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
}