output_fname = "{0}/{1}job{2:05}_output.h5".format(o.output_dir,
o.fileNamePrefix, o.job_num)
d = DataStorage.open(output_fname, 'w')
seed_gen = TrialSeedGenerator(int(o.master_seed))
out = []
overalT = 0.
################################################################################
for trial_idx in range(o.ntrials):
print("\n\t\tStarting trial no. {0}\n".format(trial_idx))
seed_gen.set_generators(trial_idx)
d['master_seed'] = int(o.master_seed)
d['invalidated'] = 1
ei_net = BasicGridCellNetwork(o, simulationOpts=None)
ei_net.endConstruction()
ei_net.beginSimulation()
data = ei_net.getNetParams()
# E --> I neurons
data['g_IE'] = ei_net.getConnMatrix("E")
# I --> E neurons
data['g_EI'] = ei_net.getConnMatrix("I")
ei_net.endSimulation()
out.append(data)
constrT, simT, totalT = ei_net.printTimes()
overalT += totalT
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 "
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,
d['trials'] = []
x_off = [0, 15, -15, 15]
y_off = [0, 15, -15, -15]
overalT = 0.
stop = False
###############################################################################
seed_gen = TrialSeedGenerator(int(o.master_seed))
for trial_idx in range(o.ntrials):
seed_gen.set_generators(trial_idx) # Each trial is reproducible
d['master_seed'] = int(o.master_seed)
d['invalidated'] = 1
#const_v = [0.0, -o.Ivel]
ei_net = BasicGridCellNetwork(o, simulationOpts=None)
d['net_params'] = ei_net.getNetParams() # Common settings will stay
# turn velocity inputs on
if o.velON:
ei_net.setVelocityCurrentInput_e()
# animal position inputs (constant)
pos = ConstPosInputs(0 + x_off[trial_idx], 0 + y_off[trial_idx])
# place cells
if o.pcON:
# activate place cells (including start place cells))
ei_net.setPlaceCells()
# start place cells
if o.spcON:
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
endPos_y = [90.0, -90.0, -90.0, 90.0]
borders = zip(zip(startPos_x, startPos_y), zip(endPos_x, endPos_y))
border_dim = max(startPos_x) - min(startPos_x), max(startPos_y) - min(
startPos_y)
overalT = 0.
stop = False
###############################################################################
seed_gen = TrialSeedGenerator(int(o.master_seed))
for trial_idx in range(o.ntrials):
seed_gen.set_generators(trial_idx) # Each trial is reproducible
d['master_seed'] = int(o.master_seed)
d['invalidated'] = 1
#const_v = [0.0, -o.Ivel]
ei_net = BasicGridCellNetwork(o, simulationOpts=None)
d['net_params'] = ei_net.getNetParams() # Common settings will stay
# turn velocity inputs on
if o.velON:
ei_net.setVelocityCurrentInput_e()
# place cells
if o.pcON:
# activate place cells (including start place cells))
ei_net.setPlaceCells(distribution='box_outline', boxSize=border_dim)
elif o.spcON:
# activate start place cells only
ei_net.setStartPlaceCells(ConstPosInputs(0, 0))
else:
pass
output_fname = "{0}/{1}job{2:05}_output.h5".format(o.output_dir,
o.fileNamePrefix, o.job_num)
d = DataStorage.open(output_fname, 'w')
seed_gen = TrialSeedGenerator(o.master_seed)
out = []
overalT = 0.
################################################################################
for trial_idx in range(o.ntrials):
print("\n\t\tStarting trial no. {0}\n".format(trial_idx))
seed_gen.set_generators(trial_idx)
d['master_seed'] = o.master_seed
d['invalidated'] = 1
ei_net = BasicGridCellNetwork(o, simulationOpts=None)
ei_net.endConstruction()
ei_net.beginSimulation()
data = ei_net.getNetParams()
# E --> I neurons
data['g_IE'] = ei_net.getConnMatrix("E")
# I --> E neurons
data['g_EI'] = ei_net.getConnMatrix("I")
ei_net.endSimulation()
out.append(data)
constrT, simT, totalT = ei_net.printTimes()
overalT += totalT
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 "
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
output_fname = "{0}/{1}job{2:05}_output.h5".format(o.output_dir,
o.fileNamePrefix, o.job_num)
d = DataStorage.open(output_fname, 'w')
d['trials'] = []
overalT = 0.
stop = False
###############################################################################
seed_gen = TrialSeedGenerator(int(o.master_seed))
for trial_idx in range(o.ntrials):
seed_gen.set_generators(trial_idx) # Each trial is reproducible
d['master_seed'] = int(o.master_seed)
d['invalidated'] = 1
#const_v = [0.0, -o.Ivel]
ei_net = BasicGridCellNetwork(o, simulationOpts=None)
d['net_params'] = ei_net.getNetParams() # Common settings will stay
# turn velocity inputs on
ei_net.setVelocityCurrentInput_e()
# activate place cells (including start place cells))
ei_net.setPlaceCells()
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()