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satrasatra
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Merge pull request #1554 from jason-wg/master
ENH: BrainSuite updates: Add interfaces for additional command line tools
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‎nipype/interfaces/brainsuite/__init__.py

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@@ -1,3 +1,4 @@
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# -*- coding: utf-8 -*-
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from .brainsuite import (Bse, Bfc, Pvc, Cerebro, Cortex, Scrubmask, Tca,
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Dewisp, Dfs, Pialmesh, Skullfinder, Hemisplit)
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Dewisp, Dfs, Pialmesh, Skullfinder, Hemisplit,
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SVReg, BDP, ThicknessPVC)

‎nipype/interfaces/brainsuite/brainsuite.py

Lines changed: 918 additions & 178 deletions
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‎nipype/interfaces/brainsuite/tests/test_auto_BDP.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from ....testing import assert_equal
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from ..brainsuite import BDP
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def test_BDP_inputs():
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input_map = dict(BVecBValPair=dict(argstr='--bvec %s --bval %s',
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mandatory=True,
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position=-1,
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xor=[u'bMatrixFile'],
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),
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args=dict(argstr='%s',
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),
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bMatrixFile=dict(argstr='--bmat %s',
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mandatory=True,
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position=-1,
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xor=[u'BVecBValPair'],
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),
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bValRatioThreshold=dict(argstr='--bval-ratio-threshold %f',
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),
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bfcFile=dict(argstr='%s',
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mandatory=True,
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position=0,
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xor=[u'noStructuralRegistration'],
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),
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customDiffusionLabel=dict(argstr='--custom-diffusion-label %s',
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),
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customLabelXML=dict(argstr='--custom-label-xml %s',
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),
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customT1Label=dict(argstr='--custom-t1-label %s',
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),
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dataSinkDelay=dict(argstr='%s',
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),
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dcorrRegMeasure=dict(argstr='--dcorr-reg-method %s',
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),
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dcorrWeight=dict(argstr='--dcorr-regularization-wt %f',
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),
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dwiMask=dict(argstr='--dwi-mask %s',
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),
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echoSpacing=dict(argstr='--echo-spacing=%f',
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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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estimateODF_3DShore=dict(argstr='--3dshore --diffusion_time_ms %f',
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),
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estimateODF_FRACT=dict(argstr='--FRACT',
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),
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estimateODF_FRT=dict(argstr='--FRT',
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),
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estimateTensors=dict(argstr='--tensors',
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),
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fieldmapCorrection=dict(argstr='--fieldmap-correction %s',
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requires=[u'echoSpacing'],
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),
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fieldmapCorrectionMethod=dict(argstr='--fieldmap-correction-method %s',
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xor=[u'skipIntensityCorr'],
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),
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fieldmapSmooth=dict(argstr='--fieldmap-smooth3=%f',
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),
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flagConfigFile=dict(argstr='--flag-conf-file %s',
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),
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forcePartialROIStats=dict(argstr='--force-partial-roi-stats',
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),
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generateStats=dict(argstr='--generate-stats',
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),
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ignoreFieldmapFOV=dict(argstr='--ignore-fieldmap-fov',
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),
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ignoreMemory=dict(argstr='--ignore-memory',
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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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inputDiffusionData=dict(argstr='--nii %s',
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mandatory=True,
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position=-2,
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),
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lowMemory=dict(argstr='--low-memory',
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),
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noStructuralRegistration=dict(argstr='--no-structural-registration',
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mandatory=True,
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position=0,
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xor=[u'bfcFile'],
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),
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odfLambta=dict(argstr='--odf-lambda <L>',
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),
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onlyStats=dict(argstr='--generate-only-stats',
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),
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outPrefix=dict(argstr='--output-fileprefix %s',
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),
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outputDiffusionCoordinates=dict(argstr='--output-diffusion-coordinate',
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),
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outputSubdir=dict(argstr='--output-subdir %s',
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),
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phaseEncodingDirection=dict(argstr='--dir=%s',
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),
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rigidRegMeasure=dict(argstr='--rigid-reg-measure %s',
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),
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skipDistortionCorr=dict(argstr='--no-distortion-correction',
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),
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skipIntensityCorr=dict(argstr='--no-intensity-correction',
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xor=[u'fieldmapCorrectionMethod'],
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),
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skipNonuniformityCorr=dict(argstr='--no-nonuniformity-correction',
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),
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t1Mask=dict(argstr='--t1-mask %s',
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),
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terminal_output=dict(nohash=True,
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),
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threads=dict(argstr='--threads=%d',
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),
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transformDataOnly=dict(argstr='--transform-data-only',
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),
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transformDiffusionSurface=dict(argstr='--transform-diffusion-surface %s',
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),
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transformDiffusionVolume=dict(argstr='--transform-diffusion-volume %s',
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),
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transformInterpolation=dict(argstr='--transform-interpolation %s',
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),
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transformT1Surface=dict(argstr='--transform-t1-surface %s',
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),
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transformT1Volume=dict(argstr='--transform-t1-volume %s',
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),
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)
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inputs = BDP.input_spec()
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for key, metadata in list(input_map.items()):
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for metakey, value in list(metadata.items()):
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yield assert_equal, getattr(inputs.traits()[key], metakey), value
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‎nipype/interfaces/brainsuite/tests/test_auto_Bse.py

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Original file line numberDiff line numberDiff line change
@@ -46,6 +46,7 @@ def test_Bse_inputs():
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hash_files=False,
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),
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outputMaskFile=dict(argstr='--mask %s',
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genfile=True,
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hash_files=False,
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),
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radius=dict(argstr='-r %f',

‎nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -31,14 +31,16 @@ def test_Cerebro_inputs():
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linearConvergence=dict(argstr='--linconv %f',
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),
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outputAffineTransformFile=dict(argstr='--air %s',
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genfile=True,
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),
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outputCerebrumMaskFile=dict(argstr='-o %s',
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genfile=True,
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),
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outputLabelMaskFile=dict(argstr='-l %s',
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outputLabelVolumeFile=dict(argstr='-l %s',
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genfile=True,
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),
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outputWarpTransformFile=dict(argstr='--warp %s',
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genfile=True,
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),
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tempDirectory=dict(argstr='--tempdir %s',
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),
@@ -65,7 +67,7 @@ def test_Cerebro_inputs():
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def test_Cerebro_outputs():
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output_map = dict(outputAffineTransformFile=dict(),
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outputCerebrumMaskFile=dict(),
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outputLabelMaskFile=dict(),
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outputLabelVolumeFile=dict(),
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outputWarpTransformFile=dict(),
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)
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outputs = Cerebro.output_spec()

‎nipype/interfaces/brainsuite/tests/test_auto_SVReg.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from ....testing import assert_equal
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from ..brainsuite import SVReg
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def test_SVReg_inputs():
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input_map = dict(args=dict(argstr='%s',
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),
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atlasFilePrefix=dict(argstr="'%s'",
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position=1,
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),
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curveMatchingInstructions=dict(argstr="'-cur %s'",
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),
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dataSinkDelay=dict(argstr='%s',
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),
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displayModuleName=dict(argstr="'-m'",
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),
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displayTimestamps=dict(argstr="'-t'",
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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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ignore_exception=dict(nohash=True,
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usedefault=True,
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),
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iterations=dict(argstr="'-H %d'",
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),
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keepIntermediates=dict(argstr="'-k'",
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),
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pialSurfaceMaskDilation=dict(argstr="'-D %d'",
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),
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refineOutputs=dict(argstr="'-r'",
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),
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shortMessages=dict(argstr="'-gui'",
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),
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skipToIntensityReg=dict(argstr="'-p'",
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),
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skipToVolumeReg=dict(argstr="'-s'",
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),
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skipVolumetricProcessing=dict(argstr="'-S'",
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),
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subjectFilePrefix=dict(argstr="'%s'",
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mandatory=True,
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position=0,
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),
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terminal_output=dict(nohash=True,
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),
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useCerebrumMask=dict(argstr="'-C'",
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),
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useManualMaskFile=dict(argstr="'-cbm'",
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),
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useMultiThreading=dict(argstr="'-P'",
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),
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useSingleThreading=dict(argstr="'-U'",
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),
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verbosity0=dict(argstr="'-v0'",
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xor=(u'verbosity0', u'verbosity1', u'verbosity2'),
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),
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verbosity1=dict(argstr="'-v1'",
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xor=(u'verbosity0', u'verbosity1', u'verbosity2'),
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),
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verbosity2=dict(argstr="'v2'",
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xor=(u'verbosity0', u'verbosity1', u'verbosity2'),
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),
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)
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inputs = SVReg.input_spec()
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for key, metadata in list(input_map.items()):
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for metakey, value in list(metadata.items()):
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yield assert_equal, getattr(inputs.traits()[key], metakey), value
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‎nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from ....testing import assert_equal
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from ..brainsuite import ThicknessPVC
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def test_ThicknessPVC_inputs():
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input_map = dict(args=dict(argstr='%s',
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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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ignore_exception=dict(nohash=True,
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usedefault=True,
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),
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subjectFilePrefix=dict(argstr='%s',
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mandatory=True,
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),
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terminal_output=dict(nohash=True,
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),
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)
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inputs = ThicknessPVC.input_spec()
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for key, metadata in list(input_map.items()):
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for metakey, value in list(metadata.items()):
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yield assert_equal, getattr(inputs.traits()[key], metakey), value
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