#include <AdThreshIF.h>

Inheritance diagram for moose::AdThreshIF:

Collaboration diagram for moose::AdThreshIF:

Public Member Functions
	AdThreshIF ()

double	getA0 (const Eref &e) const

double	getTauThresh (const Eref &e) const

double	getThreshAdaptive (const Eref &e) const

double	getThreshJump (const Eref &e) const

void	setA0 (const Eref &e, double val)

void	setTauThresh (const Eref &e, double val)

void	setThreshAdaptive (const Eref &e, double val)

void	setThreshJump (const Eref &e, double val)

void	vProcess (const Eref &e, ProcPtr p)

void	vReinit (const Eref &e, ProcPtr p)

virtual	~AdThreshIF ()

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)

Private Attributes
double	a0_

double	tauThresh_

double	threshAdaptive_

double	threshJump_

Additional Inherited Members
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 AdThreshIF.h.

Constructor & Destructor Documentation

AdThreshIF::AdThreshIF ( )

Definition at line 89 of file AdThreshIF.cpp.

References a0_, tauThresh_, threshAdaptive_, and threshJump_.

 {threshAdaptive_ = 0.0;
 tauThresh_ = 1.0;
 a0_ = 0.0;
 threshJump_ = 0.0;}

AdThreshIF::~AdThreshIF ( )

virtual

Definition at line 95 of file AdThreshIF.cpp.

96 {;}

Member Function Documentation

double AdThreshIF::getA0 ( const Eref & e ) const

Definition at line 168 of file AdThreshIF.cpp.

References a0_.

Referenced by initCinfo().

 {
     return a0_;
 }

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double AdThreshIF::getTauThresh ( const Eref & e ) const

Definition at line 158 of file AdThreshIF.cpp.

References tauThresh_.

Referenced by initCinfo().

 {
     return tauThresh_;
 }

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double AdThreshIF::getThreshAdaptive ( const Eref & e ) const

Definition at line 148 of file AdThreshIF.cpp.

References threshAdaptive_.

Referenced by initCinfo().

 {
     return threshAdaptive_;
 }

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double AdThreshIF::getThreshJump ( const Eref & e ) const

Definition at line 178 of file AdThreshIF.cpp.

References threshJump_.

Referenced by initCinfo().

 {
     return threshJump_;
 }

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const Cinfo * AdThreshIF::initCinfo ( )

static

Initializes the class info.

Definition at line 19 of file AdThreshIF.cpp.

References AdThreshIFCinfo, getA0(), getTauThresh(), getThreshAdaptive(), getThreshJump(), moose::IntFireBase::initCinfo(), setA0(), setTauThresh(), setThreshAdaptive(), and setThreshJump().

 {
     static string doc[] =
     {
         "Name", "AdThreshIF",
         "Author", "Aditya Gilra",
         "Description", "Leaky Integrate-and-Fire neuron with adaptive threshold."
         "Based on Rossant, C., Goodman, D.F.M., Platkiewicz, J., and Brette, R. (2010)."
         "Rm*Cm * dVm/dt = -(Vm-Em) + Rm*I"
         "tauThresh * d threshAdaptive / dt = a0*(Vm-Em) - threshAdaptive "
         "at each spike, threshAdaptive is increased by threshJump "
         "the spiking threshold adapts as thresh + threshAdaptive "
     };
 
     static ElementValueFinfo< AdThreshIF, double > threshAdaptive(
         "threshAdaptive",
         "adaptative part of the threshold that decays with time constant tauThresh",
         &AdThreshIF::setThreshAdaptive,
         &AdThreshIF::getThreshAdaptive
     );
 
     static ElementValueFinfo< AdThreshIF, double > tauThresh(
         "tauThresh",
         "time constant of adaptative part of the threshold",
         &AdThreshIF::setTauThresh,
         &AdThreshIF::getTauThresh
     );
 
     static ElementValueFinfo< AdThreshIF, double > a0(
         "a0",
         "factor for voltage-dependent term in evolution of adaptative threshold: "
         "tauThresh * d threshAdaptive / dt = a0*(Vm-Em) - threshAdaptive ",
         &AdThreshIF::setA0,
         &AdThreshIF::getA0
     );
 
     static ElementValueFinfo< AdThreshIF, double > threshJump(
         "threshJump",
         "threshJump is added to threshAdaptive on each spike",
         &AdThreshIF::setThreshJump,
         &AdThreshIF::getThreshJump
     );
 
     static Finfo* AdThreshIFFinfos[] = {
         &threshAdaptive,// Value
         &tauThresh,     // Value
         &a0,            // Value
         &threshJump     // Value
     };
 
     static Dinfo< AdThreshIF > dinfo;
     static Cinfo AdThreshIFCinfo(
                 "AdThreshIF",
                 IntFireBase::initCinfo(),
                 AdThreshIFFinfos,
                 sizeof( AdThreshIFFinfos ) / sizeof (Finfo*),
                 &dinfo,
                 doc,
                 sizeof(doc)/sizeof(string)
     );
 
     return &AdThreshIFCinfo;
 }

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void AdThreshIF::setA0	(	const Eref &	e,
		double	val
	)

Definition at line 163 of file AdThreshIF.cpp.

References a0_.

Referenced by initCinfo().

 {
     a0_ = val;
 }

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void AdThreshIF::setTauThresh	(	const Eref &	e,
		double	val
	)

Definition at line 153 of file AdThreshIF.cpp.

References tauThresh_.

Referenced by initCinfo().

 {
     tauThresh_ = val;
 }

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void AdThreshIF::setThreshAdaptive	(	const Eref &	e,
		double	val
	)

Definition at line 143 of file AdThreshIF.cpp.

References threshAdaptive_.

Referenced by initCinfo().

 {
     threshAdaptive_ = val;
 }

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void AdThreshIF::setThreshJump	(	const Eref &	e,
		double	val
	)

Definition at line 173 of file AdThreshIF.cpp.

References threshJump_.

Referenced by initCinfo().

 {
     threshJump_ = val;
 }

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void AdThreshIF::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 102 of file AdThreshIF.cpp.

References a0_, moose::Compartment::A_, moose::IntFireBase::activation_, moose::Compartment::B_, ProcInfo::currTime, ProcInfo::dt, moose::Compartment::Em_, moose::IntFireBase::fired_, moose::IntFireBase::lastEvent_, moose::IntFireBase::refractT_, moose::Compartment::Rm_, moose::IntFireBase::spikeOut(), moose::Compartment::sumInject_, tauThresh_, threshAdaptive_, threshJump_, moose::IntFireBase::threshold_, moose::Compartment::Vm_, moose::CompartmentBase::VmOut(), 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_ > (threshold_+threshAdaptive_) ) {
             Vm_ = vReset_;
             threshAdaptive_ += threshJump_;
             lastEvent_ = p->currTime;
             fired_ = true;
             spikeOut()->send( e, p->currTime );
             VmOut()->send( e, Vm_ );
         } else {
             threshAdaptive_ += (-threshAdaptive_ + a0_*(Vm_-Em_)) * p->dt/tauThresh_;
             Compartment::vProcess( e, p );  // this sends out Vm message also,
                                             // so do Vm_ calculations before
         }
     }
 }

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

virtual

The reinit function reinitializes all fields.

Implements moose::IntFireBase.

Definition at line 134 of file AdThreshIF.cpp.

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

 {
     activation_ = 0.0;
     threshAdaptive_ = 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::AdThreshIF::a0_

private

Definition at line 53 of file AdThreshIF.h.

Referenced by AdThreshIF(), getA0(), setA0(), and vProcess().

double moose::AdThreshIF::tauThresh_

private

Definition at line 52 of file AdThreshIF.h.

Referenced by AdThreshIF(), getTauThresh(), setTauThresh(), and vProcess().

double moose::AdThreshIF::threshAdaptive_

private

Definition at line 51 of file AdThreshIF.h.

Referenced by AdThreshIF(), getThreshAdaptive(), setThreshAdaptive(), vProcess(), and vReinit().

double moose::AdThreshIF::threshJump_

private

Definition at line 54 of file AdThreshIF.h.

Referenced by AdThreshIF(), getThreshJump(), setThreshJump(), and vProcess().

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

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

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation