angular_project_library.h

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/***************************************************************************
 *
 * Authors:     Roberto Marabini
 *
 * 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_ANGULAR_PROJECT_LIBRARY_HH
#define _PROG_ANGULAR_PROJECT_LIBRARY_HH

#include <data/sampling.h>
#include <core/symmetries.h>
#include <core/args.h>
#include <fstream>
#include <iostream>
#include <string>
#include <data/projection.h>
#include <core/xmipp_image.h>
#include <core/xmipp_funcs.h>
#include <core/xmipp_program.h>
#include <core/metadata_extension.h>
#include <reconstruction/project_real_shears.h>
#include <data/fourier_projection.h>
#include <reconstruction/project.h>

/* PDB Phantom Program Parameters ------------------------------------------ */
class ProgAngularProjectLibrary: public XmippProgram
{
public:
    Sampling mysampling;

    double sampling;

    double perturb_projection_vector;

    double psi_sampling;

    double max_tilt_angle;
    
    double min_tilt_angle;
    
    FileName output_file;

    FileName output_file_root;

    FileName fn_groups;

    projectionType projType;
    double paddFactor;
    double maxFrequency;
    int BSplineDeg;

#ifdef NEVERDEFINED

    std::vector <Matrix1D<double> > close_points_angles;
#endif

    FileName FnexperimentalImages;
    
    bool angular_distance_bool;

    bool remove_points_far_away_from_experimental_data_bool;
    
    double angular_distance;

    bool compute_closer_sampling_point_bool;
    
    bool compute_neighbors_bool;
   
    int symmetry;

    FileName        fn_sym;

     FileName        fn_sym_neigh;

    int sym_order;
    
    FileName input_volume;
    
    Image<double> inputVol;
    
    int Xdim;
    
    int Ydim;
    bool only_winner;

    /* Volume for shear projection */
    RealShearsInfo *Vshears;

    /* Volume for fourier projection */
    FourierProjector *Vfourier;

    // std::vector <Matrix1D<double> > symmetry_vectors;
public:
    ProgAngularProjectLibrary();
    ProgAngularProjectLibrary(const ProgAngularProjectLibrary &)=delete;
    ProgAngularProjectLibrary(const ProgAngularProjectLibrary &&)=delete;

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

    void readParams();

    void defineParams();

    void show();

    void run();

    void createGroupSamplingFiles(void);
    
    void get_sym_vectors(std::vector< Matrix1D<double > > &sym_points);

    void project_angle_vector(int my_init, int my_end, bool verbose = true);
#ifdef NEVERDEFINED

    void remove_points_not_close_to_experimental_points(void);
#endif
};
#endif