#include <RootCellAnalyzing.hpp>

Public Member Functions
	RootCellAnalyzing (CellAtlasAttr cellAtlasAttr, CellAtlasConfigAttr cellAtlasConfigAttr)

bool	analyzeCells (std::vector< int > &uniqueLabels, const vvGraph &segmentedMesh, const vvGraph &surfaceMesh, std::map< int, Point3d > &bMap, std::map< int, Point3d > &diffbMap, labelVertexMap &lvMap, RootCellProcessing &rcp, int firstLabel, double minVolume)

void	analyzeBezierGrid (std::vector< int > &uniqueLabels, std::map< int, Point3d > &cellCentroids, std::vector< std::vector< Point3d > > &bezier, std::map< int, Point3d > &nearestPoints, std::map< int, Point2i > &nearestIndex)

void	analyzeSurface (std::vector< int > &uniqueLabels, std::map< int, Point3d > &cellCentroids, const vvGraph &surfaceMesh, std::map< int, Point3d > &nearestSurfacePoints)

bool	createCartesianCoordSystem (RootCellProcessing &rcp)

bool	createLayerCoordSystem (const vvGraph &surfaceMesh, std::vector< std::vector< Point3d > > &bezier, RootCellProcessing &rcp)

bool	createRootCoordSystem (const vvGraph &surfaceMesh, std::map< int, Point3d > &bMap, std::map< int, Point3d > &diffbMap, RootCellProcessing &rcp)

bool	analyzeEmbryo (std::vector< int > &uniqueLabels, const vvGraph &segmentedMesh, const vvGraph &surfaceMesh, std::vector< std::vector< Point3d > > &bezGrid, std::map< int, Point3d > &bMap, std::map< int, Point3d > &diffbMap, labelVertexMap &lvMap, RootCellProcessing &rootDataBox, int firstLabel, double minVolume, QString mode)

bool	generateLabelTriangleMap (int numCells, std::vector< int > &uniqueLabels, const vvGraph &segmentedMesh, labelVertexMap &lvMap, std::map< int, triVector > &cellTriangles)

void	analyzeBezierLine (std::vector< int > &uniqueLabels, std::map< int, Point3d > &cellCentroids, std::map< int, Point3d > &bMap, std::map< int, Point3d > &diffbMap, bool flipBezier=false)

bool	analyzeCellCalcDisSurface (RootCellProcessing &rcp, const vvGraph &surfaceMesh, bool checkArc, std::map< int, double > &surfaceArclengths, std::map< int, double > &surfaceRadialDis, std::map< int, Point3d > &bMap, bool considerOrientation=false)

bool	analyzeCellCentroidsVolumes (std::map< int, triVector > &cellTriangles, RootCellProcessing &rcp, double minVolume)

bool	analyzeCellCentroids2D (std::map< int, triVector > &cellTriangles, RootCellProcessing &rcp)

void	calcCircumferentialEqual (std::vector< int > &uniqueLabels, std::map< int, Point3d > &cellCentroids)

void	writeDataFields (RootCellProcessing &rcp)

void	calcSimpleRadial (std::vector< int > &uniqueLabels, RootCellProcessing &rcp, std::map< int, Point3d > &cellCentroids)

void	calcCoordSystemCartesian (std::vector< int > &uniqueLabels)

void	calcCoordSystem (std::vector< int > &uniqueLabels, std::map< int, Point3d > &diffBezInterp, std::map< int, Point3d > &dirRad, std::map< int, Point3d > &dirLong, std::map< int, Point3d > &dirCirc)

void	createCoordSystem (std::vector< Point3d > &points, RootCellProcessing &rcp, std::map< int, Point3d > &bMap, std::map< int, Point3d > &diffbMap, std::map< int, Point3d > &bMapRadRef)

void	minMaxToBezierPerCell (vvGraph &S, std::vector< int > &uniqueLabels, std::map< int, Point3d > &bMap, bool flipBezier=false)

Point3d	organToCartesianCoords (Point3d organCoords, primDataStructure &p1)

Point3d	cartesianToOrganCoords (Point3d cartesianCoords, primDataStructure p1)

bool	generateMeshTriangleVector (const vvGraph &S, triVector &triVec)

Point3d	organToCartesianCoordsWithMap (Point3d organCoords, primDataStructure &p1)

void	generateSurfaceMap (primDataStructure &p1)

void	estimateAllCellLengths (RootCellProcessing &rcp, std::map< int, triVector > &cellTriangles)

Public Attributes
CellAtlasAttr *	data

CellAtlasConfigAttr *	config

std::map< int, double >	arclengths

std::map< int, double >	arclengthsUM

std::map< int, double >	arclengthsMinUM

std::map< int, double >	arclengthsMaxUM

std::map< int, Point3d >	diffBezInterp

std::map< int, Point3d >	bezInterp

std::map< int, double >	azimCoord

std::map< int, double >	radialDis

std::map< int, double >	scaledRadialDis

std::map< int, double >	outsideWallArea

std::map< int, double >	nrNeighbors

double	bezLength

std::map< int, Point3d >	cellCentroids

std::vector< int >	uniqueLabels

std::map< int, double >	lengthLong

std::map< int, double >	lengthRad

std::map< int, double >	lengthCirc

std::map< int, Point3d >	dirRad

std::map< int, Point3d >	dirLong

std::map< int, Point3d >	dirCirc

int	firstLabel

Point3d	firstLong

Point3d	firstRad

std::map< std::pair< int, int >, double >	surfaceMap

Static Public Attributes
static const int	radRes

Detailed Description

Definition at line 30 of file RootCellAnalyzing.hpp.

Constructor & Destructor Documentation

◆ RootCellAnalyzing()

mgx::RootCellAnalyzing::RootCellAnalyzing	(	CellAtlasAttr *	cellAtlasAttr,
		CellAtlasConfigAttr *	cellAtlasConfigAttr
	)

inline

Definition at line 60 of file RootCellAnalyzing.hpp.

Member Function Documentation

◆ analyzeBezierGrid()

void mgx::RootCellAnalyzing::analyzeBezierGrid	(	std::vector< int > &	uniqueLabels,
		std::map< int, Point3d > &	cellCentroids,
		std::vector< std::vector< Point3d > > &	bezier,
		std::map< int, Point3d > &	nearestPoints,
		std::map< int, Point2i > &	nearestIndex
	)

◆ analyzeBezierLine()

void mgx::RootCellAnalyzing::analyzeBezierLine	(	std::vector< int > &	uniqueLabels,
		std::map< int, Point3d > &	cellCentroids,
		std::map< int, Point3d > &	bMap,
		std::map< int, Point3d > &	diffbMap,
		bool	flipBezier = `false`
	)

◆ analyzeCellCalcDisSurface()

bool mgx::RootCellAnalyzing::analyzeCellCalcDisSurface	(	RootCellProcessing &	rcp,
		const vvGraph &	surfaceMesh,
		bool	checkArc,
		std::map< int, double > &	surfaceArclengths,
		std::map< int, double > &	surfaceRadialDis,
		std::map< int, Point3d > &	bMap,
		bool	considerOrientation = `false`
	)

◆ analyzeCellCentroids2D()

bool mgx::RootCellAnalyzing::analyzeCellCentroids2D	(	std::map< int, triVector > &	cellTriangles,
		RootCellProcessing &	rcp
	)

◆ analyzeCellCentroidsVolumes()

bool mgx::RootCellAnalyzing::analyzeCellCentroidsVolumes	(	std::map< int, triVector > &	cellTriangles,
		RootCellProcessing &	rcp,
		double	minVolume
	)

◆ analyzeCells()

bool mgx::RootCellAnalyzing::analyzeCells	(	std::vector< int > &	uniqueLabels,
		const vvGraph &	segmentedMesh,
		const vvGraph &	surfaceMesh,
		std::map< int, Point3d > &	bMap,
		std::map< int, Point3d > &	diffbMap,
		labelVertexMap &	lvMap,
		RootCellProcessing &	rcp,
		int	firstLabel,
		double	minVolume
	)

◆ analyzeEmbryo()

bool mgx::RootCellAnalyzing::analyzeEmbryo	(	std::vector< int > &	uniqueLabels,
		const vvGraph &	segmentedMesh,
		const vvGraph &	surfaceMesh,
		std::vector< std::vector< Point3d > > &	bezGrid,
		std::map< int, Point3d > &	bMap,
		std::map< int, Point3d > &	diffbMap,
		labelVertexMap &	lvMap,
		RootCellProcessing &	rootDataBox,
		int	firstLabel,
		double	minVolume,
		QString	mode
	)

◆ analyzeSurface()

void mgx::RootCellAnalyzing::analyzeSurface	(	std::vector< int > &	uniqueLabels,
		std::map< int, Point3d > &	cellCentroids,
		const vvGraph &	surfaceMesh,
		std::map< int, Point3d > &	nearestSurfacePoints
	)

◆ calcCircumferentialEqual()

void mgx::RootCellAnalyzing::calcCircumferentialEqual	(	std::vector< int > &	uniqueLabels,
		std::map< int, Point3d > &	cellCentroids
	)

◆ calcCoordSystem()

void mgx::RootCellAnalyzing::calcCoordSystem	(	std::vector< int > &	uniqueLabels,
		std::map< int, Point3d > &	diffBezInterp,
		std::map< int, Point3d > &	dirRad,
		std::map< int, Point3d > &	dirLong,
		std::map< int, Point3d > &	dirCirc
	)

◆ calcCoordSystemCartesian()

void mgx::RootCellAnalyzing::calcCoordSystemCartesian ( std::vector< int > & uniqueLabels )

◆ calcSimpleRadial()

void mgx::RootCellAnalyzing::calcSimpleRadial	(	std::vector< int > &	uniqueLabels,
		RootCellProcessing &	rcp,
		std::map< int, Point3d > &	cellCentroids
	)

◆ cartesianToOrganCoords()

Point3d mgx::RootCellAnalyzing::cartesianToOrganCoords	(	Point3d	cartesianCoords,
		primDataStructure	p1
	)

◆ createCartesianCoordSystem()

bool mgx::RootCellAnalyzing::createCartesianCoordSystem ( RootCellProcessing & rcp )

◆ createCoordSystem()

void mgx::RootCellAnalyzing::createCoordSystem	(	std::vector< Point3d > &	points,
		RootCellProcessing &	rcp,
		std::map< int, Point3d > &	bMap,
		std::map< int, Point3d > &	diffbMap,
		std::map< int, Point3d > &	bMapRadRef
	)

◆ createLayerCoordSystem()

bool mgx::RootCellAnalyzing::createLayerCoordSystem	(	const vvGraph &	surfaceMesh,
		std::vector< std::vector< Point3d > > &	bezier,
		RootCellProcessing &	rcp
	)

◆ createRootCoordSystem()

bool mgx::RootCellAnalyzing::createRootCoordSystem	(	const vvGraph &	surfaceMesh,
		std::map< int, Point3d > &	bMap,
		std::map< int, Point3d > &	diffbMap,
		RootCellProcessing &	rcp
	)

◆ estimateAllCellLengths()

void mgx::RootCellAnalyzing::estimateAllCellLengths	(	RootCellProcessing &	rcp,
		std::map< int, triVector > &	cellTriangles
	)

◆ generateLabelTriangleMap()

bool mgx::RootCellAnalyzing::generateLabelTriangleMap	(	int	numCells,
		std::vector< int > &	uniqueLabels,
		const vvGraph &	segmentedMesh,
		labelVertexMap &	lvMap,
		std::map< int, triVector > &	cellTriangles
	)

◆ generateMeshTriangleVector()

bool mgx::RootCellAnalyzing::generateMeshTriangleVector	(	const vvGraph &	S,
		triVector &	triVec
	)

◆ generateSurfaceMap()

void mgx::RootCellAnalyzing::generateSurfaceMap ( primDataStructure & p1 )

◆ minMaxToBezierPerCell()

void mgx::RootCellAnalyzing::minMaxToBezierPerCell	(	vvGraph &	S,
		std::vector< int > &	uniqueLabels,
		std::map< int, Point3d > &	bMap,
		bool	flipBezier = `false`
	)

◆ organToCartesianCoords()

Point3d mgx::RootCellAnalyzing::organToCartesianCoords	(	Point3d	organCoords,
		primDataStructure &	p1
	)

◆ organToCartesianCoordsWithMap()

Point3d mgx::RootCellAnalyzing::organToCartesianCoordsWithMap	(	Point3d	organCoords,
		primDataStructure &	p1
	)

◆ writeDataFields()

void mgx::RootCellAnalyzing::writeDataFields ( RootCellProcessing & rcp )

Member Data Documentation

◆ arclengths

std::map<int,double> mgx::RootCellAnalyzing::arclengths

Definition at line 37 of file RootCellAnalyzing.hpp.

◆ arclengthsMaxUM

std::map<int,double> mgx::RootCellAnalyzing::arclengthsMaxUM

Definition at line 40 of file RootCellAnalyzing.hpp.

◆ arclengthsMinUM

std::map<int,double> mgx::RootCellAnalyzing::arclengthsMinUM

Definition at line 39 of file RootCellAnalyzing.hpp.

◆ arclengthsUM

std::map<int,double> mgx::RootCellAnalyzing::arclengthsUM

Definition at line 38 of file RootCellAnalyzing.hpp.

◆ azimCoord

std::map<int,double> mgx::RootCellAnalyzing::azimCoord

Definition at line 43 of file RootCellAnalyzing.hpp.

◆ bezInterp

std::map<int,Point3d> mgx::RootCellAnalyzing::bezInterp

Definition at line 42 of file RootCellAnalyzing.hpp.

◆ bezLength

double mgx::RootCellAnalyzing::bezLength

Definition at line 45 of file RootCellAnalyzing.hpp.

◆ cellCentroids

std::map<int,Point3d> mgx::RootCellAnalyzing::cellCentroids

Definition at line 47 of file RootCellAnalyzing.hpp.

◆ config

CellAtlasConfigAttr* mgx::RootCellAnalyzing::config

Definition at line 35 of file RootCellAnalyzing.hpp.

◆ data

CellAtlasAttr* mgx::RootCellAnalyzing::data

Definition at line 34 of file RootCellAnalyzing.hpp.

◆ diffBezInterp

std::map<int,Point3d> mgx::RootCellAnalyzing::diffBezInterp

Definition at line 41 of file RootCellAnalyzing.hpp.

◆ dirCirc

std::map<int, Point3d> mgx::RootCellAnalyzing::dirCirc

Definition at line 51 of file RootCellAnalyzing.hpp.

◆ dirLong

std::map<int, Point3d> mgx::RootCellAnalyzing::dirLong

Definition at line 51 of file RootCellAnalyzing.hpp.

◆ dirRad

std::map<int, Point3d> mgx::RootCellAnalyzing::dirRad

Definition at line 51 of file RootCellAnalyzing.hpp.

◆ firstLabel

int mgx::RootCellAnalyzing::firstLabel

Definition at line 53 of file RootCellAnalyzing.hpp.

◆ firstLong

Point3d mgx::RootCellAnalyzing::firstLong

Definition at line 54 of file RootCellAnalyzing.hpp.

◆ firstRad

Point3d mgx::RootCellAnalyzing::firstRad

Definition at line 55 of file RootCellAnalyzing.hpp.

◆ lengthCirc

std::map<int,double> mgx::RootCellAnalyzing::lengthCirc

Definition at line 50 of file RootCellAnalyzing.hpp.

◆ lengthLong

std::map<int,double> mgx::RootCellAnalyzing::lengthLong

Definition at line 50 of file RootCellAnalyzing.hpp.

◆ lengthRad

std::map<int,double> mgx::RootCellAnalyzing::lengthRad

Definition at line 50 of file RootCellAnalyzing.hpp.

◆ nrNeighbors

std::map<int,double> mgx::RootCellAnalyzing::nrNeighbors

Definition at line 43 of file RootCellAnalyzing.hpp.

◆ outsideWallArea

std::map<int,double> mgx::RootCellAnalyzing::outsideWallArea

Definition at line 43 of file RootCellAnalyzing.hpp.

◆ radialDis

std::map<int,double> mgx::RootCellAnalyzing::radialDis

Definition at line 43 of file RootCellAnalyzing.hpp.

◆ radRes

const int mgx::RootCellAnalyzing::radRes

static

Definition at line 57 of file RootCellAnalyzing.hpp.

◆ scaledRadialDis

std::map<int,double> mgx::RootCellAnalyzing::scaledRadialDis

Definition at line 43 of file RootCellAnalyzing.hpp.

◆ surfaceMap

std::map<std::pair<int,int>, double> mgx::RootCellAnalyzing::surfaceMap

Definition at line 58 of file RootCellAnalyzing.hpp.

◆ uniqueLabels

std::vector<int> mgx::RootCellAnalyzing::uniqueLabels

Definition at line 48 of file RootCellAnalyzing.hpp.

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

AddOns/CellAtlas/RootCellAnalyzing.hpp

Public Member Functions

Public Attributes

Static Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ RootCellAnalyzing()

Member Function Documentation

◆ analyzeBezierGrid()

◆ analyzeBezierLine()

◆ analyzeCellCalcDisSurface()

◆ analyzeCellCentroids2D()

◆ analyzeCellCentroidsVolumes()

◆ analyzeCells()

◆ analyzeEmbryo()

◆ analyzeSurface()

◆ calcCircumferentialEqual()

◆ calcCoordSystem()

◆ calcCoordSystemCartesian()

◆ calcSimpleRadial()

◆ cartesianToOrganCoords()

◆ createCartesianCoordSystem()

◆ createCoordSystem()

◆ createLayerCoordSystem()

◆ createRootCoordSystem()

◆ estimateAllCellLengths()

◆ generateLabelTriangleMap()

◆ generateMeshTriangleVector()

◆ generateSurfaceMap()

◆ minMaxToBezierPerCell()

◆ organToCartesianCoords()

◆ organToCartesianCoordsWithMap()

◆ writeDataFields()

Member Data Documentation

◆ arclengths

◆ arclengthsMaxUM

◆ arclengthsMinUM

◆ arclengthsUM

◆ azimCoord

◆ bezInterp

◆ bezLength

◆ cellCentroids

◆ config

◆ data

◆ diffBezInterp

◆ dirCirc

◆ dirLong

◆ dirRad

◆ firstLabel

◆ firstLong

◆ firstRad

◆ lengthCirc

◆ lengthLong

◆ lengthRad

◆ nrNeighbors

◆ outsideWallArea

◆ radialDis

◆ radRes

◆ scaledRadialDis

◆ surfaceMap

◆ uniqueLabels