forward_art_zernike3d_subtomos.h

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/***************************************************************************
 *
 * Authors:    David Herreros Calero dherreros@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_FORWARD_ART_ZERNIKE3D_SUBTOMOS
#define _PROG_FORWARD_ART_ZERNIKE3D_SUBTOMOS

#include <core/xmipp_metadata_program.h>
#include <core/matrix1d.h>
#include <core/xmipp_image.h>
#include <data/fourier_filter.h>
#include <data/fourier_projection.h>
#include <core/xmipp_error.h>
#include <data/blobs.h>


class ProgForwardArtZernike3DSubtomos: public XmippMetadataProgram
{
public:
    FileName fnVolR;
    FileName fnMaskR;
    FileName fnVolO;
    FileName fnOutDir;
    // Metadata with already processed images
    // FileName fnDone;
    int L1, L2;
    Matrix1D<int> vL1, vN, vL2, vM;
    double Ts;
    int RmaxDef;
    // Phase Flipped
    bool phaseFlipped;
    // Ignore CTF
    bool ignoreCTF;
    // Regularization ART
    double lambda;
    // Save each # iter
    int save_iter;
    // Correct CTF
    bool useCTF;
    // Apply Zernike
    bool useZernike;
    // Flag for enable/disabled image
    int flagEnabled;
    // Tilt angles
    double t1, t2;

public:
    bool resume;
    // Number of ART iterations
    int niter;
    // Sort last N projections
    int sort_last_N;
    // 2D and 3D masks in real space
    MultidimArray<int> mask2D;
    // Volume size
    size_t Xdim;
    // Input image
    Image<double> V, Vrefined, Vout, Ifilteredp;
    // INput image
    Image<double> I;
    // Spherical mask
    MultidimArray<int> Vmask;
    // Theoretical projection
    Image<double> P;
    // Weight Image
    Image<double> W;
    // Difference Image
    Image<double> Idiff;
    // Transformation matrix
    Matrix2D<double> A;
    // Original angles
    double rot, tilt, psi;
    // Original shift
    double shiftX, shiftY, shiftZ;
    // Original flip
    bool flip;
    // CTF Check
    bool hasCTF;
    // Original defocus
    double defocusU, defocusV, defocusAngle;
    // CTF
    CTFDescription ctf;
    // CTF filter
    FourierFilter FilterCTF;
    // Vector Size
    int vecSize;
    // Vector containing the degree of the spherical harmonics
    std::vector<double> clnm;
    // Show optimization
    bool showOptimization;
    // Row ids ordered in a orthogonal fashion
    MultidimArray<size_t> ordered_list;
    // Save iter counter
    int current_save_iter;
    // Image counter
    int num_images;
    // Current ART iteration
    int current_iter;
    // Volume dimensions
    int initX, endX, initY, endY, initZ, endZ;
    // Blob
    int loop_step;
    struct blobtype blob;
    double blob_r;
    double sigma, sigma4;
    // Gaussian projection table
    MultidimArray<double> gaussian3d, gaussian_mw;
    // Fourier transformer 
    FourierTransformer transformer;
public:
    enum class Mode { Proj, Vol };

    ProgForwardArtZernike3DSubtomos();

    ~ProgForwardArtZernike3DSubtomos();

    void readParams();

    void show();

    void defineParams();

    void preProcess();

    // virtual void createWorkFiles();

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

    void numCoefficients(int l1, int l2, int &vecSize);

    void fillVectorTerms(int l1, int l2, Matrix1D<int> &vL1, Matrix1D<int> &vN, 
                         Matrix1D<int> &vL2, Matrix1D<int> &vM);

    void deformVol(MultidimArray<double> &mP, MultidimArray<double> &mW,
                   const MultidimArray<double> &mV,
                   double rot, double tilt, double psi);
    
    void recoverVol();
    virtual void finishProcessing();

    void applyMissingWedge(MultidimArray<double> &mV);

    // void updateCTFImage(double defocusU, double defocusV, double angle);

  private:
    enum class Direction { Forward, Backward };

    // ART algorithm
    template <Direction DIRECTION>
    void artModel();

    // Apply Zernike codeformation
    template<bool USESZERNIKE, Direction DIRECTION>
    void zernikeModel();

    // Spaltting at position r
    void splattingAtPos(std::array<double, 3> r, double weight, 
                        MultidimArray<double> &mP, MultidimArray<double> &mW, 
                        MultidimArray<double> &mV);

    void updateVoxel(std::array<double, 3> r, double &voxel, MultidimArray<double> &mV);

    // virtual void checkPoint();

    virtual void run();

    // Sort images in an orthogonal fashion
    void sortOrthogonal();

};
#endif