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Fix: fsl.WarpUtils #906

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Merged
merged 3 commits into from
Sep 1, 2014
Merged

Fix: fsl.WarpUtils #906

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3f8c154
bugfix: for unknown reasons WarpUtils produced wrong command lines
oesteban Aug 14, 2014
fa11ffd
bugfix: for unknown reasons WarpUtils produced wrong command lines (ii)
oesteban Aug 14, 2014
72e1c51
Merge branch 'master' into bug/fnirtfileutils
oesteban Sep 1, 2014
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17 changes: 9 additions & 8 deletions nipype/interfaces/fsl/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1513,7 +1513,7 @@ class WarpUtilsInputSpec(FSLCommandInputSpec):
'would typically be the file that was specified '
'with the --in argument when running fnirt.'))

out_format = traits.Either('field', 'spline', argstr='--outformat=%s',
out_format = traits.Either('spline', 'field', argstr='--outformat=%s',
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@oesteban - shouldn't this be an Enum?

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Yep, fixing...

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@satra is there any way to avoid opening a new branch and a new PR to apply such minor patches? (sorry for my ignorance about git and github). I've done that to fix it, but I feel it potentially annoying, isn't it?

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unfortunately no. and a change like this also requires make specs to run.

desc=('Specifies the output format. If set to field (default) '
'the output will be a (4D) field-file. If set to spline '
'the format will be a (4D) file of spline coefficients.'))
Expand Down Expand Up @@ -1557,10 +1557,8 @@ class WarpUtilsInputSpec(FSLCommandInputSpec):
'stored separately from the displacements).'))

class WarpUtilsOutputSpec(TraitedSpec):
out_file = File(exists=True,
desc=('Name of output file, containing the warp as field or coefficients.'))
out_jacobian = File(exists=True,
desc=('Name of output file, containing the map of the determinant of '
out_file = File(desc=('Name of output file, containing the warp as field or coefficients.'))
out_jacobian = File(desc=('Name of output file, containing the map of the determinant of '
'the Jacobian'))


Expand Down Expand Up @@ -1603,9 +1601,12 @@ def _parse_inputs(self, skip=None):

if self.inputs.write_jacobian:
if not isdefined(self.inputs.out_jacobian):
trait_spec = self.inputs.trait('out_jacobian')
trait_spec.name_source = ['in_file']
trait_spec.name_template = '%s_jac'
jac_spec = self.inputs.trait('out_jacobian')
jac_spec.name_source = ['in_file']
jac_spec.name_template = '%s_jac'
jac_spec.output_name = 'out_jacobian'
else:
skip+=['out_jacobian']

skip+=['write_jacobian']
return super(WarpUtils, self)._parse_inputs(skip=skip)
Expand Down