symmetries.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'
 ***************************************************************************/
/* ------------------------------------------------------------------------- */
/* SYMMETRIES                                                                */
/* ------------------------------------------------------------------------- */
#ifndef _CORE_SYMMETRIES_HH
#define _CORE_SYMMETRIES_HH

#include "matrix1d.h"
#include "matrix2d.h"
#include "xmipp_funcs.h"
#include "args.h"
#include "transformations.h"
#include "metadata_base.h"
#include "metadata_row_base.h"

//define the  crystallographic groups
//symmetry matices from http://cci.lbl.gov/asu_gallery/
#define sym_undefined    -1
#define sym_P1            1
#define sym_P2            3//c-axis, b-axis
#define sym_P2_1          4
#define sym_C2           12
#define sym_P222         16
#define sym_P2_122       17
#define sym_P22_12       1717
//#define sym_P22_12       17
#define sym_P22_12_1     18
#define sym_P4           75
#define sym_P422         89
#define sym_P42_12       90
#define sym_P3          143
#define sym_P312        150
#define sym_P6          168
#define sym_P622        177
// This constant is obsolete and should be revised with the use of
// matrix euality accuracy
#define SYM_ACCURACY 1e-6
//point group symmetries
#define pg_CI  200
#define pg_CS  201
#define pg_CN  202
#define pg_CNV 203
#define pg_CNH 204
#define pg_SN  205
#define pg_DN  206
#define pg_DNV 207
#define pg_DNH 208
#define pg_T   209
#define pg_TD  210
#define pg_TH  211
#define pg_O   212
#define pg_OH  213
#define pg_I   214  //default xmipp icosahedaral symmetry
#define pg_IH  215

#define pg_I1   216 //no crowther 222
#define pg_I2   217 //crowther 222-> default in xmipp
#define pg_I3   218 //52 as used by spider
#define pg_I4   219 //another 52
#define pg_I5   220 //another another 52 (used by EMBL-matfb)

#define pg_I1H  221 //no crowther 222, + mirror plane
#define pg_I2H  222 //crowther 222-> default in xmipp+ mirror plane
#define pg_I3H  223 //52 as used by spider+ mirror plane
#define pg_I4H  224 //another 52+ mirror plane
#define pg_I5H  225 //another another 52 (used by EMBL-matfb)+ mirror plane

#define SYMINDEX(SL, sym_no, i, numIMG) \
    numIMG+SL.__L.mdimy/4*i+sym_no

class SymList
{
private:
    // Crystallographic space group. This is only a guess based on angles.
    // No check on vectors magnitude is made
    int  space_group;
public:
    // L and R matrices
    Matrix2D<double> __L, __R;
    Matrix2D<double> __shift;  // It is used for crystallographic symmetries
    Matrix1D<int>    __chain_length;

    // As the symmetry elements form a subgroup, this is the number of
    // true symmetry elements belonging to the list, the rest of
    // the list are simply the elements to fill the subgroup
    int true_symNo;

    // Number of Axis, mirrors, ...
    int              __sym_elements;

public:
    SymList()
    {
        __sym_elements = true_symNo = space_group = 0;
    }

    SymList(const FileName& fn_sym, double accuracy = SYM_ACCURACY)
    {
        readSymmetryFile(fn_sym, accuracy);
    }

    bool isSymmetryGroup(FileName fn_sym, int &pgGroup, int &pgOrder);

    void fillSymmetryClass(const FileName &symmetry, int pgGroup, int pgOrder,
                             std::vector<std::string> &fileContent);

    void getMatrices(int i, Matrix2D<double> &L, Matrix2D<double> &R,
                      bool homogeneous=true) const;

    void setMatrices(int i, const Matrix2D<double> &L,
                      const Matrix2D<double> &R);

    void getShift(int i, Matrix1D<double> &shift) const;

    void setShift(int i, const Matrix1D<double> &shift);

    void addShift(const Matrix1D<double> &shift);

    int readSymmetryFile(FileName fn_sym, double accuracy = SYM_ACCURACY);

    void addMatrices(const Matrix2D<double> &L, const Matrix2D<double> &R,
                      int chain_length);

    void computeSubgroup(double accuracy = SYM_ACCURACY);

    int symsNo() const
    {
        return MAT_YSIZE(__L) / 4;
    }
    int spaceGroup() const
    {
        return space_group;
    }
    int trueSymsNo() const
    {
        return true_symNo;
    }

    int  crystallographicSpaceGroup(double mag_a,
                                      double mag_b,
                                      double ang_a2b_deg) const;

    double nonRedundantProjectionSphere(int pgGroup, int pgOrder);

    double computeDistance(double rot1, double tilt1,
                           double psi1, double &rot2, double &tilt2, double &psi2,
                           bool projdir_mode, bool check_mirrors, bool object_rotation=false,
                           bool write_mirrors = true);
    void computeDistance(MetaData &md,
                           bool projdir_mode, bool check_mirrors,
                           bool object_rotation=false);
    void breakSymmetry(double rot1, double tilt1, double psi1,
                                  double &rot2, double &tilt2, double &psi2
                                  );

};
#endif