def test_multiple_connections_between_same_populations(self):
p1 = pyNN.Population(no_neurons,
pyNN.IF_curr_exp,
cell_params_lif,
label="LIF Pop")
p2 = pyNN.Population(no_neurons,
pyNN.IF_curr_exp,
cell_params_lif,
label="LIF Pop")
pyNN.Projection(p1, p2, pyNN.OneToOneConnector(1, 1))
self.assertIsInstance(
pyNN.Projection(p1, p2, pyNN.OneToOneConnector(1, 1)), Projection,
"Failed to create multiple connections between"
" the same pair of populations")
def test_projection_params(self):
populations = list()
projection_details = list()
populations = list()
weight_to_spike = 2
delay = 5
populations.append(
pyNN.Population(no_neurons,
pyNN.IF_curr_exp,
cell_params_lif,
label="LIF Pop"))
populations.append(
pyNN.Population(no_neurons,
pyNN.IF_curr_dual_exp,
cell_params_lif2exp,
label="IF_curr_dual_exp Pop"))
populations.append(
pyNN.Population(no_neurons,
pyNN.IF_cond_exp,
cell_params_lifexp,
label="IF_cond_exp Pop"))
populations.append(
pyNN.Population(no_neurons,
pyNN.IZK_curr_exp,
cell_params_izk,
label="IZK_curr_exp Pop"))
for i in range(4):
for j in range(4):
projection_details.append({
'presyn':
populations[i],
'postsyn':
populations[j],
'connector':
pyNN.OneToOneConnector(weight_to_spike, delay)
})
projections.append(
pyNN.Projection(
populations[i], populations[j],
pyNN.OneToOneConnector(weight_to_spike, delay)))
for i in range(4):
for j in range(4):
self.assertEqual(
projections[i + j]._projection_edge._pre_vertex,
projection_details[i + j]['presyn']._vertex)
self.assertEqual(
projections[i + j]._projection_edge._post_vertex,
projection_details[i + j]['postsyn']._vertex)
def test_setup(self):
global projections
weight_to_spike = 2
delay = 5
populations.append(
pyNN.Population(no_neurons,
pyNN.IF_curr_exp,
cell_params_lif,
label="LIF Pop"))
populations.append(
pyNN.Population(no_neurons,
pyNN.IF_curr_dual_exp,
cell_params_lif2exp,
label="IF_curr_dual_exp Pop"))
populations.append(
pyNN.Population(no_neurons,
pyNN.IF_cond_exp,
cell_params_lifexp,
label="IF_cond_exp Pop"))
populations.append(
pyNN.Population(no_neurons,
pyNN.IZK_curr_exp,
cell_params_izk,
label="IZK_curr_exp Pop"))
populations.append(
pyNN.Population(no_neurons,
pyNN.SpikeSourceArray,
spike_array,
label="SpikeSourceArray Pop"))
populations.append(
pyNN.Population(no_neurons,
pyNN.SpikeSourcePoisson,
spike_array_poisson,
label="SpikeSourcePoisson Pop"))
for i in range(4):
projection_details.append({
'presyn':
populations[0],
'postsyn':
populations[i],
'connector':
pyNN.OneToOneConnector(weight_to_spike, delay)
})
projections.append(
pyNN.Projection(populations[0], populations[i],
pyNN.OneToOneConnector(weight_to_spike,
delay)))
def test_source_populations_as_postsynaptic(self):
global projections
weight_to_spike = 2
delay = 5
with self.assertRaises(exc.ConfigurationException):
for i in range(4, 6):
projections.append(
pyNN.Projection(
populations[0], populations[i],
pyNN.OneToOneConnector(weight_to_spike, delay)))
def test_recording_numerious_element(self):
p.setup(timestep=1.0, min_delay=1.0, max_delay=144.0)
n_neurons = 20 # number of neurons in each population
p.set_number_of_neurons_per_core("IF_curr_exp", n_neurons / 2)
cell_params_lif = {
'cm': 0.25,
'i_offset': 0.0,
'tau_m': 20.0,
'tau_refrac': 2.0,
'tau_syn_E': 5.0,
'tau_syn_I': 5.0,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -50.0
}
populations = list()
projections = list()
boxed_array = numpy.zeros(shape=(0, 2))
spike_array = list()
for neuron_id in range(0, n_neurons):
spike_array.append(list())
for random_time in range(0, 20):
random_time2 = random.randint(0, 5000)
boxed_array = numpy.append(boxed_array,
[[neuron_id, random_time2]],
axis=0)
spike_array[neuron_id].append(random_time)
spike_array_params = {'spike_times': spike_array}
populations.append(
p.Population(n_neurons,
p.IF_curr_exp,
cell_params_lif,
label='pop_1'))
populations.append(
p.Population(n_neurons,
p.SpikeSourceArray,
spike_array_params,
label='inputSpikes_1'))
projections.append(
p.Projection(populations[1], populations[0],
p.OneToOneConnector()))
populations[1].record()
p.run(5000)
spike_array_spikes = populations[1].getSpikes()
boxed_array = boxed_array[numpy.lexsort(
(boxed_array[:, 1], boxed_array[:, 0]))]
numpy.testing.assert_array_equal(spike_array_spikes, boxed_array)
p.end()
def test_inhibitory_connector(self):
weight_to_spike = 2
delay = 5
p1 = pyNN.Population(no_neurons,
pyNN.IF_curr_exp,
cell_params_lif,
label="LIF Pop")
p2 = pyNN.Population(no_neurons,
pyNN.IF_curr_exp,
cell_params_lif,
label="LIF Pop")
s12_2 = pyNN.Projection(p1,
p2,
pyNN.OneToOneConnector(weight_to_spike, delay),
target='inhibitory')
s21 = pyNN.Projection(p2,
p1,
pyNN.OneToOneConnector(weight_to_spike, delay),
target='excitatory')
def test_connector_populations_of_different_sizes(self):
weight = 2
delay = 5
p1 = pyNN.Population(10,
pyNN.IF_curr_exp,
cell_params_lif,
label="pop 1")
p2 = pyNN.Population(5,
pyNN.IF_curr_exp,
cell_params_lif,
label="pop 2")
with self.assertRaises(ConfigurationException):
pyNN.Projection(p1, p2, pyNN.OneToOneConnector(weight, delay))
def test_one_to_one_connector_from_high_to_low(self):
weight_to_spike, delay = 2, 5
second_population = pyNN.Population(no_neurons,
pyNN.IF_curr_exp,
cell_params_lif,
label="LIF Pop")
different_population = pyNN.Population(
20,
pyNN.IF_curr_exp,
cell_params_lif,
label="A random sized population")
with self.assertRaises(exc.ConfigurationException):
pyNN.Projection(different_population, second_population,
pyNN.OneToOneConnector(weight_to_spike, delay))
def test_synapse_list_generation_for_different_sized_populations(self):
number_of_neurons = 10
first_population = pyNN.Population(number_of_neurons,
pyNN.IF_curr_exp,
cell_params_lif,
label="One pop")
second_population = pyNN.Population(number_of_neurons + 5,
pyNN.IF_curr_exp,
cell_params_lif,
label="Second pop")
weight = 2
delay = 1
connection = pyNN.OneToOneConnector(weight, delay)
with self.assertRaises(ConfigurationException):
connection.generate_synapse_list(first_population,
second_population, 1, 1.0, 0)
def test_self_connect_population(self):
number_of_neurons = 10
first_population = pyNN.Population(number_of_neurons,
pyNN.IF_curr_exp,
cell_params_lif,
label="One pop")
weight = 2
delay = 1
synapse_type = 0
connection = pyNN.OneToOneConnector(weight, delay)
synaptic_list = connection.generate_synapse_list(
first_population, first_population, 1, 1.0, synapse_type)
self.assertEqual(synaptic_list.get_max_weight(), weight)
self.assertEqual(synaptic_list.get_min_weight(), weight)
pp(synaptic_list.get_rows())
self.assertEqual(synaptic_list.get_n_rows(), number_of_neurons)
self.assertEqual(synaptic_list.get_max_delay(), delay)
self.assertEqual(synaptic_list.get_min_delay(), delay)
def test_recording_poisson_spikes_rate_0(self):
p.setup(timestep=1.0, min_delay=1.0, max_delay=144.0)
n_neurons = 256 # number of neurons in each population
p.set_number_of_neurons_per_core("IF_curr_exp", n_neurons / 2)
cell_params_lif = {
'cm': 0.25,
'i_offset': 0.0,
'tau_m': 20.0,
'tau_refrac': 2.0,
'tau_syn_E': 5.0,
'tau_syn_I': 5.0,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -50.0
}
populations = list()
projections = list()
populations.append(
p.Population(n_neurons,
p.IF_curr_exp,
cell_params_lif,
label='pop_1'))
populations.append(
p.Population(n_neurons,
p.SpikeSourcePoisson, {'rate': 0},
label='inputSpikes_1'))
projections.append(
p.Projection(populations[1], populations[0],
p.OneToOneConnector()))
populations[1].record()
p.run(5000)
spikes = populations[1].getSpikes()
print spikes
p.end()
def simulate(self, spinnaker, input_spike_times):
# Cell parameters
cell_params = {
'tau_m': 20.0,
'v_rest': -60.0,
'v_reset': -60.0,
'v_thresh': -40.0,
'tau_syn_E': 2.0,
'tau_syn_I': 2.0,
'tau_refrac': 2.0,
'cm': 0.25,
'i_offset': 0.0,
}
rng = p.NumpyRNG(seed=28375)
v_init = p.RandomDistribution('uniform', [-60, -40], rng)
p.setup(timestep=1.0, min_delay=1.0, max_delay=10.0)
pop = p.Population(1, p.IF_curr_exp, cell_params, label='population')
pop.randomInit(v_init)
pop.record()
pop.record_v()
noise = p.Population(1, p.SpikeSourceArray,
{"spike_times": input_spike_times})
p.Projection(noise,
pop,
p.OneToOneConnector(weights=0.4, delays=1),
target='excitatory')
# Simulate
p.run(self.simtime)
pop_voltages = pop.get_v(compatible_output=True)
pop_spikes = pop.getSpikes(compatible_output=True)
p.end()
return pop_voltages, pop_spikes
def test_connect_two_different_populations(self):
number_of_neurons = 10
first_population = pyNN.Population(number_of_neurons,
pyNN.IF_curr_exp,
cell_params_lif,
label="One pop")
second_population = pyNN.Population(number_of_neurons,
pyNN.IF_curr_exp,
cell_params_lif,
label="Second pop")
weight = 2
delay = 1
synapse_type = first_population._vertex.get_synapse_id('excitatory')
connection = pyNN.OneToOneConnector(weight, delay)
synaptic_list = connection.generate_synapse_list(
first_population, second_population, 1, 1.0, synapse_type)
self.assertEqual(synaptic_list.get_max_weight(), weight)
self.assertEqual(synaptic_list.get_min_weight(), weight)
pp(synaptic_list.get_rows())
self.assertEqual(synaptic_list.get_n_rows(), number_of_neurons)
self.assertEqual(synaptic_list.get_max_delay(), delay)
self.assertEqual(synaptic_list.get_min_delay(), delay)
cell_params_lif,
label='pop_backward')
# Create injection populations
injector_forward = Frontend.Population(n_neurons,
ExternalDevices.SpikeInjector,
cell_params_spike_injector_with_key,
label='spike_injector_forward')
injector_backward = Frontend.Population(n_neurons,
ExternalDevices.SpikeInjector,
cell_params_spike_injector,
label='spike_injector_backward')
# Create a connection from the injector into the populations
Frontend.Projection(injector_forward, pop_forward,
Frontend.OneToOneConnector(weights=weight_to_spike))
Frontend.Projection(injector_backward, pop_backward,
Frontend.OneToOneConnector(weights=weight_to_spike))
# Synfire chain connections where each neuron is connected to its next neuron
# NOTE: there is no recurrent connection so that each chain stops once it
# reaches the end
loop_forward = list()
loop_backward = list()
for i in range(0, n_neurons - 1):
loop_forward.append((i, (i + 1) % n_neurons, weight_to_spike, 3))
loop_backward.append(((i + 1) % n_neurons, i, weight_to_spike, 3))
Frontend.Projection(pop_forward, pop_forward,
Frontend.FromListConnector(loop_forward))
Frontend.Projection(pop_backward, pop_backward,
Frontend.FromListConnector(loop_backward))
# spindle population
spindle_pop = p.Population(n_fibers * 2,
MuscleSpindle, {
"primary": [1] * n_fibers + [0] * n_fibers,
"v_thresh": 100.0,
"receive_port": 12345
},
label="spindle_pop")
spindle_pop.record()
# dynamic fusimotor drive
gamma_dyn = p.Population(1, p.SpikeSourcePoisson, {'rate': 70.0})
p.Projection(gamma_dyn,
spindle_pop,
p.OneToOneConnector(weights=weight),
target="dynamic")
# static fusimotor drive
gamma_st = p.Population(1, p.SpikeSourcePoisson, {'rate': 40.0})
p.Projection(gamma_st,
spindle_pop,
p.OneToOneConnector(weights=weight),
target="static")
# database for live communication
spynnaker_external_devices = SpynnakerExternalDevicePluginManager()
def create_database():
database_notify_port_num = conf.config.getint("Database", "notify_port")
]})
post_stim = sim.Population(
pop_size, sim.SpikeSourceArray, {
'spike_times': [
[
i for i in range(pairing_start_time, pairing_end_time,
time_between_pairs)
],
]
})
# +-------------------------------------------------------------------+
# | Creation of connections |
# +-------------------------------------------------------------------+
# Connection type between noise poisson generator and excitatory populations
ee_connector = sim.OneToOneConnector(weights=2)
sim.Projection(pre_stim, pre_pop, ee_connector, target='excitatory')
sim.Projection(post_stim, post_pop, ee_connector, target='excitatory')
# Plastic Connections between pre_pop and post_pop
stdp_model = sim.STDPMechanism(
timing_dependence=sim.SpikePairRule(tau_plus=20.0, tau_minus=50.0),
weight_dependence=sim.AdditiveWeightDependence(w_min=0,
w_max=1,
A_plus=0.02,
A_minus=0.02))
sim.Projection(pre_pop,
post_pop,
sim.OneToOneConnector(),
def test_script(self):
"""
test that tests the printing of v from a pre determined recording
:return:
"""
p.setup(timestep=0.1, min_delay=1.0, max_delay=14.0)
n_neurons = 128 * 128 # number of neurons in each population
p.set_number_of_neurons_per_core("IF_cond_exp", 256)
cell_params_lif = {
'cm': 0.25,
'i_offset': 0.0,
'tau_m': 20.0,
'tau_refrac': 2.0,
'tau_syn_E': 5.0,
'tau_syn_I': 5.0,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -50.0,
'e_rev_E': 0.,
'e_rev_I': -80.
}
populations = list()
projections = list()
weight_to_spike = 0.035
delay = 1.7
spikes = read_spikefile('test.spikes', n_neurons)
print spikes
spike_array = {'spike_times': spikes}
populations.append(
p.Population(n_neurons,
p.SpikeSourceArray,
spike_array,
label='inputSpikes_1'))
populations.append(
p.Population(n_neurons,
p.IF_cond_exp,
cell_params_lif,
label='pop_1'))
projections.append(
p.Projection(
populations[0], populations[1],
p.OneToOneConnector(weights=weight_to_spike, delays=delay)))
populations[1].record()
p.run(100)
spikes = populations[1].getSpikes(compatible_output=True)
if spikes is not None:
print spikes
pylab.figure()
pylab.plot([i[1] for i in spikes], [i[0] for i in spikes], ".")
pylab.xlabel('Time/ms')
pylab.ylabel('spikes')
pylab.title('spikes')
pylab.show()
else:
print "No spikes received"
p.end()
import spynnaker.pyNN as p
p.setup(timestep=1.0, min_delay=1.0, max_delay=144.0)
nNeurons = 100
#p.set_number_of_neurons_per_core("IF_curr_exp", nNeurons)
input = p.Population(1024, p.SpikeSourcePoisson, {'rate': 10}, "input")
relay_on = p.Population(1024, p.IF_curr_exp, {}, "input")
weight_to_spike = 2.0
delay = 17
t_rule_LGN = p.SpikePairRule (tau_plus=17, tau_minus=34)
w_rule_LGN = p.AdditiveWeightDependence (w_min=0.0, w_max=0.3, A_plus=0.01, A_minus=0.0085)
stdp_model_LGN = p.STDPMechanism (timing_dependence = t_rule_LGN, weight_dependence = w_rule_LGN)
s_d_LGN = p.SynapseDynamics(slow = stdp_model_LGN)
in_to_relay_on = p.Projection(input, relay_on, p.OneToOneConnector(weights=1),synapse_dynamics = s_d_LGN, target='excitatory')
p.run(1000)
p.end()
# | Creation of neuron populations |
# +-------------------------------------------------------------------+
# Neuron populations
pre_pop = p.Population(pop_size, model, cell_params)
post_pop = p.Population(pop_size, model, cell_params)
# Stimulating populations
pre_stim = p.Population(pop_size, p.SpikeSourceArray, {'spike_times': [[i for i in range(0, sim_time, time_between_pairs)],]})
post_stim = p.Population(pop_size, p.SpikeSourceArray, {'spike_times': [[i for i in range(pairing_start_time, pairing_end_time, time_between_pairs)],]})
# +-------------------------------------------------------------------+
# | Creation of connections |
# +-------------------------------------------------------------------+
# Connection type between noise poisson generator and excitatory populations
ee_connector = p.OneToOneConnector(weights=2)
p.Projection(pre_stim, pre_pop, ee_connector, target='excitatory')
p.Projection(post_stim, post_pop, ee_connector, target='excitatory')
# Plastic Connections between pre_pop and post_pop
stdp_model = p.STDPMechanism(
timing_dependence = p.SpikePairRule(tau_plus = 20.0, tau_minus = 50.0),
weight_dependence = p.AdditiveWeightDependence(w_min = 0, w_max = 1, A_plus=0.02, A_minus = 0.02)
)
p.Projection(pre_pop, post_pop, p.OneToOneConnector(),
synapse_dynamics = p.SynapseDynamics(slow= stdp_model)
)
# Record spikes
[i[2] for i in v_for_neuron])
p.setup(time_step)
input_pop = p.Population(1,
p.SpikeSourceArray, {"spike_times": spike_times},
label="input")
my_model_pop = p.Population(1,
MyModelCurrExp, {
"my_parameter": -70.0,
"i_offset": i_offset,
},
label="my_model_pop")
p.Projection(input_pop, my_model_pop, p.OneToOneConnector(weights=weight))
my_model_my_synapse_type_pop = p.Population(
1,
MyModelCurrMySynapseType, {
"my_parameter": -70.0,
"i_offset": i_offset,
"my_ex_synapse_parameter": 0.5
},
label="my_model_my_synapse_type_pop")
p.Projection(input_pop, my_model_my_synapse_type_pop,
p.OneToOneConnector(weights=weight))
my_model_my_additional_input_pop = p.Population(
1,
MyModelCurrExpMyAdditionalInput, {
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 = 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]
def main():
minutes = 0
seconds = 30
milliseconds = 0
run_time = minutes*60*1000 + seconds*1000 + milliseconds
weight_to_spike = 4.
model = sim.IF_curr_exp
cell_params = {'cm' : 0.25, # nF
'i_offset' : 0.0,
'tau_m' : 10.0,
'tau_refrac': 2.0,
'tau_syn_E' : 2.5,
'tau_syn_I' : 2.5,
'v_reset' : -70.0,
'v_rest' : -65.0,
'v_thresh' : -55.4
}
# Available resolutions
# 16, 32, 64, 128
mode = ExternalDvsEmulatorDevice.MODE_64
cam_res = int(mode)
cam_fps = 90
frames_per_saccade = cam_fps/3 - 1
polarity = ExternalDvsEmulatorDevice.MERGED_POLARITY
output_type = ExternalDvsEmulatorDevice.OUTPUT_TIME
history_weight = 1.0
behaviour = VirtualCam.BEHAVE_ATTENTION
vcam = VirtualCam("./mnist", behaviour=behaviour, fps=cam_fps,
resolution=cam_res, frames_per_saccade=frames_per_saccade)
cam_params = {'mode': mode,
'polarity': polarity,
'threshold': 12,
'adaptive_threshold': False,
'fps': cam_fps,
'inhibition': False,
'output_type': output_type,
'save_spikes': "./spikes_from_cam.pickle",
'history_weight': history_weight,
#'device_id': 0, # for an OpenCV webcam device
#'device_id': 'path/to/video/file', # to encode pre-recorded video
'device_id': vcam,
}
if polarity == ExternalDvsEmulatorDevice.MERGED_POLARITY:
num_neurons = 2*(cam_res**2)
else:
num_neurons = cam_res**2
sim.setup(timestep=1.0, min_delay=1.0, max_delay=10.0)
target = sim.Population(num_neurons, model, cell_params)
stimulation = sim.Population(num_neurons, DvsEmulatorDevice, cam_params,
label="Webcam population")
connector = sim.OneToOneConnector(weights=weight_to_spike)
projection = sim.Projection(stimulation, target, connector)
target.record()
sim.run(run_time)
spikes = target.getSpikes(compatible_output=True)
sim.end()
#stimulation._vertex.stop()
print ("Raster plot of the spikes that Spinnaker echoed back")
fig = pylab.figure()
spike_times = [spike_time for (neuron_id, spike_time) in spikes]
spike_ids = [neuron_id for (neuron_id, spike_time) in spikes]
pylab.plot(spike_times, spike_ids, ".", markerfacecolor="None",
markeredgecolor="Blue", markersize=3)
pylab.show()
pynn.setup(timestep=ts, min_delay=ts, max_delay=2.0 * ts)
pop = pynn.Population(size=n_neurons,
cellclass=pynn.IF_curr_exp,
cellparams={},
label='pop')
# The ROS_Spinnaker_Interface just needs to be initialised with these two Spike Source Parameters.
ros_interface = ROS_Spinnaker_Interface(
n_neurons_source=n_neurons, # number of neurons of the injector population
Spike_Source_Class=SpikeSourcePoisson
) # the transfer function ROS Input -> Spikes you want to use.
# Build your network, run the simulation and optionally record the spikes and voltages.
pynn.Projection(ros_interface, pop, pynn.OneToOneConnector(weights=5,
delays=1))
pop.record()
pop.record_v()
pynn.run(simulation_time)
spikes = pop.getSpikes()
pynn.end()
# Plot
import pylab
spike_times = [spike[1] for spike in spikes]
spike_ids = [spike[0] for spike in spikes]
post_times = generate_fixed_frequency_test_data(
f, start_time + t, num_pairs)
pre_stim = sim.Population(1, sim.SpikeSourceArray,
{'spike_times': [
pre_times,
]})
post_stim = sim.Population(1, sim.SpikeSourceArray,
{'spike_times': [
post_times,
]})
# Update simulation time
sim_time = max(sim_time, max(max(pre_times), max(post_times)) + 100)
# Connections between spike sources and neuron populations
ee_connector = sim.OneToOneConnector(weights=2)
sim.Projection(pre_stim, pre_pop, ee_connector, target='excitatory')
sim.Projection(post_stim, post_pop, ee_connector, target='excitatory')
# **HACK**
param_scale = 0.5
# Plastic Connection between pre_pop and post_pop
# Sjostrom visual cortex min-triplet params
stdp_model = sim.STDPMechanism(
timing_dependence=sim.PfisterSpikeTripletRule(tau_plus=16.8,
tau_minus=33.7,
tau_x=101,
tau_y=114),
weight_dependence=sim.AdditiveWeightDependence(
w_min=0.0,
label="INH2INH_conn",
target='inhibitory')
poisson_rate = 500.0
pop_poisson_exc_p = sim.Population(len(exc_neuron_idx), sim.SpikeSourcePoisson,
{"rate": poisson_rate})
pop_poisson_exc_n = sim.Population(len(exc_neuron_idx), sim.SpikeSourcePoisson,
{"rate": poisson_rate})
pop_poisson_inh_p = sim.Population(len(inh_neuron_idx), sim.SpikeSourcePoisson,
{"rate": poisson_rate})
pop_poisson_inh_n = sim.Population(len(inh_neuron_idx), sim.SpikeSourcePoisson,
{"rate": poisson_rate})
poisson_weight = 0.005
sim.Projection(pop_poisson_exc_p, pop_lsm_exc,
sim.OneToOneConnector(weights=poisson_weight))
sim.Projection(pop_poisson_exc_n, pop_lsm_exc,
sim.OneToOneConnector(weights=-poisson_weight))
sim.Projection(pop_poisson_inh_p, pop_lsm_inh,
sim.OneToOneConnector(weights=poisson_weight))
sim.Projection(pop_poisson_inh_n, pop_lsm_inh,
sim.OneToOneConnector(weights=-poisson_weight))
#
# INPUT - Setup
#
print "Liquid->Liquid connections... Input Setup"
tspk = simulation_timestep * 50 # The neurons spike after 50 time steps!
number_of_spikes = 500
def test_inhibitory_connector_memory(self):
p.setup(timestep=0.1, min_delay=1, max_delay=10.0)
weight_to_spike = 10
delay = 1
cell_params_lif = {
'cm': 0.25,
'i_offset': 0.0,
'tau_m': 20.0,
'tau_refrac': 1.0,
'tau_syn_E': 5.0,
'tau_syn_I': 8.0,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -50.0
}
spike_array = {'spike_times': [0]}
mem_access = {'spike_times': [10]}
p_initial_spike = p.Population(1,
p.SpikeSourceArray,
spike_array,
label="Initial spike pop")
p_mem = p.Population(1, p.IF_curr_exp, cell_params_lif, label="Memory")
p_out = p.Population(1, p.IF_curr_exp, cell_params_lif, label="Output")
p_bridge = p.Population(1,
p.IF_curr_exp,
cell_params_lif,
label="Bridge")
p_inhibitor = p.Population(1,
p.IF_curr_exp,
cell_params_lif,
label="Inhibitor")
p_access = p.Population(1,
p.SpikeSourceArray,
mem_access,
label="Access memory spike pop")
p_out.record()
p_mem.record()
p_inhibitor.record()
p_initial_spike.record()
p_access.record()
pr_initial_spike1 = p.Projection(
p_initial_spike, p_mem,
p.OneToOneConnector(weight_to_spike, delay))
pr_initial_spike2 = p.Projection(
p_initial_spike, p_inhibitor,
p.OneToOneConnector(weight_to_spike, delay))
pr_mem_access = p.Projection(p_access,
p_inhibitor,
p.OneToOneConnector(
weight_to_spike, delay),
target='inhibitory')
pr_inhibitor_self = p.Projection(
p_inhibitor, p_inhibitor,
p.OneToOneConnector(weight_to_spike, delay))
pr_inhibitor_bridge = p.Projection(p_inhibitor,
p_bridge,
p.OneToOneConnector(
weight_to_spike, delay),
target='inhibitory')
pr_mem_self = p.Projection(p_mem, p_mem,
p.OneToOneConnector(weight_to_spike, delay))
pr_mem_bridge = p.Projection(
p_mem, p_bridge, p.OneToOneConnector(weight_to_spike, delay))
pr_bridge_output = p.Projection(
p_bridge, p_out, p.OneToOneConnector(weight_to_spike, delay))
pr_bridge_inhibitor = p.Projection(
p_bridge, p_inhibitor, p.OneToOneConnector(weight_to_spike, delay))
p_mem.record_v()
p_mem.record_gsyn()
p_mem.record()
p.run(30)
v = None
gsyn = None
spikes = None
v = p_mem.get_v(compatible_output=True)
gsyn = p_mem.get_gsyn(compatible_output=True)
spikes = p_mem.getSpikes(compatible_output=True)
if spikes != None:
print spikes
pylab.figure()
pylab.plot([i[1] for i in spikes], [i[0] for i in spikes], ".")
pylab.xlabel('Time/ms')
pylab.ylabel('spikes')
pylab.title('spikes')
pylab.show()
else:
print "No spikes received"
# Make some graphs
ticks = len(v) / 1
if v != None:
pylab.figure()
pylab.xlabel('Time/ms')
pylab.ylabel('v')
pylab.title('v')
for pos in range(0, 1, 20):
v_for_neuron = v[pos * ticks:(pos + 1) * ticks]
pylab.plot([i[1] for i in v_for_neuron],
[i[2] for i in v_for_neuron])
pylab.show()
if gsyn != None:
pylab.figure()
pylab.xlabel('Time/ms')
pylab.ylabel('gsyn')
pylab.title('gsyn')
for pos in range(0, 1, 20):
gsyn_for_neuron = gsyn[pos * ticks:(pos + 1) * ticks]
pylab.plot([i[1] for i in gsyn_for_neuron],
[i[2] for i in gsyn_for_neuron])
pylab.show()
p.end()
w_max=1.0,
A_plus=0.1,
A_minus=0.5))
# Connections between spike sources and neuron populations
####### SET HERE THE PARALLEL FIBER-PURKINJE CELL LEARNING RULE
ee_connector = sim.AllToAllConnector(weights=0.5)
projection_pf = sim.Projection(
pre_stim,
population,
ee_connector,
synapse_dynamics=sim.SynapseDynamics(slow=stdp_model),
target='excitatory')
# SET HERE THE TEACHING SIGNAL PROJECTION
ee_connector = sim.OneToOneConnector()
proj_teaching = sim.Projection(teaching_stim,
population,
ee_connector,
target='supervision')
print("Simulating for %us" % (sim_time / 1000))
# Run simulation
sim.run(sim_time)
# Get weight from each projection
end_w = projection_pf.getWeights(
) #[p.getWeights()[0] for p in projections_pf]
print end_w
label=spikeInjectionPopLabel1)
populations.append(pop_spikes_in_1)
pop_spikes_in_2 = spynn.Population(nNeurons2,
ExternalDevices.SpikeInjector,
cell_params_spike_injector_2,
label=spikeInjectionPopLabel2)
populations.append(pop_spikes_in_2)
pop_spikes_out_1.record()
#ExternalDevices.activate_live_output_for(pop_spikes_out_1)
pop_spikes_out_2.record()
#ExternalDevices.activate_live_output_for(pop_spikes_out_2)
projections.append(
spynn.Projection(pop_spikes_in_1, pop_spikes_out_1,
spynn.OneToOneConnector(weights=weight_to_spike)))
projections.append(
spynn.Projection(pop_spikes_in_2, pop_spikes_out_2,
spynn.OneToOneConnector(weights=weight_to_spike)))
spynn.run(runTimeMs + 1000) #add extra second to get all downstream spikes
spikes1 = pop_spikes_out_1.getSpikes(compatible_output=True)
spikes2 = pop_spikes_out_2.getSpikes(compatible_output=True)
#For raster plot of all together, we need to convert neuron ids to be global not local to each pop
for j in spikes2:
j[0] = j[0] + nNeurons1
totalSpikes = len(spikes1) + len(spikes1)
print 'Total spikes generated: ', totalSpikes
if totalSpikes > 0:
populations.append(
p.Population(1, p.SpikeSourceArray, spikeArray, label='pop_0'))
#populations.append(p.Population(nNeurons, p.IF_curr_exp, input_cell_params, label='pop_0'))
populations.append(
p.Population(nNeurons, p.IF_curr_exp, cell_params_lif, label='pop_1'))
populations.append(
p.Population(nNeurons, p.IF_curr_exp, cell_params_lif, label='pop_2'))
#projections.append(p.Projection(populations[0], populations[1], p.OneToOneConnector(weights=weight_to_spike, delays=delay)))
projections.append(
p.Projection(
populations[0], populations[1],
p.AllToAllConnector(weights=weight_to_spike, delays=injection_delay)))
projections.append(
p.Projection(populations[1], populations[2],
p.OneToOneConnector(weights=weight_to_spike, delays=delay)))
#projections.append(p.Projection(populations[1], populations[0], p.FromListConnector([(0, 0, weight_to_spike, injection_delay)])))
populations[1].record_v()
populations[1].record()
p.run(100)
v = None
gsyn = None
spikes = None
v = populations[1].get_v(compatible_output=True)
spikes = populations[1].getSpikes(compatible_output=True)
if spikes != None:
ros_interface = ROS_Spinnaker_Interface(
Spike_Sink_Class=
SpikeSinkSmoothing, # the transfer function Spikes -> ROS Output you want to use.
# You can choose from the transfer_functions module
# or write one yourself.
output_population=pop) # the pynn population you wish to receive the
# live spikes from.
# Notice that ros_interface will now be None, because there is no SpikeInjector for receiver only.
# You need a different Spike Source.
# Build your network, run the simulation and optionally record the spikes and voltages.
spike_source = pynn.Population(n_neurons, pynn.SpikeSourcePoisson,
{'rate': 10})
pynn.Projection(spike_source, pop, pynn.OneToOneConnector(weights=5, delays=1))
pop.record()
pop.record_v()
pynn.run(simulation_time)
spikes = pop.getSpikes()
pynn.end()
# Plot
import pylab
spike_times = [spike[1] for spike in spikes]
spike_ids = [spike[0] for spike in spikes]
