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[ENH] Update ants.LaplacianThickness to use name_source #2747

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Merged
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Oct 24, 2018
Merged

[ENH] Update ants.LaplacianThickness to use name_source #2747

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45afd83
[ENH] Move ``nipype.interfaces.ants.LaplacianThickness`` to use ``nam…
oesteban Oct 24, 2018
8502192
update specs
oesteban Oct 24, 2018
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23 changes: 6 additions & 17 deletions nipype/interfaces/ants/segmentation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand All @@ -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'
Expand All @@ -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(
Expand Down
4 changes: 3 additions & 1 deletion nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py
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Expand Up @@ -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(
Expand Down