TTK
Loading...
Searching...
No Matches
Public Member Functions | List of all members
ttk::MergeTreeNeuralLayer Class Reference
base

#include <MergeTreeNeuralLayer.h>

Inheritance diagram for ttk::MergeTreeNeuralLayer:
ttk::Debug ttk::MergeTreeNeuralBase ttk::BaseClass ttk::Debug ttk::MergeTreeAxesAlgorithmBase ttk::BaseClass ttk::Debug ttk::MergeTreeBase ttk::BaseClass ttk::Debug ttk::BaseClass

Public Member Functions

 MergeTreeNeuralLayer ()
 
- Public Member Functions inherited from ttk::Debug
 Debug ()
 
 ~Debug () override
 
virtual int setDebugLevel (const int &debugLevel)
 
int setWrapper (const Wrapper *wrapper) override
 
int printMsg (const std::string &msg, const debug::Priority &priority=debug::Priority::INFO, const debug::LineMode &lineMode=debug::LineMode::NEW, std::ostream &stream=std::cout) const
 
int printMsg (const std::vector< std::string > &msgs, const debug::Priority &priority=debug::Priority::INFO, const debug::LineMode &lineMode=debug::LineMode::NEW, std::ostream &stream=std::cout) const
 
int printErr (const std::string &msg, const debug::LineMode &lineMode=debug::LineMode::NEW, std::ostream &stream=std::cerr) const
 
int printWrn (const std::string &msg, const debug::LineMode &lineMode=debug::LineMode::NEW, std::ostream &stream=std::cerr) const
 
int printMsg (const std::string &msg, const double &progress, const double &time, const int &threads, const double &memory, const debug::LineMode &lineMode=debug::LineMode::NEW, const debug::Priority &priority=debug::Priority::PERFORMANCE, std::ostream &stream=std::cout) const
 
int printMsg (const std::string &msg, const double &progress, const double &time, const debug::LineMode &lineMode=debug::LineMode::NEW, const debug::Priority &priority=debug::Priority::PERFORMANCE, std::ostream &stream=std::cout) const
 
int printMsg (const std::string &msg, const double &progress, const double &time, const int &threads, const debug::LineMode &lineMode=debug::LineMode::NEW, const debug::Priority &priority=debug::Priority::PERFORMANCE, std::ostream &stream=std::cout) const
 
int printMsg (const std::string &msg, const double &progress, const debug::LineMode &lineMode=debug::LineMode::NEW, const debug::Priority &priority=debug::Priority::PERFORMANCE, std::ostream &stream=std::cout) const
 
int printMsg (const std::string &msg, const double &progress, const debug::Priority &priority, const debug::LineMode &lineMode=debug::LineMode::NEW, std::ostream &stream=std::cout) const
 
int printMsg (const std::vector< std::vector< std::string > > &rows, const debug::Priority &priority=debug::Priority::INFO, const bool hasHeader=true, const debug::LineMode &lineMode=debug::LineMode::NEW, std::ostream &stream=std::cout) const
 
int printMsg (const debug::Separator &separator, const debug::LineMode &lineMode=debug::LineMode::NEW, const debug::Priority &priority=debug::Priority::INFO, std::ostream &stream=std::cout) const
 
int printMsg (const debug::Separator &separator, const debug::Priority &priority, const debug::LineMode &lineMode=debug::LineMode::NEW, std::ostream &stream=std::cout) const
 
int printMsg (const std::string &msg, const debug::Separator &separator, const debug::LineMode &lineMode=debug::LineMode::NEW, const debug::Priority &priority=debug::Priority::INFO, std::ostream &stream=std::cout) const
 
void setDebugMsgPrefix (const std::string &prefix)
 
- Public Member Functions inherited from ttk::BaseClass
 BaseClass ()
 
virtual ~BaseClass ()=default
 
int getThreadNumber () const
 
virtual int setThreadNumber (const int threadNumber)
 
- Public Member Functions inherited from ttk::MergeTreeNeuralBase
 MergeTreeNeuralBase ()
 
- Public Member Functions inherited from ttk::MergeTreeAxesAlgorithmBase
 MergeTreeAxesAlgorithmBase ()
 
void setDeterministic (const bool deterministic)
 
void setNumberOfProjectionSteps (const unsigned int k)
 
void setBarycenterSizeLimitPercent (const double barycenterSizeLimitPercent)
 
void setProbabilisticVectorsInit (const bool probabilisticVectorsInit)
 
template<class dataType>
void computeOneDistance (const ftm::MergeTree< dataType > &tree1, const 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 (const ftm::MergeTree< dataType > &tree1, const 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 axeNumber, 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 > > &inputToAxesDistances, 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, int barycenterInitIndex, bool oneIter, 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, 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>
std::tuple< dataType, dataType > getParametrizedBirthDeath (ftm::FTMTree_MT *tree, ftm::idNode node)
 
template<class dataType>
void computeBranchesCorrelationMatrix (const 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)
 
- Public Member Functions inherited from ttk::MergeTreeBase
 MergeTreeBase ()
 
void setAssignmentSolver (int assignmentSolver)
 
void setEpsilon1UseFarthestSaddle (bool b)
 
void setEpsilonTree1 (double epsilon)
 
void setEpsilonTree2 (double epsilon)
 
void setEpsilon2Tree1 (double epsilon)
 
void setEpsilon2Tree2 (double epsilon)
 
void setEpsilon3Tree1 (double epsilon)
 
void setEpsilon3Tree2 (double epsilon)
 
void setPersistenceThreshold (double pt)
 
void setParallelize (bool para)
 
void setNodePerTask (int npt)
 
void setBranchDecomposition (bool useBD)
 
void setNormalizedWasserstein (bool normalizedWasserstein)
 
void setKeepSubtree (bool keepSubtree)
 
void setNonMatchingWeight (double weight)
 
void setBarycenterMergeTree (bool imt)
 
void setDistanceSquaredRoot (bool distanceSquaredRoot)
 
void setUseMinMaxPair (bool useMinMaxPair)
 
void setDeleteMultiPersPairs (bool deleteMultiPersPairsT)
 
void setCleanTree (bool clean)
 
void setIsPersistenceDiagram (bool isPD)
 
void setJoinSplitMixtureCoefficient (const double mixtureCoefficient)
 
void setUseDoubleInput (const bool useDoubleInput)
 
std::vector< std::vector< int > > getTreesNodeCorr ()
 
double mixDistancesMinMaxPairWeight (bool isFirstInput)
 
double mixDistancesWeight (bool isFirstInput)
 
template<class dataType>
double mixDistances (dataType distance1, dataType distance2)
 
template<class dataType>
void mixDistancesMatrix (std::vector< std::vector< dataType > > &distanceMatrix, std::vector< std::vector< dataType > > &distanceMatrix2)
 
template<class dataType>
void mergeSaddle (ftm::FTMTree_MT *tree, double epsilon, std::vector< std::vector< ftm::idNode > > &treeNodeMerged, bool mergeByPersistence=false)
 
template<class dataType>
void persistenceMerging (ftm::FTMTree_MT *tree, double epsilon2, double epsilon3=100)
 
void deletePersistenceDiagramsPairs (ftm::FTMTree_MT *tree, std::vector< ftm::idNode > &nodes)
 
template<class dataType>
void keepMostImportantPairs (ftm::FTMTree_MT *tree, int n, bool useBD)
 
template<class dataType>
void persistenceThresholding (ftm::FTMTree_MT *tree, double persistenceThresholdT, std::vector< ftm::idNode > &deletedNodes)
 
template<class dataType>
void persistenceThresholding (ftm::FTMTree_MT *tree, std::vector< ftm::idNode > &deletedNodes)
 
template<class dataType>
void persistenceThresholding (ftm::FTMTree_MT *tree, double persistenceThresholdT)
 
template<class dataType>
void persistenceThresholding (ftm::FTMTree_MT *tree)
 
template<class dataType>
void verifyOrigins (ftm::FTMTree_MT *tree)
 
template<class dataType>
void preprocessTree (ftm::FTMTree_MT *tree, bool deleteInconsistentNodes=true)
 
template<class dataType>
ftm::FTMTree_MT * computeBranchDecomposition (ftm::FTMTree_MT *tree, std::vector< std::vector< ftm::idNode > > &treeNodeMerged)
 
template<class dataType>
void dontUseMinMaxPair (ftm::FTMTree_MT *tree)
 
void verifyPairsTree (ftm::FTMTree_MT *tree)
 
template<class dataType>
void deleteMultiPersPairs (ftm::FTMTree_MT *tree, bool useBD)
 
template<class dataType>
void preprocessingPipeline (ftm::MergeTree< dataType > &mTree, double epsilonTree, double epsilon2Tree, double epsilon3Tree, bool branchDecompositionT, bool useMinMaxPairT, bool cleanTreeT, double persistenceThreshold, std::vector< int > &nodeCorr, bool deleteInconsistentNodes=true)
 
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 (const ftm::FTMTree_MT *tree, ftm::idNode nodeId)
 
template<class dataType>
dataType insertCost (const ftm::FTMTree_MT *tree, ftm::idNode nodeId)
 
template<class dataType>
dataType relabelCostOnly (const ftm::FTMTree_MT *tree1, ftm::idNode nodeId1, const ftm::FTMTree_MT *tree2, ftm::idNode nodeId2)
 
template<class dataType>
dataType relabelCost (const ftm::FTMTree_MT *tree1, ftm::idNode nodeId1, const ftm::FTMTree_MT *tree2, ftm::idNode nodeId2)
 
void getParamNames (std::vector< std::string > &paramNames)
 
double getParamValueFromName (std::string &paramName)
 
void setParamValueFromName (std::string &paramName, double value)
 
void getTreesStats (std::vector< ftm::FTMTree_MT * > &trees, std::array< double, 3 > &stats)
 
void printTreesStats (std::vector< ftm::FTMTree_MT * > &trees)
 
template<class dataType>
void printTreesStats (std::vector< ftm::MergeTree< dataType > > &trees)
 
template<class dataType>
void printTableVector (std::vector< std::vector< dataType > > &table)
 
template<class dataType>
void printTable (dataType *table, int nRows, int nCols)
 
void printMatching (std::vector< MatchingType > &matchings)
 
void printMatching (std::vector< std::tuple< ftm::idNode, ftm::idNode, double > > &matchings)
 
void printMatching (std::vector< std::tuple< ftm::idNode, ftm::idNode > > &matchings)
 
template<class dataType>
void printPairs (std::vector< std::tuple< SimplexId, SimplexId, dataType > > &treePairs)
 
template<class dataType>
void printOutputMatching (std::vector< std::tuple< ftm::idNode, ftm::idNode > > &outputMatching, ftm::FTMTree_MT *tree1, ftm::FTMTree_MT *tree2, bool computeCosts=true)
 

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::MergeTreeNeuralBase
double dropout_ = 0.0
 
bool euclideanVectorsInit_ = false
 
bool randomAxesInit_ = false
 
bool initBarycenterRandom_ = false
 
bool initBarycenterOneIter_ = false
 
bool initOriginPrimeStructByCopy_ = true
 
bool initOriginPrimeValuesByCopy_ = true
 
double initOriginPrimeValuesByCopyRandomness_ = 0.0
 
bool activate_ = true
 
unsigned int activationFunction_ = 1
 
bool useGpu_ = false
 
float bigValuesThreshold_ = 0
 
- Protected Attributes inherited from ttk::MergeTreeAxesAlgorithmBase
bool deterministic_ = true
 
unsigned int numberOfAxes_ = 2
 
unsigned int k_ = 16
 
double barycenterSizeLimitPercent_ = 20.0
 
bool probabilisticVectorsInit_ = false
 
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
 
double nonMatchingWeight_ = 1.0
 
bool distanceSquaredRoot_ = true
 
bool useFullMerge_ = false
 
bool isPersistenceDiagram_ = false
 
bool convertToDiagram_ = false
 
double mixtureCoefficient_ = 0.5
 
bool useDoubleInput_ = false
 
bool parallelize_ = true
 
int nodePerTask_ = 32
 
bool cleanTree_ = true
 
std::vector< std::vector< int > > treesNodeCorr_
 
- Static Protected Attributes inherited from ttk::Debug
static COMMON_EXPORTS debug::LineMode lastLineMode = ttk::debug::LineMode::NEW
 

Detailed Description

The MergeTreeNeuralLayer class provides methods to define and use a wasserstein layer able to process merge trees or persistence diagrams.

Author
Mathieu Pont mathi.nosp@m.eu.p.nosp@m.ont@l.nosp@m.ip6..nosp@m.fr
Date
2023.

This module defines the MergeTreeNeuralLayer class that provide methods to define and use a wasserstein layer able to process merge trees or persistence diagrams.

To initialize the layer you can use the following functions: "initInputBasisOrigin" and "initInputBasisVectors" for the input basis, then "initOutputBasis" for the output basis. Please refer to the documentation of these functions for how to use them.

Then, you should call the "requires_grad" function, with a parameter sets to true, to enable torch to compute gradient for this layer for it to be optimized.

The layer can then be used with the "forward" function to pass a topological representation as input and get the topological representation at the output of the layer (the transformed input).

Related publication:
"Wasserstein Auto-Encoders of Merge Trees (and Persistence Diagrams)"
Mathieu Pont, Julien Tierny.
IEEE Transactions on Visualization and Computer Graphics, 2023

Definition at line 47 of file MergeTreeNeuralLayer.h.

Constructor & Destructor Documentation

◆ MergeTreeNeuralLayer()

ttk::MergeTreeNeuralLayer::MergeTreeNeuralLayer ( )

Definition at line 8 of file MergeTreeNeuralLayer.cpp.

The documentation for this class was generated from the following files:
Generated on Fri Apr 10 2026 10:02:13 for TTK by doxygen 1.13.2