#include <laplacianEigenmaps.h>

Inheritance diagram for LaplacianEigenmap:

Collaboration diagram for LaplacianEigenmap:

Public Member Functions
void	setSpecificParameters (double sigma=1.0, size_t numberOfNeighbours=7)
	Set specific parameters. More...

void	reduceDimensionality ()
	Reduce dimensionality. More...

Public Member Functions inherited from DimRedAlgorithm
	DimRedAlgorithm ()
	Empty constructor. More...

void	setInputData (Matrix2D< double > &X)
	Set input data. More...

void	setOutputDimensionality (size_t outputDim)
	Set output dimensionality. More...

const Matrix2D< double > &	getReducedData ()
	Get reduced data. More...

Public Attributes
double	sigma

size_t	numberOfNeighbours

Public Attributes inherited from DimRedAlgorithm
Matrix2D< double > *	X
	Pointer to input data. More...

size_t	outputDim
	Output dim. More...

Matrix2D< double >	Y
	Output data. More...

DimRedDistance2	distance
	Distance function. More...

FileName	fnMapping
	Save mapping. More...

Detailed Description

Class for making a Kernel PCA dimensionality reduction

Definition at line 37 of file laplacianEigenmaps.h.

Member Function Documentation

◆ reduceDimensionality()

void LaplacianEigenmap::reduceDimensionality ( )

virtual

Reduce dimensionality.

Implements DimRedAlgorithm.

Definition at line 35 of file laplacianEigenmaps.cpp.

 {
     Matrix2D<double> G,L,D;
     Matrix1D<double> mappedX;
     //Construct neighborhood graph
     computeDistanceToNeighbours(*X,numberOfNeighbours,G,distance,false);
     //Compute Gaussian kernel(heat kernel based weights)
     computeSimilarityMatrix(G,sigma,true,true);
     //Compute Laplacian
     computeGraphLaplacian(G,L);
     //Construct diagonal weight matrix
     D.initZeros(MAT_YSIZE(G),MAT_YSIZE(G));
     FOR_ALL_ELEMENTS_IN_MATRIX2D(G)
         MAT_ELEM(D,i,i)+=MAT_ELEM(G,i,j);
     //Construct eigenmaps
     generalizedEigs(L,D,mappedX,Y);
     keepColumns(Y,1,(int)outputDim);
 }

◆ setSpecificParameters()

void LaplacianEigenmap::setSpecificParameters	(	double	sigma = `1.0`,
		size_t	numberOfNeighbours = `7`
	)

Set specific parameters.

Definition at line 29 of file laplacianEigenmaps.cpp.

 {
     this->sigma=sigma;
     this->numberOfNeighbours=numberOfNeighbours;
 }

Member Data Documentation

◆ numberOfNeighbours

size_t LaplacianEigenmap::numberOfNeighbours

Definition at line 41 of file laplacianEigenmaps.h.

◆ sigma

double LaplacianEigenmap::sigma

Definition at line 40 of file laplacianEigenmaps.h.

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

xmipp/libraries/dimred/laplacianEigenmaps.h
xmipp/libraries/dimred/laplacianEigenmaps.cpp

Public Member Functions