def inhibitory_connect(layers, source, dest1, dest2, dest3, weight):
sim.Projection(layers[source].population, layers[dest1].population,
sim.OneToOneConnector(),
sim.StaticSynapse(weight=weight))
sim.Projection(layers[source].population, layers[dest2].population,
sim.OneToOneConnector(),
sim.StaticSynapse(weight=weight))
sim.Projection(layers[source].population, layers[dest3].population,
sim.OneToOneConnector(),
sim.StaticSynapse(weight=weight))
def set_distal_connections(self, connections):
for src, tgt, sgm in connections:
soma = pynn.PopulationView(self.soma, [int(src)])
segment = pynn.PopulationView(self.distal,
[2 * int(tgt) + int(sgm)])
pynn.Projection(soma, segment,
pynn.OneToOneConnector(weights=0.014))
def connect(self):
# connect populations
self.injection = pynn.Projection(self.sources,
self.columns,
pynn.FixedProbabilityConnector(
0.02, weights=0.0033 * 2),
target='excitatory',
rng=pynn.random.NumpyRNG(seed=5337))
self.recurrent_excitation = pynn.Projection(
self.columns,
self.columns,
pynn.OneToOneConnector(weights=0.01 * 2),
target='excitatory')
self.lateral_inhibition = pynn.Projection(
self.columns,
self.columns,
pynn.DistanceDependentProbabilityConnector('d < 10',
weights=0.004 * 2),
target='inhibitory',
rng=pynn.random.NumpyRNG(seed=5337))
self.global_inhibition = pynn.Projection(
self.inhibitory_pool,
self.columns,
pynn.FixedProbabilityConnector(0.8, weights=0.0012 * 2),
target='inhibitory',
rng=pynn.random.NumpyRNG(seed=5337))
self.forward_inhibition = pynn.Projection(
self.sources,
self.inhibitory_pool,
pynn.FixedProbabilityConnector(0.8, weights=0.0035),
target='excitatory',
rng=pynn.random.NumpyRNG(seed=5337))
def test_ticket244():
nest = pyNN.nest
nest.setup(threads=4)
p1 = nest.Population(4, nest.IF_curr_exp())
p1.record('spikes')
poisson_generator = nest.Population(3, nest.SpikeSourcePoisson(rate=1000.0))
conn = nest.OneToOneConnector()
syn = nest.StaticSynapse(weight=1.0)
nest.Projection(poisson_generator, p1.sample(3), conn, syn, receptor_type="excitatory")
nest.run(15)
p1.get_data()
def create_corner_layer_for(input_layers):
shape = input_layers[0].shape
total_output_neurons = np.prod(shape)
output_population = sim.Population(total_output_neurons,
sim.IF_curr_exp(),
label='corner')
for layer in input_layers:
sim.Projection(layer.population, output_population,
sim.OneToOneConnector(),
sim.StaticSynapse(weight=1., delay=0.5))
return Layer(output_population, shape)
def connect(self):
n_cells = self.parameters.config.n_cells
n_segments = self.parameters.config.n_segments
# connect populations
pynn.Projection(self.distal_input, self.distal,
pynn.OneToOneConnector(weights=0.025))
for i in range(self.parameters.config.n_columns):
# get "compartments" for all cells in this column
inhibitions = self.inhibitory[i * n_cells:(i + 1) * n_cells]
somas = self.soma[i * n_cells:(i + 1) * n_cells]
proximal_input = pynn.PopulationView(self.proximal_input, [i])
# set up connections with columnar symmetry
pynn.Projection(inhibitions,
somas,
pynn.DistanceDependentProbabilityConnector(
'd>=1', weights=0.2),
target='SYN_2') # 4
pynn.Projection(proximal_input,
somas,
pynn.AllToAllConnector(weights=0.08),
target='SYN_1') # 1
pynn.Projection(proximal_input, inhibitions,
pynn.AllToAllConnector(weights=0.042)) # 2
for j in range(self.parameters.config.n_cells):
# get "compartments" for this specific cell
segments = self.distal[i * n_cells * n_segments + j *
n_segments:i * n_cells * n_segments +
(j + 1) * n_segments]
inhibition = pynn.PopulationView(self.inhibitory,
[i * n_cells + j])
soma = pynn.PopulationView(self.soma, [i * n_cells + j])
# set up connections with cellular symmetry
pynn.Projection(segments,
inhibition,
pynn.AllToAllConnector(weights=0.15),
target='inhibitory') # 3
pynn.Projection(segments,
soma,
pynn.AllToAllConnector(weights=0.15),
target='SYN_3') # 3
def connect(self):
"""Setup connections between populations"""
params = self.parameters.projections
# generate weights with normal distributed jitter and set up stimulus
w = params.stimulus.weight + np.random.normal(
0, params.stimulus.jitter, len(self.columns))
stimulus_connector = pynn.OneToOneConnector(weights=w)
pynn.Projection(self.stimulus, self.columns, stimulus_connector)
# projection to accumulate/count the number of active columns
accumulation_connector = pynn.AllToAllConnector(
weights=params.accumulation.weight)
pynn.Projection(self.columns, self.kill_switch, accumulation_connector)
# projection to inhibit all columns
inhibition_connector = pynn.AllToAllConnector(
weights=params.inhibition.weight)
pynn.Projection(self.kill_switch,
self.columns,
inhibition_connector,
target='inhibitory')
# forward inhibition
forward_inhibition_connector = pynn.FixedProbabilityConnector(
params.forward_inhibition.probability,
weights=params.forward_inhibition.weight)
pynn.Projection(self.stimulus,
self.columns,
forward_inhibition_connector,
target='inhibitory')
# calculate connectivity matrix
n_columns = self.parameters.populations.columns.size
n_inputs = self.parameters.config.input_size
self.connections = (np.random.uniform(0, 1, n_columns * n_inputs) >
0.60).reshape(len(self.columns),
n_inputs).astype(np.int64)
self.permanences = np.random.normal(.3, .05,
n_columns * n_inputs).reshape(
len(self.columns), n_inputs)
def test_callback(data_input):
global message
message = data_input.actual.positions
msg_list = list(message)
#msg_list[0] = int(message[0].encode('hex'),16)
#for i in
#msg_list = int(message.encode('hex'),16)
#print('============= Received image data.',message)
rospy.loginfo('=====received data %r', msg_list[0])
timer = Timer()
dt = 0.1
p.setup(timestep=dt) # 0.1ms
pop_1 = p.Population(1, p.IF_curr_exp, {}, label="pop_1")
#input = p.Population(1, p.SpikeSourceArray, {'spike_times': [[0,3,6]]}, label='input')
input = p.Population(1, p.SpikeSourcePoisson,
{'rate': (msg_list[0] + 1.6) * 100})
stat_syn = p.StaticSynapse(weight=50.0, delay=1)
input_proj = p.Projection(input,
pop_1,
p.OneToOneConnector(),
synapse_type=stat_syn,
receptor_type='excitatory')
pop_1.record(['v', 'spikes'])
p.run(10)
pop_1_data = pop_1.get_data()
spikes = pop_1_data.segments[0].spiketrains[0]
mean_rate = int(gaussian_convolution(spikes, dt))
rospy.loginfo('=====mean_rate %r', mean_rate) # mean_rate = 64
rate_command = mean_rate
# rate coding of the spike train
'''
pub = rospy.Publisher('/cmd_vel_mux/input/teleop', Twist, queue_size=10)
# construct the output command
command = Twist()
command.linear.x = rate_command*0.02
command.angular.z = rate_command/50000.
pub.publish(command)
'''
pub = rospy.Publisher('/arm_controller/follow_joint_trajectory/goal',
FollowJointTrajectoryActionGoal,
queue_size=10)
command = FollowJointTrajectoryActionGoal()
command.header.stamp = rospy.Time.now()
command.goal.trajectory.joint_names = ['elbow']
point = JointTrajectoryPoint()
point.positions = [rate_command / 10]
point.time_from_start = rospy.Duration(1)
command.goal.trajectory.points.append(point)
pub.publish(command)
rospy.loginfo('=====send command %r', command.goal.trajectory.points[0])
fig_settings = {
'lines.linewidth': 0.5,
'axes.linewidth': 0.5,
'axes.labelsize': 'small',
'legend.fontsize': 'small',
'font.size': 8
}
plt.rcParams.update(fig_settings)
fig1 = plt.figure(1, figsize=(6, 8))
def plot_spiketrains(segment):
for spiketrain in segment.spiketrains:
y = np.ones_like(spiketrain) * spiketrain.annotations['source_id']
plt.plot(spiketrain, y, '.')
plt.ylabel(segment.name)
plt.setp(plt.gca().get_xticklabels(), visible=False)
def plot_signal(signal, index, colour='b'):
label = "Neuron %d" % signal.annotations['source_ids'][index]
plt.plot(signal.times, signal[:, index], colour, label=label)
plt.ylabel("%s (%s)" %
(signal.name, signal.units._dimensionality.string))
plt.setp(plt.gca().get_xticklabels(), visible=False)
plt.legend()
print("now plotting the network---------------")
rospy.loginfo('--------now plotting---------------')
n_panels = sum(a.shape[1]
for a in pop_1_data.segments[0].analogsignalarrays) + 2
plt.subplot(n_panels, 1, 1)
plot_spiketrains(pop_1_data.segments[0])
panel = 3
for array in pop_1_data.segments[0].analogsignalarrays:
for i in range(array.shape[1]):
plt.subplot(n_panels, 1, panel)
plot_signal(array, i, colour='bg'[panel % 2])
panel += 1
plt.xlabel("time (%s)" % array.times.units._dimensionality.string)
plt.setp(plt.gca().get_xticklabels(), visible=True) #
# cells.initialize('regime', 1002) # temporary hack
cells.initialize('Regime9ML', 1.0) # temporary hack
# from numpy import r
input = sim.Population(3, sim.SpikeSourceArray)
numpy.random.seed(12345)
input[0].spike_times = numpy.add.accumulate(
numpy.random.exponential(1000.0 / 100.0, size=1000))
input[1].spike_times = numpy.add.accumulate(
numpy.random.exponential(1000.0 / 20.0, size=1000))
input[2].spike_times = numpy.add.accumulate(
numpy.random.exponential(1000.0 / 50.0, size=1000))
connector = sim.OneToOneConnector(weights=1.0, delays=0.5)
conn = [
sim.Projection(input[0:1], cells, connector, target='AMPA_spikeinput'),
sim.Projection(input[1:2], cells, connector, target='GABAa_spikeinput'),
sim.Projection(input[2:3], cells, connector, target='GABAb_spikeinput')
]
cells._record('iaf_V')
cells._record('AMPA_g')
cells._record('GABAa_g')
cells._record('GABAb_g')
cells.record()
sim.run(100.0)
V1 = network.get_population("V1LayerToPlot")
V2 = network.get_population("V2LayerToPlot")
V4Bright = network.get_population("V4Brightness")
V4Dark = network.get_population("V4Darkness")
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 useSurfaceSegmentation:
SurfaceSegmentationOff = network.get_population(
"SurfaceSegmentationOff")
SurfaceSegmentationOn = network.get_population("SurfaceSegmentationOn")
if useBoundarySegmentation:
BoundarySegmentationOff = network.get_population(
"BoundarySegmentationOff")
BoundarySegmentationOn = network.get_population(
"BoundarySegmentationOn")
network.get_population("BoundarySegmentationOnInter3").inject(
sim.DCSource(amplitude=constantInput, start=0.0, stop=simTime))
sim.IF_cond_alpha(**cell_params),
label="inhib_pop")
spike_source_1 = sim.Population(
1, sim.SpikeSourceArray(spike_times=spike_time_for_id_1))
spike_source_2 = sim.Population(
1, sim.SpikeSourceArray(spike_times=spike_time_for_id_2))
spike_source_3 = sim.Population(
1, sim.SpikeSourceArray(spike_times=spike_time_for_id_3))
spike_source_4 = sim.Population(
1, sim.SpikeSourceArray(spike_times=spike_time_for_id_4))
spike_source_9 = sim.Population(
1, sim.SpikeSourceArray(spike_times=spike_time_for_id_9))
spike_2_conn_for_1 = sim.Projection(spike_source_1, cann_pop[1:2],
sim.OneToOneConnector(),
sim.StaticSynapse(weight=0.002, delay=0.1))
spike_2_conn_for_2 = sim.Projection(spike_source_2, cann_pop[2:3],
sim.OneToOneConnector(),
sim.StaticSynapse(weight=0.002, delay=0.1))
spike_2_conn_for_3 = sim.Projection(spike_source_3, cann_pop[3:4],
sim.OneToOneConnector(),
sim.StaticSynapse(weight=0.002, delay=0.1))
spike_2_conn_for_4 = sim.Projection(spike_source_4, cann_pop[4:5],
sim.OneToOneConnector(),
sim.StaticSynapse(weight=0.002, delay=0.1))
spike_2_conn_for_9 = sim.Projection(spike_source_9, cann_pop[9:10],
sim.OneToOneConnector(),
sim.StaticSynapse(weight=0.002, delay=0.1))
cann_2_cann = sim.Projection(
#generate_spike_times = [[0], [500], [1000], [1500], [2000], [2500], [3000],
# [3500], [4000], [4500]] #, [5000]]
#spike_source = sim.Population(n_neurons,
# sim.SpikeSourceArray(
# spike_times = generate_spike_times))
spike_source = sim.Population(
n_neurons, sim.SpikeSourceArray(spike_times=[0, 1000, 3000]))
# populations and projections
layer_1 = sim.Population(n_neurons, sim.IF_curr_alpha(), label="layer_1")
'''
layer_2 = sim.Population(n_neurons, sim.IF_curr_alpha(),
label = "layer_2")
'''
proj_src_2_l1 = sim.Projection(spike_source, layer_1, sim.OneToOneConnector())
'''
proj_l1_2_l2 = sim.Projection(layer_1, layer_2,
sim.OneToOneConnector())
'''
sim.run(sim_time)
layer_1.record(('spikes', 'v'))
#layer_2.record(['spikes', 'v'])
#layer_1.record(['v', 'spikes'])
#layer_2.record(['v', 'spikes'])
# plot the spikes
data_1 = layer_1.get_data().segments[0]
vm = data_1.filter(name="v")
Figure(Panel(vm, ylabel="Memb. Pot."),
'''
#output poission
pop = p.Population(
num_output,
p.SpikeSourcePoisson,
{
'rate': MIN_rate, #test_x[i],
'start': (epo * num_epo + i) * (dur_train + silence),
'duration': dur_train
})
temp_popv = p.PopulationView(pop, np.nonzero(train_y[ind])[0])
temp_popv.set('rate', teaching_rate)
TeachingPoission.append(pop)
#print ImagePoission[10].get('start')
ee_connector = p.OneToOneConnector(weights=3.0)
for i in range(num_train * num_epo * 1):
p.Projection(ImagePoission[i],
pop_input,
ee_connector,
target='excitatory')
pop_output = p.Population(num_output, p.IF_curr_exp, cell_params_lif)
weight_max = 1.3
stdp_model = p.STDPMechanism(
timing_dependence=p.SpikePairRule(tau_plus=10., tau_minus=10.0),
weight_dependence=p.MultiplicativeWeightDependence(w_min=0.0,
w_max=weight_max,
A_plus=0.01,
A_minus=0.01)
#AdditiveWeightDependence
label='Background Noise')
background_noise_to_exc = simulator.Projection(
noise_population, cortical_neurons_exc, simulator.AllToAllConnector(),
noise_syn)
background_noise_to_inh = simulator.Projection(
noise_population, cortical_neurons_inh, simulator.AllToAllConnector(),
noise_syn)
else:
# If correlated is False, all cortical neurons receive independent noise
noise_population_exc = simulator.Population(
Ncell_exc**2, noise_model, label='Background Noise to Exc')
noise_population_inh = simulator.Population(
Ncell_inh**2, noise_model, label='Background Noise to Inh')
background_noise_to_exc = simulator.Projection(
noise_population_exc, cortical_neurons_exc,
simulator.OneToOneConnector(), noise_syn)
background_noise_to_inh = simulator.Projection(
noise_population_inh, cortical_neurons_inh,
simulator.OneToOneConnector(), noise_syn)
#############################
## Thalamo-Cortical connections
#############################
# Sample random phases and orientations
phases_space = np.linspace(-180, 180, 20)
orientation_space = np.linspace(-90, 90, 20)
phases_exc = np.random.rand(Ncell_exc**2) * 360 # Phases continium
#phases_exc = np.random.choice(phases_space, Ncell_exc*2) # Phases discrete
spike_times = spike_input))
neg_spike_src = sim.Population(1, sim.SpikeSourceArray(
spike_times = neg_spike_times))
#spike_2_conn_for_1 = sim.Projection(spike_source_1, hd_cann_pop[1:2], sim.OneToOneConnector(),
# sim.StaticSynapse(weight = 0.002, delay = 0.1))
#spike_2_conn_for_2 = sim.Projection(spike_source_2, hd_cann_pop[2:3], sim.OneToOneConnector(),
# sim.StaticSynapse(weight = 0.002, delay = 0.1))
spike_2_conn_for_3 = sim.Projection(hd_spike_src, hd_cann_pop[3:4], sim.AllToAllConnector(),
sim.StaticSynapse(weight = 0.002, delay = 0.1))
#spike_2_conn_for_4 = sim.Projection(spike_source_4, hd_cann_pop[4:5], sim.OneToOneConnector(),
# sim.StaticSynapse(weight = 0.002, delay = 0.1))
#spike_2_conn_for_9 = sim.Projection(spike_source_9, hd_cann_pop[9:10], sim.OneToOneConnector(),
# sim.StaticSynapse(weight = 0.002, delay = 0.1))
pos_spikes = sim.Projection(pos_spike_src, pos_rot_conj[3:4], sim.OneToOneConnector(),
sim.StaticSynapse(weight = 0.2, delay = 0.1))
neg_spikes = sim.Projection(neg_spike_src, neg_rot_conj[4:5], sim.OneToOneConnector(),
sim.StaticSynapse(weight = 0.2, delay = 0.1))
# Connections/ Projections
hd_cann_2_hd_cann = sim.Projection(hd_cann_pop, hd_cann_pop,
sim.FromListConnector(hd_cann_connector, column_names=["weight"]),
sim.StaticSynapse(weight = 0.0001, delay = 75))
hd_cann_2_inh = sim.Projection(hd_cann_pop, inhib_pop, sim.AllToAllConnector(),
sim.StaticSynapse(weight = 0.02, delay = 0.1),
receptor_type = "excitatory")
def create_brain():
"""
Initializes PyNN with the neuronal network that has to be simulated for the experiment
"""
GR_PARAMS = {'cm': 0.002,
'v_rest': -70.0,
'tau_m': 100.0,
'e_rev_E': 0.0,
'e_rev_I': -75.0,
'v_reset': -70.0,
'v_thresh': -40.0,
'tau_refrac': 1.0,
'tau_syn_E': 0.5,
'tau_syn_I': 2.0}
GO_PARAMS = {'cm': 0.002,
'v_rest': -70.0,
'tau_m': 100.0,
'e_rev_E': 0.0,
'e_rev_I': -75.0,
'v_reset': -70.0,
'v_thresh': -40.0,
'tau_refrac': 1.0,
'tau_syn_E': 0.5,
'tau_syn_I': 2.0}
PC_PARAMS = {'C_m': 0.314,
'g_L': 0.012,
'E_L': -70.0,
'E_ex': 0.0,
'E_in': -75.0,
'e_cs': 0.0,
'V_reset': -70.0,
'V_th': -52.0,
't_ref': 1.0,
'tau_syn_ex': 0.85,
'tau_syn_in': 5.45,
'tau_syn_cs': 0.85}
VN_PARAMS = {'C_m': 0.002,
'g_L': 0.0002,
'E_L': -70.0,
'E_ex': 0.0,
'E_in': -80.0,
'e_ts': 0.0,
'V_reset': -70.5,
'V_th': -40.0,
't_ref': 1.0,
'tau_syn_ex': 0.5,
'tau_syn_in': 7.0,
'tau_syn_ts': 0.85,
'tau_cos': 10.0,
'exponent': 2.0}
##THIS MODULE CAN BE DOWNLOADED FROM https://github.com/jgarridoalcazar/SpikingCerebellum/
#try:
# nest.Install('cerebellummodule')
#except nest.NESTError:
# pass
parrot_neuron = sim.native_cell_type('parrot_neuron')
# Create MF population
MF_population = sim.Population(num_MF_neurons,parrot_neuron,{},label='MFLayer')
# Create GOC population
GOC_population = sim.Population(num_GOC_neurons,sim.IF_cond_alpha(**GO_PARAMS),label='GOCLayer')
# Create MF-GO connections
mf_go_connections = sim.Projection(MF_population,
GOC_population,
sim.OneToOneConnector(),
sim.StaticSynapse(delay=1.0, weight=mf_go_weights))
# Create GrC population
GC_population = sim.Population(num_GC_neurons,sim.IF_cond_alpha(**GR_PARAMS),label='GCLayer')
# Random distribution for synapses delays and weights
delay_distr = RandomDistribution('uniform', (1.0, 10.0), rng=NumpyRNG(seed=85524))
weight_distr_MF = RandomDistribution('uniform', (mf_gc_weights*0.8, mf_gc_weights*1.2), rng=NumpyRNG(seed=85524))
weight_distr_GO = RandomDistribution('uniform', (go_gc_weights*0.8, go_gc_weights*1.2), rng=NumpyRNG(seed=24568))
# Create MF-GC and GO-GC connections
float_num_MF_neurons = float (num_MF_neurons)
for i in range (num_MF_neurons):
GC_medium_index = int(round((i / float_num_MF_neurons) * num_GC_neurons))
GC_lower_index = GC_medium_index - 40
GC_upper_index = GC_medium_index + 60
if(GC_lower_index < 0):
GC_lower_index = 0
elif(GC_upper_index > num_GC_neurons):
GC_upper_index = num_GC_neurons
if(GC_lower_index < GC_medium_index):
GO_GC_con1 = sim.Projection(sim.PopulationView(GOC_population, range(i, i+1)),
sim.PopulationView(GC_population, range(GC_lower_index, GC_medium_index)),
sim.AllToAllConnector(),
sim.StaticSynapse(delay=delay_distr, weight=weight_distr_GO))
MF_GC_con2 = sim.Projection(sim.PopulationView(MF_population, range(i, i+1)),
sim.PopulationView(GC_population, range(GC_medium_index, GC_medium_index + 20)),
sim.AllToAllConnector(),
sim.StaticSynapse(delay=delay_distr, weight=weight_distr_MF))
if((GC_medium_index + 20) < GC_upper_index):
GO_GC_con3 = sim.Projection(sim.PopulationView(GOC_population, range(i, i+1)),
sim.PopulationView(GC_population, range(GC_medium_index + 20, GC_upper_index)),
sim.AllToAllConnector(),
sim.StaticSynapse(delay=delay_distr, weight=weight_distr_GO))
# Create PC population (THIS MODEL HAS BEEN DEFINED IN THE CEREBELLUMMODULE PACKAGE: https://github.com/jgarridoalcazar/SpikingCerebellum/)
pc_neuron = sim.native_cell_type('iaf_cond_exp_cs')
PC_population = sim.Population(num_PC_neurons,pc_neuron(**PC_PARAMS),label='PCLayer')
# Create VN population (THIS MODEL HAS BEEN DEFINED IN THE CEREBELLUMMODULE PACKAGE: https://github.com/jgarridoalcazar/SpikingCerebellum/)
vn_neuron = sim.native_cell_type('iaf_cond_exp_cos')
VN_population = sim.Population(num_VN_neurons,vn_neuron(**VN_PARAMS),label='VNLayer')
# Create IO population
IO_population = sim.Population(num_IO_neurons,parrot_neuron,{},label='IOLayer')
# Create MF-VN learning rule (THIS MODEL HAS BEEN DEFINED IN THE CEREBELLUMMODULE PACKAGE: https://github.com/jgarridoalcazar/SpikingCerebellum/)
stdp_cos = sim.native_synapse_type('stdp_cos_synapse')(**{'weight':mf_vn_weights,
'delay':1.0,
'exponent': 2.0,
'tau_cos': 5.0,
'A_plus': 0.0000009,
'A_minus': 0.00001,
'Wmin': 0.0005,
'Wmax': 0.007})
# Create MF-VN connections
mf_vn_connections = sim.Projection(MF_population,
VN_population,
sim.AllToAllConnector(),
receptor_type='AMPA',
# synapse_type = sim.StaticSynapse(delay=1.0, weight=mf_vn_weights))
synapse_type = stdp_cos)
# Create PC-VN connections
pc_vn_connections = sim.Projection(PC_population,
VN_population,
sim.OneToOneConnector(),
receptor_type='GABA',
synapse_type = sim.StaticSynapse(delay=1.0, weight=pc_vn_weights))
# This second synapse with "receptor_type=TEACHING_SIGNAL" propagates the learning signals that drive the plasticity mechanisms in MF-VN synapses
pc_vn_connections = sim.Projection(PC_population,
VN_population,
sim.OneToOneConnector(),
receptor_type='TEACHING_SIGNAL',
synapse_type = sim.StaticSynapse(delay=1.0, weight=0.0))
# Create MF-VN learning rule (THIS MODEL HAS BEEN DEFINED IN THE CEREBELLUMMODULE PACKAGE: https://github.com/jgarridoalcazar/SpikingCerebellum/)
stdp_syn = sim.native_synapse_type('stdp_sin_synapse')(**{'weight':gc_pc_weights,
'delay':1.0,
'exponent': 10,
'peak': 100.0,
'A_plus': 0.000014,
'A_minus': 0.00008,
'Wmin': 0.000,
'Wmax': 0.010})
# Create GC-PC connections
gc_pc_connections = sim.Projection(GC_population,
PC_population,
sim.AllToAllConnector(),
receptor_type='AMPA',
# synapse_type = sim.StaticSynapse(delay=1.0, weight=gc_pc_weights))
synapse_type = stdp_syn)
# Create IO-PC connections. This synapse with "receptor_type=COMPLEX_SPIKE" propagates the learning signals that drive the plasticity mechanisms in GC-PC synapses
io_pc_connections = sim.Projection(IO_population,
PC_population,
sim.OneToOneConnector(),
receptor_type='COMPLEX_SPIKE',
synapse_type = sim.StaticSynapse(delay=1.0, weight=io_pc_weights))
# Group all neural layers
population = MF_population + GOC_population + GC_population + PC_population + VN_population + IO_population
# Set Vm to resting potential
# sim.initialize(PC_population, V_m=PC_population.get('E_L'))
# sim.initialize(VN_population, V_m=VN_population.get('E_L'))
return population
def create_S2_layers(C1_layers: Dict[float, Sequence[Layer]], feature_size,
s2_prototype_cells, refrac_s2=.1, stdp=True,
inhibition=True)\
-> Dict[float, List[Layer]]:
"""
Creates all prototype S2 layers for all sizes.
Parameters:
`layers_dict`: A dictionary containing for each size a list of C1
layers, for each feature one
`feature_size`:
`s2_prototype_cells`:
`refrac_s2`:
`stdp`:
Returns:
A dictionary containing for each size a list of different S2
layers, for each prototype one.
"""
f_s = feature_size
initial_weight = 25 / (f_s * f_s)
weight_rng = rnd.RandomDistribution('normal',
mu=initial_weight,
sigma=initial_weight / 20)
i_offset_rng = rnd.RandomDistribution('normal', mu=.5, sigma=.45)
weights = list(
map(lambda x: weight_rng.next() * 1000, range(4 * f_s * f_s)))
S2_layers = {}
i_offsets = list(
map(lambda x: i_offset_rng.next(), range(s2_prototype_cells)))
ndicts = list(map(lambda x: {}, range(s2_prototype_cells)))
ondicts = list(map(lambda x: {}, range(s2_prototype_cells)))
omdicts = list(map(lambda x: {}, range(s2_prototype_cells)))
for size, layers in C1_layers.items():
n, m = how_many_squares_in_shape(layers[0].shape, (f_s, f_s), f_s)
if stdp:
l_i_offsets = [list(map(lambda x: rnd.RandomDistribution('normal',
mu=i_offsets[i], sigma=.25).next(), range(n * m)))\
for i in range(s2_prototype_cells)]
else:
l_i_offsets = np.zeros((s2_prototype_cells, n * m))
print('S2 Shape', n, m)
layer_list = list(
map(
lambda i: Layer(
sim.Population(n * m,
sim.IF_curr_exp(i_offset=l_i_offsets[i],
tau_refrac=refrac_s2),
structure=space.Grid2D(aspect_ratio=m / n),
label=str(i)), (n, m)),
range(s2_prototype_cells)))
for S2_layer in layer_list:
for C1_layer in layers:
S2_layer.projections[C1_layer.population.label] =\
connect_layer_to_layer(C1_layer, S2_layer, (f_s, f_s), f_s,
[[w] for w in weights[:f_s * f_s]],
stdp=stdp,
initial_weight=initial_weight,
ndicts=ndicts, ondicts=ondicts,
omdicts=omdicts)
S2_layers[size] = layer_list
# Set the labels of the shared connections
if stdp:
t = time.clock()
print('Set shared labels')
for s2_label_dicts in [ndicts, ondicts, omdicts]:
for i in range(s2_prototype_cells):
w_iter = weights.__iter__()
for label, (source, target) in s2_label_dicts[i].items():
conns = nest.GetConnections(source=source, target=target)
nest.SetStatus(conns, {
'label': label,
'weight': w_iter.__next__()
})
print('Setting labels took', time.clock() - t)
if inhibition:
# Create inhibitory connections between the S2 cells
# First between the neurons of the same layer...
inh_weight = -10
inh_delay = .1
print('Create S2 self inhibitory connections')
for layer_list in S2_layers.values():
for layer in layer_list:
sim.Projection(
layer.population, layer.population,
sim.AllToAllConnector(allow_self_connections=False),
sim.StaticSynapse(weight=inh_weight, delay=inh_delay))
# ...and between the layers
print('Create S2 cross-scale inhibitory connections')
for i in range(s2_prototype_cells):
for layer_list1 in S2_layers.values():
for layer_list2 in S2_layers.values():
if layer_list1[i] != layer_list2[i]:
sim.Projection(
layer_list1[i].population,
layer_list2[i].population, sim.AllToAllConnector(),
sim.StaticSynapse(weight=inh_weight,
delay=inh_delay))
if stdp:
# Create the inhibition between different prototype layers
print('Create S2 cross-prototype inhibitory connections')
for layer_list in S2_layers.values():
for layer1 in layer_list:
for layer2 in layer_list:
if layer1 != layer2:
sim.Projection(
layer1.population, layer2.population,
sim.OneToOneConnector(),
sim.StaticSynapse(weight=inh_weight - 1,
delay=inh_delay))
return S2_layers
def run_retina(params):
"""Run the retina using the specified parameters."""
print "Setting up simulation"
timer = Timer()
timer.start() # start timer on construction
pyNN.setup(timestep=params['dt'],
max_delay=params['syn_delay'],
threads=params['threads'],
rng_seeds=params['kernelseeds'])
N = params['N']
phr_ON = pyNN.Population((N, N), pyNN.native_cell_type('dc_generator')())
phr_OFF = pyNN.Population((N, N), pyNN.native_cell_type('dc_generator')())
noise_ON = pyNN.Population(
(N, N),
pyNN.native_cell_type('noise_generator')(mean=0.0,
std=params['noise_std']))
noise_OFF = pyNN.Population(
(N, N),
pyNN.native_cell_type('noise_generator')(mean=0.0,
std=params['noise_std']))
phr_ON.set(start=params['simtime'] / 4,
stop=params['simtime'] / 4 * 3,
amplitude=params['amplitude'] * params['snr'])
phr_OFF.set(start=params['simtime'] / 4,
stop=params['simtime'] / 4 * 3,
amplitude=-params['amplitude'] * params['snr'])
# target ON and OFF populations
v_init = params['parameters_gc'].pop('Vinit')
out_ON = pyNN.Population((N, N),
pyNN.native_cell_type('iaf_cond_exp_sfa_rr')(
**params['parameters_gc']))
out_OFF = pyNN.Population((N, N),
pyNN.native_cell_type('iaf_cond_exp_sfa_rr')(
**params['parameters_gc']))
out_ON.initialize(v=v_init)
out_OFF.initialize(v=v_init)
#print "Connecting the network"
retina_proj_ON = pyNN.Projection(phr_ON, out_ON, pyNN.OneToOneConnector())
retina_proj_ON.set(weight=params['weight'])
retina_proj_OFF = pyNN.Projection(phr_OFF, out_OFF,
pyNN.OneToOneConnector())
retina_proj_OFF.set(weight=params['weight'])
noise_proj_ON = pyNN.Projection(noise_ON, out_ON, pyNN.OneToOneConnector())
noise_proj_ON.set(weight=params['weight'])
noise_proj_OFF = pyNN.Projection(noise_OFF, out_OFF,
pyNN.OneToOneConnector())
noise_proj_OFF.set(weight=params['weight'])
out_ON.record('spikes')
out_OFF.record('spikes')
# reads out time used for building
buildCPUTime = timer.elapsedTime()
print "Running simulation"
timer.start() # start timer on construction
pyNN.run(params['simtime'])
simCPUTime = timer.elapsedTime()
out_ON_DATA = out_ON.get_data().segments[0]
out_OFF_DATA = out_OFF.get_data().segments[0]
print "\nRetina Network Simulation:"
print(params['description'])
print "Number of Neurons : ", N**2
print "Output rate (ON) : ", out_ON.mean_spike_count(), \
"spikes/neuron in ", params['simtime'], "ms"
print "Output rate (OFF) : ", out_OFF.mean_spike_count(), \
"spikes/neuron in ", params['simtime'], "ms"
print "Build time : ", buildCPUTime, "s"
print "Simulation time : ", simCPUTime, "s"
return out_ON_DATA, out_OFF_DATA
stimSpikes = np.arange(stimInterval, (stimNoSpikes + 0.5) * stimInterval,
stimInterval)
measureSpikes = stimSpikes + delayStimMeasure
stim = pynn.Population(1, pynn.SpikeSourceArray, {'spike_times': stimSpikes})
measure = pynn.Population(1, pynn.SpikeSourceArray,
{'spike_times': measureSpikes})
#create neuron
neuron = pynn.Population(1, pynn.IF_cond_exp)
#init and import custom NEST synapse model
pynn.nest.SetDefaults(synapseModel, synapseParams)
stdpModel = pynn.NativeSynapseDynamics(synapseModel)
#connect stimuli
connStim = pynn.OneToOneConnector(weights=stimWeight)
connMeasure = pynn.OneToOneConnector(weights=measureWeight)
pynn.Projection(stim, neuron, connStim, target='excitatory')
prj = pynn.Projection(measure,
neuron,
connMeasure,
synapse_dynamics=stdpModel,
target='excitatory')
#record spike times and membrane potential
neuron.record()
neuron.record_v()
connSTDP = pynn.nest.FindConnections(measure)
weightList = []
aCausalList = []
}
sim.setup()
neuron1 = sim.Population(n, sim.IF_cond_alpha(**cell_params), label="neuron1")
neuron2 = sim.Population(n, sim.IF_cond_alpha(**cell_params), label="neuron2")
spike_times = [1000., 2000.]
spike_source = sim.Population(1, sim.SpikeSourceArray(spike_times=spike_times))
conn = sim.Projection(spike_source, neuron1[spiky:spiky + 1],
sim.AllToAllConnector(),
sim.StaticSynapse(weight=0.002, delay=1.))
n2n_conn = sim.Projection(neuron1, neuron2, sim.OneToOneConnector(),
sim.StaticSynapse(weight=0.002, delay=1.))
spike_source.record('spikes')
neuron1.record(('v', 'spikes'))
neuron2.record(('v', 'spikes'))
sim.run(5000.0)
#print neuron1.get_spike_counts()
from pyNN.utility.plotting import Figure, Panel
data1 = neuron1.get_data().segments[0]
data2 = neuron1.get_data().segments[0]
vm = data1.filter(name="v")[0]
Figure(Panel(vm, ylabel="Membrane potential (mV)", yticks=True),
def estimate_kb(cell_params_lif):
cell_para = copy.deepcopy(cell_params_lif)
random.seed(0)
p.setup(timestep=1.0, min_delay=1.0, max_delay=16.0)
run_s = 10.
runtime = 1000. * run_s
max_rate = 1000.
ee_connector = p.OneToOneConnector(weights=1.0, delays=2.0)
pop_list = []
pop_output = []
pop_source = []
x = np.arange(0., 1.01, 0.1)
count = 0
trail = 10
for i in x:
for j in range(trail): #trails for average
pop_output.append(p.Population(1, p.IF_curr_exp, cell_para))
poisson_spikes = mu.poisson_generator(i * max_rate, 0, runtime)
pop_source.append(
p.Population(1, p.SpikeSourceArray,
{'spike_times': poisson_spikes}))
p.Projection(pop_source[count],
pop_output[count],
ee_connector,
target='excitatory')
pop_output[count].record()
count += 1
count = 0
for i in x:
cell_para['i_offset'] = i
pop_list.append(p.Population(1, p.IF_curr_exp, cell_para))
pop_list[count].record()
count += 1
pop_list[count - 1].record_v()
p.run(runtime)
rate_I = np.zeros(count)
rate_P = np.zeros(count)
rate_P_max = np.zeros(count)
rate_P_min = np.ones(count) * 1000.
for i in range(count):
spikes = pop_list[i].getSpikes(compatible_output=True)
rate_I[i] = len(spikes) / run_s
for j in range(trail):
spikes = pop_output[i * trail +
j].getSpikes(compatible_output=True)
spike_num = len(spikes) / run_s
rate_P[i] += spike_num
if spike_num > rate_P_max[i]:
rate_P_max[i] = spike_num
if spike_num < rate_P_min[i]:
rate_P_min[i] = spike_num
rate_P[i] /= trail
'''
#plot_spikes(spikes, 'Current = 10. mA')
plt.plot(x, rate_I, label='current',)
plt.plot(x, rate_P, label='Poisson input')
plt.fill_between(x, rate_P_min, rate_P_max, facecolor = 'green', alpha=0.3)
'''
x0 = np.where(rate_P > 1.)[0][0]
x1 = 4
k = (rate_P[x1] - rate_P[x0]) / (x[x1] - x[x0])
'''
plt.plot(x, k*(x-x[x0])+rate_P[x0], label='linear')
plt.legend(loc='upper left', shadow=True)
plt.grid('on')
plt.show()
'''
p.end()
return k, x[x0], rate_P[x0]
inp = sim.Population(
1,
sim.SpikeSourcePoisson(duration=simparams['duration'],
rate=simparams['input_rate']))
inp.label = 'input cell'
outp = sim.Population(1, sim.IF_curr_exp, cellparams=cellparams)
outp.label = 'output cell'
inp.record('spikes')
outp.record(['v', 'spikes'])
synapse = sim.StaticSynapse(weight=1, delay=simparams['delay'])
connector = sim.OneToOneConnector()
connection = sim.Projection(inp, outp, connector, synapse)
def report_time(t):
print("Time: {}".format(t))
return t + simparams['dt']
par = 'i_offset'
for p in [0.01]:
outp.set(**{par: p})
cellparams[par] = p
outp.initialize(v=cellparams['v_rest'])
sim.run(simparams['duration'], callbacks=[report_time])
sim.reset(annotations={par: p})
def __init__(self, sim_params=None, cell_params=None, verbose=True):
'''
Parameters : Stimulus, Population, Synapses, Recording, Running
'''
self.verbose = verbose
self.sim_params = sim_params
self.cell_params = cell_params
sim.setup() #spike_precision='on_grid')#timestep = .1)
N_inh = int(sim_params['nb_neurons'] *
sim_params['p']) #total pop * proportion of inhib
self.spike_source = sim.Population(
N_inh,
sim.SpikeSourcePoisson(rate=sim_params['input_rate'],
duration=sim_params['simtime'] / 2))
#orientation stimulus, see bottom section of notebook
angle = 1. * np.arange(N_inh)
rates = self.tuning_function(angle,
sim_params['angle_input'] / 180. * N_inh,
sim_params['b_input'], N_inh)
rates /= rates.mean()
rates *= sim_params['input_rate']
for i, cell in enumerate(self.spike_source):
cell.set_parameters(rate=rates[i])
#neuron model selection
if sim_params['neuron_model'] == 'IF_cond_alpha':
model = sim.IF_cond_alpha #LIF with nice dynamics
else:
model = sim.IF_cond_exp #LIF with exp dynamics
#populations
E_neurons = sim.Population(
N_inh,
model(**cell_params),
initial_values={
'v':
rnd('uniform',
(sim_params['v_init_min'], sim_params['v_init_max']))
},
label="Excitateurs")
I_neurons = sim.Population(
int(sim_params['nb_neurons'] - N_inh),
model(**cell_params),
initial_values={
'v':
rnd('uniform',
(sim_params['v_init_min'], sim_params['v_init_max']))
},
label="Inhibiteurs")
#input to excitatories
input_exc = sim.Projection(
self.spike_source, E_neurons, sim.OneToOneConnector(),
sim.StaticSynapse(weight=sim_params['w_input_exc'],
delay=sim_params['s_input_exc']))
#loop through connections type and use associated params, can be a bit slow
conn_types = ['exc_inh', 'inh_exc', 'exc_exc',
'inh_inh'] #connection types
'''
self.proj = self.set_synapses(conn_types = conn_types, sim_params =sim_params,
E_neurons = E_neurons, I_neurons = I_neurons,
N_inh = N_inh)
'''
#Multi threading support NE MARCHE PAS LAISSER LE NJOBS EN 1
self.proj = Parallel(n_jobs=1, backend='multiprocessing')(
delayed(self.set_synapses)(conn_type,
sim_params=sim_params,
E_neurons=E_neurons,
I_neurons=I_neurons,
N_inh=N_inh,
conn_types=conn_types,
verbose=verbose)
for conn_type in range(len(conn_types)))
if verbose: print('Done building synapses !')
#record
self.spike_source.record('spikes')
E_neurons.record('spikes')
I_neurons.record('spikes')
#run
if verbose: print('Running simulation..')
sim.run(sim_params['simtime'])
if verbose: print('Done running !')
#get the spikes
self.E_spikes = E_neurons #.get_data().segments[0]
self.I_spikes = I_neurons #.get_data().segments[0]
self.P_spikes = self.spike_source #.get_data().segments[0]
plt.interactive(False)
sim.setup(0.1)
neurons = sim.Population(64, sim.IF_curr_exp, {}, label="neurons")
print(neurons.celltype.recordable)
params = {
'rate': 10000.0, # Mean spike frequency (Hz)
'start': 0.0, # Start time (ms)
'duration': 1e10 # Duration of spike sequence (ms)
}
input = sim.Population(64, sim.SpikeSourcePoisson(**params), label="input")
input_proj = sim.Projection(
input, neurons, sim.OneToOneConnector(), receptor_type='excitatory'
) ##https://github.com/NeuralEnsemble/PyNN/issues/273
def twoDto1D(x):
return (8 * x[0] + x[1])
def oneDto2D(n):
return np.array([int(n / 8.), int(n - 8 * (int(n / 8.)))])
def plot_spiketrains(segment):
for spiketrain in segment.spiketrains:
y = np.ones_like(spiketrain) * spiketrain.annotations['source_id']
plt.plot(spiketrain, y, '.')
