def pop_act_time_course(DATA, Model, t0=400., smoothing=10,
FIGSIZE=(4,2),
YTICKS=[0, 15, 30], XTICKS=[0, 500, 1000]):
tstop = Model['T2']+2.*Model['DT2']
t = np.arange(int(tstop/Model['dt']))*Model['dt']
ismooth = int(smoothing/Model['dt'])
MEAN_FE, MEAN_FI, MEAN_FD = [np.zeros((len(DATA), len(t))) for i in range(3)]
for n, data in enumerate(DATA):
MEAN_FE[n, :] = gaussian_smoothing(data['POP_ACT_RecExc'], ismooth)
MEAN_FI[n, :] = gaussian_smoothing(data['POP_ACT_RecInh'], ismooth)
MEAN_FD[n, :] = gaussian_smoothing(data['POP_ACT_DsInh'], ismooth)
faff = waveform(t, Model)
cond = (t>t0)
t -= (Model['T1']-Model['DT1'])
fig3, ax = plt.subplots(1, figsize=FIGSIZE)
for vec, label, color in zip([MEAN_FE, MEAN_FI, MEAN_FD],
['$\\nu_e$', '$\\nu_i$', '$\\nu_d$'],
[Green, Red, Purple]):
plt.plot(t[cond], vec.mean(axis=0)[cond], color=color, label=label, lw=3)
plt.fill_between(t[cond],
vec.mean(axis=0)[cond]-vec.std(axis=0)[cond],
vec.mean(axis=0)[cond]+vec.std(axis=0)[cond],
color=color, alpha=.5)
ax.legend(frameon=False)
set_plot(ax, yticks=YTICKS, xticks=XTICKS,
ylabel='rate (Hz)', xlabel='time (ms)')
return fig3
def compute_relationship_smooth_and_plot(cbins,
pop_hist,
num_hist,
ax,
Nsmooth=10):
x, y, sy = [], [], []
for xx, ph, N in zip(cbins, pop_hist, num_hist):
if len(ph) > 1:
x.append(xx)
y.append(np.sum(np.array(ph) * np.array(N) / np.sum(N)))
sy.append(
np.sqrt(
np.sum(
(np.array(ph) - y[-1])**2 * np.array(N) / np.sum(N))))
xx, yy, ss = np.linspace(np.min(x), np.max(x),
int(Nsmooth / 2 * len(x))), np.zeros(
int(Nsmooth / 2 * len(x))), np.zeros(
int(Nsmooth / 2 * len(x)))
for i in range(len(xx)):
i0 = np.argmin((xx[i] - x)**2)
yy[i], ss[i] = y[i0], sy[i0]
yy, ss = gaussian_smoothing(yy, Nsmooth), gaussian_smoothing(ss, Nsmooth)
ax.plot(xx, yy, 'k-', lw=1.5)
ax.fill_between(xx, yy + ss, yy - ss, color='k', alpha=.5, lw=0)
def conductance_time_course(DATA, Model, t0=400., smoothing=10,
FIGSIZE=(4,2),
YTICKS=[0, 4, 8], XTICKS=[-400, 0, 400, 800]):
fig2, ax = plt.subplots(1, figsize=FIGSIZE)
tstop = Model['T2']+2.*Model['DT2']
t = np.arange(int(tstop/Model['dt']))*Model['dt']
ismooth = int(smoothing/Model['dt'])
MEAN_GE, STD_GE = np.zeros((len(DATA), len(t))), np.zeros((len(DATA), len(t)))
MEAN_GI, STD_GI = np.zeros((len(DATA), len(t))), np.zeros((len(DATA), len(t)))
for n in range(len(DATA)):
data = DATA[n].copy()
# smoothing conductances
for i, gsyn in enumerate(data['GSYNe_RecExc']):
data['GSYNe_RecExc'][i] = gaussian_smoothing(gsyn, ismooth)
for i, gsyn in enumerate(data['GSYNi_RecExc']):
data['GSYNi_RecExc'][i] = gaussian_smoothing(gsyn, ismooth)
MEAN_GE[n, :] = np.array(data['GSYNe_RecExc']).mean(axis=0)/Model['RecExc_Gl']
STD_GE[n, :] = np.array(data['GSYNe_RecExc']).std(axis=0)/Model['RecExc_Gl']
MEAN_GI[n, :] = np.array(data['GSYNi_RecExc']).mean(axis=0)/Model['RecExc_Gl']
STD_GI[n, :] = np.array(data['GSYNi_RecExc']).std(axis=0)/Model['RecExc_Gl']
cond = (t>t0)
t -= (Model['T1']-Model['DT1'])
ax.plot(t[cond], MEAN_GE.mean(axis=0)[cond], color=Green, lw=2, label=r'$G_{e}$')
ax.plot(t[cond], MEAN_GI.mean(axis=0)[cond], color=Red, lw=2, label=r'$G_{i}$')
ax.fill_between(t[cond],
MEAN_GE.mean(axis=0)[cond]-STD_GE.mean(axis=0)[cond],
MEAN_GE.mean(axis=0)[cond]+STD_GE.mean(axis=0)[cond],
alpha=.6, color=Green)
ax.fill_between(t[cond],
MEAN_GI.mean(axis=0)[cond]-STD_GI.mean(axis=0)[cond],
MEAN_GI.mean(axis=0)[cond]+STD_GI.mean(axis=0)[cond],
alpha=.6, color=Red)
ax.legend(frameon=False)
set_plot(ax, yticks=YTICKS, xticks=XTICKS,
ylabel='$G_{syn}$/$g_L$', xlabel='time (ms)')
return fig2, ax
def spike_train_distance(Pattern1, Pattern2, data, tau=5e-3):
"""
A similarity coef for spike trains
"""
t = np.arange(int(data['stim_duration'] / data['dt'])) * data['dt']
train1, train2 = 0 * t, 0 * t
for tspike in Pattern1:
if (tspike >= 0) and (tspike < data['stim_duration']):
train1[int(tspike / data['dt'])] = 1
for tspike in Pattern2:
if (tspike >= 0) and (tspike < data['stim_duration']):
train2[int(tspike / data['dt'])] = 1
train1 = gaussian_smoothing(train1, int(tau / data['dt']))
train2 = gaussian_smoothing(train2, int(tau / data['dt']))
std1, std2 = np.std(train1), np.std(train2)
if (std1 > 0) and (std2 > 0):
# so that corrcoef works
return np.corrcoef(train1, train2)[0, 1]
else:
return -1
def compare_two_regimes(Model, smooth=20):
for f, color in zip(['sas.zip', 'bs.zip'], [Blue, Orange]):
Model['filename'] = f
F_aff, DATA = get_scan(Model)
F_out = []
for i, data in enumerate(DATA):
cond = data['t'] > 350
Fout.append(
gaussian_smoothing(data['POP_ACT_RecExc'],
int(smooth / data['dt']))[cond].max())
ax.plot(F_aff, F_out, color=color)
set_plot(ax,
xlabel=' $\delta \\nu_a $ (Hz)',
ylabel=' $\\delta \nu_e$ (Hz)')
def analyze_scan(Model, smooth=10, filename=None):
F_aff, seeds, Model, DATA = get_scan(Model, filename=filename)
fig1, ax1 = plt.subplots(1, figsize=(4, 2.5))
plt.subplots_adjust(left=.3, bottom=.4)
fig2, ax2 = plt.subplots(1, figsize=(4, 2.5))
plt.subplots_adjust(left=.3, bottom=.4)
for i in range(len(F_aff)):
TRACES = []
for j in range(len(seeds)):
data = DATA[i * len(seeds) + j]
# TRACES.append(data['POP_ACT_RecExc'])
TRACES.append(
gaussian_smoothing(data['POP_ACT_RecExc'],
int(smooth / data['dt'])))
mean = np.array(TRACES).mean(axis=0)
std = np.array(TRACES).std(axis=0)
# smoothing
cond = data['t'] > 350
ax1.plot(data['t'][cond],
mean[cond],
color=cm.copper(i / len(F_aff)),
lw=2)
ax1.fill_between(data['t'][cond],
mean[cond] - std[cond],
mean[cond] + std[cond],
color=cm.copper(i / len(F_aff)),
alpha=.5)
ax2.plot(data['t'][cond],
data['faff'][cond],
color=cm.copper(i / len(F_aff)))
set_plot(ax1, xlabel='time (ms)', ylabel='rate (Hz)')
set_plot(ax2, xlabel='time (ms)', ylabel='rate (Hz)')
# put_list_of_figs_to_svg_fig([fig1, fig2])
return fig1, fig2
def make_single_resp_fig(F_aff,
seeds,
Model,
DATA_SA,
DATA_BA,
smoothing=30,
t0=430,
XTICKS=np.arange(4) * 250,
tstart_vis=350,
tend_vis=700,
t_after_stim_for_bsl=1400.):
fig1, ax1 = plt.subplots(1, figsize=(4, 2.5))
plt.subplots_adjust(left=.3, bottom=.4)
fig2, ax2 = plt.subplots(1, figsize=(4, 2.5))
plt.subplots_adjust(left=.3, bottom=.4)
fig3, ax3 = plt.subplots(1, figsize=(4, 2.5))
plt.subplots_adjust(left=.3, bottom=.4)
for i in range(len(F_aff)):
SA_TRACES, BA_TRACES = [], []
for j in range(len(seeds)):
data = DATA_SA[i * len(seeds) + j]
v = gaussian_smoothing(data['POP_ACT_RecExc'],
int(smoothing / Model['dt']))
SA_TRACES.append(v)
data = DATA_BA[i * len(seeds) + j]
v = gaussian_smoothing(data['POP_ACT_RecExc'],
int(smoothing / Model['dt']))
BA_TRACES.append(v)
SA_mean, SA_std = np.array(SA_TRACES).mean(
axis=0), np.array(SA_TRACES).std(axis=0)
BA_mean, BA_std = np.array(BA_TRACES).mean(
axis=0), np.array(BA_TRACES).std(axis=0)
data = DATA_SA[i * len(seeds) + j]
cond, cond2 = (data['t'] > tstart_vis) & (
data['t'] < tend_vis), data['t'] > t_after_stim_for_bsl
ax2.plot(data['t'][cond] - t0,
SA_mean[cond] - SA_mean[cond2].mean(),
color=cm.viridis(i / len(F_aff)),
lw=2)
ax2.fill_between(data['t'][cond] - t0,
SA_mean[cond] - SA_std[cond] - SA_mean[cond2].mean(),
SA_mean[cond] + SA_std[cond] - SA_mean[cond2].mean(),
color=cm.viridis(i / len(F_aff)),
alpha=.5)
ax3.plot(data['t'][cond] - t0,
BA_mean[cond] - BA_mean[cond2].mean(),
color=cm.viridis(i / len(F_aff)),
lw=2)
ax3.fill_between(data['t'][cond] - t0,
BA_mean[cond] - BA_std[cond] - BA_mean[cond2].mean(),
BA_mean[cond] + BA_std[cond] - BA_mean[cond2].mean(),
color=cm.viridis(i / len(F_aff)),
alpha=.5)
ax1.plot(data['t'][cond] - t0,
data['faff'][cond] - data['faff'][cond2].mean(),
color=cm.viridis(i / len(F_aff)),
lw=3)
set_plot(ax1,
xlabel='time (ms)',
ylabel='$\delta \\nu_a$ (Hz)',
xticks=XTICKS)
set_plot(ax2,
xlabel='time (ms)',
ylabel='$\delta \\nu_e$ (Hz)',
xticks=XTICKS)
set_plot(ax3,
xlabel='time (ms)',
ylabel='$\delta \\nu_e$ (Hz)',
xticks=XTICKS)
return fig1, fig2, fig3
parser.add_argument("-a", "--analyze", help="perform analysis of params space",
action="store_true")
parser.add_argument("-rm", "--run_multiple_seeds", help="run with multiple seeds",
action="store_true")
parser.add_argument("--debug", help="debug", action="store_true")
args = parser.parse_args()
Model = vars(args)
if args.analyze:
analyze_sim(Model)
ntwk.show()
elif args.run_multiple_seeds:
Model['filename'] = 'sparse_vs_balanced/data/time_varying_input.h5'
run_scan(Model)
elif args.debug:
Model, seeds, DATA = get_scan({}, filename='sparse_vs_balanced/data/time_varying_input.zip')
hist_of_Vm_pre_post(DATA, Model, nbin=30)
# one_Vm_fig(DATA[0], Model)
ntwk.show()
else:
Model['filename'] = 'data/time_varying_input_debug.h5'
NTWK = run_sim(Model)
Nue, Nui, Nud = NTWK['POP_ACT'][0].rate/ntwk.Hz, NTWK['POP_ACT'][1].rate/ntwk.Hz,\
NTWK['POP_ACT'][2].rate/ntwk.Hz
ntwk.plot(NTWK['POP_ACT'][0].t/ntwk.ms, gaussian_smoothing(Nue,int(20./0.1)))
ntwk.plot(NTWK['POP_ACT'][0].t/ntwk.ms, gaussian_smoothing(Nui,int(20./0.1)))
ntwk.plot(NTWK['POP_ACT'][0].t/ntwk.ms, gaussian_smoothing(Nud,int(20./0.1)))
ntwk.show()
if __name__ == '__main__':
from data_analysis.processing.signanalysis import gaussian_smoothing
# import the model defined in root directory
sys.path.append(str(pathlib.Path(__file__).resolve().parents[2]))
from model import *
args = parser.parse_args()
Model = vars(args)
if Model['p_AffExc_DsInh'] == 0.:
print(
'---------------------------------------------------------------------------'
)
print(
'to run the 3 pop model, you need to set an afferent connectivity proba !'
)
print(
'e.g run: \n python running_3pop_model.py --p_AffExc_DsInh 0.1'
)
print(
'---------------------------------------------------------------------------'
)
else:
NTWK = run_3pop_ntwk_model(Model, tstop=400)
Nue = NTWK['POP_ACT'][0].rate / ntwk.Hz
ntwk.plot(NTWK['POP_ACT'][0].t / ntwk.ms,
gaussian_smoothing(Nue, int(20. / 0.1)))
ntwk.show()
def load_data(
fn,
args,
fraction_extent_of_data=[0., 1.], # for cross-validation
verbose=False,
with_spiking_activity=True,
chosen_window_only=True,
full_processing=False,
with_Vm_low_freq=False):
if verbose:
print('analyzing :', fn)
with open(fn.replace(s1, s2).replace('abf', 'json')) as f:
props = json.load(f)
if chosen_window_only:
t0, t1 = np.float(props['t0']), np.float(props['t1'])
else:
t0, t1 = 0, np.inf
raw_data = load_file(fn, zoom=[t0, t1])
data_full = {
't': raw_data[0] - raw_data[0][0],
'Vm': raw_data[1][1],
'Extra': raw_data[1][0]
}
# in case
cond = (np.arange(len(data_full['t']))>=int(len(data_full['t'])*fraction_extent_of_data[0])) &\
(np.arange(len(data_full['t']))<=int(len(data_full['t'])*fraction_extent_of_data[1]))
data = {
't': data_full['t'][cond],
'Vm': data_full['Vm'][cond],
'Extra': data_full['Extra'][cond],
'name': fn.split(os.path.sep)[-1],
'filename': fn
}
data['dt'] = data['t'][1] - data['t'][0]
if 'offset' in props:
data['Vm'] += float(props['offset'])
isubsampling = int(args.subsampling_period / data['dt'])
data['sbsmpl_Vm'] = data['Vm'][::isubsampling][:-1]
data['sbsmpl_Extra'] = data['Extra'][::isubsampling][:-1]
data['sbsmpl_t'] = data['t'][::isubsampling][:-1]
data['sbsmpl_dt'] = data['dt'] * isubsampling
if full_processing:
# compute the pLFP
if verbose:
print('processing LFP')
functions.preprocess_LFP(data,
freqs=np.linspace(args.f0 / args.w0,
args.f0 * args.w0,
args.wavelet_number),
new_dt=args.subsampling_period,
percentile_for_p0=args.percentile_for_p0,
smoothing=args.T0)
data['pLFP'] = data['pLFP'][:min(
[len(data['pLFP']), len(data['sbsmpl_t'])])]
# compute the Network State Index
if verbose:
print('computing NSI')
functions.compute_Network_State_Index(
data,
freqs=np.linspace(args.delta_band[0], args.delta_band[1],
8), # freqs in delta band
Tstate=args.Tstate,
Var_criteria=data['p0'], # HERE TAKING NOISE AS CRITERIA !!!
alpha=args.alpha,
T_sliding_mean=args.T_sliding_mean,
with_Vm_low_freq=with_Vm_low_freq)
# extract delta and gamma power from LFP
if verbose:
print('computing delta and gamma')
functions.compute_delta_and_gamma(data, args)
# MUA from extracellular signal
if with_spiking_activity:
if verbose:
print('computing MUA, spikes and FR')
data['MUA'] = gaussian_smoothing(\
np.abs(butter_bandpass_filter(data['Extra'],\
args.MUA_band[0], args.MUA_band[1], 1./data['dt'], order=5)),\
int(args.MUA_smoothing/data['dt']))
data['sbsmpl_MUA'] = 1e-3 * data['MUA'][::int(
args.subsampling_period / data['dt'])][:-1] # in uV
# Spike times from Vm
data['tspikes'] = data['t'][np.argwhere(
(data['Vm'][:-1] <= args.spike_threshold)
& (data['Vm'][1:] > args.spike_threshold)).flatten()]
Vpeaks = []
for tt in data['tspikes']:
Vpeaks.append(
np.max(data['Vm'][(data['t'] > tt - 5e-3)
& (data['t'] < tt + 5e-3)])
) # max in Vm surrouding spike time
data['Vpeak_spikes'] = np.array(Vpeaks)
data['sbsmpl_FR'] = np.histogram(
data['tspikes'], bins=data['sbsmpl_t'])[0] / data['sbsmpl_dt']
return data