ttk::MergeTreePrincipalGeodesics Class Reference

#include <MergeTreePrincipalGeodesics.h>

Inheritance diagram for ttk::MergeTreePrincipalGeodesics:

Classes
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Public Member Functions
	MergeTreePrincipalGeodesics ()
unsigned int	getGeodesicNumber ()
template<class dataType >
void	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)
double	orthogonalCost (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)
double	regularizerCost (std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2)
double	projectionCost (std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, std::vector< std::vector< std::vector< double > > > &vS, std::vector< std::vector< std::vector< double > > > &v2s, double optMapCost)
template<class dataType >
double	barycentricProjection (ftm::MergeTree< dataType > &barycenter, ftm::MergeTree< dataType > &extremity, std::vector< std::vector< double > > &v, bool isV1, bool useDoubleInput=false, bool isFirstInput=true)
template<class dataType >
double	optimalMappingSetProjection (ftm::MergeTree< dataType > &barycenter, std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, ftm::MergeTree< dataType > &barycenter2, std::vector< std::vector< double > > &trees2V, std::vector< std::vector< double > > &trees2V2, bool useSecondInput=false)
void	trueGeneralizedGeodesicProjection (std::vector< std::vector< double > > &v1, std::vector< std::vector< double > > &v2)
void	orthogonalProjection (std::vector< std::vector< double > > &v1, std::vector< std::vector< double > > &v2, std::vector< std::vector< std::vector< double > > > &vS, std::vector< std::vector< std::vector< double > > > &v2s)
template<class dataType >
double	projectionStep (int geodesicNumber, ftm::MergeTree< dataType > &barycenter, std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, std::vector< std::vector< std::vector< double > > > &vS, std::vector< std::vector< std::vector< double > > > &v2s, ftm::MergeTree< dataType > &barycenter2, std::vector< std::vector< double > > &trees2V, std::vector< std::vector< double > > &trees2V2, std::vector< std::vector< std::vector< double > > > &trees2Vs, std::vector< std::vector< std::vector< double > > > &trees2V2s, bool useSecondInput, unsigned int noProjectionStep)
template<class dataType >
void	assignmentImpl (ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &trees, std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, ftm::MergeTree< dataType > &barycenter2, std::vector< ftm::MergeTree< dataType > > &trees2, std::vector< std::vector< double > > &trees2V, std::vector< std::vector< double > > &trees2V2, std::vector< std::vector< double > > &allTreesTs, 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< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings2, std::vector< double > &ts, std::vector< double > &distances)
template<class dataType >
void	assignmentStep (ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &trees, std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, ftm::MergeTree< dataType > &barycenter2, std::vector< ftm::MergeTree< dataType > > &trees2, std::vector< std::vector< double > > &trees2V, std::vector< std::vector< double > > &trees2V2, std::vector< std::vector< double > > &allTreesTs, 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< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings2, std::vector< double > &ts, std::vector< double > &distances)
template<class dataType >
void	updateClosedForm (int geodesicNumber, ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &trees, std::vector< ftm::MergeTree< dataType > > &allInterpolated, std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings, std::vector< std::vector< double > > &tss, std::vector< std::vector< double > > &vR, std::vector< std::vector< double > > &vR2, std::vector< bool > &isUniform)
template<class dataType >
void	manageIndividualTs (int geodesicNumber, ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &trees, std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, std::vector< std::vector< std::vector< double > > > &vS, std::vector< std::vector< std::vector< double > > > &v2s, std::vector< double > &ts, std::vector< std::vector< double > > &allTreesTs, std::vector< ftm::MergeTree< dataType > > &allInterpolated, std::vector< bool > &isUniform, std::vector< std::vector< double > > &tss, unsigned int &noUniform, bool &foundAllUniform)
template<class dataType >
bool	updateClosedFormStep (int geodesicNumber, ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &trees, std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings, std::vector< std::vector< std::vector< double > > > &vS, std::vector< std::vector< std::vector< double > > > &v2s, ftm::MergeTree< dataType > &barycenter2, std::vector< ftm::MergeTree< dataType > > &trees2, std::vector< std::vector< double > > &trees2V, std::vector< std::vector< double > > &trees2V2, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings2, std::vector< std::vector< std::vector< double > > > &trees2Vs, std::vector< std::vector< std::vector< double > > > &trees2V2s, std::vector< double > &ts, std::vector< std::vector< double > > &allTreesTs)
template<class dataType >
bool	updateStep (int geodesicNumber, ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &trees, std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings, std::vector< std::vector< std::vector< double > > > &vS, std::vector< std::vector< std::vector< double > > > &v2s, ftm::MergeTree< dataType > &barycenter2, std::vector< ftm::MergeTree< dataType > > &trees2, std::vector< std::vector< double > > &trees2V, std::vector< std::vector< double > > &trees2V2, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &matchings2, std::vector< std::vector< std::vector< double > > > &trees2Vs, std::vector< std::vector< std::vector< double > > > &trees2V2s, std::vector< double > &ts, std::vector< std::vector< double > > &allTreesTs)
template<class dataType >
bool	convergenceStep (std::vector< double > &distances, std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, dataType &oldFrechetEnergy, dataType &minFrechetEnergy, int &cptBlocked, bool &converged, double optMapCost)
template<class dataType >
void	computePrincipalGeodesic (unsigned int geodesicNumber, ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &trees, ftm::MergeTree< dataType > &barycenter2, std::vector< ftm::MergeTree< dataType > > &trees2)
template<class dataType >
void	computePrincipalGeodesics (std::vector< ftm::MergeTree< dataType > > &trees, std::vector< ftm::MergeTree< dataType > > &trees2)
template<class dataType >
void	execute (std::vector< ftm::MergeTree< dataType > > &trees, std::vector< ftm::MergeTree< dataType > > &trees2)
void	copyMinMaxPairVector (std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, std::vector< std::vector< double > > &trees2V, std::vector< std::vector< double > > &trees2V2)
template<class dataType >
void	computeGeodesicExtremities ()
template<class dataType >
void	computeBranchesCorrelationMatrix (ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &trees)
template<class dataType >
void	printIterationVariances (ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &trees, ftm::MergeTree< dataType > &barycenter2, std::vector< ftm::MergeTree< dataType > > &trees2, int geodesicNumber, double globalVariance)
double	verifyOrthogonality (std::vector< std::vector< std::vector< double > > > &vS, std::vector< std::vector< std::vector< double > > > &v2s, bool doPrint=true)
double	verifyOrthogonality (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, bool doPrint=true)
template<class dataType >
dataType	computeVarianceFromDistances (std::vector< dataType > &distances)
template<class dataType >
double	computeExplainedVariance (ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &trees, std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, std::vector< double > &ts, bool computeGlobalVariance=false)
template<class dataType >
double	computeGlobalVariance (ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &trees)
template<class dataType >
double	computeSurfaceExplainedVariance (ftm::MergeTree< dataType > &barycenter, std::vector< ftm::MergeTree< dataType > > &trees, std::vector< std::vector< std::vector< double > > > &vS, std::vector< std::vector< std::vector< double > > > &v2s, std::vector< std::vector< double > > &ts)
template<class dataType >
void	computeProjectionDistances (ftm::MergeTree< dataType > &barycenter, std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, std::vector< double > &ts, std::vector< double > &distances, bool useDoubleInput=false, bool isFirstInput=true)
template<class dataType >
double	computeExplainedVarianceT (ftm::MergeTree< dataType > &barycenter, std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, std::vector< double > &ts)
template<class dataType >
double	computeExplainedVarianceT (ftm::MergeTree< dataType > &barycenter, std::vector< std::vector< double > > &v, std::vector< std::vector< double > > &v2, ftm::MergeTree< dataType > &barycenter2, std::vector< std::vector< double > > &trees2V, std::vector< std::vector< double > > &trees2V2, std::vector< double > &ts)
template<class dataType >
void	verifyMinMaxPair (ftm::MergeTree< dataType > &mTree1, ftm::MergeTree< dataType > &mTree)
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	doComputeReconstructionError_ = false
bool	keepState_ = false
unsigned int	noProjectionStep_ = 2
bool	projectInitializedVectors_ = true
double	t_vectorCopy_time_ = 0.0
double	t_allVectorCopy_time_ = 0.0
std::vector< double >	inputToBaryDistances_
std::vector< std::vector< double > >	inputToGeodesicsDistances_
ftm::MergeTree< double >	barycenter_
ftm::MergeTree< double >	barycenterInput2_
ftm::MergeTree< double >	barycenterBDT_
ftm::MergeTree< double >	barycenterInput2BDT_
bool	barycenterWasComputed_ = false
int	newVectorOffset_ = 0
double	cumulVariance_ = 0.0
double	cumulTVariance_ = 0.0
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::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 MergeTreePrincipalGeodesics class provides methods to compute Principal Geodesic Analysis on the space of merge trees or persistence diagrams, that is, a set of orthogonal geodesic axes defining a basis with the barycenter as origin.

Author

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

Date

2021

This module defines the MergeTreePrincipalGeodesics class that computes Principal Geodesic Analysis on the space of merge trees or persistence diagrams, that is, a set of orthogonal geodesic axes defining a basis with the barycenter as origin.

Related publication:
"Principal Geodesic Analysis of Merge Trees (and Persistence Diagrams)"
Mathieu Pont, Jules Vidal, Julien Tierny.
IEEE Transactions on Visualization and Computer Graphics, 2022

Online examples:

• Merge Tree Principal Geodesic Analysis example
  

Definition at line 35 of file MergeTreePrincipalGeodesics.h.

Constructor & Destructor Documentation

MergeTreePrincipalGeodesics()

ttk::MergeTreePrincipalGeodesics::MergeTreePrincipalGeodesics ( )

inline

Definition at line 61 of file MergeTreePrincipalGeodesics.h.

Member Function Documentation

assignmentImpl()

template<class dataType >

void ttk::MergeTreePrincipalGeodesics::assignmentImpl ( ftm::MergeTree< dataType > &  barycenter, std::vector< ftm::MergeTree< dataType > > &  trees, std::vector< std::vector< double > > &  v, std::vector< std::vector< double > > &  v2, ftm::MergeTree< dataType > &  barycenter2, std::vector< ftm::MergeTree< dataType > > &  trees2, std::vector< std::vector< double > > &  trees2V, std::vector< std::vector< double > > &  trees2V2, std::vector< std::vector< double > > &  allTreesTs, 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< std::tuple< ftm::idNode, ftm::idNode, double > > > &  matchings, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &  matchings2, std::vector< double > &  ts, std::vector< double > &  distances  )

inline

Definition at line 383 of file MergeTreePrincipalGeodesics.h.

assignmentStep()

template<class dataType >

void ttk::MergeTreePrincipalGeodesics::assignmentStep ( ftm::MergeTree< dataType > &  barycenter, std::vector< ftm::MergeTree< dataType > > &  trees, std::vector< std::vector< double > > &  v, std::vector< std::vector< double > > &  v2, ftm::MergeTree< dataType > &  barycenter2, std::vector< ftm::MergeTree< dataType > > &  trees2, std::vector< std::vector< double > > &  trees2V, std::vector< std::vector< double > > &  trees2V2, std::vector< std::vector< double > > &  allTreesTs, 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< std::tuple< ftm::idNode, ftm::idNode, double > > > &  matchings, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &  matchings2, std::vector< double > &  ts, std::vector< double > &  distances  )

inline

Definition at line 484 of file MergeTreePrincipalGeodesics.h.

barycentricProjection()

template<class dataType >

double ttk::MergeTreePrincipalGeodesics::barycentricProjection ( ftm::MergeTree< dataType > &  barycenter, ftm::MergeTree< dataType > &  extremity, std::vector< std::vector< double > > &  v, bool  isV1, bool  useDoubleInput = false, bool  isFirstInput = true  )

inline

Definition at line 154 of file MergeTreePrincipalGeodesics.h.

computeBranchesCorrelationMatrix()

template<class dataType >

void ttk::MergeTreePrincipalGeodesics::computeBranchesCorrelationMatrix ( ftm::MergeTree< dataType > &  barycenter, std::vector< ftm::MergeTree< dataType > > &  trees  )

inline

Definition at line 1180 of file MergeTreePrincipalGeodesics.h.

computeExplainedVariance()

template<class dataType >

double ttk::MergeTreePrincipalGeodesics::computeExplainedVariance	(	ftm::MergeTree< dataType > &	barycenter,
		std::vector< ftm::MergeTree< dataType > > &	trees,
		std::vector< std::vector< double > > &	v,
		std::vector< std::vector< double > > &	v2,
		std::vector< double > &	ts,
		bool	computeGlobalVariance = false
	)

Definition at line 16 of file MergeTreePrincipalGeodesicsUtils.h.

computeExplainedVarianceT() [1/2]

template<class dataType >

double ttk::MergeTreePrincipalGeodesics::computeExplainedVarianceT	(	ftm::MergeTree< dataType > &	barycenter,
		std::vector< std::vector< double > > &	v,
		std::vector< std::vector< double > > &	v2,
		ftm::MergeTree< dataType > &	barycenter2,
		std::vector< std::vector< double > > &	trees2V,
		std::vector< std::vector< double > > &	trees2V2,
		std::vector< double > &	ts
	)

Definition at line 126 of file MergeTreePrincipalGeodesicsUtils.h.

computeExplainedVarianceT() [2/2]

template<class dataType >

double ttk::MergeTreePrincipalGeodesics::computeExplainedVarianceT	(	ftm::MergeTree< dataType > &	barycenter,
		std::vector< std::vector< double > > &	v,
		std::vector< std::vector< double > > &	v2,
		std::vector< double > &	ts
	)

Definition at line 115 of file MergeTreePrincipalGeodesicsUtils.h.

computeGeodesicExtremities()

template<class dataType >

void ttk::MergeTreePrincipalGeodesics::computeGeodesicExtremities ( )

inline

Definition at line 1141 of file MergeTreePrincipalGeodesics.h.

computeGlobalVariance()

template<class dataType >

double ttk::MergeTreePrincipalGeodesics::computeGlobalVariance	(	ftm::MergeTree< dataType > &	barycenter,
		std::vector< ftm::MergeTree< dataType > > &	trees
	)

Definition at line 50 of file MergeTreePrincipalGeodesicsUtils.h.

computePrincipalGeodesic()

template<class dataType >

void ttk::MergeTreePrincipalGeodesics::computePrincipalGeodesic ( unsigned int  geodesicNumber, ftm::MergeTree< dataType > &  barycenter, std::vector< ftm::MergeTree< dataType > > &  trees, ftm::MergeTree< dataType > &  barycenter2, std::vector< ftm::MergeTree< dataType > > &  trees2  )

inline

Definition at line 849 of file MergeTreePrincipalGeodesics.h.

computePrincipalGeodesics()

template<class dataType >

void ttk::MergeTreePrincipalGeodesics::computePrincipalGeodesics ( std::vector< ftm::MergeTree< dataType > > &  trees, std::vector< ftm::MergeTree< dataType > > &  trees2  )

inline

Definition at line 970 of file MergeTreePrincipalGeodesics.h.

computeProjectionDistances()

template<class dataType >

void ttk::MergeTreePrincipalGeodesics::computeProjectionDistances	(	ftm::MergeTree< dataType > &	barycenter,
		std::vector< std::vector< double > > &	v,
		std::vector< std::vector< double > > &	v2,
		std::vector< double > &	ts,
		std::vector< double > &	distances,
		bool	useDoubleInput = false,
		bool	isFirstInput = true
	)

Definition at line 90 of file MergeTreePrincipalGeodesicsUtils.h.

computeSurfaceExplainedVariance()

template<class dataType >

double ttk::MergeTreePrincipalGeodesics::computeSurfaceExplainedVariance	(	ftm::MergeTree< dataType > &	barycenter,
		std::vector< ftm::MergeTree< dataType > > &	trees,
		std::vector< std::vector< std::vector< double > > > &	vS,
		std::vector< std::vector< std::vector< double > > > &	v2s,
		std::vector< std::vector< double > > &	ts
	)

Definition at line 60 of file MergeTreePrincipalGeodesicsUtils.h.

computeVarianceFromDistances()

template<class dataType >

dataType ttk::MergeTreePrincipalGeodesics::computeVarianceFromDistances

(

std::vector< dataType > &

distances

)

Definition at line 7 of file MergeTreePrincipalGeodesicsUtils.h.

convergenceStep()

template<class dataType >

bool ttk::MergeTreePrincipalGeodesics::convergenceStep ( std::vector< double > &  distances, std::vector< std::vector< double > > &  v, std::vector< std::vector< double > > &  v2, dataType &  oldFrechetEnergy, dataType &  minFrechetEnergy, int &  cptBlocked, bool &  converged, double  optMapCost  )

inline

Definition at line 793 of file MergeTreePrincipalGeodesics.h.

copyMinMaxPairVector()

void ttk::MergeTreePrincipalGeodesics::copyMinMaxPairVector ( std::vector< std::vector< double > > &  v, std::vector< std::vector< double > > &  v2, std::vector< std::vector< double > > &  trees2V, std::vector< std::vector< double > > &  trees2V2  )

inline

Definition at line 1130 of file MergeTreePrincipalGeodesics.h.

execute()

template<class dataType >

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

inline

Definition at line 1075 of file MergeTreePrincipalGeodesics.h.

getGeodesicNumber()

unsigned int ttk::MergeTreePrincipalGeodesics::getGeodesicNumber ( )

inline

Definition at line 70 of file MergeTreePrincipalGeodesics.h.

initVectors()

template<class dataType >

void ttk::MergeTreePrincipalGeodesics::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  )

inline

Definition at line 88 of file MergeTreePrincipalGeodesics.h.

manageIndividualTs()

template<class dataType >

void ttk::MergeTreePrincipalGeodesics::manageIndividualTs ( int  geodesicNumber, ftm::MergeTree< dataType > &  barycenter, std::vector< ftm::MergeTree< dataType > > &  trees, std::vector< std::vector< double > > &  v, std::vector< std::vector< double > > &  v2, std::vector< std::vector< std::vector< double > > > &  vS, std::vector< std::vector< std::vector< double > > > &  v2s, std::vector< double > &  ts, std::vector< std::vector< double > > &  allTreesTs, std::vector< ftm::MergeTree< dataType > > &  allInterpolated, std::vector< bool > &  isUniform, std::vector< std::vector< double > > &  tss, unsigned int &  noUniform, bool &  foundAllUniform  )

inline

Definition at line 652 of file MergeTreePrincipalGeodesics.h.

optimalMappingSetProjection()

template<class dataType >

double ttk::MergeTreePrincipalGeodesics::optimalMappingSetProjection ( ftm::MergeTree< dataType > &  barycenter, std::vector< std::vector< double > > &  v, std::vector< std::vector< double > > &  v2, ftm::MergeTree< dataType > &  barycenter2, std::vector< std::vector< double > > &  trees2V, std::vector< std::vector< double > > &  trees2V2, bool  useSecondInput = false  )

inline

Definition at line 208 of file MergeTreePrincipalGeodesics.h.

orthogonalCost()

double ttk::MergeTreePrincipalGeodesics::orthogonalCost ( 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  )

inline

Definition at line 126 of file MergeTreePrincipalGeodesics.h.

orthogonalProjection()

void ttk::MergeTreePrincipalGeodesics::orthogonalProjection ( std::vector< std::vector< double > > &  v1, std::vector< std::vector< double > > &  v2, std::vector< std::vector< std::vector< double > > > &  vS, std::vector< std::vector< std::vector< double > > > &  v2s  )

inline

Definition at line 262 of file MergeTreePrincipalGeodesics.h.

printIterationVariances()

template<class dataType >

void ttk::MergeTreePrincipalGeodesics::printIterationVariances ( ftm::MergeTree< dataType > &  barycenter, std::vector< ftm::MergeTree< dataType > > &  trees, ftm::MergeTree< dataType > &  barycenter2, std::vector< ftm::MergeTree< dataType > > &  trees2, int  geodesicNumber, double  globalVariance  )

inline

Definition at line 1192 of file MergeTreePrincipalGeodesics.h.

projectionCost()

double ttk::MergeTreePrincipalGeodesics::projectionCost ( std::vector< std::vector< double > > &  v, std::vector< std::vector< double > > &  v2, std::vector< std::vector< std::vector< double > > > &  vS, std::vector< std::vector< std::vector< double > > > &  v2s, double  optMapCost  )

inline

Definition at line 141 of file MergeTreePrincipalGeodesics.h.

projectionStep()

template<class dataType >

double ttk::MergeTreePrincipalGeodesics::projectionStep ( int  geodesicNumber, ftm::MergeTree< dataType > &  barycenter, std::vector< std::vector< double > > &  v, std::vector< std::vector< double > > &  v2, std::vector< std::vector< std::vector< double > > > &  vS, std::vector< std::vector< std::vector< double > > > &  v2s, ftm::MergeTree< dataType > &  barycenter2, std::vector< std::vector< double > > &  trees2V, std::vector< std::vector< double > > &  trees2V2, std::vector< std::vector< std::vector< double > > > &  trees2Vs, std::vector< std::vector< std::vector< double > > > &  trees2V2s, bool  useSecondInput, unsigned int  noProjectionStep  )

inline

Definition at line 287 of file MergeTreePrincipalGeodesics.h.

regularizerCost()

double ttk::MergeTreePrincipalGeodesics::regularizerCost ( std::vector< std::vector< double > > &  v, std::vector< std::vector< double > > &  v2  )

inline

Definition at line 133 of file MergeTreePrincipalGeodesics.h.

trueGeneralizedGeodesicProjection()

void ttk::MergeTreePrincipalGeodesics::trueGeneralizedGeodesicProjection ( std::vector< std::vector< double > > &  v1, std::vector< std::vector< double > > &  v2  )

inline

Definition at line 245 of file MergeTreePrincipalGeodesics.h.

updateClosedForm()

template<class dataType >

void ttk::MergeTreePrincipalGeodesics::updateClosedForm ( int  geodesicNumber, ftm::MergeTree< dataType > &  barycenter, std::vector< ftm::MergeTree< dataType > > &  trees, std::vector< ftm::MergeTree< dataType > > &  allInterpolated, std::vector< std::vector< double > > &  v, std::vector< std::vector< double > > &  v2, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &  matchings, std::vector< std::vector< double > > &  tss, std::vector< std::vector< double > > &  vR, std::vector< std::vector< double > > &  vR2, std::vector< bool > &  isUniform  )

inline

Definition at line 520 of file MergeTreePrincipalGeodesics.h.

updateClosedFormStep()

template<class dataType >

bool ttk::MergeTreePrincipalGeodesics::updateClosedFormStep ( int  geodesicNumber, ftm::MergeTree< dataType > &  barycenter, std::vector< ftm::MergeTree< dataType > > &  trees, std::vector< std::vector< double > > &  v, std::vector< std::vector< double > > &  v2, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &  matchings, std::vector< std::vector< std::vector< double > > > &  vS, std::vector< std::vector< std::vector< double > > > &  v2s, ftm::MergeTree< dataType > &  barycenter2, std::vector< ftm::MergeTree< dataType > > &  trees2, std::vector< std::vector< double > > &  trees2V, std::vector< std::vector< double > > &  trees2V2, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &  matchings2, std::vector< std::vector< std::vector< double > > > &  trees2Vs, std::vector< std::vector< std::vector< double > > > &  trees2V2s, std::vector< double > &  ts, std::vector< std::vector< double > > &  allTreesTs  )

inline

Definition at line 695 of file MergeTreePrincipalGeodesics.h.

updateStep()

template<class dataType >

bool ttk::MergeTreePrincipalGeodesics::updateStep ( int  geodesicNumber, ftm::MergeTree< dataType > &  barycenter, std::vector< ftm::MergeTree< dataType > > &  trees, std::vector< std::vector< double > > &  v, std::vector< std::vector< double > > &  v2, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &  matchings, std::vector< std::vector< std::vector< double > > > &  vS, std::vector< std::vector< std::vector< double > > > &  v2s, ftm::MergeTree< dataType > &  barycenter2, std::vector< ftm::MergeTree< dataType > > &  trees2, std::vector< std::vector< double > > &  trees2V, std::vector< std::vector< double > > &  trees2V2, std::vector< std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > > &  matchings2, std::vector< std::vector< std::vector< double > > > &  trees2Vs, std::vector< std::vector< std::vector< double > > > &  trees2V2s, std::vector< double > &  ts, std::vector< std::vector< double > > &  allTreesTs  )

inline

Definition at line 763 of file MergeTreePrincipalGeodesics.h.

verifyMinMaxPair()

template<class dataType >

void ttk::MergeTreePrincipalGeodesics::verifyMinMaxPair ( ftm::MergeTree< dataType > &  mTree1, ftm::MergeTree< dataType > &  mTree  )

inline

Definition at line 1326 of file MergeTreePrincipalGeodesics.h.

verifyOrthogonality() [1/2]

double ttk::MergeTreePrincipalGeodesics::verifyOrthogonality	(	std::vector< std::vector< std::vector< double > > > &	vS,
		std::vector< std::vector< std::vector< double > > > &	v2s,
		bool	doPrint = true
	)

Definition at line 4 of file MergeTreePrincipalGeodesics.cpp.

verifyOrthogonality() [2/2]

double ttk::MergeTreePrincipalGeodesics::verifyOrthogonality	(	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,
		bool	doPrint = true
	)

Definition at line 34 of file MergeTreePrincipalGeodesics.cpp.

Member Data Documentation

barycenter_

ftm::MergeTree<double> ttk::MergeTreePrincipalGeodesics::barycenter_

protected

Definition at line 53 of file MergeTreePrincipalGeodesics.h.

barycenterBDT_

ftm::MergeTree<double> ttk::MergeTreePrincipalGeodesics::barycenterBDT_

protected

Definition at line 53 of file MergeTreePrincipalGeodesics.h.

barycenterInput2_

ftm::MergeTree<double> ttk::MergeTreePrincipalGeodesics::barycenterInput2_

protected

Definition at line 53 of file MergeTreePrincipalGeodesics.h.

barycenterInput2BDT_

ftm::MergeTree<double> ttk::MergeTreePrincipalGeodesics::barycenterInput2BDT_

protected

Definition at line 54 of file MergeTreePrincipalGeodesics.h.

barycenterWasComputed_

bool ttk::MergeTreePrincipalGeodesics::barycenterWasComputed_ = false

protected

Definition at line 55 of file MergeTreePrincipalGeodesics.h.

cumulTVariance_

double ttk::MergeTreePrincipalGeodesics::cumulTVariance_ = 0.0

protected

Definition at line 58 of file MergeTreePrincipalGeodesics.h.

cumulVariance_

double ttk::MergeTreePrincipalGeodesics::cumulVariance_ = 0.0

protected

Definition at line 58 of file MergeTreePrincipalGeodesics.h.

doComputeReconstructionError_

bool ttk::MergeTreePrincipalGeodesics::doComputeReconstructionError_ = false

protected

Definition at line 39 of file MergeTreePrincipalGeodesics.h.

inputToBaryDistances_

std::vector<double> ttk::MergeTreePrincipalGeodesics::inputToBaryDistances_

protected

Definition at line 51 of file MergeTreePrincipalGeodesics.h.

inputToGeodesicsDistances_

std::vector<std::vector<double> > ttk::MergeTreePrincipalGeodesics::inputToGeodesicsDistances_

protected

Definition at line 52 of file MergeTreePrincipalGeodesics.h.

keepState_

bool ttk::MergeTreePrincipalGeodesics::keepState_ = false

protected

Definition at line 41 of file MergeTreePrincipalGeodesics.h.

newVectorOffset_

int ttk::MergeTreePrincipalGeodesics::newVectorOffset_ = 0

protected

Definition at line 57 of file MergeTreePrincipalGeodesics.h.

noProjectionStep_

unsigned int ttk::MergeTreePrincipalGeodesics::noProjectionStep_ = 2

protected

Definition at line 42 of file MergeTreePrincipalGeodesics.h.

projectInitializedVectors_

bool ttk::MergeTreePrincipalGeodesics::projectInitializedVectors_ = true

protected

Definition at line 45 of file MergeTreePrincipalGeodesics.h.

t_allVectorCopy_time_

double ttk::MergeTreePrincipalGeodesics::t_allVectorCopy_time_ = 0.0

protected

Definition at line 48 of file MergeTreePrincipalGeodesics.h.

t_vectorCopy_time_

double ttk::MergeTreePrincipalGeodesics::t_vectorCopy_time_ = 0.0

protected

Definition at line 48 of file MergeTreePrincipalGeodesics.h.

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

• /home/julien/Pro/git/github/ttk-tierny/core/base/mergeTreePrincipalGeodesics/MergeTreePrincipalGeodesics.h
• /home/julien/Pro/git/github/ttk-tierny/core/base/mergeTreePrincipalGeodesics/MergeTreePrincipalGeodesics.cpp
• /home/julien/Pro/git/github/ttk-tierny/core/base/mergeTreePrincipalGeodesics/MergeTreePrincipalGeodesicsUtils.h