basic_art.h

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/***************************************************************************
 *
 * Authors:     Carlos Oscar S. 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 _BASIC_ART_HH
#define _BASIC_ART_HH

#include "core/symmetries.h"
#include "core/xmipp_filename.h"
#include "core/metadata_label.h"
#include "data/basis.h"
#include "data/fourier_projection.h"


struct ReconsInfo
{
    FileName fn_proj;
    MDRowVec    row;
    FileName fn_ctf;
    double  rot;
    double  tilt;
    double  psi;
    int    sym;
    int    seed;
};

/* ART parameters ---------------------------------------------------------- */
class BasicARTParameters
{
public:
    // Type of the parallel processing
    typedef enum {ART, pCAV, pAVSP, pSART, pBiCAV, pSIRT, pfSIRT, SIRT } ARTParallelMode;

    /* User parameters ...................................................... */
    Basis basis;

    int no_it;

    Matrix1D<double> lambda_list;

    ARTParallelMode parallel_mode;

    int block_size;

    int eq_mode;

    bool random_sort;

    bool dont_sort;

    int sort_last_N;

    bool WLS;

    Matrix1D<double> kappa_list;

    std::vector<Projection> residual_imgs;

    double sum_weight;

    double grid_relative_size;

    int grid_type;

    int proj_ext;

    double R;

    int Xoutput_volume_size;

    int Youtput_volume_size;

    int Zoutput_volume_size;

    double sampling;

    FileName fn_sym;

    int sym_each;

    double max_tilt;

    int ref_trans_after;

    double ref_trans_step;

    double sparseEps;

    double diffusionWeight;

    int force_sym;

    bool do_not_generate_subgroup;

    bool do_not_use_symproj;

    FileName fn_surface_mask;

    FileName fn_sel;

    double goldmask;

    bool shiftedTomograms;

    FileName fn_out, fn_root;

    FileName fn_start;

    int stop_at;

    double known_volume;

    FileName fn_ctf;

    bool unmatched;

    double ray_length;

    bool apply_shifts;

    bool positivity;

    bool print_system_matrix;

    bool is_crystal;

    bool variability_analysis;

    bool refine;

    bool noisy_reconstruction;

    bool using_MPI;

    int threads;

#define TELL_IV                    0x100
#define TELL_ONLY_SYM              0x80
#define TELL_USE_INPUT_BASISVOLUME 0x40
#define TELL_SHOW_ERROR            0x20
#define TELL_MANUAL_ORDER          0x10
#define TELL_SAVE_AT_EACH_STEP     0x8
#define TELL_SAVE_INTERMIDIATE     0x4
#define TELL_SAVE_BASIS            0x2
#define TELL_STATS                 0x1

    int tell;

    int save_intermidiate_every;

    int verbose;

    FileName fn_control;

    /* ART Side information ................................................. */
    SymList         SL;

    size_t          projXdim;

    size_t          projYdim;

    std::ofstream        *fh_hist=nullptr;

    ReconsInfo     *IMG_Inf=nullptr;

    MultidimArray<int>   ordered_list;

    int             numIMG;

    int             trueIMG;

    Matrix2D<double> *D=nullptr;
    Matrix2D<double> *Dinv=nullptr;

    Image<double> *surface_mask=nullptr;

    int POCS_freq;

    GridVolumeT<int> *GVNeq=nullptr;
public:
    BasicARTParameters() = default;
    BasicARTParameters(const BasicARTParameters &)=delete;
    BasicARTParameters(const BasicARTParameters &&)=delete;

    ~BasicARTParameters();
    BasicARTParameters & operator =(const BasicARTParameters &)=delete;
    BasicARTParameters & operator =(const BasicARTParameters &&)=delete;

    void defaultValues();

    static void defineParams(XmippProgram * program, bool mpiMode = false);

    void readParams(XmippProgram * program);

#define BASIC 0
#define FULL  1

    void produceSideInfo(GridVolume &vol_basis0, int level = FULL, int rank = -1);

    void computeCAVWeights(GridVolume &vol_basis0,
                           int numProjs_node, int debug_level = 0);

    double lambda(int n)
    {
        int imax = VEC_XSIZE(lambda_list);
        if (imax == 0)
            REPORT_ERROR(ERR_MULTIDIM_SIZE, "Basic_art: There are no lambdas\n");
        if (n >= imax)
            return lambda_list(imax -1);
        else
            return lambda_list(n);
    }

    double kappa(int n)
    {
        int imax = VEC_XSIZE(kappa_list);
        if (imax == 0)
            REPORT_ERROR(ERR_MULTIDIM_SIZE, "Basic_art: There are no kappas\n");
        if (n >= imax)
            return kappa_list(imax -1);
        else
            return kappa_list(n);
    }

    int ProjXdim();

    int ProjYdim();

};

#endif