Demonstrate using the simulator for a surface simulation, deterministic integration.

Run time: approximately 27 seconds (workstation circa 2010). Memory requirement: ~ 1 GB



In [2]:

    
from tvb.datatypes.cortex import Cortex

from tvb.simulator.lab import *



In [3]:

    
LOG.info("Configuring...")



In [4]:

    
#Initialise a Model, Coupling, and Connectivity.
oscillator = models.Generic2dOscillator()
white_matter = connectivity.Connectivity(load_default=True)
white_matter.speed = numpy.array([4.0])

white_matter_coupling = coupling.Difference(a=0.014)



In [5]:

    
#Initialise an Integrator
heunint = integrators.HeunDeterministic(dt=2 ** -4)



In [7]:

    
#Initialise some Monitors with period in physical time
mon_tavg = monitors.TemporalAverage(period=2 ** -2)
mon_savg = monitors.SpatialAverage(period=2 ** -2)
mon_eeg = monitors.EEG(period=2 ** -2)
#Bundle them
what_to_watch = (mon_tavg, mon_savg, mon_eeg)



In [8]:

    
#Initialise a surface fully loaded
local_coupling_strength = numpy.array([2 ** -10])
default_cortex = Cortex(load_default=True)
default_cortex.coupling_strength = local_coupling_strength



In [9]:

    
#Initialise Simulator -- Model, Connectivity, Integrator, Monitors, and surface.
sim = simulator.Simulator(model=oscillator, connectivity=white_matter,
                          coupling=white_matter_coupling,
                          integrator=heunint, monitors=what_to_watch,
                          surface=default_cortex)
sim.configure()



In [10]:

    
LOG.info("Starting simulation...")
#Perform the simulation
tavg_data = []
tavg_time = []
savg_data = []
savg_time = []
eeg_data = []
eeg_time = []

for tavg, savg, eeg in sim(simulation_length=2 ** 2):
    if not tavg is None:
        tavg_time.append(tavg[0])
        tavg_data.append(tavg[1])
    
    if not savg is None:
        savg_time.append(savg[0])
        savg_data.append(savg[1])
    
    if not eeg is None:
        eeg_time.append(eeg[0])
        eeg_data.append(eeg[1])

LOG.info("finished simulation.")

Plot pretty pictures of what we just did



In [11]:

    
#Make the lists numpy.arrays for easier use.
TAVG = numpy.array(tavg_data)
SAVG = numpy.array(savg_data)
EEG = numpy.array(eeg_data)

#Plot region averaged time series
figure(3)
plot(savg_time, SAVG[:, 0, :, 0])
title("Region average")

#Plot EEG time series
figure(4)

color_idx = numpy.linspace(0, 1, EEG.shape[2])
for i in color_idx:
    plot(eeg_time, EEG[:, 0, :, 0], color=cm.cool(i), lw=3, alpha=0.2)
title("EEG")

#Show them
show()

#Surface movie, requires mayavi.malb
if IMPORTED_MAYAVI:
    st = surface_timeseries(sim.surface, TAVG[:, 0, :, 0])