This file gathers various function dedicated to data conversion in order to convert various type of GATE files (macro file, root datafile) to the CASToR file formats. More...

#include "gVariables.hh"
#include "gOptions.hh"
#include "iDataFilePET.hh"
#include "sOutputManager.hh"
#include "sScannerManager.hh"
#include "oInterfileIO.hh"

Macros
#define	GATE_SYS_UNKNOWN -1

#define	GATE_SYS_CYLINDRICAL 0

#define	GATE_SYS_ECAT 1

#define	GATE_SYS_SPECT 2

#define	GATE_NB_MAX_LAYERS 4

Functions
vector< string >	CheckGATECommand (const string &a_key, const string &a_line)
	Check if the line contains the provided GATE command. In this case, parse the line and returns the values in a vector of strings. More...

vector< string >	Split (string a_line)
	Split the line provided in parameter into a vector of strings (separator is blankspace) More...

void	ConvertValuesTomm (vector< string > &values)
	Check if the vector of strings passed in parameter contains the 'cm' unit In this case, convert all its values in mm. More...

template<class T >
string	toString (T a_val)

template<typename T >
int	WriteVector (ofstream &file, const string &a_key, vector< T > a_vals)
	Write the key and its values in the file provided in parameter. More...

int	WriteVector (ofstream &file, const string &a_key, vector< string > a_vals)
	Write the key and its values in the file provided in parameter. More...

int	WriteVector (ofstream &file, const string &a_key, vector< vector< string > > a_vals)
	Write the key and its values contained in a 2 level vector of strings in the file provided in parameter. More...

int	GetGATESystemType (const string &a_pathMac)
	Read a GATE macro file and identify the system type from the 'gate/systems/' command lines. More...

int	GetGATEMacFiles (const string &a_pathMac, vector< string > &ap_pathToMacFiles)
	Extract the paths to each macro file contained in the main macro file. More...

int	GetGATEAliasesCylindrical (vector< string > path_mac_files, string &rsector_name, string &module_name, string &submodule_name, string &crystal_name, vector< string > &layers_name, int vb)
	Loop over a list of path to GATE macro files passed in parameter to recover aliases of the different parts of a cylindricalPET. More...

int	GetGATEAliasesEcat (vector< string > path_mac_files, string &block_name, string &crystal_name, int vb)
	Loop over a list of path to GATE macro files passed in parameter to recover aliases of the different parts of an ecat system. More...

int	GetGATEAliasesSPECT (vector< string > path_mac_files, string &base_name, string &crystal_name, string &pixel_name, int vb)
	Loop over a list of path to GATE macro files passed in parameter to recover aliases of the different parts of an ecat system. More...

uint32_t	ConvertIDecat (int32_t nBlocksPerRing, int32_t nBlocksLine, int32_t nCrystalsTransaxial, int32_t nCrystalsAxial, int32_t crystalID, int32_t blockID)
	Compute a CASToR crystal index of a GATE ecat system from its indexes (block/crystal) and the system layout. More...

uint32_t	ConvertIDSPECTRoot1 (int32_t a_headID, float_t a_rotAngle, float_t a_angStep, uint32_t a_nProjectionsByHead)
	Compute a CASToR projection index of a GATE SPECThead system. More...

uint32_t	ConvertIDSPECTRoot2 (uint32_t a_nbSimulatedPixels, uint32_t a_nPixTrs, uint32_t a_nPixAxl, int32_t a_headID, int32_t a_crystalID, int32_t a_pixelID, float_t a_rotAngle, float_t a_headAngPitch, float_t a_crystalSizeAxl, float_t a_crystalSizeTrs, float_t a_gPosX, float_t a_gPosY, float_t a_gPosZ)
	Compute a CASToR crystal index of a GATE SPECThead system. More...

uint32_t	ConvertIDcylindrical (uint32_t nRsectorsAngPos, uint32_t nRsectorsAxial, bool a_invertDetOrder, int a_rsectorIdOrder, bool a_lyrRptFlag, uint32_t nModulesTransaxial, uint32_t nModulesAxial, uint32_t nSubmodulesTransaxial, uint32_t nSubmodulesAxial, uint32_t nCrystalsTransaxial, uint32_t nCrystalsAxial, uint8_t nLayers, uint32_t *nCrystalPerLayer, vector< uint32_t > nLayersRptTransaxial, vector< uint32_t > nLayersRptAxial, int32_t layerID, int32_t crystalID, int32_t submoduleID, int32_t moduleID, int32_t rsectorID)

int	ComputeKindGATEEvent (int32_t eventID1, int32_t eventID2, int comptonPhantom1, int comptonPhantom2, int rayleighPhantom1, int rayleighPhantom2)

int	ReadMacECAT (string a_pathMac, uint32_t &nCrystalsTot, uint32_t &nCrystalsAxial, uint32_t &nCrystalsTransaxial, uint32_t &nBlocksLine, uint32_t &nBlocksPerRing, uint32_t &start_time_ms, uint32_t &duration_ms, FLTNB &pet_coinc_window, int vb)

int	ReadMacSPECT (string a_pathMac, float_t &distToDetector, uint32_t &nHeads, uint32_t &nPixAxl, uint32_t &nPixTrs, float_t &crystalSizeAxl, float_t &crystalSizeTrs, uint32_t &nProjectionsTot, uint32_t &nProjectionsByHead, float_t &head1stAngle, float_t &headAngPitch, float_t &headAngStepDeg, int &headRotDirection, uint32_t &start_time_ms, uint32_t &duration_ms, int vb)
	Recover informations about the scanner element of an ECAT system, and acquisition duration, from a GATE macro file. More...

int	ReadIntfSPECT (string a_pathIntf, float_t &ap_distToDetector, uint32_t &ap_nHeads, uint32_t &ap_nPixAxl, uint32_t &ap_nPixTrs, float_t &ap_crystalSizeAxl, float_t &ap_crystalSizeTrs, uint32_t &ap_nProjectionsTot, uint32_t &ap_nProjectionsByHead, float_t &ap_head1stAngle, float_t &ap_headAngPitch, float_t &headAngStepDeg, int &ap_headRotDirection, uint32_t &ap_start_time_ms, uint32_t &ap_duration_ms, int vb)
	Recover informations about the scanner element of an ECAT system, and acquisition duration, from a GATE macro file. More...

int	ReadMacCylindrical (string a_pathMac, uint8_t &nLayers, uint32_t *nb_crystal_per_layer, uint32_t &nCrystalsTot, uint32_t &nCrystalsAxial, uint32_t &nCrystalsTransaxial, vector< uint32_t > &nLayersRptAxial, vector< uint32_t > &nLayersRptTransaxial, uint32_t &nSubmodulesAxial, uint32_t &nSubmodulesTransaxial, uint32_t &nModulesAxial, uint32_t &nModulesTransaxial, uint32_t &nRsectorsAxial, uint32_t &nRsectorsAngPos, bool &invert_det_order, int &rsector_id_order, uint32_t &start_time_ms, uint32_t &duration_ms, FLTNB &pet_coinc_window, bool &lyr_rpt_flag, int vb)

int	CreateGeomWithECAT (string a_pathMac, string a_pathGeom)
	Read a GATE macro file containing the description of an ecat system, and convert it to a geom file. More...

int	CreateGeomWithCylindrical (string a_pathMac, string a_pathGeom)
	Read a GATE macro file containing the description of a cylindricalPET system, and convert it to a geom file. More...

int	CreateGeomWithSPECT (string a_pathMac, string a_pathGeom)
	Read a GATE macro file containing the description of a SPECThead system, and convert it to a geom file. More...

Detailed Description

This file gathers various function dedicated to data conversion in order to convert various type of GATE files (macro file, root datafile) to the CASToR file formats.

Definition in file include/management/gDataConversionUtilities.hh.

Macro Definition Documentation

◆ GATE_NB_MAX_LAYERS

#define GATE_NB_MAX_LAYERS 4

Definition at line 50 of file include/management/gDataConversionUtilities.hh.

Function Documentation

◆ CheckGATECommand()

vector<string> CheckGATECommand	(	const string &	a_key,
		const string &	a_line
	)

Check if the line contains the provided GATE command. In this case, parse the line and returns the values in a vector of strings.

Parameters

a_key	string containing a GATE command to recover
a_line	: string containing the line to check

Values are converted in mm if 'cm' is found in the line

Returns: the vector of strings containing the elements of the line.

Definition at line 30 of file code/src/management/gDataConversionUtilities.cc.

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◆ ComputeKindGATEEvent()

int ComputeKindGATEEvent	(	int32_t	eventID1,
		int32_t	eventID2,
		int	comptonPhantom1,
		int	comptonPhantom2,
		int	rayleighPhantom1,
		int	rayleighPhantom2
	)

Definition at line 1001 of file code/src/management/gDataConversionUtilities.cc.

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◆ ConvertIDcylindrical()

uint32_t ConvertIDcylindrical	(	uint32_t	nRsectorsAngPos,
		uint32_t	nRsectorsAxial,
		bool	a_invertDetOrder,
		int	a_rsectorIdOrder,
		bool	a_lyrRptFlag,
		uint32_t	nModulesTransaxial,
		uint32_t	nModulesAxial,
		uint32_t	nSubmodulesTransaxial,
		uint32_t	nSubmodulesAxial,
		uint32_t	nCrystalsTransaxial,
		uint32_t	nCrystalsAxial,
		uint8_t	nLayers,
		uint32_t *	nCrystalPerLayer,
		vector< uint32_t >	nLayersRptTransaxial,
		vector< uint32_t >	nLayersRptAxial,
		int32_t	layerID,
		int32_t	crystalID,
		int32_t	submoduleID,
		int32_t	moduleID,
		int32_t	rsectorID
	)

Definition at line 806 of file src/management/gDataConversionUtilities.cc.

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◆ ConvertIDecat()

uint32_t ConvertIDecat	(	int32_t	nBlocksPerRing,
		int32_t	nBlocksLine,
		int32_t	nCrystalsTransaxial,
		int32_t	nCrystalsAxial,
		int32_t	crystalID,
		int32_t	blockID
	)

Compute a CASToR crystal index of a GATE ecat system from its indexes (block/crystal) and the system layout.

Parameters

nBlocksPerRing
nBlocksLine
nCrystalsTransaxial
nCrystalsAxial
crystalID
blockID

Returns: CASToR crystal index

Definition at line 672 of file code/src/management/gDataConversionUtilities.cc.

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◆ ConvertIDSPECTRoot1()

uint32_t ConvertIDSPECTRoot1	(	int32_t	a_headID,
		float_t	a_rotAngle,
		float_t	a_angStep,
		uint32_t	a_nProjectionsByHead
	)

Compute a CASToR projection index of a GATE SPECThead system.

Parameters

a_headID	: head index as provided in the root file
a_rotAngle	: rotation angle (deg) as provided in the root file
a_angStep	: angular step (deg) computed from the macro file
a_nProjectionsByHead	: total number of projections for each head

Returns: CASToR projection index for a SPECThead system

Definition at line 706 of file code/src/management/gDataConversionUtilities.cc.

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◆ ConvertIDSPECTRoot2()

uint32_t ConvertIDSPECTRoot2	(	uint32_t	a_nbSimulatedPixels,
		uint32_t	a_nPixTrs,
		uint32_t	a_nPixAxl,
		int32_t	a_headID,
		int32_t	a_crystalID,
		int32_t	a_pixelID,
		float_t	a_rotAngle,
		float_t	a_headAngPitch,
		float_t	a_crystalSizeAxl,
		float_t	a_crystalSizeTrs,
		float_t	a_gPosX,
		float_t	a_gPosY,
		float_t	a_gPosZ
	)

Compute a CASToR crystal index of a GATE SPECThead system.

Parameters

a_nbSimulatedPixels
a_nPixTrs
a_nPixAxl
a_headID
a_crystalID
a_pixelID
a_rotAngle
a_headAngPitch
a_crystalSizeAxl
a_crystalSizeTrs
a_gPosX
a_gPosY
a_gPosZ

Returns: CASToR crystal index. Return a higher number than the max index if error

Definition at line 745 of file code/src/management/gDataConversionUtilities.cc.

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◆ ConvertValuesTomm()

void ConvertValuesTomm ( vector< string > & ap_v )

Check if the vector of strings passed in parameter contains the 'cm' unit In this case, convert all its values in mm.

Parameters

ap_v	: vector of strings

Definition at line 90 of file code/src/management/gDataConversionUtilities.cc.

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◆ CreateGeomWithCylindrical()

int CreateGeomWithCylindrical	(	string	a_pathMac,
		string	a_pathGeom
	)

Read a GATE macro file containing the description of a cylindricalPET system, and convert it to a geom file.

Parameters

a_pathMac	: string containing the path to a GATE macro file
a_pathGeom	: string containing the path to a CASToR output geom file

Returns: 0 if success, positive value otherwise

Definition at line 2764 of file code/src/management/gDataConversionUtilities.cc.

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◆ CreateGeomWithECAT()

int CreateGeomWithECAT	(	string	a_pathMac,
		string	a_pathGeom
	)

Read a GATE macro file containing the description of an ecat system, and convert it to a geom file.

Parameters

a_pathMac	: string containing the path to a GATE macro file
a_pathGeom	: string containing the path to a CASToR output geom file

Returns: 0 if success, positive value otherwise

Definition at line 4370 of file code/src/management/gDataConversionUtilities.cc.

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◆ CreateGeomWithSPECT()

int CreateGeomWithSPECT	(	string	a_pathMac,
		string	a_pathGeom
	)

Read a GATE macro file containing the description of a SPECThead system, and convert it to a geom file.

Parameters

a_pathMac	: string containing the path to a GATE macro file
a_pathGeom	: string containing the path to a CASToR output geom file

Returns: 0 if success, positive value otherwise

Definition at line 4906 of file code/src/management/gDataConversionUtilities.cc.

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◆ GetGATEAliasesCylindrical()

int GetGATEAliasesCylindrical	(	vector< string >	path_mac_files,
		string &	rsector_name,
		string &	module_name,
		string &	submodule_name,
		string &	crystal_name,
		vector< string > &	layers_name,
		int	vb
	)

Loop over a list of path to GATE macro files passed in parameter to recover aliases of the different parts of a cylindricalPET.

Parameters

path_mac_files
rsector_name
module_name
submodule_name
crystal_name
layers_name

Returns: 0 if success, positive value otherwise

Definition at line 362 of file code/src/management/gDataConversionUtilities.cc.

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◆ GetGATEAliasesEcat()

int GetGATEAliasesEcat	(	vector< string >	path_mac_files,
		string &	block_name,
		string &	crystal_name,
		int	vb
	)

Loop over a list of path to GATE macro files passed in parameter to recover aliases of the different parts of an ecat system.

Parameters

path_mac_files
block_name
crystal_name
vb

Returns: 0 if success, positive value otherwise

Definition at line 502 of file code/src/management/gDataConversionUtilities.cc.

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◆ GetGATEAliasesSPECT()

int GetGATEAliasesSPECT	(	vector< string >	path_mac_files,
		string &	base_name,
		string &	crystal_name,
		string &	pixel_name,
		int	vb
	)

Loop over a list of path to GATE macro files passed in parameter to recover aliases of the different parts of an ecat system.

Parameters

path_mac_files
base_name
crystal_name
pixel_name
vb

Returns: 0 if success, positive value otherwise

Definition at line 586 of file code/src/management/gDataConversionUtilities.cc.

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◆ GetGATEMacFiles()

int GetGATEMacFiles	(	const string &	a_pathMac,
		vector< string > &	ap_pathToMacFiles
	)

Extract the paths to each macro file contained in the main macro file.

Parameters

a_pathMac	: path to a GATE main macro file
ap_pathToMacFiles	: array containing the paths of macro files

Returns: 0 if success, positive value otherwise

Definition at line 221 of file code/src/management/gDataConversionUtilities.cc.

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◆ GetGATESystemType()

int GetGATESystemType ( const string & a_pathMac )

Read a GATE macro file and identify the system type from the 'gate/systems/' command lines.

Parameters

a_pathMac : path to a GATE macro file

Returns: system type, as described by the macro GATE_SYS_TYPE, -1 if error

Definition at line 273 of file code/src/management/gDataConversionUtilities.cc.

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◆ ReadIntfSPECT()

int ReadIntfSPECT	(	string	a_pathIntf,
		float_t &	a_distToDetector,
		uint32_t &	a_nHeads,
		uint32_t &	a_nPixAxl,
		uint32_t &	a_nPixTrs,
		float_t &	a_crystalSizeAxl,
		float_t &	a_crystalSizeTrs,
		uint32_t &	a_nProjectionsTot,
		uint32_t &	a_nProjectionsByHead,
		float_t &	a_head1stAngle,
		float_t &	a_headAngPitchDeg,
		float_t &	a_headAngStepDeg,
		int &	a_headRotDirection,
		uint32_t &	a_start_time_ms,
		uint32_t &	a_duration_ms,
		int	vb
	)

Recover informations about the scanner element of an ECAT system, and acquisition duration, from a GATE macro file.

Parameters

a_pathIntf	: path to the interfile header
distToDetector	: distance between center of rotation and detector surface
nHeads	: nb of cameras
nPixAxl	: nb of transaxial pixels
nPixTrs	: nb of axial pixels
crystalSizeAxl	: crystal axial dimension
crystalSizeTrs	: crystal transaxial dimension
head1stAngle	: head first angle
headAngPitch	: angular pitch between heads
headRotSpeed	: angle between projection
headRotDirection	: rotation direction of the head (CW or CCW)
start_time_ms	: acquisition start time converted in ms
duration_ms	: acquisition duration converted in ms
Intf_fiels	: Interfile key structure to initialize with projection image parameters
vb	: verbosity

Returns: 0 if success, positive value otherwise

Definition at line 2534 of file code/src/management/gDataConversionUtilities.cc.

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◆ ReadMacCylindrical()

int ReadMacCylindrical	(	string	a_pathMac,
		uint8_t &	nLayers,
		uint32_t *	nb_crystal_per_layer,
		uint32_t &	nCrystalsTot,
		uint32_t &	nCrystalsAxial,
		uint32_t &	nCrystalsTransaxial,
		vector< uint32_t > &	nLayersRptAxial,
		vector< uint32_t > &	nLayersRptTransaxial,
		uint32_t &	nSubmodulesAxial,
		uint32_t &	nSubmodulesTransaxial,
		uint32_t &	nModulesAxial,
		uint32_t &	nModulesTransaxial,
		uint32_t &	nRsectorsAxial,
		uint32_t &	nRsectorsAngPos,
		bool &	invert_det_order,
		int &	rsector_id_order,
		uint32_t &	start_time_ms,
		uint32_t &	duration_ms,
		FLTNB &	pet_coinc_window,
		bool &	lyr_rpt_flag,
		int	vb
	)

Definition at line 1063 of file src/management/gDataConversionUtilities.cc.

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◆ ReadMacECAT()

int ReadMacECAT	(	string	a_pathMac,
		uint32_t &	nCrystalsTot,
		uint32_t &	nCrystalsAxial,
		uint32_t &	nCrystalsTransaxial,
		uint32_t &	nBlocksLine,
		uint32_t &	nBlocksPerRing,
		uint32_t &	start_time_ms,
		uint32_t &	duration_ms,
		FLTNB &	pet_coinc_window,
		int	vb
	)

Definition at line 1869 of file code/src/management/gDataConversionUtilities.cc.

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◆ ReadMacSPECT()

int ReadMacSPECT	(	string	a_pathMac,
		float_t &	a_distToDetector,
		uint32_t &	a_nHeads,
		uint32_t &	a_nPixAxl,
		uint32_t &	a_nPixTrs,
		float_t &	a_crystalSizeAxl,
		float_t &	a_crystalSizeTrs,
		uint32_t &	a_nProjectionsTot,
		uint32_t &	a_nProjectionsByHead,
		float_t &	a_head1stAngle,
		float_t &	a_headAngPitch,
		float_t &	a_headAngStepDeg,
		int &	a_headRotDirection,
		uint32_t &	a_start_time_ms,
		uint32_t &	a_duration_ms,
		int	vb
	)

Recover informations about the scanner element of an ECAT system, and acquisition duration, from a GATE macro file.

Parameters

a_pathMac	: path to a macro file
distToDetector	: distance between center of rotation and detector surface
nHeads	: nb of cameras
nPixAxl	: nb of transaxial pixels
nPixTrs	: nb of axial pixels
crystalSizeAxl	: crystal axial dimension
crystalSizeTrs	: crystal transaxial dimension
nProjectionsTot	: total number of projections (cumulated over each head)
nProjectionsByHead	: total number of projections for each head
head1stAngle	: head first angle
headAngPitch	: angular pitch between heads
headAngStepDeg	: angular step between each projection
headRotDirection	: rotation direction of the head (CW or CCW)
start_time_ms	: acquisition start time converted in ms
duration_ms	: acquisition duration converted in ms
vb	: verbosity