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[ENH] ants.ApplyTransform - Accept 'identity' keyword #2239

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Merged
merged 3 commits into from
Oct 21, 2017
Merged

[ENH] ants.ApplyTransform - Accept 'identity' keyword #2239

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acf3a69
[ENH] ants.ApplyTransform - Accept 'identity' keyword
oesteban Oct 19, 2017
dc1284f
Merge remote-tracking branch 'upstream/master' into fr/2126
oesteban Oct 20, 2017
5cd113d
fix doctest
oesteban Oct 20, 2017
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27 changes: 20 additions & 7 deletions nipype/interfaces/ants/resampling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -243,13 +243,15 @@ class ApplyTransformsInputSpec(ANTSCommandInputSpec):
'Gaussian',
'BSpline',
argstr='%s', usedefault=True)
interpolation_parameters = traits.Either(traits.Tuple(traits.Int()), # BSpline (order)
traits.Tuple(traits.Float(), # Gaussian/MultiLabel (sigma, alpha)
traits.Float())
)
transforms = InputMultiPath(File(exists=True), argstr='%s', mandatory=True,
desc='transform files: will be applied in reverse order. For '
'example, the last specified transform will be applied first.')
interpolation_parameters = traits.Either(
traits.Tuple(traits.Int()), # BSpline (order)
traits.Tuple(traits.Float(), # Gaussian/MultiLabel (sigma, alpha)
traits.Float())
)
transforms = traits.Either(
InputMultiPath(File(exists=True)), 'identity', argstr='%s', mandatory=True,
desc='transform files: will be applied in reverse order. For '
'example, the last specified transform will be applied first.')
invert_transform_flags = InputMultiPath(traits.Bool())
default_value = traits.Float(0.0, argstr='--default-value %g', usedefault=True)
print_out_composite_warp_file = traits.Bool(False, requires=["output_image"],
Expand All @@ -269,6 +271,15 @@ class ApplyTransforms(ANTSCommand):
--------

>>> from nipype.interfaces.ants import ApplyTransforms
>>> at = ApplyTransforms()
>>> at.inputs.input_image = 'moving1.nii'
>>> at.inputs.reference_image = 'fixed1.nii'
>>> at.inputs.transforms = 'identity'
>>> at.cmdline # doctest: +ALLOW_UNICODE
'antsApplyTransforms --default-value 0 --input moving1.nii \
--interpolation Linear --output moving1_trans.nii \
--reference-image fixed1.nii -t identity'

>>> at = ApplyTransforms()
>>> at.inputs.dimension = 3
>>> at.inputs.input_image = 'moving1.nii'
Expand Down Expand Up @@ -338,6 +349,8 @@ def _format_arg(self, opt, spec, val):
if opt == "output_image":
return self._get_output_warped_filename()
elif opt == "transforms":
if val == 'identity':
return '-t identity'
return self._get_transform_filenames()
elif opt == 'interpolation':
if self.inputs.interpolation in ['BSpline', 'MultiLabel', 'Gaussian'] and \
Expand Down