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Afni deconvolve #2

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Merged
merged 2 commits into from
Jun 22, 2017
Merged

Afni deconvolve #2

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a3a48fa
Merge pull request #3 from rmarkello/afni_deconvolve
tsalo Jun 22, 2017
7f15322
Drop output spec and map outputs in list_outputs.
tsalo Jun 22, 2017
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17 changes: 10 additions & 7 deletions nipype/interfaces/afni/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -158,10 +158,6 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
requires=['glt_sym'])


class DeconvolveOutputSpec(TraitedSpec):
pass


class Deconvolve(AFNICommand):
"""Performs OLS regression given a 4D neuroimage file and stimulus timings

Expand All @@ -179,19 +175,23 @@ class Deconvolve(AFNICommand):
>>> stim_times = [(1, 'stims1.txt', 'SPMG1(4)'), (2, 'stims2.txt', 'SPMG2(4)')]
>>> deconvolve.inputs.stim_times = stim_times
>>> deconvolve.cmdline # doctest: +ALLOW_UNICODE
'3dDeconvolve -input functional.nii -bucket output.nii -x1D output.1D -stim_times 1 stims1.txt SPMG1(4) 2 stims2.txt SPMG2(4)'
'3dDeconvolve -input functional.nii -bucket output.nii -x1D output -stim_times 1 stims1.txt SPMG1(4) 2 stims2.txt SPMG2(4)'
>>> res = deconvolve.run() # doctest: +SKIP
"""

_cmd = '3dDeconvolve'
input_spec = DeconvolveInputSpec
output_spec = DeconvolveOutputSpec
output_spec = AFNICommandOutputSpec

def _list_outputs(self):
outputs = self.output_spec().get()
if isdefined(self.inputs.x1D):
if not self.inputs.x1D.endswith('.xmat.1D'):
outputs['x1D'] = outputs['x1D'] + '.xmat.1D'
outputs['x1D'] = self.inputs.x1D + '.xmat.1D'
else:
outputs['x1D'] = self.inputs.x1D

outputs['bucket'] = self.inputs.bucket
return outputs

def _format_arg(self, name, trait_spec, value):
Expand All @@ -206,5 +206,8 @@ def _format_arg(self, name, trait_spec, value):
arg += trait_spec.argstr % value
arg = arg.rstrip()
return arg

if name == 'stim_times':
self.inputs.num_stimts = len(value)
elif name == 'glt_sym':
self.inputs.num_glt = len(value)