TTK VTK-filter that apply dimension reduction algorithms on input. More...

#include <DimensionReduction.h>

Inheritance diagram for ttk::DimensionReduction:

Public Types
enum class	METHOD { SE = 0 , LLE = 1 , MDS = 2 , T_SNE = 3 , ISOMAP = 4 , PCA = 5 , TOPOMAP = 6 }

Public Member Functions
	DimensionReduction ()

void	setSEParameters (const std::string &Affinity, const float Gamma, const std::string &EigenSolver, const bool InputIsADistanceMatrix)

void	setLLEParameters (const float Regularization, const std::string &EigenSolver, const float Tolerance, const int MaxIteration, const std::string &Method_s, const float HessianTolerance, const float ModifiedTolerance, const std::string &NeighborsAlgorithm)

void	setMDSParameters (const bool Metric, const int Init, const int MaxIteration, const int Verbose, const float Epsilon, const bool Dissimilarity)

void	setTSNEParameters (const float Perplexity, const float Exaggeration, const float LearningRate, const int MaxIteration, const int MaxIterationProgress, const float GradientThreshold, const std::string &Metric, const std::string &Init, const int Verbose, const std::string &Method_s, const float Angle)

void	setISOParameters (const std::string &EigenSolver, const float Tolerance, const int MaxIteration, const std::string &PathMethod, const std::string &NeighborsAlgorithm)

void	setPCAParameters (const bool Copy, const bool Whiten, const std::string &SVDSolver, const float Tolerance, const std::string &MaxIteration)

void	setTopoParameters (const size_t AngularSampleNb, bool CheckMST)

void	setInputModulePath (const std::string &modulePath)

void	setInputModuleName (const std::string &moduleName)

void	setInputFunctionName (const std::string &functionName)

void	setInputMethod (METHOD method)

void	setInputNumberOfComponents (const int numberOfComponents)

void	setInputNumberOfNeighbors (const int numberOfNeighbors)

void	setInputIsDeterministic (const int isDeterm)

void	setIsInputDistanceMatrix (const bool data)

int	execute (std::vector< std::vector< double > > &outputEmbedding, const std::vector< double > &inputMatrix, const int nRows, const int nColumns, int *insertionTimeForTopoMap=nullptr) const

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)

Protected Attributes
std::string	se_Affinity {"nearest_neighbors"}

float	se_Gamma {1}

std::string	se_EigenSolver {"None"}

float	lle_Regularization {1e-3}

std::string	lle_EigenSolver {"auto"}

float	lle_Tolerance {1e-3}

int	lle_MaxIteration {300}

std::string	lle_Method {"standard"}

float	lle_HessianTolerance {1e-3}

float	lle_ModifiedTolerance {1e-3}

std::string	lle_NeighborsAlgorithm {"auto"}

bool	mds_Metric {true}

int	mds_Init {4}

int	mds_MaxIteration {300}

int	mds_Verbose {0}

float	mds_Epsilon {0}

std::string	mds_Dissimilarity {"euclidean"}

float	tsne_Perplexity {30}

float	tsne_Exaggeration {12}

float	tsne_LearningRate {200}

int	tsne_MaxIteration {1000}

int	tsne_MaxIterationProgress {300}

float	tsne_GradientThreshold {1e-7}

std::string	tsne_Metric {"euclidean"}

std::string	tsne_Init {"random"}

int	tsne_Verbose {0}

std::string	tsne_Method {"barnes_hut"}

float	tsne_Angle {0.5}

std::string	iso_EigenSolver {"auto"}

float	iso_Tolerance {1e-3}

int	iso_MaxIteration {300}

std::string	iso_PathMethod {"auto"}

std::string	iso_NeighborsAlgorithm {"auto"}

std::string	iso_Metric {"euclidean"}

bool	pca_Copy {true}

bool	pca_Whiten {false}

std::string	pca_SVDSolver {"auto"}

float	pca_Tolerance {0}

std::string	pca_MaxIteration {"auto"}

size_t	topomap_AngularSampleNb

bool	topomap_CheckMST

TopoMap::STRATEGY	topomap_Strategy {TopoMap::STRATEGY::KRUSKAL}

std::string	ModulePath {"default"}

std::string	ModuleName {"dimensionReduction"}

std::string	FunctionName {"doIt"}

METHOD	Method

int	NumberOfComponents {2}

int	NumberOfNeighbors {5}

int	IsDeterministic {true}

char	majorVersion_ {'0'}

bool	IsInputADistanceMatrix {false}

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_

Additional Inherited Members
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)

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

Detailed Description

TTK VTK-filter that apply dimension reduction algorithms on input.

Author: Guillaume Favelier guill.nosp@m.aume.nosp@m..fave.nosp@m.lier.nosp@m.@lip6.nosp@m..fr

Date: September 2018

Parameters

Input	Input scalar field (vtkTable)
Output	Output scalar field (vtkTable)

TTK VTK-filter that takes a matrix (vtkTable) as input and apply a dimension reduction algorithm from scikit-learn.

See also: ttk::Triangulation; ttkDimensionReduction.cpp for a usage example.

Online examples:

Definition at line 60 of file DimensionReduction.h.

Member Enumeration Documentation

◆ METHOD

enum class ttk::DimensionReduction::METHOD

strong

Scikit-Learn Dimension Reduction algorithms

Enumerator
SE	Spectral Embedding
LLE	Locally Linear Embedding
MDS	Multi-Dimensional Scaling
T_SNE	t-distributed Stochastic Neighbor Embedding
ISOMAP	IsoMap Embedding
PCA	Principal Component Analysis
TOPOMAP	TopoMap

Definition at line 66 of file DimensionReduction.h.

Constructor & Destructor Documentation

◆ DimensionReduction()

DimensionReduction::DimensionReduction ( )

Definition at line 18 of file DimensionReduction.cpp.

Member Function Documentation

◆ execute()

int DimensionReduction::execute	(	std::vector< std::vector< double > > &	outputEmbedding,
		const std::vector< double > &	inputMatrix,
		const int	nRows,
		const int	nColumns,
		int *	insertionTimeForTopoMap = `nullptr`
	)		const

Definition at line 45 of file DimensionReduction.cpp.

◆ setInputFunctionName()

void ttk::DimensionReduction::setInputFunctionName ( const std::string & functionName )

inline

Definition at line 192 of file DimensionReduction.h.

◆ setInputIsDeterministic()

void ttk::DimensionReduction::setInputIsDeterministic ( const int isDeterm )

inline

Definition at line 243 of file DimensionReduction.h.

◆ setInputMethod()

void ttk::DimensionReduction::setInputMethod ( METHOD method )

inline

Definition at line 196 of file DimensionReduction.h.

◆ setInputModuleName()

void ttk::DimensionReduction::setInputModuleName ( const std::string & moduleName )

inline

Definition at line 188 of file DimensionReduction.h.

◆ setInputModulePath()

void ttk::DimensionReduction::setInputModulePath ( const std::string & modulePath )

inline

Definition at line 184 of file DimensionReduction.h.

◆ setInputNumberOfComponents()

void ttk::DimensionReduction::setInputNumberOfComponents ( const int numberOfComponents )

inline

Definition at line 235 of file DimensionReduction.h.

◆ setInputNumberOfNeighbors()

void ttk::DimensionReduction::setInputNumberOfNeighbors ( const int numberOfNeighbors )

inline

Definition at line 239 of file DimensionReduction.h.

◆ setIsInputDistanceMatrix()

void ttk::DimensionReduction::setIsInputDistanceMatrix ( const bool data )

inline

Definition at line 247 of file DimensionReduction.h.

◆ setISOParameters()

void ttk::DimensionReduction::setISOParameters	(	const std::string &	EigenSolver,
		const float	Tolerance,
		const int	MaxIteration,
		const std::string &	PathMethod,
		const std::string &	NeighborsAlgorithm
	)

inline

Definition at line 156 of file DimensionReduction.h.

◆ setLLEParameters()

void ttk::DimensionReduction::setLLEParameters	(	const float	Regularization,
		const std::string &	EigenSolver,
		const float	Tolerance,
		const int	MaxIteration,
		const std::string &	Method_s,
		const float	HessianTolerance,
		const float	ModifiedTolerance,
		const std::string &	NeighborsAlgorithm
	)

inline

Definition at line 96 of file DimensionReduction.h.

◆ setMDSParameters()

void ttk::DimensionReduction::setMDSParameters	(	const bool	Metric,
		const int	Init,
		const int	MaxIteration,
		const int	Verbose,
		const float	Epsilon,
		const bool	Dissimilarity
	)

inline

Definition at line 114 of file DimensionReduction.h.

◆ setPCAParameters()

void ttk::DimensionReduction::setPCAParameters	(	const bool	Copy,
		const bool	Whiten,
		const std::string &	SVDSolver,
		const float	Tolerance,
		const std::string &	MaxIteration
	)

inline

Definition at line 168 of file DimensionReduction.h.

◆ setSEParameters()

void ttk::DimensionReduction::setSEParameters	(	const std::string &	Affinity,
		const float	Gamma,
		const std::string &	EigenSolver,
		const bool	InputIsADistanceMatrix
	)

inline

Definition at line 83 of file DimensionReduction.h.

◆ setTopoParameters()

void ttk::DimensionReduction::setTopoParameters	(	const size_t	AngularSampleNb,
		bool	CheckMST
	)

inline

Definition at line 179 of file DimensionReduction.h.

◆ setTSNEParameters()

void ttk::DimensionReduction::setTSNEParameters	(	const float	Perplexity,
		const float	Exaggeration,
		const float	LearningRate,
		const int	MaxIteration,
		const int	MaxIterationProgress,
		const float	GradientThreshold,
		const std::string &	Metric,
		const std::string &	Init,
		const int	Verbose,
		const std::string &	Method_s,
		const float	Angle
	)

inline

Definition at line 132 of file DimensionReduction.h.

Member Data Documentation

◆ FunctionName

std::string ttk::DimensionReduction::FunctionName {"doIt"}

protected

Definition at line 328 of file DimensionReduction.h.

◆ IsDeterministic

int ttk::DimensionReduction::IsDeterministic {true}

protected

Definition at line 334 of file DimensionReduction.h.

◆ IsInputADistanceMatrix

bool ttk::DimensionReduction::IsInputADistanceMatrix {false}

protected

Definition at line 336 of file DimensionReduction.h.

◆ iso_EigenSolver

std::string ttk::DimensionReduction::iso_EigenSolver {"auto"}

protected

Definition at line 306 of file DimensionReduction.h.

◆ iso_MaxIteration

int ttk::DimensionReduction::iso_MaxIteration {300}

protected

Definition at line 308 of file DimensionReduction.h.

◆ iso_Metric

std::string ttk::DimensionReduction::iso_Metric {"euclidean"}

protected

Definition at line 311 of file DimensionReduction.h.

◆ iso_NeighborsAlgorithm

std::string ttk::DimensionReduction::iso_NeighborsAlgorithm {"auto"}

protected

Definition at line 310 of file DimensionReduction.h.

◆ iso_PathMethod

std::string ttk::DimensionReduction::iso_PathMethod {"auto"}

protected

Definition at line 309 of file DimensionReduction.h.

◆ iso_Tolerance

float ttk::DimensionReduction::iso_Tolerance {1e-3}

protected

Definition at line 307 of file DimensionReduction.h.

◆ lle_EigenSolver

std::string ttk::DimensionReduction::lle_EigenSolver {"auto"}

protected

Definition at line 276 of file DimensionReduction.h.

◆ lle_HessianTolerance

float ttk::DimensionReduction::lle_HessianTolerance {1e-3}

protected

Definition at line 280 of file DimensionReduction.h.

◆ lle_MaxIteration

int ttk::DimensionReduction::lle_MaxIteration {300}

protected

Definition at line 278 of file DimensionReduction.h.

◆ lle_Method

std::string ttk::DimensionReduction::lle_Method {"standard"}

protected

Definition at line 279 of file DimensionReduction.h.

◆ lle_ModifiedTolerance

float ttk::DimensionReduction::lle_ModifiedTolerance {1e-3}

protected

Definition at line 281 of file DimensionReduction.h.

◆ lle_NeighborsAlgorithm

std::string ttk::DimensionReduction::lle_NeighborsAlgorithm {"auto"}

protected

Definition at line 282 of file DimensionReduction.h.

◆ lle_Regularization

float ttk::DimensionReduction::lle_Regularization {1e-3}

protected

Definition at line 275 of file DimensionReduction.h.

◆ lle_Tolerance

float ttk::DimensionReduction::lle_Tolerance {1e-3}

protected

Definition at line 277 of file DimensionReduction.h.

◆ majorVersion_

char ttk::DimensionReduction::majorVersion_ {'0'}

protected

Definition at line 335 of file DimensionReduction.h.

◆ mds_Dissimilarity

std::string ttk::DimensionReduction::mds_Dissimilarity {"euclidean"}

protected

Definition at line 290 of file DimensionReduction.h.

◆ mds_Epsilon

float ttk::DimensionReduction::mds_Epsilon {0}

protected

Definition at line 289 of file DimensionReduction.h.

◆ mds_Init

int ttk::DimensionReduction::mds_Init {4}

protected

Definition at line 286 of file DimensionReduction.h.

◆ mds_MaxIteration

int ttk::DimensionReduction::mds_MaxIteration {300}

protected

Definition at line 287 of file DimensionReduction.h.

◆ mds_Metric

bool ttk::DimensionReduction::mds_Metric {true}

protected

Definition at line 285 of file DimensionReduction.h.

◆ mds_Verbose

int ttk::DimensionReduction::mds_Verbose {0}

protected

Definition at line 288 of file DimensionReduction.h.

◆ Method

METHOD ttk::DimensionReduction::Method

protected

Definition at line 330 of file DimensionReduction.h.

◆ ModuleName

std::string ttk::DimensionReduction::ModuleName {"dimensionReduction"}

protected

Definition at line 327 of file DimensionReduction.h.

◆ ModulePath

std::string ttk::DimensionReduction::ModulePath {"default"}

protected

Definition at line 326 of file DimensionReduction.h.

◆ NumberOfComponents

int ttk::DimensionReduction::NumberOfComponents {2}

protected

Definition at line 332 of file DimensionReduction.h.

◆ NumberOfNeighbors

int ttk::DimensionReduction::NumberOfNeighbors {5}

protected

Definition at line 333 of file DimensionReduction.h.

◆ pca_Copy

bool ttk::DimensionReduction::pca_Copy {true}

protected

Definition at line 314 of file DimensionReduction.h.

◆ pca_MaxIteration

std::string ttk::DimensionReduction::pca_MaxIteration {"auto"}

protected

Definition at line 318 of file DimensionReduction.h.

◆ pca_SVDSolver

std::string ttk::DimensionReduction::pca_SVDSolver {"auto"}

protected

Definition at line 316 of file DimensionReduction.h.

◆ pca_Tolerance

float ttk::DimensionReduction::pca_Tolerance {0}

protected

Definition at line 317 of file DimensionReduction.h.

◆ pca_Whiten

bool ttk::DimensionReduction::pca_Whiten {false}

protected

Definition at line 315 of file DimensionReduction.h.

◆ se_Affinity

std::string ttk::DimensionReduction::se_Affinity {"nearest_neighbors"}

protected

Definition at line 270 of file DimensionReduction.h.

◆ se_EigenSolver

std::string ttk::DimensionReduction::se_EigenSolver {"None"}

protected

Definition at line 272 of file DimensionReduction.h.

◆ se_Gamma

float ttk::DimensionReduction::se_Gamma {1}

protected

Definition at line 271 of file DimensionReduction.h.

◆ topomap_AngularSampleNb

size_t ttk::DimensionReduction::topomap_AngularSampleNb

protected

Definition at line 321 of file DimensionReduction.h.

◆ topomap_CheckMST

bool ttk::DimensionReduction::topomap_CheckMST

protected

Definition at line 322 of file DimensionReduction.h.

◆ topomap_Strategy

TopoMap::STRATEGY ttk::DimensionReduction::topomap_Strategy {TopoMap::STRATEGY::KRUSKAL}

protected

Definition at line 323 of file DimensionReduction.h.

◆ tsne_Angle

float ttk::DimensionReduction::tsne_Angle {0.5}

protected

Definition at line 303 of file DimensionReduction.h.

◆ tsne_Exaggeration

float ttk::DimensionReduction::tsne_Exaggeration {12}

protected

Definition at line 294 of file DimensionReduction.h.

◆ tsne_GradientThreshold

float ttk::DimensionReduction::tsne_GradientThreshold {1e-7}

protected

Definition at line 298 of file DimensionReduction.h.

◆ tsne_Init

std::string ttk::DimensionReduction::tsne_Init {"random"}

protected

Definition at line 300 of file DimensionReduction.h.

◆ tsne_LearningRate

float ttk::DimensionReduction::tsne_LearningRate {200}

protected

Definition at line 295 of file DimensionReduction.h.

◆ tsne_MaxIteration

int ttk::DimensionReduction::tsne_MaxIteration {1000}

protected

Definition at line 296 of file DimensionReduction.h.

◆ tsne_MaxIterationProgress

int ttk::DimensionReduction::tsne_MaxIterationProgress {300}

protected

Definition at line 297 of file DimensionReduction.h.

◆ tsne_Method

std::string ttk::DimensionReduction::tsne_Method {"barnes_hut"}

protected

Definition at line 302 of file DimensionReduction.h.

◆ tsne_Metric

std::string ttk::DimensionReduction::tsne_Metric {"euclidean"}

protected

Definition at line 299 of file DimensionReduction.h.

◆ tsne_Perplexity

float ttk::DimensionReduction::tsne_Perplexity {30}

protected

Definition at line 293 of file DimensionReduction.h.

◆ tsne_Verbose

int ttk::DimensionReduction::tsne_Verbose {0}

protected

Definition at line 301 of file DimensionReduction.h.

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

/home/julien/Pro/git/github/ttk-tierny/core/base/dimensionReduction/DimensionReduction.h
/home/julien/Pro/git/github/ttk-tierny/core/base/dimensionReduction/DimensionReduction.cpp

Public Types

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ METHOD

Constructor & Destructor Documentation

◆ DimensionReduction()

Member Function Documentation

◆ execute()

◆ setInputFunctionName()

◆ setInputIsDeterministic()

◆ setInputMethod()

◆ setInputModuleName()

◆ setInputModulePath()

◆ setInputNumberOfComponents()

◆ setInputNumberOfNeighbors()

◆ setIsInputDistanceMatrix()

◆ setISOParameters()

◆ setLLEParameters()

◆ setMDSParameters()

◆ setPCAParameters()

◆ setSEParameters()

◆ setTopoParameters()

◆ setTSNEParameters()

Member Data Documentation

◆ FunctionName

◆ IsDeterministic

◆ IsInputADistanceMatrix

◆ iso_EigenSolver

◆ iso_MaxIteration

◆ iso_Metric

◆ iso_NeighborsAlgorithm

◆ iso_PathMethod

◆ iso_Tolerance

◆ lle_EigenSolver

◆ lle_HessianTolerance

◆ lle_MaxIteration

◆ lle_Method

◆ lle_ModifiedTolerance

◆ lle_NeighborsAlgorithm

◆ lle_Regularization

◆ lle_Tolerance

◆ majorVersion_

◆ mds_Dissimilarity

◆ mds_Epsilon

◆ mds_Init

◆ mds_MaxIteration

◆ mds_Metric

◆ mds_Verbose

◆ Method

◆ ModuleName

◆ ModulePath

◆ NumberOfComponents

◆ NumberOfNeighbors

◆ pca_Copy

◆ pca_MaxIteration

◆ pca_SVDSolver

◆ pca_Tolerance

◆ pca_Whiten

◆ se_Affinity

◆ se_EigenSolver

◆ se_Gamma

◆ topomap_AngularSampleNb

◆ topomap_CheckMST

◆ topomap_Strategy

◆ tsne_Angle

◆ tsne_Exaggeration

◆ tsne_GradientThreshold

◆ tsne_Init

◆ tsne_LearningRate

◆ tsne_MaxIteration

◆ tsne_MaxIterationProgress

◆ tsne_Method

◆ tsne_Metric

◆ tsne_Perplexity

◆ tsne_Verbose