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satrasatra
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Merge pull request #1305 from jason-wg/patch-1
Create brainsuite.py
2 parents fc4bc55 + 98fdb3d commit 355591b

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lines changed

‎CHANGES

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Next release
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============
3-
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* ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
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* FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)
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* FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)
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* FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)

‎nipype/interfaces/brainsuite/__init__.py

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from .brainsuite import (Bse, Bfc, Pvc, Cerebro, Cortex, Scrubmask, Tca,
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Dewisp, Dfs, Pialmesh, Skullfinder, Hemisplit)

‎nipype/interfaces/brainsuite/brainsuite.py

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‎nipype/interfaces/brainsuite/tests/__init__.py

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‎nipype/interfaces/brainsuite/tests/test_auto_Bfc.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 Bfc
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def test_Bfc_inputs():
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input_map = dict(args=dict(argstr='%s',
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),
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biasEstimateConvergenceThreshold=dict(argstr='--beps %f',
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),
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biasEstimateSpacing=dict(argstr='-s %d',
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),
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biasFieldEstimatesOutputPrefix=dict(argstr='--biasprefix %s',
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),
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biasRange=dict(argstr='%s',
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),
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controlPointSpacing=dict(argstr='-c %d',
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),
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convergenceThreshold=dict(argstr='--eps %f',
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),
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correctWholeVolume=dict(argstr='--extrapolate',
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),
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correctedImagesOutputPrefix=dict(argstr='--prefix %s',
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),
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correctionScheduleFile=dict(argstr='--schedule %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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histogramRadius=dict(argstr='-r %d',
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),
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histogramType=dict(argstr='%s',
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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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inputMRIFile=dict(argstr='-i %s',
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mandatory=True,
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),
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inputMaskFile=dict(argstr='-m %s',
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hash_files=False,
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),
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intermediate_file_type=dict(argstr='%s',
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),
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iterativeMode=dict(argstr='--iterate',
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),
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maxBias=dict(argstr='-U %f',
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usedefault=True,
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),
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minBias=dict(argstr='-L %f',
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usedefault=True,
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),
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outputBiasField=dict(argstr='--bias %s',
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hash_files=False,
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),
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outputMRIVolume=dict(argstr='-o %s',
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genfile=True,
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hash_files=False,
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),
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outputMaskedBiasField=dict(argstr='--maskedbias %s',
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hash_files=False,
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),
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splineLambda=dict(argstr='-w %f',
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),
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terminal_output=dict(nohash=True,
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),
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timer=dict(argstr='--timer',
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),
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verbosityLevel=dict(argstr='-v %d',
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),
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)
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inputs = Bfc.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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def test_Bfc_outputs():
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output_map = dict(correctionScheduleFile=dict(),
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outputBiasField=dict(),
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outputMRIVolume=dict(),
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outputMaskedBiasField=dict(),
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)
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outputs = Bfc.output_spec()
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for key, metadata in list(output_map.items()):
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for metakey, value in list(metadata.items()):
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yield assert_equal, getattr(outputs.traits()[key], metakey), value

‎nipype/interfaces/brainsuite/tests/test_auto_Bse.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 Bse
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def test_Bse_inputs():
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input_map = dict(args=dict(argstr='%s',
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),
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diffusionConstant=dict(argstr='-d %f',
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usedefault=True,
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),
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diffusionIterations=dict(argstr='-n %d',
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usedefault=True,
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),
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dilateFinalMask=dict(argstr='-p',
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usedefault=True,
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),
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edgeDetectionConstant=dict(argstr='-s %f',
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usedefault=True,
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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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inputMRIFile=dict(argstr='-i %s',
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mandatory=True,
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),
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noRotate=dict(argstr='--norotate',
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),
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outputCortexFile=dict(argstr='--cortex %s',
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hash_files=False,
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),
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outputDetailedBrainMask=dict(argstr='--hires %s',
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hash_files=False,
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),
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outputDiffusionFilter=dict(argstr='--adf %s',
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hash_files=False,
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),
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outputEdgeMap=dict(argstr='--edge %s',
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hash_files=False,
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),
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outputMRIVolume=dict(argstr='-o %s',
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genfile=True,
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hash_files=False,
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),
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outputMaskFile=dict(argstr='--mask %s',
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hash_files=False,
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),
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radius=dict(argstr='-r %f',
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usedefault=True,
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),
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terminal_output=dict(nohash=True,
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),
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timer=dict(argstr='--timer',
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),
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trim=dict(argstr='--trim',
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usedefault=True,
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),
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verbosityLevel=dict(argstr='-v %f',
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usedefault=True,
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),
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)
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inputs = Bse.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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def test_Bse_outputs():
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output_map = dict(outputCortexFile=dict(),
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outputDetailedBrainMask=dict(),
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outputDiffusionFilter=dict(),
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outputEdgeMap=dict(),
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outputMRIVolume=dict(),
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outputMaskFile=dict(),
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)
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outputs = Bse.output_spec()
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for key, metadata in list(output_map.items()):
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for metakey, value in list(metadata.items()):
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yield assert_equal, getattr(outputs.traits()[key], metakey), value

‎nipype/interfaces/brainsuite/tests/test_auto_Cerebro.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 Cerebro
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def test_Cerebro_inputs():
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input_map = dict(args=dict(argstr='%s',
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),
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costFunction=dict(argstr='-c %d',
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usedefault=True,
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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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inputAtlasLabelFile=dict(argstr='--atlaslabels %s',
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mandatory=True,
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),
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inputAtlasMRIFile=dict(argstr='--atlas %s',
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mandatory=True,
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),
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inputBrainMaskFile=dict(argstr='-m %s',
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),
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inputMRIFile=dict(argstr='-i %s',
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mandatory=True,
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),
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keepTempFiles=dict(argstr='--keep',
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),
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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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),
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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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genfile=True,
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),
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outputWarpTransformFile=dict(argstr='--warp %s',
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),
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tempDirectory=dict(argstr='--tempdir %s',
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),
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tempDirectoryBase=dict(argstr='--tempdirbase %s',
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),
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terminal_output=dict(nohash=True,
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),
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useCentroids=dict(argstr='--centroids',
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),
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verbosity=dict(argstr='-v %d',
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),
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warpConvergence=dict(argstr='--warpconv %f',
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),
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warpLabel=dict(argstr='--warplevel %d',
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),
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)
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inputs = Cerebro.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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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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outputWarpTransformFile=dict(),
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)
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outputs = Cerebro.output_spec()
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for key, metadata in list(output_map.items()):
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for metakey, value in list(metadata.items()):
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yield assert_equal, getattr(outputs.traits()[key], metakey), value

‎nipype/interfaces/brainsuite/tests/test_auto_Cortex.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 Cortex
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def test_Cortex_inputs():
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input_map = dict(args=dict(argstr='%s',
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),
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computeGCBoundary=dict(argstr='-g',
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),
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computeWGBoundary=dict(argstr='-w',
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usedefault=True,
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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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includeAllSubcorticalAreas=dict(argstr='-a',
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usedefault=True,
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),
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inputHemisphereLabelFile=dict(argstr='-h %s',
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mandatory=True,
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),
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inputTissueFractionFile=dict(argstr='-f %s',
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mandatory=True,
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),
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outputCerebrumMask=dict(argstr='-o %s',
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genfile=True,
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),
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terminal_output=dict(nohash=True,
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),
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timer=dict(argstr='--timer',
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),
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tissueFractionThreshold=dict(argstr='-p %f',
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usedefault=True,
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),
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verbosity=dict(argstr='-v %d',
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),
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)
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inputs = Cortex.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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def test_Cortex_outputs():
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output_map = dict(outputCerebrumMask=dict(),
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)
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outputs = Cortex.output_spec()
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for key, metadata in list(output_map.items()):
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for metakey, value in list(metadata.items()):
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yield assert_equal, getattr(outputs.traits()[key], metakey), value

‎nipype/interfaces/brainsuite/tests/test_auto_Dewisp.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 Dewisp
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def test_Dewisp_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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inputMaskFile=dict(argstr='-i %s',
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mandatory=True,
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),
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maximumIterations=dict(argstr='-n %d',
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),
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outputMaskFile=dict(argstr='-o %s',
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genfile=True,
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),
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sizeThreshold=dict(argstr='-t %d',
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),
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terminal_output=dict(nohash=True,
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),
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timer=dict(argstr='--timer',
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),
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verbosity=dict(argstr='-v %d',
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),
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)
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inputs = Dewisp.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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def test_Dewisp_outputs():
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output_map = dict(outputMaskFile=dict(),
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)
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outputs = Dewisp.output_spec()
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for key, metadata in list(output_map.items()):
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for metakey, value in list(metadata.items()):
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yield assert_equal, getattr(outputs.traits()[key], metakey), value

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