XPLOR image format is in ASCII: More...

#include <xplorio.h>

Inheritance diagram for EMAN::XplorIO:

Collaboration diagram for EMAN::XplorIO:

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

	~XplorIO ()

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

bool	is_new_file

int	nlines_in_header

int	nx

int	ny

int	nz

float	apix_x

float	apix_y

float	apix_z

float	cell_alpha

float	cell_beta

float	cell_gama

Static Private Attributes
static const string	SECTION_MODE = "ZYX"

static const int	NFLOAT_PER_LINE = 6

static const int	INTEGER_SIZE = 8

static const int	FLOAT_SIZE = 12

static const char *	OUTFORMAT = "%12.5E"

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

XPLOR image format is in ASCII:

header: (note: each integer takes 8 Bytes space, each float is 12.5E format.) line 1: empty line 2: int: number of lines for title (ntitle) next ntitle lines: string: titles line ntitle+3: 9 int: nx, xmin, xmax, ny, ymin, ymax, nz, zmin, zmax line ntitle+4: 6 float: cell size (x, y, z), cell angles (alpha, beta, gamma) line ntitle+5: string: ZYX (this is the section mode. always ZYX)
data

for zindex = 1 to nz: zindex nx*ny floats. each line has 6 floats. each float is in 12.5E format.

A XPLOR file contains one 2D or 3D image.

Definition at line 60 of file xplorio.h.

Constructor & Destructor Documentation

◆ XplorIO()

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

explicit

Definition at line 56 of file xplorio.cpp.

:       ImageIO(fname, rw)
{
        is_big_endian = ByteOrder::is_host_big_endian();
        is_new_file = false;
        nlines_in_header = 0;
 
        nx = 0;
        ny = 0;
        nz = 0;
 
        apix_x = 0;
        apix_y = 0;
        apix_z = 0;
 
        cell_alpha = 0;
        cell_beta = 0;
        cell_gama = 0;
}

References apix_x, apix_y, apix_z, cell_alpha, cell_beta, cell_gama, is_big_endian, EMAN::ByteOrder::is_host_big_endian(), is_new_file, nlines_in_header, nx, ny, and nz.

◆ ~XplorIO()

XplorIO::~XplorIO ( )

Definition at line 76 of file xplorio.cpp.

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

References EMAN::ImageIO::file.

Member Function Documentation

◆ is_valid()

bool XplorIO::is_valid ( const void * first_block )

static

Definition at line 148 of file xplorio.cpp.

{
        ENTERFUNC;
        if (!first_block) {
                return false;
        }
        char *buf = (char *)(first_block);
        string line1 = Util::get_line_from_string(&buf);
        bool result = true;
 
        if (line1.size() != 0) {
                result = false;
        }
        else {
                string line2 = Util::get_line_from_string(&buf);
                int ntitle = 0;
 
                if ((int)line2.size() != INTEGER_SIZE) {
                        result = false;
                }
                else {
                        ntitle = atoi(line2.c_str());
                        if (ntitle < 0 || ntitle > 50) {
                                result = false;
                        }
 
                        else {
                                for (int i = 0; i < ntitle+2; i++) {
                                        Util::get_line_from_string(&buf);
                                }
 
                                string modeline = Util::get_line_from_string(&buf);
                                if (modeline != SECTION_MODE) {
                                        result = false;
                                }
                        }
                }
        }
 
        EXITFUNC;
        return result;
}

References ENTERFUNC, EXITFUNC, EMAN::Util::get_line_from_string(), INTEGER_SIZE, and SECTION_MODE.

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

Member Data Documentation

◆ apix_x

float EMAN::XplorIO::apix_x

private

Definition at line 78 of file xplorio.h.

Referenced by XplorIO().

◆ apix_y

float EMAN::XplorIO::apix_y

private

Definition at line 79 of file xplorio.h.

Referenced by XplorIO().

◆ apix_z

float EMAN::XplorIO::apix_z

private

Definition at line 80 of file xplorio.h.

Referenced by XplorIO().

◆ cell_alpha

float EMAN::XplorIO::cell_alpha

private

Definition at line 82 of file xplorio.h.

Referenced by XplorIO().

◆ cell_beta

float EMAN::XplorIO::cell_beta

private

Definition at line 83 of file xplorio.h.

Referenced by XplorIO().

◆ cell_gama

float EMAN::XplorIO::cell_gama

private

Definition at line 84 of file xplorio.h.

Referenced by XplorIO().

◆ DEFINE_IMAGEIO_FUNC

EMAN::XplorIO::DEFINE_IMAGEIO_FUNC

Definition at line 66 of file xplorio.h.

◆ FLOAT_SIZE

const int XplorIO::FLOAT_SIZE = 12

staticprivate

Definition at line 89 of file xplorio.h.

◆ INTEGER_SIZE

const int XplorIO::INTEGER_SIZE = 8

staticprivate

Definition at line 88 of file xplorio.h.

Referenced by is_valid().

◆ is_big_endian

bool EMAN::XplorIO::is_big_endian

private

Definition at line 70 of file xplorio.h.

Referenced by XplorIO().

◆ is_new_file

bool EMAN::XplorIO::is_new_file

private

Definition at line 71 of file xplorio.h.

Referenced by XplorIO().

◆ NFLOAT_PER_LINE

const int XplorIO::NFLOAT_PER_LINE = 6

staticprivate

Definition at line 87 of file xplorio.h.

◆ nlines_in_header

int EMAN::XplorIO::nlines_in_header

private

Definition at line 72 of file xplorio.h.

Referenced by XplorIO().

◆ nx

int EMAN::XplorIO::nx

private

Definition at line 74 of file xplorio.h.

Referenced by XplorIO().

◆ ny

int EMAN::XplorIO::ny

private

Definition at line 75 of file xplorio.h.

Referenced by XplorIO().

◆ nz

int EMAN::XplorIO::nz

private

Definition at line 76 of file xplorio.h.

Referenced by XplorIO().

◆ OUTFORMAT

const char * XplorIO::OUTFORMAT = "%12.5E"

staticprivate

Definition at line 90 of file xplorio.h.

◆ SECTION_MODE

const string XplorIO::SECTION_MODE = "ZYX"

staticprivate

Definition at line 86 of file xplorio.h.

Referenced by is_valid().

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

◆ XplorIO()

◆ ~XplorIO()

Member Function Documentation

◆ is_valid()

Member Data Documentation

◆ apix_x

◆ apix_y

◆ apix_z

◆ cell_alpha

◆ cell_beta

◆ cell_gama

◆ DEFINE_IMAGEIO_FUNC

◆ FLOAT_SIZE

◆ INTEGER_SIZE

◆ is_big_endian

◆ is_new_file

◆ NFLOAT_PER_LINE

◆ nlines_in_header

◆ nx

◆ ny

◆ nz

◆ OUTFORMAT

◆ SECTION_MODE