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