art_crystal.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 _PROG_ART_CRYSTAL_HH
#  define _PROG_ART_CRYSTAL_HH

#include <core/xmipp_image.h>
#include <core/matrix1d.h>
#include <core/matrix2d.h>
#include <core/symmetries.h>

#include "base_art_recons.h"

class CrystalARTRecons: public ARTReconsBase
{
public:
    /* User parameters ...................................................... */
    double a_mag;
    double b_mag;
    double ang_a2b_deg;
    double ang_x2a_deg;
    Matrix1D<double> avox;
    Matrix1D<double> bvox;
    bool fill_space;

    /* Side information ..................................................... */
    Matrix1D<double> a;
    Matrix1D<double> b;
    Matrix1D<double> aint;
    Matrix1D<double> bint;
    Matrix1D<double> ai;
    Matrix1D<double> bi;
    int space_group;
    MultidimArray<int> unit_cell_mask;

public:

    static void defineParams(XmippProgram * program, const char* prefix=nullptr, const char* comment=nullptr);

    void readParams(XmippProgram * program);

    void print(std::ostream &o) const;


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

    void singleStep(GridVolume &vol_in, GridVolume *vol_out,
                    Projection &theo_proj, Projection &read_proj,
                    int sym_no,
                    Projection &diff_proj, Projection &corr_proj, Projection &alig_proj,
                    double &mean_error, int numIMG, double lambda, int act_proj,
                    const FileName &fn_ctf, const MultidimArray<int> *maskPtr,
                    bool refine);

    /* Finish ART iterations.
       Expand output volume to fill space if necessary. */
    void postProcess(GridVolume &vol_basis);

    void applySymmetry(GridVolume &vol_in, GridVolume *vol_out,int grid_type);
};

void computeIntegerLattice(const Matrix1D<double> &a,
                             const Matrix1D<double> &b,
                             double a_mag, double b_mag,
                             double ang_a2b_deg,
                             Matrix1D<double> &aint,
                             Matrix1D<double> &bint,
                             Matrix2D<double> &V,
                             int space_group);

void expandToFillSpace(const BasicARTParameters &prm,
                          const CrystalARTRecons &eprm, GridVolume &vol);


#endif