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satrasatra
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Merge pull request nipy#322 from satra/fix/cleanup
Fix/cleanup
2 parents 845d809 + e028db0 commit 09c00b7

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+280
-211
lines changed

‎examples/dmri_group_connectivity_camino.py

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@@ -54,7 +54,7 @@
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import os.path as op # system functions
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import cmp
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from nipype.workflows.dmri.camino.group_connectivity import create_group_connectivity_pipeline
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from nipype.workflows.dmri.connectivity.group_connectivity import (create_merge_networks_by_group_workflow,
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from nipype.workflows.dmri.connectivity.group_connectivity import (create_merge_networks_by_group_workflow,
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create_merge_group_networks_workflow, create_average_networks_by_group_workflow)
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"""

‎nipype/interfaces/ants/__init__.py

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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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"""Top-level namespace for ants."""
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from nipype.interfaces.ants.base import ANTSCommand
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from nipype.interfaces.ants.normalize import (BuildTemplate,
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WarpImageMultiTransform, GenWarpFields)
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from .normalize import (BuildTemplate, WarpImageMultiTransform, GenWarpFields)
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‎nipype/interfaces/ants/base.py

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# vi: set ft=python sts=4 ts=4 sw=4 et:
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"""The ants module provides basic functions for interfacing with ANTS tools."""
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__docformat__ = 'restructuredtext'
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# Standard library imports
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import os
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from copy import deepcopy
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# Third-party imports
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import numpy as np
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# Local imports
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from nipype.interfaces.base import (TraitedSpec, File, traits,
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Directory, InputMultiPath,
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OutputMultiPath, CommandLine,
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CommandLineInputSpec, isdefined)
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from nipype.interfaces.base import (CommandLine, CommandLineInputSpec, traits,
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isdefined)
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import logging
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logger = logging.getLogger('iflogger')
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class ANTSCommandInputSpec(CommandLineInputSpec):
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"""Base Input Specification for all ANTS Commands
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"""
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num_threads = traits.Int(1, usedefault=True,
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desc="Number of ITK threads to use")
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class ANTSCommand(CommandLine):
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"""Base class for ANTS interfaces
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"""
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input_spec = ANTSCommandInputSpec
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_num_threads = 1
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def __init__(self, **inputs):
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self.inputs.environ['ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS']='1'
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return super(ANTSCommand, self).__init__(**inputs)
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super(ANTSCommand, self).__init__(**inputs)
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self.inputs.on_trait_change(self._num_threads_update, 'num_threads')
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if not isdefined(self.inputs.num_threads):
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self.inputs.num_threads = self._num_threads
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else:
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self._num_threads_update()
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def _num_threads_update(self):
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self._num_threads = self.inputs.num_threads
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self.inputs.environ.update({'ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS':
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'%s' % self.inputs.num_threads})
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@classmethod
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def set_default_num_threads(cls, num_threads):
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"""Set the default number of threads for ITK calls
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This method is used to set the default number of ITK threads for all
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the ANTS interfaces. However, setting this will not update the output
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type for any existing instances. For these, assign the
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<instance>.inputs.num_threads
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"""
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cls._num_threads = num_threads

‎nipype/interfaces/ants/normalize.py

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‎nipype/interfaces/cmtk/nx.py

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@@ -505,7 +505,7 @@ class AverageNetworks(BaseInterface):
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"""
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Calculates and outputs the average network given a set of input NetworkX gpickle files
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This interface will only keep an edge in the averaged network if that edge is present in
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This interface will only keep an edge in the averaged network if that edge is present in
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at least half of the input networks.
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Example

‎nipype/interfaces/setup.py

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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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def configuration(parent_package='',top_path=None):
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def configuration(parent_package='', top_path=None):
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from numpy.distutils.misc_util import Configuration
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config = Configuration('interfaces', parent_package, top_path)
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config.add_subpackage('afni')
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config.add_subpackage('ants')
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config.add_subpackage('camino')
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config.add_subpackage('camino2trackvis')
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config.add_subpackage('cmtk')

‎nipype/interfaces/spm/preprocess.py

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@@ -1056,7 +1056,7 @@ class ApplyDeformationFieldInputSpec(SPMCommandInputSpec):
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reference_volume = File(exists=True, mandatory=True, field='comp{2}.id.space')
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interp = traits.Range(low=0, high=7, field='interp',
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desc='degree of b-spline used for interpolation')
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class ApplyDeformationFieldOutputSpec(TraitedSpec):
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out_files = OutputMultiPath(File(exists=True))

‎nipype/testing/data/ants_Affine.txt

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‎nipype/testing/data/ants_Warp.nii.gz

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‎nipype/testing/data/ants_deformed.nii.gz

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