def load_annotation_file(file_path, end_frame, dims):
with h5py.File(file_path, 'r') as f:
# shape(frame, neuron_num), temporal fluorescence traces
if 'C' in f.keys():
C = np.array(f.get('C')).T[:, :end_frame]
neuron_num = C.shape[0]
else:
C = None
if 'C_raw' in f.keys():
C_raw = np.array(f.get('C_raw')).T[:, :end_frame]
neuron_num = C_raw.shape[0]
else:
C_raw = None
# C = np.array(f.get('C_raw')).T[:, :end_frame]
# C = np.where(C < 0, 0, C)
# neuron_num = C.shape[0]
# shape(neuron_num, height * width), spatial components
A = np.array(f.get('A'),
dtype='float32').T.reshape(dims[0], dims[1], neuron_num)
A = csc_matrix(A.transpose(1, 0, 2).reshape(-1, neuron_num))
estimates = Estimates(A=A, b=None, C=C, f=None, R=None, dims=dims)
estimates.C_raw = C_raw
return estimates
opts = params.CNMFParams(params_dict=params_dict)
cnm = load_CNMF(fname_new[:-5] + '_cnmf_gsig.hdf5')
# %% prepare ground truth masks
gt_file = os.path.join(
os.path.split(fname_new)[0],
os.path.split(fname_new)[1][:-4] + 'match_masks.npz')
with np.load(gt_file, encoding='latin1') as ld:
print(ld.keys())
Cn_orig = ld['Cn']
gt_estimate = Estimates(A=scipy.sparse.csc_matrix(ld['A_gt'][()]),
b=ld['b_gt'],
C=ld['C_gt'],
f=ld['f_gt'],
R=ld['YrA_gt'],
dims=(ld['d1'], ld['d2']))
min_size_neuro = 3 * 2 * np.pi
max_size_neuro = (2 * params_dict['gSig'][0])**2 * np.pi
gt_estimate.threshold_spatial_components(maxthr=0.2, dview=dview)
gt_estimate.remove_small_large_neurons(min_size_neuro, max_size_neuro)
_ = gt_estimate.remove_duplicates(predictions=None,
r_values=None,
dist_thr=0.1,
min_dist=10,
thresh_subset=0.6)
print(gt_estimate.A_thr.shape)
for gr_snr in SNRs_grid:
C_gt = ld['C_gt']
Cn_orig = ld['Cn']
if ds_factor > 1:
A_gt2 = np.concatenate([
cv2.resize(A_gt[:, fr_].reshape(dims_or, order='F'),
cnm.dims[::-1]).reshape(-1, order='F')[:, None]
for fr_ in range(A_gt.shape[-1])
],
axis=1)
Cn_orig = cv2.resize(Cn_orig, cnm.dims[::-1])
else:
A_gt2 = A_gt.copy()
gt_estimate = Estimates(A=scipy.sparse.csc_matrix(A_gt2),
b=None,
C=C_gt,
f=None,
R=None,
dims=cnm.dims)
gt_estimate.threshold_spatial_components(maxthr=global_params['max_thr'],
dview=None)
gt_estimate.remove_small_large_neurons(min_size_neuro, max_size_neuro)
_ = gt_estimate.remove_duplicates(predictions=None,
r_values=None,
dist_thr=0.1,
min_dist=10,
thresh_subset=0.6)
print(gt_estimate.A.shape)
# %% compute performance and plot against consensus annotations
tp_gt, tp_comp, fn_gt, fp_comp, performance_cons_off = compare_components(
gt_estimate,
plt.figure()
plt.plot(vpy.estimates['recons_signal'][n][:2000])
from caiman.source_extraction.cnmf.estimates import Estimates
import scipy
estimates = vpy.estimates.copy()
A = np.array(estimates['spatial_filter']).transpose([1,2,0]).reshape((-1, len(estimates['spatial_filter'])),order='F')
A = A / A.max(axis=0)
b = np.zeros((A.shape[0],2))
A = scipy.sparse.csc_matrix(A)
b = scipy.sparse.csc_matrix(b)
C = np.array(estimates['t_rec'])
f = np.zeros((2, C.shape[1]))
R = np.array(estimates['t']) - C
est = Estimates(A=A, C=C, b=b, f=f, R=R, dims=(100,100))
est.YrA = R
#est.plot_contours(img=summary_image[:,:,2])
# now load the file
Yr, dims, T = cm.load_memmap(fname_new)
images = np.reshape(Yr.T, [T] + list(dims), order='F')
est.dview = dview
#est.view_components(img=summary_image[:,:,2])
est.play_movie(imgs=images, magnification=4)
est = np.load('/home/nel/data/voltage_data/volpy_paper/reconstructed/estimates.npz',allow_pickle=True)['arr_0'].item()
fnames = ['/home/nel/data/voltage_data/volpy_paper/memory/403106_3min_10000._rig__d1_512_d2_128_d3_1_order_F_frames_10000_.mmap']
def OnACID_A_init(fr, fnames, out, hfile, epochs=2):
# %% set up some parameters
decay_time = .4 # approximate length of transient event in seconds
gSig = (4, 4) # expected half size of neurons
p = 1 # order of AR indicator dynamics
thresh_CNN_noisy = 0.8 #0.65 # CNN threshold for candidate components
gnb = 2 # number of background components
init_method = 'cnmf' # initialization method
min_SNR = 2.5 # signal to noise ratio for accepting a component
rval_thr = 0.8 # space correlation threshold for accepting a component
ds_factor = 1 # spatial downsampling factor, newImg=img/ds_factor(increases speed but may lose some fine structure)
# K = 25 # number of components per patch
patch_size = 32 # size of patch
stride = 3 # amount of overlap between patches
max_num_added = 5
max_comp_update_shape = np.inf
update_num_comps = False
gSig = tuple(np.ceil(
np.array(gSig) /
ds_factor).astype('int')) # recompute gSig if downsampling is involved
mot_corr = True # flag for online motion correction
pw_rigid = False # flag for pw-rigid motion correction (slower but potentially more accurate)
max_shifts_online = np.ceil(10. / ds_factor).astype(
'int') # maximum allowed shift during motion correction
sniper_mode = False # use a CNN to detect new neurons (o/w space correlation)
# set up some additional supporting parameters needed for the algorithm
# (these are default values but can change depending on dataset properties)
init_batch = 500 # number of frames for initialization (presumably from the first file)
K = 2 # initial number of components
show_movie = False # show the movie as the data gets processed
print("Frame rate: {}".format(fr))
params_dict = {
'fr': fr,
'fnames': fnames,
'decay_time': decay_time,
'gSig': gSig,
'gnb': gnb,
'p': p,
'min_SNR': min_SNR,
'rval_thr': rval_thr,
'ds_factor': ds_factor,
'nb': gnb,
'motion_correct': mot_corr,
'normalize': True,
'sniper_mode': sniper_mode,
'K': K,
'use_cnn': False,
'epochs': epochs,
'max_shifts_online': max_shifts_online,
'pw_rigid': pw_rigid,
'min_num_trial': 10,
'show_movie': show_movie,
'save_online_movie': False,
"max_num_added": max_num_added,
"max_comp_update_shape": max_comp_update_shape,
"update_num_comps": update_num_comps,
"dist_shape_update": update_num_comps,
'init_batch': init_batch,
'init_method': init_method,
'rf': patch_size // 2,
'stride': stride,
'thresh_CNN_noisy': thresh_CNN_noisy
}
opts = CNMFParams(params_dict=params_dict)
with h5py.File(hfile, 'r') as hf:
ests = Estimates(A=load_A(hf))
cnm = online_cnmf.OnACID(params=opts, estimates=ests)
cnm.estimates = ests
cnm.fit_online()
cnm.save(out)