ttkPersistenceDiagram Class Reference

TTK VTK-filter for the computation of persistence diagrams. More...

#include <ttkPersistenceDiagram.h>

Inheritance diagram for ttkPersistenceDiagram:

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	SetForceInputOffsetScalarField (bool)
virtual bool	GetForceInputOffsetScalarField ()
virtual void	SetShowInsideDomain (bool)
virtual bool	GetShowInsideDomain ()
virtual void	SetBackEnd (int _arg)
virtual void	SetBackEnd (BACKEND)
virtual BACKEND	GetBackEnd () const
virtual int	GetStartingResolutionLevel ()
virtual void	SetStartingResolutionLevel (int)
virtual int	GetStoppingResolutionLevel ()
virtual void	SetStoppingResolutionLevel (int)
virtual bool	GetIsResumable ()
virtual void	SetIsResumable (bool)
virtual double	GetTimeLimit ()
virtual void	SetTimeLimit (double)
virtual double	GetEpsilon ()
virtual void	SetEpsilon (double)
virtual void	SetIgnoreBoundary (bool)
virtual bool	GetIgnoreBoundary ()
void	SetComputeMinSad (const bool data)
void	SetComputeSadSad (const bool data)
void	SetComputeSadMax (const bool data)
void	SetDMSDimensions (const int data)
virtual void	SetClearDGCache (bool)
virtual bool	GetClearDGCache ()
Public Member Functions inherited from ttkAlgorithm
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, ttk::Triangulation *triangulation, const bool getGlobalOrder=false, const int orderArrayIdx=0, const bool enforceOrderArrayIdx=false)
vtkDataArray *	checkForGlobalAndComputeOrderArray (vtkDataSet *const inputData, vtkDataArray *scalarArray, const int scalarArrayIdx, const bool getGlobalOrder, vtkDataArray *orderArray, ttk::Triangulation *triangulation, const bool enforceOrderArrayIdx)
vtkDataArray *	ComputeOrderArray (vtkDataSet *const inputData, vtkDataArray *scalarArray, const int scalarArrayIdx, const bool getGlobalOrder, vtkDataArray *oldOrderArray, ttk::Triangulation *triangulation)
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)

Static Public Member Functions
static ttkPersistenceDiagram *	New ()
static int	IsTypeOf (const char *type)
static ttkPersistenceDiagram *	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
	ttkPersistenceDiagram ()
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, std::map< int, int > &neighToId, 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, std::map< int, int > &neighborsToId)
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::PersistenceDiagram
	PersistenceDiagram ()
void	setBackend (const BACKEND be)
void	setComputeMinSad (const bool data)
void	setComputeSadSad (const bool data)
void	setComputeSadMax (const bool data)
template<typename scalarType , typename triangulationType >
void	augmentPersistenceDiagram (std::vector< PersistencePair > &persistencePairs, const scalarType *const scalars, const triangulationType *triangulation)
	Complete a ttk::DiagramType instance with scalar field values (useful for persistence) and 3D coordinates of critical vertices.
ttk::CriticalType	getNodeType (ftm::FTMTree_MT *tree, ftm::TreeType treeType, const SimplexId vertexId) const
void	sortPersistenceDiagram (std::vector< PersistencePair > &diagram, const SimplexId *const offsets) const
template<typename scalarType >
int	computeCTPersistenceDiagram (ftm::FTMTreePP &tree, const std::vector< std::tuple< ttk::SimplexId, ttk::SimplexId, scalarType, bool > > &pairs, std::vector< PersistencePair > &diagram) const
template<typename scalarType , class triangulationType >
int	execute (std::vector< PersistencePair > &CTDiagram, const scalarType *inputScalars, const size_t scalarsMTime, const SimplexId *inputOffsets, const triangulationType *triangulation, const std::vector< bool > *updateMask=nullptr)
template<typename scalarType , class triangulationType >
int	executeFTM (std::vector< PersistencePair > &CTDiagram, const scalarType *inputScalars, const SimplexId *inputOffsets, const triangulationType *triangulation)
template<class triangulationType >
int	executeProgressiveTopology (std::vector< PersistencePair > &CTDiagram, const SimplexId *inputOffsets, const triangulationType *triangulation)
template<typename scalarType , class triangulationType >
int	executeApproximateTopology (std::vector< PersistencePair > &CTDiagram, const scalarType *inputScalars, const triangulationType *triangulation)
template<class triangulationType >
int	executePersistentSimplex (std::vector< PersistencePair > &CTDiagram, const SimplexId *inputOffsets, const triangulationType *triangulation)
template<typename scalarType , class triangulationType >
int	executeDiscreteMorseSandwich (std::vector< PersistencePair > &CTDiagram, const scalarType *inputScalars, const size_t scalarsMTime, const SimplexId *inputOffsets, const triangulationType *triangulation, const std::vector< bool > *updateMask=nullptr)
template<class triangulationType >
void	checkProgressivityRequirement (const triangulationType *triangulation)
template<class triangulationType >
void	checkManifold (const triangulationType *const triangulation)
void	preconditionTriangulation (AbstractTriangulation *triangulation)
void	setOutputMonotonyOffsets (void *data)
void	setOutputOffsets (void *data)
void	setOutputScalars (void *data)
void	setDeltaApproximate (double data)
template<class triangulationType >
void	checkProgressivityRequirement (const triangulationType *ttkNotUsed(triangulation))

Additional Inherited Members
Protected Types inherited from ttk::PersistenceDiagram
enum class	BACKEND {   FTM = 0 , PROGRESSIVE_TOPOLOGY = 1 , DISCRETE_MORSE_SANDWICH = 2 , APPROXIMATE_TOPOLOGY = 3 ,   PERSISTENT_SIMPLEX = 4 }
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::PersistenceDiagram
bool	IgnoreBoundary {false}
ftm::FTMTreePP	contourTree_ {}
dcg::DiscreteGradient	dcg_ {}
PersistentSimplexPairs	psp_ {}
DiscreteMorseSandwich	dms_ {}
BACKEND	BackEnd {BACKEND::DISCRETE_MORSE_SANDWICH}
ttk::ProgressiveTopology	progT_ {}
ttk::ApproximateTopology	approxT_ {}
int	StartingResolutionLevel {0}
int	StoppingResolutionLevel {-1}
bool	IsResumable {false}
double	TimeLimit {}
void *	outputScalars_ {}
void *	outputOffsets_ {}
void *	outputMonotonyOffsets_ {}
double	Epsilon
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 persistence diagrams.

Author

Guillaume Favelier guill.nosp@m.aume.nosp@m..fave.nosp@m.lier.nosp@m.@lip6.nosp@m..fr

Julien Tierny julie.nosp@m.n.ti.nosp@m.erny@.nosp@m.lip6.nosp@m..fr

Date

September 2016.

This filter computes the persistence diagram of the extremum-saddle pairs of an input scalar field. The X-coordinate of each pair corresponds to its birth, while its smallest and highest Y-coordinates correspond to its birth and death respectively.

In practice, the diagram is represented by a vtkUnstructuredGrid. Each vertex of this mesh represent a critical point of the input data. It is associated with point data (vertexId, critical type). Each vertical edge of this mesh represent a persistence pair. It is associated with cell data (persistence of the pair, critical index of the extremum of the pair).

Persistence diagrams are useful and stable concise representations of the topological features of a data-set. It is useful to fine-tune persistence thresholds for topological simplification or for fast similarity estimations for instance.

Parameters

Input	Input scalar field, either 2D or 3D, regular grid or triangulation (vtkDataSet)
Output	Output persistence diagram (vtkUnstructuredGrid)

This filter can be used as any other VTK filter (for instance, by using the sequence of calls SetInputData(), Update(), GetOutput()).

See the related ParaView example state files for usage examples within a VTK pipeline.

Related publication
"Computational Topology: An Introduction"
Herbert Edelsbrunner and John Harer
American Mathematical Society, 2010

Five backends are available for the computation:

1) FTM
Related publication
"Task-based Augmented Contour Trees with Fibonacci Heaps" Charles Gueunet, Pierre Fortin, Julien Jomier, Julien Tierny IEEE Transactions on Parallel and Distributed Systems, 2019

2) Progressive Approach
Related publication
"A Progressive Approach to Scalar Field Topology"
Jules Vidal, Pierre Guillou, Julien Tierny
IEEE Transactions on Visualization and Computer Graphics, 2021

3) Discrete Morse Sandwich (default)
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.
Fast and versatile algorithm for persistence diagram computation.

4) Approximate Approach
Related publication
"Fast Approximation of Persistence Diagrams with Guarantees"
Jules Vidal, Julien Tierny
IEEE Symposium on Large Data Visualization and Analysis (LDAV), 2021

5) Persistent Simplex
This is a textbook (and very slow) algorithm, described in "Algorithm and Theory of Computation Handbook (Second Edition) - Special Topics and Techniques" by Atallah and Blanton on page 97.

See also

ttkMergeTreePP

ttkPersistenceCurve

ttkScalarFieldCriticalPoints

ttkTopologicalSimplification

ttk::PersistenceDiagram

Online examples:

• 1-Manifold Learning example
  
• 1-Manifold Learning Circles example
  
• 2-Manifold Learning example
  
• BuiltInExample1
  
• Clustering Kelvin Helmholtz Instabilities example
  
• CT Bones example
  
• Dragon example
  
• Harmonic Skeleton example
  
• Image Processing example
  
• Interaction sites
  
• Karhunen-Love Digits 64-Dimensions example
  
• Morse Persistence example
  
• Morse-Smale Quadrangulation example
  
• Persistence clustering 0 example
  
• Persistence clustering 1 example
  
• Persistence clustering 2 example
  
• Persistence clustering 3 example
  
• Persistence clustering 4 example
  
• Persistence Diagram Clustering example
  
• Persistence Diagram Distance example
  
• Persistence Diagram Principal Geodesic Analysis example
  
• Tectonic Puzzle example
  
• Topological Optimization DarkSky example
  
• Topological Optimization for Pegasus Genus Repair example
  
• Topological Optimization for Torus Repair example
  
• Tribute example
  
• Uncertain Starting Vortex example
  

Definition at line 176 of file ttkPersistenceDiagram.h.

Member Typedef Documentation

Superclass

typedef ttkAlgorithm ttkPersistenceDiagram::Superclass

Definition at line 183 of file ttkPersistenceDiagram.h.

Constructor & Destructor Documentation

ttkPersistenceDiagram()

ttkPersistenceDiagram::ttkPersistenceDiagram ( )

protected

Definition at line 17 of file ttkPersistenceDiagram.cpp.

Member Function Documentation

FillInputPortInformation()

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

overrideprotected

Definition at line 22 of file ttkPersistenceDiagram.cpp.

FillOutputPortInformation()

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

overrideprotected

Definition at line 31 of file ttkPersistenceDiagram.cpp.

GetBackEnd()

virtual BACKEND ttkPersistenceDiagram::GetBackEnd ( ) const

virtual

GetClassName()

virtual const char * ttkPersistenceDiagram::GetClassName ( )

virtual

Reimplemented from ttkAlgorithm.

GetClearDGCache()

virtual bool ttkPersistenceDiagram::GetClearDGCache ( )

virtual

GetEpsilon()

virtual double ttkPersistenceDiagram::GetEpsilon ( )

virtual

GetForceInputOffsetScalarField()

virtual bool ttkPersistenceDiagram::GetForceInputOffsetScalarField ( )

virtual

GetIgnoreBoundary()

virtual bool ttkPersistenceDiagram::GetIgnoreBoundary ( )

virtual

GetIsResumable()

virtual bool ttkPersistenceDiagram::GetIsResumable ( )

virtual

GetShowInsideDomain()

virtual bool ttkPersistenceDiagram::GetShowInsideDomain ( )

virtual

GetStartingResolutionLevel()

virtual int ttkPersistenceDiagram::GetStartingResolutionLevel ( )

virtual

GetStoppingResolutionLevel()

virtual int ttkPersistenceDiagram::GetStoppingResolutionLevel ( )

virtual

GetTimeLimit()

virtual double ttkPersistenceDiagram::GetTimeLimit ( )

virtual

IsA()

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

virtual

Reimplemented from ttkAlgorithm.

IsTypeOf()

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

static

New()

static ttkPersistenceDiagram * ttkPersistenceDiagram::New ( )

static

RequestData()

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

overrideprotected

Definition at line 94 of file ttkPersistenceDiagram.cpp.

SafeDownCast()

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

static

SetBackEnd() [1/2]

virtual void ttkPersistenceDiagram::SetBackEnd ( BACKEND  )

virtual

SetBackEnd() [2/2]

virtual void ttkPersistenceDiagram::SetBackEnd ( int  _arg )

virtual

SetClearDGCache()

virtual void ttkPersistenceDiagram::SetClearDGCache ( bool  )

virtual

SetComputeMinSad()

void ttkPersistenceDiagram::SetComputeMinSad ( const bool  data )

inline

Definition at line 212 of file ttkPersistenceDiagram.h.

SetComputeSadMax()

void ttkPersistenceDiagram::SetComputeSadMax ( const bool  data )

inline

Definition at line 222 of file ttkPersistenceDiagram.h.

SetComputeSadSad()

void ttkPersistenceDiagram::SetComputeSadSad ( const bool  data )

inline

Definition at line 217 of file ttkPersistenceDiagram.h.

SetDMSDimensions()

void ttkPersistenceDiagram::SetDMSDimensions ( const int  data )

inline

Definition at line 227 of file ttkPersistenceDiagram.h.

SetEpsilon()

virtual void ttkPersistenceDiagram::SetEpsilon ( double  )

virtual

SetForceInputOffsetScalarField()

virtual void ttkPersistenceDiagram::SetForceInputOffsetScalarField ( bool  )

virtual

SetIgnoreBoundary()

virtual void ttkPersistenceDiagram::SetIgnoreBoundary ( bool  )

virtual

SetIsResumable()

virtual void ttkPersistenceDiagram::SetIsResumable ( bool  )

virtual

SetShowInsideDomain()

virtual void ttkPersistenceDiagram::SetShowInsideDomain ( bool  )

virtual

SetStartingResolutionLevel()

virtual void ttkPersistenceDiagram::SetStartingResolutionLevel ( int  )

virtual

SetStoppingResolutionLevel()

virtual void ttkPersistenceDiagram::SetStoppingResolutionLevel ( int  )

virtual

SetTimeLimit()

virtual void ttkPersistenceDiagram::SetTimeLimit ( double  )

virtual

---

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

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