def _test_integrator(self, Integrator, delays=False):
dt = 0.01
if issubclass(Integrator, IntegratorStochastic):
integrator = Integrator(dt=dt, noise=Additive(nsig=np.r_[dt]))
integrator.noise.dt = integrator.dt
else:
integrator = Integrator(dt=dt)
if isinstance(integrator, (Identity, IdentityStochastic)):
self._test_mvar(integrator, delays=delays)
else:
self._test_mpr(integrator, delays=delays)
def _test_integrator(self, Integrator):
if issubclass(Integrator, IntegratorStochastic):
integrator = Integrator(dt=0.1, noise=Additive(nsig=np.r_[0.01]))
integrator.noise.dt = integrator.dt
else:
integrator = Integrator(dt=0.1)
nn = 76
state = np.random.randn(2, 1, nn)
weights = np.random.randn(nn, nn)
cx = weights.dot(state[:, 0].T).T
assert cx.shape == (2, nn)
expected = integrator.scheme(state[:, 0], self._test_dfun, cx, 0, 0)
actual = state.copy()
np.random.seed(42)
self._eval_cg(integrator, actual, weights)
np.testing.assert_allclose(actual[:, 0], expected)
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.")