def run_network(options):
'''Run network with given `options` and return the dictionary that would be
saved to an output file.
'''
o = options
seed_gen = TrialSeedGenerator(o.master_seed)
stateMonParams = {'start': o.time - o.stateMonDur}
nrec_spikes_e = None # all neurons
nrec_spikes_i = 10
d = {}
if "trials" not in d.keys():
d['trials'] = []
overalT = 0.
################################################################################
for trial_idx in range(len(d['trials']), o.ntrials):
print("\n\t\tStarting trial no. {0}\n".format(trial_idx))
seed_gen.set_generators(trial_idx)
d['invalidated'] = 1
ei_net = BasicGridCellNetwork(o,
simulationOpts=None,
nrec_spikes=(nrec_spikes_e,
nrec_spikes_i),
stateRecParams=(stateMonParams,
stateMonParams))
if o.velON and not o.constantPosition:
ei_net.setVelocityCurrentInput_e()
posIn = ConstPosInputs(0, 0) if o.constantPosition else None
ei_net.setPlaceCells(posIn=posIn)
try:
ei_net.simulate(o.time, printTime=o.printTime)
except NESTError as e:
print("Simulation interrupted. Message: {0}".format(str(e)))
print("Trying to save the simulated data if possible...")
ei_net.endSimulation()
d['trials'].append(ei_net.getAllData())
constrT, simT, totalT = ei_net.printTimes()
overalT += totalT
print("Script total run time: {0} s".format(overalT))
################################################################################
return d
def run_network(options):
'''Run network with given `options` and return the dictionary that would be
saved to an output file.
'''
o = options
seed_gen = TrialSeedGenerator(o.master_seed)
stateMonParams = {
'start' : o.time - o.stateMonDur
}
nrec_spikes_e = None # all neurons
nrec_spikes_i = 10
d = {}
if "trials" not in d.keys():
d['trials'] = []
overalT = 0.
################################################################################
for trial_idx in range(len(d['trials']), o.ntrials):
print("\n\t\tStarting trial no. {0}\n".format(trial_idx))
seed_gen.set_generators(trial_idx)
d['invalidated'] = 1
ei_net = BasicGridCellNetwork(o, simulationOpts=None,
nrec_spikes=(nrec_spikes_e, nrec_spikes_i),
stateRecParams=(stateMonParams, stateMonParams))
if o.velON and not o.constantPosition:
ei_net.setVelocityCurrentInput_e()
posIn = ConstPosInputs(0, 0) if o.constantPosition else None
ei_net.setPlaceCells(posIn=posIn)
try:
ei_net.simulate(o.time, printTime=o.printTime)
except NESTError as e:
print("Simulation interrupted. Message: {0}".format(str(e)))
print("Trying to save the simulated data if possible...")
ei_net.endSimulation()
d['trials'].append(ei_net.getAllData())
constrT, simT, totalT = ei_net.printTimes()
overalT += totalT
print("Script total run time: {0} s".format(overalT))
################################################################################
return d
stateRecF_e = choice(ei_net.E_pop, options.gammaNSample, replace=False)
stateRecF_i = choice(ei_net.I_pop, options.gammaNSample, replace=False)
stateMonF_e_params = {
'withtime': False,
'interval': options.sim_dt * 10,
'record_from': ['I_clamp_GABA_A']
}
stateMonF_e = ei_net.getGenericStateMonitor(stateRecF_e,
stateMonF_e_params,
'stateMonF_e')
d['net_params'] = ei_net.getNetParams() # Common settings will stay
d.flush()
ei_net.simulate(options.time, printTime=options.printTime)
ei_net.endSimulation()
d['trials'].append(signal_analysis(ei_net.getAllData()))
d.flush()
constrT, simT, totalT = ei_net.printTimes()
overalT += totalT
except NESTError as e:
print("Simulation interrupted. Message: {0}".format(str(e)))
print("Trying to save the simulated data if possible...")
break
d.close()
print("Script total run time: {0} s".format(overalT))
###############################################################################
else:
# Here the start PCs must be set explicitly
ei_net.setStartPlaceCells(ConstPosInputs(0, 0))
if o.ipc_ON:
if o.constantPosition:
raise RuntimeError("Place cells connected to I cells cannot be "
"used when the constantPosition parameter is "
"ON.")
ei_net.setIPlaceCells()
d['net_params'] = ei_net.getNetParams() # Common settings will stay
d.flush()
try:
ei_net.simulate(o.time, printTime=o.printTime)
except NESTError as e:
print("Simulation interrupted. Message: {0}".format(str(e)))
print("Trying to save the simulated data if possible...")
stop = True
ei_net.endSimulation()
d['trials'].append(ei_net.getAllData())
d.flush()
constrT, simT, totalT = ei_net.printTimes()
overalT += totalT
if stop:
break
d.close()
print("Script total run time: {0} s".format(overalT))
################################################################################
ei_net.connect_border_cells_line_method(o.bc_conn_weight)
elif o.bcConnMethod == "place":
ei_net.connect_border_cells_modified_place_cell_method(
o.bc_conn_weight)
elif o.bcConnMethod == "none":
pass
try:
ei_net.simulate(o.time, printTime=o.printTime)
except NESTError as e:
print("Simulation interrupted. Message: {0}".format(str(e)))
print("Not saving the data. Trying to clean up if possible...")
stop = True
ei_net.endSimulation()
# get simulation data
sim_data = ei_net.getAllData()
# add connection matrices if selected
if o.getConnMatrices:
print("Getting connection matrices...")
sim_data['connections'] = ei_net.getConnections()
# save simulation data
d['trials'].append(sim_data)
d.flush()
constrT, simT, totalT = ei_net.printTimes()
overalT += totalT
if stop:
break
d.close()
print("Script total run time: {0} s".format(overalT))
###############################################################################
ei_net.setStartPlaceCells(ConstPosInputs(0, 0))
if o.ipc_ON:
if o.constantPosition:
raise RuntimeError("Place cells connected to I cells cannot be "
"used when the constantPosition parameter is "
"ON.")
ei_net.setIPlaceCells()
d['net_params'] = ei_net.getNetParams() # Common settings will stay
d.flush()
try:
ei_net.simulate(o.time, printTime=o.printTime)
except NESTError as e:
print("Simulation interrupted. Message: {0}".format(str(e)))
print("Trying to save the simulated data if possible...")
stop = True
ei_net.endSimulation()
d['trials'].append(ei_net.getAllData())
d.flush()
constrT, simT, totalT = ei_net.printTimes()
overalT += totalT
if stop:
break
d.close()
print("Script total run time: {0} s".format(overalT))
################################################################################
