def build_from_ensemble_connection(model, conn):
"""Build the parameters object for a connection from an Ensemble."""
# Create a random number generator
rng = np.random.RandomState(model.seeds[conn])
# Get the transform
transform = full_transform(conn, slice_pre=False)
# Use Nengo upstream to build parameters for the solver
eval_points, activities, targets = connection_b.build_linear_system(
model, conn, rng
)
# Use cached solver
solver = model.decoder_cache.wrap_solver(conn.solver)
if conn.solver.weights:
raise NotImplementedError(
"SpiNNaker does not currently support neuron to neuron connections"
)
else:
decoders, solver_info = solver(activities, targets, rng=rng)
# Return the parameters
return BuiltConnection(
decoders=decoders,
eval_points=eval_points,
transform=transform,
solver_info=solver_info
)
def test_build_linear_system(seed, rng, plt, allclose):
func = lambda x: x**2
with nengo.Network(seed=seed) as net:
conn = nengo.Connection(nengo.Ensemble(60, 1),
nengo.Ensemble(50, 1),
function=func)
model = Model()
model.build(net)
eval_points, activities, targets = build_linear_system(model, conn, rng)
assert eval_points.shape[1] == 1
assert targets.shape[1] == 1
assert activities.shape[1] == 60
assert eval_points.shape[0] == activities.shape[0] == targets.shape[0]
X = eval_points
AA = activities.T.dot(activities)
AX = activities.T.dot(eval_points)
AY = activities.T.dot(targets)
WX = np.linalg.solve(AA, AX)
WY = np.linalg.solve(AA, AY)
Xhat = activities.dot(WX)
Yhat = activities.dot(WY)
i = np.argsort(eval_points.ravel())
plt.plot(X[i], Xhat[i])
plt.plot(X[i], Yhat[i])
assert allclose(Xhat, X, atol=1e-1)
assert allclose(Yhat, func(X), atol=1e-1)
def test_build_linear_system_zeroact(seed, rng):
eval_points = np.linspace(-0.1, 0.1, 100)[:, None]
with nengo.Network(seed=seed) as net:
a = nengo.Ensemble(5, 1, intercepts=nengo.dists.Choice([0.9]))
b = nengo.Ensemble(5, 1, intercepts=nengo.dists.Choice([0.9]))
model = Model()
model.build(net)
conn = nengo.Connection(a,
b,
eval_points=eval_points,
add_to_container=False)
with pytest.raises(BuildError, match="'activities' matrix is all zero"):
build_linear_system(model, conn, rng)
def build_nrn_connection(model, conn):
# Create random number generator
rng = np.random.RandomState(model.seeds[conn])
# Check pre-conditions
assert isinstance(conn.pre, nengo.Ensemble)
assert not isinstance(conn.pre.neuron_type, nengo.neurons.Direct)
# FIXME assert no rate neurons are used. How to do that?
# Get input signal
# FIXME this should probably be
# model.sig[conn]['in'] = model.sig[conn.pre]["out"]
# in both cases
if isinstance(conn.pre, nengo.ensemble.Neurons):
model.sig[conn]["in"] = model.sig[conn.pre.ensemble]["out"]
else:
model.sig[conn]["in"] = model.sig[conn.pre]["out"]
# Figure out type of connection
if isinstance(conn.post, nengo.ensemble.Neurons):
raise NotImplementedError() # TODO
elif isinstance(conn.post.neuron_type, Compartmental):
pass
else:
raise AssertionError("This function should only be called if post neurons are " "compartmental.")
# Solve for weights
# FIXME just assuming solver is a weight solver, may that break?
# Default solver should probably also produce sparse solutions for
# performance reasons
eval_points, activities, targets = build_linear_system(model, conn, rng=rng)
# account for transform
transform = full_transform(conn)
targets = np.dot(targets, transform.T)
weights, solver_info = conn.solver(activities, targets, rng=rng, E=model.params[conn.post].scaled_encoders.T)
# Synapse type
synapse = conn.synapse
if is_number(synapse):
synapse = ExpSyn(synapse)
# Connect
# TODO: Why is this adjustment of the weights necessary?
weights = weights / synapse.tau / 5.0 * 0.1
connections = [[] for i in range(len(weights))]
for i, cell in enumerate(ens_to_cells[conn.post]):
for j, w in enumerate(weights[:, i]):
if w >= 0.0:
x = np.random.rand()
connections[j].append(synapse.create(cell.neuron.apical(x), w * (x + 1)))
else:
connections[j].append(synapse.create(cell.neuron.soma(0.5), w))
# 3. Add operator creating events for synapses if pre neuron fired
model.add_op(NrnTransmitSpikes(model.sig[conn]["in"], connections))
# a = nengo.Ensemble(n, im_dims)
v = nengo.Node(size_in=im_dims, size_out=im_dims)
c = nengo.Connection(a, v, eval_points=eval_points, synapse=0.01)
w1 = nengo.Node(video_plot, size_in=im_dims)
w2 = nengo.Node(rmse_recorder, size_in=im_dims)
nengo.Connection(v, w1, synapse=None)
nengo.Connection(v, w2, synapse=None)
sim = nengo.Simulator(net)
# show reconstructed images
if 1:
from nengo.builder.connection import build_linear_system
plt.figure(3)
plt.clf()
_, A, y = build_linear_system(sim.model, c, None)
x = sim.data[c].decoders.T
r, c = 2, 5
axes = [[plt.subplot2grid((2 * r, c), (2 * i + k, j)) for k in range(2)]
for i in range(r) for j in range(c)]
for i in range(r * c):
show_image(axes[i][0], y[i].reshape(im_shape))
show_image(axes[i][1], np.dot(A[i], x).reshape(im_shape))
sim.run(1.)
print(rmse_total)
def build_nrn_connection(model, conn):
# Create random number generator
rng = np.random.RandomState(model.seeds[conn])
# Check pre-conditions
assert isinstance(conn.pre, nengo.Ensemble)
assert not isinstance(conn.pre.neuron_type, nengo.neurons.Direct)
# FIXME assert no rate neurons are used. How to do that?
# Get input signal
# FIXME this should probably be
# model.sig[conn]['in'] = model.sig[conn.pre]["out"]
# in both cases
if isinstance(conn.pre, nengo.ensemble.Neurons):
model.sig[conn]['in'] = model.sig[conn.pre.ensemble]['out']
else:
model.sig[conn]['in'] = model.sig[conn.pre]["out"]
# Figure out type of connection
if isinstance(conn.post, nengo.ensemble.Neurons):
raise NotImplementedError() # TODO
elif isinstance(conn.post.neuron_type, Compartmental):
pass
else:
raise AssertionError(
"This function should only be called if post neurons are "
"compartmental.")
# Solve for weights
# FIXME just assuming solver is a weight solver, may that break?
# Default solver should probably also produce sparse solutions for
# performance reasons
eval_points, activities, targets = build_linear_system(model,
conn,
rng=rng)
# account for transform
transform = full_transform(conn)
targets = np.dot(targets, transform.T)
weights, solver_info = conn.solver(
activities,
targets,
rng=rng,
E=model.params[conn.post].scaled_encoders.T)
# Synapse type
synapse = conn.synapse
if is_number(synapse):
synapse = ExpSyn(synapse)
# Connect
# TODO: Why is this adjustment of the weights necessary?
weights = weights / synapse.tau / 5. * .1
connections = [[] for i in range(len(weights))]
for i, cell in enumerate(ens_to_cells[conn.post]):
for j, w in enumerate(weights[:, i]):
if w >= 0.0:
x = np.random.rand()
connections[j].append(
synapse.create(cell.neuron.apical(x), w * (x + 1)))
else:
connections[j].append(synapse.create(cell.neuron.soma(0.5), w))
# 3. Add operator creating events for synapses if pre neuron fired
model.add_op(NrnTransmitSpikes(model.sig[conn]['in'], connections))