A SAL image is an image from Perkin Elmer PDS Microdensitometer. More...

#include <salio.h>

Inheritance diagram for EMAN::SalIO:

Collaboration diagram for EMAN::SalIO:

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

	~SalIO ()

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	ScanAxis { X_SCAN_AXIS , Y_SCAN_AXIS }

enum	ScanMode { NON_RASTER_SCAN , RASTER_SCAN }

Private Attributes
int	nx

int	ny

int	record_length

ScanMode	scan_mode

float	pixel

Static Private Attributes
static const char *	HDR_EXT = "hdr"

static const char *	IMG_EXT = "img"

static const char *	MAGIC = " IDENTIFICATION"

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

A SAL image is an image from Perkin Elmer PDS Microdensitometer.

A SAL image consists of 2 files: 1 header file "X.hdr" and a data file "X.img". Header file is in ASCII format. Data file is in binary format.

Each pair of hdr/img SAL files contains 1 2D image.

Definition at line 47 of file salio.h.

Member Enumeration Documentation

◆ ScanAxis

enum EMAN::SalIO::ScanAxis

private

Enumerator
X_SCAN_AXIS
Y_SCAN_AXIS

Definition at line 61 of file salio.h.

                {
                        X_SCAN_AXIS,
                        Y_SCAN_AXIS
                };

◆ ScanMode

enum EMAN::SalIO::ScanMode

private

Enumerator
NON_RASTER_SCAN
RASTER_SCAN

Definition at line 67 of file salio.h.

                {
                        NON_RASTER_SCAN,
                        RASTER_SCAN
                };

Constructor & Destructor Documentation

◆ SalIO()

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

explicit

Definition at line 53 of file salio.cpp.

:       ImageIO(fname, rw)
{
        nx = 0;
        ny = 0;
        record_length = 512;
        scan_mode = NON_RASTER_SCAN;
        pixel = 4.6667f;
}

References NON_RASTER_SCAN, nx, ny, pixel, record_length, and scan_mode.

◆ ~SalIO()

SalIO::~SalIO ( )

Definition at line 63 of file salio.cpp.

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

References EMAN::ImageIO::file.

Member Function Documentation

◆ is_valid()

bool SalIO::is_valid ( const void * first_block )

static

Definition at line 141 of file salio.cpp.

{
        ENTERFUNC;
        bool result = false;
 
        if (!first_block) {
                result = false;
        }
        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::SalIO::DEFINE_IMAGEIO_FUNC

Definition at line 53 of file salio.h.

◆ HDR_EXT

const char * SalIO::HDR_EXT = "hdr"

staticprivate

Definition at line 57 of file salio.h.

◆ IMG_EXT

const char * SalIO::IMG_EXT = "img"

staticprivate

Definition at line 58 of file salio.h.

◆ MAGIC

const char * SalIO::MAGIC = " IDENTIFICATION"

staticprivate

Definition at line 59 of file salio.h.

Referenced by is_valid().

◆ nx

int EMAN::SalIO::nx

private

Definition at line 74 of file salio.h.

Referenced by SalIO().

◆ ny

int EMAN::SalIO::ny

private

Definition at line 75 of file salio.h.

Referenced by SalIO().

◆ pixel

float EMAN::SalIO::pixel

private

Definition at line 78 of file salio.h.

Referenced by SalIO().

◆ record_length

int EMAN::SalIO::record_length

private

Definition at line 76 of file salio.h.

Referenced by SalIO().

◆ scan_mode

ScanMode EMAN::SalIO::scan_mode

private

Definition at line 77 of file salio.h.

Referenced by SalIO().

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

Public Member Functions

Static Public Member Functions

Public Attributes

Private Types

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ ScanAxis

◆ ScanMode

Constructor & Destructor Documentation

◆ SalIO()

◆ ~SalIO()

Member Function Documentation

◆ is_valid()

Member Data Documentation

◆ DEFINE_IMAGEIO_FUNC

◆ HDR_EXT

◆ IMG_EXT

◆ MAGIC

◆ nx

◆ ny

◆ pixel

◆ record_length

◆ scan_mode