Pynest microcircuit example

Example file to run the microcircuit.

This example uses the function GetNodes, which is deprecated. A deprecation warning is therefore issued. For details about deprecated functions, see documentation.

Import the necessary modules

import time
import numpy as np
import network
from network_params import net_dict
from sim_params import sim_dict
from stimulus_params import stim_dict

Initialize the network and pass parameters to it.

tic = time.time()
net = network.Network(sim_dict, net_dict, stim_dict)
toc = time.time() - tic
print("Time to initialize the network: %.2f s" % toc)
# Connect all nodes.
tic = time.time()
net.setup()
toc = time.time() - tic
print("Time to create the connections: %.2f s" % toc)
# Simulate.
tic = time.time()
net.simulate()
toc = time.time() - tic
print("Time to simulate: %.2f s" % toc)

Plot a raster plot of the spikes of the simulated neurons and the average spike rate of all populations. For visual purposes only spikes 100 ms before and 100 ms after the thalamic stimulus time are plotted here by default. The computation of spike rates discards the first 500 ms of the simulation to exclude initialization artifacts.

raster_plot_time_idx = np.array(
    [stim_dict['th_start'] - 100.0, stim_dict['th_start'] + 100.0]
    )
fire_rate_time_idx = np.array([500.0, sim_dict['t_sim']])
net.evaluate(raster_plot_time_idx, fire_rate_time_idx)