TTK VTK-filter for the computation of persistent generators. More...

#include <ttkPersistentGenerators.h>

Inheritance diagram for ttkPersistentGenerators:

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)

virtual void	SetPruneHandlesGenerators (bool)

virtual bool	GetPruneHandlesGenerators ()

virtual void	SetForceInputOffsetScalarField (bool)

virtual bool	GetForceInputOffsetScalarField ()

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 ttkPersistentGenerators *	New ()

static int	IsTypeOf (const char *type)

static ttkPersistentGenerators *	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
	ttkPersistentGenerators ()

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

int	FillInputPortInformation (int port, vtkInformation *info) override

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

template<typename triangulationType >
int	computePersistentGenerators (std::vector< GeneratorType > &generators, std::vector< std::vector< SimplexId > > &connComps, const SimplexId *const offsets, const triangulationType &triangulation)
	Compute the persistence generators from the discrete gradient.

Protected Member Functions inherited from ttk::DiscreteMorseSandwich
template<typename triangulationType >
std::vector< std::vector< SimplexId > >	getSaddle1ToMinima (const std::vector< SimplexId > &criticalEdges, const triangulationType &triangulation) const
	Follow the descending 1-separatrices to compute the saddles -> minima association.

template<typename triangulationType , typename GFS , typename GFSN , typename OB >
std::vector< std::vector< SimplexId > >	getSaddle2ToMaxima (const std::vector< SimplexId > &criticalCells, const GFS &getFaceStar, const GFSN &getFaceStarNumber, const OB &isOnBoundary, const triangulationType &triangulation) const
	Follow the ascending 1-separatrices to compute the saddles -> maxima association.

template<typename triangulationType >
void	getMinSaddlePairs (std::vector< PersistencePair > &pairs, std::vector< bool > &pairedMinima, std::vector< bool > &paired1Saddles, const std::vector< SimplexId > &criticalEdges, const std::vector< SimplexId > &critEdgesOrder, const SimplexId *const offsets, const triangulationType &triangulation) const
	Compute the pairs of dimension 0.

template<typename triangulationType >
void	getMaxSaddlePairs (std::vector< PersistencePair > &pairs, std::vector< bool > &pairedMaxima, std::vector< bool > &pairedSaddles, const std::vector< SimplexId > &criticalSaddles, const std::vector< SimplexId > &critSaddlesOrder, const std::vector< SimplexId > &critMaxsOrder, const triangulationType &triangulation) const
	Compute the pairs of dimension dim - 1.

template<typename triangulationType >
void	getSaddleSaddlePairs (std::vector< PersistencePair > &pairs, std::vector< bool > &paired1Saddles, std::vector< bool > &paired2Saddles, const bool exportBoundaries, std::vector< GeneratorType > &boundaries, const std::vector< SimplexId > &critical1Saddles, const std::vector< SimplexId > &critical2Saddles, const std::vector< SimplexId > &crit1SaddlesOrder, const triangulationType &triangulation) const
	Compute the saddle-saddle pairs (in 3D)

template<typename triangulationType >
void	extractCriticalCells (std::array< std::vector< SimplexId >, 4 > &criticalCellsByDim, std::array< std::vector< SimplexId >, 4 > &critCellsOrder, const SimplexId *const offsets, const triangulationType &triangulation, const bool sortEdges) const
	Extract & sort critical cell from the DiscreteGradient.

void	displayStats (const std::vector< PersistencePair > &pairs, const std::array< std::vector< SimplexId >, 4 > &criticalCellsByDim, const std::vector< bool > &pairedMinima, const std::vector< bool > &paired1Saddles, const std::vector< bool > &paired2Saddles, const std::vector< bool > &pairedMaxima) const
	Print number of pairs, critical cells per dimension & unpaired cells.

void	tripletsToPersistencePairs (std::vector< PersistencePair > &pairs, std::vector< bool > &pairedExtrema, std::vector< bool > &pairedSaddles, std::vector< SimplexId > &reps, std::vector< tripletType > &triplets, const SimplexId const saddlesOrder, const SimplexId const extremaOrder, const SimplexId pairDim) const
	Compute persistence pairs from triplets.

template<typename triangulationType , typename Container >
SimplexId	eliminateBoundariesSandwich (const SimplexId s2, std::vector< bool > &onBoundary, std::vector< Container > &s2Boundaries, const std::vector< SimplexId > &s2Mapping, const std::vector< SimplexId > &s1Mapping, std::vector< SimplexId > &partners, std::vector< Lock > &s1Locks, std::vector< Lock > &s2Locks, const triangulationType &triangulation) const
	Detect 1-saddles paired to a given 2-saddle.

template<typename triangulationType >
void	alloc (const triangulationType &triangulation)

void	clear ()

	DiscreteMorseSandwich ()

void	preconditionTriangulation (AbstractTriangulation *const data)

void	setInputOffsets (const SimplexId *const offsets)

void	setComputeMinSad (const bool data)

void	setComputeSadSad (const bool data)

void	setComputeSadMax (const bool data)

template<typename triangulationType >
int	buildGradient (const void const scalars, const size_t scalarsMTime, const SimplexId const offsets, const triangulationType &triangulation)

void	setGradient (ttk::dcg::DiscreteGradient &&dg)
	Ugly hack to avoid a call to buildGradient()

ttk::dcg::DiscreteGradient &&	getGradient ()

template<typename triangulationType >
SimplexId	getCellGreaterVertex (const dcg::Cell &c, const triangulationType &triangulation)

const std::vector< std::vector< SimplexId > > &	get2SaddlesChildren () const

template<typename triangulationType >
int	computePersistencePairs (std::vector< PersistencePair > &pairs, const SimplexId *const offsets, const triangulationType &triangulation, const bool ignoreBoundary, const bool compute2SaddlesChildren=false)
	Compute the persistence pairs from the discrete gradient.

Additional Inherited Members
Protected Types inherited from ttk::DiscreteMorseSandwich
using	tripletType = std::array< SimplexId, 3 >
	Triplet type for persistence pairs.

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::PersistentGenerators
bool	PruneHandlesGenerators {false}

Protected Attributes inherited from ttk::DiscreteMorseSandwich
dcg::DiscreteGradient	dg_ {}

std::vector< SimplexId >	firstRepMin_ {}

std::vector< SimplexId >	firstRepMax_ {}

std::vector< SimplexId >	edgeTrianglePartner_ {}

std::vector< SimplexId >	s2Mapping_ {}

std::vector< SimplexId >	s1Mapping_ {}

std::vector< EdgeSimplex >	critEdges_ {}

std::array< std::vector< bool >, 4 >	pairedCritCells_ {}

std::vector< bool >	onBoundary_ {}

std::array< std::vector< SimplexId >, 4 >	critCellsOrder_ {}

std::vector< std::vector< SimplexId > >	s2Children_ {}

bool	ComputeMinSad {true}

bool	ComputeSadSad {true}

bool	ComputeSadMax {true}

bool	Compute2SaddlesChildren {false}

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

Detailed Description

TTK VTK-filter for the computation of persistent generators.

Author: Pierre Guillou pierr.nosp@m.e.gu.nosp@m.illou.nosp@m.@lip.nosp@m.6.fr

Date: February 2022.

Related publication
"Discrete Morse Sandwich: Fast Computation of Persistence Diagrams for Scalar Data -- An Algorithm and A Benchmark"
Pierre Guillou, Jules Vidal, Julien Tierny
IEEE Transactions on Visualization and Computer Graphics, 2023.
arXiv:2206.13932, 2023.

Online examples:

Definition at line 53 of file ttkPersistentGenerators.h.

Member Typedef Documentation

◆ Superclass

typedef ttkAlgorithm ttkPersistentGenerators::Superclass

Definition at line 60 of file ttkPersistentGenerators.h.

Constructor & Destructor Documentation

◆ ttkPersistentGenerators()

ttkPersistentGenerators::ttkPersistentGenerators ( )

protected

Definition at line 19 of file ttkPersistentGenerators.cpp.

Member Function Documentation

◆ FillInputPortInformation()

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

overrideprotected

Definition at line 25 of file ttkPersistentGenerators.cpp.

◆ FillOutputPortInformation()

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

overrideprotected

Definition at line 34 of file ttkPersistentGenerators.cpp.

◆ GetClassName()

virtual const char * ttkPersistentGenerators::GetClassName ( )

virtual

Reimplemented from ttkAlgorithm.

◆ GetForceInputOffsetScalarField()

virtual bool ttkPersistentGenerators::GetForceInputOffsetScalarField ( )

virtual

◆ GetPruneHandlesGenerators()

virtual bool ttkPersistentGenerators::GetPruneHandlesGenerators ( )

virtual

◆ IsA()

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

virtual

Reimplemented from ttkAlgorithm.

◆ IsTypeOf()

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

static

◆ New()

static ttkPersistentGenerators * ttkPersistentGenerators::New ( )

static

◆ RequestData()

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

overrideprotected

Definition at line 179 of file ttkPersistentGenerators.cpp.

◆ SafeDownCast()

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

static

◆ SetForceInputOffsetScalarField()

virtual void ttkPersistentGenerators::SetForceInputOffsetScalarField ( bool )

virtual

◆ SetPruneHandlesGenerators()

virtual void ttkPersistentGenerators::SetPruneHandlesGenerators ( bool )

virtual

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

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

◆ ttkPersistentGenerators()

Member Function Documentation

◆ FillInputPortInformation()

◆ FillOutputPortInformation()

◆ GetClassName()

◆ GetForceInputOffsetScalarField()

◆ GetPruneHandlesGenerators()

◆ IsA()

◆ IsTypeOf()

◆ New()

◆ RequestData()

◆ SafeDownCast()

◆ SetForceInputOffsetScalarField()

◆ SetPruneHandlesGenerators()