Merge remote-tracking branch 'origin/pr/849'

Conflicts:
	CHANGES

Author: chrisgorgo

.travis.yml

@@ -12,7 +12,7 @@ before_install:
   - sudo rm -rf /dev/shm
   - sudo ln -s /run/shm /dev/shm
   - bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh)
-  - travis_retry sudo apt-get install -qq --no-install-recommends fsl afni
+  - travis_retry sudo apt-get install -qq --no-install-recommends fsl afni elastix
   - travis_retry sudo apt-get install -qq fsl-atlases
   - source /etc/fsl/fsl.sh
 

CHANGES

@@ -6,6 +6,8 @@ Next Release
        ``from nipype.interfaces import fsl``).
 * ENH: New FSL interface: ProbTrackX2
 * ENH: New misc algorithm: NormalizeProbabilityMapSet
+* ENH: Support for elastix via a set of new interfaces: Registration, ApplyWarp, 
+       AnalyzeWarp, PointsWarp, and EditTransform
 * ENH: New ANTs interface: ApplyTransformsToPoints
 * ENH: New metrics group in algorithms. Now Distance, Overlap, and FuzzyOverlap
        are found in nipype.algorithms.metrics instead of misc

nipype/interfaces/elastix/__init__.py

@@ -0,0 +1,13 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# @Author: oesteban - code@oscaresteban.es
+# @Date:   2014-06-02 12:06:07
+# @Last Modified by:   oesteban
+# @Last Modified time: 2014-06-17 10:59:20
+"""Top-level namespace for elastix."""
+
+from registration import Registration, ApplyWarp, AnalyzeWarp, PointsWarp
+from utils import EditTransform

nipype/interfaces/elastix/base.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# @Author: oesteban - code@oscaresteban.es
+# @Date:   2014-06-03 13:42:46
+# @Last Modified by:   oesteban
+# @Last Modified time: 2014-06-17 10:17:43
+"""The :py:mod:`nipype.interfaces.elastix` provides the interface to
+the elastix registration software.
+
+.. note:: http://elastix.isi.uu.nl/
+
+
+"""
+
+from ..base import (CommandLine, CommandLineInputSpec, isdefined,
+                    TraitedSpec, File, traits, InputMultiPath)
+from ... import logging
+logger = logging.getLogger('interface')
+
+
+class ElastixBaseInputSpec(CommandLineInputSpec):
+    output_path = traits.Directory('./', exists=True, mandatory=True, usedefault=True,
+                              argstr='-out %s', desc='output directory')
+    num_threads = traits.Int(1, argstr='-threads %01d',
+                             desc='set the maximum number of threads of elastix')

nipype/interfaces/elastix/registration.py

@@ -0,0 +1,240 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# @Author: oesteban - code@oscaresteban.es
+# @Date:   2014-06-02 12:06:50
+# @Last Modified by:   oesteban
+# @Last Modified time: 2014-06-17 10:19:23
+"""
+Interfaces to perform image registrations and to apply the resulting
+displacement maps to images and points.
+
+"""
+
+import os.path as op
+import re
+
+from ..base import (CommandLine, CommandLineInputSpec, isdefined,
+                    TraitedSpec, File, traits, InputMultiPath)
+
+
+from base import ElastixBaseInputSpec
+
+from ... import logging
+logger = logging.getLogger('interface')
+
+
+class RegistrationInputSpec(ElastixBaseInputSpec):
+    fixed_image = File(exists=True, mandatory=True, argstr='-f %s',
+           desc='fixed image')
+    moving_image = File(exists=True, mandatory=True, argstr='-m %s',
+           desc='moving image')
+
+    parameters = InputMultiPath(File(exists=True), mandatory=True, argstr='-p %s...',
+                                desc='parameter file, elastix handles 1 or more -p')
+
+    fixed_mask = File(exists=True, argstr='-fMask %s', desc='mask for fixed image')
+    moving_mask = File(exists=True, argstr='-mMask %s', desc='mask for moving image')
+    initial_transform = File(exists=True, argstr='-t0 %s',
+                             desc='parameter file for initial transform')
+
+
+class RegistrationOutputSpec(TraitedSpec):
+    transform = InputMultiPath(File(exists=True), desc='output transform')
+    warped_file = File(desc='input moving image warped to fixed image')
+    warped_files = InputMultiPath(File(exists=False),
+                                  desc=('input moving image warped to fixed image at each level'))
+    warped_files_flags = traits.List(traits.Bool(False),
+                                    desc='flag indicating if warped image was generated')
+
+
+class Registration(CommandLine):
+    """Elastix nonlinear registration interface
+
+    Example
+    -------
+
+    >>> from nipype.interfaces.elastix import Registration
+    >>> reg = Registration()
+    >>> reg.inputs.fixed_image = 'fixed1.nii'
+    >>> reg.inputs.moving_image = 'moving1.nii'
+    >>> reg.inputs.parameters = ['elastix.txt']
+    >>> reg.cmdline
+    'elastix -f fixed1.nii -m moving1.nii -out ./ -p elastix.txt'
+    """
+
+    _cmd = 'elastix'
+    input_spec = RegistrationInputSpec
+    output_spec = RegistrationOutputSpec
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+
+        out_dir = op.abspath(self.inputs.output_path)
+
+        opts = [ 'WriteResultImage', 'ResultImageFormat' ]
+        regex = re.compile(r'^\((\w+)\s(.+)\)$')
+
+        outputs['transform'] = []
+        outputs['warped_files'] = []
+        outputs['warped_files_flags'] = []
+
+        for i,params in enumerate(self.inputs.parameters):
+            config = {}
+
+            with open(params, 'r') as f:
+                for line in f.readlines():
+                    line = line.strip()
+                    if not line.startswith('//') and line:
+                        m = regex.search(line)
+                        if m:
+                            value = self._cast(m.group(2).strip())
+                            config[m.group(1).strip()] = value
+
+            outputs['transform'].append(op.join(out_dir,
+                                        'TransformParameters.%01d.txt' % i ))
+
+            warped_file = None
+            if config['WriteResultImage']:
+                warped_file = op.join(out_dir,
+                                      'result.%01d.%s' %(i,config['ResultImageFormat']))
+
+            outputs['warped_files'].append(warped_file)
+            outputs['warped_files_flags'].append(config['WriteResultImage'])
+
+        if outputs['warped_files_flags'][-1]:
+            outputs['warped_file'] = outputs['warped_files'][-1]
+
+        return outputs
+
+
+    def _cast(self,val):
+        if val.startswith('"') and val.endswith('"'):
+            if val == '"true"':
+                return True
+            elif val == '"false"':
+                return False
+            else:
+                return val[1:-1]
+
+        try:
+            return int(val)
+        except ValueError:
+            try:
+                return float(val)
+            except ValueError:
+                return val
+
+class ApplyWarpInputSpec(ElastixBaseInputSpec):
+    transform_file = File(exists=True, mandatory=True, argstr='-tp %s',
+                          desc='transform-parameter file, only 1')
+
+    moving_image = File(exists=True, argstr='-in %s', mandatory=True,
+                        desc='input image to deform')
+
+
+
+class ApplyWarpOutputSpec(TraitedSpec):
+    warped_file = File(desc='input moving image warped to fixed image')
+
+class ApplyWarp(CommandLine):
+    """Use `transformix` to apply a transform on an input image.
+    The transform is specified in the transform-parameter file.
+
+    Example::
+
+    >>> from nipype.interfaces.elastix import ApplyWarp
+    >>> reg = ApplyWarp()
+    >>> reg.inputs.moving_image = 'moving1.nii'
+    >>> reg.inputs.transform_file = 'TransformParameters.0.txt'
+    >>> reg.cmdline
+    'transformix -in moving1.nii -out ./ -tp TransformParameters.0.txt'
+    """
+
+    _cmd = 'transformix'
+    input_spec = ApplyWarpInputSpec
+    output_spec = ApplyWarpOutputSpec
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        out_dir = op.abspath(self.inputs.output_path)
+        outputs['warped_file'] = op.join(out_dir,'result.nii.gz')
+        return outputs
+
+
+class AnalyzeWarpInputSpec(ElastixBaseInputSpec):
+    transform_file = File(exists=True, mandatory=True, argstr='-tp %s',
+                          desc='transform-parameter file, only 1')
+
+
+class AnalyzeWarpOutputSpec(TraitedSpec):
+    disp_field = File(exists=True, desc='displacements field')
+    jacdet_map = File(exists=True, desc='det(Jacobian) map')
+    jacmat_map = File(exists=True, desc='Jacobian matrix map')
+
+class AnalyzeWarp(CommandLine):
+    """Use `transformix` to get details from the input transform (generate
+    the corresponding deformation field, generate the determinant of the
+    Jacobian map or the Jacobian map itself)
+
+    Example::
+
+    >>> from nipype.interfaces.elastix import AnalyzeWarp
+    >>> reg = AnalyzeWarp()
+    >>> reg.inputs.transform_file = 'TransformParameters.0.txt'
+    >>> reg.cmdline
+    'transformix -def all -jac all -jacmat all -out ./ -tp TransformParameters.0.txt'
+    """
+
+    _cmd = 'transformix -def all -jac all -jacmat all'
+    input_spec = AnalyzeWarpInputSpec
+    output_spec = AnalyzeWarpOutputSpec
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        out_dir = op.abspath(self.inputs.output_path)
+        outputs['disp_field'] = op.join(out_dir,'deformationField.nii.gz')
+        outputs['jacdet_map'] = op.join(out_dir,'spatialJacobian.nii.gz')
+        outputs['jacmat_map'] = op.join(out_dir,'fullSpatialJacobian.nii.gz')
+        return outputs
+
+
+class PointsWarpInputSpec(ElastixBaseInputSpec):
+    points_file = File(exists=True, argstr='-def %s', mandatory=True,
+                       desc='input points (accepts .vtk triangular meshes).')
+    transform_file = File(exists=True, mandatory=True, argstr='-tp %s',
+                          desc='transform-parameter file, only 1')
+
+
+
+class PointsWarpOutputSpec(TraitedSpec):
+    warped_file = File(desc='input points displaced in fixed image domain')
+
+class PointsWarp(CommandLine):
+    """Use `transformix` to apply a transform on an input point set.
+    The transform is specified in the transform-parameter file.
+
+    Example::
+
+    >>> from nipype.interfaces.elastix import PointsWarp
+    >>> reg = PointsWarp()
+    >>> reg.inputs.points_file = 'surf1.vtk'
+    >>> reg.inputs.transform_file = 'TransformParameters.0.txt'
+    >>> reg.cmdline
+    'transformix -out ./ -def surf1.vtk -tp TransformParameters.0.txt'
+    """
+
+    _cmd = 'transformix'
+    input_spec = PointsWarpInputSpec
+    output_spec = PointsWarpOutputSpec
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        out_dir = op.abspath(self.inputs.output_path)
+
+        fname, ext = op.splitext(op.basename(self.inputs.points_file))
+
+        outputs['warped_file'] = op.join(out_dir,'outputpoints%s' % ext)
+        return outputs

nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py

@@ -0,0 +1,43 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.elastix.registration import AnalyzeWarp
+
+def test_AnalyzeWarp_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    num_threads=dict(argstr='-threads %01d',
+    ),
+    output_path=dict(argstr='-out %s',
+    mandatory=True,
+    usedefault=True,
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    transform_file=dict(argstr='-tp %s',
+    mandatory=True,
+    ),
+    )
+    inputs = AnalyzeWarp.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_AnalyzeWarp_outputs():
+    output_map = dict(disp_field=dict(),
+    jacdet_map=dict(),
+    jacmat_map=dict(),
+    )
+    outputs = AnalyzeWarp.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+

nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py

@@ -0,0 +1,44 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.elastix.registration import ApplyWarp
+
+def test_ApplyWarp_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    moving_image=dict(argstr='-in %s',
+    mandatory=True,
+    ),
+    num_threads=dict(argstr='-threads %01d',
+    ),
+    output_path=dict(argstr='-out %s',
+    mandatory=True,
+    usedefault=True,
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    transform_file=dict(argstr='-tp %s',
+    mandatory=True,
+    ),
+    )
+    inputs = ApplyWarp.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_ApplyWarp_outputs():
+    output_map = dict(warped_file=dict(),
+    )
+    outputs = ApplyWarp.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+