def test_simple_pyfunc(self):
dt = 0.001
m = nengo.Model("test_simple_pyfunc")
time = Signal(np.zeros(1), name='time')
sig = Signal(np.zeros(1), name='sig')
pop = nengo.PythonFunction(fn=lambda t, x: np.sin(x), n_in=1)
m.operators = []
b = Builder()
b.model = m
b.build_pyfunc(pop)
m.operators += [
ProdUpdate(Signal(dt), Signal(1), Signal(1), time),
DotInc(Signal([[1.0]]), time, pop.input_signal),
ProdUpdate(Signal([[1.0]]), pop.output_signal, Signal(0), sig),
]
sim = self.Simulator(m, dt=dt, builder=testbuilder)
sim.step()
for i in range(5):
sim.step()
t = (i + 2) * dt
self.assertTrue(np.allclose(sim.signals[time], t),
msg='%s != %s' % (sim.signals[time], t))
self.assertTrue(
np.allclose(
sim.signals[sig], np.sin(t - dt*2)),
msg='%s != %s' % (sim.signals[sig], np.sin(t - dt*2)))
def _test_lif_base(self, cls=nengo.LIF):
"""Test that the dynamic model approximately matches the rates"""
rng = np.random.RandomState(85243)
dt = 0.001
d = 1
n = 5000
m = nengo.Model("")
ins = Signal(0.5 * np.ones(d), name='ins')
lif = cls(n)
lif.set_gain_bias(max_rates=rng.uniform(low=10, high=200, size=n),
intercepts=rng.uniform(low=-1, high=1, size=n))
m.operators = []
b = Builder()
b.model = m
b._builders[cls](lif)
m.operators += [DotInc(Signal(np.ones((n, d))), ins, lif.input_signal)]
sim = self.Simulator(m, dt=dt, builder=testbuilder)
t_final = 1.0
spikes = np.zeros(n)
for i in range(int(np.round(t_final / dt))):
sim.step()
spikes += sim.signals[lif.output_signal]
math_rates = lif.rates(sim.signals[lif.input_signal] - lif.bias)
sim_rates = spikes / t_final
logger.debug("ME = %f", (sim_rates - math_rates).mean())
logger.debug("RMSE = %f",
rms(sim_rates - math_rates) / (rms(math_rates) + 1e-20))
self.assertTrue(np.sum(math_rates > 0) > 0.5*n,
"At least 50% of neurons must fire")
self.assertTrue(np.allclose(sim_rates, math_rates, atol=1, rtol=0.02))
def test_encoder_decoder_pathway(self):
"""Verifies (like by hand) that the simulator does the right
things in the right order."""
m = nengo.Model("")
dt = 0.001
foo = Signal([1.0], name='foo')
pop = nengo.PythonFunction(fn=lambda t, x: x + 1, n_in=2, label='pop')
decoders = np.asarray([.2, .1])
decs = Signal(decoders * 0.5)
m.operators = []
b = Builder()
b.model = m
b.build_pyfunc(pop)
m.operators += [
DotInc(Signal([[1.0], [2.0]]), foo, pop.input_signal),
ProdUpdate(decs, pop.output_signal, Signal(0.2), foo)
]
def check(sig, target):
self.assertTrue(np.allclose(sim.signals[sig], target),
"%s: value %s is not close to target %s" %
(sig, sim.signals[sig], target))
sim = self.Simulator(m, dt=dt, builder=testbuilder)
check(foo, 1.0)
check(pop.input_signal, 0)
check(pop.output_signal, 0)
sim.step()
#DotInc to pop.input_signal (input=[1.0,2.0])
#produpdate updates foo (foo=[0.2])
#pop updates pop.output_signal (output=[2,3])
check(pop.input_signal, [1, 2])
check(pop.output_signal, [2, 3])
check(foo, .2)
check(decs, [.1, .05])
sim.step()
#DotInc to pop.input_signal (input=[0.2,0.4])
# (note that pop resets its own input signal each timestep)
#produpdate updates foo (foo=[0.39]) 0.2*0.5*2+0.1*0.5*3 + 0.2*0.2
#pop updates pop.output_signal (output=[1.2,1.4])
check(decs, [.1, .05])
check(pop.input_signal, [0.2, 0.4])
check(pop.output_signal, [1.2, 1.4])
# -- foo is computed as a prodUpdate of the *previous* output signal
# foo <- .2 * foo + dot(decoders * .5, output_signal)
# .2 * .2 + dot([.2, .1] * .5, [2, 3])
# .04 + (.2 + .15)
# <- .39
check(foo, .39)
def test_simple_direct_mode(self):
dt = 0.001
m = nengo.Model("test_simple_direct_mode")
time = Signal(n=1, name='time')
sig = Signal(n=1, name='sig')
pop = Direct(n_in=1, n_out=1, fn=np.sin)
m.signals = [sig, time]
m.operators = []
Builder().build_direct(pop, m, dt)
m.operators += [
ProdUpdate(Constant(dt), Constant(1), Constant(1), time),
DotInc(Constant([[1.0]]), time, pop.input_signal),
ProdUpdate(Constant([[1.0]]), pop.output_signal, Constant(0), sig)
]
sim = m.simulator(sim_class=self.Simulator, dt=dt, builder=testbuilder)
sim.step()
for i in range(5):
sim.step()
t = (i + 2) * dt
self.assertTrue(np.allclose(sim.signals[time], t),
msg='%s != %s' % (sim.signals[time], t))
self.assertTrue(np.allclose(sim.signals[sig], np.sin(t - dt * 2)),
msg='%s != %s' %
(sim.signals[sig], np.sin(t - dt * 2)))
def test_encoder_decoder_with_views(self):
m = nengo.Model("")
dt = 0.001
foo = Signal([1.0], name='foo')
pop = nengo.PythonFunction(fn=lambda t, x: x + 1, n_in=2, label='pop')
decoders = np.asarray([.2, .1])
m.operators = []
b = Builder()
b.model = m
b.build_pyfunc(pop)
m.operators += [
DotInc(Signal([[1.0], [2.0]]), foo[:], pop.input_signal),
ProdUpdate(
Signal(decoders * 0.5), pop.output_signal, Signal(0.2), foo[:])
]
def check(sig, target):
self.assertTrue(np.allclose(sim.signals[sig], target),
"%s: value %s is not close to target %s" %
(sig, sim.signals[sig], target))
sim = self.Simulator(m, dt=dt, builder=testbuilder)
#pop.input_signal = [0,0]
#pop.output_signal = [0,0]
sim.step()
#DotInc to pop.input_signal (input=[1.0,2.0])
#produpdate updates foo (foo=[0.2])
#pop updates pop.output_signal (output=[2,3])
check(foo, .2)
check(pop.input_signal, [1, 2])
check(pop.output_signal, [2, 3])
sim.step()
#DotInc to pop.input_signal (input=[0.2,0.4])
# (note that pop resets its own input signal each timestep)
#produpdate updates foo (foo=[0.39]) 0.2*0.5*2+0.1*0.5*3 + 0.2*0.2
#pop updates pop.output_signal (output=[1.2,1.4])
check(foo, .39)
check(pop.input_signal, [0.2, 0.4])
check(pop.output_signal, [1.2, 1.4])
def test_pyfunc(self):
"""Test Python Function nonlinearity"""
dt = 0.001
d = 3
n_steps = 3
n_trials = 3
rng = np.random.RandomState(seed=987)
for i in range(n_trials):
A = rng.normal(size=(d, d))
fn = lambda t, x: np.cos(np.dot(A, x))
x = np.random.normal(size=d)
m = nengo.Model("")
ins = Signal(x, name='ins')
pop = nengo.PythonFunction(fn=fn, n_in=d)
m.operators = []
b = Builder()
b.model = m
b.build_pyfunc(pop)
m.operators += [
DotInc(Signal(np.eye(d)), ins, pop.input_signal),
ProdUpdate(
Signal(np.eye(d)), pop.output_signal, Signal(0), ins)
]
sim = self.Simulator(m, dt=dt, builder=testbuilder)
p0 = np.zeros(d)
s0 = np.array(x)
for j in range(n_steps):
tmp = p0
p0 = fn(0, s0)
s0 = tmp
sim.step()
assert_allclose(self, logger, s0, sim.signals[ins])
assert_allclose(
self, logger, p0, sim.signals[pop.output_signal])
def test_custom_type(Simulator, allclose):
"""Test with custom learning rule type.
A custom learning type may have ``size_in`` not equal to 0, 1, or None.
"""
class TestRule(nengo.learning_rules.LearningRuleType):
modifies = "decoders"
def __init__(self):
super().__init__(1.0, size_in=3)
def build_test_rule(model, _, rule):
error = Signal(np.zeros(rule.connection.size_in))
model.add_op(Reset(error))
model.sig[rule]["in"] = error[:rule.size_in]
model.add_op(Copy(error, model.sig[rule]["delta"]))
Builder.register(TestRule)(build_test_rule)
with nengo.Network() as net:
a = nengo.Ensemble(10, 1)
b = nengo.Ensemble(10, 1)
conn = nengo.Connection(a.neurons,
b,
transform=np.zeros((1, 10)),
learning_rule_type=TestRule())
err = nengo.Node([1, 2, 3])
nengo.Connection(err, conn.learning_rule, synapse=None)
p = nengo.Probe(conn, "weights")
with Simulator(net) as sim:
sim.run(sim.dt * 5)
assert allclose(sim.data[p][:, 0, :3],
np.outer(np.arange(1, 6), np.arange(1, 4)))
assert allclose(sim.data[p][:, :, 3:], 0)
def test_encoder_decoder_with_views(self):
m = nengo.Model("")
dt = 0.001
foo = Signal(n=1, name='foo')
pop = Direct(n_in=2, n_out=2, fn=lambda x: x + 1, name='pop')
decoders = np.asarray([.2, .1])
m.signals = [foo]
m.operators = []
Builder().build_direct(pop, m, dt)
m.operators += [
DotInc(Constant([[1.0], [2.0]]), foo[:], pop.input_signal),
ProdUpdate(Constant(decoders * 0.5), pop.output_signal,
Constant(0.2), foo[:])
]
def check(sig, target):
self.assertTrue(
np.allclose(sim.signals[sig],
target), "%s: value %s is not close to target %s" %
(sig, sim.signals[sig], target))
sim = m.simulator(sim_class=self.Simulator, dt=dt, builder=testbuilder)
#set initial value of foo (foo=1.0)
sim.signals[foo] = np.asarray([1.0])
#pop.input_signal = [0,0]
#pop.output_signal = [0,0]
sim.step()
#DotInc to pop.input_signal (input=[1.0,2.0])
#produpdate updates foo (foo=[0.2])
#pop updates pop.output_signal (output=[2,3])
check(foo, .2)
check(pop.input_signal, [1, 2])
check(pop.output_signal, [2, 3])
sim.step()
#DotInc to pop.input_signal (input=[0.2,0.4])
# (note that pop resets its own input signal each timestep)
#produpdate updates foo (foo=[0.39]) 0.2*0.5*2+0.1*0.5*3 + 0.2*0.2
#pop updates pop.output_signal (output=[1.2,1.4])
check(foo, .39)
check(pop.input_signal, [0.2, 0.4])
check(pop.output_signal, [1.2, 1.4])
def test_direct(self):
"""Test direct mode"""
dt = 0.001
d = 3
n_steps = 3
n_trials = 3
rng = np.random.RandomState(seed=987)
for i in xrange(n_trials):
A = rng.normal(size=(d, d))
fn = lambda x: np.cos(np.dot(A, x))
x = np.random.normal(size=d)
m = nengo.Model("")
ins = Signal(n=d, name='ins')
pop = Direct(n_in=d, n_out=d, fn=fn)
m.signals = [ins]
m.operators = []
Builder().build_direct(pop, m, dt)
m.operators += [
DotInc(Constant(np.eye(d)), ins, pop.input_signal),
ProdUpdate(Constant(np.eye(d)), pop.output_signal, Constant(0),
ins)
]
sim = m.simulator(sim_class=self.Simulator,
dt=dt,
builder=testbuilder)
sim.signals[ins] = x
p0 = np.zeros(d)
s0 = np.array(x)
for j in xrange(n_steps):
tmp = p0
p0 = fn(s0)
s0 = tmp
sim.step()
assert np.allclose(s0, sim.signals[ins])
assert np.allclose(p0, sim.signals[pop.output_signal])
def _test_lif_base(self, cls=LIF):
"""Test that the dynamic model approximately matches the rates"""
rng = np.random.RandomState(85243)
dt = 0.001
d = 1
n = 5e3
m = nengo.Model("")
ins = Signal(n=d, name='ins')
lif = cls(n)
lif.set_gain_bias(max_rates=rng.uniform(low=10, high=200, size=n),
intercepts=rng.uniform(low=-1, high=1, size=n))
m.signals = [ins]
m.operators = []
b = Builder()
b._builders[cls](lif, m, dt)
m.operators += [
DotInc(Constant(np.ones((n, d))), ins, lif.input_signal)
]
sim = m.simulator(sim_class=self.Simulator, dt=dt, builder=testbuilder)
sim.signals[ins] = 0.5 * np.ones(d)
t_final = 1.0
spikes = np.zeros(n)
for i in xrange(int(np.round(t_final / dt))):
sim.step()
spikes += sim.signals[lif.output_signal]
math_rates = lif.rates(sim.signals[lif.input_signal] - lif.bias)
sim_rates = spikes / t_final
logger.debug("ME = %f", (sim_rates - math_rates).mean())
logger.debug("RMSE = %f",
rms(sim_rates - math_rates) / (rms(math_rates) + 1e-20))
self.assertTrue(
np.sum(math_rates > 0) > 0.5 * n,
"At least 50% of neurons must fire")
self.assertTrue(np.allclose(sim_rates, math_rates, atol=1, rtol=0.02))
def __init__(self, network, dt=0.001, seed=None, model=None):
"""Initialize the simulator with a network and (optionally) a model.
Most of the time, you will pass in a network and sometimes a dt::
sim1 = nengo.Simulator(my_network) # Uses default 0.001s dt
sim2 = nengo.Simulator(my_network, dt=0.01) # Uses 0.01s dt
For more advanced use cases, you can initialize the model yourself,
and also pass in a network that will be built into the same model
that you pass in::
sim = nengo.Simulator(my_network, model=my_model)
If you want full control over the build process, then you can build
your network into the model manually. If you do this, then you must
explicitly pass in ``None`` for the network::
sim = nengo.Simulator(None, model=my_model)
Parameters
----------
network : nengo.Network instance or None
A network object to the built and then simulated.
If a fully built ``model`` is passed in, then you can skip
building the network by passing in network=None.
dt : float
The length of a simulator timestep, in seconds.
seed : int
A seed for all stochastic operators used in this simulator.
Note that there are not stochastic operators implemented
currently, so this parameters does nothing.
model : nengo.builder.Model instance or None
A model object that contains build artifacts to be simulated.
Usually the simulator will build this model for you; however,
if you want to build the network manually, or to inject some
build artifacts in the Model before building the network,
then you can pass in a ``nengo.builder.Model`` instance.
"""
self.dt = dt
if model is None:
self.model = Model(dt=self.dt, label="%s, dt=%f" % (network.label, dt), seed=network.seed)
else:
self.model = model
if network is not None:
# Build the network into the model
Builder.build(network, model=self.model)
# Use model seed as simulator seed if the seed is not provided
# Note: seed is not used right now, but one day...
self.seed = self.model.seed if seed is None else seed
# -- map from Signal.base -> ndarray
self.signals = SignalDict(__time__=np.asarray(0.0, dtype=np.float64))
for op in self.model.operators:
op.init_signals(self.signals, self.dt)
self.dg = operator_depencency_graph(self.model.operators)
self._step_order = [node for node in toposort(self.dg) if hasattr(node, "make_step")]
self._steps = [node.make_step(self.signals, self.dt) for node in self._step_order]
self.n_steps = 0
# Add built states to the probe dictionary
self._probe_outputs = self.model.params
# Provide a nicer interface to probe outputs
self.data = ProbeDict(self._probe_outputs)
def test_encoder_decoder_pathway(self):
#
# This test is a very short and small simulation that
# verifies (like by hand) that the simulator does the right
# things in the right order.
#
m = nengo.Model("")
dt = 0.001
foo = Signal(n=1, name='foo')
pop = Direct(n_in=2, n_out=2, fn=lambda x: x + 1, name='pop')
decoders = np.asarray([.2, .1])
decs = Constant(decoders * 0.5)
m.signals = [foo, decs]
m.operators = []
Builder().build_direct(pop, m, dt)
m.operators += [
DotInc(Constant([[1.0], [2.0]]), foo, pop.input_signal),
ProdUpdate(decs, pop.output_signal, Constant(0.2), foo)
]
def check(sig, target):
self.assertTrue(
np.allclose(sim.signals[sig],
target), "%s: value %s is not close to target %s" %
(sig, sim.signals[sig], target))
sim = m.simulator(sim_class=self.Simulator, dt=dt, builder=testbuilder)
# -- initialize things
sim.signals[foo] = np.asarray([1.0])
check(foo, 1.0)
check(pop.input_signal, 0)
check(pop.output_signal, 0)
sim.step()
#DotInc to pop.input_signal (input=[1.0,2.0])
#produpdate updates foo (foo=[0.2])
#pop updates pop.output_signal (output=[2,3])
check(pop.input_signal, [1, 2])
check(pop.output_signal, [2, 3])
check(foo, .2)
check(decs, [.1, .05])
sim.step()
#DotInc to pop.input_signal (input=[0.2,0.4])
# (note that pop resets its own input signal each timestep)
#produpdate updates foo (foo=[0.39]) 0.2*0.5*2+0.1*0.5*3 + 0.2*0.2
#pop updates pop.output_signal (output=[1.2,1.4])
check(decs, [.1, .05])
check(pop.input_signal, [0.2, 0.4])
check(pop.output_signal, [1.2, 1.4])
# -- foo is computed as a prodUpdate of the *previous* output signal
# foo <- .2 * foo + dot(decoders * .5, output_signal)
# .2 * .2 + dot([.2, .1] * .5, [2, 3])
# .04 + (.2 + .15)
# <- .39
check(foo, .39)
def __init__(self, network, dt=0.001, seed=None, model=None):
"""Initialize the simulator with a network and (optionally) a model.
Most of the time, you will pass in a network and sometimes a dt::
sim1 = nengo.Simulator(my_network) # Uses default 0.001s dt
sim2 = nengo.Simulator(my_network, dt=0.01) # Uses 0.01s dt
For more advanced use cases, you can initialize the model yourself,
and also pass in a network that will be built into the same model
that you pass in::
sim = nengo.Simulator(my_network, model=my_model)
If you want full control over the build process, then you can build
your network into the model manually. If you do this, then you must
explicitly pass in ``None`` for the network::
sim = nengo.Simulator(None, model=my_model)
Parameters
----------
network : nengo.Network instance or None
A network object to the built and then simulated.
If a fully built ``model`` is passed in, then you can skip
building the network by passing in network=None.
dt : float
The length of a simulator timestep, in seconds.
seed : int
A seed for all stochastic operators used in this simulator.
Note that there are not stochastic operators implemented
currently, so this parameters does nothing.
model : nengo.builder.Model instance or None
A model object that contains build artifacts to be simulated.
Usually the simulator will build this model for you; however,
if you want to build the network manually, or to inject some
build artifacts in the Model before building the network,
then you can pass in a ``nengo.builder.Model`` instance.
"""
self.dt = dt
if model is None:
self.model = Model(dt=self.dt,
label="%s, dt=%f" % (network.label, dt),
seed=network.seed)
else:
self.model = model
if network is not None:
# Build the network into the model
Builder.build(network, model=self.model)
# Use model seed as simulator seed if the seed is not provided
# Note: seed is not used right now, but one day...
self.seed = self.model.seed if seed is None else seed
# -- map from Signal.base -> ndarray
self.signals = SignalDict(__time__=np.asarray(0.0, dtype=np.float64))
for op in self.model.operators:
op.init_signals(self.signals, self.dt)
self.dg = operator_depencency_graph(self.model.operators)
self._step_order = [node for node in toposort(self.dg)
if hasattr(node, 'make_step')]
self._steps = [node.make_step(self.signals, self.dt)
for node in self._step_order]
self.n_steps = 0
# Add built states to the probe dictionary
self._probe_outputs = self.model.params
# Provide a nicer interface to probe outputs
self.data = ProbeDict(self._probe_outputs)