Neuron Class Reference

#include <Neuron.h>

Collaboration diagram for Neuron:

Public Member Functions
	Neuron ()
	Neuron (const Neuron &other)
void	setRM (double v)
double	getRM () const
void	setRA (double v)
double	getRA () const
void	setCM (double v)
double	getCM () const
void	setEm (double v)
double	getEm () const
void	setTheta (double v)
double	getTheta () const
void	setPhi (double v)
double	getPhi () const
void	setSourceFile (string v)
string	getSourceFile () const
void	setCompartmentLengthInLambdas (double v)
double	getCompartmentLengthInLambdas () const
unsigned int	getNumCompartments () const
unsigned int	getNumBranches () const
vector< double >	getPathDistFromSoma () const
vector< double >	getGeomDistFromSoma () const
vector< double >	getElecDistFromSoma () const
vector< ObjId >	getCompartments () const
vector< ObjId >	getExprElist (const Eref &e, string line) const
vector< double >	getExprVal (const Eref &e, string line) const
vector< ObjId >	getSpinesFromExpression (const Eref &e, string line) const
void	setChannelDistribution (const Eref &e, vector< string > v)
vector< string >	getChannelDistribution (const Eref &e) const
void	setPassiveDistribution (const Eref &e, vector< string > v)
vector< string >	getPassiveDistribution (const Eref &e) const
void	setSpineDistribution (const Eref &e, vector< string > v)
vector< string >	getSpineDistribution (const Eref &e) const
void	buildSegmentTree (const Eref &e)
	Fills up vector of segments. First entry is soma.
void	setSpineAndPsdMesh (Id spineMesh, Id psdMesh)
	Fills up vector of segments. First entry is soma.
void	setSpineAndPsdDsolve (Id spineDsolve, Id psdDsolve)
void	updateSegmentLengths ()
void	installSpines (const vector< ObjId > &elist, const vector< double > &val, const vector< string > &line)
void	makeSpacingDistrib (const vector< ObjId > &elist, const vector< double > &val, vector< unsigned int > &seglistIndex, vector< unsigned int > &elistIndex, vector< double > &pos, const vector< string > &line) const
void	parseMechSpec (const Eref &e)
void	installMechanism (const string &name, const vector< ObjId > &elist, const vector< double > &val, const vector< string > &line)
void	buildElist (const Eref &e, const vector< string > &line, vector< ObjId > &elist, vector< double > &val)
void	evalExprForElist (const vector< ObjId > &elist, const string &expn, vector< double > &val) const
Spine *	lookupSpine (unsigned int index)
void	setNumSpines (unsigned int num)
unsigned int	getNumSpines () const
const vector< Id > &	spineIds (unsigned int index) const
void	scaleBufAndRates (unsigned int spineNum, double lenScale, double diaScale) const
void	scaleShaftDiffusion (unsigned int spineNum, double len, double dia) const
	Scale the diffusion parameters due to a change in the shaft dimensions.
void	scaleHeadDiffusion (unsigned int spineNum, double len, double dia) const
	Scale the diffusion parameters due to a change in the head dimensions.
Static Public Member Functions
static const Cinfo *	initCinfo ()

Detailed Description

The Neuron class to hold the Compartment class elements.

Constructor & Destructor Documentation

Neuron::Neuron ( )

Neuron::Neuron ( const Neuron & other )

Member Function Documentation

void Neuron::buildElist	(	const Eref &	e,
		const vector< string > &	line,
		vector< ObjId > &	elist,
		vector< double > &	val
	)

void Neuron::buildSegmentTree ( const Eref & e )

Fills up vector of segments. First entry is soma.

References Neutral::children(), fillSegIndex(), Eref::id(), Id::path(), and updateSegmentLengths().

Referenced by initCinfo().

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void Neuron::evalExprForElist	(	const vector< ObjId > &	elist,
		const string &	expn,
		vector< double > &	val
	)			const

vector< string > Neuron::getChannelDistribution ( const Eref & e ) const

Referenced by initCinfo().

double Neuron::getCM ( ) const

Referenced by initCinfo().

double Neuron::getCompartmentLengthInLambdas ( ) const

Referenced by initCinfo().

vector< ObjId > Neuron::getCompartments ( ) const

Referenced by initCinfo().

vector< double > Neuron::getElecDistFromSoma ( ) const

Referenced by initCinfo().

double Neuron::getEm ( ) const

Referenced by initCinfo().

vector< ObjId > Neuron::getExprElist	(	const Eref &	e,
		string	line
	)			const

Referenced by initCinfo().

vector< double > Neuron::getExprVal	(	const Eref &	e,
		string	line
	)			const

Referenced by initCinfo().

vector< double > Neuron::getGeomDistFromSoma ( ) const

Referenced by initCinfo().

unsigned int Neuron::getNumBranches ( ) const

Referenced by initCinfo().

unsigned int Neuron::getNumCompartments ( ) const

Referenced by initCinfo().

unsigned int Neuron::getNumSpines ( ) const

Referenced by initCinfo().

vector< string > Neuron::getPassiveDistribution ( const Eref & e ) const

Referenced by initCinfo().

vector< double > Neuron::getPathDistFromSoma ( ) const

Referenced by initCinfo().

double Neuron::getPhi ( ) const

Referenced by initCinfo().

double Neuron::getRA ( ) const

Referenced by initCinfo().

double Neuron::getRM ( ) const

Referenced by initCinfo().

string Neuron::getSourceFile ( ) const

Referenced by initCinfo().

vector< string > Neuron::getSpineDistribution ( const Eref & e ) const

Referenced by initCinfo().

vector< ObjId > Neuron::getSpinesFromExpression	(	const Eref &	e,
		string	line
	)			const

Referenced by initCinfo().

double Neuron::getTheta ( ) const

Referenced by initCinfo().

const Cinfo * Neuron::initCinfo ( ) [static]

Initializes the class info.

References buildSegmentTree(), getChannelDistribution(), getCM(), getCompartmentLengthInLambdas(), getCompartments(), getElecDistFromSoma(), getEm(), getExprElist(), getExprVal(), getGeomDistFromSoma(), getNumBranches(), getNumCompartments(), getNumSpines(), getPassiveDistribution(), getPathDistFromSoma(), getPhi(), getRA(), getRM(), getSourceFile(), getSpineDistribution(), getSpinesFromExpression(), getTheta(), Neutral::initCinfo(), Spine::initCinfo(), lookupSpine(), setChannelDistribution(), setCM(), setCompartmentLengthInLambdas(), setEm(), setNumSpines(), setPassiveDistribution(), setPhi(), setRA(), setRM(), setSourceFile(), setSpineAndPsdDsolve(), setSpineAndPsdMesh(), setSpineDistribution(), and setTheta().

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void Neuron::installMechanism	(	const string &	name,
		const vector< ObjId > &	elist,
		const vector< double > &	val,
		const vector< string > &	line
	)

void Neuron::installSpines	(	const vector< ObjId > &	elist,
		const vector< double > &	val,
		const vector< string > &	line
	)

Spine * Neuron::lookupSpine ( unsigned int index )

Referenced by initCinfo().

void Neuron::makeSpacingDistrib	(	const vector< ObjId > &	elist,
		const vector< double > &	val,
		vector< unsigned int > &	seglistIndex,
		vector< unsigned int > &	elistIndex,
		vector< double > &	pos,
		const vector< string > &	line
	)			const

void Neuron::parseMechSpec ( const Eref & e )

void Neuron::scaleBufAndRates	(	unsigned int	spineNum,
		double	lenScale,
		double	diaScale
	)			const

Referenced by Spine::setHeadDiameter(), and Spine::setHeadLength().

void Neuron::scaleHeadDiffusion	(	unsigned int	spineNum,
		double	len,
		double	dia
	)			const

Scale the diffusion parameters due to a change in the head dimensions.

References PI.

Referenced by Spine::setHeadDiameter(), and Spine::setHeadLength().

void Neuron::scaleShaftDiffusion	(	unsigned int	spineNum,
		double	len,
		double	dia
	)			const

Scale the diffusion parameters due to a change in the shaft dimensions.

References PI.

Referenced by Spine::setShaftDiameter(), and Spine::setShaftLength().

void Neuron::setChannelDistribution	(	const Eref &	e,
		vector< string >	v
	)

Referenced by initCinfo().

void Neuron::setCM ( double v )

Referenced by initCinfo().

void Neuron::setCompartmentLengthInLambdas ( double v )

Referenced by initCinfo().

void Neuron::setEm ( double v )

Referenced by initCinfo().

void Neuron::setNumSpines ( unsigned int num )

Ignore it. the number of spines is set when we build the tree.

Referenced by initCinfo().

void Neuron::setPassiveDistribution	(	const Eref &	e,
		vector< string >	v
	)

Referenced by initCinfo().

void Neuron::setPhi ( double v )

Referenced by initCinfo().

void Neuron::setRA ( double v )

Referenced by initCinfo().

void Neuron::setRM ( double v )

Referenced by initCinfo().

void Neuron::setSourceFile ( string v )

Referenced by initCinfo().

void Neuron::setSpineAndPsdDsolve	(	Id	spineDsolve,
		Id	psdDsolve
	)

Referenced by initCinfo().

void Neuron::setSpineAndPsdMesh	(	Id	spineMesh,
		Id	psdMesh
	)

Fills up vector of segments. First entry is soma.

References Neutral::child(), Element::cinfo(), Id::element(), Id::eref(), Cinfo::isA(), and Id::path().

Referenced by initCinfo().

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void Neuron::setSpineDistribution	(	const Eref &	e,
		vector< string >	v
	)

Referenced by initCinfo().

void Neuron::setTheta ( double v )

Referenced by initCinfo().

const vector< Id > & Neuron::spineIds ( unsigned int index ) const

Referenced by Spine::getHeadDiameter(), Spine::getHeadLength(), Spine::getShaftDiameter(), Spine::getShaftLength(), Spine::setHeadDiameter(), Spine::setHeadLength(), Spine::setShaftDiameter(), and Spine::setShaftLength().

void Neuron::updateSegmentLengths ( )

Referenced by buildSegmentTree().

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

biophysics/Neuron.h
biophysics/Neuron.cpp

Neuron Class Reference

Public Member Functions

Static Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation