ttkPersistenceDiagramClustering Class Reference

TTK processing package for the computation of Wasserstein barycenters and K-Means clusterings of a set of persistence diagrams. More...

#include <ttkPersistenceDiagramClustering.h>

Inheritance diagram for ttkPersistenceDiagramClustering:

Public Types
enum class	DISPLAY { COMPACT = 0 , STARS = 1 , MATCHINGS = 2 }
enum class	METHOD { PROGRESSIVE = 0 , AUCTION = 1 }
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	SetWassersteinMetric (int)
virtual int	GetWassersteinMetric ()
virtual void	SetUseProgressive (bool)
virtual bool	GetUseProgressive ()
virtual void	SetTimeLimit (double)
virtual double	GetTimeLimit ()
void	SetAlpha (const double alpha)
void	SetAntiAlpha (const double antiAlpha)
virtual double	GetAlpha ()
virtual void	SetDeltaLim (double)
virtual double	GetDeltaLim ()
virtual void	SetLambda (double)
virtual double	GetLambda ()
virtual void	SetNumberOfClusters (int)
virtual int	GetNumberOfClusters ()
virtual void	SetUseAccelerated (bool)
virtual bool	GetUseAccelerated ()
virtual void	SetUseKmeansppInit (bool)
virtual bool	GetUseKmeansppInit ()
virtual void	SetForceUseOfAlgorithm (bool)
virtual bool	GetForceUseOfAlgorithm ()
virtual void	SetDeterministic (bool)
virtual bool	GetDeterministic ()
virtual void	SetPairTypeClustering (int)
virtual int	GetPairTypeClustering ()
void	SetSpacing (double spacing)
virtual double	GetSpacing ()
void	SetDisplayMethod (int displayMethod)
virtual DISPLAY	GetDisplayMethod () const
virtual void	SetUseAdditionalPrecision (bool)
virtual bool	GetUseAdditionalPrecision ()
virtual void	SetDistanceWritingOptions (int)
virtual int	GetDistanceWritingOptions ()
virtual void	SetUseInterruptible (bool)
virtual bool	GetUseInterruptible ()
virtual void	SetMethod (int _arg)
virtual void	SetMethod (METHOD)
virtual METHOD	GetMethod () const
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 ttkPersistenceDiagramClustering *	New ()
static int	IsTypeOf (const char *type)
static ttkPersistenceDiagramClustering *	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
	ttkPersistenceDiagramClustering ()
int	FillInputPortInformation (int port, vtkInformation *info) override
int	FillOutputPortInformation (int port, vtkInformation *info) override
void	Modified () override
void	outputClusteredDiagrams (vtkMultiBlockDataSet *output, const std::vector< vtkUnstructuredGrid * > &diagsVTU, const std::vector< ttk::DiagramType > &diags, const std::vector< std::vector< std::vector< ttk::MatchingType > > > &matchingsPerCluster, const std::vector< int > &inv_clustering, const DISPLAY dm, const double spacing, const double max_persistence) const
void	outputCentroids (vtkMultiBlockDataSet *output, const std::vector< ttk::DiagramType > &final_centroids, const std::vector< std::vector< std::vector< ttk::MatchingType > > > &matchingsPerCluster, vtkUnstructuredGrid *const someInputDiag, const DISPLAY dm, const double spacing, const double max_persistence) const
void	outputMatchings (vtkMultiBlockDataSet *output, const size_t nClusters, const std::vector< ttk::DiagramType > &diags, const std::vector< std::vector< std::vector< ttk::MatchingType > > > &matchingsPerCluster, const std::vector< ttk::DiagramType > &centroids, const std::vector< int > &inv_clustering, const ttkPersistenceDiagramClustering::DISPLAY dm, const double spacing, const double max_persistence) const
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::PersistenceDiagramClustering
	PersistenceDiagramClustering ()
	~PersistenceDiagramClustering () override=default
std::vector< int >	execute (std::vector< DiagramType > &intermediateDiagrams, std::vector< DiagramType > &centroids, std::vector< std::vector< std::vector< MatchingType > > > &all_matchings)
std::array< double, 3 >	getDistances () const

Additional Inherited Members
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::PersistenceDiagramClustering
std::array< double, 3 >	distances {}
int	DistanceWritingOptions {0}
int	PairTypeClustering {-1}
bool	Deterministic {true}
int	WassersteinMetric {2}
bool	UseProgressive {true}
bool	ForceUseOfAlgorithm {false}
bool	UseInterruptible {true}
double	Alpha {1.0}
bool	UseAdditionalPrecision {false}
double	DeltaLim {0.01}
double	Lambda {1.0}
double	TimeLimit {999999}
int	NumberOfClusters {1}
bool	UseAccelerated {false}
bool	UseKmeansppInit {false}
int	points_added_
int	points_deleted_
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 Wasserstein barycenters and K-Means clusterings of a set of persistence diagrams.

Author

Jules Vidal jules.nosp@m..vid.nosp@m.al@li.nosp@m.p6.f.nosp@m.r

Joseph Budin josep.nosp@m.h.bu.nosp@m.din@p.nosp@m.olyt.nosp@m.echni.nosp@m.que..nosp@m.edu

Date

September 2019

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

PersistenceDiagramClustering

Online examples:

• Clustering Kelvin Helmholtz Instabilities example
  
• Persistence Diagram Clustering example
  
• Persistence Diagram Distance example
  

Definition at line 46 of file ttkPersistenceDiagramClustering.h.

Member Typedef Documentation

Superclass

typedef ttkAlgorithm ttkPersistenceDiagramClustering::Superclass

Definition at line 53 of file ttkPersistenceDiagramClustering.h.

Member Enumeration Documentation

DISPLAY

enum class ttkPersistenceDiagramClustering::DISPLAY

strong

Enumerator
COMPACT
STARS
MATCHINGS

Definition at line 55 of file ttkPersistenceDiagramClustering.h.

METHOD

enum class ttkPersistenceDiagramClustering::METHOD

strong

Enumerator
PROGRESSIVE
AUCTION

Definition at line 61 of file ttkPersistenceDiagramClustering.h.

Constructor & Destructor Documentation

ttkPersistenceDiagramClustering()

ttkPersistenceDiagramClustering::ttkPersistenceDiagramClustering ( )

protected

Definition at line 23 of file ttkPersistenceDiagramClustering.cpp.

Member Function Documentation

FillInputPortInformation()

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

overrideprotected

Definition at line 28 of file ttkPersistenceDiagramClustering.cpp.

FillOutputPortInformation()

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

overrideprotected

Definition at line 38 of file ttkPersistenceDiagramClustering.cpp.

GetAlpha()

virtual double ttkPersistenceDiagramClustering::GetAlpha ( )

virtual

GetClassName()

virtual const char * ttkPersistenceDiagramClustering::GetClassName ( )

virtual

Reimplemented from ttkAlgorithm.

GetDeltaLim()

virtual double ttkPersistenceDiagramClustering::GetDeltaLim ( )

virtual

GetDeterministic()

virtual bool ttkPersistenceDiagramClustering::GetDeterministic ( )

virtual

GetDisplayMethod()

virtual DISPLAY ttkPersistenceDiagramClustering::GetDisplayMethod ( ) const

virtual

GetDistanceWritingOptions()

virtual int ttkPersistenceDiagramClustering::GetDistanceWritingOptions ( )

virtual

GetForceUseOfAlgorithm()

virtual bool ttkPersistenceDiagramClustering::GetForceUseOfAlgorithm ( )

virtual

GetLambda()

virtual double ttkPersistenceDiagramClustering::GetLambda ( )

virtual

GetMethod()

virtual METHOD ttkPersistenceDiagramClustering::GetMethod ( ) const

virtual

GetNumberOfClusters()

virtual int ttkPersistenceDiagramClustering::GetNumberOfClusters ( )

virtual

GetPairTypeClustering()

virtual int ttkPersistenceDiagramClustering::GetPairTypeClustering ( )

virtual

GetSpacing()

virtual double ttkPersistenceDiagramClustering::GetSpacing ( )

virtual

GetTimeLimit()

virtual double ttkPersistenceDiagramClustering::GetTimeLimit ( )

virtual

GetUseAccelerated()

virtual bool ttkPersistenceDiagramClustering::GetUseAccelerated ( )

virtual

GetUseAdditionalPrecision()

virtual bool ttkPersistenceDiagramClustering::GetUseAdditionalPrecision ( )

virtual

GetUseInterruptible()

virtual bool ttkPersistenceDiagramClustering::GetUseInterruptible ( )

virtual

GetUseKmeansppInit()

virtual bool ttkPersistenceDiagramClustering::GetUseKmeansppInit ( )

virtual

GetUseProgressive()

virtual bool ttkPersistenceDiagramClustering::GetUseProgressive ( )

virtual

GetWassersteinMetric()

virtual int ttkPersistenceDiagramClustering::GetWassersteinMetric ( )

virtual

IsA()

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

virtual

Reimplemented from ttkAlgorithm.

IsTypeOf()

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

static

Modified()

void ttkPersistenceDiagramClustering::Modified ( )

overrideprotected

Definition at line 48 of file ttkPersistenceDiagramClustering.cpp.

New()

static ttkPersistenceDiagramClustering * ttkPersistenceDiagramClustering::New ( )

static

outputCentroids()

void ttkPersistenceDiagramClustering::outputCentroids ( vtkMultiBlockDataSet *  output, const std::vector< ttk::DiagramType > &  final_centroids, const std::vector< std::vector< std::vector< ttk::MatchingType > > > &  matchingsPerCluster, vtkUnstructuredGrid *const  someInputDiag, const DISPLAY  dm, const double  spacing, const double  max_persistence  ) const

protected

Definition at line 326 of file ttkPersistenceDiagramClustering.cpp.

outputClusteredDiagrams()

void ttkPersistenceDiagramClustering::outputClusteredDiagrams ( vtkMultiBlockDataSet *  output, const std::vector< vtkUnstructuredGrid * > &  diagsVTU, const std::vector< ttk::DiagramType > &  diags, const std::vector< std::vector< std::vector< ttk::MatchingType > > > &  matchingsPerCluster, const std::vector< int > &  inv_clustering, const DISPLAY  dm, const double  spacing, const double  max_persistence  ) const

protected

Definition at line 203 of file ttkPersistenceDiagramClustering.cpp.

outputMatchings()

void ttkPersistenceDiagramClustering::outputMatchings ( vtkMultiBlockDataSet *  output, const size_t  nClusters, const std::vector< ttk::DiagramType > &  diags, const std::vector< std::vector< std::vector< ttk::MatchingType > > > &  matchingsPerCluster, const std::vector< ttk::DiagramType > &  centroids, const std::vector< int > &  inv_clustering, const ttkPersistenceDiagramClustering::DISPLAY  dm, const double  spacing, const double  max_persistence  ) const

protected

Definition at line 413 of file ttkPersistenceDiagramClustering.cpp.

RequestData()

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

overrideprotected

Definition at line 53 of file ttkPersistenceDiagramClustering.cpp.

SafeDownCast()

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

static

SetAlpha()

void ttkPersistenceDiagramClustering::SetAlpha ( const double  alpha )

inline

Definition at line 75 of file ttkPersistenceDiagramClustering.h.

SetAntiAlpha()

void ttkPersistenceDiagramClustering::SetAntiAlpha ( const double  antiAlpha )

inline

Definition at line 79 of file ttkPersistenceDiagramClustering.h.

SetDeltaLim()

virtual void ttkPersistenceDiagramClustering::SetDeltaLim ( double  )

virtual

SetDeterministic()

virtual void ttkPersistenceDiagramClustering::SetDeterministic ( bool  )

virtual

SetDisplayMethod()

void ttkPersistenceDiagramClustering::SetDisplayMethod ( int  displayMethod )

inline

Definition at line 118 of file ttkPersistenceDiagramClustering.h.

SetDistanceWritingOptions()

virtual void ttkPersistenceDiagramClustering::SetDistanceWritingOptions ( int  )

virtual

SetForceUseOfAlgorithm()

virtual void ttkPersistenceDiagramClustering::SetForceUseOfAlgorithm ( bool  )

virtual

SetLambda()

virtual void ttkPersistenceDiagramClustering::SetLambda ( double  )

virtual

SetMethod() [1/2]

virtual void ttkPersistenceDiagramClustering::SetMethod ( int  _arg )

virtual

SetMethod() [2/2]

virtual void ttkPersistenceDiagramClustering::SetMethod ( METHOD  )

virtual

SetNumberOfClusters()

virtual void ttkPersistenceDiagramClustering::SetNumberOfClusters ( int  )

virtual

SetPairTypeClustering()

virtual void ttkPersistenceDiagramClustering::SetPairTypeClustering ( int  )

virtual

SetSpacing()

void ttkPersistenceDiagramClustering::SetSpacing ( double  spacing )

inline

Definition at line 108 of file ttkPersistenceDiagramClustering.h.

SetTimeLimit()

virtual void ttkPersistenceDiagramClustering::SetTimeLimit ( double  )

virtual

SetUseAccelerated()

virtual void ttkPersistenceDiagramClustering::SetUseAccelerated ( bool  )

virtual

SetUseAdditionalPrecision()

virtual void ttkPersistenceDiagramClustering::SetUseAdditionalPrecision ( bool  )

virtual

SetUseInterruptible()

virtual void ttkPersistenceDiagramClustering::SetUseInterruptible ( bool  )

virtual

SetUseKmeansppInit()

virtual void ttkPersistenceDiagramClustering::SetUseKmeansppInit ( bool  )

virtual

SetUseProgressive()

virtual void ttkPersistenceDiagramClustering::SetUseProgressive ( bool  )

virtual

SetWassersteinMetric()

virtual void ttkPersistenceDiagramClustering::SetWassersteinMetric ( int  )

virtual

---

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

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