HadrontherapyLet.cc

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// Hadrontherapy advanced example for Geant4
// See more at: https://twiki.cern.ch/twiki/bin/view/Geant4/AdvancedExamplesHadrontherapy

#include "HadrontherapyDetectorConstruction.hh"
#include "HadrontherapyLet.hh"
#include "HadrontherapyAnalysisManager.hh"
#include "HadrontherapyInteractionParameters.hh"
#include "HadrontherapyPrimaryGeneratorAction.hh"
#include "HadrontherapyMatrix.hh"
#include "G4RunManager.hh"
#include "G4SystemOfUnits.hh"
#include <cmath>

HadrontherapyLet* HadrontherapyLet::instance = NULL;
G4bool HadrontherapyLet::doCalculation = false;

HadrontherapyLet* HadrontherapyLet::GetInstance(HadrontherapyDetectorConstruction *pDet)
{
    if (instance) delete instance;
    instance = new HadrontherapyLet(pDet);
    return instance;
}

HadrontherapyLet* HadrontherapyLet::GetInstance()
{
    return instance;
}

HadrontherapyLet::HadrontherapyLet(HadrontherapyDetectorConstruction* pDet)
  :filename("Let.out"),matrix(0) // Default output filename
{
    
    matrix = HadrontherapyMatrix::GetInstance();
    
    if (!matrix) 
      G4Exception("HadrontherapyLet::HadrontherapyLet",
          "Hadrontherapy0005", FatalException, 
          "HadrontherapyMatrix not found. Firstly create an instance of it.");
    
    nVoxels = matrix -> GetNvoxel();
    
    numberOfVoxelAlongX = matrix -> GetNumberOfVoxelAlongX();
    numberOfVoxelAlongY = matrix -> GetNumberOfVoxelAlongY();
    numberOfVoxelAlongZ = matrix -> GetNumberOfVoxelAlongZ();
    
    G4RunManager *runManager = G4RunManager::GetRunManager();
    pPGA = (HadrontherapyPrimaryGeneratorAction*)runManager -> GetUserPrimaryGeneratorAction();
    // Pointer to the detector material
    detectorMat = pDet -> GetDetectorLogicalVolume() -> GetMaterial();
    density = detectorMat -> GetDensity();
    // Instances for Total LET
    totalLetD =      new G4double[nVoxels];
    DtotalLetD =     new G4double[nVoxels];
    
}

HadrontherapyLet::~HadrontherapyLet()
{
    Clear();
    delete [] totalLetD;
    delete [] DtotalLetD;
}

// Fill energy spectrum for every voxel (local energy spectrum)
void HadrontherapyLet::Initialize()
{
    for(G4int v=0; v < nVoxels; v++) totalLetD[v] = DtotalLetD[v] = 0.;
    Clear();
}
void HadrontherapyLet::Clear()
{
    for (size_t i=0; i < ionLetStore.size(); i++)
    {
        delete [] ionLetStore[i].letDN;
        delete [] ionLetStore[i].letDD;
    }
    ionLetStore.clear();
}
void  HadrontherapyLet::FillEnergySpectrum(G4int trackID,
                                           G4ParticleDefinition* particleDef,
                                           /*G4double kinEnergy,*/
                                           G4double DE,
                                           G4double DX,
                                           G4int i, G4int j, G4int k)
{
    if (DE <= 0. || DX <=0.) return;
    if (!doCalculation) return;
    G4int Z = particleDef -> GetAtomicNumber();
    
    
    G4int PDGencoding = particleDef -> GetPDGEncoding();
    PDGencoding -= PDGencoding%10;
    
    G4int voxel = matrix -> Index(i,j,k);
    // Total LET calculation...
    totalLetD[voxel]  += DE*(DE/DX);
    DtotalLetD[voxel] += DE;
    // Single ion LET
    if (Z>=1)
    {
        // Search for already allocated data...
        size_t l;
        for (l=0; l < ionLetStore.size(); l++)
        {
            if (ionLetStore[l].PDGencoding == PDGencoding)
                if ( ((trackID ==1) && (ionLetStore[l].isPrimary)) || ((trackID !=1) && (!ionLetStore[l].isPrimary)))
                    break;
        }
        
        if (l == ionLetStore.size()) // Just another type of ion/particle for our store...
        {
            
            G4int A = particleDef -> GetAtomicMass();
            
            G4String fullName = particleDef -> GetParticleName();
            G4String name = fullName.substr (0, fullName.find("[") ); // cut excitation energy [x.y]
            
            ionLet ion =
            {
                (trackID == 1) ? true:false, // is it the primary particle?
                PDGencoding,
                fullName,
                name,
                Z,
                A,
                new G4double[nVoxels], // Let Dose Numerator
                new G4double[nVoxels]  // Let Dose Denominator
            };
            
            // Initialize let
            for(G4int v=0; v < nVoxels; v++) ion.letDN[v] = ion.letDD[v] = 0.;
            ionLetStore.push_back(ion);
            //G4cout << "Allocated LET data for " << ion.name << G4endl;
            
        }
        ionLetStore[l].letDN[voxel] += DE*(DE/DX);
        ionLetStore[l].letDD[voxel] += DE;
    }
}




void HadrontherapyLet::LetOutput()
{
    for(G4int v=0; v < nVoxels; v++) if (DtotalLetD[v]>0.) totalLetD[v] = totalLetD[v]/DtotalLetD[v];
    // Sort ions by A and then by Z ...
    std::sort(ionLetStore.begin(), ionLetStore.end());
    // Compute Let Track and Let Dose for any single ion
    
    for(G4int v=0; v < nVoxels; v++)
    {
        for (size_t ion=0; ion < ionLetStore.size(); ion++)
        {
            if (ionLetStore[ion].letDD[v] >0.) ionLetStore[ion].letDN[v] = ionLetStore[ion].letDN[v] / ionLetStore[ion].letDD[v];
            
        }// end loop over ions
    }
    
}// end loop over voxels

void HadrontherapyLet::StoreLetAscii()
{
#define width 15L
    if(ionLetStore.size())
    {
        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";
            ofs <<  std::setw(width) << "LDT";
            for (size_t l=0; l < ionLetStore.size(); l++)
            {
                G4String a = (ionLetStore[l].isPrimary) ? "_1":"";
                ofs << std::setw(width) << ionLetStore[l].name  + a ;
            }
            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 v = matrix -> Index(i, j, k);
                        // row write
                        for (size_t l=0; l < ionLetStore.size(); l++)
                        {
                            // Write only not identically null data lines
                            if(ionLetStore[l].letDN)
                            {
                                ofs << G4endl;
                                ofs << i << '\t' << j << '\t' << k << '\t';
                                
                                ofs << std::setw(width) << totalLetD[v]/(keV/um);
                                for (size_t ll=0; ll < ionLetStore.size(); ll++)
                                {
                                    ofs << std::setw(width) << ionLetStore[ll].letDN[v]/(keV/um) ;
                                }
                                break;
                            }
                        }
                    }
            ofs.close();
            G4cout << "Let is being written to " << filename << G4endl;
        }
        
    }
}

void HadrontherapyLet::StoreLetRoot()
{
#ifdef G4ANALYSIS_USE_ROOT
    
    HadrontherapyAnalysisManager* analysis = HadrontherapyAnalysisManager::GetInstance();
    
    for(G4int i = 0; i < numberOfVoxelAlongX; i++)
        for(G4int j = 0; j < numberOfVoxelAlongY; j++) 
            for(G4int k = 0; k < numberOfVoxelAlongZ; k++) 
            {
                G4int v = matrix -> Index(i, j, k);
                for (size_t ion=0; ion < ionLetStore.size(); ion++)
                {
                    
                    analysis -> FillLetFragmentTuple( i, j, k, ionLetStore[ion].A, ionLetStore[ion].Z, ionLetStore[ion].letDN[v]);
                    
                    
                }
            }
    
#endif
}