From 81248238192178269ebeb36ec2340872e61b5523 Mon Sep 17 00:00:00 2001 From: oesteban Date: Mon, 15 Jul 2019 18:32:32 -0700 Subject: [PATCH 01/19] ENH: Modify ``Directory`` and ``File`` traits to get along with pathlib Ref #2944 --- nipype/info.py | 29 ++-- nipype/interfaces/base/traits_extension.py | 168 ++++++++------------- 2 files changed, 79 insertions(+), 118 deletions(-) diff --git a/nipype/info.py b/nipype/info.py index d4a5df9cac..b5b0dac0f8 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -135,26 +135,27 @@ def get_nipype_gitversion(): VERSION = __version__ PROVIDES = ['nipype'] REQUIRES = [ - 'nibabel>=%s' % NIBABEL_MIN_VERSION, - 'networkx>=%s,<=%s ; python_version < "3.0"' % (NETWORKX_MIN_VERSION, NETWORKX_MAX_VERSION_27), + 'click>=%s' % CLICK_MIN_VERSION, + 'configparser; python_version <= "3.4"', + 'funcsigs', + 'future>=%s' % FUTURE_MIN_VERSION, + 'futures; python_version == "2.7"', 'networkx>=%s ; python_version >= "3.0"' % NETWORKX_MIN_VERSION, - 'numpy>=%s,!=%s ; python_version == "2.7"' % (NUMPY_MIN_VERSION, NUMPY_BAD_VERSION_27), + 'networkx>=%s,<=%s ; python_version < "3.0"' % (NETWORKX_MIN_VERSION, NETWORKX_MAX_VERSION_27), + 'neurdflib', + 'nibabel>=%s' % NIBABEL_MIN_VERSION, 'numpy>=%s ; python_version > "3.0" and python_version < "3.7"' % NUMPY_MIN_VERSION, 'numpy>=%s ; python_version >= "3.7"' % NUMPY_MIN_VERSION_37, + 'numpy>=%s,!=%s ; python_version == "2.7"' % (NUMPY_MIN_VERSION, NUMPY_BAD_VERSION_27), + 'packaging', + 'pathlib2; python_version <= "3.4"', + 'prov>=%s' % PROV_VERSION, + 'pydot>=%s' % PYDOT_MIN_VERSION, + 'pydotplus', 'python-dateutil>=%s' % DATEUTIL_MIN_VERSION, 'scipy>=%s' % SCIPY_MIN_VERSION, - 'traits>=%s,!=5.0' % TRAITS_MIN_VERSION, - 'future>=%s' % FUTURE_MIN_VERSION, 'simplejson>=%s' % SIMPLEJSON_MIN_VERSION, - 'prov>=%s' % PROV_VERSION, - 'neurdflib', - 'click>=%s' % CLICK_MIN_VERSION, - 'funcsigs', - 'pydotplus', - 'pydot>=%s' % PYDOT_MIN_VERSION, - 'packaging', - 'futures; python_version == "2.7"', - 'configparser; python_version <= "3.4"', + 'traits>=%s,!=5.0' % TRAITS_MIN_VERSION, ] TESTS_REQUIRES = [ diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py index 7a464cc557..35fbc59ada 100644 --- a/nipype/interfaces/base/traits_extension.py +++ b/nipype/interfaces/base/traits_extension.py @@ -24,17 +24,16 @@ absolute_import) from builtins import str, bytes -import os from collections import Sequence +from pathlib import Path # perform all external trait imports here from traits import __version__ as traits_version import traits.api as traits -from traits.trait_handlers import TraitDictObject, TraitListObject +from traits.trait_handlers import TraitType, NoDefaultSpecified, TraitDictObject, TraitListObject from traits.trait_errors import TraitError -from traits.trait_base import _Undefined, class_of +from traits.trait_base import _Undefined -from traits.api import BaseUnicode from traits.api import Unicode from future import standard_library @@ -45,7 +44,7 @@ class Str(Unicode): - """Replacement for the default traits.Str based in bytes""" + """Replaces the default traits.Str based in bytes.""" # Monkeypatch Str and DictStrStr for Python 2 compatibility @@ -54,125 +53,86 @@ class Str(Unicode): traits.DictStrStr = DictStrStr -class File(BaseUnicode): - """ Defines a trait whose value must be the name of a file. - """ +class BasePath(TraitType): + """Defines a trait whose value must be a valid filesystem path.""" # A description of the type of value this trait accepts: - info_text = 'a file name' + info_text = 'a pathlike object or string' + exists = False + pathlike = False + resolve = False + _is_file = False + _is_dir = False + + def __init__(self, default_value=NoDefaultSpecified, exists=False, + pathlike=False, resolve=False, **metadata): + """Create a BasePath trait.""" + self.exists = exists + self.resolve = resolve + self.pathlike = pathlike # For backwards compatibility for now + # self.pathlike = pathlike or exists + if any((exists, self._is_file, self._is_dir)): + self.info_text += ' representing a' + if exists: + self.info_text += 'n existing' + if self._is_file: + self.info_text += ' file' + elif self._is_dir: + self.info_text += ' directory' + else: + self.info_text += ' file or directory' - def __init__(self, - value='', - filter=None, - auto_set=False, - entries=0, - exists=False, - **metadata): - """ Creates a File trait. + super(BasePath, self).__init__(default_value=default_value, **metadata) - Parameters - ---------- - value : string - The default value for the trait - filter : string - A wildcard string to filter filenames in the file dialog box used by - the attribute trait editor. - auto_set : boolean - Indicates whether the file editor updates the trait value after - every key stroke. - exists : boolean - Indicates whether the trait value must be an existing file or - not. - - Default Value - ------------- - *value* or '' - """ - self.filter = filter - self.auto_set = auto_set - self.entries = entries - self.exists = exists + def validate(self, object, name, value): + """Validate a value change.""" + try: + value = Path(value) # Use pathlib's validation + except Exception: + self.error(object, name, str(value)) - if exists: - self.info_text = 'an existing file name' + if self.exists: + if self.exists and not value.exists(): + self.error(object, name, str(value)) - super(File, self).__init__(value, **metadata) + if self._is_file and not value.is_file(): + self.error(object, name, str(value)) - def validate(self, object, name, value): - """ Validates that a specified value is valid for this trait.""" - validated_value = super(File, self).validate(object, name, value) - if not self.exists: - return validated_value - elif os.path.isfile(value): - return validated_value - else: - raise TraitError( - args='The trait \'{}\' of {} instance is {}, but the path ' - ' \'{}\' does not exist.'.format(name, class_of(object), - self.info_text, value)) + if self._is_dir and not value.is_dir(): + self.error(object, name, str(value)) - self.error(object, name, value) + if self.resolve: + value = value.resolve() + if not self.pathlike: + value = str(value) -# ------------------------------------------------------------------------------- -# 'Directory' trait -# ------------------------------------------------------------------------------- + return value -class Directory(BaseUnicode): - """ - Defines a trait whose value must be the name of a directory. +class Directory(BasePath): """ + Defines a trait whose value must be a directory path. - # A description of the type of value this trait accepts: - info_text = 'a directory name' + >>> from nipype.interfaces.base import Directory, TraitedSpec + >>> class A(TraitedSpec): + ... foo = Directory(exists=False) + >>> a = A() + >>> a.foo + - def __init__(self, - value='', - auto_set=False, - entries=0, - exists=False, - **metadata): - """ Creates a Directory trait. + >>> a.foo = '/some/made/out/path' + '/some/made/out/path' - Parameters - ---------- - value : string - The default value for the trait - auto_set : boolean - Indicates whether the directory editor updates the trait value - after every key stroke. - exists : boolean - Indicates whether the trait value must be an existing directory or - not. - - Default Value - ------------- - *value* or '' - """ - self.entries = entries - self.auto_set = auto_set - self.exists = exists + """ - if exists: - self.info_text = 'an existing directory name' + _is_dir = True - super(Directory, self).__init__(value, **metadata) - def validate(self, object, name, value): - """ Validates that a specified value is valid for this trait.""" - if isinstance(value, (str, bytes)): - if not self.exists: - return value - if os.path.isdir(value): - return value - else: - raise TraitError( - args='The trait \'{}\' of {} instance is {}, but the path ' - ' \'{}\' does not exist.'.format(name, class_of(object), - self.info_text, value)) +class File(BasePath): + """Defines a trait whose value must be a file path.""" - self.error(object, name, value) + _is_file = True # lists of tuples From 7aee40db7d3e94ca0819f92a2c0569fd42b487cc Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Tue, 16 Jul 2019 00:20:21 -0700 Subject: [PATCH 02/19] fix(traits): update ``ImageFile`` trait to match new ``File`` --- nipype/interfaces/base/tests/test_specs.py | 9 +- nipype/interfaces/base/traits_extension.py | 218 +++++++++++++-------- 2 files changed, 135 insertions(+), 92 deletions(-) diff --git a/nipype/interfaces/base/tests/test_specs.py b/nipype/interfaces/base/tests/test_specs.py index bab112e96d..b27daea6a8 100644 --- a/nipype/interfaces/base/tests/test_specs.py +++ b/nipype/interfaces/base/tests/test_specs.py @@ -2,9 +2,9 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: from __future__ import print_function, unicode_literals -from future import standard_library import os import warnings +from future import standard_library import pytest @@ -420,7 +420,8 @@ def test_ImageFile(): # setup traits x.add_trait('nifti', nib.ImageFile(types=['nifti1', 'dicom'])) x.add_trait('anytype', nib.ImageFile()) - x.add_trait('newtype', nib.ImageFile(types=['nifti10'])) + with pytest.raises(ValueError): + x.add_trait('newtype', nib.ImageFile(types=['nifti10'])) x.add_trait('nocompress', nib.ImageFile(types=['mgh'], allow_compressed=False)) @@ -428,10 +429,8 @@ def test_ImageFile(): x.nifti = 'test.mgz' x.nifti = 'test.nii' x.anytype = 'test.xml' - with pytest.raises(AttributeError): - x.newtype = 'test.nii' with pytest.raises(nib.TraitError): - x.nocompress = 'test.nii.gz' + x.nocompress = 'test.mgz' x.nocompress = 'test.mgh' diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py index 35fbc59ada..c7a5427898 100644 --- a/nipype/interfaces/base/traits_extension.py +++ b/nipype/interfaces/base/traits_extension.py @@ -42,6 +42,18 @@ standard_library.install_aliases() +IMG_FORMATS = { + 'afni': ('.HEAD', '.BRIK'), + 'cifti2': ('.nii', '.nii.gz'), + 'dicom': ('.dcm', '.IMA', '.tar', '.tar.gz'), + 'gifti': ('.gii', '.gii.gz'), + 'mgh': ('.mgh', '.mgz', '.mgh.gz'), + 'nifti1': ('.nii', '.nii.gz', '.hdr', '.img', '.img.gz'), + 'nifti2': ('.nii', '.nii.gz'), + 'nrrd': ('.nrrd', '.nhdr'), +} +IMG_ZIP_FMT = set(['.nii.gz', 'tar.gz', '.gii.gz', '.mgz', '.mgh.gz', 'img.gz']) + class Str(Unicode): """Replaces the default traits.Str based in bytes.""" @@ -64,8 +76,7 @@ class BasePath(TraitType): _is_file = False _is_dir = False - def __init__(self, default_value=NoDefaultSpecified, exists=False, - pathlike=False, resolve=False, **metadata): + def __init__(self, exists=False, pathlike=False, resolve=False, **metadata): """Create a BasePath trait.""" self.exists = exists self.resolve = resolve @@ -82,9 +93,9 @@ def __init__(self, default_value=NoDefaultSpecified, exists=False, else: self.info_text += ' file or directory' - super(BasePath, self).__init__(default_value=default_value, **metadata) + super(BasePath, self).__init__(**metadata) - def validate(self, object, name, value): + def validate(self, object, name, value, return_pathlike=False): """Validate a value change.""" try: value = Path(value) # Use pathlib's validation @@ -104,7 +115,7 @@ def validate(self, object, name, value): if self.resolve: value = value.resolve() - if not self.pathlike: + if not return_pathlike and not self.pathlike: value = str(value) return value @@ -114,7 +125,9 @@ class Directory(BasePath): """ Defines a trait whose value must be a directory path. - >>> from nipype.interfaces.base import Directory, TraitedSpec + Examples:: + + >>> from nipype.interfaces.base import Directory, TraitedSpec, TraitError >>> class A(TraitedSpec): ... foo = Directory(exists=False) >>> a = A() @@ -122,103 +135,134 @@ class Directory(BasePath): >>> a.foo = '/some/made/out/path' + >>> a.foo '/some/made/out/path' + >>> class A(TraitedSpec): + ... foo = Directory(exists=False, resolve=True) + >>> a = A(foo='relative_dir') + >>> a.foo # doctest: +ELLIPSIS + '.../relative_dir' + + >>> class A(TraitedSpec): + ... foo = Directory(exists=True, resolve=True) + >>> a = A() + >>> a.foo = 'relative_dir' # doctest: +IGNORE_EXCEPTION_DETAIL + Traceback (most recent call last): + TraitError: + + >>> from os import mkdir + >>> mkdir('relative_dir') + >>> a.foo = 'relative_dir' + >>> a.foo # doctest: +ELLIPSIS + '.../relative_dir' + + """ _is_dir = True class File(BasePath): - """Defines a trait whose value must be a file path.""" + """ + Defines a trait whose value must be a file path. + + >>> from nipype.interfaces.base import File, TraitedSpec, TraitError + >>> class A(TraitedSpec): + ... foo = File() + >>> a = A() + >>> a.foo + + + >>> a.foo = '/some/made/out/path/to/file' + >>> a.foo + '/some/made/out/path/to/file' + + >>> class A(TraitedSpec): + ... foo = File(exists=False, resolve=True) + >>> a = A(foo='idontexist.txt') + >>> a.foo # doctest: +ELLIPSIS + '.../idontexist.txt' + + >>> class A(TraitedSpec): + ... foo = File(exists=True, resolve=True) + >>> a = A() + >>> a.foo = 'idontexist.txt' # doctest: +IGNORE_EXCEPTION_DETAIL + Traceback (most recent call last): + TraitError: + + >>> open('idoexist.txt', 'w').close() + >>> a.foo = 'idoexist.txt' + >>> a.foo # doctest: +ELLIPSIS + '.../idoexist.txt' + + >>> class A(TraitedSpec): + ... foo = File(exists=True, resolve=True, extensions=['.txt', 'txt.gz']) + >>> a = A() + >>> a.foo = 'idoexist.badtxt' # doctest: +IGNORE_EXCEPTION_DETAIL + Traceback (most recent call last): + TraitError: + + >>> a.foo = 'idoexist.txt' + >>> a.foo # doctest: +ELLIPSIS + '.../idoexist.txt' + + """ _is_file = True + _exts = None + def __init__(self, exists=False, pathlike=False, resolve=False, allow_compressed=True, + extensions=None, **metadata): + """Create a File trait.""" + if extensions is not None: + if isinstance(extensions, (bytes, str)): + extensions = [extensions] -# lists of tuples -# each element consists of : -# - uncompressed (tuple[0]) extension -# - compressed (tuple[1]) extension -img_fmt_types = { - 'nifti1': [('.nii', '.nii.gz'), (('.hdr', '.img'), ('.hdr', '.img.gz'))], - 'mgh': [('.mgh', '.mgz'), ('.mgh', '.mgh.gz')], - 'nifti2': [('.nii', '.nii.gz')], - 'cifti2': [('.nii', '.nii.gz')], - 'gifti': [('.gii', '.gii.gz')], - 'dicom': [('.dcm', '.dcm'), ('.IMA', '.IMA'), ('.tar', '.tar.gz')], - 'nrrd': [('.nrrd', 'nrrd'), ('nhdr', 'nhdr')], - 'afni': [('.HEAD', '.HEAD'), ('.BRIK', '.BRIK')] -} + if allow_compressed is False: + extensions = list(set(extensions) - IMG_ZIP_FMT) + self._exts = sorted(set(['.%s' % ext if not ext.startswith('.') else ext + for ext in extensions])) -class ImageFile(File): - """ Defines a trait of specific neuroimaging files """ - - def __init__(self, - value='', - filter=None, - auto_set=False, - entries=0, - exists=False, - types=[], - allow_compressed=True, - **metadata): - """ Trait handles neuroimaging files. - - Parameters - ---------- - types : list - Strings of file format types accepted - compressed : boolean - Indicates whether the file format can compressed - """ - self.types = types - self.allow_compressed = allow_compressed - super(ImageFile, self).__init__(value, filter, auto_set, entries, - exists, **metadata) - - def info(self): - existing = 'n existing' if self.exists else '' - comma = ',' if self.exists and not self.allow_compressed else '' - uncompressed = ' uncompressed' if not self.allow_compressed else '' - with_ext = ' (valid extensions: [{}])'.format( - ', '.join(self.grab_exts())) if self.types else '' - return 'a{existing}{comma}{uncompressed} file{with_ext}'.format( - existing=existing, comma=comma, uncompressed=uncompressed, - with_ext=with_ext) - - def grab_exts(self): - # TODO: file type validation - exts = [] - for fmt in self.types: - if fmt in img_fmt_types: - exts.extend( - sum([[u for u in y[0]] - if isinstance(y[0], tuple) else [y[0]] - for y in img_fmt_types[fmt]], [])) - if self.allow_compressed: - exts.extend( - sum([[u for u in y[-1]] - if isinstance(y[-1], tuple) else [y[-1]] - for y in img_fmt_types[fmt]], [])) - else: - raise AttributeError( - 'Information has not been added for format' - ' type {} yet. Supported formats include: ' - '{}'.format(fmt, ', '.join(img_fmt_types.keys()))) - return list(set(exts)) + super(File, self).__init__(exists=exists, pathlike=pathlike, + resolve=True, **metadata) def validate(self, object, name, value): - """ Validates that a specified value is valid for this trait. - """ - validated_value = super(ImageFile, self).validate(object, name, value) - if validated_value and self.types: - _exts = self.grab_exts() - if not any(validated_value.endswith(x) for x in _exts): - raise TraitError( - args="{} is not included in allowed types: {}".format( - validated_value, ', '.join(_exts))) - return validated_value + """Validate a value change.""" + value = super(File, self).validate(object, name, value, return_pathlike=True) + if self._exts: + ext = ''.join(value.suffixes) + if ext not in self._exts: + self.error(object, name, str(value)) + + if not self.pathlike: + value = str(value) + + return value + + +class ImageFile(File): + """Defines a trait whose value must be a known neuroimaging file.""" + + def __init__(self, exists=False, pathlike=False, resolve=False, + types=None, **metadata): + """Create an ImageFile trait.""" + extensions = None + if types is not None: + if isinstance(types, (bytes, str)): + types = [types] + + if set(types) - set(IMG_FORMATS.keys()): + invalid = set(types) - set(IMG_FORMATS.keys()) + raise ValueError("""\ +Unknown value(s) %s for metadata type of an ImageFile input.\ +""" % ', '.join(['"%s"' % t for t in invalid])) + extensions = [ext for t in types for ext in IMG_FORMATS[t]] + + super(ImageFile, self).__init__( + exists=exists, extensions=extensions, + pathlike=pathlike, resolve=True, **metadata) """ From a2c53fb3c4d386e569da8f37b96b7f422507edcf Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Tue, 16 Jul 2019 01:43:36 -0700 Subject: [PATCH 03/19] fix(traits): set ``usedefault`` metadata to ``True`` --- nipype/interfaces/base/traits_extension.py | 96 +++++++++++++--------- 1 file changed, 56 insertions(+), 40 deletions(-) diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py index c7a5427898..2f8672f4b9 100644 --- a/nipype/interfaces/base/traits_extension.py +++ b/nipype/interfaces/base/traits_extension.py @@ -54,6 +54,35 @@ } IMG_ZIP_FMT = set(['.nii.gz', 'tar.gz', '.gii.gz', '.mgz', '.mgh.gz', 'img.gz']) +""" +The functions that pop-up the Traits GUIs, edit_traits and +configure_traits, were failing because all of our inputs default to +Undefined deep and down in traits/ui/wx/list_editor.py it checks for +the len() of the elements of the list. The _Undefined class in traits +does not define the __len__ method and would error. I tried defining +our own Undefined and even sublassing Undefined, but both of those +failed with a TraitError in our initializer when we assign the +Undefined to the inputs because of an incompatible type: + +TraitError: The 'vertical_gradient' trait of a BetInputSpec instance must be \ +a float, but a value of was specified. + +So... in order to keep the same type but add the missing method, I +monkey patched. +""" + + +def _length(self): + return 0 + + +########################################################################## +# Apply monkeypatch here +_Undefined.__len__ = _length +########################################################################## + +Undefined = _Undefined() + class Str(Unicode): """Replaces the default traits.Str based in bytes.""" @@ -76,12 +105,12 @@ class BasePath(TraitType): _is_file = False _is_dir = False - def __init__(self, exists=False, pathlike=False, resolve=False, **metadata): + def __init__(self, default_value=Undefined, + exists=False, pathlike=False, resolve=False, **metadata): """Create a BasePath trait.""" self.exists = exists self.resolve = resolve - self.pathlike = pathlike # For backwards compatibility for now - # self.pathlike = pathlike or exists + self.pathlike = pathlike if any((exists, self._is_file, self._is_dir)): self.info_text += ' representing a' if exists: @@ -93,7 +122,8 @@ def __init__(self, exists=False, pathlike=False, resolve=False, **metadata): else: self.info_text += ' file or directory' - super(BasePath, self).__init__(**metadata) + metadata['usedefault'] = True + super(BasePath, self).__init__(default_value, **metadata) def validate(self, object, name, value, return_pathlike=False): """Validate a value change.""" @@ -120,6 +150,15 @@ def validate(self, object, name, value, return_pathlike=False): return value + def get_value(self, object, name, trait=None): + value = super(BasePath, self).get_value(object, name) + if value is Undefined: + return self.default_value + + if self.pathlike: + return value + return str(value) + class Directory(BasePath): """ @@ -158,6 +197,12 @@ class Directory(BasePath): '.../relative_dir' + >>> class A(TraitedSpec): + ... foo = Directory('tmpdir', resolve=True) + >>> a = A() + >>> a.foo # doctest: +ELLIPSIS + 'tmpdir' + """ _is_dir = True @@ -212,8 +257,8 @@ class File(BasePath): _is_file = True _exts = None - def __init__(self, exists=False, pathlike=False, resolve=False, allow_compressed=True, - extensions=None, **metadata): + def __init__(self, default_value=NoDefaultSpecified, exists=False, pathlike=False, + resolve=False, allow_compressed=True, extensions=None, **metadata): """Create a File trait.""" if extensions is not None: if isinstance(extensions, (bytes, str)): @@ -225,8 +270,8 @@ def __init__(self, exists=False, pathlike=False, resolve=False, allow_compressed self._exts = sorted(set(['.%s' % ext if not ext.startswith('.') else ext for ext in extensions])) - super(File, self).__init__(exists=exists, pathlike=pathlike, - resolve=True, **metadata) + super(File, self).__init__(default_value=default_value, exists=exists, + pathlike=pathlike, resolve=True, **metadata) def validate(self, object, name, value): """Validate a value change.""" @@ -245,8 +290,8 @@ def validate(self, object, name, value): class ImageFile(File): """Defines a trait whose value must be a known neuroimaging file.""" - def __init__(self, exists=False, pathlike=False, resolve=False, - types=None, **metadata): + def __init__(self, default_value=NoDefaultSpecified, exists=False, + pathlike=False, resolve=False, types=None, **metadata): """Create an ImageFile trait.""" extensions = None if types is not None: @@ -261,39 +306,10 @@ def __init__(self, exists=False, pathlike=False, resolve=False, extensions = [ext for t in types for ext in IMG_FORMATS[t]] super(ImageFile, self).__init__( - exists=exists, extensions=extensions, + default_value=default_value, exists=exists, extensions=extensions, pathlike=pathlike, resolve=True, **metadata) -""" -The functions that pop-up the Traits GUIs, edit_traits and -configure_traits, were failing because all of our inputs default to -Undefined deep and down in traits/ui/wx/list_editor.py it checks for -the len() of the elements of the list. The _Undefined class in traits -does not define the __len__ method and would error. I tried defining -our own Undefined and even sublassing Undefined, but both of those -failed with a TraitError in our initializer when we assign the -Undefined to the inputs because of an incompatible type: - -TraitError: The 'vertical_gradient' trait of a BetInputSpec instance must be a float, but a value of was specified. - -So... in order to keep the same type but add the missing method, I -monkey patched. -""" - - -def length(self): - return 0 - - -########################################################################## -# Apply monkeypatch here -_Undefined.__len__ = length -########################################################################## - -Undefined = _Undefined() - - def isdefined(object): return not isinstance(object, _Undefined) From a8f55bb2be1db81582881e9cc5ddbf1f3f6d0076 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Tue, 16 Jul 2019 06:44:28 -0700 Subject: [PATCH 04/19] fix(traits): ``resolve`` meta was forced to ``True`` for ``File`` --- nipype/interfaces/base/traits_extension.py | 28 +++++++++++++++------- 1 file changed, 20 insertions(+), 8 deletions(-) diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py index 2f8672f4b9..f7b2ceec93 100644 --- a/nipype/interfaces/base/traits_extension.py +++ b/nipype/interfaces/base/traits_extension.py @@ -150,14 +150,14 @@ def validate(self, object, name, value, return_pathlike=False): return value - def get_value(self, object, name, trait=None): - value = super(BasePath, self).get_value(object, name) - if value is Undefined: - return self.default_value + # def get_value(self, object, name, trait=None): + # value = super(BasePath, self).get_value(object, name) + # if value is Undefined: + # return self.default_value - if self.pathlike: - return value - return str(value) + # if self.pathlike: + # return value + # return str(value) class Directory(BasePath): @@ -196,6 +196,12 @@ class Directory(BasePath): >>> a.foo # doctest: +ELLIPSIS '.../relative_dir' + >>> class A(TraitedSpec): + ... foo = Directory(exists=True, resolve=False) + >>> a = A(foo='relative_dir') + >>> a.foo + 'relative_dir' + >>> class A(TraitedSpec): ... foo = Directory('tmpdir', resolve=True) @@ -241,6 +247,12 @@ class File(BasePath): >>> a.foo # doctest: +ELLIPSIS '.../idoexist.txt' + >>> class A(TraitedSpec): + ... foo = File(exists=True, resolve=False) + >>> a = A(foo='idoexist.txt') + >>> a.foo + 'idoexist.txt' + >>> class A(TraitedSpec): ... foo = File(exists=True, resolve=True, extensions=['.txt', 'txt.gz']) >>> a = A() @@ -271,7 +283,7 @@ def __init__(self, default_value=NoDefaultSpecified, exists=False, pathlike=Fals for ext in extensions])) super(File, self).__init__(default_value=default_value, exists=exists, - pathlike=pathlike, resolve=True, **metadata) + pathlike=pathlike, resolve=resolve, **metadata) def validate(self, object, name, value): """Validate a value change.""" From 5f99d935a649e872d30c13c190ec9a1ab4e26ce4 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Tue, 16 Jul 2019 06:45:18 -0700 Subject: [PATCH 05/19] fix(traits): ``resolve`` of ``ImageFiles``, ``ImageFileSPM`` adapted to new ``ImageFile`` --- nipype/interfaces/base/traits_extension.py | 2 +- nipype/interfaces/spm/base.py | 20 ++++++-------------- 2 files changed, 7 insertions(+), 15 deletions(-) diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py index f7b2ceec93..785e2f3741 100644 --- a/nipype/interfaces/base/traits_extension.py +++ b/nipype/interfaces/base/traits_extension.py @@ -319,7 +319,7 @@ def __init__(self, default_value=NoDefaultSpecified, exists=False, super(ImageFile, self).__init__( default_value=default_value, exists=exists, extensions=extensions, - pathlike=pathlike, resolve=True, **metadata) + pathlike=pathlike, resolve=resolve, **metadata) def isdefined(object): diff --git a/nipype/interfaces/spm/base.py b/nipype/interfaces/spm/base.py index fd93dfc522..9503d15f11 100644 --- a/nipype/interfaces/spm/base.py +++ b/nipype/interfaces/spm/base.py @@ -32,6 +32,7 @@ from ..base import (BaseInterface, traits, isdefined, InputMultiPath, BaseInterfaceInputSpec, Directory, Undefined, ImageFile, PackageInfo) +from ..base.traits_extension import NoDefaultSpecified from ..matlab import MatlabCommand from ...external.due import due, Doi, BibTeX @@ -601,15 +602,8 @@ class ImageFileSPM(ImageFile): Defines an ImageFile trait specific to SPM interfaces. """ - def __init__(self, - value='', - filter=None, - auto_set=False, - entries=0, - exists=False, - types=['nifti1', 'nifti2'], - allow_compressed=False, - **metadata): + def __init__(self, default_value=NoDefaultSpecified, exists=False, + pathlike=False, resolve=False, **metadata): """ Trait handles neuroimaging files. Parameters @@ -619,8 +613,6 @@ def __init__(self, compressed : boolean Indicates whether the file format can compressed """ - self.types = types - self.allow_compressed = allow_compressed - super(ImageFileSPM, - self).__init__(value, filter, auto_set, entries, exists, types, - allow_compressed, **metadata) + super(ImageFileSPM, self).__init__( + default_value=default_value, exists=exists, types=['nifti1', 'nifti2'], + pathlike=pathlike, resolve=resolve, **metadata) From addadb32840480a8bbedb817a8ff9f1d61f0060e Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Tue, 16 Jul 2019 08:31:24 -0700 Subject: [PATCH 06/19] fix(traits): ensuring backwards compatibility of new traits --- nipype/interfaces/base/support.py | 2 +- nipype/interfaces/base/traits_extension.py | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/nipype/interfaces/base/support.py b/nipype/interfaces/base/support.py index de9d46f61a..0fd1d27674 100644 --- a/nipype/interfaces/base/support.py +++ b/nipype/interfaces/base/support.py @@ -278,7 +278,7 @@ def _inputs_help(cls): >>> from nipype.interfaces.afni import GCOR >>> _inputs_help(GCOR) # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE - ['Inputs::', '', '\t[Mandatory]', '\tin_file: (an existing file name)', ... + ['Inputs::', '', '\t[Mandatory]', '\tin_file: (a pathlike object or string... """ helpstr = ['Inputs::'] diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py index 785e2f3741..d6de198ddf 100644 --- a/nipype/interfaces/base/traits_extension.py +++ b/nipype/interfaces/base/traits_extension.py @@ -105,7 +105,7 @@ class BasePath(TraitType): _is_file = False _is_dir = False - def __init__(self, default_value=Undefined, + def __init__(self, value=Undefined, exists=False, pathlike=False, resolve=False, **metadata): """Create a BasePath trait.""" self.exists = exists @@ -123,7 +123,7 @@ def __init__(self, default_value=Undefined, self.info_text += ' file or directory' metadata['usedefault'] = True - super(BasePath, self).__init__(default_value, **metadata) + super(BasePath, self).__init__(value, **metadata) def validate(self, object, name, value, return_pathlike=False): """Validate a value change.""" @@ -269,7 +269,7 @@ class File(BasePath): _is_file = True _exts = None - def __init__(self, default_value=NoDefaultSpecified, exists=False, pathlike=False, + def __init__(self, value=NoDefaultSpecified, exists=False, pathlike=False, resolve=False, allow_compressed=True, extensions=None, **metadata): """Create a File trait.""" if extensions is not None: @@ -282,7 +282,7 @@ def __init__(self, default_value=NoDefaultSpecified, exists=False, pathlike=Fals self._exts = sorted(set(['.%s' % ext if not ext.startswith('.') else ext for ext in extensions])) - super(File, self).__init__(default_value=default_value, exists=exists, + super(File, self).__init__(value=value, exists=exists, pathlike=pathlike, resolve=resolve, **metadata) def validate(self, object, name, value): @@ -302,7 +302,7 @@ def validate(self, object, name, value): class ImageFile(File): """Defines a trait whose value must be a known neuroimaging file.""" - def __init__(self, default_value=NoDefaultSpecified, exists=False, + def __init__(self, value=NoDefaultSpecified, exists=False, pathlike=False, resolve=False, types=None, **metadata): """Create an ImageFile trait.""" extensions = None @@ -318,7 +318,7 @@ def __init__(self, default_value=NoDefaultSpecified, exists=False, extensions = [ext for t in types for ext in IMG_FORMATS[t]] super(ImageFile, self).__init__( - default_value=default_value, exists=exists, extensions=extensions, + value=value, exists=exists, extensions=extensions, pathlike=pathlike, resolve=resolve, **metadata) From 72f7feda51977c0ceac8ffb20e5798d5dac2b7f3 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Tue, 16 Jul 2019 08:33:28 -0700 Subject: [PATCH 07/19] fix(interfaces): minor amends to SPM and AFNI interfaces --- nipype/interfaces/afni/base.py | 6 -- nipype/interfaces/afni/preprocess.py | 103 ++++++++++++++++----------- nipype/interfaces/spm/base.py | 18 ++--- 3 files changed, 64 insertions(+), 63 deletions(-) diff --git a/nipype/interfaces/afni/base.py b/nipype/interfaces/afni/base.py index d4b8e474ff..1851b42654 100644 --- a/nipype/interfaces/afni/base.py +++ b/nipype/interfaces/afni/base.py @@ -115,12 +115,6 @@ class AFNICommandInputSpec(CommandLineInputSpec): 1, usedefault=True, nohash=True, desc='set number of threads') outputtype = traits.Enum( 'AFNI', list(Info.ftypes.keys()), desc='AFNI output filetype') - out_file = File( - name_template="%s_afni", - desc='output image file name', - argstr='-prefix %s', - name_source=["in_file"]) - class AFNICommandOutputSpec(TraitedSpec): out_file = File(desc='output file', exists=True) diff --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py index c2ccb1988a..75f0cedcc7 100644 --- a/nipype/interfaces/afni/preprocess.py +++ b/nipype/interfaces/afni/preprocess.py @@ -13,7 +13,7 @@ from ...utils.filemanip import (load_json, save_json, split_filename, fname_presuffix) from ..base import (CommandLineInputSpec, CommandLine, TraitedSpec, traits, - isdefined, File, InputMultiPath, Undefined, Str, + isdefined, File, Directory, InputMultiPath, Undefined, Str, InputMultiObject) from .base import (AFNICommandBase, AFNICommand, AFNICommandInputSpec, @@ -757,8 +757,7 @@ class BandpassInputSpec(AFNICommandInputSpec): desc='output file from 3dBandpass', argstr='-prefix %s', position=1, - name_source='in_file', - genfile=True) + name_source='in_file') lowpass = traits.Float( desc='lowpass', argstr='%f', position=-2, mandatory=True) highpass = traits.Float( @@ -909,6 +908,11 @@ class BlurToFWHMInputSpec(AFNICommandInputSpec): argstr='-input %s', mandatory=True, exists=True) + out_file = File( + name_template='%s_afni', + desc='output image file name', + argstr='-prefix %s', + name_source='in_file') automask = traits.Bool( desc='Create an automask from the input dataset.', argstr='-automask') fwhm = traits.Float( @@ -1042,6 +1046,11 @@ class DegreeCentralityInputSpec(CentralityInputSpec): mandatory=True, exists=True, copyfile=False) + out_file = File( + name_template='%s_afni', + desc='output image file name', + argstr='-prefix %s', + name_source='in_file') sparsity = traits.Float( desc='only take the top percent of connections', argstr='-sparsity %f') oned_file = Str( @@ -1188,6 +1197,11 @@ class ECMInputSpec(CentralityInputSpec): mandatory=True, exists=True, copyfile=False) + out_file = File( + name_template='%s_afni', + desc='output image file name', + argstr='-prefix %s', + name_source='in_file') sparsity = traits.Float( desc='only take the top percent of connections', argstr='-sparsity %f') full = traits.Bool( @@ -1453,6 +1467,11 @@ class LFCDInputSpec(CentralityInputSpec): mandatory=True, exists=True, copyfile=False) + out_file = File( + name_template='%s_afni', + desc='output image file name', + argstr='-prefix %s', + name_source='in_file') class LFCD(AFNICommand): @@ -3072,15 +3091,13 @@ def _list_outputs(self): class QwarpInputSpec(AFNICommandInputSpec): in_file = File( - desc= - 'Source image (opposite phase encoding direction than base image).', + desc='Source image (opposite phase encoding direction than base image).', argstr='-source %s', mandatory=True, exists=True, copyfile=False) base_file = File( - desc= - 'Base image (opposite phase encoding direction than source image).', + desc='Base image (opposite phase encoding direction than source image).', argstr='-base %s', mandatory=True, exists=True, @@ -3088,42 +3105,42 @@ class QwarpInputSpec(AFNICommandInputSpec): out_file = File( argstr='-prefix %s', name_template='%s_QW', - name_source=['in_file'], - genfile=True, - desc='out_file ppp' - 'Sets the prefix for the output datasets.' - '* The source dataset is warped to match the base' - 'and gets prefix \'ppp\'. (Except if \'-plusminus\' is used.)' - '* The final interpolation to this output dataset is' - 'done using the \'wsinc5\' method. See the output of' - ' 3dAllineate -HELP' - '(in the "Modifying \'-final wsinc5\'" section) for' - 'the lengthy technical details.' - '* The 3D warp used is saved in a dataset with' - 'prefix \'ppp_WARP\' -- this dataset can be used' - 'with 3dNwarpApply and 3dNwarpCat, for example.' - '* To be clear, this is the warp from source dataset' - ' coordinates to base dataset coordinates, where the' - ' values at each base grid point are the xyz displacments' - ' needed to move that grid point\'s xyz values to the' - ' corresponding xyz values in the source dataset:' - ' base( (x,y,z) + WARP(x,y,z) ) matches source(x,y,z)' - ' Another way to think of this warp is that it \'pulls\'' - ' values back from source space to base space.' - '* 3dNwarpApply would use \'ppp_WARP\' to transform datasets' - 'aligned with the source dataset to be aligned with the' - 'base dataset.' - '** If you do NOT want this warp saved, use the option \'-nowarp\'.' - '-->> (However, this warp is usually the most valuable possible output!)' - '* If you want to calculate and save the inverse 3D warp,' - 'use the option \'-iwarp\'. This inverse warp will then be' - 'saved in a dataset with prefix \'ppp_WARPINV\'.' - '* This inverse warp could be used to transform data from base' - 'space to source space, if you need to do such an operation.' - '* You can easily compute the inverse later, say by a command like' - ' 3dNwarpCat -prefix Z_WARPINV \'INV(Z_WARP+tlrc)\'' - 'or the inverse can be computed as needed in 3dNwarpApply, like' - ' 3dNwarpApply -nwarp \'INV(Z_WARP+tlrc)\' -source Dataset.nii ...') + name_source='in_file', + desc="""\ +out_file ppp\ +Sets the prefix for the output datasets.\ +* The source dataset is warped to match the base\ +and gets prefix \'ppp\'. (Except if \'-plusminus\' is used.)\ +* The final interpolation to this output dataset is\ +done using the \'wsinc5\' method. See the output of\ + 3dAllineate -HELP\ +(in the "Modifying \'-final wsinc5\'" section) for\ +the lengthy technical details.\ +* The 3D warp used is saved in a dataset with\ +prefix \'ppp_WARP\' -- this dataset can be used\ +with 3dNwarpApply and 3dNwarpCat, for example.\ +* To be clear, this is the warp from source dataset\ + coordinates to base dataset coordinates, where the\ + values at each base grid point are the xyz displacments\ + needed to move that grid point\'s xyz values to the\ + corresponding xyz values in the source dataset:\ + base( (x,y,z) + WARP(x,y,z) ) matches source(x,y,z)\ + Another way to think of this warp is that it \'pulls\'\ + values back from source space to base space.\ +* 3dNwarpApply would use \'ppp_WARP\' to transform datasets\ +aligned with the source dataset to be aligned with the\ +base dataset.\ +** If you do NOT want this warp saved, use the option \'-nowarp\'.\ +-->> (However, this warp is usually the most valuable possible output!)\ +* If you want to calculate and save the inverse 3D warp,\ +use the option \'-iwarp\'. This inverse warp will then be\ +saved in a dataset with prefix \'ppp_WARPINV\'.\ +* This inverse warp could be used to transform data from base\ +space to source space, if you need to do such an operation.\ +* You can easily compute the inverse later, say by a command like\ + 3dNwarpCat -prefix Z_WARPINV \'INV(Z_WARP+tlrc)\'\ +or the inverse can be computed as needed in 3dNwarpApply, like\ + 3dNwarpApply -nwarp \'INV(Z_WARP+tlrc)\' -source Dataset.nii ...""") resample = traits.Bool( desc='This option simply resamples the source dataset to match the' 'base dataset grid. You can use this if the two datasets' diff --git a/nipype/interfaces/spm/base.py b/nipype/interfaces/spm/base.py index 9503d15f11..bbabbf42ba 100644 --- a/nipype/interfaces/spm/base.py +++ b/nipype/interfaces/spm/base.py @@ -598,21 +598,11 @@ def _make_matlab_command(self, contents, postscript=None): class ImageFileSPM(ImageFile): - """ - Defines an ImageFile trait specific to SPM interfaces. - """ + """Defines a trait whose value must be a NIfTI file.""" - def __init__(self, default_value=NoDefaultSpecified, exists=False, + def __init__(self, value=NoDefaultSpecified, exists=False, pathlike=False, resolve=False, **metadata): - """ Trait handles neuroimaging files. - - Parameters - ---------- - types : list - Strings of file format types accepted - compressed : boolean - Indicates whether the file format can compressed - """ + """Create an ImageFileSPM trait.""" super(ImageFileSPM, self).__init__( - default_value=default_value, exists=exists, types=['nifti1', 'nifti2'], + value=value, exists=exists, types=['nifti1', 'nifti2'], pathlike=pathlike, resolve=resolve, **metadata) From c8457e6dbe6a3e586693eec199a7d68a1c506728 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Tue, 16 Jul 2019 08:34:11 -0700 Subject: [PATCH 08/19] maint(specs): make specs --- nipype/algorithms/tests/test_auto_ACompCor.py | 11 +- .../tests/test_auto_ActivationCount.py | 6 +- .../tests/test_auto_AddCSVColumn.py | 7 +- .../algorithms/tests/test_auto_AddCSVRow.py | 2 +- nipype/algorithms/tests/test_auto_AddNoise.py | 11 +- .../tests/test_auto_ArtifactDetect.py | 2 +- .../test_auto_CalculateNormalizedMoments.py | 5 +- .../tests/test_auto_ComputeDVARS.py | 24 ++-- .../tests/test_auto_ComputeMeshWarp.py | 14 ++- .../algorithms/tests/test_auto_CreateNifti.py | 12 +- nipype/algorithms/tests/test_auto_Distance.py | 14 ++- .../tests/test_auto_FramewiseDisplacement.py | 9 +- .../tests/test_auto_FuzzyOverlap.py | 2 +- nipype/algorithms/tests/test_auto_Gunzip.py | 8 +- nipype/algorithms/tests/test_auto_ICC.py | 11 +- .../algorithms/tests/test_auto_Matlab2CSV.py | 5 +- .../tests/test_auto_MergeCSVFiles.py | 2 +- .../algorithms/tests/test_auto_MergeROIs.py | 4 +- .../tests/test_auto_MeshWarpMaths.py | 9 +- .../tests/test_auto_NonSteadyStateDetector.py | 6 +- .../test_auto_NormalizeProbabilityMapSet.py | 2 +- .../algorithms/tests/test_auto_P2PDistance.py | 14 ++- .../algorithms/tests/test_auto_PickAtlas.py | 9 +- .../algorithms/tests/test_auto_Similarity.py | 14 ++- .../tests/test_auto_SpecifySparseModel.py | 4 +- .../algorithms/tests/test_auto_SplitROIs.py | 7 +- .../tests/test_auto_StimulusCorrelation.py | 5 +- nipype/algorithms/tests/test_auto_TCompCor.py | 11 +- .../algorithms/tests/test_auto_WarpPoints.py | 13 ++- .../afni/tests/test_auto_ABoverlap.py | 5 +- .../afni/tests/test_auto_AFNICommand.py | 5 - .../afni/tests/test_auto_AFNIPythonCommand.py | 5 - .../afni/tests/test_auto_AFNItoNIFTI.py | 4 +- .../afni/tests/test_auto_AlignEpiAnatPy.py | 22 ++-- .../afni/tests/test_auto_Allineate.py | 33 ++++-- .../afni/tests/test_auto_AutoTLRC.py | 3 +- .../afni/tests/test_auto_AutoTcorrelate.py | 10 +- .../afni/tests/test_auto_Autobox.py | 4 +- .../afni/tests/test_auto_Automask.py | 7 +- .../afni/tests/test_auto_Axialize.py | 4 +- .../afni/tests/test_auto_Bandpass.py | 11 +- .../afni/tests/test_auto_BlurInMask.py | 14 ++- .../afni/tests/test_auto_BlurToFWHM.py | 16 ++- .../afni/tests/test_auto_BrickStat.py | 2 + .../interfaces/afni/tests/test_auto_Bucket.py | 3 +- .../interfaces/afni/tests/test_auto_Calc.py | 11 +- nipype/interfaces/afni/tests/test_auto_Cat.py | 2 +- .../afni/tests/test_auto_CatMatvec.py | 3 +- .../afni/tests/test_auto_CenterMass.py | 11 +- .../afni/tests/test_auto_ClipLevel.py | 1 + .../afni/tests/test_auto_ConvertDset.py | 4 +- .../interfaces/afni/tests/test_auto_Copy.py | 4 +- .../afni/tests/test_auto_Deconvolve.py | 38 +++++-- .../afni/tests/test_auto_DegreeCentrality.py | 13 ++- .../afni/tests/test_auto_Despike.py | 4 +- .../afni/tests/test_auto_Detrend.py | 4 +- nipype/interfaces/afni/tests/test_auto_Dot.py | 8 +- nipype/interfaces/afni/tests/test_auto_ECM.py | 11 +- .../interfaces/afni/tests/test_auto_Edge3.py | 4 +- .../interfaces/afni/tests/test_auto_Eval.py | 11 +- .../interfaces/afni/tests/test_auto_FWHMx.py | 17 ++- nipype/interfaces/afni/tests/test_auto_Fim.py | 5 +- .../afni/tests/test_auto_Fourier.py | 4 +- .../interfaces/afni/tests/test_auto_GCOR.py | 2 + .../interfaces/afni/tests/test_auto_Hist.py | 12 +- .../interfaces/afni/tests/test_auto_LFCD.py | 11 +- .../afni/tests/test_auto_LocalBistat.py | 4 +- .../afni/tests/test_auto_Localstat.py | 3 +- .../afni/tests/test_auto_MaskTool.py | 3 +- .../afni/tests/test_auto_Maskave.py | 5 +- .../interfaces/afni/tests/test_auto_Means.py | 5 +- .../interfaces/afni/tests/test_auto_Merge.py | 3 +- .../interfaces/afni/tests/test_auto_Notes.py | 8 +- .../afni/tests/test_auto_NwarpAdjust.py | 3 +- .../afni/tests/test_auto_NwarpApply.py | 3 +- 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.../afni/tests/test_auto_TCorrMap.py | 51 +++++---- .../afni/tests/test_auto_TCorrelate.py | 5 +- .../interfaces/afni/tests/test_auto_TNorm.py | 4 +- .../afni/tests/test_auto_TProject.py | 24 +++- .../interfaces/afni/tests/test_auto_TShift.py | 6 +- .../interfaces/afni/tests/test_auto_TStat.py | 9 +- .../interfaces/afni/tests/test_auto_To3D.py | 4 +- .../interfaces/afni/tests/test_auto_Undump.py | 9 +- .../afni/tests/test_auto_Unifize.py | 11 +- .../interfaces/afni/tests/test_auto_Volreg.py | 14 ++- .../interfaces/afni/tests/test_auto_Warp.py | 21 +++- .../interfaces/afni/tests/test_auto_ZCutUp.py | 4 +- .../interfaces/afni/tests/test_auto_Zcat.py | 3 +- .../afni/tests/test_auto_Zeropad.py | 4 +- .../interfaces/ants/tests/test_auto_ANTS.py | 10 +- .../ants/tests/test_auto_AffineInitializer.py | 4 +- .../ants/tests/test_auto_AntsJointFusion.py | 12 +- .../ants/tests/test_auto_ApplyTransforms.py | 4 +- .../test_auto_ApplyTransformsToPoints.py | 3 +- .../ants/tests/test_auto_Atropos.py | 4 +- .../tests/test_auto_AverageAffineTransform.py | 3 +- .../ants/tests/test_auto_AverageImages.py | 2 +- .../ants/tests/test_auto_BrainExtraction.py | 44 ++++---- .../tests/test_auto_ComposeMultiTransform.py | 4 +- .../tests/test_auto_CompositeTransformUtil.py | 7 +- .../test_auto_ConvertScalarImageToRGB.py | 3 +- .../ants/tests/test_auto_CorticalThickness.py | 35 +++--- ...est_auto_CreateJacobianDeterminantImage.py | 4 +- .../ants/tests/test_auto_CreateTiledMosaic.py | 9 +- .../ants/tests/test_auto_DenoiseImage.py | 7 +- .../ants/tests/test_auto_GenWarpFields.py | 12 +- .../ants/tests/test_auto_JointFusion.py | 8 +- .../ants/tests/test_auto_KellyKapowski.py | 20 +++- .../ants/tests/test_auto_LabelGeometry.py | 3 +- .../tests/test_auto_LaplacianThickness.py | 5 +- .../tests/test_auto_MeasureImageSimilarity.py | 20 +++- .../ants/tests/test_auto_MultiplyImages.py | 4 +- .../tests/test_auto_N4BiasFieldCorrection.py | 20 +++- .../ants/tests/test_auto_Registration.py | 22 ++-- .../tests/test_auto_RegistrationSynQuick.py | 10 +- .../test_auto_WarpImageMultiTransform.py | 5 +- ..._auto_WarpTimeSeriesImageMultiTransform.py | 4 +- .../ants/tests/test_auto_antsIntroduction.py | 12 +- .../tests/test_auto_buildtemplateparallel.py | 2 +- .../brainsuite/tests/test_auto_BDP.py | 52 +++++++-- .../brainsuite/tests/test_auto_Bfc.py | 18 ++- .../brainsuite/tests/test_auto_Bse.py | 19 +++- .../brainsuite/tests/test_auto_Cerebro.py | 20 +++- .../brainsuite/tests/test_auto_Cortex.py | 5 +- .../brainsuite/tests/test_auto_Dewisp.py | 4 +- .../brainsuite/tests/test_auto_Dfs.py | 9 +- .../brainsuite/tests/test_auto_Hemisplit.py | 19 +++- .../brainsuite/tests/test_auto_Pialmesh.py | 6 +- .../brainsuite/tests/test_auto_Pvc.py | 12 +- .../brainsuite/tests/test_auto_Scrubmask.py | 4 +- .../brainsuite/tests/test_auto_Skullfinder.py | 5 +- .../brainsuite/tests/test_auto_Tca.py | 4 +- .../camino/tests/test_auto_AnalyzeHeader.py | 10 +- .../tests/test_auto_ComputeEigensystem.py | 3 +- .../test_auto_ComputeFractionalAnisotropy.py | 4 +- .../tests/test_auto_ComputeMeanDiffusivity.py | 5 +- .../tests/test_auto_ComputeTensorTrace.py | 4 +- .../camino/tests/test_auto_Conmat.py | 13 ++- .../camino/tests/test_auto_DT2NIfTI.py | 9 +- .../camino/tests/test_auto_DTIFit.py | 9 +- .../camino/tests/test_auto_DTLUTGen.py | 3 +- .../camino/tests/test_auto_DTMetric.py | 9 +- .../camino/tests/test_auto_FSL2Scheme.py | 4 +- .../camino/tests/test_auto_Image2Voxel.py | 3 +- .../camino/tests/test_auto_ImageStats.py | 3 +- .../camino/tests/test_auto_LinRecon.py | 10 +- .../interfaces/camino/tests/test_auto_MESD.py | 9 +- .../camino/tests/test_auto_ModelFit.py | 29 ++++- .../camino/tests/test_auto_NIfTIDT2Camino.py | 18 ++- .../camino/tests/test_auto_PicoPDFs.py | 3 +- .../camino/tests/test_auto_ProcStreamlines.py | 33 ++++-- .../camino/tests/test_auto_QBallMX.py | 3 +- .../camino/tests/test_auto_SFLUTGen.py | 6 +- .../camino/tests/test_auto_SFPICOCalibData.py | 6 +- 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.../cmtk/tests/test_auto_NetworkXMetrics.py | 34 ++++-- .../cmtk/tests/test_auto_Parcellate.py | 25 +++-- .../interfaces/cmtk/tests/test_auto_ROIGen.py | 29 +++-- .../tests/test_auto_DTIRecon.py | 31 +++--- .../tests/test_auto_DTITracker.py | 13 ++- .../tests/test_auto_HARDIMat.py | 23 +++- .../tests/test_auto_ODFRecon.py | 12 +- .../tests/test_auto_ODFTracker.py | 14 ++- .../tests/test_auto_SplineFilter.py | 3 +- .../tests/test_auto_TrackMerge.py | 2 +- .../dipy/tests/test_auto_APMQball.py | 19 +++- nipype/interfaces/dipy/tests/test_auto_CSD.py | 25 +++-- nipype/interfaces/dipy/tests/test_auto_DTI.py | 29 +++-- .../dipy/tests/test_auto_Denoise.py | 13 ++- .../tests/test_auto_DipyDiffusionInterface.py | 15 ++- .../tests/test_auto_EstimateResponseSH.py | 26 +++-- .../dipy/tests/test_auto_RESTORE.py | 33 ++++-- .../dipy/tests/test_auto_Resample.py | 7 +- .../tests/test_auto_SimulateMultiTensor.py | 21 ++-- .../tests/test_auto_StreamlineTractography.py | 23 ++-- .../dipy/tests/test_auto_TensorMode.py | 19 +++- .../dipy/tests/test_auto_TrackDensityMap.py | 9 +- .../dtitk/tests/test_auto_AffScalarVol.py | 6 +- .../tests/test_auto_AffSymTensor3DVol.py | 6 +- .../dtitk/tests/test_auto_Affine.py | 7 +- .../dtitk/tests/test_auto_AffineTask.py | 7 +- .../dtitk/tests/test_auto_BinThresh.py | 4 +- .../dtitk/tests/test_auto_BinThreshTask.py | 4 +- .../dtitk/tests/test_auto_ComposeXfm.py | 5 +- .../dtitk/tests/test_auto_ComposeXfmTask.py | 5 +- .../dtitk/tests/test_auto_Diffeo.py | 7 +- .../dtitk/tests/test_auto_DiffeoScalarVol.py | 6 +- .../tests/test_auto_DiffeoSymTensor3DVol.py | 6 +- .../dtitk/tests/test_auto_DiffeoTask.py | 7 +- .../interfaces/dtitk/tests/test_auto_Rigid.py | 7 +- .../dtitk/tests/test_auto_RigidTask.py | 7 +- .../dtitk/tests/test_auto_SVAdjustVoxSp.py | 5 +- .../tests/test_auto_SVAdjustVoxSpTask.py | 5 +- .../dtitk/tests/test_auto_SVResample.py | 5 +- .../dtitk/tests/test_auto_SVResampleTask.py | 5 +- 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22 +++- .../tests/test_auto_ApplyVolTransform.py | 17 ++- .../freesurfer/tests/test_auto_Binarize.py | 18 ++- .../freesurfer/tests/test_auto_CALabel.py | 18 ++- .../freesurfer/tests/test_auto_CANormalize.py | 23 +++- .../freesurfer/tests/test_auto_CARegister.py | 15 ++- .../test_auto_CheckTalairachAlignment.py | 3 +- .../freesurfer/tests/test_auto_Concatenate.py | 15 ++- .../tests/test_auto_ConcatenateLTA.py | 6 +- .../freesurfer/tests/test_auto_Contrast.py | 28 +++-- .../freesurfer/tests/test_auto_Curvature.py | 7 +- .../tests/test_auto_CurvatureStats.py | 12 +- .../tests/test_auto_DICOMConvert.py | 14 ++- .../freesurfer/tests/test_auto_EMRegister.py | 17 ++- .../tests/test_auto_EditWMwithAseg.py | 8 +- .../freesurfer/tests/test_auto_EulerNumber.py | 5 +- .../tests/test_auto_ExtractMainComponent.py | 4 +- .../freesurfer/tests/test_auto_FSCommand.py | 2 +- .../tests/test_auto_FSCommandOpenMP.py | 2 +- .../tests/test_auto_FSScriptCommand.py | 2 +- .../freesurfer/tests/test_auto_FitMSParams.py | 9 +- .../freesurfer/tests/test_auto_FixTopology.py | 24 +++- .../tests/test_auto_FuseSegmentations.py | 5 +- .../freesurfer/tests/test_auto_GLMFit.py | 53 ++++++--- .../freesurfer/tests/test_auto_ImageInfo.py | 5 +- .../freesurfer/tests/test_auto_Jacobian.py | 7 +- .../freesurfer/tests/test_auto_LTAConvert.py | 25 +++-- .../freesurfer/tests/test_auto_Label2Annot.py | 14 ++- .../freesurfer/tests/test_auto_Label2Label.py | 26 ++++- .../freesurfer/tests/test_auto_Label2Vol.py | 20 +++- .../tests/test_auto_MNIBiasCorrection.py | 16 ++- .../freesurfer/tests/test_auto_MPRtoMNI305.py | 4 +- .../freesurfer/tests/test_auto_MRIConvert.py | 44 ++++++-- .../freesurfer/tests/test_auto_MRICoreg.py | 13 ++- .../freesurfer/tests/test_auto_MRIFill.py | 23 +++- .../tests/test_auto_MRIMarchingCubes.py | 6 +- .../freesurfer/tests/test_auto_MRIPretess.py | 7 +- .../freesurfer/tests/test_auto_MRISPreproc.py | 7 +- .../tests/test_auto_MRISPreprocReconAll.py | 18 ++- .../tests/test_auto_MRITessellate.py | 6 +- .../freesurfer/tests/test_auto_MRIsCALabel.py | 22 +++- .../freesurfer/tests/test_auto_MRIsCalc.py | 7 +- .../freesurfer/tests/test_auto_MRIsCombine.py | 5 +- .../freesurfer/tests/test_auto_MRIsConvert.py | 36 ++++-- .../freesurfer/tests/test_auto_MRIsExpand.py | 5 +- .../freesurfer/tests/test_auto_MRIsInflate.py | 13 ++- .../freesurfer/tests/test_auto_MS_LDA.py | 6 +- .../tests/test_auto_MakeAverageSubject.py | 2 +- .../tests/test_auto_MakeSurfaces.py | 48 +++++--- .../freesurfer/tests/test_auto_Normalize.py | 16 ++- .../tests/test_auto_OneSampleTTest.py | 53 ++++++--- .../freesurfer/tests/test_auto_Paint.py | 7 +- .../tests/test_auto_ParcellationStats.py | 58 +++++++--- .../tests/test_auto_ParseDICOMDir.py | 5 +- .../freesurfer/tests/test_auto_ReconAll.py | 65 ++++++++--- .../freesurfer/tests/test_auto_Register.py | 13 ++- .../tests/test_auto_RegisterAVItoTalairach.py | 5 +- .../tests/test_auto_RelabelHypointensities.py | 12 +- .../tests/test_auto_RemoveIntersection.py | 6 +- .../freesurfer/tests/test_auto_RemoveNeck.py | 8 +- .../freesurfer/tests/test_auto_Resample.py | 6 +- .../tests/test_auto_RobustRegister.py | 35 ++++-- .../tests/test_auto_RobustTemplate.py | 4 +- .../tests/test_auto_SampleToSurface.py | 17 ++- .../freesurfer/tests/test_auto_SegStats.py | 39 +++++-- .../tests/test_auto_SegStatsReconAll.py | 78 +++++++++---- .../freesurfer/tests/test_auto_SegmentCC.py | 14 ++- .../freesurfer/tests/test_auto_SegmentWM.py | 6 +- .../freesurfer/tests/test_auto_Smooth.py | 7 +- .../tests/test_auto_SmoothTessellation.py | 16 ++- .../freesurfer/tests/test_auto_Sphere.py | 11 +- .../tests/test_auto_SphericalAverage.py | 11 +- .../tests/test_auto_Surface2VolTransform.py | 13 ++- .../tests/test_auto_SurfaceSmooth.py | 6 +- .../tests/test_auto_SurfaceSnapshots.py | 16 ++- .../tests/test_auto_SurfaceTransform.py | 7 +- .../tests/test_auto_SynthesizeFLASH.py | 7 +- .../tests/test_auto_TalairachAVI.py | 4 +- .../freesurfer/tests/test_auto_TalairachQC.py | 3 +- .../freesurfer/tests/test_auto_Tkregister2.py | 25 +++-- .../tests/test_auto_UnpackSDICOMDir.py | 20 +++- .../freesurfer/tests/test_auto_VolumeMask.py | 34 ++++-- .../tests/test_auto_WatershedSkullStrip.py | 7 +- .../fsl/tests/test_auto_AR1Image.py | 4 +- .../fsl/tests/test_auto_AccuracyTester.py | 3 + .../fsl/tests/test_auto_ApplyMask.py | 5 +- .../fsl/tests/test_auto_ApplyTOPUP.py | 6 +- .../fsl/tests/test_auto_ApplyWarp.py | 25 ++++- .../fsl/tests/test_auto_ApplyXFM.py | 36 ++++-- .../interfaces/fsl/tests/test_auto_AvScale.py | 2 + .../interfaces/fsl/tests/test_auto_B0Calc.py | 4 +- .../fsl/tests/test_auto_BEDPOSTX5.py | 31 ++++-- nipype/interfaces/fsl/tests/test_auto_BET.py | 25 +++-- .../fsl/tests/test_auto_BinaryMaths.py | 5 +- .../fsl/tests/test_auto_ChangeDataType.py | 4 +- .../fsl/tests/test_auto_Classifier.py | 6 +- .../interfaces/fsl/tests/test_auto_Cleaner.py | 3 +- .../interfaces/fsl/tests/test_auto_Cluster.py | 32 ++++-- .../interfaces/fsl/tests/test_auto_Complex.py | 21 +++- .../fsl/tests/test_auto_ContrastMgr.py | 9 +- .../fsl/tests/test_auto_ConvertWarp.py | 34 ++++-- .../fsl/tests/test_auto_ConvertXFM.py | 5 +- .../fsl/tests/test_auto_CopyGeom.py | 4 +- .../interfaces/fsl/tests/test_auto_DTIFit.py | 38 ++++--- .../fsl/tests/test_auto_DilateImage.py | 5 +- .../fsl/tests/test_auto_DistanceMap.py | 11 +- .../fsl/tests/test_auto_DualRegression.py | 5 +- .../fsl/tests/test_auto_EPIDeWarp.py | 20 +++- nipype/interfaces/fsl/tests/test_auto_Eddy.py | 40 +++++-- .../fsl/tests/test_auto_EddyCorrect.py | 4 +- .../fsl/tests/test_auto_EddyQuad.py | 29 +++-- .../interfaces/fsl/tests/test_auto_EpiReg.py | 56 ++++++---- .../fsl/tests/test_auto_ErodeImage.py | 5 +- .../fsl/tests/test_auto_ExtractROI.py | 4 +- nipype/interfaces/fsl/tests/test_auto_FAST.py | 21 +++- nipype/interfaces/fsl/tests/test_auto_FEAT.py | 3 +- .../fsl/tests/test_auto_FEATModel.py | 11 +- .../fsl/tests/test_auto_FEATRegister.py | 7 +- 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.../fsl/tests/test_auto_Randomise.py | 18 ++- .../fsl/tests/test_auto_Reorient2Std.py | 4 +- .../fsl/tests/test_auto_RobustFOV.py | 7 +- nipype/interfaces/fsl/tests/test_auto_SMM.py | 8 +- .../interfaces/fsl/tests/test_auto_SUSAN.py | 4 +- .../interfaces/fsl/tests/test_auto_SigLoss.py | 9 +- .../interfaces/fsl/tests/test_auto_Slice.py | 1 + .../fsl/tests/test_auto_SliceTimer.py | 14 ++- .../interfaces/fsl/tests/test_auto_Slicer.py | 6 +- .../interfaces/fsl/tests/test_auto_Smooth.py | 4 +- .../fsl/tests/test_auto_SmoothEstimate.py | 3 + .../fsl/tests/test_auto_SpatialFilter.py | 5 +- .../interfaces/fsl/tests/test_auto_Split.py | 1 + .../fsl/tests/test_auto_StdImage.py | 4 +- .../fsl/tests/test_auto_SwapDimensions.py | 4 +- .../interfaces/fsl/tests/test_auto_TOPUP.py | 18 ++- .../fsl/tests/test_auto_TemporalFilter.py | 4 +- .../fsl/tests/test_auto_Threshold.py | 4 +- .../fsl/tests/test_auto_TractSkeleton.py | 26 +++-- .../fsl/tests/test_auto_Training.py | 2 +- 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...est_auto_JistCortexSurfaceMeshInflation.py | 9 +- .../test_auto_JistIntensityMp2rageMasking.py | 23 ++-- .../test_auto_JistLaminarProfileCalculator.py | 12 +- .../test_auto_JistLaminarProfileGeometry.py | 7 +- .../test_auto_JistLaminarProfileSampling.py | 19 +++- .../test_auto_JistLaminarROIAveraging.py | 17 ++- ...test_auto_JistLaminarVolumetricLayering.py | 16 ++- ...test_auto_MedicAlgorithmImageCalculator.py | 12 +- .../test_auto_MedicAlgorithmLesionToads.py | 48 +++++--- .../test_auto_MedicAlgorithmMipavReorient.py | 5 +- .../mipav/tests/test_auto_MedicAlgorithmN3.py | 9 +- .../test_auto_MedicAlgorithmSPECTRE2010.py | 28 +++-- .../mipav/tests/test_auto_RandomVol.py | 2 +- .../mne/tests/test_auto_WatershedBEM.py | 21 +++- ..._auto_ConstrainedSphericalDeconvolution.py | 9 +- .../test_auto_DWI2SphericalHarmonicsImage.py | 5 +- .../mrtrix/tests/test_auto_DWI2Tensor.py | 4 +- ...est_auto_DiffusionTensorStreamlineTrack.py | 9 +- .../tests/test_auto_Directions2Amplitude.py | 9 +- 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.../brains/tests/test_auto_SimilarityIndex.py | 15 ++- .../diffusion/tests/test_auto_DWIConvert.py | 35 ++++-- .../tests/test_auto_compareTractInclusion.py | 10 +- .../diffusion/tests/test_auto_dtiaverage.py | 2 +- .../diffusion/tests/test_auto_dtiestim.py | 23 ++-- .../diffusion/tests/test_auto_dtiprocess.py | 60 ++++++---- .../tests/test_auto_extractNrrdVectorIndex.py | 7 +- .../tests/test_auto_gtractAnisotropyMap.py | 7 +- .../tests/test_auto_gtractAverageBvalues.py | 7 +- .../tests/test_auto_gtractClipAnisotropy.py | 7 +- .../tests/test_auto_gtractCoRegAnatomy.py | 17 ++- .../tests/test_auto_gtractConcatDwi.py | 2 +- .../test_auto_gtractCopyImageOrientation.py | 12 +- .../tests/test_auto_gtractCoregBvalues.py | 14 ++- .../tests/test_auto_gtractCostFastMarching.py | 18 ++- .../tests/test_auto_gtractCreateGuideFiber.py | 7 +- .../test_auto_gtractFastMarchingTracking.py | 21 +++- .../tests/test_auto_gtractFiberTracking.py | 25 ++++- .../tests/test_auto_gtractImageConformity.py | 12 +- 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.../tests/test_auto_DWIRicianLMMSEFilter.py | 7 +- .../tests/test_auto_DWIToDTIEstimation.py | 16 ++- ..._auto_DiffusionTensorScalarMeasurements.py | 7 +- ...est_auto_DiffusionWeightedVolumeMasking.py | 11 +- .../tests/test_auto_ResampleDTIVolume.py | 22 +++- .../test_auto_TractographyLabelMapSeeding.py | 13 ++- .../tests/test_auto_AddScalarVolumes.py | 8 +- .../tests/test_auto_CastScalarVolume.py | 7 +- .../tests/test_auto_CheckerBoardFilter.py | 8 +- ...test_auto_CurvatureAnisotropicDiffusion.py | 7 +- .../tests/test_auto_ExtractSkeleton.py | 7 +- .../test_auto_GaussianBlurImageFilter.py | 7 +- .../test_auto_GradientAnisotropicDiffusion.py | 7 +- .../test_auto_GrayscaleFillHoleImageFilter.py | 7 +- ...test_auto_GrayscaleGrindPeakImageFilter.py | 7 +- .../tests/test_auto_HistogramMatching.py | 8 +- .../tests/test_auto_ImageLabelCombine.py | 8 +- .../tests/test_auto_MaskScalarVolume.py | 8 +- .../tests/test_auto_MedianImageFilter.py | 7 +- .../tests/test_auto_MultiplyScalarVolumes.py | 8 +- .../test_auto_N4ITKBiasFieldCorrection.py | 19 +++- ...test_auto_ResampleScalarVectorDWIVolume.py | 22 +++- .../tests/test_auto_SubtractScalarVolumes.py | 8 +- .../tests/test_auto_ThresholdScalarVolume.py | 7 +- ...auto_VotingBinaryHoleFillingImageFilter.py | 7 +- ...est_auto_DWIUnbiasedNonLocalMeansFilter.py | 7 +- .../tests/test_auto_AffineRegistration.py | 11 +- ...test_auto_BSplineDeformableRegistration.py | 13 ++- .../test_auto_BSplineToDeformationField.py | 12 +- .../test_auto_ExpertAutomatedRegistration.py | 16 ++- .../tests/test_auto_LinearRegistration.py | 11 +- ..._auto_MultiResolutionAffineRegistration.py | 11 +- .../test_auto_OtsuThresholdImageFilter.py | 7 +- .../test_auto_OtsuThresholdSegmentation.py | 7 +- .../tests/test_auto_ResampleScalarVolume.py | 7 +- .../tests/test_auto_RigidRegistration.py | 11 +- .../test_auto_IntensityDifferenceMetric.py | 10 +- ..._auto_PETStandardUptakeValueComputation.py | 22 +++- .../tests/test_auto_ACPCTransform.py | 2 +- .../tests/test_auto_BRAINSDemonWarp.py | 35 ++++-- .../registration/tests/test_auto_BRAINSFit.py | 39 +++++-- .../tests/test_auto_BRAINSResample.py | 22 +++- .../tests/test_auto_FiducialRegistration.py | 2 +- .../tests/test_auto_VBRAINSDemonWarp.py | 25 +++-- .../tests/test_auto_BRAINSROIAuto.py | 9 +- .../tests/test_auto_EMSegmentCommandLine.py | 19 +++- .../test_auto_RobustStatisticsSegmenter.py | 8 +- ...st_auto_SimpleRegionGrowingSegmentation.py | 7 +- .../tests/test_auto_DicomToNrrdConverter.py | 7 +- ...test_auto_EMSegmentTransformToNewFormat.py | 7 +- .../tests/test_auto_GrayscaleModelMaker.py | 7 +- .../tests/test_auto_LabelMapSmoothing.py | 7 +- .../slicer/tests/test_auto_MergeModels.py | 8 +- .../slicer/tests/test_auto_ModelMaker.py | 6 +- .../slicer/tests/test_auto_ModelToLabelMap.py | 8 +- .../tests/test_auto_OrientScalarVolume.py | 7 +- .../tests/test_auto_ProbeVolumeWithModel.py | 8 +- .../spm/tests/test_auto_Analyze2nii.py | 7 +- .../spm/tests/test_auto_ApplyDeformations.py | 2 + .../test_auto_ApplyInverseDeformation.py | 7 +- .../spm/tests/test_auto_ApplyTransform.py | 13 ++- .../spm/tests/test_auto_CalcCoregAffine.py | 14 ++- .../spm/tests/test_auto_Coregister.py | 1 + .../interfaces/spm/tests/test_auto_DARTEL.py | 2 +- .../spm/tests/test_auto_DARTELNorm2MNI.py | 3 +- .../spm/tests/test_auto_EstimateContrast.py | 4 +- .../spm/tests/test_auto_EstimateModel.py | 11 +- .../spm/tests/test_auto_FactorialDesign.py | 12 +- .../spm/tests/test_auto_FieldMap.py | 7 +- .../spm/tests/test_auto_Level1Design.py | 12 +- .../test_auto_MultipleRegressionDesign.py | 12 +- .../spm/tests/test_auto_Normalize.py | 4 + .../spm/tests/test_auto_Normalize12.py | 3 + .../tests/test_auto_OneSampleTTestDesign.py | 12 +- .../spm/tests/test_auto_PairedTTestDesign.py | 12 +- .../interfaces/spm/tests/test_auto_Realign.py | 7 +- .../spm/tests/test_auto_RealignUnwarp.py | 8 +- .../interfaces/spm/tests/test_auto_Reslice.py | 14 ++- .../spm/tests/test_auto_ResliceToReference.py | 5 +- .../interfaces/spm/tests/test_auto_Segment.py | 30 ++--- .../spm/tests/test_auto_Threshold.py | 6 +- .../tests/test_auto_ThresholdStatistics.py | 2 + .../tests/test_auto_TwoSampleTTestDesign.py | 12 +- .../spm/tests/test_auto_VBMSegment.py | 9 +- .../tests/test_auto_BIDSDataGrabber.py | 5 +- nipype/interfaces/tests/test_auto_Bru2.py | 3 +- nipype/interfaces/tests/test_auto_C3d.py | 1 + .../tests/test_auto_C3dAffineTool.py | 5 +- nipype/interfaces/tests/test_auto_CopyMeta.py | 12 +- .../interfaces/tests/test_auto_DataGrabber.py | 2 +- nipype/interfaces/tests/test_auto_DataSink.py | 4 +- nipype/interfaces/tests/test_auto_Dcm2nii.py | 3 + nipype/interfaces/tests/test_auto_Dcm2niix.py | 1 + nipype/interfaces/tests/test_auto_DcmStack.py | 4 +- .../tests/test_auto_FreeSurferSource.py | 60 ++++++++-- .../tests/test_auto_GroupAndStack.py | 2 +- .../tests/test_auto_JSONFileGrabber.py | 2 +- .../tests/test_auto_JSONFileSink.py | 4 +- .../interfaces/tests/test_auto_LookupMeta.py | 5 +- .../tests/test_auto_MatlabCommand.py | 5 +- .../interfaces/tests/test_auto_MergeNifti.py | 4 +- nipype/interfaces/tests/test_auto_MeshFix.py | 5 +- .../interfaces/tests/test_auto_MySQLSink.py | 1 + nipype/interfaces/tests/test_auto_PETPVC.py | 5 +- .../interfaces/tests/test_auto_Quickshear.py | 5 +- nipype/interfaces/tests/test_auto_Reorient.py | 9 +- nipype/interfaces/tests/test_auto_Rescale.py | 12 +- .../tests/test_auto_S3DataGrabber.py | 2 +- .../interfaces/tests/test_auto_SQLiteSink.py | 5 +- .../interfaces/tests/test_auto_SelectFiles.py | 2 +- .../tests/test_auto_SignalExtraction.py | 7 +- .../interfaces/tests/test_auto_SplitNifti.py | 7 +- nipype/interfaces/tests/test_auto_XNATSink.py | 3 +- .../interfaces/tests/test_auto_XNATSource.py | 3 +- .../utility/tests/test_auto_AssertEqual.py | 10 +- .../utility/tests/test_auto_CSVReader.py | 5 +- .../utility/tests/test_auto_Rename.py | 5 +- .../vista/tests/test_auto_Vnifti2Image.py | 5 +- .../vista/tests/test_auto_VtoMat.py | 4 +- .../workbench/tests/test_auto_CiftiSmooth.py | 11 +- .../tests/test_auto_MetricResample.py | 11 +- 781 files changed, 6777 insertions(+), 2429 deletions(-) diff --git a/nipype/algorithms/tests/test_auto_ACompCor.py b/nipype/algorithms/tests/test_auto_ACompCor.py index e28c77d467..ff33a4f94d 100644 --- a/nipype/algorithms/tests/test_auto_ACompCor.py +++ b/nipype/algorithms/tests/test_auto_ACompCor.py @@ -22,7 +22,10 @@ def test_ACompCor_inputs(): ), num_components=dict(xor=['variance_threshold'], ), pre_filter=dict(usedefault=True, ), - realigned_file=dict(mandatory=True, ), + realigned_file=dict( + mandatory=True, + usedefault=True, + ), regress_poly_degree=dict(usedefault=True, ), repetition_time=dict(), save_metadata=dict(usedefault=True, ), @@ -40,9 +43,9 @@ def test_ACompCor_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ACompCor_outputs(): output_map = dict( - components_file=dict(), - metadata_file=dict(), - pre_filter_file=dict(), + components_file=dict(usedefault=True, ), + metadata_file=dict(usedefault=True, ), + pre_filter_file=dict(usedefault=True, ), ) outputs = ACompCor.output_spec() diff --git a/nipype/algorithms/tests/test_auto_ActivationCount.py b/nipype/algorithms/tests/test_auto_ActivationCount.py index d6e3ff7165..5bbc837c74 100644 --- a/nipype/algorithms/tests/test_auto_ActivationCount.py +++ b/nipype/algorithms/tests/test_auto_ActivationCount.py @@ -15,9 +15,9 @@ def test_ActivationCount_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ActivationCount_outputs(): output_map = dict( - acm_neg=dict(), - acm_pos=dict(), - out_file=dict(), + acm_neg=dict(usedefault=True, ), + acm_pos=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), ) outputs = ActivationCount.output_spec() diff --git a/nipype/algorithms/tests/test_auto_AddCSVColumn.py b/nipype/algorithms/tests/test_auto_AddCSVColumn.py index feedcf46e8..82fba10b80 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVColumn.py +++ b/nipype/algorithms/tests/test_auto_AddCSVColumn.py @@ -7,7 +7,10 @@ def test_AddCSVColumn_inputs(): input_map = dict( extra_column_heading=dict(), extra_field=dict(), - in_file=dict(mandatory=True, ), + in_file=dict( + mandatory=True, + usedefault=True, + ), out_file=dict(usedefault=True, ), ) inputs = AddCSVColumn.input_spec() @@ -16,7 +19,7 @@ def test_AddCSVColumn_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AddCSVColumn_outputs(): - output_map = dict(csv_file=dict(), ) + output_map = dict(csv_file=dict(usedefault=True, ), ) outputs = AddCSVColumn.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_AddCSVRow.py b/nipype/algorithms/tests/test_auto_AddCSVRow.py index 4666a147d2..e96cef284f 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVRow.py +++ b/nipype/algorithms/tests/test_auto_AddCSVRow.py @@ -14,7 +14,7 @@ def test_AddCSVRow_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AddCSVRow_outputs(): - output_map = dict(csv_file=dict(), ) + output_map = dict(csv_file=dict(usedefault=True, ), ) outputs = AddCSVRow.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_AddNoise.py b/nipype/algorithms/tests/test_auto_AddNoise.py index 6e0655a93e..3348f938ab 100644 --- a/nipype/algorithms/tests/test_auto_AddNoise.py +++ b/nipype/algorithms/tests/test_auto_AddNoise.py @@ -13,9 +13,12 @@ def test_AddNoise_inputs(): mandatory=True, usedefault=True, ), - in_file=dict(mandatory=True, ), - in_mask=dict(), - out_file=dict(), + in_file=dict( + mandatory=True, + usedefault=True, + ), + in_mask=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), snr=dict(usedefault=True, ), ) inputs = AddNoise.input_spec() @@ -24,7 +27,7 @@ def test_AddNoise_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AddNoise_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = AddNoise.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_ArtifactDetect.py b/nipype/algorithms/tests/test_auto_ArtifactDetect.py index 85c57b8823..900a55c6a1 100644 --- a/nipype/algorithms/tests/test_auto_ArtifactDetect.py +++ b/nipype/algorithms/tests/test_auto_ArtifactDetect.py @@ -8,7 +8,7 @@ def test_ArtifactDetect_inputs(): bound_by_brainmask=dict(usedefault=True, ), global_threshold=dict(usedefault=True, ), intersect_mask=dict(usedefault=True, ), - mask_file=dict(), + mask_file=dict(usedefault=True, ), mask_threshold=dict(), mask_type=dict(mandatory=True, ), norm_threshold=dict( diff --git a/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py b/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py index 3dbbd772c8..18d1c3488f 100644 --- a/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py +++ b/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py @@ -6,7 +6,10 @@ def test_CalculateNormalizedMoments_inputs(): input_map = dict( moment=dict(mandatory=True, ), - timeseries_file=dict(mandatory=True, ), + timeseries_file=dict( + mandatory=True, + usedefault=True, + ), ) inputs = CalculateNormalizedMoments.input_spec() diff --git a/nipype/algorithms/tests/test_auto_ComputeDVARS.py b/nipype/algorithms/tests/test_auto_ComputeDVARS.py index ca263c77ac..ddb06bb364 100644 --- a/nipype/algorithms/tests/test_auto_ComputeDVARS.py +++ b/nipype/algorithms/tests/test_auto_ComputeDVARS.py @@ -8,8 +8,14 @@ def test_ComputeDVARS_inputs(): figdpi=dict(usedefault=True, ), figformat=dict(usedefault=True, ), figsize=dict(usedefault=True, ), - in_file=dict(mandatory=True, ), - in_mask=dict(mandatory=True, ), + in_file=dict( + mandatory=True, + usedefault=True, + ), + in_mask=dict( + mandatory=True, + usedefault=True, + ), intensity_normalization=dict(usedefault=True, ), remove_zerovariance=dict(usedefault=True, ), save_all=dict(usedefault=True, ), @@ -29,13 +35,13 @@ def test_ComputeDVARS_outputs(): avg_nstd=dict(), avg_std=dict(), avg_vxstd=dict(), - fig_nstd=dict(), - fig_std=dict(), - fig_vxstd=dict(), - out_all=dict(), - out_nstd=dict(), - out_std=dict(), - out_vxstd=dict(), + fig_nstd=dict(usedefault=True, ), + fig_std=dict(usedefault=True, ), + fig_vxstd=dict(usedefault=True, ), + out_all=dict(usedefault=True, ), + out_nstd=dict(usedefault=True, ), + out_std=dict(usedefault=True, ), + out_vxstd=dict(usedefault=True, ), ) outputs = ComputeDVARS.output_spec() diff --git a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py index 0308653786..47aac34917 100644 --- a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py +++ b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py @@ -8,8 +8,14 @@ def test_ComputeMeshWarp_inputs(): metric=dict(usedefault=True, ), out_file=dict(usedefault=True, ), out_warp=dict(usedefault=True, ), - surface1=dict(mandatory=True, ), - surface2=dict(mandatory=True, ), + surface1=dict( + mandatory=True, + usedefault=True, + ), + surface2=dict( + mandatory=True, + usedefault=True, + ), weighting=dict(usedefault=True, ), ) inputs = ComputeMeshWarp.input_spec() @@ -20,8 +26,8 @@ def test_ComputeMeshWarp_inputs(): def test_ComputeMeshWarp_outputs(): output_map = dict( distance=dict(), - out_file=dict(), - out_warp=dict(), + out_file=dict(usedefault=True, ), + out_warp=dict(usedefault=True, ), ) outputs = ComputeMeshWarp.output_spec() diff --git a/nipype/algorithms/tests/test_auto_CreateNifti.py b/nipype/algorithms/tests/test_auto_CreateNifti.py index f8bf8a405f..bf607edbe3 100644 --- a/nipype/algorithms/tests/test_auto_CreateNifti.py +++ b/nipype/algorithms/tests/test_auto_CreateNifti.py @@ -6,8 +6,14 @@ def test_CreateNifti_inputs(): input_map = dict( affine=dict(), - data_file=dict(mandatory=True, ), - header_file=dict(mandatory=True, ), + data_file=dict( + mandatory=True, + usedefault=True, + ), + header_file=dict( + mandatory=True, + usedefault=True, + ), ) inputs = CreateNifti.input_spec() @@ -15,7 +21,7 @@ def test_CreateNifti_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CreateNifti_outputs(): - output_map = dict(nifti_file=dict(), ) + output_map = dict(nifti_file=dict(usedefault=True, ), ) outputs = CreateNifti.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_Distance.py b/nipype/algorithms/tests/test_auto_Distance.py index 2c5d098d73..3dfe5817e3 100644 --- a/nipype/algorithms/tests/test_auto_Distance.py +++ b/nipype/algorithms/tests/test_auto_Distance.py @@ -5,10 +5,16 @@ def test_Distance_inputs(): input_map = dict( - mask_volume=dict(), + mask_volume=dict(usedefault=True, ), method=dict(usedefault=True, ), - volume1=dict(mandatory=True, ), - volume2=dict(mandatory=True, ), + volume1=dict( + mandatory=True, + usedefault=True, + ), + volume2=dict( + mandatory=True, + usedefault=True, + ), ) inputs = Distance.input_spec() @@ -18,7 +24,7 @@ def test_Distance_inputs(): def test_Distance_outputs(): output_map = dict( distance=dict(), - histogram=dict(), + histogram=dict(usedefault=True, ), point1=dict(), point2=dict(), ) diff --git a/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py b/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py index 685dec61e8..e33f793b52 100644 --- a/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py +++ b/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py @@ -7,7 +7,10 @@ def test_FramewiseDisplacement_inputs(): input_map = dict( figdpi=dict(usedefault=True, ), figsize=dict(usedefault=True, ), - in_file=dict(mandatory=True, ), + in_file=dict( + mandatory=True, + usedefault=True, + ), normalize=dict(usedefault=True, ), out_figure=dict(usedefault=True, ), out_file=dict(usedefault=True, ), @@ -24,8 +27,8 @@ def test_FramewiseDisplacement_inputs(): def test_FramewiseDisplacement_outputs(): output_map = dict( fd_average=dict(), - out_figure=dict(), - out_file=dict(), + out_figure=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), ) outputs = FramewiseDisplacement.output_spec() diff --git a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py index e9e28aaa44..8f11f836fd 100644 --- a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py +++ b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py @@ -5,7 +5,7 @@ def test_FuzzyOverlap_inputs(): input_map = dict( - in_mask=dict(), + in_mask=dict(usedefault=True, ), in_ref=dict(mandatory=True, ), in_tst=dict(mandatory=True, ), out_file=dict(usedefault=True, ), diff --git a/nipype/algorithms/tests/test_auto_Gunzip.py b/nipype/algorithms/tests/test_auto_Gunzip.py index f12e1f9b45..bf04db015d 100644 --- a/nipype/algorithms/tests/test_auto_Gunzip.py +++ b/nipype/algorithms/tests/test_auto_Gunzip.py @@ -4,14 +4,18 @@ def test_Gunzip_inputs(): - input_map = dict(in_file=dict(mandatory=True, ), ) + input_map = dict( + in_file=dict( + mandatory=True, + usedefault=True, + ), ) inputs = Gunzip.input_spec() for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Gunzip_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Gunzip.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_ICC.py b/nipype/algorithms/tests/test_auto_ICC.py index 1a4a2b1517..98260c3db1 100644 --- a/nipype/algorithms/tests/test_auto_ICC.py +++ b/nipype/algorithms/tests/test_auto_ICC.py @@ -5,7 +5,10 @@ def test_ICC_inputs(): input_map = dict( - mask=dict(mandatory=True, ), + mask=dict( + mandatory=True, + usedefault=True, + ), subjects_sessions=dict(mandatory=True, ), ) inputs = ICC.input_spec() @@ -15,9 +18,9 @@ def test_ICC_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ICC_outputs(): output_map = dict( - icc_map=dict(), - session_var_map=dict(), - subject_var_map=dict(), + icc_map=dict(usedefault=True, ), + session_var_map=dict(usedefault=True, ), + subject_var_map=dict(usedefault=True, ), ) outputs = ICC.output_spec() diff --git a/nipype/algorithms/tests/test_auto_Matlab2CSV.py b/nipype/algorithms/tests/test_auto_Matlab2CSV.py index fcc1648bf9..648248e12f 100644 --- a/nipype/algorithms/tests/test_auto_Matlab2CSV.py +++ b/nipype/algorithms/tests/test_auto_Matlab2CSV.py @@ -5,7 +5,10 @@ def test_Matlab2CSV_inputs(): input_map = dict( - in_file=dict(mandatory=True, ), + in_file=dict( + mandatory=True, + usedefault=True, + ), reshape_matrix=dict(usedefault=True, ), ) inputs = Matlab2CSV.input_spec() diff --git a/nipype/algorithms/tests/test_auto_MergeCSVFiles.py b/nipype/algorithms/tests/test_auto_MergeCSVFiles.py index fd882e850a..b2091d39c5 100644 --- a/nipype/algorithms/tests/test_auto_MergeCSVFiles.py +++ b/nipype/algorithms/tests/test_auto_MergeCSVFiles.py @@ -19,7 +19,7 @@ def test_MergeCSVFiles_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MergeCSVFiles_outputs(): - output_map = dict(csv_file=dict(), ) + output_map = dict(csv_file=dict(usedefault=True, ), ) outputs = MergeCSVFiles.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_MergeROIs.py b/nipype/algorithms/tests/test_auto_MergeROIs.py index 01b2b097a8..fc2298c1b5 100644 --- a/nipype/algorithms/tests/test_auto_MergeROIs.py +++ b/nipype/algorithms/tests/test_auto_MergeROIs.py @@ -7,7 +7,7 @@ def test_MergeROIs_inputs(): input_map = dict( in_files=dict(), in_index=dict(), - in_reference=dict(), + in_reference=dict(usedefault=True, ), ) inputs = MergeROIs.input_spec() @@ -15,7 +15,7 @@ def test_MergeROIs_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MergeROIs_outputs(): - output_map = dict(merged_file=dict(), ) + output_map = dict(merged_file=dict(usedefault=True, ), ) outputs = MergeROIs.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py index f89b16017b..a633a3f657 100644 --- a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py +++ b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py @@ -6,7 +6,10 @@ def test_MeshWarpMaths_inputs(): input_map = dict( float_trait=dict(), - in_surf=dict(mandatory=True, ), + in_surf=dict( + mandatory=True, + usedefault=True, + ), operation=dict(usedefault=True, ), operator=dict( mandatory=True, @@ -22,8 +25,8 @@ def test_MeshWarpMaths_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MeshWarpMaths_outputs(): output_map = dict( - out_file=dict(), - out_warp=dict(), + out_file=dict(usedefault=True, ), + out_warp=dict(usedefault=True, ), ) outputs = MeshWarpMaths.output_spec() diff --git a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py index b86fe3df03..94ee5f1103 100644 --- a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py +++ b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py @@ -4,7 +4,11 @@ def test_NonSteadyStateDetector_inputs(): - input_map = dict(in_file=dict(mandatory=True, ), ) + input_map = dict( + in_file=dict( + mandatory=True, + usedefault=True, + ), ) inputs = NonSteadyStateDetector.input_spec() for key, metadata in list(input_map.items()): diff --git a/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py b/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py index 4c9a5584d0..298207c8ef 100644 --- a/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py +++ b/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py @@ -6,7 +6,7 @@ def test_NormalizeProbabilityMapSet_inputs(): input_map = dict( in_files=dict(), - in_mask=dict(), + in_mask=dict(usedefault=True, ), ) inputs = NormalizeProbabilityMapSet.input_spec() diff --git a/nipype/algorithms/tests/test_auto_P2PDistance.py b/nipype/algorithms/tests/test_auto_P2PDistance.py index 9948e3675e..4671c89fdb 100644 --- a/nipype/algorithms/tests/test_auto_P2PDistance.py +++ b/nipype/algorithms/tests/test_auto_P2PDistance.py @@ -8,8 +8,14 @@ def test_P2PDistance_inputs(): metric=dict(usedefault=True, ), out_file=dict(usedefault=True, ), out_warp=dict(usedefault=True, ), - surface1=dict(mandatory=True, ), - surface2=dict(mandatory=True, ), + surface1=dict( + mandatory=True, + usedefault=True, + ), + surface2=dict( + mandatory=True, + usedefault=True, + ), weighting=dict(usedefault=True, ), ) inputs = P2PDistance.input_spec() @@ -20,8 +26,8 @@ def test_P2PDistance_inputs(): def test_P2PDistance_outputs(): output_map = dict( distance=dict(), - out_file=dict(), - out_warp=dict(), + out_file=dict(usedefault=True, ), + out_warp=dict(usedefault=True, ), ) outputs = P2PDistance.output_spec() diff --git a/nipype/algorithms/tests/test_auto_PickAtlas.py b/nipype/algorithms/tests/test_auto_PickAtlas.py index 3b15c302e5..604e883674 100644 --- a/nipype/algorithms/tests/test_auto_PickAtlas.py +++ b/nipype/algorithms/tests/test_auto_PickAtlas.py @@ -5,11 +5,14 @@ def test_PickAtlas_inputs(): input_map = dict( - atlas=dict(mandatory=True, ), + atlas=dict( + mandatory=True, + usedefault=True, + ), dilation_size=dict(usedefault=True, ), hemi=dict(usedefault=True, ), labels=dict(mandatory=True, ), - output_file=dict(), + output_file=dict(usedefault=True, ), ) inputs = PickAtlas.input_spec() @@ -17,7 +20,7 @@ def test_PickAtlas_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PickAtlas_outputs(): - output_map = dict(mask_file=dict(), ) + output_map = dict(mask_file=dict(usedefault=True, ), ) outputs = PickAtlas.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_Similarity.py b/nipype/algorithms/tests/test_auto_Similarity.py index b2ad79b5eb..97fb6a2490 100644 --- a/nipype/algorithms/tests/test_auto_Similarity.py +++ b/nipype/algorithms/tests/test_auto_Similarity.py @@ -5,11 +5,17 @@ def test_Similarity_inputs(): input_map = dict( - mask1=dict(), - mask2=dict(), + mask1=dict(usedefault=True, ), + mask2=dict(usedefault=True, ), metric=dict(usedefault=True, ), - volume1=dict(mandatory=True, ), - volume2=dict(mandatory=True, ), + volume1=dict( + mandatory=True, + usedefault=True, + ), + volume2=dict( + mandatory=True, + usedefault=True, + ), ) inputs = Similarity.input_spec() diff --git a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py index dc12dd3a89..128aad5aa5 100644 --- a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py @@ -53,8 +53,8 @@ def test_SpecifySparseModel_inputs(): def test_SpecifySparseModel_outputs(): output_map = dict( session_info=dict(), - sparse_png_file=dict(), - sparse_svg_file=dict(), + sparse_png_file=dict(usedefault=True, ), + sparse_svg_file=dict(usedefault=True, ), ) outputs = SpecifySparseModel.output_spec() diff --git a/nipype/algorithms/tests/test_auto_SplitROIs.py b/nipype/algorithms/tests/test_auto_SplitROIs.py index 963926666d..fd718624f3 100644 --- a/nipype/algorithms/tests/test_auto_SplitROIs.py +++ b/nipype/algorithms/tests/test_auto_SplitROIs.py @@ -5,8 +5,11 @@ def test_SplitROIs_inputs(): input_map = dict( - in_file=dict(mandatory=True, ), - in_mask=dict(), + in_file=dict( + mandatory=True, + usedefault=True, + ), + in_mask=dict(usedefault=True, ), roi_size=dict(), ) inputs = SplitROIs.input_spec() diff --git a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py index 8c7ef276d9..e18a219045 100644 --- a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py +++ b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py @@ -8,7 +8,10 @@ def test_StimulusCorrelation_inputs(): concatenated_design=dict(mandatory=True, ), intensity_values=dict(mandatory=True, ), realignment_parameters=dict(mandatory=True, ), - spm_mat_file=dict(mandatory=True, ), + spm_mat_file=dict( + mandatory=True, + usedefault=True, + ), ) inputs = StimulusCorrelation.input_spec() diff --git a/nipype/algorithms/tests/test_auto_TCompCor.py b/nipype/algorithms/tests/test_auto_TCompCor.py index c3bdcac192..3982b6f5fa 100644 --- a/nipype/algorithms/tests/test_auto_TCompCor.py +++ b/nipype/algorithms/tests/test_auto_TCompCor.py @@ -23,7 +23,10 @@ def test_TCompCor_inputs(): num_components=dict(xor=['variance_threshold'], ), percentile_threshold=dict(usedefault=True, ), pre_filter=dict(usedefault=True, ), - realigned_file=dict(mandatory=True, ), + realigned_file=dict( + mandatory=True, + usedefault=True, + ), regress_poly_degree=dict(usedefault=True, ), repetition_time=dict(), save_metadata=dict(usedefault=True, ), @@ -41,10 +44,10 @@ def test_TCompCor_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TCompCor_outputs(): output_map = dict( - components_file=dict(), + components_file=dict(usedefault=True, ), high_variance_masks=dict(), - metadata_file=dict(), - pre_filter_file=dict(), + metadata_file=dict(usedefault=True, ), + pre_filter_file=dict(usedefault=True, ), ) outputs = TCompCor.output_spec() diff --git a/nipype/algorithms/tests/test_auto_WarpPoints.py b/nipype/algorithms/tests/test_auto_WarpPoints.py index b6965065a2..e3967a8523 100644 --- a/nipype/algorithms/tests/test_auto_WarpPoints.py +++ b/nipype/algorithms/tests/test_auto_WarpPoints.py @@ -14,9 +14,16 @@ def test_WarpPoints_inputs(): name_source='points', name_template='%s_warped', output_name='out_points', + usedefault=True, + ), + points=dict( + mandatory=True, + usedefault=True, + ), + warp=dict( + mandatory=True, + usedefault=True, ), - points=dict(mandatory=True, ), - warp=dict(mandatory=True, ), ) inputs = WarpPoints.input_spec() @@ -24,7 +31,7 @@ def test_WarpPoints_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpPoints_outputs(): - output_map = dict(out_points=dict(), ) + output_map = dict(out_points=dict(usedefault=True, ), ) outputs = WarpPoints.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_ABoverlap.py b/nipype/interfaces/afni/tests/test_auto_ABoverlap.py index 55cb12c27f..67f8157add 100644 --- a/nipype/interfaces/afni/tests/test_auto_ABoverlap.py +++ b/nipype/interfaces/afni/tests/test_auto_ABoverlap.py @@ -15,12 +15,14 @@ def test_ABoverlap_inputs(): copyfile=False, mandatory=True, position=-3, + usedefault=True, ), in_file_b=dict( argstr='%s', copyfile=False, mandatory=True, position=-2, + usedefault=True, ), no_automask=dict(argstr='-no_automask', ), num_threads=dict( @@ -30,6 +32,7 @@ def test_ABoverlap_inputs(): out_file=dict( argstr=' |& tee %s', position=-1, + usedefault=True, ), outputtype=dict(), quiet=dict(argstr='-quiet', ), @@ -41,7 +44,7 @@ def test_ABoverlap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ABoverlap_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ABoverlap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py index 724c98dcb2..6d051d49b7 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py @@ -14,11 +14,6 @@ def test_AFNICommand_inputs(): nohash=True, usedefault=True, ), - out_file=dict( - argstr='-prefix %s', - name_source=['in_file'], - name_template='%s_afni', - ), outputtype=dict(), ) inputs = AFNICommand.input_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py b/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py index ba2411edfb..a3903c652b 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNIPythonCommand.py @@ -14,11 +14,6 @@ def test_AFNIPythonCommand_inputs(): nohash=True, usedefault=True, ), - out_file=dict( - argstr='-prefix %s', - name_source=['in_file'], - name_template='%s_afni', - ), outputtype=dict(), ) inputs = AFNIPythonCommand.input_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py index d89519d571..3aecfd48aa 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py @@ -16,6 +16,7 @@ def test_AFNItoNIFTI_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, ), newid=dict( argstr='-newid', @@ -34,6 +35,7 @@ def test_AFNItoNIFTI_inputs(): hash_files=False, name_source='in_file', name_template='%s.nii', + usedefault=True, ), outputtype=dict(), pure=dict(argstr='-pure', ), @@ -44,7 +46,7 @@ def test_AFNItoNIFTI_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AFNItoNIFTI_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = AFNItoNIFTI.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py b/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py index dfbfc648f7..15db355b43 100644 --- a/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py +++ b/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py @@ -9,6 +9,7 @@ def test_AlignEpiAnatPy_inputs(): argstr='-anat %s', copyfile=False, mandatory=True, + usedefault=True, ), anat2epi=dict(argstr='-anat2epi', ), args=dict(argstr='%s', ), @@ -26,6 +27,7 @@ def test_AlignEpiAnatPy_inputs(): argstr='-epi %s', copyfile=False, mandatory=True, + usedefault=True, ), outputtype=dict(), py27_path=dict(usedefault=True, ), @@ -50,16 +52,16 @@ def test_AlignEpiAnatPy_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_AlignEpiAnatPy_outputs(): output_map = dict( - anat_al_mat=dict(), - anat_al_orig=dict(), - epi_al_mat=dict(), - epi_al_orig=dict(), - epi_al_tlrc_mat=dict(), - epi_reg_al_mat=dict(), - epi_tlrc_al=dict(), - epi_vr_al_mat=dict(), - epi_vr_motion=dict(), - skullstrip=dict(), + anat_al_mat=dict(usedefault=True, ), + anat_al_orig=dict(usedefault=True, ), + epi_al_mat=dict(usedefault=True, ), + epi_al_orig=dict(usedefault=True, ), + epi_al_tlrc_mat=dict(usedefault=True, ), + epi_reg_al_mat=dict(usedefault=True, ), + epi_tlrc_al=dict(usedefault=True, ), + epi_vr_al_mat=dict(usedefault=True, ), + epi_vr_motion=dict(usedefault=True, ), + skullstrip=dict(usedefault=True, ), ) outputs = AlignEpiAnatPy.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Allineate.py b/nipype/interfaces/afni/tests/test_auto_Allineate.py index be02af14da..20678a52e2 100644 --- a/nipype/interfaces/afni/tests/test_auto_Allineate.py +++ b/nipype/interfaces/afni/tests/test_auto_Allineate.py @@ -8,6 +8,7 @@ def test_Allineate_inputs(): allcostx=dict( argstr='-allcostx |& tee %s', position=-1, + usedefault=True, xor=[ 'out_file', 'out_matrix', 'out_param_file', 'out_weight_file' ], @@ -31,18 +32,24 @@ def test_Allineate_inputs(): argstr='-source %s', copyfile=False, mandatory=True, + usedefault=True, ), in_matrix=dict( argstr='-1Dmatrix_apply %s', position=-3, + usedefault=True, xor=['out_matrix'], ), in_param_file=dict( argstr='-1Dparam_apply %s', + usedefault=True, xor=['out_param_file'], ), interpolation=dict(argstr='-interp %s', ), - master=dict(argstr='-master %s', ), + master=dict( + argstr='-master %s', + usedefault=True, + ), maxrot=dict(argstr='-maxrot %f', ), maxscl=dict(argstr='-maxscl %f', ), maxshf=dict(argstr='-maxshf %f', ), @@ -64,14 +71,17 @@ def test_Allineate_inputs(): hash_files=False, name_source='in_file', name_template='%s_allineate', + usedefault=True, xor=['allcostx'], ), out_matrix=dict( argstr='-1Dmatrix_save %s', + usedefault=True, xor=['in_matrix', 'allcostx'], ), out_param_file=dict( argstr='-1Dparam_save %s', + usedefault=True, xor=['in_param_file', 'allcostx'], ), out_weight_file=dict( @@ -81,11 +91,17 @@ def test_Allineate_inputs(): outputtype=dict(), overwrite=dict(argstr='-overwrite', ), quiet=dict(argstr='-quiet', ), - reference=dict(argstr='-base %s', ), + reference=dict( + argstr='-base %s', + usedefault=True, + ), replacebase=dict(argstr='-replacebase', ), replacemeth=dict(argstr='-replacemeth %s', ), source_automask=dict(argstr='-source_automask+%d', ), - source_mask=dict(argstr='-source_mask %s', ), + source_mask=dict( + argstr='-source_mask %s', + usedefault=True, + ), two_best=dict(argstr='-twobest %d', ), two_blur=dict(argstr='-twoblur %f', ), two_first=dict(argstr='-twofirst', ), @@ -99,6 +115,7 @@ def test_Allineate_inputs(): argstr='-weight %s', deprecated='1.0.0', new_name='weight', + usedefault=True, ), zclip=dict(argstr='-zclip', ), ) @@ -109,11 +126,11 @@ def test_Allineate_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Allineate_outputs(): output_map = dict( - allcostx=dict(), - out_file=dict(), - out_matrix=dict(), - out_param_file=dict(), - out_weight_file=dict(), + allcostx=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), + out_matrix=dict(usedefault=True, ), + out_param_file=dict(usedefault=True, ), + out_weight_file=dict(usedefault=True, ), ) outputs = Allineate.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py b/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py index bb00b3b585..ef4e07abcf 100644 --- a/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py +++ b/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py @@ -18,6 +18,7 @@ def test_AutoTLRC_inputs(): argstr='-input %s', copyfile=False, mandatory=True, + usedefault=True, ), no_ss=dict(argstr='-no_ss', ), outputtype=dict(), @@ -28,7 +29,7 @@ def test_AutoTLRC_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AutoTLRC_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = AutoTLRC.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py index 424b7d25b1..feb6f09dde 100644 --- a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py @@ -16,14 +16,19 @@ def test_AutoTcorrelate_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, + ), + mask=dict( + argstr='-mask %s', + usedefault=True, ), - mask=dict(argstr='-mask %s', ), mask_only_targets=dict( argstr='-mask_only_targets', xor=['mask_source'], ), mask_source=dict( argstr='-mask_source %s', + usedefault=True, xor=['mask_only_targets'], ), num_threads=dict( @@ -34,6 +39,7 @@ def test_AutoTcorrelate_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_similarity_matrix.1D', + usedefault=True, ), outputtype=dict(), polort=dict(argstr='-polort %d', ), @@ -44,7 +50,7 @@ def test_AutoTcorrelate_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AutoTcorrelate_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = AutoTcorrelate.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Autobox.py b/nipype/interfaces/afni/tests/test_auto_Autobox.py index f158263c54..fa303b8595 100644 --- a/nipype/interfaces/afni/tests/test_auto_Autobox.py +++ b/nipype/interfaces/afni/tests/test_auto_Autobox.py @@ -14,6 +14,7 @@ def test_Autobox_inputs(): argstr='-input %s', copyfile=False, mandatory=True, + usedefault=True, ), no_clustering=dict(argstr='-noclust', ), num_threads=dict( @@ -24,6 +25,7 @@ def test_Autobox_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_autobox', + usedefault=True, ), outputtype=dict(), padding=dict(argstr='-npad %d', ), @@ -35,7 +37,7 @@ def test_Autobox_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Autobox_outputs(): output_map = dict( - out_file=dict(), + out_file=dict(usedefault=True, ), x_max=dict(), x_min=dict(), y_max=dict(), diff --git a/nipype/interfaces/afni/tests/test_auto_Automask.py b/nipype/interfaces/afni/tests/test_auto_Automask.py index efffd19cba..3e8be0b9f9 100644 --- a/nipype/interfaces/afni/tests/test_auto_Automask.py +++ b/nipype/interfaces/afni/tests/test_auto_Automask.py @@ -10,6 +10,7 @@ def test_Automask_inputs(): argstr='-apply_prefix %s', name_source='in_file', name_template='%s_masked', + usedefault=True, ), clfrac=dict(argstr='-clfrac %s', ), dilate=dict(argstr='-dilate %s', ), @@ -23,6 +24,7 @@ def test_Automask_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, ), num_threads=dict( nohash=True, @@ -32,6 +34,7 @@ def test_Automask_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_mask', + usedefault=True, ), outputtype=dict(), ) @@ -42,8 +45,8 @@ def test_Automask_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Automask_outputs(): output_map = dict( - brain_file=dict(), - out_file=dict(), + brain_file=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), ) outputs = Automask.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Axialize.py b/nipype/interfaces/afni/tests/test_auto_Axialize.py index 62b425c932..10fd904487 100644 --- a/nipype/interfaces/afni/tests/test_auto_Axialize.py +++ b/nipype/interfaces/afni/tests/test_auto_Axialize.py @@ -23,6 +23,7 @@ def test_Axialize_inputs(): copyfile=False, mandatory=True, position=-2, + usedefault=True, ), num_threads=dict( nohash=True, @@ -33,6 +34,7 @@ def test_Axialize_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_axialize', + usedefault=True, ), outputtype=dict(), sagittal=dict( @@ -47,7 +49,7 @@ def test_Axialize_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Axialize_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Axialize.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Bandpass.py b/nipype/interfaces/afni/tests/test_auto_Bandpass.py index fb0861a747..b20c770e6d 100644 --- a/nipype/interfaces/afni/tests/test_auto_Bandpass.py +++ b/nipype/interfaces/afni/tests/test_auto_Bandpass.py @@ -23,6 +23,7 @@ def test_Bandpass_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, ), localPV=dict(argstr='-localPV %f', ), lowpass=dict( @@ -33,6 +34,7 @@ def test_Bandpass_inputs(): mask=dict( argstr='-mask %s', position=2, + usedefault=True, ), nfft=dict(argstr='-nfft %d', ), no_detrend=dict(argstr='-nodetrend', ), @@ -42,14 +44,17 @@ def test_Bandpass_inputs(): nohash=True, usedefault=True, ), - orthogonalize_dset=dict(argstr='-dsort %s', ), + orthogonalize_dset=dict( + argstr='-dsort %s', + usedefault=True, + ), orthogonalize_file=dict(argstr='-ort %s', ), out_file=dict( argstr='-prefix %s', - genfile=True, name_source='in_file', name_template='%s_bp', position=1, + usedefault=True, ), outputtype=dict(), tr=dict(argstr='-dt %f', ), @@ -60,7 +65,7 @@ def test_Bandpass_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Bandpass_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Bandpass.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py index 334116d945..a6ba4a84ac 100644 --- a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py +++ b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py @@ -21,9 +21,16 @@ def test_BlurInMask_inputs(): copyfile=False, mandatory=True, position=1, + usedefault=True, + ), + mask=dict( + argstr='-mask %s', + usedefault=True, + ), + multimask=dict( + argstr='-Mmask %s', + usedefault=True, ), - mask=dict(argstr='-mask %s', ), - multimask=dict(argstr='-Mmask %s', ), num_threads=dict( nohash=True, usedefault=True, @@ -37,6 +44,7 @@ def test_BlurInMask_inputs(): name_source='in_file', name_template='%s_blur', position=-1, + usedefault=True, ), outputtype=dict(), preserve=dict(argstr='-preserve', ), @@ -47,7 +55,7 @@ def test_BlurInMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BlurInMask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = BlurInMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py b/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py index 2f88a1edcb..a20133f62a 100644 --- a/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py +++ b/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py @@ -7,7 +7,10 @@ def test_BlurToFWHM_inputs(): input_map = dict( args=dict(argstr='%s', ), automask=dict(argstr='-automask', ), - blurmaster=dict(argstr='-blurmaster %s', ), + blurmaster=dict( + argstr='-blurmaster %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -17,16 +20,21 @@ def test_BlurToFWHM_inputs(): in_file=dict( argstr='-input %s', mandatory=True, + usedefault=True, + ), + mask=dict( + argstr='-mask %s', + usedefault=True, ), - mask=dict(argstr='-mask %s', ), num_threads=dict( nohash=True, usedefault=True, ), out_file=dict( argstr='-prefix %s', - name_source=['in_file'], + name_source='in_file', name_template='%s_afni', + usedefault=True, ), outputtype=dict(), ) @@ -36,7 +44,7 @@ def test_BlurToFWHM_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BlurToFWHM_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = BlurToFWHM.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_BrickStat.py b/nipype/interfaces/afni/tests/test_auto_BrickStat.py index 0056df5980..5bab8eeba5 100644 --- a/nipype/interfaces/afni/tests/test_auto_BrickStat.py +++ b/nipype/interfaces/afni/tests/test_auto_BrickStat.py @@ -14,10 +14,12 @@ def test_BrickStat_inputs(): argstr='%s', mandatory=True, position=-1, + usedefault=True, ), mask=dict( argstr='-mask %s', position=2, + usedefault=True, ), max=dict(argstr='-max', ), mean=dict(argstr='-mean', ), diff --git a/nipype/interfaces/afni/tests/test_auto_Bucket.py b/nipype/interfaces/afni/tests/test_auto_Bucket.py index c3faf87a09..93aa40d738 100644 --- a/nipype/interfaces/afni/tests/test_auto_Bucket.py +++ b/nipype/interfaces/afni/tests/test_auto_Bucket.py @@ -22,6 +22,7 @@ def test_Bucket_inputs(): out_file=dict( argstr='-prefix %s', name_template='buck', + usedefault=True, ), outputtype=dict(), ) @@ -31,7 +32,7 @@ def test_Bucket_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Bucket_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Bucket.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Calc.py b/nipype/interfaces/afni/tests/test_auto_Calc.py index 28863d5a4b..bc8a362782 100644 --- a/nipype/interfaces/afni/tests/test_auto_Calc.py +++ b/nipype/interfaces/afni/tests/test_auto_Calc.py @@ -19,24 +19,31 @@ def test_Calc_inputs(): argstr='-a %s', mandatory=True, position=0, + usedefault=True, ), in_file_b=dict( argstr='-b %s', position=1, + usedefault=True, ), in_file_c=dict( argstr='-c %s', position=2, + usedefault=True, ), num_threads=dict( nohash=True, usedefault=True, ), - other=dict(argstr='', ), + other=dict( + argstr='', + usedefault=True, + ), out_file=dict( argstr='-prefix %s', name_source='in_file_a', name_template='%s_calc', + usedefault=True, ), outputtype=dict(), overwrite=dict(argstr='-overwrite', ), @@ -50,7 +57,7 @@ def test_Calc_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Calc_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Calc.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Cat.py b/nipype/interfaces/afni/tests/test_auto_Cat.py index 3da86c66d6..92e4099ea5 100644 --- a/nipype/interfaces/afni/tests/test_auto_Cat.py +++ b/nipype/interfaces/afni/tests/test_auto_Cat.py @@ -67,7 +67,7 @@ def test_Cat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Cat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Cat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_CatMatvec.py b/nipype/interfaces/afni/tests/test_auto_CatMatvec.py index b67ab485d4..e678afc632 100644 --- a/nipype/interfaces/afni/tests/test_auto_CatMatvec.py +++ b/nipype/interfaces/afni/tests/test_auto_CatMatvec.py @@ -38,6 +38,7 @@ def test_CatMatvec_inputs(): name_source='in_file', name_template='%s_cat.aff12.1D', position=-1, + usedefault=True, ), outputtype=dict(), ) @@ -47,7 +48,7 @@ def test_CatMatvec_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CatMatvec_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = CatMatvec.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_CenterMass.py b/nipype/interfaces/afni/tests/test_auto_CenterMass.py index 322218a50d..de6475ed3d 100644 --- a/nipype/interfaces/afni/tests/test_auto_CenterMass.py +++ b/nipype/interfaces/afni/tests/test_auto_CenterMass.py @@ -15,6 +15,7 @@ def test_CenterMass_inputs(): name_source='in_file', name_template='%s_cm.out', position=-1, + usedefault=True, ), environ=dict( nohash=True, @@ -25,9 +26,13 @@ def test_CenterMass_inputs(): copyfile=True, mandatory=True, position=-2, + usedefault=True, ), local_ijk=dict(argstr='-local_ijk', ), - mask_file=dict(argstr='-mask %s', ), + mask_file=dict( + argstr='-mask %s', + usedefault=True, + ), roi_vals=dict(argstr='-roi_vals %s', ), set_cm=dict(argstr='-set %f %f %f', ), ) @@ -39,8 +44,8 @@ def test_CenterMass_inputs(): def test_CenterMass_outputs(): output_map = dict( cm=dict(), - cm_file=dict(), - out_file=dict(), + cm_file=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), ) outputs = CenterMass.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py index 8b8c61208d..47db0633f7 100644 --- a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py +++ b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py @@ -24,6 +24,7 @@ def test_ClipLevel_inputs(): argstr='%s', mandatory=True, position=-1, + usedefault=True, ), mfrac=dict( argstr='-mfrac %s', diff --git a/nipype/interfaces/afni/tests/test_auto_ConvertDset.py b/nipype/interfaces/afni/tests/test_auto_ConvertDset.py index 06ba3a54f2..66625253a4 100644 --- a/nipype/interfaces/afni/tests/test_auto_ConvertDset.py +++ b/nipype/interfaces/afni/tests/test_auto_ConvertDset.py @@ -14,6 +14,7 @@ def test_ConvertDset_inputs(): argstr='-input %s', mandatory=True, position=-2, + usedefault=True, ), num_threads=dict( nohash=True, @@ -23,6 +24,7 @@ def test_ConvertDset_inputs(): argstr='-prefix %s', mandatory=True, position=-1, + usedefault=True, ), out_type=dict( argstr='-o_%s', @@ -37,7 +39,7 @@ def test_ConvertDset_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConvertDset_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ConvertDset.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Copy.py b/nipype/interfaces/afni/tests/test_auto_Copy.py index a8e67d5607..dcc3a546b2 100644 --- a/nipype/interfaces/afni/tests/test_auto_Copy.py +++ b/nipype/interfaces/afni/tests/test_auto_Copy.py @@ -15,6 +15,7 @@ def test_Copy_inputs(): copyfile=False, mandatory=True, position=-2, + usedefault=True, ), num_threads=dict( nohash=True, @@ -25,6 +26,7 @@ def test_Copy_inputs(): name_source='in_file', name_template='%s_copy', position=-1, + usedefault=True, ), outputtype=dict(), verbose=dict(argstr='-verb', ), @@ -35,7 +37,7 @@ def test_Copy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Copy_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Copy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Deconvolve.py b/nipype/interfaces/afni/tests/test_auto_Deconvolve.py index ae42a77019..6f66bbaf9c 100644 --- a/nipype/interfaces/afni/tests/test_auto_Deconvolve.py +++ b/nipype/interfaces/afni/tests/test_auto_Deconvolve.py @@ -5,13 +5,19 @@ def test_Deconvolve_inputs(): input_map = dict( - STATmask=dict(argstr='-STATmask %s', ), + STATmask=dict( + argstr='-STATmask %s', + usedefault=True, + ), TR_1D=dict(argstr='-TR_1D %f', ), allzero_OK=dict(argstr='-allzero_OK', ), args=dict(argstr='%s', ), automask=dict(argstr='-automask', ), cbucket=dict(argstr='-cbucket %s', ), - censor=dict(argstr='-censor %s', ), + censor=dict( + argstr='-censor %s', + usedefault=True, + ), dmbase=dict(argstr='-dmbase', ), dname=dict(argstr='-D%s=%s', ), environ=dict( @@ -43,13 +49,19 @@ def test_Deconvolve_inputs(): position=1, sep=' ', ), - input1D=dict(argstr='-input1D %s', ), + input1D=dict( + argstr='-input1D %s', + usedefault=True, + ), legendre=dict(argstr='-legendre', ), local_times=dict( argstr='-local_times', xor=['global_times'], ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + usedefault=True, + ), noblock=dict(argstr='-noblock', ), nocond=dict(argstr='-nocond', ), nodmbase=dict(argstr='-nodmbase', ), @@ -69,7 +81,10 @@ def test_Deconvolve_inputs(): nohash=True, ), ortvec=dict(argstr='-ortvec %s %s', ), - out_file=dict(argstr='-bucket %s', ), + out_file=dict( + argstr='-bucket %s', + usedefault=True, + ), outputtype=dict(), polort=dict(argstr='-polort %d', ), rmsmin=dict(argstr='-rmsmin %f', ), @@ -96,7 +111,10 @@ def test_Deconvolve_inputs(): xor=['sat'], ), vout=dict(argstr='-vout', ), - x1D=dict(argstr='-x1D %s', ), + x1D=dict( + argstr='-x1D %s', + usedefault=True, + ), x1D_stop=dict(argstr='-x1D_stop', ), ) inputs = Deconvolve.input_spec() @@ -106,10 +124,10 @@ def test_Deconvolve_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Deconvolve_outputs(): output_map = dict( - cbucket=dict(), - out_file=dict(), - reml_script=dict(), - x1D=dict(), + cbucket=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), + reml_script=dict(usedefault=True, ), + x1D=dict(usedefault=True, ), ) outputs = Deconvolve.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py b/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py index 664cca5985..a64e48cedf 100644 --- a/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py +++ b/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py @@ -17,8 +17,12 @@ def test_DegreeCentrality_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, + ), + mask=dict( + argstr='-mask %s', + usedefault=True, ), - mask=dict(argstr='-mask %s', ), num_threads=dict( nohash=True, usedefault=True, @@ -26,8 +30,9 @@ def test_DegreeCentrality_inputs(): oned_file=dict(argstr='-out1D %s', ), out_file=dict( argstr='-prefix %s', - name_source=['in_file'], + name_source='in_file', name_template='%s_afni', + usedefault=True, ), outputtype=dict(), polort=dict(argstr='-polort %d', ), @@ -41,8 +46,8 @@ def test_DegreeCentrality_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DegreeCentrality_outputs(): output_map = dict( - oned_file=dict(), - out_file=dict(), + oned_file=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), ) outputs = DegreeCentrality.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Despike.py b/nipype/interfaces/afni/tests/test_auto_Despike.py index ff0b8b532a..08031c8d4a 100644 --- a/nipype/interfaces/afni/tests/test_auto_Despike.py +++ b/nipype/interfaces/afni/tests/test_auto_Despike.py @@ -15,6 +15,7 @@ def test_Despike_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, ), num_threads=dict( nohash=True, @@ -24,6 +25,7 @@ def test_Despike_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_despike', + usedefault=True, ), outputtype=dict(), ) @@ -33,7 +35,7 @@ def test_Despike_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Despike_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Despike.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Detrend.py b/nipype/interfaces/afni/tests/test_auto_Detrend.py index 1938529cf7..5f75cf079b 100644 --- a/nipype/interfaces/afni/tests/test_auto_Detrend.py +++ b/nipype/interfaces/afni/tests/test_auto_Detrend.py @@ -15,6 +15,7 @@ def test_Detrend_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, ), num_threads=dict( nohash=True, @@ -24,6 +25,7 @@ def test_Detrend_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_detrend', + usedefault=True, ), outputtype=dict(), ) @@ -33,7 +35,7 @@ def test_Detrend_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Detrend_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Detrend.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Dot.py b/nipype/interfaces/afni/tests/test_auto_Dot.py index 7623e90ca7..610f226961 100644 --- a/nipype/interfaces/afni/tests/test_auto_Dot.py +++ b/nipype/interfaces/afni/tests/test_auto_Dot.py @@ -22,7 +22,10 @@ def test_Dot_inputs(): argstr='%s ...', position=-2, ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + usedefault=True, + ), mrange=dict(argstr='-mrange %s %s', ), num_threads=dict( nohash=True, @@ -31,6 +34,7 @@ def test_Dot_inputs(): out_file=dict( argstr=' |& tee %s', position=-1, + usedefault=True, ), outputtype=dict(), show_labels=dict(argstr='-show_labels', ), @@ -42,7 +46,7 @@ def test_Dot_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Dot_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Dot.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_ECM.py b/nipype/interfaces/afni/tests/test_auto_ECM.py index 8a4793fb7f..ab5c438035 100644 --- a/nipype/interfaces/afni/tests/test_auto_ECM.py +++ b/nipype/interfaces/afni/tests/test_auto_ECM.py @@ -20,8 +20,12 @@ def test_ECM_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, + ), + mask=dict( + argstr='-mask %s', + usedefault=True, ), - mask=dict(argstr='-mask %s', ), max_iter=dict(argstr='-max_iter %d', ), memory=dict(argstr='-memory %f', ), num_threads=dict( @@ -30,8 +34,9 @@ def test_ECM_inputs(): ), out_file=dict( argstr='-prefix %s', - name_source=['in_file'], + name_source='in_file', name_template='%s_afni', + usedefault=True, ), outputtype=dict(), polort=dict(argstr='-polort %d', ), @@ -46,7 +51,7 @@ def test_ECM_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ECM_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ECM.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Edge3.py b/nipype/interfaces/afni/tests/test_auto_Edge3.py index 8fc6953c28..64f3e8785b 100644 --- a/nipype/interfaces/afni/tests/test_auto_Edge3.py +++ b/nipype/interfaces/afni/tests/test_auto_Edge3.py @@ -24,6 +24,7 @@ def test_Edge3_inputs(): copyfile=False, mandatory=True, position=0, + usedefault=True, ), nscale=dict( argstr='-nscale', @@ -36,6 +37,7 @@ def test_Edge3_inputs(): out_file=dict( argstr='-prefix %s', position=-1, + usedefault=True, ), outputtype=dict(), scale_floats=dict( @@ -50,7 +52,7 @@ def test_Edge3_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Edge3_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Edge3.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Eval.py b/nipype/interfaces/afni/tests/test_auto_Eval.py index 35c1360a6e..0f43128ae0 100644 --- a/nipype/interfaces/afni/tests/test_auto_Eval.py +++ b/nipype/interfaces/afni/tests/test_auto_Eval.py @@ -19,25 +19,32 @@ def test_Eval_inputs(): argstr='-a %s', mandatory=True, position=0, + usedefault=True, ), in_file_b=dict( argstr='-b %s', position=1, + usedefault=True, ), in_file_c=dict( argstr='-c %s', position=2, + usedefault=True, ), num_threads=dict( nohash=True, usedefault=True, ), - other=dict(argstr='', ), + other=dict( + argstr='', + usedefault=True, + ), out1D=dict(argstr='-1D', ), out_file=dict( argstr='-prefix %s', name_source='in_file_a', name_template='%s_calc', + usedefault=True, ), outputtype=dict(), single_idx=dict(), @@ -50,7 +57,7 @@ def test_Eval_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Eval_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Eval.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_FWHMx.py b/nipype/interfaces/afni/tests/test_auto_FWHMx.py index 14ab26fa4f..1c0e9c7f1e 100644 --- a/nipype/interfaces/afni/tests/test_auto_FWHMx.py +++ b/nipype/interfaces/afni/tests/test_auto_FWHMx.py @@ -40,13 +40,18 @@ def test_FWHMx_inputs(): in_file=dict( argstr='-input %s', mandatory=True, + usedefault=True, + ), + mask=dict( + argstr='-mask %s', + usedefault=True, ), - mask=dict(argstr='-mask %s', ), out_detrend=dict( argstr='-detprefix %s', keep_extension=False, name_source='in_file', name_template='%s_detrend', + usedefault=True, ), out_file=dict( argstr='> %s', @@ -54,12 +59,14 @@ def test_FWHMx_inputs(): name_source='in_file', name_template='%s_fwhmx.out', position=-1, + usedefault=True, ), out_subbricks=dict( argstr='-out %s', keep_extension=False, name_source='in_file', name_template='%s_subbricks.out', + usedefault=True, ), unif=dict(argstr='-unif', ), ) @@ -72,10 +79,10 @@ def test_FWHMx_outputs(): output_map = dict( acf_param=dict(), fwhm=dict(), - out_acf=dict(), - out_detrend=dict(), - out_file=dict(), - out_subbricks=dict(), + out_acf=dict(usedefault=True, ), + out_detrend=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), + out_subbricks=dict(usedefault=True, ), ) outputs = FWHMx.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Fim.py b/nipype/interfaces/afni/tests/test_auto_Fim.py index 931e5ff244..a8cb1c22da 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fim.py +++ b/nipype/interfaces/afni/tests/test_auto_Fim.py @@ -18,12 +18,14 @@ def test_Fim_inputs(): argstr='-ideal_file %s', mandatory=True, position=2, + usedefault=True, ), in_file=dict( argstr='-input %s', copyfile=False, mandatory=True, position=1, + usedefault=True, ), num_threads=dict( nohash=True, @@ -37,6 +39,7 @@ def test_Fim_inputs(): argstr='-bucket %s', name_source='in_file', name_template='%s_fim', + usedefault=True, ), outputtype=dict(), ) @@ -46,7 +49,7 @@ def test_Fim_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Fim_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Fim.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Fourier.py b/nipype/interfaces/afni/tests/test_auto_Fourier.py index 69cd955cbc..14feefd617 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fourier.py +++ b/nipype/interfaces/afni/tests/test_auto_Fourier.py @@ -19,6 +19,7 @@ def test_Fourier_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, ), lowpass=dict( argstr='-lowpass %f', @@ -32,6 +33,7 @@ def test_Fourier_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_fourier', + usedefault=True, ), outputtype=dict(), retrend=dict(argstr='-retrend', ), @@ -42,7 +44,7 @@ def test_Fourier_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Fourier_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Fourier.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_GCOR.py b/nipype/interfaces/afni/tests/test_auto_GCOR.py index 9d603dda36..71d9b6b0f7 100644 --- a/nipype/interfaces/afni/tests/test_auto_GCOR.py +++ b/nipype/interfaces/afni/tests/test_auto_GCOR.py @@ -15,10 +15,12 @@ def test_GCOR_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, ), mask=dict( argstr='-mask %s', copyfile=False, + usedefault=True, ), nfirst=dict(argstr='-nfirst %d', ), no_demean=dict(argstr='-no_demean', ), diff --git a/nipype/interfaces/afni/tests/test_auto_Hist.py b/nipype/interfaces/afni/tests/test_auto_Hist.py index 48499a9605..a06d661547 100644 --- a/nipype/interfaces/afni/tests/test_auto_Hist.py +++ b/nipype/interfaces/afni/tests/test_auto_Hist.py @@ -16,8 +16,12 @@ def test_Hist_inputs(): copyfile=False, mandatory=True, position=1, + usedefault=True, + ), + mask=dict( + argstr='-mask %s', + usedefault=True, ), - mask=dict(argstr='-mask %s', ), max_value=dict(argstr='-max %f', ), min_value=dict(argstr='-min %f', ), nbin=dict(argstr='-nbin %d', ), @@ -26,6 +30,7 @@ def test_Hist_inputs(): keep_extension=False, name_source=['in_file'], name_template='%s_hist', + usedefault=True, ), out_show=dict( argstr='> %s', @@ -33,6 +38,7 @@ def test_Hist_inputs(): name_source='in_file', name_template='%s_hist.out', position=-1, + usedefault=True, ), showhist=dict( argstr='-showhist', @@ -46,8 +52,8 @@ def test_Hist_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Hist_outputs(): output_map = dict( - out_file=dict(), - out_show=dict(), + out_file=dict(usedefault=True, ), + out_show=dict(usedefault=True, ), ) outputs = Hist.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_LFCD.py b/nipype/interfaces/afni/tests/test_auto_LFCD.py index 9cbde10b56..6a99d09cb6 100644 --- a/nipype/interfaces/afni/tests/test_auto_LFCD.py +++ b/nipype/interfaces/afni/tests/test_auto_LFCD.py @@ -17,16 +17,21 @@ def test_LFCD_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, + ), + mask=dict( + argstr='-mask %s', + usedefault=True, ), - mask=dict(argstr='-mask %s', ), num_threads=dict( nohash=True, usedefault=True, ), out_file=dict( argstr='-prefix %s', - name_source=['in_file'], + name_source='in_file', name_template='%s_afni', + usedefault=True, ), outputtype=dict(), polort=dict(argstr='-polort %d', ), @@ -38,7 +43,7 @@ def test_LFCD_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LFCD_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = LFCD.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_LocalBistat.py b/nipype/interfaces/afni/tests/test_auto_LocalBistat.py index 22f0b717d8..13c31f02c7 100644 --- a/nipype/interfaces/afni/tests/test_auto_LocalBistat.py +++ b/nipype/interfaces/afni/tests/test_auto_LocalBistat.py @@ -18,11 +18,13 @@ def test_LocalBistat_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), in_file2=dict( argstr='%s', mandatory=True, position=-1, + usedefault=True, ), mask_file=dict(argstr='-mask %s', ), neighborhood=dict( @@ -56,7 +58,7 @@ def test_LocalBistat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LocalBistat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = LocalBistat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Localstat.py b/nipype/interfaces/afni/tests/test_auto_Localstat.py index c2f53c3db0..4ad85d0728 100644 --- a/nipype/interfaces/afni/tests/test_auto_Localstat.py +++ b/nipype/interfaces/afni/tests/test_auto_Localstat.py @@ -19,6 +19,7 @@ def test_Localstat_inputs(): argstr='%s', mandatory=True, position=-1, + usedefault=True, ), mask_file=dict(argstr='-mask %s', ), neighborhood=dict( @@ -63,7 +64,7 @@ def test_Localstat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Localstat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Localstat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_MaskTool.py b/nipype/interfaces/afni/tests/test_auto_MaskTool.py index 1644bee878..ef4464b6ca 100644 --- a/nipype/interfaces/afni/tests/test_auto_MaskTool.py +++ b/nipype/interfaces/afni/tests/test_auto_MaskTool.py @@ -38,6 +38,7 @@ def test_MaskTool_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_mask', + usedefault=True, ), outputtype=dict(), union=dict(argstr='-union', ), @@ -49,7 +50,7 @@ def test_MaskTool_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MaskTool_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MaskTool.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Maskave.py b/nipype/interfaces/afni/tests/test_auto_Maskave.py index a318e685a9..462ed4e3cf 100644 --- a/nipype/interfaces/afni/tests/test_auto_Maskave.py +++ b/nipype/interfaces/afni/tests/test_auto_Maskave.py @@ -15,10 +15,12 @@ def test_Maskave_inputs(): copyfile=False, mandatory=True, position=-2, + usedefault=True, ), mask=dict( argstr='-mask %s', position=1, + usedefault=True, ), num_threads=dict( nohash=True, @@ -30,6 +32,7 @@ def test_Maskave_inputs(): name_source='in_file', name_template='%s_maskave.1D', position=-1, + usedefault=True, ), outputtype=dict(), quiet=dict( @@ -43,7 +46,7 @@ def test_Maskave_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Maskave_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Maskave.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Means.py b/nipype/interfaces/afni/tests/test_auto_Means.py index 2e422e68db..c1830e2e23 100644 --- a/nipype/interfaces/afni/tests/test_auto_Means.py +++ b/nipype/interfaces/afni/tests/test_auto_Means.py @@ -16,10 +16,12 @@ def test_Means_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), in_file_b=dict( argstr='%s', position=-1, + usedefault=True, ), mask_inter=dict(argstr='-mask_inter', ), mask_union=dict(argstr='-mask_union', ), @@ -32,6 +34,7 @@ def test_Means_inputs(): argstr='-prefix %s', name_source='in_file_a', name_template='%s_mean', + usedefault=True, ), outputtype=dict(), scale=dict(argstr='-%sscale', ), @@ -45,7 +48,7 @@ def test_Means_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Means_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Means.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Merge.py b/nipype/interfaces/afni/tests/test_auto_Merge.py index c36ee6f7a1..6dfe98c9f4 100644 --- a/nipype/interfaces/afni/tests/test_auto_Merge.py +++ b/nipype/interfaces/afni/tests/test_auto_Merge.py @@ -29,6 +29,7 @@ def test_Merge_inputs(): argstr='-prefix %s', name_source='in_files', name_template='%s_merge', + usedefault=True, ), outputtype=dict(), ) @@ -38,7 +39,7 @@ def test_Merge_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Merge_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Merge.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Notes.py b/nipype/interfaces/afni/tests/test_auto_Notes.py index 965bacb000..1ac8f2df04 100644 --- a/nipype/interfaces/afni/tests/test_auto_Notes.py +++ b/nipype/interfaces/afni/tests/test_auto_Notes.py @@ -21,12 +21,16 @@ def test_Notes_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, ), num_threads=dict( nohash=True, usedefault=True, ), - out_file=dict(argstr='%s', ), + out_file=dict( + argstr='%s', + usedefault=True, + ), outputtype=dict(), rep_history=dict( argstr='-HH "%s"', @@ -40,7 +44,7 @@ def test_Notes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Notes_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Notes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_NwarpAdjust.py b/nipype/interfaces/afni/tests/test_auto_NwarpAdjust.py index 48b59a2968..d6d9f23dd1 100644 --- a/nipype/interfaces/afni/tests/test_auto_NwarpAdjust.py +++ b/nipype/interfaces/afni/tests/test_auto_NwarpAdjust.py @@ -21,6 +21,7 @@ def test_NwarpAdjust_inputs(): name_source='in_files', name_template='%s_NwarpAdjust', requires=['in_files'], + usedefault=True, ), outputtype=dict(), warps=dict( @@ -34,7 +35,7 @@ def test_NwarpAdjust_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NwarpAdjust_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = NwarpAdjust.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_NwarpApply.py b/nipype/interfaces/afni/tests/test_auto_NwarpApply.py index 63f6baa044..df04e5dc3d 100644 --- a/nipype/interfaces/afni/tests/test_auto_NwarpApply.py +++ b/nipype/interfaces/afni/tests/test_auto_NwarpApply.py @@ -25,6 +25,7 @@ def test_NwarpApply_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_Nwarp', + usedefault=True, ), quiet=dict( argstr='-quiet', @@ -46,7 +47,7 @@ def test_NwarpApply_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NwarpApply_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = NwarpApply.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_NwarpCat.py b/nipype/interfaces/afni/tests/test_auto_NwarpCat.py index c6b3689c9e..0aaa040442 100644 --- a/nipype/interfaces/afni/tests/test_auto_NwarpCat.py +++ b/nipype/interfaces/afni/tests/test_auto_NwarpCat.py @@ -29,6 +29,7 @@ def test_NwarpCat_inputs(): argstr='-prefix %s', name_source='in_files', name_template='%s_NwarpCat', + usedefault=True, ), outputtype=dict(), space=dict(argstr='-space %s', ), @@ -40,7 +41,7 @@ def test_NwarpCat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NwarpCat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = NwarpCat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py b/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py index fe037851af..dd805be5cc 100644 --- a/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py +++ b/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py @@ -17,9 +17,11 @@ def test_OneDToolPy_inputs(): in_file=dict( argstr='-infile %s', mandatory=True, + usedefault=True, ), out_file=dict( argstr='-write %s', + usedefault=True, xor=['show_cormat_warnings'], ), outputtype=dict(), @@ -41,7 +43,7 @@ def test_OneDToolPy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OneDToolPy_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = OneDToolPy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_OutlierCount.py b/nipype/interfaces/afni/tests/test_auto_OutlierCount.py index a63fbb8bef..14a6fa0fe6 100644 --- a/nipype/interfaces/afni/tests/test_auto_OutlierCount.py +++ b/nipype/interfaces/afni/tests/test_auto_OutlierCount.py @@ -28,6 +28,7 @@ def test_OutlierCount_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), interval=dict( argstr='-range', @@ -39,12 +40,14 @@ def test_OutlierCount_inputs(): ), mask=dict( argstr='-mask %s', + usedefault=True, xor=['autoclip', 'automask'], ), out_file=dict( keep_extension=False, name_source=['in_file'], name_template='%s_outliers', + usedefault=True, ), outliers_file=dict( argstr='-save %s', @@ -52,6 +55,7 @@ def test_OutlierCount_inputs(): name_source=['in_file'], name_template='%s_outliers', output_name='out_outliers', + usedefault=True, ), polort=dict(argstr='-polort %d', ), qthr=dict( @@ -67,8 +71,8 @@ def test_OutlierCount_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_OutlierCount_outputs(): output_map = dict( - out_file=dict(), - out_outliers=dict(), + out_file=dict(usedefault=True, ), + out_outliers=dict(usedefault=True, ), ) outputs = OutlierCount.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_QualityIndex.py b/nipype/interfaces/afni/tests/test_auto_QualityIndex.py index 679a3e0393..0c85e0d585 100644 --- a/nipype/interfaces/afni/tests/test_auto_QualityIndex.py +++ b/nipype/interfaces/afni/tests/test_auto_QualityIndex.py @@ -25,6 +25,7 @@ def test_QualityIndex_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), interval=dict( argstr='-range', @@ -32,6 +33,7 @@ def test_QualityIndex_inputs(): ), mask=dict( argstr='-mask %s', + usedefault=True, xor=['autoclip', 'automask'], ), out_file=dict( @@ -40,6 +42,7 @@ def test_QualityIndex_inputs(): name_source=['in_file'], name_template='%s_tqual', position=-1, + usedefault=True, ), quadrant=dict( argstr='-quadrant', @@ -56,7 +59,7 @@ def test_QualityIndex_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_QualityIndex_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = QualityIndex.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Qwarp.py b/nipype/interfaces/afni/tests/test_auto_Qwarp.py index f6df3d0ab5..ffaf1a5a3f 100644 --- a/nipype/interfaces/afni/tests/test_auto_Qwarp.py +++ b/nipype/interfaces/afni/tests/test_auto_Qwarp.py @@ -25,6 +25,7 @@ def test_Qwarp_inputs(): argstr='-base %s', copyfile=False, mandatory=True, + usedefault=True, ), baxopt=dict( argstr='-boxopt', @@ -41,6 +42,7 @@ def test_Qwarp_inputs(): emask=dict( argstr='-emask %s', copyfile=False, + usedefault=True, ), environ=dict( nohash=True, @@ -53,6 +55,7 @@ def test_Qwarp_inputs(): gridlist=dict( argstr='-gridlist %s', copyfile=False, + usedefault=True, xor=['duplo', 'plusminus'], ), hel=dict( @@ -63,6 +66,7 @@ def test_Qwarp_inputs(): argstr='-source %s', copyfile=False, mandatory=True, + usedefault=True, ), inilev=dict( argstr='-inilev %d', @@ -117,9 +121,9 @@ def test_Qwarp_inputs(): ), out_file=dict( argstr='-prefix %s', - genfile=True, - name_source=['in_file'], + name_source='in_file', name_template='%s_QW', + usedefault=True, ), out_weight_file=dict(argstr='-wtprefix %s', ), outputtype=dict(), @@ -141,7 +145,10 @@ def test_Qwarp_inputs(): xor=['quiet'], ), wball=dict(argstr='-wball %s', ), - weight=dict(argstr='-weight %s', ), + weight=dict( + argstr='-weight %s', + usedefault=True, + ), wmask=dict(argstr='-wpass %s %f', ), workhard=dict( argstr='-workhard', @@ -155,11 +162,11 @@ def test_Qwarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Qwarp_outputs(): output_map = dict( - base_warp=dict(), - source_warp=dict(), - warped_base=dict(), - warped_source=dict(), - weights=dict(), + base_warp=dict(usedefault=True, ), + source_warp=dict(usedefault=True, ), + warped_base=dict(usedefault=True, ), + warped_source=dict(usedefault=True, ), + weights=dict(usedefault=True, ), ) outputs = Qwarp.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py b/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py index 340f3a0e4a..3c3b1fde90 100644 --- a/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py +++ b/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py @@ -25,6 +25,7 @@ def test_QwarpPlusMinus_inputs(): argstr='-base %s', copyfile=False, mandatory=True, + usedefault=True, ), baxopt=dict( argstr='-boxopt', @@ -41,6 +42,7 @@ def test_QwarpPlusMinus_inputs(): emask=dict( argstr='-emask %s', copyfile=False, + usedefault=True, ), environ=dict( nohash=True, @@ -53,6 +55,7 @@ def test_QwarpPlusMinus_inputs(): gridlist=dict( argstr='-gridlist %s', copyfile=False, + usedefault=True, xor=['duplo', 'plusminus'], ), hel=dict( @@ -63,6 +66,7 @@ def test_QwarpPlusMinus_inputs(): argstr='-source %s', copyfile=False, mandatory=True, + usedefault=True, ), inilev=dict( argstr='-inilev %d', @@ -142,13 +146,17 @@ def test_QwarpPlusMinus_inputs(): copyfile=False, deprecated='1.1.2', new_name='in_file', + usedefault=True, ), verb=dict( argstr='-verb', xor=['quiet'], ), wball=dict(argstr='-wball %s', ), - weight=dict(argstr='-weight %s', ), + weight=dict( + argstr='-weight %s', + usedefault=True, + ), wmask=dict(argstr='-wpass %s %f', ), workhard=dict( argstr='-workhard', @@ -162,11 +170,11 @@ def test_QwarpPlusMinus_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_QwarpPlusMinus_outputs(): output_map = dict( - base_warp=dict(), - source_warp=dict(), - warped_base=dict(), - warped_source=dict(), - weights=dict(), + base_warp=dict(usedefault=True, ), + source_warp=dict(usedefault=True, ), + warped_base=dict(usedefault=True, ), + warped_source=dict(usedefault=True, ), + weights=dict(usedefault=True, ), ) outputs = QwarpPlusMinus.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_ROIStats.py b/nipype/interfaces/afni/tests/test_auto_ROIStats.py index fbda92e9a5..9dc1c87943 100644 --- a/nipype/interfaces/afni/tests/test_auto_ROIStats.py +++ b/nipype/interfaces/afni/tests/test_auto_ROIStats.py @@ -23,15 +23,20 @@ def test_ROIStats_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), mask=dict( argstr='-mask %s', deprecated='1.1.4', new_name='mask_file', position=3, + usedefault=True, ), mask_f2short=dict(argstr='-mask_f2short', ), - mask_file=dict(argstr='-mask %s', ), + mask_file=dict( + argstr='-mask %s', + usedefault=True, + ), nobriklab=dict(argstr='-nobriklab', ), nomeanout=dict(argstr='-nomeanout', ), num_roi=dict(argstr='-numroi %s', ), @@ -41,6 +46,7 @@ def test_ROIStats_inputs(): name_source='in_file', name_template='%s_roistat.1D', position=-1, + usedefault=True, ), quiet=dict(argstr='-quiet', ), roisel=dict(argstr='-roisel %s', ), @@ -56,7 +62,7 @@ def test_ROIStats_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ROIStats_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ROIStats.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_ReHo.py b/nipype/interfaces/afni/tests/test_auto_ReHo.py index 1809759485..491cb6e337 100644 --- a/nipype/interfaces/afni/tests/test_auto_ReHo.py +++ b/nipype/interfaces/afni/tests/test_auto_ReHo.py @@ -19,8 +19,12 @@ def test_ReHo_inputs(): argstr='-inset %s', mandatory=True, position=1, + usedefault=True, + ), + label_set=dict( + argstr='-in_rois %s', + usedefault=True, ), - label_set=dict(argstr='-in_rois %s', ), mask_file=dict(argstr='-mask %s', ), neighborhood=dict( argstr='-nneigh %s', @@ -46,8 +50,8 @@ def test_ReHo_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ReHo_outputs(): output_map = dict( - out_file=dict(), - out_vals=dict(), + out_file=dict(usedefault=True, ), + out_vals=dict(usedefault=True, ), ) outputs = ReHo.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Refit.py b/nipype/interfaces/afni/tests/test_auto_Refit.py index 4983eafc81..f1727686a9 100644 --- a/nipype/interfaces/afni/tests/test_auto_Refit.py +++ b/nipype/interfaces/afni/tests/test_auto_Refit.py @@ -11,7 +11,10 @@ def test_Refit_inputs(): atrint=dict(argstr='-atrint %s %s', ), atrstring=dict(argstr='-atrstring %s %s', ), deoblique=dict(argstr='-deoblique', ), - duporigin_file=dict(argstr='-duporigin %s', ), + duporigin_file=dict( + argstr='-duporigin %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -21,6 +24,7 @@ def test_Refit_inputs(): copyfile=True, mandatory=True, position=-1, + usedefault=True, ), nosaveatr=dict(argstr='-nosaveatr', ), saveatr=dict(argstr='-saveatr', ), @@ -39,7 +43,7 @@ def test_Refit_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Refit_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Refit.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Remlfit.py b/nipype/interfaces/afni/tests/test_auto_Remlfit.py index 4cdc8b2ff2..69ca9642d0 100644 --- a/nipype/interfaces/afni/tests/test_auto_Remlfit.py +++ b/nipype/interfaces/afni/tests/test_auto_Remlfit.py @@ -5,7 +5,10 @@ def test_Remlfit_inputs(): input_map = dict( - STATmask=dict(argstr='-STATmask %s', ), + STATmask=dict( + argstr='-STATmask %s', + usedefault=True, + ), addbase=dict( argstr='-addbase %s', copyfile=False, @@ -19,6 +22,7 @@ def test_Remlfit_inputs(): dsort=dict( argstr='-dsort %s', copyfile=False, + usedefault=True, ), dsort_nods=dict( argstr='-dsort_nods', @@ -28,10 +32,19 @@ def test_Remlfit_inputs(): nohash=True, usedefault=True, ), - errts_file=dict(argstr='-Rerrts %s', ), - fitts_file=dict(argstr='-Rfitts %s', ), + errts_file=dict( + argstr='-Rerrts %s', + usedefault=True, + ), + fitts_file=dict( + argstr='-Rfitts %s', + usedefault=True, + ), fout=dict(argstr='-fout', ), - glt_file=dict(argstr='-Rglt %s', ), + glt_file=dict( + argstr='-Rglt %s', + usedefault=True, + ), gltsym=dict(argstr='-gltsym "%s" %s...', ), in_files=dict( argstr='-input "%s"', @@ -39,7 +52,10 @@ def test_Remlfit_inputs(): mandatory=True, sep=' ', ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + usedefault=True, + ), matim=dict( argstr='-matim %s', xor=['matrix'], @@ -47,6 +63,7 @@ def test_Remlfit_inputs(): matrix=dict( argstr='-matrix %s', mandatory=True, + usedefault=True, ), nobout=dict(argstr='-nobout', ), nodmbase=dict( @@ -58,28 +75,58 @@ def test_Remlfit_inputs(): nohash=True, usedefault=True, ), - obeta=dict(argstr='-Obeta %s', ), - obuck=dict(argstr='-Obuck %s', ), - oerrts=dict(argstr='-Oerrts %s', ), - ofitts=dict(argstr='-Ofitts %s', ), - oglt=dict(argstr='-Oglt %s', ), - out_file=dict(argstr='-Rbuck %s', ), + obeta=dict( + argstr='-Obeta %s', + usedefault=True, + ), + obuck=dict( + argstr='-Obuck %s', + usedefault=True, + ), + oerrts=dict( + argstr='-Oerrts %s', + usedefault=True, + ), + ofitts=dict( + argstr='-Ofitts %s', + usedefault=True, + ), + oglt=dict( + argstr='-Oglt %s', + usedefault=True, + ), + out_file=dict( + argstr='-Rbuck %s', + usedefault=True, + ), outputtype=dict(), - ovar=dict(argstr='-Ovar %s', ), + ovar=dict( + argstr='-Ovar %s', + usedefault=True, + ), polort=dict( argstr='-polort %d', xor=['matrix'], ), quiet=dict(argstr='-quiet', ), - rbeta_file=dict(argstr='-Rbeta %s', ), + rbeta_file=dict( + argstr='-Rbeta %s', + usedefault=True, + ), rout=dict(argstr='-rout', ), slibase=dict(argstr='-slibase %s', ), slibase_sm=dict(argstr='-slibase_sm %s', ), tout=dict(argstr='-tout', ), usetemp=dict(argstr='-usetemp', ), - var_file=dict(argstr='-Rvar %s', ), + var_file=dict( + argstr='-Rvar %s', + usedefault=True, + ), verb=dict(argstr='-verb', ), - wherr_file=dict(argstr='-Rwherr %s', ), + wherr_file=dict( + argstr='-Rwherr %s', + usedefault=True, + ), ) inputs = Remlfit.input_spec() @@ -88,19 +135,19 @@ def test_Remlfit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Remlfit_outputs(): output_map = dict( - errts_file=dict(), - fitts_file=dict(), - glt_file=dict(), - obeta=dict(), - obuck=dict(), - oerrts=dict(), - ofitts=dict(), - oglt=dict(), - out_file=dict(), - ovar=dict(), - rbeta_file=dict(), - var_file=dict(), - wherr_file=dict(), + errts_file=dict(usedefault=True, ), + fitts_file=dict(usedefault=True, ), + glt_file=dict(usedefault=True, ), + obeta=dict(usedefault=True, ), + obuck=dict(usedefault=True, ), + oerrts=dict(usedefault=True, ), + ofitts=dict(usedefault=True, ), + oglt=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), + ovar=dict(usedefault=True, ), + rbeta_file=dict(usedefault=True, ), + var_file=dict(usedefault=True, ), + wherr_file=dict(usedefault=True, ), ) outputs = Remlfit.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Resample.py b/nipype/interfaces/afni/tests/test_auto_Resample.py index 9ab2309307..b6be4c083a 100644 --- a/nipype/interfaces/afni/tests/test_auto_Resample.py +++ b/nipype/interfaces/afni/tests/test_auto_Resample.py @@ -15,6 +15,7 @@ def test_Resample_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, ), master=dict(argstr='-master %s', ), num_threads=dict( @@ -26,6 +27,7 @@ def test_Resample_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_resample', + usedefault=True, ), outputtype=dict(), resample_mode=dict(argstr='-rmode %s', ), @@ -37,7 +39,7 @@ def test_Resample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Resample_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Resample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Retroicor.py b/nipype/interfaces/afni/tests/test_auto_Retroicor.py index 4c2a1c2393..9b79ea0623 100644 --- a/nipype/interfaces/afni/tests/test_auto_Retroicor.py +++ b/nipype/interfaces/afni/tests/test_auto_Retroicor.py @@ -9,11 +9,13 @@ def test_Retroicor_inputs(): card=dict( argstr='-card %s', position=-2, + usedefault=True, ), cardphase=dict( argstr='-cardphase %s', hash_files=False, position=-6, + usedefault=True, ), environ=dict( nohash=True, @@ -24,6 +26,7 @@ def test_Retroicor_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, ), num_threads=dict( nohash=True, @@ -38,16 +41,19 @@ def test_Retroicor_inputs(): name_source=['in_file'], name_template='%s_retroicor', position=1, + usedefault=True, ), outputtype=dict(), resp=dict( argstr='-resp %s', position=-3, + usedefault=True, ), respphase=dict( argstr='-respphase %s', hash_files=False, position=-7, + usedefault=True, ), threshold=dict( argstr='-threshold %d', @@ -60,7 +66,7 @@ def test_Retroicor_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Retroicor_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Retroicor.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTest.py b/nipype/interfaces/afni/tests/test_auto_SVMTest.py index 4b31d3a11c..e4349149e1 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTest.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTest.py @@ -14,6 +14,7 @@ def test_SVMTest_inputs(): in_file=dict( argstr='-testvol %s', mandatory=True, + usedefault=True, ), model=dict( argstr='-model %s', @@ -30,9 +31,13 @@ def test_SVMTest_inputs(): out_file=dict( argstr='-predictions %s', name_template='%s_predictions', + usedefault=True, ), outputtype=dict(), - testlabels=dict(argstr='-testlabels %s', ), + testlabels=dict( + argstr='-testlabels %s', + usedefault=True, + ), ) inputs = SVMTest.input_spec() @@ -40,7 +45,7 @@ def test_SVMTest_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SVMTest_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = SVMTest.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py index ddb3f8c05f..54d326a561 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py @@ -10,9 +10,13 @@ def test_SVMTrain_inputs(): name_source='in_file', name_template='%s_alphas', suffix='_alphas', + usedefault=True, ), args=dict(argstr='%s', ), - censor=dict(argstr='-censor %s', ), + censor=dict( + argstr='-censor %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -21,12 +25,14 @@ def test_SVMTrain_inputs(): argstr='-trainvol %s', copyfile=False, mandatory=True, + usedefault=True, ), kernel=dict(argstr='-kernel %s', ), mask=dict( argstr='-mask %s', copyfile=False, position=-1, + usedefault=True, ), max_iterations=dict(argstr='-max_iterations %d', ), model=dict( @@ -34,6 +40,7 @@ def test_SVMTrain_inputs(): name_source='in_file', name_template='%s_model', suffix='_model', + usedefault=True, ), nomodelmask=dict(argstr='-nomodelmask', ), num_threads=dict( @@ -46,9 +53,13 @@ def test_SVMTrain_inputs(): name_source='in_file', name_template='%s_vectors', suffix='_bucket', + usedefault=True, ), outputtype=dict(), - trainlabels=dict(argstr='-trainlabels %s', ), + trainlabels=dict( + argstr='-trainlabels %s', + usedefault=True, + ), ttype=dict( argstr='-type %s', mandatory=True, @@ -62,9 +73,9 @@ def test_SVMTrain_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SVMTrain_outputs(): output_map = dict( - alphas=dict(), - model=dict(), - out_file=dict(), + alphas=dict(usedefault=True, ), + model=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), ) outputs = SVMTrain.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Seg.py b/nipype/interfaces/afni/tests/test_auto_Seg.py index e93d81a7aa..a30d59b1cb 100644 --- a/nipype/interfaces/afni/tests/test_auto_Seg.py +++ b/nipype/interfaces/afni/tests/test_auto_Seg.py @@ -20,6 +20,7 @@ def test_Seg_inputs(): copyfile=True, mandatory=True, position=-1, + usedefault=True, ), main_N=dict(argstr='-main_N %d', ), mask=dict( @@ -37,7 +38,7 @@ def test_Seg_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Seg_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Seg.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py index e960369787..3b56af7aa2 100644 --- a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py +++ b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py @@ -15,6 +15,7 @@ def test_SkullStrip_inputs(): copyfile=False, mandatory=True, position=1, + usedefault=True, ), num_threads=dict( nohash=True, @@ -24,6 +25,7 @@ def test_SkullStrip_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_skullstrip', + usedefault=True, ), outputtype=dict(), ) @@ -33,7 +35,7 @@ def test_SkullStrip_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SkullStrip_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = SkullStrip.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Synthesize.py b/nipype/interfaces/afni/tests/test_auto_Synthesize.py index 87278098fb..bdbf66c858 100644 --- a/nipype/interfaces/afni/tests/test_auto_Synthesize.py +++ b/nipype/interfaces/afni/tests/test_auto_Synthesize.py @@ -11,6 +11,7 @@ def test_Synthesize_inputs(): argstr='-cbucket %s', copyfile=False, mandatory=True, + usedefault=True, ), cenfill=dict(argstr='-cenfill %s', ), dry_run=dict(argstr='-dry', ), @@ -22,6 +23,7 @@ def test_Synthesize_inputs(): argstr='-matrix %s', copyfile=False, mandatory=True, + usedefault=True, ), num_threads=dict( nohash=True, @@ -30,6 +32,7 @@ def test_Synthesize_inputs(): out_file=dict( argstr='-prefix %s', name_template='syn', + usedefault=True, ), outputtype=dict(), select=dict( @@ -43,7 +46,7 @@ def test_Synthesize_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Synthesize_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Synthesize.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TCat.py b/nipype/interfaces/afni/tests/test_auto_TCat.py index 5c51b02637..900b977540 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCat.py +++ b/nipype/interfaces/afni/tests/test_auto_TCat.py @@ -24,6 +24,7 @@ def test_TCat_inputs(): argstr='-prefix %s', name_source='in_files', name_template='%s_tcat', + usedefault=True, ), outputtype=dict(), rlt=dict( @@ -38,7 +39,7 @@ def test_TCat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TCat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TCat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py b/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py index 09b21ea408..3d3e650a98 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py +++ b/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py @@ -23,6 +23,7 @@ def test_TCatSubBrick_inputs(): out_file=dict( argstr='-prefix %s', genfile=True, + usedefault=True, ), outputtype=dict(), rlt=dict( @@ -36,7 +37,7 @@ def test_TCatSubBrick_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TCatSubBrick_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TCatSubBrick.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py index e1b23a3387..3c04561a81 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py @@ -24,6 +24,7 @@ def test_TCorr1D_inputs(): keep_extension=True, name_source='xset', name_template='%s_correlation.nii.gz', + usedefault=True, ), outputtype=dict(), pearson=dict( @@ -46,11 +47,13 @@ def test_TCorr1D_inputs(): copyfile=False, mandatory=True, position=-2, + usedefault=True, ), y_1d=dict( argstr=' %s', mandatory=True, position=-1, + usedefault=True, ), ) inputs = TCorr1D.input_spec() @@ -59,7 +62,7 @@ def test_TCorr1D_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TCorr1D_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TCorr1D.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py index 32778fcf11..5efb91365b 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py @@ -9,6 +9,7 @@ def test_TCorrMap_inputs(): argstr='-Thresh %f %s', name_source='in_file', suffix='_thresh', + usedefault=True, xor=('absolute_threshold', 'var_absolute_threshold', 'var_absolute_threshold_normalize'), ), @@ -18,12 +19,14 @@ def test_TCorrMap_inputs(): argstr='-Aexpr %s %s', name_source='in_file', suffix='_aexpr', + usedefault=True, xor=('average_expr', 'average_expr_nonzero', 'sum_expr'), ), average_expr_nonzero=dict( argstr='-Cexpr %s %s', name_source='in_file', suffix='_cexpr', + usedefault=True, xor=('average_expr', 'average_expr_nonzero', 'sum_expr'), ), bandpass=dict(argstr='-bpass %f %f', ), @@ -31,10 +34,12 @@ def test_TCorrMap_inputs(): correlation_maps=dict( argstr='-CorrMap %s', name_source='in_file', + usedefault=True, ), correlation_maps_masked=dict( argstr='-CorrMask %s', name_source='in_file', + usedefault=True, ), environ=dict( nohash=True, @@ -45,43 +50,47 @@ def test_TCorrMap_inputs(): argstr='-Hist %d %s', name_source='in_file', suffix='_hist', + usedefault=True, ), histogram_bin_numbers=dict(), in_file=dict( argstr='-input %s', copyfile=False, mandatory=True, + usedefault=True, + ), + mask=dict( + argstr='-mask %s', + usedefault=True, ), - mask=dict(argstr='-mask %s', ), mean_file=dict( argstr='-Mean %s', name_source='in_file', suffix='_mean', + usedefault=True, ), num_threads=dict( nohash=True, usedefault=True, ), - out_file=dict( - argstr='-prefix %s', - name_source=['in_file'], - name_template='%s_afni', - ), outputtype=dict(), pmean=dict( argstr='-Pmean %s', name_source='in_file', suffix='_pmean', + usedefault=True, ), polort=dict(argstr='-polort %d', ), qmean=dict( argstr='-Qmean %s', name_source='in_file', suffix='_qmean', + usedefault=True, ), regress_out_timeseries=dict(argstr='-ort %s', ), seeds=dict( argstr='-seed %s', + usedefault=True, xor='seeds_width', ), seeds_width=dict( @@ -92,6 +101,7 @@ def test_TCorrMap_inputs(): argstr='-Sexpr %s %s', name_source='in_file', suffix='_sexpr', + usedefault=True, xor=('average_expr', 'average_expr_nonzero', 'sum_expr'), ), thresholds=dict(), @@ -99,6 +109,7 @@ def test_TCorrMap_inputs(): argstr='-VarThresh %f %f %f %s', name_source='in_file', suffix='_varthresh', + usedefault=True, xor=('absolute_threshold', 'var_absolute_threshold', 'var_absolute_threshold_normalize'), ), @@ -106,6 +117,7 @@ def test_TCorrMap_inputs(): argstr='-VarThreshN %f %f %f %s', name_source='in_file', suffix='_varthreshn', + usedefault=True, xor=('absolute_threshold', 'var_absolute_threshold', 'var_absolute_threshold_normalize'), ), @@ -113,6 +125,7 @@ def test_TCorrMap_inputs(): argstr='-Zmean %s', name_source='in_file', suffix='_zmean', + usedefault=True, ), ) inputs = TCorrMap.input_spec() @@ -122,19 +135,19 @@ def test_TCorrMap_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TCorrMap_outputs(): output_map = dict( - absolute_threshold=dict(), - average_expr=dict(), - average_expr_nonzero=dict(), - correlation_maps=dict(), - correlation_maps_masked=dict(), - histogram=dict(), - mean_file=dict(), - pmean=dict(), - qmean=dict(), - sum_expr=dict(), - var_absolute_threshold=dict(), - var_absolute_threshold_normalize=dict(), - zmean=dict(), + absolute_threshold=dict(usedefault=True, ), + average_expr=dict(usedefault=True, ), + average_expr_nonzero=dict(usedefault=True, ), + correlation_maps=dict(usedefault=True, ), + correlation_maps_masked=dict(usedefault=True, ), + histogram=dict(usedefault=True, ), + mean_file=dict(usedefault=True, ), + pmean=dict(usedefault=True, ), + qmean=dict(usedefault=True, ), + sum_expr=dict(usedefault=True, ), + var_absolute_threshold=dict(usedefault=True, ), + var_absolute_threshold_normalize=dict(usedefault=True, ), + zmean=dict(usedefault=True, ), ) outputs = TCorrMap.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py index 8d773f429e..283fe966ae 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py @@ -18,6 +18,7 @@ def test_TCorrelate_inputs(): argstr='-prefix %s', name_source='xset', name_template='%s_tcorr', + usedefault=True, ), outputtype=dict(), pearson=dict(argstr='-pearson', ), @@ -27,12 +28,14 @@ def test_TCorrelate_inputs(): copyfile=False, mandatory=True, position=-2, + usedefault=True, ), yset=dict( argstr='%s', copyfile=False, mandatory=True, position=-1, + usedefault=True, ), ) inputs = TCorrelate.input_spec() @@ -41,7 +44,7 @@ def test_TCorrelate_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TCorrelate_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TCorrelate.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TNorm.py b/nipype/interfaces/afni/tests/test_auto_TNorm.py index 3fb246684b..23d2a43841 100644 --- a/nipype/interfaces/afni/tests/test_auto_TNorm.py +++ b/nipype/interfaces/afni/tests/test_auto_TNorm.py @@ -16,6 +16,7 @@ def test_TNorm_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, ), norm1=dict(argstr='-norm1', ), norm2=dict(argstr='-norm2', ), @@ -29,6 +30,7 @@ def test_TNorm_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_tnorm', + usedefault=True, ), outputtype=dict(), polort=dict(argstr='-polort %s', ), @@ -39,7 +41,7 @@ def test_TNorm_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TNorm_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TNorm.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TProject.py b/nipype/interfaces/afni/tests/test_auto_TProject.py index ba4efd6189..c07c6fd602 100644 --- a/nipype/interfaces/afni/tests/test_auto_TProject.py +++ b/nipype/interfaces/afni/tests/test_auto_TProject.py @@ -14,9 +14,15 @@ def test_TProject_inputs(): bandpass=dict(argstr='-bandpass %g %g', ), blur=dict(argstr='-blur %g', ), cenmode=dict(argstr='-cenmode %s', ), - censor=dict(argstr='-censor %s', ), + censor=dict( + argstr='-censor %s', + usedefault=True, + ), censortr=dict(argstr='-CENSORTR %s', ), - concat=dict(argstr='-concat %s', ), + concat=dict( + argstr='-concat %s', + usedefault=True, + ), dsort=dict(argstr='-dsort %s...', ), environ=dict( nohash=True, @@ -27,20 +33,28 @@ def test_TProject_inputs(): copyfile=False, mandatory=True, position=1, + usedefault=True, + ), + mask=dict( + argstr='-mask %s', + usedefault=True, ), - mask=dict(argstr='-mask %s', ), noblock=dict(argstr='-noblock', ), norm=dict(argstr='-norm', ), num_threads=dict( nohash=True, usedefault=True, ), - ort=dict(argstr='-ort %s', ), + ort=dict( + argstr='-ort %s', + usedefault=True, + ), out_file=dict( argstr='-prefix %s', name_source='in_file', name_template='%s_tproject', position=-1, + usedefault=True, ), outputtype=dict(), polort=dict(argstr='-polort %d', ), @@ -52,7 +66,7 @@ def test_TProject_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TProject_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TProject.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TShift.py b/nipype/interfaces/afni/tests/test_auto_TShift.py index b267986952..2a66792be7 100644 --- a/nipype/interfaces/afni/tests/test_auto_TShift.py +++ b/nipype/interfaces/afni/tests/test_auto_TShift.py @@ -16,6 +16,7 @@ def test_TShift_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, ), interp=dict(argstr='-%s', ), num_threads=dict( @@ -26,6 +27,7 @@ def test_TShift_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_tshift', + usedefault=True, ), outputtype=dict(), rlt=dict(argstr='-rlt', ), @@ -56,8 +58,8 @@ def test_TShift_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TShift_outputs(): output_map = dict( - out_file=dict(), - timing_file=dict(), + out_file=dict(usedefault=True, ), + timing_file=dict(usedefault=True, ), ) outputs = TShift.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_TStat.py b/nipype/interfaces/afni/tests/test_auto_TStat.py index 5a3ebd8a21..021b39bac3 100644 --- a/nipype/interfaces/afni/tests/test_auto_TStat.py +++ b/nipype/interfaces/afni/tests/test_auto_TStat.py @@ -15,8 +15,12 @@ def test_TStat_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, + ), + mask=dict( + argstr='-mask %s', + usedefault=True, ), - mask=dict(argstr='-mask %s', ), num_threads=dict( nohash=True, usedefault=True, @@ -26,6 +30,7 @@ def test_TStat_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_tstat', + usedefault=True, ), outputtype=dict(), ) @@ -35,7 +40,7 @@ def test_TStat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TStat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TStat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_To3D.py b/nipype/interfaces/afni/tests/test_auto_To3D.py index 66ccabefcb..0edf3f255d 100644 --- a/nipype/interfaces/afni/tests/test_auto_To3D.py +++ b/nipype/interfaces/afni/tests/test_auto_To3D.py @@ -18,6 +18,7 @@ def test_To3D_inputs(): argstr='%s/*.dcm', mandatory=True, position=-1, + usedefault=True, ), num_threads=dict( nohash=True, @@ -27,6 +28,7 @@ def test_To3D_inputs(): argstr='-prefix %s', name_source=['in_folder'], name_template='%s', + usedefault=True, ), outputtype=dict(), skipoutliers=dict(argstr='-skip_outliers', ), @@ -37,7 +39,7 @@ def test_To3D_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_To3D_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = To3D.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Undump.py b/nipype/interfaces/afni/tests/test_auto_Undump.py index 07d0ff8e81..572e7e3bcb 100644 --- a/nipype/interfaces/afni/tests/test_auto_Undump.py +++ b/nipype/interfaces/afni/tests/test_auto_Undump.py @@ -20,8 +20,12 @@ def test_Undump_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, + ), + mask_file=dict( + argstr='-mask %s', + usedefault=True, ), - mask_file=dict(argstr='-mask %s', ), num_threads=dict( nohash=True, usedefault=True, @@ -30,6 +34,7 @@ def test_Undump_inputs(): out_file=dict( argstr='-prefix %s', name_source='in_file', + usedefault=True, ), outputtype=dict(), srad=dict(argstr='-srad %f', ), @@ -40,7 +45,7 @@ def test_Undump_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Undump_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Undump.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Unifize.py b/nipype/interfaces/afni/tests/test_auto_Unifize.py index 3215d51e64..c5c89a0793 100644 --- a/nipype/interfaces/afni/tests/test_auto_Unifize.py +++ b/nipype/interfaces/afni/tests/test_auto_Unifize.py @@ -22,6 +22,7 @@ def test_Unifize_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, ), no_duplo=dict(argstr='-noduplo', ), num_threads=dict( @@ -32,11 +33,15 @@ def test_Unifize_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_unifized', + usedefault=True, ), outputtype=dict(), quiet=dict(argstr='-quiet', ), rbt=dict(argstr='-rbt %f %f %f', ), - scale_file=dict(argstr='-ssave %s', ), + scale_file=dict( + argstr='-ssave %s', + usedefault=True, + ), t2=dict(argstr='-T2', ), t2_up=dict(argstr='-T2up %f', ), urad=dict(argstr='-Urad %s', ), @@ -48,8 +53,8 @@ def test_Unifize_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Unifize_outputs(): output_map = dict( - out_file=dict(), - scale_file=dict(), + out_file=dict(usedefault=True, ), + scale_file=dict(usedefault=True, ), ) outputs = Unifize.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Volreg.py b/nipype/interfaces/afni/tests/test_auto_Volreg.py index 293b7613e8..179e1fa3e3 100644 --- a/nipype/interfaces/afni/tests/test_auto_Volreg.py +++ b/nipype/interfaces/afni/tests/test_auto_Volreg.py @@ -9,6 +9,7 @@ def test_Volreg_inputs(): basefile=dict( argstr='-base %s', position=-6, + usedefault=True, ), copyorigin=dict(argstr='-twodup', ), environ=dict( @@ -20,6 +21,7 @@ def test_Volreg_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, ), in_weight_volume=dict(argstr="-weight '%s[%d]'", ), interp=dict(argstr='-%s', ), @@ -29,6 +31,7 @@ def test_Volreg_inputs(): name_source='in_file', name_template='%s_md.1D', position=-4, + usedefault=True, ), num_threads=dict( nohash=True, @@ -39,17 +42,20 @@ def test_Volreg_inputs(): keep_extension=True, name_source='in_file', name_template='%s.1D', + usedefault=True, ), oned_matrix_save=dict( argstr='-1Dmatrix_save %s', keep_extension=True, name_source='in_file', name_template='%s.aff12.1D', + usedefault=True, ), out_file=dict( argstr='-prefix %s', name_source='in_file', name_template='%s_volreg', + usedefault=True, ), outputtype=dict(), timeshift=dict(argstr='-tshift 0', ), @@ -66,10 +72,10 @@ def test_Volreg_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Volreg_outputs(): output_map = dict( - md1d_file=dict(), - oned_file=dict(), - oned_matrix_save=dict(), - out_file=dict(), + md1d_file=dict(usedefault=True, ), + oned_file=dict(usedefault=True, ), + oned_matrix_save=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), ) outputs = Volreg.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Warp.py b/nipype/interfaces/afni/tests/test_auto_Warp.py index b85692310a..c5bee6a063 100644 --- a/nipype/interfaces/afni/tests/test_auto_Warp.py +++ b/nipype/interfaces/afni/tests/test_auto_Warp.py @@ -11,27 +11,38 @@ def test_Warp_inputs(): nohash=True, usedefault=True, ), - gridset=dict(argstr='-gridset %s', ), + gridset=dict( + argstr='-gridset %s', + usedefault=True, + ), in_file=dict( argstr='%s', copyfile=False, mandatory=True, position=-1, + usedefault=True, ), interp=dict(argstr='-%s', ), - matparent=dict(argstr='-matparent %s', ), + matparent=dict( + argstr='-matparent %s', + usedefault=True, + ), mni2tta=dict(argstr='-mni2tta', ), newgrid=dict(argstr='-newgrid %f', ), num_threads=dict( nohash=True, usedefault=True, ), - oblique_parent=dict(argstr='-oblique_parent %s', ), + oblique_parent=dict( + argstr='-oblique_parent %s', + usedefault=True, + ), out_file=dict( argstr='-prefix %s', keep_extension=True, name_source='in_file', name_template='%s_warp', + usedefault=True, ), outputtype=dict(), save_warp=dict(requires=['verbose'], ), @@ -46,8 +57,8 @@ def test_Warp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Warp_outputs(): output_map = dict( - out_file=dict(), - warp_file=dict(), + out_file=dict(usedefault=True, ), + warp_file=dict(usedefault=True, ), ) outputs = Warp.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py index cacb6b1534..353a98d76a 100644 --- a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py +++ b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py @@ -15,6 +15,7 @@ def test_ZCutUp_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, ), keep=dict(argstr='-keep %s', ), num_threads=dict( @@ -25,6 +26,7 @@ def test_ZCutUp_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_zcutup', + usedefault=True, ), outputtype=dict(), ) @@ -34,7 +36,7 @@ def test_ZCutUp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ZCutUp_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ZCutUp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Zcat.py b/nipype/interfaces/afni/tests/test_auto_Zcat.py index 3a2b7ff853..6dc0430c09 100644 --- a/nipype/interfaces/afni/tests/test_auto_Zcat.py +++ b/nipype/interfaces/afni/tests/test_auto_Zcat.py @@ -33,6 +33,7 @@ def test_Zcat_inputs(): argstr='-prefix %s', name_source='in_files', name_template='%s_zcat', + usedefault=True, ), outputtype=dict(), verb=dict(argstr='-verb', ), @@ -43,7 +44,7 @@ def test_Zcat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Zcat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Zcat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Zeropad.py b/nipype/interfaces/afni/tests/test_auto_Zeropad.py index cfba8e2f3c..427eef0f67 100644 --- a/nipype/interfaces/afni/tests/test_auto_Zeropad.py +++ b/nipype/interfaces/afni/tests/test_auto_Zeropad.py @@ -51,6 +51,7 @@ def test_Zeropad_inputs(): copyfile=False, mandatory=True, position=-1, + usedefault=True, ), master=dict( argstr='-master %s', @@ -67,6 +68,7 @@ def test_Zeropad_inputs(): out_file=dict( argstr='-prefix %s', name_template='zeropad', + usedefault=True, ), outputtype=dict(), z=dict( @@ -80,7 +82,7 @@ def test_Zeropad_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Zeropad_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Zeropad.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_ANTS.py b/nipype/interfaces/ants/tests/test_auto_ANTS.py index 7c7ef6682c..24ddbadadf 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTS.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTS.py @@ -84,11 +84,11 @@ def test_ANTS_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ANTS_outputs(): output_map = dict( - affine_transform=dict(), - inverse_warp_transform=dict(), - metaheader=dict(), - metaheader_raw=dict(), - warp_transform=dict(), + affine_transform=dict(usedefault=True, ), + inverse_warp_transform=dict(usedefault=True, ), + metaheader=dict(usedefault=True, ), + metaheader_raw=dict(usedefault=True, ), + warp_transform=dict(usedefault=True, ), ) outputs = ANTS.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py b/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py index fed21cdbef..96d839a0dc 100644 --- a/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py +++ b/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py @@ -19,6 +19,7 @@ def test_AffineInitializer_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), local_search=dict( argstr='%d', @@ -29,6 +30,7 @@ def test_AffineInitializer_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), num_threads=dict( nohash=True, @@ -61,7 +63,7 @@ def test_AffineInitializer_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AffineInitializer_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = AffineInitializer.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py index 341f250a2c..cf39a7c3c4 100644 --- a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py @@ -36,7 +36,10 @@ def test_AntsJointFusion_inputs(): argstr='-e %s', requires=['exclusion_image'], ), - mask_image=dict(argstr='-x %s', ), + mask_image=dict( + argstr='-x %s', + usedefault=True, + ), num_threads=dict( nohash=True, usedefault=True, @@ -50,10 +53,11 @@ def test_AntsJointFusion_inputs(): out_label_fusion=dict( argstr='%s', hash_files=False, + usedefault=True, ), out_label_post_prob_name_format=dict( - requires=['out_label_fusion', - 'out_intensity_fusion_name_format'], ), + requires=['out_label_fusion', 'out_intensity_fusion_name_format'], + ), patch_metric=dict(argstr='-m %s', ), patch_radius=dict( argstr='-p %s', @@ -88,7 +92,7 @@ def test_AntsJointFusion_outputs(): output_map = dict( out_atlas_voting_weight_name_format=dict(), out_intensity_fusion_name_format=dict(), - out_label_fusion=dict(), + out_label_fusion=dict(usedefault=True, ), out_label_post_prob_name_format=dict(), ) outputs = AntsJointFusion.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py index c2bbffa14f..82cd9dfc29 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py @@ -22,6 +22,7 @@ def test_ApplyTransforms_inputs(): input_image=dict( argstr='--input %s', mandatory=True, + usedefault=True, ), input_image_type=dict(argstr='--input-image-type %d', ), interpolation=dict( @@ -44,6 +45,7 @@ def test_ApplyTransforms_inputs(): reference_image=dict( argstr='--reference-image %s', mandatory=True, + usedefault=True, ), transforms=dict( argstr='%s', @@ -56,7 +58,7 @@ def test_ApplyTransforms_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyTransforms_outputs(): - output_map = dict(output_image=dict(), ) + output_map = dict(output_image=dict(usedefault=True, ), ) outputs = ApplyTransforms.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py index 92c6c21ec1..58fc69e72d 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py @@ -14,6 +14,7 @@ def test_ApplyTransformsToPoints_inputs(): input_file=dict( argstr='--input %s', mandatory=True, + usedefault=True, ), invert_transform_flags=dict(), num_threads=dict( @@ -37,7 +38,7 @@ def test_ApplyTransformsToPoints_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyTransformsToPoints_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = ApplyTransformsToPoints.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_Atropos.py b/nipype/interfaces/ants/tests/test_auto_Atropos.py index 90bc13778a..b3b9252858 100644 --- a/nipype/interfaces/ants/tests/test_auto_Atropos.py +++ b/nipype/interfaces/ants/tests/test_auto_Atropos.py @@ -29,6 +29,7 @@ def test_Atropos_inputs(): mask_image=dict( argstr='--mask-image %s', mandatory=True, + usedefault=True, ), maximum_number_of_icm_terations=dict( requires=['icm_use_synchronous_update'], ), @@ -44,6 +45,7 @@ def test_Atropos_inputs(): argstr='%s', genfile=True, hash_files=False, + usedefault=True, ), output_posteriors_name_template=dict(usedefault=True, ), posterior_formulation=dict(argstr='%s', ), @@ -65,7 +67,7 @@ def test_Atropos_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Atropos_outputs(): output_map = dict( - classified_image=dict(), + classified_image=dict(usedefault=True, ), posteriors=dict(), ) outputs = Atropos.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py index 3fe3abe5cf..4fad7f75d5 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py @@ -23,6 +23,7 @@ def test_AverageAffineTransform_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), transforms=dict( argstr='%s', @@ -36,7 +37,7 @@ def test_AverageAffineTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AverageAffineTransform_outputs(): - output_map = dict(affine_transform=dict(), ) + output_map = dict(affine_transform=dict(usedefault=True, ), ) outputs = AverageAffineTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_AverageImages.py b/nipype/interfaces/ants/tests/test_auto_AverageImages.py index 41e0c99007..dba08b8ae7 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageImages.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageImages.py @@ -42,7 +42,7 @@ def test_AverageImages_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AverageImages_outputs(): - output_map = dict(output_average_image=dict(), ) + output_map = dict(output_average_image=dict(usedefault=True, ), ) outputs = AverageImages.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py b/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py index 2d48192199..e25d66f914 100644 --- a/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py +++ b/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py @@ -8,16 +8,19 @@ def test_BrainExtraction_inputs(): anatomical_image=dict( argstr='-a %s', mandatory=True, + usedefault=True, ), args=dict(argstr='%s', ), brain_probability_mask=dict( argstr='-m %s', copyfile=False, mandatory=True, + usedefault=True, ), brain_template=dict( argstr='-e %s', mandatory=True, + usedefault=True, ), debug=dict(argstr='-z 1', ), dimension=dict( @@ -28,7 +31,10 @@ def test_BrainExtraction_inputs(): nohash=True, usedefault=True, ), - extraction_registration_mask=dict(argstr='-f %s', ), + extraction_registration_mask=dict( + argstr='-f %s', + usedefault=True, + ), image_suffix=dict( argstr='-s %s', usedefault=True, @@ -52,24 +58,24 @@ def test_BrainExtraction_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BrainExtraction_outputs(): output_map = dict( - BrainExtractionBrain=dict(), - BrainExtractionCSF=dict(), - BrainExtractionGM=dict(), - BrainExtractionInitialAffine=dict(), - BrainExtractionInitialAffineFixed=dict(), - BrainExtractionInitialAffineMoving=dict(), - BrainExtractionLaplacian=dict(), - BrainExtractionMask=dict(), - BrainExtractionPrior0GenericAffine=dict(), - BrainExtractionPrior1InverseWarp=dict(), - BrainExtractionPrior1Warp=dict(), - BrainExtractionPriorWarped=dict(), - BrainExtractionSegmentation=dict(), - BrainExtractionTemplateLaplacian=dict(), - BrainExtractionTmp=dict(), - BrainExtractionWM=dict(), - N4Corrected0=dict(), - N4Truncated0=dict(), + BrainExtractionBrain=dict(usedefault=True, ), + BrainExtractionCSF=dict(usedefault=True, ), + BrainExtractionGM=dict(usedefault=True, ), + BrainExtractionInitialAffine=dict(usedefault=True, ), + BrainExtractionInitialAffineFixed=dict(usedefault=True, ), + BrainExtractionInitialAffineMoving=dict(usedefault=True, ), + BrainExtractionLaplacian=dict(usedefault=True, ), + BrainExtractionMask=dict(usedefault=True, ), + BrainExtractionPrior0GenericAffine=dict(usedefault=True, ), + BrainExtractionPrior1InverseWarp=dict(usedefault=True, ), + BrainExtractionPrior1Warp=dict(usedefault=True, ), + BrainExtractionPriorWarped=dict(usedefault=True, ), + BrainExtractionSegmentation=dict(usedefault=True, ), + BrainExtractionTemplateLaplacian=dict(usedefault=True, ), + BrainExtractionTmp=dict(usedefault=True, ), + BrainExtractionWM=dict(usedefault=True, ), + N4Corrected0=dict(usedefault=True, ), + N4Truncated0=dict(usedefault=True, ), ) outputs = BrainExtraction.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py index 83fb2ed2aa..8363a98834 100644 --- a/nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py @@ -25,10 +25,12 @@ def test_ComposeMultiTransform_inputs(): name_source=['transforms'], name_template='%s_composed', position=1, + usedefault=True, ), reference_image=dict( argstr='%s', position=2, + usedefault=True, ), transforms=dict( argstr='%s', @@ -42,7 +44,7 @@ def test_ComposeMultiTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComposeMultiTransform_outputs(): - output_map = dict(output_transform=dict(), ) + output_map = dict(output_transform=dict(usedefault=True, ), ) outputs = ComposeMultiTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_CompositeTransformUtil.py b/nipype/interfaces/ants/tests/test_auto_CompositeTransformUtil.py index d2e6f943e2..abe9a62427 100644 --- a/nipype/interfaces/ants/tests/test_auto_CompositeTransformUtil.py +++ b/nipype/interfaces/ants/tests/test_auto_CompositeTransformUtil.py @@ -22,6 +22,7 @@ def test_CompositeTransformUtil_inputs(): out_file=dict( argstr='%s', position=2, + usedefault=True, ), output_prefix=dict( argstr='%s', @@ -41,9 +42,9 @@ def test_CompositeTransformUtil_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CompositeTransformUtil_outputs(): output_map = dict( - affine_transform=dict(), - displacement_field=dict(), - out_file=dict(), + affine_transform=dict(usedefault=True, ), + displacement_field=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), ) outputs = CompositeTransformUtil.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py index ea9a16cbe2..43471662ab 100644 --- a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py +++ b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py @@ -31,6 +31,7 @@ def test_ConvertScalarImageToRGB_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), mask_image=dict( argstr='%s', @@ -73,7 +74,7 @@ def test_ConvertScalarImageToRGB_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConvertScalarImageToRGB_outputs(): - output_map = dict(output_image=dict(), ) + output_map = dict(output_image=dict(usedefault=True, ), ) outputs = ConvertScalarImageToRGB.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py index e2595a710f..6c45c795d5 100644 --- a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py @@ -8,6 +8,7 @@ def test_CorticalThickness_inputs(): anatomical_image=dict( argstr='-a %s', mandatory=True, + usedefault=True, ), args=dict(argstr='%s', ), b_spline_smoothing=dict(argstr='-v', ), @@ -15,12 +16,14 @@ def test_CorticalThickness_inputs(): argstr='-m %s', copyfile=False, mandatory=True, + usedefault=True, ), brain_template=dict( argstr='-e %s', mandatory=True, + usedefault=True, ), - cortical_label_image=dict(), + cortical_label_image=dict(usedefault=True, ), debug=dict(argstr='-z 1', ), dimension=dict( argstr='-d %d', @@ -30,7 +33,10 @@ def test_CorticalThickness_inputs(): nohash=True, usedefault=True, ), - extraction_registration_mask=dict(argstr='-f %s', ), + extraction_registration_mask=dict( + argstr='-f %s', + usedefault=True, + ), image_suffix=dict( argstr='-s %s', usedefault=True, @@ -57,6 +63,7 @@ def test_CorticalThickness_inputs(): t1_registration_template=dict( argstr='-t %s', mandatory=True, + usedefault=True, ), use_floatingpoint_precision=dict(argstr='-j %d', ), use_random_seeding=dict(argstr='-u %d', ), @@ -68,19 +75,19 @@ def test_CorticalThickness_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CorticalThickness_outputs(): output_map = dict( - BrainExtractionMask=dict(), - BrainSegmentation=dict(), - BrainSegmentationN4=dict(), + BrainExtractionMask=dict(usedefault=True, ), + BrainSegmentation=dict(usedefault=True, ), + BrainSegmentationN4=dict(usedefault=True, ), BrainSegmentationPosteriors=dict(), - BrainVolumes=dict(), - CorticalThickness=dict(), - CorticalThicknessNormedToTemplate=dict(), - ExtractedBrainN4=dict(), - SubjectToTemplate0GenericAffine=dict(), - SubjectToTemplate1Warp=dict(), - SubjectToTemplateLogJacobian=dict(), - TemplateToSubject0Warp=dict(), - TemplateToSubject1GenericAffine=dict(), + BrainVolumes=dict(usedefault=True, ), + CorticalThickness=dict(usedefault=True, ), + CorticalThicknessNormedToTemplate=dict(usedefault=True, ), + ExtractedBrainN4=dict(usedefault=True, ), + SubjectToTemplate0GenericAffine=dict(usedefault=True, ), + SubjectToTemplate1Warp=dict(usedefault=True, ), + SubjectToTemplateLogJacobian=dict(usedefault=True, ), + TemplateToSubject0Warp=dict(usedefault=True, ), + TemplateToSubject1GenericAffine=dict(usedefault=True, ), ) outputs = CorticalThickness.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py b/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py index b32e7b98e0..c3d5aca2bf 100644 --- a/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py +++ b/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py @@ -10,6 +10,7 @@ def test_CreateJacobianDeterminantImage_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), doLogJacobian=dict( argstr='%d', @@ -32,6 +33,7 @@ def test_CreateJacobianDeterminantImage_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), useGeometric=dict( argstr='%d', @@ -44,7 +46,7 @@ def test_CreateJacobianDeterminantImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CreateJacobianDeterminantImage_outputs(): - output_map = dict(jacobian_image=dict(), ) + output_map = dict(jacobian_image=dict(usedefault=True, ), ) outputs = CreateJacobianDeterminantImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py index 74c2b0a7c2..ec56617940 100644 --- a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py +++ b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py @@ -16,8 +16,12 @@ def test_CreateTiledMosaic_inputs(): input_image=dict( argstr='-i %s', mandatory=True, + usedefault=True, + ), + mask_image=dict( + argstr='-x %s', + usedefault=True, ), - mask_image=dict(argstr='-x %s', ), num_threads=dict( nohash=True, usedefault=True, @@ -31,6 +35,7 @@ def test_CreateTiledMosaic_inputs(): rgb_image=dict( argstr='-r %s', mandatory=True, + usedefault=True, ), slices=dict(argstr='-s %s', ), tile_geometry=dict(argstr='-t %s', ), @@ -41,7 +46,7 @@ def test_CreateTiledMosaic_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CreateTiledMosaic_outputs(): - output_map = dict(output_image=dict(), ) + output_map = dict(output_image=dict(usedefault=True, ), ) outputs = CreateTiledMosaic.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py b/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py index 882cb21854..fea1094a13 100644 --- a/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py +++ b/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py @@ -14,12 +14,14 @@ def test_DenoiseImage_inputs(): input_image=dict( argstr='-i %s', mandatory=True, + usedefault=True, ), noise_image=dict( hash_files=False, keep_extension=True, name_source=['input_image'], name_template='%s_noise', + usedefault=True, ), noise_model=dict( argstr='-n %s', @@ -35,6 +37,7 @@ def test_DenoiseImage_inputs(): keep_extension=True, name_source=['input_image'], name_template='%s_noise_corrected', + usedefault=True, ), save_noise=dict( mandatory=True, @@ -54,8 +57,8 @@ def test_DenoiseImage_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DenoiseImage_outputs(): output_map = dict( - noise_image=dict(), - output_image=dict(), + noise_image=dict(usedefault=True, ), + output_image=dict(usedefault=True, ), ) outputs = DenoiseImage.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py index af91f9a8af..2a6b175a8c 100644 --- a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py +++ b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py @@ -21,6 +21,7 @@ def test_GenWarpFields_inputs(): argstr='-i %s', copyfile=False, mandatory=True, + usedefault=True, ), inverse_warp_template_labels=dict(argstr='-l', ), max_iterations=dict( @@ -40,6 +41,7 @@ def test_GenWarpFields_inputs(): argstr='-r %s', copyfile=True, mandatory=True, + usedefault=True, ), similarity_metric=dict(argstr='-s %s', ), transformation_model=dict( @@ -54,11 +56,11 @@ def test_GenWarpFields_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_GenWarpFields_outputs(): output_map = dict( - affine_transformation=dict(), - input_file=dict(), - inverse_warp_field=dict(), - output_file=dict(), - warp_field=dict(), + affine_transformation=dict(usedefault=True, ), + input_file=dict(usedefault=True, ), + inverse_warp_field=dict(usedefault=True, ), + output_file=dict(usedefault=True, ), + warp_field=dict(usedefault=True, ), ) outputs = GenWarpFields.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_JointFusion.py b/nipype/interfaces/ants/tests/test_auto_JointFusion.py index 9e82584729..0da922535a 100644 --- a/nipype/interfaces/ants/tests/test_auto_JointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_JointFusion.py @@ -26,7 +26,10 @@ def test_JointFusion_inputs(): nohash=True, usedefault=True, ), - exclusion_region=dict(argstr='-x %s', ), + exclusion_region=dict( + argstr='-x %s', + usedefault=True, + ), method=dict( argstr='-m %s', usedefault=True, @@ -46,6 +49,7 @@ def test_JointFusion_inputs(): name_template='%s', output_name='output_label_image', position=-1, + usedefault=True, ), patch_radius=dict( argstr='-rp %s', @@ -76,7 +80,7 @@ def test_JointFusion_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JointFusion_outputs(): - output_map = dict(output_label_image=dict(), ) + output_map = dict(output_label_image=dict(usedefault=True, ), ) outputs = JointFusion.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py b/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py index 6129670d39..7a26ae8d17 100644 --- a/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py +++ b/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py @@ -16,6 +16,7 @@ def test_KellyKapowski_inputs(): keep_extension=True, name_source=['segmentation_image'], name_template='%s_cortical_thickness', + usedefault=True, ), dimension=dict( argstr='--image-dimensionality %d', @@ -31,7 +32,9 @@ def test_KellyKapowski_inputs(): ), gray_matter_label=dict(usedefault=True, ), gray_matter_prob_image=dict( - argstr='--gray-matter-probability-image "%s"', ), + argstr='--gray-matter-probability-image "%s"', + usedefault=True, + ), max_invert_displacement_field_iters=dict( argstr= '--maximum-number-of-invert-displacement-field-iterations %d', @@ -48,6 +51,7 @@ def test_KellyKapowski_inputs(): segmentation_image=dict( argstr='--segmentation-image "%s"', mandatory=True, + usedefault=True, ), smoothing_variance=dict( argstr='--smoothing-variance %f', @@ -61,17 +65,23 @@ def test_KellyKapowski_inputs(): argstr='--thickness-prior-estimate %f', usedefault=True, ), - thickness_prior_image=dict(argstr='--thickness-prior-image "%s"', ), + thickness_prior_image=dict( + argstr='--thickness-prior-image "%s"', + usedefault=True, + ), use_bspline_smoothing=dict(argstr='--use-bspline-smoothing 1', ), warped_white_matter=dict( hash_files=False, keep_extension=True, name_source=['segmentation_image'], name_template='%s_warped_white_matter', + usedefault=True, ), white_matter_label=dict(usedefault=True, ), white_matter_prob_image=dict( - argstr='--white-matter-probability-image "%s"', ), + argstr='--white-matter-probability-image "%s"', + usedefault=True, + ), ) inputs = KellyKapowski.input_spec() @@ -80,8 +90,8 @@ def test_KellyKapowski_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_KellyKapowski_outputs(): output_map = dict( - cortical_thickness=dict(), - warped_white_matter=dict(), + cortical_thickness=dict(usedefault=True, ), + warped_white_matter=dict(usedefault=True, ), ) outputs = KellyKapowski.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_LabelGeometry.py b/nipype/interfaces/ants/tests/test_auto_LabelGeometry.py index a5de244711..0eaca9e911 100644 --- a/nipype/interfaces/ants/tests/test_auto_LabelGeometry.py +++ b/nipype/interfaces/ants/tests/test_auto_LabelGeometry.py @@ -25,6 +25,7 @@ def test_LabelGeometry_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), num_threads=dict( nohash=True, @@ -43,7 +44,7 @@ def test_LabelGeometry_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LabelGeometry_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = LabelGeometry.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py index 608ba10889..ed3b5d49a7 100644 --- a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py @@ -20,12 +20,14 @@ def test_LaplacianThickness_inputs(): copyfile=True, mandatory=True, position=2, + usedefault=True, ), input_wm=dict( argstr='%s', copyfile=True, mandatory=True, position=1, + usedefault=True, ), num_threads=dict( nohash=True, @@ -38,6 +40,7 @@ def test_LaplacianThickness_inputs(): name_source=['input_wm'], name_template='%s_thickness', position=3, + usedefault=True, ), prior_thickness=dict( argstr='%s', @@ -65,7 +68,7 @@ def test_LaplacianThickness_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LaplacianThickness_outputs(): - output_map = dict(output_image=dict(), ) + output_map = dict(output_image=dict(usedefault=True, ), ) outputs = LaplacianThickness.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py b/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py index 1a5041ae74..5edc7f859b 100644 --- a/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py +++ b/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py @@ -14,8 +14,14 @@ def test_MeasureImageSimilarity_inputs(): nohash=True, usedefault=True, ), - fixed_image=dict(mandatory=True, ), - fixed_image_mask=dict(argstr='%s', ), + fixed_image=dict( + mandatory=True, + usedefault=True, + ), + fixed_image_mask=dict( + argstr='%s', + usedefault=True, + ), metric=dict( argstr='%s', mandatory=True, @@ -24,8 +30,14 @@ def test_MeasureImageSimilarity_inputs(): requires=['metric'], usedefault=True, ), - moving_image=dict(mandatory=True, ), - moving_image_mask=dict(requires=['fixed_image_mask'], ), + moving_image=dict( + mandatory=True, + usedefault=True, + ), + moving_image_mask=dict( + requires=['fixed_image_mask'], + usedefault=True, + ), num_threads=dict( nohash=True, usedefault=True, diff --git a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py index 1bf787018d..7d3756b044 100644 --- a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py +++ b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py @@ -19,6 +19,7 @@ def test_MultiplyImages_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), num_threads=dict( nohash=True, @@ -28,6 +29,7 @@ def test_MultiplyImages_inputs(): argstr='%s', mandatory=True, position=3, + usedefault=True, ), second_input=dict( argstr='%s', @@ -41,7 +43,7 @@ def test_MultiplyImages_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MultiplyImages_outputs(): - output_map = dict(output_product_image=dict(), ) + output_map = dict(output_product_image=dict(usedefault=True, ), ) outputs = MultiplyImages.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py index 66edf0c3d6..029c7dd3a9 100644 --- a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py +++ b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py @@ -6,7 +6,10 @@ def test_N4BiasFieldCorrection_inputs(): input_map = dict( args=dict(argstr='%s', ), - bias_image=dict(hash_files=False, ), + bias_image=dict( + hash_files=False, + usedefault=True, + ), bspline_fitting_distance=dict(argstr='--bspline-fitting %s', ), bspline_order=dict(requires=['bspline_fitting_distance'], ), convergence_threshold=dict(requires=['n_iterations'], ), @@ -25,8 +28,12 @@ def test_N4BiasFieldCorrection_inputs(): input_image=dict( argstr='--input-image %s', mandatory=True, + usedefault=True, + ), + mask_image=dict( + argstr='--mask-image %s', + usedefault=True, ), - mask_image=dict(argstr='--mask-image %s', ), n_iterations=dict(argstr='--convergence %s', ), num_threads=dict( nohash=True, @@ -43,7 +50,10 @@ def test_N4BiasFieldCorrection_inputs(): xor=['bias_image'], ), shrink_factor=dict(argstr='--shrink-factor %d', ), - weight_image=dict(argstr='--weight-image %s', ), + weight_image=dict( + argstr='--weight-image %s', + usedefault=True, + ), ) inputs = N4BiasFieldCorrection.input_spec() @@ -52,8 +62,8 @@ def test_N4BiasFieldCorrection_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_N4BiasFieldCorrection_outputs(): output_map = dict( - bias_image=dict(), - output_image=dict(), + bias_image=dict(usedefault=True, ), + output_image=dict(usedefault=True, ), ) outputs = N4BiasFieldCorrection.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_Registration.py b/nipype/interfaces/ants/tests/test_auto_Registration.py index 4bd253c3d0..1e3fd9dfd7 100644 --- a/nipype/interfaces/ants/tests/test_auto_Registration.py +++ b/nipype/interfaces/ants/tests/test_auto_Registration.py @@ -30,6 +30,7 @@ def test_Registration_inputs(): fixed_image_mask=dict( argstr='%s', max_ver='2.1.0', + usedefault=True, xor=['fixed_image_masks'], ), fixed_image_masks=dict( @@ -72,6 +73,7 @@ def test_Registration_inputs(): moving_image_mask=dict( max_ver='2.1.0', requires=['fixed_image_mask'], + usedefault=True, xor=['moving_image_masks'], ), moving_image_masks=dict( @@ -98,7 +100,10 @@ def test_Registration_inputs(): requires=['metric_weight'], usedefault=True, ), - restore_state=dict(argstr='--restore-state %s', ), + restore_state=dict( + argstr='--restore-state %s', + usedefault=True, + ), restrict_deformation=dict(), sampling_percentage=dict(requires=['sampling_strategy'], ), sampling_percentage_item_trait=dict(), @@ -106,7 +111,10 @@ def test_Registration_inputs(): sampling_strategy=dict(requires=['metric_weight'], ), sampling_strategy_item_trait=dict(), sampling_strategy_stage_trait=dict(), - save_state=dict(argstr='--save-state %s', ), + save_state=dict( + argstr='--save-state %s', + usedefault=True, + ), shrink_factors=dict(mandatory=True, ), sigma_units=dict(requires=['smoothing_sigmas'], ), smoothing_sigmas=dict(mandatory=True, ), @@ -141,17 +149,17 @@ def test_Registration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Registration_outputs(): output_map = dict( - composite_transform=dict(), + composite_transform=dict(usedefault=True, ), elapsed_time=dict(), forward_invert_flags=dict(), forward_transforms=dict(), - inverse_composite_transform=dict(), - inverse_warped_image=dict(), + inverse_composite_transform=dict(usedefault=True, ), + inverse_warped_image=dict(usedefault=True, ), metric_value=dict(), reverse_invert_flags=dict(), reverse_transforms=dict(), - save_state=dict(), - warped_image=dict(), + save_state=dict(usedefault=True, ), + warped_image=dict(usedefault=True, ), ) outputs = Registration.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_RegistrationSynQuick.py b/nipype/interfaces/ants/tests/test_auto_RegistrationSynQuick.py index 8bc79392e1..c8a9ab90bc 100644 --- a/nipype/interfaces/ants/tests/test_auto_RegistrationSynQuick.py +++ b/nipype/interfaces/ants/tests/test_auto_RegistrationSynQuick.py @@ -55,11 +55,11 @@ def test_RegistrationSynQuick_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RegistrationSynQuick_outputs(): output_map = dict( - forward_warp_field=dict(), - inverse_warp_field=dict(), - inverse_warped_image=dict(), - out_matrix=dict(), - warped_image=dict(), + forward_warp_field=dict(usedefault=True, ), + inverse_warp_field=dict(usedefault=True, ), + inverse_warped_image=dict(usedefault=True, ), + out_matrix=dict(usedefault=True, ), + warped_image=dict(usedefault=True, ), ) outputs = RegistrationSynQuick.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py index 42020f6db9..52985afe86 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py @@ -19,6 +19,7 @@ def test_WarpImageMultiTransform_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), invert_affine=dict(), num_threads=dict( @@ -35,10 +36,12 @@ def test_WarpImageMultiTransform_inputs(): genfile=True, hash_files=False, position=3, + usedefault=True, xor=['out_postfix'], ), reference_image=dict( argstr='-R %s', + usedefault=True, xor=['tightest_box'], ), reslice_by_header=dict(argstr='--reslice-by-header', ), @@ -60,7 +63,7 @@ def test_WarpImageMultiTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpImageMultiTransform_outputs(): - output_map = dict(output_image=dict(), ) + output_map = dict(output_image=dict(usedefault=True, ), ) outputs = WarpImageMultiTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py index de3131f056..9ccde564d4 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py @@ -19,6 +19,7 @@ def test_WarpTimeSeriesImageMultiTransform_inputs(): argstr='%s', copyfile=True, mandatory=True, + usedefault=True, ), invert_affine=dict(), num_threads=dict( @@ -31,6 +32,7 @@ def test_WarpTimeSeriesImageMultiTransform_inputs(): ), reference_image=dict( argstr='-R %s', + usedefault=True, xor=['tightest_box'], ), reslice_by_header=dict(argstr='--reslice-by-header', ), @@ -52,7 +54,7 @@ def test_WarpTimeSeriesImageMultiTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpTimeSeriesImageMultiTransform_outputs(): - output_map = dict(output_image=dict(), ) + output_map = dict(output_image=dict(usedefault=True, ), ) outputs = WarpTimeSeriesImageMultiTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py index fe21858500..f681af7d8b 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py +++ b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py @@ -21,6 +21,7 @@ def test_antsIntroduction_inputs(): argstr='-i %s', copyfile=False, mandatory=True, + usedefault=True, ), inverse_warp_template_labels=dict(argstr='-l', ), max_iterations=dict( @@ -40,6 +41,7 @@ def test_antsIntroduction_inputs(): argstr='-r %s', copyfile=True, mandatory=True, + usedefault=True, ), similarity_metric=dict(argstr='-s %s', ), transformation_model=dict( @@ -54,11 +56,11 @@ def test_antsIntroduction_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_antsIntroduction_outputs(): output_map = dict( - affine_transformation=dict(), - input_file=dict(), - inverse_warp_field=dict(), - output_file=dict(), - warp_field=dict(), + affine_transformation=dict(usedefault=True, ), + input_file=dict(usedefault=True, ), + inverse_warp_field=dict(usedefault=True, ), + output_file=dict(usedefault=True, ), + warp_field=dict(usedefault=True, ), ) outputs = antsIntroduction.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py index 8513003c29..bfd7f6bdca 100644 --- a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py +++ b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py @@ -61,7 +61,7 @@ def test_buildtemplateparallel_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_buildtemplateparallel_outputs(): output_map = dict( - final_template_file=dict(), + final_template_file=dict(usedefault=True, ), subject_outfiles=dict(), template_files=dict(), ) diff --git a/nipype/interfaces/brainsuite/tests/test_auto_BDP.py b/nipype/interfaces/brainsuite/tests/test_auto_BDP.py index ff705edfeb..1db0577519 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_BDP.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_BDP.py @@ -16,6 +16,7 @@ def test_BDP_inputs(): argstr='--bmat %s', mandatory=True, position=-1, + usedefault=True, xor=['BVecBValPair'], ), bValRatioThreshold=dict(argstr='--bval-ratio-threshold %f', ), @@ -23,15 +24,28 @@ def test_BDP_inputs(): argstr='%s', mandatory=True, position=0, + usedefault=True, xor=['noStructuralRegistration'], ), - customDiffusionLabel=dict(argstr='--custom-diffusion-label %s', ), - customLabelXML=dict(argstr='--custom-label-xml %s', ), - customT1Label=dict(argstr='--custom-t1-label %s', ), + customDiffusionLabel=dict( + argstr='--custom-diffusion-label %s', + usedefault=True, + ), + customLabelXML=dict( + argstr='--custom-label-xml %s', + usedefault=True, + ), + customT1Label=dict( + argstr='--custom-t1-label %s', + usedefault=True, + ), dataSinkDelay=dict(argstr='%s', ), dcorrRegMeasure=dict(argstr='--dcorr-reg-method %s', ), dcorrWeight=dict(argstr='--dcorr-regularization-wt %f', ), - dwiMask=dict(argstr='--dwi-mask %s', ), + dwiMask=dict( + argstr='--dwi-mask %s', + usedefault=True, + ), echoSpacing=dict(argstr='--echo-spacing=%f', ), environ=dict( nohash=True, @@ -44,13 +58,17 @@ def test_BDP_inputs(): fieldmapCorrection=dict( argstr='--fieldmap-correction %s', requires=['echoSpacing'], + usedefault=True, ), fieldmapCorrectionMethod=dict( argstr='--fieldmap-correction-method %s', xor=['skipIntensityCorr'], ), fieldmapSmooth=dict(argstr='--fieldmap-smooth3=%f', ), - flagConfigFile=dict(argstr='--flag-conf-file %s', ), + flagConfigFile=dict( + argstr='--flag-conf-file %s', + usedefault=True, + ), forcePartialROIStats=dict(argstr='--force-partial-roi-stats', ), generateStats=dict(argstr='--generate-stats', ), ignoreFieldmapFOV=dict(argstr='--ignore-fieldmap-fov', ), @@ -59,6 +77,7 @@ def test_BDP_inputs(): argstr='--nii %s', mandatory=True, position=-2, + usedefault=True, ), lowMemory=dict(argstr='--low-memory', ), noStructuralRegistration=dict( @@ -81,16 +100,29 @@ def test_BDP_inputs(): xor=['fieldmapCorrectionMethod'], ), skipNonuniformityCorr=dict(argstr='--no-nonuniformity-correction', ), - t1Mask=dict(argstr='--t1-mask %s', ), + t1Mask=dict( + argstr='--t1-mask %s', + usedefault=True, + ), threads=dict(argstr='--threads=%d', ), transformDataOnly=dict(argstr='--transform-data-only', ), transformDiffusionSurface=dict( - argstr='--transform-diffusion-surface %s', ), + argstr='--transform-diffusion-surface %s', + usedefault=True, + ), transformDiffusionVolume=dict( - argstr='--transform-diffusion-volume %s', ), + argstr='--transform-diffusion-volume %s', + usedefault=True, + ), transformInterpolation=dict(argstr='--transform-interpolation %s', ), - transformT1Surface=dict(argstr='--transform-t1-surface %s', ), - transformT1Volume=dict(argstr='--transform-t1-volume %s', ), + transformT1Surface=dict( + argstr='--transform-t1-surface %s', + usedefault=True, + ), + transformT1Volume=dict( + argstr='--transform-t1-volume %s', + usedefault=True, + ), ) inputs = BDP.input_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py b/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py index 01200e50fc..e9e56894e1 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py @@ -14,7 +14,10 @@ def test_Bfc_inputs(): convergenceThreshold=dict(argstr='--eps %f', ), correctWholeVolume=dict(argstr='--extrapolate', ), correctedImagesOutputPrefix=dict(argstr='--prefix %s', ), - correctionScheduleFile=dict(argstr='--schedule %s', ), + correctionScheduleFile=dict( + argstr='--schedule %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -24,10 +27,12 @@ def test_Bfc_inputs(): inputMRIFile=dict( argstr='-i %s', mandatory=True, + usedefault=True, ), inputMaskFile=dict( argstr='-m %s', hash_files=False, + usedefault=True, ), intermediate_file_type=dict(argstr='%s', ), iterativeMode=dict(argstr='--iterate', ), @@ -42,15 +47,18 @@ def test_Bfc_inputs(): outputBiasField=dict( argstr='--bias %s', hash_files=False, + usedefault=True, ), outputMRIVolume=dict( argstr='-o %s', genfile=True, hash_files=False, + usedefault=True, ), outputMaskedBiasField=dict( argstr='--maskedbias %s', hash_files=False, + usedefault=True, ), splineLambda=dict(argstr='-w %f', ), timer=dict(argstr='--timer', ), @@ -63,10 +71,10 @@ def test_Bfc_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Bfc_outputs(): output_map = dict( - correctionScheduleFile=dict(), - outputBiasField=dict(), - outputMRIVolume=dict(), - outputMaskedBiasField=dict(), + correctionScheduleFile=dict(usedefault=True, ), + outputBiasField=dict(usedefault=True, ), + outputMRIVolume=dict(usedefault=True, ), + outputMaskedBiasField=dict(usedefault=True, ), ) outputs = Bfc.output_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Bse.py b/nipype/interfaces/brainsuite/tests/test_auto_Bse.py index bbd154bc24..2ff6264ed5 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Bse.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Bse.py @@ -29,33 +29,40 @@ def test_Bse_inputs(): inputMRIFile=dict( argstr='-i %s', mandatory=True, + usedefault=True, ), noRotate=dict(argstr='--norotate', ), outputCortexFile=dict( argstr='--cortex %s', hash_files=False, + usedefault=True, ), outputDetailedBrainMask=dict( argstr='--hires %s', hash_files=False, + usedefault=True, ), outputDiffusionFilter=dict( argstr='--adf %s', hash_files=False, + usedefault=True, ), outputEdgeMap=dict( argstr='--edge %s', hash_files=False, + usedefault=True, ), outputMRIVolume=dict( argstr='-o %s', genfile=True, hash_files=False, + usedefault=True, ), outputMaskFile=dict( argstr='--mask %s', genfile=True, hash_files=False, + usedefault=True, ), radius=dict( argstr='-r %f', @@ -78,12 +85,12 @@ def test_Bse_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Bse_outputs(): output_map = dict( - outputCortexFile=dict(), - outputDetailedBrainMask=dict(), - outputDiffusionFilter=dict(), - outputEdgeMap=dict(), - outputMRIVolume=dict(), - outputMaskFile=dict(), + outputCortexFile=dict(usedefault=True, ), + outputDetailedBrainMask=dict(usedefault=True, ), + outputDiffusionFilter=dict(usedefault=True, ), + outputEdgeMap=dict(usedefault=True, ), + outputMRIVolume=dict(usedefault=True, ), + outputMaskFile=dict(usedefault=True, ), ) outputs = Bse.output_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py b/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py index 808e4347c3..0734b7f831 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py @@ -17,33 +17,43 @@ def test_Cerebro_inputs(): inputAtlasLabelFile=dict( argstr='--atlaslabels %s', mandatory=True, + usedefault=True, ), inputAtlasMRIFile=dict( argstr='--atlas %s', mandatory=True, + usedefault=True, + ), + inputBrainMaskFile=dict( + argstr='-m %s', + usedefault=True, ), - inputBrainMaskFile=dict(argstr='-m %s', ), inputMRIFile=dict( argstr='-i %s', mandatory=True, + usedefault=True, ), keepTempFiles=dict(argstr='--keep', ), linearConvergence=dict(argstr='--linconv %f', ), outputAffineTransformFile=dict( argstr='--air %s', genfile=True, + usedefault=True, ), outputCerebrumMaskFile=dict( argstr='-o %s', genfile=True, + usedefault=True, ), outputLabelVolumeFile=dict( argstr='-l %s', genfile=True, + usedefault=True, ), outputWarpTransformFile=dict( argstr='--warp %s', genfile=True, + usedefault=True, ), tempDirectory=dict(argstr='--tempdir %s', ), tempDirectoryBase=dict(argstr='--tempdirbase %s', ), @@ -59,10 +69,10 @@ def test_Cerebro_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Cerebro_outputs(): output_map = dict( - outputAffineTransformFile=dict(), - outputCerebrumMaskFile=dict(), - outputLabelVolumeFile=dict(), - outputWarpTransformFile=dict(), + outputAffineTransformFile=dict(usedefault=True, ), + outputCerebrumMaskFile=dict(usedefault=True, ), + outputLabelVolumeFile=dict(usedefault=True, ), + outputWarpTransformFile=dict(usedefault=True, ), ) outputs = Cerebro.output_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py b/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py index 536cb158f2..61e7ecfb76 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py @@ -22,14 +22,17 @@ def test_Cortex_inputs(): inputHemisphereLabelFile=dict( argstr='-h %s', mandatory=True, + usedefault=True, ), inputTissueFractionFile=dict( argstr='-f %s', mandatory=True, + usedefault=True, ), outputCerebrumMask=dict( argstr='-o %s', genfile=True, + usedefault=True, ), timer=dict(argstr='--timer', ), tissueFractionThreshold=dict( @@ -44,7 +47,7 @@ def test_Cortex_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Cortex_outputs(): - output_map = dict(outputCerebrumMask=dict(), ) + output_map = dict(outputCerebrumMask=dict(usedefault=True, ), ) outputs = Cortex.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py b/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py index ba430fb1fd..297f72b857 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py @@ -13,11 +13,13 @@ def test_Dewisp_inputs(): inputMaskFile=dict( argstr='-i %s', mandatory=True, + usedefault=True, ), maximumIterations=dict(argstr='-n %d', ), outputMaskFile=dict( argstr='-o %s', genfile=True, + usedefault=True, ), sizeThreshold=dict(argstr='-t %d', ), timer=dict(argstr='--timer', ), @@ -29,7 +31,7 @@ def test_Dewisp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Dewisp_outputs(): - output_map = dict(outputMaskFile=dict(), ) + output_map = dict(outputMaskFile=dict(usedefault=True, ), ) outputs = Dewisp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py b/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py index c69232fd01..c4f3fbf8cf 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py @@ -14,10 +14,14 @@ def test_Dfs_inputs(): nohash=True, usedefault=True, ), - inputShadingVolume=dict(argstr='-c %s', ), + inputShadingVolume=dict( + argstr='-c %s', + usedefault=True, + ), inputVolumeFile=dict( argstr='-i %s', mandatory=True, + usedefault=True, ), noNormalsFlag=dict(argstr='--nonormals', ), nonZeroTessellation=dict( @@ -27,6 +31,7 @@ def test_Dfs_inputs(): outputSurfaceFile=dict( argstr='-o %s', genfile=True, + usedefault=True, ), postSmoothFlag=dict(argstr='--postsmooth', ), scalingPercentile=dict(argstr='-f %f', ), @@ -55,7 +60,7 @@ def test_Dfs_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Dfs_outputs(): - output_map = dict(outputSurfaceFile=dict(), ) + output_map = dict(outputSurfaceFile=dict(usedefault=True, ), ) outputs = Dfs.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py b/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py index 9e3db80dd9..40984870f1 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py @@ -13,28 +13,37 @@ def test_Hemisplit_inputs(): inputHemisphereLabelFile=dict( argstr='-l %s', mandatory=True, + usedefault=True, ), inputSurfaceFile=dict( argstr='-i %s', mandatory=True, + usedefault=True, ), outputLeftHemisphere=dict( argstr='--left %s', genfile=True, + usedefault=True, ), outputLeftPialHemisphere=dict( argstr='-pl %s', genfile=True, + usedefault=True, ), outputRightHemisphere=dict( argstr='--right %s', genfile=True, + usedefault=True, ), outputRightPialHemisphere=dict( argstr='-pr %s', genfile=True, + usedefault=True, + ), + pialSurfaceFile=dict( + argstr='-p %s', + usedefault=True, ), - pialSurfaceFile=dict(argstr='-p %s', ), timer=dict(argstr='--timer', ), verbosity=dict(argstr='-v %d', ), ) @@ -45,10 +54,10 @@ def test_Hemisplit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Hemisplit_outputs(): output_map = dict( - outputLeftHemisphere=dict(), - outputLeftPialHemisphere=dict(), - outputRightHemisphere=dict(), - outputRightPialHemisphere=dict(), + outputLeftHemisphere=dict(usedefault=True, ), + outputLeftPialHemisphere=dict(usedefault=True, ), + outputRightHemisphere=dict(usedefault=True, ), + outputRightPialHemisphere=dict(usedefault=True, ), ) outputs = Hemisplit.output_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py b/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py index afc621a56e..da7e3a2f12 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py @@ -14,14 +14,17 @@ def test_Pialmesh_inputs(): inputMaskFile=dict( argstr='-m %s', mandatory=True, + usedefault=True, ), inputSurfaceFile=dict( argstr='-i %s', mandatory=True, + usedefault=True, ), inputTissueFractionFile=dict( argstr='-f %s', mandatory=True, + usedefault=True, ), laplacianSmoothing=dict( argstr='--smooth %f', @@ -46,6 +49,7 @@ def test_Pialmesh_inputs(): outputSurfaceFile=dict( argstr='-o %s', genfile=True, + usedefault=True, ), recomputeNormals=dict(argstr='--norm', ), searchRadius=dict( @@ -70,7 +74,7 @@ def test_Pialmesh_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Pialmesh_outputs(): - output_map = dict(outputSurfaceFile=dict(), ) + output_map = dict(outputSurfaceFile=dict(usedefault=True, ), ) outputs = Pialmesh.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py b/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py index d425d4ddac..ca3156ac3b 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py @@ -13,15 +13,21 @@ def test_Pvc_inputs(): inputMRIFile=dict( argstr='-i %s', mandatory=True, + usedefault=True, + ), + inputMaskFile=dict( + argstr='-m %s', + usedefault=True, ), - inputMaskFile=dict(argstr='-m %s', ), outputLabelFile=dict( argstr='-o %s', genfile=True, + usedefault=True, ), outputTissueFractionFile=dict( argstr='-f %s', genfile=True, + usedefault=True, ), spatialPrior=dict(argstr='-l %f', ), threeClassFlag=dict(argstr='-3', ), @@ -35,8 +41,8 @@ def test_Pvc_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Pvc_outputs(): output_map = dict( - outputLabelFile=dict(), - outputTissueFractionFile=dict(), + outputLabelFile=dict(usedefault=True, ), + outputTissueFractionFile=dict(usedefault=True, ), ) outputs = Pvc.output_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py b/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py index eb672d12b7..9937f51878 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py @@ -21,11 +21,13 @@ def test_Scrubmask_inputs(): inputMaskFile=dict( argstr='-i %s', mandatory=True, + usedefault=True, ), numberIterations=dict(argstr='-n %d', ), outputMaskFile=dict( argstr='-o %s', genfile=True, + usedefault=True, ), timer=dict(argstr='--timer', ), verbosity=dict(argstr='-v %d', ), @@ -36,7 +38,7 @@ def test_Scrubmask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Scrubmask_outputs(): - output_map = dict(outputMaskFile=dict(), ) + output_map = dict(outputMaskFile=dict(usedefault=True, ), ) outputs = Scrubmask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py b/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py index 2191f7b133..e85ac9fb77 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py @@ -15,15 +15,18 @@ def test_Skullfinder_inputs(): inputMRIFile=dict( argstr='-i %s', mandatory=True, + usedefault=True, ), inputMaskFile=dict( argstr='-m %s', mandatory=True, + usedefault=True, ), lowerThreshold=dict(argstr='-l %d', ), outputLabelFile=dict( argstr='-o %s', genfile=True, + usedefault=True, ), performFinalOpening=dict(argstr='--finalOpening', ), scalpLabelValue=dict(argstr='--scalplabel %d', ), @@ -39,7 +42,7 @@ def test_Skullfinder_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Skullfinder_outputs(): - output_map = dict(outputLabelFile=dict(), ) + output_map = dict(outputLabelFile=dict(usedefault=True, ), ) outputs = Skullfinder.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Tca.py b/nipype/interfaces/brainsuite/tests/test_auto_Tca.py index ec2886b42f..3e237a7472 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Tca.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Tca.py @@ -17,6 +17,7 @@ def test_Tca_inputs(): inputMaskFile=dict( argstr='-i %s', mandatory=True, + usedefault=True, ), maxCorrectionSize=dict(argstr='-n %d', ), minCorrectionSize=dict( @@ -26,6 +27,7 @@ def test_Tca_inputs(): outputMaskFile=dict( argstr='-o %s', genfile=True, + usedefault=True, ), timer=dict(argstr='--timer', ), verbosity=dict(argstr='-v %d', ), @@ -36,7 +38,7 @@ def test_Tca_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Tca_outputs(): - output_map = dict(outputMaskFile=dict(), ) + output_map = dict(outputMaskFile=dict(usedefault=True, ), ) outputs = Tca.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py index 5d796126cc..d797170db6 100644 --- a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py +++ b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py @@ -31,10 +31,12 @@ def test_AnalyzeHeader_inputs(): argstr='< %s', mandatory=True, position=1, + usedefault=True, ), initfromheader=dict( argstr='-initfromheader %s', position=3, + usedefault=True, ), intelbyteorder=dict(argstr='-intelbyteorder', ), networkbyteorder=dict(argstr='-networkbyteorder', ), @@ -58,22 +60,27 @@ def test_AnalyzeHeader_inputs(): printbigendian=dict( argstr='-printbigendian %s', position=3, + usedefault=True, ), printimagedims=dict( argstr='-printimagedims %s', position=3, + usedefault=True, ), printintelbyteorder=dict( argstr='-printintelbyteorder %s', position=3, + usedefault=True, ), printprogargs=dict( argstr='-printprogargs %s', position=3, + usedefault=True, ), readheader=dict( argstr='-readheader %s', position=3, + usedefault=True, ), scaleinter=dict( argstr='-scaleinter %d', @@ -86,6 +93,7 @@ def test_AnalyzeHeader_inputs(): scheme_file=dict( argstr='%s', position=2, + usedefault=True, ), voxel_dims=dict( argstr='-voxeldims %s', @@ -98,7 +106,7 @@ def test_AnalyzeHeader_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AnalyzeHeader_outputs(): - output_map = dict(header=dict(), ) + output_map = dict(header=dict(usedefault=True, ), ) outputs = AnalyzeHeader.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py index caee9e68cf..3ea63e2e21 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py @@ -14,6 +14,7 @@ def test_ComputeEigensystem_inputs(): argstr='< %s', mandatory=True, position=1, + usedefault=True, ), inputdatatype=dict( argstr='-inputdatatype %s', @@ -37,7 +38,7 @@ def test_ComputeEigensystem_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeEigensystem_outputs(): - output_map = dict(eigen=dict(), ) + output_map = dict(eigen=dict(usedefault=True, ), ) outputs = ComputeEigensystem.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py index 49cfdfd96a..bc07cde8df 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py @@ -14,6 +14,7 @@ def test_ComputeFractionalAnisotropy_inputs(): argstr='< %s', mandatory=True, position=1, + usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict(argstr='-inputmodel %s', ), @@ -26,6 +27,7 @@ def test_ComputeFractionalAnisotropy_inputs(): scheme_file=dict( argstr='%s', position=2, + usedefault=True, ), ) inputs = ComputeFractionalAnisotropy.input_spec() @@ -34,7 +36,7 @@ def test_ComputeFractionalAnisotropy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeFractionalAnisotropy_outputs(): - output_map = dict(fa=dict(), ) + output_map = dict(fa=dict(usedefault=True, ), ) outputs = ComputeFractionalAnisotropy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py index 212477d149..6ac6cba916 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py @@ -14,6 +14,7 @@ def test_ComputeMeanDiffusivity_inputs(): argstr='< %s', mandatory=True, position=1, + usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict(argstr='-inputmodel %s', ), @@ -21,11 +22,13 @@ def test_ComputeMeanDiffusivity_inputs(): argstr='> %s', genfile=True, position=-1, + usedefault=True, ), outputdatatype=dict(argstr='-outputdatatype %s', ), scheme_file=dict( argstr='%s', position=2, + usedefault=True, ), ) inputs = ComputeMeanDiffusivity.input_spec() @@ -34,7 +37,7 @@ def test_ComputeMeanDiffusivity_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeMeanDiffusivity_outputs(): - output_map = dict(md=dict(), ) + output_map = dict(md=dict(usedefault=True, ), ) outputs = ComputeMeanDiffusivity.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py index 1112c7c743..adb3abeb02 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py @@ -14,6 +14,7 @@ def test_ComputeTensorTrace_inputs(): argstr='< %s', mandatory=True, position=1, + usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict(argstr='-inputmodel %s', ), @@ -26,6 +27,7 @@ def test_ComputeTensorTrace_inputs(): scheme_file=dict( argstr='%s', position=2, + usedefault=True, ), ) inputs = ComputeTensorTrace.input_spec() @@ -34,7 +36,7 @@ def test_ComputeTensorTrace_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeTensorTrace_outputs(): - output_map = dict(trace=dict(), ) + output_map = dict(trace=dict(usedefault=True, ), ) outputs = ComputeTensorTrace.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_Conmat.py b/nipype/interfaces/camino/tests/test_auto_Conmat.py index 06a76fdf2b..e84de0c1b2 100644 --- a/nipype/interfaces/camino/tests/test_auto_Conmat.py +++ b/nipype/interfaces/camino/tests/test_auto_Conmat.py @@ -13,20 +13,27 @@ def test_Conmat_inputs(): in_file=dict( argstr='-inputfile %s', mandatory=True, + usedefault=True, ), output_root=dict( argstr='-outputroot %s', genfile=True, + usedefault=True, ), scalar_file=dict( argstr='-scalarfile %s', requires=['tract_stat'], + usedefault=True, ), target_file=dict( argstr='-targetfile %s', mandatory=True, + usedefault=True, + ), + targetname_file=dict( + argstr='-targetnamefile %s', + usedefault=True, ), - targetname_file=dict(argstr='-targetnamefile %s', ), tract_prop=dict( argstr='-tractstat %s', units='NA', @@ -46,8 +53,8 @@ def test_Conmat_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Conmat_outputs(): output_map = dict( - conmat_sc=dict(), - conmat_ts=dict(), + conmat_sc=dict(usedefault=True, ), + conmat_ts=dict(usedefault=True, ), ) outputs = Conmat.output_spec() diff --git a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py index b20dcbf3bf..70569cafb6 100644 --- a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py +++ b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py @@ -14,16 +14,19 @@ def test_DT2NIfTI_inputs(): argstr='-header %s', mandatory=True, position=3, + usedefault=True, ), in_file=dict( argstr='-inputfile %s', mandatory=True, position=1, + usedefault=True, ), output_root=dict( argstr='-outputroot %s', genfile=True, position=2, + usedefault=True, ), ) inputs = DT2NIfTI.input_spec() @@ -33,9 +36,9 @@ def test_DT2NIfTI_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DT2NIfTI_outputs(): output_map = dict( - dt=dict(), - exitcode=dict(), - lns0=dict(), + dt=dict(usedefault=True, ), + exitcode=dict(usedefault=True, ), + lns0=dict(usedefault=True, ), ) outputs = DT2NIfTI.output_spec() diff --git a/nipype/interfaces/camino/tests/test_auto_DTIFit.py b/nipype/interfaces/camino/tests/test_auto_DTIFit.py index a23da89552..5124db3f1f 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/camino/tests/test_auto_DTIFit.py @@ -6,7 +6,10 @@ def test_DTIFit_inputs(): input_map = dict( args=dict(argstr='%s', ), - bgmask=dict(argstr='-bgmask %s', ), + bgmask=dict( + argstr='-bgmask %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -15,6 +18,7 @@ def test_DTIFit_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), non_linear=dict( argstr='-nonlinear', @@ -29,6 +33,7 @@ def test_DTIFit_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), ) inputs = DTIFit.input_spec() @@ -37,7 +42,7 @@ def test_DTIFit_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DTIFit_outputs(): - output_map = dict(tensor_fitted=dict(), ) + output_map = dict(tensor_fitted=dict(usedefault=True, ), ) outputs = DTIFit.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py index 95e8e0bea5..618d40c99d 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py @@ -39,6 +39,7 @@ def test_DTLUTGen_inputs(): argstr='-schemefile %s', mandatory=True, position=2, + usedefault=True, ), snr=dict( argstr='-snr %f', @@ -60,7 +61,7 @@ def test_DTLUTGen_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DTLUTGen_outputs(): - output_map = dict(dtLUT=dict(), ) + output_map = dict(dtLUT=dict(usedefault=True, ), ) outputs = DTLUTGen.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_DTMetric.py b/nipype/interfaces/camino/tests/test_auto_DTMetric.py index 12256a50d8..8fd0852d50 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTMetric.py +++ b/nipype/interfaces/camino/tests/test_auto_DTMetric.py @@ -6,10 +6,14 @@ def test_DTMetric_inputs(): input_map = dict( args=dict(argstr='%s', ), - data_header=dict(argstr='-header %s', ), + data_header=dict( + argstr='-header %s', + usedefault=True, + ), eigen_data=dict( argstr='-inputfile %s', mandatory=True, + usedefault=True, ), environ=dict( nohash=True, @@ -30,6 +34,7 @@ def test_DTMetric_inputs(): outputfile=dict( argstr='-outputfile %s', genfile=True, + usedefault=True, ), ) inputs = DTMetric.input_spec() @@ -38,7 +43,7 @@ def test_DTMetric_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DTMetric_outputs(): - output_map = dict(metric_stats=dict(), ) + output_map = dict(metric_stats=dict(usedefault=True, ), ) outputs = DTMetric.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py index a2ebfbf0a6..583738ac14 100644 --- a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py +++ b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py @@ -14,11 +14,13 @@ def test_FSL2Scheme_inputs(): argstr='-bvalfile %s', mandatory=True, position=2, + usedefault=True, ), bvec_file=dict( argstr='-bvecfile %s', mandatory=True, position=1, + usedefault=True, ), diffusiontime=dict( argstr='-diffusiontime %f', @@ -49,7 +51,7 @@ def test_FSL2Scheme_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FSL2Scheme_outputs(): - output_map = dict(scheme=dict(), ) + output_map = dict(scheme=dict(usedefault=True, ), ) outputs = FSL2Scheme.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py index adae10f0bb..d0591b3004 100644 --- a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py +++ b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py @@ -14,6 +14,7 @@ def test_Image2Voxel_inputs(): argstr='-4dimage %s', mandatory=True, position=1, + usedefault=True, ), out_file=dict( argstr='> %s', @@ -32,7 +33,7 @@ def test_Image2Voxel_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Image2Voxel_outputs(): - output_map = dict(voxel_order=dict(), ) + output_map = dict(voxel_order=dict(usedefault=True, ), ) outputs = Image2Voxel.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ImageStats.py b/nipype/interfaces/camino/tests/test_auto_ImageStats.py index 3813051025..30f7c13573 100644 --- a/nipype/interfaces/camino/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/camino/tests/test_auto_ImageStats.py @@ -22,6 +22,7 @@ def test_ImageStats_inputs(): output_root=dict( argstr='-outputroot %s', mandatory=True, + usedefault=True, ), stat=dict( argstr='-stat %s', @@ -35,7 +36,7 @@ def test_ImageStats_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ImageStats_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ImageStats.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_LinRecon.py b/nipype/interfaces/camino/tests/test_auto_LinRecon.py index 8998f42602..3e02e6641a 100644 --- a/nipype/interfaces/camino/tests/test_auto_LinRecon.py +++ b/nipype/interfaces/camino/tests/test_auto_LinRecon.py @@ -6,7 +6,10 @@ def test_LinRecon_inputs(): input_map = dict( args=dict(argstr='%s', ), - bgmask=dict(argstr='-bgmask %s', ), + bgmask=dict( + argstr='-bgmask %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -15,6 +18,7 @@ def test_LinRecon_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), log=dict(argstr='-log', ), normalize=dict(argstr='-normalize', ), @@ -27,11 +31,13 @@ def test_LinRecon_inputs(): argstr='%s', mandatory=True, position=3, + usedefault=True, ), scheme_file=dict( argstr='%s', mandatory=True, position=2, + usedefault=True, ), ) inputs = LinRecon.input_spec() @@ -40,7 +46,7 @@ def test_LinRecon_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LinRecon_outputs(): - output_map = dict(recon_data=dict(), ) + output_map = dict(recon_data=dict(usedefault=True, ), ) outputs = LinRecon.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_MESD.py b/nipype/interfaces/camino/tests/test_auto_MESD.py index 73089a3395..8b99faf461 100644 --- a/nipype/interfaces/camino/tests/test_auto_MESD.py +++ b/nipype/interfaces/camino/tests/test_auto_MESD.py @@ -6,7 +6,10 @@ def test_MESD_inputs(): input_map = dict( args=dict(argstr='%s', ), - bgmask=dict(argstr='-bgmask %s', ), + bgmask=dict( + argstr='-bgmask %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -19,6 +22,7 @@ def test_MESD_inputs(): argstr='-inputfile %s', mandatory=True, position=1, + usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inverter=dict( @@ -44,6 +48,7 @@ def test_MESD_inputs(): scheme_file=dict( argstr='-schemefile %s', mandatory=True, + usedefault=True, ), ) inputs = MESD.input_spec() @@ -52,7 +57,7 @@ def test_MESD_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MESD_outputs(): - output_map = dict(mesd_data=dict(), ) + output_map = dict(mesd_data=dict(usedefault=True, ), ) outputs = MESD.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ModelFit.py b/nipype/interfaces/camino/tests/test_auto_ModelFit.py index 04d22bbe59..0f7b332e25 100644 --- a/nipype/interfaces/camino/tests/test_auto_ModelFit.py +++ b/nipype/interfaces/camino/tests/test_auto_ModelFit.py @@ -6,7 +6,10 @@ def test_ModelFit_inputs(): input_map = dict( args=dict(argstr='%s', ), - bgmask=dict(argstr='-bgmask %s', ), + bgmask=dict( + argstr='-bgmask %s', + usedefault=True, + ), bgthresh=dict(argstr='-bgthresh %G', ), cfthresh=dict(argstr='-csfthresh %G', ), environ=dict( @@ -18,24 +21,38 @@ def test_ModelFit_inputs(): in_file=dict( argstr='-inputfile %s', mandatory=True, + usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), model=dict( argstr='-model %s', mandatory=True, ), - noisemap=dict(argstr='-noisemap %s', ), + noisemap=dict( + argstr='-noisemap %s', + usedefault=True, + ), out_file=dict( argstr='> %s', genfile=True, position=-1, ), - outlier=dict(argstr='-outliermap %s', ), - outputfile=dict(argstr='-outputfile %s', ), - residualmap=dict(argstr='-residualmap %s', ), + outlier=dict( + argstr='-outliermap %s', + usedefault=True, + ), + outputfile=dict( + argstr='-outputfile %s', + usedefault=True, + ), + residualmap=dict( + argstr='-residualmap %s', + usedefault=True, + ), scheme_file=dict( argstr='-schemefile %s', mandatory=True, + usedefault=True, ), sigma=dict(argstr='-sigma %G', ), tau=dict(argstr='-tau %G', ), @@ -46,7 +63,7 @@ def test_ModelFit_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ModelFit_outputs(): - output_map = dict(fitted_data=dict(), ) + output_map = dict(fitted_data=dict(usedefault=True, ), ) outputs = ModelFit.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py index 9a4867a73c..d31ab64eb0 100644 --- a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py +++ b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py @@ -6,7 +6,10 @@ def test_NIfTIDT2Camino_inputs(): input_map = dict( args=dict(argstr='%s', ), - bgmask=dict(argstr='-bgmask %s', ), + bgmask=dict( + argstr='-bgmask %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -15,14 +18,21 @@ def test_NIfTIDT2Camino_inputs(): argstr='-inputfile %s', mandatory=True, position=1, + usedefault=True, + ), + lns0_file=dict( + argstr='-lns0 %s', + usedefault=True, ), - lns0_file=dict(argstr='-lns0 %s', ), out_file=dict( argstr='> %s', genfile=True, position=-1, ), - s0_file=dict(argstr='-s0 %s', ), + s0_file=dict( + argstr='-s0 %s', + usedefault=True, + ), scaleinter=dict(argstr='-scaleinter %s', ), scaleslope=dict(argstr='-scaleslope %s', ), uppertriangular=dict(argstr='-uppertriangular %s', ), @@ -33,7 +43,7 @@ def test_NIfTIDT2Camino_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NIfTIDT2Camino_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = NIfTIDT2Camino.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py index f2b59666a2..9c0fec3085 100644 --- a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py +++ b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py @@ -15,6 +15,7 @@ def test_PicoPDFs_inputs(): argstr='< %s', mandatory=True, position=1, + usedefault=True, ), inputmodel=dict( argstr='-inputmodel %s', @@ -50,7 +51,7 @@ def test_PicoPDFs_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PicoPDFs_outputs(): - output_map = dict(pdfs=dict(), ) + output_map = dict(pdfs=dict(usedefault=True, ), ) outputs = PicoPDFs.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py index 8838bb72cf..7ad506e894 100644 --- a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py @@ -16,17 +16,24 @@ def test_ProcStreamlines_inputs(): units='NA', ), discardloops=dict(argstr='-discardloops', ), - endpointfile=dict(argstr='-endpointfile %s', ), + endpointfile=dict( + argstr='-endpointfile %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, ), - exclusionfile=dict(argstr='-exclusionfile %s', ), + exclusionfile=dict( + argstr='-exclusionfile %s', + usedefault=True, + ), gzip=dict(argstr='-gzip', ), in_file=dict( argstr='-inputfile %s', mandatory=True, position=1, + usedefault=True, ), inputmodel=dict( argstr='-inputmodel %s', @@ -70,7 +77,10 @@ def test_ProcStreamlines_inputs(): argstr='-outputcp', requires=['outputroot', 'seedfile'], ), - outputroot=dict(argstr='-outputroot %s', ), + outputroot=dict( + argstr='-outputroot %s', + usedefault=True, + ), outputsc=dict( argstr='-outputsc', requires=['outputroot', 'seedfile'], @@ -84,7 +94,10 @@ def test_ProcStreamlines_inputs(): argstr='-resamplestepsize %d', units='NA', ), - seedfile=dict(argstr='-seedfile %s', ), + seedfile=dict( + argstr='-seedfile %s', + usedefault=True, + ), seedpointmm=dict( argstr='-seedpointmm %s', units='mm', @@ -93,14 +106,20 @@ def test_ProcStreamlines_inputs(): argstr='-seedpointvox %s', units='voxels', ), - targetfile=dict(argstr='-targetfile %s', ), + targetfile=dict( + argstr='-targetfile %s', + usedefault=True, + ), truncateinexclusion=dict(argstr='-truncateinexclusion', ), truncateloops=dict(argstr='-truncateloops', ), voxeldims=dict( argstr='-voxeldims %s', units='mm', ), - waypointfile=dict(argstr='-waypointfile %s', ), + waypointfile=dict( + argstr='-waypointfile %s', + usedefault=True, + ), ) inputs = ProcStreamlines.input_spec() @@ -110,7 +129,7 @@ def test_ProcStreamlines_inputs(): def test_ProcStreamlines_outputs(): output_map = dict( outputroot_files=dict(), - proc=dict(), + proc=dict(usedefault=True, ), ) outputs = ProcStreamlines.output_spec() diff --git a/nipype/interfaces/camino/tests/test_auto_QBallMX.py b/nipype/interfaces/camino/tests/test_auto_QBallMX.py index e965cb606a..c59a8e1253 100644 --- a/nipype/interfaces/camino/tests/test_auto_QBallMX.py +++ b/nipype/interfaces/camino/tests/test_auto_QBallMX.py @@ -34,6 +34,7 @@ def test_QBallMX_inputs(): scheme_file=dict( argstr='-schemefile %s', mandatory=True, + usedefault=True, ), smoothingsigma=dict( argstr='-smoothingsigma %f', @@ -46,7 +47,7 @@ def test_QBallMX_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_QBallMX_outputs(): - output_map = dict(qmat=dict(), ) + output_map = dict(qmat=dict(usedefault=True, ), ) outputs = QBallMX.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py index c52ca04929..178392e90d 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py @@ -18,10 +18,12 @@ def test_SFLUTGen_inputs(): in_file=dict( argstr='-inputfile %s', mandatory=True, + usedefault=True, ), info_file=dict( argstr='-infofile %s', mandatory=True, + usedefault=True, ), minvectsperbin=dict( argstr='-minvectsperbin %d', @@ -52,8 +54,8 @@ def test_SFLUTGen_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SFLUTGen_outputs(): output_map = dict( - lut_one_fibre=dict(), - lut_two_fibres=dict(), + lut_one_fibre=dict(usedefault=True, ), + lut_two_fibres=dict(usedefault=True, ), ) outputs = SFLUTGen.output_spec() diff --git a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py index e83a01e2c3..1f6f132038 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py @@ -15,6 +15,7 @@ def test_SFPICOCalibData_inputs(): genfile=True, hash_files=False, mandatory=True, + usedefault=True, ), onedtfarange=dict( argstr='-onedtfarange %s', @@ -32,6 +33,7 @@ def test_SFPICOCalibData_inputs(): scheme_file=dict( argstr='-schemefile %s', mandatory=True, + usedefault=True, ), seed=dict( argstr='-seed %f', @@ -77,8 +79,8 @@ def test_SFPICOCalibData_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SFPICOCalibData_outputs(): output_map = dict( - PICOCalib=dict(), - calib_info=dict(), + PICOCalib=dict(usedefault=True, ), + calib_info=dict(usedefault=True, ), ) outputs = SFPICOCalibData.output_spec() diff --git a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py index 959545d042..b06ae65202 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py @@ -17,6 +17,7 @@ def test_SFPeaks_inputs(): in_file=dict( argstr='-inputfile %s', mandatory=True, + usedefault=True, ), inputmodel=dict( argstr='-inputmodel %s', @@ -52,7 +53,10 @@ def test_SFPeaks_inputs(): argstr='-rbfpointset %d', units='NA', ), - scheme_file=dict(argstr='%s', ), + scheme_file=dict( + argstr='%s', + usedefault=True, + ), searchradius=dict( argstr='-searchradius %f', units='NA', @@ -68,7 +72,7 @@ def test_SFPeaks_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SFPeaks_outputs(): - output_map = dict(peaks=dict(), ) + output_map = dict(peaks=dict(usedefault=True, ), ) outputs = SFPeaks.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_Shredder.py b/nipype/interfaces/camino/tests/test_auto_Shredder.py index 1099693874..2018b7dc5a 100644 --- a/nipype/interfaces/camino/tests/test_auto_Shredder.py +++ b/nipype/interfaces/camino/tests/test_auto_Shredder.py @@ -19,6 +19,7 @@ def test_Shredder_inputs(): argstr='< %s', mandatory=True, position=-2, + usedefault=True, ), offset=dict( argstr='%d', @@ -42,7 +43,7 @@ def test_Shredder_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Shredder_outputs(): - output_map = dict(shredded=dict(), ) + output_map = dict(shredded=dict(usedefault=True, ), ) outputs = Shredder.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_Track.py b/nipype/interfaces/camino/tests/test_auto_Track.py index ad8d3ff2bb..b83157f8d4 100644 --- a/nipype/interfaces/camino/tests/test_auto_Track.py +++ b/nipype/interfaces/camino/tests/test_auto_Track.py @@ -5,7 +5,10 @@ def test_Track_inputs(): input_map = dict( - anisfile=dict(argstr='-anisfile %s', ), + anisfile=dict( + argstr='-anisfile %s', + usedefault=True, + ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curveinterval=dict( @@ -25,6 +28,7 @@ def test_Track_inputs(): in_file=dict( argstr='-inputfile %s', position=1, + usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict( @@ -45,15 +49,18 @@ def test_Track_inputs(): argstr='-outputfile %s', genfile=True, position=-1, + usedefault=True, ), output_root=dict( argstr='-outputroot %s', position=-1, + usedefault=True, ), outputtracts=dict(argstr='-outputtracts %s', ), seed_file=dict( argstr='-seedfile %s', position=2, + usedefault=True, ), stepsize=dict( argstr='-stepsize %f', @@ -74,7 +81,7 @@ def test_Track_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Track_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(usedefault=True, ), ) outputs = Track.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py index 89515cef55..ddc48c71d4 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py @@ -5,7 +5,10 @@ def test_TrackBallStick_inputs(): input_map = dict( - anisfile=dict(argstr='-anisfile %s', ), + anisfile=dict( + argstr='-anisfile %s', + usedefault=True, + ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curveinterval=dict( @@ -25,6 +28,7 @@ def test_TrackBallStick_inputs(): in_file=dict( argstr='-inputfile %s', position=1, + usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict( @@ -45,15 +49,18 @@ def test_TrackBallStick_inputs(): argstr='-outputfile %s', genfile=True, position=-1, + usedefault=True, ), output_root=dict( argstr='-outputroot %s', position=-1, + usedefault=True, ), outputtracts=dict(argstr='-outputtracts %s', ), seed_file=dict( argstr='-seedfile %s', position=2, + usedefault=True, ), stepsize=dict( argstr='-stepsize %f', @@ -74,7 +81,7 @@ def test_TrackBallStick_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackBallStick_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(usedefault=True, ), ) outputs = TrackBallStick.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py index 2815ef18ee..481405062b 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py @@ -5,7 +5,10 @@ def test_TrackBayesDirac_inputs(): input_map = dict( - anisfile=dict(argstr='-anisfile %s', ), + anisfile=dict( + argstr='-anisfile %s', + usedefault=True, + ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curveinterval=dict( @@ -25,11 +28,15 @@ def test_TrackBayesDirac_inputs(): usedefault=True, ), extpriordatatype=dict(argstr='-extpriordatatype %s', ), - extpriorfile=dict(argstr='-extpriorfile %s', ), + extpriorfile=dict( + argstr='-extpriorfile %s', + usedefault=True, + ), gzip=dict(argstr='-gzip', ), in_file=dict( argstr='-inputfile %s', position=1, + usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict( @@ -54,10 +61,12 @@ def test_TrackBayesDirac_inputs(): argstr='-outputfile %s', genfile=True, position=-1, + usedefault=True, ), output_root=dict( argstr='-outputroot %s', position=-1, + usedefault=True, ), outputtracts=dict(argstr='-outputtracts %s', ), pdf=dict(argstr='-pdf %s', ), @@ -65,10 +74,12 @@ def test_TrackBayesDirac_inputs(): scheme_file=dict( argstr='-schemefile %s', mandatory=True, + usedefault=True, ), seed_file=dict( argstr='-seedfile %s', position=2, + usedefault=True, ), stepsize=dict( argstr='-stepsize %f', @@ -89,7 +100,7 @@ def test_TrackBayesDirac_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackBayesDirac_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(usedefault=True, ), ) outputs = TrackBayesDirac.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py index 827dbb2f27..629ee39f78 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py @@ -5,12 +5,16 @@ def test_TrackBedpostxDeter_inputs(): input_map = dict( - anisfile=dict(argstr='-anisfile %s', ), + anisfile=dict( + argstr='-anisfile %s', + usedefault=True, + ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), bedpostxdir=dict( argstr='-bedpostxdir %s', mandatory=True, + usedefault=True, ), curveinterval=dict( argstr='-curveinterval %f', @@ -29,6 +33,7 @@ def test_TrackBedpostxDeter_inputs(): in_file=dict( argstr='-inputfile %s', position=1, + usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict( @@ -53,15 +58,18 @@ def test_TrackBedpostxDeter_inputs(): argstr='-outputfile %s', genfile=True, position=-1, + usedefault=True, ), output_root=dict( argstr='-outputroot %s', position=-1, + usedefault=True, ), outputtracts=dict(argstr='-outputtracts %s', ), seed_file=dict( argstr='-seedfile %s', position=2, + usedefault=True, ), stepsize=dict( argstr='-stepsize %f', @@ -82,7 +90,7 @@ def test_TrackBedpostxDeter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackBedpostxDeter_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(usedefault=True, ), ) outputs = TrackBedpostxDeter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py index e250ec9c40..af2f9ea808 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py @@ -5,12 +5,16 @@ def test_TrackBedpostxProba_inputs(): input_map = dict( - anisfile=dict(argstr='-anisfile %s', ), + anisfile=dict( + argstr='-anisfile %s', + usedefault=True, + ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), bedpostxdir=dict( argstr='-bedpostxdir %s', mandatory=True, + usedefault=True, ), curveinterval=dict( argstr='-curveinterval %f', @@ -29,6 +33,7 @@ def test_TrackBedpostxProba_inputs(): in_file=dict( argstr='-inputfile %s', position=1, + usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict( @@ -57,15 +62,18 @@ def test_TrackBedpostxProba_inputs(): argstr='-outputfile %s', genfile=True, position=-1, + usedefault=True, ), output_root=dict( argstr='-outputroot %s', position=-1, + usedefault=True, ), outputtracts=dict(argstr='-outputtracts %s', ), seed_file=dict( argstr='-seedfile %s', position=2, + usedefault=True, ), stepsize=dict( argstr='-stepsize %f', @@ -86,7 +94,7 @@ def test_TrackBedpostxProba_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackBedpostxProba_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(usedefault=True, ), ) outputs = TrackBedpostxProba.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py index 90ffd05a2d..6d7b0be071 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py @@ -5,10 +5,16 @@ def test_TrackBootstrap_inputs(): input_map = dict( - anisfile=dict(argstr='-anisfile %s', ), + anisfile=dict( + argstr='-anisfile %s', + usedefault=True, + ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), - bgmask=dict(argstr='-bgmask %s', ), + bgmask=dict( + argstr='-bgmask %s', + usedefault=True, + ), bsdatafiles=dict( argstr='-bsdatafile %s', mandatory=True, @@ -30,6 +36,7 @@ def test_TrackBootstrap_inputs(): in_file=dict( argstr='-inputfile %s', position=1, + usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict( @@ -55,19 +62,23 @@ def test_TrackBootstrap_inputs(): argstr='-outputfile %s', genfile=True, position=-1, + usedefault=True, ), output_root=dict( argstr='-outputroot %s', position=-1, + usedefault=True, ), outputtracts=dict(argstr='-outputtracts %s', ), scheme_file=dict( argstr='-schemefile %s', mandatory=True, + usedefault=True, ), seed_file=dict( argstr='-seedfile %s', position=2, + usedefault=True, ), stepsize=dict( argstr='-stepsize %f', @@ -88,7 +99,7 @@ def test_TrackBootstrap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackBootstrap_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(usedefault=True, ), ) outputs = TrackBootstrap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackDT.py b/nipype/interfaces/camino/tests/test_auto_TrackDT.py index 7ab3772468..2669d42651 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackDT.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackDT.py @@ -5,7 +5,10 @@ def test_TrackDT_inputs(): input_map = dict( - anisfile=dict(argstr='-anisfile %s', ), + anisfile=dict( + argstr='-anisfile %s', + usedefault=True, + ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curveinterval=dict( @@ -25,6 +28,7 @@ def test_TrackDT_inputs(): in_file=dict( argstr='-inputfile %s', position=1, + usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict( @@ -45,15 +49,18 @@ def test_TrackDT_inputs(): argstr='-outputfile %s', genfile=True, position=-1, + usedefault=True, ), output_root=dict( argstr='-outputroot %s', position=-1, + usedefault=True, ), outputtracts=dict(argstr='-outputtracts %s', ), seed_file=dict( argstr='-seedfile %s', position=2, + usedefault=True, ), stepsize=dict( argstr='-stepsize %f', @@ -74,7 +81,7 @@ def test_TrackDT_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackDT_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(usedefault=True, ), ) outputs = TrackDT.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py index 30ff12db9f..16232d11d2 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py @@ -5,7 +5,10 @@ def test_TrackPICo_inputs(): input_map = dict( - anisfile=dict(argstr='-anisfile %s', ), + anisfile=dict( + argstr='-anisfile %s', + usedefault=True, + ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curveinterval=dict( @@ -25,6 +28,7 @@ def test_TrackPICo_inputs(): in_file=dict( argstr='-inputfile %s', position=1, + usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict( @@ -49,16 +53,19 @@ def test_TrackPICo_inputs(): argstr='-outputfile %s', genfile=True, position=-1, + usedefault=True, ), output_root=dict( argstr='-outputroot %s', position=-1, + usedefault=True, ), outputtracts=dict(argstr='-outputtracts %s', ), pdf=dict(argstr='-pdf %s', ), seed_file=dict( argstr='-seedfile %s', position=2, + usedefault=True, ), stepsize=dict( argstr='-stepsize %f', @@ -79,7 +86,7 @@ def test_TrackPICo_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackPICo_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(usedefault=True, ), ) outputs = TrackPICo.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TractShredder.py b/nipype/interfaces/camino/tests/test_auto_TractShredder.py index c9cf40e1c3..952ef69b43 100644 --- a/nipype/interfaces/camino/tests/test_auto_TractShredder.py +++ b/nipype/interfaces/camino/tests/test_auto_TractShredder.py @@ -19,6 +19,7 @@ def test_TractShredder_inputs(): argstr='< %s', mandatory=True, position=-2, + usedefault=True, ), offset=dict( argstr='%d', @@ -42,7 +43,7 @@ def test_TractShredder_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TractShredder_outputs(): - output_map = dict(shredded=dict(), ) + output_map = dict(shredded=dict(usedefault=True, ), ) outputs = TractShredder.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py index 8dc8bd03e9..0bbe7ca4e9 100644 --- a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py @@ -15,6 +15,7 @@ def test_VtkStreamlines_inputs(): argstr=' < %s', mandatory=True, position=-2, + usedefault=True, ), inputmodel=dict( argstr='-inputmodel %s', @@ -30,14 +31,17 @@ def test_VtkStreamlines_inputs(): scalar_file=dict( argstr='-scalarfile %s', position=3, + usedefault=True, ), seed_file=dict( argstr='-seedfile %s', position=1, + usedefault=True, ), target_file=dict( argstr='-targetfile %s', position=2, + usedefault=True, ), voxeldims=dict( argstr='-voxeldims %s', @@ -51,7 +55,7 @@ def test_VtkStreamlines_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_VtkStreamlines_outputs(): - output_map = dict(vtk=dict(), ) + output_map = dict(vtk=dict(usedefault=True, ), ) outputs = VtkStreamlines.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py index b4d5092dab..109a116bce 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py @@ -20,6 +20,7 @@ def test_Camino2Trackvis_inputs(): argstr='-i %s', mandatory=True, position=1, + usedefault=True, ), min_length=dict( argstr='-l %d', @@ -29,11 +30,13 @@ def test_Camino2Trackvis_inputs(): nifti_file=dict( argstr='--nifti %s', position=7, + usedefault=True, ), out_file=dict( argstr='-o %s', genfile=True, position=2, + usedefault=True, ), voxel_dims=dict( argstr='-x %s', @@ -45,6 +48,7 @@ def test_Camino2Trackvis_inputs(): argstr='--voxel-order %s', mandatory=True, position=6, + usedefault=True, ), ) inputs = Camino2Trackvis.input_spec() @@ -53,7 +57,7 @@ def test_Camino2Trackvis_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Camino2Trackvis_outputs(): - output_map = dict(trackvis=dict(), ) + output_map = dict(trackvis=dict(usedefault=True, ), ) outputs = Camino2Trackvis.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py index 978b2439a2..9f7b512ec5 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py @@ -8,6 +8,7 @@ def test_Trackvis2Camino_inputs(): append_file=dict( argstr='-a %s', position=2, + usedefault=True, ), args=dict(argstr='%s', ), environ=dict( @@ -18,11 +19,13 @@ def test_Trackvis2Camino_inputs(): argstr='-i %s', mandatory=True, position=1, + usedefault=True, ), out_file=dict( argstr='-o %s', genfile=True, position=2, + usedefault=True, ), ) inputs = Trackvis2Camino.input_spec() @@ -31,7 +34,7 @@ def test_Trackvis2Camino_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Trackvis2Camino_outputs(): - output_map = dict(camino=dict(), ) + output_map = dict(camino=dict(usedefault=True, ), ) outputs = Trackvis2Camino.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py index a80bbe757a..b8ed8ce13f 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py @@ -7,9 +7,9 @@ def test_AverageNetworks_inputs(): input_map = dict( group_id=dict(usedefault=True, ), in_files=dict(mandatory=True, ), - out_gexf_groupavg=dict(), - out_gpickled_groupavg=dict(), - resolution_network_file=dict(), + out_gexf_groupavg=dict(usedefault=True, ), + out_gpickled_groupavg=dict(usedefault=True, ), + resolution_network_file=dict(usedefault=True, ), ) inputs = AverageNetworks.input_spec() @@ -18,8 +18,8 @@ def test_AverageNetworks_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_AverageNetworks_outputs(): output_map = dict( - gexf_groupavg=dict(), - gpickled_groupavg=dict(), + gexf_groupavg=dict(usedefault=True, ), + gpickled_groupavg=dict(usedefault=True, ), matlab_groupavgs=dict(), ) outputs = AverageNetworks.output_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py index 00a1acea98..9c9e5b1bc5 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py @@ -32,7 +32,7 @@ def test_CFFConverter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CFFConverter_outputs(): - output_map = dict(connectome_file=dict(), ) + output_map = dict(connectome_file=dict(usedefault=True, ), ) outputs = CFFConverter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py b/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py index 60e8596f5e..4f575506d6 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py @@ -6,16 +6,43 @@ def test_CreateMatrix_inputs(): input_map = dict( count_region_intersections=dict(usedefault=True, ), - out_endpoint_array_name=dict(genfile=True, ), - out_fiber_length_std_matrix_mat_file=dict(genfile=True, ), - out_intersection_matrix_mat_file=dict(genfile=True, ), - out_matrix_file=dict(genfile=True, ), + out_endpoint_array_name=dict( + genfile=True, + usedefault=True, + ), + out_fiber_length_std_matrix_mat_file=dict( + genfile=True, + usedefault=True, + ), + out_intersection_matrix_mat_file=dict( + genfile=True, + usedefault=True, + ), + out_matrix_file=dict( + genfile=True, + usedefault=True, + ), out_matrix_mat_file=dict(usedefault=True, ), - out_mean_fiber_length_matrix_mat_file=dict(genfile=True, ), - out_median_fiber_length_matrix_mat_file=dict(genfile=True, ), - resolution_network_file=dict(mandatory=True, ), - roi_file=dict(mandatory=True, ), - tract_file=dict(mandatory=True, ), + out_mean_fiber_length_matrix_mat_file=dict( + genfile=True, + usedefault=True, + ), + out_median_fiber_length_matrix_mat_file=dict( + genfile=True, + usedefault=True, + ), + resolution_network_file=dict( + mandatory=True, + usedefault=True, + ), + roi_file=dict( + mandatory=True, + usedefault=True, + ), + tract_file=dict( + mandatory=True, + usedefault=True, + ), ) inputs = CreateMatrix.input_spec() @@ -24,24 +51,24 @@ def test_CreateMatrix_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CreateMatrix_outputs(): output_map = dict( - endpoint_file=dict(), - endpoint_file_mm=dict(), - fiber_label_file=dict(), - fiber_labels_noorphans=dict(), - fiber_length_file=dict(), - fiber_length_std_matrix_mat_file=dict(), + endpoint_file=dict(usedefault=True, ), + endpoint_file_mm=dict(usedefault=True, ), + fiber_label_file=dict(usedefault=True, ), + fiber_labels_noorphans=dict(usedefault=True, ), + fiber_length_file=dict(usedefault=True, ), + fiber_length_std_matrix_mat_file=dict(usedefault=True, ), filtered_tractographies=dict(), - filtered_tractography=dict(), - filtered_tractography_by_intersections=dict(), - intersection_matrix_file=dict(), - intersection_matrix_mat_file=dict(), + filtered_tractography=dict(usedefault=True, ), + filtered_tractography_by_intersections=dict(usedefault=True, ), + intersection_matrix_file=dict(usedefault=True, ), + intersection_matrix_mat_file=dict(usedefault=True, ), matlab_matrix_files=dict(), - matrix_file=dict(), + matrix_file=dict(usedefault=True, ), matrix_files=dict(), - matrix_mat_file=dict(), - mean_fiber_length_matrix_mat_file=dict(), - median_fiber_length_matrix_mat_file=dict(), - stats_file=dict(), + matrix_mat_file=dict(usedefault=True, ), + mean_fiber_length_matrix_mat_file=dict(usedefault=True, ), + median_fiber_length_matrix_mat_file=dict(usedefault=True, ), + stats_file=dict(usedefault=True, ), ) outputs = CreateMatrix.output_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py index 3635f21e59..4018c04a85 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py @@ -6,8 +6,14 @@ def test_CreateNodes_inputs(): input_map = dict( out_filename=dict(usedefault=True, ), - resolution_network_file=dict(mandatory=True, ), - roi_file=dict(mandatory=True, ), + resolution_network_file=dict( + mandatory=True, + usedefault=True, + ), + roi_file=dict( + mandatory=True, + usedefault=True, + ), ) inputs = CreateNodes.input_spec() @@ -15,7 +21,7 @@ def test_CreateNodes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CreateNodes_outputs(): - output_map = dict(node_network=dict(), ) + output_map = dict(node_network=dict(usedefault=True, ), ) outputs = CreateNodes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py index ceaa6d8dea..2b86746313 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py @@ -14,7 +14,7 @@ def test_MergeCNetworks_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MergeCNetworks_outputs(): - output_map = dict(connectome_file=dict(), ) + output_map = dict(connectome_file=dict(usedefault=True, ), ) outputs = MergeCNetworks.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py index e3220e4790..1481b540ee 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py @@ -8,10 +8,10 @@ def test_NetworkBasedStatistic_inputs(): edge_key=dict(usedefault=True, ), in_group1=dict(mandatory=True, ), in_group2=dict(mandatory=True, ), - node_position_network=dict(), + node_position_network=dict(usedefault=True, ), number_of_permutations=dict(usedefault=True, ), - out_nbs_network=dict(), - out_nbs_pval_network=dict(), + out_nbs_network=dict(usedefault=True, ), + out_nbs_pval_network=dict(usedefault=True, ), t_tail=dict(usedefault=True, ), threshold=dict(usedefault=True, ), ) @@ -22,8 +22,8 @@ def test_NetworkBasedStatistic_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_NetworkBasedStatistic_outputs(): output_map = dict( - nbs_network=dict(), - nbs_pval_network=dict(), + nbs_network=dict(usedefault=True, ), + nbs_pval_network=dict(usedefault=True, ), network_files=dict(), ) outputs = NetworkBasedStatistic.output_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py index d9a3f0c740..837f0a8f76 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py @@ -6,13 +6,25 @@ def test_NetworkXMetrics_inputs(): input_map = dict( compute_clique_related_measures=dict(usedefault=True, ), - in_file=dict(mandatory=True, ), - out_edge_metrics_matlab=dict(genfile=True, ), - out_global_metrics_matlab=dict(genfile=True, ), + in_file=dict( + mandatory=True, + usedefault=True, + ), + out_edge_metrics_matlab=dict( + genfile=True, + usedefault=True, + ), + out_global_metrics_matlab=dict( + genfile=True, + usedefault=True, + ), out_k_core=dict(usedefault=True, ), out_k_crust=dict(usedefault=True, ), out_k_shell=dict(usedefault=True, ), - out_node_metrics_matlab=dict(genfile=True, ), + out_node_metrics_matlab=dict( + genfile=True, + usedefault=True, + ), out_pickled_extra_measures=dict(usedefault=True, ), treat_as_weighted_graph=dict(usedefault=True, ), ) @@ -24,18 +36,18 @@ def test_NetworkXMetrics_inputs(): def test_NetworkXMetrics_outputs(): output_map = dict( edge_measure_networks=dict(), - edge_measures_matlab=dict(), - global_measures_matlab=dict(), + edge_measures_matlab=dict(usedefault=True, ), + global_measures_matlab=dict(usedefault=True, ), gpickled_network_files=dict(), - k_core=dict(), - k_crust=dict(), + k_core=dict(usedefault=True, ), + k_crust=dict(usedefault=True, ), k_networks=dict(), - k_shell=dict(), + k_shell=dict(usedefault=True, ), matlab_dict_measures=dict(), matlab_matrix_files=dict(), node_measure_networks=dict(), - node_measures_matlab=dict(), - pickled_extra_measures=dict(), + node_measures_matlab=dict(usedefault=True, ), + pickled_extra_measures=dict(usedefault=True, ), ) outputs = NetworkXMetrics.output_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py index edcdf2e7a1..e4a876db18 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py +++ b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py @@ -6,11 +6,14 @@ def test_Parcellate_inputs(): input_map = dict( dilation=dict(usedefault=True, ), - freesurfer_dir=dict(), - out_roi_file=dict(genfile=True, ), + freesurfer_dir=dict(usedefault=True, ), + out_roi_file=dict( + genfile=True, + usedefault=True, + ), parcellation_name=dict(usedefault=True, ), subject_id=dict(mandatory=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = Parcellate.input_spec() @@ -19,14 +22,14 @@ def test_Parcellate_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Parcellate_outputs(): output_map = dict( - aseg_file=dict(), - cc_unknown_file=dict(), - dilated_roi_file_in_structural_space=dict(), - ribbon_file=dict(), - roi_file=dict(), - roi_file_in_structural_space=dict(), - roiv_file=dict(), - white_matter_mask_file=dict(), + aseg_file=dict(usedefault=True, ), + cc_unknown_file=dict(usedefault=True, ), + dilated_roi_file_in_structural_space=dict(usedefault=True, ), + ribbon_file=dict(usedefault=True, ), + roi_file=dict(usedefault=True, ), + roi_file_in_structural_space=dict(usedefault=True, ), + roiv_file=dict(usedefault=True, ), + white_matter_mask_file=dict(usedefault=True, ), ) outputs = Parcellate.output_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py index dd2ce50aec..bc7d997ca8 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py +++ b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py @@ -5,11 +5,26 @@ def test_ROIGen_inputs(): input_map = dict( - LUT_file=dict(xor=['use_freesurfer_LUT'], ), - aparc_aseg_file=dict(mandatory=True, ), - freesurfer_dir=dict(requires=['use_freesurfer_LUT'], ), - out_dict_file=dict(genfile=True, ), - out_roi_file=dict(genfile=True, ), + LUT_file=dict( + usedefault=True, + xor=['use_freesurfer_LUT'], + ), + aparc_aseg_file=dict( + mandatory=True, + usedefault=True, + ), + freesurfer_dir=dict( + requires=['use_freesurfer_LUT'], + usedefault=True, + ), + out_dict_file=dict( + genfile=True, + usedefault=True, + ), + out_roi_file=dict( + genfile=True, + usedefault=True, + ), use_freesurfer_LUT=dict(xor=['LUT_file'], ), ) inputs = ROIGen.input_spec() @@ -19,8 +34,8 @@ def test_ROIGen_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ROIGen_outputs(): output_map = dict( - dict_file=dict(), - roi_file=dict(), + dict_file=dict(usedefault=True, ), + roi_file=dict(usedefault=True, ), ) outputs = ROIGen.output_spec() diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py index a39dbf6c3b..9513ba2c56 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py @@ -9,13 +9,18 @@ def test_DTIRecon_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), args=dict(argstr='%s', ), b0_threshold=dict(argstr='-b0_th', ), - bvals=dict(mandatory=True, ), + bvals=dict( + mandatory=True, + usedefault=True, + ), bvecs=dict( argstr='-gm %s', mandatory=True, + usedefault=True, ), environ=dict( nohash=True, @@ -41,18 +46,18 @@ def test_DTIRecon_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DTIRecon_outputs(): output_map = dict( - ADC=dict(), - B0=dict(), - FA=dict(), - FA_color=dict(), - L1=dict(), - L2=dict(), - L3=dict(), - V1=dict(), - V2=dict(), - V3=dict(), - exp=dict(), - tensor=dict(), + ADC=dict(usedefault=True, ), + B0=dict(usedefault=True, ), + FA=dict(usedefault=True, ), + FA_color=dict(usedefault=True, ), + L1=dict(usedefault=True, ), + L2=dict(usedefault=True, ), + L3=dict(usedefault=True, ), + V1=dict(usedefault=True, ), + V2=dict(usedefault=True, ), + V3=dict(usedefault=True, ), + exp=dict(usedefault=True, ), + tensor=dict(usedefault=True, ), ) outputs = DTIRecon.output_spec() diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py index cf483d00d0..a80c4ac3c4 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py @@ -25,11 +25,13 @@ def test_DTITracker_inputs(): argstr='-m %s', mandatory=True, position=2, + usedefault=True, ), mask1_threshold=dict(position=3, ), mask2_file=dict( argstr='-m2 %s', position=4, + usedefault=True, ), mask2_threshold=dict(position=5, ), output_file=dict( @@ -37,14 +39,17 @@ def test_DTITracker_inputs(): position=1, usedefault=True, ), - output_mask=dict(argstr='-om %s', ), + output_mask=dict( + argstr='-om %s', + usedefault=True, + ), primary_vector=dict(argstr='-%s', ), random_seed=dict(argstr='-rseed %d', ), step_length=dict(argstr='-l %f', ), swap_xy=dict(argstr='-sxy', ), swap_yz=dict(argstr='-syz', ), swap_zx=dict(argstr='-szx', ), - tensor_file=dict(), + tensor_file=dict(usedefault=True, ), tracking_method=dict(argstr='-%s', ), ) inputs = DTITracker.input_spec() @@ -54,8 +59,8 @@ def test_DTITracker_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DTITracker_outputs(): output_map = dict( - mask_file=dict(), - track_file=dict(), + mask_file=dict(usedefault=True, ), + track_file=dict(usedefault=True, ), ) outputs = DTITracker.output_spec() diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py index 59bc8c25a5..5f04836ce9 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py @@ -6,27 +6,40 @@ def test_HARDIMat_inputs(): input_map = dict( args=dict(argstr='%s', ), - bvals=dict(mandatory=True, ), + bvals=dict( + mandatory=True, + usedefault=True, + ), bvecs=dict( argstr='%s', mandatory=True, position=1, + usedefault=True, ), environ=dict( nohash=True, usedefault=True, ), - image_info=dict(argstr='-info %s', ), + image_info=dict( + argstr='-info %s', + usedefault=True, + ), image_orientation_vectors=dict(argstr='-iop %f', ), oblique_correction=dict(argstr='-oc', ), - odf_file=dict(argstr='-odf %s', ), + odf_file=dict( + argstr='-odf %s', + usedefault=True, + ), order=dict(argstr='-order %s', ), out_file=dict( argstr='%s', position=2, usedefault=True, ), - reference_file=dict(argstr='-ref %s', ), + reference_file=dict( + argstr='-ref %s', + usedefault=True, + ), ) inputs = HARDIMat.input_spec() @@ -34,7 +47,7 @@ def test_HARDIMat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_HARDIMat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = HARDIMat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py index 1e66b93bec..d23f176cdc 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py @@ -9,6 +9,7 @@ def test_ODFRecon_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), args=dict(argstr='%s', ), dsi=dict(argstr='-dsi', ), @@ -21,6 +22,7 @@ def test_ODFRecon_inputs(): matrix=dict( argstr='-mat %s', mandatory=True, + usedefault=True, ), n_b0=dict( argstr='-b0 %s', @@ -57,11 +59,11 @@ def test_ODFRecon_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ODFRecon_outputs(): output_map = dict( - B0=dict(), - DWI=dict(), - ODF=dict(), - entropy=dict(), - max=dict(), + B0=dict(usedefault=True, ), + DWI=dict(usedefault=True, ), + ODF=dict(usedefault=True, ), + entropy=dict(usedefault=True, ), + max=dict(usedefault=True, ), ) outputs = ODFRecon.output_spec() diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py index 41b2d530f6..291f6987fe 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py @@ -5,7 +5,10 @@ def test_ODFTracker_inputs(): input_map = dict( - ODF=dict(mandatory=True, ), + ODF=dict( + mandatory=True, + usedefault=True, + ), angle_threshold=dict(argstr='-at %f', ), args=dict(argstr='%s', ), disc=dict(argstr='-disc', ), @@ -32,14 +35,19 @@ def test_ODFTracker_inputs(): argstr='-m %s', mandatory=True, position=2, + usedefault=True, ), mask1_threshold=dict(position=3, ), mask2_file=dict( argstr='-m2 %s', position=4, + usedefault=True, ), mask2_threshold=dict(position=5, ), - max=dict(mandatory=True, ), + max=dict( + mandatory=True, + usedefault=True, + ), out_file=dict( argstr='%s', position=1, @@ -60,7 +68,7 @@ def test_ODFTracker_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ODFTracker_outputs(): - output_map = dict(track_file=dict(), ) + output_map = dict(track_file=dict(usedefault=True, ), ) outputs = ODFTracker.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py index 8648a1f1f9..e939cdba72 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py @@ -24,6 +24,7 @@ def test_SplineFilter_inputs(): argstr='%s', mandatory=True, position=0, + usedefault=True, ), ) inputs = SplineFilter.input_spec() @@ -32,7 +33,7 @@ def test_SplineFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SplineFilter_outputs(): - output_map = dict(smoothed_track_file=dict(), ) + output_map = dict(smoothed_track_file=dict(usedefault=True, ), ) outputs = SplineFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py index b004678175..0333b8283c 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py @@ -27,7 +27,7 @@ def test_TrackMerge_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackMerge_outputs(): - output_map = dict(track_file=dict(), ) + output_map = dict(track_file=dict(usedefault=True, ), ) outputs = TrackMerge.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dipy/tests/test_auto_APMQball.py b/nipype/interfaces/dipy/tests/test_auto_APMQball.py index f6f3f2e4c6..4696370434 100644 --- a/nipype/interfaces/dipy/tests/test_auto_APMQball.py +++ b/nipype/interfaces/dipy/tests/test_auto_APMQball.py @@ -6,10 +6,19 @@ def test_APMQball_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict(mandatory=True, ), - in_bvec=dict(mandatory=True, ), - in_file=dict(mandatory=True, ), - mask_file=dict(), + in_bval=dict( + mandatory=True, + usedefault=True, + ), + in_bvec=dict( + mandatory=True, + usedefault=True, + ), + in_file=dict( + mandatory=True, + usedefault=True, + ), + mask_file=dict(usedefault=True, ), out_prefix=dict(), ) inputs = APMQball.input_spec() @@ -18,7 +27,7 @@ def test_APMQball_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_APMQball_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = APMQball.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dipy/tests/test_auto_CSD.py b/nipype/interfaces/dipy/tests/test_auto_CSD.py index a30efaa3cc..c0372e0436 100644 --- a/nipype/interfaces/dipy/tests/test_auto_CSD.py +++ b/nipype/interfaces/dipy/tests/test_auto_CSD.py @@ -6,13 +6,22 @@ def test_CSD_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict(mandatory=True, ), - in_bvec=dict(mandatory=True, ), - in_file=dict(mandatory=True, ), - in_mask=dict(), - out_fods=dict(), + in_bval=dict( + mandatory=True, + usedefault=True, + ), + in_bvec=dict( + mandatory=True, + usedefault=True, + ), + in_file=dict( + mandatory=True, + usedefault=True, + ), + in_mask=dict(usedefault=True, ), + out_fods=dict(usedefault=True, ), out_prefix=dict(), - response=dict(), + response=dict(usedefault=True, ), save_fods=dict(usedefault=True, ), sh_order=dict(usedefault=True, ), ) @@ -23,8 +32,8 @@ def test_CSD_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CSD_outputs(): output_map = dict( - model=dict(), - out_fods=dict(), + model=dict(usedefault=True, ), + out_fods=dict(usedefault=True, ), ) outputs = CSD.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_DTI.py b/nipype/interfaces/dipy/tests/test_auto_DTI.py index f543856065..f8416f25a0 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DTI.py +++ b/nipype/interfaces/dipy/tests/test_auto_DTI.py @@ -6,10 +6,19 @@ def test_DTI_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict(mandatory=True, ), - in_bvec=dict(mandatory=True, ), - in_file=dict(mandatory=True, ), - mask_file=dict(), + in_bval=dict( + mandatory=True, + usedefault=True, + ), + in_bvec=dict( + mandatory=True, + usedefault=True, + ), + in_file=dict( + mandatory=True, + usedefault=True, + ), + mask_file=dict(usedefault=True, ), out_prefix=dict(), ) inputs = DTI.input_spec() @@ -19,12 +28,12 @@ def test_DTI_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DTI_outputs(): output_map = dict( - ad_file=dict(), - color_fa_file=dict(), - fa_file=dict(), - md_file=dict(), - out_file=dict(), - rd_file=dict(), + ad_file=dict(usedefault=True, ), + color_fa_file=dict(usedefault=True, ), + fa_file=dict(usedefault=True, ), + md_file=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), + rd_file=dict(usedefault=True, ), ) outputs = DTI.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_Denoise.py b/nipype/interfaces/dipy/tests/test_auto_Denoise.py index 88a1bc5314..a799d22b8d 100644 --- a/nipype/interfaces/dipy/tests/test_auto_Denoise.py +++ b/nipype/interfaces/dipy/tests/test_auto_Denoise.py @@ -6,15 +6,18 @@ def test_Denoise_inputs(): input_map = dict( block_radius=dict(usedefault=True, ), - in_file=dict(mandatory=True, ), - in_mask=dict(), - noise_mask=dict(), + in_file=dict( + mandatory=True, + usedefault=True, + ), + in_mask=dict(usedefault=True, ), + noise_mask=dict(usedefault=True, ), noise_model=dict( mandatory=True, usedefault=True, ), patch_radius=dict(usedefault=True, ), - signal_mask=dict(), + signal_mask=dict(usedefault=True, ), snr=dict(), ) inputs = Denoise.input_spec() @@ -23,7 +26,7 @@ def test_Denoise_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Denoise_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Denoise.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py b/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py index ee9022ca58..3820a6f42e 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py +++ b/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py @@ -6,9 +6,18 @@ def test_DipyDiffusionInterface_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict(mandatory=True, ), - in_bvec=dict(mandatory=True, ), - in_file=dict(mandatory=True, ), + in_bval=dict( + mandatory=True, + usedefault=True, + ), + in_bvec=dict( + mandatory=True, + usedefault=True, + ), + in_file=dict( + mandatory=True, + usedefault=True, + ), out_prefix=dict(), ) inputs = DipyDiffusionInterface.input_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py b/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py index 1270d94b13..c152a2e226 100644 --- a/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py +++ b/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py @@ -8,11 +8,23 @@ def test_EstimateResponseSH_inputs(): auto=dict(xor=['recursive'], ), b0_thres=dict(usedefault=True, ), fa_thresh=dict(usedefault=True, ), - in_bval=dict(mandatory=True, ), - in_bvec=dict(mandatory=True, ), - in_evals=dict(mandatory=True, ), - in_file=dict(mandatory=True, ), - in_mask=dict(), + in_bval=dict( + mandatory=True, + usedefault=True, + ), + in_bvec=dict( + mandatory=True, + usedefault=True, + ), + in_evals=dict( + mandatory=True, + usedefault=True, + ), + in_file=dict( + mandatory=True, + usedefault=True, + ), + in_mask=dict(usedefault=True, ), out_mask=dict(usedefault=True, ), out_prefix=dict(), recursive=dict(xor=['auto'], ), @@ -26,8 +38,8 @@ def test_EstimateResponseSH_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EstimateResponseSH_outputs(): output_map = dict( - out_mask=dict(), - response=dict(), + out_mask=dict(usedefault=True, ), + response=dict(usedefault=True, ), ) outputs = EstimateResponseSH.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_RESTORE.py b/nipype/interfaces/dipy/tests/test_auto_RESTORE.py index 9f62d05e0c..f6f4a87466 100644 --- a/nipype/interfaces/dipy/tests/test_auto_RESTORE.py +++ b/nipype/interfaces/dipy/tests/test_auto_RESTORE.py @@ -6,11 +6,20 @@ def test_RESTORE_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict(mandatory=True, ), - in_bvec=dict(mandatory=True, ), - in_file=dict(mandatory=True, ), - in_mask=dict(), - noise_mask=dict(), + in_bval=dict( + mandatory=True, + usedefault=True, + ), + in_bvec=dict( + mandatory=True, + usedefault=True, + ), + in_file=dict( + mandatory=True, + usedefault=True, + ), + in_mask=dict(usedefault=True, ), + noise_mask=dict(usedefault=True, ), out_prefix=dict(), ) inputs = RESTORE.input_spec() @@ -20,13 +29,13 @@ def test_RESTORE_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RESTORE_outputs(): output_map = dict( - evals=dict(), - evecs=dict(), - fa=dict(), - md=dict(), - mode=dict(), - rd=dict(), - trace=dict(), + evals=dict(usedefault=True, ), + evecs=dict(usedefault=True, ), + fa=dict(usedefault=True, ), + md=dict(usedefault=True, ), + mode=dict(usedefault=True, ), + rd=dict(usedefault=True, ), + trace=dict(usedefault=True, ), ) outputs = RESTORE.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_Resample.py b/nipype/interfaces/dipy/tests/test_auto_Resample.py index ff51e0efe4..261bab77ce 100644 --- a/nipype/interfaces/dipy/tests/test_auto_Resample.py +++ b/nipype/interfaces/dipy/tests/test_auto_Resample.py @@ -5,7 +5,10 @@ def test_Resample_inputs(): input_map = dict( - in_file=dict(mandatory=True, ), + in_file=dict( + mandatory=True, + usedefault=True, + ), interp=dict( mandatory=True, usedefault=True, @@ -18,7 +21,7 @@ def test_Resample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Resample_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Resample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py index db46a3b982..31db2179c1 100644 --- a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py +++ b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py @@ -5,16 +5,19 @@ def test_SimulateMultiTensor_inputs(): input_map = dict( - baseline=dict(mandatory=True, ), + baseline=dict( + mandatory=True, + usedefault=True, + ), bvalues=dict(usedefault=True, ), diff_iso=dict(usedefault=True, ), diff_sf=dict(usedefault=True, ), - gradients=dict(), - in_bval=dict(), - in_bvec=dict(), + gradients=dict(usedefault=True, ), + in_bval=dict(usedefault=True, ), + in_bvec=dict(usedefault=True, ), in_dirs=dict(mandatory=True, ), in_frac=dict(mandatory=True, ), - in_mask=dict(), + in_mask=dict(usedefault=True, ), in_vfms=dict(mandatory=True, ), n_proc=dict(usedefault=True, ), num_dirs=dict(usedefault=True, ), @@ -31,10 +34,10 @@ def test_SimulateMultiTensor_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SimulateMultiTensor_outputs(): output_map = dict( - out_bval=dict(), - out_bvec=dict(), - out_file=dict(), - out_mask=dict(), + out_bval=dict(usedefault=True, ), + out_bvec=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), + out_mask=dict(usedefault=True, ), ) outputs = SimulateMultiTensor.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py b/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py index 1bc1a2ea97..420f9686bd 100644 --- a/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py +++ b/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py @@ -9,9 +9,12 @@ def test_StreamlineTractography_inputs(): mandatory=True, usedefault=True, ), - in_file=dict(mandatory=True, ), - in_model=dict(), - in_peaks=dict(), + in_file=dict( + mandatory=True, + usedefault=True, + ), + in_model=dict(usedefault=True, ), + in_peaks=dict(usedefault=True, ), min_angle=dict( mandatory=True, usedefault=True, @@ -33,9 +36,9 @@ def test_StreamlineTractography_inputs(): mandatory=True, usedefault=True, ), - seed_coord=dict(), - seed_mask=dict(), - tracking_mask=dict(), + seed_coord=dict(usedefault=True, ), + seed_mask=dict(usedefault=True, ), + tracking_mask=dict(usedefault=True, ), ) inputs = StreamlineTractography.input_spec() @@ -44,10 +47,10 @@ def test_StreamlineTractography_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_StreamlineTractography_outputs(): output_map = dict( - gfa=dict(), - odf_peaks=dict(), - out_seeds=dict(), - tracks=dict(), + gfa=dict(usedefault=True, ), + odf_peaks=dict(usedefault=True, ), + out_seeds=dict(usedefault=True, ), + tracks=dict(usedefault=True, ), ) outputs = StreamlineTractography.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py index d072af78fc..319b38d094 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py +++ b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py @@ -6,10 +6,19 @@ def test_TensorMode_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict(mandatory=True, ), - in_bvec=dict(mandatory=True, ), - in_file=dict(mandatory=True, ), - mask_file=dict(), + in_bval=dict( + mandatory=True, + usedefault=True, + ), + in_bvec=dict( + mandatory=True, + usedefault=True, + ), + in_file=dict( + mandatory=True, + usedefault=True, + ), + mask_file=dict(usedefault=True, ), out_prefix=dict(), ) inputs = TensorMode.input_spec() @@ -18,7 +27,7 @@ def test_TensorMode_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TensorMode_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TensorMode.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py index 79af3b5940..31d68631ca 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py +++ b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py @@ -6,10 +6,13 @@ def test_TrackDensityMap_inputs(): input_map = dict( data_dims=dict(), - in_file=dict(mandatory=True, ), + in_file=dict( + mandatory=True, + usedefault=True, + ), out_filename=dict(usedefault=True, ), points_space=dict(usedefault=True, ), - reference=dict(), + reference=dict(usedefault=True, ), voxel_dims=dict(), ) inputs = TrackDensityMap.input_spec() @@ -18,7 +21,7 @@ def test_TrackDensityMap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackDensityMap_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TrackDensityMap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_AffScalarVol.py b/nipype/interfaces/dtitk/tests/test_auto_AffScalarVol.py index 5f9262d788..ef9cd8ceab 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_AffScalarVol.py +++ b/nipype/interfaces/dtitk/tests/test_auto_AffScalarVol.py @@ -21,6 +21,7 @@ def test_AffScalarVol_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), interpolation=dict( argstr='-interp %s', @@ -31,13 +32,16 @@ def test_AffScalarVol_inputs(): keep_extension=True, name_source='in_file', name_template='%s_affxfmd', + usedefault=True, ), target=dict( argstr='-target %s', + usedefault=True, xor=['transform'], ), transform=dict( argstr='-trans %s', + usedefault=True, xor=['target', 'translation', 'euler', 'deformation'], ), translation=dict( @@ -51,7 +55,7 @@ def test_AffScalarVol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AffScalarVol_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = AffScalarVol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_AffSymTensor3DVol.py b/nipype/interfaces/dtitk/tests/test_auto_AffSymTensor3DVol.py index 6d7abc852a..83077db6fd 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_AffSymTensor3DVol.py +++ b/nipype/interfaces/dtitk/tests/test_auto_AffSymTensor3DVol.py @@ -21,6 +21,7 @@ def test_AffSymTensor3DVol_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), interpolation=dict( argstr='-interp %s', @@ -31,6 +32,7 @@ def test_AffSymTensor3DVol_inputs(): keep_extension=True, name_source='in_file', name_template='%s_affxfmd', + usedefault=True, ), reorient=dict( argstr='-reorient %s', @@ -38,10 +40,12 @@ def test_AffSymTensor3DVol_inputs(): ), target=dict( argstr='-target %s', + usedefault=True, xor=['transform'], ), transform=dict( argstr='-trans %s', + usedefault=True, xor=['target', 'translation', 'euler', 'deformation'], ), translation=dict( @@ -55,7 +59,7 @@ def test_AffSymTensor3DVol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AffSymTensor3DVol_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = AffSymTensor3DVol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_Affine.py b/nipype/interfaces/dtitk/tests/test_auto_Affine.py index 78d2e6f011..2631304823 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_Affine.py +++ b/nipype/interfaces/dtitk/tests/test_auto_Affine.py @@ -15,6 +15,7 @@ def test_Affine_inputs(): copyfile=False, mandatory=True, position=0, + usedefault=True, ), ftol=dict( argstr='%g', @@ -26,12 +27,14 @@ def test_Affine_inputs(): argstr='%s', copyfile=True, position=5, + usedefault=True, ), moving_file=dict( argstr='%s', copyfile=False, mandatory=True, position=1, + usedefault=True, ), sampling_xyz=dict( argstr='%g %g %g', @@ -53,8 +56,8 @@ def test_Affine_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Affine_outputs(): output_map = dict( - out_file=dict(), - out_file_xfm=dict(), + out_file=dict(usedefault=True, ), + out_file_xfm=dict(usedefault=True, ), ) outputs = Affine.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_AffineTask.py b/nipype/interfaces/dtitk/tests/test_auto_AffineTask.py index 5f3b43153a..5737bb29a7 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_AffineTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_AffineTask.py @@ -15,6 +15,7 @@ def test_AffineTask_inputs(): copyfile=False, mandatory=True, position=0, + usedefault=True, ), ftol=dict( argstr='%g', @@ -26,12 +27,14 @@ def test_AffineTask_inputs(): argstr='%s', copyfile=True, position=5, + usedefault=True, ), moving_file=dict( argstr='%s', copyfile=False, mandatory=True, position=1, + usedefault=True, ), sampling_xyz=dict( argstr='%g %g %g', @@ -53,8 +56,8 @@ def test_AffineTask_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_AffineTask_outputs(): output_map = dict( - out_file=dict(), - out_file_xfm=dict(), + out_file=dict(usedefault=True, ), + out_file_xfm=dict(usedefault=True, ), ) outputs = AffineTask.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_BinThresh.py b/nipype/interfaces/dtitk/tests/test_auto_BinThresh.py index cbd4efccb2..c63046d31a 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_BinThresh.py +++ b/nipype/interfaces/dtitk/tests/test_auto_BinThresh.py @@ -14,6 +14,7 @@ def test_BinThresh_inputs(): argstr='%s', mandatory=True, position=0, + usedefault=True, ), inside_value=dict( argstr='%g', @@ -33,6 +34,7 @@ def test_BinThresh_inputs(): name_source='in_file', name_template='%s_thrbin', position=1, + usedefault=True, ), outside_value=dict( argstr='%g', @@ -53,7 +55,7 @@ def test_BinThresh_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinThresh_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = BinThresh.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_BinThreshTask.py b/nipype/interfaces/dtitk/tests/test_auto_BinThreshTask.py index dcd396abe2..c76c9653a7 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_BinThreshTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_BinThreshTask.py @@ -14,6 +14,7 @@ def test_BinThreshTask_inputs(): argstr='%s', mandatory=True, position=0, + usedefault=True, ), inside_value=dict( argstr='%g', @@ -33,6 +34,7 @@ def test_BinThreshTask_inputs(): name_source='in_file', name_template='%s_thrbin', position=1, + usedefault=True, ), outside_value=dict( argstr='%g', @@ -53,7 +55,7 @@ def test_BinThreshTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinThreshTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = BinThreshTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_ComposeXfm.py b/nipype/interfaces/dtitk/tests/test_auto_ComposeXfm.py index 09fcdc186e..bd62da2e94 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_ComposeXfm.py +++ b/nipype/interfaces/dtitk/tests/test_auto_ComposeXfm.py @@ -13,14 +13,17 @@ def test_ComposeXfm_inputs(): in_aff=dict( argstr='-aff %s', mandatory=True, + usedefault=True, ), in_df=dict( argstr='-df %s', mandatory=True, + usedefault=True, ), out_file=dict( argstr='-out %s', genfile=True, + usedefault=True, ), ) inputs = ComposeXfm.input_spec() @@ -29,7 +32,7 @@ def test_ComposeXfm_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComposeXfm_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ComposeXfm.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_ComposeXfmTask.py b/nipype/interfaces/dtitk/tests/test_auto_ComposeXfmTask.py index 99c6f6d340..2f552d4171 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_ComposeXfmTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_ComposeXfmTask.py @@ -13,14 +13,17 @@ def test_ComposeXfmTask_inputs(): in_aff=dict( argstr='-aff %s', mandatory=True, + usedefault=True, ), in_df=dict( argstr='-df %s', mandatory=True, + usedefault=True, ), out_file=dict( argstr='-out %s', genfile=True, + usedefault=True, ), ) inputs = ComposeXfmTask.input_spec() @@ -29,7 +32,7 @@ def test_ComposeXfmTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComposeXfmTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ComposeXfmTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_Diffeo.py b/nipype/interfaces/dtitk/tests/test_auto_Diffeo.py index ad532bd631..698ede9270 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_Diffeo.py +++ b/nipype/interfaces/dtitk/tests/test_auto_Diffeo.py @@ -13,6 +13,7 @@ def test_Diffeo_inputs(): fixed_file=dict( argstr='%s', position=0, + usedefault=True, ), ftol=dict( argstr='%g', @@ -29,11 +30,13 @@ def test_Diffeo_inputs(): mask_file=dict( argstr='%s', position=2, + usedefault=True, ), moving_file=dict( argstr='%s', copyfile=False, position=1, + usedefault=True, ), n_iters=dict( argstr='%d', @@ -49,8 +52,8 @@ def test_Diffeo_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Diffeo_outputs(): output_map = dict( - out_file=dict(), - out_file_xfm=dict(), + out_file=dict(usedefault=True, ), + out_file_xfm=dict(usedefault=True, ), ) outputs = Diffeo.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_DiffeoScalarVol.py b/nipype/interfaces/dtitk/tests/test_auto_DiffeoScalarVol.py index 7d1305d384..925943ede4 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_DiffeoScalarVol.py +++ b/nipype/interfaces/dtitk/tests/test_auto_DiffeoScalarVol.py @@ -14,6 +14,7 @@ def test_DiffeoScalarVol_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), interpolation=dict( argstr='-interp %s', @@ -24,15 +25,18 @@ def test_DiffeoScalarVol_inputs(): keep_extension=True, name_source='in_file', name_template='%s_diffeoxfmd', + usedefault=True, ), resampling_type=dict(argstr='-type %s', ), target=dict( argstr='-target %s', + usedefault=True, xor=['voxel_size'], ), transform=dict( argstr='-trans %s', mandatory=True, + usedefault=True, ), voxel_size=dict( argstr='-vsize %g %g %g', @@ -45,7 +49,7 @@ def test_DiffeoScalarVol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DiffeoScalarVol_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = DiffeoScalarVol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_DiffeoSymTensor3DVol.py b/nipype/interfaces/dtitk/tests/test_auto_DiffeoSymTensor3DVol.py index b934c56d2b..a73c6236ed 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_DiffeoSymTensor3DVol.py +++ b/nipype/interfaces/dtitk/tests/test_auto_DiffeoSymTensor3DVol.py @@ -18,6 +18,7 @@ def test_DiffeoSymTensor3DVol_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), interpolation=dict( argstr='-interp %s', @@ -28,6 +29,7 @@ def test_DiffeoSymTensor3DVol_inputs(): keep_extension=True, name_source='in_file', name_template='%s_diffeoxfmd', + usedefault=True, ), reorient=dict( argstr='-reorient %s', @@ -36,11 +38,13 @@ def test_DiffeoSymTensor3DVol_inputs(): resampling_type=dict(argstr='-type %s', ), target=dict( argstr='-target %s', + usedefault=True, xor=['voxel_size'], ), transform=dict( argstr='-trans %s', mandatory=True, + usedefault=True, ), voxel_size=dict( argstr='-vsize %g %g %g', @@ -53,7 +57,7 @@ def test_DiffeoSymTensor3DVol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DiffeoSymTensor3DVol_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = DiffeoSymTensor3DVol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_DiffeoTask.py b/nipype/interfaces/dtitk/tests/test_auto_DiffeoTask.py index 5aea665d4c..d3b5bc813d 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_DiffeoTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_DiffeoTask.py @@ -13,6 +13,7 @@ def test_DiffeoTask_inputs(): fixed_file=dict( argstr='%s', position=0, + usedefault=True, ), ftol=dict( argstr='%g', @@ -29,11 +30,13 @@ def test_DiffeoTask_inputs(): mask_file=dict( argstr='%s', position=2, + usedefault=True, ), moving_file=dict( argstr='%s', copyfile=False, position=1, + usedefault=True, ), n_iters=dict( argstr='%d', @@ -49,8 +52,8 @@ def test_DiffeoTask_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DiffeoTask_outputs(): output_map = dict( - out_file=dict(), - out_file_xfm=dict(), + out_file=dict(usedefault=True, ), + out_file_xfm=dict(usedefault=True, ), ) outputs = DiffeoTask.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_Rigid.py b/nipype/interfaces/dtitk/tests/test_auto_Rigid.py index ecb7c2d33b..48e8d00138 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_Rigid.py +++ b/nipype/interfaces/dtitk/tests/test_auto_Rigid.py @@ -15,6 +15,7 @@ def test_Rigid_inputs(): copyfile=False, mandatory=True, position=0, + usedefault=True, ), ftol=dict( argstr='%g', @@ -26,12 +27,14 @@ def test_Rigid_inputs(): argstr='%s', copyfile=True, position=5, + usedefault=True, ), moving_file=dict( argstr='%s', copyfile=False, mandatory=True, position=1, + usedefault=True, ), sampling_xyz=dict( argstr='%g %g %g', @@ -53,8 +56,8 @@ def test_Rigid_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Rigid_outputs(): output_map = dict( - out_file=dict(), - out_file_xfm=dict(), + out_file=dict(usedefault=True, ), + out_file_xfm=dict(usedefault=True, ), ) outputs = Rigid.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_RigidTask.py b/nipype/interfaces/dtitk/tests/test_auto_RigidTask.py index c627fda741..277c906fb7 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_RigidTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_RigidTask.py @@ -15,6 +15,7 @@ def test_RigidTask_inputs(): copyfile=False, mandatory=True, position=0, + usedefault=True, ), ftol=dict( argstr='%g', @@ -26,12 +27,14 @@ def test_RigidTask_inputs(): argstr='%s', copyfile=True, position=5, + usedefault=True, ), moving_file=dict( argstr='%s', copyfile=False, mandatory=True, position=1, + usedefault=True, ), sampling_xyz=dict( argstr='%g %g %g', @@ -53,8 +56,8 @@ def test_RigidTask_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RigidTask_outputs(): output_map = dict( - out_file=dict(), - out_file_xfm=dict(), + out_file=dict(usedefault=True, ), + out_file_xfm=dict(usedefault=True, ), ) outputs = RigidTask.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSp.py b/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSp.py index 3574906455..387de8ca89 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSp.py +++ b/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSp.py @@ -13,6 +13,7 @@ def test_SVAdjustVoxSp_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), origin=dict( argstr='-origin %g %g %g', @@ -23,9 +24,11 @@ def test_SVAdjustVoxSp_inputs(): keep_extension=True, name_source='in_file', name_template='%s_avs', + usedefault=True, ), target_file=dict( argstr='-target %s', + usedefault=True, xor=['voxel_size', 'origin'], ), voxel_size=dict( @@ -39,7 +42,7 @@ def test_SVAdjustVoxSp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SVAdjustVoxSp_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = SVAdjustVoxSp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSpTask.py b/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSpTask.py index 40a7592c19..acd986d585 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSpTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSpTask.py @@ -13,6 +13,7 @@ def test_SVAdjustVoxSpTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), origin=dict( argstr='-origin %g %g %g', @@ -23,9 +24,11 @@ def test_SVAdjustVoxSpTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_avs', + usedefault=True, ), target_file=dict( argstr='-target %s', + usedefault=True, xor=['voxel_size', 'origin'], ), voxel_size=dict( @@ -39,7 +42,7 @@ def test_SVAdjustVoxSpTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SVAdjustVoxSpTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = SVAdjustVoxSpTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_SVResample.py b/nipype/interfaces/dtitk/tests/test_auto_SVResample.py index 91ca638f22..d37306197c 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_SVResample.py +++ b/nipype/interfaces/dtitk/tests/test_auto_SVResample.py @@ -18,6 +18,7 @@ def test_SVResample_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), origin=dict( argstr='-origin %g %g %g', @@ -28,9 +29,11 @@ def test_SVResample_inputs(): keep_extension=True, name_source='in_file', name_template='%s_resampled', + usedefault=True, ), target_file=dict( argstr='-target %s', + usedefault=True, xor=['array_size', 'voxel_size', 'origin'], ), voxel_size=dict( @@ -44,7 +47,7 @@ def test_SVResample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SVResample_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = SVResample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_SVResampleTask.py b/nipype/interfaces/dtitk/tests/test_auto_SVResampleTask.py index 8a7574bfd8..65200bf04c 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_SVResampleTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_SVResampleTask.py @@ -18,6 +18,7 @@ def test_SVResampleTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), origin=dict( argstr='-origin %g %g %g', @@ -28,9 +29,11 @@ def test_SVResampleTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_resampled', + usedefault=True, ), target_file=dict( argstr='-target %s', + usedefault=True, xor=['array_size', 'voxel_size', 'origin'], ), voxel_size=dict( @@ -44,7 +47,7 @@ def test_SVResampleTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SVResampleTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = SVResampleTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustOriginTask.py b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustOriginTask.py index bda9128369..0c9a1d0d90 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustOriginTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustOriginTask.py @@ -13,6 +13,7 @@ def test_TVAdjustOriginTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), origin=dict( argstr='-origin %g %g %g', @@ -23,9 +24,11 @@ def test_TVAdjustOriginTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_avs', + usedefault=True, ), target_file=dict( argstr='-target %s', + usedefault=True, xor=['voxel_size', 'origin'], ), voxel_size=dict( @@ -39,7 +42,7 @@ def test_TVAdjustOriginTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVAdjustOriginTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TVAdjustOriginTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSp.py b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSp.py index b8ce9039d5..9912f3c1a7 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSp.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSp.py @@ -13,6 +13,7 @@ def test_TVAdjustVoxSp_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), origin=dict( argstr='-origin %g %g %g', @@ -23,9 +24,11 @@ def test_TVAdjustVoxSp_inputs(): keep_extension=True, name_source='in_file', name_template='%s_avs', + usedefault=True, ), target_file=dict( argstr='-target %s', + usedefault=True, xor=['voxel_size', 'origin'], ), voxel_size=dict( @@ -39,7 +42,7 @@ def test_TVAdjustVoxSp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVAdjustVoxSp_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TVAdjustVoxSp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSpTask.py b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSpTask.py index e9ef8137dc..0cdc3871a0 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSpTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSpTask.py @@ -13,6 +13,7 @@ def test_TVAdjustVoxSpTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), origin=dict( argstr='-origin %g %g %g', @@ -23,9 +24,11 @@ def test_TVAdjustVoxSpTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_avs', + usedefault=True, ), target_file=dict( argstr='-target %s', + usedefault=True, xor=['voxel_size', 'origin'], ), voxel_size=dict( @@ -39,7 +42,7 @@ def test_TVAdjustVoxSpTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVAdjustVoxSpTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TVAdjustVoxSpTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVResample.py b/nipype/interfaces/dtitk/tests/test_auto_TVResample.py index aefafc6430..f706ba9ff6 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVResample.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVResample.py @@ -18,6 +18,7 @@ def test_TVResample_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), interpolation=dict(argstr='-interp %s', ), origin=dict( @@ -29,9 +30,11 @@ def test_TVResample_inputs(): keep_extension=True, name_source='in_file', name_template='%s_resampled', + usedefault=True, ), target_file=dict( argstr='-target %s', + usedefault=True, xor=['array_size', 'voxel_size', 'origin'], ), voxel_size=dict( @@ -45,7 +48,7 @@ def test_TVResample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVResample_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TVResample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVResampleTask.py b/nipype/interfaces/dtitk/tests/test_auto_TVResampleTask.py index b3c70bb729..f1c0193a4e 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVResampleTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVResampleTask.py @@ -18,6 +18,7 @@ def test_TVResampleTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), interpolation=dict(argstr='-interp %s', ), origin=dict( @@ -29,9 +30,11 @@ def test_TVResampleTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_resampled', + usedefault=True, ), target_file=dict( argstr='-target %s', + usedefault=True, xor=['array_size', 'voxel_size', 'origin'], ), voxel_size=dict( @@ -45,7 +48,7 @@ def test_TVResampleTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVResampleTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TVResampleTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVtool.py b/nipype/interfaces/dtitk/tests/test_auto_TVtool.py index 2267228631..c13dbcb967 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVtool.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVtool.py @@ -13,11 +13,13 @@ def test_TVtool_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), in_flag=dict(argstr='-%s', ), out_file=dict( argstr='-out %s', genfile=True, + usedefault=True, ), ) inputs = TVtool.input_spec() @@ -26,7 +28,7 @@ def test_TVtool_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVtool_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TVtool.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVtoolTask.py b/nipype/interfaces/dtitk/tests/test_auto_TVtoolTask.py index 252d7c9d0a..2e5547f5a0 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVtoolTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVtoolTask.py @@ -13,11 +13,13 @@ def test_TVtoolTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), in_flag=dict(argstr='-%s', ), out_file=dict( argstr='-out %s', genfile=True, + usedefault=True, ), ) inputs = TVtoolTask.input_spec() @@ -26,7 +28,7 @@ def test_TVtoolTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVtoolTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TVtoolTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_affScalarVolTask.py b/nipype/interfaces/dtitk/tests/test_auto_affScalarVolTask.py index 72330737b6..958818eeb9 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_affScalarVolTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_affScalarVolTask.py @@ -21,6 +21,7 @@ def test_affScalarVolTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), interpolation=dict( argstr='-interp %s', @@ -31,13 +32,16 @@ def test_affScalarVolTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_affxfmd', + usedefault=True, ), target=dict( argstr='-target %s', + usedefault=True, xor=['transform'], ), transform=dict( argstr='-trans %s', + usedefault=True, xor=['target', 'translation', 'euler', 'deformation'], ), translation=dict( @@ -51,7 +55,7 @@ def test_affScalarVolTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_affScalarVolTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = affScalarVolTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_affSymTensor3DVolTask.py b/nipype/interfaces/dtitk/tests/test_auto_affSymTensor3DVolTask.py index da8fae25cc..746304d997 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_affSymTensor3DVolTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_affSymTensor3DVolTask.py @@ -21,6 +21,7 @@ def test_affSymTensor3DVolTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), interpolation=dict( argstr='-interp %s', @@ -31,6 +32,7 @@ def test_affSymTensor3DVolTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_affxfmd', + usedefault=True, ), reorient=dict( argstr='-reorient %s', @@ -38,10 +40,12 @@ def test_affSymTensor3DVolTask_inputs(): ), target=dict( argstr='-target %s', + usedefault=True, xor=['transform'], ), transform=dict( argstr='-trans %s', + usedefault=True, xor=['target', 'translation', 'euler', 'deformation'], ), translation=dict( @@ -55,7 +59,7 @@ def test_affSymTensor3DVolTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_affSymTensor3DVolTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = affSymTensor3DVolTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_diffeoScalarVolTask.py b/nipype/interfaces/dtitk/tests/test_auto_diffeoScalarVolTask.py index 10965b7077..d6786572a3 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_diffeoScalarVolTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_diffeoScalarVolTask.py @@ -14,6 +14,7 @@ def test_diffeoScalarVolTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), interpolation=dict( argstr='-interp %s', @@ -24,15 +25,18 @@ def test_diffeoScalarVolTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_diffeoxfmd', + usedefault=True, ), resampling_type=dict(argstr='-type %s', ), target=dict( argstr='-target %s', + usedefault=True, xor=['voxel_size'], ), transform=dict( argstr='-trans %s', mandatory=True, + usedefault=True, ), voxel_size=dict( argstr='-vsize %g %g %g', @@ -45,7 +49,7 @@ def test_diffeoScalarVolTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_diffeoScalarVolTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = diffeoScalarVolTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_diffeoSymTensor3DVolTask.py b/nipype/interfaces/dtitk/tests/test_auto_diffeoSymTensor3DVolTask.py index 52112735b1..b99bd69a4a 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_diffeoSymTensor3DVolTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_diffeoSymTensor3DVolTask.py @@ -18,6 +18,7 @@ def test_diffeoSymTensor3DVolTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), interpolation=dict( argstr='-interp %s', @@ -28,6 +29,7 @@ def test_diffeoSymTensor3DVolTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_diffeoxfmd', + usedefault=True, ), reorient=dict( argstr='-reorient %s', @@ -36,11 +38,13 @@ def test_diffeoSymTensor3DVolTask_inputs(): resampling_type=dict(argstr='-type %s', ), target=dict( argstr='-target %s', + usedefault=True, xor=['voxel_size'], ), transform=dict( argstr='-trans %s', mandatory=True, + usedefault=True, ), voxel_size=dict( argstr='-vsize %g %g %g', @@ -53,7 +57,7 @@ def test_diffeoSymTensor3DVolTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_diffeoSymTensor3DVolTask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = diffeoSymTensor3DVolTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py index f05821d9c1..d2d69581bf 100644 --- a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py @@ -18,7 +18,10 @@ def test_AnalyzeWarp_inputs(): argstr='-jacmat %s', usedefault=True, ), - moving_image=dict(argstr='-in %s', ), + moving_image=dict( + argstr='-in %s', + usedefault=True, + ), num_threads=dict( argstr='-threads %01d', nohash=True, @@ -37,6 +40,7 @@ def test_AnalyzeWarp_inputs(): transform_file=dict( argstr='-tp %s', mandatory=True, + usedefault=True, ), ) inputs = AnalyzeWarp.input_spec() @@ -46,9 +50,9 @@ def test_AnalyzeWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_AnalyzeWarp_outputs(): output_map = dict( - disp_field=dict(), - jacdet_map=dict(), - jacmat_map=dict(), + disp_field=dict(usedefault=True, ), + jacdet_map=dict(usedefault=True, ), + jacmat_map=dict(usedefault=True, ), ) outputs = AnalyzeWarp.output_spec() diff --git a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py index 16f2b54079..b199bbeca3 100644 --- a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py @@ -13,6 +13,7 @@ def test_ApplyWarp_inputs(): moving_image=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), num_threads=dict( argstr='-threads %01d', @@ -27,6 +28,7 @@ def test_ApplyWarp_inputs(): transform_file=dict( argstr='-tp %s', mandatory=True, + usedefault=True, ), ) inputs = ApplyWarp.input_spec() @@ -35,7 +37,7 @@ def test_ApplyWarp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyWarp_outputs(): - output_map = dict(warped_file=dict(), ) + output_map = dict(warped_file=dict(usedefault=True, ), ) outputs = ApplyWarp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py index ef227da7f8..b6dba08d2e 100644 --- a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py +++ b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py @@ -9,11 +9,14 @@ def test_EditTransform_inputs(): argstr='FinalBSplineInterpolationOrder', usedefault=True, ), - output_file=dict(), + output_file=dict(usedefault=True, ), output_format=dict(argstr='ResultImageFormat', ), output_type=dict(argstr='ResultImagePixelType', ), - reference_image=dict(), - transform_file=dict(mandatory=True, ), + reference_image=dict(usedefault=True, ), + transform_file=dict( + mandatory=True, + usedefault=True, + ), ) inputs = EditTransform.input_spec() @@ -21,7 +24,7 @@ def test_EditTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EditTransform_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = EditTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py index c93a0526c1..f5115e1e04 100644 --- a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py @@ -23,10 +23,12 @@ def test_PointsWarp_inputs(): points_file=dict( argstr='-def %s', mandatory=True, + usedefault=True, ), transform_file=dict( argstr='-tp %s', mandatory=True, + usedefault=True, ), ) inputs = PointsWarp.input_spec() @@ -35,7 +37,7 @@ def test_PointsWarp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PointsWarp_outputs(): - output_map = dict(warped_file=dict(), ) + output_map = dict(warped_file=dict(usedefault=True, ), ) outputs = PointsWarp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/elastix/tests/test_auto_Registration.py b/nipype/interfaces/elastix/tests/test_auto_Registration.py index 4e774ab036..7c63e433cc 100644 --- a/nipype/interfaces/elastix/tests/test_auto_Registration.py +++ b/nipype/interfaces/elastix/tests/test_auto_Registration.py @@ -13,14 +13,25 @@ def test_Registration_inputs(): fixed_image=dict( argstr='-f %s', mandatory=True, + usedefault=True, + ), + fixed_mask=dict( + argstr='-fMask %s', + usedefault=True, + ), + initial_transform=dict( + argstr='-t0 %s', + usedefault=True, ), - fixed_mask=dict(argstr='-fMask %s', ), - initial_transform=dict(argstr='-t0 %s', ), moving_image=dict( argstr='-m %s', mandatory=True, + usedefault=True, + ), + moving_mask=dict( + argstr='-mMask %s', + usedefault=True, ), - moving_mask=dict(argstr='-mMask %s', ), num_threads=dict( argstr='-threads %01d', nohash=True, @@ -44,7 +55,7 @@ def test_Registration_inputs(): def test_Registration_outputs(): output_map = dict( transform=dict(), - warped_file=dict(), + warped_file=dict(usedefault=True, ), warped_files=dict(), warped_files_flags=dict(), ) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py b/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py index ed32693df5..0aac5b03fb 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py @@ -15,17 +15,19 @@ def test_AddXFormToHeader_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), out_file=dict( argstr='%s', position=-1, usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), transform=dict( argstr='%s', mandatory=True, position=-3, + usedefault=True, ), verbose=dict(argstr='-v', ), ) @@ -35,7 +37,7 @@ def test_AddXFormToHeader_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AddXFormToHeader_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = AddXFormToHeader.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py index fc5bc39b6f..7388dc8e4f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py @@ -7,36 +7,70 @@ def test_Aparc2Aseg_inputs(): input_map = dict( a2009s=dict(argstr='--a2009s', ), args=dict(argstr='%s', ), - aseg=dict(argstr='--aseg %s', ), + aseg=dict( + argstr='--aseg %s', + usedefault=True, + ), copy_inputs=dict(), - ctxseg=dict(argstr='--ctxseg %s', ), + ctxseg=dict( + argstr='--ctxseg %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, ), - filled=dict(), + filled=dict(usedefault=True, ), hypo_wm=dict(argstr='--hypo-as-wm', ), label_wm=dict(argstr='--labelwm', ), - lh_annotation=dict(mandatory=True, ), - lh_pial=dict(mandatory=True, ), - lh_ribbon=dict(mandatory=True, ), - lh_white=dict(mandatory=True, ), + lh_annotation=dict( + mandatory=True, + usedefault=True, + ), + lh_pial=dict( + mandatory=True, + usedefault=True, + ), + lh_ribbon=dict( + mandatory=True, + usedefault=True, + ), + lh_white=dict( + mandatory=True, + usedefault=True, + ), out_file=dict( argstr='--o %s', mandatory=True, + usedefault=True, + ), + rh_annotation=dict( + mandatory=True, + usedefault=True, + ), + rh_pial=dict( + mandatory=True, + usedefault=True, + ), + rh_ribbon=dict( + mandatory=True, + usedefault=True, + ), + rh_white=dict( + mandatory=True, + usedefault=True, + ), + ribbon=dict( + mandatory=True, + usedefault=True, ), - rh_annotation=dict(mandatory=True, ), - rh_pial=dict(mandatory=True, ), - rh_ribbon=dict(mandatory=True, ), - rh_white=dict(mandatory=True, ), - ribbon=dict(mandatory=True, ), rip_unknown=dict(argstr='--rip-unknown', ), subject_id=dict( argstr='--s %s', mandatory=True, usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), volmask=dict(argstr='--volmask', ), ) inputs = Aparc2Aseg.input_spec() @@ -45,7 +79,11 @@ def test_Aparc2Aseg_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Aparc2Aseg_outputs(): - output_map = dict(out_file=dict(argstr='%s', ), ) + output_map = dict( + out_file=dict( + argstr='%s', + usedefault=True, + ), ) outputs = Aparc2Aseg.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py index 7044fdde2f..7e535391fb 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py @@ -13,12 +13,14 @@ def test_Apas2Aseg_inputs(): in_file=dict( argstr='--i %s', mandatory=True, + usedefault=True, ), out_file=dict( argstr='--o %s', mandatory=True, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = Apas2Aseg.input_spec() @@ -26,7 +28,11 @@ def test_Apas2Aseg_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Apas2Aseg_outputs(): - output_map = dict(out_file=dict(argstr='%s', ), ) + output_map = dict( + out_file=dict( + argstr='%s', + usedefault=True, + ), ) outputs = Apas2Aseg.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py index 69f56d7dde..6d71752071 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py @@ -14,6 +14,7 @@ def test_ApplyMask_inputs(): argstr='%s', mandatory=True, position=-3, + usedefault=True, ), invert_xfm=dict(argstr='-invert', ), keep_mask_deletion_edits=dict(argstr='-keep_mask_deletion_edits', ), @@ -21,6 +22,7 @@ def test_ApplyMask_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), mask_thresh=dict(argstr='-T %.4f', ), out_file=dict( @@ -30,13 +32,23 @@ def test_ApplyMask_inputs(): name_source=['in_file'], name_template='%s_masked', position=-1, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), transfer=dict(argstr='-transfer %d', ), use_abs=dict(argstr='-abs', ), - xfm_file=dict(argstr='-xform %s', ), - xfm_source=dict(argstr='-lta_src %s', ), - xfm_target=dict(argstr='-lta_dst %s', ), + xfm_file=dict( + argstr='-xform %s', + usedefault=True, + ), + xfm_source=dict( + argstr='-lta_src %s', + usedefault=True, + ), + xfm_target=dict( + argstr='-lta_dst %s', + usedefault=True, + ), ) inputs = ApplyMask.input_spec() @@ -44,7 +56,7 @@ def test_ApplyMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyMask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ApplyMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py index c9e8f85904..cb62cf70b7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py @@ -19,6 +19,7 @@ def test_ApplyVolTransform_inputs(): fsl_reg_file=dict( argstr='--fsl %s', mandatory=True, + usedefault=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), ), @@ -31,16 +32,21 @@ def test_ApplyVolTransform_inputs(): lta_file=dict( argstr='--lta %s', mandatory=True, + usedefault=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), ), lta_inv_file=dict( argstr='--lta-inv %s', mandatory=True, + usedefault=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), ), - m3z_file=dict(argstr='--m3z %s', ), + m3z_file=dict( + argstr='--m3z %s', + usedefault=True, + ), mni_152_reg=dict( argstr='--regheader', mandatory=True, @@ -55,6 +61,7 @@ def test_ApplyVolTransform_inputs(): reg_file=dict( argstr='--reg %s', mandatory=True, + usedefault=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), ), @@ -68,6 +75,7 @@ def test_ApplyVolTransform_inputs(): argstr='--mov %s', copyfile=False, mandatory=True, + usedefault=True, ), subject=dict( argstr='--s %s', @@ -75,7 +83,7 @@ def test_ApplyVolTransform_inputs(): xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), tal=dict( argstr='--tal', mandatory=True, @@ -85,15 +93,18 @@ def test_ApplyVolTransform_inputs(): target_file=dict( argstr='--targ %s', mandatory=True, + usedefault=True, xor=('target_file', 'tal', 'fs_target'), ), transformed_file=dict( argstr='--o %s', genfile=True, + usedefault=True, ), xfm_reg_file=dict( argstr='--xfm %s', mandatory=True, + usedefault=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), ), @@ -104,7 +115,7 @@ def test_ApplyVolTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyVolTransform_outputs(): - output_map = dict(transformed_file=dict(), ) + output_map = dict(transformed_file=dict(usedefault=True, ), ) outputs = ApplyVolTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py index 93db55cd30..7b7a6b9229 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py @@ -13,6 +13,7 @@ def test_Binarize_inputs(): binary_file=dict( argstr='--o %s', genfile=True, + usedefault=True, ), count_file=dict(argstr='--count %s', ), dilate=dict(argstr='--dilate %d', ), @@ -27,16 +28,23 @@ def test_Binarize_inputs(): argstr='--i %s', copyfile=False, mandatory=True, + usedefault=True, ), invert=dict(argstr='--inv', ), - mask_file=dict(argstr='--mask maskvol', ), + mask_file=dict( + argstr='--mask maskvol', + usedefault=True, + ), mask_thresh=dict(argstr='--mask-thresh %f', ), match=dict(argstr='--match %d...', ), max=dict( argstr='--max %f', xor=['wm_ven_csf'], ), - merge_file=dict(argstr='--merge %s', ), + merge_file=dict( + argstr='--merge %s', + usedefault=True, + ), min=dict( argstr='--min %f', xor=['wm_ven_csf'], @@ -44,7 +52,7 @@ def test_Binarize_inputs(): out_type=dict(argstr='', ), rmax=dict(argstr='--rmax %f', ), rmin=dict(argstr='--rmin %f', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ventricles=dict(argstr='--ventricles', ), wm=dict(argstr='--wm', ), wm_ven_csf=dict( @@ -61,8 +69,8 @@ def test_Binarize_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Binarize_outputs(): output_map = dict( - binary_file=dict(), - count_file=dict(), + binary_file=dict(usedefault=True, ), + count_file=dict(usedefault=True, ), ) outputs = Binarize.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py index 1cf35fcedb..9785dd78c1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py @@ -16,9 +16,16 @@ def test_CALabel_inputs(): argstr='%s', mandatory=True, position=-4, + usedefault=True, + ), + in_vol=dict( + argstr='-r %s', + usedefault=True, + ), + intensities=dict( + argstr='-r %s', + usedefault=True, ), - in_vol=dict(argstr='-r %s', ), - intensities=dict(argstr='-r %s', ), label=dict(argstr='-l %s', ), no_big_ventricles=dict(argstr='-nobigventricles', ), num_threads=dict(), @@ -26,19 +33,22 @@ def test_CALabel_inputs(): argstr='%s', mandatory=True, position=-1, + usedefault=True, ), prior=dict(argstr='-prior %.1f', ), relabel_unlikely=dict(argstr='-relabel_unlikely %d %.1f', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), template=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), transform=dict( argstr='%s', mandatory=True, position=-3, + usedefault=True, ), ) inputs = CALabel.input_spec() @@ -47,7 +57,7 @@ def test_CALabel_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CALabel_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = CALabel.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py index 0e8ec025ec..2a13aa8eb9 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py @@ -10,8 +10,12 @@ def test_CANormalize_inputs(): argstr='%s', mandatory=True, position=-3, + usedefault=True, + ), + control_points=dict( + argstr='-c %s', + usedefault=True, ), - control_points=dict(argstr='-c %s', ), environ=dict( nohash=True, usedefault=True, @@ -20,9 +24,16 @@ def test_CANormalize_inputs(): argstr='%s', mandatory=True, position=-4, + usedefault=True, + ), + long_file=dict( + argstr='-long %s', + usedefault=True, + ), + mask=dict( + argstr='-mask %s', + usedefault=True, ), - long_file=dict(argstr='-long %s', ), - mask=dict(argstr='-mask %s', ), out_file=dict( argstr='%s', hash_files=False, @@ -30,12 +41,14 @@ def test_CANormalize_inputs(): name_source=['in_file'], name_template='%s_norm', position=-1, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), transform=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), ) inputs = CANormalize.input_spec() @@ -45,7 +58,7 @@ def test_CANormalize_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CANormalize_outputs(): output_map = dict( - control_points=dict(), + control_points=dict(usedefault=True, ), out_file=dict(), ) outputs = CANormalize.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py b/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py index e3cbf52f10..6425104219 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py @@ -16,6 +16,7 @@ def test_CARegister_inputs(): argstr='%s', mandatory=True, position=-3, + usedefault=True, ), invert_and_save=dict( argstr='-invert-and-save', @@ -23,20 +24,28 @@ def test_CARegister_inputs(): ), l_files=dict(argstr='-l %s', ), levels=dict(argstr='-levels %d', ), - mask=dict(argstr='-mask %s', ), + mask=dict( + argstr='-mask %s', + usedefault=True, + ), no_big_ventricles=dict(argstr='-nobigventricles', ), num_threads=dict(), out_file=dict( argstr='%s', genfile=True, position=-1, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), template=dict( argstr='%s', position=-2, + usedefault=True, + ), + transform=dict( + argstr='-T %s', + usedefault=True, ), - transform=dict(argstr='-T %s', ), ) inputs = CARegister.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py index a7d3ad3bb0..82072d0635 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py @@ -14,6 +14,7 @@ def test_CheckTalairachAlignment_inputs(): argstr='-xfm %s', mandatory=True, position=-1, + usedefault=True, xor=['subject'], ), subject=dict( @@ -22,7 +23,7 @@ def test_CheckTalairachAlignment_inputs(): position=-1, xor=['in_file'], ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), threshold=dict( argstr='-T %.3f', usedefault=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py index e4e8efb718..c7fd82daea 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py @@ -11,6 +11,7 @@ def test_Concatenate_inputs(): concatenated_file=dict( argstr='--o %s', genfile=True, + usedefault=True, ), environ=dict( nohash=True, @@ -22,17 +23,23 @@ def test_Concatenate_inputs(): mandatory=True, ), keep_dtype=dict(argstr='--keep-datatype', ), - mask_file=dict(argstr='--mask %s', ), + mask_file=dict( + argstr='--mask %s', + usedefault=True, + ), max_bonfcor=dict(argstr='--max-bonfcor', ), max_index=dict(argstr='--max-index', ), mean_div_n=dict(argstr='--mean-div-n', ), multiply_by=dict(argstr='--mul %f', ), - multiply_matrix_file=dict(argstr='--mtx %s', ), + multiply_matrix_file=dict( + argstr='--mtx %s', + usedefault=True, + ), paired_stats=dict(argstr='--paired-%s', ), sign=dict(argstr='--%s', ), sort=dict(argstr='--sort', ), stats=dict(argstr='--%s', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), vote=dict(argstr='--vote', ), ) inputs = Concatenate.input_spec() @@ -41,7 +48,7 @@ def test_Concatenate_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Concatenate_outputs(): - output_map = dict(concatenated_file=dict(), ) + output_map = dict(concatenated_file=dict(usedefault=True, ), ) outputs = Concatenate.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py b/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py index 40a465b249..50806c9a5d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py @@ -14,6 +14,7 @@ def test_ConcatenateLTA_inputs(): argstr='%s', mandatory=True, position=-3, + usedefault=True, ), in_lta2=dict( argstr='%s', @@ -30,10 +31,11 @@ def test_ConcatenateLTA_inputs(): name_source=['in_lta1'], name_template='%s_concat', position=-1, + usedefault=True, ), out_type=dict(argstr='-out_type %d', ), subject=dict(argstr='-subject %s', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), tal_source_file=dict( argstr='-tal %s', position=-5, @@ -51,7 +53,7 @@ def test_ConcatenateLTA_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConcatenateLTA_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ConcatenateLTA.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py index 7999001813..a8b530cf5e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py @@ -17,16 +17,28 @@ def test_Contrast_inputs(): argstr='--%s-only', mandatory=True, ), - orig=dict(mandatory=True, ), - rawavg=dict(mandatory=True, ), + orig=dict( + mandatory=True, + usedefault=True, + ), + rawavg=dict( + mandatory=True, + usedefault=True, + ), subject_id=dict( argstr='--s %s', mandatory=True, usedefault=True, ), - subjects_dir=dict(), - thickness=dict(mandatory=True, ), - white=dict(mandatory=True, ), + subjects_dir=dict(usedefault=True, ), + thickness=dict( + mandatory=True, + usedefault=True, + ), + white=dict( + mandatory=True, + usedefault=True, + ), ) inputs = Contrast.input_spec() @@ -35,9 +47,9 @@ def test_Contrast_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Contrast_outputs(): output_map = dict( - out_contrast=dict(), - out_log=dict(), - out_stats=dict(), + out_contrast=dict(usedefault=True, ), + out_log=dict(usedefault=True, ), + out_stats=dict(usedefault=True, ), ) outputs = Contrast.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py b/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py index f29b76df29..9bfad24622 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py @@ -18,10 +18,11 @@ def test_Curvature_inputs(): copyfile=True, mandatory=True, position=-2, + usedefault=True, ), n=dict(argstr='-n', ), save=dict(argstr='-w', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), threshold=dict(argstr='-thresh %.3f', ), ) inputs = Curvature.input_spec() @@ -31,8 +32,8 @@ def test_Curvature_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Curvature_outputs(): output_map = dict( - out_gauss=dict(), - out_mean=dict(), + out_gauss=dict(usedefault=True, ), + out_mean=dict(usedefault=True, ), ) outputs = Curvature.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py b/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py index 19d6a4772e..e42db217a4 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py @@ -11,11 +11,13 @@ def test_CurvatureStats_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), curvfile2=dict( argstr='%s', mandatory=True, position=-1, + usedefault=True, ), environ=dict( nohash=True, @@ -32,6 +34,7 @@ def test_CurvatureStats_inputs(): hash_files=False, name_source=['hemisphere'], name_template='%s.curv.stats', + usedefault=True, ), subject_id=dict( argstr='%s', @@ -39,8 +42,11 @@ def test_CurvatureStats_inputs(): position=-4, usedefault=True, ), - subjects_dir=dict(), - surface=dict(argstr='-F %s', ), + subjects_dir=dict(usedefault=True, ), + surface=dict( + argstr='-F %s', + usedefault=True, + ), values=dict(argstr='-G', ), write=dict(argstr='--writeCurvatureFiles', ), ) @@ -50,7 +56,7 @@ def test_CurvatureStats_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CurvatureStats_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = CurvatureStats.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py index efd53fb773..c4b0f2667f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py @@ -6,9 +6,15 @@ def test_DICOMConvert_inputs(): input_map = dict( args=dict(argstr='%s', ), - base_output_dir=dict(mandatory=True, ), - dicom_dir=dict(mandatory=True, ), - dicom_info=dict(), + base_output_dir=dict( + mandatory=True, + usedefault=True, + ), + dicom_dir=dict( + mandatory=True, + usedefault=True, + ), + dicom_info=dict(usedefault=True, ), environ=dict( nohash=True, usedefault=True, @@ -19,7 +25,7 @@ def test_DICOMConvert_inputs(): seq_list=dict(requires=['dicom_info'], ), subject_dir_template=dict(usedefault=True, ), subject_id=dict(), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = DICOMConvert.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py index e681a03871..2323f7ae24 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py @@ -14,8 +14,12 @@ def test_EMRegister_inputs(): argstr='%s', mandatory=True, position=-3, + usedefault=True, + ), + mask=dict( + argstr='-mask %s', + usedefault=True, ), - mask=dict(argstr='-mask %s', ), nbrspacing=dict(argstr='-uns %d', ), num_threads=dict(), out_file=dict( @@ -25,15 +29,20 @@ def test_EMRegister_inputs(): name_source=['in_file'], name_template='%s_transform.lta', position=-1, + usedefault=True, ), skull=dict(argstr='-skull', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), template=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, + ), + transform=dict( + argstr='-t %s', + usedefault=True, ), - transform=dict(argstr='-t %s', ), ) inputs = EMRegister.input_spec() @@ -41,7 +50,7 @@ def test_EMRegister_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EMRegister_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = EMRegister.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py b/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py index f971f4fab9..c24f977b00 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py @@ -10,6 +10,7 @@ def test_EditWMwithAseg_inputs(): argstr='%s', mandatory=True, position=-3, + usedefault=True, ), environ=dict( nohash=True, @@ -19,19 +20,22 @@ def test_EditWMwithAseg_inputs(): argstr='%s', mandatory=True, position=-4, + usedefault=True, ), keep_in=dict(argstr='-keep-in', ), out_file=dict( argstr='%s', mandatory=True, position=-1, + usedefault=True, ), seg_file=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = EditWMwithAseg.input_spec() @@ -39,7 +43,7 @@ def test_EditWMwithAseg_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EditWMwithAseg_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = EditWMwithAseg.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py b/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py index 996d079b48..3a14dea036 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py @@ -14,8 +14,9 @@ def test_EulerNumber_inputs(): argstr='%s', mandatory=True, position=-1, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = EulerNumber.input_spec() @@ -23,7 +24,7 @@ def test_EulerNumber_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EulerNumber_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = EulerNumber.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py index f3f4896a75..1415471ab3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py @@ -14,12 +14,14 @@ def test_ExtractMainComponent_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), out_file=dict( argstr='%s', name_source='in_file', name_template='%s.maincmp', position=2, + usedefault=True, ), ) inputs = ExtractMainComponent.input_spec() @@ -28,7 +30,7 @@ def test_ExtractMainComponent_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ExtractMainComponent_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ExtractMainComponent.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py index 0546d99006..98fe0664ae 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py @@ -10,7 +10,7 @@ def test_FSCommand_inputs(): nohash=True, usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = FSCommand.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py b/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py index 5b8bca1484..97de836a9e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py @@ -11,7 +11,7 @@ def test_FSCommandOpenMP_inputs(): usedefault=True, ), num_threads=dict(), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = FSCommandOpenMP.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py b/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py index e791bb5976..0df666e23c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py @@ -10,7 +10,7 @@ def test_FSScriptCommand_inputs(): nohash=True, usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = FSScriptCommand.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py index 9e6b1cbc8b..01687c2eff 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py @@ -20,8 +20,9 @@ def test_FitMSParams_inputs(): argstr='%s', genfile=True, position=-1, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), te_list=dict(), tr_list=dict(), xfm_list=dict(), @@ -33,9 +34,9 @@ def test_FitMSParams_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FitMSParams_outputs(): output_map = dict( - pd_image=dict(), - t1_image=dict(), - t2star_image=dict(), + pd_image=dict(usedefault=True, ), + t1_image=dict(usedefault=True, ), + t2star_image=dict(usedefault=True, ), ) outputs = FitMSParams.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py index 8b61823b42..9ef951e5d8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py @@ -17,10 +17,22 @@ def test_FixTopology_inputs(): mandatory=True, position=-1, ), - in_brain=dict(mandatory=True, ), - in_inflated=dict(mandatory=True, ), - in_orig=dict(mandatory=True, ), - in_wm=dict(mandatory=True, ), + in_brain=dict( + mandatory=True, + usedefault=True, + ), + in_inflated=dict( + mandatory=True, + usedefault=True, + ), + in_orig=dict( + mandatory=True, + usedefault=True, + ), + in_wm=dict( + mandatory=True, + usedefault=True, + ), mgz=dict(argstr='-mgz', ), seed=dict(argstr='-seed %d', ), sphere=dict(argstr='-sphere %s', ), @@ -30,7 +42,7 @@ def test_FixTopology_inputs(): position=-2, usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = FixTopology.input_spec() @@ -38,7 +50,7 @@ def test_FixTopology_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FixTopology_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = FixTopology.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py b/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py index 8608444fc8..0c1dd31a66 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py @@ -25,12 +25,13 @@ def test_FuseSegmentations_inputs(): out_file=dict( mandatory=True, position=-1, + usedefault=True, ), subject_id=dict( argstr='%s', position=-3, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), timepoints=dict( argstr='%s', mandatory=True, @@ -43,7 +44,7 @@ def test_FuseSegmentations_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FuseSegmentations_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = FuseSegmentations.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py index 828bbfab03..de629db007 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py @@ -19,6 +19,7 @@ def test_GLMFit_inputs(): debug=dict(argstr='--debug', ), design=dict( argstr='--X %s', + usedefault=True, xor=('fsgd', 'design', 'one_sample'), ), diag=dict(argstr='--diag %d', ), @@ -33,9 +34,13 @@ def test_GLMFit_inputs(): ), fixed_fx_dof_file=dict( argstr='--ffxdofdat %d', + usedefault=True, xor=['fixed_fx_dof'], ), - fixed_fx_var=dict(argstr='--yffxvar %s', ), + fixed_fx_var=dict( + argstr='--yffxvar %s', + usedefault=True, + ), force_perm=dict(argstr='--perm-force', ), fsgd=dict( argstr='--fsgd %s %s', @@ -51,13 +56,18 @@ def test_GLMFit_inputs(): argstr='--y %s', copyfile=False, mandatory=True, + usedefault=True, ), invert_mask=dict(argstr='--mask-inv', ), label_file=dict( argstr='--label %s', + usedefault=True, xor=['cortex'], ), - mask_file=dict(argstr='--mask %s', ), + mask_file=dict( + argstr='--mask %s', + usedefault=True, + ), no_contrast_ok=dict(argstr='--no-contrasts-ok', ), no_est_fwhm=dict(argstr='--no-est-fwhm', ), no_mask_smooth=dict(argstr='--no-mask-smooth', ), @@ -84,11 +94,14 @@ def test_GLMFit_inputs(): save_residual=dict(argstr='--eres-save', ), seed=dict(argstr='--seed %d', ), self_reg=dict(argstr='--selfreg %d %d %d', ), - sim_done_file=dict(argstr='--sim-done %s', ), + sim_done_file=dict( + argstr='--sim-done %s', + usedefault=True, + ), sim_sign=dict(argstr='--sim-sign %s', ), simulation=dict(argstr='--sim %s %d %f %s', ), subject_id=dict(), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), surf=dict( argstr='--surf %s %s %s', requires=['subject_id', 'hemi'], @@ -98,7 +111,10 @@ def test_GLMFit_inputs(): uniform=dict(argstr='--uniform %f %f', ), var_fwhm=dict(argstr='--var-fwhm %f', ), vox_dump=dict(argstr='--voxdump %d %d %d', ), - weight_file=dict(xor=['weighted_ls'], ), + weight_file=dict( + usedefault=True, + xor=['weighted_ls'], + ), weight_inv=dict( argstr='--w-inv', xor=['weighted_ls'], @@ -109,6 +125,7 @@ def test_GLMFit_inputs(): ), weighted_ls=dict( argstr='--wls %s', + usedefault=True, xor=('weight_file', 'weight_inv', 'weight_sqrt'), ), ) @@ -119,23 +136,23 @@ def test_GLMFit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_GLMFit_outputs(): output_map = dict( - beta_file=dict(), - dof_file=dict(), - error_file=dict(), - error_stddev_file=dict(), - error_var_file=dict(), - estimate_file=dict(), - frame_eigenvectors=dict(), + beta_file=dict(usedefault=True, ), + dof_file=dict(usedefault=True, ), + error_file=dict(usedefault=True, ), + error_stddev_file=dict(usedefault=True, ), + error_var_file=dict(usedefault=True, ), + estimate_file=dict(usedefault=True, ), + frame_eigenvectors=dict(usedefault=True, ), ftest_file=dict(), - fwhm_file=dict(), + fwhm_file=dict(usedefault=True, ), gamma_file=dict(), gamma_var_file=dict(), - glm_dir=dict(), - mask_file=dict(), + glm_dir=dict(usedefault=True, ), + mask_file=dict(usedefault=True, ), sig_file=dict(), - singular_values=dict(), - spatial_eigenvectors=dict(), - svd_stats_file=dict(), + singular_values=dict(usedefault=True, ), + spatial_eigenvectors=dict(usedefault=True, ), + svd_stats_file=dict(usedefault=True, ), ) outputs = GLMFit.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py index 2fa225e87e..58e987f6a4 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py @@ -13,8 +13,9 @@ def test_ImageInfo_inputs(): in_file=dict( argstr='%s', position=1, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = ImageInfo.input_spec() @@ -31,7 +32,7 @@ def test_ImageInfo_outputs(): file_format=dict(), info=dict(), orientation=dict(), - out_file=dict(), + out_file=dict(usedefault=True, ), ph_enc_dir=dict(), vox_sizes=dict(), ) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py b/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py index 49f5e6b48f..22c3fed709 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py @@ -14,11 +14,13 @@ def test_Jacobian_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), in_origsurf=dict( argstr='%s', mandatory=True, position=-3, + usedefault=True, ), out_file=dict( argstr='%s', @@ -27,8 +29,9 @@ def test_Jacobian_inputs(): name_source=['in_origsurf'], name_template='%s.jacobian', position=-1, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = Jacobian.input_spec() @@ -36,7 +39,7 @@ def test_Jacobian_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Jacobian_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Jacobian.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py index bcbf971d01..a0876c3e13 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py @@ -13,12 +13,14 @@ def test_LTAConvert_inputs(): in_fsl=dict( argstr='--infsl %s', mandatory=True, + usedefault=True, xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'), ), in_itk=dict( argstr='--initk %s', mandatory=True, + usedefault=True, xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'), ), @@ -31,18 +33,21 @@ def test_LTAConvert_inputs(): in_mni=dict( argstr='--inmni %s', mandatory=True, + usedefault=True, xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'), ), in_niftyreg=dict( argstr='--inniftyreg %s', mandatory=True, + usedefault=True, xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'), ), in_reg=dict( argstr='--inreg %s', mandatory=True, + usedefault=True, xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'), ), @@ -56,9 +61,15 @@ def test_LTAConvert_inputs(): out_lta=dict(argstr='--outlta %s', ), out_mni=dict(argstr='--outmni %s', ), out_reg=dict(argstr='--outreg %s', ), - source_file=dict(argstr='--src %s', ), + source_file=dict( + argstr='--src %s', + usedefault=True, + ), target_conform=dict(argstr='--trgconform', ), - target_file=dict(argstr='--trg %s', ), + target_file=dict( + argstr='--trg %s', + usedefault=True, + ), ) inputs = LTAConvert.input_spec() @@ -67,11 +78,11 @@ def test_LTAConvert_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_LTAConvert_outputs(): output_map = dict( - out_fsl=dict(), - out_itk=dict(), - out_lta=dict(), - out_mni=dict(), - out_reg=dict(), + out_fsl=dict(usedefault=True, ), + out_itk=dict(usedefault=True, ), + out_lta=dict(usedefault=True, ), + out_mni=dict(usedefault=True, ), + out_reg=dict(usedefault=True, ), ) outputs = LTAConvert.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py index 2d7761006b..1e4ef551f9 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py @@ -6,7 +6,10 @@ def test_Label2Annot_inputs(): input_map = dict( args=dict(argstr='%s', ), - color_table=dict(argstr='--ctab %s', ), + color_table=dict( + argstr='--ctab %s', + usedefault=True, + ), copy_inputs=dict(), environ=dict( nohash=True, @@ -21,7 +24,10 @@ def test_Label2Annot_inputs(): mandatory=True, ), keep_max=dict(argstr='--maxstatwinner', ), - orig=dict(mandatory=True, ), + orig=dict( + mandatory=True, + usedefault=True, + ), out_annot=dict( argstr='--a %s', mandatory=True, @@ -31,7 +37,7 @@ def test_Label2Annot_inputs(): mandatory=True, usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), verbose_off=dict(argstr='--noverbose', ), ) inputs = Label2Annot.input_spec() @@ -40,7 +46,7 @@ def test_Label2Annot_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Label2Annot_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Label2Annot.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py index 7511cd0dbb..e62b00a7cb 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py @@ -21,6 +21,7 @@ def test_Label2Label_inputs(): keep_extension=True, name_source=['source_label'], name_template='%s_converted', + usedefault=True, ), registration_method=dict( argstr='--regmethod %s', @@ -29,21 +30,34 @@ def test_Label2Label_inputs(): source_label=dict( argstr='--srclabel %s', mandatory=True, + usedefault=True, + ), + source_sphere_reg=dict( + mandatory=True, + usedefault=True, ), - source_sphere_reg=dict(mandatory=True, ), source_subject=dict( argstr='--srcsubject %s', mandatory=True, ), - source_white=dict(mandatory=True, ), - sphere_reg=dict(mandatory=True, ), + source_white=dict( + mandatory=True, + usedefault=True, + ), + sphere_reg=dict( + mandatory=True, + usedefault=True, + ), subject_id=dict( argstr='--trgsubject %s', mandatory=True, usedefault=True, ), - subjects_dir=dict(), - white=dict(mandatory=True, ), + subjects_dir=dict(usedefault=True, ), + white=dict( + mandatory=True, + usedefault=True, + ), ) inputs = Label2Label.input_spec() @@ -51,7 +65,7 @@ def test_Label2Label_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Label2Label_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Label2Label.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py index fb2726635f..dc17d6a604 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py @@ -10,6 +10,7 @@ def test_Label2Vol_inputs(): copyfile=False, mandatory=True, requires=('subject_id', 'hemi'), + usedefault=True, xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'), ), aparc_aseg=dict( @@ -35,9 +36,15 @@ def test_Label2Vol_inputs(): mandatory=True, xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'), ), - label_hit_file=dict(argstr='--hits %s', ), + label_hit_file=dict( + argstr='--hits %s', + usedefault=True, + ), label_voxel_volume=dict(argstr='--labvoxvol %f', ), - map_label_stat=dict(argstr='--label-stat %s', ), + map_label_stat=dict( + argstr='--label-stat %s', + usedefault=True, + ), native_vox2ras=dict(argstr='--native-vox2ras', ), proj=dict( argstr='--proj %s %f %f %f', @@ -45,28 +52,33 @@ def test_Label2Vol_inputs(): ), reg_file=dict( argstr='--reg %s', + usedefault=True, xor=('reg_file', 'reg_header', 'identity'), ), reg_header=dict( argstr='--regheader %s', + usedefault=True, xor=('reg_file', 'reg_header', 'identity'), ), seg_file=dict( argstr='--seg %s', copyfile=False, mandatory=True, + usedefault=True, xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'), ), subject_id=dict(argstr='--subject %s', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), surface=dict(argstr='--surf %s', ), template_file=dict( argstr='--temp %s', mandatory=True, + usedefault=True, ), vol_label_file=dict( argstr='--o %s', genfile=True, + usedefault=True, ), ) inputs = Label2Vol.input_spec() @@ -75,7 +87,7 @@ def test_Label2Vol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Label2Vol_outputs(): - output_map = dict(vol_label_file=dict(), ) + output_map = dict(vol_label_file=dict(usedefault=True, ), ) outputs = Label2Vol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py b/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py index 7b6ae4a945..986c4e808c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py @@ -14,12 +14,16 @@ def test_MNIBiasCorrection_inputs(): in_file=dict( argstr='--i %s', mandatory=True, + usedefault=True, ), iterations=dict( argstr='--n %d', usedefault=True, ), - mask=dict(argstr='--mask %s', ), + mask=dict( + argstr='--mask %s', + usedefault=True, + ), no_rescale=dict(argstr='--no-rescale', ), out_file=dict( argstr='--o %s', @@ -27,12 +31,16 @@ def test_MNIBiasCorrection_inputs(): keep_extension=True, name_source=['in_file'], name_template='%s_output', + usedefault=True, ), protocol_iterations=dict(argstr='--proto-iters %d', ), shrink=dict(argstr='--shrink %d', ), stop=dict(argstr='--stop %f', ), - subjects_dir=dict(), - transform=dict(argstr='--uchar %s', ), + subjects_dir=dict(usedefault=True, ), + transform=dict( + argstr='--uchar %s', + usedefault=True, + ), ) inputs = MNIBiasCorrection.input_spec() @@ -40,7 +48,7 @@ def test_MNIBiasCorrection_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MNIBiasCorrection_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MNIBiasCorrection.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py b/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py index b4b7436120..c712a08211 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py @@ -18,7 +18,7 @@ def test_MPRtoMNI305_inputs(): mandatory=True, usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), target=dict( mandatory=True, usedefault=True, @@ -32,7 +32,7 @@ def test_MPRtoMNI305_inputs(): def test_MPRtoMNI305_outputs(): output_map = dict( log_file=dict(usedefault=True, ), - out_file=dict(), + out_file=dict(usedefault=True, ), ) outputs = MPRtoMNI305.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py index b44cf7a308..911702da45 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py @@ -5,12 +5,24 @@ def test_MRIConvert_inputs(): input_map = dict( - apply_inv_transform=dict(argstr='--apply_inverse_transform %s', ), - apply_transform=dict(argstr='--apply_transform %s', ), + apply_inv_transform=dict( + argstr='--apply_inverse_transform %s', + usedefault=True, + ), + apply_transform=dict( + argstr='--apply_transform %s', + usedefault=True, + ), args=dict(argstr='%s', ), ascii=dict(argstr='--ascii', ), - autoalign_matrix=dict(argstr='--autoalign %s', ), - color_file=dict(argstr='--color_file %s', ), + autoalign_matrix=dict( + argstr='--autoalign %s', + usedefault=True, + ), + color_file=dict( + argstr='--color_file %s', + usedefault=True, + ), conform=dict(argstr='--conform', ), conform_min=dict(argstr='--conform_min', ), conform_size=dict(argstr='--conform_size %s', ), @@ -35,6 +47,7 @@ def test_MRIConvert_inputs(): argstr='--input_volume %s', mandatory=True, position=-2, + usedefault=True, ), in_i_dir=dict(argstr='--in_i_direction %f %f %f', ), in_i_size=dict(argstr='--in_i_size %d', ), @@ -43,7 +56,10 @@ def test_MRIConvert_inputs(): in_j_size=dict(argstr='--in_j_size %d', ), in_k_dir=dict(argstr='--in_k_direction %f %f %f', ), in_k_size=dict(argstr='--in_k_size %d', ), - in_like=dict(argstr='--in_like %s', ), + in_like=dict( + argstr='--in_like %s', + usedefault=True, + ), in_matrix=dict(argstr='--in_matrix', ), in_orientation=dict(argstr='--in_orientation %s', ), in_scale=dict(argstr='--scale %f', ), @@ -61,6 +77,7 @@ def test_MRIConvert_inputs(): argstr='--output_volume %s', genfile=True, position=-1, + usedefault=True, ), out_i_count=dict(argstr='--out_i_count %d', ), out_i_dir=dict(argstr='--out_i_direction %f %f %f', ), @@ -81,8 +98,14 @@ def test_MRIConvert_inputs(): read_only=dict(argstr='--read_only', ), reorder=dict(argstr='--reorder %d %d %d', ), resample_type=dict(argstr='--resample_type %s', ), - reslice_like=dict(argstr='--reslice_like %s', ), - sdcm_list=dict(argstr='--sdcmlist %s', ), + reslice_like=dict( + argstr='--reslice_like %s', + usedefault=True, + ), + sdcm_list=dict( + argstr='--sdcmlist %s', + usedefault=True, + ), skip_n=dict(argstr='--nskip %d', ), slice_bias=dict(argstr='--slice-bias %f', ), slice_crop=dict(argstr='--slice-crop %d %d', ), @@ -90,9 +113,12 @@ def test_MRIConvert_inputs(): smooth_parcellation=dict(argstr='--smooth_parcellation', ), sphinx=dict(argstr='--sphinx', ), split=dict(argstr='--split', ), - status_file=dict(argstr='--status %s', ), + status_file=dict( + argstr='--status %s', + usedefault=True, + ), subject_name=dict(argstr='--subject_name %s', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), te=dict(argstr='-te %d', ), template_info=dict(argstr='--template_info', ), template_type=dict(argstr='--template_type %s', ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py b/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py index 6c12cabdc2..c80c21b614 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py @@ -44,6 +44,7 @@ def test_MRICoreg_inputs(): argstr='--ref %s', copyfile=False, mandatory=True, + usedefault=True, xor=['subject_id'], ), reference_mask=dict( @@ -56,6 +57,7 @@ def test_MRICoreg_inputs(): argstr='--mov %s', copyfile=False, mandatory=True, + usedefault=True, ), source_mask=dict(argstr='--mov-mask', ), source_oob=dict(argstr='--mov-oob', ), @@ -66,7 +68,10 @@ def test_MRICoreg_inputs(): requires=['subjects_dir'], xor=['reference_file'], ), - subjects_dir=dict(argstr='--sd %s', ), + subjects_dir=dict( + argstr='--sd %s', + usedefault=True, + ), ) inputs = MRICoreg.input_spec() @@ -75,9 +80,9 @@ def test_MRICoreg_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MRICoreg_outputs(): output_map = dict( - out_lta_file=dict(), - out_params_file=dict(), - out_reg_file=dict(), + out_lta_file=dict(usedefault=True, ), + out_params_file=dict(usedefault=True, ), + out_reg_file=dict(usedefault=True, ), ) outputs = MRICoreg.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py index 719986961d..79057d3233 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py @@ -14,16 +14,27 @@ def test_MRIFill_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, + ), + log_file=dict( + argstr='-a %s', + usedefault=True, ), - log_file=dict(argstr='-a %s', ), out_file=dict( argstr='%s', mandatory=True, position=-1, + usedefault=True, + ), + segmentation=dict( + argstr='-segmentation %s', + usedefault=True, + ), + subjects_dir=dict(usedefault=True, ), + transform=dict( + argstr='-xform %s', + usedefault=True, ), - segmentation=dict(argstr='-segmentation %s', ), - subjects_dir=dict(), - transform=dict(argstr='-xform %s', ), ) inputs = MRIFill.input_spec() @@ -32,8 +43,8 @@ def test_MRIFill_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MRIFill_outputs(): output_map = dict( - log_file=dict(), - out_file=dict(), + log_file=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), ) outputs = MRIFill.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py index f43d217256..84164b8ddf 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py @@ -19,6 +19,7 @@ def test_MRIMarchingCubes_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), label_value=dict( argstr='%d', @@ -29,8 +30,9 @@ def test_MRIMarchingCubes_inputs(): argstr='./%s', genfile=True, position=-2, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = MRIMarchingCubes.input_spec() @@ -38,7 +40,7 @@ def test_MRIMarchingCubes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIMarchingCubes_outputs(): - output_map = dict(surface=dict(), ) + output_map = dict(surface=dict(usedefault=True, ), ) outputs = MRIMarchingCubes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py index 2e7c7d2ea5..682dbd68f4 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py @@ -14,11 +14,13 @@ def test_MRIPretess_inputs(): argstr='%s', mandatory=True, position=-4, + usedefault=True, ), in_norm=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), keep=dict(argstr='-keep', ), label=dict( @@ -34,8 +36,9 @@ def test_MRIPretess_inputs(): name_source=['in_filled'], name_template='%s_pretesswm', position=-1, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), test=dict(argstr='-test', ), ) inputs = MRIPretess.input_spec() @@ -44,7 +47,7 @@ def test_MRIPretess_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIPretess_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MRIPretess.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py index c92b4fea15..99b60abfcd 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py @@ -12,6 +12,7 @@ def test_MRISPreproc_inputs(): ), fsgd_file=dict( argstr='--fsgd %s', + usedefault=True, xor=('subjects', 'fsgd_file', 'subject_file'), ), fwhm=dict( @@ -37,19 +38,21 @@ def test_MRISPreproc_inputs(): out_file=dict( argstr='--out %s', genfile=True, + usedefault=True, ), proj_frac=dict(argstr='--projfrac %s', ), smooth_cortex_only=dict(argstr='--smooth-cortex-only', ), source_format=dict(argstr='--srcfmt %s', ), subject_file=dict( argstr='--f %s', + usedefault=True, xor=('subjects', 'fsgd_file', 'subject_file'), ), subjects=dict( argstr='--s %s...', xor=('subjects', 'fsgd_file', 'subject_file'), ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), surf_area=dict( argstr='--area %s', xor=('surf_measure', 'surf_measure_file', 'surf_area'), @@ -75,7 +78,7 @@ def test_MRISPreproc_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRISPreproc_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MRISPreproc.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py index e72d8adb9e..8074cd14b2 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py @@ -13,6 +13,7 @@ def test_MRISPreprocReconAll_inputs(): ), fsgd_file=dict( argstr='--fsgd %s', + usedefault=True, xor=('subjects', 'fsgd_file', 'subject_file'), ), fwhm=dict( @@ -27,7 +28,10 @@ def test_MRISPreprocReconAll_inputs(): argstr='--hemi %s', mandatory=True, ), - lh_surfreg_target=dict(requires=['surfreg_files'], ), + lh_surfreg_target=dict( + requires=['surfreg_files'], + usedefault=True, + ), num_iters=dict( argstr='--niters %d', xor=['fwhm'], @@ -39,13 +43,18 @@ def test_MRISPreprocReconAll_inputs(): out_file=dict( argstr='--out %s', genfile=True, + usedefault=True, ), proj_frac=dict(argstr='--projfrac %s', ), - rh_surfreg_target=dict(requires=['surfreg_files'], ), + rh_surfreg_target=dict( + requires=['surfreg_files'], + usedefault=True, + ), smooth_cortex_only=dict(argstr='--smooth-cortex-only', ), source_format=dict(argstr='--srcfmt %s', ), subject_file=dict( argstr='--f %s', + usedefault=True, xor=('subjects', 'fsgd_file', 'subject_file'), ), subject_id=dict( @@ -57,7 +66,7 @@ def test_MRISPreprocReconAll_inputs(): argstr='--s %s...', xor=('subjects', 'fsgd_file', 'subject_file'), ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), surf_area=dict( argstr='--area %s', xor=('surf_measure', 'surf_measure_file', 'surf_area'), @@ -69,6 +78,7 @@ def test_MRISPreprocReconAll_inputs(): ), surf_measure_file=dict( argstr='--meas %s', + usedefault=True, xor=('surf_measure', 'surf_measure_file', 'surf_area'), ), surfreg_files=dict( @@ -87,7 +97,7 @@ def test_MRISPreprocReconAll_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRISPreprocReconAll_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MRISPreprocReconAll.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py index a5899cfe70..40cc4a8c4e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py @@ -14,6 +14,7 @@ def test_MRITessellate_inputs(): argstr='%s', mandatory=True, position=-3, + usedefault=True, ), label_value=dict( argstr='%d', @@ -24,8 +25,9 @@ def test_MRITessellate_inputs(): argstr='%s', genfile=True, position=-1, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), tesselate_all_voxels=dict(argstr='-a', ), use_real_RAS_coordinates=dict(argstr='-n', ), ) @@ -35,7 +37,7 @@ def test_MRITessellate_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRITessellate_outputs(): - output_map = dict(surface=dict(), ) + output_map = dict(surface=dict(usedefault=True, ), ) outputs = MRITessellate.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py index 441be3e0a4..0d9af752e7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py @@ -11,14 +11,19 @@ def test_MRIsCALabel_inputs(): argstr='%s', mandatory=True, position=-3, + usedefault=True, ), classifier=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), copy_inputs=dict(), - curv=dict(mandatory=True, ), + curv=dict( + mandatory=True, + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -37,17 +42,24 @@ def test_MRIsCALabel_inputs(): name_source=['hemisphere'], name_template='%s.aparc.annot', position=-1, + usedefault=True, ), seed=dict(argstr='-seed %d', ), - smoothwm=dict(mandatory=True, ), + smoothwm=dict( + mandatory=True, + usedefault=True, + ), subject_id=dict( argstr='%s', mandatory=True, position=-5, usedefault=True, ), - subjects_dir=dict(), - sulc=dict(mandatory=True, ), + subjects_dir=dict(usedefault=True, ), + sulc=dict( + mandatory=True, + usedefault=True, + ), ) inputs = MRIsCALabel.input_spec() @@ -55,7 +67,7 @@ def test_MRIsCALabel_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsCALabel_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MRIsCALabel.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py index cbd68c8457..7c0f19b38a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py @@ -19,10 +19,12 @@ def test_MRIsCalc_inputs(): argstr='%s', mandatory=True, position=-3, + usedefault=True, ), in_file2=dict( argstr='%s', position=-1, + usedefault=True, xor=['in_float', 'in_int'], ), in_float=dict( @@ -38,8 +40,9 @@ def test_MRIsCalc_inputs(): out_file=dict( argstr='-o %s', mandatory=True, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = MRIsCalc.input_spec() @@ -47,7 +50,7 @@ def test_MRIsCalc_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsCalc_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MRIsCalc.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py index 657292c5c7..e63dde7322 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py @@ -20,8 +20,9 @@ def test_MRIsCombine_inputs(): genfile=True, mandatory=True, position=-1, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = MRIsCombine.input_spec() @@ -29,7 +30,7 @@ def test_MRIsCombine_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsCombine_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MRIsCombine.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py index 21622b2449..5e8aef895b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py @@ -5,21 +5,34 @@ def test_MRIsConvert_inputs(): input_map = dict( - annot_file=dict(argstr='--annot %s', ), + annot_file=dict( + argstr='--annot %s', + usedefault=True, + ), args=dict(argstr='%s', ), dataarray_num=dict(argstr='--da_num %d', ), environ=dict( nohash=True, usedefault=True, ), - functional_file=dict(argstr='-f %s', ), + functional_file=dict( + argstr='-f %s', + usedefault=True, + ), in_file=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, + ), + label_file=dict( + argstr='--label %s', + usedefault=True, + ), + labelstats_outfile=dict( + argstr='--labelstats %s', + usedefault=True, ), - label_file=dict(argstr='--label %s', ), - labelstats_outfile=dict(argstr='--labelstats %s', ), normal=dict(argstr='-n', ), origname=dict(argstr='-o %s', ), out_datatype=dict( @@ -31,14 +44,21 @@ def test_MRIsConvert_inputs(): genfile=True, mandatory=True, position=-1, + usedefault=True, xor=['out_datatype'], ), - parcstats_file=dict(argstr='--parcstats %s', ), + parcstats_file=dict( + argstr='--parcstats %s', + usedefault=True, + ), patch=dict(argstr='-p', ), rescale=dict(argstr='-r', ), - scalarcurv_file=dict(argstr='-c %s', ), + scalarcurv_file=dict( + argstr='-c %s', + usedefault=True, + ), scale=dict(argstr='-s %.3f', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), talairachxfm_subjid=dict(argstr='-t %s', ), to_scanner=dict(argstr='--to-scanner', ), to_tkr=dict(argstr='--to-tkr', ), @@ -51,7 +71,7 @@ def test_MRIsConvert_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsConvert_outputs(): - output_map = dict(converted=dict(), ) + output_map = dict(converted=dict(usedefault=True, ), ) outputs = MRIsConvert.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py index 8639c1e7b6..5c09580639 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py @@ -21,6 +21,7 @@ def test_MRIsExpand_inputs(): copyfile=False, mandatory=True, position=-3, + usedefault=True, ), nsurfaces=dict(argstr='-N %d', ), out_name=dict( @@ -38,7 +39,7 @@ def test_MRIsExpand_inputs(): usedefault=True, ), spring=dict(argstr='-S %g', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), thickness=dict(argstr='-thickness', ), thickness_name=dict( argstr='-thickness_name %s', @@ -52,7 +53,7 @@ def test_MRIsExpand_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsExpand_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MRIsExpand.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py index 73e48a2521..ef736757cb 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py @@ -15,6 +15,7 @@ def test_MRIsInflate_inputs(): copyfile=True, mandatory=True, position=-2, + usedefault=True, ), no_save_sulc=dict( argstr='-no-save-sulc', @@ -27,9 +28,13 @@ def test_MRIsInflate_inputs(): name_source=['in_file'], name_template='%s.inflated', position=-1, + usedefault=True, + ), + out_sulc=dict( + usedefault=True, + xor=['no_save_sulc'], ), - out_sulc=dict(xor=['no_save_sulc'], ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = MRIsInflate.input_spec() @@ -38,8 +43,8 @@ def test_MRIsInflate_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsInflate_outputs(): output_map = dict( - out_file=dict(), - out_sulc=dict(), + out_file=dict(usedefault=True, ), + out_sulc=dict(usedefault=True, ), ) outputs = MRIsInflate.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py index f3453818c5..dd7ed03a1b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py @@ -25,7 +25,7 @@ def test_MS_LDA_inputs(): ), mask_file=dict(argstr='-mask %s', ), shift=dict(argstr='-shift %d', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), use_weights=dict(argstr='-W', ), vol_synth_file=dict( argstr='-synth %s', @@ -43,8 +43,8 @@ def test_MS_LDA_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MS_LDA_outputs(): output_map = dict( - vol_synth_file=dict(), - weight_file=dict(), + vol_synth_file=dict(usedefault=True, ), + weight_file=dict(usedefault=True, ), ) outputs = MS_LDA.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py index 5dfb555346..68b1d33455 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py @@ -14,7 +14,7 @@ def test_MakeAverageSubject_inputs(): argstr='--out %s', usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), subjects_ids=dict( argstr='--subjects %s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py index 7ff18eeba6..0b26f19ca0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py @@ -17,16 +17,32 @@ def test_MakeSurfaces_inputs(): mandatory=True, position=-1, ), - in_T1=dict(argstr='-T1 %s', ), - in_aseg=dict(argstr='-aseg %s', ), - in_filled=dict(mandatory=True, ), - in_label=dict(xor=['noaparc'], ), + in_T1=dict( + argstr='-T1 %s', + usedefault=True, + ), + in_aseg=dict( + argstr='-aseg %s', + usedefault=True, + ), + in_filled=dict( + mandatory=True, + usedefault=True, + ), + in_label=dict( + usedefault=True, + xor=['noaparc'], + ), in_orig=dict( argstr='-orig %s', mandatory=True, + usedefault=True, + ), + in_white=dict(usedefault=True, ), + in_wm=dict( + mandatory=True, + usedefault=True, ), - in_white=dict(), - in_wm=dict(mandatory=True, ), longitudinal=dict(argstr='-long', ), maximum=dict(argstr='-max %.1f', ), mgz=dict(argstr='-mgz', ), @@ -38,15 +54,19 @@ def test_MakeSurfaces_inputs(): orig_pial=dict( argstr='-orig_pial %s', requires=['in_label'], + usedefault=True, + ), + orig_white=dict( + argstr='-orig_white %s', + usedefault=True, ), - orig_white=dict(argstr='-orig_white %s', ), subject_id=dict( argstr='%s', mandatory=True, position=-2, usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), white=dict(argstr='-white %s', ), white_only=dict(argstr='-whiteonly', ), ) @@ -57,12 +77,12 @@ def test_MakeSurfaces_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MakeSurfaces_outputs(): output_map = dict( - out_area=dict(), - out_cortex=dict(), - out_curv=dict(), - out_pial=dict(), - out_thickness=dict(), - out_white=dict(), + out_area=dict(usedefault=True, ), + out_cortex=dict(usedefault=True, ), + out_curv=dict(usedefault=True, ), + out_pial=dict(usedefault=True, ), + out_thickness=dict(usedefault=True, ), + out_white=dict(usedefault=True, ), ) outputs = MakeSurfaces.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py index 1923b5ceed..ff50a476cb 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py @@ -15,8 +15,12 @@ def test_Normalize_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, + ), + mask=dict( + argstr='-mask %s', + usedefault=True, ), - mask=dict(argstr='-mask %s', ), out_file=dict( argstr='%s', hash_files=False, @@ -24,10 +28,14 @@ def test_Normalize_inputs(): name_source=['in_file'], name_template='%s_norm', position=-1, + usedefault=True, + ), + segmentation=dict( + argstr='-aseg %s', + usedefault=True, ), - segmentation=dict(argstr='-aseg %s', ), - subjects_dir=dict(), - transform=dict(), + subjects_dir=dict(usedefault=True, ), + transform=dict(usedefault=True, ), ) inputs = Normalize.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py index 1091bdbdc3..b0c31b42b6 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py @@ -19,6 +19,7 @@ def test_OneSampleTTest_inputs(): debug=dict(argstr='--debug', ), design=dict( argstr='--X %s', + usedefault=True, xor=('fsgd', 'design', 'one_sample'), ), diag=dict(argstr='--diag %d', ), @@ -33,9 +34,13 @@ def test_OneSampleTTest_inputs(): ), fixed_fx_dof_file=dict( argstr='--ffxdofdat %d', + usedefault=True, xor=['fixed_fx_dof'], ), - fixed_fx_var=dict(argstr='--yffxvar %s', ), + fixed_fx_var=dict( + argstr='--yffxvar %s', + usedefault=True, + ), force_perm=dict(argstr='--perm-force', ), fsgd=dict( argstr='--fsgd %s %s', @@ -51,13 +56,18 @@ def test_OneSampleTTest_inputs(): argstr='--y %s', copyfile=False, mandatory=True, + usedefault=True, ), invert_mask=dict(argstr='--mask-inv', ), label_file=dict( argstr='--label %s', + usedefault=True, xor=['cortex'], ), - mask_file=dict(argstr='--mask %s', ), + mask_file=dict( + argstr='--mask %s', + usedefault=True, + ), no_contrast_ok=dict(argstr='--no-contrasts-ok', ), no_est_fwhm=dict(argstr='--no-est-fwhm', ), no_mask_smooth=dict(argstr='--no-mask-smooth', ), @@ -84,11 +94,14 @@ def test_OneSampleTTest_inputs(): save_residual=dict(argstr='--eres-save', ), seed=dict(argstr='--seed %d', ), self_reg=dict(argstr='--selfreg %d %d %d', ), - sim_done_file=dict(argstr='--sim-done %s', ), + sim_done_file=dict( + argstr='--sim-done %s', + usedefault=True, + ), sim_sign=dict(argstr='--sim-sign %s', ), simulation=dict(argstr='--sim %s %d %f %s', ), subject_id=dict(), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), surf=dict( argstr='--surf %s %s %s', requires=['subject_id', 'hemi'], @@ -98,7 +111,10 @@ def test_OneSampleTTest_inputs(): uniform=dict(argstr='--uniform %f %f', ), var_fwhm=dict(argstr='--var-fwhm %f', ), vox_dump=dict(argstr='--voxdump %d %d %d', ), - weight_file=dict(xor=['weighted_ls'], ), + weight_file=dict( + usedefault=True, + xor=['weighted_ls'], + ), weight_inv=dict( argstr='--w-inv', xor=['weighted_ls'], @@ -109,6 +125,7 @@ def test_OneSampleTTest_inputs(): ), weighted_ls=dict( argstr='--wls %s', + usedefault=True, xor=('weight_file', 'weight_inv', 'weight_sqrt'), ), ) @@ -119,23 +136,23 @@ def test_OneSampleTTest_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_OneSampleTTest_outputs(): output_map = dict( - beta_file=dict(), - dof_file=dict(), - error_file=dict(), - error_stddev_file=dict(), - error_var_file=dict(), - estimate_file=dict(), - frame_eigenvectors=dict(), + beta_file=dict(usedefault=True, ), + dof_file=dict(usedefault=True, ), + error_file=dict(usedefault=True, ), + error_stddev_file=dict(usedefault=True, ), + error_var_file=dict(usedefault=True, ), + estimate_file=dict(usedefault=True, ), + frame_eigenvectors=dict(usedefault=True, ), ftest_file=dict(), - fwhm_file=dict(), + fwhm_file=dict(usedefault=True, ), gamma_file=dict(), gamma_var_file=dict(), - glm_dir=dict(), - mask_file=dict(), + glm_dir=dict(usedefault=True, ), + mask_file=dict(usedefault=True, ), sig_file=dict(), - singular_values=dict(), - spatial_eigenvectors=dict(), - svd_stats_file=dict(), + singular_values=dict(usedefault=True, ), + spatial_eigenvectors=dict(usedefault=True, ), + svd_stats_file=dict(usedefault=True, ), ) outputs = OneSampleTTest.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Paint.py b/nipype/interfaces/freesurfer/tests/test_auto_Paint.py index c452594e55..41c07e0c90 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Paint.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Paint.py @@ -15,6 +15,7 @@ def test_Paint_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), out_file=dict( argstr='%s', @@ -23,12 +24,14 @@ def test_Paint_inputs(): name_source=['in_surf'], name_template='%s.avg_curv', position=-1, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), template=dict( argstr='%s', mandatory=True, position=-3, + usedefault=True, ), template_param=dict(), ) @@ -38,7 +41,7 @@ def test_Paint_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Paint_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Paint.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py b/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py index 81ac276b2f..29eeb7d760 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py @@ -6,10 +6,16 @@ def test_ParcellationStats_inputs(): input_map = dict( args=dict(argstr='%s', ), - aseg=dict(mandatory=True, ), - brainmask=dict(mandatory=True, ), + aseg=dict( + mandatory=True, + usedefault=True, + ), + brainmask=dict( + mandatory=True, + usedefault=True, + ), copy_inputs=dict(), - cortex_label=dict(), + cortex_label=dict(usedefault=True, ), environ=dict( nohash=True, usedefault=True, @@ -28,8 +34,14 @@ def test_ParcellationStats_inputs(): argstr='-l %s', xor=['in_annotatoin', 'out_color'], ), - lh_pial=dict(mandatory=True, ), - lh_white=dict(mandatory=True, ), + lh_pial=dict( + mandatory=True, + usedefault=True, + ), + lh_white=dict( + mandatory=True, + usedefault=True, + ), mgz=dict(argstr='-mgz', ), out_color=dict( argstr='-c %s', @@ -41,16 +53,25 @@ def test_ParcellationStats_inputs(): genfile=True, requires=['tabular_output'], ), - rh_pial=dict(mandatory=True, ), - rh_white=dict(mandatory=True, ), - ribbon=dict(mandatory=True, ), + rh_pial=dict( + mandatory=True, + usedefault=True, + ), + rh_white=dict( + mandatory=True, + usedefault=True, + ), + ribbon=dict( + mandatory=True, + usedefault=True, + ), subject_id=dict( argstr='%s', mandatory=True, position=-3, usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), surface=dict( argstr='%s', position=-1, @@ -60,9 +81,18 @@ def test_ParcellationStats_inputs(): argstr='-th3', requires=['cortex_label'], ), - thickness=dict(mandatory=True, ), - transform=dict(mandatory=True, ), - wm=dict(mandatory=True, ), + thickness=dict( + mandatory=True, + usedefault=True, + ), + transform=dict( + mandatory=True, + usedefault=True, + ), + wm=dict( + mandatory=True, + usedefault=True, + ), ) inputs = ParcellationStats.input_spec() @@ -71,8 +101,8 @@ def test_ParcellationStats_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ParcellationStats_outputs(): output_map = dict( - out_color=dict(), - out_table=dict(), + out_color=dict(usedefault=True, ), + out_table=dict(usedefault=True, ), ) outputs = ParcellationStats.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py index 93254ddcb3..232f363e72 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py @@ -9,6 +9,7 @@ def test_ParseDICOMDir_inputs(): dicom_dir=dict( argstr='--d %s', mandatory=True, + usedefault=True, ), dicom_info_file=dict( argstr='--o %s', @@ -19,7 +20,7 @@ def test_ParseDICOMDir_inputs(): usedefault=True, ), sortbyrun=dict(argstr='--sortbyrun', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), summarize=dict(argstr='--summarize', ), ) inputs = ParseDICOMDir.input_spec() @@ -28,7 +29,7 @@ def test_ParseDICOMDir_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ParseDICOMDir_outputs(): - output_map = dict(dicom_info_file=dict(), ) + output_map = dict(dicom_info_file=dict(usedefault=True, ), ) outputs = ParseDICOMDir.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py index 39f6a8c942..72b256c3ea 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py @@ -8,11 +8,13 @@ def test_ReconAll_inputs(): FLAIR_file=dict( argstr='-FLAIR %s', min_ver='5.3.0', + usedefault=True, ), T1_files=dict(argstr='-i %s...', ), T2_file=dict( argstr='-T2 %s', min_ver='5.3.0', + usedefault=True, ), args=dict(argstr='%s', ), big_ventricles=dict(argstr='-bigventricles', ), @@ -26,7 +28,10 @@ def test_ReconAll_inputs(): nohash=True, usedefault=True, ), - expert=dict(argstr='-expert %s', ), + expert=dict( + argstr='-expert %s', + usedefault=True, + ), flags=dict(argstr='%s', ), hemi=dict(argstr='-hemi %s', ), hippocampal_subfields_T1=dict( @@ -77,6 +82,7 @@ def test_ReconAll_inputs(): argstr='-sd %s', genfile=True, hash_files=False, + usedefault=True, ), talairach=dict(xor=['expert'], ), use_FLAIR=dict( @@ -102,7 +108,10 @@ def test_ReconAll_outputs(): altkey='BA', loc='stats', ), - T1=dict(loc='mri', ), + T1=dict( + loc='mri', + usedefault=True, + ), annot=dict( altkey='*annot', loc='label', @@ -123,14 +132,23 @@ def test_ReconAll_outputs(): altkey='area.pial', loc='surf', ), - aseg=dict(loc='mri', ), + aseg=dict( + loc='mri', + usedefault=True, + ), aseg_stats=dict( altkey='aseg', loc='stats', ), avg_curv=dict(loc='surf', ), - brain=dict(loc='mri', ), - brainmask=dict(loc='mri', ), + brain=dict( + loc='mri', + usedefault=True, + ), + brainmask=dict( + loc='mri', + usedefault=True, + ), curv=dict(loc='surf', ), curv_pial=dict( altkey='curv.pial', @@ -144,7 +162,10 @@ def test_ReconAll_outputs(): altkey='entorhinal_exvivo', loc='stats', ), - filled=dict(loc='mri', ), + filled=dict( + loc='mri', + usedefault=True, + ), graymid=dict( altkey=['graymid', 'midthickness'], loc='surf', @@ -155,11 +176,23 @@ def test_ReconAll_outputs(): altkey='*label', loc='label', ), - norm=dict(loc='mri', ), - nu=dict(loc='mri', ), - orig=dict(loc='mri', ), + norm=dict( + loc='mri', + usedefault=True, + ), + nu=dict( + loc='mri', + usedefault=True, + ), + orig=dict( + loc='mri', + usedefault=True, + ), pial=dict(loc='surf', ), - rawavg=dict(loc='mri', ), + rawavg=dict( + loc='mri', + usedefault=True, + ), ribbon=dict( altkey='*ribbon', loc='mri', @@ -171,13 +204,19 @@ def test_ReconAll_outputs(): loc='surf', ), subject_id=dict(), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), sulc=dict(loc='surf', ), thickness=dict(loc='surf', ), volume=dict(loc='surf', ), white=dict(loc='surf', ), - wm=dict(loc='mri', ), - wmparc=dict(loc='mri', ), + wm=dict( + loc='mri', + usedefault=True, + ), + wmparc=dict( + loc='mri', + usedefault=True, + ), wmparc_stats=dict( altkey='wmparc', loc='stats', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Register.py b/nipype/interfaces/freesurfer/tests/test_auto_Register.py index b4eff5133c..ef13270f35 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Register.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Register.py @@ -14,27 +14,34 @@ def test_Register_inputs(): nohash=True, usedefault=True, ), - in_smoothwm=dict(copyfile=True, ), + in_smoothwm=dict( + copyfile=True, + usedefault=True, + ), in_sulc=dict( copyfile=True, mandatory=True, + usedefault=True, ), in_surf=dict( argstr='%s', copyfile=True, mandatory=True, position=-3, + usedefault=True, ), out_file=dict( argstr='%s', genfile=True, position=-1, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), target=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), ) inputs = Register.input_spec() @@ -43,7 +50,7 @@ def test_Register_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Register_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Register.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py index 0bc88bf935..7bd2387e07 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py @@ -14,22 +14,25 @@ def test_RegisterAVItoTalairach_inputs(): argstr='%s', mandatory=True, position=0, + usedefault=True, ), out_file=dict( argstr='%s', position=3, usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), target=dict( argstr='%s', mandatory=True, position=1, + usedefault=True, ), vox2vox=dict( argstr='%s', mandatory=True, position=2, + usedefault=True, ), ) inputs = RegisterAVItoTalairach.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py b/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py index 859aff0820..c0181e302e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py @@ -10,6 +10,7 @@ def test_RelabelHypointensities_inputs(): argstr='%s', mandatory=True, position=-3, + usedefault=True, ), environ=dict( nohash=True, @@ -18,6 +19,7 @@ def test_RelabelHypointensities_inputs(): lh_white=dict( copyfile=True, mandatory=True, + usedefault=True, ), out_file=dict( argstr='%s', @@ -26,12 +28,14 @@ def test_RelabelHypointensities_inputs(): name_source=['aseg'], name_template='%s.hypos.mgz', position=-1, + usedefault=True, ), rh_white=dict( copyfile=True, mandatory=True, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), surf_directory=dict( argstr='%s', position=-2, @@ -44,7 +48,11 @@ def test_RelabelHypointensities_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RelabelHypointensities_outputs(): - output_map = dict(out_file=dict(argstr='%s', ), ) + output_map = dict( + out_file=dict( + argstr='%s', + usedefault=True, + ), ) outputs = RelabelHypointensities.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py b/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py index 69e1d453a4..73ae626aaf 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py @@ -15,6 +15,7 @@ def test_RemoveIntersection_inputs(): copyfile=True, mandatory=True, position=-2, + usedefault=True, ), out_file=dict( argstr='%s', @@ -23,8 +24,9 @@ def test_RemoveIntersection_inputs(): name_source=['in_file'], name_template='%s', position=-1, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = RemoveIntersection.input_spec() @@ -32,7 +34,7 @@ def test_RemoveIntersection_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RemoveIntersection_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = RemoveIntersection.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py b/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py index 9e095ddba0..f83b2393ef 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py @@ -14,6 +14,7 @@ def test_RemoveNeck_inputs(): argstr='%s', mandatory=True, position=-4, + usedefault=True, ), out_file=dict( argstr='%s', @@ -22,18 +23,21 @@ def test_RemoveNeck_inputs(): name_source=['in_file'], name_template='%s_noneck', position=-1, + usedefault=True, ), radius=dict(argstr='-radius %d', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), template=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), transform=dict( argstr='%s', mandatory=True, position=-3, + usedefault=True, ), ) inputs = RemoveNeck.input_spec() @@ -42,7 +46,7 @@ def test_RemoveNeck_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RemoveNeck_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = RemoveNeck.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py index ecb939d89a..96e3c3cf6c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py @@ -14,13 +14,15 @@ def test_Resample_inputs(): argstr='-i %s', mandatory=True, position=-2, + usedefault=True, ), resampled_file=dict( argstr='-o %s', genfile=True, position=-1, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), voxel_size=dict( argstr='-vs %.2f %.2f %.2f', mandatory=True, @@ -32,7 +34,7 @@ def test_Resample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Resample_outputs(): - output_map = dict(resampled_file=dict(), ) + output_map = dict(resampled_file=dict(usedefault=True, ), ) outputs = Resample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py index af9020c278..6275b8d322 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py @@ -24,12 +24,21 @@ def test_RobustRegister_inputs(): half_targ_xfm=dict(argstr='--halfdstlta %s', ), half_weights=dict(argstr='--halfweights %s', ), high_iterations=dict(argstr='--highit %d', ), - in_xfm_file=dict(argstr='--transform', ), + in_xfm_file=dict( + argstr='--transform', + usedefault=True, + ), init_orient=dict(argstr='--initorient', ), iteration_thresh=dict(argstr='--epsit %.3f', ), least_squares=dict(argstr='--leastsquares', ), - mask_source=dict(argstr='--maskmov %s', ), - mask_target=dict(argstr='--maskdst %s', ), + mask_source=dict( + argstr='--maskmov %s', + usedefault=True, + ), + mask_target=dict( + argstr='--maskdst %s', + usedefault=True, + ), max_iterations=dict(argstr='--maxit %d', ), no_init=dict(argstr='--noinit', ), no_multi=dict(argstr='--nomulti', ), @@ -47,12 +56,14 @@ def test_RobustRegister_inputs(): source_file=dict( argstr='--mov %s', mandatory=True, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), subsample_thresh=dict(argstr='--subsample %d', ), target_file=dict( argstr='--dst %s', mandatory=True, + usedefault=True, ), trans_only=dict(argstr='--transonly', ), weights_file=dict(argstr='--weights %s', ), @@ -65,14 +76,14 @@ def test_RobustRegister_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RobustRegister_outputs(): output_map = dict( - half_source=dict(), - half_source_xfm=dict(), - half_targ=dict(), - half_targ_xfm=dict(), - half_weights=dict(), - out_reg_file=dict(), - registered_file=dict(), - weights_file=dict(), + half_source=dict(usedefault=True, ), + half_source_xfm=dict(usedefault=True, ), + half_targ=dict(usedefault=True, ), + half_targ_xfm=dict(usedefault=True, ), + half_weights=dict(usedefault=True, ), + out_reg_file=dict(usedefault=True, ), + registered_file=dict(usedefault=True, ), + weights_file=dict(usedefault=True, ), ) outputs = RobustRegister.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py b/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py index e845a764e4..675cd41f2b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py @@ -38,7 +38,7 @@ def test_RobustTemplate_inputs(): xor=['auto_detect_sensitivity'], ), scaled_intensity_outputs=dict(argstr='--iscaleout %s', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), subsample_threshold=dict(argstr='--subsample %d', ), transform_outputs=dict(argstr='--lta %s', ), ) @@ -49,7 +49,7 @@ def test_RobustTemplate_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RobustTemplate_outputs(): output_map = dict( - out_file=dict(), + out_file=dict(usedefault=True, ), scaled_intensity_outputs=dict(), transform_outputs=dict(), ) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py index 0926eebba2..04b1352ff6 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py @@ -32,6 +32,7 @@ def test_SampleToSurface_inputs(): interp_method=dict(argstr='--interp %s', ), mask_label=dict( argstr='--mask %s', + usedefault=True, xor=['cortex_mask'], ), mni152reg=dict( @@ -46,6 +47,7 @@ def test_SampleToSurface_inputs(): out_file=dict( argstr='--o %s', genfile=True, + usedefault=True, ), out_type=dict(argstr='--out_type %s', ), override_reg_subj=dict( @@ -56,10 +58,14 @@ def test_SampleToSurface_inputs(): mandatory=True, xor=['sampling_method'], ), - reference_file=dict(argstr='--ref %s', ), + reference_file=dict( + argstr='--ref %s', + usedefault=True, + ), reg_file=dict( argstr='--reg %s', mandatory=True, + usedefault=True, xor=['reg_file', 'reg_header', 'mni152reg'], ), reg_header=dict( @@ -87,9 +93,10 @@ def test_SampleToSurface_inputs(): source_file=dict( argstr='--mov %s', mandatory=True, + usedefault=True, ), subject_id=dict(), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), surf_reg=dict( argstr='--surfreg %s', requires=['target_subject'], @@ -105,9 +112,9 @@ def test_SampleToSurface_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SampleToSurface_outputs(): output_map = dict( - hits_file=dict(), - out_file=dict(), - vox_file=dict(), + hits_file=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), + vox_file=dict(usedefault=True, ), ) outputs = SampleToSurface.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py index 8feb61d9d8..a38d9b5b5f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py @@ -14,11 +14,15 @@ def test_SegStats_inputs(): avgwf_file=dict(argstr='--avgwfvol %s', ), avgwf_txt_file=dict(argstr='--avgwf %s', ), brain_vol=dict(argstr='--%s', ), - brainmask_file=dict(argstr='--brainmask %s', ), + brainmask_file=dict( + argstr='--brainmask %s', + usedefault=True, + ), calc_power=dict(argstr='--%s', ), calc_snr=dict(argstr='--snr', ), color_table_file=dict( argstr='--ctab %s', + usedefault=True, xor=('color_table_file', 'default_color_table', 'gca_color_table'), ), cortex_vol_from_surf=dict(argstr='--surf-ctx-vol', ), @@ -39,36 +43,51 @@ def test_SegStats_inputs(): frame=dict(argstr='--frame %d', ), gca_color_table=dict( argstr='--ctab-gca %s', + usedefault=True, xor=('color_table_file', 'default_color_table', 'gca_color_table'), ), - in_file=dict(argstr='--i %s', ), - in_intensity=dict(argstr='--in %s --in-intensity-name %s', ), + in_file=dict( + argstr='--i %s', + usedefault=True, + ), + in_intensity=dict( + argstr='--in %s --in-intensity-name %s', + usedefault=True, + ), intensity_units=dict( argstr='--in-intensity-units %s', requires=['in_intensity'], ), mask_erode=dict(argstr='--maskerode %d', ), - mask_file=dict(argstr='--mask %s', ), + mask_file=dict( + argstr='--mask %s', + usedefault=True, + ), mask_frame=dict(requires=['mask_file'], ), mask_invert=dict(argstr='--maskinvert', ), mask_sign=dict(), mask_thresh=dict(argstr='--maskthresh %f', ), multiply=dict(argstr='--mul %f', ), non_empty_only=dict(argstr='--nonempty', ), - partial_volume_file=dict(argstr='--pv %s', ), + partial_volume_file=dict( + argstr='--pv %s', + usedefault=True, + ), segment_id=dict(argstr='--id %s...', ), segmentation_file=dict( argstr='--seg %s', mandatory=True, + usedefault=True, xor=('segmentation_file', 'annot', 'surf_label'), ), sf_avg_file=dict(argstr='--sfavg %s', ), subcort_gm=dict(argstr='--subcortgray', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), summary_file=dict( argstr='--sum %s', genfile=True, position=-1, + usedefault=True, ), supratent=dict(argstr='--supratent', ), surf_label=dict( @@ -87,10 +106,10 @@ def test_SegStats_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SegStats_outputs(): output_map = dict( - avgwf_file=dict(), - avgwf_txt_file=dict(), - sf_avg_file=dict(), - summary_file=dict(), + avgwf_file=dict(usedefault=True, ), + avgwf_txt_file=dict(usedefault=True, ), + sf_avg_file=dict(usedefault=True, ), + summary_file=dict(usedefault=True, ), ) outputs = SegStats.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py index e65dc82e3b..e27c24651f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py @@ -11,15 +11,19 @@ def test_SegStatsReconAll_inputs(): xor=('segmentation_file', 'annot', 'surf_label'), ), args=dict(argstr='%s', ), - aseg=dict(), + aseg=dict(usedefault=True, ), avgwf_file=dict(argstr='--avgwfvol %s', ), avgwf_txt_file=dict(argstr='--avgwf %s', ), brain_vol=dict(argstr='--%s', ), - brainmask_file=dict(argstr='--brainmask %s', ), + brainmask_file=dict( + argstr='--brainmask %s', + usedefault=True, + ), calc_power=dict(argstr='--%s', ), calc_snr=dict(argstr='--snr', ), color_table_file=dict( argstr='--ctab %s', + usedefault=True, xor=('color_table_file', 'default_color_table', 'gca_color_table'), ), copy_inputs=dict(), @@ -41,35 +45,67 @@ def test_SegStatsReconAll_inputs(): frame=dict(argstr='--frame %d', ), gca_color_table=dict( argstr='--ctab-gca %s', + usedefault=True, xor=('color_table_file', 'default_color_table', 'gca_color_table'), ), - in_file=dict(argstr='--i %s', ), - in_intensity=dict(argstr='--in %s --in-intensity-name %s', ), + in_file=dict( + argstr='--i %s', + usedefault=True, + ), + in_intensity=dict( + argstr='--in %s --in-intensity-name %s', + usedefault=True, + ), intensity_units=dict( argstr='--in-intensity-units %s', requires=['in_intensity'], ), - lh_orig_nofix=dict(mandatory=True, ), - lh_pial=dict(mandatory=True, ), - lh_white=dict(mandatory=True, ), + lh_orig_nofix=dict( + mandatory=True, + usedefault=True, + ), + lh_pial=dict( + mandatory=True, + usedefault=True, + ), + lh_white=dict( + mandatory=True, + usedefault=True, + ), mask_erode=dict(argstr='--maskerode %d', ), - mask_file=dict(argstr='--mask %s', ), + mask_file=dict( + argstr='--mask %s', + usedefault=True, + ), mask_frame=dict(requires=['mask_file'], ), mask_invert=dict(argstr='--maskinvert', ), mask_sign=dict(), mask_thresh=dict(argstr='--maskthresh %f', ), multiply=dict(argstr='--mul %f', ), non_empty_only=dict(argstr='--nonempty', ), - partial_volume_file=dict(argstr='--pv %s', ), - presurf_seg=dict(), - rh_orig_nofix=dict(mandatory=True, ), - rh_pial=dict(mandatory=True, ), - rh_white=dict(mandatory=True, ), + partial_volume_file=dict( + argstr='--pv %s', + usedefault=True, + ), + presurf_seg=dict(usedefault=True, ), + rh_orig_nofix=dict( + mandatory=True, + usedefault=True, + ), + rh_pial=dict( + mandatory=True, + usedefault=True, + ), + rh_white=dict( + mandatory=True, + usedefault=True, + ), ribbon=dict(mandatory=True, ), segment_id=dict(argstr='--id %s...', ), segmentation_file=dict( argstr='--seg %s', mandatory=True, + usedefault=True, xor=('segmentation_file', 'annot', 'surf_label'), ), sf_avg_file=dict(argstr='--sfavg %s', ), @@ -79,11 +115,12 @@ def test_SegStatsReconAll_inputs(): mandatory=True, usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), summary_file=dict( argstr='--sum %s', genfile=True, position=-1, + usedefault=True, ), supratent=dict(argstr='--supratent', ), surf_label=dict( @@ -92,7 +129,10 @@ def test_SegStatsReconAll_inputs(): xor=('segmentation_file', 'annot', 'surf_label'), ), total_gray=dict(argstr='--totalgray', ), - transform=dict(mandatory=True, ), + transform=dict( + mandatory=True, + usedefault=True, + ), vox=dict(argstr='--vox %s', ), wm_vol_from_surf=dict(argstr='--surf-wm-vol', ), ) @@ -103,10 +143,10 @@ def test_SegStatsReconAll_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SegStatsReconAll_outputs(): output_map = dict( - avgwf_file=dict(), - avgwf_txt_file=dict(), - sf_avg_file=dict(), - summary_file=dict(), + avgwf_file=dict(usedefault=True, ), + avgwf_txt_file=dict(usedefault=True, ), + sf_avg_file=dict(usedefault=True, ), + summary_file=dict(usedefault=True, ), ) outputs = SegStatsReconAll.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py b/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py index e6b5fb2679..679f5449eb 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py @@ -14,18 +14,24 @@ def test_SegmentCC_inputs(): in_file=dict( argstr='-aseg %s', mandatory=True, + usedefault=True, + ), + in_norm=dict( + mandatory=True, + usedefault=True, ), - in_norm=dict(mandatory=True, ), out_file=dict( argstr='-o %s', hash_files=False, keep_extension=False, name_source=['in_file'], name_template='%s.auto.mgz', + usedefault=True, ), out_rotation=dict( argstr='-lta %s', mandatory=True, + usedefault=True, ), subject_id=dict( argstr='%s', @@ -33,7 +39,7 @@ def test_SegmentCC_inputs(): position=-1, usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = SegmentCC.input_spec() @@ -42,8 +48,8 @@ def test_SegmentCC_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SegmentCC_outputs(): output_map = dict( - out_file=dict(), - out_rotation=dict(), + out_file=dict(usedefault=True, ), + out_rotation=dict(usedefault=True, ), ) outputs = SegmentCC.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py b/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py index aa742e8fea..15895f4ec2 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py @@ -14,13 +14,15 @@ def test_SegmentWM_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), out_file=dict( argstr='%s', mandatory=True, position=-1, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = SegmentWM.input_spec() @@ -28,7 +30,7 @@ def test_SegmentWM_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SegmentWM_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = SegmentWM.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py index fe4581dee0..85a6179e7f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py @@ -13,6 +13,7 @@ def test_Smooth_inputs(): in_file=dict( argstr='--i %s', mandatory=True, + usedefault=True, ), num_iters=dict( argstr='--niters %d', @@ -30,12 +31,14 @@ def test_Smooth_inputs(): reg_file=dict( argstr='--reg %s', mandatory=True, + usedefault=True, ), smoothed_file=dict( argstr='--o %s', genfile=True, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), surface_fwhm=dict( argstr='--fwhm %f', mandatory=True, @@ -50,7 +53,7 @@ def test_Smooth_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Smooth_outputs(): - output_map = dict(smoothed_file=dict(), ) + output_map = dict(smoothed_file=dict(usedefault=True, ), ) outputs = Smooth.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py index 8ce4dce075..259805e6c2 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py @@ -19,19 +19,27 @@ def test_SmoothTessellation_inputs(): copyfile=True, mandatory=True, position=-2, + usedefault=True, ), normalize_area=dict(argstr='-area', ), - out_area_file=dict(argstr='-b %s', ), - out_curvature_file=dict(argstr='-c %s', ), + out_area_file=dict( + argstr='-b %s', + usedefault=True, + ), + out_curvature_file=dict( + argstr='-c %s', + usedefault=True, + ), out_file=dict( argstr='%s', genfile=True, position=-1, + usedefault=True, ), seed=dict(argstr='-seed %d', ), smoothing_iterations=dict(argstr='-n %d', ), snapshot_writing_iterations=dict(argstr='-w %d', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), use_gaussian_curvature_smoothing=dict(argstr='-g', ), use_momentum=dict(argstr='-m', ), ) @@ -41,7 +49,7 @@ def test_SmoothTessellation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SmoothTessellation_outputs(): - output_map = dict(surface=dict(), ) + output_map = dict(surface=dict(usedefault=True, ), ) outputs = SmoothTessellation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py b/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py index 461398e6a8..242be862a5 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py @@ -15,8 +15,12 @@ def test_Sphere_inputs(): copyfile=True, mandatory=True, position=-2, + usedefault=True, + ), + in_smoothwm=dict( + copyfile=True, + usedefault=True, ), - in_smoothwm=dict(copyfile=True, ), magic=dict(argstr='-q', ), num_threads=dict(), out_file=dict( @@ -25,9 +29,10 @@ def test_Sphere_inputs(): name_source=['in_file'], name_template='%s.sphere', position=-1, + usedefault=True, ), seed=dict(argstr='-seed %d', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = Sphere.input_spec() @@ -35,7 +40,7 @@ def test_Sphere_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Sphere_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Sphere.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py index efdc032787..54c24a96dd 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py @@ -26,22 +26,27 @@ def test_SphericalAverage_inputs(): genfile=True, position=-2, ), - in_orig=dict(argstr='-orig %s', ), + in_orig=dict( + argstr='-orig %s', + usedefault=True, + ), in_surf=dict( argstr='%s', mandatory=True, position=-3, + usedefault=True, ), out_file=dict( argstr='%s', genfile=True, position=-1, + usedefault=True, ), subject_id=dict( argstr='-o %s', mandatory=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), threshold=dict(argstr='-t %.1f', ), which=dict( argstr='%s', @@ -55,7 +60,7 @@ def test_SphericalAverage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SphericalAverage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = SphericalAverage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py index ca3f96c42b..7ab924576c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py @@ -22,12 +22,14 @@ def test_Surface2VolTransform_inputs(): reg_file=dict( argstr='--volreg %s', mandatory=True, + usedefault=True, xor=['subject_id'], ), source_file=dict( argstr='--surfval %s', copyfile=False, mandatory=True, + usedefault=True, xor=['mkmask'], ), subject_id=dict( @@ -36,18 +38,23 @@ def test_Surface2VolTransform_inputs(): ), subjects_dir=dict(argstr='--sd %s', ), surf_name=dict(argstr='--surf %s', ), - template_file=dict(argstr='--template %s', ), + template_file=dict( + argstr='--template %s', + usedefault=True, + ), transformed_file=dict( argstr='--outvol %s', hash_files=False, name_source=['source_file'], name_template='%s_asVol.nii', + usedefault=True, ), vertexvol_file=dict( argstr='--vtxvol %s', hash_files=False, name_source=['source_file'], name_template='%s_asVol_vertex.nii', + usedefault=True, ), ) inputs = Surface2VolTransform.input_spec() @@ -57,8 +64,8 @@ def test_Surface2VolTransform_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Surface2VolTransform_outputs(): output_map = dict( - transformed_file=dict(), - vertexvol_file=dict(), + transformed_file=dict(usedefault=True, ), + vertexvol_file=dict(usedefault=True, ), ) outputs = Surface2VolTransform.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py index 84bef6ed7a..2fde5bd6c2 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py @@ -25,10 +25,12 @@ def test_SurfaceSmooth_inputs(): in_file=dict( argstr='--sval %s', mandatory=True, + usedefault=True, ), out_file=dict( argstr='--tval %s', genfile=True, + usedefault=True, ), reshape=dict(argstr='--reshape', ), smooth_iters=dict( @@ -39,7 +41,7 @@ def test_SurfaceSmooth_inputs(): argstr='--s %s', mandatory=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = SurfaceSmooth.input_spec() @@ -47,7 +49,7 @@ def test_SurfaceSmooth_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SurfaceSmooth_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = SurfaceSmooth.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py index a413d410b1..1024780411 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py @@ -7,6 +7,7 @@ def test_SurfaceSnapshots_inputs(): input_map = dict( annot_file=dict( argstr='-annotation %s', + usedefault=True, xor=['annot_name'], ), annot_name=dict( @@ -14,7 +15,10 @@ def test_SurfaceSnapshots_inputs(): xor=['annot_file'], ), args=dict(argstr='%s', ), - colortable=dict(argstr='-colortable %s', ), + colortable=dict( + argstr='-colortable %s', + usedefault=True, + ), demean_overlay=dict(argstr='-zm', ), environ=dict( nohash=True, @@ -32,6 +36,7 @@ def test_SurfaceSnapshots_inputs(): invert_overlay=dict(argstr='-invphaseflag 1', ), label_file=dict( argstr='-label %s', + usedefault=True, xor=['label_name'], ), label_name=dict( @@ -48,6 +53,7 @@ def test_SurfaceSnapshots_inputs(): overlay=dict( argstr='-overlay %s', requires=['overlay_range'], + usedefault=True, ), overlay_range=dict(argstr='%s', ), overlay_range_offset=dict(argstr='-foffset %.3f', ), @@ -55,7 +61,10 @@ def test_SurfaceSnapshots_inputs(): argstr='-overlay-reg %s', xor=['overlay_reg', 'identity_reg', 'mni152_reg'], ), - patch_file=dict(argstr='-patch %s', ), + patch_file=dict( + argstr='-patch %s', + usedefault=True, + ), reverse_overlay=dict(argstr='-revphaseflag 1', ), screenshot_stem=dict(), show_color_scale=dict(argstr='-colscalebarflag 1', ), @@ -76,7 +85,7 @@ def test_SurfaceSnapshots_inputs(): mandatory=True, position=1, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), surface=dict( argstr='%s', mandatory=True, @@ -85,6 +94,7 @@ def test_SurfaceSnapshots_inputs(): tcl_script=dict( argstr='%s', genfile=True, + usedefault=True, ), truncate_overlay=dict(argstr='-truncphaseflag 1', ), ) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py index 0546a275dc..f700f4e470 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py @@ -17,17 +17,20 @@ def test_SurfaceTransform_inputs(): out_file=dict( argstr='--tval %s', genfile=True, + usedefault=True, ), reshape=dict(argstr='--reshape', ), reshape_factor=dict(argstr='--reshape-factor', ), source_annot_file=dict( argstr='--sval-annot %s', mandatory=True, + usedefault=True, xor=['source_file'], ), source_file=dict( argstr='--sval %s', mandatory=True, + usedefault=True, xor=['source_annot_file'], ), source_subject=dict( @@ -38,7 +41,7 @@ def test_SurfaceTransform_inputs(): argstr='--sfmt %s', requires=['source_file'], ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), target_ico_order=dict(argstr='--trgicoorder %d', ), target_subject=dict( argstr='--trgsubject %s', @@ -52,7 +55,7 @@ def test_SurfaceTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SurfaceTransform_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = SurfaceTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py index ea121d877e..4f1756672f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py @@ -22,17 +22,20 @@ def test_SynthesizeFLASH_inputs(): out_file=dict( argstr='%s', genfile=True, + usedefault=True, ), pd_image=dict( argstr='%s', mandatory=True, position=6, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), t1_image=dict( argstr='%s', mandatory=True, position=5, + usedefault=True, ), te=dict( argstr='%.3f', @@ -51,7 +54,7 @@ def test_SynthesizeFLASH_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SynthesizeFLASH_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = SynthesizeFLASH.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py index 8ce925fcc7..913d41e595 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py @@ -14,12 +14,14 @@ def test_TalairachAVI_inputs(): in_file=dict( argstr='--i %s', mandatory=True, + usedefault=True, ), out_file=dict( argstr='--xfm %s', mandatory=True, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = TalairachAVI.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py index d07e572365..11ddab6588 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py @@ -14,8 +14,9 @@ def test_TalairachQC_inputs(): argstr='%s', mandatory=True, position=0, + usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = TalairachQC.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py index 17f8e53a1f..bd785e45cc 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py @@ -10,7 +10,10 @@ def test_Tkregister2_inputs(): nohash=True, usedefault=True, ), - fsl_in_matrix=dict(argstr='--fsl %s', ), + fsl_in_matrix=dict( + argstr='--fsl %s', + usedefault=True, + ), fsl_out=dict(argstr='--fslregout %s', ), fstal=dict( argstr='--fstal', @@ -25,11 +28,15 @@ def test_Tkregister2_inputs(): argstr='--ltaout-inv', requires=['lta_in'], ), - lta_in=dict(argstr='--lta %s', ), + lta_in=dict( + argstr='--lta %s', + usedefault=True, + ), lta_out=dict(argstr='--ltaout %s', ), moving_image=dict( argstr='--mov %s', mandatory=True, + usedefault=True, ), movscale=dict(argstr='--movscale %f', ), noedit=dict( @@ -43,12 +50,16 @@ def test_Tkregister2_inputs(): ), reg_header=dict(argstr='--regheader', ), subject_id=dict(argstr='--s %s', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), target_image=dict( argstr='--targ %s', + usedefault=True, xor=['fstarg'], ), - xfm=dict(argstr='--xfm %s', ), + xfm=dict( + argstr='--xfm %s', + usedefault=True, + ), ) inputs = Tkregister2.input_spec() @@ -57,9 +68,9 @@ def test_Tkregister2_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Tkregister2_outputs(): output_map = dict( - fsl_file=dict(), - lta_file=dict(), - reg_file=dict(), + fsl_file=dict(usedefault=True, ), + lta_file=dict(usedefault=True, ), + reg_file=dict(usedefault=True, ), ) outputs = Tkregister2.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py index 9427e60940..3f2168c4ca 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py @@ -9,6 +9,7 @@ def test_UnpackSDICOMDir_inputs(): config=dict( argstr='-cfg %s', mandatory=True, + usedefault=True, xor=('run_info', 'config', 'seq_config'), ), dir_structure=dict(argstr='-%s', ), @@ -16,27 +17,38 @@ def test_UnpackSDICOMDir_inputs(): nohash=True, usedefault=True, ), - log_file=dict(argstr='-log %s', ), + log_file=dict( + argstr='-log %s', + usedefault=True, + ), no_info_dump=dict(argstr='-noinfodump', ), no_unpack_err=dict(argstr='-no-unpackerr', ), - output_dir=dict(argstr='-targ %s', ), + output_dir=dict( + argstr='-targ %s', + usedefault=True, + ), run_info=dict( argstr='-run %d %s %s %s', mandatory=True, xor=('run_info', 'config', 'seq_config'), ), - scan_only=dict(argstr='-scanonly %s', ), + scan_only=dict( + argstr='-scanonly %s', + usedefault=True, + ), seq_config=dict( argstr='-seqcfg %s', mandatory=True, + usedefault=True, xor=('run_info', 'config', 'seq_config'), ), source_dir=dict( argstr='-src %s', mandatory=True, + usedefault=True, ), spm_zeropad=dict(argstr='-nspmzeropad %d', ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = UnpackSDICOMDir.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py b/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py index 3e898a81f7..0fb8d0e709 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py @@ -6,7 +6,10 @@ def test_VolumeMask_inputs(): input_map = dict( args=dict(argstr='%s', ), - aseg=dict(xor=['in_aseg'], ), + aseg=dict( + usedefault=True, + xor=['in_aseg'], + ), copy_inputs=dict(), environ=dict( nohash=True, @@ -14,6 +17,7 @@ def test_VolumeMask_inputs(): ), in_aseg=dict( argstr='--aseg_name %s', + usedefault=True, xor=['aseg'], ), left_ribbonlabel=dict( @@ -24,10 +28,22 @@ def test_VolumeMask_inputs(): argstr='--label_left_white %d', mandatory=True, ), - lh_pial=dict(mandatory=True, ), - lh_white=dict(mandatory=True, ), - rh_pial=dict(mandatory=True, ), - rh_white=dict(mandatory=True, ), + lh_pial=dict( + mandatory=True, + usedefault=True, + ), + lh_white=dict( + mandatory=True, + usedefault=True, + ), + rh_pial=dict( + mandatory=True, + usedefault=True, + ), + rh_white=dict( + mandatory=True, + usedefault=True, + ), right_ribbonlabel=dict( argstr='--label_right_ribbon %d', mandatory=True, @@ -43,7 +59,7 @@ def test_VolumeMask_inputs(): position=-1, usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), ) inputs = VolumeMask.input_spec() @@ -52,9 +68,9 @@ def test_VolumeMask_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_VolumeMask_outputs(): output_map = dict( - lh_ribbon=dict(), - out_ribbon=dict(), - rh_ribbon=dict(), + lh_ribbon=dict(usedefault=True, ), + out_ribbon=dict(usedefault=True, ), + rh_ribbon=dict(usedefault=True, ), ) outputs = VolumeMask.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py b/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py index 3586e7d234..e7b777f54a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py @@ -9,6 +9,7 @@ def test_WatershedSkullStrip_inputs(): brain_atlas=dict( argstr='-brain_atlas %s', position=-4, + usedefault=True, ), environ=dict( nohash=True, @@ -18,6 +19,7 @@ def test_WatershedSkullStrip_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), out_file=dict( argstr='%s', @@ -25,11 +27,12 @@ def test_WatershedSkullStrip_inputs(): position=-1, usedefault=True, ), - subjects_dir=dict(), + subjects_dir=dict(usedefault=True, ), t1=dict(argstr='-T1', ), transform=dict( argstr='%s', position=-3, + usedefault=True, ), ) inputs = WatershedSkullStrip.input_spec() @@ -38,7 +41,7 @@ def test_WatershedSkullStrip_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WatershedSkullStrip_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = WatershedSkullStrip.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_AR1Image.py b/nipype/interfaces/fsl/tests/test_auto_AR1Image.py index 32efb1826e..a579e1ddd0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AR1Image.py +++ b/nipype/interfaces/fsl/tests/test_auto_AR1Image.py @@ -19,6 +19,7 @@ def test_AR1Image_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -33,6 +34,7 @@ def test_AR1Image_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -46,7 +48,7 @@ def test_AR1Image_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AR1Image_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = AR1Image.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py b/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py index 062d6367f7..615a8b366e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py +++ b/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py @@ -20,11 +20,13 @@ def test_AccuracyTester_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), trained_wts_file=dict( argstr='%s', mandatory=True, position=1, + usedefault=True, ), ) inputs = AccuracyTester.input_spec() @@ -37,6 +39,7 @@ def test_AccuracyTester_outputs(): output_directory=dict( argstr='%s', position=1, + usedefault=True, ), ) outputs = AccuracyTester.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py index 8a39956c18..4d7f79dcfd 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py @@ -14,6 +14,7 @@ def test_ApplyMask_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -23,6 +24,7 @@ def test_ApplyMask_inputs(): argstr='-mas %s', mandatory=True, position=4, + usedefault=True, ), nan2zeros=dict( argstr='-nan', @@ -33,6 +35,7 @@ def test_ApplyMask_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -46,7 +49,7 @@ def test_ApplyMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyMask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ApplyMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py index 7a803f9695..8a8c03dc3d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py @@ -10,6 +10,7 @@ def test_ApplyTOPUP_inputs(): encoding_file=dict( argstr='--datain=%s', mandatory=True, + usedefault=True, ), environ=dict( nohash=True, @@ -28,10 +29,12 @@ def test_ApplyTOPUP_inputs(): argstr='--topup=%s', copyfile=False, requires=['in_topup_movpar'], + usedefault=True, ), in_topup_movpar=dict( copyfile=False, requires=['in_topup_fieldcoef'], + usedefault=True, ), interp=dict(argstr='--interp=%s', ), method=dict(argstr='--method=%s', ), @@ -39,6 +42,7 @@ def test_ApplyTOPUP_inputs(): argstr='--out=%s', name_source=['in_files'], name_template='%s_corrected', + usedefault=True, ), output_type=dict(), ) @@ -48,7 +52,7 @@ def test_ApplyTOPUP_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyTOPUP_outputs(): - output_map = dict(out_corrected=dict(), ) + output_map = dict(out_corrected=dict(usedefault=True, ), ) outputs = ApplyTOPUP.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py index 71977cb873..5fa27c8d36 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py @@ -15,30 +15,45 @@ def test_ApplyWarp_inputs(): nohash=True, usedefault=True, ), - field_file=dict(argstr='--warp=%s', ), + field_file=dict( + argstr='--warp=%s', + usedefault=True, + ), in_file=dict( argstr='--in=%s', mandatory=True, position=0, + usedefault=True, ), interp=dict( argstr='--interp=%s', position=-2, ), - mask_file=dict(argstr='--mask=%s', ), + mask_file=dict( + argstr='--mask=%s', + usedefault=True, + ), out_file=dict( argstr='--out=%s', genfile=True, hash_files=False, position=2, + usedefault=True, ), output_type=dict(), - postmat=dict(argstr='--postmat=%s', ), - premat=dict(argstr='--premat=%s', ), + postmat=dict( + argstr='--postmat=%s', + usedefault=True, + ), + premat=dict( + argstr='--premat=%s', + usedefault=True, + ), ref_file=dict( argstr='--ref=%s', mandatory=True, position=1, + usedefault=True, ), relwarp=dict( argstr='--rel', @@ -54,7 +69,7 @@ def test_ApplyWarp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyWarp_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ApplyWarp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py b/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py index f515be1f04..9f1b52b701 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py @@ -45,10 +45,12 @@ def test_ApplyXFM_inputs(): fieldmap=dict( argstr='-fieldmap %s', min_ver='5.0.0', + usedefault=True, ), fieldmapmask=dict( argstr='-fieldmapmask %s', min_ver='5.0.0', + usedefault=True, ), fine_search=dict( argstr='-finesearch %d', @@ -59,9 +61,16 @@ def test_ApplyXFM_inputs(): argstr='-in %s', mandatory=True, position=0, + usedefault=True, + ), + in_matrix_file=dict( + argstr='-init %s', + usedefault=True, + ), + in_weight=dict( + argstr='-inweight %s', + usedefault=True, ), - in_matrix_file=dict(argstr='-init %s', ), - in_weight=dict(argstr='-inweight %s', ), interp=dict(argstr='-interp %s', ), min_sampling=dict( argstr='-minsampling %f', @@ -77,12 +86,14 @@ def test_ApplyXFM_inputs(): name_source=['in_file'], name_template='%s_flirt', position=2, + usedefault=True, ), out_log=dict( keep_extension=True, name_source=['in_file'], name_template='%s_flirt.log', requires=['save_log'], + usedefault=True, ), out_matrix_file=dict( argstr='-omat %s', @@ -91,6 +102,7 @@ def test_ApplyXFM_inputs(): name_source=['in_file'], name_template='%s_flirt.mat', position=3, + usedefault=True, ), output_type=dict(), padding_size=dict( @@ -101,15 +113,22 @@ def test_ApplyXFM_inputs(): argstr='-pedir %d', min_ver='5.0.0', ), - ref_weight=dict(argstr='-refweight %s', ), + ref_weight=dict( + argstr='-refweight %s', + usedefault=True, + ), reference=dict( argstr='-ref %s', mandatory=True, position=1, + usedefault=True, ), rigid2D=dict(argstr='-2D', ), save_log=dict(), - schedule=dict(argstr='-schedule %s', ), + schedule=dict( + argstr='-schedule %s', + usedefault=True, + ), searchr_x=dict( argstr='-searchrx %s', units='degrees', @@ -132,14 +151,17 @@ def test_ApplyXFM_inputs(): wm_seg=dict( argstr='-wmseg %s', min_ver='5.0.0', + usedefault=True, ), wmcoords=dict( argstr='-wmcoords %s', min_ver='5.0.0', + usedefault=True, ), wmnorms=dict( argstr='-wmnorms %s', min_ver='5.0.0', + usedefault=True, ), ) inputs = ApplyXFM.input_spec() @@ -149,9 +171,9 @@ def test_ApplyXFM_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyXFM_outputs(): output_map = dict( - out_file=dict(), - out_log=dict(), - out_matrix_file=dict(), + out_file=dict(usedefault=True, ), + out_log=dict(usedefault=True, ), + out_matrix_file=dict(usedefault=True, ), ) outputs = ApplyXFM.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_AvScale.py b/nipype/interfaces/fsl/tests/test_auto_AvScale.py index 762ada916d..0c0f6cc21a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AvScale.py +++ b/nipype/interfaces/fsl/tests/test_auto_AvScale.py @@ -14,10 +14,12 @@ def test_AvScale_inputs(): mat_file=dict( argstr='%s', position=-2, + usedefault=True, ), ref_file=dict( argstr='%s', position=-1, + usedefault=True, ), ) inputs = AvScale.input_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_B0Calc.py b/nipype/interfaces/fsl/tests/test_auto_B0Calc.py index 96ec6b949c..6037a02cff 100644 --- a/nipype/interfaces/fsl/tests/test_auto_B0Calc.py +++ b/nipype/interfaces/fsl/tests/test_auto_B0Calc.py @@ -34,6 +34,7 @@ def test_B0Calc_inputs(): argstr='-i %s', mandatory=True, position=0, + usedefault=True, ), out_file=dict( argstr='-o %s', @@ -41,6 +42,7 @@ def test_B0Calc_inputs(): name_template='%s_b0field', output_name='out_file', position=1, + usedefault=True, ), output_type=dict(), x_b0=dict( @@ -81,7 +83,7 @@ def test_B0Calc_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_B0Calc_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = B0Calc.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py index 1ac5db111b..ab53f454a4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py +++ b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py @@ -18,13 +18,22 @@ def test_BEDPOSTX5_inputs(): argstr='--burnin_noard=%d', usedefault=True, ), - bvals=dict(mandatory=True, ), - bvecs=dict(mandatory=True, ), + bvals=dict( + mandatory=True, + usedefault=True, + ), + bvecs=dict( + mandatory=True, + usedefault=True, + ), cnlinear=dict( argstr='--cnonlinear', xor=('no_spat', 'non_linear', 'cnlinear'), ), - dwi=dict(mandatory=True, ), + dwi=dict( + mandatory=True, + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -42,10 +51,16 @@ def test_BEDPOSTX5_inputs(): usedefault=True, ), fudge=dict(argstr='-w %d', ), - grad_dev=dict(), + grad_dev=dict(usedefault=True, ), gradnonlin=dict(argstr='-g', ), - logdir=dict(argstr='--logdir=%s', ), - mask=dict(mandatory=True, ), + logdir=dict( + argstr='--logdir=%s', + usedefault=True, + ), + mask=dict( + mandatory=True, + usedefault=True, + ), model=dict(argstr='-model %d', ), n_fibres=dict( argstr='-n %d', @@ -96,8 +111,8 @@ def test_BEDPOSTX5_outputs(): output_map = dict( dyads=dict(), dyads_dispersion=dict(), - mean_S0samples=dict(), - mean_dsamples=dict(), + mean_S0samples=dict(usedefault=True, ), + mean_dsamples=dict(usedefault=True, ), mean_fsamples=dict(), mean_phsamples=dict(), mean_thsamples=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_BET.py b/nipype/interfaces/fsl/tests/test_auto_BET.py index eccf348b3e..d7f8341811 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BET.py +++ b/nipype/interfaces/fsl/tests/test_auto_BET.py @@ -24,6 +24,7 @@ def test_BET_inputs(): argstr='%s', mandatory=True, position=0, + usedefault=True, ), mask=dict(argstr='-m', ), mesh=dict(argstr='-e', ), @@ -33,6 +34,7 @@ def test_BET_inputs(): genfile=True, hash_files=False, position=1, + usedefault=True, ), outline=dict(argstr='-o', ), output_type=dict(), @@ -68,6 +70,7 @@ def test_BET_inputs(): ), t2_guided=dict( argstr='-A2 %s', + usedefault=True, xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), ), @@ -81,17 +84,17 @@ def test_BET_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BET_outputs(): output_map = dict( - inskull_mask_file=dict(), - inskull_mesh_file=dict(), - mask_file=dict(), - meshfile=dict(), - out_file=dict(), - outline_file=dict(), - outskin_mask_file=dict(), - outskin_mesh_file=dict(), - outskull_mask_file=dict(), - outskull_mesh_file=dict(), - skull_mask_file=dict(), + inskull_mask_file=dict(usedefault=True, ), + inskull_mesh_file=dict(usedefault=True, ), + mask_file=dict(usedefault=True, ), + meshfile=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), + outline_file=dict(usedefault=True, ), + outskin_mask_file=dict(usedefault=True, ), + outskin_mesh_file=dict(usedefault=True, ), + outskull_mask_file=dict(usedefault=True, ), + outskull_mesh_file=dict(usedefault=True, ), + skull_mask_file=dict(usedefault=True, ), ) outputs = BET.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py index 2548ae68e5..c33648ccda 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py @@ -14,6 +14,7 @@ def test_BinaryMaths_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -27,6 +28,7 @@ def test_BinaryMaths_inputs(): argstr='%s', mandatory=True, position=5, + usedefault=True, xor=['operand_value'], ), operand_value=dict( @@ -45,6 +47,7 @@ def test_BinaryMaths_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -58,7 +61,7 @@ def test_BinaryMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinaryMaths_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = BinaryMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py index aab508f2bf..c4f60c5862 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py +++ b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py @@ -14,6 +14,7 @@ def test_ChangeDataType_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -28,6 +29,7 @@ def test_ChangeDataType_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -42,7 +44,7 @@ def test_ChangeDataType_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ChangeDataType_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ChangeDataType.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Classifier.py b/nipype/interfaces/fsl/tests/test_auto_Classifier.py index a8db888acb..784e75a250 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Classifier.py +++ b/nipype/interfaces/fsl/tests/test_auto_Classifier.py @@ -6,7 +6,7 @@ def test_Classifier_inputs(): input_map = dict( args=dict(argstr='%s', ), - artifacts_list_file=dict(), + artifacts_list_file=dict(usedefault=True, ), environ=dict( nohash=True, usedefault=True, @@ -15,6 +15,7 @@ def test_Classifier_inputs(): argstr='%s', copyfile=False, position=1, + usedefault=True, ), thresh=dict( argstr='%d', @@ -26,6 +27,7 @@ def test_Classifier_inputs(): copyfile=False, mandatory=True, position=2, + usedefault=True, ), ) inputs = Classifier.input_spec() @@ -34,7 +36,7 @@ def test_Classifier_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Classifier_outputs(): - output_map = dict(artifacts_list_file=dict(), ) + output_map = dict(artifacts_list_file=dict(usedefault=True, ), ) outputs = Classifier.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Cleaner.py b/nipype/interfaces/fsl/tests/test_auto_Cleaner.py index 5fc505a174..e5fac9f4f8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cleaner.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cleaner.py @@ -14,6 +14,7 @@ def test_Cleaner_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), cleanup_motion=dict( argstr='-m', @@ -47,7 +48,7 @@ def test_Cleaner_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Cleaner_outputs(): - output_map = dict(cleaned_functional_file=dict(), ) + output_map = dict(cleaned_functional_file=dict(usedefault=True, ), ) outputs = Cleaner.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Cluster.py b/nipype/interfaces/fsl/tests/test_auto_Cluster.py index f876f85e64..ac36533a80 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cluster.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cluster.py @@ -24,6 +24,7 @@ def test_Cluster_inputs(): in_file=dict( argstr='--in=%s', mandatory=True, + usedefault=True, ), minclustersize=dict( argstr='--minclustersize', @@ -72,7 +73,10 @@ def test_Cluster_inputs(): argstr='--pthresh=%.10f', requires=['dlh', 'volume'], ), - std_space_file=dict(argstr='--stdvol=%s', ), + std_space_file=dict( + argstr='--stdvol=%s', + usedefault=True, + ), threshold=dict( argstr='--thresh=%.10f', mandatory=True, @@ -82,8 +86,14 @@ def test_Cluster_inputs(): usedefault=True, ), volume=dict(argstr='--volume=%d', ), - warpfield_file=dict(argstr='--warpvol=%s', ), - xfm_file=dict(argstr='--xfm=%s', ), + warpfield_file=dict( + argstr='--warpvol=%s', + usedefault=True, + ), + xfm_file=dict( + argstr='--xfm=%s', + usedefault=True, + ), ) inputs = Cluster.input_spec() @@ -92,14 +102,14 @@ def test_Cluster_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Cluster_outputs(): output_map = dict( - index_file=dict(), - localmax_txt_file=dict(), - localmax_vol_file=dict(), - max_file=dict(), - mean_file=dict(), - pval_file=dict(), - size_file=dict(), - threshold_file=dict(), + index_file=dict(usedefault=True, ), + localmax_txt_file=dict(usedefault=True, ), + localmax_vol_file=dict(usedefault=True, ), + max_file=dict(usedefault=True, ), + mean_file=dict(usedefault=True, ), + pval_file=dict(usedefault=True, ), + size_file=dict(usedefault=True, ), + threshold_file=dict(usedefault=True, ), ) outputs = Cluster.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Complex.py b/nipype/interfaces/fsl/tests/test_auto_Complex.py index 7e49bcdfa8..31f83f5b75 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Complex.py +++ b/nipype/interfaces/fsl/tests/test_auto_Complex.py @@ -17,10 +17,12 @@ def test_Complex_inputs(): complex_in_file=dict( argstr='%s', position=2, + usedefault=True, ), complex_in_file2=dict( argstr='%s', position=3, + usedefault=True, ), complex_merge=dict( argstr='-complexmerge', @@ -35,6 +37,7 @@ def test_Complex_inputs(): argstr='%s', genfile=True, position=-3, + usedefault=True, xor=[ 'complex_out_file', 'magnitude_out_file', 'phase_out_file', 'real_out_file', 'imaginary_out_file', 'real_polar', @@ -68,11 +71,13 @@ def test_Complex_inputs(): imaginary_in_file=dict( argstr='%s', position=3, + usedefault=True, ), imaginary_out_file=dict( argstr='%s', genfile=True, position=-3, + usedefault=True, xor=[ 'complex_out_file', 'magnitude_out_file', 'phase_out_file', 'real_polar', 'complex_cartesian', 'complex_polar', @@ -82,11 +87,13 @@ def test_Complex_inputs(): magnitude_in_file=dict( argstr='%s', position=2, + usedefault=True, ), magnitude_out_file=dict( argstr='%s', genfile=True, position=-4, + usedefault=True, xor=[ 'complex_out_file', 'real_out_file', 'imaginary_out_file', 'real_cartesian', 'complex_cartesian', 'complex_polar', @@ -97,11 +104,13 @@ def test_Complex_inputs(): phase_in_file=dict( argstr='%s', position=3, + usedefault=True, ), phase_out_file=dict( argstr='%s', genfile=True, position=-3, + usedefault=True, xor=[ 'complex_out_file', 'real_out_file', 'imaginary_out_file', 'real_cartesian', 'complex_cartesian', 'complex_polar', @@ -119,11 +128,13 @@ def test_Complex_inputs(): real_in_file=dict( argstr='%s', position=2, + usedefault=True, ), real_out_file=dict( argstr='%s', genfile=True, position=-4, + usedefault=True, xor=[ 'complex_out_file', 'magnitude_out_file', 'phase_out_file', 'real_polar', 'complex_cartesian', 'complex_polar', @@ -150,11 +161,11 @@ def test_Complex_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Complex_outputs(): output_map = dict( - complex_out_file=dict(), - imaginary_out_file=dict(), - magnitude_out_file=dict(), - phase_out_file=dict(), - real_out_file=dict(), + complex_out_file=dict(usedefault=True, ), + imaginary_out_file=dict(usedefault=True, ), + magnitude_out_file=dict(usedefault=True, ), + phase_out_file=dict(usedefault=True, ), + real_out_file=dict(usedefault=True, ), ) outputs = Complex.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py index a82ea8fe43..928f84fcf7 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py +++ b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py @@ -10,17 +10,22 @@ def test_ContrastMgr_inputs(): corrections=dict( copyfile=False, mandatory=True, + usedefault=True, ), dof_file=dict( argstr='', copyfile=False, mandatory=True, + usedefault=True, ), environ=dict( nohash=True, usedefault=True, ), - fcon_file=dict(argstr='-f %s', ), + fcon_file=dict( + argstr='-f %s', + usedefault=True, + ), output_type=dict(), param_estimates=dict( argstr='', @@ -32,12 +37,14 @@ def test_ContrastMgr_inputs(): copyfile=False, mandatory=True, position=-2, + usedefault=True, ), suffix=dict(argstr='-suffix %s', ), tcon_file=dict( argstr='%s', mandatory=True, position=-1, + usedefault=True, ), ) inputs = ContrastMgr.input_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py index 2ed14aaad2..3bb8bebf8b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py @@ -17,7 +17,10 @@ def test_ConvertWarp_inputs(): ), jacobian_max=dict(argstr='--jmax=%f', ), jacobian_min=dict(argstr='--jmin=%f', ), - midmat=dict(argstr='--midmat=%s', ), + midmat=dict( + argstr='--midmat=%s', + usedefault=True, + ), out_abswarp=dict( argstr='--absout', xor=['out_relwarp'], @@ -28,18 +31,26 @@ def test_ConvertWarp_inputs(): name_template='%s_concatwarp', output_name='out_file', position=-1, + usedefault=True, ), out_relwarp=dict( argstr='--relout', xor=['out_abswarp'], ), output_type=dict(), - postmat=dict(argstr='--postmat=%s', ), - premat=dict(argstr='--premat=%s', ), + postmat=dict( + argstr='--postmat=%s', + usedefault=True, + ), + premat=dict( + argstr='--premat=%s', + usedefault=True, + ), reference=dict( argstr='--ref=%s', mandatory=True, position=1, + usedefault=True, ), relwarp=dict( argstr='--rel', @@ -49,9 +60,18 @@ def test_ConvertWarp_inputs(): argstr='--shiftdir=%s', requires=['shift_in_file'], ), - shift_in_file=dict(argstr='--shiftmap=%s', ), - warp1=dict(argstr='--warp1=%s', ), - warp2=dict(argstr='--warp2=%s', ), + shift_in_file=dict( + argstr='--shiftmap=%s', + usedefault=True, + ), + warp1=dict( + argstr='--warp1=%s', + usedefault=True, + ), + warp2=dict( + argstr='--warp2=%s', + usedefault=True, + ), ) inputs = ConvertWarp.input_spec() @@ -59,7 +79,7 @@ def test_ConvertWarp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConvertWarp_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ConvertWarp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py index c017a39a52..dd23d7dbde 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py @@ -26,10 +26,12 @@ def test_ConvertXFM_inputs(): argstr='%s', mandatory=True, position=-1, + usedefault=True, ), in_file2=dict( argstr='%s', position=-2, + usedefault=True, ), invert_xfm=dict( argstr='-inverse', @@ -41,6 +43,7 @@ def test_ConvertXFM_inputs(): genfile=True, hash_files=False, position=1, + usedefault=True, ), output_type=dict(), ) @@ -50,7 +53,7 @@ def test_ConvertXFM_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConvertXFM_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ConvertXFM.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py index c66feff211..499e76adc3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py +++ b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py @@ -14,6 +14,7 @@ def test_CopyGeom_inputs(): name_template='%s', output_name='out_file', position=1, + usedefault=True, ), environ=dict( nohash=True, @@ -27,6 +28,7 @@ def test_CopyGeom_inputs(): argstr='%s', mandatory=True, position=0, + usedefault=True, ), output_type=dict(), ) @@ -36,7 +38,7 @@ def test_CopyGeom_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CopyGeom_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = CopyGeom.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py index b1d3b4822d..260d59b11a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py @@ -15,28 +15,38 @@ def test_DTIFit_inputs(): argstr='-b %s', mandatory=True, position=4, + usedefault=True, ), bvecs=dict( argstr='-r %s', mandatory=True, position=3, + usedefault=True, + ), + cni=dict( + argstr='--cni=%s', + usedefault=True, ), - cni=dict(argstr='--cni=%s', ), dwi=dict( argstr='-k %s', mandatory=True, position=0, + usedefault=True, ), environ=dict( nohash=True, usedefault=True, ), - gradnonlin=dict(argstr='--gradnonlin=%s', ), + gradnonlin=dict( + argstr='--gradnonlin=%s', + usedefault=True, + ), little_bit=dict(argstr='--littlebit', ), mask=dict( argstr='-m %s', mandatory=True, position=2, + usedefault=True, ), max_x=dict(argstr='-X %d', ), max_y=dict(argstr='-Y %d', ), @@ -55,18 +65,18 @@ def test_DTIFit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DTIFit_outputs(): output_map = dict( - FA=dict(), - L1=dict(), - L2=dict(), - L3=dict(), - MD=dict(), - MO=dict(), - S0=dict(), - V1=dict(), - V2=dict(), - V3=dict(), - sse=dict(), - tensor=dict(), + FA=dict(usedefault=True, ), + L1=dict(usedefault=True, ), + L2=dict(usedefault=True, ), + L3=dict(usedefault=True, ), + MD=dict(usedefault=True, ), + MO=dict(usedefault=True, ), + S0=dict(usedefault=True, ), + V1=dict(usedefault=True, ), + V2=dict(usedefault=True, ), + V3=dict(usedefault=True, ), + sse=dict(usedefault=True, ), + tensor=dict(usedefault=True, ), ) outputs = DTIFit.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py index 3ed43fbd22..9d748e6edc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py @@ -14,6 +14,7 @@ def test_DilateImage_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -22,6 +23,7 @@ def test_DilateImage_inputs(): kernel_file=dict( argstr='%s', position=5, + usedefault=True, xor=['kernel_size'], ), kernel_shape=dict( @@ -47,6 +49,7 @@ def test_DilateImage_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -60,7 +63,7 @@ def test_DilateImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DilateImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = DilateImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py index 5f3321de78..1caf8a1926 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py +++ b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py @@ -10,6 +10,7 @@ def test_DistanceMap_inputs(): argstr='--out=%s', genfile=True, hash_files=False, + usedefault=True, ), environ=dict( nohash=True, @@ -18,13 +19,17 @@ def test_DistanceMap_inputs(): in_file=dict( argstr='--in=%s', mandatory=True, + usedefault=True, ), invert_input=dict(argstr='--invert', ), local_max_file=dict( argstr='--localmax=%s', hash_files=False, ), - mask_file=dict(argstr='--mask=%s', ), + mask_file=dict( + argstr='--mask=%s', + usedefault=True, + ), output_type=dict(), ) inputs = DistanceMap.input_spec() @@ -34,8 +39,8 @@ def test_DistanceMap_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DistanceMap_outputs(): output_map = dict( - distance_map=dict(), - local_max_file=dict(), + distance_map=dict(usedefault=True, ), + local_max_file=dict(usedefault=True, ), ) outputs = DistanceMap.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_DualRegression.py b/nipype/interfaces/fsl/tests/test_auto_DualRegression.py index 4c2fdd3ceb..4d69e0609f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DualRegression.py +++ b/nipype/interfaces/fsl/tests/test_auto_DualRegression.py @@ -9,6 +9,7 @@ def test_DualRegression_inputs(): con_file=dict( argstr='%s', position=4, + usedefault=True, ), des_norm=dict( argstr='%i', @@ -18,6 +19,7 @@ def test_DualRegression_inputs(): design_file=dict( argstr='%s', position=3, + usedefault=True, ), environ=dict( nohash=True, @@ -27,6 +29,7 @@ def test_DualRegression_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), in_files=dict( argstr='%s', @@ -57,7 +60,7 @@ def test_DualRegression_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DualRegression_outputs(): - output_map = dict(out_dir=dict(), ) + output_map = dict(out_dir=dict(usedefault=True, ), ) outputs = DualRegression.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py index 2a5f0c86b6..eb226f6bee 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py @@ -10,12 +10,16 @@ def test_EPIDeWarp_inputs(): dph_file=dict( argstr='--dph %s', mandatory=True, + usedefault=True, ), environ=dict( nohash=True, usedefault=True, ), - epi_file=dict(argstr='--epi %s', ), + epi_file=dict( + argstr='--epi %s', + usedefault=True, + ), epidw=dict( argstr='--epidw %s', genfile=False, @@ -24,7 +28,10 @@ def test_EPIDeWarp_inputs(): argstr='--esp %s', usedefault=True, ), - exf_file=dict(argstr='--exf %s', ), + exf_file=dict( + argstr='--exf %s', + usedefault=True, + ), exfdw=dict( argstr='--exfdw %s', genfile=True, @@ -33,6 +40,7 @@ def test_EPIDeWarp_inputs(): argstr='--mag %s', mandatory=True, position=0, + usedefault=True, ), nocleanup=dict( argstr='--nocleanup', @@ -63,10 +71,10 @@ def test_EPIDeWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EPIDeWarp_outputs(): output_map = dict( - exf_mask=dict(), - exfdw=dict(), - unwarped_file=dict(), - vsm_file=dict(), + exf_mask=dict(usedefault=True, ), + exfdw=dict(usedefault=True, ), + unwarped_file=dict(usedefault=True, ), + vsm_file=dict(usedefault=True, ), ) outputs = EPIDeWarp.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Eddy.py b/nipype/interfaces/fsl/tests/test_auto_Eddy.py index 55d9409e17..6457370353 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Eddy.py +++ b/nipype/interfaces/fsl/tests/test_auto_Eddy.py @@ -18,7 +18,10 @@ def test_Eddy_inputs(): ), fep=dict(argstr='--fep', ), field=dict(argstr='--field=%s', ), - field_mat=dict(argstr='--field_mat=%s', ), + field_mat=dict( + argstr='--field_mat=%s', + usedefault=True, + ), flm=dict(argstr='--flm=%s', ), fudge_factor=dict( argstr='--ff=%s', @@ -28,32 +31,42 @@ def test_Eddy_inputs(): in_acqp=dict( argstr='--acqp=%s', mandatory=True, + usedefault=True, ), in_bval=dict( argstr='--bvals=%s', mandatory=True, + usedefault=True, ), in_bvec=dict( argstr='--bvecs=%s', mandatory=True, + usedefault=True, ), in_file=dict( argstr='--imain=%s', mandatory=True, + usedefault=True, ), in_index=dict( argstr='--index=%s', mandatory=True, + usedefault=True, ), in_mask=dict( argstr='--mask=%s', mandatory=True, + usedefault=True, ), in_topup_fieldcoef=dict( argstr='--topup=%s', requires=['in_topup_movpar'], + usedefault=True, + ), + in_topup_movpar=dict( + requires=['in_topup_fieldcoef'], + usedefault=True, ), - in_topup_movpar=dict(requires=['in_topup_fieldcoef'], ), interp=dict(argstr='--interp=%s', ), is_shelled=dict(argstr='--data_is_shelled', ), method=dict(argstr='--resamp=%s', ), @@ -79,7 +92,10 @@ def test_Eddy_inputs(): argstr='--residuals', min_ver='5.0.10', ), - session=dict(argstr='--session=%s', ), + session=dict( + argstr='--session=%s', + usedefault=True, + ), slm=dict(argstr='--slm=%s', ), use_cuda=dict(), ) @@ -90,15 +106,15 @@ def test_Eddy_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Eddy_outputs(): output_map = dict( - out_cnr_maps=dict(), - out_corrected=dict(), - out_movement_rms=dict(), - out_outlier_report=dict(), - out_parameter=dict(), - out_residuals=dict(), - out_restricted_movement_rms=dict(), - out_rotated_bvecs=dict(), - out_shell_alignment_parameters=dict(), + out_cnr_maps=dict(usedefault=True, ), + out_corrected=dict(usedefault=True, ), + out_movement_rms=dict(usedefault=True, ), + out_outlier_report=dict(usedefault=True, ), + out_parameter=dict(usedefault=True, ), + out_residuals=dict(usedefault=True, ), + out_restricted_movement_rms=dict(usedefault=True, ), + out_rotated_bvecs=dict(usedefault=True, ), + out_shell_alignment_parameters=dict(usedefault=True, ), ) outputs = Eddy.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py index e88219aa04..41de073264 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py +++ b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py @@ -14,6 +14,7 @@ def test_EddyCorrect_inputs(): argstr='%s', mandatory=True, position=0, + usedefault=True, ), out_file=dict( argstr='%s', @@ -21,6 +22,7 @@ def test_EddyCorrect_inputs(): name_template='%s_edc', output_name='eddy_corrected', position=1, + usedefault=True, ), output_type=dict(), ref_num=dict( @@ -36,7 +38,7 @@ def test_EddyCorrect_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EddyCorrect_outputs(): - output_map = dict(eddy_corrected=dict(), ) + output_map = dict(eddy_corrected=dict(usedefault=True, ), ) outputs = EddyCorrect.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py b/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py index 3cc6da2027..35afe6da13 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py +++ b/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py @@ -14,20 +14,29 @@ def test_EddyQuad_inputs(): bval_file=dict( argstr='--bvals %s', mandatory=True, + usedefault=True, + ), + bvec_file=dict( + argstr='--bvecs %s', + usedefault=True, ), - bvec_file=dict(argstr='--bvecs %s', ), environ=dict( nohash=True, usedefault=True, ), - field=dict(argstr='--field %s', ), + field=dict( + argstr='--field %s', + usedefault=True, + ), idx_file=dict( argstr='--eddyIdx %s', mandatory=True, + usedefault=True, ), mask_file=dict( argstr='--mask %s', mandatory=True, + usedefault=True, ), output_dir=dict( argstr='--output-dir %s', @@ -38,8 +47,12 @@ def test_EddyQuad_inputs(): param_file=dict( argstr='--eddyParams %s', mandatory=True, + usedefault=True, + ), + slice_spec=dict( + argstr='--slspec %s', + usedefault=True, ), - slice_spec=dict(argstr='--slspec %s', ), verbose=dict(argstr='--verbose', ), ) inputs = EddyQuad.input_spec() @@ -51,12 +64,12 @@ def test_EddyQuad_outputs(): output_map = dict( avg_b0_pe_png=dict(), avg_b_png=dict(), - clean_volumes=dict(), + clean_volumes=dict(usedefault=True, ), cnr_png=dict(), - qc_json=dict(), - qc_pdf=dict(), - residuals=dict(), - vdm_png=dict(), + qc_json=dict(usedefault=True, ), + qc_pdf=dict(usedefault=True, ), + residuals=dict(usedefault=True, ), + vdm_png=dict(usedefault=True, ), ) outputs = EddyQuad.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py index 634a75e376..351c4684ac 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py @@ -15,10 +15,20 @@ def test_EpiReg_inputs(): argstr='--epi=%s', mandatory=True, position=-4, + usedefault=True, + ), + fmap=dict( + argstr='--fmap=%s', + usedefault=True, + ), + fmapmag=dict( + argstr='--fmapmag=%s', + usedefault=True, + ), + fmapmagbrain=dict( + argstr='--fmapmagbrain=%s', + usedefault=True, ), - fmap=dict(argstr='--fmap=%s', ), - fmapmag=dict(argstr='--fmapmag=%s', ), - fmapmagbrain=dict(argstr='--fmapmagbrain=%s', ), no_clean=dict( argstr='--noclean', usedefault=True, @@ -35,14 +45,22 @@ def test_EpiReg_inputs(): argstr='--t1brain=%s', mandatory=True, position=-2, + usedefault=True, ), t1_head=dict( argstr='--t1=%s', mandatory=True, position=-3, + usedefault=True, + ), + weight_image=dict( + argstr='--weight=%s', + usedefault=True, + ), + wmseg=dict( + argstr='--wmseg=%s', + usedefault=True, ), - weight_image=dict(argstr='--weight=%s', ), - wmseg=dict(argstr='--wmseg=%s', ), ) inputs = EpiReg.input_spec() @@ -51,20 +69,20 @@ def test_EpiReg_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EpiReg_outputs(): output_map = dict( - epi2str_inv=dict(), - epi2str_mat=dict(), - fmap2epi_mat=dict(), - fmap2str_mat=dict(), - fmap_epi=dict(), - fmap_str=dict(), - fmapmag_str=dict(), - fullwarp=dict(), - out_1vol=dict(), - out_file=dict(), - seg=dict(), - shiftmap=dict(), - wmedge=dict(), - wmseg=dict(), + epi2str_inv=dict(usedefault=True, ), + epi2str_mat=dict(usedefault=True, ), + fmap2epi_mat=dict(usedefault=True, ), + fmap2str_mat=dict(usedefault=True, ), + fmap_epi=dict(usedefault=True, ), + fmap_str=dict(usedefault=True, ), + fmapmag_str=dict(usedefault=True, ), + fullwarp=dict(usedefault=True, ), + out_1vol=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), + seg=dict(usedefault=True, ), + shiftmap=dict(usedefault=True, ), + wmedge=dict(usedefault=True, ), + wmseg=dict(usedefault=True, ), ) outputs = EpiReg.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py index 797a403d45..997f810204 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py @@ -14,6 +14,7 @@ def test_ErodeImage_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -22,6 +23,7 @@ def test_ErodeImage_inputs(): kernel_file=dict( argstr='%s', position=5, + usedefault=True, xor=['kernel_size'], ), kernel_shape=dict( @@ -47,6 +49,7 @@ def test_ErodeImage_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -60,7 +63,7 @@ def test_ErodeImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ErodeImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ErodeImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py index df8de64144..4eec8dd12d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py +++ b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py @@ -22,6 +22,7 @@ def test_ExtractROI_inputs(): argstr='%s', mandatory=True, position=0, + usedefault=True, ), output_type=dict(), roi_file=dict( @@ -29,6 +30,7 @@ def test_ExtractROI_inputs(): genfile=True, hash_files=False, position=1, + usedefault=True, ), t_min=dict( argstr='%d', @@ -69,7 +71,7 @@ def test_ExtractROI_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ExtractROI_outputs(): - output_map = dict(roi_file=dict(), ) + output_map = dict(roi_file=dict(usedefault=True, ), ) outputs = ExtractROI.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_FAST.py b/nipype/interfaces/fsl/tests/test_auto_FAST.py index 0b983181af..51bf1329ba 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FAST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FAST.py @@ -24,15 +24,24 @@ def test_FAST_inputs(): position=-1, ), init_seg_smooth=dict(argstr='-f %.3f', ), - init_transform=dict(argstr='-a %s', ), + init_transform=dict( + argstr='-a %s', + usedefault=True, + ), iters_afterbias=dict(argstr='-O %d', ), - manual_seg=dict(argstr='-s %s', ), + manual_seg=dict( + argstr='-s %s', + usedefault=True, + ), mixel_smooth=dict(argstr='-R %.2f', ), no_bias=dict(argstr='-N', ), no_pve=dict(argstr='--nopve', ), number_classes=dict(argstr='-n %d', ), other_priors=dict(argstr='-A %s', ), - out_basename=dict(argstr='-o %s', ), + out_basename=dict( + argstr='-o %s', + usedefault=True, + ), output_biascorrected=dict(argstr='-B', ), output_biasfield=dict(argstr='-b', ), output_type=dict(), @@ -50,13 +59,13 @@ def test_FAST_inputs(): def test_FAST_outputs(): output_map = dict( bias_field=dict(), - mixeltype=dict(), + mixeltype=dict(usedefault=True, ), partial_volume_files=dict(), - partial_volume_map=dict(), + partial_volume_map=dict(usedefault=True, ), probability_maps=dict(), restored_image=dict(), tissue_class_files=dict(), - tissue_class_map=dict(), + tissue_class_map=dict(usedefault=True, ), ) outputs = FAST.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FEAT.py b/nipype/interfaces/fsl/tests/test_auto_FEAT.py index 01fc72506f..c2f96f43e2 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEAT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEAT.py @@ -14,6 +14,7 @@ def test_FEAT_inputs(): argstr='%s', mandatory=True, position=0, + usedefault=True, ), output_type=dict(), ) @@ -23,7 +24,7 @@ def test_FEAT_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FEAT_outputs(): - output_map = dict(feat_dir=dict(), ) + output_map = dict(feat_dir=dict(usedefault=True, ), ) outputs = FEAT.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py index 34ea37d47f..8fe45da4b7 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py @@ -21,6 +21,7 @@ def test_FEATModel_inputs(): copyfile=False, mandatory=True, position=0, + usedefault=True, ), output_type=dict(), ) @@ -31,11 +32,11 @@ def test_FEATModel_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FEATModel_outputs(): output_map = dict( - con_file=dict(), - design_cov=dict(), - design_file=dict(), - design_image=dict(), - fcon_file=dict(), + con_file=dict(usedefault=True, ), + design_cov=dict(usedefault=True, ), + design_file=dict(usedefault=True, ), + design_image=dict(usedefault=True, ), + fcon_file=dict(usedefault=True, ), ) outputs = FEATModel.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py index a8f59a0ec3..af21df478b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py @@ -7,7 +7,10 @@ def test_FEATRegister_inputs(): input_map = dict( feat_dirs=dict(mandatory=True, ), reg_dof=dict(usedefault=True, ), - reg_image=dict(mandatory=True, ), + reg_image=dict( + mandatory=True, + usedefault=True, + ), ) inputs = FEATRegister.input_spec() @@ -15,7 +18,7 @@ def test_FEATRegister_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FEATRegister_outputs(): - output_map = dict(fsf_file=dict(), ) + output_map = dict(fsf_file=dict(usedefault=True, ), ) outputs = FEATRegister.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_FIRST.py b/nipype/interfaces/fsl/tests/test_auto_FIRST.py index 964ee4922c..514a4fbbb1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FIRST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FIRST.py @@ -8,6 +8,7 @@ def test_FIRST_inputs(): affine_file=dict( argstr='-a %s', position=6, + usedefault=True, ), args=dict(argstr='%s', ), brain_extracted=dict( @@ -23,6 +24,7 @@ def test_FIRST_inputs(): copyfile=False, mandatory=True, position=-2, + usedefault=True, ), list_of_specific_structures=dict( argstr='-s %s', @@ -64,8 +66,8 @@ def test_FIRST_inputs(): def test_FIRST_outputs(): output_map = dict( bvars=dict(), - original_segmentations=dict(), - segmentation_file=dict(), + original_segmentations=dict(usedefault=True, ), + segmentation_file=dict(usedefault=True, ), vtk_surfaces=dict(), ) outputs = FIRST.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py index bd335282e3..5a455f9c92 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py @@ -10,21 +10,30 @@ def test_FLAMEO_inputs(): cope_file=dict( argstr='--copefile=%s', mandatory=True, + usedefault=True, ), cov_split_file=dict( argstr='--covsplitfile=%s', mandatory=True, + usedefault=True, ), design_file=dict( argstr='--designfile=%s', mandatory=True, + usedefault=True, + ), + dof_var_cope_file=dict( + argstr='--dofvarcopefile=%s', + usedefault=True, ), - dof_var_cope_file=dict(argstr='--dofvarcopefile=%s', ), environ=dict( nohash=True, usedefault=True, ), - f_con_file=dict(argstr='--fcontrastsfile=%s', ), + f_con_file=dict( + argstr='--fcontrastsfile=%s', + usedefault=True, + ), fix_mean=dict(argstr='--fixmean', ), infer_outliers=dict(argstr='--inferoutliers', ), log_dir=dict( @@ -34,6 +43,7 @@ def test_FLAMEO_inputs(): mask_file=dict( argstr='--maskfile=%s', mandatory=True, + usedefault=True, ), n_jumps=dict(argstr='--njumps=%d', ), no_pe_outputs=dict(argstr='--nopeoutput', ), @@ -48,8 +58,12 @@ def test_FLAMEO_inputs(): t_con_file=dict( argstr='--tcontrastsfile=%s', mandatory=True, + usedefault=True, + ), + var_cope_file=dict( + argstr='--varcopefile=%s', + usedefault=True, ), - var_cope_file=dict(argstr='--varcopefile=%s', ), ) inputs = FLAMEO.input_spec() @@ -63,7 +77,7 @@ def test_FLAMEO_outputs(): mrefvars=dict(), pes=dict(), res4d=dict(), - stats_dir=dict(), + stats_dir=dict(usedefault=True, ), tdof=dict(), tstats=dict(), var_copes=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py index 0b59550e5a..4794488674 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py @@ -42,10 +42,12 @@ def test_FLIRT_inputs(): fieldmap=dict( argstr='-fieldmap %s', min_ver='5.0.0', + usedefault=True, ), fieldmapmask=dict( argstr='-fieldmapmask %s', min_ver='5.0.0', + usedefault=True, ), fine_search=dict( argstr='-finesearch %d', @@ -56,9 +58,16 @@ def test_FLIRT_inputs(): argstr='-in %s', mandatory=True, position=0, + usedefault=True, + ), + in_matrix_file=dict( + argstr='-init %s', + usedefault=True, + ), + in_weight=dict( + argstr='-inweight %s', + usedefault=True, ), - in_matrix_file=dict(argstr='-init %s', ), - in_weight=dict(argstr='-inweight %s', ), interp=dict(argstr='-interp %s', ), min_sampling=dict( argstr='-minsampling %f', @@ -74,12 +83,14 @@ def test_FLIRT_inputs(): name_source=['in_file'], name_template='%s_flirt', position=2, + usedefault=True, ), out_log=dict( keep_extension=True, name_source=['in_file'], name_template='%s_flirt.log', requires=['save_log'], + usedefault=True, ), out_matrix_file=dict( argstr='-omat %s', @@ -88,6 +99,7 @@ def test_FLIRT_inputs(): name_source=['in_file'], name_template='%s_flirt.mat', position=3, + usedefault=True, ), output_type=dict(), padding_size=dict( @@ -98,15 +110,22 @@ def test_FLIRT_inputs(): argstr='-pedir %d', min_ver='5.0.0', ), - ref_weight=dict(argstr='-refweight %s', ), + ref_weight=dict( + argstr='-refweight %s', + usedefault=True, + ), reference=dict( argstr='-ref %s', mandatory=True, position=1, + usedefault=True, ), rigid2D=dict(argstr='-2D', ), save_log=dict(), - schedule=dict(argstr='-schedule %s', ), + schedule=dict( + argstr='-schedule %s', + usedefault=True, + ), searchr_x=dict( argstr='-searchrx %s', units='degrees', @@ -129,14 +148,17 @@ def test_FLIRT_inputs(): wm_seg=dict( argstr='-wmseg %s', min_ver='5.0.0', + usedefault=True, ), wmcoords=dict( argstr='-wmcoords %s', min_ver='5.0.0', + usedefault=True, ), wmnorms=dict( argstr='-wmnorms %s', min_ver='5.0.0', + usedefault=True, ), ) inputs = FLIRT.input_spec() @@ -146,9 +168,9 @@ def test_FLIRT_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FLIRT_outputs(): output_map = dict( - out_file=dict(), - out_log=dict(), - out_matrix_file=dict(), + out_file=dict(usedefault=True, ), + out_log=dict(usedefault=True, ), + out_matrix_file=dict(usedefault=True, ), ) outputs = FLIRT.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py index 2b7d0b1b00..052cc20231 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py @@ -5,7 +5,10 @@ def test_FNIRT_inputs(): input_map = dict( - affine_file=dict(argstr='--aff=%s', ), + affine_file=dict( + argstr='--aff=%s', + usedefault=True, + ), apply_inmask=dict( argstr='--applyinmask=%s', sep=',', @@ -39,6 +42,7 @@ def test_FNIRT_inputs(): in_file=dict( argstr='--in=%s', mandatory=True, + usedefault=True, ), in_fwhm=dict( argstr='--infwhm=%s', @@ -48,11 +52,17 @@ def test_FNIRT_inputs(): argstr='--intin=%s', copyfile=False, ), - inmask_file=dict(argstr='--inmask=%s', ), + inmask_file=dict( + argstr='--inmask=%s', + usedefault=True, + ), inmask_val=dict(argstr='--impinval=%f', ), intensity_mapping_model=dict(argstr='--intmod=%s', ), intensity_mapping_order=dict(argstr='--intorder=%d', ), - inwarp_file=dict(argstr='--inwarp=%s', ), + inwarp_file=dict( + argstr='--inwarp=%s', + usedefault=True, + ), jacobian_file=dict( argstr='--jout=%s', hash_files=False, @@ -62,6 +72,7 @@ def test_FNIRT_inputs(): argstr='--logout=%s', genfile=True, hash_files=False, + usedefault=True, ), max_nonlin_iter=dict( argstr='--miter=%s', @@ -79,12 +90,16 @@ def test_FNIRT_inputs(): ref_file=dict( argstr='--ref=%s', mandatory=True, + usedefault=True, ), ref_fwhm=dict( argstr='--reffwhm=%s', sep=',', ), - refmask_file=dict(argstr='--refmask=%s', ), + refmask_file=dict( + argstr='--refmask=%s', + usedefault=True, + ), refmask_val=dict(argstr='--imprefval=%f', ), regularization_lambda=dict( argstr='--lambda=%s', @@ -116,6 +131,7 @@ def test_FNIRT_inputs(): argstr='--iout=%s', genfile=True, hash_files=False, + usedefault=True, ), ) inputs = FNIRT.input_spec() @@ -125,13 +141,13 @@ def test_FNIRT_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FNIRT_outputs(): output_map = dict( - field_file=dict(), - fieldcoeff_file=dict(), - jacobian_file=dict(), - log_file=dict(), - modulatedref_file=dict(), + field_file=dict(usedefault=True, ), + fieldcoeff_file=dict(usedefault=True, ), + jacobian_file=dict(usedefault=True, ), + log_file=dict(usedefault=True, ), + modulatedref_file=dict(usedefault=True, ), out_intensitymap_file=dict(), - warped_file=dict(), + warped_file=dict(usedefault=True, ), ) outputs = FNIRT.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py index fd85eee3bf..23399e58f5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py @@ -21,10 +21,12 @@ def test_FSLXCommand_inputs(): bvals=dict( argstr='--bvals=%s', mandatory=True, + usedefault=True, ), bvecs=dict( argstr='--bvecs=%s', mandatory=True, + usedefault=True, ), cnlinear=dict( argstr='--cnonlinear', @@ -33,6 +35,7 @@ def test_FSLXCommand_inputs(): dwi=dict( argstr='--data=%s', mandatory=True, + usedefault=True, ), environ=dict( nohash=True, @@ -58,6 +61,7 @@ def test_FSLXCommand_inputs(): mask=dict( argstr='--mask=%s', mandatory=True, + usedefault=True, ), model=dict(argstr='--model=%d', ), n_fibres=dict( @@ -102,10 +106,10 @@ def test_FSLXCommand_outputs(): output_map = dict( dyads=dict(), fsamples=dict(), - mean_S0samples=dict(), - mean_dsamples=dict(), + mean_S0samples=dict(usedefault=True, ), + mean_dsamples=dict(usedefault=True, ), mean_fsamples=dict(), - mean_tausamples=dict(), + mean_tausamples=dict(usedefault=True, ), phsamples=dict(), thsamples=dict(), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py index 0e96f1e867..399555fd1a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py +++ b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py @@ -15,8 +15,14 @@ def test_FUGUE_inputs(): nohash=True, usedefault=True, ), - fmap_in_file=dict(argstr='--loadfmap=%s', ), - fmap_out_file=dict(argstr='--savefmap=%s', ), + fmap_in_file=dict( + argstr='--loadfmap=%s', + usedefault=True, + ), + fmap_out_file=dict( + argstr='--savefmap=%s', + usedefault=True, + ), forward_warping=dict(usedefault=True, ), fourier_order=dict(argstr='--fourier=%d', ), icorr=dict( @@ -27,8 +33,14 @@ def test_FUGUE_inputs(): argstr='--icorronly', requires=['unwarped_file'], ), - in_file=dict(argstr='--in=%s', ), - mask_file=dict(argstr='--mask=%s', ), + in_file=dict( + argstr='--in=%s', + usedefault=True, + ), + mask_file=dict( + argstr='--mask=%s', + usedefault=True, + ), median_2dfilter=dict(argstr='--median', ), no_extend=dict(argstr='--noextend', ), no_gap_fill=dict(argstr='--nofill', ), @@ -36,7 +48,10 @@ def test_FUGUE_inputs(): output_type=dict(), pava=dict(argstr='--pava', ), phase_conjugate=dict(argstr='--phaseconj', ), - phasemap_in_file=dict(argstr='--phasemap=%s', ), + phasemap_in_file=dict( + argstr='--phasemap=%s', + usedefault=True, + ), poly_order=dict(argstr='--poly=%d', ), save_fmap=dict(xor=['save_unmasked_fmap'], ), save_shift=dict(xor=['save_unmasked_shift'], ), @@ -48,19 +63,27 @@ def test_FUGUE_inputs(): argstr='--unmaskshift', xor=['save_shift'], ), - shift_in_file=dict(argstr='--loadshift=%s', ), - shift_out_file=dict(argstr='--saveshift=%s', ), + shift_in_file=dict( + argstr='--loadshift=%s', + usedefault=True, + ), + shift_out_file=dict( + argstr='--saveshift=%s', + usedefault=True, + ), smooth2d=dict(argstr='--smooth2=%.2f', ), smooth3d=dict(argstr='--smooth3=%.2f', ), unwarp_direction=dict(argstr='--unwarpdir=%s', ), unwarped_file=dict( argstr='--unwarp=%s', requires=['in_file'], + usedefault=True, xor=['warped_file'], ), warped_file=dict( argstr='--warp=%s', requires=['in_file'], + usedefault=True, xor=['unwarped_file'], ), ) @@ -71,10 +94,10 @@ def test_FUGUE_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FUGUE_outputs(): output_map = dict( - fmap_out_file=dict(), - shift_out_file=dict(), - unwarped_file=dict(), - warped_file=dict(), + fmap_out_file=dict(usedefault=True, ), + shift_out_file=dict(usedefault=True, ), + unwarped_file=dict(usedefault=True, ), + warped_file=dict(usedefault=True, ), ) outputs = FUGUE.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py b/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py index 3945c40a87..5cd92366b7 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py +++ b/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py @@ -14,6 +14,7 @@ def test_FeatureExtractor_inputs(): argstr='%s', copyfile=False, position=-1, + usedefault=True, ), ) inputs = FeatureExtractor.input_spec() @@ -27,6 +28,7 @@ def test_FeatureExtractor_outputs(): argstr='%s', copyfile=False, position=-1, + usedefault=True, ), ) outputs = FeatureExtractor.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py index 36cbb979d7..fed7784be3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py +++ b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py @@ -10,6 +10,7 @@ def test_FilterRegressor_inputs(): argstr='-d %s', mandatory=True, position=3, + usedefault=True, ), environ=dict( nohash=True, @@ -31,13 +32,18 @@ def test_FilterRegressor_inputs(): argstr='-i %s', mandatory=True, position=1, + usedefault=True, + ), + mask=dict( + argstr='-m %s', + usedefault=True, ), - mask=dict(argstr='-m %s', ), out_file=dict( argstr='-o %s', genfile=True, hash_files=False, position=2, + usedefault=True, ), out_vnscales=dict(argstr='--out_vnscales', ), output_type=dict(), @@ -49,7 +55,7 @@ def test_FilterRegressor_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FilterRegressor_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = FilterRegressor.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py index 3731c842e7..2162579d00 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py +++ b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py @@ -20,6 +20,7 @@ def test_FindTheBiggest_inputs(): genfile=True, hash_files=False, position=2, + usedefault=True, ), output_type=dict(), ) @@ -29,7 +30,11 @@ def test_FindTheBiggest_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FindTheBiggest_outputs(): - output_map = dict(out_file=dict(argstr='%s', ), ) + output_map = dict( + out_file=dict( + argstr='%s', + usedefault=True, + ), ) outputs = FindTheBiggest.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_GLM.py b/nipype/interfaces/fsl/tests/test_auto_GLM.py index 1dbf7eba19..39273b51e4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_GLM.py +++ b/nipype/interfaces/fsl/tests/test_auto_GLM.py @@ -6,7 +6,10 @@ def test_GLM_inputs(): input_map = dict( args=dict(argstr='%s', ), - contrasts=dict(argstr='-c %s', ), + contrasts=dict( + argstr='-c %s', + usedefault=True, + ), dat_norm=dict(argstr='--dat_norm', ), demean=dict(argstr='--demean', ), des_norm=dict(argstr='--des_norm', ), @@ -14,6 +17,7 @@ def test_GLM_inputs(): argstr='-d %s', mandatory=True, position=2, + usedefault=True, ), dof=dict(argstr='--dof=%d', ), environ=dict( @@ -24,26 +28,64 @@ def test_GLM_inputs(): argstr='-i %s', mandatory=True, position=1, + usedefault=True, + ), + mask=dict( + argstr='-m %s', + usedefault=True, + ), + out_cope=dict( + argstr='--out_cope=%s', + usedefault=True, + ), + out_data_name=dict( + argstr='--out_data=%s', + usedefault=True, + ), + out_f_name=dict( + argstr='--out_f=%s', + usedefault=True, ), - mask=dict(argstr='-m %s', ), - out_cope=dict(argstr='--out_cope=%s', ), - out_data_name=dict(argstr='--out_data=%s', ), - out_f_name=dict(argstr='--out_f=%s', ), out_file=dict( argstr='-o %s', keep_extension=True, name_source='in_file', name_template='%s_glm', position=3, + usedefault=True, + ), + out_p_name=dict( + argstr='--out_p=%s', + usedefault=True, + ), + out_pf_name=dict( + argstr='--out_pf=%s', + usedefault=True, + ), + out_res_name=dict( + argstr='--out_res=%s', + usedefault=True, + ), + out_sigsq_name=dict( + argstr='--out_sigsq=%s', + usedefault=True, + ), + out_t_name=dict( + argstr='--out_t=%s', + usedefault=True, + ), + out_varcb_name=dict( + argstr='--out_varcb=%s', + usedefault=True, + ), + out_vnscales_name=dict( + argstr='--out_vnscales=%s', + usedefault=True, + ), + out_z_name=dict( + argstr='--out_z=%s', + usedefault=True, ), - out_p_name=dict(argstr='--out_p=%s', ), - out_pf_name=dict(argstr='--out_pf=%s', ), - out_res_name=dict(argstr='--out_res=%s', ), - out_sigsq_name=dict(argstr='--out_sigsq=%s', ), - out_t_name=dict(argstr='--out_t=%s', ), - out_varcb_name=dict(argstr='--out_varcb=%s', ), - out_vnscales_name=dict(argstr='--out_vnscales=%s', ), - out_z_name=dict(argstr='--out_z=%s', ), output_type=dict(), var_norm=dict(argstr='--vn', ), ) @@ -57,7 +99,7 @@ def test_GLM_outputs(): out_cope=dict(), out_data=dict(), out_f=dict(), - out_file=dict(), + out_file=dict(usedefault=True, ), out_p=dict(), out_pf=dict(), out_res=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py b/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py index 05bbb5b106..f22397d1bf 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py +++ b/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py @@ -20,31 +20,40 @@ def test_ICA_AROMA_inputs(): feat_dir=dict( argstr='-feat %s', mandatory=True, + usedefault=True, xor=[ 'in_file', 'mat_file', 'fnirt_warp_file', 'motion_parameters' ], ), fnirt_warp_file=dict( argstr='-warp %s', + usedefault=True, xor=['feat_dir'], ), in_file=dict( argstr='-i %s', mandatory=True, + usedefault=True, xor=['feat_dir'], ), mask=dict( argstr='-m %s', + usedefault=True, xor=['feat_dir'], ), mat_file=dict( argstr='-affmat %s', + usedefault=True, xor=['feat_dir'], ), - melodic_dir=dict(argstr='-meldir %s', ), + melodic_dir=dict( + argstr='-meldir %s', + usedefault=True, + ), motion_parameters=dict( argstr='-mc %s', mandatory=True, + usedefault=True, xor=['feat_dir'], ), out_dir=dict( @@ -60,9 +69,9 @@ def test_ICA_AROMA_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ICA_AROMA_outputs(): output_map = dict( - aggr_denoised_file=dict(), - nonaggr_denoised_file=dict(), - out_dir=dict(), + aggr_denoised_file=dict(usedefault=True, ), + nonaggr_denoised_file=dict(usedefault=True, ), + out_dir=dict(usedefault=True, ), ) outputs = ICA_AROMA.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py index 6d4e06827e..0323144aca 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py @@ -14,12 +14,17 @@ def test_ImageMaths_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), in_file2=dict( argstr='%s', position=3, + usedefault=True, + ), + mask_file=dict( + argstr='-mas %s', + usedefault=True, ), - mask_file=dict(argstr='-mas %s', ), op_string=dict( argstr='%s', position=2, @@ -33,6 +38,7 @@ def test_ImageMaths_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_type=dict(), suffix=dict(), @@ -43,7 +49,7 @@ def test_ImageMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ImageMaths_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ImageMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py index 042f93112b..3c0165915a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py @@ -15,8 +15,12 @@ def test_ImageMeants_inputs(): argstr='-i %s', mandatory=True, position=0, + usedefault=True, + ), + mask=dict( + argstr='-m %s', + usedefault=True, ), - mask=dict(argstr='-m %s', ), nobin=dict(argstr='--no_bin', ), order=dict( argstr='--order=%d', @@ -26,6 +30,7 @@ def test_ImageMeants_inputs(): argstr='-o %s', genfile=True, hash_files=False, + usedefault=True, ), output_type=dict(), show_all=dict(argstr='--showall', ), @@ -39,7 +44,7 @@ def test_ImageMeants_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ImageMeants_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ImageMeants.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py index 91a6059798..072e308455 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py @@ -14,8 +14,12 @@ def test_ImageStats_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, + ), + mask_file=dict( + argstr='', + usedefault=True, ), - mask_file=dict(argstr='', ), op_string=dict( argstr='%s', mandatory=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py index 973f42ea34..cedfb5ad80 100644 --- a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py @@ -19,6 +19,7 @@ def test_InvWarp_inputs(): hash_files=False, name_source=['warp'], name_template='%s_inverse', + usedefault=True, ), jacobian_max=dict(argstr='--jmax=%f', ), jacobian_min=dict(argstr='--jmin=%f', ), @@ -28,6 +29,7 @@ def test_InvWarp_inputs(): reference=dict( argstr='--ref=%s', mandatory=True, + usedefault=True, ), regularise=dict(argstr='--regularise=%f', ), relative=dict( @@ -37,6 +39,7 @@ def test_InvWarp_inputs(): warp=dict( argstr='--warp=%s', mandatory=True, + usedefault=True, ), ) inputs = InvWarp.input_spec() @@ -45,7 +48,7 @@ def test_InvWarp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_InvWarp_outputs(): - output_map = dict(inverse_warp=dict(), ) + output_map = dict(inverse_warp=dict(usedefault=True, ), ) outputs = InvWarp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py index 4b6192c98d..5b110e99dc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py @@ -20,6 +20,7 @@ def test_IsotropicSmooth_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -34,6 +35,7 @@ def test_IsotropicSmooth_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -53,7 +55,7 @@ def test_IsotropicSmooth_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_IsotropicSmooth_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = IsotropicSmooth.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_L2Model.py b/nipype/interfaces/fsl/tests/test_auto_L2Model.py index 9d3588666f..c188a82b36 100644 --- a/nipype/interfaces/fsl/tests/test_auto_L2Model.py +++ b/nipype/interfaces/fsl/tests/test_auto_L2Model.py @@ -12,9 +12,9 @@ def test_L2Model_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_L2Model_outputs(): output_map = dict( - design_con=dict(), - design_grp=dict(), - design_mat=dict(), + design_con=dict(usedefault=True, ), + design_grp=dict(usedefault=True, ), + design_mat=dict(usedefault=True, ), ) outputs = L2Model.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py index daeca07b10..b586d758b3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py @@ -17,17 +17,25 @@ def test_MCFLIRT_inputs(): argstr='-in %s', mandatory=True, position=0, + usedefault=True, + ), + init=dict( + argstr='-init %s', + usedefault=True, ), - init=dict(argstr='-init %s', ), interpolation=dict(argstr='-%s_final', ), mean_vol=dict(argstr='-meanvol', ), out_file=dict( argstr='-out %s', genfile=True, hash_files=False, + usedefault=True, ), output_type=dict(), - ref_file=dict(argstr='-reffile %s', ), + ref_file=dict( + argstr='-reffile %s', + usedefault=True, + ), ref_vol=dict(argstr='-refvol %d', ), rotation=dict(argstr='-rotation %d', ), save_mats=dict(argstr='-mats', ), @@ -48,12 +56,12 @@ def test_MCFLIRT_inputs(): def test_MCFLIRT_outputs(): output_map = dict( mat_file=dict(), - mean_img=dict(), - out_file=dict(), - par_file=dict(), + mean_img=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), + par_file=dict(usedefault=True, ), rms_files=dict(), - std_img=dict(), - variance_img=dict(), + std_img=dict(usedefault=True, ), + variance_img=dict(usedefault=True, ), ) outputs = MCFLIRT.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py index b22078c450..e5bd64e8ca 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py +++ b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py @@ -5,10 +5,16 @@ def test_MELODIC_inputs(): input_map = dict( - ICs=dict(argstr='--ICs=%s', ), + ICs=dict( + argstr='--ICs=%s', + usedefault=True, + ), approach=dict(argstr='-a %s', ), args=dict(argstr='%s', ), - bg_image=dict(argstr='--bgimage=%s', ), + bg_image=dict( + argstr='--bgimage=%s', + usedefault=True, + ), bg_threshold=dict(argstr='--bgthreshold=%f', ), cov_weight=dict(argstr='--covarweight=%f', ), dim=dict(argstr='-d %d', ), @@ -26,14 +32,20 @@ def test_MELODIC_inputs(): sep=',', ), log_power=dict(argstr='--logPower', ), - mask=dict(argstr='-m %s', ), + mask=dict( + argstr='-m %s', + usedefault=True, + ), max_restart=dict(argstr='--maxrestart=%d', ), maxit=dict(argstr='--maxit=%d', ), migp=dict(argstr='--migp', ), migpN=dict(argstr='--migpN %d', ), migp_factor=dict(argstr='--migp_factor %d', ), migp_shuffle=dict(argstr='--migp_shuffle', ), - mix=dict(argstr='--mix=%s', ), + mix=dict( + argstr='--mix=%s', + usedefault=True, + ), mm_thresh=dict(argstr='--mmthresh=%f', ), no_bet=dict(argstr='--nobet', ), no_mask=dict(argstr='--nomask', ), @@ -44,6 +56,7 @@ def test_MELODIC_inputs(): out_dir=dict( argstr='-o %s', genfile=True, + usedefault=True, ), out_mean=dict(argstr='--Omean', ), out_orig=dict(argstr='--Oorig', ), @@ -57,13 +70,28 @@ def test_MELODIC_inputs(): remove_deriv=dict(argstr='--remove_deriv', ), report=dict(argstr='--report', ), report_maps=dict(argstr='--report_maps=%s', ), - s_con=dict(argstr='--Scon=%s', ), - s_des=dict(argstr='--Sdes=%s', ), + s_con=dict( + argstr='--Scon=%s', + usedefault=True, + ), + s_des=dict( + argstr='--Sdes=%s', + usedefault=True, + ), sep_vn=dict(argstr='--sep_vn', ), sep_whiten=dict(argstr='--sep_whiten', ), - smode=dict(argstr='--smode=%s', ), - t_con=dict(argstr='--Tcon=%s', ), - t_des=dict(argstr='--Tdes=%s', ), + smode=dict( + argstr='--smode=%s', + usedefault=True, + ), + t_con=dict( + argstr='--Tcon=%s', + usedefault=True, + ), + t_des=dict( + argstr='--Tdes=%s', + usedefault=True, + ), tr_sec=dict(argstr='--tr=%f', ), update_mask=dict(argstr='--update_mask', ), var_norm=dict(argstr='--vn', ), @@ -75,8 +103,8 @@ def test_MELODIC_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MELODIC_outputs(): output_map = dict( - out_dir=dict(), - report_dir=dict(), + out_dir=dict(usedefault=True, ), + report_dir=dict(usedefault=True, ), ) outputs = MELODIC.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py index c7a5a3e465..38f955a3f6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py +++ b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py @@ -13,6 +13,7 @@ def test_MakeDyadicVectors_inputs(): mask=dict( argstr='%s', position=2, + usedefault=True, ), output=dict( argstr='%s', @@ -29,11 +30,13 @@ def test_MakeDyadicVectors_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), theta_vol=dict( argstr='%s', mandatory=True, position=0, + usedefault=True, ), ) inputs = MakeDyadicVectors.input_spec() @@ -43,8 +46,8 @@ def test_MakeDyadicVectors_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MakeDyadicVectors_outputs(): output_map = dict( - dispersion=dict(), - dyads=dict(), + dispersion=dict(usedefault=True, ), + dyads=dict(usedefault=True, ), ) outputs = MakeDyadicVectors.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py index 64b0f8b089..e2dde50f6c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py @@ -14,6 +14,7 @@ def test_MathsCommand_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -28,6 +29,7 @@ def test_MathsCommand_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -41,7 +43,7 @@ def test_MathsCommand_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MathsCommand_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MathsCommand.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py index 9910f9c4e8..c77c8bbaa1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py @@ -19,6 +19,7 @@ def test_MaxImage_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -33,6 +34,7 @@ def test_MaxImage_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -46,7 +48,7 @@ def test_MaxImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MaxImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MaxImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py b/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py index f49c5f462c..47fd14ded4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py @@ -19,6 +19,7 @@ def test_MaxnImage_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -33,6 +34,7 @@ def test_MaxnImage_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -46,7 +48,7 @@ def test_MaxnImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MaxnImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MaxnImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py index 2172dcfa9e..31a3751c77 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py @@ -19,6 +19,7 @@ def test_MeanImage_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -33,6 +34,7 @@ def test_MeanImage_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -46,7 +48,7 @@ def test_MeanImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MeanImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MeanImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MedianImage.py b/nipype/interfaces/fsl/tests/test_auto_MedianImage.py index c14bf8d839..c8cb6c88e0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MedianImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MedianImage.py @@ -19,6 +19,7 @@ def test_MedianImage_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -33,6 +34,7 @@ def test_MedianImage_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -46,7 +48,7 @@ def test_MedianImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MedianImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MedianImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Merge.py b/nipype/interfaces/fsl/tests/test_auto_Merge.py index 826270239e..39c4f1b09c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Merge.py +++ b/nipype/interfaces/fsl/tests/test_auto_Merge.py @@ -26,6 +26,7 @@ def test_Merge_inputs(): name_source='in_files', name_template='%s_merged', position=1, + usedefault=True, ), output_type=dict(), tr=dict( @@ -39,7 +40,7 @@ def test_Merge_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Merge_outputs(): - output_map = dict(merged_file=dict(), ) + output_map = dict(merged_file=dict(usedefault=True, ), ) outputs = Merge.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MinImage.py b/nipype/interfaces/fsl/tests/test_auto_MinImage.py index 4e9002c259..cf6b14fe60 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MinImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MinImage.py @@ -19,6 +19,7 @@ def test_MinImage_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -33,6 +34,7 @@ def test_MinImage_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -46,7 +48,7 @@ def test_MinImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MinImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MinImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py index 97d2426b53..a3acf1458f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py +++ b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py @@ -14,8 +14,12 @@ def test_MotionOutliers_inputs(): in_file=dict( argstr='-i %s', mandatory=True, + usedefault=True, + ), + mask=dict( + argstr='-m %s', + usedefault=True, ), - mask=dict(argstr='-m %s', ), metric=dict(argstr='--%s', ), no_motion_correction=dict(argstr='--nomoco', ), out_file=dict( @@ -24,6 +28,7 @@ def test_MotionOutliers_inputs(): keep_extension=True, name_source='in_file', name_template='%s_outliers.txt', + usedefault=True, ), out_metric_plot=dict( argstr='-p %s', @@ -31,6 +36,7 @@ def test_MotionOutliers_inputs(): keep_extension=True, name_source='in_file', name_template='%s_metrics.png', + usedefault=True, ), out_metric_values=dict( argstr='-s %s', @@ -38,6 +44,7 @@ def test_MotionOutliers_inputs(): keep_extension=True, name_source='in_file', name_template='%s_metrics.txt', + usedefault=True, ), output_type=dict(), threshold=dict(argstr='--thresh=%g', ), @@ -49,9 +56,9 @@ def test_MotionOutliers_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MotionOutliers_outputs(): output_map = dict( - out_file=dict(), - out_metric_plot=dict(), - out_metric_values=dict(), + out_file=dict(usedefault=True, ), + out_metric_plot=dict(usedefault=True, ), + out_metric_values=dict(usedefault=True, ), ) outputs = MotionOutliers.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py index 50a2977a4c..d1ae4c8a9b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py @@ -14,6 +14,7 @@ def test_MultiImageMaths_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -34,6 +35,7 @@ def test_MultiImageMaths_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -47,7 +49,7 @@ def test_MultiImageMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MultiImageMaths_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MultiImageMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py index 78bd97ff85..96ead7d20c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py @@ -16,10 +16,10 @@ def test_MultipleRegressDesign_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MultipleRegressDesign_outputs(): output_map = dict( - design_con=dict(), - design_fts=dict(), - design_grp=dict(), - design_mat=dict(), + design_con=dict(usedefault=True, ), + design_fts=dict(usedefault=True, ), + design_grp=dict(usedefault=True, ), + design_mat=dict(usedefault=True, ), ) outputs = MultipleRegressDesign.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Overlay.py b/nipype/interfaces/fsl/tests/test_auto_Overlay.py index 9818ae1eda..fa139b9254 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Overlay.py +++ b/nipype/interfaces/fsl/tests/test_auto_Overlay.py @@ -16,6 +16,7 @@ def test_Overlay_inputs(): argstr='%s', mandatory=True, position=4, + usedefault=True, ), bg_thresh=dict( argstr='%.3f %.3f', @@ -38,6 +39,7 @@ def test_Overlay_inputs(): genfile=True, hash_files=False, position=-1, + usedefault=True, ), out_type=dict( argstr='%s', @@ -54,10 +56,12 @@ def test_Overlay_inputs(): argstr='%s', mandatory=True, position=6, + usedefault=True, ), stat_image2=dict( argstr='%s', position=9, + usedefault=True, xor=['show_negative_stats'], ), stat_thresh=dict( @@ -85,7 +89,7 @@ def test_Overlay_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Overlay_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Overlay.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py index 328a8e3272..5709018ae8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py +++ b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py @@ -9,6 +9,7 @@ def test_PRELUDE_inputs(): complex_phase_file=dict( argstr='--complex=%s', mandatory=True, + usedefault=True, xor=['magnitude_file', 'phase_file'], ), end=dict(argstr='--end=%d', ), @@ -19,19 +20,25 @@ def test_PRELUDE_inputs(): label_file=dict( argstr='--labels=%s', hash_files=False, + usedefault=True, ), labelprocess2d=dict(argstr='--labelslices', ), magnitude_file=dict( argstr='--abs=%s', mandatory=True, + usedefault=True, xor=['complex_phase_file'], ), - mask_file=dict(argstr='--mask=%s', ), + mask_file=dict( + argstr='--mask=%s', + usedefault=True, + ), num_partitions=dict(argstr='--numphasesplit=%d', ), output_type=dict(), phase_file=dict( argstr='--phase=%s', mandatory=True, + usedefault=True, xor=['complex_phase_file'], ), process2d=dict( @@ -45,11 +52,13 @@ def test_PRELUDE_inputs(): rawphase_file=dict( argstr='--rawphase=%s', hash_files=False, + usedefault=True, ), removeramps=dict(argstr='--removeramps', ), savemask_file=dict( argstr='--savemask=%s', hash_files=False, + usedefault=True, ), start=dict(argstr='--start=%d', ), threshold=dict(argstr='--thresh=%.10f', ), @@ -57,6 +66,7 @@ def test_PRELUDE_inputs(): argstr='--unwrap=%s', genfile=True, hash_files=False, + usedefault=True, ), ) inputs = PRELUDE.input_spec() @@ -65,7 +75,7 @@ def test_PRELUDE_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PRELUDE_outputs(): - output_map = dict(unwrapped_phase_file=dict(), ) + output_map = dict(unwrapped_phase_file=dict(usedefault=True, ), ) outputs = PRELUDE.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py b/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py index 4e08c18db0..a9deb42a8e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py @@ -19,6 +19,7 @@ def test_PercentileImage_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -33,6 +34,7 @@ def test_PercentileImage_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -50,7 +52,7 @@ def test_PercentileImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PercentileImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = PercentileImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py index 45a5b43945..1b6d3ccaa7 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py @@ -20,6 +20,7 @@ def test_PlotMotionParams_inputs(): argstr='-o %s', genfile=True, hash_files=False, + usedefault=True, ), output_type=dict(), plot_size=dict(argstr='%s', ), @@ -34,7 +35,7 @@ def test_PlotMotionParams_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PlotMotionParams_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = PlotMotionParams.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py index 62ced498e1..448cbb35be 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py @@ -16,11 +16,15 @@ def test_PlotTimeSeries_inputs(): position=1, ), labels=dict(argstr='%s', ), - legend_file=dict(argstr='--legend=%s', ), + legend_file=dict( + argstr='--legend=%s', + usedefault=True, + ), out_file=dict( argstr='-o %s', genfile=True, hash_files=False, + usedefault=True, ), output_type=dict(), plot_finish=dict( @@ -62,7 +66,7 @@ def test_PlotTimeSeries_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PlotTimeSeries_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = PlotTimeSeries.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py index 18a812c00b..28ed263c1b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py +++ b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py @@ -14,12 +14,14 @@ def test_PowerSpectrum_inputs(): argstr='%s', mandatory=True, position=0, + usedefault=True, ), out_file=dict( argstr='%s', genfile=True, hash_files=False, position=1, + usedefault=True, ), output_type=dict(), ) @@ -29,7 +31,7 @@ def test_PowerSpectrum_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PowerSpectrum_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = PowerSpectrum.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py index 66bfd51fab..f93508a22a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py +++ b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py @@ -20,11 +20,13 @@ def test_PrepareFieldmap_inputs(): argstr='%s', mandatory=True, position=3, + usedefault=True, ), in_phase=dict( argstr='%s', mandatory=True, position=2, + usedefault=True, ), nocheck=dict( argstr='--nocheck', @@ -34,6 +36,7 @@ def test_PrepareFieldmap_inputs(): out_fieldmap=dict( argstr='%s', position=4, + usedefault=True, ), output_type=dict(), scanner=dict( @@ -48,7 +51,7 @@ def test_PrepareFieldmap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PrepareFieldmap_outputs(): - output_map = dict(out_fieldmap=dict(), ) + output_map = dict(out_fieldmap=dict(usedefault=True, ), ) outputs = PrepareFieldmap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py index 5368d0dd37..e44d1a3370 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py @@ -6,7 +6,10 @@ def test_ProbTrackX_inputs(): input_map = dict( args=dict(argstr='%s', ), - avoid_mp=dict(argstr='--avoid=%s', ), + avoid_mp=dict( + argstr='--avoid=%s', + usedefault=True, + ), c_thresh=dict(argstr='--cthr=%.3f', ), correct_path_distribution=dict(argstr='--pd', ), dist_thresh=dict(argstr='--distthresh=%.3f', ), @@ -20,14 +23,24 @@ def test_ProbTrackX_inputs(): usedefault=True, ), fsamples=dict(mandatory=True, ), - inv_xfm=dict(argstr='--invxfm=%s', ), + inv_xfm=dict( + argstr='--invxfm=%s', + usedefault=True, + ), loop_check=dict(argstr='--loopcheck', ), mask=dict( argstr='-m %s', mandatory=True, + usedefault=True, + ), + mask2=dict( + argstr='--mask2=%s', + usedefault=True, + ), + mesh=dict( + argstr='--mesh=%s', + usedefault=True, ), - mask2=dict(argstr='--mask2=%s', ), - mesh=dict(argstr='--mesh=%s', ), mod_euler=dict(argstr='--modeuler', ), mode=dict( argstr='--mode=%s', @@ -47,6 +60,7 @@ def test_ProbTrackX_inputs(): out_dir=dict( argstr='--dir=%s', genfile=True, + usedefault=True, ), output_type=dict(), phsamples=dict(mandatory=True, ), @@ -62,15 +76,27 @@ def test_ProbTrackX_inputs(): argstr='--seed=%s', mandatory=True, ), - seed_ref=dict(argstr='--seedref=%s', ), + seed_ref=dict( + argstr='--seedref=%s', + usedefault=True, + ), step_length=dict(argstr='--steplength=%.3f', ), - stop_mask=dict(argstr='--stop=%s', ), + stop_mask=dict( + argstr='--stop=%s', + usedefault=True, + ), target_masks=dict(argstr='--targetmasks=%s', ), thsamples=dict(mandatory=True, ), use_anisotropy=dict(argstr='--usef', ), verbose=dict(argstr='--verbose=%d', ), - waypoints=dict(argstr='--waypoints=%s', ), - xfm=dict(argstr='--xfm=%s', ), + waypoints=dict( + argstr='--waypoints=%s', + usedefault=True, + ), + xfm=dict( + argstr='--xfm=%s', + usedefault=True, + ), ) inputs = ProbTrackX.input_spec() @@ -80,10 +106,10 @@ def test_ProbTrackX_inputs(): def test_ProbTrackX_outputs(): output_map = dict( fdt_paths=dict(), - log=dict(), + log=dict(usedefault=True, ), particle_files=dict(), targets=dict(), - way_total=dict(), + way_total=dict(usedefault=True, ), ) outputs = ProbTrackX.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py index 8592b5ae1a..a1ca70b2b5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py @@ -6,9 +6,15 @@ def test_ProbTrackX2_inputs(): input_map = dict( args=dict(argstr='%s', ), - avoid_mp=dict(argstr='--avoid=%s', ), + avoid_mp=dict( + argstr='--avoid=%s', + usedefault=True, + ), c_thresh=dict(argstr='--cthr=%.3f', ), - colmask4=dict(argstr='--colmask4=%s', ), + colmask4=dict( + argstr='--colmask4=%s', + usedefault=True, + ), correct_path_distribution=dict(argstr='--pd', ), dist_thresh=dict(argstr='--distthresh=%.3f', ), distthresh1=dict(argstr='--distthresh1=%.3f', ), @@ -18,18 +24,28 @@ def test_ProbTrackX2_inputs(): usedefault=True, ), fibst=dict(argstr='--fibst=%d', ), - fopd=dict(argstr='--fopd=%s', ), + fopd=dict( + argstr='--fopd=%s', + usedefault=True, + ), force_dir=dict( argstr='--forcedir', usedefault=True, ), fsamples=dict(mandatory=True, ), - inv_xfm=dict(argstr='--invxfm=%s', ), + inv_xfm=dict( + argstr='--invxfm=%s', + usedefault=True, + ), loop_check=dict(argstr='--loopcheck', ), - lrtarget3=dict(argstr='--lrtarget3=%s', ), + lrtarget3=dict( + argstr='--lrtarget3=%s', + usedefault=True, + ), mask=dict( argstr='-m %s', mandatory=True, + usedefault=True, ), meshspace=dict(argstr='--meshspace=%s', ), mod_euler=dict(argstr='--modeuler', ), @@ -58,6 +74,7 @@ def test_ProbTrackX2_inputs(): out_dir=dict( argstr='--dir=%s', genfile=True, + usedefault=True, ), output_type=dict(), phsamples=dict(mandatory=True, ), @@ -73,21 +90,42 @@ def test_ProbTrackX2_inputs(): argstr='--seed=%s', mandatory=True, ), - seed_ref=dict(argstr='--seedref=%s', ), + seed_ref=dict( + argstr='--seedref=%s', + usedefault=True, + ), simple=dict(argstr='--simple', ), step_length=dict(argstr='--steplength=%.3f', ), - stop_mask=dict(argstr='--stop=%s', ), - target2=dict(argstr='--target2=%s', ), - target3=dict(argstr='--target3=%s', ), - target4=dict(argstr='--target4=%s', ), + stop_mask=dict( + argstr='--stop=%s', + usedefault=True, + ), + target2=dict( + argstr='--target2=%s', + usedefault=True, + ), + target3=dict( + argstr='--target3=%s', + usedefault=True, + ), + target4=dict( + argstr='--target4=%s', + usedefault=True, + ), target_masks=dict(argstr='--targetmasks=%s', ), thsamples=dict(mandatory=True, ), use_anisotropy=dict(argstr='--usef', ), verbose=dict(argstr='--verbose=%d', ), waycond=dict(argstr='--waycond=%s', ), wayorder=dict(argstr='--wayorder', ), - waypoints=dict(argstr='--waypoints=%s', ), - xfm=dict(argstr='--xfm=%s', ), + waypoints=dict( + argstr='--waypoints=%s', + usedefault=True, + ), + xfm=dict( + argstr='--xfm=%s', + usedefault=True, + ), ) inputs = ProbTrackX2.input_spec() @@ -97,15 +135,15 @@ def test_ProbTrackX2_inputs(): def test_ProbTrackX2_outputs(): output_map = dict( fdt_paths=dict(), - log=dict(), - lookup_tractspace=dict(), - matrix1_dot=dict(), - matrix2_dot=dict(), - matrix3_dot=dict(), - network_matrix=dict(), + log=dict(usedefault=True, ), + lookup_tractspace=dict(usedefault=True, ), + matrix1_dot=dict(usedefault=True, ), + matrix2_dot=dict(usedefault=True, ), + matrix3_dot=dict(usedefault=True, ), + network_matrix=dict(usedefault=True, ), particle_files=dict(), targets=dict(), - way_total=dict(), + way_total=dict(usedefault=True, ), ) outputs = ProbTrackX2.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Randomise.py b/nipype/interfaces/fsl/tests/test_auto_Randomise.py index 3d52347265..423b5b9f07 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Randomise.py +++ b/nipype/interfaces/fsl/tests/test_auto_Randomise.py @@ -17,6 +17,7 @@ def test_Randomise_inputs(): design_mat=dict( argstr='-d %s', position=2, + usedefault=True, ), environ=dict( nohash=True, @@ -25,13 +26,20 @@ def test_Randomise_inputs(): f_c_thresh=dict(argstr='-F %.2f', ), f_cm_thresh=dict(argstr='-S %.2f', ), f_only=dict(argstr='--f_only', ), - fcon=dict(argstr='-f %s', ), + fcon=dict( + argstr='-f %s', + usedefault=True, + ), in_file=dict( argstr='-i %s', mandatory=True, position=0, + usedefault=True, + ), + mask=dict( + argstr='-m %s', + usedefault=True, ), - mask=dict(argstr='-m %s', ), num_perm=dict(argstr='-n %d', ), one_sample_group_mean=dict(argstr='-1', ), output_type=dict(), @@ -43,6 +51,7 @@ def test_Randomise_inputs(): tcon=dict( argstr='-t %s', position=3, + usedefault=True, ), tfce=dict(argstr='-T', ), tfce2D=dict(argstr='--T2', ), @@ -51,7 +60,10 @@ def test_Randomise_inputs(): tfce_H=dict(argstr='--tfce_H=%.2f', ), var_smooth=dict(argstr='-v %d', ), vox_p_values=dict(argstr='-x', ), - x_block_labels=dict(argstr='-e %s', ), + x_block_labels=dict( + argstr='-e %s', + usedefault=True, + ), ) inputs = Randomise.input_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py index 76647d82d8..ba24ac7e92 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py +++ b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py @@ -13,11 +13,13 @@ def test_Reorient2Std_inputs(): in_file=dict( argstr='%s', mandatory=True, + usedefault=True, ), out_file=dict( argstr='%s', genfile=True, hash_files=False, + usedefault=True, ), output_type=dict(), ) @@ -27,7 +29,7 @@ def test_Reorient2Std_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Reorient2Std_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Reorient2Std.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py index e1cbac6fc9..3178abf8c1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py +++ b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py @@ -15,18 +15,21 @@ def test_RobustFOV_inputs(): argstr='-i %s', mandatory=True, position=0, + usedefault=True, ), out_roi=dict( argstr='-r %s', hash_files=False, name_source=['in_file'], name_template='%s_ROI', + usedefault=True, ), out_transform=dict( argstr='-m %s', hash_files=False, name_source=['in_file'], name_template='%s_to_ROI', + usedefault=True, ), output_type=dict(), ) @@ -37,8 +40,8 @@ def test_RobustFOV_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RobustFOV_outputs(): output_map = dict( - out_roi=dict(), - out_transform=dict(), + out_roi=dict(usedefault=True, ), + out_transform=dict(usedefault=True, ), ) outputs = RobustFOV.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_SMM.py b/nipype/interfaces/fsl/tests/test_auto_SMM.py index 1e1cc308cc..64ef65f0e4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SMM.py +++ b/nipype/interfaces/fsl/tests/test_auto_SMM.py @@ -15,6 +15,7 @@ def test_SMM_inputs(): copyfile=False, mandatory=True, position=1, + usedefault=True, ), no_deactivation_class=dict( argstr='--zfstatmode', @@ -26,6 +27,7 @@ def test_SMM_inputs(): copyfile=False, mandatory=True, position=0, + usedefault=True, ), ) inputs = SMM.input_spec() @@ -35,9 +37,9 @@ def test_SMM_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SMM_outputs(): output_map = dict( - activation_p_map=dict(), - deactivation_p_map=dict(), - null_p_map=dict(), + activation_p_map=dict(usedefault=True, ), + deactivation_p_map=dict(usedefault=True, ), + null_p_map=dict(usedefault=True, ), ) outputs = SMM.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py index ebbef0d427..bf82a06086 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py +++ b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py @@ -29,12 +29,14 @@ def test_SUSAN_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), out_file=dict( argstr='%s', genfile=True, hash_files=False, position=-1, + usedefault=True, ), output_type=dict(), usans=dict( @@ -54,7 +56,7 @@ def test_SUSAN_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SUSAN_outputs(): - output_map = dict(smoothed_file=dict(), ) + output_map = dict(smoothed_file=dict(usedefault=True, ), ) outputs = SUSAN.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py index f3be97b350..ae19dff835 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py +++ b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py @@ -14,11 +14,16 @@ def test_SigLoss_inputs(): in_file=dict( argstr='-i %s', mandatory=True, + usedefault=True, + ), + mask_file=dict( + argstr='-m %s', + usedefault=True, ), - mask_file=dict(argstr='-m %s', ), out_file=dict( argstr='-s %s', genfile=True, + usedefault=True, ), output_type=dict(), slice_direction=dict(argstr='-d %s', ), @@ -29,7 +34,7 @@ def test_SigLoss_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SigLoss_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = SigLoss.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Slice.py b/nipype/interfaces/fsl/tests/test_auto_Slice.py index d1e9093e37..52545e8375 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Slice.py +++ b/nipype/interfaces/fsl/tests/test_auto_Slice.py @@ -15,6 +15,7 @@ def test_Slice_inputs(): copyfile=False, mandatory=True, position=0, + usedefault=True, ), out_base_name=dict( argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py index 75b9918ad9..5ffd052768 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py +++ b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py @@ -6,8 +6,14 @@ def test_SliceTimer_inputs(): input_map = dict( args=dict(argstr='%s', ), - custom_order=dict(argstr='--ocustom=%s', ), - custom_timings=dict(argstr='--tcustom=%s', ), + custom_order=dict( + argstr='--ocustom=%s', + usedefault=True, + ), + custom_timings=dict( + argstr='--tcustom=%s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -17,6 +23,7 @@ def test_SliceTimer_inputs(): argstr='--in=%s', mandatory=True, position=0, + usedefault=True, ), index_dir=dict(argstr='--down', ), interleaved=dict(argstr='--odd', ), @@ -24,6 +31,7 @@ def test_SliceTimer_inputs(): argstr='--out=%s', genfile=True, hash_files=False, + usedefault=True, ), output_type=dict(), slice_direction=dict(argstr='--direction=%d', ), @@ -35,7 +43,7 @@ def test_SliceTimer_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SliceTimer_outputs(): - output_map = dict(slice_time_corrected_file=dict(), ) + output_map = dict(slice_time_corrected_file=dict(usedefault=True, ), ) outputs = SliceTimer.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Slicer.py b/nipype/interfaces/fsl/tests/test_auto_Slicer.py index d313cda474..823c8ae1a8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Slicer.py +++ b/nipype/interfaces/fsl/tests/test_auto_Slicer.py @@ -15,6 +15,7 @@ def test_Slicer_inputs(): colour_map=dict( argstr='-l %s', position=4, + usedefault=True, ), dither_edges=dict( argstr='-t', @@ -27,6 +28,7 @@ def test_Slicer_inputs(): image_edges=dict( argstr='%s', position=2, + usedefault=True, ), image_width=dict( argstr='%d', @@ -36,6 +38,7 @@ def test_Slicer_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), intensity_range=dict( argstr='-i %.3f %.3f', @@ -60,6 +63,7 @@ def test_Slicer_inputs(): genfile=True, hash_files=False, position=-1, + usedefault=True, ), output_type=dict(), sample_axial=dict( @@ -98,7 +102,7 @@ def test_Slicer_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Slicer_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Slicer.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Smooth.py b/nipype/interfaces/fsl/tests/test_auto_Smooth.py index e8d8e06117..df9427bde0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Smooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_Smooth.py @@ -20,6 +20,7 @@ def test_Smooth_inputs(): argstr='%s', mandatory=True, position=0, + usedefault=True, ), output_type=dict(), sigma=dict( @@ -34,6 +35,7 @@ def test_Smooth_inputs(): name_source=['in_file'], name_template='%s_smooth', position=2, + usedefault=True, ), ) inputs = Smooth.input_spec() @@ -42,7 +44,7 @@ def test_Smooth_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Smooth_outputs(): - output_map = dict(smoothed_file=dict(), ) + output_map = dict(smoothed_file=dict(usedefault=True, ), ) outputs = Smooth.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py index df7544f931..6a9a0593da 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py +++ b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py @@ -18,14 +18,17 @@ def test_SmoothEstimate_inputs(): mask_file=dict( argstr='--mask=%s', mandatory=True, + usedefault=True, ), output_type=dict(), residual_fit_file=dict( argstr='--res=%s', requires=['dof'], + usedefault=True, ), zstat_file=dict( argstr='--zstat=%s', + usedefault=True, xor=['dof'], ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py index d62f904655..06d1d43277 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py @@ -14,6 +14,7 @@ def test_SpatialFilter_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -22,6 +23,7 @@ def test_SpatialFilter_inputs(): kernel_file=dict( argstr='%s', position=5, + usedefault=True, xor=['kernel_size'], ), kernel_shape=dict( @@ -47,6 +49,7 @@ def test_SpatialFilter_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -60,7 +63,7 @@ def test_SpatialFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SpatialFilter_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = SpatialFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Split.py b/nipype/interfaces/fsl/tests/test_auto_Split.py index cec2ab462d..8097db6fd8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Split.py +++ b/nipype/interfaces/fsl/tests/test_auto_Split.py @@ -19,6 +19,7 @@ def test_Split_inputs(): argstr='%s', mandatory=True, position=0, + usedefault=True, ), out_base_name=dict( argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_StdImage.py b/nipype/interfaces/fsl/tests/test_auto_StdImage.py index 302ab9c4c2..0f47f02b4e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_StdImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_StdImage.py @@ -19,6 +19,7 @@ def test_StdImage_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -33,6 +34,7 @@ def test_StdImage_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -46,7 +48,7 @@ def test_StdImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_StdImage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = StdImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py index 7cbb57491c..ebf6866487 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py +++ b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py @@ -14,6 +14,7 @@ def test_SwapDimensions_inputs(): argstr='%s', mandatory=True, position='1', + usedefault=True, ), new_dims=dict( argstr='%s %s %s', @@ -23,6 +24,7 @@ def test_SwapDimensions_inputs(): argstr='%s', genfile=True, hash_files=False, + usedefault=True, ), output_type=dict(), ) @@ -32,7 +34,7 @@ def test_SwapDimensions_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SwapDimensions_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = SwapDimensions.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py index 3f91b3722a..544167f904 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py @@ -19,6 +19,7 @@ def test_TOPUP_inputs(): encoding_file=dict( argstr='--datain=%s', mandatory=True, + usedefault=True, xor=['encoding_direction'], ), environ=dict( @@ -30,6 +31,7 @@ def test_TOPUP_inputs(): in_file=dict( argstr='--imain=%s', mandatory=True, + usedefault=True, ), interp=dict(argstr='--interp=%s', ), max_iter=dict(argstr='--miter=%d', ), @@ -40,18 +42,21 @@ def test_TOPUP_inputs(): hash_files=False, name_source=['in_file'], name_template='%s_base', + usedefault=True, ), out_corrected=dict( argstr='--iout=%s', hash_files=False, name_source=['in_file'], name_template='%s_corrected', + usedefault=True, ), out_field=dict( argstr='--fout=%s', hash_files=False, name_source=['in_file'], name_template='%s_field', + usedefault=True, ), out_jac_prefix=dict( argstr='--jacout=%s', @@ -64,6 +69,7 @@ def test_TOPUP_inputs(): keep_extension=True, name_source=['in_file'], name_template='%s_topup.log', + usedefault=True, ), out_mat_prefix=dict( argstr='--rbmout=%s', @@ -97,14 +103,14 @@ def test_TOPUP_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TOPUP_outputs(): output_map = dict( - out_corrected=dict(), - out_enc_file=dict(), - out_field=dict(), - out_fieldcoef=dict(), + out_corrected=dict(usedefault=True, ), + out_enc_file=dict(usedefault=True, ), + out_field=dict(usedefault=True, ), + out_fieldcoef=dict(usedefault=True, ), out_jacs=dict(), - out_logfile=dict(), + out_logfile=dict(usedefault=True, ), out_mats=dict(), - out_movpar=dict(), + out_movpar=dict(usedefault=True, ), out_warps=dict(), ) outputs = TOPUP.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py index c762b99d31..d567dcd085 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py @@ -19,6 +19,7 @@ def test_TemporalFilter_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -38,6 +39,7 @@ def test_TemporalFilter_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -51,7 +53,7 @@ def test_TemporalFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TemporalFilter_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TemporalFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Threshold.py b/nipype/interfaces/fsl/tests/test_auto_Threshold.py index 5c2bb46cc8..996bcfd928 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Threshold.py +++ b/nipype/interfaces/fsl/tests/test_auto_Threshold.py @@ -15,6 +15,7 @@ def test_Threshold_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -29,6 +30,7 @@ def test_Threshold_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -49,7 +51,7 @@ def test_Threshold_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Threshold_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Threshold.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py index 4308ee8153..b900074a51 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py +++ b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py @@ -5,11 +5,17 @@ def test_TractSkeleton_inputs(): input_map = dict( - alt_data_file=dict(argstr='-a %s', ), - alt_skeleton=dict(argstr='-s %s', ), + alt_data_file=dict( + argstr='-a %s', + usedefault=True, + ), + alt_skeleton=dict( + argstr='-s %s', + usedefault=True, + ), args=dict(argstr='%s', ), - data_file=dict(), - distance_map=dict(), + data_file=dict(usedefault=True, ), + distance_map=dict(usedefault=True, ), environ=dict( nohash=True, usedefault=True, @@ -17,14 +23,18 @@ def test_TractSkeleton_inputs(): in_file=dict( argstr='-i %s', mandatory=True, + usedefault=True, ), output_type=dict(), project_data=dict( argstr='-p %.3f %s %s %s %s', requires=['threshold', 'distance_map', 'data_file'], ), - projected_data=dict(), - search_mask_file=dict(xor=['use_cingulum_mask'], ), + projected_data=dict(usedefault=True, ), + search_mask_file=dict( + usedefault=True, + xor=['use_cingulum_mask'], + ), skeleton_file=dict(argstr='-o %s', ), threshold=dict(), use_cingulum_mask=dict( @@ -39,8 +49,8 @@ def test_TractSkeleton_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TractSkeleton_outputs(): output_map = dict( - projected_data=dict(), - skeleton_file=dict(), + projected_data=dict(usedefault=True, ), + skeleton_file=dict(usedefault=True, ), ) outputs = TractSkeleton.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Training.py b/nipype/interfaces/fsl/tests/test_auto_Training.py index 91d48e4c01..d9943d7033 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Training.py +++ b/nipype/interfaces/fsl/tests/test_auto_Training.py @@ -30,7 +30,7 @@ def test_Training_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Training_outputs(): - output_map = dict(trained_wts_file=dict(), ) + output_map = dict(trained_wts_file=dict(usedefault=True, ), ) outputs = Training.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py index a0dcf2610d..322bfc8baa 100644 --- a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py @@ -14,6 +14,7 @@ def test_UnaryMaths_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -33,6 +34,7 @@ def test_UnaryMaths_inputs(): genfile=True, hash_files=False, position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -46,7 +48,7 @@ def test_UnaryMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_UnaryMaths_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = UnaryMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_VecReg.py b/nipype/interfaces/fsl/tests/test_auto_VecReg.py index 61a28f7369..b5a75f168b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_VecReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_VecReg.py @@ -5,7 +5,10 @@ def test_VecReg_inputs(): input_map = dict( - affine_mat=dict(argstr='-t %s', ), + affine_mat=dict( + argstr='-t %s', + usedefault=True, + ), args=dict(argstr='%s', ), environ=dict( nohash=True, @@ -14,23 +17,41 @@ def test_VecReg_inputs(): in_file=dict( argstr='-i %s', mandatory=True, + usedefault=True, ), interpolation=dict(argstr='--interp=%s', ), - mask=dict(argstr='-m %s', ), + mask=dict( + argstr='-m %s', + usedefault=True, + ), out_file=dict( argstr='-o %s', genfile=True, hash_files=False, + usedefault=True, ), output_type=dict(), - ref_mask=dict(argstr='--refmask=%s', ), + ref_mask=dict( + argstr='--refmask=%s', + usedefault=True, + ), ref_vol=dict( argstr='-r %s', mandatory=True, + usedefault=True, + ), + rotation_mat=dict( + argstr='--rotmat=%s', + usedefault=True, + ), + rotation_warp=dict( + argstr='--rotwarp=%s', + usedefault=True, + ), + warp_field=dict( + argstr='-w %s', + usedefault=True, ), - rotation_mat=dict(argstr='--rotmat=%s', ), - rotation_warp=dict(argstr='--rotwarp=%s', ), - warp_field=dict(argstr='-w %s', ), ) inputs = VecReg.input_spec() @@ -38,7 +59,7 @@ def test_VecReg_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_VecReg_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = VecReg.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py index 30924223cf..64258eb6ce 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py @@ -17,6 +17,7 @@ def test_WarpPoints_inputs(): dest_file=dict( argstr='-dest %s', mandatory=True, + usedefault=True, ), environ=dict( nohash=True, @@ -26,22 +27,27 @@ def test_WarpPoints_inputs(): argstr='%s', mandatory=True, position=-1, + usedefault=True, ), out_file=dict( name_source='in_coords', name_template='%s_warped', output_name='out_file', + usedefault=True, ), src_file=dict( argstr='-src %s', mandatory=True, + usedefault=True, ), warp_file=dict( argstr='-warp %s', + usedefault=True, xor=['xfm_file'], ), xfm_file=dict( argstr='-xfm %s', + usedefault=True, xor=['warp_file'], ), ) @@ -51,7 +57,7 @@ def test_WarpPoints_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpPoints_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = WarpPoints.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py b/nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py index 627ef60ad6..8aa6a7b2ee 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py @@ -21,22 +21,27 @@ def test_WarpPointsFromStd_inputs(): img_file=dict( argstr='-img %s', mandatory=True, + usedefault=True, ), in_coords=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), std_file=dict( argstr='-std %s', mandatory=True, + usedefault=True, ), warp_file=dict( argstr='-warp %s', + usedefault=True, xor=['xfm_file'], ), xfm_file=dict( argstr='-xfm %s', + usedefault=True, xor=['warp_file'], ), ) @@ -46,7 +51,7 @@ def test_WarpPointsFromStd_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpPointsFromStd_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = WarpPointsFromStd.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py index 3d37ad1486..adc1b0fb77 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py @@ -21,28 +21,37 @@ def test_WarpPointsToStd_inputs(): img_file=dict( argstr='-img %s', mandatory=True, + usedefault=True, ), in_coords=dict( argstr='%s', mandatory=True, position=-1, + usedefault=True, ), out_file=dict( name_source='in_coords', name_template='%s_warped', output_name='out_file', + usedefault=True, + ), + premat_file=dict( + argstr='-premat %s', + usedefault=True, ), - premat_file=dict(argstr='-premat %s', ), std_file=dict( argstr='-std %s', mandatory=True, + usedefault=True, ), warp_file=dict( argstr='-warp %s', + usedefault=True, xor=['xfm_file'], ), xfm_file=dict( argstr='-xfm %s', + usedefault=True, xor=['warp_file'], ), ) @@ -52,7 +61,7 @@ def test_WarpPointsToStd_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpPointsToStd_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = WarpPointsToStd.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py index 04d3a05f14..96eedbbe51 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py @@ -13,6 +13,7 @@ def test_WarpUtils_inputs(): in_file=dict( argstr='--in=%s', mandatory=True, + usedefault=True, ), knot_space=dict(argstr='--knotspace=%d,%d,%d', ), out_file=dict( @@ -20,13 +21,18 @@ def test_WarpUtils_inputs(): name_source=['in_file'], output_name='out_file', position=-1, + usedefault=True, ), out_format=dict(argstr='--outformat=%s', ), - out_jacobian=dict(argstr='--jac=%s', ), + out_jacobian=dict( + argstr='--jac=%s', + usedefault=True, + ), output_type=dict(), reference=dict( argstr='--ref=%s', mandatory=True, + usedefault=True, ), warp_resolution=dict(argstr='--warpres=%0.4f,%0.4f,%0.4f', ), with_affine=dict(argstr='--withaff', ), @@ -42,8 +48,8 @@ def test_WarpUtils_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_WarpUtils_outputs(): output_map = dict( - out_file=dict(), - out_jacobian=dict(), + out_file=dict(usedefault=True, ), + out_jacobian=dict(usedefault=True, ), ) outputs = WarpUtils.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py index d72bb3bb4b..490bb7a17b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py +++ b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py @@ -21,10 +21,12 @@ def test_XFibres5_inputs(): bvals=dict( argstr='--bvals=%s', mandatory=True, + usedefault=True, ), bvecs=dict( argstr='--bvecs=%s', mandatory=True, + usedefault=True, ), cnlinear=dict( argstr='--cnonlinear', @@ -33,6 +35,7 @@ def test_XFibres5_inputs(): dwi=dict( argstr='--data=%s', mandatory=True, + usedefault=True, ), environ=dict( nohash=True, @@ -51,7 +54,10 @@ def test_XFibres5_inputs(): usedefault=True, ), fudge=dict(argstr='--fudge=%d', ), - gradnonlin=dict(argstr='--gradnonlin=%s', ), + gradnonlin=dict( + argstr='--gradnonlin=%s', + usedefault=True, + ), logdir=dict( argstr='--logdir=%s', usedefault=True, @@ -59,6 +65,7 @@ def test_XFibres5_inputs(): mask=dict( argstr='--mask=%s', mandatory=True, + usedefault=True, ), model=dict(argstr='--model=%d', ), n_fibres=dict( @@ -103,10 +110,10 @@ def test_XFibres5_outputs(): output_map = dict( dyads=dict(), fsamples=dict(), - mean_S0samples=dict(), - mean_dsamples=dict(), + mean_S0samples=dict(usedefault=True, ), + mean_dsamples=dict(usedefault=True, ), mean_fsamples=dict(), - mean_tausamples=dict(), + mean_tausamples=dict(usedefault=True, ), phsamples=dict(), thsamples=dict(), ) diff --git a/nipype/interfaces/minc/tests/test_auto_Average.py b/nipype/interfaces/minc/tests/test_auto_Average.py index 57bdc5ccd2..8883e6fe04 100644 --- a/nipype/interfaces/minc/tests/test_auto_Average.py +++ b/nipype/interfaces/minc/tests/test_auto_Average.py @@ -120,6 +120,7 @@ def test_Average_inputs(): name_source=['input_files'], name_template='%s_averaged.mnc', position=-1, + usedefault=True, ), quiet=dict( argstr='-quiet', @@ -147,7 +148,7 @@ def test_Average_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Average_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = Average.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_BBox.py b/nipype/interfaces/minc/tests/test_auto_BBox.py index a34aeab9b5..f168f3c242 100644 --- a/nipype/interfaces/minc/tests/test_auto_BBox.py +++ b/nipype/interfaces/minc/tests/test_auto_BBox.py @@ -17,6 +17,7 @@ def test_BBox_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), one_line=dict( argstr='-one_line', @@ -33,6 +34,7 @@ def test_BBox_inputs(): name_source=['input_file'], name_template='%s_bbox.txt', position=-1, + usedefault=True, ), threshold=dict(argstr='-threshold', ), two_lines=dict( @@ -46,7 +48,7 @@ def test_BBox_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BBox_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = BBox.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Beast.py b/nipype/interfaces/minc/tests/test_auto_Beast.py index 4834cf3c4a..eea3348e8b 100644 --- a/nipype/interfaces/minc/tests/test_auto_Beast.py +++ b/nipype/interfaces/minc/tests/test_auto_Beast.py @@ -78,7 +78,7 @@ def test_Beast_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Beast_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = Beast.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_BestLinReg.py b/nipype/interfaces/minc/tests/test_auto_BestLinReg.py index fb9061040a..f38b22f27a 100644 --- a/nipype/interfaces/minc/tests/test_auto_BestLinReg.py +++ b/nipype/interfaces/minc/tests/test_auto_BestLinReg.py @@ -22,6 +22,7 @@ def test_BestLinReg_inputs(): name_source=['source'], name_template='%s_bestlinreg.mnc', position=-1, + usedefault=True, ), output_xfm=dict( argstr='%s', @@ -31,16 +32,19 @@ def test_BestLinReg_inputs(): name_source=['source'], name_template='%s_bestlinreg.xfm', position=-2, + usedefault=True, ), source=dict( argstr='%s', mandatory=True, position=-4, + usedefault=True, ), target=dict( argstr='%s', mandatory=True, position=-3, + usedefault=True, ), verbose=dict(argstr='-verbose', ), ) @@ -51,8 +55,8 @@ def test_BestLinReg_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BestLinReg_outputs(): output_map = dict( - output_mnc=dict(), - output_xfm=dict(), + output_mnc=dict(usedefault=True, ), + output_xfm=dict(usedefault=True, ), ) outputs = BestLinReg.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_BigAverage.py b/nipype/interfaces/minc/tests/test_auto_BigAverage.py index ce1fb2b91e..7f722afa23 100644 --- a/nipype/interfaces/minc/tests/test_auto_BigAverage.py +++ b/nipype/interfaces/minc/tests/test_auto_BigAverage.py @@ -27,6 +27,7 @@ def test_BigAverage_inputs(): name_source=['input_files'], name_template='%s_bigaverage.mnc', position=-1, + usedefault=True, ), output_float=dict(argstr='--float', ), robust=dict(argstr='-robust', ), @@ -35,8 +36,12 @@ def test_BigAverage_inputs(): hash_files=False, name_source=['input_files'], name_template='%s_bigaverage_stdev.mnc', + usedefault=True, + ), + tmpdir=dict( + argstr='-tmpdir %s', + usedefault=True, ), - tmpdir=dict(argstr='-tmpdir %s', ), verbose=dict(argstr='--verbose', ), ) inputs = BigAverage.input_spec() @@ -46,8 +51,8 @@ def test_BigAverage_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BigAverage_outputs(): output_map = dict( - output_file=dict(), - sd_file=dict(), + output_file=dict(usedefault=True, ), + sd_file=dict(usedefault=True, ), ) outputs = BigAverage.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Blob.py b/nipype/interfaces/minc/tests/test_auto_Blob.py index b489ac944a..c7bfe318e0 100644 --- a/nipype/interfaces/minc/tests/test_auto_Blob.py +++ b/nipype/interfaces/minc/tests/test_auto_Blob.py @@ -15,6 +15,7 @@ def test_Blob_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), magnitude=dict(argstr='-magnitude', ), output_file=dict( @@ -24,6 +25,7 @@ def test_Blob_inputs(): name_source=['input_file'], name_template='%s_blob.mnc', position=-1, + usedefault=True, ), trace=dict(argstr='-trace', ), translation=dict(argstr='-translation', ), @@ -34,7 +36,7 @@ def test_Blob_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Blob_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = Blob.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Blur.py b/nipype/interfaces/minc/tests/test_auto_Blur.py index fb6e405012..b6ecfc8e23 100644 --- a/nipype/interfaces/minc/tests/test_auto_Blur.py +++ b/nipype/interfaces/minc/tests/test_auto_Blur.py @@ -34,11 +34,13 @@ def test_Blur_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), no_apodize=dict(argstr='-no_apodize', ), output_file_base=dict( argstr='%s', position=-1, + usedefault=True, ), partial=dict(argstr='-partial', ), rect=dict( @@ -58,12 +60,12 @@ def test_Blur_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Blur_outputs(): output_map = dict( - gradient_dxyz=dict(), - output_file=dict(), - partial_dx=dict(), - partial_dxyz=dict(), - partial_dy=dict(), - partial_dz=dict(), + gradient_dxyz=dict(usedefault=True, ), + output_file=dict(usedefault=True, ), + partial_dx=dict(usedefault=True, ), + partial_dxyz=dict(usedefault=True, ), + partial_dy=dict(usedefault=True, ), + partial_dz=dict(usedefault=True, ), ) outputs = Blur.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Calc.py b/nipype/interfaces/minc/tests/test_auto_Calc.py index 7bec782c1c..7f8a4ee0fe 100644 --- a/nipype/interfaces/minc/tests/test_auto_Calc.py +++ b/nipype/interfaces/minc/tests/test_auto_Calc.py @@ -117,6 +117,7 @@ def test_Calc_inputs(): name_source=['input_files'], name_template='%s_calc.mnc', position=-1, + usedefault=True, ), output_illegal=dict( argstr='-illegal_value', @@ -148,7 +149,7 @@ def test_Calc_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Calc_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = Calc.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Convert.py b/nipype/interfaces/minc/tests/test_auto_Convert.py index 6df596c682..ee1d8429b6 100644 --- a/nipype/interfaces/minc/tests/test_auto_Convert.py +++ b/nipype/interfaces/minc/tests/test_auto_Convert.py @@ -20,6 +20,7 @@ def test_Convert_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), output_file=dict( argstr='%s', @@ -28,6 +29,7 @@ def test_Convert_inputs(): name_source=['input_file'], name_template='%s_convert_output.mnc', position=-1, + usedefault=True, ), template=dict(argstr='-template', ), two=dict(argstr='-2', ), @@ -38,7 +40,7 @@ def test_Convert_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Convert_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = Convert.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Copy.py b/nipype/interfaces/minc/tests/test_auto_Copy.py index e91470ba6d..2e87caa55b 100644 --- a/nipype/interfaces/minc/tests/test_auto_Copy.py +++ b/nipype/interfaces/minc/tests/test_auto_Copy.py @@ -14,6 +14,7 @@ def test_Copy_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), output_file=dict( argstr='%s', @@ -22,6 +23,7 @@ def test_Copy_inputs(): name_source=['input_file'], name_template='%s_copy.mnc', position=-1, + usedefault=True, ), pixel_values=dict( argstr='-pixel_values', @@ -38,7 +40,7 @@ def test_Copy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Copy_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = Copy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Dump.py b/nipype/interfaces/minc/tests/test_auto_Dump.py index bcca2a4801..1dc7a96d78 100644 --- a/nipype/interfaces/minc/tests/test_auto_Dump.py +++ b/nipype/interfaces/minc/tests/test_auto_Dump.py @@ -30,6 +30,7 @@ def test_Dump_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), line_length=dict(argstr='-l %d', ), netcdf_name=dict(argstr='-n %s', ), @@ -44,6 +45,7 @@ def test_Dump_inputs(): name_source=['input_file'], name_template='%s_dump.txt', position=-1, + usedefault=True, ), precision=dict(argstr='%s', ), variables=dict( @@ -57,7 +59,7 @@ def test_Dump_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Dump_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = Dump.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Extract.py b/nipype/interfaces/minc/tests/test_auto_Extract.py index 77126eac18..4f37eecab3 100644 --- a/nipype/interfaces/minc/tests/test_auto_Extract.py +++ b/nipype/interfaces/minc/tests/test_auto_Extract.py @@ -72,6 +72,7 @@ def test_Extract_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), nonormalize=dict( argstr='-nonormalize', @@ -92,6 +93,7 @@ def test_Extract_inputs(): name_source=['input_file'], name_template='%s.raw', position=-1, + usedefault=True, ), start=dict( argstr='-start %s', @@ -155,7 +157,7 @@ def test_Extract_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Extract_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = Extract.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py b/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py index c89dc65de6..255acdb0b3 100644 --- a/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py +++ b/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py @@ -15,7 +15,10 @@ def test_Gennlxfm_inputs(): usedefault=True, ), ident=dict(argstr='-ident', ), - like=dict(argstr='-like %s', ), + like=dict( + argstr='-like %s', + usedefault=True, + ), output_file=dict( argstr='%s', genfile=True, @@ -23,6 +26,7 @@ def test_Gennlxfm_inputs(): name_source=['like'], name_template='%s_gennlxfm.xfm', position=-1, + usedefault=True, ), step=dict(argstr='-step %s', ), verbose=dict(argstr='-verbose', ), @@ -34,8 +38,8 @@ def test_Gennlxfm_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Gennlxfm_outputs(): output_map = dict( - output_file=dict(), - output_grid=dict(), + output_file=dict(usedefault=True, ), + output_grid=dict(usedefault=True, ), ) outputs = Gennlxfm.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Math.py b/nipype/interfaces/minc/tests/test_auto_Math.py index 1d011034d2..d1f6bf58b1 100644 --- a/nipype/interfaces/minc/tests/test_auto_Math.py +++ b/nipype/interfaces/minc/tests/test_auto_Math.py @@ -127,6 +127,7 @@ def test_Math_inputs(): name_source=['input_files'], name_template='%s_mincmath.mnc', position=-1, + usedefault=True, ), output_illegal=dict( argstr='-illegal_value', @@ -161,7 +162,7 @@ def test_Math_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Math_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = Math.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_NlpFit.py b/nipype/interfaces/minc/tests/test_auto_NlpFit.py index 1a728a90dd..c67a423fa3 100644 --- a/nipype/interfaces/minc/tests/test_auto_NlpFit.py +++ b/nipype/interfaces/minc/tests/test_auto_NlpFit.py @@ -13,6 +13,7 @@ def test_NlpFit_inputs(): config_file=dict( argstr='-config_file %s', mandatory=True, + usedefault=True, ), environ=dict( nohash=True, @@ -21,26 +22,31 @@ def test_NlpFit_inputs(): init_xfm=dict( argstr='-init_xfm %s', mandatory=True, + usedefault=True, ), input_grid_files=dict(), output_xfm=dict( argstr='%s', genfile=True, position=-1, + usedefault=True, ), source=dict( argstr='%s', mandatory=True, position=-3, + usedefault=True, ), source_mask=dict( argstr='-source_mask %s', mandatory=True, + usedefault=True, ), target=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), verbose=dict(argstr='-verbose', ), ) @@ -51,8 +57,8 @@ def test_NlpFit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_NlpFit_outputs(): output_map = dict( - output_grid=dict(), - output_xfm=dict(), + output_grid=dict(usedefault=True, ), + output_xfm=dict(usedefault=True, ), ) outputs = NlpFit.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Norm.py b/nipype/interfaces/minc/tests/test_auto_Norm.py index 3a0d28f06d..96511610a4 100644 --- a/nipype/interfaces/minc/tests/test_auto_Norm.py +++ b/nipype/interfaces/minc/tests/test_auto_Norm.py @@ -23,6 +23,7 @@ def test_Norm_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), lower=dict(argstr='-lower %s', ), mask=dict(argstr='-mask %s', ), @@ -35,6 +36,7 @@ def test_Norm_inputs(): name_source=['input_file'], name_template='%s_norm.mnc', position=-1, + usedefault=True, ), output_threshold_mask=dict( argstr='-threshold_mask %s', @@ -55,8 +57,8 @@ def test_Norm_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Norm_outputs(): output_map = dict( - output_file=dict(), - output_threshold_mask=dict(), + output_file=dict(usedefault=True, ), + output_threshold_mask=dict(usedefault=True, ), ) outputs = Norm.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Pik.py b/nipype/interfaces/minc/tests/test_auto_Pik.py index d74d9a86ad..406355ca28 100644 --- a/nipype/interfaces/minc/tests/test_auto_Pik.py +++ b/nipype/interfaces/minc/tests/test_auto_Pik.py @@ -32,6 +32,7 @@ def test_Pik_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), jpg=dict(xor=('jpg', 'png'), ), lookup=dict(argstr='--lookup %s', ), @@ -44,6 +45,7 @@ def test_Pik_inputs(): name_source=['input_file'], name_template='%s.png', position=-1, + usedefault=True, ), png=dict(xor=('jpg', 'png'), ), sagittal_offset=dict(argstr='--sagittal_offset %s', ), @@ -84,7 +86,7 @@ def test_Pik_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Pik_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = Pik.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Resample.py b/nipype/interfaces/minc/tests/test_auto_Resample.py index bd00bd224d..d842c6983b 100644 --- a/nipype/interfaces/minc/tests/test_auto_Resample.py +++ b/nipype/interfaces/minc/tests/test_auto_Resample.py @@ -86,6 +86,7 @@ def test_Resample_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), input_grid_files=dict(), invert_transformation=dict(argstr='-invert_transformation', ), @@ -123,6 +124,7 @@ def test_Resample_inputs(): name_source=['input_file'], name_template='%s_resample.mnc', position=-1, + usedefault=True, ), output_range=dict(argstr='-range %s %s', ), sagittal_slices=dict( @@ -243,7 +245,7 @@ def test_Resample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Resample_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = Resample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Reshape.py b/nipype/interfaces/minc/tests/test_auto_Reshape.py index 45e6ddeb4a..5291f9b463 100644 --- a/nipype/interfaces/minc/tests/test_auto_Reshape.py +++ b/nipype/interfaces/minc/tests/test_auto_Reshape.py @@ -26,6 +26,7 @@ def test_Reshape_inputs(): name_source=['input_file'], name_template='%s_reshape.mnc', position=-1, + usedefault=True, ), verbose=dict(argstr='-verbose', ), write_short=dict(argstr='-short', ), @@ -36,7 +37,7 @@ def test_Reshape_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Reshape_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = Reshape.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_ToEcat.py b/nipype/interfaces/minc/tests/test_auto_ToEcat.py index 26a3ac0436..eedfbbf47a 100644 --- a/nipype/interfaces/minc/tests/test_auto_ToEcat.py +++ b/nipype/interfaces/minc/tests/test_auto_ToEcat.py @@ -23,6 +23,7 @@ def test_ToEcat_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), no_decay_corr_fctr=dict(argstr='-no_decay_corr_fctr', ), output_file=dict( @@ -33,6 +34,7 @@ def test_ToEcat_inputs(): name_source=['input_file'], name_template='%s_to_ecat.v', position=-1, + usedefault=True, ), voxels_as_integers=dict(argstr='-label', ), ) @@ -42,7 +44,7 @@ def test_ToEcat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ToEcat_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = ToEcat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_ToRaw.py b/nipype/interfaces/minc/tests/test_auto_ToRaw.py index e010da322d..afc831c807 100644 --- a/nipype/interfaces/minc/tests/test_auto_ToRaw.py +++ b/nipype/interfaces/minc/tests/test_auto_ToRaw.py @@ -14,6 +14,7 @@ def test_ToRaw_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), nonormalize=dict( argstr='-nonormalize', @@ -34,6 +35,7 @@ def test_ToRaw_inputs(): name_source=['input_file'], name_template='%s.raw', position=-1, + usedefault=True, ), write_byte=dict( argstr='-byte', @@ -81,7 +83,7 @@ def test_ToRaw_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ToRaw_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = ToRaw.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_VolSymm.py b/nipype/interfaces/minc/tests/test_auto_VolSymm.py index 048ffcde9b..99ba96a29a 100644 --- a/nipype/interfaces/minc/tests/test_auto_VolSymm.py +++ b/nipype/interfaces/minc/tests/test_auto_VolSymm.py @@ -10,7 +10,10 @@ def test_VolSymm_inputs(): argstr='-clobber', usedefault=True, ), - config_file=dict(argstr='-config_file %s', ), + config_file=dict( + argstr='-config_file %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -31,6 +34,7 @@ def test_VolSymm_inputs(): name_source=['input_file'], name_template='%s_vol_symm.mnc', position=-1, + usedefault=True, ), trans_file=dict( argstr='%s', @@ -53,9 +57,9 @@ def test_VolSymm_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_VolSymm_outputs(): output_map = dict( - output_file=dict(), - output_grid=dict(), - trans_file=dict(), + output_file=dict(usedefault=True, ), + output_grid=dict(usedefault=True, ), + trans_file=dict(usedefault=True, ), ) outputs = VolSymm.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Volcentre.py b/nipype/interfaces/minc/tests/test_auto_Volcentre.py index b095751a4d..4abbcf66aa 100644 --- a/nipype/interfaces/minc/tests/test_auto_Volcentre.py +++ b/nipype/interfaces/minc/tests/test_auto_Volcentre.py @@ -20,6 +20,7 @@ def test_Volcentre_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), output_file=dict( argstr='%s', @@ -28,6 +29,7 @@ def test_Volcentre_inputs(): name_source=['input_file'], name_template='%s_volcentre.mnc', position=-1, + usedefault=True, ), verbose=dict(argstr='-verbose', ), zero_dircos=dict(argstr='-zero_dircos', ), @@ -38,7 +40,7 @@ def test_Volcentre_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Volcentre_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = Volcentre.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Voliso.py b/nipype/interfaces/minc/tests/test_auto_Voliso.py index 967642a328..a16b8da063 100644 --- a/nipype/interfaces/minc/tests/test_auto_Voliso.py +++ b/nipype/interfaces/minc/tests/test_auto_Voliso.py @@ -19,6 +19,7 @@ def test_Voliso_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), maxstep=dict(argstr='--maxstep %s', ), minstep=dict(argstr='--minstep %s', ), @@ -29,6 +30,7 @@ def test_Voliso_inputs(): name_source=['input_file'], name_template='%s_voliso.mnc', position=-1, + usedefault=True, ), verbose=dict(argstr='--verbose', ), ) @@ -38,7 +40,7 @@ def test_Voliso_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Voliso_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = Voliso.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Volpad.py b/nipype/interfaces/minc/tests/test_auto_Volpad.py index 865bc79e69..1c29b0a1c4 100644 --- a/nipype/interfaces/minc/tests/test_auto_Volpad.py +++ b/nipype/interfaces/minc/tests/test_auto_Volpad.py @@ -21,6 +21,7 @@ def test_Volpad_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), output_file=dict( argstr='%s', @@ -29,6 +30,7 @@ def test_Volpad_inputs(): name_source=['input_file'], name_template='%s_volpad.mnc', position=-1, + usedefault=True, ), smooth=dict(argstr='-smooth', ), smooth_distance=dict(argstr='-smooth_distance %s', ), @@ -40,7 +42,7 @@ def test_Volpad_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Volpad_outputs(): - output_map = dict(output_file=dict(), ) + output_map = dict(output_file=dict(usedefault=True, ), ) outputs = Volpad.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_XfmAvg.py b/nipype/interfaces/minc/tests/test_auto_XfmAvg.py index 6d036a0c0e..6ba7d2811d 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmAvg.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmAvg.py @@ -29,6 +29,7 @@ def test_XfmAvg_inputs(): argstr='%s', genfile=True, position=-1, + usedefault=True, ), verbose=dict(argstr='-verbose', ), ) @@ -39,8 +40,8 @@ def test_XfmAvg_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_XfmAvg_outputs(): output_map = dict( - output_file=dict(), - output_grid=dict(), + output_file=dict(usedefault=True, ), + output_grid=dict(usedefault=True, ), ) outputs = XfmAvg.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_XfmConcat.py b/nipype/interfaces/minc/tests/test_auto_XfmConcat.py index eb748953ef..8453286669 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmConcat.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmConcat.py @@ -28,6 +28,7 @@ def test_XfmConcat_inputs(): name_source=['input_files'], name_template='%s_xfmconcat.xfm', position=-1, + usedefault=True, ), verbose=dict(argstr='-verbose', ), ) @@ -38,7 +39,7 @@ def test_XfmConcat_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_XfmConcat_outputs(): output_map = dict( - output_file=dict(), + output_file=dict(usedefault=True, ), output_grids=dict(), ) outputs = XfmConcat.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py index d729e90639..ff7455cb6e 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py @@ -23,6 +23,7 @@ def test_XfmInvert_inputs(): argstr='%s', genfile=True, position=-1, + usedefault=True, ), verbose=dict(argstr='-verbose', ), ) @@ -33,8 +34,8 @@ def test_XfmInvert_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_XfmInvert_outputs(): output_map = dict( - output_file=dict(), - output_grid=dict(), + output_file=dict(usedefault=True, ), + output_grid=dict(usedefault=True, ), ) outputs = XfmInvert.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py index 16605acbb7..79f466bb69 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py @@ -11,18 +11,36 @@ def test_JistBrainMgdmSegmentation_inputs(): usedefault=True, ), inAdjust=dict(argstr='--inAdjust %s', ), - inAtlas=dict(argstr='--inAtlas %s', ), + inAtlas=dict( + argstr='--inAtlas %s', + usedefault=True, + ), inCompute=dict(argstr='--inCompute %s', ), inCurvature=dict(argstr='--inCurvature %f', ), inData=dict(argstr='--inData %f', ), - inFLAIR=dict(argstr='--inFLAIR %s', ), - inMP2RAGE=dict(argstr='--inMP2RAGE %s', ), - inMP2RAGE2=dict(argstr='--inMP2RAGE2 %s', ), - inMPRAGE=dict(argstr='--inMPRAGE %s', ), + inFLAIR=dict( + argstr='--inFLAIR %s', + usedefault=True, + ), + inMP2RAGE=dict( + argstr='--inMP2RAGE %s', + usedefault=True, + ), + inMP2RAGE2=dict( + argstr='--inMP2RAGE2 %s', + usedefault=True, + ), + inMPRAGE=dict( + argstr='--inMPRAGE %s', + usedefault=True, + ), inMax=dict(argstr='--inMax %d', ), inMin=dict(argstr='--inMin %f', ), inOutput=dict(argstr='--inOutput %s', ), - inPV=dict(argstr='--inPV %s', ), + inPV=dict( + argstr='--inPV %s', + usedefault=True, + ), inPosterior=dict(argstr='--inPosterior %f', ), inSteps=dict(argstr='--inSteps %d', ), inTopology=dict(argstr='--inTopology %s', ), @@ -57,10 +75,10 @@ def test_JistBrainMgdmSegmentation_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistBrainMgdmSegmentation_outputs(): output_map = dict( - outLevelset=dict(), - outPosterior2=dict(), - outPosterior3=dict(), - outSegmented=dict(), + outLevelset=dict(usedefault=True, ), + outPosterior2=dict(usedefault=True, ), + outPosterior3=dict(usedefault=True, ), + outSegmented=dict(usedefault=True, ), ) outputs = JistBrainMgdmSegmentation.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py index ebb65bb789..17a5d5be33 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py @@ -11,8 +11,14 @@ def test_JistBrainMp2rageDuraEstimation_inputs(): usedefault=True, ), inDistance=dict(argstr='--inDistance %f', ), - inSecond=dict(argstr='--inSecond %s', ), - inSkull=dict(argstr='--inSkull %s', ), + inSecond=dict( + argstr='--inSecond %s', + usedefault=True, + ), + inSkull=dict( + argstr='--inSkull %s', + usedefault=True, + ), inoutput=dict(argstr='--inoutput %s', ), null=dict(argstr='--null %s', ), outDura=dict( @@ -32,7 +38,7 @@ def test_JistBrainMp2rageDuraEstimation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JistBrainMp2rageDuraEstimation_outputs(): - output_map = dict(outDura=dict(), ) + output_map = dict(outDura=dict(usedefault=True, ), ) outputs = JistBrainMp2rageDuraEstimation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py index abf794b662..6f54ace63e 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py @@ -10,11 +10,23 @@ def test_JistBrainMp2rageSkullStripping_inputs(): nohash=True, usedefault=True, ), - inFilter=dict(argstr='--inFilter %s', ), - inSecond=dict(argstr='--inSecond %s', ), + inFilter=dict( + argstr='--inFilter %s', + usedefault=True, + ), + inSecond=dict( + argstr='--inSecond %s', + usedefault=True, + ), inSkip=dict(argstr='--inSkip %s', ), - inT1=dict(argstr='--inT1 %s', ), - inT1weighted=dict(argstr='--inT1weighted %s', ), + inT1=dict( + argstr='--inT1 %s', + usedefault=True, + ), + inT1weighted=dict( + argstr='--inT1weighted %s', + usedefault=True, + ), null=dict(argstr='--null %s', ), outBrain=dict( argstr='--outBrain %s', @@ -46,10 +58,10 @@ def test_JistBrainMp2rageSkullStripping_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistBrainMp2rageSkullStripping_outputs(): output_map = dict( - outBrain=dict(), - outMasked=dict(), - outMasked2=dict(), - outMasked3=dict(), + outBrain=dict(usedefault=True, ), + outMasked=dict(usedefault=True, ), + outMasked2=dict(usedefault=True, ), + outMasked3=dict(usedefault=True, ), ) outputs = JistBrainMp2rageSkullStripping.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py index bb86144c20..7cdf00bf5b 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py @@ -10,7 +10,10 @@ def test_JistBrainPartialVolumeFilter_inputs(): nohash=True, usedefault=True, ), - inInput=dict(argstr='--inInput %s', ), + inInput=dict( + argstr='--inInput %s', + usedefault=True, + ), inPV=dict(argstr='--inPV %s', ), inoutput=dict(argstr='--inoutput %s', ), null=dict(argstr='--null %s', ), @@ -31,7 +34,7 @@ def test_JistBrainPartialVolumeFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JistBrainPartialVolumeFilter_outputs(): - output_map = dict(outPartial=dict(), ) + output_map = dict(outPartial=dict(usedefault=True, ), ) outputs = JistBrainPartialVolumeFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py index 407b9755ca..21c31aa4e9 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py @@ -10,7 +10,10 @@ def test_JistCortexSurfaceMeshInflation_inputs(): nohash=True, usedefault=True, ), - inLevelset=dict(argstr='--inLevelset %s', ), + inLevelset=dict( + argstr='--inLevelset %s', + usedefault=True, + ), inLorentzian=dict(argstr='--inLorentzian %s', ), inMax=dict(argstr='--inMax %d', ), inMean=dict(argstr='--inMean %f', ), @@ -40,8 +43,8 @@ def test_JistCortexSurfaceMeshInflation_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistCortexSurfaceMeshInflation_outputs(): output_map = dict( - outInflated=dict(), - outOriginal=dict(), + outInflated=dict(usedefault=True, ), + outOriginal=dict(usedefault=True, ), ) outputs = JistCortexSurfaceMeshInflation.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py index bfdace4944..90fee34bb7 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py @@ -12,10 +12,19 @@ def test_JistIntensityMp2rageMasking_inputs(): ), inBackground=dict(argstr='--inBackground %s', ), inMasking=dict(argstr='--inMasking %s', ), - inQuantitative=dict(argstr='--inQuantitative %s', ), - inSecond=dict(argstr='--inSecond %s', ), + inQuantitative=dict( + argstr='--inQuantitative %s', + usedefault=True, + ), + inSecond=dict( + argstr='--inSecond %s', + usedefault=True, + ), inSkip=dict(argstr='--inSkip %s', ), - inT1weighted=dict(argstr='--inT1weighted %s', ), + inT1weighted=dict( + argstr='--inT1weighted %s', + usedefault=True, + ), null=dict(argstr='--null %s', ), outMasked=dict( argstr='--outMasked_T1_Map %s', @@ -47,10 +56,10 @@ def test_JistIntensityMp2rageMasking_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistIntensityMp2rageMasking_outputs(): output_map = dict( - outMasked=dict(), - outMasked2=dict(), - outSignal=dict(), - outSignal2=dict(), + outMasked=dict(usedefault=True, ), + outMasked2=dict(usedefault=True, ), + outSignal=dict(usedefault=True, ), + outSignal2=dict(usedefault=True, ), ) outputs = JistIntensityMp2rageMasking.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py index 12203a1aa6..529de041ca 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py @@ -10,8 +10,14 @@ def test_JistLaminarProfileCalculator_inputs(): nohash=True, usedefault=True, ), - inIntensity=dict(argstr='--inIntensity %s', ), - inMask=dict(argstr='--inMask %s', ), + inIntensity=dict( + argstr='--inIntensity %s', + usedefault=True, + ), + inMask=dict( + argstr='--inMask %s', + usedefault=True, + ), incomputed=dict(argstr='--incomputed %s', ), null=dict(argstr='--null %s', ), outResult=dict( @@ -31,7 +37,7 @@ def test_JistLaminarProfileCalculator_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarProfileCalculator_outputs(): - output_map = dict(outResult=dict(), ) + output_map = dict(outResult=dict(usedefault=True, ), ) outputs = JistLaminarProfileCalculator.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py index ddc4d5d922..f346559abf 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py @@ -10,7 +10,10 @@ def test_JistLaminarProfileGeometry_inputs(): nohash=True, usedefault=True, ), - inProfile=dict(argstr='--inProfile %s', ), + inProfile=dict( + argstr='--inProfile %s', + usedefault=True, + ), incomputed=dict(argstr='--incomputed %s', ), inoutside=dict(argstr='--inoutside %f', ), inregularization=dict(argstr='--inregularization %s', ), @@ -33,7 +36,7 @@ def test_JistLaminarProfileGeometry_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarProfileGeometry_outputs(): - output_map = dict(outResult=dict(), ) + output_map = dict(outResult=dict(usedefault=True, ), ) outputs = JistLaminarProfileGeometry.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py index 58de472b85..f8a593d9ae 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py @@ -10,9 +10,18 @@ def test_JistLaminarProfileSampling_inputs(): nohash=True, usedefault=True, ), - inCortex=dict(argstr='--inCortex %s', ), - inIntensity=dict(argstr='--inIntensity %s', ), - inProfile=dict(argstr='--inProfile %s', ), + inCortex=dict( + argstr='--inCortex %s', + usedefault=True, + ), + inIntensity=dict( + argstr='--inIntensity %s', + usedefault=True, + ), + inProfile=dict( + argstr='--inProfile %s', + usedefault=True, + ), null=dict(argstr='--null %s', ), outProfile2=dict( argstr='--outProfile2 %s', @@ -36,8 +45,8 @@ def test_JistLaminarProfileSampling_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarProfileSampling_outputs(): output_map = dict( - outProfile2=dict(), - outProfilemapped=dict(), + outProfile2=dict(usedefault=True, ), + outProfilemapped=dict(usedefault=True, ), ) outputs = JistLaminarProfileSampling.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py index bb9577ccee..9eb23ab2d8 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py @@ -10,9 +10,18 @@ def test_JistLaminarROIAveraging_inputs(): nohash=True, usedefault=True, ), - inIntensity=dict(argstr='--inIntensity %s', ), - inMask=dict(argstr='--inMask %s', ), - inROI=dict(argstr='--inROI %s', ), + inIntensity=dict( + argstr='--inIntensity %s', + usedefault=True, + ), + inMask=dict( + argstr='--inMask %s', + usedefault=True, + ), + inROI=dict( + argstr='--inROI %s', + usedefault=True, + ), inROI2=dict(argstr='--inROI2 %s', ), null=dict(argstr='--null %s', ), outROI3=dict( @@ -32,7 +41,7 @@ def test_JistLaminarROIAveraging_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarROIAveraging_outputs(): - output_map = dict(outROI3=dict(), ) + output_map = dict(outROI3=dict(usedefault=True, ), ) outputs = JistLaminarROIAveraging.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py index 4aa9f9d77b..40df4113c7 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py @@ -10,13 +10,19 @@ def test_JistLaminarVolumetricLayering_inputs(): nohash=True, usedefault=True, ), - inInner=dict(argstr='--inInner %s', ), + inInner=dict( + argstr='--inInner %s', + usedefault=True, + ), inLayering=dict(argstr='--inLayering %s', ), inLayering2=dict(argstr='--inLayering2 %s', ), inMax=dict(argstr='--inMax %d', ), inMin=dict(argstr='--inMin %f', ), inNumber=dict(argstr='--inNumber %d', ), - inOuter=dict(argstr='--inOuter %s', ), + inOuter=dict( + argstr='--inOuter %s', + usedefault=True, + ), inTopology=dict(argstr='--inTopology %s', ), incurvature=dict(argstr='--incurvature %d', ), inpresmooth=dict(argstr='--inpresmooth %s', ), @@ -48,9 +54,9 @@ def test_JistLaminarVolumetricLayering_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarVolumetricLayering_outputs(): output_map = dict( - outContinuous=dict(), - outDiscrete=dict(), - outLayer=dict(), + outContinuous=dict(usedefault=True, ), + outDiscrete=dict(usedefault=True, ), + outLayer=dict(usedefault=True, ), ) outputs = JistLaminarVolumetricLayering.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py index 016beee263..42a0a3fff7 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py @@ -11,8 +11,14 @@ def test_MedicAlgorithmImageCalculator_inputs(): usedefault=True, ), inOperation=dict(argstr='--inOperation %s', ), - inVolume=dict(argstr='--inVolume %s', ), - inVolume2=dict(argstr='--inVolume2 %s', ), + inVolume=dict( + argstr='--inVolume %s', + usedefault=True, + ), + inVolume2=dict( + argstr='--inVolume2 %s', + usedefault=True, + ), null=dict(argstr='--null %s', ), outResult=dict( argstr='--outResult %s', @@ -31,7 +37,7 @@ def test_MedicAlgorithmImageCalculator_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmImageCalculator_outputs(): - output_map = dict(outResult=dict(), ) + output_map = dict(outResult=dict(usedefault=True, ), ) outputs = MedicAlgorithmImageCalculator.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py index 87f9ab6a72..dd707bc061 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py @@ -11,14 +11,26 @@ def test_MedicAlgorithmLesionToads_inputs(): usedefault=True, ), inAtlas=dict(argstr='--inAtlas %s', ), - inAtlas2=dict(argstr='--inAtlas2 %s', ), - inAtlas3=dict(argstr='--inAtlas3 %s', ), - inAtlas4=dict(argstr='--inAtlas4 %s', ), + inAtlas2=dict( + argstr='--inAtlas2 %s', + usedefault=True, + ), + inAtlas3=dict( + argstr='--inAtlas3 %s', + usedefault=True, + ), + inAtlas4=dict( + argstr='--inAtlas4 %s', + usedefault=True, + ), inAtlas5=dict(argstr='--inAtlas5 %f', ), inAtlas6=dict(argstr='--inAtlas6 %s', ), inConnectivity=dict(argstr='--inConnectivity %s', ), inCorrect=dict(argstr='--inCorrect %s', ), - inFLAIR=dict(argstr='--inFLAIR %s', ), + inFLAIR=dict( + argstr='--inFLAIR %s', + usedefault=True, + ), inInclude=dict(argstr='--inInclude %s', ), inMaximum=dict(argstr='--inMaximum %d', ), inMaximum2=dict(argstr='--inMaximum2 %d', ), @@ -29,8 +41,14 @@ def test_MedicAlgorithmLesionToads_inputs(): inOutput2=dict(argstr='--inOutput2 %s', ), inOutput3=dict(argstr='--inOutput3 %s', ), inSmooting=dict(argstr='--inSmooting %f', ), - inT1_MPRAGE=dict(argstr='--inT1_MPRAGE %s', ), - inT1_SPGR=dict(argstr='--inT1_SPGR %s', ), + inT1_MPRAGE=dict( + argstr='--inT1_MPRAGE %s', + usedefault=True, + ), + inT1_SPGR=dict( + argstr='--inT1_SPGR %s', + usedefault=True, + ), null=dict(argstr='--null %s', ), outCortical=dict( argstr='--outCortical %s', @@ -82,15 +100,15 @@ def test_MedicAlgorithmLesionToads_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmLesionToads_outputs(): output_map = dict( - outCortical=dict(), - outFilled=dict(), - outHard=dict(), - outHard2=dict(), - outInhomogeneity=dict(), - outLesion=dict(), - outMembership=dict(), - outSulcal=dict(), - outWM=dict(), + outCortical=dict(usedefault=True, ), + outFilled=dict(usedefault=True, ), + outHard=dict(usedefault=True, ), + outHard2=dict(usedefault=True, ), + outInhomogeneity=dict(usedefault=True, ), + outLesion=dict(usedefault=True, ), + outMembership=dict(usedefault=True, ), + outSulcal=dict(usedefault=True, ), + outWM=dict(usedefault=True, ), ) outputs = MedicAlgorithmLesionToads.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py index 7c8c7248ad..b05edb5d73 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py @@ -17,7 +17,10 @@ def test_MedicAlgorithmMipavReorient_inputs(): argstr='--inSource %s', sep=';', ), - inTemplate=dict(argstr='--inTemplate %s', ), + inTemplate=dict( + argstr='--inTemplate %s', + usedefault=True, + ), inUser=dict(argstr='--inUser %s', ), inUser2=dict(argstr='--inUser2 %s', ), inUser3=dict(argstr='--inUser3 %s', ), diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py index 9d5a148a24..a5bbd301a1 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py @@ -13,7 +13,10 @@ def test_MedicAlgorithmN3_inputs(): inAutomatic=dict(argstr='--inAutomatic %s', ), inEnd=dict(argstr='--inEnd %f', ), inField=dict(argstr='--inField %f', ), - inInput=dict(argstr='--inInput %s', ), + inInput=dict( + argstr='--inInput %s', + usedefault=True, + ), inKernel=dict(argstr='--inKernel %f', ), inMaximum=dict(argstr='--inMaximum %d', ), inSignal=dict(argstr='--inSignal %f', ), @@ -42,8 +45,8 @@ def test_MedicAlgorithmN3_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmN3_outputs(): output_map = dict( - outInhomogeneity=dict(), - outInhomogeneity2=dict(), + outInhomogeneity=dict(usedefault=True, ), + outInhomogeneity2=dict(usedefault=True, ), ) outputs = MedicAlgorithmN3.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py index b2d247e9dc..df87186aa6 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py @@ -11,7 +11,10 @@ def test_MedicAlgorithmSPECTRE2010_inputs(): usedefault=True, ), inApply=dict(argstr='--inApply %s', ), - inAtlas=dict(argstr='--inAtlas %s', ), + inAtlas=dict( + argstr='--inAtlas %s', + usedefault=True, + ), inBackground=dict(argstr='--inBackground %f', ), inCoarse=dict(argstr='--inCoarse %f', ), inCost=dict(argstr='--inCost %s', ), @@ -22,7 +25,10 @@ def test_MedicAlgorithmSPECTRE2010_inputs(): inInhomogeneity=dict(argstr='--inInhomogeneity %s', ), inInitial=dict(argstr='--inInitial %d', ), inInitial2=dict(argstr='--inInitial2 %f', ), - inInput=dict(argstr='--inInput %s', ), + inInput=dict( + argstr='--inInput %s', + usedefault=True, + ), inMMC=dict(argstr='--inMMC %d', ), inMMC2=dict(argstr='--inMMC2 %d', ), inMaximum=dict(argstr='--inMaximum %f', ), @@ -95,15 +101,15 @@ def test_MedicAlgorithmSPECTRE2010_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmSPECTRE2010_outputs(): output_map = dict( - outFANTASM=dict(), - outMask=dict(), - outMidsagittal=dict(), - outOriginal=dict(), - outPrior=dict(), - outSegmentation=dict(), - outSplitHalves=dict(), - outStripped=dict(), - outd0=dict(), + outFANTASM=dict(usedefault=True, ), + outMask=dict(usedefault=True, ), + outMidsagittal=dict(usedefault=True, ), + outOriginal=dict(usedefault=True, ), + outPrior=dict(usedefault=True, ), + outSegmentation=dict(usedefault=True, ), + outSplitHalves=dict(usedefault=True, ), + outStripped=dict(usedefault=True, ), + outd0=dict(usedefault=True, ), ) outputs = MedicAlgorithmSPECTRE2010.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py index d3d92142c4..6817d55b5b 100644 --- a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py +++ b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py @@ -37,7 +37,7 @@ def test_RandomVol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RandomVol_outputs(): - output_map = dict(outRand1=dict(), ) + output_map = dict(outRand1=dict(usedefault=True, ), ) outputs = RandomVol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py index 4ced8de75a..d4e4e02b40 100644 --- a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py +++ b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py @@ -35,7 +35,10 @@ def test_WatershedBEM_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_WatershedBEM_outputs(): output_map = dict( - brain_surface=dict(loc='bem/watershed', ), + brain_surface=dict( + loc='bem/watershed', + usedefault=True, + ), cor_files=dict( altkey='COR', loc='bem/watershed/ws', @@ -43,11 +46,21 @@ def test_WatershedBEM_outputs(): fif_file=dict( altkey='fif', loc='bem', + usedefault=True, + ), + inner_skull_surface=dict( + loc='bem/watershed', + usedefault=True, ), - inner_skull_surface=dict(loc='bem/watershed', ), mesh_files=dict(), - outer_skin_surface=dict(loc='bem/watershed', ), - outer_skull_surface=dict(loc='bem/watershed', ), + outer_skin_surface=dict( + loc='bem/watershed', + usedefault=True, + ), + outer_skull_surface=dict( + loc='bem/watershed', + usedefault=True, + ), ) outputs = WatershedBEM.output_spec() diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py index 78a275f6a7..fe71be10c2 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py @@ -10,10 +10,12 @@ def test_ConstrainedSphericalDeconvolution_inputs(): directions_file=dict( argstr='-directions %s', position=-2, + usedefault=True, ), encoding_file=dict( argstr='-grad %s', position=1, + usedefault=True, ), environ=dict( nohash=True, @@ -22,17 +24,20 @@ def test_ConstrainedSphericalDeconvolution_inputs(): filter_file=dict( argstr='-filter %s', position=-2, + usedefault=True, ), in_file=dict( argstr='%s', mandatory=True, position=-3, + usedefault=True, ), iterations=dict(argstr='-niter %s', ), lambda_value=dict(argstr='-lambda %s', ), mask_image=dict( argstr='-mask %s', position=2, + usedefault=True, ), maximum_harmonic_order=dict(argstr='-lmax %s', ), normalise=dict( @@ -43,11 +48,13 @@ def test_ConstrainedSphericalDeconvolution_inputs(): argstr='%s', genfile=True, position=-1, + usedefault=True, ), response_file=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), threshold_value=dict(argstr='-threshold %s', ), ) @@ -57,7 +64,7 @@ def test_ConstrainedSphericalDeconvolution_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConstrainedSphericalDeconvolution_outputs(): - output_map = dict(spherical_harmonics_image=dict(), ) + output_map = dict(spherical_harmonics_image=dict(usedefault=True, ), ) outputs = ConstrainedSphericalDeconvolution.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py index dc95cff525..7d78b93639 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py @@ -10,6 +10,7 @@ def test_DWI2SphericalHarmonicsImage_inputs(): argstr='-grad %s', mandatory=True, position=1, + usedefault=True, ), environ=dict( nohash=True, @@ -19,6 +20,7 @@ def test_DWI2SphericalHarmonicsImage_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), maximum_harmonic_order=dict(argstr='-lmax %s', ), normalise=dict( @@ -29,6 +31,7 @@ def test_DWI2SphericalHarmonicsImage_inputs(): argstr='%s', genfile=True, position=-1, + usedefault=True, ), ) inputs = DWI2SphericalHarmonicsImage.input_spec() @@ -37,7 +40,7 @@ def test_DWI2SphericalHarmonicsImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWI2SphericalHarmonicsImage_outputs(): - output_map = dict(spherical_harmonics_image=dict(), ) + output_map = dict(spherical_harmonics_image=dict(usedefault=True, ), ) outputs = DWI2SphericalHarmonicsImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py index 86975950bf..2ede931519 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py @@ -13,6 +13,7 @@ def test_DWI2Tensor_inputs(): encoding_file=dict( argstr='-grad %s', position=2, + usedefault=True, ), environ=dict( nohash=True, @@ -39,6 +40,7 @@ def test_DWI2Tensor_inputs(): name_template='%s_tensor.mif', output_name='tensor', position=-1, + usedefault=True, ), quiet=dict( argstr='-quiet', @@ -51,7 +53,7 @@ def test_DWI2Tensor_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWI2Tensor_outputs(): - output_map = dict(tensor=dict(), ) + output_map = dict(tensor=dict(usedefault=True, ), ) outputs = DWI2Tensor.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py index 2c6417fe3a..25cbdbb7ba 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py @@ -18,6 +18,7 @@ def test_DiffusionTensorStreamlineTrack_inputs(): ), exclude_file=dict( argstr='-exclude %s', + usedefault=True, xor=['exclude_file', 'exclude_spec'], ), exclude_spec=dict( @@ -31,14 +32,17 @@ def test_DiffusionTensorStreamlineTrack_inputs(): argstr='-grad %s', mandatory=True, position=-2, + usedefault=True, ), in_file=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), include_file=dict( argstr='-include %s', + usedefault=True, xor=['include_file', 'include_spec'], ), include_spec=dict( @@ -63,6 +67,7 @@ def test_DiffusionTensorStreamlineTrack_inputs(): ), mask_file=dict( argstr='-mask %s', + usedefault=True, xor=['mask_file', 'mask_spec'], ), mask_spec=dict( @@ -92,9 +97,11 @@ def test_DiffusionTensorStreamlineTrack_inputs(): name_template='%s_tracked.tck', output_name='tracked', position=-1, + usedefault=True, ), seed_file=dict( argstr='-seed %s', + usedefault=True, xor=['seed_file', 'seed_spec'], ), seed_spec=dict( @@ -117,7 +124,7 @@ def test_DiffusionTensorStreamlineTrack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DiffusionTensorStreamlineTrack_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(usedefault=True, ), ) outputs = DiffusionTensorStreamlineTrack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py index b5474bd18c..fdfd71f3a9 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py @@ -16,6 +16,7 @@ def test_Directions2Amplitude_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), num_peaks=dict(argstr='-num %s', ), out_file=dict( @@ -25,12 +26,16 @@ def test_Directions2Amplitude_inputs(): name_source=['in_file'], name_template='%s_amplitudes.mif', position=-1, + usedefault=True, ), peak_directions=dict( argstr='-direction %s', sep=' ', ), - peaks_image=dict(argstr='-peaks %s', ), + peaks_image=dict( + argstr='-peaks %s', + usedefault=True, + ), quiet_display=dict(argstr='-quiet', ), ) inputs = Directions2Amplitude.input_spec() @@ -39,7 +44,7 @@ def test_Directions2Amplitude_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Directions2Amplitude_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Directions2Amplitude.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py index 6215593ab0..a38693054f 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py @@ -22,12 +22,14 @@ def test_Erode_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), number_of_passes=dict(argstr='-npass %s', ), out_filename=dict( argstr='%s', genfile=True, position=-1, + usedefault=True, ), quiet=dict( argstr='-quiet', @@ -40,7 +42,7 @@ def test_Erode_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Erode_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Erode.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py index 983433104e..a3844813bd 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py @@ -11,6 +11,7 @@ def test_EstimateResponseForSH_inputs(): argstr='-grad %s', mandatory=True, position=1, + usedefault=True, ), environ=dict( nohash=True, @@ -20,11 +21,13 @@ def test_EstimateResponseForSH_inputs(): argstr='%s', mandatory=True, position=-3, + usedefault=True, ), mask_image=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), maximum_harmonic_order=dict(argstr='-lmax %s', ), normalise=dict(argstr='-normalise', ), @@ -32,6 +35,7 @@ def test_EstimateResponseForSH_inputs(): argstr='%s', genfile=True, position=-1, + usedefault=True, ), quiet=dict(argstr='-quiet', ), ) @@ -41,7 +45,7 @@ def test_EstimateResponseForSH_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EstimateResponseForSH_outputs(): - output_map = dict(response=dict(), ) + output_map = dict(response=dict(usedefault=True, ), ) outputs = EstimateResponseForSH.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py b/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py index 6261b6b0a5..c07d531de9 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py @@ -5,12 +5,21 @@ def test_FSL2MRTrix_inputs(): input_map = dict( - bval_file=dict(mandatory=True, ), - bvec_file=dict(mandatory=True, ), + bval_file=dict( + mandatory=True, + usedefault=True, + ), + bvec_file=dict( + mandatory=True, + usedefault=True, + ), invert_x=dict(usedefault=True, ), invert_y=dict(usedefault=True, ), invert_z=dict(usedefault=True, ), - out_encoding_file=dict(genfile=True, ), + out_encoding_file=dict( + genfile=True, + usedefault=True, + ), ) inputs = FSL2MRTrix.input_spec() @@ -18,7 +27,7 @@ def test_FSL2MRTrix_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FSL2MRTrix_outputs(): - output_map = dict(encoding_file=dict(), ) + output_map = dict(encoding_file=dict(usedefault=True, ), ) outputs = FSL2MRTrix.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py index 6e0e670d06..92b302e199 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py @@ -16,6 +16,7 @@ def test_FilterTracks_inputs(): ), exclude_file=dict( argstr='-exclude %s', + usedefault=True, xor=['exclude_file', 'exclude_spec'], ), exclude_spec=dict( @@ -29,9 +30,11 @@ def test_FilterTracks_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), include_file=dict( argstr='-include %s', + usedefault=True, xor=['include_file', 'include_spec'], ), include_spec=dict( @@ -53,6 +56,7 @@ def test_FilterTracks_inputs(): name_source=['in_file'], name_template='%s_filt', position=-1, + usedefault=True, ), quiet=dict( argstr='-quiet', @@ -65,7 +69,7 @@ def test_FilterTracks_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FilterTracks_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = FilterTracks.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py index 5d9f51739c..dabc3cc1eb 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py @@ -10,6 +10,7 @@ def test_FindShPeaks_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), display_debug=dict(argstr='-debug', ), display_info=dict(argstr='-info', ), @@ -21,6 +22,7 @@ def test_FindShPeaks_inputs(): argstr='%s', mandatory=True, position=-3, + usedefault=True, ), num_peaks=dict(argstr='-num %s', ), out_file=dict( @@ -30,13 +32,17 @@ def test_FindShPeaks_inputs(): name_source=['in_file'], name_template='%s_peak_dirs.mif', position=-1, + usedefault=True, ), peak_directions=dict( argstr='-direction %s', sep=' ', ), peak_threshold=dict(argstr='-threshold %s', ), - peaks_image=dict(argstr='-peaks %s', ), + peaks_image=dict( + argstr='-peaks %s', + usedefault=True, + ), quiet_display=dict(argstr='-quiet', ), ) inputs = FindShPeaks.input_spec() @@ -45,7 +51,7 @@ def test_FindShPeaks_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FindShPeaks_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = FindShPeaks.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py index 2cfd89bb6f..10eafc7472 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py @@ -24,6 +24,7 @@ def test_GenerateDirections_inputs(): name_source=['num_dirs'], name_template='directions_%d.txt', position=-1, + usedefault=True, ), power=dict(argstr='-power %s', ), quiet_display=dict(argstr='-quiet', ), @@ -34,7 +35,7 @@ def test_GenerateDirections_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateDirections_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = GenerateDirections.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py index 6a0305f9e2..edbc3fe8d3 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py @@ -10,11 +10,13 @@ def test_GenerateWhiteMatterMask_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), encoding_file=dict( argstr='-grad %s', mandatory=True, position=1, + usedefault=True, ), environ=dict( nohash=True, @@ -24,12 +26,14 @@ def test_GenerateWhiteMatterMask_inputs(): argstr='%s', mandatory=True, position=-3, + usedefault=True, ), noise_level_margin=dict(argstr='-margin %s', ), out_WMProb_filename=dict( argstr='%s', genfile=True, position=-1, + usedefault=True, ), ) inputs = GenerateWhiteMatterMask.input_spec() @@ -38,7 +42,7 @@ def test_GenerateWhiteMatterMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateWhiteMatterMask_outputs(): - output_map = dict(WMprobabilitymap=dict(), ) + output_map = dict(WMprobabilitymap=dict(usedefault=True, ), ) outputs = GenerateWhiteMatterMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py index 5aef0bfd13..582cba026d 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py @@ -27,6 +27,7 @@ def test_MRConvert_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), layout=dict( argstr='-output %s', @@ -41,6 +42,7 @@ def test_MRConvert_inputs(): argstr='%s', genfile=True, position=-1, + usedefault=True, ), output_datatype=dict( argstr='-output %s', @@ -71,7 +73,7 @@ def test_MRConvert_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRConvert_outputs(): - output_map = dict(converted=dict(), ) + output_map = dict(converted=dict(usedefault=True, ), ) outputs = MRConvert.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py index a5a864289a..00ec1e3069 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py @@ -23,6 +23,7 @@ def test_MRMultiply_inputs(): argstr='%s', genfile=True, position=-1, + usedefault=True, ), quiet=dict( argstr='-quiet', @@ -35,7 +36,7 @@ def test_MRMultiply_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRMultiply_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MRMultiply.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py index d6a3db0a1d..1ea25aed2d 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py @@ -31,6 +31,7 @@ def test_MRTransform_inputs(): argstr='%s', genfile=True, position=-1, + usedefault=True, ), quiet=dict( argstr='-quiet', @@ -39,6 +40,7 @@ def test_MRTransform_inputs(): reference_image=dict( argstr='-reference %s', position=1, + usedefault=True, ), replace_transform=dict( argstr='-replace', @@ -47,10 +49,12 @@ def test_MRTransform_inputs(): template_image=dict( argstr='-template %s', position=1, + usedefault=True, ), transformation_file=dict( argstr='-transform %s', position=1, + usedefault=True, ), ) inputs = MRTransform.input_spec() @@ -59,7 +63,7 @@ def test_MRTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRTransform_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MRTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py index b6fefac9a0..e7a560a357 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py @@ -5,14 +5,17 @@ def test_MRTrix2TrackVis_inputs(): input_map = dict( - image_file=dict(), - in_file=dict(mandatory=True, ), - matrix_file=dict(), + image_file=dict(usedefault=True, ), + in_file=dict( + mandatory=True, + usedefault=True, + ), + matrix_file=dict(usedefault=True, ), out_filename=dict( genfile=True, usedefault=True, ), - registration_image_file=dict(), + registration_image_file=dict(usedefault=True, ), ) inputs = MRTrix2TrackVis.input_spec() @@ -20,7 +23,7 @@ def test_MRTrix2TrackVis_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRTrix2TrackVis_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MRTrix2TrackVis.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py index 0022de4d7a..6cd2054d6c 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py @@ -14,6 +14,7 @@ def test_MRTrixInfo_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), ) inputs = MRTrixInfo.input_spec() diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py index 0e7daabcaa..83910cecc2 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py @@ -18,11 +18,13 @@ def test_MedianFilter3D_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), out_filename=dict( argstr='%s', genfile=True, position=-1, + usedefault=True, ), quiet=dict( argstr='-quiet', @@ -35,7 +37,7 @@ def test_MedianFilter3D_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MedianFilter3D_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MedianFilter3D.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py index 6d75b1b9a2..72dbf54a9e 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py @@ -18,6 +18,7 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): ), exclude_file=dict( argstr='-exclude %s', + usedefault=True, xor=['exclude_file', 'exclude_spec'], ), exclude_spec=dict( @@ -31,9 +32,11 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), include_file=dict( argstr='-include %s', + usedefault=True, xor=['include_file', 'include_spec'], ), include_spec=dict( @@ -58,6 +61,7 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): ), mask_file=dict( argstr='-mask %s', + usedefault=True, xor=['mask_file', 'mask_spec'], ), mask_spec=dict( @@ -88,9 +92,11 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): name_template='%s_tracked.tck', output_name='tracked', position=-1, + usedefault=True, ), seed_file=dict( argstr='-seed %s', + usedefault=True, xor=['seed_file', 'seed_spec'], ), seed_spec=dict( @@ -113,7 +119,7 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(usedefault=True, ), ) outputs = ProbabilisticSphericallyDeconvolutedStreamlineTrack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py index 9bed95276d..d207afa2af 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py @@ -18,6 +18,7 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): ), exclude_file=dict( argstr='-exclude %s', + usedefault=True, xor=['exclude_file', 'exclude_spec'], ), exclude_spec=dict( @@ -31,9 +32,11 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), include_file=dict( argstr='-include %s', + usedefault=True, xor=['include_file', 'include_spec'], ), include_spec=dict( @@ -58,6 +61,7 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): ), mask_file=dict( argstr='-mask %s', + usedefault=True, xor=['mask_file', 'mask_spec'], ), mask_spec=dict( @@ -87,9 +91,11 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): name_template='%s_tracked.tck', output_name='tracked', position=-1, + usedefault=True, ), seed_file=dict( argstr='-seed %s', + usedefault=True, xor=['seed_file', 'seed_spec'], ), seed_spec=dict( @@ -112,7 +118,7 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SphericallyDeconvolutedStreamlineTrack_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(usedefault=True, ), ) outputs = SphericallyDeconvolutedStreamlineTrack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py index c898a60eb3..824ff883e8 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py @@ -18,6 +18,7 @@ def test_StreamlineTrack_inputs(): ), exclude_file=dict( argstr='-exclude %s', + usedefault=True, xor=['exclude_file', 'exclude_spec'], ), exclude_spec=dict( @@ -31,9 +32,11 @@ def test_StreamlineTrack_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), include_file=dict( argstr='-include %s', + usedefault=True, xor=['include_file', 'include_spec'], ), include_spec=dict( @@ -58,6 +61,7 @@ def test_StreamlineTrack_inputs(): ), mask_file=dict( argstr='-mask %s', + usedefault=True, xor=['mask_file', 'mask_spec'], ), mask_spec=dict( @@ -87,9 +91,11 @@ def test_StreamlineTrack_inputs(): name_template='%s_tracked.tck', output_name='tracked', position=-1, + usedefault=True, ), seed_file=dict( argstr='-seed %s', + usedefault=True, xor=['seed_file', 'seed_spec'], ), seed_spec=dict( @@ -112,7 +118,7 @@ def test_StreamlineTrack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_StreamlineTrack_outputs(): - output_map = dict(tracked=dict(), ) + output_map = dict(tracked=dict(usedefault=True, ), ) outputs = StreamlineTrack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py index e9546d7e90..67560fff57 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py @@ -18,11 +18,13 @@ def test_Tensor2ApparentDiffusion_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), out_filename=dict( argstr='%s', genfile=True, position=-1, + usedefault=True, ), quiet=dict( argstr='-quiet', @@ -35,7 +37,7 @@ def test_Tensor2ApparentDiffusion_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Tensor2ApparentDiffusion_outputs(): - output_map = dict(ADC=dict(), ) + output_map = dict(ADC=dict(usedefault=True, ), ) outputs = Tensor2ApparentDiffusion.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py index d16a907f62..ea2d63a4f8 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py @@ -18,11 +18,13 @@ def test_Tensor2FractionalAnisotropy_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), out_filename=dict( argstr='%s', genfile=True, position=-1, + usedefault=True, ), quiet=dict( argstr='-quiet', @@ -35,7 +37,7 @@ def test_Tensor2FractionalAnisotropy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Tensor2FractionalAnisotropy_outputs(): - output_map = dict(FA=dict(), ) + output_map = dict(FA=dict(usedefault=True, ), ) outputs = Tensor2FractionalAnisotropy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py index c07d0a8db4..91fba8183b 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py @@ -18,11 +18,13 @@ def test_Tensor2Vector_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), out_filename=dict( argstr='%s', genfile=True, position=-1, + usedefault=True, ), quiet=dict( argstr='-quiet', @@ -35,7 +37,7 @@ def test_Tensor2Vector_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Tensor2Vector_outputs(): - output_map = dict(vector=dict(), ) + output_map = dict(vector=dict(usedefault=True, ), ) outputs = Tensor2Vector.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py index 39fbf14d2c..84f42965fc 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py @@ -19,6 +19,7 @@ def test_Threshold_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), invert=dict( argstr='-invert', @@ -28,6 +29,7 @@ def test_Threshold_inputs(): argstr='%s', genfile=True, position=-1, + usedefault=True, ), percentage_threshold_value=dict(argstr='-percent %s', ), quiet=dict( @@ -45,7 +47,7 @@ def test_Threshold_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Threshold_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Threshold.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py index f984203ab1..b4c930d0f9 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py @@ -22,11 +22,13 @@ def test_Tracks2Prob_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), out_filename=dict( argstr='%s', genfile=True, position=-1, + usedefault=True, ), output_datatype=dict( argstr='-datatype %s', @@ -40,6 +42,7 @@ def test_Tracks2Prob_inputs(): template_file=dict( argstr='-template %s', position=1, + usedefault=True, ), voxel_dims=dict( argstr='-vox %s', @@ -53,7 +56,7 @@ def test_Tracks2Prob_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Tracks2Prob_outputs(): - output_map = dict(tract_image=dict(), ) + output_map = dict(tract_image=dict(usedefault=True, ), ) outputs = Tracks2Prob.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py index abb3ba6831..055490f1da 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py @@ -14,6 +14,7 @@ def test_ACTPrepareFSL_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), out_file=dict( argstr='%s', @@ -28,7 +29,7 @@ def test_ACTPrepareFSL_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ACTPrepareFSL_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ACTPrepareFSL.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py index c318be0bfd..bcdb6be17d 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py @@ -11,14 +11,21 @@ def test_BrainMask_inputs(): nohash=True, usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + usedefault=True, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(usedefault=True, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + usedefault=True, + ), in_file=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), nthreads=dict( argstr='-nthreads %d', @@ -37,7 +44,7 @@ def test_BrainMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BrainMask_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = BrainMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py index 95e5797d06..dd5cee6eda 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py @@ -14,13 +14,21 @@ def test_BuildConnectome_inputs(): argstr='%s', mandatory=True, position=-3, + usedefault=True, ), in_parc=dict( argstr='%s', position=-2, + usedefault=True, + ), + in_scalar=dict( + argstr='-image %s', + usedefault=True, + ), + in_weights=dict( + argstr='-tck_weights_in %s', + usedefault=True, ), - in_scalar=dict(argstr='-image %s', ), - in_weights=dict(argstr='-tck_weights_in %s', ), keep_unassigned=dict(argstr='-keep_unassigned', ), metric=dict(argstr='-metric %s', ), nthreads=dict( @@ -45,7 +53,7 @@ def test_BuildConnectome_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BuildConnectome_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = BuildConnectome.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py index 38369e8fe5..61c86e489c 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py @@ -8,7 +8,10 @@ def test_ComputeTDI_inputs(): args=dict(argstr='%s', ), contrast=dict(argstr='-constrast %s', ), data_type=dict(argstr='-datatype %s', ), - dixel=dict(argstr='-dixel %s', ), + dixel=dict( + argstr='-dixel %s', + usedefault=True, + ), ends_only=dict(argstr='-ends_only', ), environ=dict( nohash=True, @@ -19,8 +22,12 @@ def test_ComputeTDI_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, + ), + in_map=dict( + argstr='-image %s', + usedefault=True, ), - in_map=dict(argstr='-image %s', ), map_zero=dict(argstr='-map_zero', ), max_tod=dict(argstr='-tod %d', ), nthreads=dict( @@ -33,10 +40,16 @@ def test_ComputeTDI_inputs(): usedefault=True, ), precise=dict(argstr='-precise', ), - reference=dict(argstr='-template %s', ), + reference=dict( + argstr='-template %s', + usedefault=True, + ), stat_tck=dict(argstr='-stat_tck %s', ), stat_vox=dict(argstr='-stat_vox %s', ), - tck_weights=dict(argstr='-tck_weights_in %s', ), + tck_weights=dict( + argstr='-tck_weights_in %s', + usedefault=True, + ), upsample=dict(argstr='-upsample %d', ), use_dec=dict(argstr='-dec', ), vox_size=dict( @@ -50,7 +63,7 @@ def test_ComputeTDI_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeTDI_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ComputeTDI.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py b/nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py index ea4d3f05d8..e5c25b3bd8 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py @@ -6,7 +6,10 @@ def test_DWIBiasCorrect_inputs(): input_map = dict( args=dict(argstr='%s', ), - bias=dict(argstr='-bias %s', ), + bias=dict( + argstr='-bias %s', + usedefault=True, + ), bval_scale=dict(argstr='-bvalue_scaling %s', ), environ=dict( nohash=True, @@ -14,20 +17,32 @@ def test_DWIBiasCorrect_inputs(): ), fsl_grad=dict( argstr='-fslgrad %s %s', + usedefault=True, xor=('mrtrix_grad', 'fsl_grad'), ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + usedefault=True, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(usedefault=True, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + usedefault=True, + ), in_file=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, + ), + in_mask=dict( + argstr='-mask %s', + usedefault=True, ), - in_mask=dict(argstr='-mask %s', ), mrtrix_grad=dict( argstr='-grad %s', + usedefault=True, xor=('mrtrix_grad', 'fsl_grad'), ), nthreads=dict( @@ -41,6 +56,7 @@ def test_DWIBiasCorrect_inputs(): name_source='in_file', name_template='%s_biascorr', position=-1, + usedefault=True, ), use_ants=dict( argstr='-ants', @@ -60,8 +76,8 @@ def test_DWIBiasCorrect_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DWIBiasCorrect_outputs(): output_map = dict( - bias=dict(), - out_file=dict(), + bias=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), ) outputs = DWIBiasCorrect.output_spec() diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py b/nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py index 7b6930ee82..8c5f88b12e 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py @@ -12,20 +12,31 @@ def test_DWIDenoise_inputs(): usedefault=True, ), extent=dict(argstr='-extent %d,%d,%d', ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + usedefault=True, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(usedefault=True, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + usedefault=True, + ), in_file=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), mask=dict( argstr='-mask %s', position=1, + usedefault=True, + ), + noise=dict( + argstr='-noise %s', + usedefault=True, ), - noise=dict(argstr='-noise %s', ), nthreads=dict( argstr='-nthreads %d', nohash=True, @@ -37,6 +48,7 @@ def test_DWIDenoise_inputs(): name_source='in_file', name_template='%s_denoised', position=-1, + usedefault=True, ), ) inputs = DWIDenoise.input_spec() @@ -46,8 +58,8 @@ def test_DWIDenoise_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DWIDenoise_outputs(): output_map = dict( - noise=dict(), - out_file=dict(), + noise=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), ) outputs = DWIDenoise.output_spec() diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py b/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py index 0114c5efe0..ef17cc7fe7 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py @@ -12,14 +12,21 @@ def test_DWIExtract_inputs(): nohash=True, usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + usedefault=True, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(usedefault=True, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + usedefault=True, + ), in_file=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), nobzero=dict(argstr='-no_bzero', ), nthreads=dict( @@ -30,6 +37,7 @@ def test_DWIExtract_inputs(): argstr='%s', mandatory=True, position=-1, + usedefault=True, ), shell=dict( argstr='-shell %s', @@ -43,7 +51,7 @@ def test_DWIExtract_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWIExtract_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = DWIExtract.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py index a5c152e928..3d18672b6b 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py @@ -20,6 +20,7 @@ def test_EstimateFOD_inputs(): csf_txt=dict( argstr='%s', position=-2, + usedefault=True, ), environ=dict( nohash=True, @@ -33,18 +34,32 @@ def test_EstimateFOD_inputs(): gm_txt=dict( argstr='%s', position=-4, + usedefault=True, + ), + grad_file=dict( + argstr='-grad %s', + usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), - in_dirs=dict(argstr='-directions %s', ), + in_bval=dict(usedefault=True, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + usedefault=True, + ), + in_dirs=dict( + argstr='-directions %s', + usedefault=True, + ), in_file=dict( argstr='%s', mandatory=True, position=-7, + usedefault=True, + ), + mask_file=dict( + argstr='-mask %s', + usedefault=True, ), - mask_file=dict(argstr='-mask %s', ), max_sh=dict( argstr='-lmax %d', usedefault=True, @@ -67,6 +82,7 @@ def test_EstimateFOD_inputs(): argstr='%s', mandatory=True, position=-6, + usedefault=True, ), ) inputs = EstimateFOD.input_spec() @@ -76,9 +92,18 @@ def test_EstimateFOD_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EstimateFOD_outputs(): output_map = dict( - csf_odf=dict(argstr='%s', ), - gm_odf=dict(argstr='%s', ), - wm_odf=dict(argstr='%s', ), + csf_odf=dict( + argstr='%s', + usedefault=True, + ), + gm_odf=dict( + argstr='%s', + usedefault=True, + ), + wm_odf=dict( + argstr='%s', + usedefault=True, + ), ) outputs = EstimateFOD.output_spec() diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py index 85c103cc10..dabea06823 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py @@ -11,16 +11,26 @@ def test_FitTensor_inputs(): nohash=True, usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + usedefault=True, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(usedefault=True, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + usedefault=True, + ), in_file=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, + ), + in_mask=dict( + argstr='-mask %s', + usedefault=True, ), - in_mask=dict(argstr='-mask %s', ), method=dict(argstr='-method %s', ), nthreads=dict( argstr='-nthreads %d', @@ -43,7 +53,7 @@ def test_FitTensor_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FitTensor_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = FitTensor.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py index dcfbe1fc6f..55ef543167 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py @@ -16,14 +16,21 @@ def test_Generate5tt_inputs(): nohash=True, usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + usedefault=True, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(usedefault=True, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + usedefault=True, + ), in_file=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), nthreads=dict( argstr='-nthreads %d', @@ -33,6 +40,7 @@ def test_Generate5tt_inputs(): argstr='%s', mandatory=True, position=-1, + usedefault=True, ), ) inputs = Generate5tt.input_spec() @@ -41,7 +49,7 @@ def test_Generate5tt_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Generate5tt_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Generate5tt.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py index 2de0e6c115..d137914b87 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py @@ -13,16 +13,30 @@ def test_LabelConfig_inputs(): in_config=dict( argstr='%s', position=-2, + usedefault=True, ), in_file=dict( argstr='%s', mandatory=True, position=-3, + usedefault=True, + ), + lut_aal=dict( + argstr='-lut_aal %s', + usedefault=True, + ), + lut_basic=dict( + argstr='-lut_basic %s', + usedefault=True, + ), + lut_fs=dict( + argstr='-lut_freesurfer %s', + usedefault=True, + ), + lut_itksnap=dict( + argstr='-lut_itksnap %s', + usedefault=True, ), - lut_aal=dict(argstr='-lut_aal %s', ), - lut_basic=dict(argstr='-lut_basic %s', ), - lut_fs=dict(argstr='-lut_freesurfer %s', ), - lut_itksnap=dict(argstr='-lut_itksnap %s', ), nthreads=dict( argstr='-nthreads %d', nohash=True, @@ -33,7 +47,10 @@ def test_LabelConfig_inputs(): position=-1, usedefault=True, ), - spine=dict(argstr='-spine %s', ), + spine=dict( + argstr='-spine %s', + usedefault=True, + ), ) inputs = LabelConfig.input_spec() @@ -41,7 +58,7 @@ def test_LabelConfig_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LabelConfig_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = LabelConfig.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConvert.py b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConvert.py index 1e93ae82d8..d9c3138625 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConvert.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConvert.py @@ -13,16 +13,19 @@ def test_LabelConvert_inputs(): in_config=dict( argstr='%s', position=-2, + usedefault=True, ), in_file=dict( argstr='%s', mandatory=True, position=-4, + usedefault=True, ), in_lut=dict( argstr='%s', mandatory=True, position=-3, + usedefault=True, ), num_threads=dict( argstr='-nthreads %d', @@ -34,7 +37,10 @@ def test_LabelConvert_inputs(): position=-1, usedefault=True, ), - spine=dict(argstr='-spine %s', ), + spine=dict( + argstr='-spine %s', + usedefault=True, + ), ) inputs = LabelConvert.input_spec() @@ -42,7 +48,7 @@ def test_LabelConvert_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LabelConvert_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = LabelConvert.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py index ece24e1d47..acd1609dbc 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py @@ -19,14 +19,21 @@ def test_MRConvert_inputs(): nohash=True, usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + usedefault=True, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(usedefault=True, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + usedefault=True, + ), in_file=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), nthreads=dict( argstr='-nthreads %d', @@ -53,7 +60,7 @@ def test_MRConvert_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRConvert_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MRConvert.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py index c9290b562b..10b5edf453 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py @@ -18,14 +18,21 @@ def test_MRDeGibbs_inputs(): nohash=True, usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + usedefault=True, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(usedefault=True, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + usedefault=True, + ), in_file=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), maxW=dict( argstr='-maxW %d', @@ -50,6 +57,7 @@ def test_MRDeGibbs_inputs(): name_source='in_file', name_template='%s_unr', position=-1, + usedefault=True, ), ) inputs = MRDeGibbs.input_spec() @@ -58,7 +66,7 @@ def test_MRDeGibbs_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRDeGibbs_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MRDeGibbs.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py index eec06b6276..5e86fc316b 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py @@ -12,14 +12,21 @@ def test_MRMath_inputs(): nohash=True, usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + usedefault=True, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(usedefault=True, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + usedefault=True, + ), in_file=dict( argstr='%s', mandatory=True, position=-3, + usedefault=True, ), nthreads=dict( argstr='-nthreads %d', @@ -34,6 +41,7 @@ def test_MRMath_inputs(): argstr='%s', mandatory=True, position=-1, + usedefault=True, ), ) inputs = MRMath.input_spec() @@ -42,7 +50,7 @@ def test_MRMath_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRMath_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MRMath.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py index 9aa29acbe8..4ab14ad7a8 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py @@ -14,8 +14,12 @@ def test_Mesh2PVE_inputs(): argstr='%s', mandatory=True, position=-3, + usedefault=True, + ), + in_first=dict( + argstr='-first %s', + usedefault=True, ), - in_first=dict(argstr='-first %s', ), out_file=dict( argstr='%s', mandatory=True, @@ -26,6 +30,7 @@ def test_Mesh2PVE_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), ) inputs = Mesh2PVE.input_spec() @@ -34,7 +39,7 @@ def test_Mesh2PVE_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Mesh2PVE_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Mesh2PVE.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py index 502a0f7fb1..5753ebcf27 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py @@ -13,16 +13,19 @@ def test_ReplaceFSwithFIRST_inputs(): in_config=dict( argstr='%s', position=-2, + usedefault=True, ), in_file=dict( argstr='%s', mandatory=True, position=-4, + usedefault=True, ), in_t1w=dict( argstr='%s', mandatory=True, position=-3, + usedefault=True, ), out_file=dict( argstr='%s', @@ -37,7 +40,7 @@ def test_ReplaceFSwithFIRST_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ReplaceFSwithFIRST_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ReplaceFSwithFIRST.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py index f4b4660d78..55edbd4280 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py @@ -15,6 +15,7 @@ def test_ResponseSD_inputs(): csf_file=dict( argstr='%s', position=-1, + usedefault=True, ), environ=dict( nohash=True, @@ -23,17 +24,28 @@ def test_ResponseSD_inputs(): gm_file=dict( argstr='%s', position=-2, + usedefault=True, + ), + grad_file=dict( + argstr='-grad %s', + usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(usedefault=True, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + usedefault=True, + ), in_file=dict( argstr='%s', mandatory=True, position=-5, + usedefault=True, + ), + in_mask=dict( + argstr='-mask %s', + usedefault=True, ), - in_mask=dict(argstr='-mask %s', ), max_sh=dict( argstr='-lmax %s', sep=',', @@ -41,6 +53,7 @@ def test_ResponseSD_inputs(): mtt_file=dict( argstr='%s', position=-4, + usedefault=True, ), nthreads=dict( argstr='-nthreads %d', @@ -59,9 +72,18 @@ def test_ResponseSD_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ResponseSD_outputs(): output_map = dict( - csf_file=dict(argstr='%s', ), - gm_file=dict(argstr='%s', ), - wm_file=dict(argstr='%s', ), + csf_file=dict( + argstr='%s', + usedefault=True, + ), + gm_file=dict( + argstr='%s', + usedefault=True, + ), + wm_file=dict( + argstr='%s', + usedefault=True, + ), ) outputs = ResponseSD.output_spec() diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py index 93a39484f8..e637da109d 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py @@ -14,6 +14,7 @@ def test_TCK2VTK_inputs(): argstr='%s', mandatory=True, position=-2, + usedefault=True, ), nthreads=dict( argstr='-nthreads %d', @@ -24,8 +25,14 @@ def test_TCK2VTK_inputs(): position=-1, usedefault=True, ), - reference=dict(argstr='-image %s', ), - voxel=dict(argstr='-image %s', ), + reference=dict( + argstr='-image %s', + usedefault=True, + ), + voxel=dict( + argstr='-image %s', + usedefault=True, + ), ) inputs = TCK2VTK.input_spec() @@ -33,7 +40,7 @@ def test_TCK2VTK_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TCK2VTK_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TCK2VTK.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py index ae532c9910..7e67c2b11b 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py @@ -19,13 +19,29 @@ def test_TensorMetrics_inputs(): argstr='%s', mandatory=True, position=-1, + usedefault=True, + ), + in_mask=dict( + argstr='-mask %s', + usedefault=True, ), - in_mask=dict(argstr='-mask %s', ), modulate=dict(argstr='-modulate %s', ), - out_adc=dict(argstr='-adc %s', ), - out_eval=dict(argstr='-value %s', ), - out_evec=dict(argstr='-vector %s', ), - out_fa=dict(argstr='-fa %s', ), + out_adc=dict( + argstr='-adc %s', + usedefault=True, + ), + out_eval=dict( + argstr='-value %s', + usedefault=True, + ), + out_evec=dict( + argstr='-vector %s', + usedefault=True, + ), + out_fa=dict( + argstr='-fa %s', + usedefault=True, + ), ) inputs = TensorMetrics.input_spec() @@ -34,10 +50,10 @@ def test_TensorMetrics_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TensorMetrics_outputs(): output_map = dict( - out_adc=dict(), - out_eval=dict(), - out_evec=dict(), - out_fa=dict(), + out_adc=dict(usedefault=True, ), + out_eval=dict(usedefault=True, ), + out_evec=dict(usedefault=True, ), + out_fa=dict(usedefault=True, ), ) outputs = TensorMetrics.output_spec() diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py index c79fce8867..13f779d63d 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py @@ -5,7 +5,10 @@ def test_Tractography_inputs(): input_map = dict( - act_file=dict(argstr='-act %s', ), + act_file=dict( + argstr='-act %s', + usedefault=True, + ), algorithm=dict( argstr='-algorithm %s', usedefault=True, @@ -22,14 +25,21 @@ def test_Tractography_inputs(): nohash=True, usedefault=True, ), - grad_file=dict(argstr='-grad %s', ), + grad_file=dict( + argstr='-grad %s', + usedefault=True, + ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(), - in_bvec=dict(argstr='-fslgrad %s %s', ), + in_bval=dict(usedefault=True, ), + in_bvec=dict( + argstr='-fslgrad %s %s', + usedefault=True, + ), in_file=dict( argstr='%s', mandatory=True, position=-2, + usedefault=True, ), init_dir=dict(argstr='-initdirection %f,%f,%f', ), max_length=dict(argstr='-maxlength %f', ), @@ -64,17 +74,27 @@ def test_Tractography_inputs(): roi_excl=dict(argstr='-exclude %s', ), roi_incl=dict(argstr='-include %s', ), roi_mask=dict(argstr='-mask %s', ), - seed_dynamic=dict(argstr='-seed_dynamic %s', ), + seed_dynamic=dict( + argstr='-seed_dynamic %s', + usedefault=True, + ), seed_gmwmi=dict( argstr='-seed_gmwmi %s', requires=['act_file'], + usedefault=True, ), seed_grid_voxel=dict( argstr='-seed_grid_per_voxel %s %d', xor=['seed_image', 'seed_rnd_voxel'], ), - seed_image=dict(argstr='-seed_image %s', ), - seed_rejection=dict(argstr='-seed_rejection %s', ), + seed_image=dict( + argstr='-seed_image %s', + usedefault=True, + ), + seed_rejection=dict( + argstr='-seed_rejection %s', + usedefault=True, + ), seed_rnd_voxel=dict( argstr='-seed_random_per_voxel %s %d', xor=['seed_image', 'seed_grid_voxel'], @@ -97,8 +117,8 @@ def test_Tractography_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Tractography_outputs(): output_map = dict( - out_file=dict(), - out_seeds=dict(), + out_file=dict(usedefault=True, ), + out_seeds=dict(usedefault=True, ), ) outputs = Tractography.output_spec() diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py b/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py index 0505ee514c..bf5b08e3de 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py @@ -12,6 +12,7 @@ def test_FitQt1_inputs(): argstr='-comp %s', name_source=['source_file'], name_template='%s_comp.nii.gz', + usedefault=True, ), environ=dict( nohash=True, @@ -21,6 +22,7 @@ def test_FitQt1_inputs(): argstr='-error %s', name_source=['source_file'], name_template='%s_error.nii.gz', + usedefault=True, ), flips=dict( argstr='-flips %s', @@ -43,10 +45,12 @@ def test_FitQt1_inputs(): argstr='-m0map %s', name_source=['source_file'], name_template='%s_m0map.nii.gz', + usedefault=True, ), mask=dict( argstr='-mask %s', position=2, + usedefault=True, ), maxit=dict( argstr='-maxit %d', @@ -56,6 +60,7 @@ def test_FitQt1_inputs(): argstr='-mcmap %s', name_source=['source_file'], name_template='%s_mcmap.nii.gz', + usedefault=True, ), mcmaxit=dict(argstr='-mcmaxit %d', ), mcout=dict(argstr='-mcout %s', ), @@ -67,11 +72,13 @@ def test_FitQt1_inputs(): prior=dict( argstr='-prior %s', position=3, + usedefault=True, ), res_file=dict( argstr='-res %s', name_source=['source_file'], name_template='%s_res.nii.gz', + usedefault=True, ), slice_no=dict( argstr='-slice %d', @@ -81,6 +88,7 @@ def test_FitQt1_inputs(): argstr='-source %s', mandatory=True, position=1, + usedefault=True, ), spgr=dict(argstr='-SPGR', ), sr_flag=dict( @@ -91,12 +99,14 @@ def test_FitQt1_inputs(): argstr='-syn %s', name_source=['source_file'], name_template='%s_syn.nii.gz', + usedefault=True, ), t1_list=dict(argstr='-T1list %s', ), t1map_file=dict( argstr='-t1map %s', name_source=['source_file'], name_template='%s_t1map.nii.gz', + usedefault=True, ), t1max=dict(argstr='-T1max %f', ), t1min=dict(argstr='-T1min %f', ), @@ -126,13 +136,13 @@ def test_FitQt1_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FitQt1_outputs(): output_map = dict( - comp_file=dict(), - error_file=dict(), - m0map_file=dict(), - mcmap_file=dict(), - res_file=dict(), - syn_file=dict(), - t1map_file=dict(), + comp_file=dict(usedefault=True, ), + error_file=dict(usedefault=True, ), + m0map_file=dict(usedefault=True, ), + mcmap_file=dict(usedefault=True, ), + res_file=dict(usedefault=True, ), + syn_file=dict(usedefault=True, ), + t1map_file=dict(usedefault=True, ), ) outputs = FitQt1.output_spec() diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py b/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py index 9507f53fa9..e6554137f3 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py @@ -10,6 +10,7 @@ def test_RegAladin_inputs(): argstr='-aff %s', name_source=['flo_file'], name_template='%s_aff.txt', + usedefault=True, ), args=dict(argstr='%s', ), cog_flag=dict(argstr='-cog', ), @@ -20,13 +21,20 @@ def test_RegAladin_inputs(): flo_file=dict( argstr='-flo %s', mandatory=True, + usedefault=True, ), flo_low_val=dict(argstr='-floLowThr %f', ), flo_up_val=dict(argstr='-floUpThr %f', ), - fmask_file=dict(argstr='-fmask %s', ), + fmask_file=dict( + argstr='-fmask %s', + usedefault=True, + ), gpuid_val=dict(argstr='-gpuid %i', ), i_val=dict(argstr='-pi %d', ), - in_aff_file=dict(argstr='-inaff %s', ), + in_aff_file=dict( + argstr='-inaff %s', + usedefault=True, + ), ln_val=dict(argstr='-ln %d', ), lp_val=dict(argstr='-lp %d', ), maxit_val=dict(argstr='-maxit %d', ), @@ -40,6 +48,7 @@ def test_RegAladin_inputs(): ref_file=dict( argstr='-ref %s', mandatory=True, + usedefault=True, ), ref_low_val=dict(argstr='-refLowThr %f', ), ref_up_val=dict(argstr='-refUpThr %f', ), @@ -47,9 +56,13 @@ def test_RegAladin_inputs(): argstr='-res %s', name_source=['flo_file'], name_template='%s_res.nii.gz', + usedefault=True, ), rig_only_flag=dict(argstr='-rigOnly', ), - rmask_file=dict(argstr='-rmask %s', ), + rmask_file=dict( + argstr='-rmask %s', + usedefault=True, + ), smoo_f_val=dict(argstr='-smooF %f', ), smoo_r_val=dict(argstr='-smooR %f', ), v_val=dict(argstr='-pv %d', ), @@ -62,9 +75,9 @@ def test_RegAladin_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RegAladin_outputs(): output_map = dict( - aff_file=dict(), + aff_file=dict(usedefault=True, ), avg_output=dict(), - res_file=dict(), + res_file=dict(usedefault=True, ), ) outputs = RegAladin.output_spec() diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py b/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py index 2510a46eb8..cce87139dd 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py @@ -28,6 +28,7 @@ def test_RegAverage_inputs(): argstr='-avg_tran %s', position=1, requires=['warp_files'], + usedefault=True, xor=[ 'avg_files', 'avg_lts_files', 'demean1_ref_file', 'demean2_ref_file', 'demean3_ref_file' @@ -37,6 +38,7 @@ def test_RegAverage_inputs(): argstr='-demean1 %s', position=1, requires=['warp_files'], + usedefault=True, xor=[ 'avg_files', 'avg_lts_files', 'avg_ref_file', 'demean2_ref_file', 'demean3_ref_file' @@ -46,6 +48,7 @@ def test_RegAverage_inputs(): argstr='-demean2 %s', position=1, requires=['warp_files'], + usedefault=True, xor=[ 'avg_files', 'avg_lts_files', 'avg_ref_file', 'demean1_ref_file', 'demean3_ref_file' @@ -55,6 +58,7 @@ def test_RegAverage_inputs(): argstr='-demean3 %s', position=1, requires=['warp_files'], + usedefault=True, xor=[ 'avg_files', 'avg_lts_files', 'avg_ref_file', 'demean1_ref_file', 'demean2_ref_file' @@ -72,6 +76,7 @@ def test_RegAverage_inputs(): argstr='%s', genfile=True, position=0, + usedefault=True, ), warp_files=dict( argstr='%s', @@ -86,7 +91,7 @@ def test_RegAverage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegAverage_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = RegAverage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py b/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py index e9bdab82c0..94f0ed45dd 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py @@ -5,7 +5,10 @@ def test_RegF3D_inputs(): input_map = dict( - aff_file=dict(argstr='-aff %s', ), + aff_file=dict( + argstr='-aff %s', + usedefault=True, + ), amc_flag=dict(argstr='-amc', ), args=dict(argstr='%s', ), be_val=dict(argstr='-be %f', ), @@ -13,6 +16,7 @@ def test_RegF3D_inputs(): argstr='-cpp %s', name_source=['flo_file'], name_template='%s_cpp.nii.gz', + usedefault=True, ), environ=dict( nohash=True, @@ -23,14 +27,21 @@ def test_RegF3D_inputs(): flo_file=dict( argstr='-flo %s', mandatory=True, + usedefault=True, ), flo_smooth_val=dict(argstr='-smooF %f', ), flwth2_thr_val=dict(argstr='-fLwTh %d %f', ), flwth_thr_val=dict(argstr='--fLwTh %f', ), - fmask_file=dict(argstr='-fmask %s', ), + fmask_file=dict( + argstr='-fmask %s', + usedefault=True, + ), fupth2_thr_val=dict(argstr='-fUpTh %d %f', ), fupth_thr_val=dict(argstr='--fUpTh %f', ), - incpp_file=dict(argstr='-incpp %s', ), + incpp_file=dict( + argstr='-incpp %s', + usedefault=True, + ), jl_val=dict(argstr='-jl %f', ), kld2_flag=dict(argstr='-kld %d', ), kld_flag=dict(argstr='--kld', ), @@ -58,16 +69,21 @@ def test_RegF3D_inputs(): ref_file=dict( argstr='-ref %s', mandatory=True, + usedefault=True, ), ref_smooth_val=dict(argstr='-smooR %f', ), res_file=dict( argstr='-res %s', name_source=['flo_file'], name_template='%s_res.nii.gz', + usedefault=True, ), rlwth2_thr_val=dict(argstr='-rLwTh %d %f', ), rlwth_thr_val=dict(argstr='--rLwTh %f', ), - rmask_file=dict(argstr='-rmask %s', ), + rmask_file=dict( + argstr='-rmask %s', + usedefault=True, + ), rupth2_thr_val=dict(argstr='-rUpTh %d %f', ), rupth_thr_val=dict(argstr='--rUpTh %f', ), smooth_grad_val=dict(argstr='-smoothGrad %f', ), @@ -87,10 +103,10 @@ def test_RegF3D_inputs(): def test_RegF3D_outputs(): output_map = dict( avg_output=dict(), - cpp_file=dict(), - invcpp_file=dict(), - invres_file=dict(), - res_file=dict(), + cpp_file=dict(usedefault=True, ), + invcpp_file=dict(usedefault=True, ), + invres_file=dict(usedefault=True, ), + res_file=dict(usedefault=True, ), ) outputs = RegF3D.output_spec() diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py b/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py index 63f917c683..360e940c1e 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py @@ -19,11 +19,16 @@ def test_RegJacobian_inputs(): name_source=['trans_file'], name_template='%s', position=-1, + usedefault=True, + ), + ref_file=dict( + argstr='-ref %s', + usedefault=True, ), - ref_file=dict(argstr='-ref %s', ), trans_file=dict( argstr='-trans %s', mandatory=True, + usedefault=True, ), type=dict( argstr='-%s', @@ -37,7 +42,7 @@ def test_RegJacobian_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegJacobian_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = RegJacobian.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py b/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py index 3321d87afc..97493a2761 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py @@ -13,6 +13,7 @@ def test_RegMeasure_inputs(): flo_file=dict( argstr='-flo %s', mandatory=True, + usedefault=True, ), measure_type=dict( argstr='-%s', @@ -26,10 +27,12 @@ def test_RegMeasure_inputs(): argstr='-out %s', name_source=['flo_file'], name_template='%s', + usedefault=True, ), ref_file=dict( argstr='-ref %s', mandatory=True, + usedefault=True, ), ) inputs = RegMeasure.input_spec() @@ -38,7 +41,7 @@ def test_RegMeasure_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegMeasure_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = RegMeasure.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py b/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py index 06b2b48401..d4674d292e 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py @@ -13,6 +13,7 @@ def test_RegResample_inputs(): flo_file=dict( argstr='-flo %s', mandatory=True, + usedefault=True, ), inter_val=dict(argstr='-inter %d', ), omp_core_val=dict( @@ -24,6 +25,7 @@ def test_RegResample_inputs(): name_source=['flo_file'], name_template='%s', position=-1, + usedefault=True, ), pad_val=dict(argstr='-pad %f', ), psf_alg=dict(argstr='-psf_alg %d', ), @@ -31,9 +33,13 @@ def test_RegResample_inputs(): ref_file=dict( argstr='-ref %s', mandatory=True, + usedefault=True, ), tensor_flag=dict(argstr='-tensor ', ), - trans_file=dict(argstr='-trans %s', ), + trans_file=dict( + argstr='-trans %s', + usedefault=True, + ), type=dict( argstr='-%s', position=-2, @@ -47,7 +53,7 @@ def test_RegResample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegResample_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = RegResample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py b/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py index 5deb4206e6..3e08535ee1 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py @@ -18,10 +18,14 @@ def test_RegTools_inputs(): in_file=dict( argstr='-in %s', mandatory=True, + usedefault=True, ), inter_val=dict(argstr='-interp %d', ), iso_flag=dict(argstr='-iso', ), - mask_file=dict(argstr='-nan %s', ), + mask_file=dict( + argstr='-nan %s', + usedefault=True, + ), mul_val=dict(argstr='-mul %s', ), noscl_flag=dict(argstr='-noscl', ), omp_core_val=dict( @@ -32,8 +36,12 @@ def test_RegTools_inputs(): argstr='-out %s', name_source=['in_file'], name_template='%s_tools.nii.gz', + usedefault=True, + ), + rms_val=dict( + argstr='-rms %s', + usedefault=True, ), - rms_val=dict(argstr='-rms %s', ), smo_g_val=dict(argstr='-smoG %f %f %f', ), smo_s_val=dict(argstr='-smoS %f %f %f', ), sub_val=dict(argstr='-sub %s', ), @@ -45,7 +53,7 @@ def test_RegTools_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegTools_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = RegTools.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py b/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py index 57c1b0ad86..d91b77a05a 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py @@ -8,6 +8,7 @@ def test_RegTransform_inputs(): aff_2_rig_input=dict( argstr='-aff2rig %s', position=-2, + usedefault=True, xor=[ 'def_input', 'disp_input', 'flow_input', 'comp_input', 'upd_s_form_input', 'inv_aff_input', 'inv_nrr_input', @@ -19,6 +20,7 @@ def test_RegTransform_inputs(): argstr='-comp %s', position=-3, requires=['comp_input2'], + usedefault=True, xor=[ 'def_input', 'disp_input', 'flow_input', 'upd_s_form_input', 'inv_aff_input', 'inv_nrr_input', 'half_input', @@ -28,10 +30,12 @@ def test_RegTransform_inputs(): comp_input2=dict( argstr='%s', position=-2, + usedefault=True, ), def_input=dict( argstr='-def %s', position=-2, + usedefault=True, xor=[ 'disp_input', 'flow_input', 'comp_input', 'upd_s_form_input', 'inv_aff_input', 'inv_nrr_input', 'half_input', @@ -41,6 +45,7 @@ def test_RegTransform_inputs(): disp_input=dict( argstr='-disp %s', position=-2, + usedefault=True, xor=[ 'def_input', 'flow_input', 'comp_input', 'upd_s_form_input', 'inv_aff_input', 'inv_nrr_input', 'half_input', @@ -63,6 +68,7 @@ def test_RegTransform_inputs(): flow_input=dict( argstr='-flow %s', position=-2, + usedefault=True, xor=[ 'def_input', 'disp_input', 'comp_input', 'upd_s_form_input', 'inv_aff_input', 'inv_nrr_input', 'half_input', @@ -72,6 +78,7 @@ def test_RegTransform_inputs(): half_input=dict( argstr='-half %s', position=-2, + usedefault=True, xor=[ 'def_input', 'disp_input', 'flow_input', 'comp_input', 'upd_s_form_input', 'inv_aff_input', 'inv_nrr_input', @@ -81,6 +88,7 @@ def test_RegTransform_inputs(): inv_aff_input=dict( argstr='-invAff %s', position=-2, + usedefault=True, xor=[ 'def_input', 'disp_input', 'flow_input', 'comp_input', 'upd_s_form_input', 'inv_nrr_input', 'half_input', @@ -113,20 +121,24 @@ def test_RegTransform_inputs(): argstr='%s', genfile=True, position=-1, + usedefault=True, ), ref1_file=dict( argstr='-ref %s', position=0, + usedefault=True, ), ref2_file=dict( argstr='-ref2 %s', position=1, requires=['ref1_file'], + usedefault=True, ), upd_s_form_input=dict( argstr='-updSform %s', position=-3, requires=['upd_s_form_input2'], + usedefault=True, xor=[ 'def_input', 'disp_input', 'flow_input', 'comp_input', 'inv_aff_input', 'inv_nrr_input', 'half_input', @@ -137,6 +149,7 @@ def test_RegTransform_inputs(): argstr='%s', position=-2, requires=['upd_s_form_input'], + usedefault=True, ), ) inputs = RegTransform.input_spec() @@ -145,7 +158,7 @@ def test_RegTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegTransform_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = RegTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py index cc7bc896c6..0f04ca1f2e 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py @@ -14,11 +14,13 @@ def test_BinaryMaths_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), operand_file=dict( argstr='%s', mandatory=True, position=5, + usedefault=True, xor=['operand_value', 'operand_str'], ), operand_str=dict( @@ -43,6 +45,7 @@ def test_BinaryMaths_inputs(): name_source=['in_file'], name_template='%s', position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -55,7 +58,7 @@ def test_BinaryMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinaryMaths_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = BinaryMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py index 464ed6f6c4..a0901f4ee7 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py @@ -14,6 +14,7 @@ def test_BinaryMathsInteger_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), operand_value=dict( argstr='%d', @@ -30,6 +31,7 @@ def test_BinaryMathsInteger_inputs(): name_source=['in_file'], name_template='%s', position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -42,7 +44,7 @@ def test_BinaryMathsInteger_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinaryMathsInteger_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = BinaryMathsInteger.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py index 0771d72f5c..9ae998eb23 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py @@ -14,6 +14,7 @@ def test_BinaryStats_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), larger_voxel=dict( argstr='-t %f', @@ -22,11 +23,13 @@ def test_BinaryStats_inputs(): mask_file=dict( argstr='-m %s', position=-2, + usedefault=True, ), operand_file=dict( argstr='%s', mandatory=True, position=5, + usedefault=True, xor=['operand_value'], ), operand_value=dict( diff --git a/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py b/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py index dceea837c0..485fd5a0ce 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py @@ -14,13 +14,17 @@ def test_CalcTopNCC_inputs(): argstr='-target %s', mandatory=True, position=1, + usedefault=True, ), in_templates=dict( argstr='%s', mandatory=True, position=3, ), - mask_file=dict(argstr='-mask %s', ), + mask_file=dict( + argstr='-mask %s', + usedefault=True, + ), num_templates=dict( argstr='-templates %s', mandatory=True, diff --git a/nipype/interfaces/niftyseg/tests/test_auto_EM.py b/nipype/interfaces/niftyseg/tests/test_auto_EM.py index fc270ed22f..39a7ce70a0 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_EM.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_EM.py @@ -22,8 +22,12 @@ def test_EM_inputs(): argstr='-in %s', mandatory=True, position=4, + usedefault=True, + ), + mask_file=dict( + argstr='-mask %s', + usedefault=True, ), - mask_file=dict(argstr='-mask %s', ), max_iter=dict( argstr='-max_iter %s', usedefault=True, @@ -42,21 +46,25 @@ def test_EM_inputs(): argstr='-bc_out %s', name_source=['in_file'], name_template='%s_bc_em.nii.gz', + usedefault=True, ), out_file=dict( argstr='-out %s', name_source=['in_file'], name_template='%s_em.nii.gz', + usedefault=True, ), out_outlier_file=dict( argstr='-out_outlier %s', name_source=['in_file'], name_template='%s_outlier_em.nii.gz', + usedefault=True, ), outlier_val=dict(argstr='-outlier %s %s', ), prior_4D=dict( argstr='-prior4D %s', mandatory=True, + usedefault=True, xor=['no_prior', 'priors'], ), priors=dict( @@ -74,9 +82,9 @@ def test_EM_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EM_outputs(): output_map = dict( - out_bc_file=dict(), - out_file=dict(), - out_outlier_file=dict(), + out_bc_file=dict(usedefault=True, ), + out_file=dict(usedefault=True, ), + out_outlier_file=dict(usedefault=True, ), ) outputs = EM.output_spec() diff --git a/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py b/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py index 7cbfe58c6c..003dcab9a1 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py @@ -6,7 +6,10 @@ def test_FillLesions_inputs(): input_map = dict( args=dict(argstr='%s', ), - bin_mask=dict(argstr='-mask %s', ), + bin_mask=dict( + argstr='-mask %s', + usedefault=True, + ), cwf=dict(argstr='-cwf %f', ), debug=dict(argstr='-debug', ), environ=dict( @@ -18,11 +21,13 @@ def test_FillLesions_inputs(): argstr='-i %s', mandatory=True, position=1, + usedefault=True, ), lesion_mask=dict( argstr='-l %s', mandatory=True, position=2, + usedefault=True, ), match=dict(argstr='-match %f', ), other=dict(argstr='-other', ), @@ -32,6 +37,7 @@ def test_FillLesions_inputs(): name_source=['in_file'], name_template='%s_lesions_filled.nii.gz', position=3, + usedefault=True, ), search=dict(argstr='-search %f', ), size=dict(argstr='-size %d', ), @@ -45,7 +51,7 @@ def test_FillLesions_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FillLesions_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = FillLesions.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py b/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py index eea345e1df..f0ac597ea7 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py @@ -17,20 +17,28 @@ def test_LabelFusion_inputs(): nohash=True, usedefault=True, ), - file_to_seg=dict(mandatory=True, ), + file_to_seg=dict( + mandatory=True, + usedefault=True, + ), in_file=dict( argstr='-in %s', mandatory=True, position=1, + usedefault=True, ), kernel_size=dict(), - mask_file=dict(argstr='-mask %s', ), + mask_file=dict( + argstr='-mask %s', + usedefault=True, + ), max_iter=dict(argstr='-max_iter %d', ), mrf_value=dict(argstr='-MRF_beta %f', ), out_file=dict( argstr='-out %s', name_source=['in_file'], name_template='%s', + usedefault=True, ), prob_flag=dict(argstr='-outProb', ), prob_update_flag=dict(argstr='-prop_update', ), @@ -41,7 +49,7 @@ def test_LabelFusion_inputs(): position=3, usedefault=True, ), - template_file=dict(), + template_file=dict(usedefault=True, ), template_num=dict(), unc=dict(argstr='-unc', ), unc_thresh=dict(argstr='-uncthres %f', ), @@ -53,7 +61,7 @@ def test_LabelFusion_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LabelFusion_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = LabelFusion.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py b/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py index 247dc9773e..24a122f2eb 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py @@ -14,12 +14,14 @@ def test_MathsCommand_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), out_file=dict( argstr='%s', name_source=['in_file'], name_template='%s', position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -32,7 +34,7 @@ def test_MathsCommand_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MathsCommand_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MathsCommand.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_Merge.py b/nipype/interfaces/niftyseg/tests/test_auto_Merge.py index c53e4edf40..1b328500cc 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_Merge.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_Merge.py @@ -15,6 +15,7 @@ def test_Merge_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), merge_files=dict( argstr='%s', @@ -26,6 +27,7 @@ def test_Merge_inputs(): name_source=['in_file'], name_template='%s', position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -38,7 +40,7 @@ def test_Merge_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Merge_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Merge.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py b/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py index bfeded6eef..ba5b81c0d1 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py @@ -11,6 +11,7 @@ def test_PatchMatch_inputs(): argstr='-db %s', mandatory=True, position=3, + usedefault=True, ), environ=dict( nohash=True, @@ -20,12 +21,14 @@ def test_PatchMatch_inputs(): argstr='-i %s', mandatory=True, position=1, + usedefault=True, ), it_num=dict(argstr='-it %i', ), mask_file=dict( argstr='-m %s', mandatory=True, position=2, + usedefault=True, ), match_num=dict(argstr='-match %i', ), out_file=dict( @@ -33,6 +36,7 @@ def test_PatchMatch_inputs(): name_source=['in_file'], name_template='%s_pm.nii.gz', position=4, + usedefault=True, ), patch_size=dict(argstr='-size %i', ), pm_num=dict(argstr='-pm %i', ), @@ -43,7 +47,7 @@ def test_PatchMatch_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PatchMatch_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = PatchMatch.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py b/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py index e845e18952..9d47371a46 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py @@ -14,6 +14,7 @@ def test_StatsCommand_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), larger_voxel=dict( argstr='-t %f', @@ -22,6 +23,7 @@ def test_StatsCommand_inputs(): mask_file=dict( argstr='-m %s', position=-2, + usedefault=True, ), ) inputs = StatsCommand.input_spec() diff --git a/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py index 7241264eee..754990431c 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py @@ -14,17 +14,20 @@ def test_TupleMaths_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), operand_file1=dict( argstr='%s', mandatory=True, position=5, + usedefault=True, xor=['operand_value1'], ), operand_file2=dict( argstr='%s', mandatory=True, position=6, + usedefault=True, xor=['operand_value2'], ), operand_value1=dict( @@ -49,6 +52,7 @@ def test_TupleMaths_inputs(): name_source=['in_file'], name_template='%s', position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -61,7 +65,7 @@ def test_TupleMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TupleMaths_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = TupleMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py index 9b1cd7d194..5f903212af 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py @@ -14,6 +14,7 @@ def test_UnaryMaths_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), operation=dict( argstr='-%s', @@ -25,6 +26,7 @@ def test_UnaryMaths_inputs(): name_source=['in_file'], name_template='%s', position=-2, + usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -37,7 +39,7 @@ def test_UnaryMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_UnaryMaths_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = UnaryMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py b/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py index 34edf1a190..8e0cb27515 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py @@ -14,6 +14,7 @@ def test_UnaryStats_inputs(): argstr='%s', mandatory=True, position=2, + usedefault=True, ), larger_voxel=dict( argstr='-t %f', @@ -22,6 +23,7 @@ def test_UnaryStats_inputs(): mask_file=dict( argstr='-m %s', position=-2, + usedefault=True, ), operation=dict( argstr='-%s', diff --git a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py index f0f2453274..3e27a7ea09 100644 --- a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py +++ b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py @@ -8,8 +8,11 @@ def test_ComputeMask_inputs(): M=dict(), cc=dict(), m=dict(), - mean_volume=dict(mandatory=True, ), - reference_volume=dict(), + mean_volume=dict( + mandatory=True, + usedefault=True, + ), + reference_volume=dict(usedefault=True, ), ) inputs = ComputeMask.input_spec() @@ -17,7 +20,7 @@ def test_ComputeMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeMask_outputs(): - output_map = dict(brain_mask=dict(), ) + output_map = dict(brain_mask=dict(usedefault=True, ), ) outputs = ComputeMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py index 383d1cbea3..c3647fdcc8 100644 --- a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py @@ -6,14 +6,20 @@ def test_EstimateContrast_inputs(): input_map = dict( axis=dict(mandatory=True, ), - beta=dict(mandatory=True, ), + beta=dict( + mandatory=True, + usedefault=True, + ), constants=dict(mandatory=True, ), contrasts=dict(mandatory=True, ), dof=dict(mandatory=True, ), mask=dict(), nvbeta=dict(mandatory=True, ), reg_names=dict(mandatory=True, ), - s2=dict(mandatory=True, ), + s2=dict( + mandatory=True, + usedefault=True, + ), ) inputs = EstimateContrast.input_spec() diff --git a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py index 4ac3aa720e..17c68df3c7 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py +++ b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py @@ -23,15 +23,15 @@ def test_FitGLM_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FitGLM_outputs(): output_map = dict( - a=dict(), + a=dict(usedefault=True, ), axis=dict(), - beta=dict(), + beta=dict(usedefault=True, ), constants=dict(), dof=dict(), nvbeta=dict(), reg_names=dict(), residuals=dict(), - s2=dict(), + s2=dict(usedefault=True, ), ) outputs = FitGLM.output_spec() diff --git a/nipype/interfaces/nipy/tests/test_auto_Similarity.py b/nipype/interfaces/nipy/tests/test_auto_Similarity.py index fbdb6fffa6..5b4f9269cc 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Similarity.py +++ b/nipype/interfaces/nipy/tests/test_auto_Similarity.py @@ -5,11 +5,17 @@ def test_Similarity_inputs(): input_map = dict( - mask1=dict(), - mask2=dict(), + mask1=dict(usedefault=True, ), + mask2=dict(usedefault=True, ), metric=dict(usedefault=True, ), - volume1=dict(mandatory=True, ), - volume2=dict(mandatory=True, ), + volume1=dict( + mandatory=True, + usedefault=True, + ), + volume2=dict( + mandatory=True, + usedefault=True, + ), ) inputs = Similarity.input_spec() diff --git a/nipype/interfaces/nipy/tests/test_auto_Trim.py b/nipype/interfaces/nipy/tests/test_auto_Trim.py index 6073c9082b..4ba09246d3 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Trim.py +++ b/nipype/interfaces/nipy/tests/test_auto_Trim.py @@ -7,8 +7,11 @@ def test_Trim_inputs(): input_map = dict( begin_index=dict(usedefault=True, ), end_index=dict(usedefault=True, ), - in_file=dict(mandatory=True, ), - out_file=dict(), + in_file=dict( + mandatory=True, + usedefault=True, + ), + out_file=dict(usedefault=True, ), suffix=dict(usedefault=True, ), ) inputs = Trim.input_spec() @@ -17,7 +20,7 @@ def test_Trim_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Trim_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Trim.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py index 4a641ebb50..efe443a759 100644 --- a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py +++ b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py @@ -10,10 +10,13 @@ def test_CoherenceAnalyzer_inputs(): figure_type=dict(usedefault=True, ), frequency_range=dict(usedefault=True, ), in_TS=dict(), - in_file=dict(requires=('TR', ), ), + in_file=dict( + requires=('TR', ), + usedefault=True, + ), n_overlap=dict(usedefault=True, ), - output_csv_file=dict(), - output_figure_file=dict(), + output_csv_file=dict(usedefault=True, ), + output_figure_file=dict(usedefault=True, ), ) inputs = CoherenceAnalyzer.input_spec() @@ -23,11 +26,11 @@ def test_CoherenceAnalyzer_inputs(): def test_CoherenceAnalyzer_outputs(): output_map = dict( coherence_array=dict(), - coherence_csv=dict(), - coherence_fig=dict(), + coherence_csv=dict(usedefault=True, ), + coherence_fig=dict(usedefault=True, ), timedelay_array=dict(), - timedelay_csv=dict(), - timedelay_fig=dict(), + timedelay_csv=dict(usedefault=True, ), + timedelay_fig=dict(usedefault=True, ), ) outputs = CoherenceAnalyzer.output_spec() diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py index 81a22bfe38..0f0e0e3b8e 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py @@ -10,13 +10,34 @@ def test_BRAINSPosteriorToContinuousClass_inputs(): nohash=True, usedefault=True, ), - inputBasalGmVolume=dict(argstr='--inputBasalGmVolume %s', ), - inputCrblGmVolume=dict(argstr='--inputCrblGmVolume %s', ), - inputCrblWmVolume=dict(argstr='--inputCrblWmVolume %s', ), - inputCsfVolume=dict(argstr='--inputCsfVolume %s', ), - inputSurfaceGmVolume=dict(argstr='--inputSurfaceGmVolume %s', ), - inputVbVolume=dict(argstr='--inputVbVolume %s', ), - inputWhiteVolume=dict(argstr='--inputWhiteVolume %s', ), + inputBasalGmVolume=dict( + argstr='--inputBasalGmVolume %s', + usedefault=True, + ), + inputCrblGmVolume=dict( + argstr='--inputCrblGmVolume %s', + usedefault=True, + ), + inputCrblWmVolume=dict( + argstr='--inputCrblWmVolume %s', + usedefault=True, + ), + inputCsfVolume=dict( + argstr='--inputCsfVolume %s', + usedefault=True, + ), + inputSurfaceGmVolume=dict( + argstr='--inputSurfaceGmVolume %s', + usedefault=True, + ), + inputVbVolume=dict( + argstr='--inputVbVolume %s', + usedefault=True, + ), + inputWhiteVolume=dict( + argstr='--inputWhiteVolume %s', + usedefault=True, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -28,7 +49,7 @@ def test_BRAINSPosteriorToContinuousClass_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSPosteriorToContinuousClass_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = BRAINSPosteriorToContinuousClass.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py index ac589ad6dc..77c5170628 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py @@ -30,7 +30,10 @@ def test_BRAINSTalairach_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), outputBox=dict( argstr='--outputBox %s', hash_files=False, @@ -47,8 +50,8 @@ def test_BRAINSTalairach_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTalairach_outputs(): output_map = dict( - outputBox=dict(), - outputGrid=dict(), + outputBox=dict(usedefault=True, ), + outputGrid=dict(usedefault=True, ), ) outputs = BRAINSTalairach.output_spec() diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py index 5ada1576e7..d37f45fb6e 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py @@ -12,13 +12,22 @@ def test_BRAINSTalairachMask_inputs(): ), expand=dict(argstr='--expand ', ), hemisphereMode=dict(argstr='--hemisphereMode %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, ), - talairachBox=dict(argstr='--talairachBox %s', ), - talairachParameters=dict(argstr='--talairachParameters %s', ), + talairachBox=dict( + argstr='--talairachBox %s', + usedefault=True, + ), + talairachParameters=dict( + argstr='--talairachParameters %s', + usedefault=True, + ), ) inputs = BRAINSTalairachMask.input_spec() @@ -26,7 +35,7 @@ def test_BRAINSTalairachMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTalairachMask_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = BRAINSTalairachMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py b/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py index eb4bdcffae..1b67912450 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py @@ -11,7 +11,10 @@ def test_GenerateEdgeMapImage_inputs(): usedefault=True, ), inputMRVolumes=dict(argstr='--inputMRVolumes %s...', ), - inputMask=dict(argstr='--inputMask %s', ), + inputMask=dict( + argstr='--inputMask %s', + usedefault=True, + ), lowerPercentileMatching=dict(argstr='--lowerPercentileMatching %f', ), maximumOutputRange=dict(argstr='--maximumOutputRange %d', ), minimumOutputRange=dict(argstr='--minimumOutputRange %d', ), @@ -33,8 +36,8 @@ def test_GenerateEdgeMapImage_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateEdgeMapImage_outputs(): output_map = dict( - outputEdgeMap=dict(), - outputMaximumGradientImage=dict(), + outputEdgeMap=dict(usedefault=True, ), + outputMaximumGradientImage=dict(usedefault=True, ), ) outputs = GenerateEdgeMapImage.output_spec() diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py b/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py index ae16bc8fab..c1f7943b76 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py @@ -27,7 +27,7 @@ def test_GeneratePurePlugMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GeneratePurePlugMask_outputs(): - output_map = dict(outputMaskFile=dict(), ) + output_map = dict(outputMaskFile=dict(usedefault=True, ), ) outputs = GeneratePurePlugMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py index 1377072149..90450e9e26 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py @@ -11,16 +11,28 @@ def test_HistogramMatchingFilter_inputs(): usedefault=True, ), histogramAlgorithm=dict(argstr='--histogramAlgorithm %s', ), - inputBinaryVolume=dict(argstr='--inputBinaryVolume %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputBinaryVolume=dict( + argstr='--inputBinaryVolume %s', + usedefault=True, + ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', ), numberOfMatchPoints=dict(argstr='--numberOfMatchPoints %d', ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, ), - referenceBinaryVolume=dict(argstr='--referenceBinaryVolume %s', ), - referenceVolume=dict(argstr='--referenceVolume %s', ), + referenceBinaryVolume=dict( + argstr='--referenceBinaryVolume %s', + usedefault=True, + ), + referenceVolume=dict( + argstr='--referenceVolume %s', + usedefault=True, + ), verbose=dict(argstr='--verbose ', ), writeHistogram=dict(argstr='--writeHistogram %s', ), ) @@ -30,7 +42,7 @@ def test_HistogramMatchingFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_HistogramMatchingFilter_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = HistogramMatchingFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py index 534488ad10..68d0d1b8cf 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py @@ -5,14 +5,23 @@ def test_SimilarityIndex_inputs(): input_map = dict( - ANNContinuousVolume=dict(argstr='--ANNContinuousVolume %s', ), + ANNContinuousVolume=dict( + argstr='--ANNContinuousVolume %s', + usedefault=True, + ), args=dict(argstr='%s', ), environ=dict( nohash=True, usedefault=True, ), - inputManualVolume=dict(argstr='--inputManualVolume %s', ), - outputCSVFilename=dict(argstr='--outputCSVFilename %s', ), + inputManualVolume=dict( + argstr='--inputManualVolume %s', + usedefault=True, + ), + outputCSVFilename=dict( + argstr='--outputCSVFilename %s', + usedefault=True, + ), thresholdInterval=dict(argstr='--thresholdInterval %f', ), ) inputs = SimilarityIndex.input_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py index 05593527fb..2103f17918 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py @@ -13,15 +13,30 @@ def test_DWIConvert_inputs(): usedefault=True, ), fMRI=dict(argstr='--fMRI ', ), - fslNIFTIFile=dict(argstr='--fslNIFTIFile %s', ), + fslNIFTIFile=dict( + argstr='--fslNIFTIFile %s', + usedefault=True, + ), gradientVectorFile=dict( argstr='--gradientVectorFile %s', hash_files=False, ), - inputBValues=dict(argstr='--inputBValues %s', ), - inputBVectors=dict(argstr='--inputBVectors %s', ), - inputDicomDirectory=dict(argstr='--inputDicomDirectory %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputBValues=dict( + argstr='--inputBValues %s', + usedefault=True, + ), + inputBVectors=dict( + argstr='--inputBVectors %s', + usedefault=True, + ), + inputDicomDirectory=dict( + argstr='--inputDicomDirectory %s', + usedefault=True, + ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), outputBValues=dict( argstr='--outputBValues %s', hash_files=False, @@ -54,11 +69,11 @@ def test_DWIConvert_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DWIConvert_outputs(): output_map = dict( - gradientVectorFile=dict(), - outputBValues=dict(), - outputBVectors=dict(), - outputDirectory=dict(), - outputVolume=dict(), + gradientVectorFile=dict(usedefault=True, ), + outputBValues=dict(usedefault=True, ), + outputBVectors=dict(usedefault=True, ), + outputDirectory=dict(usedefault=True, ), + outputVolume=dict(usedefault=True, ), ) outputs = DWIConvert.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py index eb9d8c6184..b6ec40ddba 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py @@ -13,8 +13,14 @@ def test_compareTractInclusion_inputs(): ), numberOfPoints=dict(argstr='--numberOfPoints %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), - standardFiber=dict(argstr='--standardFiber %s', ), - testFiber=dict(argstr='--testFiber %s', ), + standardFiber=dict( + argstr='--standardFiber %s', + usedefault=True, + ), + testFiber=dict( + argstr='--testFiber %s', + usedefault=True, + ), testForBijection=dict(argstr='--testForBijection ', ), testForFiberCardinality=dict(argstr='--testForFiberCardinality ', ), writeXMLPolyDataFile=dict(argstr='--writeXMLPolyDataFile ', ), diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py index 92c00853f4..078e2774ca 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py @@ -24,7 +24,7 @@ def test_dtiaverage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_dtiaverage_outputs(): - output_map = dict(tensor_output=dict(), ) + output_map = dict(tensor_output=dict(usedefault=True, ), ) outputs = dtiaverage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py index 440fd4df07..376f92459a 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py @@ -15,14 +15,23 @@ def test_dtiestim_inputs(): ), DTI_double=dict(argstr='--DTI_double ', ), args=dict(argstr='%s', ), - bad_region_mask=dict(argstr='--bad_region_mask %s', ), - brain_mask=dict(argstr='--brain_mask %s', ), + bad_region_mask=dict( + argstr='--bad_region_mask %s', + usedefault=True, + ), + brain_mask=dict( + argstr='--brain_mask %s', + usedefault=True, + ), correction=dict(argstr='--correction %s', ), defaultTensor=dict( argstr='--defaultTensor %s', sep=',', ), - dwi_image=dict(argstr='--dwi_image %s', ), + dwi_image=dict( + argstr='--dwi_image %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -51,10 +60,10 @@ def test_dtiestim_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_dtiestim_outputs(): output_map = dict( - B0=dict(), - B0_mask_output=dict(), - idwi=dict(), - tensor_output=dict(), + B0=dict(usedefault=True, ), + B0_mask_output=dict(usedefault=True, ), + idwi=dict(usedefault=True, ), + tensor_output=dict(usedefault=True, ), ) outputs = dtiestim.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py index 3148d1edb5..a8c7de8d9a 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py @@ -10,7 +10,10 @@ def test_dtiprocess_inputs(): argstr='--RD_output %s', hash_files=False, ), - affineitk_file=dict(argstr='--affineitk_file %s', ), + affineitk_file=dict( + argstr='--affineitk_file %s', + usedefault=True, + ), args=dict(argstr='%s', ), color_fa_output=dict( argstr='--color_fa_output %s', @@ -21,8 +24,14 @@ def test_dtiprocess_inputs(): argstr='--deformation_output %s', hash_files=False, ), - dof_file=dict(argstr='--dof_file %s', ), - dti_image=dict(argstr='--dti_image %s', ), + dof_file=dict( + argstr='--dof_file %s', + usedefault=True, + ), + dti_image=dict( + argstr='--dti_image %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -39,7 +48,10 @@ def test_dtiprocess_inputs(): argstr='--fa_output %s', hash_files=False, ), - forward=dict(argstr='--forward %s', ), + forward=dict( + argstr='--forward %s', + usedefault=True, + ), frobenius_norm_output=dict( argstr='--frobenius_norm_output %s', hash_files=False, @@ -58,7 +70,10 @@ def test_dtiprocess_inputs(): argstr='--lambda3_output %s', hash_files=False, ), - mask=dict(argstr='--mask %s', ), + mask=dict( + argstr='--mask %s', + usedefault=True, + ), md_output=dict( argstr='--md_output %s', hash_files=False, @@ -67,7 +82,10 @@ def test_dtiprocess_inputs(): argstr='--negative_eigenvector_output %s', hash_files=False, ), - newdof_file=dict(argstr='--newdof_file %s', ), + newdof_file=dict( + argstr='--newdof_file %s', + usedefault=True, + ), outmask=dict( argstr='--outmask %s', hash_files=False, @@ -92,21 +110,21 @@ def test_dtiprocess_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_dtiprocess_outputs(): output_map = dict( - RD_output=dict(), - color_fa_output=dict(), - deformation_output=dict(), - fa_gradient_output=dict(), - fa_gradmag_output=dict(), - fa_output=dict(), - frobenius_norm_output=dict(), - lambda1_output=dict(), - lambda2_output=dict(), - lambda3_output=dict(), - md_output=dict(), - negative_eigenvector_output=dict(), - outmask=dict(), - principal_eigenvector_output=dict(), - rot_output=dict(), + RD_output=dict(usedefault=True, ), + color_fa_output=dict(usedefault=True, ), + deformation_output=dict(usedefault=True, ), + fa_gradient_output=dict(usedefault=True, ), + fa_gradmag_output=dict(usedefault=True, ), + fa_output=dict(usedefault=True, ), + frobenius_norm_output=dict(usedefault=True, ), + lambda1_output=dict(usedefault=True, ), + lambda2_output=dict(usedefault=True, ), + lambda3_output=dict(usedefault=True, ), + md_output=dict(usedefault=True, ), + negative_eigenvector_output=dict(usedefault=True, ), + outmask=dict(usedefault=True, ), + principal_eigenvector_output=dict(usedefault=True, ), + rot_output=dict(usedefault=True, ), ) outputs = dtiprocess.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py index ac5784f1c7..cca7af405e 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py @@ -10,7 +10,10 @@ def test_extractNrrdVectorIndex_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -25,7 +28,7 @@ def test_extractNrrdVectorIndex_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_extractNrrdVectorIndex_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = extractNrrdVectorIndex.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py index 195d7dc3e1..2225121f02 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py @@ -11,7 +11,10 @@ def test_gtractAnisotropyMap_inputs(): nohash=True, usedefault=True, ), - inputTensorVolume=dict(argstr='--inputTensorVolume %s', ), + inputTensorVolume=dict( + argstr='--inputTensorVolume %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -24,7 +27,7 @@ def test_gtractAnisotropyMap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractAnisotropyMap_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = gtractAnisotropyMap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py index fbb5bd6a55..96a0ee96e8 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py @@ -12,7 +12,10 @@ def test_gtractAverageBvalues_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -25,7 +28,7 @@ def test_gtractAverageBvalues_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractAverageBvalues_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = gtractAverageBvalues.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py index fed980c463..c1e3e04156 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py @@ -12,7 +12,10 @@ def test_gtractClipAnisotropy_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -25,7 +28,7 @@ def test_gtractClipAnisotropy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractClipAnisotropy_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = gtractClipAnisotropy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py index 456e1e79fa..9522b2be08 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py @@ -17,9 +17,18 @@ def test_gtractCoRegAnatomy_inputs(): argstr='--gridSize %s', sep=',', ), - inputAnatomicalVolume=dict(argstr='--inputAnatomicalVolume %s', ), - inputRigidTransform=dict(argstr='--inputRigidTransform %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputAnatomicalVolume=dict( + argstr='--inputAnatomicalVolume %s', + usedefault=True, + ), + inputRigidTransform=dict( + argstr='--inputRigidTransform %s', + usedefault=True, + ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), maxBSplineDisplacement=dict(argstr='--maxBSplineDisplacement %f', ), maximumStepSize=dict(argstr='--maximumStepSize %f', ), minimumStepSize=dict(argstr='--minimumStepSize %f', ), @@ -47,7 +56,7 @@ def test_gtractCoRegAnatomy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractCoRegAnatomy_outputs(): - output_map = dict(outputTransformName=dict(), ) + output_map = dict(outputTransformName=dict(usedefault=True, ), ) outputs = gtractCoRegAnatomy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py index 7b75858eff..75561455d7 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py @@ -24,7 +24,7 @@ def test_gtractConcatDwi_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractConcatDwi_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = gtractConcatDwi.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py index d9e0b725c8..456f5f1eb5 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py @@ -10,8 +10,14 @@ def test_gtractCopyImageOrientation_inputs(): nohash=True, usedefault=True, ), - inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputReferenceVolume=dict( + argstr='--inputReferenceVolume %s', + usedefault=True, + ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -24,7 +30,7 @@ def test_gtractCopyImageOrientation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractCopyImageOrientation_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = gtractCopyImageOrientation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py index 3143b16dfb..ef467f8957 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py @@ -12,11 +12,17 @@ def test_gtractCoregBvalues_inputs(): nohash=True, usedefault=True, ), - fixedVolume=dict(argstr='--fixedVolume %s', ), + fixedVolume=dict( + argstr='--fixedVolume %s', + usedefault=True, + ), fixedVolumeIndex=dict(argstr='--fixedVolumeIndex %d', ), maximumStepSize=dict(argstr='--maximumStepSize %f', ), minimumStepSize=dict(argstr='--minimumStepSize %f', ), - movingVolume=dict(argstr='--movingVolume %s', ), + movingVolume=dict( + argstr='--movingVolume %s', + usedefault=True, + ), numberOfIterations=dict(argstr='--numberOfIterations %d', ), numberOfSpatialSamples=dict(argstr='--numberOfSpatialSamples %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -40,8 +46,8 @@ def test_gtractCoregBvalues_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_gtractCoregBvalues_outputs(): output_map = dict( - outputTransform=dict(), - outputVolume=dict(), + outputTransform=dict(usedefault=True, ), + outputVolume=dict(usedefault=True, ), ) outputs = gtractCoregBvalues.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py index 32d1e68898..3e8d6ce899 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py @@ -11,10 +11,18 @@ def test_gtractCostFastMarching_inputs(): nohash=True, usedefault=True, ), - inputAnisotropyVolume=dict(argstr='--inputAnisotropyVolume %s', ), + inputAnisotropyVolume=dict( + argstr='--inputAnisotropyVolume %s', + usedefault=True, + ), inputStartingSeedsLabelMapVolume=dict( - argstr='--inputStartingSeedsLabelMapVolume %s', ), - inputTensorVolume=dict(argstr='--inputTensorVolume %s', ), + argstr='--inputStartingSeedsLabelMapVolume %s', + usedefault=True, + ), + inputTensorVolume=dict( + argstr='--inputTensorVolume %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputCostVolume=dict( argstr='--outputCostVolume %s', @@ -35,8 +43,8 @@ def test_gtractCostFastMarching_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_gtractCostFastMarching_outputs(): output_map = dict( - outputCostVolume=dict(), - outputSpeedVolume=dict(), + outputCostVolume=dict(usedefault=True, ), + outputSpeedVolume=dict(usedefault=True, ), ) outputs = gtractCostFastMarching.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py index bbe375bbb9..7d77f81257 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py @@ -10,7 +10,10 @@ def test_gtractCreateGuideFiber_inputs(): nohash=True, usedefault=True, ), - inputFiber=dict(argstr='--inputFiber %s', ), + inputFiber=dict( + argstr='--inputFiber %s', + usedefault=True, + ), numberOfPoints=dict(argstr='--numberOfPoints %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputFiber=dict( @@ -25,7 +28,7 @@ def test_gtractCreateGuideFiber_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractCreateGuideFiber_outputs(): - output_map = dict(outputFiber=dict(), ) + output_map = dict(outputFiber=dict(usedefault=True, ), ) outputs = gtractCreateGuideFiber.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py index ec3a99b91e..0f3400b5c5 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py @@ -11,11 +11,22 @@ def test_gtractFastMarchingTracking_inputs(): nohash=True, usedefault=True, ), - inputAnisotropyVolume=dict(argstr='--inputAnisotropyVolume %s', ), - inputCostVolume=dict(argstr='--inputCostVolume %s', ), + inputAnisotropyVolume=dict( + argstr='--inputAnisotropyVolume %s', + usedefault=True, + ), + inputCostVolume=dict( + argstr='--inputCostVolume %s', + usedefault=True, + ), inputStartingSeedsLabelMapVolume=dict( - argstr='--inputStartingSeedsLabelMapVolume %s', ), - inputTensorVolume=dict(argstr='--inputTensorVolume %s', ), + argstr='--inputStartingSeedsLabelMapVolume %s', + usedefault=True, + ), + inputTensorVolume=dict( + argstr='--inputTensorVolume %s', + usedefault=True, + ), maximumStepSize=dict(argstr='--maximumStepSize %f', ), minimumStepSize=dict(argstr='--minimumStepSize %f', ), numberOfIterations=dict(argstr='--numberOfIterations %d', ), @@ -35,7 +46,7 @@ def test_gtractFastMarchingTracking_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractFastMarchingTracking_outputs(): - output_map = dict(outputTract=dict(), ) + output_map = dict(outputTract=dict(usedefault=True, ), ) outputs = gtractFastMarchingTracking.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py index 96c93b8b64..214838457e 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py @@ -16,13 +16,26 @@ def test_gtractFiberTracking_inputs(): ), guidedCurvatureThreshold=dict( argstr='--guidedCurvatureThreshold %f', ), - inputAnisotropyVolume=dict(argstr='--inputAnisotropyVolume %s', ), + inputAnisotropyVolume=dict( + argstr='--inputAnisotropyVolume %s', + usedefault=True, + ), inputEndingSeedsLabelMapVolume=dict( - argstr='--inputEndingSeedsLabelMapVolume %s', ), + argstr='--inputEndingSeedsLabelMapVolume %s', + usedefault=True, + ), inputStartingSeedsLabelMapVolume=dict( - argstr='--inputStartingSeedsLabelMapVolume %s', ), - inputTensorVolume=dict(argstr='--inputTensorVolume %s', ), - inputTract=dict(argstr='--inputTract %s', ), + argstr='--inputStartingSeedsLabelMapVolume %s', + usedefault=True, + ), + inputTensorVolume=dict( + argstr='--inputTensorVolume %s', + usedefault=True, + ), + inputTract=dict( + argstr='--inputTract %s', + usedefault=True, + ), maximumBranchPoints=dict(argstr='--maximumBranchPoints %d', ), maximumGuideDistance=dict(argstr='--maximumGuideDistance %f', ), maximumLength=dict(argstr='--maximumLength %f', ), @@ -51,7 +64,7 @@ def test_gtractFiberTracking_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractFiberTracking_outputs(): - output_map = dict(outputTract=dict(), ) + output_map = dict(outputTract=dict(usedefault=True, ), ) outputs = gtractFiberTracking.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py index 9ddde832b2..1930bc3d0f 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py @@ -10,8 +10,14 @@ def test_gtractImageConformity_inputs(): nohash=True, usedefault=True, ), - inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputReferenceVolume=dict( + argstr='--inputReferenceVolume %s', + usedefault=True, + ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -24,7 +30,7 @@ def test_gtractImageConformity_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractImageConformity_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = gtractImageConformity.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py index ca642ceb66..2e09633ce5 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py @@ -10,8 +10,14 @@ def test_gtractInvertBSplineTransform_inputs(): nohash=True, usedefault=True, ), - inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), - inputTransform=dict(argstr='--inputTransform %s', ), + inputReferenceVolume=dict( + argstr='--inputReferenceVolume %s', + usedefault=True, + ), + inputTransform=dict( + argstr='--inputTransform %s', + usedefault=True, + ), landmarkDensity=dict( argstr='--landmarkDensity %s', sep=',', @@ -28,7 +34,7 @@ def test_gtractInvertBSplineTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractInvertBSplineTransform_outputs(): - output_map = dict(outputTransform=dict(), ) + output_map = dict(outputTransform=dict(usedefault=True, ), ) outputs = gtractInvertBSplineTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py index e4fd213d39..f65b49c1b8 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py @@ -6,8 +6,14 @@ def test_gtractInvertDisplacementField_inputs(): input_map = dict( args=dict(argstr='%s', ), - baseImage=dict(argstr='--baseImage %s', ), - deformationImage=dict(argstr='--deformationImage %s', ), + baseImage=dict( + argstr='--baseImage %s', + usedefault=True, + ), + deformationImage=dict( + argstr='--deformationImage %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -25,7 +31,7 @@ def test_gtractInvertDisplacementField_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractInvertDisplacementField_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = gtractInvertDisplacementField.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py index c035862663..51ba4f126b 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py @@ -10,7 +10,10 @@ def test_gtractInvertRigidTransform_inputs(): nohash=True, usedefault=True, ), - inputTransform=dict(argstr='--inputTransform %s', ), + inputTransform=dict( + argstr='--inputTransform %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputTransform=dict( argstr='--outputTransform %s', @@ -23,7 +26,7 @@ def test_gtractInvertRigidTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractInvertRigidTransform_outputs(): - output_map = dict(outputTransform=dict(), ) + output_map = dict(outputTransform=dict(usedefault=True, ), ) outputs = gtractInvertRigidTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py index 43f428b233..52a3d57f4e 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py @@ -10,9 +10,18 @@ def test_gtractResampleAnisotropy_inputs(): nohash=True, usedefault=True, ), - inputAnatomicalVolume=dict(argstr='--inputAnatomicalVolume %s', ), - inputAnisotropyVolume=dict(argstr='--inputAnisotropyVolume %s', ), - inputTransform=dict(argstr='--inputTransform %s', ), + inputAnatomicalVolume=dict( + argstr='--inputAnatomicalVolume %s', + usedefault=True, + ), + inputAnisotropyVolume=dict( + argstr='--inputAnisotropyVolume %s', + usedefault=True, + ), + inputTransform=dict( + argstr='--inputTransform %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -26,7 +35,7 @@ def test_gtractResampleAnisotropy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleAnisotropy_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = gtractResampleAnisotropy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py index 812afca5c0..c7a3d596eb 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py @@ -10,9 +10,18 @@ def test_gtractResampleB0_inputs(): nohash=True, usedefault=True, ), - inputAnatomicalVolume=dict(argstr='--inputAnatomicalVolume %s', ), - inputTransform=dict(argstr='--inputTransform %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputAnatomicalVolume=dict( + argstr='--inputAnatomicalVolume %s', + usedefault=True, + ), + inputTransform=dict( + argstr='--inputTransform %s', + usedefault=True, + ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -27,7 +36,7 @@ def test_gtractResampleB0_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleB0_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = gtractResampleB0.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py index decc017c60..037e0600b3 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py @@ -10,9 +10,18 @@ def test_gtractResampleCodeImage_inputs(): nohash=True, usedefault=True, ), - inputCodeVolume=dict(argstr='--inputCodeVolume %s', ), - inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), - inputTransform=dict(argstr='--inputTransform %s', ), + inputCodeVolume=dict( + argstr='--inputCodeVolume %s', + usedefault=True, + ), + inputReferenceVolume=dict( + argstr='--inputReferenceVolume %s', + usedefault=True, + ), + inputTransform=dict( + argstr='--inputTransform %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -26,7 +35,7 @@ def test_gtractResampleCodeImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleCodeImage_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = gtractResampleCodeImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py index b815d3d3d6..48cfcbb024 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py @@ -15,8 +15,14 @@ def test_gtractResampleDWIInPlace_inputs(): argstr='--imageOutputSize %s', sep=',', ), - inputTransform=dict(argstr='--inputTransform %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputTransform=dict( + argstr='--inputTransform %s', + usedefault=True, + ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputResampledB0=dict( argstr='--outputResampledB0 %s', @@ -26,8 +32,14 @@ def test_gtractResampleDWIInPlace_inputs(): argstr='--outputVolume %s', hash_files=False, ), - referenceVolume=dict(argstr='--referenceVolume %s', ), - warpDWITransform=dict(argstr='--warpDWITransform %s', ), + referenceVolume=dict( + argstr='--referenceVolume %s', + usedefault=True, + ), + warpDWITransform=dict( + argstr='--warpDWITransform %s', + usedefault=True, + ), ) inputs = gtractResampleDWIInPlace.input_spec() @@ -36,8 +48,8 @@ def test_gtractResampleDWIInPlace_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleDWIInPlace_outputs(): output_map = dict( - outputResampledB0=dict(), - outputVolume=dict(), + outputResampledB0=dict(usedefault=True, ), + outputVolume=dict(usedefault=True, ), ) outputs = gtractResampleDWIInPlace.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py index d0d2cd5664..2d42314a38 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py @@ -11,10 +11,17 @@ def test_gtractResampleFibers_inputs(): usedefault=True, ), inputForwardDeformationFieldVolume=dict( - argstr='--inputForwardDeformationFieldVolume %s', ), + argstr='--inputForwardDeformationFieldVolume %s', + usedefault=True, + ), inputReverseDeformationFieldVolume=dict( - argstr='--inputReverseDeformationFieldVolume %s', ), - inputTract=dict(argstr='--inputTract %s', ), + argstr='--inputReverseDeformationFieldVolume %s', + usedefault=True, + ), + inputTract=dict( + argstr='--inputTract %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputTract=dict( argstr='--outputTract %s', @@ -28,7 +35,7 @@ def test_gtractResampleFibers_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleFibers_outputs(): - output_map = dict(outputTract=dict(), ) + output_map = dict(outputTract=dict(usedefault=True, ), ) outputs = gtractResampleFibers.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py index ead96d1c71..5eccecfb14 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py @@ -18,9 +18,15 @@ def test_gtractTensor_inputs(): argstr='--ignoreIndex %s', sep=',', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), maskProcessingMode=dict(argstr='--maskProcessingMode %s', ), - maskVolume=dict(argstr='--maskVolume %s', ), + maskVolume=dict( + argstr='--maskVolume %s', + usedefault=True, + ), medianFilterSize=dict( argstr='--medianFilterSize %s', sep=',', @@ -39,7 +45,7 @@ def test_gtractTensor_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractTensor_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = gtractTensor.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py index 2dfde189e2..2e38e05bef 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py @@ -10,8 +10,14 @@ def test_gtractTransformToDisplacementField_inputs(): nohash=True, usedefault=True, ), - inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), - inputTransform=dict(argstr='--inputTransform %s', ), + inputReferenceVolume=dict( + argstr='--inputReferenceVolume %s', + usedefault=True, + ), + inputTransform=dict( + argstr='--inputTransform %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputDeformationFieldVolume=dict( argstr='--outputDeformationFieldVolume %s', @@ -24,7 +30,7 @@ def test_gtractTransformToDisplacementField_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractTransformToDisplacementField_outputs(): - output_map = dict(outputDeformationFieldVolume=dict(), ) + output_map = dict(outputDeformationFieldVolume=dict(usedefault=True, ), ) outputs = gtractTransformToDisplacementField.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py index cc06c5ede5..9fcde55991 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py @@ -10,7 +10,10 @@ def test_maxcurvature_inputs(): nohash=True, usedefault=True, ), - image=dict(argstr='--image %s', ), + image=dict( + argstr='--image %s', + usedefault=True, + ), output=dict( argstr='--output %s', hash_files=False, @@ -24,7 +27,7 @@ def test_maxcurvature_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_maxcurvature_outputs(): - output_map = dict(output=dict(), ) + output_map = dict(output=dict(usedefault=True, ), ) outputs = maxcurvature.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py index 7c61974ef3..b938d61201 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py @@ -10,7 +10,10 @@ def test_UKFTractography_inputs(): Qw=dict(argstr='--Qw %f', ), Rs=dict(argstr='--Rs %f', ), args=dict(argstr='%s', ), - dwiFile=dict(argstr='--dwiFile %s', ), + dwiFile=dict( + argstr='--dwiFile %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -21,7 +24,10 @@ def test_UKFTractography_inputs(): argstr='--labels %s', sep=',', ), - maskFile=dict(argstr='--maskFile %s', ), + maskFile=dict( + argstr='--maskFile %s', + usedefault=True, + ), maxBranchingAngle=dict(argstr='--maxBranchingAngle %f', ), maxHalfFiberLength=dict(argstr='--maxHalfFiberLength %f', ), minBranchingAngle=dict(argstr='--minBranchingAngle %f', ), @@ -38,7 +44,10 @@ def test_UKFTractography_inputs(): recordTensors=dict(argstr='--recordTensors ', ), recordTrace=dict(argstr='--recordTrace ', ), seedFALimit=dict(argstr='--seedFALimit %f', ), - seedsFile=dict(argstr='--seedsFile %s', ), + seedsFile=dict( + argstr='--seedsFile %s', + usedefault=True, + ), seedsPerVoxel=dict(argstr='--seedsPerVoxel %d', ), stepLength=dict(argstr='--stepLength %f', ), storeGlyphs=dict(argstr='--storeGlyphs ', ), @@ -60,8 +69,8 @@ def test_UKFTractography_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_UKFTractography_outputs(): output_map = dict( - tracts=dict(), - tractsWithSecondTensor=dict(), + tracts=dict(usedefault=True, ), + tractsWithSecondTensor=dict(usedefault=True, ), ) outputs = UKFTractography.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py index b4756a9406..ec5ee174ed 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py @@ -6,23 +6,35 @@ def test_fiberprocess_inputs(): input_map = dict( args=dict(argstr='%s', ), - displacement_field=dict(argstr='--displacement_field %s', ), + displacement_field=dict( + argstr='--displacement_field %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, ), - fiber_file=dict(argstr='--fiber_file %s', ), + fiber_file=dict( + argstr='--fiber_file %s', + usedefault=True, + ), fiber_output=dict( argstr='--fiber_output %s', hash_files=False, ), fiber_radius=dict(argstr='--fiber_radius %f', ), - h_field=dict(argstr='--h_field %s', ), + h_field=dict( + argstr='--h_field %s', + usedefault=True, + ), index_space=dict(argstr='--index_space ', ), noDataChange=dict(argstr='--noDataChange ', ), no_warp=dict(argstr='--no_warp ', ), saveProperties=dict(argstr='--saveProperties ', ), - tensor_volume=dict(argstr='--tensor_volume %s', ), + tensor_volume=dict( + argstr='--tensor_volume %s', + usedefault=True, + ), verbose=dict(argstr='--verbose ', ), voxel_label=dict(argstr='--voxel_label %d', ), voxelize=dict( @@ -38,8 +50,8 @@ def test_fiberprocess_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_fiberprocess_outputs(): output_map = dict( - fiber_output=dict(), - voxelize=dict(), + fiber_output=dict(usedefault=True, ), + voxelize=dict(usedefault=True, ), ) outputs = fiberprocess.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py index d6f3a5cd50..a7df93f305 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py @@ -10,7 +10,10 @@ def test_fiberstats_inputs(): nohash=True, usedefault=True, ), - fiber_file=dict(argstr='--fiber_file %s', ), + fiber_file=dict( + argstr='--fiber_file %s', + usedefault=True, + ), verbose=dict(argstr='--verbose ', ), ) inputs = fiberstats.input_spec() diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py index 33e57c0ca3..085f99bc37 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py @@ -12,8 +12,14 @@ def test_fibertrack_inputs(): ), forbidden_label=dict(argstr='--forbidden_label %d', ), force=dict(argstr='--force ', ), - input_roi_file=dict(argstr='--input_roi_file %s', ), - input_tensor_file=dict(argstr='--input_tensor_file %s', ), + input_roi_file=dict( + argstr='--input_roi_file %s', + usedefault=True, + ), + input_tensor_file=dict( + argstr='--input_tensor_file %s', + usedefault=True, + ), max_angle=dict(argstr='--max_angle %f', ), min_fa=dict(argstr='--min_fa %f', ), output_fiber_file=dict( @@ -33,7 +39,7 @@ def test_fibertrack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_fibertrack_outputs(): - output_map = dict(output_fiber_file=dict(), ) + output_map = dict(output_fiber_file=dict(usedefault=True, ), ) outputs = fibertrack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py index cfbee7449c..bdbb02059d 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py @@ -10,7 +10,10 @@ def test_CannyEdge_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), lowerThreshold=dict(argstr='--lowerThreshold %f', ), outputVolume=dict( argstr='--outputVolume %s', @@ -25,7 +28,7 @@ def test_CannyEdge_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CannyEdge_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = CannyEdge.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py index b4196db823..7ce651cd47 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py @@ -13,9 +13,15 @@ def test_CannySegmentationLevelSetImageFilter_inputs(): nohash=True, usedefault=True, ), - initialModel=dict(argstr='--initialModel %s', ), + initialModel=dict( + argstr='--initialModel %s', + usedefault=True, + ), initialModelIsovalue=dict(argstr='--initialModelIsovalue %f', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), maxIterations=dict(argstr='--maxIterations %d', ), outputSpeedVolume=dict( argstr='--outputSpeedVolume %s', @@ -33,8 +39,8 @@ def test_CannySegmentationLevelSetImageFilter_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CannySegmentationLevelSetImageFilter_outputs(): output_map = dict( - outputSpeedVolume=dict(), - outputVolume=dict(), + outputSpeedVolume=dict(usedefault=True, ), + outputVolume=dict(usedefault=True, ), ) outputs = CannySegmentationLevelSetImageFilter.output_spec() diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py index 7945ec8ade..bfecea83e7 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py @@ -10,9 +10,15 @@ def test_DilateImage_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), + inputMaskVolume=dict( + argstr='--inputMaskVolume %s', + usedefault=True, + ), inputRadius=dict(argstr='--inputRadius %d', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -24,7 +30,7 @@ def test_DilateImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DilateImage_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = DilateImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py index 6bd6235e80..7af627bb4a 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py @@ -10,8 +10,14 @@ def test_DilateMask_inputs(): nohash=True, usedefault=True, ), - inputBinaryVolume=dict(argstr='--inputBinaryVolume %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputBinaryVolume=dict( + argstr='--inputBinaryVolume %s', + usedefault=True, + ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), lowerThreshold=dict(argstr='--lowerThreshold %f', ), outputVolume=dict( argstr='--outputVolume %s', @@ -25,7 +31,7 @@ def test_DilateMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DilateMask_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = DilateMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py index f7aaf722c4..9cd90e0621 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py @@ -10,8 +10,14 @@ def test_DistanceMaps_inputs(): nohash=True, usedefault=True, ), - inputLabelVolume=dict(argstr='--inputLabelVolume %s', ), - inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), + inputLabelVolume=dict( + argstr='--inputLabelVolume %s', + usedefault=True, + ), + inputMaskVolume=dict( + argstr='--inputMaskVolume %s', + usedefault=True, + ), inputTissueLabel=dict(argstr='--inputTissueLabel %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -24,7 +30,7 @@ def test_DistanceMaps_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DistanceMaps_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = DistanceMaps.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py index 320bb76b77..f5e98d3053 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py @@ -10,8 +10,14 @@ def test_DumpBinaryTrainingVectors_inputs(): nohash=True, usedefault=True, ), - inputHeaderFilename=dict(argstr='--inputHeaderFilename %s', ), - inputVectorFilename=dict(argstr='--inputVectorFilename %s', ), + inputHeaderFilename=dict( + argstr='--inputHeaderFilename %s', + usedefault=True, + ), + inputVectorFilename=dict( + argstr='--inputVectorFilename %s', + usedefault=True, + ), ) inputs = DumpBinaryTrainingVectors.input_spec() diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py index 9e096b0062..b9f280d795 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py @@ -10,9 +10,15 @@ def test_ErodeImage_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), + inputMaskVolume=dict( + argstr='--inputMaskVolume %s', + usedefault=True, + ), inputRadius=dict(argstr='--inputRadius %d', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -24,7 +30,7 @@ def test_ErodeImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ErodeImage_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = ErodeImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py index 539660f73b..1607a834d0 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py @@ -10,8 +10,14 @@ def test_FlippedDifference_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputMaskVolume=dict( + argstr='--inputMaskVolume %s', + usedefault=True, + ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -23,7 +29,7 @@ def test_FlippedDifference_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FlippedDifference_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = FlippedDifference.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py index 0a211f23d2..4226a4dce8 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py @@ -10,8 +10,14 @@ def test_GenerateBrainClippedImage_inputs(): nohash=True, usedefault=True, ), - inputImg=dict(argstr='--inputImg %s', ), - inputMsk=dict(argstr='--inputMsk %s', ), + inputImg=dict( + argstr='--inputImg %s', + usedefault=True, + ), + inputMsk=dict( + argstr='--inputMsk %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputFileName=dict( argstr='--outputFileName %s', @@ -24,7 +30,7 @@ def test_GenerateBrainClippedImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateBrainClippedImage_outputs(): - output_map = dict(outputFileName=dict(), ) + output_map = dict(outputFileName=dict(usedefault=True, ), ) outputs = GenerateBrainClippedImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py index 58d3f35c5a..a797efb90f 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py @@ -11,8 +11,14 @@ def test_GenerateSummedGradientImage_inputs(): nohash=True, usedefault=True, ), - inputVolume1=dict(argstr='--inputVolume1 %s', ), - inputVolume2=dict(argstr='--inputVolume2 %s', ), + inputVolume1=dict( + argstr='--inputVolume1 %s', + usedefault=True, + ), + inputVolume2=dict( + argstr='--inputVolume2 %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputFileName=dict( argstr='--outputFileName %s', @@ -25,7 +31,7 @@ def test_GenerateSummedGradientImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateSummedGradientImage_outputs(): - output_map = dict(outputFileName=dict(), ) + output_map = dict(outputFileName=dict(usedefault=True, ), ) outputs = GenerateSummedGradientImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py index 1348e61d4b..e85da77db7 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py @@ -10,7 +10,10 @@ def test_GenerateTestImage_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), lowerBoundOfOutputVolume=dict( argstr='--lowerBoundOfOutputVolume %f', ), outputVolume=dict( @@ -27,7 +30,7 @@ def test_GenerateTestImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateTestImage_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = GenerateTestImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py index 27ebb18d29..a4fe09a024 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py @@ -11,7 +11,10 @@ def test_GradientAnisotropicDiffusionImageFilter_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), numberOfIterations=dict(argstr='--numberOfIterations %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -25,7 +28,7 @@ def test_GradientAnisotropicDiffusionImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GradientAnisotropicDiffusionImageFilter_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = GradientAnisotropicDiffusionImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py index 9ad82598bb..2d97ec8100 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py @@ -12,9 +12,18 @@ def test_HammerAttributeCreator_inputs(): nohash=True, usedefault=True, ), - inputCSFVolume=dict(argstr='--inputCSFVolume %s', ), - inputGMVolume=dict(argstr='--inputGMVolume %s', ), - inputWMVolume=dict(argstr='--inputWMVolume %s', ), + inputCSFVolume=dict( + argstr='--inputCSFVolume %s', + usedefault=True, + ), + inputGMVolume=dict( + argstr='--inputGMVolume %s', + usedefault=True, + ), + inputWMVolume=dict( + argstr='--inputWMVolume %s', + usedefault=True, + ), outputVolumeBase=dict(argstr='--outputVolumeBase %s', ), ) inputs = HammerAttributeCreator.input_spec() diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py index c6b1ef20a9..81afd305dc 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py @@ -10,9 +10,15 @@ def test_NeighborhoodMean_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), + inputMaskVolume=dict( + argstr='--inputMaskVolume %s', + usedefault=True, + ), inputRadius=dict(argstr='--inputRadius %d', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -24,7 +30,7 @@ def test_NeighborhoodMean_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NeighborhoodMean_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = NeighborhoodMean.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py index 2c2b2d585f..b7b165cc97 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py @@ -10,9 +10,15 @@ def test_NeighborhoodMedian_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), + inputMaskVolume=dict( + argstr='--inputMaskVolume %s', + usedefault=True, + ), inputRadius=dict(argstr='--inputRadius %d', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -24,7 +30,7 @@ def test_NeighborhoodMedian_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NeighborhoodMedian_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = NeighborhoodMedian.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py index 75bb83315f..2ce9c6a0aa 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py @@ -23,7 +23,7 @@ def test_STAPLEAnalysis_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_STAPLEAnalysis_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = STAPLEAnalysis.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py index cd4b4a1af2..348018b3e1 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py @@ -11,7 +11,10 @@ def test_TextureFromNoiseImageFilter_inputs(): usedefault=True, ), inputRadius=dict(argstr='--inputRadius %d', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -23,7 +26,7 @@ def test_TextureFromNoiseImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TextureFromNoiseImageFilter_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = TextureFromNoiseImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py index 0ad523c7d0..2587252a3a 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py @@ -11,8 +11,14 @@ def test_TextureMeasureFilter_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputMaskVolume=dict( + argstr='--inputMaskVolume %s', + usedefault=True, + ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), insideROIValue=dict(argstr='--insideROIValue %f', ), outputFilename=dict( argstr='--outputFilename %s', @@ -25,7 +31,7 @@ def test_TextureMeasureFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TextureMeasureFilter_outputs(): - output_map = dict(outputFilename=dict(), ) + output_map = dict(outputFilename=dict(usedefault=True, ), ) outputs = TextureMeasureFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py index b84cda1fc3..af98570055 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py @@ -14,6 +14,7 @@ def test_UnbiasedNonLocalMeans_inputs(): inputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), outputVolume=dict( argstr='%s', @@ -37,7 +38,11 @@ def test_UnbiasedNonLocalMeans_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_UnbiasedNonLocalMeans_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = UnbiasedNonLocalMeans.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py index f9ff60cfd9..802c3d817b 100644 --- a/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py +++ b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py @@ -6,13 +6,19 @@ def test_scalartransform_inputs(): input_map = dict( args=dict(argstr='%s', ), - deformation=dict(argstr='--deformation %s', ), + deformation=dict( + argstr='--deformation %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, ), h_field=dict(argstr='--h_field ', ), - input_image=dict(argstr='--input_image %s', ), + input_image=dict( + argstr='--input_image %s', + usedefault=True, + ), interpolation=dict(argstr='--interpolation %s', ), invert=dict(argstr='--invert ', ), output_image=dict( @@ -31,8 +37,8 @@ def test_scalartransform_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_scalartransform_outputs(): output_map = dict( - output_image=dict(), - transformation=dict(), + output_image=dict(usedefault=True, ), + transformation=dict(usedefault=True, ), ) outputs = scalartransform.output_spec() diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py index c631f9b96e..5ac8f5f353 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py @@ -19,14 +19,25 @@ def test_BRAINSDemonWarp_inputs(): nohash=True, usedefault=True, ), - fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), - fixedVolume=dict(argstr='--fixedVolume %s', ), + fixedBinaryVolume=dict( + argstr='--fixedBinaryVolume %s', + usedefault=True, + ), + fixedVolume=dict( + argstr='--fixedVolume %s', + usedefault=True, + ), gradient_type=dict(argstr='--gradient_type %s', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), initializeWithDisplacementField=dict( - argstr='--initializeWithDisplacementField %s', ), - initializeWithTransform=dict(argstr='--initializeWithTransform %s', ), + argstr='--initializeWithDisplacementField %s', + usedefault=True, + ), + initializeWithTransform=dict( + argstr='--initializeWithTransform %s', + usedefault=True, + ), inputPixelType=dict(argstr='--inputPixelType %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), lowerThresholdForBOBF=dict(argstr='--lowerThresholdForBOBF %d', ), @@ -44,8 +55,14 @@ def test_BRAINSDemonWarp_inputs(): argstr='--minimumMovingPyramid %s', sep=',', ), - movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), - movingVolume=dict(argstr='--movingVolume %s', ), + movingBinaryVolume=dict( + argstr='--movingBinaryVolume %s', + usedefault=True, + ), + movingVolume=dict( + argstr='--movingVolume %s', + usedefault=True, + ), neighborhoodForBOBF=dict( argstr='--neighborhoodForBOBF %s', sep=',', @@ -92,9 +109,9 @@ def test_BRAINSDemonWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSDemonWarp_outputs(): output_map = dict( - outputCheckerboardVolume=dict(), - outputDisplacementFieldVolume=dict(), - outputVolume=dict(), + outputCheckerboardVolume=dict(usedefault=True, ), + outputDisplacementFieldVolume=dict(usedefault=True, ), + outputVolume=dict(usedefault=True, ), ) outputs = BRAINSDemonWarp.output_spec() diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py index 18059c4f57..5fde41901c 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py @@ -22,13 +22,25 @@ def test_BRAINSFit_inputs(): usedefault=True, ), failureExitCode=dict(argstr='--failureExitCode %d', ), - fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), - fixedVolume=dict(argstr='--fixedVolume %s', ), - fixedVolume2=dict(argstr='--fixedVolume2 %s', ), + fixedBinaryVolume=dict( + argstr='--fixedBinaryVolume %s', + usedefault=True, + ), + fixedVolume=dict( + argstr='--fixedVolume %s', + usedefault=True, + ), + fixedVolume2=dict( + argstr='--fixedVolume2 %s', + usedefault=True, + ), fixedVolumeTimeIndex=dict(argstr='--fixedVolumeTimeIndex %d', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), - initialTransform=dict(argstr='--initialTransform %s', ), + initialTransform=dict( + argstr='--initialTransform %s', + usedefault=True, + ), initializeRegistrationByCurrentGenericTransform=dict( argstr='--initializeRegistrationByCurrentGenericTransform ', ), initializeTransformMode=dict(argstr='--initializeTransformMode %s', ), @@ -59,9 +71,18 @@ def test_BRAINSFit_inputs(): argstr='--minimumStepLength %s', sep=',', ), - movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), - movingVolume=dict(argstr='--movingVolume %s', ), - movingVolume2=dict(argstr='--movingVolume2 %s', ), + movingBinaryVolume=dict( + argstr='--movingBinaryVolume %s', + usedefault=True, + ), + movingVolume=dict( + argstr='--movingVolume %s', + usedefault=True, + ), + movingVolume2=dict( + argstr='--movingVolume2 %s', + usedefault=True, + ), movingVolumeTimeIndex=dict(argstr='--movingVolumeTimeIndex %d', ), numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', ), numberOfIterations=dict( @@ -129,14 +150,14 @@ def test_BRAINSFit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSFit_outputs(): output_map = dict( - bsplineTransform=dict(), - linearTransform=dict(), - logFileReport=dict(), - outputFixedVolumeROI=dict(), - outputMovingVolumeROI=dict(), - outputTransform=dict(), - outputVolume=dict(), - strippedOutputTransform=dict(), + bsplineTransform=dict(usedefault=True, ), + linearTransform=dict(usedefault=True, ), + logFileReport=dict(usedefault=True, ), + outputFixedVolumeROI=dict(usedefault=True, ), + outputMovingVolumeROI=dict(usedefault=True, ), + outputTransform=dict(usedefault=True, ), + outputVolume=dict(usedefault=True, ), + strippedOutputTransform=dict(usedefault=True, ), ) outputs = BRAINSFit.output_spec() diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py index 98ec5f4ff3..38758ac585 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py @@ -7,7 +7,10 @@ def test_BRAINSResample_inputs(): input_map = dict( args=dict(argstr='%s', ), defaultValue=dict(argstr='--defaultValue %f', ), - deformationVolume=dict(argstr='--deformationVolume %s', ), + deformationVolume=dict( + argstr='--deformationVolume %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -16,7 +19,10 @@ def test_BRAINSResample_inputs(): argstr='--gridSpacing %s', sep=',', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), interpolationMode=dict(argstr='--interpolationMode %s', ), inverseTransform=dict(argstr='--inverseTransform ', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -25,8 +31,14 @@ def test_BRAINSResample_inputs(): hash_files=False, ), pixelType=dict(argstr='--pixelType %s', ), - referenceVolume=dict(argstr='--referenceVolume %s', ), - warpTransform=dict(argstr='--warpTransform %s', ), + referenceVolume=dict( + argstr='--referenceVolume %s', + usedefault=True, + ), + warpTransform=dict( + argstr='--warpTransform %s', + usedefault=True, + ), ) inputs = BRAINSResample.input_spec() @@ -34,7 +46,7 @@ def test_BRAINSResample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSResample_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = BRAINSResample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py index 4ce0d7159c..8326816fc9 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py @@ -10,7 +10,10 @@ def test_BRAINSResize_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -24,7 +27,7 @@ def test_BRAINSResize_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSResize_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = BRAINSResize.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py index 2a700eaac7..4d3b90959e 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py @@ -11,9 +11,15 @@ def test_BRAINSTransformFromFiducials_inputs(): usedefault=True, ), fixedLandmarks=dict(argstr='--fixedLandmarks %s...', ), - fixedLandmarksFile=dict(argstr='--fixedLandmarksFile %s', ), + fixedLandmarksFile=dict( + argstr='--fixedLandmarksFile %s', + usedefault=True, + ), movingLandmarks=dict(argstr='--movingLandmarks %s...', ), - movingLandmarksFile=dict(argstr='--movingLandmarksFile %s', ), + movingLandmarksFile=dict( + argstr='--movingLandmarksFile %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), saveTransform=dict( argstr='--saveTransform %s', @@ -27,7 +33,7 @@ def test_BRAINSTransformFromFiducials_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTransformFromFiducials_outputs(): - output_map = dict(saveTransform=dict(), ) + output_map = dict(saveTransform=dict(usedefault=True, ), ) outputs = BRAINSTransformFromFiducials.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py index b3255da1d3..17d6d7715d 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -19,14 +19,22 @@ def test_VBRAINSDemonWarp_inputs(): nohash=True, usedefault=True, ), - fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), + fixedBinaryVolume=dict( + argstr='--fixedBinaryVolume %s', + usedefault=True, + ), fixedVolume=dict(argstr='--fixedVolume %s...', ), gradient_type=dict(argstr='--gradient_type %s', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), initializeWithDisplacementField=dict( - argstr='--initializeWithDisplacementField %s', ), - initializeWithTransform=dict(argstr='--initializeWithTransform %s', ), + argstr='--initializeWithDisplacementField %s', + usedefault=True, + ), + initializeWithTransform=dict( + argstr='--initializeWithTransform %s', + usedefault=True, + ), inputPixelType=dict(argstr='--inputPixelType %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), lowerThresholdForBOBF=dict(argstr='--lowerThresholdForBOBF %d', ), @@ -44,7 +52,10 @@ def test_VBRAINSDemonWarp_inputs(): argstr='--minimumMovingPyramid %s', sep=',', ), - movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), + movingBinaryVolume=dict( + argstr='--movingBinaryVolume %s', + usedefault=True, + ), movingVolume=dict(argstr='--movingVolume %s...', ), neighborhoodForBOBF=dict( argstr='--neighborhoodForBOBF %s', @@ -96,9 +107,9 @@ def test_VBRAINSDemonWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_VBRAINSDemonWarp_outputs(): output_map = dict( - outputCheckerboardVolume=dict(), - outputDisplacementFieldVolume=dict(), - outputVolume=dict(), + outputCheckerboardVolume=dict(usedefault=True, ), + outputDisplacementFieldVolume=dict(usedefault=True, ), + outputVolume=dict(usedefault=True, ), ) outputs = VBRAINSDemonWarp.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py index 2d66884522..0f29a199f6 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py @@ -6,7 +6,10 @@ def test_BRAINSABC_inputs(): input_map = dict( args=dict(argstr='%s', ), - atlasDefinition=dict(argstr='--atlasDefinition %s', ), + atlasDefinition=dict( + argstr='--atlasDefinition %s', + usedefault=True, + ), atlasToSubjectInitialTransform=dict( argstr='--atlasToSubjectInitialTransform %s', hash_files=False, @@ -71,7 +74,10 @@ def test_BRAINSABC_inputs(): ), posteriorTemplate=dict(argstr='--posteriorTemplate %s', ), purePlugsThreshold=dict(argstr='--purePlugsThreshold %f', ), - restoreState=dict(argstr='--restoreState %s', ), + restoreState=dict( + argstr='--restoreState %s', + usedefault=True, + ), saveState=dict( argstr='--saveState %s', hash_files=False, @@ -88,14 +94,14 @@ def test_BRAINSABC_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSABC_outputs(): output_map = dict( - atlasToSubjectInitialTransform=dict(), - atlasToSubjectTransform=dict(), + atlasToSubjectInitialTransform=dict(usedefault=True, ), + atlasToSubjectTransform=dict(usedefault=True, ), implicitOutputs=dict(), - outputDir=dict(), - outputDirtyLabels=dict(), - outputLabels=dict(), + outputDir=dict(usedefault=True, ), + outputDirtyLabels=dict(usedefault=True, ), + outputLabels=dict(usedefault=True, ), outputVolumes=dict(), - saveState=dict(), + saveState=dict(usedefault=True, ), ) outputs = BRAINSABC.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py index 9b2d10061c..311b1df2a1 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py @@ -6,12 +6,24 @@ def test_BRAINSConstellationDetector_inputs(): input_map = dict( BackgroundFillValue=dict(argstr='--BackgroundFillValue %s', ), - LLSModel=dict(argstr='--LLSModel %s', ), + LLSModel=dict( + argstr='--LLSModel %s', + usedefault=True, + ), acLowerBound=dict(argstr='--acLowerBound %f', ), args=dict(argstr='%s', ), - atlasLandmarkWeights=dict(argstr='--atlasLandmarkWeights %s', ), - atlasLandmarks=dict(argstr='--atlasLandmarks %s', ), - atlasVolume=dict(argstr='--atlasVolume %s', ), + atlasLandmarkWeights=dict( + argstr='--atlasLandmarkWeights %s', + usedefault=True, + ), + atlasLandmarks=dict( + argstr='--atlasLandmarks %s', + usedefault=True, + ), + atlasVolume=dict( + argstr='--atlasVolume %s', + usedefault=True, + ), cutOutHeadInOutputVolume=dict(argstr='--cutOutHeadInOutputVolume ', ), debug=dict(argstr='--debug ', ), environ=dict( @@ -37,9 +49,18 @@ def test_BRAINSConstellationDetector_inputs(): sep=',', ), houghEyeDetectorMode=dict(argstr='--houghEyeDetectorMode %d', ), - inputLandmarksEMSP=dict(argstr='--inputLandmarksEMSP %s', ), - inputTemplateModel=dict(argstr='--inputTemplateModel %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputLandmarksEMSP=dict( + argstr='--inputLandmarksEMSP %s', + usedefault=True, + ), + inputTemplateModel=dict( + argstr='--inputTemplateModel %s', + usedefault=True, + ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), interpolationMode=dict(argstr='--interpolationMode %s', ), mspQualityLevel=dict(argstr='--mspQualityLevel %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -105,16 +126,16 @@ def test_BRAINSConstellationDetector_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSConstellationDetector_outputs(): output_map = dict( - outputLandmarksInACPCAlignedSpace=dict(), - outputLandmarksInInputSpace=dict(), - outputMRML=dict(), - outputResampledVolume=dict(), - outputTransform=dict(), - outputUntransformedClippedVolume=dict(), - outputVerificationScript=dict(), - outputVolume=dict(), - resultsDir=dict(), - writeBranded2DImage=dict(), + outputLandmarksInACPCAlignedSpace=dict(usedefault=True, ), + outputLandmarksInInputSpace=dict(usedefault=True, ), + outputMRML=dict(usedefault=True, ), + outputResampledVolume=dict(usedefault=True, ), + outputTransform=dict(usedefault=True, ), + outputUntransformedClippedVolume=dict(usedefault=True, ), + outputVerificationScript=dict(usedefault=True, ), + outputVolume=dict(usedefault=True, ), + resultsDir=dict(usedefault=True, ), + writeBranded2DImage=dict(usedefault=True, ), ) outputs = BRAINSConstellationDetector.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py index 9f2b00c311..cde17297dc 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py @@ -24,7 +24,10 @@ def test_BRAINSCreateLabelMapFromProbabilityMaps_inputs(): ), inclusionThreshold=dict(argstr='--inclusionThreshold %f', ), inputProbabilityVolume=dict(argstr='--inputProbabilityVolume %s...', ), - nonAirRegionMask=dict(argstr='--nonAirRegionMask %s', ), + nonAirRegionMask=dict( + argstr='--nonAirRegionMask %s', + usedefault=True, + ), priorLabelCodes=dict( argstr='--priorLabelCodes %s', sep=',', @@ -37,8 +40,8 @@ def test_BRAINSCreateLabelMapFromProbabilityMaps_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSCreateLabelMapFromProbabilityMaps_outputs(): output_map = dict( - cleanLabelVolume=dict(), - dirtyLabelVolume=dict(), + cleanLabelVolume=dict(usedefault=True, ), + dirtyLabelVolume=dict(usedefault=True, ), ) outputs = BRAINSCreateLabelMapFromProbabilityMaps.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py index 9d66d4a463..f14fc12f3e 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py @@ -19,10 +19,15 @@ def test_BRAINSCut_inputs(): histogramEqualization=dict(argstr='--histogramEqualization ', ), method=dict(argstr='--method %s', ), modelConfigurationFilename=dict( - argstr='--modelConfigurationFilename %s', ), + argstr='--modelConfigurationFilename %s', + usedefault=True, + ), modelFilename=dict(argstr='--modelFilename %s', ), multiStructureThreshold=dict(argstr='--multiStructureThreshold ', ), - netConfiguration=dict(argstr='--netConfiguration %s', ), + netConfiguration=dict( + argstr='--netConfiguration %s', + usedefault=True, + ), numberOfTrees=dict(argstr='--numberOfTrees %d', ), randomTreeDepth=dict(argstr='--randomTreeDepth %d', ), trainModel=dict(argstr='--trainModel ', ), diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py index 826ec19f0e..f4495cbda0 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py @@ -10,7 +10,10 @@ def test_BRAINSMultiSTAPLE_inputs(): nohash=True, usedefault=True, ), - inputCompositeT1Volume=dict(argstr='--inputCompositeT1Volume %s', ), + inputCompositeT1Volume=dict( + argstr='--inputCompositeT1Volume %s', + usedefault=True, + ), inputLabelVolume=dict(argstr='--inputLabelVolume %s...', ), inputTransform=dict(argstr='--inputTransform %s...', ), labelForUndecidedPixels=dict(argstr='--labelForUndecidedPixels %d', ), @@ -32,8 +35,8 @@ def test_BRAINSMultiSTAPLE_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSMultiSTAPLE_outputs(): output_map = dict( - outputConfusionMatrix=dict(), - outputMultiSTAPLE=dict(), + outputConfusionMatrix=dict(usedefault=True, ), + outputMultiSTAPLE=dict(usedefault=True, ), ) outputs = BRAINSMultiSTAPLE.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py index 3e70b75883..f222d7f4ae 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -13,7 +13,10 @@ def test_BRAINSROIAuto_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), maskOutput=dict(argstr='--maskOutput ', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), otsuPercentileThreshold=dict(argstr='--otsuPercentileThreshold %f', ), @@ -36,8 +39,8 @@ def test_BRAINSROIAuto_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSROIAuto_outputs(): output_map = dict( - outputROIMaskVolume=dict(), - outputVolume=dict(), + outputROIMaskVolume=dict(usedefault=True, ), + outputVolume=dict(usedefault=True, ), ) outputs = BRAINSROIAuto.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py index d71e7003ff..97100404e1 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py @@ -10,7 +10,10 @@ def test_BinaryMaskEditorBasedOnLandmarks_inputs(): nohash=True, usedefault=True, ), - inputBinaryVolume=dict(argstr='--inputBinaryVolume %s', ), + inputBinaryVolume=dict( + argstr='--inputBinaryVolume %s', + usedefault=True, + ), inputLandmarkNames=dict( argstr='--inputLandmarkNames %s', sep=',', @@ -19,7 +22,10 @@ def test_BinaryMaskEditorBasedOnLandmarks_inputs(): argstr='--inputLandmarkNamesForObliquePlane %s', sep=',', ), - inputLandmarksFilename=dict(argstr='--inputLandmarksFilename %s', ), + inputLandmarksFilename=dict( + argstr='--inputLandmarksFilename %s', + usedefault=True, + ), outputBinaryVolume=dict( argstr='--outputBinaryVolume %s', hash_files=False, @@ -39,7 +45,7 @@ def test_BinaryMaskEditorBasedOnLandmarks_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinaryMaskEditorBasedOnLandmarks_outputs(): - output_map = dict(outputBinaryVolume=dict(), ) + output_map = dict(outputBinaryVolume=dict(usedefault=True, ), ) outputs = BinaryMaskEditorBasedOnLandmarks.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py index 2e099b4f56..d5a05c0a97 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py @@ -12,7 +12,10 @@ def test_ESLR_inputs(): usedefault=True, ), high=dict(argstr='--high %d', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), low=dict(argstr='--low %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), openingSize=dict(argstr='--openingSize %d', ), @@ -29,7 +32,7 @@ def test_ESLR_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ESLR_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = ESLR.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py index c00b0cc36f..704f89bd58 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py @@ -10,8 +10,14 @@ def test_DWICompare_inputs(): nohash=True, usedefault=True, ), - inputVolume1=dict(argstr='--inputVolume1 %s', ), - inputVolume2=dict(argstr='--inputVolume2 %s', ), + inputVolume1=dict( + argstr='--inputVolume1 %s', + usedefault=True, + ), + inputVolume2=dict( + argstr='--inputVolume2 %s', + usedefault=True, + ), ) inputs = DWICompare.input_spec() diff --git a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py index e515bc613c..239b092e33 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py @@ -11,8 +11,14 @@ def test_DWISimpleCompare_inputs(): nohash=True, usedefault=True, ), - inputVolume1=dict(argstr='--inputVolume1 %s', ), - inputVolume2=dict(argstr='--inputVolume2 %s', ), + inputVolume1=dict( + argstr='--inputVolume1 %s', + usedefault=True, + ), + inputVolume2=dict( + argstr='--inputVolume2 %s', + usedefault=True, + ), ) inputs = DWISimpleCompare.input_spec() diff --git a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py index 63f45831af..f5a881004b 100644 --- a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py +++ b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py @@ -10,7 +10,10 @@ def test_GenerateCsfClippedFromClassifiedImage_inputs(): nohash=True, usedefault=True, ), - inputCassifiedVolume=dict(argstr='--inputCassifiedVolume %s', ), + inputCassifiedVolume=dict( + argstr='--inputCassifiedVolume %s', + usedefault=True, + ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -22,7 +25,7 @@ def test_GenerateCsfClippedFromClassifiedImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateCsfClippedFromClassifiedImage_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = GenerateCsfClippedFromClassifiedImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py index 27b65a4eba..d1ab2a10a5 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py @@ -15,7 +15,10 @@ def test_BRAINSAlignMSP_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), interpolationMode=dict(argstr='--interpolationMode %s', ), mspQualityLevel=dict(argstr='--mspQualityLevel %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -40,8 +43,8 @@ def test_BRAINSAlignMSP_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSAlignMSP_outputs(): output_map = dict( - OutputresampleMSP=dict(), - resultsDir=dict(), + OutputresampleMSP=dict(usedefault=True, ), + resultsDir=dict(usedefault=True, ), ) outputs = BRAINSAlignMSP.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py index 7a0528f201..2479c5f233 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py @@ -12,7 +12,10 @@ def test_BRAINSClipInferior_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -25,7 +28,7 @@ def test_BRAINSClipInferior_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSClipInferior_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = BRAINSClipInferior.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py index a124ad60d9..7c29d75f85 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py @@ -11,7 +11,10 @@ def test_BRAINSConstellationModeler_inputs(): nohash=True, usedefault=True, ), - inputTrainingList=dict(argstr='--inputTrainingList %s', ), + inputTrainingList=dict( + argstr='--inputTrainingList %s', + usedefault=True, + ), mspQualityLevel=dict(argstr='--mspQualityLevel %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), optimizedLandmarksFilenameExtender=dict( @@ -42,8 +45,8 @@ def test_BRAINSConstellationModeler_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSConstellationModeler_outputs(): output_map = dict( - outputModel=dict(), - resultsDir=dict(), + outputModel=dict(usedefault=True, ), + resultsDir=dict(usedefault=True, ), ) outputs = BRAINSConstellationModeler.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py index 9df3c8b8d6..0339ae0bea 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py @@ -11,7 +11,10 @@ def test_BRAINSEyeDetector_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -24,7 +27,7 @@ def test_BRAINSEyeDetector_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSEyeDetector_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = BRAINSEyeDetector.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py index bc3807f9f8..fafa298559 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py @@ -10,7 +10,10 @@ def test_BRAINSInitializedControlPoints_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputLandmarksFile=dict(argstr='--outputLandmarksFile %s', ), outputVolume=dict( @@ -32,7 +35,7 @@ def test_BRAINSInitializedControlPoints_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSInitializedControlPoints_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = BRAINSInitializedControlPoints.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py index 2456b8fb4d..7804d04d92 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py @@ -11,10 +11,17 @@ def test_BRAINSLandmarkInitializer_inputs(): usedefault=True, ), inputFixedLandmarkFilename=dict( - argstr='--inputFixedLandmarkFilename %s', ), + argstr='--inputFixedLandmarkFilename %s', + usedefault=True, + ), inputMovingLandmarkFilename=dict( - argstr='--inputMovingLandmarkFilename %s', ), - inputWeightFilename=dict(argstr='--inputWeightFilename %s', ), + argstr='--inputMovingLandmarkFilename %s', + usedefault=True, + ), + inputWeightFilename=dict( + argstr='--inputWeightFilename %s', + usedefault=True, + ), outputTransformFilename=dict( argstr='--outputTransformFilename %s', hash_files=False, @@ -26,7 +33,7 @@ def test_BRAINSLandmarkInitializer_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSLandmarkInitializer_outputs(): - output_map = dict(outputTransformFilename=dict(), ) + output_map = dict(outputTransformFilename=dict(usedefault=True, ), ) outputs = BRAINSLandmarkInitializer.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py index b6b83baa12..99d7fa217b 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py @@ -10,7 +10,10 @@ def test_BRAINSLinearModelerEPCA_inputs(): nohash=True, usedefault=True, ), - inputTrainingList=dict(argstr='--inputTrainingList %s', ), + inputTrainingList=dict( + argstr='--inputTrainingList %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), ) inputs = BRAINSLinearModelerEPCA.input_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py index 262d948029..7b75451d10 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py @@ -10,10 +10,22 @@ def test_BRAINSLmkTransform_inputs(): nohash=True, usedefault=True, ), - inputFixedLandmarks=dict(argstr='--inputFixedLandmarks %s', ), - inputMovingLandmarks=dict(argstr='--inputMovingLandmarks %s', ), - inputMovingVolume=dict(argstr='--inputMovingVolume %s', ), - inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), + inputFixedLandmarks=dict( + argstr='--inputFixedLandmarks %s', + usedefault=True, + ), + inputMovingLandmarks=dict( + argstr='--inputMovingLandmarks %s', + usedefault=True, + ), + inputMovingVolume=dict( + argstr='--inputMovingVolume %s', + usedefault=True, + ), + inputReferenceVolume=dict( + argstr='--inputReferenceVolume %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputAffineTransform=dict( argstr='--outputAffineTransform %s', @@ -31,8 +43,8 @@ def test_BRAINSLmkTransform_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSLmkTransform_outputs(): output_map = dict( - outputAffineTransform=dict(), - outputResampledVolume=dict(), + outputAffineTransform=dict(usedefault=True, ), + outputResampledVolume=dict(usedefault=True, ), ) outputs = BRAINSLmkTransform.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py index 9627258bcf..1797a4ab8b 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py @@ -20,9 +20,18 @@ def test_BRAINSMush_inputs(): nohash=True, usedefault=True, ), - inputFirstVolume=dict(argstr='--inputFirstVolume %s', ), - inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), - inputSecondVolume=dict(argstr='--inputSecondVolume %s', ), + inputFirstVolume=dict( + argstr='--inputFirstVolume %s', + usedefault=True, + ), + inputMaskVolume=dict( + argstr='--inputMaskVolume %s', + usedefault=True, + ), + inputSecondVolume=dict( + argstr='--inputSecondVolume %s', + usedefault=True, + ), lowerThresholdFactor=dict(argstr='--lowerThresholdFactor %f', ), lowerThresholdFactorPre=dict(argstr='--lowerThresholdFactorPre %f', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -52,9 +61,9 @@ def test_BRAINSMush_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSMush_outputs(): output_map = dict( - outputMask=dict(), - outputVolume=dict(), - outputWeightsFile=dict(), + outputMask=dict(usedefault=True, ), + outputVolume=dict(usedefault=True, ), + outputWeightsFile=dict(usedefault=True, ), ) outputs = BRAINSMush.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py index 1b803956e7..146ae01a5b 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py @@ -39,7 +39,7 @@ def test_BRAINSSnapShotWriter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSSnapShotWriter_outputs(): - output_map = dict(outputFilename=dict(), ) + output_map = dict(outputFilename=dict(usedefault=True, ), ) outputs = BRAINSSnapShotWriter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py index c6d10736d7..5a5bba170d 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py @@ -14,14 +14,20 @@ def test_BRAINSTransformConvert_inputs(): nohash=True, usedefault=True, ), - inputTransform=dict(argstr='--inputTransform %s', ), + inputTransform=dict( + argstr='--inputTransform %s', + usedefault=True, + ), outputPrecisionType=dict(argstr='--outputPrecisionType %s', ), outputTransform=dict( argstr='--outputTransform %s', hash_files=False, ), outputTransformType=dict(argstr='--outputTransformType %s', ), - referenceVolume=dict(argstr='--referenceVolume %s', ), + referenceVolume=dict( + argstr='--referenceVolume %s', + usedefault=True, + ), ) inputs = BRAINSTransformConvert.input_spec() @@ -30,8 +36,8 @@ def test_BRAINSTransformConvert_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTransformConvert_outputs(): output_map = dict( - displacementVolume=dict(), - outputTransform=dict(), + displacementVolume=dict(usedefault=True, ), + outputTransform=dict(usedefault=True, ), ) outputs = BRAINSTransformConvert.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py index d2f3b74140..8f0d95f919 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py @@ -14,7 +14,10 @@ def test_BRAINSTrimForegroundInDirection_inputs(): usedefault=True, ), headSizeLimit=dict(argstr='--headSizeLimit %f', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), otsuPercentileThreshold=dict(argstr='--otsuPercentileThreshold %f', ), outputVolume=dict( @@ -28,7 +31,7 @@ def test_BRAINSTrimForegroundInDirection_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTrimForegroundInDirection_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = BRAINSTrimForegroundInDirection.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py index 46924bf180..b7041c94ea 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py @@ -40,8 +40,14 @@ def test_FindCenterOfBrain_inputs(): generateDebugImages=dict(argstr='--generateDebugImages ', ), headSizeEstimate=dict(argstr='--headSizeEstimate %f', ), headSizeLimit=dict(argstr='--headSizeLimit %f', ), - imageMask=dict(argstr='--imageMask %s', ), - inputVolume=dict(argstr='--inputVolume %s', ), + imageMask=dict( + argstr='--imageMask %s', + usedefault=True, + ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), maximize=dict(argstr='--maximize ', ), otsuPercentileThreshold=dict(argstr='--otsuPercentileThreshold %f', ), ) @@ -52,12 +58,12 @@ def test_FindCenterOfBrain_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FindCenterOfBrain_outputs(): output_map = dict( - clippedImageMask=dict(), - debugAfterGridComputationsForegroundImage=dict(), - debugClippedImageMask=dict(), - debugDistanceImage=dict(), - debugGridImage=dict(), - debugTrimmedImage=dict(), + clippedImageMask=dict(usedefault=True, ), + debugAfterGridComputationsForegroundImage=dict(usedefault=True, ), + debugClippedImageMask=dict(usedefault=True, ), + debugDistanceImage=dict(usedefault=True, ), + debugGridImage=dict(usedefault=True, ), + debugTrimmedImage=dict(usedefault=True, ), ) outputs = FindCenterOfBrain.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py index 9087d6667b..f1de4189fa 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py @@ -23,7 +23,7 @@ def test_GenerateLabelMapFromProbabilityMap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateLabelMapFromProbabilityMap_outputs(): - output_map = dict(outputLabelVolume=dict(), ) + output_map = dict(outputLabelVolume=dict(usedefault=True, ), ) outputs = GenerateLabelMapFromProbabilityMap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py index f5372a240e..6d40209c22 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py @@ -10,10 +10,22 @@ def test_ImageRegionPlotter_inputs(): nohash=True, usedefault=True, ), - inputBinaryROIVolume=dict(argstr='--inputBinaryROIVolume %s', ), - inputLabelVolume=dict(argstr='--inputLabelVolume %s', ), - inputVolume1=dict(argstr='--inputVolume1 %s', ), - inputVolume2=dict(argstr='--inputVolume2 %s', ), + inputBinaryROIVolume=dict( + argstr='--inputBinaryROIVolume %s', + usedefault=True, + ), + inputLabelVolume=dict( + argstr='--inputLabelVolume %s', + usedefault=True, + ), + inputVolume1=dict( + argstr='--inputVolume1 %s', + usedefault=True, + ), + inputVolume2=dict( + argstr='--inputVolume2 %s', + usedefault=True, + ), numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', ), outputJointHistogramData=dict( argstr='--outputJointHistogramData %s', ), diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py index daf6d5634f..995a0a6a29 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py @@ -10,10 +10,22 @@ def test_JointHistogram_inputs(): nohash=True, usedefault=True, ), - inputMaskVolumeInXAxis=dict(argstr='--inputMaskVolumeInXAxis %s', ), - inputMaskVolumeInYAxis=dict(argstr='--inputMaskVolumeInYAxis %s', ), - inputVolumeInXAxis=dict(argstr='--inputVolumeInXAxis %s', ), - inputVolumeInYAxis=dict(argstr='--inputVolumeInYAxis %s', ), + inputMaskVolumeInXAxis=dict( + argstr='--inputMaskVolumeInXAxis %s', + usedefault=True, + ), + inputMaskVolumeInYAxis=dict( + argstr='--inputMaskVolumeInYAxis %s', + usedefault=True, + ), + inputVolumeInXAxis=dict( + argstr='--inputVolumeInXAxis %s', + usedefault=True, + ), + inputVolumeInYAxis=dict( + argstr='--inputVolumeInYAxis %s', + usedefault=True, + ), outputJointHistogramImage=dict( argstr='--outputJointHistogramImage %s', ), verbose=dict(argstr='--verbose ', ), diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py index 7bea38e2f1..cfd3390db5 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py @@ -10,7 +10,10 @@ def test_ShuffleVectorsModule_inputs(): nohash=True, usedefault=True, ), - inputVectorFileBaseName=dict(argstr='--inputVectorFileBaseName %s', ), + inputVectorFileBaseName=dict( + argstr='--inputVectorFileBaseName %s', + usedefault=True, + ), outputVectorFileBaseName=dict( argstr='--outputVectorFileBaseName %s', hash_files=False, @@ -23,7 +26,7 @@ def test_ShuffleVectorsModule_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ShuffleVectorsModule_outputs(): - output_map = dict(outputVectorFileBaseName=dict(), ) + output_map = dict(outputVectorFileBaseName=dict(usedefault=True, ), ) outputs = ShuffleVectorsModule.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py b/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py index 32e6ce65cd..91d5424458 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py @@ -11,7 +11,10 @@ def test_fcsv_to_hdf5_inputs(): usedefault=True, ), landmarkGlobPattern=dict(argstr='--landmarkGlobPattern %s', ), - landmarkTypesList=dict(argstr='--landmarkTypesList %s', ), + landmarkTypesList=dict( + argstr='--landmarkTypesList %s', + usedefault=True, + ), landmarksInformationFile=dict( argstr='--landmarksInformationFile %s', hash_files=False, @@ -30,8 +33,8 @@ def test_fcsv_to_hdf5_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_fcsv_to_hdf5_outputs(): output_map = dict( - landmarksInformationFile=dict(), - modelFile=dict(), + landmarksInformationFile=dict(usedefault=True, ), + modelFile=dict(usedefault=True, ), ) outputs = fcsv_to_hdf5.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py index 196b09b304..746380b899 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py @@ -10,7 +10,10 @@ def test_insertMidACPCpoint_inputs(): nohash=True, usedefault=True, ), - inputLandmarkFile=dict(argstr='--inputLandmarkFile %s', ), + inputLandmarkFile=dict( + argstr='--inputLandmarkFile %s', + usedefault=True, + ), outputLandmarkFile=dict( argstr='--outputLandmarkFile %s', hash_files=False, @@ -22,7 +25,7 @@ def test_insertMidACPCpoint_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_insertMidACPCpoint_outputs(): - output_map = dict(outputLandmarkFile=dict(), ) + output_map = dict(outputLandmarkFile=dict(usedefault=True, ), ) outputs = insertMidACPCpoint.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py index 151a2c7b3a..e7ed3ecd59 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py @@ -10,7 +10,10 @@ def test_landmarksConstellationAligner_inputs(): nohash=True, usedefault=True, ), - inputLandmarksPaired=dict(argstr='--inputLandmarksPaired %s', ), + inputLandmarksPaired=dict( + argstr='--inputLandmarksPaired %s', + usedefault=True, + ), outputLandmarksPaired=dict( argstr='--outputLandmarksPaired %s', hash_files=False, @@ -22,7 +25,7 @@ def test_landmarksConstellationAligner_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_landmarksConstellationAligner_outputs(): - output_map = dict(outputLandmarksPaired=dict(), ) + output_map = dict(outputLandmarksPaired=dict(usedefault=True, ), ) outputs = landmarksConstellationAligner.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py index 0bcd747d36..afe12a43d3 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py @@ -5,14 +5,23 @@ def test_landmarksConstellationWeights_inputs(): input_map = dict( - LLSModel=dict(argstr='--LLSModel %s', ), + LLSModel=dict( + argstr='--LLSModel %s', + usedefault=True, + ), args=dict(argstr='%s', ), environ=dict( nohash=True, usedefault=True, ), - inputTemplateModel=dict(argstr='--inputTemplateModel %s', ), - inputTrainingList=dict(argstr='--inputTrainingList %s', ), + inputTemplateModel=dict( + argstr='--inputTemplateModel %s', + usedefault=True, + ), + inputTrainingList=dict( + argstr='--inputTrainingList %s', + usedefault=True, + ), outputWeightsList=dict( argstr='--outputWeightsList %s', hash_files=False, @@ -24,7 +33,7 @@ def test_landmarksConstellationWeights_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_landmarksConstellationWeights_outputs(): - output_map = dict(outputWeightsList=dict(), ) + output_map = dict(outputWeightsList=dict(usedefault=True, ), ) outputs = landmarksConstellationWeights.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py index c8d5df2ba2..2f86ec6bdf 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py @@ -13,6 +13,7 @@ def test_DTIexport_inputs(): inputTensor=dict( argstr='%s', position=-2, + usedefault=True, ), outputFile=dict( argstr='%s', @@ -26,7 +27,11 @@ def test_DTIexport_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DTIexport_outputs(): - output_map = dict(outputFile=dict(position=-1, ), ) + output_map = dict( + outputFile=dict( + position=-1, + usedefault=True, + ), ) outputs = DTIexport.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py index ec1d66bc0b..04381b63b4 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py @@ -13,6 +13,7 @@ def test_DTIimport_inputs(): inputFile=dict( argstr='%s', position=-2, + usedefault=True, ), outputTensor=dict( argstr='%s', @@ -27,7 +28,11 @@ def test_DTIimport_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DTIimport_outputs(): - output_map = dict(outputTensor=dict(position=-1, ), ) + output_map = dict( + outputTensor=dict( + position=-1, + usedefault=True, + ), ) outputs = DTIimport.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py index a2caa2f633..99e13e5df2 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py @@ -14,6 +14,7 @@ def test_DWIJointRicianLMMSEFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), ng=dict(argstr='--ng %d', ), outputVolume=dict( @@ -36,7 +37,11 @@ def test_DWIJointRicianLMMSEFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWIJointRicianLMMSEFilter_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = DWIJointRicianLMMSEFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py index 7eff851562..64cc981a5c 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py @@ -15,6 +15,7 @@ def test_DWIRicianLMMSEFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), iter=dict(argstr='--iter %d', ), maxnstd=dict(argstr='--maxnstd %d', ), @@ -42,7 +43,11 @@ def test_DWIRicianLMMSEFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWIRicianLMMSEFilter_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = DWIRicianLMMSEFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py index 217f91edf0..67cfdd61fc 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py @@ -14,8 +14,12 @@ def test_DWIToDTIEstimation_inputs(): inputVolume=dict( argstr='%s', position=-3, + usedefault=True, + ), + mask=dict( + argstr='--mask %s', + usedefault=True, ), - mask=dict(argstr='--mask %s', ), outputBaseline=dict( argstr='%s', hash_files=False, @@ -35,8 +39,14 @@ def test_DWIToDTIEstimation_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DWIToDTIEstimation_outputs(): output_map = dict( - outputBaseline=dict(position=-1, ), - outputTensor=dict(position=-2, ), + outputBaseline=dict( + position=-1, + usedefault=True, + ), + outputTensor=dict( + position=-2, + usedefault=True, + ), ) outputs = DWIToDTIEstimation.output_spec() diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py index b75989c349..5a7676b5c2 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py @@ -14,6 +14,7 @@ def test_DiffusionTensorScalarMeasurements_inputs(): inputVolume=dict( argstr='%s', position=-3, + usedefault=True, ), outputScalar=dict( argstr='%s', @@ -27,7 +28,11 @@ def test_DiffusionTensorScalarMeasurements_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DiffusionTensorScalarMeasurements_outputs(): - output_map = dict(outputScalar=dict(position=-1, ), ) + output_map = dict( + outputScalar=dict( + position=-1, + usedefault=True, + ), ) outputs = DiffusionTensorScalarMeasurements.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py index 5e8c39a4ac..56c18cf862 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py @@ -13,6 +13,7 @@ def test_DiffusionWeightedVolumeMasking_inputs(): inputVolume=dict( argstr='%s', position=-4, + usedefault=True, ), otsuomegathreshold=dict(argstr='--otsuomegathreshold %f', ), outputBaseline=dict( @@ -34,8 +35,14 @@ def test_DiffusionWeightedVolumeMasking_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DiffusionWeightedVolumeMasking_outputs(): output_map = dict( - outputBaseline=dict(position=-2, ), - thresholdMask=dict(position=-1, ), + outputBaseline=dict( + position=-2, + usedefault=True, + ), + thresholdMask=dict( + position=-1, + usedefault=True, + ), ) outputs = DiffusionWeightedVolumeMasking.output_spec() diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py index 30860d9da0..2789f95aa6 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py @@ -7,11 +7,17 @@ def test_ResampleDTIVolume_inputs(): input_map = dict( Inverse_ITK_Transformation=dict( argstr='--Inverse_ITK_Transformation ', ), - Reference=dict(argstr='--Reference %s', ), + Reference=dict( + argstr='--Reference %s', + usedefault=True, + ), args=dict(argstr='%s', ), centered_transform=dict(argstr='--centered_transform ', ), correction=dict(argstr='--correction %s', ), - defField=dict(argstr='--defField %s', ), + defField=dict( + argstr='--defField %s', + usedefault=True, + ), default_pixel_value=dict(argstr='--default_pixel_value %f', ), direction_matrix=dict( argstr='--direction_matrix %s', @@ -26,6 +32,7 @@ def test_ResampleDTIVolume_inputs(): inputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), interpolation=dict(argstr='--interpolation %s', ), notbulk=dict(argstr='--notbulk ', ), @@ -54,7 +61,10 @@ def test_ResampleDTIVolume_inputs(): ), transform_order=dict(argstr='--transform_order %s', ), transform_tensor_method=dict(argstr='--transform_tensor_method %s', ), - transformationFile=dict(argstr='--transformationFile %s', ), + transformationFile=dict( + argstr='--transformationFile %s', + usedefault=True, + ), window_function=dict(argstr='--window_function %s', ), ) inputs = ResampleDTIVolume.input_spec() @@ -63,7 +73,11 @@ def test_ResampleDTIVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ResampleDTIVolume_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = ResampleDTIVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py index 31fb7d5c0d..737e1cea44 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py @@ -8,6 +8,7 @@ def test_TractographyLabelMapSeeding_inputs(): InputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), OutputFibers=dict( argstr='%s', @@ -20,7 +21,10 @@ def test_TractographyLabelMapSeeding_inputs(): nohash=True, usedefault=True, ), - inputroi=dict(argstr='--inputroi %s', ), + inputroi=dict( + argstr='--inputroi %s', + usedefault=True, + ), integrationsteplength=dict(argstr='--integrationsteplength %f', ), label=dict(argstr='--label %d', ), maximumlength=dict(argstr='--maximumlength %f', ), @@ -45,8 +49,11 @@ def test_TractographyLabelMapSeeding_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TractographyLabelMapSeeding_outputs(): output_map = dict( - OutputFibers=dict(position=-1, ), - outputdirectory=dict(), + OutputFibers=dict( + position=-1, + usedefault=True, + ), + outputdirectory=dict(usedefault=True, ), ) outputs = TractographyLabelMapSeeding.output_spec() diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py index 9f2209c1eb..0f4dedb338 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py @@ -13,10 +13,12 @@ def test_AddScalarVolumes_inputs(): inputVolume1=dict( argstr='%s', position=-3, + usedefault=True, ), inputVolume2=dict( argstr='%s', position=-2, + usedefault=True, ), order=dict(argstr='--order %s', ), outputVolume=dict( @@ -31,7 +33,11 @@ def test_AddScalarVolumes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AddScalarVolumes_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = AddScalarVolumes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py index a659aa47f7..265d763858 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py @@ -8,6 +8,7 @@ def test_CastScalarVolume_inputs(): InputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), OutputVolume=dict( argstr='%s', @@ -27,7 +28,11 @@ def test_CastScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CastScalarVolume_outputs(): - output_map = dict(OutputVolume=dict(position=-1, ), ) + output_map = dict( + OutputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = CastScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py index ae662cf2ba..7937c9b217 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py @@ -17,10 +17,12 @@ def test_CheckerBoardFilter_inputs(): inputVolume1=dict( argstr='%s', position=-3, + usedefault=True, ), inputVolume2=dict( argstr='%s', position=-2, + usedefault=True, ), outputVolume=dict( argstr='%s', @@ -34,7 +36,11 @@ def test_CheckerBoardFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CheckerBoardFilter_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = CheckerBoardFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py index 5613eb0c4c..ae6aca11c0 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py @@ -14,6 +14,7 @@ def test_CurvatureAnisotropicDiffusion_inputs(): inputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), iterations=dict(argstr='--iterations %d', ), outputVolume=dict( @@ -29,7 +30,11 @@ def test_CurvatureAnisotropicDiffusion_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CurvatureAnisotropicDiffusion_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = CurvatureAnisotropicDiffusion.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py index 5db6c65c7e..924fcd5665 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py @@ -8,6 +8,7 @@ def test_ExtractSkeleton_inputs(): InputImageFileName=dict( argstr='%s', position=-2, + usedefault=True, ), OutputImageFileName=dict( argstr='%s', @@ -30,7 +31,11 @@ def test_ExtractSkeleton_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ExtractSkeleton_outputs(): - output_map = dict(OutputImageFileName=dict(position=-1, ), ) + output_map = dict( + OutputImageFileName=dict( + position=-1, + usedefault=True, + ), ) outputs = ExtractSkeleton.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py index ff46d6d308..d95490e3f8 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py @@ -13,6 +13,7 @@ def test_GaussianBlurImageFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), outputVolume=dict( argstr='%s', @@ -27,7 +28,11 @@ def test_GaussianBlurImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GaussianBlurImageFilter_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = GaussianBlurImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py index 8ec7dbb156..0cda5dfa38 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py @@ -14,6 +14,7 @@ def test_GradientAnisotropicDiffusion_inputs(): inputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), iterations=dict(argstr='--iterations %d', ), outputVolume=dict( @@ -29,7 +30,11 @@ def test_GradientAnisotropicDiffusion_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GradientAnisotropicDiffusion_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = GradientAnisotropicDiffusion.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py index 062a23c293..6565bb7b21 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py @@ -13,6 +13,7 @@ def test_GrayscaleFillHoleImageFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), outputVolume=dict( argstr='%s', @@ -26,7 +27,11 @@ def test_GrayscaleFillHoleImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GrayscaleFillHoleImageFilter_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = GrayscaleFillHoleImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py index edb6081ed3..a05db51667 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py @@ -13,6 +13,7 @@ def test_GrayscaleGrindPeakImageFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), outputVolume=dict( argstr='%s', @@ -26,7 +27,11 @@ def test_GrayscaleGrindPeakImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GrayscaleGrindPeakImageFilter_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = GrayscaleGrindPeakImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py index f73690586d..8423192ff0 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py @@ -13,6 +13,7 @@ def test_HistogramMatching_inputs(): inputVolume=dict( argstr='%s', position=-3, + usedefault=True, ), numberOfHistogramLevels=dict(argstr='--numberOfHistogramLevels %d', ), numberOfMatchPoints=dict(argstr='--numberOfMatchPoints %d', ), @@ -24,6 +25,7 @@ def test_HistogramMatching_inputs(): referenceVolume=dict( argstr='%s', position=-2, + usedefault=True, ), threshold=dict(argstr='--threshold ', ), ) @@ -33,7 +35,11 @@ def test_HistogramMatching_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_HistogramMatching_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = HistogramMatching.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py index 0bae22c342..90f0bf1df4 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py @@ -8,10 +8,12 @@ def test_ImageLabelCombine_inputs(): InputLabelMap_A=dict( argstr='%s', position=-3, + usedefault=True, ), InputLabelMap_B=dict( argstr='%s', position=-2, + usedefault=True, ), OutputLabelMap=dict( argstr='%s', @@ -31,7 +33,11 @@ def test_ImageLabelCombine_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ImageLabelCombine_outputs(): - output_map = dict(OutputLabelMap=dict(position=-1, ), ) + output_map = dict( + OutputLabelMap=dict( + position=-1, + usedefault=True, + ), ) outputs = ImageLabelCombine.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py index cd04072890..6af542ced3 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py @@ -8,10 +8,12 @@ def test_MaskScalarVolume_inputs(): InputVolume=dict( argstr='%s', position=-3, + usedefault=True, ), MaskVolume=dict( argstr='%s', position=-2, + usedefault=True, ), OutputVolume=dict( argstr='%s', @@ -32,7 +34,11 @@ def test_MaskScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MaskScalarVolume_outputs(): - output_map = dict(OutputVolume=dict(position=-1, ), ) + output_map = dict( + OutputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = MaskScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py index 35bb9496c9..14e8404ac5 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py @@ -13,6 +13,7 @@ def test_MedianImageFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), neighborhood=dict( argstr='--neighborhood %s', @@ -30,7 +31,11 @@ def test_MedianImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MedianImageFilter_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = MedianImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py index 6590c4b133..8d442e83ca 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py @@ -13,10 +13,12 @@ def test_MultiplyScalarVolumes_inputs(): inputVolume1=dict( argstr='%s', position=-3, + usedefault=True, ), inputVolume2=dict( argstr='%s', position=-2, + usedefault=True, ), order=dict(argstr='--order %s', ), outputVolume=dict( @@ -31,7 +33,11 @@ def test_MultiplyScalarVolumes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MultiplyScalarVolumes_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = MultiplyScalarVolumes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py index c6ad0bf24d..74a7e497a5 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py @@ -16,12 +16,18 @@ def test_N4ITKBiasFieldCorrection_inputs(): argstr='--histogramsharpening %s', sep=',', ), - inputimage=dict(argstr='--inputimage %s', ), + inputimage=dict( + argstr='--inputimage %s', + usedefault=True, + ), iterations=dict( argstr='--iterations %s', sep=',', ), - maskimage=dict(argstr='--maskimage %s', ), + maskimage=dict( + argstr='--maskimage %s', + usedefault=True, + ), meshresolution=dict( argstr='--meshresolution %s', sep=',', @@ -36,7 +42,10 @@ def test_N4ITKBiasFieldCorrection_inputs(): ), shrinkfactor=dict(argstr='--shrinkfactor %d', ), splinedistance=dict(argstr='--splinedistance %f', ), - weightimage=dict(argstr='--weightimage %s', ), + weightimage=dict( + argstr='--weightimage %s', + usedefault=True, + ), ) inputs = N4ITKBiasFieldCorrection.input_spec() @@ -45,8 +54,8 @@ def test_N4ITKBiasFieldCorrection_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_N4ITKBiasFieldCorrection_outputs(): output_map = dict( - outputbiasfield=dict(), - outputimage=dict(), + outputbiasfield=dict(usedefault=True, ), + outputimage=dict(usedefault=True, ), ) outputs = N4ITKBiasFieldCorrection.output_spec() diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py index ebe34fd9b3..589feab548 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py @@ -7,10 +7,16 @@ def test_ResampleScalarVectorDWIVolume_inputs(): input_map = dict( Inverse_ITK_Transformation=dict( argstr='--Inverse_ITK_Transformation ', ), - Reference=dict(argstr='--Reference %s', ), + Reference=dict( + argstr='--Reference %s', + usedefault=True, + ), args=dict(argstr='%s', ), centered_transform=dict(argstr='--centered_transform ', ), - defField=dict(argstr='--defField %s', ), + defField=dict( + argstr='--defField %s', + usedefault=True, + ), default_pixel_value=dict(argstr='--default_pixel_value %f', ), direction_matrix=dict( argstr='--direction_matrix %s', @@ -25,6 +31,7 @@ def test_ResampleScalarVectorDWIVolume_inputs(): inputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), interpolation=dict(argstr='--interpolation %s', ), notbulk=dict(argstr='--notbulk ', ), @@ -52,7 +59,10 @@ def test_ResampleScalarVectorDWIVolume_inputs(): sep=',', ), transform_order=dict(argstr='--transform_order %s', ), - transformationFile=dict(argstr='--transformationFile %s', ), + transformationFile=dict( + argstr='--transformationFile %s', + usedefault=True, + ), window_function=dict(argstr='--window_function %s', ), ) inputs = ResampleScalarVectorDWIVolume.input_spec() @@ -61,7 +71,11 @@ def test_ResampleScalarVectorDWIVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ResampleScalarVectorDWIVolume_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = ResampleScalarVectorDWIVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py index d62589881f..49614c4383 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py @@ -13,10 +13,12 @@ def test_SubtractScalarVolumes_inputs(): inputVolume1=dict( argstr='%s', position=-3, + usedefault=True, ), inputVolume2=dict( argstr='%s', position=-2, + usedefault=True, ), order=dict(argstr='--order %s', ), outputVolume=dict( @@ -31,7 +33,11 @@ def test_SubtractScalarVolumes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SubtractScalarVolumes_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = SubtractScalarVolumes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py index 34de317104..adb89adc9a 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py @@ -8,6 +8,7 @@ def test_ThresholdScalarVolume_inputs(): InputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), OutputVolume=dict( argstr='%s', @@ -31,7 +32,11 @@ def test_ThresholdScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ThresholdScalarVolume_outputs(): - output_map = dict(OutputVolume=dict(position=-1, ), ) + output_map = dict( + OutputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = ThresholdScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py index 8e7890de85..0be5e18f93 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py @@ -15,6 +15,7 @@ def test_VotingBinaryHoleFillingImageFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), majorityThreshold=dict(argstr='--majorityThreshold %d', ), outputVolume=dict( @@ -33,7 +34,11 @@ def test_VotingBinaryHoleFillingImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_VotingBinaryHoleFillingImageFilter_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = VotingBinaryHoleFillingImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py index 0e25ffad9a..a25de38c5d 100644 --- a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py +++ b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py @@ -14,6 +14,7 @@ def test_DWIUnbiasedNonLocalMeansFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), ng=dict(argstr='--ng %d', ), outputVolume=dict( @@ -40,7 +41,11 @@ def test_DWIUnbiasedNonLocalMeansFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWIUnbiasedNonLocalMeansFilter_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = DWIUnbiasedNonLocalMeansFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py index 949cdc7f61..df91b32b72 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py @@ -8,10 +8,12 @@ def test_AffineRegistration_inputs(): FixedImageFileName=dict( argstr='%s', position=-2, + usedefault=True, ), MovingImageFileName=dict( argstr='%s', position=-1, + usedefault=True, ), args=dict(argstr='%s', ), environ=dict( @@ -20,7 +22,10 @@ def test_AffineRegistration_inputs(): ), fixedsmoothingfactor=dict(argstr='--fixedsmoothingfactor %d', ), histogrambins=dict(argstr='--histogrambins %d', ), - initialtransform=dict(argstr='--initialtransform %s', ), + initialtransform=dict( + argstr='--initialtransform %s', + usedefault=True, + ), iterations=dict(argstr='--iterations %d', ), movingsmoothingfactor=dict(argstr='--movingsmoothingfactor %d', ), outputtransform=dict( @@ -41,8 +46,8 @@ def test_AffineRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_AffineRegistration_outputs(): output_map = dict( - outputtransform=dict(), - resampledmovingfilename=dict(), + outputtransform=dict(usedefault=True, ), + resampledmovingfilename=dict(usedefault=True, ), ) outputs = AffineRegistration.output_spec() diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py index 17339f8859..a7a780110d 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py @@ -8,10 +8,12 @@ def test_BSplineDeformableRegistration_inputs(): FixedImageFileName=dict( argstr='%s', position=-2, + usedefault=True, ), MovingImageFileName=dict( argstr='%s', position=-1, + usedefault=True, ), args=dict(argstr='%s', ), constrain=dict(argstr='--constrain ', ), @@ -22,7 +24,10 @@ def test_BSplineDeformableRegistration_inputs(): ), gridSize=dict(argstr='--gridSize %d', ), histogrambins=dict(argstr='--histogrambins %d', ), - initialtransform=dict(argstr='--initialtransform %s', ), + initialtransform=dict( + argstr='--initialtransform %s', + usedefault=True, + ), iterations=dict(argstr='--iterations %d', ), maximumDeformation=dict(argstr='--maximumDeformation %f', ), outputtransform=dict( @@ -46,9 +51,9 @@ def test_BSplineDeformableRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BSplineDeformableRegistration_outputs(): output_map = dict( - outputtransform=dict(), - outputwarp=dict(), - resampledmovingfilename=dict(), + outputtransform=dict(usedefault=True, ), + outputwarp=dict(usedefault=True, ), + resampledmovingfilename=dict(usedefault=True, ), ) outputs = BSplineDeformableRegistration.output_spec() diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py index 8335515c13..14742b11f3 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py @@ -14,8 +14,14 @@ def test_BSplineToDeformationField_inputs(): nohash=True, usedefault=True, ), - refImage=dict(argstr='--refImage %s', ), - tfm=dict(argstr='--tfm %s', ), + refImage=dict( + argstr='--refImage %s', + usedefault=True, + ), + tfm=dict( + argstr='--tfm %s', + usedefault=True, + ), ) inputs = BSplineToDeformationField.input_spec() @@ -23,7 +29,7 @@ def test_BSplineToDeformationField_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BSplineToDeformationField_outputs(): - output_map = dict(defImage=dict(), ) + output_map = dict(defImage=dict(usedefault=True, ), ) outputs = BSplineToDeformationField.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py index 7fa8b77d63..916a96119d 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py @@ -22,17 +22,25 @@ def test_ExpertAutomatedRegistration_inputs(): fixedImage=dict( argstr='%s', position=-2, + usedefault=True, + ), + fixedImageMask=dict( + argstr='--fixedImageMask %s', + usedefault=True, ), - fixedImageMask=dict(argstr='--fixedImageMask %s', ), fixedLandmarks=dict(argstr='--fixedLandmarks %s...', ), initialization=dict(argstr='--initialization %s', ), interpolation=dict(argstr='--interpolation %s', ), - loadTransform=dict(argstr='--loadTransform %s', ), + loadTransform=dict( + argstr='--loadTransform %s', + usedefault=True, + ), metric=dict(argstr='--metric %s', ), minimizeMemory=dict(argstr='--minimizeMemory ', ), movingImage=dict( argstr='%s', position=-1, + usedefault=True, ), movingLandmarks=dict(argstr='--movingLandmarks %s...', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -58,8 +66,8 @@ def test_ExpertAutomatedRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ExpertAutomatedRegistration_outputs(): output_map = dict( - resampledImage=dict(), - saveTransform=dict(), + resampledImage=dict(usedefault=True, ), + saveTransform=dict(usedefault=True, ), ) outputs = ExpertAutomatedRegistration.output_spec() diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py index a55432f9b0..cd1bf18500 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py @@ -8,10 +8,12 @@ def test_LinearRegistration_inputs(): FixedImageFileName=dict( argstr='%s', position=-2, + usedefault=True, ), MovingImageFileName=dict( argstr='%s', position=-1, + usedefault=True, ), args=dict(argstr='%s', ), environ=dict( @@ -20,7 +22,10 @@ def test_LinearRegistration_inputs(): ), fixedsmoothingfactor=dict(argstr='--fixedsmoothingfactor %d', ), histogrambins=dict(argstr='--histogrambins %d', ), - initialtransform=dict(argstr='--initialtransform %s', ), + initialtransform=dict( + argstr='--initialtransform %s', + usedefault=True, + ), iterations=dict( argstr='--iterations %s', sep=',', @@ -48,8 +53,8 @@ def test_LinearRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_LinearRegistration_outputs(): output_map = dict( - outputtransform=dict(), - resampledmovingfilename=dict(), + outputtransform=dict(usedefault=True, ), + resampledmovingfilename=dict(usedefault=True, ), ) outputs = LinearRegistration.output_spec() diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py index 7903fd1d5c..0461f6a91a 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py @@ -13,13 +13,18 @@ def test_MultiResolutionAffineRegistration_inputs(): fixedImage=dict( argstr='%s', position=-2, + usedefault=True, + ), + fixedImageMask=dict( + argstr='--fixedImageMask %s', + usedefault=True, ), - fixedImageMask=dict(argstr='--fixedImageMask %s', ), fixedImageROI=dict(argstr='--fixedImageROI %s', ), metricTolerance=dict(argstr='--metricTolerance %f', ), movingImage=dict( argstr='%s', position=-1, + usedefault=True, ), numIterations=dict(argstr='--numIterations %d', ), numLineIterations=dict(argstr='--numLineIterations %d', ), @@ -41,8 +46,8 @@ def test_MultiResolutionAffineRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MultiResolutionAffineRegistration_outputs(): output_map = dict( - resampledImage=dict(), - saveTransform=dict(), + resampledImage=dict(usedefault=True, ), + saveTransform=dict(usedefault=True, ), ) outputs = MultiResolutionAffineRegistration.output_spec() diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py index a1af6c71b3..b1ae9800fe 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py @@ -13,6 +13,7 @@ def test_OtsuThresholdImageFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), insideValue=dict(argstr='--insideValue %d', ), numberOfBins=dict(argstr='--numberOfBins %d', ), @@ -29,7 +30,11 @@ def test_OtsuThresholdImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OtsuThresholdImageFilter_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = OtsuThresholdImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py index 02beeee464..87178c9f27 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py @@ -15,6 +15,7 @@ def test_OtsuThresholdSegmentation_inputs(): inputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), minimumObjectSize=dict(argstr='--minimumObjectSize %d', ), numberOfBins=dict(argstr='--numberOfBins %d', ), @@ -30,7 +31,11 @@ def test_OtsuThresholdSegmentation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OtsuThresholdSegmentation_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = OtsuThresholdSegmentation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py index baa698246c..0210093054 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py @@ -8,6 +8,7 @@ def test_ResampleScalarVolume_inputs(): InputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), OutputVolume=dict( argstr='%s', @@ -31,7 +32,11 @@ def test_ResampleScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ResampleScalarVolume_outputs(): - output_map = dict(OutputVolume=dict(position=-1, ), ) + output_map = dict( + OutputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = ResampleScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py index 6c2a0eb072..c77095ae3e 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py @@ -8,10 +8,12 @@ def test_RigidRegistration_inputs(): FixedImageFileName=dict( argstr='%s', position=-2, + usedefault=True, ), MovingImageFileName=dict( argstr='%s', position=-1, + usedefault=True, ), args=dict(argstr='%s', ), environ=dict( @@ -20,7 +22,10 @@ def test_RigidRegistration_inputs(): ), fixedsmoothingfactor=dict(argstr='--fixedsmoothingfactor %d', ), histogrambins=dict(argstr='--histogrambins %d', ), - initialtransform=dict(argstr='--initialtransform %s', ), + initialtransform=dict( + argstr='--initialtransform %s', + usedefault=True, + ), iterations=dict( argstr='--iterations %s', sep=',', @@ -49,8 +54,8 @@ def test_RigidRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RigidRegistration_outputs(): output_map = dict( - outputtransform=dict(), - resampledmovingfilename=dict(), + outputtransform=dict(usedefault=True, ), + resampledmovingfilename=dict(usedefault=True, ), ) outputs = RigidRegistration.output_spec() diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py index e46f046add..2353b8fecd 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py @@ -9,10 +9,12 @@ def test_IntensityDifferenceMetric_inputs(): baselineSegmentationVolume=dict( argstr='%s', position=-3, + usedefault=True, ), baselineVolume=dict( argstr='%s', position=-4, + usedefault=True, ), changingBandSize=dict(argstr='--changingBandSize %d', ), environ=dict( @@ -22,6 +24,7 @@ def test_IntensityDifferenceMetric_inputs(): followupVolume=dict( argstr='%s', position=-2, + usedefault=True, ), outputVolume=dict( argstr='%s', @@ -41,8 +44,11 @@ def test_IntensityDifferenceMetric_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_IntensityDifferenceMetric_outputs(): output_map = dict( - outputVolume=dict(position=-1, ), - reportFileName=dict(), + outputVolume=dict( + position=-1, + usedefault=True, + ), + reportFileName=dict(usedefault=True, ), ) outputs = IntensityDifferenceMetric.output_spec() diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py index 61141f65db..314edc7dd8 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py @@ -11,7 +11,10 @@ def test_PETStandardUptakeValueComputation_inputs(): SUVMean=dict(argstr='--SUVMean %s', ), SUVMin=dict(argstr='--SUVMin %s', ), args=dict(argstr='%s', ), - color=dict(argstr='--color %s', ), + color=dict( + argstr='--color %s', + usedefault=True, + ), csvFile=dict( argstr='--csvFile %s', hash_files=False, @@ -20,9 +23,18 @@ def test_PETStandardUptakeValueComputation_inputs(): nohash=True, usedefault=True, ), - labelMap=dict(argstr='--labelMap %s', ), - petDICOMPath=dict(argstr='--petDICOMPath %s', ), - petVolume=dict(argstr='--petVolume %s', ), + labelMap=dict( + argstr='--labelMap %s', + usedefault=True, + ), + petDICOMPath=dict( + argstr='--petDICOMPath %s', + usedefault=True, + ), + petVolume=dict( + argstr='--petVolume %s', + usedefault=True, + ), ) inputs = PETStandardUptakeValueComputation.input_spec() @@ -30,7 +42,7 @@ def test_PETStandardUptakeValueComputation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PETStandardUptakeValueComputation_outputs(): - output_map = dict(csvFile=dict(), ) + output_map = dict(csvFile=dict(usedefault=True, ), ) outputs = PETStandardUptakeValueComputation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py index 454e290102..d9b331cb34 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py @@ -24,7 +24,7 @@ def test_ACPCTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ACPCTransform_outputs(): - output_map = dict(outputTransform=dict(), ) + output_map = dict(outputTransform=dict(usedefault=True, ), ) outputs = ACPCTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py index c631f9b96e..5ac8f5f353 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py @@ -19,14 +19,25 @@ def test_BRAINSDemonWarp_inputs(): nohash=True, usedefault=True, ), - fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), - fixedVolume=dict(argstr='--fixedVolume %s', ), + fixedBinaryVolume=dict( + argstr='--fixedBinaryVolume %s', + usedefault=True, + ), + fixedVolume=dict( + argstr='--fixedVolume %s', + usedefault=True, + ), gradient_type=dict(argstr='--gradient_type %s', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), initializeWithDisplacementField=dict( - argstr='--initializeWithDisplacementField %s', ), - initializeWithTransform=dict(argstr='--initializeWithTransform %s', ), + argstr='--initializeWithDisplacementField %s', + usedefault=True, + ), + initializeWithTransform=dict( + argstr='--initializeWithTransform %s', + usedefault=True, + ), inputPixelType=dict(argstr='--inputPixelType %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), lowerThresholdForBOBF=dict(argstr='--lowerThresholdForBOBF %d', ), @@ -44,8 +55,14 @@ def test_BRAINSDemonWarp_inputs(): argstr='--minimumMovingPyramid %s', sep=',', ), - movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), - movingVolume=dict(argstr='--movingVolume %s', ), + movingBinaryVolume=dict( + argstr='--movingBinaryVolume %s', + usedefault=True, + ), + movingVolume=dict( + argstr='--movingVolume %s', + usedefault=True, + ), neighborhoodForBOBF=dict( argstr='--neighborhoodForBOBF %s', sep=',', @@ -92,9 +109,9 @@ def test_BRAINSDemonWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSDemonWarp_outputs(): output_map = dict( - outputCheckerboardVolume=dict(), - outputDisplacementFieldVolume=dict(), - outputVolume=dict(), + outputCheckerboardVolume=dict(usedefault=True, ), + outputDisplacementFieldVolume=dict(usedefault=True, ), + outputVolume=dict(usedefault=True, ), ) outputs = BRAINSDemonWarp.output_spec() diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py index bb62633d94..679ab82bf7 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py @@ -28,13 +28,22 @@ def test_BRAINSFit_inputs(): usedefault=True, ), failureExitCode=dict(argstr='--failureExitCode %d', ), - fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), - fixedVolume=dict(argstr='--fixedVolume %s', ), + fixedBinaryVolume=dict( + argstr='--fixedBinaryVolume %s', + usedefault=True, + ), + fixedVolume=dict( + argstr='--fixedVolume %s', + usedefault=True, + ), fixedVolumeTimeIndex=dict(argstr='--fixedVolumeTimeIndex %d', ), forceMINumberOfThreads=dict(argstr='--forceMINumberOfThreads %d', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), - initialTransform=dict(argstr='--initialTransform %s', ), + initialTransform=dict( + argstr='--initialTransform %s', + usedefault=True, + ), initializeTransformMode=dict(argstr='--initializeTransformMode %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), linearTransform=dict( @@ -54,8 +63,14 @@ def test_BRAINSFit_inputs(): argstr='--minimumStepLength %s', sep=',', ), - movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), - movingVolume=dict(argstr='--movingVolume %s', ), + movingBinaryVolume=dict( + argstr='--movingBinaryVolume %s', + usedefault=True, + ), + movingVolume=dict( + argstr='--movingVolume %s', + usedefault=True, + ), movingVolumeTimeIndex=dict(argstr='--movingVolumeTimeIndex %d', ), numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', ), numberOfIterations=dict( @@ -127,13 +142,13 @@ def test_BRAINSFit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSFit_outputs(): output_map = dict( - bsplineTransform=dict(), - linearTransform=dict(), - outputFixedVolumeROI=dict(), - outputMovingVolumeROI=dict(), - outputTransform=dict(), - outputVolume=dict(), - strippedOutputTransform=dict(), + bsplineTransform=dict(usedefault=True, ), + linearTransform=dict(usedefault=True, ), + outputFixedVolumeROI=dict(usedefault=True, ), + outputMovingVolumeROI=dict(usedefault=True, ), + outputTransform=dict(usedefault=True, ), + outputVolume=dict(usedefault=True, ), + strippedOutputTransform=dict(usedefault=True, ), ) outputs = BRAINSFit.output_spec() diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py index 98ec5f4ff3..38758ac585 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py @@ -7,7 +7,10 @@ def test_BRAINSResample_inputs(): input_map = dict( args=dict(argstr='%s', ), defaultValue=dict(argstr='--defaultValue %f', ), - deformationVolume=dict(argstr='--deformationVolume %s', ), + deformationVolume=dict( + argstr='--deformationVolume %s', + usedefault=True, + ), environ=dict( nohash=True, usedefault=True, @@ -16,7 +19,10 @@ def test_BRAINSResample_inputs(): argstr='--gridSpacing %s', sep=',', ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), interpolationMode=dict(argstr='--interpolationMode %s', ), inverseTransform=dict(argstr='--inverseTransform ', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -25,8 +31,14 @@ def test_BRAINSResample_inputs(): hash_files=False, ), pixelType=dict(argstr='--pixelType %s', ), - referenceVolume=dict(argstr='--referenceVolume %s', ), - warpTransform=dict(argstr='--warpTransform %s', ), + referenceVolume=dict( + argstr='--referenceVolume %s', + usedefault=True, + ), + warpTransform=dict( + argstr='--warpTransform %s', + usedefault=True, + ), ) inputs = BRAINSResample.input_spec() @@ -34,7 +46,7 @@ def test_BRAINSResample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSResample_outputs(): - output_map = dict(outputVolume=dict(), ) + output_map = dict(outputVolume=dict(usedefault=True, ), ) outputs = BRAINSResample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py index 36d42fe8df..a4ae5f1b6f 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py @@ -26,7 +26,7 @@ def test_FiducialRegistration_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FiducialRegistration_outputs(): - output_map = dict(saveTransform=dict(), ) + output_map = dict(saveTransform=dict(usedefault=True, ), ) outputs = FiducialRegistration.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py index b3255da1d3..17d6d7715d 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -19,14 +19,22 @@ def test_VBRAINSDemonWarp_inputs(): nohash=True, usedefault=True, ), - fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), + fixedBinaryVolume=dict( + argstr='--fixedBinaryVolume %s', + usedefault=True, + ), fixedVolume=dict(argstr='--fixedVolume %s...', ), gradient_type=dict(argstr='--gradient_type %s', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), initializeWithDisplacementField=dict( - argstr='--initializeWithDisplacementField %s', ), - initializeWithTransform=dict(argstr='--initializeWithTransform %s', ), + argstr='--initializeWithDisplacementField %s', + usedefault=True, + ), + initializeWithTransform=dict( + argstr='--initializeWithTransform %s', + usedefault=True, + ), inputPixelType=dict(argstr='--inputPixelType %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), lowerThresholdForBOBF=dict(argstr='--lowerThresholdForBOBF %d', ), @@ -44,7 +52,10 @@ def test_VBRAINSDemonWarp_inputs(): argstr='--minimumMovingPyramid %s', sep=',', ), - movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), + movingBinaryVolume=dict( + argstr='--movingBinaryVolume %s', + usedefault=True, + ), movingVolume=dict(argstr='--movingVolume %s...', ), neighborhoodForBOBF=dict( argstr='--neighborhoodForBOBF %s', @@ -96,9 +107,9 @@ def test_VBRAINSDemonWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_VBRAINSDemonWarp_outputs(): output_map = dict( - outputCheckerboardVolume=dict(), - outputDisplacementFieldVolume=dict(), - outputVolume=dict(), + outputCheckerboardVolume=dict(usedefault=True, ), + outputDisplacementFieldVolume=dict(usedefault=True, ), + outputVolume=dict(usedefault=True, ), ) outputs = VBRAINSDemonWarp.output_spec() diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py index 89863fb730..1f990681d0 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -12,7 +12,10 @@ def test_BRAINSROIAuto_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict(argstr='--inputVolume %s', ), + inputVolume=dict( + argstr='--inputVolume %s', + usedefault=True, + ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), otsuPercentileThreshold=dict(argstr='--otsuPercentileThreshold %f', ), outputClippedVolumeROI=dict( @@ -34,8 +37,8 @@ def test_BRAINSROIAuto_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSROIAuto_outputs(): output_map = dict( - outputClippedVolumeROI=dict(), - outputROIMaskVolume=dict(), + outputClippedVolumeROI=dict(usedefault=True, ), + outputROIMaskVolume=dict(usedefault=True, ), ) outputs = BRAINSROIAuto.output_spec() diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py index 09b0b1300f..f47dceaeb9 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py @@ -21,11 +21,16 @@ def test_EMSegmentCommandLine_inputs(): hash_files=False, ), intermediateResultsDirectory=dict( - argstr='--intermediateResultsDirectory %s', ), + argstr='--intermediateResultsDirectory %s', + usedefault=True, + ), keepTempFiles=dict(argstr='--keepTempFiles ', ), loadAtlasNonCentered=dict(argstr='--loadAtlasNonCentered ', ), loadTargetCentered=dict(argstr='--loadTargetCentered ', ), - mrmlSceneFileName=dict(argstr='--mrmlSceneFileName %s', ), + mrmlSceneFileName=dict( + argstr='--mrmlSceneFileName %s', + usedefault=True, + ), parametersMRMLNodeName=dict(argstr='--parametersMRMLNodeName %s', ), registrationAffineType=dict(argstr='--registrationAffineType %d', ), registrationDeformableType=dict( @@ -36,7 +41,9 @@ def test_EMSegmentCommandLine_inputs(): hash_files=False, ), resultStandardVolumeFileName=dict( - argstr='--resultStandardVolumeFileName %s', ), + argstr='--resultStandardVolumeFileName %s', + usedefault=True, + ), resultVolumeFileName=dict( argstr='--resultVolumeFileName %s', hash_files=False, @@ -53,9 +60,9 @@ def test_EMSegmentCommandLine_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EMSegmentCommandLine_outputs(): output_map = dict( - generateEmptyMRMLSceneAndQuit=dict(), - resultMRMLSceneFileName=dict(), - resultVolumeFileName=dict(), + generateEmptyMRMLSceneAndQuit=dict(usedefault=True, ), + resultMRMLSceneFileName=dict(usedefault=True, ), + resultVolumeFileName=dict(usedefault=True, ), ) outputs = EMSegmentCommandLine.output_spec() diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py index ed46177df0..51a38cdb53 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py @@ -16,12 +16,14 @@ def test_RobustStatisticsSegmenter_inputs(): labelImageFileName=dict( argstr='%s', position=-2, + usedefault=True, ), labelValue=dict(argstr='--labelValue %d', ), maxRunningTime=dict(argstr='--maxRunningTime %f', ), originalImageFileName=dict( argstr='%s', position=-3, + usedefault=True, ), segmentedImageFileName=dict( argstr='%s', @@ -35,7 +37,11 @@ def test_RobustStatisticsSegmenter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RobustStatisticsSegmenter_outputs(): - output_map = dict(segmentedImageFileName=dict(position=-1, ), ) + output_map = dict( + segmentedImageFileName=dict( + position=-1, + usedefault=True, + ), ) outputs = RobustStatisticsSegmenter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py index 3c5e2124d0..1d9792fdaf 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py @@ -13,6 +13,7 @@ def test_SimpleRegionGrowingSegmentation_inputs(): inputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), iterations=dict(argstr='--iterations %d', ), labelvalue=dict(argstr='--labelvalue %d', ), @@ -33,7 +34,11 @@ def test_SimpleRegionGrowingSegmentation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SimpleRegionGrowingSegmentation_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = SimpleRegionGrowingSegmentation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py index 2997e805f9..6f01502c60 100644 --- a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py +++ b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py @@ -10,7 +10,10 @@ def test_DicomToNrrdConverter_inputs(): nohash=True, usedefault=True, ), - inputDicomDirectory=dict(argstr='--inputDicomDirectory %s', ), + inputDicomDirectory=dict( + argstr='--inputDicomDirectory %s', + usedefault=True, + ), outputDirectory=dict( argstr='--outputDirectory %s', hash_files=False, @@ -30,7 +33,7 @@ def test_DicomToNrrdConverter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DicomToNrrdConverter_outputs(): - output_map = dict(outputDirectory=dict(), ) + output_map = dict(outputDirectory=dict(usedefault=True, ), ) outputs = DicomToNrrdConverter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py index 279d68e0ab..2713754c67 100644 --- a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py +++ b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py @@ -10,7 +10,10 @@ def test_EMSegmentTransformToNewFormat_inputs(): nohash=True, usedefault=True, ), - inputMRMLFileName=dict(argstr='--inputMRMLFileName %s', ), + inputMRMLFileName=dict( + argstr='--inputMRMLFileName %s', + usedefault=True, + ), outputMRMLFileName=dict( argstr='--outputMRMLFileName %s', hash_files=False, @@ -23,7 +26,7 @@ def test_EMSegmentTransformToNewFormat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EMSegmentTransformToNewFormat_outputs(): - output_map = dict(outputMRMLFileName=dict(), ) + output_map = dict(outputMRMLFileName=dict(usedefault=True, ), ) outputs = EMSegmentTransformToNewFormat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py index 7ad8cac8e9..5722b10fc4 100644 --- a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py @@ -8,6 +8,7 @@ def test_GrayscaleModelMaker_inputs(): InputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), OutputGeometry=dict( argstr='%s', @@ -32,7 +33,11 @@ def test_GrayscaleModelMaker_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GrayscaleModelMaker_outputs(): - output_map = dict(OutputGeometry=dict(position=-1, ), ) + output_map = dict( + OutputGeometry=dict( + position=-1, + usedefault=True, + ), ) outputs = GrayscaleModelMaker.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py index bb3780495b..918569a017 100644 --- a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py +++ b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py @@ -14,6 +14,7 @@ def test_LabelMapSmoothing_inputs(): inputVolume=dict( argstr='%s', position=-2, + usedefault=True, ), labelToSmooth=dict(argstr='--labelToSmooth %d', ), maxRMSError=dict(argstr='--maxRMSError %f', ), @@ -30,7 +31,11 @@ def test_LabelMapSmoothing_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LabelMapSmoothing_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = LabelMapSmoothing.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py index 6453957a79..eb982af412 100644 --- a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py +++ b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py @@ -8,10 +8,12 @@ def test_MergeModels_inputs(): Model1=dict( argstr='%s', position=-3, + usedefault=True, ), Model2=dict( argstr='%s', position=-2, + usedefault=True, ), ModelOutput=dict( argstr='%s', @@ -30,7 +32,11 @@ def test_MergeModels_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MergeModels_outputs(): - output_map = dict(ModelOutput=dict(position=-1, ), ) + output_map = dict( + ModelOutput=dict( + position=-1, + usedefault=True, + ), ) outputs = MergeModels.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py index ed182137cf..1a7b9400e3 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py @@ -8,9 +8,13 @@ def test_ModelMaker_inputs(): InputVolume=dict( argstr='%s', position=-1, + usedefault=True, ), args=dict(argstr='%s', ), - color=dict(argstr='--color %s', ), + color=dict( + argstr='--color %s', + usedefault=True, + ), debug=dict(argstr='--debug ', ), decimate=dict(argstr='--decimate %f', ), end=dict(argstr='--end %d', ), diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py index efd11f1040..5c7db905d8 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py @@ -8,6 +8,7 @@ def test_ModelToLabelMap_inputs(): InputVolume=dict( argstr='%s', position=-3, + usedefault=True, ), OutputVolume=dict( argstr='%s', @@ -23,6 +24,7 @@ def test_ModelToLabelMap_inputs(): surface=dict( argstr='%s', position=-2, + usedefault=True, ), ) inputs = ModelToLabelMap.input_spec() @@ -31,7 +33,11 @@ def test_ModelToLabelMap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ModelToLabelMap_outputs(): - output_map = dict(OutputVolume=dict(position=-1, ), ) + output_map = dict( + OutputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = ModelToLabelMap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py index f3d1908cd0..d30db9f888 100644 --- a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py +++ b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py @@ -13,6 +13,7 @@ def test_OrientScalarVolume_inputs(): inputVolume1=dict( argstr='%s', position=-2, + usedefault=True, ), orientation=dict(argstr='--orientation %s', ), outputVolume=dict( @@ -27,7 +28,11 @@ def test_OrientScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OrientScalarVolume_outputs(): - output_map = dict(outputVolume=dict(position=-1, ), ) + output_map = dict( + outputVolume=dict( + position=-1, + usedefault=True, + ), ) outputs = OrientScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py index 32a2fc2139..ad86ef55a1 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py +++ b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py @@ -8,10 +8,12 @@ def test_ProbeVolumeWithModel_inputs(): InputModel=dict( argstr='%s', position=-2, + usedefault=True, ), InputVolume=dict( argstr='%s', position=-3, + usedefault=True, ), OutputModel=dict( argstr='%s', @@ -30,7 +32,11 @@ def test_ProbeVolumeWithModel_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ProbeVolumeWithModel_outputs(): - output_map = dict(OutputModel=dict(position=-1, ), ) + output_map = dict( + OutputModel=dict( + position=-1, + usedefault=True, + ), ) outputs = ProbeVolumeWithModel.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py index 1b1aa6edcd..fe8b6c4634 100644 --- a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py +++ b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py @@ -5,7 +5,10 @@ def test_Analyze2nii_inputs(): input_map = dict( - analyze_file=dict(mandatory=True, ), + analyze_file=dict( + mandatory=True, + usedefault=True, + ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), paths=dict(), @@ -24,7 +27,7 @@ def test_Analyze2nii_outputs(): output_map = dict( matlab_cmd=dict(), mfile=dict(usedefault=True, ), - nifti_file=dict(), + nifti_file=dict(usedefault=True, ), paths=dict(), use_mcr=dict(), use_v8struct=dict( diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py index bbc925ec9e..03d01a391d 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py @@ -8,6 +8,7 @@ def test_ApplyDeformations_inputs(): deformation_field=dict( field='comp{1}.def', mandatory=True, + usedefault=True, ), in_files=dict( field='fnames', @@ -20,6 +21,7 @@ def test_ApplyDeformations_inputs(): reference_volume=dict( field='comp{2}.id.space', mandatory=True, + usedefault=True, ), use_mcr=dict(), use_v8struct=dict( diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py index d1c35dbcd2..26197ab0a8 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py @@ -8,10 +8,12 @@ def test_ApplyInverseDeformation_inputs(): bounding_box=dict(field='comp{1}.inv.comp{1}.sn2def.bb', ), deformation=dict( field='comp{1}.inv.comp{1}.sn2def.matname', + usedefault=True, xor=['deformation_field'], ), deformation_field=dict( field='comp{1}.inv.comp{1}.def', + usedefault=True, xor=['deformation'], ), in_files=dict( @@ -22,7 +24,10 @@ def test_ApplyInverseDeformation_inputs(): matlab_cmd=dict(), mfile=dict(usedefault=True, ), paths=dict(), - target=dict(field='comp{1}.inv.space', ), + target=dict( + field='comp{1}.inv.space', + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict( min_ver='8', diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py index a686e95485..30a3080071 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py @@ -8,11 +8,18 @@ def test_ApplyTransform_inputs(): in_file=dict( copyfile=True, mandatory=True, + usedefault=True, + ), + mat=dict( + mandatory=True, + usedefault=True, ), - mat=dict(mandatory=True, ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), - out_file=dict(genfile=True, ), + out_file=dict( + genfile=True, + usedefault=True, + ), paths=dict(), use_mcr=dict(), use_v8struct=dict( @@ -26,7 +33,7 @@ def test_ApplyTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyTransform_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = ApplyTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py index 69695ca7b5..5cac290da6 100644 --- a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py +++ b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py @@ -5,16 +5,20 @@ def test_CalcCoregAffine_inputs(): input_map = dict( - invmat=dict(), - mat=dict(), + invmat=dict(usedefault=True, ), + mat=dict(usedefault=True, ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), moving=dict( copyfile=False, mandatory=True, + usedefault=True, ), paths=dict(), - target=dict(mandatory=True, ), + target=dict( + mandatory=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict( min_ver='8', @@ -28,8 +32,8 @@ def test_CalcCoregAffine_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CalcCoregAffine_outputs(): output_map = dict( - invmat=dict(), - mat=dict(), + invmat=dict(usedefault=True, ), + mat=dict(usedefault=True, ), ) outputs = CalcCoregAffine.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_Coregister.py b/nipype/interfaces/spm/tests/test_auto_Coregister.py index 957a2c84a9..6318b1ab88 100644 --- a/nipype/interfaces/spm/tests/test_auto_Coregister.py +++ b/nipype/interfaces/spm/tests/test_auto_Coregister.py @@ -29,6 +29,7 @@ def test_Coregister_inputs(): copyfile=False, field='ref', mandatory=True, + usedefault=True, ), tolerance=dict(field='eoptions.tol', ), use_mcr=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_DARTEL.py b/nipype/interfaces/spm/tests/test_auto_DARTEL.py index cc1b9eee1b..e7d261a99a 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTEL.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTEL.py @@ -34,7 +34,7 @@ def test_DARTEL_inputs(): def test_DARTEL_outputs(): output_map = dict( dartel_flow_fields=dict(), - final_template_file=dict(), + final_template_file=dict(usedefault=True, ), template_files=dict(), ) outputs = DARTEL.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py index d25bde2e5d..24d7690916 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py @@ -24,6 +24,7 @@ def test_DARTELNorm2MNI_inputs(): copyfile=False, field='mni_norm.template', mandatory=True, + usedefault=True, ), use_mcr=dict(), use_v8struct=dict( @@ -39,7 +40,7 @@ def test_DARTELNorm2MNI_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DARTELNorm2MNI_outputs(): output_map = dict( - normalization_parameter_file=dict(), + normalization_parameter_file=dict(usedefault=True, ), normalized_files=dict(), ) outputs = DARTELNorm2MNI.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py index bc9bb9006e..1bd4678c3a 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py @@ -17,11 +17,13 @@ def test_EstimateContrast_inputs(): residual_image=dict( copyfile=False, mandatory=True, + usedefault=True, ), spm_mat_file=dict( copyfile=True, field='spmmat', mandatory=True, + usedefault=True, ), use_derivs=dict(xor=['group_contrast'], ), use_mcr=dict(), @@ -41,7 +43,7 @@ def test_EstimateContrast_outputs(): ess_images=dict(), spmF_images=dict(), spmT_images=dict(), - spm_mat_file=dict(), + spm_mat_file=dict(usedefault=True, ), ) outputs = EstimateContrast.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py index 05f511a0bd..7d058fa76e 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py @@ -17,6 +17,7 @@ def test_EstimateModel_inputs(): copyfile=True, field='spmmat', mandatory=True, + usedefault=True, ), use_mcr=dict(), use_v8struct=dict( @@ -34,15 +35,15 @@ def test_EstimateModel_outputs(): output_map = dict( ARcoef=dict(), Cbetas=dict(), - RPVimage=dict(), + RPVimage=dict(usedefault=True, ), SDbetas=dict(), SDerror=dict(), beta_images=dict(), - labels=dict(), - mask_image=dict(), - residual_image=dict(), + labels=dict(usedefault=True, ), + mask_image=dict(usedefault=True, ), + residual_image=dict(usedefault=True, ), residual_images=dict(), - spm_mat_file=dict(), + spm_mat_file=dict(usedefault=True, ), ) outputs = EstimateModel.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py index 38d2b1c6fb..2a181918c5 100644 --- a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py @@ -6,7 +6,10 @@ def test_FactorialDesign_inputs(): input_map = dict( covariates=dict(field='cov', ), - explicit_mask_file=dict(field='masking.em', ), + explicit_mask_file=dict( + field='masking.em', + usedefault=True, + ), global_calc_mean=dict( field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], @@ -24,7 +27,10 @@ def test_FactorialDesign_inputs(): mfile=dict(usedefault=True, ), no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), paths=dict(), - spm_mat_dir=dict(field='dir', ), + spm_mat_dir=dict( + field='dir', + usedefault=True, + ), threshold_mask_absolute=dict( field='masking.tm.tma.athresh', xor=['threshold_mask_none', 'threshold_mask_relative'], @@ -50,7 +56,7 @@ def test_FactorialDesign_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FactorialDesign_outputs(): - output_map = dict(spm_mat_file=dict(), ) + output_map = dict(spm_mat_file=dict(usedefault=True, ), ) outputs = FactorialDesign.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_FieldMap.py b/nipype/interfaces/spm/tests/test_auto_FieldMap.py index 43fbbcb8f4..bc2751220a 100644 --- a/nipype/interfaces/spm/tests/test_auto_FieldMap.py +++ b/nipype/interfaces/spm/tests/test_auto_FieldMap.py @@ -8,6 +8,7 @@ def test_FieldMap_inputs(): anat_file=dict( copyfile=False, field='subj.anat', + usedefault=True, ), blip_direction=dict( field='subj.defaults.defaultsval.blipdir', @@ -21,6 +22,7 @@ def test_FieldMap_inputs(): copyfile=False, field='subj.session.epi', mandatory=True, + usedefault=True, ), epifm=dict( field='subj.defaults.defaultsval.epifm', @@ -35,6 +37,7 @@ def test_FieldMap_inputs(): copyfile=False, field='subj.data.presubphasemag.magnitude', mandatory=True, + usedefault=True, ), mask_fwhm=dict( field='subj.defaults.defaultsval.mflags.fwhm', @@ -75,6 +78,7 @@ def test_FieldMap_inputs(): copyfile=False, field='subj.data.presubphasemag.phase', mandatory=True, + usedefault=True, ), reg=dict( field='subj.defaults.defaultsval.mflags.reg', @@ -87,6 +91,7 @@ def test_FieldMap_inputs(): template=dict( copyfile=False, field='subj.defaults.defaultsval.mflags.template', + usedefault=True, ), thresh=dict( field='subj.defaults.defaultsval.mflags.thresh', @@ -120,7 +125,7 @@ def test_FieldMap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FieldMap_outputs(): - output_map = dict(vdm=dict(), ) + output_map = dict(vdm=dict(usedefault=True, ), ) outputs = FieldMap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_Level1Design.py b/nipype/interfaces/spm/tests/test_auto_Level1Design.py index 7dce3dda2a..d84d5ca907 100644 --- a/nipype/interfaces/spm/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/spm/tests/test_auto_Level1Design.py @@ -16,7 +16,10 @@ def test_Level1Design_inputs(): field='timing.RT', mandatory=True, ), - mask_image=dict(field='mask', ), + mask_image=dict( + field='mask', + usedefault=True, + ), mask_threshold=dict(usedefault=True, ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), @@ -28,7 +31,10 @@ def test_Level1Design_inputs(): field='sess', mandatory=True, ), - spm_mat_dir=dict(field='dir', ), + spm_mat_dir=dict( + field='dir', + usedefault=True, + ), timing_units=dict( field='timing.units', mandatory=True, @@ -46,7 +52,7 @@ def test_Level1Design_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Level1Design_outputs(): - output_map = dict(spm_mat_file=dict(), ) + output_map = dict(spm_mat_file=dict(usedefault=True, ), ) outputs = Level1Design.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py index 26957f2fbb..dc8e73d77c 100644 --- a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py @@ -6,7 +6,10 @@ def test_MultipleRegressionDesign_inputs(): input_map = dict( covariates=dict(field='cov', ), - explicit_mask_file=dict(field='masking.em', ), + explicit_mask_file=dict( + field='masking.em', + usedefault=True, + ), global_calc_mean=dict( field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], @@ -32,7 +35,10 @@ def test_MultipleRegressionDesign_inputs(): mfile=dict(usedefault=True, ), no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), paths=dict(), - spm_mat_dir=dict(field='dir', ), + spm_mat_dir=dict( + field='dir', + usedefault=True, + ), threshold_mask_absolute=dict( field='masking.tm.tma.athresh', xor=['threshold_mask_none', 'threshold_mask_relative'], @@ -59,7 +65,7 @@ def test_MultipleRegressionDesign_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MultipleRegressionDesign_outputs(): - output_map = dict(spm_mat_file=dict(), ) + output_map = dict(spm_mat_file=dict(usedefault=True, ), ) outputs = MultipleRegressionDesign.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize.py b/nipype/interfaces/spm/tests/test_auto_Normalize.py index fde0bf7fff..d2018122b3 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize.py @@ -24,6 +24,7 @@ def test_Normalize_inputs(): copyfile=False, field='subj.matname', mandatory=True, + usedefault=True, xor=['source', 'template'], ), paths=dict(), @@ -37,17 +38,20 @@ def test_Normalize_inputs(): source_weight=dict( copyfile=False, field='subj.wtsrc', + usedefault=True, ), template=dict( copyfile=False, field='eoptions.template', mandatory=True, + usedefault=True, xor=['parameter_file'], ), template_image_smoothing=dict(field='eoptions.smoref', ), template_weight=dict( copyfile=False, field='eoptions.weight', + usedefault=True, ), use_mcr=dict(), use_v8struct=dict( diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize12.py b/nipype/interfaces/spm/tests/test_auto_Normalize12.py index bf8da2dba1..3428df38b5 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize12.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize12.py @@ -16,12 +16,14 @@ def test_Normalize12_inputs(): copyfile=False, field='subj.def', mandatory=True, + usedefault=True, xor=['image_to_align', 'tpm'], ), image_to_align=dict( copyfile=True, field='subj.vol', mandatory=True, + usedefault=True, xor=['deformation_file'], ), jobtype=dict(usedefault=True, ), @@ -37,6 +39,7 @@ def test_Normalize12_inputs(): tpm=dict( copyfile=False, field='eoptions.tpm', + usedefault=True, xor=['deformation_file'], ), use_mcr=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py index dbb02a6275..a57ba3b3f9 100644 --- a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py @@ -6,7 +6,10 @@ def test_OneSampleTTestDesign_inputs(): input_map = dict( covariates=dict(field='cov', ), - explicit_mask_file=dict(field='masking.em', ), + explicit_mask_file=dict( + field='masking.em', + usedefault=True, + ), global_calc_mean=dict( field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], @@ -28,7 +31,10 @@ def test_OneSampleTTestDesign_inputs(): mfile=dict(usedefault=True, ), no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), paths=dict(), - spm_mat_dir=dict(field='dir', ), + spm_mat_dir=dict( + field='dir', + usedefault=True, + ), threshold_mask_absolute=dict( field='masking.tm.tma.athresh', xor=['threshold_mask_none', 'threshold_mask_relative'], @@ -54,7 +60,7 @@ def test_OneSampleTTestDesign_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OneSampleTTestDesign_outputs(): - output_map = dict(spm_mat_file=dict(), ) + output_map = dict(spm_mat_file=dict(usedefault=True, ), ) outputs = OneSampleTTestDesign.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py index 3e1662268a..12bc0f4a16 100644 --- a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py @@ -7,7 +7,10 @@ def test_PairedTTestDesign_inputs(): input_map = dict( ancova=dict(field='des.pt.ancova', ), covariates=dict(field='cov', ), - explicit_mask_file=dict(field='masking.em', ), + explicit_mask_file=dict( + field='masking.em', + usedefault=True, + ), global_calc_mean=dict( field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], @@ -30,7 +33,10 @@ def test_PairedTTestDesign_inputs(): mandatory=True, ), paths=dict(), - spm_mat_dir=dict(field='dir', ), + spm_mat_dir=dict( + field='dir', + usedefault=True, + ), threshold_mask_absolute=dict( field='masking.tm.tma.athresh', xor=['threshold_mask_none', 'threshold_mask_relative'], @@ -56,7 +62,7 @@ def test_PairedTTestDesign_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PairedTTestDesign_outputs(): - output_map = dict(spm_mat_file=dict(), ) + output_map = dict(spm_mat_file=dict(usedefault=True, ), ) outputs = PairedTTestDesign.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_Realign.py b/nipype/interfaces/spm/tests/test_auto_Realign.py index ac2f5bbd92..10f5f6a0a6 100644 --- a/nipype/interfaces/spm/tests/test_auto_Realign.py +++ b/nipype/interfaces/spm/tests/test_auto_Realign.py @@ -28,7 +28,10 @@ def test_Realign_inputs(): min_ver='8', usedefault=True, ), - weight_img=dict(field='eoptions.weight', ), + weight_img=dict( + field='eoptions.weight', + usedefault=True, + ), wrap=dict(field='eoptions.wrap', ), write_interp=dict(field='roptions.interp', ), write_mask=dict(field='roptions.mask', ), @@ -47,7 +50,7 @@ def test_Realign_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Realign_outputs(): output_map = dict( - mean_image=dict(), + mean_image=dict(usedefault=True, ), modified_in_files=dict(), realigned_files=dict(), realignment_parameters=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py b/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py index 5c7c36f80b..0bafbfbd30 100644 --- a/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py +++ b/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py @@ -45,6 +45,7 @@ def test_RealignUnwarp_inputs(): phase_map=dict( copyfile=False, field='data.pmscan', + usedefault=True, ), quality=dict(field='eoptions.quality', ), register_to_mean=dict(field='eoptions.rtm', ), @@ -63,7 +64,10 @@ def test_RealignUnwarp_inputs(): min_ver='8', usedefault=True, ), - weight_img=dict(field='eoptions.weight', ), + weight_img=dict( + field='eoptions.weight', + usedefault=True, + ), wrap=dict(field='eoptions.ewrap', ), ) inputs = RealignUnwarp.input_spec() @@ -73,7 +77,7 @@ def test_RealignUnwarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RealignUnwarp_outputs(): output_map = dict( - mean_image=dict(), + mean_image=dict(usedefault=True, ), modified_in_files=dict(), realigned_unwarped_files=dict(), realignment_parameters=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_Reslice.py b/nipype/interfaces/spm/tests/test_auto_Reslice.py index 81299fc748..b51d753b8d 100644 --- a/nipype/interfaces/spm/tests/test_auto_Reslice.py +++ b/nipype/interfaces/spm/tests/test_auto_Reslice.py @@ -5,13 +5,19 @@ def test_Reslice_inputs(): input_map = dict( - in_file=dict(mandatory=True, ), + in_file=dict( + mandatory=True, + usedefault=True, + ), interp=dict(usedefault=True, ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), - out_file=dict(), + out_file=dict(usedefault=True, ), paths=dict(), - space_defining=dict(mandatory=True, ), + space_defining=dict( + mandatory=True, + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict( min_ver='8', @@ -24,7 +30,7 @@ def test_Reslice_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Reslice_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Reslice.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py index 3e39ade181..89a4885328 100644 --- a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py +++ b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py @@ -14,7 +14,10 @@ def test_ResliceToReference_inputs(): matlab_cmd=dict(), mfile=dict(usedefault=True, ), paths=dict(), - target=dict(field='comp{1}.id.space', ), + target=dict( + field='comp{1}.id.space', + usedefault=True, + ), use_mcr=dict(), use_v8struct=dict( min_ver='8', diff --git a/nipype/interfaces/spm/tests/test_auto_Segment.py b/nipype/interfaces/spm/tests/test_auto_Segment.py index f6df46e1de..6327f62d35 100644 --- a/nipype/interfaces/spm/tests/test_auto_Segment.py +++ b/nipype/interfaces/spm/tests/test_auto_Segment.py @@ -17,7 +17,10 @@ def test_Segment_inputs(): ), gaussians_per_class=dict(field='opts.ngaus', ), gm_output_type=dict(field='output.GM', ), - mask_image=dict(field='opts.msk', ), + mask_image=dict( + field='opts.msk', + usedefault=True, + ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), paths=dict(), @@ -40,22 +43,23 @@ def test_Segment_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Segment_outputs(): output_map = dict( - bias_corrected_image=dict(), - inverse_transformation_mat=dict(), - modulated_csf_image=dict(), - modulated_gm_image=dict(), + bias_corrected_image=dict(usedefault=True, ), + inverse_transformation_mat=dict(usedefault=True, ), + modulated_csf_image=dict(usedefault=True, ), + modulated_gm_image=dict(usedefault=True, ), modulated_input_image=dict( deprecated='0.10', new_name='bias_corrected_image', + usedefault=True, ), - modulated_wm_image=dict(), - native_csf_image=dict(), - native_gm_image=dict(), - native_wm_image=dict(), - normalized_csf_image=dict(), - normalized_gm_image=dict(), - normalized_wm_image=dict(), - transformation_mat=dict(), + modulated_wm_image=dict(usedefault=True, ), + native_csf_image=dict(usedefault=True, ), + native_gm_image=dict(usedefault=True, ), + native_wm_image=dict(usedefault=True, ), + normalized_csf_image=dict(usedefault=True, ), + normalized_gm_image=dict(usedefault=True, ), + normalized_wm_image=dict(usedefault=True, ), + transformation_mat=dict(usedefault=True, ), ) outputs = Segment.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_Threshold.py b/nipype/interfaces/spm/tests/test_auto_Threshold.py index 078adb3a1b..8aa01622fd 100644 --- a/nipype/interfaces/spm/tests/test_auto_Threshold.py +++ b/nipype/interfaces/spm/tests/test_auto_Threshold.py @@ -17,10 +17,12 @@ def test_Threshold_inputs(): spm_mat_file=dict( copyfile=True, mandatory=True, + usedefault=True, ), stat_image=dict( copyfile=False, mandatory=True, + usedefault=True, ), use_fwe_correction=dict(usedefault=True, ), use_mcr=dict(), @@ -40,9 +42,9 @@ def test_Threshold_outputs(): activation_forced=dict(), cluster_forming_thr=dict(), n_clusters=dict(), - pre_topo_fdr_map=dict(), + pre_topo_fdr_map=dict(usedefault=True, ), pre_topo_n_clusters=dict(), - thresholded_map=dict(), + thresholded_map=dict(usedefault=True, ), ) outputs = Threshold.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py index ccdc441e04..2477e75ecd 100644 --- a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py +++ b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py @@ -14,10 +14,12 @@ def test_ThresholdStatistics_inputs(): spm_mat_file=dict( copyfile=True, mandatory=True, + usedefault=True, ), stat_image=dict( copyfile=False, mandatory=True, + usedefault=True, ), use_mcr=dict(), use_v8struct=dict( diff --git a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py index 4dfbc12570..f1720acff7 100644 --- a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py @@ -7,7 +7,10 @@ def test_TwoSampleTTestDesign_inputs(): input_map = dict( covariates=dict(field='cov', ), dependent=dict(field='des.t2.dept', ), - explicit_mask_file=dict(field='masking.em', ), + explicit_mask_file=dict( + field='masking.em', + usedefault=True, + ), global_calc_mean=dict( field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], @@ -33,7 +36,10 @@ def test_TwoSampleTTestDesign_inputs(): mfile=dict(usedefault=True, ), no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), paths=dict(), - spm_mat_dir=dict(field='dir', ), + spm_mat_dir=dict( + field='dir', + usedefault=True, + ), threshold_mask_absolute=dict( field='masking.tm.tma.athresh', xor=['threshold_mask_none', 'threshold_mask_relative'], @@ -60,7 +66,7 @@ def test_TwoSampleTTestDesign_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TwoSampleTTestDesign_outputs(): - output_map = dict(spm_mat_file=dict(), ) + output_map = dict(spm_mat_file=dict(usedefault=True, ), ) outputs = TwoSampleTTestDesign.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py index 6aaac2b489..095e42c2a8 100644 --- a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py +++ b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py @@ -46,7 +46,9 @@ def test_VBMSegment_inputs(): usedefault=True, ), dartel_template=dict( - field='estwrite.extopts.dartelwarp.normhigh.darteltpm', ), + field='estwrite.extopts.dartelwarp.normhigh.darteltpm', + usedefault=True, + ), deformation_field=dict( field='estwrite.output.warps', usedefault=True, @@ -105,7 +107,10 @@ def test_VBMSegment_inputs(): usedefault=True, ), spatial_normalization=dict(usedefault=True, ), - tissues=dict(field='estwrite.tpm', ), + tissues=dict( + field='estwrite.tpm', + usedefault=True, + ), use_mcr=dict(), use_sanlm_denoising_filter=dict( field='estwrite.extopts.sanlm', diff --git a/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py b/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py index 24cbda657b..d65f8726e7 100644 --- a/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py +++ b/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py @@ -5,7 +5,10 @@ def test_BIDSDataGrabber_inputs(): input_map = dict( - base_dir=dict(mandatory=True, ), + base_dir=dict( + mandatory=True, + usedefault=True, + ), extra_derivatives=dict(), index_derivatives=dict( mandatory=True, diff --git a/nipype/interfaces/tests/test_auto_Bru2.py b/nipype/interfaces/tests/test_auto_Bru2.py index ce436ac03e..d77c1f429a 100644 --- a/nipype/interfaces/tests/test_auto_Bru2.py +++ b/nipype/interfaces/tests/test_auto_Bru2.py @@ -18,6 +18,7 @@ def test_Bru2_inputs(): argstr='%s', mandatory=True, position=-1, + usedefault=True, ), output_filename=dict( argstr='-o %s', @@ -30,7 +31,7 @@ def test_Bru2_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Bru2_outputs(): - output_map = dict(nii_file=dict(), ) + output_map = dict(nii_file=dict(usedefault=True, ), ) outputs = Bru2.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_C3d.py b/nipype/interfaces/tests/test_auto_C3d.py index 9e74e82e2a..cae646af71 100644 --- a/nipype/interfaces/tests/test_auto_C3d.py +++ b/nipype/interfaces/tests/test_auto_C3d.py @@ -25,6 +25,7 @@ def test_C3d_inputs(): out_file=dict( argstr='-o %s', position=-1, + usedefault=True, xor=['out_files'], ), out_files=dict( diff --git a/nipype/interfaces/tests/test_auto_C3dAffineTool.py b/nipype/interfaces/tests/test_auto_C3dAffineTool.py index 510ea2f02a..3875b1a4a3 100644 --- a/nipype/interfaces/tests/test_auto_C3dAffineTool.py +++ b/nipype/interfaces/tests/test_auto_C3dAffineTool.py @@ -22,14 +22,17 @@ def test_C3dAffineTool_inputs(): reference_file=dict( argstr='-ref %s', position=1, + usedefault=True, ), source_file=dict( argstr='-src %s', position=2, + usedefault=True, ), transform_file=dict( argstr='%s', position=3, + usedefault=True, ), ) inputs = C3dAffineTool.input_spec() @@ -38,7 +41,7 @@ def test_C3dAffineTool_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_C3dAffineTool_outputs(): - output_map = dict(itk_transform=dict(), ) + output_map = dict(itk_transform=dict(usedefault=True, ), ) outputs = C3dAffineTool.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_CopyMeta.py b/nipype/interfaces/tests/test_auto_CopyMeta.py index 012edfa886..2fa5fc6102 100644 --- a/nipype/interfaces/tests/test_auto_CopyMeta.py +++ b/nipype/interfaces/tests/test_auto_CopyMeta.py @@ -5,10 +5,16 @@ def test_CopyMeta_inputs(): input_map = dict( - dest_file=dict(mandatory=True, ), + dest_file=dict( + mandatory=True, + usedefault=True, + ), exclude_classes=dict(), include_classes=dict(), - src_file=dict(mandatory=True, ), + src_file=dict( + mandatory=True, + usedefault=True, + ), ) inputs = CopyMeta.input_spec() @@ -16,7 +22,7 @@ def test_CopyMeta_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CopyMeta_outputs(): - output_map = dict(dest_file=dict(), ) + output_map = dict(dest_file=dict(usedefault=True, ), ) outputs = CopyMeta.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_DataGrabber.py b/nipype/interfaces/tests/test_auto_DataGrabber.py index d39db0b527..da4f8b9081 100644 --- a/nipype/interfaces/tests/test_auto_DataGrabber.py +++ b/nipype/interfaces/tests/test_auto_DataGrabber.py @@ -5,7 +5,7 @@ def test_DataGrabber_inputs(): input_map = dict( - base_directory=dict(), + base_directory=dict(usedefault=True, ), drop_blank_outputs=dict(usedefault=True, ), raise_on_empty=dict(usedefault=True, ), sort_filelist=dict(mandatory=True, ), diff --git a/nipype/interfaces/tests/test_auto_DataSink.py b/nipype/interfaces/tests/test_auto_DataSink.py index da26854451..2d6e70f224 100644 --- a/nipype/interfaces/tests/test_auto_DataSink.py +++ b/nipype/interfaces/tests/test_auto_DataSink.py @@ -6,7 +6,7 @@ def test_DataSink_inputs(): input_map = dict( _outputs=dict(usedefault=True, ), - base_directory=dict(), + base_directory=dict(usedefault=True, ), bucket=dict(), container=dict(), creds_path=dict(), @@ -15,7 +15,7 @@ def test_DataSink_inputs(): parameterization=dict(usedefault=True, ), regexp_substitutions=dict(), remove_dest_dir=dict(usedefault=True, ), - strip_dir=dict(), + strip_dir=dict(usedefault=True, ), substitutions=dict(), ) inputs = DataSink.input_spec() diff --git a/nipype/interfaces/tests/test_auto_Dcm2nii.py b/nipype/interfaces/tests/test_auto_Dcm2nii.py index 0caa45a1f1..531177d915 100644 --- a/nipype/interfaces/tests/test_auto_Dcm2nii.py +++ b/nipype/interfaces/tests/test_auto_Dcm2nii.py @@ -17,6 +17,7 @@ def test_Dcm2nii_inputs(): config_file=dict( argstr='-b %s', genfile=True, + usedefault=True, ), convert_all_pars=dict( argstr='-v', @@ -49,6 +50,7 @@ def test_Dcm2nii_inputs(): output_dir=dict( argstr='-o %s', genfile=True, + usedefault=True, ), protocol_in_filename=dict( argstr='-p', @@ -63,6 +65,7 @@ def test_Dcm2nii_inputs(): argstr='%s', mandatory=True, position=-1, + usedefault=True, xor=['source_names'], ), source_in_filename=dict( diff --git a/nipype/interfaces/tests/test_auto_Dcm2niix.py b/nipype/interfaces/tests/test_auto_Dcm2niix.py index 5917f48583..950b571d9e 100644 --- a/nipype/interfaces/tests/test_auto_Dcm2niix.py +++ b/nipype/interfaces/tests/test_auto_Dcm2niix.py @@ -52,6 +52,7 @@ def test_Dcm2niix_inputs(): argstr='%s', mandatory=True, position=-1, + usedefault=True, xor=['source_names'], ), source_names=dict( diff --git a/nipype/interfaces/tests/test_auto_DcmStack.py b/nipype/interfaces/tests/test_auto_DcmStack.py index 53a5259af5..825805e09d 100644 --- a/nipype/interfaces/tests/test_auto_DcmStack.py +++ b/nipype/interfaces/tests/test_auto_DcmStack.py @@ -12,7 +12,7 @@ def test_DcmStack_inputs(): include_regexes=dict(), out_ext=dict(usedefault=True, ), out_format=dict(), - out_path=dict(), + out_path=dict(usedefault=True, ), ) inputs = DcmStack.input_spec() @@ -20,7 +20,7 @@ def test_DcmStack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DcmStack_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = DcmStack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_FreeSurferSource.py b/nipype/interfaces/tests/test_auto_FreeSurferSource.py index 15ea9c66cd..da75606a40 100644 --- a/nipype/interfaces/tests/test_auto_FreeSurferSource.py +++ b/nipype/interfaces/tests/test_auto_FreeSurferSource.py @@ -7,7 +7,10 @@ def test_FreeSurferSource_inputs(): input_map = dict( hemi=dict(usedefault=True, ), subject_id=dict(mandatory=True, ), - subjects_dir=dict(mandatory=True, ), + subjects_dir=dict( + mandatory=True, + usedefault=True, + ), ) inputs = FreeSurferSource.input_spec() @@ -20,7 +23,10 @@ def test_FreeSurferSource_outputs(): altkey='BA', loc='stats', ), - T1=dict(loc='mri', ), + T1=dict( + loc='mri', + usedefault=True, + ), annot=dict( altkey='*annot', loc='label', @@ -41,14 +47,23 @@ def test_FreeSurferSource_outputs(): altkey='area.pial', loc='surf', ), - aseg=dict(loc='mri', ), + aseg=dict( + loc='mri', + usedefault=True, + ), aseg_stats=dict( altkey='aseg', loc='stats', ), avg_curv=dict(loc='surf', ), - brain=dict(loc='mri', ), - brainmask=dict(loc='mri', ), + brain=dict( + loc='mri', + usedefault=True, + ), + brainmask=dict( + loc='mri', + usedefault=True, + ), curv=dict(loc='surf', ), curv_pial=dict( altkey='curv.pial', @@ -62,7 +77,10 @@ def test_FreeSurferSource_outputs(): altkey='entorhinal_exvivo', loc='stats', ), - filled=dict(loc='mri', ), + filled=dict( + loc='mri', + usedefault=True, + ), graymid=dict( altkey=['graymid', 'midthickness'], loc='surf', @@ -73,11 +91,23 @@ def test_FreeSurferSource_outputs(): altkey='*label', loc='label', ), - norm=dict(loc='mri', ), - nu=dict(loc='mri', ), - orig=dict(loc='mri', ), + norm=dict( + loc='mri', + usedefault=True, + ), + nu=dict( + loc='mri', + usedefault=True, + ), + orig=dict( + loc='mri', + usedefault=True, + ), pial=dict(loc='surf', ), - rawavg=dict(loc='mri', ), + rawavg=dict( + loc='mri', + usedefault=True, + ), ribbon=dict( altkey='*ribbon', loc='mri', @@ -92,8 +122,14 @@ def test_FreeSurferSource_outputs(): thickness=dict(loc='surf', ), volume=dict(loc='surf', ), white=dict(loc='surf', ), - wm=dict(loc='mri', ), - wmparc=dict(loc='mri', ), + wm=dict( + loc='mri', + usedefault=True, + ), + wmparc=dict( + loc='mri', + usedefault=True, + ), wmparc_stats=dict( altkey='wmparc', loc='stats', diff --git a/nipype/interfaces/tests/test_auto_GroupAndStack.py b/nipype/interfaces/tests/test_auto_GroupAndStack.py index a8f30e32f9..ef56cebf15 100644 --- a/nipype/interfaces/tests/test_auto_GroupAndStack.py +++ b/nipype/interfaces/tests/test_auto_GroupAndStack.py @@ -12,7 +12,7 @@ def test_GroupAndStack_inputs(): include_regexes=dict(), out_ext=dict(usedefault=True, ), out_format=dict(), - out_path=dict(), + out_path=dict(usedefault=True, ), ) inputs = GroupAndStack.input_spec() diff --git a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py index 03a65cf6c2..363f5ac8a3 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py +++ b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py @@ -6,7 +6,7 @@ def test_JSONFileGrabber_inputs(): input_map = dict( defaults=dict(), - in_file=dict(), + in_file=dict(usedefault=True, ), ) inputs = JSONFileGrabber.input_spec() diff --git a/nipype/interfaces/tests/test_auto_JSONFileSink.py b/nipype/interfaces/tests/test_auto_JSONFileSink.py index 002997912b..fdcc2bf441 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileSink.py +++ b/nipype/interfaces/tests/test_auto_JSONFileSink.py @@ -7,7 +7,7 @@ def test_JSONFileSink_inputs(): input_map = dict( _outputs=dict(usedefault=True, ), in_dict=dict(usedefault=True, ), - out_file=dict(), + out_file=dict(usedefault=True, ), ) inputs = JSONFileSink.input_spec() @@ -15,7 +15,7 @@ def test_JSONFileSink_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JSONFileSink_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = JSONFileSink.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_LookupMeta.py b/nipype/interfaces/tests/test_auto_LookupMeta.py index 29100aaef7..b37a94c82c 100644 --- a/nipype/interfaces/tests/test_auto_LookupMeta.py +++ b/nipype/interfaces/tests/test_auto_LookupMeta.py @@ -5,7 +5,10 @@ def test_LookupMeta_inputs(): input_map = dict( - in_file=dict(mandatory=True, ), + in_file=dict( + mandatory=True, + usedefault=True, + ), meta_keys=dict(mandatory=True, ), ) inputs = LookupMeta.input_spec() diff --git a/nipype/interfaces/tests/test_auto_MatlabCommand.py b/nipype/interfaces/tests/test_auto_MatlabCommand.py index c1b971d25d..45427e1222 100644 --- a/nipype/interfaces/tests/test_auto_MatlabCommand.py +++ b/nipype/interfaces/tests/test_auto_MatlabCommand.py @@ -10,7 +10,10 @@ def test_MatlabCommand_inputs(): nohash=True, usedefault=True, ), - logfile=dict(argstr='-logfile %s', ), + logfile=dict( + argstr='-logfile %s', + usedefault=True, + ), mfile=dict(usedefault=True, ), nodesktop=dict( argstr='-nodesktop', diff --git a/nipype/interfaces/tests/test_auto_MergeNifti.py b/nipype/interfaces/tests/test_auto_MergeNifti.py index 9e0a017c60..7015091abc 100644 --- a/nipype/interfaces/tests/test_auto_MergeNifti.py +++ b/nipype/interfaces/tests/test_auto_MergeNifti.py @@ -9,7 +9,7 @@ def test_MergeNifti_inputs(): merge_dim=dict(), out_ext=dict(usedefault=True, ), out_format=dict(), - out_path=dict(), + out_path=dict(usedefault=True, ), sort_order=dict(), ) inputs = MergeNifti.input_spec() @@ -18,7 +18,7 @@ def test_MergeNifti_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MergeNifti_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = MergeNifti.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_MeshFix.py b/nipype/interfaces/tests/test_auto_MeshFix.py index f306f4abed..2d1693eb67 100644 --- a/nipype/interfaces/tests/test_auto_MeshFix.py +++ b/nipype/interfaces/tests/test_auto_MeshFix.py @@ -43,10 +43,12 @@ def test_MeshFix_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), in_file2=dict( argstr='%s', position=2, + usedefault=True, ), join_closest_components=dict( argstr='-jc', @@ -61,6 +63,7 @@ def test_MeshFix_inputs(): out_filename=dict( argstr='-o %s', genfile=True, + usedefault=True, ), output_type=dict(usedefault=True, ), quiet_mode=dict(argstr='-q', ), @@ -94,7 +97,7 @@ def test_MeshFix_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MeshFix_outputs(): - output_map = dict(mesh_file=dict(), ) + output_map = dict(mesh_file=dict(usedefault=True, ), ) outputs = MeshFix.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_MySQLSink.py b/nipype/interfaces/tests/test_auto_MySQLSink.py index 048699659a..38cb32f9b1 100644 --- a/nipype/interfaces/tests/test_auto_MySQLSink.py +++ b/nipype/interfaces/tests/test_auto_MySQLSink.py @@ -7,6 +7,7 @@ def test_MySQLSink_inputs(): input_map = dict( config=dict( mandatory=True, + usedefault=True, xor=['host'], ), database_name=dict(mandatory=True, ), diff --git a/nipype/interfaces/tests/test_auto_PETPVC.py b/nipype/interfaces/tests/test_auto_PETPVC.py index c5283435d5..9aa510aef5 100644 --- a/nipype/interfaces/tests/test_auto_PETPVC.py +++ b/nipype/interfaces/tests/test_auto_PETPVC.py @@ -33,10 +33,12 @@ def test_PETPVC_inputs(): in_file=dict( argstr='-i %s', mandatory=True, + usedefault=True, ), mask_file=dict( argstr='-m %s', mandatory=True, + usedefault=True, ), n_deconv=dict( argstr='-k %d', @@ -50,6 +52,7 @@ def test_PETPVC_inputs(): argstr='-o %s', genfile=True, hash_files=False, + usedefault=True, ), pvc=dict( argstr='-p %s', @@ -66,7 +69,7 @@ def test_PETPVC_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PETPVC_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = PETPVC.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_Quickshear.py b/nipype/interfaces/tests/test_auto_Quickshear.py index 7f39a6bc96..b62c77e77a 100644 --- a/nipype/interfaces/tests/test_auto_Quickshear.py +++ b/nipype/interfaces/tests/test_auto_Quickshear.py @@ -18,11 +18,13 @@ def test_Quickshear_inputs(): argstr='%s', mandatory=True, position=1, + usedefault=True, ), mask_file=dict( argstr='%s', mandatory=True, position=2, + usedefault=True, ), out_file=dict( argstr='%s', @@ -30,6 +32,7 @@ def test_Quickshear_inputs(): name_source='in_file', name_template='%s_defaced', position=3, + usedefault=True, ), ) inputs = Quickshear.input_spec() @@ -38,7 +41,7 @@ def test_Quickshear_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Quickshear_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Quickshear.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_Reorient.py b/nipype/interfaces/tests/test_auto_Reorient.py index 2e45a1ca7f..27a6cba17e 100644 --- a/nipype/interfaces/tests/test_auto_Reorient.py +++ b/nipype/interfaces/tests/test_auto_Reorient.py @@ -5,7 +5,10 @@ def test_Reorient_inputs(): input_map = dict( - in_file=dict(mandatory=True, ), + in_file=dict( + mandatory=True, + usedefault=True, + ), orientation=dict(usedefault=True, ), ) inputs = Reorient.input_spec() @@ -15,8 +18,8 @@ def test_Reorient_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Reorient_outputs(): output_map = dict( - out_file=dict(), - transform=dict(), + out_file=dict(usedefault=True, ), + transform=dict(usedefault=True, ), ) outputs = Reorient.output_spec() diff --git a/nipype/interfaces/tests/test_auto_Rescale.py b/nipype/interfaces/tests/test_auto_Rescale.py index e180c82988..021b05e998 100644 --- a/nipype/interfaces/tests/test_auto_Rescale.py +++ b/nipype/interfaces/tests/test_auto_Rescale.py @@ -5,10 +5,16 @@ def test_Rescale_inputs(): input_map = dict( - in_file=dict(mandatory=True, ), + in_file=dict( + mandatory=True, + usedefault=True, + ), invert=dict(), percentile=dict(usedefault=True, ), - ref_file=dict(mandatory=True, ), + ref_file=dict( + mandatory=True, + usedefault=True, + ), ) inputs = Rescale.input_spec() @@ -16,7 +22,7 @@ def test_Rescale_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Rescale_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Rescale.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_S3DataGrabber.py b/nipype/interfaces/tests/test_auto_S3DataGrabber.py index 7c69413eb0..990347f56d 100644 --- a/nipype/interfaces/tests/test_auto_S3DataGrabber.py +++ b/nipype/interfaces/tests/test_auto_S3DataGrabber.py @@ -8,7 +8,7 @@ def test_S3DataGrabber_inputs(): anon=dict(usedefault=True, ), bucket=dict(mandatory=True, ), bucket_path=dict(usedefault=True, ), - local_directory=dict(), + local_directory=dict(usedefault=True, ), raise_on_empty=dict(usedefault=True, ), region=dict(usedefault=True, ), sort_filelist=dict(mandatory=True, ), diff --git a/nipype/interfaces/tests/test_auto_SQLiteSink.py b/nipype/interfaces/tests/test_auto_SQLiteSink.py index ea03663c4c..3972583753 100644 --- a/nipype/interfaces/tests/test_auto_SQLiteSink.py +++ b/nipype/interfaces/tests/test_auto_SQLiteSink.py @@ -5,7 +5,10 @@ def test_SQLiteSink_inputs(): input_map = dict( - database_file=dict(mandatory=True, ), + database_file=dict( + mandatory=True, + usedefault=True, + ), table_name=dict(mandatory=True, ), ) inputs = SQLiteSink.input_spec() diff --git a/nipype/interfaces/tests/test_auto_SelectFiles.py b/nipype/interfaces/tests/test_auto_SelectFiles.py index bf438fb826..f037d8824c 100644 --- a/nipype/interfaces/tests/test_auto_SelectFiles.py +++ b/nipype/interfaces/tests/test_auto_SelectFiles.py @@ -5,7 +5,7 @@ def test_SelectFiles_inputs(): input_map = dict( - base_directory=dict(), + base_directory=dict(usedefault=True, ), force_lists=dict(usedefault=True, ), raise_on_empty=dict(usedefault=True, ), sort_filelist=dict(usedefault=True, ), diff --git a/nipype/interfaces/tests/test_auto_SignalExtraction.py b/nipype/interfaces/tests/test_auto_SignalExtraction.py index bc76f5261a..c74ab279da 100644 --- a/nipype/interfaces/tests/test_auto_SignalExtraction.py +++ b/nipype/interfaces/tests/test_auto_SignalExtraction.py @@ -7,7 +7,10 @@ def test_SignalExtraction_inputs(): input_map = dict( class_labels=dict(mandatory=True, ), detrend=dict(usedefault=True, ), - in_file=dict(mandatory=True, ), + in_file=dict( + mandatory=True, + usedefault=True, + ), incl_shared_variance=dict(usedefault=True, ), include_global=dict(usedefault=True, ), label_files=dict(mandatory=True, ), @@ -19,7 +22,7 @@ def test_SignalExtraction_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SignalExtraction_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = SignalExtraction.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_SplitNifti.py b/nipype/interfaces/tests/test_auto_SplitNifti.py index e1f6539fab..43d22ac4b2 100644 --- a/nipype/interfaces/tests/test_auto_SplitNifti.py +++ b/nipype/interfaces/tests/test_auto_SplitNifti.py @@ -5,10 +5,13 @@ def test_SplitNifti_inputs(): input_map = dict( - in_file=dict(mandatory=True, ), + in_file=dict( + mandatory=True, + usedefault=True, + ), out_ext=dict(usedefault=True, ), out_format=dict(), - out_path=dict(), + out_path=dict(usedefault=True, ), split_dim=dict(), ) inputs = SplitNifti.input_spec() diff --git a/nipype/interfaces/tests/test_auto_XNATSink.py b/nipype/interfaces/tests/test_auto_XNATSink.py index b4db5ec8d3..9357443afa 100644 --- a/nipype/interfaces/tests/test_auto_XNATSink.py +++ b/nipype/interfaces/tests/test_auto_XNATSink.py @@ -7,9 +7,10 @@ def test_XNATSink_inputs(): input_map = dict( _outputs=dict(usedefault=True, ), assessor_id=dict(xor=['reconstruction_id'], ), - cache_dir=dict(), + cache_dir=dict(usedefault=True, ), config=dict( mandatory=True, + usedefault=True, xor=['server'], ), experiment_id=dict(mandatory=True, ), diff --git a/nipype/interfaces/tests/test_auto_XNATSource.py b/nipype/interfaces/tests/test_auto_XNATSource.py index 8faa79af81..1403dc1c18 100644 --- a/nipype/interfaces/tests/test_auto_XNATSource.py +++ b/nipype/interfaces/tests/test_auto_XNATSource.py @@ -5,9 +5,10 @@ def test_XNATSource_inputs(): input_map = dict( - cache_dir=dict(), + cache_dir=dict(usedefault=True, ), config=dict( mandatory=True, + usedefault=True, xor=['server'], ), pwd=dict(), diff --git a/nipype/interfaces/utility/tests/test_auto_AssertEqual.py b/nipype/interfaces/utility/tests/test_auto_AssertEqual.py index 284e0f4d62..78502aeed6 100644 --- a/nipype/interfaces/utility/tests/test_auto_AssertEqual.py +++ b/nipype/interfaces/utility/tests/test_auto_AssertEqual.py @@ -5,8 +5,14 @@ def test_AssertEqual_inputs(): input_map = dict( - volume1=dict(mandatory=True, ), - volume2=dict(mandatory=True, ), + volume1=dict( + mandatory=True, + usedefault=True, + ), + volume2=dict( + mandatory=True, + usedefault=True, + ), ) inputs = AssertEqual.input_spec() diff --git a/nipype/interfaces/utility/tests/test_auto_CSVReader.py b/nipype/interfaces/utility/tests/test_auto_CSVReader.py index 8a51ca4170..2fbbd73545 100644 --- a/nipype/interfaces/utility/tests/test_auto_CSVReader.py +++ b/nipype/interfaces/utility/tests/test_auto_CSVReader.py @@ -6,7 +6,10 @@ def test_CSVReader_inputs(): input_map = dict( header=dict(usedefault=True, ), - in_file=dict(mandatory=True, ), + in_file=dict( + mandatory=True, + usedefault=True, + ), ) inputs = CSVReader.input_spec() diff --git a/nipype/interfaces/utility/tests/test_auto_Rename.py b/nipype/interfaces/utility/tests/test_auto_Rename.py index 1e6e1cab34..a01e76d30a 100644 --- a/nipype/interfaces/utility/tests/test_auto_Rename.py +++ b/nipype/interfaces/utility/tests/test_auto_Rename.py @@ -6,7 +6,10 @@ def test_Rename_inputs(): input_map = dict( format_string=dict(mandatory=True, ), - in_file=dict(mandatory=True, ), + in_file=dict( + mandatory=True, + usedefault=True, + ), keep_ext=dict(), parse_string=dict(), use_fullpath=dict(usedefault=True, ), diff --git a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py index 785e87e8b1..5bdfacde58 100644 --- a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py +++ b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py @@ -9,6 +9,7 @@ def test_Vnifti2Image_inputs(): attributes=dict( argstr='-attr %s', position=2, + usedefault=True, ), environ=dict( nohash=True, @@ -18,6 +19,7 @@ def test_Vnifti2Image_inputs(): argstr='-in %s', mandatory=True, position=1, + usedefault=True, ), out_file=dict( argstr='-out %s', @@ -26,6 +28,7 @@ def test_Vnifti2Image_inputs(): name_source=['in_file'], name_template='%s.v', position=-1, + usedefault=True, ), ) inputs = Vnifti2Image.input_spec() @@ -34,7 +37,7 @@ def test_Vnifti2Image_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Vnifti2Image_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = Vnifti2Image.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/vista/tests/test_auto_VtoMat.py b/nipype/interfaces/vista/tests/test_auto_VtoMat.py index ee16266402..33f9ea354d 100644 --- a/nipype/interfaces/vista/tests/test_auto_VtoMat.py +++ b/nipype/interfaces/vista/tests/test_auto_VtoMat.py @@ -14,6 +14,7 @@ def test_VtoMat_inputs(): argstr='-in %s', mandatory=True, position=1, + usedefault=True, ), out_file=dict( argstr='-out %s', @@ -22,6 +23,7 @@ def test_VtoMat_inputs(): name_source=['in_file'], name_template='%s.mat', position=-1, + usedefault=True, ), ) inputs = VtoMat.input_spec() @@ -30,7 +32,7 @@ def test_VtoMat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_VtoMat_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = VtoMat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/workbench/tests/test_auto_CiftiSmooth.py b/nipype/interfaces/workbench/tests/test_auto_CiftiSmooth.py index b510a3b34e..ac7a3f3032 100644 --- a/nipype/interfaces/workbench/tests/test_auto_CiftiSmooth.py +++ b/nipype/interfaces/workbench/tests/test_auto_CiftiSmooth.py @@ -10,14 +10,17 @@ def test_CiftiSmooth_inputs(): argstr='cerebellum-corrected-areas %s', position=10, requires=['cerebellum_surf'], + usedefault=True, ), cerebellum_surf=dict( argstr='-cerebellum-surface %s', position=9, + usedefault=True, ), cifti_roi=dict( argstr='-cifti-roi %s', position=11, + usedefault=True, ), direction=dict( argstr='%s', @@ -40,15 +43,18 @@ def test_CiftiSmooth_inputs(): argstr='%s', mandatory=True, position=0, + usedefault=True, ), left_corrected_areas=dict( argstr='-left-corrected-areas %s', position=6, + usedefault=True, ), left_surf=dict( argstr='-left-surface %s', mandatory=True, position=5, + usedefault=True, ), merged_volume=dict( argstr='-merged-volume', @@ -60,15 +66,18 @@ def test_CiftiSmooth_inputs(): name_source=['in_file'], name_template='smoothed_%s.nii', position=4, + usedefault=True, ), right_corrected_areas=dict( argstr='-right-corrected-areas %s', position=8, + usedefault=True, ), right_surf=dict( argstr='-right-surface %s', mandatory=True, position=7, + usedefault=True, ), sigma_surf=dict( argstr='%s', @@ -87,7 +96,7 @@ def test_CiftiSmooth_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CiftiSmooth_outputs(): - output_map = dict(out_file=dict(), ) + output_map = dict(out_file=dict(usedefault=True, ), ) outputs = CiftiSmooth.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/workbench/tests/test_auto_MetricResample.py b/nipype/interfaces/workbench/tests/test_auto_MetricResample.py index 46a66aa728..f652a02fc0 100644 --- a/nipype/interfaces/workbench/tests/test_auto_MetricResample.py +++ b/nipype/interfaces/workbench/tests/test_auto_MetricResample.py @@ -19,11 +19,13 @@ def test_MetricResample_inputs(): current_area=dict( argstr='%s', position=6, + usedefault=True, ), current_sphere=dict( argstr='%s', mandatory=True, position=1, + usedefault=True, ), environ=dict( nohash=True, @@ -33,6 +35,7 @@ def test_MetricResample_inputs(): argstr='%s', mandatory=True, position=0, + usedefault=True, ), largest=dict( argstr='-largest', @@ -46,11 +49,13 @@ def test_MetricResample_inputs(): new_area=dict( argstr='%s', position=7, + usedefault=True, ), new_sphere=dict( argstr='%s', mandatory=True, position=2, + usedefault=True, ), out_file=dict( argstr='%s', @@ -58,10 +63,12 @@ def test_MetricResample_inputs(): name_source=['new_sphere'], name_template='%s.out', position=4, + usedefault=True, ), roi_metric=dict( argstr='-current-roi %s', position=8, + usedefault=True, ), valid_roi_out=dict( argstr='-valid-roi-out', @@ -75,8 +82,8 @@ def test_MetricResample_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MetricResample_outputs(): output_map = dict( - out_file=dict(), - roi_file=dict(), + out_file=dict(usedefault=True, ), + roi_file=dict(usedefault=True, ), ) outputs = MetricResample.output_spec() From 281f516741fd5fb2582616648163638f0525683a Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 16 Jul 2019 09:57:17 -0700 Subject: [PATCH 09/19] fix(traits): restore old ``usedefault`` behavior of ``File``s --- nipype/interfaces/base/traits_extension.py | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py index d6de198ddf..6786c10939 100644 --- a/nipype/interfaces/base/traits_extension.py +++ b/nipype/interfaces/base/traits_extension.py @@ -122,7 +122,6 @@ def __init__(self, value=Undefined, else: self.info_text += ' file or directory' - metadata['usedefault'] = True super(BasePath, self).__init__(value, **metadata) def validate(self, object, name, value, return_pathlike=False): @@ -204,7 +203,14 @@ class Directory(BasePath): >>> class A(TraitedSpec): - ... foo = Directory('tmpdir', resolve=True) + ... foo = Directory('tmpdir') + >>> a = A() + >>> a.foo # doctest: +ELLIPSIS + + + + >>> class A(TraitedSpec): + ... foo = Directory('tmpdir', usedefault=True) >>> a = A() >>> a.foo # doctest: +ELLIPSIS 'tmpdir' @@ -248,8 +254,14 @@ class File(BasePath): '.../idoexist.txt' >>> class A(TraitedSpec): - ... foo = File(exists=True, resolve=False) - >>> a = A(foo='idoexist.txt') + ... foo = File('idoexist.txt') + >>> a = A() + >>> a.foo + + + >>> class A(TraitedSpec): + ... foo = File('idoexist.txt', usedefault=True) + >>> a = A() >>> a.foo 'idoexist.txt' From 6dbd76defe7c0a0250279fe66dc568b222de44e9 Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 16 Jul 2019 09:59:09 -0700 Subject: [PATCH 10/19] fix(interfaces): revise test that should pass --- nipype/algorithms/tests/test_rapidart.py | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/nipype/algorithms/tests/test_rapidart.py b/nipype/algorithms/tests/test_rapidart.py index 9c29648626..ab149da0a6 100644 --- a/nipype/algorithms/tests/test_rapidart.py +++ b/nipype/algorithms/tests/test_rapidart.py @@ -79,12 +79,13 @@ def test_sc_init(): def test_sc_populate_inputs(): sc = ra.StimulusCorrelation() - inputs = Bunch( - realignment_parameters=None, - intensity_values=None, - spm_mat_file=None, - concatenated_design=None) - assert set(sc.inputs.__dict__.keys()) == set(inputs.__dict__.keys()) + expected = [ + 'concatenated_design', + 'intensity_values', + 'realignment_parameters', + 'spm_mat_file', + ] + assert sorted(sc.inputs.get().keys()) == expected def test_sc_output_filenames(): From 98d830867076359703af7e00d401c1d3fa50b00b Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 16 Jul 2019 09:59:42 -0700 Subject: [PATCH 11/19] fix(deps): add pathlib2 to requirements.txt --- requirements.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements.txt b/requirements.txt index 0d951f49c0..64fb55cc2a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,3 +14,4 @@ configparser pydotplus pydot>=1.2.3 packaging +pathlib2 From 4b6e390a721d75c5d7db61fe4db2a25adcb37107 Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 16 Jul 2019 10:01:16 -0700 Subject: [PATCH 12/19] fix(specs): update specs --- nipype/algorithms/tests/test_auto_ACompCor.py | 11 +- .../tests/test_auto_ActivationCount.py | 6 +- .../tests/test_auto_AddCSVColumn.py | 7 +- .../algorithms/tests/test_auto_AddCSVRow.py | 2 +- nipype/algorithms/tests/test_auto_AddNoise.py | 11 +- .../tests/test_auto_ArtifactDetect.py | 2 +- .../test_auto_CalculateNormalizedMoments.py | 5 +- .../tests/test_auto_ComputeDVARS.py | 24 ++-- .../tests/test_auto_ComputeMeshWarp.py | 14 +-- .../algorithms/tests/test_auto_CreateNifti.py | 12 +- nipype/algorithms/tests/test_auto_Distance.py | 14 +-- .../tests/test_auto_FramewiseDisplacement.py | 9 +- .../tests/test_auto_FuzzyOverlap.py | 2 +- nipype/algorithms/tests/test_auto_Gunzip.py | 8 +- nipype/algorithms/tests/test_auto_ICC.py | 11 +- .../algorithms/tests/test_auto_Matlab2CSV.py | 5 +- .../tests/test_auto_MergeCSVFiles.py | 2 +- .../algorithms/tests/test_auto_MergeROIs.py | 4 +- .../tests/test_auto_MeshWarpMaths.py | 9 +- .../tests/test_auto_NonSteadyStateDetector.py | 6 +- .../test_auto_NormalizeProbabilityMapSet.py | 2 +- .../algorithms/tests/test_auto_P2PDistance.py | 14 +-- .../algorithms/tests/test_auto_PickAtlas.py | 9 +- .../algorithms/tests/test_auto_Similarity.py | 14 +-- .../tests/test_auto_SpecifySparseModel.py | 4 +- .../algorithms/tests/test_auto_SplitROIs.py | 7 +- .../tests/test_auto_StimulusCorrelation.py | 5 +- nipype/algorithms/tests/test_auto_TCompCor.py | 11 +- .../algorithms/tests/test_auto_WarpPoints.py | 13 +-- .../afni/tests/test_auto_ABoverlap.py | 5 +- .../afni/tests/test_auto_AFNItoNIFTI.py | 4 +- .../afni/tests/test_auto_AlignEpiAnatPy.py | 22 ++-- .../afni/tests/test_auto_Allineate.py | 33 ++---- .../afni/tests/test_auto_AutoTLRC.py | 3 +- .../afni/tests/test_auto_AutoTcorrelate.py | 10 +- .../afni/tests/test_auto_Autobox.py | 4 +- .../afni/tests/test_auto_Automask.py | 7 +- .../afni/tests/test_auto_Axialize.py | 4 +- .../afni/tests/test_auto_Bandpass.py | 10 +- .../afni/tests/test_auto_BlurInMask.py | 14 +-- .../afni/tests/test_auto_BlurToFWHM.py | 14 +-- .../afni/tests/test_auto_BrickStat.py | 2 - .../interfaces/afni/tests/test_auto_Bucket.py | 3 +- .../interfaces/afni/tests/test_auto_Calc.py | 11 +- nipype/interfaces/afni/tests/test_auto_Cat.py | 2 +- .../afni/tests/test_auto_CatMatvec.py | 3 +- .../afni/tests/test_auto_CenterMass.py | 11 +- .../afni/tests/test_auto_ClipLevel.py | 1 - .../afni/tests/test_auto_ConvertDset.py | 4 +- .../interfaces/afni/tests/test_auto_Copy.py | 4 +- .../afni/tests/test_auto_Deconvolve.py | 38 ++----- .../afni/tests/test_auto_DegreeCentrality.py | 11 +- .../afni/tests/test_auto_Despike.py | 4 +- .../afni/tests/test_auto_Detrend.py | 4 +- nipype/interfaces/afni/tests/test_auto_Dot.py | 8 +- nipype/interfaces/afni/tests/test_auto_ECM.py | 9 +- .../interfaces/afni/tests/test_auto_Edge3.py | 4 +- .../interfaces/afni/tests/test_auto_Eval.py | 11 +- .../interfaces/afni/tests/test_auto_FWHMx.py | 17 +-- nipype/interfaces/afni/tests/test_auto_Fim.py | 5 +- .../afni/tests/test_auto_Fourier.py | 4 +- .../interfaces/afni/tests/test_auto_GCOR.py | 2 - .../interfaces/afni/tests/test_auto_Hist.py | 12 +- .../interfaces/afni/tests/test_auto_LFCD.py | 9 +- .../afni/tests/test_auto_LocalBistat.py | 4 +- .../afni/tests/test_auto_Localstat.py | 3 +- .../afni/tests/test_auto_MaskTool.py | 3 +- .../afni/tests/test_auto_Maskave.py | 5 +- .../interfaces/afni/tests/test_auto_Means.py | 5 +- .../interfaces/afni/tests/test_auto_Merge.py | 3 +- .../interfaces/afni/tests/test_auto_Notes.py | 8 +- .../afni/tests/test_auto_NwarpAdjust.py | 3 +- .../afni/tests/test_auto_NwarpApply.py | 3 +- .../afni/tests/test_auto_NwarpCat.py | 3 +- .../afni/tests/test_auto_OneDToolPy.py | 4 +- .../afni/tests/test_auto_OutlierCount.py | 8 +- .../afni/tests/test_auto_QualityIndex.py | 5 +- .../interfaces/afni/tests/test_auto_Qwarp.py | 20 +--- .../afni/tests/test_auto_QwarpPlusMinus.py | 20 +--- .../afni/tests/test_auto_ROIStats.py | 10 +- .../interfaces/afni/tests/test_auto_ReHo.py | 10 +- .../interfaces/afni/tests/test_auto_Refit.py | 8 +- .../afni/tests/test_auto_Remlfit.py | 103 +++++------------- .../afni/tests/test_auto_Resample.py | 4 +- .../afni/tests/test_auto_Retroicor.py | 8 +- .../afni/tests/test_auto_SVMTest.py | 9 +- .../afni/tests/test_auto_SVMTrain.py | 21 +--- nipype/interfaces/afni/tests/test_auto_Seg.py | 3 +- .../afni/tests/test_auto_SkullStrip.py | 4 +- .../afni/tests/test_auto_Synthesize.py | 5 +- .../interfaces/afni/tests/test_auto_TCat.py | 3 +- .../afni/tests/test_auto_TCatSubBrick.py | 3 +- .../afni/tests/test_auto_TCorr1D.py | 5 +- .../afni/tests/test_auto_TCorrMap.py | 46 +++----- .../afni/tests/test_auto_TCorrelate.py | 5 +- .../interfaces/afni/tests/test_auto_TNorm.py | 4 +- .../afni/tests/test_auto_TProject.py | 24 +--- .../interfaces/afni/tests/test_auto_TShift.py | 6 +- .../interfaces/afni/tests/test_auto_TStat.py | 9 +- .../interfaces/afni/tests/test_auto_To3D.py | 4 +- .../interfaces/afni/tests/test_auto_Undump.py | 9 +- .../afni/tests/test_auto_Unifize.py | 11 +- .../interfaces/afni/tests/test_auto_Volreg.py | 14 +-- .../interfaces/afni/tests/test_auto_Warp.py | 21 +--- .../interfaces/afni/tests/test_auto_ZCutUp.py | 4 +- .../interfaces/afni/tests/test_auto_Zcat.py | 3 +- .../afni/tests/test_auto_Zeropad.py | 4 +- .../interfaces/ants/tests/test_auto_ANTS.py | 10 +- .../ants/tests/test_auto_AffineInitializer.py | 4 +- .../ants/tests/test_auto_AntsJointFusion.py | 12 +- .../ants/tests/test_auto_ApplyTransforms.py | 4 +- .../test_auto_ApplyTransformsToPoints.py | 3 +- .../ants/tests/test_auto_Atropos.py | 4 +- .../tests/test_auto_AverageAffineTransform.py | 3 +- .../ants/tests/test_auto_AverageImages.py | 2 +- .../ants/tests/test_auto_BrainExtraction.py | 44 ++++---- .../tests/test_auto_ComposeMultiTransform.py | 4 +- .../tests/test_auto_CompositeTransformUtil.py | 7 +- .../test_auto_ConvertScalarImageToRGB.py | 3 +- .../ants/tests/test_auto_CorticalThickness.py | 35 +++--- ...est_auto_CreateJacobianDeterminantImage.py | 4 +- .../ants/tests/test_auto_CreateTiledMosaic.py | 9 +- .../ants/tests/test_auto_DenoiseImage.py | 7 +- .../ants/tests/test_auto_GenWarpFields.py | 12 +- .../ants/tests/test_auto_JointFusion.py | 8 +- .../ants/tests/test_auto_KellyKapowski.py | 20 +--- .../ants/tests/test_auto_LabelGeometry.py | 3 +- .../tests/test_auto_LaplacianThickness.py | 5 +- .../tests/test_auto_MeasureImageSimilarity.py | 20 +--- .../ants/tests/test_auto_MultiplyImages.py | 4 +- .../tests/test_auto_N4BiasFieldCorrection.py | 20 +--- .../ants/tests/test_auto_Registration.py | 22 ++-- .../tests/test_auto_RegistrationSynQuick.py | 10 +- .../test_auto_WarpImageMultiTransform.py | 5 +- ..._auto_WarpTimeSeriesImageMultiTransform.py | 4 +- .../ants/tests/test_auto_antsIntroduction.py | 12 +- .../tests/test_auto_buildtemplateparallel.py | 2 +- .../brainsuite/tests/test_auto_BDP.py | 52 ++------- .../brainsuite/tests/test_auto_Bfc.py | 18 +-- .../brainsuite/tests/test_auto_Bse.py | 19 +--- .../brainsuite/tests/test_auto_Cerebro.py | 20 +--- .../brainsuite/tests/test_auto_Cortex.py | 5 +- .../brainsuite/tests/test_auto_Dewisp.py | 4 +- .../brainsuite/tests/test_auto_Dfs.py | 9 +- .../brainsuite/tests/test_auto_Hemisplit.py | 19 +--- .../brainsuite/tests/test_auto_Pialmesh.py | 6 +- .../brainsuite/tests/test_auto_Pvc.py | 12 +- .../brainsuite/tests/test_auto_Scrubmask.py | 4 +- .../brainsuite/tests/test_auto_Skullfinder.py | 5 +- .../brainsuite/tests/test_auto_Tca.py | 4 +- .../camino/tests/test_auto_AnalyzeHeader.py | 10 +- .../tests/test_auto_ComputeEigensystem.py | 3 +- .../test_auto_ComputeFractionalAnisotropy.py | 4 +- .../tests/test_auto_ComputeMeanDiffusivity.py | 5 +- .../tests/test_auto_ComputeTensorTrace.py | 4 +- .../camino/tests/test_auto_Conmat.py | 13 +-- .../camino/tests/test_auto_DT2NIfTI.py | 9 +- .../camino/tests/test_auto_DTIFit.py | 9 +- .../camino/tests/test_auto_DTLUTGen.py | 3 +- .../camino/tests/test_auto_DTMetric.py | 9 +- .../camino/tests/test_auto_FSL2Scheme.py | 4 +- .../camino/tests/test_auto_Image2Voxel.py | 3 +- .../camino/tests/test_auto_ImageStats.py | 3 +- .../camino/tests/test_auto_LinRecon.py | 10 +- .../interfaces/camino/tests/test_auto_MESD.py | 9 +- .../camino/tests/test_auto_ModelFit.py | 29 +---- .../camino/tests/test_auto_NIfTIDT2Camino.py | 18 +-- .../camino/tests/test_auto_PicoPDFs.py | 3 +- .../camino/tests/test_auto_ProcStreamlines.py | 33 ++---- .../camino/tests/test_auto_QBallMX.py | 3 +- .../camino/tests/test_auto_SFLUTGen.py | 6 +- .../camino/tests/test_auto_SFPICOCalibData.py | 6 +- .../camino/tests/test_auto_SFPeaks.py | 8 +- .../camino/tests/test_auto_Shredder.py | 3 +- .../camino/tests/test_auto_Track.py | 11 +- .../camino/tests/test_auto_TrackBallStick.py | 11 +- .../camino/tests/test_auto_TrackBayesDirac.py | 17 +-- .../tests/test_auto_TrackBedpostxDeter.py | 12 +- .../tests/test_auto_TrackBedpostxProba.py | 12 +- .../camino/tests/test_auto_TrackBootstrap.py | 17 +-- .../camino/tests/test_auto_TrackDT.py | 11 +- .../camino/tests/test_auto_TrackPICo.py | 11 +- .../camino/tests/test_auto_TractShredder.py | 3 +- .../camino/tests/test_auto_VtkStreamlines.py | 6 +- .../tests/test_auto_Camino2Trackvis.py | 6 +- .../tests/test_auto_Trackvis2Camino.py | 5 +- .../cmtk/tests/test_auto_AverageNetworks.py | 10 +- .../cmtk/tests/test_auto_CFFConverter.py | 2 +- .../cmtk/tests/test_auto_CreateMatrix.py | 75 ++++--------- .../cmtk/tests/test_auto_CreateNodes.py | 12 +- .../cmtk/tests/test_auto_MergeCNetworks.py | 2 +- .../tests/test_auto_NetworkBasedStatistic.py | 10 +- .../cmtk/tests/test_auto_NetworkXMetrics.py | 34 ++---- .../cmtk/tests/test_auto_Parcellate.py | 25 ++--- .../interfaces/cmtk/tests/test_auto_ROIGen.py | 29 ++--- .../tests/test_auto_DTIRecon.py | 31 +++--- .../tests/test_auto_DTITracker.py | 13 +-- .../tests/test_auto_HARDIMat.py | 23 +--- .../tests/test_auto_ODFRecon.py | 12 +- .../tests/test_auto_ODFTracker.py | 14 +-- .../tests/test_auto_SplineFilter.py | 3 +- .../tests/test_auto_TrackMerge.py | 2 +- .../dipy/tests/test_auto_APMQball.py | 19 +--- nipype/interfaces/dipy/tests/test_auto_CSD.py | 25 ++--- nipype/interfaces/dipy/tests/test_auto_DTI.py | 29 ++--- .../dipy/tests/test_auto_Denoise.py | 13 +-- .../tests/test_auto_DipyDiffusionInterface.py | 15 +-- .../tests/test_auto_EstimateResponseSH.py | 26 ++--- .../dipy/tests/test_auto_RESTORE.py | 33 ++---- .../dipy/tests/test_auto_Resample.py | 7 +- .../tests/test_auto_SimulateMultiTensor.py | 21 ++-- .../tests/test_auto_StreamlineTractography.py | 23 ++-- .../dipy/tests/test_auto_TensorMode.py | 19 +--- .../dipy/tests/test_auto_TrackDensityMap.py | 9 +- .../dtitk/tests/test_auto_AffScalarVol.py | 6 +- .../tests/test_auto_AffSymTensor3DVol.py | 6 +- .../dtitk/tests/test_auto_Affine.py | 7 +- .../dtitk/tests/test_auto_AffineTask.py | 7 +- .../dtitk/tests/test_auto_BinThresh.py | 4 +- .../dtitk/tests/test_auto_BinThreshTask.py | 4 +- .../dtitk/tests/test_auto_ComposeXfm.py | 5 +- .../dtitk/tests/test_auto_ComposeXfmTask.py | 5 +- .../dtitk/tests/test_auto_Diffeo.py | 7 +- .../dtitk/tests/test_auto_DiffeoScalarVol.py | 6 +- .../tests/test_auto_DiffeoSymTensor3DVol.py | 6 +- .../dtitk/tests/test_auto_DiffeoTask.py | 7 +- .../interfaces/dtitk/tests/test_auto_Rigid.py | 7 +- .../dtitk/tests/test_auto_RigidTask.py | 7 +- .../dtitk/tests/test_auto_SVAdjustVoxSp.py | 5 +- .../tests/test_auto_SVAdjustVoxSpTask.py | 5 +- .../dtitk/tests/test_auto_SVResample.py | 5 +- .../dtitk/tests/test_auto_SVResampleTask.py | 5 +- .../tests/test_auto_TVAdjustOriginTask.py | 5 +- .../dtitk/tests/test_auto_TVAdjustVoxSp.py | 5 +- .../tests/test_auto_TVAdjustVoxSpTask.py | 5 +- .../dtitk/tests/test_auto_TVResample.py | 5 +- .../dtitk/tests/test_auto_TVResampleTask.py | 5 +- .../dtitk/tests/test_auto_TVtool.py | 4 +- .../dtitk/tests/test_auto_TVtoolTask.py | 4 +- .../dtitk/tests/test_auto_affScalarVolTask.py | 6 +- .../tests/test_auto_affSymTensor3DVolTask.py | 6 +- .../tests/test_auto_diffeoScalarVolTask.py | 6 +- .../test_auto_diffeoSymTensor3DVolTask.py | 6 +- .../elastix/tests/test_auto_AnalyzeWarp.py | 12 +- .../elastix/tests/test_auto_ApplyWarp.py | 4 +- .../elastix/tests/test_auto_EditTransform.py | 11 +- .../elastix/tests/test_auto_PointsWarp.py | 4 +- .../elastix/tests/test_auto_Registration.py | 19 +--- .../tests/test_auto_AddXFormToHeader.py | 6 +- .../freesurfer/tests/test_auto_Aparc2Aseg.py | 66 +++-------- .../freesurfer/tests/test_auto_Apas2Aseg.py | 10 +- .../freesurfer/tests/test_auto_ApplyMask.py | 22 +--- .../tests/test_auto_ApplyVolTransform.py | 17 +-- .../freesurfer/tests/test_auto_Binarize.py | 18 +-- .../freesurfer/tests/test_auto_CALabel.py | 18 +-- .../freesurfer/tests/test_auto_CANormalize.py | 23 +--- .../freesurfer/tests/test_auto_CARegister.py | 15 +-- .../test_auto_CheckTalairachAlignment.py | 3 +- .../freesurfer/tests/test_auto_Concatenate.py | 15 +-- .../tests/test_auto_ConcatenateLTA.py | 6 +- .../freesurfer/tests/test_auto_Contrast.py | 28 ++--- .../freesurfer/tests/test_auto_Curvature.py | 7 +- .../tests/test_auto_CurvatureStats.py | 12 +- .../tests/test_auto_DICOMConvert.py | 14 +-- .../freesurfer/tests/test_auto_EMRegister.py | 17 +-- .../tests/test_auto_EditWMwithAseg.py | 8 +- .../freesurfer/tests/test_auto_EulerNumber.py | 5 +- .../tests/test_auto_ExtractMainComponent.py | 4 +- .../freesurfer/tests/test_auto_FSCommand.py | 2 +- .../tests/test_auto_FSCommandOpenMP.py | 2 +- .../tests/test_auto_FSScriptCommand.py | 2 +- .../freesurfer/tests/test_auto_FitMSParams.py | 9 +- .../freesurfer/tests/test_auto_FixTopology.py | 24 +--- .../tests/test_auto_FuseSegmentations.py | 5 +- .../freesurfer/tests/test_auto_GLMFit.py | 53 +++------ .../freesurfer/tests/test_auto_ImageInfo.py | 5 +- .../freesurfer/tests/test_auto_Jacobian.py | 7 +- .../freesurfer/tests/test_auto_LTAConvert.py | 25 ++--- .../freesurfer/tests/test_auto_Label2Annot.py | 14 +-- .../freesurfer/tests/test_auto_Label2Label.py | 26 +---- .../freesurfer/tests/test_auto_Label2Vol.py | 20 +--- .../tests/test_auto_MNIBiasCorrection.py | 16 +-- .../freesurfer/tests/test_auto_MPRtoMNI305.py | 4 +- .../freesurfer/tests/test_auto_MRIConvert.py | 44 ++------ .../freesurfer/tests/test_auto_MRICoreg.py | 13 +-- .../freesurfer/tests/test_auto_MRIFill.py | 23 +--- .../tests/test_auto_MRIMarchingCubes.py | 6 +- .../freesurfer/tests/test_auto_MRIPretess.py | 7 +- .../freesurfer/tests/test_auto_MRISPreproc.py | 7 +- .../tests/test_auto_MRISPreprocReconAll.py | 18 +-- .../tests/test_auto_MRITessellate.py | 6 +- .../freesurfer/tests/test_auto_MRIsCALabel.py | 22 +--- .../freesurfer/tests/test_auto_MRIsCalc.py | 7 +- .../freesurfer/tests/test_auto_MRIsCombine.py | 5 +- .../freesurfer/tests/test_auto_MRIsConvert.py | 36 ++---- .../freesurfer/tests/test_auto_MRIsExpand.py | 5 +- .../freesurfer/tests/test_auto_MRIsInflate.py | 13 +-- .../freesurfer/tests/test_auto_MS_LDA.py | 6 +- .../tests/test_auto_MakeAverageSubject.py | 2 +- .../tests/test_auto_MakeSurfaces.py | 48 +++----- .../freesurfer/tests/test_auto_Normalize.py | 16 +-- .../tests/test_auto_OneSampleTTest.py | 53 +++------ .../freesurfer/tests/test_auto_Paint.py | 7 +- .../tests/test_auto_ParcellationStats.py | 58 +++------- .../tests/test_auto_ParseDICOMDir.py | 5 +- .../freesurfer/tests/test_auto_ReconAll.py | 65 +++-------- .../freesurfer/tests/test_auto_Register.py | 13 +-- .../tests/test_auto_RegisterAVItoTalairach.py | 5 +- .../tests/test_auto_RelabelHypointensities.py | 12 +- .../tests/test_auto_RemoveIntersection.py | 6 +- .../freesurfer/tests/test_auto_RemoveNeck.py | 8 +- .../freesurfer/tests/test_auto_Resample.py | 6 +- .../tests/test_auto_RobustRegister.py | 35 ++---- .../tests/test_auto_RobustTemplate.py | 4 +- .../tests/test_auto_SampleToSurface.py | 17 +-- .../freesurfer/tests/test_auto_SegStats.py | 39 ++----- .../tests/test_auto_SegStatsReconAll.py | 78 ++++--------- .../freesurfer/tests/test_auto_SegmentCC.py | 14 +-- .../freesurfer/tests/test_auto_SegmentWM.py | 6 +- .../freesurfer/tests/test_auto_Smooth.py | 7 +- .../tests/test_auto_SmoothTessellation.py | 16 +-- .../freesurfer/tests/test_auto_Sphere.py | 11 +- .../tests/test_auto_SphericalAverage.py | 11 +- .../tests/test_auto_Surface2VolTransform.py | 13 +-- .../tests/test_auto_SurfaceSmooth.py | 6 +- .../tests/test_auto_SurfaceSnapshots.py | 16 +-- .../tests/test_auto_SurfaceTransform.py | 7 +- .../tests/test_auto_SynthesizeFLASH.py | 7 +- .../tests/test_auto_TalairachAVI.py | 4 +- .../freesurfer/tests/test_auto_TalairachQC.py | 3 +- .../freesurfer/tests/test_auto_Tkregister2.py | 25 ++--- .../tests/test_auto_UnpackSDICOMDir.py | 20 +--- .../freesurfer/tests/test_auto_VolumeMask.py | 34 ++---- .../tests/test_auto_WatershedSkullStrip.py | 7 +- .../fsl/tests/test_auto_AR1Image.py | 4 +- .../fsl/tests/test_auto_AccuracyTester.py | 3 - .../fsl/tests/test_auto_ApplyMask.py | 5 +- .../fsl/tests/test_auto_ApplyTOPUP.py | 6 +- .../fsl/tests/test_auto_ApplyWarp.py | 25 +---- .../fsl/tests/test_auto_ApplyXFM.py | 36 ++---- .../interfaces/fsl/tests/test_auto_AvScale.py | 2 - .../interfaces/fsl/tests/test_auto_B0Calc.py | 4 +- .../fsl/tests/test_auto_BEDPOSTX5.py | 31 ++---- nipype/interfaces/fsl/tests/test_auto_BET.py | 25 ++--- .../fsl/tests/test_auto_BinaryMaths.py | 5 +- .../fsl/tests/test_auto_ChangeDataType.py | 4 +- .../fsl/tests/test_auto_Classifier.py | 6 +- .../interfaces/fsl/tests/test_auto_Cleaner.py | 3 +- .../interfaces/fsl/tests/test_auto_Cluster.py | 32 ++---- .../interfaces/fsl/tests/test_auto_Complex.py | 21 +--- .../fsl/tests/test_auto_ContrastMgr.py | 9 +- .../fsl/tests/test_auto_ConvertWarp.py | 34 ++---- .../fsl/tests/test_auto_ConvertXFM.py | 5 +- .../fsl/tests/test_auto_CopyGeom.py | 4 +- .../interfaces/fsl/tests/test_auto_DTIFit.py | 38 +++---- .../fsl/tests/test_auto_DilateImage.py | 5 +- .../fsl/tests/test_auto_DistanceMap.py | 11 +- .../fsl/tests/test_auto_DualRegression.py | 5 +- .../fsl/tests/test_auto_EPIDeWarp.py | 20 +--- nipype/interfaces/fsl/tests/test_auto_Eddy.py | 40 ++----- .../fsl/tests/test_auto_EddyCorrect.py | 4 +- .../fsl/tests/test_auto_EddyQuad.py | 29 ++--- .../interfaces/fsl/tests/test_auto_EpiReg.py | 56 ++++------ .../fsl/tests/test_auto_ErodeImage.py | 5 +- .../fsl/tests/test_auto_ExtractROI.py | 4 +- nipype/interfaces/fsl/tests/test_auto_FAST.py | 21 +--- nipype/interfaces/fsl/tests/test_auto_FEAT.py | 3 +- .../fsl/tests/test_auto_FEATModel.py | 11 +- .../fsl/tests/test_auto_FEATRegister.py | 7 +- .../interfaces/fsl/tests/test_auto_FIRST.py | 6 +- .../interfaces/fsl/tests/test_auto_FLAMEO.py | 22 +--- .../interfaces/fsl/tests/test_auto_FLIRT.py | 36 ++---- .../interfaces/fsl/tests/test_auto_FNIRT.py | 36 ++---- .../fsl/tests/test_auto_FSLXCommand.py | 10 +- .../interfaces/fsl/tests/test_auto_FUGUE.py | 45 ++------ .../fsl/tests/test_auto_FeatureExtractor.py | 2 - .../fsl/tests/test_auto_FilterRegressor.py | 10 +- .../fsl/tests/test_auto_FindTheBiggest.py | 7 +- nipype/interfaces/fsl/tests/test_auto_GLM.py | 70 +++--------- .../fsl/tests/test_auto_ICA_AROMA.py | 17 +-- .../fsl/tests/test_auto_ImageMaths.py | 10 +- .../fsl/tests/test_auto_ImageMeants.py | 9 +- .../fsl/tests/test_auto_ImageStats.py | 6 +- .../interfaces/fsl/tests/test_auto_InvWarp.py | 5 +- .../fsl/tests/test_auto_IsotropicSmooth.py | 4 +- .../interfaces/fsl/tests/test_auto_L2Model.py | 6 +- .../interfaces/fsl/tests/test_auto_MCFLIRT.py | 22 ++-- .../interfaces/fsl/tests/test_auto_MELODIC.py | 50 ++------- .../fsl/tests/test_auto_MakeDyadicVectors.py | 7 +- .../fsl/tests/test_auto_MathsCommand.py | 4 +- .../fsl/tests/test_auto_MaxImage.py | 4 +- .../fsl/tests/test_auto_MaxnImage.py | 4 +- .../fsl/tests/test_auto_MeanImage.py | 4 +- .../fsl/tests/test_auto_MedianImage.py | 4 +- .../interfaces/fsl/tests/test_auto_Merge.py | 3 +- .../fsl/tests/test_auto_MinImage.py | 4 +- .../fsl/tests/test_auto_MotionOutliers.py | 15 +-- .../fsl/tests/test_auto_MultiImageMaths.py | 4 +- .../tests/test_auto_MultipleRegressDesign.py | 8 +- .../interfaces/fsl/tests/test_auto_Overlay.py | 6 +- .../interfaces/fsl/tests/test_auto_PRELUDE.py | 14 +-- .../fsl/tests/test_auto_PercentileImage.py | 4 +- .../fsl/tests/test_auto_PlotMotionParams.py | 3 +- .../fsl/tests/test_auto_PlotTimeSeries.py | 8 +- .../fsl/tests/test_auto_PowerSpectrum.py | 4 +- .../fsl/tests/test_auto_PrepareFieldmap.py | 5 +- .../fsl/tests/test_auto_ProbTrackX.py | 46 ++------ .../fsl/tests/test_auto_ProbTrackX2.py | 76 ++++--------- .../fsl/tests/test_auto_Randomise.py | 18 +-- .../fsl/tests/test_auto_Reorient2Std.py | 4 +- .../fsl/tests/test_auto_RobustFOV.py | 7 +- nipype/interfaces/fsl/tests/test_auto_SMM.py | 8 +- .../interfaces/fsl/tests/test_auto_SUSAN.py | 4 +- .../interfaces/fsl/tests/test_auto_SigLoss.py | 9 +- .../interfaces/fsl/tests/test_auto_Slice.py | 1 - .../fsl/tests/test_auto_SliceTimer.py | 14 +-- .../interfaces/fsl/tests/test_auto_Slicer.py | 6 +- .../interfaces/fsl/tests/test_auto_Smooth.py | 4 +- .../fsl/tests/test_auto_SmoothEstimate.py | 3 - .../fsl/tests/test_auto_SpatialFilter.py | 5 +- .../interfaces/fsl/tests/test_auto_Split.py | 1 - .../fsl/tests/test_auto_StdImage.py | 4 +- .../fsl/tests/test_auto_SwapDimensions.py | 4 +- .../interfaces/fsl/tests/test_auto_TOPUP.py | 18 +-- .../fsl/tests/test_auto_TemporalFilter.py | 4 +- .../fsl/tests/test_auto_Threshold.py | 4 +- .../fsl/tests/test_auto_TractSkeleton.py | 26 ++--- .../fsl/tests/test_auto_Training.py | 2 +- .../fsl/tests/test_auto_UnaryMaths.py | 4 +- .../interfaces/fsl/tests/test_auto_VecReg.py | 35 ++---- .../fsl/tests/test_auto_WarpPoints.py | 8 +- .../fsl/tests/test_auto_WarpPointsFromStd.py | 7 +- .../fsl/tests/test_auto_WarpPointsToStd.py | 13 +-- .../fsl/tests/test_auto_WarpUtils.py | 12 +- .../fsl/tests/test_auto_XFibres5.py | 15 +-- .../minc/tests/test_auto_Average.py | 3 +- .../interfaces/minc/tests/test_auto_BBox.py | 4 +- .../interfaces/minc/tests/test_auto_Beast.py | 2 +- .../minc/tests/test_auto_BestLinReg.py | 8 +- .../minc/tests/test_auto_BigAverage.py | 11 +- .../interfaces/minc/tests/test_auto_Blob.py | 4 +- .../interfaces/minc/tests/test_auto_Blur.py | 14 +-- .../interfaces/minc/tests/test_auto_Calc.py | 3 +- .../minc/tests/test_auto_Convert.py | 4 +- .../interfaces/minc/tests/test_auto_Copy.py | 4 +- .../interfaces/minc/tests/test_auto_Dump.py | 4 +- .../minc/tests/test_auto_Extract.py | 4 +- .../minc/tests/test_auto_Gennlxfm.py | 10 +- .../interfaces/minc/tests/test_auto_Math.py | 3 +- .../interfaces/minc/tests/test_auto_NlpFit.py | 10 +- .../interfaces/minc/tests/test_auto_Norm.py | 6 +- nipype/interfaces/minc/tests/test_auto_Pik.py | 4 +- .../minc/tests/test_auto_Resample.py | 4 +- .../minc/tests/test_auto_Reshape.py | 3 +- .../interfaces/minc/tests/test_auto_ToEcat.py | 4 +- .../interfaces/minc/tests/test_auto_ToRaw.py | 4 +- .../minc/tests/test_auto_VolSymm.py | 12 +- .../minc/tests/test_auto_Volcentre.py | 4 +- .../interfaces/minc/tests/test_auto_Voliso.py | 4 +- .../interfaces/minc/tests/test_auto_Volpad.py | 4 +- .../interfaces/minc/tests/test_auto_XfmAvg.py | 5 +- .../minc/tests/test_auto_XfmConcat.py | 3 +- .../minc/tests/test_auto_XfmInvert.py | 5 +- .../test_auto_JistBrainMgdmSegmentation.py | 38 ++----- ...est_auto_JistBrainMp2rageDuraEstimation.py | 12 +- ...est_auto_JistBrainMp2rageSkullStripping.py | 28 ++--- .../test_auto_JistBrainPartialVolumeFilter.py | 7 +- ...est_auto_JistCortexSurfaceMeshInflation.py | 9 +- .../test_auto_JistIntensityMp2rageMasking.py | 23 ++-- .../test_auto_JistLaminarProfileCalculator.py | 12 +- .../test_auto_JistLaminarProfileGeometry.py | 7 +- .../test_auto_JistLaminarProfileSampling.py | 19 +--- .../test_auto_JistLaminarROIAveraging.py | 17 +-- ...test_auto_JistLaminarVolumetricLayering.py | 16 +-- ...test_auto_MedicAlgorithmImageCalculator.py | 12 +- .../test_auto_MedicAlgorithmLesionToads.py | 48 +++----- .../test_auto_MedicAlgorithmMipavReorient.py | 5 +- .../mipav/tests/test_auto_MedicAlgorithmN3.py | 9 +- .../test_auto_MedicAlgorithmSPECTRE2010.py | 28 ++--- .../mipav/tests/test_auto_RandomVol.py | 2 +- .../mne/tests/test_auto_WatershedBEM.py | 21 +--- ..._auto_ConstrainedSphericalDeconvolution.py | 9 +- .../test_auto_DWI2SphericalHarmonicsImage.py | 5 +- .../mrtrix/tests/test_auto_DWI2Tensor.py | 4 +- ...est_auto_DiffusionTensorStreamlineTrack.py | 9 +- .../tests/test_auto_Directions2Amplitude.py | 9 +- .../mrtrix/tests/test_auto_Erode.py | 4 +- .../tests/test_auto_EstimateResponseForSH.py | 6 +- .../mrtrix/tests/test_auto_FSL2MRTrix.py | 17 +-- .../mrtrix/tests/test_auto_FilterTracks.py | 6 +- .../mrtrix/tests/test_auto_FindShPeaks.py | 10 +- .../tests/test_auto_GenerateDirections.py | 3 +- .../test_auto_GenerateWhiteMatterMask.py | 6 +- .../mrtrix/tests/test_auto_MRConvert.py | 4 +- .../mrtrix/tests/test_auto_MRMultiply.py | 3 +- .../mrtrix/tests/test_auto_MRTransform.py | 6 +- .../mrtrix/tests/test_auto_MRTrix2TrackVis.py | 13 +-- .../mrtrix/tests/test_auto_MRTrixInfo.py | 1 - .../mrtrix/tests/test_auto_MedianFilter3D.py | 4 +- ...cSphericallyDeconvolutedStreamlineTrack.py | 8 +- ..._SphericallyDeconvolutedStreamlineTrack.py | 8 +- .../mrtrix/tests/test_auto_StreamlineTrack.py | 8 +- .../test_auto_Tensor2ApparentDiffusion.py | 4 +- .../test_auto_Tensor2FractionalAnisotropy.py | 4 +- .../mrtrix/tests/test_auto_Tensor2Vector.py | 4 +- .../mrtrix/tests/test_auto_Threshold.py | 4 +- .../mrtrix/tests/test_auto_Tracks2Prob.py | 5 +- .../mrtrix3/tests/test_auto_ACTPrepareFSL.py | 3 +- .../mrtrix3/tests/test_auto_BrainMask.py | 15 +-- .../tests/test_auto_BuildConnectome.py | 14 +-- .../mrtrix3/tests/test_auto_ComputeTDI.py | 23 +--- .../mrtrix3/tests/test_auto_DWIBiasCorrect.py | 30 ++--- .../mrtrix3/tests/test_auto_DWIDenoise.py | 24 +--- .../mrtrix3/tests/test_auto_DWIExtract.py | 16 +-- .../mrtrix3/tests/test_auto_EstimateFOD.py | 41 ++----- .../mrtrix3/tests/test_auto_FitTensor.py | 20 +--- .../mrtrix3/tests/test_auto_Generate5tt.py | 16 +-- .../mrtrix3/tests/test_auto_LabelConfig.py | 29 +---- .../mrtrix3/tests/test_auto_LabelConvert.py | 10 +- .../mrtrix3/tests/test_auto_MRConvert.py | 15 +-- .../mrtrix3/tests/test_auto_MRDeGibbs.py | 16 +-- .../mrtrix3/tests/test_auto_MRMath.py | 16 +-- .../mrtrix3/tests/test_auto_Mesh2PVE.py | 9 +- .../tests/test_auto_ReplaceFSwithFIRST.py | 5 +- .../mrtrix3/tests/test_auto_ResponseSD.py | 36 ++---- .../mrtrix3/tests/test_auto_TCK2VTK.py | 13 +-- .../mrtrix3/tests/test_auto_TensorMetrics.py | 34 ++---- .../mrtrix3/tests/test_auto_Tractography.py | 38 ++----- .../niftyfit/tests/test_auto_FitQt1.py | 24 ++-- .../niftyreg/tests/test_auto_RegAladin.py | 23 +--- .../niftyreg/tests/test_auto_RegAverage.py | 7 +- .../niftyreg/tests/test_auto_RegF3D.py | 32 ++---- .../niftyreg/tests/test_auto_RegJacobian.py | 9 +- .../niftyreg/tests/test_auto_RegMeasure.py | 5 +- .../niftyreg/tests/test_auto_RegResample.py | 10 +- .../niftyreg/tests/test_auto_RegTools.py | 14 +-- .../niftyreg/tests/test_auto_RegTransform.py | 15 +-- .../niftyseg/tests/test_auto_BinaryMaths.py | 5 +- .../tests/test_auto_BinaryMathsInteger.py | 4 +- .../niftyseg/tests/test_auto_BinaryStats.py | 3 - .../niftyseg/tests/test_auto_CalcTopNCC.py | 6 +- .../interfaces/niftyseg/tests/test_auto_EM.py | 16 +-- .../niftyseg/tests/test_auto_FillLesions.py | 10 +- .../niftyseg/tests/test_auto_LabelFusion.py | 16 +-- .../niftyseg/tests/test_auto_MathsCommand.py | 4 +- .../niftyseg/tests/test_auto_Merge.py | 4 +- .../niftyseg/tests/test_auto_PatchMatch.py | 6 +- .../niftyseg/tests/test_auto_StatsCommand.py | 2 - .../niftyseg/tests/test_auto_TupleMaths.py | 6 +- .../niftyseg/tests/test_auto_UnaryMaths.py | 4 +- .../niftyseg/tests/test_auto_UnaryStats.py | 2 - .../nipy/tests/test_auto_ComputeMask.py | 9 +- .../nipy/tests/test_auto_EstimateContrast.py | 10 +- .../interfaces/nipy/tests/test_auto_FitGLM.py | 6 +- .../nipy/tests/test_auto_Similarity.py | 14 +-- .../interfaces/nipy/tests/test_auto_Trim.py | 9 +- .../tests/test_auto_CoherenceAnalyzer.py | 17 ++- ...t_auto_BRAINSPosteriorToContinuousClass.py | 37 ++----- .../brains/tests/test_auto_BRAINSTalairach.py | 9 +- .../tests/test_auto_BRAINSTalairachMask.py | 17 +-- .../tests/test_auto_GenerateEdgeMapImage.py | 9 +- .../tests/test_auto_GeneratePurePlugMask.py | 2 +- .../test_auto_HistogramMatchingFilter.py | 22 +--- .../brains/tests/test_auto_SimilarityIndex.py | 15 +-- .../diffusion/tests/test_auto_DWIConvert.py | 35 ++---- .../tests/test_auto_compareTractInclusion.py | 10 +- .../diffusion/tests/test_auto_dtiaverage.py | 2 +- .../diffusion/tests/test_auto_dtiestim.py | 23 ++-- .../diffusion/tests/test_auto_dtiprocess.py | 60 ++++------ .../tests/test_auto_extractNrrdVectorIndex.py | 7 +- .../tests/test_auto_gtractAnisotropyMap.py | 7 +- .../tests/test_auto_gtractAverageBvalues.py | 7 +- .../tests/test_auto_gtractClipAnisotropy.py | 7 +- .../tests/test_auto_gtractCoRegAnatomy.py | 17 +-- .../tests/test_auto_gtractConcatDwi.py | 2 +- .../test_auto_gtractCopyImageOrientation.py | 12 +- .../tests/test_auto_gtractCoregBvalues.py | 14 +-- .../tests/test_auto_gtractCostFastMarching.py | 18 +-- .../tests/test_auto_gtractCreateGuideFiber.py | 7 +- .../test_auto_gtractFastMarchingTracking.py | 21 +--- .../tests/test_auto_gtractFiberTracking.py | 25 +---- .../tests/test_auto_gtractImageConformity.py | 12 +- .../test_auto_gtractInvertBSplineTransform.py | 12 +- ...test_auto_gtractInvertDisplacementField.py | 12 +- .../test_auto_gtractInvertRigidTransform.py | 7 +- .../test_auto_gtractResampleAnisotropy.py | 17 +-- .../tests/test_auto_gtractResampleB0.py | 17 +-- .../test_auto_gtractResampleCodeImage.py | 17 +-- .../test_auto_gtractResampleDWIInPlace.py | 24 +--- .../tests/test_auto_gtractResampleFibers.py | 15 +-- .../diffusion/tests/test_auto_gtractTensor.py | 12 +- ...auto_gtractTransformToDisplacementField.py | 12 +- .../diffusion/tests/test_auto_maxcurvature.py | 7 +- .../tests/test_auto_UKFTractography.py | 19 +--- .../tests/test_auto_fiberprocess.py | 24 +--- .../tests/test_auto_fiberstats.py | 5 +- .../tests/test_auto_fibertrack.py | 12 +- .../filtering/tests/test_auto_CannyEdge.py | 7 +- ...to_CannySegmentationLevelSetImageFilter.py | 14 +-- .../filtering/tests/test_auto_DilateImage.py | 12 +- .../filtering/tests/test_auto_DilateMask.py | 12 +- .../filtering/tests/test_auto_DistanceMaps.py | 12 +- .../test_auto_DumpBinaryTrainingVectors.py | 10 +- .../filtering/tests/test_auto_ErodeImage.py | 12 +- .../tests/test_auto_FlippedDifference.py | 12 +- .../test_auto_GenerateBrainClippedImage.py | 12 +- .../test_auto_GenerateSummedGradientImage.py | 12 +- .../tests/test_auto_GenerateTestImage.py | 7 +- ...GradientAnisotropicDiffusionImageFilter.py | 7 +- .../tests/test_auto_HammerAttributeCreator.py | 15 +-- .../tests/test_auto_NeighborhoodMean.py | 12 +- .../tests/test_auto_NeighborhoodMedian.py | 12 +- .../tests/test_auto_STAPLEAnalysis.py | 2 +- .../test_auto_TextureFromNoiseImageFilter.py | 7 +- .../tests/test_auto_TextureMeasureFilter.py | 12 +- .../tests/test_auto_UnbiasedNonLocalMeans.py | 7 +- .../legacy/tests/test_auto_scalartransform.py | 14 +-- .../tests/test_auto_BRAINSDemonWarp.py | 35 ++---- .../registration/tests/test_auto_BRAINSFit.py | 51 +++------ .../tests/test_auto_BRAINSResample.py | 22 +--- .../tests/test_auto_BRAINSResize.py | 7 +- .../test_auto_BRAINSTransformFromFiducials.py | 12 +- .../tests/test_auto_VBRAINSDemonWarp.py | 25 ++--- .../segmentation/tests/test_auto_BRAINSABC.py | 22 ++-- .../test_auto_BRAINSConstellationDetector.py | 55 +++------- ...BRAINSCreateLabelMapFromProbabilityMaps.py | 9 +- .../segmentation/tests/test_auto_BRAINSCut.py | 9 +- .../tests/test_auto_BRAINSMultiSTAPLE.py | 9 +- .../tests/test_auto_BRAINSROIAuto.py | 9 +- ...t_auto_BinaryMaskEditorBasedOnLandmarks.py | 12 +- .../segmentation/tests/test_auto_ESLR.py | 7 +- .../semtools/tests/test_auto_DWICompare.py | 10 +- .../tests/test_auto_DWISimpleCompare.py | 10 +- ...o_GenerateCsfClippedFromClassifiedImage.py | 7 +- .../tests/test_auto_BRAINSAlignMSP.py | 9 +- .../tests/test_auto_BRAINSClipInferior.py | 7 +- .../test_auto_BRAINSConstellationModeler.py | 9 +- .../tests/test_auto_BRAINSEyeDetector.py | 7 +- ...est_auto_BRAINSInitializedControlPoints.py | 7 +- .../test_auto_BRAINSLandmarkInitializer.py | 15 +-- .../test_auto_BRAINSLinearModelerEPCA.py | 5 +- .../tests/test_auto_BRAINSLmkTransform.py | 24 +--- .../utilities/tests/test_auto_BRAINSMush.py | 21 +--- .../tests/test_auto_BRAINSSnapShotWriter.py | 2 +- .../tests/test_auto_BRAINSTransformConvert.py | 14 +-- ...st_auto_BRAINSTrimForegroundInDirection.py | 7 +- .../tests/test_auto_FindCenterOfBrain.py | 22 ++-- ...auto_GenerateLabelMapFromProbabilityMap.py | 2 +- .../tests/test_auto_ImageRegionPlotter.py | 20 +--- .../tests/test_auto_JointHistogram.py | 20 +--- .../tests/test_auto_ShuffleVectorsModule.py | 7 +- .../utilities/tests/test_auto_fcsv_to_hdf5.py | 9 +- .../tests/test_auto_insertMidACPCpoint.py | 7 +- ...test_auto_landmarksConstellationAligner.py | 7 +- ...test_auto_landmarksConstellationWeights.py | 17 +-- .../diffusion/tests/test_auto_DTIexport.py | 7 +- .../diffusion/tests/test_auto_DTIimport.py | 7 +- .../test_auto_DWIJointRicianLMMSEFilter.py | 7 +- .../tests/test_auto_DWIRicianLMMSEFilter.py | 7 +- .../tests/test_auto_DWIToDTIEstimation.py | 16 +-- ..._auto_DiffusionTensorScalarMeasurements.py | 7 +- ...est_auto_DiffusionWeightedVolumeMasking.py | 11 +- .../tests/test_auto_ResampleDTIVolume.py | 22 +--- .../test_auto_TractographyLabelMapSeeding.py | 13 +-- .../tests/test_auto_AddScalarVolumes.py | 8 +- .../tests/test_auto_CastScalarVolume.py | 7 +- .../tests/test_auto_CheckerBoardFilter.py | 8 +- ...test_auto_CurvatureAnisotropicDiffusion.py | 7 +- .../tests/test_auto_ExtractSkeleton.py | 7 +- .../test_auto_GaussianBlurImageFilter.py | 7 +- .../test_auto_GradientAnisotropicDiffusion.py | 7 +- .../test_auto_GrayscaleFillHoleImageFilter.py | 7 +- ...test_auto_GrayscaleGrindPeakImageFilter.py | 7 +- .../tests/test_auto_HistogramMatching.py | 8 +- .../tests/test_auto_ImageLabelCombine.py | 8 +- .../tests/test_auto_MaskScalarVolume.py | 8 +- .../tests/test_auto_MedianImageFilter.py | 7 +- .../tests/test_auto_MultiplyScalarVolumes.py | 8 +- .../test_auto_N4ITKBiasFieldCorrection.py | 19 +--- ...test_auto_ResampleScalarVectorDWIVolume.py | 22 +--- .../tests/test_auto_SubtractScalarVolumes.py | 8 +- .../tests/test_auto_ThresholdScalarVolume.py | 7 +- ...auto_VotingBinaryHoleFillingImageFilter.py | 7 +- ...est_auto_DWIUnbiasedNonLocalMeansFilter.py | 7 +- .../tests/test_auto_AffineRegistration.py | 11 +- ...test_auto_BSplineDeformableRegistration.py | 13 +-- .../test_auto_BSplineToDeformationField.py | 12 +- .../test_auto_ExpertAutomatedRegistration.py | 16 +-- .../tests/test_auto_LinearRegistration.py | 11 +- ..._auto_MultiResolutionAffineRegistration.py | 11 +- .../test_auto_OtsuThresholdImageFilter.py | 7 +- .../test_auto_OtsuThresholdSegmentation.py | 7 +- .../tests/test_auto_ResampleScalarVolume.py | 7 +- .../tests/test_auto_RigidRegistration.py | 11 +- .../test_auto_IntensityDifferenceMetric.py | 10 +- ..._auto_PETStandardUptakeValueComputation.py | 22 +--- .../tests/test_auto_ACPCTransform.py | 2 +- .../tests/test_auto_BRAINSDemonWarp.py | 35 ++---- .../registration/tests/test_auto_BRAINSFit.py | 39 ++----- .../tests/test_auto_BRAINSResample.py | 22 +--- .../tests/test_auto_FiducialRegistration.py | 2 +- .../tests/test_auto_VBRAINSDemonWarp.py | 25 ++--- .../tests/test_auto_BRAINSROIAuto.py | 9 +- .../tests/test_auto_EMSegmentCommandLine.py | 19 +--- .../test_auto_RobustStatisticsSegmenter.py | 8 +- ...st_auto_SimpleRegionGrowingSegmentation.py | 7 +- .../tests/test_auto_DicomToNrrdConverter.py | 7 +- ...test_auto_EMSegmentTransformToNewFormat.py | 7 +- .../tests/test_auto_GrayscaleModelMaker.py | 7 +- .../tests/test_auto_LabelMapSmoothing.py | 7 +- .../slicer/tests/test_auto_MergeModels.py | 8 +- .../slicer/tests/test_auto_ModelMaker.py | 6 +- .../slicer/tests/test_auto_ModelToLabelMap.py | 8 +- .../tests/test_auto_OrientScalarVolume.py | 7 +- .../tests/test_auto_ProbeVolumeWithModel.py | 8 +- .../spm/tests/test_auto_Analyze2nii.py | 7 +- .../spm/tests/test_auto_ApplyDeformations.py | 2 - .../test_auto_ApplyInverseDeformation.py | 7 +- .../spm/tests/test_auto_ApplyTransform.py | 13 +-- .../spm/tests/test_auto_CalcCoregAffine.py | 14 +-- .../spm/tests/test_auto_Coregister.py | 1 - .../interfaces/spm/tests/test_auto_DARTEL.py | 2 +- .../spm/tests/test_auto_DARTELNorm2MNI.py | 3 +- .../spm/tests/test_auto_EstimateContrast.py | 4 +- .../spm/tests/test_auto_EstimateModel.py | 11 +- .../spm/tests/test_auto_FactorialDesign.py | 12 +- .../spm/tests/test_auto_FieldMap.py | 7 +- .../spm/tests/test_auto_Level1Design.py | 12 +- .../test_auto_MultipleRegressionDesign.py | 12 +- .../spm/tests/test_auto_Normalize.py | 4 - .../spm/tests/test_auto_Normalize12.py | 3 - .../tests/test_auto_OneSampleTTestDesign.py | 12 +- .../spm/tests/test_auto_PairedTTestDesign.py | 12 +- .../interfaces/spm/tests/test_auto_Realign.py | 7 +- .../spm/tests/test_auto_RealignUnwarp.py | 8 +- .../interfaces/spm/tests/test_auto_Reslice.py | 14 +-- .../spm/tests/test_auto_ResliceToReference.py | 5 +- .../interfaces/spm/tests/test_auto_Segment.py | 30 +++-- .../spm/tests/test_auto_Threshold.py | 6 +- .../tests/test_auto_ThresholdStatistics.py | 2 - .../tests/test_auto_TwoSampleTTestDesign.py | 12 +- .../spm/tests/test_auto_VBMSegment.py | 9 +- .../tests/test_auto_BIDSDataGrabber.py | 5 +- nipype/interfaces/tests/test_auto_Bru2.py | 3 +- nipype/interfaces/tests/test_auto_C3d.py | 1 - .../tests/test_auto_C3dAffineTool.py | 5 +- nipype/interfaces/tests/test_auto_CopyMeta.py | 12 +- .../interfaces/tests/test_auto_DataGrabber.py | 2 +- nipype/interfaces/tests/test_auto_DataSink.py | 4 +- nipype/interfaces/tests/test_auto_Dcm2nii.py | 3 - nipype/interfaces/tests/test_auto_Dcm2niix.py | 1 - nipype/interfaces/tests/test_auto_DcmStack.py | 4 +- .../tests/test_auto_FreeSurferSource.py | 60 ++-------- .../tests/test_auto_GroupAndStack.py | 2 +- .../tests/test_auto_JSONFileGrabber.py | 2 +- .../tests/test_auto_JSONFileSink.py | 4 +- .../interfaces/tests/test_auto_LookupMeta.py | 5 +- .../tests/test_auto_MatlabCommand.py | 5 +- .../interfaces/tests/test_auto_MergeNifti.py | 4 +- nipype/interfaces/tests/test_auto_MeshFix.py | 5 +- .../interfaces/tests/test_auto_MySQLSink.py | 1 - nipype/interfaces/tests/test_auto_PETPVC.py | 5 +- .../interfaces/tests/test_auto_Quickshear.py | 5 +- nipype/interfaces/tests/test_auto_Reorient.py | 9 +- nipype/interfaces/tests/test_auto_Rescale.py | 12 +- .../tests/test_auto_S3DataGrabber.py | 2 +- .../interfaces/tests/test_auto_SQLiteSink.py | 5 +- .../interfaces/tests/test_auto_SelectFiles.py | 2 +- .../tests/test_auto_SignalExtraction.py | 7 +- .../interfaces/tests/test_auto_SplitNifti.py | 7 +- nipype/interfaces/tests/test_auto_XNATSink.py | 3 +- .../interfaces/tests/test_auto_XNATSource.py | 3 +- .../utility/tests/test_auto_AssertEqual.py | 10 +- .../utility/tests/test_auto_CSVReader.py | 5 +- .../utility/tests/test_auto_Rename.py | 5 +- .../vista/tests/test_auto_Vnifti2Image.py | 5 +- .../vista/tests/test_auto_VtoMat.py | 4 +- .../workbench/tests/test_auto_CiftiSmooth.py | 11 +- .../tests/test_auto_MetricResample.py | 11 +- 779 files changed, 2407 insertions(+), 6772 deletions(-) diff --git a/nipype/algorithms/tests/test_auto_ACompCor.py b/nipype/algorithms/tests/test_auto_ACompCor.py index ff33a4f94d..e28c77d467 100644 --- a/nipype/algorithms/tests/test_auto_ACompCor.py +++ b/nipype/algorithms/tests/test_auto_ACompCor.py @@ -22,10 +22,7 @@ def test_ACompCor_inputs(): ), num_components=dict(xor=['variance_threshold'], ), pre_filter=dict(usedefault=True, ), - realigned_file=dict( - mandatory=True, - usedefault=True, - ), + realigned_file=dict(mandatory=True, ), regress_poly_degree=dict(usedefault=True, ), repetition_time=dict(), save_metadata=dict(usedefault=True, ), @@ -43,9 +40,9 @@ def test_ACompCor_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ACompCor_outputs(): output_map = dict( - components_file=dict(usedefault=True, ), - metadata_file=dict(usedefault=True, ), - pre_filter_file=dict(usedefault=True, ), + components_file=dict(), + metadata_file=dict(), + pre_filter_file=dict(), ) outputs = ACompCor.output_spec() diff --git a/nipype/algorithms/tests/test_auto_ActivationCount.py b/nipype/algorithms/tests/test_auto_ActivationCount.py index 5bbc837c74..d6e3ff7165 100644 --- a/nipype/algorithms/tests/test_auto_ActivationCount.py +++ b/nipype/algorithms/tests/test_auto_ActivationCount.py @@ -15,9 +15,9 @@ def test_ActivationCount_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ActivationCount_outputs(): output_map = dict( - acm_neg=dict(usedefault=True, ), - acm_pos=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), + acm_neg=dict(), + acm_pos=dict(), + out_file=dict(), ) outputs = ActivationCount.output_spec() diff --git a/nipype/algorithms/tests/test_auto_AddCSVColumn.py b/nipype/algorithms/tests/test_auto_AddCSVColumn.py index 82fba10b80..feedcf46e8 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVColumn.py +++ b/nipype/algorithms/tests/test_auto_AddCSVColumn.py @@ -7,10 +7,7 @@ def test_AddCSVColumn_inputs(): input_map = dict( extra_column_heading=dict(), extra_field=dict(), - in_file=dict( - mandatory=True, - usedefault=True, - ), + in_file=dict(mandatory=True, ), out_file=dict(usedefault=True, ), ) inputs = AddCSVColumn.input_spec() @@ -19,7 +16,7 @@ def test_AddCSVColumn_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AddCSVColumn_outputs(): - output_map = dict(csv_file=dict(usedefault=True, ), ) + output_map = dict(csv_file=dict(), ) outputs = AddCSVColumn.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_AddCSVRow.py b/nipype/algorithms/tests/test_auto_AddCSVRow.py index e96cef284f..4666a147d2 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVRow.py +++ b/nipype/algorithms/tests/test_auto_AddCSVRow.py @@ -14,7 +14,7 @@ def test_AddCSVRow_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AddCSVRow_outputs(): - output_map = dict(csv_file=dict(usedefault=True, ), ) + output_map = dict(csv_file=dict(), ) outputs = AddCSVRow.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_AddNoise.py b/nipype/algorithms/tests/test_auto_AddNoise.py index 3348f938ab..6e0655a93e 100644 --- a/nipype/algorithms/tests/test_auto_AddNoise.py +++ b/nipype/algorithms/tests/test_auto_AddNoise.py @@ -13,12 +13,9 @@ def test_AddNoise_inputs(): mandatory=True, usedefault=True, ), - in_file=dict( - mandatory=True, - usedefault=True, - ), - in_mask=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), + in_file=dict(mandatory=True, ), + in_mask=dict(), + out_file=dict(), snr=dict(usedefault=True, ), ) inputs = AddNoise.input_spec() @@ -27,7 +24,7 @@ def test_AddNoise_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AddNoise_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = AddNoise.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_ArtifactDetect.py b/nipype/algorithms/tests/test_auto_ArtifactDetect.py index 900a55c6a1..85c57b8823 100644 --- a/nipype/algorithms/tests/test_auto_ArtifactDetect.py +++ b/nipype/algorithms/tests/test_auto_ArtifactDetect.py @@ -8,7 +8,7 @@ def test_ArtifactDetect_inputs(): bound_by_brainmask=dict(usedefault=True, ), global_threshold=dict(usedefault=True, ), intersect_mask=dict(usedefault=True, ), - mask_file=dict(usedefault=True, ), + mask_file=dict(), mask_threshold=dict(), mask_type=dict(mandatory=True, ), norm_threshold=dict( diff --git a/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py b/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py index 18d1c3488f..3dbbd772c8 100644 --- a/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py +++ b/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py @@ -6,10 +6,7 @@ def test_CalculateNormalizedMoments_inputs(): input_map = dict( moment=dict(mandatory=True, ), - timeseries_file=dict( - mandatory=True, - usedefault=True, - ), + timeseries_file=dict(mandatory=True, ), ) inputs = CalculateNormalizedMoments.input_spec() diff --git a/nipype/algorithms/tests/test_auto_ComputeDVARS.py b/nipype/algorithms/tests/test_auto_ComputeDVARS.py index ddb06bb364..ca263c77ac 100644 --- a/nipype/algorithms/tests/test_auto_ComputeDVARS.py +++ b/nipype/algorithms/tests/test_auto_ComputeDVARS.py @@ -8,14 +8,8 @@ def test_ComputeDVARS_inputs(): figdpi=dict(usedefault=True, ), figformat=dict(usedefault=True, ), figsize=dict(usedefault=True, ), - in_file=dict( - mandatory=True, - usedefault=True, - ), - in_mask=dict( - mandatory=True, - usedefault=True, - ), + in_file=dict(mandatory=True, ), + in_mask=dict(mandatory=True, ), intensity_normalization=dict(usedefault=True, ), remove_zerovariance=dict(usedefault=True, ), save_all=dict(usedefault=True, ), @@ -35,13 +29,13 @@ def test_ComputeDVARS_outputs(): avg_nstd=dict(), avg_std=dict(), avg_vxstd=dict(), - fig_nstd=dict(usedefault=True, ), - fig_std=dict(usedefault=True, ), - fig_vxstd=dict(usedefault=True, ), - out_all=dict(usedefault=True, ), - out_nstd=dict(usedefault=True, ), - out_std=dict(usedefault=True, ), - out_vxstd=dict(usedefault=True, ), + fig_nstd=dict(), + fig_std=dict(), + fig_vxstd=dict(), + out_all=dict(), + out_nstd=dict(), + out_std=dict(), + out_vxstd=dict(), ) outputs = ComputeDVARS.output_spec() diff --git a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py index 47aac34917..0308653786 100644 --- a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py +++ b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py @@ -8,14 +8,8 @@ def test_ComputeMeshWarp_inputs(): metric=dict(usedefault=True, ), out_file=dict(usedefault=True, ), out_warp=dict(usedefault=True, ), - surface1=dict( - mandatory=True, - usedefault=True, - ), - surface2=dict( - mandatory=True, - usedefault=True, - ), + surface1=dict(mandatory=True, ), + surface2=dict(mandatory=True, ), weighting=dict(usedefault=True, ), ) inputs = ComputeMeshWarp.input_spec() @@ -26,8 +20,8 @@ def test_ComputeMeshWarp_inputs(): def test_ComputeMeshWarp_outputs(): output_map = dict( distance=dict(), - out_file=dict(usedefault=True, ), - out_warp=dict(usedefault=True, ), + out_file=dict(), + out_warp=dict(), ) outputs = ComputeMeshWarp.output_spec() diff --git a/nipype/algorithms/tests/test_auto_CreateNifti.py b/nipype/algorithms/tests/test_auto_CreateNifti.py index bf607edbe3..f8bf8a405f 100644 --- a/nipype/algorithms/tests/test_auto_CreateNifti.py +++ b/nipype/algorithms/tests/test_auto_CreateNifti.py @@ -6,14 +6,8 @@ def test_CreateNifti_inputs(): input_map = dict( affine=dict(), - data_file=dict( - mandatory=True, - usedefault=True, - ), - header_file=dict( - mandatory=True, - usedefault=True, - ), + data_file=dict(mandatory=True, ), + header_file=dict(mandatory=True, ), ) inputs = CreateNifti.input_spec() @@ -21,7 +15,7 @@ def test_CreateNifti_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CreateNifti_outputs(): - output_map = dict(nifti_file=dict(usedefault=True, ), ) + output_map = dict(nifti_file=dict(), ) outputs = CreateNifti.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_Distance.py b/nipype/algorithms/tests/test_auto_Distance.py index 3dfe5817e3..2c5d098d73 100644 --- a/nipype/algorithms/tests/test_auto_Distance.py +++ b/nipype/algorithms/tests/test_auto_Distance.py @@ -5,16 +5,10 @@ def test_Distance_inputs(): input_map = dict( - mask_volume=dict(usedefault=True, ), + mask_volume=dict(), method=dict(usedefault=True, ), - volume1=dict( - mandatory=True, - usedefault=True, - ), - volume2=dict( - mandatory=True, - usedefault=True, - ), + volume1=dict(mandatory=True, ), + volume2=dict(mandatory=True, ), ) inputs = Distance.input_spec() @@ -24,7 +18,7 @@ def test_Distance_inputs(): def test_Distance_outputs(): output_map = dict( distance=dict(), - histogram=dict(usedefault=True, ), + histogram=dict(), point1=dict(), point2=dict(), ) diff --git a/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py b/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py index e33f793b52..685dec61e8 100644 --- a/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py +++ b/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py @@ -7,10 +7,7 @@ def test_FramewiseDisplacement_inputs(): input_map = dict( figdpi=dict(usedefault=True, ), figsize=dict(usedefault=True, ), - in_file=dict( - mandatory=True, - usedefault=True, - ), + in_file=dict(mandatory=True, ), normalize=dict(usedefault=True, ), out_figure=dict(usedefault=True, ), out_file=dict(usedefault=True, ), @@ -27,8 +24,8 @@ def test_FramewiseDisplacement_inputs(): def test_FramewiseDisplacement_outputs(): output_map = dict( fd_average=dict(), - out_figure=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), + out_figure=dict(), + out_file=dict(), ) outputs = FramewiseDisplacement.output_spec() diff --git a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py index 8f11f836fd..e9e28aaa44 100644 --- a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py +++ b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py @@ -5,7 +5,7 @@ def test_FuzzyOverlap_inputs(): input_map = dict( - in_mask=dict(usedefault=True, ), + in_mask=dict(), in_ref=dict(mandatory=True, ), in_tst=dict(mandatory=True, ), out_file=dict(usedefault=True, ), diff --git a/nipype/algorithms/tests/test_auto_Gunzip.py b/nipype/algorithms/tests/test_auto_Gunzip.py index bf04db015d..f12e1f9b45 100644 --- a/nipype/algorithms/tests/test_auto_Gunzip.py +++ b/nipype/algorithms/tests/test_auto_Gunzip.py @@ -4,18 +4,14 @@ def test_Gunzip_inputs(): - input_map = dict( - in_file=dict( - mandatory=True, - usedefault=True, - ), ) + input_map = dict(in_file=dict(mandatory=True, ), ) inputs = Gunzip.input_spec() for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Gunzip_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Gunzip.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_ICC.py b/nipype/algorithms/tests/test_auto_ICC.py index 98260c3db1..1a4a2b1517 100644 --- a/nipype/algorithms/tests/test_auto_ICC.py +++ b/nipype/algorithms/tests/test_auto_ICC.py @@ -5,10 +5,7 @@ def test_ICC_inputs(): input_map = dict( - mask=dict( - mandatory=True, - usedefault=True, - ), + mask=dict(mandatory=True, ), subjects_sessions=dict(mandatory=True, ), ) inputs = ICC.input_spec() @@ -18,9 +15,9 @@ def test_ICC_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ICC_outputs(): output_map = dict( - icc_map=dict(usedefault=True, ), - session_var_map=dict(usedefault=True, ), - subject_var_map=dict(usedefault=True, ), + icc_map=dict(), + session_var_map=dict(), + subject_var_map=dict(), ) outputs = ICC.output_spec() diff --git a/nipype/algorithms/tests/test_auto_Matlab2CSV.py b/nipype/algorithms/tests/test_auto_Matlab2CSV.py index 648248e12f..fcc1648bf9 100644 --- a/nipype/algorithms/tests/test_auto_Matlab2CSV.py +++ b/nipype/algorithms/tests/test_auto_Matlab2CSV.py @@ -5,10 +5,7 @@ def test_Matlab2CSV_inputs(): input_map = dict( - in_file=dict( - mandatory=True, - usedefault=True, - ), + in_file=dict(mandatory=True, ), reshape_matrix=dict(usedefault=True, ), ) inputs = Matlab2CSV.input_spec() diff --git a/nipype/algorithms/tests/test_auto_MergeCSVFiles.py b/nipype/algorithms/tests/test_auto_MergeCSVFiles.py index b2091d39c5..fd882e850a 100644 --- a/nipype/algorithms/tests/test_auto_MergeCSVFiles.py +++ b/nipype/algorithms/tests/test_auto_MergeCSVFiles.py @@ -19,7 +19,7 @@ def test_MergeCSVFiles_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MergeCSVFiles_outputs(): - output_map = dict(csv_file=dict(usedefault=True, ), ) + output_map = dict(csv_file=dict(), ) outputs = MergeCSVFiles.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_MergeROIs.py b/nipype/algorithms/tests/test_auto_MergeROIs.py index fc2298c1b5..01b2b097a8 100644 --- a/nipype/algorithms/tests/test_auto_MergeROIs.py +++ b/nipype/algorithms/tests/test_auto_MergeROIs.py @@ -7,7 +7,7 @@ def test_MergeROIs_inputs(): input_map = dict( in_files=dict(), in_index=dict(), - in_reference=dict(usedefault=True, ), + in_reference=dict(), ) inputs = MergeROIs.input_spec() @@ -15,7 +15,7 @@ def test_MergeROIs_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MergeROIs_outputs(): - output_map = dict(merged_file=dict(usedefault=True, ), ) + output_map = dict(merged_file=dict(), ) outputs = MergeROIs.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py index a633a3f657..f89b16017b 100644 --- a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py +++ b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py @@ -6,10 +6,7 @@ def test_MeshWarpMaths_inputs(): input_map = dict( float_trait=dict(), - in_surf=dict( - mandatory=True, - usedefault=True, - ), + in_surf=dict(mandatory=True, ), operation=dict(usedefault=True, ), operator=dict( mandatory=True, @@ -25,8 +22,8 @@ def test_MeshWarpMaths_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MeshWarpMaths_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - out_warp=dict(usedefault=True, ), + out_file=dict(), + out_warp=dict(), ) outputs = MeshWarpMaths.output_spec() diff --git a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py index 94ee5f1103..b86fe3df03 100644 --- a/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py +++ b/nipype/algorithms/tests/test_auto_NonSteadyStateDetector.py @@ -4,11 +4,7 @@ def test_NonSteadyStateDetector_inputs(): - input_map = dict( - in_file=dict( - mandatory=True, - usedefault=True, - ), ) + input_map = dict(in_file=dict(mandatory=True, ), ) inputs = NonSteadyStateDetector.input_spec() for key, metadata in list(input_map.items()): diff --git a/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py b/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py index 298207c8ef..4c9a5584d0 100644 --- a/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py +++ b/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py @@ -6,7 +6,7 @@ def test_NormalizeProbabilityMapSet_inputs(): input_map = dict( in_files=dict(), - in_mask=dict(usedefault=True, ), + in_mask=dict(), ) inputs = NormalizeProbabilityMapSet.input_spec() diff --git a/nipype/algorithms/tests/test_auto_P2PDistance.py b/nipype/algorithms/tests/test_auto_P2PDistance.py index 4671c89fdb..9948e3675e 100644 --- a/nipype/algorithms/tests/test_auto_P2PDistance.py +++ b/nipype/algorithms/tests/test_auto_P2PDistance.py @@ -8,14 +8,8 @@ def test_P2PDistance_inputs(): metric=dict(usedefault=True, ), out_file=dict(usedefault=True, ), out_warp=dict(usedefault=True, ), - surface1=dict( - mandatory=True, - usedefault=True, - ), - surface2=dict( - mandatory=True, - usedefault=True, - ), + surface1=dict(mandatory=True, ), + surface2=dict(mandatory=True, ), weighting=dict(usedefault=True, ), ) inputs = P2PDistance.input_spec() @@ -26,8 +20,8 @@ def test_P2PDistance_inputs(): def test_P2PDistance_outputs(): output_map = dict( distance=dict(), - out_file=dict(usedefault=True, ), - out_warp=dict(usedefault=True, ), + out_file=dict(), + out_warp=dict(), ) outputs = P2PDistance.output_spec() diff --git a/nipype/algorithms/tests/test_auto_PickAtlas.py b/nipype/algorithms/tests/test_auto_PickAtlas.py index 604e883674..3b15c302e5 100644 --- a/nipype/algorithms/tests/test_auto_PickAtlas.py +++ b/nipype/algorithms/tests/test_auto_PickAtlas.py @@ -5,14 +5,11 @@ def test_PickAtlas_inputs(): input_map = dict( - atlas=dict( - mandatory=True, - usedefault=True, - ), + atlas=dict(mandatory=True, ), dilation_size=dict(usedefault=True, ), hemi=dict(usedefault=True, ), labels=dict(mandatory=True, ), - output_file=dict(usedefault=True, ), + output_file=dict(), ) inputs = PickAtlas.input_spec() @@ -20,7 +17,7 @@ def test_PickAtlas_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PickAtlas_outputs(): - output_map = dict(mask_file=dict(usedefault=True, ), ) + output_map = dict(mask_file=dict(), ) outputs = PickAtlas.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/algorithms/tests/test_auto_Similarity.py b/nipype/algorithms/tests/test_auto_Similarity.py index 97fb6a2490..b2ad79b5eb 100644 --- a/nipype/algorithms/tests/test_auto_Similarity.py +++ b/nipype/algorithms/tests/test_auto_Similarity.py @@ -5,17 +5,11 @@ def test_Similarity_inputs(): input_map = dict( - mask1=dict(usedefault=True, ), - mask2=dict(usedefault=True, ), + mask1=dict(), + mask2=dict(), metric=dict(usedefault=True, ), - volume1=dict( - mandatory=True, - usedefault=True, - ), - volume2=dict( - mandatory=True, - usedefault=True, - ), + volume1=dict(mandatory=True, ), + volume2=dict(mandatory=True, ), ) inputs = Similarity.input_spec() diff --git a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py index 128aad5aa5..dc12dd3a89 100644 --- a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py @@ -53,8 +53,8 @@ def test_SpecifySparseModel_inputs(): def test_SpecifySparseModel_outputs(): output_map = dict( session_info=dict(), - sparse_png_file=dict(usedefault=True, ), - sparse_svg_file=dict(usedefault=True, ), + sparse_png_file=dict(), + sparse_svg_file=dict(), ) outputs = SpecifySparseModel.output_spec() diff --git a/nipype/algorithms/tests/test_auto_SplitROIs.py b/nipype/algorithms/tests/test_auto_SplitROIs.py index fd718624f3..963926666d 100644 --- a/nipype/algorithms/tests/test_auto_SplitROIs.py +++ b/nipype/algorithms/tests/test_auto_SplitROIs.py @@ -5,11 +5,8 @@ def test_SplitROIs_inputs(): input_map = dict( - in_file=dict( - mandatory=True, - usedefault=True, - ), - in_mask=dict(usedefault=True, ), + in_file=dict(mandatory=True, ), + in_mask=dict(), roi_size=dict(), ) inputs = SplitROIs.input_spec() diff --git a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py index e18a219045..8c7ef276d9 100644 --- a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py +++ b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py @@ -8,10 +8,7 @@ def test_StimulusCorrelation_inputs(): concatenated_design=dict(mandatory=True, ), intensity_values=dict(mandatory=True, ), realignment_parameters=dict(mandatory=True, ), - spm_mat_file=dict( - mandatory=True, - usedefault=True, - ), + spm_mat_file=dict(mandatory=True, ), ) inputs = StimulusCorrelation.input_spec() diff --git a/nipype/algorithms/tests/test_auto_TCompCor.py b/nipype/algorithms/tests/test_auto_TCompCor.py index 3982b6f5fa..c3bdcac192 100644 --- a/nipype/algorithms/tests/test_auto_TCompCor.py +++ b/nipype/algorithms/tests/test_auto_TCompCor.py @@ -23,10 +23,7 @@ def test_TCompCor_inputs(): num_components=dict(xor=['variance_threshold'], ), percentile_threshold=dict(usedefault=True, ), pre_filter=dict(usedefault=True, ), - realigned_file=dict( - mandatory=True, - usedefault=True, - ), + realigned_file=dict(mandatory=True, ), regress_poly_degree=dict(usedefault=True, ), repetition_time=dict(), save_metadata=dict(usedefault=True, ), @@ -44,10 +41,10 @@ def test_TCompCor_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TCompCor_outputs(): output_map = dict( - components_file=dict(usedefault=True, ), + components_file=dict(), high_variance_masks=dict(), - metadata_file=dict(usedefault=True, ), - pre_filter_file=dict(usedefault=True, ), + metadata_file=dict(), + pre_filter_file=dict(), ) outputs = TCompCor.output_spec() diff --git a/nipype/algorithms/tests/test_auto_WarpPoints.py b/nipype/algorithms/tests/test_auto_WarpPoints.py index e3967a8523..b6965065a2 100644 --- a/nipype/algorithms/tests/test_auto_WarpPoints.py +++ b/nipype/algorithms/tests/test_auto_WarpPoints.py @@ -14,16 +14,9 @@ def test_WarpPoints_inputs(): name_source='points', name_template='%s_warped', output_name='out_points', - usedefault=True, - ), - points=dict( - mandatory=True, - usedefault=True, - ), - warp=dict( - mandatory=True, - usedefault=True, ), + points=dict(mandatory=True, ), + warp=dict(mandatory=True, ), ) inputs = WarpPoints.input_spec() @@ -31,7 +24,7 @@ def test_WarpPoints_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpPoints_outputs(): - output_map = dict(out_points=dict(usedefault=True, ), ) + output_map = dict(out_points=dict(), ) outputs = WarpPoints.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_ABoverlap.py b/nipype/interfaces/afni/tests/test_auto_ABoverlap.py index 67f8157add..55cb12c27f 100644 --- a/nipype/interfaces/afni/tests/test_auto_ABoverlap.py +++ b/nipype/interfaces/afni/tests/test_auto_ABoverlap.py @@ -15,14 +15,12 @@ def test_ABoverlap_inputs(): copyfile=False, mandatory=True, position=-3, - usedefault=True, ), in_file_b=dict( argstr='%s', copyfile=False, mandatory=True, position=-2, - usedefault=True, ), no_automask=dict(argstr='-no_automask', ), num_threads=dict( @@ -32,7 +30,6 @@ def test_ABoverlap_inputs(): out_file=dict( argstr=' |& tee %s', position=-1, - usedefault=True, ), outputtype=dict(), quiet=dict(argstr='-quiet', ), @@ -44,7 +41,7 @@ def test_ABoverlap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ABoverlap_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ABoverlap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py index 3aecfd48aa..d89519d571 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py @@ -16,7 +16,6 @@ def test_AFNItoNIFTI_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, ), newid=dict( argstr='-newid', @@ -35,7 +34,6 @@ def test_AFNItoNIFTI_inputs(): hash_files=False, name_source='in_file', name_template='%s.nii', - usedefault=True, ), outputtype=dict(), pure=dict(argstr='-pure', ), @@ -46,7 +44,7 @@ def test_AFNItoNIFTI_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AFNItoNIFTI_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = AFNItoNIFTI.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py b/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py index 15db355b43..dfbfc648f7 100644 --- a/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py +++ b/nipype/interfaces/afni/tests/test_auto_AlignEpiAnatPy.py @@ -9,7 +9,6 @@ def test_AlignEpiAnatPy_inputs(): argstr='-anat %s', copyfile=False, mandatory=True, - usedefault=True, ), anat2epi=dict(argstr='-anat2epi', ), args=dict(argstr='%s', ), @@ -27,7 +26,6 @@ def test_AlignEpiAnatPy_inputs(): argstr='-epi %s', copyfile=False, mandatory=True, - usedefault=True, ), outputtype=dict(), py27_path=dict(usedefault=True, ), @@ -52,16 +50,16 @@ def test_AlignEpiAnatPy_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_AlignEpiAnatPy_outputs(): output_map = dict( - anat_al_mat=dict(usedefault=True, ), - anat_al_orig=dict(usedefault=True, ), - epi_al_mat=dict(usedefault=True, ), - epi_al_orig=dict(usedefault=True, ), - epi_al_tlrc_mat=dict(usedefault=True, ), - epi_reg_al_mat=dict(usedefault=True, ), - epi_tlrc_al=dict(usedefault=True, ), - epi_vr_al_mat=dict(usedefault=True, ), - epi_vr_motion=dict(usedefault=True, ), - skullstrip=dict(usedefault=True, ), + anat_al_mat=dict(), + anat_al_orig=dict(), + epi_al_mat=dict(), + epi_al_orig=dict(), + epi_al_tlrc_mat=dict(), + epi_reg_al_mat=dict(), + epi_tlrc_al=dict(), + epi_vr_al_mat=dict(), + epi_vr_motion=dict(), + skullstrip=dict(), ) outputs = AlignEpiAnatPy.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Allineate.py b/nipype/interfaces/afni/tests/test_auto_Allineate.py index 20678a52e2..be02af14da 100644 --- a/nipype/interfaces/afni/tests/test_auto_Allineate.py +++ b/nipype/interfaces/afni/tests/test_auto_Allineate.py @@ -8,7 +8,6 @@ def test_Allineate_inputs(): allcostx=dict( argstr='-allcostx |& tee %s', position=-1, - usedefault=True, xor=[ 'out_file', 'out_matrix', 'out_param_file', 'out_weight_file' ], @@ -32,24 +31,18 @@ def test_Allineate_inputs(): argstr='-source %s', copyfile=False, mandatory=True, - usedefault=True, ), in_matrix=dict( argstr='-1Dmatrix_apply %s', position=-3, - usedefault=True, xor=['out_matrix'], ), in_param_file=dict( argstr='-1Dparam_apply %s', - usedefault=True, xor=['out_param_file'], ), interpolation=dict(argstr='-interp %s', ), - master=dict( - argstr='-master %s', - usedefault=True, - ), + master=dict(argstr='-master %s', ), maxrot=dict(argstr='-maxrot %f', ), maxscl=dict(argstr='-maxscl %f', ), maxshf=dict(argstr='-maxshf %f', ), @@ -71,17 +64,14 @@ def test_Allineate_inputs(): hash_files=False, name_source='in_file', name_template='%s_allineate', - usedefault=True, xor=['allcostx'], ), out_matrix=dict( argstr='-1Dmatrix_save %s', - usedefault=True, xor=['in_matrix', 'allcostx'], ), out_param_file=dict( argstr='-1Dparam_save %s', - usedefault=True, xor=['in_param_file', 'allcostx'], ), out_weight_file=dict( @@ -91,17 +81,11 @@ def test_Allineate_inputs(): outputtype=dict(), overwrite=dict(argstr='-overwrite', ), quiet=dict(argstr='-quiet', ), - reference=dict( - argstr='-base %s', - usedefault=True, - ), + reference=dict(argstr='-base %s', ), replacebase=dict(argstr='-replacebase', ), replacemeth=dict(argstr='-replacemeth %s', ), source_automask=dict(argstr='-source_automask+%d', ), - source_mask=dict( - argstr='-source_mask %s', - usedefault=True, - ), + source_mask=dict(argstr='-source_mask %s', ), two_best=dict(argstr='-twobest %d', ), two_blur=dict(argstr='-twoblur %f', ), two_first=dict(argstr='-twofirst', ), @@ -115,7 +99,6 @@ def test_Allineate_inputs(): argstr='-weight %s', deprecated='1.0.0', new_name='weight', - usedefault=True, ), zclip=dict(argstr='-zclip', ), ) @@ -126,11 +109,11 @@ def test_Allineate_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Allineate_outputs(): output_map = dict( - allcostx=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), - out_matrix=dict(usedefault=True, ), - out_param_file=dict(usedefault=True, ), - out_weight_file=dict(usedefault=True, ), + allcostx=dict(), + out_file=dict(), + out_matrix=dict(), + out_param_file=dict(), + out_weight_file=dict(), ) outputs = Allineate.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py b/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py index ef4e07abcf..bb00b3b585 100644 --- a/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py +++ b/nipype/interfaces/afni/tests/test_auto_AutoTLRC.py @@ -18,7 +18,6 @@ def test_AutoTLRC_inputs(): argstr='-input %s', copyfile=False, mandatory=True, - usedefault=True, ), no_ss=dict(argstr='-no_ss', ), outputtype=dict(), @@ -29,7 +28,7 @@ def test_AutoTLRC_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AutoTLRC_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = AutoTLRC.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py index feb6f09dde..424b7d25b1 100644 --- a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py @@ -16,19 +16,14 @@ def test_AutoTcorrelate_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, - ), - mask=dict( - argstr='-mask %s', - usedefault=True, ), + mask=dict(argstr='-mask %s', ), mask_only_targets=dict( argstr='-mask_only_targets', xor=['mask_source'], ), mask_source=dict( argstr='-mask_source %s', - usedefault=True, xor=['mask_only_targets'], ), num_threads=dict( @@ -39,7 +34,6 @@ def test_AutoTcorrelate_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_similarity_matrix.1D', - usedefault=True, ), outputtype=dict(), polort=dict(argstr='-polort %d', ), @@ -50,7 +44,7 @@ def test_AutoTcorrelate_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AutoTcorrelate_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = AutoTcorrelate.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Autobox.py b/nipype/interfaces/afni/tests/test_auto_Autobox.py index fa303b8595..f158263c54 100644 --- a/nipype/interfaces/afni/tests/test_auto_Autobox.py +++ b/nipype/interfaces/afni/tests/test_auto_Autobox.py @@ -14,7 +14,6 @@ def test_Autobox_inputs(): argstr='-input %s', copyfile=False, mandatory=True, - usedefault=True, ), no_clustering=dict(argstr='-noclust', ), num_threads=dict( @@ -25,7 +24,6 @@ def test_Autobox_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_autobox', - usedefault=True, ), outputtype=dict(), padding=dict(argstr='-npad %d', ), @@ -37,7 +35,7 @@ def test_Autobox_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Autobox_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), + out_file=dict(), x_max=dict(), x_min=dict(), y_max=dict(), diff --git a/nipype/interfaces/afni/tests/test_auto_Automask.py b/nipype/interfaces/afni/tests/test_auto_Automask.py index 3e8be0b9f9..efffd19cba 100644 --- a/nipype/interfaces/afni/tests/test_auto_Automask.py +++ b/nipype/interfaces/afni/tests/test_auto_Automask.py @@ -10,7 +10,6 @@ def test_Automask_inputs(): argstr='-apply_prefix %s', name_source='in_file', name_template='%s_masked', - usedefault=True, ), clfrac=dict(argstr='-clfrac %s', ), dilate=dict(argstr='-dilate %s', ), @@ -24,7 +23,6 @@ def test_Automask_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, ), num_threads=dict( nohash=True, @@ -34,7 +32,6 @@ def test_Automask_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_mask', - usedefault=True, ), outputtype=dict(), ) @@ -45,8 +42,8 @@ def test_Automask_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Automask_outputs(): output_map = dict( - brain_file=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), + brain_file=dict(), + out_file=dict(), ) outputs = Automask.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Axialize.py b/nipype/interfaces/afni/tests/test_auto_Axialize.py index 10fd904487..62b425c932 100644 --- a/nipype/interfaces/afni/tests/test_auto_Axialize.py +++ b/nipype/interfaces/afni/tests/test_auto_Axialize.py @@ -23,7 +23,6 @@ def test_Axialize_inputs(): copyfile=False, mandatory=True, position=-2, - usedefault=True, ), num_threads=dict( nohash=True, @@ -34,7 +33,6 @@ def test_Axialize_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_axialize', - usedefault=True, ), outputtype=dict(), sagittal=dict( @@ -49,7 +47,7 @@ def test_Axialize_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Axialize_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Axialize.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Bandpass.py b/nipype/interfaces/afni/tests/test_auto_Bandpass.py index b20c770e6d..d225136e94 100644 --- a/nipype/interfaces/afni/tests/test_auto_Bandpass.py +++ b/nipype/interfaces/afni/tests/test_auto_Bandpass.py @@ -23,7 +23,6 @@ def test_Bandpass_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, ), localPV=dict(argstr='-localPV %f', ), lowpass=dict( @@ -34,7 +33,6 @@ def test_Bandpass_inputs(): mask=dict( argstr='-mask %s', position=2, - usedefault=True, ), nfft=dict(argstr='-nfft %d', ), no_detrend=dict(argstr='-nodetrend', ), @@ -44,17 +42,13 @@ def test_Bandpass_inputs(): nohash=True, usedefault=True, ), - orthogonalize_dset=dict( - argstr='-dsort %s', - usedefault=True, - ), + orthogonalize_dset=dict(argstr='-dsort %s', ), orthogonalize_file=dict(argstr='-ort %s', ), out_file=dict( argstr='-prefix %s', name_source='in_file', name_template='%s_bp', position=1, - usedefault=True, ), outputtype=dict(), tr=dict(argstr='-dt %f', ), @@ -65,7 +59,7 @@ def test_Bandpass_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Bandpass_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Bandpass.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py index a6ba4a84ac..334116d945 100644 --- a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py +++ b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py @@ -21,16 +21,9 @@ def test_BlurInMask_inputs(): copyfile=False, mandatory=True, position=1, - usedefault=True, - ), - mask=dict( - argstr='-mask %s', - usedefault=True, - ), - multimask=dict( - argstr='-Mmask %s', - usedefault=True, ), + mask=dict(argstr='-mask %s', ), + multimask=dict(argstr='-Mmask %s', ), num_threads=dict( nohash=True, usedefault=True, @@ -44,7 +37,6 @@ def test_BlurInMask_inputs(): name_source='in_file', name_template='%s_blur', position=-1, - usedefault=True, ), outputtype=dict(), preserve=dict(argstr='-preserve', ), @@ -55,7 +47,7 @@ def test_BlurInMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BlurInMask_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = BlurInMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py b/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py index a20133f62a..4fd8bef47e 100644 --- a/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py +++ b/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py @@ -7,10 +7,7 @@ def test_BlurToFWHM_inputs(): input_map = dict( args=dict(argstr='%s', ), automask=dict(argstr='-automask', ), - blurmaster=dict( - argstr='-blurmaster %s', - usedefault=True, - ), + blurmaster=dict(argstr='-blurmaster %s', ), environ=dict( nohash=True, usedefault=True, @@ -20,12 +17,8 @@ def test_BlurToFWHM_inputs(): in_file=dict( argstr='-input %s', mandatory=True, - usedefault=True, - ), - mask=dict( - argstr='-mask %s', - usedefault=True, ), + mask=dict(argstr='-mask %s', ), num_threads=dict( nohash=True, usedefault=True, @@ -34,7 +27,6 @@ def test_BlurToFWHM_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_afni', - usedefault=True, ), outputtype=dict(), ) @@ -44,7 +36,7 @@ def test_BlurToFWHM_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BlurToFWHM_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = BlurToFWHM.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_BrickStat.py b/nipype/interfaces/afni/tests/test_auto_BrickStat.py index 5bab8eeba5..0056df5980 100644 --- a/nipype/interfaces/afni/tests/test_auto_BrickStat.py +++ b/nipype/interfaces/afni/tests/test_auto_BrickStat.py @@ -14,12 +14,10 @@ def test_BrickStat_inputs(): argstr='%s', mandatory=True, position=-1, - usedefault=True, ), mask=dict( argstr='-mask %s', position=2, - usedefault=True, ), max=dict(argstr='-max', ), mean=dict(argstr='-mean', ), diff --git a/nipype/interfaces/afni/tests/test_auto_Bucket.py b/nipype/interfaces/afni/tests/test_auto_Bucket.py index 93aa40d738..c3faf87a09 100644 --- a/nipype/interfaces/afni/tests/test_auto_Bucket.py +++ b/nipype/interfaces/afni/tests/test_auto_Bucket.py @@ -22,7 +22,6 @@ def test_Bucket_inputs(): out_file=dict( argstr='-prefix %s', name_template='buck', - usedefault=True, ), outputtype=dict(), ) @@ -32,7 +31,7 @@ def test_Bucket_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Bucket_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Bucket.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Calc.py b/nipype/interfaces/afni/tests/test_auto_Calc.py index bc8a362782..28863d5a4b 100644 --- a/nipype/interfaces/afni/tests/test_auto_Calc.py +++ b/nipype/interfaces/afni/tests/test_auto_Calc.py @@ -19,31 +19,24 @@ def test_Calc_inputs(): argstr='-a %s', mandatory=True, position=0, - usedefault=True, ), in_file_b=dict( argstr='-b %s', position=1, - usedefault=True, ), in_file_c=dict( argstr='-c %s', position=2, - usedefault=True, ), num_threads=dict( nohash=True, usedefault=True, ), - other=dict( - argstr='', - usedefault=True, - ), + other=dict(argstr='', ), out_file=dict( argstr='-prefix %s', name_source='in_file_a', name_template='%s_calc', - usedefault=True, ), outputtype=dict(), overwrite=dict(argstr='-overwrite', ), @@ -57,7 +50,7 @@ def test_Calc_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Calc_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Calc.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Cat.py b/nipype/interfaces/afni/tests/test_auto_Cat.py index 92e4099ea5..3da86c66d6 100644 --- a/nipype/interfaces/afni/tests/test_auto_Cat.py +++ b/nipype/interfaces/afni/tests/test_auto_Cat.py @@ -67,7 +67,7 @@ def test_Cat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Cat_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Cat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_CatMatvec.py b/nipype/interfaces/afni/tests/test_auto_CatMatvec.py index e678afc632..b67ab485d4 100644 --- a/nipype/interfaces/afni/tests/test_auto_CatMatvec.py +++ b/nipype/interfaces/afni/tests/test_auto_CatMatvec.py @@ -38,7 +38,6 @@ def test_CatMatvec_inputs(): name_source='in_file', name_template='%s_cat.aff12.1D', position=-1, - usedefault=True, ), outputtype=dict(), ) @@ -48,7 +47,7 @@ def test_CatMatvec_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CatMatvec_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = CatMatvec.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_CenterMass.py b/nipype/interfaces/afni/tests/test_auto_CenterMass.py index de6475ed3d..322218a50d 100644 --- a/nipype/interfaces/afni/tests/test_auto_CenterMass.py +++ b/nipype/interfaces/afni/tests/test_auto_CenterMass.py @@ -15,7 +15,6 @@ def test_CenterMass_inputs(): name_source='in_file', name_template='%s_cm.out', position=-1, - usedefault=True, ), environ=dict( nohash=True, @@ -26,13 +25,9 @@ def test_CenterMass_inputs(): copyfile=True, mandatory=True, position=-2, - usedefault=True, ), local_ijk=dict(argstr='-local_ijk', ), - mask_file=dict( - argstr='-mask %s', - usedefault=True, - ), + mask_file=dict(argstr='-mask %s', ), roi_vals=dict(argstr='-roi_vals %s', ), set_cm=dict(argstr='-set %f %f %f', ), ) @@ -44,8 +39,8 @@ def test_CenterMass_inputs(): def test_CenterMass_outputs(): output_map = dict( cm=dict(), - cm_file=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), + cm_file=dict(), + out_file=dict(), ) outputs = CenterMass.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py index 47db0633f7..8b8c61208d 100644 --- a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py +++ b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py @@ -24,7 +24,6 @@ def test_ClipLevel_inputs(): argstr='%s', mandatory=True, position=-1, - usedefault=True, ), mfrac=dict( argstr='-mfrac %s', diff --git a/nipype/interfaces/afni/tests/test_auto_ConvertDset.py b/nipype/interfaces/afni/tests/test_auto_ConvertDset.py index 66625253a4..06ba3a54f2 100644 --- a/nipype/interfaces/afni/tests/test_auto_ConvertDset.py +++ b/nipype/interfaces/afni/tests/test_auto_ConvertDset.py @@ -14,7 +14,6 @@ def test_ConvertDset_inputs(): argstr='-input %s', mandatory=True, position=-2, - usedefault=True, ), num_threads=dict( nohash=True, @@ -24,7 +23,6 @@ def test_ConvertDset_inputs(): argstr='-prefix %s', mandatory=True, position=-1, - usedefault=True, ), out_type=dict( argstr='-o_%s', @@ -39,7 +37,7 @@ def test_ConvertDset_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConvertDset_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ConvertDset.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Copy.py b/nipype/interfaces/afni/tests/test_auto_Copy.py index dcc3a546b2..a8e67d5607 100644 --- a/nipype/interfaces/afni/tests/test_auto_Copy.py +++ b/nipype/interfaces/afni/tests/test_auto_Copy.py @@ -15,7 +15,6 @@ def test_Copy_inputs(): copyfile=False, mandatory=True, position=-2, - usedefault=True, ), num_threads=dict( nohash=True, @@ -26,7 +25,6 @@ def test_Copy_inputs(): name_source='in_file', name_template='%s_copy', position=-1, - usedefault=True, ), outputtype=dict(), verbose=dict(argstr='-verb', ), @@ -37,7 +35,7 @@ def test_Copy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Copy_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Copy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Deconvolve.py b/nipype/interfaces/afni/tests/test_auto_Deconvolve.py index 6f66bbaf9c..ae42a77019 100644 --- a/nipype/interfaces/afni/tests/test_auto_Deconvolve.py +++ b/nipype/interfaces/afni/tests/test_auto_Deconvolve.py @@ -5,19 +5,13 @@ def test_Deconvolve_inputs(): input_map = dict( - STATmask=dict( - argstr='-STATmask %s', - usedefault=True, - ), + STATmask=dict(argstr='-STATmask %s', ), TR_1D=dict(argstr='-TR_1D %f', ), allzero_OK=dict(argstr='-allzero_OK', ), args=dict(argstr='%s', ), automask=dict(argstr='-automask', ), cbucket=dict(argstr='-cbucket %s', ), - censor=dict( - argstr='-censor %s', - usedefault=True, - ), + censor=dict(argstr='-censor %s', ), dmbase=dict(argstr='-dmbase', ), dname=dict(argstr='-D%s=%s', ), environ=dict( @@ -49,19 +43,13 @@ def test_Deconvolve_inputs(): position=1, sep=' ', ), - input1D=dict( - argstr='-input1D %s', - usedefault=True, - ), + input1D=dict(argstr='-input1D %s', ), legendre=dict(argstr='-legendre', ), local_times=dict( argstr='-local_times', xor=['global_times'], ), - mask=dict( - argstr='-mask %s', - usedefault=True, - ), + mask=dict(argstr='-mask %s', ), noblock=dict(argstr='-noblock', ), nocond=dict(argstr='-nocond', ), nodmbase=dict(argstr='-nodmbase', ), @@ -81,10 +69,7 @@ def test_Deconvolve_inputs(): nohash=True, ), ortvec=dict(argstr='-ortvec %s %s', ), - out_file=dict( - argstr='-bucket %s', - usedefault=True, - ), + out_file=dict(argstr='-bucket %s', ), outputtype=dict(), polort=dict(argstr='-polort %d', ), rmsmin=dict(argstr='-rmsmin %f', ), @@ -111,10 +96,7 @@ def test_Deconvolve_inputs(): xor=['sat'], ), vout=dict(argstr='-vout', ), - x1D=dict( - argstr='-x1D %s', - usedefault=True, - ), + x1D=dict(argstr='-x1D %s', ), x1D_stop=dict(argstr='-x1D_stop', ), ) inputs = Deconvolve.input_spec() @@ -124,10 +106,10 @@ def test_Deconvolve_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Deconvolve_outputs(): output_map = dict( - cbucket=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), - reml_script=dict(usedefault=True, ), - x1D=dict(usedefault=True, ), + cbucket=dict(), + out_file=dict(), + reml_script=dict(), + x1D=dict(), ) outputs = Deconvolve.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py b/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py index a64e48cedf..056712dd38 100644 --- a/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py +++ b/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py @@ -17,12 +17,8 @@ def test_DegreeCentrality_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, - ), - mask=dict( - argstr='-mask %s', - usedefault=True, ), + mask=dict(argstr='-mask %s', ), num_threads=dict( nohash=True, usedefault=True, @@ -32,7 +28,6 @@ def test_DegreeCentrality_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_afni', - usedefault=True, ), outputtype=dict(), polort=dict(argstr='-polort %d', ), @@ -46,8 +41,8 @@ def test_DegreeCentrality_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DegreeCentrality_outputs(): output_map = dict( - oned_file=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), + oned_file=dict(), + out_file=dict(), ) outputs = DegreeCentrality.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Despike.py b/nipype/interfaces/afni/tests/test_auto_Despike.py index 08031c8d4a..ff0b8b532a 100644 --- a/nipype/interfaces/afni/tests/test_auto_Despike.py +++ b/nipype/interfaces/afni/tests/test_auto_Despike.py @@ -15,7 +15,6 @@ def test_Despike_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, ), num_threads=dict( nohash=True, @@ -25,7 +24,6 @@ def test_Despike_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_despike', - usedefault=True, ), outputtype=dict(), ) @@ -35,7 +33,7 @@ def test_Despike_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Despike_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Despike.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Detrend.py b/nipype/interfaces/afni/tests/test_auto_Detrend.py index 5f75cf079b..1938529cf7 100644 --- a/nipype/interfaces/afni/tests/test_auto_Detrend.py +++ b/nipype/interfaces/afni/tests/test_auto_Detrend.py @@ -15,7 +15,6 @@ def test_Detrend_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, ), num_threads=dict( nohash=True, @@ -25,7 +24,6 @@ def test_Detrend_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_detrend', - usedefault=True, ), outputtype=dict(), ) @@ -35,7 +33,7 @@ def test_Detrend_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Detrend_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Detrend.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Dot.py b/nipype/interfaces/afni/tests/test_auto_Dot.py index 610f226961..7623e90ca7 100644 --- a/nipype/interfaces/afni/tests/test_auto_Dot.py +++ b/nipype/interfaces/afni/tests/test_auto_Dot.py @@ -22,10 +22,7 @@ def test_Dot_inputs(): argstr='%s ...', position=-2, ), - mask=dict( - argstr='-mask %s', - usedefault=True, - ), + mask=dict(argstr='-mask %s', ), mrange=dict(argstr='-mrange %s %s', ), num_threads=dict( nohash=True, @@ -34,7 +31,6 @@ def test_Dot_inputs(): out_file=dict( argstr=' |& tee %s', position=-1, - usedefault=True, ), outputtype=dict(), show_labels=dict(argstr='-show_labels', ), @@ -46,7 +42,7 @@ def test_Dot_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Dot_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Dot.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_ECM.py b/nipype/interfaces/afni/tests/test_auto_ECM.py index ab5c438035..0b59b2aaf5 100644 --- a/nipype/interfaces/afni/tests/test_auto_ECM.py +++ b/nipype/interfaces/afni/tests/test_auto_ECM.py @@ -20,12 +20,8 @@ def test_ECM_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, - ), - mask=dict( - argstr='-mask %s', - usedefault=True, ), + mask=dict(argstr='-mask %s', ), max_iter=dict(argstr='-max_iter %d', ), memory=dict(argstr='-memory %f', ), num_threads=dict( @@ -36,7 +32,6 @@ def test_ECM_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_afni', - usedefault=True, ), outputtype=dict(), polort=dict(argstr='-polort %d', ), @@ -51,7 +46,7 @@ def test_ECM_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ECM_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ECM.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Edge3.py b/nipype/interfaces/afni/tests/test_auto_Edge3.py index 64f3e8785b..8fc6953c28 100644 --- a/nipype/interfaces/afni/tests/test_auto_Edge3.py +++ b/nipype/interfaces/afni/tests/test_auto_Edge3.py @@ -24,7 +24,6 @@ def test_Edge3_inputs(): copyfile=False, mandatory=True, position=0, - usedefault=True, ), nscale=dict( argstr='-nscale', @@ -37,7 +36,6 @@ def test_Edge3_inputs(): out_file=dict( argstr='-prefix %s', position=-1, - usedefault=True, ), outputtype=dict(), scale_floats=dict( @@ -52,7 +50,7 @@ def test_Edge3_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Edge3_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Edge3.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Eval.py b/nipype/interfaces/afni/tests/test_auto_Eval.py index 0f43128ae0..35c1360a6e 100644 --- a/nipype/interfaces/afni/tests/test_auto_Eval.py +++ b/nipype/interfaces/afni/tests/test_auto_Eval.py @@ -19,32 +19,25 @@ def test_Eval_inputs(): argstr='-a %s', mandatory=True, position=0, - usedefault=True, ), in_file_b=dict( argstr='-b %s', position=1, - usedefault=True, ), in_file_c=dict( argstr='-c %s', position=2, - usedefault=True, ), num_threads=dict( nohash=True, usedefault=True, ), - other=dict( - argstr='', - usedefault=True, - ), + other=dict(argstr='', ), out1D=dict(argstr='-1D', ), out_file=dict( argstr='-prefix %s', name_source='in_file_a', name_template='%s_calc', - usedefault=True, ), outputtype=dict(), single_idx=dict(), @@ -57,7 +50,7 @@ def test_Eval_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Eval_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Eval.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_FWHMx.py b/nipype/interfaces/afni/tests/test_auto_FWHMx.py index 1c0e9c7f1e..14ab26fa4f 100644 --- a/nipype/interfaces/afni/tests/test_auto_FWHMx.py +++ b/nipype/interfaces/afni/tests/test_auto_FWHMx.py @@ -40,18 +40,13 @@ def test_FWHMx_inputs(): in_file=dict( argstr='-input %s', mandatory=True, - usedefault=True, - ), - mask=dict( - argstr='-mask %s', - usedefault=True, ), + mask=dict(argstr='-mask %s', ), out_detrend=dict( argstr='-detprefix %s', keep_extension=False, name_source='in_file', name_template='%s_detrend', - usedefault=True, ), out_file=dict( argstr='> %s', @@ -59,14 +54,12 @@ def test_FWHMx_inputs(): name_source='in_file', name_template='%s_fwhmx.out', position=-1, - usedefault=True, ), out_subbricks=dict( argstr='-out %s', keep_extension=False, name_source='in_file', name_template='%s_subbricks.out', - usedefault=True, ), unif=dict(argstr='-unif', ), ) @@ -79,10 +72,10 @@ def test_FWHMx_outputs(): output_map = dict( acf_param=dict(), fwhm=dict(), - out_acf=dict(usedefault=True, ), - out_detrend=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), - out_subbricks=dict(usedefault=True, ), + out_acf=dict(), + out_detrend=dict(), + out_file=dict(), + out_subbricks=dict(), ) outputs = FWHMx.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Fim.py b/nipype/interfaces/afni/tests/test_auto_Fim.py index a8cb1c22da..931e5ff244 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fim.py +++ b/nipype/interfaces/afni/tests/test_auto_Fim.py @@ -18,14 +18,12 @@ def test_Fim_inputs(): argstr='-ideal_file %s', mandatory=True, position=2, - usedefault=True, ), in_file=dict( argstr='-input %s', copyfile=False, mandatory=True, position=1, - usedefault=True, ), num_threads=dict( nohash=True, @@ -39,7 +37,6 @@ def test_Fim_inputs(): argstr='-bucket %s', name_source='in_file', name_template='%s_fim', - usedefault=True, ), outputtype=dict(), ) @@ -49,7 +46,7 @@ def test_Fim_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Fim_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Fim.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Fourier.py b/nipype/interfaces/afni/tests/test_auto_Fourier.py index 14feefd617..69cd955cbc 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fourier.py +++ b/nipype/interfaces/afni/tests/test_auto_Fourier.py @@ -19,7 +19,6 @@ def test_Fourier_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, ), lowpass=dict( argstr='-lowpass %f', @@ -33,7 +32,6 @@ def test_Fourier_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_fourier', - usedefault=True, ), outputtype=dict(), retrend=dict(argstr='-retrend', ), @@ -44,7 +42,7 @@ def test_Fourier_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Fourier_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Fourier.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_GCOR.py b/nipype/interfaces/afni/tests/test_auto_GCOR.py index 71d9b6b0f7..9d603dda36 100644 --- a/nipype/interfaces/afni/tests/test_auto_GCOR.py +++ b/nipype/interfaces/afni/tests/test_auto_GCOR.py @@ -15,12 +15,10 @@ def test_GCOR_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, ), mask=dict( argstr='-mask %s', copyfile=False, - usedefault=True, ), nfirst=dict(argstr='-nfirst %d', ), no_demean=dict(argstr='-no_demean', ), diff --git a/nipype/interfaces/afni/tests/test_auto_Hist.py b/nipype/interfaces/afni/tests/test_auto_Hist.py index a06d661547..48499a9605 100644 --- a/nipype/interfaces/afni/tests/test_auto_Hist.py +++ b/nipype/interfaces/afni/tests/test_auto_Hist.py @@ -16,12 +16,8 @@ def test_Hist_inputs(): copyfile=False, mandatory=True, position=1, - usedefault=True, - ), - mask=dict( - argstr='-mask %s', - usedefault=True, ), + mask=dict(argstr='-mask %s', ), max_value=dict(argstr='-max %f', ), min_value=dict(argstr='-min %f', ), nbin=dict(argstr='-nbin %d', ), @@ -30,7 +26,6 @@ def test_Hist_inputs(): keep_extension=False, name_source=['in_file'], name_template='%s_hist', - usedefault=True, ), out_show=dict( argstr='> %s', @@ -38,7 +33,6 @@ def test_Hist_inputs(): name_source='in_file', name_template='%s_hist.out', position=-1, - usedefault=True, ), showhist=dict( argstr='-showhist', @@ -52,8 +46,8 @@ def test_Hist_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Hist_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - out_show=dict(usedefault=True, ), + out_file=dict(), + out_show=dict(), ) outputs = Hist.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_LFCD.py b/nipype/interfaces/afni/tests/test_auto_LFCD.py index 6a99d09cb6..9be4450e57 100644 --- a/nipype/interfaces/afni/tests/test_auto_LFCD.py +++ b/nipype/interfaces/afni/tests/test_auto_LFCD.py @@ -17,12 +17,8 @@ def test_LFCD_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, - ), - mask=dict( - argstr='-mask %s', - usedefault=True, ), + mask=dict(argstr='-mask %s', ), num_threads=dict( nohash=True, usedefault=True, @@ -31,7 +27,6 @@ def test_LFCD_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_afni', - usedefault=True, ), outputtype=dict(), polort=dict(argstr='-polort %d', ), @@ -43,7 +38,7 @@ def test_LFCD_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LFCD_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = LFCD.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_LocalBistat.py b/nipype/interfaces/afni/tests/test_auto_LocalBistat.py index 13c31f02c7..22f0b717d8 100644 --- a/nipype/interfaces/afni/tests/test_auto_LocalBistat.py +++ b/nipype/interfaces/afni/tests/test_auto_LocalBistat.py @@ -18,13 +18,11 @@ def test_LocalBistat_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), in_file2=dict( argstr='%s', mandatory=True, position=-1, - usedefault=True, ), mask_file=dict(argstr='-mask %s', ), neighborhood=dict( @@ -58,7 +56,7 @@ def test_LocalBistat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LocalBistat_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = LocalBistat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Localstat.py b/nipype/interfaces/afni/tests/test_auto_Localstat.py index 4ad85d0728..c2f53c3db0 100644 --- a/nipype/interfaces/afni/tests/test_auto_Localstat.py +++ b/nipype/interfaces/afni/tests/test_auto_Localstat.py @@ -19,7 +19,6 @@ def test_Localstat_inputs(): argstr='%s', mandatory=True, position=-1, - usedefault=True, ), mask_file=dict(argstr='-mask %s', ), neighborhood=dict( @@ -64,7 +63,7 @@ def test_Localstat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Localstat_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Localstat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_MaskTool.py b/nipype/interfaces/afni/tests/test_auto_MaskTool.py index ef4464b6ca..1644bee878 100644 --- a/nipype/interfaces/afni/tests/test_auto_MaskTool.py +++ b/nipype/interfaces/afni/tests/test_auto_MaskTool.py @@ -38,7 +38,6 @@ def test_MaskTool_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_mask', - usedefault=True, ), outputtype=dict(), union=dict(argstr='-union', ), @@ -50,7 +49,7 @@ def test_MaskTool_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MaskTool_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MaskTool.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Maskave.py b/nipype/interfaces/afni/tests/test_auto_Maskave.py index 462ed4e3cf..a318e685a9 100644 --- a/nipype/interfaces/afni/tests/test_auto_Maskave.py +++ b/nipype/interfaces/afni/tests/test_auto_Maskave.py @@ -15,12 +15,10 @@ def test_Maskave_inputs(): copyfile=False, mandatory=True, position=-2, - usedefault=True, ), mask=dict( argstr='-mask %s', position=1, - usedefault=True, ), num_threads=dict( nohash=True, @@ -32,7 +30,6 @@ def test_Maskave_inputs(): name_source='in_file', name_template='%s_maskave.1D', position=-1, - usedefault=True, ), outputtype=dict(), quiet=dict( @@ -46,7 +43,7 @@ def test_Maskave_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Maskave_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Maskave.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Means.py b/nipype/interfaces/afni/tests/test_auto_Means.py index c1830e2e23..2e422e68db 100644 --- a/nipype/interfaces/afni/tests/test_auto_Means.py +++ b/nipype/interfaces/afni/tests/test_auto_Means.py @@ -16,12 +16,10 @@ def test_Means_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), in_file_b=dict( argstr='%s', position=-1, - usedefault=True, ), mask_inter=dict(argstr='-mask_inter', ), mask_union=dict(argstr='-mask_union', ), @@ -34,7 +32,6 @@ def test_Means_inputs(): argstr='-prefix %s', name_source='in_file_a', name_template='%s_mean', - usedefault=True, ), outputtype=dict(), scale=dict(argstr='-%sscale', ), @@ -48,7 +45,7 @@ def test_Means_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Means_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Means.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Merge.py b/nipype/interfaces/afni/tests/test_auto_Merge.py index 6dfe98c9f4..c36ee6f7a1 100644 --- a/nipype/interfaces/afni/tests/test_auto_Merge.py +++ b/nipype/interfaces/afni/tests/test_auto_Merge.py @@ -29,7 +29,6 @@ def test_Merge_inputs(): argstr='-prefix %s', name_source='in_files', name_template='%s_merge', - usedefault=True, ), outputtype=dict(), ) @@ -39,7 +38,7 @@ def test_Merge_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Merge_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Merge.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Notes.py b/nipype/interfaces/afni/tests/test_auto_Notes.py index 1ac8f2df04..965bacb000 100644 --- a/nipype/interfaces/afni/tests/test_auto_Notes.py +++ b/nipype/interfaces/afni/tests/test_auto_Notes.py @@ -21,16 +21,12 @@ def test_Notes_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, ), num_threads=dict( nohash=True, usedefault=True, ), - out_file=dict( - argstr='%s', - usedefault=True, - ), + out_file=dict(argstr='%s', ), outputtype=dict(), rep_history=dict( argstr='-HH "%s"', @@ -44,7 +40,7 @@ def test_Notes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Notes_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Notes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_NwarpAdjust.py b/nipype/interfaces/afni/tests/test_auto_NwarpAdjust.py index d6d9f23dd1..48b59a2968 100644 --- a/nipype/interfaces/afni/tests/test_auto_NwarpAdjust.py +++ b/nipype/interfaces/afni/tests/test_auto_NwarpAdjust.py @@ -21,7 +21,6 @@ def test_NwarpAdjust_inputs(): name_source='in_files', name_template='%s_NwarpAdjust', requires=['in_files'], - usedefault=True, ), outputtype=dict(), warps=dict( @@ -35,7 +34,7 @@ def test_NwarpAdjust_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NwarpAdjust_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = NwarpAdjust.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_NwarpApply.py b/nipype/interfaces/afni/tests/test_auto_NwarpApply.py index df04e5dc3d..63f6baa044 100644 --- a/nipype/interfaces/afni/tests/test_auto_NwarpApply.py +++ b/nipype/interfaces/afni/tests/test_auto_NwarpApply.py @@ -25,7 +25,6 @@ def test_NwarpApply_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_Nwarp', - usedefault=True, ), quiet=dict( argstr='-quiet', @@ -47,7 +46,7 @@ def test_NwarpApply_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NwarpApply_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = NwarpApply.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_NwarpCat.py b/nipype/interfaces/afni/tests/test_auto_NwarpCat.py index 0aaa040442..c6b3689c9e 100644 --- a/nipype/interfaces/afni/tests/test_auto_NwarpCat.py +++ b/nipype/interfaces/afni/tests/test_auto_NwarpCat.py @@ -29,7 +29,6 @@ def test_NwarpCat_inputs(): argstr='-prefix %s', name_source='in_files', name_template='%s_NwarpCat', - usedefault=True, ), outputtype=dict(), space=dict(argstr='-space %s', ), @@ -41,7 +40,7 @@ def test_NwarpCat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NwarpCat_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = NwarpCat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py b/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py index dd805be5cc..fe037851af 100644 --- a/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py +++ b/nipype/interfaces/afni/tests/test_auto_OneDToolPy.py @@ -17,11 +17,9 @@ def test_OneDToolPy_inputs(): in_file=dict( argstr='-infile %s', mandatory=True, - usedefault=True, ), out_file=dict( argstr='-write %s', - usedefault=True, xor=['show_cormat_warnings'], ), outputtype=dict(), @@ -43,7 +41,7 @@ def test_OneDToolPy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OneDToolPy_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = OneDToolPy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_OutlierCount.py b/nipype/interfaces/afni/tests/test_auto_OutlierCount.py index 14a6fa0fe6..a63fbb8bef 100644 --- a/nipype/interfaces/afni/tests/test_auto_OutlierCount.py +++ b/nipype/interfaces/afni/tests/test_auto_OutlierCount.py @@ -28,7 +28,6 @@ def test_OutlierCount_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), interval=dict( argstr='-range', @@ -40,14 +39,12 @@ def test_OutlierCount_inputs(): ), mask=dict( argstr='-mask %s', - usedefault=True, xor=['autoclip', 'automask'], ), out_file=dict( keep_extension=False, name_source=['in_file'], name_template='%s_outliers', - usedefault=True, ), outliers_file=dict( argstr='-save %s', @@ -55,7 +52,6 @@ def test_OutlierCount_inputs(): name_source=['in_file'], name_template='%s_outliers', output_name='out_outliers', - usedefault=True, ), polort=dict(argstr='-polort %d', ), qthr=dict( @@ -71,8 +67,8 @@ def test_OutlierCount_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_OutlierCount_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - out_outliers=dict(usedefault=True, ), + out_file=dict(), + out_outliers=dict(), ) outputs = OutlierCount.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_QualityIndex.py b/nipype/interfaces/afni/tests/test_auto_QualityIndex.py index 0c85e0d585..679a3e0393 100644 --- a/nipype/interfaces/afni/tests/test_auto_QualityIndex.py +++ b/nipype/interfaces/afni/tests/test_auto_QualityIndex.py @@ -25,7 +25,6 @@ def test_QualityIndex_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), interval=dict( argstr='-range', @@ -33,7 +32,6 @@ def test_QualityIndex_inputs(): ), mask=dict( argstr='-mask %s', - usedefault=True, xor=['autoclip', 'automask'], ), out_file=dict( @@ -42,7 +40,6 @@ def test_QualityIndex_inputs(): name_source=['in_file'], name_template='%s_tqual', position=-1, - usedefault=True, ), quadrant=dict( argstr='-quadrant', @@ -59,7 +56,7 @@ def test_QualityIndex_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_QualityIndex_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = QualityIndex.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Qwarp.py b/nipype/interfaces/afni/tests/test_auto_Qwarp.py index ffaf1a5a3f..1a2a1ee216 100644 --- a/nipype/interfaces/afni/tests/test_auto_Qwarp.py +++ b/nipype/interfaces/afni/tests/test_auto_Qwarp.py @@ -25,7 +25,6 @@ def test_Qwarp_inputs(): argstr='-base %s', copyfile=False, mandatory=True, - usedefault=True, ), baxopt=dict( argstr='-boxopt', @@ -42,7 +41,6 @@ def test_Qwarp_inputs(): emask=dict( argstr='-emask %s', copyfile=False, - usedefault=True, ), environ=dict( nohash=True, @@ -55,7 +53,6 @@ def test_Qwarp_inputs(): gridlist=dict( argstr='-gridlist %s', copyfile=False, - usedefault=True, xor=['duplo', 'plusminus'], ), hel=dict( @@ -66,7 +63,6 @@ def test_Qwarp_inputs(): argstr='-source %s', copyfile=False, mandatory=True, - usedefault=True, ), inilev=dict( argstr='-inilev %d', @@ -123,7 +119,6 @@ def test_Qwarp_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_QW', - usedefault=True, ), out_weight_file=dict(argstr='-wtprefix %s', ), outputtype=dict(), @@ -145,10 +140,7 @@ def test_Qwarp_inputs(): xor=['quiet'], ), wball=dict(argstr='-wball %s', ), - weight=dict( - argstr='-weight %s', - usedefault=True, - ), + weight=dict(argstr='-weight %s', ), wmask=dict(argstr='-wpass %s %f', ), workhard=dict( argstr='-workhard', @@ -162,11 +154,11 @@ def test_Qwarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Qwarp_outputs(): output_map = dict( - base_warp=dict(usedefault=True, ), - source_warp=dict(usedefault=True, ), - warped_base=dict(usedefault=True, ), - warped_source=dict(usedefault=True, ), - weights=dict(usedefault=True, ), + base_warp=dict(), + source_warp=dict(), + warped_base=dict(), + warped_source=dict(), + weights=dict(), ) outputs = Qwarp.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py b/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py index 3c3b1fde90..340f3a0e4a 100644 --- a/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py +++ b/nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py @@ -25,7 +25,6 @@ def test_QwarpPlusMinus_inputs(): argstr='-base %s', copyfile=False, mandatory=True, - usedefault=True, ), baxopt=dict( argstr='-boxopt', @@ -42,7 +41,6 @@ def test_QwarpPlusMinus_inputs(): emask=dict( argstr='-emask %s', copyfile=False, - usedefault=True, ), environ=dict( nohash=True, @@ -55,7 +53,6 @@ def test_QwarpPlusMinus_inputs(): gridlist=dict( argstr='-gridlist %s', copyfile=False, - usedefault=True, xor=['duplo', 'plusminus'], ), hel=dict( @@ -66,7 +63,6 @@ def test_QwarpPlusMinus_inputs(): argstr='-source %s', copyfile=False, mandatory=True, - usedefault=True, ), inilev=dict( argstr='-inilev %d', @@ -146,17 +142,13 @@ def test_QwarpPlusMinus_inputs(): copyfile=False, deprecated='1.1.2', new_name='in_file', - usedefault=True, ), verb=dict( argstr='-verb', xor=['quiet'], ), wball=dict(argstr='-wball %s', ), - weight=dict( - argstr='-weight %s', - usedefault=True, - ), + weight=dict(argstr='-weight %s', ), wmask=dict(argstr='-wpass %s %f', ), workhard=dict( argstr='-workhard', @@ -170,11 +162,11 @@ def test_QwarpPlusMinus_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_QwarpPlusMinus_outputs(): output_map = dict( - base_warp=dict(usedefault=True, ), - source_warp=dict(usedefault=True, ), - warped_base=dict(usedefault=True, ), - warped_source=dict(usedefault=True, ), - weights=dict(usedefault=True, ), + base_warp=dict(), + source_warp=dict(), + warped_base=dict(), + warped_source=dict(), + weights=dict(), ) outputs = QwarpPlusMinus.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_ROIStats.py b/nipype/interfaces/afni/tests/test_auto_ROIStats.py index 9dc1c87943..fbda92e9a5 100644 --- a/nipype/interfaces/afni/tests/test_auto_ROIStats.py +++ b/nipype/interfaces/afni/tests/test_auto_ROIStats.py @@ -23,20 +23,15 @@ def test_ROIStats_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), mask=dict( argstr='-mask %s', deprecated='1.1.4', new_name='mask_file', position=3, - usedefault=True, ), mask_f2short=dict(argstr='-mask_f2short', ), - mask_file=dict( - argstr='-mask %s', - usedefault=True, - ), + mask_file=dict(argstr='-mask %s', ), nobriklab=dict(argstr='-nobriklab', ), nomeanout=dict(argstr='-nomeanout', ), num_roi=dict(argstr='-numroi %s', ), @@ -46,7 +41,6 @@ def test_ROIStats_inputs(): name_source='in_file', name_template='%s_roistat.1D', position=-1, - usedefault=True, ), quiet=dict(argstr='-quiet', ), roisel=dict(argstr='-roisel %s', ), @@ -62,7 +56,7 @@ def test_ROIStats_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ROIStats_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ROIStats.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_ReHo.py b/nipype/interfaces/afni/tests/test_auto_ReHo.py index 491cb6e337..1809759485 100644 --- a/nipype/interfaces/afni/tests/test_auto_ReHo.py +++ b/nipype/interfaces/afni/tests/test_auto_ReHo.py @@ -19,12 +19,8 @@ def test_ReHo_inputs(): argstr='-inset %s', mandatory=True, position=1, - usedefault=True, - ), - label_set=dict( - argstr='-in_rois %s', - usedefault=True, ), + label_set=dict(argstr='-in_rois %s', ), mask_file=dict(argstr='-mask %s', ), neighborhood=dict( argstr='-nneigh %s', @@ -50,8 +46,8 @@ def test_ReHo_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ReHo_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - out_vals=dict(usedefault=True, ), + out_file=dict(), + out_vals=dict(), ) outputs = ReHo.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Refit.py b/nipype/interfaces/afni/tests/test_auto_Refit.py index f1727686a9..4983eafc81 100644 --- a/nipype/interfaces/afni/tests/test_auto_Refit.py +++ b/nipype/interfaces/afni/tests/test_auto_Refit.py @@ -11,10 +11,7 @@ def test_Refit_inputs(): atrint=dict(argstr='-atrint %s %s', ), atrstring=dict(argstr='-atrstring %s %s', ), deoblique=dict(argstr='-deoblique', ), - duporigin_file=dict( - argstr='-duporigin %s', - usedefault=True, - ), + duporigin_file=dict(argstr='-duporigin %s', ), environ=dict( nohash=True, usedefault=True, @@ -24,7 +21,6 @@ def test_Refit_inputs(): copyfile=True, mandatory=True, position=-1, - usedefault=True, ), nosaveatr=dict(argstr='-nosaveatr', ), saveatr=dict(argstr='-saveatr', ), @@ -43,7 +39,7 @@ def test_Refit_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Refit_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Refit.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Remlfit.py b/nipype/interfaces/afni/tests/test_auto_Remlfit.py index 69ca9642d0..4cdc8b2ff2 100644 --- a/nipype/interfaces/afni/tests/test_auto_Remlfit.py +++ b/nipype/interfaces/afni/tests/test_auto_Remlfit.py @@ -5,10 +5,7 @@ def test_Remlfit_inputs(): input_map = dict( - STATmask=dict( - argstr='-STATmask %s', - usedefault=True, - ), + STATmask=dict(argstr='-STATmask %s', ), addbase=dict( argstr='-addbase %s', copyfile=False, @@ -22,7 +19,6 @@ def test_Remlfit_inputs(): dsort=dict( argstr='-dsort %s', copyfile=False, - usedefault=True, ), dsort_nods=dict( argstr='-dsort_nods', @@ -32,19 +28,10 @@ def test_Remlfit_inputs(): nohash=True, usedefault=True, ), - errts_file=dict( - argstr='-Rerrts %s', - usedefault=True, - ), - fitts_file=dict( - argstr='-Rfitts %s', - usedefault=True, - ), + errts_file=dict(argstr='-Rerrts %s', ), + fitts_file=dict(argstr='-Rfitts %s', ), fout=dict(argstr='-fout', ), - glt_file=dict( - argstr='-Rglt %s', - usedefault=True, - ), + glt_file=dict(argstr='-Rglt %s', ), gltsym=dict(argstr='-gltsym "%s" %s...', ), in_files=dict( argstr='-input "%s"', @@ -52,10 +39,7 @@ def test_Remlfit_inputs(): mandatory=True, sep=' ', ), - mask=dict( - argstr='-mask %s', - usedefault=True, - ), + mask=dict(argstr='-mask %s', ), matim=dict( argstr='-matim %s', xor=['matrix'], @@ -63,7 +47,6 @@ def test_Remlfit_inputs(): matrix=dict( argstr='-matrix %s', mandatory=True, - usedefault=True, ), nobout=dict(argstr='-nobout', ), nodmbase=dict( @@ -75,58 +58,28 @@ def test_Remlfit_inputs(): nohash=True, usedefault=True, ), - obeta=dict( - argstr='-Obeta %s', - usedefault=True, - ), - obuck=dict( - argstr='-Obuck %s', - usedefault=True, - ), - oerrts=dict( - argstr='-Oerrts %s', - usedefault=True, - ), - ofitts=dict( - argstr='-Ofitts %s', - usedefault=True, - ), - oglt=dict( - argstr='-Oglt %s', - usedefault=True, - ), - out_file=dict( - argstr='-Rbuck %s', - usedefault=True, - ), + obeta=dict(argstr='-Obeta %s', ), + obuck=dict(argstr='-Obuck %s', ), + oerrts=dict(argstr='-Oerrts %s', ), + ofitts=dict(argstr='-Ofitts %s', ), + oglt=dict(argstr='-Oglt %s', ), + out_file=dict(argstr='-Rbuck %s', ), outputtype=dict(), - ovar=dict( - argstr='-Ovar %s', - usedefault=True, - ), + ovar=dict(argstr='-Ovar %s', ), polort=dict( argstr='-polort %d', xor=['matrix'], ), quiet=dict(argstr='-quiet', ), - rbeta_file=dict( - argstr='-Rbeta %s', - usedefault=True, - ), + rbeta_file=dict(argstr='-Rbeta %s', ), rout=dict(argstr='-rout', ), slibase=dict(argstr='-slibase %s', ), slibase_sm=dict(argstr='-slibase_sm %s', ), tout=dict(argstr='-tout', ), usetemp=dict(argstr='-usetemp', ), - var_file=dict( - argstr='-Rvar %s', - usedefault=True, - ), + var_file=dict(argstr='-Rvar %s', ), verb=dict(argstr='-verb', ), - wherr_file=dict( - argstr='-Rwherr %s', - usedefault=True, - ), + wherr_file=dict(argstr='-Rwherr %s', ), ) inputs = Remlfit.input_spec() @@ -135,19 +88,19 @@ def test_Remlfit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Remlfit_outputs(): output_map = dict( - errts_file=dict(usedefault=True, ), - fitts_file=dict(usedefault=True, ), - glt_file=dict(usedefault=True, ), - obeta=dict(usedefault=True, ), - obuck=dict(usedefault=True, ), - oerrts=dict(usedefault=True, ), - ofitts=dict(usedefault=True, ), - oglt=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), - ovar=dict(usedefault=True, ), - rbeta_file=dict(usedefault=True, ), - var_file=dict(usedefault=True, ), - wherr_file=dict(usedefault=True, ), + errts_file=dict(), + fitts_file=dict(), + glt_file=dict(), + obeta=dict(), + obuck=dict(), + oerrts=dict(), + ofitts=dict(), + oglt=dict(), + out_file=dict(), + ovar=dict(), + rbeta_file=dict(), + var_file=dict(), + wherr_file=dict(), ) outputs = Remlfit.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Resample.py b/nipype/interfaces/afni/tests/test_auto_Resample.py index b6be4c083a..9ab2309307 100644 --- a/nipype/interfaces/afni/tests/test_auto_Resample.py +++ b/nipype/interfaces/afni/tests/test_auto_Resample.py @@ -15,7 +15,6 @@ def test_Resample_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, ), master=dict(argstr='-master %s', ), num_threads=dict( @@ -27,7 +26,6 @@ def test_Resample_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_resample', - usedefault=True, ), outputtype=dict(), resample_mode=dict(argstr='-rmode %s', ), @@ -39,7 +37,7 @@ def test_Resample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Resample_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Resample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Retroicor.py b/nipype/interfaces/afni/tests/test_auto_Retroicor.py index 9b79ea0623..4c2a1c2393 100644 --- a/nipype/interfaces/afni/tests/test_auto_Retroicor.py +++ b/nipype/interfaces/afni/tests/test_auto_Retroicor.py @@ -9,13 +9,11 @@ def test_Retroicor_inputs(): card=dict( argstr='-card %s', position=-2, - usedefault=True, ), cardphase=dict( argstr='-cardphase %s', hash_files=False, position=-6, - usedefault=True, ), environ=dict( nohash=True, @@ -26,7 +24,6 @@ def test_Retroicor_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, ), num_threads=dict( nohash=True, @@ -41,19 +38,16 @@ def test_Retroicor_inputs(): name_source=['in_file'], name_template='%s_retroicor', position=1, - usedefault=True, ), outputtype=dict(), resp=dict( argstr='-resp %s', position=-3, - usedefault=True, ), respphase=dict( argstr='-respphase %s', hash_files=False, position=-7, - usedefault=True, ), threshold=dict( argstr='-threshold %d', @@ -66,7 +60,7 @@ def test_Retroicor_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Retroicor_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Retroicor.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTest.py b/nipype/interfaces/afni/tests/test_auto_SVMTest.py index e4349149e1..4b31d3a11c 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTest.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTest.py @@ -14,7 +14,6 @@ def test_SVMTest_inputs(): in_file=dict( argstr='-testvol %s', mandatory=True, - usedefault=True, ), model=dict( argstr='-model %s', @@ -31,13 +30,9 @@ def test_SVMTest_inputs(): out_file=dict( argstr='-predictions %s', name_template='%s_predictions', - usedefault=True, ), outputtype=dict(), - testlabels=dict( - argstr='-testlabels %s', - usedefault=True, - ), + testlabels=dict(argstr='-testlabels %s', ), ) inputs = SVMTest.input_spec() @@ -45,7 +40,7 @@ def test_SVMTest_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SVMTest_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = SVMTest.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py index 54d326a561..ddb3f8c05f 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py @@ -10,13 +10,9 @@ def test_SVMTrain_inputs(): name_source='in_file', name_template='%s_alphas', suffix='_alphas', - usedefault=True, ), args=dict(argstr='%s', ), - censor=dict( - argstr='-censor %s', - usedefault=True, - ), + censor=dict(argstr='-censor %s', ), environ=dict( nohash=True, usedefault=True, @@ -25,14 +21,12 @@ def test_SVMTrain_inputs(): argstr='-trainvol %s', copyfile=False, mandatory=True, - usedefault=True, ), kernel=dict(argstr='-kernel %s', ), mask=dict( argstr='-mask %s', copyfile=False, position=-1, - usedefault=True, ), max_iterations=dict(argstr='-max_iterations %d', ), model=dict( @@ -40,7 +34,6 @@ def test_SVMTrain_inputs(): name_source='in_file', name_template='%s_model', suffix='_model', - usedefault=True, ), nomodelmask=dict(argstr='-nomodelmask', ), num_threads=dict( @@ -53,13 +46,9 @@ def test_SVMTrain_inputs(): name_source='in_file', name_template='%s_vectors', suffix='_bucket', - usedefault=True, ), outputtype=dict(), - trainlabels=dict( - argstr='-trainlabels %s', - usedefault=True, - ), + trainlabels=dict(argstr='-trainlabels %s', ), ttype=dict( argstr='-type %s', mandatory=True, @@ -73,9 +62,9 @@ def test_SVMTrain_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SVMTrain_outputs(): output_map = dict( - alphas=dict(usedefault=True, ), - model=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), + alphas=dict(), + model=dict(), + out_file=dict(), ) outputs = SVMTrain.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Seg.py b/nipype/interfaces/afni/tests/test_auto_Seg.py index a30d59b1cb..e93d81a7aa 100644 --- a/nipype/interfaces/afni/tests/test_auto_Seg.py +++ b/nipype/interfaces/afni/tests/test_auto_Seg.py @@ -20,7 +20,6 @@ def test_Seg_inputs(): copyfile=True, mandatory=True, position=-1, - usedefault=True, ), main_N=dict(argstr='-main_N %d', ), mask=dict( @@ -38,7 +37,7 @@ def test_Seg_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Seg_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Seg.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py index 3b56af7aa2..e960369787 100644 --- a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py +++ b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py @@ -15,7 +15,6 @@ def test_SkullStrip_inputs(): copyfile=False, mandatory=True, position=1, - usedefault=True, ), num_threads=dict( nohash=True, @@ -25,7 +24,6 @@ def test_SkullStrip_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_skullstrip', - usedefault=True, ), outputtype=dict(), ) @@ -35,7 +33,7 @@ def test_SkullStrip_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SkullStrip_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = SkullStrip.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Synthesize.py b/nipype/interfaces/afni/tests/test_auto_Synthesize.py index bdbf66c858..87278098fb 100644 --- a/nipype/interfaces/afni/tests/test_auto_Synthesize.py +++ b/nipype/interfaces/afni/tests/test_auto_Synthesize.py @@ -11,7 +11,6 @@ def test_Synthesize_inputs(): argstr='-cbucket %s', copyfile=False, mandatory=True, - usedefault=True, ), cenfill=dict(argstr='-cenfill %s', ), dry_run=dict(argstr='-dry', ), @@ -23,7 +22,6 @@ def test_Synthesize_inputs(): argstr='-matrix %s', copyfile=False, mandatory=True, - usedefault=True, ), num_threads=dict( nohash=True, @@ -32,7 +30,6 @@ def test_Synthesize_inputs(): out_file=dict( argstr='-prefix %s', name_template='syn', - usedefault=True, ), outputtype=dict(), select=dict( @@ -46,7 +43,7 @@ def test_Synthesize_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Synthesize_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Synthesize.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TCat.py b/nipype/interfaces/afni/tests/test_auto_TCat.py index 900b977540..5c51b02637 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCat.py +++ b/nipype/interfaces/afni/tests/test_auto_TCat.py @@ -24,7 +24,6 @@ def test_TCat_inputs(): argstr='-prefix %s', name_source='in_files', name_template='%s_tcat', - usedefault=True, ), outputtype=dict(), rlt=dict( @@ -39,7 +38,7 @@ def test_TCat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TCat_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TCat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py b/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py index 3d3e650a98..09b21ea408 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py +++ b/nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py @@ -23,7 +23,6 @@ def test_TCatSubBrick_inputs(): out_file=dict( argstr='-prefix %s', genfile=True, - usedefault=True, ), outputtype=dict(), rlt=dict( @@ -37,7 +36,7 @@ def test_TCatSubBrick_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TCatSubBrick_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TCatSubBrick.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py index 3c04561a81..e1b23a3387 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py @@ -24,7 +24,6 @@ def test_TCorr1D_inputs(): keep_extension=True, name_source='xset', name_template='%s_correlation.nii.gz', - usedefault=True, ), outputtype=dict(), pearson=dict( @@ -47,13 +46,11 @@ def test_TCorr1D_inputs(): copyfile=False, mandatory=True, position=-2, - usedefault=True, ), y_1d=dict( argstr=' %s', mandatory=True, position=-1, - usedefault=True, ), ) inputs = TCorr1D.input_spec() @@ -62,7 +59,7 @@ def test_TCorr1D_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TCorr1D_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TCorr1D.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py index 5efb91365b..823762fdad 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py @@ -9,7 +9,6 @@ def test_TCorrMap_inputs(): argstr='-Thresh %f %s', name_source='in_file', suffix='_thresh', - usedefault=True, xor=('absolute_threshold', 'var_absolute_threshold', 'var_absolute_threshold_normalize'), ), @@ -19,14 +18,12 @@ def test_TCorrMap_inputs(): argstr='-Aexpr %s %s', name_source='in_file', suffix='_aexpr', - usedefault=True, xor=('average_expr', 'average_expr_nonzero', 'sum_expr'), ), average_expr_nonzero=dict( argstr='-Cexpr %s %s', name_source='in_file', suffix='_cexpr', - usedefault=True, xor=('average_expr', 'average_expr_nonzero', 'sum_expr'), ), bandpass=dict(argstr='-bpass %f %f', ), @@ -34,12 +31,10 @@ def test_TCorrMap_inputs(): correlation_maps=dict( argstr='-CorrMap %s', name_source='in_file', - usedefault=True, ), correlation_maps_masked=dict( argstr='-CorrMask %s', name_source='in_file', - usedefault=True, ), environ=dict( nohash=True, @@ -50,24 +45,18 @@ def test_TCorrMap_inputs(): argstr='-Hist %d %s', name_source='in_file', suffix='_hist', - usedefault=True, ), histogram_bin_numbers=dict(), in_file=dict( argstr='-input %s', copyfile=False, mandatory=True, - usedefault=True, - ), - mask=dict( - argstr='-mask %s', - usedefault=True, ), + mask=dict(argstr='-mask %s', ), mean_file=dict( argstr='-Mean %s', name_source='in_file', suffix='_mean', - usedefault=True, ), num_threads=dict( nohash=True, @@ -78,19 +67,16 @@ def test_TCorrMap_inputs(): argstr='-Pmean %s', name_source='in_file', suffix='_pmean', - usedefault=True, ), polort=dict(argstr='-polort %d', ), qmean=dict( argstr='-Qmean %s', name_source='in_file', suffix='_qmean', - usedefault=True, ), regress_out_timeseries=dict(argstr='-ort %s', ), seeds=dict( argstr='-seed %s', - usedefault=True, xor='seeds_width', ), seeds_width=dict( @@ -101,7 +87,6 @@ def test_TCorrMap_inputs(): argstr='-Sexpr %s %s', name_source='in_file', suffix='_sexpr', - usedefault=True, xor=('average_expr', 'average_expr_nonzero', 'sum_expr'), ), thresholds=dict(), @@ -109,7 +94,6 @@ def test_TCorrMap_inputs(): argstr='-VarThresh %f %f %f %s', name_source='in_file', suffix='_varthresh', - usedefault=True, xor=('absolute_threshold', 'var_absolute_threshold', 'var_absolute_threshold_normalize'), ), @@ -117,7 +101,6 @@ def test_TCorrMap_inputs(): argstr='-VarThreshN %f %f %f %s', name_source='in_file', suffix='_varthreshn', - usedefault=True, xor=('absolute_threshold', 'var_absolute_threshold', 'var_absolute_threshold_normalize'), ), @@ -125,7 +108,6 @@ def test_TCorrMap_inputs(): argstr='-Zmean %s', name_source='in_file', suffix='_zmean', - usedefault=True, ), ) inputs = TCorrMap.input_spec() @@ -135,19 +117,19 @@ def test_TCorrMap_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TCorrMap_outputs(): output_map = dict( - absolute_threshold=dict(usedefault=True, ), - average_expr=dict(usedefault=True, ), - average_expr_nonzero=dict(usedefault=True, ), - correlation_maps=dict(usedefault=True, ), - correlation_maps_masked=dict(usedefault=True, ), - histogram=dict(usedefault=True, ), - mean_file=dict(usedefault=True, ), - pmean=dict(usedefault=True, ), - qmean=dict(usedefault=True, ), - sum_expr=dict(usedefault=True, ), - var_absolute_threshold=dict(usedefault=True, ), - var_absolute_threshold_normalize=dict(usedefault=True, ), - zmean=dict(usedefault=True, ), + absolute_threshold=dict(), + average_expr=dict(), + average_expr_nonzero=dict(), + correlation_maps=dict(), + correlation_maps_masked=dict(), + histogram=dict(), + mean_file=dict(), + pmean=dict(), + qmean=dict(), + sum_expr=dict(), + var_absolute_threshold=dict(), + var_absolute_threshold_normalize=dict(), + zmean=dict(), ) outputs = TCorrMap.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py index 283fe966ae..8d773f429e 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py @@ -18,7 +18,6 @@ def test_TCorrelate_inputs(): argstr='-prefix %s', name_source='xset', name_template='%s_tcorr', - usedefault=True, ), outputtype=dict(), pearson=dict(argstr='-pearson', ), @@ -28,14 +27,12 @@ def test_TCorrelate_inputs(): copyfile=False, mandatory=True, position=-2, - usedefault=True, ), yset=dict( argstr='%s', copyfile=False, mandatory=True, position=-1, - usedefault=True, ), ) inputs = TCorrelate.input_spec() @@ -44,7 +41,7 @@ def test_TCorrelate_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TCorrelate_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TCorrelate.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TNorm.py b/nipype/interfaces/afni/tests/test_auto_TNorm.py index 23d2a43841..3fb246684b 100644 --- a/nipype/interfaces/afni/tests/test_auto_TNorm.py +++ b/nipype/interfaces/afni/tests/test_auto_TNorm.py @@ -16,7 +16,6 @@ def test_TNorm_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, ), norm1=dict(argstr='-norm1', ), norm2=dict(argstr='-norm2', ), @@ -30,7 +29,6 @@ def test_TNorm_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_tnorm', - usedefault=True, ), outputtype=dict(), polort=dict(argstr='-polort %s', ), @@ -41,7 +39,7 @@ def test_TNorm_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TNorm_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TNorm.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TProject.py b/nipype/interfaces/afni/tests/test_auto_TProject.py index c07c6fd602..ba4efd6189 100644 --- a/nipype/interfaces/afni/tests/test_auto_TProject.py +++ b/nipype/interfaces/afni/tests/test_auto_TProject.py @@ -14,15 +14,9 @@ def test_TProject_inputs(): bandpass=dict(argstr='-bandpass %g %g', ), blur=dict(argstr='-blur %g', ), cenmode=dict(argstr='-cenmode %s', ), - censor=dict( - argstr='-censor %s', - usedefault=True, - ), + censor=dict(argstr='-censor %s', ), censortr=dict(argstr='-CENSORTR %s', ), - concat=dict( - argstr='-concat %s', - usedefault=True, - ), + concat=dict(argstr='-concat %s', ), dsort=dict(argstr='-dsort %s...', ), environ=dict( nohash=True, @@ -33,28 +27,20 @@ def test_TProject_inputs(): copyfile=False, mandatory=True, position=1, - usedefault=True, - ), - mask=dict( - argstr='-mask %s', - usedefault=True, ), + mask=dict(argstr='-mask %s', ), noblock=dict(argstr='-noblock', ), norm=dict(argstr='-norm', ), num_threads=dict( nohash=True, usedefault=True, ), - ort=dict( - argstr='-ort %s', - usedefault=True, - ), + ort=dict(argstr='-ort %s', ), out_file=dict( argstr='-prefix %s', name_source='in_file', name_template='%s_tproject', position=-1, - usedefault=True, ), outputtype=dict(), polort=dict(argstr='-polort %d', ), @@ -66,7 +52,7 @@ def test_TProject_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TProject_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TProject.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_TShift.py b/nipype/interfaces/afni/tests/test_auto_TShift.py index 2a66792be7..b267986952 100644 --- a/nipype/interfaces/afni/tests/test_auto_TShift.py +++ b/nipype/interfaces/afni/tests/test_auto_TShift.py @@ -16,7 +16,6 @@ def test_TShift_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, ), interp=dict(argstr='-%s', ), num_threads=dict( @@ -27,7 +26,6 @@ def test_TShift_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_tshift', - usedefault=True, ), outputtype=dict(), rlt=dict(argstr='-rlt', ), @@ -58,8 +56,8 @@ def test_TShift_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TShift_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - timing_file=dict(usedefault=True, ), + out_file=dict(), + timing_file=dict(), ) outputs = TShift.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_TStat.py b/nipype/interfaces/afni/tests/test_auto_TStat.py index 021b39bac3..5a3ebd8a21 100644 --- a/nipype/interfaces/afni/tests/test_auto_TStat.py +++ b/nipype/interfaces/afni/tests/test_auto_TStat.py @@ -15,12 +15,8 @@ def test_TStat_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, - ), - mask=dict( - argstr='-mask %s', - usedefault=True, ), + mask=dict(argstr='-mask %s', ), num_threads=dict( nohash=True, usedefault=True, @@ -30,7 +26,6 @@ def test_TStat_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_tstat', - usedefault=True, ), outputtype=dict(), ) @@ -40,7 +35,7 @@ def test_TStat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TStat_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TStat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_To3D.py b/nipype/interfaces/afni/tests/test_auto_To3D.py index 0edf3f255d..66ccabefcb 100644 --- a/nipype/interfaces/afni/tests/test_auto_To3D.py +++ b/nipype/interfaces/afni/tests/test_auto_To3D.py @@ -18,7 +18,6 @@ def test_To3D_inputs(): argstr='%s/*.dcm', mandatory=True, position=-1, - usedefault=True, ), num_threads=dict( nohash=True, @@ -28,7 +27,6 @@ def test_To3D_inputs(): argstr='-prefix %s', name_source=['in_folder'], name_template='%s', - usedefault=True, ), outputtype=dict(), skipoutliers=dict(argstr='-skip_outliers', ), @@ -39,7 +37,7 @@ def test_To3D_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_To3D_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = To3D.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Undump.py b/nipype/interfaces/afni/tests/test_auto_Undump.py index 572e7e3bcb..07d0ff8e81 100644 --- a/nipype/interfaces/afni/tests/test_auto_Undump.py +++ b/nipype/interfaces/afni/tests/test_auto_Undump.py @@ -20,12 +20,8 @@ def test_Undump_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, - ), - mask_file=dict( - argstr='-mask %s', - usedefault=True, ), + mask_file=dict(argstr='-mask %s', ), num_threads=dict( nohash=True, usedefault=True, @@ -34,7 +30,6 @@ def test_Undump_inputs(): out_file=dict( argstr='-prefix %s', name_source='in_file', - usedefault=True, ), outputtype=dict(), srad=dict(argstr='-srad %f', ), @@ -45,7 +40,7 @@ def test_Undump_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Undump_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Undump.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Unifize.py b/nipype/interfaces/afni/tests/test_auto_Unifize.py index c5c89a0793..3215d51e64 100644 --- a/nipype/interfaces/afni/tests/test_auto_Unifize.py +++ b/nipype/interfaces/afni/tests/test_auto_Unifize.py @@ -22,7 +22,6 @@ def test_Unifize_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, ), no_duplo=dict(argstr='-noduplo', ), num_threads=dict( @@ -33,15 +32,11 @@ def test_Unifize_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_unifized', - usedefault=True, ), outputtype=dict(), quiet=dict(argstr='-quiet', ), rbt=dict(argstr='-rbt %f %f %f', ), - scale_file=dict( - argstr='-ssave %s', - usedefault=True, - ), + scale_file=dict(argstr='-ssave %s', ), t2=dict(argstr='-T2', ), t2_up=dict(argstr='-T2up %f', ), urad=dict(argstr='-Urad %s', ), @@ -53,8 +48,8 @@ def test_Unifize_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Unifize_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - scale_file=dict(usedefault=True, ), + out_file=dict(), + scale_file=dict(), ) outputs = Unifize.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Volreg.py b/nipype/interfaces/afni/tests/test_auto_Volreg.py index 179e1fa3e3..293b7613e8 100644 --- a/nipype/interfaces/afni/tests/test_auto_Volreg.py +++ b/nipype/interfaces/afni/tests/test_auto_Volreg.py @@ -9,7 +9,6 @@ def test_Volreg_inputs(): basefile=dict( argstr='-base %s', position=-6, - usedefault=True, ), copyorigin=dict(argstr='-twodup', ), environ=dict( @@ -21,7 +20,6 @@ def test_Volreg_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, ), in_weight_volume=dict(argstr="-weight '%s[%d]'", ), interp=dict(argstr='-%s', ), @@ -31,7 +29,6 @@ def test_Volreg_inputs(): name_source='in_file', name_template='%s_md.1D', position=-4, - usedefault=True, ), num_threads=dict( nohash=True, @@ -42,20 +39,17 @@ def test_Volreg_inputs(): keep_extension=True, name_source='in_file', name_template='%s.1D', - usedefault=True, ), oned_matrix_save=dict( argstr='-1Dmatrix_save %s', keep_extension=True, name_source='in_file', name_template='%s.aff12.1D', - usedefault=True, ), out_file=dict( argstr='-prefix %s', name_source='in_file', name_template='%s_volreg', - usedefault=True, ), outputtype=dict(), timeshift=dict(argstr='-tshift 0', ), @@ -72,10 +66,10 @@ def test_Volreg_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Volreg_outputs(): output_map = dict( - md1d_file=dict(usedefault=True, ), - oned_file=dict(usedefault=True, ), - oned_matrix_save=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), + md1d_file=dict(), + oned_file=dict(), + oned_matrix_save=dict(), + out_file=dict(), ) outputs = Volreg.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_Warp.py b/nipype/interfaces/afni/tests/test_auto_Warp.py index c5bee6a063..b85692310a 100644 --- a/nipype/interfaces/afni/tests/test_auto_Warp.py +++ b/nipype/interfaces/afni/tests/test_auto_Warp.py @@ -11,38 +11,27 @@ def test_Warp_inputs(): nohash=True, usedefault=True, ), - gridset=dict( - argstr='-gridset %s', - usedefault=True, - ), + gridset=dict(argstr='-gridset %s', ), in_file=dict( argstr='%s', copyfile=False, mandatory=True, position=-1, - usedefault=True, ), interp=dict(argstr='-%s', ), - matparent=dict( - argstr='-matparent %s', - usedefault=True, - ), + matparent=dict(argstr='-matparent %s', ), mni2tta=dict(argstr='-mni2tta', ), newgrid=dict(argstr='-newgrid %f', ), num_threads=dict( nohash=True, usedefault=True, ), - oblique_parent=dict( - argstr='-oblique_parent %s', - usedefault=True, - ), + oblique_parent=dict(argstr='-oblique_parent %s', ), out_file=dict( argstr='-prefix %s', keep_extension=True, name_source='in_file', name_template='%s_warp', - usedefault=True, ), outputtype=dict(), save_warp=dict(requires=['verbose'], ), @@ -57,8 +46,8 @@ def test_Warp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Warp_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - warp_file=dict(usedefault=True, ), + out_file=dict(), + warp_file=dict(), ) outputs = Warp.output_spec() diff --git a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py index 353a98d76a..cacb6b1534 100644 --- a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py +++ b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py @@ -15,7 +15,6 @@ def test_ZCutUp_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, ), keep=dict(argstr='-keep %s', ), num_threads=dict( @@ -26,7 +25,6 @@ def test_ZCutUp_inputs(): argstr='-prefix %s', name_source='in_file', name_template='%s_zcutup', - usedefault=True, ), outputtype=dict(), ) @@ -36,7 +34,7 @@ def test_ZCutUp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ZCutUp_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ZCutUp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Zcat.py b/nipype/interfaces/afni/tests/test_auto_Zcat.py index 6dc0430c09..3a2b7ff853 100644 --- a/nipype/interfaces/afni/tests/test_auto_Zcat.py +++ b/nipype/interfaces/afni/tests/test_auto_Zcat.py @@ -33,7 +33,6 @@ def test_Zcat_inputs(): argstr='-prefix %s', name_source='in_files', name_template='%s_zcat', - usedefault=True, ), outputtype=dict(), verb=dict(argstr='-verb', ), @@ -44,7 +43,7 @@ def test_Zcat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Zcat_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Zcat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/afni/tests/test_auto_Zeropad.py b/nipype/interfaces/afni/tests/test_auto_Zeropad.py index 427eef0f67..cfba8e2f3c 100644 --- a/nipype/interfaces/afni/tests/test_auto_Zeropad.py +++ b/nipype/interfaces/afni/tests/test_auto_Zeropad.py @@ -51,7 +51,6 @@ def test_Zeropad_inputs(): copyfile=False, mandatory=True, position=-1, - usedefault=True, ), master=dict( argstr='-master %s', @@ -68,7 +67,6 @@ def test_Zeropad_inputs(): out_file=dict( argstr='-prefix %s', name_template='zeropad', - usedefault=True, ), outputtype=dict(), z=dict( @@ -82,7 +80,7 @@ def test_Zeropad_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Zeropad_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Zeropad.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_ANTS.py b/nipype/interfaces/ants/tests/test_auto_ANTS.py index 24ddbadadf..7c7ef6682c 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTS.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTS.py @@ -84,11 +84,11 @@ def test_ANTS_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ANTS_outputs(): output_map = dict( - affine_transform=dict(usedefault=True, ), - inverse_warp_transform=dict(usedefault=True, ), - metaheader=dict(usedefault=True, ), - metaheader_raw=dict(usedefault=True, ), - warp_transform=dict(usedefault=True, ), + affine_transform=dict(), + inverse_warp_transform=dict(), + metaheader=dict(), + metaheader_raw=dict(), + warp_transform=dict(), ) outputs = ANTS.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py b/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py index 96d839a0dc..fed21cdbef 100644 --- a/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py +++ b/nipype/interfaces/ants/tests/test_auto_AffineInitializer.py @@ -19,7 +19,6 @@ def test_AffineInitializer_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), local_search=dict( argstr='%d', @@ -30,7 +29,6 @@ def test_AffineInitializer_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), num_threads=dict( nohash=True, @@ -63,7 +61,7 @@ def test_AffineInitializer_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AffineInitializer_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = AffineInitializer.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py index cf39a7c3c4..341f250a2c 100644 --- a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py @@ -36,10 +36,7 @@ def test_AntsJointFusion_inputs(): argstr='-e %s', requires=['exclusion_image'], ), - mask_image=dict( - argstr='-x %s', - usedefault=True, - ), + mask_image=dict(argstr='-x %s', ), num_threads=dict( nohash=True, usedefault=True, @@ -53,11 +50,10 @@ def test_AntsJointFusion_inputs(): out_label_fusion=dict( argstr='%s', hash_files=False, - usedefault=True, ), out_label_post_prob_name_format=dict( - requires=['out_label_fusion', 'out_intensity_fusion_name_format'], - ), + requires=['out_label_fusion', + 'out_intensity_fusion_name_format'], ), patch_metric=dict(argstr='-m %s', ), patch_radius=dict( argstr='-p %s', @@ -92,7 +88,7 @@ def test_AntsJointFusion_outputs(): output_map = dict( out_atlas_voting_weight_name_format=dict(), out_intensity_fusion_name_format=dict(), - out_label_fusion=dict(usedefault=True, ), + out_label_fusion=dict(), out_label_post_prob_name_format=dict(), ) outputs = AntsJointFusion.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py index 82cd9dfc29..c2bbffa14f 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py @@ -22,7 +22,6 @@ def test_ApplyTransforms_inputs(): input_image=dict( argstr='--input %s', mandatory=True, - usedefault=True, ), input_image_type=dict(argstr='--input-image-type %d', ), interpolation=dict( @@ -45,7 +44,6 @@ def test_ApplyTransforms_inputs(): reference_image=dict( argstr='--reference-image %s', mandatory=True, - usedefault=True, ), transforms=dict( argstr='%s', @@ -58,7 +56,7 @@ def test_ApplyTransforms_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyTransforms_outputs(): - output_map = dict(output_image=dict(usedefault=True, ), ) + output_map = dict(output_image=dict(), ) outputs = ApplyTransforms.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py index 58fc69e72d..92c6c21ec1 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py @@ -14,7 +14,6 @@ def test_ApplyTransformsToPoints_inputs(): input_file=dict( argstr='--input %s', mandatory=True, - usedefault=True, ), invert_transform_flags=dict(), num_threads=dict( @@ -38,7 +37,7 @@ def test_ApplyTransformsToPoints_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyTransformsToPoints_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = ApplyTransformsToPoints.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_Atropos.py b/nipype/interfaces/ants/tests/test_auto_Atropos.py index b3b9252858..90bc13778a 100644 --- a/nipype/interfaces/ants/tests/test_auto_Atropos.py +++ b/nipype/interfaces/ants/tests/test_auto_Atropos.py @@ -29,7 +29,6 @@ def test_Atropos_inputs(): mask_image=dict( argstr='--mask-image %s', mandatory=True, - usedefault=True, ), maximum_number_of_icm_terations=dict( requires=['icm_use_synchronous_update'], ), @@ -45,7 +44,6 @@ def test_Atropos_inputs(): argstr='%s', genfile=True, hash_files=False, - usedefault=True, ), output_posteriors_name_template=dict(usedefault=True, ), posterior_formulation=dict(argstr='%s', ), @@ -67,7 +65,7 @@ def test_Atropos_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Atropos_outputs(): output_map = dict( - classified_image=dict(usedefault=True, ), + classified_image=dict(), posteriors=dict(), ) outputs = Atropos.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py index 4fad7f75d5..3fe3abe5cf 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py @@ -23,7 +23,6 @@ def test_AverageAffineTransform_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), transforms=dict( argstr='%s', @@ -37,7 +36,7 @@ def test_AverageAffineTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AverageAffineTransform_outputs(): - output_map = dict(affine_transform=dict(usedefault=True, ), ) + output_map = dict(affine_transform=dict(), ) outputs = AverageAffineTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_AverageImages.py b/nipype/interfaces/ants/tests/test_auto_AverageImages.py index dba08b8ae7..41e0c99007 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageImages.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageImages.py @@ -42,7 +42,7 @@ def test_AverageImages_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AverageImages_outputs(): - output_map = dict(output_average_image=dict(usedefault=True, ), ) + output_map = dict(output_average_image=dict(), ) outputs = AverageImages.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py b/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py index e25d66f914..2d48192199 100644 --- a/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py +++ b/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py @@ -8,19 +8,16 @@ def test_BrainExtraction_inputs(): anatomical_image=dict( argstr='-a %s', mandatory=True, - usedefault=True, ), args=dict(argstr='%s', ), brain_probability_mask=dict( argstr='-m %s', copyfile=False, mandatory=True, - usedefault=True, ), brain_template=dict( argstr='-e %s', mandatory=True, - usedefault=True, ), debug=dict(argstr='-z 1', ), dimension=dict( @@ -31,10 +28,7 @@ def test_BrainExtraction_inputs(): nohash=True, usedefault=True, ), - extraction_registration_mask=dict( - argstr='-f %s', - usedefault=True, - ), + extraction_registration_mask=dict(argstr='-f %s', ), image_suffix=dict( argstr='-s %s', usedefault=True, @@ -58,24 +52,24 @@ def test_BrainExtraction_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BrainExtraction_outputs(): output_map = dict( - BrainExtractionBrain=dict(usedefault=True, ), - BrainExtractionCSF=dict(usedefault=True, ), - BrainExtractionGM=dict(usedefault=True, ), - BrainExtractionInitialAffine=dict(usedefault=True, ), - BrainExtractionInitialAffineFixed=dict(usedefault=True, ), - BrainExtractionInitialAffineMoving=dict(usedefault=True, ), - BrainExtractionLaplacian=dict(usedefault=True, ), - BrainExtractionMask=dict(usedefault=True, ), - BrainExtractionPrior0GenericAffine=dict(usedefault=True, ), - BrainExtractionPrior1InverseWarp=dict(usedefault=True, ), - BrainExtractionPrior1Warp=dict(usedefault=True, ), - BrainExtractionPriorWarped=dict(usedefault=True, ), - BrainExtractionSegmentation=dict(usedefault=True, ), - BrainExtractionTemplateLaplacian=dict(usedefault=True, ), - BrainExtractionTmp=dict(usedefault=True, ), - BrainExtractionWM=dict(usedefault=True, ), - N4Corrected0=dict(usedefault=True, ), - N4Truncated0=dict(usedefault=True, ), + BrainExtractionBrain=dict(), + BrainExtractionCSF=dict(), + BrainExtractionGM=dict(), + BrainExtractionInitialAffine=dict(), + BrainExtractionInitialAffineFixed=dict(), + BrainExtractionInitialAffineMoving=dict(), + BrainExtractionLaplacian=dict(), + BrainExtractionMask=dict(), + BrainExtractionPrior0GenericAffine=dict(), + BrainExtractionPrior1InverseWarp=dict(), + BrainExtractionPrior1Warp=dict(), + BrainExtractionPriorWarped=dict(), + BrainExtractionSegmentation=dict(), + BrainExtractionTemplateLaplacian=dict(), + BrainExtractionTmp=dict(), + BrainExtractionWM=dict(), + N4Corrected0=dict(), + N4Truncated0=dict(), ) outputs = BrainExtraction.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py index 8363a98834..83fb2ed2aa 100644 --- a/nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_ComposeMultiTransform.py @@ -25,12 +25,10 @@ def test_ComposeMultiTransform_inputs(): name_source=['transforms'], name_template='%s_composed', position=1, - usedefault=True, ), reference_image=dict( argstr='%s', position=2, - usedefault=True, ), transforms=dict( argstr='%s', @@ -44,7 +42,7 @@ def test_ComposeMultiTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComposeMultiTransform_outputs(): - output_map = dict(output_transform=dict(usedefault=True, ), ) + output_map = dict(output_transform=dict(), ) outputs = ComposeMultiTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_CompositeTransformUtil.py b/nipype/interfaces/ants/tests/test_auto_CompositeTransformUtil.py index abe9a62427..d2e6f943e2 100644 --- a/nipype/interfaces/ants/tests/test_auto_CompositeTransformUtil.py +++ b/nipype/interfaces/ants/tests/test_auto_CompositeTransformUtil.py @@ -22,7 +22,6 @@ def test_CompositeTransformUtil_inputs(): out_file=dict( argstr='%s', position=2, - usedefault=True, ), output_prefix=dict( argstr='%s', @@ -42,9 +41,9 @@ def test_CompositeTransformUtil_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CompositeTransformUtil_outputs(): output_map = dict( - affine_transform=dict(usedefault=True, ), - displacement_field=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), + affine_transform=dict(), + displacement_field=dict(), + out_file=dict(), ) outputs = CompositeTransformUtil.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py index 43471662ab..ea9a16cbe2 100644 --- a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py +++ b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py @@ -31,7 +31,6 @@ def test_ConvertScalarImageToRGB_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), mask_image=dict( argstr='%s', @@ -74,7 +73,7 @@ def test_ConvertScalarImageToRGB_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConvertScalarImageToRGB_outputs(): - output_map = dict(output_image=dict(usedefault=True, ), ) + output_map = dict(output_image=dict(), ) outputs = ConvertScalarImageToRGB.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py index 6c45c795d5..e2595a710f 100644 --- a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py @@ -8,7 +8,6 @@ def test_CorticalThickness_inputs(): anatomical_image=dict( argstr='-a %s', mandatory=True, - usedefault=True, ), args=dict(argstr='%s', ), b_spline_smoothing=dict(argstr='-v', ), @@ -16,14 +15,12 @@ def test_CorticalThickness_inputs(): argstr='-m %s', copyfile=False, mandatory=True, - usedefault=True, ), brain_template=dict( argstr='-e %s', mandatory=True, - usedefault=True, ), - cortical_label_image=dict(usedefault=True, ), + cortical_label_image=dict(), debug=dict(argstr='-z 1', ), dimension=dict( argstr='-d %d', @@ -33,10 +30,7 @@ def test_CorticalThickness_inputs(): nohash=True, usedefault=True, ), - extraction_registration_mask=dict( - argstr='-f %s', - usedefault=True, - ), + extraction_registration_mask=dict(argstr='-f %s', ), image_suffix=dict( argstr='-s %s', usedefault=True, @@ -63,7 +57,6 @@ def test_CorticalThickness_inputs(): t1_registration_template=dict( argstr='-t %s', mandatory=True, - usedefault=True, ), use_floatingpoint_precision=dict(argstr='-j %d', ), use_random_seeding=dict(argstr='-u %d', ), @@ -75,19 +68,19 @@ def test_CorticalThickness_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CorticalThickness_outputs(): output_map = dict( - BrainExtractionMask=dict(usedefault=True, ), - BrainSegmentation=dict(usedefault=True, ), - BrainSegmentationN4=dict(usedefault=True, ), + BrainExtractionMask=dict(), + BrainSegmentation=dict(), + BrainSegmentationN4=dict(), BrainSegmentationPosteriors=dict(), - BrainVolumes=dict(usedefault=True, ), - CorticalThickness=dict(usedefault=True, ), - CorticalThicknessNormedToTemplate=dict(usedefault=True, ), - ExtractedBrainN4=dict(usedefault=True, ), - SubjectToTemplate0GenericAffine=dict(usedefault=True, ), - SubjectToTemplate1Warp=dict(usedefault=True, ), - SubjectToTemplateLogJacobian=dict(usedefault=True, ), - TemplateToSubject0Warp=dict(usedefault=True, ), - TemplateToSubject1GenericAffine=dict(usedefault=True, ), + BrainVolumes=dict(), + CorticalThickness=dict(), + CorticalThicknessNormedToTemplate=dict(), + ExtractedBrainN4=dict(), + SubjectToTemplate0GenericAffine=dict(), + SubjectToTemplate1Warp=dict(), + SubjectToTemplateLogJacobian=dict(), + TemplateToSubject0Warp=dict(), + TemplateToSubject1GenericAffine=dict(), ) outputs = CorticalThickness.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py b/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py index c3d5aca2bf..b32e7b98e0 100644 --- a/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py +++ b/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py @@ -10,7 +10,6 @@ def test_CreateJacobianDeterminantImage_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), doLogJacobian=dict( argstr='%d', @@ -33,7 +32,6 @@ def test_CreateJacobianDeterminantImage_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), useGeometric=dict( argstr='%d', @@ -46,7 +44,7 @@ def test_CreateJacobianDeterminantImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CreateJacobianDeterminantImage_outputs(): - output_map = dict(jacobian_image=dict(usedefault=True, ), ) + output_map = dict(jacobian_image=dict(), ) outputs = CreateJacobianDeterminantImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py index ec56617940..74c2b0a7c2 100644 --- a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py +++ b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py @@ -16,12 +16,8 @@ def test_CreateTiledMosaic_inputs(): input_image=dict( argstr='-i %s', mandatory=True, - usedefault=True, - ), - mask_image=dict( - argstr='-x %s', - usedefault=True, ), + mask_image=dict(argstr='-x %s', ), num_threads=dict( nohash=True, usedefault=True, @@ -35,7 +31,6 @@ def test_CreateTiledMosaic_inputs(): rgb_image=dict( argstr='-r %s', mandatory=True, - usedefault=True, ), slices=dict(argstr='-s %s', ), tile_geometry=dict(argstr='-t %s', ), @@ -46,7 +41,7 @@ def test_CreateTiledMosaic_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CreateTiledMosaic_outputs(): - output_map = dict(output_image=dict(usedefault=True, ), ) + output_map = dict(output_image=dict(), ) outputs = CreateTiledMosaic.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py b/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py index fea1094a13..882cb21854 100644 --- a/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py +++ b/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py @@ -14,14 +14,12 @@ def test_DenoiseImage_inputs(): input_image=dict( argstr='-i %s', mandatory=True, - usedefault=True, ), noise_image=dict( hash_files=False, keep_extension=True, name_source=['input_image'], name_template='%s_noise', - usedefault=True, ), noise_model=dict( argstr='-n %s', @@ -37,7 +35,6 @@ def test_DenoiseImage_inputs(): keep_extension=True, name_source=['input_image'], name_template='%s_noise_corrected', - usedefault=True, ), save_noise=dict( mandatory=True, @@ -57,8 +54,8 @@ def test_DenoiseImage_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DenoiseImage_outputs(): output_map = dict( - noise_image=dict(usedefault=True, ), - output_image=dict(usedefault=True, ), + noise_image=dict(), + output_image=dict(), ) outputs = DenoiseImage.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py index 2a6b175a8c..af91f9a8af 100644 --- a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py +++ b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py @@ -21,7 +21,6 @@ def test_GenWarpFields_inputs(): argstr='-i %s', copyfile=False, mandatory=True, - usedefault=True, ), inverse_warp_template_labels=dict(argstr='-l', ), max_iterations=dict( @@ -41,7 +40,6 @@ def test_GenWarpFields_inputs(): argstr='-r %s', copyfile=True, mandatory=True, - usedefault=True, ), similarity_metric=dict(argstr='-s %s', ), transformation_model=dict( @@ -56,11 +54,11 @@ def test_GenWarpFields_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_GenWarpFields_outputs(): output_map = dict( - affine_transformation=dict(usedefault=True, ), - input_file=dict(usedefault=True, ), - inverse_warp_field=dict(usedefault=True, ), - output_file=dict(usedefault=True, ), - warp_field=dict(usedefault=True, ), + affine_transformation=dict(), + input_file=dict(), + inverse_warp_field=dict(), + output_file=dict(), + warp_field=dict(), ) outputs = GenWarpFields.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_JointFusion.py b/nipype/interfaces/ants/tests/test_auto_JointFusion.py index 0da922535a..9e82584729 100644 --- a/nipype/interfaces/ants/tests/test_auto_JointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_JointFusion.py @@ -26,10 +26,7 @@ def test_JointFusion_inputs(): nohash=True, usedefault=True, ), - exclusion_region=dict( - argstr='-x %s', - usedefault=True, - ), + exclusion_region=dict(argstr='-x %s', ), method=dict( argstr='-m %s', usedefault=True, @@ -49,7 +46,6 @@ def test_JointFusion_inputs(): name_template='%s', output_name='output_label_image', position=-1, - usedefault=True, ), patch_radius=dict( argstr='-rp %s', @@ -80,7 +76,7 @@ def test_JointFusion_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JointFusion_outputs(): - output_map = dict(output_label_image=dict(usedefault=True, ), ) + output_map = dict(output_label_image=dict(), ) outputs = JointFusion.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py b/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py index 7a26ae8d17..6129670d39 100644 --- a/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py +++ b/nipype/interfaces/ants/tests/test_auto_KellyKapowski.py @@ -16,7 +16,6 @@ def test_KellyKapowski_inputs(): keep_extension=True, name_source=['segmentation_image'], name_template='%s_cortical_thickness', - usedefault=True, ), dimension=dict( argstr='--image-dimensionality %d', @@ -32,9 +31,7 @@ def test_KellyKapowski_inputs(): ), gray_matter_label=dict(usedefault=True, ), gray_matter_prob_image=dict( - argstr='--gray-matter-probability-image "%s"', - usedefault=True, - ), + argstr='--gray-matter-probability-image "%s"', ), max_invert_displacement_field_iters=dict( argstr= '--maximum-number-of-invert-displacement-field-iterations %d', @@ -51,7 +48,6 @@ def test_KellyKapowski_inputs(): segmentation_image=dict( argstr='--segmentation-image "%s"', mandatory=True, - usedefault=True, ), smoothing_variance=dict( argstr='--smoothing-variance %f', @@ -65,23 +61,17 @@ def test_KellyKapowski_inputs(): argstr='--thickness-prior-estimate %f', usedefault=True, ), - thickness_prior_image=dict( - argstr='--thickness-prior-image "%s"', - usedefault=True, - ), + thickness_prior_image=dict(argstr='--thickness-prior-image "%s"', ), use_bspline_smoothing=dict(argstr='--use-bspline-smoothing 1', ), warped_white_matter=dict( hash_files=False, keep_extension=True, name_source=['segmentation_image'], name_template='%s_warped_white_matter', - usedefault=True, ), white_matter_label=dict(usedefault=True, ), white_matter_prob_image=dict( - argstr='--white-matter-probability-image "%s"', - usedefault=True, - ), + argstr='--white-matter-probability-image "%s"', ), ) inputs = KellyKapowski.input_spec() @@ -90,8 +80,8 @@ def test_KellyKapowski_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_KellyKapowski_outputs(): output_map = dict( - cortical_thickness=dict(usedefault=True, ), - warped_white_matter=dict(usedefault=True, ), + cortical_thickness=dict(), + warped_white_matter=dict(), ) outputs = KellyKapowski.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_LabelGeometry.py b/nipype/interfaces/ants/tests/test_auto_LabelGeometry.py index 0eaca9e911..a5de244711 100644 --- a/nipype/interfaces/ants/tests/test_auto_LabelGeometry.py +++ b/nipype/interfaces/ants/tests/test_auto_LabelGeometry.py @@ -25,7 +25,6 @@ def test_LabelGeometry_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), num_threads=dict( nohash=True, @@ -44,7 +43,7 @@ def test_LabelGeometry_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LabelGeometry_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = LabelGeometry.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py index ed3b5d49a7..608ba10889 100644 --- a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py @@ -20,14 +20,12 @@ def test_LaplacianThickness_inputs(): copyfile=True, mandatory=True, position=2, - usedefault=True, ), input_wm=dict( argstr='%s', copyfile=True, mandatory=True, position=1, - usedefault=True, ), num_threads=dict( nohash=True, @@ -40,7 +38,6 @@ def test_LaplacianThickness_inputs(): name_source=['input_wm'], name_template='%s_thickness', position=3, - usedefault=True, ), prior_thickness=dict( argstr='%s', @@ -68,7 +65,7 @@ def test_LaplacianThickness_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LaplacianThickness_outputs(): - output_map = dict(output_image=dict(usedefault=True, ), ) + output_map = dict(output_image=dict(), ) outputs = LaplacianThickness.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py b/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py index 5edc7f859b..1a5041ae74 100644 --- a/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py +++ b/nipype/interfaces/ants/tests/test_auto_MeasureImageSimilarity.py @@ -14,14 +14,8 @@ def test_MeasureImageSimilarity_inputs(): nohash=True, usedefault=True, ), - fixed_image=dict( - mandatory=True, - usedefault=True, - ), - fixed_image_mask=dict( - argstr='%s', - usedefault=True, - ), + fixed_image=dict(mandatory=True, ), + fixed_image_mask=dict(argstr='%s', ), metric=dict( argstr='%s', mandatory=True, @@ -30,14 +24,8 @@ def test_MeasureImageSimilarity_inputs(): requires=['metric'], usedefault=True, ), - moving_image=dict( - mandatory=True, - usedefault=True, - ), - moving_image_mask=dict( - requires=['fixed_image_mask'], - usedefault=True, - ), + moving_image=dict(mandatory=True, ), + moving_image_mask=dict(requires=['fixed_image_mask'], ), num_threads=dict( nohash=True, usedefault=True, diff --git a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py index 7d3756b044..1bf787018d 100644 --- a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py +++ b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py @@ -19,7 +19,6 @@ def test_MultiplyImages_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), num_threads=dict( nohash=True, @@ -29,7 +28,6 @@ def test_MultiplyImages_inputs(): argstr='%s', mandatory=True, position=3, - usedefault=True, ), second_input=dict( argstr='%s', @@ -43,7 +41,7 @@ def test_MultiplyImages_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MultiplyImages_outputs(): - output_map = dict(output_product_image=dict(usedefault=True, ), ) + output_map = dict(output_product_image=dict(), ) outputs = MultiplyImages.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py index 029c7dd3a9..66edf0c3d6 100644 --- a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py +++ b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py @@ -6,10 +6,7 @@ def test_N4BiasFieldCorrection_inputs(): input_map = dict( args=dict(argstr='%s', ), - bias_image=dict( - hash_files=False, - usedefault=True, - ), + bias_image=dict(hash_files=False, ), bspline_fitting_distance=dict(argstr='--bspline-fitting %s', ), bspline_order=dict(requires=['bspline_fitting_distance'], ), convergence_threshold=dict(requires=['n_iterations'], ), @@ -28,12 +25,8 @@ def test_N4BiasFieldCorrection_inputs(): input_image=dict( argstr='--input-image %s', mandatory=True, - usedefault=True, - ), - mask_image=dict( - argstr='--mask-image %s', - usedefault=True, ), + mask_image=dict(argstr='--mask-image %s', ), n_iterations=dict(argstr='--convergence %s', ), num_threads=dict( nohash=True, @@ -50,10 +43,7 @@ def test_N4BiasFieldCorrection_inputs(): xor=['bias_image'], ), shrink_factor=dict(argstr='--shrink-factor %d', ), - weight_image=dict( - argstr='--weight-image %s', - usedefault=True, - ), + weight_image=dict(argstr='--weight-image %s', ), ) inputs = N4BiasFieldCorrection.input_spec() @@ -62,8 +52,8 @@ def test_N4BiasFieldCorrection_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_N4BiasFieldCorrection_outputs(): output_map = dict( - bias_image=dict(usedefault=True, ), - output_image=dict(usedefault=True, ), + bias_image=dict(), + output_image=dict(), ) outputs = N4BiasFieldCorrection.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_Registration.py b/nipype/interfaces/ants/tests/test_auto_Registration.py index 1e3fd9dfd7..4bd253c3d0 100644 --- a/nipype/interfaces/ants/tests/test_auto_Registration.py +++ b/nipype/interfaces/ants/tests/test_auto_Registration.py @@ -30,7 +30,6 @@ def test_Registration_inputs(): fixed_image_mask=dict( argstr='%s', max_ver='2.1.0', - usedefault=True, xor=['fixed_image_masks'], ), fixed_image_masks=dict( @@ -73,7 +72,6 @@ def test_Registration_inputs(): moving_image_mask=dict( max_ver='2.1.0', requires=['fixed_image_mask'], - usedefault=True, xor=['moving_image_masks'], ), moving_image_masks=dict( @@ -100,10 +98,7 @@ def test_Registration_inputs(): requires=['metric_weight'], usedefault=True, ), - restore_state=dict( - argstr='--restore-state %s', - usedefault=True, - ), + restore_state=dict(argstr='--restore-state %s', ), restrict_deformation=dict(), sampling_percentage=dict(requires=['sampling_strategy'], ), sampling_percentage_item_trait=dict(), @@ -111,10 +106,7 @@ def test_Registration_inputs(): sampling_strategy=dict(requires=['metric_weight'], ), sampling_strategy_item_trait=dict(), sampling_strategy_stage_trait=dict(), - save_state=dict( - argstr='--save-state %s', - usedefault=True, - ), + save_state=dict(argstr='--save-state %s', ), shrink_factors=dict(mandatory=True, ), sigma_units=dict(requires=['smoothing_sigmas'], ), smoothing_sigmas=dict(mandatory=True, ), @@ -149,17 +141,17 @@ def test_Registration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Registration_outputs(): output_map = dict( - composite_transform=dict(usedefault=True, ), + composite_transform=dict(), elapsed_time=dict(), forward_invert_flags=dict(), forward_transforms=dict(), - inverse_composite_transform=dict(usedefault=True, ), - inverse_warped_image=dict(usedefault=True, ), + inverse_composite_transform=dict(), + inverse_warped_image=dict(), metric_value=dict(), reverse_invert_flags=dict(), reverse_transforms=dict(), - save_state=dict(usedefault=True, ), - warped_image=dict(usedefault=True, ), + save_state=dict(), + warped_image=dict(), ) outputs = Registration.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_RegistrationSynQuick.py b/nipype/interfaces/ants/tests/test_auto_RegistrationSynQuick.py index c8a9ab90bc..8bc79392e1 100644 --- a/nipype/interfaces/ants/tests/test_auto_RegistrationSynQuick.py +++ b/nipype/interfaces/ants/tests/test_auto_RegistrationSynQuick.py @@ -55,11 +55,11 @@ def test_RegistrationSynQuick_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RegistrationSynQuick_outputs(): output_map = dict( - forward_warp_field=dict(usedefault=True, ), - inverse_warp_field=dict(usedefault=True, ), - inverse_warped_image=dict(usedefault=True, ), - out_matrix=dict(usedefault=True, ), - warped_image=dict(usedefault=True, ), + forward_warp_field=dict(), + inverse_warp_field=dict(), + inverse_warped_image=dict(), + out_matrix=dict(), + warped_image=dict(), ) outputs = RegistrationSynQuick.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py index 52985afe86..42020f6db9 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py @@ -19,7 +19,6 @@ def test_WarpImageMultiTransform_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), invert_affine=dict(), num_threads=dict( @@ -36,12 +35,10 @@ def test_WarpImageMultiTransform_inputs(): genfile=True, hash_files=False, position=3, - usedefault=True, xor=['out_postfix'], ), reference_image=dict( argstr='-R %s', - usedefault=True, xor=['tightest_box'], ), reslice_by_header=dict(argstr='--reslice-by-header', ), @@ -63,7 +60,7 @@ def test_WarpImageMultiTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpImageMultiTransform_outputs(): - output_map = dict(output_image=dict(usedefault=True, ), ) + output_map = dict(output_image=dict(), ) outputs = WarpImageMultiTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py index 9ccde564d4..de3131f056 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py @@ -19,7 +19,6 @@ def test_WarpTimeSeriesImageMultiTransform_inputs(): argstr='%s', copyfile=True, mandatory=True, - usedefault=True, ), invert_affine=dict(), num_threads=dict( @@ -32,7 +31,6 @@ def test_WarpTimeSeriesImageMultiTransform_inputs(): ), reference_image=dict( argstr='-R %s', - usedefault=True, xor=['tightest_box'], ), reslice_by_header=dict(argstr='--reslice-by-header', ), @@ -54,7 +52,7 @@ def test_WarpTimeSeriesImageMultiTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpTimeSeriesImageMultiTransform_outputs(): - output_map = dict(output_image=dict(usedefault=True, ), ) + output_map = dict(output_image=dict(), ) outputs = WarpTimeSeriesImageMultiTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py index f681af7d8b..fe21858500 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py +++ b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py @@ -21,7 +21,6 @@ def test_antsIntroduction_inputs(): argstr='-i %s', copyfile=False, mandatory=True, - usedefault=True, ), inverse_warp_template_labels=dict(argstr='-l', ), max_iterations=dict( @@ -41,7 +40,6 @@ def test_antsIntroduction_inputs(): argstr='-r %s', copyfile=True, mandatory=True, - usedefault=True, ), similarity_metric=dict(argstr='-s %s', ), transformation_model=dict( @@ -56,11 +54,11 @@ def test_antsIntroduction_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_antsIntroduction_outputs(): output_map = dict( - affine_transformation=dict(usedefault=True, ), - input_file=dict(usedefault=True, ), - inverse_warp_field=dict(usedefault=True, ), - output_file=dict(usedefault=True, ), - warp_field=dict(usedefault=True, ), + affine_transformation=dict(), + input_file=dict(), + inverse_warp_field=dict(), + output_file=dict(), + warp_field=dict(), ) outputs = antsIntroduction.output_spec() diff --git a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py index bfd7f6bdca..8513003c29 100644 --- a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py +++ b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py @@ -61,7 +61,7 @@ def test_buildtemplateparallel_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_buildtemplateparallel_outputs(): output_map = dict( - final_template_file=dict(usedefault=True, ), + final_template_file=dict(), subject_outfiles=dict(), template_files=dict(), ) diff --git a/nipype/interfaces/brainsuite/tests/test_auto_BDP.py b/nipype/interfaces/brainsuite/tests/test_auto_BDP.py index 1db0577519..ff705edfeb 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_BDP.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_BDP.py @@ -16,7 +16,6 @@ def test_BDP_inputs(): argstr='--bmat %s', mandatory=True, position=-1, - usedefault=True, xor=['BVecBValPair'], ), bValRatioThreshold=dict(argstr='--bval-ratio-threshold %f', ), @@ -24,28 +23,15 @@ def test_BDP_inputs(): argstr='%s', mandatory=True, position=0, - usedefault=True, xor=['noStructuralRegistration'], ), - customDiffusionLabel=dict( - argstr='--custom-diffusion-label %s', - usedefault=True, - ), - customLabelXML=dict( - argstr='--custom-label-xml %s', - usedefault=True, - ), - customT1Label=dict( - argstr='--custom-t1-label %s', - usedefault=True, - ), + customDiffusionLabel=dict(argstr='--custom-diffusion-label %s', ), + customLabelXML=dict(argstr='--custom-label-xml %s', ), + customT1Label=dict(argstr='--custom-t1-label %s', ), dataSinkDelay=dict(argstr='%s', ), dcorrRegMeasure=dict(argstr='--dcorr-reg-method %s', ), dcorrWeight=dict(argstr='--dcorr-regularization-wt %f', ), - dwiMask=dict( - argstr='--dwi-mask %s', - usedefault=True, - ), + dwiMask=dict(argstr='--dwi-mask %s', ), echoSpacing=dict(argstr='--echo-spacing=%f', ), environ=dict( nohash=True, @@ -58,17 +44,13 @@ def test_BDP_inputs(): fieldmapCorrection=dict( argstr='--fieldmap-correction %s', requires=['echoSpacing'], - usedefault=True, ), fieldmapCorrectionMethod=dict( argstr='--fieldmap-correction-method %s', xor=['skipIntensityCorr'], ), fieldmapSmooth=dict(argstr='--fieldmap-smooth3=%f', ), - flagConfigFile=dict( - argstr='--flag-conf-file %s', - usedefault=True, - ), + flagConfigFile=dict(argstr='--flag-conf-file %s', ), forcePartialROIStats=dict(argstr='--force-partial-roi-stats', ), generateStats=dict(argstr='--generate-stats', ), ignoreFieldmapFOV=dict(argstr='--ignore-fieldmap-fov', ), @@ -77,7 +59,6 @@ def test_BDP_inputs(): argstr='--nii %s', mandatory=True, position=-2, - usedefault=True, ), lowMemory=dict(argstr='--low-memory', ), noStructuralRegistration=dict( @@ -100,29 +81,16 @@ def test_BDP_inputs(): xor=['fieldmapCorrectionMethod'], ), skipNonuniformityCorr=dict(argstr='--no-nonuniformity-correction', ), - t1Mask=dict( - argstr='--t1-mask %s', - usedefault=True, - ), + t1Mask=dict(argstr='--t1-mask %s', ), threads=dict(argstr='--threads=%d', ), transformDataOnly=dict(argstr='--transform-data-only', ), transformDiffusionSurface=dict( - argstr='--transform-diffusion-surface %s', - usedefault=True, - ), + argstr='--transform-diffusion-surface %s', ), transformDiffusionVolume=dict( - argstr='--transform-diffusion-volume %s', - usedefault=True, - ), + argstr='--transform-diffusion-volume %s', ), transformInterpolation=dict(argstr='--transform-interpolation %s', ), - transformT1Surface=dict( - argstr='--transform-t1-surface %s', - usedefault=True, - ), - transformT1Volume=dict( - argstr='--transform-t1-volume %s', - usedefault=True, - ), + transformT1Surface=dict(argstr='--transform-t1-surface %s', ), + transformT1Volume=dict(argstr='--transform-t1-volume %s', ), ) inputs = BDP.input_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py b/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py index e9e56894e1..01200e50fc 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py @@ -14,10 +14,7 @@ def test_Bfc_inputs(): convergenceThreshold=dict(argstr='--eps %f', ), correctWholeVolume=dict(argstr='--extrapolate', ), correctedImagesOutputPrefix=dict(argstr='--prefix %s', ), - correctionScheduleFile=dict( - argstr='--schedule %s', - usedefault=True, - ), + correctionScheduleFile=dict(argstr='--schedule %s', ), environ=dict( nohash=True, usedefault=True, @@ -27,12 +24,10 @@ def test_Bfc_inputs(): inputMRIFile=dict( argstr='-i %s', mandatory=True, - usedefault=True, ), inputMaskFile=dict( argstr='-m %s', hash_files=False, - usedefault=True, ), intermediate_file_type=dict(argstr='%s', ), iterativeMode=dict(argstr='--iterate', ), @@ -47,18 +42,15 @@ def test_Bfc_inputs(): outputBiasField=dict( argstr='--bias %s', hash_files=False, - usedefault=True, ), outputMRIVolume=dict( argstr='-o %s', genfile=True, hash_files=False, - usedefault=True, ), outputMaskedBiasField=dict( argstr='--maskedbias %s', hash_files=False, - usedefault=True, ), splineLambda=dict(argstr='-w %f', ), timer=dict(argstr='--timer', ), @@ -71,10 +63,10 @@ def test_Bfc_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Bfc_outputs(): output_map = dict( - correctionScheduleFile=dict(usedefault=True, ), - outputBiasField=dict(usedefault=True, ), - outputMRIVolume=dict(usedefault=True, ), - outputMaskedBiasField=dict(usedefault=True, ), + correctionScheduleFile=dict(), + outputBiasField=dict(), + outputMRIVolume=dict(), + outputMaskedBiasField=dict(), ) outputs = Bfc.output_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Bse.py b/nipype/interfaces/brainsuite/tests/test_auto_Bse.py index 2ff6264ed5..bbd154bc24 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Bse.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Bse.py @@ -29,40 +29,33 @@ def test_Bse_inputs(): inputMRIFile=dict( argstr='-i %s', mandatory=True, - usedefault=True, ), noRotate=dict(argstr='--norotate', ), outputCortexFile=dict( argstr='--cortex %s', hash_files=False, - usedefault=True, ), outputDetailedBrainMask=dict( argstr='--hires %s', hash_files=False, - usedefault=True, ), outputDiffusionFilter=dict( argstr='--adf %s', hash_files=False, - usedefault=True, ), outputEdgeMap=dict( argstr='--edge %s', hash_files=False, - usedefault=True, ), outputMRIVolume=dict( argstr='-o %s', genfile=True, hash_files=False, - usedefault=True, ), outputMaskFile=dict( argstr='--mask %s', genfile=True, hash_files=False, - usedefault=True, ), radius=dict( argstr='-r %f', @@ -85,12 +78,12 @@ def test_Bse_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Bse_outputs(): output_map = dict( - outputCortexFile=dict(usedefault=True, ), - outputDetailedBrainMask=dict(usedefault=True, ), - outputDiffusionFilter=dict(usedefault=True, ), - outputEdgeMap=dict(usedefault=True, ), - outputMRIVolume=dict(usedefault=True, ), - outputMaskFile=dict(usedefault=True, ), + outputCortexFile=dict(), + outputDetailedBrainMask=dict(), + outputDiffusionFilter=dict(), + outputEdgeMap=dict(), + outputMRIVolume=dict(), + outputMaskFile=dict(), ) outputs = Bse.output_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py b/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py index 0734b7f831..808e4347c3 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py @@ -17,43 +17,33 @@ def test_Cerebro_inputs(): inputAtlasLabelFile=dict( argstr='--atlaslabels %s', mandatory=True, - usedefault=True, ), inputAtlasMRIFile=dict( argstr='--atlas %s', mandatory=True, - usedefault=True, - ), - inputBrainMaskFile=dict( - argstr='-m %s', - usedefault=True, ), + inputBrainMaskFile=dict(argstr='-m %s', ), inputMRIFile=dict( argstr='-i %s', mandatory=True, - usedefault=True, ), keepTempFiles=dict(argstr='--keep', ), linearConvergence=dict(argstr='--linconv %f', ), outputAffineTransformFile=dict( argstr='--air %s', genfile=True, - usedefault=True, ), outputCerebrumMaskFile=dict( argstr='-o %s', genfile=True, - usedefault=True, ), outputLabelVolumeFile=dict( argstr='-l %s', genfile=True, - usedefault=True, ), outputWarpTransformFile=dict( argstr='--warp %s', genfile=True, - usedefault=True, ), tempDirectory=dict(argstr='--tempdir %s', ), tempDirectoryBase=dict(argstr='--tempdirbase %s', ), @@ -69,10 +59,10 @@ def test_Cerebro_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Cerebro_outputs(): output_map = dict( - outputAffineTransformFile=dict(usedefault=True, ), - outputCerebrumMaskFile=dict(usedefault=True, ), - outputLabelVolumeFile=dict(usedefault=True, ), - outputWarpTransformFile=dict(usedefault=True, ), + outputAffineTransformFile=dict(), + outputCerebrumMaskFile=dict(), + outputLabelVolumeFile=dict(), + outputWarpTransformFile=dict(), ) outputs = Cerebro.output_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py b/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py index 61e7ecfb76..536cb158f2 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py @@ -22,17 +22,14 @@ def test_Cortex_inputs(): inputHemisphereLabelFile=dict( argstr='-h %s', mandatory=True, - usedefault=True, ), inputTissueFractionFile=dict( argstr='-f %s', mandatory=True, - usedefault=True, ), outputCerebrumMask=dict( argstr='-o %s', genfile=True, - usedefault=True, ), timer=dict(argstr='--timer', ), tissueFractionThreshold=dict( @@ -47,7 +44,7 @@ def test_Cortex_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Cortex_outputs(): - output_map = dict(outputCerebrumMask=dict(usedefault=True, ), ) + output_map = dict(outputCerebrumMask=dict(), ) outputs = Cortex.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py b/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py index 297f72b857..ba430fb1fd 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py @@ -13,13 +13,11 @@ def test_Dewisp_inputs(): inputMaskFile=dict( argstr='-i %s', mandatory=True, - usedefault=True, ), maximumIterations=dict(argstr='-n %d', ), outputMaskFile=dict( argstr='-o %s', genfile=True, - usedefault=True, ), sizeThreshold=dict(argstr='-t %d', ), timer=dict(argstr='--timer', ), @@ -31,7 +29,7 @@ def test_Dewisp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Dewisp_outputs(): - output_map = dict(outputMaskFile=dict(usedefault=True, ), ) + output_map = dict(outputMaskFile=dict(), ) outputs = Dewisp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py b/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py index c4f3fbf8cf..c69232fd01 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py @@ -14,14 +14,10 @@ def test_Dfs_inputs(): nohash=True, usedefault=True, ), - inputShadingVolume=dict( - argstr='-c %s', - usedefault=True, - ), + inputShadingVolume=dict(argstr='-c %s', ), inputVolumeFile=dict( argstr='-i %s', mandatory=True, - usedefault=True, ), noNormalsFlag=dict(argstr='--nonormals', ), nonZeroTessellation=dict( @@ -31,7 +27,6 @@ def test_Dfs_inputs(): outputSurfaceFile=dict( argstr='-o %s', genfile=True, - usedefault=True, ), postSmoothFlag=dict(argstr='--postsmooth', ), scalingPercentile=dict(argstr='-f %f', ), @@ -60,7 +55,7 @@ def test_Dfs_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Dfs_outputs(): - output_map = dict(outputSurfaceFile=dict(usedefault=True, ), ) + output_map = dict(outputSurfaceFile=dict(), ) outputs = Dfs.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py b/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py index 40984870f1..9e3db80dd9 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py @@ -13,37 +13,28 @@ def test_Hemisplit_inputs(): inputHemisphereLabelFile=dict( argstr='-l %s', mandatory=True, - usedefault=True, ), inputSurfaceFile=dict( argstr='-i %s', mandatory=True, - usedefault=True, ), outputLeftHemisphere=dict( argstr='--left %s', genfile=True, - usedefault=True, ), outputLeftPialHemisphere=dict( argstr='-pl %s', genfile=True, - usedefault=True, ), outputRightHemisphere=dict( argstr='--right %s', genfile=True, - usedefault=True, ), outputRightPialHemisphere=dict( argstr='-pr %s', genfile=True, - usedefault=True, - ), - pialSurfaceFile=dict( - argstr='-p %s', - usedefault=True, ), + pialSurfaceFile=dict(argstr='-p %s', ), timer=dict(argstr='--timer', ), verbosity=dict(argstr='-v %d', ), ) @@ -54,10 +45,10 @@ def test_Hemisplit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Hemisplit_outputs(): output_map = dict( - outputLeftHemisphere=dict(usedefault=True, ), - outputLeftPialHemisphere=dict(usedefault=True, ), - outputRightHemisphere=dict(usedefault=True, ), - outputRightPialHemisphere=dict(usedefault=True, ), + outputLeftHemisphere=dict(), + outputLeftPialHemisphere=dict(), + outputRightHemisphere=dict(), + outputRightPialHemisphere=dict(), ) outputs = Hemisplit.output_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py b/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py index da7e3a2f12..afc621a56e 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py @@ -14,17 +14,14 @@ def test_Pialmesh_inputs(): inputMaskFile=dict( argstr='-m %s', mandatory=True, - usedefault=True, ), inputSurfaceFile=dict( argstr='-i %s', mandatory=True, - usedefault=True, ), inputTissueFractionFile=dict( argstr='-f %s', mandatory=True, - usedefault=True, ), laplacianSmoothing=dict( argstr='--smooth %f', @@ -49,7 +46,6 @@ def test_Pialmesh_inputs(): outputSurfaceFile=dict( argstr='-o %s', genfile=True, - usedefault=True, ), recomputeNormals=dict(argstr='--norm', ), searchRadius=dict( @@ -74,7 +70,7 @@ def test_Pialmesh_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Pialmesh_outputs(): - output_map = dict(outputSurfaceFile=dict(usedefault=True, ), ) + output_map = dict(outputSurfaceFile=dict(), ) outputs = Pialmesh.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py b/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py index ca3156ac3b..d425d4ddac 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py @@ -13,21 +13,15 @@ def test_Pvc_inputs(): inputMRIFile=dict( argstr='-i %s', mandatory=True, - usedefault=True, - ), - inputMaskFile=dict( - argstr='-m %s', - usedefault=True, ), + inputMaskFile=dict(argstr='-m %s', ), outputLabelFile=dict( argstr='-o %s', genfile=True, - usedefault=True, ), outputTissueFractionFile=dict( argstr='-f %s', genfile=True, - usedefault=True, ), spatialPrior=dict(argstr='-l %f', ), threeClassFlag=dict(argstr='-3', ), @@ -41,8 +35,8 @@ def test_Pvc_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Pvc_outputs(): output_map = dict( - outputLabelFile=dict(usedefault=True, ), - outputTissueFractionFile=dict(usedefault=True, ), + outputLabelFile=dict(), + outputTissueFractionFile=dict(), ) outputs = Pvc.output_spec() diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py b/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py index 9937f51878..eb672d12b7 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py @@ -21,13 +21,11 @@ def test_Scrubmask_inputs(): inputMaskFile=dict( argstr='-i %s', mandatory=True, - usedefault=True, ), numberIterations=dict(argstr='-n %d', ), outputMaskFile=dict( argstr='-o %s', genfile=True, - usedefault=True, ), timer=dict(argstr='--timer', ), verbosity=dict(argstr='-v %d', ), @@ -38,7 +36,7 @@ def test_Scrubmask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Scrubmask_outputs(): - output_map = dict(outputMaskFile=dict(usedefault=True, ), ) + output_map = dict(outputMaskFile=dict(), ) outputs = Scrubmask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py b/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py index e85ac9fb77..2191f7b133 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py @@ -15,18 +15,15 @@ def test_Skullfinder_inputs(): inputMRIFile=dict( argstr='-i %s', mandatory=True, - usedefault=True, ), inputMaskFile=dict( argstr='-m %s', mandatory=True, - usedefault=True, ), lowerThreshold=dict(argstr='-l %d', ), outputLabelFile=dict( argstr='-o %s', genfile=True, - usedefault=True, ), performFinalOpening=dict(argstr='--finalOpening', ), scalpLabelValue=dict(argstr='--scalplabel %d', ), @@ -42,7 +39,7 @@ def test_Skullfinder_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Skullfinder_outputs(): - output_map = dict(outputLabelFile=dict(usedefault=True, ), ) + output_map = dict(outputLabelFile=dict(), ) outputs = Skullfinder.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Tca.py b/nipype/interfaces/brainsuite/tests/test_auto_Tca.py index 3e237a7472..ec2886b42f 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Tca.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Tca.py @@ -17,7 +17,6 @@ def test_Tca_inputs(): inputMaskFile=dict( argstr='-i %s', mandatory=True, - usedefault=True, ), maxCorrectionSize=dict(argstr='-n %d', ), minCorrectionSize=dict( @@ -27,7 +26,6 @@ def test_Tca_inputs(): outputMaskFile=dict( argstr='-o %s', genfile=True, - usedefault=True, ), timer=dict(argstr='--timer', ), verbosity=dict(argstr='-v %d', ), @@ -38,7 +36,7 @@ def test_Tca_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Tca_outputs(): - output_map = dict(outputMaskFile=dict(usedefault=True, ), ) + output_map = dict(outputMaskFile=dict(), ) outputs = Tca.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py index d797170db6..5d796126cc 100644 --- a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py +++ b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py @@ -31,12 +31,10 @@ def test_AnalyzeHeader_inputs(): argstr='< %s', mandatory=True, position=1, - usedefault=True, ), initfromheader=dict( argstr='-initfromheader %s', position=3, - usedefault=True, ), intelbyteorder=dict(argstr='-intelbyteorder', ), networkbyteorder=dict(argstr='-networkbyteorder', ), @@ -60,27 +58,22 @@ def test_AnalyzeHeader_inputs(): printbigendian=dict( argstr='-printbigendian %s', position=3, - usedefault=True, ), printimagedims=dict( argstr='-printimagedims %s', position=3, - usedefault=True, ), printintelbyteorder=dict( argstr='-printintelbyteorder %s', position=3, - usedefault=True, ), printprogargs=dict( argstr='-printprogargs %s', position=3, - usedefault=True, ), readheader=dict( argstr='-readheader %s', position=3, - usedefault=True, ), scaleinter=dict( argstr='-scaleinter %d', @@ -93,7 +86,6 @@ def test_AnalyzeHeader_inputs(): scheme_file=dict( argstr='%s', position=2, - usedefault=True, ), voxel_dims=dict( argstr='-voxeldims %s', @@ -106,7 +98,7 @@ def test_AnalyzeHeader_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AnalyzeHeader_outputs(): - output_map = dict(header=dict(usedefault=True, ), ) + output_map = dict(header=dict(), ) outputs = AnalyzeHeader.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py index 3ea63e2e21..caee9e68cf 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py @@ -14,7 +14,6 @@ def test_ComputeEigensystem_inputs(): argstr='< %s', mandatory=True, position=1, - usedefault=True, ), inputdatatype=dict( argstr='-inputdatatype %s', @@ -38,7 +37,7 @@ def test_ComputeEigensystem_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeEigensystem_outputs(): - output_map = dict(eigen=dict(usedefault=True, ), ) + output_map = dict(eigen=dict(), ) outputs = ComputeEigensystem.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py index bc07cde8df..49cfdfd96a 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py @@ -14,7 +14,6 @@ def test_ComputeFractionalAnisotropy_inputs(): argstr='< %s', mandatory=True, position=1, - usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict(argstr='-inputmodel %s', ), @@ -27,7 +26,6 @@ def test_ComputeFractionalAnisotropy_inputs(): scheme_file=dict( argstr='%s', position=2, - usedefault=True, ), ) inputs = ComputeFractionalAnisotropy.input_spec() @@ -36,7 +34,7 @@ def test_ComputeFractionalAnisotropy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeFractionalAnisotropy_outputs(): - output_map = dict(fa=dict(usedefault=True, ), ) + output_map = dict(fa=dict(), ) outputs = ComputeFractionalAnisotropy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py index 6ac6cba916..212477d149 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py @@ -14,7 +14,6 @@ def test_ComputeMeanDiffusivity_inputs(): argstr='< %s', mandatory=True, position=1, - usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict(argstr='-inputmodel %s', ), @@ -22,13 +21,11 @@ def test_ComputeMeanDiffusivity_inputs(): argstr='> %s', genfile=True, position=-1, - usedefault=True, ), outputdatatype=dict(argstr='-outputdatatype %s', ), scheme_file=dict( argstr='%s', position=2, - usedefault=True, ), ) inputs = ComputeMeanDiffusivity.input_spec() @@ -37,7 +34,7 @@ def test_ComputeMeanDiffusivity_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeMeanDiffusivity_outputs(): - output_map = dict(md=dict(usedefault=True, ), ) + output_map = dict(md=dict(), ) outputs = ComputeMeanDiffusivity.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py index adb3abeb02..1112c7c743 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py @@ -14,7 +14,6 @@ def test_ComputeTensorTrace_inputs(): argstr='< %s', mandatory=True, position=1, - usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict(argstr='-inputmodel %s', ), @@ -27,7 +26,6 @@ def test_ComputeTensorTrace_inputs(): scheme_file=dict( argstr='%s', position=2, - usedefault=True, ), ) inputs = ComputeTensorTrace.input_spec() @@ -36,7 +34,7 @@ def test_ComputeTensorTrace_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeTensorTrace_outputs(): - output_map = dict(trace=dict(usedefault=True, ), ) + output_map = dict(trace=dict(), ) outputs = ComputeTensorTrace.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_Conmat.py b/nipype/interfaces/camino/tests/test_auto_Conmat.py index e84de0c1b2..06a76fdf2b 100644 --- a/nipype/interfaces/camino/tests/test_auto_Conmat.py +++ b/nipype/interfaces/camino/tests/test_auto_Conmat.py @@ -13,27 +13,20 @@ def test_Conmat_inputs(): in_file=dict( argstr='-inputfile %s', mandatory=True, - usedefault=True, ), output_root=dict( argstr='-outputroot %s', genfile=True, - usedefault=True, ), scalar_file=dict( argstr='-scalarfile %s', requires=['tract_stat'], - usedefault=True, ), target_file=dict( argstr='-targetfile %s', mandatory=True, - usedefault=True, - ), - targetname_file=dict( - argstr='-targetnamefile %s', - usedefault=True, ), + targetname_file=dict(argstr='-targetnamefile %s', ), tract_prop=dict( argstr='-tractstat %s', units='NA', @@ -53,8 +46,8 @@ def test_Conmat_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Conmat_outputs(): output_map = dict( - conmat_sc=dict(usedefault=True, ), - conmat_ts=dict(usedefault=True, ), + conmat_sc=dict(), + conmat_ts=dict(), ) outputs = Conmat.output_spec() diff --git a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py index 70569cafb6..b20dcbf3bf 100644 --- a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py +++ b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py @@ -14,19 +14,16 @@ def test_DT2NIfTI_inputs(): argstr='-header %s', mandatory=True, position=3, - usedefault=True, ), in_file=dict( argstr='-inputfile %s', mandatory=True, position=1, - usedefault=True, ), output_root=dict( argstr='-outputroot %s', genfile=True, position=2, - usedefault=True, ), ) inputs = DT2NIfTI.input_spec() @@ -36,9 +33,9 @@ def test_DT2NIfTI_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DT2NIfTI_outputs(): output_map = dict( - dt=dict(usedefault=True, ), - exitcode=dict(usedefault=True, ), - lns0=dict(usedefault=True, ), + dt=dict(), + exitcode=dict(), + lns0=dict(), ) outputs = DT2NIfTI.output_spec() diff --git a/nipype/interfaces/camino/tests/test_auto_DTIFit.py b/nipype/interfaces/camino/tests/test_auto_DTIFit.py index 5124db3f1f..a23da89552 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/camino/tests/test_auto_DTIFit.py @@ -6,10 +6,7 @@ def test_DTIFit_inputs(): input_map = dict( args=dict(argstr='%s', ), - bgmask=dict( - argstr='-bgmask %s', - usedefault=True, - ), + bgmask=dict(argstr='-bgmask %s', ), environ=dict( nohash=True, usedefault=True, @@ -18,7 +15,6 @@ def test_DTIFit_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), non_linear=dict( argstr='-nonlinear', @@ -33,7 +29,6 @@ def test_DTIFit_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), ) inputs = DTIFit.input_spec() @@ -42,7 +37,7 @@ def test_DTIFit_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DTIFit_outputs(): - output_map = dict(tensor_fitted=dict(usedefault=True, ), ) + output_map = dict(tensor_fitted=dict(), ) outputs = DTIFit.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py index 618d40c99d..95e8e0bea5 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py @@ -39,7 +39,6 @@ def test_DTLUTGen_inputs(): argstr='-schemefile %s', mandatory=True, position=2, - usedefault=True, ), snr=dict( argstr='-snr %f', @@ -61,7 +60,7 @@ def test_DTLUTGen_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DTLUTGen_outputs(): - output_map = dict(dtLUT=dict(usedefault=True, ), ) + output_map = dict(dtLUT=dict(), ) outputs = DTLUTGen.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_DTMetric.py b/nipype/interfaces/camino/tests/test_auto_DTMetric.py index 8fd0852d50..12256a50d8 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTMetric.py +++ b/nipype/interfaces/camino/tests/test_auto_DTMetric.py @@ -6,14 +6,10 @@ def test_DTMetric_inputs(): input_map = dict( args=dict(argstr='%s', ), - data_header=dict( - argstr='-header %s', - usedefault=True, - ), + data_header=dict(argstr='-header %s', ), eigen_data=dict( argstr='-inputfile %s', mandatory=True, - usedefault=True, ), environ=dict( nohash=True, @@ -34,7 +30,6 @@ def test_DTMetric_inputs(): outputfile=dict( argstr='-outputfile %s', genfile=True, - usedefault=True, ), ) inputs = DTMetric.input_spec() @@ -43,7 +38,7 @@ def test_DTMetric_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DTMetric_outputs(): - output_map = dict(metric_stats=dict(usedefault=True, ), ) + output_map = dict(metric_stats=dict(), ) outputs = DTMetric.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py index 583738ac14..a2ebfbf0a6 100644 --- a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py +++ b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py @@ -14,13 +14,11 @@ def test_FSL2Scheme_inputs(): argstr='-bvalfile %s', mandatory=True, position=2, - usedefault=True, ), bvec_file=dict( argstr='-bvecfile %s', mandatory=True, position=1, - usedefault=True, ), diffusiontime=dict( argstr='-diffusiontime %f', @@ -51,7 +49,7 @@ def test_FSL2Scheme_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FSL2Scheme_outputs(): - output_map = dict(scheme=dict(usedefault=True, ), ) + output_map = dict(scheme=dict(), ) outputs = FSL2Scheme.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py index d0591b3004..adae10f0bb 100644 --- a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py +++ b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py @@ -14,7 +14,6 @@ def test_Image2Voxel_inputs(): argstr='-4dimage %s', mandatory=True, position=1, - usedefault=True, ), out_file=dict( argstr='> %s', @@ -33,7 +32,7 @@ def test_Image2Voxel_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Image2Voxel_outputs(): - output_map = dict(voxel_order=dict(usedefault=True, ), ) + output_map = dict(voxel_order=dict(), ) outputs = Image2Voxel.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ImageStats.py b/nipype/interfaces/camino/tests/test_auto_ImageStats.py index 30f7c13573..3813051025 100644 --- a/nipype/interfaces/camino/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/camino/tests/test_auto_ImageStats.py @@ -22,7 +22,6 @@ def test_ImageStats_inputs(): output_root=dict( argstr='-outputroot %s', mandatory=True, - usedefault=True, ), stat=dict( argstr='-stat %s', @@ -36,7 +35,7 @@ def test_ImageStats_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ImageStats_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ImageStats.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_LinRecon.py b/nipype/interfaces/camino/tests/test_auto_LinRecon.py index 3e02e6641a..8998f42602 100644 --- a/nipype/interfaces/camino/tests/test_auto_LinRecon.py +++ b/nipype/interfaces/camino/tests/test_auto_LinRecon.py @@ -6,10 +6,7 @@ def test_LinRecon_inputs(): input_map = dict( args=dict(argstr='%s', ), - bgmask=dict( - argstr='-bgmask %s', - usedefault=True, - ), + bgmask=dict(argstr='-bgmask %s', ), environ=dict( nohash=True, usedefault=True, @@ -18,7 +15,6 @@ def test_LinRecon_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), log=dict(argstr='-log', ), normalize=dict(argstr='-normalize', ), @@ -31,13 +27,11 @@ def test_LinRecon_inputs(): argstr='%s', mandatory=True, position=3, - usedefault=True, ), scheme_file=dict( argstr='%s', mandatory=True, position=2, - usedefault=True, ), ) inputs = LinRecon.input_spec() @@ -46,7 +40,7 @@ def test_LinRecon_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LinRecon_outputs(): - output_map = dict(recon_data=dict(usedefault=True, ), ) + output_map = dict(recon_data=dict(), ) outputs = LinRecon.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_MESD.py b/nipype/interfaces/camino/tests/test_auto_MESD.py index 8b99faf461..73089a3395 100644 --- a/nipype/interfaces/camino/tests/test_auto_MESD.py +++ b/nipype/interfaces/camino/tests/test_auto_MESD.py @@ -6,10 +6,7 @@ def test_MESD_inputs(): input_map = dict( args=dict(argstr='%s', ), - bgmask=dict( - argstr='-bgmask %s', - usedefault=True, - ), + bgmask=dict(argstr='-bgmask %s', ), environ=dict( nohash=True, usedefault=True, @@ -22,7 +19,6 @@ def test_MESD_inputs(): argstr='-inputfile %s', mandatory=True, position=1, - usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inverter=dict( @@ -48,7 +44,6 @@ def test_MESD_inputs(): scheme_file=dict( argstr='-schemefile %s', mandatory=True, - usedefault=True, ), ) inputs = MESD.input_spec() @@ -57,7 +52,7 @@ def test_MESD_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MESD_outputs(): - output_map = dict(mesd_data=dict(usedefault=True, ), ) + output_map = dict(mesd_data=dict(), ) outputs = MESD.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ModelFit.py b/nipype/interfaces/camino/tests/test_auto_ModelFit.py index 0f7b332e25..04d22bbe59 100644 --- a/nipype/interfaces/camino/tests/test_auto_ModelFit.py +++ b/nipype/interfaces/camino/tests/test_auto_ModelFit.py @@ -6,10 +6,7 @@ def test_ModelFit_inputs(): input_map = dict( args=dict(argstr='%s', ), - bgmask=dict( - argstr='-bgmask %s', - usedefault=True, - ), + bgmask=dict(argstr='-bgmask %s', ), bgthresh=dict(argstr='-bgthresh %G', ), cfthresh=dict(argstr='-csfthresh %G', ), environ=dict( @@ -21,38 +18,24 @@ def test_ModelFit_inputs(): in_file=dict( argstr='-inputfile %s', mandatory=True, - usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), model=dict( argstr='-model %s', mandatory=True, ), - noisemap=dict( - argstr='-noisemap %s', - usedefault=True, - ), + noisemap=dict(argstr='-noisemap %s', ), out_file=dict( argstr='> %s', genfile=True, position=-1, ), - outlier=dict( - argstr='-outliermap %s', - usedefault=True, - ), - outputfile=dict( - argstr='-outputfile %s', - usedefault=True, - ), - residualmap=dict( - argstr='-residualmap %s', - usedefault=True, - ), + outlier=dict(argstr='-outliermap %s', ), + outputfile=dict(argstr='-outputfile %s', ), + residualmap=dict(argstr='-residualmap %s', ), scheme_file=dict( argstr='-schemefile %s', mandatory=True, - usedefault=True, ), sigma=dict(argstr='-sigma %G', ), tau=dict(argstr='-tau %G', ), @@ -63,7 +46,7 @@ def test_ModelFit_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ModelFit_outputs(): - output_map = dict(fitted_data=dict(usedefault=True, ), ) + output_map = dict(fitted_data=dict(), ) outputs = ModelFit.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py index d31ab64eb0..9a4867a73c 100644 --- a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py +++ b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py @@ -6,10 +6,7 @@ def test_NIfTIDT2Camino_inputs(): input_map = dict( args=dict(argstr='%s', ), - bgmask=dict( - argstr='-bgmask %s', - usedefault=True, - ), + bgmask=dict(argstr='-bgmask %s', ), environ=dict( nohash=True, usedefault=True, @@ -18,21 +15,14 @@ def test_NIfTIDT2Camino_inputs(): argstr='-inputfile %s', mandatory=True, position=1, - usedefault=True, - ), - lns0_file=dict( - argstr='-lns0 %s', - usedefault=True, ), + lns0_file=dict(argstr='-lns0 %s', ), out_file=dict( argstr='> %s', genfile=True, position=-1, ), - s0_file=dict( - argstr='-s0 %s', - usedefault=True, - ), + s0_file=dict(argstr='-s0 %s', ), scaleinter=dict(argstr='-scaleinter %s', ), scaleslope=dict(argstr='-scaleslope %s', ), uppertriangular=dict(argstr='-uppertriangular %s', ), @@ -43,7 +33,7 @@ def test_NIfTIDT2Camino_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NIfTIDT2Camino_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = NIfTIDT2Camino.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py index 9c0fec3085..f2b59666a2 100644 --- a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py +++ b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py @@ -15,7 +15,6 @@ def test_PicoPDFs_inputs(): argstr='< %s', mandatory=True, position=1, - usedefault=True, ), inputmodel=dict( argstr='-inputmodel %s', @@ -51,7 +50,7 @@ def test_PicoPDFs_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PicoPDFs_outputs(): - output_map = dict(pdfs=dict(usedefault=True, ), ) + output_map = dict(pdfs=dict(), ) outputs = PicoPDFs.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py index 7ad506e894..8838bb72cf 100644 --- a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py @@ -16,24 +16,17 @@ def test_ProcStreamlines_inputs(): units='NA', ), discardloops=dict(argstr='-discardloops', ), - endpointfile=dict( - argstr='-endpointfile %s', - usedefault=True, - ), + endpointfile=dict(argstr='-endpointfile %s', ), environ=dict( nohash=True, usedefault=True, ), - exclusionfile=dict( - argstr='-exclusionfile %s', - usedefault=True, - ), + exclusionfile=dict(argstr='-exclusionfile %s', ), gzip=dict(argstr='-gzip', ), in_file=dict( argstr='-inputfile %s', mandatory=True, position=1, - usedefault=True, ), inputmodel=dict( argstr='-inputmodel %s', @@ -77,10 +70,7 @@ def test_ProcStreamlines_inputs(): argstr='-outputcp', requires=['outputroot', 'seedfile'], ), - outputroot=dict( - argstr='-outputroot %s', - usedefault=True, - ), + outputroot=dict(argstr='-outputroot %s', ), outputsc=dict( argstr='-outputsc', requires=['outputroot', 'seedfile'], @@ -94,10 +84,7 @@ def test_ProcStreamlines_inputs(): argstr='-resamplestepsize %d', units='NA', ), - seedfile=dict( - argstr='-seedfile %s', - usedefault=True, - ), + seedfile=dict(argstr='-seedfile %s', ), seedpointmm=dict( argstr='-seedpointmm %s', units='mm', @@ -106,20 +93,14 @@ def test_ProcStreamlines_inputs(): argstr='-seedpointvox %s', units='voxels', ), - targetfile=dict( - argstr='-targetfile %s', - usedefault=True, - ), + targetfile=dict(argstr='-targetfile %s', ), truncateinexclusion=dict(argstr='-truncateinexclusion', ), truncateloops=dict(argstr='-truncateloops', ), voxeldims=dict( argstr='-voxeldims %s', units='mm', ), - waypointfile=dict( - argstr='-waypointfile %s', - usedefault=True, - ), + waypointfile=dict(argstr='-waypointfile %s', ), ) inputs = ProcStreamlines.input_spec() @@ -129,7 +110,7 @@ def test_ProcStreamlines_inputs(): def test_ProcStreamlines_outputs(): output_map = dict( outputroot_files=dict(), - proc=dict(usedefault=True, ), + proc=dict(), ) outputs = ProcStreamlines.output_spec() diff --git a/nipype/interfaces/camino/tests/test_auto_QBallMX.py b/nipype/interfaces/camino/tests/test_auto_QBallMX.py index c59a8e1253..e965cb606a 100644 --- a/nipype/interfaces/camino/tests/test_auto_QBallMX.py +++ b/nipype/interfaces/camino/tests/test_auto_QBallMX.py @@ -34,7 +34,6 @@ def test_QBallMX_inputs(): scheme_file=dict( argstr='-schemefile %s', mandatory=True, - usedefault=True, ), smoothingsigma=dict( argstr='-smoothingsigma %f', @@ -47,7 +46,7 @@ def test_QBallMX_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_QBallMX_outputs(): - output_map = dict(qmat=dict(usedefault=True, ), ) + output_map = dict(qmat=dict(), ) outputs = QBallMX.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py index 178392e90d..c52ca04929 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py @@ -18,12 +18,10 @@ def test_SFLUTGen_inputs(): in_file=dict( argstr='-inputfile %s', mandatory=True, - usedefault=True, ), info_file=dict( argstr='-infofile %s', mandatory=True, - usedefault=True, ), minvectsperbin=dict( argstr='-minvectsperbin %d', @@ -54,8 +52,8 @@ def test_SFLUTGen_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SFLUTGen_outputs(): output_map = dict( - lut_one_fibre=dict(usedefault=True, ), - lut_two_fibres=dict(usedefault=True, ), + lut_one_fibre=dict(), + lut_two_fibres=dict(), ) outputs = SFLUTGen.output_spec() diff --git a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py index 1f6f132038..e83a01e2c3 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py @@ -15,7 +15,6 @@ def test_SFPICOCalibData_inputs(): genfile=True, hash_files=False, mandatory=True, - usedefault=True, ), onedtfarange=dict( argstr='-onedtfarange %s', @@ -33,7 +32,6 @@ def test_SFPICOCalibData_inputs(): scheme_file=dict( argstr='-schemefile %s', mandatory=True, - usedefault=True, ), seed=dict( argstr='-seed %f', @@ -79,8 +77,8 @@ def test_SFPICOCalibData_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SFPICOCalibData_outputs(): output_map = dict( - PICOCalib=dict(usedefault=True, ), - calib_info=dict(usedefault=True, ), + PICOCalib=dict(), + calib_info=dict(), ) outputs = SFPICOCalibData.output_spec() diff --git a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py index b06ae65202..959545d042 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py @@ -17,7 +17,6 @@ def test_SFPeaks_inputs(): in_file=dict( argstr='-inputfile %s', mandatory=True, - usedefault=True, ), inputmodel=dict( argstr='-inputmodel %s', @@ -53,10 +52,7 @@ def test_SFPeaks_inputs(): argstr='-rbfpointset %d', units='NA', ), - scheme_file=dict( - argstr='%s', - usedefault=True, - ), + scheme_file=dict(argstr='%s', ), searchradius=dict( argstr='-searchradius %f', units='NA', @@ -72,7 +68,7 @@ def test_SFPeaks_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SFPeaks_outputs(): - output_map = dict(peaks=dict(usedefault=True, ), ) + output_map = dict(peaks=dict(), ) outputs = SFPeaks.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_Shredder.py b/nipype/interfaces/camino/tests/test_auto_Shredder.py index 2018b7dc5a..1099693874 100644 --- a/nipype/interfaces/camino/tests/test_auto_Shredder.py +++ b/nipype/interfaces/camino/tests/test_auto_Shredder.py @@ -19,7 +19,6 @@ def test_Shredder_inputs(): argstr='< %s', mandatory=True, position=-2, - usedefault=True, ), offset=dict( argstr='%d', @@ -43,7 +42,7 @@ def test_Shredder_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Shredder_outputs(): - output_map = dict(shredded=dict(usedefault=True, ), ) + output_map = dict(shredded=dict(), ) outputs = Shredder.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_Track.py b/nipype/interfaces/camino/tests/test_auto_Track.py index b83157f8d4..ad8d3ff2bb 100644 --- a/nipype/interfaces/camino/tests/test_auto_Track.py +++ b/nipype/interfaces/camino/tests/test_auto_Track.py @@ -5,10 +5,7 @@ def test_Track_inputs(): input_map = dict( - anisfile=dict( - argstr='-anisfile %s', - usedefault=True, - ), + anisfile=dict(argstr='-anisfile %s', ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curveinterval=dict( @@ -28,7 +25,6 @@ def test_Track_inputs(): in_file=dict( argstr='-inputfile %s', position=1, - usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict( @@ -49,18 +45,15 @@ def test_Track_inputs(): argstr='-outputfile %s', genfile=True, position=-1, - usedefault=True, ), output_root=dict( argstr='-outputroot %s', position=-1, - usedefault=True, ), outputtracts=dict(argstr='-outputtracts %s', ), seed_file=dict( argstr='-seedfile %s', position=2, - usedefault=True, ), stepsize=dict( argstr='-stepsize %f', @@ -81,7 +74,7 @@ def test_Track_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Track_outputs(): - output_map = dict(tracked=dict(usedefault=True, ), ) + output_map = dict(tracked=dict(), ) outputs = Track.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py index ddc48c71d4..89515cef55 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py @@ -5,10 +5,7 @@ def test_TrackBallStick_inputs(): input_map = dict( - anisfile=dict( - argstr='-anisfile %s', - usedefault=True, - ), + anisfile=dict(argstr='-anisfile %s', ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curveinterval=dict( @@ -28,7 +25,6 @@ def test_TrackBallStick_inputs(): in_file=dict( argstr='-inputfile %s', position=1, - usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict( @@ -49,18 +45,15 @@ def test_TrackBallStick_inputs(): argstr='-outputfile %s', genfile=True, position=-1, - usedefault=True, ), output_root=dict( argstr='-outputroot %s', position=-1, - usedefault=True, ), outputtracts=dict(argstr='-outputtracts %s', ), seed_file=dict( argstr='-seedfile %s', position=2, - usedefault=True, ), stepsize=dict( argstr='-stepsize %f', @@ -81,7 +74,7 @@ def test_TrackBallStick_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackBallStick_outputs(): - output_map = dict(tracked=dict(usedefault=True, ), ) + output_map = dict(tracked=dict(), ) outputs = TrackBallStick.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py index 481405062b..2815ef18ee 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py @@ -5,10 +5,7 @@ def test_TrackBayesDirac_inputs(): input_map = dict( - anisfile=dict( - argstr='-anisfile %s', - usedefault=True, - ), + anisfile=dict(argstr='-anisfile %s', ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curveinterval=dict( @@ -28,15 +25,11 @@ def test_TrackBayesDirac_inputs(): usedefault=True, ), extpriordatatype=dict(argstr='-extpriordatatype %s', ), - extpriorfile=dict( - argstr='-extpriorfile %s', - usedefault=True, - ), + extpriorfile=dict(argstr='-extpriorfile %s', ), gzip=dict(argstr='-gzip', ), in_file=dict( argstr='-inputfile %s', position=1, - usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict( @@ -61,12 +54,10 @@ def test_TrackBayesDirac_inputs(): argstr='-outputfile %s', genfile=True, position=-1, - usedefault=True, ), output_root=dict( argstr='-outputroot %s', position=-1, - usedefault=True, ), outputtracts=dict(argstr='-outputtracts %s', ), pdf=dict(argstr='-pdf %s', ), @@ -74,12 +65,10 @@ def test_TrackBayesDirac_inputs(): scheme_file=dict( argstr='-schemefile %s', mandatory=True, - usedefault=True, ), seed_file=dict( argstr='-seedfile %s', position=2, - usedefault=True, ), stepsize=dict( argstr='-stepsize %f', @@ -100,7 +89,7 @@ def test_TrackBayesDirac_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackBayesDirac_outputs(): - output_map = dict(tracked=dict(usedefault=True, ), ) + output_map = dict(tracked=dict(), ) outputs = TrackBayesDirac.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py index 629ee39f78..827dbb2f27 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py @@ -5,16 +5,12 @@ def test_TrackBedpostxDeter_inputs(): input_map = dict( - anisfile=dict( - argstr='-anisfile %s', - usedefault=True, - ), + anisfile=dict(argstr='-anisfile %s', ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), bedpostxdir=dict( argstr='-bedpostxdir %s', mandatory=True, - usedefault=True, ), curveinterval=dict( argstr='-curveinterval %f', @@ -33,7 +29,6 @@ def test_TrackBedpostxDeter_inputs(): in_file=dict( argstr='-inputfile %s', position=1, - usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict( @@ -58,18 +53,15 @@ def test_TrackBedpostxDeter_inputs(): argstr='-outputfile %s', genfile=True, position=-1, - usedefault=True, ), output_root=dict( argstr='-outputroot %s', position=-1, - usedefault=True, ), outputtracts=dict(argstr='-outputtracts %s', ), seed_file=dict( argstr='-seedfile %s', position=2, - usedefault=True, ), stepsize=dict( argstr='-stepsize %f', @@ -90,7 +82,7 @@ def test_TrackBedpostxDeter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackBedpostxDeter_outputs(): - output_map = dict(tracked=dict(usedefault=True, ), ) + output_map = dict(tracked=dict(), ) outputs = TrackBedpostxDeter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py index af2f9ea808..e250ec9c40 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py @@ -5,16 +5,12 @@ def test_TrackBedpostxProba_inputs(): input_map = dict( - anisfile=dict( - argstr='-anisfile %s', - usedefault=True, - ), + anisfile=dict(argstr='-anisfile %s', ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), bedpostxdir=dict( argstr='-bedpostxdir %s', mandatory=True, - usedefault=True, ), curveinterval=dict( argstr='-curveinterval %f', @@ -33,7 +29,6 @@ def test_TrackBedpostxProba_inputs(): in_file=dict( argstr='-inputfile %s', position=1, - usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict( @@ -62,18 +57,15 @@ def test_TrackBedpostxProba_inputs(): argstr='-outputfile %s', genfile=True, position=-1, - usedefault=True, ), output_root=dict( argstr='-outputroot %s', position=-1, - usedefault=True, ), outputtracts=dict(argstr='-outputtracts %s', ), seed_file=dict( argstr='-seedfile %s', position=2, - usedefault=True, ), stepsize=dict( argstr='-stepsize %f', @@ -94,7 +86,7 @@ def test_TrackBedpostxProba_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackBedpostxProba_outputs(): - output_map = dict(tracked=dict(usedefault=True, ), ) + output_map = dict(tracked=dict(), ) outputs = TrackBedpostxProba.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py index 6d7b0be071..90ffd05a2d 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py @@ -5,16 +5,10 @@ def test_TrackBootstrap_inputs(): input_map = dict( - anisfile=dict( - argstr='-anisfile %s', - usedefault=True, - ), + anisfile=dict(argstr='-anisfile %s', ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), - bgmask=dict( - argstr='-bgmask %s', - usedefault=True, - ), + bgmask=dict(argstr='-bgmask %s', ), bsdatafiles=dict( argstr='-bsdatafile %s', mandatory=True, @@ -36,7 +30,6 @@ def test_TrackBootstrap_inputs(): in_file=dict( argstr='-inputfile %s', position=1, - usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict( @@ -62,23 +55,19 @@ def test_TrackBootstrap_inputs(): argstr='-outputfile %s', genfile=True, position=-1, - usedefault=True, ), output_root=dict( argstr='-outputroot %s', position=-1, - usedefault=True, ), outputtracts=dict(argstr='-outputtracts %s', ), scheme_file=dict( argstr='-schemefile %s', mandatory=True, - usedefault=True, ), seed_file=dict( argstr='-seedfile %s', position=2, - usedefault=True, ), stepsize=dict( argstr='-stepsize %f', @@ -99,7 +88,7 @@ def test_TrackBootstrap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackBootstrap_outputs(): - output_map = dict(tracked=dict(usedefault=True, ), ) + output_map = dict(tracked=dict(), ) outputs = TrackBootstrap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackDT.py b/nipype/interfaces/camino/tests/test_auto_TrackDT.py index 2669d42651..7ab3772468 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackDT.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackDT.py @@ -5,10 +5,7 @@ def test_TrackDT_inputs(): input_map = dict( - anisfile=dict( - argstr='-anisfile %s', - usedefault=True, - ), + anisfile=dict(argstr='-anisfile %s', ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curveinterval=dict( @@ -28,7 +25,6 @@ def test_TrackDT_inputs(): in_file=dict( argstr='-inputfile %s', position=1, - usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict( @@ -49,18 +45,15 @@ def test_TrackDT_inputs(): argstr='-outputfile %s', genfile=True, position=-1, - usedefault=True, ), output_root=dict( argstr='-outputroot %s', position=-1, - usedefault=True, ), outputtracts=dict(argstr='-outputtracts %s', ), seed_file=dict( argstr='-seedfile %s', position=2, - usedefault=True, ), stepsize=dict( argstr='-stepsize %f', @@ -81,7 +74,7 @@ def test_TrackDT_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackDT_outputs(): - output_map = dict(tracked=dict(usedefault=True, ), ) + output_map = dict(tracked=dict(), ) outputs = TrackDT.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py index 16232d11d2..30ff12db9f 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py @@ -5,10 +5,7 @@ def test_TrackPICo_inputs(): input_map = dict( - anisfile=dict( - argstr='-anisfile %s', - usedefault=True, - ), + anisfile=dict(argstr='-anisfile %s', ), anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curveinterval=dict( @@ -28,7 +25,6 @@ def test_TrackPICo_inputs(): in_file=dict( argstr='-inputfile %s', position=1, - usedefault=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), inputmodel=dict( @@ -53,19 +49,16 @@ def test_TrackPICo_inputs(): argstr='-outputfile %s', genfile=True, position=-1, - usedefault=True, ), output_root=dict( argstr='-outputroot %s', position=-1, - usedefault=True, ), outputtracts=dict(argstr='-outputtracts %s', ), pdf=dict(argstr='-pdf %s', ), seed_file=dict( argstr='-seedfile %s', position=2, - usedefault=True, ), stepsize=dict( argstr='-stepsize %f', @@ -86,7 +79,7 @@ def test_TrackPICo_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackPICo_outputs(): - output_map = dict(tracked=dict(usedefault=True, ), ) + output_map = dict(tracked=dict(), ) outputs = TrackPICo.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_TractShredder.py b/nipype/interfaces/camino/tests/test_auto_TractShredder.py index 952ef69b43..c9cf40e1c3 100644 --- a/nipype/interfaces/camino/tests/test_auto_TractShredder.py +++ b/nipype/interfaces/camino/tests/test_auto_TractShredder.py @@ -19,7 +19,6 @@ def test_TractShredder_inputs(): argstr='< %s', mandatory=True, position=-2, - usedefault=True, ), offset=dict( argstr='%d', @@ -43,7 +42,7 @@ def test_TractShredder_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TractShredder_outputs(): - output_map = dict(shredded=dict(usedefault=True, ), ) + output_map = dict(shredded=dict(), ) outputs = TractShredder.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py index 0bbe7ca4e9..8dc8bd03e9 100644 --- a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py @@ -15,7 +15,6 @@ def test_VtkStreamlines_inputs(): argstr=' < %s', mandatory=True, position=-2, - usedefault=True, ), inputmodel=dict( argstr='-inputmodel %s', @@ -31,17 +30,14 @@ def test_VtkStreamlines_inputs(): scalar_file=dict( argstr='-scalarfile %s', position=3, - usedefault=True, ), seed_file=dict( argstr='-seedfile %s', position=1, - usedefault=True, ), target_file=dict( argstr='-targetfile %s', position=2, - usedefault=True, ), voxeldims=dict( argstr='-voxeldims %s', @@ -55,7 +51,7 @@ def test_VtkStreamlines_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_VtkStreamlines_outputs(): - output_map = dict(vtk=dict(usedefault=True, ), ) + output_map = dict(vtk=dict(), ) outputs = VtkStreamlines.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py index 109a116bce..b4d5092dab 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py @@ -20,7 +20,6 @@ def test_Camino2Trackvis_inputs(): argstr='-i %s', mandatory=True, position=1, - usedefault=True, ), min_length=dict( argstr='-l %d', @@ -30,13 +29,11 @@ def test_Camino2Trackvis_inputs(): nifti_file=dict( argstr='--nifti %s', position=7, - usedefault=True, ), out_file=dict( argstr='-o %s', genfile=True, position=2, - usedefault=True, ), voxel_dims=dict( argstr='-x %s', @@ -48,7 +45,6 @@ def test_Camino2Trackvis_inputs(): argstr='--voxel-order %s', mandatory=True, position=6, - usedefault=True, ), ) inputs = Camino2Trackvis.input_spec() @@ -57,7 +53,7 @@ def test_Camino2Trackvis_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Camino2Trackvis_outputs(): - output_map = dict(trackvis=dict(usedefault=True, ), ) + output_map = dict(trackvis=dict(), ) outputs = Camino2Trackvis.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py index 9f7b512ec5..978b2439a2 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py @@ -8,7 +8,6 @@ def test_Trackvis2Camino_inputs(): append_file=dict( argstr='-a %s', position=2, - usedefault=True, ), args=dict(argstr='%s', ), environ=dict( @@ -19,13 +18,11 @@ def test_Trackvis2Camino_inputs(): argstr='-i %s', mandatory=True, position=1, - usedefault=True, ), out_file=dict( argstr='-o %s', genfile=True, position=2, - usedefault=True, ), ) inputs = Trackvis2Camino.input_spec() @@ -34,7 +31,7 @@ def test_Trackvis2Camino_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Trackvis2Camino_outputs(): - output_map = dict(camino=dict(usedefault=True, ), ) + output_map = dict(camino=dict(), ) outputs = Trackvis2Camino.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py index b8ed8ce13f..a80bbe757a 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py @@ -7,9 +7,9 @@ def test_AverageNetworks_inputs(): input_map = dict( group_id=dict(usedefault=True, ), in_files=dict(mandatory=True, ), - out_gexf_groupavg=dict(usedefault=True, ), - out_gpickled_groupavg=dict(usedefault=True, ), - resolution_network_file=dict(usedefault=True, ), + out_gexf_groupavg=dict(), + out_gpickled_groupavg=dict(), + resolution_network_file=dict(), ) inputs = AverageNetworks.input_spec() @@ -18,8 +18,8 @@ def test_AverageNetworks_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_AverageNetworks_outputs(): output_map = dict( - gexf_groupavg=dict(usedefault=True, ), - gpickled_groupavg=dict(usedefault=True, ), + gexf_groupavg=dict(), + gpickled_groupavg=dict(), matlab_groupavgs=dict(), ) outputs = AverageNetworks.output_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py index 9c9e5b1bc5..00a1acea98 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py @@ -32,7 +32,7 @@ def test_CFFConverter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CFFConverter_outputs(): - output_map = dict(connectome_file=dict(usedefault=True, ), ) + output_map = dict(connectome_file=dict(), ) outputs = CFFConverter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py b/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py index 4f575506d6..60e8596f5e 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py @@ -6,43 +6,16 @@ def test_CreateMatrix_inputs(): input_map = dict( count_region_intersections=dict(usedefault=True, ), - out_endpoint_array_name=dict( - genfile=True, - usedefault=True, - ), - out_fiber_length_std_matrix_mat_file=dict( - genfile=True, - usedefault=True, - ), - out_intersection_matrix_mat_file=dict( - genfile=True, - usedefault=True, - ), - out_matrix_file=dict( - genfile=True, - usedefault=True, - ), + out_endpoint_array_name=dict(genfile=True, ), + out_fiber_length_std_matrix_mat_file=dict(genfile=True, ), + out_intersection_matrix_mat_file=dict(genfile=True, ), + out_matrix_file=dict(genfile=True, ), out_matrix_mat_file=dict(usedefault=True, ), - out_mean_fiber_length_matrix_mat_file=dict( - genfile=True, - usedefault=True, - ), - out_median_fiber_length_matrix_mat_file=dict( - genfile=True, - usedefault=True, - ), - resolution_network_file=dict( - mandatory=True, - usedefault=True, - ), - roi_file=dict( - mandatory=True, - usedefault=True, - ), - tract_file=dict( - mandatory=True, - usedefault=True, - ), + out_mean_fiber_length_matrix_mat_file=dict(genfile=True, ), + out_median_fiber_length_matrix_mat_file=dict(genfile=True, ), + resolution_network_file=dict(mandatory=True, ), + roi_file=dict(mandatory=True, ), + tract_file=dict(mandatory=True, ), ) inputs = CreateMatrix.input_spec() @@ -51,24 +24,24 @@ def test_CreateMatrix_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CreateMatrix_outputs(): output_map = dict( - endpoint_file=dict(usedefault=True, ), - endpoint_file_mm=dict(usedefault=True, ), - fiber_label_file=dict(usedefault=True, ), - fiber_labels_noorphans=dict(usedefault=True, ), - fiber_length_file=dict(usedefault=True, ), - fiber_length_std_matrix_mat_file=dict(usedefault=True, ), + endpoint_file=dict(), + endpoint_file_mm=dict(), + fiber_label_file=dict(), + fiber_labels_noorphans=dict(), + fiber_length_file=dict(), + fiber_length_std_matrix_mat_file=dict(), filtered_tractographies=dict(), - filtered_tractography=dict(usedefault=True, ), - filtered_tractography_by_intersections=dict(usedefault=True, ), - intersection_matrix_file=dict(usedefault=True, ), - intersection_matrix_mat_file=dict(usedefault=True, ), + filtered_tractography=dict(), + filtered_tractography_by_intersections=dict(), + intersection_matrix_file=dict(), + intersection_matrix_mat_file=dict(), matlab_matrix_files=dict(), - matrix_file=dict(usedefault=True, ), + matrix_file=dict(), matrix_files=dict(), - matrix_mat_file=dict(usedefault=True, ), - mean_fiber_length_matrix_mat_file=dict(usedefault=True, ), - median_fiber_length_matrix_mat_file=dict(usedefault=True, ), - stats_file=dict(usedefault=True, ), + matrix_mat_file=dict(), + mean_fiber_length_matrix_mat_file=dict(), + median_fiber_length_matrix_mat_file=dict(), + stats_file=dict(), ) outputs = CreateMatrix.output_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py index 4018c04a85..3635f21e59 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py @@ -6,14 +6,8 @@ def test_CreateNodes_inputs(): input_map = dict( out_filename=dict(usedefault=True, ), - resolution_network_file=dict( - mandatory=True, - usedefault=True, - ), - roi_file=dict( - mandatory=True, - usedefault=True, - ), + resolution_network_file=dict(mandatory=True, ), + roi_file=dict(mandatory=True, ), ) inputs = CreateNodes.input_spec() @@ -21,7 +15,7 @@ def test_CreateNodes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CreateNodes_outputs(): - output_map = dict(node_network=dict(usedefault=True, ), ) + output_map = dict(node_network=dict(), ) outputs = CreateNodes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py index 2b86746313..ceaa6d8dea 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py @@ -14,7 +14,7 @@ def test_MergeCNetworks_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MergeCNetworks_outputs(): - output_map = dict(connectome_file=dict(usedefault=True, ), ) + output_map = dict(connectome_file=dict(), ) outputs = MergeCNetworks.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py index 1481b540ee..e3220e4790 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py @@ -8,10 +8,10 @@ def test_NetworkBasedStatistic_inputs(): edge_key=dict(usedefault=True, ), in_group1=dict(mandatory=True, ), in_group2=dict(mandatory=True, ), - node_position_network=dict(usedefault=True, ), + node_position_network=dict(), number_of_permutations=dict(usedefault=True, ), - out_nbs_network=dict(usedefault=True, ), - out_nbs_pval_network=dict(usedefault=True, ), + out_nbs_network=dict(), + out_nbs_pval_network=dict(), t_tail=dict(usedefault=True, ), threshold=dict(usedefault=True, ), ) @@ -22,8 +22,8 @@ def test_NetworkBasedStatistic_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_NetworkBasedStatistic_outputs(): output_map = dict( - nbs_network=dict(usedefault=True, ), - nbs_pval_network=dict(usedefault=True, ), + nbs_network=dict(), + nbs_pval_network=dict(), network_files=dict(), ) outputs = NetworkBasedStatistic.output_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py index 837f0a8f76..d9a3f0c740 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py @@ -6,25 +6,13 @@ def test_NetworkXMetrics_inputs(): input_map = dict( compute_clique_related_measures=dict(usedefault=True, ), - in_file=dict( - mandatory=True, - usedefault=True, - ), - out_edge_metrics_matlab=dict( - genfile=True, - usedefault=True, - ), - out_global_metrics_matlab=dict( - genfile=True, - usedefault=True, - ), + in_file=dict(mandatory=True, ), + out_edge_metrics_matlab=dict(genfile=True, ), + out_global_metrics_matlab=dict(genfile=True, ), out_k_core=dict(usedefault=True, ), out_k_crust=dict(usedefault=True, ), out_k_shell=dict(usedefault=True, ), - out_node_metrics_matlab=dict( - genfile=True, - usedefault=True, - ), + out_node_metrics_matlab=dict(genfile=True, ), out_pickled_extra_measures=dict(usedefault=True, ), treat_as_weighted_graph=dict(usedefault=True, ), ) @@ -36,18 +24,18 @@ def test_NetworkXMetrics_inputs(): def test_NetworkXMetrics_outputs(): output_map = dict( edge_measure_networks=dict(), - edge_measures_matlab=dict(usedefault=True, ), - global_measures_matlab=dict(usedefault=True, ), + edge_measures_matlab=dict(), + global_measures_matlab=dict(), gpickled_network_files=dict(), - k_core=dict(usedefault=True, ), - k_crust=dict(usedefault=True, ), + k_core=dict(), + k_crust=dict(), k_networks=dict(), - k_shell=dict(usedefault=True, ), + k_shell=dict(), matlab_dict_measures=dict(), matlab_matrix_files=dict(), node_measure_networks=dict(), - node_measures_matlab=dict(usedefault=True, ), - pickled_extra_measures=dict(usedefault=True, ), + node_measures_matlab=dict(), + pickled_extra_measures=dict(), ) outputs = NetworkXMetrics.output_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py index e4a876db18..edcdf2e7a1 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py +++ b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py @@ -6,14 +6,11 @@ def test_Parcellate_inputs(): input_map = dict( dilation=dict(usedefault=True, ), - freesurfer_dir=dict(usedefault=True, ), - out_roi_file=dict( - genfile=True, - usedefault=True, - ), + freesurfer_dir=dict(), + out_roi_file=dict(genfile=True, ), parcellation_name=dict(usedefault=True, ), subject_id=dict(mandatory=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = Parcellate.input_spec() @@ -22,14 +19,14 @@ def test_Parcellate_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Parcellate_outputs(): output_map = dict( - aseg_file=dict(usedefault=True, ), - cc_unknown_file=dict(usedefault=True, ), - dilated_roi_file_in_structural_space=dict(usedefault=True, ), - ribbon_file=dict(usedefault=True, ), - roi_file=dict(usedefault=True, ), - roi_file_in_structural_space=dict(usedefault=True, ), - roiv_file=dict(usedefault=True, ), - white_matter_mask_file=dict(usedefault=True, ), + aseg_file=dict(), + cc_unknown_file=dict(), + dilated_roi_file_in_structural_space=dict(), + ribbon_file=dict(), + roi_file=dict(), + roi_file_in_structural_space=dict(), + roiv_file=dict(), + white_matter_mask_file=dict(), ) outputs = Parcellate.output_spec() diff --git a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py index bc7d997ca8..dd2ce50aec 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py +++ b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py @@ -5,26 +5,11 @@ def test_ROIGen_inputs(): input_map = dict( - LUT_file=dict( - usedefault=True, - xor=['use_freesurfer_LUT'], - ), - aparc_aseg_file=dict( - mandatory=True, - usedefault=True, - ), - freesurfer_dir=dict( - requires=['use_freesurfer_LUT'], - usedefault=True, - ), - out_dict_file=dict( - genfile=True, - usedefault=True, - ), - out_roi_file=dict( - genfile=True, - usedefault=True, - ), + LUT_file=dict(xor=['use_freesurfer_LUT'], ), + aparc_aseg_file=dict(mandatory=True, ), + freesurfer_dir=dict(requires=['use_freesurfer_LUT'], ), + out_dict_file=dict(genfile=True, ), + out_roi_file=dict(genfile=True, ), use_freesurfer_LUT=dict(xor=['LUT_file'], ), ) inputs = ROIGen.input_spec() @@ -34,8 +19,8 @@ def test_ROIGen_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ROIGen_outputs(): output_map = dict( - dict_file=dict(usedefault=True, ), - roi_file=dict(usedefault=True, ), + dict_file=dict(), + roi_file=dict(), ) outputs = ROIGen.output_spec() diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py index 9513ba2c56..a39dbf6c3b 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py @@ -9,18 +9,13 @@ def test_DTIRecon_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), args=dict(argstr='%s', ), b0_threshold=dict(argstr='-b0_th', ), - bvals=dict( - mandatory=True, - usedefault=True, - ), + bvals=dict(mandatory=True, ), bvecs=dict( argstr='-gm %s', mandatory=True, - usedefault=True, ), environ=dict( nohash=True, @@ -46,18 +41,18 @@ def test_DTIRecon_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DTIRecon_outputs(): output_map = dict( - ADC=dict(usedefault=True, ), - B0=dict(usedefault=True, ), - FA=dict(usedefault=True, ), - FA_color=dict(usedefault=True, ), - L1=dict(usedefault=True, ), - L2=dict(usedefault=True, ), - L3=dict(usedefault=True, ), - V1=dict(usedefault=True, ), - V2=dict(usedefault=True, ), - V3=dict(usedefault=True, ), - exp=dict(usedefault=True, ), - tensor=dict(usedefault=True, ), + ADC=dict(), + B0=dict(), + FA=dict(), + FA_color=dict(), + L1=dict(), + L2=dict(), + L3=dict(), + V1=dict(), + V2=dict(), + V3=dict(), + exp=dict(), + tensor=dict(), ) outputs = DTIRecon.output_spec() diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py index a80c4ac3c4..cf483d00d0 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py @@ -25,13 +25,11 @@ def test_DTITracker_inputs(): argstr='-m %s', mandatory=True, position=2, - usedefault=True, ), mask1_threshold=dict(position=3, ), mask2_file=dict( argstr='-m2 %s', position=4, - usedefault=True, ), mask2_threshold=dict(position=5, ), output_file=dict( @@ -39,17 +37,14 @@ def test_DTITracker_inputs(): position=1, usedefault=True, ), - output_mask=dict( - argstr='-om %s', - usedefault=True, - ), + output_mask=dict(argstr='-om %s', ), primary_vector=dict(argstr='-%s', ), random_seed=dict(argstr='-rseed %d', ), step_length=dict(argstr='-l %f', ), swap_xy=dict(argstr='-sxy', ), swap_yz=dict(argstr='-syz', ), swap_zx=dict(argstr='-szx', ), - tensor_file=dict(usedefault=True, ), + tensor_file=dict(), tracking_method=dict(argstr='-%s', ), ) inputs = DTITracker.input_spec() @@ -59,8 +54,8 @@ def test_DTITracker_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DTITracker_outputs(): output_map = dict( - mask_file=dict(usedefault=True, ), - track_file=dict(usedefault=True, ), + mask_file=dict(), + track_file=dict(), ) outputs = DTITracker.output_spec() diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py index 5f04836ce9..59bc8c25a5 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py @@ -6,40 +6,27 @@ def test_HARDIMat_inputs(): input_map = dict( args=dict(argstr='%s', ), - bvals=dict( - mandatory=True, - usedefault=True, - ), + bvals=dict(mandatory=True, ), bvecs=dict( argstr='%s', mandatory=True, position=1, - usedefault=True, ), environ=dict( nohash=True, usedefault=True, ), - image_info=dict( - argstr='-info %s', - usedefault=True, - ), + image_info=dict(argstr='-info %s', ), image_orientation_vectors=dict(argstr='-iop %f', ), oblique_correction=dict(argstr='-oc', ), - odf_file=dict( - argstr='-odf %s', - usedefault=True, - ), + odf_file=dict(argstr='-odf %s', ), order=dict(argstr='-order %s', ), out_file=dict( argstr='%s', position=2, usedefault=True, ), - reference_file=dict( - argstr='-ref %s', - usedefault=True, - ), + reference_file=dict(argstr='-ref %s', ), ) inputs = HARDIMat.input_spec() @@ -47,7 +34,7 @@ def test_HARDIMat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_HARDIMat_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = HARDIMat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py index d23f176cdc..1e66b93bec 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py @@ -9,7 +9,6 @@ def test_ODFRecon_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), args=dict(argstr='%s', ), dsi=dict(argstr='-dsi', ), @@ -22,7 +21,6 @@ def test_ODFRecon_inputs(): matrix=dict( argstr='-mat %s', mandatory=True, - usedefault=True, ), n_b0=dict( argstr='-b0 %s', @@ -59,11 +57,11 @@ def test_ODFRecon_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ODFRecon_outputs(): output_map = dict( - B0=dict(usedefault=True, ), - DWI=dict(usedefault=True, ), - ODF=dict(usedefault=True, ), - entropy=dict(usedefault=True, ), - max=dict(usedefault=True, ), + B0=dict(), + DWI=dict(), + ODF=dict(), + entropy=dict(), + max=dict(), ) outputs = ODFRecon.output_spec() diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py index 291f6987fe..41b2d530f6 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py @@ -5,10 +5,7 @@ def test_ODFTracker_inputs(): input_map = dict( - ODF=dict( - mandatory=True, - usedefault=True, - ), + ODF=dict(mandatory=True, ), angle_threshold=dict(argstr='-at %f', ), args=dict(argstr='%s', ), disc=dict(argstr='-disc', ), @@ -35,19 +32,14 @@ def test_ODFTracker_inputs(): argstr='-m %s', mandatory=True, position=2, - usedefault=True, ), mask1_threshold=dict(position=3, ), mask2_file=dict( argstr='-m2 %s', position=4, - usedefault=True, ), mask2_threshold=dict(position=5, ), - max=dict( - mandatory=True, - usedefault=True, - ), + max=dict(mandatory=True, ), out_file=dict( argstr='%s', position=1, @@ -68,7 +60,7 @@ def test_ODFTracker_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ODFTracker_outputs(): - output_map = dict(track_file=dict(usedefault=True, ), ) + output_map = dict(track_file=dict(), ) outputs = ODFTracker.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py index e939cdba72..8648a1f1f9 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py @@ -24,7 +24,6 @@ def test_SplineFilter_inputs(): argstr='%s', mandatory=True, position=0, - usedefault=True, ), ) inputs = SplineFilter.input_spec() @@ -33,7 +32,7 @@ def test_SplineFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SplineFilter_outputs(): - output_map = dict(smoothed_track_file=dict(usedefault=True, ), ) + output_map = dict(smoothed_track_file=dict(), ) outputs = SplineFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py index 0333b8283c..b004678175 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py @@ -27,7 +27,7 @@ def test_TrackMerge_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackMerge_outputs(): - output_map = dict(track_file=dict(usedefault=True, ), ) + output_map = dict(track_file=dict(), ) outputs = TrackMerge.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dipy/tests/test_auto_APMQball.py b/nipype/interfaces/dipy/tests/test_auto_APMQball.py index 4696370434..f6f3f2e4c6 100644 --- a/nipype/interfaces/dipy/tests/test_auto_APMQball.py +++ b/nipype/interfaces/dipy/tests/test_auto_APMQball.py @@ -6,19 +6,10 @@ def test_APMQball_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict( - mandatory=True, - usedefault=True, - ), - in_bvec=dict( - mandatory=True, - usedefault=True, - ), - in_file=dict( - mandatory=True, - usedefault=True, - ), - mask_file=dict(usedefault=True, ), + in_bval=dict(mandatory=True, ), + in_bvec=dict(mandatory=True, ), + in_file=dict(mandatory=True, ), + mask_file=dict(), out_prefix=dict(), ) inputs = APMQball.input_spec() @@ -27,7 +18,7 @@ def test_APMQball_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_APMQball_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = APMQball.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dipy/tests/test_auto_CSD.py b/nipype/interfaces/dipy/tests/test_auto_CSD.py index c0372e0436..a30efaa3cc 100644 --- a/nipype/interfaces/dipy/tests/test_auto_CSD.py +++ b/nipype/interfaces/dipy/tests/test_auto_CSD.py @@ -6,22 +6,13 @@ def test_CSD_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict( - mandatory=True, - usedefault=True, - ), - in_bvec=dict( - mandatory=True, - usedefault=True, - ), - in_file=dict( - mandatory=True, - usedefault=True, - ), - in_mask=dict(usedefault=True, ), - out_fods=dict(usedefault=True, ), + in_bval=dict(mandatory=True, ), + in_bvec=dict(mandatory=True, ), + in_file=dict(mandatory=True, ), + in_mask=dict(), + out_fods=dict(), out_prefix=dict(), - response=dict(usedefault=True, ), + response=dict(), save_fods=dict(usedefault=True, ), sh_order=dict(usedefault=True, ), ) @@ -32,8 +23,8 @@ def test_CSD_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CSD_outputs(): output_map = dict( - model=dict(usedefault=True, ), - out_fods=dict(usedefault=True, ), + model=dict(), + out_fods=dict(), ) outputs = CSD.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_DTI.py b/nipype/interfaces/dipy/tests/test_auto_DTI.py index f8416f25a0..f543856065 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DTI.py +++ b/nipype/interfaces/dipy/tests/test_auto_DTI.py @@ -6,19 +6,10 @@ def test_DTI_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict( - mandatory=True, - usedefault=True, - ), - in_bvec=dict( - mandatory=True, - usedefault=True, - ), - in_file=dict( - mandatory=True, - usedefault=True, - ), - mask_file=dict(usedefault=True, ), + in_bval=dict(mandatory=True, ), + in_bvec=dict(mandatory=True, ), + in_file=dict(mandatory=True, ), + mask_file=dict(), out_prefix=dict(), ) inputs = DTI.input_spec() @@ -28,12 +19,12 @@ def test_DTI_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DTI_outputs(): output_map = dict( - ad_file=dict(usedefault=True, ), - color_fa_file=dict(usedefault=True, ), - fa_file=dict(usedefault=True, ), - md_file=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), - rd_file=dict(usedefault=True, ), + ad_file=dict(), + color_fa_file=dict(), + fa_file=dict(), + md_file=dict(), + out_file=dict(), + rd_file=dict(), ) outputs = DTI.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_Denoise.py b/nipype/interfaces/dipy/tests/test_auto_Denoise.py index a799d22b8d..88a1bc5314 100644 --- a/nipype/interfaces/dipy/tests/test_auto_Denoise.py +++ b/nipype/interfaces/dipy/tests/test_auto_Denoise.py @@ -6,18 +6,15 @@ def test_Denoise_inputs(): input_map = dict( block_radius=dict(usedefault=True, ), - in_file=dict( - mandatory=True, - usedefault=True, - ), - in_mask=dict(usedefault=True, ), - noise_mask=dict(usedefault=True, ), + in_file=dict(mandatory=True, ), + in_mask=dict(), + noise_mask=dict(), noise_model=dict( mandatory=True, usedefault=True, ), patch_radius=dict(usedefault=True, ), - signal_mask=dict(usedefault=True, ), + signal_mask=dict(), snr=dict(), ) inputs = Denoise.input_spec() @@ -26,7 +23,7 @@ def test_Denoise_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Denoise_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Denoise.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py b/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py index 3820a6f42e..ee9022ca58 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py +++ b/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py @@ -6,18 +6,9 @@ def test_DipyDiffusionInterface_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict( - mandatory=True, - usedefault=True, - ), - in_bvec=dict( - mandatory=True, - usedefault=True, - ), - in_file=dict( - mandatory=True, - usedefault=True, - ), + in_bval=dict(mandatory=True, ), + in_bvec=dict(mandatory=True, ), + in_file=dict(mandatory=True, ), out_prefix=dict(), ) inputs = DipyDiffusionInterface.input_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py b/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py index c152a2e226..1270d94b13 100644 --- a/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py +++ b/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py @@ -8,23 +8,11 @@ def test_EstimateResponseSH_inputs(): auto=dict(xor=['recursive'], ), b0_thres=dict(usedefault=True, ), fa_thresh=dict(usedefault=True, ), - in_bval=dict( - mandatory=True, - usedefault=True, - ), - in_bvec=dict( - mandatory=True, - usedefault=True, - ), - in_evals=dict( - mandatory=True, - usedefault=True, - ), - in_file=dict( - mandatory=True, - usedefault=True, - ), - in_mask=dict(usedefault=True, ), + in_bval=dict(mandatory=True, ), + in_bvec=dict(mandatory=True, ), + in_evals=dict(mandatory=True, ), + in_file=dict(mandatory=True, ), + in_mask=dict(), out_mask=dict(usedefault=True, ), out_prefix=dict(), recursive=dict(xor=['auto'], ), @@ -38,8 +26,8 @@ def test_EstimateResponseSH_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EstimateResponseSH_outputs(): output_map = dict( - out_mask=dict(usedefault=True, ), - response=dict(usedefault=True, ), + out_mask=dict(), + response=dict(), ) outputs = EstimateResponseSH.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_RESTORE.py b/nipype/interfaces/dipy/tests/test_auto_RESTORE.py index f6f4a87466..9f62d05e0c 100644 --- a/nipype/interfaces/dipy/tests/test_auto_RESTORE.py +++ b/nipype/interfaces/dipy/tests/test_auto_RESTORE.py @@ -6,20 +6,11 @@ def test_RESTORE_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict( - mandatory=True, - usedefault=True, - ), - in_bvec=dict( - mandatory=True, - usedefault=True, - ), - in_file=dict( - mandatory=True, - usedefault=True, - ), - in_mask=dict(usedefault=True, ), - noise_mask=dict(usedefault=True, ), + in_bval=dict(mandatory=True, ), + in_bvec=dict(mandatory=True, ), + in_file=dict(mandatory=True, ), + in_mask=dict(), + noise_mask=dict(), out_prefix=dict(), ) inputs = RESTORE.input_spec() @@ -29,13 +20,13 @@ def test_RESTORE_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RESTORE_outputs(): output_map = dict( - evals=dict(usedefault=True, ), - evecs=dict(usedefault=True, ), - fa=dict(usedefault=True, ), - md=dict(usedefault=True, ), - mode=dict(usedefault=True, ), - rd=dict(usedefault=True, ), - trace=dict(usedefault=True, ), + evals=dict(), + evecs=dict(), + fa=dict(), + md=dict(), + mode=dict(), + rd=dict(), + trace=dict(), ) outputs = RESTORE.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_Resample.py b/nipype/interfaces/dipy/tests/test_auto_Resample.py index 261bab77ce..ff51e0efe4 100644 --- a/nipype/interfaces/dipy/tests/test_auto_Resample.py +++ b/nipype/interfaces/dipy/tests/test_auto_Resample.py @@ -5,10 +5,7 @@ def test_Resample_inputs(): input_map = dict( - in_file=dict( - mandatory=True, - usedefault=True, - ), + in_file=dict(mandatory=True, ), interp=dict( mandatory=True, usedefault=True, @@ -21,7 +18,7 @@ def test_Resample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Resample_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Resample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py index 31db2179c1..db46a3b982 100644 --- a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py +++ b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py @@ -5,19 +5,16 @@ def test_SimulateMultiTensor_inputs(): input_map = dict( - baseline=dict( - mandatory=True, - usedefault=True, - ), + baseline=dict(mandatory=True, ), bvalues=dict(usedefault=True, ), diff_iso=dict(usedefault=True, ), diff_sf=dict(usedefault=True, ), - gradients=dict(usedefault=True, ), - in_bval=dict(usedefault=True, ), - in_bvec=dict(usedefault=True, ), + gradients=dict(), + in_bval=dict(), + in_bvec=dict(), in_dirs=dict(mandatory=True, ), in_frac=dict(mandatory=True, ), - in_mask=dict(usedefault=True, ), + in_mask=dict(), in_vfms=dict(mandatory=True, ), n_proc=dict(usedefault=True, ), num_dirs=dict(usedefault=True, ), @@ -34,10 +31,10 @@ def test_SimulateMultiTensor_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SimulateMultiTensor_outputs(): output_map = dict( - out_bval=dict(usedefault=True, ), - out_bvec=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), - out_mask=dict(usedefault=True, ), + out_bval=dict(), + out_bvec=dict(), + out_file=dict(), + out_mask=dict(), ) outputs = SimulateMultiTensor.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py b/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py index 420f9686bd..1bc1a2ea97 100644 --- a/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py +++ b/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py @@ -9,12 +9,9 @@ def test_StreamlineTractography_inputs(): mandatory=True, usedefault=True, ), - in_file=dict( - mandatory=True, - usedefault=True, - ), - in_model=dict(usedefault=True, ), - in_peaks=dict(usedefault=True, ), + in_file=dict(mandatory=True, ), + in_model=dict(), + in_peaks=dict(), min_angle=dict( mandatory=True, usedefault=True, @@ -36,9 +33,9 @@ def test_StreamlineTractography_inputs(): mandatory=True, usedefault=True, ), - seed_coord=dict(usedefault=True, ), - seed_mask=dict(usedefault=True, ), - tracking_mask=dict(usedefault=True, ), + seed_coord=dict(), + seed_mask=dict(), + tracking_mask=dict(), ) inputs = StreamlineTractography.input_spec() @@ -47,10 +44,10 @@ def test_StreamlineTractography_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_StreamlineTractography_outputs(): output_map = dict( - gfa=dict(usedefault=True, ), - odf_peaks=dict(usedefault=True, ), - out_seeds=dict(usedefault=True, ), - tracks=dict(usedefault=True, ), + gfa=dict(), + odf_peaks=dict(), + out_seeds=dict(), + tracks=dict(), ) outputs = StreamlineTractography.output_spec() diff --git a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py index 319b38d094..d072af78fc 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py +++ b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py @@ -6,19 +6,10 @@ def test_TensorMode_inputs(): input_map = dict( b0_thres=dict(usedefault=True, ), - in_bval=dict( - mandatory=True, - usedefault=True, - ), - in_bvec=dict( - mandatory=True, - usedefault=True, - ), - in_file=dict( - mandatory=True, - usedefault=True, - ), - mask_file=dict(usedefault=True, ), + in_bval=dict(mandatory=True, ), + in_bvec=dict(mandatory=True, ), + in_file=dict(mandatory=True, ), + mask_file=dict(), out_prefix=dict(), ) inputs = TensorMode.input_spec() @@ -27,7 +18,7 @@ def test_TensorMode_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TensorMode_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TensorMode.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py index 31d68631ca..79af3b5940 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py +++ b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py @@ -6,13 +6,10 @@ def test_TrackDensityMap_inputs(): input_map = dict( data_dims=dict(), - in_file=dict( - mandatory=True, - usedefault=True, - ), + in_file=dict(mandatory=True, ), out_filename=dict(usedefault=True, ), points_space=dict(usedefault=True, ), - reference=dict(usedefault=True, ), + reference=dict(), voxel_dims=dict(), ) inputs = TrackDensityMap.input_spec() @@ -21,7 +18,7 @@ def test_TrackDensityMap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TrackDensityMap_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TrackDensityMap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_AffScalarVol.py b/nipype/interfaces/dtitk/tests/test_auto_AffScalarVol.py index ef9cd8ceab..5f9262d788 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_AffScalarVol.py +++ b/nipype/interfaces/dtitk/tests/test_auto_AffScalarVol.py @@ -21,7 +21,6 @@ def test_AffScalarVol_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), interpolation=dict( argstr='-interp %s', @@ -32,16 +31,13 @@ def test_AffScalarVol_inputs(): keep_extension=True, name_source='in_file', name_template='%s_affxfmd', - usedefault=True, ), target=dict( argstr='-target %s', - usedefault=True, xor=['transform'], ), transform=dict( argstr='-trans %s', - usedefault=True, xor=['target', 'translation', 'euler', 'deformation'], ), translation=dict( @@ -55,7 +51,7 @@ def test_AffScalarVol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AffScalarVol_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = AffScalarVol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_AffSymTensor3DVol.py b/nipype/interfaces/dtitk/tests/test_auto_AffSymTensor3DVol.py index 83077db6fd..6d7abc852a 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_AffSymTensor3DVol.py +++ b/nipype/interfaces/dtitk/tests/test_auto_AffSymTensor3DVol.py @@ -21,7 +21,6 @@ def test_AffSymTensor3DVol_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), interpolation=dict( argstr='-interp %s', @@ -32,7 +31,6 @@ def test_AffSymTensor3DVol_inputs(): keep_extension=True, name_source='in_file', name_template='%s_affxfmd', - usedefault=True, ), reorient=dict( argstr='-reorient %s', @@ -40,12 +38,10 @@ def test_AffSymTensor3DVol_inputs(): ), target=dict( argstr='-target %s', - usedefault=True, xor=['transform'], ), transform=dict( argstr='-trans %s', - usedefault=True, xor=['target', 'translation', 'euler', 'deformation'], ), translation=dict( @@ -59,7 +55,7 @@ def test_AffSymTensor3DVol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AffSymTensor3DVol_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = AffSymTensor3DVol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_Affine.py b/nipype/interfaces/dtitk/tests/test_auto_Affine.py index 2631304823..78d2e6f011 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_Affine.py +++ b/nipype/interfaces/dtitk/tests/test_auto_Affine.py @@ -15,7 +15,6 @@ def test_Affine_inputs(): copyfile=False, mandatory=True, position=0, - usedefault=True, ), ftol=dict( argstr='%g', @@ -27,14 +26,12 @@ def test_Affine_inputs(): argstr='%s', copyfile=True, position=5, - usedefault=True, ), moving_file=dict( argstr='%s', copyfile=False, mandatory=True, position=1, - usedefault=True, ), sampling_xyz=dict( argstr='%g %g %g', @@ -56,8 +53,8 @@ def test_Affine_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Affine_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - out_file_xfm=dict(usedefault=True, ), + out_file=dict(), + out_file_xfm=dict(), ) outputs = Affine.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_AffineTask.py b/nipype/interfaces/dtitk/tests/test_auto_AffineTask.py index 5737bb29a7..5f3b43153a 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_AffineTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_AffineTask.py @@ -15,7 +15,6 @@ def test_AffineTask_inputs(): copyfile=False, mandatory=True, position=0, - usedefault=True, ), ftol=dict( argstr='%g', @@ -27,14 +26,12 @@ def test_AffineTask_inputs(): argstr='%s', copyfile=True, position=5, - usedefault=True, ), moving_file=dict( argstr='%s', copyfile=False, mandatory=True, position=1, - usedefault=True, ), sampling_xyz=dict( argstr='%g %g %g', @@ -56,8 +53,8 @@ def test_AffineTask_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_AffineTask_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - out_file_xfm=dict(usedefault=True, ), + out_file=dict(), + out_file_xfm=dict(), ) outputs = AffineTask.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_BinThresh.py b/nipype/interfaces/dtitk/tests/test_auto_BinThresh.py index c63046d31a..cbd4efccb2 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_BinThresh.py +++ b/nipype/interfaces/dtitk/tests/test_auto_BinThresh.py @@ -14,7 +14,6 @@ def test_BinThresh_inputs(): argstr='%s', mandatory=True, position=0, - usedefault=True, ), inside_value=dict( argstr='%g', @@ -34,7 +33,6 @@ def test_BinThresh_inputs(): name_source='in_file', name_template='%s_thrbin', position=1, - usedefault=True, ), outside_value=dict( argstr='%g', @@ -55,7 +53,7 @@ def test_BinThresh_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinThresh_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = BinThresh.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_BinThreshTask.py b/nipype/interfaces/dtitk/tests/test_auto_BinThreshTask.py index c76c9653a7..dcd396abe2 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_BinThreshTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_BinThreshTask.py @@ -14,7 +14,6 @@ def test_BinThreshTask_inputs(): argstr='%s', mandatory=True, position=0, - usedefault=True, ), inside_value=dict( argstr='%g', @@ -34,7 +33,6 @@ def test_BinThreshTask_inputs(): name_source='in_file', name_template='%s_thrbin', position=1, - usedefault=True, ), outside_value=dict( argstr='%g', @@ -55,7 +53,7 @@ def test_BinThreshTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinThreshTask_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = BinThreshTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_ComposeXfm.py b/nipype/interfaces/dtitk/tests/test_auto_ComposeXfm.py index bd62da2e94..09fcdc186e 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_ComposeXfm.py +++ b/nipype/interfaces/dtitk/tests/test_auto_ComposeXfm.py @@ -13,17 +13,14 @@ def test_ComposeXfm_inputs(): in_aff=dict( argstr='-aff %s', mandatory=True, - usedefault=True, ), in_df=dict( argstr='-df %s', mandatory=True, - usedefault=True, ), out_file=dict( argstr='-out %s', genfile=True, - usedefault=True, ), ) inputs = ComposeXfm.input_spec() @@ -32,7 +29,7 @@ def test_ComposeXfm_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComposeXfm_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ComposeXfm.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_ComposeXfmTask.py b/nipype/interfaces/dtitk/tests/test_auto_ComposeXfmTask.py index 2f552d4171..99c6f6d340 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_ComposeXfmTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_ComposeXfmTask.py @@ -13,17 +13,14 @@ def test_ComposeXfmTask_inputs(): in_aff=dict( argstr='-aff %s', mandatory=True, - usedefault=True, ), in_df=dict( argstr='-df %s', mandatory=True, - usedefault=True, ), out_file=dict( argstr='-out %s', genfile=True, - usedefault=True, ), ) inputs = ComposeXfmTask.input_spec() @@ -32,7 +29,7 @@ def test_ComposeXfmTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComposeXfmTask_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ComposeXfmTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_Diffeo.py b/nipype/interfaces/dtitk/tests/test_auto_Diffeo.py index 698ede9270..ad532bd631 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_Diffeo.py +++ b/nipype/interfaces/dtitk/tests/test_auto_Diffeo.py @@ -13,7 +13,6 @@ def test_Diffeo_inputs(): fixed_file=dict( argstr='%s', position=0, - usedefault=True, ), ftol=dict( argstr='%g', @@ -30,13 +29,11 @@ def test_Diffeo_inputs(): mask_file=dict( argstr='%s', position=2, - usedefault=True, ), moving_file=dict( argstr='%s', copyfile=False, position=1, - usedefault=True, ), n_iters=dict( argstr='%d', @@ -52,8 +49,8 @@ def test_Diffeo_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Diffeo_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - out_file_xfm=dict(usedefault=True, ), + out_file=dict(), + out_file_xfm=dict(), ) outputs = Diffeo.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_DiffeoScalarVol.py b/nipype/interfaces/dtitk/tests/test_auto_DiffeoScalarVol.py index 925943ede4..7d1305d384 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_DiffeoScalarVol.py +++ b/nipype/interfaces/dtitk/tests/test_auto_DiffeoScalarVol.py @@ -14,7 +14,6 @@ def test_DiffeoScalarVol_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), interpolation=dict( argstr='-interp %s', @@ -25,18 +24,15 @@ def test_DiffeoScalarVol_inputs(): keep_extension=True, name_source='in_file', name_template='%s_diffeoxfmd', - usedefault=True, ), resampling_type=dict(argstr='-type %s', ), target=dict( argstr='-target %s', - usedefault=True, xor=['voxel_size'], ), transform=dict( argstr='-trans %s', mandatory=True, - usedefault=True, ), voxel_size=dict( argstr='-vsize %g %g %g', @@ -49,7 +45,7 @@ def test_DiffeoScalarVol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DiffeoScalarVol_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = DiffeoScalarVol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_DiffeoSymTensor3DVol.py b/nipype/interfaces/dtitk/tests/test_auto_DiffeoSymTensor3DVol.py index a73c6236ed..b934c56d2b 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_DiffeoSymTensor3DVol.py +++ b/nipype/interfaces/dtitk/tests/test_auto_DiffeoSymTensor3DVol.py @@ -18,7 +18,6 @@ def test_DiffeoSymTensor3DVol_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), interpolation=dict( argstr='-interp %s', @@ -29,7 +28,6 @@ def test_DiffeoSymTensor3DVol_inputs(): keep_extension=True, name_source='in_file', name_template='%s_diffeoxfmd', - usedefault=True, ), reorient=dict( argstr='-reorient %s', @@ -38,13 +36,11 @@ def test_DiffeoSymTensor3DVol_inputs(): resampling_type=dict(argstr='-type %s', ), target=dict( argstr='-target %s', - usedefault=True, xor=['voxel_size'], ), transform=dict( argstr='-trans %s', mandatory=True, - usedefault=True, ), voxel_size=dict( argstr='-vsize %g %g %g', @@ -57,7 +53,7 @@ def test_DiffeoSymTensor3DVol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DiffeoSymTensor3DVol_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = DiffeoSymTensor3DVol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_DiffeoTask.py b/nipype/interfaces/dtitk/tests/test_auto_DiffeoTask.py index d3b5bc813d..5aea665d4c 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_DiffeoTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_DiffeoTask.py @@ -13,7 +13,6 @@ def test_DiffeoTask_inputs(): fixed_file=dict( argstr='%s', position=0, - usedefault=True, ), ftol=dict( argstr='%g', @@ -30,13 +29,11 @@ def test_DiffeoTask_inputs(): mask_file=dict( argstr='%s', position=2, - usedefault=True, ), moving_file=dict( argstr='%s', copyfile=False, position=1, - usedefault=True, ), n_iters=dict( argstr='%d', @@ -52,8 +49,8 @@ def test_DiffeoTask_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DiffeoTask_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - out_file_xfm=dict(usedefault=True, ), + out_file=dict(), + out_file_xfm=dict(), ) outputs = DiffeoTask.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_Rigid.py b/nipype/interfaces/dtitk/tests/test_auto_Rigid.py index 48e8d00138..ecb7c2d33b 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_Rigid.py +++ b/nipype/interfaces/dtitk/tests/test_auto_Rigid.py @@ -15,7 +15,6 @@ def test_Rigid_inputs(): copyfile=False, mandatory=True, position=0, - usedefault=True, ), ftol=dict( argstr='%g', @@ -27,14 +26,12 @@ def test_Rigid_inputs(): argstr='%s', copyfile=True, position=5, - usedefault=True, ), moving_file=dict( argstr='%s', copyfile=False, mandatory=True, position=1, - usedefault=True, ), sampling_xyz=dict( argstr='%g %g %g', @@ -56,8 +53,8 @@ def test_Rigid_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Rigid_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - out_file_xfm=dict(usedefault=True, ), + out_file=dict(), + out_file_xfm=dict(), ) outputs = Rigid.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_RigidTask.py b/nipype/interfaces/dtitk/tests/test_auto_RigidTask.py index 277c906fb7..c627fda741 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_RigidTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_RigidTask.py @@ -15,7 +15,6 @@ def test_RigidTask_inputs(): copyfile=False, mandatory=True, position=0, - usedefault=True, ), ftol=dict( argstr='%g', @@ -27,14 +26,12 @@ def test_RigidTask_inputs(): argstr='%s', copyfile=True, position=5, - usedefault=True, ), moving_file=dict( argstr='%s', copyfile=False, mandatory=True, position=1, - usedefault=True, ), sampling_xyz=dict( argstr='%g %g %g', @@ -56,8 +53,8 @@ def test_RigidTask_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RigidTask_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - out_file_xfm=dict(usedefault=True, ), + out_file=dict(), + out_file_xfm=dict(), ) outputs = RigidTask.output_spec() diff --git a/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSp.py b/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSp.py index 387de8ca89..3574906455 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSp.py +++ b/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSp.py @@ -13,7 +13,6 @@ def test_SVAdjustVoxSp_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), origin=dict( argstr='-origin %g %g %g', @@ -24,11 +23,9 @@ def test_SVAdjustVoxSp_inputs(): keep_extension=True, name_source='in_file', name_template='%s_avs', - usedefault=True, ), target_file=dict( argstr='-target %s', - usedefault=True, xor=['voxel_size', 'origin'], ), voxel_size=dict( @@ -42,7 +39,7 @@ def test_SVAdjustVoxSp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SVAdjustVoxSp_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = SVAdjustVoxSp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSpTask.py b/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSpTask.py index acd986d585..40a7592c19 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSpTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_SVAdjustVoxSpTask.py @@ -13,7 +13,6 @@ def test_SVAdjustVoxSpTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), origin=dict( argstr='-origin %g %g %g', @@ -24,11 +23,9 @@ def test_SVAdjustVoxSpTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_avs', - usedefault=True, ), target_file=dict( argstr='-target %s', - usedefault=True, xor=['voxel_size', 'origin'], ), voxel_size=dict( @@ -42,7 +39,7 @@ def test_SVAdjustVoxSpTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SVAdjustVoxSpTask_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = SVAdjustVoxSpTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_SVResample.py b/nipype/interfaces/dtitk/tests/test_auto_SVResample.py index d37306197c..91ca638f22 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_SVResample.py +++ b/nipype/interfaces/dtitk/tests/test_auto_SVResample.py @@ -18,7 +18,6 @@ def test_SVResample_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), origin=dict( argstr='-origin %g %g %g', @@ -29,11 +28,9 @@ def test_SVResample_inputs(): keep_extension=True, name_source='in_file', name_template='%s_resampled', - usedefault=True, ), target_file=dict( argstr='-target %s', - usedefault=True, xor=['array_size', 'voxel_size', 'origin'], ), voxel_size=dict( @@ -47,7 +44,7 @@ def test_SVResample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SVResample_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = SVResample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_SVResampleTask.py b/nipype/interfaces/dtitk/tests/test_auto_SVResampleTask.py index 65200bf04c..8a7574bfd8 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_SVResampleTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_SVResampleTask.py @@ -18,7 +18,6 @@ def test_SVResampleTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), origin=dict( argstr='-origin %g %g %g', @@ -29,11 +28,9 @@ def test_SVResampleTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_resampled', - usedefault=True, ), target_file=dict( argstr='-target %s', - usedefault=True, xor=['array_size', 'voxel_size', 'origin'], ), voxel_size=dict( @@ -47,7 +44,7 @@ def test_SVResampleTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SVResampleTask_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = SVResampleTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustOriginTask.py b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustOriginTask.py index 0c9a1d0d90..bda9128369 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustOriginTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustOriginTask.py @@ -13,7 +13,6 @@ def test_TVAdjustOriginTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), origin=dict( argstr='-origin %g %g %g', @@ -24,11 +23,9 @@ def test_TVAdjustOriginTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_avs', - usedefault=True, ), target_file=dict( argstr='-target %s', - usedefault=True, xor=['voxel_size', 'origin'], ), voxel_size=dict( @@ -42,7 +39,7 @@ def test_TVAdjustOriginTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVAdjustOriginTask_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TVAdjustOriginTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSp.py b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSp.py index 9912f3c1a7..b8ce9039d5 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSp.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSp.py @@ -13,7 +13,6 @@ def test_TVAdjustVoxSp_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), origin=dict( argstr='-origin %g %g %g', @@ -24,11 +23,9 @@ def test_TVAdjustVoxSp_inputs(): keep_extension=True, name_source='in_file', name_template='%s_avs', - usedefault=True, ), target_file=dict( argstr='-target %s', - usedefault=True, xor=['voxel_size', 'origin'], ), voxel_size=dict( @@ -42,7 +39,7 @@ def test_TVAdjustVoxSp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVAdjustVoxSp_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TVAdjustVoxSp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSpTask.py b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSpTask.py index 0cdc3871a0..e9ef8137dc 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSpTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVAdjustVoxSpTask.py @@ -13,7 +13,6 @@ def test_TVAdjustVoxSpTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), origin=dict( argstr='-origin %g %g %g', @@ -24,11 +23,9 @@ def test_TVAdjustVoxSpTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_avs', - usedefault=True, ), target_file=dict( argstr='-target %s', - usedefault=True, xor=['voxel_size', 'origin'], ), voxel_size=dict( @@ -42,7 +39,7 @@ def test_TVAdjustVoxSpTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVAdjustVoxSpTask_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TVAdjustVoxSpTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVResample.py b/nipype/interfaces/dtitk/tests/test_auto_TVResample.py index f706ba9ff6..aefafc6430 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVResample.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVResample.py @@ -18,7 +18,6 @@ def test_TVResample_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), interpolation=dict(argstr='-interp %s', ), origin=dict( @@ -30,11 +29,9 @@ def test_TVResample_inputs(): keep_extension=True, name_source='in_file', name_template='%s_resampled', - usedefault=True, ), target_file=dict( argstr='-target %s', - usedefault=True, xor=['array_size', 'voxel_size', 'origin'], ), voxel_size=dict( @@ -48,7 +45,7 @@ def test_TVResample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVResample_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TVResample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVResampleTask.py b/nipype/interfaces/dtitk/tests/test_auto_TVResampleTask.py index f1c0193a4e..b3c70bb729 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVResampleTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVResampleTask.py @@ -18,7 +18,6 @@ def test_TVResampleTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), interpolation=dict(argstr='-interp %s', ), origin=dict( @@ -30,11 +29,9 @@ def test_TVResampleTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_resampled', - usedefault=True, ), target_file=dict( argstr='-target %s', - usedefault=True, xor=['array_size', 'voxel_size', 'origin'], ), voxel_size=dict( @@ -48,7 +45,7 @@ def test_TVResampleTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVResampleTask_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TVResampleTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVtool.py b/nipype/interfaces/dtitk/tests/test_auto_TVtool.py index c13dbcb967..2267228631 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVtool.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVtool.py @@ -13,13 +13,11 @@ def test_TVtool_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), in_flag=dict(argstr='-%s', ), out_file=dict( argstr='-out %s', genfile=True, - usedefault=True, ), ) inputs = TVtool.input_spec() @@ -28,7 +26,7 @@ def test_TVtool_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVtool_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TVtool.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_TVtoolTask.py b/nipype/interfaces/dtitk/tests/test_auto_TVtoolTask.py index 2e5547f5a0..252d7c9d0a 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_TVtoolTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_TVtoolTask.py @@ -13,13 +13,11 @@ def test_TVtoolTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), in_flag=dict(argstr='-%s', ), out_file=dict( argstr='-out %s', genfile=True, - usedefault=True, ), ) inputs = TVtoolTask.input_spec() @@ -28,7 +26,7 @@ def test_TVtoolTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TVtoolTask_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TVtoolTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_affScalarVolTask.py b/nipype/interfaces/dtitk/tests/test_auto_affScalarVolTask.py index 958818eeb9..72330737b6 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_affScalarVolTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_affScalarVolTask.py @@ -21,7 +21,6 @@ def test_affScalarVolTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), interpolation=dict( argstr='-interp %s', @@ -32,16 +31,13 @@ def test_affScalarVolTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_affxfmd', - usedefault=True, ), target=dict( argstr='-target %s', - usedefault=True, xor=['transform'], ), transform=dict( argstr='-trans %s', - usedefault=True, xor=['target', 'translation', 'euler', 'deformation'], ), translation=dict( @@ -55,7 +51,7 @@ def test_affScalarVolTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_affScalarVolTask_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = affScalarVolTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_affSymTensor3DVolTask.py b/nipype/interfaces/dtitk/tests/test_auto_affSymTensor3DVolTask.py index 746304d997..da8fae25cc 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_affSymTensor3DVolTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_affSymTensor3DVolTask.py @@ -21,7 +21,6 @@ def test_affSymTensor3DVolTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), interpolation=dict( argstr='-interp %s', @@ -32,7 +31,6 @@ def test_affSymTensor3DVolTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_affxfmd', - usedefault=True, ), reorient=dict( argstr='-reorient %s', @@ -40,12 +38,10 @@ def test_affSymTensor3DVolTask_inputs(): ), target=dict( argstr='-target %s', - usedefault=True, xor=['transform'], ), transform=dict( argstr='-trans %s', - usedefault=True, xor=['target', 'translation', 'euler', 'deformation'], ), translation=dict( @@ -59,7 +55,7 @@ def test_affSymTensor3DVolTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_affSymTensor3DVolTask_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = affSymTensor3DVolTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_diffeoScalarVolTask.py b/nipype/interfaces/dtitk/tests/test_auto_diffeoScalarVolTask.py index d6786572a3..10965b7077 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_diffeoScalarVolTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_diffeoScalarVolTask.py @@ -14,7 +14,6 @@ def test_diffeoScalarVolTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), interpolation=dict( argstr='-interp %s', @@ -25,18 +24,15 @@ def test_diffeoScalarVolTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_diffeoxfmd', - usedefault=True, ), resampling_type=dict(argstr='-type %s', ), target=dict( argstr='-target %s', - usedefault=True, xor=['voxel_size'], ), transform=dict( argstr='-trans %s', mandatory=True, - usedefault=True, ), voxel_size=dict( argstr='-vsize %g %g %g', @@ -49,7 +45,7 @@ def test_diffeoScalarVolTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_diffeoScalarVolTask_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = diffeoScalarVolTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/dtitk/tests/test_auto_diffeoSymTensor3DVolTask.py b/nipype/interfaces/dtitk/tests/test_auto_diffeoSymTensor3DVolTask.py index b99bd69a4a..52112735b1 100644 --- a/nipype/interfaces/dtitk/tests/test_auto_diffeoSymTensor3DVolTask.py +++ b/nipype/interfaces/dtitk/tests/test_auto_diffeoSymTensor3DVolTask.py @@ -18,7 +18,6 @@ def test_diffeoSymTensor3DVolTask_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), interpolation=dict( argstr='-interp %s', @@ -29,7 +28,6 @@ def test_diffeoSymTensor3DVolTask_inputs(): keep_extension=True, name_source='in_file', name_template='%s_diffeoxfmd', - usedefault=True, ), reorient=dict( argstr='-reorient %s', @@ -38,13 +36,11 @@ def test_diffeoSymTensor3DVolTask_inputs(): resampling_type=dict(argstr='-type %s', ), target=dict( argstr='-target %s', - usedefault=True, xor=['voxel_size'], ), transform=dict( argstr='-trans %s', mandatory=True, - usedefault=True, ), voxel_size=dict( argstr='-vsize %g %g %g', @@ -57,7 +53,7 @@ def test_diffeoSymTensor3DVolTask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_diffeoSymTensor3DVolTask_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = diffeoSymTensor3DVolTask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py index d2d69581bf..f05821d9c1 100644 --- a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py @@ -18,10 +18,7 @@ def test_AnalyzeWarp_inputs(): argstr='-jacmat %s', usedefault=True, ), - moving_image=dict( - argstr='-in %s', - usedefault=True, - ), + moving_image=dict(argstr='-in %s', ), num_threads=dict( argstr='-threads %01d', nohash=True, @@ -40,7 +37,6 @@ def test_AnalyzeWarp_inputs(): transform_file=dict( argstr='-tp %s', mandatory=True, - usedefault=True, ), ) inputs = AnalyzeWarp.input_spec() @@ -50,9 +46,9 @@ def test_AnalyzeWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_AnalyzeWarp_outputs(): output_map = dict( - disp_field=dict(usedefault=True, ), - jacdet_map=dict(usedefault=True, ), - jacmat_map=dict(usedefault=True, ), + disp_field=dict(), + jacdet_map=dict(), + jacmat_map=dict(), ) outputs = AnalyzeWarp.output_spec() diff --git a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py index b199bbeca3..16f2b54079 100644 --- a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py @@ -13,7 +13,6 @@ def test_ApplyWarp_inputs(): moving_image=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), num_threads=dict( argstr='-threads %01d', @@ -28,7 +27,6 @@ def test_ApplyWarp_inputs(): transform_file=dict( argstr='-tp %s', mandatory=True, - usedefault=True, ), ) inputs = ApplyWarp.input_spec() @@ -37,7 +35,7 @@ def test_ApplyWarp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyWarp_outputs(): - output_map = dict(warped_file=dict(usedefault=True, ), ) + output_map = dict(warped_file=dict(), ) outputs = ApplyWarp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py index b6dba08d2e..ef227da7f8 100644 --- a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py +++ b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py @@ -9,14 +9,11 @@ def test_EditTransform_inputs(): argstr='FinalBSplineInterpolationOrder', usedefault=True, ), - output_file=dict(usedefault=True, ), + output_file=dict(), output_format=dict(argstr='ResultImageFormat', ), output_type=dict(argstr='ResultImagePixelType', ), - reference_image=dict(usedefault=True, ), - transform_file=dict( - mandatory=True, - usedefault=True, - ), + reference_image=dict(), + transform_file=dict(mandatory=True, ), ) inputs = EditTransform.input_spec() @@ -24,7 +21,7 @@ def test_EditTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EditTransform_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = EditTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py index f5115e1e04..c93a0526c1 100644 --- a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py @@ -23,12 +23,10 @@ def test_PointsWarp_inputs(): points_file=dict( argstr='-def %s', mandatory=True, - usedefault=True, ), transform_file=dict( argstr='-tp %s', mandatory=True, - usedefault=True, ), ) inputs = PointsWarp.input_spec() @@ -37,7 +35,7 @@ def test_PointsWarp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PointsWarp_outputs(): - output_map = dict(warped_file=dict(usedefault=True, ), ) + output_map = dict(warped_file=dict(), ) outputs = PointsWarp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/elastix/tests/test_auto_Registration.py b/nipype/interfaces/elastix/tests/test_auto_Registration.py index 7c63e433cc..4e774ab036 100644 --- a/nipype/interfaces/elastix/tests/test_auto_Registration.py +++ b/nipype/interfaces/elastix/tests/test_auto_Registration.py @@ -13,25 +13,14 @@ def test_Registration_inputs(): fixed_image=dict( argstr='-f %s', mandatory=True, - usedefault=True, - ), - fixed_mask=dict( - argstr='-fMask %s', - usedefault=True, - ), - initial_transform=dict( - argstr='-t0 %s', - usedefault=True, ), + fixed_mask=dict(argstr='-fMask %s', ), + initial_transform=dict(argstr='-t0 %s', ), moving_image=dict( argstr='-m %s', mandatory=True, - usedefault=True, - ), - moving_mask=dict( - argstr='-mMask %s', - usedefault=True, ), + moving_mask=dict(argstr='-mMask %s', ), num_threads=dict( argstr='-threads %01d', nohash=True, @@ -55,7 +44,7 @@ def test_Registration_inputs(): def test_Registration_outputs(): output_map = dict( transform=dict(), - warped_file=dict(usedefault=True, ), + warped_file=dict(), warped_files=dict(), warped_files_flags=dict(), ) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py b/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py index 0aac5b03fb..ed32693df5 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py @@ -15,19 +15,17 @@ def test_AddXFormToHeader_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), out_file=dict( argstr='%s', position=-1, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), transform=dict( argstr='%s', mandatory=True, position=-3, - usedefault=True, ), verbose=dict(argstr='-v', ), ) @@ -37,7 +35,7 @@ def test_AddXFormToHeader_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AddXFormToHeader_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = AddXFormToHeader.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py index 7388dc8e4f..fc5bc39b6f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py @@ -7,70 +7,36 @@ def test_Aparc2Aseg_inputs(): input_map = dict( a2009s=dict(argstr='--a2009s', ), args=dict(argstr='%s', ), - aseg=dict( - argstr='--aseg %s', - usedefault=True, - ), + aseg=dict(argstr='--aseg %s', ), copy_inputs=dict(), - ctxseg=dict( - argstr='--ctxseg %s', - usedefault=True, - ), + ctxseg=dict(argstr='--ctxseg %s', ), environ=dict( nohash=True, usedefault=True, ), - filled=dict(usedefault=True, ), + filled=dict(), hypo_wm=dict(argstr='--hypo-as-wm', ), label_wm=dict(argstr='--labelwm', ), - lh_annotation=dict( - mandatory=True, - usedefault=True, - ), - lh_pial=dict( - mandatory=True, - usedefault=True, - ), - lh_ribbon=dict( - mandatory=True, - usedefault=True, - ), - lh_white=dict( - mandatory=True, - usedefault=True, - ), + lh_annotation=dict(mandatory=True, ), + lh_pial=dict(mandatory=True, ), + lh_ribbon=dict(mandatory=True, ), + lh_white=dict(mandatory=True, ), out_file=dict( argstr='--o %s', mandatory=True, - usedefault=True, - ), - rh_annotation=dict( - mandatory=True, - usedefault=True, - ), - rh_pial=dict( - mandatory=True, - usedefault=True, - ), - rh_ribbon=dict( - mandatory=True, - usedefault=True, - ), - rh_white=dict( - mandatory=True, - usedefault=True, - ), - ribbon=dict( - mandatory=True, - usedefault=True, ), + rh_annotation=dict(mandatory=True, ), + rh_pial=dict(mandatory=True, ), + rh_ribbon=dict(mandatory=True, ), + rh_white=dict(mandatory=True, ), + ribbon=dict(mandatory=True, ), rip_unknown=dict(argstr='--rip-unknown', ), subject_id=dict( argstr='--s %s', mandatory=True, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), volmask=dict(argstr='--volmask', ), ) inputs = Aparc2Aseg.input_spec() @@ -79,11 +45,7 @@ def test_Aparc2Aseg_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Aparc2Aseg_outputs(): - output_map = dict( - out_file=dict( - argstr='%s', - usedefault=True, - ), ) + output_map = dict(out_file=dict(argstr='%s', ), ) outputs = Aparc2Aseg.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py index 7e535391fb..7044fdde2f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py @@ -13,14 +13,12 @@ def test_Apas2Aseg_inputs(): in_file=dict( argstr='--i %s', mandatory=True, - usedefault=True, ), out_file=dict( argstr='--o %s', mandatory=True, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = Apas2Aseg.input_spec() @@ -28,11 +26,7 @@ def test_Apas2Aseg_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Apas2Aseg_outputs(): - output_map = dict( - out_file=dict( - argstr='%s', - usedefault=True, - ), ) + output_map = dict(out_file=dict(argstr='%s', ), ) outputs = Apas2Aseg.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py index 6d71752071..69f56d7dde 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py @@ -14,7 +14,6 @@ def test_ApplyMask_inputs(): argstr='%s', mandatory=True, position=-3, - usedefault=True, ), invert_xfm=dict(argstr='-invert', ), keep_mask_deletion_edits=dict(argstr='-keep_mask_deletion_edits', ), @@ -22,7 +21,6 @@ def test_ApplyMask_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), mask_thresh=dict(argstr='-T %.4f', ), out_file=dict( @@ -32,23 +30,13 @@ def test_ApplyMask_inputs(): name_source=['in_file'], name_template='%s_masked', position=-1, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), transfer=dict(argstr='-transfer %d', ), use_abs=dict(argstr='-abs', ), - xfm_file=dict( - argstr='-xform %s', - usedefault=True, - ), - xfm_source=dict( - argstr='-lta_src %s', - usedefault=True, - ), - xfm_target=dict( - argstr='-lta_dst %s', - usedefault=True, - ), + xfm_file=dict(argstr='-xform %s', ), + xfm_source=dict(argstr='-lta_src %s', ), + xfm_target=dict(argstr='-lta_dst %s', ), ) inputs = ApplyMask.input_spec() @@ -56,7 +44,7 @@ def test_ApplyMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyMask_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ApplyMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py index cb62cf70b7..c9e8f85904 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py @@ -19,7 +19,6 @@ def test_ApplyVolTransform_inputs(): fsl_reg_file=dict( argstr='--fsl %s', mandatory=True, - usedefault=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), ), @@ -32,21 +31,16 @@ def test_ApplyVolTransform_inputs(): lta_file=dict( argstr='--lta %s', mandatory=True, - usedefault=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), ), lta_inv_file=dict( argstr='--lta-inv %s', mandatory=True, - usedefault=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), ), - m3z_file=dict( - argstr='--m3z %s', - usedefault=True, - ), + m3z_file=dict(argstr='--m3z %s', ), mni_152_reg=dict( argstr='--regheader', mandatory=True, @@ -61,7 +55,6 @@ def test_ApplyVolTransform_inputs(): reg_file=dict( argstr='--reg %s', mandatory=True, - usedefault=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), ), @@ -75,7 +68,6 @@ def test_ApplyVolTransform_inputs(): argstr='--mov %s', copyfile=False, mandatory=True, - usedefault=True, ), subject=dict( argstr='--s %s', @@ -83,7 +75,7 @@ def test_ApplyVolTransform_inputs(): xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), tal=dict( argstr='--tal', mandatory=True, @@ -93,18 +85,15 @@ def test_ApplyVolTransform_inputs(): target_file=dict( argstr='--targ %s', mandatory=True, - usedefault=True, xor=('target_file', 'tal', 'fs_target'), ), transformed_file=dict( argstr='--o %s', genfile=True, - usedefault=True, ), xfm_reg_file=dict( argstr='--xfm %s', mandatory=True, - usedefault=True, xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'), ), @@ -115,7 +104,7 @@ def test_ApplyVolTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyVolTransform_outputs(): - output_map = dict(transformed_file=dict(usedefault=True, ), ) + output_map = dict(transformed_file=dict(), ) outputs = ApplyVolTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py index 7b7a6b9229..93db55cd30 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py @@ -13,7 +13,6 @@ def test_Binarize_inputs(): binary_file=dict( argstr='--o %s', genfile=True, - usedefault=True, ), count_file=dict(argstr='--count %s', ), dilate=dict(argstr='--dilate %d', ), @@ -28,23 +27,16 @@ def test_Binarize_inputs(): argstr='--i %s', copyfile=False, mandatory=True, - usedefault=True, ), invert=dict(argstr='--inv', ), - mask_file=dict( - argstr='--mask maskvol', - usedefault=True, - ), + mask_file=dict(argstr='--mask maskvol', ), mask_thresh=dict(argstr='--mask-thresh %f', ), match=dict(argstr='--match %d...', ), max=dict( argstr='--max %f', xor=['wm_ven_csf'], ), - merge_file=dict( - argstr='--merge %s', - usedefault=True, - ), + merge_file=dict(argstr='--merge %s', ), min=dict( argstr='--min %f', xor=['wm_ven_csf'], @@ -52,7 +44,7 @@ def test_Binarize_inputs(): out_type=dict(argstr='', ), rmax=dict(argstr='--rmax %f', ), rmin=dict(argstr='--rmin %f', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ventricles=dict(argstr='--ventricles', ), wm=dict(argstr='--wm', ), wm_ven_csf=dict( @@ -69,8 +61,8 @@ def test_Binarize_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Binarize_outputs(): output_map = dict( - binary_file=dict(usedefault=True, ), - count_file=dict(usedefault=True, ), + binary_file=dict(), + count_file=dict(), ) outputs = Binarize.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py index 9785dd78c1..1cf35fcedb 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py @@ -16,16 +16,9 @@ def test_CALabel_inputs(): argstr='%s', mandatory=True, position=-4, - usedefault=True, - ), - in_vol=dict( - argstr='-r %s', - usedefault=True, - ), - intensities=dict( - argstr='-r %s', - usedefault=True, ), + in_vol=dict(argstr='-r %s', ), + intensities=dict(argstr='-r %s', ), label=dict(argstr='-l %s', ), no_big_ventricles=dict(argstr='-nobigventricles', ), num_threads=dict(), @@ -33,22 +26,19 @@ def test_CALabel_inputs(): argstr='%s', mandatory=True, position=-1, - usedefault=True, ), prior=dict(argstr='-prior %.1f', ), relabel_unlikely=dict(argstr='-relabel_unlikely %d %.1f', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), template=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), transform=dict( argstr='%s', mandatory=True, position=-3, - usedefault=True, ), ) inputs = CALabel.input_spec() @@ -57,7 +47,7 @@ def test_CALabel_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CALabel_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = CALabel.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py index 2a13aa8eb9..0e8ec025ec 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py @@ -10,12 +10,8 @@ def test_CANormalize_inputs(): argstr='%s', mandatory=True, position=-3, - usedefault=True, - ), - control_points=dict( - argstr='-c %s', - usedefault=True, ), + control_points=dict(argstr='-c %s', ), environ=dict( nohash=True, usedefault=True, @@ -24,16 +20,9 @@ def test_CANormalize_inputs(): argstr='%s', mandatory=True, position=-4, - usedefault=True, - ), - long_file=dict( - argstr='-long %s', - usedefault=True, - ), - mask=dict( - argstr='-mask %s', - usedefault=True, ), + long_file=dict(argstr='-long %s', ), + mask=dict(argstr='-mask %s', ), out_file=dict( argstr='%s', hash_files=False, @@ -41,14 +30,12 @@ def test_CANormalize_inputs(): name_source=['in_file'], name_template='%s_norm', position=-1, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), transform=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), ) inputs = CANormalize.input_spec() @@ -58,7 +45,7 @@ def test_CANormalize_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CANormalize_outputs(): output_map = dict( - control_points=dict(usedefault=True, ), + control_points=dict(), out_file=dict(), ) outputs = CANormalize.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py b/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py index 6425104219..e3cbf52f10 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py @@ -16,7 +16,6 @@ def test_CARegister_inputs(): argstr='%s', mandatory=True, position=-3, - usedefault=True, ), invert_and_save=dict( argstr='-invert-and-save', @@ -24,28 +23,20 @@ def test_CARegister_inputs(): ), l_files=dict(argstr='-l %s', ), levels=dict(argstr='-levels %d', ), - mask=dict( - argstr='-mask %s', - usedefault=True, - ), + mask=dict(argstr='-mask %s', ), no_big_ventricles=dict(argstr='-nobigventricles', ), num_threads=dict(), out_file=dict( argstr='%s', genfile=True, position=-1, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), template=dict( argstr='%s', position=-2, - usedefault=True, - ), - transform=dict( - argstr='-T %s', - usedefault=True, ), + transform=dict(argstr='-T %s', ), ) inputs = CARegister.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py index 82072d0635..a7d3ad3bb0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py @@ -14,7 +14,6 @@ def test_CheckTalairachAlignment_inputs(): argstr='-xfm %s', mandatory=True, position=-1, - usedefault=True, xor=['subject'], ), subject=dict( @@ -23,7 +22,7 @@ def test_CheckTalairachAlignment_inputs(): position=-1, xor=['in_file'], ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), threshold=dict( argstr='-T %.3f', usedefault=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py index c7fd82daea..e4e8efb718 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py @@ -11,7 +11,6 @@ def test_Concatenate_inputs(): concatenated_file=dict( argstr='--o %s', genfile=True, - usedefault=True, ), environ=dict( nohash=True, @@ -23,23 +22,17 @@ def test_Concatenate_inputs(): mandatory=True, ), keep_dtype=dict(argstr='--keep-datatype', ), - mask_file=dict( - argstr='--mask %s', - usedefault=True, - ), + mask_file=dict(argstr='--mask %s', ), max_bonfcor=dict(argstr='--max-bonfcor', ), max_index=dict(argstr='--max-index', ), mean_div_n=dict(argstr='--mean-div-n', ), multiply_by=dict(argstr='--mul %f', ), - multiply_matrix_file=dict( - argstr='--mtx %s', - usedefault=True, - ), + multiply_matrix_file=dict(argstr='--mtx %s', ), paired_stats=dict(argstr='--paired-%s', ), sign=dict(argstr='--%s', ), sort=dict(argstr='--sort', ), stats=dict(argstr='--%s', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), vote=dict(argstr='--vote', ), ) inputs = Concatenate.input_spec() @@ -48,7 +41,7 @@ def test_Concatenate_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Concatenate_outputs(): - output_map = dict(concatenated_file=dict(usedefault=True, ), ) + output_map = dict(concatenated_file=dict(), ) outputs = Concatenate.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py b/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py index 50806c9a5d..40a465b249 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py @@ -14,7 +14,6 @@ def test_ConcatenateLTA_inputs(): argstr='%s', mandatory=True, position=-3, - usedefault=True, ), in_lta2=dict( argstr='%s', @@ -31,11 +30,10 @@ def test_ConcatenateLTA_inputs(): name_source=['in_lta1'], name_template='%s_concat', position=-1, - usedefault=True, ), out_type=dict(argstr='-out_type %d', ), subject=dict(argstr='-subject %s', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), tal_source_file=dict( argstr='-tal %s', position=-5, @@ -53,7 +51,7 @@ def test_ConcatenateLTA_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConcatenateLTA_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ConcatenateLTA.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py index a8b530cf5e..7999001813 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py @@ -17,28 +17,16 @@ def test_Contrast_inputs(): argstr='--%s-only', mandatory=True, ), - orig=dict( - mandatory=True, - usedefault=True, - ), - rawavg=dict( - mandatory=True, - usedefault=True, - ), + orig=dict(mandatory=True, ), + rawavg=dict(mandatory=True, ), subject_id=dict( argstr='--s %s', mandatory=True, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), - thickness=dict( - mandatory=True, - usedefault=True, - ), - white=dict( - mandatory=True, - usedefault=True, - ), + subjects_dir=dict(), + thickness=dict(mandatory=True, ), + white=dict(mandatory=True, ), ) inputs = Contrast.input_spec() @@ -47,9 +35,9 @@ def test_Contrast_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Contrast_outputs(): output_map = dict( - out_contrast=dict(usedefault=True, ), - out_log=dict(usedefault=True, ), - out_stats=dict(usedefault=True, ), + out_contrast=dict(), + out_log=dict(), + out_stats=dict(), ) outputs = Contrast.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py b/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py index 9bfad24622..f29b76df29 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py @@ -18,11 +18,10 @@ def test_Curvature_inputs(): copyfile=True, mandatory=True, position=-2, - usedefault=True, ), n=dict(argstr='-n', ), save=dict(argstr='-w', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), threshold=dict(argstr='-thresh %.3f', ), ) inputs = Curvature.input_spec() @@ -32,8 +31,8 @@ def test_Curvature_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Curvature_outputs(): output_map = dict( - out_gauss=dict(usedefault=True, ), - out_mean=dict(usedefault=True, ), + out_gauss=dict(), + out_mean=dict(), ) outputs = Curvature.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py b/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py index e42db217a4..19d6a4772e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py @@ -11,13 +11,11 @@ def test_CurvatureStats_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), curvfile2=dict( argstr='%s', mandatory=True, position=-1, - usedefault=True, ), environ=dict( nohash=True, @@ -34,7 +32,6 @@ def test_CurvatureStats_inputs(): hash_files=False, name_source=['hemisphere'], name_template='%s.curv.stats', - usedefault=True, ), subject_id=dict( argstr='%s', @@ -42,11 +39,8 @@ def test_CurvatureStats_inputs(): position=-4, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), - surface=dict( - argstr='-F %s', - usedefault=True, - ), + subjects_dir=dict(), + surface=dict(argstr='-F %s', ), values=dict(argstr='-G', ), write=dict(argstr='--writeCurvatureFiles', ), ) @@ -56,7 +50,7 @@ def test_CurvatureStats_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CurvatureStats_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = CurvatureStats.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py index c4b0f2667f..efd53fb773 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py @@ -6,15 +6,9 @@ def test_DICOMConvert_inputs(): input_map = dict( args=dict(argstr='%s', ), - base_output_dir=dict( - mandatory=True, - usedefault=True, - ), - dicom_dir=dict( - mandatory=True, - usedefault=True, - ), - dicom_info=dict(usedefault=True, ), + base_output_dir=dict(mandatory=True, ), + dicom_dir=dict(mandatory=True, ), + dicom_info=dict(), environ=dict( nohash=True, usedefault=True, @@ -25,7 +19,7 @@ def test_DICOMConvert_inputs(): seq_list=dict(requires=['dicom_info'], ), subject_dir_template=dict(usedefault=True, ), subject_id=dict(), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = DICOMConvert.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py index 2323f7ae24..e681a03871 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py @@ -14,12 +14,8 @@ def test_EMRegister_inputs(): argstr='%s', mandatory=True, position=-3, - usedefault=True, - ), - mask=dict( - argstr='-mask %s', - usedefault=True, ), + mask=dict(argstr='-mask %s', ), nbrspacing=dict(argstr='-uns %d', ), num_threads=dict(), out_file=dict( @@ -29,20 +25,15 @@ def test_EMRegister_inputs(): name_source=['in_file'], name_template='%s_transform.lta', position=-1, - usedefault=True, ), skull=dict(argstr='-skull', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), template=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, - ), - transform=dict( - argstr='-t %s', - usedefault=True, ), + transform=dict(argstr='-t %s', ), ) inputs = EMRegister.input_spec() @@ -50,7 +41,7 @@ def test_EMRegister_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EMRegister_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = EMRegister.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py b/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py index c24f977b00..f971f4fab9 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py @@ -10,7 +10,6 @@ def test_EditWMwithAseg_inputs(): argstr='%s', mandatory=True, position=-3, - usedefault=True, ), environ=dict( nohash=True, @@ -20,22 +19,19 @@ def test_EditWMwithAseg_inputs(): argstr='%s', mandatory=True, position=-4, - usedefault=True, ), keep_in=dict(argstr='-keep-in', ), out_file=dict( argstr='%s', mandatory=True, position=-1, - usedefault=True, ), seg_file=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = EditWMwithAseg.input_spec() @@ -43,7 +39,7 @@ def test_EditWMwithAseg_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EditWMwithAseg_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = EditWMwithAseg.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py b/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py index 3a14dea036..996d079b48 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py @@ -14,9 +14,8 @@ def test_EulerNumber_inputs(): argstr='%s', mandatory=True, position=-1, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = EulerNumber.input_spec() @@ -24,7 +23,7 @@ def test_EulerNumber_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EulerNumber_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = EulerNumber.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py index 1415471ab3..f3f4896a75 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py @@ -14,14 +14,12 @@ def test_ExtractMainComponent_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), out_file=dict( argstr='%s', name_source='in_file', name_template='%s.maincmp', position=2, - usedefault=True, ), ) inputs = ExtractMainComponent.input_spec() @@ -30,7 +28,7 @@ def test_ExtractMainComponent_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ExtractMainComponent_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ExtractMainComponent.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py index 98fe0664ae..0546d99006 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py @@ -10,7 +10,7 @@ def test_FSCommand_inputs(): nohash=True, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = FSCommand.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py b/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py index 97de836a9e..5b8bca1484 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py @@ -11,7 +11,7 @@ def test_FSCommandOpenMP_inputs(): usedefault=True, ), num_threads=dict(), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = FSCommandOpenMP.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py b/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py index 0df666e23c..e791bb5976 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py @@ -10,7 +10,7 @@ def test_FSScriptCommand_inputs(): nohash=True, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = FSScriptCommand.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py index 01687c2eff..9e6b1cbc8b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py @@ -20,9 +20,8 @@ def test_FitMSParams_inputs(): argstr='%s', genfile=True, position=-1, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), te_list=dict(), tr_list=dict(), xfm_list=dict(), @@ -34,9 +33,9 @@ def test_FitMSParams_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FitMSParams_outputs(): output_map = dict( - pd_image=dict(usedefault=True, ), - t1_image=dict(usedefault=True, ), - t2star_image=dict(usedefault=True, ), + pd_image=dict(), + t1_image=dict(), + t2star_image=dict(), ) outputs = FitMSParams.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py index 9ef951e5d8..8b61823b42 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py @@ -17,22 +17,10 @@ def test_FixTopology_inputs(): mandatory=True, position=-1, ), - in_brain=dict( - mandatory=True, - usedefault=True, - ), - in_inflated=dict( - mandatory=True, - usedefault=True, - ), - in_orig=dict( - mandatory=True, - usedefault=True, - ), - in_wm=dict( - mandatory=True, - usedefault=True, - ), + in_brain=dict(mandatory=True, ), + in_inflated=dict(mandatory=True, ), + in_orig=dict(mandatory=True, ), + in_wm=dict(mandatory=True, ), mgz=dict(argstr='-mgz', ), seed=dict(argstr='-seed %d', ), sphere=dict(argstr='-sphere %s', ), @@ -42,7 +30,7 @@ def test_FixTopology_inputs(): position=-2, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = FixTopology.input_spec() @@ -50,7 +38,7 @@ def test_FixTopology_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FixTopology_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = FixTopology.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py b/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py index 0c1dd31a66..8608444fc8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py @@ -25,13 +25,12 @@ def test_FuseSegmentations_inputs(): out_file=dict( mandatory=True, position=-1, - usedefault=True, ), subject_id=dict( argstr='%s', position=-3, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), timepoints=dict( argstr='%s', mandatory=True, @@ -44,7 +43,7 @@ def test_FuseSegmentations_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FuseSegmentations_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = FuseSegmentations.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py index de629db007..828bbfab03 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py @@ -19,7 +19,6 @@ def test_GLMFit_inputs(): debug=dict(argstr='--debug', ), design=dict( argstr='--X %s', - usedefault=True, xor=('fsgd', 'design', 'one_sample'), ), diag=dict(argstr='--diag %d', ), @@ -34,13 +33,9 @@ def test_GLMFit_inputs(): ), fixed_fx_dof_file=dict( argstr='--ffxdofdat %d', - usedefault=True, xor=['fixed_fx_dof'], ), - fixed_fx_var=dict( - argstr='--yffxvar %s', - usedefault=True, - ), + fixed_fx_var=dict(argstr='--yffxvar %s', ), force_perm=dict(argstr='--perm-force', ), fsgd=dict( argstr='--fsgd %s %s', @@ -56,18 +51,13 @@ def test_GLMFit_inputs(): argstr='--y %s', copyfile=False, mandatory=True, - usedefault=True, ), invert_mask=dict(argstr='--mask-inv', ), label_file=dict( argstr='--label %s', - usedefault=True, xor=['cortex'], ), - mask_file=dict( - argstr='--mask %s', - usedefault=True, - ), + mask_file=dict(argstr='--mask %s', ), no_contrast_ok=dict(argstr='--no-contrasts-ok', ), no_est_fwhm=dict(argstr='--no-est-fwhm', ), no_mask_smooth=dict(argstr='--no-mask-smooth', ), @@ -94,14 +84,11 @@ def test_GLMFit_inputs(): save_residual=dict(argstr='--eres-save', ), seed=dict(argstr='--seed %d', ), self_reg=dict(argstr='--selfreg %d %d %d', ), - sim_done_file=dict( - argstr='--sim-done %s', - usedefault=True, - ), + sim_done_file=dict(argstr='--sim-done %s', ), sim_sign=dict(argstr='--sim-sign %s', ), simulation=dict(argstr='--sim %s %d %f %s', ), subject_id=dict(), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), surf=dict( argstr='--surf %s %s %s', requires=['subject_id', 'hemi'], @@ -111,10 +98,7 @@ def test_GLMFit_inputs(): uniform=dict(argstr='--uniform %f %f', ), var_fwhm=dict(argstr='--var-fwhm %f', ), vox_dump=dict(argstr='--voxdump %d %d %d', ), - weight_file=dict( - usedefault=True, - xor=['weighted_ls'], - ), + weight_file=dict(xor=['weighted_ls'], ), weight_inv=dict( argstr='--w-inv', xor=['weighted_ls'], @@ -125,7 +109,6 @@ def test_GLMFit_inputs(): ), weighted_ls=dict( argstr='--wls %s', - usedefault=True, xor=('weight_file', 'weight_inv', 'weight_sqrt'), ), ) @@ -136,23 +119,23 @@ def test_GLMFit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_GLMFit_outputs(): output_map = dict( - beta_file=dict(usedefault=True, ), - dof_file=dict(usedefault=True, ), - error_file=dict(usedefault=True, ), - error_stddev_file=dict(usedefault=True, ), - error_var_file=dict(usedefault=True, ), - estimate_file=dict(usedefault=True, ), - frame_eigenvectors=dict(usedefault=True, ), + beta_file=dict(), + dof_file=dict(), + error_file=dict(), + error_stddev_file=dict(), + error_var_file=dict(), + estimate_file=dict(), + frame_eigenvectors=dict(), ftest_file=dict(), - fwhm_file=dict(usedefault=True, ), + fwhm_file=dict(), gamma_file=dict(), gamma_var_file=dict(), - glm_dir=dict(usedefault=True, ), - mask_file=dict(usedefault=True, ), + glm_dir=dict(), + mask_file=dict(), sig_file=dict(), - singular_values=dict(usedefault=True, ), - spatial_eigenvectors=dict(usedefault=True, ), - svd_stats_file=dict(usedefault=True, ), + singular_values=dict(), + spatial_eigenvectors=dict(), + svd_stats_file=dict(), ) outputs = GLMFit.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py index 58e987f6a4..2fa225e87e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py @@ -13,9 +13,8 @@ def test_ImageInfo_inputs(): in_file=dict( argstr='%s', position=1, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = ImageInfo.input_spec() @@ -32,7 +31,7 @@ def test_ImageInfo_outputs(): file_format=dict(), info=dict(), orientation=dict(), - out_file=dict(usedefault=True, ), + out_file=dict(), ph_enc_dir=dict(), vox_sizes=dict(), ) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py b/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py index 22c3fed709..49f5e6b48f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py @@ -14,13 +14,11 @@ def test_Jacobian_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), in_origsurf=dict( argstr='%s', mandatory=True, position=-3, - usedefault=True, ), out_file=dict( argstr='%s', @@ -29,9 +27,8 @@ def test_Jacobian_inputs(): name_source=['in_origsurf'], name_template='%s.jacobian', position=-1, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = Jacobian.input_spec() @@ -39,7 +36,7 @@ def test_Jacobian_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Jacobian_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Jacobian.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py index a0876c3e13..bcbf971d01 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py @@ -13,14 +13,12 @@ def test_LTAConvert_inputs(): in_fsl=dict( argstr='--infsl %s', mandatory=True, - usedefault=True, xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'), ), in_itk=dict( argstr='--initk %s', mandatory=True, - usedefault=True, xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'), ), @@ -33,21 +31,18 @@ def test_LTAConvert_inputs(): in_mni=dict( argstr='--inmni %s', mandatory=True, - usedefault=True, xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'), ), in_niftyreg=dict( argstr='--inniftyreg %s', mandatory=True, - usedefault=True, xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'), ), in_reg=dict( argstr='--inreg %s', mandatory=True, - usedefault=True, xor=('in_lta', 'in_fsl', 'in_mni', 'in_reg', 'in_niftyreg', 'in_itk'), ), @@ -61,15 +56,9 @@ def test_LTAConvert_inputs(): out_lta=dict(argstr='--outlta %s', ), out_mni=dict(argstr='--outmni %s', ), out_reg=dict(argstr='--outreg %s', ), - source_file=dict( - argstr='--src %s', - usedefault=True, - ), + source_file=dict(argstr='--src %s', ), target_conform=dict(argstr='--trgconform', ), - target_file=dict( - argstr='--trg %s', - usedefault=True, - ), + target_file=dict(argstr='--trg %s', ), ) inputs = LTAConvert.input_spec() @@ -78,11 +67,11 @@ def test_LTAConvert_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_LTAConvert_outputs(): output_map = dict( - out_fsl=dict(usedefault=True, ), - out_itk=dict(usedefault=True, ), - out_lta=dict(usedefault=True, ), - out_mni=dict(usedefault=True, ), - out_reg=dict(usedefault=True, ), + out_fsl=dict(), + out_itk=dict(), + out_lta=dict(), + out_mni=dict(), + out_reg=dict(), ) outputs = LTAConvert.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py index 1e4ef551f9..2d7761006b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py @@ -6,10 +6,7 @@ def test_Label2Annot_inputs(): input_map = dict( args=dict(argstr='%s', ), - color_table=dict( - argstr='--ctab %s', - usedefault=True, - ), + color_table=dict(argstr='--ctab %s', ), copy_inputs=dict(), environ=dict( nohash=True, @@ -24,10 +21,7 @@ def test_Label2Annot_inputs(): mandatory=True, ), keep_max=dict(argstr='--maxstatwinner', ), - orig=dict( - mandatory=True, - usedefault=True, - ), + orig=dict(mandatory=True, ), out_annot=dict( argstr='--a %s', mandatory=True, @@ -37,7 +31,7 @@ def test_Label2Annot_inputs(): mandatory=True, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), verbose_off=dict(argstr='--noverbose', ), ) inputs = Label2Annot.input_spec() @@ -46,7 +40,7 @@ def test_Label2Annot_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Label2Annot_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Label2Annot.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py index e62b00a7cb..7511cd0dbb 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py @@ -21,7 +21,6 @@ def test_Label2Label_inputs(): keep_extension=True, name_source=['source_label'], name_template='%s_converted', - usedefault=True, ), registration_method=dict( argstr='--regmethod %s', @@ -30,34 +29,21 @@ def test_Label2Label_inputs(): source_label=dict( argstr='--srclabel %s', mandatory=True, - usedefault=True, - ), - source_sphere_reg=dict( - mandatory=True, - usedefault=True, ), + source_sphere_reg=dict(mandatory=True, ), source_subject=dict( argstr='--srcsubject %s', mandatory=True, ), - source_white=dict( - mandatory=True, - usedefault=True, - ), - sphere_reg=dict( - mandatory=True, - usedefault=True, - ), + source_white=dict(mandatory=True, ), + sphere_reg=dict(mandatory=True, ), subject_id=dict( argstr='--trgsubject %s', mandatory=True, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), - white=dict( - mandatory=True, - usedefault=True, - ), + subjects_dir=dict(), + white=dict(mandatory=True, ), ) inputs = Label2Label.input_spec() @@ -65,7 +51,7 @@ def test_Label2Label_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Label2Label_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Label2Label.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py index dc17d6a604..fb2726635f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py @@ -10,7 +10,6 @@ def test_Label2Vol_inputs(): copyfile=False, mandatory=True, requires=('subject_id', 'hemi'), - usedefault=True, xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'), ), aparc_aseg=dict( @@ -36,15 +35,9 @@ def test_Label2Vol_inputs(): mandatory=True, xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'), ), - label_hit_file=dict( - argstr='--hits %s', - usedefault=True, - ), + label_hit_file=dict(argstr='--hits %s', ), label_voxel_volume=dict(argstr='--labvoxvol %f', ), - map_label_stat=dict( - argstr='--label-stat %s', - usedefault=True, - ), + map_label_stat=dict(argstr='--label-stat %s', ), native_vox2ras=dict(argstr='--native-vox2ras', ), proj=dict( argstr='--proj %s %f %f %f', @@ -52,33 +45,28 @@ def test_Label2Vol_inputs(): ), reg_file=dict( argstr='--reg %s', - usedefault=True, xor=('reg_file', 'reg_header', 'identity'), ), reg_header=dict( argstr='--regheader %s', - usedefault=True, xor=('reg_file', 'reg_header', 'identity'), ), seg_file=dict( argstr='--seg %s', copyfile=False, mandatory=True, - usedefault=True, xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'), ), subject_id=dict(argstr='--subject %s', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), surface=dict(argstr='--surf %s', ), template_file=dict( argstr='--temp %s', mandatory=True, - usedefault=True, ), vol_label_file=dict( argstr='--o %s', genfile=True, - usedefault=True, ), ) inputs = Label2Vol.input_spec() @@ -87,7 +75,7 @@ def test_Label2Vol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Label2Vol_outputs(): - output_map = dict(vol_label_file=dict(usedefault=True, ), ) + output_map = dict(vol_label_file=dict(), ) outputs = Label2Vol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py b/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py index 986c4e808c..7b6ae4a945 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py @@ -14,16 +14,12 @@ def test_MNIBiasCorrection_inputs(): in_file=dict( argstr='--i %s', mandatory=True, - usedefault=True, ), iterations=dict( argstr='--n %d', usedefault=True, ), - mask=dict( - argstr='--mask %s', - usedefault=True, - ), + mask=dict(argstr='--mask %s', ), no_rescale=dict(argstr='--no-rescale', ), out_file=dict( argstr='--o %s', @@ -31,16 +27,12 @@ def test_MNIBiasCorrection_inputs(): keep_extension=True, name_source=['in_file'], name_template='%s_output', - usedefault=True, ), protocol_iterations=dict(argstr='--proto-iters %d', ), shrink=dict(argstr='--shrink %d', ), stop=dict(argstr='--stop %f', ), - subjects_dir=dict(usedefault=True, ), - transform=dict( - argstr='--uchar %s', - usedefault=True, - ), + subjects_dir=dict(), + transform=dict(argstr='--uchar %s', ), ) inputs = MNIBiasCorrection.input_spec() @@ -48,7 +40,7 @@ def test_MNIBiasCorrection_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MNIBiasCorrection_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MNIBiasCorrection.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py b/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py index c712a08211..b4b7436120 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py @@ -18,7 +18,7 @@ def test_MPRtoMNI305_inputs(): mandatory=True, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), target=dict( mandatory=True, usedefault=True, @@ -32,7 +32,7 @@ def test_MPRtoMNI305_inputs(): def test_MPRtoMNI305_outputs(): output_map = dict( log_file=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), + out_file=dict(), ) outputs = MPRtoMNI305.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py index 911702da45..b44cf7a308 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py @@ -5,24 +5,12 @@ def test_MRIConvert_inputs(): input_map = dict( - apply_inv_transform=dict( - argstr='--apply_inverse_transform %s', - usedefault=True, - ), - apply_transform=dict( - argstr='--apply_transform %s', - usedefault=True, - ), + apply_inv_transform=dict(argstr='--apply_inverse_transform %s', ), + apply_transform=dict(argstr='--apply_transform %s', ), args=dict(argstr='%s', ), ascii=dict(argstr='--ascii', ), - autoalign_matrix=dict( - argstr='--autoalign %s', - usedefault=True, - ), - color_file=dict( - argstr='--color_file %s', - usedefault=True, - ), + autoalign_matrix=dict(argstr='--autoalign %s', ), + color_file=dict(argstr='--color_file %s', ), conform=dict(argstr='--conform', ), conform_min=dict(argstr='--conform_min', ), conform_size=dict(argstr='--conform_size %s', ), @@ -47,7 +35,6 @@ def test_MRIConvert_inputs(): argstr='--input_volume %s', mandatory=True, position=-2, - usedefault=True, ), in_i_dir=dict(argstr='--in_i_direction %f %f %f', ), in_i_size=dict(argstr='--in_i_size %d', ), @@ -56,10 +43,7 @@ def test_MRIConvert_inputs(): in_j_size=dict(argstr='--in_j_size %d', ), in_k_dir=dict(argstr='--in_k_direction %f %f %f', ), in_k_size=dict(argstr='--in_k_size %d', ), - in_like=dict( - argstr='--in_like %s', - usedefault=True, - ), + in_like=dict(argstr='--in_like %s', ), in_matrix=dict(argstr='--in_matrix', ), in_orientation=dict(argstr='--in_orientation %s', ), in_scale=dict(argstr='--scale %f', ), @@ -77,7 +61,6 @@ def test_MRIConvert_inputs(): argstr='--output_volume %s', genfile=True, position=-1, - usedefault=True, ), out_i_count=dict(argstr='--out_i_count %d', ), out_i_dir=dict(argstr='--out_i_direction %f %f %f', ), @@ -98,14 +81,8 @@ def test_MRIConvert_inputs(): read_only=dict(argstr='--read_only', ), reorder=dict(argstr='--reorder %d %d %d', ), resample_type=dict(argstr='--resample_type %s', ), - reslice_like=dict( - argstr='--reslice_like %s', - usedefault=True, - ), - sdcm_list=dict( - argstr='--sdcmlist %s', - usedefault=True, - ), + reslice_like=dict(argstr='--reslice_like %s', ), + sdcm_list=dict(argstr='--sdcmlist %s', ), skip_n=dict(argstr='--nskip %d', ), slice_bias=dict(argstr='--slice-bias %f', ), slice_crop=dict(argstr='--slice-crop %d %d', ), @@ -113,12 +90,9 @@ def test_MRIConvert_inputs(): smooth_parcellation=dict(argstr='--smooth_parcellation', ), sphinx=dict(argstr='--sphinx', ), split=dict(argstr='--split', ), - status_file=dict( - argstr='--status %s', - usedefault=True, - ), + status_file=dict(argstr='--status %s', ), subject_name=dict(argstr='--subject_name %s', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), te=dict(argstr='-te %d', ), template_info=dict(argstr='--template_info', ), template_type=dict(argstr='--template_type %s', ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py b/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py index c80c21b614..6c12cabdc2 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py @@ -44,7 +44,6 @@ def test_MRICoreg_inputs(): argstr='--ref %s', copyfile=False, mandatory=True, - usedefault=True, xor=['subject_id'], ), reference_mask=dict( @@ -57,7 +56,6 @@ def test_MRICoreg_inputs(): argstr='--mov %s', copyfile=False, mandatory=True, - usedefault=True, ), source_mask=dict(argstr='--mov-mask', ), source_oob=dict(argstr='--mov-oob', ), @@ -68,10 +66,7 @@ def test_MRICoreg_inputs(): requires=['subjects_dir'], xor=['reference_file'], ), - subjects_dir=dict( - argstr='--sd %s', - usedefault=True, - ), + subjects_dir=dict(argstr='--sd %s', ), ) inputs = MRICoreg.input_spec() @@ -80,9 +75,9 @@ def test_MRICoreg_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MRICoreg_outputs(): output_map = dict( - out_lta_file=dict(usedefault=True, ), - out_params_file=dict(usedefault=True, ), - out_reg_file=dict(usedefault=True, ), + out_lta_file=dict(), + out_params_file=dict(), + out_reg_file=dict(), ) outputs = MRICoreg.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py index 79057d3233..719986961d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py @@ -14,27 +14,16 @@ def test_MRIFill_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, - ), - log_file=dict( - argstr='-a %s', - usedefault=True, ), + log_file=dict(argstr='-a %s', ), out_file=dict( argstr='%s', mandatory=True, position=-1, - usedefault=True, - ), - segmentation=dict( - argstr='-segmentation %s', - usedefault=True, - ), - subjects_dir=dict(usedefault=True, ), - transform=dict( - argstr='-xform %s', - usedefault=True, ), + segmentation=dict(argstr='-segmentation %s', ), + subjects_dir=dict(), + transform=dict(argstr='-xform %s', ), ) inputs = MRIFill.input_spec() @@ -43,8 +32,8 @@ def test_MRIFill_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MRIFill_outputs(): output_map = dict( - log_file=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), + log_file=dict(), + out_file=dict(), ) outputs = MRIFill.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py index 84164b8ddf..f43d217256 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py @@ -19,7 +19,6 @@ def test_MRIMarchingCubes_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), label_value=dict( argstr='%d', @@ -30,9 +29,8 @@ def test_MRIMarchingCubes_inputs(): argstr='./%s', genfile=True, position=-2, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = MRIMarchingCubes.input_spec() @@ -40,7 +38,7 @@ def test_MRIMarchingCubes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIMarchingCubes_outputs(): - output_map = dict(surface=dict(usedefault=True, ), ) + output_map = dict(surface=dict(), ) outputs = MRIMarchingCubes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py index 682dbd68f4..2e7c7d2ea5 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py @@ -14,13 +14,11 @@ def test_MRIPretess_inputs(): argstr='%s', mandatory=True, position=-4, - usedefault=True, ), in_norm=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), keep=dict(argstr='-keep', ), label=dict( @@ -36,9 +34,8 @@ def test_MRIPretess_inputs(): name_source=['in_filled'], name_template='%s_pretesswm', position=-1, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), test=dict(argstr='-test', ), ) inputs = MRIPretess.input_spec() @@ -47,7 +44,7 @@ def test_MRIPretess_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIPretess_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MRIPretess.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py index 99b60abfcd..c92b4fea15 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py @@ -12,7 +12,6 @@ def test_MRISPreproc_inputs(): ), fsgd_file=dict( argstr='--fsgd %s', - usedefault=True, xor=('subjects', 'fsgd_file', 'subject_file'), ), fwhm=dict( @@ -38,21 +37,19 @@ def test_MRISPreproc_inputs(): out_file=dict( argstr='--out %s', genfile=True, - usedefault=True, ), proj_frac=dict(argstr='--projfrac %s', ), smooth_cortex_only=dict(argstr='--smooth-cortex-only', ), source_format=dict(argstr='--srcfmt %s', ), subject_file=dict( argstr='--f %s', - usedefault=True, xor=('subjects', 'fsgd_file', 'subject_file'), ), subjects=dict( argstr='--s %s...', xor=('subjects', 'fsgd_file', 'subject_file'), ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), surf_area=dict( argstr='--area %s', xor=('surf_measure', 'surf_measure_file', 'surf_area'), @@ -78,7 +75,7 @@ def test_MRISPreproc_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRISPreproc_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MRISPreproc.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py index 8074cd14b2..e72d8adb9e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py @@ -13,7 +13,6 @@ def test_MRISPreprocReconAll_inputs(): ), fsgd_file=dict( argstr='--fsgd %s', - usedefault=True, xor=('subjects', 'fsgd_file', 'subject_file'), ), fwhm=dict( @@ -28,10 +27,7 @@ def test_MRISPreprocReconAll_inputs(): argstr='--hemi %s', mandatory=True, ), - lh_surfreg_target=dict( - requires=['surfreg_files'], - usedefault=True, - ), + lh_surfreg_target=dict(requires=['surfreg_files'], ), num_iters=dict( argstr='--niters %d', xor=['fwhm'], @@ -43,18 +39,13 @@ def test_MRISPreprocReconAll_inputs(): out_file=dict( argstr='--out %s', genfile=True, - usedefault=True, ), proj_frac=dict(argstr='--projfrac %s', ), - rh_surfreg_target=dict( - requires=['surfreg_files'], - usedefault=True, - ), + rh_surfreg_target=dict(requires=['surfreg_files'], ), smooth_cortex_only=dict(argstr='--smooth-cortex-only', ), source_format=dict(argstr='--srcfmt %s', ), subject_file=dict( argstr='--f %s', - usedefault=True, xor=('subjects', 'fsgd_file', 'subject_file'), ), subject_id=dict( @@ -66,7 +57,7 @@ def test_MRISPreprocReconAll_inputs(): argstr='--s %s...', xor=('subjects', 'fsgd_file', 'subject_file'), ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), surf_area=dict( argstr='--area %s', xor=('surf_measure', 'surf_measure_file', 'surf_area'), @@ -78,7 +69,6 @@ def test_MRISPreprocReconAll_inputs(): ), surf_measure_file=dict( argstr='--meas %s', - usedefault=True, xor=('surf_measure', 'surf_measure_file', 'surf_area'), ), surfreg_files=dict( @@ -97,7 +87,7 @@ def test_MRISPreprocReconAll_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRISPreprocReconAll_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MRISPreprocReconAll.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py index 40cc4a8c4e..a5899cfe70 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py @@ -14,7 +14,6 @@ def test_MRITessellate_inputs(): argstr='%s', mandatory=True, position=-3, - usedefault=True, ), label_value=dict( argstr='%d', @@ -25,9 +24,8 @@ def test_MRITessellate_inputs(): argstr='%s', genfile=True, position=-1, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), tesselate_all_voxels=dict(argstr='-a', ), use_real_RAS_coordinates=dict(argstr='-n', ), ) @@ -37,7 +35,7 @@ def test_MRITessellate_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRITessellate_outputs(): - output_map = dict(surface=dict(usedefault=True, ), ) + output_map = dict(surface=dict(), ) outputs = MRITessellate.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py index 0d9af752e7..441be3e0a4 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py @@ -11,19 +11,14 @@ def test_MRIsCALabel_inputs(): argstr='%s', mandatory=True, position=-3, - usedefault=True, ), classifier=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), copy_inputs=dict(), - curv=dict( - mandatory=True, - usedefault=True, - ), + curv=dict(mandatory=True, ), environ=dict( nohash=True, usedefault=True, @@ -42,24 +37,17 @@ def test_MRIsCALabel_inputs(): name_source=['hemisphere'], name_template='%s.aparc.annot', position=-1, - usedefault=True, ), seed=dict(argstr='-seed %d', ), - smoothwm=dict( - mandatory=True, - usedefault=True, - ), + smoothwm=dict(mandatory=True, ), subject_id=dict( argstr='%s', mandatory=True, position=-5, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), - sulc=dict( - mandatory=True, - usedefault=True, - ), + subjects_dir=dict(), + sulc=dict(mandatory=True, ), ) inputs = MRIsCALabel.input_spec() @@ -67,7 +55,7 @@ def test_MRIsCALabel_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsCALabel_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MRIsCALabel.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py index 7c0f19b38a..cbd68c8457 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py @@ -19,12 +19,10 @@ def test_MRIsCalc_inputs(): argstr='%s', mandatory=True, position=-3, - usedefault=True, ), in_file2=dict( argstr='%s', position=-1, - usedefault=True, xor=['in_float', 'in_int'], ), in_float=dict( @@ -40,9 +38,8 @@ def test_MRIsCalc_inputs(): out_file=dict( argstr='-o %s', mandatory=True, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = MRIsCalc.input_spec() @@ -50,7 +47,7 @@ def test_MRIsCalc_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsCalc_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MRIsCalc.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py index e63dde7322..657292c5c7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py @@ -20,9 +20,8 @@ def test_MRIsCombine_inputs(): genfile=True, mandatory=True, position=-1, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = MRIsCombine.input_spec() @@ -30,7 +29,7 @@ def test_MRIsCombine_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsCombine_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MRIsCombine.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py index 5e8aef895b..21622b2449 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py @@ -5,34 +5,21 @@ def test_MRIsConvert_inputs(): input_map = dict( - annot_file=dict( - argstr='--annot %s', - usedefault=True, - ), + annot_file=dict(argstr='--annot %s', ), args=dict(argstr='%s', ), dataarray_num=dict(argstr='--da_num %d', ), environ=dict( nohash=True, usedefault=True, ), - functional_file=dict( - argstr='-f %s', - usedefault=True, - ), + functional_file=dict(argstr='-f %s', ), in_file=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, - ), - label_file=dict( - argstr='--label %s', - usedefault=True, - ), - labelstats_outfile=dict( - argstr='--labelstats %s', - usedefault=True, ), + label_file=dict(argstr='--label %s', ), + labelstats_outfile=dict(argstr='--labelstats %s', ), normal=dict(argstr='-n', ), origname=dict(argstr='-o %s', ), out_datatype=dict( @@ -44,21 +31,14 @@ def test_MRIsConvert_inputs(): genfile=True, mandatory=True, position=-1, - usedefault=True, xor=['out_datatype'], ), - parcstats_file=dict( - argstr='--parcstats %s', - usedefault=True, - ), + parcstats_file=dict(argstr='--parcstats %s', ), patch=dict(argstr='-p', ), rescale=dict(argstr='-r', ), - scalarcurv_file=dict( - argstr='-c %s', - usedefault=True, - ), + scalarcurv_file=dict(argstr='-c %s', ), scale=dict(argstr='-s %.3f', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), talairachxfm_subjid=dict(argstr='-t %s', ), to_scanner=dict(argstr='--to-scanner', ), to_tkr=dict(argstr='--to-tkr', ), @@ -71,7 +51,7 @@ def test_MRIsConvert_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsConvert_outputs(): - output_map = dict(converted=dict(usedefault=True, ), ) + output_map = dict(converted=dict(), ) outputs = MRIsConvert.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py index 5c09580639..8639c1e7b6 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py @@ -21,7 +21,6 @@ def test_MRIsExpand_inputs(): copyfile=False, mandatory=True, position=-3, - usedefault=True, ), nsurfaces=dict(argstr='-N %d', ), out_name=dict( @@ -39,7 +38,7 @@ def test_MRIsExpand_inputs(): usedefault=True, ), spring=dict(argstr='-S %g', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), thickness=dict(argstr='-thickness', ), thickness_name=dict( argstr='-thickness_name %s', @@ -53,7 +52,7 @@ def test_MRIsExpand_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsExpand_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MRIsExpand.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py index ef736757cb..73e48a2521 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py @@ -15,7 +15,6 @@ def test_MRIsInflate_inputs(): copyfile=True, mandatory=True, position=-2, - usedefault=True, ), no_save_sulc=dict( argstr='-no-save-sulc', @@ -28,13 +27,9 @@ def test_MRIsInflate_inputs(): name_source=['in_file'], name_template='%s.inflated', position=-1, - usedefault=True, - ), - out_sulc=dict( - usedefault=True, - xor=['no_save_sulc'], ), - subjects_dir=dict(usedefault=True, ), + out_sulc=dict(xor=['no_save_sulc'], ), + subjects_dir=dict(), ) inputs = MRIsInflate.input_spec() @@ -43,8 +38,8 @@ def test_MRIsInflate_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MRIsInflate_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - out_sulc=dict(usedefault=True, ), + out_file=dict(), + out_sulc=dict(), ) outputs = MRIsInflate.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py index dd7ed03a1b..f3453818c5 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py @@ -25,7 +25,7 @@ def test_MS_LDA_inputs(): ), mask_file=dict(argstr='-mask %s', ), shift=dict(argstr='-shift %d', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), use_weights=dict(argstr='-W', ), vol_synth_file=dict( argstr='-synth %s', @@ -43,8 +43,8 @@ def test_MS_LDA_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MS_LDA_outputs(): output_map = dict( - vol_synth_file=dict(usedefault=True, ), - weight_file=dict(usedefault=True, ), + vol_synth_file=dict(), + weight_file=dict(), ) outputs = MS_LDA.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py index 68b1d33455..5dfb555346 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py @@ -14,7 +14,7 @@ def test_MakeAverageSubject_inputs(): argstr='--out %s', usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), subjects_ids=dict( argstr='--subjects %s', mandatory=True, diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py index 0b26f19ca0..7ff18eeba6 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py @@ -17,32 +17,16 @@ def test_MakeSurfaces_inputs(): mandatory=True, position=-1, ), - in_T1=dict( - argstr='-T1 %s', - usedefault=True, - ), - in_aseg=dict( - argstr='-aseg %s', - usedefault=True, - ), - in_filled=dict( - mandatory=True, - usedefault=True, - ), - in_label=dict( - usedefault=True, - xor=['noaparc'], - ), + in_T1=dict(argstr='-T1 %s', ), + in_aseg=dict(argstr='-aseg %s', ), + in_filled=dict(mandatory=True, ), + in_label=dict(xor=['noaparc'], ), in_orig=dict( argstr='-orig %s', mandatory=True, - usedefault=True, - ), - in_white=dict(usedefault=True, ), - in_wm=dict( - mandatory=True, - usedefault=True, ), + in_white=dict(), + in_wm=dict(mandatory=True, ), longitudinal=dict(argstr='-long', ), maximum=dict(argstr='-max %.1f', ), mgz=dict(argstr='-mgz', ), @@ -54,19 +38,15 @@ def test_MakeSurfaces_inputs(): orig_pial=dict( argstr='-orig_pial %s', requires=['in_label'], - usedefault=True, - ), - orig_white=dict( - argstr='-orig_white %s', - usedefault=True, ), + orig_white=dict(argstr='-orig_white %s', ), subject_id=dict( argstr='%s', mandatory=True, position=-2, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), white=dict(argstr='-white %s', ), white_only=dict(argstr='-whiteonly', ), ) @@ -77,12 +57,12 @@ def test_MakeSurfaces_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MakeSurfaces_outputs(): output_map = dict( - out_area=dict(usedefault=True, ), - out_cortex=dict(usedefault=True, ), - out_curv=dict(usedefault=True, ), - out_pial=dict(usedefault=True, ), - out_thickness=dict(usedefault=True, ), - out_white=dict(usedefault=True, ), + out_area=dict(), + out_cortex=dict(), + out_curv=dict(), + out_pial=dict(), + out_thickness=dict(), + out_white=dict(), ) outputs = MakeSurfaces.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py index ff50a476cb..1923b5ceed 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py @@ -15,12 +15,8 @@ def test_Normalize_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, - ), - mask=dict( - argstr='-mask %s', - usedefault=True, ), + mask=dict(argstr='-mask %s', ), out_file=dict( argstr='%s', hash_files=False, @@ -28,14 +24,10 @@ def test_Normalize_inputs(): name_source=['in_file'], name_template='%s_norm', position=-1, - usedefault=True, - ), - segmentation=dict( - argstr='-aseg %s', - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), - transform=dict(usedefault=True, ), + segmentation=dict(argstr='-aseg %s', ), + subjects_dir=dict(), + transform=dict(), ) inputs = Normalize.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py index b0c31b42b6..1091bdbdc3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py @@ -19,7 +19,6 @@ def test_OneSampleTTest_inputs(): debug=dict(argstr='--debug', ), design=dict( argstr='--X %s', - usedefault=True, xor=('fsgd', 'design', 'one_sample'), ), diag=dict(argstr='--diag %d', ), @@ -34,13 +33,9 @@ def test_OneSampleTTest_inputs(): ), fixed_fx_dof_file=dict( argstr='--ffxdofdat %d', - usedefault=True, xor=['fixed_fx_dof'], ), - fixed_fx_var=dict( - argstr='--yffxvar %s', - usedefault=True, - ), + fixed_fx_var=dict(argstr='--yffxvar %s', ), force_perm=dict(argstr='--perm-force', ), fsgd=dict( argstr='--fsgd %s %s', @@ -56,18 +51,13 @@ def test_OneSampleTTest_inputs(): argstr='--y %s', copyfile=False, mandatory=True, - usedefault=True, ), invert_mask=dict(argstr='--mask-inv', ), label_file=dict( argstr='--label %s', - usedefault=True, xor=['cortex'], ), - mask_file=dict( - argstr='--mask %s', - usedefault=True, - ), + mask_file=dict(argstr='--mask %s', ), no_contrast_ok=dict(argstr='--no-contrasts-ok', ), no_est_fwhm=dict(argstr='--no-est-fwhm', ), no_mask_smooth=dict(argstr='--no-mask-smooth', ), @@ -94,14 +84,11 @@ def test_OneSampleTTest_inputs(): save_residual=dict(argstr='--eres-save', ), seed=dict(argstr='--seed %d', ), self_reg=dict(argstr='--selfreg %d %d %d', ), - sim_done_file=dict( - argstr='--sim-done %s', - usedefault=True, - ), + sim_done_file=dict(argstr='--sim-done %s', ), sim_sign=dict(argstr='--sim-sign %s', ), simulation=dict(argstr='--sim %s %d %f %s', ), subject_id=dict(), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), surf=dict( argstr='--surf %s %s %s', requires=['subject_id', 'hemi'], @@ -111,10 +98,7 @@ def test_OneSampleTTest_inputs(): uniform=dict(argstr='--uniform %f %f', ), var_fwhm=dict(argstr='--var-fwhm %f', ), vox_dump=dict(argstr='--voxdump %d %d %d', ), - weight_file=dict( - usedefault=True, - xor=['weighted_ls'], - ), + weight_file=dict(xor=['weighted_ls'], ), weight_inv=dict( argstr='--w-inv', xor=['weighted_ls'], @@ -125,7 +109,6 @@ def test_OneSampleTTest_inputs(): ), weighted_ls=dict( argstr='--wls %s', - usedefault=True, xor=('weight_file', 'weight_inv', 'weight_sqrt'), ), ) @@ -136,23 +119,23 @@ def test_OneSampleTTest_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_OneSampleTTest_outputs(): output_map = dict( - beta_file=dict(usedefault=True, ), - dof_file=dict(usedefault=True, ), - error_file=dict(usedefault=True, ), - error_stddev_file=dict(usedefault=True, ), - error_var_file=dict(usedefault=True, ), - estimate_file=dict(usedefault=True, ), - frame_eigenvectors=dict(usedefault=True, ), + beta_file=dict(), + dof_file=dict(), + error_file=dict(), + error_stddev_file=dict(), + error_var_file=dict(), + estimate_file=dict(), + frame_eigenvectors=dict(), ftest_file=dict(), - fwhm_file=dict(usedefault=True, ), + fwhm_file=dict(), gamma_file=dict(), gamma_var_file=dict(), - glm_dir=dict(usedefault=True, ), - mask_file=dict(usedefault=True, ), + glm_dir=dict(), + mask_file=dict(), sig_file=dict(), - singular_values=dict(usedefault=True, ), - spatial_eigenvectors=dict(usedefault=True, ), - svd_stats_file=dict(usedefault=True, ), + singular_values=dict(), + spatial_eigenvectors=dict(), + svd_stats_file=dict(), ) outputs = OneSampleTTest.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Paint.py b/nipype/interfaces/freesurfer/tests/test_auto_Paint.py index 41c07e0c90..c452594e55 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Paint.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Paint.py @@ -15,7 +15,6 @@ def test_Paint_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), out_file=dict( argstr='%s', @@ -24,14 +23,12 @@ def test_Paint_inputs(): name_source=['in_surf'], name_template='%s.avg_curv', position=-1, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), template=dict( argstr='%s', mandatory=True, position=-3, - usedefault=True, ), template_param=dict(), ) @@ -41,7 +38,7 @@ def test_Paint_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Paint_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Paint.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py b/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py index 29eeb7d760..81ac276b2f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py @@ -6,16 +6,10 @@ def test_ParcellationStats_inputs(): input_map = dict( args=dict(argstr='%s', ), - aseg=dict( - mandatory=True, - usedefault=True, - ), - brainmask=dict( - mandatory=True, - usedefault=True, - ), + aseg=dict(mandatory=True, ), + brainmask=dict(mandatory=True, ), copy_inputs=dict(), - cortex_label=dict(usedefault=True, ), + cortex_label=dict(), environ=dict( nohash=True, usedefault=True, @@ -34,14 +28,8 @@ def test_ParcellationStats_inputs(): argstr='-l %s', xor=['in_annotatoin', 'out_color'], ), - lh_pial=dict( - mandatory=True, - usedefault=True, - ), - lh_white=dict( - mandatory=True, - usedefault=True, - ), + lh_pial=dict(mandatory=True, ), + lh_white=dict(mandatory=True, ), mgz=dict(argstr='-mgz', ), out_color=dict( argstr='-c %s', @@ -53,25 +41,16 @@ def test_ParcellationStats_inputs(): genfile=True, requires=['tabular_output'], ), - rh_pial=dict( - mandatory=True, - usedefault=True, - ), - rh_white=dict( - mandatory=True, - usedefault=True, - ), - ribbon=dict( - mandatory=True, - usedefault=True, - ), + rh_pial=dict(mandatory=True, ), + rh_white=dict(mandatory=True, ), + ribbon=dict(mandatory=True, ), subject_id=dict( argstr='%s', mandatory=True, position=-3, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), surface=dict( argstr='%s', position=-1, @@ -81,18 +60,9 @@ def test_ParcellationStats_inputs(): argstr='-th3', requires=['cortex_label'], ), - thickness=dict( - mandatory=True, - usedefault=True, - ), - transform=dict( - mandatory=True, - usedefault=True, - ), - wm=dict( - mandatory=True, - usedefault=True, - ), + thickness=dict(mandatory=True, ), + transform=dict(mandatory=True, ), + wm=dict(mandatory=True, ), ) inputs = ParcellationStats.input_spec() @@ -101,8 +71,8 @@ def test_ParcellationStats_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ParcellationStats_outputs(): output_map = dict( - out_color=dict(usedefault=True, ), - out_table=dict(usedefault=True, ), + out_color=dict(), + out_table=dict(), ) outputs = ParcellationStats.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py index 232f363e72..93254ddcb3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py @@ -9,7 +9,6 @@ def test_ParseDICOMDir_inputs(): dicom_dir=dict( argstr='--d %s', mandatory=True, - usedefault=True, ), dicom_info_file=dict( argstr='--o %s', @@ -20,7 +19,7 @@ def test_ParseDICOMDir_inputs(): usedefault=True, ), sortbyrun=dict(argstr='--sortbyrun', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), summarize=dict(argstr='--summarize', ), ) inputs = ParseDICOMDir.input_spec() @@ -29,7 +28,7 @@ def test_ParseDICOMDir_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ParseDICOMDir_outputs(): - output_map = dict(dicom_info_file=dict(usedefault=True, ), ) + output_map = dict(dicom_info_file=dict(), ) outputs = ParseDICOMDir.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py index 72b256c3ea..39f6a8c942 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py @@ -8,13 +8,11 @@ def test_ReconAll_inputs(): FLAIR_file=dict( argstr='-FLAIR %s', min_ver='5.3.0', - usedefault=True, ), T1_files=dict(argstr='-i %s...', ), T2_file=dict( argstr='-T2 %s', min_ver='5.3.0', - usedefault=True, ), args=dict(argstr='%s', ), big_ventricles=dict(argstr='-bigventricles', ), @@ -28,10 +26,7 @@ def test_ReconAll_inputs(): nohash=True, usedefault=True, ), - expert=dict( - argstr='-expert %s', - usedefault=True, - ), + expert=dict(argstr='-expert %s', ), flags=dict(argstr='%s', ), hemi=dict(argstr='-hemi %s', ), hippocampal_subfields_T1=dict( @@ -82,7 +77,6 @@ def test_ReconAll_inputs(): argstr='-sd %s', genfile=True, hash_files=False, - usedefault=True, ), talairach=dict(xor=['expert'], ), use_FLAIR=dict( @@ -108,10 +102,7 @@ def test_ReconAll_outputs(): altkey='BA', loc='stats', ), - T1=dict( - loc='mri', - usedefault=True, - ), + T1=dict(loc='mri', ), annot=dict( altkey='*annot', loc='label', @@ -132,23 +123,14 @@ def test_ReconAll_outputs(): altkey='area.pial', loc='surf', ), - aseg=dict( - loc='mri', - usedefault=True, - ), + aseg=dict(loc='mri', ), aseg_stats=dict( altkey='aseg', loc='stats', ), avg_curv=dict(loc='surf', ), - brain=dict( - loc='mri', - usedefault=True, - ), - brainmask=dict( - loc='mri', - usedefault=True, - ), + brain=dict(loc='mri', ), + brainmask=dict(loc='mri', ), curv=dict(loc='surf', ), curv_pial=dict( altkey='curv.pial', @@ -162,10 +144,7 @@ def test_ReconAll_outputs(): altkey='entorhinal_exvivo', loc='stats', ), - filled=dict( - loc='mri', - usedefault=True, - ), + filled=dict(loc='mri', ), graymid=dict( altkey=['graymid', 'midthickness'], loc='surf', @@ -176,23 +155,11 @@ def test_ReconAll_outputs(): altkey='*label', loc='label', ), - norm=dict( - loc='mri', - usedefault=True, - ), - nu=dict( - loc='mri', - usedefault=True, - ), - orig=dict( - loc='mri', - usedefault=True, - ), + norm=dict(loc='mri', ), + nu=dict(loc='mri', ), + orig=dict(loc='mri', ), pial=dict(loc='surf', ), - rawavg=dict( - loc='mri', - usedefault=True, - ), + rawavg=dict(loc='mri', ), ribbon=dict( altkey='*ribbon', loc='mri', @@ -204,19 +171,13 @@ def test_ReconAll_outputs(): loc='surf', ), subject_id=dict(), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), sulc=dict(loc='surf', ), thickness=dict(loc='surf', ), volume=dict(loc='surf', ), white=dict(loc='surf', ), - wm=dict( - loc='mri', - usedefault=True, - ), - wmparc=dict( - loc='mri', - usedefault=True, - ), + wm=dict(loc='mri', ), + wmparc=dict(loc='mri', ), wmparc_stats=dict( altkey='wmparc', loc='stats', diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Register.py b/nipype/interfaces/freesurfer/tests/test_auto_Register.py index ef13270f35..b4eff5133c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Register.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Register.py @@ -14,34 +14,27 @@ def test_Register_inputs(): nohash=True, usedefault=True, ), - in_smoothwm=dict( - copyfile=True, - usedefault=True, - ), + in_smoothwm=dict(copyfile=True, ), in_sulc=dict( copyfile=True, mandatory=True, - usedefault=True, ), in_surf=dict( argstr='%s', copyfile=True, mandatory=True, position=-3, - usedefault=True, ), out_file=dict( argstr='%s', genfile=True, position=-1, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), target=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), ) inputs = Register.input_spec() @@ -50,7 +43,7 @@ def test_Register_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Register_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Register.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py index 7bd2387e07..0bc88bf935 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py @@ -14,25 +14,22 @@ def test_RegisterAVItoTalairach_inputs(): argstr='%s', mandatory=True, position=0, - usedefault=True, ), out_file=dict( argstr='%s', position=3, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), target=dict( argstr='%s', mandatory=True, position=1, - usedefault=True, ), vox2vox=dict( argstr='%s', mandatory=True, position=2, - usedefault=True, ), ) inputs = RegisterAVItoTalairach.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py b/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py index c0181e302e..859aff0820 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py @@ -10,7 +10,6 @@ def test_RelabelHypointensities_inputs(): argstr='%s', mandatory=True, position=-3, - usedefault=True, ), environ=dict( nohash=True, @@ -19,7 +18,6 @@ def test_RelabelHypointensities_inputs(): lh_white=dict( copyfile=True, mandatory=True, - usedefault=True, ), out_file=dict( argstr='%s', @@ -28,14 +26,12 @@ def test_RelabelHypointensities_inputs(): name_source=['aseg'], name_template='%s.hypos.mgz', position=-1, - usedefault=True, ), rh_white=dict( copyfile=True, mandatory=True, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), surf_directory=dict( argstr='%s', position=-2, @@ -48,11 +44,7 @@ def test_RelabelHypointensities_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RelabelHypointensities_outputs(): - output_map = dict( - out_file=dict( - argstr='%s', - usedefault=True, - ), ) + output_map = dict(out_file=dict(argstr='%s', ), ) outputs = RelabelHypointensities.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py b/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py index 73ae626aaf..69e1d453a4 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py @@ -15,7 +15,6 @@ def test_RemoveIntersection_inputs(): copyfile=True, mandatory=True, position=-2, - usedefault=True, ), out_file=dict( argstr='%s', @@ -24,9 +23,8 @@ def test_RemoveIntersection_inputs(): name_source=['in_file'], name_template='%s', position=-1, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = RemoveIntersection.input_spec() @@ -34,7 +32,7 @@ def test_RemoveIntersection_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RemoveIntersection_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = RemoveIntersection.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py b/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py index f83b2393ef..9e095ddba0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py @@ -14,7 +14,6 @@ def test_RemoveNeck_inputs(): argstr='%s', mandatory=True, position=-4, - usedefault=True, ), out_file=dict( argstr='%s', @@ -23,21 +22,18 @@ def test_RemoveNeck_inputs(): name_source=['in_file'], name_template='%s_noneck', position=-1, - usedefault=True, ), radius=dict(argstr='-radius %d', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), template=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), transform=dict( argstr='%s', mandatory=True, position=-3, - usedefault=True, ), ) inputs = RemoveNeck.input_spec() @@ -46,7 +42,7 @@ def test_RemoveNeck_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RemoveNeck_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = RemoveNeck.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py index 96e3c3cf6c..ecb939d89a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py @@ -14,15 +14,13 @@ def test_Resample_inputs(): argstr='-i %s', mandatory=True, position=-2, - usedefault=True, ), resampled_file=dict( argstr='-o %s', genfile=True, position=-1, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), voxel_size=dict( argstr='-vs %.2f %.2f %.2f', mandatory=True, @@ -34,7 +32,7 @@ def test_Resample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Resample_outputs(): - output_map = dict(resampled_file=dict(usedefault=True, ), ) + output_map = dict(resampled_file=dict(), ) outputs = Resample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py index 6275b8d322..af9020c278 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py @@ -24,21 +24,12 @@ def test_RobustRegister_inputs(): half_targ_xfm=dict(argstr='--halfdstlta %s', ), half_weights=dict(argstr='--halfweights %s', ), high_iterations=dict(argstr='--highit %d', ), - in_xfm_file=dict( - argstr='--transform', - usedefault=True, - ), + in_xfm_file=dict(argstr='--transform', ), init_orient=dict(argstr='--initorient', ), iteration_thresh=dict(argstr='--epsit %.3f', ), least_squares=dict(argstr='--leastsquares', ), - mask_source=dict( - argstr='--maskmov %s', - usedefault=True, - ), - mask_target=dict( - argstr='--maskdst %s', - usedefault=True, - ), + mask_source=dict(argstr='--maskmov %s', ), + mask_target=dict(argstr='--maskdst %s', ), max_iterations=dict(argstr='--maxit %d', ), no_init=dict(argstr='--noinit', ), no_multi=dict(argstr='--nomulti', ), @@ -56,14 +47,12 @@ def test_RobustRegister_inputs(): source_file=dict( argstr='--mov %s', mandatory=True, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), subsample_thresh=dict(argstr='--subsample %d', ), target_file=dict( argstr='--dst %s', mandatory=True, - usedefault=True, ), trans_only=dict(argstr='--transonly', ), weights_file=dict(argstr='--weights %s', ), @@ -76,14 +65,14 @@ def test_RobustRegister_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RobustRegister_outputs(): output_map = dict( - half_source=dict(usedefault=True, ), - half_source_xfm=dict(usedefault=True, ), - half_targ=dict(usedefault=True, ), - half_targ_xfm=dict(usedefault=True, ), - half_weights=dict(usedefault=True, ), - out_reg_file=dict(usedefault=True, ), - registered_file=dict(usedefault=True, ), - weights_file=dict(usedefault=True, ), + half_source=dict(), + half_source_xfm=dict(), + half_targ=dict(), + half_targ_xfm=dict(), + half_weights=dict(), + out_reg_file=dict(), + registered_file=dict(), + weights_file=dict(), ) outputs = RobustRegister.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py b/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py index 675cd41f2b..e845a764e4 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py @@ -38,7 +38,7 @@ def test_RobustTemplate_inputs(): xor=['auto_detect_sensitivity'], ), scaled_intensity_outputs=dict(argstr='--iscaleout %s', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), subsample_threshold=dict(argstr='--subsample %d', ), transform_outputs=dict(argstr='--lta %s', ), ) @@ -49,7 +49,7 @@ def test_RobustTemplate_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RobustTemplate_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), + out_file=dict(), scaled_intensity_outputs=dict(), transform_outputs=dict(), ) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py index 04b1352ff6..0926eebba2 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py @@ -32,7 +32,6 @@ def test_SampleToSurface_inputs(): interp_method=dict(argstr='--interp %s', ), mask_label=dict( argstr='--mask %s', - usedefault=True, xor=['cortex_mask'], ), mni152reg=dict( @@ -47,7 +46,6 @@ def test_SampleToSurface_inputs(): out_file=dict( argstr='--o %s', genfile=True, - usedefault=True, ), out_type=dict(argstr='--out_type %s', ), override_reg_subj=dict( @@ -58,14 +56,10 @@ def test_SampleToSurface_inputs(): mandatory=True, xor=['sampling_method'], ), - reference_file=dict( - argstr='--ref %s', - usedefault=True, - ), + reference_file=dict(argstr='--ref %s', ), reg_file=dict( argstr='--reg %s', mandatory=True, - usedefault=True, xor=['reg_file', 'reg_header', 'mni152reg'], ), reg_header=dict( @@ -93,10 +87,9 @@ def test_SampleToSurface_inputs(): source_file=dict( argstr='--mov %s', mandatory=True, - usedefault=True, ), subject_id=dict(), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), surf_reg=dict( argstr='--surfreg %s', requires=['target_subject'], @@ -112,9 +105,9 @@ def test_SampleToSurface_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SampleToSurface_outputs(): output_map = dict( - hits_file=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), - vox_file=dict(usedefault=True, ), + hits_file=dict(), + out_file=dict(), + vox_file=dict(), ) outputs = SampleToSurface.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py index a38d9b5b5f..8feb61d9d8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py @@ -14,15 +14,11 @@ def test_SegStats_inputs(): avgwf_file=dict(argstr='--avgwfvol %s', ), avgwf_txt_file=dict(argstr='--avgwf %s', ), brain_vol=dict(argstr='--%s', ), - brainmask_file=dict( - argstr='--brainmask %s', - usedefault=True, - ), + brainmask_file=dict(argstr='--brainmask %s', ), calc_power=dict(argstr='--%s', ), calc_snr=dict(argstr='--snr', ), color_table_file=dict( argstr='--ctab %s', - usedefault=True, xor=('color_table_file', 'default_color_table', 'gca_color_table'), ), cortex_vol_from_surf=dict(argstr='--surf-ctx-vol', ), @@ -43,51 +39,36 @@ def test_SegStats_inputs(): frame=dict(argstr='--frame %d', ), gca_color_table=dict( argstr='--ctab-gca %s', - usedefault=True, xor=('color_table_file', 'default_color_table', 'gca_color_table'), ), - in_file=dict( - argstr='--i %s', - usedefault=True, - ), - in_intensity=dict( - argstr='--in %s --in-intensity-name %s', - usedefault=True, - ), + in_file=dict(argstr='--i %s', ), + in_intensity=dict(argstr='--in %s --in-intensity-name %s', ), intensity_units=dict( argstr='--in-intensity-units %s', requires=['in_intensity'], ), mask_erode=dict(argstr='--maskerode %d', ), - mask_file=dict( - argstr='--mask %s', - usedefault=True, - ), + mask_file=dict(argstr='--mask %s', ), mask_frame=dict(requires=['mask_file'], ), mask_invert=dict(argstr='--maskinvert', ), mask_sign=dict(), mask_thresh=dict(argstr='--maskthresh %f', ), multiply=dict(argstr='--mul %f', ), non_empty_only=dict(argstr='--nonempty', ), - partial_volume_file=dict( - argstr='--pv %s', - usedefault=True, - ), + partial_volume_file=dict(argstr='--pv %s', ), segment_id=dict(argstr='--id %s...', ), segmentation_file=dict( argstr='--seg %s', mandatory=True, - usedefault=True, xor=('segmentation_file', 'annot', 'surf_label'), ), sf_avg_file=dict(argstr='--sfavg %s', ), subcort_gm=dict(argstr='--subcortgray', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), summary_file=dict( argstr='--sum %s', genfile=True, position=-1, - usedefault=True, ), supratent=dict(argstr='--supratent', ), surf_label=dict( @@ -106,10 +87,10 @@ def test_SegStats_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SegStats_outputs(): output_map = dict( - avgwf_file=dict(usedefault=True, ), - avgwf_txt_file=dict(usedefault=True, ), - sf_avg_file=dict(usedefault=True, ), - summary_file=dict(usedefault=True, ), + avgwf_file=dict(), + avgwf_txt_file=dict(), + sf_avg_file=dict(), + summary_file=dict(), ) outputs = SegStats.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py index e27c24651f..e65dc82e3b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py @@ -11,19 +11,15 @@ def test_SegStatsReconAll_inputs(): xor=('segmentation_file', 'annot', 'surf_label'), ), args=dict(argstr='%s', ), - aseg=dict(usedefault=True, ), + aseg=dict(), avgwf_file=dict(argstr='--avgwfvol %s', ), avgwf_txt_file=dict(argstr='--avgwf %s', ), brain_vol=dict(argstr='--%s', ), - brainmask_file=dict( - argstr='--brainmask %s', - usedefault=True, - ), + brainmask_file=dict(argstr='--brainmask %s', ), calc_power=dict(argstr='--%s', ), calc_snr=dict(argstr='--snr', ), color_table_file=dict( argstr='--ctab %s', - usedefault=True, xor=('color_table_file', 'default_color_table', 'gca_color_table'), ), copy_inputs=dict(), @@ -45,67 +41,35 @@ def test_SegStatsReconAll_inputs(): frame=dict(argstr='--frame %d', ), gca_color_table=dict( argstr='--ctab-gca %s', - usedefault=True, xor=('color_table_file', 'default_color_table', 'gca_color_table'), ), - in_file=dict( - argstr='--i %s', - usedefault=True, - ), - in_intensity=dict( - argstr='--in %s --in-intensity-name %s', - usedefault=True, - ), + in_file=dict(argstr='--i %s', ), + in_intensity=dict(argstr='--in %s --in-intensity-name %s', ), intensity_units=dict( argstr='--in-intensity-units %s', requires=['in_intensity'], ), - lh_orig_nofix=dict( - mandatory=True, - usedefault=True, - ), - lh_pial=dict( - mandatory=True, - usedefault=True, - ), - lh_white=dict( - mandatory=True, - usedefault=True, - ), + lh_orig_nofix=dict(mandatory=True, ), + lh_pial=dict(mandatory=True, ), + lh_white=dict(mandatory=True, ), mask_erode=dict(argstr='--maskerode %d', ), - mask_file=dict( - argstr='--mask %s', - usedefault=True, - ), + mask_file=dict(argstr='--mask %s', ), mask_frame=dict(requires=['mask_file'], ), mask_invert=dict(argstr='--maskinvert', ), mask_sign=dict(), mask_thresh=dict(argstr='--maskthresh %f', ), multiply=dict(argstr='--mul %f', ), non_empty_only=dict(argstr='--nonempty', ), - partial_volume_file=dict( - argstr='--pv %s', - usedefault=True, - ), - presurf_seg=dict(usedefault=True, ), - rh_orig_nofix=dict( - mandatory=True, - usedefault=True, - ), - rh_pial=dict( - mandatory=True, - usedefault=True, - ), - rh_white=dict( - mandatory=True, - usedefault=True, - ), + partial_volume_file=dict(argstr='--pv %s', ), + presurf_seg=dict(), + rh_orig_nofix=dict(mandatory=True, ), + rh_pial=dict(mandatory=True, ), + rh_white=dict(mandatory=True, ), ribbon=dict(mandatory=True, ), segment_id=dict(argstr='--id %s...', ), segmentation_file=dict( argstr='--seg %s', mandatory=True, - usedefault=True, xor=('segmentation_file', 'annot', 'surf_label'), ), sf_avg_file=dict(argstr='--sfavg %s', ), @@ -115,12 +79,11 @@ def test_SegStatsReconAll_inputs(): mandatory=True, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), summary_file=dict( argstr='--sum %s', genfile=True, position=-1, - usedefault=True, ), supratent=dict(argstr='--supratent', ), surf_label=dict( @@ -129,10 +92,7 @@ def test_SegStatsReconAll_inputs(): xor=('segmentation_file', 'annot', 'surf_label'), ), total_gray=dict(argstr='--totalgray', ), - transform=dict( - mandatory=True, - usedefault=True, - ), + transform=dict(mandatory=True, ), vox=dict(argstr='--vox %s', ), wm_vol_from_surf=dict(argstr='--surf-wm-vol', ), ) @@ -143,10 +103,10 @@ def test_SegStatsReconAll_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SegStatsReconAll_outputs(): output_map = dict( - avgwf_file=dict(usedefault=True, ), - avgwf_txt_file=dict(usedefault=True, ), - sf_avg_file=dict(usedefault=True, ), - summary_file=dict(usedefault=True, ), + avgwf_file=dict(), + avgwf_txt_file=dict(), + sf_avg_file=dict(), + summary_file=dict(), ) outputs = SegStatsReconAll.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py b/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py index 679f5449eb..e6b5fb2679 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py @@ -14,24 +14,18 @@ def test_SegmentCC_inputs(): in_file=dict( argstr='-aseg %s', mandatory=True, - usedefault=True, - ), - in_norm=dict( - mandatory=True, - usedefault=True, ), + in_norm=dict(mandatory=True, ), out_file=dict( argstr='-o %s', hash_files=False, keep_extension=False, name_source=['in_file'], name_template='%s.auto.mgz', - usedefault=True, ), out_rotation=dict( argstr='-lta %s', mandatory=True, - usedefault=True, ), subject_id=dict( argstr='%s', @@ -39,7 +33,7 @@ def test_SegmentCC_inputs(): position=-1, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = SegmentCC.input_spec() @@ -48,8 +42,8 @@ def test_SegmentCC_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SegmentCC_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - out_rotation=dict(usedefault=True, ), + out_file=dict(), + out_rotation=dict(), ) outputs = SegmentCC.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py b/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py index 15895f4ec2..aa742e8fea 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py @@ -14,15 +14,13 @@ def test_SegmentWM_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), out_file=dict( argstr='%s', mandatory=True, position=-1, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = SegmentWM.input_spec() @@ -30,7 +28,7 @@ def test_SegmentWM_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SegmentWM_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = SegmentWM.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py index 85a6179e7f..fe4581dee0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py @@ -13,7 +13,6 @@ def test_Smooth_inputs(): in_file=dict( argstr='--i %s', mandatory=True, - usedefault=True, ), num_iters=dict( argstr='--niters %d', @@ -31,14 +30,12 @@ def test_Smooth_inputs(): reg_file=dict( argstr='--reg %s', mandatory=True, - usedefault=True, ), smoothed_file=dict( argstr='--o %s', genfile=True, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), surface_fwhm=dict( argstr='--fwhm %f', mandatory=True, @@ -53,7 +50,7 @@ def test_Smooth_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Smooth_outputs(): - output_map = dict(smoothed_file=dict(usedefault=True, ), ) + output_map = dict(smoothed_file=dict(), ) outputs = Smooth.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py index 259805e6c2..8ce4dce075 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py @@ -19,27 +19,19 @@ def test_SmoothTessellation_inputs(): copyfile=True, mandatory=True, position=-2, - usedefault=True, ), normalize_area=dict(argstr='-area', ), - out_area_file=dict( - argstr='-b %s', - usedefault=True, - ), - out_curvature_file=dict( - argstr='-c %s', - usedefault=True, - ), + out_area_file=dict(argstr='-b %s', ), + out_curvature_file=dict(argstr='-c %s', ), out_file=dict( argstr='%s', genfile=True, position=-1, - usedefault=True, ), seed=dict(argstr='-seed %d', ), smoothing_iterations=dict(argstr='-n %d', ), snapshot_writing_iterations=dict(argstr='-w %d', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), use_gaussian_curvature_smoothing=dict(argstr='-g', ), use_momentum=dict(argstr='-m', ), ) @@ -49,7 +41,7 @@ def test_SmoothTessellation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SmoothTessellation_outputs(): - output_map = dict(surface=dict(usedefault=True, ), ) + output_map = dict(surface=dict(), ) outputs = SmoothTessellation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py b/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py index 242be862a5..461398e6a8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py @@ -15,12 +15,8 @@ def test_Sphere_inputs(): copyfile=True, mandatory=True, position=-2, - usedefault=True, - ), - in_smoothwm=dict( - copyfile=True, - usedefault=True, ), + in_smoothwm=dict(copyfile=True, ), magic=dict(argstr='-q', ), num_threads=dict(), out_file=dict( @@ -29,10 +25,9 @@ def test_Sphere_inputs(): name_source=['in_file'], name_template='%s.sphere', position=-1, - usedefault=True, ), seed=dict(argstr='-seed %d', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = Sphere.input_spec() @@ -40,7 +35,7 @@ def test_Sphere_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Sphere_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Sphere.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py index 54c24a96dd..efdc032787 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py @@ -26,27 +26,22 @@ def test_SphericalAverage_inputs(): genfile=True, position=-2, ), - in_orig=dict( - argstr='-orig %s', - usedefault=True, - ), + in_orig=dict(argstr='-orig %s', ), in_surf=dict( argstr='%s', mandatory=True, position=-3, - usedefault=True, ), out_file=dict( argstr='%s', genfile=True, position=-1, - usedefault=True, ), subject_id=dict( argstr='-o %s', mandatory=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), threshold=dict(argstr='-t %.1f', ), which=dict( argstr='%s', @@ -60,7 +55,7 @@ def test_SphericalAverage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SphericalAverage_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = SphericalAverage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py index 7ab924576c..ca3f96c42b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py @@ -22,14 +22,12 @@ def test_Surface2VolTransform_inputs(): reg_file=dict( argstr='--volreg %s', mandatory=True, - usedefault=True, xor=['subject_id'], ), source_file=dict( argstr='--surfval %s', copyfile=False, mandatory=True, - usedefault=True, xor=['mkmask'], ), subject_id=dict( @@ -38,23 +36,18 @@ def test_Surface2VolTransform_inputs(): ), subjects_dir=dict(argstr='--sd %s', ), surf_name=dict(argstr='--surf %s', ), - template_file=dict( - argstr='--template %s', - usedefault=True, - ), + template_file=dict(argstr='--template %s', ), transformed_file=dict( argstr='--outvol %s', hash_files=False, name_source=['source_file'], name_template='%s_asVol.nii', - usedefault=True, ), vertexvol_file=dict( argstr='--vtxvol %s', hash_files=False, name_source=['source_file'], name_template='%s_asVol_vertex.nii', - usedefault=True, ), ) inputs = Surface2VolTransform.input_spec() @@ -64,8 +57,8 @@ def test_Surface2VolTransform_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Surface2VolTransform_outputs(): output_map = dict( - transformed_file=dict(usedefault=True, ), - vertexvol_file=dict(usedefault=True, ), + transformed_file=dict(), + vertexvol_file=dict(), ) outputs = Surface2VolTransform.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py index 2fde5bd6c2..84bef6ed7a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py @@ -25,12 +25,10 @@ def test_SurfaceSmooth_inputs(): in_file=dict( argstr='--sval %s', mandatory=True, - usedefault=True, ), out_file=dict( argstr='--tval %s', genfile=True, - usedefault=True, ), reshape=dict(argstr='--reshape', ), smooth_iters=dict( @@ -41,7 +39,7 @@ def test_SurfaceSmooth_inputs(): argstr='--s %s', mandatory=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = SurfaceSmooth.input_spec() @@ -49,7 +47,7 @@ def test_SurfaceSmooth_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SurfaceSmooth_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = SurfaceSmooth.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py index 1024780411..a413d410b1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py @@ -7,7 +7,6 @@ def test_SurfaceSnapshots_inputs(): input_map = dict( annot_file=dict( argstr='-annotation %s', - usedefault=True, xor=['annot_name'], ), annot_name=dict( @@ -15,10 +14,7 @@ def test_SurfaceSnapshots_inputs(): xor=['annot_file'], ), args=dict(argstr='%s', ), - colortable=dict( - argstr='-colortable %s', - usedefault=True, - ), + colortable=dict(argstr='-colortable %s', ), demean_overlay=dict(argstr='-zm', ), environ=dict( nohash=True, @@ -36,7 +32,6 @@ def test_SurfaceSnapshots_inputs(): invert_overlay=dict(argstr='-invphaseflag 1', ), label_file=dict( argstr='-label %s', - usedefault=True, xor=['label_name'], ), label_name=dict( @@ -53,7 +48,6 @@ def test_SurfaceSnapshots_inputs(): overlay=dict( argstr='-overlay %s', requires=['overlay_range'], - usedefault=True, ), overlay_range=dict(argstr='%s', ), overlay_range_offset=dict(argstr='-foffset %.3f', ), @@ -61,10 +55,7 @@ def test_SurfaceSnapshots_inputs(): argstr='-overlay-reg %s', xor=['overlay_reg', 'identity_reg', 'mni152_reg'], ), - patch_file=dict( - argstr='-patch %s', - usedefault=True, - ), + patch_file=dict(argstr='-patch %s', ), reverse_overlay=dict(argstr='-revphaseflag 1', ), screenshot_stem=dict(), show_color_scale=dict(argstr='-colscalebarflag 1', ), @@ -85,7 +76,7 @@ def test_SurfaceSnapshots_inputs(): mandatory=True, position=1, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), surface=dict( argstr='%s', mandatory=True, @@ -94,7 +85,6 @@ def test_SurfaceSnapshots_inputs(): tcl_script=dict( argstr='%s', genfile=True, - usedefault=True, ), truncate_overlay=dict(argstr='-truncphaseflag 1', ), ) diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py index f700f4e470..0546a275dc 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py @@ -17,20 +17,17 @@ def test_SurfaceTransform_inputs(): out_file=dict( argstr='--tval %s', genfile=True, - usedefault=True, ), reshape=dict(argstr='--reshape', ), reshape_factor=dict(argstr='--reshape-factor', ), source_annot_file=dict( argstr='--sval-annot %s', mandatory=True, - usedefault=True, xor=['source_file'], ), source_file=dict( argstr='--sval %s', mandatory=True, - usedefault=True, xor=['source_annot_file'], ), source_subject=dict( @@ -41,7 +38,7 @@ def test_SurfaceTransform_inputs(): argstr='--sfmt %s', requires=['source_file'], ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), target_ico_order=dict(argstr='--trgicoorder %d', ), target_subject=dict( argstr='--trgsubject %s', @@ -55,7 +52,7 @@ def test_SurfaceTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SurfaceTransform_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = SurfaceTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py index 4f1756672f..ea121d877e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py @@ -22,20 +22,17 @@ def test_SynthesizeFLASH_inputs(): out_file=dict( argstr='%s', genfile=True, - usedefault=True, ), pd_image=dict( argstr='%s', mandatory=True, position=6, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), t1_image=dict( argstr='%s', mandatory=True, position=5, - usedefault=True, ), te=dict( argstr='%.3f', @@ -54,7 +51,7 @@ def test_SynthesizeFLASH_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SynthesizeFLASH_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = SynthesizeFLASH.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py index 913d41e595..8ce925fcc7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py @@ -14,14 +14,12 @@ def test_TalairachAVI_inputs(): in_file=dict( argstr='--i %s', mandatory=True, - usedefault=True, ), out_file=dict( argstr='--xfm %s', mandatory=True, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = TalairachAVI.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py index 11ddab6588..d07e572365 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py @@ -14,9 +14,8 @@ def test_TalairachQC_inputs(): argstr='%s', mandatory=True, position=0, - usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = TalairachQC.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py index bd785e45cc..17f8e53a1f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py @@ -10,10 +10,7 @@ def test_Tkregister2_inputs(): nohash=True, usedefault=True, ), - fsl_in_matrix=dict( - argstr='--fsl %s', - usedefault=True, - ), + fsl_in_matrix=dict(argstr='--fsl %s', ), fsl_out=dict(argstr='--fslregout %s', ), fstal=dict( argstr='--fstal', @@ -28,15 +25,11 @@ def test_Tkregister2_inputs(): argstr='--ltaout-inv', requires=['lta_in'], ), - lta_in=dict( - argstr='--lta %s', - usedefault=True, - ), + lta_in=dict(argstr='--lta %s', ), lta_out=dict(argstr='--ltaout %s', ), moving_image=dict( argstr='--mov %s', mandatory=True, - usedefault=True, ), movscale=dict(argstr='--movscale %f', ), noedit=dict( @@ -50,16 +43,12 @@ def test_Tkregister2_inputs(): ), reg_header=dict(argstr='--regheader', ), subject_id=dict(argstr='--s %s', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), target_image=dict( argstr='--targ %s', - usedefault=True, xor=['fstarg'], ), - xfm=dict( - argstr='--xfm %s', - usedefault=True, - ), + xfm=dict(argstr='--xfm %s', ), ) inputs = Tkregister2.input_spec() @@ -68,9 +57,9 @@ def test_Tkregister2_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Tkregister2_outputs(): output_map = dict( - fsl_file=dict(usedefault=True, ), - lta_file=dict(usedefault=True, ), - reg_file=dict(usedefault=True, ), + fsl_file=dict(), + lta_file=dict(), + reg_file=dict(), ) outputs = Tkregister2.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py index 3f2168c4ca..9427e60940 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py @@ -9,7 +9,6 @@ def test_UnpackSDICOMDir_inputs(): config=dict( argstr='-cfg %s', mandatory=True, - usedefault=True, xor=('run_info', 'config', 'seq_config'), ), dir_structure=dict(argstr='-%s', ), @@ -17,38 +16,27 @@ def test_UnpackSDICOMDir_inputs(): nohash=True, usedefault=True, ), - log_file=dict( - argstr='-log %s', - usedefault=True, - ), + log_file=dict(argstr='-log %s', ), no_info_dump=dict(argstr='-noinfodump', ), no_unpack_err=dict(argstr='-no-unpackerr', ), - output_dir=dict( - argstr='-targ %s', - usedefault=True, - ), + output_dir=dict(argstr='-targ %s', ), run_info=dict( argstr='-run %d %s %s %s', mandatory=True, xor=('run_info', 'config', 'seq_config'), ), - scan_only=dict( - argstr='-scanonly %s', - usedefault=True, - ), + scan_only=dict(argstr='-scanonly %s', ), seq_config=dict( argstr='-seqcfg %s', mandatory=True, - usedefault=True, xor=('run_info', 'config', 'seq_config'), ), source_dir=dict( argstr='-src %s', mandatory=True, - usedefault=True, ), spm_zeropad=dict(argstr='-nspmzeropad %d', ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = UnpackSDICOMDir.input_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py b/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py index 0fb8d0e709..3e898a81f7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py @@ -6,10 +6,7 @@ def test_VolumeMask_inputs(): input_map = dict( args=dict(argstr='%s', ), - aseg=dict( - usedefault=True, - xor=['in_aseg'], - ), + aseg=dict(xor=['in_aseg'], ), copy_inputs=dict(), environ=dict( nohash=True, @@ -17,7 +14,6 @@ def test_VolumeMask_inputs(): ), in_aseg=dict( argstr='--aseg_name %s', - usedefault=True, xor=['aseg'], ), left_ribbonlabel=dict( @@ -28,22 +24,10 @@ def test_VolumeMask_inputs(): argstr='--label_left_white %d', mandatory=True, ), - lh_pial=dict( - mandatory=True, - usedefault=True, - ), - lh_white=dict( - mandatory=True, - usedefault=True, - ), - rh_pial=dict( - mandatory=True, - usedefault=True, - ), - rh_white=dict( - mandatory=True, - usedefault=True, - ), + lh_pial=dict(mandatory=True, ), + lh_white=dict(mandatory=True, ), + rh_pial=dict(mandatory=True, ), + rh_white=dict(mandatory=True, ), right_ribbonlabel=dict( argstr='--label_right_ribbon %d', mandatory=True, @@ -59,7 +43,7 @@ def test_VolumeMask_inputs(): position=-1, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), ) inputs = VolumeMask.input_spec() @@ -68,9 +52,9 @@ def test_VolumeMask_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_VolumeMask_outputs(): output_map = dict( - lh_ribbon=dict(usedefault=True, ), - out_ribbon=dict(usedefault=True, ), - rh_ribbon=dict(usedefault=True, ), + lh_ribbon=dict(), + out_ribbon=dict(), + rh_ribbon=dict(), ) outputs = VolumeMask.output_spec() diff --git a/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py b/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py index e7b777f54a..3586e7d234 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py @@ -9,7 +9,6 @@ def test_WatershedSkullStrip_inputs(): brain_atlas=dict( argstr='-brain_atlas %s', position=-4, - usedefault=True, ), environ=dict( nohash=True, @@ -19,7 +18,6 @@ def test_WatershedSkullStrip_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), out_file=dict( argstr='%s', @@ -27,12 +25,11 @@ def test_WatershedSkullStrip_inputs(): position=-1, usedefault=True, ), - subjects_dir=dict(usedefault=True, ), + subjects_dir=dict(), t1=dict(argstr='-T1', ), transform=dict( argstr='%s', position=-3, - usedefault=True, ), ) inputs = WatershedSkullStrip.input_spec() @@ -41,7 +38,7 @@ def test_WatershedSkullStrip_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WatershedSkullStrip_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = WatershedSkullStrip.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_AR1Image.py b/nipype/interfaces/fsl/tests/test_auto_AR1Image.py index a579e1ddd0..32efb1826e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AR1Image.py +++ b/nipype/interfaces/fsl/tests/test_auto_AR1Image.py @@ -19,7 +19,6 @@ def test_AR1Image_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -34,7 +33,6 @@ def test_AR1Image_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -48,7 +46,7 @@ def test_AR1Image_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AR1Image_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = AR1Image.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py b/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py index 615a8b366e..062d6367f7 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py +++ b/nipype/interfaces/fsl/tests/test_auto_AccuracyTester.py @@ -20,13 +20,11 @@ def test_AccuracyTester_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), trained_wts_file=dict( argstr='%s', mandatory=True, position=1, - usedefault=True, ), ) inputs = AccuracyTester.input_spec() @@ -39,7 +37,6 @@ def test_AccuracyTester_outputs(): output_directory=dict( argstr='%s', position=1, - usedefault=True, ), ) outputs = AccuracyTester.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py index 4d7f79dcfd..8a39956c18 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py @@ -14,7 +14,6 @@ def test_ApplyMask_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -24,7 +23,6 @@ def test_ApplyMask_inputs(): argstr='-mas %s', mandatory=True, position=4, - usedefault=True, ), nan2zeros=dict( argstr='-nan', @@ -35,7 +33,6 @@ def test_ApplyMask_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -49,7 +46,7 @@ def test_ApplyMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyMask_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ApplyMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py index 8a8c03dc3d..7a803f9695 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py @@ -10,7 +10,6 @@ def test_ApplyTOPUP_inputs(): encoding_file=dict( argstr='--datain=%s', mandatory=True, - usedefault=True, ), environ=dict( nohash=True, @@ -29,12 +28,10 @@ def test_ApplyTOPUP_inputs(): argstr='--topup=%s', copyfile=False, requires=['in_topup_movpar'], - usedefault=True, ), in_topup_movpar=dict( copyfile=False, requires=['in_topup_fieldcoef'], - usedefault=True, ), interp=dict(argstr='--interp=%s', ), method=dict(argstr='--method=%s', ), @@ -42,7 +39,6 @@ def test_ApplyTOPUP_inputs(): argstr='--out=%s', name_source=['in_files'], name_template='%s_corrected', - usedefault=True, ), output_type=dict(), ) @@ -52,7 +48,7 @@ def test_ApplyTOPUP_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyTOPUP_outputs(): - output_map = dict(out_corrected=dict(usedefault=True, ), ) + output_map = dict(out_corrected=dict(), ) outputs = ApplyTOPUP.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py index 5fa27c8d36..71977cb873 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py @@ -15,45 +15,30 @@ def test_ApplyWarp_inputs(): nohash=True, usedefault=True, ), - field_file=dict( - argstr='--warp=%s', - usedefault=True, - ), + field_file=dict(argstr='--warp=%s', ), in_file=dict( argstr='--in=%s', mandatory=True, position=0, - usedefault=True, ), interp=dict( argstr='--interp=%s', position=-2, ), - mask_file=dict( - argstr='--mask=%s', - usedefault=True, - ), + mask_file=dict(argstr='--mask=%s', ), out_file=dict( argstr='--out=%s', genfile=True, hash_files=False, position=2, - usedefault=True, ), output_type=dict(), - postmat=dict( - argstr='--postmat=%s', - usedefault=True, - ), - premat=dict( - argstr='--premat=%s', - usedefault=True, - ), + postmat=dict(argstr='--postmat=%s', ), + premat=dict(argstr='--premat=%s', ), ref_file=dict( argstr='--ref=%s', mandatory=True, position=1, - usedefault=True, ), relwarp=dict( argstr='--rel', @@ -69,7 +54,7 @@ def test_ApplyWarp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyWarp_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ApplyWarp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py b/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py index 9f1b52b701..f515be1f04 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py @@ -45,12 +45,10 @@ def test_ApplyXFM_inputs(): fieldmap=dict( argstr='-fieldmap %s', min_ver='5.0.0', - usedefault=True, ), fieldmapmask=dict( argstr='-fieldmapmask %s', min_ver='5.0.0', - usedefault=True, ), fine_search=dict( argstr='-finesearch %d', @@ -61,16 +59,9 @@ def test_ApplyXFM_inputs(): argstr='-in %s', mandatory=True, position=0, - usedefault=True, - ), - in_matrix_file=dict( - argstr='-init %s', - usedefault=True, - ), - in_weight=dict( - argstr='-inweight %s', - usedefault=True, ), + in_matrix_file=dict(argstr='-init %s', ), + in_weight=dict(argstr='-inweight %s', ), interp=dict(argstr='-interp %s', ), min_sampling=dict( argstr='-minsampling %f', @@ -86,14 +77,12 @@ def test_ApplyXFM_inputs(): name_source=['in_file'], name_template='%s_flirt', position=2, - usedefault=True, ), out_log=dict( keep_extension=True, name_source=['in_file'], name_template='%s_flirt.log', requires=['save_log'], - usedefault=True, ), out_matrix_file=dict( argstr='-omat %s', @@ -102,7 +91,6 @@ def test_ApplyXFM_inputs(): name_source=['in_file'], name_template='%s_flirt.mat', position=3, - usedefault=True, ), output_type=dict(), padding_size=dict( @@ -113,22 +101,15 @@ def test_ApplyXFM_inputs(): argstr='-pedir %d', min_ver='5.0.0', ), - ref_weight=dict( - argstr='-refweight %s', - usedefault=True, - ), + ref_weight=dict(argstr='-refweight %s', ), reference=dict( argstr='-ref %s', mandatory=True, position=1, - usedefault=True, ), rigid2D=dict(argstr='-2D', ), save_log=dict(), - schedule=dict( - argstr='-schedule %s', - usedefault=True, - ), + schedule=dict(argstr='-schedule %s', ), searchr_x=dict( argstr='-searchrx %s', units='degrees', @@ -151,17 +132,14 @@ def test_ApplyXFM_inputs(): wm_seg=dict( argstr='-wmseg %s', min_ver='5.0.0', - usedefault=True, ), wmcoords=dict( argstr='-wmcoords %s', min_ver='5.0.0', - usedefault=True, ), wmnorms=dict( argstr='-wmnorms %s', min_ver='5.0.0', - usedefault=True, ), ) inputs = ApplyXFM.input_spec() @@ -171,9 +149,9 @@ def test_ApplyXFM_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyXFM_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - out_log=dict(usedefault=True, ), - out_matrix_file=dict(usedefault=True, ), + out_file=dict(), + out_log=dict(), + out_matrix_file=dict(), ) outputs = ApplyXFM.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_AvScale.py b/nipype/interfaces/fsl/tests/test_auto_AvScale.py index 0c0f6cc21a..762ada916d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AvScale.py +++ b/nipype/interfaces/fsl/tests/test_auto_AvScale.py @@ -14,12 +14,10 @@ def test_AvScale_inputs(): mat_file=dict( argstr='%s', position=-2, - usedefault=True, ), ref_file=dict( argstr='%s', position=-1, - usedefault=True, ), ) inputs = AvScale.input_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_B0Calc.py b/nipype/interfaces/fsl/tests/test_auto_B0Calc.py index 6037a02cff..96ec6b949c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_B0Calc.py +++ b/nipype/interfaces/fsl/tests/test_auto_B0Calc.py @@ -34,7 +34,6 @@ def test_B0Calc_inputs(): argstr='-i %s', mandatory=True, position=0, - usedefault=True, ), out_file=dict( argstr='-o %s', @@ -42,7 +41,6 @@ def test_B0Calc_inputs(): name_template='%s_b0field', output_name='out_file', position=1, - usedefault=True, ), output_type=dict(), x_b0=dict( @@ -83,7 +81,7 @@ def test_B0Calc_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_B0Calc_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = B0Calc.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py index ab53f454a4..1ac5db111b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py +++ b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py @@ -18,22 +18,13 @@ def test_BEDPOSTX5_inputs(): argstr='--burnin_noard=%d', usedefault=True, ), - bvals=dict( - mandatory=True, - usedefault=True, - ), - bvecs=dict( - mandatory=True, - usedefault=True, - ), + bvals=dict(mandatory=True, ), + bvecs=dict(mandatory=True, ), cnlinear=dict( argstr='--cnonlinear', xor=('no_spat', 'non_linear', 'cnlinear'), ), - dwi=dict( - mandatory=True, - usedefault=True, - ), + dwi=dict(mandatory=True, ), environ=dict( nohash=True, usedefault=True, @@ -51,16 +42,10 @@ def test_BEDPOSTX5_inputs(): usedefault=True, ), fudge=dict(argstr='-w %d', ), - grad_dev=dict(usedefault=True, ), + grad_dev=dict(), gradnonlin=dict(argstr='-g', ), - logdir=dict( - argstr='--logdir=%s', - usedefault=True, - ), - mask=dict( - mandatory=True, - usedefault=True, - ), + logdir=dict(argstr='--logdir=%s', ), + mask=dict(mandatory=True, ), model=dict(argstr='-model %d', ), n_fibres=dict( argstr='-n %d', @@ -111,8 +96,8 @@ def test_BEDPOSTX5_outputs(): output_map = dict( dyads=dict(), dyads_dispersion=dict(), - mean_S0samples=dict(usedefault=True, ), - mean_dsamples=dict(usedefault=True, ), + mean_S0samples=dict(), + mean_dsamples=dict(), mean_fsamples=dict(), mean_phsamples=dict(), mean_thsamples=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_BET.py b/nipype/interfaces/fsl/tests/test_auto_BET.py index d7f8341811..eccf348b3e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BET.py +++ b/nipype/interfaces/fsl/tests/test_auto_BET.py @@ -24,7 +24,6 @@ def test_BET_inputs(): argstr='%s', mandatory=True, position=0, - usedefault=True, ), mask=dict(argstr='-m', ), mesh=dict(argstr='-e', ), @@ -34,7 +33,6 @@ def test_BET_inputs(): genfile=True, hash_files=False, position=1, - usedefault=True, ), outline=dict(argstr='-o', ), output_type=dict(), @@ -70,7 +68,6 @@ def test_BET_inputs(): ), t2_guided=dict( argstr='-A2 %s', - usedefault=True, xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), ), @@ -84,17 +81,17 @@ def test_BET_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BET_outputs(): output_map = dict( - inskull_mask_file=dict(usedefault=True, ), - inskull_mesh_file=dict(usedefault=True, ), - mask_file=dict(usedefault=True, ), - meshfile=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), - outline_file=dict(usedefault=True, ), - outskin_mask_file=dict(usedefault=True, ), - outskin_mesh_file=dict(usedefault=True, ), - outskull_mask_file=dict(usedefault=True, ), - outskull_mesh_file=dict(usedefault=True, ), - skull_mask_file=dict(usedefault=True, ), + inskull_mask_file=dict(), + inskull_mesh_file=dict(), + mask_file=dict(), + meshfile=dict(), + out_file=dict(), + outline_file=dict(), + outskin_mask_file=dict(), + outskin_mesh_file=dict(), + outskull_mask_file=dict(), + outskull_mesh_file=dict(), + skull_mask_file=dict(), ) outputs = BET.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py index c33648ccda..2548ae68e5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py @@ -14,7 +14,6 @@ def test_BinaryMaths_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -28,7 +27,6 @@ def test_BinaryMaths_inputs(): argstr='%s', mandatory=True, position=5, - usedefault=True, xor=['operand_value'], ), operand_value=dict( @@ -47,7 +45,6 @@ def test_BinaryMaths_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -61,7 +58,7 @@ def test_BinaryMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinaryMaths_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = BinaryMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py index c4f60c5862..aab508f2bf 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py +++ b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py @@ -14,7 +14,6 @@ def test_ChangeDataType_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -29,7 +28,6 @@ def test_ChangeDataType_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -44,7 +42,7 @@ def test_ChangeDataType_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ChangeDataType_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ChangeDataType.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Classifier.py b/nipype/interfaces/fsl/tests/test_auto_Classifier.py index 784e75a250..a8db888acb 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Classifier.py +++ b/nipype/interfaces/fsl/tests/test_auto_Classifier.py @@ -6,7 +6,7 @@ def test_Classifier_inputs(): input_map = dict( args=dict(argstr='%s', ), - artifacts_list_file=dict(usedefault=True, ), + artifacts_list_file=dict(), environ=dict( nohash=True, usedefault=True, @@ -15,7 +15,6 @@ def test_Classifier_inputs(): argstr='%s', copyfile=False, position=1, - usedefault=True, ), thresh=dict( argstr='%d', @@ -27,7 +26,6 @@ def test_Classifier_inputs(): copyfile=False, mandatory=True, position=2, - usedefault=True, ), ) inputs = Classifier.input_spec() @@ -36,7 +34,7 @@ def test_Classifier_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Classifier_outputs(): - output_map = dict(artifacts_list_file=dict(usedefault=True, ), ) + output_map = dict(artifacts_list_file=dict(), ) outputs = Classifier.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Cleaner.py b/nipype/interfaces/fsl/tests/test_auto_Cleaner.py index e5fac9f4f8..5fc505a174 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cleaner.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cleaner.py @@ -14,7 +14,6 @@ def test_Cleaner_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), cleanup_motion=dict( argstr='-m', @@ -48,7 +47,7 @@ def test_Cleaner_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Cleaner_outputs(): - output_map = dict(cleaned_functional_file=dict(usedefault=True, ), ) + output_map = dict(cleaned_functional_file=dict(), ) outputs = Cleaner.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Cluster.py b/nipype/interfaces/fsl/tests/test_auto_Cluster.py index ac36533a80..f876f85e64 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cluster.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cluster.py @@ -24,7 +24,6 @@ def test_Cluster_inputs(): in_file=dict( argstr='--in=%s', mandatory=True, - usedefault=True, ), minclustersize=dict( argstr='--minclustersize', @@ -73,10 +72,7 @@ def test_Cluster_inputs(): argstr='--pthresh=%.10f', requires=['dlh', 'volume'], ), - std_space_file=dict( - argstr='--stdvol=%s', - usedefault=True, - ), + std_space_file=dict(argstr='--stdvol=%s', ), threshold=dict( argstr='--thresh=%.10f', mandatory=True, @@ -86,14 +82,8 @@ def test_Cluster_inputs(): usedefault=True, ), volume=dict(argstr='--volume=%d', ), - warpfield_file=dict( - argstr='--warpvol=%s', - usedefault=True, - ), - xfm_file=dict( - argstr='--xfm=%s', - usedefault=True, - ), + warpfield_file=dict(argstr='--warpvol=%s', ), + xfm_file=dict(argstr='--xfm=%s', ), ) inputs = Cluster.input_spec() @@ -102,14 +92,14 @@ def test_Cluster_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Cluster_outputs(): output_map = dict( - index_file=dict(usedefault=True, ), - localmax_txt_file=dict(usedefault=True, ), - localmax_vol_file=dict(usedefault=True, ), - max_file=dict(usedefault=True, ), - mean_file=dict(usedefault=True, ), - pval_file=dict(usedefault=True, ), - size_file=dict(usedefault=True, ), - threshold_file=dict(usedefault=True, ), + index_file=dict(), + localmax_txt_file=dict(), + localmax_vol_file=dict(), + max_file=dict(), + mean_file=dict(), + pval_file=dict(), + size_file=dict(), + threshold_file=dict(), ) outputs = Cluster.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Complex.py b/nipype/interfaces/fsl/tests/test_auto_Complex.py index 31f83f5b75..7e49bcdfa8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Complex.py +++ b/nipype/interfaces/fsl/tests/test_auto_Complex.py @@ -17,12 +17,10 @@ def test_Complex_inputs(): complex_in_file=dict( argstr='%s', position=2, - usedefault=True, ), complex_in_file2=dict( argstr='%s', position=3, - usedefault=True, ), complex_merge=dict( argstr='-complexmerge', @@ -37,7 +35,6 @@ def test_Complex_inputs(): argstr='%s', genfile=True, position=-3, - usedefault=True, xor=[ 'complex_out_file', 'magnitude_out_file', 'phase_out_file', 'real_out_file', 'imaginary_out_file', 'real_polar', @@ -71,13 +68,11 @@ def test_Complex_inputs(): imaginary_in_file=dict( argstr='%s', position=3, - usedefault=True, ), imaginary_out_file=dict( argstr='%s', genfile=True, position=-3, - usedefault=True, xor=[ 'complex_out_file', 'magnitude_out_file', 'phase_out_file', 'real_polar', 'complex_cartesian', 'complex_polar', @@ -87,13 +82,11 @@ def test_Complex_inputs(): magnitude_in_file=dict( argstr='%s', position=2, - usedefault=True, ), magnitude_out_file=dict( argstr='%s', genfile=True, position=-4, - usedefault=True, xor=[ 'complex_out_file', 'real_out_file', 'imaginary_out_file', 'real_cartesian', 'complex_cartesian', 'complex_polar', @@ -104,13 +97,11 @@ def test_Complex_inputs(): phase_in_file=dict( argstr='%s', position=3, - usedefault=True, ), phase_out_file=dict( argstr='%s', genfile=True, position=-3, - usedefault=True, xor=[ 'complex_out_file', 'real_out_file', 'imaginary_out_file', 'real_cartesian', 'complex_cartesian', 'complex_polar', @@ -128,13 +119,11 @@ def test_Complex_inputs(): real_in_file=dict( argstr='%s', position=2, - usedefault=True, ), real_out_file=dict( argstr='%s', genfile=True, position=-4, - usedefault=True, xor=[ 'complex_out_file', 'magnitude_out_file', 'phase_out_file', 'real_polar', 'complex_cartesian', 'complex_polar', @@ -161,11 +150,11 @@ def test_Complex_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Complex_outputs(): output_map = dict( - complex_out_file=dict(usedefault=True, ), - imaginary_out_file=dict(usedefault=True, ), - magnitude_out_file=dict(usedefault=True, ), - phase_out_file=dict(usedefault=True, ), - real_out_file=dict(usedefault=True, ), + complex_out_file=dict(), + imaginary_out_file=dict(), + magnitude_out_file=dict(), + phase_out_file=dict(), + real_out_file=dict(), ) outputs = Complex.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py index 928f84fcf7..a82ea8fe43 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py +++ b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py @@ -10,22 +10,17 @@ def test_ContrastMgr_inputs(): corrections=dict( copyfile=False, mandatory=True, - usedefault=True, ), dof_file=dict( argstr='', copyfile=False, mandatory=True, - usedefault=True, ), environ=dict( nohash=True, usedefault=True, ), - fcon_file=dict( - argstr='-f %s', - usedefault=True, - ), + fcon_file=dict(argstr='-f %s', ), output_type=dict(), param_estimates=dict( argstr='', @@ -37,14 +32,12 @@ def test_ContrastMgr_inputs(): copyfile=False, mandatory=True, position=-2, - usedefault=True, ), suffix=dict(argstr='-suffix %s', ), tcon_file=dict( argstr='%s', mandatory=True, position=-1, - usedefault=True, ), ) inputs = ContrastMgr.input_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py index 3bb8bebf8b..2ed14aaad2 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py @@ -17,10 +17,7 @@ def test_ConvertWarp_inputs(): ), jacobian_max=dict(argstr='--jmax=%f', ), jacobian_min=dict(argstr='--jmin=%f', ), - midmat=dict( - argstr='--midmat=%s', - usedefault=True, - ), + midmat=dict(argstr='--midmat=%s', ), out_abswarp=dict( argstr='--absout', xor=['out_relwarp'], @@ -31,26 +28,18 @@ def test_ConvertWarp_inputs(): name_template='%s_concatwarp', output_name='out_file', position=-1, - usedefault=True, ), out_relwarp=dict( argstr='--relout', xor=['out_abswarp'], ), output_type=dict(), - postmat=dict( - argstr='--postmat=%s', - usedefault=True, - ), - premat=dict( - argstr='--premat=%s', - usedefault=True, - ), + postmat=dict(argstr='--postmat=%s', ), + premat=dict(argstr='--premat=%s', ), reference=dict( argstr='--ref=%s', mandatory=True, position=1, - usedefault=True, ), relwarp=dict( argstr='--rel', @@ -60,18 +49,9 @@ def test_ConvertWarp_inputs(): argstr='--shiftdir=%s', requires=['shift_in_file'], ), - shift_in_file=dict( - argstr='--shiftmap=%s', - usedefault=True, - ), - warp1=dict( - argstr='--warp1=%s', - usedefault=True, - ), - warp2=dict( - argstr='--warp2=%s', - usedefault=True, - ), + shift_in_file=dict(argstr='--shiftmap=%s', ), + warp1=dict(argstr='--warp1=%s', ), + warp2=dict(argstr='--warp2=%s', ), ) inputs = ConvertWarp.input_spec() @@ -79,7 +59,7 @@ def test_ConvertWarp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConvertWarp_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ConvertWarp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py index dd23d7dbde..c017a39a52 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py @@ -26,12 +26,10 @@ def test_ConvertXFM_inputs(): argstr='%s', mandatory=True, position=-1, - usedefault=True, ), in_file2=dict( argstr='%s', position=-2, - usedefault=True, ), invert_xfm=dict( argstr='-inverse', @@ -43,7 +41,6 @@ def test_ConvertXFM_inputs(): genfile=True, hash_files=False, position=1, - usedefault=True, ), output_type=dict(), ) @@ -53,7 +50,7 @@ def test_ConvertXFM_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConvertXFM_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ConvertXFM.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py index 499e76adc3..c66feff211 100644 --- a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py +++ b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py @@ -14,7 +14,6 @@ def test_CopyGeom_inputs(): name_template='%s', output_name='out_file', position=1, - usedefault=True, ), environ=dict( nohash=True, @@ -28,7 +27,6 @@ def test_CopyGeom_inputs(): argstr='%s', mandatory=True, position=0, - usedefault=True, ), output_type=dict(), ) @@ -38,7 +36,7 @@ def test_CopyGeom_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CopyGeom_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = CopyGeom.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py index 260d59b11a..b1d3b4822d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py @@ -15,38 +15,28 @@ def test_DTIFit_inputs(): argstr='-b %s', mandatory=True, position=4, - usedefault=True, ), bvecs=dict( argstr='-r %s', mandatory=True, position=3, - usedefault=True, - ), - cni=dict( - argstr='--cni=%s', - usedefault=True, ), + cni=dict(argstr='--cni=%s', ), dwi=dict( argstr='-k %s', mandatory=True, position=0, - usedefault=True, ), environ=dict( nohash=True, usedefault=True, ), - gradnonlin=dict( - argstr='--gradnonlin=%s', - usedefault=True, - ), + gradnonlin=dict(argstr='--gradnonlin=%s', ), little_bit=dict(argstr='--littlebit', ), mask=dict( argstr='-m %s', mandatory=True, position=2, - usedefault=True, ), max_x=dict(argstr='-X %d', ), max_y=dict(argstr='-Y %d', ), @@ -65,18 +55,18 @@ def test_DTIFit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DTIFit_outputs(): output_map = dict( - FA=dict(usedefault=True, ), - L1=dict(usedefault=True, ), - L2=dict(usedefault=True, ), - L3=dict(usedefault=True, ), - MD=dict(usedefault=True, ), - MO=dict(usedefault=True, ), - S0=dict(usedefault=True, ), - V1=dict(usedefault=True, ), - V2=dict(usedefault=True, ), - V3=dict(usedefault=True, ), - sse=dict(usedefault=True, ), - tensor=dict(usedefault=True, ), + FA=dict(), + L1=dict(), + L2=dict(), + L3=dict(), + MD=dict(), + MO=dict(), + S0=dict(), + V1=dict(), + V2=dict(), + V3=dict(), + sse=dict(), + tensor=dict(), ) outputs = DTIFit.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py index 9d748e6edc..3ed43fbd22 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py @@ -14,7 +14,6 @@ def test_DilateImage_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -23,7 +22,6 @@ def test_DilateImage_inputs(): kernel_file=dict( argstr='%s', position=5, - usedefault=True, xor=['kernel_size'], ), kernel_shape=dict( @@ -49,7 +47,6 @@ def test_DilateImage_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -63,7 +60,7 @@ def test_DilateImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DilateImage_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = DilateImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py index 1caf8a1926..5f3321de78 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py +++ b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py @@ -10,7 +10,6 @@ def test_DistanceMap_inputs(): argstr='--out=%s', genfile=True, hash_files=False, - usedefault=True, ), environ=dict( nohash=True, @@ -19,17 +18,13 @@ def test_DistanceMap_inputs(): in_file=dict( argstr='--in=%s', mandatory=True, - usedefault=True, ), invert_input=dict(argstr='--invert', ), local_max_file=dict( argstr='--localmax=%s', hash_files=False, ), - mask_file=dict( - argstr='--mask=%s', - usedefault=True, - ), + mask_file=dict(argstr='--mask=%s', ), output_type=dict(), ) inputs = DistanceMap.input_spec() @@ -39,8 +34,8 @@ def test_DistanceMap_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DistanceMap_outputs(): output_map = dict( - distance_map=dict(usedefault=True, ), - local_max_file=dict(usedefault=True, ), + distance_map=dict(), + local_max_file=dict(), ) outputs = DistanceMap.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_DualRegression.py b/nipype/interfaces/fsl/tests/test_auto_DualRegression.py index 4d69e0609f..4c2fdd3ceb 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DualRegression.py +++ b/nipype/interfaces/fsl/tests/test_auto_DualRegression.py @@ -9,7 +9,6 @@ def test_DualRegression_inputs(): con_file=dict( argstr='%s', position=4, - usedefault=True, ), des_norm=dict( argstr='%i', @@ -19,7 +18,6 @@ def test_DualRegression_inputs(): design_file=dict( argstr='%s', position=3, - usedefault=True, ), environ=dict( nohash=True, @@ -29,7 +27,6 @@ def test_DualRegression_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), in_files=dict( argstr='%s', @@ -60,7 +57,7 @@ def test_DualRegression_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DualRegression_outputs(): - output_map = dict(out_dir=dict(usedefault=True, ), ) + output_map = dict(out_dir=dict(), ) outputs = DualRegression.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py index eb226f6bee..2a5f0c86b6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py @@ -10,16 +10,12 @@ def test_EPIDeWarp_inputs(): dph_file=dict( argstr='--dph %s', mandatory=True, - usedefault=True, ), environ=dict( nohash=True, usedefault=True, ), - epi_file=dict( - argstr='--epi %s', - usedefault=True, - ), + epi_file=dict(argstr='--epi %s', ), epidw=dict( argstr='--epidw %s', genfile=False, @@ -28,10 +24,7 @@ def test_EPIDeWarp_inputs(): argstr='--esp %s', usedefault=True, ), - exf_file=dict( - argstr='--exf %s', - usedefault=True, - ), + exf_file=dict(argstr='--exf %s', ), exfdw=dict( argstr='--exfdw %s', genfile=True, @@ -40,7 +33,6 @@ def test_EPIDeWarp_inputs(): argstr='--mag %s', mandatory=True, position=0, - usedefault=True, ), nocleanup=dict( argstr='--nocleanup', @@ -71,10 +63,10 @@ def test_EPIDeWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EPIDeWarp_outputs(): output_map = dict( - exf_mask=dict(usedefault=True, ), - exfdw=dict(usedefault=True, ), - unwarped_file=dict(usedefault=True, ), - vsm_file=dict(usedefault=True, ), + exf_mask=dict(), + exfdw=dict(), + unwarped_file=dict(), + vsm_file=dict(), ) outputs = EPIDeWarp.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Eddy.py b/nipype/interfaces/fsl/tests/test_auto_Eddy.py index 6457370353..55d9409e17 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Eddy.py +++ b/nipype/interfaces/fsl/tests/test_auto_Eddy.py @@ -18,10 +18,7 @@ def test_Eddy_inputs(): ), fep=dict(argstr='--fep', ), field=dict(argstr='--field=%s', ), - field_mat=dict( - argstr='--field_mat=%s', - usedefault=True, - ), + field_mat=dict(argstr='--field_mat=%s', ), flm=dict(argstr='--flm=%s', ), fudge_factor=dict( argstr='--ff=%s', @@ -31,42 +28,32 @@ def test_Eddy_inputs(): in_acqp=dict( argstr='--acqp=%s', mandatory=True, - usedefault=True, ), in_bval=dict( argstr='--bvals=%s', mandatory=True, - usedefault=True, ), in_bvec=dict( argstr='--bvecs=%s', mandatory=True, - usedefault=True, ), in_file=dict( argstr='--imain=%s', mandatory=True, - usedefault=True, ), in_index=dict( argstr='--index=%s', mandatory=True, - usedefault=True, ), in_mask=dict( argstr='--mask=%s', mandatory=True, - usedefault=True, ), in_topup_fieldcoef=dict( argstr='--topup=%s', requires=['in_topup_movpar'], - usedefault=True, - ), - in_topup_movpar=dict( - requires=['in_topup_fieldcoef'], - usedefault=True, ), + in_topup_movpar=dict(requires=['in_topup_fieldcoef'], ), interp=dict(argstr='--interp=%s', ), is_shelled=dict(argstr='--data_is_shelled', ), method=dict(argstr='--resamp=%s', ), @@ -92,10 +79,7 @@ def test_Eddy_inputs(): argstr='--residuals', min_ver='5.0.10', ), - session=dict( - argstr='--session=%s', - usedefault=True, - ), + session=dict(argstr='--session=%s', ), slm=dict(argstr='--slm=%s', ), use_cuda=dict(), ) @@ -106,15 +90,15 @@ def test_Eddy_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Eddy_outputs(): output_map = dict( - out_cnr_maps=dict(usedefault=True, ), - out_corrected=dict(usedefault=True, ), - out_movement_rms=dict(usedefault=True, ), - out_outlier_report=dict(usedefault=True, ), - out_parameter=dict(usedefault=True, ), - out_residuals=dict(usedefault=True, ), - out_restricted_movement_rms=dict(usedefault=True, ), - out_rotated_bvecs=dict(usedefault=True, ), - out_shell_alignment_parameters=dict(usedefault=True, ), + out_cnr_maps=dict(), + out_corrected=dict(), + out_movement_rms=dict(), + out_outlier_report=dict(), + out_parameter=dict(), + out_residuals=dict(), + out_restricted_movement_rms=dict(), + out_rotated_bvecs=dict(), + out_shell_alignment_parameters=dict(), ) outputs = Eddy.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py index 41de073264..e88219aa04 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py +++ b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py @@ -14,7 +14,6 @@ def test_EddyCorrect_inputs(): argstr='%s', mandatory=True, position=0, - usedefault=True, ), out_file=dict( argstr='%s', @@ -22,7 +21,6 @@ def test_EddyCorrect_inputs(): name_template='%s_edc', output_name='eddy_corrected', position=1, - usedefault=True, ), output_type=dict(), ref_num=dict( @@ -38,7 +36,7 @@ def test_EddyCorrect_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EddyCorrect_outputs(): - output_map = dict(eddy_corrected=dict(usedefault=True, ), ) + output_map = dict(eddy_corrected=dict(), ) outputs = EddyCorrect.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py b/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py index 35afe6da13..3cc6da2027 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py +++ b/nipype/interfaces/fsl/tests/test_auto_EddyQuad.py @@ -14,29 +14,20 @@ def test_EddyQuad_inputs(): bval_file=dict( argstr='--bvals %s', mandatory=True, - usedefault=True, - ), - bvec_file=dict( - argstr='--bvecs %s', - usedefault=True, ), + bvec_file=dict(argstr='--bvecs %s', ), environ=dict( nohash=True, usedefault=True, ), - field=dict( - argstr='--field %s', - usedefault=True, - ), + field=dict(argstr='--field %s', ), idx_file=dict( argstr='--eddyIdx %s', mandatory=True, - usedefault=True, ), mask_file=dict( argstr='--mask %s', mandatory=True, - usedefault=True, ), output_dir=dict( argstr='--output-dir %s', @@ -47,12 +38,8 @@ def test_EddyQuad_inputs(): param_file=dict( argstr='--eddyParams %s', mandatory=True, - usedefault=True, - ), - slice_spec=dict( - argstr='--slspec %s', - usedefault=True, ), + slice_spec=dict(argstr='--slspec %s', ), verbose=dict(argstr='--verbose', ), ) inputs = EddyQuad.input_spec() @@ -64,12 +51,12 @@ def test_EddyQuad_outputs(): output_map = dict( avg_b0_pe_png=dict(), avg_b_png=dict(), - clean_volumes=dict(usedefault=True, ), + clean_volumes=dict(), cnr_png=dict(), - qc_json=dict(usedefault=True, ), - qc_pdf=dict(usedefault=True, ), - residuals=dict(usedefault=True, ), - vdm_png=dict(usedefault=True, ), + qc_json=dict(), + qc_pdf=dict(), + residuals=dict(), + vdm_png=dict(), ) outputs = EddyQuad.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py index 351c4684ac..634a75e376 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py @@ -15,20 +15,10 @@ def test_EpiReg_inputs(): argstr='--epi=%s', mandatory=True, position=-4, - usedefault=True, - ), - fmap=dict( - argstr='--fmap=%s', - usedefault=True, - ), - fmapmag=dict( - argstr='--fmapmag=%s', - usedefault=True, - ), - fmapmagbrain=dict( - argstr='--fmapmagbrain=%s', - usedefault=True, ), + fmap=dict(argstr='--fmap=%s', ), + fmapmag=dict(argstr='--fmapmag=%s', ), + fmapmagbrain=dict(argstr='--fmapmagbrain=%s', ), no_clean=dict( argstr='--noclean', usedefault=True, @@ -45,22 +35,14 @@ def test_EpiReg_inputs(): argstr='--t1brain=%s', mandatory=True, position=-2, - usedefault=True, ), t1_head=dict( argstr='--t1=%s', mandatory=True, position=-3, - usedefault=True, - ), - weight_image=dict( - argstr='--weight=%s', - usedefault=True, - ), - wmseg=dict( - argstr='--wmseg=%s', - usedefault=True, ), + weight_image=dict(argstr='--weight=%s', ), + wmseg=dict(argstr='--wmseg=%s', ), ) inputs = EpiReg.input_spec() @@ -69,20 +51,20 @@ def test_EpiReg_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EpiReg_outputs(): output_map = dict( - epi2str_inv=dict(usedefault=True, ), - epi2str_mat=dict(usedefault=True, ), - fmap2epi_mat=dict(usedefault=True, ), - fmap2str_mat=dict(usedefault=True, ), - fmap_epi=dict(usedefault=True, ), - fmap_str=dict(usedefault=True, ), - fmapmag_str=dict(usedefault=True, ), - fullwarp=dict(usedefault=True, ), - out_1vol=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), - seg=dict(usedefault=True, ), - shiftmap=dict(usedefault=True, ), - wmedge=dict(usedefault=True, ), - wmseg=dict(usedefault=True, ), + epi2str_inv=dict(), + epi2str_mat=dict(), + fmap2epi_mat=dict(), + fmap2str_mat=dict(), + fmap_epi=dict(), + fmap_str=dict(), + fmapmag_str=dict(), + fullwarp=dict(), + out_1vol=dict(), + out_file=dict(), + seg=dict(), + shiftmap=dict(), + wmedge=dict(), + wmseg=dict(), ) outputs = EpiReg.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py index 997f810204..797a403d45 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py @@ -14,7 +14,6 @@ def test_ErodeImage_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -23,7 +22,6 @@ def test_ErodeImage_inputs(): kernel_file=dict( argstr='%s', position=5, - usedefault=True, xor=['kernel_size'], ), kernel_shape=dict( @@ -49,7 +47,6 @@ def test_ErodeImage_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -63,7 +60,7 @@ def test_ErodeImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ErodeImage_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ErodeImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py index 4eec8dd12d..df8de64144 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py +++ b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py @@ -22,7 +22,6 @@ def test_ExtractROI_inputs(): argstr='%s', mandatory=True, position=0, - usedefault=True, ), output_type=dict(), roi_file=dict( @@ -30,7 +29,6 @@ def test_ExtractROI_inputs(): genfile=True, hash_files=False, position=1, - usedefault=True, ), t_min=dict( argstr='%d', @@ -71,7 +69,7 @@ def test_ExtractROI_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ExtractROI_outputs(): - output_map = dict(roi_file=dict(usedefault=True, ), ) + output_map = dict(roi_file=dict(), ) outputs = ExtractROI.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_FAST.py b/nipype/interfaces/fsl/tests/test_auto_FAST.py index 51bf1329ba..0b983181af 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FAST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FAST.py @@ -24,24 +24,15 @@ def test_FAST_inputs(): position=-1, ), init_seg_smooth=dict(argstr='-f %.3f', ), - init_transform=dict( - argstr='-a %s', - usedefault=True, - ), + init_transform=dict(argstr='-a %s', ), iters_afterbias=dict(argstr='-O %d', ), - manual_seg=dict( - argstr='-s %s', - usedefault=True, - ), + manual_seg=dict(argstr='-s %s', ), mixel_smooth=dict(argstr='-R %.2f', ), no_bias=dict(argstr='-N', ), no_pve=dict(argstr='--nopve', ), number_classes=dict(argstr='-n %d', ), other_priors=dict(argstr='-A %s', ), - out_basename=dict( - argstr='-o %s', - usedefault=True, - ), + out_basename=dict(argstr='-o %s', ), output_biascorrected=dict(argstr='-B', ), output_biasfield=dict(argstr='-b', ), output_type=dict(), @@ -59,13 +50,13 @@ def test_FAST_inputs(): def test_FAST_outputs(): output_map = dict( bias_field=dict(), - mixeltype=dict(usedefault=True, ), + mixeltype=dict(), partial_volume_files=dict(), - partial_volume_map=dict(usedefault=True, ), + partial_volume_map=dict(), probability_maps=dict(), restored_image=dict(), tissue_class_files=dict(), - tissue_class_map=dict(usedefault=True, ), + tissue_class_map=dict(), ) outputs = FAST.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FEAT.py b/nipype/interfaces/fsl/tests/test_auto_FEAT.py index c2f96f43e2..01fc72506f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEAT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEAT.py @@ -14,7 +14,6 @@ def test_FEAT_inputs(): argstr='%s', mandatory=True, position=0, - usedefault=True, ), output_type=dict(), ) @@ -24,7 +23,7 @@ def test_FEAT_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FEAT_outputs(): - output_map = dict(feat_dir=dict(usedefault=True, ), ) + output_map = dict(feat_dir=dict(), ) outputs = FEAT.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py index 8fe45da4b7..34ea37d47f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py @@ -21,7 +21,6 @@ def test_FEATModel_inputs(): copyfile=False, mandatory=True, position=0, - usedefault=True, ), output_type=dict(), ) @@ -32,11 +31,11 @@ def test_FEATModel_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FEATModel_outputs(): output_map = dict( - con_file=dict(usedefault=True, ), - design_cov=dict(usedefault=True, ), - design_file=dict(usedefault=True, ), - design_image=dict(usedefault=True, ), - fcon_file=dict(usedefault=True, ), + con_file=dict(), + design_cov=dict(), + design_file=dict(), + design_image=dict(), + fcon_file=dict(), ) outputs = FEATModel.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py index af21df478b..a8f59a0ec3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py @@ -7,10 +7,7 @@ def test_FEATRegister_inputs(): input_map = dict( feat_dirs=dict(mandatory=True, ), reg_dof=dict(usedefault=True, ), - reg_image=dict( - mandatory=True, - usedefault=True, - ), + reg_image=dict(mandatory=True, ), ) inputs = FEATRegister.input_spec() @@ -18,7 +15,7 @@ def test_FEATRegister_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FEATRegister_outputs(): - output_map = dict(fsf_file=dict(usedefault=True, ), ) + output_map = dict(fsf_file=dict(), ) outputs = FEATRegister.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_FIRST.py b/nipype/interfaces/fsl/tests/test_auto_FIRST.py index 514a4fbbb1..964ee4922c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FIRST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FIRST.py @@ -8,7 +8,6 @@ def test_FIRST_inputs(): affine_file=dict( argstr='-a %s', position=6, - usedefault=True, ), args=dict(argstr='%s', ), brain_extracted=dict( @@ -24,7 +23,6 @@ def test_FIRST_inputs(): copyfile=False, mandatory=True, position=-2, - usedefault=True, ), list_of_specific_structures=dict( argstr='-s %s', @@ -66,8 +64,8 @@ def test_FIRST_inputs(): def test_FIRST_outputs(): output_map = dict( bvars=dict(), - original_segmentations=dict(usedefault=True, ), - segmentation_file=dict(usedefault=True, ), + original_segmentations=dict(), + segmentation_file=dict(), vtk_surfaces=dict(), ) outputs = FIRST.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py index 5a455f9c92..bd335282e3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py @@ -10,30 +10,21 @@ def test_FLAMEO_inputs(): cope_file=dict( argstr='--copefile=%s', mandatory=True, - usedefault=True, ), cov_split_file=dict( argstr='--covsplitfile=%s', mandatory=True, - usedefault=True, ), design_file=dict( argstr='--designfile=%s', mandatory=True, - usedefault=True, - ), - dof_var_cope_file=dict( - argstr='--dofvarcopefile=%s', - usedefault=True, ), + dof_var_cope_file=dict(argstr='--dofvarcopefile=%s', ), environ=dict( nohash=True, usedefault=True, ), - f_con_file=dict( - argstr='--fcontrastsfile=%s', - usedefault=True, - ), + f_con_file=dict(argstr='--fcontrastsfile=%s', ), fix_mean=dict(argstr='--fixmean', ), infer_outliers=dict(argstr='--inferoutliers', ), log_dir=dict( @@ -43,7 +34,6 @@ def test_FLAMEO_inputs(): mask_file=dict( argstr='--maskfile=%s', mandatory=True, - usedefault=True, ), n_jumps=dict(argstr='--njumps=%d', ), no_pe_outputs=dict(argstr='--nopeoutput', ), @@ -58,12 +48,8 @@ def test_FLAMEO_inputs(): t_con_file=dict( argstr='--tcontrastsfile=%s', mandatory=True, - usedefault=True, - ), - var_cope_file=dict( - argstr='--varcopefile=%s', - usedefault=True, ), + var_cope_file=dict(argstr='--varcopefile=%s', ), ) inputs = FLAMEO.input_spec() @@ -77,7 +63,7 @@ def test_FLAMEO_outputs(): mrefvars=dict(), pes=dict(), res4d=dict(), - stats_dir=dict(usedefault=True, ), + stats_dir=dict(), tdof=dict(), tstats=dict(), var_copes=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py index 4794488674..0b59550e5a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py @@ -42,12 +42,10 @@ def test_FLIRT_inputs(): fieldmap=dict( argstr='-fieldmap %s', min_ver='5.0.0', - usedefault=True, ), fieldmapmask=dict( argstr='-fieldmapmask %s', min_ver='5.0.0', - usedefault=True, ), fine_search=dict( argstr='-finesearch %d', @@ -58,16 +56,9 @@ def test_FLIRT_inputs(): argstr='-in %s', mandatory=True, position=0, - usedefault=True, - ), - in_matrix_file=dict( - argstr='-init %s', - usedefault=True, - ), - in_weight=dict( - argstr='-inweight %s', - usedefault=True, ), + in_matrix_file=dict(argstr='-init %s', ), + in_weight=dict(argstr='-inweight %s', ), interp=dict(argstr='-interp %s', ), min_sampling=dict( argstr='-minsampling %f', @@ -83,14 +74,12 @@ def test_FLIRT_inputs(): name_source=['in_file'], name_template='%s_flirt', position=2, - usedefault=True, ), out_log=dict( keep_extension=True, name_source=['in_file'], name_template='%s_flirt.log', requires=['save_log'], - usedefault=True, ), out_matrix_file=dict( argstr='-omat %s', @@ -99,7 +88,6 @@ def test_FLIRT_inputs(): name_source=['in_file'], name_template='%s_flirt.mat', position=3, - usedefault=True, ), output_type=dict(), padding_size=dict( @@ -110,22 +98,15 @@ def test_FLIRT_inputs(): argstr='-pedir %d', min_ver='5.0.0', ), - ref_weight=dict( - argstr='-refweight %s', - usedefault=True, - ), + ref_weight=dict(argstr='-refweight %s', ), reference=dict( argstr='-ref %s', mandatory=True, position=1, - usedefault=True, ), rigid2D=dict(argstr='-2D', ), save_log=dict(), - schedule=dict( - argstr='-schedule %s', - usedefault=True, - ), + schedule=dict(argstr='-schedule %s', ), searchr_x=dict( argstr='-searchrx %s', units='degrees', @@ -148,17 +129,14 @@ def test_FLIRT_inputs(): wm_seg=dict( argstr='-wmseg %s', min_ver='5.0.0', - usedefault=True, ), wmcoords=dict( argstr='-wmcoords %s', min_ver='5.0.0', - usedefault=True, ), wmnorms=dict( argstr='-wmnorms %s', min_ver='5.0.0', - usedefault=True, ), ) inputs = FLIRT.input_spec() @@ -168,9 +146,9 @@ def test_FLIRT_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FLIRT_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - out_log=dict(usedefault=True, ), - out_matrix_file=dict(usedefault=True, ), + out_file=dict(), + out_log=dict(), + out_matrix_file=dict(), ) outputs = FLIRT.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py index 052cc20231..2b7d0b1b00 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py @@ -5,10 +5,7 @@ def test_FNIRT_inputs(): input_map = dict( - affine_file=dict( - argstr='--aff=%s', - usedefault=True, - ), + affine_file=dict(argstr='--aff=%s', ), apply_inmask=dict( argstr='--applyinmask=%s', sep=',', @@ -42,7 +39,6 @@ def test_FNIRT_inputs(): in_file=dict( argstr='--in=%s', mandatory=True, - usedefault=True, ), in_fwhm=dict( argstr='--infwhm=%s', @@ -52,17 +48,11 @@ def test_FNIRT_inputs(): argstr='--intin=%s', copyfile=False, ), - inmask_file=dict( - argstr='--inmask=%s', - usedefault=True, - ), + inmask_file=dict(argstr='--inmask=%s', ), inmask_val=dict(argstr='--impinval=%f', ), intensity_mapping_model=dict(argstr='--intmod=%s', ), intensity_mapping_order=dict(argstr='--intorder=%d', ), - inwarp_file=dict( - argstr='--inwarp=%s', - usedefault=True, - ), + inwarp_file=dict(argstr='--inwarp=%s', ), jacobian_file=dict( argstr='--jout=%s', hash_files=False, @@ -72,7 +62,6 @@ def test_FNIRT_inputs(): argstr='--logout=%s', genfile=True, hash_files=False, - usedefault=True, ), max_nonlin_iter=dict( argstr='--miter=%s', @@ -90,16 +79,12 @@ def test_FNIRT_inputs(): ref_file=dict( argstr='--ref=%s', mandatory=True, - usedefault=True, ), ref_fwhm=dict( argstr='--reffwhm=%s', sep=',', ), - refmask_file=dict( - argstr='--refmask=%s', - usedefault=True, - ), + refmask_file=dict(argstr='--refmask=%s', ), refmask_val=dict(argstr='--imprefval=%f', ), regularization_lambda=dict( argstr='--lambda=%s', @@ -131,7 +116,6 @@ def test_FNIRT_inputs(): argstr='--iout=%s', genfile=True, hash_files=False, - usedefault=True, ), ) inputs = FNIRT.input_spec() @@ -141,13 +125,13 @@ def test_FNIRT_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FNIRT_outputs(): output_map = dict( - field_file=dict(usedefault=True, ), - fieldcoeff_file=dict(usedefault=True, ), - jacobian_file=dict(usedefault=True, ), - log_file=dict(usedefault=True, ), - modulatedref_file=dict(usedefault=True, ), + field_file=dict(), + fieldcoeff_file=dict(), + jacobian_file=dict(), + log_file=dict(), + modulatedref_file=dict(), out_intensitymap_file=dict(), - warped_file=dict(usedefault=True, ), + warped_file=dict(), ) outputs = FNIRT.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py index 23399e58f5..fd85eee3bf 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py @@ -21,12 +21,10 @@ def test_FSLXCommand_inputs(): bvals=dict( argstr='--bvals=%s', mandatory=True, - usedefault=True, ), bvecs=dict( argstr='--bvecs=%s', mandatory=True, - usedefault=True, ), cnlinear=dict( argstr='--cnonlinear', @@ -35,7 +33,6 @@ def test_FSLXCommand_inputs(): dwi=dict( argstr='--data=%s', mandatory=True, - usedefault=True, ), environ=dict( nohash=True, @@ -61,7 +58,6 @@ def test_FSLXCommand_inputs(): mask=dict( argstr='--mask=%s', mandatory=True, - usedefault=True, ), model=dict(argstr='--model=%d', ), n_fibres=dict( @@ -106,10 +102,10 @@ def test_FSLXCommand_outputs(): output_map = dict( dyads=dict(), fsamples=dict(), - mean_S0samples=dict(usedefault=True, ), - mean_dsamples=dict(usedefault=True, ), + mean_S0samples=dict(), + mean_dsamples=dict(), mean_fsamples=dict(), - mean_tausamples=dict(usedefault=True, ), + mean_tausamples=dict(), phsamples=dict(), thsamples=dict(), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py index 399555fd1a..0e96f1e867 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py +++ b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py @@ -15,14 +15,8 @@ def test_FUGUE_inputs(): nohash=True, usedefault=True, ), - fmap_in_file=dict( - argstr='--loadfmap=%s', - usedefault=True, - ), - fmap_out_file=dict( - argstr='--savefmap=%s', - usedefault=True, - ), + fmap_in_file=dict(argstr='--loadfmap=%s', ), + fmap_out_file=dict(argstr='--savefmap=%s', ), forward_warping=dict(usedefault=True, ), fourier_order=dict(argstr='--fourier=%d', ), icorr=dict( @@ -33,14 +27,8 @@ def test_FUGUE_inputs(): argstr='--icorronly', requires=['unwarped_file'], ), - in_file=dict( - argstr='--in=%s', - usedefault=True, - ), - mask_file=dict( - argstr='--mask=%s', - usedefault=True, - ), + in_file=dict(argstr='--in=%s', ), + mask_file=dict(argstr='--mask=%s', ), median_2dfilter=dict(argstr='--median', ), no_extend=dict(argstr='--noextend', ), no_gap_fill=dict(argstr='--nofill', ), @@ -48,10 +36,7 @@ def test_FUGUE_inputs(): output_type=dict(), pava=dict(argstr='--pava', ), phase_conjugate=dict(argstr='--phaseconj', ), - phasemap_in_file=dict( - argstr='--phasemap=%s', - usedefault=True, - ), + phasemap_in_file=dict(argstr='--phasemap=%s', ), poly_order=dict(argstr='--poly=%d', ), save_fmap=dict(xor=['save_unmasked_fmap'], ), save_shift=dict(xor=['save_unmasked_shift'], ), @@ -63,27 +48,19 @@ def test_FUGUE_inputs(): argstr='--unmaskshift', xor=['save_shift'], ), - shift_in_file=dict( - argstr='--loadshift=%s', - usedefault=True, - ), - shift_out_file=dict( - argstr='--saveshift=%s', - usedefault=True, - ), + shift_in_file=dict(argstr='--loadshift=%s', ), + shift_out_file=dict(argstr='--saveshift=%s', ), smooth2d=dict(argstr='--smooth2=%.2f', ), smooth3d=dict(argstr='--smooth3=%.2f', ), unwarp_direction=dict(argstr='--unwarpdir=%s', ), unwarped_file=dict( argstr='--unwarp=%s', requires=['in_file'], - usedefault=True, xor=['warped_file'], ), warped_file=dict( argstr='--warp=%s', requires=['in_file'], - usedefault=True, xor=['unwarped_file'], ), ) @@ -94,10 +71,10 @@ def test_FUGUE_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FUGUE_outputs(): output_map = dict( - fmap_out_file=dict(usedefault=True, ), - shift_out_file=dict(usedefault=True, ), - unwarped_file=dict(usedefault=True, ), - warped_file=dict(usedefault=True, ), + fmap_out_file=dict(), + shift_out_file=dict(), + unwarped_file=dict(), + warped_file=dict(), ) outputs = FUGUE.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py b/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py index 5cd92366b7..3945c40a87 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py +++ b/nipype/interfaces/fsl/tests/test_auto_FeatureExtractor.py @@ -14,7 +14,6 @@ def test_FeatureExtractor_inputs(): argstr='%s', copyfile=False, position=-1, - usedefault=True, ), ) inputs = FeatureExtractor.input_spec() @@ -28,7 +27,6 @@ def test_FeatureExtractor_outputs(): argstr='%s', copyfile=False, position=-1, - usedefault=True, ), ) outputs = FeatureExtractor.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py index fed7784be3..36cbb979d7 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py +++ b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py @@ -10,7 +10,6 @@ def test_FilterRegressor_inputs(): argstr='-d %s', mandatory=True, position=3, - usedefault=True, ), environ=dict( nohash=True, @@ -32,18 +31,13 @@ def test_FilterRegressor_inputs(): argstr='-i %s', mandatory=True, position=1, - usedefault=True, - ), - mask=dict( - argstr='-m %s', - usedefault=True, ), + mask=dict(argstr='-m %s', ), out_file=dict( argstr='-o %s', genfile=True, hash_files=False, position=2, - usedefault=True, ), out_vnscales=dict(argstr='--out_vnscales', ), output_type=dict(), @@ -55,7 +49,7 @@ def test_FilterRegressor_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FilterRegressor_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = FilterRegressor.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py index 2162579d00..3731c842e7 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py +++ b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py @@ -20,7 +20,6 @@ def test_FindTheBiggest_inputs(): genfile=True, hash_files=False, position=2, - usedefault=True, ), output_type=dict(), ) @@ -30,11 +29,7 @@ def test_FindTheBiggest_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FindTheBiggest_outputs(): - output_map = dict( - out_file=dict( - argstr='%s', - usedefault=True, - ), ) + output_map = dict(out_file=dict(argstr='%s', ), ) outputs = FindTheBiggest.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_GLM.py b/nipype/interfaces/fsl/tests/test_auto_GLM.py index 39273b51e4..1dbf7eba19 100644 --- a/nipype/interfaces/fsl/tests/test_auto_GLM.py +++ b/nipype/interfaces/fsl/tests/test_auto_GLM.py @@ -6,10 +6,7 @@ def test_GLM_inputs(): input_map = dict( args=dict(argstr='%s', ), - contrasts=dict( - argstr='-c %s', - usedefault=True, - ), + contrasts=dict(argstr='-c %s', ), dat_norm=dict(argstr='--dat_norm', ), demean=dict(argstr='--demean', ), des_norm=dict(argstr='--des_norm', ), @@ -17,7 +14,6 @@ def test_GLM_inputs(): argstr='-d %s', mandatory=True, position=2, - usedefault=True, ), dof=dict(argstr='--dof=%d', ), environ=dict( @@ -28,64 +24,26 @@ def test_GLM_inputs(): argstr='-i %s', mandatory=True, position=1, - usedefault=True, - ), - mask=dict( - argstr='-m %s', - usedefault=True, - ), - out_cope=dict( - argstr='--out_cope=%s', - usedefault=True, - ), - out_data_name=dict( - argstr='--out_data=%s', - usedefault=True, - ), - out_f_name=dict( - argstr='--out_f=%s', - usedefault=True, ), + mask=dict(argstr='-m %s', ), + out_cope=dict(argstr='--out_cope=%s', ), + out_data_name=dict(argstr='--out_data=%s', ), + out_f_name=dict(argstr='--out_f=%s', ), out_file=dict( argstr='-o %s', keep_extension=True, name_source='in_file', name_template='%s_glm', position=3, - usedefault=True, - ), - out_p_name=dict( - argstr='--out_p=%s', - usedefault=True, - ), - out_pf_name=dict( - argstr='--out_pf=%s', - usedefault=True, - ), - out_res_name=dict( - argstr='--out_res=%s', - usedefault=True, - ), - out_sigsq_name=dict( - argstr='--out_sigsq=%s', - usedefault=True, - ), - out_t_name=dict( - argstr='--out_t=%s', - usedefault=True, - ), - out_varcb_name=dict( - argstr='--out_varcb=%s', - usedefault=True, - ), - out_vnscales_name=dict( - argstr='--out_vnscales=%s', - usedefault=True, - ), - out_z_name=dict( - argstr='--out_z=%s', - usedefault=True, ), + out_p_name=dict(argstr='--out_p=%s', ), + out_pf_name=dict(argstr='--out_pf=%s', ), + out_res_name=dict(argstr='--out_res=%s', ), + out_sigsq_name=dict(argstr='--out_sigsq=%s', ), + out_t_name=dict(argstr='--out_t=%s', ), + out_varcb_name=dict(argstr='--out_varcb=%s', ), + out_vnscales_name=dict(argstr='--out_vnscales=%s', ), + out_z_name=dict(argstr='--out_z=%s', ), output_type=dict(), var_norm=dict(argstr='--vn', ), ) @@ -99,7 +57,7 @@ def test_GLM_outputs(): out_cope=dict(), out_data=dict(), out_f=dict(), - out_file=dict(usedefault=True, ), + out_file=dict(), out_p=dict(), out_pf=dict(), out_res=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py b/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py index f22397d1bf..05bbb5b106 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py +++ b/nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py @@ -20,40 +20,31 @@ def test_ICA_AROMA_inputs(): feat_dir=dict( argstr='-feat %s', mandatory=True, - usedefault=True, xor=[ 'in_file', 'mat_file', 'fnirt_warp_file', 'motion_parameters' ], ), fnirt_warp_file=dict( argstr='-warp %s', - usedefault=True, xor=['feat_dir'], ), in_file=dict( argstr='-i %s', mandatory=True, - usedefault=True, xor=['feat_dir'], ), mask=dict( argstr='-m %s', - usedefault=True, xor=['feat_dir'], ), mat_file=dict( argstr='-affmat %s', - usedefault=True, xor=['feat_dir'], ), - melodic_dir=dict( - argstr='-meldir %s', - usedefault=True, - ), + melodic_dir=dict(argstr='-meldir %s', ), motion_parameters=dict( argstr='-mc %s', mandatory=True, - usedefault=True, xor=['feat_dir'], ), out_dir=dict( @@ -69,9 +60,9 @@ def test_ICA_AROMA_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ICA_AROMA_outputs(): output_map = dict( - aggr_denoised_file=dict(usedefault=True, ), - nonaggr_denoised_file=dict(usedefault=True, ), - out_dir=dict(usedefault=True, ), + aggr_denoised_file=dict(), + nonaggr_denoised_file=dict(), + out_dir=dict(), ) outputs = ICA_AROMA.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py index 0323144aca..6d4e06827e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py @@ -14,17 +14,12 @@ def test_ImageMaths_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), in_file2=dict( argstr='%s', position=3, - usedefault=True, - ), - mask_file=dict( - argstr='-mas %s', - usedefault=True, ), + mask_file=dict(argstr='-mas %s', ), op_string=dict( argstr='%s', position=2, @@ -38,7 +33,6 @@ def test_ImageMaths_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_type=dict(), suffix=dict(), @@ -49,7 +43,7 @@ def test_ImageMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ImageMaths_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ImageMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py index 3c0165915a..042f93112b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py @@ -15,12 +15,8 @@ def test_ImageMeants_inputs(): argstr='-i %s', mandatory=True, position=0, - usedefault=True, - ), - mask=dict( - argstr='-m %s', - usedefault=True, ), + mask=dict(argstr='-m %s', ), nobin=dict(argstr='--no_bin', ), order=dict( argstr='--order=%d', @@ -30,7 +26,6 @@ def test_ImageMeants_inputs(): argstr='-o %s', genfile=True, hash_files=False, - usedefault=True, ), output_type=dict(), show_all=dict(argstr='--showall', ), @@ -44,7 +39,7 @@ def test_ImageMeants_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ImageMeants_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ImageMeants.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py index 072e308455..91a6059798 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py @@ -14,12 +14,8 @@ def test_ImageStats_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, - ), - mask_file=dict( - argstr='', - usedefault=True, ), + mask_file=dict(argstr='', ), op_string=dict( argstr='%s', mandatory=True, diff --git a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py index cedfb5ad80..973f42ea34 100644 --- a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py @@ -19,7 +19,6 @@ def test_InvWarp_inputs(): hash_files=False, name_source=['warp'], name_template='%s_inverse', - usedefault=True, ), jacobian_max=dict(argstr='--jmax=%f', ), jacobian_min=dict(argstr='--jmin=%f', ), @@ -29,7 +28,6 @@ def test_InvWarp_inputs(): reference=dict( argstr='--ref=%s', mandatory=True, - usedefault=True, ), regularise=dict(argstr='--regularise=%f', ), relative=dict( @@ -39,7 +37,6 @@ def test_InvWarp_inputs(): warp=dict( argstr='--warp=%s', mandatory=True, - usedefault=True, ), ) inputs = InvWarp.input_spec() @@ -48,7 +45,7 @@ def test_InvWarp_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_InvWarp_outputs(): - output_map = dict(inverse_warp=dict(usedefault=True, ), ) + output_map = dict(inverse_warp=dict(), ) outputs = InvWarp.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py index 5b110e99dc..4b6192c98d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py @@ -20,7 +20,6 @@ def test_IsotropicSmooth_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -35,7 +34,6 @@ def test_IsotropicSmooth_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -55,7 +53,7 @@ def test_IsotropicSmooth_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_IsotropicSmooth_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = IsotropicSmooth.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_L2Model.py b/nipype/interfaces/fsl/tests/test_auto_L2Model.py index c188a82b36..9d3588666f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_L2Model.py +++ b/nipype/interfaces/fsl/tests/test_auto_L2Model.py @@ -12,9 +12,9 @@ def test_L2Model_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_L2Model_outputs(): output_map = dict( - design_con=dict(usedefault=True, ), - design_grp=dict(usedefault=True, ), - design_mat=dict(usedefault=True, ), + design_con=dict(), + design_grp=dict(), + design_mat=dict(), ) outputs = L2Model.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py index b586d758b3..daeca07b10 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py @@ -17,25 +17,17 @@ def test_MCFLIRT_inputs(): argstr='-in %s', mandatory=True, position=0, - usedefault=True, - ), - init=dict( - argstr='-init %s', - usedefault=True, ), + init=dict(argstr='-init %s', ), interpolation=dict(argstr='-%s_final', ), mean_vol=dict(argstr='-meanvol', ), out_file=dict( argstr='-out %s', genfile=True, hash_files=False, - usedefault=True, ), output_type=dict(), - ref_file=dict( - argstr='-reffile %s', - usedefault=True, - ), + ref_file=dict(argstr='-reffile %s', ), ref_vol=dict(argstr='-refvol %d', ), rotation=dict(argstr='-rotation %d', ), save_mats=dict(argstr='-mats', ), @@ -56,12 +48,12 @@ def test_MCFLIRT_inputs(): def test_MCFLIRT_outputs(): output_map = dict( mat_file=dict(), - mean_img=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), - par_file=dict(usedefault=True, ), + mean_img=dict(), + out_file=dict(), + par_file=dict(), rms_files=dict(), - std_img=dict(usedefault=True, ), - variance_img=dict(usedefault=True, ), + std_img=dict(), + variance_img=dict(), ) outputs = MCFLIRT.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py index e5bd64e8ca..b22078c450 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py +++ b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py @@ -5,16 +5,10 @@ def test_MELODIC_inputs(): input_map = dict( - ICs=dict( - argstr='--ICs=%s', - usedefault=True, - ), + ICs=dict(argstr='--ICs=%s', ), approach=dict(argstr='-a %s', ), args=dict(argstr='%s', ), - bg_image=dict( - argstr='--bgimage=%s', - usedefault=True, - ), + bg_image=dict(argstr='--bgimage=%s', ), bg_threshold=dict(argstr='--bgthreshold=%f', ), cov_weight=dict(argstr='--covarweight=%f', ), dim=dict(argstr='-d %d', ), @@ -32,20 +26,14 @@ def test_MELODIC_inputs(): sep=',', ), log_power=dict(argstr='--logPower', ), - mask=dict( - argstr='-m %s', - usedefault=True, - ), + mask=dict(argstr='-m %s', ), max_restart=dict(argstr='--maxrestart=%d', ), maxit=dict(argstr='--maxit=%d', ), migp=dict(argstr='--migp', ), migpN=dict(argstr='--migpN %d', ), migp_factor=dict(argstr='--migp_factor %d', ), migp_shuffle=dict(argstr='--migp_shuffle', ), - mix=dict( - argstr='--mix=%s', - usedefault=True, - ), + mix=dict(argstr='--mix=%s', ), mm_thresh=dict(argstr='--mmthresh=%f', ), no_bet=dict(argstr='--nobet', ), no_mask=dict(argstr='--nomask', ), @@ -56,7 +44,6 @@ def test_MELODIC_inputs(): out_dir=dict( argstr='-o %s', genfile=True, - usedefault=True, ), out_mean=dict(argstr='--Omean', ), out_orig=dict(argstr='--Oorig', ), @@ -70,28 +57,13 @@ def test_MELODIC_inputs(): remove_deriv=dict(argstr='--remove_deriv', ), report=dict(argstr='--report', ), report_maps=dict(argstr='--report_maps=%s', ), - s_con=dict( - argstr='--Scon=%s', - usedefault=True, - ), - s_des=dict( - argstr='--Sdes=%s', - usedefault=True, - ), + s_con=dict(argstr='--Scon=%s', ), + s_des=dict(argstr='--Sdes=%s', ), sep_vn=dict(argstr='--sep_vn', ), sep_whiten=dict(argstr='--sep_whiten', ), - smode=dict( - argstr='--smode=%s', - usedefault=True, - ), - t_con=dict( - argstr='--Tcon=%s', - usedefault=True, - ), - t_des=dict( - argstr='--Tdes=%s', - usedefault=True, - ), + smode=dict(argstr='--smode=%s', ), + t_con=dict(argstr='--Tcon=%s', ), + t_des=dict(argstr='--Tdes=%s', ), tr_sec=dict(argstr='--tr=%f', ), update_mask=dict(argstr='--update_mask', ), var_norm=dict(argstr='--vn', ), @@ -103,8 +75,8 @@ def test_MELODIC_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MELODIC_outputs(): output_map = dict( - out_dir=dict(usedefault=True, ), - report_dir=dict(usedefault=True, ), + out_dir=dict(), + report_dir=dict(), ) outputs = MELODIC.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py index 38f955a3f6..c7a5a3e465 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py +++ b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py @@ -13,7 +13,6 @@ def test_MakeDyadicVectors_inputs(): mask=dict( argstr='%s', position=2, - usedefault=True, ), output=dict( argstr='%s', @@ -30,13 +29,11 @@ def test_MakeDyadicVectors_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), theta_vol=dict( argstr='%s', mandatory=True, position=0, - usedefault=True, ), ) inputs = MakeDyadicVectors.input_spec() @@ -46,8 +43,8 @@ def test_MakeDyadicVectors_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MakeDyadicVectors_outputs(): output_map = dict( - dispersion=dict(usedefault=True, ), - dyads=dict(usedefault=True, ), + dispersion=dict(), + dyads=dict(), ) outputs = MakeDyadicVectors.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py index e2dde50f6c..64b0f8b089 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py @@ -14,7 +14,6 @@ def test_MathsCommand_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -29,7 +28,6 @@ def test_MathsCommand_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -43,7 +41,7 @@ def test_MathsCommand_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MathsCommand_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MathsCommand.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py index c77c8bbaa1..9910f9c4e8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py @@ -19,7 +19,6 @@ def test_MaxImage_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -34,7 +33,6 @@ def test_MaxImage_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -48,7 +46,7 @@ def test_MaxImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MaxImage_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MaxImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py b/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py index 47fd14ded4..f49c5f462c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MaxnImage.py @@ -19,7 +19,6 @@ def test_MaxnImage_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -34,7 +33,6 @@ def test_MaxnImage_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -48,7 +46,7 @@ def test_MaxnImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MaxnImage_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MaxnImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py index 31a3751c77..2172dcfa9e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py @@ -19,7 +19,6 @@ def test_MeanImage_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -34,7 +33,6 @@ def test_MeanImage_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -48,7 +46,7 @@ def test_MeanImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MeanImage_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MeanImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MedianImage.py b/nipype/interfaces/fsl/tests/test_auto_MedianImage.py index c8cb6c88e0..c14bf8d839 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MedianImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MedianImage.py @@ -19,7 +19,6 @@ def test_MedianImage_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -34,7 +33,6 @@ def test_MedianImage_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -48,7 +46,7 @@ def test_MedianImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MedianImage_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MedianImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Merge.py b/nipype/interfaces/fsl/tests/test_auto_Merge.py index 39c4f1b09c..826270239e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Merge.py +++ b/nipype/interfaces/fsl/tests/test_auto_Merge.py @@ -26,7 +26,6 @@ def test_Merge_inputs(): name_source='in_files', name_template='%s_merged', position=1, - usedefault=True, ), output_type=dict(), tr=dict( @@ -40,7 +39,7 @@ def test_Merge_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Merge_outputs(): - output_map = dict(merged_file=dict(usedefault=True, ), ) + output_map = dict(merged_file=dict(), ) outputs = Merge.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MinImage.py b/nipype/interfaces/fsl/tests/test_auto_MinImage.py index cf6b14fe60..4e9002c259 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MinImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MinImage.py @@ -19,7 +19,6 @@ def test_MinImage_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -34,7 +33,6 @@ def test_MinImage_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -48,7 +46,7 @@ def test_MinImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MinImage_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MinImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py index a3acf1458f..97d2426b53 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py +++ b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py @@ -14,12 +14,8 @@ def test_MotionOutliers_inputs(): in_file=dict( argstr='-i %s', mandatory=True, - usedefault=True, - ), - mask=dict( - argstr='-m %s', - usedefault=True, ), + mask=dict(argstr='-m %s', ), metric=dict(argstr='--%s', ), no_motion_correction=dict(argstr='--nomoco', ), out_file=dict( @@ -28,7 +24,6 @@ def test_MotionOutliers_inputs(): keep_extension=True, name_source='in_file', name_template='%s_outliers.txt', - usedefault=True, ), out_metric_plot=dict( argstr='-p %s', @@ -36,7 +31,6 @@ def test_MotionOutliers_inputs(): keep_extension=True, name_source='in_file', name_template='%s_metrics.png', - usedefault=True, ), out_metric_values=dict( argstr='-s %s', @@ -44,7 +38,6 @@ def test_MotionOutliers_inputs(): keep_extension=True, name_source='in_file', name_template='%s_metrics.txt', - usedefault=True, ), output_type=dict(), threshold=dict(argstr='--thresh=%g', ), @@ -56,9 +49,9 @@ def test_MotionOutliers_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MotionOutliers_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - out_metric_plot=dict(usedefault=True, ), - out_metric_values=dict(usedefault=True, ), + out_file=dict(), + out_metric_plot=dict(), + out_metric_values=dict(), ) outputs = MotionOutliers.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py index d1ae4c8a9b..50a2977a4c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py @@ -14,7 +14,6 @@ def test_MultiImageMaths_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -35,7 +34,6 @@ def test_MultiImageMaths_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -49,7 +47,7 @@ def test_MultiImageMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MultiImageMaths_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MultiImageMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py index 96ead7d20c..78bd97ff85 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py @@ -16,10 +16,10 @@ def test_MultipleRegressDesign_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MultipleRegressDesign_outputs(): output_map = dict( - design_con=dict(usedefault=True, ), - design_fts=dict(usedefault=True, ), - design_grp=dict(usedefault=True, ), - design_mat=dict(usedefault=True, ), + design_con=dict(), + design_fts=dict(), + design_grp=dict(), + design_mat=dict(), ) outputs = MultipleRegressDesign.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Overlay.py b/nipype/interfaces/fsl/tests/test_auto_Overlay.py index fa139b9254..9818ae1eda 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Overlay.py +++ b/nipype/interfaces/fsl/tests/test_auto_Overlay.py @@ -16,7 +16,6 @@ def test_Overlay_inputs(): argstr='%s', mandatory=True, position=4, - usedefault=True, ), bg_thresh=dict( argstr='%.3f %.3f', @@ -39,7 +38,6 @@ def test_Overlay_inputs(): genfile=True, hash_files=False, position=-1, - usedefault=True, ), out_type=dict( argstr='%s', @@ -56,12 +54,10 @@ def test_Overlay_inputs(): argstr='%s', mandatory=True, position=6, - usedefault=True, ), stat_image2=dict( argstr='%s', position=9, - usedefault=True, xor=['show_negative_stats'], ), stat_thresh=dict( @@ -89,7 +85,7 @@ def test_Overlay_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Overlay_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Overlay.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py index 5709018ae8..328a8e3272 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py +++ b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py @@ -9,7 +9,6 @@ def test_PRELUDE_inputs(): complex_phase_file=dict( argstr='--complex=%s', mandatory=True, - usedefault=True, xor=['magnitude_file', 'phase_file'], ), end=dict(argstr='--end=%d', ), @@ -20,25 +19,19 @@ def test_PRELUDE_inputs(): label_file=dict( argstr='--labels=%s', hash_files=False, - usedefault=True, ), labelprocess2d=dict(argstr='--labelslices', ), magnitude_file=dict( argstr='--abs=%s', mandatory=True, - usedefault=True, xor=['complex_phase_file'], ), - mask_file=dict( - argstr='--mask=%s', - usedefault=True, - ), + mask_file=dict(argstr='--mask=%s', ), num_partitions=dict(argstr='--numphasesplit=%d', ), output_type=dict(), phase_file=dict( argstr='--phase=%s', mandatory=True, - usedefault=True, xor=['complex_phase_file'], ), process2d=dict( @@ -52,13 +45,11 @@ def test_PRELUDE_inputs(): rawphase_file=dict( argstr='--rawphase=%s', hash_files=False, - usedefault=True, ), removeramps=dict(argstr='--removeramps', ), savemask_file=dict( argstr='--savemask=%s', hash_files=False, - usedefault=True, ), start=dict(argstr='--start=%d', ), threshold=dict(argstr='--thresh=%.10f', ), @@ -66,7 +57,6 @@ def test_PRELUDE_inputs(): argstr='--unwrap=%s', genfile=True, hash_files=False, - usedefault=True, ), ) inputs = PRELUDE.input_spec() @@ -75,7 +65,7 @@ def test_PRELUDE_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PRELUDE_outputs(): - output_map = dict(unwrapped_phase_file=dict(usedefault=True, ), ) + output_map = dict(unwrapped_phase_file=dict(), ) outputs = PRELUDE.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py b/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py index a9deb42a8e..4e08c18db0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_PercentileImage.py @@ -19,7 +19,6 @@ def test_PercentileImage_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -34,7 +33,6 @@ def test_PercentileImage_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -52,7 +50,7 @@ def test_PercentileImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PercentileImage_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = PercentileImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py index 1b6d3ccaa7..45a5b43945 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py @@ -20,7 +20,6 @@ def test_PlotMotionParams_inputs(): argstr='-o %s', genfile=True, hash_files=False, - usedefault=True, ), output_type=dict(), plot_size=dict(argstr='%s', ), @@ -35,7 +34,7 @@ def test_PlotMotionParams_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PlotMotionParams_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = PlotMotionParams.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py index 448cbb35be..62ced498e1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py @@ -16,15 +16,11 @@ def test_PlotTimeSeries_inputs(): position=1, ), labels=dict(argstr='%s', ), - legend_file=dict( - argstr='--legend=%s', - usedefault=True, - ), + legend_file=dict(argstr='--legend=%s', ), out_file=dict( argstr='-o %s', genfile=True, hash_files=False, - usedefault=True, ), output_type=dict(), plot_finish=dict( @@ -66,7 +62,7 @@ def test_PlotTimeSeries_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PlotTimeSeries_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = PlotTimeSeries.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py index 28ed263c1b..18a812c00b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py +++ b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py @@ -14,14 +14,12 @@ def test_PowerSpectrum_inputs(): argstr='%s', mandatory=True, position=0, - usedefault=True, ), out_file=dict( argstr='%s', genfile=True, hash_files=False, position=1, - usedefault=True, ), output_type=dict(), ) @@ -31,7 +29,7 @@ def test_PowerSpectrum_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PowerSpectrum_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = PowerSpectrum.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py index f93508a22a..66bfd51fab 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py +++ b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py @@ -20,13 +20,11 @@ def test_PrepareFieldmap_inputs(): argstr='%s', mandatory=True, position=3, - usedefault=True, ), in_phase=dict( argstr='%s', mandatory=True, position=2, - usedefault=True, ), nocheck=dict( argstr='--nocheck', @@ -36,7 +34,6 @@ def test_PrepareFieldmap_inputs(): out_fieldmap=dict( argstr='%s', position=4, - usedefault=True, ), output_type=dict(), scanner=dict( @@ -51,7 +48,7 @@ def test_PrepareFieldmap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PrepareFieldmap_outputs(): - output_map = dict(out_fieldmap=dict(usedefault=True, ), ) + output_map = dict(out_fieldmap=dict(), ) outputs = PrepareFieldmap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py index e44d1a3370..5368d0dd37 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py @@ -6,10 +6,7 @@ def test_ProbTrackX_inputs(): input_map = dict( args=dict(argstr='%s', ), - avoid_mp=dict( - argstr='--avoid=%s', - usedefault=True, - ), + avoid_mp=dict(argstr='--avoid=%s', ), c_thresh=dict(argstr='--cthr=%.3f', ), correct_path_distribution=dict(argstr='--pd', ), dist_thresh=dict(argstr='--distthresh=%.3f', ), @@ -23,24 +20,14 @@ def test_ProbTrackX_inputs(): usedefault=True, ), fsamples=dict(mandatory=True, ), - inv_xfm=dict( - argstr='--invxfm=%s', - usedefault=True, - ), + inv_xfm=dict(argstr='--invxfm=%s', ), loop_check=dict(argstr='--loopcheck', ), mask=dict( argstr='-m %s', mandatory=True, - usedefault=True, - ), - mask2=dict( - argstr='--mask2=%s', - usedefault=True, - ), - mesh=dict( - argstr='--mesh=%s', - usedefault=True, ), + mask2=dict(argstr='--mask2=%s', ), + mesh=dict(argstr='--mesh=%s', ), mod_euler=dict(argstr='--modeuler', ), mode=dict( argstr='--mode=%s', @@ -60,7 +47,6 @@ def test_ProbTrackX_inputs(): out_dir=dict( argstr='--dir=%s', genfile=True, - usedefault=True, ), output_type=dict(), phsamples=dict(mandatory=True, ), @@ -76,27 +62,15 @@ def test_ProbTrackX_inputs(): argstr='--seed=%s', mandatory=True, ), - seed_ref=dict( - argstr='--seedref=%s', - usedefault=True, - ), + seed_ref=dict(argstr='--seedref=%s', ), step_length=dict(argstr='--steplength=%.3f', ), - stop_mask=dict( - argstr='--stop=%s', - usedefault=True, - ), + stop_mask=dict(argstr='--stop=%s', ), target_masks=dict(argstr='--targetmasks=%s', ), thsamples=dict(mandatory=True, ), use_anisotropy=dict(argstr='--usef', ), verbose=dict(argstr='--verbose=%d', ), - waypoints=dict( - argstr='--waypoints=%s', - usedefault=True, - ), - xfm=dict( - argstr='--xfm=%s', - usedefault=True, - ), + waypoints=dict(argstr='--waypoints=%s', ), + xfm=dict(argstr='--xfm=%s', ), ) inputs = ProbTrackX.input_spec() @@ -106,10 +80,10 @@ def test_ProbTrackX_inputs(): def test_ProbTrackX_outputs(): output_map = dict( fdt_paths=dict(), - log=dict(usedefault=True, ), + log=dict(), particle_files=dict(), targets=dict(), - way_total=dict(usedefault=True, ), + way_total=dict(), ) outputs = ProbTrackX.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py index a1ca70b2b5..8592b5ae1a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py @@ -6,15 +6,9 @@ def test_ProbTrackX2_inputs(): input_map = dict( args=dict(argstr='%s', ), - avoid_mp=dict( - argstr='--avoid=%s', - usedefault=True, - ), + avoid_mp=dict(argstr='--avoid=%s', ), c_thresh=dict(argstr='--cthr=%.3f', ), - colmask4=dict( - argstr='--colmask4=%s', - usedefault=True, - ), + colmask4=dict(argstr='--colmask4=%s', ), correct_path_distribution=dict(argstr='--pd', ), dist_thresh=dict(argstr='--distthresh=%.3f', ), distthresh1=dict(argstr='--distthresh1=%.3f', ), @@ -24,28 +18,18 @@ def test_ProbTrackX2_inputs(): usedefault=True, ), fibst=dict(argstr='--fibst=%d', ), - fopd=dict( - argstr='--fopd=%s', - usedefault=True, - ), + fopd=dict(argstr='--fopd=%s', ), force_dir=dict( argstr='--forcedir', usedefault=True, ), fsamples=dict(mandatory=True, ), - inv_xfm=dict( - argstr='--invxfm=%s', - usedefault=True, - ), + inv_xfm=dict(argstr='--invxfm=%s', ), loop_check=dict(argstr='--loopcheck', ), - lrtarget3=dict( - argstr='--lrtarget3=%s', - usedefault=True, - ), + lrtarget3=dict(argstr='--lrtarget3=%s', ), mask=dict( argstr='-m %s', mandatory=True, - usedefault=True, ), meshspace=dict(argstr='--meshspace=%s', ), mod_euler=dict(argstr='--modeuler', ), @@ -74,7 +58,6 @@ def test_ProbTrackX2_inputs(): out_dir=dict( argstr='--dir=%s', genfile=True, - usedefault=True, ), output_type=dict(), phsamples=dict(mandatory=True, ), @@ -90,42 +73,21 @@ def test_ProbTrackX2_inputs(): argstr='--seed=%s', mandatory=True, ), - seed_ref=dict( - argstr='--seedref=%s', - usedefault=True, - ), + seed_ref=dict(argstr='--seedref=%s', ), simple=dict(argstr='--simple', ), step_length=dict(argstr='--steplength=%.3f', ), - stop_mask=dict( - argstr='--stop=%s', - usedefault=True, - ), - target2=dict( - argstr='--target2=%s', - usedefault=True, - ), - target3=dict( - argstr='--target3=%s', - usedefault=True, - ), - target4=dict( - argstr='--target4=%s', - usedefault=True, - ), + stop_mask=dict(argstr='--stop=%s', ), + target2=dict(argstr='--target2=%s', ), + target3=dict(argstr='--target3=%s', ), + target4=dict(argstr='--target4=%s', ), target_masks=dict(argstr='--targetmasks=%s', ), thsamples=dict(mandatory=True, ), use_anisotropy=dict(argstr='--usef', ), verbose=dict(argstr='--verbose=%d', ), waycond=dict(argstr='--waycond=%s', ), wayorder=dict(argstr='--wayorder', ), - waypoints=dict( - argstr='--waypoints=%s', - usedefault=True, - ), - xfm=dict( - argstr='--xfm=%s', - usedefault=True, - ), + waypoints=dict(argstr='--waypoints=%s', ), + xfm=dict(argstr='--xfm=%s', ), ) inputs = ProbTrackX2.input_spec() @@ -135,15 +97,15 @@ def test_ProbTrackX2_inputs(): def test_ProbTrackX2_outputs(): output_map = dict( fdt_paths=dict(), - log=dict(usedefault=True, ), - lookup_tractspace=dict(usedefault=True, ), - matrix1_dot=dict(usedefault=True, ), - matrix2_dot=dict(usedefault=True, ), - matrix3_dot=dict(usedefault=True, ), - network_matrix=dict(usedefault=True, ), + log=dict(), + lookup_tractspace=dict(), + matrix1_dot=dict(), + matrix2_dot=dict(), + matrix3_dot=dict(), + network_matrix=dict(), particle_files=dict(), targets=dict(), - way_total=dict(usedefault=True, ), + way_total=dict(), ) outputs = ProbTrackX2.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Randomise.py b/nipype/interfaces/fsl/tests/test_auto_Randomise.py index 423b5b9f07..3d52347265 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Randomise.py +++ b/nipype/interfaces/fsl/tests/test_auto_Randomise.py @@ -17,7 +17,6 @@ def test_Randomise_inputs(): design_mat=dict( argstr='-d %s', position=2, - usedefault=True, ), environ=dict( nohash=True, @@ -26,20 +25,13 @@ def test_Randomise_inputs(): f_c_thresh=dict(argstr='-F %.2f', ), f_cm_thresh=dict(argstr='-S %.2f', ), f_only=dict(argstr='--f_only', ), - fcon=dict( - argstr='-f %s', - usedefault=True, - ), + fcon=dict(argstr='-f %s', ), in_file=dict( argstr='-i %s', mandatory=True, position=0, - usedefault=True, - ), - mask=dict( - argstr='-m %s', - usedefault=True, ), + mask=dict(argstr='-m %s', ), num_perm=dict(argstr='-n %d', ), one_sample_group_mean=dict(argstr='-1', ), output_type=dict(), @@ -51,7 +43,6 @@ def test_Randomise_inputs(): tcon=dict( argstr='-t %s', position=3, - usedefault=True, ), tfce=dict(argstr='-T', ), tfce2D=dict(argstr='--T2', ), @@ -60,10 +51,7 @@ def test_Randomise_inputs(): tfce_H=dict(argstr='--tfce_H=%.2f', ), var_smooth=dict(argstr='-v %d', ), vox_p_values=dict(argstr='-x', ), - x_block_labels=dict( - argstr='-e %s', - usedefault=True, - ), + x_block_labels=dict(argstr='-e %s', ), ) inputs = Randomise.input_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py index ba24ac7e92..76647d82d8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py +++ b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py @@ -13,13 +13,11 @@ def test_Reorient2Std_inputs(): in_file=dict( argstr='%s', mandatory=True, - usedefault=True, ), out_file=dict( argstr='%s', genfile=True, hash_files=False, - usedefault=True, ), output_type=dict(), ) @@ -29,7 +27,7 @@ def test_Reorient2Std_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Reorient2Std_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Reorient2Std.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py index 3178abf8c1..e1cbac6fc9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py +++ b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py @@ -15,21 +15,18 @@ def test_RobustFOV_inputs(): argstr='-i %s', mandatory=True, position=0, - usedefault=True, ), out_roi=dict( argstr='-r %s', hash_files=False, name_source=['in_file'], name_template='%s_ROI', - usedefault=True, ), out_transform=dict( argstr='-m %s', hash_files=False, name_source=['in_file'], name_template='%s_to_ROI', - usedefault=True, ), output_type=dict(), ) @@ -40,8 +37,8 @@ def test_RobustFOV_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RobustFOV_outputs(): output_map = dict( - out_roi=dict(usedefault=True, ), - out_transform=dict(usedefault=True, ), + out_roi=dict(), + out_transform=dict(), ) outputs = RobustFOV.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_SMM.py b/nipype/interfaces/fsl/tests/test_auto_SMM.py index 64ef65f0e4..1e1cc308cc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SMM.py +++ b/nipype/interfaces/fsl/tests/test_auto_SMM.py @@ -15,7 +15,6 @@ def test_SMM_inputs(): copyfile=False, mandatory=True, position=1, - usedefault=True, ), no_deactivation_class=dict( argstr='--zfstatmode', @@ -27,7 +26,6 @@ def test_SMM_inputs(): copyfile=False, mandatory=True, position=0, - usedefault=True, ), ) inputs = SMM.input_spec() @@ -37,9 +35,9 @@ def test_SMM_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_SMM_outputs(): output_map = dict( - activation_p_map=dict(usedefault=True, ), - deactivation_p_map=dict(usedefault=True, ), - null_p_map=dict(usedefault=True, ), + activation_p_map=dict(), + deactivation_p_map=dict(), + null_p_map=dict(), ) outputs = SMM.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py index bf82a06086..ebbef0d427 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py +++ b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py @@ -29,14 +29,12 @@ def test_SUSAN_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), out_file=dict( argstr='%s', genfile=True, hash_files=False, position=-1, - usedefault=True, ), output_type=dict(), usans=dict( @@ -56,7 +54,7 @@ def test_SUSAN_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SUSAN_outputs(): - output_map = dict(smoothed_file=dict(usedefault=True, ), ) + output_map = dict(smoothed_file=dict(), ) outputs = SUSAN.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py index ae19dff835..f3be97b350 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py +++ b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py @@ -14,16 +14,11 @@ def test_SigLoss_inputs(): in_file=dict( argstr='-i %s', mandatory=True, - usedefault=True, - ), - mask_file=dict( - argstr='-m %s', - usedefault=True, ), + mask_file=dict(argstr='-m %s', ), out_file=dict( argstr='-s %s', genfile=True, - usedefault=True, ), output_type=dict(), slice_direction=dict(argstr='-d %s', ), @@ -34,7 +29,7 @@ def test_SigLoss_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SigLoss_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = SigLoss.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Slice.py b/nipype/interfaces/fsl/tests/test_auto_Slice.py index 52545e8375..d1e9093e37 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Slice.py +++ b/nipype/interfaces/fsl/tests/test_auto_Slice.py @@ -15,7 +15,6 @@ def test_Slice_inputs(): copyfile=False, mandatory=True, position=0, - usedefault=True, ), out_base_name=dict( argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py index 5ffd052768..75b9918ad9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py +++ b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py @@ -6,14 +6,8 @@ def test_SliceTimer_inputs(): input_map = dict( args=dict(argstr='%s', ), - custom_order=dict( - argstr='--ocustom=%s', - usedefault=True, - ), - custom_timings=dict( - argstr='--tcustom=%s', - usedefault=True, - ), + custom_order=dict(argstr='--ocustom=%s', ), + custom_timings=dict(argstr='--tcustom=%s', ), environ=dict( nohash=True, usedefault=True, @@ -23,7 +17,6 @@ def test_SliceTimer_inputs(): argstr='--in=%s', mandatory=True, position=0, - usedefault=True, ), index_dir=dict(argstr='--down', ), interleaved=dict(argstr='--odd', ), @@ -31,7 +24,6 @@ def test_SliceTimer_inputs(): argstr='--out=%s', genfile=True, hash_files=False, - usedefault=True, ), output_type=dict(), slice_direction=dict(argstr='--direction=%d', ), @@ -43,7 +35,7 @@ def test_SliceTimer_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SliceTimer_outputs(): - output_map = dict(slice_time_corrected_file=dict(usedefault=True, ), ) + output_map = dict(slice_time_corrected_file=dict(), ) outputs = SliceTimer.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Slicer.py b/nipype/interfaces/fsl/tests/test_auto_Slicer.py index 823c8ae1a8..d313cda474 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Slicer.py +++ b/nipype/interfaces/fsl/tests/test_auto_Slicer.py @@ -15,7 +15,6 @@ def test_Slicer_inputs(): colour_map=dict( argstr='-l %s', position=4, - usedefault=True, ), dither_edges=dict( argstr='-t', @@ -28,7 +27,6 @@ def test_Slicer_inputs(): image_edges=dict( argstr='%s', position=2, - usedefault=True, ), image_width=dict( argstr='%d', @@ -38,7 +36,6 @@ def test_Slicer_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), intensity_range=dict( argstr='-i %.3f %.3f', @@ -63,7 +60,6 @@ def test_Slicer_inputs(): genfile=True, hash_files=False, position=-1, - usedefault=True, ), output_type=dict(), sample_axial=dict( @@ -102,7 +98,7 @@ def test_Slicer_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Slicer_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Slicer.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Smooth.py b/nipype/interfaces/fsl/tests/test_auto_Smooth.py index df9427bde0..e8d8e06117 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Smooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_Smooth.py @@ -20,7 +20,6 @@ def test_Smooth_inputs(): argstr='%s', mandatory=True, position=0, - usedefault=True, ), output_type=dict(), sigma=dict( @@ -35,7 +34,6 @@ def test_Smooth_inputs(): name_source=['in_file'], name_template='%s_smooth', position=2, - usedefault=True, ), ) inputs = Smooth.input_spec() @@ -44,7 +42,7 @@ def test_Smooth_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Smooth_outputs(): - output_map = dict(smoothed_file=dict(usedefault=True, ), ) + output_map = dict(smoothed_file=dict(), ) outputs = Smooth.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py index 6a9a0593da..df7544f931 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py +++ b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py @@ -18,17 +18,14 @@ def test_SmoothEstimate_inputs(): mask_file=dict( argstr='--mask=%s', mandatory=True, - usedefault=True, ), output_type=dict(), residual_fit_file=dict( argstr='--res=%s', requires=['dof'], - usedefault=True, ), zstat_file=dict( argstr='--zstat=%s', - usedefault=True, xor=['dof'], ), ) diff --git a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py index 06d1d43277..d62f904655 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py @@ -14,7 +14,6 @@ def test_SpatialFilter_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -23,7 +22,6 @@ def test_SpatialFilter_inputs(): kernel_file=dict( argstr='%s', position=5, - usedefault=True, xor=['kernel_size'], ), kernel_shape=dict( @@ -49,7 +47,6 @@ def test_SpatialFilter_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -63,7 +60,7 @@ def test_SpatialFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SpatialFilter_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = SpatialFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Split.py b/nipype/interfaces/fsl/tests/test_auto_Split.py index 8097db6fd8..cec2ab462d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Split.py +++ b/nipype/interfaces/fsl/tests/test_auto_Split.py @@ -19,7 +19,6 @@ def test_Split_inputs(): argstr='%s', mandatory=True, position=0, - usedefault=True, ), out_base_name=dict( argstr='%s', diff --git a/nipype/interfaces/fsl/tests/test_auto_StdImage.py b/nipype/interfaces/fsl/tests/test_auto_StdImage.py index 0f47f02b4e..302ab9c4c2 100644 --- a/nipype/interfaces/fsl/tests/test_auto_StdImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_StdImage.py @@ -19,7 +19,6 @@ def test_StdImage_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -34,7 +33,6 @@ def test_StdImage_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -48,7 +46,7 @@ def test_StdImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_StdImage_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = StdImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py index ebf6866487..7cbb57491c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py +++ b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py @@ -14,7 +14,6 @@ def test_SwapDimensions_inputs(): argstr='%s', mandatory=True, position='1', - usedefault=True, ), new_dims=dict( argstr='%s %s %s', @@ -24,7 +23,6 @@ def test_SwapDimensions_inputs(): argstr='%s', genfile=True, hash_files=False, - usedefault=True, ), output_type=dict(), ) @@ -34,7 +32,7 @@ def test_SwapDimensions_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SwapDimensions_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = SwapDimensions.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py index 544167f904..3f91b3722a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py @@ -19,7 +19,6 @@ def test_TOPUP_inputs(): encoding_file=dict( argstr='--datain=%s', mandatory=True, - usedefault=True, xor=['encoding_direction'], ), environ=dict( @@ -31,7 +30,6 @@ def test_TOPUP_inputs(): in_file=dict( argstr='--imain=%s', mandatory=True, - usedefault=True, ), interp=dict(argstr='--interp=%s', ), max_iter=dict(argstr='--miter=%d', ), @@ -42,21 +40,18 @@ def test_TOPUP_inputs(): hash_files=False, name_source=['in_file'], name_template='%s_base', - usedefault=True, ), out_corrected=dict( argstr='--iout=%s', hash_files=False, name_source=['in_file'], name_template='%s_corrected', - usedefault=True, ), out_field=dict( argstr='--fout=%s', hash_files=False, name_source=['in_file'], name_template='%s_field', - usedefault=True, ), out_jac_prefix=dict( argstr='--jacout=%s', @@ -69,7 +64,6 @@ def test_TOPUP_inputs(): keep_extension=True, name_source=['in_file'], name_template='%s_topup.log', - usedefault=True, ), out_mat_prefix=dict( argstr='--rbmout=%s', @@ -103,14 +97,14 @@ def test_TOPUP_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TOPUP_outputs(): output_map = dict( - out_corrected=dict(usedefault=True, ), - out_enc_file=dict(usedefault=True, ), - out_field=dict(usedefault=True, ), - out_fieldcoef=dict(usedefault=True, ), + out_corrected=dict(), + out_enc_file=dict(), + out_field=dict(), + out_fieldcoef=dict(), out_jacs=dict(), - out_logfile=dict(usedefault=True, ), + out_logfile=dict(), out_mats=dict(), - out_movpar=dict(usedefault=True, ), + out_movpar=dict(), out_warps=dict(), ) outputs = TOPUP.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py index d567dcd085..c762b99d31 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py @@ -19,7 +19,6 @@ def test_TemporalFilter_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -39,7 +38,6 @@ def test_TemporalFilter_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -53,7 +51,7 @@ def test_TemporalFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TemporalFilter_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TemporalFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_Threshold.py b/nipype/interfaces/fsl/tests/test_auto_Threshold.py index 996bcfd928..5c2bb46cc8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Threshold.py +++ b/nipype/interfaces/fsl/tests/test_auto_Threshold.py @@ -15,7 +15,6 @@ def test_Threshold_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -30,7 +29,6 @@ def test_Threshold_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -51,7 +49,7 @@ def test_Threshold_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Threshold_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Threshold.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py index b900074a51..4308ee8153 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py +++ b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py @@ -5,17 +5,11 @@ def test_TractSkeleton_inputs(): input_map = dict( - alt_data_file=dict( - argstr='-a %s', - usedefault=True, - ), - alt_skeleton=dict( - argstr='-s %s', - usedefault=True, - ), + alt_data_file=dict(argstr='-a %s', ), + alt_skeleton=dict(argstr='-s %s', ), args=dict(argstr='%s', ), - data_file=dict(usedefault=True, ), - distance_map=dict(usedefault=True, ), + data_file=dict(), + distance_map=dict(), environ=dict( nohash=True, usedefault=True, @@ -23,18 +17,14 @@ def test_TractSkeleton_inputs(): in_file=dict( argstr='-i %s', mandatory=True, - usedefault=True, ), output_type=dict(), project_data=dict( argstr='-p %.3f %s %s %s %s', requires=['threshold', 'distance_map', 'data_file'], ), - projected_data=dict(usedefault=True, ), - search_mask_file=dict( - usedefault=True, - xor=['use_cingulum_mask'], - ), + projected_data=dict(), + search_mask_file=dict(xor=['use_cingulum_mask'], ), skeleton_file=dict(argstr='-o %s', ), threshold=dict(), use_cingulum_mask=dict( @@ -49,8 +39,8 @@ def test_TractSkeleton_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TractSkeleton_outputs(): output_map = dict( - projected_data=dict(usedefault=True, ), - skeleton_file=dict(usedefault=True, ), + projected_data=dict(), + skeleton_file=dict(), ) outputs = TractSkeleton.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_Training.py b/nipype/interfaces/fsl/tests/test_auto_Training.py index d9943d7033..91d48e4c01 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Training.py +++ b/nipype/interfaces/fsl/tests/test_auto_Training.py @@ -30,7 +30,7 @@ def test_Training_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Training_outputs(): - output_map = dict(trained_wts_file=dict(usedefault=True, ), ) + output_map = dict(trained_wts_file=dict(), ) outputs = Training.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py index 322bfc8baa..a0dcf2610d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py @@ -14,7 +14,6 @@ def test_UnaryMaths_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), internal_datatype=dict( argstr='-dt %s', @@ -34,7 +33,6 @@ def test_UnaryMaths_inputs(): genfile=True, hash_files=False, position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -48,7 +46,7 @@ def test_UnaryMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_UnaryMaths_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = UnaryMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_VecReg.py b/nipype/interfaces/fsl/tests/test_auto_VecReg.py index b5a75f168b..61a28f7369 100644 --- a/nipype/interfaces/fsl/tests/test_auto_VecReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_VecReg.py @@ -5,10 +5,7 @@ def test_VecReg_inputs(): input_map = dict( - affine_mat=dict( - argstr='-t %s', - usedefault=True, - ), + affine_mat=dict(argstr='-t %s', ), args=dict(argstr='%s', ), environ=dict( nohash=True, @@ -17,41 +14,23 @@ def test_VecReg_inputs(): in_file=dict( argstr='-i %s', mandatory=True, - usedefault=True, ), interpolation=dict(argstr='--interp=%s', ), - mask=dict( - argstr='-m %s', - usedefault=True, - ), + mask=dict(argstr='-m %s', ), out_file=dict( argstr='-o %s', genfile=True, hash_files=False, - usedefault=True, ), output_type=dict(), - ref_mask=dict( - argstr='--refmask=%s', - usedefault=True, - ), + ref_mask=dict(argstr='--refmask=%s', ), ref_vol=dict( argstr='-r %s', mandatory=True, - usedefault=True, - ), - rotation_mat=dict( - argstr='--rotmat=%s', - usedefault=True, - ), - rotation_warp=dict( - argstr='--rotwarp=%s', - usedefault=True, - ), - warp_field=dict( - argstr='-w %s', - usedefault=True, ), + rotation_mat=dict(argstr='--rotmat=%s', ), + rotation_warp=dict(argstr='--rotwarp=%s', ), + warp_field=dict(argstr='-w %s', ), ) inputs = VecReg.input_spec() @@ -59,7 +38,7 @@ def test_VecReg_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_VecReg_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = VecReg.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py index 64258eb6ce..30924223cf 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py @@ -17,7 +17,6 @@ def test_WarpPoints_inputs(): dest_file=dict( argstr='-dest %s', mandatory=True, - usedefault=True, ), environ=dict( nohash=True, @@ -27,27 +26,22 @@ def test_WarpPoints_inputs(): argstr='%s', mandatory=True, position=-1, - usedefault=True, ), out_file=dict( name_source='in_coords', name_template='%s_warped', output_name='out_file', - usedefault=True, ), src_file=dict( argstr='-src %s', mandatory=True, - usedefault=True, ), warp_file=dict( argstr='-warp %s', - usedefault=True, xor=['xfm_file'], ), xfm_file=dict( argstr='-xfm %s', - usedefault=True, xor=['warp_file'], ), ) @@ -57,7 +51,7 @@ def test_WarpPoints_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpPoints_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = WarpPoints.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py b/nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py index 8aa6a7b2ee..627ef60ad6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPointsFromStd.py @@ -21,27 +21,22 @@ def test_WarpPointsFromStd_inputs(): img_file=dict( argstr='-img %s', mandatory=True, - usedefault=True, ), in_coords=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), std_file=dict( argstr='-std %s', mandatory=True, - usedefault=True, ), warp_file=dict( argstr='-warp %s', - usedefault=True, xor=['xfm_file'], ), xfm_file=dict( argstr='-xfm %s', - usedefault=True, xor=['warp_file'], ), ) @@ -51,7 +46,7 @@ def test_WarpPointsFromStd_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpPointsFromStd_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = WarpPointsFromStd.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py index adc1b0fb77..3d37ad1486 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py @@ -21,37 +21,28 @@ def test_WarpPointsToStd_inputs(): img_file=dict( argstr='-img %s', mandatory=True, - usedefault=True, ), in_coords=dict( argstr='%s', mandatory=True, position=-1, - usedefault=True, ), out_file=dict( name_source='in_coords', name_template='%s_warped', output_name='out_file', - usedefault=True, - ), - premat_file=dict( - argstr='-premat %s', - usedefault=True, ), + premat_file=dict(argstr='-premat %s', ), std_file=dict( argstr='-std %s', mandatory=True, - usedefault=True, ), warp_file=dict( argstr='-warp %s', - usedefault=True, xor=['xfm_file'], ), xfm_file=dict( argstr='-xfm %s', - usedefault=True, xor=['warp_file'], ), ) @@ -61,7 +52,7 @@ def test_WarpPointsToStd_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_WarpPointsToStd_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = WarpPointsToStd.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py index 96eedbbe51..04d3a05f14 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py @@ -13,7 +13,6 @@ def test_WarpUtils_inputs(): in_file=dict( argstr='--in=%s', mandatory=True, - usedefault=True, ), knot_space=dict(argstr='--knotspace=%d,%d,%d', ), out_file=dict( @@ -21,18 +20,13 @@ def test_WarpUtils_inputs(): name_source=['in_file'], output_name='out_file', position=-1, - usedefault=True, ), out_format=dict(argstr='--outformat=%s', ), - out_jacobian=dict( - argstr='--jac=%s', - usedefault=True, - ), + out_jacobian=dict(argstr='--jac=%s', ), output_type=dict(), reference=dict( argstr='--ref=%s', mandatory=True, - usedefault=True, ), warp_resolution=dict(argstr='--warpres=%0.4f,%0.4f,%0.4f', ), with_affine=dict(argstr='--withaff', ), @@ -48,8 +42,8 @@ def test_WarpUtils_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_WarpUtils_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - out_jacobian=dict(usedefault=True, ), + out_file=dict(), + out_jacobian=dict(), ) outputs = WarpUtils.output_spec() diff --git a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py index 490bb7a17b..d72bb3bb4b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py +++ b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py @@ -21,12 +21,10 @@ def test_XFibres5_inputs(): bvals=dict( argstr='--bvals=%s', mandatory=True, - usedefault=True, ), bvecs=dict( argstr='--bvecs=%s', mandatory=True, - usedefault=True, ), cnlinear=dict( argstr='--cnonlinear', @@ -35,7 +33,6 @@ def test_XFibres5_inputs(): dwi=dict( argstr='--data=%s', mandatory=True, - usedefault=True, ), environ=dict( nohash=True, @@ -54,10 +51,7 @@ def test_XFibres5_inputs(): usedefault=True, ), fudge=dict(argstr='--fudge=%d', ), - gradnonlin=dict( - argstr='--gradnonlin=%s', - usedefault=True, - ), + gradnonlin=dict(argstr='--gradnonlin=%s', ), logdir=dict( argstr='--logdir=%s', usedefault=True, @@ -65,7 +59,6 @@ def test_XFibres5_inputs(): mask=dict( argstr='--mask=%s', mandatory=True, - usedefault=True, ), model=dict(argstr='--model=%d', ), n_fibres=dict( @@ -110,10 +103,10 @@ def test_XFibres5_outputs(): output_map = dict( dyads=dict(), fsamples=dict(), - mean_S0samples=dict(usedefault=True, ), - mean_dsamples=dict(usedefault=True, ), + mean_S0samples=dict(), + mean_dsamples=dict(), mean_fsamples=dict(), - mean_tausamples=dict(usedefault=True, ), + mean_tausamples=dict(), phsamples=dict(), thsamples=dict(), ) diff --git a/nipype/interfaces/minc/tests/test_auto_Average.py b/nipype/interfaces/minc/tests/test_auto_Average.py index 8883e6fe04..57bdc5ccd2 100644 --- a/nipype/interfaces/minc/tests/test_auto_Average.py +++ b/nipype/interfaces/minc/tests/test_auto_Average.py @@ -120,7 +120,6 @@ def test_Average_inputs(): name_source=['input_files'], name_template='%s_averaged.mnc', position=-1, - usedefault=True, ), quiet=dict( argstr='-quiet', @@ -148,7 +147,7 @@ def test_Average_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Average_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = Average.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_BBox.py b/nipype/interfaces/minc/tests/test_auto_BBox.py index f168f3c242..a34aeab9b5 100644 --- a/nipype/interfaces/minc/tests/test_auto_BBox.py +++ b/nipype/interfaces/minc/tests/test_auto_BBox.py @@ -17,7 +17,6 @@ def test_BBox_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), one_line=dict( argstr='-one_line', @@ -34,7 +33,6 @@ def test_BBox_inputs(): name_source=['input_file'], name_template='%s_bbox.txt', position=-1, - usedefault=True, ), threshold=dict(argstr='-threshold', ), two_lines=dict( @@ -48,7 +46,7 @@ def test_BBox_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BBox_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = BBox.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Beast.py b/nipype/interfaces/minc/tests/test_auto_Beast.py index eea3348e8b..4834cf3c4a 100644 --- a/nipype/interfaces/minc/tests/test_auto_Beast.py +++ b/nipype/interfaces/minc/tests/test_auto_Beast.py @@ -78,7 +78,7 @@ def test_Beast_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Beast_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = Beast.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_BestLinReg.py b/nipype/interfaces/minc/tests/test_auto_BestLinReg.py index f38b22f27a..fb9061040a 100644 --- a/nipype/interfaces/minc/tests/test_auto_BestLinReg.py +++ b/nipype/interfaces/minc/tests/test_auto_BestLinReg.py @@ -22,7 +22,6 @@ def test_BestLinReg_inputs(): name_source=['source'], name_template='%s_bestlinreg.mnc', position=-1, - usedefault=True, ), output_xfm=dict( argstr='%s', @@ -32,19 +31,16 @@ def test_BestLinReg_inputs(): name_source=['source'], name_template='%s_bestlinreg.xfm', position=-2, - usedefault=True, ), source=dict( argstr='%s', mandatory=True, position=-4, - usedefault=True, ), target=dict( argstr='%s', mandatory=True, position=-3, - usedefault=True, ), verbose=dict(argstr='-verbose', ), ) @@ -55,8 +51,8 @@ def test_BestLinReg_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BestLinReg_outputs(): output_map = dict( - output_mnc=dict(usedefault=True, ), - output_xfm=dict(usedefault=True, ), + output_mnc=dict(), + output_xfm=dict(), ) outputs = BestLinReg.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_BigAverage.py b/nipype/interfaces/minc/tests/test_auto_BigAverage.py index 7f722afa23..ce1fb2b91e 100644 --- a/nipype/interfaces/minc/tests/test_auto_BigAverage.py +++ b/nipype/interfaces/minc/tests/test_auto_BigAverage.py @@ -27,7 +27,6 @@ def test_BigAverage_inputs(): name_source=['input_files'], name_template='%s_bigaverage.mnc', position=-1, - usedefault=True, ), output_float=dict(argstr='--float', ), robust=dict(argstr='-robust', ), @@ -36,12 +35,8 @@ def test_BigAverage_inputs(): hash_files=False, name_source=['input_files'], name_template='%s_bigaverage_stdev.mnc', - usedefault=True, - ), - tmpdir=dict( - argstr='-tmpdir %s', - usedefault=True, ), + tmpdir=dict(argstr='-tmpdir %s', ), verbose=dict(argstr='--verbose', ), ) inputs = BigAverage.input_spec() @@ -51,8 +46,8 @@ def test_BigAverage_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BigAverage_outputs(): output_map = dict( - output_file=dict(usedefault=True, ), - sd_file=dict(usedefault=True, ), + output_file=dict(), + sd_file=dict(), ) outputs = BigAverage.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Blob.py b/nipype/interfaces/minc/tests/test_auto_Blob.py index c7bfe318e0..b489ac944a 100644 --- a/nipype/interfaces/minc/tests/test_auto_Blob.py +++ b/nipype/interfaces/minc/tests/test_auto_Blob.py @@ -15,7 +15,6 @@ def test_Blob_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), magnitude=dict(argstr='-magnitude', ), output_file=dict( @@ -25,7 +24,6 @@ def test_Blob_inputs(): name_source=['input_file'], name_template='%s_blob.mnc', position=-1, - usedefault=True, ), trace=dict(argstr='-trace', ), translation=dict(argstr='-translation', ), @@ -36,7 +34,7 @@ def test_Blob_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Blob_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = Blob.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Blur.py b/nipype/interfaces/minc/tests/test_auto_Blur.py index b6ecfc8e23..fb6e405012 100644 --- a/nipype/interfaces/minc/tests/test_auto_Blur.py +++ b/nipype/interfaces/minc/tests/test_auto_Blur.py @@ -34,13 +34,11 @@ def test_Blur_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), no_apodize=dict(argstr='-no_apodize', ), output_file_base=dict( argstr='%s', position=-1, - usedefault=True, ), partial=dict(argstr='-partial', ), rect=dict( @@ -60,12 +58,12 @@ def test_Blur_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Blur_outputs(): output_map = dict( - gradient_dxyz=dict(usedefault=True, ), - output_file=dict(usedefault=True, ), - partial_dx=dict(usedefault=True, ), - partial_dxyz=dict(usedefault=True, ), - partial_dy=dict(usedefault=True, ), - partial_dz=dict(usedefault=True, ), + gradient_dxyz=dict(), + output_file=dict(), + partial_dx=dict(), + partial_dxyz=dict(), + partial_dy=dict(), + partial_dz=dict(), ) outputs = Blur.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Calc.py b/nipype/interfaces/minc/tests/test_auto_Calc.py index 7f8a4ee0fe..7bec782c1c 100644 --- a/nipype/interfaces/minc/tests/test_auto_Calc.py +++ b/nipype/interfaces/minc/tests/test_auto_Calc.py @@ -117,7 +117,6 @@ def test_Calc_inputs(): name_source=['input_files'], name_template='%s_calc.mnc', position=-1, - usedefault=True, ), output_illegal=dict( argstr='-illegal_value', @@ -149,7 +148,7 @@ def test_Calc_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Calc_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = Calc.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Convert.py b/nipype/interfaces/minc/tests/test_auto_Convert.py index ee1d8429b6..6df596c682 100644 --- a/nipype/interfaces/minc/tests/test_auto_Convert.py +++ b/nipype/interfaces/minc/tests/test_auto_Convert.py @@ -20,7 +20,6 @@ def test_Convert_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), output_file=dict( argstr='%s', @@ -29,7 +28,6 @@ def test_Convert_inputs(): name_source=['input_file'], name_template='%s_convert_output.mnc', position=-1, - usedefault=True, ), template=dict(argstr='-template', ), two=dict(argstr='-2', ), @@ -40,7 +38,7 @@ def test_Convert_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Convert_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = Convert.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Copy.py b/nipype/interfaces/minc/tests/test_auto_Copy.py index 2e87caa55b..e91470ba6d 100644 --- a/nipype/interfaces/minc/tests/test_auto_Copy.py +++ b/nipype/interfaces/minc/tests/test_auto_Copy.py @@ -14,7 +14,6 @@ def test_Copy_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), output_file=dict( argstr='%s', @@ -23,7 +22,6 @@ def test_Copy_inputs(): name_source=['input_file'], name_template='%s_copy.mnc', position=-1, - usedefault=True, ), pixel_values=dict( argstr='-pixel_values', @@ -40,7 +38,7 @@ def test_Copy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Copy_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = Copy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Dump.py b/nipype/interfaces/minc/tests/test_auto_Dump.py index 1dc7a96d78..bcca2a4801 100644 --- a/nipype/interfaces/minc/tests/test_auto_Dump.py +++ b/nipype/interfaces/minc/tests/test_auto_Dump.py @@ -30,7 +30,6 @@ def test_Dump_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), line_length=dict(argstr='-l %d', ), netcdf_name=dict(argstr='-n %s', ), @@ -45,7 +44,6 @@ def test_Dump_inputs(): name_source=['input_file'], name_template='%s_dump.txt', position=-1, - usedefault=True, ), precision=dict(argstr='%s', ), variables=dict( @@ -59,7 +57,7 @@ def test_Dump_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Dump_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = Dump.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Extract.py b/nipype/interfaces/minc/tests/test_auto_Extract.py index 4f37eecab3..77126eac18 100644 --- a/nipype/interfaces/minc/tests/test_auto_Extract.py +++ b/nipype/interfaces/minc/tests/test_auto_Extract.py @@ -72,7 +72,6 @@ def test_Extract_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), nonormalize=dict( argstr='-nonormalize', @@ -93,7 +92,6 @@ def test_Extract_inputs(): name_source=['input_file'], name_template='%s.raw', position=-1, - usedefault=True, ), start=dict( argstr='-start %s', @@ -157,7 +155,7 @@ def test_Extract_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Extract_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = Extract.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py b/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py index 255acdb0b3..c89dc65de6 100644 --- a/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py +++ b/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py @@ -15,10 +15,7 @@ def test_Gennlxfm_inputs(): usedefault=True, ), ident=dict(argstr='-ident', ), - like=dict( - argstr='-like %s', - usedefault=True, - ), + like=dict(argstr='-like %s', ), output_file=dict( argstr='%s', genfile=True, @@ -26,7 +23,6 @@ def test_Gennlxfm_inputs(): name_source=['like'], name_template='%s_gennlxfm.xfm', position=-1, - usedefault=True, ), step=dict(argstr='-step %s', ), verbose=dict(argstr='-verbose', ), @@ -38,8 +34,8 @@ def test_Gennlxfm_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Gennlxfm_outputs(): output_map = dict( - output_file=dict(usedefault=True, ), - output_grid=dict(usedefault=True, ), + output_file=dict(), + output_grid=dict(), ) outputs = Gennlxfm.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Math.py b/nipype/interfaces/minc/tests/test_auto_Math.py index d1f6bf58b1..1d011034d2 100644 --- a/nipype/interfaces/minc/tests/test_auto_Math.py +++ b/nipype/interfaces/minc/tests/test_auto_Math.py @@ -127,7 +127,6 @@ def test_Math_inputs(): name_source=['input_files'], name_template='%s_mincmath.mnc', position=-1, - usedefault=True, ), output_illegal=dict( argstr='-illegal_value', @@ -162,7 +161,7 @@ def test_Math_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Math_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = Math.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_NlpFit.py b/nipype/interfaces/minc/tests/test_auto_NlpFit.py index c67a423fa3..1a728a90dd 100644 --- a/nipype/interfaces/minc/tests/test_auto_NlpFit.py +++ b/nipype/interfaces/minc/tests/test_auto_NlpFit.py @@ -13,7 +13,6 @@ def test_NlpFit_inputs(): config_file=dict( argstr='-config_file %s', mandatory=True, - usedefault=True, ), environ=dict( nohash=True, @@ -22,31 +21,26 @@ def test_NlpFit_inputs(): init_xfm=dict( argstr='-init_xfm %s', mandatory=True, - usedefault=True, ), input_grid_files=dict(), output_xfm=dict( argstr='%s', genfile=True, position=-1, - usedefault=True, ), source=dict( argstr='%s', mandatory=True, position=-3, - usedefault=True, ), source_mask=dict( argstr='-source_mask %s', mandatory=True, - usedefault=True, ), target=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), verbose=dict(argstr='-verbose', ), ) @@ -57,8 +51,8 @@ def test_NlpFit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_NlpFit_outputs(): output_map = dict( - output_grid=dict(usedefault=True, ), - output_xfm=dict(usedefault=True, ), + output_grid=dict(), + output_xfm=dict(), ) outputs = NlpFit.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Norm.py b/nipype/interfaces/minc/tests/test_auto_Norm.py index 96511610a4..3a0d28f06d 100644 --- a/nipype/interfaces/minc/tests/test_auto_Norm.py +++ b/nipype/interfaces/minc/tests/test_auto_Norm.py @@ -23,7 +23,6 @@ def test_Norm_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), lower=dict(argstr='-lower %s', ), mask=dict(argstr='-mask %s', ), @@ -36,7 +35,6 @@ def test_Norm_inputs(): name_source=['input_file'], name_template='%s_norm.mnc', position=-1, - usedefault=True, ), output_threshold_mask=dict( argstr='-threshold_mask %s', @@ -57,8 +55,8 @@ def test_Norm_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Norm_outputs(): output_map = dict( - output_file=dict(usedefault=True, ), - output_threshold_mask=dict(usedefault=True, ), + output_file=dict(), + output_threshold_mask=dict(), ) outputs = Norm.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Pik.py b/nipype/interfaces/minc/tests/test_auto_Pik.py index 406355ca28..d74d9a86ad 100644 --- a/nipype/interfaces/minc/tests/test_auto_Pik.py +++ b/nipype/interfaces/minc/tests/test_auto_Pik.py @@ -32,7 +32,6 @@ def test_Pik_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), jpg=dict(xor=('jpg', 'png'), ), lookup=dict(argstr='--lookup %s', ), @@ -45,7 +44,6 @@ def test_Pik_inputs(): name_source=['input_file'], name_template='%s.png', position=-1, - usedefault=True, ), png=dict(xor=('jpg', 'png'), ), sagittal_offset=dict(argstr='--sagittal_offset %s', ), @@ -86,7 +84,7 @@ def test_Pik_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Pik_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = Pik.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Resample.py b/nipype/interfaces/minc/tests/test_auto_Resample.py index d842c6983b..bd00bd224d 100644 --- a/nipype/interfaces/minc/tests/test_auto_Resample.py +++ b/nipype/interfaces/minc/tests/test_auto_Resample.py @@ -86,7 +86,6 @@ def test_Resample_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), input_grid_files=dict(), invert_transformation=dict(argstr='-invert_transformation', ), @@ -124,7 +123,6 @@ def test_Resample_inputs(): name_source=['input_file'], name_template='%s_resample.mnc', position=-1, - usedefault=True, ), output_range=dict(argstr='-range %s %s', ), sagittal_slices=dict( @@ -245,7 +243,7 @@ def test_Resample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Resample_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = Resample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Reshape.py b/nipype/interfaces/minc/tests/test_auto_Reshape.py index 5291f9b463..45e6ddeb4a 100644 --- a/nipype/interfaces/minc/tests/test_auto_Reshape.py +++ b/nipype/interfaces/minc/tests/test_auto_Reshape.py @@ -26,7 +26,6 @@ def test_Reshape_inputs(): name_source=['input_file'], name_template='%s_reshape.mnc', position=-1, - usedefault=True, ), verbose=dict(argstr='-verbose', ), write_short=dict(argstr='-short', ), @@ -37,7 +36,7 @@ def test_Reshape_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Reshape_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = Reshape.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_ToEcat.py b/nipype/interfaces/minc/tests/test_auto_ToEcat.py index eedfbbf47a..26a3ac0436 100644 --- a/nipype/interfaces/minc/tests/test_auto_ToEcat.py +++ b/nipype/interfaces/minc/tests/test_auto_ToEcat.py @@ -23,7 +23,6 @@ def test_ToEcat_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), no_decay_corr_fctr=dict(argstr='-no_decay_corr_fctr', ), output_file=dict( @@ -34,7 +33,6 @@ def test_ToEcat_inputs(): name_source=['input_file'], name_template='%s_to_ecat.v', position=-1, - usedefault=True, ), voxels_as_integers=dict(argstr='-label', ), ) @@ -44,7 +42,7 @@ def test_ToEcat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ToEcat_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = ToEcat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_ToRaw.py b/nipype/interfaces/minc/tests/test_auto_ToRaw.py index afc831c807..e010da322d 100644 --- a/nipype/interfaces/minc/tests/test_auto_ToRaw.py +++ b/nipype/interfaces/minc/tests/test_auto_ToRaw.py @@ -14,7 +14,6 @@ def test_ToRaw_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), nonormalize=dict( argstr='-nonormalize', @@ -35,7 +34,6 @@ def test_ToRaw_inputs(): name_source=['input_file'], name_template='%s.raw', position=-1, - usedefault=True, ), write_byte=dict( argstr='-byte', @@ -83,7 +81,7 @@ def test_ToRaw_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ToRaw_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = ToRaw.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_VolSymm.py b/nipype/interfaces/minc/tests/test_auto_VolSymm.py index 99ba96a29a..048ffcde9b 100644 --- a/nipype/interfaces/minc/tests/test_auto_VolSymm.py +++ b/nipype/interfaces/minc/tests/test_auto_VolSymm.py @@ -10,10 +10,7 @@ def test_VolSymm_inputs(): argstr='-clobber', usedefault=True, ), - config_file=dict( - argstr='-config_file %s', - usedefault=True, - ), + config_file=dict(argstr='-config_file %s', ), environ=dict( nohash=True, usedefault=True, @@ -34,7 +31,6 @@ def test_VolSymm_inputs(): name_source=['input_file'], name_template='%s_vol_symm.mnc', position=-1, - usedefault=True, ), trans_file=dict( argstr='%s', @@ -57,9 +53,9 @@ def test_VolSymm_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_VolSymm_outputs(): output_map = dict( - output_file=dict(usedefault=True, ), - output_grid=dict(usedefault=True, ), - trans_file=dict(usedefault=True, ), + output_file=dict(), + output_grid=dict(), + trans_file=dict(), ) outputs = VolSymm.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_Volcentre.py b/nipype/interfaces/minc/tests/test_auto_Volcentre.py index 4abbcf66aa..b095751a4d 100644 --- a/nipype/interfaces/minc/tests/test_auto_Volcentre.py +++ b/nipype/interfaces/minc/tests/test_auto_Volcentre.py @@ -20,7 +20,6 @@ def test_Volcentre_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), output_file=dict( argstr='%s', @@ -29,7 +28,6 @@ def test_Volcentre_inputs(): name_source=['input_file'], name_template='%s_volcentre.mnc', position=-1, - usedefault=True, ), verbose=dict(argstr='-verbose', ), zero_dircos=dict(argstr='-zero_dircos', ), @@ -40,7 +38,7 @@ def test_Volcentre_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Volcentre_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = Volcentre.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Voliso.py b/nipype/interfaces/minc/tests/test_auto_Voliso.py index a16b8da063..967642a328 100644 --- a/nipype/interfaces/minc/tests/test_auto_Voliso.py +++ b/nipype/interfaces/minc/tests/test_auto_Voliso.py @@ -19,7 +19,6 @@ def test_Voliso_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), maxstep=dict(argstr='--maxstep %s', ), minstep=dict(argstr='--minstep %s', ), @@ -30,7 +29,6 @@ def test_Voliso_inputs(): name_source=['input_file'], name_template='%s_voliso.mnc', position=-1, - usedefault=True, ), verbose=dict(argstr='--verbose', ), ) @@ -40,7 +38,7 @@ def test_Voliso_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Voliso_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = Voliso.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_Volpad.py b/nipype/interfaces/minc/tests/test_auto_Volpad.py index 1c29b0a1c4..865bc79e69 100644 --- a/nipype/interfaces/minc/tests/test_auto_Volpad.py +++ b/nipype/interfaces/minc/tests/test_auto_Volpad.py @@ -21,7 +21,6 @@ def test_Volpad_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), output_file=dict( argstr='%s', @@ -30,7 +29,6 @@ def test_Volpad_inputs(): name_source=['input_file'], name_template='%s_volpad.mnc', position=-1, - usedefault=True, ), smooth=dict(argstr='-smooth', ), smooth_distance=dict(argstr='-smooth_distance %s', ), @@ -42,7 +40,7 @@ def test_Volpad_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Volpad_outputs(): - output_map = dict(output_file=dict(usedefault=True, ), ) + output_map = dict(output_file=dict(), ) outputs = Volpad.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/minc/tests/test_auto_XfmAvg.py b/nipype/interfaces/minc/tests/test_auto_XfmAvg.py index 6ba7d2811d..6d036a0c0e 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmAvg.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmAvg.py @@ -29,7 +29,6 @@ def test_XfmAvg_inputs(): argstr='%s', genfile=True, position=-1, - usedefault=True, ), verbose=dict(argstr='-verbose', ), ) @@ -40,8 +39,8 @@ def test_XfmAvg_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_XfmAvg_outputs(): output_map = dict( - output_file=dict(usedefault=True, ), - output_grid=dict(usedefault=True, ), + output_file=dict(), + output_grid=dict(), ) outputs = XfmAvg.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_XfmConcat.py b/nipype/interfaces/minc/tests/test_auto_XfmConcat.py index 8453286669..eb748953ef 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmConcat.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmConcat.py @@ -28,7 +28,6 @@ def test_XfmConcat_inputs(): name_source=['input_files'], name_template='%s_xfmconcat.xfm', position=-1, - usedefault=True, ), verbose=dict(argstr='-verbose', ), ) @@ -39,7 +38,7 @@ def test_XfmConcat_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_XfmConcat_outputs(): output_map = dict( - output_file=dict(usedefault=True, ), + output_file=dict(), output_grids=dict(), ) outputs = XfmConcat.output_spec() diff --git a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py index ff7455cb6e..d729e90639 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py @@ -23,7 +23,6 @@ def test_XfmInvert_inputs(): argstr='%s', genfile=True, position=-1, - usedefault=True, ), verbose=dict(argstr='-verbose', ), ) @@ -34,8 +33,8 @@ def test_XfmInvert_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_XfmInvert_outputs(): output_map = dict( - output_file=dict(usedefault=True, ), - output_grid=dict(usedefault=True, ), + output_file=dict(), + output_grid=dict(), ) outputs = XfmInvert.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py index 79f466bb69..16605acbb7 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py @@ -11,36 +11,18 @@ def test_JistBrainMgdmSegmentation_inputs(): usedefault=True, ), inAdjust=dict(argstr='--inAdjust %s', ), - inAtlas=dict( - argstr='--inAtlas %s', - usedefault=True, - ), + inAtlas=dict(argstr='--inAtlas %s', ), inCompute=dict(argstr='--inCompute %s', ), inCurvature=dict(argstr='--inCurvature %f', ), inData=dict(argstr='--inData %f', ), - inFLAIR=dict( - argstr='--inFLAIR %s', - usedefault=True, - ), - inMP2RAGE=dict( - argstr='--inMP2RAGE %s', - usedefault=True, - ), - inMP2RAGE2=dict( - argstr='--inMP2RAGE2 %s', - usedefault=True, - ), - inMPRAGE=dict( - argstr='--inMPRAGE %s', - usedefault=True, - ), + inFLAIR=dict(argstr='--inFLAIR %s', ), + inMP2RAGE=dict(argstr='--inMP2RAGE %s', ), + inMP2RAGE2=dict(argstr='--inMP2RAGE2 %s', ), + inMPRAGE=dict(argstr='--inMPRAGE %s', ), inMax=dict(argstr='--inMax %d', ), inMin=dict(argstr='--inMin %f', ), inOutput=dict(argstr='--inOutput %s', ), - inPV=dict( - argstr='--inPV %s', - usedefault=True, - ), + inPV=dict(argstr='--inPV %s', ), inPosterior=dict(argstr='--inPosterior %f', ), inSteps=dict(argstr='--inSteps %d', ), inTopology=dict(argstr='--inTopology %s', ), @@ -75,10 +57,10 @@ def test_JistBrainMgdmSegmentation_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistBrainMgdmSegmentation_outputs(): output_map = dict( - outLevelset=dict(usedefault=True, ), - outPosterior2=dict(usedefault=True, ), - outPosterior3=dict(usedefault=True, ), - outSegmented=dict(usedefault=True, ), + outLevelset=dict(), + outPosterior2=dict(), + outPosterior3=dict(), + outSegmented=dict(), ) outputs = JistBrainMgdmSegmentation.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py index 17a5d5be33..ebb65bb789 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py @@ -11,14 +11,8 @@ def test_JistBrainMp2rageDuraEstimation_inputs(): usedefault=True, ), inDistance=dict(argstr='--inDistance %f', ), - inSecond=dict( - argstr='--inSecond %s', - usedefault=True, - ), - inSkull=dict( - argstr='--inSkull %s', - usedefault=True, - ), + inSecond=dict(argstr='--inSecond %s', ), + inSkull=dict(argstr='--inSkull %s', ), inoutput=dict(argstr='--inoutput %s', ), null=dict(argstr='--null %s', ), outDura=dict( @@ -38,7 +32,7 @@ def test_JistBrainMp2rageDuraEstimation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JistBrainMp2rageDuraEstimation_outputs(): - output_map = dict(outDura=dict(usedefault=True, ), ) + output_map = dict(outDura=dict(), ) outputs = JistBrainMp2rageDuraEstimation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py index 6f54ace63e..abf794b662 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py @@ -10,23 +10,11 @@ def test_JistBrainMp2rageSkullStripping_inputs(): nohash=True, usedefault=True, ), - inFilter=dict( - argstr='--inFilter %s', - usedefault=True, - ), - inSecond=dict( - argstr='--inSecond %s', - usedefault=True, - ), + inFilter=dict(argstr='--inFilter %s', ), + inSecond=dict(argstr='--inSecond %s', ), inSkip=dict(argstr='--inSkip %s', ), - inT1=dict( - argstr='--inT1 %s', - usedefault=True, - ), - inT1weighted=dict( - argstr='--inT1weighted %s', - usedefault=True, - ), + inT1=dict(argstr='--inT1 %s', ), + inT1weighted=dict(argstr='--inT1weighted %s', ), null=dict(argstr='--null %s', ), outBrain=dict( argstr='--outBrain %s', @@ -58,10 +46,10 @@ def test_JistBrainMp2rageSkullStripping_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistBrainMp2rageSkullStripping_outputs(): output_map = dict( - outBrain=dict(usedefault=True, ), - outMasked=dict(usedefault=True, ), - outMasked2=dict(usedefault=True, ), - outMasked3=dict(usedefault=True, ), + outBrain=dict(), + outMasked=dict(), + outMasked2=dict(), + outMasked3=dict(), ) outputs = JistBrainMp2rageSkullStripping.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py index 7cdf00bf5b..bb86144c20 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py @@ -10,10 +10,7 @@ def test_JistBrainPartialVolumeFilter_inputs(): nohash=True, usedefault=True, ), - inInput=dict( - argstr='--inInput %s', - usedefault=True, - ), + inInput=dict(argstr='--inInput %s', ), inPV=dict(argstr='--inPV %s', ), inoutput=dict(argstr='--inoutput %s', ), null=dict(argstr='--null %s', ), @@ -34,7 +31,7 @@ def test_JistBrainPartialVolumeFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JistBrainPartialVolumeFilter_outputs(): - output_map = dict(outPartial=dict(usedefault=True, ), ) + output_map = dict(outPartial=dict(), ) outputs = JistBrainPartialVolumeFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py index 21c31aa4e9..407b9755ca 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py @@ -10,10 +10,7 @@ def test_JistCortexSurfaceMeshInflation_inputs(): nohash=True, usedefault=True, ), - inLevelset=dict( - argstr='--inLevelset %s', - usedefault=True, - ), + inLevelset=dict(argstr='--inLevelset %s', ), inLorentzian=dict(argstr='--inLorentzian %s', ), inMax=dict(argstr='--inMax %d', ), inMean=dict(argstr='--inMean %f', ), @@ -43,8 +40,8 @@ def test_JistCortexSurfaceMeshInflation_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistCortexSurfaceMeshInflation_outputs(): output_map = dict( - outInflated=dict(usedefault=True, ), - outOriginal=dict(usedefault=True, ), + outInflated=dict(), + outOriginal=dict(), ) outputs = JistCortexSurfaceMeshInflation.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py index 90fee34bb7..bfdace4944 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py @@ -12,19 +12,10 @@ def test_JistIntensityMp2rageMasking_inputs(): ), inBackground=dict(argstr='--inBackground %s', ), inMasking=dict(argstr='--inMasking %s', ), - inQuantitative=dict( - argstr='--inQuantitative %s', - usedefault=True, - ), - inSecond=dict( - argstr='--inSecond %s', - usedefault=True, - ), + inQuantitative=dict(argstr='--inQuantitative %s', ), + inSecond=dict(argstr='--inSecond %s', ), inSkip=dict(argstr='--inSkip %s', ), - inT1weighted=dict( - argstr='--inT1weighted %s', - usedefault=True, - ), + inT1weighted=dict(argstr='--inT1weighted %s', ), null=dict(argstr='--null %s', ), outMasked=dict( argstr='--outMasked_T1_Map %s', @@ -56,10 +47,10 @@ def test_JistIntensityMp2rageMasking_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistIntensityMp2rageMasking_outputs(): output_map = dict( - outMasked=dict(usedefault=True, ), - outMasked2=dict(usedefault=True, ), - outSignal=dict(usedefault=True, ), - outSignal2=dict(usedefault=True, ), + outMasked=dict(), + outMasked2=dict(), + outSignal=dict(), + outSignal2=dict(), ) outputs = JistIntensityMp2rageMasking.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py index 529de041ca..12203a1aa6 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py @@ -10,14 +10,8 @@ def test_JistLaminarProfileCalculator_inputs(): nohash=True, usedefault=True, ), - inIntensity=dict( - argstr='--inIntensity %s', - usedefault=True, - ), - inMask=dict( - argstr='--inMask %s', - usedefault=True, - ), + inIntensity=dict(argstr='--inIntensity %s', ), + inMask=dict(argstr='--inMask %s', ), incomputed=dict(argstr='--incomputed %s', ), null=dict(argstr='--null %s', ), outResult=dict( @@ -37,7 +31,7 @@ def test_JistLaminarProfileCalculator_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarProfileCalculator_outputs(): - output_map = dict(outResult=dict(usedefault=True, ), ) + output_map = dict(outResult=dict(), ) outputs = JistLaminarProfileCalculator.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py index f346559abf..ddc4d5d922 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py @@ -10,10 +10,7 @@ def test_JistLaminarProfileGeometry_inputs(): nohash=True, usedefault=True, ), - inProfile=dict( - argstr='--inProfile %s', - usedefault=True, - ), + inProfile=dict(argstr='--inProfile %s', ), incomputed=dict(argstr='--incomputed %s', ), inoutside=dict(argstr='--inoutside %f', ), inregularization=dict(argstr='--inregularization %s', ), @@ -36,7 +33,7 @@ def test_JistLaminarProfileGeometry_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarProfileGeometry_outputs(): - output_map = dict(outResult=dict(usedefault=True, ), ) + output_map = dict(outResult=dict(), ) outputs = JistLaminarProfileGeometry.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py index f8a593d9ae..58de472b85 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py @@ -10,18 +10,9 @@ def test_JistLaminarProfileSampling_inputs(): nohash=True, usedefault=True, ), - inCortex=dict( - argstr='--inCortex %s', - usedefault=True, - ), - inIntensity=dict( - argstr='--inIntensity %s', - usedefault=True, - ), - inProfile=dict( - argstr='--inProfile %s', - usedefault=True, - ), + inCortex=dict(argstr='--inCortex %s', ), + inIntensity=dict(argstr='--inIntensity %s', ), + inProfile=dict(argstr='--inProfile %s', ), null=dict(argstr='--null %s', ), outProfile2=dict( argstr='--outProfile2 %s', @@ -45,8 +36,8 @@ def test_JistLaminarProfileSampling_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarProfileSampling_outputs(): output_map = dict( - outProfile2=dict(usedefault=True, ), - outProfilemapped=dict(usedefault=True, ), + outProfile2=dict(), + outProfilemapped=dict(), ) outputs = JistLaminarProfileSampling.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py index 9eb23ab2d8..bb9577ccee 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py @@ -10,18 +10,9 @@ def test_JistLaminarROIAveraging_inputs(): nohash=True, usedefault=True, ), - inIntensity=dict( - argstr='--inIntensity %s', - usedefault=True, - ), - inMask=dict( - argstr='--inMask %s', - usedefault=True, - ), - inROI=dict( - argstr='--inROI %s', - usedefault=True, - ), + inIntensity=dict(argstr='--inIntensity %s', ), + inMask=dict(argstr='--inMask %s', ), + inROI=dict(argstr='--inROI %s', ), inROI2=dict(argstr='--inROI2 %s', ), null=dict(argstr='--null %s', ), outROI3=dict( @@ -41,7 +32,7 @@ def test_JistLaminarROIAveraging_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarROIAveraging_outputs(): - output_map = dict(outROI3=dict(usedefault=True, ), ) + output_map = dict(outROI3=dict(), ) outputs = JistLaminarROIAveraging.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py index 40df4113c7..4aa9f9d77b 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py @@ -10,19 +10,13 @@ def test_JistLaminarVolumetricLayering_inputs(): nohash=True, usedefault=True, ), - inInner=dict( - argstr='--inInner %s', - usedefault=True, - ), + inInner=dict(argstr='--inInner %s', ), inLayering=dict(argstr='--inLayering %s', ), inLayering2=dict(argstr='--inLayering2 %s', ), inMax=dict(argstr='--inMax %d', ), inMin=dict(argstr='--inMin %f', ), inNumber=dict(argstr='--inNumber %d', ), - inOuter=dict( - argstr='--inOuter %s', - usedefault=True, - ), + inOuter=dict(argstr='--inOuter %s', ), inTopology=dict(argstr='--inTopology %s', ), incurvature=dict(argstr='--incurvature %d', ), inpresmooth=dict(argstr='--inpresmooth %s', ), @@ -54,9 +48,9 @@ def test_JistLaminarVolumetricLayering_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarVolumetricLayering_outputs(): output_map = dict( - outContinuous=dict(usedefault=True, ), - outDiscrete=dict(usedefault=True, ), - outLayer=dict(usedefault=True, ), + outContinuous=dict(), + outDiscrete=dict(), + outLayer=dict(), ) outputs = JistLaminarVolumetricLayering.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py index 42a0a3fff7..016beee263 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py @@ -11,14 +11,8 @@ def test_MedicAlgorithmImageCalculator_inputs(): usedefault=True, ), inOperation=dict(argstr='--inOperation %s', ), - inVolume=dict( - argstr='--inVolume %s', - usedefault=True, - ), - inVolume2=dict( - argstr='--inVolume2 %s', - usedefault=True, - ), + inVolume=dict(argstr='--inVolume %s', ), + inVolume2=dict(argstr='--inVolume2 %s', ), null=dict(argstr='--null %s', ), outResult=dict( argstr='--outResult %s', @@ -37,7 +31,7 @@ def test_MedicAlgorithmImageCalculator_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmImageCalculator_outputs(): - output_map = dict(outResult=dict(usedefault=True, ), ) + output_map = dict(outResult=dict(), ) outputs = MedicAlgorithmImageCalculator.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py index dd707bc061..87f9ab6a72 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py @@ -11,26 +11,14 @@ def test_MedicAlgorithmLesionToads_inputs(): usedefault=True, ), inAtlas=dict(argstr='--inAtlas %s', ), - inAtlas2=dict( - argstr='--inAtlas2 %s', - usedefault=True, - ), - inAtlas3=dict( - argstr='--inAtlas3 %s', - usedefault=True, - ), - inAtlas4=dict( - argstr='--inAtlas4 %s', - usedefault=True, - ), + inAtlas2=dict(argstr='--inAtlas2 %s', ), + inAtlas3=dict(argstr='--inAtlas3 %s', ), + inAtlas4=dict(argstr='--inAtlas4 %s', ), inAtlas5=dict(argstr='--inAtlas5 %f', ), inAtlas6=dict(argstr='--inAtlas6 %s', ), inConnectivity=dict(argstr='--inConnectivity %s', ), inCorrect=dict(argstr='--inCorrect %s', ), - inFLAIR=dict( - argstr='--inFLAIR %s', - usedefault=True, - ), + inFLAIR=dict(argstr='--inFLAIR %s', ), inInclude=dict(argstr='--inInclude %s', ), inMaximum=dict(argstr='--inMaximum %d', ), inMaximum2=dict(argstr='--inMaximum2 %d', ), @@ -41,14 +29,8 @@ def test_MedicAlgorithmLesionToads_inputs(): inOutput2=dict(argstr='--inOutput2 %s', ), inOutput3=dict(argstr='--inOutput3 %s', ), inSmooting=dict(argstr='--inSmooting %f', ), - inT1_MPRAGE=dict( - argstr='--inT1_MPRAGE %s', - usedefault=True, - ), - inT1_SPGR=dict( - argstr='--inT1_SPGR %s', - usedefault=True, - ), + inT1_MPRAGE=dict(argstr='--inT1_MPRAGE %s', ), + inT1_SPGR=dict(argstr='--inT1_SPGR %s', ), null=dict(argstr='--null %s', ), outCortical=dict( argstr='--outCortical %s', @@ -100,15 +82,15 @@ def test_MedicAlgorithmLesionToads_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmLesionToads_outputs(): output_map = dict( - outCortical=dict(usedefault=True, ), - outFilled=dict(usedefault=True, ), - outHard=dict(usedefault=True, ), - outHard2=dict(usedefault=True, ), - outInhomogeneity=dict(usedefault=True, ), - outLesion=dict(usedefault=True, ), - outMembership=dict(usedefault=True, ), - outSulcal=dict(usedefault=True, ), - outWM=dict(usedefault=True, ), + outCortical=dict(), + outFilled=dict(), + outHard=dict(), + outHard2=dict(), + outInhomogeneity=dict(), + outLesion=dict(), + outMembership=dict(), + outSulcal=dict(), + outWM=dict(), ) outputs = MedicAlgorithmLesionToads.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py index b05edb5d73..7c8c7248ad 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py @@ -17,10 +17,7 @@ def test_MedicAlgorithmMipavReorient_inputs(): argstr='--inSource %s', sep=';', ), - inTemplate=dict( - argstr='--inTemplate %s', - usedefault=True, - ), + inTemplate=dict(argstr='--inTemplate %s', ), inUser=dict(argstr='--inUser %s', ), inUser2=dict(argstr='--inUser2 %s', ), inUser3=dict(argstr='--inUser3 %s', ), diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py index a5bbd301a1..9d5a148a24 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py @@ -13,10 +13,7 @@ def test_MedicAlgorithmN3_inputs(): inAutomatic=dict(argstr='--inAutomatic %s', ), inEnd=dict(argstr='--inEnd %f', ), inField=dict(argstr='--inField %f', ), - inInput=dict( - argstr='--inInput %s', - usedefault=True, - ), + inInput=dict(argstr='--inInput %s', ), inKernel=dict(argstr='--inKernel %f', ), inMaximum=dict(argstr='--inMaximum %d', ), inSignal=dict(argstr='--inSignal %f', ), @@ -45,8 +42,8 @@ def test_MedicAlgorithmN3_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmN3_outputs(): output_map = dict( - outInhomogeneity=dict(usedefault=True, ), - outInhomogeneity2=dict(usedefault=True, ), + outInhomogeneity=dict(), + outInhomogeneity2=dict(), ) outputs = MedicAlgorithmN3.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py index df87186aa6..b2d247e9dc 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py @@ -11,10 +11,7 @@ def test_MedicAlgorithmSPECTRE2010_inputs(): usedefault=True, ), inApply=dict(argstr='--inApply %s', ), - inAtlas=dict( - argstr='--inAtlas %s', - usedefault=True, - ), + inAtlas=dict(argstr='--inAtlas %s', ), inBackground=dict(argstr='--inBackground %f', ), inCoarse=dict(argstr='--inCoarse %f', ), inCost=dict(argstr='--inCost %s', ), @@ -25,10 +22,7 @@ def test_MedicAlgorithmSPECTRE2010_inputs(): inInhomogeneity=dict(argstr='--inInhomogeneity %s', ), inInitial=dict(argstr='--inInitial %d', ), inInitial2=dict(argstr='--inInitial2 %f', ), - inInput=dict( - argstr='--inInput %s', - usedefault=True, - ), + inInput=dict(argstr='--inInput %s', ), inMMC=dict(argstr='--inMMC %d', ), inMMC2=dict(argstr='--inMMC2 %d', ), inMaximum=dict(argstr='--inMaximum %f', ), @@ -101,15 +95,15 @@ def test_MedicAlgorithmSPECTRE2010_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmSPECTRE2010_outputs(): output_map = dict( - outFANTASM=dict(usedefault=True, ), - outMask=dict(usedefault=True, ), - outMidsagittal=dict(usedefault=True, ), - outOriginal=dict(usedefault=True, ), - outPrior=dict(usedefault=True, ), - outSegmentation=dict(usedefault=True, ), - outSplitHalves=dict(usedefault=True, ), - outStripped=dict(usedefault=True, ), - outd0=dict(usedefault=True, ), + outFANTASM=dict(), + outMask=dict(), + outMidsagittal=dict(), + outOriginal=dict(), + outPrior=dict(), + outSegmentation=dict(), + outSplitHalves=dict(), + outStripped=dict(), + outd0=dict(), ) outputs = MedicAlgorithmSPECTRE2010.output_spec() diff --git a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py index 6817d55b5b..d3d92142c4 100644 --- a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py +++ b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py @@ -37,7 +37,7 @@ def test_RandomVol_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RandomVol_outputs(): - output_map = dict(outRand1=dict(usedefault=True, ), ) + output_map = dict(outRand1=dict(), ) outputs = RandomVol.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py index d4e4e02b40..4ced8de75a 100644 --- a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py +++ b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py @@ -35,10 +35,7 @@ def test_WatershedBEM_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_WatershedBEM_outputs(): output_map = dict( - brain_surface=dict( - loc='bem/watershed', - usedefault=True, - ), + brain_surface=dict(loc='bem/watershed', ), cor_files=dict( altkey='COR', loc='bem/watershed/ws', @@ -46,21 +43,11 @@ def test_WatershedBEM_outputs(): fif_file=dict( altkey='fif', loc='bem', - usedefault=True, - ), - inner_skull_surface=dict( - loc='bem/watershed', - usedefault=True, ), + inner_skull_surface=dict(loc='bem/watershed', ), mesh_files=dict(), - outer_skin_surface=dict( - loc='bem/watershed', - usedefault=True, - ), - outer_skull_surface=dict( - loc='bem/watershed', - usedefault=True, - ), + outer_skin_surface=dict(loc='bem/watershed', ), + outer_skull_surface=dict(loc='bem/watershed', ), ) outputs = WatershedBEM.output_spec() diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py index fe71be10c2..78a275f6a7 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py @@ -10,12 +10,10 @@ def test_ConstrainedSphericalDeconvolution_inputs(): directions_file=dict( argstr='-directions %s', position=-2, - usedefault=True, ), encoding_file=dict( argstr='-grad %s', position=1, - usedefault=True, ), environ=dict( nohash=True, @@ -24,20 +22,17 @@ def test_ConstrainedSphericalDeconvolution_inputs(): filter_file=dict( argstr='-filter %s', position=-2, - usedefault=True, ), in_file=dict( argstr='%s', mandatory=True, position=-3, - usedefault=True, ), iterations=dict(argstr='-niter %s', ), lambda_value=dict(argstr='-lambda %s', ), mask_image=dict( argstr='-mask %s', position=2, - usedefault=True, ), maximum_harmonic_order=dict(argstr='-lmax %s', ), normalise=dict( @@ -48,13 +43,11 @@ def test_ConstrainedSphericalDeconvolution_inputs(): argstr='%s', genfile=True, position=-1, - usedefault=True, ), response_file=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), threshold_value=dict(argstr='-threshold %s', ), ) @@ -64,7 +57,7 @@ def test_ConstrainedSphericalDeconvolution_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ConstrainedSphericalDeconvolution_outputs(): - output_map = dict(spherical_harmonics_image=dict(usedefault=True, ), ) + output_map = dict(spherical_harmonics_image=dict(), ) outputs = ConstrainedSphericalDeconvolution.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py index 7d78b93639..dc95cff525 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py @@ -10,7 +10,6 @@ def test_DWI2SphericalHarmonicsImage_inputs(): argstr='-grad %s', mandatory=True, position=1, - usedefault=True, ), environ=dict( nohash=True, @@ -20,7 +19,6 @@ def test_DWI2SphericalHarmonicsImage_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), maximum_harmonic_order=dict(argstr='-lmax %s', ), normalise=dict( @@ -31,7 +29,6 @@ def test_DWI2SphericalHarmonicsImage_inputs(): argstr='%s', genfile=True, position=-1, - usedefault=True, ), ) inputs = DWI2SphericalHarmonicsImage.input_spec() @@ -40,7 +37,7 @@ def test_DWI2SphericalHarmonicsImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWI2SphericalHarmonicsImage_outputs(): - output_map = dict(spherical_harmonics_image=dict(usedefault=True, ), ) + output_map = dict(spherical_harmonics_image=dict(), ) outputs = DWI2SphericalHarmonicsImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py index 2ede931519..86975950bf 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py @@ -13,7 +13,6 @@ def test_DWI2Tensor_inputs(): encoding_file=dict( argstr='-grad %s', position=2, - usedefault=True, ), environ=dict( nohash=True, @@ -40,7 +39,6 @@ def test_DWI2Tensor_inputs(): name_template='%s_tensor.mif', output_name='tensor', position=-1, - usedefault=True, ), quiet=dict( argstr='-quiet', @@ -53,7 +51,7 @@ def test_DWI2Tensor_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWI2Tensor_outputs(): - output_map = dict(tensor=dict(usedefault=True, ), ) + output_map = dict(tensor=dict(), ) outputs = DWI2Tensor.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py index 25cbdbb7ba..2c6417fe3a 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py @@ -18,7 +18,6 @@ def test_DiffusionTensorStreamlineTrack_inputs(): ), exclude_file=dict( argstr='-exclude %s', - usedefault=True, xor=['exclude_file', 'exclude_spec'], ), exclude_spec=dict( @@ -32,17 +31,14 @@ def test_DiffusionTensorStreamlineTrack_inputs(): argstr='-grad %s', mandatory=True, position=-2, - usedefault=True, ), in_file=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), include_file=dict( argstr='-include %s', - usedefault=True, xor=['include_file', 'include_spec'], ), include_spec=dict( @@ -67,7 +63,6 @@ def test_DiffusionTensorStreamlineTrack_inputs(): ), mask_file=dict( argstr='-mask %s', - usedefault=True, xor=['mask_file', 'mask_spec'], ), mask_spec=dict( @@ -97,11 +92,9 @@ def test_DiffusionTensorStreamlineTrack_inputs(): name_template='%s_tracked.tck', output_name='tracked', position=-1, - usedefault=True, ), seed_file=dict( argstr='-seed %s', - usedefault=True, xor=['seed_file', 'seed_spec'], ), seed_spec=dict( @@ -124,7 +117,7 @@ def test_DiffusionTensorStreamlineTrack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DiffusionTensorStreamlineTrack_outputs(): - output_map = dict(tracked=dict(usedefault=True, ), ) + output_map = dict(tracked=dict(), ) outputs = DiffusionTensorStreamlineTrack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py index fdfd71f3a9..b5474bd18c 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py @@ -16,7 +16,6 @@ def test_Directions2Amplitude_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), num_peaks=dict(argstr='-num %s', ), out_file=dict( @@ -26,16 +25,12 @@ def test_Directions2Amplitude_inputs(): name_source=['in_file'], name_template='%s_amplitudes.mif', position=-1, - usedefault=True, ), peak_directions=dict( argstr='-direction %s', sep=' ', ), - peaks_image=dict( - argstr='-peaks %s', - usedefault=True, - ), + peaks_image=dict(argstr='-peaks %s', ), quiet_display=dict(argstr='-quiet', ), ) inputs = Directions2Amplitude.input_spec() @@ -44,7 +39,7 @@ def test_Directions2Amplitude_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Directions2Amplitude_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Directions2Amplitude.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py index a38693054f..6215593ab0 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py @@ -22,14 +22,12 @@ def test_Erode_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), number_of_passes=dict(argstr='-npass %s', ), out_filename=dict( argstr='%s', genfile=True, position=-1, - usedefault=True, ), quiet=dict( argstr='-quiet', @@ -42,7 +40,7 @@ def test_Erode_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Erode_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Erode.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py index a3844813bd..983433104e 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py @@ -11,7 +11,6 @@ def test_EstimateResponseForSH_inputs(): argstr='-grad %s', mandatory=True, position=1, - usedefault=True, ), environ=dict( nohash=True, @@ -21,13 +20,11 @@ def test_EstimateResponseForSH_inputs(): argstr='%s', mandatory=True, position=-3, - usedefault=True, ), mask_image=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), maximum_harmonic_order=dict(argstr='-lmax %s', ), normalise=dict(argstr='-normalise', ), @@ -35,7 +32,6 @@ def test_EstimateResponseForSH_inputs(): argstr='%s', genfile=True, position=-1, - usedefault=True, ), quiet=dict(argstr='-quiet', ), ) @@ -45,7 +41,7 @@ def test_EstimateResponseForSH_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EstimateResponseForSH_outputs(): - output_map = dict(response=dict(usedefault=True, ), ) + output_map = dict(response=dict(), ) outputs = EstimateResponseForSH.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py b/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py index c07d531de9..6261b6b0a5 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py @@ -5,21 +5,12 @@ def test_FSL2MRTrix_inputs(): input_map = dict( - bval_file=dict( - mandatory=True, - usedefault=True, - ), - bvec_file=dict( - mandatory=True, - usedefault=True, - ), + bval_file=dict(mandatory=True, ), + bvec_file=dict(mandatory=True, ), invert_x=dict(usedefault=True, ), invert_y=dict(usedefault=True, ), invert_z=dict(usedefault=True, ), - out_encoding_file=dict( - genfile=True, - usedefault=True, - ), + out_encoding_file=dict(genfile=True, ), ) inputs = FSL2MRTrix.input_spec() @@ -27,7 +18,7 @@ def test_FSL2MRTrix_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FSL2MRTrix_outputs(): - output_map = dict(encoding_file=dict(usedefault=True, ), ) + output_map = dict(encoding_file=dict(), ) outputs = FSL2MRTrix.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py index 92b302e199..6e0e670d06 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py @@ -16,7 +16,6 @@ def test_FilterTracks_inputs(): ), exclude_file=dict( argstr='-exclude %s', - usedefault=True, xor=['exclude_file', 'exclude_spec'], ), exclude_spec=dict( @@ -30,11 +29,9 @@ def test_FilterTracks_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), include_file=dict( argstr='-include %s', - usedefault=True, xor=['include_file', 'include_spec'], ), include_spec=dict( @@ -56,7 +53,6 @@ def test_FilterTracks_inputs(): name_source=['in_file'], name_template='%s_filt', position=-1, - usedefault=True, ), quiet=dict( argstr='-quiet', @@ -69,7 +65,7 @@ def test_FilterTracks_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FilterTracks_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = FilterTracks.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py index dabc3cc1eb..5d9f51739c 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py @@ -10,7 +10,6 @@ def test_FindShPeaks_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), display_debug=dict(argstr='-debug', ), display_info=dict(argstr='-info', ), @@ -22,7 +21,6 @@ def test_FindShPeaks_inputs(): argstr='%s', mandatory=True, position=-3, - usedefault=True, ), num_peaks=dict(argstr='-num %s', ), out_file=dict( @@ -32,17 +30,13 @@ def test_FindShPeaks_inputs(): name_source=['in_file'], name_template='%s_peak_dirs.mif', position=-1, - usedefault=True, ), peak_directions=dict( argstr='-direction %s', sep=' ', ), peak_threshold=dict(argstr='-threshold %s', ), - peaks_image=dict( - argstr='-peaks %s', - usedefault=True, - ), + peaks_image=dict(argstr='-peaks %s', ), quiet_display=dict(argstr='-quiet', ), ) inputs = FindShPeaks.input_spec() @@ -51,7 +45,7 @@ def test_FindShPeaks_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FindShPeaks_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = FindShPeaks.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py index 10eafc7472..2cfd89bb6f 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py @@ -24,7 +24,6 @@ def test_GenerateDirections_inputs(): name_source=['num_dirs'], name_template='directions_%d.txt', position=-1, - usedefault=True, ), power=dict(argstr='-power %s', ), quiet_display=dict(argstr='-quiet', ), @@ -35,7 +34,7 @@ def test_GenerateDirections_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateDirections_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = GenerateDirections.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py index edbc3fe8d3..6a0305f9e2 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py @@ -10,13 +10,11 @@ def test_GenerateWhiteMatterMask_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), encoding_file=dict( argstr='-grad %s', mandatory=True, position=1, - usedefault=True, ), environ=dict( nohash=True, @@ -26,14 +24,12 @@ def test_GenerateWhiteMatterMask_inputs(): argstr='%s', mandatory=True, position=-3, - usedefault=True, ), noise_level_margin=dict(argstr='-margin %s', ), out_WMProb_filename=dict( argstr='%s', genfile=True, position=-1, - usedefault=True, ), ) inputs = GenerateWhiteMatterMask.input_spec() @@ -42,7 +38,7 @@ def test_GenerateWhiteMatterMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateWhiteMatterMask_outputs(): - output_map = dict(WMprobabilitymap=dict(usedefault=True, ), ) + output_map = dict(WMprobabilitymap=dict(), ) outputs = GenerateWhiteMatterMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py index 582cba026d..5aef0bfd13 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py @@ -27,7 +27,6 @@ def test_MRConvert_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), layout=dict( argstr='-output %s', @@ -42,7 +41,6 @@ def test_MRConvert_inputs(): argstr='%s', genfile=True, position=-1, - usedefault=True, ), output_datatype=dict( argstr='-output %s', @@ -73,7 +71,7 @@ def test_MRConvert_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRConvert_outputs(): - output_map = dict(converted=dict(usedefault=True, ), ) + output_map = dict(converted=dict(), ) outputs = MRConvert.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py index 00ec1e3069..a5a864289a 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py @@ -23,7 +23,6 @@ def test_MRMultiply_inputs(): argstr='%s', genfile=True, position=-1, - usedefault=True, ), quiet=dict( argstr='-quiet', @@ -36,7 +35,7 @@ def test_MRMultiply_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRMultiply_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MRMultiply.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py index 1ea25aed2d..d6a3db0a1d 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py @@ -31,7 +31,6 @@ def test_MRTransform_inputs(): argstr='%s', genfile=True, position=-1, - usedefault=True, ), quiet=dict( argstr='-quiet', @@ -40,7 +39,6 @@ def test_MRTransform_inputs(): reference_image=dict( argstr='-reference %s', position=1, - usedefault=True, ), replace_transform=dict( argstr='-replace', @@ -49,12 +47,10 @@ def test_MRTransform_inputs(): template_image=dict( argstr='-template %s', position=1, - usedefault=True, ), transformation_file=dict( argstr='-transform %s', position=1, - usedefault=True, ), ) inputs = MRTransform.input_spec() @@ -63,7 +59,7 @@ def test_MRTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRTransform_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MRTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py index e7a560a357..b6fefac9a0 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py @@ -5,17 +5,14 @@ def test_MRTrix2TrackVis_inputs(): input_map = dict( - image_file=dict(usedefault=True, ), - in_file=dict( - mandatory=True, - usedefault=True, - ), - matrix_file=dict(usedefault=True, ), + image_file=dict(), + in_file=dict(mandatory=True, ), + matrix_file=dict(), out_filename=dict( genfile=True, usedefault=True, ), - registration_image_file=dict(usedefault=True, ), + registration_image_file=dict(), ) inputs = MRTrix2TrackVis.input_spec() @@ -23,7 +20,7 @@ def test_MRTrix2TrackVis_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRTrix2TrackVis_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MRTrix2TrackVis.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py index 6cd2054d6c..0022de4d7a 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py @@ -14,7 +14,6 @@ def test_MRTrixInfo_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), ) inputs = MRTrixInfo.input_spec() diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py index 83910cecc2..0e7daabcaa 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py @@ -18,13 +18,11 @@ def test_MedianFilter3D_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), out_filename=dict( argstr='%s', genfile=True, position=-1, - usedefault=True, ), quiet=dict( argstr='-quiet', @@ -37,7 +35,7 @@ def test_MedianFilter3D_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MedianFilter3D_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MedianFilter3D.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py index 72dbf54a9e..6d75b1b9a2 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py @@ -18,7 +18,6 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): ), exclude_file=dict( argstr='-exclude %s', - usedefault=True, xor=['exclude_file', 'exclude_spec'], ), exclude_spec=dict( @@ -32,11 +31,9 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), include_file=dict( argstr='-include %s', - usedefault=True, xor=['include_file', 'include_spec'], ), include_spec=dict( @@ -61,7 +58,6 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): ), mask_file=dict( argstr='-mask %s', - usedefault=True, xor=['mask_file', 'mask_spec'], ), mask_spec=dict( @@ -92,11 +88,9 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): name_template='%s_tracked.tck', output_name='tracked', position=-1, - usedefault=True, ), seed_file=dict( argstr='-seed %s', - usedefault=True, xor=['seed_file', 'seed_spec'], ), seed_spec=dict( @@ -119,7 +113,7 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_outputs(): - output_map = dict(tracked=dict(usedefault=True, ), ) + output_map = dict(tracked=dict(), ) outputs = ProbabilisticSphericallyDeconvolutedStreamlineTrack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py index d207afa2af..9bed95276d 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py @@ -18,7 +18,6 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): ), exclude_file=dict( argstr='-exclude %s', - usedefault=True, xor=['exclude_file', 'exclude_spec'], ), exclude_spec=dict( @@ -32,11 +31,9 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), include_file=dict( argstr='-include %s', - usedefault=True, xor=['include_file', 'include_spec'], ), include_spec=dict( @@ -61,7 +58,6 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): ), mask_file=dict( argstr='-mask %s', - usedefault=True, xor=['mask_file', 'mask_spec'], ), mask_spec=dict( @@ -91,11 +87,9 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): name_template='%s_tracked.tck', output_name='tracked', position=-1, - usedefault=True, ), seed_file=dict( argstr='-seed %s', - usedefault=True, xor=['seed_file', 'seed_spec'], ), seed_spec=dict( @@ -118,7 +112,7 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SphericallyDeconvolutedStreamlineTrack_outputs(): - output_map = dict(tracked=dict(usedefault=True, ), ) + output_map = dict(tracked=dict(), ) outputs = SphericallyDeconvolutedStreamlineTrack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py index 824ff883e8..c898a60eb3 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py @@ -18,7 +18,6 @@ def test_StreamlineTrack_inputs(): ), exclude_file=dict( argstr='-exclude %s', - usedefault=True, xor=['exclude_file', 'exclude_spec'], ), exclude_spec=dict( @@ -32,11 +31,9 @@ def test_StreamlineTrack_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), include_file=dict( argstr='-include %s', - usedefault=True, xor=['include_file', 'include_spec'], ), include_spec=dict( @@ -61,7 +58,6 @@ def test_StreamlineTrack_inputs(): ), mask_file=dict( argstr='-mask %s', - usedefault=True, xor=['mask_file', 'mask_spec'], ), mask_spec=dict( @@ -91,11 +87,9 @@ def test_StreamlineTrack_inputs(): name_template='%s_tracked.tck', output_name='tracked', position=-1, - usedefault=True, ), seed_file=dict( argstr='-seed %s', - usedefault=True, xor=['seed_file', 'seed_spec'], ), seed_spec=dict( @@ -118,7 +112,7 @@ def test_StreamlineTrack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_StreamlineTrack_outputs(): - output_map = dict(tracked=dict(usedefault=True, ), ) + output_map = dict(tracked=dict(), ) outputs = StreamlineTrack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py index 67560fff57..e9546d7e90 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py @@ -18,13 +18,11 @@ def test_Tensor2ApparentDiffusion_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), out_filename=dict( argstr='%s', genfile=True, position=-1, - usedefault=True, ), quiet=dict( argstr='-quiet', @@ -37,7 +35,7 @@ def test_Tensor2ApparentDiffusion_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Tensor2ApparentDiffusion_outputs(): - output_map = dict(ADC=dict(usedefault=True, ), ) + output_map = dict(ADC=dict(), ) outputs = Tensor2ApparentDiffusion.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py index ea2d63a4f8..d16a907f62 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py @@ -18,13 +18,11 @@ def test_Tensor2FractionalAnisotropy_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), out_filename=dict( argstr='%s', genfile=True, position=-1, - usedefault=True, ), quiet=dict( argstr='-quiet', @@ -37,7 +35,7 @@ def test_Tensor2FractionalAnisotropy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Tensor2FractionalAnisotropy_outputs(): - output_map = dict(FA=dict(usedefault=True, ), ) + output_map = dict(FA=dict(), ) outputs = Tensor2FractionalAnisotropy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py index 91fba8183b..c07d0a8db4 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py @@ -18,13 +18,11 @@ def test_Tensor2Vector_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), out_filename=dict( argstr='%s', genfile=True, position=-1, - usedefault=True, ), quiet=dict( argstr='-quiet', @@ -37,7 +35,7 @@ def test_Tensor2Vector_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Tensor2Vector_outputs(): - output_map = dict(vector=dict(usedefault=True, ), ) + output_map = dict(vector=dict(), ) outputs = Tensor2Vector.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py index 84f42965fc..39fbf14d2c 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py @@ -19,7 +19,6 @@ def test_Threshold_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), invert=dict( argstr='-invert', @@ -29,7 +28,6 @@ def test_Threshold_inputs(): argstr='%s', genfile=True, position=-1, - usedefault=True, ), percentage_threshold_value=dict(argstr='-percent %s', ), quiet=dict( @@ -47,7 +45,7 @@ def test_Threshold_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Threshold_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Threshold.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py index b4c930d0f9..f984203ab1 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py @@ -22,13 +22,11 @@ def test_Tracks2Prob_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), out_filename=dict( argstr='%s', genfile=True, position=-1, - usedefault=True, ), output_datatype=dict( argstr='-datatype %s', @@ -42,7 +40,6 @@ def test_Tracks2Prob_inputs(): template_file=dict( argstr='-template %s', position=1, - usedefault=True, ), voxel_dims=dict( argstr='-vox %s', @@ -56,7 +53,7 @@ def test_Tracks2Prob_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Tracks2Prob_outputs(): - output_map = dict(tract_image=dict(usedefault=True, ), ) + output_map = dict(tract_image=dict(), ) outputs = Tracks2Prob.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py index 055490f1da..abb3ba6831 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py @@ -14,7 +14,6 @@ def test_ACTPrepareFSL_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), out_file=dict( argstr='%s', @@ -29,7 +28,7 @@ def test_ACTPrepareFSL_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ACTPrepareFSL_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ACTPrepareFSL.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py index bcdb6be17d..c318be0bfd 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py @@ -11,21 +11,14 @@ def test_BrainMask_inputs(): nohash=True, usedefault=True, ), - grad_file=dict( - argstr='-grad %s', - usedefault=True, - ), + grad_file=dict(argstr='-grad %s', ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(usedefault=True, ), - in_bvec=dict( - argstr='-fslgrad %s %s', - usedefault=True, - ), + in_bval=dict(), + in_bvec=dict(argstr='-fslgrad %s %s', ), in_file=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), nthreads=dict( argstr='-nthreads %d', @@ -44,7 +37,7 @@ def test_BrainMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BrainMask_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = BrainMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py index dd5cee6eda..95e5797d06 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py @@ -14,21 +14,13 @@ def test_BuildConnectome_inputs(): argstr='%s', mandatory=True, position=-3, - usedefault=True, ), in_parc=dict( argstr='%s', position=-2, - usedefault=True, - ), - in_scalar=dict( - argstr='-image %s', - usedefault=True, - ), - in_weights=dict( - argstr='-tck_weights_in %s', - usedefault=True, ), + in_scalar=dict(argstr='-image %s', ), + in_weights=dict(argstr='-tck_weights_in %s', ), keep_unassigned=dict(argstr='-keep_unassigned', ), metric=dict(argstr='-metric %s', ), nthreads=dict( @@ -53,7 +45,7 @@ def test_BuildConnectome_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BuildConnectome_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = BuildConnectome.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py index 61c86e489c..38369e8fe5 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py @@ -8,10 +8,7 @@ def test_ComputeTDI_inputs(): args=dict(argstr='%s', ), contrast=dict(argstr='-constrast %s', ), data_type=dict(argstr='-datatype %s', ), - dixel=dict( - argstr='-dixel %s', - usedefault=True, - ), + dixel=dict(argstr='-dixel %s', ), ends_only=dict(argstr='-ends_only', ), environ=dict( nohash=True, @@ -22,12 +19,8 @@ def test_ComputeTDI_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, - ), - in_map=dict( - argstr='-image %s', - usedefault=True, ), + in_map=dict(argstr='-image %s', ), map_zero=dict(argstr='-map_zero', ), max_tod=dict(argstr='-tod %d', ), nthreads=dict( @@ -40,16 +33,10 @@ def test_ComputeTDI_inputs(): usedefault=True, ), precise=dict(argstr='-precise', ), - reference=dict( - argstr='-template %s', - usedefault=True, - ), + reference=dict(argstr='-template %s', ), stat_tck=dict(argstr='-stat_tck %s', ), stat_vox=dict(argstr='-stat_vox %s', ), - tck_weights=dict( - argstr='-tck_weights_in %s', - usedefault=True, - ), + tck_weights=dict(argstr='-tck_weights_in %s', ), upsample=dict(argstr='-upsample %d', ), use_dec=dict(argstr='-dec', ), vox_size=dict( @@ -63,7 +50,7 @@ def test_ComputeTDI_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeTDI_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ComputeTDI.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py b/nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py index e5c25b3bd8..ea4d3f05d8 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_DWIBiasCorrect.py @@ -6,10 +6,7 @@ def test_DWIBiasCorrect_inputs(): input_map = dict( args=dict(argstr='%s', ), - bias=dict( - argstr='-bias %s', - usedefault=True, - ), + bias=dict(argstr='-bias %s', ), bval_scale=dict(argstr='-bvalue_scaling %s', ), environ=dict( nohash=True, @@ -17,32 +14,20 @@ def test_DWIBiasCorrect_inputs(): ), fsl_grad=dict( argstr='-fslgrad %s %s', - usedefault=True, xor=('mrtrix_grad', 'fsl_grad'), ), - grad_file=dict( - argstr='-grad %s', - usedefault=True, - ), + grad_file=dict(argstr='-grad %s', ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(usedefault=True, ), - in_bvec=dict( - argstr='-fslgrad %s %s', - usedefault=True, - ), + in_bval=dict(), + in_bvec=dict(argstr='-fslgrad %s %s', ), in_file=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, - ), - in_mask=dict( - argstr='-mask %s', - usedefault=True, ), + in_mask=dict(argstr='-mask %s', ), mrtrix_grad=dict( argstr='-grad %s', - usedefault=True, xor=('mrtrix_grad', 'fsl_grad'), ), nthreads=dict( @@ -56,7 +41,6 @@ def test_DWIBiasCorrect_inputs(): name_source='in_file', name_template='%s_biascorr', position=-1, - usedefault=True, ), use_ants=dict( argstr='-ants', @@ -76,8 +60,8 @@ def test_DWIBiasCorrect_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DWIBiasCorrect_outputs(): output_map = dict( - bias=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), + bias=dict(), + out_file=dict(), ) outputs = DWIBiasCorrect.output_spec() diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py b/nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py index 8c5f88b12e..7b6930ee82 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_DWIDenoise.py @@ -12,31 +12,20 @@ def test_DWIDenoise_inputs(): usedefault=True, ), extent=dict(argstr='-extent %d,%d,%d', ), - grad_file=dict( - argstr='-grad %s', - usedefault=True, - ), + grad_file=dict(argstr='-grad %s', ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(usedefault=True, ), - in_bvec=dict( - argstr='-fslgrad %s %s', - usedefault=True, - ), + in_bval=dict(), + in_bvec=dict(argstr='-fslgrad %s %s', ), in_file=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), mask=dict( argstr='-mask %s', position=1, - usedefault=True, - ), - noise=dict( - argstr='-noise %s', - usedefault=True, ), + noise=dict(argstr='-noise %s', ), nthreads=dict( argstr='-nthreads %d', nohash=True, @@ -48,7 +37,6 @@ def test_DWIDenoise_inputs(): name_source='in_file', name_template='%s_denoised', position=-1, - usedefault=True, ), ) inputs = DWIDenoise.input_spec() @@ -58,8 +46,8 @@ def test_DWIDenoise_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DWIDenoise_outputs(): output_map = dict( - noise=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), + noise=dict(), + out_file=dict(), ) outputs = DWIDenoise.output_spec() diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py b/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py index ef17cc7fe7..0114c5efe0 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_DWIExtract.py @@ -12,21 +12,14 @@ def test_DWIExtract_inputs(): nohash=True, usedefault=True, ), - grad_file=dict( - argstr='-grad %s', - usedefault=True, - ), + grad_file=dict(argstr='-grad %s', ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(usedefault=True, ), - in_bvec=dict( - argstr='-fslgrad %s %s', - usedefault=True, - ), + in_bval=dict(), + in_bvec=dict(argstr='-fslgrad %s %s', ), in_file=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), nobzero=dict(argstr='-no_bzero', ), nthreads=dict( @@ -37,7 +30,6 @@ def test_DWIExtract_inputs(): argstr='%s', mandatory=True, position=-1, - usedefault=True, ), shell=dict( argstr='-shell %s', @@ -51,7 +43,7 @@ def test_DWIExtract_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWIExtract_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = DWIExtract.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py index 3d18672b6b..a5c152e928 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py @@ -20,7 +20,6 @@ def test_EstimateFOD_inputs(): csf_txt=dict( argstr='%s', position=-2, - usedefault=True, ), environ=dict( nohash=True, @@ -34,32 +33,18 @@ def test_EstimateFOD_inputs(): gm_txt=dict( argstr='%s', position=-4, - usedefault=True, - ), - grad_file=dict( - argstr='-grad %s', - usedefault=True, ), + grad_file=dict(argstr='-grad %s', ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(usedefault=True, ), - in_bvec=dict( - argstr='-fslgrad %s %s', - usedefault=True, - ), - in_dirs=dict( - argstr='-directions %s', - usedefault=True, - ), + in_bval=dict(), + in_bvec=dict(argstr='-fslgrad %s %s', ), + in_dirs=dict(argstr='-directions %s', ), in_file=dict( argstr='%s', mandatory=True, position=-7, - usedefault=True, - ), - mask_file=dict( - argstr='-mask %s', - usedefault=True, ), + mask_file=dict(argstr='-mask %s', ), max_sh=dict( argstr='-lmax %d', usedefault=True, @@ -82,7 +67,6 @@ def test_EstimateFOD_inputs(): argstr='%s', mandatory=True, position=-6, - usedefault=True, ), ) inputs = EstimateFOD.input_spec() @@ -92,18 +76,9 @@ def test_EstimateFOD_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EstimateFOD_outputs(): output_map = dict( - csf_odf=dict( - argstr='%s', - usedefault=True, - ), - gm_odf=dict( - argstr='%s', - usedefault=True, - ), - wm_odf=dict( - argstr='%s', - usedefault=True, - ), + csf_odf=dict(argstr='%s', ), + gm_odf=dict(argstr='%s', ), + wm_odf=dict(argstr='%s', ), ) outputs = EstimateFOD.output_spec() diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py index dabea06823..85c103cc10 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py @@ -11,26 +11,16 @@ def test_FitTensor_inputs(): nohash=True, usedefault=True, ), - grad_file=dict( - argstr='-grad %s', - usedefault=True, - ), + grad_file=dict(argstr='-grad %s', ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(usedefault=True, ), - in_bvec=dict( - argstr='-fslgrad %s %s', - usedefault=True, - ), + in_bval=dict(), + in_bvec=dict(argstr='-fslgrad %s %s', ), in_file=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, - ), - in_mask=dict( - argstr='-mask %s', - usedefault=True, ), + in_mask=dict(argstr='-mask %s', ), method=dict(argstr='-method %s', ), nthreads=dict( argstr='-nthreads %d', @@ -53,7 +43,7 @@ def test_FitTensor_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FitTensor_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = FitTensor.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py index 55ef543167..dcfbe1fc6f 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py @@ -16,21 +16,14 @@ def test_Generate5tt_inputs(): nohash=True, usedefault=True, ), - grad_file=dict( - argstr='-grad %s', - usedefault=True, - ), + grad_file=dict(argstr='-grad %s', ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(usedefault=True, ), - in_bvec=dict( - argstr='-fslgrad %s %s', - usedefault=True, - ), + in_bval=dict(), + in_bvec=dict(argstr='-fslgrad %s %s', ), in_file=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), nthreads=dict( argstr='-nthreads %d', @@ -40,7 +33,6 @@ def test_Generate5tt_inputs(): argstr='%s', mandatory=True, position=-1, - usedefault=True, ), ) inputs = Generate5tt.input_spec() @@ -49,7 +41,7 @@ def test_Generate5tt_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Generate5tt_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Generate5tt.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py index d137914b87..2de0e6c115 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py @@ -13,30 +13,16 @@ def test_LabelConfig_inputs(): in_config=dict( argstr='%s', position=-2, - usedefault=True, ), in_file=dict( argstr='%s', mandatory=True, position=-3, - usedefault=True, - ), - lut_aal=dict( - argstr='-lut_aal %s', - usedefault=True, - ), - lut_basic=dict( - argstr='-lut_basic %s', - usedefault=True, - ), - lut_fs=dict( - argstr='-lut_freesurfer %s', - usedefault=True, - ), - lut_itksnap=dict( - argstr='-lut_itksnap %s', - usedefault=True, ), + lut_aal=dict(argstr='-lut_aal %s', ), + lut_basic=dict(argstr='-lut_basic %s', ), + lut_fs=dict(argstr='-lut_freesurfer %s', ), + lut_itksnap=dict(argstr='-lut_itksnap %s', ), nthreads=dict( argstr='-nthreads %d', nohash=True, @@ -47,10 +33,7 @@ def test_LabelConfig_inputs(): position=-1, usedefault=True, ), - spine=dict( - argstr='-spine %s', - usedefault=True, - ), + spine=dict(argstr='-spine %s', ), ) inputs = LabelConfig.input_spec() @@ -58,7 +41,7 @@ def test_LabelConfig_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LabelConfig_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = LabelConfig.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConvert.py b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConvert.py index d9c3138625..1e93ae82d8 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConvert.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConvert.py @@ -13,19 +13,16 @@ def test_LabelConvert_inputs(): in_config=dict( argstr='%s', position=-2, - usedefault=True, ), in_file=dict( argstr='%s', mandatory=True, position=-4, - usedefault=True, ), in_lut=dict( argstr='%s', mandatory=True, position=-3, - usedefault=True, ), num_threads=dict( argstr='-nthreads %d', @@ -37,10 +34,7 @@ def test_LabelConvert_inputs(): position=-1, usedefault=True, ), - spine=dict( - argstr='-spine %s', - usedefault=True, - ), + spine=dict(argstr='-spine %s', ), ) inputs = LabelConvert.input_spec() @@ -48,7 +42,7 @@ def test_LabelConvert_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LabelConvert_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = LabelConvert.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py index acd1609dbc..ece24e1d47 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRConvert.py @@ -19,21 +19,14 @@ def test_MRConvert_inputs(): nohash=True, usedefault=True, ), - grad_file=dict( - argstr='-grad %s', - usedefault=True, - ), + grad_file=dict(argstr='-grad %s', ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(usedefault=True, ), - in_bvec=dict( - argstr='-fslgrad %s %s', - usedefault=True, - ), + in_bval=dict(), + in_bvec=dict(argstr='-fslgrad %s %s', ), in_file=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), nthreads=dict( argstr='-nthreads %d', @@ -60,7 +53,7 @@ def test_MRConvert_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRConvert_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MRConvert.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py index 10b5edf453..c9290b562b 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py @@ -18,21 +18,14 @@ def test_MRDeGibbs_inputs(): nohash=True, usedefault=True, ), - grad_file=dict( - argstr='-grad %s', - usedefault=True, - ), + grad_file=dict(argstr='-grad %s', ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(usedefault=True, ), - in_bvec=dict( - argstr='-fslgrad %s %s', - usedefault=True, - ), + in_bval=dict(), + in_bvec=dict(argstr='-fslgrad %s %s', ), in_file=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), maxW=dict( argstr='-maxW %d', @@ -57,7 +50,6 @@ def test_MRDeGibbs_inputs(): name_source='in_file', name_template='%s_unr', position=-1, - usedefault=True, ), ) inputs = MRDeGibbs.input_spec() @@ -66,7 +58,7 @@ def test_MRDeGibbs_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRDeGibbs_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MRDeGibbs.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py index 5e86fc316b..eec06b6276 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRMath.py @@ -12,21 +12,14 @@ def test_MRMath_inputs(): nohash=True, usedefault=True, ), - grad_file=dict( - argstr='-grad %s', - usedefault=True, - ), + grad_file=dict(argstr='-grad %s', ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(usedefault=True, ), - in_bvec=dict( - argstr='-fslgrad %s %s', - usedefault=True, - ), + in_bval=dict(), + in_bvec=dict(argstr='-fslgrad %s %s', ), in_file=dict( argstr='%s', mandatory=True, position=-3, - usedefault=True, ), nthreads=dict( argstr='-nthreads %d', @@ -41,7 +34,6 @@ def test_MRMath_inputs(): argstr='%s', mandatory=True, position=-1, - usedefault=True, ), ) inputs = MRMath.input_spec() @@ -50,7 +42,7 @@ def test_MRMath_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MRMath_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MRMath.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py index 4ab14ad7a8..9aa29acbe8 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py @@ -14,12 +14,8 @@ def test_Mesh2PVE_inputs(): argstr='%s', mandatory=True, position=-3, - usedefault=True, - ), - in_first=dict( - argstr='-first %s', - usedefault=True, ), + in_first=dict(argstr='-first %s', ), out_file=dict( argstr='%s', mandatory=True, @@ -30,7 +26,6 @@ def test_Mesh2PVE_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), ) inputs = Mesh2PVE.input_spec() @@ -39,7 +34,7 @@ def test_Mesh2PVE_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Mesh2PVE_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Mesh2PVE.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py index 5753ebcf27..502a0f7fb1 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py @@ -13,19 +13,16 @@ def test_ReplaceFSwithFIRST_inputs(): in_config=dict( argstr='%s', position=-2, - usedefault=True, ), in_file=dict( argstr='%s', mandatory=True, position=-4, - usedefault=True, ), in_t1w=dict( argstr='%s', mandatory=True, position=-3, - usedefault=True, ), out_file=dict( argstr='%s', @@ -40,7 +37,7 @@ def test_ReplaceFSwithFIRST_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ReplaceFSwithFIRST_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ReplaceFSwithFIRST.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py index 55edbd4280..f4b4660d78 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py @@ -15,7 +15,6 @@ def test_ResponseSD_inputs(): csf_file=dict( argstr='%s', position=-1, - usedefault=True, ), environ=dict( nohash=True, @@ -24,28 +23,17 @@ def test_ResponseSD_inputs(): gm_file=dict( argstr='%s', position=-2, - usedefault=True, - ), - grad_file=dict( - argstr='-grad %s', - usedefault=True, ), + grad_file=dict(argstr='-grad %s', ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(usedefault=True, ), - in_bvec=dict( - argstr='-fslgrad %s %s', - usedefault=True, - ), + in_bval=dict(), + in_bvec=dict(argstr='-fslgrad %s %s', ), in_file=dict( argstr='%s', mandatory=True, position=-5, - usedefault=True, - ), - in_mask=dict( - argstr='-mask %s', - usedefault=True, ), + in_mask=dict(argstr='-mask %s', ), max_sh=dict( argstr='-lmax %s', sep=',', @@ -53,7 +41,6 @@ def test_ResponseSD_inputs(): mtt_file=dict( argstr='%s', position=-4, - usedefault=True, ), nthreads=dict( argstr='-nthreads %d', @@ -72,18 +59,9 @@ def test_ResponseSD_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ResponseSD_outputs(): output_map = dict( - csf_file=dict( - argstr='%s', - usedefault=True, - ), - gm_file=dict( - argstr='%s', - usedefault=True, - ), - wm_file=dict( - argstr='%s', - usedefault=True, - ), + csf_file=dict(argstr='%s', ), + gm_file=dict(argstr='%s', ), + wm_file=dict(argstr='%s', ), ) outputs = ResponseSD.output_spec() diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py index e637da109d..93a39484f8 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py @@ -14,7 +14,6 @@ def test_TCK2VTK_inputs(): argstr='%s', mandatory=True, position=-2, - usedefault=True, ), nthreads=dict( argstr='-nthreads %d', @@ -25,14 +24,8 @@ def test_TCK2VTK_inputs(): position=-1, usedefault=True, ), - reference=dict( - argstr='-image %s', - usedefault=True, - ), - voxel=dict( - argstr='-image %s', - usedefault=True, - ), + reference=dict(argstr='-image %s', ), + voxel=dict(argstr='-image %s', ), ) inputs = TCK2VTK.input_spec() @@ -40,7 +33,7 @@ def test_TCK2VTK_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TCK2VTK_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TCK2VTK.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py index 7e67c2b11b..ae532c9910 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py @@ -19,29 +19,13 @@ def test_TensorMetrics_inputs(): argstr='%s', mandatory=True, position=-1, - usedefault=True, - ), - in_mask=dict( - argstr='-mask %s', - usedefault=True, ), + in_mask=dict(argstr='-mask %s', ), modulate=dict(argstr='-modulate %s', ), - out_adc=dict( - argstr='-adc %s', - usedefault=True, - ), - out_eval=dict( - argstr='-value %s', - usedefault=True, - ), - out_evec=dict( - argstr='-vector %s', - usedefault=True, - ), - out_fa=dict( - argstr='-fa %s', - usedefault=True, - ), + out_adc=dict(argstr='-adc %s', ), + out_eval=dict(argstr='-value %s', ), + out_evec=dict(argstr='-vector %s', ), + out_fa=dict(argstr='-fa %s', ), ) inputs = TensorMetrics.input_spec() @@ -50,10 +34,10 @@ def test_TensorMetrics_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TensorMetrics_outputs(): output_map = dict( - out_adc=dict(usedefault=True, ), - out_eval=dict(usedefault=True, ), - out_evec=dict(usedefault=True, ), - out_fa=dict(usedefault=True, ), + out_adc=dict(), + out_eval=dict(), + out_evec=dict(), + out_fa=dict(), ) outputs = TensorMetrics.output_spec() diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py index 13f779d63d..c79fce8867 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py @@ -5,10 +5,7 @@ def test_Tractography_inputs(): input_map = dict( - act_file=dict( - argstr='-act %s', - usedefault=True, - ), + act_file=dict(argstr='-act %s', ), algorithm=dict( argstr='-algorithm %s', usedefault=True, @@ -25,21 +22,14 @@ def test_Tractography_inputs(): nohash=True, usedefault=True, ), - grad_file=dict( - argstr='-grad %s', - usedefault=True, - ), + grad_file=dict(argstr='-grad %s', ), grad_fsl=dict(argstr='-fslgrad %s %s', ), - in_bval=dict(usedefault=True, ), - in_bvec=dict( - argstr='-fslgrad %s %s', - usedefault=True, - ), + in_bval=dict(), + in_bvec=dict(argstr='-fslgrad %s %s', ), in_file=dict( argstr='%s', mandatory=True, position=-2, - usedefault=True, ), init_dir=dict(argstr='-initdirection %f,%f,%f', ), max_length=dict(argstr='-maxlength %f', ), @@ -74,27 +64,17 @@ def test_Tractography_inputs(): roi_excl=dict(argstr='-exclude %s', ), roi_incl=dict(argstr='-include %s', ), roi_mask=dict(argstr='-mask %s', ), - seed_dynamic=dict( - argstr='-seed_dynamic %s', - usedefault=True, - ), + seed_dynamic=dict(argstr='-seed_dynamic %s', ), seed_gmwmi=dict( argstr='-seed_gmwmi %s', requires=['act_file'], - usedefault=True, ), seed_grid_voxel=dict( argstr='-seed_grid_per_voxel %s %d', xor=['seed_image', 'seed_rnd_voxel'], ), - seed_image=dict( - argstr='-seed_image %s', - usedefault=True, - ), - seed_rejection=dict( - argstr='-seed_rejection %s', - usedefault=True, - ), + seed_image=dict(argstr='-seed_image %s', ), + seed_rejection=dict(argstr='-seed_rejection %s', ), seed_rnd_voxel=dict( argstr='-seed_random_per_voxel %s %d', xor=['seed_image', 'seed_grid_voxel'], @@ -117,8 +97,8 @@ def test_Tractography_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Tractography_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - out_seeds=dict(usedefault=True, ), + out_file=dict(), + out_seeds=dict(), ) outputs = Tractography.output_spec() diff --git a/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py b/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py index bf5b08e3de..0505ee514c 100644 --- a/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py +++ b/nipype/interfaces/niftyfit/tests/test_auto_FitQt1.py @@ -12,7 +12,6 @@ def test_FitQt1_inputs(): argstr='-comp %s', name_source=['source_file'], name_template='%s_comp.nii.gz', - usedefault=True, ), environ=dict( nohash=True, @@ -22,7 +21,6 @@ def test_FitQt1_inputs(): argstr='-error %s', name_source=['source_file'], name_template='%s_error.nii.gz', - usedefault=True, ), flips=dict( argstr='-flips %s', @@ -45,12 +43,10 @@ def test_FitQt1_inputs(): argstr='-m0map %s', name_source=['source_file'], name_template='%s_m0map.nii.gz', - usedefault=True, ), mask=dict( argstr='-mask %s', position=2, - usedefault=True, ), maxit=dict( argstr='-maxit %d', @@ -60,7 +56,6 @@ def test_FitQt1_inputs(): argstr='-mcmap %s', name_source=['source_file'], name_template='%s_mcmap.nii.gz', - usedefault=True, ), mcmaxit=dict(argstr='-mcmaxit %d', ), mcout=dict(argstr='-mcout %s', ), @@ -72,13 +67,11 @@ def test_FitQt1_inputs(): prior=dict( argstr='-prior %s', position=3, - usedefault=True, ), res_file=dict( argstr='-res %s', name_source=['source_file'], name_template='%s_res.nii.gz', - usedefault=True, ), slice_no=dict( argstr='-slice %d', @@ -88,7 +81,6 @@ def test_FitQt1_inputs(): argstr='-source %s', mandatory=True, position=1, - usedefault=True, ), spgr=dict(argstr='-SPGR', ), sr_flag=dict( @@ -99,14 +91,12 @@ def test_FitQt1_inputs(): argstr='-syn %s', name_source=['source_file'], name_template='%s_syn.nii.gz', - usedefault=True, ), t1_list=dict(argstr='-T1list %s', ), t1map_file=dict( argstr='-t1map %s', name_source=['source_file'], name_template='%s_t1map.nii.gz', - usedefault=True, ), t1max=dict(argstr='-T1max %f', ), t1min=dict(argstr='-T1min %f', ), @@ -136,13 +126,13 @@ def test_FitQt1_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FitQt1_outputs(): output_map = dict( - comp_file=dict(usedefault=True, ), - error_file=dict(usedefault=True, ), - m0map_file=dict(usedefault=True, ), - mcmap_file=dict(usedefault=True, ), - res_file=dict(usedefault=True, ), - syn_file=dict(usedefault=True, ), - t1map_file=dict(usedefault=True, ), + comp_file=dict(), + error_file=dict(), + m0map_file=dict(), + mcmap_file=dict(), + res_file=dict(), + syn_file=dict(), + t1map_file=dict(), ) outputs = FitQt1.output_spec() diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py b/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py index e6554137f3..9507f53fa9 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py @@ -10,7 +10,6 @@ def test_RegAladin_inputs(): argstr='-aff %s', name_source=['flo_file'], name_template='%s_aff.txt', - usedefault=True, ), args=dict(argstr='%s', ), cog_flag=dict(argstr='-cog', ), @@ -21,20 +20,13 @@ def test_RegAladin_inputs(): flo_file=dict( argstr='-flo %s', mandatory=True, - usedefault=True, ), flo_low_val=dict(argstr='-floLowThr %f', ), flo_up_val=dict(argstr='-floUpThr %f', ), - fmask_file=dict( - argstr='-fmask %s', - usedefault=True, - ), + fmask_file=dict(argstr='-fmask %s', ), gpuid_val=dict(argstr='-gpuid %i', ), i_val=dict(argstr='-pi %d', ), - in_aff_file=dict( - argstr='-inaff %s', - usedefault=True, - ), + in_aff_file=dict(argstr='-inaff %s', ), ln_val=dict(argstr='-ln %d', ), lp_val=dict(argstr='-lp %d', ), maxit_val=dict(argstr='-maxit %d', ), @@ -48,7 +40,6 @@ def test_RegAladin_inputs(): ref_file=dict( argstr='-ref %s', mandatory=True, - usedefault=True, ), ref_low_val=dict(argstr='-refLowThr %f', ), ref_up_val=dict(argstr='-refUpThr %f', ), @@ -56,13 +47,9 @@ def test_RegAladin_inputs(): argstr='-res %s', name_source=['flo_file'], name_template='%s_res.nii.gz', - usedefault=True, ), rig_only_flag=dict(argstr='-rigOnly', ), - rmask_file=dict( - argstr='-rmask %s', - usedefault=True, - ), + rmask_file=dict(argstr='-rmask %s', ), smoo_f_val=dict(argstr='-smooF %f', ), smoo_r_val=dict(argstr='-smooR %f', ), v_val=dict(argstr='-pv %d', ), @@ -75,9 +62,9 @@ def test_RegAladin_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RegAladin_outputs(): output_map = dict( - aff_file=dict(usedefault=True, ), + aff_file=dict(), avg_output=dict(), - res_file=dict(usedefault=True, ), + res_file=dict(), ) outputs = RegAladin.output_spec() diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py b/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py index cce87139dd..2510a46eb8 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegAverage.py @@ -28,7 +28,6 @@ def test_RegAverage_inputs(): argstr='-avg_tran %s', position=1, requires=['warp_files'], - usedefault=True, xor=[ 'avg_files', 'avg_lts_files', 'demean1_ref_file', 'demean2_ref_file', 'demean3_ref_file' @@ -38,7 +37,6 @@ def test_RegAverage_inputs(): argstr='-demean1 %s', position=1, requires=['warp_files'], - usedefault=True, xor=[ 'avg_files', 'avg_lts_files', 'avg_ref_file', 'demean2_ref_file', 'demean3_ref_file' @@ -48,7 +46,6 @@ def test_RegAverage_inputs(): argstr='-demean2 %s', position=1, requires=['warp_files'], - usedefault=True, xor=[ 'avg_files', 'avg_lts_files', 'avg_ref_file', 'demean1_ref_file', 'demean3_ref_file' @@ -58,7 +55,6 @@ def test_RegAverage_inputs(): argstr='-demean3 %s', position=1, requires=['warp_files'], - usedefault=True, xor=[ 'avg_files', 'avg_lts_files', 'avg_ref_file', 'demean1_ref_file', 'demean2_ref_file' @@ -76,7 +72,6 @@ def test_RegAverage_inputs(): argstr='%s', genfile=True, position=0, - usedefault=True, ), warp_files=dict( argstr='%s', @@ -91,7 +86,7 @@ def test_RegAverage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegAverage_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = RegAverage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py b/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py index 94f0ed45dd..e9bdab82c0 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py @@ -5,10 +5,7 @@ def test_RegF3D_inputs(): input_map = dict( - aff_file=dict( - argstr='-aff %s', - usedefault=True, - ), + aff_file=dict(argstr='-aff %s', ), amc_flag=dict(argstr='-amc', ), args=dict(argstr='%s', ), be_val=dict(argstr='-be %f', ), @@ -16,7 +13,6 @@ def test_RegF3D_inputs(): argstr='-cpp %s', name_source=['flo_file'], name_template='%s_cpp.nii.gz', - usedefault=True, ), environ=dict( nohash=True, @@ -27,21 +23,14 @@ def test_RegF3D_inputs(): flo_file=dict( argstr='-flo %s', mandatory=True, - usedefault=True, ), flo_smooth_val=dict(argstr='-smooF %f', ), flwth2_thr_val=dict(argstr='-fLwTh %d %f', ), flwth_thr_val=dict(argstr='--fLwTh %f', ), - fmask_file=dict( - argstr='-fmask %s', - usedefault=True, - ), + fmask_file=dict(argstr='-fmask %s', ), fupth2_thr_val=dict(argstr='-fUpTh %d %f', ), fupth_thr_val=dict(argstr='--fUpTh %f', ), - incpp_file=dict( - argstr='-incpp %s', - usedefault=True, - ), + incpp_file=dict(argstr='-incpp %s', ), jl_val=dict(argstr='-jl %f', ), kld2_flag=dict(argstr='-kld %d', ), kld_flag=dict(argstr='--kld', ), @@ -69,21 +58,16 @@ def test_RegF3D_inputs(): ref_file=dict( argstr='-ref %s', mandatory=True, - usedefault=True, ), ref_smooth_val=dict(argstr='-smooR %f', ), res_file=dict( argstr='-res %s', name_source=['flo_file'], name_template='%s_res.nii.gz', - usedefault=True, ), rlwth2_thr_val=dict(argstr='-rLwTh %d %f', ), rlwth_thr_val=dict(argstr='--rLwTh %f', ), - rmask_file=dict( - argstr='-rmask %s', - usedefault=True, - ), + rmask_file=dict(argstr='-rmask %s', ), rupth2_thr_val=dict(argstr='-rUpTh %d %f', ), rupth_thr_val=dict(argstr='--rUpTh %f', ), smooth_grad_val=dict(argstr='-smoothGrad %f', ), @@ -103,10 +87,10 @@ def test_RegF3D_inputs(): def test_RegF3D_outputs(): output_map = dict( avg_output=dict(), - cpp_file=dict(usedefault=True, ), - invcpp_file=dict(usedefault=True, ), - invres_file=dict(usedefault=True, ), - res_file=dict(usedefault=True, ), + cpp_file=dict(), + invcpp_file=dict(), + invres_file=dict(), + res_file=dict(), ) outputs = RegF3D.output_spec() diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py b/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py index 360e940c1e..63f917c683 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegJacobian.py @@ -19,16 +19,11 @@ def test_RegJacobian_inputs(): name_source=['trans_file'], name_template='%s', position=-1, - usedefault=True, - ), - ref_file=dict( - argstr='-ref %s', - usedefault=True, ), + ref_file=dict(argstr='-ref %s', ), trans_file=dict( argstr='-trans %s', mandatory=True, - usedefault=True, ), type=dict( argstr='-%s', @@ -42,7 +37,7 @@ def test_RegJacobian_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegJacobian_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = RegJacobian.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py b/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py index 97493a2761..3321d87afc 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegMeasure.py @@ -13,7 +13,6 @@ def test_RegMeasure_inputs(): flo_file=dict( argstr='-flo %s', mandatory=True, - usedefault=True, ), measure_type=dict( argstr='-%s', @@ -27,12 +26,10 @@ def test_RegMeasure_inputs(): argstr='-out %s', name_source=['flo_file'], name_template='%s', - usedefault=True, ), ref_file=dict( argstr='-ref %s', mandatory=True, - usedefault=True, ), ) inputs = RegMeasure.input_spec() @@ -41,7 +38,7 @@ def test_RegMeasure_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegMeasure_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = RegMeasure.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py b/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py index d4674d292e..06b2b48401 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegResample.py @@ -13,7 +13,6 @@ def test_RegResample_inputs(): flo_file=dict( argstr='-flo %s', mandatory=True, - usedefault=True, ), inter_val=dict(argstr='-inter %d', ), omp_core_val=dict( @@ -25,7 +24,6 @@ def test_RegResample_inputs(): name_source=['flo_file'], name_template='%s', position=-1, - usedefault=True, ), pad_val=dict(argstr='-pad %f', ), psf_alg=dict(argstr='-psf_alg %d', ), @@ -33,13 +31,9 @@ def test_RegResample_inputs(): ref_file=dict( argstr='-ref %s', mandatory=True, - usedefault=True, ), tensor_flag=dict(argstr='-tensor ', ), - trans_file=dict( - argstr='-trans %s', - usedefault=True, - ), + trans_file=dict(argstr='-trans %s', ), type=dict( argstr='-%s', position=-2, @@ -53,7 +47,7 @@ def test_RegResample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegResample_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = RegResample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py b/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py index 3e08535ee1..5deb4206e6 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegTools.py @@ -18,14 +18,10 @@ def test_RegTools_inputs(): in_file=dict( argstr='-in %s', mandatory=True, - usedefault=True, ), inter_val=dict(argstr='-interp %d', ), iso_flag=dict(argstr='-iso', ), - mask_file=dict( - argstr='-nan %s', - usedefault=True, - ), + mask_file=dict(argstr='-nan %s', ), mul_val=dict(argstr='-mul %s', ), noscl_flag=dict(argstr='-noscl', ), omp_core_val=dict( @@ -36,12 +32,8 @@ def test_RegTools_inputs(): argstr='-out %s', name_source=['in_file'], name_template='%s_tools.nii.gz', - usedefault=True, - ), - rms_val=dict( - argstr='-rms %s', - usedefault=True, ), + rms_val=dict(argstr='-rms %s', ), smo_g_val=dict(argstr='-smoG %f %f %f', ), smo_s_val=dict(argstr='-smoS %f %f %f', ), sub_val=dict(argstr='-sub %s', ), @@ -53,7 +45,7 @@ def test_RegTools_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegTools_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = RegTools.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py b/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py index d91b77a05a..57c1b0ad86 100644 --- a/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py +++ b/nipype/interfaces/niftyreg/tests/test_auto_RegTransform.py @@ -8,7 +8,6 @@ def test_RegTransform_inputs(): aff_2_rig_input=dict( argstr='-aff2rig %s', position=-2, - usedefault=True, xor=[ 'def_input', 'disp_input', 'flow_input', 'comp_input', 'upd_s_form_input', 'inv_aff_input', 'inv_nrr_input', @@ -20,7 +19,6 @@ def test_RegTransform_inputs(): argstr='-comp %s', position=-3, requires=['comp_input2'], - usedefault=True, xor=[ 'def_input', 'disp_input', 'flow_input', 'upd_s_form_input', 'inv_aff_input', 'inv_nrr_input', 'half_input', @@ -30,12 +28,10 @@ def test_RegTransform_inputs(): comp_input2=dict( argstr='%s', position=-2, - usedefault=True, ), def_input=dict( argstr='-def %s', position=-2, - usedefault=True, xor=[ 'disp_input', 'flow_input', 'comp_input', 'upd_s_form_input', 'inv_aff_input', 'inv_nrr_input', 'half_input', @@ -45,7 +41,6 @@ def test_RegTransform_inputs(): disp_input=dict( argstr='-disp %s', position=-2, - usedefault=True, xor=[ 'def_input', 'flow_input', 'comp_input', 'upd_s_form_input', 'inv_aff_input', 'inv_nrr_input', 'half_input', @@ -68,7 +63,6 @@ def test_RegTransform_inputs(): flow_input=dict( argstr='-flow %s', position=-2, - usedefault=True, xor=[ 'def_input', 'disp_input', 'comp_input', 'upd_s_form_input', 'inv_aff_input', 'inv_nrr_input', 'half_input', @@ -78,7 +72,6 @@ def test_RegTransform_inputs(): half_input=dict( argstr='-half %s', position=-2, - usedefault=True, xor=[ 'def_input', 'disp_input', 'flow_input', 'comp_input', 'upd_s_form_input', 'inv_aff_input', 'inv_nrr_input', @@ -88,7 +81,6 @@ def test_RegTransform_inputs(): inv_aff_input=dict( argstr='-invAff %s', position=-2, - usedefault=True, xor=[ 'def_input', 'disp_input', 'flow_input', 'comp_input', 'upd_s_form_input', 'inv_nrr_input', 'half_input', @@ -121,24 +113,20 @@ def test_RegTransform_inputs(): argstr='%s', genfile=True, position=-1, - usedefault=True, ), ref1_file=dict( argstr='-ref %s', position=0, - usedefault=True, ), ref2_file=dict( argstr='-ref2 %s', position=1, requires=['ref1_file'], - usedefault=True, ), upd_s_form_input=dict( argstr='-updSform %s', position=-3, requires=['upd_s_form_input2'], - usedefault=True, xor=[ 'def_input', 'disp_input', 'flow_input', 'comp_input', 'inv_aff_input', 'inv_nrr_input', 'half_input', @@ -149,7 +137,6 @@ def test_RegTransform_inputs(): argstr='%s', position=-2, requires=['upd_s_form_input'], - usedefault=True, ), ) inputs = RegTransform.input_spec() @@ -158,7 +145,7 @@ def test_RegTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RegTransform_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = RegTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py index 0f04ca1f2e..cc7bc896c6 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMaths.py @@ -14,13 +14,11 @@ def test_BinaryMaths_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), operand_file=dict( argstr='%s', mandatory=True, position=5, - usedefault=True, xor=['operand_value', 'operand_str'], ), operand_str=dict( @@ -45,7 +43,6 @@ def test_BinaryMaths_inputs(): name_source=['in_file'], name_template='%s', position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -58,7 +55,7 @@ def test_BinaryMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinaryMaths_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = BinaryMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py index a0901f4ee7..464ed6f6c4 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryMathsInteger.py @@ -14,7 +14,6 @@ def test_BinaryMathsInteger_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), operand_value=dict( argstr='%d', @@ -31,7 +30,6 @@ def test_BinaryMathsInteger_inputs(): name_source=['in_file'], name_template='%s', position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -44,7 +42,7 @@ def test_BinaryMathsInteger_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinaryMathsInteger_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = BinaryMathsInteger.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py b/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py index 9ae998eb23..0771d72f5c 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_BinaryStats.py @@ -14,7 +14,6 @@ def test_BinaryStats_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), larger_voxel=dict( argstr='-t %f', @@ -23,13 +22,11 @@ def test_BinaryStats_inputs(): mask_file=dict( argstr='-m %s', position=-2, - usedefault=True, ), operand_file=dict( argstr='%s', mandatory=True, position=5, - usedefault=True, xor=['operand_value'], ), operand_value=dict( diff --git a/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py b/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py index 485fd5a0ce..dceea837c0 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_CalcTopNCC.py @@ -14,17 +14,13 @@ def test_CalcTopNCC_inputs(): argstr='-target %s', mandatory=True, position=1, - usedefault=True, ), in_templates=dict( argstr='%s', mandatory=True, position=3, ), - mask_file=dict( - argstr='-mask %s', - usedefault=True, - ), + mask_file=dict(argstr='-mask %s', ), num_templates=dict( argstr='-templates %s', mandatory=True, diff --git a/nipype/interfaces/niftyseg/tests/test_auto_EM.py b/nipype/interfaces/niftyseg/tests/test_auto_EM.py index 39a7ce70a0..fc270ed22f 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_EM.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_EM.py @@ -22,12 +22,8 @@ def test_EM_inputs(): argstr='-in %s', mandatory=True, position=4, - usedefault=True, - ), - mask_file=dict( - argstr='-mask %s', - usedefault=True, ), + mask_file=dict(argstr='-mask %s', ), max_iter=dict( argstr='-max_iter %s', usedefault=True, @@ -46,25 +42,21 @@ def test_EM_inputs(): argstr='-bc_out %s', name_source=['in_file'], name_template='%s_bc_em.nii.gz', - usedefault=True, ), out_file=dict( argstr='-out %s', name_source=['in_file'], name_template='%s_em.nii.gz', - usedefault=True, ), out_outlier_file=dict( argstr='-out_outlier %s', name_source=['in_file'], name_template='%s_outlier_em.nii.gz', - usedefault=True, ), outlier_val=dict(argstr='-outlier %s %s', ), prior_4D=dict( argstr='-prior4D %s', mandatory=True, - usedefault=True, xor=['no_prior', 'priors'], ), priors=dict( @@ -82,9 +74,9 @@ def test_EM_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EM_outputs(): output_map = dict( - out_bc_file=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), - out_outlier_file=dict(usedefault=True, ), + out_bc_file=dict(), + out_file=dict(), + out_outlier_file=dict(), ) outputs = EM.output_spec() diff --git a/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py b/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py index 003dcab9a1..7cbfe58c6c 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_FillLesions.py @@ -6,10 +6,7 @@ def test_FillLesions_inputs(): input_map = dict( args=dict(argstr='%s', ), - bin_mask=dict( - argstr='-mask %s', - usedefault=True, - ), + bin_mask=dict(argstr='-mask %s', ), cwf=dict(argstr='-cwf %f', ), debug=dict(argstr='-debug', ), environ=dict( @@ -21,13 +18,11 @@ def test_FillLesions_inputs(): argstr='-i %s', mandatory=True, position=1, - usedefault=True, ), lesion_mask=dict( argstr='-l %s', mandatory=True, position=2, - usedefault=True, ), match=dict(argstr='-match %f', ), other=dict(argstr='-other', ), @@ -37,7 +32,6 @@ def test_FillLesions_inputs(): name_source=['in_file'], name_template='%s_lesions_filled.nii.gz', position=3, - usedefault=True, ), search=dict(argstr='-search %f', ), size=dict(argstr='-size %d', ), @@ -51,7 +45,7 @@ def test_FillLesions_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FillLesions_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = FillLesions.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py b/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py index f0ac597ea7..eea345e1df 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_LabelFusion.py @@ -17,28 +17,20 @@ def test_LabelFusion_inputs(): nohash=True, usedefault=True, ), - file_to_seg=dict( - mandatory=True, - usedefault=True, - ), + file_to_seg=dict(mandatory=True, ), in_file=dict( argstr='-in %s', mandatory=True, position=1, - usedefault=True, ), kernel_size=dict(), - mask_file=dict( - argstr='-mask %s', - usedefault=True, - ), + mask_file=dict(argstr='-mask %s', ), max_iter=dict(argstr='-max_iter %d', ), mrf_value=dict(argstr='-MRF_beta %f', ), out_file=dict( argstr='-out %s', name_source=['in_file'], name_template='%s', - usedefault=True, ), prob_flag=dict(argstr='-outProb', ), prob_update_flag=dict(argstr='-prop_update', ), @@ -49,7 +41,7 @@ def test_LabelFusion_inputs(): position=3, usedefault=True, ), - template_file=dict(usedefault=True, ), + template_file=dict(), template_num=dict(), unc=dict(argstr='-unc', ), unc_thresh=dict(argstr='-uncthres %f', ), @@ -61,7 +53,7 @@ def test_LabelFusion_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LabelFusion_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = LabelFusion.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py b/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py index 24a122f2eb..247dc9773e 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_MathsCommand.py @@ -14,14 +14,12 @@ def test_MathsCommand_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), out_file=dict( argstr='%s', name_source=['in_file'], name_template='%s', position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -34,7 +32,7 @@ def test_MathsCommand_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MathsCommand_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MathsCommand.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_Merge.py b/nipype/interfaces/niftyseg/tests/test_auto_Merge.py index 1b328500cc..c53e4edf40 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_Merge.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_Merge.py @@ -15,7 +15,6 @@ def test_Merge_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), merge_files=dict( argstr='%s', @@ -27,7 +26,6 @@ def test_Merge_inputs(): name_source=['in_file'], name_template='%s', position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -40,7 +38,7 @@ def test_Merge_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Merge_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Merge.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py b/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py index ba5b81c0d1..bfeded6eef 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_PatchMatch.py @@ -11,7 +11,6 @@ def test_PatchMatch_inputs(): argstr='-db %s', mandatory=True, position=3, - usedefault=True, ), environ=dict( nohash=True, @@ -21,14 +20,12 @@ def test_PatchMatch_inputs(): argstr='-i %s', mandatory=True, position=1, - usedefault=True, ), it_num=dict(argstr='-it %i', ), mask_file=dict( argstr='-m %s', mandatory=True, position=2, - usedefault=True, ), match_num=dict(argstr='-match %i', ), out_file=dict( @@ -36,7 +33,6 @@ def test_PatchMatch_inputs(): name_source=['in_file'], name_template='%s_pm.nii.gz', position=4, - usedefault=True, ), patch_size=dict(argstr='-size %i', ), pm_num=dict(argstr='-pm %i', ), @@ -47,7 +43,7 @@ def test_PatchMatch_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PatchMatch_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = PatchMatch.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py b/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py index 9d47371a46..e845e18952 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_StatsCommand.py @@ -14,7 +14,6 @@ def test_StatsCommand_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), larger_voxel=dict( argstr='-t %f', @@ -23,7 +22,6 @@ def test_StatsCommand_inputs(): mask_file=dict( argstr='-m %s', position=-2, - usedefault=True, ), ) inputs = StatsCommand.input_spec() diff --git a/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py index 754990431c..7241264eee 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_TupleMaths.py @@ -14,20 +14,17 @@ def test_TupleMaths_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), operand_file1=dict( argstr='%s', mandatory=True, position=5, - usedefault=True, xor=['operand_value1'], ), operand_file2=dict( argstr='%s', mandatory=True, position=6, - usedefault=True, xor=['operand_value2'], ), operand_value1=dict( @@ -52,7 +49,6 @@ def test_TupleMaths_inputs(): name_source=['in_file'], name_template='%s', position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -65,7 +61,7 @@ def test_TupleMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TupleMaths_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = TupleMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py b/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py index 5f903212af..9b1cd7d194 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_UnaryMaths.py @@ -14,7 +14,6 @@ def test_UnaryMaths_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), operation=dict( argstr='-%s', @@ -26,7 +25,6 @@ def test_UnaryMaths_inputs(): name_source=['in_file'], name_template='%s', position=-2, - usedefault=True, ), output_datatype=dict( argstr='-odt %s', @@ -39,7 +37,7 @@ def test_UnaryMaths_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_UnaryMaths_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = UnaryMaths.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py b/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py index 8e0cb27515..34edf1a190 100644 --- a/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py +++ b/nipype/interfaces/niftyseg/tests/test_auto_UnaryStats.py @@ -14,7 +14,6 @@ def test_UnaryStats_inputs(): argstr='%s', mandatory=True, position=2, - usedefault=True, ), larger_voxel=dict( argstr='-t %f', @@ -23,7 +22,6 @@ def test_UnaryStats_inputs(): mask_file=dict( argstr='-m %s', position=-2, - usedefault=True, ), operation=dict( argstr='-%s', diff --git a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py index 3e27a7ea09..f0f2453274 100644 --- a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py +++ b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py @@ -8,11 +8,8 @@ def test_ComputeMask_inputs(): M=dict(), cc=dict(), m=dict(), - mean_volume=dict( - mandatory=True, - usedefault=True, - ), - reference_volume=dict(usedefault=True, ), + mean_volume=dict(mandatory=True, ), + reference_volume=dict(), ) inputs = ComputeMask.input_spec() @@ -20,7 +17,7 @@ def test_ComputeMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ComputeMask_outputs(): - output_map = dict(brain_mask=dict(usedefault=True, ), ) + output_map = dict(brain_mask=dict(), ) outputs = ComputeMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py index c3647fdcc8..383d1cbea3 100644 --- a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py @@ -6,20 +6,14 @@ def test_EstimateContrast_inputs(): input_map = dict( axis=dict(mandatory=True, ), - beta=dict( - mandatory=True, - usedefault=True, - ), + beta=dict(mandatory=True, ), constants=dict(mandatory=True, ), contrasts=dict(mandatory=True, ), dof=dict(mandatory=True, ), mask=dict(), nvbeta=dict(mandatory=True, ), reg_names=dict(mandatory=True, ), - s2=dict( - mandatory=True, - usedefault=True, - ), + s2=dict(mandatory=True, ), ) inputs = EstimateContrast.input_spec() diff --git a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py index 17c68df3c7..4ac3aa720e 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py +++ b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py @@ -23,15 +23,15 @@ def test_FitGLM_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FitGLM_outputs(): output_map = dict( - a=dict(usedefault=True, ), + a=dict(), axis=dict(), - beta=dict(usedefault=True, ), + beta=dict(), constants=dict(), dof=dict(), nvbeta=dict(), reg_names=dict(), residuals=dict(), - s2=dict(usedefault=True, ), + s2=dict(), ) outputs = FitGLM.output_spec() diff --git a/nipype/interfaces/nipy/tests/test_auto_Similarity.py b/nipype/interfaces/nipy/tests/test_auto_Similarity.py index 5b4f9269cc..fbdb6fffa6 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Similarity.py +++ b/nipype/interfaces/nipy/tests/test_auto_Similarity.py @@ -5,17 +5,11 @@ def test_Similarity_inputs(): input_map = dict( - mask1=dict(usedefault=True, ), - mask2=dict(usedefault=True, ), + mask1=dict(), + mask2=dict(), metric=dict(usedefault=True, ), - volume1=dict( - mandatory=True, - usedefault=True, - ), - volume2=dict( - mandatory=True, - usedefault=True, - ), + volume1=dict(mandatory=True, ), + volume2=dict(mandatory=True, ), ) inputs = Similarity.input_spec() diff --git a/nipype/interfaces/nipy/tests/test_auto_Trim.py b/nipype/interfaces/nipy/tests/test_auto_Trim.py index 4ba09246d3..6073c9082b 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Trim.py +++ b/nipype/interfaces/nipy/tests/test_auto_Trim.py @@ -7,11 +7,8 @@ def test_Trim_inputs(): input_map = dict( begin_index=dict(usedefault=True, ), end_index=dict(usedefault=True, ), - in_file=dict( - mandatory=True, - usedefault=True, - ), - out_file=dict(usedefault=True, ), + in_file=dict(mandatory=True, ), + out_file=dict(), suffix=dict(usedefault=True, ), ) inputs = Trim.input_spec() @@ -20,7 +17,7 @@ def test_Trim_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Trim_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Trim.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py index efe443a759..4a641ebb50 100644 --- a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py +++ b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py @@ -10,13 +10,10 @@ def test_CoherenceAnalyzer_inputs(): figure_type=dict(usedefault=True, ), frequency_range=dict(usedefault=True, ), in_TS=dict(), - in_file=dict( - requires=('TR', ), - usedefault=True, - ), + in_file=dict(requires=('TR', ), ), n_overlap=dict(usedefault=True, ), - output_csv_file=dict(usedefault=True, ), - output_figure_file=dict(usedefault=True, ), + output_csv_file=dict(), + output_figure_file=dict(), ) inputs = CoherenceAnalyzer.input_spec() @@ -26,11 +23,11 @@ def test_CoherenceAnalyzer_inputs(): def test_CoherenceAnalyzer_outputs(): output_map = dict( coherence_array=dict(), - coherence_csv=dict(usedefault=True, ), - coherence_fig=dict(usedefault=True, ), + coherence_csv=dict(), + coherence_fig=dict(), timedelay_array=dict(), - timedelay_csv=dict(usedefault=True, ), - timedelay_fig=dict(usedefault=True, ), + timedelay_csv=dict(), + timedelay_fig=dict(), ) outputs = CoherenceAnalyzer.output_spec() diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py index 0f0e0e3b8e..81a22bfe38 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py @@ -10,34 +10,13 @@ def test_BRAINSPosteriorToContinuousClass_inputs(): nohash=True, usedefault=True, ), - inputBasalGmVolume=dict( - argstr='--inputBasalGmVolume %s', - usedefault=True, - ), - inputCrblGmVolume=dict( - argstr='--inputCrblGmVolume %s', - usedefault=True, - ), - inputCrblWmVolume=dict( - argstr='--inputCrblWmVolume %s', - usedefault=True, - ), - inputCsfVolume=dict( - argstr='--inputCsfVolume %s', - usedefault=True, - ), - inputSurfaceGmVolume=dict( - argstr='--inputSurfaceGmVolume %s', - usedefault=True, - ), - inputVbVolume=dict( - argstr='--inputVbVolume %s', - usedefault=True, - ), - inputWhiteVolume=dict( - argstr='--inputWhiteVolume %s', - usedefault=True, - ), + inputBasalGmVolume=dict(argstr='--inputBasalGmVolume %s', ), + inputCrblGmVolume=dict(argstr='--inputCrblGmVolume %s', ), + inputCrblWmVolume=dict(argstr='--inputCrblWmVolume %s', ), + inputCsfVolume=dict(argstr='--inputCsfVolume %s', ), + inputSurfaceGmVolume=dict(argstr='--inputSurfaceGmVolume %s', ), + inputVbVolume=dict(argstr='--inputVbVolume %s', ), + inputWhiteVolume=dict(argstr='--inputWhiteVolume %s', ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -49,7 +28,7 @@ def test_BRAINSPosteriorToContinuousClass_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSPosteriorToContinuousClass_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = BRAINSPosteriorToContinuousClass.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py index 77c5170628..ac589ad6dc 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py @@ -30,10 +30,7 @@ def test_BRAINSTalairach_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), outputBox=dict( argstr='--outputBox %s', hash_files=False, @@ -50,8 +47,8 @@ def test_BRAINSTalairach_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTalairach_outputs(): output_map = dict( - outputBox=dict(usedefault=True, ), - outputGrid=dict(usedefault=True, ), + outputBox=dict(), + outputGrid=dict(), ) outputs = BRAINSTalairach.output_spec() diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py index d37f45fb6e..5ada1576e7 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py @@ -12,22 +12,13 @@ def test_BRAINSTalairachMask_inputs(): ), expand=dict(argstr='--expand ', ), hemisphereMode=dict(argstr='--hemisphereMode %s', ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, ), - talairachBox=dict( - argstr='--talairachBox %s', - usedefault=True, - ), - talairachParameters=dict( - argstr='--talairachParameters %s', - usedefault=True, - ), + talairachBox=dict(argstr='--talairachBox %s', ), + talairachParameters=dict(argstr='--talairachParameters %s', ), ) inputs = BRAINSTalairachMask.input_spec() @@ -35,7 +26,7 @@ def test_BRAINSTalairachMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTalairachMask_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = BRAINSTalairachMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py b/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py index 1b67912450..eb4bdcffae 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py @@ -11,10 +11,7 @@ def test_GenerateEdgeMapImage_inputs(): usedefault=True, ), inputMRVolumes=dict(argstr='--inputMRVolumes %s...', ), - inputMask=dict( - argstr='--inputMask %s', - usedefault=True, - ), + inputMask=dict(argstr='--inputMask %s', ), lowerPercentileMatching=dict(argstr='--lowerPercentileMatching %f', ), maximumOutputRange=dict(argstr='--maximumOutputRange %d', ), minimumOutputRange=dict(argstr='--minimumOutputRange %d', ), @@ -36,8 +33,8 @@ def test_GenerateEdgeMapImage_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateEdgeMapImage_outputs(): output_map = dict( - outputEdgeMap=dict(usedefault=True, ), - outputMaximumGradientImage=dict(usedefault=True, ), + outputEdgeMap=dict(), + outputMaximumGradientImage=dict(), ) outputs = GenerateEdgeMapImage.output_spec() diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py b/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py index c1f7943b76..ae16bc8fab 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py @@ -27,7 +27,7 @@ def test_GeneratePurePlugMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GeneratePurePlugMask_outputs(): - output_map = dict(outputMaskFile=dict(usedefault=True, ), ) + output_map = dict(outputMaskFile=dict(), ) outputs = GeneratePurePlugMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py index 90450e9e26..1377072149 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py @@ -11,28 +11,16 @@ def test_HistogramMatchingFilter_inputs(): usedefault=True, ), histogramAlgorithm=dict(argstr='--histogramAlgorithm %s', ), - inputBinaryVolume=dict( - argstr='--inputBinaryVolume %s', - usedefault=True, - ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputBinaryVolume=dict(argstr='--inputBinaryVolume %s', ), + inputVolume=dict(argstr='--inputVolume %s', ), numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', ), numberOfMatchPoints=dict(argstr='--numberOfMatchPoints %d', ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, ), - referenceBinaryVolume=dict( - argstr='--referenceBinaryVolume %s', - usedefault=True, - ), - referenceVolume=dict( - argstr='--referenceVolume %s', - usedefault=True, - ), + referenceBinaryVolume=dict(argstr='--referenceBinaryVolume %s', ), + referenceVolume=dict(argstr='--referenceVolume %s', ), verbose=dict(argstr='--verbose ', ), writeHistogram=dict(argstr='--writeHistogram %s', ), ) @@ -42,7 +30,7 @@ def test_HistogramMatchingFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_HistogramMatchingFilter_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = HistogramMatchingFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py index 68d0d1b8cf..534488ad10 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py @@ -5,23 +5,14 @@ def test_SimilarityIndex_inputs(): input_map = dict( - ANNContinuousVolume=dict( - argstr='--ANNContinuousVolume %s', - usedefault=True, - ), + ANNContinuousVolume=dict(argstr='--ANNContinuousVolume %s', ), args=dict(argstr='%s', ), environ=dict( nohash=True, usedefault=True, ), - inputManualVolume=dict( - argstr='--inputManualVolume %s', - usedefault=True, - ), - outputCSVFilename=dict( - argstr='--outputCSVFilename %s', - usedefault=True, - ), + inputManualVolume=dict(argstr='--inputManualVolume %s', ), + outputCSVFilename=dict(argstr='--outputCSVFilename %s', ), thresholdInterval=dict(argstr='--thresholdInterval %f', ), ) inputs = SimilarityIndex.input_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py index 2103f17918..05593527fb 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py @@ -13,30 +13,15 @@ def test_DWIConvert_inputs(): usedefault=True, ), fMRI=dict(argstr='--fMRI ', ), - fslNIFTIFile=dict( - argstr='--fslNIFTIFile %s', - usedefault=True, - ), + fslNIFTIFile=dict(argstr='--fslNIFTIFile %s', ), gradientVectorFile=dict( argstr='--gradientVectorFile %s', hash_files=False, ), - inputBValues=dict( - argstr='--inputBValues %s', - usedefault=True, - ), - inputBVectors=dict( - argstr='--inputBVectors %s', - usedefault=True, - ), - inputDicomDirectory=dict( - argstr='--inputDicomDirectory %s', - usedefault=True, - ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputBValues=dict(argstr='--inputBValues %s', ), + inputBVectors=dict(argstr='--inputBVectors %s', ), + inputDicomDirectory=dict(argstr='--inputDicomDirectory %s', ), + inputVolume=dict(argstr='--inputVolume %s', ), outputBValues=dict( argstr='--outputBValues %s', hash_files=False, @@ -69,11 +54,11 @@ def test_DWIConvert_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DWIConvert_outputs(): output_map = dict( - gradientVectorFile=dict(usedefault=True, ), - outputBValues=dict(usedefault=True, ), - outputBVectors=dict(usedefault=True, ), - outputDirectory=dict(usedefault=True, ), - outputVolume=dict(usedefault=True, ), + gradientVectorFile=dict(), + outputBValues=dict(), + outputBVectors=dict(), + outputDirectory=dict(), + outputVolume=dict(), ) outputs = DWIConvert.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py index b6ec40ddba..eb9d8c6184 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py @@ -13,14 +13,8 @@ def test_compareTractInclusion_inputs(): ), numberOfPoints=dict(argstr='--numberOfPoints %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), - standardFiber=dict( - argstr='--standardFiber %s', - usedefault=True, - ), - testFiber=dict( - argstr='--testFiber %s', - usedefault=True, - ), + standardFiber=dict(argstr='--standardFiber %s', ), + testFiber=dict(argstr='--testFiber %s', ), testForBijection=dict(argstr='--testForBijection ', ), testForFiberCardinality=dict(argstr='--testForFiberCardinality ', ), writeXMLPolyDataFile=dict(argstr='--writeXMLPolyDataFile ', ), diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py index 078e2774ca..92c00853f4 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py @@ -24,7 +24,7 @@ def test_dtiaverage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_dtiaverage_outputs(): - output_map = dict(tensor_output=dict(usedefault=True, ), ) + output_map = dict(tensor_output=dict(), ) outputs = dtiaverage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py index 376f92459a..440fd4df07 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py @@ -15,23 +15,14 @@ def test_dtiestim_inputs(): ), DTI_double=dict(argstr='--DTI_double ', ), args=dict(argstr='%s', ), - bad_region_mask=dict( - argstr='--bad_region_mask %s', - usedefault=True, - ), - brain_mask=dict( - argstr='--brain_mask %s', - usedefault=True, - ), + bad_region_mask=dict(argstr='--bad_region_mask %s', ), + brain_mask=dict(argstr='--brain_mask %s', ), correction=dict(argstr='--correction %s', ), defaultTensor=dict( argstr='--defaultTensor %s', sep=',', ), - dwi_image=dict( - argstr='--dwi_image %s', - usedefault=True, - ), + dwi_image=dict(argstr='--dwi_image %s', ), environ=dict( nohash=True, usedefault=True, @@ -60,10 +51,10 @@ def test_dtiestim_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_dtiestim_outputs(): output_map = dict( - B0=dict(usedefault=True, ), - B0_mask_output=dict(usedefault=True, ), - idwi=dict(usedefault=True, ), - tensor_output=dict(usedefault=True, ), + B0=dict(), + B0_mask_output=dict(), + idwi=dict(), + tensor_output=dict(), ) outputs = dtiestim.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py index a8c7de8d9a..3148d1edb5 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py @@ -10,10 +10,7 @@ def test_dtiprocess_inputs(): argstr='--RD_output %s', hash_files=False, ), - affineitk_file=dict( - argstr='--affineitk_file %s', - usedefault=True, - ), + affineitk_file=dict(argstr='--affineitk_file %s', ), args=dict(argstr='%s', ), color_fa_output=dict( argstr='--color_fa_output %s', @@ -24,14 +21,8 @@ def test_dtiprocess_inputs(): argstr='--deformation_output %s', hash_files=False, ), - dof_file=dict( - argstr='--dof_file %s', - usedefault=True, - ), - dti_image=dict( - argstr='--dti_image %s', - usedefault=True, - ), + dof_file=dict(argstr='--dof_file %s', ), + dti_image=dict(argstr='--dti_image %s', ), environ=dict( nohash=True, usedefault=True, @@ -48,10 +39,7 @@ def test_dtiprocess_inputs(): argstr='--fa_output %s', hash_files=False, ), - forward=dict( - argstr='--forward %s', - usedefault=True, - ), + forward=dict(argstr='--forward %s', ), frobenius_norm_output=dict( argstr='--frobenius_norm_output %s', hash_files=False, @@ -70,10 +58,7 @@ def test_dtiprocess_inputs(): argstr='--lambda3_output %s', hash_files=False, ), - mask=dict( - argstr='--mask %s', - usedefault=True, - ), + mask=dict(argstr='--mask %s', ), md_output=dict( argstr='--md_output %s', hash_files=False, @@ -82,10 +67,7 @@ def test_dtiprocess_inputs(): argstr='--negative_eigenvector_output %s', hash_files=False, ), - newdof_file=dict( - argstr='--newdof_file %s', - usedefault=True, - ), + newdof_file=dict(argstr='--newdof_file %s', ), outmask=dict( argstr='--outmask %s', hash_files=False, @@ -110,21 +92,21 @@ def test_dtiprocess_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_dtiprocess_outputs(): output_map = dict( - RD_output=dict(usedefault=True, ), - color_fa_output=dict(usedefault=True, ), - deformation_output=dict(usedefault=True, ), - fa_gradient_output=dict(usedefault=True, ), - fa_gradmag_output=dict(usedefault=True, ), - fa_output=dict(usedefault=True, ), - frobenius_norm_output=dict(usedefault=True, ), - lambda1_output=dict(usedefault=True, ), - lambda2_output=dict(usedefault=True, ), - lambda3_output=dict(usedefault=True, ), - md_output=dict(usedefault=True, ), - negative_eigenvector_output=dict(usedefault=True, ), - outmask=dict(usedefault=True, ), - principal_eigenvector_output=dict(usedefault=True, ), - rot_output=dict(usedefault=True, ), + RD_output=dict(), + color_fa_output=dict(), + deformation_output=dict(), + fa_gradient_output=dict(), + fa_gradmag_output=dict(), + fa_output=dict(), + frobenius_norm_output=dict(), + lambda1_output=dict(), + lambda2_output=dict(), + lambda3_output=dict(), + md_output=dict(), + negative_eigenvector_output=dict(), + outmask=dict(), + principal_eigenvector_output=dict(), + rot_output=dict(), ) outputs = dtiprocess.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py index cca7af405e..ac5784f1c7 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py @@ -10,10 +10,7 @@ def test_extractNrrdVectorIndex_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -28,7 +25,7 @@ def test_extractNrrdVectorIndex_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_extractNrrdVectorIndex_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = extractNrrdVectorIndex.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py index 2225121f02..195d7dc3e1 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py @@ -11,10 +11,7 @@ def test_gtractAnisotropyMap_inputs(): nohash=True, usedefault=True, ), - inputTensorVolume=dict( - argstr='--inputTensorVolume %s', - usedefault=True, - ), + inputTensorVolume=dict(argstr='--inputTensorVolume %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -27,7 +24,7 @@ def test_gtractAnisotropyMap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractAnisotropyMap_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = gtractAnisotropyMap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py index 96a0ee96e8..fbb5bd6a55 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py @@ -12,10 +12,7 @@ def test_gtractAverageBvalues_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -28,7 +25,7 @@ def test_gtractAverageBvalues_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractAverageBvalues_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = gtractAverageBvalues.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py index c1e3e04156..fed980c463 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py @@ -12,10 +12,7 @@ def test_gtractClipAnisotropy_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -28,7 +25,7 @@ def test_gtractClipAnisotropy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractClipAnisotropy_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = gtractClipAnisotropy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py index 9522b2be08..456e1e79fa 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py @@ -17,18 +17,9 @@ def test_gtractCoRegAnatomy_inputs(): argstr='--gridSize %s', sep=',', ), - inputAnatomicalVolume=dict( - argstr='--inputAnatomicalVolume %s', - usedefault=True, - ), - inputRigidTransform=dict( - argstr='--inputRigidTransform %s', - usedefault=True, - ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputAnatomicalVolume=dict(argstr='--inputAnatomicalVolume %s', ), + inputRigidTransform=dict(argstr='--inputRigidTransform %s', ), + inputVolume=dict(argstr='--inputVolume %s', ), maxBSplineDisplacement=dict(argstr='--maxBSplineDisplacement %f', ), maximumStepSize=dict(argstr='--maximumStepSize %f', ), minimumStepSize=dict(argstr='--minimumStepSize %f', ), @@ -56,7 +47,7 @@ def test_gtractCoRegAnatomy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractCoRegAnatomy_outputs(): - output_map = dict(outputTransformName=dict(usedefault=True, ), ) + output_map = dict(outputTransformName=dict(), ) outputs = gtractCoRegAnatomy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py index 75561455d7..7b75858eff 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py @@ -24,7 +24,7 @@ def test_gtractConcatDwi_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractConcatDwi_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = gtractConcatDwi.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py index 456f5f1eb5..d9e0b725c8 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py @@ -10,14 +10,8 @@ def test_gtractCopyImageOrientation_inputs(): nohash=True, usedefault=True, ), - inputReferenceVolume=dict( - argstr='--inputReferenceVolume %s', - usedefault=True, - ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), + inputVolume=dict(argstr='--inputVolume %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -30,7 +24,7 @@ def test_gtractCopyImageOrientation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractCopyImageOrientation_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = gtractCopyImageOrientation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py index ef467f8957..3143b16dfb 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py @@ -12,17 +12,11 @@ def test_gtractCoregBvalues_inputs(): nohash=True, usedefault=True, ), - fixedVolume=dict( - argstr='--fixedVolume %s', - usedefault=True, - ), + fixedVolume=dict(argstr='--fixedVolume %s', ), fixedVolumeIndex=dict(argstr='--fixedVolumeIndex %d', ), maximumStepSize=dict(argstr='--maximumStepSize %f', ), minimumStepSize=dict(argstr='--minimumStepSize %f', ), - movingVolume=dict( - argstr='--movingVolume %s', - usedefault=True, - ), + movingVolume=dict(argstr='--movingVolume %s', ), numberOfIterations=dict(argstr='--numberOfIterations %d', ), numberOfSpatialSamples=dict(argstr='--numberOfSpatialSamples %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -46,8 +40,8 @@ def test_gtractCoregBvalues_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_gtractCoregBvalues_outputs(): output_map = dict( - outputTransform=dict(usedefault=True, ), - outputVolume=dict(usedefault=True, ), + outputTransform=dict(), + outputVolume=dict(), ) outputs = gtractCoregBvalues.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py index 3e8d6ce899..32d1e68898 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py @@ -11,18 +11,10 @@ def test_gtractCostFastMarching_inputs(): nohash=True, usedefault=True, ), - inputAnisotropyVolume=dict( - argstr='--inputAnisotropyVolume %s', - usedefault=True, - ), + inputAnisotropyVolume=dict(argstr='--inputAnisotropyVolume %s', ), inputStartingSeedsLabelMapVolume=dict( - argstr='--inputStartingSeedsLabelMapVolume %s', - usedefault=True, - ), - inputTensorVolume=dict( - argstr='--inputTensorVolume %s', - usedefault=True, - ), + argstr='--inputStartingSeedsLabelMapVolume %s', ), + inputTensorVolume=dict(argstr='--inputTensorVolume %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputCostVolume=dict( argstr='--outputCostVolume %s', @@ -43,8 +35,8 @@ def test_gtractCostFastMarching_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_gtractCostFastMarching_outputs(): output_map = dict( - outputCostVolume=dict(usedefault=True, ), - outputSpeedVolume=dict(usedefault=True, ), + outputCostVolume=dict(), + outputSpeedVolume=dict(), ) outputs = gtractCostFastMarching.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py index 7d77f81257..bbe375bbb9 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py @@ -10,10 +10,7 @@ def test_gtractCreateGuideFiber_inputs(): nohash=True, usedefault=True, ), - inputFiber=dict( - argstr='--inputFiber %s', - usedefault=True, - ), + inputFiber=dict(argstr='--inputFiber %s', ), numberOfPoints=dict(argstr='--numberOfPoints %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputFiber=dict( @@ -28,7 +25,7 @@ def test_gtractCreateGuideFiber_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractCreateGuideFiber_outputs(): - output_map = dict(outputFiber=dict(usedefault=True, ), ) + output_map = dict(outputFiber=dict(), ) outputs = gtractCreateGuideFiber.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py index 0f3400b5c5..ec3a99b91e 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py @@ -11,22 +11,11 @@ def test_gtractFastMarchingTracking_inputs(): nohash=True, usedefault=True, ), - inputAnisotropyVolume=dict( - argstr='--inputAnisotropyVolume %s', - usedefault=True, - ), - inputCostVolume=dict( - argstr='--inputCostVolume %s', - usedefault=True, - ), + inputAnisotropyVolume=dict(argstr='--inputAnisotropyVolume %s', ), + inputCostVolume=dict(argstr='--inputCostVolume %s', ), inputStartingSeedsLabelMapVolume=dict( - argstr='--inputStartingSeedsLabelMapVolume %s', - usedefault=True, - ), - inputTensorVolume=dict( - argstr='--inputTensorVolume %s', - usedefault=True, - ), + argstr='--inputStartingSeedsLabelMapVolume %s', ), + inputTensorVolume=dict(argstr='--inputTensorVolume %s', ), maximumStepSize=dict(argstr='--maximumStepSize %f', ), minimumStepSize=dict(argstr='--minimumStepSize %f', ), numberOfIterations=dict(argstr='--numberOfIterations %d', ), @@ -46,7 +35,7 @@ def test_gtractFastMarchingTracking_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractFastMarchingTracking_outputs(): - output_map = dict(outputTract=dict(usedefault=True, ), ) + output_map = dict(outputTract=dict(), ) outputs = gtractFastMarchingTracking.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py index 214838457e..96c93b8b64 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py @@ -16,26 +16,13 @@ def test_gtractFiberTracking_inputs(): ), guidedCurvatureThreshold=dict( argstr='--guidedCurvatureThreshold %f', ), - inputAnisotropyVolume=dict( - argstr='--inputAnisotropyVolume %s', - usedefault=True, - ), + inputAnisotropyVolume=dict(argstr='--inputAnisotropyVolume %s', ), inputEndingSeedsLabelMapVolume=dict( - argstr='--inputEndingSeedsLabelMapVolume %s', - usedefault=True, - ), + argstr='--inputEndingSeedsLabelMapVolume %s', ), inputStartingSeedsLabelMapVolume=dict( - argstr='--inputStartingSeedsLabelMapVolume %s', - usedefault=True, - ), - inputTensorVolume=dict( - argstr='--inputTensorVolume %s', - usedefault=True, - ), - inputTract=dict( - argstr='--inputTract %s', - usedefault=True, - ), + argstr='--inputStartingSeedsLabelMapVolume %s', ), + inputTensorVolume=dict(argstr='--inputTensorVolume %s', ), + inputTract=dict(argstr='--inputTract %s', ), maximumBranchPoints=dict(argstr='--maximumBranchPoints %d', ), maximumGuideDistance=dict(argstr='--maximumGuideDistance %f', ), maximumLength=dict(argstr='--maximumLength %f', ), @@ -64,7 +51,7 @@ def test_gtractFiberTracking_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractFiberTracking_outputs(): - output_map = dict(outputTract=dict(usedefault=True, ), ) + output_map = dict(outputTract=dict(), ) outputs = gtractFiberTracking.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py index 1930bc3d0f..9ddde832b2 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py @@ -10,14 +10,8 @@ def test_gtractImageConformity_inputs(): nohash=True, usedefault=True, ), - inputReferenceVolume=dict( - argstr='--inputReferenceVolume %s', - usedefault=True, - ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), + inputVolume=dict(argstr='--inputVolume %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -30,7 +24,7 @@ def test_gtractImageConformity_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractImageConformity_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = gtractImageConformity.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py index 2e09633ce5..ca642ceb66 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py @@ -10,14 +10,8 @@ def test_gtractInvertBSplineTransform_inputs(): nohash=True, usedefault=True, ), - inputReferenceVolume=dict( - argstr='--inputReferenceVolume %s', - usedefault=True, - ), - inputTransform=dict( - argstr='--inputTransform %s', - usedefault=True, - ), + inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), + inputTransform=dict(argstr='--inputTransform %s', ), landmarkDensity=dict( argstr='--landmarkDensity %s', sep=',', @@ -34,7 +28,7 @@ def test_gtractInvertBSplineTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractInvertBSplineTransform_outputs(): - output_map = dict(outputTransform=dict(usedefault=True, ), ) + output_map = dict(outputTransform=dict(), ) outputs = gtractInvertBSplineTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py index f65b49c1b8..e4fd213d39 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py @@ -6,14 +6,8 @@ def test_gtractInvertDisplacementField_inputs(): input_map = dict( args=dict(argstr='%s', ), - baseImage=dict( - argstr='--baseImage %s', - usedefault=True, - ), - deformationImage=dict( - argstr='--deformationImage %s', - usedefault=True, - ), + baseImage=dict(argstr='--baseImage %s', ), + deformationImage=dict(argstr='--deformationImage %s', ), environ=dict( nohash=True, usedefault=True, @@ -31,7 +25,7 @@ def test_gtractInvertDisplacementField_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractInvertDisplacementField_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = gtractInvertDisplacementField.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py index 51ba4f126b..c035862663 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py @@ -10,10 +10,7 @@ def test_gtractInvertRigidTransform_inputs(): nohash=True, usedefault=True, ), - inputTransform=dict( - argstr='--inputTransform %s', - usedefault=True, - ), + inputTransform=dict(argstr='--inputTransform %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputTransform=dict( argstr='--outputTransform %s', @@ -26,7 +23,7 @@ def test_gtractInvertRigidTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractInvertRigidTransform_outputs(): - output_map = dict(outputTransform=dict(usedefault=True, ), ) + output_map = dict(outputTransform=dict(), ) outputs = gtractInvertRigidTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py index 52a3d57f4e..43f428b233 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py @@ -10,18 +10,9 @@ def test_gtractResampleAnisotropy_inputs(): nohash=True, usedefault=True, ), - inputAnatomicalVolume=dict( - argstr='--inputAnatomicalVolume %s', - usedefault=True, - ), - inputAnisotropyVolume=dict( - argstr='--inputAnisotropyVolume %s', - usedefault=True, - ), - inputTransform=dict( - argstr='--inputTransform %s', - usedefault=True, - ), + inputAnatomicalVolume=dict(argstr='--inputAnatomicalVolume %s', ), + inputAnisotropyVolume=dict(argstr='--inputAnisotropyVolume %s', ), + inputTransform=dict(argstr='--inputTransform %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -35,7 +26,7 @@ def test_gtractResampleAnisotropy_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleAnisotropy_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = gtractResampleAnisotropy.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py index c7a3d596eb..812afca5c0 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py @@ -10,18 +10,9 @@ def test_gtractResampleB0_inputs(): nohash=True, usedefault=True, ), - inputAnatomicalVolume=dict( - argstr='--inputAnatomicalVolume %s', - usedefault=True, - ), - inputTransform=dict( - argstr='--inputTransform %s', - usedefault=True, - ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputAnatomicalVolume=dict(argstr='--inputAnatomicalVolume %s', ), + inputTransform=dict(argstr='--inputTransform %s', ), + inputVolume=dict(argstr='--inputVolume %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -36,7 +27,7 @@ def test_gtractResampleB0_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleB0_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = gtractResampleB0.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py index 037e0600b3..decc017c60 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py @@ -10,18 +10,9 @@ def test_gtractResampleCodeImage_inputs(): nohash=True, usedefault=True, ), - inputCodeVolume=dict( - argstr='--inputCodeVolume %s', - usedefault=True, - ), - inputReferenceVolume=dict( - argstr='--inputReferenceVolume %s', - usedefault=True, - ), - inputTransform=dict( - argstr='--inputTransform %s', - usedefault=True, - ), + inputCodeVolume=dict(argstr='--inputCodeVolume %s', ), + inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), + inputTransform=dict(argstr='--inputTransform %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -35,7 +26,7 @@ def test_gtractResampleCodeImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleCodeImage_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = gtractResampleCodeImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py index 48cfcbb024..b815d3d3d6 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py @@ -15,14 +15,8 @@ def test_gtractResampleDWIInPlace_inputs(): argstr='--imageOutputSize %s', sep=',', ), - inputTransform=dict( - argstr='--inputTransform %s', - usedefault=True, - ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputTransform=dict(argstr='--inputTransform %s', ), + inputVolume=dict(argstr='--inputVolume %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputResampledB0=dict( argstr='--outputResampledB0 %s', @@ -32,14 +26,8 @@ def test_gtractResampleDWIInPlace_inputs(): argstr='--outputVolume %s', hash_files=False, ), - referenceVolume=dict( - argstr='--referenceVolume %s', - usedefault=True, - ), - warpDWITransform=dict( - argstr='--warpDWITransform %s', - usedefault=True, - ), + referenceVolume=dict(argstr='--referenceVolume %s', ), + warpDWITransform=dict(argstr='--warpDWITransform %s', ), ) inputs = gtractResampleDWIInPlace.input_spec() @@ -48,8 +36,8 @@ def test_gtractResampleDWIInPlace_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleDWIInPlace_outputs(): output_map = dict( - outputResampledB0=dict(usedefault=True, ), - outputVolume=dict(usedefault=True, ), + outputResampledB0=dict(), + outputVolume=dict(), ) outputs = gtractResampleDWIInPlace.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py index 2d42314a38..d0d2cd5664 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py @@ -11,17 +11,10 @@ def test_gtractResampleFibers_inputs(): usedefault=True, ), inputForwardDeformationFieldVolume=dict( - argstr='--inputForwardDeformationFieldVolume %s', - usedefault=True, - ), + argstr='--inputForwardDeformationFieldVolume %s', ), inputReverseDeformationFieldVolume=dict( - argstr='--inputReverseDeformationFieldVolume %s', - usedefault=True, - ), - inputTract=dict( - argstr='--inputTract %s', - usedefault=True, - ), + argstr='--inputReverseDeformationFieldVolume %s', ), + inputTract=dict(argstr='--inputTract %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputTract=dict( argstr='--outputTract %s', @@ -35,7 +28,7 @@ def test_gtractResampleFibers_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleFibers_outputs(): - output_map = dict(outputTract=dict(usedefault=True, ), ) + output_map = dict(outputTract=dict(), ) outputs = gtractResampleFibers.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py index 5eccecfb14..ead96d1c71 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py @@ -18,15 +18,9 @@ def test_gtractTensor_inputs(): argstr='--ignoreIndex %s', sep=',', ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), maskProcessingMode=dict(argstr='--maskProcessingMode %s', ), - maskVolume=dict( - argstr='--maskVolume %s', - usedefault=True, - ), + maskVolume=dict(argstr='--maskVolume %s', ), medianFilterSize=dict( argstr='--medianFilterSize %s', sep=',', @@ -45,7 +39,7 @@ def test_gtractTensor_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractTensor_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = gtractTensor.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py index 2e38e05bef..2dfde189e2 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py @@ -10,14 +10,8 @@ def test_gtractTransformToDisplacementField_inputs(): nohash=True, usedefault=True, ), - inputReferenceVolume=dict( - argstr='--inputReferenceVolume %s', - usedefault=True, - ), - inputTransform=dict( - argstr='--inputTransform %s', - usedefault=True, - ), + inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), + inputTransform=dict(argstr='--inputTransform %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputDeformationFieldVolume=dict( argstr='--outputDeformationFieldVolume %s', @@ -30,7 +24,7 @@ def test_gtractTransformToDisplacementField_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_gtractTransformToDisplacementField_outputs(): - output_map = dict(outputDeformationFieldVolume=dict(usedefault=True, ), ) + output_map = dict(outputDeformationFieldVolume=dict(), ) outputs = gtractTransformToDisplacementField.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py index 9fcde55991..cc06c5ede5 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py @@ -10,10 +10,7 @@ def test_maxcurvature_inputs(): nohash=True, usedefault=True, ), - image=dict( - argstr='--image %s', - usedefault=True, - ), + image=dict(argstr='--image %s', ), output=dict( argstr='--output %s', hash_files=False, @@ -27,7 +24,7 @@ def test_maxcurvature_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_maxcurvature_outputs(): - output_map = dict(output=dict(usedefault=True, ), ) + output_map = dict(output=dict(), ) outputs = maxcurvature.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py index b938d61201..7c61974ef3 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py @@ -10,10 +10,7 @@ def test_UKFTractography_inputs(): Qw=dict(argstr='--Qw %f', ), Rs=dict(argstr='--Rs %f', ), args=dict(argstr='%s', ), - dwiFile=dict( - argstr='--dwiFile %s', - usedefault=True, - ), + dwiFile=dict(argstr='--dwiFile %s', ), environ=dict( nohash=True, usedefault=True, @@ -24,10 +21,7 @@ def test_UKFTractography_inputs(): argstr='--labels %s', sep=',', ), - maskFile=dict( - argstr='--maskFile %s', - usedefault=True, - ), + maskFile=dict(argstr='--maskFile %s', ), maxBranchingAngle=dict(argstr='--maxBranchingAngle %f', ), maxHalfFiberLength=dict(argstr='--maxHalfFiberLength %f', ), minBranchingAngle=dict(argstr='--minBranchingAngle %f', ), @@ -44,10 +38,7 @@ def test_UKFTractography_inputs(): recordTensors=dict(argstr='--recordTensors ', ), recordTrace=dict(argstr='--recordTrace ', ), seedFALimit=dict(argstr='--seedFALimit %f', ), - seedsFile=dict( - argstr='--seedsFile %s', - usedefault=True, - ), + seedsFile=dict(argstr='--seedsFile %s', ), seedsPerVoxel=dict(argstr='--seedsPerVoxel %d', ), stepLength=dict(argstr='--stepLength %f', ), storeGlyphs=dict(argstr='--storeGlyphs ', ), @@ -69,8 +60,8 @@ def test_UKFTractography_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_UKFTractography_outputs(): output_map = dict( - tracts=dict(usedefault=True, ), - tractsWithSecondTensor=dict(usedefault=True, ), + tracts=dict(), + tractsWithSecondTensor=dict(), ) outputs = UKFTractography.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py index ec5ee174ed..b4756a9406 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py @@ -6,35 +6,23 @@ def test_fiberprocess_inputs(): input_map = dict( args=dict(argstr='%s', ), - displacement_field=dict( - argstr='--displacement_field %s', - usedefault=True, - ), + displacement_field=dict(argstr='--displacement_field %s', ), environ=dict( nohash=True, usedefault=True, ), - fiber_file=dict( - argstr='--fiber_file %s', - usedefault=True, - ), + fiber_file=dict(argstr='--fiber_file %s', ), fiber_output=dict( argstr='--fiber_output %s', hash_files=False, ), fiber_radius=dict(argstr='--fiber_radius %f', ), - h_field=dict( - argstr='--h_field %s', - usedefault=True, - ), + h_field=dict(argstr='--h_field %s', ), index_space=dict(argstr='--index_space ', ), noDataChange=dict(argstr='--noDataChange ', ), no_warp=dict(argstr='--no_warp ', ), saveProperties=dict(argstr='--saveProperties ', ), - tensor_volume=dict( - argstr='--tensor_volume %s', - usedefault=True, - ), + tensor_volume=dict(argstr='--tensor_volume %s', ), verbose=dict(argstr='--verbose ', ), voxel_label=dict(argstr='--voxel_label %d', ), voxelize=dict( @@ -50,8 +38,8 @@ def test_fiberprocess_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_fiberprocess_outputs(): output_map = dict( - fiber_output=dict(usedefault=True, ), - voxelize=dict(usedefault=True, ), + fiber_output=dict(), + voxelize=dict(), ) outputs = fiberprocess.output_spec() diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py index a7df93f305..d6f3a5cd50 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py @@ -10,10 +10,7 @@ def test_fiberstats_inputs(): nohash=True, usedefault=True, ), - fiber_file=dict( - argstr='--fiber_file %s', - usedefault=True, - ), + fiber_file=dict(argstr='--fiber_file %s', ), verbose=dict(argstr='--verbose ', ), ) inputs = fiberstats.input_spec() diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py index 085f99bc37..33e57c0ca3 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py @@ -12,14 +12,8 @@ def test_fibertrack_inputs(): ), forbidden_label=dict(argstr='--forbidden_label %d', ), force=dict(argstr='--force ', ), - input_roi_file=dict( - argstr='--input_roi_file %s', - usedefault=True, - ), - input_tensor_file=dict( - argstr='--input_tensor_file %s', - usedefault=True, - ), + input_roi_file=dict(argstr='--input_roi_file %s', ), + input_tensor_file=dict(argstr='--input_tensor_file %s', ), max_angle=dict(argstr='--max_angle %f', ), min_fa=dict(argstr='--min_fa %f', ), output_fiber_file=dict( @@ -39,7 +33,7 @@ def test_fibertrack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_fibertrack_outputs(): - output_map = dict(output_fiber_file=dict(usedefault=True, ), ) + output_map = dict(output_fiber_file=dict(), ) outputs = fibertrack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py index bdbb02059d..cfbee7449c 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py @@ -10,10 +10,7 @@ def test_CannyEdge_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), lowerThreshold=dict(argstr='--lowerThreshold %f', ), outputVolume=dict( argstr='--outputVolume %s', @@ -28,7 +25,7 @@ def test_CannyEdge_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CannyEdge_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = CannyEdge.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py index 7ce651cd47..b4196db823 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py @@ -13,15 +13,9 @@ def test_CannySegmentationLevelSetImageFilter_inputs(): nohash=True, usedefault=True, ), - initialModel=dict( - argstr='--initialModel %s', - usedefault=True, - ), + initialModel=dict(argstr='--initialModel %s', ), initialModelIsovalue=dict(argstr='--initialModelIsovalue %f', ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), maxIterations=dict(argstr='--maxIterations %d', ), outputSpeedVolume=dict( argstr='--outputSpeedVolume %s', @@ -39,8 +33,8 @@ def test_CannySegmentationLevelSetImageFilter_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CannySegmentationLevelSetImageFilter_outputs(): output_map = dict( - outputSpeedVolume=dict(usedefault=True, ), - outputVolume=dict(usedefault=True, ), + outputSpeedVolume=dict(), + outputVolume=dict(), ) outputs = CannySegmentationLevelSetImageFilter.output_spec() diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py index bfecea83e7..7945ec8ade 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py @@ -10,15 +10,9 @@ def test_DilateImage_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict( - argstr='--inputMaskVolume %s', - usedefault=True, - ), + inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), inputRadius=dict(argstr='--inputRadius %d', ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -30,7 +24,7 @@ def test_DilateImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DilateImage_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = DilateImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py index 7af627bb4a..6bd6235e80 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py @@ -10,14 +10,8 @@ def test_DilateMask_inputs(): nohash=True, usedefault=True, ), - inputBinaryVolume=dict( - argstr='--inputBinaryVolume %s', - usedefault=True, - ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputBinaryVolume=dict(argstr='--inputBinaryVolume %s', ), + inputVolume=dict(argstr='--inputVolume %s', ), lowerThreshold=dict(argstr='--lowerThreshold %f', ), outputVolume=dict( argstr='--outputVolume %s', @@ -31,7 +25,7 @@ def test_DilateMask_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DilateMask_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = DilateMask.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py index 9cd90e0621..f7aaf722c4 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py @@ -10,14 +10,8 @@ def test_DistanceMaps_inputs(): nohash=True, usedefault=True, ), - inputLabelVolume=dict( - argstr='--inputLabelVolume %s', - usedefault=True, - ), - inputMaskVolume=dict( - argstr='--inputMaskVolume %s', - usedefault=True, - ), + inputLabelVolume=dict(argstr='--inputLabelVolume %s', ), + inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), inputTissueLabel=dict(argstr='--inputTissueLabel %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -30,7 +24,7 @@ def test_DistanceMaps_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DistanceMaps_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = DistanceMaps.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py index f5e98d3053..320bb76b77 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py @@ -10,14 +10,8 @@ def test_DumpBinaryTrainingVectors_inputs(): nohash=True, usedefault=True, ), - inputHeaderFilename=dict( - argstr='--inputHeaderFilename %s', - usedefault=True, - ), - inputVectorFilename=dict( - argstr='--inputVectorFilename %s', - usedefault=True, - ), + inputHeaderFilename=dict(argstr='--inputHeaderFilename %s', ), + inputVectorFilename=dict(argstr='--inputVectorFilename %s', ), ) inputs = DumpBinaryTrainingVectors.input_spec() diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py index b9f280d795..9e096b0062 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py @@ -10,15 +10,9 @@ def test_ErodeImage_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict( - argstr='--inputMaskVolume %s', - usedefault=True, - ), + inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), inputRadius=dict(argstr='--inputRadius %d', ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -30,7 +24,7 @@ def test_ErodeImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ErodeImage_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = ErodeImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py index 1607a834d0..539660f73b 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py @@ -10,14 +10,8 @@ def test_FlippedDifference_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict( - argstr='--inputMaskVolume %s', - usedefault=True, - ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), + inputVolume=dict(argstr='--inputVolume %s', ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -29,7 +23,7 @@ def test_FlippedDifference_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FlippedDifference_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = FlippedDifference.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py index 4226a4dce8..0a211f23d2 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py @@ -10,14 +10,8 @@ def test_GenerateBrainClippedImage_inputs(): nohash=True, usedefault=True, ), - inputImg=dict( - argstr='--inputImg %s', - usedefault=True, - ), - inputMsk=dict( - argstr='--inputMsk %s', - usedefault=True, - ), + inputImg=dict(argstr='--inputImg %s', ), + inputMsk=dict(argstr='--inputMsk %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputFileName=dict( argstr='--outputFileName %s', @@ -30,7 +24,7 @@ def test_GenerateBrainClippedImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateBrainClippedImage_outputs(): - output_map = dict(outputFileName=dict(usedefault=True, ), ) + output_map = dict(outputFileName=dict(), ) outputs = GenerateBrainClippedImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py index a797efb90f..58d3f35c5a 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py @@ -11,14 +11,8 @@ def test_GenerateSummedGradientImage_inputs(): nohash=True, usedefault=True, ), - inputVolume1=dict( - argstr='--inputVolume1 %s', - usedefault=True, - ), - inputVolume2=dict( - argstr='--inputVolume2 %s', - usedefault=True, - ), + inputVolume1=dict(argstr='--inputVolume1 %s', ), + inputVolume2=dict(argstr='--inputVolume2 %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputFileName=dict( argstr='--outputFileName %s', @@ -31,7 +25,7 @@ def test_GenerateSummedGradientImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateSummedGradientImage_outputs(): - output_map = dict(outputFileName=dict(usedefault=True, ), ) + output_map = dict(outputFileName=dict(), ) outputs = GenerateSummedGradientImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py index e85da77db7..1348e61d4b 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py @@ -10,10 +10,7 @@ def test_GenerateTestImage_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), lowerBoundOfOutputVolume=dict( argstr='--lowerBoundOfOutputVolume %f', ), outputVolume=dict( @@ -30,7 +27,7 @@ def test_GenerateTestImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateTestImage_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = GenerateTestImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py index a4fe09a024..27ebb18d29 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py @@ -11,10 +11,7 @@ def test_GradientAnisotropicDiffusionImageFilter_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), numberOfIterations=dict(argstr='--numberOfIterations %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -28,7 +25,7 @@ def test_GradientAnisotropicDiffusionImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GradientAnisotropicDiffusionImageFilter_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = GradientAnisotropicDiffusionImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py index 2d97ec8100..9ad82598bb 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py @@ -12,18 +12,9 @@ def test_HammerAttributeCreator_inputs(): nohash=True, usedefault=True, ), - inputCSFVolume=dict( - argstr='--inputCSFVolume %s', - usedefault=True, - ), - inputGMVolume=dict( - argstr='--inputGMVolume %s', - usedefault=True, - ), - inputWMVolume=dict( - argstr='--inputWMVolume %s', - usedefault=True, - ), + inputCSFVolume=dict(argstr='--inputCSFVolume %s', ), + inputGMVolume=dict(argstr='--inputGMVolume %s', ), + inputWMVolume=dict(argstr='--inputWMVolume %s', ), outputVolumeBase=dict(argstr='--outputVolumeBase %s', ), ) inputs = HammerAttributeCreator.input_spec() diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py index 81afd305dc..c6b1ef20a9 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py @@ -10,15 +10,9 @@ def test_NeighborhoodMean_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict( - argstr='--inputMaskVolume %s', - usedefault=True, - ), + inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), inputRadius=dict(argstr='--inputRadius %d', ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -30,7 +24,7 @@ def test_NeighborhoodMean_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NeighborhoodMean_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = NeighborhoodMean.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py index b7b165cc97..2c2b2d585f 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py @@ -10,15 +10,9 @@ def test_NeighborhoodMedian_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict( - argstr='--inputMaskVolume %s', - usedefault=True, - ), + inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), inputRadius=dict(argstr='--inputRadius %d', ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -30,7 +24,7 @@ def test_NeighborhoodMedian_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_NeighborhoodMedian_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = NeighborhoodMedian.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py index 2ce9c6a0aa..75bb83315f 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py @@ -23,7 +23,7 @@ def test_STAPLEAnalysis_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_STAPLEAnalysis_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = STAPLEAnalysis.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py index 348018b3e1..cd4b4a1af2 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py @@ -11,10 +11,7 @@ def test_TextureFromNoiseImageFilter_inputs(): usedefault=True, ), inputRadius=dict(argstr='--inputRadius %d', ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -26,7 +23,7 @@ def test_TextureFromNoiseImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TextureFromNoiseImageFilter_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = TextureFromNoiseImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py index 2587252a3a..0ad523c7d0 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py @@ -11,14 +11,8 @@ def test_TextureMeasureFilter_inputs(): nohash=True, usedefault=True, ), - inputMaskVolume=dict( - argstr='--inputMaskVolume %s', - usedefault=True, - ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), + inputVolume=dict(argstr='--inputVolume %s', ), insideROIValue=dict(argstr='--insideROIValue %f', ), outputFilename=dict( argstr='--outputFilename %s', @@ -31,7 +25,7 @@ def test_TextureMeasureFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TextureMeasureFilter_outputs(): - output_map = dict(outputFilename=dict(usedefault=True, ), ) + output_map = dict(outputFilename=dict(), ) outputs = TextureMeasureFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py index af98570055..b84cda1fc3 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py @@ -14,7 +14,6 @@ def test_UnbiasedNonLocalMeans_inputs(): inputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), outputVolume=dict( argstr='%s', @@ -38,11 +37,7 @@ def test_UnbiasedNonLocalMeans_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_UnbiasedNonLocalMeans_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = UnbiasedNonLocalMeans.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py index 802c3d817b..f9ff60cfd9 100644 --- a/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py +++ b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py @@ -6,19 +6,13 @@ def test_scalartransform_inputs(): input_map = dict( args=dict(argstr='%s', ), - deformation=dict( - argstr='--deformation %s', - usedefault=True, - ), + deformation=dict(argstr='--deformation %s', ), environ=dict( nohash=True, usedefault=True, ), h_field=dict(argstr='--h_field ', ), - input_image=dict( - argstr='--input_image %s', - usedefault=True, - ), + input_image=dict(argstr='--input_image %s', ), interpolation=dict(argstr='--interpolation %s', ), invert=dict(argstr='--invert ', ), output_image=dict( @@ -37,8 +31,8 @@ def test_scalartransform_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_scalartransform_outputs(): output_map = dict( - output_image=dict(usedefault=True, ), - transformation=dict(usedefault=True, ), + output_image=dict(), + transformation=dict(), ) outputs = scalartransform.output_spec() diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py index 5ac8f5f353..c631f9b96e 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py @@ -19,25 +19,14 @@ def test_BRAINSDemonWarp_inputs(): nohash=True, usedefault=True, ), - fixedBinaryVolume=dict( - argstr='--fixedBinaryVolume %s', - usedefault=True, - ), - fixedVolume=dict( - argstr='--fixedVolume %s', - usedefault=True, - ), + fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), + fixedVolume=dict(argstr='--fixedVolume %s', ), gradient_type=dict(argstr='--gradient_type %s', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), initializeWithDisplacementField=dict( - argstr='--initializeWithDisplacementField %s', - usedefault=True, - ), - initializeWithTransform=dict( - argstr='--initializeWithTransform %s', - usedefault=True, - ), + argstr='--initializeWithDisplacementField %s', ), + initializeWithTransform=dict(argstr='--initializeWithTransform %s', ), inputPixelType=dict(argstr='--inputPixelType %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), lowerThresholdForBOBF=dict(argstr='--lowerThresholdForBOBF %d', ), @@ -55,14 +44,8 @@ def test_BRAINSDemonWarp_inputs(): argstr='--minimumMovingPyramid %s', sep=',', ), - movingBinaryVolume=dict( - argstr='--movingBinaryVolume %s', - usedefault=True, - ), - movingVolume=dict( - argstr='--movingVolume %s', - usedefault=True, - ), + movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), + movingVolume=dict(argstr='--movingVolume %s', ), neighborhoodForBOBF=dict( argstr='--neighborhoodForBOBF %s', sep=',', @@ -109,9 +92,9 @@ def test_BRAINSDemonWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSDemonWarp_outputs(): output_map = dict( - outputCheckerboardVolume=dict(usedefault=True, ), - outputDisplacementFieldVolume=dict(usedefault=True, ), - outputVolume=dict(usedefault=True, ), + outputCheckerboardVolume=dict(), + outputDisplacementFieldVolume=dict(), + outputVolume=dict(), ) outputs = BRAINSDemonWarp.output_spec() diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py index 5fde41901c..18059c4f57 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py @@ -22,25 +22,13 @@ def test_BRAINSFit_inputs(): usedefault=True, ), failureExitCode=dict(argstr='--failureExitCode %d', ), - fixedBinaryVolume=dict( - argstr='--fixedBinaryVolume %s', - usedefault=True, - ), - fixedVolume=dict( - argstr='--fixedVolume %s', - usedefault=True, - ), - fixedVolume2=dict( - argstr='--fixedVolume2 %s', - usedefault=True, - ), + fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), + fixedVolume=dict(argstr='--fixedVolume %s', ), + fixedVolume2=dict(argstr='--fixedVolume2 %s', ), fixedVolumeTimeIndex=dict(argstr='--fixedVolumeTimeIndex %d', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), - initialTransform=dict( - argstr='--initialTransform %s', - usedefault=True, - ), + initialTransform=dict(argstr='--initialTransform %s', ), initializeRegistrationByCurrentGenericTransform=dict( argstr='--initializeRegistrationByCurrentGenericTransform ', ), initializeTransformMode=dict(argstr='--initializeTransformMode %s', ), @@ -71,18 +59,9 @@ def test_BRAINSFit_inputs(): argstr='--minimumStepLength %s', sep=',', ), - movingBinaryVolume=dict( - argstr='--movingBinaryVolume %s', - usedefault=True, - ), - movingVolume=dict( - argstr='--movingVolume %s', - usedefault=True, - ), - movingVolume2=dict( - argstr='--movingVolume2 %s', - usedefault=True, - ), + movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), + movingVolume=dict(argstr='--movingVolume %s', ), + movingVolume2=dict(argstr='--movingVolume2 %s', ), movingVolumeTimeIndex=dict(argstr='--movingVolumeTimeIndex %d', ), numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', ), numberOfIterations=dict( @@ -150,14 +129,14 @@ def test_BRAINSFit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSFit_outputs(): output_map = dict( - bsplineTransform=dict(usedefault=True, ), - linearTransform=dict(usedefault=True, ), - logFileReport=dict(usedefault=True, ), - outputFixedVolumeROI=dict(usedefault=True, ), - outputMovingVolumeROI=dict(usedefault=True, ), - outputTransform=dict(usedefault=True, ), - outputVolume=dict(usedefault=True, ), - strippedOutputTransform=dict(usedefault=True, ), + bsplineTransform=dict(), + linearTransform=dict(), + logFileReport=dict(), + outputFixedVolumeROI=dict(), + outputMovingVolumeROI=dict(), + outputTransform=dict(), + outputVolume=dict(), + strippedOutputTransform=dict(), ) outputs = BRAINSFit.output_spec() diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py index 38758ac585..98ec5f4ff3 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py @@ -7,10 +7,7 @@ def test_BRAINSResample_inputs(): input_map = dict( args=dict(argstr='%s', ), defaultValue=dict(argstr='--defaultValue %f', ), - deformationVolume=dict( - argstr='--deformationVolume %s', - usedefault=True, - ), + deformationVolume=dict(argstr='--deformationVolume %s', ), environ=dict( nohash=True, usedefault=True, @@ -19,10 +16,7 @@ def test_BRAINSResample_inputs(): argstr='--gridSpacing %s', sep=',', ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), inverseTransform=dict(argstr='--inverseTransform ', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -31,14 +25,8 @@ def test_BRAINSResample_inputs(): hash_files=False, ), pixelType=dict(argstr='--pixelType %s', ), - referenceVolume=dict( - argstr='--referenceVolume %s', - usedefault=True, - ), - warpTransform=dict( - argstr='--warpTransform %s', - usedefault=True, - ), + referenceVolume=dict(argstr='--referenceVolume %s', ), + warpTransform=dict(argstr='--warpTransform %s', ), ) inputs = BRAINSResample.input_spec() @@ -46,7 +34,7 @@ def test_BRAINSResample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSResample_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = BRAINSResample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py index 8326816fc9..4ce0d7159c 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py @@ -10,10 +10,7 @@ def test_BRAINSResize_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -27,7 +24,7 @@ def test_BRAINSResize_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSResize_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = BRAINSResize.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py index 4d3b90959e..2a700eaac7 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py @@ -11,15 +11,9 @@ def test_BRAINSTransformFromFiducials_inputs(): usedefault=True, ), fixedLandmarks=dict(argstr='--fixedLandmarks %s...', ), - fixedLandmarksFile=dict( - argstr='--fixedLandmarksFile %s', - usedefault=True, - ), + fixedLandmarksFile=dict(argstr='--fixedLandmarksFile %s', ), movingLandmarks=dict(argstr='--movingLandmarks %s...', ), - movingLandmarksFile=dict( - argstr='--movingLandmarksFile %s', - usedefault=True, - ), + movingLandmarksFile=dict(argstr='--movingLandmarksFile %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), saveTransform=dict( argstr='--saveTransform %s', @@ -33,7 +27,7 @@ def test_BRAINSTransformFromFiducials_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTransformFromFiducials_outputs(): - output_map = dict(saveTransform=dict(usedefault=True, ), ) + output_map = dict(saveTransform=dict(), ) outputs = BRAINSTransformFromFiducials.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py index 17d6d7715d..b3255da1d3 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -19,22 +19,14 @@ def test_VBRAINSDemonWarp_inputs(): nohash=True, usedefault=True, ), - fixedBinaryVolume=dict( - argstr='--fixedBinaryVolume %s', - usedefault=True, - ), + fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), fixedVolume=dict(argstr='--fixedVolume %s...', ), gradient_type=dict(argstr='--gradient_type %s', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), initializeWithDisplacementField=dict( - argstr='--initializeWithDisplacementField %s', - usedefault=True, - ), - initializeWithTransform=dict( - argstr='--initializeWithTransform %s', - usedefault=True, - ), + argstr='--initializeWithDisplacementField %s', ), + initializeWithTransform=dict(argstr='--initializeWithTransform %s', ), inputPixelType=dict(argstr='--inputPixelType %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), lowerThresholdForBOBF=dict(argstr='--lowerThresholdForBOBF %d', ), @@ -52,10 +44,7 @@ def test_VBRAINSDemonWarp_inputs(): argstr='--minimumMovingPyramid %s', sep=',', ), - movingBinaryVolume=dict( - argstr='--movingBinaryVolume %s', - usedefault=True, - ), + movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), movingVolume=dict(argstr='--movingVolume %s...', ), neighborhoodForBOBF=dict( argstr='--neighborhoodForBOBF %s', @@ -107,9 +96,9 @@ def test_VBRAINSDemonWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_VBRAINSDemonWarp_outputs(): output_map = dict( - outputCheckerboardVolume=dict(usedefault=True, ), - outputDisplacementFieldVolume=dict(usedefault=True, ), - outputVolume=dict(usedefault=True, ), + outputCheckerboardVolume=dict(), + outputDisplacementFieldVolume=dict(), + outputVolume=dict(), ) outputs = VBRAINSDemonWarp.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py index 0f29a199f6..2d66884522 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py @@ -6,10 +6,7 @@ def test_BRAINSABC_inputs(): input_map = dict( args=dict(argstr='%s', ), - atlasDefinition=dict( - argstr='--atlasDefinition %s', - usedefault=True, - ), + atlasDefinition=dict(argstr='--atlasDefinition %s', ), atlasToSubjectInitialTransform=dict( argstr='--atlasToSubjectInitialTransform %s', hash_files=False, @@ -74,10 +71,7 @@ def test_BRAINSABC_inputs(): ), posteriorTemplate=dict(argstr='--posteriorTemplate %s', ), purePlugsThreshold=dict(argstr='--purePlugsThreshold %f', ), - restoreState=dict( - argstr='--restoreState %s', - usedefault=True, - ), + restoreState=dict(argstr='--restoreState %s', ), saveState=dict( argstr='--saveState %s', hash_files=False, @@ -94,14 +88,14 @@ def test_BRAINSABC_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSABC_outputs(): output_map = dict( - atlasToSubjectInitialTransform=dict(usedefault=True, ), - atlasToSubjectTransform=dict(usedefault=True, ), + atlasToSubjectInitialTransform=dict(), + atlasToSubjectTransform=dict(), implicitOutputs=dict(), - outputDir=dict(usedefault=True, ), - outputDirtyLabels=dict(usedefault=True, ), - outputLabels=dict(usedefault=True, ), + outputDir=dict(), + outputDirtyLabels=dict(), + outputLabels=dict(), outputVolumes=dict(), - saveState=dict(usedefault=True, ), + saveState=dict(), ) outputs = BRAINSABC.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py index 311b1df2a1..9b2d10061c 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py @@ -6,24 +6,12 @@ def test_BRAINSConstellationDetector_inputs(): input_map = dict( BackgroundFillValue=dict(argstr='--BackgroundFillValue %s', ), - LLSModel=dict( - argstr='--LLSModel %s', - usedefault=True, - ), + LLSModel=dict(argstr='--LLSModel %s', ), acLowerBound=dict(argstr='--acLowerBound %f', ), args=dict(argstr='%s', ), - atlasLandmarkWeights=dict( - argstr='--atlasLandmarkWeights %s', - usedefault=True, - ), - atlasLandmarks=dict( - argstr='--atlasLandmarks %s', - usedefault=True, - ), - atlasVolume=dict( - argstr='--atlasVolume %s', - usedefault=True, - ), + atlasLandmarkWeights=dict(argstr='--atlasLandmarkWeights %s', ), + atlasLandmarks=dict(argstr='--atlasLandmarks %s', ), + atlasVolume=dict(argstr='--atlasVolume %s', ), cutOutHeadInOutputVolume=dict(argstr='--cutOutHeadInOutputVolume ', ), debug=dict(argstr='--debug ', ), environ=dict( @@ -49,18 +37,9 @@ def test_BRAINSConstellationDetector_inputs(): sep=',', ), houghEyeDetectorMode=dict(argstr='--houghEyeDetectorMode %d', ), - inputLandmarksEMSP=dict( - argstr='--inputLandmarksEMSP %s', - usedefault=True, - ), - inputTemplateModel=dict( - argstr='--inputTemplateModel %s', - usedefault=True, - ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputLandmarksEMSP=dict(argstr='--inputLandmarksEMSP %s', ), + inputTemplateModel=dict(argstr='--inputTemplateModel %s', ), + inputVolume=dict(argstr='--inputVolume %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), mspQualityLevel=dict(argstr='--mspQualityLevel %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -126,16 +105,16 @@ def test_BRAINSConstellationDetector_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSConstellationDetector_outputs(): output_map = dict( - outputLandmarksInACPCAlignedSpace=dict(usedefault=True, ), - outputLandmarksInInputSpace=dict(usedefault=True, ), - outputMRML=dict(usedefault=True, ), - outputResampledVolume=dict(usedefault=True, ), - outputTransform=dict(usedefault=True, ), - outputUntransformedClippedVolume=dict(usedefault=True, ), - outputVerificationScript=dict(usedefault=True, ), - outputVolume=dict(usedefault=True, ), - resultsDir=dict(usedefault=True, ), - writeBranded2DImage=dict(usedefault=True, ), + outputLandmarksInACPCAlignedSpace=dict(), + outputLandmarksInInputSpace=dict(), + outputMRML=dict(), + outputResampledVolume=dict(), + outputTransform=dict(), + outputUntransformedClippedVolume=dict(), + outputVerificationScript=dict(), + outputVolume=dict(), + resultsDir=dict(), + writeBranded2DImage=dict(), ) outputs = BRAINSConstellationDetector.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py index cde17297dc..9f2b00c311 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py @@ -24,10 +24,7 @@ def test_BRAINSCreateLabelMapFromProbabilityMaps_inputs(): ), inclusionThreshold=dict(argstr='--inclusionThreshold %f', ), inputProbabilityVolume=dict(argstr='--inputProbabilityVolume %s...', ), - nonAirRegionMask=dict( - argstr='--nonAirRegionMask %s', - usedefault=True, - ), + nonAirRegionMask=dict(argstr='--nonAirRegionMask %s', ), priorLabelCodes=dict( argstr='--priorLabelCodes %s', sep=',', @@ -40,8 +37,8 @@ def test_BRAINSCreateLabelMapFromProbabilityMaps_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSCreateLabelMapFromProbabilityMaps_outputs(): output_map = dict( - cleanLabelVolume=dict(usedefault=True, ), - dirtyLabelVolume=dict(usedefault=True, ), + cleanLabelVolume=dict(), + dirtyLabelVolume=dict(), ) outputs = BRAINSCreateLabelMapFromProbabilityMaps.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py index f14fc12f3e..9d66d4a463 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py @@ -19,15 +19,10 @@ def test_BRAINSCut_inputs(): histogramEqualization=dict(argstr='--histogramEqualization ', ), method=dict(argstr='--method %s', ), modelConfigurationFilename=dict( - argstr='--modelConfigurationFilename %s', - usedefault=True, - ), + argstr='--modelConfigurationFilename %s', ), modelFilename=dict(argstr='--modelFilename %s', ), multiStructureThreshold=dict(argstr='--multiStructureThreshold ', ), - netConfiguration=dict( - argstr='--netConfiguration %s', - usedefault=True, - ), + netConfiguration=dict(argstr='--netConfiguration %s', ), numberOfTrees=dict(argstr='--numberOfTrees %d', ), randomTreeDepth=dict(argstr='--randomTreeDepth %d', ), trainModel=dict(argstr='--trainModel ', ), diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py index f4495cbda0..826ec19f0e 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py @@ -10,10 +10,7 @@ def test_BRAINSMultiSTAPLE_inputs(): nohash=True, usedefault=True, ), - inputCompositeT1Volume=dict( - argstr='--inputCompositeT1Volume %s', - usedefault=True, - ), + inputCompositeT1Volume=dict(argstr='--inputCompositeT1Volume %s', ), inputLabelVolume=dict(argstr='--inputLabelVolume %s...', ), inputTransform=dict(argstr='--inputTransform %s...', ), labelForUndecidedPixels=dict(argstr='--labelForUndecidedPixels %d', ), @@ -35,8 +32,8 @@ def test_BRAINSMultiSTAPLE_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSMultiSTAPLE_outputs(): output_map = dict( - outputConfusionMatrix=dict(usedefault=True, ), - outputMultiSTAPLE=dict(usedefault=True, ), + outputConfusionMatrix=dict(), + outputMultiSTAPLE=dict(), ) outputs = BRAINSMultiSTAPLE.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py index f222d7f4ae..3e70b75883 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -13,10 +13,7 @@ def test_BRAINSROIAuto_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), maskOutput=dict(argstr='--maskOutput ', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), otsuPercentileThreshold=dict(argstr='--otsuPercentileThreshold %f', ), @@ -39,8 +36,8 @@ def test_BRAINSROIAuto_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSROIAuto_outputs(): output_map = dict( - outputROIMaskVolume=dict(usedefault=True, ), - outputVolume=dict(usedefault=True, ), + outputROIMaskVolume=dict(), + outputVolume=dict(), ) outputs = BRAINSROIAuto.output_spec() diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py index 97100404e1..d71e7003ff 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py @@ -10,10 +10,7 @@ def test_BinaryMaskEditorBasedOnLandmarks_inputs(): nohash=True, usedefault=True, ), - inputBinaryVolume=dict( - argstr='--inputBinaryVolume %s', - usedefault=True, - ), + inputBinaryVolume=dict(argstr='--inputBinaryVolume %s', ), inputLandmarkNames=dict( argstr='--inputLandmarkNames %s', sep=',', @@ -22,10 +19,7 @@ def test_BinaryMaskEditorBasedOnLandmarks_inputs(): argstr='--inputLandmarkNamesForObliquePlane %s', sep=',', ), - inputLandmarksFilename=dict( - argstr='--inputLandmarksFilename %s', - usedefault=True, - ), + inputLandmarksFilename=dict(argstr='--inputLandmarksFilename %s', ), outputBinaryVolume=dict( argstr='--outputBinaryVolume %s', hash_files=False, @@ -45,7 +39,7 @@ def test_BinaryMaskEditorBasedOnLandmarks_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BinaryMaskEditorBasedOnLandmarks_outputs(): - output_map = dict(outputBinaryVolume=dict(usedefault=True, ), ) + output_map = dict(outputBinaryVolume=dict(), ) outputs = BinaryMaskEditorBasedOnLandmarks.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py index d5a05c0a97..2e099b4f56 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py @@ -12,10 +12,7 @@ def test_ESLR_inputs(): usedefault=True, ), high=dict(argstr='--high %d', ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), low=dict(argstr='--low %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), openingSize=dict(argstr='--openingSize %d', ), @@ -32,7 +29,7 @@ def test_ESLR_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ESLR_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = ESLR.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py index 704f89bd58..c00b0cc36f 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py @@ -10,14 +10,8 @@ def test_DWICompare_inputs(): nohash=True, usedefault=True, ), - inputVolume1=dict( - argstr='--inputVolume1 %s', - usedefault=True, - ), - inputVolume2=dict( - argstr='--inputVolume2 %s', - usedefault=True, - ), + inputVolume1=dict(argstr='--inputVolume1 %s', ), + inputVolume2=dict(argstr='--inputVolume2 %s', ), ) inputs = DWICompare.input_spec() diff --git a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py index 239b092e33..e515bc613c 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py @@ -11,14 +11,8 @@ def test_DWISimpleCompare_inputs(): nohash=True, usedefault=True, ), - inputVolume1=dict( - argstr='--inputVolume1 %s', - usedefault=True, - ), - inputVolume2=dict( - argstr='--inputVolume2 %s', - usedefault=True, - ), + inputVolume1=dict(argstr='--inputVolume1 %s', ), + inputVolume2=dict(argstr='--inputVolume2 %s', ), ) inputs = DWISimpleCompare.input_spec() diff --git a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py index f5a881004b..63f45831af 100644 --- a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py +++ b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py @@ -10,10 +10,7 @@ def test_GenerateCsfClippedFromClassifiedImage_inputs(): nohash=True, usedefault=True, ), - inputCassifiedVolume=dict( - argstr='--inputCassifiedVolume %s', - usedefault=True, - ), + inputCassifiedVolume=dict(argstr='--inputCassifiedVolume %s', ), outputVolume=dict( argstr='--outputVolume %s', hash_files=False, @@ -25,7 +22,7 @@ def test_GenerateCsfClippedFromClassifiedImage_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateCsfClippedFromClassifiedImage_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = GenerateCsfClippedFromClassifiedImage.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py index d1ab2a10a5..27b65a4eba 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py @@ -15,10 +15,7 @@ def test_BRAINSAlignMSP_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), mspQualityLevel=dict(argstr='--mspQualityLevel %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -43,8 +40,8 @@ def test_BRAINSAlignMSP_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSAlignMSP_outputs(): output_map = dict( - OutputresampleMSP=dict(usedefault=True, ), - resultsDir=dict(usedefault=True, ), + OutputresampleMSP=dict(), + resultsDir=dict(), ) outputs = BRAINSAlignMSP.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py index 2479c5f233..7a0528f201 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py @@ -12,10 +12,7 @@ def test_BRAINSClipInferior_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -28,7 +25,7 @@ def test_BRAINSClipInferior_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSClipInferior_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = BRAINSClipInferior.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py index 7c29d75f85..a124ad60d9 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py @@ -11,10 +11,7 @@ def test_BRAINSConstellationModeler_inputs(): nohash=True, usedefault=True, ), - inputTrainingList=dict( - argstr='--inputTrainingList %s', - usedefault=True, - ), + inputTrainingList=dict(argstr='--inputTrainingList %s', ), mspQualityLevel=dict(argstr='--mspQualityLevel %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), optimizedLandmarksFilenameExtender=dict( @@ -45,8 +42,8 @@ def test_BRAINSConstellationModeler_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSConstellationModeler_outputs(): output_map = dict( - outputModel=dict(usedefault=True, ), - resultsDir=dict(usedefault=True, ), + outputModel=dict(), + resultsDir=dict(), ) outputs = BRAINSConstellationModeler.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py index 0339ae0bea..9df3c8b8d6 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py @@ -11,10 +11,7 @@ def test_BRAINSEyeDetector_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputVolume=dict( argstr='--outputVolume %s', @@ -27,7 +24,7 @@ def test_BRAINSEyeDetector_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSEyeDetector_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = BRAINSEyeDetector.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py index fafa298559..bc3807f9f8 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py @@ -10,10 +10,7 @@ def test_BRAINSInitializedControlPoints_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputLandmarksFile=dict(argstr='--outputLandmarksFile %s', ), outputVolume=dict( @@ -35,7 +32,7 @@ def test_BRAINSInitializedControlPoints_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSInitializedControlPoints_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = BRAINSInitializedControlPoints.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py index 7804d04d92..2456b8fb4d 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py @@ -11,17 +11,10 @@ def test_BRAINSLandmarkInitializer_inputs(): usedefault=True, ), inputFixedLandmarkFilename=dict( - argstr='--inputFixedLandmarkFilename %s', - usedefault=True, - ), + argstr='--inputFixedLandmarkFilename %s', ), inputMovingLandmarkFilename=dict( - argstr='--inputMovingLandmarkFilename %s', - usedefault=True, - ), - inputWeightFilename=dict( - argstr='--inputWeightFilename %s', - usedefault=True, - ), + argstr='--inputMovingLandmarkFilename %s', ), + inputWeightFilename=dict(argstr='--inputWeightFilename %s', ), outputTransformFilename=dict( argstr='--outputTransformFilename %s', hash_files=False, @@ -33,7 +26,7 @@ def test_BRAINSLandmarkInitializer_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSLandmarkInitializer_outputs(): - output_map = dict(outputTransformFilename=dict(usedefault=True, ), ) + output_map = dict(outputTransformFilename=dict(), ) outputs = BRAINSLandmarkInitializer.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py index 99d7fa217b..b6b83baa12 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py @@ -10,10 +10,7 @@ def test_BRAINSLinearModelerEPCA_inputs(): nohash=True, usedefault=True, ), - inputTrainingList=dict( - argstr='--inputTrainingList %s', - usedefault=True, - ), + inputTrainingList=dict(argstr='--inputTrainingList %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), ) inputs = BRAINSLinearModelerEPCA.input_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py index 7b75451d10..262d948029 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py @@ -10,22 +10,10 @@ def test_BRAINSLmkTransform_inputs(): nohash=True, usedefault=True, ), - inputFixedLandmarks=dict( - argstr='--inputFixedLandmarks %s', - usedefault=True, - ), - inputMovingLandmarks=dict( - argstr='--inputMovingLandmarks %s', - usedefault=True, - ), - inputMovingVolume=dict( - argstr='--inputMovingVolume %s', - usedefault=True, - ), - inputReferenceVolume=dict( - argstr='--inputReferenceVolume %s', - usedefault=True, - ), + inputFixedLandmarks=dict(argstr='--inputFixedLandmarks %s', ), + inputMovingLandmarks=dict(argstr='--inputMovingLandmarks %s', ), + inputMovingVolume=dict(argstr='--inputMovingVolume %s', ), + inputReferenceVolume=dict(argstr='--inputReferenceVolume %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), outputAffineTransform=dict( argstr='--outputAffineTransform %s', @@ -43,8 +31,8 @@ def test_BRAINSLmkTransform_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSLmkTransform_outputs(): output_map = dict( - outputAffineTransform=dict(usedefault=True, ), - outputResampledVolume=dict(usedefault=True, ), + outputAffineTransform=dict(), + outputResampledVolume=dict(), ) outputs = BRAINSLmkTransform.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py index 1797a4ab8b..9627258bcf 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py @@ -20,18 +20,9 @@ def test_BRAINSMush_inputs(): nohash=True, usedefault=True, ), - inputFirstVolume=dict( - argstr='--inputFirstVolume %s', - usedefault=True, - ), - inputMaskVolume=dict( - argstr='--inputMaskVolume %s', - usedefault=True, - ), - inputSecondVolume=dict( - argstr='--inputSecondVolume %s', - usedefault=True, - ), + inputFirstVolume=dict(argstr='--inputFirstVolume %s', ), + inputMaskVolume=dict(argstr='--inputMaskVolume %s', ), + inputSecondVolume=dict(argstr='--inputSecondVolume %s', ), lowerThresholdFactor=dict(argstr='--lowerThresholdFactor %f', ), lowerThresholdFactorPre=dict(argstr='--lowerThresholdFactorPre %f', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -61,9 +52,9 @@ def test_BRAINSMush_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSMush_outputs(): output_map = dict( - outputMask=dict(usedefault=True, ), - outputVolume=dict(usedefault=True, ), - outputWeightsFile=dict(usedefault=True, ), + outputMask=dict(), + outputVolume=dict(), + outputWeightsFile=dict(), ) outputs = BRAINSMush.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py index 146ae01a5b..1b803956e7 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py @@ -39,7 +39,7 @@ def test_BRAINSSnapShotWriter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSSnapShotWriter_outputs(): - output_map = dict(outputFilename=dict(usedefault=True, ), ) + output_map = dict(outputFilename=dict(), ) outputs = BRAINSSnapShotWriter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py index 5a5bba170d..c6d10736d7 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py @@ -14,20 +14,14 @@ def test_BRAINSTransformConvert_inputs(): nohash=True, usedefault=True, ), - inputTransform=dict( - argstr='--inputTransform %s', - usedefault=True, - ), + inputTransform=dict(argstr='--inputTransform %s', ), outputPrecisionType=dict(argstr='--outputPrecisionType %s', ), outputTransform=dict( argstr='--outputTransform %s', hash_files=False, ), outputTransformType=dict(argstr='--outputTransformType %s', ), - referenceVolume=dict( - argstr='--referenceVolume %s', - usedefault=True, - ), + referenceVolume=dict(argstr='--referenceVolume %s', ), ) inputs = BRAINSTransformConvert.input_spec() @@ -36,8 +30,8 @@ def test_BRAINSTransformConvert_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTransformConvert_outputs(): output_map = dict( - displacementVolume=dict(usedefault=True, ), - outputTransform=dict(usedefault=True, ), + displacementVolume=dict(), + outputTransform=dict(), ) outputs = BRAINSTransformConvert.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py index 8f0d95f919..d2f3b74140 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py @@ -14,10 +14,7 @@ def test_BRAINSTrimForegroundInDirection_inputs(): usedefault=True, ), headSizeLimit=dict(argstr='--headSizeLimit %f', ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), otsuPercentileThreshold=dict(argstr='--otsuPercentileThreshold %f', ), outputVolume=dict( @@ -31,7 +28,7 @@ def test_BRAINSTrimForegroundInDirection_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTrimForegroundInDirection_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = BRAINSTrimForegroundInDirection.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py index b7041c94ea..46924bf180 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py @@ -40,14 +40,8 @@ def test_FindCenterOfBrain_inputs(): generateDebugImages=dict(argstr='--generateDebugImages ', ), headSizeEstimate=dict(argstr='--headSizeEstimate %f', ), headSizeLimit=dict(argstr='--headSizeLimit %f', ), - imageMask=dict( - argstr='--imageMask %s', - usedefault=True, - ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + imageMask=dict(argstr='--imageMask %s', ), + inputVolume=dict(argstr='--inputVolume %s', ), maximize=dict(argstr='--maximize ', ), otsuPercentileThreshold=dict(argstr='--otsuPercentileThreshold %f', ), ) @@ -58,12 +52,12 @@ def test_FindCenterOfBrain_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_FindCenterOfBrain_outputs(): output_map = dict( - clippedImageMask=dict(usedefault=True, ), - debugAfterGridComputationsForegroundImage=dict(usedefault=True, ), - debugClippedImageMask=dict(usedefault=True, ), - debugDistanceImage=dict(usedefault=True, ), - debugGridImage=dict(usedefault=True, ), - debugTrimmedImage=dict(usedefault=True, ), + clippedImageMask=dict(), + debugAfterGridComputationsForegroundImage=dict(), + debugClippedImageMask=dict(), + debugDistanceImage=dict(), + debugGridImage=dict(), + debugTrimmedImage=dict(), ) outputs = FindCenterOfBrain.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py index f1de4189fa..9087d6667b 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py @@ -23,7 +23,7 @@ def test_GenerateLabelMapFromProbabilityMap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GenerateLabelMapFromProbabilityMap_outputs(): - output_map = dict(outputLabelVolume=dict(usedefault=True, ), ) + output_map = dict(outputLabelVolume=dict(), ) outputs = GenerateLabelMapFromProbabilityMap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py index 6d40209c22..f5372a240e 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py @@ -10,22 +10,10 @@ def test_ImageRegionPlotter_inputs(): nohash=True, usedefault=True, ), - inputBinaryROIVolume=dict( - argstr='--inputBinaryROIVolume %s', - usedefault=True, - ), - inputLabelVolume=dict( - argstr='--inputLabelVolume %s', - usedefault=True, - ), - inputVolume1=dict( - argstr='--inputVolume1 %s', - usedefault=True, - ), - inputVolume2=dict( - argstr='--inputVolume2 %s', - usedefault=True, - ), + inputBinaryROIVolume=dict(argstr='--inputBinaryROIVolume %s', ), + inputLabelVolume=dict(argstr='--inputLabelVolume %s', ), + inputVolume1=dict(argstr='--inputVolume1 %s', ), + inputVolume2=dict(argstr='--inputVolume2 %s', ), numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', ), outputJointHistogramData=dict( argstr='--outputJointHistogramData %s', ), diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py index 995a0a6a29..daf6d5634f 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py @@ -10,22 +10,10 @@ def test_JointHistogram_inputs(): nohash=True, usedefault=True, ), - inputMaskVolumeInXAxis=dict( - argstr='--inputMaskVolumeInXAxis %s', - usedefault=True, - ), - inputMaskVolumeInYAxis=dict( - argstr='--inputMaskVolumeInYAxis %s', - usedefault=True, - ), - inputVolumeInXAxis=dict( - argstr='--inputVolumeInXAxis %s', - usedefault=True, - ), - inputVolumeInYAxis=dict( - argstr='--inputVolumeInYAxis %s', - usedefault=True, - ), + inputMaskVolumeInXAxis=dict(argstr='--inputMaskVolumeInXAxis %s', ), + inputMaskVolumeInYAxis=dict(argstr='--inputMaskVolumeInYAxis %s', ), + inputVolumeInXAxis=dict(argstr='--inputVolumeInXAxis %s', ), + inputVolumeInYAxis=dict(argstr='--inputVolumeInYAxis %s', ), outputJointHistogramImage=dict( argstr='--outputJointHistogramImage %s', ), verbose=dict(argstr='--verbose ', ), diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py index cfd3390db5..7bea38e2f1 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py @@ -10,10 +10,7 @@ def test_ShuffleVectorsModule_inputs(): nohash=True, usedefault=True, ), - inputVectorFileBaseName=dict( - argstr='--inputVectorFileBaseName %s', - usedefault=True, - ), + inputVectorFileBaseName=dict(argstr='--inputVectorFileBaseName %s', ), outputVectorFileBaseName=dict( argstr='--outputVectorFileBaseName %s', hash_files=False, @@ -26,7 +23,7 @@ def test_ShuffleVectorsModule_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ShuffleVectorsModule_outputs(): - output_map = dict(outputVectorFileBaseName=dict(usedefault=True, ), ) + output_map = dict(outputVectorFileBaseName=dict(), ) outputs = ShuffleVectorsModule.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py b/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py index 91d5424458..32e6ce65cd 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py @@ -11,10 +11,7 @@ def test_fcsv_to_hdf5_inputs(): usedefault=True, ), landmarkGlobPattern=dict(argstr='--landmarkGlobPattern %s', ), - landmarkTypesList=dict( - argstr='--landmarkTypesList %s', - usedefault=True, - ), + landmarkTypesList=dict(argstr='--landmarkTypesList %s', ), landmarksInformationFile=dict( argstr='--landmarksInformationFile %s', hash_files=False, @@ -33,8 +30,8 @@ def test_fcsv_to_hdf5_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_fcsv_to_hdf5_outputs(): output_map = dict( - landmarksInformationFile=dict(usedefault=True, ), - modelFile=dict(usedefault=True, ), + landmarksInformationFile=dict(), + modelFile=dict(), ) outputs = fcsv_to_hdf5.output_spec() diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py index 746380b899..196b09b304 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py @@ -10,10 +10,7 @@ def test_insertMidACPCpoint_inputs(): nohash=True, usedefault=True, ), - inputLandmarkFile=dict( - argstr='--inputLandmarkFile %s', - usedefault=True, - ), + inputLandmarkFile=dict(argstr='--inputLandmarkFile %s', ), outputLandmarkFile=dict( argstr='--outputLandmarkFile %s', hash_files=False, @@ -25,7 +22,7 @@ def test_insertMidACPCpoint_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_insertMidACPCpoint_outputs(): - output_map = dict(outputLandmarkFile=dict(usedefault=True, ), ) + output_map = dict(outputLandmarkFile=dict(), ) outputs = insertMidACPCpoint.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py index e7ed3ecd59..151a2c7b3a 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py @@ -10,10 +10,7 @@ def test_landmarksConstellationAligner_inputs(): nohash=True, usedefault=True, ), - inputLandmarksPaired=dict( - argstr='--inputLandmarksPaired %s', - usedefault=True, - ), + inputLandmarksPaired=dict(argstr='--inputLandmarksPaired %s', ), outputLandmarksPaired=dict( argstr='--outputLandmarksPaired %s', hash_files=False, @@ -25,7 +22,7 @@ def test_landmarksConstellationAligner_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_landmarksConstellationAligner_outputs(): - output_map = dict(outputLandmarksPaired=dict(usedefault=True, ), ) + output_map = dict(outputLandmarksPaired=dict(), ) outputs = landmarksConstellationAligner.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py index afe12a43d3..0bcd747d36 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py @@ -5,23 +5,14 @@ def test_landmarksConstellationWeights_inputs(): input_map = dict( - LLSModel=dict( - argstr='--LLSModel %s', - usedefault=True, - ), + LLSModel=dict(argstr='--LLSModel %s', ), args=dict(argstr='%s', ), environ=dict( nohash=True, usedefault=True, ), - inputTemplateModel=dict( - argstr='--inputTemplateModel %s', - usedefault=True, - ), - inputTrainingList=dict( - argstr='--inputTrainingList %s', - usedefault=True, - ), + inputTemplateModel=dict(argstr='--inputTemplateModel %s', ), + inputTrainingList=dict(argstr='--inputTrainingList %s', ), outputWeightsList=dict( argstr='--outputWeightsList %s', hash_files=False, @@ -33,7 +24,7 @@ def test_landmarksConstellationWeights_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_landmarksConstellationWeights_outputs(): - output_map = dict(outputWeightsList=dict(usedefault=True, ), ) + output_map = dict(outputWeightsList=dict(), ) outputs = landmarksConstellationWeights.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py index 2f86ec6bdf..c8d5df2ba2 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py @@ -13,7 +13,6 @@ def test_DTIexport_inputs(): inputTensor=dict( argstr='%s', position=-2, - usedefault=True, ), outputFile=dict( argstr='%s', @@ -27,11 +26,7 @@ def test_DTIexport_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DTIexport_outputs(): - output_map = dict( - outputFile=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputFile=dict(position=-1, ), ) outputs = DTIexport.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py index 04381b63b4..ec1d66bc0b 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py @@ -13,7 +13,6 @@ def test_DTIimport_inputs(): inputFile=dict( argstr='%s', position=-2, - usedefault=True, ), outputTensor=dict( argstr='%s', @@ -28,11 +27,7 @@ def test_DTIimport_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DTIimport_outputs(): - output_map = dict( - outputTensor=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputTensor=dict(position=-1, ), ) outputs = DTIimport.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py index 99e13e5df2..a2caa2f633 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py @@ -14,7 +14,6 @@ def test_DWIJointRicianLMMSEFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), ng=dict(argstr='--ng %d', ), outputVolume=dict( @@ -37,11 +36,7 @@ def test_DWIJointRicianLMMSEFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWIJointRicianLMMSEFilter_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = DWIJointRicianLMMSEFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py index 64cc981a5c..7eff851562 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py @@ -15,7 +15,6 @@ def test_DWIRicianLMMSEFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), iter=dict(argstr='--iter %d', ), maxnstd=dict(argstr='--maxnstd %d', ), @@ -43,11 +42,7 @@ def test_DWIRicianLMMSEFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWIRicianLMMSEFilter_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = DWIRicianLMMSEFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py index 67cfdd61fc..217f91edf0 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py @@ -14,12 +14,8 @@ def test_DWIToDTIEstimation_inputs(): inputVolume=dict( argstr='%s', position=-3, - usedefault=True, - ), - mask=dict( - argstr='--mask %s', - usedefault=True, ), + mask=dict(argstr='--mask %s', ), outputBaseline=dict( argstr='%s', hash_files=False, @@ -39,14 +35,8 @@ def test_DWIToDTIEstimation_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DWIToDTIEstimation_outputs(): output_map = dict( - outputBaseline=dict( - position=-1, - usedefault=True, - ), - outputTensor=dict( - position=-2, - usedefault=True, - ), + outputBaseline=dict(position=-1, ), + outputTensor=dict(position=-2, ), ) outputs = DWIToDTIEstimation.output_spec() diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py index 5a7676b5c2..b75989c349 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py @@ -14,7 +14,6 @@ def test_DiffusionTensorScalarMeasurements_inputs(): inputVolume=dict( argstr='%s', position=-3, - usedefault=True, ), outputScalar=dict( argstr='%s', @@ -28,11 +27,7 @@ def test_DiffusionTensorScalarMeasurements_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DiffusionTensorScalarMeasurements_outputs(): - output_map = dict( - outputScalar=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputScalar=dict(position=-1, ), ) outputs = DiffusionTensorScalarMeasurements.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py index 56c18cf862..5e8c39a4ac 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py @@ -13,7 +13,6 @@ def test_DiffusionWeightedVolumeMasking_inputs(): inputVolume=dict( argstr='%s', position=-4, - usedefault=True, ), otsuomegathreshold=dict(argstr='--otsuomegathreshold %f', ), outputBaseline=dict( @@ -35,14 +34,8 @@ def test_DiffusionWeightedVolumeMasking_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DiffusionWeightedVolumeMasking_outputs(): output_map = dict( - outputBaseline=dict( - position=-2, - usedefault=True, - ), - thresholdMask=dict( - position=-1, - usedefault=True, - ), + outputBaseline=dict(position=-2, ), + thresholdMask=dict(position=-1, ), ) outputs = DiffusionWeightedVolumeMasking.output_spec() diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py index 2789f95aa6..30860d9da0 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py @@ -7,17 +7,11 @@ def test_ResampleDTIVolume_inputs(): input_map = dict( Inverse_ITK_Transformation=dict( argstr='--Inverse_ITK_Transformation ', ), - Reference=dict( - argstr='--Reference %s', - usedefault=True, - ), + Reference=dict(argstr='--Reference %s', ), args=dict(argstr='%s', ), centered_transform=dict(argstr='--centered_transform ', ), correction=dict(argstr='--correction %s', ), - defField=dict( - argstr='--defField %s', - usedefault=True, - ), + defField=dict(argstr='--defField %s', ), default_pixel_value=dict(argstr='--default_pixel_value %f', ), direction_matrix=dict( argstr='--direction_matrix %s', @@ -32,7 +26,6 @@ def test_ResampleDTIVolume_inputs(): inputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), interpolation=dict(argstr='--interpolation %s', ), notbulk=dict(argstr='--notbulk ', ), @@ -61,10 +54,7 @@ def test_ResampleDTIVolume_inputs(): ), transform_order=dict(argstr='--transform_order %s', ), transform_tensor_method=dict(argstr='--transform_tensor_method %s', ), - transformationFile=dict( - argstr='--transformationFile %s', - usedefault=True, - ), + transformationFile=dict(argstr='--transformationFile %s', ), window_function=dict(argstr='--window_function %s', ), ) inputs = ResampleDTIVolume.input_spec() @@ -73,11 +63,7 @@ def test_ResampleDTIVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ResampleDTIVolume_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = ResampleDTIVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py index 737e1cea44..31fb7d5c0d 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py @@ -8,7 +8,6 @@ def test_TractographyLabelMapSeeding_inputs(): InputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), OutputFibers=dict( argstr='%s', @@ -21,10 +20,7 @@ def test_TractographyLabelMapSeeding_inputs(): nohash=True, usedefault=True, ), - inputroi=dict( - argstr='--inputroi %s', - usedefault=True, - ), + inputroi=dict(argstr='--inputroi %s', ), integrationsteplength=dict(argstr='--integrationsteplength %f', ), label=dict(argstr='--label %d', ), maximumlength=dict(argstr='--maximumlength %f', ), @@ -49,11 +45,8 @@ def test_TractographyLabelMapSeeding_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_TractographyLabelMapSeeding_outputs(): output_map = dict( - OutputFibers=dict( - position=-1, - usedefault=True, - ), - outputdirectory=dict(usedefault=True, ), + OutputFibers=dict(position=-1, ), + outputdirectory=dict(), ) outputs = TractographyLabelMapSeeding.output_spec() diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py index 0f4dedb338..9f2209c1eb 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py @@ -13,12 +13,10 @@ def test_AddScalarVolumes_inputs(): inputVolume1=dict( argstr='%s', position=-3, - usedefault=True, ), inputVolume2=dict( argstr='%s', position=-2, - usedefault=True, ), order=dict(argstr='--order %s', ), outputVolume=dict( @@ -33,11 +31,7 @@ def test_AddScalarVolumes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_AddScalarVolumes_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = AddScalarVolumes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py index 265d763858..a659aa47f7 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py @@ -8,7 +8,6 @@ def test_CastScalarVolume_inputs(): InputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), OutputVolume=dict( argstr='%s', @@ -28,11 +27,7 @@ def test_CastScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CastScalarVolume_outputs(): - output_map = dict( - OutputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(OutputVolume=dict(position=-1, ), ) outputs = CastScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py index 7937c9b217..ae662cf2ba 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py @@ -17,12 +17,10 @@ def test_CheckerBoardFilter_inputs(): inputVolume1=dict( argstr='%s', position=-3, - usedefault=True, ), inputVolume2=dict( argstr='%s', position=-2, - usedefault=True, ), outputVolume=dict( argstr='%s', @@ -36,11 +34,7 @@ def test_CheckerBoardFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CheckerBoardFilter_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = CheckerBoardFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py index ae6aca11c0..5613eb0c4c 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py @@ -14,7 +14,6 @@ def test_CurvatureAnisotropicDiffusion_inputs(): inputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), iterations=dict(argstr='--iterations %d', ), outputVolume=dict( @@ -30,11 +29,7 @@ def test_CurvatureAnisotropicDiffusion_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CurvatureAnisotropicDiffusion_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = CurvatureAnisotropicDiffusion.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py index 924fcd5665..5db6c65c7e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py @@ -8,7 +8,6 @@ def test_ExtractSkeleton_inputs(): InputImageFileName=dict( argstr='%s', position=-2, - usedefault=True, ), OutputImageFileName=dict( argstr='%s', @@ -31,11 +30,7 @@ def test_ExtractSkeleton_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ExtractSkeleton_outputs(): - output_map = dict( - OutputImageFileName=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(OutputImageFileName=dict(position=-1, ), ) outputs = ExtractSkeleton.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py index d95490e3f8..ff46d6d308 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py @@ -13,7 +13,6 @@ def test_GaussianBlurImageFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), outputVolume=dict( argstr='%s', @@ -28,11 +27,7 @@ def test_GaussianBlurImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GaussianBlurImageFilter_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = GaussianBlurImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py index 0cda5dfa38..8ec7dbb156 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py @@ -14,7 +14,6 @@ def test_GradientAnisotropicDiffusion_inputs(): inputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), iterations=dict(argstr='--iterations %d', ), outputVolume=dict( @@ -30,11 +29,7 @@ def test_GradientAnisotropicDiffusion_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GradientAnisotropicDiffusion_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = GradientAnisotropicDiffusion.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py index 6565bb7b21..062a23c293 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py @@ -13,7 +13,6 @@ def test_GrayscaleFillHoleImageFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), outputVolume=dict( argstr='%s', @@ -27,11 +26,7 @@ def test_GrayscaleFillHoleImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GrayscaleFillHoleImageFilter_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = GrayscaleFillHoleImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py index a05db51667..edb6081ed3 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py @@ -13,7 +13,6 @@ def test_GrayscaleGrindPeakImageFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), outputVolume=dict( argstr='%s', @@ -27,11 +26,7 @@ def test_GrayscaleGrindPeakImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GrayscaleGrindPeakImageFilter_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = GrayscaleGrindPeakImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py index 8423192ff0..f73690586d 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py @@ -13,7 +13,6 @@ def test_HistogramMatching_inputs(): inputVolume=dict( argstr='%s', position=-3, - usedefault=True, ), numberOfHistogramLevels=dict(argstr='--numberOfHistogramLevels %d', ), numberOfMatchPoints=dict(argstr='--numberOfMatchPoints %d', ), @@ -25,7 +24,6 @@ def test_HistogramMatching_inputs(): referenceVolume=dict( argstr='%s', position=-2, - usedefault=True, ), threshold=dict(argstr='--threshold ', ), ) @@ -35,11 +33,7 @@ def test_HistogramMatching_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_HistogramMatching_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = HistogramMatching.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py index 90f0bf1df4..0bae22c342 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py @@ -8,12 +8,10 @@ def test_ImageLabelCombine_inputs(): InputLabelMap_A=dict( argstr='%s', position=-3, - usedefault=True, ), InputLabelMap_B=dict( argstr='%s', position=-2, - usedefault=True, ), OutputLabelMap=dict( argstr='%s', @@ -33,11 +31,7 @@ def test_ImageLabelCombine_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ImageLabelCombine_outputs(): - output_map = dict( - OutputLabelMap=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(OutputLabelMap=dict(position=-1, ), ) outputs = ImageLabelCombine.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py index 6af542ced3..cd04072890 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py @@ -8,12 +8,10 @@ def test_MaskScalarVolume_inputs(): InputVolume=dict( argstr='%s', position=-3, - usedefault=True, ), MaskVolume=dict( argstr='%s', position=-2, - usedefault=True, ), OutputVolume=dict( argstr='%s', @@ -34,11 +32,7 @@ def test_MaskScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MaskScalarVolume_outputs(): - output_map = dict( - OutputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(OutputVolume=dict(position=-1, ), ) outputs = MaskScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py index 14e8404ac5..35bb9496c9 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py @@ -13,7 +13,6 @@ def test_MedianImageFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), neighborhood=dict( argstr='--neighborhood %s', @@ -31,11 +30,7 @@ def test_MedianImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MedianImageFilter_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = MedianImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py index 8d442e83ca..6590c4b133 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py @@ -13,12 +13,10 @@ def test_MultiplyScalarVolumes_inputs(): inputVolume1=dict( argstr='%s', position=-3, - usedefault=True, ), inputVolume2=dict( argstr='%s', position=-2, - usedefault=True, ), order=dict(argstr='--order %s', ), outputVolume=dict( @@ -33,11 +31,7 @@ def test_MultiplyScalarVolumes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MultiplyScalarVolumes_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = MultiplyScalarVolumes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py index 74a7e497a5..c6ad0bf24d 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py @@ -16,18 +16,12 @@ def test_N4ITKBiasFieldCorrection_inputs(): argstr='--histogramsharpening %s', sep=',', ), - inputimage=dict( - argstr='--inputimage %s', - usedefault=True, - ), + inputimage=dict(argstr='--inputimage %s', ), iterations=dict( argstr='--iterations %s', sep=',', ), - maskimage=dict( - argstr='--maskimage %s', - usedefault=True, - ), + maskimage=dict(argstr='--maskimage %s', ), meshresolution=dict( argstr='--meshresolution %s', sep=',', @@ -42,10 +36,7 @@ def test_N4ITKBiasFieldCorrection_inputs(): ), shrinkfactor=dict(argstr='--shrinkfactor %d', ), splinedistance=dict(argstr='--splinedistance %f', ), - weightimage=dict( - argstr='--weightimage %s', - usedefault=True, - ), + weightimage=dict(argstr='--weightimage %s', ), ) inputs = N4ITKBiasFieldCorrection.input_spec() @@ -54,8 +45,8 @@ def test_N4ITKBiasFieldCorrection_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_N4ITKBiasFieldCorrection_outputs(): output_map = dict( - outputbiasfield=dict(usedefault=True, ), - outputimage=dict(usedefault=True, ), + outputbiasfield=dict(), + outputimage=dict(), ) outputs = N4ITKBiasFieldCorrection.output_spec() diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py index 589feab548..ebe34fd9b3 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py @@ -7,16 +7,10 @@ def test_ResampleScalarVectorDWIVolume_inputs(): input_map = dict( Inverse_ITK_Transformation=dict( argstr='--Inverse_ITK_Transformation ', ), - Reference=dict( - argstr='--Reference %s', - usedefault=True, - ), + Reference=dict(argstr='--Reference %s', ), args=dict(argstr='%s', ), centered_transform=dict(argstr='--centered_transform ', ), - defField=dict( - argstr='--defField %s', - usedefault=True, - ), + defField=dict(argstr='--defField %s', ), default_pixel_value=dict(argstr='--default_pixel_value %f', ), direction_matrix=dict( argstr='--direction_matrix %s', @@ -31,7 +25,6 @@ def test_ResampleScalarVectorDWIVolume_inputs(): inputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), interpolation=dict(argstr='--interpolation %s', ), notbulk=dict(argstr='--notbulk ', ), @@ -59,10 +52,7 @@ def test_ResampleScalarVectorDWIVolume_inputs(): sep=',', ), transform_order=dict(argstr='--transform_order %s', ), - transformationFile=dict( - argstr='--transformationFile %s', - usedefault=True, - ), + transformationFile=dict(argstr='--transformationFile %s', ), window_function=dict(argstr='--window_function %s', ), ) inputs = ResampleScalarVectorDWIVolume.input_spec() @@ -71,11 +61,7 @@ def test_ResampleScalarVectorDWIVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ResampleScalarVectorDWIVolume_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = ResampleScalarVectorDWIVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py index 49614c4383..d62589881f 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py @@ -13,12 +13,10 @@ def test_SubtractScalarVolumes_inputs(): inputVolume1=dict( argstr='%s', position=-3, - usedefault=True, ), inputVolume2=dict( argstr='%s', position=-2, - usedefault=True, ), order=dict(argstr='--order %s', ), outputVolume=dict( @@ -33,11 +31,7 @@ def test_SubtractScalarVolumes_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SubtractScalarVolumes_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = SubtractScalarVolumes.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py index adb89adc9a..34de317104 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py @@ -8,7 +8,6 @@ def test_ThresholdScalarVolume_inputs(): InputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), OutputVolume=dict( argstr='%s', @@ -32,11 +31,7 @@ def test_ThresholdScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ThresholdScalarVolume_outputs(): - output_map = dict( - OutputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(OutputVolume=dict(position=-1, ), ) outputs = ThresholdScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py index 0be5e18f93..8e7890de85 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py @@ -15,7 +15,6 @@ def test_VotingBinaryHoleFillingImageFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), majorityThreshold=dict(argstr='--majorityThreshold %d', ), outputVolume=dict( @@ -34,11 +33,7 @@ def test_VotingBinaryHoleFillingImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_VotingBinaryHoleFillingImageFilter_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = VotingBinaryHoleFillingImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py index a25de38c5d..0e25ffad9a 100644 --- a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py +++ b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py @@ -14,7 +14,6 @@ def test_DWIUnbiasedNonLocalMeansFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), ng=dict(argstr='--ng %d', ), outputVolume=dict( @@ -41,11 +40,7 @@ def test_DWIUnbiasedNonLocalMeansFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DWIUnbiasedNonLocalMeansFilter_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = DWIUnbiasedNonLocalMeansFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py index df91b32b72..949cdc7f61 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py @@ -8,12 +8,10 @@ def test_AffineRegistration_inputs(): FixedImageFileName=dict( argstr='%s', position=-2, - usedefault=True, ), MovingImageFileName=dict( argstr='%s', position=-1, - usedefault=True, ), args=dict(argstr='%s', ), environ=dict( @@ -22,10 +20,7 @@ def test_AffineRegistration_inputs(): ), fixedsmoothingfactor=dict(argstr='--fixedsmoothingfactor %d', ), histogrambins=dict(argstr='--histogrambins %d', ), - initialtransform=dict( - argstr='--initialtransform %s', - usedefault=True, - ), + initialtransform=dict(argstr='--initialtransform %s', ), iterations=dict(argstr='--iterations %d', ), movingsmoothingfactor=dict(argstr='--movingsmoothingfactor %d', ), outputtransform=dict( @@ -46,8 +41,8 @@ def test_AffineRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_AffineRegistration_outputs(): output_map = dict( - outputtransform=dict(usedefault=True, ), - resampledmovingfilename=dict(usedefault=True, ), + outputtransform=dict(), + resampledmovingfilename=dict(), ) outputs = AffineRegistration.output_spec() diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py index a7a780110d..17339f8859 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py @@ -8,12 +8,10 @@ def test_BSplineDeformableRegistration_inputs(): FixedImageFileName=dict( argstr='%s', position=-2, - usedefault=True, ), MovingImageFileName=dict( argstr='%s', position=-1, - usedefault=True, ), args=dict(argstr='%s', ), constrain=dict(argstr='--constrain ', ), @@ -24,10 +22,7 @@ def test_BSplineDeformableRegistration_inputs(): ), gridSize=dict(argstr='--gridSize %d', ), histogrambins=dict(argstr='--histogrambins %d', ), - initialtransform=dict( - argstr='--initialtransform %s', - usedefault=True, - ), + initialtransform=dict(argstr='--initialtransform %s', ), iterations=dict(argstr='--iterations %d', ), maximumDeformation=dict(argstr='--maximumDeformation %f', ), outputtransform=dict( @@ -51,9 +46,9 @@ def test_BSplineDeformableRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BSplineDeformableRegistration_outputs(): output_map = dict( - outputtransform=dict(usedefault=True, ), - outputwarp=dict(usedefault=True, ), - resampledmovingfilename=dict(usedefault=True, ), + outputtransform=dict(), + outputwarp=dict(), + resampledmovingfilename=dict(), ) outputs = BSplineDeformableRegistration.output_spec() diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py index 14742b11f3..8335515c13 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py @@ -14,14 +14,8 @@ def test_BSplineToDeformationField_inputs(): nohash=True, usedefault=True, ), - refImage=dict( - argstr='--refImage %s', - usedefault=True, - ), - tfm=dict( - argstr='--tfm %s', - usedefault=True, - ), + refImage=dict(argstr='--refImage %s', ), + tfm=dict(argstr='--tfm %s', ), ) inputs = BSplineToDeformationField.input_spec() @@ -29,7 +23,7 @@ def test_BSplineToDeformationField_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BSplineToDeformationField_outputs(): - output_map = dict(defImage=dict(usedefault=True, ), ) + output_map = dict(defImage=dict(), ) outputs = BSplineToDeformationField.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py index 916a96119d..7fa8b77d63 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py @@ -22,25 +22,17 @@ def test_ExpertAutomatedRegistration_inputs(): fixedImage=dict( argstr='%s', position=-2, - usedefault=True, - ), - fixedImageMask=dict( - argstr='--fixedImageMask %s', - usedefault=True, ), + fixedImageMask=dict(argstr='--fixedImageMask %s', ), fixedLandmarks=dict(argstr='--fixedLandmarks %s...', ), initialization=dict(argstr='--initialization %s', ), interpolation=dict(argstr='--interpolation %s', ), - loadTransform=dict( - argstr='--loadTransform %s', - usedefault=True, - ), + loadTransform=dict(argstr='--loadTransform %s', ), metric=dict(argstr='--metric %s', ), minimizeMemory=dict(argstr='--minimizeMemory ', ), movingImage=dict( argstr='%s', position=-1, - usedefault=True, ), movingLandmarks=dict(argstr='--movingLandmarks %s...', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -66,8 +58,8 @@ def test_ExpertAutomatedRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_ExpertAutomatedRegistration_outputs(): output_map = dict( - resampledImage=dict(usedefault=True, ), - saveTransform=dict(usedefault=True, ), + resampledImage=dict(), + saveTransform=dict(), ) outputs = ExpertAutomatedRegistration.output_spec() diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py index cd1bf18500..a55432f9b0 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py @@ -8,12 +8,10 @@ def test_LinearRegistration_inputs(): FixedImageFileName=dict( argstr='%s', position=-2, - usedefault=True, ), MovingImageFileName=dict( argstr='%s', position=-1, - usedefault=True, ), args=dict(argstr='%s', ), environ=dict( @@ -22,10 +20,7 @@ def test_LinearRegistration_inputs(): ), fixedsmoothingfactor=dict(argstr='--fixedsmoothingfactor %d', ), histogrambins=dict(argstr='--histogrambins %d', ), - initialtransform=dict( - argstr='--initialtransform %s', - usedefault=True, - ), + initialtransform=dict(argstr='--initialtransform %s', ), iterations=dict( argstr='--iterations %s', sep=',', @@ -53,8 +48,8 @@ def test_LinearRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_LinearRegistration_outputs(): output_map = dict( - outputtransform=dict(usedefault=True, ), - resampledmovingfilename=dict(usedefault=True, ), + outputtransform=dict(), + resampledmovingfilename=dict(), ) outputs = LinearRegistration.output_spec() diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py index 0461f6a91a..7903fd1d5c 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py @@ -13,18 +13,13 @@ def test_MultiResolutionAffineRegistration_inputs(): fixedImage=dict( argstr='%s', position=-2, - usedefault=True, - ), - fixedImageMask=dict( - argstr='--fixedImageMask %s', - usedefault=True, ), + fixedImageMask=dict(argstr='--fixedImageMask %s', ), fixedImageROI=dict(argstr='--fixedImageROI %s', ), metricTolerance=dict(argstr='--metricTolerance %f', ), movingImage=dict( argstr='%s', position=-1, - usedefault=True, ), numIterations=dict(argstr='--numIterations %d', ), numLineIterations=dict(argstr='--numLineIterations %d', ), @@ -46,8 +41,8 @@ def test_MultiResolutionAffineRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MultiResolutionAffineRegistration_outputs(): output_map = dict( - resampledImage=dict(usedefault=True, ), - saveTransform=dict(usedefault=True, ), + resampledImage=dict(), + saveTransform=dict(), ) outputs = MultiResolutionAffineRegistration.output_spec() diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py index b1ae9800fe..a1af6c71b3 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py @@ -13,7 +13,6 @@ def test_OtsuThresholdImageFilter_inputs(): inputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), insideValue=dict(argstr='--insideValue %d', ), numberOfBins=dict(argstr='--numberOfBins %d', ), @@ -30,11 +29,7 @@ def test_OtsuThresholdImageFilter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OtsuThresholdImageFilter_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = OtsuThresholdImageFilter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py index 87178c9f27..02beeee464 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py @@ -15,7 +15,6 @@ def test_OtsuThresholdSegmentation_inputs(): inputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), minimumObjectSize=dict(argstr='--minimumObjectSize %d', ), numberOfBins=dict(argstr='--numberOfBins %d', ), @@ -31,11 +30,7 @@ def test_OtsuThresholdSegmentation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OtsuThresholdSegmentation_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = OtsuThresholdSegmentation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py index 0210093054..baa698246c 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py @@ -8,7 +8,6 @@ def test_ResampleScalarVolume_inputs(): InputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), OutputVolume=dict( argstr='%s', @@ -32,11 +31,7 @@ def test_ResampleScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ResampleScalarVolume_outputs(): - output_map = dict( - OutputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(OutputVolume=dict(position=-1, ), ) outputs = ResampleScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py index c77095ae3e..6c2a0eb072 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py @@ -8,12 +8,10 @@ def test_RigidRegistration_inputs(): FixedImageFileName=dict( argstr='%s', position=-2, - usedefault=True, ), MovingImageFileName=dict( argstr='%s', position=-1, - usedefault=True, ), args=dict(argstr='%s', ), environ=dict( @@ -22,10 +20,7 @@ def test_RigidRegistration_inputs(): ), fixedsmoothingfactor=dict(argstr='--fixedsmoothingfactor %d', ), histogrambins=dict(argstr='--histogrambins %d', ), - initialtransform=dict( - argstr='--initialtransform %s', - usedefault=True, - ), + initialtransform=dict(argstr='--initialtransform %s', ), iterations=dict( argstr='--iterations %s', sep=',', @@ -54,8 +49,8 @@ def test_RigidRegistration_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RigidRegistration_outputs(): output_map = dict( - outputtransform=dict(usedefault=True, ), - resampledmovingfilename=dict(usedefault=True, ), + outputtransform=dict(), + resampledmovingfilename=dict(), ) outputs = RigidRegistration.output_spec() diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py index 2353b8fecd..e46f046add 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py @@ -9,12 +9,10 @@ def test_IntensityDifferenceMetric_inputs(): baselineSegmentationVolume=dict( argstr='%s', position=-3, - usedefault=True, ), baselineVolume=dict( argstr='%s', position=-4, - usedefault=True, ), changingBandSize=dict(argstr='--changingBandSize %d', ), environ=dict( @@ -24,7 +22,6 @@ def test_IntensityDifferenceMetric_inputs(): followupVolume=dict( argstr='%s', position=-2, - usedefault=True, ), outputVolume=dict( argstr='%s', @@ -44,11 +41,8 @@ def test_IntensityDifferenceMetric_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_IntensityDifferenceMetric_outputs(): output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), - reportFileName=dict(usedefault=True, ), + outputVolume=dict(position=-1, ), + reportFileName=dict(), ) outputs = IntensityDifferenceMetric.output_spec() diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py index 314edc7dd8..61141f65db 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py @@ -11,10 +11,7 @@ def test_PETStandardUptakeValueComputation_inputs(): SUVMean=dict(argstr='--SUVMean %s', ), SUVMin=dict(argstr='--SUVMin %s', ), args=dict(argstr='%s', ), - color=dict( - argstr='--color %s', - usedefault=True, - ), + color=dict(argstr='--color %s', ), csvFile=dict( argstr='--csvFile %s', hash_files=False, @@ -23,18 +20,9 @@ def test_PETStandardUptakeValueComputation_inputs(): nohash=True, usedefault=True, ), - labelMap=dict( - argstr='--labelMap %s', - usedefault=True, - ), - petDICOMPath=dict( - argstr='--petDICOMPath %s', - usedefault=True, - ), - petVolume=dict( - argstr='--petVolume %s', - usedefault=True, - ), + labelMap=dict(argstr='--labelMap %s', ), + petDICOMPath=dict(argstr='--petDICOMPath %s', ), + petVolume=dict(argstr='--petVolume %s', ), ) inputs = PETStandardUptakeValueComputation.input_spec() @@ -42,7 +30,7 @@ def test_PETStandardUptakeValueComputation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PETStandardUptakeValueComputation_outputs(): - output_map = dict(csvFile=dict(usedefault=True, ), ) + output_map = dict(csvFile=dict(), ) outputs = PETStandardUptakeValueComputation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py index d9b331cb34..454e290102 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py @@ -24,7 +24,7 @@ def test_ACPCTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ACPCTransform_outputs(): - output_map = dict(outputTransform=dict(usedefault=True, ), ) + output_map = dict(outputTransform=dict(), ) outputs = ACPCTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py index 5ac8f5f353..c631f9b96e 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py @@ -19,25 +19,14 @@ def test_BRAINSDemonWarp_inputs(): nohash=True, usedefault=True, ), - fixedBinaryVolume=dict( - argstr='--fixedBinaryVolume %s', - usedefault=True, - ), - fixedVolume=dict( - argstr='--fixedVolume %s', - usedefault=True, - ), + fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), + fixedVolume=dict(argstr='--fixedVolume %s', ), gradient_type=dict(argstr='--gradient_type %s', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), initializeWithDisplacementField=dict( - argstr='--initializeWithDisplacementField %s', - usedefault=True, - ), - initializeWithTransform=dict( - argstr='--initializeWithTransform %s', - usedefault=True, - ), + argstr='--initializeWithDisplacementField %s', ), + initializeWithTransform=dict(argstr='--initializeWithTransform %s', ), inputPixelType=dict(argstr='--inputPixelType %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), lowerThresholdForBOBF=dict(argstr='--lowerThresholdForBOBF %d', ), @@ -55,14 +44,8 @@ def test_BRAINSDemonWarp_inputs(): argstr='--minimumMovingPyramid %s', sep=',', ), - movingBinaryVolume=dict( - argstr='--movingBinaryVolume %s', - usedefault=True, - ), - movingVolume=dict( - argstr='--movingVolume %s', - usedefault=True, - ), + movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), + movingVolume=dict(argstr='--movingVolume %s', ), neighborhoodForBOBF=dict( argstr='--neighborhoodForBOBF %s', sep=',', @@ -109,9 +92,9 @@ def test_BRAINSDemonWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSDemonWarp_outputs(): output_map = dict( - outputCheckerboardVolume=dict(usedefault=True, ), - outputDisplacementFieldVolume=dict(usedefault=True, ), - outputVolume=dict(usedefault=True, ), + outputCheckerboardVolume=dict(), + outputDisplacementFieldVolume=dict(), + outputVolume=dict(), ) outputs = BRAINSDemonWarp.output_spec() diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py index 679ab82bf7..bb62633d94 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py @@ -28,22 +28,13 @@ def test_BRAINSFit_inputs(): usedefault=True, ), failureExitCode=dict(argstr='--failureExitCode %d', ), - fixedBinaryVolume=dict( - argstr='--fixedBinaryVolume %s', - usedefault=True, - ), - fixedVolume=dict( - argstr='--fixedVolume %s', - usedefault=True, - ), + fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), + fixedVolume=dict(argstr='--fixedVolume %s', ), fixedVolumeTimeIndex=dict(argstr='--fixedVolumeTimeIndex %d', ), forceMINumberOfThreads=dict(argstr='--forceMINumberOfThreads %d', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), - initialTransform=dict( - argstr='--initialTransform %s', - usedefault=True, - ), + initialTransform=dict(argstr='--initialTransform %s', ), initializeTransformMode=dict(argstr='--initializeTransformMode %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), linearTransform=dict( @@ -63,14 +54,8 @@ def test_BRAINSFit_inputs(): argstr='--minimumStepLength %s', sep=',', ), - movingBinaryVolume=dict( - argstr='--movingBinaryVolume %s', - usedefault=True, - ), - movingVolume=dict( - argstr='--movingVolume %s', - usedefault=True, - ), + movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), + movingVolume=dict(argstr='--movingVolume %s', ), movingVolumeTimeIndex=dict(argstr='--movingVolumeTimeIndex %d', ), numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', ), numberOfIterations=dict( @@ -142,13 +127,13 @@ def test_BRAINSFit_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSFit_outputs(): output_map = dict( - bsplineTransform=dict(usedefault=True, ), - linearTransform=dict(usedefault=True, ), - outputFixedVolumeROI=dict(usedefault=True, ), - outputMovingVolumeROI=dict(usedefault=True, ), - outputTransform=dict(usedefault=True, ), - outputVolume=dict(usedefault=True, ), - strippedOutputTransform=dict(usedefault=True, ), + bsplineTransform=dict(), + linearTransform=dict(), + outputFixedVolumeROI=dict(), + outputMovingVolumeROI=dict(), + outputTransform=dict(), + outputVolume=dict(), + strippedOutputTransform=dict(), ) outputs = BRAINSFit.output_spec() diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py index 38758ac585..98ec5f4ff3 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py @@ -7,10 +7,7 @@ def test_BRAINSResample_inputs(): input_map = dict( args=dict(argstr='%s', ), defaultValue=dict(argstr='--defaultValue %f', ), - deformationVolume=dict( - argstr='--deformationVolume %s', - usedefault=True, - ), + deformationVolume=dict(argstr='--deformationVolume %s', ), environ=dict( nohash=True, usedefault=True, @@ -19,10 +16,7 @@ def test_BRAINSResample_inputs(): argstr='--gridSpacing %s', sep=',', ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), inverseTransform=dict(argstr='--inverseTransform ', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), @@ -31,14 +25,8 @@ def test_BRAINSResample_inputs(): hash_files=False, ), pixelType=dict(argstr='--pixelType %s', ), - referenceVolume=dict( - argstr='--referenceVolume %s', - usedefault=True, - ), - warpTransform=dict( - argstr='--warpTransform %s', - usedefault=True, - ), + referenceVolume=dict(argstr='--referenceVolume %s', ), + warpTransform=dict(argstr='--warpTransform %s', ), ) inputs = BRAINSResample.input_spec() @@ -46,7 +34,7 @@ def test_BRAINSResample_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSResample_outputs(): - output_map = dict(outputVolume=dict(usedefault=True, ), ) + output_map = dict(outputVolume=dict(), ) outputs = BRAINSResample.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py index a4ae5f1b6f..36d42fe8df 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py @@ -26,7 +26,7 @@ def test_FiducialRegistration_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FiducialRegistration_outputs(): - output_map = dict(saveTransform=dict(usedefault=True, ), ) + output_map = dict(saveTransform=dict(), ) outputs = FiducialRegistration.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py index 17d6d7715d..b3255da1d3 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -19,22 +19,14 @@ def test_VBRAINSDemonWarp_inputs(): nohash=True, usedefault=True, ), - fixedBinaryVolume=dict( - argstr='--fixedBinaryVolume %s', - usedefault=True, - ), + fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), fixedVolume=dict(argstr='--fixedVolume %s...', ), gradient_type=dict(argstr='--gradient_type %s', ), gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), initializeWithDisplacementField=dict( - argstr='--initializeWithDisplacementField %s', - usedefault=True, - ), - initializeWithTransform=dict( - argstr='--initializeWithTransform %s', - usedefault=True, - ), + argstr='--initializeWithDisplacementField %s', ), + initializeWithTransform=dict(argstr='--initializeWithTransform %s', ), inputPixelType=dict(argstr='--inputPixelType %s', ), interpolationMode=dict(argstr='--interpolationMode %s', ), lowerThresholdForBOBF=dict(argstr='--lowerThresholdForBOBF %d', ), @@ -52,10 +44,7 @@ def test_VBRAINSDemonWarp_inputs(): argstr='--minimumMovingPyramid %s', sep=',', ), - movingBinaryVolume=dict( - argstr='--movingBinaryVolume %s', - usedefault=True, - ), + movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), movingVolume=dict(argstr='--movingVolume %s...', ), neighborhoodForBOBF=dict( argstr='--neighborhoodForBOBF %s', @@ -107,9 +96,9 @@ def test_VBRAINSDemonWarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_VBRAINSDemonWarp_outputs(): output_map = dict( - outputCheckerboardVolume=dict(usedefault=True, ), - outputDisplacementFieldVolume=dict(usedefault=True, ), - outputVolume=dict(usedefault=True, ), + outputCheckerboardVolume=dict(), + outputDisplacementFieldVolume=dict(), + outputVolume=dict(), ) outputs = VBRAINSDemonWarp.output_spec() diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py index 1f990681d0..89863fb730 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -12,10 +12,7 @@ def test_BRAINSROIAuto_inputs(): nohash=True, usedefault=True, ), - inputVolume=dict( - argstr='--inputVolume %s', - usedefault=True, - ), + inputVolume=dict(argstr='--inputVolume %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), otsuPercentileThreshold=dict(argstr='--otsuPercentileThreshold %f', ), outputClippedVolumeROI=dict( @@ -37,8 +34,8 @@ def test_BRAINSROIAuto_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSROIAuto_outputs(): output_map = dict( - outputClippedVolumeROI=dict(usedefault=True, ), - outputROIMaskVolume=dict(usedefault=True, ), + outputClippedVolumeROI=dict(), + outputROIMaskVolume=dict(), ) outputs = BRAINSROIAuto.output_spec() diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py index f47dceaeb9..09b0b1300f 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py @@ -21,16 +21,11 @@ def test_EMSegmentCommandLine_inputs(): hash_files=False, ), intermediateResultsDirectory=dict( - argstr='--intermediateResultsDirectory %s', - usedefault=True, - ), + argstr='--intermediateResultsDirectory %s', ), keepTempFiles=dict(argstr='--keepTempFiles ', ), loadAtlasNonCentered=dict(argstr='--loadAtlasNonCentered ', ), loadTargetCentered=dict(argstr='--loadTargetCentered ', ), - mrmlSceneFileName=dict( - argstr='--mrmlSceneFileName %s', - usedefault=True, - ), + mrmlSceneFileName=dict(argstr='--mrmlSceneFileName %s', ), parametersMRMLNodeName=dict(argstr='--parametersMRMLNodeName %s', ), registrationAffineType=dict(argstr='--registrationAffineType %d', ), registrationDeformableType=dict( @@ -41,9 +36,7 @@ def test_EMSegmentCommandLine_inputs(): hash_files=False, ), resultStandardVolumeFileName=dict( - argstr='--resultStandardVolumeFileName %s', - usedefault=True, - ), + argstr='--resultStandardVolumeFileName %s', ), resultVolumeFileName=dict( argstr='--resultVolumeFileName %s', hash_files=False, @@ -60,9 +53,9 @@ def test_EMSegmentCommandLine_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_EMSegmentCommandLine_outputs(): output_map = dict( - generateEmptyMRMLSceneAndQuit=dict(usedefault=True, ), - resultMRMLSceneFileName=dict(usedefault=True, ), - resultVolumeFileName=dict(usedefault=True, ), + generateEmptyMRMLSceneAndQuit=dict(), + resultMRMLSceneFileName=dict(), + resultVolumeFileName=dict(), ) outputs = EMSegmentCommandLine.output_spec() diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py index 51a38cdb53..ed46177df0 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py @@ -16,14 +16,12 @@ def test_RobustStatisticsSegmenter_inputs(): labelImageFileName=dict( argstr='%s', position=-2, - usedefault=True, ), labelValue=dict(argstr='--labelValue %d', ), maxRunningTime=dict(argstr='--maxRunningTime %f', ), originalImageFileName=dict( argstr='%s', position=-3, - usedefault=True, ), segmentedImageFileName=dict( argstr='%s', @@ -37,11 +35,7 @@ def test_RobustStatisticsSegmenter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_RobustStatisticsSegmenter_outputs(): - output_map = dict( - segmentedImageFileName=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(segmentedImageFileName=dict(position=-1, ), ) outputs = RobustStatisticsSegmenter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py index 1d9792fdaf..3c5e2124d0 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py @@ -13,7 +13,6 @@ def test_SimpleRegionGrowingSegmentation_inputs(): inputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), iterations=dict(argstr='--iterations %d', ), labelvalue=dict(argstr='--labelvalue %d', ), @@ -34,11 +33,7 @@ def test_SimpleRegionGrowingSegmentation_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SimpleRegionGrowingSegmentation_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = SimpleRegionGrowingSegmentation.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py index 6f01502c60..2997e805f9 100644 --- a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py +++ b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py @@ -10,10 +10,7 @@ def test_DicomToNrrdConverter_inputs(): nohash=True, usedefault=True, ), - inputDicomDirectory=dict( - argstr='--inputDicomDirectory %s', - usedefault=True, - ), + inputDicomDirectory=dict(argstr='--inputDicomDirectory %s', ), outputDirectory=dict( argstr='--outputDirectory %s', hash_files=False, @@ -33,7 +30,7 @@ def test_DicomToNrrdConverter_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DicomToNrrdConverter_outputs(): - output_map = dict(outputDirectory=dict(usedefault=True, ), ) + output_map = dict(outputDirectory=dict(), ) outputs = DicomToNrrdConverter.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py index 2713754c67..279d68e0ab 100644 --- a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py +++ b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py @@ -10,10 +10,7 @@ def test_EMSegmentTransformToNewFormat_inputs(): nohash=True, usedefault=True, ), - inputMRMLFileName=dict( - argstr='--inputMRMLFileName %s', - usedefault=True, - ), + inputMRMLFileName=dict(argstr='--inputMRMLFileName %s', ), outputMRMLFileName=dict( argstr='--outputMRMLFileName %s', hash_files=False, @@ -26,7 +23,7 @@ def test_EMSegmentTransformToNewFormat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_EMSegmentTransformToNewFormat_outputs(): - output_map = dict(outputMRMLFileName=dict(usedefault=True, ), ) + output_map = dict(outputMRMLFileName=dict(), ) outputs = EMSegmentTransformToNewFormat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py index 5722b10fc4..7ad8cac8e9 100644 --- a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py @@ -8,7 +8,6 @@ def test_GrayscaleModelMaker_inputs(): InputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), OutputGeometry=dict( argstr='%s', @@ -33,11 +32,7 @@ def test_GrayscaleModelMaker_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_GrayscaleModelMaker_outputs(): - output_map = dict( - OutputGeometry=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(OutputGeometry=dict(position=-1, ), ) outputs = GrayscaleModelMaker.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py index 918569a017..bb3780495b 100644 --- a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py +++ b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py @@ -14,7 +14,6 @@ def test_LabelMapSmoothing_inputs(): inputVolume=dict( argstr='%s', position=-2, - usedefault=True, ), labelToSmooth=dict(argstr='--labelToSmooth %d', ), maxRMSError=dict(argstr='--maxRMSError %f', ), @@ -31,11 +30,7 @@ def test_LabelMapSmoothing_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_LabelMapSmoothing_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = LabelMapSmoothing.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py index eb982af412..6453957a79 100644 --- a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py +++ b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py @@ -8,12 +8,10 @@ def test_MergeModels_inputs(): Model1=dict( argstr='%s', position=-3, - usedefault=True, ), Model2=dict( argstr='%s', position=-2, - usedefault=True, ), ModelOutput=dict( argstr='%s', @@ -32,11 +30,7 @@ def test_MergeModels_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MergeModels_outputs(): - output_map = dict( - ModelOutput=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(ModelOutput=dict(position=-1, ), ) outputs = MergeModels.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py index 1a7b9400e3..ed182137cf 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py @@ -8,13 +8,9 @@ def test_ModelMaker_inputs(): InputVolume=dict( argstr='%s', position=-1, - usedefault=True, ), args=dict(argstr='%s', ), - color=dict( - argstr='--color %s', - usedefault=True, - ), + color=dict(argstr='--color %s', ), debug=dict(argstr='--debug ', ), decimate=dict(argstr='--decimate %f', ), end=dict(argstr='--end %d', ), diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py index 5c7db905d8..efd11f1040 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py @@ -8,7 +8,6 @@ def test_ModelToLabelMap_inputs(): InputVolume=dict( argstr='%s', position=-3, - usedefault=True, ), OutputVolume=dict( argstr='%s', @@ -24,7 +23,6 @@ def test_ModelToLabelMap_inputs(): surface=dict( argstr='%s', position=-2, - usedefault=True, ), ) inputs = ModelToLabelMap.input_spec() @@ -33,11 +31,7 @@ def test_ModelToLabelMap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ModelToLabelMap_outputs(): - output_map = dict( - OutputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(OutputVolume=dict(position=-1, ), ) outputs = ModelToLabelMap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py index d30db9f888..f3d1908cd0 100644 --- a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py +++ b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py @@ -13,7 +13,6 @@ def test_OrientScalarVolume_inputs(): inputVolume1=dict( argstr='%s', position=-2, - usedefault=True, ), orientation=dict(argstr='--orientation %s', ), outputVolume=dict( @@ -28,11 +27,7 @@ def test_OrientScalarVolume_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OrientScalarVolume_outputs(): - output_map = dict( - outputVolume=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(outputVolume=dict(position=-1, ), ) outputs = OrientScalarVolume.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py index ad86ef55a1..32a2fc2139 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py +++ b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py @@ -8,12 +8,10 @@ def test_ProbeVolumeWithModel_inputs(): InputModel=dict( argstr='%s', position=-2, - usedefault=True, ), InputVolume=dict( argstr='%s', position=-3, - usedefault=True, ), OutputModel=dict( argstr='%s', @@ -32,11 +30,7 @@ def test_ProbeVolumeWithModel_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ProbeVolumeWithModel_outputs(): - output_map = dict( - OutputModel=dict( - position=-1, - usedefault=True, - ), ) + output_map = dict(OutputModel=dict(position=-1, ), ) outputs = ProbeVolumeWithModel.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py index fe8b6c4634..1b1aa6edcd 100644 --- a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py +++ b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py @@ -5,10 +5,7 @@ def test_Analyze2nii_inputs(): input_map = dict( - analyze_file=dict( - mandatory=True, - usedefault=True, - ), + analyze_file=dict(mandatory=True, ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), paths=dict(), @@ -27,7 +24,7 @@ def test_Analyze2nii_outputs(): output_map = dict( matlab_cmd=dict(), mfile=dict(usedefault=True, ), - nifti_file=dict(usedefault=True, ), + nifti_file=dict(), paths=dict(), use_mcr=dict(), use_v8struct=dict( diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py index 03d01a391d..bbc925ec9e 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py @@ -8,7 +8,6 @@ def test_ApplyDeformations_inputs(): deformation_field=dict( field='comp{1}.def', mandatory=True, - usedefault=True, ), in_files=dict( field='fnames', @@ -21,7 +20,6 @@ def test_ApplyDeformations_inputs(): reference_volume=dict( field='comp{2}.id.space', mandatory=True, - usedefault=True, ), use_mcr=dict(), use_v8struct=dict( diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py index 26197ab0a8..d1c35dbcd2 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py @@ -8,12 +8,10 @@ def test_ApplyInverseDeformation_inputs(): bounding_box=dict(field='comp{1}.inv.comp{1}.sn2def.bb', ), deformation=dict( field='comp{1}.inv.comp{1}.sn2def.matname', - usedefault=True, xor=['deformation_field'], ), deformation_field=dict( field='comp{1}.inv.comp{1}.def', - usedefault=True, xor=['deformation'], ), in_files=dict( @@ -24,10 +22,7 @@ def test_ApplyInverseDeformation_inputs(): matlab_cmd=dict(), mfile=dict(usedefault=True, ), paths=dict(), - target=dict( - field='comp{1}.inv.space', - usedefault=True, - ), + target=dict(field='comp{1}.inv.space', ), use_mcr=dict(), use_v8struct=dict( min_ver='8', diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py index 30a3080071..a686e95485 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py @@ -8,18 +8,11 @@ def test_ApplyTransform_inputs(): in_file=dict( copyfile=True, mandatory=True, - usedefault=True, - ), - mat=dict( - mandatory=True, - usedefault=True, ), + mat=dict(mandatory=True, ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), - out_file=dict( - genfile=True, - usedefault=True, - ), + out_file=dict(genfile=True, ), paths=dict(), use_mcr=dict(), use_v8struct=dict( @@ -33,7 +26,7 @@ def test_ApplyTransform_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_ApplyTransform_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = ApplyTransform.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py index 5cac290da6..69695ca7b5 100644 --- a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py +++ b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py @@ -5,20 +5,16 @@ def test_CalcCoregAffine_inputs(): input_map = dict( - invmat=dict(usedefault=True, ), - mat=dict(usedefault=True, ), + invmat=dict(), + mat=dict(), matlab_cmd=dict(), mfile=dict(usedefault=True, ), moving=dict( copyfile=False, mandatory=True, - usedefault=True, ), paths=dict(), - target=dict( - mandatory=True, - usedefault=True, - ), + target=dict(mandatory=True, ), use_mcr=dict(), use_v8struct=dict( min_ver='8', @@ -32,8 +28,8 @@ def test_CalcCoregAffine_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_CalcCoregAffine_outputs(): output_map = dict( - invmat=dict(usedefault=True, ), - mat=dict(usedefault=True, ), + invmat=dict(), + mat=dict(), ) outputs = CalcCoregAffine.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_Coregister.py b/nipype/interfaces/spm/tests/test_auto_Coregister.py index 6318b1ab88..957a2c84a9 100644 --- a/nipype/interfaces/spm/tests/test_auto_Coregister.py +++ b/nipype/interfaces/spm/tests/test_auto_Coregister.py @@ -29,7 +29,6 @@ def test_Coregister_inputs(): copyfile=False, field='ref', mandatory=True, - usedefault=True, ), tolerance=dict(field='eoptions.tol', ), use_mcr=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_DARTEL.py b/nipype/interfaces/spm/tests/test_auto_DARTEL.py index e7d261a99a..cc1b9eee1b 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTEL.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTEL.py @@ -34,7 +34,7 @@ def test_DARTEL_inputs(): def test_DARTEL_outputs(): output_map = dict( dartel_flow_fields=dict(), - final_template_file=dict(usedefault=True, ), + final_template_file=dict(), template_files=dict(), ) outputs = DARTEL.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py index 24d7690916..d25bde2e5d 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py @@ -24,7 +24,6 @@ def test_DARTELNorm2MNI_inputs(): copyfile=False, field='mni_norm.template', mandatory=True, - usedefault=True, ), use_mcr=dict(), use_v8struct=dict( @@ -40,7 +39,7 @@ def test_DARTELNorm2MNI_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_DARTELNorm2MNI_outputs(): output_map = dict( - normalization_parameter_file=dict(usedefault=True, ), + normalization_parameter_file=dict(), normalized_files=dict(), ) outputs = DARTELNorm2MNI.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py index 1bd4678c3a..bc9bb9006e 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py @@ -17,13 +17,11 @@ def test_EstimateContrast_inputs(): residual_image=dict( copyfile=False, mandatory=True, - usedefault=True, ), spm_mat_file=dict( copyfile=True, field='spmmat', mandatory=True, - usedefault=True, ), use_derivs=dict(xor=['group_contrast'], ), use_mcr=dict(), @@ -43,7 +41,7 @@ def test_EstimateContrast_outputs(): ess_images=dict(), spmF_images=dict(), spmT_images=dict(), - spm_mat_file=dict(usedefault=True, ), + spm_mat_file=dict(), ) outputs = EstimateContrast.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py index 7d058fa76e..05f511a0bd 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py @@ -17,7 +17,6 @@ def test_EstimateModel_inputs(): copyfile=True, field='spmmat', mandatory=True, - usedefault=True, ), use_mcr=dict(), use_v8struct=dict( @@ -35,15 +34,15 @@ def test_EstimateModel_outputs(): output_map = dict( ARcoef=dict(), Cbetas=dict(), - RPVimage=dict(usedefault=True, ), + RPVimage=dict(), SDbetas=dict(), SDerror=dict(), beta_images=dict(), - labels=dict(usedefault=True, ), - mask_image=dict(usedefault=True, ), - residual_image=dict(usedefault=True, ), + labels=dict(), + mask_image=dict(), + residual_image=dict(), residual_images=dict(), - spm_mat_file=dict(usedefault=True, ), + spm_mat_file=dict(), ) outputs = EstimateModel.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py index 2a181918c5..38d2b1c6fb 100644 --- a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py @@ -6,10 +6,7 @@ def test_FactorialDesign_inputs(): input_map = dict( covariates=dict(field='cov', ), - explicit_mask_file=dict( - field='masking.em', - usedefault=True, - ), + explicit_mask_file=dict(field='masking.em', ), global_calc_mean=dict( field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], @@ -27,10 +24,7 @@ def test_FactorialDesign_inputs(): mfile=dict(usedefault=True, ), no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), paths=dict(), - spm_mat_dir=dict( - field='dir', - usedefault=True, - ), + spm_mat_dir=dict(field='dir', ), threshold_mask_absolute=dict( field='masking.tm.tma.athresh', xor=['threshold_mask_none', 'threshold_mask_relative'], @@ -56,7 +50,7 @@ def test_FactorialDesign_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FactorialDesign_outputs(): - output_map = dict(spm_mat_file=dict(usedefault=True, ), ) + output_map = dict(spm_mat_file=dict(), ) outputs = FactorialDesign.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_FieldMap.py b/nipype/interfaces/spm/tests/test_auto_FieldMap.py index bc2751220a..43fbbcb8f4 100644 --- a/nipype/interfaces/spm/tests/test_auto_FieldMap.py +++ b/nipype/interfaces/spm/tests/test_auto_FieldMap.py @@ -8,7 +8,6 @@ def test_FieldMap_inputs(): anat_file=dict( copyfile=False, field='subj.anat', - usedefault=True, ), blip_direction=dict( field='subj.defaults.defaultsval.blipdir', @@ -22,7 +21,6 @@ def test_FieldMap_inputs(): copyfile=False, field='subj.session.epi', mandatory=True, - usedefault=True, ), epifm=dict( field='subj.defaults.defaultsval.epifm', @@ -37,7 +35,6 @@ def test_FieldMap_inputs(): copyfile=False, field='subj.data.presubphasemag.magnitude', mandatory=True, - usedefault=True, ), mask_fwhm=dict( field='subj.defaults.defaultsval.mflags.fwhm', @@ -78,7 +75,6 @@ def test_FieldMap_inputs(): copyfile=False, field='subj.data.presubphasemag.phase', mandatory=True, - usedefault=True, ), reg=dict( field='subj.defaults.defaultsval.mflags.reg', @@ -91,7 +87,6 @@ def test_FieldMap_inputs(): template=dict( copyfile=False, field='subj.defaults.defaultsval.mflags.template', - usedefault=True, ), thresh=dict( field='subj.defaults.defaultsval.mflags.thresh', @@ -125,7 +120,7 @@ def test_FieldMap_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_FieldMap_outputs(): - output_map = dict(vdm=dict(usedefault=True, ), ) + output_map = dict(vdm=dict(), ) outputs = FieldMap.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_Level1Design.py b/nipype/interfaces/spm/tests/test_auto_Level1Design.py index d84d5ca907..7dce3dda2a 100644 --- a/nipype/interfaces/spm/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/spm/tests/test_auto_Level1Design.py @@ -16,10 +16,7 @@ def test_Level1Design_inputs(): field='timing.RT', mandatory=True, ), - mask_image=dict( - field='mask', - usedefault=True, - ), + mask_image=dict(field='mask', ), mask_threshold=dict(usedefault=True, ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), @@ -31,10 +28,7 @@ def test_Level1Design_inputs(): field='sess', mandatory=True, ), - spm_mat_dir=dict( - field='dir', - usedefault=True, - ), + spm_mat_dir=dict(field='dir', ), timing_units=dict( field='timing.units', mandatory=True, @@ -52,7 +46,7 @@ def test_Level1Design_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Level1Design_outputs(): - output_map = dict(spm_mat_file=dict(usedefault=True, ), ) + output_map = dict(spm_mat_file=dict(), ) outputs = Level1Design.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py index dc8e73d77c..26957f2fbb 100644 --- a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py @@ -6,10 +6,7 @@ def test_MultipleRegressionDesign_inputs(): input_map = dict( covariates=dict(field='cov', ), - explicit_mask_file=dict( - field='masking.em', - usedefault=True, - ), + explicit_mask_file=dict(field='masking.em', ), global_calc_mean=dict( field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], @@ -35,10 +32,7 @@ def test_MultipleRegressionDesign_inputs(): mfile=dict(usedefault=True, ), no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), paths=dict(), - spm_mat_dir=dict( - field='dir', - usedefault=True, - ), + spm_mat_dir=dict(field='dir', ), threshold_mask_absolute=dict( field='masking.tm.tma.athresh', xor=['threshold_mask_none', 'threshold_mask_relative'], @@ -65,7 +59,7 @@ def test_MultipleRegressionDesign_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MultipleRegressionDesign_outputs(): - output_map = dict(spm_mat_file=dict(usedefault=True, ), ) + output_map = dict(spm_mat_file=dict(), ) outputs = MultipleRegressionDesign.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize.py b/nipype/interfaces/spm/tests/test_auto_Normalize.py index d2018122b3..fde0bf7fff 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize.py @@ -24,7 +24,6 @@ def test_Normalize_inputs(): copyfile=False, field='subj.matname', mandatory=True, - usedefault=True, xor=['source', 'template'], ), paths=dict(), @@ -38,20 +37,17 @@ def test_Normalize_inputs(): source_weight=dict( copyfile=False, field='subj.wtsrc', - usedefault=True, ), template=dict( copyfile=False, field='eoptions.template', mandatory=True, - usedefault=True, xor=['parameter_file'], ), template_image_smoothing=dict(field='eoptions.smoref', ), template_weight=dict( copyfile=False, field='eoptions.weight', - usedefault=True, ), use_mcr=dict(), use_v8struct=dict( diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize12.py b/nipype/interfaces/spm/tests/test_auto_Normalize12.py index 3428df38b5..bf8da2dba1 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize12.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize12.py @@ -16,14 +16,12 @@ def test_Normalize12_inputs(): copyfile=False, field='subj.def', mandatory=True, - usedefault=True, xor=['image_to_align', 'tpm'], ), image_to_align=dict( copyfile=True, field='subj.vol', mandatory=True, - usedefault=True, xor=['deformation_file'], ), jobtype=dict(usedefault=True, ), @@ -39,7 +37,6 @@ def test_Normalize12_inputs(): tpm=dict( copyfile=False, field='eoptions.tpm', - usedefault=True, xor=['deformation_file'], ), use_mcr=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py index a57ba3b3f9..dbb02a6275 100644 --- a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py @@ -6,10 +6,7 @@ def test_OneSampleTTestDesign_inputs(): input_map = dict( covariates=dict(field='cov', ), - explicit_mask_file=dict( - field='masking.em', - usedefault=True, - ), + explicit_mask_file=dict(field='masking.em', ), global_calc_mean=dict( field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], @@ -31,10 +28,7 @@ def test_OneSampleTTestDesign_inputs(): mfile=dict(usedefault=True, ), no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), paths=dict(), - spm_mat_dir=dict( - field='dir', - usedefault=True, - ), + spm_mat_dir=dict(field='dir', ), threshold_mask_absolute=dict( field='masking.tm.tma.athresh', xor=['threshold_mask_none', 'threshold_mask_relative'], @@ -60,7 +54,7 @@ def test_OneSampleTTestDesign_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_OneSampleTTestDesign_outputs(): - output_map = dict(spm_mat_file=dict(usedefault=True, ), ) + output_map = dict(spm_mat_file=dict(), ) outputs = OneSampleTTestDesign.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py index 12bc0f4a16..3e1662268a 100644 --- a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py @@ -7,10 +7,7 @@ def test_PairedTTestDesign_inputs(): input_map = dict( ancova=dict(field='des.pt.ancova', ), covariates=dict(field='cov', ), - explicit_mask_file=dict( - field='masking.em', - usedefault=True, - ), + explicit_mask_file=dict(field='masking.em', ), global_calc_mean=dict( field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], @@ -33,10 +30,7 @@ def test_PairedTTestDesign_inputs(): mandatory=True, ), paths=dict(), - spm_mat_dir=dict( - field='dir', - usedefault=True, - ), + spm_mat_dir=dict(field='dir', ), threshold_mask_absolute=dict( field='masking.tm.tma.athresh', xor=['threshold_mask_none', 'threshold_mask_relative'], @@ -62,7 +56,7 @@ def test_PairedTTestDesign_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PairedTTestDesign_outputs(): - output_map = dict(spm_mat_file=dict(usedefault=True, ), ) + output_map = dict(spm_mat_file=dict(), ) outputs = PairedTTestDesign.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_Realign.py b/nipype/interfaces/spm/tests/test_auto_Realign.py index 10f5f6a0a6..ac2f5bbd92 100644 --- a/nipype/interfaces/spm/tests/test_auto_Realign.py +++ b/nipype/interfaces/spm/tests/test_auto_Realign.py @@ -28,10 +28,7 @@ def test_Realign_inputs(): min_ver='8', usedefault=True, ), - weight_img=dict( - field='eoptions.weight', - usedefault=True, - ), + weight_img=dict(field='eoptions.weight', ), wrap=dict(field='eoptions.wrap', ), write_interp=dict(field='roptions.interp', ), write_mask=dict(field='roptions.mask', ), @@ -50,7 +47,7 @@ def test_Realign_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Realign_outputs(): output_map = dict( - mean_image=dict(usedefault=True, ), + mean_image=dict(), modified_in_files=dict(), realigned_files=dict(), realignment_parameters=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py b/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py index 0bafbfbd30..5c7c36f80b 100644 --- a/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py +++ b/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py @@ -45,7 +45,6 @@ def test_RealignUnwarp_inputs(): phase_map=dict( copyfile=False, field='data.pmscan', - usedefault=True, ), quality=dict(field='eoptions.quality', ), register_to_mean=dict(field='eoptions.rtm', ), @@ -64,10 +63,7 @@ def test_RealignUnwarp_inputs(): min_ver='8', usedefault=True, ), - weight_img=dict( - field='eoptions.weight', - usedefault=True, - ), + weight_img=dict(field='eoptions.weight', ), wrap=dict(field='eoptions.ewrap', ), ) inputs = RealignUnwarp.input_spec() @@ -77,7 +73,7 @@ def test_RealignUnwarp_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_RealignUnwarp_outputs(): output_map = dict( - mean_image=dict(usedefault=True, ), + mean_image=dict(), modified_in_files=dict(), realigned_unwarped_files=dict(), realignment_parameters=dict(), diff --git a/nipype/interfaces/spm/tests/test_auto_Reslice.py b/nipype/interfaces/spm/tests/test_auto_Reslice.py index b51d753b8d..81299fc748 100644 --- a/nipype/interfaces/spm/tests/test_auto_Reslice.py +++ b/nipype/interfaces/spm/tests/test_auto_Reslice.py @@ -5,19 +5,13 @@ def test_Reslice_inputs(): input_map = dict( - in_file=dict( - mandatory=True, - usedefault=True, - ), + in_file=dict(mandatory=True, ), interp=dict(usedefault=True, ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), + out_file=dict(), paths=dict(), - space_defining=dict( - mandatory=True, - usedefault=True, - ), + space_defining=dict(mandatory=True, ), use_mcr=dict(), use_v8struct=dict( min_ver='8', @@ -30,7 +24,7 @@ def test_Reslice_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Reslice_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Reslice.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py index 89a4885328..3e39ade181 100644 --- a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py +++ b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py @@ -14,10 +14,7 @@ def test_ResliceToReference_inputs(): matlab_cmd=dict(), mfile=dict(usedefault=True, ), paths=dict(), - target=dict( - field='comp{1}.id.space', - usedefault=True, - ), + target=dict(field='comp{1}.id.space', ), use_mcr=dict(), use_v8struct=dict( min_ver='8', diff --git a/nipype/interfaces/spm/tests/test_auto_Segment.py b/nipype/interfaces/spm/tests/test_auto_Segment.py index 6327f62d35..f6df46e1de 100644 --- a/nipype/interfaces/spm/tests/test_auto_Segment.py +++ b/nipype/interfaces/spm/tests/test_auto_Segment.py @@ -17,10 +17,7 @@ def test_Segment_inputs(): ), gaussians_per_class=dict(field='opts.ngaus', ), gm_output_type=dict(field='output.GM', ), - mask_image=dict( - field='opts.msk', - usedefault=True, - ), + mask_image=dict(field='opts.msk', ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), paths=dict(), @@ -43,23 +40,22 @@ def test_Segment_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Segment_outputs(): output_map = dict( - bias_corrected_image=dict(usedefault=True, ), - inverse_transformation_mat=dict(usedefault=True, ), - modulated_csf_image=dict(usedefault=True, ), - modulated_gm_image=dict(usedefault=True, ), + bias_corrected_image=dict(), + inverse_transformation_mat=dict(), + modulated_csf_image=dict(), + modulated_gm_image=dict(), modulated_input_image=dict( deprecated='0.10', new_name='bias_corrected_image', - usedefault=True, ), - modulated_wm_image=dict(usedefault=True, ), - native_csf_image=dict(usedefault=True, ), - native_gm_image=dict(usedefault=True, ), - native_wm_image=dict(usedefault=True, ), - normalized_csf_image=dict(usedefault=True, ), - normalized_gm_image=dict(usedefault=True, ), - normalized_wm_image=dict(usedefault=True, ), - transformation_mat=dict(usedefault=True, ), + modulated_wm_image=dict(), + native_csf_image=dict(), + native_gm_image=dict(), + native_wm_image=dict(), + normalized_csf_image=dict(), + normalized_gm_image=dict(), + normalized_wm_image=dict(), + transformation_mat=dict(), ) outputs = Segment.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_Threshold.py b/nipype/interfaces/spm/tests/test_auto_Threshold.py index 8aa01622fd..078adb3a1b 100644 --- a/nipype/interfaces/spm/tests/test_auto_Threshold.py +++ b/nipype/interfaces/spm/tests/test_auto_Threshold.py @@ -17,12 +17,10 @@ def test_Threshold_inputs(): spm_mat_file=dict( copyfile=True, mandatory=True, - usedefault=True, ), stat_image=dict( copyfile=False, mandatory=True, - usedefault=True, ), use_fwe_correction=dict(usedefault=True, ), use_mcr=dict(), @@ -42,9 +40,9 @@ def test_Threshold_outputs(): activation_forced=dict(), cluster_forming_thr=dict(), n_clusters=dict(), - pre_topo_fdr_map=dict(usedefault=True, ), + pre_topo_fdr_map=dict(), pre_topo_n_clusters=dict(), - thresholded_map=dict(usedefault=True, ), + thresholded_map=dict(), ) outputs = Threshold.output_spec() diff --git a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py index 2477e75ecd..ccdc441e04 100644 --- a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py +++ b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py @@ -14,12 +14,10 @@ def test_ThresholdStatistics_inputs(): spm_mat_file=dict( copyfile=True, mandatory=True, - usedefault=True, ), stat_image=dict( copyfile=False, mandatory=True, - usedefault=True, ), use_mcr=dict(), use_v8struct=dict( diff --git a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py index f1720acff7..4dfbc12570 100644 --- a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py @@ -7,10 +7,7 @@ def test_TwoSampleTTestDesign_inputs(): input_map = dict( covariates=dict(field='cov', ), dependent=dict(field='des.t2.dept', ), - explicit_mask_file=dict( - field='masking.em', - usedefault=True, - ), + explicit_mask_file=dict(field='masking.em', ), global_calc_mean=dict( field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], @@ -36,10 +33,7 @@ def test_TwoSampleTTestDesign_inputs(): mfile=dict(usedefault=True, ), no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), paths=dict(), - spm_mat_dir=dict( - field='dir', - usedefault=True, - ), + spm_mat_dir=dict(field='dir', ), threshold_mask_absolute=dict( field='masking.tm.tma.athresh', xor=['threshold_mask_none', 'threshold_mask_relative'], @@ -66,7 +60,7 @@ def test_TwoSampleTTestDesign_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_TwoSampleTTestDesign_outputs(): - output_map = dict(spm_mat_file=dict(usedefault=True, ), ) + output_map = dict(spm_mat_file=dict(), ) outputs = TwoSampleTTestDesign.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py index 095e42c2a8..6aaac2b489 100644 --- a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py +++ b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py @@ -46,9 +46,7 @@ def test_VBMSegment_inputs(): usedefault=True, ), dartel_template=dict( - field='estwrite.extopts.dartelwarp.normhigh.darteltpm', - usedefault=True, - ), + field='estwrite.extopts.dartelwarp.normhigh.darteltpm', ), deformation_field=dict( field='estwrite.output.warps', usedefault=True, @@ -107,10 +105,7 @@ def test_VBMSegment_inputs(): usedefault=True, ), spatial_normalization=dict(usedefault=True, ), - tissues=dict( - field='estwrite.tpm', - usedefault=True, - ), + tissues=dict(field='estwrite.tpm', ), use_mcr=dict(), use_sanlm_denoising_filter=dict( field='estwrite.extopts.sanlm', diff --git a/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py b/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py index d65f8726e7..24cbda657b 100644 --- a/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py +++ b/nipype/interfaces/tests/test_auto_BIDSDataGrabber.py @@ -5,10 +5,7 @@ def test_BIDSDataGrabber_inputs(): input_map = dict( - base_dir=dict( - mandatory=True, - usedefault=True, - ), + base_dir=dict(mandatory=True, ), extra_derivatives=dict(), index_derivatives=dict( mandatory=True, diff --git a/nipype/interfaces/tests/test_auto_Bru2.py b/nipype/interfaces/tests/test_auto_Bru2.py index d77c1f429a..ce436ac03e 100644 --- a/nipype/interfaces/tests/test_auto_Bru2.py +++ b/nipype/interfaces/tests/test_auto_Bru2.py @@ -18,7 +18,6 @@ def test_Bru2_inputs(): argstr='%s', mandatory=True, position=-1, - usedefault=True, ), output_filename=dict( argstr='-o %s', @@ -31,7 +30,7 @@ def test_Bru2_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Bru2_outputs(): - output_map = dict(nii_file=dict(usedefault=True, ), ) + output_map = dict(nii_file=dict(), ) outputs = Bru2.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_C3d.py b/nipype/interfaces/tests/test_auto_C3d.py index cae646af71..9e74e82e2a 100644 --- a/nipype/interfaces/tests/test_auto_C3d.py +++ b/nipype/interfaces/tests/test_auto_C3d.py @@ -25,7 +25,6 @@ def test_C3d_inputs(): out_file=dict( argstr='-o %s', position=-1, - usedefault=True, xor=['out_files'], ), out_files=dict( diff --git a/nipype/interfaces/tests/test_auto_C3dAffineTool.py b/nipype/interfaces/tests/test_auto_C3dAffineTool.py index 3875b1a4a3..510ea2f02a 100644 --- a/nipype/interfaces/tests/test_auto_C3dAffineTool.py +++ b/nipype/interfaces/tests/test_auto_C3dAffineTool.py @@ -22,17 +22,14 @@ def test_C3dAffineTool_inputs(): reference_file=dict( argstr='-ref %s', position=1, - usedefault=True, ), source_file=dict( argstr='-src %s', position=2, - usedefault=True, ), transform_file=dict( argstr='%s', position=3, - usedefault=True, ), ) inputs = C3dAffineTool.input_spec() @@ -41,7 +38,7 @@ def test_C3dAffineTool_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_C3dAffineTool_outputs(): - output_map = dict(itk_transform=dict(usedefault=True, ), ) + output_map = dict(itk_transform=dict(), ) outputs = C3dAffineTool.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_CopyMeta.py b/nipype/interfaces/tests/test_auto_CopyMeta.py index 2fa5fc6102..012edfa886 100644 --- a/nipype/interfaces/tests/test_auto_CopyMeta.py +++ b/nipype/interfaces/tests/test_auto_CopyMeta.py @@ -5,16 +5,10 @@ def test_CopyMeta_inputs(): input_map = dict( - dest_file=dict( - mandatory=True, - usedefault=True, - ), + dest_file=dict(mandatory=True, ), exclude_classes=dict(), include_classes=dict(), - src_file=dict( - mandatory=True, - usedefault=True, - ), + src_file=dict(mandatory=True, ), ) inputs = CopyMeta.input_spec() @@ -22,7 +16,7 @@ def test_CopyMeta_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CopyMeta_outputs(): - output_map = dict(dest_file=dict(usedefault=True, ), ) + output_map = dict(dest_file=dict(), ) outputs = CopyMeta.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_DataGrabber.py b/nipype/interfaces/tests/test_auto_DataGrabber.py index da4f8b9081..d39db0b527 100644 --- a/nipype/interfaces/tests/test_auto_DataGrabber.py +++ b/nipype/interfaces/tests/test_auto_DataGrabber.py @@ -5,7 +5,7 @@ def test_DataGrabber_inputs(): input_map = dict( - base_directory=dict(usedefault=True, ), + base_directory=dict(), drop_blank_outputs=dict(usedefault=True, ), raise_on_empty=dict(usedefault=True, ), sort_filelist=dict(mandatory=True, ), diff --git a/nipype/interfaces/tests/test_auto_DataSink.py b/nipype/interfaces/tests/test_auto_DataSink.py index 2d6e70f224..da26854451 100644 --- a/nipype/interfaces/tests/test_auto_DataSink.py +++ b/nipype/interfaces/tests/test_auto_DataSink.py @@ -6,7 +6,7 @@ def test_DataSink_inputs(): input_map = dict( _outputs=dict(usedefault=True, ), - base_directory=dict(usedefault=True, ), + base_directory=dict(), bucket=dict(), container=dict(), creds_path=dict(), @@ -15,7 +15,7 @@ def test_DataSink_inputs(): parameterization=dict(usedefault=True, ), regexp_substitutions=dict(), remove_dest_dir=dict(usedefault=True, ), - strip_dir=dict(usedefault=True, ), + strip_dir=dict(), substitutions=dict(), ) inputs = DataSink.input_spec() diff --git a/nipype/interfaces/tests/test_auto_Dcm2nii.py b/nipype/interfaces/tests/test_auto_Dcm2nii.py index 531177d915..0caa45a1f1 100644 --- a/nipype/interfaces/tests/test_auto_Dcm2nii.py +++ b/nipype/interfaces/tests/test_auto_Dcm2nii.py @@ -17,7 +17,6 @@ def test_Dcm2nii_inputs(): config_file=dict( argstr='-b %s', genfile=True, - usedefault=True, ), convert_all_pars=dict( argstr='-v', @@ -50,7 +49,6 @@ def test_Dcm2nii_inputs(): output_dir=dict( argstr='-o %s', genfile=True, - usedefault=True, ), protocol_in_filename=dict( argstr='-p', @@ -65,7 +63,6 @@ def test_Dcm2nii_inputs(): argstr='%s', mandatory=True, position=-1, - usedefault=True, xor=['source_names'], ), source_in_filename=dict( diff --git a/nipype/interfaces/tests/test_auto_Dcm2niix.py b/nipype/interfaces/tests/test_auto_Dcm2niix.py index 950b571d9e..5917f48583 100644 --- a/nipype/interfaces/tests/test_auto_Dcm2niix.py +++ b/nipype/interfaces/tests/test_auto_Dcm2niix.py @@ -52,7 +52,6 @@ def test_Dcm2niix_inputs(): argstr='%s', mandatory=True, position=-1, - usedefault=True, xor=['source_names'], ), source_names=dict( diff --git a/nipype/interfaces/tests/test_auto_DcmStack.py b/nipype/interfaces/tests/test_auto_DcmStack.py index 825805e09d..53a5259af5 100644 --- a/nipype/interfaces/tests/test_auto_DcmStack.py +++ b/nipype/interfaces/tests/test_auto_DcmStack.py @@ -12,7 +12,7 @@ def test_DcmStack_inputs(): include_regexes=dict(), out_ext=dict(usedefault=True, ), out_format=dict(), - out_path=dict(usedefault=True, ), + out_path=dict(), ) inputs = DcmStack.input_spec() @@ -20,7 +20,7 @@ def test_DcmStack_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_DcmStack_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = DcmStack.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_FreeSurferSource.py b/nipype/interfaces/tests/test_auto_FreeSurferSource.py index da75606a40..15ea9c66cd 100644 --- a/nipype/interfaces/tests/test_auto_FreeSurferSource.py +++ b/nipype/interfaces/tests/test_auto_FreeSurferSource.py @@ -7,10 +7,7 @@ def test_FreeSurferSource_inputs(): input_map = dict( hemi=dict(usedefault=True, ), subject_id=dict(mandatory=True, ), - subjects_dir=dict( - mandatory=True, - usedefault=True, - ), + subjects_dir=dict(mandatory=True, ), ) inputs = FreeSurferSource.input_spec() @@ -23,10 +20,7 @@ def test_FreeSurferSource_outputs(): altkey='BA', loc='stats', ), - T1=dict( - loc='mri', - usedefault=True, - ), + T1=dict(loc='mri', ), annot=dict( altkey='*annot', loc='label', @@ -47,23 +41,14 @@ def test_FreeSurferSource_outputs(): altkey='area.pial', loc='surf', ), - aseg=dict( - loc='mri', - usedefault=True, - ), + aseg=dict(loc='mri', ), aseg_stats=dict( altkey='aseg', loc='stats', ), avg_curv=dict(loc='surf', ), - brain=dict( - loc='mri', - usedefault=True, - ), - brainmask=dict( - loc='mri', - usedefault=True, - ), + brain=dict(loc='mri', ), + brainmask=dict(loc='mri', ), curv=dict(loc='surf', ), curv_pial=dict( altkey='curv.pial', @@ -77,10 +62,7 @@ def test_FreeSurferSource_outputs(): altkey='entorhinal_exvivo', loc='stats', ), - filled=dict( - loc='mri', - usedefault=True, - ), + filled=dict(loc='mri', ), graymid=dict( altkey=['graymid', 'midthickness'], loc='surf', @@ -91,23 +73,11 @@ def test_FreeSurferSource_outputs(): altkey='*label', loc='label', ), - norm=dict( - loc='mri', - usedefault=True, - ), - nu=dict( - loc='mri', - usedefault=True, - ), - orig=dict( - loc='mri', - usedefault=True, - ), + norm=dict(loc='mri', ), + nu=dict(loc='mri', ), + orig=dict(loc='mri', ), pial=dict(loc='surf', ), - rawavg=dict( - loc='mri', - usedefault=True, - ), + rawavg=dict(loc='mri', ), ribbon=dict( altkey='*ribbon', loc='mri', @@ -122,14 +92,8 @@ def test_FreeSurferSource_outputs(): thickness=dict(loc='surf', ), volume=dict(loc='surf', ), white=dict(loc='surf', ), - wm=dict( - loc='mri', - usedefault=True, - ), - wmparc=dict( - loc='mri', - usedefault=True, - ), + wm=dict(loc='mri', ), + wmparc=dict(loc='mri', ), wmparc_stats=dict( altkey='wmparc', loc='stats', diff --git a/nipype/interfaces/tests/test_auto_GroupAndStack.py b/nipype/interfaces/tests/test_auto_GroupAndStack.py index ef56cebf15..a8f30e32f9 100644 --- a/nipype/interfaces/tests/test_auto_GroupAndStack.py +++ b/nipype/interfaces/tests/test_auto_GroupAndStack.py @@ -12,7 +12,7 @@ def test_GroupAndStack_inputs(): include_regexes=dict(), out_ext=dict(usedefault=True, ), out_format=dict(), - out_path=dict(usedefault=True, ), + out_path=dict(), ) inputs = GroupAndStack.input_spec() diff --git a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py index 363f5ac8a3..03a65cf6c2 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py +++ b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py @@ -6,7 +6,7 @@ def test_JSONFileGrabber_inputs(): input_map = dict( defaults=dict(), - in_file=dict(usedefault=True, ), + in_file=dict(), ) inputs = JSONFileGrabber.input_spec() diff --git a/nipype/interfaces/tests/test_auto_JSONFileSink.py b/nipype/interfaces/tests/test_auto_JSONFileSink.py index fdcc2bf441..002997912b 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileSink.py +++ b/nipype/interfaces/tests/test_auto_JSONFileSink.py @@ -7,7 +7,7 @@ def test_JSONFileSink_inputs(): input_map = dict( _outputs=dict(usedefault=True, ), in_dict=dict(usedefault=True, ), - out_file=dict(usedefault=True, ), + out_file=dict(), ) inputs = JSONFileSink.input_spec() @@ -15,7 +15,7 @@ def test_JSONFileSink_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_JSONFileSink_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = JSONFileSink.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_LookupMeta.py b/nipype/interfaces/tests/test_auto_LookupMeta.py index b37a94c82c..29100aaef7 100644 --- a/nipype/interfaces/tests/test_auto_LookupMeta.py +++ b/nipype/interfaces/tests/test_auto_LookupMeta.py @@ -5,10 +5,7 @@ def test_LookupMeta_inputs(): input_map = dict( - in_file=dict( - mandatory=True, - usedefault=True, - ), + in_file=dict(mandatory=True, ), meta_keys=dict(mandatory=True, ), ) inputs = LookupMeta.input_spec() diff --git a/nipype/interfaces/tests/test_auto_MatlabCommand.py b/nipype/interfaces/tests/test_auto_MatlabCommand.py index 45427e1222..c1b971d25d 100644 --- a/nipype/interfaces/tests/test_auto_MatlabCommand.py +++ b/nipype/interfaces/tests/test_auto_MatlabCommand.py @@ -10,10 +10,7 @@ def test_MatlabCommand_inputs(): nohash=True, usedefault=True, ), - logfile=dict( - argstr='-logfile %s', - usedefault=True, - ), + logfile=dict(argstr='-logfile %s', ), mfile=dict(usedefault=True, ), nodesktop=dict( argstr='-nodesktop', diff --git a/nipype/interfaces/tests/test_auto_MergeNifti.py b/nipype/interfaces/tests/test_auto_MergeNifti.py index 7015091abc..9e0a017c60 100644 --- a/nipype/interfaces/tests/test_auto_MergeNifti.py +++ b/nipype/interfaces/tests/test_auto_MergeNifti.py @@ -9,7 +9,7 @@ def test_MergeNifti_inputs(): merge_dim=dict(), out_ext=dict(usedefault=True, ), out_format=dict(), - out_path=dict(usedefault=True, ), + out_path=dict(), sort_order=dict(), ) inputs = MergeNifti.input_spec() @@ -18,7 +18,7 @@ def test_MergeNifti_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MergeNifti_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = MergeNifti.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_MeshFix.py b/nipype/interfaces/tests/test_auto_MeshFix.py index 2d1693eb67..f306f4abed 100644 --- a/nipype/interfaces/tests/test_auto_MeshFix.py +++ b/nipype/interfaces/tests/test_auto_MeshFix.py @@ -43,12 +43,10 @@ def test_MeshFix_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), in_file2=dict( argstr='%s', position=2, - usedefault=True, ), join_closest_components=dict( argstr='-jc', @@ -63,7 +61,6 @@ def test_MeshFix_inputs(): out_filename=dict( argstr='-o %s', genfile=True, - usedefault=True, ), output_type=dict(usedefault=True, ), quiet_mode=dict(argstr='-q', ), @@ -97,7 +94,7 @@ def test_MeshFix_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_MeshFix_outputs(): - output_map = dict(mesh_file=dict(usedefault=True, ), ) + output_map = dict(mesh_file=dict(), ) outputs = MeshFix.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_MySQLSink.py b/nipype/interfaces/tests/test_auto_MySQLSink.py index 38cb32f9b1..048699659a 100644 --- a/nipype/interfaces/tests/test_auto_MySQLSink.py +++ b/nipype/interfaces/tests/test_auto_MySQLSink.py @@ -7,7 +7,6 @@ def test_MySQLSink_inputs(): input_map = dict( config=dict( mandatory=True, - usedefault=True, xor=['host'], ), database_name=dict(mandatory=True, ), diff --git a/nipype/interfaces/tests/test_auto_PETPVC.py b/nipype/interfaces/tests/test_auto_PETPVC.py index 9aa510aef5..c5283435d5 100644 --- a/nipype/interfaces/tests/test_auto_PETPVC.py +++ b/nipype/interfaces/tests/test_auto_PETPVC.py @@ -33,12 +33,10 @@ def test_PETPVC_inputs(): in_file=dict( argstr='-i %s', mandatory=True, - usedefault=True, ), mask_file=dict( argstr='-m %s', mandatory=True, - usedefault=True, ), n_deconv=dict( argstr='-k %d', @@ -52,7 +50,6 @@ def test_PETPVC_inputs(): argstr='-o %s', genfile=True, hash_files=False, - usedefault=True, ), pvc=dict( argstr='-p %s', @@ -69,7 +66,7 @@ def test_PETPVC_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_PETPVC_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = PETPVC.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_Quickshear.py b/nipype/interfaces/tests/test_auto_Quickshear.py index b62c77e77a..7f39a6bc96 100644 --- a/nipype/interfaces/tests/test_auto_Quickshear.py +++ b/nipype/interfaces/tests/test_auto_Quickshear.py @@ -18,13 +18,11 @@ def test_Quickshear_inputs(): argstr='%s', mandatory=True, position=1, - usedefault=True, ), mask_file=dict( argstr='%s', mandatory=True, position=2, - usedefault=True, ), out_file=dict( argstr='%s', @@ -32,7 +30,6 @@ def test_Quickshear_inputs(): name_source='in_file', name_template='%s_defaced', position=3, - usedefault=True, ), ) inputs = Quickshear.input_spec() @@ -41,7 +38,7 @@ def test_Quickshear_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Quickshear_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Quickshear.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_Reorient.py b/nipype/interfaces/tests/test_auto_Reorient.py index 27a6cba17e..2e45a1ca7f 100644 --- a/nipype/interfaces/tests/test_auto_Reorient.py +++ b/nipype/interfaces/tests/test_auto_Reorient.py @@ -5,10 +5,7 @@ def test_Reorient_inputs(): input_map = dict( - in_file=dict( - mandatory=True, - usedefault=True, - ), + in_file=dict(mandatory=True, ), orientation=dict(usedefault=True, ), ) inputs = Reorient.input_spec() @@ -18,8 +15,8 @@ def test_Reorient_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_Reorient_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - transform=dict(usedefault=True, ), + out_file=dict(), + transform=dict(), ) outputs = Reorient.output_spec() diff --git a/nipype/interfaces/tests/test_auto_Rescale.py b/nipype/interfaces/tests/test_auto_Rescale.py index 021b05e998..e180c82988 100644 --- a/nipype/interfaces/tests/test_auto_Rescale.py +++ b/nipype/interfaces/tests/test_auto_Rescale.py @@ -5,16 +5,10 @@ def test_Rescale_inputs(): input_map = dict( - in_file=dict( - mandatory=True, - usedefault=True, - ), + in_file=dict(mandatory=True, ), invert=dict(), percentile=dict(usedefault=True, ), - ref_file=dict( - mandatory=True, - usedefault=True, - ), + ref_file=dict(mandatory=True, ), ) inputs = Rescale.input_spec() @@ -22,7 +16,7 @@ def test_Rescale_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Rescale_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Rescale.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_S3DataGrabber.py b/nipype/interfaces/tests/test_auto_S3DataGrabber.py index 990347f56d..7c69413eb0 100644 --- a/nipype/interfaces/tests/test_auto_S3DataGrabber.py +++ b/nipype/interfaces/tests/test_auto_S3DataGrabber.py @@ -8,7 +8,7 @@ def test_S3DataGrabber_inputs(): anon=dict(usedefault=True, ), bucket=dict(mandatory=True, ), bucket_path=dict(usedefault=True, ), - local_directory=dict(usedefault=True, ), + local_directory=dict(), raise_on_empty=dict(usedefault=True, ), region=dict(usedefault=True, ), sort_filelist=dict(mandatory=True, ), diff --git a/nipype/interfaces/tests/test_auto_SQLiteSink.py b/nipype/interfaces/tests/test_auto_SQLiteSink.py index 3972583753..ea03663c4c 100644 --- a/nipype/interfaces/tests/test_auto_SQLiteSink.py +++ b/nipype/interfaces/tests/test_auto_SQLiteSink.py @@ -5,10 +5,7 @@ def test_SQLiteSink_inputs(): input_map = dict( - database_file=dict( - mandatory=True, - usedefault=True, - ), + database_file=dict(mandatory=True, ), table_name=dict(mandatory=True, ), ) inputs = SQLiteSink.input_spec() diff --git a/nipype/interfaces/tests/test_auto_SelectFiles.py b/nipype/interfaces/tests/test_auto_SelectFiles.py index f037d8824c..bf438fb826 100644 --- a/nipype/interfaces/tests/test_auto_SelectFiles.py +++ b/nipype/interfaces/tests/test_auto_SelectFiles.py @@ -5,7 +5,7 @@ def test_SelectFiles_inputs(): input_map = dict( - base_directory=dict(usedefault=True, ), + base_directory=dict(), force_lists=dict(usedefault=True, ), raise_on_empty=dict(usedefault=True, ), sort_filelist=dict(usedefault=True, ), diff --git a/nipype/interfaces/tests/test_auto_SignalExtraction.py b/nipype/interfaces/tests/test_auto_SignalExtraction.py index c74ab279da..bc76f5261a 100644 --- a/nipype/interfaces/tests/test_auto_SignalExtraction.py +++ b/nipype/interfaces/tests/test_auto_SignalExtraction.py @@ -7,10 +7,7 @@ def test_SignalExtraction_inputs(): input_map = dict( class_labels=dict(mandatory=True, ), detrend=dict(usedefault=True, ), - in_file=dict( - mandatory=True, - usedefault=True, - ), + in_file=dict(mandatory=True, ), incl_shared_variance=dict(usedefault=True, ), include_global=dict(usedefault=True, ), label_files=dict(mandatory=True, ), @@ -22,7 +19,7 @@ def test_SignalExtraction_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_SignalExtraction_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = SignalExtraction.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/tests/test_auto_SplitNifti.py b/nipype/interfaces/tests/test_auto_SplitNifti.py index 43d22ac4b2..e1f6539fab 100644 --- a/nipype/interfaces/tests/test_auto_SplitNifti.py +++ b/nipype/interfaces/tests/test_auto_SplitNifti.py @@ -5,13 +5,10 @@ def test_SplitNifti_inputs(): input_map = dict( - in_file=dict( - mandatory=True, - usedefault=True, - ), + in_file=dict(mandatory=True, ), out_ext=dict(usedefault=True, ), out_format=dict(), - out_path=dict(usedefault=True, ), + out_path=dict(), split_dim=dict(), ) inputs = SplitNifti.input_spec() diff --git a/nipype/interfaces/tests/test_auto_XNATSink.py b/nipype/interfaces/tests/test_auto_XNATSink.py index 9357443afa..b4db5ec8d3 100644 --- a/nipype/interfaces/tests/test_auto_XNATSink.py +++ b/nipype/interfaces/tests/test_auto_XNATSink.py @@ -7,10 +7,9 @@ def test_XNATSink_inputs(): input_map = dict( _outputs=dict(usedefault=True, ), assessor_id=dict(xor=['reconstruction_id'], ), - cache_dir=dict(usedefault=True, ), + cache_dir=dict(), config=dict( mandatory=True, - usedefault=True, xor=['server'], ), experiment_id=dict(mandatory=True, ), diff --git a/nipype/interfaces/tests/test_auto_XNATSource.py b/nipype/interfaces/tests/test_auto_XNATSource.py index 1403dc1c18..8faa79af81 100644 --- a/nipype/interfaces/tests/test_auto_XNATSource.py +++ b/nipype/interfaces/tests/test_auto_XNATSource.py @@ -5,10 +5,9 @@ def test_XNATSource_inputs(): input_map = dict( - cache_dir=dict(usedefault=True, ), + cache_dir=dict(), config=dict( mandatory=True, - usedefault=True, xor=['server'], ), pwd=dict(), diff --git a/nipype/interfaces/utility/tests/test_auto_AssertEqual.py b/nipype/interfaces/utility/tests/test_auto_AssertEqual.py index 78502aeed6..284e0f4d62 100644 --- a/nipype/interfaces/utility/tests/test_auto_AssertEqual.py +++ b/nipype/interfaces/utility/tests/test_auto_AssertEqual.py @@ -5,14 +5,8 @@ def test_AssertEqual_inputs(): input_map = dict( - volume1=dict( - mandatory=True, - usedefault=True, - ), - volume2=dict( - mandatory=True, - usedefault=True, - ), + volume1=dict(mandatory=True, ), + volume2=dict(mandatory=True, ), ) inputs = AssertEqual.input_spec() diff --git a/nipype/interfaces/utility/tests/test_auto_CSVReader.py b/nipype/interfaces/utility/tests/test_auto_CSVReader.py index 2fbbd73545..8a51ca4170 100644 --- a/nipype/interfaces/utility/tests/test_auto_CSVReader.py +++ b/nipype/interfaces/utility/tests/test_auto_CSVReader.py @@ -6,10 +6,7 @@ def test_CSVReader_inputs(): input_map = dict( header=dict(usedefault=True, ), - in_file=dict( - mandatory=True, - usedefault=True, - ), + in_file=dict(mandatory=True, ), ) inputs = CSVReader.input_spec() diff --git a/nipype/interfaces/utility/tests/test_auto_Rename.py b/nipype/interfaces/utility/tests/test_auto_Rename.py index a01e76d30a..1e6e1cab34 100644 --- a/nipype/interfaces/utility/tests/test_auto_Rename.py +++ b/nipype/interfaces/utility/tests/test_auto_Rename.py @@ -6,10 +6,7 @@ def test_Rename_inputs(): input_map = dict( format_string=dict(mandatory=True, ), - in_file=dict( - mandatory=True, - usedefault=True, - ), + in_file=dict(mandatory=True, ), keep_ext=dict(), parse_string=dict(), use_fullpath=dict(usedefault=True, ), diff --git a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py index 5bdfacde58..785e87e8b1 100644 --- a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py +++ b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py @@ -9,7 +9,6 @@ def test_Vnifti2Image_inputs(): attributes=dict( argstr='-attr %s', position=2, - usedefault=True, ), environ=dict( nohash=True, @@ -19,7 +18,6 @@ def test_Vnifti2Image_inputs(): argstr='-in %s', mandatory=True, position=1, - usedefault=True, ), out_file=dict( argstr='-out %s', @@ -28,7 +26,6 @@ def test_Vnifti2Image_inputs(): name_source=['in_file'], name_template='%s.v', position=-1, - usedefault=True, ), ) inputs = Vnifti2Image.input_spec() @@ -37,7 +34,7 @@ def test_Vnifti2Image_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_Vnifti2Image_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = Vnifti2Image.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/vista/tests/test_auto_VtoMat.py b/nipype/interfaces/vista/tests/test_auto_VtoMat.py index 33f9ea354d..ee16266402 100644 --- a/nipype/interfaces/vista/tests/test_auto_VtoMat.py +++ b/nipype/interfaces/vista/tests/test_auto_VtoMat.py @@ -14,7 +14,6 @@ def test_VtoMat_inputs(): argstr='-in %s', mandatory=True, position=1, - usedefault=True, ), out_file=dict( argstr='-out %s', @@ -23,7 +22,6 @@ def test_VtoMat_inputs(): name_source=['in_file'], name_template='%s.mat', position=-1, - usedefault=True, ), ) inputs = VtoMat.input_spec() @@ -32,7 +30,7 @@ def test_VtoMat_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_VtoMat_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = VtoMat.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/workbench/tests/test_auto_CiftiSmooth.py b/nipype/interfaces/workbench/tests/test_auto_CiftiSmooth.py index ac7a3f3032..b510a3b34e 100644 --- a/nipype/interfaces/workbench/tests/test_auto_CiftiSmooth.py +++ b/nipype/interfaces/workbench/tests/test_auto_CiftiSmooth.py @@ -10,17 +10,14 @@ def test_CiftiSmooth_inputs(): argstr='cerebellum-corrected-areas %s', position=10, requires=['cerebellum_surf'], - usedefault=True, ), cerebellum_surf=dict( argstr='-cerebellum-surface %s', position=9, - usedefault=True, ), cifti_roi=dict( argstr='-cifti-roi %s', position=11, - usedefault=True, ), direction=dict( argstr='%s', @@ -43,18 +40,15 @@ def test_CiftiSmooth_inputs(): argstr='%s', mandatory=True, position=0, - usedefault=True, ), left_corrected_areas=dict( argstr='-left-corrected-areas %s', position=6, - usedefault=True, ), left_surf=dict( argstr='-left-surface %s', mandatory=True, position=5, - usedefault=True, ), merged_volume=dict( argstr='-merged-volume', @@ -66,18 +60,15 @@ def test_CiftiSmooth_inputs(): name_source=['in_file'], name_template='smoothed_%s.nii', position=4, - usedefault=True, ), right_corrected_areas=dict( argstr='-right-corrected-areas %s', position=8, - usedefault=True, ), right_surf=dict( argstr='-right-surface %s', mandatory=True, position=7, - usedefault=True, ), sigma_surf=dict( argstr='%s', @@ -96,7 +87,7 @@ def test_CiftiSmooth_inputs(): for metakey, value in list(metadata.items()): assert getattr(inputs.traits()[key], metakey) == value def test_CiftiSmooth_outputs(): - output_map = dict(out_file=dict(usedefault=True, ), ) + output_map = dict(out_file=dict(), ) outputs = CiftiSmooth.output_spec() for key, metadata in list(output_map.items()): diff --git a/nipype/interfaces/workbench/tests/test_auto_MetricResample.py b/nipype/interfaces/workbench/tests/test_auto_MetricResample.py index f652a02fc0..46a66aa728 100644 --- a/nipype/interfaces/workbench/tests/test_auto_MetricResample.py +++ b/nipype/interfaces/workbench/tests/test_auto_MetricResample.py @@ -19,13 +19,11 @@ def test_MetricResample_inputs(): current_area=dict( argstr='%s', position=6, - usedefault=True, ), current_sphere=dict( argstr='%s', mandatory=True, position=1, - usedefault=True, ), environ=dict( nohash=True, @@ -35,7 +33,6 @@ def test_MetricResample_inputs(): argstr='%s', mandatory=True, position=0, - usedefault=True, ), largest=dict( argstr='-largest', @@ -49,13 +46,11 @@ def test_MetricResample_inputs(): new_area=dict( argstr='%s', position=7, - usedefault=True, ), new_sphere=dict( argstr='%s', mandatory=True, position=2, - usedefault=True, ), out_file=dict( argstr='%s', @@ -63,12 +58,10 @@ def test_MetricResample_inputs(): name_source=['new_sphere'], name_template='%s.out', position=4, - usedefault=True, ), roi_metric=dict( argstr='-current-roi %s', position=8, - usedefault=True, ), valid_roi_out=dict( argstr='-valid-roi-out', @@ -82,8 +75,8 @@ def test_MetricResample_inputs(): assert getattr(inputs.traits()[key], metakey) == value def test_MetricResample_outputs(): output_map = dict( - out_file=dict(usedefault=True, ), - roi_file=dict(usedefault=True, ), + out_file=dict(), + roi_file=dict(), ) outputs = MetricResample.output_spec() From 1134a6bb850bc5700e425054d29f2ca6ac43cf59 Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 16 Jul 2019 10:40:10 -0700 Subject: [PATCH 13/19] fix(dipy): resolve issues with dipy versions dipy==0.15 apparently breaks almost all tests dipy==0.14 breaks only one test (added skip condition) dipy==0.16 (latest today) seems to work alright. --- nipype/info.py | 2 +- nipype/interfaces/dipy/base.py | 13 ++++++++++--- nipype/interfaces/dipy/tests/test_base.py | 3 ++- 3 files changed, 13 insertions(+), 5 deletions(-) diff --git a/nipype/info.py b/nipype/info.py index b5b0dac0f8..c902485c4a 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -171,7 +171,7 @@ def get_nipype_gitversion(): 'doc': ['Sphinx>=1.4', 'numpydoc', 'matplotlib', 'pydotplus', 'pydot>=1.2.3'], 'tests': TESTS_REQUIRES, 'specs': ['yapf'], - 'nipy': ['nitime', 'nilearn<0.5.0', 'dipy', 'nipy', 'matplotlib'], + 'nipy': ['nitime', 'nilearn<0.5.0', 'dipy!=0.15,>=0.14', 'nipy', 'matplotlib'], 'profiler': ['psutil>=5.0'], 'duecredit': ['duecredit'], 'xvfbwrapper': ['xvfbwrapper'], diff --git a/nipype/interfaces/dipy/base.py b/nipype/interfaces/dipy/base.py index 27f26e989a..225d6649a3 100644 --- a/nipype/interfaces/dipy/base.py +++ b/nipype/interfaces/dipy/base.py @@ -6,7 +6,6 @@ import os.path as op import inspect import numpy as np -from ... import logging from ..base import (traits, File, isdefined, LibraryBaseInterface, BaseInterfaceInputSpec, TraitedSpec) @@ -23,19 +22,27 @@ def no_dipy(): - """ Check if dipy is available """ + """Check if dipy is available.""" global HAVE_DIPY return not HAVE_DIPY def dipy_version(): - """ Check dipy version """ + """Return dipy version.""" if no_dipy(): return None return dipy.__version__ +def check_version(minversion): + """Check version is greater or equal to a given version.""" + from packaging.version import Version + if no_dipy(): + return None + return Version(dipy.__version__) >= Version(minversion) + + class DipyBaseInterface(LibraryBaseInterface): """ A base interface for py:mod:`dipy` computations diff --git a/nipype/interfaces/dipy/tests/test_base.py b/nipype/interfaces/dipy/tests/test_base.py index 1d475ac0f7..a6684a65a1 100644 --- a/nipype/interfaces/dipy/tests/test_base.py +++ b/nipype/interfaces/dipy/tests/test_base.py @@ -3,7 +3,7 @@ from ...base import traits, TraitedSpec, BaseInterfaceInputSpec from ..base import (convert_to_traits_type, create_interface_specs, dipy_to_nipype_interface, DipyBaseInterface, no_dipy, - get_dipy_workflows) + get_dipy_workflows, check_version) def test_convert_to_traits_type(): @@ -85,6 +85,7 @@ def test_create_interface_specs(): @pytest.mark.skipif(no_dipy(), reason="DIPY is not installed") +@pytest.mark.skipif(not check_version('0.16'), reason='dipy must be >=0.16') def test_dipy_to_nipype_interface(): from dipy.workflows.workflow import Workflow From 005f87e2d3432d64e7b552695e881b8eea9aa2ca Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 16 Jul 2019 10:46:21 -0700 Subject: [PATCH 14/19] fix(io): repair ``io.S3DataGrabber`` which was not expecting path-like objects --- nipype/interfaces/io.py | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py index 60e8b6fafc..4b9afd1ce1 100644 --- a/nipype/interfaces/io.py +++ b/nipype/interfaces/io.py @@ -1024,15 +1024,18 @@ def _list_outputs(self): def s3tolocal(self, s3path, bkt): import boto # path formatting - if not os.path.split(self.inputs.local_directory)[1] == '': - self.inputs.local_directory += '/' - if not os.path.split(self.inputs.bucket_path)[1] == '': - self.inputs.bucket_path += '/' - if self.inputs.template[0] == '/': - self.inputs.template = self.inputs.template[1:] - - localpath = s3path.replace(self.inputs.bucket_path, - self.inputs.local_directory) + local_directory = str(self.inputs.local_directory) + bucket_path = str(self.inputs.bucket_path) + template = str(self.inputs.template) + if not os.path.split(local_directory)[1] == '': + local_directory += '/' + if not os.path.split(bucket_path)[1] == '': + bucket_path += '/' + if template[0] == '/': + template = template[1:] + + localpath = s3path.replace(bucket_path, + local_directory) localdir = os.path.split(localpath)[0] if not os.path.exists(localdir): os.makedirs(localdir) From d0f4bf59e6dda0e1cbeb2e4a37845337b033c4d1 Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 16 Jul 2019 11:05:47 -0700 Subject: [PATCH 15/19] fix(py<3.6): workaround for ``Path.resolve(strict=value)`` --- nipype/interfaces/base/traits_extension.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py index 6786c10939..b3c56f6749 100644 --- a/nipype/interfaces/base/traits_extension.py +++ b/nipype/interfaces/base/traits_extension.py @@ -142,7 +142,13 @@ def validate(self, object, name, value, return_pathlike=False): self.error(object, name, str(value)) if self.resolve: - value = value.resolve() + try: + value = value.resolve(strict=self.exists) + except TypeError: + if self.exists: + value = value.resolve() + elif not value.is_absolute(): + value = Path() / value if not return_pathlike and not self.pathlike: value = str(value) From eeb53d0255229f92bc8a4e28dbadd02b8685d0b7 Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 16 Jul 2019 11:07:12 -0700 Subject: [PATCH 16/19] fix(pathlib2): Import pathlib2 if python < 3. --- nipype/interfaces/base/traits_extension.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py index b3c56f6749..bb59686ce5 100644 --- a/nipype/interfaces/base/traits_extension.py +++ b/nipype/interfaces/base/traits_extension.py @@ -1,4 +1,3 @@ -# -*- coding: utf-8 -*- # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: """ @@ -25,7 +24,6 @@ from builtins import str, bytes from collections import Sequence -from pathlib import Path # perform all external trait imports here from traits import __version__ as traits_version @@ -37,6 +35,12 @@ from traits.api import Unicode from future import standard_library +try: + from pathlib import Path +except ImportError: + from pathlib2 import Path + + if traits_version < '3.7.0': raise ImportError('Traits version 3.7.0 or higher must be installed') From 398697ae235e26598ae1b0c57048b8a0c6ec4f8e Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 16 Jul 2019 11:55:20 -0700 Subject: [PATCH 17/19] fix(python2): make deepcopy to work with python2 --- nipype/interfaces/base/specs.py | 52 +++++++++++++--------- nipype/interfaces/base/traits_extension.py | 2 +- 2 files changed, 33 insertions(+), 21 deletions(-) diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py index dbbc816dc9..139923d0f7 100644 --- a/nipype/interfaces/base/specs.py +++ b/nipype/interfaces/base/specs.py @@ -32,6 +32,14 @@ from ... import config, __version__ + +USING_PATHLIB2 = False +try: + from pathlib import Path +except ImportError: + from pathlib2 import Path # noqa + USING_PATHLIB2 = True + FLOAT_FORMAT = '{:.10f}'.format nipype_version = Version(__version__) @@ -314,26 +322,8 @@ def __all__(self): return self.copyable_trait_names() -class TraitedSpec(BaseTraitedSpec): - """ Create a subclass with strict traits. - - This is used in 90% of the cases. - """ - _ = traits.Disallow - - -class BaseInterfaceInputSpec(TraitedSpec): - pass - - -class DynamicTraitedSpec(BaseTraitedSpec): - """ A subclass to handle dynamic traits - - This class is a workaround for add_traits and clone_traits not - functioning well together. - """ - - def __deepcopy__(self, memo): +if USING_PATHLIB2: + def _py2deepcopy(self, memo): """ bug in deepcopy for HasTraits results in weird cloning behavior for added traits """ @@ -357,6 +347,28 @@ def __deepcopy__(self, memo): dup.trait_set(**dup_dict) return dup + BaseTraitedSpec.__deepcopy__ = _py2deepcopy + + +class TraitedSpec(BaseTraitedSpec): + """ Create a subclass with strict traits. + + This is used in 90% of the cases. + """ + _ = traits.Disallow + + +class BaseInterfaceInputSpec(TraitedSpec): + pass + + +class DynamicTraitedSpec(BaseTraitedSpec): + """ A subclass to handle dynamic traits + + This class is a workaround for add_traits and clone_traits not + functioning well together. + """ + class CommandLineInputSpec(BaseInterfaceInputSpec): args = traits.Str(argstr='%s', desc='Additional parameters to the command') diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py index bb59686ce5..6bb737a384 100644 --- a/nipype/interfaces/base/traits_extension.py +++ b/nipype/interfaces/base/traits_extension.py @@ -131,7 +131,7 @@ def __init__(self, value=Undefined, def validate(self, object, name, value, return_pathlike=False): """Validate a value change.""" try: - value = Path(value) # Use pathlib's validation + value = Path('%s' % value) # Use pathlib's validation except Exception: self.error(object, name, str(value)) From 08ddc9fc7772efb73b22ca96f2dcf28a01b931e7 Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 16 Jul 2019 12:59:20 -0700 Subject: [PATCH 18/19] fix(python3): roll patch back to ``DynamicTraitedSpec.__deepcopy__`` --- nipype/interfaces/base/specs.py | 59 +++++++++++++++++++-------------- 1 file changed, 34 insertions(+), 25 deletions(-) diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py index 139923d0f7..64eb6397e5 100644 --- a/nipype/interfaces/base/specs.py +++ b/nipype/interfaces/base/specs.py @@ -322,32 +322,37 @@ def __all__(self): return self.copyable_trait_names() +def _deepcopypatch(self, memo): + """ + Replace the ``__deepcopy__`` member with a traits-friendly implementation. + + A bug in ``__deepcopy__`` for ``HasTraits`` results in weird cloning behaviors. + Occurs for all specs in Python<3 and only for DynamicTraitedSpec in Python>2. + + """ + id_self = id(self) + if id_self in memo: + return memo[id_self] + dup_dict = deepcopy(self.trait_get(), memo) + # access all keys + for key in self.copyable_trait_names(): + if key in self.__dict__.keys(): + _ = getattr(self, key) + # clone once + dup = self.clone_traits(memo=memo) + for key in self.copyable_trait_names(): + try: + _ = getattr(dup, key) + except: + pass + # clone twice + dup = self.clone_traits(memo=memo) + dup.trait_set(**dup_dict) + return dup + + if USING_PATHLIB2: - def _py2deepcopy(self, memo): - """ bug in deepcopy for HasTraits results in weird cloning behavior for - added traits - """ - id_self = id(self) - if id_self in memo: - return memo[id_self] - dup_dict = deepcopy(self.trait_get(), memo) - # access all keys - for key in self.copyable_trait_names(): - if key in self.__dict__.keys(): - _ = getattr(self, key) - # clone once - dup = self.clone_traits(memo=memo) - for key in self.copyable_trait_names(): - try: - _ = getattr(dup, key) - except: - pass - # clone twice - dup = self.clone_traits(memo=memo) - dup.trait_set(**dup_dict) - return dup - - BaseTraitedSpec.__deepcopy__ = _py2deepcopy + BaseTraitedSpec.__deepcopy__ = _deepcopypatch class TraitedSpec(BaseTraitedSpec): @@ -370,6 +375,10 @@ class DynamicTraitedSpec(BaseTraitedSpec): """ +if not USING_PATHLIB2: + DynamicTraitedSpec.__deepcopy__ = _deepcopypatch + + class CommandLineInputSpec(BaseInterfaceInputSpec): args = traits.Str(argstr='%s', desc='Additional parameters to the command') environ = traits.DictStrStr( From 8069604ab54fc2c1ed8890749eb85f87975b69f8 Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 16 Jul 2019 14:13:43 -0700 Subject: [PATCH 19/19] fix(py>2,<3.6): fixed workaround for ``Path.resolve(strict=False)`` --- nipype/interfaces/base/traits_extension.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py index 6bb737a384..22ffc7f231 100644 --- a/nipype/interfaces/base/traits_extension.py +++ b/nipype/interfaces/base/traits_extension.py @@ -152,7 +152,7 @@ def validate(self, object, name, value, return_pathlike=False): if self.exists: value = value.resolve() elif not value.is_absolute(): - value = Path() / value + value = Path().resolve() / value if not return_pathlike and not self.pathlike: value = str(value)