#include <sstream> 
#include <string>
#include <typeinfo>
#include <fstream>
#include <iomanip>
#include <vector>
#include <map>
#include <algorithm>
#include <functional>
#include <cmath>
#include <iostream>
#include <bitset>
using namespace std;
#include "TH1F.h"
#include "TF1.h" 
#include "TF2.h" 
#include "TF3.h" 
#include "TH2F.h"
#include "TH3F.h"
#include "TImage.h"
#include "TCanvas.h"
#include "TFile.h"
#include "TExec.h"
#include "TLine.h"
#include "TProfile.h"
#include "TError.h"
#include "TNtuple.h"
#include "TVector.h"
#include "TGraph.h"
#include "TGraph2D.h"
#include "TGraphErrors.h"
#include "TMultiGraph.h"
#include "TPolyLine3D.h"
#include "TPad.h"
#include "TGaxis.h"
#include "TAttLine.h"
#include "TAttFill.h"
#include "TApplication.h"
#include "THStack.h"
#include <TGClient.h>
#include <TF1.h>
#include "TTree.h"
#include "TBranch.h"
#include "TChain.h"
#include <TRandom.h>
#include <TGButton.h>
#include <TGFrame.h>
#include <TROOT.h>
#include "TStyle.h"
#include "TTreeViewer.h"
#include "TTreeReader.h"
#include "TTreeReaderValue.h"
#include "TTreeReaderArray.h"
#include "TLegend.h"
#include "TLatex.h"
#include "TPaveStats.h"
#include <TRootEmbeddedCanvas.h>
#include <RQ_OBJECT.h>
#include <TMatrix.h>
#include <TMath.h>

#include <TMatrixD.h>
#include <TMatrixDSym.h>
#include <TFitResultPtr.h>
#include <TFitResult.h>
#include <TGLHistPainter.h>
#include <TGLParametric.h>
#include "TAxis3D.h"
#include "TView.h"
#include <TEveManager.h>
#include "TPaletteAxis.h"
#include "TDecompLU.h"
#include "TPolyMarker3D.h"
#include "TMarker3DBox.h"
#include "TGLViewer.h"
#include "TView3D.h"
#include "TRootBrowser.h"
#include "TBrowser.h"
#include "TBenchmark.h"
#include "TSystem.h"






int main(int argc, char* argv[]){

TApplication *myApp = new TApplication("myApp", &argc, argv ,0,-1);

if (argc<1+1){//I'll ask for one argument in argv
  cout<<endl<<"Missing arguments! First is the 'saveImage' bool to save the canvas' content"<<endl;
  return 0;
}

                // type your script here //

gBenchmark = new TBenchmark(); //I'm declaring the tool that will measure the time to run the code
gBenchmark->Start("all"); //starts the timer


TFile file("TenTracks-ohdu2-run300-Zoomed.root"); //opens the file
TTreeReader reader("hitSumm", &file); //declares the reader

// To create the values I want. Name and template type must match the ones in the tree
TTreeReaderValue<int> nSavedPix(reader, "nSavedPix"); 
TTreeReaderValue<int> flag(reader, "flag"); 
TTreeReaderValue<int> xMax(reader, "xMax"); 
TTreeReaderValue<int> xMin(reader, "xMin"); 
TTreeReaderValue<int> yMax(reader, "yMax"); 
TTreeReaderValue<int> yMin(reader, "yMin"); 
TTreeReaderValue<float> E0(reader, "E0"); 
TTreeReaderValue<float> gain(reader, "gainCu"); 
TTreeReaderArray<int> xPix(reader, "xPix"); 
TTreeReaderArray<int> yPix(reader, "yPix"); 
TTreeReaderArray<int> level(reader, "level"); 
TTreeReaderArray<float> ePix(reader, "ePix"); 


int TrackCounter=0; //track counter 
int TopTracks=9; //Number of tracks I'll work with (max is 9)

int zoom1=1000; int zoom2=1200; //Limits if I want to work in a sub section

bool saveImage=(bool) strtof(argv[1], NULL);
string FileNameT=Form("%dTracksFitted",TopTracks);

// Pre-defining variables I'll use later
float Chisq=0; int NDF=0;

// Start looping in the tree
while (reader.Next()) {
//I'll ask that there're no errors
    if(*flag!=0)  continue;
  
    if (*xMin<zoom1 || *xMax>zoom2) continue;
    if(TopTracks<0 || TrackCounter>=TopTracks) break;

    
    TH2F * hTracks= new TH2F("Tracks",Form("Track %d",TrackCounter+1), *xMax-*xMin+10+10,*xMin-5,*xMax+5+10, *yMax-*yMin+10+10,*yMin-5,*yMax+5+10); //To draw the whole tracks
    ostringstream hTitle; hTitle<<"Track "<<TrackCounter+1;
    hTracks->SetTitle(Form("Track %d",TrackCounter+1));

    
//     Looping over all saved pixels in the track to fill the histogram
    for (int j=0;j<*nSavedPix;++j){
      if(level[j]>0) break;// Filter pixels in level 0
//       Now I'll fill the histogram, setting the bin's content to ePix/gain=energy in keV:
      hTracks->SetBinContent(xPix[j]-(*xMin-5), yPix[j]-(*yMin-5), ePix[j]/ *gain);
    }  //ends the loop
    
    {// Begin fitting
      hTracks->Fit("pol1","Q");
      hTracks->GetFunction("pol1")->SetRange(*xMin,*xMax);
    }
    
    Chisq=hTracks->GetFunction("pol1")->GetChisquare();
    NDF=hTracks->GetFunction("pol1")->GetNDF();

    
    TCanvas *c = new TCanvas("c", "Canvas",60,60,600,600);
    c->SetFillColor(kWhite);
    c->SetFrameFillColor(kWhite);// The background is white
    gStyle->SetPalette(kRainBow); //for the rainbow palette
    TGaxis::SetMaxDigits(4); //Significant digits in both axis and colorbar
    c->SetLogz();

    hTracks->GetFunction("pol1")->SetLineColor(kBlack);

    hTracks->GetXaxis()->SetTitle("x axis");
    hTracks->GetYaxis()->SetTitle("y axis");
    hTracks->GetYaxis()->SetTitleOffset(0.95);
    hTracks->SetMinimum(0);
    hTracks->SetMaximum(10);
    
    hTracks->Draw("colz");

    {//To form a legend
      gStyle->SetOptStat(0);
      TLegend *legend = new TLegend(0.15, 0.8, 0.65, 0.9);
      ostringstream legChisq; legChisq<<"Chi square/NDF: "<<Chisq<<"/"<<NDF<<"= "<<Chisq/NDF;
      legend->AddEntry(hTracks, legChisq.str().c_str(),"");
      legend->Draw();
      c->Update();
    }
    

//     Saving the histograms in an unique pdf file
    if(saveImage){ 
      c->Draw();c->Modified(); c->Update();
      if(TopTracks>1){
        if(TrackCounter+1==1) c->Print(("Histograms/"+FileNameT+".pdf(").c_str(),"pdf");
        else if(TrackCounter+1==TopTracks) c->Print(("Histograms/"+FileNameT+".pdf)").c_str(),"pdf");
        else c->Print(("Histograms/"+FileNameT+".pdf").c_str(),"pdf");
      }
      else if(TopTracks==1) c->Print(("Histograms/"+FileNameT+".pdf").c_str(),"pdf");
      delete c;
  }

    

    TrackCounter++;
}//Ends looping the tree


cout<<"Tracks looped (flag=0): "<<TrackCounter<<endl; //prints the ammount of events in the loop




                        // stop //

gBenchmark->Stop("all"); //stops and returns the timer
cout<<endl<<"Time to run = "<< gBenchmark->GetCpuTime("all") <<"s."<<endl;
//If desired, I can print the results for the timer

cout<<endl<<"Done"<<endl;
myApp->Run();  // allows the halt of the script execution
return 0;



    
    
}