def simulate_spiking3(parameters):
x = Bunch(parameters)
tau_m_inv = 1./(x.tau_m*br.ms)
tau_e_inv = 1./(x.tau_e*br.ms)
tau_i_inv = 1./(x.tau_i*br.ms)
tau_a_inv = 1./(x.tau_a*br.ms)
GM = generative_model_data(x.Ndic, x.Ndim, x.k, positive_phi=x.positive_phi, positive_input=x.positive_input, seed=x.seed)
br.clear(all=True) # clears away all the brian objects from previous simulations.
eqs = '''
dvm/dt=((x.v_rest*br.mV-vm) + ge*(x.v_rev_e*br.mV-vm) + gi*(x.v_rev_i*br.mV-vm) + i_s)*tau_m_inv :br.mV
dge/dt = -ge*tau_e_inv :1
dgi/dt = -gi*tau_i_inv :1
da/dt = -a*tau_a_inv :br.Hz
i_s :br.mV
'''
simulation_clock = br.Clock(dt=x.dt*br.ms)
recording_clock = br.Clock(dt=1*br.ms)
P = br.NeuronGroup(x.Ndic, model=eqs, threshold=x.v_thr*br.mV, reset=x.v_reset*br.mV, refractory=x.t_refr*br.ms, clock=simulation_clock)
P.vm = (((np.random.random((x.Ndic))-0.5) * 0.5 * (x.v_rest-x.v_thr)) + x.v_rest) * br.mV
P.i_s = x.input_factor * GM["i_stim"] * br.mV
P.a = 0
G_exc = GM["G"].copy()
G_exc[G_exc>0]=0
G_exc = -1.*G_exc
G_inh = GM["G"].copy()
G_inh[G_inh<0]=0
Ce = br.Connection(P, P, 'ge')
Ce.connect(P, P, x.w_e*G_exc)
Ci = br.Connection(P, P, 'gi')
Ci.connect(P, P, x.w_i*G_inh)
Ca = br.IdentityConnection(P, P, 'a', weight=tau_a_inv)
M = br.SpikeMonitor(P)
SMs = []
SM_1 = br.StateMonitor(P, "vm", record=True, timestep=1, clock=recording_clock)
SM_2 = br.StateMonitor(P, "ge", record=True, timestep=1, clock=recording_clock)
SM_3 = br.StateMonitor(P, "gi", record=True, timestep=1, clock=recording_clock)
SM_4 = br.StateMonitor(P, "a", record=True, timestep=1, clock=recording_clock)
SM_5 = br.StateMonitor(P, "i_s", record=True, timestep=1, clock=recording_clock)
SMs.append(SM_1)
SMs.append(SM_2)
SMs.append(SM_3)
SMs.append(SM_4)
SMs.append(SM_5)
network = br.Network(P, Ce, Ci, Ca, M, *SMs)
# starting the simulation
network.run(x.t_end*br.ms)
return SMs, M, GM
def setup_sims(neuron_params, input_params, duration):
fin = input_params.get("fin")
fout = input_params.get("fout")
weight = input_params.get("weight")
num_inp = input_params.get("num_inp")
sync_configs = input_params.get("sync")
if fin is None:
fin = sl.tools.calibrate_frequencies(neuron_params,
N_in=num_inp, w_in=weight,
f_out=fout,
synchrony_conf=sync_configs)
brian.clear(True)
gc.collect()
brian.defaultclock.reinit()
neurons = NeuronGroup(N=len(sync_configs), **neuron_params)
simulation = Network(neurons)
input_groups = []
for idx, (inrate, (sync, jitter)) in enumerate(zip(fin, sync_configs)):
inp_grp = sl.tools.fast_synchronous_input_gen(num_inp,
inrate*Hz,
sync, jitter,
duration)
simulation.add(inp_grp)
inp_conn = Connection(inp_grp, neurons[idx], state='V', weight=weight)
input_groups.append(inp_grp)
simulation.add(inp_conn)
tracemon = StateMonitor(neurons, 'V', record=True)
spikemon = SpikeMonitor(neurons)
inputmons = [SpikeMonitor(igrp) for igrp in input_groups]
simulation.add(tracemon, spikemon, inputmons)
monitors = {"inputs": inputmons, "outputs": spikemon, "traces": tracemon}
return simulation, monitors
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 simulate_rate4(parameters):
x = Bunch(parameters)
GM = generative_model_data(x.Ndic, x.Ndim, x.k, positive=x.positive_GM, seed=x.seed)
tau_m_inv = 1./(x.tau_m*br.ms)
br.clear(all=True) # clears away all the brian objects from previous simulations.
def thresh_func(values, threshold, thr_type, thr_coeff, nonnegative):
vals = values.copy()
if not nonnegative:
vals[(vals<threshold) & (vals>-threshold)]=0.
if thr_type == "soft":
vals[(vals>threshold)] -= threshold
vals[(vals<-threshold)] += threshold
else:
vals[(vals<threshold)]=0.
if thr_type == "soft":
vals[(vals>threshold)] -= threshold
return thr_coeff * vals
eqs = '''
du/dt=(-u-li+i_s)*tau_m_inv :br.Hz
a :br.Hz
i_s :br.Hz
li :br.Hz
'''
simulation_clock = br.Clock(dt=x.dt*br.ms)
recording_clock = br.Clock(dt=1*br.ms)
P = br.NeuronGroup(x.Ndic, model=eqs, threshold=200000*br.Hz, clock=simulation_clock)
P.i_s = x.input_factor * GM["i_stim"]
P.a = 0
@br.network_operation(clock=simulation_clock, when="end")
def set_input(simulation_clock):
P.li = np.dot(GM["G"], P.a)
P.a = thresh_func(P.u, x.threshold, x.thr_type, x.thr_coeff, x.nonnegative)
SMs = []
SM_2 = br.StateMonitor(P, "a", record=True, timestep=1, clock=recording_clock)
SMs.append(SM_2)
network = br.Network(P, set_input, *SMs)
# starting the simulation
network.run(x.t_end*br.ms)
return 1.*SM_2[:][:,-1]/x.input_factor, GM
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
def simulate_rate5(parameters):
x = Bunch(parameters)
tau_m_inv = 1./(x.tau_m*br.ms)
br.clear(all=True) # clears away all the brian objects from previous simulations.
assert x.thresh_func, "you have to provide a threshold function"
eqs = '''
du/dt=(-u-li+i_s)*tau_m_inv :br.Hz
a :br.Hz
i_s :br.Hz
li :br.Hz
'''
simulation_clock = br.Clock(dt=x.dt*br.ms)
recording_clock = br.Clock(dt=1*br.ms)
P = br.NeuronGroup(x.Ndic, model=eqs, threshold=200000*br.Hz, clock=simulation_clock)
P.i_s = x.input_factor * x.GM["i_stim"]
P.a = 0
@br.network_operation(clock=simulation_clock, when="end")
def set_input(simulation_clock):
P.li = np.dot(x.GM["G"], P.a)
P.a = x.thresh_func(P.u, x.threshold)
SMs = []
SM_2 = br.StateMonitor(P, "a", record=True, timestep=1, clock=recording_clock)
SMs.append(SM_2)
network = br.Network(P, set_input, *SMs)
# starting the simulation
network.run(x.t_end*br.ms)
return 1.*SM_2[:]
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
def runsim(Nin, weight, fout, sync):
sim = Network()
clear(True)
gc.collect()
defaultclock.reinit()
duration = 5*second
lifeq = "dV/dt = -V/(10*ms) : volt"
nrndef = {"model": lifeq, "threshold": "V>=15*mV", "reset": "V=0*mV",
"refractory": 2*ms}
fin = load_or_calibrate(nrndef, Nin, weight, sync, fout,
Vth=15*mV, tau=10*ms)
# print("Calibrated frequencies:")
# print(", ".join(str(f) for f in fin))
inputgroups = []
connections = []
neurons = []
Nneurons = len(fin)
neurons = NeuronGroup(Nneurons, **nrndef)
for idx in range(Nneurons):
fin_i = fin[idx]
sync_i, sigma_i = sync[idx]
inputgrp = sl.tools.fast_synchronous_input_gen(Nin, fin_i,
sync_i, sigma_i,
duration)
defaultclock.reinit()
conn = Connection(inputgrp, neurons[idx], state="V", weight=weight)
inputgroups.append(inputgrp)
connections.append(conn)
voltagemon = StateMonitor(neurons, "V", record=True)
spikemon = SpikeMonitor(neurons, record=True)
sim.add(neurons, voltagemon, spikemon)
sim.add(*inputgroups)
sim.add(*connections)
print("Running {} {} {}".format(Nin, weight, fout))
sim.run(duration, report="stdout")
mnpss = []
allnpss = []
for idx in range(Nneurons):
vmon = voltagemon[idx]
smon = spikemon[idx]
# print("Desired firing rate: {}".format(fout))
# print("Actual firing rate: {}".format(len(smon)/duration))
if len(smon) > 0:
npss = sl.tools.npss(vmon, smon, 0*mV, 15*mV, 10*ms, 2*ms)
else:
npss = 0
mnpss.append(np.mean(npss))
allnpss.append(npss)
nrndeftuple = tuple(nrndef.items())
key = (nrndeftuple, Nin, weight, tuple(sync), fout, 15*mV, 10*ms)
save_data(key, allnpss)
imshape = (len(sigma), len(Sin))
imextent = (0, 1, 0, 4.0)
mnpss = np.reshape(mnpss, imshape, order="F")
plt.figure()
plt.imshow(mnpss, aspect="auto", origin="lower", extent=imextent,
interpolation="none", vmin=0, vmax=1)
cbar = plt.colorbar()
cbar.set_label("$\overline{M}$")
plt.xlabel("$S_{in}$")
plt.ylabel("$\sigma_{in}$ (ms)")
filename = "npss_{}_{}_{}".format(Nin, weight, fout).replace(".", "")
plt.savefig(filename+".pdf")
plt.savefig(filename+".png")
print("{} saved".format(filename))
voltages = voltagemon.values
spiketrains = spikemon.spiketimes.values()
pickle.dump({"voltages": voltages, "spiketrains": spiketrains},
open(filename+".pkl", 'w'))
return voltagemon, spikemon
def run_sim(ffExcInputMult=None, ffInhInputMult=None):
"""Run the cond-based LIF neuron simulation. Takes a few minutes to construct network and run
Parameters
----------
ffExcInputMult: scalar: FF input magnitude to E cells. multiply ffInputV by this value and connect to E cells
ffInhInputMult: scalar: FF input magnitude to I cells.
Returns
-------
outDict - spike times, records of continuous values from simulation
"""
# use helper to get input timecourses
(ffInputV, condAddV) = create_input_vectors(
doDebugPlot=False) # multiplied by scalars below
# setup initial state
stT = time.time()
brian.set_global_preferences(usecodegen=True)
brian.set_global_preferences(useweave=True)
brian.set_global_preferences(usecodegenweave=True)
brian.clear(erase=True, all=True)
brian.reinit_default_clock()
clk = brian.Clock(dt=0.05 * ms)
################
# create neurons, define connections
neurNetwork = brian.NeuronGroup(nNet,
model=eqs,
threshold=vthresh,
reset=vrest,
refractory=absRefractoryMs * msecond,
order=1,
compile=True,
freeze=False,
clock=clk)
# create neuron pools
neurCE = neurNetwork.subgroup(nExc)
neurCI = neurNetwork.subgroup(nInh)
connCE = brian.Connection(neurCE, neurNetwork, 'ge')
connCI = brian.Connection(neurCI, neurNetwork, 'gi')
print('n cells: %d, nE,I %d,%d, %s, absRefractoryMs: %d' %
(nNet, nExc, nInh, repr(clk), absRefractoryMs))
# connect the network to itself
connCE.connect_random(neurCE,
neurNetwork,
internalSparseness,
weight=connENetWeight)
connCI.connect_random(neurCI,
neurNetwork,
internalSparseness,
weight=connINetWeight)
# connect inputs that change spont rate
assert (
spontAddRate <= 0
), 'Spont add rate should be negative - convention: neg, excite inhibitory cells'
spontAddNInpSyn = 100
nTotalSpontNeurons = (spontAddNInpSyn * nInh * 0.02)
neurSpont = brian.PoissonGroup(nTotalSpontNeurons,
-1.0 * spontAddRate * Hz)
connCSpont = brian.Connection(neurSpont, neurCI, 'ge')
connCSpont.connect_random(
p=spontAddNInpSyn * 1.0 / nTotalSpontNeurons,
weight=connENetWeight, # match internal excitatory strengths
fixed=True)
# connect the feedforward visual (poisson) inputs to excitatory cells (ff E)
ffExcInputNInpSyn = 100
nTotalFfNeurons = (ffExcInputNInpSyn * ffExcInputNTargs * 0.02
) # one pop of input cells for both E and I FF
_ffExcInputV = ffExcInputMult * np.abs(a_(ffInputV).copy())
assert (np.all(
_ffExcInputV >= 0)), 'Negative FF rates are rectified to zero'
neurFfExcInput = brian.PoissonGroup(
nTotalFfNeurons, lambda t: _ffExcInputV[int(t * 1000)] * Hz)
connCFfExcInput = brian.Connection(neurFfExcInput, neurNetwork, 'ge')
connCFfExcInput.connect_random(neurFfExcInput,
neurCE[0:ffExcInputNTargs],
ffExcInputNInpSyn * 1.0 / nTotalFfNeurons,
weight=connENetWeight,
fixed=True)
# connect the feedforward visual (poisson) inputs to inhibitory cells (ff I)
ffInhInputNInpSyn = 100
_ffInhInputV = ffInhInputMult * np.abs(ffInputV.copy())
assert (np.all(
_ffInhInputV >= 0)), 'Negative FF rates are rectified to zero'
neurFfInhInput = brian.PoissonGroup(
nTotalFfNeurons, lambda t: _ffInhInputV[int(t * 1000)] * Hz)
connCFfInhInput = brian.Connection(neurFfInhInput, neurNetwork, 'ge')
connCFfInhInput.connect_random(
neurFfInhInput,
neurCI[0:ffInhInputNTargs],
ffInhInputNInpSyn * 1.0 / nTotalFfNeurons, # sparseness
weight=connENetWeight,
fixed=True)
# connect added step (ChR2) conductance to excitatory cells
condAddAmp = 4.0
gAdd = brian.TimedArray(condAddAmp * condAddV, dt=1 * ms)
print('Adding conductance for %d cells (can be slow): ' %
len(condAddNeurNs),
end=' ')
for (iN, tN) in enumerate(condAddNeurNs):
neurCE[tN].gAdd = gAdd
print('done')
# Initialize using some randomness so all neurons don't start in same state.
# Alternative: initialize with constant values, give net extra 100-300ms to evolve from initial state.
neurNetwork.v = (brian.randn(1) * 5.0 - 65) * mvolt
neurNetwork.ge = brian.randn(nNet) * 1.5 + 4
neurNetwork.gi = brian.randn(nNet) * 12 + 20
# Record continuous variables and spikes
monSTarg = brian.SpikeMonitor(neurNetwork)
if contRecNs is not None:
contRecClock = brian.Clock(dt=contRecStepMs * ms)
monVTarg = brian.StateMonitor(neurNetwork,
'v',
record=contRecNs,
clock=contRecClock)
monGETarg = brian.StateMonitor(neurNetwork,
'ge',
record=contRecNs,
clock=contRecClock)
monGAddTarg = brian.StateMonitor(neurNetwork,
'gAdd',
record=contRecNs,
clock=contRecClock)
monGITarg = brian.StateMonitor(neurNetwork,
'gi',
record=contRecNs,
clock=contRecClock)
# construct brian.Network before running (so brian explicitly knows what to update during run)
netL = [
neurNetwork, connCE, connCI, monSTarg, neurFfExcInput, connCFfExcInput,
neurFfInhInput, connCFfInhInput, neurSpont, connCSpont
]
if contRecNs is not None:
# noinspection PyUnboundLocalVariable
netL.append([monVTarg, monGETarg, monGAddTarg,
monGITarg]) # cont monitors
net = brian.Network(netL)
print("Network construction time: %3.1f seconds" % (time.time() - stT))
# run
print("Simulation running...")
sys.stdout.flush()
start_time = time.time()
net.run(simRunTimeS * second, report='text', report_period=30.0 * second)
durationS = time.time() - start_time
print("Simulation time: %3.1f seconds" % durationS)
outNTC = collections.namedtuple(
'outNTC',
'vm ge gadd gi clockDtS clockStartS clockEndS spiketimes contRecNs')
outNTC.__new__.__defaults__ = (None, ) * len(
outNTC._fields) # default to None
outNT = outNTC(clockDtS=float(monSTarg.clock.dt),
clockStartS=float(monSTarg.clock.start),
clockEndS=float(monSTarg.clock.end),
spiketimes=a_(monSTarg.spiketimes.values(), dtype='O'),
contRecNs=contRecNs)
if contRecNs is not None:
outNT = outNT._replace(vm=monVTarg.values,
ge=monGETarg.values,
gadd=monGAddTarg.values,
gi=monGITarg.values)
return outNT
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 runsim(fin):
clear(True)
gc.collect()
defaultclock.reinit()
weight = 0.16*mV
sim = Network()
duration = 2.0*second
Vth = 15*mV
Vreset = 13.65*mV
trefr = 2*ms
lifeq = """
dV/dt = -V/(10*ms) : volt
Vth : volt
"""
nrndef = {"model": lifeq, "threshold": "V>=Vth", "reset": "V=Vreset",
"refractory": 0.1*ms}
inputgroups = []
connections = []
neurons = []
Nneurons = len(fin)
neurons = NeuronGroup(Nneurons, **nrndef)
neurons.V = 0*mV
neurons.Vth = 15*mV
for idx in range(Nneurons):
fin_i = fin[idx]*Hz
inputgrp = PoissonGroup(50, fin_i)
conn = Connection(inputgrp, neurons[idx], state="V", weight=weight)
inputgroups.append(inputgrp)
connections.append(conn)
voltagemon = StateMonitor(neurons, "V", record=True)
spikemon = SpikeMonitor(neurons, record=True)
sim.add(neurons, voltagemon, spikemon)
sim.add(*inputgroups)
sim.add(*connections)
@network_operation
def refractory_threshold(clock):
for idx in range(Nneurons):
if (len(spikemon.spiketimes[idx])
and clock.t < spikemon.spiketimes[idx][-1]*second+trefr):
neurons.Vth[idx] = 100*mV
else:
neurons.Vth[idx] = Vth
sim.add(refractory_threshold)
print("Running simulation of {} neurons for {} s".format(Nneurons, duration))
sim.run(duration, report="stdout")
mnpss = []
allnpss = []
outisi = []
for idx in range(Nneurons):
vmon = voltagemon[idx]
smon = spikemon[idx]
if not len(smon):
continue
outisi.append(duration*1000/len(smon))
if len(smon) > 0:
npss = sl.tools.npss(vmon, smon, 0*mV, 15*mV, 10*ms, 2*ms)
else:
npss = 0
mnpss.append(np.mean(npss))
allnpss.append(npss)
return outisi, mnpss
def tearDownClass(cls):
clear(True, True)
reload(brian)
def tearDownClass(cls):
clear(True, True)
reload(brian)
def fft_std(delta_u, run_num, new_connectivity, osc, rep):
#bn.seed(int(time.time()))
bn.reinit_default_clock()
#bn.seed(1412958308+2)
bn.defaultclock.dt = 0.5 * bn.ms
#==============================================================================
# Define constants for the model.
#==============================================================================
fft_file = './std_fft_p20_'
rate_file = './std_rate_p20_'
print delta_u
print run_num
print new_connectivity
print rep
if osc:
T = 5.5 * bn.second
else:
T = 2.5 * bn.second
n_tsteps = T / bn.defaultclock.dt
fft_start = 0.5 * bn.second / bn.defaultclock.dt # Time window for the FFT computation
ro = 1.2 * bn.Hz
SEE1 = 1.0
SEE2 = 1.0
qee1 = 1.00 # Fraction of NMDA receptors for e to e connections
qee2 = 0.00
qie1 = 1.00 # Fraction of NMDA receptors for e to i connections
qie2 = 0.00
uee1 = 0.2 - delta_u
uee2 = 0.2 + delta_u
uie1 = 0.2
uie2 = 0.2
trec1 = 1000.0 * bn.ms
trec2 = 1000.0 * bn.ms
k = 0.65
#Jeo_const = 1.0#*bn.mV # Base strength of o (external) to e connections
Ne = 3200 # number of excitatory neurons
Ni = 800 # number of inhibitory neurons
No = 20000 # number of external neurons
N = Ne + Ni
pcon = 0.2 # probability of connection
Jee = 10.0 / (Ne * pcon)
Jie = 10.0 / (Ne * pcon)
Jii = k * 10.0 / (Ni * pcon)
Jei = k * 10.0 / (Ni * pcon)
Jeo = 1.0
El = -60.0 * bn.mV # leak reversal potential
Vreset = -52.0 * bn.mV # reversal potential
Vthresh = -40.0 * bn.mV # spiking threshold
tref = 2.0 * bn.ms # refractory period
te = 20.0 * bn.ms # membrane time constant of excitatory neurons
ti = 10.0 * bn.ms # membrane time constant of inhibitory neruons
tee_ampa = 10.0 * bn.ms # time const of ampa currents at excitatory neurons
tee_nmda = 100.0 * bn.ms # time const of nmda currents at excitatory neurons
tie_ampa = 10.0 * bn.ms # time const of ampa currents at inhibitory neurons
tie_nmda = 100.0 * bn.ms # time const of nmda currents at inhibitory neurons
tii_gaba = 10.0 * bn.ms # time const of GABA currents at inhibitory neurons
tei_gaba = 10.0 * bn.ms # time const of GABA currents at excitatory neurons
teo_input = 100.0 * bn.ms
#==============================================================================
# Define model structure
#==============================================================================
model = '''
dV/dt = (-(V-El)+J_ampa1*I_ampa1+J_nmda1*I_nmda1+J_ampa2*I_ampa2+J_nmda2*I_nmda2-J_gaba*I_gaba+J_input*I_input+eta)/tm : bn.volt
dI_ampa1/dt = -I_ampa1/t_ampa : bn.volt
dI_nmda1/dt = -I_nmda1/t_nmda : bn.volt
dI_ampa2/dt = -I_ampa2/t_ampa : bn.volt
dI_nmda2/dt = -I_nmda2/t_nmda : bn.volt
dI_gaba/dt = -I_gaba/t_gaba : bn.volt
dI_input/dt = (-I_input+mu)/t_input : bn.volt
dx1/dt = (1-x1)/t1_rec : 1
dx2/dt = (1-x2)/t2_rec : 1
u1 : 1
t1_rec : bn.second
u2 : 1
t2_rec : bn.second
mu : bn.volt
eta : bn.volt
J_ampa1 : 1
J_nmda1 : 1
J_ampa2 : 1
J_nmda2 : 1
J_gaba : 1
J_input : 1
tm : bn.second
t_ampa : bn.second
t_nmda : bn.second
t_gaba : bn.second
t_input : bn.second
'''
P_reset = "V=-52*bn.mV;x1+=-u1*x1;x2+=-u2*x2"
Se_model = '''
we_ampa1 : bn.volt
we_nmda1 : bn.volt
we_ampa2 : bn.volt
we_nmda2 : bn.volt
'''
Se_pre = ('I_ampa1 += x1_pre*we_ampa1', 'I_nmda1 += x1_pre*we_nmda1',
'I_ampa2 += x2_pre*we_ampa2', 'I_nmda2 += x2_pre*we_nmda2')
Si_model = '''
wi_gaba : bn.volt
'''
Si_pre = 'I_gaba += wi_gaba'
So_model = '''
wo_input : bn.volt
'''
So_pre = 'I_input += wo_input'
#==============================================================================
# Define populations
#==============================================================================
P = bn.NeuronGroup(N,
model,
threshold=Vthresh,
reset=P_reset,
refractory=tref)
Pe = P[0:Ne]
Pe.tm = te
Pe.t_ampa = tee_ampa
Pe.t_nmda = tee_nmda
Pe.t_gaba = tei_gaba
Pe.t_input = teo_input
Pe.I_ampa1 = 0 * bn.mV
Pe.I_nmda1 = 0 * bn.mV
Pe.I_ampa2 = 0 * bn.mV
Pe.I_nmda2 = 0 * bn.mV
Pe.I_gaba = 0 * bn.mV
Pe.I_input = 0 * bn.mV
Pe.V = (np.random.rand(Pe.V.size) * 12 - 52) * bn.mV
Pe.x1 = 1.0
Pe.x2 = 1.0
Pe.u1 = uee1
Pe.u2 = uee2
Pe.t1_rec = trec1
Pe.t2_rec = trec2
Pi = P[Ne:(Ne + Ni)]
Pi.tm = ti
Pi.t_ampa = tie_ampa
Pi.t_nmda = tie_nmda
Pi.t_gaba = tii_gaba
Pi.t_input = teo_input
Pi.I_ampa1 = 0 * bn.mV
Pi.I_nmda1 = 0 * bn.mV
Pi.I_ampa2 = 0 * bn.mV
Pi.I_nmda2 = 0 * bn.mV
Pi.I_gaba = 0 * bn.mV
Pi.I_input = 0 * bn.mV
Pi.V = (np.random.rand(Pi.V.size) * 12 - 52) * bn.mV
Pi.x1 = 1.0
Pi.x2 = 1.0
Pi.u1 = 0.0
Pi.u2 = 0.0
Pi.t1_rec = 1.0
Pi.t2_rec = 1.0
Pe.J_ampa1 = Jee * (1 - qee1) #*SEE1
Pe.J_nmda1 = Jee * qee1 #*SEE1
Pe.J_ampa2 = Jee * (1 - qee2) #*SEE2
Pe.J_nmda2 = Jee * qee2 #*SEE2
Pi.J_ampa1 = Jie * (1 - qie2) #*SEE2
Pi.J_nmda1 = Jie * qie2 #*SEE2
Pi.J_ampa2 = Jie * (1 - qie1) #*SEE1
Pi.J_nmda2 = Jie * qie1 #*SEE1
Pe.J_gaba = Jei
Pi.J_gaba = Jii
Pe.J_input = Jeo
Pi.J_input = Jeo
#==============================================================================
# Define inputs
#==============================================================================
if osc:
Pe.mu = 12.0 * bn.mV
holder = np.zeros((n_tsteps, ))
t_freq = np.linspace(0, 10, n_tsteps)
fo = 0.2 # Smallest frequency in the signal
fe = 10.0 # Largest frequency in the signal
F = int(fe / 0.2)
for m in range(1, F + 1):
holder = holder + np.cos(2 * np.pi * m * fo * t_freq - m *
(m - 1) * np.pi / F)
holder = holder / np.max(holder)
Pe.eta = bn.TimedArray(0.0 * bn.mV * holder) #, dt=0.5*bn.ms)
Background_eo = bn.PoissonInput(Pe,
N=1000,
rate=1.05 * bn.Hz,
weight=0.2 * bn.mV,
state='I_input')
Background_io = bn.PoissonInput(Pi,
N=1000,
rate=1.0 * bn.Hz,
weight=0.2 * bn.mV,
state='I_input')
Pi.mu = 0 * bn.mV
Pi.eta = 0 * bn.mV #, dt=0.5*bn.ms)
Po = bn.PoissonGroup(No, rates=0 * bn.Hz)
else:
Background_eo = bn.PoissonInput(Pe,
N=1000,
rate=1.05 * bn.Hz,
weight=0.2 * bn.mV,
state='I_input')
Background_io = bn.PoissonInput(Pi,
N=1000,
rate=1.0 * bn.Hz,
weight=0.2 * bn.mV,
state='I_input')
holder_pe = np.zeros((n_tsteps, ))
time_steps = np.linspace(0, T / bn.second, n_tsteps)
holder_pe[time_steps < 0.5] = 0.0 * bn.mV
holder_pe[time_steps >= 0.5] = 6.0 * bn.mV #25
holder_pe[time_steps > 1.5] = 0.0 * bn.mV #25
Pe.mu = bn.TimedArray(holder_pe)
def firing_function(t, ro):
if t > 0.5 * bn.second and t < 3.5 * bn.second:
return 0.0 * bn.Hz
else:
return 0.0 * bn.Hz
Pe.eta = 0 * bn.mV #, dt=0.5*bn.ms)
Pi.mu = 0.0 * bn.mV
Pi.eta = 0 * bn.mV #, dt=0.5*bn.ms)
Po = bn.PoissonGroup(No, rates=lambda t: firing_function(t, ro))
#==============================================================================
# Define synapses
#==============================================================================
See1 = bn.Synapses(Pe, Pe, model=Se_model, pre=Se_pre)
See2 = bn.Synapses(Pe, Pe, model=Se_model, pre=Se_pre)
Sie1 = bn.Synapses(Pe, Pi, model=Se_model, pre=Se_pre)
Sie2 = bn.Synapses(Pe, Pi, model=Se_model, pre=Se_pre)
Sei = bn.Synapses(Pi, Pe, model=Si_model, pre=Si_pre)
Sii = bn.Synapses(Pi, Pi, model=Si_model, pre=Si_pre)
Seo = bn.Synapses(Po, Pe, model=So_model, pre=So_pre)
#==============================================================================
# Define random connections
#==============================================================================
if new_connectivity:
See1.connect_random(Pe, Pe, sparseness=pcon / 2.0)
See2.connect_random(Pe, Pe, sparseness=pcon / 2.0)
Sie1.connect_random(Pe, Pi, sparseness=pcon / 2.0)
Sie2.connect_random(Pe, Pi, sparseness=pcon / 2.0)
Sii.connect_random(Pi, Pi, sparseness=pcon)
Sei.connect_random(Pi, Pe, sparseness=pcon)
Seo.connect_random(Po, Pe, sparseness=pcon)
print 'Saving'
See1.save_connectivity('./See1_connections_std_saver_p20_' +
str(run_num))
See2.save_connectivity('./See2_connections_std_saver_p20_' +
str(run_num))
Sie1.save_connectivity('./Sie1_connections_std_saver_p20_' +
str(run_num))
Sie2.save_connectivity('./Sie2_connections_std_saver_p20_' +
str(run_num))
Sii.save_connectivity('./Sii_connections_std_saver_p20_' +
str(run_num))
Sei.save_connectivity('./Sei_connections_std_saver_p20_' +
str(run_num))
Seo.save_connectivity('./Seo_connections_std_saver_p20_' +
str(run_num))
else:
print 'Loading'
See1.load_connectivity('./See1_connections_std_saver_p20_' +
str(run_num))
See2.load_connectivity('./See2_connections_std_saver_p20_' +
str(run_num))
Sie1.load_connectivity('./Sie1_connections_std_saver_p20_' +
str(run_num))
Sie2.load_connectivity('./Sie2_connections_std_saver_p20_' +
str(run_num))
Sii.load_connectivity('./Sii_connections_std_saver_p20_' +
str(run_num))
Sei.load_connectivity('./Sei_connections_std_saver_p20_' +
str(run_num))
Seo.load_connectivity('./Seo_connections_std_saver_p20_' +
str(run_num))
See1.we_ampa1 = SEE1 * 1.0 * bn.mV / tee_ampa
See1.we_nmda1 = SEE1 * 1.0 * bn.mV / tee_nmda
See1.we_ampa2 = 0.0 * bn.mV / tee_ampa
See1.we_nmda2 = 0.0 * bn.mV / tee_nmda
See2.we_ampa1 = 0.0 * bn.mV / tee_ampa
See2.we_nmda1 = 0.0 * bn.mV / tee_nmda
See2.we_ampa2 = SEE2 * 1.0 * bn.mV / tee_ampa
See2.we_nmda2 = SEE2 * 1.0 * bn.mV / tee_nmda
Sie1.we_ampa1 = 0.0 * bn.mV / tie_ampa
Sie1.we_nmda1 = 0.0 * bn.mV / tie_nmda
Sie1.we_ampa2 = SEE1 * 1.0 * bn.mV / tie_ampa
Sie1.we_nmda2 = SEE1 * 1.0 * bn.mV / tie_nmda
Sie2.we_ampa1 = SEE2 * 1.0 * bn.mV / tie_ampa
Sie2.we_nmda1 = SEE2 * 1.0 * bn.mV / tie_nmda
Sie2.we_ampa2 = 0.0 * bn.mV / tie_ampa
Sie2.we_nmda2 = 0.0 * bn.mV / tie_nmda
Sei.wi_gaba = 1.0 * bn.mV / tei_gaba
Sii.wi_gaba = 1.0 * bn.mV / tii_gaba
Seo.wo_input = 1.0 * bn.mV / teo_input
#==============================================================================
# Define monitors
#==============================================================================
Pe_mon_V = bn.StateMonitor(Pe, 'V', timestep=10, record=True)
Pe_mon_eta = bn.StateMonitor(Pe, 'eta', timestep=1, record=True)
Pe_mon_ampa1 = bn.StateMonitor(Pe, 'I_ampa1', timestep=1, record=True)
Pe_mon_nmda1 = bn.StateMonitor(Pe, 'I_nmda1', timestep=1, record=True)
Pe_mon_ampa2 = bn.StateMonitor(Pe, 'I_ampa2', timestep=1, record=True)
Pe_mon_nmda2 = bn.StateMonitor(Pe, 'I_nmda2', timestep=1, record=True)
Pe_mon_gaba = bn.StateMonitor(Pe, 'I_gaba', timestep=1, record=True)
Pe_mon_input = bn.StateMonitor(Pe, 'I_input', timestep=10, record=True)
See1_mon_x = bn.StateMonitor(Pe, 'x1', timestep=10, record=True)
See2_mon_x = bn.StateMonitor(Pe, 'x2', timestep=10, record=True)
Pe_ratemon = bn.PopulationRateMonitor(Pe, bin=10.0 * bn.ms)
Pi_ratemon = bn.PopulationRateMonitor(Pi, bin=10.0 * bn.ms)
#==============================================================================
# Run model
#==============================================================================
timer = 0 * bn.second
t_start = time.time()
bn.run(T, report='graphical')
timer = timer + T
print '-------------------------------------------------------'
print 'Time is ' + str(timer) + ' seconds'
t_end = time.time()
print 'Time to compute last ' +str(T)+' seconds is: ' + \
str(t_end - t_start) + ' seconds'
print '-------------------------------------------------------\n'
Pe_mon_ampa1_vals = Pe.J_ampa1[0] * np.mean(Pe_mon_ampa1.values.T, axis=1)
Pe_mon_nmda1_vals = Pe.J_nmda1[0] * np.mean(Pe_mon_nmda1.values.T, axis=1)
Pe_mon_ampa2_vals = Pe.J_ampa2[0] * np.mean(Pe_mon_ampa2.values.T, axis=1)
Pe_mon_nmda2_vals = Pe.J_nmda2[0] * np.mean(Pe_mon_nmda2.values.T, axis=1)
Pe_mon_ampa_vals = Pe_mon_ampa1_vals + Pe_mon_ampa2_vals
Pe_mon_nmda_vals = Pe_mon_nmda1_vals + Pe_mon_nmda2_vals
Pe_mon_gaba_vals = Pe.J_gaba[0] * np.mean(Pe_mon_gaba.values.T, axis=1)
Pe_mon_input_vals = Pe.J_input[0] * np.mean(Pe_mon_input.values.T, axis=1)
Pe_mon_V_vals = np.mean(Pe_mon_V.values.T, axis=1)
Pe_mon_all_vals = Pe_mon_ampa_vals + Pe_mon_nmda_vals - Pe_mon_gaba_vals
See1_mon_x_vals = np.mean(See1_mon_x.values.T, axis=1)
See2_mon_x_vals = np.mean(See2_mon_x.values.T, axis=1)
#==============================================================================
# Save into a Matlab file
#==============================================================================
if osc:
Pe_output = Pe.J_ampa1[0]*Pe_mon_ampa1.values+Pe.J_nmda1[0]*Pe_mon_nmda1.values + \
Pe.J_ampa2[0]*Pe_mon_ampa2.values+Pe.J_nmda2[0]*Pe_mon_nmda2.values-Pe.J_gaba[0]*Pe_mon_gaba.values
Pe_output = Pe_output[:, fft_start:, ]
Pe_V = Pe_mon_V.values[:, fft_start:, ]
Pe_glut = Pe.J_ampa1[0]*Pe_mon_ampa1.values+Pe.J_nmda1[0]*Pe_mon_nmda1.values + \
Pe.J_ampa2[0]*Pe_mon_ampa2.values+Pe.J_nmda2[0]*Pe_mon_nmda2.values
Pe_glut = Pe_glut[:, fft_start:, ]
Pe_gaba = Pe.J_gaba[0] * Pe_mon_gaba.values
Pe_gaba = Pe_gaba[:, fft_start:, ]
Pe_input = Pe_mon_eta[:, fft_start:, ]
T_step = bn.defaultclock.dt
holder = {
'Pe_output': Pe_output,
'Pe_input': Pe_input,
'Pe_V': Pe_V,
'Pe_glut': Pe_glut,
'Pe_gaba': Pe_gaba,
'T_step': T_step
}
scipy.io.savemat(fft_file + 'delta_u' + str(delta_u) + '_' + str(rep),
mdict=holder)
else:
holder = {
'Pe_rate': Pe_ratemon.rate,
'Pe_time': Pe_ratemon.times,
'uee1': uee1,
'uee2': uee2,
'uie1': uie1,
'uie2': uie2
}
scipy.io.savemat(rate_file + 'delta_q_' + str(delta_u) + '_' +
str(run_num) + 'rep' + str(rep),
mdict=holder)
bn.clear(erase=True, all=True)
def tearDownClass(BrianMonitorTest):
clear(True, True)
reload(brian)
import random
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