def test_with_proxy_bad_input(self): connectivity, coupling, integrator, monitors, sim, result, result_all = self._reference_simulation() # The modify model without proxy np.random.seed(42) init = np.concatenate((np.random.random_sample((385, 1, 76, 1)), np.random.random_sample((385, 1, 76, 1))), axis=1) np.random.seed(42) id_proxy = range(11) model = ReducedWongWangProxy(tau_s=np.random.rand(76)) synchronization_time = 1. # Initialise a Simulator -- Model, Connectivity, Integrator, and Monitors. sim_4 = CoSimulator( voi=np.array([0]), synchronization_time=synchronization_time, cosim_monitors=(RawCosim(),), proxy_inds=np.asarray(id_proxy, dtype=np.int), model=model, connectivity=connectivity, coupling=coupling, integrator=integrator, monitors=(monitors,), initial_conditions=init, ) sim_4.configure() sim_4.run() # run the first steps because the history is delayed sim_to_sync_time = int(SIMULATION_LENGTH / synchronization_time) sync_steps = int(synchronization_time / integrator.dt) result_4_all = [np.empty((0,)), np.empty((sync_steps, 2, 76, 1))] for j in range(0, sim_to_sync_time): result_4_all_step = sim_4.run( cosim_updates=[np.array([result_all[0][0][(sync_steps * j) + i] for i in range(sync_steps)]), np.ones((sync_steps, 1, len(id_proxy), 1)) * 0.7]) result_4_all[0] = np.concatenate((result_4_all[0], result_4_all_step[0][0])) result_4_all[1] = np.concatenate((result_4_all[1], result_4_all_step[0][1])) simulation_n_steps = int(SIMULATION_LENGTH / integrator.dt) # The beggining is good for rate for i in range(np.min(sim_4.connectivity.idelays[np.nonzero(sim_4.connectivity.idelays)])+1): np.testing.assert_array_equal(result_all[0][1][i][0][len(id_proxy):], result_4_all[1][i+sync_steps, 0, len(id_proxy):]) np.testing.assert_array_compare(operator.__ne__,result_all[0][1][i][0][:len(id_proxy)], result_4_all[1][i+sync_steps, 0, :len(id_proxy)]) # after the delayed impact the simulation, This create some difference for rate for i in range(np.min(sim_4.connectivity.idelays[np.nonzero(sim_4.connectivity.idelays)])+1, simulation_n_steps): diff = result_all[0][1][i][0][len(id_proxy):] - result_4_all[1][i+sync_steps, 0, len(id_proxy):] assert np.sum(diff) != 0 np.testing.assert_array_compare(operator.__ne__,result_all[0][1][i][0][:len(id_proxy)], result_4_all[1][i+sync_steps, 0, :len(id_proxy)]) # The beggining is good for S for i in range(np.min(sim_4.connectivity.idelays[np.nonzero(sim_4.connectivity.idelays)])+1): np.testing.assert_array_equal(result_all[0][1][i][1][len(id_proxy):], result_4_all[1][i+sync_steps, 1, len(id_proxy):]) np.testing.assert_array_equal(result_all[0][1][i][1][:len(id_proxy)]*np.NAN, result_4_all[1][i+sync_steps, 1, :len(id_proxy)]) # after the delayed impact the simulation, This create some difference for S for i in range(np.min(sim_4.connectivity.idelays[np.nonzero(sim_4.connectivity.idelays)])+1, simulation_n_steps): diff = result_all[0][1][i][1][len(id_proxy):] - result_4_all[1][i+sync_steps, 1, len(id_proxy):] assert np.sum(diff) != 0 np.testing.assert_array_equal(result_all[0][1][i][1][:len(id_proxy)]*np.NAN, result_4_all[1][i+sync_steps, 1, :len(id_proxy)])
def test_with_proxy_right_input(self): connectivity, coupling, integrator, monitors, sim, result, result_all = self._reference_simulation( ) # The modify model without proxy np.random.seed(42) init = np.concatenate((np.random.random_sample( (385, 1, 76, 1)), np.random.random_sample((385, 1, 76, 1))), axis=1) np.random.seed(42) id_proxy = range(11) model = ReducedWongWangProxy(tau_s=np.random.rand(76)) synchronization_time = 1.0 # Initialise a Simulator -- Model, Connectivity, Integrator, and Monitors. sim_5 = CoSimulator( voi=np.array([0]), synchronization_time=synchronization_time, cosim_monitors=(RawCosim(), ), proxy_inds=np.asarray(id_proxy, dtype=np.int), model=model, connectivity=connectivity, coupling=coupling, integrator=integrator, monitors=(monitors, ), initial_conditions=init, ) sim_5.configure() sim_5.run() # run the first steps because the history is delayed sim_to_sync_time = int(SIMULATION_LENGTH / synchronization_time) sync_steps = int(synchronization_time / integrator.dt) result_5_all = [np.empty((0, )), np.empty((sync_steps, 2, 76, 1))] for j in range(0, sim_to_sync_time): result_5_all_step = sim_5.run(cosim_updates=[ np.array([ result_all[0][0][(sync_steps * j) + i] for i in range(sync_steps) ]), np.array([ result_all[0][1][(sync_steps * j) + i][0][id_proxy] for i in range(sync_steps) ]).reshape((sync_steps, 1, len(id_proxy), 1)) ]) result_5_all[0] = np.concatenate( (result_5_all[0], result_5_all_step[0][0])) result_5_all[1] = np.concatenate( (result_5_all[1], result_5_all_step[0][1])) for i in range(int(SIMULATION_LENGTH / integrator.dt)): np.testing.assert_array_equal( result_all[0][1][i][0][len(id_proxy):], result_5_all[1][i + sync_steps, 0, len(id_proxy):]) np.testing.assert_array_equal( result_all[0][1][i][0][:len(id_proxy)], result_5_all[1][i + sync_steps, 0, :len(id_proxy)])
def test_precision_with_proxy(self): connectivity, coupling, integrator, monitors, sim, result, result_all = self._reference_simulation( self._simulation_length) # New simulator with proxy np.random.seed(42) init = np.concatenate((np.random.random_sample( (385, 1, 76, 1)), np.random.random_sample((385, 1, 76, 1))), axis=1) np.random.seed(42) model_1 = ReducedWongWangProxy(tau_s=np.random.rand(76)) synchronization_time = 1. # Initialise a Simulator -- Model, Connectivity, Integrator, and Monitors. sim_1 = CoSimulator( voi=np.array([0]), synchronization_time=synchronization_time, cosim_monitors=(RawCosim(), ), proxy_inds=np.asarray([0], dtype=np.int), model=model_1, connectivity=connectivity, coupling=coupling, integrator=integrator, monitors=(monitors, ), initial_conditions=init, ) sim_1.configure() sim_to_sync_time = int(self._simulation_length / synchronization_time) sync_steps = int(synchronization_time / integrator.dt) result_1_all = [np.empty((0, )), np.empty((sync_steps, 2, 76, 1))] sim_1.run() # run the first steps because the history is delayed for j in range(0, sim_to_sync_time): result_1_all_step = sim_1.run(cosim_updates=[ np.array([ result_all[0][0][(sync_steps * j) + i] for i in range(sync_steps) ]), np.array([ result_all[0][1][(sync_steps * j) + i][0][0] for i in range(sync_steps) ]).reshape((sync_steps, 1, 1, 1)) ]) result_1_all[0] = np.concatenate( (result_1_all[0], result_1_all_step[0][0])) result_1_all[1] = np.concatenate( (result_1_all[1], result_1_all_step[0][1])) for i in range(int(self._simulation_length / integrator.dt)): np.testing.assert_array_equal( result_all[0][1][i][0][1:], result_1_all[1][i + sync_steps, 0, 1:]) np.testing.assert_array_equal( result_all[0][1][i][0][:1], result_1_all[1][i + sync_steps, 0, :1])
def test_without_proxy(self): model, connectivity, coupling, init, integrator, monitors = self._prepare_reference_simulation() np.random.seed(42) # Initialise a Simulator -- Model, Connectivity, Integrator, and Monitors. sim = CoSimulator( voi=np.array([0]), synchronization_time=1., cosim_monitors=(RawCosim(),), proxy_inds=np.array([], dtype=np.int), model=model, connectivity=connectivity, coupling=coupling, integrator=integrator, monitors=(monitors,), initial_conditions=init, ) with pytest.raises(ValueError): sim.configure()
def test_without_proxy_coupling(self): connectivity, coupling, integrator, monitors, sim, result, result_all = self._reference_simulation( ) # The modify model without proxy np.random.seed(42) init = np.concatenate((np.random.random_sample( (385, 1, 76, 1)), np.random.random_sample((385, 1, 76, 1))), axis=1) model = ReducedWongWangProxy(tau_s=np.random.rand(76)) synchronization_time = 1.0 # Initialise a Simulator -- Model, Connectivity, Integrator, and Monitors. sim_6 = CoSimulator( voi=np.array([0]), synchronization_time=synchronization_time, cosim_monitors=(CosimCoupling(coupling=coupling), ), proxy_inds=np.asarray([0], dtype=np.int), model=model, connectivity=connectivity, coupling=coupling, integrator=integrator, monitors=(monitors, ), initial_conditions=init, ) sim_6.configure() result_2_all = sim_6.run( )[0][1][:, 0, 0, 0] # run the first steps because the history is delayed sim_to_sync_time = int(SIMULATION_LENGTH / synchronization_time) sync_steps = int(synchronization_time / integrator.dt) with pytest.raises(ValueError): coupling_future = sim_6.loop_cosim_monitor_output(sync_steps, 1) coupling_future = sim_6.loop_cosim_monitor_output() for i in range(sim_to_sync_time): result_2 = sim_6.run()[0][1][:, 0, 0, 0] np.testing.assert_array_equal( result[i * sync_steps:(i + 1) * sync_steps] * np.NAN, result_2) assert np.sum(np.isnan( sim_6.loop_cosim_monitor_output()[0][1])) == 0
def tvb_init(parameters, time_synchronize, initial_condition): """ To initialise Nest and to create the connectome model :param parameters : (model,connectivity,coupling,integrator) : parameter for the simulation without monitor :param time_synchronize : the time of synchronization for the proxy :param initial_condition: the initial condition of the model :return: sim : the TVB simulator, (weights_in,delay_in): the connectivity of disconnect region input (weights_out,delay_out): the connectivity of disconnect region ouput """ model, connectivity, coupling, integrator, id_proxy = parameters # Initialise some Monitors with period in physical time monitors = (lab.monitors.Raw(variables_of_interest=np.array(0)),) # Initialise a Simulator -- Model, Connectivity, Integrator, and Monitors. if len(id_proxy) == 0: sim = lab.simulator.Simulator( model=model, connectivity=connectivity, coupling=coupling, integrator=integrator, monitors=monitors, initial_conditions=initial_condition ) else: # Initialise a Simulator -- Model, Connectivity, Integrator, and Monitors. sim = CoSimulator( voi=np.array([0]), synchronization_time=time_synchronize, cosim_monitors=(RawCosim(),), proxy_inds=np.asarray(id_proxy, dtype=np.int), model=model, connectivity=connectivity, coupling=coupling, integrator=integrator, monitors=monitors, initial_conditions=initial_condition ) sim.configure() return sim
def test_monitor(self): connectivity, coupling, integrator, monitors, sim, result, result_all = self._reference_simulation( self._simulation_length) # New simulator with proxy np.random.seed(42) init = np.concatenate((np.random.random_sample( (385, 1, 76, 1)), np.random.random_sample((385, 1, 76, 1))), axis=1) np.random.seed(42) model_1 = ReducedWongWangProxy(tau_s=np.random.rand(76)) # Initialise a Simulator -- Model, Connectivity, Integrator, and Monitors. synchronization_time = 1.0 sim_1 = CoSimulator( voi=np.array([0]), synchronization_time=synchronization_time, cosim_monitors=(RawCosim(), RawVoiCosim(variables_of_interest=np.array([0])), RawDelayed(), RawVoiDelayed(variables_of_interest=np.array([0])), CosimCoupling(coupling=coupling), CosimCoupling(coupling=coupling, variables_of_interest=np.array([0 ]))), proxy_inds=np.asarray([0], dtype=np.int), model=model_1, connectivity=connectivity, coupling=coupling, integrator=integrator, monitors=(monitors, ), initial_conditions=init, ) sim_1.configure() sim_to_sync_time = int(self._simulation_length / synchronization_time) sync_steps = int(synchronization_time / integrator.dt) result_1_all = [np.empty((0, )), np.empty((sync_steps, 2, 76, 1))] result_cosim_monitors = [] sim_1.run() # run the first steps because the history is delayed for j in range(0, sim_to_sync_time): # This should fail for CosimCoupling that can only return FUTURE coupling values!!! result_cosim_monitors.append( sim_1.loop_cosim_monitor_output(sync_steps, 0)) result_1_all_step = sim_1.run(cosim_updates=[ np.array([ result_all[0][0][(sync_steps * j) + i] for i in range(sync_steps) ]), np.array([ result_all[0][1][(sync_steps * j) + i][0][0] for i in range(sync_steps) ]).reshape((sync_steps, 1, 1, 1)) ]) result_1_all[0] = np.concatenate( (result_1_all[0], result_1_all_step[0][0])) result_1_all[1] = np.concatenate( (result_1_all[1], result_1_all_step[0][1])) for i in range(int(self._simulation_length / integrator.dt)): np.testing.assert_array_equal( result_all[0][1][i][0][1:], result_1_all[1][i + sync_steps, 0, 1:]) np.testing.assert_array_equal( result_all[0][1][i][0][:1], result_1_all[1][i + sync_steps, 0, :1]) for i in range(sim_to_sync_time): result_step = result_cosim_monitors[i] # check the dimension of the monitors np.testing.assert_array_equal(result_step[0][1].shape, (sync_steps, 2, 76, 1)) np.testing.assert_array_equal(result_step[1][1].shape, (sync_steps, 1, 76, 1)) np.testing.assert_array_equal(result_step[3][1].shape, (sync_steps, 1, 76, 1)) np.testing.assert_array_equal(result_step[4][1].shape, (sync_steps, 1, 76, 1)) np.testing.assert_array_equal(result_step[5][1].shape, (sync_steps, 1, 76, 1)) # compare the monitors between them np.testing.assert_array_equal(result_step[2][1], result_step[3][1]) np.testing.assert_array_equal(result_step[4][1], result_step[5][1]) np.testing.assert_array_equal(result_step[0][1][:, 0, :, :], result_step[1][1][:, 0, :, :])