Images

Collaboration diagram for Images:

Modules
	Image Formats
	Extension to Image class

Classes
class	ImageOver
class	Image< T >
struct	ImageFHandler
struct	ImageInfo
struct	ApplyGeoParams
class	ImageBase
	Image base class. More...

Macros
#define	SWAPTRIG   16776960

Enumerations
enum	TransformType {   NoTransform = 0, Standard = 1, Centered = 2, Hermitian = 3,   CentHerm = 4 }
enum	WriteMode {   WRITE_READONLY, WRITE_OVERWRITE, WRITE_REPLACE, WRITE_APPEND,   WRITE_LAST_LABEL, WRITE_READONLY, WRITE_OVERWRITE, WRITE_REPLACE,   WRITE_APPEND, WRITE_LAST_LABEL }
enum	DataMode {   _NONE = -2, HEADER = -1, _HEADER_ALL = 0, DATA = 1,   _DATA_ALL = 2 }
enum	CastWriteMode { CW_CAST, CW_CONVERT, CW_ADJUST, CW_LAST_LABEL }

Variables
const size_t	rw_max_page_size = 4194304
const ApplyGeoParams	DefaultApplyGeoParams

Images Speed-up
#define	VOLMATRIX(V)   ((V).data)
#define	IMGMATRIX(I)   ((I).data)
#define	IMGPIXEL(I, i, j)   A2D_ELEM(((I).data), (i), (j))
#define	DIRECT_IMGPIXEL(I, i, j)   DIRECT_A2D_ELEM(((I).data), (i), (j))
#define	VOLVOXEL(V, k, i, j)   A3D_ELEM(((V).data), (k), (i), (j))
#define	DIRECT_VOLVOXEL(I, k, i, j)   DIRECT_A3D_ELEM(((I).data), (k), (i), (j))

Detailed Description

Macro Definition Documentation

DIRECT_IMGPIXEL

#define DIRECT_IMGPIXEL	(		I,
			i,
			j
	)		DIRECT_A2D_ELEM(((I).data), (i), (j))

Physical pixel access.

The physical pixel access gives you access to a pixel by its physical position and not by its logical one. This access shouldn't be used as a custom, use instead the logical access, but there might be cases in which this access might be interesting. Physical positions start at index 0 in C.

std::cout << "This is the first pixel stored in the Image " <<
    DIRECT_IMGPIXEL(V, 0, 0) << std::endl;

Definition at line 200 of file xmipp_image_base.h.

DIRECT_VOLVOXEL

#define DIRECT_VOLVOXEL	(		I,
			k,
			i,
			j
	)		DIRECT_A3D_ELEM(((I).data), (k), (i), (j))

Physical voxel access.

The physical voxel access gives you access to a voxel by its physical position and not by its logical one. This access shouldn't be used as a custom, use instead the logical access, but there might be cases in which this access might be interesting. Physical positions start at index 0 in C.

std::cout << "This is the first voxel stored in the Volume " <<
    DIRECT_VOLVOXEL(V, 0, 0, 0) << std::endl;

Definition at line 228 of file xmipp_image_base.h.

IMGMATRIX

#define IMGMATRIX

(

I

)

((I).data)

Image Matrix access.

This macro does the same as the normal 2D matrix access but in a faster way as no function call is generated.

IMGMATRIX(V).resize(128, 128);

IMGMATRIX(V2) = IMGMATRIX(V1) + IMGMATRIX(V2);

Definition at line 181 of file xmipp_image_base.h.

IMGPIXEL

#define IMGPIXEL	(		I,
			i,
			j
	)		A2D_ELEM(((I).data), (i), (j))

Pixel access. For fast access to pixel values (and for backwards compatibility of the code)

Definition at line 186 of file xmipp_image_base.h.

SWAPTRIG

#define SWAPTRIG   16776960

Swapping trigger. Threshold file z size above which bytes are swapped.

Definition at line 234 of file xmipp_image_base.h.

VOLMATRIX

#define VOLMATRIX

(

V

)

((V).data)

Volume Matrix access.

This macro does the same as the normal 3D matrix access but in a faster way as no function call is generated.

VOLMATRIX(V).resize(128, 128, 128);

VOLMATRIX(V2) = VOLMATRIX(V1) + VOLMATRIX(V2);

Definition at line 168 of file xmipp_image_base.h.

VOLVOXEL

#define VOLVOXEL	(		V,
			k,
			i,
			j
	)		A3D_ELEM(((V).data), (k), (i), (j))

Voxel access.

This macro does the same as the normal voxel access (remember, logical access) but in a faster way as no function call is generated.

std::cout << "Grey level of voxel (2,-3,-3) of the Volume = " <<
    VOLVOXEL(V, 2, -3, -3) << std::endl;

VOLVOXEL(I, 2, -3, -3) = VOLVOXEL(I, 2, -3, -2);

Definition at line 214 of file xmipp_image_base.h.

Enumeration Type Documentation

CastWriteMode

enum CastWriteMode

Enumerator
CW_CAST
CW_CONVERT
CW_ADJUST
CW_LAST_LABEL

Definition at line 101 of file xmipp_image_base.h.

{
    // prefix needed so extract_image_enums.py script can create the equivalent class for Java
    CW_CAST,       //Only cast the data type
    CW_CONVERT,    //Convert the data from one type to another
    CW_ADJUST,     //Adjust the histogram to fill the gray level range
    CW_LAST_LABEL                       // **** NOTE ****: Do keep this label always at the end
    // it is here for looping purposes
} CastWriteMode;

DataMode

enum DataMode

Data mode This enumerate which data will be read/write from image files We can read/write complete image or only its headers(w/o geometrical information)

Enumerator
_NONE
HEADER
_HEADER_ALL
DATA
_DATA_ALL

Definition at line 88 of file xmipp_image_base.h.

{
    _NONE = -2,  // Nothing to do. Used by ImageGeneric to check the right datatype to be used
    HEADER = -1, //Don't read image data, only info from main header(datatype and dimensions)
    _HEADER_ALL = 0, //Read complete header(main and geo), useful for header_extract and header_assign
    DATA = 1, //Read image data and main header, geometrical transformations will be ignored
    _DATA_ALL = 2  //Read data with complete header(the use of this option is not recommended, all Xmipp
                // programs should read and write geo info through metadatas
}DataMode;

TransformType

enum TransformType

Transform type. This type defines the kind of image.

Enumerator
NoTransform
Standard
Centered
Hermitian
CentHerm

Definition at line 62 of file xmipp_image_base.h.

{
    NoTransform = 0,        // No transform
    Standard = 1,           // Standard transform: origin = (0,0,0)
    Centered = 2,           // Centered transform: origin = (nx/2,ny/2,nz/2)
    Hermitian = 3,          // Hermitian half: origin = (0,0,0)
    CentHerm = 4            // Centered hermitian: origin = (0,ny/2,nz/2)
} TransformType;

WriteMode

enum WriteMode

Write mode This class defines the writing behavior.

Enumerator
WRITE_READONLY
WRITE_OVERWRITE
WRITE_REPLACE
WRITE_APPEND
WRITE_LAST_LABEL
WRITE_READONLY
WRITE_OVERWRITE
WRITE_REPLACE
WRITE_APPEND
WRITE_LAST_LABEL

Definition at line 74 of file xmipp_image_base.h.

{
    WRITE_READONLY,   //only can read the file
    WRITE_OVERWRITE, //forget about the old file and overwrite it
    WRITE_REPLACE,   //replace a particular object by another
    WRITE_APPEND,    //append and object at the end of a stack, so far can not append stacks
    WRITE_LAST_LABEL                       // **** NOTE ****: Do keep this label always at the end
    // it is here for looping purposes
} WriteMode;

Variable Documentation

DefaultApplyGeoParams

const ApplyGeoParams DefaultApplyGeoParams

Definition at line 152 of file xmipp_image_base.h.

rw_max_page_size

const size_t rw_max_page_size = 4194304

Size of the page used to read and write images from/to file

Definition at line 45 of file xmipp_image.h.