tomo_align_refinement.h

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/***************************************************************************
 *
 * Authors:    Carlos Oscar            coss@cnb.csic.es (2006)
 *
 * 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_PREDICT_TOMOGRAPHY
#define _PROG_ANGULAR_PREDICT_TOMOGRPAHY

#include "core/xmipp_image.h"
#include "core/xmipp_program.h"
#include "core/matrix2d.h"

class AlignmentTomography
{
public:
    double rot;
    double tilt;
    double psi;
    double x;
    double y;
    double corr;
    Matrix2D<double> M;
    FileName fn_img;
    FileName fn_mask;
    
    AlignmentTomography();
};

class ProgTomoAlignRefinement: public XmippProgram
{
public:
    FileName fn_ref;
    FileName fn_sel;
    FileName fn_out;
    double max_rot_change;
    double max_tilt_change;
    double max_psi_change;
    double rot_step;
    double tilt_step;
    double psi_step;
    double max_shift_change;
    double shift_step;
    bool adjustGray;
    bool generateAligned;
public:
    Image<double> V;
    std::vector<AlignmentTomography> list_of_assigned;
public:
    void readParams();

    void show();

    void defineParams();

    void produce_side_info();

    void predict_angles(size_t i, const FileName &fnImgOut);

    void run();
};
#endif