Collaboration diagram for ECAT6 ... ECAT8 support in the IO library:

Files
file	ECAT7DynamicDiscretisedDensityOutputFileFormat.cxx
	Implementation of class stir::ecat::ecat7::ECAT7DynamicDiscretisedDensityOutputFileFormat.

file	add_ecat7_header_to_sgl.cxx
	Prepend contents of ECAT7 header to a new sgl file (from list mode acquisition)

file	show_ecat7_header.cxx
	Show contents of ECAT7 header.

file	ecat6_types.h
	ECAT 6 CTI matrix parameters.

file	ecat6_utils.h
	Declaration of ECAT 6 CTI functions to access data.

file	ECAT6ImageInputFileFormat.h
	Declaration of class stir::ecat::ecat6::ECAT6ImageInputFileFormat.

file	ECAT6OutputFileFormat.h
	Declaration of class stir::ecat::ecat7::ECAT6OutputFileFormat.

file	ECAT7DynamicDiscretisedDensityInputFileFormat.h
	Declaration of class stir::ecat::ecat7::ECAT7DynamicDiscretisedDensityInputFileFormat.

file	ECAT7DynamicDiscretisedDensityOutputFileFormat.h
	Declaration of class stir::ecat::ecat7::ECAT7DynamicDiscretisedDensityOutputFileFormat.

file	ECAT7ImageInputFileFormat.h
	Declaration of class stir::ecat::ecat7::ECAT7ImageInputFileFormat.

file	ECAT7OutputFileFormat.h
	Declaration of class stir::ecat::ecat7::ECAT7OutputFileFormat.

file	ECAT7ParametricDensityOutputFileFormat.h
	Declaration of class stir::ecat::ecat7::ECAT7ParametricDensityOutputFileFormat.

file	ECAT8_32bitListmodeInputFileFormat.h
	Declaration of class stir::ecat::ECAT8_32bitListmodeInputFileFormat.

file	ECAT962ListmodeInputFileFormat.h
	Declaration of class stir::ecat::ecat7::ECAT962ListmodeInputFileFormat.

file	ECAT966ListmodeInputFileFormat.h
	Declaration of class stir::ecat::ecat7::ECAT966ListmodeInputFileFormat.

file	InterfileHeaderSiemens.h
	This file declares the classes stir::InterfileHeaderSiemens, stir::InterfileRawDataHeaderSiemens, stir::InterfilePDFSHeaderSiemens, stir::InterfileListmodeHeaderSiemens, stir:InterfileNormHeaderSiemens.

file	stir_ecat6.h
	Declaration of routines which convert ECAT6 things into our building blocks and vice versa.

file	stir_ecat7.h
	Declaration of routines which convert CTI things into our building blocks and vice versa.

file	stir_ecat_common.h
	Declaration of routines which convert ECAT things into our building blocks and vice versa.

file	ecat6_utils.cxx
	Implementation of ECAT 6 CTI functions to access data.

file	ECAT6OutputFileFormat.cxx
	Implementation of class stir::ECAT6OutputFileFormat.

file	ECAT7DynamicDiscretisedDensityInputFileFormat.cxx
	Implementation of class stir::ecat::ecat7::ECAT7DynamicDiscretisedDensityInputFileFormat.

file	ECAT7DynamicDiscretisedDensityOutputFileFormat.cxx
	Implementation of class stir::ecat::ecat7::ECAT7DynamicDiscretisedDensityOutputFileFormat.

file	ECAT7OutputFileFormat.cxx
	Implementation of class stir::ecat::ecat7::ECAT7OutputFileFormat.

file	ECAT7ParametricDensityOutputFileFormat.cxx
	Implementation of class stir::ecat::ecat7::ECAT7ParametricDensityOutputFileFormat.

file	stir_ecat6.cxx
	Implementation of routines which convert CTI things into our building blocks and vice versa.

file	stir_ecat7.cxx
	Implementation of routines which convert ECAT7 things into our building blocks and vice versa.

file	stir_ecat_common.cxx
	Implementation of routines which convert ECAT6, ECAT7 and ECAT8 things into our building blocks and vice versa.

file	add_ecat7_header_to_sgl.cxx
	Prepend contents of ECAT7 header to a new sgl file (from list mode acquisition)

file	BinNormalisationFromECAT7.cxx
	Implementation for class stir::ecat::ecat7::BinNormalisationFromECAT7.

file	BinNormalisationFromECAT8.cxx
	Implementation for class stir::ecat::BinNormalisationFromECAT8.

file	copy_ecat7_header.cxx
	Copy contents of an ECAT7 header from 1 file to another.

file	ecat_swap_corners.cxx
	A (slightly dangerous) utility to perform so-called corner-swapping for ECAT6 projection data.

file	is_ecat7_file.cxx
	A simple utility that allows to check if a file is in the ECAT7 format.

Classes
class	stir::ecat::ecat6::ECAT6ImageInputFileFormat
	Class for reading images in ECAT6 file-format. More...

class	stir::ecat::ecat6::ECAT6OutputFileFormat
	Implementation of OutputFileFormat paradigm for the ECAT6 format. More...

class	stir::ecat::ecat7::ECAT7DynamicDiscretisedDensityInputFileFormat
	Class for reading images in ECAT7 file-format. More...

class	stir::ecat::ecat7::ECAT7DynamicDiscretisedDensityOutputFileFormat
	Implementation of OutputFileFormat paradigm for the ECAT7 format. More...

class	stir::ecat::ecat7::ECAT7ImageInputFileFormat
	Class for reading images in ECAT7 file-format. More...

class	stir::ecat::ecat7::ECAT7OutputFileFormat
	Implementation of OutputFileFormat paradigm for the ECAT7 format. More...

class	stir::ecat::ecat7::ECAT7ParametricDensityOutputFileFormat< DiscretisedDensityT >
	Implementation of OutputFileFormat paradigm for the ECAT7 format. More...

class	stir::ecat::ECAT8_32bitListmodeInputFileFormat
	Class for being able to read list mode data from the ECAT 8_32bit scanner via the listmode-data registry. More...

class	stir::ecat::ecat7::ECAT962ListmodeInputFileFormat
	Class for reading list mode data from the ECAT 962 scanner. More...

class	stir::ecat::ecat7::ECAT966ListmodeInputFileFormat
	Class for reading list mode data from the ECAT 966 scanner. More...

class	stir::InterfileHeaderSiemens
	a class for Interfile keywords (and parsing) common to all types of data More...

class	stir::InterfileRawDataHeaderSiemens
	a class for Interfile keywords (and parsing) specific to Siemens PET projection, list mode data or norm data More...

class	stir::InterfilePDFSHeaderSiemens
	a class for Interfile keywords (and parsing) specific to projection data (i.e. ProjDataFromStream) for Siemens PET scanners More...

class	stir::InterfileListmodeHeaderSiemens
	a class for Interfile keywords (and parsing) specific to Siemens listmode data (in PETLINK format) More...

class	stir::InterfileNormHeaderSiemens
	a class for Interfile keywords (and parsing) specific to Siemens (component-based) normalisation data More...

class	stir::ecat::ecat7::BinNormalisationFromECAT7
	A BinNormalisation class that gets the normalisation factors from an ECAT7 3D normalisation file. More...

class	stir::ecat::BinNormalisationFromECAT8
	A BinNormalisation class that gets the normalisation factors from an ECAT8 3D normalisation file. Note that you have to point it to the "Interfile" header. More...

struct	stir::ecat::ecat6::ScanInfoRec
	ECAT 6 CTI scanner parameters. More...

Enumerations
enum	stir::ecat::ECATDataType { ECAT_unknown_data_type = 0 , ECAT_Byte_data_type = 1 , ECAT_I2_little_endian_data_type = 2 , ECAT_I4_little_endian_data_type = 3 , ECAT_R4_VAX_data_type = 4 , ECAT_R4_IEEE_big_endian_data_type = 5 , ECAT_I2_big_endian_data_type = 6 , ECAT_I4_big_endian_data_type = 7 }
	Possible values for the data_type field in ECAT headers. More...

Functions
long	stir::ecat::ecat6::cti_numcod (int frame, int plane, int gate, int data, int bed)
	Encode scan information into a single, incomprehensible number.

void	stir::ecat::ecat6::cti_numdoc (long matnum, Matval *matval)
	Unpack encoded data into a nice struct. Reverse of cti_numcod ().

int	stir::ecat::ecat6::cti_rings2plane (short nrings, short ring0, short ring1)
	Get sinogram plane from ring pair.

FILE *	stir::ecat::ecat6::cti_create (const char fname, const ECAT6_Main_header mhead)
	Open a file and write main header to it. Returns a pointer to the file, or 0 if unsuccessful.

int	stir::ecat::ecat6::cti_rblk (FILE fptr, int blkno, void bufr, int nblks)
	Read from a matrix file starting at the given block. Returns EXIT_SUCCESS if all went well.

int	stir::ecat::ecat6::cti_wblk (FILE fptr, int blkno, void bufr, int nblks)
	Write blocks from buffer into file. Returns EXIT_SUCCESS if successful.

int	stir::ecat::ecat6::cti_read_ECAT6_Main_header (FILE fptr, ECAT6_Main_header h)
	Read header data from a file and place it into a ECAT6_Main_header struct. Returns EXIT_SUCCESS if no error.

int	stir::ecat::ecat6::cti_read_scan_subheader (FILE fptr, const ECAT6_Main_header , int blknum, Scan_subheader *)
	Read header data from a file and place it into a Scan_subheader struct. Returns EXIT_SUCCESS if no error.

int	stir::ecat::ecat6::cti_read_attn_subheader (FILE fptr, const ECAT6_Main_header h, int blknum, Attn_subheader *header_ptr)
	Read header data from a file and place it into a Attn_subheader struct. Returns EXIT_SUCCESS if no error.

int	stir::ecat::ecat6::cti_read_norm_subheader (FILE fptr, const ECAT6_Main_header h, int blknum, Norm_subheader *header_ptr)
	Read header data from a file and place it into a Norm_subheader struct. Returns EXIT_SUCCESS if no error.

int	stir::ecat::ecat6::cti_read_image_subheader (FILE fptr, const ECAT6_Main_header h, int blknum, Image_subheader *header_ptr)
	Read header data from a file and place it into an Image_subheader struct. Returns EXIT_SUCCESS if no error.

int	stir::ecat::ecat6::cti_enter (FILE fptr, const ECAT6_Main_header mhead_ptr, long matnum, int nblks)
	Create entry in file corresponding to matnum, and return offset of next block. Or some such. Returns 0 if there was an error.

int	stir::ecat::ecat6::cti_lookup (FILE fptr, const ECAT6_Main_header mhead_ptr, long matnum, MatDir *entry)
	Look up a "matrix number" in the file and return the MatDir entry for it. Returns 0 if the lookup was NOT successful.

int	stir::ecat::ecat6::cti_write_idata (FILE fptr, int blk, const short data, int isize)
	Write data in blocks from buffer into file.

int	stir::ecat::ecat6::cti_write_image_subheader (FILE fptr, const ECAT6_Main_header h, int blknum, const Image_subheader *header_ptr)
	Write an image subheader into a matrix file. Returns 0 if successful.

int	stir::ecat::ecat6::cti_write_ECAT6_Main_header (FILE fptr, const ECAT6_Main_header header_ptr)
	Write an image main header into a matrix file. Returns 0 if successful.

int	stir::ecat::ecat6::cti_write_scan_subheader (FILE fptr, const ECAT6_Main_header h, int blknum, const Scan_subheader *header_ptr)
	Write a scan subheader into a matrix file.

int	stir::ecat::ecat6::cti_write_image (FILE fptr, long matnum, const ECAT6_Main_header mhead_ptr, const Image_subheader header_ptr, const short data, int data_size)
	Write an image, including headers, into a matrix file.

int	stir::ecat::ecat6::cti_write_scan (FILE fptr, long matnum, const ECAT6_Main_header mhead_ptr, const Scan_subheader header_ptr, const short data, int data_size)
	Write a scan, including headers, into a matrix file.

int	stir::ecat::ecat6::get_scanheaders (FILE fptr, long matnum, ECAT6_Main_header mhead, Scan_subheader shead, ScanInfoRec scanParams)
	Read main header and subheader from scan file. Returns EXIT_SUCCESS if no error.

int	stir::ecat::ecat6::get_scandata (FILE fptr, char scan, ScanInfoRec *scanParams)
	Read scan data from file. Returns EXIT_FAILURE if the data could not be read.

int	stir::ecat::ecat6::get_attnheaders (FILE fptr, long matnum, ECAT6_Main_header mhead, Attn_subheader shead, ScanInfoRec attnParams)
	Read main header and subheader from attn file. Returns EXIT_SUCCESS if no error.

int	stir::ecat::ecat6::get_normheaders (FILE fptr, long matnum, ECAT6_Main_header mhead, Norm_subheader shead, ScanInfoRec nrmParams)
	Read main header and subheader from normalisation file. Returns EXIT_SUCCESS if no error.

bool	stir::ecat::ecat6::is_ECAT6_file (const std::string &filename)
	checks if the file is in ECAT6 format

bool	stir::ecat::ecat6::is_ECAT6_image_file (const std::string &filename)
	checks if the file is in ECAT6 format and if the file contains images

bool	stir::ecat::ecat6::is_ECAT6_emission_file (const std::string &filename)
	checks if the file is in ECAT6 format and if the file contains emission sinograms (or blank/transmision)

bool	stir::ecat::ecat6::is_ECAT6_attenuation_file (const std::string &filename)
	checks if the file is in ECAT6 format and if the file contains attenuation correction factors

Scanner *	stir::ecat::ecat6::find_scanner_from_ECAT6_Main_header (const ECAT6_Main_header &mhead)
	determine scanner type from the ECAT6_Main_header

Succeeded	stir::ecat::ecat6::DiscretisedDensity_to_ECAT6 (DiscretisedDensity< 3, float > const &density, std::string const &cti_name, std::string const &orig_name, const Scanner &scanner, const int frame_num=1, const int gate_num=1, const int data_num=0, const int bed_num=0)
	Create a new ECAT6 image file and write the data in there.

Succeeded	stir::ecat::ecat6::DiscretisedDensity_to_ECAT6 (FILE *fptr, DiscretisedDensity< 3, float > const &density, const ECAT6_Main_header &mhead, const int frame_num=1, const int gate_num=1, const int data_num=0, const int bed_num=0)
	Write an (extra) image to an existing ECAT6 file.

Succeeded	stir::ecat::ecat6::ProjData_to_ECAT6 (ProjData const &proj_data, std::string const &cti_name, std::string const &orig_name, const int frame_num=1, const int gate_num=1, const int data_num=0, const int bed_num=0, const bool write_2D_sinograms=false)
	Create a new ECAT6 sinogram file and write the data in there.

Succeeded	stir::ecat::ecat6::ProjData_to_ECAT6 (FILE *fptr, ProjData const &proj_data, const ECAT6_Main_header &mhead, const int frame_num=1, const int gate_num=1, const int data_num=0, const int bed_num=0, const bool write_2D_sinograms=false)
	Write an (extra) set of sinograms to an existing ECAT6 file.

void	stir::ecat::ecat6::make_ECAT6_Main_header (ECAT6_Main_header &, const Scanner &, const std::string &orig_name, ExamInfo const &exam_info)
	Fill in most of the main header given a Scanner object and orig_name.

void	stir::ecat::ecat6::make_ECAT6_Main_header (ECAT6_Main_header &mhead, Scanner const &scanner, const std::string &orig_name, DiscretisedDensity< 3, float > const &density)
	Fill in most of the main header given a Scanner object and orig_name and an image.

void	stir::ecat::ecat6::make_ECAT6_Main_header (ECAT6_Main_header &mhead, const std::string &orig_name, ProjDataInfo const &proj_data_info)
	Fill in most of the main header given an orig_name and a proj_data_info.

bool	stir::ecat::ecat7::is_ECAT7_file (const std::string &filename)
	checks if the file is in ECAT7 formatThis partly relies on the implementation of matrix_open in the LLN matrix library. Additional checks are made on the main header. Current checks are:

bool	stir::ecat::ecat7::is_ECAT7_image_file (const std::string &filename)
	checks if the file is in ECAT6 format and if the file contains images

bool	stir::ecat::ecat7::is_ECAT7_emission_file (const std::string &filename)
	checks if the file is in ECAT6 format and if the file contains emission sinograms (or blank/transmision)

bool	stir::ecat::ecat7::is_ECAT7_attenuation_file (const std::string &filename)
	checks if the file is in ECAT6 format and if the file contains attenuation correction factors

void	stir::ecat::ecat7::find_scanner (shared_ptr< Scanner > &scanner_ptr, const Main_header &mhead)
	determine scanner type from the main_header

Succeeded	stir::ecat::ecat7::DiscretisedDensity_to_ECAT7 (DiscretisedDensity< 3, float > const &density, std::string const &cti_name, std::string const &orig_name, const Scanner &scanner, const int frame_num=1, const int gate_num=1, const int data_num=0, const int bed_num=0)
	Create a new ECAT7 image file and write the data in there.

Succeeded	stir::ecat::ecat7::DiscretisedDensity_to_ECAT7 (MatrixFile *mptr, DiscretisedDensity< 3, float > const &density, const int frame_num=1, const int gate_num=1, const int data_num=0, const int bed_num=0)
	Write an (extra) image to an existing ECAT7 file.

Succeeded	stir::ecat::ecat7::ProjData_to_ECAT7 (ProjData const &proj_data, NumericType output_type, std::string const &cti_name, std::string const &orig_name, const int frame_num=1, const int gate_num=1, const int data_num=0, const int bed_num=0, const bool write_as_attenuation=false, float scale_factor=0.0F)
	Create a new ECAT7 sinogram file and write the data in there.

Succeeded	stir::ecat::ecat7::ProjData_to_ECAT7 (MatrixFile *mptr, ProjData const &proj_data, const int frame_num=1, const int gate_num=1, const int data_num=0, const int bed_num=0, float scale_factor=0.0F)
	Write an (extra) set of sinograms to an existing ECAT7 file.

void	stir::ecat::ecat7::make_ECAT7_main_header (Main_header &, const Scanner &, const std::string &orig_name, ExamInfo const &exam_info)
	Fill in most of the main header given a Scanner object and orig_name.

void	stir::ecat::ecat7::make_ECAT7_main_header (Main_header &mhead, Scanner const &scanner, const std::string &orig_name, DiscretisedDensity< 3, float > const &density)
	Fill in most of the main header given a Scanner object and orig_name and an image.

NumericType	stir::ecat::ecat7::make_ECAT7_main_header (Main_header &mhead, const std::string &orig_name, ExamInfo const &exam_info, ProjDataInfo const &proj_data_info, const bool write_as_attenuation=false, NumericType output_type=NumericType::FLOAT)
	Fill in most of the main header given an orig_name and a proj_data_info.

void	stir::ecat::ecat7::make_subheader_for_ECAT7 (Attn_subheader &shead, const Main_header &mhead, const ProjDataInfo &proj_data_info)
	Fill in most of the subheader.

void	stir::ecat::ecat7::make_subheader_for_ECAT7 (Scan3D_subheader &shead, const Main_header &mhead, const ProjDataInfo &proj_data_info)
	Fill in most of the subheader.

ProjDataFromStream *	stir::ecat::ecat7::make_pdfs_from_matrix (MatrixFile const mptr, MatrixData const matrix, const shared_ptr< std::iostream > &stream_ptr)
	Make a ProjDataFromStream object that 'points' into an ECAT7 file.

Succeeded	stir::ecat::ecat7::write_basic_interfile_header_for_ECAT7 (std::string &interfile_header_name, const std::string &ECAT7_filename, const int frame_num, const int gate_num, const int data_num, const int bed_num)
	Writes an Interfile header that 'points' into an ECAT7 file.

void	stir::ecat::find_type_from_ECAT_data_type (NumericType &type, ByteOrder &byte_order, const short data_type)
	Find out which NumericType and ByteOrder corresponds to a ECAT data type.

short	stir::ecat::find_ECAT_data_type (const NumericType &type, const ByteOrder &byte_order)
	Find out which ECAT data type corresponds to a certain NumericType and ByteOrder.

short	stir::ecat::find_ECAT_system_type (const Scanner &scanner)
	Find the value used in the ECAT Main header for a given scanner.

Scanner *	stir::ecat::find_scanner_from_ECAT_system_type (const short system_type)
	Find the scanner corresponding to the system type in the main header.

std::vector< int >	stir::ecat::find_segment_sequence (const ProjDataInfo &pdi)
	Return the sequence of how Siemens stores segments.

std::vector< int >	stir::ecat::find_timing_poss_sequence (const ProjDataInfo &pdi)
	Return the sequence of how Siemens stores TOF bins.

virtual bool	stir::ecat::ecat7::ECAT7DynamicDiscretisedDensityInputFileFormat::actual_can_read (const FileSignature &signature, std::istream &input) const
	Class for reading images in ECAT7 file-format.

Detailed Description

Enumeration Type Documentation

◆ ECATDataType

enum stir::ecat::ECATDataType

Possible values for the data_type field in ECAT headers.

The data_type field is used to indicate how the data are written. Note that the VAX_float type is not the same as IEEE float with little_endian byte order.

Function Documentation

◆ cti_numdoc()

void stir::ecat::ecat6::cti_numdoc	(	long	matnum,
		Matval *	matval )

Unpack encoded data into a nice struct. Reverse of cti_numcod ().

Parameters

matnum	the thingy to decode
matval	struct containing the decoded values from matnum

References cti_numdoc().

Referenced by cti_numdoc().

◆ cti_rings2plane()

int stir::ecat::ecat6::cti_rings2plane	(	short	nrings,
		short	ring0,
		short	ring1 )

Get sinogram plane from ring pair.

Parameters

ring0	first ring in ring pair
ring1	second ring in ring pair

References cti_rings2plane().

Referenced by cti_rings2plane(), and ProjData_to_ECAT6().

◆ cti_create()

FILE * stir::ecat::ecat6::cti_create	(	const char *	fname,
		const ECAT6_Main_header *	mhead )

Open a file and write main header to it. Returns a pointer to the file, or 0 if unsuccessful.

Parameters

fname	name of file to open
mhead	pointer to main header struct to copy into the file

References cti_create().

Referenced by stir::ecat::ecat6::ECAT6OutputFileFormat::actual_write_to_file(), cti_create(), DiscretisedDensity_to_ECAT6(), and ProjData_to_ECAT6().

◆ cti_rblk()

int stir::ecat::ecat6::cti_rblk	(	FILE *	fptr,
		int	blkno,
		void *	bufr,
		int	nblks )

Read from a matrix file starting at the given block. Returns EXIT_SUCCESS if all went well.

Parameters

fptr	file pointer
blkno	first block to read
nblks	number of blocks to read

References cti_rblk().

Referenced by cti_rblk(), and get_scandata().

◆ cti_wblk()

int stir::ecat::ecat6::cti_wblk	(	FILE *	fptr,
		int	blkno,
		void *	bufr,
		int	nblks )

Write blocks from buffer into file. Returns EXIT_SUCCESS if successful.

Parameters

fptr	pointer to file.
blkno	position in file of first block to write.
nblks	number of blocks to write.

References cti_wblk().

Referenced by cti_wblk(), and cti_write_idata().

◆ cti_read_ECAT6_Main_header()

int stir::ecat::ecat6::cti_read_ECAT6_Main_header	(	FILE *	fptr,
		ECAT6_Main_header *	h )

Read header data from a file and place it into a ECAT6_Main_header struct. Returns EXIT_SUCCESS if no error.

Parameters

fptr	file containing the header data
h	struct to fill with header info

References cti_read_ECAT6_Main_header().

Referenced by cti_read_ECAT6_Main_header(), get_attnheaders(), get_normheaders(), get_scanheaders(), and stir::ecat::ecat6::ECAT6ImageInputFileFormat::read_from_file().

◆ cti_read_scan_subheader()

int stir::ecat::ecat6::cti_read_scan_subheader	(	FILE *	fptr,
		const ECAT6_Main_header *	h,
		int	blknum,
		Scan_subheader *	header_ptr )

Read header data from a file and place it into a Scan_subheader struct. Returns EXIT_SUCCESS if no error.

Parameters

fptr	file containing the header data
blknum	block number at which to begin reading
h	struct to fill

References cti_read_scan_subheader().

Referenced by cti_read_scan_subheader(), and get_scanheaders().

◆ cti_read_attn_subheader()

int stir::ecat::ecat6::cti_read_attn_subheader	(	FILE *	fptr,
		const ECAT6_Main_header *	h,
		int	blknum,
		Attn_subheader *	header_ptr )

Read header data from a file and place it into a Attn_subheader struct. Returns EXIT_SUCCESS if no error.

Parameters

fptr	file containing the header data
blknum	block number at which to begin reading
header_ptr	struct to fill

References cti_read_attn_subheader().

Referenced by cti_read_attn_subheader(), and get_attnheaders().

◆ cti_read_norm_subheader()

int stir::ecat::ecat6::cti_read_norm_subheader	(	FILE *	fptr,
		const ECAT6_Main_header *	h,
		int	blknum,
		Norm_subheader *	header_ptr )

Read header data from a file and place it into a Norm_subheader struct. Returns EXIT_SUCCESS if no error.

Parameters

fptr	file containing the header data
blknum	block number at which to begin reading
header_ptr	struct to fill

References cti_read_norm_subheader().

Referenced by cti_read_norm_subheader(), and get_normheaders().

◆ cti_read_image_subheader()

int stir::ecat::ecat6::cti_read_image_subheader	(	FILE *	fptr,
		const ECAT6_Main_header *	h,
		int	blknum,
		Image_subheader *	header_ptr )

Read header data from a file and place it into an Image_subheader struct. Returns EXIT_SUCCESS if no error.

Parameters

fptr	file containing the header data
blknum	block number at which to begin reading
header_ptr	struct to fill

References cti_read_image_subheader().

Referenced by cti_read_image_subheader().

◆ cti_enter()

int stir::ecat::ecat6::cti_enter	(	FILE *	fptr,
		const ECAT6_Main_header *	mhead_ptr,
		long	matnum,
		int	nblks )

Create entry in file corresponding to matnum, and return offset of next block. Or some such. Returns 0 if there was an error.

Parameters

fptr	pointer to file.
mhead_ptr	pointer to a main header
matnum	desired matnum.
nblks	number of blocks

References cti_enter().

Referenced by cti_enter(), cti_write_image(), and cti_write_scan().

◆ cti_lookup()

int stir::ecat::ecat6::cti_lookup	(	FILE *	fptr,
		const ECAT6_Main_header *	mhead_ptr,
		long	matnum,
		MatDir *	entry )

Look up a "matrix number" in the file and return the MatDir entry for it. Returns 0 if the lookup was NOT successful.

Parameters

fptr	file containing all the tabulated information.
mhead_ptr	pointer to a main header
matnum	index.
entry	where to put the result.

References cti_lookup().

Referenced by cti_lookup(), get_attnheaders(), get_normheaders(), and get_scanheaders().

◆ cti_write_image_subheader()

int stir::ecat::ecat6::cti_write_image_subheader	(	FILE *	fptr,
		const ECAT6_Main_header *	h,
		int	blknum,
		const Image_subheader *	header_ptr )

Write an image subheader into a matrix file. Returns 0 if successful.

Parameters

fptr	pointer to file.
blknum	offset (in blocks) in file of first block to write.
header_ptr	header to write

References cti_write_image_subheader().

Referenced by cti_write_image(), and cti_write_image_subheader().

◆ cti_write_ECAT6_Main_header()

int stir::ecat::ecat6::cti_write_ECAT6_Main_header	(	FILE *	fptr,
		const ECAT6_Main_header *	header_ptr )

Write an image main header into a matrix file. Returns 0 if successful.

Parameters

fptr	pointer to file.
header_ptr	header to write

References cti_write_ECAT6_Main_header(), cti_write_image(), cti_write_scan(), cti_write_scan_subheader(), file_data_to_host(), get_attnheaders(), get_normheaders(), get_scandata(), get_scanheaders(), img_zero_fill(), and scan_zero_fill().

Referenced by cti_write_ECAT6_Main_header().

◆ cti_write_scan_subheader()

int stir::ecat::ecat6::cti_write_scan_subheader	(	FILE *	fptr,
		const ECAT6_Main_header *	h,
		int	blknum,
		const Scan_subheader *	header_ptr )

Write a scan subheader into a matrix file.

Parameters

fptr	pointer to file.
blknum	block offset at which to begin writing
header_ptr	header to write

References cti_write_scan_subheader().

Referenced by cti_write_ECAT6_Main_header(), cti_write_scan(), and cti_write_scan_subheader().

◆ get_scanheaders()

int stir::ecat::ecat6::get_scanheaders	(	FILE *	fptr,
		long	matnum,
		ECAT6_Main_header *	mhead,
		Scan_subheader *	shead,
		ScanInfoRec *	scanParams )

Read main header and subheader from scan file. Returns EXIT_SUCCESS if no error.

Parameters

fptr	pointer to scan file
matnum	matnum for scan
mhead	where to put the main header
shead	where to put the subheader
scanParams	where to put the scan parameters

References cti_lookup(), cti_read_ECAT6_Main_header(), cti_read_scan_subheader(), and get_scanheaders().

Referenced by cti_write_ECAT6_Main_header(), and get_scanheaders().

◆ get_scandata()

int stir::ecat::ecat6::get_scandata	(	FILE *	fptr,
		char *	scan,
		ScanInfoRec *	scanParams )

Read scan data from file. Returns EXIT_FAILURE if the data could not be read.

Parameters

fptr	scan file
scan	buffer for the data, must be preallocated
scanParams	data parameters

The data will be stored according to the data_type in scanParams, but converted (i.e. byte-swapped etc.) to the hosts native format.

Warning: the scan buffer has to be allocated with size a multiple of MatBLKSIZE, even if there is actually less data in the sinogram.

References cti_rblk(), file_data_to_host(), and get_scandata().

Referenced by cti_write_ECAT6_Main_header(), and get_scandata().

◆ get_attnheaders()

int stir::ecat::ecat6::get_attnheaders	(	FILE *	fptr,
		long	matnum,
		ECAT6_Main_header *	mhead,
		Attn_subheader *	shead,
		ScanInfoRec *	attnParams )

Read main header and subheader from attn file. Returns EXIT_SUCCESS if no error.

Parameters

fptr	pointer to attn file
matnum	matnum for attn
mhead	where to put the main header
shead	where to put the subheader
attnParams	where to put the attn parameters

References cti_lookup(), cti_read_attn_subheader(), cti_read_ECAT6_Main_header(), and get_attnheaders().

Referenced by cti_write_ECAT6_Main_header(), and get_attnheaders().

◆ get_normheaders()

int stir::ecat::ecat6::get_normheaders	(	FILE *	fptr,
		long	matnum,
		ECAT6_Main_header *	mhead,
		Norm_subheader *	shead,
		ScanInfoRec *	nrmParams )

Read main header and subheader from normalisation file. Returns EXIT_SUCCESS if no error.

Parameters

fptr	pointer to nrm file
matnum	matnum for nrm
mhead	where to put the main header
shead	where to put the subheader
nrmParams	where to put the nrm parameters

References cti_lookup(), cti_read_ECAT6_Main_header(), cti_read_norm_subheader(), and get_normheaders().

Referenced by cti_write_ECAT6_Main_header(), and get_normheaders().

◆ is_ECAT6_file()

bool stir::ecat::ecat6::is_ECAT6_file ( const std::string & filename )

checks if the file is in ECAT6 format

As ECAT6 doesn't have a 'magic number' this check is somewhat heuristic. Checks are only on the main header. Current checks are:

sw_version field between 0 and 69
file_type field one of the values in the enum MatFileType
num_frames field > 0

References is_ECAT6_file().

Referenced by is_ECAT6_attenuation_file(), is_ECAT6_emission_file(), is_ECAT6_file(), is_ECAT6_image_file(), and stir::TimeFrameDefinitions::TimeFrameDefinitions().

◆ find_scanner_from_ECAT6_Main_header()

Scanner * stir::ecat::ecat6::find_scanner_from_ECAT6_Main_header ( const ECAT6_Main_header & mhead )

determine scanner type from the ECAT6_Main_header

Returns a Unknown_Scanner if it does not recognise it.

References find_scanner_from_ECAT6_Main_header(), and stir::ecat::find_scanner_from_ECAT_system_type().

Referenced by DiscretisedDensity_to_ECAT6(), and find_scanner_from_ECAT6_Main_header().

◆ DiscretisedDensity_to_ECAT6()

Succeeded stir::ecat::ecat6::DiscretisedDensity_to_ECAT6	(	FILE *	fptr,
		DiscretisedDensity< 3, float > const &	density,
		const ECAT6_Main_header &	mhead,
		const int	frame_num = 1,
		const int	gate_num = 1,
		const int	data_num = 0,
		const int	bed_num = 0 )

Write an (extra) image to an existing ECAT6 file.

Some consistency checks are performed between the image and the data in the main header

Warning: This does NOT write the main header.

References stir::convert_array(), cti_numcod(), cti_write_image(), DiscretisedDensity_to_ECAT6(), stir::Array< num_dimensions, elemT >::find_max(), stir::Array< num_dimensions, elemT >::find_min(), find_scanner_from_ECAT6_Main_header(), stir::DiscretisedDensityOnCartesianGrid< num_dimensions, elemT >::get_grid_spacing(), stir::VectorWithOffset< T >::get_length(), stir::VectorWithOffset< T >::get_min_index(), stir::DiscretisedDensity< num_dimensions, elemT >::get_origin(), img_zero_fill(), and stir::warning().

◆ ProjData_to_ECAT6() [1/2]

Succeeded stir::ecat::ecat6::ProjData_to_ECAT6	(	ProjData const &	proj_data,
		std::string const &	cti_name,
		std::string const &	orig_name,
		const int	frame_num = 1,
		const int	gate_num = 1,
		const int	data_num = 0,
		const int	bed_num = 0,
		const bool	write_2D_sinograms = false )

Create a new ECAT6 sinogram file and write the data in there.

Warning: Only data without axial compression can be handled by the ECAT6 3D sinogram format, and hence also by this function (CTI span==1), except when write_2D_sinograms==true

References cti_create(), stir::DataWithProjDataInfo::get_proj_data_info_sptr(), make_ECAT6_Main_header(), and ProjData_to_ECAT6().

Referenced by ProjData_to_ECAT6(), and ProjData_to_ECAT6().

◆ ProjData_to_ECAT6() [2/2]

Succeeded stir::ecat::ecat6::ProjData_to_ECAT6	(	FILE *	fptr,
		ProjData const &	proj_data,
		const ECAT6_Main_header &	mhead,
		const int	frame_num = 1,
		const int	gate_num = 1,
		const int	data_num = 0,
		const int	bed_num = 0,
		const bool	write_2D_sinograms = false )

Write an (extra) set of sinograms to an existing ECAT6 file.

Some consistency checks are performed between the proj_data and the data in the main header

Warning: Only data without axial compression can be handled by the ECAT6 3D sinogram format, and hence also by this function (CTI span==1), except when write_2D_sinograms==true; This does NOT write the main header.

◆ make_ECAT6_Main_header() [1/2]

void stir::ecat::ecat6::make_ECAT6_Main_header	(	ECAT6_Main_header &	mhead,
		Scanner const &	scanner,
		const std::string &	orig_name,
		DiscretisedDensity< 3, float > const &	density )

Fill in most of the main header given a Scanner object and orig_name and an image.

Sets file_type, num_planes, plane_separation as well

References stir::DiscretisedDensityOnCartesianGrid< num_dimensions, elemT >::get_grid_spacing(), stir::VectorWithOffset< T >::get_length(), and make_ECAT6_Main_header().

◆ make_ECAT6_Main_header() [2/2]

void stir::ecat::ecat6::make_ECAT6_Main_header	(	ECAT6_Main_header &	mhead,
		const std::string &	orig_name,
		ProjDataInfo const &	proj_data_info )

Fill in most of the main header given an orig_name and a proj_data_info.

It gets the scanner from the proj_data_info object. Sets file_type, num_planes, plane_separation as well

References stir::ProjDataInfo::get_max_segment_num(), stir::ProjDataInfo::get_min_segment_num(), stir::ProjDataInfo::get_num_axial_poss(), stir::ProjDataInfo::get_scanner_sptr(), make_ECAT6_Main_header(), and stir::warning().

◆ is_ECAT7_file()

bool stir::ecat::ecat7::is_ECAT7_file ( const std::string & filename )

checks if the file is in ECAT7 formatThis partly relies on the implementation of matrix_open in the LLN matrix library. Additional checks are made on the main header. Current checks are:

sw_version field between 70 and 79
file_type field one of the values in the enum MatFileType
num_frames field > 0

Warning: When the file is not readable, error() is called.

References is_ECAT7_file().

Referenced by is_ECAT7_attenuation_file(), is_ECAT7_emission_file(), is_ECAT7_file(), is_ECAT7_image_file(), stir::DiscretisedDensity< 3, float >::read_from_file(), stir::ProjData::read_from_file(), and stir::TimeFrameDefinitions::TimeFrameDefinitions().

◆ find_scanner()

void stir::ecat::ecat7::find_scanner	(	shared_ptr< Scanner > &	scanner_ptr,
		const Main_header &	mhead )

determine scanner type from the main_header

Returns a Unknown_Scanner if it does not recognise it.

References find_scanner(), and stir::ecat::find_scanner_from_ECAT_system_type().

Referenced by stir::ecat::ecat7::ECAT966ListmodeInputFileFormat::can_read(), stir::ecat::ecat7::CListModeDataECAT< CListRecordT >::CListModeDataECAT(), DiscretisedDensity_to_ECAT7(), find_scanner(), and stir::ecat::ecat7::SinglesRatesFromSglFile::read_singles_from_sgl_file().

◆ DiscretisedDensity_to_ECAT7()

Succeeded stir::ecat::ecat7::DiscretisedDensity_to_ECAT7	(	MatrixFile *	mptr,
		DiscretisedDensity< 3, float > const &	density,
		const int	frame_num = 1,
		const int	gate_num = 1,
		const int	data_num = 0,
		const int	bed_num = 0 )

Write an (extra) image to an existing ECAT7 file.

Some consistency checks are performed between the image and the data in the main header

Warning: This does NOT write the main header.

References DiscretisedDensity_to_ECAT7(), find_scanner(), stir::ecat::find_type_from_ECAT_data_type(), stir::DiscretisedDensityOnCartesianGrid< num_dimensions, elemT >::get_grid_spacing(), stir::VectorWithOffset< T >::get_length(), stir::VectorWithOffset< T >::get_max_index(), stir::VectorWithOffset< T >::get_min_index(), stir::DiscretisedDensity< num_dimensions, elemT >::get_physical_coordinates_for_indices(), and stir::warning().

◆ ProjData_to_ECAT7() [1/2]

Succeeded stir::ecat::ecat7::ProjData_to_ECAT7	(	ProjData const &	proj_data,
		NumericType	output_type,
		std::string const &	cti_name,
		std::string const &	orig_name,
		const int	frame_num = 1,
		const int	gate_num = 1,
		const int	data_num = 0,
		const int	bed_num = 0,
		const bool	write_as_attenuation = false,
		float	scale_factor = 0.0F )

Create a new ECAT7 sinogram file and write the data in there.

Note that not all output_type are supported by the ECAT7 format. If a wrong type is used, it will be forced to floats.

References stir::DataWithProjDataInfo::get_proj_data_info_sptr(), make_ECAT7_main_header(), and ProjData_to_ECAT7().

Referenced by ProjData_to_ECAT7(), and ProjData_to_ECAT7().

◆ ProjData_to_ECAT7() [2/2]

Succeeded stir::ecat::ecat7::ProjData_to_ECAT7	(	MatrixFile *	mptr,
		ProjData const &	proj_data,
		const int	frame_num = 1,
		const int	gate_num = 1,
		const int	data_num = 0,
		const int	bed_num = 0,
		float	scale_factor = 0.0F )

Write an (extra) set of sinograms to an existing ECAT7 file.

Some consistency checks are performed between the proj_data and the data in the main header pointer of mptr.

For ECAT7, the data type for the output is determined by the file_type field of the main header.

Warning: This does NOT write the main header.

References ProjData_to_ECAT7(), and stir::warning().

◆ make_ECAT7_main_header() [1/2]

void stir::ecat::ecat7::make_ECAT7_main_header	(	Main_header &	mhead,
		Scanner const &	scanner,
		const std::string &	orig_name,
		DiscretisedDensity< 3, float > const &	density )

Fill in most of the main header given a Scanner object and orig_name and an image.

Sets num_planes, plane_separation as well

References stir::DiscretisedDensityOnCartesianGrid< num_dimensions, elemT >::get_grid_spacing(), stir::VectorWithOffset< T >::get_length(), and make_ECAT7_main_header().

◆ make_ECAT7_main_header() [2/2]

NumericType stir::ecat::ecat7::make_ECAT7_main_header	(	Main_header &	mhead,
		const std::string &	orig_name,
		ExamInfo const &	exam_info,
		ProjDataInfo const &	proj_data_info,
		const bool	write_as_attenuation = false,
		NumericType	output_type = NumericType::FLOAT )

Fill in most of the main header given an orig_name and a proj_data_info.

It gets the scanner from the proj_data_info object. Sets num_planes, plane_separation as well and attempts septa_state.

Returns: the actual NumericType that should be used for further IO. This is necessary because the file_type in the ECAT7 main header depends on the output_type (sign).

Defaults mean that it will set to file_type Float3dSinogram.

Warning: Note that not all output_type are supported by the ECAT7 format. If a wrong type is used, it will be forced to floats.; The acquisition_type field will be set to either TransmissionScan or StaticEmission, depending on write_as_attenuation. This is not necessarily correct.

References stir::Scanner::get_default_bin_size(), stir::ProjDataInfo::get_max_segment_num(), stir::ProjDataInfo::get_min_segment_num(), stir::ProjDataInfo::get_num_axial_poss(), stir::ProjDataInfo::get_num_segments(), stir::ProjDataInfo::get_sampling_in_s(), stir::ProjDataInfo::get_scanner_ptr(), stir::Scanner::get_type(), stir::NumericType::id, make_ECAT7_main_header(), and stir::warning().

◆ make_subheader_for_ECAT7() [1/2]

void stir::ecat::ecat7::make_subheader_for_ECAT7	(	Attn_subheader &	shead,
		const Main_header &	mhead,
		const ProjDataInfo &	proj_data_info )

Fill in most of the subheader.

Warning: data_type and volume_mode has still to be set

References make_subheader_for_ECAT7(), and stir::warning().

Referenced by make_subheader_for_ECAT7(), and make_subheader_for_ECAT7().

◆ make_subheader_for_ECAT7() [2/2]

void stir::ecat::ecat7::make_subheader_for_ECAT7	(	Scan3D_subheader &	shead,
		const Main_header &	mhead,
		const ProjDataInfo &	proj_data_info )

Fill in most of the subheader.

Warning: data_type and volume_mode has still to be set

References make_subheader_for_ECAT7(), and stir::warning().

◆ make_pdfs_from_matrix()

ProjDataFromStream * stir::ecat::ecat7::make_pdfs_from_matrix	(	MatrixFile *const	mptr,
		MatrixData *const	matrix,
		const shared_ptr< std::iostream > &	stream_ptr )

Make a ProjDataFromStream object that 'points' into an ECAT7 file.

mptr is the LLN structure that has the file pointer etc for the ECAT7 file
matrix encodes frame, gate, data, bed numbers
stream_ptr is a pointer to a stream object corresponding to the SAME file as the ECAT7 file. This argument is necessary as it isn't possible to make a stream from a FILE pointer.
Returns
NULL when it is an unsupported data type
Only data types AttenCor, Byte3dSinogram, Short3dSinogram, Float3dSinogram can be handled. Other sinogram formats have subheaders interleaved with the data which makes it impossible to have a corresponding ProjDataFromStream

References make_pdfs_from_matrix(), and write_basic_interfile_header_for_ECAT7().

Referenced by make_pdfs_from_matrix(), and write_basic_interfile_header_for_ECAT7().

◆ write_basic_interfile_header_for_ECAT7()

Succeeded stir::ecat::ecat7::write_basic_interfile_header_for_ECAT7	(	std::string &	interfile_header_name,
		const std::string &	ECAT7_filename,
		const int	frame_num,
		const int	gate_num,
		const int	data_num,
		const int	bed_num )

Writes an Interfile header that 'points' into an ECAT7 file.

Only data types AttenCor, Byte3dSinogram, Short3dSinogram, Float3dSinogram, ByteVolume, PetVolume can be handled.

interfile_header_name will be set to the header name used. It will be of the form ECAT7_filename_extension_f1g1d0b0.hs or .hv. For example, for ECAT7_filename test.S, and frame=2, gate=3, data=4, bed=5, the header name will be test_S_f2g3d4b5.hs

References stir::find_filename(), make_pdfs_from_matrix(), stir::max_filename_length, stir::warning(), write_basic_interfile_header_for_ECAT7(), stir::write_basic_interfile_image_header(), and stir::write_basic_interfile_PDFS_header().

Referenced by make_pdfs_from_matrix(), and write_basic_interfile_header_for_ECAT7().