def setup(params, *args, **kw):
matlab_setup(['MicrotubuleTracker', '-a', 'mt_track_config.xml'],
params=params)
docker_setup('microtubuletracker',
'MicrotubuleTracker',
'matlab_runtime',
params=params)
def setup(params, *args, **kw):
python_setup("RootTipMulti.py", params)
matlab_setup('matlab/maizeG.m', bisque_deps=False, params=params)
docker_setup('roottipmulti',
'RootTipMulti',
'matlab_runtime',
params=params)
def setup(params, *args, **kw):
ensure_matlab(params)
#mex_compile(['vrl_gc.cpp'], where='vrl_tools/maxflow_kolmogorov')
matlab_setup(['GraphcutSegmentation'], params=params)
docker_setup('graphcut',
'GraphcutSegmentation',
'matlab_runtime',
params=params)
def setup(params, *args, **kw):
ensure_matlab(params)
mex_compile(['vrl_gc.cpp'], where='vrl_tools/maxflow_kolmogorov')
matlab_setup(['ImageMatting', '-a', 'vrl_tools'], params=params)
docker_setup('imagematting',
'ImageMatting',
'matlab_runtime',
params=params)
def setup(params, *args, **kw):
docker_params = read_config('runtime-bisque.cfg', "docker")
if not asbool(docker_params.get('docker.enabled', False)):
print "No Docker available... cannot set up module."
return 1
try:
# clone Dream.3D UCSB repo and build Docker image
tmp_dir = tempfile.mkdtemp()
print "Cloning code into %s..." % tmp_dir
p = Popen([
'git', 'clone', '[email protected]:wlenthe/UCSB_DREAM3D',
'%s/source' % tmp_dir
],
stdout=PIPE)
if p.wait() != 0:
print "Dream.3D repo could not be cloned... cannot set up module."
return 1
# build Docker image
print "Building Dream.3D docker image..."
p = Popen([
'timeout', '-s', 'SIGKILL', '120m', 'docker', 'build', '--tag',
'dream3d_ucsb',
'%s/source' % tmp_dir
],
stdout=PIPE)
while True:
line = p.stdout.readline()
if line == '':
break
m = re.search('\[[ ]*[0-9]+%\]', line)
if m:
print '\r\r\r\r\r\r',
print m.group(0),
sys.stdout.flush()
print
if p.wait() != 0:
print "Dream.3D image could not be built... cannot set up module."
return 1
python_setup('Dream3D.py', params=params)
docker_setup('bisque_dream3d_ucsb',
'Dream3D',
'dream3d_ucsb',
params=params)
finally:
# delete tmp_dir
shutil.rmtree(tmp_dir)
def setup(params, *args, **kw):
matlab_setup(['Phidias.m', '-a', 'phenotype_descriptors'], params=params)
docker_setup('phidiasanalyze', 'Phidias', 'matlab_runtime', params=params)
def setup(params, *args, **kw):
ensure_matlab(params)
mex_compile(['vrl_gc.cpp'], where='vrl_tools/maxflow_kolmogorov')
matlab_setup(['PlanteomeSegmenter', '-a', 'vrl_tools'], params=params)
docker_setup('imagematting', 'PlanteomeSegmenter', 'matlab_runtime', params=params)
def setup(params, *args, **kw):
matlab_setup(['Phidias.m', '-a', 'phenotype_descriptors'], params=params)
docker_setup('phidiasanalyze', 'Phidias', 'matlab_runtime', params=params)
def setup(params, *args, **kw):
matlab_setup('PhidiasModel.m', params=params)
docker_setup('phidiasmodel', 'Phidiasmodel', 'matlab_runtime', params=params)
def setup(params, *args, **kw):
matlab_setup('WatershedSegmentation', params=params)
docker_setup('watershedsegmentation',
'WatershedSegmentation',
'matlab_runtime',
params=params)
def setup(i_params, *args, **kw):
print('args={}, kw={}'.format(args, kw))
docker_setup('bisque_uplanteome',
'PlanteomeDeepSegment',
'planteomedeepsegment',
params=i_params)
def setup(params, *args, **kw):
matlab_setup('PhidiasAnnotate.m', params=params)
docker_setup('phidiasannotate',
'PhidiasAnnotate',
'matlab_runtime',
params=params)
def setup(params, *args, **kw):
python_setup('SeedSize.py', params=params)
matlab_setup('matlab/seedSize', bisque_deps=False, params=params)
docker_setup('seedsize', 'SeedSize', 'matlab_runtime', params=params)
def setup(params, *args, **kw):
python_setup('Dream3D.py', params=params)
docker_setup('bisque_dream3d', 'Dream3D', 'dream3d', params=params)
def setup(params, *args, **kw):
python_setup('PythonScriptWrapper.py', params=params)
docker_setup('segmentation',
'TwoPhasePrediction',
'twophaseprediction',
params=params)
def setup(params, *args, **kw):
matlab_setup('PHFDetector', params=params)
docker_setup('phfdetector', 'PHFDetector', 'matlab_runtime', params=params)
def setup(params, *args, **kw):
matlab_setup('NuclearDetector3D', params=params)
docker_setup('n3d', 'NuclearDetector3D', 'matlab_runtime', params=params)
def setup(*args, **kw):
python_setup('RootTip.py', params=params)
matlab_setup('matlab/araGT.m', bisque_deps=False, params=params)
docker_setup('roottip', "RootTip", "matlab_runtime", params=params)
def setup(params, *args, **kw):
matlab_setup('PhidiasModel.m', params=params)
docker_setup('phidiasmodel',
'Phidiasmodel',
'matlab_runtime',
params=params)
def setup(params, *args, **kw):
#python_setup('CellProfiler.py', params=params)
docker_setup('bisque_cellprofiler', 'CellProfiler', 'cellprofiler', params=params)
def setup(params, *args, **kw):
python_setup('PythonScriptWrapper.py', params=params)
docker_setup('cell_segmentation_2d',
'CellSegmentation2D',
'cell-segmentation-2d',
params=params)
def setup(params, *args, **kw):
matlab_setup('NuclearFilter', params=params)
docker_setup('nuclearfilter',
'NuclearFilter',
'matlab_runtime',
params=params)
def setup(params, *args, **kw):
python_setup('PythonScriptWrapper.py', params=params)
docker_setup('Composite_Strength', 'TwoPhasePrediction', 'twophaseprediction', params=params)
def setup(params, *args, **kw):
matlab_setup('FluorescentCavities', params=params)
docker_setup('fluorescentcavities',
'FluorescentCavities',
'matlab_runtime',
params=params)
def setup(params, *args, **kw):
matlab_setup('PlantcellTracking', params=params)
docker_setup('plantcelltracking',
'PlantcellTracking',
'matlab_runtime',
params=params)
def setup(params, *args, **kw):
python_setup('PythonScriptWrapper.py', params=params)
docker_setup('torch-cellseg-3dunet-v3', 'CellSegment3DUnet', 'torch-cellseg-3dunet-v2', params=params)
def setup(params, *args, **kw):
matlab_setup('PhidiasAnnotate.m', params=params)
docker_setup('phidiasannotate', 'PhidiasAnnotate', 'matlab_runtime', params=params)
def setup(params, *args, **kw):
python_setup('PythonScriptWrapper.py', params=params)
docker_setup('COVIDPredictor', params=params)
def setup(params, *args, **kw):
python_setup('ImageJ.py', params=params)
docker_setup('bisque_imagej', 'ImageJ', 'imagej', params=params)
