laplacianEigenmaps.cpp

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/***************************************************************************
 *
 * Authors:    Carlos Oscar Sanchez Sorzano      coss@cnb.csic.es (2013)
 *             Daniel Albuerne Gonzalez          d.albuerne@usp.ceu.es
 *
 * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
 * 02111-1307  USA
 *
 *  All comments concerning this program package may be sent to the
 *  e-mail address 'xmipp@cnb.csic.es'
 ***************************************************************************/

#include "laplacianEigenmaps.h"

void LaplacianEigenmap::setSpecificParameters(double sigma, size_t numberOfNeighbours)
{
    this->sigma=sigma;
    this->numberOfNeighbours=numberOfNeighbours;
}

void LaplacianEigenmap::reduceDimensionality()
{
    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);
}