def signal_probe(model, key, probe):
kwargs = model.chip2host_params.get(probe, None)
weights = None
if kwargs is not None:
assert kwargs['function'] is None
weights = kwargs['transform'].T / model.dt
if isinstance(probe.target, nengo.ensemble.Neurons):
if probe.attr == 'output':
if weights is None:
# spike probes should give values of 1.0/dt on spike events
weights = 1.0 / model.dt
if hasattr(probe.target.ensemble.neuron_type, 'amplitude'):
weights *= probe.target.ensemble.neuron_type.amplitude
# Signal probes directly probe a target signal
target = model.objs[probe.obj]['out']
loihi_probe = Probe(target=target,
key=key,
slice=probe.slice,
synapse=probe.synapse,
weights=weights)
target.add_probe(loihi_probe)
model.objs[probe]['in'] = target
model.objs[probe]['out'] = loihi_probe
def test_negative_cxbase(request, seed):
n_axons = 3
model = Model()
input = SpikeInput(n_axons)
input.add_spikes(1, list(range(n_axons)))
model.add_input(input)
axon = Axon(n_axons)
input.add_axon(axon)
block = LoihiBlock(3)
block.compartment.configure_relu()
model.add_block(block)
synapse = Synapse(n_axons)
weights = [0.1, 0.1, 0.1]
indices = [0, 1, 2]
axon_to_weight_map = list(range(n_axons))
cx_bases = [0, 1, -1]
synapse.set_population_weights(weights,
indices,
axon_to_weight_map,
cx_bases,
pop_type=32)
axon.target = synapse
block.add_synapse(synapse)
probe = Probe(target=block, key='voltage')
block.add_probe(probe)
discretize_model(model)
n_steps = 2
if request.config.getoption("--target") == 'loihi':
with HardwareInterface(model, use_snips=False, seed=seed) as sim:
sim.run_steps(n_steps)
y = sim.get_probe_output(probe)
else:
with EmulatorInterface(model, seed=seed) as sim:
sim.run_steps(n_steps)
y = sim.get_probe_output(probe)
# Compartments 0 and 2 should change from axons 0 and 1.
# Axon 2 should have no effect, and not change compartment 1 (the sum of
# its cx_base and index), or other compartments (e.g. 2 if cx_base ignored)
assert np.allclose(y[1, 1], 0), "Third axon not ignored"
assert np.allclose(y[1, 0], y[1, 2]), "Third axon targeting another"
assert not np.allclose(y[1], y[0]), "Voltage not changing"
def test_pop_tiny(pop_type, channels_last, nc, request, plt, seed, allclose):
tau_rc = 0.02
tau_ref = 0.001
tau_s = 0.0
dt = 0.001
neuron_bias = 1.
pres_time = 0.4
sti, stj = 1, 1
if nc == 1:
filters = np.array([[-0.5, 2., -0.25], [-0.75, 2., -1.0],
[-0.5, 3., -0.5], [-1.0, 6.,
-0.25]]).reshape(1, 4, 1, 3)
inp_biases = np.array([[1, 5, 1], [2, 1, 2]])
inp_biases = inp_biases[:, :, None]
elif nc == 2:
filters = np.array([[[-0.5, 2., -0.2], [-0.7, 2., -1.0],
[-0.5, 3., -0.5], [-1.0, 6., -0.2]],
[[-1.0, 2., -1.0], [-0.5, 2., -0.5],
[-0.8, 3., -0.2], [-1.0, 4.,
-0.2]]]).reshape(2, 4, 1, 3)
inp_biases = np.array([[[1, 5, 1], [2, 1, 2]], [[0, 3, 1], [4, 2, 1]]])
inp_biases = np.transpose(inp_biases, (1, 2, 0))
# rearrange to (kernel_rows, kernel_cols, in_channels, out_channels)
filters = np.transpose(filters, (2, 3, 0, 1))
inp_biases = inp_biases / (inp_biases.max() + 0.001)
# --- compute nengo_loihi outputs
ni, nj, nk = inp_biases.shape
si, sj, nc, nf = filters.shape
nij = ni * nj
nyi = 1 + (ni - si) // sti
nyj = 1 + (nj - sj) // stj
out_size = nyi * nyj * nf
assert out_size <= 1024
model = Model()
# input block
inp = LoihiBlock(ni * nj * nk, label='inp')
assert inp.n_neurons <= 1024
inp.compartment.configure_relu()
inp.compartment.bias[:] = inp_biases.ravel()
inp_ax = Axon(nij, label='inp_ax')
# we always compute the pixel/channel idxs with channels_last=True
# (not sure why?), and then set it to the correct value afterwards
inp_shape = nengo_transforms.ChannelShape((ni, nj, nk), channels_last=True)
inp_ax.set_compartment_axon_map(target_axons=conv.pixel_idxs(inp_shape),
atoms=conv.channel_idxs(inp_shape))
inp_shape.shape = (ni, nj, nk) if channels_last else (nk, ni, nj)
inp_shape.channels_last = channels_last
inp.add_axon(inp_ax)
model.add_block(inp)
# conv block
neurons = LoihiBlock(out_size, label='neurons')
assert neurons.n_neurons <= 1024
neurons.compartment.configure_lif(tau_rc=tau_rc, tau_ref=tau_ref, dt=dt)
neurons.compartment.configure_filter(tau_s, dt=dt)
neurons.compartment.bias[:] = neuron_bias
synapse = Synapse(np.prod(inp_shape.spatial_shape), label='synapse')
conv2d_transform = nengo_transforms.Convolution(
nf,
inp_shape,
strides=(sti, stj),
channels_last=channels_last,
init=filters,
kernel_size=(1, 3))
weights, indices, axon_to_weight_map, bases = conv.conv2d_loihi_weights(
conv2d_transform)
synapse.set_population_weights(weights,
indices,
axon_to_weight_map,
bases,
pop_type=pop_type)
neurons.add_synapse(synapse)
out_probe = Probe(target=neurons, key='spiked')
neurons.add_probe(out_probe)
inp_ax.target = synapse
model.add_block(neurons)
# simulation
discretize_model(model)
n_steps = int(pres_time / dt)
target = request.config.getoption("--target")
if target == 'loihi':
with HardwareInterface(model, use_snips=False, seed=seed) as sim:
sim.run_steps(n_steps)
sim_out = sim.get_probe_output(out_probe)
else:
with EmulatorInterface(model, seed=seed) as sim:
sim.run_steps(n_steps)
sim_out = sim.get_probe_output(out_probe)
sim_out = np.sum(sim_out, axis=0) * (dt / pres_time)
if channels_last:
sim_out.shape = (nyi, nyj, nf)
sim_out = np.transpose(sim_out, (2, 0, 1))
else:
sim_out.shape = (nf, nyi, nyj)
out_max = sim_out.max()
# --- plot results
rows = 1
cols = 2
ax = plt.subplot(rows, cols, 1)
plt.hist(sim_out.ravel(), bins=11)
ax = plt.subplot(rows, cols, 2)
tile(sim_out, vmin=0, vmax=out_max, grid=True, ax=ax)
# ref_out determined by emulator running code known to work
if nc == 1:
ref_out = np.array([[0.06, 0.02], [0.055, 0.], [0.0825, 0.0225],
[0.125, 0.04]])
elif nc == 2:
ref_out = np.array([[0.0975, 0.02], [0.0825, 0.02], [0.125, 0.055],
[0.2475, 0.0825]])
assert allclose(sim_out[:, :, 0], ref_out, rtol=0, atol=1e-7)
def test_conv2d_weights(channels_last, hw_opts, request, plt, seed, rng,
allclose):
def loihi_rates_n(neuron_type, x, gain, bias, dt):
"""Compute Loihi rates on higher dimensional inputs"""
y = x.reshape(-1, x.shape[-1])
gain = np.asarray(gain)
bias = np.asarray(bias)
if gain.ndim == 0:
gain = gain * np.ones(x.shape[-1])
if bias.ndim == 0:
bias = bias * np.ones(x.shape[-1])
rates = loihi_rates(neuron_type, y, gain, bias, dt)
return rates.reshape(*x.shape)
if channels_last:
plt.saveas = None
pytest.xfail("Blocked by CxBase cannot be > 256 bug")
target = request.config.getoption("--target")
if target != 'loihi' and len(hw_opts) > 0:
pytest.skip("Hardware options only available on hardware")
pop_type = 32
# load data
with open(os.path.join(test_dir, 'mnist10.pkl'), 'rb') as f:
test10 = pickle.load(f)
test_x = test10[0][0].reshape(28, 28)
test_x = test_x[3:24, 3:24]
test_x = 1.999 * test_x - 0.999
filters = Gabor(freq=Uniform(0.5, 1)).generate(8, (7, 7), rng=rng)
sti, stj = 2, 2
tau_rc = 0.02
tau_ref = 0.002
tau_s = 0.005
dt = 0.001
encode_type = nengo.SpikingRectifiedLinear()
encode_gain = 1. / dt
encode_bias = 0.
neuron_type = nengo.LIF(tau_rc=tau_rc, tau_ref=tau_ref)
neuron_gain = 1.
neuron_bias = 1.
pres_time = 0.2
# --- compute ideal outputs
def conv_pm(x, kernel):
y0 = scipy.signal.correlate2d(x[0], kernel, mode='valid')[::sti, ::stj]
y1 = scipy.signal.correlate2d(x[1], kernel, mode='valid')[::sti, ::stj]
return [y0, -y1]
ref_out = np.array([test_x, -test_x])
ref_out = loihi_rates_n(encode_type, ref_out, encode_gain, encode_bias, dt)
ref_out = ref_out / encode_gain
ref_out = np.array([conv_pm(ref_out, kernel) for kernel in filters])
ref_out = ref_out.sum(axis=1) # sum positive and negative parts
ref_out = loihi_rates_n(neuron_type, ref_out, neuron_gain, neuron_bias, dt)
# --- compute nengo_loihi outputs
inp_biases = np.stack([test_x, -test_x], axis=-1 if channels_last else 0)
inp_shape = nengo_transforms.ChannelShape(inp_biases.shape,
channels_last=channels_last)
kernel = np.array([filters, -filters]) # two channels, pos and neg
kernel = np.transpose(kernel, (2, 3, 0, 1))
conv2d_transform = nengo_transforms.Convolution(
8,
inp_shape,
strides=(sti, stj),
channels_last=channels_last,
kernel_size=(7, 7),
init=kernel)
out_size = ref_out.size
nf, nyi, nyj = ref_out.shape
assert out_size <= 1024
model = Model()
# input block
inp = LoihiBlock(inp_shape.size, label='inp')
assert inp.n_neurons <= 1024
inp.compartment.configure_relu()
inp.compartment.bias[:] = inp_biases.ravel()
inp_ax = Axon(np.prod(inp_shape.spatial_shape), label='inp_ax')
inp_ax.set_compartment_axon_map(target_axons=conv.pixel_idxs(inp_shape),
atoms=conv.channel_idxs(inp_shape))
inp.add_axon(inp_ax)
model.add_block(inp)
# conv block
neurons = LoihiBlock(out_size, label='neurons')
assert neurons.n_neurons <= 1024
neurons.compartment.configure_lif(tau_rc=tau_rc, tau_ref=tau_ref, dt=dt)
neurons.compartment.configure_filter(tau_s, dt=dt)
neurons.compartment.bias[:] = neuron_bias
synapse = Synapse(np.prod(inp_shape.spatial_shape), label='synapse')
weights, indices, axon_to_weight_map, bases = conv.conv2d_loihi_weights(
conv2d_transform)
synapse.set_population_weights(weights,
indices,
axon_to_weight_map,
bases,
pop_type=pop_type)
neurons.add_synapse(synapse)
out_probe = Probe(target=neurons, key='spiked')
neurons.add_probe(out_probe)
inp_ax.target = synapse
model.add_block(neurons)
# simulation
discretize_model(model)
n_steps = int(pres_time / dt)
if target == 'loihi':
with HardwareInterface(model, use_snips=False, seed=seed,
**hw_opts) as sim:
sim.run_steps(n_steps)
sim_out = sim.get_probe_output(out_probe)
else:
with EmulatorInterface(model, seed=seed) as sim:
sim.run_steps(n_steps)
sim_out = sim.get_probe_output(out_probe)
sim_out = np.sum(sim_out, axis=0) / pres_time
if channels_last:
sim_out.shape = (nyi, nyj, nf)
sim_out = np.transpose(sim_out, (2, 0, 1))
else:
sim_out.shape = (nf, nyi, nyj)
out_max = max(ref_out.max(), sim_out.max())
# --- plot results
rows = 2
cols = 2
ax = plt.subplot(rows, cols, 1)
tile(filters, cols=8, ax=ax)
ax = plt.subplot(rows, cols, 2)
tile(ref_out, vmin=0, vmax=out_max, cols=8, ax=ax)
ax = plt.subplot(rows, cols, 3)
plt.hist(ref_out.ravel(), bins=31)
plt.hist(sim_out.ravel(), bins=31)
ax = plt.subplot(rows, cols, 4)
# tile(sim_out, vmin=0, vmax=1, cols=8, ax=ax)
tile(sim_out, vmin=0, vmax=out_max, cols=8, ax=ax)
assert allclose(sim_out, ref_out, atol=10, rtol=1e-3)
def test_uv_overflow(n_axons, plt, allclose, monkeypatch):
# TODO: Currently this is not testing the V overflow, since it is higher
# and I haven't been able to figure out a way to make it overflow.
nt = 15
model = Model()
# n_axons controls number of input spikes and thus amount of overflow
input = SpikeInput(n_axons)
for t in np.arange(1, nt + 1):
input.add_spikes(t, np.arange(n_axons)) # send spikes to all axons
model.add_input(input)
block = LoihiBlock(1)
block.compartment.configure_relu()
block.compartment.configure_filter(0.1)
synapse = Synapse(n_axons)
synapse.set_full_weights(np.ones((n_axons, 1)))
block.add_synapse(synapse)
axon = Axon(n_axons)
axon.target = synapse
input.add_axon(axon)
probe_u = Probe(target=block, key='current')
block.add_probe(probe_u)
probe_v = Probe(target=block, key='voltage')
block.add_probe(probe_v)
probe_s = Probe(target=block, key='spiked')
block.add_probe(probe_s)
model.add_block(block)
discretize_model(model)
# must set these after `discretize` to specify discretized values
block.compartment.vmin = -2**22 + 1
block.compartment.vth[:] = VTH_MAX
assert EmulatorInterface.strict # Tests should be run in strict mode
monkeypatch.setattr(EmulatorInterface, "strict", False)
with EmulatorInterface(model) as emu:
with pytest.warns(UserWarning):
emu.run_steps(nt)
emu_u = emu.get_probe_output(probe_u)
emu_v = emu.get_probe_output(probe_v)
emu_s = emu.get_probe_output(probe_s)
with HardwareInterface(model, use_snips=False) as sim:
sim.run_steps(nt)
sim_u = sim.get_probe_output(probe_u)
sim_v = sim.get_probe_output(probe_v)
sim_s = sim.get_probe_output(probe_s)
sim_v[sim_s > 0] = 0 # since Loihi has placeholder voltage after spike
plt.subplot(311)
plt.plot(emu_u)
plt.plot(sim_u)
plt.subplot(312)
plt.plot(emu_v)
plt.plot(sim_v)
plt.subplot(313)
plt.plot(emu_s)
plt.plot(sim_s)
assert allclose(emu_u, sim_u)
assert allclose(emu_v, sim_v)
def test_population_input(request, allclose):
target = request.config.getoption("--target")
dt = 0.001
n_inputs = 3
n_axons = 1
n_cx = 2
steps = 6
spike_times_inds = [(1, [0]), (3, [1]), (5, [2])]
model = Model()
input = SpikeInput(n_inputs)
model.add_input(input)
spikes = [(input, ti, inds) for ti, inds in spike_times_inds]
input_axon = Axon(n_axons)
axon_map = np.zeros(n_inputs, dtype=int)
atoms = np.arange(n_inputs)
input_axon.set_axon_map(axon_map, atoms)
input.add_axon(input_axon)
block = LoihiBlock(n_cx)
block.compartment.configure_lif(tau_rc=0., tau_ref=0., dt=dt)
block.compartment.configure_filter(0, dt=dt)
model.add_block(block)
synapse = Synapse(n_axons)
weights = 0.1 * np.array([[[1, 2], [2, 3], [4, 5]]], dtype=float)
indices = np.array([[[0, 1], [0, 1], [0, 1]]], dtype=int)
axon_to_weight_map = np.zeros(n_axons, dtype=int)
cx_bases = np.zeros(n_axons, dtype=int)
synapse.set_population_weights(weights,
indices,
axon_to_weight_map,
cx_bases,
pop_type=32)
block.add_synapse(synapse)
input_axon.target = synapse
probe = Probe(target=block, key='voltage')
block.add_probe(probe)
discretize_model(model)
if target == 'loihi':
with HardwareInterface(model, use_snips=True) as sim:
sim.run_steps(steps, blocking=False)
for ti in range(1, steps + 1):
spikes_i = [spike for spike in spikes if spike[1] == ti]
sim.host2chip(spikes=spikes_i, errors=[])
sim.chip2host(probes_receivers={})
y = sim.get_probe_output(probe)
else:
for inp, ti, inds in spikes:
inp.add_spikes(ti, inds)
with EmulatorInterface(model) as sim:
sim.run_steps(steps)
y = sim.get_probe_output(probe)
vth = block.compartment.vth[0]
assert (block.compartment.vth == vth).all()
z = y / vth
assert allclose(z[[1, 3, 5]], weights[0], atol=4e-2, rtol=0)
def test_simulator_noise(exp, request, plt, seed, allclose):
# TODO: test that the mean falls within a number of standard errors
# of the expected mean, and that non-zero offsets work correctly.
# Currently, there is an unexpected negative bias for small noise
# exponents, apparently because there is a probability of generating
# the shifted equivalent of -128, whereas with e.g. exp = 7 all the
# generated numbers fall in [-127, 127].
offset = 0
target = request.config.getoption("--target")
n_cx = 1000
model = Model()
block = LoihiBlock(n_cx)
block.compartment.configure_relu()
block.compartment.vmin = -1
block.compartment.enableNoise[:] = 1
block.compartment.noiseExp0 = exp
block.compartment.noiseMantOffset0 = offset
block.compartment.noiseAtDendOrVm = 1
probe = Probe(target=block, key='voltage')
block.add_probe(probe)
model.add_block(block)
discretize_model(model)
exp2 = block.compartment.noiseExp0
offset2 = block.compartment.noiseMantOffset0
n_steps = 100
if target == 'loihi':
with HardwareInterface(model, use_snips=False, seed=seed) as sim:
sim.run_steps(n_steps)
y = sim.get_probe_output(probe)
else:
with EmulatorInterface(model, seed=seed) as sim:
sim.run_steps(n_steps)
y = sim.get_probe_output(probe)
t = np.arange(1, n_steps + 1)
bias = offset2 * 2.**(exp2 - 1)
std = 2.**exp2 / np.sqrt(3) # divide by sqrt(3) for std of uniform -1..1
rmean = t * bias
rstd = np.sqrt(t) * std
rerr = rstd / np.sqrt(n_cx)
ymean = y.mean(axis=1)
ystd = y.std(axis=1)
diffs = np.diff(np.vstack([np.zeros_like(y[0]), y]), axis=0)
plt.subplot(311)
plt.hist(diffs.ravel(), bins=256)
plt.subplot(312)
plt.plot(rmean, 'k')
plt.plot(rmean + 3 * rerr, 'k--')
plt.plot(rmean - 3 * rerr, 'k--')
plt.plot(ymean)
plt.title('mean')
plt.subplot(313)
plt.plot(rstd, 'k')
plt.plot(ystd)
plt.title('std')
assert allclose(ystd, rstd, rtol=0.1, atol=1)
def conn_probe(model, nengo_probe):
# Connection probes create a connection from the target, and probe
# the resulting signal (used when you want to probe the default
# output of an object, which may not have a predefined signal)
synapse = 0 # Removed internal filtering
# get any extra arguments if this probe was created to send data
# to an off-chip Node via the splitter
conn_label = (None if nengo_probe.label is None else "%s_conn" %
nengo_probe.label)
kwargs = model.chip2host_params.get(nengo_probe, None)
if kwargs is not None:
# this probe is for sending data to a Node
kwargs.setdefault('label', conn_label)
# determine the dimensionality
input_dim = nengo_probe.target.size_out
func = kwargs['function']
if func is not None:
if callable(func):
input_dim = np.asarray(
func(np.zeros(input_dim, dtype=np.float64))).size
else:
input_dim = len(func[0])
transform = np.asarray(kwargs['transform'], dtype=np.float64)
if transform.ndim <= 1:
output_dim = input_dim
elif transform.ndim == 2:
assert transform.shape[1] == input_dim
output_dim = transform.shape[0]
else:
raise NotImplementedError()
target = nengo.Node(size_in=output_dim, add_to_container=False)
conn = Connection(nengo_probe.target,
target,
synapse=synapse,
solver=nengo_probe.solver,
add_to_container=False,
**kwargs)
model.probe_conns[nengo_probe] = conn
else:
conn = Connection(
nengo_probe.target,
nengo_probe,
synapse=synapse,
solver=nengo_probe.solver,
add_to_container=False,
label=conn_label,
)
target = nengo_probe
# Set connection's seed to probe's (which isn't used elsewhere)
model.seeded[conn] = model.seeded[nengo_probe]
model.seeds[conn] = model.seeds[nengo_probe]
d = conn.size_out
if isinstance(nengo_probe.target, Ensemble):
# probed values are scaled by the target ensemble's radius
scale = nengo_probe.target.radius
w = np.diag(scale * np.ones(d))
weights = np.vstack([w, -w])
else:
raise NotImplementedError(
"Nodes cannot be onchip, connections not yet probeable")
probe = Probe(key='voltage', weights=weights, synapse=nengo_probe.synapse)
model.objs[target]['in'] = probe
model.objs[target]['out'] = probe
# add an extra entry for simulator.run_steps to read data out
model.objs[nengo_probe]['out'] = probe
# Build the connection
model.build(conn)