angular_continuous_assign2.h

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/***************************************************************************
 *
 * Authors:    Carlos Oscar Sanchez 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_ANGULAR_PREDICT_CONTINOUOS2
#define _PROG_ANGULAR_PREDICT_CONTINUOUS2

#include "core/xmipp_metadata_program.h"
#include "core/multidim_array.h"
#include "core/xmipp_image.h"
#include "data/fourier_filter.h"
#include "data/fourier_projection.h"

class FourierProjector;


constexpr int  CONTCOST_CORR = 0;
constexpr int  CONTCOST_L1 = 1;


class ProgAngularContinuousAssign2: public XmippMetadataProgram
{
public:
    FileName fnVol;
    FileName fnResiduals;
    FileName fnProjections;
    double maxShift;
    double maxScale;
    double maxAngularChange;
    double maxResol;
    double maxDefocusChange;
    double maxA;
    double maxB;
    double Ts;
    int Rmax;
    int pad;
    // Optimize gray
    bool optimizeGrayValues;
    // Optimize shift
    bool optimizeShift;
    // Optimize scale
    bool optimizeScale;
    // Optimize angles
    bool optimizeAngles;
    // Optimize defocus
    bool optimizeDefocus;
    // Ignore CTF
    bool ignoreCTF;
    // Apply transformation to this image
    String originalImageLabel;
    // Phase Flipped
    bool phaseFlipped;
    // Penalization for the average
    // double penalization;
    
    // Force defocusU = defocusV
    bool sameDefocus;

public:
    // Rank (used for MPI version)
    int rank;

    // 2D mask in real space
    MultidimArray<int> mask2D;
    // Inverse of the sum of Mask2D
    double iMask2Dsum;
    // Fourier projector
    FourierProjector *projector;
    // Volume size
    size_t Xdim;
    // Input image
    Image<double> I, Ip, E, Ifiltered, Ifilteredp;
    // Theoretical projection
    Projection P;
    // Filter
    FourierFilter filter;
    // Transformation matrix
    Matrix2D<double> A;
    // Original angles
    double old_rot, old_tilt, old_psi;
    // Original shift
    double old_shiftX, old_shiftY;
    // Original flip
    bool old_flip;
    // Original gray scale
    double old_grayA, old_grayB;
    // Has CTF
    bool hasCTF;
    // Original defocus
    double old_defocusU, old_defocusV, old_defocusAngle;
    // CTF
    CTFDescription ctf;
    // Covariance matrices
    Matrix2D<double> C0, C;
    // Image stddev
    double Istddev;
    // Continuous cost function
    int contCost;
    // Current defoci
    double currentDefocusU, currentDefocusV, currentAngle;
    // CTF image
    MultidimArray<double> *ctfImage;
    std::unique_ptr<MultidimArray<double>> ctfEnvelope;
    // Fourier Transformer
    FourierTransformer fftTransformer;
    // Fourier transforms
    MultidimArray< std::complex<double> > fftE;
public:
    ProgAngularContinuousAssign2();

    ~ProgAngularContinuousAssign2();

    void readParams();

    void show();

    void defineParams();

    void startProcessing();

    void preProcess();

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

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

    void postProcess();
};
#endif