Gatan2 Image file = header + data. More...

#include <gatan2io.h>

Inheritance diagram for EMAN::Gatan2IO:

Collaboration diagram for EMAN::Gatan2IO:

[legend]

Classes
struct	Gatan2Header

Public Member Functions
	Gatan2IO (const string &fname, IOMode rw_mode=READ_ONLY)

	~Gatan2IO ()

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)

Public Attributes
	DEFINE_IMAGEIO_FUNC

Private Types
enum	DataType { GATAN2_SHORT = 1 , GATAN2_FLOAT = 2 , GATAN2_COMPLEX = 3 , GATAN2_PACKED_COMPLEX = 5 , GATAN2_CHAR = 6 , GATAN2_INT = 7 , GATAN2_INVALID }

Private Member Functions
int	to_em_datatype (int gatan_type)

Private Attributes
Gatan2Header	gatanh

bool	is_big_endian

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

Gatan2 Image file = header + data.

header is defined in Gatan2Header. data is nx by ny. A Gatan2 file contains 1 2D image.

Definition at line 45 of file gatan2io.h.

Member Enumeration Documentation

◆ DataType

enum EMAN::Gatan2IO::DataType

private

Enumerator
GATAN2_SHORT
GATAN2_FLOAT
GATAN2_COMPLEX
GATAN2_PACKED_COMPLEX
GATAN2_CHAR
GATAN2_INT
GATAN2_INVALID

Definition at line 54 of file gatan2io.h.

                {
                        GATAN2_SHORT = 1,
                        GATAN2_FLOAT = 2,
                        GATAN2_COMPLEX = 3,
                        GATAN2_PACKED_COMPLEX = 5,
                        GATAN2_CHAR = 6,
                        GATAN2_INT = 7,
                        GATAN2_INVALID
                };

Constructor & Destructor Documentation

◆ Gatan2IO()

Gatan2IO::Gatan2IO	(	const string &	fname,
		IOMode	rw_mode = `READ_ONLY`
	)

explicit

Definition at line 39 of file gatan2io.cpp.

:       ImageIO(fname, rw)
{
        is_big_endian = ByteOrder::is_host_big_endian();
        memset(&gatanh, 0, sizeof(Gatan2Header));
}

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

◆ ~Gatan2IO()

Gatan2IO::~Gatan2IO ( )

Definition at line 46 of file gatan2io.cpp.

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

References EMAN::ImageIO::file.

Member Function Documentation

◆ is_valid()

bool Gatan2IO::is_valid ( const void * first_block )

static

Definition at line 82 of file gatan2io.cpp.

{
        ENTERFUNC;
        bool result = false;
        
        if (!first_block) {
                result = false;
        }
        else {
                const short *data = static_cast < const short *>(first_block);
                short len = data[5];
                short type = data[6];
 
                bool data_big_endian = ByteOrder::is_data_big_endian(&len);
 
                if (data_big_endian != ByteOrder::is_host_big_endian()) {
                        ByteOrder::swap_bytes(&len);
                        ByteOrder::swap_bytes(&type);
                }
 
                int double_size = sizeof(double);
                if (len > 0 && len <= double_size && type > 0 && type <= GATAN2_INVALID) {
                        result = true;
                }
        }
        EXITFUNC;
        return result;
}

References ENTERFUNC, EXITFUNC, GATAN2_INVALID, 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 Gatan2IO::to_em_datatype ( int gatan_type )

private

Definition at line 239 of file gatan2io.cpp.

{
        switch (gatan_type) {
        case GATAN2_SHORT:
                return EMUtil::EM_SHORT;
 
        case GATAN2_FLOAT:
                return EMUtil::EM_FLOAT;
 
        case GATAN2_CHAR:
                return EMUtil::EM_CHAR;
 
        case GATAN2_INT:
                return EMUtil::EM_INT;
        }
 
        return EMUtil::EM_UNKNOWN;
}

References EMAN::EMUtil::EM_CHAR, EMAN::EMUtil::EM_FLOAT, EMAN::EMUtil::EM_INT, EMAN::EMUtil::EM_SHORT, EMAN::EMUtil::EM_UNKNOWN, GATAN2_CHAR, GATAN2_FLOAT, GATAN2_INT, and GATAN2_SHORT.

Member Data Documentation

◆ DEFINE_IMAGEIO_FUNC

EMAN::Gatan2IO::DEFINE_IMAGEIO_FUNC

Definition at line 51 of file gatan2io.h.

◆ gatanh

Gatan2Header EMAN::Gatan2IO::gatanh

private

Definition at line 79 of file gatan2io.h.

Referenced by Gatan2IO().

◆ is_big_endian

bool EMAN::Gatan2IO::is_big_endian

private

Definition at line 81 of file gatan2io.h.

Referenced by Gatan2IO().

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

Classes

Public Member Functions

Static Public Member Functions

Public Attributes

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ DataType

Constructor & Destructor Documentation

◆ Gatan2IO()

◆ ~Gatan2IO()

Member Function Documentation

◆ is_valid()

◆ to_em_datatype()

Member Data Documentation

◆ DEFINE_IMAGEIO_FUNC

◆ gatanh

◆ is_big_endian