mask.cpp File Reference

#include "mask.h"
#include "core/xmipp_program.h"
#include "core/xmipp_image_generic.h"
#include "core/transformations.h"
#include "data/wavelet.h"
#include "core/xmipp_funcs.h"

Include dependency graph for mask.cpp:

Go to the source code of this file.

Macros
#define	DWTCIRCULAR2D_BLOCK(s, quadrant)
#define	DWTSPHERICALMASK_BLOCK(s, quadrant)
#define	SHOW_MODE
#define	SHOW_CENTER   std::cout << " (x0,y0,z0)=(" << x0 << "," << y0 << "," << z0 << ")\n";

Functions
void	RaisedCosineMask (MultidimArray< double > &mask, double r1, double r2, int mode, double x0, double y0, double z0)
void	RaisedCrownMask (MultidimArray< double > &mask, double r1, double r2, double pix_width, int mode, double x0, double y0, double z0)
void	KaiserMask (MultidimArray< double > &mask, double delta, double Deltaw)
void	SincMask (MultidimArray< double > &mask, double omega, int mode, double x0, double y0, double z0)
void	SincKaiserMask (MultidimArray< double > &mask, double omega, double delta, double Deltaw)
void	BlackmanMask (MultidimArray< double > &mask, int mode, double x0, double y0, double z0)
void	SincBlackmanMask (MultidimArray< double > &mask, double omega, double power_percentage, double x0, double y0, double z0)
void	BinaryCircularMask (MultidimArray< int > &mask, double radius, int mode, double x0, double y0, double z0)
void	BlobCircularMask (MultidimArray< double > &mask, double r1, blobtype blob, int mode, double x0, double y0, double z0)
void	BinaryCrownMask (MultidimArray< int > &mask, double R1, double R2, int mode, double x0, double y0, double z0)
void	BinaryTubeMask (MultidimArray< int > &mask, double R1, double R2, double H, int mode, double x0, double y0, double z0)
void	BlobCrownMask (MultidimArray< double > &mask, double r1, double r2, blobtype blob, int mode, double x0, double y0, double z0)
void	BinaryFrameMask (MultidimArray< int > &mask, int Xrect, int Yrect, int Zrect, int mode, double x0, double y0, double z0)
void	GaussianMask (MultidimArray< double > &mask, double sigma, int mode, double x0, double y0, double z0)
void	BinaryDWTCircularMask2D (MultidimArray< int > &mask, double radius, int smin, int smax, const std::string &quadrant)
void	SeparableSincKaiserMask2D (MultidimArray< double > &mask, double omega, double delta, double Deltaw)
void	mask2D_4neig (MultidimArray< int > &mask, int value, int center)
void	mask2D_8neig (MultidimArray< int > &mask, int value1, int value2, int center)
void	BinaryDWTSphericalMask3D (MultidimArray< int > &mask, double radius, int smin, int smax, const std::string &quadrant)
void	BinaryCylinderMask (MultidimArray< int > &mask, double R, double H, int mode, double x0, double y0, double z0)
void	BinaryConeMask (MultidimArray< int > &mask, double theta, int mode, bool centerOrigin)
void	BinaryWedgeMask (MultidimArray< int > &mask, double theta0, double thetaF, const Matrix2D< double > &A, bool centerOrigin)
void	mask3D_6neig (MultidimArray< int > &mask, int value, int center)
void	mask3D_18neig (MultidimArray< int > &mask, int value1, int value2, int center)
void	mask3D_26neig (MultidimArray< int > &mask, int value1, int value2, int value3, int center)
int	count_with_mask (const MultidimArray< int > &mask, const MultidimArray< std::complex< double > > &m, int mode, double th1, double th2)
void	rangeAdjust_within_mask (const MultidimArray< double > *mask, const MultidimArray< double > &m1, MultidimArray< double > &m2)
Mask Tools
All Mask tools work only in the overlapping area of the given image/volume and the mask in logical coordinates. Ie, if you have a mask defined from -2 to 2 and you apply it to an image defined from 0 to 63 then only those values of the mask between 0 and 2 will be applied. The rest of the image will remain untouched. This region where the mask is active within the overlapping area will be called in this documentation: active area.
void	apply_geo_binary_2D_mask (MultidimArray< int > &mask, const Matrix2D< double > &A)
void	apply_geo_cont_2D_mask (MultidimArray< double > &mask, const Matrix2D< double > &A)

Macro Definition Documentation

DWTCIRCULAR2D_BLOCK

#define DWTCIRCULAR2D_BLOCK	(		s,
			quadrant
	)

Value:

SelectDWTBlock(s, mask, quadrant, \
                   XX(corner1),XX(corner2),YY(corner1),YY(corner2)); \
    V2_PLUS_V2(center,corner1,corner2); \
    V2_BY_CT(center,center,0.5); \
    FOR_ALL_ELEMENTS_IN_ARRAY2D_BETWEEN(corner1,corner2) { \
        double r2=(XX(r)-XX(center))*(XX(r)-XX(center))+ \
                  (YY(r)-YY(center))*(YY(r)-YY(center)); \
        A2D_ELEM(mask,YY(r),XX(r))=(r2<=radius2); \
    }

Definition at line 346 of file mask.cpp.

DWTSPHERICALMASK_BLOCK

#define DWTSPHERICALMASK_BLOCK	(		s,
			quadrant
	)

Value:

SelectDWTBlock(s, mask, quadrant, \
                   XX(corner1),XX(corner2),YY(corner1),YY(corner2), \
                   ZZ(corner1),ZZ(corner2)); \
    V3_PLUS_V3(center,corner1,corner2); \
    V3_BY_CT(center,center,0.5); \
    FOR_ALL_ELEMENTS_IN_ARRAY3D_BETWEEN(corner1,corner2) { \
        double r2=(XX(r)-XX(center))*(XX(r)-XX(center))+ \
                  (YY(r)-YY(center))*(YY(r)-YY(center))+ \
                  (ZZ(r)-ZZ(center))*(ZZ(r)-ZZ(center)); \
        A3D_ELEM(mask,ZZ(r),YY(r),XX(r))=(r2<=radius2); \
    }

Definition at line 431 of file mask.cpp.

SHOW_CENTER

#define SHOW_CENTER   std::cout << " (x0,y0,z0)=(" << x0 << "," << y0 << "," << z0 << ")\n";

SHOW_MODE

#define SHOW_MODE

Value:

if (mode==INNER_MASK) std::cout << "   mode=INNER MASK\n"; \
    else                  std::cout << "   mode=OUTER MASK\n";

Function Documentation

BinaryCylinderMask()

void BinaryCylinderMask	(	MultidimArray< int > &	mask,
		double	R,
		double	H,
		int	mode,
		double	x0,
		double	y0,
		double	z0
	)

Definition at line 471 of file mask.cpp.

{
    mask.initZeros();
    double R2 = R * R;
    double H_2 = H / 2;
    FOR_ALL_ELEMENTS_IN_ARRAY3D(mask)
    {
        double r2 = (i - y0) * (i - y0) + (j - x0) * (j - x0);
        int in_cyilinder = (r2 <= R2 && ABS(k - z0) <= H_2);
        if (in_cyilinder  && mode == INNER_MASK)
            A3D_ELEM(mask, k, i, j) = 1;
        else if (!in_cyilinder && mode == OUTSIDE_MASK)
            A3D_ELEM(mask, k, i, j) = 1;
    }
}

BinaryDWTSphericalMask3D()

void BinaryDWTSphericalMask3D	(	MultidimArray< int > &	mask,
		double	radius,
		int	smin,
		int	smax,
		const std::string &	quadrant
	)

Definition at line 443 of file mask.cpp.

{
    mask.initZeros();
    double radius2 = radius * radius / (4 * (smin + 1));
    for (int s = smin; s <= smax; s++)
    {
        Matrix1D<int> corner1(3);
        Matrix1D<int> corner2(3);
        Matrix1D<int> r(3);
        Matrix1D<double> center(3);
        if (quadrant == "xxx")
        {
            DWTSPHERICALMASK_BLOCK(s, "001");
            DWTSPHERICALMASK_BLOCK(s, "010");
            DWTSPHERICALMASK_BLOCK(s, "011");
            DWTSPHERICALMASK_BLOCK(s, "100");
            DWTSPHERICALMASK_BLOCK(s, "101");
            DWTSPHERICALMASK_BLOCK(s, "110");
            DWTSPHERICALMASK_BLOCK(s, "111");
        }
        else
            DWTSPHERICALMASK_BLOCK(s, quadrant);
        radius2 /= 4;
    }
}

BinaryTubeMask()

void BinaryTubeMask	(	MultidimArray< int > &	mask,
		double	R1,
		double	R2,
		double	H,
		int	mode,
		double	x0,
		double	y0,
		double	z0
	)

Definition at line 261 of file mask.cpp.

{
    mask.initZeros();
    double R12 = R1 * R1;
    double R22 = R2 * R2;
    FOR_ALL_ELEMENTS_IN_ARRAY3D(mask)
    {
        double r2 = (i - y0) * (i - y0) + (j - x0) * (j - x0);
        bool in_tube = (r2 >= R12 && r2 <= R22 && ABS(k)<H);
        if (in_tube  && mode == INNER_MASK)
            A3D_ELEM(mask, k, i, j) = 1;
        else if (!in_tube && mode == OUTSIDE_MASK)
            A3D_ELEM(mask, k, i, j) = 1;
    }
}