Camino tracking interfaces update

CHANGES

@@ -1,6 +1,9 @@
 Next release
 ============
 
+* ENH: Updated Camino tracking interfaces, which can now use FSL bedpostx output.
+       New options also include choice of tracker, interpolator, stepsize and 
+       curveinterval for angle threshold (https://github.com/nipy/nipype/pull/1029)
 * FIX: Interfaces redirecting X crashed if $DISPLAY not defined (https://github.com/nipy/nipype/pull/1027)
 * FIX: Bug crashed 'make api' (https://github.com/nipy/nipype/pull/1026)
 * ENH: Updated antsIntroduction to handle RA and RI registrations (https://github.com/nipy/nipype/pull/1009)

nipype/algorithms/tests/test_auto_Overlap.py

@@ -0,0 +1,46 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.algorithms.misc import Overlap
+
+def test_Overlap_inputs():
+    input_map = dict(bg_overlap=dict(mandatory=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    mask_volume=dict(),
+    out_file=dict(usedefault=True,
+    ),
+    vol_units=dict(mandatory=True,
+    usedefault=True,
+    ),
+    volume1=dict(mandatory=True,
+    ),
+    volume2=dict(mandatory=True,
+    ),
+    weighting=dict(usedefault=True,
+    ),
+    )
+    inputs = Overlap.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_Overlap_outputs():
+    output_map = dict(dice=dict(),
+    diff_file=dict(),
+    jaccard=dict(),
+    labels=dict(),
+    roi_di=dict(),
+    roi_ji=dict(),
+    roi_voldiff=dict(),
+    volume_difference=dict(),
+    )
+    outputs = Overlap.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/camino/__init__.py

@@ -9,6 +9,7 @@
                       Shredder)
 from .dti import (DTIFit, ModelFit, DTLUTGen, PicoPDFs, Track, TrackPICo,
                   TrackBayesDirac, TrackDT, TrackBallStick, TrackBootstrap,
+                  TrackBedpostxDeter, TrackBedpostxProba,
                   ComputeFractionalAnisotropy, ComputeMeanDiffusivity,
                   ComputeTensorTrace,  ComputeEigensystem, DTMetric)
 from .calib import (SFPICOCalibData, SFLUTGen)

nipype/interfaces/camino/tests/test_auto_Track.py

@@ -9,6 +9,9 @@ def test_Track_inputs():
     ),
     args=dict(argstr='%s',
     ),
+    curveinterval=dict(argstr='-curveinterval %f',
+    requires=['curvethresh'],
+    ),
     curvethresh=dict(argstr='-curvethresh %f',
     ),
     data_dims=dict(argstr='-datadims %s',
@@ -23,14 +26,15 @@ def test_Track_inputs():
     usedefault=True,
     ),
     in_file=dict(argstr='-inputfile %s',
-    mandatory=True,
     position=1,
     ),
     inputdatatype=dict(argstr='-inputdatatype %s',
     ),
     inputmodel=dict(argstr='-inputmodel %s',
     usedefault=True,
     ),
+    interpolator=dict(argstr='-interpolator %s',
+    ),
     ipthresh=dict(argstr='-ipthresh %f',
     ),
     maxcomponents=dict(argstr='-maxcomponents %d',
@@ -51,9 +55,15 @@ def test_Track_inputs():
     seed_file=dict(argstr='-seedfile %s',
     position=2,
     ),
+    stepsize=dict(argstr='-stepsize %f',
+    requires=['tracker'],
+    ),
     terminal_output=dict(mandatory=True,
     nohash=True,
     ),
+    tracker=dict(argstr='-tracker %s',
+    usedefault=True,
+    ),
     voxel_dims=dict(argstr='-voxeldims %s',
     units='mm',
     ),

nipype/interfaces/camino/tests/test_auto_TrackBallStick.py

@@ -9,6 +9,9 @@ def test_TrackBallStick_inputs():
     ),
     args=dict(argstr='%s',
     ),
+    curveinterval=dict(argstr='-curveinterval %f',
+    requires=['curvethresh'],
+    ),
     curvethresh=dict(argstr='-curvethresh %f',
     ),
     data_dims=dict(argstr='-datadims %s',
@@ -23,14 +26,15 @@ def test_TrackBallStick_inputs():
     usedefault=True,
     ),
     in_file=dict(argstr='-inputfile %s',
-    mandatory=True,
     position=1,
     ),
     inputdatatype=dict(argstr='-inputdatatype %s',
     ),
     inputmodel=dict(argstr='-inputmodel %s',
     usedefault=True,
     ),
+    interpolator=dict(argstr='-interpolator %s',
+    ),
     ipthresh=dict(argstr='-ipthresh %f',
     ),
     maxcomponents=dict(argstr='-maxcomponents %d',
@@ -51,9 +55,15 @@ def test_TrackBallStick_inputs():
     seed_file=dict(argstr='-seedfile %s',
     position=2,
     ),
+    stepsize=dict(argstr='-stepsize %f',
+    requires=['tracker'],
+    ),
     terminal_output=dict(mandatory=True,
     nohash=True,
     ),
+    tracker=dict(argstr='-tracker %s',
+    usedefault=True,
+    ),
     voxel_dims=dict(argstr='-voxeldims %s',
     units='mm',
     ),

nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py

@@ -9,6 +9,9 @@ def test_TrackBayesDirac_inputs():
     ),
     args=dict(argstr='%s',
     ),
+    curveinterval=dict(argstr='-curveinterval %f',
+    requires=['curvethresh'],
+    ),
     curvepriorg=dict(argstr='-curvepriorg %G',
     ),
     curvepriork=dict(argstr='-curvepriork %G',
@@ -33,14 +36,15 @@ def test_TrackBayesDirac_inputs():
     usedefault=True,
     ),
     in_file=dict(argstr='-inputfile %s',
-    mandatory=True,
     position=1,
     ),
     inputdatatype=dict(argstr='-inputdatatype %s',
     ),
     inputmodel=dict(argstr='-inputmodel %s',
     usedefault=True,
     ),
+    interpolator=dict(argstr='-interpolator %s',
+    ),
     ipthresh=dict(argstr='-ipthresh %f',
     ),
     iterations=dict(argstr='-iterations %d',
@@ -71,9 +75,15 @@ def test_TrackBayesDirac_inputs():
     seed_file=dict(argstr='-seedfile %s',
     position=2,
     ),
+    stepsize=dict(argstr='-stepsize %f',
+    requires=['tracker'],
+    ),
     terminal_output=dict(mandatory=True,
     nohash=True,
     ),
+    tracker=dict(argstr='-tracker %s',
+    usedefault=True,
+    ),
     voxel_dims=dict(argstr='-voxeldims %s',
     units='mm',
     ),

nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py

@@ -0,0 +1,91 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.camino.dti import TrackBedpostxDeter
+
+def test_TrackBedpostxDeter_inputs():
+    input_map = dict(anisfile=dict(argstr='-anisfile %s',
+    ),
+    anisthresh=dict(argstr='-anisthresh %f',
+    ),
+    args=dict(argstr='%s',
+    ),
+    bedpostxdir=dict(argstr='-bedpostxdir %s',
+    mandatory=True,
+    ),
+    curveinterval=dict(argstr='-curveinterval %f',
+    requires=['curvethresh'],
+    ),
+    curvethresh=dict(argstr='-curvethresh %f',
+    ),
+    data_dims=dict(argstr='-datadims %s',
+    units='voxels',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    gzip=dict(argstr='-gzip',
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='-inputfile %s',
+    position=1,
+    ),
+    inputdatatype=dict(argstr='-inputdatatype %s',
+    ),
+    inputmodel=dict(argstr='-inputmodel %s',
+    usedefault=True,
+    ),
+    interpolator=dict(argstr='-interpolator %s',
+    ),
+    ipthresh=dict(argstr='-ipthresh %f',
+    ),
+    maxcomponents=dict(argstr='-maxcomponents %d',
+    units='NA',
+    ),
+    min_vol_frac=dict(argstr='-bedpostxminf %d',
+    units='NA',
+    ),
+    numpds=dict(argstr='-numpds %d',
+    units='NA',
+    ),
+    out_file=dict(argstr='-outputfile %s',
+    genfile=True,
+    position=-1,
+    ),
+    output_root=dict(argstr='-outputroot %s',
+    position=-1,
+    ),
+    outputtracts=dict(argstr='-outputtracts %s',
+    ),
+    seed_file=dict(argstr='-seedfile %s',
+    position=2,
+    ),
+    stepsize=dict(argstr='-stepsize %f',
+    requires=['tracker'],
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    tracker=dict(argstr='-tracker %s',
+    usedefault=True,
+    ),
+    voxel_dims=dict(argstr='-voxeldims %s',
+    units='mm',
+    ),
+    )
+    inputs = TrackBedpostxDeter.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_TrackBedpostxDeter_outputs():
+    output_map = dict(tracked=dict(),
+    )
+    outputs = TrackBedpostxDeter.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/camino/tests/test_auto_TrackBedpostxProba.py

@@ -0,0 +1,94 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.camino.dti import TrackBedpostxProba
+
+def test_TrackBedpostxProba_inputs():
+    input_map = dict(anisfile=dict(argstr='-anisfile %s',
+    ),
+    anisthresh=dict(argstr='-anisthresh %f',
+    ),
+    args=dict(argstr='%s',
+    ),
+    bedpostxdir=dict(argstr='-bedpostxdir %s',
+    mandatory=True,
+    ),
+    curveinterval=dict(argstr='-curveinterval %f',
+    requires=['curvethresh'],
+    ),
+    curvethresh=dict(argstr='-curvethresh %f',
+    ),
+    data_dims=dict(argstr='-datadims %s',
+    units='voxels',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    gzip=dict(argstr='-gzip',
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='-inputfile %s',
+    position=1,
+    ),
+    inputdatatype=dict(argstr='-inputdatatype %s',
+    ),
+    inputmodel=dict(argstr='-inputmodel %s',
+    usedefault=True,
+    ),
+    interpolator=dict(argstr='-interpolator %s',
+    ),
+    ipthresh=dict(argstr='-ipthresh %f',
+    ),
+    iterations=dict(argstr='-iterations %d',
+    units='NA',
+    ),
+    maxcomponents=dict(argstr='-maxcomponents %d',
+    units='NA',
+    ),
+    min_vol_frac=dict(argstr='-bedpostxminf %d',
+    units='NA',
+    ),
+    numpds=dict(argstr='-numpds %d',
+    units='NA',
+    ),
+    out_file=dict(argstr='-outputfile %s',
+    genfile=True,
+    position=-1,
+    ),
+    output_root=dict(argstr='-outputroot %s',
+    position=-1,
+    ),
+    outputtracts=dict(argstr='-outputtracts %s',
+    ),
+    seed_file=dict(argstr='-seedfile %s',
+    position=2,
+    ),
+    stepsize=dict(argstr='-stepsize %f',
+    requires=['tracker'],
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    tracker=dict(argstr='-tracker %s',
+    usedefault=True,
+    ),
+    voxel_dims=dict(argstr='-voxeldims %s',
+    units='mm',
+    ),
+    )
+    inputs = TrackBedpostxProba.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_TrackBedpostxProba_outputs():
+    output_map = dict(tracked=dict(),
+    )
+    outputs = TrackBedpostxProba.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+