IORTMatrix Class Reference

#include <IORTMatrix.hh>

Public Member Functions
	~IORTMatrix ()
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="")
void	StoreDoseFluenceRoot ()
G4int	Index (G4int i, G4int j, G4int k)
G4double *	GetMatrix ()
G4int	GetNvoxel ()
G4int	GetNumberOfVoxelAlongX ()
G4int	GetNumberOfVoxelAlongY ()
G4int	GetNumberOfVoxelAlongZ ()

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

Static Public Attributes
static G4bool	secondary = false

Detailed Description

Definition at line 66 of file IORTMatrix.hh.

Constructor & Destructor Documentation

IORTMatrix::~IORTMatrix

(

)

Definition at line 102 of file IORTMatrix.cc.

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

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Member Function Documentation

void IORTMatrix::Clear

(

)

Definition at line 111 of file IORTMatrix.cc.

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

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void IORTMatrix::ClearHitTrack

(

)

Definition at line 145 of file IORTMatrix.cc.

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

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

Definition at line 161 of file IORTMatrix.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/massOfVoxel;
                
                    // 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/massOfVoxel;
        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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void IORTMatrix::Fill	(	G4int	i,
		G4int	j,
		G4int	k,
		G4double	energyDeposit
	)

Definition at line 386 of file IORTMatrix.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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G4int * IORTMatrix::GetHitTrack	(	G4int	i,
		G4int	j,
		G4int	k
	)

Definition at line 150 of file IORTMatrix.cc.

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

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IORTMatrix * IORTMatrix::GetInstance ( )

static

Definition at line 61 of file IORTMatrix.cc.

{
    return instance;
}

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

static

Definition at line 67 of file IORTMatrix.cc.

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

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G4double* IORTMatrix::GetMatrix ( )

inline

Definition at line 123 of file IORTMatrix.hh.

{return matrix;}

G4int IORTMatrix::GetNumberOfVoxelAlongX ( )

inline

Definition at line 127 of file IORTMatrix.hh.

{return numberOfVoxelAlongX;}

G4int IORTMatrix::GetNumberOfVoxelAlongY ( )

inline

Definition at line 128 of file IORTMatrix.hh.

{return numberOfVoxelAlongY;}

G4int IORTMatrix::GetNumberOfVoxelAlongZ ( )

inline

Definition at line 129 of file IORTMatrix.hh.

{return numberOfVoxelAlongZ;}

G4int IORTMatrix::GetNvoxel ( )

inline

Definition at line 125 of file IORTMatrix.hh.

{return numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ;}

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

inline

Definition at line 120 of file IORTMatrix.hh.

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

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void IORTMatrix::Initialize

(

)

Definition at line 123 of file IORTMatrix.cc.

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

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void IORTMatrix::PrintNuclides

(

)

Definition at line 136 of file IORTMatrix.cc.

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

void IORTMatrix::StoreDoseData

(

)

Definition at line 280 of file IORTMatrix.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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void IORTMatrix::StoreDoseFluenceAscii

(

G4String

filename = ""

)

Definition at line 291 of file IORTMatrix.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(MeV/g)";
    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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void IORTMatrix::StoreDoseFluenceRoot

(

)

Definition at line 362 of file IORTMatrix.cc.

{
    IORTAnalysisManager* analysis = IORTAnalysisManager::GetInstance();
    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);
        for (size_t l=0; l < ionStore.size(); l++)
          
          {
        // Do the same work for .root file: fill dose/fluence ntuple  
        analysis -> FillVoxelFragmentTuple( i, j, k, 
                            ionStore[l].A, 
                            ionStore[l].Z, 
                            ionStore[l].dose[n]/massOfVoxel/doseUnit, 
                            ionStore[l].fluence[n] );
        
        
          }
        
      }
}

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void IORTMatrix::StoreFluenceData

(

)

Definition at line 273 of file IORTMatrix.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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void IORTMatrix::StoreMatrix	(	G4String	file,
		void *	data,
		size_t	psize
	)

Definition at line 241 of file IORTMatrix.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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void IORTMatrix::TotalEnergyDeposit

(

)

Definition at line 395 of file IORTMatrix.cc.

{
    // Store the information of the matrix in a ntuple and in 
    // a 1D Histogram
}

Member Data Documentation

G4bool IORTMatrix::secondary = false

static

Definition at line 83 of file IORTMatrix.hh.

---

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

• source/geant4.10.03.p03/examples/advanced/iort_therapy/include/IORTMatrix.hh
• source/geant4.10.03.p03/examples/advanced/iort_therapy/src/IORTMatrix.cc