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)
	Convert a value of any type into string. More...

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 nRsectorsPerRing, 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)
	Compute a CASToR crystal index of a GATE cylindricalPET system from its indexes (rsector/module/submodule/crystal) and the system layout. More...

int	ComputeKindGATEEvent (uint32_t eventID1, uint32_t eventID2, int comptonPhantom1, int comptonPhantom2, int rayleighPhantom1, int rayleighPhantom2)
	Determine kind of a given coincidence event, from its attributes. More...

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

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 &nRsectorsPerRing, uint32_t &start_time_ms, uint32_t &duration_ms, int vb)
	Recover informations about the scanner element of a cylindricalPET system and acquisition duration, from a GATE macro file. More...

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 gDataConversionUtilities.hh.

Macro Definition Documentation

#define GATE_NB_MAX_LAYERS 4

Definition at line 50 of file gDataConversionUtilities.hh.

Function Documentation

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 41 of file gDataConversionUtilities.cc.

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ComputeKindGATEEvent	(	uint32_t	eventID1,
		uint32_t	eventID2,
		int	comptonPhantom1,
		int	comptonPhantom2,
		int	rayleighPhantom1,
		int	rayleighPhantom2
	)

Determine kind of a given coincidence event, from its attributes.

Parameters

eventID1
eventID2
comptonPhantom1
comptonPhantom2
rayleighPhantom1
rayleighPhantom2

Returns: kind of the coincidence : unknown (=0, default), true(=1), single scat(=2), multiple scat(=3), random(=4)) (default value =0)

Definition at line 943 of file gDataConversionUtilities.cc.

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ConvertIDcylindrical	(	uint32_t	nRsectorsPerRing,
		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
	)

Compute a CASToR crystal index of a GATE cylindricalPET system from its indexes (rsector/module/submodule/crystal) and the system layout.

Parameters

nRsectorsPerRing
nModulesTransaxial
nModulesAxial
nSubmodulesTransaxial
nSubmodulesAxial
nCrystalsTransaxial
nCrystalsAxial
nLayers
nb_crystal_per_layer
nLayersRptTransaxial
nLayersRptAxial
layerID
crystalID
submoduleID
moduleID
rsectorID

Returns: CASToR crystal index

Definition at line 832 of file gDataConversionUtilities.cc.

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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 gDataConversionUtilities.cc.

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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 gDataConversionUtilities.cc.

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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 gDataConversionUtilities.cc.

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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.

Parameters

ap_v	: vector of strings

Definition at line 101 of file gDataConversionUtilities.cc.

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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 2285 of file gDataConversionUtilities.cc.

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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 3341 of file gDataConversionUtilities.cc.

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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 3835 of file gDataConversionUtilities.cc.

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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 gDataConversionUtilities.cc.

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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 gDataConversionUtilities.cc.

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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 gDataConversionUtilities.cc.

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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 232 of file gDataConversionUtilities.cc.

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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 gDataConversionUtilities.cc.

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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.

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 2055 of file gDataConversionUtilities.cc.

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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 &	nRsectorsPerRing,
		uint32_t &	start_time_ms,
		uint32_t &	duration_ms,
		int	vb
	)

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

Parameters

a_pathMac	: path to a main macro file
nLayers	: nb of crystal layers
nCrystalsAxial	: nb of axial crystals (in a submodule)
nCrystalsTransaxial	: nb of transaxial crystals (in a submodule)
nCrystalLayersAxial	: Array containing the number of axial crystals in each layer
nCrystalLayersTransaxial	: Array containing the number of transaxial crystals in each layer
nSubmodulesAxial	: nb of axial submodules (in a module)
nSubmodulesTransaxial	: nb of transaxial submodules (in a module)
nModulesAxial	: nb of axial modules (in a rsector)
nModulesTransaxial	: nb of transaxial modules (in a rsector)
nRsectorsPerRing	: nb of rsectors per ring
start_time_ms	: acquisition start time converted in ms
duration_ms	: acquisition duration converted in ms
vb	: verbosity

Returns: 0 if success, positive value otherwise

Definition at line 997 of file gDataConversionUtilities.cc.

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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,
		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 main macro file
nCrystalsAxial	: nb of axial crystals
nCrystalsTransaxial	: nb of transaxial crystals
nBlocksLine	: nb of axial blocks
nBlocksPerRing	: nb of blocks per ring
start_time_ms	: acquisition start time converted in ms
duration_ms	: acquisition duration converted in ms
vb	: verbosity

Returns: 0 if success, positive value otherwise

Definition at line 1419 of file gDataConversionUtilities.cc.

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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.

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

Returns: 0 if success, positive value otherwise

Definition at line 1656 of file gDataConversionUtilities.cc.

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Split ( string a_line )

Split the line provided in parameter into a vector of strings (separator is blankspace)

Parameters

a_line : string to split

Returns: vector of string containing the splitted elements of the line

Definition at line 76 of file gDataConversionUtilities.cc.

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template<class T >

toString ( T a_val )

Convert a value of any type into string.

Parameters

a_val : value to convert

Returns: the value in parameter converted in string

Definition at line 89 of file gDataConversionUtilities.hh.

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template<typename T >

WriteVector	(	ofstream &	file,
		const string &	a_key,
		vector< T >	a_vals
	)

Write the key and its values in the file provided in parameter.

Parameters

file	: the output file
a_key	: key to write
a_vals	: vector containing the key values

Returns: 0 if success, positive value otherwise

Definition at line 130 of file gDataConversionUtilities.cc.

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WriteVector	(	ofstream &	file,
		const string &	a_key,
		vector< string >	a_vals
	)

Write the key and its values in the file provided in parameter.

Parameters

file	: the output file
a_key	: key to write
a_vals	: vector containing the key values

Returns: 0 if success, positive value otherwise

Definition at line 169 of file gDataConversionUtilities.cc.

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.

Parameters

file	: the output file
a_key	: key to write
a_vals	: vector containing the key values

Returns: 0 if success, positive value otherwise

Definition at line 204 of file gDataConversionUtilities.cc.

Macros

Functions

Detailed Description

Macro Definition Documentation

Function Documentation