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))
