#include <iostream>
#include <stdlib.h>
#include "TFile.h"
void quicksort( Double_t* arr1, Int_t* arr2, int left, int right)
{
  auto i = left;
  auto j = right;
  auto tmp = arr1[0];
  auto pivot = arr1[(int)((left + right)/2)];

  // Partition
  while (i <= j) {
    while (arr1[i] < pivot)
      i++;
    while (arr1[j] > pivot)
      j--;
    if (i <= j) {
      // swap arr1 elements
      tmp = arr1[i];
      arr1[i] = arr1[j];
      arr1[j] = tmp;
      // swap arr2 elements
      tmp = arr2[i];
      arr2[i] = arr2[j];
      arr2[j] = tmp;
      i++;
      j--;
    }
  };
  
  // Recursion
  if (left < j)
    quicksort(arr1, arr2, left, j);
  if (i < right)
    quicksort(arr1, arr2, i, right);

  return;
}
void TimeSync()
{
    Char_t* f;    TChain* MUSICdata = new TChain("tree");
    f ="/fs2data/bavarians/MUSIC_Devel/FSUDAQ/Run_001_B0.root";
    std::cout<<f<<std::endl;
    MUSICdata->Add(f);
    f ="/fs2data/bavarians/MUSIC_Devel/FSUDAQ/Run_001_B1.root";
    std::cout<<f<<std::endl;
    MUSICdata->Add(f);
    f ="/fs2data/bavarians/MUSIC_Devel/FSUDAQ/Run_001_B2.root";
    std::cout<<f<<std::endl;
    MUSICdata->Add(f);
    f ="/fs2data/bavarians/MUSIC_Devel/FSUDAQ/Run_001_B3.root";
    std::cout<<f<<std::endl;
    MUSICdata->Add(f);
    double run_portion=0.01;

    //"""""""""""""""""""""
    //TIME synchronization of the digital board
    //"""""""""""""""""""""

	Double_t shiftTime[4] ={0.0, 0.0 , 0.0, 0.0};
    //"""""""""""""""""""""
    //MAP
    //"""""""""""""""""""""
    //Left 0->15
    //Right 16->31
    //Individual{32=Grid, 33=S0, 34=cathode, 35=S17, 40-43 pulser},
    //100=empty
    int Map_DAQCha_to_MUSICStrip[4][16]={{34,100, 1, 100, 33, 40, 5, 100, 0, 100, 9, 100, 17, 13, 100, 32},
					 {2, 100, 16, 100, 21, 41, 20, 100, 8, 100, 24, 100, 27, 28, 100, 14},
				         {19, 100, 3, 100, 6, 42, 7, 100, 25, 100, 11, 100, 12, 15, 100, 31},
					 {4, 100, 18, 36, 23, 43, 22, 100, 10, 100, 26, 100, 29, 30, 100, 35}}; 


    //"""""""""""""""""""""
    //Data tree structure
    //"""""""""""""""""""""
    MUSICdata->SetBranchStatus("*", 0);
    
    int MAX_MULTI  =100;


	unsigned short           bd[MAX_MULTI] ;
	unsigned short           ch[MAX_MULTI] ;
	unsigned long long      e_t[MAX_MULTI] ;
    
    
    MUSICdata->SetBranchStatus("ch", 1);MUSICdata->SetBranchAddress("ch", &ch);
    MUSICdata->SetBranchStatus("bd", 1);MUSICdata->SetBranchAddress("bd", &bd);
    MUSICdata->SetBranchStatus("e_t", 1);MUSICdata->SetBranchAddress("e_t", &e_t);
    

    double Ibeam = 30000.;
    int nStat = MUSICdata->GetEntries();
    std::cout<<nStat<<std::endl;


    
    //"""""""""""""""""""""
    //time alignment
    //"""""""""""""""""""""
  TH2F* ChTimeBefore = new TH2F("ChTimeBefore", ";time(0.1 ms);channel(S0->LR16)",5000, 1000,1000+1,80,0,80);
    Double_t* timestampVec = new  Double_t[nStat];    Int_t* entryVec = new Int_t[nStat];
    for(int j=0;j<nStat;j++){
        MUSICdata->GetEntry(j);
        ChTimeBefore->Fill((e_t[0]*1e-9)*1e+4 , bd[0]*16+ch[0]);
        timestampVec[j]= (e_t[0] - shiftTime[bd[0]]*1e+9);
        entryVec[j]=j;
    }
    quicksort(timestampVec, entryVec,0,nStat-1);
    std::cout<<"sorted "<<std::endl;
    int PositiveTime=0;
    for(int j=0;j<nStat;j++){
        if(timestampVec[j]>=0){
            PositiveTime=j;
            break;
        }
    }

    //"""""""""""""""""""""
    //checking synchronization
    //"""""""""""""""""""""
    Double_t TimeEv = timestampVec[PositiveTime]*1e-9;

    //"""""""""""""""""""""
    //Plot definition
    //"""""""""""""""""""""
   TH2F* ChTimeAfter = new TH2F("ChTimeAfter", ";time(0.1 ms);channel(S0->LR16)",5000, 1000, 1000+1,80,0,80);

   for(int i=0;i<nStat;i++){
            MUSICdata->GetEntry(entryVec[i]);
            ChTimeAfter->Fill((timestampVec[i]*1e-9)*1e+4, bd[0]*16+ch[0]);
    }
    TCanvas* c= new TCanvas("c","c",800,800);c->Divide(1,2);
    gStyle->SetPalette(kThermometer);
    c->cd(1);ChTimeBefore->Draw("colz");
c->cd(2);ChTimeAfter->Draw("colz");

}