#!/usr/bin/env python
# coding: utf-8

# In[1]:


get_ipython().run_line_magic('matplotlib', 'widget')
import matplotlib.pyplot as plt
import numpy
from tvb.simulator.lab import *


# # Simulate with the Jansen and Rit model. 
# 
# White noise is added to one specific state variable to emulate the external
# stochastic stimulus p(t) as described in [JansenRit_1995]

# In[2]:


jrm = models.JansenRit(mu=numpy.array([0.]), v0=numpy.array([6.]))

phi_n_scaling = (jrm.a * jrm.A * (jrm.p_max-jrm.p_min) * 0.5 )**2 / 2.
sigma         = numpy.zeros(6) 
sigma[3]      = phi_n_scaling

# the other aspects of the simulator are standard
sim = simulator.Simulator(
    model=jrm,
    connectivity=connectivity.Connectivity.from_file(),
    coupling=coupling.SigmoidalJansenRit(a=numpy.array([10.0])),
    integrator=integrators.HeunStochastic(dt=2 ** -4, noise=noise.Additive(nsig=sigma)),
    monitors=(monitors.TemporalAverage(period=2 ** -2),),
    simulation_length=1e3,
).configure()

# run it
(time, data), = sim.run()

# visualize time series
plt.figure()
plt.plot(time, data[:, 0, :, 0], 'k', alpha=0.1)
plt.title("Temporal Average")