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ENH: BrainSuite updates: Add interfaces for additional command line tools #1554

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3 changes: 2 additions & 1 deletion nipype/interfaces/brainsuite/__init__.py
@@ -1,3 +1,4 @@
# -*- coding: utf-8 -*-
from .brainsuite import (Bse, Bfc, Pvc, Cerebro, Cortex, Scrubmask, Tca,
Dewisp, Dfs, Pialmesh, Skullfinder, Hemisplit)
Dewisp, Dfs, Pialmesh, Skullfinder, Hemisplit,
SVReg, BDP, ThicknessPVC)
1,096 changes: 918 additions & 178 deletions nipype/interfaces/brainsuite/brainsuite.py

Large diffs are not rendered by default.

130 changes: 130 additions & 0 deletions nipype/interfaces/brainsuite/tests/test_auto_BDP.py
@@ -0,0 +1,130 @@
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
from ....testing import assert_equal
from ..brainsuite import BDP


def test_BDP_inputs():
input_map = dict(BVecBValPair=dict(argstr='--bvec %s --bval %s',
mandatory=True,
position=-1,
xor=[u'bMatrixFile'],
),
args=dict(argstr='%s',
),
bMatrixFile=dict(argstr='--bmat %s',
mandatory=True,
position=-1,
xor=[u'BVecBValPair'],
),
bValRatioThreshold=dict(argstr='--bval-ratio-threshold %f',
),
bfcFile=dict(argstr='%s',
mandatory=True,
position=0,
xor=[u'noStructuralRegistration'],
),
customDiffusionLabel=dict(argstr='--custom-diffusion-label %s',
),
customLabelXML=dict(argstr='--custom-label-xml %s',
),
customT1Label=dict(argstr='--custom-t1-label %s',
),
dataSinkDelay=dict(argstr='%s',
),
dcorrRegMeasure=dict(argstr='--dcorr-reg-method %s',
),
dcorrWeight=dict(argstr='--dcorr-regularization-wt %f',
),
dwiMask=dict(argstr='--dwi-mask %s',
),
echoSpacing=dict(argstr='--echo-spacing=%f',
),
environ=dict(nohash=True,
usedefault=True,
),
estimateODF_3DShore=dict(argstr='--3dshore --diffusion_time_ms %f',
),
estimateODF_FRACT=dict(argstr='--FRACT',
),
estimateODF_FRT=dict(argstr='--FRT',
),
estimateTensors=dict(argstr='--tensors',
),
fieldmapCorrection=dict(argstr='--fieldmap-correction %s',
requires=[u'echoSpacing'],
),
fieldmapCorrectionMethod=dict(argstr='--fieldmap-correction-method %s',
xor=[u'skipIntensityCorr'],
),
fieldmapSmooth=dict(argstr='--fieldmap-smooth3=%f',
),
flagConfigFile=dict(argstr='--flag-conf-file %s',
),
forcePartialROIStats=dict(argstr='--force-partial-roi-stats',
),
generateStats=dict(argstr='--generate-stats',
),
ignoreFieldmapFOV=dict(argstr='--ignore-fieldmap-fov',
),
ignoreMemory=dict(argstr='--ignore-memory',
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
inputDiffusionData=dict(argstr='--nii %s',
mandatory=True,
position=-2,
),
lowMemory=dict(argstr='--low-memory',
),
noStructuralRegistration=dict(argstr='--no-structural-registration',
mandatory=True,
position=0,
xor=[u'bfcFile'],
),
odfLambta=dict(argstr='--odf-lambda <L>',
),
onlyStats=dict(argstr='--generate-only-stats',
),
outPrefix=dict(argstr='--output-fileprefix %s',
),
outputDiffusionCoordinates=dict(argstr='--output-diffusion-coordinate',
),
outputSubdir=dict(argstr='--output-subdir %s',
),
phaseEncodingDirection=dict(argstr='--dir=%s',
),
rigidRegMeasure=dict(argstr='--rigid-reg-measure %s',
),
skipDistortionCorr=dict(argstr='--no-distortion-correction',
),
skipIntensityCorr=dict(argstr='--no-intensity-correction',
xor=[u'fieldmapCorrectionMethod'],
),
skipNonuniformityCorr=dict(argstr='--no-nonuniformity-correction',
),
t1Mask=dict(argstr='--t1-mask %s',
),
terminal_output=dict(nohash=True,
),
threads=dict(argstr='--threads=%d',
),
transformDataOnly=dict(argstr='--transform-data-only',
),
transformDiffusionSurface=dict(argstr='--transform-diffusion-surface %s',
),
transformDiffusionVolume=dict(argstr='--transform-diffusion-volume %s',
),
transformInterpolation=dict(argstr='--transform-interpolation %s',
),
transformT1Surface=dict(argstr='--transform-t1-surface %s',
),
transformT1Volume=dict(argstr='--transform-t1-volume %s',
),
)
inputs = BDP.input_spec()

for key, metadata in list(input_map.items()):
for metakey, value in list(metadata.items()):
yield assert_equal, getattr(inputs.traits()[key], metakey), value

1 change: 1 addition & 0 deletions nipype/interfaces/brainsuite/tests/test_auto_Bse.py
Expand Up @@ -46,6 +46,7 @@ def test_Bse_inputs():
hash_files=False,
),
outputMaskFile=dict(argstr='--mask %s',
genfile=True,
hash_files=False,
),
radius=dict(argstr='-r %f',
Expand Down
6 changes: 4 additions & 2 deletions nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py
Expand Up @@ -31,14 +31,16 @@ def test_Cerebro_inputs():
linearConvergence=dict(argstr='--linconv %f',
),
outputAffineTransformFile=dict(argstr='--air %s',
genfile=True,
),
outputCerebrumMaskFile=dict(argstr='-o %s',
genfile=True,
),
outputLabelMaskFile=dict(argstr='-l %s',
outputLabelVolumeFile=dict(argstr='-l %s',
genfile=True,
),
outputWarpTransformFile=dict(argstr='--warp %s',
genfile=True,
),
tempDirectory=dict(argstr='--tempdir %s',
),
Expand All @@ -65,7 +67,7 @@ def test_Cerebro_inputs():
def test_Cerebro_outputs():
output_map = dict(outputAffineTransformFile=dict(),
outputCerebrumMaskFile=dict(),
outputLabelMaskFile=dict(),
outputLabelVolumeFile=dict(),
outputWarpTransformFile=dict(),
)
outputs = Cerebro.output_spec()
Expand Down
71 changes: 71 additions & 0 deletions nipype/interfaces/brainsuite/tests/test_auto_SVReg.py
@@ -0,0 +1,71 @@
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
from ....testing import assert_equal
from ..brainsuite import SVReg


def test_SVReg_inputs():
input_map = dict(args=dict(argstr='%s',
),
atlasFilePrefix=dict(argstr="'%s'",
position=1,
),
curveMatchingInstructions=dict(argstr="'-cur %s'",
),
dataSinkDelay=dict(argstr='%s',
),
displayModuleName=dict(argstr="'-m'",
),
displayTimestamps=dict(argstr="'-t'",
),
environ=dict(nohash=True,
usedefault=True,
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
iterations=dict(argstr="'-H %d'",
),
keepIntermediates=dict(argstr="'-k'",
),
pialSurfaceMaskDilation=dict(argstr="'-D %d'",
),
refineOutputs=dict(argstr="'-r'",
),
shortMessages=dict(argstr="'-gui'",
),
skipToIntensityReg=dict(argstr="'-p'",
),
skipToVolumeReg=dict(argstr="'-s'",
),
skipVolumetricProcessing=dict(argstr="'-S'",
),
subjectFilePrefix=dict(argstr="'%s'",
mandatory=True,
position=0,
),
terminal_output=dict(nohash=True,
),
useCerebrumMask=dict(argstr="'-C'",
),
useManualMaskFile=dict(argstr="'-cbm'",
),
useMultiThreading=dict(argstr="'-P'",
),
useSingleThreading=dict(argstr="'-U'",
),
verbosity0=dict(argstr="'-v0'",
xor=(u'verbosity0', u'verbosity1', u'verbosity2'),
),
verbosity1=dict(argstr="'-v1'",
xor=(u'verbosity0', u'verbosity1', u'verbosity2'),
),
verbosity2=dict(argstr="'v2'",
xor=(u'verbosity0', u'verbosity1', u'verbosity2'),
),
)
inputs = SVReg.input_spec()

for key, metadata in list(input_map.items()):
for metakey, value in list(metadata.items()):
yield assert_equal, getattr(inputs.traits()[key], metakey), value

26 changes: 26 additions & 0 deletions nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py
@@ -0,0 +1,26 @@
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
from ....testing import assert_equal
from ..brainsuite import ThicknessPVC


def test_ThicknessPVC_inputs():
input_map = dict(args=dict(argstr='%s',
),
environ=dict(nohash=True,
usedefault=True,
),
ignore_exception=dict(nohash=True,
usedefault=True,
),
subjectFilePrefix=dict(argstr='%s',
mandatory=True,
),
terminal_output=dict(nohash=True,
),
)
inputs = ThicknessPVC.input_spec()

for key, metadata in list(input_map.items()):
for metakey, value in list(metadata.items()):
yield assert_equal, getattr(inputs.traits()[key], metakey), value