SwcSegment Class Reference

#include <SwcSegment.h>

Inheritance diagram for SwcSegment:

Collaboration diagram for SwcSegment:

Public Member Functions
	SwcSegment ()
	SwcSegment (const string &line)
	SwcSegment (int i, short type, double x, double y, double z, double r, int parent)
bool	OK () const
void	setBad ()
unsigned int	parent () const
void	setParent (unsigned int pa)
unsigned int	myIndex () const
void	addChild (unsigned int kid)
void	figureOutType ()
const vector< int > &	kids () const
void	replaceKids (const vector< int > &kids)
unsigned short	type () const
double	radius () const
double	length () const
double	L () const
double	distance (const SwcSegment &other) const
const Vec &	vec () const
void	setGeometricalDistanceFromSoma (const SwcSegment &soma)
void	setCumulativeDistance (double len, double L, double pSoma, double eSoma)
double	getPathDistFromSoma () const
double	getGeomDistFromSoma () const
double	getElecDistFromSoma () const
Static Public Attributes
static const short	UNDEF = 0
static const short	SOMA = 1
static const short	AXON = 2
static const short	DEND = 3
static const short	APICAL = 4
static const short	FORK = 5
static const short	END = 6
static const short	CUSTOM = 7
static const short	BadSegment = 8
static const short	AXON_FORK = 10
static const short	AXON_END = 11
static const short	APICAL_FORK = 12
static const short	APICAL_END = 13
static const string	typeName []
Protected Attributes
unsigned int	myIndex_
short	type_
	Index of self.
Vec	v_
double	radius_
	coordinates of end of segment
double	length_
	Radius of segment.
double	L_
	Length of segment.
unsigned int	parent_
	Number of length constants in segment.
double	pathDistanceFromSoma_
	Index of parent. Is ~0 for soma.
double	geometricalDistanceFromSoma_
	geometrical distance from soma.
double	electrotonicDistanceFromSoma_
	electrotonic dist from soma, summed along dend.
vector< int >	kids_

Detailed Description

This defines a single segment in an SWC file used in NeuroMorpho Note that this is not going to work well for dendritic spines which come off in the middle of a parent compartment, and which have to be started from the surface rather than the axis of the dendrite.

Constructor & Destructor Documentation

SwcSegment::SwcSegment ( ) [inline]

SwcSegment::SwcSegment ( const string & line )

SwcSegment::SwcSegment	(	int	i,
		short	type,
		double	x,
		double	y,
		double	z,
		double	r,
		int	parent
	)

References parent_.

Member Function Documentation

void SwcSegment::addChild ( unsigned int kid ) [inline]

References kids_.

double SwcSegment::distance ( const SwcSegment & other ) const [inline]

References Vec::distance(), and v_.

Referenced by ReadSwc::cleanZeroLength().

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void SwcSegment::figureOutType ( )

References APICAL, APICAL_END, APICAL_FORK, AXON, AXON_END, AXON_FORK, DEND, END, FORK, kids_, SOMA, and type_.

double SwcSegment::getElecDistFromSoma ( ) const [inline]

References electrotonicDistanceFromSoma_.

double SwcSegment::getGeomDistFromSoma ( ) const [inline]

References geometricalDistanceFromSoma_.

double SwcSegment::getPathDistFromSoma ( ) const [inline]

References pathDistanceFromSoma_.

const vector< int >& SwcSegment::kids ( ) const [inline]

References kids_.

Referenced by ReadSwc::cleanZeroLength(), and ReadSwc::parseBranches().

double SwcSegment::L ( ) const [inline]

References L_.

double SwcSegment::length ( ) const [inline]

References length_.

unsigned int SwcSegment::myIndex ( ) const [inline]

References myIndex_.

Referenced by ReadSwc::assignKids(), ReadSwc::build(), ReadSwc::cleanZeroLength(), SwcBranch::printDiagnostics(), and ReadSwc::validate().

bool SwcSegment::OK ( ) const [inline]

References BadSegment, CUSTOM, type_, and UNDEF.

Referenced by ReadSwc::parseBranches().

unsigned int SwcSegment::parent ( ) const [inline]

References parent_.

Referenced by ReadSwc::assignKids(), ReadSwc::build(), ReadSwc::cleanZeroLength(), SwcBranch::printDiagnostics(), and ReadSwc::validate().

double SwcSegment::radius ( ) const [inline]

References radius_.

Referenced by ReadSwc::validate().

void SwcSegment::replaceKids ( const vector< int > & kids ) [inline]

References kids_.

Referenced by ReadSwc::cleanZeroLength().

void SwcSegment::setBad ( ) [inline]

References BadSegment, and type_.

Referenced by ReadSwc::cleanZeroLength().

void SwcSegment::setCumulativeDistance	(	double	len,
		double	L,
		double	pSoma,
		double	eSoma
	)			`[inline]`

References electrotonicDistanceFromSoma_, L_, length_, and pathDistanceFromSoma_.

void SwcSegment::setGeometricalDistanceFromSoma ( const SwcSegment & soma ) [inline]

References Vec::distance(), geometricalDistanceFromSoma_, and v_.

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void SwcSegment::setParent ( unsigned int pa ) [inline]

References parent_.

Referenced by ReadSwc::cleanZeroLength().

unsigned short SwcSegment::type ( ) const [inline]

References type_.

Referenced by ReadSwc::diagnostics().

const Vec& SwcSegment::vec ( ) const [inline]

References v_.

Member Data Documentation

const short SwcSegment::APICAL = 4 [static]

Referenced by figureOutType().

const short SwcSegment::APICAL_END = 13 [static]

Referenced by figureOutType().

const short SwcSegment::APICAL_FORK = 12 [static]

Referenced by figureOutType().

const short SwcSegment::AXON = 2 [static]

Referenced by figureOutType().

const short SwcSegment::AXON_END = 11 [static]

Referenced by figureOutType().

const short SwcSegment::AXON_FORK = 10 [static]

Referenced by figureOutType().

const short SwcSegment::BadSegment = 8 [static]

Referenced by OK(), and setBad().

const short SwcSegment::CUSTOM = 7 [static]

Referenced by OK().

const short SwcSegment::DEND = 3 [static]

Referenced by figureOutType().

double SwcSegment::electrotonicDistanceFromSoma_ [protected]

electrotonic dist from soma, summed along dend.

Referenced by getElecDistFromSoma(), and setCumulativeDistance().

const short SwcSegment::END = 6 [static]

Referenced by figureOutType().

const short SwcSegment::FORK = 5 [static]

Referenced by figureOutType().

double SwcSegment::geometricalDistanceFromSoma_ [protected]

geometrical distance from soma.

Referenced by getGeomDistFromSoma(), and setGeometricalDistanceFromSoma().

vector< int > SwcSegment::kids_ [protected]

Referenced by addChild(), figureOutType(), kids(), and replaceKids().

double SwcSegment::L_ [protected]

Length of segment.

Referenced by L(), and setCumulativeDistance().

double SwcSegment::length_ [protected]

Radius of segment.

Referenced by length(), and setCumulativeDistance().

unsigned int SwcSegment::myIndex_ [protected]

Referenced by myIndex().

unsigned int SwcSegment::parent_ [protected]

Number of length constants in segment.

Referenced by parent(), setParent(), and SwcSegment().

double SwcSegment::pathDistanceFromSoma_ [protected]

Index of parent. Is ~0 for soma.

dist from soma: not direct, but threaded along dend

Referenced by getPathDistFromSoma(), and setCumulativeDistance().

double SwcSegment::radius_ [protected]

coordinates of end of segment

Referenced by radius().

const short SwcSegment::SOMA = 1 [static]

Referenced by figureOutType().

short SwcSegment::type_ [protected]

Index of self.

The type of the segment is supposedly as below for SWC files. Seems to be honored in the breach in actual files. 0 = undefined 1 = soma 2 = axon 3 = dendrite 4 = apical dendrite 5 = fork point 6 = end point 7 = custom

Referenced by figureOutType(), OK(), setBad(), and type().

const string SwcSegment::typeName [static]

Initial value:

 { 
    "undef", "soma", "axon", "dend", "apical", "dend_f", "dend_e", 
    "custom", "bad", "undef",
    "axon_f", "axon_e", "apical_f", "apical_e" }

Referenced by ReadSwc::diagnostics().

const short SwcSegment::UNDEF = 0 [static]

Referenced by OK().

Vec SwcSegment::v_ [protected]

Referenced by distance(), setGeometricalDistanceFromSoma(), and vec().

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

biophysics/SwcSegment.h
biophysics/SwcSegment.cpp

SwcSegment Class Reference

Public Member Functions

Static Public Attributes

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation