Gatan DM$ was introduced with the GMS 2.0 release. More...

#include <dm4io.h>

Inheritance diagram for EMAN::DM4IO:

Collaboration diagram for EMAN::DM4IO:

[legend]

Public Member Functions
	DM4IO (const string &fname, IOMode rw_mode=READ_ONLY)

	~DM4IO ()

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

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 = 4 }

Private Attributes
bool	is_big_endian

GatanDM4::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 DM$ was introduced with the GMS 2.0 release.

Each file starts with a TagGroupWithVersion record which saves the root TagGroup with some additional information.

Gatan DM4 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 DM4 file contains 1 2D image.

All data is saved by default with big endian encoding.

Definition at line 249 of file dm4io.h.

Member Enumeration Documentation

◆ anonymous enum

anonymous enum

private

Enumerator
NUM_ID_INT

Definition at line 260 of file dm4io.h.

260{ NUM_ID_INT = 4 }; //actually its int+long+int=16 bytes

EMAN::DM4IO::NUM_ID_INT

@ NUM_ID_INT

Definition: dm4io.h:260

Constructor & Destructor Documentation

◆ DM4IO()

DM4IO::DM4IO	(	const string &	fname,
		IOMode	rw_mode = `READ_ONLY`
	)

explicit

Definition at line 742 of file dm4io.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.

◆ ~DM4IO()

DM4IO::~DM4IO ( )

Definition at line 749 of file dm4io.cpp.

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

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

Member Function Documentation

◆ get_nimg()

int DM4IO::get_nimg ( )

virtual

Return the number of images in this image file.

Reimplemented from EMAN::ImageIO.

Definition at line 1037 of file dm4io.cpp.

{
        init();
 
        TagGroup root_group(file, tagtable, "");
        root_group.read_tag_group(true, 0, 1);
 
        return tagtable->get_image_counted();
}

References EMAN::ImageIO::file, EMAN::GatanDM4::TagTable::get_image_counted(), EMAN::ImageIO::init(), EMAN::GatanDM4::TagGroup::read_tag_group(), and tagtable.

◆ is_valid()

bool DM4IO::is_valid ( const void * first_block )

static

Definition at line 811 of file dm4io.cpp.

{
        ENTERFUNC;
 
        if (!first_block) {
                return false;
        }
 
        const int *data = static_cast < const int *>(first_block);
 
        int img_ver = data[0];
        int byte_order = data[3];
        if (ByteOrder::is_data_big_endian(&img_ver) != ByteOrder::is_host_big_endian()) {
                ByteOrder::swap_bytes(&img_ver);
                ByteOrder::swap_bytes(&byte_order);
        }
 
        if (img_ver != 4) {
                return false;
        }
 
        if (byte_order != 0 && byte_order != 1) {
                return false;
        }
 
        return true;
}

References ENTERFUNC, 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().

Member Data Documentation

◆ DEFINE_IMAGEIO_FUNC

EMAN::DM4IO::DEFINE_IMAGEIO_FUNC

Definition at line 255 of file dm4io.h.

◆ is_big_endian

bool EMAN::DM4IO::is_big_endian

private

Definition at line 262 of file dm4io.h.

Referenced by DM4IO().

◆ tagtable

GatanDM4::TagTable* EMAN::DM4IO::tagtable

private

Definition at line 263 of file dm4io.h.

Referenced by DM4IO(), get_nimg(), and ~DM4IO().

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

Public Member Functions

Static Public Member Functions

Public Attributes

Private Types

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ anonymous enum

Constructor & Destructor Documentation

◆ DM4IO()

◆ ~DM4IO()

Member Function Documentation

◆ get_nimg()

◆ is_valid()

Member Data Documentation

◆ DEFINE_IMAGEIO_FUNC

◆ is_big_endian

◆ tagtable