Symplifying interfaces using name_source/name_template when possible

Author: byvernault

nipype/interfaces/niftyreg/reg.py

@@ -120,11 +120,13 @@ class RegAladinInputSpec(CommandLineInputSpec):
                               argstr='-omp %i')
 
     # Affine output transformation matrix file
-    aff_file = File(genfile=True,
+    aff_file = File(name_source=['flo_file'],
+                    name_template='%s_aff.txt',
                     desc='The output affine matrix file',
                     argstr='-aff %s')
     # Result warped image file
-    res_file = File(genfile=True,
+    res_file = File(name_source=['flo_file'],
+                    name_template='%s_res.nii.gz',
                     desc='The affine transformed floating image',
                     argstr='-res %s')
 
@@ -155,35 +157,17 @@ class RegAladin(NiftyRegCommand):
     >>> node.inputs.flo_file = 'im2.nii'
     >>> node.inputs.rmask_file = 'mask.nii'
     >>> node.inputs.omp_core_val = 4
-    >>> node.cmdline  # doctest: +ELLIPSIS +ALLOW_UNICODE
-    'reg_aladin -aff .../im2_aff.txt -flo im2.nii -omp 4 -ref im1.nii \
--res .../im2_res.nii.gz -rmask mask.nii'
+    >>> node.cmdline  # doctest: +ALLOW_UNICODE
+    'reg_aladin -aff im2_aff.txt -flo im2.nii -omp 4 -ref im1.nii \
+-res im2_res.nii.gz -rmask mask.nii'
 
     """
     _cmd = get_custom_path('reg_aladin')
     input_spec = RegAladinInputSpec
     output_spec = RegAladinOutputSpec
 
-    def _gen_filename(self, name):
-        if name == 'aff_file':
-            return self._gen_fname(self.inputs.flo_file,
-                                   suffix='_aff', ext='.txt')
-        if name == 'res_file':
-            return self._gen_fname(self.inputs.flo_file,
-                                   suffix='_res', ext='.nii.gz')
-        return None
-
     def _list_outputs(self):
-        outputs = self.output_spec().get()
-
-        if isdefined(self.inputs.aff_file):
-            outputs['aff_file'] = self.inputs.aff_file
-        else:
-            outputs['aff_file'] = self._gen_filename('aff_file')
-        if isdefined(self.inputs.res_file):
-            outputs['res_file'] = self.inputs.aff_file
-        else:
-            outputs['res_file'] = self._gen_filename('res_file')
+        outputs = super(RegAladin, self)._list_outputs()
 
         # Make a list of the linear transformation file and the input image
         aff = os.path.abspath(outputs['aff_file'])
@@ -349,11 +333,13 @@ class RegF3DInputSpec(CommandLineInputSpec):
                               argstr='-omp %i')
 
     # Output CPP image file
-    cpp_file = File(genfile=True,
+    cpp_file = File(name_source=['flo_file'],
+                    name_template='%s_cpp.nii.gz',
                     desc='The output CPP file',
                     argstr='-cpp %s')
     # Output warped image file
-    res_file = File(genfile=True,
+    res_file = File(name_source=['flo_file'],
+                    name_template='%s_res.nii.gz',
                     desc='The output resampled image',
                     argstr='-res %s')
 
@@ -385,9 +371,9 @@ class RegF3D(NiftyRegCommand):
     >>> node.inputs.flo_file = 'im2.nii'
     >>> node.inputs.rmask_file = 'mask.nii'
     >>> node.inputs.omp_core_val = 4
-    >>> node.cmdline  # doctest: +ELLIPSIS +ALLOW_UNICODE
-    'reg_f3d -cpp .../im2_cpp.nii.gz -flo im2.nii -omp 4 -ref im1.nii \
--res .../im2_res.nii.gz -rmask mask.nii'
+    >>> node.cmdline  # doctest: +ALLOW_UNICODE
+    'reg_f3d -cpp im2_cpp.nii.gz -flo im2.nii -omp 4 -ref im1.nii \
+-res im2_res.nii.gz -rmask mask.nii'
 
     """
     _cmd = get_custom_path('reg_f3d')
@@ -399,26 +385,8 @@ def _remove_extension(in_file):
         dn, bn, _ = split_filename(in_file)
         return os.path.join(dn, bn)
 
-    def _gen_filename(self, name):
-        if name == 'res_file':
-            return self._gen_fname(self.inputs.flo_file,
-                                   suffix='_res', ext='.nii.gz')
-        if name == 'cpp_file':
-            return self._gen_fname(self.inputs.flo_file,
-                                   suffix='_cpp', ext='.nii.gz')
-
     def _list_outputs(self):
-        outputs = self.output_spec().get()
-
-        if isdefined(self.inputs.res_file):
-            outputs['res_file'] = self.inputs.res_file
-        else:
-            outputs['res_file'] = self._gen_filename('res_file')
-
-        if isdefined(self.inputs.cpp_file):
-            outputs['cpp_file'] = self.inputs.cpp_file
-        else:
-            outputs['cpp_file'] = self._gen_filename('cpp_file')
+        outputs = super(RegF3D, self)._list_outputs()
 
         if self.inputs.vel_flag is True:
             res_name = self._remove_extension(outputs['res_file'])
@@ -436,4 +404,5 @@ def _list_outputs(self):
             cpp_file = os.path.abspath(outputs['cpp_file'])
             flo_file = os.path.abspath(self.inputs.flo_file)
             outputs['avg_output'] = '%s %s' % (cpp_file, flo_file)
+
         return outputs

nipype/interfaces/niftyreg/regutils.py

@@ -206,7 +206,8 @@ class RegToolsInputSpec(CommandLineInputSpec):
                    mandatory=True)
 
     # Output file path
-    out_file = File(genfile=True,
+    out_file = File(name_source=['in_file'],
+                    name_template='%s_tools.nii.gz',
                     desc='The output file name',
                     argstr='-out %s')
 
@@ -301,8 +302,8 @@ class RegTools(NiftyRegCommand):
     >>> node.inputs.in_file = 'im1.nii'
     >>> node.inputs.mul_val = 4
     >>> node.inputs.omp_core_val = 4
-    >>> node.cmdline  # doctest: +ELLIPSIS +ALLOW_UNICODE
-    'reg_tools -in im1.nii -mul 4.0 -omp 4 -out .../im1_tools.nii.gz'
+    >>> node.cmdline  # doctest: +ALLOW_UNICODE
+    'reg_tools -in im1.nii -mul 4.0 -omp 4 -out im1_tools.nii.gz'
 
     """
     _cmd = get_custom_path('reg_tools')

nipype/interfaces/niftyreg/tests/test_auto_RegAladin.py

@@ -7,7 +7,8 @@ def test_RegAladin_inputs():
     input_map = dict(aff_direct_flag=dict(argstr='-affDirect',
     ),
     aff_file=dict(argstr='-aff %s',
-    genfile=True,
+    name_source=['flo_file'],
+    name_template='%s_aff.txt',
     ),
     args=dict(argstr='%s',
     ),
@@ -56,7 +57,8 @@ def test_RegAladin_inputs():
     ref_up_val=dict(argstr='-refUpThr %f',
     ),
     res_file=dict(argstr='-res %s',
-    genfile=True,
+    name_source=['flo_file'],
+    name_template='%s_res.nii.gz',
     ),
     rig_only_flag=dict(argstr='-rigOnly',
     ),

nipype/interfaces/niftyreg/tests/test_auto_RegF3D.py

@@ -13,7 +13,8 @@ def test_RegF3D_inputs():
     be_val=dict(argstr='-be %f',
     ),
     cpp_file=dict(argstr='-cpp %s',
-    genfile=True,
+    name_source=['flo_file'],
+    name_template='%s_cpp.nii.gz',
     ),
     environ=dict(nohash=True,
     usedefault=True,
@@ -90,7 +91,8 @@ def test_RegF3D_inputs():
     ref_smooth_val=dict(argstr='-smooR %f',
     ),
     res_file=dict(argstr='-res %s',
-    genfile=True,
+    name_source=['flo_file'],
+    name_template='%s_res.nii.gz',
     ),
     rlwth2_thr_val=dict(argstr='-rLwTh %d %f',
     ),

nipype/interfaces/niftyreg/tests/test_auto_RegTools.py

@@ -36,7 +36,8 @@ def test_RegTools_inputs():
     omp_core_val=dict(argstr='-omp %i',
     ),
     out_file=dict(argstr='-out %s',
-    genfile=True,
+    name_source=['in_file'],
+    name_template='%s_tools.nii.gz',
     ),
     rms_val=dict(argstr='-rms %s',
     ),

nipype/interfaces/niftyreg/tests/test_reg.py

@@ -2,11 +2,11 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 
+import pytest
+
 from nipype.interfaces.niftyreg import (no_niftyreg, get_custom_path,
                                         RegAladin, RegF3D)
 from nipype.testing import example_data
-import os
-import pytest
 
 
 @pytest.mark.skipif(
@@ -37,11 +37,12 @@ def test_reg_aladin():
 -rmask {rmask}'
     expected_cmd = cmd_tmp.format(
         cmd=get_custom_path('reg_aladin'),
-        aff=os.path.join(os.getcwd(), 'im2_aff.txt'),
+        aff='im2_aff.txt',
         flo=flo_file,
         ref=ref_file,
-        res=os.path.join(os.getcwd(), 'im2_res.nii.gz'),
-        rmask=rmask_file)
+        res='im2_res.nii.gz',
+        rmask=rmask_file,
+    )
 
     assert nr_aladin.cmdline == expected_cmd
 
@@ -77,10 +78,11 @@ def test_reg_f3d():
 -ref {ref} -res {res} -rmask {rmask} -vel'
     expected_cmd = cmd_tmp.format(
         cmd=get_custom_path('reg_f3d'),
-        cpp=os.path.join(os.getcwd(), 'im2_cpp.nii.gz'),
+        cpp='im2_cpp.nii.gz',
         flo=flo_file,
         ref=ref_file,
-        res=os.path.join(os.getcwd(), 'im2_res.nii.gz'),
-        rmask=rmask_file)
+        res='im2_res.nii.gz',
+        rmask=rmask_file,
+    )
 
     assert nr_f3d.cmdline == expected_cmd

nipype/interfaces/niftyreg/tests/test_regutils.py

@@ -156,7 +156,7 @@ def test_reg_tools_mul():
     expected_cmd = cmd_tmp.format(
         cmd=get_custom_path('reg_tools'),
         in_file=in_file,
-        out_file=os.path.join(os.getcwd(), 'im1_tools.nii.gz'))
+        out_file='im1_tools.nii.gz')
 
     assert nr_tools.cmdline == expected_cmd
 
@@ -169,7 +169,7 @@ def test_reg_tools_mul():
     expected_cmd = cmd_tmp.format(
         cmd=get_custom_path('reg_tools'),
         in_file=in_file,
-        out_file=os.path.join(os.getcwd(), 'im1_tools.nii.gz'))
+        out_file='im1_tools.nii.gz')
 
     assert nr_tools_2.cmdline == expected_cmd