transform_dimred.h

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/***************************************************************************
 * Authors:     AUTHOR_NAME (jvargas@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 _TRANSFROM_DIMRED
#define _TRANSFROM_DIMRED

#include "core/metadata_vec.h"
#include "data/mask.h"
#include "data/filters.h"
#include "matrix_dimred.h"

class ProgTransformDimRed: public ProgDimRed
{
public:
    FileName fnRandomSampling;
    int numGrids;
    String distance;
public:
    MetaDataVec SFin;
    Mask mask;

    // Auxiliary variables for alignment
    MultidimArray<double> I1, I2;
    Matrix2D<double> M;
    AlignmentAux aux;
    CorrelationAux aux2;
    RotationalCorrelationAux aux3;
public:
    void readParams();

    void show();

    void defineParams();

    void produceSideInfo();

    void run();

    void insertImageInDataMatrix(size_t index, const MultidimArray<double> &mImg);

    void extractImageFromDataMatrix(size_t index, MultidimArray<double> &mImg);

    double progCorrelationDistance(size_t i1, size_t i2);

    //Extract a number of random projections well sampled in the projection sphere
    void extractRandomProjections();

};
#endif