PIF(Portable Image Format for EM Data) is an image format from Purdue University. More...

#include <pifio.h>

Inheritance diagram for EMAN::PifIO:

Collaboration diagram for EMAN::PifIO:

[legend]

Classes
struct	PifColorMap

struct	PifFileHeader

struct	PifImageHeader

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

	~PifIO ()

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 Types
enum	{ PIF_MAGIC_NUM = 8 }

enum	PifDataMode { PIF_CHAR = 0 , PIF_SHORT = 1 , PIF_FLOAT_INT = 2 , PIF_SHORT_COMPLEX = 3 , PIF_FLOAT_INT_COMPLEX = 4 , PIF_BOXED_DATA = 6 , PIF_SHORT_FLOAT = 7 , PIF_SHORT_FLOAT_COMPLEX = 8 , PIF_FLOAT = 9 , PIF_FLOAT_COMPLEX = 10 , PIF_MAP_FLOAT_SHORT = 20 , PIF_MAP_FLOAT_INT = 21 , PIF_MAP_FLOAT_INT_2 = 40 , PIF_BOXED_FLOAT_INT = 46 , PIF_INVALID }

Private Member Functions
int	get_mode_size (PifDataMode mode)

bool	is_float_int (int mode)

void	fseek_to (int image_index)

int	to_em_datatype (int pif_datatype)

int	to_pif_datatype (int em_datatype)

Private Attributes
string	filename

PifFileHeader	pfh

int	mode_size

bool	is_big_endian

bool	is_new_file

float	real_scale_factor

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

PIF(Portable Image Format for EM Data) is an image format from Purdue University.

A PIF file = file header + (image header + image data) + (image header + image data) ...

A PIF file has a overall file header followed by n images. Each image has a header and data block.

EMAN only supports homogeneous PIF file, which means all images n a PIF should have the same dimensions. We also assume the (nx,ny,nz) in PifFileHeader are equal to (nx,ny,nz) in each Image header.

Definition at line 52 of file pifio.h.

Member Enumeration Documentation

◆ anonymous enum

anonymous enum

private

Enumerator
PIF_MAGIC_NUM

Definition at line 68 of file pifio.h.

                {
                        PIF_MAGIC_NUM = 8
                };

◆ PifDataMode

enum EMAN::PifIO::PifDataMode

private

Enumerator
PIF_CHAR
PIF_SHORT
PIF_FLOAT_INT
PIF_SHORT_COMPLEX
PIF_FLOAT_INT_COMPLEX
PIF_BOXED_DATA
PIF_SHORT_FLOAT
PIF_SHORT_FLOAT_COMPLEX
PIF_FLOAT
PIF_FLOAT_COMPLEX
PIF_MAP_FLOAT_SHORT
PIF_MAP_FLOAT_INT
PIF_MAP_FLOAT_INT_2
PIF_BOXED_FLOAT_INT
PIF_INVALID

Definition at line 73 of file pifio.h.

                {
                        PIF_CHAR = 0,
                        PIF_SHORT = 1,
                        PIF_FLOAT_INT = 2,
                        PIF_SHORT_COMPLEX = 3,
                        PIF_FLOAT_INT_COMPLEX = 4,
                        PIF_BOXED_DATA = 6,                     // byte, read as 0
                        PIF_SHORT_FLOAT = 7,
                        PIF_SHORT_FLOAT_COMPLEX = 8,
                        PIF_FLOAT = 9,
                        PIF_FLOAT_COMPLEX = 10,
                        PIF_MAP_FLOAT_SHORT = 20,
                        PIF_MAP_FLOAT_INT = 21,
                        PIF_MAP_FLOAT_INT_2 = 40,                       // 4 byte floatint, read as 2
                        PIF_BOXED_FLOAT_INT = 46,               // 4 byte floatint, read as 2
                        PIF_INVALID
                };

Constructor & Destructor Documentation

◆ PifIO()

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

explicit

Definition at line 44 of file pifio.cpp.

:       ImageIO(fname, rw)
{
        file = 0;
        mode_size = 0;
        is_big_endian = ByteOrder::is_host_big_endian();
        real_scale_factor = 1;
        is_new_file = false;
        memset(&pfh, 0, sizeof(PifFileHeader));
}

References EMAN::ImageIO::file, is_big_endian, EMAN::ByteOrder::is_host_big_endian(), is_new_file, mode_size, pfh, and real_scale_factor.

◆ ~PifIO()

PifIO::~PifIO ( )

Definition at line 55 of file pifio.cpp.

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

References EMAN::ImageIO::file.

Member Function Documentation

◆ fseek_to()

void PifIO::fseek_to ( int image_index )

private

Definition at line 193 of file pifio.cpp.

{
        int pih_sz = sizeof(PifImageHeader);
        int image_size = 0;
 
#if 0
        // this works for some images that PURDUE people gave to me.
        // But those images don't follow the PIF specification. So
        // I believe they are in wrong format.
        if (pfh.nimg == 1) {
                image_size = pfh.nx * pfh.ny * pfh.nz;
        }
        else {
                image_size = pfh.nx * pfh.ny;
        }
#endif
        image_size = pfh.nx * pfh.ny * pfh.nz;
 
        size_t file_offset = sizeof(PifFileHeader) +
                (pih_sz + image_size * mode_size) * image_index;
 
        portable_fseek(file, file_offset, SEEK_SET);
}

References EMAN::ImageIO::file, mode_size, EMAN::PifIO::PifFileHeader::nimg, EMAN::PifIO::PifFileHeader::nx, EMAN::PifIO::PifFileHeader::ny, EMAN::PifIO::PifFileHeader::nz, pfh, and portable_fseek().

◆ get_mode_size()

int PifIO::get_mode_size ( PifDataMode mode )

private

Definition at line 64 of file pifio.cpp.

{
        int size = 0;
 
        switch (mode) {
        case PIF_CHAR:
        case PIF_BOXED_DATA:
                size = sizeof(char);
                break;
        case PIF_SHORT:
        case PIF_SHORT_FLOAT:
        case PIF_SHORT_COMPLEX:
        case PIF_SHORT_FLOAT_COMPLEX:
        case PIF_MAP_FLOAT_SHORT:
                size = sizeof(short);
                break;
        case PIF_FLOAT:
        case PIF_FLOAT_COMPLEX:
                size = sizeof(float);
                break;
        case PIF_FLOAT_INT:
        case PIF_FLOAT_INT_COMPLEX:
        case PIF_MAP_FLOAT_INT:
        case PIF_MAP_FLOAT_INT_2:
        case PIF_BOXED_FLOAT_INT:
                size = sizeof(int);
                break;
        default:
                break;
        }
        return size;
}

References PIF_BOXED_DATA, PIF_BOXED_FLOAT_INT, PIF_CHAR, PIF_FLOAT, PIF_FLOAT_COMPLEX, PIF_FLOAT_INT, PIF_FLOAT_INT_COMPLEX, PIF_MAP_FLOAT_INT, PIF_MAP_FLOAT_INT_2, PIF_MAP_FLOAT_SHORT, PIF_SHORT, PIF_SHORT_COMPLEX, PIF_SHORT_FLOAT, and PIF_SHORT_FLOAT_COMPLEX.

◆ get_nimg()

int PifIO::get_nimg ( )

virtual

Return the number of images in this image file.

Reimplemented from EMAN::ImageIO.

Definition at line 540 of file pifio.cpp.

{
        init();
        return pfh.nimg;
}

References EMAN::ImageIO::init(), EMAN::PifIO::PifFileHeader::nimg, and pfh.

◆ is_float_int()

bool PifIO::is_float_int ( int mode )

private

Definition at line 97 of file pifio.cpp.

{
        PifDataMode mode = static_cast < PifDataMode > (m);
        switch (mode) {
        case PIF_SHORT_FLOAT:
        case PIF_SHORT_FLOAT_COMPLEX:
        //case PIF_FLOAT:
        case PIF_FLOAT_INT:
        //case PIF_FLOAT_COMPLEX:
        case PIF_FLOAT_INT_COMPLEX:
        case PIF_MAP_FLOAT_SHORT:
        case PIF_MAP_FLOAT_INT:
        case PIF_MAP_FLOAT_INT_2:
        case PIF_BOXED_FLOAT_INT:
                return true;
        default:
                break;
        }
        return false;
}

References PIF_BOXED_FLOAT_INT, PIF_FLOAT_INT, PIF_FLOAT_INT_COMPLEX, PIF_MAP_FLOAT_INT, PIF_MAP_FLOAT_INT_2, PIF_MAP_FLOAT_SHORT, PIF_SHORT_FLOAT, and PIF_SHORT_FLOAT_COMPLEX.

◆ is_single_image_format()

bool EMAN::PifIO::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 61 of file pifio.h.

                {
                        return false;
                }

◆ is_valid()

bool PifIO::is_valid ( const void * first_block )

static

Definition at line 164 of file pifio.cpp.

{
        ENTERFUNC;
        bool result = false;
 
        if (first_block) {
                const int *data = static_cast < const int *>(first_block);
                int m1 = data[0];
                int m2 = data[1];
                int endian = data[7];
                bool data_big_endian = false;
                if (endian) {
                        data_big_endian = true;
                }
 
                if (data_big_endian != ByteOrder::is_host_big_endian()) {
                        ByteOrder::swap_bytes(&m1);
                        ByteOrder::swap_bytes(&m2);
                }
 
                if (m1 == PIF_MAGIC_NUM && m2 == PIF_MAGIC_NUM) {
                         result = true;
                }
        }
 
        EXITFUNC;
        return result;
}

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

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

◆ to_em_datatype()

int PifIO::to_em_datatype ( int pif_datatype )

private

Definition at line 547 of file pifio.cpp.

{
        PifDataMode mode = static_cast < PifDataMode > (p);
        EMUtil::EMDataType e = EMUtil::EM_UNKNOWN;
 
        switch (mode) {
        case PIF_CHAR:
        case PIF_BOXED_DATA:
                e = EMUtil::EM_CHAR;
                break;
 
        case PIF_SHORT:
        case PIF_SHORT_FLOAT:
        case PIF_MAP_FLOAT_SHORT:
                e = EMUtil::EM_SHORT;
                break;
 
        case PIF_SHORT_COMPLEX:
        case PIF_SHORT_FLOAT_COMPLEX:
                e = EMUtil::EM_SHORT_COMPLEX;
                break;
 
        case PIF_FLOAT:
        case PIF_FLOAT_INT:
        case PIF_MAP_FLOAT_INT:
        case PIF_MAP_FLOAT_INT_2:
        case PIF_BOXED_FLOAT_INT:
                e = EMUtil::EM_FLOAT;
                break;
        case PIF_FLOAT_COMPLEX:
        case PIF_FLOAT_INT_COMPLEX:
                e = EMUtil::EM_FLOAT_COMPLEX;
                break;
        case PIF_INVALID:
                e = EMUtil::EM_UNKNOWN;
                break;
        }
        return e;
}

References EMAN::EMUtil::EM_CHAR, EMAN::EMUtil::EM_FLOAT, EMAN::EMUtil::EM_FLOAT_COMPLEX, EMAN::EMUtil::EM_SHORT, EMAN::EMUtil::EM_SHORT_COMPLEX, EMAN::EMUtil::EM_UNKNOWN, PIF_BOXED_DATA, PIF_BOXED_FLOAT_INT, PIF_CHAR, PIF_FLOAT, PIF_FLOAT_COMPLEX, PIF_FLOAT_INT, PIF_FLOAT_INT_COMPLEX, PIF_INVALID, PIF_MAP_FLOAT_INT, PIF_MAP_FLOAT_INT_2, PIF_MAP_FLOAT_SHORT, PIF_SHORT, PIF_SHORT_COMPLEX, PIF_SHORT_FLOAT, and PIF_SHORT_FLOAT_COMPLEX.

◆ to_pif_datatype()

int PifIO::to_pif_datatype ( int em_datatype )

private

Definition at line 587 of file pifio.cpp.

{
        PifDataMode m = PIF_INVALID;
 
        switch (e) {
        case EMUtil::EM_CHAR:
                m = PIF_BOXED_DATA;
                break;
        case EMUtil::EM_SHORT:
                m = PIF_SHORT;
                break;
        case EMUtil::EM_SHORT_COMPLEX:
                m = PIF_SHORT_COMPLEX;
                break;
        case EMUtil::EM_FLOAT:
                m = PIF_FLOAT_INT;
                break;
        case EMUtil::EM_FLOAT_COMPLEX:
                m = PIF_FLOAT_COMPLEX;
                break;
        default:
                LOGERR("unknown PIF mode: %d", e);
        }
 
        return m;
}

References EMAN::EMUtil::EM_CHAR, EMAN::EMUtil::EM_FLOAT, EMAN::EMUtil::EM_FLOAT_COMPLEX, EMAN::EMUtil::EM_SHORT, EMAN::EMUtil::EM_SHORT_COMPLEX, LOGERR, PIF_BOXED_DATA, PIF_FLOAT_COMPLEX, PIF_FLOAT_INT, PIF_INVALID, PIF_SHORT, and PIF_SHORT_COMPLEX.

Member Data Documentation

◆ DEFINE_IMAGEIO_FUNC

EMAN::PifIO::DEFINE_IMAGEIO_FUNC

Definition at line 58 of file pifio.h.

◆ filename

string EMAN::PifIO::filename

private

Definition at line 174 of file pifio.h.

◆ is_big_endian

bool EMAN::PifIO::is_big_endian

private

Definition at line 177 of file pifio.h.

Referenced by PifIO().

◆ is_new_file

bool EMAN::PifIO::is_new_file

private

Definition at line 178 of file pifio.h.

Referenced by PifIO().

◆ mode_size

int EMAN::PifIO::mode_size

private

Definition at line 176 of file pifio.h.

Referenced by fseek_to(), and PifIO().

◆ pfh

PifFileHeader EMAN::PifIO::pfh

private

Definition at line 175 of file pifio.h.

Referenced by fseek_to(), get_nimg(), and PifIO().

◆ real_scale_factor

float EMAN::PifIO::real_scale_factor

private

Definition at line 179 of file pifio.h.

Referenced by PifIO().

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

◆ anonymous enum

◆ PifDataMode

Constructor & Destructor Documentation

◆ PifIO()

◆ ~PifIO()

Member Function Documentation

◆ fseek_to()

◆ get_mode_size()

◆ get_nimg()

◆ is_float_int()

◆ is_single_image_format()

◆ is_valid()

◆ to_em_datatype()

◆ to_pif_datatype()

Member Data Documentation

◆ DEFINE_IMAGEIO_FUNC

◆ filename

◆ is_big_endian

◆ is_new_file

◆ mode_size

◆ pfh

◆ real_scale_factor