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FIX: Return afni.Qwarp outputs as absolute paths #2705

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Merged
merged 1 commit into from
Sep 19, 2018
Merged

FIX: Return afni.Qwarp outputs as absolute paths #2705

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26 changes: 18 additions & 8 deletions nipype/interfaces/afni/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3596,31 +3596,41 @@ def _list_outputs(self):
else:
ext = prefix[ext_ind:]
suffix = ''

# All outputs should be in the same directory as the prefix
out_dir = os.path.dirname(os.path.abspath(prefix))

outputs['warped_source'] = fname_presuffix(
prefix, suffix=suffix, use_ext=False) + ext
prefix, suffix=suffix, use_ext=False, newpath=out_dir) + ext
if not self.inputs.nowarp:
outputs['source_warp'] = fname_presuffix(
prefix, suffix='_WARP' + suffix, use_ext=False) + ext
prefix, suffix='_WARP' + suffix, use_ext=False,
newpath=out_dir) + ext
if self.inputs.iwarp:
outputs['base_warp'] = fname_presuffix(
prefix, suffix='_WARPINV' + suffix, use_ext=False) + ext
prefix, suffix='_WARPINV' + suffix, use_ext=False,
newpath=out_dir) + ext
if isdefined(self.inputs.out_weight_file):
outputs['weights'] = os.path.abspath(self.inputs.out_weight_file)

if self.inputs.plusminus:
outputs['warped_source'] = fname_presuffix(
prefix, suffix='_PLUS' + suffix, use_ext=False) + ext
prefix, suffix='_PLUS' + suffix, use_ext=False,
newpath=out_dir) + ext
outputs['warped_base'] = fname_presuffix(
prefix, suffix='_MINUS' + suffix, use_ext=False) + ext
prefix, suffix='_MINUS' + suffix, use_ext=False,
newpath=out_dir) + ext
outputs['source_warp'] = fname_presuffix(
prefix, suffix='_PLUS_WARP' + suffix, use_ext=False) + ext
prefix, suffix='_PLUS_WARP' + suffix, use_ext=False,
newpath=out_dir) + ext
outputs['base_warp'] = fname_presuffix(
prefix, suffix='_MINUS_WARP' + suffix, use_ext=False) + ext
prefix, suffix='_MINUS_WARP' + suffix, use_ext=False,
newpath=out_dir) + ext
return outputs

def _gen_filename(self, name):
if name == 'out_file':
return self._gen_fname(self.inputs.source_file, suffix='_QW')
return self._gen_fname(self.inputs.in_file, suffix='_QW')


class QwarpPlusMinusInputSpec(QwarpInputSpec):
Expand Down