mpi_classify_FTTRI.h

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/***************************************************************************
 *
 * Authors:    Carlos Oscar            coss@cnb.csic.es (2012)
 *             Wang Xia                wangxia@lsec.cc.ac.cn
 *             Guoliang Xu             xuguo@lsec.cc.ac.cn
 *
 * 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 _PROG_CLASSIFY_FTTRI
#define _PROG_CLASSIFY_FTTRI

#include "parallel/xmipp_mpi.h"
#include "core/xmipp_image.h"
#include "core/metadata_vec.h"


class EpsilonClass
{
public:
    std::vector<size_t> memberIdx;
    std::vector<int> neighbours;
};

class ProgClassifyFTTRI: public XmippProgram
{
public:
    FileName fnIn;

    FileName fnRoot;

    double pad;

    double fmax;

    size_t Rmax;

    double zoom;

    double sigma1;

    double sigma2;

    size_t nref;

    size_t nMinImages;

    int Niter;

    bool doPhase;
public:
    // Name of the invariants;
    FileName fnFTTRI;
    // Final size of the invariant
    int FTTRIXdim;
    int FTTRIYdim;
    // Mpi node
    std::shared_ptr<MpiNode> node;
    // FileTaskDistributor
    MpiTaskDistributor *taskDistributor;
    // MetaData In
    MetaDataVec mdIn;
    // Object Ids
    std::vector<size_t> imgsId;
    // Padded size
    int padXdim;
    // Set of classes
    std::vector< EpsilonClass > epsilonClasses;
    // Initial range for epsilon
    double dMin, dMax;
    // Copy of bestObjective
    double bestObjective;
    // Copy of bestEpsilon
    double bestEpsilon;
    // Copy of bestClass
    std::vector< EpsilonClass > bestEpsilonClasses;
    // Epsilon of each class
    Matrix1D<double> classEpsilon;
    // Epsilon max is the maximum of all class epsilons
    double epsilonMax;
    // Assigned to class
    Matrix1D<unsigned char> notAssigned;
    // Assigned to class init
    Matrix1D<unsigned char> notAssigned0;
    // All FTTRI centroids are loaded in memory
    Image<double> fttriCentroids;
    // All Image centroids are loaded in memory
    Image<double> imageCentroids;
public:
    ProgClassifyFTTRI(int argc, char **argv);

    void readParams();

    void show();

    void defineParams();

    void produceSideInfo();

    void produceFTTRI();

    void estimateEpsilonInitialRange();

    double fttri_distance(const MultidimArray<double> &fttri_i,
                          const MultidimArray<double> &fttri_j);

    void skipRandomNumberOfUnassignedClasses(
            size_t &currentPointer, size_t remaining);

    size_t wrapperFitness(double epsilon);

    void epsilonClassification(double epsilon);

    void searchOptimalEpsilon();

    void removeSmallClasses();

    int findFarthestFTTRI(const MultidimArray<double> &fttriSeed,
            const EpsilonClass &class_i);

    int findFarthest(const MultidimArray<double> &seed,
            const EpsilonClass &class_i, bool FTTRI);

    void splitLargeClasses(bool FTTRI);

    void splitLargeFTTRIClasses();

    void computeClassNeighbours(bool FTTRI);


    size_t reassignImagesToClasses(bool FTTRI);

    void writeResults(bool FTTRI);

    void alignImagesWithinClasses();

    void computeClassCentroids(bool FTTRI);

    void run();
};
#endif