if single_thread: dview = None else: try: c.close() except: print('C was not existing, creating one') print("Stopping cluster to avoid unnencessary use of memory....") sys.stdout.flush() if backend == 'SLURM': try: cm.stop_server(is_slurm=True) except: print('Nothing to stop') slurm_script = '/mnt/xfs1/home/agiovann/SOFTWARE/Constrained_NMF/SLURM/slurmStart.sh' cm.start_server(slurm_script=slurm_script) pdir, profile = os.environ['IPPPDIR'], os.environ['IPPPROFILE'] c = Client(ipython_dir=pdir, profile=profile) else: cm.stop_server() cm.start_server() c = Client() print(('Using ' + str(len(c)) + ' processes')) dview = c[:len(c)] #%% set parameters and create template by rigid motion correction t1 = time.time() #fname = 'k56_20160608_RSM_125um_41mW_zoom2p2_00001_00034.tif' #fname = 'Sue_1000.tif' fname = 'Sue_2000.tif' max_shifts = (12, 12)
if single_thread: dview = None else: try: c.close() except: print('C was not existing, creating one') print("Stopping cluster to avoid unnencessary use of memory....") sys.stdout.flush() if backend == 'SLURM': try: cm.stop_server(is_slurm=True) except: print('Nothing to stop') slurm_script = '/mnt/xfs1/home/agiovann/SOFTWARE/Constrained_NMF/SLURM/slurmStart.sh' cm.start_server(slurm_script=slurm_script) pdir, profile = os.environ['IPPPDIR'], os.environ['IPPPROFILE'] c = Client(ipython_dir=pdir, profile=profile) else: cm.stop_server() cm.start_server() c = Client() print(('Using ' + str(len(c)) + ' processes')) dview = c[:len(c)] #%% set parameters and create template by rigid motion correction t1 = time.time() fname = '20_12__002_cr.tif' max_shifts = (12, 12) splits = 28 # for parallelization split the movies in num_sqplits chuncks across time m = cm.load(fname, subindices=slice(None, None, None))