#include <ExIF.h>

Inheritance diagram for moose::ExIF:

Collaboration diagram for moose::ExIF:

Public Member Functions
	ExIF ()

double	getDeltaThresh (const Eref &e) const

double	getVPeak (const Eref &e) const

void	setDeltaThresh (const Eref &e, double val)

void	setVPeak (const Eref &e, double val)

void	vProcess (const Eref &e, ProcPtr p)

void	vReinit (const Eref &e, ProcPtr p)

virtual	~ExIF ()

Public Member Functions inherited from moose::IntFireBase
void	activation (double val)

double	getLastEventTime (const Eref &e) const

double	getRefractoryPeriod (const Eref &e) const

double	getThresh (const Eref &e) const

double	getVReset (const Eref &e) const

bool	hasFired (const Eref &e) const

	IntFireBase ()

void	setRefractoryPeriod (const Eref &e, double val)

void	setThresh (const Eref &e, double val)

void	setVReset (const Eref &e, double val)

virtual	~IntFireBase ()

Public Member Functions inherited from moose::Compartment
void	cable ()

	Compartment ()

virtual double	vGetCm (const Eref &e) const

virtual double	vGetEm (const Eref &e) const

virtual double	vGetIm (const Eref &e) const

virtual double	vGetInitVm (const Eref &e) const

virtual double	vGetInject (const Eref &e) const

virtual double	vGetRa (const Eref &e) const

virtual double	vGetRm (const Eref &e) const

virtual double	vGetVm (const Eref &e) const

void	vHandleAxial (double Vm)

void	vHandleChannel (const Eref &e, double Gk, double Ek)

void	vHandleRaxial (double Ra, double Vm)

void	vInitProc (const Eref &e, ProcPtr p)

void	vInitReinit (const Eref &e, ProcPtr p)

void	vInjectMsg (const Eref &e, double current)

void	vRandInject (const Eref &e, double prob, double current)

virtual void	vSetCm (const Eref &e, double Cm)

virtual void	vSetEm (const Eref &e, double Em)

virtual void	vSetInitVm (const Eref &e, double initVm)

virtual void	vSetInject (const Eref &e, double Inject)

virtual void	vSetRa (const Eref &e, double Ra)

virtual void	vSetRm (const Eref &e, double Rm)

virtual void	vSetVm (const Eref &e, double Vm)

virtual	~Compartment ()

Public Member Functions inherited from moose::CompartmentBase
void	cable ()

	CompartmentBase ()

void	displace (double dx, double dy, double dz)
	Displaces compartment by specified distance vector. More...

double	getCm (const Eref &e) const

double	getDiameter () const

double	getEm (const Eref &e) const

double	getIm (const Eref &e) const

double	getInitVm (const Eref &e) const

double	getInject (const Eref &e) const

double	getLength () const

double	getRa (const Eref &e) const

double	getRm (const Eref &e) const

double	getVm (const Eref &e) const

double	getX () const

double	getX0 () const

double	getY () const

double	getY0 () const

double	getZ () const

double	getZ0 () const

void	handleAxial (double Vm)

void	handleChannel (const Eref &e, double Gk, double Ek)

void	handleRaxial (double Ra, double Vm)

void	initProc (const Eref &e, ProcPtr p)

void	initReinit (const Eref &e, ProcPtr p)

void	injectMsg (const Eref &e, double current)

void	process (const Eref &e, ProcPtr p)

void	randInject (const Eref &e, double prob, double current)

bool	rangeWarning (const string &field, double value)

void	reinit (const Eref &e, ProcPtr p)

void	setCm (const Eref &e, double Cm)

void	setDiameter (double diameter)

void	setEm (const Eref &e, double Em)

void	setGeomAndElec (const Eref &e, double length, double dia)
	Scales electrical values along with setting length, dia. More...

void	setInitVm (const Eref &e, double initVm)

void	setInject (const Eref &e, double Inject)

void	setLength (double length)

void	setRa (const Eref &e, double Ra)

void	setRm (const Eref &e, double Rm)

void	setVm (const Eref &e, double Vm)

void	setX (double value)

void	setX0 (double value)

void	setY (double value)

void	setY0 (double value)

void	setZ (double value)

void	setZ0 (double value)

void	updateLength ()

virtual void	vSetSolver (const Eref &e, Id hsolve)

virtual	~CompartmentBase ()

Static Public Member Functions
static const Cinfo *	initCinfo ()

Static Public Member Functions inherited from moose::IntFireBase
static const Cinfo *	initCinfo ()

static SrcFinfo1< double > *	spikeOut ()
	Message src for outgoing spikes. More...

Static Public Member Functions inherited from moose::Compartment
static const Cinfo *	initCinfo ()

Static Public Member Functions inherited from moose::CompartmentBase
static const Cinfo *	initCinfo ()

static SrcFinfo1< double > *	VmOut ()

static void	zombify (Element orig, const Cinfo zClass, Id hsolve)

Protected Attributes
double	deltaThresh_

double	vPeak_

Protected Attributes inherited from moose::IntFireBase
double	activation_

bool	fired_

double	lastEvent_

double	refractT_

double	threshold_

double	vReset_

Protected Attributes inherited from moose::Compartment
double	A_

double	B_

double	Cm_

double	Em_

double	Im_

double	initVm_

double	inject_

double	lastIm_

double	Ra_

double	Rm_

double	sumInject_

double	Vm_

Detailed Description

The IntFire class sets up an integrate-and-fire compartment.

Definition at line 19 of file ExIF.h.

Constructor & Destructor Documentation

ExIF::ExIF ( )

Definition at line 70 of file ExIF.cpp.

References deltaThresh_, and vPeak_.

71 {vPeak_ = 0.0;

72 deltaThresh_ = 0.0;}

moose::ExIF::vPeak_

double vPeak_

Definition: ExIF.h:48

moose::ExIF::deltaThresh_

double deltaThresh_

Definition: ExIF.h:47

ExIF::~ExIF ( )

virtual

Definition at line 74 of file ExIF.cpp.

75 {;}

Member Function Documentation

double ExIF::getDeltaThresh ( const Eref & e ) const

Definition at line 125 of file ExIF.cpp.

References deltaThresh_.

Referenced by initCinfo().

 {
     return deltaThresh_;
 }

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double ExIF::getVPeak ( const Eref & e ) const

Definition at line 135 of file ExIF.cpp.

References vPeak_.

Referenced by initCinfo().

 {
     return vPeak_;
 }

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const Cinfo * ExIF::initCinfo ( )

static

Initializes the class info.

Definition at line 19 of file ExIF.cpp.

References ExIFCinfo, getDeltaThresh(), getVPeak(), moose::IntFireBase::initCinfo(), setDeltaThresh(), and setVPeak().

Referenced by moose::AdExIF::initCinfo().

 {
     static string doc[] =
     {
         "Name", "ExIF",
         "Author", "Aditya Gilra",
         "Description", "Leaky Integrate-and-Fire neuron with Exponential spike rise."
         "Rm*Cm dVm/dt = -(Vm-Em) + deltaThresh * exp((Vm-thresh)/deltaThresh) + Rm*I"
     };
 
     static ElementValueFinfo< ExIF, double > deltaThresh(
         "deltaThresh",
         "Parameter in Vm evolution equation:"
         "Rm*Cm * dVm/dt = -(Vm-Em) + deltaThresh * exp((Vm-thresh)/deltaThresh) + Rm*I",
         &ExIF::setDeltaThresh,
         &ExIF::getDeltaThresh
     );
 
     static ElementValueFinfo< ExIF, double > vPeak(
         "vPeak",
         "Vm is reset on reaching vPeak, different from spike thresh below:"
         "Rm*Cm dVm/dt = -(Vm-Em) + deltaThresh * exp((Vm-thresh)/deltaThresh) + Rm*I",
         &ExIF::setVPeak,
         &ExIF::getVPeak
     );
 
     static Finfo* ExIFFinfos[] = {
         &deltaThresh,       // Value
         &vPeak,             // Value
     };
 
     static Dinfo< ExIF > dinfo;
     static Cinfo ExIFCinfo(
                 "ExIF",
                 IntFireBase::initCinfo(),
                 ExIFFinfos,
                 sizeof( ExIFFinfos ) / sizeof (Finfo*),
                 &dinfo,
                 doc,
                 sizeof(doc)/sizeof(string)
     );
 
     return &ExIFCinfo;
 }

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void ExIF::setDeltaThresh	(	const Eref &	e,
		double	val
	)

Definition at line 120 of file ExIF.cpp.

References deltaThresh_.

Referenced by initCinfo().

 {
     deltaThresh_ = val;
 }

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void ExIF::setVPeak	(	const Eref &	e,
		double	val
	)

Definition at line 130 of file ExIF.cpp.

References vPeak_.

Referenced by initCinfo().

 {
     vPeak_ = val;
 }

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void ExIF::vProcess	(	const Eref &	e,
		ProcPtr	p
	)

virtual

The process function does the object updating and sends out messages to channels, nernsts, and so on.

Implements moose::IntFireBase.

Definition at line 81 of file ExIF.cpp.

References moose::Compartment::A_, moose::IntFireBase::activation_, moose::Compartment::B_, moose::Compartment::Cm_, ProcInfo::currTime, deltaThresh_, ProcInfo::dt, moose::IntFireBase::fired_, moose::IntFireBase::lastEvent_, moose::IntFireBase::refractT_, moose::Compartment::Rm_, moose::IntFireBase::spikeOut(), moose::Compartment::sumInject_, moose::IntFireBase::threshold_, moose::Compartment::Vm_, moose::CompartmentBase::VmOut(), vPeak_, moose::Compartment::vProcess(), and moose::IntFireBase::vReset_.

 {
     fired_ = false;
     if ( p->currTime < lastEvent_ + refractT_ ) {
         Vm_ = vReset_;
         A_ = 0.0;
         B_ = 1.0 / Rm_;
         sumInject_ = 0.0;
         VmOut()->send( e, Vm_ );
     } else {
         // activation can be a continous variable (graded synapse).
         // So integrate it at every time step, thus *dt.
         // For a delta-fn synapse, SynHandler-s divide by dt and send activation.
         // See: http://www.genesis-sim.org/GENESIS/Hyperdoc/Manual-26.html#synchan
         //          for this continuous definition of activation.
         Vm_ += activation_ * p->dt;
         activation_ = 0.0;
         if ( Vm_ >= vPeak_ ) {
             Vm_ = vReset_;
             lastEvent_ = p->currTime;
             fired_ = true;
             spikeOut()->send( e, p->currTime );
             VmOut()->send( e, Vm_ );
         } else {
             Vm_ += deltaThresh_ * exp((Vm_-threshold_)/deltaThresh_) *p->dt/Rm_/Cm_;
             Compartment::vProcess( e, p );  // this sends out Vm message also,
                                             // so do calculations before
         }
     }
 }

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void ExIF::vReinit	(	const Eref &	e,
		ProcPtr	p
	)

virtual

The reinit function reinitializes all fields.

Implements moose::IntFireBase.

Definition at line 112 of file ExIF.cpp.

References moose::IntFireBase::activation_, moose::IntFireBase::fired_, moose::IntFireBase::lastEvent_, moose::IntFireBase::refractT_, and moose::Compartment::vReinit().

 {
     activation_ = 0.0;
     fired_ = false;
     lastEvent_ = -refractT_; // Allow it to fire right away.
     Compartment::vReinit( e, p );
 }

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Member Data Documentation

double moose::ExIF::deltaThresh_

protected

Definition at line 47 of file ExIF.h.

Referenced by ExIF(), getDeltaThresh(), setDeltaThresh(), vProcess(), and moose::AdExIF::vProcess().

double moose::ExIF::vPeak_

protected

Definition at line 48 of file ExIF.h.

Referenced by ExIF(), getVPeak(), setVPeak(), vProcess(), and moose::AdExIF::vProcess().

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

moose-core/intfire/ExIF.h
moose-core/intfire/ExIF.cpp

Public Member Functions

Static Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation