def setupLayerRN(params, neuronModel, cell_params, injectionPopulations, popPoissionNoiseSource, populationsRN):
#create a single RN population divided into virtual clusters one per VR
#this will be fed by the noise population and modulated by the relevant ratecoded neuron
#to create a rate coded population
numVR = params['NUM_VR']
rnClusterSize = int(params['CLUSTER_SIZE']) #* params['NETWORK_SCALE']
rnPopSize = rnClusterSize * numVR
popName = 'popRN'
popRN = spynnaker.Population(rnPopSize, neuronModel, cell_params, label=popName)
populationsRN.append(popRN)
#connect one random poisson neuron to each RN neuron
weight = params['WEIGHT_POISSON_TO_CLUSTER_RN']
delay = params['DELAY_POISSON_TO_CLUSTER_RN']
connections = utils.fromList_OneRandomSrcForEachTarget(popPoissionNoiseSource._size,popRN._size,weight,delay)
projPoissonToClusterRN = spynnaker.Projection(popPoissionNoiseSource, popRN, spynnaker.FromListConnector(connections), target='excitatory')
vr = 0
for injectionPopn in injectionPopulations:
connections = list()
for fromNeuronIdx in range(injectionPopn._size):
#connect the correct VR ratecode neuron in popRateCodeSpikes to corresponding subsection (cluster) of the RN population
weight = params['WEIGHT_RATECODE_TO_CLUSTER_RN']
firstIndex = vr * rnClusterSize
lastIndex = firstIndex + rnClusterSize - 1
connections += utils.fromList_SpecificNeuronToRange(fromNeuronIdx,firstIndex,lastIndex,weight,params['MIN_DELAY_RATECODE_TO_CLUSTER_RN'],params['MAX_DELAY_RATECODE_TO_CLUSTER_RN'])
vr = vr + 1
#after the last neuron in the current injection pop, create a projection to the RN
projRateToClusterRN = spynnaker.Projection(injectionPopn, popRN, spynnaker.FromListConnector(connections), target='excitatory')
print 'Added projection to RN of ', len(connections), " connections from injection pop ", injectionPopn.label, "(size ", injectionPopn._size,")"
def createIntraPopulationWTA(popn, numClusters, weight, delay, connectivity,
createSingleProjection):
allConnections = []
clusterSize = popn._size / numClusters
for i in range(numClusters):
for j in range(numClusters):
if i != j:
srcFirstIdx = i * clusterSize
srcLastIdx = srcFirstIdx + clusterSize - 1
targFirstIdx = j * clusterSize
targLastIdx = targFirstIdx + clusterSize - 1
connections = fromList_fromRangeToRange(
srcFirstIdx, srcLastIdx, targFirstIdx, targLastIdx, weight,
delay, delay, connectivity)
if (createSingleProjection):
allConnections += connections
else:
projInhibitory = spynnaker.Projection(
popn,
popn,
spynnaker.FromListConnector(connections),
target='inhibitory')
#print ' WTA connections', projInhibitory.getWeights()
if (createSingleProjection):
projInhibitory = spynnaker.Projection(
popn,
popn,
spynnaker.FromListConnector(allConnections),
target='inhibitory')
def nealprojection(self, pre_neurons, post_neurons, connector_list,
inh_exc):
#projection method for SpiNNaker
conn_list = spinn.FromListConnector(connector_list)
spinn.Projection(pre_neurons,
post_neurons,
conn_list,
receptor_type=inh_exc)
def test(spikeTimes, trained_weights,label):
#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__)) #
#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
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]
f1=pplt.Figure(
# plot voltage
pplt.Panel(v, ylabel="Membrane potential (mV)", xticks=True, yticks=True, xlim=(0, runTime+100)),
# raster plot
pplt.Panel(spikes, xlabel="Time (ms)", xticks=True, yticks=True, markersize=2, xlim=(0, runTime+100)),
title='Test with label ' + str(label),
annotations='Test with label ' + str(label)
)
f1.save('plot/'+str(trylabel)+str(label)+'_test.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 setupLayerAN(params, settings, neuronModel, cell_params, popClassActivation, popPoissionNoiseSource, populationsPN, populationsAN,learning,projectionsPNAN):
#create an Association Neuron AN cluster population per class
#this will be fed by:
#1) PN clusters via plastic synapses
#2) Class activation to innervate the correct AN cluster for a given input
#3) laterally inhibit between AN clusters
numClasses = params['NUM_CLASSES']
anClusterSize = int(params['CLUSTER_SIZE']) #* params['NETWORK_SCALE']
for an in range(numClasses):
popName = 'popClusterAN_' + str(an) ;
popClusterAN = spynnaker.Population(anClusterSize, neuronModel, cell_params, label=popName)
populationsAN.append(popClusterAN)
#connect neurons in every PN popn to x% (e.g 50%) neurons in this AN cluster
for pn in range(len(populationsPN)):
if learning:
projLabel = 'Proj_PN' + str(pn) + '_AN' + str(an)
projClusterPNToClusterAN = connectClusterPNtoAN(params,populationsPN[pn],popClusterAN,float(settings['OBSERVATION_EXPOSURE_TIME_MS']),projLabel)
projectionsPNAN.append(projClusterPNToClusterAN) #keep handle to use later for saving off weights at end of learning
else:
#Without plasticity, create PNAN FromList connectors using weights saved during learning stage
connections = utils.loadListFromFile(getWeightsFilename(settings,'PNAN',pn,an))
#print 'Loaded weightsList[',pn,',',an,']',connections
tupleList = utils.createListOfTuples(connections) #new version only accepts list of tuples not list of lists
#print 'tupleList[',pn,',',an,']',tupleList
conn = spynnaker.FromListConnector(tupleList)
projClusterPNToClusterAN = spynnaker.Projection(populationsPN[pn], popClusterAN,conn, target='excitatory')
if learning:
#use the class activity input neurons to create correlated activity during learining in the corresponding class cluster
weight = params['WEIGHT_CLASS_EXCITATION_TO_CLUSTER_AN']
connections = utils.fromList_SpecificNeuronToAll(an,anClusterSize,weight,params['MIN_DELAY_CLASS_ACTIVITY_TO_CLUSTER_AN'],params['MAX_DELAY_CLASS_ACTIVITY_TO_CLUSTER_AN'])
projClassActivityToClusterAN = spynnaker.Projection(popClassActivation, popClusterAN, spynnaker.FromListConnector(connections), target='excitatory')
else: #testing
#send spikes on these outputs back to correct host port , these will be used to determine winner etc
anHostReceivePort = int(settings['AN_HOST_RECEIVE_PORT'])
ExternalDevices.activate_live_output_for(popClusterAN,port=anHostReceivePort)
#connect each AN cluster to inhibit every other AN cluster
utils.createInterPopulationWTA(populationsAN,params['WEIGHT_WTA_AN_AN'],params['DELAY_WTA_AN_AN'],float(params['CONNECTIVITY_WTA_AN_AN']))
#inhibit other non-corresponding class clusters
if learning:
weight = params['WEIGHT_CLASS_INHIBITION_TO_CLUSTER_AN']
for activeCls in range(numClasses):
connections = utils.fromList_SpecificNeuronToAll(activeCls,anClusterSize,weight,params['MIN_DELAY_CLASS_ACTIVITY_TO_CLUSTER_AN'],params['MAX_DELAY_CLASS_ACTIVITY_TO_CLUSTER_AN'])
for an in range(numClasses):
if an != activeCls:
projClassActivityToClusterAN = spynnaker.Projection(popClassActivation, populationsAN[an], spynnaker.FromListConnector(connections), target='inhibitory')
def obtain_synapses(wiring_plan):
rng = NumpyRNG(seed=64754)
delay_distr = RandomDistribution('normal', [2, 1e-1], rng=rng)
weight_distr = RandomDistribution('normal', [45, 1e-1], rng=rng)
flat_iter = [ (i,j,k,xaxis) for i,j in enumerate(filtered) for k,xaxis in enumerate(j) ]
index_exc = list(set( source for (source,j,target,xaxis) in flat_iter if xaxis==1 or xaxis == 2 ))
index_inh = list(set( source for (source,j,target,xaxis) in flat_iter if xaxis==-1 or xaxis == -2 ))
EElist = []
IIlist = []
EIlist = []
IElist = []
for (source,j,target,xaxis) in flat_iter:
delay = delay_distr.next()
weight = 1.0 # will be updated later.
if xaxis==1 or xaxis == 2:
if target in index_inh:
EIlist.append((source,target,delay,weight))
else:
EElist.append((source,target,delay,weight))
if xaxis==-1 or xaxis == -2:
if target in index_exc:
IElist.append((source,target,delay,weight))
else:
IIlist.append((source,target,delay,weight))
conn_ee = sim.FromListConnector(EElist)
conn_ie = sim.FromListConnector(IElist)
conn_ei = sim.FromListConnector(EIlist)
conn_ii = sim.FromListConnector(IIlist)
return (conn_ee, conn_ie, conn_ei, conn_ii,index_exc,index_inh)
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
#create connections
filenames=[
"0Conv2D_14x14x16",
"1Conv2D_12x12x32",
"2Conv2D_12x12x8",
"4Dense_5"
]
for i in range(len(network)-1):
ex = np.genfromtxt(filenames[i]+"_excitatory")
inh = np.genfromtxt(filenames[i]+"_inhibitory")
ex[:,2] /= weight_scale
inh[:,2] /= weight_scale
pynn.Projection(network[i], network[i+1], pynn.FromListConnector(ex, ['weight', 'delay']), receptor_type='excitatory')
pynn.Projection(network[i], network[i+1], pynn.FromListConnector(inh, ['weight', 'delay']), receptor_type='inhibitory')
#network[i+1].initialize(v=0.0, isyn_exc=0.0, isyn_inh=0.0)
#'isyn_exc': 0.0, 'isyn_inh': 0.0,
#set input
firstrun = True
for trial, j in enumerate(test_data):
if firstrun:
firstrun = False
else:
pynn.reset()
try:
for i in range(len(network)-1):
num_test = len(test_data)
# create network
network, labels, n_neurons = load_assembly(
path, "tsfold" + str(fold) + "_nest", pynn)
# load connections
for l in range(len(network) - 1):
conn = np.genfromtxt(path + "/" + labels[l + 1])
# when we switch to spinnaker we need to split the connection in ex and inh:
ex = conn[conn[:, 2] > 0]
inh = conn[conn[:, 2] < 0]
if ex.any():
ex[:, 2] *= weight_scale
pynn.Projection(network[l], network[l+1], \
pynn.FromListConnector(ex, ['weight', 'delay']), receptor_type='excitatory')
if inh.any():
inh[:, 2] *= weight_scale
pynn.Projection(network[l], network[l+1], \
pynn.FromListConnector(inh, ['weight', 'delay']), receptor_type='inhibitory')
network[l + 1].set(**cell_params)
network[l + 1].initialize(v=network[l + 1].get('v_rest'))
# record spikes
if plot:
for layer in network:
layer.record("spikes")
else:
network[-1].record("spikes")
#create connections
filenames = [
"0Conv2D_30x30x16", "1Conv2D_28x28x32", "2Conv2D_28x28x8", "4Dense_5"
]
weight_scale = 1
for i in range(len(network) - 1):
ex = np.genfromtxt(filenames[i] + "_excitatory")
inh = np.genfromtxt(filenames[i] + "_inhibitory")
ex[:, 2] /= weight_scale
inh[:, 2] /= weight_scale
pynn.Projection(network[i],
network[i + 1],
pynn.FromListConnector(ex, ['weight', 'delay']),
receptor_type='excitatory')
pynn.Projection(network[i],
network[i + 1],
pynn.FromListConnector(inh, ['weight', 'delay']),
receptor_type='inhibitory')
network[i + 1].initialize(v=0.0)
#set input
x_flat = np.ravel(data)
rescale_fac = 1000 / (1000 * dt)
#rescale_fac = 1000 / (self.config.getint('input', 'input_rate') *self._dt)
rates = 1000 * x_flat / rescale_fac
#print(rates)
network[0].set(rate=rates)
conn_prob = 0.1,
weight=input_strength,
new_format=new_conn_list)
exc2exc = dist_dep_conn_3d_3d(exc_3d, exc_3d, dist_rule = "exp(-sqrt(d*d))",
conn_prob = 0.2,
weight=input_strength,
new_format=new_conn_list)
exc2inh = dist_dep_conn_3d_3d(exc_3d, inh_3d, dist_rule = "exp(-sqrt(d*d))",
conn_prob = 0.2,
weight=input_strength,
new_format=new_conn_list)
connectors = {}
connectors['in2exc'] = sim.FromListConnector(in2exc)
connectors['in2inh'] = sim.FromListConnector(in2inh)
#connectors['in2inv'] = sim.FromListConnector(in2inv)
connectors['inh2exc'] = sim.FromListConnector(inh2exc)
connectors['inh2inh'] = sim.FromListConnector(inh2inh)
connectors['exc2inh'] = sim.FromListConnector(exc2inh)
connectors['exc2exc'] = sim.FromListConnector(exc2exc)
connectors['exc2id'] = sim.AllToAllConnector(allow_self_connections=False,
weights=normal_distribution,
delays=exc_delay_dist)
#~
#~ connectors['exc2id'] = sim.FixedProbabilityConnector(0.2, allow_self_connections=False,
#~ weights=normal_distribution,
#~ delays=exc_delay_dist
#~ )
import pyNN.spiNNaker as sim
sim.setup()
p1 = sim.Population(3, sim.SpikeSourceArray, {"spike_times": [1.0, 2.0, 3.0]})
p2 = sim.Population(3, sim.SpikeSourceArray, {"spike_times": [[10.0], [20.0], [30.0]]})
p3 = sim.Population(4, sim.IF_cond_exp, {})
sim.Projection(p2, p3, sim.FromListConnector([
(0, 0, 0.1, 1.0), (1, 1, 0.1, 1.0), (2, 2, 0.1, 1.0)]))
#sim.Projection(p1, p3, sim.FromListConnector([(0, 3, 0.1, 1.0)])) # works if this line is added
sim.run(100.0)
stdp_model = sim.STDPMechanism(
timing_dependence=sim.SpikePairRule(tau_plus=tau_plus,
tau_minus=tau_minus,
nearest=True),
weight_dependence=sim.AdditiveWeightDependence(w_min=min_weight,
w_max=max_weight,
A_plus=a_plus,
A_minus=a_minus))
rng = sim.NumpyRNG(seed=int(time.time()))
#rng = sim.NumpyRNG(seed=1)
e2e_lst, e2i_lst, i2e_lst, i2i_lst = connections(max_conn_per_neuron, num_exc,
num_inh, max_delay)
e2e_conn = sim.FromListConnector(e2e_lst)
e2i_conn = sim.FromListConnector(e2i_lst)
i2e_conn = sim.FromListConnector(i2e_lst)
i2i_conn = sim.FromListConnector(i2i_lst)
o2o_conn = sim.OneToOneConnector(weights=weight_to_spike, delays=1.)
#~ print("-----------------------------------------------------------------")
#~ print("-----------------------------------------------------------------")
#~ print("Excitatory to Excitatory connections")
#~ print("-----------------------------------------------------------------")
e2e_proj = sim.Projection(
exc_pop,
exc_pop,
e2e_conn,
target="excitatory",
def run_test(w_list, cell_para, spike_source_data):
#Du.set_trace()
pop_list = []
p.setup(timestep=1.0, min_delay=1.0, max_delay=3.0)
#input poisson layer
input_size = w_list[0].shape[0]
#print w_list[0].shape[0]
#print w_list[1].shape[0]
list = []
for j in range(input_size):
list.append(spike_source_data[j])
pop_in = p.Population(input_size, p.SpikeSourceArray,
{'spike_times': list})
pop_list.append(pop_in)
#for j in range(input_size):
#pop_in[j].spike_times = spike_source_data[j]
#pop_in = p.Population(input_size, p.SpikeSourceArray, {'spike_times' : []})
#for j in range(input_size):
#pop_in[j].spike_times = spike_source_data[j]
#pop_list.append(pop_in)
#count =0
#print w_list[0].shape[0]
for w in w_list:
input_size = w.shape[0]
#count = count+1
#print count
output_size = w.shape[1]
#pos_w = np.copy(w)
#pos_w[pos_w < 0] = 0
#neg_w = np.copy(w)
#neg_w[neg_w > 0] = 0
conn_list_exci = []
conn_list_inhi = []
#k_size=in_size-out_size+1
for x_ind in range(input_size):
for y_ind in range(output_size):
weights = w[x_ind][y_ind]
#for i in range(w.shape[1]):
if weights > 0:
conn_list_exci.append((x_ind, y_ind, weights, 1.))
elif weights < 0:
conn_list_inhi.append((x_ind, y_ind, weights, 1.))
#print output_size
pop_out = p.Population(output_size, p.IF_curr_exp, cell_para)
if len(conn_list_exci) > 0:
p.Projection(pop_in,
pop_out,
p.FromListConnector(conn_list_exci),
target='excitatory')
if len(conn_list_inhi) > 0:
p.Projection(pop_in,
pop_out,
p.FromListConnector(conn_list_inhi),
target='inhibitory')
#p.Projection(pop_in, pop_out, p.AllToAllConnector(weights = pos_w), target='excitatory')
#p.Projection(pop_in, pop_out, p.AllToAllConnector(weights = neg_w), target='inhibitory')
pop_list.append(pop_out)
pop_in = pop_out
pop_out.record()
run_time = np.ceil(np.max(spike_source_data)[0] / 1000.) * 1000
#print run_time
p.run(run_time)
spikes = pop_out.getSpikes(compatible_output=True)
return spikes
injectionConnection = [(0, 0, weight_to_spike, 1)]
all_to_one_connection = list()
for i in range(0, nNeurons):
singleConnection = (i, 0, weight_to_spike, delay)
all_to_one_connection.append(singleConnection)
spikeArray = {'spike_times': [[0]]}
populations.append(
p.Population(nNeurons, p.IF_curr_exp, cell_params_lif, label='pop_1'))
populations.append(
p.Population(1, p.SpikeSourceArray, spikeArray, label='inputSpikes_1'))
populations.append(
p.Population(nNeurons, p.IF_cond_exp, cell_params_lif, label='pop_2'))
projections.append(
p.Projection(populations[0], populations[0],
p.FromListConnector(loopConnections)))
projections.append(
p.Projection(populations[1], populations[0],
p.FromListConnector(injectionConnection)))
projections.append(
p.Projection(populations[0], populations[2],
p.FromListConnector(all_to_one_connection)))
populations[0].record_v()
populations[0].record_gsyn()
populations[0].record()
p.run(5000)
p.end()
def setupLayerPN(params, neuronModel, cell_params, populationsRN,
populationsPN):
#create a projection neuron PN cluster population per VR
#this will be fed by the equivalent RN population and will laterally
#inhibit between clusters
numVR = int(params['NUM_VR'])
#print 'PN layer, no. VR: ' , numVR
pnClusterSize = int(params['CLUSTER_SIZE'] * params['NETWORK_SCALE'])
maxNeuronsPerCore = int(params['MAX_NEURONS_PER_CORE'])
maxVrPerPop = maxNeuronsPerCore / pnClusterSize
#how many cores were needed to accomodate RN layer (1 pynn pop in this case)
numCoresRN = utils.coresRequired(populationsRN, maxNeuronsPerCore)
#print 'The RN layer is taking up ', numCoresRN, ' cores'
coresAvailablePN = int(params['CORES_ON_BOARD'] - params['NUM_CLASSES'] -
numCoresRN - 3) # 2 x input, 1 x noise source
#print 'PN layer, no. cores available:' , coresAvailablePN
vrPerPop = int(ceil(float(numVR) / float(coresAvailablePN)))
if vrPerPop > maxVrPerPop:
print 'The number of VR and/or cluster size stipulated for \
this model are too a large for the capacity of this board.'
quit
#print 'PN layer, no. VRs per population will be: ', vrPerPop
pnPopSize = pnClusterSize * vrPerPop
#print 'PN layer, neurons per population will be: ', pnPopSize
numPopPN = int(ceil(float(numVR) / float(vrPerPop)))
#print 'PN layer, number of populations(cores) used will be: ', numPopPN
#print 'PN layer, spare (unused) cores : ', coresAvailablePN - numPopPN
weightPNPN = float(params['WEIGHT_WTA_PN_PN'])
delayPNPN = int(params['DELAY_WTA_PN_PN'])
connectivityPNPN = float(params['CONNECTIVITY_WTA_PN_PN'])
for p in range(numPopPN):
popName = 'popPN_' + str(p)
popPN = spynnaker.Population(pnPopSize,
neuronModel,
cell_params,
label=popName)
#print 'created population ', popName
populationsPN.append(popPN)
#create a FromList to feed each PN neuron in this popn from its
#corresponding RN neuron in the single monolithic RN popn
weightRNPN = float(params['WEIGHT_RN_PN'])
delayRNPN = int(params['DELAY_RN_PN'])
rnStartIdx = p * pnPopSize
rnEndIdx = rnStartIdx + pnPopSize - 1
# The last PN popn will often have unneeded 'ghost' clusters at
#the end due to imperfect dstribution of VRs among cores
# As there is no RN cluster that feeds these (RN is one pop of the
#correct total size) so the connections must stop at the end of RN
rnMaxIdx = populationsRN[0]._size - 1
if rnEndIdx > rnMaxIdx:
rnEndIdx = rnMaxIdx #clamp to the end of the RN population
pnEndIdx = rnEndIdx - rnStartIdx
connections = utils.fromList_OneToOne_fromRangeToRange(
rnStartIdx, rnEndIdx, 0, pnEndIdx, weightRNPN, delayRNPN,
delayRNPN)
projClusterRNToClusterPN = spynnaker.Projection(
populationsRN[0],
popPN,
spynnaker.FromListConnector(connections),
target='excitatory')
#within this popn only, connect each PN sub-population VR
#"cluster" to inhibit every other
if vrPerPop > 1:
utils.createIntraPopulationWTA(popPN, vrPerPop, weightPNPN,
delayPNPN, connectivityPNPN, True)
#Also connect each PN cluster to inhibit every other cluster
utils.createInterPopulationWTA(populationsPN, weightPNPN, delayPNPN,
connectivityPNPN)
label=RECEIVER_LABEL2)
sim.external_devices.activate_live_output_for(synfire1)
sim.external_devices.activate_live_output_for(synfire2)
loop_conns = list()
for i in range(0, n_neurons - 1):
single_connection = (i, i + 1, weight_to_spike, delay)
loop_conns.append(single_connection)
print(loop_conns)
input_proj = sim.Projection(input,
synfire1,
sim.OneToOneConnector(),
synapse_type=sim.StaticSynapse(weight=5, delay=1))
synfire1_proj = sim.Projection(synfire1, synfire1,
sim.FromListConnector(loop_conns))
synfire2_proj = sim.Projection(synfire2, synfire2,
sim.FromListConnector(loop_conns))
"""
s_neo = synfire1.get_data(variables=["spikes"])
spikes = s_neo.segments[0].spiketrains
print spikes
s_neo = synfire2.get_data(variables=["spikes"])
spikes = s_neo.segments[0].spiketrains
print spikes
"""
sim.run(simtime)
sim.end()
})
subsampled = p.Population(
subsample_size * subsample_size, # size
p.IF_curr_exp, # Neuron Type
cell_params, # Neuron Parameters
label="Input") # Label
# select one population to observe with the visualiser in tools/visualiser
# the visualiser needs to be started with the following configuration files:
# ./visualiser -c retina_full_128.ini for observing the retina input
# ./visualiser -c retina_32_128pc.ini for observing the subsampling population
input_pol_0.record() # to visualise the retina input
#subsampled.record() # to visualise the subsampled input
p1 = p.Projection(input_pol_0,
subsampled,
p.FromListConnector(
subSamplerConnector2D(128, subsample_size, .25, 1)),
label='subsampling projection')
p2 = p.Projection(input_pol_1,
subsampled,
p.FromListConnector(
subSamplerConnector2D(128, subsample_size, .25, 1)),
label='subsampling projection')
p.run(runtime) # Simulation time
p.end()
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
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
#misc.set_cell_params(pop_1, cellparams)
pop_2 = sim.Population(size=4, cellclass=sim.IF_curr_exp(), label="2_hidden")
pop_2.set(v_thresh=0.1)
#misc.set_cell_params(pop_2, cellparams)
#pop_2.set(i_offset=s[label]['v_thresh'])
# this projection / pop_0 is only used to monitor the input spikes (actually not needed for MLP network)
input_proj = sim.Projection(input_pop,
pop_0,
sim.OneToOneConnector(),
synapse_type=sim.StaticSynapse(weight=3, delay=1))
if INHIBITORY:
inhibitory_connections_1, exitatory_connections_1 = misc.read_connections(
p1)
inhibitory_connector_1 = sim.FromListConnector(
inhibitory_connections_1, column_names=["i", "j", "delay", "weight"])
exitatory_connector_1 = sim.FromListConnector(
exitatory_connections_1, column_names=["i", "j", "delay", "weight"])
inhibitory_proj_1 = sim.Projection(pop_0,
pop_1,
inhibitory_connector_1,
receptor_type='inhibitory')
exitatory_proj_1 = sim.Projection(pop_0,
pop_1,
exitatory_connector_1,
receptor_type='excitatory')
inhibitory_connections_2, exitatory_connections_2 = misc.read_connections(
p2)
inhibitory_connector_2 = sim.FromListConnector(
inhibitory_connections_2, column_names=["i", "j", "delay", "weight"])
def train_snn(### Settings
data_dir = "data/X_train_zied.npy",
cls_dir = "data/y_train_zied.npy",
data = "load", # pass data as argument
cls = "load", # pass labels as argument
save = True, # True to save all parameters of the network
randomness = True,
reverse_src_del = False,
use_old_weights = False,
rand_data = False,
### Parameters
n_training = 2, # How many times the samples will be iterated
ts = 1., # Timestep of Spinnaker (ms)
trial_num = 10, # How many samples (trials) from data used
# Network
n_feature = 80, # Number of features (= 4 features * 20 neurons)
# Weights
wei_src_enc = .2, # From Source Array at input to Encoding Layer(Exc)
wei_enc_filt = .6, # From Encoding Layer to Filtering Layer Exc neurons (Exc)
wei_filt_inh = 0.03, # From Filtering Layer Inh neurons to Exc neurons (Inh)
wei_init_stdp = .0, # From Filtering Layer Exc neurons to Output Layer (Exc)
wei_cls_exc = 0.9, # From Output Layer Exc neurons to Inh neurons (Exc)
wei_cls_inh = 50,#0.1,#,10 # From Output Layer Inh neurons to Exc neurons (Inh)
wei_source_outp = 10., # From Source Array at output to Output Layer Exc neurons (Exc)
wei_noise_poi = 0.02,
# Delays
del_init_stdp = 1.,
del_source_outp = 1.,
del_noise_poi = 1.,
# Connection Probabilities
prob_filt_inh = .4, # Prob of connectivity inhibitory connections at FilT_Layer
prob_stdp = 1., # Prob of STDP connections
prob_output_inh = .7, # Prob of inhibitory connections at Output Layer
prob_noise_poi_conn = 0.02,
## STDP Parameters
tau_pl = 5.,
stdp_w_max = 0.4, # default 0.4
stdp_w_min = 0.0, # default 0.0
stdp_A_pl = 2,#0.02,# 0.01, # default 0.01 (below 0.01 weights don't change)
# => minus in order to get symmetric curve
# Data Extraction
scale_data = 2.): # Scale features into [0-scale_data] range
# BUG fix:
# n_feature is somehow a tuple
# try:
# trial_num = trial_num[0]
# except Exception as e:
# print("\n\n\n EXCEPTION TRIGGERED !!!! \n\n\n")
# pass
############################################################################
## Function Definitions
############################################################################
def gaussian(x, mu, sig):
return np.float16(np.exp(-np.power(x - mu, 2.) /
(2 * np.power(sig, 2.))))
def calc_pop_code(feature, rng1, rng2, num):
interval=np.float(rng2-rng1)/num
means=np.arange(rng1+interval, rng2+interval, interval)
pop_code=[gaussian(feature,mu,0.025) for mu in means]
return pop_code
def PoissonTimes2(t_str=0., t_end=100., rate=10., seed=1.):
times = [t_str]
rng = np.random.RandomState(seed=seed)
cont = True
while cont == True:
t_next = np.floor(times[-1] + 1000. * next_spike_times(rng,rate))
if t_next < t_end - 30:
times.append(t_next[0])
else:
cont=False
return times[1:]
def PoissonTimes(t_str=0., t_end=100., rate=10., seed=1., max_rate=0):
if rate>0:
interval = (t_end - t_str + 0.) / rate
# Add additional reverse_src_del
if reverse_src_del == True:
times = np.arange(t_str + 30, t_end - 40, interval)
# add reverse proportional delay
rev_del = np.ceil(max_rate / rate)
if rev_del != np.inf:
times += rev_del
else:
times = np.arange(t_str + 30, t_end - 40, interval)
return list(times)
else:
return []
def next_spike_times(rng,rate):
return -np.log(1.0-rng.rand(1)) / rate
def ismember(a, b):
b=[b]
bind = {}
for i, elt in enumerate(b):
if elt not in bind:
bind[elt] = i
aa=[bind.get(itm, -1) for itm in a]
return sum(np.array(aa)+1.)
def get_data(trial_num, test_num=10):
# trial_num: number of training samples
# test_num: number of test samples
pass
def rand_sample_of_train_set(n):
# n: number of features
# Return: np.array containing n samples of the training set
X = np.load(data_dir)
y = np.load(cls_dir)
idx = np.random.randint(len(X), size=n)
return X[idx], y[idx]
############################################################################
## Parameters
############################################################################
# Load training data
# only load n_rand_data features of training set
if rand_data == True:
data, cls = rand_sample_of_train_set(trial_num)
# load all features of training set
else: # load data if its not in passed as fuct argument
if data == "load" and cls == "load":
data = np.load(data_dir)
cls = np.load(cls_dir)
# Simulation Parameters
trial_num = len(cls) # How many samples (trials) from data will be presented
#n_training = 1 # How many times the samples will be iterated
n_trials = n_training * trial_num # Total trials
time_int_trials = 200. # (ms) Time to present each trial data
SIM_TIME = n_trials * time_int_trials # Total simulation time (ms)
#ts = 1. # Timestep of Spinnaker (ms)
min_del = ts
max_del = 144 * ts
p.setup(timestep=ts, min_delay=min_del, max_delay=max_del)
## Neuron Numbers
#n_feature = 80 # Number of features (= 4 features * 20 neurons)
# => 20 neuros: resolution of encoding
n_pop = data.shape[1] #4 # Number of neurons in one population (X dim)
n_cl = 2 # Number of classes at the output
## Connection Parameters
# Weights
# wei_src_enc = .2 # From Source Array at input to Encoding Layer(Exc)
# wei_enc_filt = .6 # From Encoding Layer to Filtering Layer Exc neurons (Exc)
# wei_filt_inh = 0.03 # From Filtering Layer Inh neurons to Exc neurons (Inh)
# wei_init_stdp = .0 # From Filtering Layer Exc neurons to Output Layer (Exc)
# wei_cls_exc = 0.9 # From Output Layer Exc neurons to Inh neurons (Exc)
# wei_cls_inh = 10 # 0.1 # From Output Layer Inh neurons to Exc neurons (Inh)
# wei_source_outp = 10. # From Source Array at output to Output Layer Exc neurons (Exc)
# wei_noise_poi = 0.02
# Delays
if randomness == True: # if True: calculate "del_src_enc" (randomly) new
# if False: load previously saved "del_src_enc"
if reverse_src_del == True:
# calc delays erversly proportional to feature value
del_src_enc = np.zeros(n_feature*n_pop)
else:
del_src_enc = [int(np.random.randint(n_pop)+1)
for _ in range(n_feature*n_pop)]
np.save("output_files/del_src_enc.npy", del_src_enc)
else:
#del_src_enc = np.load("output_files/del_src_enc.npy")
del_src_enc = np.ones(n_feature*n_pop).astype(int) #[1 for _ in range(n_feature*n_pop)]
del_enc_filt = ts
del_filt_inh = ts
# del_init_stdp = 1.
del_cls_exc = ts
del_cls_inh = ts
# del_source_outp = 1.
# del_noise_poi = 1.
# Firing Rates
noise_poi_rate = 10.
max_fr_input = 100. # maximum firing rate at the input layer
max_fr_rate_output = 20. # Maximum firing rate at output (supervisory signal)
## Connection Probabilities
# prob_filt_inh = .4 # Prob of connectivity inhibitory connections at FilT_Layer
# prob_stdp = 1. # Prob of STDP connections
# prob_output_inh = .7 # Prob of inhibitory connections at Output Layer
# prob_noise_poi_conn = 0.02
## STDP Parameters
# tau_pl = 0.3 # (0.2 - 0.3 works)
tau_min = tau_pl # default tau_pl
# stdp_w_max = 0.4 # default 0.4
# stdp_w_min = 0.0 # default 0.0
# stdp_A_pl = 0.01 # default 0.01 (below 0.01 weights don't change)
stdp_A_min = -stdp_A_pl # default - stdp_A_pl
# => minus in order to get symmetric curve
## Neuron Parameters
cell_params_lif = {'cm': 0.25,# 0.25,
'i_offset': 0.0,
'tau_m': 20.,
'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#-50
}
############################################################################
## Data Extraction
############################################################################
## Extract Feature Data
# scale_data = 2. # Scale features into [0-scale_data] range
r,c = np.shape(data)
data_rates = np.reshape(data, (1, r*c))[0]
# Threshold (to keep spikes in range)
thr_data_plus = 30
thr_data_minus = -10
#dd = [d if d<thr_data_plus else thr_data_plus for d in data_rates]
#dd = [d if d>thr_data_minus else thr_data_minus for d in dd]
# Shift and normalize data
#dd2 = np.array(dd) - min(dd)
dd2 = np.array(data_rates) - min(data_rates)
dd2 = dd2 / max(dd2) * 2
new_data_rates = []
for r in dd2:
new_data_rates += calc_pop_code(r, 0., scale_data, n_feature /
(n_pop + 0.0))
data_rates = list(max_fr_input*np.array(new_data_rates))
## Extract Class Data
# load class vector
#cls = np.load(path_y)
cls = np.reshape(cls, (len(cls),1)) # create col vector
r_cl, c_cl = np.shape(cls)
#cls = list(np.reshape(cls, (1, r_cl * c_cl))[0] - 1)
cls = list(np.reshape(cls, (1, r_cl * c_cl))[0])
## The class and rate information to be used during the simulation
outputs = n_training * cls[0:trial_num] # positiv, ints
poi_rate = n_training * data_rates[0:trial_num * n_feature]
## Save parameters to be used in test
parameter_dict = {"n_feature":n_feature, "n_pop":n_pop,"n_cl":n_cl,
"wei_src_enc":wei_src_enc, "wei_enc_filt":wei_enc_filt,
"wei_filt_inh":wei_filt_inh, "wei_cls_exc":wei_cls_exc,
"wei_cls_inh":wei_cls_inh, "del_enc_filt":del_enc_filt,
"del_init_stdp":del_init_stdp, "del_cls_exc":del_cls_exc,
"del_cls_inh":del_cls_inh, "trial_num":trial_num,
"time_int_trials":time_int_trials, "scale_data":scale_data,
"ts":ts,"max_fr_input":max_fr_input,
"max_fr_rate_output":max_fr_rate_output,
"noise_poi_rate":noise_poi_rate, "max_fr_input":max_fr_input,
"max_fr_rate_output":max_fr_rate_output, "prob_filt_inh":prob_filt_inh,
"prob_stdp":prob_stdp, "prob_output_inh":prob_output_inh,
"prob_noise_poi_conn":prob_noise_poi_conn, "tau_pl":tau_pl,
"stdp_w_max":stdp_w_max, "stdp_w_min":stdp_w_min, "stdp_A_pl":stdp_A_pl,
"wei_noise_poi":wei_noise_poi, "del_noise_poi":del_noise_poi,
"thr_data_plus":thr_data_plus, "thr_data_minus":thr_data_minus
}
if save == True:
np.save("output_files/parameters1",parameter_dict)
np.save("output_files/parameters2",del_src_enc)
############################################################################
## Create populations for different layers
############################################################################
poi_layer = []
enc_layer = []
filt_layer_exc = []
out_layer_exc = []
out_layer_inh = []
out_spike_source = []
# Calculate spike times at the input using the rate information coming from features
spike_times = [[] for i in range(n_feature)]
for i in range(n_trials):
t_st = i * time_int_trials
t_end = t_st + time_int_trials
ind = i * n_feature
for j in range(n_feature):
times = PoissonTimes(t_st, t_end, poi_rate[ind+j],
np.random.randint(100), max_rate=max(poi_rate))
for t in times:
spike_times[j].append(t)
if randomness == True: # if True: calculate "spike_times" (randomly) new
# uf False: load previously saved "spike_times"
np.save('output_files/spike_times_train.npy', spike_times)
else:
spike_times = np.load('output_files/spike_times_train.npy')
# Calculate spike times at the output (as supervisory signal)
out_spike_times=[[] for i in range(n_cl)]
for i in range(n_trials):
t_st = i * time_int_trials
t_end = t_st + time_int_trials
ind = outputs[i]
times = PoissonTimes(t_st, t_end, max_fr_rate_output,
np.random.randint(100))
for t in times:
out_spike_times[int(ind)].append(t)
if randomness == True: # if True: calculate "out_spike_times" (randomly) new
# uf False: load previously saved "out_spike_times"
np.save('output_files/out_spike_times.npy', out_spike_times)
else:
out_spike_times = np.load('output_files/out_spike_times.npy')
# Spike source of input layer
spike_source=p.Population(n_feature,
p.SpikeSourceArray,
{'spike_times':spike_times},
label='spike_source')
# Spike source of output layer (Supervisory signal)
for i in range(n_cl):
out_spike_source.append(p.Population(1, p.SpikeSourceArray,
{'spike_times':[out_spike_times[i]]}, label='out_spike_source'))
# Encoding layer and Filtering Layer definitions
enc_layer = p.Population(n_feature * n_pop,
p.IF_curr_exp,
cell_params_lif,
label='enc_layer')
filt_layer = p.Population(n_feature * n_pop,
p.IF_curr_exp,
cell_params_lif,
label='filt_layer')
# Excitatory and Inhibitory population definitions at the output
for i in range(n_cl):
out_layer_exc.append(p.Population(n_pop,
p.IF_curr_exp,
cell_params_lif,
label='out_layer_exc{}'.format(i)))
out_layer_inh.append(p.Population(n_pop,
p.IF_curr_exp,
cell_params_lif,
label='out_layer_inh{}'.format(i)))
out_layer_exc[i].record()
# Noisy poisson population at the input
poisson_input = p.Population(n_pop * 2,
p.SpikeSourcePoisson,
{"rate":noise_poi_rate})
# Record Spikes
enc_layer.record()
filt_layer.record()
#enc_layer.initialize('v',p.RandomDistribution('uniform',[-51.,-69.]))
#filt_layer.initialize('v',p.RandomDistribution('uniform',[-51.,-69.]))
############################################################################
## Projections
############################################################################
## Connection List from Spike Source Array to Encoding Layer
conn_inp_enc=[]
for i in range(n_feature):
ind=i*n_pop
for j in range(n_pop):
conn_inp_enc.append([i,ind+j,wei_src_enc,del_src_enc[ind+j]])
if save == True:
np.save("output_files/conn_inp_enc",conn_inp_enc)
## Connection List for Filtering Layer Inhibitory
if randomness == True: # if True: calculate conn_filt_inh (randomly) new
# uf False: load previously saved conn_filt_inh
conn_filt_inh=[]
for i in range(n_feature):
rng1=i*n_pop
rng2=rng1+n_pop
inp=range(rng1,rng2)
outp=range(0,rng1)+range(rng2,n_feature*n_pop)
for ii in inp:
for jj in outp:
if prob_filt_inh>np.random.rand():
conn_filt_inh.append([ii,jj,wei_filt_inh,del_filt_inh])
if save == True:
np.save('output_files/conn_filt_inh.npy', conn_filt_inh)
else:
conn_filt_inh = np.load('output_files/conn_filt_inh.npy')
## STDP Connection List
if randomness == True: # if True: calculate conn_stdp_list (randomly) new
# uf False: load previously saved conn_stdp_list
conn_stdp_list=[[] for i in range(n_cl)]
for i in range(n_cl): # For each population at output layer
if use_old_weights == True:
cl_weights = np.load(
"output_files/stdp_weights{}.npy".format(i))
w = 0
for ii in range(n_pop * n_feature): # For each neuron in filtering layer
for jj in range(n_pop): # For each neuron in each population of output layer
if prob_stdp > np.random.rand(): # If the prob of connection is satiesfied
# Make the connection
if use_old_weights == True:
conn_stdp_list[i].append([ii,
jj,
cl_weights[w],
del_init_stdp])
w += 1
else:
conn_stdp_list[i].append([ii,
jj,
wei_init_stdp,
del_init_stdp])
if use_old_weights == False or save == True:
np.save('output_files/conn_stdp_list.npy', conn_stdp_list)
else:
conn_stdp_list = np.load('output_files/conn_stdp_list.npy')
## Output Layer Inhibitory Connection List
if randomness == True: # if True: calculate conn_stdp_list (randomly) new
# uf False: load previously saved conn_stdp_list
conn_output_inh = [[] for i in range(n_cl) for j in range(n_cl) if i!=j]
c = 0
for i in range(n_cl):
for j in range(n_cl):
if i != j:
for ii in range(n_pop):
for jj in range(n_pop):
if prob_output_inh > np.random.rand():
conn_output_inh[c].append([ii,
jj,
wei_cls_inh,
del_cls_inh])
c += 1
if save == True:
np.save("output_files/conn_output_inh.npy",conn_output_inh)
else:
conn_output_inh = np.load("output_files/conn_output_inh.npy")
## Spike Source to Encoding Layer
p.Projection(spike_source, enc_layer,
p.FromListConnector(conn_inp_enc))
## Encoding Layer to Filtering Layer
p.Projection(enc_layer, filt_layer,
p.OneToOneConnector(weights=wei_enc_filt,
delays=del_enc_filt))
## Filtering Layer Inhibitory
p.Projection(filt_layer, filt_layer,
p.FromListConnector(conn_filt_inh),
target="inhibitory")
## STDP Connection between Filtering Layer and Output Layer
timing_rule = p.SpikePairRule(tau_plus=tau_pl,
tau_minus=tau_min)
weight_rule = p.AdditiveWeightDependence(w_max=stdp_w_max,
w_min=stdp_w_min,
A_plus=stdp_A_pl,
A_minus=stdp_A_min)
stdp_model = p.STDPMechanism(timing_dependence=timing_rule,
weight_dependence=weight_rule)
# STDP connection
stdp_proj = []
for j in range(n_cl):
stdp_proj.append(
p.Projection(filt_layer,out_layer_exc[j],
p.FromListConnector(conn_stdp_list[j]),
synapse_dynamics = p.SynapseDynamics(slow=stdp_model)))
## Connection between Output Layer neurons
c = 0
for i in range(n_cl):
p.Projection(out_layer_exc[i], out_layer_inh[i],
p.OneToOneConnector(weights=wei_cls_exc,
delays=del_cls_exc))
iter_array=[j for j in range(n_cl) if j!=i]
for j in iter_array:
p.Projection(out_layer_exc[i], out_layer_exc[j],
p.FromListConnector(conn_output_inh[c]),
target="inhibitory")
c += 1
## Spike Source Array to Output
for i in range(n_cl):
p.Projection(out_spike_source[i],
out_layer_exc[i],
p.AllToAllConnector(weights=wei_source_outp,
delays=del_source_outp))
iter_array = [j for j in range(n_cl) if j != i]
for j in iter_array:
p.Projection(out_spike_source[i],
out_layer_exc[j],
p.AllToAllConnector(weights=wei_source_outp,
delays=del_source_outp),
target="inhibitory")
#for i in range(n_cl):
# p.Projection(out_spike_source[i], out_layer_exc[i], p.AllToAllConnector\
# (weights=wei_source_outp, delays=del_source_outp))
# p.Projection(out_spike_source[i], out_layer_exc[1-i], p.AllToAllConnector\
# (weights=wei_source_outp, delays=del_source_outp),target="inhibitory")
## Noisy poisson connection to encoding layer
if randomness == True: # if True: connect noise to network
# if False: don't use noise in network
p.Projection(poisson_input, enc_layer,
p.FixedProbabilityConnector(p_connect=prob_noise_poi_conn,
weights=wei_noise_poi,
delays=del_noise_poi))
############################################################################
## Simulation
############################################################################
p.run(SIM_TIME)
Enc_Spikes = enc_layer.getSpikes()
Filt_Exc_Spikes = filt_layer.getSpikes()
Out_Spikes = [[] for i in range(n_cl)]
for i in range(n_cl):
Out_Spikes[i] = out_layer_exc[i].getSpikes()
wei = []
for i in range(n_cl):
ww = stdp_proj[i].getWeights()
if save == True:
np.save("output_files/stdp_weights{}".format(i), ww)
wei.append(ww)
p.end()
############################################################################
## Plot
############################################################################
## Plot 1: Encoding Layer Raster Plot
if 0:
pylab.figure()
pylab.xlabel('Time (ms)')
pylab.ylabel('Neuron ID')
pylab.title('Encoding Layer Raster Plot')
pylab.hold(True)
pylab.plot([i[1] for i in Enc_Spikes], [i[0] for i in Enc_Spikes], ".b")
pylab.hold(False)
#pylab.axis([-10,c*SIM_TIME+100,-1,numInp+numOut+numInp+3])
pylab.show()
## Plot 2-1: Filtering Layer Raster Plot
if 0:
pylab.figure()
pylab.xlabel('Time (ms)')
pylab.ylabel('Neuron ID')
pylab.title('Filtering Layer Raster Plot')
pylab.plot([i[1] for i in Filt_Exc_Spikes],
[i[0] for i in Filt_Exc_Spikes], ".b")
#pylab.axis([-10,c*SIM_TIME+100,-1,numInp+numOut+numInp+3])
pylab.show()
## Plot 2-2: Filtering Layer Layer Raster Plot
if 0:
pylab.figure()
pylab.xlabel('Time (ms)')
pylab.ylabel('Neuron ID')
pylab.title('Filtering Layer Layer Raster Plot')
pylab.hold(True)
pylab.plot([i[1] for i in Filt_Exc_Spikes],
[i[0] for i in Filt_Exc_Spikes], ".b")
time_ind=[i*time_int_trials for i in range(len(outputs))]
for i in range(len(time_ind)):
pylab.plot([time_ind[i],time_ind[i]],[0,2000],"r")
pylab.hold(False)
#pylab.axis([-10,c*SIM_TIME+100,-1,numInp+numOut+numInp+3])
pylab.show()
## Plot 3-1: Output Layer Raster Plot
if 0:
pylab.figure()
pylab.xlabel('Time (ms)')
pylab.ylabel('Neuron')
pylab.title('Output Layer Raster Plot')
pylab.hold(True)
c=0
for array in Out_Spikes:
pylab.plot([i[1] for i in array], [i[0]+c for i in array], ".b")
c+=0.2
pylab.hold(False)
pylab.axis([-10,SIM_TIME+100,-1,n_pop+3])
pylab.show()
## Plot 4: STDP WEIGHTS
if 1:
pylab.figure()
pylab.xlabel('Weight ID')
pylab.ylabel('Weight Value')
pylab.title('STDP weights at the end')
#pylab.title('STDP weights at the end' + ' (trail_num=' + str(trial_num) + ')')
pylab.hold(True)
for i in range(n_cl):
pylab.plot(wei[i])
pylab.hold(False)
pylab.axis([-10,n_pop*n_feature*n_pop*0.5+10,-stdp_w_max,2*stdp_w_max])
str_legend=["To Cl {}".format(i+1) for i in range(n_cl)]
pylab.legend(str_legend)
#pylab.show()
fname = 'plots/weights_1.png'
while True:
if os.path.isfile(fname): # if file already exists
new_num = int(fname.split('.')[0].split('_')[1]) + 1
fname = fname.split('_')[0] + '_' +str(new_num) + '.png'
# if len(fname) == 19:
# new_num = int(fname.split('.')[0][-1]) + 1
# fname = fname.split('.')[0][:-1] + str(new_num) + '.png'
# elif len(fname) == 20:
# new_num = int(fname.split('.')[0][-2:]) + 1
# fname = fname.split('.')[0][:-2] + str(new_num) + '.png'
# else:
# new_num = int(fname.split('.')[0][-3:]) + 1
# fname = fname.split('.')[0][:-3] + str(new_num) + '.png'
else:
pylab.savefig(fname)
break
#pylab.figure()
#pylab.xlabel('Weight ID')
#pylab.ylabel('Weight Value')
#pylab.title('STDP weights at the end')
#pylab.hold(True)
#pylab.plot(wei[0], "b")
#pylab.plot(wei[1], "g")
#pylab.hold(False)
#pylab.axis([-10, n_pop * n_feature * n_pop * 0.5 + 10,
# -stdp_w_max, 2 * stdp_w_max])
#pylab.legend(['To Cl 1','To Cl 2'])
#pylab.show()
## Plot 5: Spike Source Spiking Times
if 0:
pylab.figure()
pylab.hold(True)
pylab.plot(out_spike_times[0],
[1 for i in range(len(out_spike_times[0]))],"x")
pylab.plot(out_spike_times[1],
[1.05 for i in range(len(out_spike_times[1]))],"x")
pylab.hold(False)
pylab.title("Spike Source Spiking Times")
pylab.axis([-100,SIM_TIME+100,-2,3])
pylab.show()
## Calculate spiking activity of each neuron to each class inputs
sum_filt=[[0 for i in range(n_feature*n_pop)] for j in range(n_cl)]
sum_filt=np.array(sum_filt)
for i in range(n_trials):
t_st = i * time_int_trials
t_end = t_st + time_int_trials
cl = outputs[i]
for n,t in Filt_Exc_Spikes:
if t >= t_st and t < t_end:
sum_filt[int(cl),int(n)] = sum_filt[int(cl), int(n)] + 1
a4=sum_filt[0]
b4=sum_filt[1]
thr=20
diff_vec=np.abs(a4 - b4)
diff_thr=[i if i>thr else 0. for i in diff_vec]
diff_ind=[i for i in range(len(diff_thr)) if diff_thr[i]!=0]
if save == True:
np.save("output_files/diff_ind_filt",diff_ind)
diff2 = a4 - b4
diff_thr2=[i if i > thr or i <- thr else 0. for i in diff2]
diff_ind2=[i for i in range(len(diff_thr2)) if diff_thr2[i] != 0]
if save == True:
np.save("output_files/diff_ind_filt2",diff_ind2)
np.save("output_files/diff_thr2",diff_thr2)
## Plot 6: Total Spiking Activity of Neurons at Decomposition Layer for Each Class
if 0:
a4=sum_filt[0]
b4=sum_filt[1]
pylab.figure()
pylab.hold(True)
pylab.plot(a4,"b")
pylab.plot(b4,"r")
pylab.xlabel('Neuron ID')
pylab.ylabel('Total Firing Rates Through Trials')
pylab.title("Total Spiking Activity of Neurons at Decomposition Layer ",
"for Each Class")
pylab.hold(False)
pylab.legend(["Activity to AN1","Activity to AN2"])
pylab.show()
'connected_chip_coords':connected_chip_coords,
'connected_chip_edge':link,
'unique_id': 'R',
"polarity": p.ExternalRetinaDevice.DOWN_POLARITY},
label='input_pol_1down')
subsampled = p.Population(subsample_size*subsample_size, # size
p.IF_curr_exp, # Neuron Type
cell_params, # Neuron Parameters
label="Input") # Label
subsampled.initialize('v', -75)
subsampled.set_mapping_constraint({'x':0,'y':1})
#subsampled.record() # sends spikes to the visualiser (use parameters = 32)
list_input = retina_lib.subSamplerConnector2D(128,subsample_size,.2,1)
#print "input list is :"
#print list_input
p1_up = p.Projection(input_pol_1_up,
subsampled,
p.FromListConnector(list_input),
label='subsampling projection')
p2_down = p.Projection(input_pol_1_down,
subsampled,
p.FromListConnector(list_input),
label='subsampling projection')
p.run(runtime) # Simulation time
p.end()
def test_snn(randomness = False,
data_dir = "data/X_test_zied.npy",
cls_dir = "data/y_test_zied.npy",
data = "load", # pass data as argument
cls = "load"): # pass labels as argument
###############################################################################
## Function Definitions
###############################################################################
def gaussian(x, mu, sig):
return np.float16(np.exp(-np.power(x - mu, 2.) / (2 * np.power(sig, 2.))))
def calc_pop_code(feature, rng1, rng2, num):
interval = np.float(rng2 - rng1) / num
means = np.arange(rng1 + interval,rng2 + interval, interval)
pop_code = [gaussian(feature, mu, 0.025) for mu in means]
return pop_code
def PoissonTimes2(t_str=0., t_end=100., rate=10., seed=1.):
times = [t_str]
rng = np.random.RandomState(seed=seed)
cont = True
while cont == True:
t_next = np.floor(times[-1] + 1000. * next_spike_times(rng, rate))
if t_next < t_end - 30:
times.append(t_next[0])
else:
cont = False
return times[1:]
def PoissonTimes(t_str=0., t_end=100., rate=10., seed=1.):
if rate > 0:
interval = (t_end - t_str+0.) / rate
times = np.arange(t_str + 30, t_end - 40, interval)
return list(times)
else:
return []
def next_spike_times(rng,rate):
return -np.log(1.0 - rng.rand(1)) / rate
def ismember(a, b):
b = [b]
bind = {}
for i, elt in enumerate(b):
if elt not in bind:
bind[elt] = i
aa=[bind.get(itm, -1) for itm in a]
return sum(np.array(aa) + 1.)
###############################################################################
## Parameters
###############################################################################
# Load Parameter
parameters = np.load("output_files/parameters1.npy")
parameters = parameters.item()
# Load test data
if data == "load" and cls == "load":
data = np.load(data_dir)
cls = np.load(cls_dir)
# Simulation Parameters
trial_num = parameters["trial_num"] # How many samples (trials) from data will be presented
n_trials = len(cls)#10#20 #int(trial_num) # Total trials
time_int_trials = parameters["time_int_trials"] # (ms) Time to present each trial data
SIM_TIME = n_trials * time_int_trials # Total simulation time (ms)
ts = parameters["ts"] # Timestep of Spinnaker (ms)
min_del = ts
max_del = 144 * ts
p.setup(timestep=ts, min_delay=min_del, max_delay=max_del)
## Neuron Numbers
n_feature = parameters["n_feature"] # Number of features
n_pop = parameters["n_pop"] # Number of neurons in one population
n_cl = parameters["n_cl"] # Number of classes at the output
## Connection Parameters
# Weights
wei_src_enc = parameters["wei_src_enc"] # From Source Array at input to Encoding Layer(Exc)
wei_enc_filt = parameters["wei_enc_filt"] # From Encoding Layer to Filtering Layer Exc neurons (Exc)
wei_filt_inh = parameters["wei_filt_inh"] # From Filtering Layer Inh neurons to Exc neurons (Inh)
wei_cls_exc = parameters["wei_cls_exc"] # From Output Layer Exc neurons to Inh neurons (Exc)
wei_cls_inh = parameters["wei_cls_inh"] # From Output Layer Inh neurons to Exc neurons (Inh)
wei_noise_poi = parameters["wei_noise_poi"]
# Delays
del_src_enc = np.load("output_files/parameters2.npy")
del_enc_filt = parameters["del_enc_filt"]
del_init_stdp = parameters["del_init_stdp"]
del_cls_exc = parameters["del_cls_exc"]
del_cls_inh = parameters["del_cls_inh"]
del_noise_poi = parameters["del_noise_poi"]
# Firing Rates
noise_poi_rate = parameters["noise_poi_rate"]
max_fr_input = parameters["max_fr_input"] # maximum firing rate at the input layer
max_fr_rate_output = parameters["max_fr_rate_output"] # Maximum firing rate at output (supervisory signal)
## Connection Probabilities
prob_filt_inh = parameters["prob_filt_inh"] # Prob of connectivity inhi-connections at Filtering Layer
prob_stdp = parameters["prob_stdp"] # Probability of STDP connections
prob_output_inh = parameters["prob_output_inh"] # Prob of inhi-connections at Output Layer
prob_noise_poi_conn = parameters["prob_noise_poi_conn"]
## STDP Parameters
tau_pl = parameters["tau_pl"] #5
tau_min = tau_pl
stdp_w_max = parameters["stdp_w_max"]
stdp_w_min = parameters["stdp_w_min"]
stdp_A_pl = parameters["stdp_A_pl"]
stdp_A_min = -stdp_A_pl # minus in order to get symmetric curve
## Neuron Parameters
cell_params_lif = {'cm': 1.,
'i_offset': 0.0,
'tau_m': 20.,
'tau_refrac': 2.0,
'tau_syn_E': 5.0,
'tau_syn_I': 5.0,
'v_reset': -70.0,
'v_rest': -65.0,
'v_thresh': -65.0
}
###############################################################################
## Data Extraction
###############################################################################
## Extract Feature Data
scale_data = parameters["scale_data"] # Scale features into [0-scale_data] range
#data = np.load("features_without_artifact.npy")
#data = np.load('X_test.npy')
r, c = np.shape(data)
# Threshold (to keep spikes amplitudes in range)
thr_data_plus = parameters["thr_data_plus"]
thr_data_minus = parameters["thr_data_minus"]
data_rates = np.reshape(data, (1, r * c))[0]
# Shift an normalize the data
#dd = [d if d<thr_data_plus else thr_data_plus for d in data_rates]
#dd = [d if d>thr_data_minus else thr_data_minus for d in dd]
#dd2 = np.array(dd) - min(dd)
#dd2 = dd2 / max(dd2) * 2
dd2 = np.array(data_rates) - min(data_rates)
dd2 = dd2 / max(dd2) * 2
new_data_rates = []
for r in dd2:
new_data_rates += calc_pop_code(r, 0., scale_data,
n_feature / (n_pop + 0.0))
data_rates = list(max_fr_input * np.array(new_data_rates))
## Extract Class Data
#cls = np.load("classes_without_artifact.npy")
#cls = np.load("y_test.npy")
cls = cls.reshape(len(cls), 1)
r_cl, c_cl = np.shape(cls)
cls = list(np.reshape(cls, (1, r_cl * c_cl))[0])
outputs = cls[:n_trials]
poi_rate = data_rates[:n_feature * n_trials]
t1 = 0#70
t2 = int(t1 + n_trials)
outputs = cls[t1:t2]
poi_rate = data_rates[t1 * n_feature:n_feature * t2]
###############################################################################
## Create populations for different layers
###############################################################################
poi_layer = []
enc_layer = []
filt_layer_exc = []
out_layer_exc = []
out_layer_inh = []
# Calculate poisson spike times for features
spike_times = [[] for i in range(n_feature)]
for i in range(n_trials):
t_st = i * time_int_trials
t_end = t_st + time_int_trials
ind = i * n_feature
for j in range(n_feature):
times = PoissonTimes(t_st, t_end, poi_rate[ind+j],
np.random.randint(100))
for t in times:
spike_times[j].append(t)
if randomness == True: # if True: calculate "spike_times" (randomly) new
# if False: load previously saved "spike_times"
np.save('output_files/spike_times_test.npy', spike_times)
else:
spike_times = np.load('output_files/spike_times_test.npy')
# Spike source of input layer
spike_source = p.Population(n_feature,
p.SpikeSourceArray,
{'spike_times':spike_times},
label='spike_source')
enc_layer = p.Population(n_feature * n_pop,
p.IF_curr_exp,
cell_params_lif,
label='enc_layer')
filt_layer = p.Population(n_feature * n_pop,
p.IF_curr_exp,
cell_params_lif,
label='filt_layer')
#filt_layer_inh=p.Population(n_feature*n_pop, p.IF_curr_exp, cell_params_lif, label='filt_layer_inh')
for i in range(n_cl):
out_layer_exc.append(p.Population(n_pop,
p.IF_curr_exp,
cell_params_lif,
label='out_layer_exc{}'.format(i)))
out_layer_inh.append(p.Population(n_pop,
p.IF_curr_exp,
cell_params_lif,
label='out_layer_inh{}'.format(i)))
out_layer_exc[i].record()
poisson_input = p.Population(n_pop * 2,
p.SpikeSourcePoisson,
{"rate":noise_poi_rate})
enc_layer.record()
filt_layer.record()
###############################################################################
## Projections
###############################################################################
## Connection List from Spike Source Array to Encoding Layer
conn_inp_enc = np.load("output_files/conn_inp_enc.npy")
#Connection List for Filtering Layer Inhibitory
conn_filt_inh = np.load("output_files/conn_filt_inh.npy")
## STDP Connection List
conn_stdp_list = np.load("output_files/conn_stdp_list.npy")
diff_ind = np.load("output_files/diff_ind_filt.npy")
diff_ind2 = np.load("output_files/diff_ind_filt2.npy")
diff_thr2 = np.load("output_files/diff_thr2.npy")
c1 = 0
for cls_list in conn_stdp_list:
c2 = 0
cls_wei = np.load("output_files/stdp_weights{}.npy".format(c1))
mx = max(cls_wei)
for conn in cls_list:
# if ismember(diff_ind,conn[0]):
if (ismember(diff_ind2,conn[0]) and
np.sign(c1-0.5) * np.sign(diff_thr2[int(conn[0])]) == -1.):
# conn[2]=0.08*cls_wei[c2]/mx
conn[2] = 0.08#*diff_thr2[conn[0]]/36.
# conn[2]=2.*cls_wei[c2]
c2 += 1
c1 += 1
conn_stdp_list = list(conn_stdp_list)
## Output Layer Inhibitory Connection List
conn_output_inh = np.load("output_files/conn_output_inh.npy")
## Spike Source to Encoding Layer
p.Projection(spike_source,enc_layer,p.FromListConnector(conn_inp_enc))
## Encoding Layer to Filtering Layer
p.Projection(enc_layer, filt_layer,
p.OneToOneConnector(weights=wei_enc_filt,
delays=del_enc_filt))
## Filtering Layer Inhibitory
p.Projection(filt_layer,filt_layer,
p.FromListConnector(conn_filt_inh),
target="inhibitory")
## STDP Connection between Filtering Layer and Output Layer
stdp_proj = []
for j in range(n_cl):
stdp_proj.append(p.Projection(filt_layer, out_layer_exc[j],
p.FromListConnector(conn_stdp_list[j])))
## Connection between Output Layer neurons
c = 0
for i in range(n_cl):
p.Projection(out_layer_exc[i], out_layer_inh[i],
p.OneToOneConnector(weights=wei_cls_exc,
delays=del_cls_exc))
iter_array = [j for j in range(n_cl) if j != i]
for j in iter_array:
p.Projection(out_layer_inh[i], out_layer_exc[j],
p.FromListConnector(conn_output_inh[c]),
target="inhibitory")
c+=1
## Noisy poisson connection to encoding layer
if randomness == True: # if True: connect noise to network
# if False: don't use noise in network
p.Projection(poisson_input,
enc_layer,
p.FixedProbabilityConnector(p_connect=prob_noise_poi_conn,
weights=wei_noise_poi,
delays = del_noise_poi))
###############################################################################
## Simulation
###############################################################################
p.run(SIM_TIME)
Enc_Spikes = enc_layer.getSpikes()
Filt_Exc_Spikes = filt_layer.getSpikes()
#Filt_Inh_Spikes = filt_layer_inh.getSpikes()
Out_Spikes = [[] for i in range(n_cl)]
for i in range(n_cl):
Out_Spikes[i] = out_layer_exc[i].getSpikes()
p.end()
###############################################################################
## Plot
###############################################################################
## Plot 1
if 0:
pylab.figure()
pylab.xlabel('Time (ms)')
pylab.ylabel('Neuron ID')
pylab.title('Encoding Layer Raster Plot')
pylab.hold(True)
pylab.plot([i[1] for i in Enc_Spikes], [i[0] for i in Enc_Spikes], ".b")
pylab.hold(False)
#pylab.axis([-10,c*SIM_TIME+100,-1,numInp+numOut+numInp+3])
pylab.show()
## Plot 2-1
if 0:
pylab.figure()
pylab.xlabel('Time (ms)')
pylab.ylabel('Neuron ID')
pylab.title('Filtering Layer Raster Plot')
pylab.plot([i[1] for i in Filt_Exc_Spikes], [i[0] for i in Filt_Exc_Spikes], ".b")
#pylab.axis([-10,c*SIM_TIME+100,-1,numInp+numOut+numInp+3])
pylab.show()
## Plot 2-2
pylab.figure()
pylab.xlabel('Time (ms)')
pylab.ylabel('Neuron ID')
pylab.title('Filtering Layer Raster Plot')
pylab.hold(True)
pylab.plot([i[1] for i in Filt_Exc_Spikes], [i[0] for i in Filt_Exc_Spikes], ".b")
time_ind=[i*time_int_trials for i in range(len(outputs))]
for i in range(len(time_ind)):
pylab.plot([time_ind[i],time_ind[i]],[0,2000],"r")
pylab.hold(False)
#pylab.axis([-10,c*SIM_TIME+100,-1,numInp+numOut+numInp+3])
pylab.show()
## Plot 3-1
if 0:
pylab.figure()
pylab.xlabel('Time (ms)')
pylab.ylabel('Neuron ID')
pylab.title('Association Layer Raster Plot\nTest for Trial Numbers {}-{}'.format(t1,t2))
pylab.hold(True)
c=0
for array in Out_Spikes:
pylab.plot([i[1] for i in array], [i[0]+c for i in array], ".b")
c+=0.2
time_cls=[j*time_int_trials+i for j in range(len(outputs)) for i in range(int(time_int_trials))]
cls_lb=[outputs[j]+0.4 for j in range(len(outputs)) for i in range(int(time_int_trials))]
time_ind=[i*time_int_trials for i in range(len(outputs))]
for i in range(len(time_ind)):
pylab.plot([time_ind[i],time_ind[i]],[0,10],"r")
#pylab.plot(time_cls,cls_lb,".")
pylab.hold(False)
pylab.axis([-10,SIM_TIME+100,-1,n_pop+2])
pylab.show()
## Plot 3-2
pylab.figure()
pylab.xlabel('Time (ms)')
pylab.ylabel('Neuron ID')
pylab.title(('Association Layer Raster Plot\n',
'Test for Samples {}-{}').format(t1,t2))
pylab.hold(True)
pylab.plot([i[1] for i in Out_Spikes[0]],
[i[0] for i in Out_Spikes[0]],
".b")
pylab.plot([i[1] for i in Out_Spikes[1]],
[i[0] + 0.2 for i in Out_Spikes[1]],
".r")
time_ind = [i * time_int_trials for i in range(len(outputs))]
for i in range(len(time_ind)):
pylab.plot([time_ind[i], time_ind[i]], [0,n_pop], "k")
#pylab.plot(time_cls,cls_lb,".")
pylab.hold(False)
pylab.axis([-10, SIM_TIME+100, -1, n_pop + 2])
pylab.legend(["AN1","AN2" ])
pylab.show()
sum_output = [[] for i in range(n_cl)]
for i in range(n_trials):
t_st = i * time_int_trials
t_end = t_st + time_int_trials
for j in range(n_cl):
sum_output[j].append(np.sum(
[1 for n, t in Out_Spikes[j] if t >= t_st and t < t_end])
)
## Plot 4
if 0:
# pylab.figure()
# pylab.hold(True)
# pylab.plot(sum_output[0], "b.")
# pylab.plot(sum_output[1], "r.")
# out_cl0 = [i for i in range(len(outputs)) if outputs[i] == 0]
# out_cl1 = [i for i in range(len(outputs)) if outputs[i] == 1]
# pylab.plot(out_cl0,[-2 for i in range(len(out_cl0))], "xb")
# pylab.plot(out_cl1,[-2 for i in range(len(out_cl1))], "xr")
# pylab.hold(False)
# pylab.title("Total spikes at each AN population for each trial")
# pylab.xlabel("Trials")
# pylab.ylabel("Firing Rate")
# pylab.legend(["Cl0","Cl1","Winning Cl 0", "Winning Cl 1"])
# pylab.axis([-2, n_trials + 2, -4, max(max(sum_output)) + 30])
# pylab.show()
pylab.figure()
pylab.hold(True)
pylab.plot(sum_output[0], "b^")
pylab.plot(sum_output[1], "r^")
#pylab.plot(sum_output[0],"b")
#pylab.plot(sum_output[1],"r")
ppp0 = np.array(sum_output[0])
ppp1 = np.array(sum_output[1])
out_cl0 = [i for i in range(len(outputs)) if outputs[i] == 0]
out_cl1 = [i for i in range(len(outputs)) if outputs[i] == 1]
pylab.plot(out_cl0, ppp0[out_cl0], "bs")
pylab.plot(out_cl1, ppp1[out_cl1], "rs")
pylab.hold(False)
pylab.title("Total spikes at each AN population for each trial")
pylab.xlabel("Trials")
pylab.ylabel("Spike Count for Each Trial")
pylab.legend(["Cls 0", "Cls 1", "Actual Winner Cls 0",
"Actual Winner Cls 1"])
pylab.axis([-2, n_trials + 2, -4, max(max(sum_output)) + 30])
pylab.show()
## Check Classification rate
s = np.array(sum_output)
cl = np.floor((np.sign(s[1] - s[0]) + 1) / 2)
r_cl = np.array(outputs)
wrong = np.sum(np.abs(cl - r_cl))
rate = (n_trials - wrong) / n_trials
print("success rate: {}%".format(abs(rate)*100.))
print("cl:\n", cl)
print("r_cl:\n", r_cl)
## Plot 5
if 0:
pylab.figure()
cf = 0.1
pylab.hold(True)
cls_wei0 = np.load("output_files/stdp_weights{}.npy".format(0))
mx = max(cls_wei0)
cls_wei0 = cf * cls_wei0 / mx
cls_wei1 = np.load("output_files/stdp_weights{}.npy".format(1))
mx = max(cls_wei1)
cls_wei1 = cf * cls_wei1/ mx
l = min(len(cls_wei0), len(cls_wei1))
new_array0 = [cls_wei0[i] for i in range(l) if cls_wei0[i] > cls_wei1[i]]
x0 = [i for i in range(l) if cls_wei0[i] > cls_wei1[i]]
new_array1 = [cls_wei1[i] for i in range(l) if cls_wei1[i] > cls_wei0[i]]
x1 = [i for i in range(l) if cls_wei1[i] > cls_wei0[i]]
pylab.plot(x0, new_array0, "gx")
pylab.plot(x1, new_array1, "bx")
#for i in range(2):
# cls_wei=np.load("stdp_weights{}.npy".format(i))
# mx=max(cls_wei)
# cls_wei=0.05*cls_wei/mx
# pylab.plot(cls_wei,"x")
pylab.axis([-10, 2000, -0.1, 0.15])
pylab.hold(False)
pylab.show()
## Plot 7
if 0:
sum_filt = [[0 for i in range(n_feature * n_pop)] for j in range(n_cl)]
sum_filt = np.array(sum_filt)
for i in range(n_trials):
t_st = i * time_int_trials
t_end = t_st + time_int_trials
cl = outputs[i]
for n, t in Filt_Exc_Spikes:
if t >= t_st and t < t_end:
sum_filt[int(cl),int(n)] = sum_filt[(cl),int(n)] + 1
a4=sum_filt[0]
b4=sum_filt[1]
pylab.figure()
pylab.hold(True)
pylab.plot(a4,"b.")
pylab.plot(b4,"r.")
pylab.xlabel('Neuron ID')
pylab.ylabel('Total Firing Rates Through Trials')
pylab.title("Total Spiking Activity of Neurons at Decomposition Layer for Each Class")
pylab.hold(False)
pylab.legend(["Activity to AN1","Activity to AN2"])
pylab.show()
return rate
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 = []
currentMove = 0
for step in range(numberOfSteps):
for action in range(numberOfActions):
connectionList.append((step, currentMove))
currentMove += 1
first_spike_trigger_projection = sim.Projection(firstSpikeTrigger, statePopulation, sim.FromListConnector(connectionList),
synapse_type=sim.StaticSynapse(weight=5, delay=2))
statePopulation.record(["spikes", "v"])
actorPopulation.record(["spikes", "v"])
delay = 17
loopConnections = list()
for i in range(0, nNeurons):
singleConnection = (i, ((i + 1) % nNeurons), weight_to_spike, delay)
loopConnections.append(singleConnection)
injectionConnection = [(0, 0, weight_to_spike, 1)]
spikeArray = {'spike_times': [[0, 1050]]}
populations.append(p.Population(nNeurons, p.IF_curr_exp, cell_params_lif,
label='pop_1'))
populations.append(p.Population(1, p.SpikeSourceArray, spikeArray,
label='inputSpikes_1'))
projections.append(p.Projection(populations[0], populations[0],
p.FromListConnector(loopConnections)))
projections.append(p.Projection(populations[1], populations[0],
p.FromListConnector(injectionConnection)))
populations[0].record_v()
populations[0].record_gsyn()
populations[0].record()
p.run(runtime)
v = None
gsyn = None
spikes = None
v = populations[0].get_v(compatible_output=True)
gsyn = populations[0].get_gsyn(compatible_output=True)
def train(label, untrained_weights=None):
organisedStim = {}
labelSpikes = []
spikeTimes = generate_data(label)
for i in range(output_size):
labelSpikes.append([])
labelSpikes[label] = [(input_size - 1) * v_co + 1,
(input_size - 1) * v_co * 2 + 1,
(input_size - 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))) + 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=0, w_max=0.4),
dendritic_delay_fraction=1.0)
#def projections
stdp_proj = sim.Projection(layer1,
layer2,
sim.FromListConnector(connections),
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"])
print(label)
spikestim = neostim.segments[0].spiketrains
neoinput = layer1.get_data(["spikes"])
spikesinput = neoinput.segments[0].spiketrains
pplt.Figure(pplt.Panel(v,
ylabel="Membrane potential (mV)",
xticks=True,
yticks=True,
xlim=(0, runTime)),
pplt.Panel(spikesinput,
xticks=True,
yticks=True,
markersize=2,
xlim=(0, runTime)),
pplt.Panel(spikestim,
xticks=True,
yticks=True,
markersize=2,
xlim=(0, runTime)),
pplt.Panel(spikes,
xticks=True,
xlabel="Time (ms)",
yticks=True,
markersize=2,
xlim=(0, runTime)),
title="Training" + str(label),
annotations="Training" +
str(label)).save('plot1/' + str(trylabel) + str(label) +
'_training.png')
sim.end()
return weight_list[1]
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)
connectionList = []
for step in range(numberOfSteps - 1):
for action in range(numberOfActions):
connectionList.append((action, action + numberOfActions))
moves_projection = sim.Projection(post_pop,
post_pop,
sim.FromListConnector(connectionList),
synapse_type=sim.StaticSynapse(weight=5,
delay=2))
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=2))
input_projection2 = sim.Projection(input2,
def setupLayerAN(params, settings, neuronModel, cell_params,
popClassActivation, popPoissionNoiseSource, populationsPN,
populationsAN, projectionsPNAN):
#create an Association Neuron AN cluster population per class
#this will be fed by:
#1) PN clusters via plastic synapses
#2) Class activation to innervate the correct AN cluster for a given input
#3) laterally inhibit between AN clusters
numClasses = params['NUM_CLASSES']
anClusterSize = params['CLUSTER_SIZE'] * params['NETWORK_SCALE']
learning = settings['LEARNING']
for an in range(numClasses):
popName = 'popClusterAN_' + str(an)
popClusterAN = spynnaker.Population(anClusterSize,
neuronModel,
cell_params,
label=popName)
populationsAN.append(popClusterAN)
#connect neurons in every PN popn to x% (e.g 50%) neurons in
#this AN cluster
for pn in range(len(populationsPN)):
if learning:
projLabel = 'Proj_PN' + str(pn) + '_AN' + str(an)
projClusterPNToClusterAN = connectClusterPNtoAN(
params, populationsPN[pn], popClusterAN, projLabel)
projectionsPNAN.append(projClusterPNToClusterAN) #keep handle
#to use later for saving off weights at end of learning
else:
#Without plasticity, create PNAN FromList connectors
#using weights saved during learning stage
connections = utils.loadListFromFile(
getWeightsFilename(settings, 'PNAN', pn, an))
#print 'Loaded weightsList[',pn,',',an,']',connections
#print np.shape(connections)
projClusterPNToClusterAN = spynnaker.Projection(
populationsPN[pn],
popClusterAN,
spynnaker.FromListConnector(connections),
target='excitatory')
if learning:
#use the class activity input neurons to create correlated
#activity during learning in the corresponding class cluster
weight = params['WEIGHT_CLASS_ACTIVITY_TO_CLUSTER_AN']
connections = utils.fromList_SpecificNeuronToAll(
an, anClusterSize, weight,
params['MIN_DELAY_CLASS_ACTIVITY_TO_CLUSTER_AN'],
params['MAX_DELAY_CLASS_ACTIVITY_TO_CLUSTER_AN'])
projClassActivityToClusterAN = spynnaker.Projection(
popClassActivation,
popClusterAN,
spynnaker.FromListConnector(connections),
target='excitatory')
#connect each AN cluster to inhibit every other AN cluster
utils.createInterPopulationWTA(populationsAN, params['WEIGHT_WTA_AN_AN'],
params['DELAY_WTA_AN_AN'],
float(params['CONNECTIVITY_WTA_AN_AN']))
