A LSX file is a high performance ASCII file that contains a list of image numbers and file names. More...

#include <lstfastio.h>

Inheritance diagram for EMAN::LstFastIO:

Collaboration diagram for EMAN::LstFastIO:

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

	~LstFastIO ()

bool	is_single_image_format () const
	Is this image format only storing 1 image or not. More...

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...

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 Member Functions
int	calc_ref_image_index (int image_index)

Private Attributes
bool	is_big_endian

int	nimg

unsigned int	line_length

unsigned int	head_length

ImageIO *	imageio

string	ref_filename

int	last_lst_index

int	last_ref_index

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

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 LSX file is a high performance ASCII file that contains a list of image numbers and file names.

Each line of a LSX file has the following format: after the #LSX magic number are 2 lines, the second line containing

comment

line-length

Denoting the length of each line in the file. If writing additional lines to the file, this length must not be exceeded.

Additional '#' comment lines are NOT permitted within the file

lines have the form: reference_image_index reference-image-filename comments

Definition at line 54 of file lstfastio.h.

Constructor & Destructor Documentation

◆ LstFastIO()

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

explicit

Definition at line 52 of file lstfastio.cpp.

:       ImageIO(fname, rw)
{
        is_big_endian = ByteOrder::is_host_big_endian();
        nimg = 0;
        imageio = 0;
        ref_filename = "";
        last_lst_index = -1;
        last_ref_index = -1;
}

References imageio, is_big_endian, EMAN::ByteOrder::is_host_big_endian(), last_lst_index, last_ref_index, nimg, and ref_filename.

◆ ~LstFastIO()

LstFastIO::~LstFastIO ( )

Definition at line 63 of file lstfastio.cpp.

{
        if (file) {
                fclose(file);
                file = 0;
        }
        ref_filename = "";
        if(imageio) {
                delete imageio;
                imageio = 0;
        }
}

References EMAN::ImageIO::file, imageio, and ref_filename.

Member Function Documentation

◆ calc_ref_image_index()

int LstFastIO::calc_ref_image_index ( int image_index )

private

Definition at line 138 of file lstfastio.cpp.

{
        if (image_index == last_lst_index) {
                return last_ref_index;
        }
        else {
                vector<char> buf(line_length+1);
 
                fseek(file,head_length+line_length*image_index,SEEK_SET);
                if (!fgets(buf.data(), line_length, file)) {
                        LOGERR("reach EOF in file '%s' before reading %dth image",
                                   filename.c_str(), image_index);
                        return 1;
                }
 
                int ref_image_index = 0;
                char ref_image_path[MAXPATHLEN];
                vector<char> unused(line_length);
                sscanf(buf.data(), " %d %s %[ .,0-9-]", &ref_image_index, ref_image_path, unused.data());
                string newrefname = string(ref_image_path);
                if (newrefname.compare(ref_filename)==0) {      // use the existing imageio when possible, TODO: cache a few?
                        if (imageio==0) throw FileAccessException(ref_filename);
                } else {
                        ref_filename = newrefname;
                        if (!Util::is_file_exist(ref_filename)) throw FileAccessException(ref_filename);
                        if (imageio!=0) delete imageio;
                        imageio = EMUtil::get_imageio(ref_filename, rw_mode);
                }
                last_ref_index = ref_image_index;
        }
//      printf("%d\t%d\t%s\n",image_index,last_ref_index,ref_filename.c_str());
 
        last_lst_index = image_index;
 
        return last_ref_index;
}

References EMAN::ImageIO::file, FileAccessException, EMAN::ImageIO::filename, EMAN::EMUtil::get_imageio(), head_length, imageio, EMAN::Util::is_file_exist(), last_lst_index, last_ref_index, line_length, LOGERR, ref_filename, and EMAN::ImageIO::rw_mode.

◆ get_nimg()

int LstFastIO::get_nimg ( )

virtual

Return the number of images in this image file.

Reimplemented from EMAN::ImageIO.

Definition at line 235 of file lstfastio.cpp.

{
        init();
        return nimg;
}

References EMAN::ImageIO::init(), and nimg.

◆ is_single_image_format()

bool EMAN::LstFastIO::is_single_image_format ( ) const

inlinevirtual

Is this image format only storing 1 image or not.

Some image formats like MRC only store 1 image in a file, so this function returns 'true' for them. Other image formats like IMAGIC/HDF5 may store mutliple images, so this function returns 'false' for them.

Reimplemented from EMAN::ImageIO.

Definition at line 63 of file lstfastio.h.

                {
                        return false;
                }

◆ is_valid()

bool LstFastIO::is_valid ( const void * first_block )

static

Definition at line 111 of file lstfastio.cpp.

{
        ENTERFUNC;
        bool result = false;
 
        if (!first_block) {
                result = false;
        }
        else {
                result = Util::check_file_by_magic(first_block, MAGIC);
        }
 
        if (result) {
                for (int i=0; i<1024; i++) {
                        char c = ((const char *)first_block)[i];
                        if (c==0) break;
                        if (c==13) { 
//                              printf("%1024s\n",(const char *)first_block);
                                printf("ERROR: .lst file contains \\r at pos %d. This should never happen. (If you edit a .lst file with a text editor on Windows, it will corrupt the file). Aborting program.\n",i);
                                exit(1);
                        }
                }
        }
        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::LstFastIO::DEFINE_IMAGEIO_FUNC

Definition at line 60 of file lstfastio.h.

◆ head_length

unsigned int EMAN::LstFastIO::head_length

private

Definition at line 72 of file lstfastio.h.

Referenced by calc_ref_image_index().

◆ imageio

ImageIO* EMAN::LstFastIO::imageio

private

Definition at line 74 of file lstfastio.h.

Referenced by calc_ref_image_index(), LstFastIO(), and ~LstFastIO().

◆ is_big_endian

bool EMAN::LstFastIO::is_big_endian

private

Definition at line 69 of file lstfastio.h.

Referenced by LstFastIO().

◆ last_lst_index

int EMAN::LstFastIO::last_lst_index

private

Definition at line 77 of file lstfastio.h.

Referenced by calc_ref_image_index(), and LstFastIO().

◆ last_ref_index

int EMAN::LstFastIO::last_ref_index

private

Definition at line 78 of file lstfastio.h.

Referenced by calc_ref_image_index(), and LstFastIO().

◆ line_length

unsigned int EMAN::LstFastIO::line_length

private

Definition at line 71 of file lstfastio.h.

Referenced by calc_ref_image_index().

◆ MAGIC

const char * LstFastIO::MAGIC = "#LSX"

staticprivate

Definition at line 81 of file lstfastio.h.

Referenced by is_valid().

◆ nimg

int EMAN::LstFastIO::nimg

private

Definition at line 70 of file lstfastio.h.

Referenced by get_nimg(), and LstFastIO().

◆ ref_filename

string EMAN::LstFastIO::ref_filename

private

Definition at line 75 of file lstfastio.h.

Referenced by calc_ref_image_index(), LstFastIO(), and ~LstFastIO().

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

Public Member Functions

Static Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

comment

line-length

Constructor & Destructor Documentation

◆ LstFastIO()

◆ ~LstFastIO()

Member Function Documentation

◆ calc_ref_image_index()

◆ get_nimg()

◆ is_single_image_format()

◆ is_valid()

Member Data Documentation

◆ DEFINE_IMAGEIO_FUNC

◆ head_length

◆ imageio

◆ is_big_endian

◆ last_lst_index

◆ last_ref_index

◆ line_length

◆ MAGIC

◆ nimg

◆ ref_filename