def test_nest_dense_normalisation():
p1 = pynn.Population(12, pynn.IF_cond_exp(**v.DEFAULT_NEURON_PARAMETERS))
p2 = pynn.Population(10, pynn.IF_cond_exp(**v.DEFAULT_NEURON_PARAMETERS))
l = v.Dense(p1, p2, v.ReLU(), weights=1)
m = v.Model(l)
out = m.predict(np.ones(12) * 12, 50)
assert np.allclose(np.ones(10), out, atol=0.1)
def test_nest_model_predict_active():
p1 = pynn.Population(2, pynn.IF_cond_exp())
p2 = pynn.Population(2, pynn.IF_cond_exp())
l = v.Dense(p1, p2, v.ReLU(), decoder=v.spike_count, weights=1)
m = v.Model(l)
out = m.predict(np.array([1, 1]), 1000)
assert len(out) == 2
assert abs(out[0] - out[1]) <= 10 # Must be approx same spikes
def test_nest_model_predict_inactive():
p1 = pynn.Population(2, pynn.IF_cond_exp())
p2 = pynn.Population(2, pynn.IF_cond_exp())
l = v.Dense(p1, p2, v.ReLU(), decoder=v.spike_count)
m = v.Model(l)
out = m.predict(np.array([0, 0]), 10)
assert len(out) == 2
assert out.sum() < 10
def test_nest_dense_create():
p1 = pynn.Population(12, pynn.IF_cond_exp())
p2 = pynn.Population(10, pynn.IF_cond_exp())
d = v.Dense(p1, p2, v.ReLU())
expected_weights = np.ones((12, 10))
actual_weights = d.projection.get('weight', format='array')
assert not np.allclose(actual_weights, expected_weights) # Should be normal distributed
assert abs(actual_weights.sum()) <= 24
def test_nest_projection_gaussian():
p1 = pynn.Population(2, pynn.IF_cond_exp())
p2 = pynn.Population(2, pynn.IF_cond_exp())
c = pynn.Projection(p1, p2,
pynn.AllToAllConnector(allow_self_connections=False))
c.set(weight=pynn.random.RandomDistribution('normal', mu=0.5, sigma=0.1))
weights = c.get('weight', format='array')
assert len(weights[weights == 0]) < 1
def test_nest_model_linear_scaling():
p1 = pynn.Population(2, pynn.IF_cond_exp(**v.DEFAULT_NEURON_PARAMETERS))
p2 = pynn.Population(2, pynn.IF_cond_exp(**v.DEFAULT_NEURON_PARAMETERS))
l1 = v.Dense(p1, p2, v.ReLU(), decoder=v.spike_count, weights=1)
m = v.Model(l1)
xs = np.array([12, 12])
out = m.predict(xs, 50)
assert np.allclose([38, 38], out)
def test_replicate_assert_size():
p1 = pynn.Population(6, pynn.IF_cond_exp())
p2 = pynn.Population(6, pynn.IF_cond_exp())
p3 = pynn.Population(5, pynn.IF_cond_exp())
with pytest.raises(ValueError):
v.Replicate(p1, (p2, p3))
with pytest.raises(ValueError):
v.Replicate(p1, (p3, p2))
def test_nest_dense_chain():
p1 = pynn.Population(12, pynn.SpikeSourcePoisson(rate = 100))
p2 = pynn.Population(10, pynn.IF_cond_exp())
p3 = pynn.Population(2, pynn.IF_cond_exp())
p3.record('spikes')
d1 = v.Dense(p1, p2, v.ReLU())
d2 = v.Dense(p2, p3, v.ReLU())
pynn.run(1000)
assert len(p3.get_data().segments[-1].spiketrains) > 0
def setUp(self):
sim.setup()
self.p1 = sim.Population(7, sim.IF_cond_exp())
self.p2 = sim.Population(4, sim.IF_cond_exp())
self.p3 = sim.Population(5, sim.IF_curr_alpha())
self.syn_rnd = sim.StaticSynapse(weight=0.123, delay=0.5)
self.syn_a2a = sim.StaticSynapse(weight=0.456, delay=0.4)
self.random_connect = sim.FixedNumberPostConnector(n=2)
self.all2all = sim.AllToAllConnector()
def test_replicate_can_replicate():
p1 = pynn.Population(6, pynn.IF_cond_exp(i_offset=10))
p2 = pynn.Population(6, pynn.IF_cond_exp())
p3 = pynn.Population(6, pynn.IF_cond_exp())
l = v.Replicate(p1, (p2, p3), v.ReLU(), weights=(1, 1))
pynn.run(1000)
l.store_spikes()
expected = np.ones((2, 6))
assert np.allclose(expected, l.get_output())
def test_nest_create_input_populations():
p1 = pynn.Population(2, pynn.IF_cond_exp())
p2 = pynn.Population(2, pynn.IF_cond_exp())
l = v.Dense(p1, p2, v.ReLU())
m = v.Model(l)
assert len(m.input_populations) == 2
inp = np.array([1, 0.2])
m.set_input(inp)
assert m.input_populations[0].get('i_offset') == 1
assert m.input_populations[1].get('i_offset') == 0.2
def test_replicate_create():
p1 = pynn.Population(6, pynn.IF_cond_exp())
p2 = pynn.Population(6, pynn.IF_cond_exp())
p3 = pynn.Population(6, pynn.IF_cond_exp())
l = v.Replicate(p1, (p2, p3), v.ReLU(), weights=(1, 1))
pynn.run(1000)
l.store_spikes()
assert l.layer1.input.shape == (6, 0)
assert l.layer2.input.shape == (6, 0)
assert l.get_output().shape == (2, 6)
def test_nest_dense_reduced_weight_fire():
p1 = pynn.Population(1, pynn.IF_cond_exp(i_offset=10))
p2 = pynn.Population(2, pynn.IF_cond_exp())
d = v.Dense(p1, p2, v.ReLU(), weights = np.array([[1, 0]]))
pynn.run(1000)
spiketrains1 = p1.get_data().segments[-1].spiketrains
spiketrains2 = p2.get_data().segments[-1].spiketrains
assert spiketrains1[0].size > 0
assert spiketrains2[0].size > 0
assert spiketrains2[1].size == 0
def test_nest_model_spike_normalisation():
p1 = pynn.Population(2, pynn.IF_cond_exp(**v.DEFAULT_NEURON_PARAMETERS))
p2 = pynn.Population(4, pynn.IF_cond_exp(**v.DEFAULT_NEURON_PARAMETERS))
p3 = pynn.Population(4, pynn.IF_cond_exp(**v.DEFAULT_NEURON_PARAMETERS))
l1 = v.Dense(p1, p2, decoder=v.spike_rate(50), weights=1)
l2 = v.Dense(p2, p3, decoder=v.spike_rate(50), weights=1)
m = v.Model(l1, l2)
m.predict([12, 12], 50)
for rate in np.concatenate((l1.get_output(), l2.get_output())):
assert rate > 0
assert rate < 1
def test_nest_dense_backprop():
p1 = pynn.Population(4, pynn.IF_cond_exp())
p2 = pynn.Population(2, pynn.IF_cond_exp())
l = v.Dense(p1, p2, v.UnitActivation(), weights = 1, decoder = lambda x: x)
old_weights = l.get_weights()
l.input_cache = np.ones((1, 4)) # Mock spikes
errors = l.backward(np.array([[0, 1]]), lambda w, g, b, bg: (w - g, b - bg))
expected_errors = np.zeros((2, 4)) + 4
assert np.allclose(errors, expected_errors)
expected_weights = np.tile([1, -3], (4, 1))
assert np.allclose(l.get_weights(), expected_weights)
def test_nest_input_projection():
p1 = pynn.Population(2, pynn.IF_cond_exp(**v.DEFAULT_NEURON_PARAMETERS))
p2 = pynn.Population(2, pynn.IF_cond_exp(**v.DEFAULT_NEURON_PARAMETERS))
l = v.Dense(p1, p2, v.ReLU(), weights=1)
m = v.Model(l)
t = v.LinearTranslation()
assert np.allclose(l.get_weights(), np.ones((2, 2)))
assert m.input_projection[0].weight == t.weights(1, 1)
assert m.input_projection[1].weight == t.weights(1, 1)
m.predict([1, 1], 50)
spiketrains = l.output
assert abs(len(spiketrains[0]) - len(spiketrains[1])) <= 20
def test_nest_dense_restore():
p1 = pynn.Population(12, pynn.IF_cond_exp())
p2 = pynn.Population(10, pynn.IF_cond_exp())
d = v.Dense(p1, p2, v.ReLU(), weights = 2)
d.set_weights(-1)
t = v.LinearTranslation()
assert np.array_equal(d.projection.get('weight', format='array'),
t.weights(np.ones((12, 10)) * -1, 12))
d.projection.set(weight = 1) # Simulate reset()
assert np.array_equal(d.projection.get('weight', format='array'),
np.ones((12, 10)))
d.restore_weights()
assert np.array_equal(d.projection.get('weight', format='array'),
t.weights(np.ones((12, 10)) * -1, 12))
def test_nest_model_backwards():
p1 = pynn.Population(2, pynn.IF_cond_exp())
p2 = pynn.Population(3, pynn.IF_cond_exp())
l1 = v.Dense(p1, p2, v.ReLU(), decoder=v.spike_count_linear, weights=1)
m = v.Model(l1)
xs = np.array([12, 12])
spikes = m.predict(xs, 50)
def l(w, g, b, bg):
return w - g, b - bg
m.backward([0, 1, 1], l) # no learning rate
expected_weights = np.array([[1, 0, 0], [1, 0, 0]])
assert np.allclose(l1.get_weights(), expected_weights, atol=0.2)
def test_nest_dense_increased_weight_fire():
p1 = pynn.Population(1, pynn.SpikeSourcePoisson(rate = 1))
p2 = pynn.Population(1, pynn.IF_cond_exp())
p2.record('spikes')
d = v.Dense(p1, p2, v.ReLU(), weights = 2)
pynn.run(1000)
spiketrains = p2.get_data().segments[-1].spiketrains
count1 = spiketrains[0].size
pynn.reset()
p1 = pynn.Population(1, pynn.SpikeSourcePoisson(rate = 1))
p2 = pynn.Population(1, pynn.IF_cond_exp())
p2.record('spikes')
d = v.Dense(p1, p2, v.ReLU(), weights = 2)
pynn.run(1000)
spiketrains = p2.get_data().segments[-1].spiketrains
count2 = spiketrains[0].size
assert count2 >= count1 * 2
def test_nest_dense_shape():
p1 = pynn.Population(12, pynn.SpikeSourcePoisson(rate = 10))
p2 = pynn.Population(10, pynn.IF_cond_exp())
d = v.Dense(p1, p2, v.ReLU(), weights = 1)
pynn.run(1000)
d.store_spikes()
assert d.input.shape == (12,)
assert d.output.shape[0] == 10
def test_nest_model_backwards_reset():
p1 = pynn.Population(2, pynn.IF_cond_exp())
p2 = pynn.Population(2, pynn.IF_cond_exp())
l1 = v.Dense(p1, p2, v.ReLU(), decoder=v.spike_count_normalised, weights=1)
m = v.Model(l1)
xs1 = np.array([10, 10])
ys1 = np.array([0, 10])
xs2 = np.array([10, 10])
ys2 = np.array([0, 10])
# First pass
target1 = m.predict(xs1, 50)
m.backward([0, 1], lambda w, g, b, bg: (w - g, b - bg))
expected_weights = np.array([[1, 0], [1, 0]])
assert np.allclose(l1.get_weights(), expected_weights)
# Second pass
target2 = m.predict(xs2, 50)
m.backward([1, 0], lambda w, g, b, bg: (w - g, b - bg))
expected_weights = np.array([[-1, 0], [-1, 0]])
assert np.allclose(l1.get_weights(), expected_weights)
def setUp(self):
sim.setup()
self.p = sim.Population(
4,
sim.IF_cond_exp(
**{
'tau_m': 12.3,
'cm': lambda i: 0.987 + 0.01 * i,
'i_offset': np.array([-0.21, -0.20, -0.19, -0.18])
}))
def test_nest_dense_projection():
p1 = pynn.Population(12, pynn.SpikeSourcePoisson(rate = 10))
p2 = pynn.Population(10, pynn.IF_cond_exp())
p2.record('spikes')
d = v.Dense(p1, p2, v.ReLU(), weights = 1)
pynn.run(1000)
spiketrains = p2.get_data().segments[-1].spiketrains
assert len(spiketrains) == 10
avg_len = np.array(list(map(len, spiketrains))).mean()
# Should have equal activation
for train in spiketrains:
assert abs(len(train) - avg_len) <= 1
def test_reset(self, logcapture):
"""
Test the reset functionality. The reset must not unload the brain, therefore the neurons
that have been setup before must still exist after the reset.
"""
self.control.reset()
population = sim.Population(10, sim.IF_cond_exp())
# As PyNN >= 0.8 creates a multimeter and a spike_recorder per population, the ID of the
# 10th neuron of the 10th population (9 are created during setUp) must be 120
self.assertEqual(population.all_cells[9], 120)
logcapture.check(('hbp_nrp_cle.brainsim.pynn.PyNNControlAdapter', 'INFO',
'neuronal simulator reset'))
def test_projection(self):
path = tempfile.mkstemp()[1]
size_a = random.randint(1, 100)
size_b = random.randint(1, 100)
dist = pyhmf.RandomDistribution(rng=pyhmf.NativeRNG(1337))
conn_pyhmf = pyhmf.AllToAllConnector(weights=dist, delays=42)
proj_pyhmf = pyhmf.Projection(
pyhmf.Population(size_a, pyhmf.IF_cond_exp),
pyhmf.Population(size_b, pyhmf.IF_cond_exp),
conn_pyhmf)
proj_pyhmf.saveConnections(getattr(pyhmf, self.file_type)(path, 'wb'))
conn_pynn = pynn.FromFileConnector(getattr(pynn.recording.files, self.file_type)(path))
proj_pynn = pynn.Projection(
pynn.Population(size_a, pynn.IF_cond_exp()),
pynn.Population(size_b, pynn.IF_cond_exp()),
conn_pynn)
numpy.testing.assert_equal(proj_pyhmf.getWeights(format='array'), proj_pynn.getWeights(format='array'))
def test_native_stdp_model():
nest = pyNN.nest
from pyNN.utility import init_logging
init_logging(logfile=None, debug=True)
nest.setup()
p1 = nest.Population(10, nest.IF_cond_exp())
p2 = nest.Population(10, nest.SpikeSourcePoisson())
stdp_params = {'Wmax': 50.0, 'lambda': 0.015, 'weight': 0.001}
stdp = nest.native_synapse_type("stdp_synapse")(**stdp_params)
connector = nest.AllToAllConnector()
prj = nest.Projection(p2, p1, connector, receptor_type='excitatory',
synapse_type=stdp)
def test():
if not HAVE_H5PY and HAVE_NEST:
raise SkipTest
sim.setup()
p1 = sim.Population(10,
sim.IF_cond_exp(v_rest=-65,
tau_m=lambda i: 10 + 0.1 * i,
cm=RD('normal', (0.5, 0.05))),
label="population_one")
p2 = sim.Population(20,
sim.IF_curr_alpha(v_rest=-64,
tau_m=lambda i: 11 + 0.1 * i),
label="population_two")
prj = sim.Projection(p1,
p2,
sim.FixedProbabilityConnector(p_connect=0.5),
synapse_type=sim.StaticSynapse(weight=RD(
'uniform', [0.0, 0.1]),
delay=0.5),
receptor_type='excitatory')
net = Network(p1, p2, prj)
export_to_sonata(net, "tmp_serialization_test", overwrite=True)
net2 = import_from_sonata("tmp_serialization_test/circuit_config.json",
sim)
for orig_population in net.populations:
imp_population = net2.get_component(orig_population.label)
assert orig_population.size == imp_population.size
for name in orig_population.celltype.default_parameters:
assert_array_almost_equal(orig_population.get(name),
imp_population.get(name), 12)
w1 = prj.get('weight', format='array')
prj2 = net2.get_component(asciify(prj.label).decode('utf-8') + "-0")
w2 = prj2.get('weight', format='array')
assert_array_almost_equal(w1, w2, 12)
def setUp(self):
"""
Instantiates the PyNN communication and control adapter
"""
brainconfig.rng_seed = 123456
with LogCapture(('hbp_nrp_cle.brainsim.pynn.PyNNControlAdapter',
'hbp_nrp_cle.brainsim.pynn.PyNNCommunicationAdapter',
'hbp_nrp_cle.brainsim.common.__AbstractCommunicationAdapter')) as log_capt:
self.control = PyNNControlAdapter(sim)
self.assertEqual(self.control.is_alive(), False)
self.control.initialize(timestep=0.1,
min_delay=0.1,
max_delay=4.0,
num_threads=1)
self.control.initialize(timestep=0.1,
min_delay=0.1,
max_delay=4.0,
num_threads=1)
self.communicator = PyNNNestCommunicationAdapter()
self.neurons_cond = sim.Population(10, sim.IF_cond_exp())
self.neurons_curr = sim.Population(10, sim.IF_curr_exp())
self.two_neurons_pop_cond = [sim.Population(10, sim.IF_cond_exp()),
sim.Population(10, sim.IF_cond_exp())]
self.two_neurons_pop_curr = [sim.Population(10, sim.IF_curr_exp()),
sim.Population(10, sim.IF_curr_exp())]
self.three_neurons_pop_cond = [sim.Population(10, sim.IF_cond_exp()),
sim.Population(10, sim.IF_cond_exp()),
sim.Population(10, sim.IF_cond_exp())]
self.assertEqual(self.communicator.is_initialized, False)
self.assertEqual(self.communicator.detector_devices, [])
self.assertEqual(self.communicator.generator_devices, [])
log_capt.check(('hbp_nrp_cle.brainsim.pynn.PyNNControlAdapter', 'INFO',
'neuronal simulator initialized'),
('hbp_nrp_cle.brainsim.pynn.PyNNControlAdapter', 'WARNING',
'trying to initialize an already initialized controller'))
def test_nest_dense_numerical_gradient():
# Test idea from https://github.com/stephencwelch/Neural-Networks-Demystified/blob/master/partSix.py
# Use simple power function
f = lambda x: x**2
fd = lambda x: 2 * x
e = 1e-4
weights1 = np.ones((2, 3)).ravel()
weights2 = np.ones((3, 1)).ravel()
p1 = pynn.Population(2, pynn.IF_cond_exp())
p2 = pynn.Population(3, pynn.IF_cond_exp())
p3 = pynn.Population(1, pynn.IF_cond_exp())
l1 = v.Dense(p1, p2, v.Sigmoid(), decoder = lambda x: x)
l2 = v.Dense(p2, p3, v.Sigmoid(), decoder = lambda x: x)
m = v.Model(l1, l2)
error = v.SumSquared()
def forward_pass(xs):
"Simple sigmoid forward pass function"
l1.input_cache = xs
l1.output = l2.input_cache = v.Sigmoid()(np.matmul(xs, l1.weights))
l2.output = v.Sigmoid()(np.matmul(l2.input_cache, l2.weights))
return l2.output
def compute_numerical_gradient(xs, ys):
"Computes the numerical gradient of a layer"
weights1 = l1.get_weights().ravel() # 1D
weights2 = l2.get_weights().ravel()
weights = np.concatenate((weights1, weights2))
gradients = np.zeros(weights.shape)
def initialise_with_distortion(index, delta):
distortion = np.copy(weights)
distortion[index] = distortion[index] + delta
l1.set_weights(distortion[:len(weights1)].reshape(l1.weights.shape))
l2.set_weights(distortion[len(weights1):].reshape(l2.weights.shape))
forward_pass(xs)
# Calculate gradients
for index in range(len(weights)):
initialise_with_distortion(index, e)
error1 = -error(l2.output, ys)
initialise_with_distortion(index, -e)
error2 = -error(l2.output, ys)
gradients[index] = (error2 - error1) / (2 * e)
# Reset weights
l1.set_weights(weights1.reshape(2, 3))
l2.set_weights(weights2.reshape(3, 1))
return gradients
def compute_gradients(xs, ys):
class GradientOptimiser():
counter = 2
gradients1 = None
gradients2 = None
def __call__(self, w, wg, b, bg):
if self.counter > 1:
self.gradients2 = wg
else:
self.gradients1 = wg
self.counter -= 1
return (w, b)
output = forward_pass(xs)
optimiser = GradientOptimiser()
m.backward(error.prime(l2.output, ys), optimiser)
return np.concatenate((optimiser.gradients1.ravel(), optimiser.gradients2.ravel()))
# Normalise inputs
xs = np.array(([3,5], [5,1], [10,2]), dtype=float)
xs = xs - np.amax(xs, axis=0)
ys = np.array(([75], [82], [93]), dtype=float)
ys = ys / 100
# Calculate numerical gradients
numerical_gradients = compute_numerical_gradient(xs, ys)
# Calculate 'normal' gradients
gradients = compute_gradients(xs, ys)
# Calculate the ratio between the difference and the sum of vector norms
ratio = np.linalg.norm(gradients - numerical_gradients) /\
np.linalg.norm(gradients + numerical_gradients)
assert ratio < 1e-07
'v_reset': 0.0,
'v_rest': 0.0,
'e_rev_E': 10.0,
'e_rev_I': -10.0,
'i_offset': 0.0,
'cm': 0.1,
'tau_m': 0.8325,
'tau_syn_E': tau_syn,
'tau_syn_I': tau_syn,
'tau_refrac': 0.0
}
cellvalues = {'gsyn_exc': 0.0, 'v': 0.0, 'gsyn_inh': 0.0}
input_celltype = sim.SpikeSourceArray(spike_times=spike_times)
fc_celltype = sim.IF_cond_exp(**cellparams)
input_pop = sim.Population(34 * 34 * 2, input_celltype)
fc0 = sim.Population(w1.shape[0], fc_celltype)
fc0.initialize(**cellvalues)
fc0.set(v_thresh=vth0)
fc1 = sim.Population(w1.shape[0], fc_celltype)
fc1.initialize(**cellvalues)
fc1.set(v_thresh=vth1)
#fc1.set(i_offset=b1)
fc2 = sim.Population(10, fc_celltype)
fc2.initialize(**cellvalues)
fc2.set(v_thresh=vth2)
#fc2.set(i_offset=b2)