TTK filter for the computation of merge trees. More...

#include <ttkMergeTree.h>

Inheritance diagram for ttkMergeTree:

Public Types
enum class	BACKEND { FTM = 0 , EXTREEM = 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 bool	GetForceInputOffsetScalarField ()
	the offset array to use for simulation of simplicity

virtual void	SetForceInputOffsetScalarField (bool)


virtual int	GetBackend ()
	the backend to use for computations.

virtual void	SetBackend (int)


void	SetTreeType (const int type)
	the type of tree to compute (Join, Split, Contour, JoinSplit)


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

bool	GetWithSegmentation () const


void	SetWithNormalize (const bool norm)
	if true, a post process pass will ensure NodesId have a deterministic order

bool	GetWithNormalize () const


void	SetWithAdvStats (const bool adv)
	Compute additional information on the segmentation like the span and size (in nb of vertex) of each region.

bool	GetWithAdvStats () const


void	SetSuperArcSamplingLevel (int lvl)
	control the sampling level of the superarc. By default: 0

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)

Public Member Functions inherited from ttkMergeTreeBase
	ttkMergeTreeBase ()

	~ttkMergeTreeBase () override=default

int	getSkeletonNodes (vtkUnstructuredGrid *outputSkeletonNodes)

int	addDirectSkeletonArc (const ttk::ftm::idSuperArc arcId, const int cc, vtkPoints points, vtkUnstructuredGrid skeletonArcs, ttk::ftm::ArcData &arcData)

int	addSampledSkeletonArc (const ttk::ftm::idSuperArc arcId, const int cc, vtkPoints points, vtkUnstructuredGrid skeletonArcs, ttk::ftm::ArcData &arcData)

int	addCompleteSkeletonArc (const ttk::ftm::idSuperArc arcId, const int cc, vtkPoints points, vtkUnstructuredGrid skeletonArcs, ttk::ftm::ArcData &arcData)

int	getSkeletonArcs (vtkUnstructuredGrid *outputSkeletonArcs)

int	getSegmentation (vtkDataSet *outputSegmentation)

ttk::ftm::TreeType	GetTreeType () const

void	identify (vtkDataSet *ds) const

Static Public Member Functions
static ttkMergeTree *	New ()

static int	IsTypeOf (const char *type)

static ttkMergeTree *	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
	ttkMergeTree ()

int	getOffsets ()

int	getScalars ()

int	preconditionTriangulation ()

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)

Protected Member Functions inherited from ttkMergeTreeBase
template<class triangulationType >
int	getMergeTree (vtkUnstructuredGrid outputSkeletonArcs, std::vector< ttk::ExTreeM::Branch > &mergeTree, vtkDataArray inputScalars, const triangulationType *triangulation)

template<class triangulationType >
int	getMergeTreePoints (vtkUnstructuredGrid outputSkeletonNodes, std::map< ttk::SimplexId, int > cpMap, std::vector< std::pair< ttk::SimplexId, ttk::SimplexId > > &persistencePairs, vtkDataArray inputScalars, const triangulationType *triangulation)

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 ttkMergeTreeBase
bool	ForceInputOffsetScalarField = false

ttk::ftm::Params	params_

int	nbCC_

std::vector< vtkSmartPointer< vtkDataSet > >	connected_components_

std::vector< ttk::Triangulation * >	triangulation_

std::vector< ttk::ftm::LocalFTM >	ftmTree_

std::vector< vtkDataArray * >	inputScalars_

std::vector< std::vector< ttk::SimplexId > >	offsets_

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

Detailed Description

TTK filter for the computation of merge trees.

VTK-level features for merge tree representation.

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::FTMTree

The computation of the merge tree 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. The VTK wrapper will first call a connectivity filter, and then call a merge tree computation for each connected components. The final tree is then aggregated.

Parameters

Input	Input scalar field, either 2D or 3D, regular grid or triangulation (vtkDataSet)
TreeType	the Type of three to Compute: Join Tree (leaves corresponds to minima of the scalar field) Split Tree (leaves corresponds to maxima of the scalar field)
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 Merge Trees with Fibonacci Heaps"
Charles Gueunet, Pierre Fortin, Julien Jomier, Julien Tierny
2017 IEEE 7th Symposium on Large Data Analysis and Visualization (LDAV), doi: 10.1109/LDAV.2017.8231846.
"Task-based augmented contour trees with fibonacci heaps"
Charles Gueunet, Pierre Fortin, Julien Jomier, Julien Tierny
IEEE Transactions on Parallel and Distributed Systems, Volume 30, Issue 8, Pages 1889-1905

Online examples:

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::FTMTree

The computation of the merge tree 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. The VTK wrapper will first call a connectivity filter, and then call a merge tree computation for each connected components. The final tree is then aggregated.

Parameters

Input	Input scalar field, either 2D or 3D, regular grid or triangulation (vtkDataSet)
TreeType	the Type of three to Compute: Join Tree (leaves corresponds to minima of the scalar field) Split Tree (leaves corresponds to maxima of the scalar field)
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 Merge Trees with Fibonacci Heaps"
Charles Gueunet, Pierre Fortin, Julien Jomier, Julien Tierny
2017 IEEE 7th Symposium on Large Data Analysis and Visualization (LDAV), doi: 10.1109/LDAV.2017.8231846.
"Task-based augmented contour trees with fibonacci heaps"
Charles Gueunet, Pierre Fortin, Julien Jomier, Julien Tierny
IEEE Transactions on Parallel and Distributed Systems, Volume 30, Issue 8, Pages 1889-1905

Online examples:

Definition at line 93 of file ttkMergeTree.h.

Member Typedef Documentation

◆ Superclass

typedef ttkAlgorithm ttkMergeTree::Superclass

Definition at line 104 of file ttkMergeTree.h.

Member Enumeration Documentation

◆ BACKEND

enum class ttkMergeTree::BACKEND

strong

Enumerator
FTM
EXTREEM

Definition at line 97 of file ttkMergeTree.h.

Constructor & Destructor Documentation

◆ ttkMergeTree()

ttkMergeTree::ttkMergeTree ( )

protected

Definition at line 19 of file ttkMergeTree.cpp.

Member Function Documentation

◆ FillInputPortInformation()

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

overrideprotected

Definition at line 102 of file ttkMergeTree.cpp.

◆ FillOutputPortInformation()

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

overrideprotected

Definition at line 110 of file ttkMergeTree.cpp.

◆ GetBackend()

virtual int ttkMergeTree::GetBackend ( )

virtual

the backend to use for computations.

◆ GetClassName()

virtual const char * ttkMergeTree::GetClassName ( )

virtual

Reimplemented from ttkAlgorithm.

◆ GetForceInputOffsetScalarField()

virtual bool ttkMergeTree::GetForceInputOffsetScalarField ( )

virtual

the offset array to use for simulation of simplicity

◆ getOffsets()

int ttkMergeTree::getOffsets ( )

protected

Definition at line 25 of file ttkMergeTree.cpp.

◆ getScalars()

int ttkMergeTree::getScalars ( )

protected

Definition at line 53 of file ttkMergeTree.cpp.

◆ GetSuperArcSamplingLevel()

int ttkMergeTree::GetSuperArcSamplingLevel ( ) const

inline

Definition at line 169 of file ttkMergeTree.h.

◆ GetWithAdvStats()

bool ttkMergeTree::GetWithAdvStats ( ) const

inline

Definition at line 158 of file ttkMergeTree.h.

◆ GetWithNormalize()

bool ttkMergeTree::GetWithNormalize ( ) const

inline

Definition at line 146 of file ttkMergeTree.h.

◆ GetWithSegmentation()

bool ttkMergeTree::GetWithSegmentation ( ) const

inline

Definition at line 134 of file ttkMergeTree.h.

◆ IsA()

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

virtual

Reimplemented from ttkAlgorithm.

◆ IsTypeOf()

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

static

◆ New()

static ttkMergeTree * ttkMergeTree::New ( )

static

◆ preconditionTriangulation()

int ttkMergeTree::preconditionTriangulation ( )

protected

Definition at line 72 of file ttkMergeTree.cpp.

◆ RequestData()

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

overrideprotected

Definition at line 121 of file ttkMergeTree.cpp.

◆ SafeDownCast()

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

static

◆ SetBackend()

virtual void ttkMergeTree::SetBackend ( int )

virtual

◆ SetForceInputOffsetScalarField()

virtual void ttkMergeTree::SetForceInputOffsetScalarField ( bool )

virtual

◆ SetSuperArcSamplingLevel()

void ttkMergeTree::SetSuperArcSamplingLevel ( int lvl )

inline

control the sampling level of the superarc. By default: 0

Definition at line 165 of file ttkMergeTree.h.

◆ SetTreeType()

void ttkMergeTree::SetTreeType ( const int type )

inline

the type of tree to compute (Join, Split, Contour, JoinSplit)

Definition at line 122 of file ttkMergeTree.h.

◆ SetWithAdvStats()

void ttkMergeTree::SetWithAdvStats ( const bool adv )

inline

Compute additional information on the segmentation like the span and size (in nb of vertex) of each region.

Definition at line 154 of file ttkMergeTree.h.

◆ SetWithNormalize()

void ttkMergeTree::SetWithNormalize ( const bool norm )

inline

if true, a post process pass will ensure NodesId have a deterministic order

Definition at line 142 of file ttkMergeTree.h.

◆ SetWithSegmentation()

void ttkMergeTree::SetWithSegmentation ( const bool segm )

inline

control if the output should contains the segmentation information

Definition at line 130 of file ttkMergeTree.h.

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

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

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Superclass

Member Enumeration Documentation

◆ BACKEND

Constructor & Destructor Documentation

◆ ttkMergeTree()

Member Function Documentation

◆ FillInputPortInformation()

◆ FillOutputPortInformation()

◆ GetBackend()

◆ GetClassName()

◆ GetForceInputOffsetScalarField()

◆ getOffsets()

◆ getScalars()

◆ GetSuperArcSamplingLevel()

◆ GetWithAdvStats()

◆ GetWithNormalize()

◆ GetWithSegmentation()

◆ IsA()

◆ IsTypeOf()

◆ New()

◆ preconditionTriangulation()

◆ RequestData()

◆ SafeDownCast()

◆ SetBackend()

◆ SetForceInputOffsetScalarField()

◆ SetSuperArcSamplingLevel()

◆ SetTreeType()

◆ SetWithAdvStats()

◆ SetWithNormalize()

◆ SetWithSegmentation()