Merge pull request #2747 from nipy/oesteban-patch-1

[ENH] Update ``ants.LaplacianThickness`` to use ``name_source``

Author: effigies

nipype/interfaces/ants/segmentation.py

@@ -203,7 +203,9 @@ class LaplacianThicknessInputSpec(ANTSCommandInputSpec):
         desc='name of output file',
         argstr='%s',
         position=3,
-        genfile=True,
+        name_source=['input_wm'],
+        name_template='%s_thickness',
+        keep_extension=True,
         hash_files=False)
     smooth_param = traits.Float(argstr='smoothparam=%d', desc='', position=4)
     prior_thickness = traits.Float(
@@ -228,6 +230,9 @@ class LaplacianThickness(ANTSCommand):
     >>> cort_thick = LaplacianThickness()
     >>> cort_thick.inputs.input_wm = 'white_matter.nii.gz'
     >>> cort_thick.inputs.input_gm = 'gray_matter.nii.gz'
+    >>> cort_thick.cmdline
+    'LaplacianThickness white_matter.nii.gz gray_matter.nii.gz white_matter_thickness.nii.gz'
+
     >>> cort_thick.inputs.output_image = 'output_thickness.nii.gz'
     >>> cort_thick.cmdline
     'LaplacianThickness white_matter.nii.gz gray_matter.nii.gz output_thickness.nii.gz'
@@ -238,22 +243,6 @@ class LaplacianThickness(ANTSCommand):
     input_spec = LaplacianThicknessInputSpec
     output_spec = LaplacianThicknessOutputSpec
 
-    def _gen_filename(self, name):
-        if name == 'output_image':
-            output = self.inputs.output_image
-            if not isdefined(output):
-                _, name, ext = split_filename(self.inputs.input_wm)
-                output = name + '_thickness' + ext
-            return output
-        return None
-
-    def _list_outputs(self):
-        outputs = self._outputs().get()
-        if not outputs.get('output_image', None) \
-                or not isdefined(outputs['output_image']):
-            outputs['output_image'] = self._gen_filename('output_image')
-        return outputs
-
 
 class N4BiasFieldCorrectionInputSpec(ANTSCommandInputSpec):
     dimension = traits.Enum(

nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py

@@ -36,8 +36,10 @@ def test_LaplacianThickness_inputs():
         ),
         output_image=dict(
             argstr='%s',
-            genfile=True,
             hash_files=False,
+            keep_extension=True,
+            name_source=['input_wm'],
+            name_template='%s_thickness',
             position=3,
         ),
         prior_thickness=dict(