import numpy as np
from nengo.builder import Builder, Operator, Signal
from nengo.neurons import (AdaptiveLIF, AdaptiveLIFRate, Izhikevich, LIF,
LIFRate, NeuronType)
[docs]class SimNeurons(Operator):
"""Set a neuron model output for the given input current.
Implements ``neurons.step_math(dt, J, output, *states)``.
Parameters
----------
neurons : NeuronType
The `.NeuronType`, which defines a ``step_math`` function.
J : Signal
The input current.
output : Signal
The neuron output signal that will be set.
states : list, optional (Default: None)
A list of additional neuron state signals set by ``step_math``.
tag : str, optional (Default: None)
A label associated with the operator, for debugging purposes.
Attributes
----------
J : Signal
The input current.
neurons : NeuronType
The `.NeuronType`, which defines a ``step_math`` function.
output : Signal
The neuron output signal that will be set.
states : list
A list of additional neuron state signals set by ``step_math``.
tag : str or None
A label associated with the operator, for debugging purposes.
Notes
-----
1. sets ``[output] + states``
2. incs ``[]``
3. reads ``[J]``
4. updates ``[]``
"""
def __init__(self, neurons, J, output, states=None, tag=None):
self.neurons = neurons
self.J = J
self.output = output
self.states = [] if states is None else states
self.tag = tag
self.sets = [output] + self.states
self.incs = []
self.reads = [J]
self.updates = []
def _descstr(self):
return '%s, %s, %s' % (self.neurons, self.J, self.output)
def make_step(self, signals, dt, rng):
J = signals[self.J]
output = signals[self.output]
states = [signals[state] for state in self.states]
def step_simneurons():
self.neurons.step_math(dt, J, output, *states)
return step_simneurons
@Builder.register(NeuronType)
[docs]def build_neurons(model, neurontype, neurons):
"""Builds a `.NeuronType` object into a model.
This build function works with any `.NeuronType` that does not require
extra state, like `.RectifiedLinear` and `.LIFRate`. This function adds a
`.SimNeurons` operator connecting the input current to the
neural output signals.
Parameters
----------
model : Model
The model to build into.
neurontype : NeuronType
Neuron type to build.
neuron : Neurons
The neuron population object corresponding to the neuron type.
Notes
-----
Does not modify ``model.params[]`` and can therefore be called
more than once with the same `.NeuronType` instance.
"""
model.add_op(SimNeurons(neurons=neurontype,
J=model.sig[neurons]['in'],
output=model.sig[neurons]['out']))
@Builder.register(LIF)
[docs]def build_lif(model, lif, neurons):
"""Builds a `.LIF` object into a model.
In addition to adding a `.SimNeurons` operator, this build function sets up
signals to track the voltage and refractory times for each neuron.
Parameters
----------
model : Model
The model to build into.
lif : LIF
Neuron type to build.
neuron : Neurons
The neuron population object corresponding to the neuron type.
Notes
-----
Does not modify ``model.params[]`` and can therefore be called
more than once with the same `.LIF` instance.
"""
model.sig[neurons]['voltage'] = Signal(
np.zeros(neurons.size_in), name="%s.voltage" % neurons)
model.sig[neurons]['refractory_time'] = Signal(
np.zeros(neurons.size_in), name="%s.refractory_time" % neurons)
model.add_op(SimNeurons(
neurons=lif,
J=model.sig[neurons]['in'],
output=model.sig[neurons]['out'],
states=[model.sig[neurons]['voltage'],
model.sig[neurons]['refractory_time']]))
@Builder.register(AdaptiveLIFRate)
[docs]def build_alifrate(model, alifrate, neurons):
"""Builds an `.AdaptiveLIFRate` object into a model.
In addition to adding a `.SimNeurons` operator, this build function sets up
signals to track the adaptation term for each neuron.
Parameters
----------
model : Model
The model to build into.
alifrate : AdaptiveLIFRate
Neuron type to build.
neuron : Neurons
The neuron population object corresponding to the neuron type.
Notes
-----
Does not modify ``model.params[]`` and can therefore be called
more than once with the same `.AdaptiveLIFRate` instance.
"""
model.sig[neurons]['adaptation'] = Signal(
np.zeros(neurons.size_in), name="%s.adaptation" % neurons)
model.add_op(SimNeurons(neurons=alifrate,
J=model.sig[neurons]['in'],
output=model.sig[neurons]['out'],
states=[model.sig[neurons]['adaptation']]))
@Builder.register(AdaptiveLIF)
[docs]def build_alif(model, alif, neurons):
"""Builds an `.AdaptiveLIF` object into a model.
In addition to adding a `.SimNeurons` operator, this build function sets up
signals to track the voltage, refractory time, and adaptation term
for each neuron.
Parameters
----------
model : Model
The model to build into.
alif : AdaptiveLIF
Neuron type to build.
neuron : Neurons
The neuron population object corresponding to the neuron type.
Notes
-----
Does not modify ``model.params[]`` and can therefore be called
more than once with the same `.AdaptiveLIF` instance.
"""
model.sig[neurons]['voltage'] = Signal(
np.zeros(neurons.size_in), name="%s.voltage" % neurons)
model.sig[neurons]['refractory_time'] = Signal(
np.zeros(neurons.size_in), name="%s.refractory_time" % neurons)
model.sig[neurons]['adaptation'] = Signal(
np.zeros(neurons.size_in), name="%s.adaptation" % neurons)
model.add_op(SimNeurons(neurons=alif,
J=model.sig[neurons]['in'],
output=model.sig[neurons]['out'],
states=[model.sig[neurons]['voltage'],
model.sig[neurons]['refractory_time'],
model.sig[neurons]['adaptation']]))
@Builder.register(Izhikevich)
[docs]def build_izhikevich(model, izhikevich, neurons):
"""Builds an `.Izhikevich` object into a model.
In addition to adding a `.SimNeurons` operator, this build function sets up
signals to track the voltage and recovery terms for each neuron.
Parameters
----------
model : Model
The model to build into.
izhikevich : Izhikevich
Neuron type to build.
neuron : Neurons
The neuron population object corresponding to the neuron type.
Notes
-----
Does not modify ``model.params[]`` and can therefore be called
more than once with the same `.Izhikevich` instance.
"""
model.sig[neurons]['voltage'] = Signal(
np.ones(neurons.size_in) * izhikevich.reset_voltage,
name="%s.voltage" % neurons)
model.sig[neurons]['recovery'] = Signal(
np.ones(neurons.size_in)
* izhikevich.reset_voltage
* izhikevich.coupling, name="%s.recovery" % neurons)
model.add_op(SimNeurons(neurons=izhikevich,
J=model.sig[neurons]['in'],
output=model.sig[neurons]['out'],
states=[model.sig[neurons]['voltage'],
model.sig[neurons]['recovery']]))