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 "HadrontherapyMatrix.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
            
            
            G4AnalysisManager*  LetFragmentTuple = G4AnalysisManager::Instance();
            
            LetFragmentTuple->SetVerboseLevel(1);
            LetFragmentTuple->SetFirstHistoId(1);
            LetFragmentTuple->SetFirstNtupleId(1);
            LetFragmentTuple ->OpenFile("Let");
            
            
            LetFragmentTuple ->CreateNtuple("coordinate", "Let");
            
            
            LetFragmentTuple ->CreateNtupleIColumn("i");//1
            LetFragmentTuple ->CreateNtupleIColumn("j");//2
            LetFragmentTuple ->CreateNtupleIColumn("k");//3
            LetFragmentTuple ->CreateNtupleDColumn("TotalLetD");//4
            LetFragmentTuple ->CreateNtupleIColumn("A");//5
            LetFragmentTuple ->CreateNtupleIColumn("Z");//6
            LetFragmentTuple ->CreateNtupleDColumn("IonLETD");//7
            LetFragmentTuple ->FinishNtuple();
            
            
      for(G4int i = 0; i < numberOfVoxelAlongX; i++)
        for(G4int j = 0; j < numberOfVoxelAlongY; j++)
          for(G4int k = 0; k < numberOfVoxelAlongZ; k++)
          {
            LetFragmentTuple->FillNtupleIColumn(1,0, i);
                        LetFragmentTuple->FillNtupleIColumn(1,1, j);
                        LetFragmentTuple->FillNtupleIColumn(1,2, k);
                        
                        G4int v = matrix -> Index(i, j, k);
                        
            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);
                                
                                LetFragmentTuple->FillNtupleDColumn(1,3, totalLetD[v]/(keV/um));
                                
                                
                for (size_t ll=0; ll < ionLetStore.size(); ll++)
                {
                  ofs << std::setw(width) << ionLetStore[ll].letDN[v]/(keV/um) ;
                                    
                                    LetFragmentTuple->FillNtupleIColumn(1,4, ionLetStore[ll].A);
                                    LetFragmentTuple->FillNtupleIColumn(1,5, ionLetStore[ll].Z);
                                    
                                    
                                    LetFragmentTuple->FillNtupleDColumn(1,6, ionLetStore[ll].letDN[v]/(keV/um));
                                    LetFragmentTuple->AddNtupleRow(1);
                                    
                                
                                }
                break;
              }
            }
          }
      ofs.close();
            
            LetFragmentTuple->Write();
            LetFragmentTuple->CloseFile();
        }
        
  }

 }