mpi_angular_class_average.h

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/***************************************************************************
 * Authors:     AUTHOR_NAME (aerey@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 MPI_ANGULAR_CLASS_AVERAGE_H_
#define MPI_ANGULAR_CLASS_AVERAGE_H_

//mpirun -np 5 xmipp_mpi_angular_class_average --nJobs 70

#include "parallel/xmipp_mpi.h"
#include "core/metadata_db.h"
#include "core/xmipp_image.h"
#include "data/polar.h"

//Tags already defined in xmipp
//#define TAG_WORK                     0
//#define TAG_STOP                     1
constexpr int TAG_I_FINISH_WRITTING =         12;
constexpr int TAG_MAY_I_WRITE =               13;
constexpr int TAG_YES_YOU_MAY_WRITE =         14;
constexpr int TAG_DO_NOT_DARE_TO_WRITE =      15;
constexpr int TAG_I_AM_FREE =                 16;

constexpr int lockWeightIndexesSize =  5;
constexpr int index_lockIndex =  0;
constexpr int index_weight =  1;
constexpr int index_weights1 =  2;
constexpr int index_weights2 =  3;
constexpr int index_ref3d =  4;

constexpr int ArraySize =  8;
constexpr int index_DefGroup =  0;
constexpr int index_2DRef =  1;
constexpr int index_3DRef =  2;
constexpr int index_Order =  3;
constexpr int index_Count =  4;
constexpr int index_jobId =  5;
constexpr int index_Rot =  6;
constexpr int index_Tilt =  7;

constexpr int AVG_OUPUT_SIZE =  10;

constexpr int split0 =  0;
constexpr int split1 =  1;
constexpr int split2 =  2;


class MpiProgAngularClassAverage : public XmippMpiProgram
{
public:
    // Seed
    unsigned int master_seed;

    // Metadata with the list of jobs
    MetaDataDb mdJobList;

    MetaDataDb      DF, DFlib, DFscore;
    MetaDataDb      DFclassesExp;
    FileName         fn_out, fn_out1, fn_out2, fn_wien, fn_ref;
    std::string      col_select;
    double           limit0, limitF, limitRclass, limitRper;
    bool             do_limit0, do_limitF, do_limitR0class, do_limitRFclass, do_limitR0per, do_limitRFper;
    bool             do_mirrors;
    bool             do_split;
    size_t           paddim;
    double           pad;
    Image<double>    Iempty;
    bool             do_save_images_assigned_to_classes;
    bool             do_add;
    bool             do_pcaSorting;
    MultidimArray<double> Mwien;
    MetaDataDb      SFclasses, SFclasses1, SFclasses2;

    FileName inFile, refGroup;
    int Ri, Ro;
    int nr_iter;
    double eps;
    double max_shift;
    double max_shift_change, max_psi_change;
    Polar_fftw_plans global_plans;
    RotationalCorrelationAux rotAux;
    MultidimArray<double> corr;

    int ctfNum;
    int ref3dNum;
    size_t Xdim, Ydim, Zdim, Ndim;

    size_t mpi_job_size;

    //Lock structure
    MultidimArray<bool> lockArray;
    MultidimArray<double> weightArray;
    MultidimArray<double> weightArrays1;
    MultidimArray<double> weightArrays2;

    MpiProgAngularClassAverage();

    MpiProgAngularClassAverage(int argc, char **argv);

//    void read(int argc, char** argv);

    void readParams();

    void defineParams();

    void run();

    void mpi_process_loop(double * Def_3Dref_2Dref_JobNo);

    void mpi_process(double * Def_3Dref_2Dref_JobNo);

    void mpi_produceSideInfo();

    void mpi_preprocess();

    void filterInputMetadata();

    void saveDiscardedImages();

    void initFileNames();

    void initDimentions();

    void initWeights();

    void initOutputFiles();

    void mpi_postprocess();

    void createJobList();

    void mpi_write(
        size_t dirno,
        int ref3dIndex,
        Image<double> avg,
        Image<double> avg1,
        Image<double> avg2,
        double w1,
        double w2,
        double old_w,
        double old_w1,
        double old_w2);

    void mpi_writeController(
            size_t dirno,
            Image<double> avg,
            Image<double> avg1,
            Image<double> avg2,
            const MetaDataDb& SFclass,
            const MetaDataDb& SFclass1,
            const MetaDataDb& SFclass2,
            const MetaDataDb& SFclassDiscarded,
            const MetaDataDb& _DF,
            double w1,
            double w2,
        double w,
            int lockIndex);

    void mpi_writeFile(
            Image<double> avg,
            size_t dirno,
            FileName fileNameStk,
            double w_old);

    void getPolar(
            MultidimArray<double> &img,
            Polar<std::complex <double> > &fP,
            bool conjugated=false,
            float xoff = 0.,
            float yoff = 0.);

    void reAlignClass(
            Image<double> &avg1,
            Image<double> &avg2,
            MetaData &SFclass1,
            MetaData &SFclass2,
            std::vector<Image<double> > imgs,
            std::vector<int> splits,
            std::vector<int> numbers,
            size_t dirno,
            double * my_output);

    void applyWienerFilter(MultidimArray<double> &img);

};
#endif /* MPI_ANGULAR_CLASS_AVERAGE_H_ */