[FIX/REF] Switch to new MRtrix3 labelconvert CL tool (#2441)

* Fix new MrTrix3 CL tool

* Fix some tests

* fix: empty out the file

file contents not required for testing

* Add back Mrtrix3 labelconfig interface

* Apply suggestions

Author: jguillon

nipype/interfaces/mrtrix3/__init__.py

@@ -8,4 +8,4 @@
 from .preprocess import ResponseSD, ACTPrepareFSL, ReplaceFSwithFIRST
 from .tracking import Tractography
 from .reconst import FitTensor, EstimateFOD
-from .connectivity import LabelConfig, BuildConnectome
+from .connectivity import LabelConfig, LabelConvert, BuildConnectome

nipype/interfaces/mrtrix3/connectivity.py

@@ -219,3 +219,91 @@ def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs['out_file'] = op.abspath(self.inputs.out_file)
         return outputs
+
+
+class LabelConvertInputSpec(CommandLineInputSpec):
+    in_file = File(
+        exists=True,
+        argstr='%s',
+        mandatory=True,
+        position=-4,
+        desc='input anatomical image')
+    in_lut = File(
+        exists=True,
+        argstr='%s',
+        mandatory=True,
+        position=-3,
+        desc='get information from '
+        'a basic lookup table consisting of index / name pairs')
+    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')
+    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.')
+    num_threads = traits.Int(
+        argstr='-nthreads %d',
+        desc='number of threads. if zero, the number'
+        ' of available cpus will be used',
+        nohash=True)
+
+
+class LabelConvertOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='the output response file')
+
+
+class LabelConvert(MRTrix3Base):
+    """
+    Re-configure parcellation to be incrementally defined.
+
+    Example
+    -------
+
+    >>> import nipype.interfaces.mrtrix3 as mrt
+    >>> labels = mrt.LabelConvert()
+    >>> labels.inputs.in_file = 'aparc+aseg.nii'
+    >>> labels.inputs.in_config = 'mrtrix3_labelconfig.txt'
+    >>> labels.inputs.in_lut = 'FreeSurferColorLUT.txt'
+    >>> labels.cmdline
+    'labelconvert aparc+aseg.nii FreeSurferColorLUT.txt mrtrix3_labelconfig.txt parcellation.mif'
+    >>> labels.run()                                 # doctest: +SKIP
+    """
+
+    _cmd = 'labelconvert'
+    input_spec = LabelConvertInputSpec
+    output_spec = LabelConvertOutputSpec
+
+    def _parse_inputs(self, skip=None):
+        if skip is None:
+            skip = []
+
+        if not isdefined(self.inputs.in_config):
+            from nipype.utils.filemanip import which
+            path = which(self._cmd)
+            if path is None:
+                path = os.getenv(MRTRIX3_HOME, '/opt/mrtrix3')
+            else:
+                path = op.dirname(op.dirname(path))
+
+            self.inputs.in_config = op.join(
+                path, 'src/dwi/tractography/connectomics/'
+                'example_configs/fs_default.txt')
+
+        return super(LabelConvert, 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

nipype/interfaces/mrtrix3/tests/test_auto_LabelConvert.py

@@ -0,0 +1,59 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..connectivity import LabelConvert
+
+
+def test_LabelConvert_inputs():
+    input_map = dict(
+        args=dict(argstr='%s', ),
+        environ=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        ignore_exception=dict(
+            deprecated='1.0.0',
+            nohash=True,
+            usedefault=True,
+        ),
+        in_config=dict(
+            argstr='%s',
+            position=-2,
+        ),
+        in_file=dict(
+            argstr='%s',
+            mandatory=True,
+            position=-4,
+        ),
+        in_lut=dict(
+            argstr='%s',
+            mandatory=True,
+            position=-3,
+        ),
+        num_threads=dict(
+            argstr='-nthreads %d',
+            nohash=True,
+        ),
+        out_file=dict(
+            argstr='%s',
+            mandatory=True,
+            position=-1,
+            usedefault=True,
+        ),
+        spine=dict(argstr='-spine %s', ),
+        terminal_output=dict(
+            deprecated='1.0.0',
+            nohash=True,
+        ),
+    )
+    inputs = LabelConvert.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+def test_LabelConvert_outputs():
+    output_map = dict(out_file=dict(), )
+    outputs = LabelConvert.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/testing/data/FreeSurferColorLUT.txt

@@ -0,0 +1 @@
+