TTK processing package that computes the contour tree of scalar data and more (data segmentation, topological simplification, persistence diagrams, persistence curves, etc.). More...

#include <ContourTree.h>

Inheritance diagram for ttk::ContourTree:

Public Member Functions
	ContourTree ()

int	build ()

const SubLevelSetTree *	getMergeTree () const

int	getPersistencePairs (std::vector< std::pair< std::pair< int, int >, double > > &pairs, std::vector< std::pair< std::pair< int, int >, double > > mergePairs=nullptr, std::vector< std::pair< std::pair< int, int >, double > > splitPairs=nullptr) const override

int	getPersistencePlot (std::vector< std::pair< double, int > > &plot, std::vector< std::pair< std::pair< int, int >, double > > mergePairs=nullptr, std::vector< std::pair< std::pair< int, int >, double > > splitPairs=nullptr, std::vector< std::pair< std::pair< int, int >, double > > *pairs=nullptr) const

int	getPersistenceDiagram (std::vector< std::pair< double, double > > &diagram, std::vector< std::pair< std::pair< int, int >, double > > mergePairs=nullptr, std::vector< std::pair< std::pair< int, int >, double > > splitPairs=nullptr, std::vector< std::pair< std::pair< int, int >, double > > *pairs=nullptr) const

const SubLevelSetTree *	getSplitTree () const

int	maintainRegularVertices (const bool &onOff) override

int	setVertexNeighbors (const std::vector< std::vector< int > > *vertexNeighbors)

int	setVertexNeighbors (const int &vertexId, const std::vector< int > &neighborList)

int	computeSkeleton (unsigned int arcResolution=3) override

int	smoothSkeleton (unsigned int skeletonSmoothing) override

int	clearSkeleton () override

int	simplify (const double &simplificationThreshold, ContourTreeSimplificationMetric *metric=nullptr) override

Public Member Functions inherited from ttk::SubLevelSetTree
	SubLevelSetTree ()

int	build ()

int	buildExtremumList (std::vector< int > &extremumList, const bool &isSubLevelSet=true)

bool	buildPlanarLayout (const double &scaleX, const double &scaleY)

int	buildSaddleList (std::vector< int > &vertexList) const

int	clearArc (const int &vertexId0, const int &vertexId1)

int	clearRegularNode (const int &vertexId)

int	clearRoot (const int &vertexId)

int	exportPersistenceCurve (const std::string &fileName="output.plot") const

int	exportPersistenceDiagram (const std::string &fileName="output.plot") const

int	exportToSvg (const std::string &fileName, const double &scaleX=1, const double &scaleY=1)

int	exportToVtk (const std::string &fileName, const std::vector< float > origin=nullptr, const std::vector< float > voxelSize=nullptr)

int	flush ()

const Arc *	getArc (const int &arcId) const

const std::vector< int > *	getExtremumList () const

const Node *	getNode (const int &nodeId) const

const Node *	getNodeDownNeighbor (const Node *n, const int &neighborId) const

const Node *	getNodeDownNeighbor (const int &nodeId, const int &neighborId) const

const Node *	getNodeUpNeighbor (const Node *n, const int &neighborId) const

const Node *	getNodeUpNeighbor (const int &nodeId, const int &neighborId) const

double	getNodeScalar (const int &nodeId) const

int	getNumberOfArcs () const

int	getNumberOfSuperArcs () const

int	getNumberOfNodes () const

int	getPersistenceDiagram (std::vector< std::pair< double, double > > &diagram, std::vector< std::pair< std::pair< int, int >, double > > *pairs=nullptr) const

virtual int	getPersistencePairs (std::vector< std::pair< std::pair< int, int >, double > > &pairs, std::vector< std::pair< std::pair< int, int >, double > > mergePairs=nullptr, std::vector< std::pair< std::pair< int, int >, double > > splitPairs=nullptr) const

int	getPersistencePlot (std::vector< std::pair< double, int > > &plot, std::vector< std::pair< std::pair< int, int >, double > > *persistencePairs=nullptr) const

const SuperArc *	getSuperArc (const int &superArcId) const

int	getVertexScalar (const int &vertexId, double &scalar)

const SuperArc *	getVertexSuperArc (const int &vertexId) const

int	getVertexSuperArcId (const int &vertexId) const

const Node *	getVertexNode (const int &vertexId) const

int	getVertexNodeId (const int &vertexId) const

bool	isJoinTree () const

bool	isSplitTree () const

bool	isSosLowerThan (const int &vertexId0, const int &vertexId1) const

bool	isSosHigherThan (const int &vertexId0, const int &vertexId1) const

virtual int	maintainRegularVertices (const bool &onOff)

int	moveRegularNode (const Node n, const Node oldDown, const Node oldUp, const Node newDown, const Node *newUp)

int	print () const

void	setMaximumList (std::vector< int > &maximumList)

void	setMinimumList (std::vector< int > &minimumList)

void	setNumberOfVertices (const int &vertexNumber)

void	setTriangulation (const AbstractTriangulation *const triangulation)

void	setVertexPositions (std::vector< std::vector< double > > *vertexPositions)

void	setVertexScalars (const std::vector< real > *const vertexScalars)

void	setVertexSoSoffsets (std::vector< int > *vertexSoSoffsets)

virtual int	simplify (const double &simplificationThreshold, ContourTreeSimplificationMetric *metric=nullptr)

int	sample (unsigned int samplingLevel=3)

int	computeBarycenters ()

int	getSkeletonScalars (const std::vector< double > &scalars, std::vector< std::vector< double > > &skeletonScalars) const

virtual int	computeSkeleton (unsigned int arcResolution=3)

virtual int	smoothSkeleton (unsigned int skeletonSmoothing)

virtual int	clearSkeleton ()

Public Member Functions inherited from ttk::Debug
	Debug ()

	~Debug () override

virtual int	setDebugLevel (const int &debugLevel)

int	setWrapper (const Wrapper *wrapper) override

int	printMsg (const std::string &msg, const debug::Priority &priority=debug::Priority::INFO, const debug::LineMode &lineMode=debug::LineMode::NEW, std::ostream &stream=std::cout) const

int	printMsg (const std::vector< std::string > &msgs, const debug::Priority &priority=debug::Priority::INFO, const debug::LineMode &lineMode=debug::LineMode::NEW, std::ostream &stream=std::cout) const

int	printErr (const std::string &msg, const debug::LineMode &lineMode=debug::LineMode::NEW, std::ostream &stream=std::cerr) const

int	printWrn (const std::string &msg, const debug::LineMode &lineMode=debug::LineMode::NEW, std::ostream &stream=std::cerr) const

int	printMsg (const std::string &msg, const double &progress, const double &time, const int &threads, const double &memory, const debug::LineMode &lineMode=debug::LineMode::NEW, const debug::Priority &priority=debug::Priority::PERFORMANCE, std::ostream &stream=std::cout) const

int	printMsg (const std::string &msg, const double &progress, const double &time, const debug::LineMode &lineMode=debug::LineMode::NEW, const debug::Priority &priority=debug::Priority::PERFORMANCE, std::ostream &stream=std::cout) const

int	printMsg (const std::string &msg, const double &progress, const double &time, const int &threads, const debug::LineMode &lineMode=debug::LineMode::NEW, const debug::Priority &priority=debug::Priority::PERFORMANCE, std::ostream &stream=std::cout) const

int	printMsg (const std::string &msg, const double &progress, const debug::LineMode &lineMode=debug::LineMode::NEW, const debug::Priority &priority=debug::Priority::PERFORMANCE, std::ostream &stream=std::cout) const

int	printMsg (const std::string &msg, const double &progress, const debug::Priority &priority, const debug::LineMode &lineMode=debug::LineMode::NEW, std::ostream &stream=std::cout) const

int	printMsg (const std::vector< std::vector< std::string > > &rows, const debug::Priority &priority=debug::Priority::INFO, const bool hasHeader=true, const debug::LineMode &lineMode=debug::LineMode::NEW, std::ostream &stream=std::cout) const

int	printMsg (const debug::Separator &separator, const debug::LineMode &lineMode=debug::LineMode::NEW, const debug::Priority &priority=debug::Priority::INFO, std::ostream &stream=std::cout) const

int	printMsg (const debug::Separator &separator, const debug::Priority &priority, const debug::LineMode &lineMode=debug::LineMode::NEW, std::ostream &stream=std::cout) const

int	printMsg (const std::string &msg, const debug::Separator &separator, const debug::LineMode &lineMode=debug::LineMode::NEW, const debug::Priority &priority=debug::Priority::INFO, std::ostream &stream=std::cout) const

void	setDebugMsgPrefix (const std::string &prefix)

Public Member Functions inherited from ttk::BaseClass
	BaseClass ()

virtual	~BaseClass ()=default

int	getThreadNumber () const

virtual int	setThreadNumber (const int threadNumber)

virtual int	setWrapper (const Wrapper *wrapper)

Protected Member Functions
int	combineTrees ()

int	finalize ()

int	finalizeSuperArc (const int &nodeId, const int &arcId)

bool	isNodeEligible (const Node *n) const

Protected Member Functions inherited from ttk::SubLevelSetTree
int	appendRegularNode (const int &superArcId, const int &nodeId)

int	closeSuperArc (const int &superArcId, const int &nodeId)

int	exportNodeColorToVtk (const int &nodeId, std::ofstream &o)

int	exportNodePosToVtk (const int &nodeId, const int &pointId, std::vector< int > &vertexIds, const std::vector< float > origin, const std::vector< float > voxelSize, std::ofstream &o)

int	exportArcPosToVtk (const int &arcId, const int &pointId, std::vector< int > &vertexIds, const std::vector< float > origin, const std::vector< float > voxelSize, std::ofstream &o)

int	makeArc (const int &nodeId0, const int &nodeId1)

int	makeNode (const int &vertexId)

int	openSuperArc (const int &nodeId)

Protected Member Functions inherited from ttk::Debug
int	printMsgInternal (const std::string &msg, const std::string &right, const std::string &filler, const debug::Priority &priority=debug::Priority::INFO, const debug::LineMode &lineMode=debug::LineMode::NEW, std::ostream &stream=std::cout) const

int	printMsgInternal (const std::string &msg, const debug::Priority &priority, const debug::LineMode &lineMode, std::ostream &stream=std::cout) const

int	welcomeMsg (std::ostream &stream)

Protected Attributes
SubLevelSetTree	mergeTree_ {}

SubLevelSetTree	splitTree_ {}

Protected Attributes inherited from ttk::SubLevelSetTree
int	vertexNumber_ {0}

bool	maintainRegularVertices_ {true}

double	minScalar_ {}

double	maxScalar_ {}

const std::vector< real > *	vertexScalars_ {}

std::vector< int > *	vertexSoSoffsets_ {}

bool	externalOffsets_ {false}

const AbstractTriangulation *	triangulation_ {}

std::vector< int > *	minimumList_ {}

std::vector< int > *	maximumList_ {}

std::vector< Node >	nodeList_ {}

std::vector< Node >	originalNodeList_ {}

std::vector< Arc >	arcList_ {}

std::vector< SuperArc >	superArcList_ {}

std::vector< SuperArc >	originalSuperArcList_ {}

std::vector< int >	vertex2node_ {}

std::vector< int >	vertex2superArc_ {}

std::vector< int >	vertex2superArcNode_ {}

std::vector< std::vector< double > > *	vertexPositions_ {}

bool	isSkeletonComputed_ {false}

Protected Attributes inherited from ttk::Debug
int	debugLevel_

std::string	debugMsgPrefix_

std::string	debugMsgNamePrefix_

Protected Attributes inherited from ttk::BaseClass
bool	lastObject_

int	threadNumber_

Wrapper *	wrapper_

Additional Inherited Members
Static Protected Attributes inherited from ttk::Debug
static COMMON_EXPORTS debug::LineMode	lastLineMode = ttk::debug::LineMode::NEW

Detailed Description

TTK processing package that computes the contour tree of scalar data and more (data segmentation, topological simplification, persistence diagrams, persistence curves, etc.).

Author: Julien Tierny julie.nosp@m.n.ti.nosp@m.erny@.nosp@m.lip6.nosp@m..fr

Date: July 2011

Warning: SimplexId (large large datasets). This class builds and runs with the new triangulation API (SimplexId) but may need adjustments when addressing more than integers (large datasets).

Related publication
"Computing contour trees in all dimensions"
Hamish Carr, Jack Snoeyink, Ulrike Axen
Proc. of ACM SODA 2000.

Definition at line 591 of file ContourTree.h.

Constructor & Destructor Documentation

◆ ContourTree()

ContourTree::ContourTree ( )

Definition at line 2312 of file ContourTree.cpp.

Member Function Documentation

◆ build()

int ContourTree::build ( )

Definition at line 2316 of file ContourTree.cpp.

◆ clearSkeleton()

int ContourTree::clearSkeleton ( )

overridevirtual

Reimplemented from ttk::SubLevelSetTree.

Definition at line 2744 of file ContourTree.cpp.

◆ combineTrees()

int ContourTree::combineTrees ( )

protected

Definition at line 2427 of file ContourTree.cpp.

◆ computeSkeleton()

int ContourTree::computeSkeleton ( unsigned int arcResolution = 3 )

overridevirtual

Reimplemented from ttk::SubLevelSetTree.

Definition at line 2696 of file ContourTree.cpp.

◆ finalize()

int ContourTree::finalize ( )

protected

Definition at line 2581 of file ContourTree.cpp.

◆ finalizeSuperArc()

int ContourTree::finalizeSuperArc	(	const int &	nodeId,
		const int &	arcId
	)

protected

Definition at line 2611 of file ContourTree.cpp.

◆ getMergeTree()

const SubLevelSetTree * ttk::ContourTree::getMergeTree ( ) const

inline

Definition at line 597 of file ContourTree.h.

◆ getPersistenceDiagram()

int ContourTree::getPersistenceDiagram	(	std::vector< std::pair< double, double > > &	diagram,
		std::vector< std::pair< std::pair< int, int >, double > > *	mergePairs = `nullptr`,
		std::vector< std::pair< std::pair< int, int >, double > > *	splitPairs = `nullptr`,
		std::vector< std::pair< std::pair< int, int >, double > > *	pairs = `nullptr`
	)		const

Definition at line 2849 of file ContourTree.cpp.

◆ getPersistencePairs()

int ContourTree::getPersistencePairs	(	std::vector< std::pair< std::pair< int, int >, double > > &	pairs,
		std::vector< std::pair< std::pair< int, int >, double > > *	mergePairs = `nullptr`,
		std::vector< std::pair< std::pair< int, int >, double > > *	splitPairs = `nullptr`
	)		const

overridevirtual

Reimplemented from ttk::SubLevelSetTree.

Definition at line 2768 of file ContourTree.cpp.

◆ getPersistencePlot()

int ContourTree::getPersistencePlot	(	std::vector< std::pair< double, int > > &	plot,
		std::vector< std::pair< std::pair< int, int >, double > > *	mergePairs = `nullptr`,
		std::vector< std::pair< std::pair< int, int >, double > > *	splitPairs = `nullptr`,
		std::vector< std::pair< std::pair< int, int >, double > > *	pairs = `nullptr`
	)		const

Definition at line 2822 of file ContourTree.cpp.

◆ getSplitTree()

const SubLevelSetTree * ttk::ContourTree::getSplitTree ( ) const

inline

Definition at line 621 of file ContourTree.h.

◆ isNodeEligible()

bool ContourTree::isNodeEligible ( const Node * n ) const

protected

Definition at line 2652 of file ContourTree.cpp.

◆ maintainRegularVertices()

int ttk::ContourTree::maintainRegularVertices ( const bool & onOff )

inlineoverridevirtual

Reimplemented from ttk::SubLevelSetTree.

Definition at line 625 of file ContourTree.h.

◆ setVertexNeighbors() [1/2]

int ttk::ContourTree::setVertexNeighbors	(	const int &	vertexId,
		const std::vector< int > &	neighborList
	)

◆ setVertexNeighbors() [2/2]

int ttk::ContourTree::setVertexNeighbors ( const std::vector< std::vector< int > > * vertexNeighbors )

◆ simplify()

int ContourTree::simplify	(	const double &	simplificationThreshold,
		ContourTreeSimplificationMetric *	metric = `nullptr`
	)

overridevirtual

Reimplemented from ttk::SubLevelSetTree.

Definition at line 2883 of file ContourTree.cpp.

◆ smoothSkeleton()

int ContourTree::smoothSkeleton ( unsigned int skeletonSmoothing )

overridevirtual

Reimplemented from ttk::SubLevelSetTree.

Definition at line 2720 of file ContourTree.cpp.

Member Data Documentation

◆ mergeTree_

SubLevelSetTree ttk::ContourTree::mergeTree_ {}

protected

Definition at line 653 of file ContourTree.h.

◆ splitTree_

SubLevelSetTree ttk::ContourTree::splitTree_ {}

protected

Definition at line 653 of file ContourTree.h.

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

/home/julien/Pro/git/github/ttk-tierny/core/base/contourTree/ContourTree.h
/home/julien/Pro/git/github/ttk-tierny/core/base/contourTree/ContourTree.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ContourTree()

Member Function Documentation

◆ build()

◆ clearSkeleton()

◆ combineTrees()

◆ computeSkeleton()

◆ finalize()

◆ finalizeSuperArc()

◆ getMergeTree()

◆ getPersistenceDiagram()

◆ getPersistencePairs()

◆ getPersistencePlot()

◆ getSplitTree()

◆ isNodeEligible()

◆ maintainRegularVertices()

◆ setVertexNeighbors() [1/2]

◆ setVertexNeighbors() [2/2]

◆ simplify()

◆ smoothSkeleton()

Member Data Documentation

◆ mergeTree_

◆ splitTree_