Reformated inputs and added tests

Author: chrisgorgo

nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py

@@ -0,0 +1,66 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.freesurfer.utils import Surface2VolTransform
+def test_Surface2VolTransform_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    transformed_file=dict(name_source=['source_file'],
+    hash_files=False,
+    name_template='%s_asVol.nii',
+    argstr='--outvol %s',
+    ),
+    hemi=dict(mandatory=True,
+    argstr='--hemi %s',
+    ),
+    template_file=dict(argstr='--template %s',
+    ),
+    subject_id=dict(xor=['reg_file'],
+    argstr='--identity %s',
+    ),
+    args=dict(argstr='%s',
+    ),
+    surf_name=dict(argstr='--surf %s',
+    exists=True,
+    ),
+    vertexvol_file=dict(name_source=['source_file'],
+    hash_files=False,
+    name_template='%s_asVol_vertex.nii',
+    argstr='--vtxvol %s',
+    ),
+    reg_file=dict(mandatory=True,
+    argstr='--volreg %s',
+    xor=['subject_id'],
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    subjects_dir=dict(argstr='--sd %s',
+    ),
+    source_file=dict(copyfile=False,
+    mandatory=True,
+    argstr='--surfval %s',
+    ),
+    projfrac=dict(argstr='--projfrac %s',
+    exists=True,
+    ),
+    mkmask=dict(argstr='--mkmask',
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    )
+    inputs = Surface2VolTransform.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+def test_Surface2VolTransform_outputs():
+    output_map = dict(transformed_file=dict(),
+    vertexvol_file=dict(),
+    )
+    outputs = Surface2VolTransform.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/interfaces/freesurfer/utils.py

@@ -387,17 +387,21 @@ class Surface2VolTransformInputSpec(FSTraitedSpec):
                       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(desc='Output volume', argstr='--outvol %s', genfile=True)
+    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']) 
+                    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(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', genfile=True)
-    surf_file = File(exists=True, argstr='--surf %s',desc='surfname (default is white)')
-    projfrac_file = traits.Float(exists=True, argstr='--projfrac %s',desc='thickness fraction')
+    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'])
 
@@ -417,6 +421,9 @@ class Surface2VolTransform(FSCommand):
     >>> xfm2vol.inputs.reg_file = 'register.mat'
     >>> xfm2vol.inputs.hemi = 'lh'
     >>> xfm2vol.inputs.template_file = 'cope1.nii.gz'
+    >>> xfm2vol.inputs.subjects_dir = '.'
+    >>> xfm2vol.cmdline
+    'mri_surf2vol --hemi lh --volreg register.mat --surfval lh.cope1.mgz --sd . --template cope1.nii.gz --outvol lh.cope1_asVol.nii --vtxvol lh.cope1_asVol_vertex.nii'
     >>> res = xfm2vol.run()# doctest: +SKIP
 
     """
@@ -425,23 +432,6 @@ class Surface2VolTransform(FSCommand):
     input_spec = Surface2VolTransformInputSpec
     output_spec = Surface2VolTransformOutputSpec
 
-    def _get_outfile(self):
-        outfile = self.inputs.transformed_file
-        if not isdefined(outfile):
-            outfile = self._gen_fname(self.inputs.source_file,
-                                      suffix='_asVol')
-        return outfile
-
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        outputs['transformed_file'] = self._get_outfile()
-        return outputs
-
-    def _gen_filename(self, name):
-        if name == 'transformed_file':
-            return self._get_outfile()
-        return None
-
 class ApplyMaskInputSpec(FSTraitedSpec):
 
     in_file = File(exists=True, mandatory=True, position=-3, argstr="%s",