SER (Series File Format) is a file format created by Dr. More...

#include <serio.h>

Inheritance diagram for EMAN::SerIO:

Collaboration diagram for EMAN::SerIO:

[legend]

Classes
struct	SerHeader

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

	~SerIO ()

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...

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	SerImgMode { oneD = 0x4120 , twoD = 0x4122 }

enum	SerTagType { timeOnly = 0x4152 , posTime = 0x4122 }

enum	SerDataMode { SER_UCHAR = 1 , SER_USHORT , SER_UINT , SER_CHAR , SER_SHORT , SER_INT , SER_FLOAT , SER_DOUBLE , SER_COMPLEX8 , SER_COMPLEX16 , UNKNOWN }

Private Member Functions
void	read_dim_arr (Dict &dict, int idx)
	helper function to read attributes in dimension array More...

void	read_data_element (Dict &dict)
	helper function to read header attributes in data element More...

void	read_data_tag (Dict &dict)
	helper function to read header attributes in data tag More...

Private Attributes
bool	is_new_file

SerHeader	serh

uint64_t *	data_offset_array

uint64_t *	tag_offset_array

int	nimg

int	nx

int	ny

int	nz

int	datatypeid

int	datamode

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

SER (Series File Format) is a file format created by Dr.

Chris Boothroyd. The file format is used by TIA (Tecnai imaging and analysis), which is the program used on FEI Tecnai and Titan microscopes for acquiring and displaying scanned images and spectra.

Each .ser file stores a number of 1D or 2D images. We do not support complex SER image for now.

http://www.microscopy.cen.dtu.dk/~cbb/info/TIAformat/index.html

Definition at line 55 of file serio.h.

Member Enumeration Documentation

◆ SerDataMode

enum EMAN::SerIO::SerDataMode

private

Enumerator
SER_UCHAR
SER_USHORT
SER_UINT
SER_CHAR
SER_SHORT
SER_INT
SER_FLOAT
SER_DOUBLE
SER_COMPLEX8
SER_COMPLEX16
UNKNOWN

Definition at line 76 of file serio.h.

                                 {
                        SER_UCHAR = 1,
                        SER_USHORT,
                        SER_UINT,
                        SER_CHAR,
                        SER_SHORT,
                        SER_INT,
                        SER_FLOAT,
                        SER_DOUBLE,
                        SER_COMPLEX8,
                        SER_COMPLEX16,
                        UNKNOWN
                };

◆ SerImgMode

enum EMAN::SerIO::SerImgMode

private

Enumerator
oneD
twoD

Definition at line 66 of file serio.h.

                                {
                        oneD = 0x4120,
                        twoD = 0x4122
                };

◆ SerTagType

enum EMAN::SerIO::SerTagType

private

Enumerator
timeOnly
posTime

Definition at line 71 of file serio.h.

                                {
                        timeOnly = 0x4152,
                        posTime  = 0x4122
                };

Constructor & Destructor Documentation

◆ SerIO()

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

explicit

Definition at line 45 of file serio.cpp.

                                            :
                ImageIO(fname, rw),
                is_new_file(false), data_offset_array(0),tag_offset_array(0),
                nimg(0), nx(0), ny(0), nz(0), datatypeid(0), datamode(0)
{
}

◆ ~SerIO()

SerIO::~SerIO ( )

Definition at line 52 of file serio.cpp.

{
        if (file) {
                fclose(file);
                file = 0;
        }
 
        if (data_offset_array) {
                delete [] data_offset_array;
                data_offset_array = 0;
        }
 
        if (tag_offset_array) {
                delete [] tag_offset_array;
                tag_offset_array = 0;
        }
}

References data_offset_array, EMAN::ImageIO::file, and tag_offset_array.

Member Function Documentation

◆ get_nimg()

int SerIO::get_nimg ( )

virtual

Return the number of images in this image file.

Reimplemented from EMAN::ImageIO.

Definition at line 368 of file serio.cpp.

                    {
        init();
 
        portable_fseek(file, ValidNumberElementsOffset, SEEK_SET);
        int nimg;
        if (fread(&nimg, sizeof(int), 1, file) != 1) {
                throw ImageReadException(filename, "SER header");
        }
 
        return nimg;
}

References EMAN::ImageIO::file, EMAN::ImageIO::filename, ImageReadException, EMAN::ImageIO::init(), nimg, portable_fseek(), and ValidNumberElementsOffset.

◆ is_valid()

bool SerIO::is_valid ( const void * first_block )

static

Definition at line 94 of file serio.cpp.

{
        ENTERFUNC;
 
        if (!first_block) {
                return false;
        }
 
        const short *data = static_cast < const short *>(first_block);
        short ByteOrder = data[0];
        short SeriesID = data[1];
 
        if(ByteOrder != 0x4949 || SeriesID != 0x0197) {
                return false;
        }
 
        EXITFUNC;
        return true;
}

References ENTERFUNC, and EXITFUNC.

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

◆ read_data_element()

void SerIO::read_data_element ( Dict & dict )

private

helper function to read header attributes in data element

Definition at line 441 of file serio.cpp.

{
        if(this->datatypeid == oneD) {  //1D image
                double hitem4[2];
                if (fread(hitem4, sizeof(double), 2, file) != 2) {
                        throw ImageReadException(filename, "SER header");
                }
                dict["SER.CalibrationOffset"]   = hitem4[0];
                dict["SER.CalibrationDelta"]    = hitem4[1];
 
                int cali;
                if (fread(&cali, sizeof(int), 1, file) != 1) {
                        throw ImageReadException(filename, "SER header");
                }
                dict["SER.CalibrationElement"] = cali;
 
                short datatype;
                if (fread(&datatype, sizeof(short), 1, file) != 1) {
                        throw ImageReadException(filename, "SER header");
                }
                dict["SER.DataType"] = datatype;
 
                int arrlen;
                if (fread(&arrlen, sizeof(int), 1, file) != 1) {
                        throw ImageReadException(filename, "SER header");
                }
                dict["nx"] = arrlen;
                dict["ny"] = 1;
                dict["nz"] = 1;
 
                nx = arrlen;
                ny = 1;
                nz = 1;
        }
        else if(this->datatypeid == twoD) {     //2D image
                double hitem4[2];
                if (fread(hitem4, sizeof(double), 2, file) != 2) {
                        throw ImageReadException(filename, "SER header");
                }
                dict["SER.CalibrationOffsetX"]  = hitem4[0];
                dict["SER.CalibrationDeltaX"]   = hitem4[1];
 
                int calix;
                if (fread(&calix, sizeof(int), 1, file) != 1) {
                        throw ImageReadException(filename, "SER header");
                }
                dict["SER.CalibrationElementX"] = calix;
 
                double hitem5[2];
                if (fread(hitem5, sizeof(double), 2, file) != 2) {
                        throw ImageReadException(filename, "SER header");
                }
                dict["SER.CalibrationOffsetX"]  = hitem5[0];
                dict["SER.CalibrationDeltaX"]   = hitem5[1];
 
                int caliy;
                if (fread(&caliy, sizeof(int), 1, file) != 1) {
                        throw ImageReadException(filename, "SER header");
                }
                dict["SER.CalibrationElementY"] = caliy;
 
                short datatype;
                if (fread(&datatype, sizeof(short), 1, file) != 1) {
                        throw ImageReadException(filename, "SER header");
                }
                dict["SER.DataType"] = datatype;
                this->datamode = datatype;
 
                int arrsize[2];
                if (fread(&arrsize, sizeof(int), 2, file) != 2) {
                        throw ImageReadException(filename, "SER header");
                }
                dict["nx"] = arrsize[0];
                dict["ny"] = arrsize[1];
                dict["nz"] = 1;
 
                nx = arrsize[0];
                ny = arrsize[1];
                nz = 1;
        }
}

References datamode, datatypeid, EMAN::ImageIO::file, EMAN::ImageIO::filename, ImageReadException, nx, ny, nz, oneD, and twoD.

◆ read_data_tag()

void SerIO::read_data_tag ( Dict & dict )

private

helper function to read header attributes in data tag

Definition at line 523 of file serio.cpp.

{
        int tag_type = (int)dict["SER.TagTypeID"];
        if( tag_type == timeOnly ) {
                short tagtype;
                if (fread(&tagtype, sizeof(short), 1, file) != 1) {
                        throw ImageReadException(filename, "SER header");
                }
                assert((int)tagtype == tag_type);
 
                int sertime;
                if (fread(&sertime, sizeof(int), 1, file) != 1) {
                        throw ImageReadException(filename, "SER header");
                }
                dict["SER.Time"] = sertime;
        }
        else if( tag_type == posTime ) {
                short tagtype;
                if (fread(&tagtype, sizeof(short), 1, file) != 1) {
                        throw ImageReadException(filename, "SER header");
                }
                assert((int)tagtype == tag_type);
 
                int sertime;
                if (fread(&sertime, sizeof(int), 1, file) != 1) {
                        throw ImageReadException(filename, "SER header");
                }
                dict["SER.Time"] = sertime;
 
                double pos[2];
                if (fread(&pos, sizeof(double), 2, file) != 2) {
                        throw ImageReadException(filename, "SER header");
                }
                dict["SER.PosionX"] = pos[0];
                dict["SER.PosionY"] = pos[1];
        }
        else {
                throw ImageReadException(filename, "SER header, wrong TagTypeID");
        }
}

References EMAN::ImageIO::file, EMAN::ImageIO::filename, ImageReadException, posTime, and timeOnly.

◆ read_dim_arr()

void SerIO::read_dim_arr	(	Dict &	dict,
		int	idx
	)

private

helper function to read attributes in dimension array

Definition at line 380 of file serio.cpp.

{
        int dimsize;
        if (fread(&dimsize, sizeof(int), 1, file) != 1) {
                throw ImageReadException(filename, "SER header");
        }
 
        string sidx = Util::int2str(idx);
        dict["SER.DimensionSize"+sidx]  = dimsize;
 
        double hitem3[2];
        if (fread(hitem3, sizeof(double), 2, file) != 2) {
                throw ImageReadException(filename, "SER header");
        }
        dict["SER.CalibrationOffset"+sidx]      = hitem3[0];
        dict["SER.CalibrationDelta"+sidx]       = hitem3[1];
 
        int celement;
        if (fread(&celement, sizeof(int), 1, file) != 1) {
                throw ImageReadException(filename, "SER header");
        }
        dict["SER.CalibrationElement"+sidx]     = celement;
 
        int desclen;
        if (fread(&desclen, sizeof(int), 1, file) != 1) {
                throw ImageReadException(filename, "SER header");
        }
        dict["SER.DescriptionLength"+sidx]      = desclen;
 
        if(desclen != 0) {
                char * descr = new char[desclen+1];
                //char descr[desclen+1];
                if (fread(descr, sizeof(char), desclen, file) != (unsigned int)desclen) {
                        throw ImageReadException(filename, "SER header");
                }
                descr[desclen] = '\0';
                string sdescr(descr);
                dict["SER.Description"+sidx] = sdescr;
                delete [] descr;
        }
 
        int unitslen;
        if (fread(&unitslen, sizeof(int), 1, file) != 1) {
                throw ImageReadException(filename, "SER header");
        }
        dict["SER.UnitsLength"+sidx] = unitslen;
 
        if(unitslen != 0) {
                char * units = new char[unitslen+1];
                //char units[unitslen+1];
                if (fread(units, sizeof(int), unitslen, file) != (unsigned int)unitslen) {
                        throw ImageReadException(filename, "SER header");
                }
                units[unitslen] = '\0';
                string sunits(units);
                dict["SER.Units"+sidx] = sunits;
                delete [] units;
        }
 
}

References EMAN::ImageIO::file, EMAN::ImageIO::filename, ImageReadException, and EMAN::Util::int2str().

Member Data Documentation

◆ data_offset_array

uint64_t* EMAN::SerIO::data_offset_array

private

Definition at line 108 of file serio.h.

Referenced by ~SerIO().

◆ datamode

int EMAN::SerIO::datamode

private

Definition at line 116 of file serio.h.

Referenced by read_data_element().

◆ datatypeid

int EMAN::SerIO::datatypeid

private

Definition at line 115 of file serio.h.

Referenced by read_data_element().

◆ DEFINE_IMAGEIO_FUNC

EMAN::SerIO::DEFINE_IMAGEIO_FUNC

Definition at line 61 of file serio.h.

◆ is_new_file

bool EMAN::SerIO::is_new_file

private

Definition at line 104 of file serio.h.

◆ nimg

int EMAN::SerIO::nimg

private

Definition at line 111 of file serio.h.

Referenced by get_nimg().

◆ nx

int EMAN::SerIO::nx

private

Definition at line 112 of file serio.h.

Referenced by read_data_element().

◆ ny

int EMAN::SerIO::ny

private

Definition at line 113 of file serio.h.

Referenced by read_data_element().

◆ nz

int EMAN::SerIO::nz

private

Definition at line 114 of file serio.h.

Referenced by read_data_element().

◆ serh

SerHeader EMAN::SerIO::serh

private

Definition at line 106 of file serio.h.

◆ tag_offset_array

uint64_t* EMAN::SerIO::tag_offset_array

private

Definition at line 109 of file serio.h.

Referenced by ~SerIO().

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

Classes

Public Member Functions

Static Public Member Functions

Public Attributes

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ SerDataMode

◆ SerImgMode

◆ SerTagType

Constructor & Destructor Documentation

◆ SerIO()

◆ ~SerIO()

Member Function Documentation

◆ get_nimg()

◆ is_valid()

◆ read_data_element()

◆ read_data_tag()

◆ read_dim_arr()

Member Data Documentation

◆ data_offset_array

◆ datamode

◆ datatypeid

◆ DEFINE_IMAGEIO_FUNC

◆ is_new_file

◆ nimg

◆ nx

◆ ny

◆ nz

◆ serh

◆ tag_offset_array