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
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 "
"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)
#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:
# activate start place cells only
ei_net.setStartPlaceCells(pos)
# border cells
if o.bcON:
# create the border cells - "crosshair"
arena_borders = [
((0.0 + x_off[trial_idx], 90.0), (0.0 + x_off[trial_idx], -90.0)),
((-90.0, 0.0 + y_off[trial_idx]), (90.0, 0.0 + y_off[trial_idx]))
]
ei_net.create_border_cells(borders=arena_borders,
N_per_border=o.bcNum,
posIn=pos)
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
# border cells
if o.bcON:
# create the border cells
ei_net.create_border_cells(borders=borders, N_per_border=o.bcNum)
# connect border cells according to chosen method
if o.bcConnMethod == "line":
ei_net.connect_border_cells_line_method(o.bc_conn_weight)
elif o.bcConnMethod == "place":
ei_net.connect_border_cells_modified_place_cell_method(
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 "
"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)
