forward_zernike_volume.h

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/***************************************************************************
 *
 * Authors:    Carlos Oscar             coss@cnb.csic.es
 *             David Herreros Calero    dherreros@cnb.csic.es
 *
 * 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.uam.es'
 ***************************************************************************/

#ifndef _PROG_VOL_DEFORM_SPH
#define _PROG_VOL_DEFORM_SPH

#include <vector>
#include "core/xmipp_program.h"
#include "core/xmipp_image.h"
#include <data/blobs.h>

class ProgForwardZernikeVol: public XmippProgram
{
public:
    FileName fnVolI;

    FileName fnVolR;

    FileName fnVolOut;

    FileName fnMaskR, fnMaskI;

    FileName fnRoot;

    bool analyzeStrain;

    bool optimizeRadius;

    MultidimArray<int> V_maski, V_maskr, V_mask2;

    int L1, L2;

    double Rmax;

public:
    int vecSize;

    Image<double> VI, VR, VR2, VO, VO2, VI_f, Gx, Gy, Gz;

    std::vector<double> absMaxR_vec;

    //Deformation in pixels, sumVI, sumVD
    double deformation, sumVI, sumVD;

    // Regularization
    double lambda;

    // Save output volume
    bool applyTransformation;

    // Save the values of gx, gy and gz for local strain and rotation analysis
    bool saveDeformation;

    // Blob
    struct blobtype blob;
    double blob_r;

    double sigma4;
    // Gaussian projection table
    Matrix1D<double> gaussianProjectionTable;

    // Gaussian projection2 table
    Matrix1D<double> gaussianProjectionTable2;

    // Loop step
    int loop_step;

    // Vector containing the degree of the spherical harmonics
    Matrix1D<double> clnm;

    Matrix1D<int> vL1, vN, vL2, vM;

    //Copy of Optimizer steps
    Matrix1D<double> steps_cp;

    std::vector<double>vec;
    FileName fn_sph;

public:
    void defineParams();

    void readParams();

    void show();

    double distance(double *pclnm);

    void run();

    // /// Copy the coefficients from harmonical depth n-1 vector to harmonical depth n vector
    // void copyvectors(Matrix1D<double> &oldvect,Matrix1D<double> &newvect);

    // /// Determine the positions to be minimize of a vector containing spherical harmonic coefficients
    // void minimizepos(Matrix1D<double> &vectpos, Matrix1D<double> &prevpos);

    void minimizepos(int L1, int l2, Matrix1D<double> &steps);

    // ///Compute the number of spherical harmonics in l=0,1,...,depth
    // void Numsph(Matrix1D<int> &sphD);

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

    void fillVectorTerms(int l1, int l2);

    void computeStrain();

    void writeVector(std::string outPath, Matrix1D<double> v, bool append);

    void splattingAtPos(std::array<double, 3> r, double weight, MultidimArray<double> &mVO1, MultidimArray<double> &mVO2);

    template<bool SAVE_DEFORMATION>
    void deformVolume();

    double splatVal(std::array<double, 3> r, double weight, const MultidimArray<double> &mV);

    std::string readNthLine(int N) const;

    std::vector<double> string2vector(std::string const &s) const;

    void volume2Blobs(MultidimArray<double> &vol, MultidimArray<double> &vol2, const MultidimArray<double> &mV, const MultidimArray<int> &mask);

    void volume2Mask(MultidimArray<double> &vol, double thr);

    void rmsd(MultidimArray<double> vol1, MultidimArray<double> vol2, double &val);
};

#endif