#include <SwcSegment.h>

Inheritance diagram for SwcSegment:

Collaboration diagram for SwcSegment:

Public Member Functions
void	addChild (unsigned int kid)

double	distance (const SwcSegment &other) const

void	figureOutType ()

double	getElecDistFromSoma () const

double	getGeomDistFromSoma () const

double	getPathDistFromSoma () const

const vector< int > &	kids () const

double	L () const

double	length () const

unsigned int	myIndex () const

bool	OK () const

unsigned int	parent () const

double	radius () const

void	replaceKids (const vector< int > &kids)

void	setBad ()

void	setCumulativeDistance (double len, double L, double pSoma, double eSoma)

void	setGeometricalDistanceFromSoma (const SwcSegment &soma)

void	setParent (unsigned int pa)

	SwcSegment ()

	SwcSegment (const string &line)

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

unsigned short	type () const

const Vec &	vec () const

Static Public Attributes
static const short	APICAL = 4

static const short	APICAL_END = 13

static const short	APICAL_FORK = 12

static const short	AXON = 2

static const short	AXON_END = 11

static const short	AXON_FORK = 10

static const short	BadSegment = 8

static const short	CUSTOM = 7

static const short	DEND = 3

static const short	END = 6

static const short	FORK = 5

static const short	SOMA = 1

static const string	typeName []

static const short	UNDEF = 0

Protected Attributes
double	electrotonicDistanceFromSoma_
	electrotonic dist from soma, summed along dend. More...

double	geometricalDistanceFromSoma_
	geometrical distance from soma. More...

vector< int >	kids_

double	L_
	Length of segment. More...

double	length_
	Radius of segment. More...

unsigned int	myIndex_

unsigned int	parent_
	Number of length constants in segment. More...

double	pathDistanceFromSoma_
	Index of parent. Is ~0 for soma. More...

double	radius_
	coordinates of end of segment More...

short	type_
	Index of self. More...

Vec	v_

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.

Definition at line 18 of file SwcSegment.h.

Constructor & Destructor Documentation

SwcSegment::SwcSegment ( )

inline

Definition at line 21 of file SwcSegment.h.

                 : myIndex_( 0 ), type_( 0 ), radius_( 0.0 ),
                 length_( 0.0 ), L_( 0.0 ),
                 parent_( ~0U ),
                 geometricalDistanceFromSoma_( 0.0 ),
                 electrotonicDistanceFromSoma_( 0.0 )
         {;}

SwcSegment::SwcSegment ( const string & line )

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

Definition at line 69 of file SwcSegment.cpp.

References parent(), and parent_.

                 :
                         myIndex_( i ),
                         type_( type ),
                         v_( x, y, z ),
                         radius_( r ),
                         length_( 0.0 ),
                         L_( 0.0 ),
                         geometricalDistanceFromSoma_( 0.0 ),
                         electrotonicDistanceFromSoma_( 0.0 )
 {
     if ( parent >= 0 )
         parent_ = parent;
     else
         parent_ = ~0U;
 }

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Member Function Documentation

void SwcSegment::addChild ( unsigned int kid )

inline

Definition at line 56 of file SwcSegment.h.

References kids_.

                                           {
             kids_.push_back( kid );
         }

double SwcSegment::distance ( const SwcSegment & other ) const

inline

Definition at line 87 of file SwcSegment.h.

References Vec::distance(), and v_.

Referenced by ReadSwc::cleanZeroLength(), makeCompt(), ReadSwc::traverseBranch(), and traverseCumulativeDistance().

                                                           {
             return v_.distance( other.v_ );
         }

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void SwcSegment::figureOutType ( )

Definition at line 88 of file SwcSegment.cpp.

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

 {
     if ( type_ == SOMA ) // already defined as soma
         return;
     if ( type_ == DEND ) {
         if ( kids_.size() > 1 )
             type_ = FORK; // Dend fork point
         else if ( kids_.size() == 0 )
             type_ = END; // end point
     } else if ( type_ == APICAL ) {
         if ( kids_.size() > 1 )
             type_ = APICAL_FORK; // apical Dend fork point
         else if ( kids_.size() == 0 )
             type_ = APICAL_END; // apical end point
     } else if ( type_ == AXON ) {
         if ( kids_.size() > 1 )
             type_ = AXON_FORK; // apical Dend fork point
         else if ( kids_.size() == 0 )
             type_ = AXON_END; // apical end point
     }
 }

double SwcSegment::getElecDistFromSoma ( ) const

inline

Definition at line 117 of file SwcSegment.h.

References electrotonicDistanceFromSoma_.

                                             {
             return electrotonicDistanceFromSoma_;
         }

double SwcSegment::getGeomDistFromSoma ( ) const

inline

Definition at line 113 of file SwcSegment.h.

References geometricalDistanceFromSoma_.

                                             {
             return geometricalDistanceFromSoma_;
         }

double SwcSegment::getPathDistFromSoma ( ) const

inline

Definition at line 109 of file SwcSegment.h.

References pathDistanceFromSoma_.

                                             {
             return pathDistanceFromSoma_;
         }

const vector< int >& SwcSegment::kids ( ) const

inline

Definition at line 62 of file SwcSegment.h.

References kids_.

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

         {
             return kids_;
         }

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double SwcSegment::L ( ) const

inline

Definition at line 83 of file SwcSegment.h.

References L_.

Referenced by setCumulativeDistance(), and ReadSwc::traverseBranch().

                          {
             return L_;
         }

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double SwcSegment::length ( ) const

inline

Definition at line 79 of file SwcSegment.h.

References length_.

                               {
             return length_;
         }

unsigned int SwcSegment::myIndex ( ) const

inline

Definition at line 52 of file SwcSegment.h.

References myIndex_.

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

                                      {
             return myIndex_;
         }

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bool SwcSegment::OK ( ) const

inline

Definition at line 34 of file SwcSegment.h.

References BadSegment, CUSTOM, type_, and UNDEF.

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

         {
             return type_!=BadSegment && type_!=UNDEF && type_!=CUSTOM;
         }

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unsigned int SwcSegment::parent ( ) const

inline

Definition at line 44 of file SwcSegment.h.

References parent_.

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

                                     {
             return parent_;
         }

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double SwcSegment::radius ( ) const

inline

Definition at line 76 of file SwcSegment.h.

References radius_.

Referenced by makeCompt(), ReadSwc::traverseBranch(), and ReadSwc::validate().

                               {
             return radius_;
         }

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

inline

Definition at line 67 of file SwcSegment.h.

References kids(), and kids_.

Referenced by ReadSwc::cleanZeroLength().

         {
             kids_ = kids;
         }

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void SwcSegment::setBad ( )

inline

Definition at line 39 of file SwcSegment.h.

References BadSegment, and type_.

Referenced by ReadSwc::cleanZeroLength().

                       {
             type_ = BadSegment;
         }

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void SwcSegment::setCumulativeDistance	(	double	len,
		double	L,
		double	pSoma,
		double	eSoma
	)

inline

Definition at line 100 of file SwcSegment.h.

References electrotonicDistanceFromSoma_, L(), L_, length_, and pathDistanceFromSoma_.

         {
             length_ = len;
             L_ = L;
             pathDistanceFromSoma_ = pSoma;
             electrotonicDistanceFromSoma_ = eSoma;
         }

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void SwcSegment::setGeometricalDistanceFromSoma ( const SwcSegment & soma )

inline

Definition at line 95 of file SwcSegment.h.

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

         {
             geometricalDistanceFromSoma_ = v_.distance( soma.v_ );
         }

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void SwcSegment::setParent ( unsigned int pa )

inline

Definition at line 48 of file SwcSegment.h.

References parent_.

Referenced by ReadSwc::cleanZeroLength().

                                           {
             parent_ = pa;
         }

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unsigned short SwcSegment::type ( ) const

inline

Definition at line 72 of file SwcSegment.h.

References type_.

Referenced by ReadSwc::diagnostics(), and makeCompt().

                                     {
             return type_;
         }

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const Vec& SwcSegment::vec ( ) const

inline

Definition at line 91 of file SwcSegment.h.

References v_.

Referenced by makeCompt().

                                {
             return v_;
         }

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Member Data Documentation

const short SwcSegment::APICAL = 4

static

Definition at line 126 of file SwcSegment.h.

Referenced by figureOutType().

const short SwcSegment::APICAL_END = 13

static

Definition at line 135 of file SwcSegment.h.

Referenced by figureOutType().

const short SwcSegment::APICAL_FORK = 12

static

Definition at line 134 of file SwcSegment.h.

Referenced by figureOutType().

const short SwcSegment::AXON = 2

static

Definition at line 124 of file SwcSegment.h.

Referenced by figureOutType().

const short SwcSegment::AXON_END = 11

static

Definition at line 133 of file SwcSegment.h.

Referenced by figureOutType().

const short SwcSegment::AXON_FORK = 10

static

Definition at line 132 of file SwcSegment.h.

Referenced by figureOutType().

const short SwcSegment::BadSegment = 8

static

Definition at line 131 of file SwcSegment.h.

Referenced by OK(), and setBad().

const short SwcSegment::CUSTOM = 7

static

Definition at line 129 of file SwcSegment.h.

Referenced by OK().

const short SwcSegment::DEND = 3

static

Definition at line 125 of file SwcSegment.h.

Referenced by figureOutType().

double SwcSegment::electrotonicDistanceFromSoma_

protected

electrotonic dist from soma, summed along dend.

Definition at line 167 of file SwcSegment.h.

Referenced by getElecDistFromSoma(), and setCumulativeDistance().

const short SwcSegment::END = 6

static

Definition at line 128 of file SwcSegment.h.

Referenced by figureOutType().

const short SwcSegment::FORK = 5

static

Definition at line 127 of file SwcSegment.h.

Referenced by figureOutType().

double SwcSegment::geometricalDistanceFromSoma_

protected

geometrical distance from soma.

Definition at line 164 of file SwcSegment.h.

Referenced by getGeomDistFromSoma(), and setGeometricalDistanceFromSoma().

vector< int > SwcSegment::kids_

protected

Definition at line 169 of file SwcSegment.h.

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

double SwcSegment::L_

protected

Length of segment.

Definition at line 157 of file SwcSegment.h.

Referenced by L(), and setCumulativeDistance().

double SwcSegment::length_

protected

Radius of segment.

Definition at line 156 of file SwcSegment.h.

Referenced by length(), and setCumulativeDistance().

unsigned int SwcSegment::myIndex_

protected

Definition at line 140 of file SwcSegment.h.

Referenced by myIndex(), and SwcBranch::SwcBranch().

unsigned int SwcSegment::parent_

protected

Number of length constants in segment.

Definition at line 158 of file SwcSegment.h.

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

double SwcSegment::pathDistanceFromSoma_

protected

Index of parent. Is ~0 for soma.

dist from soma: not direct, but threaded along dend

Definition at line 161 of file SwcSegment.h.

Referenced by getPathDistFromSoma(), and setCumulativeDistance().

double SwcSegment::radius_

protected

coordinates of end of segment

Definition at line 155 of file SwcSegment.h.

Referenced by radius().

const short SwcSegment::SOMA = 1

static

Definition at line 123 of file SwcSegment.h.

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

Definition at line 153 of file SwcSegment.h.

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" }

Definition at line 137 of file SwcSegment.h.

Referenced by ReadSwc::diagnostics(), and makeCompt().

const short SwcSegment::UNDEF = 0

static

Definition at line 122 of file SwcSegment.h.

Referenced by OK().

Vec SwcSegment::v_

protected

Definition at line 154 of file SwcSegment.h.

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

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

moose-core/biophysics/SwcSegment.h
moose-core/biophysics/SwcSegment.cpp

Public Member Functions

Static Public Attributes

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation