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#include <string.h>
#include <stdio.h>
#include <iostream>
#include <vector>
#include <utility>
#include <TFile.h>
#include <TTree.h>
#include <TSystemDirectory.h>
#include <string.h>
#include <TFile.h>
#include <TTree.h>
#include <TH1.h>
#include <TH2.h>
#include <TNtuple.h>
#include <iostream>
#include <fstream>
#include <TRandom.h>
#include <TROOT.h>
#include <algorithm>
#include <assert.h>
#include <math.h>
#include <stdlib.h>
#include <time.h>
#include <sys/time.h>
#include <TCanvas.h>
#include <TF1.h>
#include <TProfile.h>
#include <TVectorD.h>
#include <cstdlib>
#include <cmath>
#include <vector>
#include <TApplication.h>
using namespace std;
int main(int argc, char **argv){
// Working directories
const char *dirname = "/work/leverington/beamprofilemonitor/hitdata/HIT_26-11-2016/with_timestamp/";
const char *listfile = NULL; int ion = atoi(argv[1]); if (ion==1) {listfile = "energylist_p";} else if (ion==2) {listfile = "energylist_he";} else if (ion==3) {listfile = "energylist_c";} else if (ion==4) {listfile = "energylist_o";} else {cerr<< argv[1] << " not allowed" << endl; cerr << "specify (1, 2, 3, or 4) for p, He4, C12, or O16" << endl; return 1; } ifstream in; ofstream ic1energyfile,ic2energyfile, beamenergyfile,beamenergyfile_iccorr, noisefile, focusfile,focusHITfile, skewfile, kurtfile,focusFitfile,chi2Fitfile; ofstream beamenergyfile_beta, peakFitfile; TFile *f; TTree *tree; Int_t nfiles = 0; Int_t EList = 0; Double_t Energy = 0.; Double_t F1 = 0.; Double_t Intensity = 0.; Double_t SP = 0.; char Filename[50]; Int_t id = 0; Double_t signalmean = 0.; Double_t signalmeanerror = 0.; Double_t signalmean_corr = 0.; Double_t signalmeanerror_corr = 0.; Double_t signalmean_offsetcorr = 0.; Double_t signalmeanerror_offsetcorr = 0.; Double_t ic1mean = 0.; Double_t ic1meanerror = 0.; Double_t ic2mean = 0.; Double_t ic2meanerror = 0.;
Double_t sp_air = 0.; Double_t sp_ps = 0.; Double_t sp2_air = 0.; Double_t sp2_ps = 0.;
Double_t ic_beam_ratio = 0.; Double_t ic_beam_ratioerror = 0.;
Double_t totalcurrent = 0.; Double_t totaltime = 0.; Double_t intcorr = 0.; Double_t icbpmcorrelation = 0.;
Double_t noisemean = 0.; Double_t noiseRMS = 0.; Double_t focusmean = 0.; Double_t focusRMS = 0.; Double_t skewmean = 0.; Double_t skewRMS = 0.; Double_t kurtmean = 0.; Double_t kurtRMS = 0.; Double_t focusFitmean = 0.; Double_t focusFitRMS = 0.; Double_t chi2Fitmean = 0.; Double_t chi2FitRMS = 0.; Double_t peakFitmean = 0.; Double_t peakFitRMS = 0.; Double_t beta = 0.; Double_t gamma = 0.; Double_t zsqr = 0.; cout << "Trying to open"<< Form(": %s%s",dirname, listfile)<<"... " << endl;
in.open(Form("%s%s.prn",dirname, listfile));
ic1energyfile.open(Form("%s_ic1.txt",listfile )); ic2energyfile.open(Form("%s_ic1ratio.txt",listfile ));
beamenergyfile.open(Form("%s_bpm1.txt",listfile )); beamenergyfile_beta.open(Form("%s_bpmbeta1.txt",listfile ));
beamenergyfile_iccorr.open(Form("%s_bpm1ratio.txt",listfile ));
noisefile.open(Form("%s_noise.txt",listfile )); focusfile.open(Form("%s_focus1.txt",listfile )); focusHITfile.open(Form("%s_focusHIT.txt",listfile )); skewfile.open(Form("%s_skew1.txt",listfile )); kurtfile.open(Form("%s_kurt1.txt",listfile )); focusFitfile.open(Form("%s_focusfit.txt",listfile )); chi2Fitfile.open(Form("%s_chi2fit.txt",listfile )); peakFitfile.open(Form("%s_peakfit.txt",listfile ));
TF1 * f_sp_air = new TF1("f_sp_air","[0]*pow(x,[1])+[2]", 50, 250); //stopping power of protons in Air [MeV cm2 /g]
f_sp_air->SetParameters(303.746, -0.873697,1.01335); //protons between 50 and 300 MeV
TF1 * f_sp_ps = new TF1("f_sp_ps","[0]*pow(x,[1])+[2]", 50, 250); //stopping power of protons in polystyrene [MeV cm2 /g]
f_sp_ps->SetParameters(361.936, -0.892255, 1.19133); //protons between 50 and 220 MeV
TF1 * f_h2sp_air = new TF1("f_h2sp_air","[0]*pow(x,[1])+[2]", 50, 250); //stopping power of helium in air [MeV cm2 /g]
f_h2sp_air->SetParameters(1236.51, -0.880225, 4.17041); //helium between 50 and 300 MeV
TF1 * f_h2sp_ps = new TF1("f_h2sp_ps","[0]*pow(x,[1])+[2]", 50, 250); //stopping power of helium in polystyrene [MeV cm2 /g]
f_h2sp_ps->SetParameters(1387.08, -0.882686,4.60833); //heelium between 50 and 300 MeV
TF1 * f_c12sp_air = new TF1("f_c12sp_air","[0]*pow(x,[1])+[2]", 80, 480); //stopping power of carbon in air [MeV cm2 /g]
f_c12sp_air->SetParameters(13291.2, -0.925464,45.3876); //carbon between 80 and 480 MeV
TF1 * f_c12sp_ps = new TF1("f_c12sp_ps","[0]*pow(x,[1])+[2]", 80, 480); //stopping power of carbon in polystyrene [MeV cm2 /g]
f_c12sp_ps->SetParameters(14538.9, -0.922423,49.2859); //carbon between 80 and 480 MeV
TF1 * f_o16sp_air = new TF1("f_o16sp_air","[0]*pow(x,[1])+[2]", 80, 480); //stopping power of oxygen in air [MeV cm2 /g]
f_o16sp_air->SetParameters(24624.9, -0.925425,80.6828); //oxygen between 80 and 480 MeV
TF1 * f_o16sp_ps = new TF1("f_o16sp_ps","[0]*pow(x,[1])+[2]", 80,480); //stopping power of oxygen in polystyrene [MeV cm2 /g]
f_o16sp_ps->SetParameters(26465.6, -0.928309,88.6728); //oxygen between 80 and 480 MeV
///// ic1/SP intensity correction factor = 19.8E6+/-0.1E6 particles/s per nA/(Mevcm2/g)
if (!in) { cout << Form("%s%s",dirname, listfile) << " not found." << endl; return 0;} cout << Form("%s%s",dirname, listfile) << " opened." << endl;
in >> EList >> Energy >> F1 >> Intensity >> SP >> Filename >> id;//prime the while loop
while (!in.eof()) { TFile * file = TFile::Open(Form("%s%s",dirname,Filename)); TFile * outfile = TFile::Open(Form("plots/%s_plots",Filename),"RECREATE"); cout << Filename << endl; // TH1D* signalDist = 0;
// file->GetObject("signalDist",signalDist);
// signalmean = signalDist->GetMean();
// signalmeanerror = signalDist->GetMeanError();
// cout << signalmean << " " << signalmeanerror << endl;
// delete signalDist;
// TCanvas *c1 = new TCanvas("c1");
TTree *data; file->GetObject("newdata", data); TH2D *h_beamSignal_channel = (TH2D*)file->Get("th2d_beamSignal_channel"); TH2D *h_bkg_channel = (TH2D*)file->Get("th2d_bkg_channel");
noisemean = h_bkg_channel->GetMean(2); noiseRMS = h_bkg_channel->GetRMS(2);
TVectorD *v = (TVectorD*)file->Get("icinfo"); // v->Print();
totalcurrent = (*v)[0]; totaltime = (*v)[1]; // data->Print();
TH1D* h_beamSignal_1 = new TH1D("h_beamSignal_1","h_beamSignal_1",510,-500,50000); TH1D* h_ic1_1 = new TH1D("h_ic1_1","h_ic1_1",510,-50,500); TH1D* h_ic2_1 = new TH1D("h_ic2_1","h_ic2_1",510,-50,500);
TH1D* h_ic_beam_ratio = new TH1D("h_ic_beam_ratio","h_ic_beam_ratio",500,0,500.); TH2D* h_beamSignal_v_ic = new TH2D("h_beamSignal_v_ic","h_beamSignal_v_ic",510,-50,500,510,-500,50000);
TH1D* h_beamFocusX_1 = new TH1D("h_beamFocusX_1","h_beamFocusX_1",200,0,50.); TH1D* h_beamSkewX_1 = new TH1D("h_beamSkewX_1","h_beamSkewX_1",200,-10,10.); TH1D* h_beamKurtX_1 = new TH1D("h_beamKurtX_1","h_beamKurtX_1",200,-10,10.); TH1D* h_beamFocusX_fit = new TH1D("h_beamFocusX_fit","h_beamFocusX_fit",200,0,50.); TH1D* h_beamChi2_fit = new TH1D("h_beamChi2_fit","h_beamChi2_fit",200,0,50.); TH1D* h_beamPeakX_fit = new TH1D("h_beamPeakX_fit","h_beamPeakX_fit",1000,0,8000.);
if (id>=0&&id<=26){ //protons
sp_air = f_sp_air->Eval(Energy)*(Intensity/1.0E6); sp_ps = f_sp_ps->Eval(Energy)*(Intensity/1.0E6); sp2_air = f_sp_air->Eval(Energy); sp2_ps = f_sp_ps->Eval(Energy); gamma = Energy/938.272 +1.; // gamma = E_u/M_u +1
beta = sqrt(1. - 1./(gamma*gamma)); zsqr = 1.; } else if (id>=27&&id<=52){ //helium
sp_air = f_h2sp_air->Eval(Energy)*(Intensity/1.0E6); sp_ps = f_h2sp_ps->Eval(Energy)*(Intensity/1.0E6); sp2_air = f_h2sp_air->Eval(Energy); sp2_ps = f_h2sp_ps->Eval(Energy); gamma = Energy/932.1055 +1.;// gamma = E_u/M_u +1
beta = sqrt(1. - 1./(gamma*gamma)); zsqr = 4.;
} else if (id>=53&&id<=78){ //carbon
sp_air = f_c12sp_air->Eval(Energy)*(Intensity/1.0E6); sp_ps = f_c12sp_ps->Eval(Energy)*(Intensity/1.0E6); sp2_air = f_c12sp_air->Eval(Energy); sp2_ps = f_c12sp_ps->Eval(Energy); gamma = Energy/932.3539 +1.;// gamma = E_u/M_u +1
beta = sqrt(1. - 1./(gamma*gamma)); zsqr = 36.;
} else if (id>=79&&id<=99){ //oxygen
sp_air = f_o16sp_air->Eval(Energy)*(Intensity/1.0E6); sp_ps = f_o16sp_ps->Eval(Energy)*(Intensity/1.0E6); sp2_air = f_o16sp_air->Eval(Energy); sp2_ps = f_o16sp_ps->Eval(Energy); gamma = Energy/931.4418 +1.;// gamma = E_u/M_u +1
beta = sqrt(1. - 1./(gamma*gamma)); zsqr = 64.; } else { sp_air = -1.; sp_ps = -1.; sp2_air = -1.; sp2_ps = -1.; gamma = 0.; beta = 0.; zsqr = -1.; }
// cout << Form("beamPeakX_fit*sqrt(2)*%F/2.3548",F1) << endl;
// data->Project("h_beamSignal_1","beamSignal_1","beamon==1&&beamSignal_1>50");
// data->Project("h_beamSignal_1", Form("beamPeakX_fit*sqrt(2)*%F/2.3548",F1) ,"beamon==1&&ic1_1>0.005&&beamChi2_fit<200&&beamPeakX_fit>20");
data->Project("h_beamSignal_1", "beamPeakX_fit*sqrt(2)*beamFocusX_fit/2.3548" ,"beamon==1&&ic1_1>0.001&&beamChi2_fit<200&&beamPeakX_fit>20");
data->Project("h_beamFocusX_1","beamFocusX_1","beamon==1&&ic1_1>0.005&&beamSignal_1>100"); data->Project("h_beamSkewX_1","beamSkewX_1","beamon==1&&ic1_1>0.005&&beamSignal_1>100"); data->Project("h_beamKurtX_1","beamKurtX_1","beamon==1&&ic1_1>0.005&&beamSignal_1>100"); data->Project("h_beamFocusX_fit","beamFocusX_fit","beamon==1&&ic1_1>0.005&&beamChi2_fit<200&&beamPeakX_fit>20"); data->Project("h_beamChi2_fit","beamChi2_fit","beamon==1&&ic1_1>0.005&&beamChi2_fit<200&&beamPeakX_fit>20"); data->Project("h_beamPeakX_fit","beamPeakX_fit","beamon==1&&ic1_1>0.005&&beamChi2_fit<200&&beamPeakX_fit>20");
focusmean = h_beamFocusX_1->GetMean(); focusRMS = h_beamFocusX_1->GetRMS(); skewmean = h_beamSkewX_1->GetMean(); skewRMS = h_beamSkewX_1->GetMeanError(); kurtmean = h_beamKurtX_1->GetMean(); kurtRMS = h_beamKurtX_1->GetMeanError(); focusFitmean = h_beamFocusX_fit->GetMean(); focusFitRMS = h_beamFocusX_fit->GetRMS(); chi2Fitmean = h_beamChi2_fit->GetMean(); chi2FitRMS = h_beamChi2_fit->GetRMS(); peakFitmean = h_beamPeakX_fit->GetMean(); peakFitRMS = h_beamPeakX_fit->GetRMS();
data->Project("h_ic1_1","ic1_1","ic1_1>0.01"); data->Project("h_ic2_1","ic2_1","ic2_1>0.01");
data->Project("h_beamSignal_v_ic","(beamPeakX_fit*sqrt(2)*beamFocusX_fit/2.3548):ic1_1","beamon==1&&ic1_1>0.005&&beamChi2_fit<200&&beamPeakX_fit>20"); icbpmcorrelation = h_beamSignal_v_ic->GetCorrelationFactor();
data->Project("h_ic_beam_ratio","(beamPeakX_fit*sqrt(2)*beamFocusX_fit/2.3548)/ic1_1","beamon==1&&ic1_1>0.005&&beamChi2_fit<200&&beamPeakX_fit>20"); signalmean = h_beamSignal_1->GetMean(); signalmeanerror = h_beamSignal_1->GetMeanError();
ic1mean = h_ic1_1->GetMean(); ic1meanerror = h_ic1_1->GetMeanError(); ic2mean = h_ic2_1->GetMean(); ic2meanerror = h_ic2_1->GetMeanError();
ic_beam_ratio=h_ic_beam_ratio->GetMean(); ic_beam_ratioerror=h_ic_beam_ratio->GetRMS(); // intcorr = (Intensity /19.8E6) / (totalcurrent/sp2_air/totaltime);
intcorr = (Intensity / 19.8E6) / (ic1mean/sp2_air)/ 3.11;
cout << id << " " <<sp2_air << " " << ic1mean/sp2_air << " " << intcorr << endl; // cout << id <<" " << sp2_ps << " " <<signalmean/(Intensity/1.0E6)/(ic1mean/sp_air) << " " << signalmeanerror/(Intensity/1.0E6)/(ic1mean/sp_air) << endl;
ic1energyfile << sp2_air << " " << ic1mean *intcorr/(Intensity/1.E6) << " " << (ic1meanerror/ic1mean + 0.01)*ic1mean*intcorr/(Intensity/1.E6) << " " << Filename << endl; // ic2energyfile << sp2_air << " " << ic2mean / (Intensity/1.0E6) / (0.659869 + 1.50842 * sp2_air) << " " << ic2meanerror/sp_air << " " << Filename << endl;
beamenergyfile << sp2_ps << " " << signalmean*intcorr/(Intensity/1.E6) << " " << (signalmeanerror/signalmean + 0.01)*signalmean*intcorr/(Intensity/1.E6)<< endl; beamenergyfile_beta << beta << " " << signalmean*intcorr/(Intensity/1.E6)/sp2_ps << " " << (signalmeanerror/signalmean+0.01) * signalmean*intcorr/(Intensity/1.E6)/sp2_ps << endl;
beamenergyfile_iccorr << sp2_ps << " " << (ic_beam_ratio*sp2_air/sp2_ps)/84.5 << " " << (ic_beam_ratioerror*sp2_air/sp2_ps)/84.5 << endl;
ic2energyfile << sp2_air << " " << icbpmcorrelation << endl; noisefile << sp2_ps << " " << noisemean << " " << noiseRMS << endl; focusfile << sp2_ps << " " << focusmean*0.8 << " " << focusRMS*0.8 << endl; focusHITfile << sp2_ps << " " << F1 << endl; skewfile << sp2_ps << " " << skewmean << " " << skewRMS << endl; kurtfile << sp2_ps << " " << kurtmean << " " << kurtRMS << endl; focusFitfile << sp2_ps << " " << focusFitmean*0.8 << " " << focusFitRMS*0.8 << endl; chi2Fitfile << sp2_ps << " " << chi2Fitmean << " " << chi2FitRMS << endl; peakFitfile << sp2_ps << " " << peakFitmean << " " << peakFitRMS*0.8 << endl;
// h_beamSignal_1->Draw("");
// c1->SaveAs(Form("figs/h_beamsignal_%i.pdf",nfiles));
// c1->Destructor();
// f->Close();
outfile->Write(); outfile->Close(); file->Close(); in >> EList >> Energy >> F1 >> Intensity >> SP >> Filename >> id; // cout << EList << Energy << F1 << Intensity << SP << Filename << id << endl;
nfiles++; } ic1energyfile.close(); ic2energyfile.close();
beamenergyfile.close(); beamenergyfile_iccorr.close(); beamenergyfile_beta.close(); noisefile.close(); focusfile.close(); focusHITfile.close(); skewfile.close(); kurtfile.close(); in.close(); focusFitfile.close(); chi2Fitfile.close(); return 0;}
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