def convert_dense(self, model, pre_layer, input_shape, index,
onnx_model_graph):
onnx_model_graph_node = onnx_model_graph.node
node_info = onnx_model_graph_node[index]
dense_num = self.get_dense_num(node_info, onnx_model_graph)
neuron_type = self.get_neuronType(index, onnx_model_graph_node)
with model:
x = nengo_dl.tensor_layer(pre_layer,
tf.layers.dense,
units=dense_num)
if neuron_type != "softmax":
if neuron_type == "lif":
x = nengo_dl.tensor_layer(
x, nengo.LIF(amplitude=self.amplitude))
elif neuron_type == "lifrate":
x = nengo_dl.tensor_layer(
x, nengo.LIFRate(amplitude=self.amplitude))
elif neuron_type == "adaptivelif":
x = nengo_dl.tensor_layer(
x, nengo.AdaptiveLIF(amplitude=self.amplitude))
elif neuron_type == "adaptivelifrate":
x = nengo_dl.tensor_layer(
x, nengo.AdaptiveLIFRate(amplitude=self.amplitude))
elif neuron_type == "izhikevich":
x = nengo_dl.tensor_layer(
x, nengo.Izhikevich(amplitude=self.amplitude))
elif neuron_type == "softlifrate":
x = nengo_dl.tensor_layer(
x,
nengo_dl.neurons.SoftLIFRate(amplitude=self.amplitude))
elif neuron_type == None: #default neuron_type = LIF
x = nengo_dl.tensor_layer(
x, nengo.LIF(amplitude=self.amplitude))
output_shape = [dense_num, 1]
return model, output_shape, x
def test_neuron_slicing(Simulator, plt, seed, rng, allclose):
N = 6
sa = slice(None, None, 2)
sb = slice(None, None, -2)
x = np.array([-1, -0.25, 1])
with nengo.Network(seed=seed) as m:
m.config[nengo.Ensemble].neuron_type = nengo.LIFRate()
u = nengo.Node(output=x)
a = nengo.Ensemble(N, dimensions=3, radius=1.7)
b = nengo.Ensemble(N, dimensions=3, radius=1.7)
nengo.Connection(u, a)
c = nengo.Connection(a.neurons[sa], b.neurons[sb])
c.transform = rng.normal(scale=1e-3, size=(c.size_out, c.size_in))
ap = nengo.Probe(a.neurons, synapse=0.03)
bp = nengo.Probe(b.neurons, synapse=0.03)
with Simulator(m) as sim:
sim.run(0.2)
t = sim.trange()
x = sim.data[ap]
y = np.zeros((len(t), b.n_neurons))
y[:, sb] = np.dot(x[:, sa], c.transform.init.T)
y = b.neuron_type.rates(y, sim.data[b].gain, sim.data[b].bias)
plt.plot(t, y, "k--")
plt.plot(t, sim.data[bp])
assert allclose(y[-10:], sim.data[bp][-10:], atol=3.0, rtol=0.0)
def test_lif_rate(ctx, blockify):
"""Test the `lif_rate` nonlinearity"""
rng = np.random
dt = 1e-3
n_neurons = [123459, 23456, 34567]
J = RA([rng.normal(loc=1, scale=10, size=n) for n in n_neurons])
R = RA([np.zeros(n) for n in n_neurons])
ref = 2e-3
taus = list(rng.uniform(low=15e-3, high=80e-3, size=len(n_neurons)))
queue = cl.CommandQueue(ctx)
clJ = CLRA(queue, J)
clR = CLRA(queue, R)
clTaus = CLRA(queue, RA([t * np.ones(n) for t, n in zip(taus, n_neurons)]))
# simulate host
nls = [nengo.LIFRate(tau_ref=ref, tau_rc=taus[i])
for i, n in enumerate(n_neurons)]
for i, nl in enumerate(nls):
nl.step_math(dt, J[i], R[i])
# simulate device
plan = plan_lif_rate(queue, dt, clJ, clR, ref, clTaus, blockify=blockify)
plan()
rate_sum = np.sum([np.sum(r) for r in R])
if rate_sum < 1.0:
logger.warn("LIF rate was not tested above the firing threshold!")
assert ra.allclose(J, clJ.to_host())
assert ra.allclose(R, clR.to_host())
def build(self, testY):
self.count = 0
def update(x):
"""
Kalman Filter: X_k = A * X_k_1 + B * Y_k
"""
Externalmat = np.mat(x[2:4]).T
Inputmat = np.mat(x[0:2]).T
Controlmat = np.matrix([[x[4], x[5]], [x[6], x[7]]])
next_state = np.squeeze(
np.asarray(Controlmat * Inputmat + Externalmat))
return next_state
with self.model:
Dir_Nurons = nengo.Ensemble(1,
dimensions=2 + 2 + 4,
neuron_type=nengo.Direct())
LIF_Neurons = nengo.Ensemble(
self.N_A,
dimensions=2,
intercepts=Uniform(-1, 1),
max_rates=Uniform(self.rate_A[0], self.rate_A[1]),
neuron_type=nengo.LIFRate(tau_rc=self.t_rc,
tau_ref=self.t_ref))
state_func = Piecewise({
0.0: [0.0, 0.0],
self.dt:
np.squeeze(np.asarray(np.mat([testY[0], testY[1]]).T)),
2 * self.dt: [0.0, 0.0]
})
state = nengo.Node(output=state_func)
# state_probe = nengo.Probe(state)
external_input = nengo.Node(output=lambda t: self.data(t))
# external_input_probe = nengo.Probe(external_input)
control_signal = nengo.Node(output=lambda t: self.control(t))
conn0 = nengo.Connection(state, Dir_Nurons[0:2])
#
conn1 = nengo.Connection(external_input, Dir_Nurons[2:4])
conn2 = nengo.Connection(control_signal, Dir_Nurons[4:8])
conn3 = nengo.Connection(Dir_Nurons,
LIF_Neurons[0:2],
function=update,
synapse=self.tau)
conn4 = nengo.Connection(LIF_Neurons[0:2], Dir_Nurons[0:2])
self.output = nengo.Probe(LIF_Neurons[0:2])
self.sim = nengo.Simulator(self.model, dt=self.dt)
def test_scalar_rate(Simulator, seed):
_test_RLS_network(Simulator,
seed,
dims=1,
lrate=1,
neuron_type=nengo.LIFRate(),
tau=None,
T_train=1,
T_test=0.5,
tols=[0.02, 1e-3, 0.02, 0.3])
def _test_temporal_solver(plt, Simulator, seed, neuron_type, tau, f, solver):
dt = 0.002
# we are cheating a bit here because we'll use the same training data as
# test data. this makes the unit testing a bit simpler since it's more
# obvious what will happen when comparing temporal to default
t = np.arange(0, 0.2, dt)
stim = np.sin(2 * np.pi * 10 * t)
function = (f(stim) if tau is None else nengo.Lowpass(tau).filt(f(stim),
dt=dt))
with Network(seed=seed) as model:
u = nengo.Node(output=nengo.processes.PresentInput(stim, dt))
x = nengo.Ensemble(100, 1, neuron_type=neuron_type)
output_ideal = nengo.Node(size_in=1)
post = dict(n_neurons=500,
dimensions=1,
neuron_type=nengo.LIFRate(),
seed=seed + 1)
output_temporal = nengo.Ensemble(**post)
output_default = nengo.Ensemble(**post)
nengo.Connection(u, output_ideal, synapse=tau, function=f)
nengo.Connection(u, x, synapse=None)
nengo.Connection(x,
output_temporal,
synapse=tau,
eval_points=stim[:, None],
function=function[:, None],
solver=Temporal(synapse=tau, solver=solver))
nengo.Connection(x,
output_default,
synapse=tau,
eval_points=stim[:, None],
function=f,
solver=solver)
p_ideal = nengo.Probe(output_ideal, synapse=None)
p_temporal = nengo.Probe(output_temporal, synapse=None)
p_default = nengo.Probe(output_default, synapse=None)
with Simulator(model, dt) as sim:
sim.run(t[-1])
plt.plot(sim.trange(),
sim.data[p_ideal] - sim.data[p_default],
label="Default")
plt.plot(sim.trange(),
sim.data[p_ideal] - sim.data[p_temporal],
label="Temporal")
plt.legend()
return (nrmse(sim.data[p_default], target=sim.data[p_ideal]) /
nrmse(sim.data[p_temporal], target=sim.data[p_ideal]))
def _test_rates(Simulator, rates, name=None):
if name is None:
name = rates.__name__
n = 100
max_rates = 50 * np.ones(n)
# max_rates = 200 * np.ones(n)
intercepts = np.linspace(-0.99, 0.99, n)
encoders = np.ones((n, 1))
nparams = dict(n_neurons=n)
eparams = dict(
max_rates=max_rates, intercepts=intercepts, encoders=encoders)
model = nengo.Network()
with model:
u = nengo.Node(output=whitenoise(1, 5, seed=8393))
a = nengo.Ensemble(nengo.LIFRate(**nparams), 1, **eparams)
b = nengo.Ensemble(nengo.LIF(**nparams), 1, **eparams)
nengo.Connection(u, a, synapse=0)
nengo.Connection(u, b, synapse=0)
up = nengo.Probe(u)
ap = nengo.Probe(a.neurons, "output", synapse=None)
bp = nengo.Probe(b.neurons, "output", synapse=None)
dt = 1e-3
sim = Simulator(model, dt=dt)
sim.run(2.)
t = sim.trange()
x = sim.data[up]
a_rates = sim.data[ap] / dt
spikes = sim.data[bp]
b_rates = rates(t, spikes)
with Plotter(Simulator) as plt:
ax = plt.subplot(411)
plt.plot(t, x)
ax = plt.subplot(412)
implot(plt, t, intercepts, a_rates.T, ax=ax)
ax.set_ylabel('intercept')
ax = plt.subplot(413)
implot(plt, t, intercepts, b_rates.T, ax=ax)
ax.set_ylabel('intercept')
ax = plt.subplot(414)
implot(plt, t, intercepts, (b_rates - a_rates).T, ax=ax)
ax.set_xlabel('time [s]')
ax.set_ylabel('intercept')
plt.savefig('utils.test_neurons.test_rates.%s.pdf' % name)
plt.close()
tmask = (t > 0.1) & (t < 1.9)
relative_rmse = rms(b_rates[tmask] - a_rates[tmask]) / rms(a_rates[tmask])
return relative_rmse
def convert_conv2d(self, model, pre_layer, input_shape, index,
onnx_model_graph):
onnx_model_graph_node = onnx_model_graph.node
node_info = onnx_model_graph_node[index]
neuron_type = self.get_neuronType(index, onnx_model_graph_node)
filters = self.get_filterNum(node_info, onnx_model_graph)
for index in range(len(node_info.attribute)):
if node_info.attribute[index].name == "kernel_shape":
kernel_size = node_info.attribute[index].ints[0]
elif node_info.attribute[index].name == "strides":
strides = node_info.attribute[index].ints[0]
elif node_info.attribute[index].name == "auto_pad":
padding = node_info.attribute[index].s.decode('ascii').lower()
if padding != "valid":
padding = "same"
if padding == "same":
output_shape = [input_shape[0], input_shape[1], filters]
else:
output_shape = [
int((input_shape[0] - kernel_size) / strides + 1),
int((input_shape[1] - kernel_size) / strides + 1), filters
]
with model:
x = nengo_dl.tensor_layer(pre_layer,
tf.layers.conv2d,
shape_in=(input_shape[0], input_shape[1],
input_shape[2]),
filters=filters,
kernel_size=kernel_size,
padding=padding)
if neuron_type == "lif":
x = nengo_dl.tensor_layer(x,
nengo.LIF(amplitude=self.amplitude))
elif neuron_type == "lifrate":
x = nengo_dl.tensor_layer(
x, nengo.LIFRate(amplitude=self.amplitude))
elif neuron_type == "adaptivelif":
x = nengo_dl.tensor_layer(
x, nengo.AdaptiveLIF(amplitude=self.amplitude))
elif neuron_type == "adaptivelifrate":
x = nengo_dl.tensor_layer(
x, nengo.AdaptiveLIFRate(amplitude=self.amplitude))
elif neuron_type == "izhikevich":
x = nengo_dl.tensor_layer(
x, nengo.Izhikevich(amplitude=self.amplitude))
elif neuron_type == "softlifrate":
x = nengo_dl.tensor_layer(
x, nengo_dl.neurons.SoftLIFRate(amplitude=self.amplitude))
elif neuron_type == None: #default neuron_type = LIF
x = nengo_dl.tensor_layer(x,
nengo.LIF(amplitude=self.amplitude))
return model, output_shape, x
def get_numpy_fn(kind, params):
if kind == 'lif':
lif = nengo.LIFRate(tau_rc=params['tau_rc'], tau_ref=params['tau_ref'])
return lambda x: (lif.rates(x, params['gain'], params['bias']) *
params['amp'])
elif kind == 'softlif':
softlif = SoftLIFRate(tau_rc=params['tau_rc'],
tau_ref=params['tau_ref'],
sigma=params['sigma'])
return lambda x: (softlif.rates(x, params['gain'], params['bias']) *
params['amp'])
else:
raise ValueError("Unknown neuron type '%s'" % kind)
def _test_rates(Simulator, rates, plt, seed):
n = 100
intercepts = np.linspace(-0.99, 0.99, n)
model = nengo.Network(seed=seed)
with model:
model.config[nengo.Ensemble].max_rates = nengo.dists.Choice([50])
model.config[nengo.Ensemble].encoders = nengo.dists.Choice([[1]])
u = nengo.Node(output=nengo.processes.WhiteSignal(2, high=5))
a = nengo.Ensemble(n,
1,
intercepts=intercepts,
neuron_type=nengo.LIFRate())
b = nengo.Ensemble(n,
1,
intercepts=intercepts,
neuron_type=nengo.LIF())
nengo.Connection(u, a, synapse=0)
nengo.Connection(u, b, synapse=0)
up = nengo.Probe(u)
ap = nengo.Probe(a.neurons)
bp = nengo.Probe(b.neurons)
with Simulator(model, seed=seed + 1) as sim:
sim.run(2.)
t = sim.trange()
x = sim.data[up]
a_rates = sim.data[ap]
spikes = sim.data[bp]
b_rates = rates(t, spikes)
if plt is not None:
ax = plt.subplot(411)
plt.plot(t, x)
ax = plt.subplot(412)
implot(plt, t, intercepts, a_rates.T, ax=ax)
ax.set_ylabel('intercept')
ax = plt.subplot(413)
implot(plt, t, intercepts, b_rates.T, ax=ax)
ax.set_ylabel('intercept')
ax = plt.subplot(414)
implot(plt, t, intercepts, (b_rates - a_rates).T, ax=ax)
ax.set_xlabel('time [s]')
ax.set_ylabel('intercept')
tmask = (t > 0.1) & (t < 1.9)
relative_rmse = rms(b_rates[tmask] - a_rates[tmask]) / rms(a_rates[tmask])
return relative_rmse
def _test_rates(Simulator, rates, plt, seed, name=None):
if name is None:
name = rates.__name__
n = 100
intercepts = np.linspace(-0.99, 0.99, n)
model = nengo.Network(seed=seed)
with model:
model.config[nengo.Ensemble].max_rates = Choice([50])
model.config[nengo.Ensemble].encoders = Choice([[1]])
u = nengo.Node(output=WhiteNoise(2., 5).f(
rng=np.random.RandomState(seed=seed)))
a = nengo.Ensemble(n, 1,
intercepts=intercepts, neuron_type=nengo.LIFRate())
b = nengo.Ensemble(n, 1,
intercepts=intercepts, neuron_type=nengo.LIF())
nengo.Connection(u, a, synapse=0)
nengo.Connection(u, b, synapse=0)
up = nengo.Probe(u)
ap = nengo.Probe(a.neurons)
bp = nengo.Probe(b.neurons)
sim = Simulator(model)
sim.run(2.)
t = sim.trange()
x = sim.data[up]
a_rates = sim.data[ap]
spikes = sim.data[bp]
b_rates = rates(t, spikes)
ax = plt.subplot(411)
plt.plot(t, x)
ax = plt.subplot(412)
implot(plt, t, intercepts, a_rates.T, ax=ax)
ax.set_ylabel('intercept')
ax = plt.subplot(413)
implot(plt, t, intercepts, b_rates.T, ax=ax)
ax.set_ylabel('intercept')
ax = plt.subplot(414)
implot(plt, t, intercepts, (b_rates - a_rates).T, ax=ax)
ax.set_xlabel('time [s]')
ax.set_ylabel('intercept')
plt.saveas = 'utils.test_neurons.test_rates.%s.pdf' % name
tmask = (t > 0.1) & (t < 1.9)
relative_rmse = rms(b_rates[tmask] - a_rates[tmask]) / rms(a_rates[tmask])
return relative_rmse
def __init__(self, botnet):
super(Grabbed, self).__init__()
with self:
self.has_grabbed = nengo.Ensemble(n_neurons=50, dimensions=1,
neuron_type=nengo.LIFRate())
def state(x):
if x<0.5: return 0
else: return 1
nengo.Connection(self.has_grabbed, self.has_grabbed, synapse=0.1)
def opened_gripper(x):
if x > -0.1:
return -1
else:
return 0
nengo.Connection(botnet.arm[3], self.has_grabbed,
function=opened_gripper)
def _add_neuron_layer(self, layer):
inputs = [self._get_input(layer)]
neuron = layer["neuron"]
ntype = neuron["type"]
n = layer["outputs"]
gain = 1.0
bias = 0.0
amplitude = 1.0
if ntype == "ident":
neuron_type = nengo.Direct()
elif ntype == "relu":
neuron_type = nengo.RectifiedLinear()
elif ntype == "logistic":
neuron_type = nengo.Sigmoid()
elif ntype == "softlif":
tau_ref, tau_rc, alpha, amp, sigma = [
neuron["params"][k] for k in ["t", "r", "a", "m", "g"]
]
lif_type = self.lif_type.lower()
if lif_type == "lif":
neuron_type = nengo.LIF(tau_rc=tau_rc, tau_ref=tau_ref)
elif lif_type == "lifrate":
neuron_type = nengo.LIFRate(tau_rc=tau_rc, tau_ref=tau_ref)
elif lif_type == "softlifrate":
neuron_type = SoftLIFRate(sigma=sigma,
tau_rc=tau_rc,
tau_ref=tau_ref)
else:
raise KeyError("Unrecognized LIF type %r" % self.lif_type)
gain = alpha
bias = 1.0
amplitude = amp
else:
raise NotImplementedError("Neuron type %r" % ntype)
return self.add_neuron_layer(
n,
inputs=inputs,
neuron_type=neuron_type,
synapse=self.synapse,
gain=gain,
bias=bias,
amplitude=amplitude,
name=layer["name"],
)
def test_softlifrate_rates(plt):
gain = 0.9
bias = 1.7
tau_rc = 0.03
tau_ref = 0.002
lif = nengo.LIFRate(tau_rc=tau_rc, tau_ref=tau_ref)
softlif = SoftLIFRate(tau_rc=tau_rc, tau_ref=tau_ref, sigma=0.00001)
x = np.linspace(-2, 2, 301)
lif_r = lif.rates(x, gain, bias)
softlif_r = softlif.rates(x, gain, bias)
plt.plot(x, lif_r)
plt.plot(x, softlif_r)
assert np.allclose(softlif_r, lif_r, atol=1e-3, rtol=1e-3)
def test_neuron_build_errors(Simulator):
# unsupported neuron type
with nengo.Network() as net:
nengo.Ensemble(5, 1, neuron_type=nengo.neurons.Sigmoid(tau_ref=0.005))
with pytest.raises(BuildError, match="type 'Sigmoid' cannot be simulated"):
with Simulator(net):
pass
# unsupported RegularSpiking type
with nengo.Network() as net:
nengo.Ensemble(5,
1,
neuron_type=nengo.RegularSpiking(
nengo.Sigmoid(tau_ref=0.005)))
with pytest.raises(BuildError,
match="RegularSpiking.*'Sigmoid'.*cannot be simu"):
with Simulator(net):
pass
# amplitude with RegularSpiking base type
with nengo.Network() as net:
nengo.Ensemble(5,
1,
neuron_type=nengo.RegularSpiking(
nengo.LIFRate(amplitude=0.5)))
with pytest.raises(BuildError,
match="Amplitude is not supported on RegularSpikin"):
with Simulator(net):
pass
# non-zero initial voltage warning
with nengo.Network() as net:
nengo.Ensemble(
5,
1,
neuron_type=nengo.LIF(
initial_state={"voltage": nengo.dists.Uniform(0, 1)}),
)
with pytest.warns(Warning,
match="initial values for 'voltage' being non-zero"):
with Simulator(net):
pass
def test_softlifrate_rates(plt, allclose):
gain = 0.9
bias = 1.7
tau_rc = 0.03
tau_ref = 0.002
lif = nengo.LIFRate(tau_rc=tau_rc, tau_ref=tau_ref)
softlif = SoftLIFRate(tau_rc=tau_rc, tau_ref=tau_ref, sigma=0.00001)
x = np.linspace(-2, 2, 301)
lif_r = lif.rates(x, gain, bias)
softlif_r = softlif.rates(x, gain, bias)
plt.plot(x, lif_r, label="LIF")
plt.plot(x, softlif_r, label="SoftLIF")
plt.legend(loc="best")
assert allclose(softlif_r, lif_r, atol=1e-3, rtol=1e-3)
def _add_softlif_layer(self, layer):
from .neurons import SoftLIFRate
taus = dict(tau_rc=layer.tau_rc, tau_ref=layer.tau_ref)
lif_type = self.lif_type.lower()
if lif_type == 'lif':
neuron_type = nengo.LIF(**taus)
elif lif_type == 'lifrate':
neuron_type = nengo.LIFRate(**taus)
elif lif_type == 'softlifrate':
neuron_type = SoftLIFRate(sigma=layer.sigma, **taus)
else:
raise KeyError("Unrecognized LIF type %r" % self.lif_type)
n = np.prod(layer.input_shape[1:])
return self.add_neuron_layer(
n, neuron_type=neuron_type, synapse=self.synapse,
gain=1, bias=1, amplitude=layer.amplitude, name=layer.name)
def test_minibatch(Simulator, seed):
with nengo.Network(seed=seed) as net:
inp = [
nengo.Node(output=[0.5]),
nengo.Node(output=np.sin),
nengo.Node(output=nengo.processes.WhiteSignal(5, 0.5, seed=seed))
]
ens = [
nengo.Ensemble(10, 1, neuron_type=nengo.AdaptiveLIF()),
nengo.Ensemble(10, 1, neuron_type=nengo.LIFRate()),
nengo.Ensemble(10, 2, noise=nengo.processes.WhiteNoise(seed=seed))
]
nengo.Connection(inp[0], ens[0])
nengo.Connection(inp[1], ens[1], synapse=None)
nengo.Connection(inp[2],
ens[2],
synapse=nengo.Alpha(0.1),
transform=[[1], [1]])
conn = nengo.Connection(ens[0], ens[1], learning_rule_type=nengo.PES())
nengo.Connection(inp[0], conn.learning_rule)
ps = [nengo.Probe(e) for e in ens]
with Simulator(net, minibatch_size=None) as sim:
probe_data = [[] for _ in ps]
for i in range(5):
sim.run_steps(100)
for j, p in enumerate(ps):
probe_data[j] += [sim.data[p]]
sim.reset()
probe_data = [np.stack(x, axis=0) for x in probe_data]
with Simulator(net, minibatch_size=5) as sim:
sim.run_steps(100)
assert np.allclose(sim.data[ps[0]], probe_data[0], atol=1e-6)
assert np.allclose(sim.data[ps[1]], probe_data[1], atol=1e-6)
assert np.allclose(sim.data[ps[2]], probe_data[2], atol=1e-6)
def test_neural_accuracy(Simulator, seed, rng, dims, neurons_per_product=128):
a = rng.normal(scale=np.sqrt(1.0 / dims), size=dims)
b = rng.normal(scale=np.sqrt(1.0 / dims), size=dims)
result = circconv(a, b)
model = nengo.Network(label="circular conv", seed=seed)
model.config[nengo.Ensemble].neuron_type = nengo.LIFRate()
with model:
input_a = nengo.Node(a)
input_b = nengo.Node(b)
cconv = nengo.networks.CircularConvolution(neurons_per_product, dimensions=dims)
nengo.Connection(input_a, cconv.input_a, synapse=None)
nengo.Connection(input_b, cconv.input_b, synapse=None)
res_p = nengo.Probe(cconv.output)
with Simulator(model) as sim:
sim.run(0.01)
error = rms(result - sim.data[res_p][-1])
assert error < 0.1
def _add_neuron_layer(self, layer):
neuron = layer['neuron']
ntype = neuron['type']
n = layer['outputs']
e = nengo.Ensemble(n, 1, label='%s_neurons' % layer['name'])
e.gain = np.ones(n)
e.bias = np.zeros(n)
transform = 1.
if ntype == 'ident':
e.neuron_type = nengo.Direct()
elif ntype == 'relu':
e.neuron_type = nengo.RectifiedLinear()
elif ntype == 'logistic':
e.neuron_type = nengo.Sigmoid()
elif ntype == 'softlif':
from .neurons import SoftLIFRate
tau_ref, tau_rc, alpha, amp, sigma, noise = [
neuron['params'][k] for k in ['t', 'r', 'a', 'm', 'g', 'n']]
lif_type = self.lif_type.lower()
if lif_type == 'lif':
e.neuron_type = nengo.LIF(tau_rc=tau_rc, tau_ref=tau_ref)
elif lif_type == 'lifrate':
e.neuron_type = nengo.LIFRate(tau_rc=tau_rc, tau_ref=tau_ref)
elif lif_type == 'softlifrate':
e.neuron_type = SoftLIFRate(
sigma=sigma, tau_rc=tau_rc, tau_ref=tau_ref)
else:
raise KeyError("Unrecognized LIF type %r" % self.lif_type)
e.gain = alpha * np.ones(n)
e.bias = np.ones(n)
transform = amp
else:
raise NotImplementedError("Neuron type %r" % ntype)
node = nengo.Node(size_in=n, label=layer['name'])
nengo.Connection(self._get_input(layer), e.neurons, synapse=None)
nengo.Connection(
e.neurons, node, transform=transform, synapse=self.synapse)
return node
def test_temporal_solver(plt, Simulator, seed):
plt.subplot(3, 1, 1)
for weights in (False, True):
assert 1.2 < _test_temporal_solver( # 1.5153... at dev time
plt, Simulator, seed, nengo.LIF(), 0.005, lambda x: x,
nengo.solvers.LstsqL2(weights=weights))
# LIFRate has no internal dynamics, and so the two solvers
# are actually numerically equivalent
plt.subplot(3, 1, 2)
assert np.allclose(
1,
_test_temporal_solver(plt, Simulator, seed, nengo.LIFRate(), None,
lambda x: 1 - 2 * x**2, nengo.solvers.LstsqL2()))
# We'll need to overfit slightly (small reg) to see the improvement for
# AdaptiveLIF (see thesis for a more principled way to improve)
plt.subplot(3, 1, 3)
assert 2.0 < _test_temporal_solver( # 2.2838... at dev time
plt, Simulator, seed, nengo.AdaptiveLIF(), 0.1, np.sin,
nengo.solvers.LstsqL2(reg=1e-5))
def test_learning_rate_schedule(Simulator):
with nengo.Network() as net:
a = nengo.Node([0])
b = nengo.Ensemble(10, 1, neuron_type=nengo.LIFRate())
nengo.Connection(a, b)
p = nengo.Probe(b)
with Simulator(net) as sim:
vals = [1.0, 0.1, 0.001]
with tf.device("/cpu:0"):
l_rate = tf.train.piecewise_constant(sim.training_step, [
tf.constant(4, dtype=tf.int64),
tf.constant(9, dtype=tf.int64)
], vals)
opt = tf.train.GradientDescentOptimizer(l_rate)
for i in range(3):
assert np.allclose(sim.sess.run(l_rate), vals[i])
sim.train({a: np.zeros((1, 10, 1))}, {p: np.zeros((1, 10, 1))},
opt,
n_epochs=5)
def make_vision_system(images, outputs, n_neurons = 1000, AIT_V1_strength = 0.06848695023305285, V1_r_transform = 0.11090645719111913, AIT_r_transform = 0.8079719992231219):
#represent currently attended item
vision_system = nengo.Network(label = 'vision_system')
with vision_system:
presentation_node = nengo.Node(None, size_in = images.shape[1], label = 'presentation_node')
vision_system.presentation_node = presentation_node
rng = np.random.RandomState(9)
encoders = Gabor().generate(n_neurons, (11, 11), rng=rng) # gabor encoders, work better, 11,11 apparently, why?
encoders = Mask((14, 90)).populate(encoders, rng=rng, flatten=True)
V1 = nengo.Ensemble(n_neurons, images.shape[1], eval_points=images,
neuron_type=nengo.LIFRate(),
intercepts=nengo.dists.Choice([-0.5]), #can switch these off
max_rates=nengo.dists.Choice([100]), # why?
encoders=encoders,
label = 'V1')
# 1000 neurons, nrofpix = dimensions
# visual_representation = nengo.Node(size_in=Dmid) #output, in this case 466 outputs
AIT = nengo.Ensemble(n_neurons, dimensions=outputs.shape[1], label = 'AIT') # output, in this case 466 outputs
visconn = nengo.Connection(V1, AIT, synapse=0.005,
eval_points = images, function=outputs,
solver=nengo.solvers.LstsqL2(reg=0.01))
Ait_V1_backwardsconn = nengo.Connection(AIT,V1, synapse = 0.005,
eval_points = outputs, function = images,
solver=nengo.solvers.LstsqL2(reg=0.01), transform = AIT_V1_strength) #Transform makes this connection a lot weaker then the forwards conneciton
nengo.Connection(presentation_node, V1, synapse=None)
nengo.Connection(AIT, AIT, synapse = 0.1, transform = AIT_r_transform)
nengo.Connection(V1, V1, synapse = 0.1, transform = V1_r_transform)
# display attended item
display_node = nengo.Node(display_func, size_in=presentation_node.size_out, label = 'display_node') # to show input
nengo.Connection(presentation_node, display_node, synapse=None)
# THESE PIECES MAKE EVERYTHING WORK please dont touch them
vision_system.AIT = AIT
vision_system.V1 = V1
return vision_system
def test_io(tmpdir):
tmpfile = str(tmpdir.join("model.pkl"))
m1 = nengo.Network()
with m1:
sin = nengo.Node(output=np.sin)
cons = nengo.Node(output=-.5)
factors = nengo.Ensemble(nengo.LIF(20), dimensions=2, radius=1.5)
factors.encoders = np.tile(
[[1, 1], [-1, 1], [1, -1], [-1, -1]],
(factors.n_neurons // 4, 1))
product = nengo.Ensemble(nengo.LIFRate(10), dimensions=1)
nengo.Connection(sin, factors[0])
nengo.Connection(cons, factors[1])
factors_p = nengo.Probe(
factors, 'decoded_output', sample_every=.01, synapse=.01)
assert factors_p # To suppress F841
product_p = nengo.Probe(
product, 'decoded_output', sample_every=.01, synapse=.01)
assert product_p # To suppress F841
m1.save(tmpfile)
m2 = nengo.Network.load(tmpfile)
assert m1 == m2
def _add_neuron_layer(self, layer):
inputs = [self._get_input(layer)]
neuron = layer['neuron']
ntype = neuron['type']
n = layer['outputs']
gain = 1.
bias = 0.
amplitude = 1.
if ntype == 'ident':
neuron_type = nengo.Direct()
elif ntype == 'relu':
neuron_type = nengo.RectifiedLinear()
elif ntype == 'logistic':
neuron_type = nengo.Sigmoid()
elif ntype == 'softlif':
from .neurons import SoftLIFRate
tau_ref, tau_rc, alpha, amp, sigma, noise = [
neuron['params'][k] for k in ['t', 'r', 'a', 'm', 'g', 'n']]
lif_type = self.lif_type.lower()
if lif_type == 'lif':
neuron_type = nengo.LIF(tau_rc=tau_rc, tau_ref=tau_ref)
elif lif_type == 'lifrate':
neuron_type = nengo.LIFRate(tau_rc=tau_rc, tau_ref=tau_ref)
elif lif_type == 'softlifrate':
neuron_type = SoftLIFRate(
sigma=sigma, tau_rc=tau_rc, tau_ref=tau_ref)
else:
raise KeyError("Unrecognized LIF type %r" % self.lif_type)
gain = alpha
bias = 1.
amplitude = amp
else:
raise NotImplementedError("Neuron type %r" % ntype)
return self.add_neuron_layer(
n, inputs=inputs, neuron_type=neuron_type, synapse=self.synapse,
gain=gain, bias=bias, amplitude=amplitude, name=layer['name'])
def test_input_magnitude(Simulator, seed, rng, dims=16, magnitude=10):
"""Test to make sure the magnitude scaling works.
Builds two different CircularConvolution networks, one with the correct
magnitude and one with 1.0 as the input_magnitude.
"""
neurons_per_product = 128
a = rng.normal(scale=np.sqrt(1. / dims), size=dims) * magnitude
b = rng.normal(scale=np.sqrt(1. / dims), size=dims) * magnitude
result = circconv(a, b)
model = nengo.Network(label="circular conv", seed=seed)
model.config[nengo.Ensemble].neuron_type = nengo.LIFRate()
with model:
inputA = nengo.Node(a)
inputB = nengo.Node(b)
cconv = nengo.networks.CircularConvolution(neurons_per_product,
dimensions=dims,
input_magnitude=magnitude)
nengo.Connection(inputA, cconv.A, synapse=None)
nengo.Connection(inputB, cconv.B, synapse=None)
res_p = nengo.Probe(cconv.output)
cconv_bad = nengo.networks.CircularConvolution(
neurons_per_product, dimensions=dims,
input_magnitude=1) # incorrect magnitude
nengo.Connection(inputA, cconv_bad.A, synapse=None)
nengo.Connection(inputB, cconv_bad.B, synapse=None)
res_p_bad = nengo.Probe(cconv_bad.output)
sim = Simulator(model)
sim.run(0.01)
error = rmse(result, sim.data[res_p][-1]) / (magnitude**2)
error_bad = rmse(result, sim.data[res_p_bad][-1]) / (magnitude**2)
assert error < 0.1
assert error_bad > 0.1
def test_connection(Simulator, seed, d):
with Network(seed=seed) as model:
stim = nengo.Node(output=lambda t: np.sin(t*2*np.pi), size_out=d)
x = nengo.Ensemble(1, d, intercepts=[-1], neuron_type=nengo.LIFRate())
default = nengo.Node(size_in=d)
improved = nengo.Node(size_in=d)
stim_conn = Connection(stim, x, synapse=None)
default_conn = nengo.Connection(x, default)
improved_conn = Connection(x, improved)
p_default = nengo.Probe(default)
p_improved = nengo.Probe(improved)
p_stim = nengo.Probe(stim, synapse=0.005)
assert not isinstance(stim_conn.solver, BiasedSolver)
assert not isinstance(default_conn.solver, BiasedSolver)
assert isinstance(improved_conn.solver, BiasedSolver)
with Simulator(model) as sim:
sim.run(1.0)
assert (rmse(sim.data[p_default], sim.data[p_stim]) >
rmse(sim.data[p_improved], sim.data[p_stim]))
def convert_dense(self, model, pre_layer, input_shape, index,
onnx_model_graph):
onnx_model_graph_node = onnx_model_graph.node
node_info = onnx_model_graph_node[index]
dense_num = self.get_dense_num(node_info, onnx_model_graph)
neuron_type = self.get_neuronType(
index,
onnx_model_graph_node) # node들 지나다니면서 - neuron이 op_type이 어떤건지 찾음
with model:
x = nengo_dl.Layer(
tf.keras.layers.Dense(units=dense_num))(pre_layer)
if neuron_type != "softmax":
if neuron_type == "lif":
x = nengo_dl.Layer(nengo.LIF(amplitude=self.amplitude))(x)
elif neuron_type == "lifrate":
x = nengo_dl.Layer(
nengo.LIFRate(amplitude=self.amplitude))(x)
elif neuron_type == "adaptivelif":
x = nengo_dl.Layer(
nengo.AdaptiveLIF(amplitude=self.amplitude))(x)
elif neuron_type == "adaptivelifrate":
x = nengo_dl.Layer(
nengo.AdaptiveLIFRate(amplitude=self.amplitude))(x)
elif neuron_type == "izhikevich":
x = nengo_dl.Layer(
nengo.Izhikevich(amplitude=self.amplitude))(x)
elif neuron_type == "softlifrate":
x = nengo_dl.Layer(
nengo_dl.neurons.SoftLIFRate(
amplitude=self.amplitude))(x)
elif neuron_type == None: # default neuron_type = LIF
x = nengo_dl.Layer(nengo.LIF(amplitude=self.amplitude))(x)
output_shape = [dense_num, 1]
print('convert Dense finish')
return model, output_shape, x # x를 return 하면서 모델을 계속 쌓아감
test_targets = one_hot(y_test, 10)
# --- set up network parameters
n_vis = X_train.shape[1]
n_out = train_targets.shape[1]
# n_hid = 300
n_hid = 1000
# n_hid = 3000
# encoders = rng.normal(size=(n_hid, 11, 11))
encoders = Gabor().generate(n_hid, (11, 11), rng=rng)
encoders = Mask((28, 28)).populate(encoders, rng=rng, flatten=True)
ens_params = dict(
eval_points=X_train,
neuron_type=nengo.LIFRate(),
intercepts=nengo.dists.Choice([-0.5]),
max_rates=nengo.dists.Choice([100]),
encoders=encoders,
)
solver = nengo.solvers.LstsqL2(reg=0.01)
# solver = nengo.solvers.LstsqL2(reg=0.0001)
with nengo.Network(seed=3) as model:
a = nengo.Ensemble(n_hid, n_vis, **ens_params)
v = nengo.Node(size_in=n_out)
conn = nengo.Connection(
a, v, synapse=None,
eval_points=X_train, function=train_targets, solver=solver)
def __init__(self, kp=0, kd=0, neural=False, adapt = False, num_motors=4, neuron_model=False, pes_learning_rate=1e-4):
#TODO
self.kp = kp
self.kd = kd
self.prev_time = time.time()
self.output = np.zeros(num_motors)
self.adapt = adapt
self.pes_learning_rate = pes_learning_rate
self.neuron_model = neuron_model
if neural == True:
model = nengo.Network(label="Adaptive Controller")
tau_rc = 0.02 #TODO: Check if this is in ms or s.
tau_ref = 0.002
if self.neuron_model == "RELU":
cur_model = nengo.RectifiedLinear()
elif self.neuron_model == "LIF":
cur_model = nengo.LIF(tau_rc=tau_rc, tau_ref=tau_ref) #lif model object.
elif self.neuron_model == "LIFRate":
cur_model = nengo.LIFRate(tau_rc=tau_rc, tau_ref=tau_ref) #lif model object.
def output_func(t, x):
self.output = np.copy(x)
def input_func_q(t, x):
return self.q
def input_func_dq(t, x):
return self.dq
def input_func_target(t, x):
return self.target
def input_func_d_target(t, x):
return self.d_target
with model:
output = nengo.Node(output_func, size_in=num_motors, size_out=0)
input_q = nengo.Node(input_func_q, size_in=num_motors, size_out=num_motors)
input_dq = nengo.Node(input_func_dq, size_in=num_motors, size_out=num_motors)
input_target = nengo.Node(input_func_target, size_in=num_motors, size_out=num_motors)
input_d_target = nengo.Node(input_func_d_target, size_in=num_motors, size_out=num_motors)
pes_learning_rate = 1e-4
#Adaptive component
if self.adapt:
adapt_ens = nengo.Ensemble(
n_neurons=1000, dimensions=num_motors,
radius=1.5,
neuron_type=cur_model)
learn_conn = nengo.Connection(
adapt_ens,
output,
learning_rule_type=nengo.PES(pes_learning_rate))
for i in range(num_motors):
inverter = nengo.Ensemble(500, dimensions=2, radius=1.5, neuron_type = cur_model)
proportional = nengo.Ensemble(500, dimensions=1, radius=1.5, neuron_type = cur_model)
derivative = nengo.Ensemble(500, dimensions=1, radius=1.5, neuron_type = cur_model)
control_signal = nengo.Ensemble(500, dimensions=1, radius=1.5, neuron_type = cur_model)
# invert terms that will be subtracted.
nengo.Connection(input_q[i], inverter[0], synapse=None, function=lambda x: x*-1)
nengo.Connection(input_dq[i], inverter[1], synapse=None, function=lambda x: x*-1)
# calculate proportional part
nengo.Connection(inverter[0], proportional, synapse=None, function=lambda x:x*kp)
nengo.Connection(input_target[i], proportional, synapse=None, function=lambda x:x*kp)
# calculate derivative part
nengo.Connection(inverter[1], derivative, synapse=None, function=lambda x:(x*kd))
nengo.Connection(input_d_target[i], derivative, synapse=None, function=lambda x:(x*kd))
# output
nengo.Connection(proportional, control_signal)
nengo.Connection(derivative, control_signal)
nengo.Connection(control_signal, output[i])
if self.adapt:
# adapt connections
nengo.Connection(input_q[i], adapt_ens, function=lambda x: np.zeros(num_motors), synapse=None)
nengo.Connection(control_signal, learn_conn.learning_rule[i], transform=-1, synapse=None)
# Nodes to access PID components.
# PID_Ens.append({"inverter":inverter,
# "proportional":proportional,
# "derivative": derivative, #TODO: Remove all except control signal.
# "control_signal": control_signal})
# control_signal_p = nengo.Probe(PID_Ens[0]["control_signal"], synapse=.01)
self.sim = nengo.Simulator(model)