def run_simple_split():
sim.setup(0.1, time_scale_factor=1)
sim.set_number_of_neurons_per_core(sim.IF_curr_exp, 16)
# Note, this next one is ignored on one-to-one Poisson sources
sim.set_number_of_neurons_per_core(sim.SpikeSourcePoisson, 10)
one_to_one_source = sim.Population(50,
sim.SpikeSourcePoisson(rate=10000),
additional_parameters={
"seed": 0,
"splitter":
SplitterPoissonDelegate()
})
rand_source = sim.Population(50,
sim.SpikeSourcePoisson(rate=10),
additional_parameters={
"seed": 1,
"splitter": SplitterSliceLegacy()
})
rand_source.record("spikes")
target = sim.Population(
50,
sim.IF_curr_exp(),
additional_parameters={
"splitter": SplitterAbstractPopulationVertexNeuronsSynapses(3)
})
target.record(["spikes", "packets-per-timestep"])
sim.Projection(one_to_one_source, target, sim.OneToOneConnector(),
sim.StaticSynapse(weight=0.01))
sim.Projection(rand_source, target, sim.OneToOneConnector(),
sim.StaticSynapse(weight=2.0))
sim.run(1000)
source_spikes = [
s.magnitude
for s in rand_source.get_data("spikes").segments[0].spiketrains
]
target_spikes = [
s.magnitude for s in target.get_data("spikes").segments[0].spiketrains
]
target_ppts = (numpy.nonzero(
numpy.sum([
s.magnitude for s in target.get_data("packets-per-timestep").
segments[0].filter(name='packets-per-timestep')[0]
],
axis=1))[0] - 1) / 10
sim.end()
# The only actual spikes received should be from the random source
all_source_spikes = numpy.unique(
numpy.sort(numpy.concatenate(source_spikes)))
assert (numpy.allclose(all_source_spikes, target_ppts))
# A target spike should be caused by a source spike (though not all sources
# will cause a target spike)
for s, t in zip(source_spikes, target_spikes):
assert (len(t) <= len(s))
def run_script():
n_neurons = 500
simtime = SIMTIME
sim.setup(timestep=1)
pop_1 = sim.Population(n_neurons, sim.IF_curr_exp(), label="pop_1")
input1 = sim.Population(1, sim.SpikeSourceArray(spike_times=[0]),
label="input")
sim.Projection(input1, pop_1, sim.AllToAllConnector(),
synapse_type=sim.StaticSynapse(weight=5, delay=1))
input2 = sim.Population(n_neurons, sim.SpikeSourcePoisson(
rate=100.0, seed=1), label="Stim_Exc")
sim.Projection(input2, pop_1, sim.OneToOneConnector(),
synapse_type=sim.StaticSynapse(weight=5, delay=1))
pop_1.record(['spikes', 'v', 'gsyn_exc', 'gsyn_inh'])
sim.run(simtime)
neo = pop_1.get_data()
spikes = neo.segments[0].spiketrains
v = neo.segments[0].filter(name='v')[0]
exc = neo.segments[0].filter(name='gsyn_exc')[0]
inh = neo.segments[0].filter(name='gsyn_inh')[0]
sim.end()
return spikes, v, exc, inh
def do_run(seed=None):
sim.setup(timestep=1.0, min_delay=1.0, max_delay=1.0)
simtime = 1000
if seed is None:
pg_pop1 = sim.Population(2,
sim.SpikeSourcePoisson(rate=10.0,
start=0,
duration=simtime),
label="pg_pop1")
pg_pop2 = sim.Population(2,
sim.SpikeSourcePoisson(rate=10.0,
start=0,
duration=simtime),
label="pg_pop2")
else:
pg_pop1 = sim.Population(2,
sim.SpikeSourcePoisson(rate=10.0,
start=0,
duration=simtime,
seed=seed),
label="pg_pop1")
pg_pop2 = sim.Population(2,
sim.SpikeSourcePoisson(rate=10.0,
start=0,
duration=simtime,
seed=seed + 1),
label="pg_pop2")
pg_pop1.record("spikes")
pg_pop2.record("spikes")
sim.run(simtime)
neo = pg_pop1.get_data("spikes")
spikes1 = neo_convertor.convert_spikes(neo)
neo = pg_pop2.get_data("spikes")
spikes2 = neo_convertor.convert_spikes(neo)
sim.end()
return (spikes1, spikes2)
def test_set_spikes_indexes(self):
sim.setup(timestep=1)
if_curr = sim.Population(5, sim.IF_curr_exp())
recorder = if_curr._vertex._neuron_recorder
ssa = sim.Population(
5, sim.SpikeSourceArray(spike_times=[0]))
ssp = sim.Population(5, sim.SpikeSourcePoisson(rate=100.0, seed=1))
if_curr.record("spikes", indexes=[1, 2, 4])
ssa.record("spikes", indexes=[1, 2, 4])
ssp.record("spikes", indexes=[1, 2, 4])
self.assertListEq(["spikes"], if_curr._get_all_recording_variables())
assert recorder._indexes["spikes"] == [1, 2, 4]
def test_set_spikes(self):
sim.setup(timestep=1)
if_curr = sim.Population(1, sim.IF_curr_exp())
self.assertListEq([], if_curr._get_all_recording_variables())
ssa = sim.Population(
1, sim.SpikeSourceArray(spike_times=[0]))
ssp = sim.Population(2, sim.SpikeSourcePoisson(rate=100.0, seed=1))
if_curr.record("spikes")
self.assertListEq(["spikes"], if_curr._get_all_recording_variables())
ssa.record("spikes")
ssp.record("spikes")
sim.end()
def no_reset(self):
p.setup(1.0)
inp = p.Population(100, p.SpikeSourcePoisson(rate=100), label="input")
inp.record("spikes")
p.run(100)
spikes1 = inp.spinnaker_get_data('spikes')
inp.set(rate=10)
p.run(100)
spikes2 = inp.spinnaker_get_data('spikes')
assert len(spikes1) > (len(spikes2) - len(spikes1)) * 5
p.end()
def test_set_spikes_interval(self):
sim.setup(timestep=1)
if_curr = sim.Population(1, sim.IF_curr_exp())
recorder = if_curr._vertex._neuron_recorder
self.assertListEq([], if_curr._get_all_recording_variables())
ssa = sim.Population(
1, sim.SpikeSourceArray(spike_times=[0]))
ssp = sim.Population(2, sim.SpikeSourcePoisson(rate=100.0, seed=1))
if_curr.record("spikes", sampling_interval=2)
ssa.record("spikes", sampling_interval=2)
ssp.record("spikes", sampling_interval=2)
self.assertListEq(["spikes"], if_curr._get_all_recording_variables())
assert recorder.get_neuron_sampling_interval("spikes") == 2
def run_forever_not_recorded():
sim.setup(1.0)
stim = sim.Population(1, sim.SpikeSourcePoisson(rate=10.0))
pop = sim.Population(255, sim.IF_curr_exp(tau_syn_E=1.0), label="pop")
sim.Projection(
stim, pop, sim.AllToAllConnector(), sim.StaticSynapse(weight=20.0))
conn = DatabaseConnection(
start_resume_callback_function=start_callback,
stop_pause_callback_function=stop_callback, local_port=None)
SpynnakerExternalDevicePluginManager.add_database_socket_address(
conn.local_ip_address, conn.local_port, None)
sim.external_devices.run_forever()
sim.end()
def test_set_spikes_indexes(self):
sim.setup(timestep=1)
if_curr = sim.Population(5, sim.IF_curr_exp())
recorder = if_curr._vertex.neuron_recorder
ssa = sim.Population(5, sim.SpikeSourceArray(spike_times=[0]))
ssp = sim.Population(5,
sim.SpikeSourcePoisson(rate=100.0),
additional_parameters={"seed": 1})
if_curr[1, 2, 4].record("spikes")
ssa[1, 2, 4].record("spikes")
ssp[1, 2, 4].record("spikes")
self.assertCountEqual(["spikes"],
if_curr._recorder.get_all_recording_variables())
assert recorder._indexes["spikes"] == [1, 2, 4]
def variable_rate_reset():
""" Test the ways of changing rates and ensure that they don't change the\
results
"""
p.setup(1.0)
pop = p.Population(100,
p.extra_models.SpikeSourcePoissonVariable(
rates=[1, 10, 100], starts=[0, 1000, 2000]),
additional_parameters={"seed": 0})
pop_2 = p.Population(100,
p.SpikeSourcePoisson(rate=1),
additional_parameters={
"seed": 0,
"max_rate": 100
})
pop.record("spikes")
pop_2.record("spikes")
p.run(1000)
spikes_pop_2_1 = pop_2.get_data("spikes")
nump = [s.magnitude for s in spikes_pop_2_1.segments[0].spiketrains]
numpy.savetxt("spikesp2_1.txt", nump[0])
pop_2.set(rate=10)
p.run(1000)
spikes_pop_2_2 = pop_2.get_data("spikes")
nump = [s.magnitude for s in spikes_pop_2_2.segments[0].spiketrains]
numpy.savetxt("spikesp2_2.txt", nump[0])
pop_2.set(rate=100)
p.run(1000)
p.reset()
p.run(3000)
spikes_pop = pop.get_data("spikes")
spikes_pop_2 = pop_2.get_data("spikes")
p.end()
spikes_1 = [s.magnitude for s in spikes_pop.segments[0].spiketrains]
spikes_2 = [s.magnitude for s in spikes_pop.segments[1].spiketrains]
spikes_p_2 = [s.magnitude for s in spikes_pop_2.segments[0].spiketrains]
print(spikes_1)
numpy.savetxt("spikes1.txt", spikes_1[0])
print(spikes_2)
numpy.savetxt("spikes2.txt", spikes_2[0])
print(spikes_p_2)
numpy.savetxt("spikesp2.txt", spikes_p_2[0])
for s1, s2, s3 in zip(spikes_1, spikes_2, spikes_p_2):
assert (numpy.array_equal(s1, s2))
assert (numpy.array_equal(s2, s3))
def test_set_spikes(self):
sim.setup(timestep=1)
if_curr = sim.Population(1, sim.IF_curr_exp())
self.assertCountEqual([],
if_curr._recorder.get_all_recording_variables())
ssa = sim.Population(1, sim.SpikeSourceArray(spike_times=[0]))
ssp = sim.Population(2,
sim.SpikeSourcePoisson(rate=100.0),
additional_parameters={"seed": 1})
if_curr.record("spikes")
self.assertCountEqual(["spikes"],
if_curr._recorder.get_all_recording_variables())
ssa.record("spikes")
ssp.record("spikes")
sim.end()
def test_set_all(self):
sim.setup(timestep=1)
if_curr = sim.Population(1, sim.IF_curr_exp())
ssa = sim.Population(1, sim.SpikeSourceArray(spike_times=[0]))
ssp = sim.Population(2,
sim.SpikeSourcePoisson(rate=100.0),
additional_parameters={"seed": 1})
if_curr.record("all")
self.assertListEq(["spikes", "v", "gsyn_inh", "gsyn_exc"],
if_curr._get_all_recording_variables())
ssa.record("all")
self.assertListEq(["spikes"], ssa._get_all_recording_variables())
ssp.record("all")
self.assertListEq(["spikes"], ssp._get_all_recording_variables())
sim.end()
def check_rates(self, rates, seconds, seed):
n_neurons = 100
sim.setup(timestep=1.0)
inputs = {}
for rate in rates:
input = sim.Population(n_neurons,
sim.SpikeSourcePoisson(rate),
label='inputSpikes_{}'.format(rate),
additional_parameters={"seed": seed})
input.record("spikes")
inputs[rate] = input
sim.run(seconds * 1000)
for rate in rates:
self.check_spikes(n_neurons, inputs[rate], rate * seconds)
sim.end()
def do_run(split, seed=None):
p.setup(1.0)
if split:
p.set_number_of_neurons_per_core(p.SpikeSourcePoisson, 27)
p.set_number_of_neurons_per_core(p.IF_curr_exp, 22)
inp = p.Population(100,
p.SpikeSourcePoisson(rate=100, seed=seed),
label="input")
pop = p.Population(100, p.IF_curr_exp, {}, label="pop")
p.Projection(inp,
pop,
p.OneToOneConnector(),
synapse_type=p.StaticSynapse(weight=5))
pop.record("spikes")
inp.record("spikes")
p.run(100)
inp.set(rate=10)
# pop.set("cm", 0.25)
pop.set(tau_syn_E=1)
p.run(100)
pop_spikes1 = pop.spinnaker_get_data('spikes')
inp_spikes1 = inp.spinnaker_get_data('spikes')
p.reset()
inp.set(rate=0)
pop.set(i_offset=1.0)
vs = p.RandomDistribution("uniform", [-65.0, -55.0],
rng=NumpyRNG(seed=seed))
pop.initialize(v=vs)
p.run(100)
pop_spikes2 = pop.spinnaker_get_data('spikes')
inp_spikes2 = inp.spinnaker_get_data('spikes')
p.end()
return (pop_spikes1, inp_spikes1, pop_spikes2, inp_spikes2)
def do_run():
p.setup(1.0)
inp = p.Population(100,
p.SpikeSourcePoisson(rate=2, seed=417),
label="input")
inp.record("spikes")
p.run(100)
p.reset()
inp.set(rate=30)
p.run(100)
p.end()
def test_levels(rates=(500, 1000), weights=(0.005, 0.0005)):
counter = 0
receive_pop = []
spike_input = []
p.setup(timestep=1, min_delay=1, max_delay=127)
p.set_number_of_neurons_per_core(p.IF_cond_exp, 10)
for rate in rates:
for weight in weights:
pop_size = 10
receive_pop.append(p.Population(pop_size, p.IF_cond_exp(
))) #, label="receive_pop{}-{}".format(rate, weight)))
receive_pop[counter].record(['spikes', 'v']) #["spikes"])
# Connect key spike injector to input population
spike_input.append(
p.Population(pop_size, p.SpikeSourcePoisson(rate=rate))
) #, label="input_connect{}-{}".format(rate, weight)))
p.Projection(spike_input[counter], receive_pop[counter],
p.OneToOneConnector(), p.StaticSynapse(weight=weight))
print "reached here 1"
runtime = 11000
counter += 1
p.run(runtime)
print "reached here 2"
for i in range(counter):
weight_index = i % len(weights)
rate_index = (i - weight_index) / len(weights)
print weight_index
print rate_index
# for j in range(receive_pop_size):
spikes = receive_pop[i].get_data('spikes').segments[0].spiketrains
v = receive_pop[i].get_data('v').segments[0].filter(name='v')[0]
plt.figure("rate = {} - weight = {}".format(rates[rate_index],
weights[weight_index]))
Figure(Panel(spikes, xlabel="Time (ms)", ylabel="nID", xticks=True),
Panel(v, ylabel="Membrane potential (mV)", yticks=True))
plt.show()
# End simulation
p.end()
def do_run():
p.setup(1.0)
inp = p.Population(100,
p.SpikeSourcePoisson(rate=2),
label="input",
additional_parameters={"seed": 417})
inp.record("spikes")
p.run(100)
p.reset()
inp.set(rate=30)
p.run(100)
p.end()
def mission_impossible_2():
sim.setup(0.1, time_scale_factor=1)
# Can't do structural on multiple synapse cores
source = sim.Population(1, sim.SpikeSourcePoisson(rate=10))
pop = sim.Population(128,
sim.IF_curr_exp(),
additional_parameters={
"splitter":
SplitterAbstractPopulationVertexNeuronsSynapses(2)
})
sim.Projection(
source, pop, sim.FromListConnector([]),
sim.StructuralMechanismStatic(sim.RandomSelection(),
sim.DistanceDependentFormation(),
sim.RandomByWeightElimination(0.5)))
with pytest.raises(SynapticConfigurationException):
sim.run(100)
def test_set_v(self):
sim.setup(timestep=1)
if_curr = sim.Population(1, sim.IF_curr_exp())
ssa = sim.Population(1, sim.SpikeSourceArray(spike_times=[0]))
ssp = sim.Population(2,
sim.SpikeSourcePoisson(rate=100.0),
additional_parameters={"seed": 1})
if_curr.record("v")
try:
ssa.record("v")
except Exception as e:
self.assertEqual(
"This population does not support the recording of v!", str(e))
try:
ssp.record("v")
except Exception as e:
self.assertEqual(
"This population does not support the recording of v!", str(e))
sim.end()
def test_set_v(self):
sim.setup(timestep=1)
if_curr = sim.Population(1, sim.IF_curr_exp())
ssa = sim.Population(1, sim.SpikeSourceArray(spike_times=[0]))
ssp = sim.Population(2,
sim.SpikeSourcePoisson(rate=100.0),
additional_parameters={"seed": 1})
if_curr.record("v")
# SpikeSourceArray must throw if asked to record voltage
with self.assertRaises(Exception) as e:
ssa.record("v")
self.assertEqual(
"This population does not support the recording of v!",
str(e.exception))
# SpikeSourcePoisson must throw if asked to record voltage
with self.assertRaises(Exception) as e:
ssp.record("v")
self.assertEqual(
"This population does not support the recording of v!",
str(e.exception))
sim.end()
def poisson_live_rates(self):
self._saved_label_init = None
self._saved_vertex_size = None
self._saved_run_time_ms = None
self._saved_machine_timestep_ms = None
self._saved_label_set = None
self._saved_label_stop = None
def init(label, vertex_size, run_time_ms, machine_timestep_ms):
self._saved_label_init = label
self._saved_vertex_size = vertex_size
self._saved_run_time_ms = run_time_ms
self._saved_machine_timestep_ms = machine_timestep_ms
def set_rates(label, conn):
time.sleep(1.0)
conn.set_rates(label, [(i, 50) for i in range(50)])
self._saved_label_set = label
def stop(label, _conn):
self._saved_label_stop = label
n_neurons = 100
timestep = 1.0
runtime = 2000
sim.setup(timestep=timestep)
sim.set_number_of_neurons_per_core(sim.SpikeSourcePoisson, 75)
pop_label = "pop_to_control"
pop = sim.Population(n_neurons,
sim.SpikeSourcePoisson(rate=0.0),
label=pop_label,
additional_parameters={"max_rate": 50.0})
pop.record("spikes")
conn = sim.external_devices.SpynnakerPoissonControlConnection(
poisson_labels=[pop_label], local_port=None)
conn.add_start_resume_callback(pop_label, set_rates)
conn.add_init_callback(pop_label, init)
conn.add_pause_stop_callback(pop_label, stop)
with self.assertRaises(ConfigurationException):
conn.add_receive_callback(pop_label, stop)
sim.external_devices.add_database_socket_address(
conn.local_ip_address, conn.local_port, None)
sim.external_devices.add_poisson_live_rate_control(pop)
sim.run(runtime)
neo = pop.get_data("spikes")
spikes = neo.segments[0].spiketrains
sim.end()
count_0_49 = 0
for a_spikes in spikes[0:50]:
count_0_49 += len(a_spikes)
count_50_99 = 0
for a_spikes in spikes[50:100]:
count_50_99 += len(a_spikes)
tolerance = math.sqrt(50.0)
self.assertAlmostEqual(50.0, count_0_49 / 50.0, delta=tolerance)
self.assertEqual(count_50_99, 0.0)
self.assertEqual(self._saved_label_set, pop_label)
self.assertEqual(self._saved_label_init, pop_label)
self.assertEqual(self._saved_label_stop, pop_label)
self.assertEqual(self._saved_machine_timestep_ms, timestep)
self.assertEqual(self._saved_vertex_size, n_neurons)
self.assertEqual(self._saved_run_time_ms, runtime)
def do_run(seed=None):
random.seed(seed)
# SpiNNaker setup
sim.setup(timestep=1.0, min_delay=1.0, max_delay=10.0)
# +-------------------------------------------------------------------+
# | General Parameters |
# +-------------------------------------------------------------------+
# Population parameters
model = sim.IF_curr_exp
cell_params = {
'cm': 0.25,
'i_offset': 0.0,
'tau_m': 10.0,
'tau_refrac': 2.0,
'tau_syn_E': 2.5,
'tau_syn_I': 2.5,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -55.4
}
# Other simulation parameters
e_rate = 200
in_rate = 350
n_stim_test = 5
n_stim_pairing = 10
dur_stim = 20
pop_size = 40
ISI = 150.
start_test_pre_pairing = 200.
start_pairing = 1500.
start_test_post_pairing = 700.
simtime = start_pairing + start_test_post_pairing + \
ISI*(n_stim_pairing + n_stim_test) + 550. # let's make it 5000
# Initialisations of the different types of populations
IAddPre = []
IAddPost = []
# +-------------------------------------------------------------------+
# | Creation of neuron populations |
# +-------------------------------------------------------------------+
# Neuron populations
pre_pop = sim.Population(pop_size, model(**cell_params))
post_pop = sim.Population(pop_size, model(**cell_params))
# Test of the effect of activity of the pre_pop population on the post_pop
# population prior to the "pairing" protocol : only pre_pop is stimulated
for i in range(n_stim_test):
IAddPre.append(
sim.Population(
pop_size,
sim.SpikeSourcePoisson(rate=in_rate,
start=start_test_pre_pairing + ISI *
(i),
duration=dur_stim,
seed=random.randint(0, 100000000))))
# Pairing protocol : pre_pop and post_pop are stimulated with a 10 ms
# difference
for i in range(n_stim_pairing):
IAddPre.append(
sim.Population(
pop_size,
sim.SpikeSourcePoisson(rate=in_rate,
start=start_pairing + ISI * (i),
duration=dur_stim,
seed=random.randint(0, 100000000))))
IAddPost.append(
sim.Population(
pop_size,
sim.SpikeSourcePoisson(rate=in_rate,
start=start_pairing + ISI * (i) + 10.,
duration=dur_stim,
seed=random.randint(0, 100000000))))
# Test post pairing : only pre_pop is stimulated
# (and should trigger activity in Post)
for i in range(n_stim_test):
start = start_pairing + ISI * n_stim_pairing + \
start_test_post_pairing + ISI * i
IAddPre.append(
sim.Population(
pop_size,
sim.SpikeSourcePoisson(rate=in_rate,
start=start,
duration=dur_stim,
seed=random.randint(0, 100000000))))
# Noise inputs
INoisePre = sim.Population(pop_size,
sim.SpikeSourcePoisson(rate=e_rate,
start=0,
duration=simtime,
seed=random.randint(
0, 100000000)),
label="expoisson")
INoisePost = sim.Population(pop_size,
sim.SpikeSourcePoisson(rate=e_rate,
start=0,
duration=simtime,
seed=random.randint(
0, 100000000)),
label="expoisson")
# +-------------------------------------------------------------------+
# | Creation of connections |
# +-------------------------------------------------------------------+
# Connection parameters
JEE = 3.
# Connection type between noise poisson generator and
# excitatory populations
ee_connector = sim.OneToOneConnector()
# Noise projections
sim.Projection(INoisePre,
pre_pop,
ee_connector,
receptor_type='excitatory',
synapse_type=sim.StaticSynapse(weight=JEE * 0.05))
sim.Projection(INoisePost,
post_pop,
ee_connector,
receptor_type='excitatory',
synapse_type=sim.StaticSynapse(weight=JEE * 0.05))
# Additional Inputs projections
for i in range(len(IAddPre)):
sim.Projection(IAddPre[i],
pre_pop,
ee_connector,
receptor_type='excitatory',
synapse_type=sim.StaticSynapse(weight=JEE * 0.05))
for i in range(len(IAddPost)):
sim.Projection(IAddPost[i],
post_pop,
ee_connector,
receptor_type='excitatory',
synapse_type=sim.StaticSynapse(weight=JEE * 0.05))
# Plastic Connections between pre_pop and post_pop
stdp_model = sim.STDPMechanism(
timing_dependence=sim.SpikePairRule(tau_plus=20.,
tau_minus=50.0,
A_plus=0.02,
A_minus=0.02),
weight_dependence=sim.AdditiveWeightDependence(w_min=0, w_max=0.9))
rng = NumpyRNG(seed=seed, parallel_safe=True)
plastic_projection = \
sim.Projection(pre_pop, post_pop, sim.FixedProbabilityConnector(
p_connect=0.5, rng=rng), synapse_type=stdp_model)
# +-------------------------------------------------------------------+
# | Simulation and results |
# +-------------------------------------------------------------------+
# Record spikes and neurons' potentials
pre_pop.record(['v', 'spikes'])
post_pop.record(['v', 'spikes'])
# Run simulation
sim.run(simtime)
weights = plastic_projection.get('weight', 'list')
pre_spikes = neo_convertor.convert_spikes(pre_pop.get_data('spikes'))
post_spikes = neo_convertor.convert_spikes(post_pop.get_data('spikes'))
# End simulation on SpiNNaker
sim.end()
return (pre_spikes, post_spikes, weights)
'tau_syn_E': tauSyn,
'tau_syn_I': tauSyn,
'i_offset': 0.9
}
# Set-up pynn Populations
E_pop = pynn.Population(N_E,
pynn.IF_curr_exp(**exc_cell_params),
label="E_pop")
I_pop = pynn.Population(N_I,
pynn.IF_curr_exp(**inh_cell_params),
label="I_pop")
Poiss_ext_E = pynn.Population(N_E,
pynn.SpikeSourcePoisson(rate=10.0),
label="Poisson_pop_E")
Poiss_ext_I = pynn.Population(N_I,
pynn.SpikeSourcePoisson(rate=10.0),
label="Poisson_pop_I")
# Connectors
E_conn = pynn.FixedProbabilityConnector(epsilon)
I_conn = pynn.FixedProbabilityConnector(epsilon)
# Use random delays for the external noise and
# set the inital membrance voltage below the resting potential
# to avoid the overshoot of activity in the beginning of the simulation
rng = NumpyRNG(seed=1)
delay_distr = RandomDistribution('uniform', low=1.0, high=16.0, rng=rng)
Ext_conn = pynn.OneToOneConnector()
def run_script(simtime,
n_neurons,
run_split=1,
record_spikes=False,
spike_rate=None,
spike_rec_indexes=None,
spike_get_indexes=None,
record_v=False,
v_rate=None,
v_rec_indexes=None,
v_get_indexes=None,
record_exc=False,
exc_rate=None,
exc_rec_indexes=None,
exc_get_indexes=None,
record_inh=False,
inh_rate=None,
inh_rec_indexes=None,
inh_get_indexes=None,
file_prefix=""):
sim.setup(timestep=1)
pop_1 = sim.Population(n_neurons, sim.IF_curr_exp(), label="pop_1")
input1 = sim.Population(1,
sim.SpikeSourceArray(spike_times=[0]),
label="input")
sim.Projection(input1,
pop_1,
sim.AllToAllConnector(),
synapse_type=sim.StaticSynapse(weight=5, delay=1))
input2 = sim.Population(n_neurons,
sim.SpikeSourcePoisson(rate=100.0),
label="Stim_Exc",
additional_parameters={"seed": 1})
sim.Projection(input2,
pop_1,
sim.OneToOneConnector(),
synapse_type=sim.StaticSynapse(weight=5, delay=1))
if record_spikes:
if spike_rec_indexes is None:
pop_1.record(['spikes'], sampling_interval=spike_rate)
else:
view = PopulationView(pop_1, spike_rec_indexes)
view.record(['spikes'], sampling_interval=spike_rate)
if record_v:
if v_rec_indexes is None:
pop_1.record(['v'], sampling_interval=v_rate)
else:
view = PopulationView(pop_1, v_rec_indexes)
view.record(['v'], sampling_interval=v_rate)
if record_exc:
if exc_rec_indexes is None:
pop_1.record(['gsyn_exc'], sampling_interval=exc_rate)
else:
view = PopulationView(pop_1, exc_rec_indexes)
view.record(['gsyn_exc'], sampling_interval=exc_rate)
if record_inh:
if inh_rec_indexes is None:
pop_1.record(['gsyn_inh'], sampling_interval=inh_rate)
else:
view = PopulationView(pop_1, inh_rec_indexes)
view.record(['gsyn_inh'], sampling_interval=inh_rate)
for i in range(run_split):
sim.run(simtime / run_split)
if record_spikes:
if spike_get_indexes is None:
neo = pop_1.get_data("spikes")
else:
view = PopulationView(pop_1, spike_get_indexes)
neo = view.get_data("spikes")
spikes = neo.segments[0].spiketrains
spike_file = os.path.join(current_file_path,
file_prefix + "spikes.csv")
write_spikes(spikes, spike_file)
else:
spikes = None
if record_v:
if v_get_indexes is None:
neo = pop_1.get_data("v")
else:
view = PopulationView(pop_1, v_get_indexes)
neo = view.get_data("v")
v = neo.segments[0].filter(name='v')[0]
v_file = os.path.join(current_file_path, file_prefix + "v.csv")
numpy.savetxt(v_file, v, delimiter=',')
else:
v = None
if record_exc:
if exc_get_indexes is None:
neo = pop_1.get_data('gsyn_exc')
else:
view = PopulationView(pop_1, exc_get_indexes)
neo = view.get_data('gsyn_exc')
exc = neo.segments[0].filter(name='gsyn_exc')[0]
exc_file = os.path.join(current_file_path, file_prefix + "exc.csv")
numpy.savetxt(exc_file, exc, delimiter=',')
else:
exc = None
if record_inh:
if inh_get_indexes is None:
neo = pop_1.get_data('gsyn_inh')
else:
view = PopulationView(pop_1, inh_get_indexes)
neo = view.get_data('gsyn_inh')
inh = neo.segments[0].filter(name='gsyn_inh')[0]
inh_file = os.path.join(current_file_path, file_prefix + "inh.csv")
numpy.savetxt(inh_file, inh, delimiter=',')
else:
inh = None
sim.end()
return spikes, v, exc, inh
p.StaticSynapse(weight=0.09))
null_pop.record(['spikes', 'v', 'gsyn_exc'])
# null_pop.record(['spikes', 'v'])
# null_pops = []
# for i in range(4*number_of_bins):
# null_pops.append(p.Population(1, p.IF_cond_exp(),
# label='null {}'.format(i)))
# null_pops[i].record(['spikes', 'v'])
# p.Projection(pendulum, null_pops[i],
# p.FromListConnector([[i, 0, weight, 1]]))
arm_collection = []
# input_spikes = []
rate = 5
print('rate = ', rate)
input_spikes = p.Population(force_increments, p.SpikeSourcePoisson(rate=rate))
p.Projection(input_spikes, pendulum, p.AllToAllConnector(), p.StaticSynapse())
weight = 0.1
label = '64 0.55'
from_list_conn_left = [[0, 0, weight, 1], [6, 0, weight, 1],
[3, 0, weight, 1], [11, 0, weight, 1]]
from_list_conn_right = [[2, 0, weight, 1], [8, 0, weight, 1],
[5, 0, weight, 1], [9, 0, weight, 1]]
left = 0
right = 1
from_list_conn_out = [[0, left, weight, 1], [6, left, weight, 1],
[3, left, weight, 1], [11, left, weight, 1],
[2, right, weight, 1], [8, right, weight, 1],
[5, right, weight, 1], [9, right, weight, 1]]
output_pop = p.Population(
outputs, p.IF_cond_exp(
def spinn_net():
np.random.seed(272727)
global output_labels
global input_labels
p.setup(timestep=1.0, min_delay=1, max_delay=60)
p.set_number_of_neurons_per_core(p.IF_cond_exp, 64)
n_pop_labels = []
n_pop_list = []
n_proj_list = []
spike_source_list = []
if offset != 0:
for i in range(2):
del output_labels[0]
for i in range(2):
del input_labels[0]
for i in range(no_neuron_pops):
#set up the input as a live spike source
if i < 2:
n_pop_labels.append("Input_pop{}".format(i))
input_labels.append("Input_pop{}".format(i))
n_pop_list.append(
p.Population(pop_sizes[i], p.SpikeSourcePoisson(rate=poisson_rate),
label=n_pop_labels[i]))
n_pop_list[i].record(["spikes"])
p.external_devices.add_poisson_live_rate_control(
n_pop_list[i], database_notify_port_num=(160+offset))
#set up output pop
elif i < 4:
n_pop_labels.append("Output_pop{}".format(i))
output_labels.append("Output_pop{}".format(i))
n_pop_list.append(p.Population(pop_sizes[i], p.IF_cond_exp(),
label=n_pop_labels[i]))
p.external_devices.activate_live_output_for(
n_pop_list[i], database_notify_port_num=(180+offset),
port=(17000+offset))
spike_source_list.append(p.Population(pop_sizes[i], p.SpikeSourcePoisson(rate=0.0),
label="source ".format(n_pop_labels[i])))
n_pop_list[i].record(["spikes", "v"])
#set up all other populations
else:
n_pop_labels.append("neuron{}".format(i))
n_pop_list.append(p.Population(pop_sizes[i], p.IF_cond_exp(),
label=n_pop_labels[i]))
spike_source_list.append(p.Population(pop_sizes[i], p.SpikeSourcePoisson(rate=0.0),
label="source ".format(n_pop_labels[i])))
n_pop_list[i].record(["spikes", "v"])
poisson_control = p.external_devices.SpynnakerPoissonControlConnection(
poisson_labels=input_labels, local_port=(160+offset))
poisson_control.add_start_callback(n_pop_list[0].label, from_list_poisson)
# poisson_control.add_start_callback(n_pop_list[1].label, poisson_setting)
# poisson_control.add_start_callback(n_pop_list[0].label, poisson_threading)
live_connection = p.external_devices.SpynnakerLiveSpikesConnection(
receive_labels=output_labels, local_port=(180+offset))
live_connection.add_receive_callback(n_pop_labels[2], receive_spikes)
live_connection.add_receive_callback(n_pop_labels[3], receive_spikes)
# weight_mu = 0.015
# weight_sdtev = 0.05
# delay_mu = 40
# delay_sdtev = 5
for i in range(no_neuron_pops):
np.random.seed(272727)
weights = RandomDistribution("normal_clipped", mu=weight_mu[i],
sigma=weight_stdev[i], low=0, high=np.inf)
delays = RandomDistribution("normal_clipped", mu=delay_mu[i],
sigma=delay_stdev[i], low=1, high=55)
synapse = p.StaticSynapse(weight=weights, delay=delays)
for j in range(2, no_neuron_pops):
print "\npop = {}({}) connecting to {}".format(i,pop_sizes[i],j)
if connect_prob_ex[i][j-2] > 1e-10:
print "ex = {}\tin = {}".format(connect_prob_ex[i][j-2], connect_prob_in[i][j-2])
print "\tweight mu = {}\t stdev = {}".format(weight_mu[i], weight_stdev[i])
print "\tdelay mu = {}\t stdev = {}".format(delay_mu[i], delay_stdev[i])
n_proj_list.append(
p.Projection(n_pop_list[i], n_pop_list[j],
p.FixedProbabilityConnector(connect_prob_ex[i][j-2]),#p.OneToOneConnector(),#
synapse, receptor_type="excitatory"))
n_proj_list.append(
p.Projection(n_pop_list[i], n_pop_list[j],
p.FixedProbabilityConnector(connect_prob_in[i][j-2]),#p.OneToOneConnector(),#
synapse, receptor_type="inhibitory"))
# n_proj_list.append(p.Projection(n_pop_list[i], n_pop_list[j],
# p.FixedProbabilityConnector(1),
# synapse, receptor_type="inhibitory"))
run = 0
p.run(duration/timeScaleFactor)
print "finished 1st"
run = 1
p.reset()
p.run(duration/timeScaleFactor)
total_v = list()
spikes = list()
v = list()
spikes.append(n_pop_list[0].get_data("spikes"))
spikes.append(n_pop_list[1].get_data("spikes"))
for j in range(2,no_neuron_pops):
spikes.append(n_pop_list[j].get_data("spikes"))
v.append(n_pop_list[j].get_data("v"))
Figure(
# raster plot of the presynaptic neuron spike times
Panel(spikes[0].segments[0].spiketrains,
yticks=True, markersize=2, xlim=(0, duration)),
Panel(spikes[1].segments[0].spiketrains,
yticks=True, markersize=2, xlim=(0, duration)),
Panel(spikes[2].segments[0].spiketrains,
yticks=True, markersize=2, xlim=(0, duration)),
Panel(spikes[3].segments[0].spiketrains,
yticks=True, markersize=2, xlim=(0, duration)),
# Panel(spikes[4].segments[0].spiketrains,
# yticks=True, markersize=2, xlim=(0, duration)),
# Panel(spikes[no_neuron_pops-2].segments[0].spiketrains,
# yticks=True, markersize=2, xlim=(0, duration)),
# Panel(spikes[no_neuron_pops-1].segments[0].spiketrains,
# yticks=True, markersize=2, xlim=(0, duration)),
title="Raster plot",
annotations="Simulated with {}".format(p.name())
)
plt.show()
Figure(
#membrane voltage plots
Panel(v[0].segments[0].filter(name='v')[0],
ylabel="Membrane potential (mV)", yticks=True, xlim=(0, duration)),
Panel(v[1].segments[0].filter(name='v')[0],
ylabel="Membrane potential (mV)", yticks=True, xlim=(0, duration)),
Panel(v[2].segments[0].filter(name='v')[0],
ylabel="Membrane potential (mV)", yticks=True, xlim=(0, duration)),
Panel(v[3].segments[0].filter(name='v')[0],
ylabel="Membrane potential (mV)", yticks=True, xlim=(0, duration)),
# Panel(v[4].segments[0].filter(name='v')[0],
# ylabel="Membrane potential (mV)", yticks=True, xlim=(0, duration)),
# Panel(v[no_neuron_pops-4].segments[0].filter(name='v')[0],
# ylabel="Membrane potential (mV)", yticks=True, xlim=(0, duration)),
# Panel(v[no_neuron_pops-3].segments[0].filter(name='v')[0],
# ylabel="Membrane potential (mV)", yticks=True, xlim=(0, duration)),
title="Membrane voltage plot",
)
plt.show()
# p.reset()
p.end()
poisson_control.close()
live_connection.close()
print "finished run"
# Create an excitatory population with 80% of the neurons and
# an inhibitory population with 20% of the neurons.
pop_exc = sim.Population(n_exc, sim.IF_curr_exp(), label="Excitatory")
pop_inh = sim.Population(n_inh, sim.IF_curr_exp(), label="Inhibitory")
# Create excitatory poisson stimulation population with 80%
# of the neurons and
# an inhibitory poisson stimulation population with 20% of the neurons,
# both with a rate of 1000Hz
# TODO RATE?
if rng is None:
seed = None
else:
seed = int(rng.next() * 1000)
stim_exc = sim.Population(n_exc,
sim.SpikeSourcePoisson(rate=1000.0, seed=seed),
label="Stim_Exc")
if rng is None:
seed = None
else:
seed = int(rng.next() * 1000)
stim_inh = sim.Population(n_inh,
sim.SpikeSourcePoisson(rate=1000.0,
seed=int(rng.next() * 1000)),
label="Stim_Inh")
# Create a one-to-one excitatory connection
# from the excitatory poisson stimulation population
# to the excitatory population with a weight of 0.1nA and a delay of 1.0ms
# TODO values
import spynnaker8 as sim
import pyNN.utility.plotting as plot
import matplotlib.pyplot as plt
from pyNN.random import RandomDistribution
n_neurons = 1000
n_exc = int(round(n_neurons * 0.8))
n_inh = int(round(n_neurons * 0.2))
simtime = 1000
sim.setup(timestep=0.1)
pop_exc = sim.Population(n_exc, sim.IF_curr_exp(), label="Excitatory")
pop_inh = sim.Population(n_inh, sim.IF_curr_exp(), label="Inhibitory")
stim_exc = sim.Population(n_exc,
sim.SpikeSourcePoisson(rate=10.0),
label="Stim_Exc")
stim_inh = sim.Population(n_inh,
sim.SpikeSourcePoisson(rate=10.0),
label="Stim_Inh")
synapse_exc = sim.StaticSynapse(weight=0.2, delay=2.0)
synapse_inh = sim.StaticSynapse(weight=-1.0, delay=2.0)
sim.Projection(pop_exc,
pop_exc,
sim.FixedProbabilityConnector(0.1),
synapse_type=synapse_exc,
receptor_type="excitatory")
sim.Projection(pop_exc,
pop_inh,
sim.FixedProbabilityConnector(0.1),
# === Parameters ===============================================================
n_neurons = 3 # number of neurons in each population for the Spiking Neural Network in this example
timestamp = 1.0 # simulate the network with 1.0 ms time steps
sim_time = 100 # total simulation time
# === Configure the simulator ==================================================
sim.setup(timestamp)
# === Build the network ========================================================
# Presynaptic population - Input layer - Stimuli
pop_input = sim.Population(n_neurons,
sim.SpikeSourcePoisson(rate=100, duration=sim_time),
label='pop_input')
# Synapse value as weight = 5.0 nA, delay = 1 ms
static_synapse = sim.StaticSynapse(weight=5.0, delay=1)
# I - IF_cond_exp Population
pop_cond_exp = sim.Population(n_neurons,
sim.IF_cond_exp, {},
label='if_cond_exp')
sim.Projection(pop_input,
pop_cond_exp,
sim.OneToOneConnector(),
synapse_type=static_synapse)
# II - IF_curr_exp Population
pop_curr_exp = sim.Population(n_neurons,
def test_agent(arm1, arm2):
arm = [arm1, arm2]
print "arm = ", arm
connections = read_agent()
p.setup(timestep=1.0, min_delay=1, max_delay=127)
p.set_number_of_neurons_per_core(p.IF_cond_exp, 100)
bandit = p.Population(len(arm), Bandit(arm, exposure_time, reward_based=reward, label='bandit_pop'))
[in2e, in2i, e_size, e2e, e2i, i_size, i2e, i2i, e2out, i2out] = connections
if e_size > 0:
excite = p.Population(e_size, p.IF_cond_exp(), label='excite_pop')
excite_noise = p.Population(e_size, p.SpikeSourcePoisson(rate=noise_rate))
p.Projection(excite_noise, excite, p.OneToOneConnector(),
p.StaticSynapse(weight=noise_weight), receptor_type='excitatory')
excite.record('spikes')
if i_size > 0:
inhib = p.Population(i_size, p.IF_cond_exp(), label='inhib_pop')
inhib_noise = p.Population(i_size, p.SpikeSourcePoisson(rate=noise_rate))
p.Projection(inhib_noise, inhib, p.OneToOneConnector(),
p.StaticSynapse(weight=noise_weight), receptor_type='excitatory')
inhib.record('spikes')
if len(in2e) != 0:
p.Projection(bandit, excite, p.FromListConnector(in2e),
receptor_type='excitatory')
# p.Projection(starting_pistol, excite, p.FromListConnector(in2e),
# receptor_type='excitatory')
if len(in2i) != 0:
p.Projection(bandit, inhib, p.FromListConnector(in2i),
receptor_type='excitatory')
# p.Projection(starting_pistol, inhib, p.FromListConnector(in2i),
# receptor_type='excitatory')
if len(e2e) != 0:
p.Projection(excite, excite, p.FromListConnector(e2e),
receptor_type='excitatory')
if len(e2i) != 0:
p.Projection(excite, inhib, p.FromListConnector(e2i),
receptor_type='excitatory')
if len(i2e) != 0:
p.Projection(inhib, excite, p.FromListConnector(i2e),
receptor_type='inhibitory')
if len(i2i) != 0:
p.Projection(inhib, inhib, p.FromListConnector(i2i),
receptor_type='inhibitory')
if len(e2out) != 0:
p.Projection(excite, bandit, p.FromListConnector(e2out),
receptor_type='excitatory')
if len(i2out) != 0:
p.Projection(inhib, bandit, p.FromListConnector(i2out),
receptor_type='inhibitory')
simulator = get_simulator()
p.run(runtime)
scores = get_scores(game_pop=bandit, simulator=simulator)
print scores
print arm
e_spikes = excite.get_data('spikes').segments[0].spiketrains
i_spikes = inhib.get_data('spikes').segments[0].spiketrains
# v = receive_pop[i].get_data('v').segments[0].filter(name='v')[0]
plt.figure("[{}, {}] - {}".format(arm1, arm2, scores))
Figure(
Panel(e_spikes, xlabel="Time (ms)", ylabel="nID", xticks=True),
Panel(i_spikes, xlabel="Time (ms)", ylabel="nID", xticks=True)
)
plt.show()
p.end()