TTK VTK-filter that computes an alignment for a multiblock of contourtrees. More...

#include <ttkContourTreeAlignment.h>

Inheritance diagram for ttkContourTreeAlignment:

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	SetRandomSeed (int)

virtual int	GetRandomSeed ()

virtual void	SetMatchTime (bool)

virtual bool	GetMatchTime ()

virtual void	SetArcMatchMode (int)

virtual int	GetArcMatchMode ()

virtual void	SetAlignmenttreeType (int)

virtual int	GetAlignmenttreeType ()

virtual void	SetWeightCombinatorialMatch (float)

virtual float	GetWeightCombinatorialMatch ()

virtual void	SetWeightArcMatch (float)

virtual float	GetWeightArcMatch ()

virtual void	SetWeightScalarValueMatch (float)

virtual float	GetWeightScalarValueMatch ()

virtual void	SetExportJSON (bool)

virtual bool	GetExportJSON ()

virtual void	SetExportPath (const std::string &)

virtual std::string	GetExportPath ()

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 ttkContourTreeAlignment *	New ()

static int	IsTypeOf (const char *type)

static ttkContourTreeAlignment *	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
int	FillInputPortInformation (int port, vtkInformation *info) override

int	FillOutputPortInformation (int port, vtkInformation *info) override

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

	ttkContourTreeAlignment ()

	~ttkContourTreeAlignment () override=default

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::ContourTreeAlignment
float	alignTreeBinary (const std::shared_ptr< ttk::cta::BinaryTree > &t1, const std::shared_ptr< ttk::cta::BinaryTree > &t2, std::vector< std::vector< float > > &memT, std::vector< std::vector< float > > &memF)

float	alignForestBinary (const std::shared_ptr< ttk::cta::BinaryTree > &t1, const std::shared_ptr< ttk::cta::BinaryTree > &t2, std::vector< std::vector< float > > &memT, std::vector< std::vector< float > > &memF)

std::shared_ptr< ttk::cta::AlignmentTree >	traceAlignmentTree (const std::shared_ptr< ttk::cta::BinaryTree > &t1, const std::shared_ptr< ttk::cta::BinaryTree > &t2, std::vector< std::vector< float > > &memT, std::vector< std::vector< float > > &memF)

std::vector< std::shared_ptr< ttk::cta::AlignmentTree > >	traceAlignmentForest (const std::shared_ptr< ttk::cta::BinaryTree > &t1, const std::shared_ptr< ttk::cta::BinaryTree > &t2, std::vector< std::vector< float > > &memT, std::vector< std::vector< float > > &memF)

std::shared_ptr< ttk::cta::AlignmentTree >	traceNullAlignment (const std::shared_ptr< ttk::cta::BinaryTree > &t, bool first)

float	editCost (const std::shared_ptr< ttk::cta::BinaryTree > &t1, const std::shared_ptr< ttk::cta::BinaryTree > &t2)

bool	isBinary (const std::shared_ptr< ttk::cta::Tree > &t)

std::shared_ptr< ttk::cta::BinaryTree >	rootAtNode (const std::shared_ptr< ttk::cta::AlignmentNode > &root)

std::shared_ptr< ttk::cta::BinaryTree >	computeRootedTree (const std::shared_ptr< ttk::cta::AlignmentNode > &node, const std::shared_ptr< ttk::cta::AlignmentEdge > &parent, int &id)

std::shared_ptr< ttk::cta::BinaryTree >	computeRootedDualTree (const std::shared_ptr< ttk::cta::AlignmentEdge > &arc, bool parent1, int &id)

void	computeNewAlignmenttree (const std::shared_ptr< ttk::cta::AlignmentTree > &res)

std::pair< float, std::vector< std::shared_ptr< ttk::cta::AlignmentNode > > >	pathToMax (const std::shared_ptr< ttk::cta::AlignmentNode > &root, const std::shared_ptr< ttk::cta::AlignmentNode > &parent)

std::pair< float, std::vector< std::shared_ptr< ttk::cta::AlignmentNode > > >	pathToMin (const std::shared_ptr< ttk::cta::AlignmentNode > &root, const std::shared_ptr< ttk::cta::AlignmentNode > &parent)

	ContourTreeAlignment ()
	Constructor of the Alignment Object.

	~ContourTreeAlignment () override
	Destructor of the Alignment Object.

void	setArcMatchMode (int mode)

void	setWeightCombinatorialMatch (float weight)

void	setWeightArcMatch (float weight)

void	setWeightScalarValueMatch (float weight)

void	setAlignmenttreeType (int type)

template<class scalarType >
int	execute (const std::vector< void * > &scalarsVP, const std::vector< int * > &regionSizes, const std::vector< int * > &segmentationIds, const std::vector< long long * > &topologies, const std::vector< size_t > &nVertices, const std::vector< size_t > &nEdges, const std::vector< int * > &segmentations, const std::vector< size_t > &segsizes, std::vector< float > &outputVertices, std::vector< long long > &outputFrequencies, std::vector< long long > &outputVertexIds, std::vector< long long > &outputBranchIds, std::vector< long long > &outputSegmentationIds, std::vector< long long > &outputArcIds, std::vector< int > &outputEdges, int seed)

bool	alignTree (const std::shared_ptr< ContourTree > &t)

bool	initialize (const std::shared_ptr< ContourTree > &t)

bool	alignTree_consistentRoot (const std::shared_ptr< ContourTree > &t)

bool	initialize_consistentRoot (const std::shared_ptr< ContourTree > &t, int rootIdx)

std::vector< std::pair< std::vector< std::shared_ptr< ttk::cta::CTNode > >, std::vector< std::shared_ptr< ttk::cta::CTEdge > > > >	getGraphs ()

std::vector< std::shared_ptr< ContourTree > >	getContourTrees ()

std::pair< std::vector< std::shared_ptr< ttk::cta::AlignmentNode > >, std::vector< std::shared_ptr< ttk::cta::AlignmentEdge > > >	getAlignmentGraph ()

std::shared_ptr< ttk::cta::BinaryTree >	getAlignmentGraphRooted ()

int	getAlignmentRootIdx ()

std::pair< float, std::shared_ptr< ttk::cta::AlignmentTree > >	getAlignmentBinary (const std::shared_ptr< ttk::cta::BinaryTree > &t1, const std::shared_ptr< ttk::cta::BinaryTree > &t2)

void	computeBranches ()

Additional Inherited Members
Protected Types inherited from ttk::ContourTreeAlignment
using	ContourTree = cta::ContourTree

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::ContourTreeAlignment
ttk::cta::Type_Alignmenttree	alignmenttreeType = ttk::cta::averageValues

ttk::cta::Mode_ArcMatch	arcMatchMode = ttk::cta::persistence

float	weightArcMatch = 1

float	weightCombinatorialMatch = 0

float	weightScalarValueMatch = 0

std::vector< std::shared_ptr< ttk::cta::AlignmentNode > >	nodes

std::vector< std::shared_ptr< ttk::cta::AlignmentEdge > >	arcs

std::vector< std::shared_ptr< ContourTree > >	contourtrees

std::vector< size_t >	permutation

std::shared_ptr< ttk::cta::AlignmentNode >	alignmentRoot

int	alignmentRootIdx

float	alignmentVal

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

Detailed Description

TTK VTK-filter that computes an alignment for a multiblock of contourtrees.

Author: Florian Wetzels (f_wet.nosp@m.zels.nosp@m.13@cs.nosp@m..uni.nosp@m.-kl.d.nosp@m.e), Jonas Lukasczyk (jl@jl.nosp@m.uk.d.nosp@m.e)

Date: 28.01.2020

This filter takes a multiblock of unstructured grids, where each block represents a contour tree, and computed the alignment of these contour trees. For each tree, a point array for the scalar values, a cell array for the region sizes of arcs and a cell array for the segmentation ids of arcs are required. Contour trees computed by the FTMTree module fulfill these requirements and are the recommended way to use this filter.

Parameters

Input	vtkMultiBlockDataSet representing the contour trees to align
Output	vtkUnstructuredGrid representing the alignment tree

The input data array for the scalar values needs to be specified via the standard VTK call vtkAlgorithm::SetInputArrayToProcess() with the following parameters:

Parameters

idx	0 (FIXED: the first array the algorithm requires)
port	0 (FIXED: first port)
connection	0 (FIXED: first connection)
fieldAssociation	0 (FIXED: point data)
arrayName	(DYNAMIC: string identifier of the input array)

The input data array for the region sizes needs to be specified via the standard VTK call vtkAlgorithm::SetInputArrayToProcess() with the following parameters:

Parameters

idx	1 (FIXED: the second array the algorithm requires)
port	0 (FIXED: first port)R
connection	0 (FIXED: first connection)
fieldAssociation	1 (FIXED: cell data)
arrayName	(DYNAMIC: string identifier of the input array)

The input data array for the segmentation ids needs to be specified via the standard VTK call vtkAlgorithm::SetInputArrayToProcess() with the following parameters:

Parameters

idx	2 (FIXED: the third array the algorithm requires)
port	0 (FIXED: first port)
connection	0 (FIXED: first connection)
fieldAssociation	1 (FIXED: cell data)
arrayName	(DYNAMIC: string identifier of the input array)

Related publication:
'Fuzzy contour trees: Alignment and joint layout of multiple contour trees' Anna Pia Lohfink, Florian Wetzels, Jonas Lukasczyk, Gunther H. Weber, and Christoph Garth. Comput. Graph. Forum, 39(3):343-355, 2020.

See also: ttk::ContourTreeAlignment

Online examples:

Contour Tree Alignment example

Definition at line 67 of file ttkContourTreeAlignment.h.

Member Typedef Documentation

◆ Superclass

typedef ttkAlgorithm ttkContourTreeAlignment::Superclass

Definition at line 74 of file ttkContourTreeAlignment.h.

Constructor & Destructor Documentation

◆ ttkContourTreeAlignment()

ttkContourTreeAlignment::ttkContourTreeAlignment ( )

protected

◆ ~ttkContourTreeAlignment()

ttkContourTreeAlignment::~ttkContourTreeAlignment ( )

overrideprotecteddefault

Member Function Documentation

◆ FillInputPortInformation()

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

overrideprotected

Definition at line 28 of file ttkContourTreeAlignment.cpp.

◆ FillOutputPortInformation()

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

overrideprotected

Definition at line 38 of file ttkContourTreeAlignment.cpp.

◆ GetAlignmenttreeType()

virtual int ttkContourTreeAlignment::GetAlignmenttreeType ( )

virtual

◆ GetArcMatchMode()

virtual int ttkContourTreeAlignment::GetArcMatchMode ( )

virtual

◆ GetClassName()

virtual const char * ttkContourTreeAlignment::GetClassName ( )

virtual

Reimplemented from ttkAlgorithm.

◆ GetExportJSON()

virtual bool ttkContourTreeAlignment::GetExportJSON ( )

virtual

◆ GetExportPath()

virtual std::string ttkContourTreeAlignment::GetExportPath ( )

virtual

◆ GetMatchTime()

virtual bool ttkContourTreeAlignment::GetMatchTime ( )

virtual

◆ GetRandomSeed()

virtual int ttkContourTreeAlignment::GetRandomSeed ( )

virtual

◆ GetWeightArcMatch()

virtual float ttkContourTreeAlignment::GetWeightArcMatch ( )

virtual

◆ GetWeightCombinatorialMatch()

virtual float ttkContourTreeAlignment::GetWeightCombinatorialMatch ( )

virtual

◆ GetWeightScalarValueMatch()

virtual float ttkContourTreeAlignment::GetWeightScalarValueMatch ( )

virtual

◆ IsA()

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

virtual

Reimplemented from ttkAlgorithm.

◆ IsTypeOf()

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

static

◆ New()

static ttkContourTreeAlignment * ttkContourTreeAlignment::New ( )

static

◆ RequestData()

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

overrideprotected

Definition at line 47 of file ttkContourTreeAlignment.cpp.

◆ SafeDownCast()

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

static

◆ SetAlignmenttreeType()

virtual void ttkContourTreeAlignment::SetAlignmenttreeType ( int )

virtual

◆ SetArcMatchMode()

virtual void ttkContourTreeAlignment::SetArcMatchMode ( int )

virtual

◆ SetExportJSON()

virtual void ttkContourTreeAlignment::SetExportJSON ( bool )

virtual

◆ SetExportPath()

virtual void ttkContourTreeAlignment::SetExportPath ( const std::string & )

virtual

◆ SetMatchTime()

virtual void ttkContourTreeAlignment::SetMatchTime ( bool )

virtual

◆ SetRandomSeed()

virtual void ttkContourTreeAlignment::SetRandomSeed ( int )

virtual

◆ SetWeightArcMatch()

virtual void ttkContourTreeAlignment::SetWeightArcMatch ( float )

virtual

◆ SetWeightCombinatorialMatch()

virtual void ttkContourTreeAlignment::SetWeightCombinatorialMatch ( float )

virtual

◆ SetWeightScalarValueMatch()

virtual void ttkContourTreeAlignment::SetWeightScalarValueMatch ( float )

virtual

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

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

◆ ttkContourTreeAlignment()

◆ ~ttkContourTreeAlignment()

Member Function Documentation

◆ FillInputPortInformation()

◆ FillOutputPortInformation()

◆ GetAlignmenttreeType()

◆ GetArcMatchMode()

◆ GetClassName()

◆ GetExportJSON()

◆ GetExportPath()

◆ GetMatchTime()

◆ GetRandomSeed()

◆ GetWeightArcMatch()

◆ GetWeightCombinatorialMatch()

◆ GetWeightScalarValueMatch()

◆ IsA()

◆ IsTypeOf()

◆ New()

◆ RequestData()

◆ SafeDownCast()

◆ SetAlignmenttreeType()

◆ SetArcMatchMode()

◆ SetExportJSON()

◆ SetExportPath()

◆ SetMatchTime()

◆ SetRandomSeed()

◆ SetWeightArcMatch()

◆ SetWeightCombinatorialMatch()

◆ SetWeightScalarValueMatch()