#include <MergeTreeDistanceMatrix.h>

Inheritance diagram for ttk::MergeTreeDistanceMatrix:

Public Member Functions
	MergeTreeDistanceMatrix ()
	~MergeTreeDistanceMatrix () override=default
void	setBaseModule (int m)
void	setBranchMetric (int m)
void	setPathMetric (int m)
template<class dataType>
void	execute (std::vector< ftm::MergeTree< dataType > > &trees, std::vector< ftm::MergeTree< dataType > > &trees2, std::vector< std::vector< double > > &distanceMatrix)
template<class dataType>
void	executePara (std::vector< ftm::MergeTree< dataType > > &trees, std::vector< std::vector< double > > &distanceMatrix, bool isFirstInput=true)
template<class dataType>
void	executeParaImpl (std::vector< ftm::MergeTree< dataType > > &trees, std::vector< std::vector< double > > &distanceMatrix, bool isFirstInput=true)
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)
Public Member Functions inherited from ttk::MergeTreeBase
	MergeTreeBase ()
void	setAssignmentSolver (int assignmentSolver)
void	setEpsilon1UseFarthestSaddle (bool b)
void	setEpsilonTree1 (double epsilon)
void	setEpsilonTree2 (double epsilon)
void	setEpsilon2Tree1 (double epsilon)
void	setEpsilon2Tree2 (double epsilon)
void	setEpsilon3Tree1 (double epsilon)
void	setEpsilon3Tree2 (double epsilon)
void	setPersistenceThreshold (double pt)
void	setParallelize (bool para)
void	setNodePerTask (int npt)
void	setBranchDecomposition (bool useBD)
void	setNormalizedWasserstein (bool normalizedWasserstein)
void	setKeepSubtree (bool keepSubtree)
void	setNonMatchingWeight (double weight)
void	setBarycenterMergeTree (bool imt)
void	setDistanceSquaredRoot (bool distanceSquaredRoot)
void	setUseMinMaxPair (bool useMinMaxPair)
void	setDeleteMultiPersPairs (bool deleteMultiPersPairsT)
void	setCleanTree (bool clean)
void	setIsPersistenceDiagram (bool isPD)
void	setJoinSplitMixtureCoefficient (const double mixtureCoefficient)
void	setUseDoubleInput (const bool useDoubleInput)
std::vector< std::vector< int > >	getTreesNodeCorr ()
double	mixDistancesMinMaxPairWeight (bool isFirstInput)
double	mixDistancesWeight (bool isFirstInput)
template<class dataType>
double	mixDistances (dataType distance1, dataType distance2)
template<class dataType>
void	mixDistancesMatrix (std::vector< std::vector< dataType > > &distanceMatrix, std::vector< std::vector< dataType > > &distanceMatrix2)
template<class dataType>
void	mergeSaddle (ftm::FTMTree_MT *tree, double epsilon, std::vector< std::vector< ftm::idNode > > &treeNodeMerged, bool mergeByPersistence=false)
template<class dataType>
void	persistenceMerging (ftm::FTMTree_MT *tree, double epsilon2, double epsilon3=100)
void	deletePersistenceDiagramsPairs (ftm::FTMTree_MT *tree, std::vector< ftm::idNode > &nodes)
template<class dataType>
void	keepMostImportantPairs (ftm::FTMTree_MT *tree, int n, bool useBD)
template<class dataType>
void	persistenceThresholding (ftm::FTMTree_MT *tree, double persistenceThresholdT, std::vector< ftm::idNode > &deletedNodes)
template<class dataType>
void	persistenceThresholding (ftm::FTMTree_MT *tree, std::vector< ftm::idNode > &deletedNodes)
template<class dataType>
void	persistenceThresholding (ftm::FTMTree_MT *tree, double persistenceThresholdT)
template<class dataType>
void	persistenceThresholding (ftm::FTMTree_MT *tree)
template<class dataType>
void	verifyOrigins (ftm::FTMTree_MT *tree)
template<class dataType>
void	preprocessTree (ftm::FTMTree_MT *tree, bool deleteInconsistentNodes=true)
template<class dataType>
ftm::FTMTree_MT *	computeBranchDecomposition (ftm::FTMTree_MT *tree, std::vector< std::vector< ftm::idNode > > &treeNodeMerged)
template<class dataType>
void	dontUseMinMaxPair (ftm::FTMTree_MT *tree)
void	verifyPairsTree (ftm::FTMTree_MT *tree)
template<class dataType>
void	deleteMultiPersPairs (ftm::FTMTree_MT *tree, bool useBD)
template<class dataType>
void	preprocessingPipeline (ftm::MergeTree< dataType > &mTree, double epsilonTree, double epsilon2Tree, double epsilon3Tree, bool branchDecompositionT, bool useMinMaxPairT, bool cleanTreeT, double persistenceThreshold, std::vector< int > &nodeCorr, bool deleteInconsistentNodes=true, bool removeMergedSaddles=false)
template<class dataType>
void	preprocessingPipeline (ftm::MergeTree< dataType > &mTree, double epsilonTree, double epsilon2Tree, double epsilon3Tree, bool branchDecompositionT, bool useMinMaxPairT, bool cleanTreeT, std::vector< int > &nodeCorr, bool deleteInconsistentNodes=true, bool removeMergedSaddles=false)
void	reverseNodeCorr (ftm::FTMTree_MT *tree, std::vector< int > &nodeCorr)
template<class dataType>
void	mtFlattening (ftm::MergeTree< dataType > &mt)
template<class dataType>
void	mtsFlattening (std::vector< ftm::MergeTree< dataType > > &mts)
double	getSizeLimitMetric (std::vector< ftm::FTMTree_MT * > &trees)
template<class dataType>
void	copyMinMaxPair (ftm::MergeTree< dataType > &mTree1, ftm::MergeTree< dataType > &mTree2, bool setOrigins=false)
template<class dataType>
std::tuple< int, dataType >	fixMergedRootOrigin (ftm::FTMTree_MT *tree)
template<class dataType>
void	branchDecompositionToTree (ftm::FTMTree_MT *tree)
template<class dataType>
void	putBackMergedNodes (ftm::FTMTree_MT *tree)
template<class dataType>
void	postprocessingPipeline (ftm::FTMTree_MT *tree)
template<class dataType>
void	convertBranchDecompositionMatching (ftm::FTMTree_MT tree1, ftm::FTMTree_MT tree2, std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > &outputMatching)
template<class dataType>
void	convertBranchDecompositionMatching (ftm::FTMTree_MT tree1, ftm::FTMTree_MT tree2, std::vector< std::tuple< ftm::idNode, ftm::idNode > > &outputMatching)
template<class dataType>
void	identifyRealMatching (ftm::FTMTree_MT tree1, ftm::FTMTree_MT tree2, std::vector< std::tuple< ftm::idNode, ftm::idNode > > &outputMatching, std::vector< std::tuple< ftm::idNode, ftm::idNode, bool > > &realMatching)
template<class dataType>
dataType	computeDistance (dataType x1, dataType x2, dataType y1, dataType y2, double power=2)
template<class dataType>
dataType	deleteCost (const ftm::FTMTree_MT *tree, ftm::idNode nodeId)
template<class dataType>
dataType	insertCost (const ftm::FTMTree_MT *tree, ftm::idNode nodeId)
template<class dataType>
dataType	relabelCostOnly (const ftm::FTMTree_MT tree1, ftm::idNode nodeId1, const ftm::FTMTree_MT tree2, ftm::idNode nodeId2)
template<class dataType>
dataType	relabelCost (const ftm::FTMTree_MT tree1, ftm::idNode nodeId1, const ftm::FTMTree_MT tree2, ftm::idNode nodeId2)
void	getParamNames (std::vector< std::string > &paramNames)
double	getParamValueFromName (std::string &paramName)
void	setParamValueFromName (std::string &paramName, double value)
void	getTreesStats (std::vector< ftm::FTMTree_MT * > &trees, std::array< double, 3 > &stats)
void	printTreesStats (std::vector< ftm::FTMTree_MT * > &trees)
template<class dataType>
void	printTreesStats (std::vector< ftm::MergeTree< dataType > > &trees)
template<class dataType>
void	printTableVector (std::vector< std::vector< dataType > > &table)
template<class dataType>
void	printTable (dataType *table, int nRows, int nCols)
void	printMatching (std::vector< MatchingType > &matchings)
void	printMatching (std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > &matchings)
void	printMatching (std::vector< std::tuple< ftm::idNode, ftm::idNode > > &matchings)
template<class dataType>
void	printPairs (std::vector< std::tuple< SimplexId, SimplexId, dataType > > &treePairs)
template<class dataType>
void	printOutputMatching (std::vector< std::tuple< ftm::idNode, ftm::idNode > > &outputMatching, ftm::FTMTree_MT tree1, ftm::FTMTree_MT tree2, bool computeCosts=true)

Protected Attributes
int	baseModule_ = 0
int	branchMetric_ = 0
int	pathMetric_ = 0
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_
Protected Attributes inherited from ttk::MergeTreeBase
int	assignmentSolverID_ = 0
bool	epsilon1UseFarthestSaddle_ = false
double	epsilonTree1_ = 0
double	epsilonTree2_ = 0
double	epsilon2Tree1_ = 100
double	epsilon2Tree2_ = 100
double	epsilon3Tree1_ = 100
double	epsilon3Tree2_ = 100
double	persistenceThreshold_ = 0
bool	barycenterMergeTree_ = false
bool	useMinMaxPair_ = true
bool	deleteMultiPersPairs_ = false
bool	branchDecomposition_ = true
int	wassersteinPower_ = 2
bool	normalizedWasserstein_ = true
bool	keepSubtree_ = false
double	nonMatchingWeight_ = 1.0
bool	distanceSquaredRoot_ = true
bool	useFullMerge_ = false
bool	isPersistenceDiagram_ = false
bool	convertToDiagram_ = false
double	mixtureCoefficient_ = 0.5
bool	useDoubleInput_ = false
bool	parallelize_ = true
int	nodePerTask_ = 32
bool	cleanTree_ = true
std::vector< std::vector< int > >	treesNodeCorr_

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

Detailed Description

The MergeTreeDistanceMatrix class provides methods to compute the distance between multiple merge trees and output a distance matrix.

Author: Mathieu Pont mathi.nosp@m.eu.p.nosp@m.ont@l.nosp@m.ip6..nosp@m.fr; Florian Wetzels (wetze.nosp@m.ls@c.nosp@m.s.uni.nosp@m.-kl..nosp@m.de)

Date: 2021.

This VTK filter uses the ttk::MergeTreeDistanceMatrix module to compute the distance matrix of a group of merge trees.

Related publication
"Wasserstein Distances, Geodesics and Barycenters of Merge Trees"
Mathieu Pont, Jules Vidal, Julie Delon, Julien Tierny.
Proc. of IEEE VIS 2021.
IEEE Transactions on Visualization and Computer Graphics, 2021

Related publication
"Edit Distance between Merge Trees"
R. Sridharamurthy, T. B. Masood, A. Kamakshidasan and V. Natarajan.
IEEE Transactions on Visualization and Computer Graphics, 2020.

Related publication
"Branch Decomposition-Independent Edit Distances for Merge Trees."
Florian Wetzels, Heike Leitte, and Christoph Garth.
Computer Graphics Forum, 2022.

Related publication
"A Deformation-based Edit Distance for Merge Trees"
Florian Wetzels, Christoph Garth.
TopoInVis 2022.

Online examples:

Definition at line 66 of file MergeTreeDistanceMatrix.h.

Constructor & Destructor Documentation

◆ MergeTreeDistanceMatrix()

ttk::MergeTreeDistanceMatrix::MergeTreeDistanceMatrix ( )

inline

Definition at line 74 of file MergeTreeDistanceMatrix.h.

◆ ~MergeTreeDistanceMatrix()

ttk::MergeTreeDistanceMatrix::~MergeTreeDistanceMatrix ( )

overridedefault

Member Function Documentation

◆ execute()

template<class dataType>

void ttk::MergeTreeDistanceMatrix::execute	(	std::vector< ftm::MergeTree< dataType > > &	trees,
		std::vector< ftm::MergeTree< dataType > > &	trees2,
		std::vector< std::vector< double > > &	distanceMatrix )

inline

Implementation of the algorithm.

Definition at line 98 of file MergeTreeDistanceMatrix.h.

◆ executePara()

template<class dataType>

void ttk::MergeTreeDistanceMatrix::executePara	(	std::vector< ftm::MergeTree< dataType > > &	trees,
		std::vector< std::vector< double > > &	distanceMatrix,
		bool	isFirstInput = true )

inline

Definition at line 126 of file MergeTreeDistanceMatrix.h.

◆ executeParaImpl()

template<class dataType>

void ttk::MergeTreeDistanceMatrix::executeParaImpl	(	std::vector< ftm::MergeTree< dataType > > &	trees,
		std::vector< std::vector< double > > &	distanceMatrix,
		bool	isFirstInput = true )

inline

Definition at line 142 of file MergeTreeDistanceMatrix.h.

◆ setBaseModule()

void ttk::MergeTreeDistanceMatrix::setBaseModule ( int m )

inline

Definition at line 82 of file MergeTreeDistanceMatrix.h.

◆ setBranchMetric()

void ttk::MergeTreeDistanceMatrix::setBranchMetric ( int m )

inline

Definition at line 86 of file MergeTreeDistanceMatrix.h.

◆ setPathMetric()

void ttk::MergeTreeDistanceMatrix::setPathMetric ( int m )

inline

Definition at line 90 of file MergeTreeDistanceMatrix.h.

Member Data Documentation

◆ baseModule_

int ttk::MergeTreeDistanceMatrix::baseModule_ = 0

protected

Definition at line 69 of file MergeTreeDistanceMatrix.h.

◆ branchMetric_

int ttk::MergeTreeDistanceMatrix::branchMetric_ = 0

protected

Definition at line 70 of file MergeTreeDistanceMatrix.h.

◆ pathMetric_

int ttk::MergeTreeDistanceMatrix::pathMetric_ = 0

protected

Definition at line 71 of file MergeTreeDistanceMatrix.h.

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

/data/julien/git/github/tierny/ttk-fork/core/base/mergeTreeDistanceMatrix/MergeTreeDistanceMatrix.h

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MergeTreeDistanceMatrix()

◆ ~MergeTreeDistanceMatrix()

Member Function Documentation

◆ execute()

◆ executePara()

◆ executeParaImpl()

◆ setBaseModule()

◆ setBranchMetric()

◆ setPathMetric()

Member Data Documentation

◆ baseModule_

◆ branchMetric_

◆ pathMetric_