LifNeuronBase Class Reference

A leaky-integrate-and-fire (I&F) neuron. More...

#include <LifNeuron.h>

Inheritance diagram for LifNeuronBase:

Collaboration diagram for LifNeuronBase:

List of all members.

Public Member Functions

LifNeuronBase (float Rm=1e6, float Cm=3e-8, float Vresting=-0.06, float Vthresh=-0.045, float Vreset=-0.06, float Vinit=-0.06, float Trefract=3e-3, float Inoise=0.0, float Iinject=0.0)

virtual ~LifNeuronBase ()

virtual int reset (double dt)

Reset the leaky I&F neuron.

bool refractoryQ ()

Returns true iff the neuron is in its absolute refactory period.

virtual void clearSynapticInput (void)=0

virtual double getVm ()

Get the current membrane voltage.

virtual double getManagedDelay () const

virtual int nSpikeInputPorts () const

virtual int nSpikeOutputPorts () const

virtual int nAnalogInputPorts () const

virtual int nAnalogOutputPorts () const

virtual PortType outputPortType (port_t o) const

virtual PortType inputPortType (port_t i) const

virtual double currentNoiseInput ()

Public Attributes

float Rm

The membrane resistance $R_m$ [units=Ohm; range=(0,1e30)].

float Cm

The membrane capacity $C_m$ [range=(0,1); units=F;].

float Vresting

The resting membrane voltage. [units=V; range=(-1,1);].

float Vthresh

If $V_m$ exceeds $V_{thresh}$ a spike is emmited. [units=V; range=(-10,100);].

float Vreset

The voltage to reset $V_m$ to after a spike. [units=V; range=(-1,1);].

float Vinit

The initial condition for $V_m$ at time $t=0$ . [units=V; range=(-1,1);].

float Trefract

The length of the absolute refractory period. [units=sec; range=(0,1);].

float Inoise

The standard deviation of the noise to be added each integration time constant. [range=(0,1); units=A;].

float Iinject

A constant current to be injected into the LIF neuron. [units=A; range=(-1,1);].

Protected Attributes

double Vm

The membrane voltage $V_m$ [readonly; units=V;].

int nStepsInRefr

If positive then this counter tells us how many time steps we are still in the absolute refractory period.

double C1

Internal constants for the exponential Euler integration of Vm.

double C2

double I0

double _dt

The time step.

Static Protected Attributes

static
ThreadSpecificRandomDistribution
< NormalDistribution > noise_gen

Random number generator for the noise.

Detailed Description

A leaky-integrate-and-fire (I&F) neuron.

Model

A standard leaky-integrate-and-fire neuron model is implemented where the membrane potential $V_m$ of a neuron is given by

$\tau_m \frac{d V_m}{dt} = -(V_m-V_{resting}) + R_m \cdot (I_{syn}(t)+I_{inject}+I_{noise})$

where $\tau_m=C_m\cdot R_m$ is the membrane time constant, $R_m$ is the membrane resistance, $I_{syn}(t)$ is the current supplied by the synapses, $I_{inject}$ is a non-specific background current and $I_{noise}$ is a Gaussion random variable with zero mean and a given variance noise.

At time $t=0$ $V_m$ ist set to $V_{init}$ . If $V_m$ exceeds the threshold voltage $V_{thresh}$ it is reset to $V_{reset}$ and hold there for the length $T_{refract}$ of the absolute refractory period.

Implementation

The exponential Euler method is used for numerical integration.

Definition at line 43 of file LifNeuron.h.

Constructor & Destructor Documentation

LifNeuronBase::LifNeuronBase	(	float	Rm = `1e6`,
		float	Cm = `3e-8`,
		float	Vresting = `-0.06`,
		float	Vthresh = `-0.045`,
		float	Vreset = `-0.06`,
		float	Vinit = `-0.06`,
		float	Trefract = `3e-3`,
		float	Inoise = `0.0`,
		float	Iinject = `0.0`
	)

Definition at line 16 of file LifNeuron.cpp.

virtual LifNeuronBase::~LifNeuronBase ( ) [inline, virtual]

Definition at line 56 of file LifNeuron.h.

Member Function Documentation

int LifNeuronBase::reset ( double dt ) [virtual]

Reset the leaky I&F neuron.

Reimplemented from SimObject.

Reimplemented in LIFCurrAlphaNeuron, LIFCurrExpNeuron, LIFCondAlphaNeuron, LIFCondExpNeuron, CompositeNeuron< CbLifNeuron >, and CompositeNeuron< LifNeuron >.

Definition at line 24 of file LifNeuron.cpp.

References SimObject::adjust(), clearSynapticInput(), nStepsInRefr, SingleOutputSpikeSender::reset(), Vinit, and Vm.

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bool LifNeuronBase::refractoryQ ( ) [inline]

Returns true iff the neuron is in its absolute refactory period.

Definition at line 65 of file LifNeuron.h.

References nStepsInRefr.

virtual void LifNeuronBase::clearSynapticInput ( void ) [pure virtual]

Implemented in LifNeuron, and CbLifNeuron.

Referenced by reset().

virtual double LifNeuronBase::getVm ( ) [inline, virtual]

Get the current membrane voltage.

Reimplemented in CbLifNeuron.

Definition at line 98 of file LifNeuron.h.

References Vm.

virtual double LifNeuronBase::getManagedDelay ( ) const [inline, virtual]

Reimplemented from SimObject.

Definition at line 103 of file LifNeuron.h.

virtual int LifNeuronBase::nSpikeInputPorts ( ) const [inline, virtual]

Reimplemented from SimObject.

Reimplemented in CompositeNeuron< CbLifNeuron >, and CompositeNeuron< LifNeuron >.

Definition at line 104 of file LifNeuron.h.

virtual int LifNeuronBase::nSpikeOutputPorts ( ) const [inline, virtual]

Reimplemented from SimObject.

Reimplemented in CompositeNeuron< CbLifNeuron >, and CompositeNeuron< LifNeuron >.

Definition at line 105 of file LifNeuron.h.

virtual int LifNeuronBase::nAnalogInputPorts ( ) const [inline, virtual]

Reimplemented from SimObject.

Reimplemented in DARecvLifNeuron, DARecvCbLifNeuron, CompositeNeuron< CbLifNeuron >, and CompositeNeuron< LifNeuron >.

Definition at line 106 of file LifNeuron.h.

virtual int LifNeuronBase::nAnalogOutputPorts ( ) const [inline, virtual]

Reimplemented from SimObject.

Reimplemented in CompositeNeuron< CbLifNeuron >, and CompositeNeuron< LifNeuron >.

Definition at line 107 of file LifNeuron.h.

virtual PortType LifNeuronBase::outputPortType ( port_t o ) const [inline, virtual]

Reimplemented from SimObject.

Reimplemented in CompositeNeuron< CbLifNeuron >, and CompositeNeuron< LifNeuron >.

Definition at line 108 of file LifNeuron.h.

References SimObject::spiking, and SimObject::undefined.

virtual PortType LifNeuronBase::inputPortType ( port_t i ) const [inline, virtual]

Reimplemented from SimObject.

Reimplemented in DARecvLifNeuron, and DARecvCbLifNeuron.

Definition at line 112 of file LifNeuron.h.

References SimObject::undefined.

virtual double LifNeuronBase::currentNoiseInput ( ) [inline, virtual]

Definition at line 118 of file LifNeuron.h.

Referenced by CbLifNeuron::advance(), and LifNeuron::advance().

Member Data Documentation

float LifNeuronBase::Rm

The membrane resistance $R_m$ [units=Ohm; range=(0,1e30)].

Definition at line 70 of file LifNeuron.h.

Referenced by CbLifNeuron::adjust(), LifNeuron::adjust(), CbLifNeuron::advance(), LIFCondAlphaNeuron::LIFCondAlphaNeuron(), LIFCondExpNeuron::LIFCondExpNeuron(), LIFCurrAlphaNeuron::LIFCurrAlphaNeuron(), LIFCurrExpNeuron::LIFCurrExpNeuron(), LIFCondExpNeuron::reset(), LIFCondAlphaNeuron::reset(), LIFCurrExpNeuron::reset(), and LIFCurrAlphaNeuron::reset().

float LifNeuronBase::Cm

The membrane capacity $C_m$ [range=(0,1); units=F;].

Definition at line 73 of file LifNeuron.h.

Referenced by CbLifNeuron::adjust(), LifNeuron::adjust(), CbLifNeuron::advance(), LIFCondAlphaNeuron::LIFCondAlphaNeuron(), LIFCondExpNeuron::LIFCondExpNeuron(), LIFCurrAlphaNeuron::LIFCurrAlphaNeuron(), LIFCurrExpNeuron::LIFCurrExpNeuron(), LIFCondExpNeuron::reset(), LIFCondAlphaNeuron::reset(), LIFCurrExpNeuron::reset(), and LIFCurrAlphaNeuron::reset().

float LifNeuronBase::Vresting

The resting membrane voltage. [units=V; range=(-1,1);].

Definition at line 76 of file LifNeuron.h.

Referenced by CbLifNeuron::adjust(), LifNeuron::adjust(), LIFCondAlphaNeuron::LIFCondAlphaNeuron(), LIFCondExpNeuron::LIFCondExpNeuron(), LIFCurrAlphaNeuron::LIFCurrAlphaNeuron(), and LIFCurrExpNeuron::LIFCurrExpNeuron().

float LifNeuronBase::Vthresh

If $V_m$ exceeds $V_{thresh}$ a spike is emmited. [units=V; range=(-10,100);].

Definition at line 79 of file LifNeuron.h.

Referenced by CbLifNeuron::advance(), LifNeuron::advance(), LIFCondAlphaNeuron::LIFCondAlphaNeuron(), LIFCondExpNeuron::LIFCondExpNeuron(), LIFCurrAlphaNeuron::LIFCurrAlphaNeuron(), and LIFCurrExpNeuron::LIFCurrExpNeuron().

float LifNeuronBase::Vreset

The voltage to reset $V_m$ to after a spike. [units=V; range=(-1,1);].

Definition at line 82 of file LifNeuron.h.

Referenced by CbLifNeuron::advance(), LifNeuron::advance(), LIFCondAlphaNeuron::LIFCondAlphaNeuron(), LIFCondExpNeuron::LIFCondExpNeuron(), LIFCurrAlphaNeuron::LIFCurrAlphaNeuron(), and LIFCurrExpNeuron::LIFCurrExpNeuron().

float LifNeuronBase::Vinit

The initial condition for $V_m$ at time $t=0$ . [units=V; range=(-1,1);].

Definition at line 85 of file LifNeuron.h.

Referenced by LIFCondAlphaNeuron::LIFCondAlphaNeuron(), LIFCondExpNeuron::LIFCondExpNeuron(), LIFCurrAlphaNeuron::LIFCurrAlphaNeuron(), LIFCurrExpNeuron::LIFCurrExpNeuron(), and reset().

float LifNeuronBase::Trefract

The length of the absolute refractory period. [units=sec; range=(0,1);].

Definition at line 88 of file LifNeuron.h.

Referenced by CbLifNeuron::advance(), LifNeuron::advance(), LIFCondAlphaNeuron::LIFCondAlphaNeuron(), LIFCondExpNeuron::LIFCondExpNeuron(), LIFCurrAlphaNeuron::LIFCurrAlphaNeuron(), and LIFCurrExpNeuron::LIFCurrExpNeuron().

float LifNeuronBase::Inoise

The standard deviation of the noise to be added each integration time constant. [range=(0,1); units=A;].

Definition at line 91 of file LifNeuron.h.

Referenced by CbLifNeuron::advance(), LifNeuron::advance(), LIFCondAlphaNeuron::LIFCondAlphaNeuron(), LIFCondExpNeuron::LIFCondExpNeuron(), LIFCurrAlphaNeuron::LIFCurrAlphaNeuron(), and LIFCurrExpNeuron::LIFCurrExpNeuron().

float LifNeuronBase::Iinject

A constant current to be injected into the LIF neuron. [units=A; range=(-1,1);].

Definition at line 94 of file LifNeuron.h.

Referenced by CbLifNeuron::adjust(), LifNeuron::adjust(), LIFCondAlphaNeuron::LIFCondAlphaNeuron(), LIFCondExpNeuron::LIFCondExpNeuron(), LIFCurrAlphaNeuron::LIFCurrAlphaNeuron(), and LIFCurrExpNeuron::LIFCurrExpNeuron().

double LifNeuronBase::Vm [protected]

The membrane voltage $V_m$ [readonly; units=V;].

Definition at line 125 of file LifNeuron.h.

Referenced by CbLifNeuron::advance(), LifNeuron::advance(), CbLifNeuron::getVm(), getVm(), and reset().

int LifNeuronBase::nStepsInRefr [protected]

If positive then this counter tells us how many time steps we are still in the absolute refractory period.

Definition at line 128 of file LifNeuron.h.

Referenced by CbLifNeuron::advance(), LifNeuron::advance(), refractoryQ(), and reset().

double LifNeuronBase::C1 [protected]

Internal constants for the exponential Euler integration of Vm.

Definition at line 131 of file LifNeuron.h.

Referenced by CbLifNeuron::adjust(), LifNeuron::adjust(), CbLifNeuron::advance(), and LifNeuron::advance().

double LifNeuronBase::C2 [protected]

Definition at line 131 of file LifNeuron.h.

Referenced by CbLifNeuron::adjust(), LifNeuron::adjust(), and LifNeuron::advance().

double LifNeuronBase::I0 [protected]

Definition at line 131 of file LifNeuron.h.

Referenced by CbLifNeuron::adjust(), LifNeuron::adjust(), CbLifNeuron::advance(), and LifNeuron::advance().

double LifNeuronBase::_dt [protected]

The time step.

Definition at line 134 of file LifNeuron.h.

Referenced by CbLifNeuron::adjust(), LifNeuron::adjust(), and CbLifNeuron::advance().

ThreadSpecificRandomDistribution< NormalDistribution > LifNeuronBase::noise_gen [static, protected]

Random number generator for the noise.

Definition at line 137 of file LifNeuron.h.

Referenced by CbLifNeuron::adjust(), LifNeuron::adjust(), CbLifNeuron::advance(), and LifNeuron::advance().

The documentation for this class was generated from the following files:

/home/tnatschl/PCSIM-Sandbox/pcsim/pcsim/simobjects/LifNeuron.h
/home/tnatschl/PCSIM-Sandbox/pcsim/pcsim/simobjects/LifNeuron.cpp


Public Member Functions
	LifNeuronBase (float Rm=1e6, float Cm=3e-8, float Vresting=-0.06, float Vthresh=-0.045, float Vreset=-0.06, float Vinit=-0.06, float Trefract=3e-3, float Inoise=0.0, float Iinject=0.0)
virtual	~LifNeuronBase ()
virtual int	reset (double dt)
	Reset the leaky I&F neuron.
bool	refractoryQ ()
	Returns true iff the neuron is in its absolute refactory period.
virtual void	clearSynapticInput (void)=0
virtual double	getVm ()
	Get the current membrane voltage.
virtual double	getManagedDelay () const
virtual int	nSpikeInputPorts () const
virtual int	nSpikeOutputPorts () const
virtual int	nAnalogInputPorts () const
virtual int	nAnalogOutputPorts () const
virtual PortType	outputPortType (port_t o) const
virtual PortType	inputPortType (port_t i) const
virtual double	currentNoiseInput ()
Public Attributes
float	Rm
	The membrane resistance [units=Ohm; range=(0,1e30)].
float	Cm
	The membrane capacity [range=(0,1); units=F;].
float	Vresting
	The resting membrane voltage. [units=V; range=(-1,1);].
float	Vthresh
	If exceeds $V_{thresh}$ a spike is emmited. [units=V; range=(-10,100);].
float	Vreset
	The voltage to reset to after a spike. [units=V; range=(-1,1);].
float	Vinit
	The initial condition for at time . [units=V; range=(-1,1);].
float	Trefract
	The length of the absolute refractory period. [units=sec; range=(0,1);].
float	Inoise
	The standard deviation of the noise to be added each integration time constant. [range=(0,1); units=A;].
float	Iinject
	A constant current to be injected into the LIF neuron. [units=A; range=(-1,1);].
Protected Attributes
double	Vm
	The membrane voltage [readonly; units=V;].
int	nStepsInRefr
	If positive then this counter tells us how many time steps we are still in the absolute refractory period.
double	C1
	Internal constants for the exponential Euler integration of Vm.
double	C2
double	I0
double	_dt
	The time step.
Static Protected Attributes
static ThreadSpecificRandomDistribution < NormalDistribution >	noise_gen
	Random number generator for the noise.