'DsInh_a': 0.,
'DsInh_b': 0.,
'DsInh_tauw': 1e9,
}
if sys.argv[-1] == 'plot':
# ######################
# ## ----- Plot ----- ##
# ######################
# vision_model = ntwk.earlyVis_model(from_file='drifting-grating-data.npz')
# ps = ntwk.vision_plot(model=vision_model)
# fig0 = ps.protocol_plot()
## load file
data = ntwk.load_dict_from_hdf5('visual_input_data.h5')
print(data['iRASTER_AffExc'])
print(data['tRASTER_AffExc'])
# ## plot
fig, _ = ntwk.raster_and_Vm_plot(data, ['Exc', 'Inh', 'DsInh', 'AffExc'],
smooth_population_activity=10.)
ntwk.show()
else:
if False:
params = ntwk.vision_params.copy()
params['rf_theta'] = [3 * np.pi / 12., 5. * np.pi / 12.]
'DsInh_Vreset': -70.,
'DsInh_deltaV': 0.,
'DsInh_a': 0.,
'DsInh_b': 0.,
'DsInh_tauw': 1e9
}
if __name__ == '__main__':
import sys
sys.path.append('../..')
import main as ntwk
if sys.argv[-1] == 'plot':
## load file
data = ntwk.load_dict_from_hdf5('CellRep2019_data.h5')
print(data)
# ## plot
fig, _ = ntwk.raster_and_Vm_plot(data, smooth_population_activity=10.)
ntwk.show()
else:
import numpy as np
from analyz.processing.signanalysis import smooth
NTWK = ntwk.build_populations(Model, ['RecExc', 'RecInh', 'DsInh'],
AFFERENT_POPULATIONS=['AffExc'],
with_raster=True,
with_Vm=4,
verbose=True)
Model['p_AffExc_recInh'] = 0.2
Model['p_AffExc_pyrExc'] = 0.05
# ==> NoiseExc
Model['p_NoiseExc_recInh'] = 0.1
Model['p_NoiseExc_pyrExc'] = 0.02
Model['p_NoiseExc_dsInh'] = 0.02
Model['p_NoiseExc_oscillExc'] = 0.2
if sys.argv[-1] == 'plot':
######################
## ----- Plot ----- ##
######################
## load file
data = ntwk.load_dict_from_hdf5('mean_field_data.h5')
# ## plot
fig, _ = ntwk.activity_plots(data, smooth_population_activity=10)
ntwk.show()
elif sys.argv[-1] == 'mf':
data = ntwk.load_dict_from_hdf5('mean_field_data.h5')
tstop, dt = 1e-3 * data['tstop'], 1e-2
t = np.arange(int(tstop / dt)) * dt
DYN_SYSTEM, INPUTS = {}, {}
for rec in REC_POPS:
# --> Inhibitory population (Inh, recurrent inhibition)
'Inh_Gl': 10.,
'Inh_Cm': 200.,
'Inh_Trefrac': 3.,
'Inh_El': -60.,
'Inh_Vthre': -50.,
'Inh_Vreset': -60.,
'Inh_delta_v': 0.,
'Inh_a': 0.,
'Inh_b': 0.,
'Inh_tauw': 1e9,
}
if sys.argv[-1] == 'plot':
## load file
data = ntwk.load_dict_from_hdf5('Vogels-Abbott.h5')
print('excitatory firing activity: ',
1e3 * len(data['iRASTER_Exc']) / data['tstop'] / data['N_Exc'])
print('inhibitory firing activity: ',
1e3 * len(data['iRASTER_Inh']) / data['tstop'] / data['N_Inh'])
## plot
fig, AX = plt.subplots(2)
AX[0].plot(data['tRASTER_Exc'], data['iRASTER_Exc'], 'bo', ms=2)
AX[0].plot(data['tRASTER_Inh'], -data['iRASTER_Inh'], 'ro', ms=2)
ntwk.set_plot(AX[0], [], xticks=[], yticks=[])
for v in data['VMS_Exc']:
AX[1].plot(np.arange(len(v)) * data['dt'], v, 'k-', lw=1)
ntwk.set_plot(AX[1], xlabel='time (ms)', ylabel='Vm (mV)')
ntwk.show()
else:
'Inh_El': -60.,
'Inh_Vthre': -53.,
'Inh_Vreset': -60.,
'Inh_deltaV': 0.,
'Inh_a': 0.,
'Inh_b': 0.,
'Inh_tauw': 1e9,
}
if sys.argv[-1] == 'plot':
# ######################
# ## ----- Plot ----- ##
# ######################
## load file
data = ntwk.load_dict_from_hdf5('with_correl_drive_data.h5')
# ## plot
fig, _ = ntwk.raster_and_Vm_plot(data, smooth_population_activity=10.)
plt.show()
else:
NTWK = ntwk.build_populations(
Model,
['Exc', 'Inh'],
AFFERENT_POPULATIONS=['AffExc'],
with_raster=True,
with_Vm=4,
# with_synaptic_currents=True,
'DsInh_El': -60.,
'DsInh_Vthre': -53.,
'DsInh_Vreset': -60.,
'DsInh_deltaV': 0.,
'DsInh_a': 0.,
'DsInh_b': 0.,
'DsInh_tauw': 1e9,
}
if sys.argv[-1] == 'plot':
# ######################
# ## ----- Plot ----- ##
# ######################
## load file
data = ntwk.load_dict_from_hdf5('3pop_model_data.h5')
# ## plot
fig, _ = ntwk.activity_plots(data, smooth_population_activity=10.)
plt.show()
else:
NTWK = ntwk.build_populations(
Model,
['Exc', 'Inh', 'DsInh'],
AFFERENT_POPULATIONS=['AffExc'],
with_raster=True,
with_Vm=4,
# with_synaptic_currents=True,
# with_synaptic_conductances=True,
verbose=True)
# --> Inhibitory population (Inh, recurrent inhibition)
'Inh_Gl': 10.,
'Inh_Cm': 200.,
'Inh_Trefrac': 5.,
'Inh_El': -70.,
'Inh_Vthre': -50.,
'Inh_Vreset': -70.,
'Inh_delta_v': 0.5,
'Inh_a': 0.,
'Inh_b': 0.,
'Inh_tauw': 1e9,
}
if sys.argv[-1] == 'plot':
## load file
data = ntwk.load_dict_from_hdf5('RS-FS.h5')
print('excitatory firing activity: ',
1e3 * len(data['iRASTER_Exc']) / data['tstop'] / data['N_Exc'])
print('inhibitory firing activity: ',
1e3 * len(data['iRASTER_Inh']) / data['tstop'] / data['N_Inh'])
## plot
fig, AX = plt.subplots(2)
AX[0].plot(data['tRASTER_Exc'], data['iRASTER_Exc'], 'bo', ms=2)
AX[0].plot(data['tRASTER_Inh'], -data['iRASTER_Inh'], 'ro', ms=2)
ntwk.set_plot(AX[0], [], xticks=[], yticks=[])
for v in data['VMS_Exc']:
AX[1].plot(np.arange(len(v)) * data['dt'], v, 'k-', lw=1)
ntwk.set_plot(AX[1], xlabel='time (ms)', ylabel='Vm (mV)')
ntwk.show()
else:
'VIPInh_El': -60.,
'VIPInh_Vthre': -53.,
'VIPInh_Vreset': -60.,
'VIPInh_deltaV': 0.,
'VIPInh_a': 0.,
'VIPInh_b': 0.,
'VIPInh_tauw': 1e9,
}
if sys.argv[-1] == 'plot':
# ######################
# ## ----- Plot ----- ##
# ######################
## load file
data = ntwk.load_dict_from_hdf5('sinusoidal_input_data.h5')
data['iRASTER_L4Exc'] = data['iRASTER_PRE1']
data['tRASTER_L4Exc'] = data['tRASTER_PRE1']
# # ## plot
fig, _ = ntwk.activity_plots(
data,
POP_KEYS=['L23Exc', 'PVInh', 'SOMInh', 'VIPInh'],
COLORS=['green', 'red', 'orange', 'purple'],
smooth_population_activity=10.)
plt.show()
else:
NTWK = ntwk.build_populations(Model,
['L23Exc', 'PVInh', 'SOMInh', 'VIPInh'],
AFFERENT_POPULATIONS=['L4Exc'],
with_raster=True,
with_Vm=4,
# --> Disinhibitory population (Inh, recurrent inhibition)
'oscillExc_Gl':10., 'oscillExc_Cm':200.,'oscillExc_Trefrac':3.,
'oscillExc_El':-70., 'oscillExc_Vthre':-50., 'oscillExc_Vreset':-70., 'oscillExc_deltaV':0.,
'oscillExc_Ioscill_amp':20.*10, 'oscillExc_Ioscill_freq': 3.,
'oscillExc_a':0., 'oscillExc_b': 0., 'oscillExc_tauw':1e9,
}
if sys.argv[-1]=='plot':
# ######################
# ## ----- Plot ----- ##
# ######################
## load file
data = ntwk.load_dict_from_hdf5('rhythmic_ntwk_data.h5')
# ## plot
fig, _ = ntwk.raster_and_Vm_plot(data, smooth_population_activity=10.)
plt.show()
else:
NTWK = ntwk.build_populations(Model, ['Exc', 'Inh', 'oscillExc'],
AFFERENT_POPULATIONS=['AffExc'],
with_raster=True,
with_pop_act=True,
with_Vm=4,
# with_synaptic_currents=True,
# with_synaptic_conductances=True,
'Inh_El': -70.,
'Inh_Vthre': -50.,
'Inh_Vreset': -70.,
'Inh_deltaV': 0.5,
'Inh_a': 0.,
'Inh_b': 0.,
'Inh_tauw': 1e9,
}
if sys.argv[-1] == 'plot':
# ######################
# ## ----- Plot ----- ##
# ######################
## load file
data = ntwk.load_dict_from_hdf5('ring_ntwk_data.h5')
# ## plot
fig, _ = ntwk.raster_and_Vm_plot(data, smooth_population_activity=10.)
plt.show()
else:
NTWK = ntwk.build_populations(
Model,
['Exc', 'Inh'],
AFFERENT_POPULATIONS=['AffExc'],
with_raster=True,
with_Vm=4,
# with_synaptic_currents=True,
'Inh_Gl': 10.,
'Inh_Cm': 200.,
'Inh_Trefrac': 3.,
'Inh_El': -60.,
'Inh_Vthre': -50.,
'Inh_Vreset': -60.,
'Inh_deltaV': 0.,
'Inh_a': 0.,
'Inh_b': 0.,
'Inh_tauw': 1e9,
}
if sys.argv[-1] == 'plot':
## load file
data = ntwk.load_dict_from_hdf5('coba_LIF_data.h5')
print('excitatory firing activity: ',
1e3 * len(data['iRASTER_Exc']) / data['tstop'] / data['N_Exc'])
print('inhibitory firing activity: ',
1e3 * len(data['iRASTER_Inh']) / data['tstop'] / data['N_Inh'])
# ## plot
fig, _ = ntwk.raster_and_Vm_plot(data, smooth_population_activity=10.)
plt.show()
else:
## we build and run the simulation
NTWK = ntwk.build_populations(
Model,
['Exc', 'Inh'],
