'edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculator',
'de.mpg.cbs.jist.brain.JistBrainMp2rageDuraEstimation',
'de.mpg.cbs.jist.brain.JistBrainPartialVolumeFilter',
'edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmThresholdToBinaryMask',
# 'de.mpg.cbs.jist.cortex.JistCortexFullCRUISE', # waiting for http://www.nitrc.org/tracker/index.php?func=detail&aid=7236&group_id=228&atid=942 to be fixed
'de.mpg.cbs.jist.cortex.JistCortexSurfaceMeshInflation'
]
modules_from_julia = [
'de.mpg.cbs.jist.intensity.JistIntensityMp2rageMasking',
'edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2010'
]
modules_from_leonie = [
'edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmLesionToads'
]
modules_from_yasinyazici = [
'edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmN3'
]
modules_list = list(
set(modules_list).union(modules_from_chris).union(
modules_from_leonie).union(modules_from_julia).union(
modules_from_yasinyazici).union(modules_list))
generate_all_classes(modules_list=modules_list,
launcher=["java edu.jhu.ece.iacl.jist.cli.run"],
redirect_x=True,
mipav_hacks=True)
'VBRAINSDemonWarp', 'extractNrrdVectorIndex', 'gtractAnisotropyMap', 'gtractAverageBvalues', 'gtractClipAnisotropy', 'gtractCoRegAnatomy', 'gtractConcatDwi', 'gtractCopyImageOrientation', 'gtractCoregBvalues', 'gtractCostFastMarching', 'gtractImageConformity', 'gtractInvertBSplineTransform', 'gtractInvertDisplacementField', 'gtractInvertRigidTransform', 'gtractResampleAnisotropy', 'gtractResampleB0', 'gtractResampleCodeImage', 'gtractResampleDWIInPlace', 'gtractTensor', 'gtractTransformToDisplacementField', 'GenerateLabelMapFromProbabilityMap', 'BRAINSLinearModelerEPCA', 'BRAINSCut', ] launcher=[''] generate_all_classes(modules_list=modules_list, launcher=[])
OUTPUT_PATH = os.path.join(args.output_path, 'semtools')
if os.path.exists(OUTPUT_PATH):
shutil.rmtree(OUTPUT_PATH)
os.mkdir(OUTPUT_PATH)
os.chdir(OUTPUT_PATH)
found_modules_list = list()
missing_modules_list = list()
for test_module in all_known_modules_list:
for currPath in SEARCH_PATHS:
currProgPath = os.path.join(currPath, test_module)
if os.path.exists(currProgPath):
found_modules_list.append(test_module)
break
else:
missing_modules_list.append(test_module)
generate_all_classes(modules_list=found_modules_list, launcher=[])
help_file = open(os.path.join(OUTPUT_PATH, 'generated.sh'), 'w')
help_file.write(' '.join(sys.argv) + "\n")
help_file.close()
print(("\n\nRan: ", ' '.join(sys.argv), "\n\n"))
print(("FOUND: ", found_modules_list))
for test_module in missing_modules_list:
print(("Missing Candidate Program: {prog_name}".format(
prog_name=test_module)))
modules_list = ['edu.jhu.bme.smile.demo.RandomVol',
'de.mpg.cbs.jist.laminar.JistLaminarProfileCalculator',
'de.mpg.cbs.jist.laminar.JistLaminarProfileSampling',
'de.mpg.cbs.jist.laminar.JistLaminarROIAveraging',
'de.mpg.cbs.jist.laminar.JistLaminarVolumetricLayering',
'de.mpg.cbs.jist.laminar.JistLaminarProfileGeometry',
'de.mpg.cbs.jist.brain.JistBrainMgdmSegmentation',
'de.mpg.cbs.jist.brain.JistBrainMp2rageSkullStripping',
'de.mpg.cbs.jist.brain.JistBrainPartialVolumeFilter',
'de.mpg.cbs.jist.brain.JistBrainMp2rageDuraEstimation']
modules_from_chris = ['edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2010',
'edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient',
'edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculator',
'de.mpg.cbs.jist.brain.JistBrainMp2rageDuraEstimation',
'de.mpg.cbs.jist.brain.JistBrainPartialVolumeFilter',
'edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmThresholdToBinaryMask',
# 'de.mpg.cbs.jist.cortex.JistCortexFullCRUISE', # waiting for http://www.nitrc.org/tracker/index.php?func=detail&aid=7236&group_id=228&atid=942 to be fixed
'de.mpg.cbs.jist.cortex.JistCortexSurfaceMeshInflation']
modules_from_julia = ['de.mpg.cbs.jist.intensity.JistIntensityMp2rageMasking',
'edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2010']
modules_from_leonie = ['edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmLesionToads']
modules_from_yasinyazici = ['edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmN3']
modules_list = list(set(modules_list).union(modules_from_chris).union(modules_from_leonie).union(modules_from_julia).union(modules_from_yasinyazici).union(modules_list))
generate_all_classes(modules_list=modules_list, launcher=["java edu.jhu.ece.iacl.jist.cli.run"], redirect_x=True, mipav_hacks=True)
#exec_dir = '/scratch/src/BRAINS4-build/bin'
#exec_dir = '/scratch/johnsonhj/src/BRAINS4-buld/bin'
exec_dir = '/Users/johnsonhj/src/BRAINS4-build/bin'
for candidate_exe in test_list.split():
test_command = exec_dir + "/" + candidate_exe + " --xml"
xmlReturnValue = subprocess.Popen(test_command,
stdout=subprocess.PIPE,
shell=True).communicate()[0]
isThisAnSEMExecutable = xmlReturnValue.find("<executable>")
if isThisAnSEMExecutable != -1:
SEM_exe.append(candidate_exe)
print("SEM_PROGRAMS: {0}".format(SEM_exe))
## NOTE: For now either the launcher needs to be found on the default path, or
## every tool in the modules list must be found on the default path
## AND calling the module with --xml must be supported and compliant.
## modules_list = ['BRAINSConstellationDetector','BRAINSFit', 'BRAINSResample', 'BRAINSDemonWarp', 'BRAINSROIAuto']
## SlicerExecutionModel compliant tools that are usually statically built, and don't need the Slicer3 --launcher
SEM.generate_all_classes(modules_list=SEM_exe, launcher=[])
### This uses the unsuppored "point" SEM type
### TransformFromFiducials
### This uses the unsupported "geometry" SEM type
### compareTractInclusion
### gtractCreateGuideFiber
### gtractFiberTracking
### gtractCostFastMarching
### gtractFastMarchingTracking
### gtractResampleFibers
SEM_exe = list()
# exec_dir = '/scratch/src/BRAINS4-build/bin'
# exec_dir = '/scratch/johnsonhj/src/BRAINS4-buld/bin'
exec_dir = "/Users/johnsonhj/src/BRAINS4-build/bin"
for candidate_exe in test_list.split():
test_command = exec_dir + "/" + candidate_exe + " --xml"
xmlReturnValue = subprocess.Popen(test_command, stdout=subprocess.PIPE, shell=True).communicate()[0]
isThisAnSEMExecutable = xmlReturnValue.find("<executable>")
if isThisAnSEMExecutable != -1:
SEM_exe.append(candidate_exe)
print("SEM_PROGRAMS: {0}".format(SEM_exe))
## NOTE: For now either the launcher needs to be found on the default path, or
## every tool in the modules list must be found on the default path
## AND calling the module with --xml must be supported and compliant.
## modules_list = ['BRAINSConstellationDetector','BRAINSFit', 'BRAINSResample', 'BRAINSDemonWarp', 'BRAINSROIAuto']
## SlicerExecutionModel compliant tools that are usually statically built, and don't need the Slicer3 --launcher
SEM.generate_all_classes(modules_list=SEM_exe, launcher=[])
### This uses the unsuppored "point" SEM type
### TransformFromFiducials
### This uses the unsupported "geometry" SEM type
### compareTractInclusion
### gtractCreateGuideFiber
### gtractFiberTracking
### gtractCostFastMarching
### gtractFastMarchingTracking
### gtractResampleFibers
