#include <TCanvas.h>
#include <TTree.h>
#include <TFile.h>
#include <TChain.h>
#include <vector>

#include <string>
#include <iostream>

gROOT->Reset();

void run_DATA_Muons_WZ_HQ(std::string infile = "input.txt",
	 std::string inputtype = "DATA",
	 std::string inputstream = "Muons",
	 std::string ntupletype = "WZ" 
	 )
  
{

  std::string line;
  std::ifstream ifs(infile.c_str());
  std::vector<std::string> fileList;


  if (ifs.is_open()) {
    while ( ifs.good() ) {
      getline (ifs,line);
      if (line.length() == 0) continue;
      for (size_t i=0,n; i <= line.length(); i=n+1) {
        n = line.find_first_of(',',i);
        if (n == string::npos)
          n = line.length();
        string tmp = line.substr(i,n-i);
        fileList.push_back(tmp);
      }
    }
  }
  ifs.close();
  
  // open input files
  TChain * Input_Chain = new TChain("physics");
  for (int iFile=0; iFile<fileList.size(); ++iFile)
    {
      std::cout << "open " << fileList[iFile].c_str() << std::endl;
      Input_Chain->Add(fileList[iFile].c_str());
    }
  
  
  /*TChain * Input_Chain = new TChain("physics");
    
  cout << "files in Chain: ";
  for (size_t i=0,n; i <= fileList.length(); i=n+1) {
  n = fileList.find_first_of(',',i);
  if (n == string::npos)
  n = fileList.length();
  std::string iFileName = fileList.substr(i,n-i);
  Input_Chain->Add(iFileName.c_str());
  cout << iFileName << " ";
  }
  */
  cout << endl;
  cout << "events: " << Input_Chain->GetEntries() << endl;
  
  gROOT->ProcessLine(".L checkOQ.C++");
  gROOT->ProcessLine(".L egammaSFclass.C++");
  //gROOT->ProcessLine(".L EnergyRescalerTool/EnergyRescaler.cxx++");
  //gSystem->Load("GoodRunsLists/StandAlone/GoodRunsListsLib.so");
  //gSystem->Load("PileupReweighting/StandAlone/libPileupReweightingLib.so");
  gSystem->Load("Background.so");
  //std::cout << "===> Loaded Background.so ") << endl;
  gROOT->ProcessLine(".L Background_defs.h");
  
  /////////////////////////////////////////////////////////////////////////////////////////////////////

  Background analysisObj(Input_Chain);      //Creating class Object.

  /////////////////////////////////////////////////////////////////////////////////////////////////////

  /////////////////////////////////////////////////////////////////////////////////////////////////////
  // Arguments   
  analysisObj.SetInputName(infile.c_str());   
  // WZ, TOP or 'Thomas' D3PDs
  analysisObj.SetNtupleType(ntupletype.c_str());   // Choose between OA or WZ  
  //Is Analysis on "MC" or "DATA"
  analysisObj.SetInputType(inputtype.c_str());
  //Electron or Muon streams (sets proper Triggers for DATA and MC)
  //Choose either "Egamma" or "Muons"
  analysisObj.SetInputStream(inputstream.c_str()); //Doesn't matter for MC 

  /////////////////////////////////////////////////////////////////////////////////////////////////////


  /////////////////////////////////////////////////////////////////////////////////////////////////////
  //Function Info

  analysisObj.SetFunctionInfo("On");  // On or Off 
  
  /////////////////////////////////////////////////////////////////////////////////////////////////////

  /////////////////////////////////////////////////////////////////////////////////////////////////////

  //Set Analysis Year - Only 
  analysisObj.SetInputYear("2011");  //Only needed for MC 
  //Set Athena Analysis Release
  analysisObj.SetAthenaRelease("rel16");
  //Writing Out all events despite trigger. Set "On" or "Off".  
  analysisObj.WriteAllEvents("On");
  //Set skimming "On" or "Off"
  analysisObj.SetSkimming("Off");
  //To output truth info, set "On" along with skimming "Off".
  analysisObj.SetOutputTruth("Off");
  //To output electron, muon, and jet resolutions
  analysisObj.SetOutputResolutions("Off");
  //To output some variables that may help to debug
  analysisObj.SetOutputDebuggingVariables("Off");

  /////////////////////////////////////////////////////////////////////////////////////////////////////

  /////////////////////////////////////////////////////////////////////////////////////////////////////
  //Set Triggers (if outputted: Need to set WriteEvents == "On")  

  //If no trigger is desired set to "NONE"
  analysisObj.SetElectronTrigger("EF_e20_medium");
  analysisObj.Set2ElectronTrigger("EF_2e10_medium");
  //analysisObj.Set3ElectronTrigger("EF_3e10_medium");
  analysisObj.Set3ElectronTrigger("NONE");
  analysisObj.SetMuonTrigger("EF_mu20_MG");
  analysisObj.Set2MuonTrigger("EF_2mu10");
  //analysisObj.Set3MuonTrigger("EF_3mu6");
  analysisObj.Set3MuonTrigger("NONE");
  //analysisObj.Set1Electron1MuonTrigger("EF_e10_loose_mu10");
  analysisObj.Set1Electron1MuonTrigger("NONE");
  //analysisObj.Set1Electron2MuonTrigger("EF_e10_medium_2mu6");
  analysisObj.Set1Electron2MuonTrigger("NONE");
  //analysisObj.Set2Electron1MuonTrigger("EF_2e10_medium_mu6");
  analysisObj.Set2Electron1MuonTrigger("NONE");
  analysisObj.SetJetTrigger("NONE");

  //Trigger filtering "On" or "Off"
  analysisObj.Do1ElTrigger("On");
  analysisObj.Do1MuTrigger("On");
  analysisObj.Do2ElTrigger("On");
  analysisObj.Do2MuTrigger("On");
  analysisObj.Do3ElTrigger("Off");
  analysisObj.Do3MuTrigger("Off");
  analysisObj.Do1El1MuTrigger("Off");
  analysisObj.Do1El2MuTrigger("Off");
  analysisObj.Do2El1MuTrigger("Off");
  analysisObj.Do1JetTrigger("Off");

  //Trigger Efficiencies on MC: Set "On" or "Off". Make sure that the triggers used and electron/muon tightness criteria    are the same.  
  analysisObj.DoTriggerEfficiencies("Off");

  /////////////////////////////////////////////////////////////////////////////////////////////////////
  //Truth Analysis can be set "On" or "Off". Some Oxford Analysis ntuples do not contain truth info.

  analysisObj.DoTruthAnalysis("Off");   

  /////////////////////////////////////////////////////////////////////////////////////////////////////

  /////////////////////////////////////////////////////////////////////////////////////////////////////
  //Choose Analysis: _MODE_TR, _MODE_HQ, or _MODE_EL                              

  analysisObj.SetRunMode(_MODE_HQ);
  //if HQ analysis, choose W+jets, Z+jets or both by setting the following to "On".
  analysisObj.DoWjetsReconstruction("On");
  analysisObj.DoZjetsReconstruction("On");

  /////////////////////////////////////////////////////////////////////////////////////////////////////
  //Set Electron quality 
  //Set electron quality for el container : loose=1, medium=2, mediumIso=3, tight=4, tightIso=5. 
  analysisObj.SetElectronQuality(2);
  //Set electron quality for Z reconstruction : loose=1, medium=2, mediumIso=3, tight=4, tightIso=5. 
  analysisObj.SetZelQuality(2);
  //Set electron quality for W reconstruction : loose=1, medium=2, mediumIso=3, tight=4, tightIso=5. 
  analysisObj.SetWelQuality(4);
  //Set W transverse mass cut
  analysisObj.SetWtransMassCut(40000.0);
  
  /////////////////////////////////////////////////////////////////////////////////////////////////////
  //Set MET 
  //Set to "Yes" for MET_RefFinal or to "No" for MET_LocHadTopo based MET
  analysisObj.SetMET_Ref("Yes");

  /////////////////////////////////////////////////////////////////////////////////////////////////////
  //Set Muon Algorithm
  //Choose either "mu_staco_" or "mu_muid_"

  analysisObj.SetMuonAlgorithmName_WZ("mu_staco_"); 
  
  /////////////////////////////////////////////////////////////////////////////////////////////////////
  //Set Jet Algorithm  
  
  //rel15
  //analysisObj.SetJetAlgorithmName_WZ("antikt4h1topo"); 
  //analysisObj.SetBtagType("ip3d_pb");
  //analysisObj.SetTruthJetAlgorithmName_WZ("antikt4truth");

  //rel16
  analysisObj.SetJetAlgorithmName_WZ("jet_AntiKt4TopoEM_");
  analysisObj.SetBtagType("sv0_pb");
  analysisObj.SetTruthJetAlgorithmName_WZ("jet_AntiKt4TruthAll_");

  ///////////////////////////////////////////////////////////////////////////////////////////////////// 

  /////////////////////////////////////////////////////////////////////////////////////////////////////
  // For All 
  /////////////////////////////////////////////////////////////////////////////////////////////////////

  //Vertex (PV) Cuts: (minimum number of tracks for the PV, maximum z_PV in mm)
  analysisObj.SetVertexCuts(3., 200000.);
 

  //Electron Isolation -- Set Etcone20_pt_corrected cut -- Put Large number for no cut. 
  analysisObj.SetEtCone20PtCorCut(40000000.0); //in MeV and affects only HQ analysis

  //Muon Hits And Vertex Cuts: (min # Pixel Hits (>), min # SCT Hits + SCT crossed Dead Sensors (>= 6), max # Holes, min z0 in mm, min d0 in mm) 
  analysisObj.SetMuonHitsAndVertexCuts(1, 6, 3, 10, 10);
  //Muon ptcone20/mu_pt Cut
  analysisObj.SetMuPtcone20OverPtCut(0.1);

  //Jet Pile-Up Removal jvtxf cut
  analysisObj.SetPileUpRemovalCut(1.0);

  //Smearing
  analysisObj.SetDoElectronSmearing("No");
  analysisObj.SetDoMuonSmearing("No");
  
  //Pt Cuts
  analysisObj.SetElectronPt_Cut(25000.0);
  analysisObj.SetMuonPt_Cut(25000.0);
  analysisObj.SetJetPt_Cut(20000.0); 
  analysisObj.SetMissingEtCut(10000.0); //Event is kept despite cut, but invariant mass isn't calculated
  
  //Eta Cuts
  analysisObj.SetElectronEta_Cut_min(-2.47);
  analysisObj.SetMuonEta_Cut_min(-2.4);
  analysisObj.SetJetEta_Cut_min(-4.5);

  analysisObj.SetElectronEta_Cut_max(2.47);
  analysisObj.SetMuonEta_Cut_max(2.4);
  analysisObj.SetJetEta_Cut_max(4.5);

  //e/e and mu/e DeltaR overlap removal
  analysisObj.SetDeltaRElElAndMuElOverlap_Cut(0.1, 0.1); // (e/e , mu/e) affects only TR analysis

  //Can remove two ETA ranges in the form (Range1_min, Ranges1_max, Range2_min, Ranges2_max) for electrons, muons, and jets
  analysisObj.RemoveElEtaRanges(1.37, 1.52, 0.0, 0.0);
  analysisObj.RemoveMuEtaRanges(0.0, 0.0, 0.0, 0.0);
  analysisObj.RemoveJetEtaRanges(0.0, 0.0, 0.0, 0.0);
  //Can remove two PHI ranges in the form (Range1_min, Ranges1_max, Range2_min, Ranges2_max) for electrons, muons, and jets
  analysisObj.RemoveElPhiRanges(0.0, 0.0, 0.0, 0.0);
  analysisObj.RemoveMuPhiRanges(0.0, 0.0, 0.0, 0.0);
  analysisObj.RemoveJetPhiRanges(0.0, 0.0, 0.0, 0.0);

  //W reconstruction Cuts
  analysisObj.Set_W_Pt_Cut(0.0);

  //DeltaR Cuts between the lepton and neutrino stemming from a W. Put Large number for no cut.
  analysisObj.SetDeltaRElNuCut(1000000.0);
  analysisObj.SetDeltaRMuNuCut(1000000.0);

  //Maximum to set on the vector sum of the three objects that reconstruct the heavy quark + the tagged jet. 
  analysisObj.SetVectorSum_lnujj_Cut(1000000.0); // in MeV 
  
  //Second Jet Cuts (HQ analysis)
  analysisObj.SetDeltaR_jet1_jet2_Cut(0.0); //Set min DeltaR between jet1 and jet2
  analysisObj.SetDeltaPhi_jet1_jet2_Cut(0.0); //Set min DeltaPhi between jet1 and jet2
  analysisObj.SetDeltaEta_jet1_jet2_Cut(0.0);  //Set min DeltaEta between jet1 and jet2
  analysisObj.SetDeltaR_W_jet2_Cut(0.0); //Set min DeltaR between W and jet2   
  analysisObj.SetDeltaPhi_W_jet2_Cut(0.0); //Set min DeltaPhi between W and jet2
  analysisObj.SetDeltaEta_W_jet2_Cut(0.0); //Set min DeltaEta between W and jet2
  analysisObj.SetJet2_minPt_Cut(15000.0); // in MeV.
  analysisObj.SetJet2_minEta_Cut(0.0);  //0.0 is no cut.
  analysisObj.SetJet2_maxEta_Cut(5.0);  //put same as general jet pt cut for no cut. 

  //Z reconstruction Cuts
  analysisObj.SetInv_Mass_2El_Cut_min(25000.0);
  analysisObj.SetInv_Mass_2Mu_Cut_min(25000.0);
  analysisObj.SetInv_Mass_2El_Cut_max(25000.0);
  analysisObj.SetInv_Mass_2Mu_Cut_max(25000.0);
  

  analysisObj.SetJetsBTagProb_Cut(0.5); 
  
  analysisObj.SetLeptonFakingJetDeltaR_Cut(0.2); 
    
  //Truth Matching Cuts 
  analysisObj.SetDeltaRElectronResCut(0.03);
  analysisObj.SetDeltaEMinForElTruthMatching(0.5); //The matched electron has to be within x*100% of the true energy.  

  analysisObj.SetDeltaRMuonResCut(0.03);
  analysisObj.SetDeltaEMinForMuTruthMatching(0.5); //The matched muon has to be within x*100% of the true energy.

  analysisObj.SetDeltaRJetResCut(0.2);
  

  //Composite lepton analysis cut 
  analysisObj.SetPtCutForStrandedElectron(20000.0);

  /////////////////////////////////////////////////////////////////////////////////////////////////////

  /////////////////////////////////////////////////////////////////////////////////////////////////////
  //Uncertainties
  //LES Uncertainty. Nominal = 0, Minus One Sigma = 1, Plus One Sigma = 2  
  analysisObj.SetLESUncertainty(0); 
  //JES Uncertainty. Nominal = 0, Minus One Sigma = 1, Plus One Sigma = 2  
  analysisObj.SetJESUncertainty(0);
  //JER Uncertainty. Nominal = 0, Minus One Sigma = 1, Plus One Sigma = 2  
  analysisObj.SetJERUncertainty(0);

  ////////////////////////////////////////////////////////////////////////////////////////////////////
  //Histograms 

  //To Output histograms, set the following to "On"
  analysisObj.OutputHistograms("Off");

  //Histogram settings:  (int nbins, double x min, double x max)  
  analysisObj.SetInvMassHisto(100, 0.0, 1000000.0);
  analysisObj.SetWPtHisto(100, 0.0, 400000.0);
  analysisObj.SetWTransMassHisto(100, 0.0, 100000.0);
  analysisObj.SetDeltaRLepNuHisto(100, 0.0, 10.0);
  analysisObj.SetVectorSumlnujjHisto(100, 0.0, 100000.0);
  analysisObj.SetScalarPtHisto(100, 0.0, 1000000.0);
  analysisObj.SetDeltaRWJet2Histo(100, 0.0, 10.0);
  analysisObj.SetDeltaPhiWJet2Histo(100, 0.0, 3.5);
  analysisObj.SetDeltaEtaWJet2Histo(100, 0.0, 7.0);
  analysisObj.SetDeltaRJet1Jet2Histo(100, 0.0, 10.0);
  analysisObj.SetDeltaPhiJet1Jet2Histo(100, 0.0, 3.5);
  analysisObj.SetDeltaEtaJet1Jet2Histo(100, 0.0, 7.0);
  analysisObj.SetElEHisto(100, 0, 400000.0);
  analysisObj.SetElPtHisto(100, 0, 400000.0);
  analysisObj.SetElEtaHisto(100, -3, 3);
  analysisObj.SetElPhiHisto(100, -3.5, 3.5);
  analysisObj.SetElChargeHisto(4, -2, 2);
  analysisObj.SetElnBLHitsHisto(5, 0, 5);
  analysisObj.SetElQualityHisto(6, 0, 6);
  analysisObj.SetMuEHisto(100, 0, 400000.0);
  analysisObj.SetMuPtHisto(100, 0, 400000.0);
  analysisObj.SetMuEtaHisto(100, -3, 3);
  analysisObj.SetMuPhiHisto(100, -3.5, 3.5);
  analysisObj.SetMuChargeHisto(4, -2, 2);
  analysisObj.SetMuQualityHisto(4, 0, 4);
  analysisObj.SetJetEHisto(100, 0, 400000.0);
  analysisObj.SetJetPtHisto(100, 0, 400000.0);
  analysisObj.SetJetEtaHisto(100, -3, 3);
  analysisObj.SetJetPhiHisto(100, -3.5, 3.5);
  analysisObj.SetMETHisto(100, 0, 400000.0);
  analysisObj.SetMETxHisto(100, -400000.0, 400000.0);
  analysisObj.SetMETyHisto(100, -400000.0, 400000.0);
  analysisObj.SetMETzElpHisto(100, -400000.0, 400000.0);
  analysisObj.SetMETzElnHisto(100, -400000.0, 400000.0);
  analysisObj.SetMETzElsHisto(4, -2, 2);
  analysisObj.SetMETzMupHisto(100, -400000.0, 400000.0);
  analysisObj.SetMETzMunHisto(100, -400000.0, 400000.0);
  analysisObj.SetMETzMusHisto(4, -2, 2);
  analysisObj.SetElNumberHisto(8, 0, 8);
  analysisObj.SetMuNumberHisto(8, 0, 8);
  analysisObj.SetLepNumberHisto(8, 0, 8);
  analysisObj.SetJetNumberHisto(15, 0, 15);
  
  /////////////////////////////////////////////////////////////////////////////////////////////////////
  //Number of events to run on

  //analysisObj.Loop(0,500);
  analysisObj.Loop();
  
  /////////////////////////////////////////////////////////////////////////////////////////////////////
}