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.
sens = sensors.SensorsInternal(load_default=True)
oscillator = models.Generic2dOscillator()
white_matter = connectivity.Connectivity(load_default=True)
white_matter.speed = numpy.array([4.0])
white_matter_coupling = coupling.Linear(a=0.014)
In [5]:
#Initialise an Integrator
heunint = integrators.HeunDeterministic(dt=2 ** -4)
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#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)
mon_seeg = monitors.SEEG(period=2 ** -2)
mon_seeg.sensors = sensors.SensorsInternal(load_default=True)
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#Bundle them
what_to_watch = (mon_tavg, mon_savg, mon_eeg, mon_seeg)
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#Initialise a surface
local_coupling_strength = numpy.array([2 ** -10])
default_cortex = Cortex(load_default=True)
default_cortex.coupling_strength = local_coupling_strength
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#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]:
#Perform the simulation
tavg_data = []
tavg_time = []
savg_data = []
savg_time = []
eeg_data = []
eeg_time = []
seeg_data = []
seeg_time = []
for tavg, savg, eeg, seeg 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])
if not seeg is None:
seeg_time.append(seeg[0])
seeg_data.append(seeg[1])
LOG.info("finished simulation.")
In [12]:
#Make the lists numpy.arrays for easier use.
TAVG = numpy.array(tavg_data)
SAVG = numpy.array(savg_data)
EEG = numpy.array(eeg_data)
SEEG = numpy.array(seeg_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")
#Plot SEEG time series
figure(5)
color_idx = numpy.linspace(0, 1, SEEG.shape[2])
for i in color_idx:
plot(seeg_time, SEEG[:, 0, :, 0], color=cm.cool(i), lw=3, alpha=0.2)
title("SEEG")
#Show them
show()
#Surface movie, requires mayavi.mlab
if IMPORTED_MAYAVI:
st = surface_timeseries(sim.surface, TAVG[:, 0, :, 0])