Single Spider Image I/O class. More...

#include <sspiderio.h>

Inheritance diagram for EMAN::SingleSpiderIO:

Collaboration diagram for EMAN::SingleSpiderIO:

[legend]

Public Member Functions
	SingleSpiderIO (const string &fname, IOMode rw_mode=READ_ONLY)
	SingleSpiderIO constructor. More...

	~SingleSpiderIO ()

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)
	Write a single SPIDER format header to an image. More...

int	write_data (float data, int image_index=0, const Region area=0, EMUtil::EMDataType filestoragetype=EMUtil::EM_FLOAT, bool use_host_endian=true)
	Write data to an image. More...

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

Public Member Functions inherited from EMAN::SpiderIO
	SpiderIO (const string &fname, IOMode rw_mode=READ_ONLY)

	~SpiderIO ()

int	get_nimg ()
	get the number of images in this stacked SPIDER image 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	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	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)

Static Public Member Functions inherited from EMAN::SpiderIO
static bool	is_valid (const void *first_block)

Protected Member Functions
bool	is_valid_spider (const void *first_block)
	check the data block to see if it represents valid stacked SPIDER image file header More...

Protected Member Functions inherited from EMAN::SpiderIO
int	write_single_header (const Dict &dict, const Region area, int image_index, size_t offset, SpiderHeader &hp, int ISTACK, int MAXIM=1, int IMGNUM=1, bool use_host_endian=true)
	write a SPIDER header to spider_file More...

int	write_single_data (float data, const Region area, SpiderHeader *&hp, size_t offset, int img_index, int max_nimg, bool use_host_endian=true)
	write a single image data More...

bool	need_swap () const

void	swap_data (float *data, size_t nitems)

void	swap_header (SpiderHeader *header)

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...

Additional Inherited Members
Public Types inherited from EMAN::ImageIO
enum	IOMode { READ_ONLY = 1 , READ_WRITE = 2 , WRITE_ONLY = 3 }

Public Attributes inherited from EMAN::SpiderIO
	DEFINE_IMAGEIO_FUNC

Protected Types inherited from EMAN::SpiderIO
enum	SpiderType { IMAGE_2D = 1 , IMAGE_3D = 3 , IMAGE_2D_FFT_ODD = -11 , IMAGE_2D_FFT_EVEN = -12 , IMAGE_3D_FFT_ODD = -21 , IMAGE_3D_FFT_EVEN = -22 }

enum	{ SINGLE_IMAGE_HEADER = 0 , OVERALL_STACK_HEADER = 2 , NUM_FLOATS_IN_HEADER = 211 }

Protected Attributes inherited from EMAN::SpiderIO
SpiderHeader *	first_h

SpiderHeader *	cur_h

bool	is_big_endian

bool	is_new_file

Protected Attributes inherited from EMAN::ImageIO
string	filename

IOMode	rw_mode

FILE *	file = nullptr

bool	initialized = false

Detailed Description

Single Spider Image I/O class.

For Spider and Single Spider image format, please refer spiderio.h.

See also: spiderio.h

Definition at line 44 of file sspiderio.h.

Constructor & Destructor Documentation

◆ SingleSpiderIO()

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

explicit

SingleSpiderIO constructor.

Parameters

filename	The filename of a single spider image file.
rw_mode	Read/Write file open mode.

Definition at line 40 of file sspiderio.cpp.

:       SpiderIO(fname, rw)
{
}

◆ ~SingleSpiderIO()

SingleSpiderIO::~SingleSpiderIO ( )

Definition at line 46 of file sspiderio.cpp.

47{

48}

Member Function Documentation

◆ is_single_image_format()

bool EMAN::SingleSpiderIO::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::SpiderIO.

Definition at line 86 of file sspiderio.h.

                {
                        return true;
                }

◆ is_valid()

bool SingleSpiderIO::is_valid ( const void * first_block )

static

Definition at line 71 of file sspiderio.cpp.

{
        ENTERFUNC;
        bool result = false;
        
        if (first_block) {
                const float *data = static_cast < const float *>(first_block);
                float nslice = data[0];
                float nrow = data[1];
                float iform = data[4];
                float nsam = data[11];
                float labrec = data[12];        //NO. of records in file header
                float labbyt = data[21];        //total NO. of bytes in header
                float lenbyt = data[22];        //record length in bytes
                float istack = data[23];
                
                bool big_endian = ByteOrder::is_float_big_endian(nslice);
                if (big_endian != ByteOrder::is_host_big_endian()) {
                        ByteOrder::swap_bytes(&nslice);
                        ByteOrder::swap_bytes(&nrow);
                        ByteOrder::swap_bytes(&iform);
                        ByteOrder::swap_bytes(&nsam);
                        ByteOrder::swap_bytes(&labrec);
                        ByteOrder::swap_bytes(&labbyt);
                        ByteOrder::swap_bytes(&lenbyt);
                        ByteOrder::swap_bytes(&istack);
                }
                
                if( int(nslice) != nslice || int(nrow) != nrow
                                || int(iform) != iform || int(nsam) != nsam 
                                || int(labrec) != labrec || int(labbyt) != labbyt
                                || int(lenbyt) != lenbyt ) {
                        result =  false;
                }
                else {
                        int itype = static_cast < int >(iform);
                        if( int(istack) != SINGLE_IMAGE_HEADER ) {
                                result = false; //istack>0 for overall header, istack<0 for indexed stack of image
                        }
                        else if( itype == IMAGE_2D_FFT_ODD || itype == IMAGE_2D_FFT_EVEN 
                                        || itype == IMAGE_3D_FFT_ODD || itype == IMAGE_3D_FFT_EVEN ) {
                                result = false; //Complex SPIDER image not supported in EMAN2
                        }
                        else if (itype == IMAGE_2D || itype == IMAGE_3D) {
                                result = true;
                        }
                }
                
                int ilabrec = static_cast<int>(labrec);
                int ilabbyt = static_cast<int>(labbyt);
                int ilenbyt = static_cast<int>(lenbyt);
                if( ilabbyt != ilabrec * ilenbyt ) {
                        result = false;
                }
        }
 
        EXITFUNC;
        return result;
}

References ENTERFUNC, EXITFUNC, EMAN::SpiderIO::IMAGE_2D, EMAN::SpiderIO::IMAGE_2D_FFT_EVEN, EMAN::SpiderIO::IMAGE_2D_FFT_ODD, EMAN::SpiderIO::IMAGE_3D, EMAN::SpiderIO::IMAGE_3D_FFT_EVEN, EMAN::SpiderIO::IMAGE_3D_FFT_ODD, EMAN::ByteOrder::is_float_big_endian(), EMAN::ByteOrder::is_host_big_endian(), EMAN::SpiderIO::SINGLE_IMAGE_HEADER, and EMAN::ByteOrder::swap_bytes().

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

◆ is_valid_spider()

bool SingleSpiderIO::is_valid_spider ( const void * first_block )

protectedvirtual

check the data block to see if it represents valid stacked SPIDER image file header

Parameters

first_block the pointer to first block of the file

Returns: boolean result of the check, true for valid stacked SPIDER image

Reimplemented from EMAN::SpiderIO.

Definition at line 132 of file sspiderio.cpp.

{
        return SingleSpiderIO::is_valid(first_block);
}

References is_valid().

◆ write_data()

int SingleSpiderIO::write_data	(	float *	data,
		int	image_index = `0`,
		const Region *	area = `0`,
		EMUtil::EMDataType	filestoragetype = `EMUtil::EM_FLOAT`,
		bool	use_host_endian = `true`
	)

virtual

Write data to an image.

Parameters

data	An array storing the data.
image_index	The index of the image to write.
area	The region to write data to.
filestoragetype	The image data type used in the output file.
use_host_endian	Whether to use the host machine endian to write out or not. If false, use the endian opposite to the host machine's endian.

Returns: 0 if OK; 1 if error.

Implements EMAN::ImageIO.

Definition at line 63 of file sspiderio.cpp.

{
        size_t offset = (int) first_h->headlen;
        return write_single_data(data, area, first_h, offset, 0, 1, use_host_endian);
}

References EMAN::SpiderIO::first_h, EMAN::SpiderIO::SpiderHeader::headlen, and EMAN::SpiderIO::write_single_data().

◆ write_header()

int SingleSpiderIO::write_header	(	const Dict &	dict,
		int	image_index = `0`,
		const Region *	area = `0`,
		EMUtil::EMDataType	filestoragetype = `EMUtil::EM_FLOAT`,
		bool	use_host_endian = `true`
	)

virtual

Write a single SPIDER format header to an image.

Parameters

dict	A keyed-dictionary storing the header information.
image_index	The index of the image to write.
area	The region to write data to.
filestoragetype	The image data type used in the output file.
use_host_endian	Whether to use the host machine endian to write out or not. If false, use the endian opposite to the host machine's endian.

Returns: 0 if OK; 1 if error.

Implements EMAN::ImageIO.

Definition at line 51 of file sspiderio.cpp.

{
        size_t offset = 0;
        int image_index = 0;
//      if(!use_host_endian) {
//              ByteOrder::swap_bytes((float*)first_h, NUM_FLOATS_IN_HEADER);
//      }
        return write_single_header(dict, area, image_index, offset, first_h, SINGLE_IMAGE_HEADER, 1, 1, use_host_endian);
}

References EMAN::SpiderIO::first_h, EMAN::SpiderIO::SINGLE_IMAGE_HEADER, and EMAN::SpiderIO::write_single_header().

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

Public Member Functions

Static Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SingleSpiderIO()

◆ ~SingleSpiderIO()

Member Function Documentation

◆ is_single_image_format()

◆ is_valid()

◆ is_valid_spider()

◆ write_data()

◆ write_header()