def test_simple(self):
params = dict(simulator=self.Simulator, seed=123, dt=0.001)
# Old API
net = nef.Network('test_simple', **params)
net.make_input('in', value=np.sin)
p = net.make_probe('in', dt_sample=0.001, pstc=0.0)
rawp = net._raw_probe(net.inputs['in'], dt_sample=.001)
st_probe = net._raw_probe(net.model.simtime, dt_sample=.001)
net.run(0.01)
data = p.get_data()
raw_data = rawp.get_data()
st_data = st_probe.get_data()
self.assertTrue(
np.allclose(st_data.ravel(), np.arange(0.001, 0.0105, .001)))
self.assertTrue(
np.allclose(raw_data.ravel(), np.sin(np.arange(0, 0.0095, .001))))
# -- the make_probe call induces a one-step delay
# on readout even when the pstc is really small.
self.assertTrue(
np.allclose(data.ravel()[1:], np.sin(np.arange(0, 0.0085, .001))))
# New API
m = nengo.Model('test_simple', **params)
node = m.make_node('in', output=np.sin)
m.probe('in')
m.run(0.01)
self.assertTrue(
np.allclose(m.data[m.simtime].ravel(),
np.arange(0.001, 0.0105, .001)))
self.assertTrue(
np.allclose(m.data['in'].ravel(),
np.sin(np.arange(0, 0.0095, .001))))
def test_scalar(self):
"""A network that represents sin(t)."""
simulator = self.Simulator
params = dict(simulator=simulator, seed=123, dt=0.001)
N = 30
target = np.sin(np.arange(4999) / 1000.)
target.shape = (4999, 1)
# Old API
net = nef.Network('test_scalar', **params)
net.make_input('in', value=np.sin)
net.make('A', N, 1)
net.connect('in', 'A')
in_p = net.make_probe('in', dt_sample=0.001, pstc=0.0)
a_p = net.make_probe('A', dt_sample=0.001, pstc=0.02)
net.run(5)
in_data = in_p.get_data()
a_data = a_p.get_data()
with Plotter(simulator) as plt:
t = net.model.data[net.model.simtime]
plt.plot(t, in_data, label='Input')
plt.plot(t, a_data, label='Neuron approximation, pstc=0.02')
plt.legend(loc=0)
plt.savefig('test_ensemble.test_scalar-old.pdf')
plt.close()
logger.debug("[Old API] input RMSE: %f", rmse(target, in_data))
logger.debug("[Old API] A RMSE: %f", rmse(target, a_data))
self.assertTrue(rmse(target, in_data) < 0.001)
self.assertTrue(rmse(target, a_data) < 0.1)
# New API
m = nengo.Model('test_scalar', **params)
m.make_node('in', output=np.sin)
m.make_ensemble('A', nengo.LIF(N), 1)
m.connect('in', 'A')
m.probe('in')
m.probe('A', filter=0.02)
m.run(5)
with Plotter(simulator) as plt:
t = m.data[m.simtime]
plt.plot(t, m.data['in'], label='Input')
plt.plot(t, m.data['A'], label='Neuron approximation, pstc=0.02')
plt.legend(loc=0)
plt.savefig('test_ensemble.test_scalar-new.pdf')
plt.close()
logger.debug("[New API] input RMSE: %f", rmse(target, m.data['in']))
logger.debug("[New API] A RMSE: %f", rmse(target, m.data['A']))
self.assertTrue(rmse(target, m.data['in']) < 0.001)
self.assertTrue(rmse(target, m.data['A']) < 0.1)
# Check old/new API similarity
logger.debug("Old/New API RMSE: %f", rmse(a_data, m.data['A']))
self.assertTrue(rmse(a_data, m.data['A']) < 0.1)
def test_prod(self):
def product(x):
return x[0] * x[1]
N = 250
seed = 123
net = nef.Network('Matrix Multiplication',
seed=seed,
simulator=self.Simulator)
net.make_input('sin', value=np.sin)
net.make_input('neg', value=[-.5])
net.make_array('p', 2 * N, 1, dimensions=2, radius=1.5)
net.make_array('D', N, 1, dimensions=1)
net.connect('sin', 'p', transform=[[1], [0]])
net.connect('neg', 'p', transform=[[0], [1]])
net.connect('p', 'D', func=product, pstc=0.01)
p_raw = net._probe_decoded_signals(
[net.ensembles['p'].origin['product'].sigs[0]],
dt_sample=.01,
pstc=.01)
probe_p = net.make_probe('p', dt_sample=.01, pstc=.01)
probe_d = net.make_probe('D', dt_sample=.01, pstc=.01)
net.run(6)
data_p = probe_p.get_data()
data_d = probe_d.get_data()
data_r = p_raw.get_data()
with Plotter(self.Simulator) as plt:
plt.subplot(211)
plt.plot(data_p)
plt.plot(np.sin(np.arange(0, 6, .01)))
plt.subplot(212)
plt.plot(data_d)
plt.plot(data_r)
plt.plot(-.5 * np.sin(np.arange(0, 6, .01)))
plt.savefig('test_old_api.test_prod.pdf')
plt.close()
self.assertTrue(
np.allclose(data_p[:, 0],
np.sin(np.arange(0, 6, .01)),
atol=.1,
rtol=.01))
self.assertTrue(np.allclose(data_p[20:, 1], -0.5, atol=.1, rtol=.01))
def match(a, b):
self.assertTrue(np.allclose(a, b, .1, .1))
match(data_d[:, 0], -0.5 * np.sin(np.arange(0, 6, .01)))
match(data_r[:, 0], -0.5 * np.sin(np.arange(0, 6, .01)))
def test_constant_vector(self):
"""A network that represents a constant 3D vector."""
simulator = self.Simulator
params = dict(simulator=simulator, seed=123, dt=0.001)
N = 30
vals = [0.6, 0.1, -0.5]
# Old API
net = nef.Network('test_constant_vector', **params)
net.make_input('in', value=vals)
net.make('A', N * len(vals), len(vals))
net.connect('in', 'A', transform=np.eye(len(vals)))
in_p = net.make_probe('in', dt_sample=0.001, pstc=0.0)
a_p = net.make_probe('A', dt_sample=0.001, pstc=0.1)
net.run(1)
in_data = in_p.get_data()
a_data = a_p.get_data()
with Plotter(simulator) as plt:
t = net.model.data[net.model.simtime]
plt.plot(t, in_data, label='Input')
plt.plot(t, a_data, label='Neuron approximation, pstc=0.1')
plt.legend(loc=0, prop={'size': 10})
plt.savefig('test_ensemble.test_constant_vector-old.pdf')
plt.close()
self.assertTrue(np.allclose(in_data[-10:], vals, atol=.05, rtol=.05))
self.assertTrue(np.allclose(a_data[-10:], vals, atol=.05, rtol=.05))
# New API
m = nengo.Model('test_constant_vector', **params)
m.make_node('in', output=vals)
m.make_ensemble('A', nengo.LIF(N * len(vals)), len(vals))
m.connect('in', 'A')
m.probe('in')
m.probe('A', filter=0.1)
m.run(1)
with Plotter(simulator) as plt:
t = m.data[m.simtime]
plt.plot(t, m.data['in'], label='Input')
plt.plot(t, m.data['A'], label='Neuron approximation, pstc=0.1')
plt.legend(loc=0, prop={'size': 10})
plt.savefig('test_ensemble.test_constant_vector-new.pdf')
plt.close()
self.assertTrue(
np.allclose(m.data['in'][-10:], vals, atol=.05, rtol=.05))
self.assertTrue(
np.allclose(m.data['A'][-10:], vals, atol=.05, rtol=.05))
def test_constant_scalar(self):
"""A Network that represents a constant value."""
simulator = self.Simulator
params = dict(simulator=simulator, seed=123, dt=0.001)
N = 30
val = 0.5
# old api
net = nef.Network('test_constant_scalar', **params)
net.make_input('in', value=[val])
net.make('A', N, 1)
net.connect('in', 'A')
in_p = net.make_probe('in', dt_sample=0.001, pstc=0.0)
a_p = net.make_probe('A', dt_sample=0.001, pstc=0.1)
net.run(1)
in_data = in_p.get_data()
a_data = a_p.get_data()
with Plotter(simulator) as plt:
t = net.model.data[net.model.simtime]
plt.plot(t, in_data, label='Input')
plt.plot(t, a_data, label='Neuron approximation, pstc=0.1')
plt.legend(loc=0)
plt.savefig('test_ensemble.test_constant_scalar-old.pdf')
plt.close()
self.assertTrue(np.allclose(in_data.ravel(), val, atol=.05, rtol=.05))
self.assertTrue(np.allclose(a_data[-10:], val, atol=.05, rtol=.05))
# New API
m = nengo.Model('test_constant_scalar', **params)
m.make_node('in', output=val)
m.make_ensemble('A', nengo.LIF(N), 1)
m.connect('in', 'A')
m.probe('in')
m.probe('A', filter=0.1)
m.run(1)
with Plotter(simulator) as plt:
t = m.data[m.simtime]
plt.plot(t, m.data['in'], label='Input')
plt.plot(t, m.data['A'], label='Neuron approximation, pstc=0.1')
plt.legend(loc=0)
plt.savefig('test_ensemble.test_constant_scalar-new.pdf')
plt.close()
self.assertTrue(
np.allclose(m.data['in'].ravel(), val, atol=.05, rtol=.05))
self.assertTrue(np.allclose(m.data['A'][-10:], val, atol=.05,
rtol=.05))
def test_counters(self):
params = dict(simulator=self.Simulator, seed=123, dt=0.001)
# Old API
net = nef.Network('test_counters', **params)
simtime_probe = net._raw_probe(net.model.simtime, dt_sample=.001)
steps_probe = net._raw_probe(net.model.steps, dt_sample=.001)
net.run(0.003)
simtime_data = simtime_probe.get_data()
steps_data = steps_probe.get_data()
self.assertTrue(np.allclose(simtime_data.flatten(),
[.001, .002, .003]))
self.assertTrue(np.allclose(steps_data.flatten(), [1, 2, 3]))
# New API
m = nengo.Model('test_counters', **params)
m.probe(m.simtime)
m.probe(m.steps)
m.run(0.003)
self.assertTrue(
np.allclose(m.data[m.simtime].flatten(), [.001, .002, .003]))
self.assertTrue(np.allclose(m.data[m.steps].flatten(), [1, 2, 3]))
def test_vector(self):
"""A network that represents sin(t), cos(t), arctan(t)."""
simulator = self.Simulator
params = dict(simulator=simulator, seed=123, dt=0.001)
N = 40
target = np.vstack(
(np.sin(np.arange(4999) / 1000.), np.cos(np.arange(4999) / 1000.),
np.arctan(np.arange(4999) / 1000.))).T
# Old API
net = nef.Network('test_vector', **params)
net.make_input('sin', value=np.sin)
net.make_input('cos', value=np.cos)
net.make_input('arctan', value=np.arctan)
net.make('A', N * 3, 3, radius=2)
net.connect('sin', 'A', transform=[[1], [0], [0]])
net.connect('cos', 'A', transform=[[0], [1], [0]])
net.connect('arctan', 'A', transform=[[0], [0], [1]])
sin_p = net.make_probe('sin', dt_sample=0.001, pstc=0.0)
cos_p = net.make_probe('cos', dt_sample=0.001, pstc=0.0)
arctan_p = net.make_probe('arctan', dt_sample=0.001, pstc=0.0)
a_p = net.make_probe('A', dt_sample=0.001, pstc=0.02)
net.run(5)
sin_data = sin_p.get_data()
cos_data = cos_p.get_data()
arctan_data = arctan_p.get_data()
a_data = a_p.get_data()
with Plotter(simulator) as plt:
t = net.model.data[net.model.simtime]
plt.plot(t, sin_data, label='sin')
plt.plot(t, cos_data, label='cos')
plt.plot(t, arctan_data, label='arctan')
plt.plot(t, a_data, label='Neuron approximation, pstc=0.02')
plt.legend(loc=0, prop={'size': 10})
plt.savefig('test_ensemble.test_vector-old.pdf')
plt.close()
logger.debug("[Old API] sin RMSE: %f", rmse(target[:, 0], sin_data))
logger.debug("[Old API] cos RMSE: %f", rmse(target[:, 1], cos_data))
logger.debug("[Old API] atan RMSE: %f", rmse(target[:, 2],
arctan_data))
logger.debug("[Old API] A RMSE: %f", rmse(target, a_data))
self.assertTrue(rmse(target, a_data) < 0.1)
# New API
m = nengo.Model('test_vector', **params)
m.make_node('sin', output=np.sin)
m.make_node('cos', output=np.cos)
m.make_node('arctan', output=np.arctan)
m.make_ensemble('A', nengo.LIF(N * 3), 3, radius=2)
m.connect('sin', 'A', transform=[[1], [0], [0]])
m.connect('cos', 'A', transform=[[0], [1], [0]])
m.connect('arctan', 'A', transform=[[0], [0], [1]])
m.probe('sin')
m.probe('cos')
m.probe('arctan')
m.probe('A', filter=0.02)
m.run(5)
with Plotter(simulator) as plt:
t = m.data[m.simtime]
plt.plot(t, m.data['sin'], label='sin')
plt.plot(t, m.data['cos'], label='cos')
plt.plot(t, m.data['arctan'], label='arctan')
plt.plot(t, m.data['A'], label='Neuron approximation, pstc=0.02')
plt.legend(loc=0, prop={'size': 10})
plt.savefig('test_ensemble.test_vector-new.pdf')
plt.close()
# Not sure why, but this isn't working...
logger.debug("[New API] sin RMSE: %f", rmse(target[:, 0],
m.data['sin']))
logger.debug("[New API] cos RMSE: %f", rmse(target[:, 1],
m.data['cos']))
logger.debug("[New API] atan RMSE: %f",
rmse(target[:, 2], m.data['arctan']))
logger.debug("[New API] A RMSE: %f", rmse(target, m.data['A']))
self.assertTrue(rmse(target, m.data['A']) < 0.1)
# Check old/new API similarity
logger.debug("Old/New API RMSE: %f", rmse(a_data, m.data['A']))
self.assertTrue(rmse(a_data, m.data['A']) < 0.1)
[Input] ----> (A) --'
^
[Control] -----'
Network behaviour:
A = tau * Input + Input * Control
"""
import nengo.old_api as api
### Define model parameters
tau = 0.1
### Create the nengo model
model = api.Network('Controlled Integrator')
### Create the model inputs
input_d = {0.2: 5, 0.3: 0, 0.44: -10, 0.54: 0, 0.8: 5, 0.9: 0}.items()
input_d.sort(reverse=True)
def input_f(t):
for key, value in input_d:
if t > key: return value
return 0.0
model.make_input('Input', input_f)
model.make_input('Control', [1])
v |
[Input] ---> (A) --'
Network behaviour:
A = A_matrix * A
"""
import nengo.old_api as api
import numpy as np
### Define model parameters
speed = 10 # Base frequency of oscillation
tau = 0.1 # TODO: this is supposed to be the feedback time constant
### Create the nengo model
model = api.Network('Integrator')
### Create the model inputs
def start_input(t):
if t < 0.01: return [1,0]
else: return [0,0]
model.make_input('Input', start_input)
def speed_func(t):
if t < 0.3: return 1
elif t < 0.6: return 0.5
else: return 1
model.make_input('Speed', speed_func)
def test_multidim_probe(self):
# Adjust these values to change the matrix dimensions
# Matrix A is D1xD2
# Matrix B is D2xD3
# result is D1xD3
D1 = 1
D2 = 2
D3 = 3
seed = 123
N = 200
Amat = np.asarray([[.4, .8]])
Bmat = np.asarray([[-1.0, -0.6, -.15], [0.25, .5, .7]])
net = nef.Network('V', seed=seed, simulator=self.Simulator)
# values should stay within the range (-radius,radius)
radius = 2.0
# make 2 matrices to store the input
logging.debug("make_array: input matrices A and B")
net.make_array('A',
neurons=N,
array_size=D1 * D2,
radius=radius,
neuron_type='lif')
net.make_array('B',
neurons=N,
array_size=D2 * D3,
radius=radius,
neuron_type='lif')
# connect inputs to them so we can set their value
inputA = net.make_input('input A', value=Amat.flatten())
inputB = net.make_input('input B', value=Bmat.flatten())
logging.debug("connect: input matrices A and B")
net.connect('input A', 'A')
net.connect('input B', 'B')
# the C matrix holds the intermediate product calculations
# need to compute D1*D2*D3 products to multiply 2 matrices together
logging.debug("make_array: intermediate C")
net.make_array('C',
4 * N,
D1 * D2 * D3,
dimensions=2,
radius=1.5 * radius,
encoders=[[1, 1], [1, -1], [-1, 1], [-1, -1]],
neuron_type='lif')
transformA = [[0] * (D1 * D2) for i in range(D1 * D2 * D3 * 2)]
transformB = [[0] * (D2 * D3) for i in range(D1 * D2 * D3 * 2)]
for i in range(D1):
for k in range(D3):
for j in range(D2):
tmp = (j + k * D2 + i * D2 * D3)
transformA[tmp * 2][j + i * D2] = 1
transformB[tmp * 2 + 1][k + j * D3] = 1
logging.debug("transA: %s", str(transformA))
logging.debug("transB: %s", str(transformB))
logging.debug("connect A->C")
net.connect('A', 'C', transform=transformA)
logging.debug("connect B->C")
net.connect('B', 'C', transform=transformB)
Cprobe = net.make_probe('C', dt_sample=0.01, pstc=0.01)
net.run(1)
logging.debug("Cprove.shape=%s", str(Cprobe.get_data().shape))
logging.debug("Amat=%s", str(Amat))
logging.debug("Bmat=%s", str(Bmat))
data = Cprobe.get_data()
with Plotter(self.Simulator) as plt:
for i in range(D1):
for k in range(D3):
for j in range(D2):
tmp = (j + k * D2 + i * D2 * D3)
plt.subplot(D1 * D2 * D3, 2, 1 + 2 * tmp)
plt.title('A[%i, %i]' % (i, j))
plt.axhline(Amat[i, j])
plt.ylim(-radius, radius)
plt.plot(data[:, 2 * tmp])
plt.subplot(D1 * D2 * D3, 2, 2 + 2 * tmp)
plt.title('B[%i, %i]' % (j, k))
plt.axhline(Bmat[j, k])
plt.ylim(-radius, radius)
plt.plot(data[:, 2 * tmp + 1])
plt.savefig('test_old_api.test_multidimprobe.pdf')
plt.close()
for i in range(D1):
for k in range(D3):
for j in range(D2):
tmp = (j + k * D2 + i * D2 * D3)
self.assertTrue(
np.allclose(data[-10:, 2 * tmp],
Amat[i, j],
atol=0.1,
rtol=0.1),
(data[-10:, 2 * tmp], Amat[i, j]))
self.assertTrue(
np.allclose(data[-10:, 1 + 2 * tmp],
Bmat[j, k],
atol=0.1,
rtol=0.1))
def test_matrix_mul(self):
# Adjust these values to change the matrix dimensions
# Matrix A is D1xD2
# Matrix B is D2xD3
# result is D1xD3
D1 = 1
D2 = 2
D3 = 2
seed = 123
N = 200
Amat = np.asarray([[.5, -.5]])
Bmat = np.asarray([[
0,
-1.,
], [.7, 0]])
net = nef.Network('Matrix Multiplication',
seed=seed,
simulator=self.Simulator)
# values should stay within the range (-radius,radius)
radius = 1
# make 2 matrices to store the input
logging.debug("make_array: input matrices A and B")
net.make_array('A',
neurons=N,
array_size=D1 * D2,
radius=radius,
neuron_type='lif')
net.make_array('B',
neurons=N,
array_size=D2 * D3,
radius=radius,
neuron_type='lif')
# connect inputs to them so we can set their value
inputA = net.make_input('input A', value=Amat.ravel())
inputB = net.make_input('input B', value=Bmat.ravel())
logging.debug("connect: input matrices A and B")
net.connect('input A', 'A')
net.connect('input B', 'B')
# the C matrix holds the intermediate product calculations
# need to compute D1*D2*D3 products to multiply 2 matrices together
logging.debug("make_array: intermediate C")
net.make_array('C',
4 * N,
D1 * D2 * D3,
dimensions=2,
radius=1.5 * radius,
encoders=[[1, 1], [1, -1], [-1, 1], [-1, -1]],
neuron_type='lif')
# determine the transformation matrices to get the correct pairwise
# products computed. This looks a bit like black magic but if
# you manually try multiplying two matrices together, you can see
# the underlying pattern. Basically, we need to build up D1*D2*D3
# pairs of numbers in C to compute the product of. If i,j,k are the
# indexes into the D1*D2*D3 products, we want to compute the product
# of element (i,j) in A with the element (j,k) in B. The index in
# A of (i,j) is j+i*D2 and the index in B of (j,k) is k+j*D3.
# The index in C is j+k*D2+i*D2*D3, multiplied by 2 since there are
# two values per ensemble. We add 1 to the B index so it goes into
# the second value in the ensemble.
transformA = [[0] * (D1 * D2) for i in range(D1 * D2 * D3 * 2)]
transformB = [[0] * (D2 * D3) for i in range(D1 * D2 * D3 * 2)]
for i in range(D1):
for j in range(D2):
for k in range(D3):
tmp = (j + k * D2 + i * D2 * D3)
transformA[tmp * 2][j + i * D2] = 1
transformB[tmp * 2 + 1][k + j * D3] = 1
logging.debug("connect A->C")
net.connect('A', 'C', transform=transformA)
logging.debug("connect B->C")
net.connect('B', 'C', transform=transformB)
# now compute the products and do the appropriate summing
logging.debug("make_array: output D")
net.make_array('D', N, D1 * D3, radius=radius, neuron_type='lif')
def product(x):
return x[0] * x[1]
# the mapping for this transformation is much easier, since we want to
# combine D2 pairs of elements (we sum D2 products together)
net.connect('C',
'D',
index_post=[i / D2 for i in range(D1 * D2 * D3)],
func=product)
Aprobe = net.make_probe('A', dt_sample=0.01, pstc=0.01)
Bprobe = net.make_probe('B', dt_sample=0.01, pstc=0.01)
Cprobe = net.make_probe('C', dt_sample=0.01, pstc=0.01)
Dprobe = net.make_probe('D', dt_sample=0.01, pstc=0.01)
prod_probe = net._probe_decoded_signals(
net.ensembles['C'].origin['product'].sigs,
dt_sample=0.01,
pstc=.01)
net.run(1)
Dmat = np.dot(Amat, Bmat)
data = Dprobe.get_data()
with Plotter(self.Simulator) as plt:
for i in range(D1):
for k in range(D3):
plt.subplot(D1, D3, i * D3 + k + 1)
plt.title('D[%i, %i]' % (i, k))
plt.plot(data[:, i * D3 + k])
plt.axhline(Dmat[i, k])
plt.ylim(-radius, radius)
plt.savefig('test_old_api.test_matrix_mul.pdf')
plt.close()
self.assertTrue(
np.allclose(Aprobe.get_data()[50:, 0], 0.5, atol=.1, rtol=.01))
self.assertTrue(
np.allclose(Aprobe.get_data()[50:, 1], -0.5, atol=.1, rtol=.01))
self.assertTrue(
np.allclose(Bprobe.get_data()[50:, 0], 0, atol=.1, rtol=.01))
self.assertTrue(
np.allclose(Bprobe.get_data()[50:, 1], -1, atol=.1, rtol=.01))
self.assertTrue(
np.allclose(Bprobe.get_data()[50:, 2], .7, atol=.1, rtol=.01))
self.assertTrue(
np.allclose(Bprobe.get_data()[50:, 3], 0, atol=.1, rtol=.01))
for i in range(D1):
for k in range(D3):
self.assertTrue(
np.allclose(data[-10:, i * D3 + k],
Dmat[i, k],
atol=0.1,
rtol=0.1),
(data[-10:, i * D3 + k], Dmat[i, k]))