EMAN::DM3IO Class Reference

Gatan DM3 file is a hierarchical binary image format. More...

#include <dm3io.h>

Inheritance diagram for EMAN::DM3IO:

Collaboration diagram for EMAN::DM3IO:

Public Member Functions
	DM3IO (const string &fname, IOMode rw_mode=READ_ONLY)
	~DM3IO ()
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	{ NUM_ID_INT = 3 }

Private Attributes
bool	is_big_endian
Gatan::TagTable *	tagtable

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

Gatan DM3 file is a hierarchical binary image format.

Everything in the image is a <key, value> pair, where key may be a container-type key which contains more key/value pairs. To read its header information, the whole file has to be parsed. During parsing, we check the keys that we are interested in and get their values.

The real binary data itself is also in this key/value hierarchy.

1 Gatan DM3 file contains 1 2D image.

Definition at line 242 of file dm3io.h.

Member Enumeration Documentation

anonymous enum

anonymous enum

private

Enumerator
NUM_ID_INT

Definition at line 252 of file dm3io.h.

{ NUM_ID_INT = 3 };

Constructor & Destructor Documentation

DM3IO()

DM3IO::DM3IO ( const string &  fname, IOMode  rw_mode = READ_ONLY  )

explicit

Definition at line 634 of file dm3io.cpp.

        :       ImageIO(fname, rw)
{
        is_big_endian = ByteOrder::is_host_big_endian();
        tagtable = new TagTable();
}

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

~DM3IO()

DM3IO::~DM3IO

(

)

Definition at line 641 of file dm3io.cpp.

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

References EMAN::ImageIO::file, and tagtable.

Member Function Documentation

is_valid()

bool DM3IO::is_valid ( const void *  first_block )

static

Definition at line 694 of file dm3io.cpp.

{
        ENTERFUNC;
 
        if (!first_block) {
                return false;
        }
 
        const int *data = static_cast < const int *>(first_block);
 
        int img_ver = data[0];
        int img_size = data[1];
        int byte_order = data[2];
 
        ByteOrder::become_big_endian(&img_ver);
 
        if (img_ver != 3) {
                return false;
        }
 
        ByteOrder::become_big_endian(&img_size);
        ByteOrder::become_big_endian(&byte_order);
 
        if (byte_order != 0 && byte_order != 1) {
                return false;
        }
 
        return true;
}

References EMAN::ByteOrder::become_big_endian(), and ENTERFUNC.

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

Member Data Documentation

DEFINE_IMAGEIO_FUNC

EMAN::DM3IO::DEFINE_IMAGEIO_FUNC

Definition at line 248 of file dm3io.h.

is_big_endian

bool EMAN::DM3IO::is_big_endian

private

Definition at line 256 of file dm3io.h.

Referenced by DM3IO().

tagtable

Gatan::TagTable* EMAN::DM3IO::tagtable

private

Definition at line 257 of file dm3io.h.

Referenced by DM3IO(), and ~DM3IO().

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

• dm3io.h
• dm3io.cpp