Merge remote-tracking branch 'origin/pr/848'

Conflicts:
	CHANGES

Author: chrisgorgo

CHANGES

@@ -14,6 +14,8 @@ Next Release
 * ENH: Support for elastix via a set of new interfaces: Registration, ApplyWarp, 
        AnalyzeWarp, PointsWarp, and EditTransform
 * ENH: New ANTs interface: ApplyTransformsToPoints, LaplacianThickness
+* ENH: New Diffusion Toolkit interface: TrackMerge
+* ENH: New MRtrix interface: FilterTracks
 * ENH: New metrics group in algorithms. Now Distance, Overlap, and FuzzyOverlap
        are found in nipype.algorithms.metrics instead of misc
 * ENH: New interface in algorithms.metrics: ErrorMap (a voxel-wise diff map).

nipype/interfaces/diffusion_toolkit/__init__.py

@@ -1,4 +1,4 @@
 from .base import Info
-from .postproc import SplineFilter
+from .postproc import SplineFilter, TrackMerge
 from .dti import DTIRecon, DTITracker
 from .odf import HARDIMat, ODFRecon, ODFTracker

nipype/interfaces/diffusion_toolkit/postproc.py

@@ -13,7 +13,7 @@
 __docformat__ = 'restructuredtext'
 
 from nipype.interfaces.base import (TraitedSpec, File, traits, CommandLine,
-    CommandLineInputSpec)
+    InputMultiPath, CommandLineInputSpec)
 
 class SplineFilterInputSpec(CommandLineInputSpec):
     track_file = File(exists=True, desc="file containing tracks to be filtered", position=0, argstr="%s", mandatory=True)
@@ -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
 
@@ -32,4 +49,42 @@ class SplineFilter(CommandLine):
     def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs['smoothed_track_file'] = os.path.abspath(self.inputs.output_file)
-        return outputs
+        return outputs
+
+
+class TrackMergeInputSpec(CommandLineInputSpec):
+    track_files = InputMultiPath(File(exists=True), desc="file containing tracks to be filtered", position=0, argstr="%s...", mandatory=True)
+    output_file = File("merged_tracks.trk", desc="target file for merged tracks", position=-1, argstr="%s", usedefault=True)
+
+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
+
+    _cmd = "track_merge"
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['track_file'] = os.path.abspath(self.inputs.output_file)
+        return outputs

nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py

@@ -0,0 +1,40 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.diffusion_toolkit.postproc import TrackMerge
+
+def test_TrackMerge_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    output_file=dict(argstr='%s',
+    position=-1,
+    usedefault=True,
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    track_files=dict(argstr='%s...',
+    mandatory=True,
+    position=0,
+    ),
+    )
+    inputs = TrackMerge.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_TrackMerge_outputs():
+    output_map = dict(track_file=dict(),
+    )
+    outputs = TrackMerge.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/mrtrix/__init__.py

@@ -1,6 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-from .tracking import (Tracks2Prob, StreamlineTrack,
+from .tracking import (Tracks2Prob, FilterTracks, StreamlineTrack,
                        DiffusionTensorStreamlineTrack,
                        SphericallyDeconvolutedStreamlineTrack,
                        ProbabilisticSphericallyDeconvolutedStreamlineTrack)

nipype/interfaces/mrtrix/convert.py

@@ -100,7 +100,10 @@ def track_gen(track_points):
         n_streams = 0
         iflogger.info('Reading tracks...')
         while True:
-            n_pts = track_points[n_streams]
+            try:
+                n_pts = track_points[n_streams]
+            except IndexError:
+                break
             pts_str = fileobj.read(n_pts * bytesize)
             nan_str = fileobj.read(bytesize)
             if len(pts_str) < (n_pts * bytesize):

nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py

@@ -0,0 +1,73 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.mrtrix.tracking import FilterTracks
+
+def test_FilterTracks_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    debug=dict(argstr='-debug',
+    position=1,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    exclude_file=dict(argstr='-exclude %s',
+    xor=['exclude_file', 'exclude_spec'],
+    ),
+    exclude_spec=dict(argstr='-exclude %s',
+    position=2,
+    sep=',',
+    units='mm',
+    xor=['exclude_file', 'exclude_spec'],
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='%s',
+    mandatory=True,
+    position=-2,
+    ),
+    include_file=dict(argstr='-include %s',
+    xor=['include_file', 'include_spec'],
+    ),
+    include_spec=dict(argstr='-include %s',
+    position=2,
+    sep=',',
+    units='mm',
+    xor=['include_file', 'include_spec'],
+    ),
+    invert=dict(argstr='-invert',
+    ),
+    minimum_tract_length=dict(argstr='-minlength %s',
+    units='mm',
+    ),
+    no_mask_interpolation=dict(argstr='-nomaskinterp',
+    ),
+    out_file=dict(argstr='%s',
+    hash_files=False,
+    name_source=['in_file'],
+    name_template='%s_filt',
+    position=-1,
+    ),
+    quiet=dict(argstr='-quiet',
+    position=1,
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    )
+    inputs = FilterTracks.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_FilterTracks_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = FilterTracks.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/mrtrix/tracking.py

@@ -14,6 +14,56 @@
 import os, os.path as op
 from nipype.interfaces.traits_extension import isdefined
 
+class FilterTracksInputSpec(CommandLineInputSpec):
+    in_file = File(exists=True, argstr='%s', mandatory=True, position=-2,
+        desc='input tracks to be filtered')
+    include_xor = ['include_file', 'include_spec']
+    include_file = File(exists=True, argstr='-include %s', desc='inclusion file', xor = include_xor)
+    include_spec = traits.List(traits.Float, desc='inclusion specification in mm and radius (x y z r)', position=2,
+        argstr='-include %s', minlen=4, maxlen=4, sep=',', units='mm', xor = include_xor)
+
+    exclude_xor = ['exclude_file', 'exclude_spec']
+    exclude_file = File(exists=True, argstr='-exclude %s', desc='exclusion file', xor = exclude_xor)
+    exclude_spec = traits.List(traits.Float, desc='exclusion specification in mm and radius (x y z r)', position=2,
+        argstr='-exclude %s', minlen=4, maxlen=4, sep=',', units='mm', xor = exclude_xor)
+
+    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_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.")
+
+
+    quiet = traits.Bool(argstr='-quiet', position=1, desc="Do not display information messages or progress status.")
+    debug = traits.Bool(argstr='-debug', position=1, desc="Display debugging messages.")
+
+class FilterTracksOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='the output filtered tracks')
+
+class FilterTracks(CommandLine):
+    """
+    Use regions-of-interest to select a subset of tracks
+    from a given MRtrix track file.
+
+    Example
+    -------
+
+    >>> import nipype.interfaces.mrtrix as mrt
+    >>> filt = mrt.FilterTracks()
+    >>> filt.inputs.in_file = 'tracks.tck'
+    >>> filt.run()                                 # doctest: +SKIP
+    """
+
+    _cmd = 'filter_tracks'
+    input_spec=FilterTracksInputSpec
+    output_spec=FilterTracksOutputSpec
+
+
 class Tracks2ProbInputSpec(CommandLineInputSpec):
     in_file = File(exists=True, argstr='%s', mandatory=True, position=-2,
         desc='tract file')