def deconvolve(mat, fs, tau = 1.5):
#neucoeff = 0.7 # neuropil coefficient
# for computing and subtracting baseline
baseline = 'maximin' # take the running max of the running min after smoothing with gaussian
sig_baseline = 10.0 # in bins, standard deviation of gaussian with which to smooth
win_baseline = 60.0 # in seconds, window in which to compute max/min filters
ops = {'tau': tau, 'fs': fs, #'neucoeff': neucoeff,
'baseline': baseline, 'sig_baseline': sig_baseline, 'win_baseline': win_baseline}
# get spikes
spks = dcnv.oasis(mat, ops)
return spks
def run_dcnv(opts):
#% Set up paths:
acquisition_dir = os.path.join(opts.rootdir, opts.animalid, opts.session,
opts.acquisition)
s2p_source_dir = os.path.join(acquisition_dir, opts.run, 'processed',
opts.analysis, 'suite2p', 'plane0')
#s2p files
s2p_raw_trace_fn = os.path.join(s2p_source_dir, 'F.npy')
s2p_np_trace_fn = os.path.join(s2p_source_dir, 'Fneu.npy')
s2p_stat_fn = os.path.join(s2p_source_dir, 'stat.npy')
s2p_ops_fn = os.path.join(s2p_source_dir, 'ops.npy')
#load them in
s2p_stat = np.load(s2p_stat_fn)
s2p_ops = np.load(s2p_ops_fn).item()
s2p_raw_trace_data = np.load(s2p_raw_trace_fn)
s2p_np_trace_data = np.load(s2p_np_trace_fn)
#doing spike deconv with correct tau param
#from Dana et al (2018 paper):
#In agreement with the cultured neuron results, jGCaMP7f has faster kinetics
#than the other jGCaMP7 sensors and is comparable to GCaMP6f.
#jGCaMP7s has slower decay time than all the other sensors (Fig. 5b)
#therefore using same value for tau (decay constant) as suggested by Suite2p
#for GCaMP6f data: 0.7
s2p_ops['tau'] = 0.7
#remove neuropil
Fc0 = s2p_raw_trace_data - s2p_ops['neucoeff'] * s2p_np_trace_data
#baseline operation
Fc1 = dcnv.preprocess(Fc0, s2p_ops)
print('Deconvoling trace')
# get spikes
spks = dcnv.oasis(Fc1, s2p_ops)
# print(spks.shape)
s2p_spks_fn = os.path.join(s2p_source_dir, 'spks.npy')
print('Saving to: %s' % (s2p_spks_fn))
np.save(s2p_spks_fn, spks)
def run_s2p(ops={}, db={}):
t0 = tic()
ops0 = default_ops()
ops = {**ops0, **ops}
ops = {**ops, **db}
print(db)
if 'save_path0' not in ops or len(ops['save_path0']) == 0:
if ('h5py' in ops) and len(ops['h5py']) > 0:
ops['save_path0'], tail = os.path.split(ops['h5py'])
else:
ops['save_path0'] = ops['data_path'][0]
# check if there are files already registered!
fpathops1 = os.path.join(ops['save_path0'], 'suite2p', 'ops1.npy')
if os.path.isfile(fpathops1):
files_found_flag = True
flag_binreg = True
ops1 = np.load(fpathops1, allow_pickle=True)
print('FOUND OPS IN %s' % ops1[0]['save_path'])
for i, op in enumerate(ops1):
# default behavior is to look in the ops
flag_reg = os.path.isfile(op['reg_file'])
if not flag_reg:
# otherwise look in the user defined save_path0
op['save_path'] = os.path.join(ops['save_path0'], 'suite2p',
'plane%d' % i)
op['ops_path'] = os.path.join(op['save_path'], 'ops.npy')
op['reg_file'] = os.path.join(op['save_path'], 'data.bin')
flag_reg = os.path.isfile(op['reg_file'])
files_found_flag &= flag_reg
if 'refImg' not in op or op['do_registration'] > 1:
flag_binreg = False
if i == len(ops1) - 1:
print(
"NOTE: not registered / registration forced with ops['do_registration']>1"
)
# use the new False
ops1[i] = {**op, **ops}.copy()
# for mesoscope tiffs, preserve original lines, etc
if 'lines' in op:
ops1[i]['nrois'] = op['nrois']
ops1[i]['nplanes'] = op['nplanes']
ops1[i]['lines'] = op['lines']
ops1[i]['dy'] = op['dy']
ops1[i]['dx'] = op['dx']
ops1[i]['iplane'] = op['iplane']
#ops1[i] = ops1[i].copy()
# except for registration results
ops1[i]['xrange'] = op['xrange']
ops1[i]['yrange'] = op['yrange']
else:
files_found_flag = False
flag_binreg = False
# if not set up files and copy tiffs/h5py to binary
if not files_found_flag:
# get default options
ops0 = default_ops()
# combine with user options
ops = {**ops0, **ops}
# copy tiff to a binary
if len(ops['h5py']):
ops1 = utils.h5py_to_binary(ops)
print('time %4.2f sec. Wrote h5py to binaries for %d planes' %
(toc(t0), len(ops1)))
else:
if 'mesoscan' in ops and ops['mesoscan']:
ops1 = utils.mesoscan_to_binary(ops)
print('time %4.2f sec. Wrote tifs to binaries for %d planes' %
(toc(t0), len(ops1)))
elif HAS_HAUS:
print('time %4.2f sec. Using HAUSIO')
dataset = haussio.load_haussio(ops['data_path'][0])
ops1 = dataset.tosuite2p(ops)
print('time %4.2f sec. Wrote data to binaries for %d planes' %
(toc(t0), len(ops1)))
else:
ops1 = utils.tiff_to_binary(ops)
print('time %4.2f sec. Wrote tifs to binaries for %d planes' %
(toc(t0), len(ops1)))
np.save(fpathops1, ops1) # save ops1
else:
print('FOUND BINARIES: %s' % ops1[0]['reg_file'])
ops1 = np.array(ops1)
#ops1 = utils.split_multiops(ops1)
if not ops['do_registration']:
flag_binreg = True
if flag_binreg:
print('SKIPPING REGISTRATION...')
if flag_binreg and not files_found_flag:
print('NOTE: binary file created, but registration not performed')
# set up number of CPU workers for registration and cell detection
ipl = 0
while ipl < len(ops1):
print('>>>>>>>>>>>>>>>>>>>>> PLANE %d <<<<<<<<<<<<<<<<<<<<<<' % ipl)
t1 = tic()
if not flag_binreg:
######### REGISTRATION #########
t11 = tic()
print('----------- REGISTRATION')
ops1[ipl] = register.register_binary(ops1[ipl]) # register binary
np.save(fpathops1, ops1) # save ops1
print('Total %0.2f sec' % (toc(t11)))
if 'roidetect' in ops1[ipl]:
roidetect = ops['roidetect']
else:
roidetect = True
if roidetect:
######## CELL DETECTION AND ROI EXTRACTION ##############
t11 = tic()
print('----------- ROI DETECTION AND EXTRACTION')
ops1[ipl] = roiextract.roi_detect_and_extract(ops1[ipl])
ops = ops1[ipl]
fpath = ops['save_path']
print('Total %0.2f sec.' % (toc(t11)))
######### SPIKE DECONVOLUTION ###############
t11 = tic()
print('----------- SPIKE DECONVOLUTION')
F = np.load(os.path.join(fpath, 'F.npy'))
Fneu = np.load(os.path.join(fpath, 'Fneu.npy'))
dF = F - ops['neucoeff'] * Fneu
spks = dcnv.oasis(dF, ops)
np.save(os.path.join(ops['save_path'], 'spks.npy'), spks)
print('Total %0.2f sec.' % (toc(t11)))
# save as matlab file
if ('save_mat' in ops) and ops['save_mat']:
stat = np.load(os.path.join(fpath, 'stat.npy'),
allow_pickle=True)
iscell = np.load(os.path.join(fpath, 'iscell.npy'))
matpath = os.path.join(ops['save_path'], 'Fall.mat')
io.savemat(
matpath, {
'stat': stat,
'ops': ops,
'F': F,
'Fneu': Fneu,
'spks': spks,
'iscell': iscell
})
else:
print("WARNING: skipping cell detection (ops['roidetect']=False)")
print(
'Plane %d out of %d planes processed in %0.2f sec (can open in GUI).'
% (ipl, len(ops1), toc(t1)))
print('total = %0.2f sec.' % (toc(t0)))
ipl += 1 #len(ipl)
# save final ops1 with all planes
np.save(fpathops1, ops1)
#### COMBINE PLANES or FIELDS OF VIEW ####
if len(ops1) > 1 and ops1[0]['combined'] and roidetect:
utils.combined(ops1)
# running a clean up script
if 'clean_script' in ops1[0]:
print('running clean-up script')
os.system('python ' + ops['clean_script'] + ' ' + fpathops1)
for ops in ops1:
if ('delete_bin' in ops) and ops['delete_bin']:
os.remove(ops['reg_file'])
if ops['nchannels'] > 1:
os.remove(ops['reg_file_chan2'])
print('TOTAL RUNTIME %0.2f sec' % toc(t0))
return ops1
def masks_and_traces(ops, stat, stat_orig):
''' main extraction function
inputs: ops and stat
creates cell and neuropil masks and extracts traces
returns: F (ROIs x time), Fneu (ROIs x time), F_chan2, Fneu_chan2, ops, stat
F_chan2 and Fneu_chan2 will be empty if no second channel
'''
t0 = time.time()
# Concatenate stat so a good neuropil function can be formed
stat_all = stat.copy()
for n in range(len(stat_orig)):
stat_all.append(stat_orig[n])
stat_all, cell_pix, _ = roiextract.create_cell_masks(ops, stat_all)
stat = stat_all[:len(stat)]
neuropil_masks = roiextract.create_neuropil_masks(ops, stat, cell_pix)
Ly = ops['Ly']
Lx = ops['Lx']
neuropil_masks = np.reshape(neuropil_masks, (-1, Ly * Lx))
stat0 = []
for n in range(len(stat)):
stat0.append({
'ipix': stat[n]['ipix'],
'lam': stat[n]['lam'] / stat[n]['lam'].sum()
})
print('Masks made in %0.2f sec.' % (time.time() - t0))
F, Fneu, ops = roiextract.extractF(ops, stat0, neuropil_masks,
ops['reg_file'])
if 'reg_file_chan2' in ops:
F_chan2, Fneu_chan2, ops2 = roiextract.extractF(
ops.copy(), stat0, neuropil_masks, ops['reg_file_chan2'])
ops['meanImg_chan2'] = ops2['meanImg_chan2']
else:
F_chan2, Fneu_chan2 = [], []
# compute activity statistics for classifier
npix = np.array([stat_orig[n]['npix']
for n in range(len(stat_orig))]).astype('float32')
for n in range(len(stat)):
stat[n]['npix_norm'] = stat[n]['npix'] / np.mean(
npix[:100]) # What if there are less than 100 cells?
stat[n]['compact'] = 1
stat[n]['footprint'] = 2
stat[n]['Manual'] = 1 # Add manual key
# subtract neuropil and compute skew, std from F
dF = F - ops['neucoeff'] * Fneu
sk = stats.skew(dF, axis=1)
sd = np.std(dF, axis=1)
for n in range(F.shape[0]):
stat[n]['skew'] = sk[n]
stat[n]['std'] = sd[n]
stat[n]['med'] = [np.mean(stat[n]['ypix']), np.mean(stat[n]['xpix'])]
dF = F - ops['neucoeff'] * Fneu
spks = dcnv.oasis(dF, ops)
# print('Ftrace size', np.shape(Fneu), np.shape(F))
return F, Fneu, F_chan2, Fneu_chan2, spks, ops, stat
def run_s2p(ops={}, db={}):
i0 = tic()
ops0 = default_ops()
ops = {**ops0, **ops}
ops = {**ops, **db}
if 'save_path0' not in ops or len(ops['save_path0']) == 0:
if ('h5py' in ops) and len(ops['h5py']) > 0:
ops['save_path0'], tail = os.path.split(ops['h5py'])
else:
ops['save_path0'] = ops['data_path'][0]
# check if there are files already registered
fpathops1 = os.path.join(ops['save_path0'], 'suite2p', 'ops1.npy')
if os.path.isfile(fpathops1):
files_found_flag = True
flag_binreg = True
ops1 = np.load(fpathops1)
for i, op in enumerate(ops1):
# default behavior is to look in the ops
flag_reg = os.path.isfile(op['reg_file'])
if not flag_reg:
# otherwise look in the user defined save_path0
op['save_path'] = os.path.join(ops['save_path0'], 'suite2p',
'plane%d' % i)
op['ops_path'] = os.path.join(op['save_path'], 'ops.npy')
op['reg_file'] = os.path.join(op['save_path'], 'data.bin')
flag_reg = os.path.isfile(op['reg_file'])
files_found_flag &= flag_reg
if 'refImg' not in op:
flag_binreg = False
# use the new options
ops1[i] = {**op, **ops}.copy()
#ops1[i] = ops1[i].copy()
print(ops1[i]['save_path'])
# except for registration results
ops1[i]['xrange'] = op['xrange']
ops1[i]['yrange'] = op['yrange']
else:
files_found_flag = False
flag_binreg = False
######### REGISTRATION #########
if not files_found_flag:
# get default options
ops0 = default_ops()
# combine with user options
ops = {**ops0, **ops}
# copy tiff to a binary
if len(ops['h5py']):
ops1 = utils.h5py_to_binary(ops)
print('time %4.4f. Wrote h5py to binaries for %d planes' %
(toc(i0), len(ops1)))
else:
if 'mesoscan' in ops and ops['mesoscan']:
ops1 = utils.mesoscan_to_binary(ops)
print('time %4.4f. Wrote tifs to binaries for %d planes' %
(toc(i0), len(ops1)))
elif HAS_HAUS:
print('time %4.4f. Using HAUSIO')
dataset = haussio.load_haussio(ops['data_path'][0])
ops1 = dataset.tosuite2p(ops)
print('time %4.4f. Wrote data to binaries for %d planes' %
(toc(i0), len(ops1)))
else:
ops1 = utils.tiff_to_binary(ops)
print('time %4.4f. Wrote tifs to binaries for %d planes' %
(toc(i0), len(ops1)))
np.save(fpathops1, ops1) # save ops1
ops1 = np.array(ops1)
ops1 = utils.split_multiops(ops1)
if not ops['do_registration']:
flag_binreg = True
if files_found_flag:
print('found ops1 and binaries')
print(ops1[0]['reg_file'])
if flag_binreg:
print('foundpre-registered binaries')
print('skipping registration...')
if flag_binreg and not files_found_flag:
print('binary file created, but registration not performed')
if len(ops1) > 1 and ops['num_workers_roi'] >= 0:
if ops['num_workers_roi'] == 0:
ops['num_workers_roi'] = len(ops1)
ni = ops['num_workers_roi']
else:
ni = 1
ik = 0
while ik < len(ops1):
ipl = ik + np.arange(0, min(ni, len(ops1) - ik))
if not flag_binreg:
ops1[ipl] = register.register_binary(ops1[ipl]) # register binary
np.save(fpathops1, ops1) # save ops1
print('time %4.4f. Registration complete for %d planes' %
(toc(i0), ni))
if ni > 1:
with Pool(len(ipl)) as p:
ops1[ipl] = p.map(utils.get_cells, ops1[ipl])
else:
ops1[ipl[0]] = utils.get_cells(ops1[ipl[0]])
for ops in ops1[ipl]:
fpath = ops['save_path']
F = np.load(os.path.join(fpath, 'F.npy'))
Fneu = np.load(os.path.join(fpath, 'Fneu.npy'))
dF = F - ops['neucoeff'] * Fneu
spks = dcnv.oasis(dF, ops)
np.save(os.path.join(ops['save_path'], 'spks.npy'), spks)
print('time %4.4f. Detected spikes in %d ROIs' %
(toc(i0), F.shape[0]))
stat = np.load(os.path.join(fpath, 'stat.npy'))
# apply default classifier
classfile = os.path.join(
os.path.abspath(os.path.dirname(__file__)),
'classifiers/classifier_user.npy')
print(classfile)
iscell = classifier.run(classfile, stat)
np.save(os.path.join(ops['save_path'], 'iscell.npy'), iscell)
# save as matlab file
if ('save_mat' in ops) and ops['save_mat']:
matpath = os.path.join(ops['save_path'], 'Fall.mat')
io.savemat(
matpath, {
'stat': stat,
'ops': ops,
'F': F,
'Fneu': Fneu,
'spks': spks,
'iscell': iscell
})
ik += len(ipl)
# save final ops1 with all planes
np.save(fpathops1, ops1)
#### COMBINE PLANES or FIELDS OF VIEW ####
if len(ops1) > 1 and ops1[0]['combined']:
utils.combined(ops1)
# running a clean up script
if 'clean_script' in ops1[0]:
print('running clean-up script')
os.system('python ' + ops['clean_script'] + ' ' + fpathops1)
for ops in ops1:
if ('delete_bin' in ops) and ops['delete_bin']:
os.remove(ops['reg_file'])
if ops['nchannels'] > 1:
os.remove(ops['reg_file_chan2'])
print('finished all tasks in total time %4.4f sec' % toc(i0))
return ops1
def run_s2p(ops={}, db={}):
i0 = tic()
ops = {**ops, **db}
if 'save_path0' not in ops or len(ops['save_path0']) == 0:
ops['save_path0'] = ops['data_path'][0]
# check if there are files already registered
fpathops1 = os.path.join(ops['save_path0'], 'suite2p', 'ops1.npy')
if os.path.isfile(fpathops1):
files_found_flag = True
flag_binreg = True
ops1 = np.load(fpathops1)
for i, op in enumerate(ops1):
# default behavior is to look in the ops
flag_reg = os.path.isfile(op['reg_file'])
if not flag_reg:
# otherwise look in the user defined save_path0
op['save_path'] = os.path.join(ops['save_path0'], 'suite2p',
'plane%d' % i)
op['ops_path'] = os.path.join(op['save_path'], 'ops.npy')
op['reg_file'] = os.path.join(op['save_path'], 'data.bin')
flag_reg = os.path.isfile(op['reg_file'])
files_found_flag &= flag_reg
if 'refImg' not in op:
flag_binreg = False
# use the new options
ops1[i] = {**op, **ops}
ops1[i] = ops1[i].copy()
print(ops1[i]['save_path'])
# except for registration results
ops1[i]['xrange'] = op['xrange']
ops1[i]['yrange'] = op['yrange']
else:
files_found_flag = False
flag_binreg = False
######### REGISTRATION #########
if not files_found_flag:
# get default options
ops0 = default_ops()
# combine with user options
ops = {**ops0, **ops}
# copy tiff to a binary
if len(ops['h5py']):
ops1 = utils.h5py_to_binary(ops)
print('time %4.4f. Wrote h5py to binaries for %d planes' %
(toc(i0), len(ops1)))
else:
ops1 = utils.tiff_to_binary(ops)
print('time %4.4f. Wrote tifs to binaries for %d planes' %
(toc(i0), len(ops1)))
# save ops1
np.save(fpathops1, ops1)
if not flag_binreg:
ops1 = register.register_binary(ops1) # register tiff
np.save(fpathops1, ops1) # save ops1
print('time %4.4f. Registration complete' % toc(i0))
else:
print('found ops1 and pre-registered binaries')
print(ops1[0]['reg_file'])
print('overwriting ops1 with new ops')
print('skipping registration...')
######### CELL DETECTION #########
if len(ops1) > 1 and ops['num_workers_roi'] >= 0:
if ops['num_workers_roi'] == 0:
ops['num_workers_roi'] = len(ops1)
with Pool(ops['num_workers_roi']) as p:
ops1 = p.map(utils.get_cells, ops1)
else:
for k in range(len(ops1)):
ops1[k] = utils.get_cells(ops1[k])
######### SPIKE DECONVOLUTION AND CLASSIFIER #########
for ops in ops1:
fpath = ops['save_path']
F = np.load(os.path.join(fpath, 'F.npy'))
Fneu = np.load(os.path.join(fpath, 'Fneu.npy'))
dF = F - ops['neucoeff'] * Fneu
spks = dcnv.oasis(dF, ops)
np.save(os.path.join(ops['save_path'], 'spks.npy'), spks)
print('time %4.4f. Detected spikes in %d ROIs' % (toc(i0), F.shape[0]))
stat = np.load(os.path.join(fpath, 'stat.npy'))
# apply default classifier
classfile = os.path.join(os.path.abspath(os.path.dirname(__file__)),
'classifiers/classifier_user.npy')
print(classfile)
iscell = classifier.run(classfile, stat)
np.save(os.path.join(ops['save_path'], 'iscell.npy'), iscell)
# save as matlab file
if ('save_mat' in ops) and ops['save_mat']:
matpath = os.path.join(ops['save_path'], 'Fall.mat')
scipy.io.savemat(
matpath, {
'stat': stat,
'ops': ops,
'F': F,
'Fneu': Fneu,
'spks': spks,
'iscell': iscell
})
# save final ops1 with all planes
np.save(fpathops1, ops1)
#### COMBINE PLANES or FIELDS OF VIEW ####
if len(ops1) > 1 and ops1[0]['combined']:
utils.combined(ops1)
for ops in ops1:
if ('delete_bin' in ops) and ops['delete_bin']:
os.remove(ops['reg_file'])
if ops['nchannels'] > 1:
os.remove(ops['reg_file_chan2'])
print('finished all tasks in total time %4.4f sec' % toc(i0))
return ops1
def activity_stats(parent):
i0 = int(1 - parent.iscell[parent.ichosen])
ypix = np.array([])
xpix = np.array([])
lam = np.array([])
footprints = np.array([])
F = np.zeros((0, parent.Fcell.shape[1]), np.float32)
Fneu = np.zeros((0, parent.Fcell.shape[1]), np.float32)
for n in np.array(parent.imerge):
ypix = np.append(ypix, parent.stat[n]["ypix"])
xpix = np.append(xpix, parent.stat[n]["xpix"])
lam = np.append(lam, parent.stat[n]["lam"])
footprints = np.append(footprints, parent.stat[n]["footprint"])
F = np.append(F, parent.Fcell[n, :][np.newaxis, :], axis=0)
Fneu = np.append(Fneu, parent.Fneu[n, :][np.newaxis, :], axis=0)
# remove overlaps
ipix = np.concatenate((ypix[:, np.newaxis], xpix[:, np.newaxis]), axis=1)
_, goodi = np.unique(ipix, return_index=True, axis=0)
ypix = ypix[goodi]
xpix = xpix[goodi]
lam = lam[goodi]
stat0 = {}
stat0["ypix"] = ypix.astype(np.int32)
stat0["xpix"] = xpix.astype(np.int32)
stat0["lam"] = lam
stat0['med'] = [np.median(stat0["ypix"]), np.median(stat0["xpix"])]
stat0["npix"] = ypix.size
d0 = parent.ops["diameter"]
radius = utils.fitMVGaus(ypix / d0[0], xpix / d0[1], lam, 2)[2]
stat0["radius"] = radius[0] * d0.mean()
stat0["aspect_ratio"] = 2 * radius[0] / (.01 + radius[0] + radius[1])
npix = np.array([parent.stat[n]['npix']
for n in range(len(parent.stat))]).astype('float32')
stat0["npix_norm"] = stat0["npix"] / npix.mean()
# compactness
rs, dy, dx = sparsedetect.circleMask(d0)
rsort = np.sort(rs.flatten())
r2 = ((ypix - stat0["med"][0]) / d0[0])**2 + (
(xpix - stat0["med"][1]) / d0[1])**2
r2 = r2**.5
stat0["mrs"] = np.mean(r2)
stat0["mrs0"] = np.mean(rsort[:r2.size])
stat0["compact"] = stat0["mrs"] / (1e-10 + stat0["mrs0"])
# footprint
stat0["footprint"] = footprints.mean()
F = F.mean(axis=0)
Fneu = Fneu.mean(axis=0)
dF = F - parent.ops["neucoeff"] * Fneu
# activity stats
stat0["skew"] = stats.skew(dF)
stat0["std"] = dF.std()
# compute outline and circle around cell
iext = fig.boundary(ypix, xpix)
stat0["yext"] = ypix[iext]
stat0["xext"] = xpix[iext]
ycirc, xcirc = fig.circle(stat0["med"], stat0["radius"])
goodi = ((ycirc >= 0)
& (xcirc >= 0)
& (ycirc < parent.ops["Ly"])
& (xcirc < parent.ops["Lx"]))
stat0["ycirc"] = ycirc[goodi]
stat0["xcirc"] = xcirc[goodi]
# deconvolve activity
spks = dcnv.oasis(dF[np.newaxis, :], parent.ops)
# add cell to structs
parent.stat = np.concatenate((parent.stat, np.array([stat0])), axis=0)
print(parent.stat[-1]["ypix"].shape)
parent.Fcell = np.concatenate((parent.Fcell, F[np.newaxis, :]), axis=0)
parent.Fneu = np.concatenate((parent.Fneu, Fneu[np.newaxis, :]), axis=0)
parent.Spks = np.concatenate((parent.Spks, spks), axis=0)
iscell = np.array([parent.iscell[parent.ichosen]], dtype=bool)
parent.iscell = np.concatenate((parent.iscell, iscell), axis=0)
def merge_activity_masks(parent):
print('merging activity... this may take some time')
i0 = int(1-parent.iscell[parent.ichosen])
ypix = np.array([])
xpix = np.array([])
lam = np.array([])
footprints = np.array([])
F = np.zeros((0,parent.Fcell.shape[1]), np.float32)
Fneu = np.zeros((0,parent.Fcell.shape[1]), np.float32)
probcell = []
probredcell = []
merged_cells = []
remove_merged = []
for n in np.array(parent.imerge):
if len(parent.stat[n]['imerge']) > 0:
remove_merged.append(n)
for k in parent.stat[n]['imerge']:
merged_cells.append(k)
else:
merged_cells.append(n)
merged_cells = np.unique(np.array(merged_cells))
for n in merged_cells:
ypix = np.append(ypix, parent.stat[n]["ypix"])
xpix = np.append(xpix, parent.stat[n]["xpix"])
lam = np.append(lam, parent.stat[n]["lam"])
footprints = np.append(footprints, parent.stat[n]["footprint"])
F = np.append(F, parent.Fcell[n,:][np.newaxis,:], axis=0)
Fneu = np.append(Fneu, parent.Fneu[n,:][np.newaxis,:], axis=0)
probcell.append(parent.probcell[n])
probredcell.append(parent.probredcell[n])
probcell = np.array(probcell)
probredcell = np.array(probredcell)
pmean = probcell.mean()
prmean = probredcell.mean()
# remove overlaps
ipix = np.concatenate((ypix[:,np.newaxis], xpix[:,np.newaxis]), axis=1)
_, goodi = np.unique(ipix, return_index=True, axis=0)
ypix = ypix[goodi]
xpix = xpix[goodi]
lam = lam[goodi]
stat0 = {}
if 'aspect' in parent.ops:
d0 = np.array([int(parent.ops['aspect']*10), 10])
else:
d0 = parent.ops['diameter']
if isinstance(d0, int):
d0 = [d0,d0]
### compute statistics of merges
stat0["imerge"] = merged_cells
stat0["ypix"] = ypix.astype(np.int32)
stat0["xpix"] = xpix.astype(np.int32)
stat0["lam"] = lam / lam.sum() * merged_cells.size
stat0['med'] = [np.median(stat0["ypix"]), np.median(stat0["xpix"])]
stat0["npix"] = ypix.size
radius = utils.fitMVGaus(ypix/d0[0], xpix/d0[1], lam, 2)[2]
stat0["radius"] = radius[0] * d0.mean()
stat0["aspect_ratio"] = 2 * radius[0]/(.01 + radius[0] + radius[1])
npix = np.array([parent.stat[n]['npix'] for n in range(len(parent.stat))]).astype('float32')
stat0["npix_norm"] = stat0["npix"] / npix.mean()
# compactness
rs,dy,dx = sparsedetect.circleMask(d0)
rsort = np.sort(rs.flatten())
r2 = ((ypix - stat0["med"][0])/d0[0])**2 + ((xpix - stat0["med"][1])/d0[1])**2
r2 = r2**.5
stat0["mrs"] = np.mean(r2)
stat0["mrs0"] = np.mean(rsort[:r2.size])
stat0["compact"] = stat0["mrs"] / (1e-10 + stat0["mrs0"])
# footprint
stat0["footprint"] = footprints.mean()
# inmerge
stat0["inmerge"] = 0
### compute activity of merged cells
F = F.mean(axis=0)
Fneu = Fneu.mean(axis=0)
dF = F - parent.ops["neucoeff"]*Fneu
# activity stats
stat0["skew"] = stats.skew(dF)
stat0["std"] = dF.std()
### for GUI drawing
# compute outline and circle around cell
iext = fig.boundary(ypix, xpix)
stat0["yext"] = ypix[iext].astype(np.int32)
stat0["xext"] = xpix[iext].astype(np.int32)
ycirc, xcirc = fig.circle(stat0["med"], stat0["radius"])
goodi = (
(ycirc >= 0)
& (xcirc >= 0)
& (ycirc < parent.ops["Ly"])
& (xcirc < parent.ops["Lx"])
)
stat0["ycirc"] = ycirc[goodi]
stat0["xcirc"] = xcirc[goodi]
# deconvolve activity
spks = dcnv.oasis(dF[np.newaxis, :], parent.ops)
### remove previously merged cell (do not replace)
for k in remove_merged:
remove_mask(parent, k)
np.delete(parent.stat, k, 0)
np.delete(parent.Fcell, k, 0)
np.delete(parent.Fneu, k, 0)
np.delete(parent.Spks, k, 0)
np.delete(parent.iscell, k, 0)
np.delete(parent.probcell, k, 0)
np.delete(parent.probredcell, k, 0)
np.delete(parent.redcell, k, 0)
np.delete(parent.notmerged, k, 0)
# add cell to structs
parent.stat = np.concatenate((parent.stat, np.array([stat0])), axis=0)
parent.stat = sparsedetect.get_overlaps(parent.stat, parent.ops)
parent.stat = np.array(parent.stat)
parent.Fcell = np.concatenate((parent.Fcell, F[np.newaxis,:]), axis=0)
parent.Fneu = np.concatenate((parent.Fneu, Fneu[np.newaxis,:]), axis=0)
parent.Spks = np.concatenate((parent.Spks, spks), axis=0)
iscell = np.array([parent.iscell[parent.ichosen]], dtype=bool)
parent.iscell = np.concatenate((parent.iscell, iscell), axis=0)
parent.probcell = np.append(parent.probcell, pmean)
parent.probredcell = np.append(parent.probredcell, prmean)
parent.redcell = np.append(parent.redcell, prmean > parent.chan2prob)
parent.notmerged = np.append(parent.notmerged, False)
# recompute binned F
parent.mode_change(parent.activityMode)
for n in merged_cells:
parent.stat[n]['inmerge'] = parent.stat.size-1
add_mask(parent, parent.iscell.size-1)