/usr/share/pyshared/nipype/interfaces/c3.py is in python-nipype 0.9.2-1.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 | """The ants module provides basic functions for interfacing with ants functions.
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
>>> os.chdir(datadir)
"""
from nipype.interfaces.base import (CommandLineInputSpec, traits, TraitedSpec,
File, SEMLikeCommandLine)
class C3dAffineToolInputSpec(CommandLineInputSpec):
reference_file = File(exists=True, argstr="-ref %s", position=1)
source_file = File(exists=True, argstr='-src %s', position=2)
transform_file = File(exists=True, argstr='%s', position=3)
itk_transform = traits.Either(traits.Bool, File(), hash_files=False,
desc="Export ITK transform.",
argstr="-oitk %s", position=5)
fsl2ras = traits.Bool(argstr='-fsl2ras', position=4)
class C3dAffineToolOutputSpec(TraitedSpec):
itk_transform = File(exists=True)
class C3dAffineTool(SEMLikeCommandLine):
"""Converts fsl-style Affine registration into ANTS compatible itk format
Example
=======
>>> from nipype.interfaces.c3 import C3dAffineTool
>>> c3 = C3dAffineTool()
>>> c3.inputs.source_file = 'cmatrix.mat'
>>> c3.inputs.itk_transform = 'affine.txt'
>>> c3.inputs.fsl2ras = True
>>> c3.cmdline
'c3d_affine_tool -src cmatrix.mat -fsl2ras -oitk affine.txt'
"""
input_spec = C3dAffineToolInputSpec
output_spec = C3dAffineToolOutputSpec
_cmd = 'c3d_affine_tool'
_outputs_filenames = {'itk_transform': 'affine.txt'}
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