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Merge pull request #1029 from mick-d/camino
Camino tracking interfaces update
2 parents 0d3bbdc + 115534e commit 226ff40

12 files changed

+514
-40
lines changed

‎CHANGES

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11
Next release
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============
33

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* ENH: Updated Camino tracking interfaces, which can now use FSL bedpostx output.
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New options also include choice of tracker, interpolator, stepsize and
6+
curveinterval for angle threshold (https://github.com/nipy/nipype/pull/1029)
47
* FIX: Interfaces redirecting X crashed if $DISPLAY not defined (https://github.com/nipy/nipype/pull/1027)
58
* FIX: Bug crashed 'make api' (https://github.com/nipy/nipype/pull/1026)
69
* ENH: Updated antsIntroduction to handle RA and RI registrations (https://github.com/nipy/nipype/pull/1009)

‎nipype/algorithms/tests/test_auto_Overlap.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from nipype.testing import assert_equal
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from nipype.algorithms.misc import Overlap
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def test_Overlap_inputs():
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input_map = dict(bg_overlap=dict(mandatory=True,
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usedefault=True,
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),
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ignore_exception=dict(nohash=True,
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usedefault=True,
11+
),
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mask_volume=dict(),
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out_file=dict(usedefault=True,
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),
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vol_units=dict(mandatory=True,
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usedefault=True,
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),
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volume1=dict(mandatory=True,
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),
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volume2=dict(mandatory=True,
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),
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weighting=dict(usedefault=True,
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),
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)
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inputs = Overlap.input_spec()
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for key, metadata in input_map.items():
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for metakey, value in metadata.items():
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yield assert_equal, getattr(inputs.traits()[key], metakey), value
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def test_Overlap_outputs():
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output_map = dict(dice=dict(),
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diff_file=dict(),
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jaccard=dict(),
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labels=dict(),
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roi_di=dict(),
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roi_ji=dict(),
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roi_voldiff=dict(),
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volume_difference=dict(),
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)
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outputs = Overlap.output_spec()
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for key, metadata in output_map.items():
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for metakey, value in metadata.items():
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yield assert_equal, getattr(outputs.traits()[key], metakey), value
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‎nipype/interfaces/camino/__init__.py

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

‎nipype/interfaces/camino/dti.py

Lines changed: 213 additions & 34 deletions
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‎nipype/interfaces/camino/tests/test_auto_Track.py

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

‎nipype/interfaces/camino/tests/test_auto_TrackBallStick.py

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

‎nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py

Lines changed: 11 additions & 1 deletion
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@@ -9,6 +9,9 @@ def test_TrackBayesDirac_inputs():
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),
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args=dict(argstr='%s',
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),
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curveinterval=dict(argstr='-curveinterval %f',
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requires=['curvethresh'],
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),
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curvepriorg=dict(argstr='-curvepriorg %G',
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),
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curvepriork=dict(argstr='-curvepriork %G',
@@ -33,14 +36,15 @@ def test_TrackBayesDirac_inputs():
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usedefault=True,
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),
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in_file=dict(argstr='-inputfile %s',
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mandatory=True,
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position=1,
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),
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inputdatatype=dict(argstr='-inputdatatype %s',
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),
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inputmodel=dict(argstr='-inputmodel %s',
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usedefault=True,
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),
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interpolator=dict(argstr='-interpolator %s',
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),
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ipthresh=dict(argstr='-ipthresh %f',
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),
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iterations=dict(argstr='-iterations %d',
@@ -71,9 +75,15 @@ def test_TrackBayesDirac_inputs():
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seed_file=dict(argstr='-seedfile %s',
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position=2,
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),
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stepsize=dict(argstr='-stepsize %f',
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requires=['tracker'],
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),
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terminal_output=dict(mandatory=True,
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nohash=True,
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),
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tracker=dict(argstr='-tracker %s',
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usedefault=True,
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),
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voxel_dims=dict(argstr='-voxeldims %s',
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units='mm',
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),

‎nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from nipype.testing import assert_equal
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from nipype.interfaces.camino.dti import TrackBedpostxDeter
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def test_TrackBedpostxDeter_inputs():
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input_map = dict(anisfile=dict(argstr='-anisfile %s',
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),
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anisthresh=dict(argstr='-anisthresh %f',
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),
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args=dict(argstr='%s',
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),
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bedpostxdir=dict(argstr='-bedpostxdir %s',
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mandatory=True,
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),
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curveinterval=dict(argstr='-curveinterval %f',
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requires=['curvethresh'],
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),
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curvethresh=dict(argstr='-curvethresh %f',
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),
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data_dims=dict(argstr='-datadims %s',
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units='voxels',
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),
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environ=dict(nohash=True,
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usedefault=True,
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),
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gzip=dict(argstr='-gzip',
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),
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ignore_exception=dict(nohash=True,
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usedefault=True,
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),
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in_file=dict(argstr='-inputfile %s',
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position=1,
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),
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inputdatatype=dict(argstr='-inputdatatype %s',
35+
),
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inputmodel=dict(argstr='-inputmodel %s',
37+
usedefault=True,
38+
),
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interpolator=dict(argstr='-interpolator %s',
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),
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ipthresh=dict(argstr='-ipthresh %f',
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),
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maxcomponents=dict(argstr='-maxcomponents %d',
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units='NA',
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),
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min_vol_frac=dict(argstr='-bedpostxminf %d',
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units='NA',
48+
),
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numpds=dict(argstr='-numpds %d',
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units='NA',
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),
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out_file=dict(argstr='-outputfile %s',
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genfile=True,
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position=-1,
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),
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output_root=dict(argstr='-outputroot %s',
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position=-1,
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),
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outputtracts=dict(argstr='-outputtracts %s',
60+
),
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seed_file=dict(argstr='-seedfile %s',
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position=2,
63+
),
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stepsize=dict(argstr='-stepsize %f',
65+
requires=['tracker'],
66+
),
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terminal_output=dict(mandatory=True,
68+
nohash=True,
69+
),
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tracker=dict(argstr='-tracker %s',
71+
usedefault=True,
72+
),
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voxel_dims=dict(argstr='-voxeldims %s',
74+
units='mm',
75+
),
76+
)
77+
inputs = TrackBedpostxDeter.input_spec()
78+
79+
for key, metadata in input_map.items():
80+
for metakey, value in metadata.items():
81+
yield assert_equal, getattr(inputs.traits()[key], metakey), value
82+
83+
def test_TrackBedpostxDeter_outputs():
84+
output_map = dict(tracked=dict(),
85+
)
86+
outputs = TrackBedpostxDeter.output_spec()
87+
88+
for key, metadata in output_map.items():
89+
for metakey, value in metadata.items():
90+
yield assert_equal, getattr(outputs.traits()[key], metakey), value
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‎nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from nipype.testing import assert_equal
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from nipype.interfaces.camino.dti import TrackBedpostxProba
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5+
def test_TrackBedpostxProba_inputs():
6+
input_map = dict(anisfile=dict(argstr='-anisfile %s',
7+
),
8+
anisthresh=dict(argstr='-anisthresh %f',
9+
),
10+
args=dict(argstr='%s',
11+
),
12+
bedpostxdir=dict(argstr='-bedpostxdir %s',
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mandatory=True,
14+
),
15+
curveinterval=dict(argstr='-curveinterval %f',
16+
requires=['curvethresh'],
17+
),
18+
curvethresh=dict(argstr='-curvethresh %f',
19+
),
20+
data_dims=dict(argstr='-datadims %s',
21+
units='voxels',
22+
),
23+
environ=dict(nohash=True,
24+
usedefault=True,
25+
),
26+
gzip=dict(argstr='-gzip',
27+
),
28+
ignore_exception=dict(nohash=True,
29+
usedefault=True,
30+
),
31+
in_file=dict(argstr='-inputfile %s',
32+
position=1,
33+
),
34+
inputdatatype=dict(argstr='-inputdatatype %s',
35+
),
36+
inputmodel=dict(argstr='-inputmodel %s',
37+
usedefault=True,
38+
),
39+
interpolator=dict(argstr='-interpolator %s',
40+
),
41+
ipthresh=dict(argstr='-ipthresh %f',
42+
),
43+
iterations=dict(argstr='-iterations %d',
44+
units='NA',
45+
),
46+
maxcomponents=dict(argstr='-maxcomponents %d',
47+
units='NA',
48+
),
49+
min_vol_frac=dict(argstr='-bedpostxminf %d',
50+
units='NA',
51+
),
52+
numpds=dict(argstr='-numpds %d',
53+
units='NA',
54+
),
55+
out_file=dict(argstr='-outputfile %s',
56+
genfile=True,
57+
position=-1,
58+
),
59+
output_root=dict(argstr='-outputroot %s',
60+
position=-1,
61+
),
62+
outputtracts=dict(argstr='-outputtracts %s',
63+
),
64+
seed_file=dict(argstr='-seedfile %s',
65+
position=2,
66+
),
67+
stepsize=dict(argstr='-stepsize %f',
68+
requires=['tracker'],
69+
),
70+
terminal_output=dict(mandatory=True,
71+
nohash=True,
72+
),
73+
tracker=dict(argstr='-tracker %s',
74+
usedefault=True,
75+
),
76+
voxel_dims=dict(argstr='-voxeldims %s',
77+
units='mm',
78+
),
79+
)
80+
inputs = TrackBedpostxProba.input_spec()
81+
82+
for key, metadata in input_map.items():
83+
for metakey, value in metadata.items():
84+
yield assert_equal, getattr(inputs.traits()[key], metakey), value
85+
86+
def test_TrackBedpostxProba_outputs():
87+
output_map = dict(tracked=dict(),
88+
)
89+
outputs = TrackBedpostxProba.output_spec()
90+
91+
for key, metadata in output_map.items():
92+
for metakey, value in metadata.items():
93+
yield assert_equal, getattr(outputs.traits()[key], metakey), value
94+

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