def __init__(self, filename):
bioformats.init_logger()
self.filename = filename
def setUp(self):
J.start_vm(class_path=bioformats.JARS)
J.attach()
bioformats.init_logger()
def setUp(self):
javabridge.attach()
bioformats.init_logger()
def __init__(self, filename):
bioformats.init_logger()
self.filename = filename
def setUp(self):
J.start_vm(class_path=bioformats.JARS)
J.attach()
bioformats.init_logger()
#############
# # Globals ##
#############
# results_path = 'results/segmentationfungus'
results_path = 'wtreible_results/segmentationfungus'
arg_names = ['script_name', 'experiment']
args = dict(zip(arg_names, sys.argv))
Arg_list = collections.namedtuple('Arg_list', arg_names)
args = Arg_list(*(args.get(arg, None) for arg in arg_names))
experiment = args[1]
print "Experiment:", experiment
os.system("taskset -p 0xFFFFFFFF %d" % os.getpid())
for f in os.listdir('/dev/shm'):
if 'shmmap' in f:
os.remove('/dev/shm/' + f)
statvfs = os.statvfs('/dev/shm')
if (statvfs.f_frsize * statvfs.f_bavail / 1024. ** 3) < 44:
raise Exception('Shared memory is running low. try: sudo mount -o remount,size=100% /run/shm/')
javabridge.start_vm(args=[], class_path=bioformats.JARS)
try:
bioformats.init_logger()
main(experiment)
finally:
javabridge.kill_vm()
