project_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_PROJECT_CRYSTAL_HH
#define _PROG_PROJECT_CRYSTAL_HH

class ParametersProjection;
class PROJECT_Side_Info;
class Crystal_Projection_Parameters;

#include "project.h"

/* Crystal Projection parameters ------------------------------------------- */
class Crystal_Projection_Parameters
{
public:
    int crystal_Xdim;
    int crystal_Ydim;
    bool orthogonal;
    Matrix1D<double> a;
    Matrix1D<double> b;
    double    Nshift_avg;
    double    Nshift_dev;
    double    disappearing_th;
    FileName fn_shift;
    MetaDataVec DF_shift;
    bool     DF_shift_bool;

public:
    Crystal_Projection_Parameters();

    void read(const FileName &fn_crystal, double scale = 1.0);

    void write(const FileName &fn_crystal);
};

/* Project as crystal ------------------------------------------------------ */
void project_crystal(Phantom &phantom, Projection &P,
                     const ParametersProjection &prm,
                     PROJECT_Side_Info &side, const Crystal_Projection_Parameters &prm_crystal,
                     float rot, float tilt, float psi);

void find_crystal_limits(
    const Matrix1D<double> &proj_corner1, const Matrix1D<double> &proj_corner2,
    const Matrix1D<double> &corner1, const Matrix1D<double> &corner2,
    const Matrix1D<double> &a, const Matrix1D<double> &b,
    int &iamin, int &iamax, int &ibmin, int &ibmax);

void move_following_spiral(Matrix1D<double> &r, const MultidimArray<int> &visited);

void fill_cell_positions(Projection &P,
                         Matrix1D<double> &aproj,   Matrix1D<double> &bproj,
                         Matrix1D<double> &aprojd,  Matrix1D<double> &bprojd,
                         Matrix1D<double> &corner1, Matrix1D<double> &corner2,
                         const Crystal_Projection_Parameters &prm_crystal,
                         MultidimArray<double> &cell_shiftX, MultidimArray<double> &cell_shiftY,
                         MultidimArray<double> &cell_shiftZ,
                         MultidimArray<int> &cell_inside,
                         MultidimArray<double> &exp_shifts_matrix_X,
                         MultidimArray<double> &exp_shifts_matrix_Y,
                         MultidimArray<double> &exp_shifts_matrix_Z);
void init_shift_matrix(const Crystal_Projection_Parameters &prm_crystal,
                       MultidimArray<int>    &cell_inside,
                       MultidimArray<double> &exp_shifts_matrix_X,
                       MultidimArray<double> &exp_shifts_matrix_Y,
                       MultidimArray<double> &exp_shifts_matrix_Z,
                       MultidimArray<double> &exp_normal_shifts_matrix_X,
                       MultidimArray<double> &exp_normal_shifts_matrix_Y,
                       MultidimArray<double> &exp_normal_shifts_matrix_Z,
                       double param_file_scale);

#endif