situs is a a Situs-specific format on a cubic lattice. More...

#include <situsio.h>

Inheritance diagram for EMAN::SitusIO:

Collaboration diagram for EMAN::SitusIO:

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

	~SitusIO ()

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 int	get_nimg ()
	Return the number of images in this image file. 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 Attributes
bool	is_new_file

float	apix

float	origx

float	origy

float	origz

int	nx

int	ny

int	nz

Static Private Attributes
static const int	SITUS_HEADER_LINES =2

static const int	FLOAT_SIZE = 12

static const int	NFLOAT_PER_LINE = 10

static const char *	OUTFORMAT = "%12.6f"

static const int	LINE_LENGTH = 1024

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

situs is a a Situs-specific format on a cubic lattice.

This allows Situs programs to keep track of coordinate systems and it makes the core Situs programs independent of the ever changing map format standards. In the editable (ASCII or text) Situs format, a short header holds the voxel spacing WIDTH, the map origin as defined by the 3D coordinates of the first voxel ORIGX, ORIGY, ORIGZ, and the map dimensions (number of increments) NX, NY, NZ. This minimalist header is followed by the data fields such that x increments change fastest and z increments change slowest. http://situs.biomachina.org/fguide.html#map2map

Definition at line 48 of file situsio.h.

Constructor & Destructor Documentation

◆ SitusIO()

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

explicit

Definition at line 44 of file situsio.cpp.

                                                :
                ImageIO(fname, rw),
                is_new_file(false),
                apix(0.0f), origx(0.0f), origy(0.0f), origz(0.0f),
                nx(0), ny(0), nz(0)
{
}

◆ ~SitusIO()

SitusIO::~SitusIO ( )

Definition at line 52 of file situsio.cpp.

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

References EMAN::ImageIO::file.

Member Function Documentation

◆ is_valid()

bool SitusIO::is_valid ( const void * first_block )

static

Definition at line 182 of file situsio.cpp.

{
        ENTERFUNC;
        if (!first_block) {
                return false;
        }
 
        char *buf = (char *)(first_block);
        string line1 = Util::get_line_from_string(&buf);
 
        if(line1.size()==0) return false;
 
        float apix, origx, origy, origz;
        int nx, ny, nz, missing;
 
        // We're looking for exactly 7
        if(sscanf(line1.c_str(), "%f %f %f %f %d %d %d %d", &apix, &origx, &origy, &origz, &nx, &ny, &nz,&missing) != 7) return false;
 
        if(apix<0.01 || apix>100) return false;
        if(nx<=0 || ny<0 || nz<0) return false;
 
        EXITFUNC;
        return true;
}

References apix, ENTERFUNC, EXITFUNC, EMAN::Util::get_line_from_string(), nx, ny, nz, origx, origy, and origz.

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

Member Data Documentation

◆ apix

float EMAN::SitusIO::apix

private

Definition at line 61 of file situsio.h.

Referenced by is_valid().

◆ DEFINE_IMAGEIO_FUNC

EMAN::SitusIO::DEFINE_IMAGEIO_FUNC

Definition at line 54 of file situsio.h.

◆ FLOAT_SIZE

const int SitusIO::FLOAT_SIZE = 12

staticprivate

Definition at line 65 of file situsio.h.

◆ is_new_file

bool EMAN::SitusIO::is_new_file

private

Definition at line 59 of file situsio.h.

◆ LINE_LENGTH

const int SitusIO::LINE_LENGTH = 1024

staticprivate

Definition at line 68 of file situsio.h.

const char * SitusIO::OUTFORMAT = "%12.6f"

staticprivate

Definition at line 67 of file situsio.h.

◆ SITUS_HEADER_LINES

const int SitusIO::SITUS_HEADER_LINES =2

staticprivate

Definition at line 64 of file situsio.h.

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

Public Member Functions

Static Public Member Functions

Public Attributes

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SitusIO()

◆ ~SitusIO()

Member Function Documentation

◆ is_valid()

Member Data Documentation

◆ apix

◆ DEFINE_IMAGEIO_FUNC

◆ FLOAT_SIZE

◆ is_new_file

◆ LINE_LENGTH

◆ NFLOAT_PER_LINE

◆ nx

◆ ny

◆ nz

◆ origx

◆ origy

◆ origz

◆ OUTFORMAT

◆ SITUS_HEADER_LINES