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
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() 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()
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 ei_net.endSimulation() d['trials'].append(ei_net.getAllData())
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) 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']
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 ei_net.endSimulation() d['trials'].append(ei_net.getAllData())