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"

Defines
#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.
vector< string >	Split (string a_line)
	Split the line provided in parameter into a vector of strings (separator is blankspace)
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.
template<class T >
string	toString (T a_val)
	Convert a value of any type into string.
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.
int	WriteVector (ofstream &file, const string &a_key, vector< string > a_vals)
	Write the key and its values in the file provided in parameter.
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.
int	GetGATESystemType (const string &a_pathMac)
	Read a GATE macro file and identify the system type from the 'gate/systems/' command lines.
int	GetGATEMacFiles (const string &a_pathMac, vector< string > &ap_pathToMacFiles)
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)
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.
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.
uint32_t	ConvertIDecat (int32_t nBlocksPerRing, int32_t nBlocksLine, int32_t nCrystalsTransaxial, int32_t nCrystalsAxial, int32_t crystalID, int32_t blockID)
uint32_t	ConvertIDSPECTRoot1 (int32_t a_headID, float_t a_rotAngle, float_t a_angStep, uint32_t a_nProjectionsByHead)
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)
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.
int	ComputeKindGATEEvent (uint32_t eventID1, uint32_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, 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)
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)
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)
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.
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.
int	CreateGeomWithSPECT (string a_pathMac, string a_pathGeom)

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.

Define Documentation

#define GATE_NB_MAX_LAYERS 4

Definition at line 49 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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int ComputeKindGATEEvent	(	uint32_t	eventID1,
		uint32_t	eventID2,
		int	comptonPhantom1,
		int	comptonPhantom2,
		int	rayleighPhantom1,
		int	rayleighPhantom2
	)

Definition at line 925 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 814 of file gDataConversionUtilities.cc.

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

Definition at line 655 of file gDataConversionUtilities.cc.

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

Definition at line 689 of file gDataConversionUtilities.cc.

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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
	)

Definition at line 728 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 2104 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 3020 of file gDataConversionUtilities.cc.

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int CreateGeomWithSPECT	(	string	a_pathMac,
		string	a_pathGeom
	)

Definition at line 3474 of file gDataConversionUtilities.cc.

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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
	)

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 485 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 569 of file gDataConversionUtilities.cc.

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

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

Definition at line 273 of file gDataConversionUtilities.cc.

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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
	)

Definition at line 1874 of file gDataConversionUtilities.cc.

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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
	)

Definition at line 979 of file gDataConversionUtilities.cc.

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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
	)

Definition at line 1305 of file gDataConversionUtilities.cc.

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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
	)

Definition at line 1525 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 88 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.

Defines

Functions

Detailed Description

Define Documentation

Function Documentation