DiffusionMaps Class Reference

#include <diffusionMaps.h>

Inheritance diagram for DiffusionMaps:

Collaboration diagram for DiffusionMaps:

Public Member Functions
void	setSpecificParameters (double t=1.0, 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	t
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 Diffusion Maps dimensionality reduction

Definition at line 37 of file diffusionMaps.h.

Member Function Documentation

reduceDimensionality()

void DiffusionMaps::reduceDimensionality ( )

virtual

Reduce dimensionality.

Implements DimRedAlgorithm.

Definition at line 35 of file diffusionMaps.cpp.

{
    //Normalize data (between 0 and 1)
    normalizeColumnsBetween0and1(*X);

    // Compute Gaussian Kernel Matrix.
    // First, compute the distance of all vs all.
    Matrix2D<double> L2distance;
    computeDistance(*X,L2distance,distance,false);

    // Now use this distance to build a similarity matrix
    computeSimilarityMatrix(L2distance,sigma);

    // Normalize L2distance to be a stochastic matrix
    Matrix1D<double> p;
    L2distance.rowSum(p);
    if (t!=1.)
        FOR_ALL_ELEMENTS_IN_MATRIX2D(L2distance)
            MAT_ELEM(L2distance,i,j)/=pow(VEC_ELEM(p,i)*VEC_ELEM(p,j),t);
    else
        FOR_ALL_ELEMENTS_IN_MATRIX2D(L2distance)
            MAT_ELEM(L2distance,i,j)/=VEC_ELEM(p,i);

    // Normalize L2distance again
    L2distance.rowSum(p);
    FOR_ALL_ELEMENTS_IN_MATRIX1D(p)
        VEC_ELEM(p,i)=sqrt(VEC_ELEM(p,i));
    FOR_ALL_ELEMENTS_IN_MATRIX2D(L2distance)
        MAT_ELEM(L2distance,i,j)/=VEC_ELEM(p,i)*VEC_ELEM(p,j);

    // L2distance=U*S*V^t
    Matrix2D<double> U,V;
    Matrix1D<double> S;
    svdcmp(L2distance,U,S,V);

    // Get columns 1 to outputDim of U as output
    // normalzied by the first element in its row
    Y.resizeNoCopy(MAT_YSIZE(U),outputDim);
    for (size_t i=0;i<MAT_YSIZE(U);++i)
    {
        double iK=1/MAT_ELEM(U,i,0);
        for (size_t j=1;j<=outputDim;++j)
            MAT_ELEM(Y,i,j-1)=MAT_ELEM(U,i,j)*iK;
    }
}

setSpecificParameters()

void DiffusionMaps::setSpecificParameters	(	double	t = 1.0,
		double	sigma = 1.0
	)

Set specific parameters.

Definition at line 29 of file diffusionMaps.cpp.

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

Member Data Documentation

sigma

double DiffusionMaps::sigma

Definition at line 41 of file diffusionMaps.h.

t

double DiffusionMaps::t

Definition at line 40 of file diffusionMaps.h.

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

• xmipp/libraries/dimred/diffusionMaps.h
• xmipp/libraries/dimred/diffusionMaps.cpp