tst: cleaned up tests

Author: satra

nipype/interfaces/freesurfer/model.py

@@ -782,9 +782,9 @@ class MS_LDAInputSpec(FSTraitedSpec):
     weight_file = traits.File(argstr='-weight %s', mandatory=True,
                         desc='filename for the LDA weights (input or output)')
     vol_synth_file = traits.File(exists=False, argstr='-synth %s',
-                               mandatory=True,
-                               desc='filename for the synthesized output volume',
-                               xor=['vol_synth_file', 'output_synth'])
+                                 mandatory=True,
+                                 desc=('filename for the synthesized output '
+                                       'volume'))
     label_file = traits.File(exists=True, argstr='-label %s',
                              desc='filename of the label volume')
     mask_file = traits.File(exists=True, argstr='-mask %s',

nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py

@@ -14,15 +14,8 @@ def test_MS_LDA_inputs():
     sep=' ',
     argstr='-lda %s',
     ),
-    output_synth=dict(new_name='vol_synth_file',
-    mandatory=True,
-    xor=['vol_synth_file', 'output_synth'],
-    deprecated='0.8',
-    argstr='-synth %s',
-    ),
     vol_synth_file=dict(mandatory=True,
     argstr='-synth %s',
-    xor=['vol_synth_file', 'output_synth'],
     ),
     shift=dict(argstr='-shift %d',
     ),

nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py

@@ -21,7 +21,6 @@ def test_Surface2VolTransform_inputs():
     args=dict(argstr='%s',
     ),
     surf_name=dict(argstr='--surf %s',
-    exists=True,
     ),
     vertexvol_file=dict(name_source=['source_file'],
     hash_files=False,
@@ -42,7 +41,6 @@ def test_Surface2VolTransform_inputs():
     argstr='--surfval %s',
     ),
     projfrac=dict(argstr='--projfrac %s',
-    exists=True,
     ),
     mkmask=dict(argstr='--mkmask',
     ),

nipype/interfaces/freesurfer/utils.py

@@ -382,33 +382,47 @@ def _gen_filename(self, name):
             return self._list_outputs()[name]
         return None
 
+
 class Surface2VolTransformInputSpec(FSTraitedSpec):
     source_file = File(exists=True, argstr='--surfval %s',
                       copyfile=False, mandatory=True,
                       desc='This is the source of the surface values')
-    hemi = traits.Str(argstr='--hemi %s', mandatory=True, desc='hemisphere of data')
-    transformed_file = File(name_template="%s_asVol.nii", desc='Output volume', argstr='--outvol %s',
+    hemi = traits.Str(argstr='--hemi %s', mandatory=True,
+                      desc='hemisphere of data')
+    transformed_file = File(name_template="%s_asVol.nii", desc='Output volume',
+                            argstr='--outvol %s',
                             name_source=['source_file'], hash_files=False)
     reg_file = File(exists=True, argstr='--volreg %s',
                     mandatory=True,
                     desc='tkRAS-to-tkRAS matrix   (tkregister2 format)',
                     xor=['subject_id'])
     template_file = File(exists=True, argstr='--template %s',
                       desc='Output template volume')
-    mkmask = traits.Bool(desc='make a mask instead of loading surface values', argstr='--mkmask')
-    vertexvol_file = File(name_template="%s_asVol_vertex.nii", desc='Path name of the vertex output '
-                          'volume, which is the same as output volume except that the value of each '
-                          'voxel is the vertex-id that is mapped to that voxel.',
-                          argstr='--vtxvol %s', name_source=['source_file'], hash_files=False)
-    surf_name = traits.Str(exists=True, argstr='--surf %s',desc='surfname (default is white)')
-    projfrac = traits.Float(exists=True, argstr='--projfrac %s',desc='thickness fraction')
-    subjects_dir = traits.Str(argstr='--sd %s',desc='freesurfer subjects directory defaults to $SUBJECTS_DIR')
-    subject_id = traits.Str(argstr='--identity %s',desc='subject id', xor=['reg_file'])
+    mkmask = traits.Bool(desc='make a mask instead of loading surface values',
+                         argstr='--mkmask')
+    vertexvol_file = File(name_template="%s_asVol_vertex.nii",
+                          desc=('Path name of the vertex output volume, which '
+                                'is the same as output volume except that the '
+                                'value of each voxel is the vertex-id that is '
+                                'mapped to that voxel.'),
+                          argstr='--vtxvol %s', name_source=['source_file'],
+                          hash_files=False)
+    surf_name = traits.Str(argstr='--surf %s',
+                           desc='surfname (default is white)')
+    projfrac = traits.Float(argstr='--projfrac %s', desc='thickness fraction')
+    subjects_dir = traits.Str(argstr='--sd %s',
+                              desc=('freesurfer subjects directory defaults to '
+                                    '$SUBJECTS_DIR'))
+    subject_id = traits.Str(argstr='--identity %s',desc='subject id',
+                            xor=['reg_file'])
+
 
 class Surface2VolTransformOutputSpec(TraitedSpec):
-    transformed_file = File(exists=True, desc='Path to output file if used normally')
+    transformed_file = File(exists=True,
+                            desc='Path to output file if used normally')
     vertexvol_file = File(desc='vertex map volume path id. Optional')
 
+
 class Surface2VolTransform(FSCommand):
     """Use FreeSurfer mri_surf2vol to apply a transform.
 
@@ -432,6 +446,7 @@ class Surface2VolTransform(FSCommand):
     input_spec = Surface2VolTransformInputSpec
     output_spec = Surface2VolTransformOutputSpec
 
+
 class ApplyMaskInputSpec(FSTraitedSpec):
 
     in_file = File(exists=True, mandatory=True, position=-3, argstr="%s",