def setupProjection_PN_KC(pn_population,kc_population):
connectionList = list() # Connection list between PN and KC
for each_kc_cell in xrange(NUM_KC_CELLS):
count = 6
selectedCells = random.sample(xrange(NUM_PN_CELLS),count)
for each_pn_cell in selectedCells:
single_coonection = (each_pn_cell,each_kc_cell)
connectionList.append(single_coonection)
pnkcProjection = spynnaker.Projection(pn_population,
kc_population,
spynnaker.FromListConnector(connectionList),
spynnaker.StaticSynapse(weight=WEIGHT_PN_KC, delay=DELAY_PN_KC))
return pnkcProjection
def setupProjection_PN_KC(pn_population, kc_population):
WEIGHT_PN_KC = 5
DELAY_PN_KC = 1.0
NUM_KC_CELLS = 2000
NUM_PN_CELLS = 784
connectionList = list() # Build up a connection list between PN and KC
for each_kc_cell in xrange(NUM_KC_CELLS):
count = random.randint(
5, 7) # How many pn_cells will connect to this kc_cell
selectedCells = random.sample(
xrange(NUM_PN_CELLS), count) # Index of randomly selected PN cells
for each_pn_cell in selectedCells:
single_coonection = (each_pn_cell, each_kc_cell)
connectionList.append(single_coonection)
pnkcProjection = spynnaker.Projection(
pn_population, kc_population,
spynnaker.FromListConnector(connectionList),
spynnaker.StaticSynapse(weight=WEIGHT_PN_KC, delay=DELAY_PN_KC))
return pnkcProjection
try:
import pyNN.spiNNaker as p
except Exception as e:
import spynnaker8 as p
# set up the tools
p.setup(timestep=1.0, min_delay=1.0, max_delay=32.0)
# set up the virtual chip coordinates for the motor
connected_chip_coords = {'x': 0, 'y': 0}
link = 4
populations = list()
projections = list()
input_population = p.Population(6, p.SpikeSourcePoisson(rate=10))
control_population = p.Population(6, p.IF_curr_exp())
motor_device = p.Population(
6, p.external_devices.MunichMotorDevice(spinnaker_link_id=0))
p.Projection(input_population,
control_population,
p.OneToOneConnector(),
synapse_type=p.StaticSynapse(weight=5.0))
p.external_devices.activate_live_output_to(control_population, motor_device)
p.run(1000)
p.end()
# declare python code when received spikes for a timer tick
def receive_spikes(label, time, neuron_ids):
for neuron_id in neuron_ids:
print("Received spike at time {} from {}-{}"
"".format(time, label, neuron_id))
p.setup(timestep=1.0)
p1 = p.Population(1, p.IF_curr_exp(), label="pop_1")
input_injector = p.Population(1, p.external_devices.SpikeInjector(),
label=INJECTOR_LABEL)
# set up python live spike connection
live_spikes_connection = p.external_devices.SpynnakerLiveSpikesConnection(
receive_labels=[RECEIVER_LABEL])
# register python receiver with live spike connection
live_spikes_connection.add_receive_callback(RECEIVER_LABEL, receive_spikes)
input_proj = p.Projection(input, p1, p.OneToOneConnector(),
p.StaticSynapse(weight=5, delay=3))
p1.record(["spikes", "v"])
p.run(50)
neo = p1.get_data(["spikes", "v"])
spikes = neo.segments[0].spiketrains
print(spikes)
v = neo.segments[0].filter(name='v')[0]
print(v)
'tau_syn_I': 2.5,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -55.0
}
neurons = sim.Population(100, sim.IF_cond_exp(**cell_params))
inputs = sim.Population(100, sim.SpikeSourcePoisson(rate=0.0))
# set input firing rates as a linear function of cell index
input_firing_rates = np.linspace(0.0, 1000.0, num=inputs.size)
inputs.set(rate=input_firing_rates)
# create one-to-one connections
wiring = sim.OneToOneConnector()
static_synapse = sim.StaticSynapse(weight=0.1, delay=2.0)
connections = sim.Projection(inputs, neurons, wiring, static_synapse)
# configure recording
neurons.record('spikes')
# run simulation
sim_duration = 10.0 # seconds
sim.run(sim_duration * 1000.0)
# retrieve recorded data
spike_counts = neurons.get_spike_counts()
print(spike_counts)
output_firing_rates = np.array(
[value for (key, value) in sorted(spike_counts.items())]) / sim_duration
sim.set_number_of_neurons_per_core(sim.IF_curr_exp, 100)
G1_1 = sim.Population(1, sim.IF_curr_exp(**cell_params_lif), label="G1_1")
G2_2 = sim.Population(10, sim.IF_curr_exp(**cell_params_lif), label="G2_2")
GEN1_3 = sim.Population(
1, sim.SpikeSourceArray(spike_times=[1, 2, 4, 6, 7], label="GEN1_3"))
G4_4 = sim.Population(1, sim.IF_curr_exp(**cell_params_lif), label="G4_4")
Dani_5 = sim.Population(1, sim.IF_curr_exp(**cell_params_lif), label="Dani_5")
G5_6 = sim.Population(1, sim.IF_curr_exp(**cell_params_lif), label="G5_6")
G6_7 = sim.Population(1, sim.IF_curr_exp(**cell_params_lif), label="G6_7")
input_GEN1_3G1_1 = sim.Projection(GEN1_3,
G1_1,
sim.OneToOneConnector(),
synapse_type=sim.StaticSynapse(weight=1.25,
delay=0))
input_G2_2G1_1 = sim.Projection(G2_2,
G1_1,
sim.OneToOneConnector(),
synapse_type=sim.StaticSynapse(weight=0.8,
delay=0))
input_G4_4G1_1 = sim.Projection(G4_4,
G1_1,
sim.OneToOneConnector(),
synapse_type=sim.StaticSynapse(weight=1.7,
delay=0))
input_Dani_5G1_1 = sim.Projection(Dani_5,
G1_1,
sim.OneToOneConnector(),
synapse_type=sim.StaticSynapse(weight=1.3,
delay=0))
label=label)
def get_outgoing_partition_constraints(self, partition):
return [
FixedKeyAndMaskConstraint([BaseKeyAndMask(0x12340000, 0xFFFF0000)])
]
class MySpiNNakerLinkDeviceDataHolder(DataHolder):
def __init__(self, spinnaker_link_id, label=None):
DataHolder.__init__(self, {
"spinnaker_link_id": spinnaker_link_id,
"label": label
})
@staticmethod
def build_model():
return MySpiNNakerLinkDevice
p.setup(1.0)
pop = p.Population(1, p.IF_curr_exp())
device = p.Population(1, MySpiNNakerLinkDeviceDataHolder(spinnaker_link_id=0))
p.Projection(device, pop, p.OneToOneConnector(), p.StaticSynapse(weight=1.0))
p.run(100)
p.end()
import pyNN.spiNNaker as sim import pyNN.utility.plotting as plot import matplotlib.pyplot as plt sim.setup(timestep=1.0) sim.set_number_of_neurons_per_core(sim.IF_curr_exp, 100) # Define Input neuron input = sim.Population(1, sim.SpikeSourcePoisson(), label="Input") # Define output neuron pop_1 = sim.Population(1,sim.IF_curr_exp(),label="pop_1") # Connect Input Neuron with Output neuron input_proj=sim.Projection(input,pop_1,sim.OneToOneConnector(),synapse_type=sim.StaticSynapse(weight=5,delay=1)) pop_1.record(["spikes","v"]) input.record(["spikes"]) simtime = 30000 sim.run(simtime) # Input neuron neo_input=input.get_data(variables=["spikes"]) spikes_input=neo_input.segments[0].spiketrains print(spikes_input) print( len(spikes_input[0]) ) # Pop1 neuron neo_pop1=pop_1.get_data(variables=["spikes","v"])
'tau_syn_E': 50, 'tau_syn_I': 5, 'v_reset': -70, 'v_rest': -65, 'v_thresh': -55 } sim.set_number_of_neurons_per_core(sim.IF_curr_exp, 100) GEN1_1= sim.Population(1,simSpikeSourceArray(spike_times=[0,8], label="GEN1_1") G1_2= sim.Population(1,sim.IF_curr_exp(**cell_params_lif), label="G1_2") G3_4= sim.Population(1,sim.IF_curr_exp(**cell_params_lif), label="G3_4") G4_5= sim.Population(1,sim.IF_curr_exp(**cell_params_lif), label="G4_5") G2_6= sim.Population(1,sim.IF_curr_exp(**cell_params_lif), label="G2_6") input_GEN1_1G1_2=sim.Projection(GEN1_1,G1_2, sim.OneToOneConnector(), synapse_type=sim.StaticSynapse(weight=1.25, delay=0)) input_G4_5G1_2=sim.Projection(G4_5,G1_2, sim.OneToOneConnector(), synapse_type=sim.StaticSynapse(weight=0.8, delay=0)) input_G4_5G3_4=sim.Projection(G4_5,G3_4, sim.OneToOneConnector(), synapse_type=sim.StaticSynapse(weight=0.9, delay=0)) input_G2_6G4_5=sim.Projection(G2_6,G4_5, sim.OneToOneConnector(), synapse_type=sim.StaticSynapse(weight=1, delay=0)) input_G1_2G2_6=sim.Projection(G1_2,G2_6, sim.OneToOneConnector(), synapse_type=sim.StaticSynapse(weight=1.6, delay=0)) GEN1_1.record(["spikes","v","gsyn_exc"]) simtime =50 sim.run(simtime) neo = GEN1_1.get_data(variables=["spikes","v","gsync_exc"]) spikes = neo.segments[0].spiketrains print spikes v = neo.segments[0].filter(name='v')[0] print v
def finalize_wiring(conn_ee, conn_ie, conn_ei, conn_ii):
ii_srcs, ii_tgs = get_sets(conn_ii)
ei_srcs, ei_tgs = get_sets(conn_ei)
ee_srcs, ee_tgs = get_sets(conn_ee)
ie_srcs, ie_tgs = get_sets(conn_ie)
_ = con_check_one(conn_ee,ee_srcs, ee_tgs)
_ = con_check_one(conn_ii,ii_srcs,ii_tgs)
_ = con_check_one(conn_ei,ei_srcs,ei_tgs)
_ = con_check_one(conn_ie,ie_srcs,ie_tgs)
len_es_srcs = len(list(ee_srcs))
# the network is dominated by inhibitory neurons, which is unusual for modellers.
# Plot all the Projection pairs as a connection matrix (Excitatory and Inhibitory Connections)
rng = NumpyRNG(seed=64754)
delay_distr = RandomDistribution('normal', [2, 1e-1], rng=rng)
all_cells = sim.Population(len(index_exc)+len(index_inh), sim.Izhikevich(a=0.02, b=0.2, c=-65, d=8, i_offset=0))
pop_exc = sim.PopulationView(all_cells,index_exc)
pop_inh = sim.PopulationView(all_cells,index_inh)
NEXC = len(index_exc)
NINH = len(index_inh)
# add random variation into Izhi parameters
for pe in index_exc:
pe = all_cells[pe]
r = random.uniform(0.0, 1.0)
pe.set_parameters(a=0.02, b=0.2, c=-65+15*r, d=8-r**2, i_offset=0)
for pi in index_inh:
pi = all_cells[pi]
r = random.uniform(0.0, 1.0)
pi.set_parameters(a=0.02+0.08*r, b=0.25-0.05*r, c=-65, d= 2, i_offset=0)
[ all_cells[i].get_parameters() for i,_ in enumerate(all_cells) ]
exc_syn = sim.StaticSynapse(weight = wg, delay=delay_distr)
assert np.any(conn_ee.conn_list[:,0]) < len_es_srcs
prj_exc_exc = sim.Projection(all_cells, all_cells, conn_ee, exc_syn, receptor_type='excitatory')
prj_exc_inh = sim.Projection(all_cells, all_cells, conn_ei, exc_syn, receptor_type='excitatory')
inh_syn = sim.StaticSynapse(weight = wg, delay=delay_distr)
delay_distr = RandomDistribution('normal', [1, 100e-3], rng=rng)
prj_inh_inh = sim.Projection(all_cells, all_cells, conn_ii, inh_syn, receptor_type='inhibitory')
prj_inh_exc = sim.Projection(all_cells, all_cells, conn_ie, inh_syn, receptor_type='inhibitory')
inh_distr = RandomDistribution('normal', [1, 2.1e-3], rng=rng)
prj_change(prj_exc_exc,wg)
prj_change(prj_exc_inh,wg)
prj_change(prj_inh_exc,wg)
prj_change(prj_inh_inh,wg)
prj_check(prj_exc_exc)
prj_check(prj_exc_inh)
prj_check(prj_inh_exc)
prj_check(prj_inh_inh)
try:
others = [prj_exc_exc, prj_exc_inh, inh_syn, prj_inh_inh, prj_inh_exc, inh_distr ]
except:
pass
return ( all_cells, pop_exc, pop_inh, NEXC, NINH )
all_cells, pop_exc, pop_inh, NEXC, NINH = finalize_wiring(conn_ee, conn_ie, conn_ei, conn_ii)
def run_network(current, tstop, all_cells, pop_exc, pop_inh, NEXC, NINH):
noisee,noisei = current
pop_exc.inject(noisee)
pop_inh.inject(noisei)
##
# Setup and run a simulation. Note there is no current injection into the neuron.
# All cells in the network are in a quiescent state, so its not a surprise that xthere are no spikes
##
arange = np.arange
all_cells.record(['v','spikes']) # , 'u'])
all_cells.initialize(v=-65.0, u=-14.0)
# === Run the simulation =====================================================
#tstop = 2000.0
all_cells.record("spikes")
sim.run(tstop)
vms = np.array(data.analogsignals[0].as_array().T)
cleaned = []
for i,vm in enumerate(vms):
if np.max(vm) > 900.0 or np.min(vm) <- 900.0:
else:
cleaned.append(vm)
vms = cleaned
#vm = s#.as_array()[:,
cnt = 0
vm_spiking = []
vm_not_spiking = []
spike_trains = []
binary_trains = []
for spiketrain in data.spiketrains:
y = np.ones_like(spiketrain) * spiketrain.annotations['source_id']
# argument edges is the time interval you want to be considered.
pspikes = pyspike.SpikeTrain(spiketrain,edges=(0,len(ass)))
spike_trains.append(pspikes)
if len(spiketrain) > max_spikes:
max_spikes = len(spiketrain)
if np.max(ass[spiketrain.annotations['source_id']]) > 0.0:
vm_spiking.append(vms[spiketrain.annotations['source_id']])
else:
vm_not_spiking.append(vms[spiketrain.annotations['source_id']])
cnt+= 1
for spiketrain in data.spiketrains:
x = conv.BinnedSpikeTrain(spiketrain, binsize=1 * pq.ms, t_start=0 * pq.s)
binary_trains.append(x)
end_floor = np.floor(float(mdf1.t_stop))
dt = float(mdf1.t_stop) % end_floor
data.t_start
#v = mdf1.take_slice_of_analogsignalarray_by_unit()
t_spike_axis = np.arange(float(mdf1.t_start), float(mdf1.t_stop), dt)
return data,vms,binary_trains,t_spike_axis
tau_minus=20.0,
A_plus=0.5,
A_minus=0.5)
weight_rule = sim.AdditiveWeightDependence(w_max=25.0, w_min=0.0)
stdp_model = sim.STDPMechanism(timing_dependence=timing_rule,
weight_dependence=weight_rule,
weight=2.0,
delay=1)
stdp_projection = sim.Projection(pre_pop,
post_pop,
sim.OneToOneConnector(),
synapse_type=stdp_model)
input_projection1 = sim.Projection(input1,
pre_pop,
sim.OneToOneConnector(),
synapse_type=sim.StaticSynapse(weight=5,
delay=1))
pre_pop.record(["spikes", "v"])
post_pop.record(["spikes", "v"])
simtime = 100
k = PyKeyboard()
def receive_spikes(label, time, neuron_ids):
try:
for neuron_id in neuron_ids:
if str(neuron_id) is '0':
print 'press right'
k.press_key(k.right_key)
if str(neuron_id) is '1':
def sim_runner(wg):
#import pyNN.neuron as sim
try:
import pyNN.spiNNaker as sim
except:
import pyNN.neuron as sim
nproc = sim.num_processes()
node = sim.rank()
print(nproc)
#import mpi4py
#threads = sim.rank()
threads = 1
rngseed = 98765
parallel_safe = False
#extra = {'threads' : threads}
# Get some hippocampus connectivity data, based on a conversation with
# academic researchers on GH:
# https://github.com/Hippocampome-Org/GraphTheory/issues?q=is%3Aissue+is%3Aclosed
# scrape hippocamome connectivity data, that I intend to use to program neuromorphic hardware.
# conditionally get files if they don't exist.
# This is literally the starting point of the connection map
path_xl = '_hybrid_connectivity_matrix_20171103_092033.xlsx'
if not os.path.exists(path_xl):
os.system(
'wget https://github.com/Hippocampome-Org/GraphTheory/files/1657258/_hybrid_connectivity_matrix_20171103_092033.xlsx'
)
xl = pd.ExcelFile(path_xl)
dfall = xl.parse()
dfall.loc[0].keys()
dfm = dfall.as_matrix()
rcls = dfm[:, :1] # real cell labels.
rcls = rcls[1:]
rcls = {k: v
for k, v in enumerate(rcls)
} # real cell labels, cast to dictionary
import pickle
with open('cell_names.p', 'wb') as f:
pickle.dump(rcls, f)
pd.DataFrame(rcls).to_csv('cell_names.csv', index=False)
filtered = dfm[:, 3:]
filtered = filtered[1:]
rng = NumpyRNG(seed=64754)
delay_distr = RandomDistribution('normal', [2, 1e-1], rng=rng)
weight_distr = RandomDistribution('normal', [45, 1e-1], rng=rng)
sanity_e = []
sanity_i = []
EElist = []
IIlist = []
EIlist = []
IElist = []
with open('wire_map_online.p', 'wb') as f:
pickle.dump(filtered, f)
for i, j in enumerate(filtered):
for k, xaxis in enumerate(j):
if xaxis == 1 or xaxis == 2:
source = i
sanity_e.append(i)
target = k
if xaxis == -1 or xaxis == -2:
sanity_i.append(i)
source = i
target = k
index_exc = list(set(sanity_e))
index_inh = list(set(sanity_i))
import pickle
with open('cell_indexs.p', 'wb') as f:
returned_list = [index_exc, index_inh]
pickle.dump(returned_list, f)
'''
import numpy
a = numpy.asarray(index_exc)
numpy.savetxt('pickles/'+str(k)+'excitatory_nunber_labels.csv', a, delimiter=",")
a = numpy.asarray(index_inh)
numpy.savetxt('pickles/'+str(k)+'inhibitory_nunber_labels.csv', a, delimiter=",")
'''
for i, j in enumerate(filtered):
for k, xaxis in enumerate(j):
if xaxis == 1 or xaxis == 2:
source = i
sanity_e.append(i)
target = k
delay = delay_distr.next()
weight = 1.0
if target in index_inh:
EIlist.append((source, target, delay, weight))
else:
EElist.append((source, target, delay, weight))
if xaxis == -1 or xaxis == -2:
sanity_i.append(i)
source = i
target = k
delay = delay_distr.next()
weight = 1.0
if target in index_exc:
IElist.append((source, target, delay, weight))
else:
IIlist.append((source, target, delay, weight))
internal_conn_ee = sim.FromListConnector(EElist)
ee = internal_conn_ee.conn_list
ee_srcs = ee[:, 0]
ee_tgs = ee[:, 1]
internal_conn_ie = sim.FromListConnector(IElist)
ie = internal_conn_ie.conn_list
ie_srcs = set([int(e[0]) for e in ie])
ie_tgs = set([int(e[1]) for e in ie])
internal_conn_ei = sim.FromListConnector(EIlist)
ei = internal_conn_ei.conn_list
ei_srcs = set([int(e[0]) for e in ei])
ei_tgs = set([int(e[1]) for e in ei])
internal_conn_ii = sim.FromListConnector(IIlist)
ii = internal_conn_ii.conn_list
ii_srcs = set([int(e[0]) for e in ii])
ii_tgs = set([int(e[1]) for e in ii])
for e in internal_conn_ee.conn_list:
assert e[0] in ee_srcs
assert e[1] in ee_tgs
for i in internal_conn_ii.conn_list:
assert i[0] in ii_srcs
assert i[1] in ii_tgs
ml = len(filtered[1]) + 1
pre_exc = []
post_exc = []
pre_inh = []
post_inh = []
rng = NumpyRNG(seed=64754)
delay_distr = RandomDistribution('normal', [2, 1e-1], rng=rng)
plot_EE = np.zeros(shape=(ml, ml), dtype=bool)
plot_II = np.zeros(shape=(ml, ml), dtype=bool)
plot_EI = np.zeros(shape=(ml, ml), dtype=bool)
plot_IE = np.zeros(shape=(ml, ml), dtype=bool)
for i in EElist:
plot_EE[i[0], i[1]] = int(0)
if i[0] != i[1]: # exclude self connections
plot_EE[i[0], i[1]] = int(1)
pre_exc.append(i[0])
post_exc.append(i[1])
assert len(pre_exc) == len(post_exc)
for i in IIlist:
plot_II[i[0], i[1]] = int(0)
if i[0] != i[1]:
plot_II[i[0], i[1]] = int(1)
pre_inh.append(i[0])
post_inh.append(i[1])
for i in IElist:
plot_IE[i[0], i[1]] = int(0)
if i[0] != i[1]: # exclude self connections
plot_IE[i[0], i[1]] = int(1)
pre_inh.append(i[0])
post_inh.append(i[1])
for i in EIlist:
plot_EI[i[0], i[1]] = int(0)
if i[0] != i[1]:
plot_EI[i[0], i[1]] = int(1)
pre_exc.append(i[0])
post_exc.append(i[1])
plot_excit = plot_EI + plot_EE
plot_inhib = plot_IE + plot_II
assert len(pre_inh) == len(post_inh)
num_exc = [i for i, e in enumerate(plot_excit) if sum(e) > 0]
num_inh = [y for y, i in enumerate(plot_inhib) if sum(i) > 0]
# the network is dominated by inhibitory neurons, which is unusual for modellers.
assert num_inh > num_exc
assert np.sum(plot_inhib) > np.sum(plot_excit)
assert len(num_exc) < ml
assert len(num_inh) < ml
# # Plot all the Projection pairs as a connection matrix (Excitatory and Inhibitory Connections)
nproc = sim.num_processes()
nproc = 8
host_name = socket.gethostname()
node_id = sim.setup(timestep=0.01, min_delay=1.0) #, **extra)
print("Host #%d is on %s" % (node_id + 1, host_name))
rng = NumpyRNG(seed=64754)
all_cells = sim.Population(
len(index_exc) + len(index_inh),
sim.Izhikevich(a=0.02, b=0.2, c=-65, d=8, i_offset=0))
pop_exc = sim.PopulationView(all_cells, index_exc)
pop_inh = sim.PopulationView(all_cells, index_inh)
for pe in pop_exc:
pe = all_cells[pe]
r = random.uniform(0.0, 1.0)
pe.set_parameters(a=0.02,
b=0.2,
c=-65 + 15 * r,
d=8 - r**2,
i_offset=0)
for pi in index_inh:
pi = all_cells[pi]
r = random.uniform(0.0, 1.0)
pi.set_parameters(a=0.02 + 0.08 * r,
b=0.25 - 0.05 * r,
c=-65,
d=2,
i_offset=0)
NEXC = len(num_exc)
NINH = len(num_inh)
exc_syn = sim.StaticSynapse(weight=wg, delay=delay_distr)
assert np.any(internal_conn_ee.conn_list[:, 0]) < ee_srcs.size
prj_exc_exc = sim.Projection(all_cells,
all_cells,
internal_conn_ee,
exc_syn,
receptor_type='excitatory')
prj_exc_inh = sim.Projection(all_cells,
all_cells,
internal_conn_ei,
exc_syn,
receptor_type='excitatory')
inh_syn = sim.StaticSynapse(weight=wg, delay=delay_distr)
delay_distr = RandomDistribution('normal', [1, 100e-3], rng=rng)
prj_inh_inh = sim.Projection(all_cells,
all_cells,
internal_conn_ii,
inh_syn,
receptor_type='inhibitory')
prj_inh_exc = sim.Projection(all_cells,
all_cells,
internal_conn_ie,
inh_syn,
receptor_type='inhibitory')
inh_distr = RandomDistribution('normal', [1, 2.1e-3], rng=rng)
ext_Connector = OneToOneConnector(callback=progress_bar)
ext_syn = StaticSynapse(weight=JE, delay=dt)
'''
print("%d Connecting excitatory population with connection probability %g, weight %g nA and delay %g ms." % (rank, epsilon, JE, delay))
E_to_E = Projection(E_net, E_net, connector, E_syn, receptor_type="excitatory")
print("E --> E\t\t", len(E_to_E), "connections")
I_to_E = Projection(I_net, E_net, connector, I_syn, receptor_type="inhibitory")
print("I --> E\t\t", len(I_to_E), "connections")
input_to_E = Projection(expoisson, E_net, ext_Connector, ext_syn, receptor_type="excitatory")
print("input --> E\t", len(input_to_E), "connections")
print("%d Connecting inhibitory population with connection probability %g, weight %g nA and delay %g ms." % (rank, epsilon, JI, delay))
E_to_I = Projection(E_net, I_net, connector, E_syn, receptor_type="excitatory")
print("E --> I\t\t", len(E_to_I), "connections")
I_to_I = Projection(I_net, I_net, connector, I_syn, receptor_type="inhibitory")
print("I --> I\t\t", len(I_to_I), "connections")
input_to_I = Projection(inpoisson, I_net, ext_Connector, ext_syn, receptor_type="excitatory")
print("input --> I\t", len(input_to_I), "connections")
'''
def prj_change(prj, wg):
prj.setWeights(wg)
prj_change(prj_exc_exc, wg)
prj_change(prj_exc_inh, wg)
prj_change(prj_inh_exc, wg)
prj_change(prj_inh_inh, wg)
def prj_check(prj):
for w in prj.weightHistogram():
for i in w:
print(i)
prj_check(prj_exc_exc)
prj_check(prj_exc_inh)
prj_check(prj_inh_exc)
prj_check(prj_inh_inh)
#print(rheobase['value'])
#print(float(rheobase['value']),1.25/1000.0)
'''Old values that worked
noise = sim.NoisyCurrentSource(mean=0.85/1000.0, stdev=5.00/1000.0, start=0.0, stop=2000.0, dt=1.0)
pop_exc.inject(noise)
#1000.0 pA
noise = sim.NoisyCurrentSource(mean=1.740/1000.0, stdev=5.00/1000.0, start=0.0, stop=2000.0, dt=1.0)
pop_inh.inject(noise)
#1750.0 pA
'''
noise = sim.NoisyCurrentSource(mean=0.74 / 1000.0,
stdev=4.00 / 1000.0,
start=0.0,
stop=2000.0,
dt=1.0)
pop_exc.inject(noise)
#1000.0 pA
noise = sim.NoisyCurrentSource(mean=1.440 / 1000.0,
stdev=4.00 / 1000.0,
start=0.0,
stop=2000.0,
dt=1.0)
pop_inh.inject(noise)
##
# Setup and run a simulation. Note there is no current injection into the neuron.
# All cells in the network are in a quiescent state, so its not a surprise that xthere are no spikes
##
sim = pyNN.neuron
arange = np.arange
import re
all_cells.record(['v', 'spikes']) # , 'u'])
all_cells.initialize(v=-65.0, u=-14.0)
# === Run the simulation =====================================================
tstop = 2000.0
sim.run(tstop)
data = None
data = all_cells.get_data().segments[0]
if not os.path.exists("pickles"):
os.mkdir("pickles")
#print(len(data.analogsignals[0].times))
with open('pickles/qi' + str(wg) + '.p', 'wb') as f:
pickle.dump(data, f)
# make data none or else it will grow in a loop
all_cells = None
data = None
noise = None
array_connectivity_small_world_exc_inh = sim.ArrayConnector(
connection_matrix_small_world_exc_inh)
array_connectivity_small_world_inh_exc = sim.ArrayConnector(
connection_matrix_small_world_inh_exc)
input_connectivity_exc = sim.FixedNumberPostConnector(
**connectivity_parameters['input_exc'])
input_connectivity_inh = sim.FixedNumberPostConnector(
**connectivity_parameters['input_inh'])
input_exc_exc_connections = sim.Projection(
ext_stim_exc,
exc_cells_input_subset,
input_connectivity_exc,
receptor_type='excitatory',
synapse_type=sim.StaticSynapse(**synaptic_parameters['input']),
label='Input connections')
input_inh_inh_connections = sim.Projection(
ext_stim_inh,
inh_cells_input_subset,
input_connectivity_inh,
receptor_type='excitatory',
synapse_type=sim.StaticSynapse(**synaptic_parameters['input']),
label='Input connections')
exc_exc_connections = sim.Projection(
exc_cells,
exc_cells,
array_connectivity_small_world_exc_exc,
receptor_type='excitatory',
connected_chip_details = {
"spinnaker_link_id": 0,
}
def get_updated_params(params):
params.update(connected_chip_details)
return params
# Setup
p.setup(timestep=1.0)
# FPGA Retina - Down Polarity
retina_pop = p.Population(
None, p.external_devices.ExternalFPGARetinaDevice, get_updated_params({
'retina_key': 0x5,
'mode': p.external_devices.ExternalFPGARetinaDevice.MODE_128,
'polarity': (
p.external_devices.ExternalFPGARetinaDevice.DOWN_POLARITY)}),
label='External retina')
population = p.Population(256, p.IF_curr_exp(), label='pop_1')
p.Projection(
retina_pop, population, p.FixedProbabilityConnector(0.1),
synapse_type=p.StaticSynapse(weight=0.1))
# q.activate_live_output_for(population)
p.run(1000)
p.end()
def lancement_sim(cellSourceSpikes,
path,
weight_input=0,
weight_inter=0,
max_time=800000,
TIME_STEP=TIME_STEP,
input_n=input_n,
nb_neuron_int=nb_neuron_int,
nb_neuron_out=nb_neuron_out,
delay=delay,
p_conn_in_int=p_conn_in_int,
p_conn_int_out=p_conn_int_out,
v_tresh=v_tresh):
simulator = 'spinnaker'
# le max_delay doit être inférieur à 14*time_step
sim.setup(timestep=TIME_STEP, min_delay=delay, max_delay=delay * 2)
randoms = np.random.rand(100, 1)
#defining network topology
lif_curr_exp_params = {
'cm': 1.0, # The capacitance of the LIF neuron in nano-Farads
'tau_m': 20.0, # The time-constant of the RC circuit, in milliseconds
'tau_refrac': 5.0, # The refractory period, in milliseconds
'v_reset':
-65.0, # The voltage to set the neuron at immediately after a spike
'v_rest': -65.0, # The ambient rest voltage of the neuron
'v_thresh':
-(v_tresh), # The threshold voltage at which the neuron will spike
'tau_syn_E': 5.0, # The excitatory input current decay time-constant
'tau_syn_I': 5.0, # The inhibitory input current decay time-constant
'i_offset': 0.0, # A base input current to add each timestep
}
# Population d'entrée avec comme source le SpikeSourceArray en paramètre
Input = sim.Population(input_n,
sim.SpikeSourceArray(spike_times=cellSourceSpikes),
label="Input")
Input.record("spikes")
# Définition des types de neurones et des couches intermédiaire, de sortie, ainsi que celle contenant le neurone de l'attention
LIF_Intermediate = sim.IF_curr_exp(**lif_curr_exp_params)
Intermediate = sim.Population(nb_neuron_int,
LIF_Intermediate,
label="Intermediate")
Intermediate.record(("spikes", "v"))
LIF_Output = sim.IF_curr_exp(**lif_curr_exp_params)
Output = sim.Population(nb_neuron_out, LIF_Output, label="Output")
Output.record(("spikes", "v"))
LIF_delayer = sim.IF_curr_exp(**lif_curr_exp_params)
Delay_n = sim.Population(1, LIF_delayer, label="Delay")
Delay_n.record(("spikes", "v"))
# set the stdp mechanisim parameters, we are going to use stdp in both connections between (input-intermediate) adn (intermediate-output)
python_rng = NumpyRNG(seed=98497627)
delay = delay # (ms) synaptic time delay
#A_minus
# définition des connexions entre couches de neurones entrée <=> intermédiaire, intermédiaire <=> sortie
# vérificatio pour savoir si on est dans le cas de la première simulation par défault ou si on doit injecter les poids
if ((weight_input != 0) or (weight_inter != 0)):
# cas ou l'on inject les poids
Conn_input_inter = sim.Projection(
Input,
Intermediate,
# Le fromListConnector pour injecter les poids
connector=sim.FromListConnector(weight_input),
receptor_type="excitatory",
label="Connection input to intermediate",
# des synapses static pour "suprimer" l'apprentissage
synapse_type=sim.StaticSynapse())
Conn_inter_output = sim.Projection(
Intermediate,
Output, # pre and post population
connector=sim.FromListConnector(weight_inter),
receptor_type="excitatory",
label="Connection intermediate to output",
synapse_type=sim.StaticSynapse())
else:
# cas par défault
Conn_input_inter = sim.Projection(
Input,
Intermediate,
connector=sim.FixedProbabilityConnector(
p_conn_in_int, allow_self_connections=False),
synapse_type=sim.StaticSynapse(
weight=RandomDistribution('normal', (3, 2.9), rng=python_rng)),
receptor_type="excitatory",
label="Connection input to intermediate")
Conn_inter_output = sim.Projection(
Intermediate,
Output, # pre and post population
connector=sim.FixedProbabilityConnector(
p_conn_int_out, allow_self_connections=False),
synapse_type=sim.StaticSynapse(
weight=RandomDistribution('normal', (3, 2.9), rng=python_rng)),
receptor_type="excitatory",
label="Connection intermediate to output")
# définition des connexions inhibitrices des couches intermédiaire et de sortie
FixedInhibitory_WTA = sim.StaticSynapse(weight=6)
WTA_INT = sim.Projection(
Intermediate,
Intermediate,
connector=sim.AllToAllConnector(allow_self_connections=False),
synapse_type=FixedInhibitory_WTA,
receptor_type="inhibitory",
label="Connection WTA")
WTA_OUT = sim.Projection(
Output,
Output,
connector=sim.AllToAllConnector(allow_self_connections=False),
synapse_type=FixedInhibitory_WTA,
receptor_type="inhibitory",
label="Connection WTA")
# Connexion avec le neurone de l'attention
FixedInhibitory_delayer = sim.StaticSynapse(weight=2)
Delay_out = sim.Projection(
Delay_n,
Output,
connector=sim.AllToAllConnector(allow_self_connections=False),
synapse_type=FixedInhibitory_delayer,
receptor_type="inhibitory",
label="Connection WTA")
Delay_inter = sim.Projection(
Intermediate,
Delay_n,
connector=sim.AllToAllConnector(allow_self_connections=False),
synapse_type=FixedInhibitory_delayer,
receptor_type="inhibitory",
label="Connection WTA")
# On précise le nombre de neurone par coeurs au cas ou
sim.set_number_of_neurons_per_core(sim.IF_curr_exp, 255)
# on arrondie le temps de simulation, sinon avec les callbacks, on a une boucle infinie pour des temps d'arrêts plus précis que la fréquence des callbacks
simtime = ceil(max_time)
try:
#lancement de la simulation
sim.run(simtime)
#récupération des infos sur les spike des trois couches
neo = Output.get_data(variables=["spikes", "v"])
spikes = neo.segments[0].spiketrains
#print(spikes)
v = neo.segments[0].filter(name='v')[0]
neo_in = Input.get_data(variables=["spikes"])
spikes_in = neo_in.segments[0].spiketrains
#print(spikes_in)
neo_intermediate = Intermediate.get_data(variables=["spikes", "v"])
spikes_intermediate = neo_intermediate.segments[0].spiketrains
#print(spikes_intermediate)
v_intermediate = neo_intermediate.segments[0].filter(name='v')[0]
#print(v_intermediate)
sim.reset()
sim.end()
except:
# Si la simulation fail, on set ces deux variables à zéros pour gérer l'erreur dans le script principal
v = 0
spikes = 0
# Création et sauvegarde des graphs des graphs si la simluation s'est bien passée, + envoie des sorties de la fonction
if (isinstance(spikes, list) and isinstance(v, AnalogSignal)):
plot.Figure(
# plot voltage for first ([0]) neuron
plot.Panel(v,
ylabel="Membrane potential (mV)",
data_labels=[Output.label],
yticks=True,
xlim=(0, simtime)),
# plot spikes (or in this case spike)
plot.Panel(spikes, yticks=True, markersize=5, xlim=(0, simtime)),
title="Spiking activity of the output layer during test",
annotations="Simulated with {}".format(sim.name())).save(
"./Generated_data/tests/" + path +
"/output_layer_membrane_voltage_and_spikes.png")
plot.Figure(
# plot voltage for first ([0]) neuron
plot.Panel(v_intermediate,
ylabel="Membrane potential (mV)",
data_labels=[Output.label],
yticks=True,
xlim=(0, simtime)),
# plot spikes (or in this case spike)
plot.Panel(spikes_intermediate,
yticks=True,
markersize=5,
xlim=(0, simtime)),
title="Spiking activity of the intermediate layer during test",
annotations="Simulated with {}".format(sim.name())).save(
"./Generated_data/tests/" + path +
"/intermediate_layer_membrane_voltage_and_spikes.png")
return v, spikes
else:
print(
"simulation failed with parameters : (l'affichage des paramètres ayant causés le disfonctionnement de la simulation sera traitée à une date ultérieur, merci!)"
)
return 0, 0
'v_thresh': -55.0
}
pre_cell = sim.SpikeSourceArray(pre_spikes)
post_cell = sim.SpikeSourceArray(post_spikes)
layer1 = sim.Population(1, pre_cell, label='inputspikes')
post = sim.Population(1,
sim.IF_curr_exp,
cellparams=cell_params_lif,
label='post')
layer2 = sim.Population(1, post_cell, label='outputspikes')
stim_proj = sim.Projection(layer2,
post,
sim.OneToOneConnector(),
synapse_type=sim.StaticSynapse(weight=7,
delay=0.25))
stdp = sim.STDPMechanism(
weight=0,
#weight=0.02, # this is the initial value of the weight
#delay="0.2 + 0.01*d",
timing_dependence=sim.SpikePairRule(tau_plus=30,
tau_minus=10,
A_plus=0.5,
A_minus=0.5),
#weight_dependence=sim.MultiplicativeWeightDependence(w_min=wMin, w_max=wMax),
weight_dependence=sim.AdditiveWeightDependence(w_min=0, w_max=5),
#weight_dependence=sim.AdditiveWeightDependence(w_min=0, w_max=0.4),
dendritic_delay_fraction=1.0)
stdp_proj = sim.Projection(layer1,
def train(spikeTimes,untrained_weights=None):
organisedStim = {}
labelSpikes = []
#spikeTimes = generate_data()
#for j in range(5):
# labelSpikes
#labelSpikes[label] = [(input_len-1)*v_co+1,(input_len-1)*v_co*2+1,(input_len-1)*v_co*3+1,]
if untrained_weights == None:
untrained_weights = RandomDistribution('uniform', low=wMin, high=wMaxInit).next(input_size*output_size)
#untrained_weights = RandomDistribution('normal_clipped', mu=0.1, sigma=0.05, low=wMin, high=wMaxInit).next(input_size*output_size)
untrained_weights = np.around(untrained_weights, 3)
#saveWeights(untrained_weights, 'untrained_weightssupmodel1traj')
print ("init!")
print "length untrained_weights :", len(untrained_weights)
if len(untrained_weights)>input_size:
training_weights = [[0 for j in range(output_size)] for i in range(input_size)] #np array? size 1024x25
k=0
for i in range(input_size):
for j in range(output_size):
training_weights[i][j] = untrained_weights[k]
k += 1
else:
training_weights = untrained_weights
connections = []
for n_pre in range(input_size): # len(untrained_weights) = input_size
for n_post in range(output_size): # len(untrained_weight[0]) = output_size; 0 or any n_pre
connections.append((n_pre, n_post, training_weights[n_pre][n_post], __delay__)) #index
runTime = int(max(max(spikeTimes))/3)+100
#####################
sim.setup(timestep=1)
#def populations
layer1=sim.Population(input_size,sim.SpikeSourceArray, {'spike_times': spikeTimes},label='inputspikes')
layer2=sim.Population(output_size,sim.IF_curr_exp,cellparams=cell_params_lif,label='outputspikes')
#supsignal=sim.Population(output_size,sim.SpikeSourceArray, {'spike_times': labelSpikes},label='supersignal')
#def learning rule
stdp = sim.STDPMechanism(
weight=untrained_weights,
#weight=0.02, # this is the initial value of the weight
#delay="0.2 + 0.01*d",
timing_dependence=sim.SpikePairRule(tau_plus=tauPlus, tau_minus=tauMinus,A_plus=aPlus, A_minus=aMinus),
#weight_dependence=sim.MultiplicativeWeightDependence(w_min=wMin, w_max=wMax),
weight_dependence=sim.AdditiveWeightDependence(w_min=wMin, w_max=wMax),
#weight_dependence=sim.AdditiveWeightDependence(w_min=0, w_max=0.4),
dendritic_delay_fraction=1.0)
#def projections
#stdp_proj = sim.Projection(layer1, layer2, sim.FromListConnector(connections), synapse_type=stdp)
stdp_proj = sim.Projection(layer1, layer2, sim.AllToAllConnector(), synapse_type=stdp)
inhibitory_connections = sim.Projection(layer2, layer2, sim.AllToAllConnector(allow_self_connections=False),
synapse_type=sim.StaticSynapse(weight=inhibWeight, delay=__delay__),
receptor_type='inhibitory')
#stim_proj = sim.Projection(supsignal, layer2, sim.OneToOneConnector(),
# synapse_type=sim.StaticSynapse(weight=stimWeight, delay=__delay__))
layer1.record(['spikes'])
layer2.record(['v','spikes'])
#supsignal.record(['spikes'])
sim.run(runTime)
print("Weights:{}".format(stdp_proj.get('weight', 'list')))
weight_list = [stdp_proj.get('weight', 'list'), stdp_proj.get('weight', format='list', with_address=False)]
neo = layer2.get_data(["spikes", "v"])
spikes = neo.segments[0].spiketrains
v = neo.segments[0].filter(name='v')[0]
#neostim = supsignal.get_data(["spikes"])
#spikestim = neostim.segments[0].spiketrains
neoinput= layer1.get_data(["spikes"])
spikesinput = neoinput.segments[0].spiketrains
plt.close('all')
pplt.Figure(
pplt.Panel(spikesinput,xticks=True, yticks=True, markersize=2, xlim=(0,runTime),xlabel='(a) Spikes of Input Layer'),
#pplt.Panel(spikestim, xticks=True, yticks=True, markersize=2, xlim=(0,runTime),xlabel='(c) Spikes of Supervised Layer'),
pplt.Panel(spikes, xticks=True, xlabel="(b) Spikes of Output Layer", yticks=True, markersize=2, xlim=(0,runTime)),
pplt.Panel(v, ylabel="Membrane potential (mV)", xticks=True, yticks=True, xlim=(0,runTime),xlabel='(c) Membrane Potential of Output Layer\nTime (ms)'),
title="Two Training",
annotations="Twoway Training"
).save('SNN_DVS_un/plot_for_twoway/'+str(trylabel)+'_training.png')
#plt.hist(weight_list[1], bins=100)
plt.close('all')
plt.hist([weight_list[1][0:input_size], weight_list[1][input_size:input_size*2], weight_list[1][input_size*2:]], bins=20, label=['neuron 0', 'neuron 1', 'neuron 2'], range=(0, wMax))
plt.title('weight distribution')
plt.xlabel('Weight value')
plt.ylabel('Weight count')
#plt.show()
#plt.show()
sim.end()
return weight_list[1]
# Stimulating populations
pre_times = [i for i in range(pre_phase, sim_time, time_between_pairs)]
post_times = [i for i in range(post_phase, sim_time, time_between_pairs)]
pre_stim = sim.Population(
1, sim.SpikeSourceArray(spike_times=[pre_times]))
post_stim = sim.Population(
1, sim.SpikeSourceArray(spike_times=[post_times]))
weight = 0.035
# Connections between spike sources and neuron populations
ee_connector = sim.OneToOneConnector()
sim.Projection(
pre_stim, pre_pop, ee_connector, receptor_type='excitatory',
synapse_type=sim.StaticSynapse(weight=weight))
sim.Projection(
post_stim, post_pop, ee_connector, receptor_type='excitatory',
synapse_type=sim.StaticSynapse(weight=weight))
# Plastic Connection between pre_pop and post_pop
stdp_model = sim.STDPMechanism(
timing_dependence=sim.SpikePairRule(
tau_plus=16.7, tau_minus=33.7, A_plus=0.005, A_minus=0.005),
weight_dependence=sim.AdditiveWeightDependence(
w_min=0.0, w_max=0.0175), weight=start_w)
projections.append(sim.Projection(
pre_pop, post_pop, sim.OneToOneConnector(),
synapse_type=stdp_model))
def test(spikeTimes,trained_weights):
#spikeTimes = extractSpikes(sample)
runTime = int(max(max(spikeTimes)))+100
##########################################
sim.setup(timestep=1)
pre_pop = sim.Population(input_size, sim.SpikeSourceArray, {'spike_times': spikeTimes}, label="pre_pop")
post_pop = sim.Population(output_size, sim.IF_curr_exp , cell_params_lif, label="post_pop")
if len(trained_weights) > input_size:
weigths = [[0 for j in range(output_size)] for i in range(input_size)] #np array? size 1024x25
k=0
for i in range(input_size):
for j in range(output_size):
weigths[i][j] = trained_weights[k]
k += 1
else:
weigths = trained_weights
connections = []
#k = 0
for n_pre in range(input_size): # len(untrained_weights) = input_size
for n_post in range(output_size): # len(untrained_weight[0]) = output_size; 0 or any n_pre
#connections.append((n_pre, n_post, weigths[n_pre][n_post]*(wMax), __delay__))
connections.append((n_pre, n_post, weigths[n_pre][n_post]*(wMax)/max(trained_weights), __delay__))
#connections.append((n_pre, n_post, min(weigths[n_pre][n_post],0.2), __delay__))
#connections.append((n_pre, n_post, weigths[n_pre][n_post]*(1)/max(trained_weights), __delay__))#
#k += 1
prepost_proj = sim.Projection(pre_pop, post_pop, sim.FromListConnector(connections), synapse_type=sim.StaticSynapse(), receptor_type='excitatory') # no more learning !!
inhib_proj = sim.Projection(post_pop, post_pop, sim.AllToAllConnector(), synapse_type=sim.StaticSynapse(weight=inhibWeight, delay=__delay__), receptor_type='inhibitory')
# no more lateral inhib
pre_pop.record(['spikes'])
post_pop.record(['v', 'spikes'])
sim.run(runTime)
neo = post_pop.get_data(['v', 'spikes'])
spikes = neo.segments[0].spiketrains
v = neo.segments[0].filter(name='v')[0]
neoinput= pre_pop.get_data(["spikes"])
spikesinput = neoinput.segments[0].spiketrains
plt.close('all')
pplt.Figure(
# plot voltage
# raster plot
pplt.Panel(spikesinput,xticks=True, yticks=True, markersize=2, xlim=(0,runTime),xlabel='(a) Spikes of Input Layer'),
pplt.Panel(spikes, xlabel="(b) Spikes of Output Layer", xticks=True, yticks=True, markersize=2, xlim=(0, runTime+100)),
pplt.Panel(v, ylabel="Membrane potential (mV)", xticks=True, yticks=True, xlim=(0, runTime+100),xlabel='(c) Membrane Potential of Output Layer\nTime (ms)'),
title='Twoway Test'#,
#annotations='T'
).save('SNN_DVS_un/plot_for_twoway/'+str(trylabel)+'_test2.png')
#f1.fig.texts=[]
print("Weights:{}".format(prepost_proj.get('weight', 'list')))
weight_list = [prepost_proj.get('weight', 'list'), prepost_proj.get('weight', format='list', with_address=False)]
#predict_label=
sim.end()
return spikes
def lancement_sim(cellSourceSpikes,
max_time=800000,
path="default",
TIME_STEP=TIME_STEP,
input_n=input_n,
nb_neuron_int=nb_neuron_int,
nb_neuron_out=nb_neuron_out,
delay=delay,
p_conn_in_int=p_conn_in_int,
p_conn_int_out=p_conn_int_out,
a_minus=0.6,
a_plus=0.6,
tau_minus=12.0,
tau_plus=10.0,
v_tresh=10.0):
simulator = 'spinnaker'
sim.setup(timestep=TIME_STEP, min_delay=delay, max_delay=delay * 2)
randoms = np.random.rand(100, 1)
lif_curr_exp_params = {
'cm': 1.0, # The capacitance of the LIF neuron in nano-Farads
'tau_m': 20.0, # The time-constant of the RC circuit, in milliseconds
'tau_refrac': 5.0, # The refractory period, in milliseconds
'v_reset':
-65.0, # The voltage to set the neuron at immediately after a spike
'v_rest': -65.0, # The ambient rest voltage of the neuron
'v_thresh':
-(v_tresh), # The threshold voltage at which the neuron will spike
'tau_syn_E': 5.0, # The excitatory input current decay time-constant
'tau_syn_I': 5.0, # The inhibitory input current decay time-constant
'i_offset': 0.0, # A base input current to add each timestep
}
Input = sim.Population(input_n,
sim.SpikeSourceArray(spike_times=cellSourceSpikes),
label="Input")
Input.record("spikes")
LIF_Intermediate = sim.IF_curr_exp(**lif_curr_exp_params)
Intermediate = sim.Population(nb_neuron_int,
LIF_Intermediate,
label="Intermediate")
Intermediate.record(("spikes", "v"))
LIF_Output = sim.IF_curr_exp(**lif_curr_exp_params)
Output = sim.Population(nb_neuron_out, LIF_Output, label="Output")
Output.record(("spikes", "v"))
LIF_delayer = sim.IF_curr_exp(**lif_curr_exp_params)
Delay_n = sim.Population(1, LIF_delayer, label="Delay")
Delay_n.record(("spikes", "v"))
python_rng = NumpyRNG(seed=98497627)
delay = delay # (ms) synaptic time delay
# Définition du fonctionnement de la stdp
stdp_proj = sim.STDPMechanism(
timing_dependence=sim.SpikePairRule(tau_plus=tau_plus,
tau_minus=tau_minus,
A_plus=a_plus,
A_minus=a_minus),
weight_dependence=sim.AdditiveWeightDependence(w_min=0.1, w_max=6),
weight=RandomDistribution('normal', (3, 2.9), rng=python_rng),
delay=delay)
Conn_input_inter = sim.Projection(
Input,
Intermediate,
connector=sim.FixedProbabilityConnector(p_conn_in_int,
allow_self_connections=False),
# synapse type set avec la définition de la stdp pour l'aprentsissage
synapse_type=stdp_proj,
receptor_type="excitatory",
label="Connection input to intermediate")
# second projection with stdp
Conn_inter_output = sim.Projection(
Intermediate,
Output, # pre and post population
connector=sim.FixedProbabilityConnector(p_conn_int_out,
allow_self_connections=False),
synapse_type=stdp_proj,
receptor_type="excitatory",
label="Connection intermediate to output")
FixedInhibitory_WTA = sim.StaticSynapse(weight=6)
WTA_INT = sim.Projection(
Intermediate,
Intermediate,
connector=sim.AllToAllConnector(allow_self_connections=False),
synapse_type=FixedInhibitory_WTA,
receptor_type="inhibitory",
label="Connection WTA")
WTA_OUT = sim.Projection(
Output,
Output,
connector=sim.AllToAllConnector(allow_self_connections=False),
synapse_type=FixedInhibitory_WTA,
receptor_type="inhibitory",
label="Connection WTA")
FixedInhibitory_delayer = sim.StaticSynapse(weight=2)
Delay_out = sim.Projection(
Delay_n,
Output,
connector=sim.AllToAllConnector(allow_self_connections=False),
synapse_type=FixedInhibitory_delayer,
receptor_type="inhibitory",
label="Connection WTA")
Delay_inter = sim.Projection(
Intermediate,
Delay_n,
connector=sim.AllToAllConnector(allow_self_connections=False),
synapse_type=FixedInhibitory_delayer,
receptor_type="inhibitory",
label="Connection WTA")
sim.set_number_of_neurons_per_core(sim.IF_curr_exp, 255)
# Définition des callbacks pour la récupération de l'écart-type sur les connexions entrée-intermédiaire, intermédiaire-sortie
weight_recorder1 = WeightRecorder(sampling_interval=1000.0,
projection=Conn_input_inter)
weight_recorder2 = WeightRecorder(sampling_interval=1000.0,
projection=Conn_inter_output)
simtime = ceil(max_time)
# Initialisation des tableaux pour la récupération des poids
weights_int = []
weights_out = []
try:
sim.run(simtime, callbacks=[weight_recorder1, weight_recorder2])
neo = Output.get_data(variables=["spikes", "v"])
spikes = neo.segments[0].spiketrains
#print(spikes)
v = neo.segments[0].filter(name='v')[0]
weights_int = Conn_input_inter.get(["weight"], format="list")
neo_in = Input.get_data(variables=["spikes"])
spikes_in = neo_in.segments[0].spiketrains
#print(spikes_in)
neo_intermediate = Intermediate.get_data(variables=["spikes", "v"])
spikes_intermediate = neo_intermediate.segments[0].spiketrains
#print(spikes_intermediate)
v_intermediate = neo_intermediate.segments[0].filter(name='v')[0]
#print(v_intermediate)
weights_out = Conn_inter_output.get(["weight"], format="list")
sim.reset()
sim.end()
except:
v = 0
spikes = 0
if (isinstance(spikes, list) and isinstance(v, AnalogSignal)):
# Récupération des écart-types
standard_deviation_out = weight_recorder2.get_standard_deviations()
standard_deviation_int = weight_recorder1.get_standard_deviations()
t = np.arange(0., max_time, 1.)
# Création et sauvegarde des graphs sur les spikes et écart-types
savePath = "./Generated_data/training/" + path + "/intermediate_layer_standard_deviation.png"
plt.plot(standard_deviation_int)
plt.xlabel("callbacks tick (1s)")
plt.ylabel("standard deviation of the weights( wmax=6, wmin=0.1 )")
plt.savefig(savePath)
plt.clf()
savePath = "./Generated_data/training/" + path + "/output_layer_standard_deviation.png"
plt.plot(standard_deviation_out)
plt.xlabel("callbacks tick")
plt.ylabel("standard deviation ( wmax=6, wmin=0.1 )")
plt.savefig(savePath)
plt.clf()
savePath = "./Generated_data/training/" + path + "/output_layer_membrane_voltage_and_spikes.png"
plot.Figure(
# plot voltage for first ([0]) neuron
plot.Panel(v,
ylabel="Membrane potential (mV)",
data_labels=[Output.label],
yticks=True,
xlim=(0, simtime)),
# plot spikes (or in this case spike)
plot.Panel(spikes, yticks=True, markersize=5, xlim=(0, simtime)),
title="Spiking activity of the output layer during training",
annotations="Simulated with {}".format(sim.name())).save(savePath)
savePath = "./Generated_data/training/" + path + "/intermediate_layer_membrane_voltage_and_spikes.png"
plot.Figure(
# plot voltage for first ([0]) neuron
plot.Panel(v_intermediate,
ylabel="Membrane potential (mV)",
data_labels=[Output.label],
yticks=True,
xlim=(0, simtime)),
# plot spikes (or in this case spike)
plot.Panel(spikes_intermediate,
yticks=True,
markersize=5,
xlim=(0, simtime)),
title="Spiking activity of the intermediate layer during training",
annotations="Simulated with {}".format(sim.name())).save(savePath)
return v, spikes, weights_int, weights_out
else:
print(
"simulation failed with parmaters parameters : (l'affichage des paramètres ayant causés le disfonctionnement de la simulation sera traitée à une date ultérieur, merci!)"
)
return 0, 0, 0, 0
sim.external_devices.activate_live_output_for(actorPopulation, database_notify_host="localhost", database_notify_port_num=20000)
sim.external_devices.activate_live_output_for(actorSpikeInjector, database_notify_host="localhost", database_notify_port_num=20002)
sim.external_devices.activate_live_output_for(firstSpikeTrigger, database_notify_host="localhost", database_notify_port_num=20004)
timing_rule = sim.SpikePairRule(tau_plus=50.0, tau_minus=50.0,
A_plus=0.001, A_minus=0.001)
weight_rule = sim.AdditiveWeightDependence(w_max=5.0, w_min=-5.0)
stdp_model = sim.STDPMechanism(timing_dependence=timing_rule,
weight_dependence=weight_rule,
weight=2, delay=1)
stdp_projection = sim.Projection(statePopulation, actorPopulation, sim.OneToOneConnector(),
synapse_type=stdp_model)
state_projection = sim.Projection(stateSpikeInjector, statePopulation, sim.OneToOneConnector(),
synapse_type=sim.StaticSynapse(weight=5, delay=2))
actorProjection = sim.Projection(actorSpikeInjector, actorPopulation, sim.OneToOneConnector(),
synapse_type=sim.StaticSynapse(weight=5, delay=0))
connectionList = []
for step in range(numberOfSteps-1):
for action in range(numberOfActions):
connectionList.append((action, action + numberOfActions))
moves_projection = sim.Projection(actorPopulation, actorPopulation, sim.FromListConnector(connectionList),
synapse_type=sim.StaticSynapse(weight=5, delay=2))
connectionList = []
def device_control_uses_payload(self):
return True
@property
def device_control_timesteps_between_sending(self):
return 10
@property
def device_control_partition_id(self):
return "MySpiNNakerLinkDevice"
p.setup(1.0)
pop = p.Population(1, p.SpikeSourcePoisson(rate=100))
spinnaker_link_device_control = p.external_devices.ExternalDeviceLifControl(
devices=[MySpiNNakerLinkDevice(n_atoms=1, spinnaker_link_id=1)],
create_edges=True)
spinnaker_link_device = p.Population(1, spinnaker_link_device_control)
spinnaker_link_device.record("v")
p.Projection(pop, spinnaker_link_device, p.OneToOneConnector(),
p.StaticSynapse(weight=1.0))
p.run(1000)
print spinnaker_link_device.get_data("v").segments[0].filter(name='v')
p.end()
# +-------------------------------------------------------------------+
# | Creation of connections |
# +-------------------------------------------------------------------+
# Connection parameters
JEE = 3.
# Connection type between noise poisson generator and excitatory populations
ee_connector = sim.OneToOneConnector()
# Noise projections
sim.Projection(INoisePre,
pre_pop,
ee_connector,
receptor_type='excitatory',
synapse_type=sim.StaticSynapse(weight=JEE * 0.05))
sim.Projection(INoisePost,
post_pop,
ee_connector,
receptor_type='excitatory',
synapse_type=sim.StaticSynapse(weight=JEE * 0.05))
# Additional Inputs projections
for i in range(len(IAddPre)):
sim.Projection(IAddPre[i],
pre_pop,
ee_connector,
receptor_type='excitatory',
synapse_type=sim.StaticSynapse(weight=JEE * 0.05))
for i in range(len(IAddPost)):
sim.Projection(IAddPost[i],
else:
LGNBright, LGNDark, V1, V2, V4Bright, V4Dark = network
LGNBright.record("spikes")
LGNDark.record("spikes")
V1.record("spikes")
V2.record("spikes")
V4Bright.record("spikes")
V4Dark.record("spikes")
if inputPoisson:
LGNBrightInput = sim.Population(ImageNumPixelRows * ImageNumPixelColumns,
sim.SpikeSourcePoisson())
LGNDarkInput = sim.Population(ImageNumPixelRows * ImageNumPixelColumns,
sim.SpikeSourcePoisson())
sim.Projection(LGNBrightInput, LGNBright, sim.OneToOneConnector(),
sim.StaticSynapse(weight=connections['brightInputToLGN']))
sim.Projection(LGNDarkInput, LGNDark, sim.OneToOneConnector(),
sim.StaticSynapse(weight=connections['darkInputToLGN']))
if numSegmentationLayers > 1:
if useBoundarySegmentation:
# BoundarySegmentationOnInter3.inject(sim.DCSource(amplitude=constantInput, start=0.0, stop=simTime))
BoundarySegmentationOnInter3.set('i_offset', 0.5)
########################################################################################
### Network is defined, now set up stimulus, segmentation signal and run everything! ###
########################################################################################
# Stuff to plot activity of LGN, V1, V2, etc. layers
cumplotDensityLGNBright = [[0 for j in range(ImageNumPixelColumns)]
for i in range(ImageNumPixelRows)]
cumplotDensityLGNDark = [[0 for j in range(ImageNumPixelColumns)]