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
'''Main simulation run: Only export E and I connections.'''
from __future__ import absolute_import, print_function, division
from grid_cell_model.models.parameters import getOptParser
from grid_cell_model.models.gc_net_nest import BasicGridCellNetwork
from grid_cell_model.models.seeds import TrialSeedGenerator
from simtools.storage import DataStorage
parser = getOptParser()
(o, args) = parser.parse_args()
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()
parser.add_argument("--bcON",
type=int,
choices=[0, 1],
default=0,
help="Border cell input ON?")
(o, args) = parser.parse_args()
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 = [-o.Ivel, 0.0]
ei_net = ConstantVelocityNetwork(o, simulationOpts=None, vel=const_v)
d['net_params'] = ei_net.getNetParams() # Common settings will stay
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
data['stateMonF_e'] = [data['stateMonF_e'][0]]
return data
parser = getOptParser()
(options, args) = parser.parse_args()
output_fname = "{0}/{1}job{2:05}_output.h5".format(options.output_dir,
options.fileNamePrefix,
options.job_num)
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)
logger.info('bumpCurrentSlope is NaN. Not performing the simulation')
exit(0)
else:
logger.info("bumpCurrentSlope: {0}".format(o.bumpCurrentSlope))
stateMonParams = {'start': o.time - o.stateMonDur}
nrec_spikes_e = None # all neurons
nrec_spikes_i = o.nrec_spikes_i
output_fname = "{0}/{1}job{2:05}_output.h5".format(o.output_dir,
o.fileNamePrefix, o.job_num)
d = DataStorage.open(output_fname, 'a')
if ("trials" not in d.keys()):
d['trials'] = []
seed_gen = TrialSeedGenerator(int(o.master_seed))
if len(d['trials']) == 0:
d['master_seed'] = int(o.master_seed)
else:
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)
from grid_cell_model.models.gc_net_nest import ConstantVelocityNetwork
from grid_cell_model.models.seeds import TrialSeedGenerator
from simtools.storage import DataStorage
parser = getOptParser()
(o, args) = parser.parse_args()
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 = ConstantVelocityNetwork(o, simulationOpts=None, vel=const_v)
d['net_params'] = ei_net.getNetParams() # Common settings will stay
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
len(trial['IvelData']) * o.dIvel, o.dIvel)
d.flush()
(o, args) = parser.parse_args()
o.master_seed = int(o.master_seed)
output_fname = "{0}/{1}job{2:05}_output.h5".format(o.output_dir,
o.fileNamePrefix, o.job_num)
d = DataStorage.open(output_fname, 'a')
if ("trials" not in d.keys()):
d['trials'] = []
# Initialise seeds and check their consistency with previously saved data
seed_gen = TrialSeedGenerator(o.master_seed)
if len(d['trials']) == 0:
d['master_seed'] = o.master_seed
else:
try:
seed_gen.check_master_seed(d['master_seed'], o.master_seed)
except ValueError as e:
d.close()
raise e
overalT = 0.
oldNTrials = len(d['trials'])
################################################################################
for trial_idx in range(o.ntrials):
print("\n\t\tStarting/appending to trial no. {0}\n".format(trial_idx))
if 'IvelVec' not in trial.keys() and 'IvelData' in trial.keys():
logger.info("Data present, but IvelVec is missing. Fixing...")
trial['IvelVec'] = np.arange(.0, len(trial['IvelData'])*o.dIvel, o.dIvel)
d.flush()
(o, args) = parser.parse_args()
output_fname = "{0}/{1}job{2:05}_output.h5".format(o.output_dir,
o.fileNamePrefix, o.job_num)
d = DataStorage.open(output_fname, 'a')
if ("trials" not in d.keys()):
d['trials'] = []
# Initialise seeds and check their consistency with previously saved data
seed_gen = TrialSeedGenerator(int(o.master_seed))
if len(d['trials']) == 0:
d['master_seed'] = int(o.master_seed)
else:
try:
seed_gen.check_master_seed(d['master_seed'], int(o.master_seed))
except ValueError as e:
d.close()
raise e
overalT = 0.
oldNTrials = len(d['trials'])
################################################################################
for trial_idx in range(o.ntrials):
print("\n\t\tStarting/appending to trial no. {0}\n".format(trial_idx))
if trial_idx >= oldNTrials: # Create new trial
'''Main simulation run: Only export E and I connections.'''
from __future__ import absolute_import, print_function, division
from grid_cell_model.models.parameters import getOptParser
from grid_cell_model.models.gc_net_nest import BasicGridCellNetwork
from grid_cell_model.data_storage import DataStorage
from grid_cell_model.models.seeds import TrialSeedGenerator
parser = getOptParser()
(o, args) = parser.parse_args()
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()
logger.info("bumpCurrentSlope: {0}".format(o.bumpCurrentSlope))
stateMonParams = {
'start' : o.time - o.stateMonDur
}
nrec_spikes_e = None # all neurons
nrec_spikes_i = o.nrec_spikes_i
output_fname = "{0}/{1}job{2:05}_output.h5".format(o.output_dir,
o.fileNamePrefix, o.job_num)
d = DataStorage.open(output_fname, 'a')
if ("trials" not in d.keys()):
d['trials'] = []
seed_gen = TrialSeedGenerator(int(o.master_seed))
if len(d['trials']) == 0:
d['master_seed'] = int(o.master_seed)
else:
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)