def test_precision(self):
weight = np.array([[2, 8], [3, 5]])
delay = 1.5
delays = np.array([[delay, delay], [delay, delay]])
init_value = [[0.9, 0.0], [0.9, 0.0]]
resolution_simulation = 0.1
synchronization_time = resolution_simulation * 10.0
nb_init = (int(delay / resolution_simulation)) + 1
initial_condition = np.array(init_value * nb_init).reshape(
(nb_init, 2, weight.shape[0], 1))
proxy_id = [0]
no_proxy = [1]
# simulation with one proxy
np.random.seed(42)
sim = TvbSim(weight,
delays,
proxy_id,
resolution_simulation,
synchronization_time,
initial_condition=initial_condition)
time, s, result = sim(synchronization_time, rate=True)
# full simulation
np.random.seed(42)
sim_ref = TvbSim(weight,
delays, [],
resolution_simulation,
synchronization_time,
initial_condition=initial_condition)
time_ref, s_ref, result_ref = sim_ref(synchronization_time, rate=True)
# compare with the Cosim Monitor RawCosim
np.testing.assert_array_equal(result_ref[:, no_proxy, :],
result[0][:, no_proxy, :])
np.testing.assert_array_equal(s_ref[:, no_proxy, :], s[0][:,
no_proxy, :])
for i in range(0, 1000):
time, s, result = sim(
synchronization_time,
rate_data=[time_ref, result_ref[:, proxy_id][:, :, 0]],
rate=True)
# compare with monitor delayed by synchronization_time
np.testing.assert_array_equal(result_ref[:, no_proxy, :],
result[1][:, no_proxy, :])
np.testing.assert_array_equal(result_ref[:, proxy_id, :] * np.NAN,
result[1][:, proxy_id, :])
np.testing.assert_array_equal(s_ref, s[1])
time_ref, s_ref, result_ref = sim_ref(synchronization_time,
rate=True)
# compare with the Cosim Monitor RawCosim
np.testing.assert_array_equal(result_ref[:, no_proxy, :],
result[0][:, no_proxy, :])
np.testing.assert_array_equal(s_ref[:, no_proxy, :],
s[0][:, no_proxy, :])
def test_precision_delay(self):
weight = np.array([[2, 8, 10], [0.2, 0.5, 0.1], [3, 0.6, 1]])
delay = np.array([[0.6, 0.5, 1.0], [0.7, 0.8, 3.0], [1.0, 0.5, 0.7]])
max = np.int(np.max(delay) * 10 + 1)
init_value = np.array([[[0.1, 0.0], [0.1, 0.0], [0.2, 0.0]]] * max)
initial_condition = init_value.reshape((max, 2, weight.shape[0], 1))
resolution_simulation = 0.1
synchronization_time = 0.1 * 4
proxy_id = [0]
no_proxy = [1, 2]
# simulation with one proxy
np.random.seed(42)
sim = TvbSim(weight,
delay,
proxy_id,
resolution_simulation,
synchronization_time,
initial_condition=initial_condition)
time, s, result = sim(synchronization_time, rate=True)
# full simulation
np.random.seed(42)
sim_ref = TvbSim(weight,
delay, [],
resolution_simulation,
synchronization_time,
initial_condition=initial_condition)
time, s_ref, result_ref = sim_ref(synchronization_time, rate=True)
# compare with the CosimMonitor RawCosim
np.testing.assert_array_equal(
np.squeeze(result_ref[:, no_proxy, :], axis=2),
np.squeeze(result[0][:, no_proxy, :], axis=2))
np.testing.assert_array_equal(
np.squeeze(s_ref[:, no_proxy, :], axis=2),
np.squeeze(s[0][:, no_proxy, :], axis=2))
for i in range(0, 1000):
time, s, result = sim(
synchronization_time,
rate_data=[time, result_ref[:, proxy_id][:, :, 0]],
rate=True)
# compare with RawDelayed monitor, delayed by synchronization_time
np.testing.assert_array_equal(result_ref[:, no_proxy, :],
result[1][:, no_proxy, :])
np.testing.assert_array_equal(result_ref[:, proxy_id, :] * np.NAN,
result[1][:, proxy_id, :])
np.testing.assert_array_equal(s_ref, s[1])
time, s_ref, result_ref = sim_ref(synchronization_time, rate=True)
# compare with the CosimMonitor RawCosim
np.testing.assert_array_equal(result_ref[:, no_proxy, :],
result[0][:, no_proxy, :])
np.testing.assert_array_equal(s_ref[:, no_proxy, :],
s[0][:, no_proxy, :])
def test_double_precision_complex(self):
weight = np.array([[5, 2, 4, 0], [8, 5, 4, 1], [6, 1, 7, 9], [10, 0, 5, 6]])
delay = np.array([[7, 8, 5, 1], [10, 3, 7, 9], [4, 3, 2, 8], [9, 10, 11, 5]])
max = np.int(np.max(delay)*10+1)
init_value = np.array([[[0.1,0.0], [0.1,0.0], [0.2,0.0], [0.9,0.0]]] * max)
initial_condition = init_value.reshape((max, 2, weight.shape[0], 1))
resolution_simulation = 0.1
synchronization_time = 0.1 * 10
proxy_id_1 = [1]
proxy_id_2 = [0, 2]
# simulation with one proxy
np.random.seed(42)
sim_1 = TvbSim(weight, delay, proxy_id_1, resolution_simulation,
synchronization_time, initial_condition=initial_condition)
time, result_1 = sim_1(synchronization_time)
# simulation_2 with one proxy
np.random.seed(42)
sim_2 = TvbSim(weight, delay, proxy_id_2, resolution_simulation,
synchronization_time, initial_condition=initial_condition)
time, result_2 = sim_2(synchronization_time)
# full simulation
np.random.seed(42)
sim_ref = TvbSim(weight, delay, [], resolution_simulation,
synchronization_time, initial_condition=initial_condition)
time_ref, result_ref = sim_ref(synchronization_time)
# COMPARE PROXY 1
np.testing.assert_array_equal(np.squeeze(result_ref[:, proxy_id_2, :], axis=2)[0],
np.squeeze(result_1[0][:, proxy_id_2, :], axis=2)[0])
# COMPARE PROXY 2
np.testing.assert_array_equal(np.squeeze(result_ref[:, proxy_id_1, :], axis=2)[0],
np.squeeze(result_2[0][:, proxy_id_1, :], axis=2)[0])
for i in range(0, 1000):
time, result_2 = sim_2(synchronization_time, [time, result_1[0][:, proxy_id_2][:, :, 0]])
# compare with raw monitor delayed of synchronization_time
np.testing.assert_array_equal(result_ref, result_2[1])
time, result_1 = sim_1(synchronization_time, [time_ref, result_ref[:, proxy_id_1][:, :, 0]])
# compare with raw monitor delayed of synchronization_time
np.testing.assert_array_equal(result_ref, result_1[1])
time_ref, result_ref = sim_ref(synchronization_time)
# COMPARE PROXY 1
np.testing.assert_array_equal(np.squeeze(result_ref[:, proxy_id_2, :], axis=2)[0],
np.squeeze(result_1[0][:, proxy_id_2, :], axis=2)[0])
# COMPARE PROXY 2
np.testing.assert_array_equal(np.squeeze(result_ref[:, proxy_id_1, :], axis=2)[0],
np.squeeze(result_2[0][:, proxy_id_1, :], axis=2)[0])
def test_double_precision_complex_delay_update(self):
weight = np.array([[5, 2, 4, 0], [8, 5, 4, 1], [6, 1, 7, 9], [10, 0, 5, 6]],dtype=np.float)
delay = np.array([[7, 8, 5, 1], [9, 3, 7, 9], [4, 3, 2, 8], [9, 10, 11, 5]],dtype=np.float)
max = np.int(np.max(delay)*10+1)
resolution_simulation = 0.1
time_synchronize = np.min(delay)
proxy_id_1 = [1]
proxy_id_2 = [0, 2]
# simulation with one proxy
np.random.seed(42)
sim_1 = TvbSim(weight, delay, proxy_id_1, resolution_simulation, time_synchronize)
time, result_1 = sim_1(time_synchronize)
# simulation_2 with one proxy
np.random.seed(42)
sim_2 = TvbSim(weight, delay, proxy_id_2, resolution_simulation, time_synchronize)
time, result_2 = sim_2(time_synchronize)
# full simulation
np.random.seed(42)
sim_ref = TvbSim(weight, delay, [], resolution_simulation, time_synchronize)
time_ref, result_ref = sim_ref(time_synchronize)
# COMPARE PROXY 1
np.testing.assert_array_equal(np.squeeze(result_ref[:, proxy_id_2, :], axis=2)[0],
np.squeeze(result_1[0][:, proxy_id_2, :], axis=2)[0])
# COMPARE PROXY 2
np.testing.assert_array_equal(np.squeeze(result_ref[:, proxy_id_1, :], axis=2)[0],
np.squeeze(result_2[0][:, proxy_id_1, :], axis=2)[0])
for i in range(0, 1000):
time, result_2 = sim_2(time_synchronize, [time, result_1[0][:, proxy_id_2][:, :, 0]])
# compare with raw monitor delayed of time_synchronize
np.testing.assert_array_equal(result_ref, result_2[1])
time, result_1 = sim_1(time_synchronize, [time_ref, result_ref[:, proxy_id_1][:, :, 0]])
# compare with raw monitor delayed of time_synchronize
np.testing.assert_array_equal(result_ref, result_1[1])
time_ref, result_ref = sim_ref(time_synchronize)
# COMPARE PROXY 1
np.testing.assert_array_equal(np.squeeze(result_ref[:, proxy_id_2, :], axis=2)[0],
np.squeeze(result_1[0][:, proxy_id_2, :], axis=2)[0])
# COMPARE PROXY 2
np.testing.assert_array_equal(np.squeeze(result_ref[:, proxy_id_1,:], axis=2)[0],
np.squeeze(result_2[0][:, proxy_id_1,:], axis=2)[0])
def test_precision_multiple(self):
weight = np.array([[5, 2, 4, 0], [8, 5, 4, 1], [6, 1, 7, 9],
[10, 0, 5, 6]])
delay = np.array([[0.1, 0.1, 0.1, 0.1], [0.1, 0.1, 0.1, 0.1],
[0.1, 0.1, 0.1, 0.1], [0.1, 0.1, 0.1, 0.1]]) * 10
max = np.int(np.max(delay) * 10 + 1)
init_value = np.array(
[[[0.1, 0.0], [0.1, 0.0], [0.2, 0.0], [0.2, 0.0]]] * max)
initial_condition = init_value.reshape((max, 2, weight.shape[0], 1))
resolution_simulation = 0.1
synchronization_time = 0.1 * 5
proxy_id = [0, 1, 2]
no_proxy = [3]
# simulation with one or more proxy
np.random.seed(42)
sim = TvbSim(weight,
delay,
proxy_id,
resolution_simulation,
synchronization_time,
initial_condition=initial_condition)
time, result = sim(synchronization_time)
# full simulation
np.random.seed(42)
sim_ref = TvbSim(weight,
delay, [],
resolution_simulation,
synchronization_time,
initial_condition=initial_condition)
time, result_ref = sim_ref(synchronization_time)
# compare with the CosimMonitor RawCosim
np.testing.assert_array_equal(
np.squeeze(result_ref[:, no_proxy, :], axis=1)[0],
np.squeeze(result[0][:, no_proxy, :], axis=1)[0])
for i in range(0, 1000):
time, result = sim(synchronization_time,
[time, result_ref[:, proxy_id][:, :, 0]])
# compare with Raw monitor delayed by synchronization_time
np.testing.assert_array_equal(result_ref, result[1])
time, result_ref = sim_ref(synchronization_time)
# compare with the CosimMonitor RawCosim
np.testing.assert_array_equal(result_ref[:, no_proxy, :],
result[0][:, no_proxy, :])
def test_update_model(self):
weight = np.array([[1, 1, 1, 1], [1, 1, 1, 1], [1, 1, 1, 1],
[1, 1, 1, 1]])
delay = np.array([[1.5, 1.5, 1.5, 1.5], [1.5, 1.5, 1.5, 1.5],
[1.5, 1.5, 1.5, 1.5], [1.5, 1.5, 1.5, 1.5]])
resolution_simulation = 0.1
resolution_monitor = 1.0
synchronization_time = 1.0
proxy_id = [0, 1]
firing_rate = np.array([[
20.0, 10.0
]]) * 10**-3 # time units in tvb is ms so the rate is in KHz
sim = TvbSim(weight, delay, proxy_id, resolution_simulation,
synchronization_time)
time, result = sim(resolution_monitor,
[np.array([resolution_simulation]), firing_rate])
for i in range(0, 100):
time, result = sim(synchronization_time, [
time + resolution_monitor,
np.repeat(firing_rate.reshape(1, 2),
int(resolution_monitor / resolution_simulation),
axis=0)
])
assert True
def test_precision_delay_update(self):
weight = np.array([[2, 8, 0], [0, 0, 0], [3, 0, 1]])
delay = np.array([[0.6, 0.5, 1.0], [0.7, 0.8, 3.0], [1.0, 0.5, 0.7]])
max = np.int(np.max(delay) * 10 + 1)
init_value = np.array([[[0.1, 0.0], [0.1, 0.0], [0.2, 0.0]]] * max)
initial_condition = init_value.reshape((max, 2, weight.shape[0], 1))
resolution_simulation = 0.1
synchronization_time = np.min(delay)
proxy_id = [0]
no_proxy = [1, 2]
# simulation with one proxy
np.random.seed(42)
sim = TvbSim(weight,
delay,
proxy_id,
resolution_simulation,
synchronization_time,
initial_condition=initial_condition)
time, result = sim(synchronization_time)
# full simulation
np.random.seed(42)
sim_ref = TvbSim(weight,
delay, [],
resolution_simulation,
synchronization_time,
initial_condition=initial_condition)
time, result_ref = sim_ref(synchronization_time)
# compare with TVB Raw monitor delayed by synchronization_time
np.testing.assert_array_equal(
np.squeeze(result_ref[:, no_proxy, :], axis=2)[0],
np.squeeze(result[0][:, no_proxy, :], axis=2)[0])
for i in range(0, 1000):
delay_input = [time, result_ref[:, proxy_id][:, :, 0]]
time, result = sim(synchronization_time, delay_input)
# compare with Raw monitor delayed by synchronization_time
np.testing.assert_array_equal(result_ref, result[1])
time, result_ref = sim_ref(synchronization_time)
# compare with TVB Raw monitor delayed by synchronization_time
np.testing.assert_array_equal(result_ref[:, no_proxy, :],
result[0][:, no_proxy, :])
def test_update_model(self):
weight = np.array([[1, 1, 1, 1], [1, 1, 1, 1], [1, 1, 1, 1],
[1, 1, 1, 1]])
delay = np.array([[1.5, 1.5, 1.5, 1.5], [1.5, 1.5, 1.5, 1.5],
[1.5, 1.5, 1.5, 1.5], [1.5, 1.5, 1.5, 1.5]])
resolution_simulation = 0.1
synchronization_time = 1.0
proxy_id = [0, 1]
firing_rate = np.array([[
20.0, 10.0
]]) * 10**-3 # units time in tvb is ms so the rate is in KHz
# Test the the update function
sim = TvbSim(weight, delay, proxy_id, resolution_simulation,
synchronization_time)
time, result = sim(resolution_simulation,
[np.array([resolution_simulation]), firing_rate])
for i in range(0, 100):
time, result = sim(synchronization_time, [
np.arange(i * synchronization_time,
(i + 1) * synchronization_time,
resolution_simulation),
np.repeat(firing_rate.reshape(1, 2),
int(synchronization_time / resolution_simulation),
axis=0)
])
assert True
# Test a fail function due to the time of simulation too long
with pytest.raises(ValueError):
sim(synchronization_time, [
np.arange(100 * synchronization_time,
102 * synchronization_time, resolution_simulation),
np.repeat(
firing_rate.reshape(1, 2),
int(synchronization_time / resolution_simulation) * 2,
axis=0)
])
# Test a fail function due to the resoulation time is not good
with pytest.raises(ValueError):
sim(synchronization_time, [
np.arange(100 * synchronization_time, 101 *
synchronization_time, resolution_simulation * 2),
np.repeat(
firing_rate.reshape(1, 2),
int(synchronization_time / resolution_simulation) * 2,
axis=0)
])
def test_double_proxy_precision_simple(self):
weight = np.array([[1, 1], [1, 1]])
delay = np.array([[10.0, 10.0], [10.0, 10.0]])
max = np.int(np.max(delay) * 10 + 1)
init_value = np.array([[[0.1, 0.0], [0.1, 0.0]]] * max)
initial_condition = init_value.reshape((max, 2, weight.shape[0], 1))
resolution_simulation = 0.1
synchronization_time = 0.1 * 4
proxy_id_1 = [0]
proxy_id_2 = [1]
# simulation_2 with one proxy
np.random.seed(42)
sim_2 = TvbSim(weight,
delay,
proxy_id_2,
resolution_simulation,
synchronization_time,
initial_condition=initial_condition)
time, s_2, result_2 = sim_2(synchronization_time, rate=True)
# simulation with one proxy
np.random.seed(42)
sim_1 = TvbSim(weight,
delay,
proxy_id_1,
resolution_simulation,
synchronization_time,
initial_condition=initial_condition)
time, s_1, result_1 = sim_1(synchronization_time, rate=True)
# full simulation
np.random.seed(42)
sim_ref = TvbSim(weight,
delay, [],
resolution_simulation,
synchronization_time,
initial_condition=initial_condition)
time_ref, s_ref, result_ref = sim_ref(synchronization_time, rate=True)
# COMPARE PROXY 1
np.testing.assert_array_equal(
np.squeeze(result_ref[:, proxy_id_2, :], axis=2),
np.squeeze(result_1[0][:, proxy_id_2, :], axis=2))
np.testing.assert_array_equal(
np.squeeze(s_ref[:, proxy_id_2, :], axis=2),
np.squeeze(s_1[0][:, proxy_id_2, :], axis=2))
# COMPARE PROXY 2
np.testing.assert_array_equal(
np.squeeze(result_ref[:, proxy_id_1, :], axis=2),
np.squeeze(result_2[0][:, proxy_id_1, :], axis=2))
np.testing.assert_array_equal(
np.squeeze(s_ref[:, proxy_id_1, :], axis=2),
np.squeeze(s_2[0][:, proxy_id_1, :], axis=2))
for i in range(0, 1000):
time, s_2, result_2 = sim_2(
synchronization_time,
rate_data=[time, result_1[0][:, proxy_id_2][:, :, 0]],
rate=True)
# compare with Raw monitor delayed by synchronization_time
np.testing.assert_array_equal(result_ref[:, proxy_id_1, :],
result_2[1][:, proxy_id_1, :])
np.testing.assert_array_equal(
result_ref[:, proxy_id_2, :] * np.NAN,
result_2[1][:, proxy_id_2, :])
np.testing.assert_array_equal(s_ref, s_2[1])
time, s_1, result_1 = sim_1(
synchronization_time,
rate_data=[time_ref, result_ref[:, proxy_id_1][:, :, 0]],
rate=True)
# compare with Raw monitor delayed by synchronization_time
np.testing.assert_array_equal(result_ref[:, proxy_id_2, :],
result_1[1][:, proxy_id_2, :])
np.testing.assert_array_equal(
result_ref[:, proxy_id_1, :] * np.NAN,
result_1[1][:, proxy_id_1, :])
np.testing.assert_array_equal(s_ref, s_1[1])
time_ref, s_ref, result_ref = sim_ref(synchronization_time,
rate=True)
# COMPARE PROXY 1
np.testing.assert_array_equal(
np.squeeze(result_ref[:, proxy_id_2, :], axis=2),
np.squeeze(result_1[0][:, proxy_id_2, :], axis=2))
np.testing.assert_array_equal(
np.squeeze(s_ref[:, proxy_id_2, :], axis=2),
np.squeeze(s_1[0][:, proxy_id_2, :], axis=2))
# COMPARE PROXY 2
np.testing.assert_array_equal(
np.squeeze(result_ref[:, proxy_id_1, :], axis=2),
np.squeeze(result_2[0][:, proxy_id_1, :], axis=2))
np.testing.assert_array_equal(
np.squeeze(s_ref[:, proxy_id_1, :], axis=2),
np.squeeze(s_2[0][:, proxy_id_1, :], axis=2))
def test_precision_bad(self):
weight = np.array([[2, 8], [3, 5]])
delay = 100.0
delays = np.array([[delay, delay], [delay, delay]])
max = np.int(np.max(delay)*10+1)
init_value = np.array([[0.9,0.0], [0.9,0.0]]*max)
resolution_simulation = 0.1
synchronization_time = 0.1 * 10.0
nb_init = (int(delay / resolution_simulation)) + 1
initial_condition = np.array(init_value * nb_init).reshape((nb_init, 2, weight.shape[0], 1))
proxy_id = [0]
no_proxy = [1]
# simulation with one proxy
np.random.seed(42)
sim = TvbSim(weight, delays, proxy_id, resolution_simulation, synchronization_time,
initial_condition=initial_condition)
time, result = sim(synchronization_time)
# full simulation
np.random.seed(42)
sim_ref = TvbSim(weight, delays, [], resolution_simulation, synchronization_time,
initial_condition=initial_condition)
time, result_ref = sim_ref(synchronization_time)
# the results are different because the data of the proxy is wrong
np.testing.assert_array_equal(result_ref[:, no_proxy, :], result[0][:, no_proxy, :])
# the first part of the result are correct because the wrong result are delayed
for i in range(0, 99):
time, result = sim(synchronization_time, [time, np.zeros_like(result_ref[:, proxy_id][:, :, 0])])
# compare with Raw monitor delayed by synchronization_time
np.testing.assert_array_equal(result_ref[:, no_proxy, :], result[1][:, no_proxy, :])
np.testing.assert_array_compare(operator.__ne__, result_ref[:, proxy_id, :], result[1][:, proxy_id, :])
time, result_ref = sim_ref(synchronization_time)
# compare with the CosimMonitor RawCosim
np.testing.assert_array_equal(result_ref[:, no_proxy, :], result[0][:, no_proxy, :])
# the result become of different value when the delayed result is computed
for i in range(100, 1000):
time, result = sim(synchronization_time, [time, np.zeros_like(result_ref[:, proxy_id][:, :, 0])])
# compare with Raw monitor delayed by synchronization_time
if i == 100: # as precedent
np.testing.assert_array_equal(result_ref[:, no_proxy, :], result[1][:, no_proxy, :])
np.testing.assert_array_compare(operator.__ne__, result_ref[:, proxy_id, :], result[1][:, proxy_id, :])
elif i == 101: # the first one is the same
np.testing.assert_array_equal(result_ref[:1, no_proxy, :], result[1][:1, no_proxy, :])
np.testing.assert_array_compare(operator.__ne__, result_ref[1:, proxy_id, :], result[1][1:, proxy_id, :])
np.testing.assert_array_compare(operator.__ne__, result_ref[1:, :, :], result[1][1:, :, :])
else:
np.testing.assert_array_compare(operator.__ne__,result_ref, result[1])
time, result_ref = sim_ref(synchronization_time)
# compare with the CosimMonitor RawCosim
if i == 100: # the first one is the same
np.testing.assert_array_equal(result_ref[:1, no_proxy, :], result[0][:1, no_proxy, :])
np.testing.assert_array_compare(operator.__ne__,result_ref[1:, no_proxy, :], result[0][1:, no_proxy, :])
else:
np.testing.assert_array_compare(operator.__ne__,result_ref[:, no_proxy, :], result[0][:, no_proxy, :])