Symplifying the interfaces when possible using name_source/name_template

Author: byvernault

nipype/interfaces/niftyseg/base.py

@@ -20,7 +20,7 @@
 
 """
 
-from nipype.interfaces.base import CommandLine, isdefined
+from nipype.interfaces.base import CommandLine
 from nipype.utils.filemanip import split_filename
 import os
 import subprocess
@@ -89,16 +89,3 @@ def _gen_fname(self, basename, out_dir=None, suffix=None, ext=None):
         if suffix is not None:
             final_bn = ''.join((final_bn, suffix))
         return os.path.abspath(os.path.join(out_dir, final_bn + final_ext))
-
-    def _gen_filename(self, name):
-        if name == 'out_file':
-            return self._gen_fname(self.inputs.in_file, suffix=self._suffix)
-        return None
-
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        if isdefined(self.inputs.out_file):
-            outputs['out_file'] = self.inputs.out_file
-        else:
-            outputs['out_file'] = self._gen_filename('out_file')
-        return outputs

nipype/interfaces/niftyseg/em.py

@@ -18,9 +18,7 @@
     >>> os.chdir(datadir)
 """
 
-import os
-
-from ..base import (TraitedSpec, File, traits, isdefined, CommandLineInputSpec,
+from ..base import (TraitedSpec, File, traits, CommandLineInputSpec,
                     InputMultiPath)
 from .base import NiftySegCommand, get_custom_path
 
@@ -91,14 +89,17 @@ class EMInputSpec(CommandLineInputSpec):
                                 desc=desc)
 
     # outputs
-    out_file = File(argstr='-out %s',
-                    genfile=True,
+    out_file = File(name_source=['in_file'],
+                    name_template='%s_em.nii.gz',
+                    argstr='-out %s',
                     desc='Output segmentation')
-    out_bc_file = File(argstr='-bc_out %s',
-                       genfile=True,
+    out_bc_file = File(name_source=['in_file'],
+                       name_template='%s_bc_em.nii.gz',
+                       argstr='-bc_out %s',
                        desc='Output bias corrected image')
-    out_outlier_file = File(argstr='-out_outlier %s',
-                            genfile=True,
+    out_outlier_file = File(name_source=['in_file'],
+                            name_template='%s_outlier_em.nii.gz',
+                            argstr='-out_outlier %s',
                             desc='Output outlierness image')
 
 
@@ -126,9 +127,9 @@ class EM(NiftySegCommand):
     >>> node = niftyseg.EM()
     >>> node.inputs.in_file = 'im1.nii'
     >>> node.inputs.no_prior = 4
-    >>> node.cmdline  # doctest: +ELLIPSIS +ALLOW_UNICODE
-    'seg_EM -in im1.nii -nopriors 4 -bc_out .../im1_bc_em.nii \
--out .../im1_em.nii -out_outlier .../im1_outlier_em.nii'
+    >>> node.cmdline  # doctest: +ALLOW_UNICODE
+    'seg_EM -in im1.nii -nopriors 4 -bc_out im1_bc_em.nii.gz \
+-out im1_em.nii.gz -out_outlier im1_outlier_em.nii.gz'
 
     """
     _cmd = get_custom_path('seg_EM')
@@ -143,32 +144,3 @@ def _format_arg(self, opt, spec, val):
             return '-priors %d %s' % (_nb_priors, ' '.join(self.inputs.priors))
         else:
             return super(EM, self)._format_arg(opt, spec, val)
-
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        outputs['out_file'] = self.inputs.out_file
-        if not isdefined(self.inputs.out_file):
-            outputs['out_file'] = self._gen_fname(self.inputs.in_file,
-                                                  suffix=self._suffix)
-        outputs['out_file'] = os.path.abspath(outputs['out_file'])
-        outputs['out_bc_file'] = self.inputs.out_bc_file
-        if not isdefined(self.inputs.out_bc_file):
-            outputs['out_bc_file'] = self._gen_fname(
-                    self.inputs.in_file, suffix=('_bc%s' % self._suffix))
-        outputs['out_bc_file'] = os.path.abspath(outputs['out_bc_file'])
-        outputs['out_outlier_file'] = self.inputs.out_outlier_file
-        if not isdefined(self.inputs.out_outlier_file):
-            outputs['out_outlier_file'] = self._gen_fname(
-                    self.inputs.in_file, suffix=('_outlier%s' % self._suffix))
-        outputs['out_outlier_file'] = os.path.abspath(
-                    outputs['out_outlier_file'])
-        return outputs
-
-    def _gen_filename(self, name):
-        if name == 'out_file':
-            return self._list_outputs()['out_file']
-        if name == 'out_bc_file':
-            return self._list_outputs()['out_bc_file']
-        if name == 'out_outlier_file':
-            return self._list_outputs()['out_outlier_file']
-        return None

nipype/interfaces/niftyseg/lesions.py

@@ -18,10 +18,9 @@
     >>> os.chdir(datadir)
 """
 
-import os
 import warnings
 
-from ..base import TraitedSpec, File, traits, isdefined, CommandLineInputSpec
+from ..base import TraitedSpec, File, traits, CommandLineInputSpec
 from .base import NiftySegCommand, get_custom_path
 
 
@@ -39,7 +38,9 @@ class FillLesionsInputSpec(CommandLineInputSpec):
                        desc='Lesion mask', position=2)
 
     # Output file name
-    out_file = File(desc='The output filename of the fill lesions results',
+    out_file = File(name_source=['in_file'],
+                    name_template='%s_lesions_filled.nii.gz',
+                    desc='The output filename of the fill lesions results',
                     argstr='-o %s', position=3)
 
     # Optional arguments
@@ -108,31 +109,10 @@ class FillLesions(NiftySegCommand):
     >>> node = niftyseg.FillLesions()
     >>> node.inputs.in_file = 'im1.nii'
     >>> node.inputs.lesion_mask = 'im2.nii'
-    >>> node.cmdline  # doctest: +ELLIPSIS +ALLOW_UNICODE
-    'seg_FillLesions -i im1.nii -l im2.nii -o .../im1_lesions_filled.nii'
+    >>> node.cmdline  # doctest: +ALLOW_UNICODE
+    'seg_FillLesions -i im1.nii -l im2.nii -o im1_lesions_filled.nii.gz'
 
     """
     _cmd = get_custom_path('seg_FillLesions')
     input_spec = FillLesionsInputSpec
     output_spec = FillLesionsOutputSpec
-
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        outputs['out_file'] = self.inputs.out_file
-        if not isdefined(self.inputs.out_file):
-            outputs['out_file'] = self._gen_filename('out_file')
-        outputs['out_file'] = os.path.abspath(outputs['out_file'])
-        return outputs
-
-    def _parse_inputs(self, skip=None):
-        """Set non-mandatory inputs if not given by user."""
-        skip = []
-        if not isdefined(self.inputs.out_file):
-            self.inputs.out_file = self._gen_filename('out_file')
-        return super(FillLesions, self)._parse_inputs(skip=skip)
-
-    def _gen_filename(self, name):
-        if name == 'out_file':
-            return self._gen_fname(self.inputs.in_file,
-                                   suffix='_lesions_filled')
-        return None

nipype/interfaces/niftyseg/maths.py

@@ -17,7 +17,6 @@
     >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
     >>> os.chdir(datadir)
 """
-import os
 
 from ..base import (TraitedSpec, File, traits, isdefined, CommandLineInputSpec,
                     NipypeInterfaceError)
@@ -71,6 +70,7 @@ class MathsCommand(NiftySegCommand):
     _cmd = get_custom_path('seg_maths')
     input_spec = MathsInput
     output_spec = MathsOutput
+    _suffix = '_maths'
 
     def _list_outputs(self):
         outputs = self.output_spec().get()
@@ -79,11 +79,11 @@ def _list_outputs(self):
         if suffix != '_merged' and isdefined(self.inputs.operation):
             suffix = '_' + self.inputs.operation
 
-        outputs['out_file'] = self.inputs.out_file
-        if not isdefined(self.inputs.out_file):
+        if isdefined(self.inputs.out_file):
+            outputs['out_file'] = self.inputs.out_file
+        else:
             outputs['out_file'] = self._gen_fname(self.inputs.in_file,
                                                   suffix=suffix)
-        outputs['out_file'] = os.path.abspath(outputs['out_file'])
         return outputs
 
     def _gen_filename(self, name):
@@ -149,8 +149,8 @@ class UnaryMaths(MathsCommand):
     >>> node.inputs.in_file = 'im1.nii'
     >>> node.inputs.operation = 'sqrt'
     >>> node.inputs.output_datatype = 'float'
-    >>> node.cmdline  # doctest: +ELLIPSIS +ALLOW_UNICODE
-    'seg_maths im1.nii -sqrt -odt float .../im1_sqrt.nii'
+    >>> node.cmdline  # doctest: +ALLOW_UNICODE
+    'seg_maths im1.nii -sqrt -odt float im1_sqrt.nii'
 
     """
     input_spec = UnaryMathsInput
@@ -237,8 +237,8 @@ class BinaryMaths(MathsCommand):
     >>> node.inputs.operation = 'sub'
     >>> node.inputs.operand_file = 'im2.nii'
     >>> node.inputs.output_datatype = 'float'
-    >>> node.cmdline  # doctest: +ELLIPSIS +ALLOW_UNICODE
-    'seg_maths im1.nii -sub im2.nii -odt float .../im1_sub.nii'
+    >>> node.cmdline  # doctest: +ALLOW_UNICODE
+    'seg_maths im1.nii -sub im2.nii -odt float im1_sub.nii'
 
     """
     input_spec = BinaryMathsInput
@@ -256,19 +256,12 @@ def _format_arg(self, opt, spec, val):
         return super(BinaryMaths, self)._format_arg(opt, spec, val)
 
     def _list_outputs(self):
-        outputs = self.output_spec().get()
-        self._suffix = '_' + self.inputs.operation
-
-        outputs['out_file'] = self.inputs.out_file
-        if not isdefined(self.inputs.out_file):
-            if isdefined(self.inputs.operation) and \
-               self.inputs.operation == 'hdr_copy':
-                outputs['out_file'] = self._gen_fname(self.inputs.operand_file,
-                                                      suffix=self._suffix)
-            else:
-                outputs['out_file'] = self._gen_fname(self.inputs.in_file,
-                                                      suffix=self._suffix)
-        outputs['out_file'] = os.path.abspath(outputs['out_file'])
+        outputs = super(BinaryMaths, self)._list_outputs()
+
+        if self.inputs.operation == 'hdr_copy':
+            outputs['out_file'] = self._gen_fname(
+                self.inputs.operand_file,
+                suffix='_{0}'.format(self.inputs.operation))
         return outputs
 
 
@@ -312,8 +305,8 @@ class BinaryMathsInteger(MathsCommand):
     >>> node.inputs.operation = 'dil'
     >>> node.inputs.operand_value = 2
     >>> node.inputs.output_datatype = 'float'
-    >>> node.cmdline  # doctest: +ELLIPSIS +ALLOW_UNICODE
-    'seg_maths im1.nii -dil 2 -odt float .../im1_dil.nii'
+    >>> node.cmdline  # doctest: +ALLOW_UNICODE
+    'seg_maths im1.nii -dil 2 -odt float im1_dil.nii'
 
     """
     input_spec = BinaryMathsInputInteger
@@ -383,8 +376,8 @@ class TupleMaths(MathsCommand):
     >>> node.inputs.operand_file1 = 'im2.nii'
     >>> node.inputs.operand_value2 = 2.0
     >>> node.inputs.output_datatype = 'float'
-    >>> node.cmdline  # doctest: +ELLIPSIS +ALLOW_UNICODE
-    'seg_maths im1.nii -lncc im2.nii 2.00000000 -odt float .../im1_lncc.nii'
+    >>> node.cmdline  # doctest: +ALLOW_UNICODE
+    'seg_maths im1.nii -lncc im2.nii 2.00000000 -odt float im1_lncc.nii'
 
     """
     input_spec = TupleMathsInput
@@ -424,9 +417,9 @@ class Merge(MathsCommand):
     >>> node.inputs.merge_files = files
     >>> node.inputs.dimension = 2
     >>> node.inputs.output_datatype = 'float'
-    >>> node.cmdline  # doctest: +ELLIPSIS +ALLOW_UNICODE
+    >>> node.cmdline  # doctest: +ALLOW_UNICODE
     'seg_maths im1.nii -merge 2 2 im2.nii im3.nii -odt float \
-.../im1_merged.nii'
+im1_merged.nii'
 
     """
     input_spec = MergeInput

nipype/interfaces/niftyseg/patchmatch.py

@@ -38,16 +38,17 @@ class PatchMatchInputSpec(CommandLineInputSpec):
                      position=2)
 
     database_file = File(argstr='-db %s',
-                         genfile=True,
+                         exists=True,
                          mandatory=True,
                          desc='Database with the segmentations',
                          position=3)
 
     # Output file name
-    out_file = File(desc='The output filename of the patchmatch results',
+    out_file = File(name_source=['in_file'],
+                    name_template='%s_pm.nii.gz',
+                    desc='The output filename of the patchmatch results',
                     argstr='-o %s',
-                    position=4,
-                    genfile=True)
+                    position=4)
 
     # Optional arguments
     patch_size = traits.Int(desc="Patch size, #voxels",
@@ -105,25 +106,11 @@ class PatchMatch(NiftySegCommand):
     >>> node.inputs.in_file = 'im1.nii'
     >>> node.inputs.mask_file = 'im2.nii'
     >>> node.inputs.database_file = 'db.xml'
-    >>> node.cmdline  # doctest: +ELLIPSIS +ALLOW_UNICODE
-    'seg_PatchMatch -i im1.nii -m im2.nii -db db.xml -o .../im1_pm.nii'
+    >>> node.cmdline  # doctest: +ALLOW_UNICODE
+    'seg_PatchMatch -i im1.nii -m im2.nii -db db.xml -o im1_pm.nii.gz'
 
     """
     _cmd = get_custom_path('seg_PatchMatch')
     input_spec = PatchMatchInputSpec
     output_spec = PatchMatchOutputSpec
     _suffix = '_pm'
-
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        outputs['out_file'] = self.inputs.out_file
-        if not isdefined(self.inputs.out_file):
-            outputs['out_file'] = self._gen_fname(self.inputs.in_file,
-                                                  suffix=self._suffix)
-        outputs['out_file'] = os.path.abspath(outputs['out_file'])
-        return outputs
-
-    def _gen_filename(self, name):
-        if name == 'out_file':
-            return self._list_outputs()['out_file']
-        return None