matrix_dimred.h

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/***************************************************************************
 * Authors:     AUTHOR_NAME Carlos Oscar Sorzano (coss@cnb.csic.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'
 ***************************************************************************/

#ifndef _MATRIX_DIMRED
#define _MATRIX_DIMRED

#include <core/xmipp_program.h>
#include "pca.h"
#include "npe.h"
#include "spe.h"
#include "lpp.h"
#include "ltsa.h"
#include "gplvm.h"
#include "lltsa.h"
#include "kernelPCA.h"
#include "hessianLLE.h"
#include "diffusionMaps.h"
#include "probabilisticPCA.h"
#include "laplacianEigenmaps.h"

class ProgDimRed: public XmippProgram
{
public:
    FileName fnIn;
    FileName fnOut;
    FileName fnMapping;
    int outputDim;
    String dimRefMethod, dimEstMethod;
    int kNN; // Number of nearest neighbors
    int Niter; // Number of iterations
    double t; // Markov random walk
    double sigma; // Sigma of kernel
    bool global; // Global for SPE
public:
    Matrix2D<double> X; // Input data
    DimRedAlgorithm*  algorithm;
    PCA               algorithmPCA;
    LTSA              algorithmLTSA;
    DiffusionMaps     algorithmDiffusionMaps;
    LLTSA             algorithmLLTSA;
    LPP               algorithmLPP;
    KernelPCA         algorithmKernelPCA;
    ProbabilisticPCA  algorithmProbabilisticPCA;
    LaplacianEigenmap algorithmLaplacianEigenmap;
    HessianLLE        algorithmHessianLLE;
    NPE               algorithmNPE;
    SPE               algorithmSPE;
public:
    ProgDimRed();

    virtual void readParams();

    virtual void show();

    virtual void defineParams();

    virtual void produceSideInfo();

    void estimateDimension();
};

class ProgMatrixDimRed: public ProgDimRed
{
public:
    int inputDim, Nsamples;
public:
    void readParams();

    void show();

    void defineParams();

    void produceSideInfo();

    void run();
};
#endif