Update to Camino tracking interfaces

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
+

nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py

@@ -14,6 +14,9 @@ def test_TrackBootstrap_inputs():
  bsdatafiles=dict(argstr='-bsdatafile %s',
  mandatory=True,
  ),
+ curveinterval=dict(argstr='-curveinterval %f',
+ requires=['curvethresh'],
+ ),
  curvethresh=dict(argstr='-curvethresh %f',
  ),
  data_dims=dict(argstr='-datadims %s',
@@ -28,14 +31,15 @@ def test_TrackBootstrap_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',
+ ),
  inversion=dict(argstr='-inversion %s',
  ),
  ipthresh=dict(argstr='-ipthresh %f',
@@ -64,9 +68,15 @@ def test_TrackBootstrap_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',
  ),