HadrontherapyMatrix Class Reference

#include <HadrontherapyMatrix.hh>

Collaboration diagram for HadrontherapyMatrix:

Public Member Functions
	~HadrontherapyMatrix ()
void	PrintNuclides ()
void	ClearHitTrack ()
G4int *	GetHitTrack (G4int i, G4int j, G4int k)
void	Initialize ()
void	Clear ()
G4bool	Fill (G4int, G4ParticleDefinition *particleDef, G4int i, G4int j, G4int k, G4double energyDeposit, G4bool fluence=false)
void	Fill (G4int i, G4int j, G4int k, G4double energyDeposit)
void	TotalEnergyDeposit ()
void	StoreMatrix (G4String file, void *data, size_t psize)
void	StoreFluenceData ()
void	StoreDoseData ()
void	StoreDoseFluenceAscii (G4String filename="")
G4int	Index (G4int i, G4int j, G4int k)
G4double *	GetMatrix ()
G4int	GetNvoxel ()
G4int	GetNumberOfVoxelAlongX ()
G4int	GetNumberOfVoxelAlongY ()
G4int	GetNumberOfVoxelAlongZ ()

Static Public Member Functions
static HadrontherapyMatrix *	GetInstance ()
static HadrontherapyMatrix *	GetInstance (G4int nX, G4int nY, G4int nZ, G4double mass)

Static Public Attributes
static G4bool	secondary = false

Private Member Functions
	HadrontherapyMatrix (G4int numberOfVoxelAlongX, G4int numberOfVoxelAlongY, G4int numberOfVoxelAlongZ, G4double massOfVoxel)

Private Attributes
G4int	numberOfVoxelAlongX
G4int	numberOfVoxelAlongY
G4int	numberOfVoxelAlongZ
G4double	massOfVoxel
G4double *	matrix
G4int *	hitTrack
G4String	stdFile
G4String	filename
std::ofstream	ofs
std::vector< ion >	ionStore
G4double	doseUnit

Static Private Attributes
static HadrontherapyMatrix *	instance = NULL

Detailed Description

Definition at line 55 of file HadrontherapyMatrix.hh.

Constructor & Destructor Documentation

HadrontherapyMatrix()

HadrontherapyMatrix::HadrontherapyMatrix ( G4int  numberOfVoxelAlongX, G4int  numberOfVoxelAlongY, G4int  numberOfVoxelAlongZ, G4double  massOfVoxel  )

private

Definition at line 61 of file HadrontherapyMatrix.cc.

                                                                                               :
    stdFile("Dose.out"),
    doseUnit(gray)
{  
    // Number of the voxels of the phantom
    // For Y = Z = 1 the phantom is divided in slices (and not in voxels)
    // orthogonal to the beam axis
    numberOfVoxelAlongX = voxelX;
    numberOfVoxelAlongY = voxelY;
    numberOfVoxelAlongZ = voxelZ; 
    massOfVoxel = mass;
    // Create the dose matrix
    matrix = new G4double[numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ];
    if (matrix)
    {
        G4cout << "HadrontherapyMatrix: Memory space to store physical dose into " <<  
        numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ <<
        " voxels has been allocated " << G4endl;
    }
    else G4Exception("HadrontherapyMatrix::HadrontherapyMatrix()", "Hadrontherapy0005", FatalException, "Can't allocate memory to store physical dose!");
        // Hit voxel (TrackID) marker
        // This array mark the status of voxel, if a hit occur, with the trackID of the particle
        // Must be initialized
    hitTrack = new G4int[numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ];
    ClearHitTrack();
}

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~HadrontherapyMatrix()

HadrontherapyMatrix::~HadrontherapyMatrix

(

)

Definition at line 89 of file HadrontherapyMatrix.cc.

{
    delete[] matrix;
    delete[] hitTrack;
    // free fluences/dose data memory
    Clear();
}

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Member Function Documentation

Clear()

void HadrontherapyMatrix::Clear

(

)

Definition at line 98 of file HadrontherapyMatrix.cc.

{
    for (size_t i=0; i<ionStore.size(); i++)
    {
    delete[] ionStore[i].dose; 
    delete[] ionStore[i].fluence; 
    }
    ionStore.clear();
}

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ClearHitTrack()

void HadrontherapyMatrix::ClearHitTrack

(

)

Definition at line 132 of file HadrontherapyMatrix.cc.

{
    for(G4int i=0; i<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ; i++) hitTrack[i] = 0;
}

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Fill() [1/2]

G4bool HadrontherapyMatrix::Fill	(	G4int	trackID,
		G4ParticleDefinition *	particleDef,
		G4int	i,
		G4int	j,
		G4int	k,
		G4double	energyDeposit,
		G4bool	fluence = false
	)

Definition at line 148 of file HadrontherapyMatrix.cc.

{
    if ( (energyDeposit <=0. && !fluence) || !secondary) return false;
    // Get Particle Data Group particle ID 
    G4int PDGencoding = particleDef -> GetPDGEncoding();
    PDGencoding -= PDGencoding%10;
    
    // Search for already allocated data...
    for (size_t l=0; l < ionStore.size(); l++)
    {
        if (ionStore[l].PDGencoding == PDGencoding ) 
        {   // Is it a primary or a secondary particle? 
          if ( (trackID ==1 && ionStore[l].isPrimary) || (trackID !=1 && !ionStore[l].isPrimary))
            {
                if (energyDeposit > 0.) ionStore[l].dose[Index(i, j, k)] += energyDeposit;
                
                    // Fill a matrix per each ion with the fluence
                if (fluence) ionStore[l].fluence[Index(i, j, k)]++;
                return true;
            }
        }
    }
    
    G4int Z = particleDef-> GetAtomicNumber();
    G4int A = particleDef-> GetAtomicMass();

    G4String fullName = particleDef -> GetParticleName();
    G4String name = fullName.substr (0, fullName.find("[") ); // cut excitation energy  
  // Let's put a new particle in our store...
    ion newIon = 
    {
        (trackID == 1) ? true:false,
        PDGencoding,
        name,
        name.length(), 
        Z, 
        A, 
        new G4double[numberOfVoxelAlongX * numberOfVoxelAlongY * numberOfVoxelAlongZ],
        new unsigned int[numberOfVoxelAlongX * numberOfVoxelAlongY * numberOfVoxelAlongZ]
    }; 
        // Initialize data
    if (newIon.dose && newIon.fluence)
    {
        for(G4int q=0; q<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ; q++)
        {
            newIon.dose[q] = 0.;
            newIon.fluence[q] = 0;
        }
        if (energyDeposit > 0.) newIon.dose[Index(i, j, k)] += energyDeposit;
        if (fluence) newIon.fluence[Index(i, j, k)]++;
        
        ionStore.push_back(newIon);
        
        // TODO Put some verbosity check
        /*
         G4cout << "Memory space to store the DOSE/FLUENCE into " <<  
         numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ << 
         " voxels has been allocated for the nuclide " << newIon.name << 
         " (Z = " << Z << ", A = " << A << ")" << G4endl ;
         */
        return true;
    }
    else // XXX Out of memory! XXX
    {
        return false;
    }
    
}

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Fill() [2/2]

void HadrontherapyMatrix::Fill	(	G4int	i,
		G4int	j,
		G4int	k,
		G4double	energyDeposit
	)

Definition at line 377 of file HadrontherapyMatrix.cc.

{
    if (matrix)
        matrix[Index(i,j,k)] += energyDeposit;
    
    // Store the energy deposit in the matrix element corresponding 
    // to the phantom voxel  
}

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GetHitTrack()

G4int * HadrontherapyMatrix::GetHitTrack	(	G4int	i,
		G4int	j,
		G4int	k
	)

Definition at line 137 of file HadrontherapyMatrix.cc.

{
    return &(hitTrack[Index(i,j,k)]);
}

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GetInstance() [1/2]

HadrontherapyMatrix * HadrontherapyMatrix::GetInstance ( )

static

Definition at line 48 of file HadrontherapyMatrix.cc.

{
    return instance;
}

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GetInstance() [2/2]

HadrontherapyMatrix * HadrontherapyMatrix::GetInstance ( G4int  nX, G4int  nY, G4int  nZ, G4double  mass  )

static

Definition at line 54 of file HadrontherapyMatrix.cc.

{
    if (instance) delete instance;
    instance = new HadrontherapyMatrix(voxelX, voxelY, voxelZ, mass);
    instance -> Initialize(); 
    return instance;
}

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GetMatrix()

G4double* HadrontherapyMatrix::GetMatrix ( )

inline

Definition at line 114 of file HadrontherapyMatrix.hh.

{return matrix;}

GetNumberOfVoxelAlongX()

G4int HadrontherapyMatrix::GetNumberOfVoxelAlongX ( )

inline

Definition at line 118 of file HadrontherapyMatrix.hh.

{return numberOfVoxelAlongX;}

GetNumberOfVoxelAlongY()

G4int HadrontherapyMatrix::GetNumberOfVoxelAlongY ( )

inline

Definition at line 119 of file HadrontherapyMatrix.hh.

{return numberOfVoxelAlongY;}

GetNumberOfVoxelAlongZ()

G4int HadrontherapyMatrix::GetNumberOfVoxelAlongZ ( )

inline

Definition at line 120 of file HadrontherapyMatrix.hh.

{return numberOfVoxelAlongZ;}

GetNvoxel()

G4int HadrontherapyMatrix::GetNvoxel ( )

inline

Definition at line 116 of file HadrontherapyMatrix.hh.

{return numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ;}

Index()

G4int HadrontherapyMatrix::Index ( G4int  i, G4int  j, G4int  k  )

inline

Definition at line 111 of file HadrontherapyMatrix.hh.

{ return (i * numberOfVoxelAlongY + j) * numberOfVoxelAlongZ + k; } 

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Initialize()

void HadrontherapyMatrix::Initialize

(

)

Definition at line 110 of file HadrontherapyMatrix.cc.

{ 
    // Clear ions store
    Clear();
    // Clear dose
    for(int i=0;i<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ;i++)
    {
        matrix[i] = 0;
    }
}

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PrintNuclides()

void HadrontherapyMatrix::PrintNuclides

(

)

Definition at line 123 of file HadrontherapyMatrix.cc.

{
    for (size_t i=0; i<ionStore.size(); i++)
    {
        G4cout << ionStore[i].name << G4endl;
    }
}

StoreDoseData()

void HadrontherapyMatrix::StoreDoseData

(

)

Definition at line 267 of file HadrontherapyMatrix.cc.

{
    
    for (size_t i=0; i < ionStore.size(); i++){
        StoreMatrix(ionStore[i].name + "_Dose.out", ionStore[i].dose, sizeof(G4double));
    }
}

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StoreDoseFluenceAscii()

void HadrontherapyMatrix::StoreDoseFluenceAscii

(

G4String

filename = ""

)

Definition at line 278 of file HadrontherapyMatrix.cc.

{
#define width 15L
    filename = (file=="") ? stdFile:file;
    // Sort like periodic table
    std::sort(ionStore.begin(), ionStore.end());
    G4cout << "Dose is being written to " << filename << G4endl;
    ofs.open(filename, std::ios::out);
    if (ofs.is_open())
    {
    // Write the voxels index and the list of particles/ions 
    ofs << std::setprecision(6) << std::left <<
        "i\tj\tk\t"; 
    // Total dose 
    ofs << std::setw(width) << "Dose(Gy)";
    if (secondary)
    {
        for (size_t l=0; l < ionStore.size(); l++)
        {
        G4String a = (ionStore[l].isPrimary) ? "_1":""; // is it a primary?
        ofs << std::setw(width) << ionStore[l].name + a <<
            std::setw(width) << ionStore[l].name  + a;
        }
        ofs << G4endl;

        /*
         * PDGencondig
         */
        /*
        ofs << std::setprecision(6) << std::left <<
        "0\t0\t0\t"; 

        // Total dose 
        ofs << std::setw(width) << '0';
        for (size_t l=0; l < ionStore.size(); l++)
        {
        ofs << std::setw(width) << ionStore[l].PDGencoding  <<
        std::setw(width) << ionStore[l].PDGencoding;
        }
        ofs << G4endl;
        */
    }
    // Write data
    for(G4int i = 0; i < numberOfVoxelAlongX; i++) 
        for(G4int j = 0; j < numberOfVoxelAlongY; j++) 
        for(G4int k = 0; k < numberOfVoxelAlongZ; k++) 
        {
            G4int n = Index(i, j, k);
            // Write only not identically null data lines
            if (matrix[n])
            {
            ofs << G4endl;
            ofs << i << '\t' << j << '\t' << k << '\t';
            // Total dose 
            ofs << std::setw(width) << (matrix[n]/massOfVoxel)/doseUnit; 
            if (secondary)
            {
                for (size_t l=0; l < ionStore.size(); l++)
                {
                // Fill ASCII file rows
                ofs << std::setw(width) << ionStore[l].dose[n]/massOfVoxel/doseUnit <<
                    std::setw(width) << ionStore[l].fluence[n]; 
                }
            }
            }
        }
    ofs.close();
    }
}

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StoreFluenceData()

void HadrontherapyMatrix::StoreFluenceData

(

)

Definition at line 260 of file HadrontherapyMatrix.cc.

{
    for (size_t i=0; i < ionStore.size(); i++){
        StoreMatrix(ionStore[i].name + "_Fluence.out", ionStore[i].fluence, sizeof(unsigned int));
    }
}

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StoreMatrix()

void HadrontherapyMatrix::StoreMatrix	(	G4String	file,
		void *	data,
		size_t	psize
	)

Definition at line 228 of file HadrontherapyMatrix.cc.

{
    if (data)
    {
        ofs.open(file, std::ios::out);
        if (ofs.is_open())
        {
            for(G4int i = 0; i < numberOfVoxelAlongX; i++) 
                for(G4int j = 0; j < numberOfVoxelAlongY; j++) 
                    for(G4int k = 0; k < numberOfVoxelAlongZ; k++) 
                    {
                        G4int n = Index(i, j, k);
                            // Check for data type: u_int, G4double, XXX 
                        if (psize == sizeof(unsigned int))
                        {
                            unsigned int* pdata = (unsigned int*)data;
                            if (pdata[n]) ofs << i << '\t' << j << '\t' <<
                                k << '\t' << pdata[n] << G4endl;
                        }
                        else if (psize == sizeof(G4double))
                        {
                            G4double* pdata = (G4double*)data;
                            if (pdata[n]) ofs << i << '\t' << j << '\t' <<
                                k << '\t' << pdata[n] << G4endl;
                        }
                    }
            ofs.close();
        }
    }
}

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TotalEnergyDeposit()

void HadrontherapyMatrix::TotalEnergyDeposit

(

)

Definition at line 386 of file HadrontherapyMatrix.cc.

{
    // Convert energy deposited to dose.
    // Store the information of the matrix in a ntuple and in 
    // a 1D Histogram
#ifdef G4ANALYSIS_USE_ROOT
      HadrontherapyAnalysisManager* analysis = HadrontherapyAnalysisManager::GetInstance();
#endif

    if (matrix)
    {  
    for(G4int i = 0; i < numberOfVoxelAlongX; i++) 
        for(G4int j = 0; j < numberOfVoxelAlongY; j++) 
        for(G4int k = 0; k < numberOfVoxelAlongZ; k++)
        {
#ifdef G4ANALYSIS_USE_ROOT
            G4int n = Index(i,j,k);
            if (analysis -> IsTheTFile() )
            {
            analysis -> FillEnergyDeposit(i, j, k, matrix[n]/massOfVoxel/doseUnit);
            analysis -> BraggPeak(i, matrix[n]/massOfVoxel/doseUnit);
            }
#endif
        }
    }
}

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Member Data Documentation

doseUnit

G4double HadrontherapyMatrix::doseUnit

private

Definition at line 137 of file HadrontherapyMatrix.hh.

filename

G4String HadrontherapyMatrix::filename

private

Definition at line 131 of file HadrontherapyMatrix.hh.

hitTrack

G4int* HadrontherapyMatrix::hitTrack

private

Definition at line 130 of file HadrontherapyMatrix.hh.

instance

HadrontherapyMatrix * HadrontherapyMatrix::instance = NULL

staticprivate

Definition at line 123 of file HadrontherapyMatrix.hh.

ionStore

std::vector<ion> HadrontherapyMatrix::ionStore

private

Definition at line 135 of file HadrontherapyMatrix.hh.

massOfVoxel

G4double HadrontherapyMatrix::massOfVoxel

private

Definition at line 127 of file HadrontherapyMatrix.hh.

matrix

G4double* HadrontherapyMatrix::matrix

private

Definition at line 129 of file HadrontherapyMatrix.hh.

numberOfVoxelAlongX

G4int HadrontherapyMatrix::numberOfVoxelAlongX

private

Definition at line 124 of file HadrontherapyMatrix.hh.

numberOfVoxelAlongY

G4int HadrontherapyMatrix::numberOfVoxelAlongY

private

Definition at line 125 of file HadrontherapyMatrix.hh.

numberOfVoxelAlongZ

G4int HadrontherapyMatrix::numberOfVoxelAlongZ

private

Definition at line 126 of file HadrontherapyMatrix.hh.

ofs

std::ofstream HadrontherapyMatrix::ofs

private

Definition at line 132 of file HadrontherapyMatrix.hh.

secondary

G4bool HadrontherapyMatrix::secondary = false

static

Definition at line 72 of file HadrontherapyMatrix.hh.

stdFile

G4String HadrontherapyMatrix::stdFile

private

Definition at line 131 of file HadrontherapyMatrix.hh.

---

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

• HadrontherapyMatrix.hh
• HadrontherapyMatrix.cc