Import Geant4 11.2.0 source tree
This commit is contained in:
Gabriele Cosmo
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{
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////////////////////////////////////////////
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gROOT->Reset();
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bool saveImage = true;
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string imageFileName = "microdosimetricSpectra.png";
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bool saveLinearEdep = true;
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bool saveLogEdep = true;
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bool saveydySpec = true;
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////////////////////////////////////////////
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//Open File where data has been stored
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////////////////////////////////////////////
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TFile* f = new TFile("radioprotection_t0.root");
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TDirectory* dir = (TDirectory*)f->Get("radioprotection_ntuple");
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TTree * nEdep = (TTree*)dir->Get("102");
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Double_t edep;
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nEdep->SetBranchAddress("edep", &edep);
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double meanChordLength = 1; //change based on the thickness of the sensitive volume (make sure to apply a conversion factor if converting to a tissue equivalent material)
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////////////////////////////////////////////
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//Put hits in microdosimeter into linear binned space histogram (typical of experimental setup)
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////////////////////////////////////////////
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int numberLinearBins = 4096;
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double minLinealEnergy = 0;
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double maxLinealEnergy = 1000;
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TH1D* histoLin = new TH1D("h1", "f(y)", numberLinearBins, minLinealEnergy, maxLinealEnergy);
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TH1D* histoYFY = new TH1D("h2", "yf(y)", numberLinearBins, minLinealEnergy, maxLinealEnergy);
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TH1D* histoDY = new TH1D("h3", "d(y)", numberLinearBins, minLinealEnergy, maxLinealEnergy);
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////////////////////////////////////////////
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//Create log bin for microdosimetric plotting
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////////////////////////////////////////////
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//Log bin stuff
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int B = 20; //the number of increments in each decade
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//eg if B = 10: 1 2 3 ... 9 10 20 30 ... 90 100 200 ...
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double yMin = 0.01; // y = lineal energy
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double yMax = 1000;
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double range = yMax / yMin;
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double fooRange = range;
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double fooMag = 10; //any old silly no > 1
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int order = 0;
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while (fooMag > 1)
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{
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fooMag = fooRange / 10 ;
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fooRange = fooRange / 10 ;
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order = order + 1 ;
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}
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int binsPerDecade = B;
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const int numberOfLogBins = binsPerDecade * order +1; //get the total number of bins
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vector<double> xbins;
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for (int b = 0; b < numberOfLogBins; b++)
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{
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xbins.push_back((yMin)*pow(10, ((b) / double(B))));
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// cout << b << " " << xbins[b] << endl;
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}
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TH1D* histoLog = new TH1D("l1", "edepLin", (numberOfLogBins-1), &xbins[0]);
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////////////////////////////////////////////
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//loop through the hits in the detector stored in the ntuple
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////////////////////////////////////////////
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int numberHits = nEdep->GetEntries();
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cout << "Number of hits in detector = " << numberHits << endl;
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for (int i = 0; i < numberHits; i++)
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{
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nEdep->GetEntry(i);
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if (edep <= 0)
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{
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cout << "Edep = 0" << endl;
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}
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histoLin->Fill(edep/meanChordLength);
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histoLog->Fill(edep/meanChordLength);
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}
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////////////////////////////////////////////
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//Normalise the log histogram based on the bin width
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////////////////////////////////////////////
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for (int bb = 1; bb <= numberOfLogBins-1; bb++)
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{
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histoLog->SetBinContent(bb, (histoLog->GetBinContent(bb) / histoLog->GetBinWidth(bb)));
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}
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////////////////////////////////////////////
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//---------Save values to file--------------
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////////////////////////////////////////////
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ofstream outFile;
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if (saveLinearEdep)
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{
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outFile.open("linEdepSpec.txt");
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for (int i = 1 ; i <= numberLinearBins; i++)
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{
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outFile << histoLin->GetBinCenter(i) * meanChordLength << "\t" << histoLin->GetBinContent(i) << endl;
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}
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outFile.close();
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}
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if (saveLogEdep)
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{
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outFile.open("logEdepSpec.txt");
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for (int bb = 1; bb <= numberOfLogBins-1; bb++)
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{
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outFile << histoLog->GetBinCenter(bb) * meanChordLength << "\t" << histoLog->GetBinContent(bb) << endl;
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}
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outFile.close();
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}
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////////////////////////////////////////////
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//----------Normalise Histo to get f(y)----
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////////////////////////////////////////////
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double intOfHist = histoLin->Integral("width") ; //gets counts in each histogram and multiplies by bin width
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histoLin->Scale(1./intOfHist);
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//histoLin->Sumw2();
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double intOfLogHist = histoLog->Integral("width") ;
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histoLog->Scale(1./intOfLogHist);
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//histoLog->Sumw2();
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//////////////////////////////////////////////////////////////
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//-------Calculate RBE using the modified MK model-----------
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/////////////////////////////////////////////////////////////
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//Technically the use of the modified MKM is applied in
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//therapeutic ion beams and not used for radioprotection applications
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//though it is included here for convience.
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//NOTE: the form used here is for "heavy ions" and not applicable
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//to the more dose depedent protons
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//---------------------------------
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//Constants
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//---------------------------------
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const double satPar = 150.; //saturation paramater obv. in keV/um
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double satParSqr = satPar * satPar;
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const double pi = 3.14159265359;
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const double SiToMuscleCorrection = 0.57;
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//Cell reltated numbers
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double alpha0 = 0.13;//0.164;//0.13; //Gy^-1 //0.13 for carbon
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double beta = 0.05; //Gy^-2
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double rho = 1.; //g/cm^3
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double rSV = 0.42; //um, the radius of the HSG cell
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//-----------------------------------------------------------
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//In order for consistent units, which in their raw form are:
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//(1/(Gy^2))(keV/g)(cm^3/um^3)
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// (1/Gy^2)(keV/um)(cm^3/g)(1/um^2)
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//------------------------------------------------------------
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//So convert (keV/g) into Gy it is scaled by (1.602E-16/0.001)(J/kg)
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//And to get cm^3 into um^3 just scale by 10E12
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//------------------------------------------------------------
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double scaleGray = 1.602E-16/0.001;
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double scaleLength = 1.E12;
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//-------Calculate y*--------
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double topIntegral = 0.;
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double botIntegral = 0.;
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//top integral
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for (Int_t i = 1; i <= numberLinearBins; i++)
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{
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topIntegral += (1 - exp(-(histoLin->GetBinCenter(i) * histoLin->GetBinCenter(i)) / satParSqr))*histoLin->GetBinContent(i) * histoLin->GetBinWidth(i);
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// (1 - exp(-y^2/y_{0}^2)) * f(y) * dy
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}
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//bottom integral
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for (Int_t i = 1; i <= numberLinearBins; i++)
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{
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botIntegral += (histoLin->GetBinCenter(i) * histoLin->GetBinContent(i) * histoLin->GetBinWidth(i));
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// y (size of each being time bin number) * f(y) * dy (bin size)
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}
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//cout << "Top: " << topIntegral << endl;
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//cout << "Bot: " << botIntegral << endl;
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//saturation corrected dose averaged linel energy value (y*)
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double satCor = satParSqr * topIntegral / botIntegral;
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//(y_{0})^2*top/bottom
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//cout << "--------------------------------" << endl;
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//cout << "y* = " << satCor << endl;
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//cout << "--------------------------------" << endl;
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//-----------alpha--------
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double alpha = alpha0 + (beta / (rho*pi*rSV*rSV))*satCor*scaleGray*scaleLength;
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//cout << "alpha = " << alpha << endl;
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//-----------finally RBE itself--------
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double ln01 = -2.302585093;
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double RBE10;//= (2*beta*5.)((sqrt(alpha*alpha - 4*beta*ln01) - alpha));
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double topRBE = (2 * beta*5.);
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double botRBE = (sqrt(alpha*alpha - 4 * beta*ln01) - alpha);
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RBE10 = topRBE / botRBE;
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//cout << "--------------------------------" << endl;
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cout << "RBE10 = " << RBE10 << endl;
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//cout << "--------------------------------" << endl;
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////////////////////////////////////////////
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//-----------Calculate yF-------------------
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////////////////////////////////////////////
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//yF = int(y * f(y) dy)
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double linyF = 0.;
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for (int i = 1 ; i <= numberLinearBins; i++)
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{
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linyF += histoLin->GetBinCenter(i) * histoLin->GetBinContent(i) * histoLin->GetBinWidth(i) ;
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}
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cout << "yF = " << linyF << endl;
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double logyF = 0;
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for (int i = 1 ; i <= numberOfLogBins; i++)
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{
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logyF += histoLog->GetBinCenter(i) * histoLog->GetBinContent(i) * histoLog->GetBinWidth(i) ;
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}
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cout << "Log yF = " << logyF << endl;
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////////////////////////////////////////////
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//--------------Calculate d(y)--------------
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////////////////////////////////////////////
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//d(y) = y*f(y) / yF
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for (int i = 1 ; i <= numberLinearBins; i++)
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{
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histoLin->SetBinContent(i, (histoLin->GetBinCenter(i) * histoLin->GetBinContent(i) / linyF));
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}
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//check that it's normalised to 1
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double intOfHistDy = histoLin->Integral("width") ;
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cout << "Int of d(y) = " << intOfHistDy << endl;
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for (int bb = 1; bb <= numberOfLogBins-1; bb++)
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{
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histoLog->SetBinContent(bb, (histoLog->GetBinCenter(bb)* histoLog->GetBinContent(bb) / logyF));
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}
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double intOfHistLogDy = histoLog->Integral("width") ;
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cout << "Int of log d(y) = " << intOfHistLogDy << endl;
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////////////////////////////////////////////
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//-------Calculate Average Q(y)-----------
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////////////////////////////////////////////
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//Q(y) = (a1/y)[1-exp(-(a2)y*y - (a3)y*y*y)]
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//Quality factor values from ICRP 60 report
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double qualityCoeff1 = 5510.;
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double qualityCoeff2 = 5.E-5;
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double qualityCoeff3 = 2.E-7;
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double aveQuality = 0.;
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//AveQuality = int(Q(y)d(y)dy)
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for (int i = 1 ; i <= numberLinearBins; i++)
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{
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aveQuality += (qualityCoeff1/histoLin->GetBinCenter(i))* (1 - exp(-qualityCoeff2*pow(histoLin->GetBinCenter(i), 2.)-qualityCoeff3*pow(histoLin->GetBinCenter(i), 3.)))* histoLin->GetBinContent(i)* histoLin->GetBinWidth(i) ;
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}
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cout << "<Q> = " << aveQuality << endl;
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////////////////////////////////////////////
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//---------Calculate yD--------------------
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////////////////////////////////////////////
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//yD = int (y * d(y) dy)
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double linyD = 0.;
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for (int i = 1 ; i <= numberLinearBins; i++)
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{
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linyD += histoLin->GetBinCenter(i) * histoLin->GetBinContent(i) * histoLin -> GetBinWidth(i) ;
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}
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cout << "yD = " << linyD << endl;
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double logyD = 0.;
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for (int bb = 1; bb <= numberOfLogBins-1; bb++)
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{
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logyD += histoLog->GetBinCenter(bb) * histoLog->GetBinContent(bb) * histoLog -> GetBinWidth(bb) ;
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}
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cout << "log yD = " << logyD << endl;
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////////////////////////////////////////////
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//---------Create yd(y)-------------------
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////////////////////////////////////////////
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for (int bb = 1; bb <= numberOfLogBins-1; bb++)
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{
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histoLog->SetBinContent(bb, (histoLog->GetBinCenter(bb)* histoLog->GetBinContent(bb)) );
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}
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//Scale bins by log(10)/B
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//See Appendix B of the ICRU 36 report for more details
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histoLog->Scale((log(10) / B));
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if (saveydySpec)
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{
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outFile.open("logYDYspec.txt");
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for (int bb = 1; bb <= numberOfLogBins-1; bb++)
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{
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outFile << histoLog->GetBinCenter(bb) << "\t" << histoLog->GetBinContent(bb) << endl;
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}
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outFile.close();
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}
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if (saveImage)
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{
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TCanvas *c1 = new TCanvas("c1", "", 1000, 800);
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//gStyle->SetOptStat(0); //un-comment to remove stat box on top right
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histoLog->SetTitle("");
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histoLog->GetXaxis()->SetTitle("y (keV/#mum)");
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histoLog->GetYaxis()->SetTitle("yd(y)");
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histoLog->GetYaxis()->SetLabelFont(42);
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histoLog->GetXaxis()->SetLabelFont(42);
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histoLog->GetYaxis()->SetTitleFont(42);
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histoLog->GetXaxis()->SetTitleFont(42);
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histoLog->GetYaxis()->CenterTitle(1);
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histoLog->GetXaxis()->CenterTitle(1);
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histoLog->GetXaxis()->SetTitleSize(0.045);
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histoLog->GetYaxis()->SetTitleSize(0.045);
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//histoLog->GetYaxis()->SetRangeUser(0., 1.8);
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//histoLog -> GetXaxis()->SetRangeUser(0.01., 1000.);
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histoLog->GetYaxis()->SetLabelSize(0.04);
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histoLog->GetXaxis()->SetLabelSize(0.04);
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histoLog->SetLineColor(1);
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histoLog->SetLineWidth(4);
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c1->SetLogx();
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//c1->SetLogy();
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//Plotting misbehaves in root6.XX
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histoLog->Draw("");
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c1->SaveAs(imageFileName.c_str());
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}
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}
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