Create brainsuite.py

CHANGES

@@ -1,6 +1,6 @@
 Next release
 ============
-
+* ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
 * FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)
 * FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)
 * FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)

nipype/interfaces/brainsuite/__init__.py

@@ -0,0 +1,2 @@
+from .brainsuite import (Bse, Bfc, Pvc, Cerebro, Cortex, Scrubmask, Tca,
+                         Dewisp, Dfs, Pialmesh, Skullfinder, Hemisplit)

nipype/interfaces/brainsuite/tests/test_auto_Bfc.py

@@ -0,0 +1,89 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ....testing import assert_equal
+from ..brainsuite import Bfc
+
+
+def test_Bfc_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    biasEstimateConvergenceThreshold=dict(argstr='--beps %f',
+    ),
+    biasEstimateSpacing=dict(argstr='-s %d',
+    ),
+    biasFieldEstimatesOutputPrefix=dict(argstr='--biasprefix %s',
+    ),
+    biasRange=dict(argstr='%s',
+    ),
+    controlPointSpacing=dict(argstr='-c %d',
+    ),
+    convergenceThreshold=dict(argstr='--eps %f',
+    ),
+    correctWholeVolume=dict(argstr='--extrapolate',
+    ),
+    correctedImagesOutputPrefix=dict(argstr='--prefix %s',
+    ),
+    correctionScheduleFile=dict(argstr='--schedule %s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    histogramRadius=dict(argstr='-r %d',
+    ),
+    histogramType=dict(argstr='%s',
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    inputMRIFile=dict(argstr='-i %s',
+    mandatory=True,
+    ),
+    inputMaskFile=dict(argstr='-m %s',
+    hash_files=False,
+    ),
+    intermediate_file_type=dict(argstr='%s',
+    ),
+    iterativeMode=dict(argstr='--iterate',
+    ),
+    maxBias=dict(argstr='-U %f',
+    usedefault=True,
+    ),
+    minBias=dict(argstr='-L %f',
+    usedefault=True,
+    ),
+    outputBiasField=dict(argstr='--bias %s',
+    hash_files=False,
+    ),
+    outputMRIVolume=dict(argstr='-o %s',
+    genfile=True,
+    hash_files=False,
+    ),
+    outputMaskedBiasField=dict(argstr='--maskedbias %s',
+    hash_files=False,
+    ),
+    splineLambda=dict(argstr='-w %f',
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    timer=dict(argstr='--timer',
+    ),
+    verbosityLevel=dict(argstr='-v %d',
+    ),
+    )
+    inputs = Bfc.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
+
+
+def test_Bfc_outputs():
+    output_map = dict(correctionScheduleFile=dict(),
+    outputBiasField=dict(),
+    outputMRIVolume=dict(),
+    outputMaskedBiasField=dict(),
+    )
+    outputs = Bfc.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/interfaces/brainsuite/tests/test_auto_Bse.py

@@ -0,0 +1,84 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ....testing import assert_equal
+from ..brainsuite import Bse
+
+
+def test_Bse_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    diffusionConstant=dict(argstr='-d %f',
+    usedefault=True,
+    ),
+    diffusionIterations=dict(argstr='-n %d',
+    usedefault=True,
+    ),
+    dilateFinalMask=dict(argstr='-p',
+    usedefault=True,
+    ),
+    edgeDetectionConstant=dict(argstr='-s %f',
+    usedefault=True,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    inputMRIFile=dict(argstr='-i %s',
+    mandatory=True,
+    ),
+    noRotate=dict(argstr='--norotate',
+    ),
+    outputCortexFile=dict(argstr='--cortex %s',
+    hash_files=False,
+    ),
+    outputDetailedBrainMask=dict(argstr='--hires %s',
+    hash_files=False,
+    ),
+    outputDiffusionFilter=dict(argstr='--adf %s',
+    hash_files=False,
+    ),
+    outputEdgeMap=dict(argstr='--edge %s',
+    hash_files=False,
+    ),
+    outputMRIVolume=dict(argstr='-o %s',
+    genfile=True,
+    hash_files=False,
+    ),
+    outputMaskFile=dict(argstr='--mask %s',
+    hash_files=False,
+    ),
+    radius=dict(argstr='-r %f',
+    usedefault=True,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    timer=dict(argstr='--timer',
+    ),
+    trim=dict(argstr='--trim',
+    usedefault=True,
+    ),
+    verbosityLevel=dict(argstr='-v %f',
+    usedefault=True,
+    ),
+    )
+    inputs = Bse.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
+
+
+def test_Bse_outputs():
+    output_map = dict(outputCortexFile=dict(),
+    outputDetailedBrainMask=dict(),
+    outputDiffusionFilter=dict(),
+    outputEdgeMap=dict(),
+    outputMRIVolume=dict(),
+    outputMaskFile=dict(),
+    )
+    outputs = Bse.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py

@@ -0,0 +1,75 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ....testing import assert_equal
+from ..brainsuite import Cerebro
+
+
+def test_Cerebro_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    costFunction=dict(argstr='-c %d',
+    usedefault=True,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    inputAtlasLabelFile=dict(argstr='--atlaslabels %s',
+    mandatory=True,
+    ),
+    inputAtlasMRIFile=dict(argstr='--atlas %s',
+    mandatory=True,
+    ),
+    inputBrainMaskFile=dict(argstr='-m %s',
+    ),
+    inputMRIFile=dict(argstr='-i %s',
+    mandatory=True,
+    ),
+    keepTempFiles=dict(argstr='--keep',
+    ),
+    linearConvergence=dict(argstr='--linconv %f',
+    ),
+    outputAffineTransformFile=dict(argstr='--air %s',
+    ),
+    outputCerebrumMaskFile=dict(argstr='-o %s',
+    genfile=True,
+    ),
+    outputLabelMaskFile=dict(argstr='-l %s',
+    genfile=True,
+    ),
+    outputWarpTransformFile=dict(argstr='--warp %s',
+    ),
+    tempDirectory=dict(argstr='--tempdir %s',
+    ),
+    tempDirectoryBase=dict(argstr='--tempdirbase %s',
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    useCentroids=dict(argstr='--centroids',
+    ),
+    verbosity=dict(argstr='-v %d',
+    ),
+    warpConvergence=dict(argstr='--warpconv %f',
+    ),
+    warpLabel=dict(argstr='--warplevel %d',
+    ),
+    )
+    inputs = Cerebro.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
+
+
+def test_Cerebro_outputs():
+    output_map = dict(outputAffineTransformFile=dict(),
+    outputCerebrumMaskFile=dict(),
+    outputLabelMaskFile=dict(),
+    outputWarpTransformFile=dict(),
+    )
+    outputs = Cerebro.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/interfaces/brainsuite/tests/test_auto_Cortex.py

@@ -0,0 +1,56 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ....testing import assert_equal
+from ..brainsuite import Cortex
+
+
+def test_Cortex_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    computeGCBoundary=dict(argstr='-g',
+    ),
+    computeWGBoundary=dict(argstr='-w',
+    usedefault=True,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    includeAllSubcorticalAreas=dict(argstr='-a',
+    usedefault=True,
+    ),
+    inputHemisphereLabelFile=dict(argstr='-h %s',
+    mandatory=True,
+    ),
+    inputTissueFractionFile=dict(argstr='-f %s',
+    mandatory=True,
+    ),
+    outputCerebrumMask=dict(argstr='-o %s',
+    genfile=True,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    timer=dict(argstr='--timer',
+    ),
+    tissueFractionThreshold=dict(argstr='-p %f',
+    usedefault=True,
+    ),
+    verbosity=dict(argstr='-v %d',
+    ),
+    )
+    inputs = Cortex.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
+
+
+def test_Cortex_outputs():
+    output_map = dict(outputCerebrumMask=dict(),
+    )
+    outputs = Cortex.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py

@@ -0,0 +1,46 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ....testing import assert_equal
+from ..brainsuite import Dewisp
+
+
+def test_Dewisp_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    inputMaskFile=dict(argstr='-i %s',
+    mandatory=True,
+    ),
+    maximumIterations=dict(argstr='-n %d',
+    ),
+    outputMaskFile=dict(argstr='-o %s',
+    genfile=True,
+    ),
+    sizeThreshold=dict(argstr='-t %d',
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    timer=dict(argstr='--timer',
+    ),
+    verbosity=dict(argstr='-v %d',
+    ),
+    )
+    inputs = Dewisp.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
+
+
+def test_Dewisp_outputs():
+    output_map = dict(outputMaskFile=dict(),
+    )
+    outputs = Dewisp.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value