IORTMatrix.cc

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//
// This is the *BASIC* version of IORT, a Geant4-based application
//
// Main Authors: G.Russo(a,b), C.Casarino*(c), G.C. Candiano(c), G.A.P. Cirrone(d), F.Romano(d)
// Contributor Authors: S.Guatelli(e)
// Past Authors: G.Arnetta(c), S.E.Mazzaglia(d)
//    
//   (a) Fondazione Istituto San Raffaele G.Giglio, Cefalù, Italy
//   (b) IBFM-CNR , Segrate (Milano), Italy
//   (c) LATO (Laboratorio di Tecnologie Oncologiche), Cefalù, Italy
//   (d) Laboratori Nazionali del Sud of the INFN, Catania, Italy
//   (e) University of Wallongong, Australia
//
//   *Corresponding author, email to carlo.casarino@polooncologicocefalu.it

#include <fstream>
#include <iostream>
#include <sstream>
#include <iomanip>

#include "IORTMatrix.hh"
#include "IORTAnalysisManager.hh"
#include "IORTPrimaryGeneratorAction.hh"

#include "globals.hh"
#include "G4SystemOfUnits.hh"
#include "G4RunManager.hh"
#include "G4ParticleGun.hh"

// Units definition: CLHEP/Units/SystemOfUnits.h
//
IORTMatrix* IORTMatrix::instance = NULL;
G4bool IORTMatrix::secondary = false;

// Only return a pointer to matrix
IORTMatrix* IORTMatrix::GetInstance() 
{
    return instance;
}
    // This STATIC method delete (!) the old matrix and rewrite a new object returning a pointer to it
    // TODO A check on the parameters is required!
IORTMatrix* IORTMatrix::GetInstance(G4int voxelX, G4int voxelY, G4int voxelZ, G4double mass)  
{
    if (instance) delete instance;
    instance = new IORTMatrix(voxelX, voxelY, voxelZ, mass);
    instance -> Initialize(); 
    return instance;
}
IORTMatrix::IORTMatrix(G4int voxelX, G4int voxelY, G4int voxelZ, G4double mass):
    stdFile("Dose.out"),
    doseUnit(MeV/g)
{  
    // 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 << "IORTMatrix: Memory space to store physical dose into " <<  
        numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ <<
        " voxels has been allocated " << G4endl;
    }
    else G4Exception("IORTMatrix::IORTMatrix()", "IORT0005", FatalException, "Error: 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();
}

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

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

// Initialise the elements of the matrix to zero
void IORTMatrix::Initialize()
{ 
    // Clear ions store
    Clear();
    // Clear dose
    for(int i=0;i<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ;i++)
    {
        matrix[i] = 0;
    }
}
    // Print generated nuclides list
void IORTMatrix::PrintNuclides()
{
    for (size_t i=0; i<ionStore.size(); i++)
    {
        G4cout << ionStore[i].name << G4endl;
    }
}
    // Clear Hit voxel (TrackID) markers
void IORTMatrix::ClearHitTrack()
{
    for(G4int i=0; i<numberOfVoxelAlongX*numberOfVoxelAlongY*numberOfVoxelAlongZ; i++) hitTrack[i] = 0;
}
    // Return Hit status
G4int* IORTMatrix::GetHitTrack(G4int i, G4int j, G4int k)
{
    return &(hitTrack[Index(i,j,k)]);
}
// Dose methods...
// Fill DOSE/fluence matrix for secondary particles: 
// If fluence parameter is true (default value is FALSE) then fluence at voxel (i, j, k) is increased. 
// The energyDeposit parameter fill the dose matrix for voxel (i,j,k) 

G4bool IORTMatrix::Fill(G4int trackID,
                 G4ParticleDefinition* particleDef,
                 G4int i, G4int j, G4int k, 
                 G4double energyDeposit,
                 G4bool fluence) 
{
    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;
    }
    
}
    
    // Methods to store data to filenames...
    //
    // General method to store matrix data to filename
void IORTMatrix::StoreMatrix(G4String file, void* data, size_t psize)
{
    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();
        }
    }
}

    // Store fluence per single ion in multiple files
void IORTMatrix::StoreFluenceData()
{
    for (size_t i=0; i < ionStore.size(); i++){
        StoreMatrix(ionStore[i].name + "_Fluence.out", ionStore[i].fluence, sizeof(unsigned int));
    }
}
    // Store dose per single ion in multiple files
void IORTMatrix::StoreDoseData()
{
    
    for (size_t i=0; i < ionStore.size(); i++){
        StoreMatrix(ionStore[i].name + "_Dose.out", ionStore[i].dose, sizeof(G4double));
    }
}
    // Store dose for all ions into a single file and into ntuples.
    // Please note that this function is called via messenger commands
    // defined in the IORTAnalysisFileMessenger.cc class file
void IORTMatrix::StoreDoseFluenceAscii(G4String file)
{
#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();
    }
}

#ifdef G4ANALYSIS_USE_ROOT
void IORTMatrix::StoreDoseFluenceRoot()
{
    IORTAnalysisManager* analysis = IORTAnalysisManager::GetInstance();
    if (analysis -> IsTheTFile())
    {
    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] );


            }
        }
    }
}
#endif

void IORTMatrix::Fill(G4int i, G4int j, G4int k, 
                   G4double energyDeposit)
{
    if (matrix)
        matrix[Index(i,j,k)] += energyDeposit;
    
    // Store the energy deposit in the matrix element corresponding 
    // to the phantom voxel  
}
void IORTMatrix::TotalEnergyDeposit()
{
    // Store the information of the matrix in a ntuple and in 
    // a 1D Histogram

/*
  G4int k;
  G4int j;
  G4int i;
  
  if (matrix)
    {       //  AGGIUNTO
      std::ofstream ofs;        //  AGGIUNTO
     
ofs.open("PDD9.9Mev_coll60_0gradi_s500_Sp1_6gradi_step0.01_setcuts0.01.out");  //  AGGIUNTO  
          
      for(G4int l = 0; l < numberOfVoxelAlongZ; l++) //  was "numberVoxelZ" and so in the other directions
    {
      k = l;
      
      for(G4int m = 0; m < numberOfVoxelAlongY; m++) 
        { 
          j = m * numberOfVoxelAlongZ + k; 
        
        for(G4int n = 0; n <  numberOfVoxelAlongX; n++)
          {
            i =  n* numberOfVoxelAlongZ * numberOfVoxelAlongY + j;
            if(matrix[i] != 0)
              { 
            ofs<< n <<'\t'<< m <<'\t'<< // AGGIUNTO
              k<<'\t'<<matrix[i]<<G4endl; // AGGIUNTO


                       }
          }       
          }
      }
          ofs.close();      //  AGGIUNTO
    }
*/

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

#ifdef G4ANALYSIS_USE_ROOT
            if (analysis -> IsTheTFile() )
            {
            analysis -> FillEnergyDeposit(i, j, k, matrix[n]/massOfVoxel/doseUnit);
            analysis -> BraggPeak(i, matrix[n]/massOfVoxel/doseUnit);
            }
#endif

        }
    }
*/
}