volume_align_prog.cpp File Reference

#include "interface/frm.h"
#include <fstream>
#include "core/xmipp_image.h"
#include "data/filters.h"
#include "core/geometry.h"
#include "data/mask.h"
#include "core/xmipp_program.h"
#include "core/transformations.h"

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Classes
class	AlignParams
class	ProgAlignVolumes

Macros
#define	COVARIANCE   1
#define	LEAST_SQUARES   2

Functions
void	applyTransformation (const MultidimArray< double > &V2, MultidimArray< double > &Vaux, double *p, bool wrap)
double	fitness (double *p)
double	wrapperFitness (double *p, void *params)

Macro Definition Documentation

COVARIANCE

#define COVARIANCE   1

Definition at line 39 of file volume_align_prog.cpp.

LEAST_SQUARES

#define LEAST_SQUARES   2

Definition at line 40 of file volume_align_prog.cpp.

Function Documentation

applyTransformation()

void applyTransformation	(	const MultidimArray< double > &	V2,
		MultidimArray< double > &	Vaux,
		double *	p,
		bool	wrap
	)

Definition at line 56 of file volume_align_prog.cpp.

{
    Matrix1D<double> r(3);
    Matrix2D<double> A, Aaux;

    double greyScale = p[0];
    double greyShift = p[1];
    double rot       = p[2];
    double tilt      = p[3];
    double psi       = p[4];
    double scale     = p[5];
    ZZ(r)            = p[6];
    YY(r)            = p[7];
    XX(r)            = p[8];

    Euler_angles2matrix(rot, tilt, psi, A, true);
    translation3DMatrix(r,Aaux);
    A = A * Aaux;
    scale3DMatrix(vectorR3(scale, scale, scale),Aaux);
    A = A * Aaux;

    applyGeometry(xmipp_transformation::LINEAR, Vaux, V2, A, xmipp_transformation::IS_NOT_INV, wrap);
    if (greyScale!=1 || greyShift!=0)
        FOR_ALL_DIRECT_ELEMENTS_IN_MULTIDIMARRAY(Vaux)
        DIRECT_MULTIDIM_ELEM(Vaux,n)=DIRECT_MULTIDIM_ELEM(Vaux,n)*greyScale+greyShift;
}

fitness()

double fitness

(

double *

p

)

Definition at line 88 of file volume_align_prog.cpp.

{
    applyTransformation(params.V2(),params.Vaux(),p, params.wrap);

    // Correlate
    double fit=0.;
    switch (params.alignment_method)
    {
    case COVARIANCE:
                    fit = -correlationIndex(params.V1(), params.Vaux(), params.mask_ptr);
        break;
    case LEAST_SQUARES:
                    fit = rms(params.V1(), params.Vaux(), params.mask_ptr);
        break;
    }
    return fit;
}

wrapperFitness()

double wrapperFitness	(	double *	p,
		void *	params
	)

Definition at line 107 of file volume_align_prog.cpp.

{
    return fitness(p+1);
}