def __init__(self):
# initial call to set up the front end (pynn requirement)
Frontend.setup(timestep=1.0, min_delay=1.0, max_delay=144.0)
use_c_visualiser = True
use_spike_injector = True
# neurons per population and the length of runtime in ms for the
# simulation, as well as the expected weight each spike will contain
self.n_neurons = 100
# set up gui
p = None
if use_spike_injector:
from multiprocessing import Process
from multiprocessing import Event
ready = Event()
p = Process(target=GUI, args=[self.n_neurons, ready])
p.start()
ready.wait()
# different runtimes for demostration purposes
run_time = None
if not use_c_visualiser and not use_spike_injector:
run_time = 1000
elif use_c_visualiser and not use_spike_injector:
run_time = 10000
elif use_c_visualiser and use_spike_injector:
run_time = 100000
elif not use_c_visualiser and use_spike_injector:
run_time = 10000
weight_to_spike = 2.0
# neural parameters of the IF_curr model used to respond to injected
# spikes.
# (cell params for a synfire chain)
cell_params_lif = {'cm': 0.25,
'i_offset': 0.0,
'tau_m': 20.0,
'tau_refrac': 2.0,
'tau_syn_E': 5.0,
'tau_syn_I': 5.0,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -50.0
}
##################################
# Parameters for the injector population. This is the minimal set of
# parameters required, which is for a set of spikes where the key is
# not important. Note that a virtual key *will* be assigned to the
# population, and that spikes sent which do not match this virtual key
# will be dropped; however, if spikes are sent using 16-bit keys, they
# will automatically be made to match the virtual key. The virtual
# key assigned can be obtained from the database.
##################################
cell_params_spike_injector = {
# The port on which the spiNNaker machine should listen for
# packets. Packets to be injected should be sent to this port on
# the spiNNaker machine
'port': 12345
}
##################################
# Parameters for the injector population. Note that each injector
# needs to be given a different port. The virtual key is assigned
# here, rather than being allocated later. As with the above, spikes
# injected need to match this key, and this will be done automatically
# with 16-bit keys.
##################################
cell_params_spike_injector_with_key = {
# The port on which the spiNNaker machine should listen for
# packets. Packets to be injected should be sent to this port on
# the spiNNaker machine
'port': 12346,
# This is the base key to be used for the injection, which is used
# to allow the keys to be routed around the spiNNaker machine.
# This assignment means that 32-bit keys must have the high-order
# 16-bit set to 0x7; This will automatically be prepended to
# 16-bit keys.
'virtual_key': 0x70000
}
# create synfire populations (if cur exp)
pop_forward = Frontend.Population(
self.n_neurons, Frontend.IF_curr_exp(**cell_params_lif),
label='pop_forward')
pop_backward = Frontend.Population(
self.n_neurons, Frontend.IF_curr_exp(**cell_params_lif),
label='pop_backward')
# Create injection populations
injector_forward = None
injector_backward = None
if use_spike_injector:
injector_forward = Frontend.Population(
self.n_neurons,
Frontend.external_devices.SpikeInjector(
**cell_params_spike_injector_with_key),
label='spike_injector_forward')
injector_backward = Frontend.Population(
self.n_neurons,
Frontend.external_devices.SpikeInjector(
**cell_params_spike_injector),
label='spike_injector_backward')
else:
spike_times = []
for _ in range(0, self.n_neurons):
spike_times.append([])
spike_times[0] = [0]
spike_times[20] = [(run_time / 100) * 20]
spike_times[40] = [(run_time / 100) * 40]
spike_times[60] = [(run_time / 100) * 60]
spike_times[80] = [(run_time / 100) * 80]
cell_params_forward = {'spike_times': spike_times}
spike_times_backwards = []
for _ in range(0, self.n_neurons):
spike_times_backwards.append([])
spike_times_backwards[0] = [(run_time / 100) * 80]
spike_times_backwards[20] = [(run_time / 100) * 60]
spike_times_backwards[40] = [(run_time / 100) * 40]
spike_times_backwards[60] = [(run_time / 100) * 20]
spike_times_backwards[80] = [0]
cell_params_backward = {'spike_times': spike_times_backwards}
injector_forward = Frontend.Population(
self.n_neurons, Frontend.SpikeSourceArray(
**cell_params_forward),
label='spike_injector_forward')
injector_backward = Frontend.Population(
self.n_neurons, Frontend.SpikeSourceArray(
**cell_params_backward),
label='spike_injector_backward')
# Create a connection from the injector into the populations
Frontend.Projection(
injector_forward, pop_forward,
Frontend.OneToOneConnector(),
Frontend.StaticSynapse(weight=weight_to_spike))
Frontend.Projection(
injector_backward, pop_backward,
Frontend.OneToOneConnector(),
Frontend.StaticSynapse(weight=weight_to_spike))
# Synfire chain connections where each neuron is connected to its next
# neuron
# NOTE: there is no recurrent connection so that each chain stops once
# it reaches the end
loop_forward = list()
loop_backward = list()
for i in range(0, self.n_neurons - 1):
loop_forward.append((i, (i + 1) %
self.n_neurons, weight_to_spike, 3))
loop_backward.append(((i + 1) %
self.n_neurons, i, weight_to_spike, 3))
Frontend.Projection(pop_forward, pop_forward,
Frontend.FromListConnector(loop_forward))
Frontend.Projection(pop_backward, pop_backward,
Frontend.FromListConnector(loop_backward))
# record spikes from the synfire chains so that we can read off valid
# results in a safe way afterwards, and verify the behavior
pop_forward.record('spikes')
pop_backward.record('spikes')
# Activate the sending of live spikes
Frontend.external_devices.activate_live_output_for(
pop_forward, database_notify_host="localhost",
database_notify_port_num=19996)
Frontend.external_devices.activate_live_output_for(
pop_backward, database_notify_host="localhost",
database_notify_port_num=19996)
if not use_c_visualiser:
# if not using the c visualiser, then a new spynnaker live spikes
# connection is created to define that there are python code which
# receives the outputted spikes.
live_spikes_connection_receive = \
Frontend.external_devices.SpynnakerLiveSpikesConnection(
receive_labels=["pop_forward", "pop_backward"],
local_port=19999, send_labels=None)
# Set up callbacks to occur when spikes are received
live_spikes_connection_receive.add_receive_callback(
"pop_forward", receive_spikes)
live_spikes_connection_receive.add_receive_callback(
"pop_backward", receive_spikes)
# Run the simulation on spiNNaker
Frontend.run(run_time)
# Retrieve spikes from the synfire chain population
spikes_forward = pop_forward.get_data('spikes')
spikes_backward = pop_backward.get_data('spikes')
# Clear data structures on spiNNaker to leave the machine in a clean
# state for future executions
Frontend.end()
if use_spike_injector:
p.join()
Figure(
# raster plot of the presynaptic neuron spike times
Panel(spikes_forward.segments[0].spiketrains,
yticks=True, markersize=0.2, xlim=(0, run_time)),
Panel(spikes_backward.segments[0].spiketrains,
yticks=True, markersize=0.2, xlim=(0, run_time)),
title="Simple synfire chain example with injected spikes",
annotations="Simulated with {}".format(Frontend.name())
)
plt.show()
pop_1 = sim.Population(2, sim.IF_curr_exp(), label="pop_1")
# Consisting of two input source neurons ...with default parameters Have the
# first input neuron spike at time 0.0ms and the second spike at time 1.0ms.
input = sim.Population(2,
sim.SpikeSourceArray(spike_times=[[0], [1]]),
label="input")
input_proj = sim.Projection(input,
pop_1,
sim.OneToOneConnector(),
synapse_type=sim.StaticSynapse(weight=5, delay=2))
# Record and plot the spikes received against time.
pop_1.record(["spikes"])
sim.run(simtime)
neo = pop_1.get_data(variables=["spikes"])
spikes = neo.segments[0].spiketrains
print spikes
sim.end()
plot.Figure(
# plot spikes (or in this case spike)
plot.Panel(spikes,
yticks=True,
xticks=True,
markersize=5,
xlim=(0, simtime)),
title="Simple Example",
annotations="Simulated with {}".format(sim.name()))
plt.show()
def do_run(nNeurons):
p.setup(timestep=1.0, min_delay=1.0, max_delay=32.0)
p.set_number_of_neurons_per_core(p.IF_curr_exp, 100)
cm = list()
i_off = list()
tau_m = list()
tau_re = list()
tau_syn_e = list()
tau_syn_i = list()
v_reset = list()
v_rest = list()
v_thresh = list()
cell_params_lif = {
'cm': cm,
'i_offset': i_off,
'tau_m': tau_m,
'tau_refrac': tau_re,
'tau_syn_E': tau_syn_e,
'tau_syn_I': tau_syn_i,
'v_reset': v_reset,
'v_rest': v_rest,
'v_thresh': v_thresh
}
for atom in range(0, nNeurons):
cm.append(0.25)
i_off.append(0.0)
tau_m.append(10.0)
tau_re.append(2.0)
tau_syn_e.append(0.5)
tau_syn_i.append(0.5)
v_reset.append(-65.0)
v_rest.append(-65.0)
v_thresh.append(-64.4)
gbar_na_distr = RandomDistribution('normal', (20.0, 2.0),
rng=NumpyRNG(seed=85524))
cell_params_lif = {
'cm': cm,
'i_offset': i_off,
'tau_m': tau_m,
'tau_refrac': tau_re,
'tau_syn_E': tau_syn_e,
'tau_syn_I': tau_syn_i,
'v_reset': v_reset,
'v_rest': v_rest,
'v_thresh': v_thresh
}
populations = list()
projections = list()
weight_to_spike = 2
delay = 1
connections = list()
for i in range(0, nNeurons):
singleConnection = (i, ((i + 1) % nNeurons), weight_to_spike, delay)
connections.append(singleConnection)
injectionConnection = [(0, 0, weight_to_spike, delay)]
spikeArray = {'spike_times': [[0]]}
populations.append(
p.Population(nNeurons, p.IF_curr_exp, cell_params_lif, label='pop_1'))
populations.append(
p.Population(1, p.SpikeSourceArray, spikeArray, label='inputSpikes_1'))
populations[0].set(cm=0.25)
populations[0].set(cm=cm)
populations[0].set(tau_m=tau_m, v_thresh=v_thresh)
populations[0].set(i_offset=gbar_na_distr)
populations[0].set(i_offset=i_off)
projections.append(
p.Projection(populations[0], populations[0],
p.FromListConnector(connections)))
projections.append(
p.Projection(populations[1], populations[0],
p.FromListConnector(injectionConnection)))
populations[0].record("v")
populations[0].record("gsyn_exc")
populations[0].record("spikes")
p.run(100)
neo = populations[0].get_data(["v", "spikes", "gsyn_exc"])
v = neo_convertor.convert_data(neo, name="v")
gsyn = neo_convertor.convert_data(neo, name="gsyn_exc")
spikes = neo_convertor.convert_spikes(neo)
p.end()
return (v, gsyn, spikes)
def split_potentiation_and_depression():
p.setup(1.0)
runtime = 100
initial_run = 1000 # to negate any initial conditions
# STDP parameters
a_plus = 0.01
a_minus = 0.01
tau_plus = 20
tau_minus = 20
plastic_delay = 3
initial_weight = 2.5
max_weight = 5
min_weight = 0
pre_spikes = [10, 50]
extra_spikes = [30]
for i in range(len(pre_spikes)):
pre_spikes[i] += initial_run
for i in range(len(extra_spikes)):
extra_spikes[i] += initial_run
# Spike source to send spike via plastic synapse
pre_pop = p.Population(1, p.SpikeSourceArray,
{'spike_times': pre_spikes}, label="pre")
# Spike source to send spike via static synapse to make
# post-plastic-synapse neuron fire
extra_pop = p.Population(1, p.SpikeSourceArray,
{'spike_times': extra_spikes}, label="extra")
# Post-plastic-synapse population
post_pop = p.Population(
1, p.IF_curr_exp(), label="post", additional_parameters={
"splitter": SplitterAbstractPopulationVertexNeuronsSynapses(1)})
# Create projections
p.Projection(
pre_pop, post_pop, p.OneToOneConnector(),
p.StaticSynapse(weight=5.0, delay=1), receptor_type="excitatory")
p.Projection(
extra_pop, post_pop, p.OneToOneConnector(),
p.StaticSynapse(weight=5.0, delay=1), receptor_type="excitatory")
syn_plas = p.STDPMechanism(
timing_dependence=p.SpikePairRule(tau_plus=tau_plus,
tau_minus=tau_minus,
A_plus=a_plus, A_minus=a_minus),
weight_dependence=p.AdditiveWeightDependence(w_min=min_weight,
w_max=max_weight),
weight=initial_weight, delay=plastic_delay)
plastic_synapse = p.Projection(pre_pop, post_pop,
p.OneToOneConnector(),
synapse_type=syn_plas,
receptor_type='excitatory')
# Record the spikes
post_pop.record("spikes")
# Run
p.run(initial_run + runtime)
# Get the weights
weights = plastic_synapse.get('weight', 'list',
with_address=False)
# Get the spikes
post_spikes = numpy.array(
# pylint: disable=no-member
post_pop.get_data('spikes').segments[0].spiketrains[0].magnitude)
# End the simulation as all information gathered
p.end()
new_weight_exact = calculate_spike_pair_additive_stdp_weight(
pre_spikes, post_spikes, initial_weight, plastic_delay, max_weight,
a_plus, a_minus, tau_plus, tau_minus)
print("Pre neuron spikes at: {}".format(pre_spikes))
print("Post-neuron spikes at: {}".format(post_spikes))
target_spikes = [1014, 1032, 1053]
assert(all(s1 == s2
for s1, s2 in zip(list(post_spikes), target_spikes)))
print("New weight exact: {}".format(new_weight_exact))
print("New weight SpiNNaker: {}".format(weights))
assert(numpy.allclose(weights, new_weight_exact, rtol=0.001))
def test_only_end(self):
setup_for_unittest()
sim.end()
def potentiation_and_depression(self):
p.setup(1)
runtime = 100
initial_run = 1000 # to negate any initial conditions
# STDP parameters
a_plus = 0.01
a_minus = 0.01
tau_plus = 20
tau_minus = 20
plastic_delay = 3
initial_weight = 2.5
max_weight = 5
min_weight = 0
pre_spikes = [10, 50]
extra_spikes = [30]
for i in range(len(pre_spikes)):
pre_spikes[i] += initial_run
for i in range(len(extra_spikes)):
extra_spikes[i] += initial_run
# Spike source to send spike via plastic synapse
pre_pop = p.Population(1,
p.SpikeSourceArray, {'spike_times': pre_spikes},
label="pre")
# Spike source to send spike via static synapse to make
# post-plastic-synapse neuron fire
extra_pop = p.Population(1,
p.SpikeSourceArray,
{'spike_times': extra_spikes},
label="extra")
# Post-plastic-synapse population
post_pop = p.Population(1, p.IF_curr_exp(), label="post")
# Create projections
p.Projection(pre_pop,
post_pop,
p.OneToOneConnector(),
p.StaticSynapse(weight=5.0, delay=1),
receptor_type="excitatory")
p.Projection(extra_pop,
post_pop,
p.OneToOneConnector(),
p.StaticSynapse(weight=5.0, delay=1),
receptor_type="excitatory")
syn_plas = p.STDPMechanism(
timing_dependence=p.extra_models.SpikeNearestPairRule(
tau_plus=tau_plus,
tau_minus=tau_minus,
A_plus=a_plus,
A_minus=a_minus),
weight_dependence=p.AdditiveWeightDependence(w_min=min_weight,
w_max=max_weight),
weight=initial_weight,
delay=plastic_delay)
plastic_synapse = p.Projection(pre_pop,
post_pop,
p.OneToOneConnector(),
synapse_type=syn_plas,
receptor_type='excitatory')
# Record the spikes
post_pop.record("spikes")
# Run
p.run(initial_run + runtime)
# Get the weights
weights = plastic_synapse.get('weight', 'list', with_address=False)
# Get the spikes
post_spikes = numpy.array(
post_pop.get_data('spikes').segments[0].spiketrains[0].magnitude)
# End the simulation as all information gathered
p.end()
# Get the spikes and time differences that will be considered by
# the simulation (as the last pre-spike will be considered differently)
pre_spikes = numpy.array(pre_spikes)
last_pre_spike = pre_spikes[-1]
considered_post_spikes = post_spikes[post_spikes < last_pre_spike]
considered_post_spikes += plastic_delay
potentiation_times = list()
depression_times = list()
for time in pre_spikes:
post_times = considered_post_spikes[considered_post_spikes > time]
if len(post_times) > 0:
last_time = post_times[0]
potentiation_times.append(time - last_time)
post_times = considered_post_spikes[considered_post_spikes < time]
if len(post_times) > 0:
last_time = post_times[-1]
depression_times.append(last_time - time)
potentiation_times = numpy.array(potentiation_times)
depression_times = numpy.array(depression_times)
# Work out the weight according to the rules
potentiations = max_weight * a_plus * numpy.exp(
(potentiation_times / tau_plus))
depressions = max_weight * a_minus * numpy.exp(
(depression_times / tau_minus))
new_weight_exact = \
initial_weight + numpy.sum(potentiations) - numpy.sum(depressions)
# print("Pre neuron spikes at: {}".format(pre_spikes))
# print("Post-neuron spikes at: {}".format(post_spikes))
target_spikes = [1014, 1032, 1053]
self.assertListEqual(list(post_spikes), target_spikes)
# print("Potentiation time differences: {}".format(potentiation_times))
# print("Depression time differences: {}".format(depression_times))
# print("Potentiation: {}".format(potentiations))
# print("Depressions: {}".format(depressions))
# print("New weight exact: {}".format(new_weight_exact))
# print("New weight SpiNNaker: {}".format(weights))
self.assertTrue(
numpy.allclose(weights[0], new_weight_exact, atol=0.001))
def do_run():
p.setup(1.0)
n_neurons = 2
pop_a = p.Population(n_neurons,
p.extra_models.SpikeSourcePoissonVariable(
rates=[10, 20, 50], starts=[0, 500, 1000]),
label="pop_a")
pop_a.record("spikes")
pop_b = p.Population(n_neurons,
p.extra_models.SpikeSourcePoissonVariable(
rates=[[1, 2, 5], [10, 20, 50]],
starts=[0, 500, 1000]),
label="pop_b")
pop_b.record("spikes")
pop_c = p.Population(n_neurons,
p.extra_models.SpikeSourcePoissonVariable(
rates=[10, 20, 50],
starts=[10, 600, 1200],
durations=[500, 500, 500]),
label="pop_c")
pop_c.record("spikes")
pop_d = p.Population(n_neurons,
p.extra_models.SpikeSourcePoissonVariable(
rates=[[1, 2, 5], [10, 20, 50]],
starts=[0, 500, 1000],
durations=[500, 400, 300]),
label="pop_d")
pop_d.record("spikes")
pop_e = p.Population(n_neurons,
p.extra_models.SpikeSourcePoissonVariable(
rates=[[1, 2, 5], [10, 20, 50]],
starts=[[0, 500, 1000], [100, 600, 1100]],
durations=[400, 300, 200]),
label="pop_e")
pop_e.record("spikes")
pop_f = p.Population(n_neurons,
p.extra_models.SpikeSourcePoissonVariable(
rates=[[1, 2, 5], [10, 20, 50]],
starts=[[0, 500, 1000], [100, 600, 1100]],
durations=[[400, 300, 200], [300, 200, 100]]),
label="pop_f")
pop_f.record("spikes")
pop_g = p.Population(n_neurons,
p.extra_models.SpikeSourcePoissonVariable(
rates=[[1, 2, 5], [10, 50]],
starts=[[0, 100, 200], [200, 300]]),
label="pop_g")
pop_g.record("spikes")
pop_h = p.Population(n_neurons,
p.SpikeSourcePoisson(rate=1),
label="pop_h")
pop_h.record("spikes")
pop_i = p.Population(n_neurons,
p.SpikeSourcePoisson(rate=1, start=100),
label="pop_i")
pop_i.record("spikes")
pop_j = p.Population(n_neurons,
p.SpikeSourcePoisson(rate=[1, 10]),
label="pop_j")
pop_j.record("spikes")
pop_k = p.Population(n_neurons,
p.SpikeSourcePoisson(rate=1, start=[0, 500]),
label="pop_k")
pop_k.record("spikes")
pop_l = p.Population(n_neurons,
p.SpikeSourcePoisson(rate=1, start=10, duration=500),
label="pop_l")
pop_l.record("spikes")
pop_m = p.Population(n_neurons,
p.SpikeSourcePoisson(rate=[1, 10],
start=[0, 500],
duration=500),
label="pop_m")
pop_m.record("spikes")
pop_n = p.Population(n_neurons,
p.SpikeSourcePoisson(rate=[1, 10],
start=[0, 500],
duration=[500, 800]),
label="pop_n")
pop_n.record("spikes")
pop_o = p.Population(n_neurons,
p.SpikeSourcePoisson(rate=1, duration=500),
label="pop_o")
pop_o.record("spikes")
p.run(2000)
p.end()
def record_weights_using_callback():
######################################
# Setup
######################################
sim.setup(timestep=simulationParameters["timeStep"])
######################################
# Neuron pop
######################################
# Input neurons
ILayer = sim.Population(popNeurons["ILayer"],
sim.SpikeSourceArray(spike_times=ILSpike),
label="ILayer")
# LIF neurons
LIFLayer = sim.Population(popNeurons["LIFLayer"],
sim.IF_curr_exp(**neuronParameters["LIFL"]),
label="LIFLayer")
LIFLayer.set(v=initNeuronParameters["LIFL"]["vInit"])
######################################
# Synapses
######################################
# ILayer-LIFLayer -> statics
sim.Projection(ILayer,
LIFLayer,
sim.OneToOneConnector(),
synapse_type=sim.StaticSynapse(
weight=synParameters["IL-LIFL"]["initWeight"],
delay=synParameters["IL-LIFL"]["delay"]))
# LIFLayer-ILayer -> STDP
timing_rule = sim.SpikePairRule(
tau_plus=synParameters["LIFL-LIFL"]["tau_plus"],
tau_minus=synParameters["LIFL-LIFL"]["tau_minus"],
A_plus=synParameters["LIFL-LIFL"]["A_plus"],
A_minus=synParameters["LIFL-LIFL"]["A_minus"])
weight_rule = sim.AdditiveWeightDependence(
w_max=synParameters["LIFL-LIFL"]["w_max"],
w_min=synParameters["LIFL-LIFL"]["w_min"])
stdp_model = sim.STDPMechanism(
timing_dependence=timing_rule,
weight_dependence=weight_rule,
weight=synParameters["LIFL-LIFL"]["initWeight"],
delay=synParameters["LIFL-LIFL"]["delay"])
LIFLayer_LIFLayer_conn = sim.Projection(
LIFLayer,
LIFLayer,
sim.AllToAllConnector(allow_self_connections=False),
synapse_type=stdp_model)
######################################
# Record parameters
######################################
LIFLayer.record(["spikes", "v"])
weightRecorderLIF_LIF = weight_recorder(
sampling_interval=simulationParameters["timeStep"],
projection=LIFLayer_LIFLayer_conn)
######################################
# Run simulation
######################################
sim.run(simulationParameters["simTime"], callbacks=[weightRecorderLIF_LIF])
######################################
# Recall data
######################################
populationData = LIFLayer.get_data(variables=["spikes", "v"])
LIFLSpikes = populationData.segments[0].spiketrains
vLIFL = populationData.segments[0].filter(name='v')[0]
w_LIFL_LIFL = weightRecorderLIF_LIF.get_weights()
######################################
# End simulation
######################################
sim.end()
######################################
# Return parameters
######################################
return ILSpike, LIFLSpikes, vLIFL, w_LIFL_LIFL
I_pop,
Ext_conn,
receptor_type="excitatory",
synapse_type=pynn.StaticSynapse(weight=J_E * 10,
delay=delay_distr))
# Record stuff
E_pop.record("spikes")
pynn.run(sim_time)
esp = None
isp = None
pe = None
pi = None
v_esp = None
esp = E_pop.get_data("spikes")
Figure(
# raster plot of the presynaptic neuron spike times
Panel(esp.segments[0].spiketrains,
yticks=True,
markersize=1,
xlim=(0, sim_time)),
title="Simple synfire chain example",
annotations="Simulated with {}".format(pynn.name()))
plt.show()
pynn.end()
def do_run(nNeurons, n_pops, neurons_per_core, runtime=25000):
"""
Runs the script Does the run based on the parameters
:param nNeurons: Number of Neurons in chain
:type nNeurons: int
:param n_pops: Number of populations
:type n_pops: int
:param neurons_per_core: Number of neurons per core
:type neurons_per_core: int
:param runtime: time to run the script for
:type runtime: int
"""
p.setup(timestep=1.0, min_delay=1.0, max_delay=144.0)
p.set_number_of_neurons_per_core(p.IF_curr_exp, neurons_per_core)
cell_params_lif = {
'cm': 0.25,
'i_offset': 0.0,
'tau_m': 20.0,
'tau_refrac': 2.0,
'tau_syn_E': 5.0,
'tau_syn_I': 5.0,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -50.0
}
populations = list()
projections = list()
weight_to_spike = 2.0
delay = 1
connections = list()
for i in range(0, nNeurons - 1):
singleConnection = (i, i + 1, weight_to_spike, delay)
connections.append(singleConnection)
pop_jump_connection = [(nNeurons - 1, 0, weight_to_spike, 1)]
injectionConnection = [(0, 0, weight_to_spike, 1)]
spikeArray = {'spike_times': [[0]]}
for i in range(0, n_pops):
populations.append(
p.Population(nNeurons,
p.IF_curr_exp(**cell_params_lif),
label='pop_{}'.format(i)))
populations.append(
p.Population(1,
p.SpikeSourceArray(**spikeArray),
label='inputSpikes_1'))
for i in range(0, n_pops):
projections.append(
p.Projection(presynaptic_population=populations[i],
postsynaptic_population=populations[i],
connector=p.FromListConnector(connections),
synapse_type=p.StaticSynapse()))
connector = p.FromListConnector(pop_jump_connection)
projections.append(
p.Projection(presynaptic_population=populations[i],
postsynaptic_population=populations[((i + 1) %
n_pops)],
connector=connector,
synapse_type=p.StaticSynapse()))
projections.append(
p.Projection(presynaptic_population=populations[n_pops],
postsynaptic_population=populations[0],
connector=p.FromListConnector(injectionConnection),
synapse_type=p.StaticSynapse()))
for pop_index in range(0, n_pops):
populations[pop_index].record("spikes")
p.run(runtime)
total_spikes = populations[0].spinnaker_get_data("spikes")
for pop_index in range(1, n_pops):
spikes = populations[pop_index].spinnaker_get_data("spikes")
if spikes is not None:
for spike in spikes:
spike[0] += (nNeurons * pop_index)
total_spikes = numpy.concatenate((total_spikes, spikes), axis=0)
p.end()
return total_spikes
def simulation_teardown(self):
"""Tear down the SpiNNaker simulation framework
:return: None
"""
p.end()
def do_run(plot):
p.setup(timestep=1.0, min_delay=1.0, max_delay=144.0)
p.set_number_of_neurons_per_core(p.IF_cond_exp, 100)
# Experiment Parameters
n_groups = 6 # Number of Synfire Groups
n_exc = 100 # Number of excitatory neurons per group
n_inh = 25 # Number of inhibitory neurons per group
sim_duration = 500.
# defining the initial pulse-packet
pp_a = 5 # Nr of pulses in the packet
pp_sigma = 5.0 # sigma of pulse-packet
pp_start = 50. # start = center of pulse-packet
# Neuron Parameters as in Kremkow et al. paper
cell_params = {
'cm': 0.290, # nF
'tau_m': 290.0 / 29.0, # pF / nS = ms
'v_rest': -70.0, # mV
'v_thresh': -57.0, # mV
'tau_syn_E': 1.5, # ms
'tau_syn_I': 10.0, # ms
'tau_refrac': 2.0, # ms
'v_reset': -70.0, # mV
'e_rev_E': 0.0, # mV
'e_rev_I': -75.0, # mV
}
weight_exc = 0.05 # uS weight for excitatory to excitatory connections
weight_inh = 0.002 # uS weight for inhibitory to excitatory connections
# list of excitatory populations
exc_pops = []
# list of inhibitory populations
inh_pops = []
# and Assembly of all populations
all_populations = []
# Create Groups
print("Creating ", n_groups, " SynfireGroups")
for group_index in range(n_groups):
# create the excitatory Population
exc_pop = p.Population(n_exc,
p.IF_cond_exp(**cell_params),
label=("pop_exc_%s" % group_index))
exc_pops.append(exc_pop) # append to excitatory populations
all_populations += [exc_pop] # and to the Assembly
# create the inhibitory Population
inh_pop = p.Population(n_inh,
p.IF_cond_exp(**cell_params),
label=("pop_inh_%s" % group_index))
inh_pops.append(inh_pop)
all_populations += [inh_pop]
# connect Inhibitory to excitatory Population
p.Projection(inh_pop,
exc_pop,
p.AllToAllConnector(),
synapse_type=p.StaticSynapse(weight=weight_inh, delay=8.),
receptor_type='inhibitory')
# Create Stimulus and connect it to first group
print("Create Stimulus Population")
# We create a Population of SpikeSourceArrays of the same dimension
# as excitatory neurons in a synfire group
pop_stim = p.Population(n_exc, p.SpikeSourceArray({}), label="pop_stim")
# We create a normal distribution around pp_start with sigma = pp_sigma
rd = pyNN.random.RandomDistribution('normal', [pp_start, pp_sigma])
all_spiketimes = []
# for each cell in the population, we take pp_a values from the
# random distribution
for cell in range(len(pop_stim)):
spiketimes = []
for pulse in range(pp_a):
spiketimes.append(rd.next()) # draw from the random distribution
spiketimes.sort()
all_spiketimes.append(spiketimes)
# convert into a numpy array
all_spiketimes = numpy.array(all_spiketimes)
# 'topographic' setting of parameters.
# all_spiketimes must have the same dimension as the Population
pop_stim.set(spike_times=all_spiketimes)
# Connect Groups with the subsequent ones
print("Connecting Groups with subsequent ones")
for group_index in range(n_groups - 1):
p.Projection(exc_pops[group_index % n_groups],
exc_pops[(group_index + 1) % n_groups],
p.FixedTotalNumberConnector(160),
synapse_type=p.StaticSynapse(weight=weight_exc,
delay=10.),
receptor_type='excitatory')
p.Projection(exc_pops[group_index % n_groups],
inh_pops[(group_index + 1) % n_groups],
p.FixedTotalNumberConnector(160),
synapse_type=p.StaticSynapse(weight=weight_exc,
delay=10.),
receptor_type='excitatory')
# Make another projection for testing that connects to itself
p.Projection(exc_pops[1],
exc_pops[1],
p.FixedTotalNumberConnector(50,
with_replacement=False,
allow_self_connections=False),
synapse_type=p.StaticSynapse(weight=weight_exc, delay=10.),
receptor_type='excitatory')
# Connect the Stimulus to the first group
print("Connecting Stimulus to first group")
p.Projection(pop_stim,
inh_pops[0],
p.FixedTotalNumberConnector(60),
synapse_type=p.StaticSynapse(weight=weight_exc, delay=20.),
receptor_type='excitatory')
p.Projection(pop_stim,
exc_pops[0],
p.FixedTotalNumberConnector(60),
synapse_type=p.StaticSynapse(weight=weight_exc, delay=20.),
receptor_type='excitatory')
# Recording spikes
pop_stim.record('spikes')
for pop in all_populations:
pop.record('spikes')
# Run
print("Run the simulation")
p.run(sim_duration)
# Get data
print("Simulation finished, now collect all spikes and plot them")
stim_spikes = pop_stim.spinnaker_get_data('spikes')
stim_spikes[:, 0] -= n_exc
# collect all spikes and make a raster_plot
spklist_exc = []
spklist_inh = []
for group in range(n_groups):
EXC_spikes = exc_pops[group].spinnaker_get_data('spikes')
INH_spikes = inh_pops[group].spinnaker_get_data('spikes')
EXC_spikes[:, 0] += group * (n_exc + n_inh)
INH_spikes[:, 0] += group * (n_exc + n_inh) + n_exc
spklist_exc += EXC_spikes.tolist()
spklist_inh += INH_spikes.tolist()
# Plot
if plot:
pylab.figure()
pylab.plot([i[1] for i in spklist_exc], [i[0] for i in spklist_exc],
"r.")
pylab.plot([i[1] for i in spklist_inh], [i[0] for i in spklist_inh],
"b.")
pylab.plot([i[1] for i in stim_spikes], [i[0] for i in stim_spikes],
"k.")
pylab.xlabel('Time/ms')
pylab.ylabel('spikes')
pylab.title('spikes')
for group in range(n_groups):
pylab.axhline(y=(group + 1) * (n_exc + n_inh), color="lightgrey")
pylab.axhline(y=(group + 1) * (n_exc + n_inh) - n_inh,
color="lightgrey")
pylab.axhline(y=0, color="grey", linewidth=1.5)
pylab.show()
p.end()
return stim_spikes, spklist_exc, spklist_inh
def test_is_local(self):
sim.setup(timestep=1.0)
pop_1 = sim.Population(N_NEURONS, sim.IF_curr_exp(), label=LABEL)
cells = pop_1.all_cells
assert pop_1.is_local(2) == cells[2].local
sim.end()
def do_run(self,
n_neurons,
time_step=1,
max_delay=144.0,
input_class=SpikeSourceArray,
spike_times=None,
rate=None,
start_time=None,
duration=None,
seed=None,
spike_times_list=None,
placement_constraint=None,
weight_to_spike=2.0,
delay=17,
neurons_per_core=10,
cell_class=IF_curr_exp,
constraint=None,
cell_params=CELL_PARAMS_LIF,
run_times=None,
reset=False,
extract_between_runs=True,
set_between_runs=None,
new_pop=False,
record_input_spikes=False,
record_input_spikes_7=False,
record=True,
get_spikes=None,
spike_path=None,
record_7=False,
record_v=True,
get_v=None,
v_path=None,
record_v_7=False,
v_sampling_rate=None,
record_gsyn_exc=True,
record_gsyn_inh=True,
get_gsyn_exc=None,
get_gsyn_inh=None,
gsyn_path_exc=None,
gsyn_path_inh=None,
record_gsyn_exc_7=False,
record_gsyn_inh_7=False,
gsyn_exc_sampling_rate=None,
gsyn_inh_sampling_rate=None,
get_all=False,
use_spike_connections=True,
use_wrap_around_connections=True,
get_weights=False,
get_delays=False,
end_before_print=False,
randomise_v_init=False):
"""
:param n_neurons: Number of Neurons in chain
:type n_neurons: int
:param time_step: time step value to be used in p.setup
:type time_step: float
:param max_delay: max_delay value to be used in p.setup
:type max_delay: float
:param rate: the rate of the SSP to fire at
:type rate: float
:param start_time: the start time for the SSP
:type start_time: float
:param duration: the length of time for the SSP to fire for
:type duration: float
:param seed: Random seed
:type seed: int
:param input_class: the class for inputs spikes (SSA or SSP)
:type input_class: SpikeSourceArray, SpikeSourcePoisson
:param spike_times: times the SSA sends in spikes
:type spike_times: matrix of int times the SSA sends in spikes
:param spike_times_list: list of times the SSA sends in spikes
- must be the same length as run times
- If set the spike_time parameter is ignored
:type spike_times: list of matrix of int times the SSA sends in spikes
:param weight_to_spike: weight for the OneToOne Connector.\
Not used by any test at the moment
:type weight_to_spike: float
:param delay: time delay in the single connectors in the spike chain
:type delay: float
:param neurons_per_core: Number of neurons per core.\
If set to None, no set_number_of_neurons_per_core call will be made
:type neurons_per_core: int or None
:param constraint: A Constraint to be place on populations[0]
:type constraint: AbstractConstraint
:param cell_class: class to be used for the main population.\
Not used by any test at the moment
:type cell_class: AbstractPopulationVertex
:param cell_params: values for the main population.\
Not used by any test at the moment.\
Note: the values must match what is expected by the cellclass
:type cell_params: dict
:param run_times: times for each run.\
A zero will skip run but trigger reset and get date ext as set
:type run_times: list of int
:param reset: if True will call reset after each run except the last
:type reset: bool
:param extract_between_runs: \
If True reads V, gysn and spikes between each run.
:type extract_between_runs: bool
:param set_between_runs: set instructions to be carried out between\
runs. Should be a list of tuples.
First element of each tuple is 0 or 1:
* 0 for main population
* 1 for input population
Second element a String for name of property to change.
Third element the new value
:type set_between_runs: List[(int, String, any)]
:param new_pop: If True will add a new population before the second run
:type new_pop: bool
:param record_input_spikes: check for recording input spikes
:type record_input_spikes: bool
:param record_input_spikes_7: \
Check for recording input spikes in PyNN7 format
:type record_input_spikes_7: bool
:param record: If True will asks for spikes to be recorded
:type record: bool
:param get_spikes: If set overrides the normal behaviour\
of getting spikes if and only if record is True.\
If left None the value of record is used.
:type get_spikes: bool
:param spike_path: The path to print(write) the last spike data too
:type spike_path: str or None
:param record_7: \
If True will asks for spikes to be recorded in PyNN7 format
:type record_7: bool
:param record_v: If True will ask for voltage to be recorded
:type record_v: bool
:param get_v: If set overrides the normal behaviour\
of getting v if and only if record_v is True.\
If left None the value of record_v is used.
:type get_v: bool
:param v_path: The path to print(write) the last v data too
:type v_path: str or None
:param get_v_7: If True ???????
:type get_v_7: bool
:param record_v_7: If True will ask for voltage to be recorded\
in PyNN7 format
:type record_v_7: bool
:param v_sampling_rate: Rate at which to sample v.
:type v_sampling_rate: int, float ot None
:param record_gsyn_exc: If True will aks for gsyn exc to be recorded
:param record_gsyn_exc: If True will ask for gsyn exc to be recorded
:type record_gsyn_exc: bool
:param record_gsyn_inh: If True will ask for gsyn inh to be recorded
:type record_gsyn_inh: bool
:param gsyn_path_exc: \
The path to print(write) the last gsyn exc data to.
:type gsyn_path_exc: str or None
:param get_gsyn_exc: If set overrides the normal behaviour\
of getting gsyn exc if and only if record_gsyn_exc is True.\
If left None the value of record_gsyn_exc is used.
:type get_gsyn_exc: bool
:param get_gsyn_inh: If set overrides the normal behaviour\
of getting gsyn inh if and only if record_gsyn_inh is True.\
If left None the value of record_gsyn_ihn is used.
:type get_gsyn_inh: bool
:param gsyn_path_inh: \
The path to print(write) the last gsyn in the data to.
:type gsyn_path_inh: str or None
:param record_gsyn_exc_7: \
If True will ask for gsyn exc to be recorded in PyNN 7 format
:type record_gsyn_exc_7: bool
:param record_gsyn_inh_7: \
If True will ask for gsyn inh to be recorded in PyNN 7 format
:type record_gsyn_inh_7: bool
:param get_all: if True will obtain another neo object with all the
data set to be recorded by any other parameter
:type get_all: bool
:param get_weights: If True set will add a weight value to the return
:type get_weights: bool
:param get_delays: If True delays will be gotten
:type get_delays: bool
:param end_before_print: If True will call end() before running the\
optional print commands.
Note: end will always be called twice even if no print path\
provided
WARNING: This is expected to cause an Exception \
if spike_path, v_path or gsyn_path provided
:type end_before_print: bool
:param randomise_v_init: randomises the v_init of the output pop.
:type randomise_v_init: bool
:param use_loop_connections: \
True will put looping connections in. False won't.
:type use_loop_connections: bool
:return (v, gsyn, spikes, weights .....)
v: Voltage after last or each run (if requested else None)
gysn: gysn after last or each run (if requested else None)
spikes: spikes after last or each run (if requested else None)
weights: weights after last or each run (if requested else skipped)
All three/four values will repeated once per run is requested
"""
self.__init_object_state()
# Initialise/verify various values
cell_params, run_times, set_between_runs, spike_times, get_spikes, \
get_v, get_gsyn_exc, get_gsyn_inh = self.__verify_parameters(
cell_params, run_times, set_between_runs, spike_times,
get_spikes, record, record_7, spike_path, get_v, record_v,
record_v_7, v_path, get_gsyn_exc, record_gsyn_exc,
record_gsyn_exc_7, gsyn_path_exc, get_gsyn_inh,
record_gsyn_inh, record_gsyn_inh_7, gsyn_path_inh)
p.setup(timestep=time_step, min_delay=1.0, max_delay=max_delay)
if neurons_per_core is not None:
p.set_number_of_neurons_per_core(p.IF_curr_exp, neurons_per_core)
populations, projections, run_count = self.__create_synfire_chain(
n_neurons, cell_class, cell_params, use_wrap_around_connections,
weight_to_spike, delay, spike_times, spike_times_list,
placement_constraint, randomise_v_init, seed, constraint,
input_class, rate, start_time, duration, use_spike_connections)
# handle recording
if record or record_7 or spike_path:
populations[0].record("spikes")
if record_v or record_v_7 or v_path:
populations[0].record(variables="v",
sampling_interval=v_sampling_rate)
if record_gsyn_exc or record_gsyn_exc_7 or gsyn_path_exc:
populations[0].record(variables="gsyn_exc",
sampling_interval=gsyn_exc_sampling_rate)
if record_gsyn_inh or record_gsyn_inh_7 or gsyn_path_inh:
populations[0].record(variables="gsyn_inh",
sampling_interval=gsyn_inh_sampling_rate)
if record_input_spikes or record_input_spikes_7:
populations[1].record("spikes")
results = self.__run_sim(
run_times, populations, projections, run_count, spike_times_list,
extract_between_runs, get_spikes, record_7, get_v, record_v_7,
get_gsyn_exc, record_gsyn_exc_7, get_gsyn_inh, record_gsyn_inh_7,
record_input_spikes, record_input_spikes_7, get_all, get_weights,
get_delays, new_pop, n_neurons, cell_class, cell_params,
weight_to_spike, set_between_runs, reset)
self._get_data(populations[0], populations[1], get_spikes, record_7,
get_v, record_v_7, get_gsyn_exc, record_gsyn_exc_7,
get_gsyn_inh, record_gsyn_inh_7, record_input_spikes,
record_input_spikes_7, get_all)
self._get_weight_delay(projections[0], get_weights, get_delays)
if end_before_print:
if v_path is not None or spike_path is not None or \
gsyn_path_exc is not None or gsyn_path_inh is not None:
print("NOTICE! end is being called before print.. commands "
"which could cause an exception")
p.end()
if v_path is not None:
populations[0].write_data(v_path, "v")
if spike_path is not None:
populations[0].write_data(spike_path, "spikes")
if gsyn_path_exc is not None:
populations[0].write_data(gsyn_path_exc, "gsyn_exc")
if gsyn_path_inh is not None:
populations[0].write_data(gsyn_path_inh, "gsyn_inh")
if not end_before_print:
p.end()
return results
def do_run(plot):
p.setup(timestep=1.0)
cell_params_lif = {
'cm': 0.25,
'i_offset': 0.0,
'tau_m': 20.0,
'tau_refrac': 2.0,
'tau_syn_E': 5.0,
'tau_syn_I': 5.0,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -50.0
}
# Parameters
nNeurons = 200
weight_to_spike = 2.0
delay = 17
runtime = 5000
p.set_number_of_neurons_per_core(p.IF_curr_exp, nNeurons / 2)
# Populations
pop = p.Population(nNeurons,
p.IF_curr_exp(**cell_params_lif),
label='pop_1')
pop2 = p.Population(nNeurons,
p.IF_curr_exp(**cell_params_lif),
label='pop_2')
# create loopConnections array for first population using numpy linspaces
loopConnections = numpy.zeros((nNeurons, nNeurons))
for i in range(nNeurons):
if i != (nNeurons - 1):
loopConnections[i, i + 1] = True
else:
loopConnections[i, 0] = True
# do the same for the second population, but just for even numbered neurons
loopConnections2 = numpy.zeros((nNeurons, nNeurons))
for i in range(0, nNeurons, 2):
if i != (nNeurons - 2):
loopConnections2[i, i + 2] = True
else:
loopConnections2[i, 0] = True
# SpikeInjector
injectionConnection = numpy.zeros((1, nNeurons))
injectionConnection[0, 0] = True
spikeArray = {'spike_times': [[0]]}
inj_pop = p.Population(1,
p.SpikeSourceArray(**spikeArray),
label='inputSpikes_1')
# Projection for injector
p.Projection(inj_pop, pop, p.ArrayConnector(injectionConnection),
p.StaticSynapse(weight=weight_to_spike, delay=1))
p.Projection(inj_pop, pop2, p.ArrayConnector(injectionConnection),
p.StaticSynapse(weight=weight_to_spike, delay=1))
# Projection within populations
p.Projection(pop, pop, p.ArrayConnector(loopConnections),
p.StaticSynapse(weight=weight_to_spike, delay=delay))
p.Projection(pop2, pop2, p.ArrayConnector(loopConnections2),
p.StaticSynapse(weight=weight_to_spike, delay=delay))
pop.record(['v', 'spikes'])
pop2.record(['v', 'spikes'])
p.run(runtime)
v = pop.get_data('v')
spikes = pop.get_data('spikes')
v2 = pop2.get_data('v')
spikes2 = pop2.get_data('spikes')
if plot:
Figure(
# raster plot of the presynaptic neurons' spike times
Panel(spikes.segments[0].spiketrains,
yticks=True,
markersize=1.2,
xlim=(0, runtime),
xticks=True),
# membrane potential of the postsynaptic neurons
Panel(v.segments[0].filter(name='v')[0],
ylabel="Membrane potential (mV)",
data_labels=[pop.label],
yticks=True,
xlim=(0, runtime),
xticks=True),
Panel(spikes2.segments[0].spiketrains,
yticks=True,
markersize=1.2,
xlim=(0, runtime),
xticks=True),
# membrane potential of the postsynaptic neurons
Panel(v2.segments[0].filter(name='v')[0],
ylabel="Membrane potential (mV)",
data_labels=[pop2.label],
yticks=True,
xlim=(0, runtime),
xticks=True),
title="Testing ArrayConnector",
annotations="Simulated with {}".format(p.name()))
plt.show()
p.end()
return v, spikes, v2, spikes2
def do_run(nNeurons, neurons_per_core):
p.setup(timestep=1.0, min_delay=1.0, max_delay=32.0)
p.set_number_of_neurons_per_core(p.IF_curr_exp, neurons_per_core)
nPopulations = 62
cell_params_lif = {
'cm': 0.25,
'i_offset': 0.0,
'tau_m': 20.0,
'tau_refrac': 2.0,
'tau_syn_E': 5.0,
'tau_syn_I': 5.0,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -50.0
}
populations = list()
projections = list()
weight_to_spike = 1.5
delay = 5
for i in range(0, nPopulations):
populations.append(
p.Population(nNeurons,
p.IF_curr_exp,
cell_params_lif,
label='pop_' + str(i)))
# print("++++++++++++++++")
# print("Added population %s" % (i))
# print("o-o-o-o-o-o-o-o-")
synapse_type = p.StaticSynapse(weight=weight_to_spike, delay=delay)
for i in range(0, nPopulations):
projections.append(
p.Projection(populations[i],
populations[(i + 1) % nPopulations],
p.OneToOneConnector(),
synapse_type=synapse_type,
label="Projection from pop {} to pop "
"{}".format(i, (i + 1) % nPopulations)))
# print("++++++++++++++++++++++++++++++++++++++++++++++++++++")
# print("Added projection from population %s to population %s" \
# % (i, (i + 1) % nPopulations))
# print("----------------------------------------------------")
# from pprint import pprint as pp
# pp(projections)
spikeArray = {'spike_times': [[0]]}
populations.append(
p.Population(1, p.SpikeSourceArray, spikeArray, label='inputSpikes_1'))
projections.append(
p.Projection(populations[-1],
populations[0],
p.AllToAllConnector(),
synapse_type=synapse_type))
for i in range(0, nPopulations):
populations[i].record("v")
populations[i].record("gsyn_exc")
populations[i].record("spikes")
p.run(1500)
''''
weights = projections[0].getWeights()
delays = projections[0].getDelays()
'''
neo = populations[0].get_data(["v", "spikes", "gsyn_exc"])
v = neo_convertor.convert_data(neo, name="v")
gsyn = neo_convertor.convert_data(neo, name="gsyn_exc")
spikes = neo_convertor.convert_spikes(neo)
p.end()
return (v, gsyn, spikes)
def debug(self, run_zero):
reports = [
# write_energy_report
"Detailed_energy_report.rpt",
"energy_summary_report.rpt",
# write_text_specs = False
"data_spec_text_files",
# write_router_reports
reports_names._ROUTING_FILENAME,
# write_partitioner_reports
reports_names._PARTITIONING_FILENAME,
# write_application_graph_placer_report
reports_names._PLACEMENT_VTX_GRAPH_FILENAME,
reports_names._PLACEMENT_CORE_GRAPH_FILENAME,
reports_names._SDRAM_FILENAME,
# write_machine_graph_placer_report
reports_names._PLACEMENT_VTX_SIMPLE_FILENAME,
reports_names._PLACEMENT_CORE_SIMPLE_FILENAME,
# repeats reports_names._SDRAM_FILENAME,
# write_router_info_report
reports_names._VIRTKEY_FILENAME,
# write_routing_table_reports
reports_names._ROUTING_TABLE_DIR,
reports_names._C_ROUTING_TABLE_DIR,
reports_names._COMPARED_FILENAME,
# write_routing_compression_checker_report
"routing_compression_checker_report.rpt",
# write_routing_tables_from_machine_report
routing_tables_from_machine_report,
# write_memory_map_report
# ??? used by MachineExecuteDataSpecification but not called ???
# write_network_specification_report
NetworkSpecification._FILENAME,
# write_provenance_data
"provenance_data",
# write_tag_allocation_reports
reports_names._TAGS_FILENAME,
# write_algorithm_timings
# "provenance_data/pacman.xml" = different test
# write_board_chip_report
BoardChipReport.AREA_CODE_REPORT_NAME,
]
sim.setup(1.0)
configs = globals_variables.get_simulator()._config
if (configs.getboolean("Machine", "enable_advanced_monitor_support")
and not configs.getboolean("Java", "use_java")):
# write_data_speed_up_report
reports.append(DataSpeedUpPacketGatherMachineVertex.REPORT_NAME)
pop = sim.Population(100, sim.IF_curr_exp, {}, label="pop")
pop.record("v")
inp = sim.Population(1,
sim.SpikeSourceArray(spike_times=[0]),
label="input")
sim.Projection(inp,
pop,
sim.AllToAllConnector(),
synapse_type=sim.StaticSynapse(weight=5))
if run_zero:
sim.run(0)
sim.run(1000)
pop.get_data("v")
report_directory = globals_variables.get_simulator().\
_report_default_directory
sim.end()
found = os.listdir(report_directory)
for report in reports:
self.assertIn(report, found)
def do_run(self):
p.setup(timestep=1.0, min_delay=1.0)
p.run(100)
p.end()
def do_run():
p.setup(timestep=1.0, min_delay=1.0, max_delay=144.0)
cell_params_lif = {
'cm': 0.25, # nF
'i_offset': 0.0,
'tau_m': 20.0,
'tau_refrac': 2.0,
'tau_syn_E': 5.0,
'tau_syn_I': 5.0,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -50.0
}
populations = list()
projections = list()
populations.append(
p.Population(sources, p.IF_curr_exp, cell_params_lif, label='pop_1'))
populations.append(
p.Population(targets, p.IF_curr_exp, cell_params_lif, label='pop_2'))
connectors = p.AllToAllConnector()
synapse_type = p.StaticSynapse(weight=weight_to_spike, delay=delay)
projections.append(
p.Projection(populations[0],
populations[1],
connectors,
synapse_type=synapse_type))
p.run(1)
# before
pre_delays_array = projections[0].get(attribute_names=["delay"],
format="nparray")
pre_delays_list = projections[0].get(attribute_names=["delay"],
format="list")
pre_weights_array = projections[0].get(attribute_names=["weight"],
format="array")
pre_weights_list = projections[0].get(attribute_names=["weight"],
format="list")
p.run(100)
# after
post_delays_array = projections[0].get(attribute_names=["delay"],
format="nparray")
post_delays_list = projections[0].get(attribute_names=["delay"],
format="list")
post_weights_array = projections[0].get(attribute_names=["weight"],
format="array")
post_weights_list = projections[0].get(attribute_names=["weight"],
format="list")
p.end()
return (pre_delays_array, pre_delays_list, pre_weights_array,
pre_weights_list, post_delays_array, post_delays_list,
post_weights_array, post_weights_list)
# Set up callbacks to occur when spikes are received
live_spikes_connection_receive.add_receive_callback(
"pop_forward", receive_spikes)
live_spikes_connection_receive.add_receive_callback(
"pop_backward", receive_spikes)
# Run the simulation on spiNNaker
Frontend.run(run_time)
spikes_forward = pop_forward.get_data('spikes')
spikes_backward = pop_backward.get_data('spikes')
Figure(
# raster plot of the presynaptic neuron spike times
Panel(spikes_forward.segments[0].spiketrains,
yticks=True,
markersize=0.2,
xlim=(0, run_time)),
Panel(spikes_backward.segments[0].spiketrains,
yticks=True,
markersize=0.2,
xlim=(0, run_time)),
title="Simple synfire chain example with injected spikes",
annotations="Simulated with {}".format(Frontend.name()))
plt.show()
# Clear data structures on spiNNaker to leave the machine in a clean state for
# future executions
Frontend.end()
def do_run(nNeurons):
p.setup(timestep=1.0, min_delay=1.0, max_delay=32.0)
p.set_number_of_neurons_per_core(p.IF_curr_exp, 250)
cell_params_lif = {
'cm': 0.25,
'i_offset': 0.0,
'tau_m': 20.0,
'tau_refrac': 5.0,
'tau_syn_E': 5.0,
'tau_syn_I': 5.0,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -50.0
}
populations = list()
projections = list()
weight_to_spike = 1.5
delay = 1
connections = list()
for i in range(0, nNeurons):
singleConnection = (i, ((i + 1) % nNeurons), weight_to_spike, delay)
connections.append(singleConnection)
injectionConnection = [(0, 0, weight_to_spike, delay)]
spikeArray = {'spike_times': [[0]]}
populations.append(
p.Population(nNeurons, p.IF_curr_exp, cell_params_lif, label='pop_1'))
populations.append(
p.Population(1, p.SpikeSourceArray, spikeArray, label='inputSpikes_1'))
projections.append(
p.Projection(populations[0], populations[0],
p.FromListConnector(connections)))
projections.append(
p.Projection(populations[1], populations[0],
p.FromListConnector(injectionConnection)))
populations[0].record("v")
populations[0].record("gsyn_exc")
populations[0].record("spikes")
p.run(1000)
''''
weights = projections[0].getWeights()
delays = projections[0].getDelays()
'''
neo = populations[0].get_data(["v", "spikes", "gsyn_exc"])
v = neo_convertor.convert_data(neo, name="v")
gsyn = neo_convertor.convert_data(neo, name="gsyn_exc")
spikes = neo_convertor.convert_spikes(neo)
p.end()
return (v, gsyn, spikes)
def structural_with_stdp():
p.setup(1.0)
pre_spikes = numpy.array(range(0, 10, 2))
pre_spikes_last_neuron = pre_spikes[pre_spikes > 0]
A_plus = 0.01
A_minus = 0.01
tau_plus = 20.0
tau_minus = 20.0
w_min = 0.0
w_max = 5.0
w_init_1 = 5.0
delay_1 = 2.0
w_init_2 = 4.0
delay_2 = 1.0
stim = p.Population(1, p.SpikeSourceArray(pre_spikes), label="stim")
pop = p.Population(1, p.IF_curr_exp(), label="pop")
pop_2 = p.Population(1, p.IF_curr_exp(), label="pop_2")
pop_3 = p.Population(1, p.IF_curr_exp(), label="pop_3")
pop_4 = p.Population(1, p.IF_curr_exp(), label="pop_4")
pop.record("spikes")
pop_2.record("spikes")
proj = p.Projection(
stim, pop, p.FromListConnector([]), p.StructuralMechanismSTDP(
partner_selection=p.LastNeuronSelection(),
formation=p.DistanceDependentFormation([1, 1], 1.0),
elimination=p.RandomByWeightElimination(2.0, 0, 0),
timing_dependence=p.SpikePairRule(
tau_plus, tau_minus, A_plus, A_minus),
weight_dependence=p.AdditiveWeightDependence(w_min, w_max),
f_rew=1000, initial_weight=w_init_1, initial_delay=delay_1,
s_max=1, seed=0, weight=0.0, delay=1.0))
proj_2 = p.Projection(
stim, pop_2, p.FromListConnector([]), p.StructuralMechanismSTDP(
partner_selection=p.RandomSelection(),
formation=p.DistanceDependentFormation([1, 1], 1.0),
elimination=p.RandomByWeightElimination(4.0, 0, 0),
timing_dependence=p.SpikePairRule(
tau_plus, tau_minus, A_plus, A_minus),
weight_dependence=p.AdditiveWeightDependence(w_min, w_max),
f_rew=1000, initial_weight=w_init_2, initial_delay=delay_2,
s_max=1, seed=0, weight=0.0, delay=1.0))
proj_3 = p.Projection(
stim, pop_3, p.FromListConnector([(0, 0)]),
p.StructuralMechanismSTDP(
partner_selection=p.LastNeuronSelection(),
formation=p.DistanceDependentFormation([1, 1], 0.0),
elimination=p.RandomByWeightElimination(4.0, 1.0, 1.0),
timing_dependence=p.SpikePairRule(
tau_plus, tau_minus, A_plus, A_minus),
weight_dependence=p.AdditiveWeightDependence(w_min, w_max),
f_rew=1000, initial_weight=2.0, initial_delay=5.0,
s_max=1, seed=0, weight=0.0, delay=1.0))
proj_4 = p.Projection(
stim, pop_4, p.FromListConnector([(0, 0)]),
p.StructuralMechanismSTDP(
partner_selection=p.RandomSelection(),
formation=p.DistanceDependentFormation([1, 1], 0.0),
elimination=p.RandomByWeightElimination(4.0, 1.0, 1.0),
timing_dependence=p.SpikePairRule(
tau_plus, tau_minus, A_plus, A_minus),
weight_dependence=p.AdditiveWeightDependence(w_min, w_max),
f_rew=1000, initial_weight=4.0, initial_delay=3.0,
s_max=1, seed=0, weight=0.0, delay=1.0))
p.run(10)
conns = list(proj.get(["weight", "delay"], "list"))
conns_2 = list(proj_2.get(["weight", "delay"], "list"))
conns_3 = list(proj_3.get(["weight", "delay"], "list"))
conns_4 = list(proj_4.get(["weight", "delay"], "list"))
spikes_1 = [s.magnitude
for s in pop.get_data("spikes").segments[0].spiketrains]
spikes_2 = [s.magnitude
for s in pop_2.get_data("spikes").segments[0].spiketrains]
p.end()
print(conns)
print(conns_2)
print(conns_3)
print(conns_4)
w_final_1 = calculate_spike_pair_additive_stdp_weight(
pre_spikes_last_neuron, spikes_1[0], w_init_1, delay_1, w_max,
A_plus, A_minus, tau_plus, tau_minus)
w_final_2 = calculate_spike_pair_additive_stdp_weight(
pre_spikes, spikes_2[0], w_init_2, delay_2, w_max, A_plus, A_minus,
tau_plus, tau_minus)
print(w_final_1, spikes_1[0])
print(w_final_2, spikes_2[0])
assert(len(conns) == 1)
assert(conns[0][3] == delay_1)
assert(conns[0][2] >= w_final_1 - 0.01 and
conns[0][2] <= w_final_1 + 0.01)
assert(len(conns_2) == 1)
assert(conns_2[0][3] == delay_2)
assert(conns_2[0][2] >= w_final_2 - 0.01 and
conns_2[0][2] <= w_final_2 + 0.01)
assert(len(conns_3) == 0)
assert(len(conns_4) == 0)
def test_double_end(self):
sim.setup(1.0)
sim.end()
sim.end()
def do_run():
# 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}
delta_t = 10
time_between_pairs = 150
num_pre_pairs = 10
num_pairs = 100
num_post_pairs = 10
pop_size = 1
pairing_start_time = (num_pre_pairs * time_between_pairs) + delta_t
pairing_end_time = pairing_start_time + (num_pairs * time_between_pairs)
sim_time = pairing_end_time + (num_post_pairs * time_between_pairs)
# +-------------------------------------------------------------------+
# | Creation of neuron populations |
# +-------------------------------------------------------------------+
# Neuron populations
pre_pop = sim.Population(pop_size, model, cell_params)
post_pop = sim.Population(pop_size, model, cell_params)
# Stimulating populations
pre_stim = sim.Population(pop_size, sim.SpikeSourceArray,
{'spike_times':
[[i for i in range(0, sim_time,
time_between_pairs)], ]})
post_stim = sim.Population(pop_size, sim.SpikeSourceArray,
{'spike_times':
[[i for i in range(pairing_start_time,
pairing_end_time,
time_between_pairs)], ]})
# +-------------------------------------------------------------------+
# | Creation of connections |
# +-------------------------------------------------------------------+
# Connection type between noise poisson generator and
# excitatory populations
ee_connector = sim.OneToOneConnector()
synapse_type = sim.StaticSynapse(weight=2)
sim.Projection(pre_stim, pre_pop, ee_connector, synapse_type=synapse_type,
receptor_type='excitatory')
sim.Projection(post_stim, post_pop, ee_connector,
synapse_type=synapse_type, receptor_type='excitatory')
# Plastic Connections between pre_pop and post_pop
stdp_model = sim.STDPMechanism(
timing_dependence=sim.SpikePairRule(tau_plus=20.0, tau_minus=50.0,
A_plus=0.02, A_minus=0.02),
weight_dependence=sim.AdditiveWeightDependence(w_min=0, w_max=1))
sim.Projection(pre_pop, post_pop, sim.OneToOneConnector(),
synapse_type=stdp_model)
# Record spikes
pre_pop.record("spikes")
post_pop.record("spikes")
# Run simulation
sim.run(sim_time)
neo = pre_pop.get_data("spikes")
pre_spikes = neo_convertor.convert_spikes(neo)
neo = post_pop.get_data("spikes")
post_spikes = neo_convertor.convert_spikes(neo)
# End simulation on SpiNNaker
sim.end()
return (pre_spikes, post_spikes)
def do_run(plot):
p.setup(timestep=1.0)
cell_params_lif = {'cm': 0.25,
'i_offset': 0.0,
'tau_m': 20.0,
'tau_refrac': 2.0,
'tau_syn_E': 5.0,
'tau_syn_I': 5.0,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -40.0
}
# Parameters
n = 256
weight_to_spike = 5.0
delay = 5
runtime = 200
# Populations
exc_pop = p.Population(n, p.IF_curr_exp(**cell_params_lif),
label='exc_pop')
inh_pop = p.Population(n, p.IF_curr_exp(**cell_params_lif),
label='inh_pop')
# SpikeInjector
injectionConnection = [(0, 0)]
spikeArray = {'spike_times': [[0]]}
inj_pop = p.Population(1, p.SpikeSourceArray(**spikeArray),
label='inputSpikes_1')
# Projection for injector
p.Projection(inj_pop, exc_pop, p.FromListConnector(injectionConnection),
p.StaticSynapse(weight=weight_to_spike, delay=delay))
# Set up fromfileconnector
current_file_path = os.path.dirname(os.path.abspath(__file__))
file1 = os.path.join(current_file_path, "large.connections")
file_connector1 = p.FromFileConnector(file1)
# Projections between populations
p.Projection(exc_pop, inh_pop, file_connector1,
p.StaticSynapse(weight=2.0, delay=5))
p.Projection(inh_pop, exc_pop, file_connector1,
p.StaticSynapse(weight=1.5, delay=10))
p.Projection(inh_pop, exc_pop, file_connector1,
p.StaticSynapse(weight=1.0, delay=1))
exc_pop.record(['v', 'spikes'])
inh_pop.record(['v', 'spikes'])
p.run(runtime)
v_exc = exc_pop.get_data('v')
spikes_exc = exc_pop.get_data('spikes')
if plot:
# pylint: disable=no-member
Figure(
# raster plot of the presynaptic neurons' spike times
Panel(spikes_exc.segments[0].spiketrains,
yticks=True, markersize=1.2, xlim=(0, runtime), xticks=True),
# membrane potential of the postsynaptic neurons
Panel(v_exc.segments[0].filter(name='v')[0],
ylabel="Membrane potential (mV)",
data_labels=[exc_pop.label], yticks=True,
xlim=(0, runtime), xticks=True),
title="Testing FromFileConnector",
annotations="Simulated with {}".format(p.name())
)
plt.show()
p.end()
return v_exc, spikes_exc
def do_run(plot):
p.setup(timestep=1.0)
cell_params_lif = {'cm': 0.25,
'i_offset': 0.0,
'tau_m': 20.0,
'tau_refrac': 2.0,
'tau_syn_E': 5.0,
'tau_syn_I': 5.0,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -40.0
}
def create_grid(n, label, dx=1.0, dy=1.0):
grid_structure = p.Grid2D(dx=dx, dy=dy, x0=0.0, y0=0.0)
return p.Population(n*n, p.IF_curr_exp(**cell_params_lif),
structure=grid_structure, label=label)
n = 4
weight_to_spike = 5.0
delay = 5
runtime = 200
# Network
grid = create_grid(n, 'grid')
# SpikeInjector
injectionConnection = [(0, 0)]
spikeArray = {'spike_times': [[0]]}
inj_pop = p.Population(1, p.SpikeSourceArray(**spikeArray),
label='inputSpikes_1')
p.Projection(inj_pop, grid, p.FromListConnector(injectionConnection),
p.StaticSynapse(weight=weight_to_spike, delay=delay))
# Connectors
exc_connector = p.AllToAllConnector()
inh_connector = p.FixedProbabilityConnector(0.5, rng=NumpyRNG(seed=10101))
# Wire grid
exc_proj = p.Projection(grid, grid, exc_connector,
p.StaticSynapse(
weight="1.0 + (2.0*exp(-d))", delay=5))
inh_proj = p.Projection(grid, grid, inh_connector,
p.StaticSynapse(
weight=1.5, delay="2 + 2.0*d"))
grid.record(['v', 'spikes'])
p.run(runtime)
v = grid.get_data('v')
spikes = grid.get_data('spikes')
exc_weights_delays = exc_proj.get(['weight', 'delay'], 'list')
inh_weights_delays = inh_proj.get(['weight', 'delay'], 'list')
if plot:
Figure(
# raster plot of the presynaptic neurons' spike times
Panel(spikes.segments[0].spiketrains,
yticks=True, markersize=0.2, xlim=(0, runtime), xticks=True),
# membrane potential of the postsynaptic neurons
Panel(v.segments[0].filter(name='v')[0],
ylabel="Membrane potential (mV)",
data_labels=[grid.label], yticks=True, xlim=(0, runtime),
xticks=True),
title="Simple 2D grid distance-dependent weights and delays",
annotations="Simulated with {}".format(p.name())
)
plt.show()
p.end()
return exc_weights_delays, inh_weights_delays
weight_to_spike = 2.0
delay = 17
loopConnections = list()
for i in range(0, nNeurons):
singleConnection = ((i, (i + 1) % nNeurons, weight_to_spike, delay))
loopConnections.append(singleConnection)
injectionConnection = [(0, 0)]
spikeArray = {'spike_times': [[0]]}
populations.append(
p.Population(nNeurons, p.IF_curr_exp(**cell_params_lif), label='pop_1'))
populations.append(
p.Population(1, p.SpikeSourceArray(**spikeArray), label='inputSpikes_1'))
projections.append(
p.Projection(populations[0], populations[0],
p.FromListConnector(loopConnections),
p.StaticSynapse(weight=weight_to_spike, delay=delay)))
projections.append(
p.Projection(populations[1], populations[0],
p.FromListConnector(injectionConnection),
p.StaticSynapse(weight=weight_to_spike, delay=1)))
p.run(runtime)
print projections[0].get(['weight', 'delay'], 'list')
p.end()
def split_structural_without_stdp():
p.setup(1.0)
stim = p.Population(1, p.SpikeSourceArray(range(10)), label="stim")
# These populations should experience formation
pop = p.Population(1,
p.IF_curr_exp(),
label="pop",
additional_parameters={
"splitter":
SplitterAbstractPopulationVertexNeuronsSynapses(1)
})
pop_2 = p.Population(1,
p.IF_curr_exp(),
label="pop_2",
additional_parameters={
"splitter":
SplitterAbstractPopulationVertexNeuronsSynapses(1)
})
# These populations should experience elimination
pop_3 = p.Population(1,
p.IF_curr_exp(),
label="pop_3",
additional_parameters={
"splitter":
SplitterAbstractPopulationVertexNeuronsSynapses(1)
})
pop_4 = p.Population(1,
p.IF_curr_exp(),
label="pop_4",
additional_parameters={
"splitter":
SplitterAbstractPopulationVertexNeuronsSynapses(1)
})
# Formation with last-neuron selection (0 probability elimination)
proj = p.Projection(
stim, pop, p.FromListConnector([]),
p.StructuralMechanismStatic(
partner_selection=p.LastNeuronSelection(),
formation=p.DistanceDependentFormation([1, 1], 1.0),
elimination=p.RandomByWeightElimination(2.0, 0, 0),
f_rew=1000,
initial_weight=2.0,
initial_delay=5.0,
s_max=1,
seed=0,
weight=0.0,
delay=1.0))
# Formation with random selection (0 probability elimination)
proj_2 = p.Projection(
stim, pop_2, p.FromListConnector([]),
p.StructuralMechanismStatic(
partner_selection=p.RandomSelection(),
formation=p.DistanceDependentFormation([1, 1], 1.0),
elimination=p.RandomByWeightElimination(4.0, 0, 0),
f_rew=1000,
initial_weight=4.0,
initial_delay=3.0,
s_max=1,
seed=0,
weight=0.0,
delay=1.0))
# Elimination with last neuron selection (0 probability formation)
proj_3 = p.Projection(
stim, pop_3, p.FromListConnector([(0, 0)]),
p.StructuralMechanismStatic(
partner_selection=p.LastNeuronSelection(),
formation=p.DistanceDependentFormation([1, 1], 0.0),
elimination=p.RandomByWeightElimination(4.0, 1.0, 1.0),
f_rew=1000,
initial_weight=2.0,
initial_delay=5.0,
s_max=1,
seed=0,
weight=0.0,
delay=1.0))
# Elimination with random selection (0 probability formation)
proj_4 = p.Projection(
stim, pop_4, p.FromListConnector([(0, 0)]),
p.StructuralMechanismStatic(
partner_selection=p.RandomSelection(),
formation=p.DistanceDependentFormation([1, 1], 0.0),
elimination=p.RandomByWeightElimination(4.0, 1.0, 1.0),
f_rew=1000,
initial_weight=4.0,
initial_delay=3.0,
s_max=1,
seed=0,
weight=0.0,
delay=1.0))
p.run(10)
# Get the final connections
conns = list(proj.get(["weight", "delay"], "list"))
conns_2 = list(proj_2.get(["weight", "delay"], "list"))
conns_3 = list(proj_3.get(["weight", "delay"], "list"))
conns_4 = list(proj_4.get(["weight", "delay"], "list"))
p.end()
print(conns)
print(conns_2)
print(conns_3)
print(conns_4)
# These should be formed with specified parameters
assert (len(conns) == 1)
assert (tuple(conns[0]) == (0, 0, 2.0, 5.0))
assert (len(conns_2) == 1)
assert (tuple(conns_2[0]) == (0, 0, 4.0, 3.0))
# These should have no connections since eliminated
assert (len(conns_3) == 0)
assert (len(conns_4) == 0)
def agent_fitness(agent, light_distance, light_theta, print_move):
global port_offset
global number_of_runs
global counter
global current_agent
global current_fitness
global current_light_distance
global current_light_theta
global currently_running
current_agent = agent
print "\n\nStarting agent - {}\n\n".format(agent)
p.setup(timestep=1.0, min_delay=delay_min, max_delay=delay_max)
p.set_number_of_neurons_per_core(p.IF_cond_exp, 20)
# setup of different neuronal populations
#neuron_pop = list();
neuron_pop = []
if port_offset != 1:
for i in range(agent_neurons):
del neuron_labels[0]
inhibitory_count = 0
excitatory_count = 0
for i in range(agent_neurons):
if agent_pop[agent][inhibitory_loc + i] == -1:
neuron_labels.append("Inhibitory{}-neuron{}-agent{}-port{}".format(
inhibitory_count, i, agent, port_offset))
neuron_pop.append(
p.Population(neuron_pop_size,
p.IF_cond_exp(),
label=neuron_labels[i]))
inhibitory_count += 1
else:
neuron_labels.append("Excitatory{}-neuron{}-agent{}-port{}".format(
excitatory_count, i, agent, port_offset))
neuron_pop.append(
p.Population(neuron_pop_size,
p.IF_cond_exp(),
label=neuron_labels[i]))
excitatory_count += 1
# if print_move == True:
# neuron_pop[i].record(["spikes", "v"])
# connect neuronal population according to genentic instructions
projection_list = list()
for i in range(agent_neurons):
for j in range(agent_neurons):
# if theres a connection connect
if agent_pop[agent][set2loc + (i * agent_neurons) + j] != 0:
# if connection is inhibitory set as such
if agent_pop[agent][inhibitory_loc + i] == -1:
synapse = p.StaticSynapse(
weight=-agent_pop[agent][(i * agent_neurons) + j],
delay=agent_pop[agent][delay_loc +
((i * agent_neurons) + j)])
projection_list.append(
p.Projection(neuron_pop[i],
neuron_pop[j],
p.AllToAllConnector(),
synapse,
receptor_type="inhibitory"))
# set as excitatory
else:
synapse = p.StaticSynapse(
weight=agent_pop[agent][(i * agent_neurons) + j],
delay=agent_pop[agent][delay_loc +
((i * agent_neurons) + j)])
projection_list.append(
p.Projection(neuron_pop[i],
neuron_pop[j],
p.AllToAllConnector(),
synapse,
receptor_type="excitatory"))
# set STDP, weight goes to negative if inhibitory?
# stdp_model = p.STDPMechanism(
# timing_dependence=p.SpikePairRule(
# tau_plus=20., tau_minus=20.0, A_plus=0.5, A_minus=0.5),
# weight_dependence=p.AdditiveWeightDependence(w_min=weight_min, w_max=weight_max))
# connect in and out live links
#visual_input = list()
visual_input = []
visual_projection = [] #list()
input_labels = [] #list()
#sensor_poisson = [0 for j in range(visual_discrete)]
sensor_poisson = poisson_rate(agent, light_distance, light_theta)
for i in range(visual_discrete):
print i
input_labels.append("input_spikes{}".format(i))
visual_input.append(
p.Population(1,
p.SpikeSourcePoisson(rate=sensor_poisson[i]),
label=input_labels[i]))
visual_projection.append(
p.Projection(
visual_input[i], neuron_pop[i], p.OneToOneConnector(),
p.StaticSynapse(weight=visual_weight, delay=visual_delay)))
p.external_devices.add_poisson_live_rate_control(
visual_input[i], database_notify_port_num=16000 + port_offset)
# poisson_control = p.external_devices.SpynnakerPoissonControlConnection(poisson_labels=[visual_input[i].label])#,local_port=18000+(port_offset*visual_discrete)+i)
# poisson_control.add_start_callback(visual_input[i].label, poisson_setting)
# visual_input = p.Population(visual_discrete, p.SpikeSourcePoisson(rate=sensor_poisson), label=input)
# p.Projection(
# visual_input, neuron_pop[(i for i in range(0,visual_discrete))], p.OneToOneConnector(), p.StaticSynapse(weight=visual_weight, delay=visual_delay))
# p.external_devices.add_poisson_live_rate_control(visual_input)
poisson_control = p.external_devices.SpynnakerPoissonControlConnection(
poisson_labels=input_labels, local_port=16000 + port_offset)
poisson_control.add_start_callback(visual_input[0].label, poisson_setting)
# poisson_control.add_start_callback(visual_input[1].label, empty_function)
# poisson_control2 = p.external_devices.SpynnakerPoissonControlConnection(poisson_labels=[visual_input[1].label],local_port=19998)#+(port_offset*visual_discrete)+i)
# poisson_control2.add_start_callback(visual_input[1].label, poisson_setting2)
# poisson_control.add_start_callback(visual_input[1].label, poisson_setting)
# for i in range(visual_discrete):
# print i
# input_labels.append("input_spikes{}".format(i))
# visual_input.append(p.Population(
# 1, p.SpikeSourcePoisson(rate=sensor_poisson[i]), label=input_labels[i]))
# visual_projection.append(p.Projection(
# visual_input[i], neuron_pop[i], p.OneToOneConnector(), p.StaticSynapse(
# weight=visual_weight, delay=visual_delay)))
# p.external_devices.add_poisson_live_rate_control(visual_input[i]) #possible all at once
# poisson_control = p.external_devices.SpynnakerPoissonControlConnection(poisson_labels=[input_labels[0], input_labels[1]])
# #for i in range(visual_discrete):
# poisson_control.add_start_callback(input_labels[i], poisson_setting)
# for i in range(4):
# del motor_labels[0]
motor_labels = []
for i in range(4):
print i
motor_labels.append(neuron_labels[agent_neurons - (i + 1)])
p.external_devices.activate_live_output_for(
neuron_pop[agent_neurons - (i + 1)],
database_notify_port_num=18000 + port_offset)
live_connection = p.external_devices.SpynnakerLiveSpikesConnection(
receive_labels=[
motor_labels[0], motor_labels[1], motor_labels[2], motor_labels[3]
],
local_port=(18000 + port_offset))
for i in range(4):
live_connection.add_receive_callback(motor_labels[i], receive_spikes)
#fitness = 0
# spikes = list()
# v = list()
current_fitness = 0
current_light_theta = light_theta
current_light_distance = light_distance
currently_running = True
p.run(total_runtime)
currently_running = False
no_move_distance = light_distance * total_runtime / time_slice
fitness = current_fitness
if abs(fitness - no_move_distance) < 1e-10:
fitness *= no_move_punishment
print "agent failed to move so was punished"
# if print_move == True:
# spikes = []
# v = []
# for j in range(agent_neurons):
# spikes.append(neuron_pop[j].get_data("spikes"))
# v.append(neuron_pop[j].get_data("v"))
live_connection.close()
live_connection._handle_possible_rerun_state()
p.end()
if counter != number_of_runs:
counter += 1
port_offset += 1
reset_agent(agent)
if print_move == True:
with open(
'movement {}.csv'.format(
(port_offset - counter) / number_of_runs),
'a') as file:
writer = csv.writer(file, delimiter=',', lineterminator='\n')
writer.writerow([
light_distance * np.sin(light_theta),
light_distance * np.cos(light_theta)
])
port_recurse_check = port_offset
fitness += agent_fitness(agent, light_distance, -light_theta,
print_move)
else:
counter = 1
port_offset -= 1
port_offset += 1
reset_agent(agent)
return fitness
def do_run():
simulator_name = 'spiNNaker'
timer = Timer()
# === Define parameters =========================================
rngseed = 98766987
parallel_safe = True
n = 1500 # number of cells
# number of excitatory cells:number of inhibitory cells
r_ei = 4.0
pconn = 0.02 # connection probability
dt = 0.1 # (ms) simulation timestep
tstop = 200 # (ms) simulaton duration
delay = 1
# Cell parameters
area = 20000. # (µm²)
tau_m = 20. # (ms)
cm = 1. # (µF/cm²)
g_leak = 5e-5 # (S/cm²)
e_leak = -49. # (mV)
v_thresh = -50. # (mV)
v_reset = -60. # (mV)
t_refrac = 5. # (ms) (clamped at v_reset)
# (mV) 'mean' membrane potential, for calculating CUBA weights
v_mean = -60.
tau_exc = 5. # (ms)
tau_inh = 10. # (ms)
# (nS) #Those weights should be similar to the COBA weights
g_exc = 0.27
# (nS) # but the delpolarising drift should be taken into account
g_inh = 4.5
e_rev_exc = 0. # (mV)
e_rev_inh = -80. # (mV)
# === Calculate derived parameters ===============================
area *= 1e-8 # convert to cm²
cm *= area * 1000 # convert to nF
r_m = 1e-6 / (g_leak * area) # membrane resistance in MΩ
assert tau_m == cm * r_m # just to check
# number of excitatory cells
n_exc = int(round((n * r_ei / (1 + r_ei))))
n_inh = n - n_exc # number of inhibitory cells
celltype = p.IF_curr_exp
# (nA) weight of excitatory synapses
w_exc = 1e-3 * g_exc * (e_rev_exc - v_mean)
w_inh = 1e-3 * g_inh * (e_rev_inh - v_mean) # (nA)
assert w_exc > 0
assert w_inh < 0
# === Build the network ==========================================
p.setup(timestep=dt, min_delay=delay, max_delay=delay)
if simulator_name == 'spiNNaker':
# this will set 100 neurons per core
p.set_number_of_neurons_per_core(p.IF_curr_exp, 10)
# this will set 50 neurons per core
p.set_number_of_neurons_per_core(p.IF_cond_exp, 10)
# node_id = 1
# np = 1
# host_name = socket.gethostname()
cell_params = {'tau_m': tau_m, 'tau_syn_E': tau_exc, 'tau_syn_I': tau_inh,
'v_rest': e_leak, 'v_reset': v_reset, 'v_thresh': v_thresh,
'cm': cm, 'tau_refrac': t_refrac, 'i_offset': 0}
timer.start()
exc_cells = p.Population(n_exc, celltype, cell_params,
label="Excitatory_Cells")
inh_cells = p.Population(n_inh, celltype, cell_params,
label="Inhibitory_Cells")
p.NativeRNG(12345)
rng = NumpyRNG(seed=rngseed, parallel_safe=parallel_safe)
uniform_distr = RandomDistribution('uniform', [v_reset, v_thresh], rng=rng)
exc_cells.initialize(v=uniform_distr)
inh_cells.initialize(v=uniform_distr)
exc_conn = p.FixedProbabilityConnector(pconn, rng=rng)
synapse_exc = p.StaticSynapse(weight=w_exc, delay=delay)
inh_conn = p.FixedProbabilityConnector(pconn, rng=rng)
synapse_inh = p.StaticSynapse(weight=w_inh, delay=delay)
connections = dict()
connections['e2e'] = p.Projection(exc_cells, exc_cells, exc_conn,
synapse_type=synapse_exc,
receptor_type='excitatory')
connections['e2i'] = p.Projection(exc_cells, inh_cells, exc_conn,
synapse_type=synapse_exc,
receptor_type='excitatory')
connections['i2e'] = p.Projection(inh_cells, exc_cells, inh_conn,
synapse_type=synapse_inh,
receptor_type='inhibitory')
connections['i2i'] = p.Projection(inh_cells, inh_cells, inh_conn,
synapse_type=synapse_inh,
receptor_type='inhibitory')
# === Setup recording ==============================
exc_cells.record("spikes")
# === Run simulation ================================
p.run(tstop)
exc_spikes = exc_cells.get_data("spikes")
exc_cells.write_data(neo_path, "spikes")
p.end()
return exc_spikes