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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,121 @@ | ||
| ################################################### | ||
| ### validation_microcircuit ### | ||
| ### a modification of the microcircuit.py ### | ||
| ################################################### | ||
|
|
||
| import os | ||
| import sys | ||
| from sim_params import simulator_params, system_params | ||
| sys.path.append(system_params['backend_path']) | ||
| sys.path.append(system_params['pyNN_path']) | ||
| from network_params import * | ||
| # import logging # TODO! Remove if it runs without this line | ||
| import pyNN | ||
| import time | ||
| from neo.io import PyNNTextIO | ||
| import plotting | ||
|
|
||
|
|
||
| # prepare simulation | ||
| #logging.basicConfig() # TODO! Remove if it runs without this line | ||
| simulator = simulator_params.keys()[0] | ||
| exec('import pyNN.%s as sim' % simulator) | ||
| sim.setup(**simulator_params[simulator]) | ||
| import network | ||
|
|
||
| # Uncomment the two lines below when networkunit is installed | ||
| #import sciunit | ||
| #from networkunit.capabilities import ProducesSpikeTrains | ||
|
|
||
| # ===================SciUnit Interface===================== | ||
|
|
||
| # Uncomment the two lines below when networkunit is installed | ||
| #class Potjans2014Microcircuit( sciunit.Model, | ||
| # ProducesSpikeTrains ): | ||
| # Comment the line below when networkunit is installed | ||
| class Potjans2014Microcircuit(): | ||
| ''' | ||
| Use case: | ||
| ''' | ||
| def __init__(self): | ||
| # prepare simulation | ||
| #exec('import pyNN.%s as sim' % simulator) | ||
| sim.setup(**simulator_params[simulator]) | ||
|
|
||
| # The network takes a good amount of time so rather than make the user | ||
| # wait to produce some capability it is better to create the network | ||
| # when the capability is evoked | ||
| def create_network(self): | ||
| # create network | ||
| start_netw = time.time() | ||
| self.n = network.Network(sim) | ||
| self.n.setup(sim) | ||
| end_netw = time.time() | ||
| if sim.rank() == 0 : | ||
| print('Creating the network took %g s' % (end_netw - start_netw,)) | ||
|
|
||
| def simulate(self): | ||
| # simulate | ||
| if sim.rank() == 0 : | ||
| print("Simulating...") | ||
| start_sim = time.time() | ||
| t = sim.run(simulator_params[simulator]['sim_duration']) | ||
| end_sim = time.time() | ||
| if sim.rank() == 0 : | ||
| print('Simulation took %g s' % (end_sim - start_sim,)) | ||
|
|
||
| def write_spiketrains(self): | ||
| start_writing = time.time() | ||
| for layer in self.n.pops : | ||
| for pop in self.n.pops[layer] : | ||
| io = PyNNTextIO(filename=system_params['output_path'] \ | ||
| + "/spikes_" + layer \ | ||
| + '_' + pop \ | ||
| + '_' + str(sim.rank()) \ | ||
| + ".txt") | ||
| spikes = self.n.pops[layer][pop].get_data('spikes', | ||
| gather=False) | ||
| for segment in spikes.segments : | ||
| io.write_segment(segment) | ||
| if record_v : | ||
| io = PyNNTextIO(filename=system_params['output_path'] \ | ||
| + "/vm_" + layer \ | ||
| + '_' + pop \ | ||
| + '_' + str(sim.rank()) \ | ||
| + ".txt") | ||
| vm = self.n.pops[layer][pop].get_data('v', | ||
| gather=False) | ||
| for segment in vm.segments : | ||
| try : | ||
| io.write_segment(segment) | ||
| except AssertionError : | ||
| pass | ||
| end_writing = time.time() | ||
| print("Writing data took %g s" % (end_writing - start_writing,)) | ||
|
|
||
| def plot_and_save(self): | ||
| if create_raster_plot and sim.rank() == 0 : | ||
| # Numbers of neurons from which spikes were recorded | ||
| n_rec = [[0] * n_pops_per_layer] * n_layers | ||
| for layer, i in layers.items() : | ||
| for pop, j in pops.items() : | ||
| if record_fraction: | ||
| n_rec[i][j] = round(N_full[layer][pop] * N_scaling * frac_record_spikes) | ||
| else: | ||
| n_rec[i][j] = n_record | ||
| plotting.show_raster_bars(raster_t_min, raster_t_max, n_rec, | ||
| frac_to_plot, system_params['output_path'] + '/') | ||
|
|
||
| def create_results_directory(self): | ||
| current_directory = os.getcwd() | ||
| build_path = current_directory + os.sep + "results" | ||
| if not os.path.exists("results"): | ||
| os.makedirs(build_path) | ||
|
|
||
| def produce_spiketrains(self): | ||
| self.create_network() | ||
| self.simulate() | ||
| self.create_results_directory() | ||
| self.write_spiketrains() | ||
| sim.end() | ||
| print ("The model " + self.__class__.__name__ + " produces_spiketrains.") |
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