def _create_sim(self, integrator=None, inhom_mmpr=False, delays=False,
run_sim=True):
mpr = MontbrioPazoRoxin()
conn = Connectivity.from_file()
if inhom_mmpr:
dispersion = 1 + np.random.randn(conn.weights.shape[0])*0.1
mpr = MontbrioPazoRoxin(eta=mpr.eta*dispersion)
conn.speed = np.r_[3.0 if delays else np.inf]
if integrator is None:
dt = 0.01
integrator = EulerDeterministic(dt=dt)
else:
dt = integrator.dt
sim = Simulator(connectivity=conn, model=mpr, integrator=integrator,
monitors=[Raw()],
simulation_length=0.1) # 10 steps
sim.configure()
if not delays:
self.assertTrue((conn.idelays == 0).all())
buf = sim.history.buffer[...,0]
# kernel has history in reverse order except 1st element 🤕
rbuf = np.concatenate((buf[0:1], buf[1:][::-1]), axis=0)
state = np.transpose(rbuf, (1, 0, 2)).astype('f')
self.assertEqual(state.shape[0], 2)
self.assertEqual(state.shape[2], conn.weights.shape[0])
if isinstance(sim.integrator, IntegratorStochastic):
sim.integrator.noise.reset_random_stream()
if run_sim:
(t,y), = sim.run()
return sim, state, t, y
else:
return sim
def main_example(tvb_sim_model,
connectivity_zip=CONFIGURED.DEFAULT_CONNECTIVITY_ZIP,
dt=0.1,
noise_strength=0.001,
simulation_length=100.0,
config=CONFIGURED):
plotter = Plotter(config)
# --------------------------------------1. Load TVB connectivity----------------------------------------------------
connectivity = Connectivity.from_file(connectivity_zip)
connectivity.configure()
plotter.plot_tvb_connectivity(connectivity)
# ----------------------2. Define a TVB simulator (model, integrator, monitors...)----------------------------------
# Create a TVB simulator and set all desired inputs
# (connectivity, model, surface, stimuli etc)
# We choose all defaults in this example
simulator = Simulator()
simulator.integrator = HeunStochastic(dt=dt)
simulator.integrator.noise.nsig = np.array(ensure_list(noise_strength))
simulator.model = tvb_sim_model
simulator.connectivity = connectivity
mon_raw = Raw(period=simulator.integrator.dt)
simulator.monitors = (mon_raw, )
# -----------------------------------3. Simulate and gather results-------------------------------------------------
# Configure the simulator with the TVB-NEST interface...
# simulator.configure(tvb_nest_interface=tvb_nest_model)
simulator.configure()
# ...and simulate!
t_start = time.time()
results = simulator.run(simulation_length=simulation_length)
print("\nSimulated in %f secs!" % (time.time() - t_start))
# -------------------------------------------6. Plot results--------------------------------------------------------
plot_results(results, simulator, None, "State Variables",
simulator.model.variables_of_interest, plotter)
return connectivity, results
