#include <kernelPCA.h>

Inheritance diagram for KernelPCA:

Collaboration diagram for KernelPCA:

Public Member Functions
void	setSpecificParameters (double sigma=1.0)
	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

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 17 of file kernelPCA.h.

Member Function Documentation

◆ reduceDimensionality()

void KernelPCA::reduceDimensionality ( )

virtual

Reduce dimensionality.

Implements DimRedAlgorithm.

Definition at line 13 of file kernelPCA.cpp.

                                      {
     // Compute Gram matrix
     Matrix2D<double> D2;
     computeDistance(*X, D2, distance, false);
     computeSimilarityMatrix(D2,sigma);
 
     // Normalize it
     Matrix1D<double> mean_i;
     D2.rowSum(mean_i);
     mean_i/=MAT_XSIZE(D2);
     double mean=mean_i.computeMean();
     FOR_ALL_ELEMENTS_IN_MATRIX2D(D2)
         MAT_ELEM(D2,i,j)+=mean-VEC_ELEM(mean_i,i)-VEC_ELEM(mean_i,j);
 
     // Compute the largest eigenvalues
     Matrix1D<double> lambda;
     firstEigs(D2,outputDim,lambda,Y);
 
     // Readjust variances
     FOR_ALL_ELEMENTS_IN_MATRIX1D(lambda)
         VEC_ELEM(lambda,i)=sqrt(VEC_ELEM(lambda,i));
     FOR_ALL_ELEMENTS_IN_MATRIX2D(Y)
         MAT_ELEM(Y,i,j)*=VEC_ELEM(lambda,j);
 }

◆ setSpecificParameters()

void KernelPCA::setSpecificParameters ( double sigma = 1.0 )

Set specific parameters.

Definition at line 9 of file kernelPCA.cpp.

                                                   {
     this->sigma = sigma;
 }

Member Data Documentation

◆ sigma

double KernelPCA::sigma

Definition at line 20 of file kernelPCA.h.

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

xmipp/libraries/dimred/kernelPCA.h
xmipp/libraries/dimred/kernelPCA.cpp