Amira file = ASCII header + binary data. More...

#include <amiraio.h>

Inheritance diagram for EMAN::AmiraIO:

Collaboration diagram for EMAN::AmiraIO:

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

	~AmiraIO ()

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 Attributes
bool	is_big_endian

EMUtil::EMDataType	dt

int	nx

int	ny

int	nz

float	pixel

float	xorigin

float	yorigin

float	zorigin

Static Private Attributes
static const char *	MAGIC = "# AmiraMesh"

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

Amira file = ASCII header + binary data.

Its first line has some magic name to label it as an Amira image. The first few lines of the file is the ASCII header. Followed the header is the data in binary format. The data has nx x ny x nz pixels.

An Amira file has only 1 2D or 3D image.

Definition at line 48 of file amiraio.h.

Constructor & Destructor Documentation

◆ AmiraIO()

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

Definition at line 48 of file amiraio.cpp.

:       ImageIO(fname, rw),
        is_big_endian(true), dt(EMUtil::EM_UNKNOWN),
         nx(0), ny(0), nz(0),
         pixel(0), xorigin(0), yorigin(0), zorigin(0)
{
}

◆ ~AmiraIO()

AmiraIO::~AmiraIO ( )

Definition at line 56 of file amiraio.cpp.

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

References EMAN::ImageIO::file.

Member Function Documentation

◆ is_valid()

bool AmiraIO::is_valid ( const void * first_block )

static

Definition at line 100 of file amiraio.cpp.

{
        ENTERFUNC;
        bool result = false;
        if (!first_block) {
                result = false;
        }
        else {
                result = Util::check_file_by_magic(first_block, MAGIC);
        }
        EXITFUNC;
        return result;
}

References EMAN::Util::check_file_by_magic(), ENTERFUNC, EXITFUNC, and MAGIC.

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

Member Data Documentation

◆ DEFINE_IMAGEIO_FUNC

EMAN::AmiraIO::DEFINE_IMAGEIO_FUNC

Definition at line 54 of file amiraio.h.

◆ dt

EMUtil::EMDataType EMAN::AmiraIO::dt

private

Definition at line 59 of file amiraio.h.

◆ is_big_endian

bool EMAN::AmiraIO::is_big_endian

private

Definition at line 58 of file amiraio.h.

◆ MAGIC

const char * AmiraIO::MAGIC = "# AmiraMesh"

staticprivate

Definition at line 66 of file amiraio.h.

Referenced by is_valid().

◆ nx

int EMAN::AmiraIO::nx

private

Definition at line 60 of file amiraio.h.

◆ ny

int EMAN::AmiraIO::ny

private

Definition at line 61 of file amiraio.h.

◆ nz

int EMAN::AmiraIO::nz

private

Definition at line 62 of file amiraio.h.

◆ pixel

float EMAN::AmiraIO::pixel

private

Definition at line 63 of file amiraio.h.

◆ xorigin

float EMAN::AmiraIO::xorigin

private

Definition at line 64 of file amiraio.h.

◆ yorigin

float EMAN::AmiraIO::yorigin

private

Definition at line 64 of file amiraio.h.

◆ zorigin

float EMAN::AmiraIO::zorigin

private

Definition at line 64 of file amiraio.h.

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

Public Member Functions

Static Public Member Functions

Public Attributes

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ AmiraIO()

◆ ~AmiraIO()

Member Function Documentation

◆ is_valid()

Member Data Documentation

◆ DEFINE_IMAGEIO_FUNC

◆ dt

◆ is_big_endian

◆ MAGIC

◆ nx

◆ ny

◆ nz

◆ pixel

◆ xorigin

◆ yorigin

◆ zorigin