TTK processing package for the computation of a matrix of Wasserstein distances between persistence diagrams. More...

#include <ttkPersistenceDiagramDistanceMatrix.h>

Inheritance diagram for ttkPersistenceDiagramDistanceMatrix:

Public Types
typedef ttkAlgorithm	Superclass

Public Types inherited from ttkAlgorithm
typedef vtkAlgorithm	Superclass

Public Member Functions
virtual const char *	GetClassName ()

virtual int	IsA (const char *type)

void	SetWassersteinMetric (const std::string &data)

std::string	GetWassersteinMetric ()

void	SetAntiAlpha (double data)

virtual double	GetAlpha ()

virtual void	SetDeltaLim (double)

virtual double	GetDeltaLim ()

virtual void	SetLambda (double)

virtual double	GetLambda ()

void	SetPairType (const int data)

int	GetPairType ()

void	SetConstraint (const int arg_)

int	GetConstraint ()

virtual void	SetMaxNumberOfPairs (unsigned int)

virtual unsigned int	GetMaxNumberOfPairs ()

virtual void	SetMinPersistence (double)

virtual double	GetMinPersistence ()

Public Member Functions inherited from ttkAlgorithm
virtual const char *	GetClassName ()

virtual int	IsA (const char *type)

void	UpdateThreadNumber ()

void	SetThreadNumber (int threadNumber)

void	SetUseAllCores (bool useAllCores)

void	SetDebugLevel (int debugLevel)

void	SetCompactTriangulationCacheSize (float cacheSize)

vtkDataArray *	GetOptionalArray (const bool &enforceArrayIndex, const int &arrayIndex, const std::string &arrayName, vtkDataSet *const inputData, const int &inputPort=0)

vtkDataArray *	GetOrderArray (vtkDataSet *const inputData, const int scalarArrayIdx, const int orderArrayIdx=0, const bool enforceOrderArrayIdx=false)

ttk::SimplexId *	GetIdentifierArrayPtr (const bool &enforceArrayIndex, const int &arrayIndex, const std::string &arrayName, vtkDataSet *const inputData, std::vector< ttk::SimplexId > &spareStorage, const int inputPort=0, const bool printErr=true)

ttk::Triangulation *	GetTriangulation (vtkDataSet *dataSet)

int	ProcessRequest (vtkInformation request, vtkInformationVector inputVectors, vtkInformationVector outputVector) override

vtkDataSet *	GetOutput ()

vtkDataSet *	GetOutput (int)

void	SetInputData (vtkDataSet *)

void	SetInputData (int, vtkDataSet *)

void	AddInputData (vtkDataSet *)

void	AddInputData (int, vtkDataSet *)

template<typename inputType >
int	checkEmptyMPIInput (inputType *input)
	This method tests whether the input is a nullptr. If the computation is being done on multiple processes, it is possible that the domain of one process or more is empty, but not others, therefore in that particular case the rest of the filter will not be computed but an error message will not be sent.

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)

Static Public Member Functions
static ttkPersistenceDiagramDistanceMatrix *	New ()

static int	IsTypeOf (const char *type)

static ttkPersistenceDiagramDistanceMatrix *	SafeDownCast (vtkObject *o)

Static Public Member Functions inherited from ttkAlgorithm
static ttkAlgorithm *	New ()

static int	IsTypeOf (const char *type)

static ttkAlgorithm *	SafeDownCast (vtkObject *o)

static std::string	GetOrderArrayName (vtkDataArray *const array)

static vtkInformationIntegerKey *	SAME_DATA_TYPE_AS_INPUT_PORT ()

Protected Member Functions
	ttkPersistenceDiagramDistanceMatrix ()

	~ttkPersistenceDiagramDistanceMatrix () override=default

int	FillInputPortInformation (int port, vtkInformation *info) override

int	FillOutputPortInformation (int port, vtkInformation *info) override

int	RequestData (vtkInformation request, vtkInformationVector inputVector, vtkInformationVector outputVector) override

Protected Member Functions inherited from ttkAlgorithm
	ttkAlgorithm ()

	~ttkAlgorithm () override

void	MPIGhostPipelinePreconditioning (vtkDataSet *input)

void	MPIPipelinePreconditioning (vtkDataSet input, std::vector< int > &neighbors, ttk::Triangulation triangulation=nullptr)

bool	checkGlobalIdValidity (ttk::LongSimplexId globalIds, ttk::SimplexId simplexNumber, unsigned char ghost, int *rankArray)

int	GenerateGlobalIds (vtkDataSet *input, std::unordered_map< ttk::SimplexId, ttk::SimplexId > &vertGtoL, std::vector< int > &neighborRanks)

void	MPITriangulationPreconditioning (ttk::Triangulation triangulation, vtkDataSet input)

virtual int	RequestDataObject (vtkInformation request, vtkInformationVector inputVectors, vtkInformationVector outputVector)

virtual int	RequestInformation (vtkInformation ttkNotUsed(request), vtkInformationVector ttkNotUsed(inputVectors), vtkInformationVector ttkNotUsed(outputVector))

virtual int	RequestUpdateTime (vtkInformation ttkNotUsed(request), vtkInformationVector ttkNotUsed(inputVectors), vtkInformationVector ttkNotUsed(outputVector))

virtual int	RequestUpdateTimeDependentInformation (vtkInformation ttkNotUsed(request), vtkInformationVector ttkNotUsed(inputVectors), vtkInformationVector ttkNotUsed(outputVector))

virtual int	RequestUpdateExtent (vtkInformation ttkNotUsed(request), vtkInformationVector ttkNotUsed(inputVectors), vtkInformationVector ttkNotUsed(outputVector))

virtual int	RequestDataNotGenerated (vtkInformation ttkNotUsed(request), vtkInformationVector ttkNotUsed(inputVectors), vtkInformationVector ttkNotUsed(outputVector))

virtual int	RequestData (vtkInformation ttkNotUsed(request), vtkInformationVector ttkNotUsed(inputVectors), vtkInformationVector ttkNotUsed(outputVector))

int	FillInputPortInformation (int ttkNotUsed(port), vtkInformation *ttkNotUsed(info)) override

int	FillOutputPortInformation (int ttkNotUsed(port), vtkInformation *ttkNotUsed(info)) override

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 Member Functions inherited from ttk::PersistenceDiagramDistanceMatrix
double	getMostPersistent (const std::vector< BidderDiagram > &bidder_diags) const

double	computePowerDistance (const BidderDiagram &D1, const BidderDiagram &D2) const

void	getDiagramsDistMat (const std::array< size_t, 2 > &nInputs, std::vector< std::vector< double > > &distanceMatrix, const std::vector< BidderDiagram > &diags_min, const std::vector< BidderDiagram > &diags_sad, const std::vector< BidderDiagram > &diags_max) const

void	setBidderDiagrams (const size_t nInputs, std::vector< DiagramType > &inputDiagrams, std::vector< BidderDiagram > &bidder_diags) const

void	enrichCurrentBidderDiagrams (const std::vector< BidderDiagram > &bidder_diags, std::vector< BidderDiagram > &current_bidder_diags, const std::vector< double > &maxDiagPersistence) const

	PersistenceDiagramDistanceMatrix ()

std::vector< std::vector< double > >	execute (const std::vector< DiagramType > &intermediateDiagrams, const std::array< size_t, 2 > &nInputs) const

void	setWasserstein (const int data)

void	setDos (const bool min, const bool sad, const bool max)

void	setAlpha (const double alpha)

void	setLambda (const double lambda)

void	setDeltaLim (const double deltaLim)

void	setMaxNumberOfPairs (const size_t data)

void	setMinPersistence (const double data)

void	setConstraint (const int data)

Additional Inherited Members
Protected Types inherited from ttk::PersistenceDiagramDistanceMatrix
enum class	ConstraintType { FULL_DIAGRAMS , NUMBER_PAIRS , ABSOLUTE_PERSISTENCE , RELATIVE_PERSISTENCE_PER_DIAG , RELATIVE_PERSISTENCE_GLOBAL }

Protected Attributes inherited from ttkAlgorithm
float	CompactTriangulationCacheSize {0.2f}

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::PersistenceDiagramDistanceMatrix
int	Wasserstein {2}

double	Alpha {1.0}

double	DeltaLim {0.01}

double	Lambda

size_t	MaxNumberOfPairs {20}

double	MinPersistence {0.1}

bool	do_min_ {true}

bool	do_sad_ {true}

bool	do_max_ {true}

ConstraintType	Constraint {ConstraintType::RELATIVE_PERSISTENCE_GLOBAL}

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

Detailed Description

TTK processing package for the computation of a matrix of Wasserstein distances between persistence diagrams.

Author: Jules Vidal jules.nosp@m..vid.nosp@m.al@li.nosp@m.p6.f.nosp@m.r; Pierre Guillou pierr.nosp@m.e.gu.nosp@m.illou.nosp@m.@lip.nosp@m.6.fr

Date: March 2020

Related publication
"Progressive Wasserstein Barycenters of Persistence Diagrams"
Jules Vidal, Joseph Budin and Julien Tierny
Proc. of IEEE VIS 2019.
IEEE Transactions on Visualization and Computer Graphics, 2019.

See also: PersistenceDiagramDistanceMatrix

Online examples:

Clustering Kelvin Helmholtz Instabilities example

Definition at line 36 of file ttkPersistenceDiagramDistanceMatrix.h.

Member Typedef Documentation

◆ Superclass

typedef ttkAlgorithm ttkPersistenceDiagramDistanceMatrix::Superclass

Definition at line 44 of file ttkPersistenceDiagramDistanceMatrix.h.

Constructor & Destructor Documentation

◆ ttkPersistenceDiagramDistanceMatrix()

ttkPersistenceDiagramDistanceMatrix::ttkPersistenceDiagramDistanceMatrix ( )

protected

Definition at line 22 of file ttkPersistenceDiagramDistanceMatrix.cpp.

◆ ~ttkPersistenceDiagramDistanceMatrix()

ttkPersistenceDiagramDistanceMatrix::~ttkPersistenceDiagramDistanceMatrix ( )

overrideprotecteddefault

Member Function Documentation

◆ FillInputPortInformation()

int ttkPersistenceDiagramDistanceMatrix::FillInputPortInformation	(	int	port,
		vtkInformation *	info
	)

overrideprotected

Definition at line 27 of file ttkPersistenceDiagramDistanceMatrix.cpp.

◆ FillOutputPortInformation()

int ttkPersistenceDiagramDistanceMatrix::FillOutputPortInformation	(	int	port,
		vtkInformation *	info
	)

overrideprotected

Definition at line 37 of file ttkPersistenceDiagramDistanceMatrix.cpp.

◆ GetAlpha()

virtual double ttkPersistenceDiagramDistanceMatrix::GetAlpha ( )

virtual

◆ GetClassName()

virtual const char * ttkPersistenceDiagramDistanceMatrix::GetClassName ( )

virtual

Reimplemented from ttkAlgorithm.

◆ GetConstraint()

int ttkPersistenceDiagramDistanceMatrix::GetConstraint ( )

inline

Definition at line 107 of file ttkPersistenceDiagramDistanceMatrix.h.

◆ GetDeltaLim()

virtual double ttkPersistenceDiagramDistanceMatrix::GetDeltaLim ( )

virtual

◆ GetLambda()

virtual double ttkPersistenceDiagramDistanceMatrix::GetLambda ( )

virtual

◆ GetMaxNumberOfPairs()

virtual unsigned int ttkPersistenceDiagramDistanceMatrix::GetMaxNumberOfPairs ( )

virtual

◆ GetMinPersistence()

virtual double ttkPersistenceDiagramDistanceMatrix::GetMinPersistence ( )

virtual

◆ GetPairType()

int ttkPersistenceDiagramDistanceMatrix::GetPairType ( )

inline

Definition at line 90 of file ttkPersistenceDiagramDistanceMatrix.h.

◆ GetWassersteinMetric()

std::string ttkPersistenceDiagramDistanceMatrix::GetWassersteinMetric ( )

inline

Definition at line 50 of file ttkPersistenceDiagramDistanceMatrix.h.

◆ IsA()

virtual int ttkPersistenceDiagramDistanceMatrix::IsA ( const char * type )

virtual

Reimplemented from ttkAlgorithm.

◆ IsTypeOf()

static int ttkPersistenceDiagramDistanceMatrix::IsTypeOf ( const char * type )

static

◆ New()

static ttkPersistenceDiagramDistanceMatrix * ttkPersistenceDiagramDistanceMatrix::New ( )

static

◆ RequestData()

int ttkPersistenceDiagramDistanceMatrix::RequestData	(	vtkInformation *	request,
		vtkInformationVector **	inputVector,
		vtkInformationVector *	outputVector
	)

overrideprotected

Definition at line 47 of file ttkPersistenceDiagramDistanceMatrix.cpp.

◆ SafeDownCast()

static ttkPersistenceDiagramDistanceMatrix * ttkPersistenceDiagramDistanceMatrix::SafeDownCast ( vtkObject * o )

static

◆ SetAntiAlpha()

void ttkPersistenceDiagramDistanceMatrix::SetAntiAlpha ( double data )

inline

Definition at line 54 of file ttkPersistenceDiagramDistanceMatrix.h.

◆ SetConstraint()

void ttkPersistenceDiagramDistanceMatrix::SetConstraint ( const int arg_ )

inline

Definition at line 103 of file ttkPersistenceDiagramDistanceMatrix.h.

◆ SetDeltaLim()

virtual void ttkPersistenceDiagramDistanceMatrix::SetDeltaLim ( double )

virtual

◆ SetLambda()

virtual void ttkPersistenceDiagramDistanceMatrix::SetLambda ( double )

virtual

◆ SetMaxNumberOfPairs()

virtual void ttkPersistenceDiagramDistanceMatrix::SetMaxNumberOfPairs ( unsigned int )

virtual

◆ SetMinPersistence()

virtual void ttkPersistenceDiagramDistanceMatrix::SetMinPersistence ( double )

virtual

◆ SetPairType()

void ttkPersistenceDiagramDistanceMatrix::SetPairType ( const int data )

inline

Definition at line 73 of file ttkPersistenceDiagramDistanceMatrix.h.

◆ SetWassersteinMetric()

void ttkPersistenceDiagramDistanceMatrix::SetWassersteinMetric ( const std::string & data )

inline

Definition at line 46 of file ttkPersistenceDiagramDistanceMatrix.h.

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

/home/julien/Pro/git/github/ttk-tierny/core/vtk/ttkPersistenceDiagramDistanceMatrix/ttkPersistenceDiagramDistanceMatrix.h
/home/julien/Pro/git/github/ttk-tierny/core/vtk/ttkPersistenceDiagramDistanceMatrix/ttkPersistenceDiagramDistanceMatrix.cpp

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Superclass

Constructor & Destructor Documentation

◆ ttkPersistenceDiagramDistanceMatrix()

◆ ~ttkPersistenceDiagramDistanceMatrix()

Member Function Documentation

◆ FillInputPortInformation()

◆ FillOutputPortInformation()

◆ GetAlpha()

◆ GetClassName()

◆ GetConstraint()

◆ GetDeltaLim()

◆ GetLambda()

◆ GetMaxNumberOfPairs()

◆ GetMinPersistence()

◆ GetPairType()

◆ GetWassersteinMetric()

◆ IsA()

◆ IsTypeOf()

◆ New()

◆ RequestData()

◆ SafeDownCast()

◆ SetAntiAlpha()

◆ SetConstraint()

◆ SetDeltaLim()

◆ SetLambda()

◆ SetMaxNumberOfPairs()

◆ SetMinPersistence()

◆ SetPairType()

◆ SetWassersteinMetric()