plt.figure()
plt.plot(1e3 * stc.times, stc.data[pick_vertex, :].T * 1e9, 'ro-')
plt.xlabel('time (ms)')
plt.ylabel('%s value (nAM)' % method)
plt.xlim((0, 150))
plt.axhline(0)
plt.show()
###############################################################################
# Now, let us try to simulate the same with MNE-neuron
import os.path as op
import hnn_core
from hnn_core import simulate_dipole, read_params, Network
hnn_core_root = op.dirname(hnn_core.__file__)
params_fname = op.join(hnn_core_root, 'param', 'N20.json')
params = read_params(params_fname)
net = Network(params)
dpl = simulate_dipole(net, n_trials=1)
import matplotlib.pyplot as plt
fig, axes = plt.subplots(2, 1, sharex=True, figsize=(6, 6))
dpl[0].plot(ax=axes[0], show=False)
net.plot_input(ax=axes[1])
net.spikes.plot()
net.plot_cells()
###############################################################################
# Now let's simulate the dipole, running 2 trials with the Joblib backend.
# To run them in parallel we could set n_jobs to equal the number of trials.
from hnn_core import JoblibBackend
with JoblibBackend(n_jobs=1):
dpls = simulate_dipole(net, n_trials=2)
###############################################################################
# and then plot it
import matplotlib.pyplot as plt
fig, axes = plt.subplots(2, 1, sharex=True, figsize=(6, 6))
plot_dipole(dpls, ax=axes[0], layer='agg', show=False)
net.plot_input(ax=axes[1])
###############################################################################
# Also, we can plot the spikes and write them to txt files.
# Note that we can use formatting syntax to specify the filename pattern
# with which each trial will be written. To read spikes back in, we can use
# wildcard expressions.
net.spikes.plot()
with tempfile.TemporaryDirectory() as tmp_dir_name:
net.spikes.write(op.join(tmp_dir_name, 'spk_%d.txt'))
spikes = read_spikes(op.join(tmp_dir_name, 'spk_*.txt'))
spikes.plot()
###############################################################################
# Now, let us try to make the exogenous driving inputs to the cells
# synchronous and see what happens