#include "blobs.h"
#include "core/histogram.h"
#include "core/xmipp_metadata_program.h"

Include dependency graph for mask.h:

Classes
class	MultidimArray< T >

class	Matrix2D< T >

class	Mask

class	ProgMask

Macros
#define	NO_MASK 0

#define	BINARY_CIRCULAR_MASK 1

#define	BINARY_CROWN_MASK 2

#define	BINARY_CYLINDER_MASK 3

#define	BINARY_FRAME_MASK 4

#define	GAUSSIAN_MASK 5

#define	RAISED_COSINE_MASK 6

#define	BLACKMAN_MASK 7

#define	SINC_MASK 8

#define	SINC_BLACKMAN_MASK 9

#define	READ_BINARY_MASK 10

#define	READ_REAL_MASK 11

#define	RAISED_CROWN_MASK 12

#define	BINARY_DWT_CIRCULAR_MASK 13

#define	BINARY_DWT_SPHERICAL_MASK 14

#define	BINARY_CONE_MASK 15

#define	BINARY_WEDGE_MASK 16

#define	BLOB_CIRCULAR_MASK 17

#define	BLOB_CROWN_MASK 18

#define	BINARY_TUBE 19

#define	INT_MASK 1

#define	DOUBLE_MASK 2

#define	ALL_KINDS INT_MASK \| DOUBLE_MASK

#define	COMPUTESTATS(type) computeStats_within_binary_mask(mask,((MultidimArray<type>)m.im),min_val,max_val,avg,stddev);

Functions
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)

Actual masks
void	RaisedCosineMask (MultidimArray< double > &mask, double r1, double r2, int mode=INNER_MASK, double x0=0, double y0=0, double z0=0)

void	RaisedCrownMask (MultidimArray< double > &mask, double r1, double r2, double pix_width, int mode=INNER_MASK, double x0=0, double y0=0, double z0=0)

void	KaiserMask (MultidimArray< double > &mask, double delta=0.01, double Deltaw=1.0/12.0)

void	SincMask (MultidimArray< double > &mask, double omega, int mode=INNER_MASK, double x0=0, double y0=0, double z0=0)

void	SincKaiserMask (MultidimArray< double > &mask, double omega, double delta=0.01, double Deltaw=1.0/12.0)

void	BlackmanMask (MultidimArray< double > &mask, int mode=INNER_MASK, double x0=0, double y0=0, double z0=0)

void	SincBlackmanMask (MultidimArray< double > &mask, double omega, double power_percentage, double x0=0, double y0=0, double z0=0)

void	BinaryCircularMask (MultidimArray< int > &mask, double radius, int mode=INNER_MASK, double x0=0, double y0=0, double z0=0)

void	BlobCircularMask (MultidimArray< double > &mask, double r1, blobtype blob, int mode, double x0=0, double y0=0, double z0=0)

void	BinaryCrownMask (MultidimArray< int > &mask, double R1, double R2, int mode=INNER_MASK, double x0=0, double y0=0, double z0=0)

void	BlobCrownMask (MultidimArray< double > &mask, double r1, double r2, blobtype blob, int mode, double x0=0, double y0=0, double z0=0)

void	GaussianMask (MultidimArray< double > &mask, double sigma, int mode=INNER_MASK, double x0=0, double y0=0, double z0=0)

void	BinaryDWTCircularMask2D (MultidimArray< int > &mask, double radius, int smin, int smax, const std::string &quadrant)

void	SeparableSincKaiserMask2D (MultidimArray< double > &mask, double omega, double delta=0.01, double Deltaw=1.0/12.0)

void	mask2D_4neig (MultidimArray< int > &mask, int value=1, int center=NO_ACTIVATE)

void	mask2D_8neig (MultidimArray< int > &mask, int value1=1, int value2=1, int center=NO_ACTIVATE)

void	BinaryDWTSphericalMask2D (MultidimArray< int > &mask, double radius, int smin, int smax, const std::string &quadrant)

void	BinaryCylinderMask (MultidimArray< int > &mask, double R, double H, int mode=INNER_MASK, double x0=0, double y0=0, int z0=0)

void	BinaryFrameMask (MultidimArray< int > &mask, int Xrect, int Yrect, int Zrect, int mode=INNER_MASK, double x0=0, double y0=0, double z0=0)

void	BinaryConeMask (MultidimArray< int > &mask, double theta, int mode=INNER_MASK, bool centerOrigin=false)

void	BinaryWedgeMask (MultidimArray< int > &mask, double theta0, double thetaF, const Matrix2D< double > &A, bool centerOrigin=false)

void	mask3D_6neig (MultidimArray< int > &mask, int value=1, int center=NO_ACTIVATE)

void	mask3D_18neig (MultidimArray< int > &mask, int value1=1, int value2=1, int center=NO_ACTIVATE)

void	mask3D_26neig (MultidimArray< int > &mask, int value1=1, int value2=1, int value3=1, int center=NO_ACTIVATE)

Variables
constexpr int	INNER_MASK = 1

constexpr int	OUTSIDE_MASK = 2

constexpr int	NO_ACTIVATE = 0

constexpr int	ACTIVATE = 1

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.
#define	count_with_mask_above(mask, m, th) count_with_mask(mask, m, COUNT_ABOVE, th, 0);

#define	count_with_mask_below(mask, m, th) count_with_mask(mask, m, COUNT_BELOW, th, 0);

#define	count_with_mask_between(mask, m, th1, th2) count_with_mask(mask, m, COUNT_BETWEEN, th1, th2);

constexpr int	COUNT_ABOVE = 1

constexpr int	COUNT_BELOW = 2

constexpr int	COUNT_BETWEEN = 3

template<typename T1 , typename T >
void	computeStats_within_binary_mask (const MultidimArray< T1 > &mask, const MultidimArray< T > &m, double &min_val, double &max_val, double &avg, double &stddev)

void	computeStats_within_binary_mask (const MultidimArray< int > &mask, const MultidimArrayGeneric &m, double &min_val, double &max_val, double &avg, double &stddev)

template<typename T >
void	apply_binary_mask (const MultidimArray< int > &mask, const MultidimArray< T > &m_in, MultidimArray< T > &m_out, T subs_val=(T) 0)

template<typename T >
void	apply_cont_mask (const MultidimArray< double > &mask, const MultidimArray< T > &m_in, MultidimArray< T > &m_out)

template<typename T >
void	compute_hist_within_binary_mask (const MultidimArray< int > &mask, MultidimArray< T > &v, Histogram1D &hist, int no_steps)

template<typename T >
void	compute_hist_within_binary_mask (const MultidimArray< int > &mask, const MultidimArray< T > &v, Histogram1D &hist, T min, T max, int no_steps)

template<typename T >
int	count_with_mask (const MultidimArray< int > &mask, const MultidimArray< T > &m, int mode, double th1, double th2)

int	count_with_mask (const MultidimArray< int > &mask, const MultidimArray< std::complex< double > > &m, int mode, double th1, double th2)

template<typename T >
void	invert_binary_mask (MultidimArray< T > &mask)

void	rangeAdjust_within_mask (const MultidimArray< double > *mask, const MultidimArray< double > &m1, MultidimArray< double > &m2)

Macro Definition Documentation

◆ ALL_KINDS

#define ALL_KINDS INT_MASK | DOUBLE_MASK

Definition at line 387 of file mask.h.

◆ BINARY_CIRCULAR_MASK

#define BINARY_CIRCULAR_MASK 1

Definition at line 365 of file mask.h.

◆ BINARY_CONE_MASK

#define BINARY_CONE_MASK 15

Definition at line 379 of file mask.h.

◆ BINARY_CROWN_MASK

#define BINARY_CROWN_MASK 2

Definition at line 366 of file mask.h.

◆ BINARY_CYLINDER_MASK

#define BINARY_CYLINDER_MASK 3

Definition at line 367 of file mask.h.

◆ BINARY_DWT_CIRCULAR_MASK

#define BINARY_DWT_CIRCULAR_MASK 13

Definition at line 377 of file mask.h.

◆ BINARY_DWT_SPHERICAL_MASK

#define BINARY_DWT_SPHERICAL_MASK 14

Definition at line 378 of file mask.h.

◆ BINARY_FRAME_MASK

#define BINARY_FRAME_MASK 4

Definition at line 368 of file mask.h.

◆ BINARY_TUBE

#define BINARY_TUBE 19

Definition at line 383 of file mask.h.

◆ BINARY_WEDGE_MASK

#define BINARY_WEDGE_MASK 16

Definition at line 380 of file mask.h.

◆ BLACKMAN_MASK

#define BLACKMAN_MASK 7

Definition at line 371 of file mask.h.

◆ BLOB_CIRCULAR_MASK

#define BLOB_CIRCULAR_MASK 17

Definition at line 381 of file mask.h.

◆ BLOB_CROWN_MASK

#define BLOB_CROWN_MASK 18

Definition at line 382 of file mask.h.

◆ COMPUTESTATS

#define COMPUTESTATS ( type ) computeStats_within_binary_mask(mask,*((MultidimArray<type>*)m.im),min_val,max_val,avg,stddev);

◆ DOUBLE_MASK

#define DOUBLE_MASK 2

Definition at line 386 of file mask.h.

◆ GAUSSIAN_MASK

#define GAUSSIAN_MASK 5

Definition at line 369 of file mask.h.

◆ INT_MASK

#define INT_MASK 1

Definition at line 385 of file mask.h.

◆ NO_MASK

#define NO_MASK 0

Definition at line 364 of file mask.h.

◆ RAISED_COSINE_MASK

#define RAISED_COSINE_MASK 6

Definition at line 370 of file mask.h.

◆ RAISED_CROWN_MASK

#define RAISED_CROWN_MASK 12

Definition at line 376 of file mask.h.

◆ READ_BINARY_MASK

#define READ_BINARY_MASK 10

Definition at line 374 of file mask.h.

◆ READ_REAL_MASK

#define READ_REAL_MASK 11

Definition at line 375 of file mask.h.

◆ SINC_BLACKMAN_MASK

#define SINC_BLACKMAN_MASK 9

Definition at line 373 of file mask.h.

◆ SINC_MASK

#define SINC_MASK 8

Definition at line 372 of file mask.h.

Classes

Macros

Functions

Variables

Mask Tools