EmIO defines I/O operations on EM image format. More...

#include <emio.h>

Inheritance diagram for EMAN::EmIO:

Collaboration diagram for EMAN::EmIO:

[legend]

Classes
struct	EMHeader

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

	~EmIO ()

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)

static size_t	get_mode_size (char data_type)

static int	get_machine_type ()

static int	to_em_datatype (char t)

Public Attributes
	DEFINE_IMAGEIO_FUNC

Private Types
enum	DataType { EM_EM_CHAR = 1 , EM_EM_SHORT = 2 , EM_EM_INT = 4 , EM_EM_FLOAT = 5 , EM_EM_COMPLEX = 8 , EM_EM_DOUBLE = 9 , EM_EM_UNKNOWN }

enum	MachineType { EM_OS8 = 0 , EM_VAX = 1 , EM_CONVEX = 2 , EM_SGI = 3 , EM_MAC = 5 , EM_PC = 6 , EM_UNKNOWN_MACHINE }

Private Attributes
EMHeader	emh

size_t	mode_size

DataType	mode

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

EmIO defines I/O operations on EM image format.

EM image = header + data with (data = nx * ny * nz).

An EM image file stores 1 single 2D or 3D image.

Definition at line 44 of file emio.h.

Member Enumeration Documentation

◆ DataType

enum EMAN::EmIO::DataType

private

Enumerator
EM_EM_CHAR
EM_EM_SHORT
EM_EM_INT
EM_EM_FLOAT
EM_EM_COMPLEX
EM_EM_DOUBLE
EM_EM_UNKNOWN

Definition at line 73 of file emio.h.

                {
                        EM_EM_CHAR = 1,
                        EM_EM_SHORT = 2,
                        EM_EM_INT = 4,
                        EM_EM_FLOAT = 5,
                        EM_EM_COMPLEX = 8,
                        EM_EM_DOUBLE = 9,
                        EM_EM_UNKNOWN
                };

◆ MachineType

enum EMAN::EmIO::MachineType

private

Enumerator
EM_OS8
EM_VAX
EM_CONVEX
EM_SGI
EM_MAC
EM_PC
EM_UNKNOWN_MACHINE

Definition at line 84 of file emio.h.

                {
                        EM_OS8 = 0,
                        EM_VAX = 1,
                        EM_CONVEX = 2,
                        EM_SGI = 3,
                        EM_MAC = 5,
                        EM_PC = 6,
                        EM_UNKNOWN_MACHINE
                };

Constructor & Destructor Documentation

◆ EmIO()

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

explicit

Definition at line 38 of file emio.cpp.

:       ImageIO(fname, rw)
{
        mode_size = 0;
        mode = EM_EM_UNKNOWN;
        is_big_endian = ByteOrder::is_host_big_endian();
        is_new_file = false;
        memset(&emh, 0, sizeof(EMHeader));
}

References EM_EM_UNKNOWN, emh, is_big_endian, EMAN::ByteOrder::is_host_big_endian(), is_new_file, mode, and mode_size.

◆ ~EmIO()

EmIO::~EmIO ( )

Definition at line 48 of file emio.cpp.

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

References EMAN::ImageIO::file.

Member Function Documentation

◆ get_machine_type()

int EmIO::get_machine_type ( )

static

Definition at line 324 of file emio.cpp.

{
        int m = EM_UNKNOWN_MACHINE;
#ifdef __sgi
        m = EM_SGI;
#elif defined __linux__
        m = EM_PC;
#elif defined __CYGWIN__
        m = EM_PC;
#elif defined WIN32
        m = EM_PC;
#elif defined MACOS
        m = EM_MAC;
#elif defined macintosh
        m = EM_MAC;
#elif defined __darwin__
        m = EM_MAC;
#elif defined __APPLE__
        m = EM_MAC;
#else
        m = EM_UNKNOWN_MACHINE;
#endif
        return m;
}

References EM_MAC, EM_PC, EM_SGI, and EM_UNKNOWN_MACHINE.

◆ get_mode_size()

size_t EmIO::get_mode_size ( char data_type )

static

Definition at line 349 of file emio.cpp.

{
        int mode = (int) data_type;
        switch (mode) {
        case EM_EM_CHAR:
                return sizeof(char);
        case EM_EM_SHORT:
                return sizeof(short);
        case EM_EM_INT:
        case EM_EM_FLOAT:
        case EM_EM_COMPLEX:
                return sizeof(int);
        case EM_EM_DOUBLE:
                return sizeof(double);
        }
        return 0;
}

References EM_EM_CHAR, EM_EM_COMPLEX, EM_EM_DOUBLE, EM_EM_FLOAT, EM_EM_INT, EM_EM_SHORT, and mode.

Referenced by is_valid().

◆ is_valid()

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

static

Definition at line 95 of file emio.cpp.

{
        ENTERFUNC;
 
        if (!first_block) {
                return false;
        }
 
        const char *data = static_cast < const char *>(first_block);
        char machine = data[0];
        char is_new_ver = data[1];
        char data_type = data[3];
 
        const int *data1 = static_cast < const int *>(first_block);
        int nx = data1[1];
        int ny = data1[2];
        int nz = data1[3];
 
        bool data_big_endian = ByteOrder::is_data_big_endian(&nz);
        if (data_big_endian != ByteOrder::is_host_big_endian()) {
                ByteOrder::swap_bytes(&nx);
                ByteOrder::swap_bytes(&ny);
                ByteOrder::swap_bytes(&nz);
        }
 
        const int max_dim = 1 << 20;
 
        if (((int) machine >= EM_OS8 && machine <= EM_PC) &&
                (is_new_ver == 0 || is_new_ver == 1) &&
                (data_type >= EM_EM_CHAR && data_type <= EM_EM_DOUBLE) &&
                (nx > 1 && nx < max_dim) && (ny > 0 && ny < max_dim) && (nz > 0 && nz < max_dim)) {
                if (file_size > 0) {
                        off_t file_size1 = (off_t)nx * (off_t)ny * (off_t)nz * (off_t)get_mode_size(data_type) + (off_t)sizeof(EMHeader);
                        if (file_size == file_size1) {
                                return true;
                        }
                }
                else {
                        return true;
                }
        }
 
        return false;
}

References EM_EM_CHAR, EM_EM_DOUBLE, EM_OS8, EM_PC, ENTERFUNC, get_mode_size(), EMAN::ByteOrder::is_data_big_endian(), 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().

◆ to_em_datatype()

int EmIO::to_em_datatype ( char t )

static

Definition at line 302 of file emio.cpp.

{
        DataType type = static_cast < DataType > (t);
        switch (type) {
        case EM_EM_CHAR:
                return EMUtil::EM_CHAR;
        case EM_EM_SHORT:
                return EMUtil::EM_SHORT;
        case EM_EM_INT:
                return EMUtil::EM_INT;
        case EM_EM_FLOAT:
                return EMUtil::EM_FLOAT;
        case EM_EM_DOUBLE:
                return EMUtil::EM_DOUBLE;
        case EM_EM_COMPLEX:
                return EMUtil::EM_FLOAT_COMPLEX;
        default:
                break;
        }
        return EMUtil::EM_UNKNOWN;
}

References EMAN::EMUtil::EM_CHAR, EMAN::EMUtil::EM_DOUBLE, EM_EM_CHAR, EM_EM_COMPLEX, EM_EM_DOUBLE, EM_EM_FLOAT, EM_EM_INT, EM_EM_SHORT, EMAN::EMUtil::EM_FLOAT, EMAN::EMUtil::EM_FLOAT_COMPLEX, EMAN::EMUtil::EM_INT, EMAN::EMUtil::EM_SHORT, and EMAN::EMUtil::EM_UNKNOWN.

Member Data Documentation

◆ DEFINE_IMAGEIO_FUNC

EMAN::EmIO::DEFINE_IMAGEIO_FUNC

Definition at line 50 of file emio.h.

◆ emh

EMHeader EMAN::EmIO::emh

private

Definition at line 96 of file emio.h.

Referenced by EmIO().

◆ is_big_endian

bool EMAN::EmIO::is_big_endian

private

Definition at line 100 of file emio.h.

Referenced by EmIO().

◆ is_new_file

bool EMAN::EmIO::is_new_file

private

Definition at line 101 of file emio.h.

Referenced by EmIO().

◆ mode

DataType EMAN::EmIO::mode

private

Definition at line 99 of file emio.h.

Referenced by EmIO(), and get_mode_size().

◆ mode_size

size_t EMAN::EmIO::mode_size

private

Definition at line 98 of file emio.h.

Referenced by EmIO().

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

Classes

Public Member Functions

Static Public Member Functions

Public Attributes

Private Types

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ DataType

◆ MachineType

Constructor & Destructor Documentation

◆ EmIO()

◆ ~EmIO()

Member Function Documentation

◆ get_machine_type()

◆ get_mode_size()

◆ is_valid()

◆ to_em_datatype()

Member Data Documentation

◆ DEFINE_IMAGEIO_FUNC

◆ emh

◆ is_big_endian

◆ is_new_file

◆ mode

◆ mode_size