Implementation of class gDataConversionUtilities functions. More...

#include "gVariables.hh"
#include "gDataConversionUtilities.hh"
#include <iomanip>

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 > &ap_v)
	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 >
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...

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

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

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. 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	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	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

Implementation of class gDataConversionUtilities functions.

Definition in file gDataConversionUtilities.cc.

Function Documentation

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 53 of file gDataConversionUtilities.cc.

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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.

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 995 of file gDataConversionUtilities.cc.

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uint32_t ConvertIDcylindrical	(	uint32_t	nRsectorsAngPos,
		uint32_t	nRsectorsAxial,
		int	a_rsectorIdOrder,
		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

nRsectorsAngPos
nRsectorsAxial
a_rsectorIdOrder
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 845 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
	)

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 684 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
	)

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 718 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
	)

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 757 of file gDataConversionUtilities.cc.

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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 113 of file gDataConversionUtilities.cc.

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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 2378 of file gDataConversionUtilities.cc.

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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 3592 of file gDataConversionUtilities.cc.

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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 4078 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
	)

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 374 of file gDataConversionUtilities.cc.

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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 514 of file gDataConversionUtilities.cc.

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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 598 of file gDataConversionUtilities.cc.

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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 244 of file gDataConversionUtilities.cc.

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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 285 of file gDataConversionUtilities.cc.

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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 2148 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 &	nRsectorsAxial,
		uint32_t &	nRsectorsAngPos,
		int &	rsector_id_order,
		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)
nRsectorsAxial	: nb of axial rsectors
nRsectorsAngPos	: nb of rsectors per ring
rsector_id_order	: ordering of rsector id
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 1051 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
	)

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 1512 of file gDataConversionUtilities.cc.

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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

Returns: 0 if success, positive value otherwise

Definition at line 1749 of file gDataConversionUtilities.cc.

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vector<string> 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 88 of file gDataConversionUtilities.cc.

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template<class 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.

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 142 of file gDataConversionUtilities.cc.

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

int 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 181 of file gDataConversionUtilities.cc.

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.

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 216 of file gDataConversionUtilities.cc.

Functions

Detailed Description

Function Documentation