add labelconfig interface

Author: oesteban

nipype/interfaces/mrtrix3/__init__.py

@@ -6,3 +6,4 @@
 from preprocess import ResponseSD, ACTPrepareFSL
 from tracking import Tractography
 from reconst import FitTensor, EstimateFOD
+from connectivity import LabelConfig

nipype/interfaces/mrtrix3/connectivity.py

@@ -0,0 +1,94 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+# -*- coding: utf-8 -*-
+
+"""
+    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)
+
+"""
+import os
+import os.path as op
+
+from base import MRTrix3BaseInputSpec, MRTrix3Base
+from nipype.interfaces.base import (
+    CommandLineInputSpec, CommandLine, traits, TraitedSpec, File)
+
+from nipype.utils.filemanip import split_filename
+from nipype.interfaces.traits_extension import isdefined
+
+
+class LabelConfigInputSpec(CommandLineInputSpec):
+    in_file = File(exists=True, argstr='%s', mandatory=True, position=-3,
+                   desc='input anatomical image')
+    in_config = File(exists=True, argstr='%s', position=-2,
+                     desc='connectome configuration file')
+    out_file = File(
+        'parcellation.mif', argstr='%s', mandatory=True, position=-1,
+        usedefault=True, desc='output file after processing')
+
+    lut_basic = File(argstr='-lut_basic %s', desc='get information from '
+                     'a basic lookup table consisting of index / name pairs')
+    lut_fs = File(argstr='-lut_freesurfer %s', desc='get information from '
+                  'a FreeSurfer lookup table(typically "FreeSurferColorLUT'
+                  '.txt")')
+    lut_aal = File(argstr='-lut_aal %s', desc='get information from the AAL '
+                   'lookup table (typically "ROI_MNI_V4.txt")')
+    lut_itksnap = File(argstr='-lut_itksnap %s', desc='get information from an'
+                       ' ITK - SNAP lookup table(this includes the IIT atlas '
+                       'file "LUT_GM.txt")')
+    spine = File(argstr='-spine %s', desc='provide a manually-defined '
+                 'segmentation of the base of the spine where the streamlines'
+                 ' terminate, so that this can become a node in the connection'
+                 ' matrix.')
+    nthreads = traits.Int(
+        argstr='-nthreads %d', desc='number of threads. if zero, the number'
+        ' of available cpus will be used')
+
+
+class LabelConfigOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='the output response file')
+
+
+class LabelConfig(MRTrix3Base):
+
+    """
+    Generate anatomical information necessary for Anatomically
+    Constrained Tractography (ACT).
+
+    Example
+    -------
+
+    >>> import nipype.interfaces.mrtrix3 as mrt
+    >>> labels = mrt.LabelConfig()
+    >>> labels.inputs.in_file = 'aparc+aseg.nii.gz'
+    >>> labels.inputs.in_config = 'mrtrix3_labelconfig.txt'
+    >>> labels.cmdline                               # doctest: +ELLIPSIS
+    'labelconfig aparc+aseg.nii.gz mrtrix3_labelconfig.txt parcellation.mif'
+    >>> labels.run()                                 # doctest: +SKIP
+    """
+
+    _cmd = 'labelconfig:'
+    input_spec = LabelConfigInputSpec
+    output_spec = LabelConfigOutputSpec
+
+    def _parse_inputs(self, skip=None):
+        if skip is None:
+            skip = []
+
+        if not isdefined(self.inputs.in_config):
+            from distutils.spawn import find_executable
+            path = op.dirname(find_executable(self._cmd))
+            self.inputs.in_config = op.abspath(
+                op.join(path, '../src/dwi/tractography/connectomics/'
+                              'example_configs/fs_default.txt'))
+        return super(LabelConfig, self)._parse_inputs(skip=skip)
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['out_file'] = op.abspath(self.inputs.out_file)
+        return outputs