symmetries.cpp File Reference

#include <stdio.h>
#include <limits>
#include <chrono>
#include <random>
#include "symmetries.h"

Include dependency graph for symmetries.cpp:

Go to the source code of this file.

Macros
#define	Symmetrize_Vol(X)
#define	put_inside(j, j_min, j_max, jint)

Functions
void	symmetrizeCrystalVectors (Matrix1D< double > &aint, Matrix1D< double > &bint, Matrix1D< double > &shift, int space_group, int sym_no, const Matrix1D< double > &eprm_aint, const Matrix1D< double > &eprm_bint)
void	symmetrizeCrystalVolume (GridVolume &vol_in, const Matrix1D< double > &eprm_aint, const Matrix1D< double > &eprm_bint, int eprm_space_group, const MultidimArray< int > &mask, int grid_type)
void	symmetry_P2_122 (Image< double > &vol, const SimpleGrid &grid, const Matrix1D< double > &eprm_aint, const Matrix1D< double > &eprm_bint, const MultidimArray< int > &mask, int volume_no, int grid_type)
void	symmetry_P22_12 (Image< double > &vol, const SimpleGrid &grid, const Matrix1D< double > &eprm_aint, const Matrix1D< double > &eprm_bint, const MultidimArray< int > &mask, int volume_no, int grid_type)
void	symmetry_P4 (Image< double > &vol, const SimpleGrid &grid, const Matrix1D< double > &eprm_aint, const Matrix1D< double > &eprm_bint, const MultidimArray< int > &mask, int volume_no, int grid_type)
void	symmetry_P42_12 (Image< double > &vol, const SimpleGrid &grid, const Matrix1D< double > &eprm_aint, const Matrix1D< double > &eprm_bint, const MultidimArray< int > &mask, int volume_no, int grid_type)
void	symmetry_P6 (Image< double > &vol, const SimpleGrid &grid, const Matrix1D< double > &eprm_aint, const Matrix1D< double > &eprm_bint, const MultidimArray< int > &mask, int volume_no, int grid_type)
double	interpolatedElement3DHelical (const MultidimArray< double > &Vin, double x, double y, double z, double zHelical, double sinRotHelical, double cosRotHelical)
double	interpolatedElement3DHelicalInt (const MultidimArray< double > &Vin, int x, int y, int z, double zHelical, double sinRotHelical, double cosRotHelical)
void	symmetry_Helical (MultidimArray< double > &Vout, const MultidimArray< double > &Vin, double zHelical, double rotHelical, double rot0, MultidimArray< int > *mask, bool dihedral, double heightFraction, int Cn)
void	symmetry_HelicalLowRes (MultidimArray< double > &Vout, const MultidimArray< double > &Vin, double zHelical, double rotHelical, double rot0, MultidimArray< int > *mask, double heightFraction)
void	symmetry_Dihedral (MultidimArray< double > &Vout, const MultidimArray< double > &Vin, double rotStep, double zmin, double zmax, double zStep, MultidimArray< int > *mask)

Macro Definition Documentation

put_inside

#define put_inside	(		j,
			j_min,
			j_max,
			jint
	)

Value:

if( (j) < (j_min) ) { (j) = (j) + (jint);}\
    else if( (j) > (j_max) ) { (j) = (j) - (jint);};

Definition at line 360 of file symmetries.cpp.

Symmetrize_Vol

#define Symmetrize_Vol

(

X

)

Value:

{\
        for (size_t i=0; i<vol_in.VolumesNo(); i++)\
            X(vol_in(i),vol_in.grid(i),eprm_aint,eprm_bint,mask,i, \
              grid_type);\
    }

Definition at line 292 of file symmetries.cpp.

Function Documentation

interpolatedElement3DHelical()

double interpolatedElement3DHelical	(	const MultidimArray< double > &	Vin,
		double	x,
		double	y,
		double	z,
		double	zHelical,
		double	sinRotHelical,
		double	cosRotHelical
	)

Definition at line 1598 of file symmetries.cpp.

{
    int x0 = floor(x);
    double fx = x - x0;
    int x1 = x0 + 1;

    int y0 = floor(y);
    double fy = y - y0;
    int y1 = y0 + 1;

    int z0 = floor(z);
    double fz = z - z0;
    int z1 = z0 + 1;

    double d000 = interpolatedElement3DHelicalInt(Vin, x0, y0, z0, zHelical, sinRotHelical, cosRotHelical);
    double d001 = interpolatedElement3DHelicalInt(Vin, x1, y0, z0, zHelical, sinRotHelical, cosRotHelical);
    double d010 = interpolatedElement3DHelicalInt(Vin, x0, y1, z0, zHelical, sinRotHelical, cosRotHelical);
    double d011 = interpolatedElement3DHelicalInt(Vin, x1, y1, z0, zHelical, sinRotHelical, cosRotHelical);
    double d100 = interpolatedElement3DHelicalInt(Vin, x0, y0, z1, zHelical, sinRotHelical, cosRotHelical);
    double d101 = interpolatedElement3DHelicalInt(Vin, x1, y0, z1, zHelical, sinRotHelical, cosRotHelical);
    double d110 = interpolatedElement3DHelicalInt(Vin, x0, y1, z1, zHelical, sinRotHelical, cosRotHelical);
    double d111 = interpolatedElement3DHelicalInt(Vin, x1, y1, z1, zHelical, sinRotHelical, cosRotHelical);

    double dx00 = LIN_INTERP(fx, d000, d001);
    double dx01 = LIN_INTERP(fx, d100, d101);
    double dx10 = LIN_INTERP(fx, d010, d011);
    double dx11 = LIN_INTERP(fx, d110, d111);
    double dxy0 = LIN_INTERP(fy, dx00, dx10);
    double dxy1 = LIN_INTERP(fy, dx01, dx11);

    return LIN_INTERP(fz, dxy0, dxy1);
}

interpolatedElement3DHelicalInt()

double interpolatedElement3DHelicalInt	(	const MultidimArray< double > &	Vin,
		int	x,
		int	y,
		int	z,
		double	zHelical,
		double	sinRotHelical,
		double	cosRotHelical
	)

Definition at line 1577 of file symmetries.cpp.

{
    if (x<STARTINGX(Vin) || x>FINISHINGX(Vin) || y<STARTINGY(Vin) || y>FINISHINGY(Vin))
        return 0.0;
    if (z>=STARTINGZ(Vin) && z<=FINISHINGZ(Vin))
        return A3D_ELEM(Vin,z,y,x);
    else if (z<STARTINGZ(Vin))
    {
        double newx=cosRotHelical*x-sinRotHelical*y;
        double newy=sinRotHelical*x+cosRotHelical*y;
        return interpolatedElement3DHelical(Vin,newx,newy,z+zHelical,zHelical, sinRotHelical, cosRotHelical);
    }
    else
    {
        double newx=cosRotHelical*x+sinRotHelical*y;
        double newy=-sinRotHelical*x+cosRotHelical*y;
        return interpolatedElement3DHelical(Vin,newx,newy,z-zHelical,zHelical, sinRotHelical, cosRotHelical);
    }
}

symmetry_HelicalLowRes()

void symmetry_HelicalLowRes	(	MultidimArray< double > &	Vout,
		const MultidimArray< double > &	Vin,
		double	zHelical,
		double	rotHelical,
		double	rot0,
		MultidimArray< int > *	mask,
		double	heightFraction
	)

Definition at line 1707 of file symmetries.cpp.

{
    MultidimArray<double> Vaux;
    Vout.initZeros(Vin);
    double helicalStep=rotHelical/zHelical;
    Matrix2D<double> A;

    for (int k=0; k<(int)ZSIZE(Vin); ++k)
    {
        double angle=RAD2DEG(helicalStep*k)+rot0;
        rotation3DMatrix(angle,'Z',A,true);
        MAT_ELEM(A,2,3)=-k;
        applyGeometry(xmipp_transformation::LINEAR,Vaux,Vin,A,xmipp_transformation::IS_NOT_INV,false,0.0);
        Vout+=Vaux;

        rotation3DMatrix(-angle,'Z',A,true);
        MAT_ELEM(A,2,3)=k;
        applyGeometry(xmipp_transformation::LINEAR,Vaux,Vin,A,xmipp_transformation::IS_NOT_INV,false,0.0);
        Vout+=Vaux;
    }
    Vout/=2*ZSIZE(Vin);
    if (mask!=nullptr)
        FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(Vout)
        if (!DIRECT_MULTIDIM_ELEM(*mask,n))
            DIRECT_MULTIDIM_ELEM(Vout,n)=0.0;
}