#include <MergeTreeTemporalReduction.h>

Inheritance diagram for ttk::MergeTreeTemporalReduction:

Public Member Functions
	MergeTreeTemporalReduction ()

void	setRemovalPercentage (double rs)

void	setUseL2Distance (bool useL2)

template<class dataType >
dataType	computeL2Distance (std::vector< dataType > &img1, std::vector< dataType > &img2, bool emptyFieldDistance=false)

template<class dataType >
std::vector< dataType >	computeL2Barycenter (std::vector< dataType > &img1, std::vector< dataType > &img2, double alpha)

template<class dataType >
dataType	computeDistance (ftm::MergeTree< dataType > &mTree1, ftm::MergeTree< dataType > &mTree2, bool emptyTreeDistance=false)

template<class dataType >
ftm::MergeTree< dataType >	computeBarycenter (ftm::MergeTree< dataType > &mTree1, ftm::MergeTree< dataType > &mTree2, double alpha)

double	computeAlpha (int index1, int middleIndex, int index2)

template<class dataType >
void	temporalSubsampling (std::vector< ftm::MergeTree< dataType > > &mTrees, std::vector< int > &removed, std::vector< ftm::MergeTree< dataType > > &barycenters, std::vector< std::vector< dataType > > &barycentersL2)

template<class dataType >
std::vector< int >	execute (std::vector< ftm::MergeTree< dataType > > &mTrees, std::vector< double > &emptyTreeDistances, std::vector< ftm::MergeTree< dataType > > &allMT)

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)

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)

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)

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)

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 (ftm::FTMTree_MT *tree, ftm::idNode nodeId)

template<class dataType >
dataType	insertCost (ftm::FTMTree_MT *tree, ftm::idNode nodeId)

template<class dataType >
dataType	relabelCostOnly (ftm::FTMTree_MT tree1, ftm::idNode nodeId1, ftm::FTMTree_MT tree2, ftm::idNode nodeId2)

template<class dataType >
dataType	relabelCost (ftm::FTMTree_MT tree1, ftm::idNode nodeId1, 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
double	removalPercentage_ = 50.

bool	useL2Distance_ = false

std::vector< std::vector< double > >	fieldL2_

bool	useCustomTimeVariable_ = false

std::vector< double >	timeVariable_

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 MergeTreeTemporalReduction class provides methods to compute a temporal reduction of a sequence of merge trees.

Author: Mathieu Pont (mathi.nosp@m.eu.p.nosp@m.ont@l.nosp@m.ip6..nosp@m.fr)

Date: 2021.

This module defines the MergeTreeTemporalReduction class that computes a temporal reduction of a sequence 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

Online examples:

Merge Tree Temporal Reduction

Definition at line 36 of file MergeTreeTemporalReduction.h.

Constructor & Destructor Documentation

◆ MergeTreeTemporalReduction()

ttk::MergeTreeTemporalReduction::MergeTreeTemporalReduction ( )

Definition at line 3 of file MergeTreeTemporalReduction.cpp.

Member Function Documentation

◆ computeAlpha()

double ttk::MergeTreeTemporalReduction::computeAlpha	(	int	index1,
		int	middleIndex,
		int	index2
	)

inline

Definition at line 159 of file MergeTreeTemporalReduction.h.

◆ computeBarycenter()

template<class dataType >

ftm::MergeTree< dataType > ttk::MergeTreeTemporalReduction::computeBarycenter	(	ftm::MergeTree< dataType > &	mTree1,
		ftm::MergeTree< dataType > &	mTree2,
		double	alpha
	)

inline

Definition at line 124 of file MergeTreeTemporalReduction.h.

◆ computeDistance()

template<class dataType >

dataType ttk::MergeTreeTemporalReduction::computeDistance	(	ftm::MergeTree< dataType > &	mTree1,
		ftm::MergeTree< dataType > &	mTree2,
		bool	emptyTreeDistance = `false`
	)

inline

Definition at line 91 of file MergeTreeTemporalReduction.h.

◆ computeL2Barycenter()

template<class dataType >

std::vector< dataType > ttk::MergeTreeTemporalReduction::computeL2Barycenter	(	std::vector< dataType > &	img1,
		std::vector< dataType > &	img2,
		double	alpha
	)

inline

Definition at line 77 of file MergeTreeTemporalReduction.h.

◆ computeL2Distance()

template<class dataType >

dataType ttk::MergeTreeTemporalReduction::computeL2Distance	(	std::vector< dataType > &	img1,
		std::vector< dataType > &	img2,
		bool	emptyFieldDistance = `false`
	)

inline

Definition at line 57 of file MergeTreeTemporalReduction.h.

◆ execute()

template<class dataType >

std::vector< int > ttk::MergeTreeTemporalReduction::execute	(	std::vector< ftm::MergeTree< dataType > > &	mTrees,
		std::vector< double > &	emptyTreeDistances,
		std::vector< ftm::MergeTree< dataType > > &	allMT
	)

inline

Definition at line 309 of file MergeTreeTemporalReduction.h.

◆ setRemovalPercentage()

void ttk::MergeTreeTemporalReduction::setRemovalPercentage ( double rs )

inline

Definition at line 48 of file MergeTreeTemporalReduction.h.

◆ setUseL2Distance()

void ttk::MergeTreeTemporalReduction::setUseL2Distance ( bool useL2 )

inline

Definition at line 52 of file MergeTreeTemporalReduction.h.

◆ temporalSubsampling()

template<class dataType >

void ttk::MergeTreeTemporalReduction::temporalSubsampling	(	std::vector< ftm::MergeTree< dataType > > &	mTrees,
		std::vector< int > &	removed,
		std::vector< ftm::MergeTree< dataType > > &	barycenters,
		std::vector< std::vector< dataType > > &	barycentersL2
	)

inline

Definition at line 168 of file MergeTreeTemporalReduction.h.

Member Data Documentation

◆ fieldL2_

std::vector<std::vector<double> > ttk::MergeTreeTemporalReduction::fieldL2_

protected

Definition at line 41 of file MergeTreeTemporalReduction.h.

◆ removalPercentage_

double ttk::MergeTreeTemporalReduction::removalPercentage_ = 50.

protected

Definition at line 39 of file MergeTreeTemporalReduction.h.

◆ timeVariable_

std::vector<double> ttk::MergeTreeTemporalReduction::timeVariable_

protected

Definition at line 43 of file MergeTreeTemporalReduction.h.

◆ useCustomTimeVariable_

bool ttk::MergeTreeTemporalReduction::useCustomTimeVariable_ = false

protected

Definition at line 42 of file MergeTreeTemporalReduction.h.

◆ useL2Distance_

bool ttk::MergeTreeTemporalReduction::useL2Distance_ = false

protected

Definition at line 40 of file MergeTreeTemporalReduction.h.

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

/home/julien/Pro/git/github/ttk-tierny/core/base/mergeTreeTemporalReduction/MergeTreeTemporalReduction.h
/home/julien/Pro/git/github/ttk-tierny/core/base/mergeTreeTemporalReduction/MergeTreeTemporalReduction.cpp

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MergeTreeTemporalReduction()

Member Function Documentation

◆ computeAlpha()

◆ computeBarycenter()

◆ computeDistance()

◆ computeL2Barycenter()

◆ computeL2Distance()

◆ execute()

◆ setRemovalPercentage()

◆ setUseL2Distance()

◆ temporalSubsampling()

Member Data Documentation

◆ fieldL2_

◆ removalPercentage_

◆ timeVariable_

◆ useCustomTimeVariable_

◆ useL2Distance_