def create_prototypes(vth=255, logicalCoreId=-1, noisy=0, synscale=1):
prototypes = {}
prototypes['vth'] = vth
#setup compartment prototypes
c_prototypes = {}
n_prototypes = {}
s_prototypes = {}
#Q Neuron
c_prototypes['somaProto'] = nx.CompartmentPrototype(
vThMant=vth,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
logicalCoreId=logicalCoreId,
enableNoise=0,
**noise_kwargs)
c_prototypes['spkProto'] = nx.CompartmentPrototype(
vThMant=vth,
biasMant=int(vth / 2),
biasExp=6,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
thresholdBehavior=2,
logicalCoreId=logicalCoreId,
enableNoise=noisy,
**noise_kwargs)
c_prototypes['ememProto'] = nx.CompartmentPrototype(
vThMant=vth,
#vMaxExp=15,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
thresholdBehavior=3,
logicalCoreId=logicalCoreId,
enableNoise=0,
**noise_kwargs)
c_prototypes['somaProto'].addDendrite([c_prototypes['spkProto']],
nx.COMPARTMENT_JOIN_OPERATION.OR)
c_prototypes['spkProto'].addDendrite([c_prototypes['ememProto']],
nx.COMPARTMENT_JOIN_OPERATION.ADD)
n_prototypes['qProto'] = nx.NeuronPrototype(c_prototypes['somaProto'])
#Soft Reset Neuron
c_prototypes['srSomaProto'] = nx.CompartmentPrototype(
vThMant=vth,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
logicalCoreId=logicalCoreId,
enableNoise=0,
**noise_kwargs)
c_prototypes['srSpkProto'] = nx.CompartmentPrototype(
vThMant=vth,
biasMant=0,
biasExp=6,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
thresholdBehavior=2,
logicalCoreId=logicalCoreId,
enableNoise=noisy,
**noise_kwargs)
c_prototypes['intProto'] = nx.CompartmentPrototype(
vThMant=vth,
#vMaxExp=15,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=4095,
thresholdBehavior=0,
logicalCoreId=logicalCoreId,
enableNoise=0,
**noise_kwargs)
c_prototypes['srSomaProto'].addDendrite([c_prototypes['srSpkProto']],
nx.COMPARTMENT_JOIN_OPERATION.OR)
c_prototypes['srSpkProto'].addDendrite([c_prototypes['intProto']],
nx.COMPARTMENT_JOIN_OPERATION.ADD)
n_prototypes['srProto'] = nx.NeuronPrototype(c_prototypes['srSomaProto'])
#FF Neuron
c_prototypes['ffSomaProto'] = nx.CompartmentPrototype(
vThMant=1,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
logicalCoreId=logicalCoreId,
enableNoise=0,
**noise_kwargs)
c_prototypes['ffSomaProto'].addDendrite([c_prototypes['ememProto']],
nx.COMPARTMENT_JOIN_OPERATION.ADD)
n_prototypes['ffProto'] = nx.NeuronPrototype(c_prototypes['ffSomaProto'])
#Inverter compartment
c_prototypes['invProto'] = nx.CompartmentPrototype(
vThMant=1,
biasMant=2,
biasExp=6,
compartmentVoltageDecay=0,
functionalState=2,
logicalCoreId=logicalCoreId,
enableNoise=0,
**noise_kwargs)
#buffer / OR
c_prototypes['bufferProto'] = nx.CompartmentPrototype(
vThMant=1,
compartmentVoltageDecay=4095,
compartmentCurrentDecay=4095,
logicalCoreId=logicalCoreId,
enableNoise=0,
**noise_kwargs)
#AND
c_prototypes['andProto'] = nx.CompartmentPrototype(
vThMant=vth,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=4095,
logicalCoreId=logicalCoreId,
enableNoise=0,
**noise_kwargs)
#Counter
v_th_max = 2**17 - 1
c_prototypes['counterProto'] = nx.CompartmentPrototype(
vThMant=v_th_max,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
logicalCoreId=logicalCoreId,
enableNoise=0,
**noise_kwargs)
#Connections
#scaled vth used when synscale is being used to increase dynamic range
vth = vth / synscale
s_prototypes['econn'] = nx.ConnectionPrototype(weight=2)
s_prototypes['iconn'] = nx.ConnectionPrototype(weight=-2)
s_prototypes['invconn'] = nx.ConnectionPrototype(weight=-1)
s_prototypes['vthconn'] = nx.ConnectionPrototype(weight=-vth)
s_prototypes['spkconn'] = nx.ConnectionPrototype(weight=vth)
s_prototypes['halfconn'] = nx.ConnectionPrototype(weight=int(vth / 2) + 1)
s_prototypes['thirdconn'] = nx.ConnectionPrototype(weight=int(vth / 3) + 1)
s_prototypes['single'] = nx.ConnectionPrototype(weight=2)
prototypes['c_prototypes'] = c_prototypes
prototypes['n_prototypes'] = n_prototypes
prototypes['s_prototypes'] = s_prototypes
return prototypes
def _create_prototypes(self):
#setup compartment prototypes
c_prototypes = {}
n_prototypes = {}
s_prototypes = {}
#Q Neuron
c_prototypes['somaProto'] = nx.CompartmentPrototype(
vThMant=self.vth,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0)
c_prototypes['spkProto'] = nx.CompartmentPrototype(
vThMant=self.vth,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
thresholdBehavior=2)
c_prototypes['ememProto'] = nx.CompartmentPrototype(
vThMant=self.vth,
#vMaxExp=15,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
thresholdBehavior=3)
c_prototypes['somaProto'].addDendrite([c_prototypes['spkProto']],
nx.COMPARTMENT_JOIN_OPERATION.OR)
c_prototypes['spkProto'].addDendrite([c_prototypes['ememProto']],
nx.COMPARTMENT_JOIN_OPERATION.ADD)
n_prototypes['qProto'] = nx.NeuronPrototype(c_prototypes['somaProto'])
#S Inverter
c_prototypes['invProto'] = nx.CompartmentPrototype(
vThMant=self.vth - 1,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
thresholdBehavior=0,
functionalState=2)
c_prototypes['spkProto'] = nx.CompartmentPrototype(
vThMant=self.vth - 1,
biasMant=self.vth,
biasExp=6,
thresholdBehavior=0,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
functionalState=2)
c_prototypes['receiverProto'] = nx.CompartmentPrototype(
vThMant=self.vth - 1,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
thresholdBehavior=0)
c_prototypes['invProto'].addDendrite(
[c_prototypes['receiverProto']],
nx.COMPARTMENT_JOIN_OPERATION.BLOCK)
n_prototypes['invNeuron'] = nx.NeuronPrototype(
c_prototypes['invProto'])
#AND
c_prototypes['andProto'] = nx.CompartmentPrototype(
vThMant=self.vth,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=4095)
#Counter (debug)
v_th_max = 2**17 - 1
c_prototypes['counterProto'] = nx.CompartmentPrototype(
vThMant=v_th_max,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0)
#Connections
s_prototypes['econn'] = nx.ConnectionPrototype(weight=2)
s_prototypes['iconn'] = nx.ConnectionPrototype(weight=-2)
s_prototypes['vthconn'] = nx.ConnectionPrototype(weight=-self.vth)
s_prototypes['spkconn'] = nx.ConnectionPrototype(weight=self.vth)
s_prototypes['halfconn'] = nx.ConnectionPrototype(
weight=int(self.vth / 2) + 1)
s_prototypes['single'] = nx.ConnectionPrototype(weight=2)
self.c_prototypes = c_prototypes
self.n_prototypes = n_prototypes
self.s_prototypes = s_prototypes
def __init__(self, params, net=None, name=None):
"""
The STDE_group contains the sTDE neurons.
One neuron consists of 4 compartments that are connected as follows:
D (main/soma)
|
C (current)
/ \\
(trigger) A B (facilitator)
A is the gate and lets B's current pass whenever it spikes.
C receives B's current on its voltage variable and decays
D receives C's voltage and integrates it, so C is basically a second current input to D
The two inputs are called trigger and facilitator following Milde (2018)
params are
'tau_fac': current tau of facilitator input
'tau_trigg': current tau of trigger input
'tau_v': voltage tau of TDE Neuron
'tau_c': current tau of TDE Neuron
'weight_fac': amplitude of the facilitator spike
'do_probes' : can be 'all', 'spikes' or None
'num_neurons' : number of sTDE neurons that are created
"""
if net is None:
net = nx.NxNet()
self.net = net
self.num_neurons = params['num_neurons']
self.neurongroups = {}
self.probes = {}
self.spikegens = {}
weight_fac, exponent_fac = calculate_mant_exp(
params['weight_fac'] / params['tau_fac'], 7)
# Create auxiliary compartments
cpA = nx.CompartmentPrototype(
vThMant=1,
compartmentCurrentDecay=int(1 / 1 * 2**12),
compartmentVoltageDecay=4095,
# thresholdBehavior=nx.COMPARTMENT_THRESHOLD_MODE.NO_SPIKE_AND_PASS_V_LG_VTH_TO_PARENT
)
cpB = nx.CompartmentPrototype(vThMant=100,
compartmentCurrentDecay=int(
1 / params['tau_fac'] * 2**12),
compartmentVoltageDecay=4095)
cpC = nx.CompartmentPrototype(
vThMant=1000,
compartmentCurrentDecay=int(1 / 1 * 2**12),
compartmentVoltageDecay=int(1 / params['tau_trigg'] * 2**12),
thresholdBehavior=nx.COMPARTMENT_THRESHOLD_MODE.
NO_SPIKE_AND_PASS_V_LG_VTH_TO_PARENT)
# Create main compartment
cpD = nx.CompartmentPrototype(
vThMant=100,
compartmentCurrentDecay=int(1 / params['tau_v'] * 2**12),
compartmentVoltageDecay=int(1 / params['tau_c'] * 2**12),
)
# build compartment tree
cpC.addDendrites(prototypeA=cpA,
prototypeB=cpB,
joinOp=nx.COMPARTMENT_JOIN_OPERATION.PASS)
cpD.addDendrite(prototype=[cpC],
joinOp=nx.COMPARTMENT_JOIN_OPERATION.ADD)
num_neurons = params['num_neurons']
neuronPrototype = nx.NeuronPrototype(cpD)
neurongroup = net.createNeuronGroup(prototype=neuronPrototype,
size=num_neurons)
sgpA = net.createSpikeGenProcess(numPorts=num_neurons)
sgpB = net.createSpikeGenProcess(numPorts=num_neurons)
# sgpC = net.createSpikeGenProcess(numPorts=1)
connProto = nx.ConnectionPrototype(weight=weight_fac,
weightExponent=exponent_fac)
sgpA.connect(neurongroup.dendrites[0].dendrites[1],
prototype=connProto,
connectionMask=sp.sparse.identity(num_neurons))
sgpB.connect(neurongroup.dendrites[0].dendrites[0],
prototype=connProto,
connectionMask=sp.sparse.identity(num_neurons))
spikegens = [sgpA, sgpB]
if params['do_probes'] == 'all':
(uA, vA, sA) = neurongroup.dendrites[0].dendrites[1].probe([
nx.ProbeParameter.COMPARTMENT_CURRENT,
nx.ProbeParameter.COMPARTMENT_VOLTAGE, nx.ProbeParameter.SPIKE
])
(uB, vB, sB) = neurongroup.dendrites[0].dendrites[0].probe([
nx.ProbeParameter.COMPARTMENT_CURRENT,
nx.ProbeParameter.COMPARTMENT_VOLTAGE, nx.ProbeParameter.SPIKE
])
(uC, vC, sC) = neurongroup.dendrites[0].probe([
nx.ProbeParameter.COMPARTMENT_CURRENT,
nx.ProbeParameter.COMPARTMENT_VOLTAGE, nx.ProbeParameter.SPIKE
])
(uD, vD, sD) = neurongroup.soma.probe([
nx.ProbeParameter.COMPARTMENT_CURRENT,
nx.ProbeParameter.COMPARTMENT_VOLTAGE, nx.ProbeParameter.SPIKE
])
probes = {
'A_current': uA,
'A_voltage': vA,
'A_spikes': sA,
'B_current': uB,
'B_voltage': vB,
'B_spikes': sB,
'C_current': uC,
'C_voltage': vC,
'C_spikes': sC,
'D_current': uD,
'D_voltage': vD,
'D_spikes': sD,
}
elif params['do_probes'] == 'spikes':
sA = neurongroup.dendrites[0].dendrites[1].probe(
[nx.ProbeParameter.SPIKE])
sB = neurongroup.dendrites[0].dendrites[0].probe(
[nx.ProbeParameter.SPIKE])
sC = neurongroup.dendrites[0].probe([nx.ProbeParameter.SPIKE])
sD = neurongroup.soma.probe([nx.ProbeParameter.SPIKE])
probes = {
'A_spikes': sA,
'B_spikes': sB,
'C_spikes': sC,
'D_spikes': sD,
}
else:
probes = None
self.neurongroup = neurongroup
self.probes = probes
self.spikegens = spikegens
self.input0 = neurongroup.dendrites[0].dendrites[0]
self.input1 = neurongroup.dendrites[0].dendrites[1]
def create_prototypes(self, vth=255, logicalCoreId=-1):
prototypes = {}
prototypes['vth'] = vth
#setup compartment prototypes
c_prototypes = {}
n_prototypes = {}
s_prototypes = {}
#Q Neuron
c_prototypes['somaProto'] = nx.CompartmentPrototype(
vThMant=vth,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
logicalCoreId=logicalCoreId)
c_prototypes['spkProto'] = nx.CompartmentPrototype(
vThMant=vth,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
thresholdBehavior=2,
logicalCoreId=logicalCoreId)
c_prototypes['ememProto'] = nx.CompartmentPrototype(
vThMant=vth,
#vMaxExp=15,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
thresholdBehavior=3,
logicalCoreId=logicalCoreId)
c_prototypes['somaProto'].addDendrite([c_prototypes['spkProto']],
nx.COMPARTMENT_JOIN_OPERATION.OR)
c_prototypes['spkProto'].addDendrite([c_prototypes['ememProto']],
nx.COMPARTMENT_JOIN_OPERATION.ADD)
n_prototypes['qProto'] = nx.NeuronPrototype(c_prototypes['somaProto'])
#S Inverter
c_prototypes['invProto'] = nx.CompartmentPrototype(
vThMant=vth - 1,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
thresholdBehavior=0,
functionalState=2,
logicalCoreId=logicalCoreId)
c_prototypes['spkProto'] = nx.CompartmentPrototype(
vThMant=vth - 1,
biasMant=vth,
biasExp=6,
thresholdBehavior=0,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
functionalState=2,
logicalCoreId=logicalCoreId)
c_prototypes['receiverProto'] = nx.CompartmentPrototype(
vThMant=vth - 1,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
thresholdBehavior=0,
logicalCoreId=logicalCoreId)
c_prototypes['invProto'].addDendrite([c_prototypes['receiverProto']],
nx.COMPARTMENT_JOIN_OPERATION.BLOCK)
n_prototypes['invNeuron'] = nx.NeuronPrototype(c_prototypes['invProto'])
c_prototypes['bufferProto'] = nx.CompartmentPrototype(
vThMant=1,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=4095,
logicalCoreId=logicalCoreId)
#AND
c_prototypes['andProto'] = nx.CompartmentPrototype(
vThMant=vth,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=4095,
logicalCoreId=logicalCoreId)
#Counter (debug)
v_th_max = 2**17 - 1
c_prototypes['counterProto'] = nx.CompartmentPrototype(
vThMant=v_th_max,
compartmentCurrentDecay=4095,
compartmentVoltageDecay=0,
logicalCoreId=logicalCoreId)
#Connections
s_prototypes['econn'] = nx.ConnectionPrototype(weight=2)
s_prototypes['iconn'] = nx.ConnectionPrototype(weight=-2)
s_prototypes['vthconn'] = nx.ConnectionPrototype(weight=-vth)
s_prototypes['spkconn'] = nx.ConnectionPrototype(weight=vth)
s_prototypes['halfconn'] = nx.ConnectionPrototype(weight=int(vth / 2) + 1)
s_prototypes['thirdconn'] = nx.ConnectionPrototype(weight=int(vth / 3) + 1)
s_prototypes['single'] = nx.ConnectionPrototype(weight=2)
prototypes['c_prototypes'] = c_prototypes
prototypes['n_prototypes'] = n_prototypes
prototypes['s_prototypes'] = s_prototypes
return prototypes