Updated CHANGES, removed genfile, added docstrings, updated tests for DTK and MRtrix

Author: Erik Ziegler

CHANGES

@@ -1,6 +1,8 @@
 Next Release
 ============
 
+* ENH: New Diffusion Toolkit interface: TrackMerge
+* ENH: New MRtrix interface: FilterTracks
 * ENH: New FSL interface: EpiReg
 * ENH: New Freesurfer interface: Tkregister2 (for conversion of fsl style matrices to freesurfer format)
 * ENH: New FSL interfaces: WarpPoints, WarpPointsToStd.

nipype/interfaces/diffusion_toolkit/postproc.py

@@ -24,6 +24,23 @@ class SplineFilterOutputSpec(TraitedSpec):
     smoothed_track_file = File(exists=True)
 
 class SplineFilter(CommandLine):
+    """
+    Smoothes TrackVis track files with a B-Spline filter.
+
+    Helps remove redundant track points and segments
+    (thus reducing the size of the track file) and also
+    make tracks nicely smoothed. It will NOT change the
+    quality of the tracks or lose any original information.
+
+    Example
+    -------
+
+    >>> import nipype.interfaces.diffusion_toolkit as dtk
+    >>> filt = dtk.SplineFilter()
+    >>> filt.inputs.track_file = 'tracks.trk'
+    >>> filt.inputs.step_length = 0.5
+    >>> filt.run()                                 # doctest: +SKIP
+    """
     input_spec=SplineFilterInputSpec
     output_spec=SplineFilterOutputSpec
 
@@ -43,6 +60,25 @@ class TrackMergeOutputSpec(TraitedSpec):
     track_file = File(exists=True)
 
 class TrackMerge(CommandLine):
+    """
+    Merges several TrackVis track files into a single track
+    file.
+
+    An id type property tag is added to each track in the
+    newly merged file, with each unique id representing where
+    the track was originally from. When the merged file is
+    loaded in TrackVis, a property filter will show up in
+    Track Property panel. Users can adjust that to distinguish
+    and sub-group tracks by its id (origin).
+
+    Example
+    -------
+
+    >>> import nipype.interfaces.diffusion_toolkit as dtk
+    >>> mrg = dtk.TrackMerge()
+    >>> mrg.inputs.track_files = ['track1.trk','track2.trk']
+    >>> mrg.run()                                 # doctest: +SKIP
+    """
     input_spec=TrackMergeInputSpec
     output_spec=TrackMergeOutputSpec
 

nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py

@@ -43,8 +43,10 @@ def test_FilterTracks_inputs():
     ),
     no_mask_interpolation=dict(argstr='-nomaskinterp',
     ),
-    out_filename=dict(argstr='%s',
-    genfile=True,
+    out_file=dict(argstr='%s',
+    hash_files=False,
+    name_source=['in_file'],
+    name_template='%s_filt',
     position=-1,
     ),
     quiet=dict(argstr='-quiet',

nipype/interfaces/mrtrix/tracking.py

@@ -30,7 +30,10 @@ class FilterTracksInputSpec(CommandLineInputSpec):
     minimum_tract_length = traits.Float(argstr='-minlength %s', units='mm',
         desc="Sets the minimum length of any track in millimeters (default is 10 mm).")
 
-    out_filename = File(genfile=True, argstr='%s', position=-1, desc='Output filtered track filename')
+
+    out_file = File(argstr='%s', position=-1, desc='Output filtered track filename',
+            name_source=['in_file'], hash_files=False, name_template='%s_filt')
+
     no_mask_interpolation = traits.Bool(argstr='-nomaskinterp', desc="Turns off trilinear interpolation of mask images.")
     invert = traits.Bool(argstr='-invert', desc="invert the matching process, so that tracks that would" \
                 "otherwise have been included are now excluded and vice-versa.")
@@ -60,25 +63,6 @@ class FilterTracks(CommandLine):
     input_spec=FilterTracksInputSpec
     output_spec=FilterTracksOutputSpec
 
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        outputs['out_file'] = op.abspath(self._gen_outfilename())
-        return outputs
-
-    def _gen_filename(self, name):
-        if name is 'out_filename':
-            return self._gen_outfilename()
-        else:
-            return None
-
-    def _gen_outfilename(self):
-        if isdefined(self.inputs.out_filename):
-            path, name , _ = split_filename(self.inputs.out_filename)
-            return op.join(path, name + '.tck')
-        else:
-            _, name , _ = split_filename(self.inputs.in_file)
-            return op.abspath(name + '_filt.tck')
-
 
 class Tracks2ProbInputSpec(CommandLineInputSpec):
     in_file = File(exists=True, argstr='%s', mandatory=True, position=-2,