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Commit 311e9b3

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TheChymeraTheChymera
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CompositeTransformUtil, new ANTs interface
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‎nipype/interfaces/ants/__init__.py

Copy file name to clipboardExpand all lines: nipype/interfaces/ants/__init__.py
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@@ -5,7 +5,7 @@
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# Registraiton programs
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from .registration import (ANTS, Registration, RegistrationSynQuick,
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MeasureImageSimilarity)
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CompositeTransformUtil, MeasureImageSimilarity)
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# Resampling Programs
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from .resampling import (ApplyTransforms, ApplyTransformsToPoints,

‎nipype/interfaces/ants/registration.py

Copy file name to clipboardExpand all lines: nipype/interfaces/ants/registration.py
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@@ -1596,3 +1596,77 @@ def _list_outputs(self):
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outputs['forward_warp_field'] = out_base + '1Warp.nii.gz'
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outputs['inverse_warp_field'] = out_base + '1InverseWarp.nii.gz'
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return outputs
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class CompositeTransformUtilInputSpec(ANTSCommandInputSpec):
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process = traits.Enum('assemble', 'disassemble', argstr='--%s',
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position=1, usedefault=True,
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desc='What to do with the transform inputs (assemble or disassemble)',
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)
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out_file = File(exists=False, argstr='%s', position=2,
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desc='Output file path (only used for disassembly).')
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in_file = InputMultiPath(File(exists=True), mandatory=True, argstr='%s...',
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position=3, desc='Input transform file(s)')
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output_prefix = Str("transform", usedefault=True, argstr='%s', position=4,
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desc="A prefix that is prepended to all output files (only used for assembly).")
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class CompositeTransformUtilOutputSpec(TraitedSpec):
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affine_transform = File(desc="Affine transform component")
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displacement_field = File(desc="Displacement field component")
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out_file = File(desc="Compound transformation file")
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class CompositeTransformUtil(ANTSCommand):
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"""
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ANTs utility which can combine or break apart transform files into their individual
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constituent components.
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Examples
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--------
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>>> from nipype.interfaces.ants import CompositeTransformUtil
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>>> tran = CompositeTransformUtil()
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>>> tran.inputs.process = 'disassemble'
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>>> tran.inputs.in_file = 'output_Composite.h5'
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>>> tran.cmdline
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'CompositeTransformUtil --disassemble output_Composite.h5 transform'
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>>> tran.run() # doctest: +SKIP
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example for assembling transformation files
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>>> from nipype.interfaces.ants import CompositeTransformUtil
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>>> tran = CompositeTransformUtil()
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>>> tran.inputs.process = 'assemble'
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>>> tran.inputs.out_file = 'my.h5'
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>>> tran.inputs.in_file = ['AffineTransform.mat', 'DisplacementFieldTransform.nii.gz']
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>>> tran.cmdline
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'CompositeTransformUtil --assemble my.h5 AffineTransform.mat DisplacementFieldTransform.nii.gz '
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>>> tran.run() # doctest: +SKIP
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"""
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_cmd = 'CompositeTransformUtil'
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input_spec = CompositeTransformUtilInputSpec
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output_spec = CompositeTransformUtilOutputSpec
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def _num_threads_update(self):
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"""
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CompositeTransformUtil ignores environment variables,
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so override environment update from ANTSCommand class
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"""
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pass
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def _format_arg(self, name, spec, value):
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if name == 'output_prefix' and self.inputs.process == 'assemble':
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value = ''
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if name == 'out_file' and self.inputs.process == 'disassemble':
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value = ''
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return super(CompositeTransformUtil, self)._format_arg(name, spec, value)
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def _list_outputs(self):
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outputs = self.output_spec().get()
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if self.inputs.process == 'disassemble':
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outputs['affine_transform'] = os.path.abspath(
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'00_{}_AffineTransform.mat'.format(self.inputs.output_prefix))
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outputs['displacement_field'] = os.path.abspath(
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'01_{}_DisplacementFieldTransform.nii.gz'.format(self.inputs.output_prefix))
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if self.inputs.process == 'assemble':
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outputs['out_file'] = os.path.abspath(self.inputs.out_file)
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return outputs

‎nipype/testing/data/AffineTransform.mat

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‎nipype/testing/data/DisplacementFieldTransform.nii.gz

Copy file name to clipboardExpand all lines: nipype/testing/data/DisplacementFieldTransform.nii.gz
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‎nipype/testing/data/output_Composite.h5

Copy file name to clipboardExpand all lines: nipype/testing/data/output_Composite.h5
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