Merge branch 'master' into enh/revising-popen-calls

Author: mgxd

CHANGES

@@ -1,12 +1,14 @@
 Upcoming release
 ================
 
+
 0.14.0 (<TBD>)
 ==============
 
 ###### [Full changelog](https://github.com/nipy/nipype/milestone/13)
 
 * MAINT: Revise use of `subprocess.Popen` (https://github.com/nipy/nipype/pull/2289)
+* ENH: Memorize version checks (https://github.com/nipy/nipype/pull/2274, https://github.com/nipy/nipype/pull/2295)
 
 
 0.14.0rc1 (November 21, 2017)

nipype/interfaces/afni/tests/test_auto_Unifize.py

@@ -32,6 +32,8 @@ def test_Unifize_inputs():
     name_source='in_file',
     ),
     outputtype=dict(),
+    rbt=dict(argstr='-rbt %f %f %f',
+    ),
     scale_file=dict(argstr='-ssave %s',
     ),
     t2=dict(argstr='-T2',

nipype/interfaces/afni/utils.py

@@ -2329,6 +2329,14 @@ class UnifizeInputSpec(AFNICommandInputSpec):
         argstr='-EPI',
         requires=['no_duplo', 't2'],
         xor=['gm'])
+    rbt = traits.Tuple(
+        traits.Float(), traits.Float(), traits.Float(),
+        desc='Option for AFNI experts only.'
+             'Specify the 3 parameters for the algorithm:\n'
+             'R = radius; same as given by option \'-Urad\', [default=18.3]\n'
+             'b = bottom percentile of normalizing data range, [default=70.0]\n'
+             'r = top percentile of normalizing data range, [default=80.0]\n',
+        argstr='-rbt %f %f %f')
 
 
 class UnifizeOutputSpec(TraitedSpec):

nipype/interfaces/fsl/base.py

@@ -26,56 +26,47 @@
 
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
-from builtins import open, object
 
 from glob import glob
 import os
 
 from ... import logging
 from ...utils.filemanip import fname_presuffix
-from ..base import traits, isdefined, CommandLine, CommandLineInputSpec
+from ..base import traits, isdefined, CommandLine, CommandLineInputSpec, PackageInfo
 from ...external.due import BibTeX
 
 IFLOGGER = logging.getLogger('interface')
 
 
-class Info(object):
-    """Handle fsl output type and version information.
-
-    version refers to the version of fsl on the system
+class Info(PackageInfo):
+    """
+    Handle FSL ``output_type`` and version information.
 
     output type refers to the type of file fsl defaults to writing
     eg, NIFTI, NIFTI_GZ
 
+    Examples
+    --------
+
+    >>> from nipype.interfaces.fsl import Info
+    >>> Info.version()  # doctest: +SKIP
+    >>> Info.output_type()  # doctest: +SKIP
+
+
     """
 
     ftypes = {'NIFTI': '.nii',
               'NIFTI_PAIR': '.img',
               'NIFTI_GZ': '.nii.gz',
               'NIFTI_PAIR_GZ': '.img.gz'}
 
-    @staticmethod
-    def version():
-        """Check for fsl version on system
-
-        Parameters
-        ----------
-        None
-
-        Returns
-        -------
-        version : str
-           Version number as string or None if FSL not found
+    if os.getenv('FSLDIR'):
+        version_file = os.path.join(
+            os.getenv('FSLDIR'), 'etc', 'fslversion')
 
-        """
-        # find which fsl being used....and get version from
-        # /path/to/fsl/etc/fslversion
-        try:
-            basedir = os.environ['FSLDIR']
-        except KeyError:
-            return None
-        out = open('%s/etc/fslversion' % (basedir)).read()
-        return out.strip('\n')
+    @staticmethod
+    def parse_version(raw_info):
+        return raw_info.splitlines()[0]
 
     @classmethod
     def output_type_to_ext(cls, output_type):