def build_simulator(self, n=4):
self.conn = numpy.zeros((n, n)) # , numpy.int32)
for i in range(self.conn.shape[0] - 1):
self.conn[i, i + 1] = 1
self.dist = numpy.r_[:n * n].reshape((n, n))
self.dist = numpy.array(self.dist, dtype=float)
self.sim = Simulator(
conduction_speed=1.0,
coupling=IdCoupling(),
surface=None,
stimulus=None,
integrator=Identity(dt=1.0),
initial_conditions=numpy.ones((n * n, 1, n, 1)),
simulation_length=10.0,
connectivity=Connectivity(region_labels=numpy.array(['']),
weights=self.conn,
tract_lengths=self.dist,
speed=numpy.array([1.0]),
centres=numpy.array([0.0])),
model=Sum(),
monitors=(Raw(), ),
)
self.sim.configure()
def _prep_sim(self, coupling) -> Simulator:
"Prepare simulator for testing a coupling function."
con = Connectivity.from_file()
con.weights[:] = 1.0
# con = Connectivity(
# region_labels=np.array(['']),
# weights=con.weights[:5][:,:5],
# tract_lengths=con.tract_lengths[:5][:,:5],
# speed=np.array([10.0]),
# centres=np.array([0.0]))
sim = Simulator(connectivity=con,
model=LinearModel(gamma=np.r_[0.0]),
coupling=coupling,
integrator=Identity(dt=1.0),
monitors=[Raw()],
simulation_length=0.5)
sim.configure()
return sim