def Run(T,
v0,
u0,
bench,
number,
input_neurons,
liquid_neurons,
hidden_neurons,
output_neurons,
Sin,
Sliq,
Sa,
Sb,
M,
Mv,
Mu,
S_in,
S_hidden,
S_out,
train=False,
letter=None):
br.forget(Sin, Sliq)
for i in range(len(Sa)):
br.forget(Sa[i])
br.forget(Sb)
br.reinit(states=False)
br.recall(Sin, Sliq)
for i in range(len(Sa)):
br.recall(Sa[i])
br.recall(Sb)
img, label = ReadImg(number=number, bench=bench, letter=letter)
spikes = GetInSpikes(img, bench=bench)
if number >= 0 and number < 4:
input_neurons.set_spiketimes(spikes)
else:
input_neurons.set_spiketimes([])
for i in range(len(liquid_neurons)):
liquid_neurons[i].v = v0
liquid_neurons[i].u = u0
liquid_neurons[i].I = 0
liquid_neurons[i].ge = 0
for i in range(len(hidden_neurons)):
hidden_neurons[i].v = v0
hidden_neurons[i].u = u0
hidden_neurons[i].I = 0
hidden_neurons[i].ge = 0
#pudb.set_trace()
output_neurons.v = v0
output_neurons.u = u0
output_neurons.I = 0
output_neurons.ge = 0
br.run(T * br.msecond, report='text')
return label
def run_network(self, traj):
"""Top-level simulation function, pass this to the environment
Performs an individual network run during parameter exploration.
`run_network` does not need to be called by the user. If the top-level
`~pypet.brian.network.run_network` method (not this one of the NetworkManager)
is passed to an :class:`~pypet.environment.Environment` with this NetworkManager,
`run_network` and :func:`~pypet.brian.network.NetworkManager.build`
are automatically called for each individual experimental run.
This function will create a new `BRIAN network`_ in case one was not pre-run.
The execution of the network run is carried out by
the :class:`~pypet.brian.network.NetworkRunner` and it's
:func:`~pypet.brian.network.NetworkRunner.execute_network_run` (also take
a look at this function's documentation to see the structure of a network run).
.. `BRIAN network`_: http://briansimulator.org/docs/reference-network.html#brian.Network
:param traj: Trajectory container
"""
# Check if the network was pre-built
if self._pre_built:
# If yes check for multiprocessing or if a single core processing is forced
multiproc = traj.f_get("config.environment.%s.multiproc" % traj.v_environment_name).f_get()
if multiproc:
self._run_network(traj)
else:
if self._force_single_core:
self._logger.warning(
"Running Single Core Mode. Be aware that the network "
"evolves over ALL your runs and is not reset. "
"Use this setting only for debugging purposes "
"because your results will be not correct in case "
"your trajectory contains more than a single run. "
)
self._run_network(traj)
else:
raise RuntimeError(
"You cannot run a pre-built network without "
"multiprocessing.\n"
"The network configuration must be copied either by "
"pickling (using a `multiproc=True` and `use_pool=True` in "
"your environment) or by forking ( multiprocessing with "
"`use_pool=False`).\n If your network "
"cannot be pickled use the latter. "
"In order to come close to iterative processing "
"you could use multiprocessing with `ncores=1`. \n"
"If you do not care about messing up initial conditions "
"(i.e. you are debugging) use `force_single_core=True` "
"in your network manager."
)
else:
clear(True, True)
reinit()
self._run_network(traj)
def run_network(self, traj):
"""Top-level simulation function, pass this to the environment
Performs an individual network run during parameter exploration.
`run_network` does not need to be called by the user. If the top-level
`~pypet.brian.network.run_network` method (not this one of the NetworkManager)
is passed to an :class:`~pypet.environment.Environment` with this NetworkManager,
`run_network` and :func:`~pypet.brian.network.NetworkManager.build`
are automatically called for each individual experimental run.
This function will create a new `BRIAN network`_ in case one was not pre-run.
The execution of the network run is carried out by
the :class:`~pypet.brian.network.NetworkRunner` and it's
:func:`~pypet.brian.network.NetworkRunner.execute_network_run` (also take
a look at this function's documentation to see the structure of a network run).
.. `BRIAN network`_: http://briansimulator.org/docs/reference-network.html#brian.Network
:param traj: Trajectory container
"""
# Check if the network was pre-built
if self._pre_built:
# If yes check for multiprocessing or if a single core processing is forced
multiproc = traj.f_get('config.environment.%s.multiproc' %
traj.v_environment_name).f_get()
if multiproc:
self._run_network(traj)
else:
if self._force_single_core:
self._logger.warning(
'Running Single Core Mode. Be aware that the network '
'evolves over ALL your runs and is not reset. '
'Use this setting only for debugging purposes '
'because your results will be not correct in case '
'your trajectory contains more than a single run. ')
self._run_network(traj)
else:
raise RuntimeError(
'You cannot run a pre-built network without '
'multiprocessing.\n'
'The network configuration must be copied either by '
'pickling (using a `multiproc=True` and `use_pool=True` in '
'your environment) or by forking ( multiprocessing with '
'`use_pool=False`).\n If your network '
'cannot be pickled use the latter. '
'In order to come close to iterative processing '
'you could use multiprocessing with `ncores=1`. \n'
'If you do not care about messing up initial conditions '
'(i.e. you are debugging) use `force_single_core=True` '
'in your network manager.')
else:
clear(True, True)
reinit()
self._run_network(traj)
def run_sim(number_neurons=default_number_neurons,
connection_probability=default_connection_probability,
synaptic_weights=default_synaptic_weights,
synaptic_time_constant=default_synaptic_time_constant,
tend=300):
'''run a simulation of a population of leaky integrate-and-fire excitatory neurons that are
randomly connected. The population is injected with a transient current.'''
from brian.units import mvolt, msecond, namp, Mohm
import brian
brian.clear()
El = 0 * mvolt
tau_m = 30 * msecond
tau_syn = synaptic_time_constant * msecond
R = 20 * Mohm
v_threshold = 30 * mvolt
v_reset = 0 * mvolt
tau_refractory = 4 * msecond
eqs = brian.Equations('''
dv/dt = (-(v - El) + R*I)/tau_m : volt
I = I_syn + I_stim : amp
dI_syn/dt = -I_syn/tau_syn : amp
I_stim : amp
''')
external_current = np.zeros(tend)
external_current[np.arange(0, 100)] = 5 * namp
group = brian.NeuronGroup(
model=eqs,
N=number_neurons, threshold=v_threshold, reset=v_reset, refractory=tau_refractory)
group.I_stim = brian.TimedArray(external_current, dt=1*msecond)
connections = brian.Connection(group, group, 'I_syn')
connections.connect_random(sparseness=connection_probability, weight=synaptic_weights*namp)
spike_monitor = brian.SpikeMonitor(group)
population_rate_monitor = brian.PopulationRateMonitor(group, bin=10*msecond)
brian.reinit()
brian.run(tend * msecond)
return spike_monitor, population_rate_monitor
def poisson_input(active, N_input, r, time_input, t1, t2):
"function to built a poisson input"
"with no zero firing rates"
from brian import PoissonGroup,SpikeMonitor,reinit,clear,run,Hz,second
import random as pyrandom
reinit(states = True)
clear(erase = True, all = True)
N = 1000
P = PoissonGroup(N)
S = SpikeMonitor(P)
run(t1)
P.rate = r
run(time_input)
P.rate = 0*Hz
run(t2)
s = []
remove = []
for i in xrange(N):
s.append(len(S[i]))
if len(S[i]) == 0:
remove.append(i)
pos = [x for x in range(N) if x not in remove]
pos = pyrandom.sample(pos, len(active))
C = []
for ii in xrange(len(pos)):
D = list(S.spiketimes[pos[ii]])
D = [(active[ii],x) for x in D]
C += D
C = [(i,t *second) for (i,t) in C]
C = sorted(C, key=lambda x: x[1])
reinit(states = True)
clear(erase = True, all = True)
return C
import brian
import numpy as np
import os, sys
nruns = int(sys.argv[1])
for nrun in xrange(1, nruns + 1):
brian.seed(nrun)
print 'RUN: ' + str(nrun)
brian.reinit(states=True)
brian.clear(erase=True, all=True)
rate = int(sys.argv[2])
foldername = 'rate' + str(rate) + '/run_' + str(nrun)
os.system('mkdir -p -v ' + foldername)
N = 1000
time_input = 23000 * brian.ms
P = brian.PoissonGroup(N)
S = brian.SpikeMonitor(P)
P.rate = rate * brian.Hz
brian.run(time_input, report='text', report_period=10 * brian.second)
fname = 'noise_'
for s in xrange(len(S.spiketimes)):
spiketimes = [round(1000 * x, 1) + 50 for x in list(S.spiketimes[s])]
np.savetxt(foldername + '/' + fname + str(s) + '.txt',
spiketimes,
fmt='%10.1f',
newline='\n')
def run_simulation(realizations=1, trials=1, t=3000 * ms, alpha=1, ree=1, k=50, winlen=50 * ms, verbose=True, t_stim=0):
"""
Run the whole simulation with the specified parameters. All model parameter are set in the function.
Keyword arguments:
:param realizations: number of repititions of the whole simulation, number of network instances
:param trials: number of trials for network instance
:param t: simulation time
:param alpha: scaling factor for number of neurons in the network
:param ree: clustering coefficient
:param k: number of clusters
:param t_stim : duration of stimulation of a subset of clusters
:param winlen: length of window in ms
:param verbose: plotting flag
:return: numpy matrices with spike times
"""
# The equations defining our neuron model
eqs_string = """
dV/dt = (mu - V)/tau + x: volt
dx/dt = -1.0/tau_2*(x - y/tau_1) : volt/second
dy/dt = -y/tau_1 : volt
mu : volt
tau: second
tau_2: second
tau_1: second
"""
# Model parameters
n_e = int(4000 * alpha) # number of exc neurons
n_i = int(1000 * alpha) # number of inh neurons
tau_e = 15 * ms # membrane time constant (for excitatory synapses)
tau_i = 10 * ms # membrane time constant (for inhibitory synapses)
tau_syn_2_e = 3 * ms # exc synaptic time constant tau2 in paper
tau_syn_2_i = 2 * ms # inh synaptic time constant tau2 in paper
tau_syn_1 = 1 * ms # exc/inh synaptic time constant tau1 in paper
vt = -50 * mV # firing threshold
vr = -65 * mV # reset potential
dv = vt - vr # delta v
refrac = 5 * ms # absolute refractory period
# scale the weights to ensure same variance in the inputs
wee = 0.024 * dv * np.sqrt(1.0 / alpha)
wie = 0.014 * dv * np.sqrt(1.0 / alpha)
wii = -0.057 * dv * np.sqrt(1.0 / alpha)
wei = -0.045 * dv * np.sqrt(1.0 / alpha)
# Connection probability
p_ee = 0.2
p_ii = 0.5
p_ie = 0.5
p_ei = 0.5
# determine probs for inside and outside of clusters
p_in, p_out = get_cluster_connection_probs(ree, k, p_ee)
mu_min_e, mu_max_e = 1.1, 1.2
mu_min_i, mu_max_i = 1.0, 1.05
# increase cluster weights if there are clusters
wee_cluster = wee if p_in == p_out else 1.9 * wee
# define numpy array for data storing
all_data = np.zeros((realizations, trials, n_e + n_i, int(t / winlen) // 2))
for realization in range(realizations):
# clear workspace to make sure that is a new realization of the network
clear(True, True)
reinit()
# set up new random bias parameter for every type of neuron
mu_e = vr + np.random.uniform(mu_min_e, mu_max_e, n_e) * dv # bias for excitatory neurons
mu_i = vr + np.random.uniform(mu_min_i, mu_max_i, n_i) * dv # bias for excitatory neurons
# Let's create an equation object from our string and parameters
model_eqs = Equations(eqs_string)
# Let's create 5000 neurons
all_neurons = NeuronGroup(
N=n_e + n_i,
model=model_eqs,
threshold=vt,
reset=vr,
refractory=refrac,
freeze=True,
method="Euler",
compile=True,
)
# Divide the neurons into excitatory and inhibitory ones
neurons_e = all_neurons[0:n_e]
neurons_i = all_neurons[n_e : n_e + n_i]
# set the bias
neurons_e.mu = mu_e
neurons_i.mu = mu_i
neurons_e.tau = tau_e
neurons_i.tau = tau_i
neurons_e.tau_2 = tau_syn_2_e
neurons_i.tau_2 = tau_syn_2_i
all_neurons.tau_1 = tau_syn_1
# set up connections
connections = Connection(all_neurons, all_neurons, "y")
# do the cluster connection like cross validation: cluster neuron := test idx; other neurons := train idx
kf = KFold(n=n_e, n_folds=k)
for idx_out, idx_in in kf: # idx_out holds all other neurons; idx_in holds all cluster neurons
# connect current cluster to itself
connections.connect_random(
all_neurons[idx_in[0] : idx_in[-1]],
all_neurons[idx_in[0] : idx_in[-1]],
sparseness=p_in,
weight=wee_cluster,
)
# connect current cluster to other neurons
connections.connect_random(
all_neurons[idx_in[0] : idx_in[-1]], all_neurons[idx_out[0] : idx_out[-1]], sparseness=p_out, weight=wee
)
# connect all excitatory to all inhibitory, irrespective of clustering
connections.connect_random(all_neurons[0:n_e], all_neurons[n_e : (n_e + n_i)], sparseness=p_ie, weight=wie)
# connect all inhibitory to all excitatory
connections.connect_random(all_neurons[n_e : (n_e + n_i)], all_neurons[0:n_e], sparseness=p_ei, weight=wei)
# connect all inhibitory to all inhibitory
connections.connect_random(
all_neurons[n_e : (n_e + n_i)], all_neurons[n_e : (n_e + n_i)], sparseness=p_ii, weight=wii
)
# set up spike monitors
spike_mon_e = SpikeMonitor(neurons_e)
spike_mon_i = SpikeMonitor(neurons_i)
# set up network with monitors
network = Network(all_neurons, connections, spike_mon_e, spike_mon_i)
# run this network for some number of trials, every time with
for trial in range(trials):
# different initial values
all_neurons.V = vr + (vt - vr) * np.random.rand(len(all_neurons)) * 1.4
# Calibration phase
# run for the first half of the time to let the neurons adapt
network.run(t / 2)
# reset monitors to start recording phase
spike_mon_i.reinit()
spike_mon_e.reinit()
# stimulation if duration is given
# define index variable for the stimulation possibility (is 0 for stimulation time=0)
t_stim_idx = int(t_stim / (winlen / ms))
if not (t_stim == 0):
# Stimulation phase, increase input to subset of clusters
all_neurons[:400].mu += 0.07 * dv
network.run(t_stim * ms, report="text")
# set back to normal
all_neurons[:400].mu -= 0.07 * dv
# save data
all_data[realization, trial, :n_e, :t_stim_idx] = spikes_counter(spike_mon_e, winlen)
all_data[realization, trial, n_e:, :t_stim_idx] = spikes_counter(spike_mon_i, winlen)
# reset monitors
spike_mon_e.reinit()
spike_mon_i.reinit()
# run the remaining time of the simulation
network.run((t / 2) - t_stim * ms, report="text")
# save results
all_data[realization, trial, :n_e, t_stim_idx:] = spikes_counter(spike_mon_e, winlen)
all_data[realization, trial, n_e:, t_stim_idx:] = spikes_counter(spike_mon_i, winlen)
if verbose:
plt.ion()
plt.figure()
raster_plot(spike_mon_e)
plt.title("Excitatory neurons")
spike_mon_e.reinit()
spike_mon_i.reinit()
return all_data
import string
import struct
from brian import Network, Equations, NeuronGroup, Connection,\
SpikeMonitor, raster_plot, StateMonitor, clear, reinit
from brian.stdunits import ms, mV, nS, pA, pF, Hz
for i in range(len(sys.argv)):
if sys.argv[i] == "-rEE":
rEE = float(sys.argv[i+1])
#%matplotlib inline
pylab.rcParams['figure.figsize'] = 12, 8 # changes figure size (width, height) for larger images
clear(True, True)
reinit()# To reinit brain clocks and remove all old brian objects from namespace,
# it's usually a good idea to put this at the beginning of a script
# The equations defining our neuron model
eqs_string = ''' dV/dt = (1.0/tau)*(myu-V) + Isyn : 1
Isyn = Isyne - Isyni : hertz
dIsyne/dt = -(1/tau1)*(Isyne + ye) : hertz
dye/dt = -(1/tau2)*ye : hertz
dIsyni/dt = -(1/tau1)*(Isyni + yi) : hertz
dyi/dt = -(1/tau2)*yi : hertz
myu : 1
'''
def run_simulation(realizations=1, trials=1, t=3000 * ms, alpha=1, ree=1,
k=50, winlen = 50 * ms, verbose=True, t_stim = 0):
"""
Run the whole simulation with the specified parameters. All model parameter are set in the function.
Keyword arguments:
:param realizations: number of repititions of the whole simulation, number of network instances
:param trials: number of trials for network instance
:param t: simulation time
:param alpha: scaling factor for number of neurons in the network
:param ree: clustering coefficient
:param k: number of clusters
:param t_stim : duration of stimulation of a subset of clusters
:param winlen: length of window in ms
:param verbose: plotting flag
:return: numpy matrices with spike times
"""
# The equations defining our neuron model
eqs_string = '''
dV/dt = (mu - V)/tau + x: volt
dx/dt = -1.0/tau_2*(x - y/tau_1) : volt/second
dy/dt = -y/tau_1 : volt
mu : volt
tau: second
tau_2: second
tau_1: second
'''
# Model parameters
n_e = int(4000 * alpha) # number of exc neurons
n_i = int(1000 * alpha) # number of inh neurons
tau_e = 15 * ms # membrane time constant (for excitatory synapses)
tau_i = 10 * ms # membrane time constant (for inhibitory synapses)
tau_syn_2_e = 3 * ms # exc synaptic time constant tau2 in paper
tau_syn_2_i = 2 * ms # inh synaptic time constant tau2 in paper
tau_syn_1 = 1 * ms # exc/inh synaptic time constant tau1 in paper
vt = -50 * mV # firing threshold
vr = -65 * mV # reset potential
dv = vt - vr # delta v
refrac = 5 * ms # absolute refractory period
# scale the weights to ensure same variance in the inputs
wee = 0.024 * dv * np.sqrt(1. / alpha)
wie = 0.014 * dv * np.sqrt(1. / alpha)
wii = -0.057 * dv * np.sqrt(1. / alpha)
wei = -0.045 * dv * np.sqrt(1. / alpha)
# Connection probability
p_ee = 0.2
p_ii = 0.5
p_ie = 0.5
p_ei = 0.5
# determine probs for inside and outside of clusters
p_in, p_out = get_cluster_connection_probs(ree, k, p_ee)
mu_min_e, mu_max_e = 1.1, 1.2
mu_min_i, mu_max_i = 1.0, 1.05
# increase cluster weights if there are clusters
wee_cluster = wee if p_in == p_out else 1.9 * wee
# define numpy array for data storing
all_data = np.zeros((realizations, trials, n_e+n_i, int(t/winlen)//2))
for realization in range(realizations):
# clear workspace to make sure that is a new realization of the network
clear(True, True)
reinit()
# set up new random bias parameter for every type of neuron
mu_e = vr + np.random.uniform(mu_min_e, mu_max_e, n_e) * dv # bias for excitatory neurons
mu_i = vr + np.random.uniform(mu_min_i, mu_max_i, n_i) * dv # bias for excitatory neurons
# Let's create an equation object from our string and parameters
model_eqs = Equations(eqs_string)
# Let's create 5000 neurons
all_neurons = NeuronGroup(N=n_e + n_i,
model=model_eqs,
threshold=vt,
reset=vr,
refractory=refrac,
freeze=True,
method='Euler',
compile=True)
# Divide the neurons into excitatory and inhibitory ones
neurons_e = all_neurons[0:n_e]
neurons_i = all_neurons[n_e:n_e + n_i]
# set the bias
neurons_e.mu = mu_e
neurons_i.mu = mu_i
neurons_e.tau = tau_e
neurons_i.tau = tau_i
neurons_e.tau_2 = tau_syn_2_e
neurons_i.tau_2 = tau_syn_2_i
all_neurons.tau_1 = tau_syn_1
# set up connections
connections = Connection(all_neurons, all_neurons, 'y')
# do the cluster connection like cross validation: cluster neuron := test idx; other neurons := train idx
kf = KFold(n=n_e, n_folds=k)
for idx_out, idx_in in kf: # idx_out holds all other neurons; idx_in holds all cluster neurons
# connect current cluster to itself
connections.connect_random(all_neurons[idx_in[0]:idx_in[-1]], all_neurons[idx_in[0]:idx_in[-1]],
sparseness=p_in, weight=wee_cluster)
# connect current cluster to other neurons
connections.connect_random(all_neurons[idx_in[0]:idx_in[-1]], all_neurons[idx_out[0]:idx_out[-1]],
sparseness=p_out, weight=wee)
# connect all excitatory to all inhibitory, irrespective of clustering
connections.connect_random(all_neurons[0:n_e], all_neurons[n_e:(n_e + n_i)], sparseness=p_ie, weight=wie)
# connect all inhibitory to all excitatory
connections.connect_random(all_neurons[n_e:(n_e + n_i)], all_neurons[0:n_e], sparseness=p_ei, weight=wei)
# connect all inhibitory to all inhibitory
connections.connect_random(all_neurons[n_e:(n_e + n_i)], all_neurons[n_e:(n_e + n_i)], sparseness=p_ii,
weight=wii)
# set up spike monitors
spike_mon_e = SpikeMonitor(neurons_e)
spike_mon_i = SpikeMonitor(neurons_i)
# set up network with monitors
network = Network(all_neurons, connections, spike_mon_e, spike_mon_i)
# run this network for some number of trials, every time with
for trial in range(trials):
# different initial values
all_neurons.V = vr + (vt - vr) * np.random.rand(len(all_neurons)) * 1.4
# Calibration phase
# run for the first half of the time to let the neurons adapt
network.run(t/2)
# reset monitors to start recording phase
spike_mon_i.reinit()
spike_mon_e.reinit()
# stimulation if duration is given
# define index variable for the stimulation possibility (is 0 for stimulation time=0)
t_stim_idx = int(t_stim / (winlen/ms))
if not(t_stim==0):
# Stimulation phase, increase input to subset of clusters
all_neurons[:400].mu += 0.07 * dv
network.run(t_stim * ms, report='text')
# set back to normal
all_neurons[:400].mu -= 0.07 * dv
# save data
all_data[realization, trial, :n_e, :t_stim_idx] = spikes_counter(spike_mon_e, winlen)
all_data[realization, trial, n_e:, :t_stim_idx] = spikes_counter(spike_mon_i, winlen)
# reset monitors
spike_mon_e.reinit()
spike_mon_i.reinit()
# run the remaining time of the simulation
network.run((t/2) - t_stim*ms, report='text')
# save results
all_data[realization, trial, :n_e, t_stim_idx:] = spikes_counter(spike_mon_e, winlen)
all_data[realization, trial, n_e:, t_stim_idx:] = spikes_counter(spike_mon_i, winlen)
if verbose:
plt.ion()
plt.figure()
raster_plot(spike_mon_e)
plt.title('Excitatory neurons')
spike_mon_e.reinit()
spike_mon_i.reinit()
return all_data
def _return_generator(self, simulation):
'''
Defines a simulation using a python generator.
'''
import brian
import numpy
print "Starting the simulation!"
print "Reseting the Brian Simulation object...",
brian.reinit(
) # This is only necessary when using the same enviroment over and over (like with iPython).
print "Done!"
clock_mult = self.step_size
brian.defaultclock.dt = clock_mult * brian.ms
print "Initial simulation time:", brian.defaultclock.t
print "Simulation step:", brian.defaultclock.dt
# Calls the user function with the Brian objects to be used in the simulation
Input_layer, Output_layer, pop_objects, syn_objects, monitors_objects = simulation(
brian.defaultclock, brian)
output_spikes = []
output_spikes_time = []
# Every time spikes occur at the SpikeMonitor related to the output neuron group, this function is called
def output_spikes_proc(spikes):
if len(spikes):
output_spikes.append(spikes.tolist(
)) # Saves the indexes of the neurons who generated spikes
output_spikes_time.append(
1000 * float(brian.defaultclock.t)
) # Converts and save the actual time in ms
# The spike monitor and all this code could be replaced by the .get_spikes() method of neurongroups.
# I need to check what is fastest way!
OutputMonitor = brian.SpikeMonitor(Output_layer,
record=False,
function=output_spikes_proc)
# Because it is not saving, the system is not going to run out of memory after a long simulation.
net = brian.Network(pop_objects + syn_objects + monitors_objects +
[OutputMonitor])
r = 0
while True:
spiketimes = yield # Receives the content from the Python generator method .send()
if spiketimes:
spiketimes = [
(i, brian.defaultclock.t) for i in spiketimes
] # The spikes received are inserted as the last simulated time
Input_layer.set_spiketimes(spiketimes)
net.run(clock_mult * brian.ms
) # I'm running one step each time this function is called
r += 1
yield (
r,
float(brian.defaultclock.t) * 1000,
numpy.array(Input_layer.get_spiketimes()).astype(
dtype=numpy.float
), # I'm doing this way to prove the spikes were received
output_spikes,
output_spikes_time
) # After the .send method, the generator executes this line and stops here
output_spikes = [
] # Cleans the output_spikes list so only the last spikes generated are sent
output_spikes_time = [
] # Cleans the output_spikes list so only the last spikes generated are sent