Merge branch 'master' of https://github.com/nipy/nipype

Author: mgxd

nipype/interfaces/afni/utils.py

@@ -619,8 +619,9 @@ class CatMatvec(AFNICommand):
 
     def _format_arg(self, name, spec, value):
         if name == 'in_file':
-            return spec.argstr % (' '.join([i[0] + ' -' + i[1]
-                                            for i in value]))
+            # Concatenate a series of filenames, with optional opkeys
+            return ' '.join('%s -%s' % (mfile, opkey) if opkey else mfile
+                           for mfile, opkey in value)
         return super(CatMatvec, self)._format_arg(name, spec, value)
 
 

nipype/interfaces/base/core.py

@@ -476,9 +476,9 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
                 setattr(outputs, key, val)
             except TraitError as error:
                 if 'an existing' in getattr(error, 'info', 'default'):
-                    msg = "No such file or directory for output '%s' of a %s interface" % \
-                        (key, self.__class__.__name__)
-                    raise FileNotFoundError(val, message=msg)
+                    msg = "No such file or directory '%s' for output '%s' of a %s interface" % \
+                        (val, key, self.__class__.__name__)
+                    raise FileNotFoundError(msg)
                 raise error
         return outputs
 

nipype/interfaces/mrtrix3/__init__.py

@@ -4,7 +4,8 @@
 # -*- coding: utf-8 -*-
 
 from .utils import (Mesh2PVE, Generate5tt, BrainMask, TensorMetrics,
-                    ComputeTDI, TCK2VTK, MRMath, MRConvert, DWIExtract)
+                    ComputeTDI, TCK2VTK, MRMath, MRConvert, MRResize,
+                    DWIExtract)
 from .preprocess import (ResponseSD, ACTPrepareFSL, ReplaceFSwithFIRST,
                          DWIDenoise, MRDeGibbs, DWIBiasCorrect)
 from .tracking import Tractography

nipype/interfaces/mrtrix3/tests/test_auto_MRResize.py

@@ -0,0 +1,77 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import MRResize
+
+
+def test_MRResize_inputs():
+    input_map = dict(
+        args=dict(argstr='%s', ),
+        bval_scale=dict(argstr='-bvalue_scaling %s', ),
+        environ=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        grad_file=dict(
+            argstr='-grad %s',
+            extensions=None,
+            xor=['grad_fsl'],
+        ),
+        grad_fsl=dict(
+            argstr='-fslgrad %s %s',
+            xor=['grad_file'],
+        ),
+        image_size=dict(
+            argstr='-size %d,%d,%d',
+            mandatory=True,
+            xor=['voxel_size', 'scale_factor'],
+        ),
+        in_bval=dict(extensions=None, ),
+        in_bvec=dict(
+            argstr='-fslgrad %s %s',
+            extensions=None,
+        ),
+        in_file=dict(
+            argstr='%s',
+            extensions=None,
+            mandatory=True,
+            position=-2,
+        ),
+        interpolation=dict(
+            argstr='-interp %s',
+            usedefault=True,
+        ),
+        nthreads=dict(
+            argstr='-nthreads %d',
+            nohash=True,
+        ),
+        out_file=dict(
+            argstr='%s',
+            extensions=None,
+            keep_extension=True,
+            name_source=['in_file'],
+            name_template='%s_resized',
+            position=-1,
+        ),
+        scale_factor=dict(
+            argstr='-scale %g,%g,%g',
+            mandatory=True,
+            xor=['image_size', 'voxel_size'],
+        ),
+        voxel_size=dict(
+            argstr='-voxel %g,%g,%g',
+            mandatory=True,
+            xor=['image_size', 'scale_factor'],
+        ),
+    )
+    inputs = MRResize.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_MRResize_outputs():
+    output_map = dict(out_file=dict(extensions=None, ), )
+    outputs = MRResize.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/mrtrix3/utils.py

@@ -677,3 +677,99 @@ def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs['out_file'] = op.abspath(self.inputs.out_file)
         return outputs
+
+
+class MRResizeInputSpec(MRTrix3BaseInputSpec):
+    in_file = File(
+        exists=True,
+        argstr='%s',
+        position=-2,
+        mandatory=True,
+        desc='input DWI image'
+    )
+    image_size = traits.Tuple(
+        (traits.Int, traits.Int, traits.Int),
+        argstr='-size %d,%d,%d',
+        mandatory=True,
+        desc='Number of voxels in each dimension of output image',
+        xor=['voxel_size', 'scale_factor'],
+    )
+    voxel_size = traits.Tuple(
+        (traits.Float, traits.Float, traits.Float),
+        argstr='-voxel %g,%g,%g',
+        mandatory=True,
+        desc='Desired voxel size in mm for the output image',
+        xor=['image_size', 'scale_factor'],
+    )
+    scale_factor = traits.Tuple(
+        (traits.Float, traits.Float, traits.Float),
+        argstr='-scale %g,%g,%g',
+        mandatory=True,
+        desc='Scale factors to rescale the image by in each dimension',
+        xor=['image_size', 'voxel_size'],
+    )
+    interpolation = traits.Enum(
+        'cubic',
+        'nearest',
+        'linear',
+        'sinc',
+        argstr='-interp %s',
+        usedefault=True,
+        desc='set the interpolation method to use when resizing (choices: '
+        'nearest, linear, cubic, sinc. Default: cubic).',
+    )
+    out_file = File(
+        argstr='%s',
+        name_template='%s_resized',
+        name_source=['in_file'],
+        keep_extension=True,
+        position=-1,
+        desc='the output resized DWI image',
+    )
+
+
+class MRResizeOutputSpec(TraitedSpec):
+    out_file = File(desc='the output resized DWI image', exists=True)
+
+
+class MRResize(MRTrix3Base):
+    """
+    Resize an image by defining the new image resolution, voxel size or a
+    scale factor. If the image is 4D, then only the first 3 dimensions can be
+    resized. Also, if the image is down-sampled, the appropriate smoothing is
+    automatically applied using Gaussian smoothing.
+    For more information, see
+    <https://mrtrix.readthedocs.io/en/latest/reference/commands/mrresize.html>
+
+    Example
+    -------
+    >>> import nipype.interfaces.mrtrix3 as mrt
+
+    Defining the new image resolution:
+    >>> image_resize = mrt.MRResize()
+    >>> image_resize.inputs.in_file = 'dwi.mif'
+    >>> image_resize.inputs.image_size = (256, 256, 144)
+    >>> image_resize.cmdline                               # doctest: +ELLIPSIS
+    'mrresize -size 256,256,144 -interp cubic dwi.mif dwi_resized.mif'
+    >>> image_resize.run()                                 # doctest: +SKIP
+
+    Defining the new image's voxel size:
+    >>> voxel_resize = mrt.MRResize()
+    >>> voxel_resize.inputs.in_file = 'dwi.mif'
+    >>> voxel_resize.inputs.voxel_size = (1, 1, 1)
+    >>> voxel_resize.cmdline                               # doctest: +ELLIPSIS
+    'mrresize -interp cubic -voxel 1,1,1 dwi.mif dwi_resized.mif'
+    >>> voxel_resize.run()                                 # doctest: +SKIP
+
+    Defining the scale factor of each image dimension:
+    >>> scale_resize = mrt.MRResize()
+    >>> scale_resize.inputs.in_file = 'dwi.mif'
+    >>> scale_resize.inputs.scale_factor = (0.5,0.5,0.5)
+    >>> scale_resize.cmdline                               # doctest: +ELLIPSIS
+    'mrresize -interp cubic -scale 0.5,0.5,0.5 dwi.mif dwi_resized.mif'
+    >>> scale_resize.run()                                 # doctest: +SKIP
+    """
+
+    _cmd = 'mrresize'
+    input_spec = MRResizeInputSpec
+    output_spec = MRResizeOutputSpec

nipype/utils/filemanip.py

@@ -40,14 +40,16 @@
 
 PY3 = sys.version_info[0] >= 3
 
-
-class FileNotFoundError(OSError):  # noqa
-    """Defines the exception for Python 2."""
-
-    def __init__(self, path):
-        """Initialize the exception."""
-        super(FileNotFoundError, self).__init__(
-            2, 'No such file or directory', '%s' % path)
+try:
+    from builtins import FileNotFoundError
+except ImportError:  # PY27
+    class FileNotFoundError(OSError):  # noqa
+        """Defines the exception for Python 2."""
+
+        def __init__(self, path):
+            """Initialize the exception."""
+            super(FileNotFoundError, self).__init__(
+                2, 'No such file or directory', '%s' % path)
 
 
 USING_PATHLIB2 = False