EMAN::EerIO Class Reference

#include <eerio.h>

Inheritance diagram for EMAN::EerIO:

Collaboration diagram for EMAN::EerIO:

Public Member Functions
	EerIO (const string &fname, IOMode rw_mode=READ_ONLY, Decoder &dec=decoder0x)
	~EerIO ()
int	get_nimg ()
	Return the number of images in this image file. More...
bool	is_single_image_format () const override
	Is this image format only storing 1 image or not. More...
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 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...
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

Public Attributes
	DEFINE_IMAGEIO_FUNC

Private Attributes
bool	is_big_endian
TIFF *	tiff_file
size_t	num_frames = 0
Dict	acquisition_data_dict
Decoder &	decoder

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

Definition at line 180 of file eerio.h.

Constructor & Destructor Documentation

EerIO()

EerIO::EerIO	(	const string &	fname,
		IOMode	rw_mode = READ_ONLY,
		Decoder &	dec = decoder0x
	)

Definition at line 150 of file eerio.cpp.

:       ImageIO(fname, rw), decoder(dec)
{
        TIFFSetWarningHandler(TIFFOutputWarning);
 
        tiff_file = TIFFOpen(filename.c_str(), "r");
 
        auto acquisition_metadata = read_acquisition_metadata(tiff_file);
        acquisition_data_dict = parse_acquisition_data(acquisition_metadata);
 
        for( ; TIFFReadDirectory(tiff_file); )
                num_frames = TIFFCurrentDirectory(tiff_file) + 1;
 
}

References acquisition_data_dict, EMAN::ImageIO::filename, num_frames, parse_acquisition_data(), read_acquisition_metadata(), tiff_file, and TIFFOutputWarning().

~EerIO()

EerIO::~EerIO

(

)

Definition at line 165 of file eerio.cpp.

{
        TIFFClose(tiff_file);
}

References tiff_file.

Member Function Documentation

get_nimg()

int EerIO::get_nimg ( )

virtual

Return the number of images in this image file.

Reimplemented from EMAN::ImageIO.

Definition at line 177 of file eerio.cpp.

{
        return num_frames;
}

References num_frames.

is_single_image_format()

bool EerIO::is_single_image_format ( ) const

overridevirtual

Is this image format only storing 1 image or not.

Some image formats like MRC only store 1 image in a file, so this function returns 'true' for them. Other image formats like IMAGIC/HDF5 may store mutliple images, so this function returns 'false' for them.

Reimplemented from EMAN::ImageIO.

Definition at line 257 of file eerio.cpp.

{
        return false;
}

Member Data Documentation

acquisition_data_dict

Dict EMAN::EerIO::acquisition_data_dict

private

Definition at line 196 of file eerio.h.

Referenced by EerIO().

decoder

Decoder& EMAN::EerIO::decoder

private

Definition at line 198 of file eerio.h.

DEFINE_IMAGEIO_FUNC

EMAN::EerIO::DEFINE_IMAGEIO_FUNC

Definition at line 190 of file eerio.h.

is_big_endian

bool EMAN::EerIO::is_big_endian

private

Definition at line 193 of file eerio.h.

num_frames

size_t EMAN::EerIO::num_frames = 0

private

Definition at line 195 of file eerio.h.

Referenced by EerIO(), and get_nimg().

tiff_file

TIFF* EMAN::EerIO::tiff_file

private

Definition at line 194 of file eerio.h.

Referenced by EerIO(), and ~EerIO().

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

• eerio.h
• eerio.cpp