MRC file = header + data (nx x ny x nz). More...

#include <fitsio.h>

Inheritance diagram for EMAN::FitsIO:

Collaboration diagram for EMAN::FitsIO:

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

	~FitsIO ()

int	read_ctf (Ctf &ctf, int image_index=0)
	Read CTF data from this image. More...

void	write_ctf (const Ctf &ctf, int image_index=0)
	Write CTF data to this image. 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 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 int	get_mode_size (int mm)

static int	to_em_datatype (int mrcmode)

static int	to_mrcmode (int em_datatype, int is_complex)

Public Attributes
	DEFINE_IMAGEIO_FUNC

Private Attributes
bool	is_big_endian

bool	is_new_file

int	dstart

int	dtype

int	nx

int	ny

int	nz

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

MRC file = header + data (nx x ny x nz).

A MRC image file stores 1D, 2D or 3D image. The image's dimensions and pixel type are defined in the header.

Definition at line 44 of file fitsio.h.

Constructor & Destructor Documentation

◆ FitsIO()

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

explicit

Definition at line 41 of file fitsio.cpp.

:       ImageIO(fname, rw)
{
        is_big_endian = ByteOrder::is_host_big_endian();
        is_new_file = false;
}

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

◆ ~FitsIO()

FitsIO::~FitsIO ( )

Definition at line 48 of file fitsio.cpp.

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

References EMAN::ImageIO::file.

Member Function Documentation

◆ get_mode_size()

static int EMAN::FitsIO::get_mode_size ( int mm )

static

◆ is_valid()

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

static

Definition at line 77 of file fitsio.cpp.

{
        ENTERFUNC;
 
        if (!first_block) {
                return false;
        }
 
        if (strncmp("SIMPLE  ",(const char *)first_block,8)==0) return true;
 
        EXITFUNC;
        return false;
}

References ENTERFUNC, and EXITFUNC.

Referenced by EMAN::EMUtil::get_image_type().

◆ read_ctf()

int FitsIO::read_ctf	(	Ctf &	ctf,
		int	image_index = `0`
	)

virtual

Read CTF data from this image.

Parameters

ctf	Used to store the CTF data.
image_index	The index of the image to read.

Returns: 0 if OK; 1 if error.

Reimplemented from EMAN::ImageIO.

Definition at line 233 of file fitsio.cpp.

{
        ENTERFUNC;
        init();
        EXITFUNC;
        return 0;
}

References ENTERFUNC, EXITFUNC, and EMAN::ImageIO::init().

◆ to_em_datatype()

static int EMAN::FitsIO::to_em_datatype ( int mrcmode )

static

◆ to_mrcmode()

static int EMAN::FitsIO::to_mrcmode	(	int	em_datatype,
		int	is_complex
	)

static

◆ write_ctf()

void FitsIO::write_ctf	(	const Ctf &	ctf,
		int	image_index = `0`
	)

virtual

Write CTF data to this image.

Parameters

ctf	Ctf instance storing the CTF data.
image_index	The index of the image to write.

Returns: 0 if OK; 1 if error.

Reimplemented from EMAN::ImageIO.

Definition at line 241 of file fitsio.cpp.

{
        ENTERFUNC;
        init();
 
        EXITFUNC;
}

References ENTERFUNC, EXITFUNC, and EMAN::ImageIO::init().

Member Data Documentation

◆ DEFINE_IMAGEIO_FUNC

EMAN::FitsIO::DEFINE_IMAGEIO_FUNC

Definition at line 50 of file fitsio.h.

◆ dstart

int EMAN::FitsIO::dstart

private

Definition at line 63 of file fitsio.h.

◆ dtype

int EMAN::FitsIO::dtype

private

Definition at line 64 of file fitsio.h.

◆ is_big_endian

bool EMAN::FitsIO::is_big_endian

private

Definition at line 61 of file fitsio.h.

Referenced by FitsIO().

◆ is_new_file

bool EMAN::FitsIO::is_new_file

private

Definition at line 62 of file fitsio.h.

Referenced by FitsIO().

◆ nx

int EMAN::FitsIO::nx

private

Definition at line 65 of file fitsio.h.

◆ ny

int EMAN::FitsIO::ny

private

Definition at line 65 of file fitsio.h.

◆ nz

int EMAN::FitsIO::nz

private

Definition at line 65 of file fitsio.h.

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

Public Member Functions

Static Public Member Functions

Public Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FitsIO()

◆ ~FitsIO()

Member Function Documentation

◆ get_mode_size()

◆ is_valid()

◆ read_ctf()

◆ to_em_datatype()

◆ to_mrcmode()

◆ write_ctf()

Member Data Documentation

◆ DEFINE_IMAGEIO_FUNC

◆ dstart

◆ dtype

◆ is_big_endian

◆ is_new_file

◆ nx

◆ ny

◆ nz