def test_defaults(self):
G = LCA(integrator_mode=True,
leak=-1.0,
noise=0.0,
time_step_size=0.02,
function=Linear,
self_excitation=1.0,
competition=-1.0)
# - - - - - LCA integrator functions - - - - -
# X = previous_value + (rate * previous_value + variable) * self.time_step_size + noise
# f(X) = 1.0*X + 0
np.testing.assert_allclose(G.execute(), np.array([[0.0]]))
# X = 0.0 + (0.0 + 0.0)*0.02 + 0.0
# X = 0.0 <--- previous value 0.0
# f(X) = 1.0*0.0 <--- return 0.0, recurrent projection 0.0
np.testing.assert_allclose(G.execute(1.0), np.array([[0.02]]))
# X = 0.0 + (0.0 + 1.0)*0.02 + 0.0
# X = 0.02 <--- previous value 0.02
# f(X) = 1.0*0.02 <--- return 0.02, recurrent projection 0.02
# Outside of a system, previous value works (integrator) but recurrent projection does NOT
np.testing.assert_allclose(G.execute(1.0), np.array([[0.0396]]))
def test_reinitialize_run(self):
L = LCA(name="L",
function=Linear,
initial_value=0.5,
integrator_mode=True,
leak=0.1,
competition=0,
self_excitation=1.0,
time_step_size=1.0,
noise=0.0)
P = Process(name="P", pathway=[L])
S = System(name="S", processes=[P])
assert np.allclose(L.previous_value, 0.5)
assert np.allclose(L.initial_value, 0.5)
assert np.allclose(L.integrator_function.initializer, 0.5)
S.run(inputs={L: 1.0},
num_trials=2,
initialize=True,
initial_values={L: 0.0})
# Integrator fn: previous_value + (rate*previous_value + new_value)*time_step_size + noise*(time_step_size**0.5)
# Trial 1 | variable = 1.0 + 0.0
# integration: 0.5 + (0.1*0.5 + 1.0)*1.0 + 0.0 = 1.55
# linear fn: 1.55*1.0 = 1.55
# Trial 2 | variable = 1.0 + 1.55
# integration: 1.55 + (0.1*1.55 + 2.55)*1.0 + 0.0 = 4.255
# linear fn: 4.255*1.0 = 4.255
assert np.allclose(L.previous_value, 4.255)
assert np.allclose(L.initial_value, 0.5)
assert np.allclose(L.integrator_function.initializer, 0.5)
L.integrator_function.reinitialize(0.9)
assert np.allclose(L.previous_value, 0.9)
assert np.allclose(L.initial_value, 0.5)
assert np.allclose(L.integrator_function.initializer, 0.9)
assert np.allclose(L.value, 4.255)
L.reinitialize(0.5)
assert np.allclose(L.previous_value, 0.5)
assert np.allclose(L.initial_value, 0.5)
assert np.allclose(L.integrator_function.initializer, 0.5)
assert np.allclose(L.value, 0.5)
S.run(inputs={L: 1.0}, num_trials=2)
# Trial 3 | variable = 1.0 + 0.5
# integration: 0.5 + (0.1*0.5 + 1.5)*1.0 + 0.0 = 2.05
# linear fn: 2.05*1.0 = 2.05
# Trial 4 | variable = 1.0 + 2.05
# integration: 2.05 + (0.1*2.05 + 3.05)*1.0 + 0.0 = 5.305
# linear fn: 5.305*1.0 = 5.305
assert np.allclose(L.previous_value, 5.305)
assert np.allclose(L.initial_value, 0.5)
assert np.allclose(L.integrator_function.initializer, 0.5)
def test_clip_2d_array(self):
L = LCA(default_variable=[[0.0, 0.0, 0.0], [0.0, 0.0, 0.0],
[0.0, 0.0, 0.0]],
clip=[-2.0, 2.0],
function=Linear,
integrator_mode=False)
assert np.allclose(
L.execute([[-5.0, -1.0, 5.0], [5.0, -5.0, 1.0], [1.0, 5.0, 5.0]]),
[[-2.0, -1.0, 2.0], [2.0, -2.0, 1.0], [1.0, 2.0, 2.0]])
def test_LCA_length_1(self):
T = TransferMechanism(function=Linear(slope=1.0))
L = LCA(
function=Linear(slope=2.0),
self_excitation=3.0,
leak=0.5,
competition=
1.0, # competition does not matter because we only have one unit
time_step_size=0.1)
P = Process(pathway=[T, L])
S = System(processes=[P])
L.reinitialize_when = Never()
# - - - - - - - Equations to be executed - - - - - - -
# new_transfer_input =
# previous_transfer_input
# + (leak * previous_transfer_input_1 + self_excitation * result1 + competition * result2 + outside_input1) * dt
# + noise
# result = new_transfer_input*2.0
# recurrent_matrix = [[3.0]]
# - - - - - - - - - - - - - - - - - - - - - - - - - -
results = []
def record_execution():
results.append(L.value[0][0])
S.run(inputs={T: [1.0]},
num_trials=3,
call_after_trial=record_execution)
# - - - - - - - TRIAL 1 - - - - - - -
# new_transfer_input = 0.0 + ( 0.5 * 0.0 + 3.0 * 0.0 + 0.0 + 1.0)*0.1 + 0.0 = 0.1
# f(new_transfer_input) = 0.1 * 2.0 = 0.2
# - - - - - - - TRIAL 2 - - - - - - -
# new_transfer_input = 0.1 + ( 0.5 * 0.1 + 3.0 * 0.2 + 0.0 + 1.0)*0.1 + 0.0 = 0.265
# f(new_transfer_input) = 0.265 * 2.0 = 0.53
# - - - - - - - TRIAL 3 - - - - - - -
# new_transfer_input = 0.265 + ( 0.5 * 0.265 + 3.0 * 0.53 + 0.0 + 1.0)*0.1 + 0.0 = 0.53725
# f(new_transfer_input) = 0.53725 * 2.0 = 1.0745
assert np.allclose(results, [0.2, 0.53, 1.0745])
def test_previous_value_stored(self):
G = LCA(integrator_mode=True,
leak=-1.0,
noise=0.0,
time_step_size=0.02,
function=Linear(slope=2.0),
self_excitation=1.0,
competition=-1.0,
initial_value=np.array([[1.0]]))
P = Process(pathway=[G])
S = System(processes=[P])
G.output_state.value = [0.0]
# - - - - - LCA integrator functions - - - - -
# X = previous_value + (rate * previous_value + variable) * self.time_step_size + noise
# f(X) = 2.0*X + 0
# - - - - - starting values - - - - -
# variable = G.output_state.value + stimulus = 0.0 + 1.0 = 1.0
# previous_value = initial_value = 1.0
# single_run = S.execute([[1.0]])
# np.testing.assert_allclose(single_run, np.array([[2.0]]))
np.testing.assert_allclose(S.execute([[1.0]]), np.array([[2.0]]))
# X = 1.0 + (-1.0 + 1.0)*0.02 + 0.0
# X = 1.0 + 0.0 + 0.0 = 1.0 <--- previous value 1.0
# f(X) = 2.0*1.0 <--- return 2.0, recurrent projection 2.0
np.testing.assert_allclose(S.execute([[1.0]]), np.array([[2.08]]))
# X = 1.0 + (-1.0 + 3.0)*0.02 + 0.0
# X = 1.0 + 0.04 = 1.04 <--- previous value 1.04
# f(X) = 2.0*1.04 <--- return 2.08
np.testing.assert_allclose(S.execute([[1.0]]), np.array([[2.1616]]))
def test_LCA_length_2(self):
T = TransferMechanism(function=Linear(slope=1.0), size=2)
L = LCA(function=Linear(slope=2.0),
size=2,
self_excitation=3.0,
leak=0.5,
competition=1.0,
time_step_size=0.1)
P = Process(pathway=[T, L])
S = System(processes=[P])
# - - - - - - - Equations to be executed - - - - - - -
# new_transfer_input =
# previous_transfer_input
# + (leak * previous_transfer_input_1 + self_excitation * result1 + competition * result2 + outside_input1) * dt
# + noise
# result = new_transfer_input*2.0
# recurrent_matrix = [[3.0]]
# - - - - - - - - - - - - - - - - - - - - - - - - - -
results = []
def record_execution():
results.append(L.value[0])
S.run(inputs={T: [1.0, 2.0]},
num_trials=3,
call_after_trial=record_execution)
# - - - - - - - TRIAL 1 - - - - - - -
# new_transfer_input_1 = 0.0 + ( 0.5 * 0.0 + 3.0 * 0.0 - 1.0*0.0 + 1.0)*0.1 + 0.0 = 0.1
# f(new_transfer_input_1) = 0.1 * 2.0 = 0.2
# new_transfer_input_2 = 0.0 + ( 0.5 * 0.0 + 3.0 * 0.0 - 1.0*0.0 + 2.0)*0.1 + 0.0 = 0.2
# f(new_transfer_input_2) = 0.2 * 2.0 = 0.4
# - - - - - - - TRIAL 2 - - - - - - -
# new_transfer_input = 0.1 + ( 0.5 * 0.1 + 3.0 * 0.2 - 1.0*0.4 + 1.0)*0.1 + 0.0 = 0.225
# f(new_transfer_input) = 0.265 * 2.0 = 0.45
# new_transfer_input_2 = 0.2 + ( 0.5 * 0.2 + 3.0 * 0.4 - 1.0*0.2 + 2.0)*0.1 + 0.0 = 0.51
# f(new_transfer_input_2) = 0.1 * 2.0 = 1.02
# - - - - - - - TRIAL 3 - - - - - - -
# new_transfer_input = 0.225 + ( 0.5 * 0.225 + 3.0 * 0.45 - 1.0*1.02 + 1.0)*0.1 + 0.0 = 0.36925
# f(new_transfer_input) = 0.36925 * 2.0 = 0.7385
# new_transfer_input_2 = 0.51 + ( 0.5 * 0.51 + 3.0 * 1.02 - 1.0*0.45 + 2.0)*0.1 + 0.0 = 0.9965
# f(new_transfer_input_2) = 0.9965 * 2.0 = 1.463
assert np.allclose(results,
[[0.2, 0.4], [0.45, 1.02], [0.7385, 1.993]])
def test_clip_float(self):
L = LCA(clip=[-2.0, 2.0], function=Linear, integrator_mode=False)
assert np.allclose(L.execute(3.0), 2.0)
assert np.allclose(L.execute(-3.0), -2.0)