Merge remote-tracking branch 'upstream/master' into enh/openfmri

* upstream/master:
  Updated CHANGES file
  FIX fix split_filename behaviour when path has no filename
  TST correct fail case in test_filemanip:test_split_filename
  TST: add fail case in test_filemanip:test_split_filename
  Updated CHANGES file
  Updated test for FSL DTIFit
  Added option to correct for gradient non linearities in dtifit
  CHANGES file updated to include Camino tracking updates
  Test overlap not included before
  Update to Camino tracking interfaces
  Fix conflicts
  delete line instead comment out
  update CHANGES
  make specs
  fix KeyError when using redirect_x in CommandLineInterface

Author: satra

CHANGES

@@ -1,5 +1,12 @@
 Next release
 ============
+
+* FIX: Fix split_filename behaviour when path has no file component (https://github.com/nipy/nipype/pull/1035)
+* ENH: Updated FSL dtifit to include option for grad non-linearities (https://github.com/nipy/nipype/pull/1032)
+* 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)
 * ENH: Updated N4BiasCorrection input spec to include weight image and spline order. Made 

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/base.py

@@ -758,12 +758,12 @@ def _get_trait_desc(self, inputs, name, spec):
         manhelpstr = ['\t%s' % name]
 
         type_info = spec.full_info(inputs, name, None)
-        default = ''
 
+        default = ''
         if spec.usedefault:
             default = ', nipype default value: %s' % str(spec.default_value()[1])
-
         line = "(%s%s)" % (type_info, default)
+
         manhelpstr = wrap(line, 70,
                           initial_indent=manhelpstr[0]+': ',
                           subsequent_indent='\t\t ')
@@ -991,7 +991,7 @@ def run(self, **inputs):
                     time.sleep(0.2)  # give Xvfb time to start
                     if xvfb_proc.poll() is not None:
                         raise Exception('Error: Xvfb did not start')
-                    old_displaynum = os.environ['DISPLAY']
+
                     runtime.environ['DISPLAY'] = ':%s' % vdisplay_num
 
             runtime = self._run_interface(runtime)

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/dti.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_Track.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_TrackBallStick.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_TrackBayesDirac.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
+