volume_correct_bfactor.h

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/***************************************************************************
 *
 * Author:     Sjors H.W. Scheres               (scheres@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 VOLUME_CORRECT_BFACTOR_H
#define VOLUME_CORRECT_BFACTOR_H

#include "core/geometry.h"
#include "core/xmipp_metadata_program.h"

class ProgVolumeCorrectBfactor: public XmippMetadataProgram
{
protected:

    double fit_minres, fit_maxres, apply_maxres;
    double sampling_rate;

    enum class MODES {
        BFACTOR_AUTO = 1,
        BFACTOR_REF = 2,
        BFACTOR_ADHOC = 3,
        ALLPOINTS_REF = 4
    };

    MODES bMode;

    int xsize;

    FileName fn_ref;

    double adhocB;

    FileName fn_fsc;

    void show();
    void defineParams();
    void readParams();
    void processImage(const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut);

public:

    ProgVolumeCorrectBfactor();

    ~ProgVolumeCorrectBfactor()
    { }
    ;

    void make_guinier_plot(MultidimArray< std::complex< double > > &m1,
                           std::vector<fit_point2D> &guinier);

    void apply_bfactor(MultidimArray< std::complex< double > > &FT1,
                       double bfactor);

    void apply_allpoints(MultidimArray< std::complex< double > > &FT1,
                         std::vector<fit_point2D> &guinier_diff);

    void get_snr_weights(std::vector<double> &snr);

    void apply_snr_weights(MultidimArray< std::complex< double > > &FT1,
                           std::vector<double> &snr);

    void write_guinierfile(const FileName& fn_guinier,
                           std::vector<fit_point2D> &guinierin,
                           std::vector<fit_point2D> &guinierweighted,
                           std::vector<fit_point2D> &guiniernew,
                           double intercept,
                           std::vector<fit_point2D> &guinierref);

    void bfactor_correction(MultidimArray< double > &m1, const FileName &fn_guinier);
};
#endif