def test_Generic2D(self):
from tvb.simulator.models.oscillator import Generic2dOscillator
from tvb.simulator._opencl.cl_models import CL_Generic2D
self.validate(Generic2dOscillator(), CL_Generic2D(), CL_Generic2D.n_states)
def generate_region_demo_data(file_path=os.path.join(os.getcwd(), "demo_data_region_16s_2048Hz.npy")):
"""
Generate 16 seconds of 2048Hz data at the region level, stochastic integration.
``Run time``: approximately 4 minutes (workstation circa 2010)
``Memory requirement``: < 1GB
``Storage requirement``: ~ 19MB
.. moduleauthor:: Stuart A. Knock <*****@*****.**>
"""
##----------------------------------------------------------------------------##
##- Perform the simulation -##
##----------------------------------------------------------------------------##
LOG.info("Configuring...")
# Initialise a Model, Coupling, and Connectivity.
pars = {'a': np.array([1.05]),
'b': np.array([-1]),
'c': np.array([0.0]),
'd': np.array([0.1]),
'e': np.array([0.0]),
'f': np.array([1 / 3.]),
'g': np.array([1.0]),
'alpha': np.array([1.0]),
'beta': np.array([0.2]),
'tau': np.array([1.25]),
'gamma': np.array([-1.0])}
oscillator = Generic2dOscillator(**pars)
white_matter = Connectivity.from_file()
white_matter.speed = np.array([4.0])
white_matter_coupling = Linear(a=np.array([0.033]))
# Initialise an Integrator
hiss = Additive(nsig=np.array([2 ** -10, ]))
heunint = HeunStochastic(dt=0.06103515625, noise=hiss)
# Initialise a Monitor with period in physical time
what_to_watch = TemporalAverage(period=0.48828125) # 2048Hz => period=1000.0/2048.0
# Initialise a Simulator -- Model, Connectivity, Integrator, and Monitors.
sim = Simulator(model=oscillator, connectivity=white_matter,
coupling=white_matter_coupling,
integrator=heunint, monitors=[what_to_watch])
sim.configure()
# Perform the simulation
tavg_data = []
tavg_time = []
LOG.info("Starting simulation...")
for tavg in sim(simulation_length=16000):
if tavg is not None:
tavg_time.append(tavg[0][0]) # TODO:The first [0] is a hack for single monitor
tavg_data.append(tavg[0][1]) # TODO:The first [0] is a hack for single monitor
LOG.info("Finished simulation.")
##----------------------------------------------------------------------------##
##- Save the data to a file -##
##----------------------------------------------------------------------------##
# Make the list a numpy.array.
LOG.info("Converting result to array...")
TAVG = np.array(tavg_data)
# Save it
LOG.info("Saving array to %s..." % file_path)
np.save(file_path, TAVG)
LOG.info("Done.")