add tck2vtk

Author: oesteban

nipype/interfaces/mrtrix3/__init__.py

@@ -2,7 +2,8 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 # -*- coding: utf-8 -*-
 
-from utils import Mesh2PVE, Generate5tt, BrainMask, TensorMetrics, ComputeTDI
+from utils import (Mesh2PVE, Generate5tt, BrainMask, TensorMetrics,
+                   ComputeTDI, TCK2VTK)
 from preprocess import ResponseSD, ACTPrepareFSL, ReplaceFSwithFIRST
 from tracking import Tractography
 from reconst import FitTensor, EstimateFOD

nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py

@@ -0,0 +1,46 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.mrtrix3.utils import TCK2VTK
+
+def test_TCK2VTK_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='%s',
+    mandatory=True,
+    position=-2,
+    ),
+    nthreads=dict(argstr='-nthreads %d',
+    nohash=True,
+    ),
+    out_file=dict(argstr='%s',
+    position=-1,
+    usedefault=True,
+    ),
+    reference=dict(argstr='-image %s',
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    voxel=dict(argstr='-image %s',
+    ),
+    )
+    inputs = TCK2VTK.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_TCK2VTK_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = TCK2VTK.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/mrtrix3/utils.py

@@ -351,3 +351,53 @@ def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs['out_file'] = op.abspath(self.inputs.out_file)
         return outputs
+
+
+class TCK2VTKInputSpec(CommandLineInputSpec):
+    in_file = File(exists=True, argstr='%s', mandatory=True, position=-2,
+                   desc='input tractography')
+    out_file = File('tracked.vtk', argstr='%s', usedefault=True, position=-1,
+                    desc='output VTK file')
+    reference = File(
+        exists=True, argstr='-image %s', desc='if specified, the properties of'
+        ' this image will be used to convert track point positions from real '
+        '(scanner) coordinates into image coordinates (in mm).')
+    voxel = File(
+        exists=True, argstr='-image %s', desc='if specified, the properties of'
+        ' this image will be used to convert track point positions from real '
+        '(scanner) coordinates into image coordinates.')
+
+    nthreads = traits.Int(
+        argstr='-nthreads %d', desc='number of threads. if zero, the number'
+        ' of available cpus will be used', nohash=True)
+
+
+class TCK2VTKOutputSpec(TraitedSpec):
+    out_file = File(desc='output VTK file')
+
+
+class TCK2VTK(MRTrix3Base):
+
+    """
+
+
+    Example
+    -------
+
+    >>> import nipype.interfaces.mrtrix3 as mrt
+    >>> vtk = mrt.TCK2VTK()
+    >>> vtk.inputs.in_file = 'tracked.tck'
+    >>> vtk.inputs.reference = 'dwi.nii.gz'
+    >>> vtk.cmdline                               # doctest: +ELLIPSIS
+    'tck2vtk -image dwi.nii.gz tracked.tck tracked.vtk'
+    >>> vtk.run()                                 # doctest: +SKIP
+    """
+
+    _cmd = 'tck2vtk'
+    input_spec = TCK2VTKInputSpec
+    output_spec = TCK2VTKOutputSpec
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['out_file'] = op.abspath(self.inputs.out_file)
+        return outputs