TTK base package defining the standard types. More...

Namespaces
namespace	dcg
namespace	debug
namespace	cf
namespace	cta
namespace	gph
namespace	Dijkstra
namespace	dcvf
namespace	ftm
namespace	ftr
namespace	Geometry
namespace	intgl
namespace	Laplacian
namespace	lts
namespace	mth
namespace	mtu
namespace	axa
namespace	pcp
namespace	persistenceSort
namespace	rpd
namespace	Statistics
namespace	periodicGhosts

Classes
class	AbstractTriangulation
	AbstractTriangulation is an interface class that defines an interface for efficient traversal methods on triangulations of piecewise linear manifolds. More...
class	ApproximateTopology
	TTK processing package for progressive Topological Data Analysis. More...
class	ArrayPreconditioning
class	AssignmentAuction
class	AssignmentExhaustive
class	AssignmentMunkres
class	AssignmentSolver
class	BarycentricSubdivision
	Subdivise a triangulation according to triangle barycenter. More...
class	BottleneckDistance
class	GabowTarjan
class	BoundingVolumeHierarchy
	Acceleration structure for native ray tracer. Based on implementation described in Physically Based Rendering: From Theory to Implementation by Matt Pharr, Wenzel Jakob and Greg Humphreys. More...
class	Ray
	Data structure for a ray. More...
class	CinemaImaging
	TTK modules that generates images of a dataset. More...
class	CinemaImagingEmbree
	TTK CinemaImagingEmbree processing package. More...
class	CinemaImagingNative
	Native renderer that uses a bounding volume hierarchy for accelerated raycasting. More...
class	CinemaQuery
	TTK cinemaQuery processing package. More...
class	ClusteringMetrics
class	ArrayLinkedList
	This class describes a dynamic size data structure for thread safe computation. It is a linked list of arrays that also stores the current number of elements. Its key feature is that the addition of an element will never cause the moving of the data structure in memory, unlike an std::vector, making the access to an element thread safe even if another thread is adding elements. More...
class	BaseClass
class	LRUCache
	LRU cache implementation. More...
class	CommandLineParser
	Basic command line parsing. More...
class	Debug
	Minimalist debugging class. More...
class	DebugTimer
	Legacy backward compatibility. More...
class	DebugMemory
	Legacy backward compatibility. More...
class	FlatJaggedArray
	Replacement for std::vector<std::vector<SimplexId>>. More...
class	Lock
	RAII wrapper around OpenMP lock. More...
class	OsCall
	Os-specifics. More...
class	Memory
class	ProgramBase
	Base editor class for standalone programs. This class parses the the command line, execute the TTK module and takes care of the IO. More...
class	Program
class	Timer
class	VisitedMask
	Auto-cleaning re-usable graph propagations data structure. More...
class	Wrapper
	Wrapper class to wrap ttk code. More...
class	ImplicitCluster
class	CompactTriangulation
	CompactTriangulation is a class implemented based on the TopoCluster data structure, which is a localized data structure for simplicial meshes. The key idea of TopoCluster is to subdivide the simplicial mesh into clusters. Then, the connectivity information is computed locally for each cluster and discarded when it is no longer needed. The simplicial mesh needs to be subdivided before using TopoCluster, i.e., there has to be a scalar field named "ttkCompactTriangulationIndex" to denote the cluster index of each vertex. Note Topocluster will reindex the simplices based on the clustering input array. Related publications "TopoCluster: A Localized Data Structure for Topology-based Visualization" Guoxi Liu, Federico Iuricich, Riccardo Fellegara, and Leila De Floriani IEEE Transactions on Visualization and Computer Graphics, 2021. More...
class	CompactTriangulationPreconditioning
	TTK processing package for mesh preprocessing before using TopoCluster. More...
class	ConnectedComponents
	TTK connectedComponents processing package. More...
class	ContinuousScatterPlot
	TTK processing package that computes the continuous scatterplot of bivariate volumetric data. More...
class	ContourAroundPoint
	TTK contourAroundPoint processing package. More...
class	Arc
class	SuperArc
class	Node
class	ContourTreeSimplificationMetric
class	PersistenceMetric
class	SubLevelSetTree
class	ContourTree
	TTK processing package that computes the contour tree of scalar data and more (data segmentation, topological simplification, persistence diagrams, persistence curves, etc.). More...
class	ContourTreeAlignment
	TTK contourTreeAlignment processing package. More...
class	DelaunayRipsPersistenceDiagram
	TTK base class that computes the persistence diagram of a Delaunay-Rips filtration. More...
class	DepthImageBasedGeometryApproximation
	This module approximates the depicted geometry of a depth image. More...
class	DimensionReduction
	TTK VTK-filter that apply dimension reduction algorithms on input. More...
class	DimensionReductionMetrics
	TTK base class that computes different scores for the quality of a dimension reduction. More...
class	DiscreteMorseSandwich
	TTK DiscreteMorseSandwich processing package. More...
class	DistanceField
	TTK processing package for distance field computation on PL manifolds. More...
class	DistanceMatrixDistortion
struct	DynTreeNode
	class representing a node of a tree and the link to its parent if not the root More...
class	DynamicTree
	Implements the Dynamic Tree data-structure (or ST-Tree). More...
class	EigenField
	TTK processing package for computing eigenfunctions of a triangular mesh. More...
class	ExplicitTriangulation
	ExplicitTriangulation is a class that provides time efficient traversal methods on triangulations of piecewise linear manifolds. More...
class	ExTreeM
class	FiberSurface
	TTK processing package that computes fiber surfaces. More...
class	FTMAtomicVector
class	FTRAtomicVector
class	GaussianPointCloud
	TTK gaussianPointCloud processing package that generates a 1D, 2D or 3D point cloud by randomly casting samples from a Gaussian distribution. More...
class	HarmonicField
	TTK processing package for the topological simplification of scalar data. More...
class	HelloWorld
class	Icosphere
class	Identifiers
class	ImplicitWithPreconditions
	Implicit Triangulation class with preconditioning. More...
class	ImplicitNoPreconditions
	Implicit Triangulation class without preconditioning. More...
class	ImplicitTriangulation
	ImplicitTriangulation is a class that provides time and memory efficient traversal methods on triangulations of piecewise linear manifolds represented by regular grids. More...
class	ImplicitTriangulationCRTP
class	IntegralLines
	TTK processing package for the computation of edge-based integral lines of the gradient of an input scalar field defined on a PL manifold. More...
class	JacobiSet
	TTK processing package for the computation of the Jacobi set of bivariate volumetric data. More...
class	KDTree
	TTK KD-Tree. More...
class	LDistance
	TTK lDistance processing package. More...
class	LDistanceMatrix
class	SweepCmp
class	LegacyTopologicalSimplification
	TTK processing package for the topological simplification of scalar data. More...
class	LowestCommonAncestor
	Class to answer the lowest common ancestor requests of pairs of nodes in a tree in constant time after a linear time preprocess. More...
class	Graph
struct	criticalPointPairComparison
	Comparison between critical point pairs ( (Extremum,Saddle), dist(M,S) ). More...
struct	mandatorySaddleComparison
	Comparison between mandatory saddles (Saddle id, Number of merged extrema). More...
struct	pairComparison
	Comparison of the second member of a std::pair<int,double>. More...
class	MandatoryCriticalPoints
	TTK processing package for the computation of mandatory critical points in uncertain scalar data. More...
class	ManifoldCheck
	TTK processing package for manifold checks. More...
class	MarchingTetrahedra
	TTK processing package for Marching Tetra/Triangles computations. More...
class	MergeTreeAutoencoder
class	MergeTreeAutoencoderDecoding
class	BranchMappingDistance
class	MergeTreeBarycenter
class	MergeTreeBase
class	MergeTreeClustering
class	MergeTreeDistance
class	PathMappingDistance
class	MergeTreeDistanceMatrix
class	MergeTreeNeuralBase
class	MergeTreeNeuralLayer
class	MergeTreeNeuralNetwork
class	MergeTreeAxesAlgorithmBase
class	MergeTreePrincipalGeodesics
class	MergeTreePrincipalGeodesicsBase
class	MergeTreePrincipalGeodesicsDecoding
class	MergeTreeTemporalReduction
class	MergeTreeTemporalReductionDecoding
class	MeshGraph
	TTK meshGraph processing package. More...
class	MetricDistortion
class	MorphologicalOperators
	TTK morphologicalOperators processing package. More...
class	MorseSmaleComplex
	TTK processing package for the computation of Morse-Smale complexes. More...
class	MorseSmaleQuadrangulation
	TTK processing package for the topological simplification of scalar data. More...
class	MultiresTopology
	TTK processing package for progressive Topological Data Analysis. More...
class	MultiresTriangulation
	MultiresTriangulation. More...
class	PathCompression
	TTK processing package for the computation of Morse-Smale segmentations using Path Compression. More...
class	PeriodicImplicitTriangulation
	TTK triangulation class for grids with periodic boundary conditions implemented in all directions. More...
class	PeriodicImplicitTriangulationCRTP
class	PeriodicWithPreconditions
	Periodic implicit Triangulation class with preconditioning. More...
class	PeriodicNoPreconditions
	Periodic implicit Triangulation class without preconditioning. More...
class	PersistenceCurve
	TTK processing package for the computation of persistence curves. More...
class	PersistenceDiagram
	TTK processing package for the computation of persistence diagrams. More...
struct	CriticalVertex
	Critical Vertex. More...
struct	PersistencePair
	Persistence Pair. More...
class	PersistenceDiagramAuction
struct	Compare
class	PersistenceDiagramAuctionActor
class	Good
class	Bidder
class	PDBarycenter
class	PDClustering
class	PersistenceDiagramBarycenter
class	PersistenceDiagramClustering
	TTK processing package for the computation of Wasserstein barycenters and K-Means clusterings of a set of persistence diagrams. More...
class	InitRandomDict
class	PersistenceDiagramConstrainedOptimization
class	PersistenceDiagramDictionary
class	PersistenceDiagramDictionaryBorderInitializer
class	PersistenceDiagramDictionaryDecoding
	TTK processing package for the computation of a Dictionary of Persistence Diagrams and barycentric weights to approximate an ensemble of Persistence Diagrams. More...
class	PersistenceDiagramDistanceMatrix
class	PersistenceDiagramWarmRestartAuction
	TTK base class that computes the Wasserstein distance between two persistence diagrams. More...
class	PersistentGenerators
	TTK PersistentGenerators processing package. More...
class	PersistentSimplexPairs
	Textbook algorithm to find persistence pairs. More...
class	MergeTreeVisualization
class	PlanarGraphLayout
	TTK planarGraphLayout processing package. More...
class	ProgressiveTopology
	TTK processing package for progressive Topological Data Analysis. More...
class	ProjectionFromTable
class	Quadrangulation
class	QuadrangulationSubdivision
	TTK processing package for the topological simplification of scalar data. More...
class	RangeDrivenOctree
	TTK optional package for octree based range queries in bivariate volumetric data. More...
class	RangeMinimumQuery
	Class to answer range minimum queries in an array in constant time after a linearithmic time preprocess. More...
class	ReebSpace
	TTK processing package that efficiently computes the Reeb space of bivariate volumetric data. More...
class	RegularGridTriangulation
	RegularGridTriangulation is an abstract subclass of ttk::AbstractTriangulation that exposes a common MPI API for triangulation on regular grids. The virtual methods in this class are meant to be implemented in ttk::ImplicitTriangulation and ttk::PeriodicImplicitTriangulation. This meta-class only holds an interface for MPI-related features for the moment but will maybe be enlarged in the future. More...
class	RipsComplex
	TTK VTK-filter that computes a Rips complex. More...
class	RipsPersistenceDiagram
	TTK base class that computes the persistence diagram of a Rips complex. More...
class	RipsPersistenceGenerators
	TTK base class that computes 1-dimensional persistence generators in a Rips filtration. More...
class	ScalarFieldCriticalPoints
	TTK processing package for the computation of critical points in PL scalar fields defined on PL manifolds. More...
class	ScalarFieldSmoother
	TTK processing package for scalar field smoothing. More...
class	SeparatrixStability
	Compute the occurrence rate of separatrices in an ensemble. More...
class	SignedDistanceField
	This filter computes a signed distance field given a surface in input. More...
class	CellArray
	CellArray generic array of cells More...
class	OneSkeleton
	OneSkeleton processing package. More...
class	ThreeSkeleton
	ThreeSkeleton processing package. More...
class	TwoSkeleton
	TwoSkeleton processing package. More...
class	ZeroSkeleton
	ZeroSkeleton processing package. More...
class	SurfaceGeometrySmoother
	TTK VTK-filter for smoothing meshes on surfaces. More...
class	TopologicalCompression
	TTK topologicalCompression processing package. More...
class	TopologicalDimensionReduction
	TTK base class that embeds points into 2D, under topological constraints. More...
class	TopologicalLoss
	TTK base class for representing differentiable topological losses to be used in dimension reduction. More...
class	TopologicalOptimization
class	TopologicalSimplification
	TTK processing package for the topological simplification of scalar data. More...
class	TopologicalSkeleton
	TTK processing package for the computation of Topological Skeleton of Vector Fields. The skeleton consists of four components: critical points, 1-separatrices(including orbits), 2-separatrices, and segmentation of where cells flow to and from. More...
class	TopoMap
class	TrackingFromCriticalPoints
class	TrackingFromFields
class	TrackingFromOverlap
	TTK trackingFromOverlap processing package that tracks labeled point sets. More...
class	TrackingFromPersistenceDiagrams
class	TrackingPostProcessing
	TTK processing package for post-processing tracked trajectories: linearization, fusion (chaining), and merge-tree-based segmentation statistics. More...
class	Triangulation
	Triangulation is a class that provides time and memory efficient traversal methods on triangulations of piecewise linear manifolds. It provides the following features: More...
class	PDFBounds
class	PDFHistograms
class	UncertainDataEstimator
	TTK processing package that takes an input ensemble data set (represented by a list of scalar fields) and which computes various vertexwise statistics (PDF estimation, bounds, moments, etc.). More...
class	UnionFind
	Union Find implementation for connectivity tracking. More...
class	VectorSimplification
	TTK VectorSimplification processing package. More...
class	VectorWeightCurve
	TTK processing package for the computation of weight curve associated with the discrete vector field topology. More...
class	WebSocketIO
class	ttkCinemaImagingEmbree
class	ttkCinemaImagingNative
class	ttkCinemaImagingVTK

Typedefs
using	triplet = std::tuple<ttk::SimplexId, ttk::SimplexId, ttk::SimplexId>
	Persistence pair type (with persistence in double).
using	polarity = unsigned char
using	LongSimplexId = long long int
	Identifier type for simplices of any dimension.
using	SimplexId = int
	Identifier type for simplices of any dimension.
using	ThreadId = int
	Identifier type for threads (i.e. with OpenMP).
using	TaskId = int
	Identifier type for tasks (i.e. with OpenMP).
using	real = double
using	DiagramType = std::vector<PersistencePair>
	Persistence Diagram type as a vector of Persistence pairs.
using	MatchingType
	Matching between two Persistence Diagram pairs.
using	GoodDiagram = std::vector<Good>
using	BidderDiagram = std::vector<Bidder>
using	Matrix = std::vector<std::vector<double>>
using	Matrice = std::vector<std::vector<double>>
using	VectorMatchingTuple = std::vector<MatchingType>
using	RipsPersistencePair
using	ValuesPair = std::pair<double, double>
using	trackingTuple = std::tuple<int, int, std::vector<SimplexId>>

Enumerations
enum class	CriticalType { Local_minimum = 0 , Saddle1 , Saddle2 , Local_maximum , Degenerate , Regular }
	default value for critical index More...
enum	Direction { Forward = 0 , Backward }
enum class	CompressionType { PersistenceDiagram = 0 , Other = 1 }

Functions
template<class dataType>
dataType	getMaxValue (std::vector< std::vector< dataType > > &matrix, bool balancedAsgn)
template<typename dataType>
dataType	getLowerBoundCost (std::vector< std::vector< dataType > > &costMatrix)
constexpr unsigned long long	str2int (const char *str, int h=0)
template<typename scalarType, typename idType>
void	sortVertices (const size_t nVerts, const scalarType const scalars, const idType const offsets, SimplexId *const order, const int nThreads)
	Sort vertices according to scalars disambiguated by offsets.
template<typename scalarType>
void	preconditionOrderArray (const size_t nVerts, const scalarType const scalars, SimplexId const order, const int nThreads=ttk::globalThreadNumber_)
	Precondition an order array to be consumed by the base layer API.
template<typename T, typename U>
void	shuffle (std::vector< T > &toShuffle, U &&rng)
	Platform-independent alternative to std::shuffle implementing the Fisher-Yates shuffle algorithm.
template<class dataType>
bool	isDeathHigher (ftm::FTMTree_MT tree1, ftm::idNode tree1Node, ftm::FTMTree_MT tree2, ftm::idNode tree2Node)
template<class dataType>
dataType	getMinMaxLocal (const ftm::FTMTree_MT *tree, ftm::idNode nodeId, bool getMin=true)
template<class dataType>
std::tuple< dataType, dataType >	getMinMaxLocalT (ftm::FTMTree_MT *tree, ftm::idNode nodeId)
template<class dataType>
std::tuple< dataType, dataType >	getNormalizedBirthDeath (const ftm::FTMTree_MT *tree, ftm::idNode nodeId, dataType newMin=0.0, dataType newMax=1.0)
template<class dataType>
std::tuple< dataType, dataType >	getParametrizedBirthDeath (ftm::FTMTree_MT *tree, ftm::idNode node, bool normalize)
template<class dataType>
dataType	getMinMaxLocalFromVector (ftm::FTMTree_MT *tree, ftm::idNode nodeId, std::vector< dataType > &scalarsVector, bool getMin=true)
template<class dataType>
std::shared_ptr< ftm::FTMTree_MT >	makeFakeTree (dataType *nodesScalar, std::vector< SimplexId > &nodes, std::vector< std::tuple< ftm::idNode, ftm::idNode > > &arcs)
template<class dataType>
ftm::MergeTree< dataType >	makeFakeMergeTree (std::vector< dataType > &scalarsVector, std::vector< std::tuple< ftm::idNode, ftm::idNode > > &arcs)
void	computeWeightedBarycenter (std::vector< DiagramType > &intermediateDiagrams, std::vector< double > &weights, DiagramType &barycenter, std::vector< std::vector< MatchingType > > &matchings, const ttk::Debug &dbg, const bool ProgBarycenter)

Variables
COMMON_EXPORTS int	globalThreadNumber_ = 1
COMMON_EXPORTS int	MPIrank_ = -1
COMMON_EXPORTS int	MPIsize_ = -1
const char	MaskScalarFieldName [] = "ttkMaskScalarField"
	default name for mask scalar field
const char	VertexScalarFieldName [] = "ttkVertexScalarField"
	default name for vertex scalar field
const char	CellScalarFieldName [] = "ttkCellScalarField"
	default name for cell scalar field
const char	OffsetScalarFieldName [] = "ttkOffsetScalarField"
	default name for offset scalar field
const char	OffsetFieldUName [] = "ttkOffsetFieldU"
	default name for bivariate offset fields
const char	OffsetFieldVName [] = "ttkOffsetFieldV"
const char	MorseSmaleCellDimensionName [] = "CellDimension"
const char	MorseSmaleCellIdName [] = "CellId"
const char	MorseSmaleBoundaryName [] = "IsOnBoundary"
const char	MorseSmaleManifoldSizeName [] = "ManifoldSize"
const char	MorseSmaleSourceIdName [] = "SourceId"
const char	MorseSmaleDestinationIdName [] = "DestinationId"
const char	MorseSmaleSeparatrixIdName [] = "SeparatrixId"
const char	MorseSmaleSeparatrixTypeName [] = "SeparatrixType"
const char	MorseSmaleSeparatrixMaximumName [] = "SeparatrixFunctionMaximum"
const char	MorseSmaleSeparatrixMinimumName [] = "SeparatrixFunctionMinimum"
const char	MorseSmaleSeparatrixDifferenceName [] = "SeparatrixFunctionDifference"
const char	MorseSmaleCriticalPointsOnBoundaryName [] = "NumberOfCriticalPointsOnBoundary"
const char	MorseSmaleAscendingName [] = "AscendingManifold"
const char	MorseSmaleDescendingName [] = "DescendingManifold"
const char	MorseSmaleManifoldName [] = "MorseSmaleManifold"
const char	SeparatrixStabilityOccurrenceCount [] = "Occurrence"
const char	SeparatrixStabilityIsomorphismClassId [] = "IsomorphismClassId"
const char	SeparatrixStabilityMatchingIdName [] = "MatchingIdInBlock"
const char	SeparatrixStabilityMatchingIdSeparatrixName [] = "SeparatrixMatchingIdInBlock"
const char	PersistenceCriticalTypeName [] = "CriticalType"
const char	PersistenceBirthName [] = "Birth"
const char	PersistenceDeathName [] = "Death"
const char	PersistenceCoordinatesName [] = "Coordinates"
const char	PersistencePairIdentifierName [] = "PairIdentifier"
const char	PersistenceName [] = "Persistence"
const char	PersistencePairTypeName [] = "PairType"
const char	PersistenceIsFinite [] = "IsFinite"
const char	compactTriangulationIndex [] = "ttkCompactTriangulationIndex"
const int	CriticalTypeNumber = 6
	number of different critical types
COMMON_EXPORTS bool	welcomeMsg_ = true
COMMON_EXPORTS bool	goodbyeMsg_ = true
COMMON_EXPORTS int	globalDebugLevel_ = 0

Detailed Description

TTK base package defining the standard types.

Minimalist namespace that handles simple statistics computations (mean, variance, correlation etc.).

Provide methods related to Merge Trees and their management with Torch.

Minimalist namespace that handles simple geometric computations (operations on std::vectors, barycentric coordinates, etc.).

TTK classes for the segmentation of an arc in the Reeb Graph.

TTK DataType management for the reeb graph.

TTK structures for the reeb graph.

TTK processing package that manage a parallel version of vector Same as in FTM: Common ?.

Union find compliant with parallel find and maintaining the current local propagation inspired by ttk::UnionFind.

TTK processing package that add persistence pairs features.

TTK container representing a node of the FTMTree_MT.

TTK processing package that manage a parallel vecrion of vector.

TTK processing package that efficiently computes the sublevel set tree of scalar data and more (data segmentation, topological simplification, persistence diagrams, persistence curves, etc.).

TTK class representing a SuperArc of a tree, containing regular vertices.

TTK structures for the contour tree.

TTK classes for the segmentation of the contour tree.

TTK container representing a node of the MergeTree.

TTK processing package that efficiently computes the contour tree of scalar data and more (data segmentation, topological simplification, persistence diagrams, persistence curves, etc.).

The Topology ToolKit.

Parameters

dataType Data type of the input scalar field (char, float, etc.).

Related publication
"Contour Forests: Fast Multi-threaded Augmented Contour Trees"
Charles Gueunet, Pierre Fortin, Julien Jomier, Julien Tierny
Proc. of IEEE LDAV 2016.

See also: ttkContourForests.cpp for a usage example.

Parameters

dataType Data type of the input scalar field (char, float, etc.).

Related publication
"Contour Forests: Fast Multi-threaded Augmented Contour Trees"
Charles Gueunet, Pierre Fortin, Julien Jomier, Julien Tierny
Proc. of IEEE LDAV 2016.

Related publication:
"Topomap: A 0-dimensional homology preserving projection of high-dimensional data"
Harish Doraiswamy, Julien Tierny, Paulo J. S. Silva, Luis Gustavo Nonato, and Claudio Silva
Proc. of IEEE VIS 2020.
IEEE Transactions on Visualization and Computer Graphics 27(2): 561-571, 2020.
"Topological Autoencoders"
Michael Moor, Max Horn, Bastian Rieck, Karsten Borgwardt,
Proceedings of the 37th International Conference on Machine Learning,

"Optimizing persistent homology-based functions"
Mathieu Carriere, Frederic Chazal, Marc Glisse, Yuichi Ike, Hariprasad Kannan, Yuhei Umeda,
Proceedings of the 38th International Conference on Machine Learning,
"Topological Autoencoders++: Fast and Accurate Cycle-Aware Dimensionality Reduction"
MattÃ©o ClÃ©mot, Julie Digne, Julien Tierny,
IEEE Transactions on Visualization and Computer Graphics. Accepted, to be presented at IEEE VIS 2026.

Parameters

dataType Data type of the input scalar field (char, float, etc.).

See also: ttkContourForests.cpp for a usage example.

Parameters

dataType	Data type of the input scalar field (char, float, etc.).
dataType	Data type of the input scalar field (char, float, etc.).

See also: ttkFTMTree.cpp for a usage example.

Online examples:

Author: Mathieu Pont (mathi.nosp@m.eu.p.nosp@m.ont@l.nosp@m.ip6..nosp@m.fr)

Date: 2021.

Utils function for manipulating FTMTree class

Parameters

dataType Data type of the input scalar field (char, float, etc.).

See also: ttkPersistenceDiagram.cpp for a usage example.; ftrGraph

Author: Charles Gueunet charl.nosp@m.es.g.nosp@m.ueune.nosp@m.t@li.nosp@m.p6.fr

Date: 2018-01-22

See also: ttkFTRGraph.h for a usage example.

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

Date: February 2016.

Related publication
"Merge Tree Geodesics and Barycenters with Path Mappings"
F. Wetzels, M. Pont, J. Tierny and C. Garth.
Proc. of IEEE VIS 2023.
IEEE Transactions on Visualization and Computer Graphics, 2024

Author: Mathieu Pont mathi.nosp@m.eu.p.nosp@m.ont@l.nosp@m.ip6..nosp@m.fr

Date: 2023.

Related publication
"Merge Tree Geodesics and Barycenters with Path Mappings"
F. Wetzels, M. Pont, J. Tierny and C. Garth.
Proc. of IEEE VIS 2023.
IEEE Transactions on Visualization and Computer Graphics, 2024

Online examples:

Merge Tree Temporal Reduction

It is used in ttk::ProgressiveTopology for the definition of efficient progressive algorithms for the computation of critical points and extremum-saddle persistence diagrams.

It is also used in ttk::ApproximateTopology for the approximate computation of the extremum-saddle persistence diagrams with guarantees.

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

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

See also: ProgressiveTopology; ApproximateTopology

Author: Mathieu Pont mathi.nosp@m.eu.p.nosp@m.ont@l.nosp@m.ip6..nosp@m.fr

Date: September 2022.

Typedef Documentation

◆ BidderDiagram

using ttk::BidderDiagram = std::vector<Bidder>

Definition at line 326 of file PersistenceDiagramAuctionActor.h.

◆ DiagramType

using ttk::DiagramType = std::vector<PersistencePair>

Persistence Diagram type as a vector of Persistence pairs.

Definition at line 60 of file PersistenceDiagramUtils.h.

◆ GoodDiagram

using ttk::GoodDiagram = std::vector<Good>

Definition at line 194 of file PersistenceDiagramAuctionActor.h.

◆ LongSimplexId

using ttk::LongSimplexId = long long int

Identifier type for simplices of any dimension.

Definition at line 15 of file DataTypes.h.

◆ MatchingType

typedef std::tuple< int, int, double > ttk::MatchingType

Initial value:

std::tuple<int,
                                 int,
                                 double
                                 >

Matching between two Persistence Diagram pairs.

id of first matching pair id of second matching pair matching cost

Definition at line 65 of file PersistenceDiagramUtils.h.

◆ Matrice

using ttk::Matrice = std::vector<std::vector<double>>

Definition at line 36 of file PersistenceDiagramDictionaryDecoding.h.

◆ Matrix

using ttk::Matrix = std::vector<std::vector<double>>

Definition at line 7 of file InitDictRandomly.h.

◆ polarity

using ttk::polarity = unsigned char

Definition at line 34 of file ApproximateTopology.h.

◆ real

using ttk::real = double

Definition at line 58 of file Os.h.

◆ RipsPersistencePair

using ttk::RipsPersistencePair

Initial value:

std::pair<std::pair<std::vector<int>, double>,

std::pair<std::vector<int>, double>>

Definition at line 19 of file PersistenceDiagramWarmRestartAuction.h.

◆ SimplexId

using ttk::SimplexId = int

Identifier type for simplices of any dimension.

Definition at line 22 of file DataTypes.h.

◆ TaskId

using ttk::TaskId = int

Identifier type for tasks (i.e. with OpenMP).

Definition at line 29 of file DataTypes.h.

◆ ThreadId

using ttk::ThreadId = int

Identifier type for threads (i.e. with OpenMP).

Definition at line 26 of file DataTypes.h.

◆ trackingTuple

using ttk::trackingTuple = std::tuple<int, int, std::vector<SimplexId>>

Definition at line 20 of file TrackingFromCriticalPoints.h.

◆ triplet

typedef std::tuple< ttk::SimplexId, ttk::SimplexId, ttk::SimplexId > ttk::triplet = std::tuple<ttk::SimplexId, ttk::SimplexId, ttk::SimplexId>

Persistence pair type (with persistence in double).

Definition at line 33 of file ApproximateTopology.h.

◆ ValuesPair

using ttk::ValuesPair = std::pair<double, double>

Definition at line 21 of file PersistenceDiagramWarmRestartAuction.h.

◆ VectorMatchingTuple

using ttk::VectorMatchingTuple = std::vector<MatchingType>

Definition at line 37 of file PersistenceDiagramDictionaryDecoding.h.

Enumeration Type Documentation

◆ CompressionType

enum class ttk::CompressionType

strong

Enumerator
PersistenceDiagram
Other

Definition at line 28 of file TopologicalCompression.h.

◆ CriticalType

enum class ttk::CriticalType

strong

default value for critical index

Enumerator
Local_minimum
Saddle1
Saddle2
Local_maximum
Degenerate
Regular

Definition at line 88 of file DataTypes.h.

◆ Direction

enum ttk::Direction

Enumerator
Forward
Backward

Definition at line 117 of file IntegralLines.h.

Function Documentation

◆ computeWeightedBarycenter()

void ttk::computeWeightedBarycenter	(	std::vector< DiagramType > &	intermediateDiagrams,
		std::vector< double > &	weights,
		DiagramType &	barycenter,
		std::vector< std::vector< MatchingType > > &	matchings,
		const ttk::Debug &	dbg,
		const bool	ProgBarycenter )

Definition at line 3 of file PersistenceDiagramClustering.cpp.

◆ getLowerBoundCost()

template<typename dataType>

dataType ttk::getLowerBoundCost ( std::vector< std::vector< dataType > > & costMatrix )

Definition at line 232 of file AssignmentAuction.h.

◆ getMaxValue()

template<class dataType>

dataType ttk::getMaxValue	(	std::vector< std::vector< dataType > > &	matrix,
		bool	balancedAsgn )

Definition at line 105 of file AssignmentAuction.h.

◆ getMinMaxLocal()

template<class dataType>

dataType ttk::getMinMaxLocal	(	const ftm::FTMTree_MT *	tree,
		ftm::idNode	nodeId,
		bool	getMin = true )

Definition at line 30 of file MergeTreeUtils.h.

◆ getMinMaxLocalFromVector()

template<class dataType>

dataType ttk::getMinMaxLocalFromVector	(	ftm::FTMTree_MT *	tree,
		ftm::idNode	nodeId,
		std::vector< dataType > &	scalarsVector,
		bool	getMin = true )

Definition at line 91 of file MergeTreeUtils.h.

◆ getMinMaxLocalT()

template<class dataType>

std::tuple< dataType, dataType > ttk::getMinMaxLocalT	(	ftm::FTMTree_MT *	tree,
		ftm::idNode	nodeId )

Definition at line 56 of file MergeTreeUtils.h.

◆ getNormalizedBirthDeath()

template<class dataType>

std::tuple< dataType, dataType > ttk::getNormalizedBirthDeath	(	const ftm::FTMTree_MT *	tree,
		ftm::idNode	nodeId,
		dataType	newMin = 0.0,
		dataType	newMax = 1.0 )

Definition at line 65 of file MergeTreeUtils.h.

◆ getParametrizedBirthDeath()

template<class dataType>

std::tuple< dataType, dataType > ttk::getParametrizedBirthDeath	(	ftm::FTMTree_MT *	tree,
		ftm::idNode	node,
		bool	normalize )

Definition at line 84 of file MergeTreeUtils.h.

◆ isDeathHigher()

template<class dataType>

bool ttk::isDeathHigher	(	ftm::FTMTree_MT *	tree1,
		ftm::idNode	tree1Node,
		ftm::FTMTree_MT *	tree2,
		ftm::idNode	tree2Node )

Definition at line 15 of file MergeTreeUtils.h.

◆ makeFakeMergeTree()

template<class dataType>

ftm::MergeTree< dataType > ttk::makeFakeMergeTree	(	std::vector< dataType > &	scalarsVector,
		std::vector< std::tuple< ftm::idNode, ftm::idNode > > &	arcs )

Definition at line 144 of file MergeTreeUtils.h.

◆ makeFakeTree()

template<class dataType>

std::shared_ptr< ftm::FTMTree_MT > ttk::makeFakeTree	(	dataType *	nodesScalar,
		std::vector< SimplexId > &	nodes,
		std::vector< std::tuple< ftm::idNode, ftm::idNode > > &	arcs )

Definition at line 117 of file MergeTreeUtils.h.

◆ preconditionOrderArray()

template<typename scalarType>

void ttk::preconditionOrderArray	(	const size_t	nVerts,
		const scalarType *const	scalars,
		SimplexId *const	order,
		const int	nThreads = ttk::globalThreadNumber_ )

inline

Precondition an order array to be consumed by the base layer API.

Parameters

[in]	nVerts	number of vertices
[in]	scalars	pointer to scalar field buffer of size `nVerts`
[out]	order	pointer to pre-allocated order buffer of size `nVerts`
[in]	nThreads	number of threads to be used

Definition at line 70 of file OrderDisambiguation.h.

◆ shuffle()

template<typename T, typename U>

void ttk::shuffle	(	std::vector< T > &	toShuffle,
		U &&	rng )

Platform-independent alternative to std::shuffle implementing the Fisher-Yates shuffle algorithm.

Parameters

[in,out]	toShuffle	Vector of elements to be shuffled
[in]	rng	Random number generator

Definition at line 13 of file Shuffle.h.

◆ sortVertices()

template<typename scalarType, typename idType>

void ttk::sortVertices	(	const size_t	nVerts,
		const scalarType *const	scalars,
		const idType *const	offsets,
		SimplexId *const	order,
		const int	nThreads )

Sort vertices according to scalars disambiguated by offsets.

Parameters

[in]	nVerts	number of vertices
[in]	scalars	array of size nVerts, main vertex comparator
[in]	offsets	array of size nVerts, disambiguate scalars on plateaux
[out]	order	array of size nVerts, computed order of vertices
[in]	nThreads	number of parallel threads

Definition at line 20 of file OrderDisambiguation.h.

◆ str2int()

unsigned long long ttk::str2int	(	const char *	str,
		int	h = 0 )

constexpr

Definition at line 11 of file BottleneckDistance.h.

Variable Documentation

◆ CellScalarFieldName

const char ttk::CellScalarFieldName[] = "ttkCellScalarField"

default name for cell scalar field

Definition at line 38 of file DataTypes.h.

◆ compactTriangulationIndex

const char ttk::compactTriangulationIndex[] = "ttkCompactTriangulationIndex"

Definition at line 85 of file DataTypes.h.

◆ CriticalTypeNumber

const int ttk::CriticalTypeNumber = 6

number of different critical types

Definition at line 97 of file DataTypes.h.

◆ globalDebugLevel_

COMMON_EXPORTS int ttk::globalDebugLevel_ = 0

extern

Definition at line 8 of file Debug.cpp.

◆ globalThreadNumber_

COMMON_EXPORTS int ttk::globalThreadNumber_ = 1

extern

Definition at line 6 of file BaseClass.cpp.

◆ goodbyeMsg_

COMMON_EXPORTS bool ttk::goodbyeMsg_ = true

extern

Definition at line 7 of file Debug.cpp.

◆ MaskScalarFieldName

const char ttk::MaskScalarFieldName[] = "ttkMaskScalarField"

default name for mask scalar field

Definition at line 32 of file DataTypes.h.

◆ MorseSmaleAscendingName

const char ttk::MorseSmaleAscendingName[] = "AscendingManifold"

Definition at line 62 of file DataTypes.h.

◆ MorseSmaleBoundaryName

const char ttk::MorseSmaleBoundaryName[] = "IsOnBoundary"

Definition at line 50 of file DataTypes.h.

◆ MorseSmaleCellDimensionName

const char ttk::MorseSmaleCellDimensionName[] = "CellDimension"

Definition at line 48 of file DataTypes.h.

◆ MorseSmaleCellIdName

const char ttk::MorseSmaleCellIdName[] = "CellId"

Definition at line 49 of file DataTypes.h.

◆ MorseSmaleCriticalPointsOnBoundaryName

const char ttk::MorseSmaleCriticalPointsOnBoundaryName[] = "NumberOfCriticalPointsOnBoundary"

Definition at line 60 of file DataTypes.h.

◆ MorseSmaleDescendingName

const char ttk::MorseSmaleDescendingName[] = "DescendingManifold"

Definition at line 63 of file DataTypes.h.

◆ MorseSmaleDestinationIdName

const char ttk::MorseSmaleDestinationIdName[] = "DestinationId"

Definition at line 53 of file DataTypes.h.

◆ MorseSmaleManifoldName

const char ttk::MorseSmaleManifoldName[] = "MorseSmaleManifold"

Definition at line 64 of file DataTypes.h.

◆ MorseSmaleManifoldSizeName

const char ttk::MorseSmaleManifoldSizeName[] = "ManifoldSize"

Definition at line 51 of file DataTypes.h.

◆ MorseSmaleSeparatrixDifferenceName

const char ttk::MorseSmaleSeparatrixDifferenceName[] = "SeparatrixFunctionDifference"

Definition at line 58 of file DataTypes.h.

◆ MorseSmaleSeparatrixIdName

const char ttk::MorseSmaleSeparatrixIdName[] = "SeparatrixId"

Definition at line 54 of file DataTypes.h.

◆ MorseSmaleSeparatrixMaximumName

const char ttk::MorseSmaleSeparatrixMaximumName[] = "SeparatrixFunctionMaximum"

Definition at line 56 of file DataTypes.h.

◆ MorseSmaleSeparatrixMinimumName

const char ttk::MorseSmaleSeparatrixMinimumName[] = "SeparatrixFunctionMinimum"

Definition at line 57 of file DataTypes.h.

◆ MorseSmaleSeparatrixTypeName

const char ttk::MorseSmaleSeparatrixTypeName[] = "SeparatrixType"

Definition at line 55 of file DataTypes.h.

◆ MorseSmaleSourceIdName

const char ttk::MorseSmaleSourceIdName[] = "SourceId"

Definition at line 52 of file DataTypes.h.

◆ MPIrank_

COMMON_EXPORTS int ttk::MPIrank_ = -1

extern

Definition at line 9 of file BaseClass.cpp.

◆ MPIsize_

COMMON_EXPORTS int ttk::MPIsize_ = -1

extern

Definition at line 10 of file BaseClass.cpp.

◆ OffsetFieldUName

const char ttk::OffsetFieldUName[] = "ttkOffsetFieldU"

default name for bivariate offset fields

Definition at line 44 of file DataTypes.h.

◆ OffsetFieldVName

const char ttk::OffsetFieldVName[] = "ttkOffsetFieldV"

Definition at line 45 of file DataTypes.h.

◆ OffsetScalarFieldName

const char ttk::OffsetScalarFieldName[] = "ttkOffsetScalarField"

default name for offset scalar field

Definition at line 41 of file DataTypes.h.

◆ PersistenceBirthName

const char ttk::PersistenceBirthName[] = "Birth"

Definition at line 76 of file DataTypes.h.

◆ PersistenceCoordinatesName

const char ttk::PersistenceCoordinatesName[] = "Coordinates"

Definition at line 78 of file DataTypes.h.

◆ PersistenceCriticalTypeName

const char ttk::PersistenceCriticalTypeName[] = "CriticalType"

Definition at line 75 of file DataTypes.h.

◆ PersistenceDeathName

const char ttk::PersistenceDeathName[] = "Death"

Definition at line 77 of file DataTypes.h.

◆ PersistenceIsFinite

const char ttk::PersistenceIsFinite[] = "IsFinite"

Definition at line 82 of file DataTypes.h.

◆ PersistenceName

const char ttk::PersistenceName[] = "Persistence"

Definition at line 80 of file DataTypes.h.

◆ PersistencePairIdentifierName

const char ttk::PersistencePairIdentifierName[] = "PairIdentifier"

Definition at line 79 of file DataTypes.h.

◆ PersistencePairTypeName

const char ttk::PersistencePairTypeName[] = "PairType"

Definition at line 81 of file DataTypes.h.

◆ SeparatrixStabilityIsomorphismClassId

const char ttk::SeparatrixStabilityIsomorphismClassId[] = "IsomorphismClassId"

Definition at line 69 of file DataTypes.h.

◆ SeparatrixStabilityMatchingIdName

const char ttk::SeparatrixStabilityMatchingIdName[] = "MatchingIdInBlock"

Definition at line 70 of file DataTypes.h.

◆ SeparatrixStabilityMatchingIdSeparatrixName

const char ttk::SeparatrixStabilityMatchingIdSeparatrixName[] = "SeparatrixMatchingIdInBlock"

Definition at line 71 of file DataTypes.h.

◆ SeparatrixStabilityOccurrenceCount

const char ttk::SeparatrixStabilityOccurrenceCount[] = "Occurrence"

Definition at line 68 of file DataTypes.h.

◆ VertexScalarFieldName

const char ttk::VertexScalarFieldName[] = "ttkVertexScalarField"

default name for vertex scalar field

Definition at line 35 of file DataTypes.h.

◆ welcomeMsg_

COMMON_EXPORTS bool ttk::welcomeMsg_ = true

extern

Definition at line 6 of file Debug.cpp.

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Detailed Description

Typedef Documentation

◆ BidderDiagram

◆ DiagramType

◆ GoodDiagram

◆ LongSimplexId

◆ MatchingType

◆ Matrice

◆ Matrix

◆ polarity

◆ real

◆ RipsPersistencePair

◆ SimplexId

◆ TaskId

◆ ThreadId

◆ trackingTuple

◆ triplet

◆ ValuesPair

◆ VectorMatchingTuple

Enumeration Type Documentation

◆ CompressionType

◆ CriticalType

◆ Direction

Function Documentation

◆ computeWeightedBarycenter()

◆ getLowerBoundCost()

◆ getMaxValue()

◆ getMinMaxLocal()

◆ getMinMaxLocalFromVector()

◆ getMinMaxLocalT()

◆ getNormalizedBirthDeath()

◆ getParametrizedBirthDeath()

◆ isDeathHigher()

◆ makeFakeMergeTree()

◆ makeFakeTree()

◆ preconditionOrderArray()

◆ shuffle()

◆ sortVertices()

◆ str2int()

Variable Documentation

◆ CellScalarFieldName

◆ compactTriangulationIndex

◆ CriticalTypeNumber

◆ globalDebugLevel_

◆ globalThreadNumber_

◆ goodbyeMsg_

◆ MaskScalarFieldName

◆ MorseSmaleAscendingName

◆ MorseSmaleBoundaryName

◆ MorseSmaleCellDimensionName

◆ MorseSmaleCellIdName

◆ MorseSmaleCriticalPointsOnBoundaryName

◆ MorseSmaleDescendingName

◆ MorseSmaleDestinationIdName

◆ MorseSmaleManifoldName

◆ MorseSmaleManifoldSizeName

◆ MorseSmaleSeparatrixDifferenceName

◆ MorseSmaleSeparatrixIdName

◆ MorseSmaleSeparatrixMaximumName

◆ MorseSmaleSeparatrixMinimumName

◆ MorseSmaleSeparatrixTypeName

◆ MorseSmaleSourceIdName

◆ MPIrank_

◆ MPIsize_

◆ OffsetFieldUName

◆ OffsetFieldVName

◆ OffsetScalarFieldName

◆ PersistenceBirthName

◆ PersistenceCoordinatesName

◆ PersistenceCriticalTypeName

◆ PersistenceDeathName

◆ PersistenceIsFinite

◆ PersistenceName

◆ PersistencePairIdentifierName