add mesh2pve interface

Author: oesteban

nipype/interfaces/mrtrix3/utils.py

@@ -0,0 +1,67 @@
+# 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 nipype.interfaces.base import (
+    CommandLineInputSpec, CommandLine, traits, TraitedSpec, File)
+
+from nipype.utils.filemanip import split_filename
+from nipype.interfaces.traits_extension import isdefined
+
+
+class Mesh2PVEInputSpec(CommandLineInputSpec):
+    in_file = File(exists=True, argstr='%s', mandatory=True, position=-3,
+                   desc='input diffusion weighted images')
+    reference = File(exists=True, argstr='%s', mandatory=True, position=-2,
+                     desc='input diffusion weighted images')
+    in_first = File(
+        exists=True, argstr='-first %s',
+        desc='indicates that the mesh file is provided by FSL FIRST')
+
+    out_file = File(
+        'mesh2volume.nii.gz', argstr='%s', mandatory=True, position=-1,
+        usedefault=True, desc='output file containing SH coefficients')
+
+
+class Mesh2PVEOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='the output response file')
+
+
+class Mesh2PVE(CommandLine):
+
+    """
+    Performs tractography after selecting the appropriate algorithm
+
+    Example
+    -------
+
+    >>> import nipype.interfaces.mrtrix3 as mrt
+    >>> m2p = mrt.Mesh2PVE()
+    >>> m2p.inputs.in_file = 'surf.vtk'
+    >>> m2p.inputs.reference = 'dwi.nii.gz'
+    >>> m2p.inputs.in_first = 'T1.nii.gz'
+    >>> m2p.cmdline                               # doctest: +ELLIPSIS
+    'mesh2pve -first T1.nii.gz surf.vtk dwi.nii.gz mesh2volume.nii.gz'
+    >>> resp.run()                                 # doctest: +SKIP
+    """
+
+    _cmd = 'mesh2pve'
+    input_spec = Mesh2PVEInputSpec
+    output_spec = Mesh2PVEOutputSpec
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['out_file'] = op.abspath(self.inputs.out_file)
+        return outputs