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
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)
Total running time of the script: ( 0 minutes 0.000 seconds)