Support multi-step composite transforms from Nibabies (#1365)

Co-authored-by: Matt Cieslak <mattcieslak@gmail.com>

Author: tsalo

xcp_d/interfaces/__init__.py

@@ -5,7 +5,6 @@
 from xcp_d.interfaces import (
     ants,
     bids,
-    c3,
     censoring,
     connectivity,
     execsummary,
@@ -19,7 +18,6 @@
 __all__ = [
     'ants',
     'bids',
-    'c3',
     'connectivity',
     'execsummary',
     'nilearn',

xcp_d/interfaces/ants.py

@@ -1,19 +1,8 @@
 """ANTS interfaces."""
 
 import logging
-import os
 
-from nipype.interfaces.ants.base import ANTSCommand, ANTSCommandInputSpec
-from nipype.interfaces.base import (
-    CommandLine,
-    CommandLineInputSpec,
-    File,
-    InputMultiPath,
-    Str,
-    TraitedSpec,
-    isdefined,
-    traits,
-)
+from nipype.interfaces.base import isdefined, traits
 from niworkflows.interfaces.fixes import (
     FixHeaderApplyTransforms,
     _FixTraitApplyTransformsInputSpec,
@@ -24,156 +13,6 @@
 LOGGER = logging.getLogger('nipype.interface')
 
 
-class _ConvertTransformFileInputSpec(CommandLineInputSpec):
-    dimension = traits.Enum(3, 2, usedefault=True, argstr='%d', position=0)
-    in_transform = traits.File(exists=True, argstr='%s', mandatory=True, position=1)
-    out_transform = traits.File(
-        argstr='%s',
-        name_source='in_transform',
-        name_template='%s.txt',
-        keep_extension=False,
-        position=2,
-        exists=False,
-    )
-
-
-class _ConvertTransformFileOutputSpec(TraitedSpec):
-    out_transform = traits.File(exists=True)
-
-
-class ConvertTransformFile(CommandLine):
-    """Wrapper for the ANTS ConvertTransformFile command.
-
-    Utility to read in a transform file (presumed to be in binary format) and output it in various
-    formats.
-    Default output is legacy human-readable text format.
-    Without any options, the output filename extension must be .txt or .tfm to signify a
-    text-formatted transform file.
-    """
-
-    _cmd = 'ConvertTransformFile'
-    input_spec = _ConvertTransformFileInputSpec
-    output_spec = _ConvertTransformFileOutputSpec
-
-
-class _CompositeTransformUtilInputSpec(ANTSCommandInputSpec):
-    """Input specification for CompositeTransformUtil."""
-
-    process = traits.Enum(
-        'assemble',
-        'disassemble',
-        argstr='--%s',
-        position=1,
-        usedefault=True,
-        desc='What to do with the transform inputs (assemble or disassemble)',
-    )
-    inverse = traits.Bool(
-        False,
-        usedefault=True,
-        desc='Whether to invert the order of the transform components. Not used by the command.',
-    )
-    out_file = File(
-        exists=False,
-        argstr='%s',
-        position=2,
-        desc='Output file path (only used for disassembly).',
-    )
-    in_file = InputMultiPath(
-        File(exists=True),
-        mandatory=True,
-        argstr='%s...',
-        position=3,
-        desc='Input transform file(s)',
-    )
-    output_prefix = Str(
-        'transform',
-        usedefault=True,
-        argstr='%s',
-        position=4,
-        desc='A prefix that is prepended to all output files (only used for assembly).',
-    )
-
-
-class _CompositeTransformUtilOutputSpec(TraitedSpec):
-    """Output specification for CompositeTransformUtil."""
-
-    affine_transform = File(desc='Affine transform component')
-    displacement_field = File(desc='Displacement field component')
-    out_file = File(desc='Compound transformation file')
-
-
-class CompositeTransformUtil(ANTSCommand):
-    """Wrapper for the ANTS CompositeTransformUtil command.
-
-    ANTs utility which can combine or break apart transform files into their individual
-    constituent components.
-
-    Examples
-    --------
-    >>> from nipype.interfaces.ants import CompositeTransformUtil
-    >>> tran = CompositeTransformUtil()
-    >>> tran.inputs.process = 'disassemble'
-    >>> tran.inputs.in_file = 'output_Composite.h5'
-    >>> tran.cmdline
-    'CompositeTransformUtil --disassemble output_Composite.h5 transform'
-    >>> tran.run()  # doctest: +SKIP
-    example for assembling transformation files
-    >>> from nipype.interfaces.ants import CompositeTransformUtil
-    >>> tran = CompositeTransformUtil(inverse=False)
-    >>> tran.inputs.process = 'assemble'
-    >>> tran.inputs.out_file = 'my.h5'
-    >>> tran.inputs.in_file = ['AffineTransform.mat', 'DisplacementFieldTransform.nii.gz']
-    >>> tran.cmdline
-    'CompositeTransformUtil --assemble my.h5 AffineTransform.mat
-     DisplacementFieldTransform.nii.gz '
-    >>> tran.run()  # doctest: +SKIP
-    """
-
-    _cmd = 'CompositeTransformUtil'
-    input_spec = _CompositeTransformUtilInputSpec
-    output_spec = _CompositeTransformUtilOutputSpec
-
-    def _num_threads_update(self):
-        """Do not update the number of threads environment variable.
-
-        CompositeTransformUtil ignores environment variables,
-        so override environment update from ANTSCommand class.
-        """
-        pass
-
-    def _format_arg(self, name, spec, value):
-        if name == 'output_prefix' and self.inputs.process == 'assemble':
-            return ''
-        if name == 'out_file' and self.inputs.process == 'disassemble':
-            return ''
-        return super()._format_arg(name, spec, value)
-
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        if self.inputs.inverse:
-            if self.inputs.process == 'disassemble':
-                outputs['affine_transform'] = os.path.abspath(
-                    f'{self.inputs.output_prefix}_01_AffineTransform.mat'
-                )
-                outputs['displacement_field'] = os.path.abspath(
-                    f'{self.inputs.output_prefix}_00_DisplacementFieldTransform.nii.gz'
-                )
-            elif self.inputs.process == 'assemble':
-                outputs['out_file'] = os.path.abspath(self.inputs.out_file)
-        else:
-            if self.inputs.process == 'disassemble':
-                outputs['affine_transform'] = os.path.abspath(
-                    f'{self.inputs.output_prefix}_00_AffineTransform.mat'
-                )
-                outputs['displacement_field'] = os.path.abspath(
-                    f'{self.inputs.output_prefix}_01_DisplacementFieldTransform.nii.gz'
-                )
-            elif self.inputs.process == 'assemble':
-                outputs['out_file'] = os.path.abspath(self.inputs.out_file)
-
-        return outputs
-
-
 class _ApplyTransformsInputSpec(_FixTraitApplyTransformsInputSpec):
     # Nipype's version doesn't have GenericLabel
     interpolation = traits.Enum(