void Read(TString source, TString physics_list){
// Create output file geant4_dose.txt with the dose rate distribution, calculated
// with the simulation results containted in brachytherapy.root
gROOT -> Reset();
TString fileName="brachytherapy_"+source+"_"+physics_list+".root";
std::cout<< "Reading " << fileName << std::endl;
//const char * c = fileName.c_str();
TFile f(fileName);
Double_t Seed_length = 0.35; //seed length in cm
Double_t EnergyMap[401]; //2D map of total energy in "radial distance (mm)" and "angle (5 degrees)"
Int_t Voxels[401]; //the number of voxels used to provide dose to each element of the energy map
Double_t normDose[401]; //Energy map divided by voxels used to make cell, normalised to energy deposition at 1cm, 90 degrees
Double_t GeomFunction[401]; //Geometry Function, normalised to the geometry function at the reference point
Double_t GeometryFunctionZero; //Geometry function at reference point, 1cm and 90 degrees
Double_t beta; //beta angle for Geometry Function calculation
Double_t R; //radial distance in cm
Double_t K; //polar angle in radians
Double_t Radial[401]; //radial dose function
Double_t radius; //radius (mm)
Int_t radInt; //nearest integer of radius (mm)
Int_t numberOfBins=801;
for (int i=0; i <401; i++)
{
EnergyMap[i]=0.;
Voxels[i]=0.;
}
//Build Energy Deposition Map
for (int k=0; k< numberOfBins; k++)
{
for (int m=0; m< numberOfBins; m++)
{
Double_t xx_histo = h20->GetXaxis()->GetBinCenter(k);
Double_t yy_histo = h20->GetYaxis()->GetBinCenter(m);
Double_t edep_histo=h20->GetBinContent(k, m);
radius = sqrt(xx_histo*xx_histo+yy_histo*yy_histo);
// if ((edep_histo!=0) && radius < 12. && radius > 9) std::cout << "histo: " << xx_histo << ", " << yy_histo
// << ", radius: " << radius <<", edep: "<< edep_histo << std::endl;
if (radius != 0){
radInt = TMath::Nint(4*radius);
if ((radInt>0)&&(radInt<=400))
{
EnergyMap[radInt]+= edep_histo;
Voxels[radInt]+= 1;
// if (radius < 12. && radius > 9 && edep_histo!=0)std::cout<< "Radius: " << radius << ", radInt:"<<radInt << ", EnergyMap: "<< EnergyMap[radInt]<< ", voxels: " << Voxels[radInt]<< std::endl;
}
}
}}
//Create Normalised Dose Map
std::cout << "The energy deposition at the reference point is " << EnergyMap[40] << std::endl;
Double_t tempNormValue = EnergyMap[40]/Voxels[40];
//value at 1cm, 90 degrees, the normalisation point
std::cout << "Dose rate ditribution (distances in cm)" << std::endl;
ofstream myfile;
TString outputFileName ="geant4_dose_"+ source+"_"+physics_list+".txt";
//const char * cOutputFileName = fileName.c_str();
myfile.open(outputFileName);
std::cout << "file " << outputFileName << " is created "<<std::endl;
for (int i=0; i<=400; i++)
{
R = double(i)/40; //distance in CM!!!
if (Voxels[i]>0) normDose[i] = EnergyMap[i]/Voxels[i]/tempNormValue;
else normDose[i] = 0;
if (R> 0.05)
{
// cout << R << " " << normDose[i] << endl;
myfile << R << " " << normDose[i] << "\n";
}
}
myfile.close();
}