DSN6 MAP is composed of a series of records which are all 512 bytes long. More...

#include <omapio.h>

Inheritance diagram for EMAN::OmapIO:

Collaboration diagram for EMAN::OmapIO:

[legend]

Classes
struct	OmapHeader
	The data in the header is composed of 256 short integers. More...

Public Member Functions
	OmapIO (const string &fname, IOMode rw_mode=READ_ONLY)

	~OmapIO ()

Public Member Functions inherited from EMAN::ImageIO
	ImageIO (const string &fname, IOMode rw)

virtual	~ImageIO ()

virtual int	read_header (Dict &dict, int image_index=0, const Region *area=0, bool is_3d=false)=0
	Read the header from an image. More...

virtual int	write_header (const Dict &dict, int image_index=0, const Region *area=0, EMUtil::EMDataType filestoragetype=EMUtil::EM_FLOAT, bool use_host_endian=true)=0
	Write a header to an image. More...

virtual int	read_data (float data, int image_index=0, const Region area=0, bool is_3d=false)=0
	Read the data from an image. More...

virtual int	read_data_8bit (unsigned char data, int image_index=0, const Region area=0, bool is_3d=false, float minval=0.0f, float maxval=0.0f)
	Read the data from an image as an 8 bit array, regardless of format. More...

virtual int	write_data (float data, int image_index=0, const Region area=0, EMUtil::EMDataType filestoragetype=EMUtil::EM_FLOAT, bool use_host_endian=true)=0
	Write data to an image. More...

virtual int	read_ctf (Ctf &ctf, int image_index=0)
	Read CTF data from this image. More...

virtual void	write_ctf (const Ctf &ctf, int image_index=0)
	Write CTF data to this image. More...

virtual void	flush ()=0
	Flush the IO buffer. More...

virtual int	get_nimg ()
	Return the number of images in this image file. More...

virtual bool	is_complex_mode ()=0
	Is this an complex image or not. More...

virtual bool	is_image_big_endian ()=0
	Is this image in big endian or not. More...

virtual bool	is_single_image_format () const
	Is this image format only storing 1 image or not. More...

template<class T >
void	become_host_endian (T *data, size_t n=1)
	Convert data of this image into host endian format. More...

string	get_filename () const

Static Public Member Functions
static bool	is_valid (const void *first_block, off_t file_size=0)

Public Attributes
	DEFINE_IMAGEIO_FUNC

Private Attributes
OmapHeader	omaph

bool	is_big_endian

bool	is_new_file

Additional Inherited Members
Public Types inherited from EMAN::ImageIO
enum	IOMode { READ_ONLY = 1 , READ_WRITE = 2 , WRITE_ONLY = 3 }

Protected Member Functions inherited from EMAN::ImageIO
virtual void	init ()=0
	Do some initialization before doing the read/write. More...

void	check_read_access (int image_index)
	Validate 'image_index' in file reading. More...

void	check_read_access (int image_index, const float *data)
	Validate 'image_index' and 'data' in file reading. More...

void	check_write_access (IOMode rw_mode, int image_index, int max_nimg=0)
	Validate rw_mode and image_index in file writing. More...

void	check_write_access (IOMode rw_mode, int image_index, int max_nimg, const float *data)
	Validate rw_mode, image_index, and data pointer in file writing. More...

void	check_region (const Region *area, const FloatSize &max_size, bool is_new_file=false, bool inbounds_only=true)
	Validate image I/O region. More...

void	check_region (const Region *area, const IntSize &max_size, bool is_new_file=false, bool inbounds_only=true)
	Validate image I/O region. More...

FILE *	sfopen (const string &filename, IOMode mode, bool *is_new=0, bool overwrite=false)
	Run fopen safely. More...

Protected Attributes inherited from EMAN::ImageIO
string	filename

IOMode	rw_mode

FILE *	file = nullptr

bool	initialized = false

Detailed Description

DSN6 MAP is composed of a series of records which are all 512 bytes long.

The first is a header which contains all the information required to intercept the rest of the file. The subsequent bricks contain blocks of electron density. Each density sample is one byte in size. The order of the samples within a brick is "x fast, y medium, and z slow". http://www.uoxray.uoregon.edu/tnt/manual/node104.html

BRICK (BINARY; input only) - treated as DSN6
BRIX (BINARY; input and output) - similar to DSN6, but has a human-readable first record that contains the cell constants etc.
OMAP (input and output) - treated as DSN6

Definition at line 50 of file omapio.h.

Constructor & Destructor Documentation

◆ OmapIO()

OmapIO::OmapIO	(	const string &	fname,
		IOMode	rw_mode = `READ_ONLY`
	)

explicit

Definition at line 37 of file omapio.cpp.

                                              :
                ImageIO(fname, rw),
                is_big_endian(false), is_new_file(false)
{
        memset(&omaph, 0, sizeof(OmapHeader));
        is_big_endian = ByteOrder::is_host_big_endian();
}

References is_big_endian, EMAN::ByteOrder::is_host_big_endian(), and omaph.

◆ ~OmapIO()

OmapIO::~OmapIO ( )

Definition at line 45 of file omapio.cpp.

{
        if (file) {
                fclose(file);
                file = 0;
        }
}

References EMAN::ImageIO::file.

Member Function Documentation

◆ is_valid()

bool OmapIO::is_valid	(	const void *	first_block,
		off_t	file_size = `0`
	)

static

Definition at line 236 of file omapio.cpp.

{
        ENTERFUNC;
 
        if (!first_block) {
                return false;
        }
 
        const short *data = static_cast < const short *>(first_block);
        short xstart = data[0];
        short ystart = data[1];
        short zstart = data[2];
        short nx = data[3];
        short ny = data[4];
        short nz = data[5];
        short const_value = data[18];
 
        if(!ByteOrder::is_host_big_endian()) {
                ByteOrder::swap_bytes(&xstart);
                ByteOrder::swap_bytes(&ystart);
                ByteOrder::swap_bytes(&zstart);
                ByteOrder::swap_bytes(&nx);
                ByteOrder::swap_bytes(&ny);
                ByteOrder::swap_bytes(&nz);
                ByteOrder::swap_bytes(&const_value);
        }
 
        if(const_value != 100) return false;
        if(nx<=0 || ny<=0 || nz<=0 || nx>10000 || ny>10000 || nz>10000) return false;
 
        EXITFUNC;
        return true;
}

References ENTERFUNC, EXITFUNC, EMAN::ByteOrder::is_host_big_endian(), and EMAN::ByteOrder::swap_bytes().

Referenced by EMAN::EMUtil::fast_get_image_type(), and EMAN::EMUtil::get_image_type().

Member Data Documentation

◆ DEFINE_IMAGEIO_FUNC

EMAN::OmapIO::DEFINE_IMAGEIO_FUNC

Definition at line 56 of file omapio.h.

◆ is_big_endian

bool EMAN::OmapIO::is_big_endian

private

Definition at line 94 of file omapio.h.

Referenced by OmapIO().

◆ is_new_file

bool EMAN::OmapIO::is_new_file

private

Definition at line 95 of file omapio.h.

◆ omaph

OmapHeader EMAN::OmapIO::omaph

private

Definition at line 92 of file omapio.h.

Referenced by OmapIO().

The documentation for this class was generated from the following files:

Classes

Public Member Functions

Static Public Member Functions

Public Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ OmapIO()

◆ ~OmapIO()

Member Function Documentation

◆ is_valid()

Member Data Documentation

◆ DEFINE_IMAGEIO_FUNC

◆ is_big_endian

◆ is_new_file

◆ omaph