common_lines.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_COMMONLINES_HH
#define _PROG_COMMONLINES_HH

#include "core/matrix1d.h"
#include "core/matrix2d.h"
#include "core/metadata_vec.h"
#include "core/xmipp_program.h"

template<typename T>
class MultidimArray;

/* Parameters -------------------------------------------------------------- */
class CommonLine
{
public:
    double angi=0.0;
    double angj=0.0;
    double distanceij=-1;
    int jmax=0;
    double percentile=-1;
};

class ProgCommonLine: public XmippProgram
{
public:
    FileName        fn_sel;
    FileName        fn_out;
    String          outputStyle;
    bool scaleDistance;
    double outlierFraction;
    double          lpf;
    double          hpf;
    double          stepAng;

    double          mem;
    int             Nthr;
    int             Nmpi;
    int rank;
public:
    ProgCommonLine(): rank(0) {};

    void readParams();

    void defineParams();

    void produceSideInfo();

    void processBlock(int i, int j);

    void getAndPrepareBlock(int i,
        std::vector< MultidimArray<std::complex<double> > > &blockRTFs,
        std::vector<MultidimArray<double> > &blockRTs);

    void show();

    void qualifyCommonLines();

    void solveForShifts();

    void writeResults();
    
    void run();
public:
    // Block size
    int Nblock;

    // Input selfile
    MetaDataVec SF;

    // Number of images
    int Nimg;

    // Xdim size of the images
    size_t Xdim;

    // Common line matrix
    std::vector<CommonLine> CLmatrix;

    // Estimated shifts
    Matrix1D<double> shift;
};

#define POW2(x) (x*x)


class CommonLineInfo
{
public:
    size_t nRays; //Number of rays in Fourier space
    int k[2]; //image projection indexes;
    int idx[2]; //commonlines indexes in k1 and k2;
    DVector vector; //direction vector

    CommonLineInfo(int n, int k1=0, int k2=0)
    {
        nRays = n;
        setImages(k1, k2);
        idx[0] = idx[1] = 0;
        vector.initZeros(3);
    }

    int getImage(int i)
    {
        return k[i];
    }

    int getIndex(int i)
    {
        return idx[i];
    }

    void setImages(int k1, int k2)
    {
        k[0] = k1;
        k[1] = k2;
    }

    void setIndex(int i, double theta)
    {
        idx[i] = ROUND(theta/TWOPI * nRays) % nRays;
    }
}
;//class CommonLineInfo

void randomQuaternions(int k, DMatrix &qArray);

void saveMatrix(const char *fn, DMatrix &array);

void quaternionToMatrix(const DVector &q, DMatrix &rotMatrix);

void quaternionCommonLines(const DMatrix &quaternions, CommonLineInfo &clInfo);

void commonlineMatrixCheat(const DMatrix &quaternions, size_t nRays,
                           DMatrix &clMatrix, DMatrix &clCorr);

void anglesRotationMatrix(size_t nRays, int i, int j, DMatrix &U);

constexpr signed int  SMALL_TRIANGLE = -101;
int tripletRotationMatrix(const DMatrix &clMatrix, size_t nRays, int k1, int k2, int k3, DMatrix &R);

void computeSyncMatrix(const DMatrix &clMatrix, size_t nRays, DMatrix &sMatrix);

void rotationsFromSyncMatrix(const DMatrix &sMatrix);




#endif