#include <MergeTreeClustering.h>

Inheritance diagram for ttk::MergeTreeClustering< dataType2 >:

Public Member Functions
	MergeTreeClustering ()

	~MergeTreeClustering () override=default

void	setNoCentroids (unsigned int noCentroidsT)

void	setMixtureCoefficient (double coef)

std::vector< std::vector< int > >	getTrees2NodeCorr ()

template<class dataType >
void	initCentroids (std::vector< ftm::FTMTree_MT * > &trees, std::vector< ftm::FTMTree_MT * > &trees2, std::vector< std::vector< ftm::MergeTree< dataType > > > &allCentroids)

template<class dataType >
void	initNewCentroid (std::vector< ftm::FTMTree_MT * > &trees, ftm::MergeTree< dataType > &centroid, int noNewCentroid)

template<class dataType >
void	initAcceleratedKMeansVectors (std::vector< ftm::FTMTree_MT * > &trees, std::vector< ftm::MergeTree< dataType > > &centroids, std::vector< ftm::FTMTree_MT * > &ttkNotUsed(trees2))

template<class dataType >
void	initAcceleratedKMeans (std::vector< ftm::FTMTree_MT * > &trees, std::vector< ftm::MergeTree< dataType > > &centroids, std::vector< ftm::FTMTree_MT * > &trees2, std::vector< ftm::MergeTree< dataType > > &centroids2)

template<class dataType >
void	copyCentroids (std::vector< ftm::MergeTree< dataType > > &centroids, std::vector< ftm::MergeTree< dataType > > &oldCentroids)

template<class dataType >
void	assignmentCentroidsAccelerated (std::vector< ftm::FTMTree_MT * > &trees, std::vector< ftm::MergeTree< dataType > > &centroids, std::vector< std::tuple< int, int > > &assignmentC, std::vector< dataType > &bestDistanceT, std::vector< ftm::FTMTree_MT * > &trees2, std::vector< ftm::MergeTree< dataType > > &centroids2)

template<class dataType >
void	assignmentCentroids (std::vector< ftm::FTMTree_MT * > &trees, std::vector< ftm::MergeTree< dataType > > &centroids, std::vector< std::tuple< int, int > > &assignmentC, std::vector< dataType > &bestDistanceT, std::vector< ftm::FTMTree_MT * > &trees2, std::vector< ftm::MergeTree< dataType > > &centroids2)

template<class dataType >
void	finalAssignmentCentroids (std::vector< ftm::FTMTree_MT * > &trees, std::vector< ftm::MergeTree< dataType > > &centroids, matchingVectorType &matchingsC, std::vector< std::tuple< int, int > > &assignmentC, std::vector< dataType > &bestDistanceT, std::vector< ftm::FTMTree_MT * > &trees2, std::vector< ftm::MergeTree< dataType > > &centroids2, matchingVectorType &matchingsC2)

template<class dataType >
void	assignmentCentroidsNaive (std::vector< ftm::FTMTree_MT * > &trees, std::vector< ftm::MergeTree< dataType > > &centroids, std::vector< std::tuple< int, int > > &assignmentC, std::vector< dataType > &bestDistanceT, std::vector< ftm::FTMTree_MT * > &trees2, std::vector< ftm::MergeTree< dataType > > &centroids2)

template<class dataType >
void	getCentroidsDistanceMatrix (std::vector< ftm::MergeTree< dataType > > &centroids, std::vector< std::vector< double > > &distanceMatrix, bool useDoubleInput=false, bool isFirstInput=true)

void	matchingCorrespondence (treesMatchingVector &matchingT, std::vector< int > &nodeCorr, std::vector< int > &assignedTreesIndex)

bool	samePreviousAssignment (int clusterId)

template<class dataType >
bool	updateCentroids (std::vector< ftm::FTMTree_MT * > &trees, std::vector< ftm::MergeTree< dataType > > &centroids, std::vector< double > &alphas, std::vector< std::tuple< int, int > > &assignmentC)

template<class dataType >
void	computeOneBarycenter (std::vector< ftm::FTMTree_MT * > &trees, ftm::MergeTree< dataType > &baryMergeTree, std::vector< double > &alphas, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &finalMatchings)

template<class dataType >
void	computeCentroids (std::vector< ftm::FTMTree_MT * > &trees, std::vector< ftm::MergeTree< dataType > > &centroids, matchingVectorType &outputMatching, std::vector< double > &alphas, std::vector< int > &clusteringAssignment, std::vector< ftm::FTMTree_MT * > &trees2, std::vector< ftm::MergeTree< dataType > > &centroids2, matchingVectorType &outputMatching2)

template<class dataType >
void	execute (std::vector< ftm::MergeTree< dataType > > &trees, matchingVectorType &outputMatching, std::vector< double > &alphas, std::vector< int > &clusteringAssignment, std::vector< ftm::MergeTree< dataType > > &trees2, matchingVectorType &outputMatching2, std::vector< ftm::MergeTree< dataType > > &centroids, std::vector< ftm::MergeTree< dataType > > &centroids2)

template<class dataType >
void	execute (std::vector< ftm::MergeTree< dataType > > &trees, matchingVectorType &outputMatching, std::vector< int > &clusteringAssignment, std::vector< ftm::MergeTree< dataType > > &trees2, matchingVectorType &outputMatching2, std::vector< ftm::MergeTree< dataType > > &centroids, std::vector< ftm::MergeTree< dataType > > &centroids2)

template<class dataType >
void	execute (std::vector< ftm::MergeTree< dataType > > &trees, matchingVectorType &outputMatching, std::vector< int > &clusteringAssignment, std::vector< ftm::MergeTree< dataType > > &centroids)

template<class dataType >
void	preprocessingClustering (std::vector< ftm::MergeTree< dataType > > &trees, std::vector< std::vector< int > > &nodeCorr, bool useMinMaxPairT=true)

template<class dataType >
void	fixMergedRootOriginClustering (std::vector< ftm::MergeTree< dataType > > &centroids)

template<class dataType >
void	putBackMinMaxPair (std::vector< ftm::MergeTree< dataType > > &centroids, std::vector< ftm::MergeTree< dataType > > &centroids2)

template<class dataType >
void	postprocessingClustering (std::vector< ftm::MergeTree< dataType > > &trees, std::vector< ftm::MergeTree< dataType > > &centroids, matchingVectorType &outputMatching, std::vector< int > &clusteringAssignment)

template<class dataType >
void	printCentroidsStats (std::vector< ftm::MergeTree< dataType > > &centroids, std::vector< ftm::MergeTree< dataType > > &centroids2)

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)

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

	~MergeTreeBarycenter () override=default

void	setTol (double tolT)

void	setAddNodes (bool addNodesT)

void	setDeterministic (bool deterministicT)

void	setProgressiveBarycenter (bool progressive)

void	setProgressiveSpeedDivisor (double progSpeed)

void	setIsCalled (bool ic)

double	getAllDistanceTime ()

double	getAddDeletedNodesTime ()

void	setAlpha (double alpha)

void	setBarycenterMaximumNumberOfPairs (unsigned int maxi)

void	setBarycenterSizeLimitPercent (double percent)

void	setPreprocess (bool preproc)

void	setPostprocess (bool postproc)

std::vector< double >	getFinalDistances ()

template<class dataType >
void	getDistanceMatrix (std::vector< ftm::FTMTree_MT * > &trees, std::vector< ftm::FTMTree_MT * > &trees2, std::vector< std::vector< double > > &distanceMatrix, bool useDoubleInput=false, bool isFirstInput=true)

template<class dataType >
void	getDistanceMatrix (std::vector< ftm::FTMTree_MT * > &trees, std::vector< std::vector< double > > &distanceMatrix, bool useDoubleInput=false, bool isFirstInput=true)

template<class dataType >
void	getSizeLimitedTrees (std::vector< ftm::FTMTree_MT * > &trees, unsigned int barycenterMaximumNumberOfPairs, double sizeLimitPercent, std::vector< ftm::MergeTree< dataType > > &mTreesLimited)

template<class dataType >
void	getSizeLimitedDistanceMatrix (std::vector< ftm::FTMTree_MT * > &trees, std::vector< std::vector< double > > &distanceMatrix, unsigned int barycenterMaximumNumberOfPairs, double sizeLimitPercent, bool useDoubleInput=false, bool isFirstInput=true)

template<class dataType >
void	getParametrizedDistanceMatrix (std::vector< ftm::FTMTree_MT * > &trees, std::vector< std::vector< double > > &distanceMatrix, unsigned int barycenterMaximumNumberOfPairs, double sizeLimitPercent, bool useDoubleInput=false, bool isFirstInput=true)

template<class dataType >
int	getBestInitTreeIndex (std::vector< ftm::FTMTree_MT * > &trees, std::vector< ftm::FTMTree_MT * > &trees2, unsigned int barycenterMaximumNumberOfPairs, double sizeLimitPercent, bool distMinimizer=true)

template<class dataType >
int	getBestInitTreeIndex (std::vector< ftm::FTMTree_MT * > &trees, std::vector< ftm::FTMTree_MT * > &trees2, double sizeLimitPercent, bool distMinimizer=true)

template<class dataType >
int	getBestInitTreeIndex (std::vector< ftm::FTMTree_MT * > &trees, bool distMinimizer=true)

template<class dataType >
void	initBarycenterTree (std::vector< ftm::FTMTree_MT * > &trees, ftm::MergeTree< dataType > &baryTree, bool distMinimizer=true)

template<class dataType >
ftm::idNode	getNodesAndScalarsToAdd (ftm::MergeTree< dataType > &ttkNotUsed(mTree1), ftm::idNode nodeId1, ftm::FTMTree_MT *tree2, ftm::idNode nodeId2, std::vector< dataType > &newScalarsVector, std::vector< std::tuple< ftm::idNode, ftm::idNode, int > > &nodesToProcess, ftm::idNode nodeCpt, int i)

template<class dataType >
void	addNodes (ftm::MergeTree< dataType > &mTree1, int noTrees, std::vector< std::tuple< ftm::idNode, ftm::idNode, int > > &nodesToProcess, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode > > > &nodesProcessed)

template<class dataType >
void	updateNodesAndScalars (ftm::MergeTree< dataType > &mTree1, int noTrees, std::vector< std::tuple< ftm::idNode, ftm::idNode, int > > &nodesToProcess, std::vector< dataType > &newScalarsVector, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode > > > &nodesProcessed)

template<class dataType >
void	updateBarycenterTreeStructure (std::vector< ftm::FTMTree_MT * > &trees, ftm::MergeTree< dataType > &baryMergeTree, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings)

template<class dataType >
std::tuple< dataType, dataType >	getParametrizedBirthDeath (ftm::FTMTree_MT *tree1, ftm::idNode nodeId1)

template<class dataType >
std::tuple< dataType, dataType >	interpolation (ftm::MergeTree< dataType > &baryMergeTree, ftm::idNode nodeId, std::vector< dataType > &newScalarsVector, std::vector< ftm::FTMTree_MT * > &trees, std::vector< ftm::idNode > &nodes, std::vector< double > &alphas)

template<class dataType >
std::tuple< dataType, dataType >	interpolationAdded (ftm::FTMTree_MT *tree, ftm::idNode nodeId, double alpha, ftm::MergeTree< dataType > &baryMergeTree, ftm::idNode nodeB, std::vector< dataType > &newScalarsVector)

template<class dataType >
void	updateBarycenterTreeScalars (std::vector< ftm::FTMTree_MT * > &trees, ftm::MergeTree< dataType > &baryMergeTree, std::vector< double > &alphas, unsigned int indexAddedNodes, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings)

template<class dataType >
void	updateBarycenterTree (std::vector< ftm::FTMTree_MT * > &trees, ftm::MergeTree< dataType > &baryMergeTree, std::vector< double > &alphas, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings)

template<class dataType >
void	computeOneDistance (ftm::FTMTree_MT tree, ftm::FTMTree_MT baryTree, std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > &matching, dataType &distance, bool useDoubleInput=false, bool isFirstInput=true)

template<class dataType >
void	computeOneDistance (ftm::FTMTree_MT *tree, ftm::MergeTree< dataType > &baryMergeTree, std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > &matching, dataType &distance, bool useDoubleInput=false, bool isFirstInput=true)

template<class dataType >
void	computeOneDistance (ftm::MergeTree< dataType > &baryMergeTree, ftm::MergeTree< dataType > &baryMergeTree2, std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > &matching, dataType &distance, bool useDoubleInput=false, bool isFirstInput=true)

template<class dataType >
void	assignment (std::vector< ftm::FTMTree_MT * > &trees, ftm::MergeTree< dataType > &baryMergeTree, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings, std::vector< dataType > &distances, bool useDoubleInput=false, bool isFirstInput=true)

template<class dataType >
void	assignmentPara (std::vector< ftm::FTMTree_MT * > &trees, ftm::MergeTree< dataType > &baryMergeTree, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings, std::vector< dataType > &distances, bool useDoubleInput=false, bool isFirstInput=true)

template<class dataType >
void	assignmentTask (std::vector< ftm::FTMTree_MT * > &trees, ftm::MergeTree< dataType > &baryMergeTree, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings, std::vector< dataType > &distances, bool useDoubleInput=false, bool isFirstInput=true)

template<class dataType >
unsigned int	persistenceScaling (std::vector< ftm::FTMTree_MT * > &trees, std::vector< ftm::MergeTree< dataType > > &mergeTrees, std::vector< ftm::FTMTree_MT * > &oriTrees, int iterationNumber, std::vector< std::vector< ftm::idNode > > &deletedNodes)

template<class dataType >
void	addScaledDeletedNodesCost (std::vector< ftm::FTMTree_MT * > &oriTrees, std::vector< std::vector< ftm::idNode > > &deletedNodes, std::vector< dataType > &distances)

template<class dataType >
void	computeBarycenter (std::vector< ftm::FTMTree_MT * > &trees, ftm::MergeTree< dataType > &baryMergeTree, std::vector< double > &alphas, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &finalMatchings, bool finalAsgnDoubleInput=false, bool finalAsgnFirstInput=true)

template<class dataType >
void	execute (std::vector< ftm::MergeTree< dataType > > &trees, std::vector< double > &alphas, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &finalMatchings, ftm::MergeTree< dataType > &baryMergeTree, bool finalAsgnDoubleInput=false, bool finalAsgnFirstInput=true)

template<class dataType >
void	execute (std::vector< ftm::MergeTree< dataType > > &trees, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &finalMatchings, ftm::MergeTree< dataType > &baryMergeTree, bool finalAsgnDoubleInput=false, bool finalAsgnFirstInput=true)

template<class dataType >
void	limitSizePercent (ftm::MergeTree< dataType > &bary, std::vector< ftm::FTMTree_MT * > &trees, double percent, bool useBD)

template<class dataType >
void	limitSizeBarycenter (ftm::MergeTree< dataType > &bary, std::vector< ftm::FTMTree_MT * > &trees, unsigned int barycenterMaximumNumberOfPairs, double percent, bool useBD=true)

template<class dataType >
void	limitSizeBarycenter (ftm::MergeTree< dataType > &bary, std::vector< ftm::FTMTree_MT * > &trees, double percent, bool useBD=true)

template<class dataType >
void	limitSizeBarycenter (ftm::MergeTree< dataType > &bary, std::vector< ftm::FTMTree_MT * > &trees, bool useBD=true)

template<class dataType >
void	fixMergedRootOriginBarycenter (ftm::MergeTree< dataType > &barycenter)

void	printBaryStats (ftm::FTMTree_MT *baryTree, const debug::Priority &priority=debug::Priority::INFO)

template<class dataType >
void	verifyBarycenterTwoTrees (std::vector< ftm::FTMTree_MT * > &trees, ftm::MergeTree< dataType > &baryMergeTree, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &finalMatchings, std::vector< dataType > distances)

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	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)

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)

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::MergeTreeBarycenter
double	tol_ = 0.0

bool	addNodes_ = true

bool	deterministic_ = true

bool	isCalled_ = false

bool	progressiveBarycenter_ = false

double	progressiveSpeedDivisor_ = 4.0

double	alpha_ = 0.5

unsigned int	barycenterMaximumNumberOfPairs_ = 0

double	barycenterSizeLimitPercent_ = 0.0

double	allDistanceTime_ = 0

double	addDeletedNodesTime_ = 0

bool	preprocess_ = true

bool	postprocess_ = true

std::vector< double >	finalDistances_

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

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_

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

Detailed Description

template<class dataType2>
class ttk::MergeTreeClustering< dataType2 >

The MergeTreeClustering class that computes a clustering of an ensemble of merge trees in k clusters

Definition at line 47 of file MergeTreeClustering.h.

Constructor & Destructor Documentation

◆ MergeTreeClustering()

template<class dataType2 >

ttk::MergeTreeClustering< dataType2 >::MergeTreeClustering ( )

inline

Definition at line 71 of file MergeTreeClustering.h.

◆ ~MergeTreeClustering()

template<class dataType2 >

ttk::MergeTreeClustering< dataType2 >::~MergeTreeClustering ( )

overridedefault

Member Function Documentation

◆ assignmentCentroids()

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::assignmentCentroids	(	std::vector< ftm::FTMTree_MT * > &	trees,
		std::vector< ftm::MergeTree< dataType > > &	centroids,
		std::vector< std::tuple< int, int > > &	assignmentC,
		std::vector< dataType > &	bestDistanceT,
		std::vector< ftm::FTMTree_MT * > &	trees2,
		std::vector< ftm::MergeTree< dataType > > &	centroids2
	)

inline

Definition at line 398 of file MergeTreeClustering.h.

◆ assignmentCentroidsAccelerated()

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::assignmentCentroidsAccelerated	(	std::vector< ftm::FTMTree_MT * > &	trees,
		std::vector< ftm::MergeTree< dataType > > &	centroids,
		std::vector< std::tuple< int, int > > &	assignmentC,
		std::vector< dataType > &	bestDistanceT,
		std::vector< ftm::FTMTree_MT * > &	trees2,
		std::vector< ftm::MergeTree< dataType > > &	centroids2
	)

inline

Definition at line 258 of file MergeTreeClustering.h.

◆ assignmentCentroidsNaive()

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::assignmentCentroidsNaive	(	std::vector< ftm::FTMTree_MT * > &	trees,
		std::vector< ftm::MergeTree< dataType > > &	centroids,
		std::vector< std::tuple< int, int > > &	assignmentC,
		std::vector< dataType > &	bestDistanceT,
		std::vector< ftm::FTMTree_MT * > &	trees2,
		std::vector< ftm::MergeTree< dataType > > &	centroids2
	)

inline

Definition at line 458 of file MergeTreeClustering.h.

◆ computeCentroids()

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::computeCentroids	(	std::vector< ftm::FTMTree_MT * > &	trees,
		std::vector< ftm::MergeTree< dataType > > &	centroids,
		matchingVectorType &	outputMatching,
		std::vector< double > &	alphas,
		std::vector< int > &	clusteringAssignment,
		std::vector< ftm::FTMTree_MT * > &	trees2,
		std::vector< ftm::MergeTree< dataType > > &	centroids2,
		matchingVectorType &	outputMatching2
	)

inline

Definition at line 643 of file MergeTreeClustering.h.

◆ computeOneBarycenter()

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::computeOneBarycenter	(	std::vector< ftm::FTMTree_MT * > &	trees,
		ftm::MergeTree< dataType > &	baryMergeTree,
		std::vector< double > &	alphas,
		std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &	finalMatchings
	)

inline

Definition at line 611 of file MergeTreeClustering.h.

◆ copyCentroids()

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::copyCentroids	(	std::vector< ftm::MergeTree< dataType > > &	centroids,
		std::vector< ftm::MergeTree< dataType > > &	oldCentroids
	)

inline

Definition at line 247 of file MergeTreeClustering.h.

◆ execute() [1/3]

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::execute	(	std::vector< ftm::MergeTree< dataType > > &	trees,
		matchingVectorType &	outputMatching,
		std::vector< double > &	alphas,
		std::vector< int > &	clusteringAssignment,
		std::vector< ftm::MergeTree< dataType > > &	trees2,
		matchingVectorType &	outputMatching2,
		std::vector< ftm::MergeTree< dataType > > &	centroids,
		std::vector< ftm::MergeTree< dataType > > &	centroids2
	)

inline

Definition at line 758 of file MergeTreeClustering.h.

◆ execute() [2/3]

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::execute	(	std::vector< ftm::MergeTree< dataType > > &	trees,
		matchingVectorType &	outputMatching,
		std::vector< int > &	clusteringAssignment,
		std::vector< ftm::MergeTree< dataType > > &	centroids
	)

inline

Definition at line 833 of file MergeTreeClustering.h.

◆ execute() [3/3]

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::execute	(	std::vector< ftm::MergeTree< dataType > > &	trees,
		matchingVectorType &	outputMatching,
		std::vector< int > &	clusteringAssignment,
		std::vector< ftm::MergeTree< dataType > > &	trees2,
		matchingVectorType &	outputMatching2,
		std::vector< ftm::MergeTree< dataType > > &	centroids,
		std::vector< ftm::MergeTree< dataType > > &	centroids2
	)

inline

Definition at line 814 of file MergeTreeClustering.h.

◆ finalAssignmentCentroids()

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::finalAssignmentCentroids	(	std::vector< ftm::FTMTree_MT * > &	trees,
		std::vector< ftm::MergeTree< dataType > > &	centroids,
		matchingVectorType &	matchingsC,
		std::vector< std::tuple< int, int > > &	assignmentC,
		std::vector< dataType > &	bestDistanceT,
		std::vector< ftm::FTMTree_MT * > &	trees2,
		std::vector< ftm::MergeTree< dataType > > &	centroids2,
		matchingVectorType &	matchingsC2
	)

inline

Definition at line 410 of file MergeTreeClustering.h.

◆ fixMergedRootOriginClustering()

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::fixMergedRootOriginClustering ( std::vector< ftm::MergeTree< dataType > > & centroids )

inline

Definition at line 864 of file MergeTreeClustering.h.

◆ getCentroidsDistanceMatrix()

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::getCentroidsDistanceMatrix	(	std::vector< ftm::MergeTree< dataType > > &	centroids,
		std::vector< std::vector< double > > &	distanceMatrix,
		bool	useDoubleInput = `false`,
		bool	isFirstInput = `true`
	)

inline

Definition at line 497 of file MergeTreeClustering.h.

◆ getTrees2NodeCorr()

template<class dataType2 >

std::vector< std::vector< int > > ttk::MergeTreeClustering< dataType2 >::getTrees2NodeCorr ( )

inline

Definition at line 86 of file MergeTreeClustering.h.

◆ initAcceleratedKMeans()

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::initAcceleratedKMeans	(	std::vector< ftm::FTMTree_MT * > &	trees,
		std::vector< ftm::MergeTree< dataType > > &	centroids,
		std::vector< ftm::FTMTree_MT * > &	trees2,
		std::vector< ftm::MergeTree< dataType > > &	centroids2
	)

inline

Definition at line 228 of file MergeTreeClustering.h.

◆ initAcceleratedKMeansVectors()

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::initAcceleratedKMeansVectors	(	std::vector< ftm::FTMTree_MT * > &	trees,
		std::vector< ftm::MergeTree< dataType > > &	centroids,
		std::vector< ftm::FTMTree_MT * > &	ttkNotUsedtrees2
	)

inline

Definition at line 207 of file MergeTreeClustering.h.

◆ initCentroids()

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::initCentroids	(	std::vector< ftm::FTMTree_MT * > &	trees,
		std::vector< ftm::FTMTree_MT * > &	trees2,
		std::vector< std::vector< ftm::MergeTree< dataType > > > &	allCentroids
	)

inline

Implementation of the algorithm.

Definition at line 99 of file MergeTreeClustering.h.

◆ initNewCentroid()

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::initNewCentroid	(	std::vector< ftm::FTMTree_MT * > &	trees,
		ftm::MergeTree< dataType > &	centroid,
		int	noNewCentroid
	)

inline

Definition at line 192 of file MergeTreeClustering.h.

◆ matchingCorrespondence()

template<class dataType2 >

void ttk::MergeTreeClustering< dataType2 >::matchingCorrespondence	(	treesMatchingVector &	matchingT,
		std::vector< int > &	nodeCorr,
		std::vector< int > &	assignedTreesIndex
	)

inline

Definition at line 510 of file MergeTreeClustering.h.

◆ postprocessingClustering()

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::postprocessingClustering	(	std::vector< ftm::MergeTree< dataType > > &	trees,
		std::vector< ftm::MergeTree< dataType > > &	centroids,
		matchingVectorType &	outputMatching,
		std::vector< int > &	clusteringAssignment
	)

inline

Definition at line 879 of file MergeTreeClustering.h.

◆ preprocessingClustering()

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::preprocessingClustering	(	std::vector< ftm::MergeTree< dataType > > &	trees,
		std::vector< std::vector< int > > &	nodeCorr,
		bool	useMinMaxPairT = `true`
	)

inline

Definition at line 847 of file MergeTreeClustering.h.

◆ printCentroidsStats()

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::printCentroidsStats	(	std::vector< ftm::MergeTree< dataType > > &	centroids,
		std::vector< ftm::MergeTree< dataType > > &	centroids2
	)

inline

Definition at line 899 of file MergeTreeClustering.h.

◆ putBackMinMaxPair()

template<class dataType2 >

template<class dataType >

void ttk::MergeTreeClustering< dataType2 >::putBackMinMaxPair	(	std::vector< ftm::MergeTree< dataType > > &	centroids,
		std::vector< ftm::MergeTree< dataType > > &	centroids2
	)

inline

Definition at line 871 of file MergeTreeClustering.h.

◆ samePreviousAssignment()

template<class dataType2 >

bool ttk::MergeTreeClustering< dataType2 >::samePreviousAssignment ( int clusterId )

inline

Definition at line 525 of file MergeTreeClustering.h.

◆ setMixtureCoefficient()

template<class dataType2 >

void ttk::MergeTreeClustering< dataType2 >::setMixtureCoefficient ( double coef )

inline

Definition at line 82 of file MergeTreeClustering.h.

◆ setNoCentroids()

template<class dataType2 >

void ttk::MergeTreeClustering< dataType2 >::setNoCentroids ( unsigned int noCentroidsT )

inline

Definition at line 78 of file MergeTreeClustering.h.

◆ updateCentroids()

template<class dataType2 >

template<class dataType >

bool ttk::MergeTreeClustering< dataType2 >::updateCentroids	(	std::vector< ftm::FTMTree_MT * > &	trees,
		std::vector< ftm::MergeTree< dataType > > &	centroids,
		std::vector< double > &	alphas,
		std::vector< std::tuple< int, int > > &	assignmentC
	)

inline

Definition at line 534 of file MergeTreeClustering.h.

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

/home/julien/Pro/git/github/ttk-tierny/core/base/mergeTreeClustering/MergeTreeClustering.h

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MergeTreeClustering()

◆ ~MergeTreeClustering()

Member Function Documentation

◆ assignmentCentroids()

◆ assignmentCentroidsAccelerated()

◆ assignmentCentroidsNaive()

◆ computeCentroids()

◆ computeOneBarycenter()

◆ copyCentroids()

◆ execute() [1/3]

◆ execute() [2/3]

◆ execute() [3/3]

◆ finalAssignmentCentroids()

◆ fixMergedRootOriginClustering()

◆ getCentroidsDistanceMatrix()

◆ getTrees2NodeCorr()

◆ initAcceleratedKMeans()

◆ initAcceleratedKMeansVectors()

◆ initCentroids()

◆ initNewCentroid()

◆ matchingCorrespondence()

◆ postprocessingClustering()

◆ preprocessingClustering()

◆ printCentroidsStats()

◆ putBackMinMaxPair()

◆ samePreviousAssignment()

◆ setMixtureCoefficient()

◆ setNoCentroids()

◆ updateCentroids()