if save_results:
np.savez(os.path.join(base_folder, 'results_analysis_patch.npz'),
A_tot=A_tot.todense(), C_tot=C_tot, sn_tot=sn_tot, d1=d1, d2=d2, b=b, f=f)
#%% if you have many components this might take long!
pl.figure()
crd = cse.utilities.plot_contours(A_tot, Cn, thr=0.9)
#%% set parameters for full field of view analysis
options = cse.utilities.CNMFSetParms(
Y, n_processes, p=0, gSig=gSig, K=A_tot.shape[-1], thr=merge_thresh)
pix_proc = np.minimum(np.int((d1 * d2) / n_processes / (old_div(T, 2000.))),
np.int(old_div((d1 * d2), n_processes))) # regulates the amount of memory used
options['spatial_params']['n_pixels_per_process'] = pix_proc
options['temporal_params']['n_pixels_per_process'] = pix_proc
#%% merge spatially overlaping and temporally correlated components
if 1:
A_m, C_m, nr_m, merged_ROIs, S_m, bl_m, c1_m, sn_m, g_m = cse.merge_components(Yr, A_tot, [], np.array(C_tot), [], np.array(
C_tot), [], options['temporal_params'], options['spatial_params'], dview=dview, thr=options['merging']['thr'], mx=np.Inf)
else:
A_m, C_m, f_m = A_tot, C_tot, f
cse.utilities.view_patches_bar(Yr, A_m, C_m, b, f_m, d1, d2, C_m, img=Cn)
#%% update temporal to get Y_r
options['temporal_params']['p'] = 0
# change ifdenoised traces time constant is wrong
options['temporal_params']['fudge_factor'] = 0.96
options['temporal_params']['backend'] = 'ipyparallel'
C_m, A_m, b, f_m, S_m, bl_m, c1_m, neurons_sn_m, g2_m, YrA_m = cse.temporal.update_temporal_components(
Yr, A_m, np.atleast_2d(b).T, C_m, f, dview=dview, bl=None, c1=None, sn=None, g=None, **options['temporal_params'])
#%% get rid of evenrually noisy components.
# But check by visual inspection to have a feeling fot the threshold. Try to be loose, you will be able to get rid of more of them later!
print 'Number of components:' + str(A_tot.shape[-1])
times.append(time.time() - t0)
#if save_results:
# np.savez('results_analysis_patch.npz',A_tot=A_tot.todense(), C_tot=C_tot, sn_tot=sn_tot,d1=d1,d2=d2)
# if you have many components this might take long!
#pl.figure()
#crd = cse.utilities.plot_contours(A_tot,Cn,thr=0.9)
# set parameters for full field of view analysis
options = cse.utilities.CNMFSetParms(Y,n_processes,p=0,gSig=gSig,K=A_tot.shape[-1],thr=merge_thresh)
pix_proc=np.minimum(np.int((d1*d2)/n_processes/(T/2000.)),np.int((d1*d2)/n_processes)) # regulates the amount of memory used
options['spatial_params']['n_pixels_per_process']=pix_proc
options['temporal_params']['n_pixels_per_process']=pix_proc
# merge spatially overlaping and temporally correlated components
A_m,C_m,nr_m,merged_ROIs,S_m,bl_m,c1_m,sn_m,g_m=cse.merge_components(Yr,A_tot,[],np.array(C_tot),[],np.array(C_tot),[],options['temporal_params'],options['spatial_params'],thr=options['merging']['thr'],mx=np.Inf)
#ti
print 'Number of components:' + str(A_m.shape[-1])
# UPDATE SPATIAL COMPONENTS
options['spatial_params']['backend']='ipyparallel' #parallelize with ipyparallel
t1 = time.time()
#%
A2,b2,C2 = cse.spatial.update_spatial_components(Yr, C_m, f, A_m, sn=sn_tot, **options['spatial_params'])
print time.time() - t1
times.append(time.time() - t1)
#
# UPDATE TEMPORAL COMPONENTS
options['temporal_params']['p']= 2
options['temporal_params']['fudge_factor']=0.98 #change ifdenoised traces time constant is wrong
options['temporal_params']['backend']='ipyparallel'
np.savez(os.path.join(folder_in,'images','results_analysis_patch_3.npz'),A_tot=A_tot.todense(), C_tot=C_tot, sn_tot=sn_tot,d1=d1,d2=d2,b=b,f=f,Cn=Cn)
#%% if you have many components this might take long!
#
#pl.figure();crd = cse.utilities.plot_contours(A_tot,Cn,thr=0.9)
#%% set parameters for full field of view analysis
options = cse.utilities.CNMFSetParms(Y,n_processes,p=0,gSig=gSig,K=A_tot.shape[-1],thr=merge_thresh)
pix_proc=np.minimum(np.int((d1*d2)/n_processes/(old_div(T,2000.))),np.int(old_div((d1*d2),n_processes))) # regulates the amount of memory used
options['spatial_params']['n_pixels_per_process']=pix_proc
options['temporal_params']['n_pixels_per_process']=pix_proc
#%% merge spatially overlaping and temporally correlated components
merged_ROIs=[0]
A_m=scipy.sparse.coo_matrix(A_tot)
C_m=C_tot
while len(merged_ROIs)>0:
A_m,C_m,nr_m,merged_ROIs,S_m,bl_m,c1_m,sn_m,g_m=cse.merge_components(Yr,A_m,[],np.array(C_m),[],np.array(C_m),[],options['temporal_params'],options['spatial_params'],dview=dview,thr=options['merging']['thr'],mx=np.Inf)
# pl.figure();crd = cse.utilities.plot_contours(A_m,Cn,thr=0.9)
#%% update temporal to get Y_r
options['temporal_params']['p']=0
options['temporal_params']['fudge_factor']=0.96 #change ifdenoised traces time constant is wrong
options['temporal_params']['backend']='ipyparallel'
C_m,f_m,S_m,bl_m,c1_m,neurons_sn_m,g2_m,YrA_m = cse.temporal.update_temporal_components(Yr,A_m,np.atleast_2d(b).T,C_m,f,dview=dview,bl=None,c1=None,sn=None,g=None,**options['temporal_params'])
#%% get rid of evenrually noisy components.
# But check by visual inspection to have a feeling fot the threshold. Try to be loose, you will be able to get rid of more of them later!
tB = np.minimum(-2,np.floor(-5./30*final_frate))
tA = np.maximum(5,np.ceil(25./30*final_frate))
Npeaks=10
traces=C_m+YrA_m
# traces_a=traces-scipy.ndimage.percentile_filter(traces,8,size=[1,np.shape(traces)[-1]/5])
# traces_b=np.diff(traces,axis=1)
pix_proc = np.minimum(
np.int((d1 * d2) / n_processes / (old_div(T, 2000.))),
np.int(old_div((d1 * d2),
n_processes))) # regulates the amount of memory used
options['spatial_params']['n_pixels_per_process'] = pix_proc
options['temporal_params']['n_pixels_per_process'] = pix_proc
#%% merge spatially overlaping and temporally correlated components
merged_ROIs = [0]
A_m = scipy.sparse.coo_matrix(A_tot)
C_m = C_tot
while len(merged_ROIs) > 0:
A_m, C_m, nr_m, merged_ROIs, S_m, bl_m, c1_m, sn_m, g_m = cse.merge_components(
Yr,
A_m, [],
np.array(C_m), [],
np.array(C_m), [],
options['temporal_params'],
options['spatial_params'],
dview=dview,
thr=options['merging']['thr'],
mx=np.Inf)
# pl.figure();crd = cse.utilities.plot_contours(A_m,Cn,thr=0.9)
#%% update temporal to get Y_r
options['temporal_params']['p'] = 0
# change ifdenoised traces time constant is wrong
options['temporal_params']['fudge_factor'] = 0.96
options['temporal_params']['backend'] = 'ipyparallel'
C_m, A_m, b, f_m, S_m, bl_m, c1_m, neurons_sn_m, g2_m, YrA_m = cse.temporal.update_temporal_components(
Yr,
A_m,
np.atleast_2d(b).T,
C_m,
def process_data(haussio_data, mask=None, p=2, nrois_init=200):
fn_cnmf = haussio_data.dirname_comp + '_cnmf.mat'
tiffs_to_cnmf(haussio_data, mask)
sys.stdout.write('Loading from {0}... '.format(
haussio_data.dirname_comp + '_Y*.npy'))
Y = np.load(haussio_data.dirname_comp + '_Y.npy', mmap_mode='r')
d1, d2, T = Y.shape
if not os.path.exists(fn_cnmf):
cse.utilities.stop_server()
sys.stdout.flush()
t0 = time.time()
Yr = np.load(haussio_data.dirname_comp + '_Yr.npy', mmap_mode='r')
sys.stdout.write('took {0:.2f} s\n'.format(time.time()-t0))
# how to subdivide the work among processes
n_pixels_per_process = d1*d2/NCPUS
options = cse.utilities.CNMFSetParms(Y, K=nrois_init, p=p, gSig=[9, 9])
options['preprocess_params']['n_processes'] = NCPUS
options['preprocess_params'][
'n_pixels_per_process'] = n_pixels_per_process
options['init_params']['nIter'] = 10
options['init_params']['maxIter'] = 10
options['init_params']['use_hals'] = False
options['spatial_params']['n_processes'] = NCPUS
options['spatial_params'][
'n_pixels_per_process'] = n_pixels_per_process
options['temporal_params']['n_processes'] = NCPUS
options['temporal_params'][
'n_pixels_per_process'] = n_pixels_per_process
cse.utilities.start_server(NCPUS)
t0 = time.time()
sys.stdout.write("Preprocessing... ")
sys.stdout.flush()
Yr, sn, g = cse.preprocess_data(Yr, **options['preprocess_params'])
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
# 224.94s
t0 = time.time()
sys.stdout.write("Initializing components... ")
sys.stdout.flush()
Ain, Cin, b_in, f_in, center = cse.initialize_components(
Y, **options['init_params'])
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
# 2281.37s
t0 = time.time()
sys.stdout.write("Updating spatial components... ")
sys.stdout.flush()
A, b, Cin = cse.update_spatial_components(
Yr, Cin, f_in, Ain, sn=sn, **options['spatial_params'])
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
# 252.57s
t0 = time.time()
sys.stdout.write("Updating temporal components... ")
sys.stdout.flush()
C, f, S, bl, c1, neurons_sn, g, YrA = \
cse.update_temporal_components(
Yr, A, b, Cin, f_in, bl=None, c1=None, sn=None, g=None,
**options['temporal_params'])
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
# 455.14s
t0 = time.time()
sys.stdout.write("Merging ROIs... ")
sys.stdout.flush()
A_m, C_m, nr_m, merged_ROIs, S_m, bl_m, c1_m, sn_m, g_m = \
cse.merge_components(
Yr, A, b, C, f, S, sn, options['temporal_params'],
options['spatial_params'], bl=bl, c1=c1, sn=neurons_sn, g=g,
thr=0.7, mx=100, fast_merge=True)
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
# 702.55s
t0 = time.time()
sys.stdout.write("Updating spatial components... ")
sys.stdout.flush()
A2, b2, C2 = cse.update_spatial_components(
Yr, C_m, f, A_m, sn=sn, **options['spatial_params'])
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
# 77.16s
t0 = time.time()
sys.stdout.write("Updating temporal components... ")
sys.stdout.flush()
C2, f2, S2, bl2, c12, neurons_sn2, g21, YrA = \
cse.update_temporal_components(
Yr, A2, b2, C2, f, bl=None, c1=None, sn=None, g=None,
**options['temporal_params'])
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
# 483.41s
# A: spatial components (ROIs)
# C: denoised [Ca2+]
# YrA: residuals ("noise")
# S: Spikes
savemat(fn_cnmf, {"A": A2, "C": C2, "YrA": YrA, "S": S2, "bl": bl2})
else:
resdict = loadmat(fn_cnmf)
A2 = resdict["A"]
C2 = resdict["C"]
YrA = resdict["YrA"]
S2 = resdict["S"]
bl2 = resdict["bl"]
proj_fn = haussio_data.dirname_comp + "_proj.npy"
if not os.path.exists(proj_fn):
zproj = utils.zproject(np.transpose(Y, (2, 0, 1)))
np.save(proj_fn, zproj)
else:
zproj = np.load(proj_fn)
# DF_F, DF = cse.extract_DF_F(Y.reshape(d1*d2, T), A2, C2)
t0 = time.time()
sys.stdout.write("Ordering components... ")
sys.stdout.flush()
A_or, C_or, srt = cse.order_components(A2, C2)
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
cse.utilities.stop_server()
polygons = contour(A2, d1, d2, thr=0.9)
rois = ROIList([sima.ROI.ROI(polygons=poly) for poly in polygons])
return rois, C2, haussio_data, zproj, S2, Y, YrA
def extract_rois_patch(file_name,d1,d2,rf=5,stride = 2):
not_completed, in_progress
rf=6
stride = 2
idx_flat,idx_2d=extract_patch_coordinates(d1, d2, rf=rf,stride = stride)
perctl=95
n_components=2
tol=1e-6
max_iter=5000
args_in=[]
for id_f,id_2d in zip(idx_flat,idx_2d):
args_in.append((file_name, id_f,id_2d[0].shape, perctl,n_components,tol,max_iter))
st=time.time()
try:
if 1:
c = Client()
dview=c[:]
file_res = dview.map_sync(nmf_patches, args_in)
else:
file_res = map(nmf_patches, args_in)
finally:
dview.results.clear()
c.purge_results('all')
c.purge_everything()
c.close()
print time.time()-st
A1=lil_matrix((d1*d2,len(file_res)))
C1=[]
A2=lil_matrix((d1*d2,len(file_res)))
C2=[]
A_tot=lil_matrix((d1*d2,n_components*len(file_res)))
C_tot=[];
count_out=0
for count,f in enumerate(file_res):
idx_,flt,ca,d=f
print count_out
#flt,ca,_=cse.order_components(coo_matrix(flt),ca)
# A1[idx_,count]=flt[:,0][:,np.newaxis]/np.sqrt(np.sum(flt[:,0]**2))
# A2[idx_,count]=flt[:,1][:,np.newaxis] /np.sqrt(np.sum(flt[:,1]**2))
# C1.append(ca[0,:])
# C2.append(ca[1,:])
for ccc in range(n_components):
A_tot[idx_,count_out]=flt[:,ccc][:,np.newaxis]/np.sqrt(np.sum(flt[:,ccc]**2))
C_tot.append(ca[ccc,:])
count_out+=1
# pl.imshow(np.reshape(flt[:,0],d,order='F'),vmax=10)
# pl.pause(.1)
correlations=np.corrcoef(np.array(C_tot))
centers=cse.com(A_tot.todense(),d1,d2)
distances=sklearn.metrics.pairwise.euclidean_distances(centers)
pl.imshow((correlations>0.8) & (distances<10))
Yr=np.load('Yr.npy',mmap_mode='r')
[d,T]=Yr.shape
Y=np.reshape(Yr,(d1,d2,T),order='F')
options=cse.utilities.CNMFSetParms(Y,p=0)
res_merge=cse.merge_components(Yr,A_tot,[],np.array(C_tot),[],np.array(C_tot),[],options['temporal_params'],options['spatial_params'],thr=0.8)
A_m,C_m,nr_m,merged_ROIs,S_m,bl_m,c1_m,sn_m,g_m=res_merge
A_norm=np.array([A_m[:,rr].toarray()/np.sqrt(np.sum(A_m[:,rr].toarray()**2)) for rr in range(A_m.shape[-1])]).T
options=cse.utilities.CNMFSetParms(Y,p=2,K=np.shape(A_m)[-1])
Yr,sn,g=cse.pre_processing.preprocess_data(Yr,**options['preprocess_params'])
epsilon=1e-2
pixels_bckgrnd=np.nonzero(A_norm.sum(axis=-1)<epsilon)[0]
f=np.sum(Yr[pixels_bckgrnd,:],axis=0)
A2,b2,C2 = cse.spatial.update_spatial_components(Yr, C_m, f, A_m, sn=sn, **options['spatial_params'])
A_or2, C_or2, srt2 = cse.utilities.order_components(A2,C2)
A_norm2=np.array([A_or2[:,rr]/np.sqrt(np.sum(A_or2[:,rr]**2)) for rr in range(A_or2.shape[-1])]).T
options['temporal_params']['p'] = 2 # set it back to original value to perform full deconvolution
C2,f2,S2,bl2,c12,neurons_sn2,g21,YrA = cse.temporal.update_temporal_components(Yr,A2,b2,C2,f,bl=None,c1=None,sn=None,g=None,**options['temporal_params'])
A_or, C_or, srt = cse.utilities.order_components(A2,C2)
return A1,A2,C1
def process_data(haussio_data, mask=None, p=2, nrois_init=400):
fn_cnmf = haussio_data.dirname_comp + '_cnmf.mat'
tiffs_to_cnmf(haussio_data, mask)
sys.stdout.write('Loading from {0}... '.format(
haussio_data.dirname_comp + '_Y*.npy'))
Y = np.load(haussio_data.dirname_comp + '_Y.npy', mmap_mode='r')
d1, d2, T = Y.shape
if not os.path.exists(fn_cnmf):
cse.utilities.stop_server()
sys.stdout.flush()
t0 = time.time()
Yr = np.load(haussio_data.dirname_comp + '_Yr.npy', mmap_mode='r')
sys.stdout.write('took {0:.2f} s\n'.format(time.time()-t0))
# how to subdivide the work among processes
n_pixels_per_process = d1*d2/NCPUS
options = cse.utilities.CNMFSetParms(
Y, NCPUS, K=nrois_init, p=p, gSig=[9, 9], ssub=2, tsub=2)
options['preprocess_params']['n_processes'] = NCPUS
options['preprocess_params'][
'n_pixels_per_process'] = n_pixels_per_process
options['init_params']['nIter'] = 10
options['init_params']['maxIter'] = 10
options['init_params']['use_hals'] = True
options['spatial_params']['n_processes'] = NCPUS
options['spatial_params'][
'n_pixels_per_process'] = n_pixels_per_process
options['temporal_params']['n_processes'] = NCPUS
options['temporal_params'][
'n_pixels_per_process'] = n_pixels_per_process
cse.utilities.start_server()
t0 = time.time()
sys.stdout.write("Preprocessing... ")
sys.stdout.flush()
Yr, sn, g, psx = cse.preprocess_data(Yr, **options['preprocess_params'])
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
# 224.94s
# 2016-05-24: 146.30s
t0 = time.time()
sys.stdout.write("Initializing components... ")
sys.stdout.flush()
Ain, Cin, b_in, f_in, center = cse.initialize_components(
Y, **options['init_params'])
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
# 2281.37s
# 2016-05-24: 1054.72s
t0 = time.time()
sys.stdout.write("Updating spatial components... ")
sys.stdout.flush()
A, b, Cin = cse.update_spatial_components(
Yr, Cin, f_in, Ain, sn=sn, **options['spatial_params'])
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
# 252.57s
# 2016-05-24: 445.95s
t0 = time.time()
sys.stdout.write("Updating temporal components... ")
sys.stdout.flush()
C, f, S, bl, c1, neurons_sn, g, YrA = \
cse.update_temporal_components(
Yr, A, b, Cin, f_in, bl=None, c1=None, sn=None, g=None,
**options['temporal_params'])
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
# 455.14s
# 2016-05-24: 86.10s
t0 = time.time()
sys.stdout.write("Merging ROIs... ")
sys.stdout.flush()
A_m, C_m, nr_m, merged_ROIs, S_m, bl_m, c1_m, sn_m, g_m = \
cse.merge_components(
Yr, A, b, C, f, S, sn, options['temporal_params'],
options['spatial_params'], bl=bl, c1=c1, sn=neurons_sn, g=g,
thr=0.7, mx=100, fast_merge=True)
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
# 702.55s
# 2016-05-24: 11.75s
t0 = time.time()
sys.stdout.write("Updating spatial components... ")
sys.stdout.flush()
A2, b2, C2 = cse.update_spatial_components(
Yr, C_m, f, A_m, sn=sn, **options['spatial_params'])
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
# 77.16s
# 2016-05-24: 99.22s
t0 = time.time()
sys.stdout.write("Updating temporal components... ")
sys.stdout.flush()
C2, f2, S2, bl2, c12, neurons_sn2, g21, YrA = \
cse.update_temporal_components(
Yr, A2, b2, C2, f, bl=None, c1=None, sn=None, g=None,
**options['temporal_params'])
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
# 483.41s
# 2016-05-24: 74.81s
# A: spatial components (ROIs)
# C: denoised [Ca2+]
# YrA: residuals ("noise")
# S: Spikes
savemat(fn_cnmf, {"A": A2, "C": C2, "YrA": YrA, "S": S2, "bl": bl2})
else:
resdict = loadmat(fn_cnmf)
A2 = resdict["A"]
C2 = resdict["C"]
YrA = resdict["YrA"]
S2 = resdict["S"]
bl2 = resdict["bl"]
proj_fn = haussio_data.dirname_comp + "_proj.npy"
if not os.path.exists(proj_fn):
zproj = utils.zproject(np.transpose(Y, (2, 0, 1)))
np.save(proj_fn, zproj)
else:
zproj = np.load(proj_fn)
# DF_F, DF = cse.extract_DF_F(Y.reshape(d1*d2, T), A2, C2)
t0 = time.time()
sys.stdout.write("Ordering components... ")
sys.stdout.flush()
A_or, C_or, srt = cse.order_components(A2, C2)
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
cse.utilities.stop_server()
polygons = contour(A2, d1, d2, thr=0.9)
rois = ROIList([sima.ROI.ROI(polygons=poly) for poly in polygons])
return rois, C2, zproj, S2, Y, YrA
def process_data_patches(
haussio_data, mask=None, p=2, nrois_init=400, roi_iceberg=0.9):
fn_cnmf = haussio_data.dirname_comp + '_cnmf.mat'
tiffs_to_cnmf(haussio_data, mask)
sys.stdout.write('Loading from {0}... '.format(
haussio_data.dirname_comp + '_Y*.npy'))
Y = np.load(haussio_data.dirname_comp + '_Y.npy', mmap_mode='r')
d1, d2, T = Y.shape
if not os.path.exists(fn_cnmf):
cse.utilities.stop_server()
sys.stdout.flush()
t0 = time.time()
fname_new = haussio_data.dirname_comp + '_Yr.npy'
Yr = np.load(fname_new, mmap_mode='r')
sys.stdout.write('took {0:.2f} s\n'.format(time.time()-t0))
# how to subdivide the work among processes
n_pixels_per_process = d1*d2/NCPUS_PATCHES
options = cse.utilities.CNMFSetParms(
Y, NCPUS, K=np.max((int(nrois_init/NCPUS), 1)), p=p, gSig=[9, 9],
ssub=1, tsub=1)
options['preprocess_params']['n_processes'] = NCPUS
options['preprocess_params'][
'n_pixels_per_process'] = n_pixels_per_process
options['init_params']['nIter'] = 10
options['init_params']['maxIter'] = 10
options['init_params']['use_hals'] = True
options['spatial_params']['n_processes'] = NCPUS
options['spatial_params'][
'n_pixels_per_process'] = n_pixels_per_process
options['temporal_params']['n_processes'] = NCPUS
options['temporal_params'][
'n_pixels_per_process'] = n_pixels_per_process
options['temporal_params']['backend'] = 'ipyparallel'
rf = 16 # half-size of the patches in pixels. rf=25, patches are 50x50
stride = 2 # amounpl of overlap between the patches in pixels
cse.utilities.start_server()
cl = Client()
dview = cl[:len(cl)]
t0 = time.time()
sys.stdout.write("CNMF patches... ")
sys.stdout.flush()
A_tot, C_tot, b, f, sn_tot, opt_out = cse.map_reduce.run_CNMF_patches(
fname_new, (d1, d2, T), options, rf=rf, stride=stride,
n_processes=NCPUS_PATCHES, dview=dview, memory_fact=4.0)
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
options = cse.utilities.CNMFSetParms(
Y, NCPUS, K=A_tot.shape[-1], p=p, gSig=[9, 9], ssub=1, tsub=1)
pix_proc = np.minimum(
np.int((d1*d2)/NCPUS/(T/2000.)),
np.int((d1*d2)/NCPUS)) # regulates the amount of memory used
options['preprocess_params']['n_processes'] = NCPUS
options['preprocess_params'][
'n_pixels_per_process'] = n_pixels_per_process
options['init_params']['nIter'] = 10
options['init_params']['maxIter'] = 10
options['init_params']['use_hals'] = True
options['spatial_params']['n_processes'] = NCPUS
options['temporal_params']['n_processes'] = NCPUS
options['spatial_params']['n_pixels_per_process'] = pix_proc
options['temporal_params']['n_pixels_per_process'] = pix_proc
t0 = time.time()
sys.stdout.write("Merging ROIs... ")
sys.stdout.flush()
A_m, C_m, nr_m, merged_ROIs, S_m, bl_m, c1_m, sn_m, g_m = \
cse.merge_components(
Yr, A_tot, [], np.array(C_tot), [], np.array(C_tot), [],
options['temporal_params'],
options['spatial_params'], thr=options['merging']['thr'],
mx=np.Inf)
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
t0 = time.time()
sys.stdout.write("Updating spatial components... ")
sys.stdout.flush()
A2, b2, C2 = cse.spatial.update_spatial_components(
Yr, C_m, f, A_m, sn=sn_tot, **options['spatial_params'])
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
# 77.16s
# 2016-05-24: 99.22s
t0 = time.time()
sys.stdout.write("Updating temporal components... ")
sys.stdout.flush()
C2, f2, S2, bl2, c12, neurons_sn2, g21, YrA = \
cse.temporal.update_temporal_components(
Yr, A2, b2, C2, f, bl=None, c1=None, sn=None, g=None,
**options['temporal_params'])
sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
# 483.41s
# 2016-05-24: 74.81s
# A: spatial components (ROIs)
# C: denoised [Ca2+]
# YrA: residuals ("noise")
# S: Spikes
savemat(fn_cnmf, {"A": A2, "C": C2, "YrA": YrA, "S": S2, "bl": bl2})
else:
resdict = loadmat(fn_cnmf)
A2 = resdict["A"]
C2 = resdict["C"]
YrA = resdict["YrA"]
S2 = resdict["S"]
bl2 = resdict["bl"]
proj_fn = haussio_data.dirname_comp + "_proj.npy"
if not os.path.exists(proj_fn):
zproj = utils.zproject(np.transpose(Y, (2, 0, 1)))
np.save(proj_fn, zproj)
else:
zproj = np.load(proj_fn)
# DF_F, DF = cse.extract_DF_F(Y.reshape(d1*d2, T), A2, C2)
# t0 = time.time()
# sys.stdout.write("Ordering components... ")
# sys.stdout.flush()
# A_or, C_or, srt = cse.order_components(A2, C2)
# sys.stdout.write(' took {0:.2f} s\n'.format(time.time()-t0))
cse.utilities.stop_server()
polygons = contour(A2, d1, d2, thr=roi_iceberg)
rois = ROIList([sima.ROI.ROI(polygons=poly) for poly in polygons])
return rois, C2, zproj, S2, Y, YrA