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Added EditTransform interface
Now, basic operations (change reference image, and setting interpolator, output pixel type, and/or output image format) are available.
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‎nipype/interfaces/elastix/__init__.py

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# @Author: oesteban - code@oscaresteban.es
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# @Date: 2014-06-02 12:06:07
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# @Last Modified by: oesteban
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# @Last Modified time: 2014-06-05 11:55:07
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# @Last Modified time: 2014-06-17 10:59:20
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"""Top-level namespace for elastix."""
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from registration import Registration, ApplyWarp, AnalyzeWarp, PointsWarp
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from utils import EditTransform

‎nipype/interfaces/elastix/base.py

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# @Author: oesteban - code@oscaresteban.es
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# @Date: 2014-06-03 13:42:46
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# @Last Modified by: oesteban
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# @Last Modified time: 2014-06-03 13:43:50
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# @Last Modified time: 2014-06-17 10:17:43
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"""The :py:mod:`nipype.interfaces.elastix` provides the interface to
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the elastix registration software.
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.. note:: http://elastix.isi.uu.nl/
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"""
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from ..base import (CommandLine, CommandLineInputSpec, isdefined,
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TraitedSpec, File, traits, InputMultiPath)

‎nipype/interfaces/elastix/registration.py

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# @Author: oesteban - code@oscaresteban.es
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# @Date: 2014-06-02 12:06:50
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# @Last Modified by: oesteban
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# @Last Modified time: 2014-06-05 14:41:30
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"""The :py:mod:`nipype.interfaces.elastix` provides the interface to
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the elastix registration software.
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.. note:: http://elastix.isi.uu.nl/
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# @Last Modified time: 2014-06-17 10:19:23
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"""
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Interfaces to perform image registrations and to apply the resulting
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displacement maps to images and points.
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"""
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‎nipype/interfaces/elastix/tests/test_auto_EditTransform.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from nipype.testing import assert_equal
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from nipype.interfaces.elastix.utils import EditTransform
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def test_EditTransform_inputs():
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input_map = dict(ignore_exception=dict(nohash=True,
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usedefault=True,
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),
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interpolation=dict(argstr='FinalBSplineInterpolationOrder',
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usedefault=True,
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),
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output_file=dict(),
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output_format=dict(argstr='ResultImageFormat',
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),
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output_type=dict(argstr='ResultImagePixelType',
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),
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reference_image=dict(mandatory=False,
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),
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transform_file=dict(mandatory=True,
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),
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)
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inputs = EditTransform.input_spec()
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for key, metadata in input_map.items():
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for metakey, value in metadata.items():
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yield assert_equal, getattr(inputs.traits()[key], metakey), value
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def test_EditTransform_outputs():
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output_map = dict(output_file=dict(),
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)
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outputs = EditTransform.output_spec()
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for key, metadata in output_map.items():
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for metakey, value in metadata.items():
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yield assert_equal, getattr(outputs.traits()[key], metakey), value
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‎nipype/interfaces/elastix/utils.py

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#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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#
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# @Author: oesteban - code@oscaresteban.es
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# @Date: 2014-06-17 10:17:07
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# @Last Modified by: oesteban
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# @Last Modified time: 2014-06-17 13:15:54
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"""
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Generic interfaces to manipulate registration parameters files, including
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transform files (to configure warpings)
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"""
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import os.path as op
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import re
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from nipype.interfaces.base import (BaseInterface, BaseInterfaceInputSpec, isdefined,
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TraitedSpec, File, traits, InputMultiPath)
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from nipype import logging
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logger = logging.getLogger('interface')
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class EditTransformInputSpec(BaseInterfaceInputSpec):
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transform_file = File(exists=True, mandatory=True,
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desc='transform-parameter file, only 1')
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reference_image = File(exists=True, mandatory=False,
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desc='set a new reference image to change the target coordinate system.')
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interpolation = traits.Enum('cubic','linear','nearest', usedefault=True,
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argstr='FinalBSplineInterpolationOrder',
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desc='set a new interpolator for transformation')
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output_type = traits.Enum('float', 'unsigned char', 'unsigned short','short',
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'unsigned long','long','double',
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argstr='ResultImagePixelType',
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desc='set a new output pixel type for resampled images')
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output_format = traits.Enum('nii.gz', 'nii', 'mhd', 'hdr', 'vtk',
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argstr='ResultImageFormat',
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desc='set a new image format for resampled images')
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output_file = File(desc='the filename for the resulting transform file')
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class EditTransformOutputSpec(TraitedSpec):
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output_file = File(exists=True, desc='output transform file')
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class EditTransform(BaseInterface):
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"""
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Manipulates an existing transform file generated with elastix
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Example::
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>>> from nipype.interfaces.elastix import EditTransform
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>>> tfm = EditTransform()
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>>> tfm.inputs.transform_file = 'TransformParameters.0.txt'
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>>> tfm.inputs.reference_image = 'fixed1.nii'
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>>> tfm.inputs.output_type = 'unsigned char'
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>>> tfm.run() # doctest: +SKIP
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"""
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input_spec = EditTransformInputSpec
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output_spec = EditTransformOutputSpec
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_out_file = ''
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_pattern = '\((?P<entry>%s\s\"?)([-\.\s\w]+)(\"?\))'
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_interp = { 'nearest': 0, 'linear': 1, 'cubic': 3 }
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def _run_interface(self, runtime):
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import re
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import nibabel as nb
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import numpy as np
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contents = ''
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with open(self.inputs.transform_file, 'r') as f:
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contents = f.read()
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if isdefined(self.inputs.output_type):
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p = re.compile((self._pattern % 'ResultImagePixelType').decode('string-escape'))
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rep = '(\g<entry>%s\g<3>' % self.inputs.output_type
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contents = p.sub(rep, contents)
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if isdefined(self.inputs.output_format):
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p = re.compile((self._pattern % 'ResultImageFormat').decode('string-escape'))
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rep = '(\g<entry>%s\g<3>' % self.inputs.output_format
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contents = p.sub(rep, contents)
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if isdefined(self.inputs.interpolation):
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p = re.compile((self._pattern % 'FinalBSplineInterpolationOrder').decode('string-escape'))
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rep = '(\g<entry>%s\g<3>' % self._interp[self.inputs.interpolation]
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contents = p.sub(rep, contents)
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if isdefined(self.inputs.reference_image):
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im = nb.load(self.inputs.reference_image)
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if len(im.get_header().get_zooms()) == 4:
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im = nb.func.four_to_three(im)[0]
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size = ' '.join(["%01d" % s for s in im.get_shape() ])
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p = re.compile((self._pattern % 'Size').decode('string-escape'))
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rep = '(\g<entry>%s\g<3>' % size
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contents = p.sub(rep, contents)
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index = ' '.join(["0" for s in im.get_shape() ])
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p = re.compile((self._pattern % 'Index').decode('string-escape'))
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rep = '(\g<entry>%s\g<3>' % index
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contents = p.sub(rep, contents)
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spacing = ' '.join(["%0.4f" % f for f in im.get_header().get_zooms()])
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p = re.compile((self._pattern % 'Spacing').decode('string-escape'))
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rep = '(\g<entry>%s\g<3>' % spacing
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contents = p.sub(rep, contents)
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itkmat = np.eye(4)
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itkmat[0,0] = -1
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itkmat[1,1] = -1
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affine = np.dot( itkmat, im.get_affine() )
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dirs = ' '.join(['%0.4f' % f for f in affine[0:3,0:3].reshape(-1)])
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orig = ' '.join(['%0.4f' % f for f in affine[0:3,3].reshape(-1)])
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p = re.compile((self._pattern % 'Direction').decode('string-escape'))
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rep = '(\g<entry>%s\g<3>' % dirs
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contents = p.sub(rep, contents)
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p = re.compile((self._pattern % 'Origin').decode('string-escape'))
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rep = '(\g<entry>%s\g<3>' % orig
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contents = p.sub(rep, contents)
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with open(self._get_outfile(), 'w') as of:
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of.write(contents)
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return runtime
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def _list_outputs(self):
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outputs = self.output_spec().get()
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outputs['output_file'] = getattr(self, '_out_file')
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return outputs
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def _get_outfile(self):
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val = getattr(self,'_out_file')
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if not val is None and not val=='':
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return val
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if isdefined(self.inputs.output_file):
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setattr(self,'_out_file',self.inputs.output_file)
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return self.inputs.output_file
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out_file = op.abspath(op.basename(self.inputs.transform_file))
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setattr(self, '_out_file', out_file)
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return out_file

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