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
d = DataStorage.open(output_fname, 'a')
if "trials" not in d.keys():
d['trials'] = []
seed_gen = TrialSeedGenerator(int(options.master_seed))
overalT = 0.
###############################################################################
for trial_idx in range(len(d['trials']), options.ntrials):
print("\n\t\tStarting trial no. {0}\n".format(trial_idx))
seed_gen.set_generators(trial_idx)
d['master_seed'] = int(options.master_seed)
d['invalidated'] = 1
try:
ei_net = BasicGridCellNetwork(options, simulationOpts=None)
const_v = [0.0, 0.0]
ei_net.setConstantVelocityCurrent_e(const_v)
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,
try:
seed_gen.check_master_seed(d['master_seed'], int(o.master_seed))
except ValueError as e:
d.close()
raise e
overalT = 0.
stop = False
###############################################################################
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),
rec_spikes_probabilistic=o.rec_spikes_probabilistic)
if o.velON and not o.constantPosition:
ei_net.setVelocityCurrentInput_e()
if o.pcON:
# This also sets the start PCs
posIn = ConstPosInputs(0, 0) if o.constantPosition else None
ei_net.setPlaceCells(posIn=posIn)
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 "
