symmetrize (Symmetrize a volume or image)

Collaboration diagram for symmetrize (Symmetrize a volume or image):

Classes
class	ProgSymmetrize
	Symmetrize Parameters. More...

Functions
void	symmetrizeVolume (const SymList &SL, const MultidimArray< double > &V_in, MultidimArray< double > &V_out, int spline=xmipp_transformation::BSPLINE3, bool wrap=xmipp_transformation::WRAP, bool do_outside_avg=false, bool sum=false, bool helical=false, bool dihedral=false, bool helicalDihedral=false, double rotHelical=0.0, double rotPhaseHelical=0.0, double zHelical=0.0, double heightFraction=0.95, const MultidimArray< double > *mask=nullptr, int Cn=1)
void	symmetrizeImage (int symorder, const MultidimArray< double > &I_in, MultidimArray< double > &I_out, int spline=xmipp_transformation::BSPLINE3, bool wrap=xmipp_transformation::WRAP, bool do_outside_avg=false, bool sum=false)

Detailed Description

Function Documentation

symmetrizeImage()

void symmetrizeImage	(	int	symorder,
		const MultidimArray< double > &	I_in,
		MultidimArray< double > &	I_out,
		int	spline = xmipp_transformation::BSPLINE3,
		bool	wrap = xmipp_transformation::WRAP,
		bool	do_outside_avg = false,
		bool	sum = false
	)

Symmetrize image.

symmetrizeVolume()

void symmetrizeVolume	(	const SymList &	SL,
		const MultidimArray< double > &	V_in,
		MultidimArray< double > &	V_out,
		int	spline = xmipp_transformation::BSPLINE3,
		bool	wrap = xmipp_transformation::WRAP,
		bool	do_outside_avg = false,
		bool	sum = false,
		bool	helical = false,
		bool	dihedral = false,
		bool	helicalDihedral = false,
		double	rotHelical = 0.0,
		double	rotPhaseHelical = 0.0,
		double	zHelical = 0.0,
		double	heightFraction = 0.95,
		const MultidimArray< double > *	mask = nullptr,
		int	Cn = 1
	)

Symmetrize volume.

Definition at line 117 of file symmetrize.cpp.

{
    Matrix2D<double> L(4, 4), R(4, 4); // A matrix from the list
    MultidimArray<double> V_aux;
    Matrix1D<double> sh(3);
    double avg = 0.;

    if (do_outside_avg)
    {
        MultidimArray<int> mask1;
        mask1.resizeNoCopy(V_in);
        mask1.setXmippOrigin();
        size_t rad = XMIPP_MIN(XSIZE(V_in), YSIZE(V_in));
        rad = XMIPP_MIN(rad, ZSIZE(V_in));
        BinaryCircularMask(mask1, rad / 2, OUTSIDE_MASK);
        double dum;
        computeStats_within_binary_mask(mask1, V_in, dum, dum, avg, dum);
    }
    V_out = V_in;

    if (!helical && !dihedral && !helicalDihedral)
    {
        MultidimArray<double> Bcoeffs;
        MultidimArray<double> *BcoeffsPtr=nullptr;
        if (spline==3)
        {
            produceSplineCoefficients(xmipp_transformation::BSPLINE3, Bcoeffs, V_in);
            BcoeffsPtr=&Bcoeffs;
        }
        for (int i = 0; i < SL.symsNo(); i++)
        {
            SL.getMatrices(i, L, R);
            /*FIXME: I do not think this make sense since V_aux is empty. ROB
               SL.getShift(i, sh);
               R(3, 0) = sh(0) * XSIZE(V_aux);
               R(3, 1) = sh(1) * YSIZE(V_aux);
               R(3, 2) = sh(2) * ZSIZE(V_aux);
            */
            applyGeometry(spline, V_aux, V_in, R.transpose(), xmipp_transformation::IS_NOT_INV, wrap, avg, BcoeffsPtr);

            if ( mask==nullptr)
                arrayByArray(V_out, V_aux, V_out, '+');
            else               // op1, op2 ,  result
                selfArrayByArrayMask(V_in, V_aux, V_out, '+', mask);
        }

        if (!sum)
            arrayByScalar(V_out, 1.0/(SL.symsNo() + 1.0f), V_out, '*');
    }
    else if (helical)
        symmetry_Helical(V_out,V_in,zHelical,rotHelical,rotPhaseHelical,nullptr,false,heightFraction,Cn);
    else if (helicalDihedral)
    {
        symmetry_Helical(V_out,V_in,zHelical,rotHelical,rotPhaseHelical,nullptr,true,heightFraction,Cn);
        MultidimArray<double> Vrotated;
        rotate(spline,Vrotated,V_out,180.0,'X',xmipp_transformation::WRAP);
        V_out+=Vrotated;
        V_out*=0.5;
    }
    else if (dihedral)
    {
        auto zmax=(int)(0.1*ZSIZE(V_in));
        symmetry_Dihedral(V_out,V_in,1,-zmax,zmax,0.5);
    }
}