def test_recurrent_mech_change_learning_rate(self):
R = RecurrentTransferMechanism(size=4,
function=Linear,
enable_learning=True,
learning_rate=0.1
)
p = Process(pathway=[R])
s = System(processes=[p])
assert R.learning_rate == 0.1
assert R.learning_mechanism.learning_rate == 0.1
# assert R.learning_mechanism.function.learning_rate == 0.1
s.run(inputs=[[1.0, 1.0, 1.0, 1.0]])
matrix_1 = [[0., 1.1, 1.1, 1.1],
[1.1, 0., 1.1, 1.1],
[1.1, 1.1, 0., 1.1],
[1.1, 1.1, 1.1, 0.]]
assert np.allclose(R.recurrent_projection.mod_matrix, matrix_1)
print(R.recurrent_projection.mod_matrix)
R.learning_rate = 0.9
assert R.learning_rate == 0.9
assert R.learning_mechanism.learning_rate == 0.9
# assert R.learning_mechanism.function.learning_rate == 0.9
s.run(inputs=[[1.0, 1.0, 1.0, 1.0]])
matrix_2 = [[0., 1.911125, 1.911125, 1.911125],
[1.911125, 0., 1.911125, 1.911125],
[1.911125, 1.911125, 0., 1.911125],
[1.911125, 1.911125, 1.911125, 0.]]
# assert np.allclose(R.recurrent_projection.mod_matrix, matrix_2)
print(R.recurrent_projection.mod_matrix)
def test_rt_without_custom_comb_fct(self):
R1 = RecurrentTransferMechanism(
has_recurrent_input_state=True,
size=2,
)
result = R1.execute([1,2])
np.testing.assert_allclose(result, [[1,2]])
def test_recurrent_mech_inputs_mismatched_with_default_shorter(self):
with pytest.raises(MechanismError) as error_text:
R = RecurrentTransferMechanism(
name='R',
size=6
)
R.execute([1, 2, 3, 4, 5])
assert "does not match required length" in str(error_text.value)
def test_recurrent_mech_function_logistic(self):
R = RecurrentTransferMechanism(
name='R',
size=10,
function=Logistic(gain=2, offset=1)
)
val = R.execute(np.ones(10))
np.testing.assert_allclose(val, [np.full(10, 0.7310585786300049)])
def test_recurrent_mech_inputs_list_of_strings(self):
with pytest.raises(UtilitiesError) as error_text:
R = RecurrentTransferMechanism(
name='R',
default_variable=[0, 0, 0, 0],
integrator_mode=True
)
R.execute(["one", "two", "three", "four"])
assert "has non-numeric entries" in str(error_text.value)
def test_rt_with_custom_comb_fct(self):
def my_fct(x):
return x[0] * x[1] if len(x) == 2 else x[0]
R2 = RecurrentTransferMechanism(
has_recurrent_input_state=True,
size=2,
combination_function=my_fct
)
result = R2.execute([1,2])
np.testing.assert_allclose(result, [[0,0]])
def test_recurrent_mech_auto_array_matrix_spec(self):
R = RecurrentTransferMechanism(
name='R',
size=4,
auto=[1.1, 2.2, 3.3, 4.4],
matrix=[[1, 2, 3, 4]] * 4
)
val = R.execute([10, 11, 12, 13])
np.testing.assert_allclose(val, [[10., 11., 12., 13.]])
np.testing.assert_allclose(R.matrix, [[1.1, 2, 3, 4], [1, 2.2, 3, 4], [1, 2, 3.3, 4], [1, 2, 3, 4.4]])
def test_recurrent_mech_matrix_auto_hetero_spec_size_1(self):
R = RecurrentTransferMechanism(
name='R',
size=1,
auto=-2,
hetero=4.4
)
val = R.execute([10])
np.testing.assert_allclose(val, [[10.]])
assert isinstance(R.matrix, np.ndarray)
np.testing.assert_allclose(R.matrix, [[-2]])
def test_recurrent_mech_function_psyneulink(self):
a = Logistic(gain=2, offset=1)
R = RecurrentTransferMechanism(
name='R',
size=7,
function=a
)
val = R.execute(np.zeros(7))
np.testing.assert_allclose(val, [np.full(7, 0.2689414213699951)])
def test_recurrent_mech_reduce_fun(self):
with pytest.raises(TransferError) as error_text:
R = RecurrentTransferMechanism(
name='R',
default_variable=[0, 0, 0, 0],
function=Reduce(),
integration_rate=1.0,
integrator_mode=True
)
R.execute([0, 0, 0, 0])
assert "must be a TRANSFER FUNCTION TYPE" in str(error_text.value)
def test_recurrent_mech_matrix_auto_hetero_spec_size_4(self):
R = RecurrentTransferMechanism(
name='R',
size=4,
auto=2.2,
hetero=-3
)
val = R.execute([10, 10, 10, 10])
np.testing.assert_allclose(val, [[10., 10., 10., 10.]])
np.testing.assert_allclose(R.matrix, [[2.2, -3, -3, -3], [-3, 2.2, -3, -3], [-3, -3, 2.2, -3], [-3, -3, -3, 2.2]])
assert isinstance(R.matrix, np.ndarray)
def test_recurrent_mech_integration_rate_0_8_initial_1_2(self):
R = RecurrentTransferMechanism(
name='R',
default_variable=[0, 0, 0, 0],
function=Linear(),
integration_rate=0.8,
initial_value=np.array([[-1, 1, -2, 2]]),
integrator_mode=True
)
val = R.execute([3, 2, 1, 0])
np.testing.assert_allclose(val, [[2.2, 1.8, .40000000000000013, .3999999999999999]])
def test_recurrent_mech_auto_matrix_spec(self):
# auto should override the diagonal only
R = RecurrentTransferMechanism(
name='R',
size=4,
auto=2.2,
matrix=[[1, 2, 3, 4]] * 4
)
val = R.execute([10, 11, 12, 13])
np.testing.assert_allclose(val, [[10., 11., 12., 13.]])
np.testing.assert_allclose(R.matrix, [[2.2, 2, 3, 4], [1, 2.2, 3, 4], [1, 2, 2.2, 4], [1, 2, 3, 2.2]])
def test_recurrent_mech_matrix_keyword_spec(self, matrix):
if matrix == RANDOM_CONNECTIVITY_MATRIX:
pytest.skip("Random test")
R = RecurrentTransferMechanism(
name='R',
size=4,
matrix=matrix
)
val = R.execute([10, 10, 10, 10])
np.testing.assert_allclose(val, [[10., 10., 10., 10.]])
np.testing.assert_allclose(R.recurrent_projection.matrix, get_matrix(matrix, R.size[0], R.size[0]))
def test_recurrent_mech_integration_rate_0_8(self):
R = RecurrentTransferMechanism(
name='R',
default_variable=[0, 0, 0, 0],
function=Linear(),
integration_rate=0.8,
integrator_mode=True
)
val = R.execute([1, 1, 1, 1])
np.testing.assert_allclose(val, [[0.8, 0.8, 0.8, 0.8]])
val = R.execute([1, 1, 1, 1])
np.testing.assert_allclose(val, [[.96, .96, .96, .96]])
def test_recurrent_mech_hetero_matrix_matrix_spec(self):
R = RecurrentTransferMechanism(
name='R',
size=4,
hetero=np.array([[-4, -3, -2, -1]] * 4),
matrix=[[1, 2, 3, 4]] * 4
)
val = R.execute([1, 2, 3, 4])
np.testing.assert_allclose(val, [[1., 2., 3., 4.]])
np.testing.assert_allclose(
R.matrix,
[[1, -3, -2, -1], [-4, 2, -2, -1], [-4, -3, 3, -1], [-4, -3, -2, 4]]
)
def test_recurrent_mech_matrix_auto_hetero_matrix_spec(self):
# when auto, hetero, and matrix are all specified, auto and hetero should take precedence
R = RecurrentTransferMechanism(
name='R',
size=4,
auto=2.2,
hetero=-3,
matrix=[[1, 2, 3, 4]] * 4
)
val = R.execute([10, 10, 10, 10])
np.testing.assert_allclose(val, [[10., 10., 10., 10.]])
np.testing.assert_allclose(R.matrix, [[2.2, -3, -3, -3], [-3, 2.2, -3, -3], [-3, -3, 2.2, -3], [-3, -3, -3, 2.2]])
assert isinstance(R.matrix, np.ndarray)
def test_recurrent_mech_matrix_other_spec(self, matrix):
R = RecurrentTransferMechanism(
name='R',
size=2,
matrix=matrix
)
val = R.execute([10, 10])
np.testing.assert_allclose(val, [[10., 10.]])
assert isinstance(R.matrix, np.ndarray)
np.testing.assert_allclose(R.matrix, [[1, 2], [3, 4]])
np.testing.assert_allclose(R.recurrent_projection.matrix, [[1, 2], [3, 4]])
assert isinstance(R.recurrent_projection.matrix, np.ndarray)
def test_ris_simple(self):
R2 = RecurrentTransferMechanism(default_variable=[[0.0, 0.0, 0.0]],
matrix=[[1.0, 2.0, 3.0],
[2.0, 1.0, 2.0],
[3.0, 2.0, 1.0]],
has_recurrent_input_state=True)
R2.execute(input=[1, 3, 2])
p2 = Process(pathway=[R2])
s2 = System(processes=[p2])
s2.run(inputs=[[1, 3, 2]])
np.testing.assert_allclose(R2.parameters.value.get(s2), [[14., 12., 13.]])
assert len(R2.input_states) == 2
assert "Recurrent Input State" not in R2.input_state.name # make sure recurrent input state isn't primary
def test_recurrent_mech_integration_rate_0_8_initial_0_5(self):
R = RecurrentTransferMechanism(
name='R',
default_variable=[0, 0, 0, 0],
function=Linear(),
integration_rate=0.8,
initial_value=np.array([[0.5, 0.5, 0.5, 0.5]]),
integrator_mode=True
)
val = R.execute([1, 1, 1, 1])
np.testing.assert_allclose(val, [[0.9, 0.9, 0.9, 0.9]])
val = R.execute([1, 2, 3, 4])
np.testing.assert_allclose(val, [[.98, 1.78, 2.5800000000000005, 3.3800000000000003]]) # due to inevitable floating point errors
def test_recurrent_mech_auto_hetero_matrix_spec_v3(self):
R = RecurrentTransferMechanism(
name='R',
size=4,
auto=[3],
hetero=2,
matrix=[[1, 2, 3, 4]] * 4
)
val = R.execute([1, 2, 3, 4])
np.testing.assert_allclose(val, [[1., 2., 3., 4.]])
np.testing.assert_allclose(
R.matrix,
[[3, 2, 2, 2], [2, 3, 2, 2], [2, 2, 3, 2], [2, 2, 2, 3]]
)
def test_recurrent_mech_hetero_float_matrix_spec(self):
# hetero should override off-diagonal only
R = RecurrentTransferMechanism(
name='R',
size=4,
hetero=-2.2,
matrix=[[1, 2, 3, 4]] * 4
)
val = R.execute([1, 2, 3, 4])
np.testing.assert_allclose(val, [[1., 2., 3., 4.]])
np.testing.assert_allclose(
R.matrix,
[[1, -2.2, -2.2, -2.2], [-2.2, 2, -2.2, -2.2], [-2.2, -2.2, 3, -2.2], [-2.2, -2.2, -2.2, 4]]
)
def test_recurrent_mech_with_learning(self):
R = RecurrentTransferMechanism(size=4,
function=Linear,
matrix=np.full((4, 4), 0.1),
enable_learning=True
)
# Test that all of these are the same:
np.testing.assert_allclose(
R.recurrent_projection.mod_matrix,
[
[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]
]
)
np.testing.assert_allclose(R.recurrent_projection.matrix, R.matrix)
np.testing.assert_allclose(R.input_state.path_afferents[0].matrix, R.matrix)
# Test that activity is properly computed prior to learning
p = Process(pathway=[R])
R.learning_enabled = False
p.execute([1, 1, 0, 0])
p.execute([1, 1, 0, 0])
np.testing.assert_allclose(R.parameters.value.get(p), [[1.2, 1.2, 0.2, 0.2]])
# Test that activity and weight changes are properly computed with learning
R.learning_enabled = True
p.execute([1, 1, 0, 0])
np.testing.assert_allclose(R.parameters.value.get(p), [[1.28, 1.28, 0.28, 0.28]])
np.testing.assert_allclose(
R.recurrent_projection.get_mod_matrix(p),
[
[0.1, 0.18192000000000003, 0.11792000000000001, 0.11792000000000001],
[0.18192000000000003, 0.1, 0.11792000000000001, 0.11792000000000001],
[0.11792000000000001, 0.11792000000000001, 0.1, 0.10392000000000001],
[0.11792000000000001, 0.11792000000000001, 0.10392000000000001, 0.1]
]
)
p.execute([1, 1, 0, 0])
np.testing.assert_allclose(R.parameters.value.get(p), [[1.4268928, 1.4268928, 0.3589728, 0.3589728]])
np.testing.assert_allclose(
R.recurrent_projection.get_mod_matrix(p),
[
[0.1, 0.28372115, 0.14353079, 0.14353079],
[0.28372115, 0.1, 0.14353079, 0.14353079],
[0.14353079, 0.14353079, 0.1, 0.11036307],
[0.14353079, 0.14353079, 0.11036307, 0.1]
]
)
def test_recurrent_mech_integration_rate_0_8_initial_1_8(self):
R = RecurrentTransferMechanism(
name='R',
default_variable=[0, 0, 0, 0],
function=Linear(),
integration_rate=0.8,
initial_value=np.array([[1.8, 1.8, 1.8, 1.8]]),
integrator_mode=True
)
val = R.execute([1, 1, 1, 1])
np.testing.assert_allclose(val, [[1.16, 1.16, 1.16, 1.16]])
val = R.execute([2, 2, 2, 2])
np.testing.assert_allclose(val, [[1.832, 1.832, 1.832, 1.832]])
val = R.execute([-4, -3, 0, 1])
np.testing.assert_allclose(val, [[-2.8336, -2.0336000000000003, .36639999999999995, 1.1663999999999999]])
def test_recurrent_mech_auto_hetero_matrix_spec_v1(self):
# auto and hetero should override matrix
R = RecurrentTransferMechanism(
name='R',
size=4,
auto=[1, 3, 5, 7],
hetero=np.array([[-4, -3, -2, -1]] * 4),
matrix=[[1, 2, 3, 4]] * 4
)
val = R.execute([1, 2, 3, 4])
np.testing.assert_allclose(val, [[1., 2., 3., 4.]])
np.testing.assert_allclose(
R.matrix,
[[1, -3, -2, -1], [-4, 3, -2, -1], [-4, -3, 5, -1], [-4, -3, -2, 7]]
)
def test_initialize_mechanisms(self):
A = TransferMechanism(name='A')
B = TransferMechanism(name='B')
C = RecurrentTransferMechanism(name='C', auto=1.0)
abc_process = Process(pathway=[A, B, C])
abc_system = System(processes=[abc_process])
C.log.set_log_conditions('value')
abc_system.run(inputs={A: [1.0, 2.0, 3.0]},
initial_values={
A: 1.0,
B: 1.5,
C: 2.0
},
initialize=True)
abc_system.run(inputs={A: [1.0, 2.0, 3.0]},
initial_values={
A: 1.0,
B: 1.5,
C: 2.0
},
initialize=False)
# Run 1 --> Execution 1: 1 + 2 = 3 | Execution 2: 3 + 2 = 5 | Execution 3: 5 + 3 = 8
# Run 2 --> Execution 1: 8 + 1 = 9 | Execution 2: 9 + 2 = 11 | Execution 3: 11 + 3 = 14
assert np.allclose(
C.log.nparray_dictionary('value')[abc_system.default_execution_id]
['value'], [[[3]], [[5]], [[8]], [[9]], [[11]], [[14]]])
def test_recurrent_transfer_origin(self):
R = RecurrentTransferMechanism(has_recurrent_input_state=True)
P = Process(pathway=[R])
S = System(processes=[P])
S.run(inputs={R: [[1.0], [2.0], [3.0]]})
print(S.results)
def test_recurrent_mech_integrator(self, benchmark, mode):
R = RecurrentTransferMechanism(size=2,
function=Logistic(),
hetero=-2.0,
integrator_mode=True,
integration_rate=0.01,
output_states = [RECURRENT_OUTPUT.RESULT])
if mode == 'Python':
EX = R.execute
elif mode == 'LLVM':
e = pnlvm.execution.MechExecution(R)
EX = e.execute
elif mode == 'PTX':
e = pnlvm.execution.MechExecution(R)
EX = e.cuda_execute
val1 = EX([[1.0, 2.0]])
val2 = EX([[1.0, 2.0]])
# execute 10 times
for i in range(10):
val = EX([[1.0, 2.0]])
benchmark(EX, [[1.0, 2.0]])
assert np.allclose(val1, [[0.50249998, 0.50499983]])
assert np.allclose(val2, [[0.50497484, 0.50994869]])
assert np.allclose(val, [[0.52837327, 0.55656439]])
def test_recurrent_mech_check_proj_attrs(self):
R = RecurrentTransferMechanism(
name='R',
size=3
)
np.testing.assert_allclose(R.recurrent_projection.matrix, R.matrix)
assert R.recurrent_projection.sender is R.output_state
assert R.recurrent_projection.receiver is R.input_state
def test_recurrent_mech_matrix_3d(self):
with pytest.raises(FunctionError) as error_text:
R = RecurrentTransferMechanism(
name='R',
size=2,
matrix=[[[1, 3], [2, 4]], [[5, 7], [6, 8]]]
)
assert "more than 2d" in str(error_text.value)