ODESystemBasedSpikingNeuron Class Reference

#include <ODESystemBasedSpikingNeuron.h>

Inheritance diagram for ODESystemBasedSpikingNeuron:

Collaboration diagram for ODESystemBasedSpikingNeuron:

List of all members.

Public Member Functions

ODESystemBasedSpikingNeuron (size_t dim)

virtual ~ODESystemBasedSpikingNeuron ()

virtual int init (InitializeInfo *ii)

Called during network initialization (prior to reset).

virtual int adjust (double dt)

Adjust to time grid of dt.

int reset (double dt, double *y0)

Reset the neuron.

virtual int advance (AdvanceInfo const &)

Advance the neuron (integration an spike checking ).

virtual void copySolverStateToFields ()

derived classes can copy the values from the solver to SimObject Fields be overwritting this method

virtual double getVm ()

Get the current membrane voltage.

Definition of input and output ports

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 getAnalogOutput (analog_port_id_t port=0) const

Return the analog value currently associated with the given port.

Manage synaptic input

virtual void clearSynapticInput (void)

virtual void currentInput (double i)

virtual void conductanceInput (double g, double Erev)

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 detected. [units=V; range=(-10,100);].

float Vinit

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

double Em

Leak reversal potential.

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.

odeiv::Solver * solver

A solver for the differential equations.

int nStepsInRefr

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

double Isyn

Summation point for all synaptic input currents.

double Gsyn

Summation point for all synaptic input conductances.

double G0

double I0

Static Protected Attributes

static
ThreadSpecificRandomDistribution
< NormalDistribution > noise

Random number generator for the noise.

Detailed Description

Author:: Thomas Natschläger

Definition at line 24 of file ODESystemBasedSpikingNeuron.h.

Constructor & Destructor Documentation

ODESystemBasedSpikingNeuron::ODESystemBasedSpikingNeuron ( size_t dim )

Definition at line 20 of file ODESystemBasedSpikingNeuron.cpp.

References solver.

ODESystemBasedSpikingNeuron::~ODESystemBasedSpikingNeuron ( ) [virtual]

Definition at line 33 of file ODESystemBasedSpikingNeuron.cpp.

References solver.

Member Function Documentation

int ODESystemBasedSpikingNeuron::init ( InitializeInfo * ii ) [virtual]

Called during network initialization (prior to reset).

Reimplemented from SimObject.

Definition at line 24 of file ODESystemBasedSpikingNeuron.cpp.

References odeiv::ODESystem::setSystem(), and solver.

Referenced by reset().

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int ODESystemBasedSpikingNeuron::adjust ( double dt ) [virtual]

Adjust to time grid of dt.

Reimplemented from SimObject.

Definition at line 51 of file ODESystemBasedSpikingNeuron.cpp.

References noise, and ThreadSpecificRandomDistribution< Dist >::set().

Referenced by reset().

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int ODESystemBasedSpikingNeuron::reset	(	double	dt,
		double *	y0
	)

Reset the neuron.

Definition at line 38 of file ODESystemBasedSpikingNeuron.cpp.

References adjust(), clearSynapticInput(), init(), nStepsInRefr, odeiv::Solver::reset(), SingleOutputSpikeSender::reset(), solver, and Vm.

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int ODESystemBasedSpikingNeuron::advance ( AdvanceInfo const & ai ) [virtual]

Advance the neuron (integration an spike checking ).

Reimplemented from SimObject.

Definition at line 56 of file ODESystemBasedSpikingNeuron.cpp.

References odeiv::Solver::advance(), ADVANCEFLAG_HASSPIKED, clearSynapticInput(), copySolverStateToFields(), AdvanceInfo::dt, Em, G0, Gsyn, I0, Iinject, Time::in_sec(), Inoise, Isyn, noise, nStepsInRefr, SingleOutputSpikeSender::out_port, Rm, SpikeOutputPort::setSpike(), solver, AdvanceInfo::t, Trefract, Vm, Vthresh, and odeiv::Solver::y().

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virtual void ODESystemBasedSpikingNeuron::copySolverStateToFields ( ) [inline, virtual]

derived classes can copy the values from the solver to SimObject Fields be overwritting this method

Definition at line 70 of file ODESystemBasedSpikingNeuron.h.

References solver, Vm, and odeiv::Solver::y().

Referenced by advance().

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

Get the current membrane voltage.

Reimplemented from ConductanceInputTarget.

Definition at line 75 of file ODESystemBasedSpikingNeuron.h.

References solver, and odeiv::Solver::y().

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

Reimplemented from SimObject.

Definition at line 83 of file ODESystemBasedSpikingNeuron.h.

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

Reimplemented from SimObject.

Definition at line 86 of file ODESystemBasedSpikingNeuron.h.

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

Reimplemented from SimObject.

Definition at line 89 of file ODESystemBasedSpikingNeuron.h.

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

Reimplemented from SimObject.

Definition at line 92 of file ODESystemBasedSpikingNeuron.h.

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

Reimplemented from SimObject.

Definition at line 95 of file ODESystemBasedSpikingNeuron.h.

References odeiv::ODESystem::dimension().

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

Reimplemented from SimObject.

Definition at line 99 of file ODESystemBasedSpikingNeuron.h.

References SimObject::analog, odeiv::ODESystem::dimension(), SimObject::spiking, and SimObject::undefined.

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

Reimplemented from SimObject.

Definition at line 108 of file ODESystemBasedSpikingNeuron.h.

References SimObject::undefined.

virtual double ODESystemBasedSpikingNeuron::getAnalogOutput ( analog_port_id_t port = 0 ) const [inline, virtual]

Return the analog value currently associated with the given port.

Reimplemented from SimObject.

Definition at line 112 of file ODESystemBasedSpikingNeuron.h.

References solver, and odeiv::Solver::y().

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virtual void ODESystemBasedSpikingNeuron::clearSynapticInput ( void ) [inline, virtual]

Definition at line 122 of file ODESystemBasedSpikingNeuron.h.

References Gsyn, and Isyn.

Referenced by advance(), and reset().

virtual void ODESystemBasedSpikingNeuron::currentInput ( double i ) [inline, virtual]

Reimplemented from CurrentInputTarget.

Definition at line 126 of file ODESystemBasedSpikingNeuron.h.

References Isyn.

virtual void ODESystemBasedSpikingNeuron::conductanceInput	(	double	g,
		double	Erev
	)			`[inline, virtual]`

Reimplemented from ConductanceInputTarget.

Definition at line 130 of file ODESystemBasedSpikingNeuron.h.

References Gsyn, and Isyn.

Member Data Documentation

float ODESystemBasedSpikingNeuron::Rm

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

Definition at line 32 of file ODESystemBasedSpikingNeuron.h.

Referenced by advance(), HHINeuron::HHINeuron(), HHNeuron::HHNeuron(), HHNeuronTraubMiles91::HHNeuronTraubMiles91(), HHNeuronTraubMiles91::reset(), HHINeuron::reset(), and HHNeuron::reset().

float ODESystemBasedSpikingNeuron::Cm

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

Definition at line 35 of file ODESystemBasedSpikingNeuron.h.

Referenced by HHNeuronTraubMiles91::derivatives(), HHINeuron::derivatives(), HHNeuron::derivatives(), HHINeuron::HHINeuron(), HHNeuron::HHNeuron(), and HHNeuronTraubMiles91::HHNeuronTraubMiles91().

float ODESystemBasedSpikingNeuron::Vresting

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

Definition at line 38 of file ODESystemBasedSpikingNeuron.h.

Referenced by HHINeuron::HHINeuron(), HHNeuron::HHNeuron(), HHNeuronTraubMiles91::HHNeuronTraubMiles91(), HHNeuronTraubMiles91::reset(), HHINeuron::reset(), and HHNeuron::reset().

float ODESystemBasedSpikingNeuron::Vthresh

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

Definition at line 41 of file ODESystemBasedSpikingNeuron.h.

Referenced by advance(), HHINeuron::HHINeuron(), HHNeuron::HHNeuron(), and HHNeuronTraubMiles91::HHNeuronTraubMiles91().

float ODESystemBasedSpikingNeuron::Vinit

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

Definition at line 44 of file ODESystemBasedSpikingNeuron.h.

Referenced by HHINeuron::HHINeuron(), HHNeuron::HHNeuron(), HHNeuronTraubMiles91::HHNeuronTraubMiles91(), HHNeuronTraubMiles91::reset(), HHINeuron::reset(), and HHNeuron::reset().

double ODESystemBasedSpikingNeuron::Em

Leak reversal potential.

Definition at line 47 of file ODESystemBasedSpikingNeuron.h.

Referenced by advance(), HHNeuronTraubMiles91::reset(), HHINeuron::reset(), and HHNeuron::reset().

float ODESystemBasedSpikingNeuron::Trefract

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

Definition at line 50 of file ODESystemBasedSpikingNeuron.h.

Referenced by advance(), HHINeuron::HHINeuron(), HHNeuron::HHNeuron(), and HHNeuronTraubMiles91::HHNeuronTraubMiles91().

float ODESystemBasedSpikingNeuron::Inoise

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

Definition at line 53 of file ODESystemBasedSpikingNeuron.h.

Referenced by advance(), HHINeuron::HHINeuron(), HHNeuron::HHNeuron(), and HHNeuronTraubMiles91::HHNeuronTraubMiles91().

float ODESystemBasedSpikingNeuron::Iinject

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

Definition at line 56 of file ODESystemBasedSpikingNeuron.h.

Referenced by advance(), HHINeuron::HHINeuron(), HHNeuron::HHNeuron(), and HHNeuronTraubMiles91::HHNeuronTraubMiles91().

double ODESystemBasedSpikingNeuron::Vm [protected]

The membrane voltage.

Definition at line 133 of file ODESystemBasedSpikingNeuron.h.

Referenced by advance(), copySolverStateToFields(), and reset().

odeiv::Solver* ODESystemBasedSpikingNeuron::solver [protected]

A solver for the differential equations.

Definition at line 143 of file ODESystemBasedSpikingNeuron.h.

Referenced by advance(), copySolverStateToFields(), getAnalogOutput(), getVm(), init(), ODESystemBasedSpikingNeuron(), reset(), and ~ODESystemBasedSpikingNeuron().

int ODESystemBasedSpikingNeuron::nStepsInRefr [protected]

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

Definition at line 146 of file ODESystemBasedSpikingNeuron.h.

Referenced by advance(), and reset().

ThreadSpecificRandomDistribution< NormalDistribution > ODESystemBasedSpikingNeuron::noise [static, protected]

Random number generator for the noise.

Definition at line 149 of file ODESystemBasedSpikingNeuron.h.

Referenced by adjust(), and advance().

double ODESystemBasedSpikingNeuron::Isyn [protected]

Summation point for all synaptic input currents.

Definition at line 152 of file ODESystemBasedSpikingNeuron.h.

Referenced by advance(), clearSynapticInput(), conductanceInput(), and currentInput().

double ODESystemBasedSpikingNeuron::Gsyn [protected]

Summation point for all synaptic input conductances.

Definition at line 155 of file ODESystemBasedSpikingNeuron.h.

Referenced by advance(), clearSynapticInput(), and conductanceInput().

double ODESystemBasedSpikingNeuron::G0 [protected]

Definition at line 158 of file ODESystemBasedSpikingNeuron.h.

Referenced by advance(), HHNeuronTraubMiles91::derivatives(), HHINeuron::derivatives(), and HHNeuron::derivatives().

double ODESystemBasedSpikingNeuron::I0 [protected]

Definition at line 158 of file ODESystemBasedSpikingNeuron.h.

Referenced by advance(), HHNeuronTraubMiles91::derivatives(), HHINeuron::derivatives(), and HHNeuron::derivatives().

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

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


Public Member Functions
	ODESystemBasedSpikingNeuron (size_t dim)
virtual	~ODESystemBasedSpikingNeuron ()
virtual int	init (InitializeInfo *ii)
	Called during network initialization (prior to reset).
virtual int	adjust (double dt)
	Adjust to time grid of dt.
int	reset (double dt, double *y0)
	Reset the neuron.
virtual int	advance (AdvanceInfo const &)
	Advance the neuron (integration an spike checking ).
virtual void	copySolverStateToFields ()
	derived classes can copy the values from the solver to SimObject Fields be overwritting this method
virtual double	getVm ()
	Get the current membrane voltage.
Definition of input and output ports
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	getAnalogOutput (analog_port_id_t port=0) const
	Return the analog value currently associated with the given port.
Manage synaptic input
virtual void	clearSynapticInput (void)
virtual void	currentInput (double i)
virtual void	conductanceInput (double g, double Erev)
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 detected. [units=V; range=(-10,100);].
float	Vinit
	The initial condition for at time . [units=V; range=(-1,1);].
double	Em
	Leak reversal potential.
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.
odeiv::Solver *	solver
	A solver for the differential equations.
int	nStepsInRefr
	If positive then this counter tells us how many time steps we are still in the absolute refractory period.
double	Isyn
	Summation point for all synaptic input currents.
double	Gsyn
	Summation point for all synaptic input conductances.
double	G0
double	I0
Static Protected Attributes
static ThreadSpecificRandomDistribution < NormalDistribution >	noise
	Random number generator for the noise.