project.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_PROJECTION_HH
#define _PROG_PROJECTION_HH

#include <core/xmipp_funcs.h>
#include <core/metadata_vec.h>
#include <data/projection.h>
#include <core/xmipp_program.h>
#include <data/pdb.h>

#include <data/phantom.h>
#include "project_crystal.h"
#include <data/ctf.h>

enum projectionType {REALSPACE, SHEARS, FOURIER};
/* Projection Program Parameters ------------------------------------------- */
class ProgProject: public XmippProgram
{
public:
    FileName fn_proj_param;
    FileName  fnPhantom;
    FileName  fnOut;
    FileName fn_crystal;
    FileName fn_sym;
    int projSize;
    double samplingRate;
    double highTs;
    bool only_create_angles;
    bool singleProjection;
    double rotSingle;
    double tiltSingle;
    double psiSingle;
    double xShift;
    double yShift;
    projectionType projType;
    double paddFactor;
    double maxFrequency;
    int BSplineDeg;

public:
    void readParams();

    void defineParams();

    void run();
};

/* Angular range ----------------------------------------------------------- */
struct Angle_range
{
    double    ang0;
    double    angF;
    int      samples;

#define ANGLE_RANGE_DETERMINISTIC 0
#define ANGLE_RANGE_RANDOM_GROUPS 1
#define ANGLE_RANGE_RANDOM        2
#define ANGLE_EVENLY              3

    int      randomness;
    double    Navg;
    double    Ndev;
};

/* Projection parameters --------------------------------------------------- */
class ParametersProjection
{
public:
    int      proj_Xdim;
    int      proj_Ydim;

    int tell;

    bool enable_angle_range;
    Angle_range rot_range;
    Angle_range tilt_range;
    Angle_range psi_range;

    //Do phase flip
    bool doPhaseFlip;
    //Apply shift
    bool applyShift;
    //Do CTF correction
    bool doCTFCorrection;

    FileName fn_angle;

    double    Npixel_avg;
    double    Npixel_dev;

    double    Ncenter_avg;
    double    Ncenter_dev;
public:

    ParametersProjection();
    void from_prog_params(const ProgProject &prog_prm);

    void read(const FileName &fn_proj_param);
};

class PROJECT_Side_Info
{
public:
    MetaDataVec    DF;
    enum PhantomType {VOXEL, XMIPP, PDB};
    PhantomType    phantomMode;
    Image<double>  phantomVol;
    Phantom        phantomDescr;
    PDBPhantom     phantomPDB;
    AtomInterpolator interpolator;
    double paddFactor;
    double maxFrequency;
    int BSplineDeg;
    bool doCrystal;

public:
    void produce_Side_Info(ParametersProjection &prm,
                           ProgProject &prog_prm);
};

/* Assigning angles -------------------------------------------------------- */
int PROJECT_Assign_angles(MetaData &DF, const ParametersProjection &prm);

/* Effectively project ----------------------------------------------------- */
int PROJECT_Effectively_project(const FileName &fnOut,
                                bool singleProjection,
                                int projType,
                                const ParametersProjection &prm,
                                PROJECT_Side_Info &side,
                                const Crystal_Projection_Parameters &prm_crystal,
                                Projection &proj, MetaData &SF);

/* Main routine ------------------------------------------------------------ */
int ROUT_project(ProgProject &prm, Projection &proj, MetaData &SF);
#endif