lpp.cpp

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/***************************************************************************
 *
 * Authors:    Oscar Hueros Fernandez      o.hueros@gmail.com (2013)
 *
 * Universidad San Pablo CEU
 *
 * 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 "lpp.h"

void LPP::setSpecificParameters(int k, double sigma)
{
    this->k=k;
    this->sigma=sigma;
}
void LPP::reduceDimensionality()
{
    // Compute the distance to the k nearest neighbors
    Matrix2D<double> D2;
    computeDistanceToNeighbours(*X, k, D2, distance, false);

    // Compute similarity matrix
    computeSimilarityMatrix(D2,sigma,true,true);

    // Compute graph laplacian
    Matrix2D<double> L;
    computeGraphLaplacian(D2,L);

    Matrix2D<double> DP, LP;
    matrixOperation_XtAX_symmetric(*X,D2,DP);
    matrixOperation_XtAX_symmetric(*X,L,LP);

    // Compute eigenvalues and eigenvectors resolving the generalized eigenvector problem
    Matrix2D<double> Peigvec, eigvector;
    Matrix1D<double> Deigval;
    generalizedEigs(LP, DP, Deigval, Peigvec);

    // Sort the eigenvalues in ascending order
    Matrix1D<int> idx;
    Deigval.indexSort(idx);

    // Sort the eigenvalues in descending order and get the smallest eigenvectors
    eigvector.resizeNoCopy(MAT_YSIZE(Peigvec),outputDim);
    for (size_t j=0; j<outputDim; ++j)
    {
        int idxj=VEC_ELEM(idx,j)-1;
        for (int i=0; i<MAT_YSIZE(Peigvec); ++i)
            MAT_ELEM(eigvector,i,j)=MAT_ELEM(Peigvec,i,idxj);
    }

    // Compute the result of the reduce dimensionality method
    Y=*X * eigvector;
    if (fnMapping!="")
        eigvector.write(fnMapping);
}