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plot_ESTIM_anim.py
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Fri, May 3, 15:53

plot_ESTIM_anim.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2016-10-11 20:35:38
# @Email: theo.lemaire@epfl.ch
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2018-09-21 16:10:53
""" Run simulations of the HH system with injected electric current,
and plot resulting dynamics. """
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import matplotlib.patches as patches
from PySONIC.neurons import *
# -------------- SIMULATION -----------------
# Create channels mechanism
neuron = CorticalIB()
for i in range(len(neuron.states_names)):
print('{}0 = {:.2f}'.format(neuron.states_names[i], neuron.states0[i]))
# Set pulse parameters
tstim = 500e-3 # s
toffset = 300e-3 # s
Amin = -20.0
Amax = 20.0
amps = np.arange(Amin, Amax + 0.5, 1.0)
nA = len(amps)
root = 'C:/Users/Theo/Documents/E-STIM output/IB/anim'
mymap = cm.get_cmap('coolwarm')
sm = plt.cm.ScalarMappable(cmap=mymap, norm=plt.Normalize(Amin, Amax))
sm._A = []
i = 0
for Astim in amps:
i += 1
# Run simulation
print('sim {}/{} ({:.2f} mA/m2, {:.0f} ms)'.format(i, nA, Astim, tstim * 1e3))
t, y, _ = neuron.simulate(Astim, tstim, toffset)
Vm = y[0, :]
# Plot membrane potential profile
fs = 12
fig, ax = plt.subplots(figsize=(10, 3.5))
ax.set_xlabel('$time\ (ms)$', fontsize=fs)
ax.set_ylabel('$V_m\ (mV)$', fontsize=fs)
ax.set_ylim(-150.0, 60.0)
ax.set_xticks([0.0, 500.0])
ax.set_yticks([-100, 50.0])
ax.locator_params(axis='y', nbins=2)
for item in ax.get_yticklabels():
item.set_fontsize(fs)
for item in ax.get_xticklabels():
item.set_fontsize(fs)
(ybottom, ytop) = ax.get_ylim()
ax.add_patch(patches.Rectangle((0.0, ybottom), tstim * 1e3, ytop - ybottom,
facecolor='gold', alpha=0.2))
ax.plot(t * 1e3, Vm, linewidth=2)
plt.tight_layout()
fig.subplots_adjust(right=0.80)
cbar_ax = fig.add_axes([0.82, 0.2, 0.02, 0.75])
fig.add_axes()
fig.colorbar(sm, cax=cbar_ax, ticks=[Astim])
cbar_ax.set_yticklabels(['{:.2f} mA/m2'.format(Astim)], fontsize=fs)
fig.savefig('{}/fig{:03d}.png'.format(root, i))
plt.close(fig)

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