TTK VTK-filter for the computation of Reeb Graphs. More...

#include <ttkReebGraph.h>

Inheritance diagram for ttkReebGraph:

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 ()

int	getSkeletonNodes (const ttk::ftr::Graph &graph, vtkUnstructuredGrid *outputSkeletonNodes)

int	addDirectSkeletonArc (const ttk::ftr::Graph &graph, const ttk::ftr::idSuperArc arcId, vtkPoints points, vtkUnstructuredGrid skeletonArcs, ttk::ftr::ArcData &arcData)

int	addSampledSkeletonArc (const ttk::ftr::Graph &graph, const ttk::ftr::idSuperArc arcId, vtkPoints points, vtkUnstructuredGrid skeletonArcs, ttk::ftr::ArcData &arcData)

int	addCompleteSkeletonArc (const ttk::ftr::Graph &graph, const ttk::ftr::idSuperArc arcId, vtkPoints points, vtkUnstructuredGrid skeletonArcs, ttk::ftr::ArcData &arcData)

int	getSkeletonArcs (const ttk::ftr::Graph &graph, vtkUnstructuredGrid *outputSkeletonArcs)

int	getSegmentation (const ttk::ftr::Graph &graph, vtkDataSet *outputSegmentation)

template<typename VTK_TT , typename TTK_TT >
int	dispatch (ttk::ftr::Graph &graph)


void	SetSingleSweep (const bool ss)
	control whether the computation should start from min and max (default) or use a single sweep starting only from the min (may be more robust)

bool	GetSingleSweep () const


void	SetWithSegmentation (const bool segm)
	control if the output should contains the segmentation information

bool	GetWithSegmentation () const


void	SetWithNormalize (const bool norm)
	if set to true, a post processing pass will be used to enforce consistent node ids between executions

bool	GetWithNormalize () const


void	SetSampling (int lvl)
	control the sampling level of the superarcs

int	GetSuperArcSamplingLevel () const

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 ttkReebGraph *	New ()

static int	IsTypeOf (const char *type)

static ttkReebGraph *	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
	ttkReebGraph ()

void	identify (vtkDataSet *ds) const

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, 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)

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_

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 Reeb Graphs.

Author: Charles Gueunet charl.nosp@m.es.g.nosp@m.ueune.nosp@m.t@ki.nosp@m.tware.nosp@m..com

Date: June 2017.

See also: ttk::ftm::FTRGraph

The computation of the Reeb graph done by this package is done in parallel if TTK_ENABLE_OPENMP is set to ON, using a task based approach described in the article mention below.

Parameters

Input	Input scalar field, either 2D or 3D, regular grid or triangulation (vtkDataSet)
SingleSweep	control if the computation should start from both minima and maxima simultaneously. If you encounter troubled with FTR, you should try to use the single sweep. It is slower but may be more robust.
Segmentation	control wethear or not the output should be augmented with the segmentation.
SuperArcSamplingLevel	control the number of subdivision of each superarc. Intermediate point will be located on the barycenter of the corresponding portion of vertex.
Output	the output of this filter is composed of: The nodes of the tree The arcs of the tree The semgentation of the initial dataset The structure of the tree (Nodes+Arcs) have a concept of nodeId, which is an id that is consistent between execution if SetWithNormalize is set to True. The downNodeId of an arc is its starting node (directed towards the leaves as the computation starts here) and the upNodeId it the ending node, in direction of the Root of the tree. The segmentation also contains some basics metrics like the size of each region (RegionSpan) or its number of vertex (RegionSize)

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

Related publication
"Task-based Augmented Reeb Graphs with Dynamic ST-Trees"
Charles Gueunet, Pierre Fortin, Julien Jomier, Julien Tierny
EGPGV19: Eurographics Symposium on Parallel Graphics and Visualization

Online examples:

Harmonic Skeleton example

Definition at line 63 of file ttkReebGraph.h.

Member Typedef Documentation

◆ Superclass

typedef ttkAlgorithm ttkReebGraph::Superclass

Definition at line 66 of file ttkReebGraph.h.

Constructor & Destructor Documentation

◆ ttkReebGraph()

ttkReebGraph::ttkReebGraph ( )

protected

Definition at line 14 of file ttkReebGraph.cpp.

Member Function Documentation

◆ addCompleteSkeletonArc()

int ttkReebGraph::addCompleteSkeletonArc	(	const ttk::ftr::Graph &	graph,
		const ttk::ftr::idSuperArc	arcId,
		vtkPoints *	points,
		vtkUnstructuredGrid *	skeletonArcs,
		ttk::ftr::ArcData &	arcData
	)

Definition at line 39 of file ttkReebGraph.cpp.

◆ addDirectSkeletonArc()

int ttkReebGraph::addDirectSkeletonArc	(	const ttk::ftr::Graph &	graph,
		const ttk::ftr::idSuperArc	arcId,
		vtkPoints *	points,
		vtkUnstructuredGrid *	skeletonArcs,
		ttk::ftr::ArcData &	arcData
	)

Definition at line 111 of file ttkReebGraph.cpp.

◆ addSampledSkeletonArc()

int ttkReebGraph::addSampledSkeletonArc	(	const ttk::ftr::Graph &	graph,
		const ttk::ftr::idSuperArc	arcId,
		vtkPoints *	points,
		vtkUnstructuredGrid *	skeletonArcs,
		ttk::ftr::ArcData &	arcData
	)

Definition at line 158 of file ttkReebGraph.cpp.

◆ dispatch()

template<typename VTK_TT , typename TTK_TT >

int ttkReebGraph::dispatch ( ttk::ftr::Graph & graph )

Definition at line 262 of file ttkReebGraph.cpp.

◆ FillInputPortInformation()

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

overrideprotected

Definition at line 20 of file ttkReebGraph.cpp.

◆ FillOutputPortInformation()

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

overrideprotected

Definition at line 28 of file ttkReebGraph.cpp.

◆ GetClassName()

virtual const char * ttkReebGraph::GetClassName ( )

virtual

Reimplemented from ttkAlgorithm.

◆ GetForceInputOffsetScalarField()

virtual bool ttkReebGraph::GetForceInputOffsetScalarField ( )

virtual

◆ getSegmentation()

int ttkReebGraph::getSegmentation	(	const ttk::ftr::Graph &	graph,
		vtkDataSet *	outputSegmentation
	)

Definition at line 359 of file ttkReebGraph.cpp.

◆ GetSingleSweep()

bool ttkReebGraph::GetSingleSweep ( ) const

inline

Definition at line 79 of file ttkReebGraph.h.

◆ getSkeletonArcs()

int ttkReebGraph::getSkeletonArcs	(	const ttk::ftr::Graph &	graph,
		vtkUnstructuredGrid *	outputSkeletonArcs
	)

Definition at line 376 of file ttkReebGraph.cpp.

◆ getSkeletonNodes()

int ttkReebGraph::getSkeletonNodes	(	const ttk::ftr::Graph &	graph,
		vtkUnstructuredGrid *	outputSkeletonNodes
	)

Definition at line 422 of file ttkReebGraph.cpp.

◆ GetSuperArcSamplingLevel()

int ttkReebGraph::GetSuperArcSamplingLevel ( ) const

inline

Definition at line 113 of file ttkReebGraph.h.

◆ GetWithNormalize()

bool ttkReebGraph::GetWithNormalize ( ) const

inline

Definition at line 102 of file ttkReebGraph.h.

◆ GetWithSegmentation()

bool ttkReebGraph::GetWithSegmentation ( ) const

inline

Definition at line 90 of file ttkReebGraph.h.

◆ identify()

void ttkReebGraph::identify ( vtkDataSet * ds ) const

protected

Definition at line 451 of file ttkReebGraph.cpp.

◆ IsA()

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

virtual

Reimplemented from ttkAlgorithm.

◆ IsTypeOf()

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

static

◆ New()

static ttkReebGraph * ttkReebGraph::New ( )

static

◆ RequestData()

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

overrideprotected

Definition at line 284 of file ttkReebGraph.cpp.

◆ SafeDownCast()

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

static

◆ SetForceInputOffsetScalarField()

virtual void ttkReebGraph::SetForceInputOffsetScalarField ( bool )

virtual

◆ SetSampling()

void ttkReebGraph::SetSampling ( int lvl )

inline

control the sampling level of the superarcs

Definition at line 109 of file ttkReebGraph.h.

◆ SetSingleSweep()

void ttkReebGraph::SetSingleSweep ( const bool ss )

inline

control whether the computation should start from min and max (default) or use a single sweep starting only from the min (may be more robust)

Definition at line 75 of file ttkReebGraph.h.

◆ SetWithNormalize()

void ttkReebGraph::SetWithNormalize ( const bool norm )

inline

if set to true, a post processing pass will be used to enforce consistent node ids between executions

Definition at line 98 of file ttkReebGraph.h.

◆ SetWithSegmentation()

void ttkReebGraph::SetWithSegmentation ( const bool segm )

inline

control if the output should contains the segmentation information

Definition at line 86 of file ttkReebGraph.h.

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

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

◆ ttkReebGraph()

Member Function Documentation

◆ addCompleteSkeletonArc()

◆ addDirectSkeletonArc()

◆ addSampledSkeletonArc()

◆ dispatch()

◆ FillInputPortInformation()

◆ FillOutputPortInformation()

◆ GetClassName()

◆ GetForceInputOffsetScalarField()

◆ getSegmentation()

◆ GetSingleSweep()

◆ getSkeletonArcs()

◆ getSkeletonNodes()

◆ GetSuperArcSamplingLevel()

◆ GetWithNormalize()

◆ GetWithSegmentation()

◆ identify()

◆ IsA()

◆ IsTypeOf()

◆ New()

◆ RequestData()

◆ SafeDownCast()

◆ SetForceInputOffsetScalarField()

◆ SetSampling()

◆ SetSingleSweep()

◆ SetWithNormalize()

◆ SetWithSegmentation()