A class to represent a single phantom for scoring dose in egs_brachy. More...

#include <phantom.h>

Inheritance diagram for EB_Phantom:

Collaboration diagram for EB_Phantom:

Public Types
enum	GeomDirections { XDIR , YDIR , ZDIR }

Public Member Functions
	EB_Phantom (EGS_Application , EGS_BaseGeometry , set< int > global_regions, int nsource, Publisher *publisher)
	EB_Phantom constructor.

	~EB_Phantom ()
	EB_Phantom destructor.

void	scoreTlen (int ir, EGS_Float dose, EGS_Particle *p)
	add tracklength dose to region ir

void	scoreEdep (int ir, EGS_Float dose)
	add energy deposition dose to region ir

void	getCurrentScore (int ireg, double &sum, double &sum2)
	get current tlen score for region

double	getTlenNorm (int ireg)

void	setDoseScale (EGS_Float)
	set dose scaling factor for output

void	update (EB_Message message, void *data)

bool	hasVolCor (int ireg)

EGS_Float	getCorrectedVolume (int ireg)
	get uncorrected volume for a given region

EGS_Float	getVolumeUncertainty (int ireg)
	get volume unc

EGS_Float	getUncorrectedVolume (int ireg)
	get corrected volume for a given region

vector< int >	getRegionsWithCorrections ()
	return a vector of all regions which were corrected

void	setCorrectedVolume (int ir, double fraction, double unc=0)
	Allow user to tell phantom what the actual volume of a region is.

void	enableTLenScoring ()
	enableTLenScoring must be called before simulation begins if you want to score dose with tracklength estimator in addition to tracklength scoring

void	enableInteractionScoring ()
	enableInteractionScoring must be called before simulation begins if you want to score dose with interaction scoring in addition to tracklength scoring

void	enableScatterScoring ()
	enableInteractionScoring must be called before simulation begins if you want to score dose with interaction scoring in addition to tracklength scoring

void	setHistory (EGS_I64 current_case)
	set current history on scoring arrays for proper statistics

void	setEffectiveHistories (EGS_Float current_case)
	set number of effective histories for normalizing scoring arrays

EGS_Float	avgVoxelVol ()
	return average voxel volume

void	outputVoxelInfo (string format)
	write voxel volumes, mass, desnity etc

void	writeVoxelInfo (ostream &)
	write voxel info file

void	outputVolumeCorrection (string format)
	intialize and output write voxel volumes to file

void	writeVolumeCorrection (ostream &)
	write voxel volumes to file

void	outputResults (int top_n=20, string output_3ddose="text", string output_egsphant="text", string output_voxinfo="text", string output_volcor="text")
	tell phantom to output its results.

bool	globalRegIsInPhant (int global_reg)
	check whether a global region falls within this phantom

int	globalToLocal (int global_reg)
	convert global region to local phantom region

int	outputData (ostream *ofile)

int	readData (istream *ifile)

void	resetCounter ()

int	addState (istream &ifile)

EGS_Float	getRealRho (int ireg)
	return actual density for region

EGS_Float	getRealMass (int ireg)
	return (corrected) real mass for region

EGS_Float	getUncorrectedMass (int ireg)
	return uncorrected for region

void	getResult (EGS_ScoringArray *, int ireg, string type, EGS_Float &r, EGS_Float &dr)
	get result for region from scoring array and normalize based on the type requested.

Public Member Functions inherited from Subscriber
virtual	~Subscriber ()

Static Public Member Functions
static bool	needsUserVolumes (const string &geom_type)
	function for checking whether a given geometry type requires user specified volumes

static bool	canWrite3ddose (const string &geom_type)
	function for checking whether a given geometry type can output 3ddose files

Public Attributes
EGS_BaseGeometry *	geometry
	the phantom geometry object

set< int >	global_regions
	the set of all global regions contained in this phantom

int	global_reg_start
	starting global region index for this phantom

int	global_reg_stop
	ending global region index for this phantom

bool	needs_user_geoms
	this phantom requires user specified geometries

bool	can_write_3ddose
	this phantom can output 3ddose files

Private Member Functions
void	outputDoseStats (EGS_ScoringArray *score, string type)
	write some stats about dose arrays

void	outputTopDoses (int top_n, vector< RegionResult > region_results)
	write the top_n doses to console

void	output3ddoseResults (string)
	write the phantom boundaries, doses and uncertainties to 3ddose file

void	output3DDoses (ostream &out, EGS_ScoringArray *score, string type)
	write input scoring array to 3ddose file

void	output3DBounds (ostream &out)
	write the phantom bounds to 3ddose file

void	outputEGSPhant (string)
	initialize and write an egsphant file for this phantom

void	writeEGSPhant (ostream &)
	write actual egsphant data to file for this phantom

string	medIndex (int medium)
	get medium index 1-9A-Z

vector< RegionResult >	getRegionResults ()
	create a vector of RegionResult structs which can then be sorted by dose value. used for output routines

void	getScoringArrays (vector< EGS_ScoringArray * > &scores, vector< string > &types, vector< string > &descriptions)
	get all active scoring arrays, their types and descriptions

void	getEGSdatScoringArrays (vector< EGS_ScoringArray * > &scores)
	get all active scoring arrays for writing to egsdat file

Private Attributes
EGS_Application *	app
	Parent application instance. Required for constructing filenames.

EGS_ScoringArray *	tlen_score
	Tracklength dose scoring array.

EGS_ScoringArray *	edep_score
	Interaction scored dose scoring array.

EGS_ScoringArray *	prim_score
	Tracklenth scored dose from primary particles.

EGS_ScoringArray *	sscat_score
	Tracklenth scored dose from single scattered particles.

EGS_ScoringArray *	mscat_score
	Tracklenth scored dose from multiple scattered particles.

int	nsources

EGS_Float	dose_scale

EGS_Float	total_radiant_e

EGS_I64	cur_history

EGS_Float	effective_histories

Publisher *	publisher

std::map< int, double >	corrected_volumes
	Corrected volume in a given region.

std::map< int, double >	volume_uncertainty

Static Private Attributes
static const string	autovol_phantom_geom_types [] = {"EGS_cSpheres", "EGS_cSphericalShell", "EGS_XYZGeometry", "EGS_XYZGeometryT", "EGS_RZ"}

static const string	threeddose_geom_types [] = {"EGS_cSpheres", "EGS_cSphericalShell", "EGS_XYZGeometry", "EGS_XYZGeometryT", "EGS_RZ"}

Detailed Description

A class to represent a single phantom for scoring dose in egs_brachy.

A simulation may have an arbitrary number of these phantoms. This class handles scoring both tracklength and interaction scoring, outputing the top N doses to the console and output to 3ddose files.

Region numbers are all 'local' region numbers. That is the phantom does not know anything about its global region number. egs_brachy should convert to local region number before calling any method taking a region number as input.

Definition at line 71 of file phantom.h.

Member Enumeration Documentation

◆ GeomDirections

enum EB_Phantom::GeomDirections

Enumerator
XDIR	XDIR=0 x dir for rectilinear, r dir for spherical, z dir for cylindrical.
YDIR	YDIR=1 y dir for rectilinear, r dir for cylindrical.
ZDIR	ZDIR=2 z dir for rectilinear.

Definition at line 135 of file phantom.h.

Constructor & Destructor Documentation

◆ EB_Phantom()

EB_Phantom::EB_Phantom	(	EGS_Application *	parent,
		EGS_BaseGeometry *	geom,
		set< int >	global_regions,
		int	nsource,
		Publisher *	publisher
	)

EB_Phantom constructor.

Definition at line 104 of file phantom.cpp.

◆ ~EB_Phantom()

EB_Phantom::~EB_Phantom ( )

inline

EB_Phantom destructor.

Definition at line 145 of file phantom.h.

Member Function Documentation

◆ addState()

int EB_Phantom::addState ( istream & ifile )

Definition at line 996 of file phantom.cpp.

◆ avgVoxelVol()

EGS_Float EB_Phantom::avgVoxelVol ( )

return average voxel volume

Definition at line 855 of file phantom.cpp.

◆ canWrite3ddose()

bool EB_Phantom::canWrite3ddose ( const string & geom_type )

static

function for checking whether a given geometry type can output 3ddose files

Definition at line 180 of file phantom.cpp.

◆ enableInteractionScoring()

void EB_Phantom::enableInteractionScoring ( )

enableInteractionScoring must be called before simulation begins if you want to score dose with interaction scoring in addition to tracklength scoring

Definition at line 215 of file phantom.cpp.

◆ enableScatterScoring()

void EB_Phantom::enableScatterScoring ( )

enableInteractionScoring must be called before simulation begins if you want to score dose with interaction scoring in addition to tracklength scoring

Definition at line 222 of file phantom.cpp.

◆ enableTLenScoring()

void EB_Phantom::enableTLenScoring ( )

enableTLenScoring must be called before simulation begins if you want to score dose with tracklength estimator in addition to tracklength scoring

Definition at line 208 of file phantom.cpp.

◆ getCorrectedVolume()

EGS_Float EB_Phantom::getCorrectedVolume ( int ireg )

get uncorrected volume for a given region

Definition at line 314 of file phantom.cpp.

◆ getCurrentScore()

void EB_Phantom::getCurrentScore	(	int	ireg,
		double &	sum,
		double &	sum2
	)

get current tlen score for region

Definition at line 332 of file phantom.cpp.

◆ getEGSdatScoringArrays()

void EB_Phantom::getEGSdatScoringArrays ( vector< EGS_ScoringArray * > & scores )

private

get all active scoring arrays for writing to egsdat file

Definition at line 668 of file phantom.cpp.

◆ getRealMass()

EGS_Float EB_Phantom::getRealMass ( int ireg )

return (corrected) real mass for region

Definition at line 291 of file phantom.cpp.

◆ getRealRho()

EGS_Float EB_Phantom::getRealRho ( int ireg )

return actual density for region

Definition at line 285 of file phantom.cpp.

◆ getRegionResults()

vector< RegionResult > EB_Phantom::getRegionResults ( )

private

create a vector of RegionResult structs which can then be sorted by dose value. used for output routines

Definition at line 377 of file phantom.cpp.

◆ getRegionsWithCorrections()

vector< int > EB_Phantom::getRegionsWithCorrections ( )

return a vector of all regions which were corrected

Definition at line 194 of file phantom.cpp.

◆ getResult()

void EB_Phantom::getResult	(	EGS_ScoringArray *	score,
		int	ireg,
		string	type,
		EGS_Float &	r,
		EGS_Float &	dr
	)

get result for region from scoring array and normalize based on the type requested.

Definition at line 349 of file phantom.cpp.

◆ getScoringArrays()

void EB_Phantom::getScoringArrays	(	vector< EGS_ScoringArray * > &	scores,
		vector< string > &	types,
		vector< string > &	descriptions
	)

private

get all active scoring arrays, their types and descriptions

Definition at line 636 of file phantom.cpp.

◆ getTlenNorm()

double EB_Phantom::getTlenNorm ( int ireg )

Definition at line 344 of file phantom.cpp.

◆ getUncorrectedMass()

EGS_Float EB_Phantom::getUncorrectedMass ( int ireg )

return uncorrected for region

Definition at line 298 of file phantom.cpp.

◆ getUncorrectedVolume()

EGS_Float EB_Phantom::getUncorrectedVolume ( int ireg )

get corrected volume for a given region

Definition at line 302 of file phantom.cpp.

◆ getVolumeUncertainty()

EGS_Float EB_Phantom::getVolumeUncertainty ( int ireg )

get volume unc

Definition at line 323 of file phantom.cpp.

◆ globalRegIsInPhant()

bool EB_Phantom::globalRegIsInPhant ( int global_reg )

inline

check whether a global region falls within this phantom

Definition at line 249 of file phantom.h.

◆ globalToLocal()

int EB_Phantom::globalToLocal ( int global_reg )

inline

convert global region to local phantom region

Definition at line 254 of file phantom.h.

◆ hasVolCor()

bool EB_Phantom::hasVolCor ( int ireg )

Definition at line 310 of file phantom.cpp.

◆ medIndex()

string EB_Phantom::medIndex ( int medium )

private

get medium index 1-9A-Z

Definition at line 823 of file phantom.cpp.

◆ needsUserVolumes()

bool EB_Phantom::needsUserVolumes ( const string & geom_type )

static

function for checking whether a given geometry type requires user specified volumes

Definition at line 166 of file phantom.cpp.

◆ output3DBounds()

void EB_Phantom::output3DBounds ( ostream & out )

private

write the phantom bounds to 3ddose file

Definition at line 735 of file phantom.cpp.

◆ output3ddoseResults()

void EB_Phantom::output3ddoseResults ( string format )

private

write the phantom boundaries, doses and uncertainties to 3ddose file

Definition at line 688 of file phantom.cpp.

◆ output3DDoses()

void EB_Phantom::output3DDoses	(	ostream &	out,
		EGS_ScoringArray *	score,
		string	type
	)

private

write input scoring array to 3ddose file

Definition at line 758 of file phantom.cpp.

◆ outputData()

int EB_Phantom::outputData ( ostream * ofile )

Definition at line 958 of file phantom.cpp.

◆ outputDoseStats()

void EB_Phantom::outputDoseStats	(	EGS_ScoringArray *	score,
		string	type
	)

private

write some stats about dose arrays

Definition at line 408 of file phantom.cpp.

◆ outputEGSPhant()

void EB_Phantom::outputEGSPhant ( string format )

private

initialize and write an egsphant file for this phantom

Definition at line 833 of file phantom.cpp.

◆ outputResults()

void EB_Phantom::outputResults	(	int	top_n = `20`,
		string	output_3ddose = `"text"`,
		string	output_egsphant = `"text"`,
		string	output_voxinfo = `"text"`,
		string	output_volcor = `"text"`
	)

tell phantom to output its results.

Definition at line 259 of file phantom.cpp.

◆ outputTopDoses()

void EB_Phantom::outputTopDoses	(	int	top_n,
		vector< RegionResult >	region_results
	)

private

write the top_n doses to console

Definition at line 567 of file phantom.cpp.

◆ outputVolumeCorrection()

void EB_Phantom::outputVolumeCorrection ( string format )

intialize and output write voxel volumes to file

Definition at line 934 of file phantom.cpp.

◆ outputVoxelInfo()

void EB_Phantom::outputVoxelInfo ( string format )

write voxel volumes, mass, desnity etc

Definition at line 897 of file phantom.cpp.

◆ readData()

int EB_Phantom::readData ( istream * ifile )

Definition at line 977 of file phantom.cpp.

◆ resetCounter()

void EB_Phantom::resetCounter ( )

Definition at line 1022 of file phantom.cpp.

◆ scoreEdep()

void EB_Phantom::scoreEdep	(	int	ir,
		EGS_Float	dose
	)

add energy deposition dose to region ir

Definition at line 155 of file phantom.cpp.

◆ scoreTlen()

void EB_Phantom::scoreTlen	(	int	ir,
		EGS_Float	dose,
		EGS_Particle *	p
	)

add tracklength dose to region ir

Definition at line 133 of file phantom.cpp.

◆ setCorrectedVolume()

void EB_Phantom::setCorrectedVolume	(	int	ir,
		double	fraction,
		double	unc = `0`
	)

Allow user to tell phantom what the actual volume of a region is.

Definition at line 202 of file phantom.cpp.

◆ setDoseScale()

void EB_Phantom::setDoseScale ( EGS_Float scale )

set dose scaling factor for output

add energy deposition dose to region ir

Definition at line 162 of file phantom.cpp.

◆ setEffectiveHistories()

void EB_Phantom::setEffectiveHistories ( EGS_Float current_case )

set number of effective histories for normalizing scoring arrays

Definition at line 253 of file phantom.cpp.

◆ setHistory()

void EB_Phantom::setHistory ( EGS_I64 current_case )

set current history on scoring arrays for proper statistics

Definition at line 234 of file phantom.cpp.

◆ update()

void EB_Phantom::update	(	EB_Message	message,
		void *	data
	)

virtual

Implements Subscriber.

Definition at line 124 of file phantom.cpp.

◆ writeEGSPhant()

void EB_Phantom::writeEGSPhant ( ostream & out )

private

write actual egsphant data to file for this phantom

Definition at line 781 of file phantom.cpp.

◆ writeVolumeCorrection()

void EB_Phantom::writeVolumeCorrection ( ostream & out )

write voxel volumes to file

Definition at line 922 of file phantom.cpp.

◆ writeVoxelInfo()

void EB_Phantom::writeVoxelInfo ( ostream & out )

write voxel info file

Definition at line 865 of file phantom.cpp.

Member Data Documentation

◆ app

EGS_Application* EB_Phantom::app

private

Parent application instance. Required for constructing filenames.

Definition at line 78 of file phantom.h.

◆ autovol_phantom_geom_types

const string EB_Phantom::autovol_phantom_geom_types = {"EGS_cSpheres", "EGS_cSphericalShell", "EGS_XYZGeometry", "EGS_XYZGeometryT", "EGS_RZ"}

staticprivate

Definition at line 97 of file phantom.h.

◆ can_write_3ddose

bool EB_Phantom::can_write_3ddose

this phantom can output 3ddose files

Definition at line 297 of file phantom.h.

◆ corrected_volumes

std::map<int, double> EB_Phantom::corrected_volumes

private

Corrected volume in a given region.

Definition at line 95 of file phantom.h.

◆ cur_history

EGS_I64 EB_Phantom::cur_history

private

Definition at line 90 of file phantom.h.

◆ dose_scale

EGS_Float EB_Phantom::dose_scale

private

Definition at line 87 of file phantom.h.

◆ edep_score

EGS_ScoringArray* EB_Phantom::edep_score

private

Interaction scored dose scoring array.

Definition at line 80 of file phantom.h.

◆ effective_histories

EGS_Float EB_Phantom::effective_histories

private

Definition at line 91 of file phantom.h.

◆ geometry

EGS_BaseGeometry* EB_Phantom::geometry

the phantom geometry object

Definition at line 284 of file phantom.h.

◆ global_reg_start

int EB_Phantom::global_reg_start

starting global region index for this phantom

Definition at line 293 of file phantom.h.

◆ global_reg_stop

int EB_Phantom::global_reg_stop

ending global region index for this phantom

Definition at line 294 of file phantom.h.

◆ global_regions

set<int> EB_Phantom::global_regions

the set of all global regions contained in this phantom

Definition at line 291 of file phantom.h.

◆ mscat_score

EGS_ScoringArray* EB_Phantom::mscat_score

private

Tracklenth scored dose from multiple scattered particles.

Definition at line 84 of file phantom.h.

◆ needs_user_geoms

bool EB_Phantom::needs_user_geoms

this phantom requires user specified geometries

Definition at line 296 of file phantom.h.

◆ nsources

int EB_Phantom::nsources

private

Definition at line 86 of file phantom.h.

◆ prim_score

EGS_ScoringArray* EB_Phantom::prim_score

private

Tracklenth scored dose from primary particles.

Definition at line 81 of file phantom.h.

◆ publisher

Publisher* EB_Phantom::publisher

private

Definition at line 93 of file phantom.h.

◆ sscat_score

EGS_ScoringArray* EB_Phantom::sscat_score

private

Tracklenth scored dose from single scattered particles.

Definition at line 82 of file phantom.h.

◆ threeddose_geom_types

const string EB_Phantom::threeddose_geom_types = {"EGS_cSpheres", "EGS_cSphericalShell", "EGS_XYZGeometry", "EGS_XYZGeometryT", "EGS_RZ"}

staticprivate

Definition at line 101 of file phantom.h.

◆ tlen_score

EGS_ScoringArray* EB_Phantom::tlen_score

private

Tracklength dose scoring array.

Definition at line 79 of file phantom.h.

◆ total_radiant_e

EGS_Float EB_Phantom::total_radiant_e

private

Definition at line 89 of file phantom.h.

◆ volume_uncertainty

std::map<int, double> EB_Phantom::volume_uncertainty

private

Definition at line 96 of file phantom.h.

The documentation for this class was generated from the following files:

/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/phantom.h
/Users/marc/Developer/EGSnrc/HEN_HOUSE/user_codes/egs_brachy/egs_brachy/phantom.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Member Enumeration Documentation

◆ GeomDirections

Constructor & Destructor Documentation

◆ EB_Phantom()

◆ ~EB_Phantom()

Member Function Documentation

◆ addState()

◆ avgVoxelVol()

◆ canWrite3ddose()

◆ enableInteractionScoring()

◆ enableScatterScoring()

◆ enableTLenScoring()

◆ getCorrectedVolume()

◆ getCurrentScore()

◆ getEGSdatScoringArrays()

◆ getRealMass()

◆ getRealRho()

◆ getRegionResults()

◆ getRegionsWithCorrections()

◆ getResult()

◆ getScoringArrays()

◆ getTlenNorm()

◆ getUncorrectedMass()

◆ getUncorrectedVolume()

◆ getVolumeUncertainty()

◆ globalRegIsInPhant()

◆ globalToLocal()

◆ hasVolCor()

◆ medIndex()

◆ needsUserVolumes()

◆ output3DBounds()

◆ output3ddoseResults()

◆ output3DDoses()

◆ outputData()

◆ outputDoseStats()

◆ outputEGSPhant()

◆ outputResults()

◆ outputTopDoses()

◆ outputVolumeCorrection()

◆ outputVoxelInfo()

◆ readData()

◆ resetCounter()

◆ scoreEdep()

◆ scoreTlen()

◆ setCorrectedVolume()

◆ setDoseScale()

◆ setEffectiveHistories()

◆ setHistory()

◆ update()

◆ writeEGSPhant()

◆ writeVolumeCorrection()

◆ writeVoxelInfo()

Member Data Documentation

◆ app

◆ autovol_phantom_geom_types

◆ can_write_3ddose

◆ corrected_volumes

◆ cur_history

◆ dose_scale

◆ edep_score

◆ effective_histories

◆ geometry

◆ global_reg_start

◆ global_reg_stop

◆ global_regions

◆ mscat_score

◆ needs_user_geoms

◆ nsources

◆ prim_score

◆ publisher

◆ sscat_score

◆ threeddose_geom_types