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()
############# # # 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()