#include <MergeTreePrincipalGeodesicsDecoding.h>

Inheritance diagram for ttk::MergeTreePrincipalGeodesicsDecoding:

Public Member Functions
	MergeTreePrincipalGeodesicsDecoding ()

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

template<class dataType >
void	processInputTrees (std::vector< ttk::ftm::MergeTree< dataType > > &inputTrees)

template<class dataType >
void	getGeodesicsMiddle (ftm::MergeTree< dataType > &barycenter, std::vector< std::vector< double * > > &vS, std::vector< std::vector< double * > > &v2s, size_t vSize, std::array< double, 2 > &middle)

template<class dataType >
void	computeGeodesicsDistance (std::vector< ttk::ftm::MergeTree< dataType > > &barycenters)

template<class dataType >
void	reconstruction (ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &inputTrees, std::vector< ftm::MergeTree< dataType > > &reconstructedTrees, std::vector< double > &reconstructionErrors, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &recInputMatchings, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &recBaryMatchings, bool isSecondInput=false)

template<class dataType >
void	constructGeodesicsTrees (ftm::MergeTree< dataType > &barycenter, std::vector< std::vector< ftm::MergeTree< dataType > > > &geodesicsTrees, bool isSecondInput=false)

template<class dataType >
void	constructGeodesicsEllipses (ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &geodesicsEllipses, bool isSecondInput=false)

unsigned int	getNumberOfRectangles (unsigned int rectangleMultiplier=1)

template<class dataType >
void	constructGeodesicsRectangle (ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &geodesicsRectangle, unsigned int rectangleMultiplier=1, bool isSecondInput=false)

template<class dataType >
void	constructGeodesicsSurface (ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &geodesicsSurface, bool isSecondInput=false)

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::MergeTreePrincipalGeodesicsBase
	MergeTreePrincipalGeodesicsBase ()

template<class dataType >
dataType	computeReconstructionError (ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &inputTrees, std::vector< std::vector< double * > > &vS, std::vector< std::vector< double * > > &v2s, size_t vSize, std::vector< std::vector< double > > &allTreesTs, std::vector< double > &reconstructionErrors, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings, bool transposeVector=true)

template<class dataType >
dataType	computeReconstructionError (ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &inputTrees, std::vector< std::vector< std::vector< double > > > &vS, std::vector< std::vector< std::vector< double > > > &v2s, std::vector< std::vector< double > > &allTreesTs, std::vector< double > &reconstructionErrors)

template<class dataType >
dataType	computeReconstructionError (ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &inputTrees, std::vector< std::vector< std::vector< double > > > &vS, std::vector< std::vector< std::vector< double > > > &v2s, std::vector< std::vector< double > > &allTreesTs)

double	getGeodesicVectorMiddle (std::vector< double > &v, std::vector< double > &v2)

double	getAdjustedTMax (double tMin, double m)

double	getAdjustedTMin (double tMax, double m)

void	updateT (double newT, double m, double &tMin, double &tMax, bool updateTMin)

template<class dataType >
bool	adjustDiagonalT (dataType baryBirth, dataType baryDeath, ftm::idNode node, std::vector< std::vector< double > > &vNew, std::vector< std::vector< double > > &v2New, double &tMin, double &tMax)

template<class dataType >
bool	adjustNestingT (ftm::MergeTree< dataType > &ttkNotUsed(barycenter), dataType baryBirth, dataType baryDeath, ftm::idNode node, std::vector< std::vector< double > > &vNew, std::vector< std::vector< double > > &v2New, double &tMin, double &tMax)

template<class dataType >
void	getInterpolationVectorDebugMsg (dataType birth, dataType death, std::vector< std::vector< double > > &vNew, std::vector< std::vector< double > > &v2New, int i, double t, double tMin, double tMax, const std::string &msg, std::stringstream &ssT)

template<class dataType >
double	getTNew (ftm::MergeTree< dataType > &barycenter, std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, int i, double t)

template<class dataType >
void	getInterpolationVector (ftm::MergeTree< dataType > &barycenter, std::vector< double * > &v, std::vector< double * > &v2, size_t vSize, double t, std::vector< dataType > &interpolationVectorT, bool transposeVector)

template<class dataType >
void	getInterpolation (ftm::MergeTree< dataType > &barycenter, std::vector< double * > &v, std::vector< double * > &v2, size_t vSize, double t, ftm::MergeTree< dataType > &interpolated, bool transposeVector=true)

template<class dataType >
void	getInterpolation (ftm::MergeTree< dataType > &barycenter, std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, double t, ftm::MergeTree< dataType > &interpolated)

template<class dataType >
void	getMultiInterpolation (ftm::MergeTree< dataType > &barycenter, std::vector< std::vector< double * > > &vS, std::vector< std::vector< double * > > &v2s, size_t vSize, std::vector< double > &ts, ftm::MergeTree< dataType > &interpolated, bool transposeVector=true)

template<class dataType >
void	getMultiInterpolation (ftm::MergeTree< dataType > &barycenter, std::vector< std::vector< std::vector< double > > > &vS, std::vector< std::vector< std::vector< double > > > &v2s, std::vector< double > &ts, ftm::MergeTree< dataType > &interpolated)

template<class dataType >
void	getMultiInterpolation (ftm::MergeTree< dataType > &barycenter, std::vector< std::vector< std::vector< double > > > &vS, std::vector< std::vector< std::vector< double > > > &v2s, std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, std::vector< double > &ts, double t, ftm::MergeTree< dataType > &interpolated)

void	callGramSchmidt (std::vector< std::vector< double > > &vS, std::vector< double > &v, std::vector< double > &newV)

void	vectorToPointer (std::vector< double > &vec, double *&pVec)

void	vectorsToPointers (std::vector< std::vector< double > > &vec, std::vector< double * > &pVec)

void	vectorOfVectorsToPointers (std::vector< std::vector< std::vector< double > > > &vS, std::vector< std::vector< double * > > &pVS)

void	pointerToVector (double *pVec, size_t size, std::vector< double > &vec)

void	pointersToVectors (std::vector< double * > &pVec, std::vector< size_t > sizes, std::vector< std::vector< double > > &vec)

void	pointersToVectors (std::vector< double * > &pVec, size_t size, std::vector< std::vector< double > > &vec)

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

template<class dataType >
void	computeOneDistance (ftm::MergeTree< dataType > &tree1, ftm::MergeTree< dataType > &tree2, std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > &matching, dataType &distance, bool isCalled=false, bool useDoubleInput=false, bool isFirstInput=true)

template<class dataType >
void	computeOneDistance (ftm::MergeTree< dataType > &tree1, ftm::MergeTree< dataType > &tree2, dataType &distance, bool isCalled=false, bool useDoubleInput=false, bool isFirstInput=true)

template<class dataType >
void	initVectorFromMatching (ftm::MergeTree< dataType > &barycenter, ftm::MergeTree< dataType > &tree, std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > &matching, std::vector< std::vector< double > > &v)

template<class dataType >
void	initRandomVector (ftm::MergeTree< dataType > &barycenter, std::vector< std::vector< double > > &v, std::vector< std::vector< std::vector< double > > > &vS, std::vector< std::vector< std::vector< double > > > &v2s)

template<class dataType , typename F >
int	initVectors (int geodesicNumber, ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &trees, ftm::MergeTree< dataType > &barycenter2, std::vector< ftm::MergeTree< dataType > > &trees2, std::vector< std::vector< double > > &v1, std::vector< std::vector< double > > &v2, std::vector< std::vector< double > > &trees2V1, std::vector< std::vector< double > > &trees2V2, int newVectorOffset, std::vector< double > &inputToOriginDistances, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &baryMatchings, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &baryMatchings2, std::vector< std::vector< double > > &inputToGeodesicsDistances, std::vector< std::vector< std::vector< double > > > &vS, std::vector< std::vector< std::vector< double > > > &v2s, std::vector< std::vector< std::vector< double > > > &trees2Vs, std::vector< std::vector< std::vector< double > > > &trees2V2s, bool projectInitializedVectors, F initializedVectorsProjection)

template<class dataType >
void	computeOneBarycenter (std::vector< ftm::MergeTree< dataType > > &trees, ftm::MergeTree< dataType > &baryMergeTree, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings, std::vector< double > &finalDistances, double barycenterSizeLimitPercent, unsigned int barycenterMaximumNumberOfPairs, bool useDoubleInput=false, bool isFirstInput=true)

template<class dataType >
void	computeOneBarycenter (std::vector< ftm::MergeTree< dataType > > &trees, ftm::MergeTree< dataType > &baryMergeTree, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings, std::vector< double > &finalDistances, double barycenterSizeLimitPercent, bool useDoubleInput=false, bool isFirstInput=true)

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

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

template<class dataType >
void	computeOneBarycenter (std::vector< ftm::MergeTree< dataType > > &trees, ftm::MergeTree< dataType > &baryMergeTree)

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

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

template<class dataType >
void	getMatchingVector (ftm::MergeTree< dataType > &barycenter, ftm::MergeTree< dataType > &tree, std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > &matchings, std::vector< ftm::idNode > &matchingVector)

template<class dataType >
void	getInverseMatchingVector (ftm::MergeTree< dataType > &barycenter, ftm::MergeTree< dataType > &tree, std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > &matchings, std::vector< ftm::idNode > &matchingVector)

template<class dataType >
void	getMatchingMatrix (ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &trees, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings, std::vector< std::vector< ftm::idNode > > &matchingMatrix)

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

template<class dataType >
void	computeBranchesCorrelationMatrix (ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &trees, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &baryMatchings, std::vector< std::vector< double > > &allTs, std::vector< std::vector< double > > &branchesCorrelationMatrix, std::vector< std::vector< double > > &persCorrelationMatrix)

void	zeroPadding (std::string &colName, const size_t numberCols, const size_t colIdx)

std::string	getTableCoefficientName (int noGeodesics, int geodesicNum)

std::string	getTableCoefficientNormName (int noGeodesics, int geodesicNum)

std::string	getTableVectorName (int noGeodesics, int geodesicNum, int vId, int vComp, bool isSecondInput=false)

std::string	getTableCorrelationName (int noGeodesics, int geodesicNum)

std::string	getTableCorrelationPersName (int noGeodesics, int geodesicNum)

std::string	getTableCorrelationTreeName (int noTrees, int treeNum)

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)

Protected Attributes
bool	computeReconstructionError_ = false

bool	transferInputTreesInformation_ = false

bool	transferBarycenterInformation_ = false

std::vector< std::vector< double * > >	pVS_

std::vector< std::vector< double * > >	pV2s_

std::vector< std::vector< double * > >	pTrees2Vs_

std::vector< std::vector< double * > >	pTrees2V2s_

size_t	vSize_

size_t	vSize2_

std::vector< double * >	pBranchesCorrelationMatrix_

std::vector< double * >	pPersCorrelationMatrix_

std::vector< std::vector< double > >	tEllipses_

std::vector< std::vector< double > >	tRectangle_

std::vector< std::vector< double > >	tSurface_

std::vector< std::vector< std::vector< double > > >	tGeodesics_

std::vector< double >	geodesicsDistances_

std::vector< bool >	surfaceIsBoundary_

std::vector< int >	surfaceBoundaryID_

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::MergeTreePrincipalGeodesicsBase
std::vector< std::vector< std::vector< double > > >	vS_

std::vector< std::vector< std::vector< double > > >	v2s_

std::vector< std::vector< std::vector< double > > >	trees2Vs_

std::vector< std::vector< std::vector< double > > >	trees2V2s_

std::vector< std::vector< double > >	allTs_

std::vector< std::vector< double > >	allScaledTs_

std::vector< std::vector< double > >	allTreesTs_

std::vector< std::vector< double > >	branchesCorrelationMatrix_

std::vector< std::vector< double > >	persCorrelationMatrix_

std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > >	baryMatchings_

std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > >	baryMatchings2_

Protected Attributes inherited from ttk::MergeTreeAxesAlgorithmBase
bool	deterministic_ = true

unsigned int	numberOfGeodesics_ = 1

unsigned int	k_ = 10

double	barycenterSizeLimitPercent_ = 0.0

std::vector< std::vector< int > >	trees2NodeCorr_

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_

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 MergeTreePrincipalGeodesicsDecoding class provides methods to compute the reconstruction of merge trees or persistence diagrams given a Principal Geodesic Analysis basis and projection coefficients.

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

Date: 2022.

This module defines the MergeTreePrincipalGeodesicsDecoding class that computes the reconstruction of merge trees or persistence diagrams given a Principal Geodesic Analysis basis and projection coefficients.

Related publication:
"Principal Geodesic Analysis of Merge Trees (and Persistence Diagrams)"
Mathieu Pont, Jules Vidal, Julien Tierny.
Online examples:

Merge Tree Principal Geodesic Analysis example

Definition at line 32 of file MergeTreePrincipalGeodesicsDecoding.h.

Constructor & Destructor Documentation

◆ MergeTreePrincipalGeodesicsDecoding()

ttk::MergeTreePrincipalGeodesicsDecoding::MergeTreePrincipalGeodesicsDecoding ( )

Definition at line 3 of file MergeTreePrincipalGeodesicsDecoding.cpp.

Member Function Documentation

◆ computeGeodesicsDistance()

template<class dataType >

void ttk::MergeTreePrincipalGeodesicsDecoding::computeGeodesicsDistance ( std::vector< ttk::ftm::MergeTree< dataType > > & barycenters )

inline

Definition at line 112 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ constructGeodesicsEllipses()

template<class dataType >

void ttk::MergeTreePrincipalGeodesicsDecoding::constructGeodesicsEllipses	(	ftm::MergeTree< dataType > &	barycenter,
		std::vector< ftm::MergeTree< dataType > > &	geodesicsEllipses,
		bool	isSecondInput = `false`
	)

inline

Definition at line 284 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ constructGeodesicsRectangle()

template<class dataType >

void ttk::MergeTreePrincipalGeodesicsDecoding::constructGeodesicsRectangle	(	ftm::MergeTree< dataType > &	barycenter,
		std::vector< ftm::MergeTree< dataType > > &	geodesicsRectangle,
		unsigned int	rectangleMultiplier = `1`,
		bool	isSecondInput = `false`
	)

inline

Definition at line 355 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ constructGeodesicsSurface()

template<class dataType >

void ttk::MergeTreePrincipalGeodesicsDecoding::constructGeodesicsSurface	(	ftm::MergeTree< dataType > &	barycenter,
		std::vector< ftm::MergeTree< dataType > > &	geodesicsSurface,
		bool	isSecondInput = `false`
	)

inline

Definition at line 424 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ constructGeodesicsTrees()

template<class dataType >

void ttk::MergeTreePrincipalGeodesicsDecoding::constructGeodesicsTrees	(	ftm::MergeTree< dataType > &	barycenter,
		std::vector< std::vector< ftm::MergeTree< dataType > > > &	geodesicsTrees,
		bool	isSecondInput = `false`
	)

inline

Definition at line 238 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ getGeodesicsMiddle()

template<class dataType >

void ttk::MergeTreePrincipalGeodesicsDecoding::getGeodesicsMiddle	(	ftm::MergeTree< dataType > &	barycenter,
		std::vector< std::vector< double * > > &	vS,
		std::vector< std::vector< double * > > &	v2s,
		size_t	vSize,
		std::array< double, 2 > &	middle
	)

inline

Definition at line 85 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ getNumberOfRectangles()

unsigned int ttk::MergeTreePrincipalGeodesicsDecoding::getNumberOfRectangles ( unsigned int rectangleMultiplier = 1 )

inline

Definition at line 350 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ preprocessBarycenter()

template<class dataType >

void ttk::MergeTreePrincipalGeodesicsDecoding::preprocessBarycenter ( ftm::MergeTree< dataType > & barycenter )

inline

Definition at line 61 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ processInputTrees()

template<class dataType >

void ttk::MergeTreePrincipalGeodesicsDecoding::processInputTrees ( std::vector< ttk::ftm::MergeTree< dataType > > & inputTrees )

inline

Definition at line 74 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ reconstruction()

template<class dataType >

void ttk::MergeTreePrincipalGeodesicsDecoding::reconstruction	(	ftm::MergeTree< dataType > &	barycenter,
		std::vector< ftm::MergeTree< dataType > > &	inputTrees,
		std::vector< ftm::MergeTree< dataType > > &	reconstructedTrees,
		std::vector< double > &	reconstructionErrors,
		std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &	recInputMatchings,
		std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &	recBaryMatchings,
		bool	isSecondInput = `false`
	)

inline

Definition at line 161 of file MergeTreePrincipalGeodesicsDecoding.h.

Member Data Documentation

◆ computeReconstructionError_

bool ttk::MergeTreePrincipalGeodesicsDecoding::computeReconstructionError_ = false

protected

Definition at line 37 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ geodesicsDistances_

std::vector<double> ttk::MergeTreePrincipalGeodesicsDecoding::geodesicsDistances_

protected

Definition at line 49 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ pBranchesCorrelationMatrix_

std::vector<double *> ttk::MergeTreePrincipalGeodesicsDecoding::pBranchesCorrelationMatrix_

protected

Definition at line 43 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ pPersCorrelationMatrix_

std::vector<double *> ttk::MergeTreePrincipalGeodesicsDecoding::pPersCorrelationMatrix_

protected

Definition at line 43 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ pTrees2V2s_

std::vector<std::vector<double *> > ttk::MergeTreePrincipalGeodesicsDecoding::pTrees2V2s_

protected

Definition at line 41 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ pTrees2Vs_

std::vector<std::vector<double *> > ttk::MergeTreePrincipalGeodesicsDecoding::pTrees2Vs_

protected

Definition at line 41 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ pV2s_

std::vector<std::vector<double *> > ttk::MergeTreePrincipalGeodesicsDecoding::pV2s_

protected

Definition at line 41 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ pVS_

std::vector<std::vector<double *> > ttk::MergeTreePrincipalGeodesicsDecoding::pVS_

protected

Definition at line 41 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ surfaceBoundaryID_

std::vector<int> ttk::MergeTreePrincipalGeodesicsDecoding::surfaceBoundaryID_

protected

Definition at line 52 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ surfaceIsBoundary_

std::vector<bool> ttk::MergeTreePrincipalGeodesicsDecoding::surfaceIsBoundary_

protected

Definition at line 51 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ tEllipses_

std::vector<std::vector<double> > ttk::MergeTreePrincipalGeodesicsDecoding::tEllipses_

protected

Definition at line 46 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ tGeodesics_

std::vector<std::vector<std::vector<double> > > ttk::MergeTreePrincipalGeodesicsDecoding::tGeodesics_

protected

Definition at line 47 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ transferBarycenterInformation_

bool ttk::MergeTreePrincipalGeodesicsDecoding::transferBarycenterInformation_ = false

protected

Definition at line 39 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ transferInputTreesInformation_

bool ttk::MergeTreePrincipalGeodesicsDecoding::transferInputTreesInformation_ = false

protected

Definition at line 38 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ tRectangle_

std::vector<std::vector<double> > ttk::MergeTreePrincipalGeodesicsDecoding::tRectangle_

protected

Definition at line 46 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ tSurface_

std::vector<std::vector<double> > ttk::MergeTreePrincipalGeodesicsDecoding::tSurface_

protected

Definition at line 46 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ vSize2_

size_t ttk::MergeTreePrincipalGeodesicsDecoding::vSize2_

protected

Definition at line 42 of file MergeTreePrincipalGeodesicsDecoding.h.

◆ vSize_

size_t ttk::MergeTreePrincipalGeodesicsDecoding::vSize_

protected

Definition at line 42 of file MergeTreePrincipalGeodesicsDecoding.h.

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

/home/julien/Pro/git/github/ttk-tierny/core/base/mergeTreePrincipalGeodesicsDecoding/MergeTreePrincipalGeodesicsDecoding.h
/home/julien/Pro/git/github/ttk-tierny/core/base/mergeTreePrincipalGeodesicsDecoding/MergeTreePrincipalGeodesicsDecoding.cpp

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MergeTreePrincipalGeodesicsDecoding()

Member Function Documentation

◆ computeGeodesicsDistance()

◆ constructGeodesicsEllipses()

◆ constructGeodesicsRectangle()

◆ constructGeodesicsSurface()

◆ constructGeodesicsTrees()

◆ getGeodesicsMiddle()

◆ getNumberOfRectangles()

◆ preprocessBarycenter()

◆ processInputTrees()

◆ reconstruction()

Member Data Documentation

◆ computeReconstructionError_

◆ geodesicsDistances_

◆ pBranchesCorrelationMatrix_

◆ pPersCorrelationMatrix_

◆ pTrees2V2s_

◆ pTrees2Vs_

◆ pV2s_

◆ pVS_

◆ surfaceBoundaryID_

◆ surfaceIsBoundary_

◆ tEllipses_

◆ tGeodesics_

◆ transferBarycenterInformation_

◆ transferInputTreesInformation_

◆ tRectangle_

◆ tSurface_

◆ vSize2_

◆ vSize_