EMAN::ImagicIO Class Reference

IMAGIC-5 Header File Format. More...

#include <imagicio.h>

Inheritance diagram for EMAN::ImagicIO:

Collaboration diagram for EMAN::ImagicIO:

Classes
struct	ImagicHeader

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

Static Public Attributes
static const char *	HED_EXT = "hed"
static const char *	IMG_EXT = "img"

Private Types
enum	DataType {   IMAGIC_UCHAR , IMAGIC_USHORT , IMAGIC_FLOAT , IMAGIC_FLOAT_COMPLEX ,   IMAGIC_FFT_FLOAT_COMPLEX , IMAGIC_UNKNOWN_TYPE }
enum	{ NUM_4BYTES_PRE_IXOLD = 14 , NUM_4BYTES_AFTER_IXOLD = 14 , NUM_4BYTES_AFTER_SPACE = 207 }

Private Member Functions
size_t	get_datatype_size (DataType t)
int	to_em_datatype (DataType t)
void	make_header_host_endian (ImagicHeader &hed)
void	swap_header (ImagicHeader &hed)
DataType	get_datatype_from_name (const char *name)
Ctf *	read_ctf (const ImagicHeader &hed) const
	the Ctf object is a EMAN1Ctf object. More...
void	write_ctf (const Ctf *const ctf, int image_index=0)

Private Attributes
string	hed_filename
string	img_filename
FILE *	hed_file
FILE *	img_file
ImagicHeader	imagich
bool	is_big_endian
bool	is_new_hed
bool	is_new_img
DataType	datatype
int	nz

Static Private Attributes
static const char *	REAL_TYPE_MAGIC = "REAL"
static const char *	CTF_MAGIC = "!-"

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

IMAGIC-5 Header File Format.

An IMAGIC-5 file has 2 files: a) a header file with extension ".hed". It contains information for every image. b) an image file with extension ".img". It contains raw data.

The header file contains one (fixed-size) record per image stored. Every header record consists of 256 REAL/float for every image.

The image file contains only the raw data. Depending on the internal IMAGIC-5 format used, which can be REAL, INTG, PACK or COMP, the data is stored as REAL/float, INTEGER/int, INTEGER*1/byte or 2x REAL/float, respectively. The first pixel stored is the upper left one. The data is stored line by line, section by section, volume by volume.

3D imagic uses the same format to 2D. it is a bunch of 2D slices. use the 'hint' IS_3D to treat "2D slices" as 3D volume.

imagic doesn't store multiple 3D images in one file (header/data pair).

Definition at line 65 of file imagicio.h.

Member Enumeration Documentation

anonymous enum

anonymous enum

private

Enumerator
NUM_4BYTES_PRE_IXOLD
NUM_4BYTES_AFTER_IXOLD
NUM_4BYTES_AFTER_SPACE

Definition at line 99 of file imagicio.h.

                {
                        NUM_4BYTES_PRE_IXOLD = 14,
                        NUM_4BYTES_AFTER_IXOLD = 14,
                        NUM_4BYTES_AFTER_SPACE = 207
                };

DataType

enum EMAN::ImagicIO::DataType

private

Enumerator
IMAGIC_UCHAR
IMAGIC_USHORT
IMAGIC_FLOAT
IMAGIC_FLOAT_COMPLEX
IMAGIC_FFT_FLOAT_COMPLEX
IMAGIC_UNKNOWN_TYPE

Definition at line 89 of file imagicio.h.

                {
                        IMAGIC_UCHAR,
                        IMAGIC_USHORT,
                        IMAGIC_FLOAT,
                        IMAGIC_FLOAT_COMPLEX,
                        IMAGIC_FFT_FLOAT_COMPLEX,
                        IMAGIC_UNKNOWN_TYPE
                };

Constructor & Destructor Documentation

ImagicIO()

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

explicit

Definition at line 50 of file imagicio.cpp.

:       ImageIO(fname, rw), hed_file(0), img_file(0)
{
        hed_filename = Util::change_filename_ext(filename, HED_EXT);
        img_filename = Util::change_filename_ext(filename, IMG_EXT);
 
        is_big_endian = ByteOrder::is_host_big_endian();
        is_new_hed = false;
        is_new_img = false;
        memset(&imagich, 0, sizeof(ImagicHeader));
        imagich.count = -1;
        datatype = IMAGIC_UNKNOWN_TYPE;
        nz = 0;
}

References EMAN::Util::change_filename_ext(), EMAN::ImagicIO::ImagicHeader::count, datatype, EMAN::ImageIO::filename, HED_EXT, hed_filename, IMAGIC_UNKNOWN_TYPE, imagich, IMG_EXT, img_filename, is_big_endian, EMAN::ByteOrder::is_host_big_endian(), is_new_hed, is_new_img, and nz.

~ImagicIO()

ImagicIO::~ImagicIO

(

)

Definition at line 65 of file imagicio.cpp.

{
        if (hed_file) {
                fclose(hed_file);
                hed_file = 0;
        }
 
        if (img_file) {
                fclose(img_file);
                img_file = 0;
        }
}

References hed_file, and img_file.

Member Function Documentation

get_datatype_from_name()

ImagicIO::DataType ImagicIO::get_datatype_from_name ( const char *  name )

private

Definition at line 628 of file imagicio.cpp.

{
        DataType t = IMAGIC_UNKNOWN_TYPE;
 
        if (strncmp(name, "PACK",4) == 0) {
                t = IMAGIC_UCHAR;
        }
        else if (strncmp(name, "INTG",4) == 0) {
                t = IMAGIC_USHORT;
        }
        else if (strncmp(name, REAL_TYPE_MAGIC,4) == 0) {
                t = IMAGIC_FLOAT;
        }
        else if (strncmp(name, "COMP",4) == 0) {
                t = IMAGIC_FLOAT_COMPLEX;
        }
        else if (strncmp(name, "RECO",4) == 0) {
                t = IMAGIC_FFT_FLOAT_COMPLEX;
        }
        return t;
}

References IMAGIC_FFT_FLOAT_COMPLEX, IMAGIC_FLOAT, IMAGIC_FLOAT_COMPLEX, IMAGIC_UCHAR, IMAGIC_UNKNOWN_TYPE, IMAGIC_USHORT, and REAL_TYPE_MAGIC.

get_datatype_size()

size_t ImagicIO::get_datatype_size ( DataType  t )

private

Definition at line 650 of file imagicio.cpp.

{
        size_t s = 0;
        switch (t) {
        case IMAGIC_UCHAR:
                s = sizeof(unsigned char);
                break;
        case IMAGIC_USHORT:
                s = sizeof(unsigned short);
                break;
        case IMAGIC_FLOAT:
        case IMAGIC_FLOAT_COMPLEX:
        case IMAGIC_FFT_FLOAT_COMPLEX:
                s = sizeof(float);
                break;
        default:
                s = 0;
        }
 
        return s;
}

References IMAGIC_FFT_FLOAT_COMPLEX, IMAGIC_FLOAT, IMAGIC_FLOAT_COMPLEX, IMAGIC_UCHAR, and IMAGIC_USHORT.

get_nimg()

int ImagicIO::get_nimg ( )

virtual

Return the number of images in this image file.

Reimplemented from EMAN::ImageIO.

Definition at line 622 of file imagicio.cpp.

{
        init();
        return (imagich.count + 1);
}

References EMAN::ImagicIO::ImagicHeader::count, imagich, and EMAN::ImageIO::init().

is_single_image_format()

bool EMAN::ImagicIO::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 77 of file imagicio.h.

                {
                        return false;
                }

is_valid()

bool ImagicIO::is_valid ( const void *  first_block )

static

Definition at line 121 of file imagicio.cpp.

{
        ENTERFUNC;
 
        if (!first_block) {
                return false;
        }
 
        const int *data = static_cast < const int *>(first_block);
        int count = data[1];
        int headrec = data[3];
        int month = data[5];
        int hour = data[7];
        int nx = data[13];
        int ny = data[12];
        
        bool data_big_endian = ByteOrder::is_data_big_endian(&headrec);
 
        if (data_big_endian != ByteOrder::is_host_big_endian()) {
                ByteOrder::swap_bytes(&count);
                ByteOrder::swap_bytes(&headrec);
                ByteOrder::swap_bytes(&month);
                ByteOrder::swap_bytes(&hour);
                ByteOrder::swap_bytes(&nx);
                ByteOrder::swap_bytes(&ny);
        }
 
        const int max_dim = 1 << 20;
        bool result = false;
 
        if (headrec == 1 &&
                count >= 0 && count < max_dim &&
                nx > 0 && nx < max_dim &&
                ny > 0 && ny < max_dim && month >= 0 && hour >= 0 && hour <= 24) {
                result = true;
        }
 
        EXITFUNC;
        return result;
}

References ENTERFUNC, EXITFUNC, EMAN::ByteOrder::is_data_big_endian(), EMAN::ByteOrder::is_host_big_endian(), and EMAN::ByteOrder::swap_bytes().

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

make_header_host_endian()

void ImagicIO::make_header_host_endian ( ImagicHeader &  hed )

private

Definition at line 690 of file imagicio.cpp.

{
        if (is_big_endian != ByteOrder::is_host_big_endian()) {
                swap_header(hed);
        }
}

References is_big_endian, EMAN::ByteOrder::is_host_big_endian(), and swap_header().

read_ctf()

Ctf * ImagicIO::read_ctf ( const ImagicHeader &  hed ) const

private

the Ctf object is a EMAN1Ctf object.

Definition at line 567 of file imagicio.cpp.

{
        ENTERFUNC;
 
        Ctf * ctf_ = 0;
        size_t n = strlen(CTF_MAGIC);
 
        if (strncmp(imagich.label, CTF_MAGIC, n) == 0) {
                ctf_ = new EMAN1Ctf();
                string header_label(hed.label);
                // Note: this block was making things crash because it assumed the following if statement
                // was true - I added the if statement (d.woolford)
                if (header_label.size() > 2) {
                        string sctf = "O" + header_label.substr(2);
                        ctf_->from_string(sctf);
                }
        }
 
        EXITFUNC;
        return ctf_;
}

References CTF_MAGIC, ENTERFUNC, EXITFUNC, EMAN::Ctf::from_string(), imagich, and EMAN::ImagicIO::ImagicHeader::label.

swap_header()

void ImagicIO::swap_header ( ImagicHeader &  hed )

private

Definition at line 698 of file imagicio.cpp.

{
        ByteOrder::swap_bytes((int *) &hed, NUM_4BYTES_PRE_IXOLD);
        ByteOrder::swap_bytes(&hed.ixold, NUM_4BYTES_AFTER_IXOLD);
        ByteOrder::swap_bytes((int *) &hed.space, NUM_4BYTES_AFTER_SPACE);
}

References EMAN::ImagicIO::ImagicHeader::ixold, NUM_4BYTES_AFTER_IXOLD, NUM_4BYTES_AFTER_SPACE, NUM_4BYTES_PRE_IXOLD, EMAN::ImagicIO::ImagicHeader::space, and EMAN::ByteOrder::swap_bytes().

Referenced by make_header_host_endian().

to_em_datatype()

int ImagicIO::to_em_datatype ( DataType  t )

private

Definition at line 672 of file imagicio.cpp.

{
        switch (t) {
        case IMAGIC_UCHAR:
                return EMUtil::EM_UCHAR;
        case IMAGIC_USHORT:
                return EMUtil::EM_USHORT;
        case IMAGIC_FLOAT:
                return EMUtil::EM_FLOAT;
        case IMAGIC_FLOAT_COMPLEX:
                return EMUtil::EM_FLOAT_COMPLEX;
        default:
                break;
        }
 
        return EMUtil::EM_UNKNOWN;
}

References EMAN::EMUtil::EM_FLOAT, EMAN::EMUtil::EM_FLOAT_COMPLEX, EMAN::EMUtil::EM_UCHAR, EMAN::EMUtil::EM_UNKNOWN, EMAN::EMUtil::EM_USHORT, IMAGIC_FLOAT, IMAGIC_FLOAT_COMPLEX, IMAGIC_UCHAR, and IMAGIC_USHORT.

write_ctf()

void ImagicIO::write_ctf ( const Ctf *const  ctf, int  image_index = 0  )

private

Definition at line 589 of file imagicio.cpp.

{
        ENTERFUNC;
        init();
 
        size_t n = strlen(CTF_MAGIC);
        strcpy(imagich.label, CTF_MAGIC);
        string ctf_ = ctf->to_string().substr(1);
        strncpy(&imagich.label[n], ctf_.c_str(), sizeof(imagich.label) - n);
 
        rewind(hed_file);
        if (fwrite(&imagich, sizeof(ImagicHeader), 1, hed_file) != 1) {
                throw ImageWriteException(hed_filename, "Imagic Header");
        }
 
        EXITFUNC;
}

References CTF_MAGIC, ENTERFUNC, EXITFUNC, hed_file, hed_filename, ImageWriteException, imagich, EMAN::ImageIO::init(), EMAN::ImagicIO::ImagicHeader::label, and EMAN::Ctf::to_string().

Member Data Documentation

CTF_MAGIC

const char * ImagicIO::CTF_MAGIC = "!-"

staticprivate

Definition at line 86 of file imagicio.h.

Referenced by read_ctf(), and write_ctf().

datatype

DataType EMAN::ImagicIO::datatype

private

Definition at line 193 of file imagicio.h.

Referenced by ImagicIO().

DEFINE_IMAGEIO_FUNC

EMAN::ImagicIO::DEFINE_IMAGEIO_FUNC

Definition at line 74 of file imagicio.h.

HED_EXT

const char * ImagicIO::HED_EXT = "hed"

static

Definition at line 68 of file imagicio.h.

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

hed_file

FILE* EMAN::ImagicIO::hed_file

private

Definition at line 185 of file imagicio.h.

Referenced by write_ctf(), and ~ImagicIO().

hed_filename

string EMAN::ImagicIO::hed_filename

private

Definition at line 182 of file imagicio.h.

Referenced by ImagicIO(), and write_ctf().

imagich

ImagicHeader EMAN::ImagicIO::imagich

private

Definition at line 188 of file imagicio.h.

Referenced by get_nimg(), ImagicIO(), read_ctf(), and write_ctf().

IMG_EXT

const char * ImagicIO::IMG_EXT = "img"

static

Definition at line 69 of file imagicio.h.

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

img_file

FILE* EMAN::ImagicIO::img_file

private

Definition at line 186 of file imagicio.h.

Referenced by ~ImagicIO().

img_filename

string EMAN::ImagicIO::img_filename

private

Definition at line 183 of file imagicio.h.

Referenced by ImagicIO().

is_big_endian

bool EMAN::ImagicIO::is_big_endian

private

Definition at line 189 of file imagicio.h.

Referenced by ImagicIO(), and make_header_host_endian().

is_new_hed

bool EMAN::ImagicIO::is_new_hed

private

Definition at line 190 of file imagicio.h.

Referenced by ImagicIO().

is_new_img

bool EMAN::ImagicIO::is_new_img

private

Definition at line 191 of file imagicio.h.

Referenced by ImagicIO().

nz

int EMAN::ImagicIO::nz

private

Definition at line 194 of file imagicio.h.

Referenced by ImagicIO().

REAL_TYPE_MAGIC

const char * ImagicIO::REAL_TYPE_MAGIC = "REAL"

staticprivate

Definition at line 85 of file imagicio.h.

Referenced by get_datatype_from_name().

---

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

• imagicio.h
• imagicio.cpp