예제 #1
0
int main(int argc, char *argv[]) {
  FILE *ofile = fopen("ee_numbering.dat", "w");
  FILE *ofile_2 = fopen("ee_next_to_boundary.dat", "w");
  int hi = -1;
  try {
    for (int iz = -1; iz < 2; iz += 2) {
      for (int ix = EEDetId::IX_MIN; ix <= EEDetId::IX_MAX; ix++) {
        for (int iy = nBegin[ix - 1]; iy <= 100 - nBegin[ix - 1] + 1; iy++) {
          hi = -1;
          if (EEDetId::validDetId(ix, iy, iz)) {
            EEDetId id = EEDetId(ix, iy, iz);
            hi = id.hashedIndex();
            assert(EEDetId::unhashIndex(hi) == id);
            //std::cout << id << " " << hi << " " << EEDetId::unhashIndex( hi ) << std::endl;
            fprintf(ofile, "%d %d %d %d %d\n", ix, iy, iz, hi, 1);
            if (EEDetId::isNextToBoundary(id)) {
              fprintf(ofile_2, "%d %d %d %d %d\n", ix, iy, iz, hi, 1);
            } else {
              fprintf(ofile_2, "%d %d %d %d %d\n", ix, iy, iz, hi, 0);
            }
          } else {
            fprintf(ofile, "%d %d %d %d %d\n", ix, iy, iz, hi, 0);
            //std::cout << "Invalid detId " << ix << " " << iy << " " << iz << std::endl;
          }
        }
      }
    }
    for (int i = 0; i < 15480; i++) {
      EEDetId id = EEDetId::unhashIndex(hi);
      assert(EEDetId::validDetId(id.ix(), id.iy(), id.zside()));
    }
  } catch (std::exception &e) {
    std::cerr << e.what();
  }
  fclose(ofile);
  fclose(ofile_2);
}
// ****************************************************************
//XXX: main
int main(int argc, char* argv[])
{
  //
  // **** May 20 2010 update ****
  // Usage: CreateEcalTimingCalibsEE fileWithTree options...
  //

  using namespace std;
  // Ao dependent timing corrections
  timeCorrectionEE_ = new TF1("timeCorrectionEE_","pol4(0)",0,1.2);
  //coefficients obtained in the interval (0, 1.5) from Low eta region < 2.2, run 144011
  timeCorrectionEE_->SetParameters(-0.461192,0.0876435,-0.234752,0.143774,-0.051990);

  // For selection cuts
  string inBxs, inOrbits, inTrig, inTTrig, inLumi, inRuns;
  float avgTimeMin, avgTimeMax;
  float minAmpEB, minAmpEE;
  float maxE1E9, maxSwissCrossNoise;  // EB only, no spikes seen in EE
  float maxHitTimeEE, minHitTimeEE;
  // init to sensible defaults
  avgTimeMin = -1; // in ns
  avgTimeMax = 1; // in ns
  minAmpEB = 5; // GeV
  minAmpEE = 5; // GeV
  maxHitTimeEE = 15; // ns
  minHitTimeEE = -15; // ns
  maxE1E9 = 0.95; // EB only
  maxSwissCrossNoise = 0.95; // EB only
  inBxs = "-1";
  inOrbits = "-1";
  inTrig = "-1";
  inTTrig = "-1";
  inLumi = "-1";
  inRuns = "-1";

  char* infile = argv[1];
  if (!infile)
  {
    cout << " No input file specified !" << endl;
    return -1;
  }

  //TODO: Replace this with the parseArguments function from the pi0 binary
  std::string stringGenericOption    = "--";
  for (int i=1 ; i<argc ; i++) {
    if (argv[i] == std::string("-bxs") && argc>i+1) inBxs = std::string(argv[i+1]);
    if (argv[i] == std::string("-orbits") && argc>i+1) inOrbits = std::string(argv[i+1]);
    if (argv[i] == std::string("-trig") && argc>i+1) inTrig = std::string(argv[i+1]);
    if (argv[i] == std::string("-ttrig") && argc>i+1) inTTrig = std::string(argv[i+1]);
    if (argv[i] == std::string("-lumi") && argc>i+1) inLumi = std::string(argv[i+1]);
    if (argv[i] == std::string("-runs") && argc>i+1) inRuns = std::string(argv[i+1]);
    if (argv[i] == std::string("-ebampmin") && argc>i+1) minAmpEB = atof(argv[i+1]);
    if (argv[i] == std::string("-eeampmin") && argc>i+1) minAmpEE = atof(argv[i+1]);
    if (argv[i] == std::string("-e1e9max") && argc>i+1) maxE1E9 = atof(argv[i+1]);
    if (argv[i] == std::string("-swisskmax") && argc>i+1) maxSwissCrossNoise = atof(argv[i+1]);
    if (argv[i] == std::string("-avgtimemin") && argc>i+1) avgTimeMin = atof(argv[i+1]);
    if (argv[i] == std::string("-avgtimemax") && argc>i+1) avgTimeMax = atof(argv[i+1]);
    if (argv[i] == std::string("-eehittimemax") && argc>i+1) maxHitTimeEE = atof(argv[i+1]);
    if (argv[i] == std::string("-eehittimemin") && argc>i+1) minHitTimeEE = atof(argv[i+1]);
    // handle here the case of multiple arguments for input files
    if (argv[i] == std::string("--i"))// && argc>i+1)
    {
      for (int u=i+1; u<argc; u++)
      {
        if ( 0==std::string(argv[u]).find( stringGenericOption ) )
        {
          if ( 0==listOfFiles_.size())  {std::cout << "no input files listed" << std::cout;}
          else  {std::cout << "no more files listed, found: " << argv[u] << std::cout;}
          break;
        }
        else
        {
          listOfFiles_.push_back(argv[u]);
          i++;
        }
      }// loop on arguments following --i
      continue;
    }//end 'if input files'

  }
  // Open the input files
  if (listOfFiles_.size()==0){
    std::cout << "\tno input file found" << std::endl;
    return(1);
  }
  else{
    std::cout << "\tfound " << listOfFiles_.size() << " input files: " << std::endl;
    for(std::vector<std::string>::const_iterator  file_itr=listOfFiles_.begin(); file_itr!=listOfFiles_.end(); file_itr++){
      std::cout << "\t" << (*file_itr) << std::endl;
    }
  }
  // Tree construction
  TChain* chain = new TChain ("EcalTimeAnalysis") ;
  std::vector<std::string>::const_iterator file_itr;
  for(file_itr=listOfFiles_.begin(); file_itr!=listOfFiles_.end(); file_itr++){
    chain->Add( (*file_itr).c_str() );
  }


  cout << "Running with options: "
    << "avgTimeMin: " << avgTimeMin << " avgTimeMax: " << avgTimeMax
    << " minAmpEB: " << minAmpEB << " minAmpEE: " << minAmpEE
    << " maxHitTimeEE: " << maxHitTimeEE << " minHitTimeEE: " << minHitTimeEE
    << " inTrig: " << inTrig << " inTTrig: " << inTTrig << " inLumi: " << inLumi 
    << " inBxs: " << inBxs << " inRuns: " << inRuns << " inOrbits: " << inOrbits
    << endl;

  // Ignore warnings
  gErrorIgnoreLevel = 2001;

  setBranchAddresses(chain,treeVars_);

  // Generate all the vectors for skipping selections
  std::vector<std::vector<double> > bxIncludeVector;
  std::vector<std::vector<double> > bxExcludeVector;
  std::vector<std::vector<double> > orbitIncludeVector;
  std::vector<std::vector<double> > orbitExcludeVector;
  std::vector<std::vector<double> > trigIncludeVector;
  std::vector<std::vector<double> > trigExcludeVector;
  std::vector<std::vector<double> > ttrigIncludeVector;
  std::vector<std::vector<double> > ttrigExcludeVector;
  std::vector<std::vector<double> > lumiIncludeVector;
  std::vector<std::vector<double> > lumiExcludeVector;
  std::vector<std::vector<double> > runIncludeVector;
  std::vector<std::vector<double> > runExcludeVector;
  //recall: string inBxs, inOrbits, inTrig, inTTrig, inLumi, inRuns;
  genIncludeExcludeVectors(inBxs,bxIncludeVector,bxExcludeVector);
  genIncludeExcludeVectors(inOrbits,orbitIncludeVector,orbitExcludeVector);
  genIncludeExcludeVectors(inTrig,trigIncludeVector,trigExcludeVector);
  genIncludeExcludeVectors(inTTrig,ttrigIncludeVector,ttrigExcludeVector);
  genIncludeExcludeVectors(inLumi,lumiIncludeVector,lumiExcludeVector);
  genIncludeExcludeVectors(inRuns,runIncludeVector,runExcludeVector);

  // Open output file and book hists
  string fileNameBeg = "timingCalibsEE";
  string rootFilename = fileNameBeg+".root";
  TFile* outfile = new TFile(rootFilename.c_str(),"RECREATE");
  outfile->cd();

  TH1F* calibHistEE = new TH1F("timingCalibsEE","timingCalibs EE [ns]",2000,-100,100);
  TH1F* calibErrorHistEE = new TH1F("timingCalibErrorEE","timingCalibError EE [ns]",500,0,5);
  calibHistEE->Sumw2();
  calibErrorHistEE->Sumw2();

  TH2F* calibsVsErrors = new TH2F("timingCalibsAndErrors","TimingCalibs vs. errors [ns]",500,0,5,100,0,10);
  calibsVsErrors->Sumw2();

  //TH2F* calibMapEE = new TH2F("calibMapEE","time calib map EE",360,1,361,170,-86,86);
  //TH2F* calibMapEEFlip = new TH2F("calibMapEEFlip","time calib map EE",170,-86,86,360,1,361);
  //TH2F* calibMapEEPhase = new TH2F("calibMapEEPhase","time calib map EE (phase of Tmax)",360,1,361,170,-86,86);
  
  //TH2F* calibMapEtaAvgEE = new TH2F("calibMapEtaAvgEE","time calibs raw eta avg map EE",360,1,361,170,-86,86);
  //TH1F* calibHistEtaAvgEE = new TH1F("timingCalibsEtaAvgEE","EtaAvgTimingCalibs EE [ns]",2000,-100,100);

  TH2F* hitsPerCryMapEEM = new TH2F("hitsPerCryMapEEM","Hits per cry EEM;ix;iy",100,1,101,100,1,101);
  TH2F* hitsPerCryMapEEP = new TH2F("hitsPerCryMapEEP","Hits per cry EEP;ix;iy",100,1,101,100,1,101);
  TH1F* hitsPerCryHistEEM = new TH1F("hitsPerCryHistEEM","Hits per cry EEM;hashedIndex",14648,0,14648);
  TH1F* hitsPerCryHistEEP = new TH1F("hitsPerCryHistEEP","Hits per cry EEP;hashedIndex",14648,0,14648);
  //TH1C* eventsEEMHist = new TH1C("numEventsEEM","Number of events, EEM",100,0,100);
  //TH1C* eventsEEPHist = new TH1C("numEventsEEP","Number of events, EEP",100,0,100);
  TProfile* ampProfileEEM = new TProfile("ampProfileEEM","Amp. profile EEM;hashedIndex",14648,0,14648);
  TProfile* ampProfileEEP = new TProfile("ampProfileEEP","Amp. profile EEP;hashedIndex",14648,0,14648);
  TProfile2D* ampProfileMapEEP = new TProfile2D("ampProfileMapEEP","Amp. profile EEP;ix;iy",100,1,101,100,1,101);
  TProfile2D* ampProfileMapEEM = new TProfile2D("ampProfileMapEEM","Amp. profile EEM;ix;iy",100,1,101,100,1,101);

  //TH1F* eventsEEHist = new TH1F("numEventsEE","Number of events, EE",100,0,100);
  //TH1F* calibSigmaHist = new TH1F("timingSpreadEE","Crystal timing spread [ns]",1000,-5,5);

  TH1F* sigmaHistEE = new TH1F("sigmaCalibsEE"," Sigma of calib distributions EE [ns]",100,0,1);

  //TH1F* chiSquaredEachEventHist = new TH1F("chi2eachEvent","Chi2 of each event",500,0,500);
  //TH2F* chiSquaredVsAmpEachEventHist = new TH2F("chi2VsAmpEachEvent","Chi2 vs. amplitude of each event",500,0,500,750,0,750);
  //TH2F* chiSquaredHighMap = new TH2F("chi2HighMap","Channels with event #Chi^{2} > 100",360,1,361,170,-86,86);
  //TH1F* chiSquaredTotalHist = new TH1F("chi2Total","Total chi2 of all events in each crystal",500,0,500);
  //TH1F* chiSquaredSingleOverTotalHist = new TH1F("chi2SingleOverTotal","Chi2 of each event over total chi2",100,0,1);
  //TH1F* ampEachEventHist = new TH1F("energyEachEvent","Energy of all events [GeV]",1000,0,10);
  //TH1F* numPointsErasedHist = new TH1F("numPointsErased","Number of points erased per crystal",25,0,25);
  
  //TProfile2D* myAmpProfile = (TProfile2D*)EBampProfile->Clone();
  //myAmpProfile->Write();
  TH1F* expectedStatPresHistEEM = new TH1F("expectedStatPresEEM","Avg. expected statistical precision EEM [ns], all crys",200,0,2);
  TH2F* expectedStatPresVsObservedMeanErrHistEEM = new TH2F("expectedStatPresVsObsEEM","Expected stat. pres. vs. obs. error on mean each event EEM [ns]",200,0,2,200,0,2);
  TH1F* expectedStatPresEachEventHistEEM = new TH1F("expectedStatPresSingleEventEEM","Expected stat. pres. each event EEM [ns]",200,0,2);
  TH1F* expectedStatPresHistEEP = new TH1F("expectedStatPresEEP","Avg. expected statistical precision EEP [ns], all crys",200,0,2);
  TH2F* expectedStatPresVsObservedMeanErrHistEEP = new TH2F("expectedStatPresVsObsEEP","Expected stat. pres. vs. obs. error on mean each event [ns] EEP",200,0,2,200,0,2);
  TH1F* expectedStatPresEachEventHistEEP = new TH1F("expectedStatPresSingleEventEEP","Expected stat. pres. each event EEP [ns]",200,0,2);
  
  TH2F* errorOnMeanVsNumEvtsHist = new TH2F("errorOnMeanVsNumEvts","Error_on_mean vs. number of events",50,0,50,200,0,2);
  errorOnMeanVsNumEvtsHist->Sumw2();
  
  TH1F* calibHistEEM = new TH1F("timingCalibsEEM","timingCalibs EEM [ns]",500,-25,25);
  TH1F* calibHistEEP = new TH1F("timingCalibsEEP","timingCalibs EEP [ns]",500,-25,25);
  TH1F* calibErrorHistEEM = new TH1F("calibErrorEEM","timingCalibError EEM [ns]",250,0,5);
  TH1F* calibErrorHistEEP = new TH1F("calibErrorEEP","timingCalibError EEP [ns]",250,0,5);
  calibHistEEM->Sumw2();
  calibHistEEP->Sumw2();
  calibErrorHistEEM->Sumw2();
  calibErrorHistEEP->Sumw2();

  TH2F* calibMapEEM = new TH2F("calibMapEEM","time calib map EEM",100,1,101,100,1,101);
  TH2F* calibMapEEP = new TH2F("calibMapEEP","time calib map EEP",100,1,101,100,1,101);
  calibMapEEM->Sumw2();
  calibMapEEP->Sumw2();

  TH2F* sigmaMapEEM = new TH2F("sigmaMapEEM","Sigma of time calib map EEM [ns];ix;iy",100,1.,101.,100,1,101);
  TH2F* sigmaMapEEP = new TH2F("sigmaMapEEP","Sigma of time calib map EEP [ns];ix;iy",100,1.,101.,100,1,101);
  TH2F* calibErrorMapEEM = new TH2F("calibErrorMapEEM","Error of time calib map EEM [ns];ix;iy",100,1.,101.,100,1,101);
  TH2F* calibErrorMapEEP = new TH2F("calibErrorMapEEP","Error of time calib map EEP [ns];ix;iy",100,1.,101.,100,1,101);

  TDirectory* cryDirEEP = gDirectory->mkdir("crystalTimingHistsEEP");
  cryDirEEP->cd();
  TH1C* cryTimingHistsEEP[100][100]; // [0][0] = ix 1, iy 1
  for(int x=0; x < 100; ++x)
  {
    for(int y=0; y < 100; ++y)
    {
      if(!EEDetId::validDetId(x+1,y+1,1))
        continue;
      string histname = "EEP_cryTiming_ix";
      histname+=intToString(x+1);
      histname+="_iy";
      histname+=intToString(y+1);
      cryTimingHistsEEP[x][y] = new TH1C(histname.c_str(),histname.c_str(),660,-33,33);
      cryTimingHistsEEP[x][y]->Sumw2();
    }
  }
  outfile->cd();
  TDirectory* cryDirEEM = gDirectory->mkdir("crystalTimingHistsEEM");
  cryDirEEM->cd();
  TH1C* cryTimingHistsEEM[100][100]; // [0][0] = ix 1, iy 1
  for(int x=0; x < 100; ++x)
  {
    for(int y=0; y < 100; ++y)
    {
      if(!EEDetId::validDetId(x+1,y+1,-1))
        continue;
      string histname = "EEM_cryTiming_ix";
      histname+=intToString(x+1);
      histname+="_iy";
      histname+=intToString(y+1);
      cryTimingHistsEEM[x][y] = new TH1C(histname.c_str(),histname.c_str(),660,-33,33);
      cryTimingHistsEEM[x][y]->Sumw2();
    }
  }
  outfile->cd();
  
  cout << "Making calibs..." << endl;

  CrystalCalibration* eeCryCalibs[14648];
  //XXX: Making calibs with weighted/unweighted mean
  for(int i=0; i < 14648; ++i)
    eeCryCalibs[i] = new CrystalCalibration(); //use weighted mean!
    //eeCryCalibs[i] = new CrystalCalibration(false); //don't use weighted mean!

  cout << "Looping over TTree...";

  // Loop over the TTree
  int numEventsUsed = 0;
  int nEntries = chain->GetEntries();
  cout << "Begin loop over TTree." << endl;

  for(int entry = 0; entry < nEntries; ++entry)
  {
    chain->GetEntry(entry);

    // Loop once to calculate average event time
    float sumTime = 0;
    int numCrysEE = 0;
    for(int bCluster=0; bCluster < treeVars_.nClusters; bCluster++)
    {
      if(treeVars_.xtalInBCIEta[bCluster][0] != -999999) continue; // skip EB clusters
      for(int cryInBC=0; cryInBC < treeVars_.nXtalsInCluster[bCluster]; cryInBC++)
      {
        sumTime += treeVars_.xtalInBCTime[bCluster][cryInBC];
        numCrysEE++;
      }
    }
    //debug
    //cout << "Number of EE crys in event: " << numEEcrys << endl;

    //XXX: Event cuts
    if(sumTime/numCrysEE > avgTimeMax || sumTime/numCrysEE < avgTimeMin)
    {
      //cout << "Average event time: " << sumTime/numCrysEE  << " so event rejected." << endl;
      continue;
    }
    // check BX, orbit, lumi, run, L1 tech/phys triggers
    bool keepEvent = includeEvent(treeVars_.bx,bxIncludeVector,bxExcludeVector)
      && includeEvent(treeVars_.orbit,orbitIncludeVector,orbitExcludeVector)
      && includeEvent(treeVars_.lumiSection,lumiIncludeVector,lumiExcludeVector)
      && includeEvent(treeVars_.runId,runIncludeVector,runExcludeVector)
      && includeEvent(treeVars_.l1ActiveTriggers,
          treeVars_.l1NActiveTriggers,trigIncludeVector,trigExcludeVector)
      && includeEvent(treeVars_.l1ActiveTechTriggers,
          treeVars_.l1NActiveTechTriggers,ttrigIncludeVector,ttrigExcludeVector);
    if(!keepEvent)
      continue;
      
    numEventsUsed++;

    // Loop over the EE crys and fill the map
    for(int bCluster=0; bCluster < treeVars_.nClusters; bCluster++)
    {
      if(treeVars_.xtalInBCIEta[bCluster][0] != -999999) continue; // skip EB clusters
      for(int cryInBC=0; cryInBC < treeVars_.nXtalsInCluster[bCluster]; cryInBC++)
      {
        int hashedIndex = treeVars_.xtalInBCHashedIndex[bCluster][cryInBC];
        float cryTime = treeVars_.xtalInBCTime[bCluster][cryInBC];
        float cryTimeError = treeVars_.xtalInBCTimeErr[bCluster][cryInBC];
        float cryAmp = treeVars_.xtalInBCAmplitudeADC[bCluster][cryInBC];
	float Ao = cryAmp/sigmaNoiseEE;
	float AoLog = log10(Ao/25);

        EEDetId det = EEDetId::unhashIndex(hashedIndex);
        if(det==EEDetId()) // make sure DetId is valid
          continue;

        int ix = det.ix();
        int iy = det.iy();

        //XXX: RecHit cuts
        bool keepHit = cryAmp >= minAmpEE
          && cryTime > minHitTimeEE
          && cryTime < maxHitTimeEE
	  && AoLog > 0
          && AoLog < 1.2;
        if(!keepHit)
          continue;

        //cout << "STUPID DEBUG: " << hashedIndex << " cryTime: " << cryTime << " cryTimeError: " << cryTimeError << " cryAmp: " << cryAmp << endl;

	// Timing correction to take out the energy dependence if log10(ampliOverSigOfThis/25)
        // is between 0 and 1.2 (about 1 and 13 GeV)
	// amplitude dependent timing corrections
        float timing = cryTime - timeCorrectionEE_->Eval(AoLog);
        //FIXME
        cryTimeError = 1;
        eeCryCalibs[hashedIndex]->insertEvent(cryAmp,timing,cryTimeError,false);

        //SIC Use when we don't have time_error available
        //eeCryCalibs[hashedIndex]->insertEvent(cryAmp,cryTime,35/(cryAmp/1.2),false);
        if(det.zside() < 0)
        {
          ampProfileEEM->Fill(hashedIndex,cryAmp);
          ampProfileMapEEM->Fill(ix,iy,cryAmp);
        }
        else
        {
          ampProfileEEP->Fill(hashedIndex,cryAmp);
          ampProfileMapEEP->Fill(ix,iy,cryAmp);
        }
      }
    }
  }

  //create output text file
  ofstream fileStream;
  string fileName = fileNameBeg+".calibs.txt";
  fileStream.open(fileName.c_str());
  if(!fileStream.good() || !fileStream.is_open())
  {
    cout << "Couldn't open text file." << endl;
    return -1;
  }
  //create problem channels text file
  ofstream fileStreamProb;
  string fileName2 = fileNameBeg+".problems.txt";
  fileStreamProb.open(fileName2.c_str());
  if(!fileStreamProb.good() || !fileStreamProb.is_open())
  {
    cout << "Couldn't open text file." << endl;
    return -1;
  }

  // Create calibration container objects
  EcalTimeCalibConstants timeCalibConstants;
  EcalTimeCalibErrors timeCalibErrors;

  cout << "Using " << numEventsUsed << " out of " << nEntries << " in the tree." << endl;
  cout << "Creating calibs..." << endl;
  float cryCalibAvg = 0;
  int numCrysCalibrated = 0;
  vector<int> hashesToCalibrateToAvg;
  //Loop over all the crys
  for(int hashedIndex=0; hashedIndex < 14648; ++hashedIndex)
  {
    EEDetId det = EEDetId::unhashIndex(hashedIndex);
    if(det==EEDetId())
      continue;
    CrystalCalibration cryCalib = *(eeCryCalibs[hashedIndex]);
    int x = det.ix();
    int y = det.iy();

    //chiSquaredTotalHist->Fill(cryCalib.totalChi2);
    //expectedStatPresHistEB->Fill(sqrt(1/expectedPresSumEB));
    //expectedStatPresVsObservedMeanErrHistEB->Fill(sigmaM,sqrt(1/expectedPresSumEB));

    //XXX: Filter events at default 0.5*meanE threshold
    cryCalib.filterOutliers();
    
    //numPointsErasedHist->Fill(numPointsErased);
    
    //Write cryTimingHists
    vector<TimingEvent> times = cryCalib.timingEvents;
    for(vector<TimingEvent>::const_iterator timeItr = times.begin();
        timeItr != times.end(); ++timeItr)
    {
      if(det.zside() < 0)
      {
        float weight = 1/((timeItr->sigmaTime)*(timeItr->sigmaTime));
        cryTimingHistsEEM[x-1][y-1]->Fill(timeItr->time,weight);
      }
      else
      {
        float weight = 1/((timeItr->sigmaTime)*(timeItr->sigmaTime));
        cryTimingHistsEEP[x-1][y-1]->Fill(timeItr->time,weight);
      }
    }
    if(det.zside() < 0)
    {
      cryDirEEM->cd();
      cryTimingHistsEEM[x-1][y-1]->Write();
    }
    else
    {
      cryDirEEP->cd();
      cryTimingHistsEEP[x-1][y-1]->Write();
    }
    outfile->cd();

    if(det.zside() < 0)
    {
      hitsPerCryHistEEM->SetBinContent(hashedIndex+1,cryCalib.timingEvents.size());
      hitsPerCryMapEEM->Fill(x,y,cryCalib.timingEvents.size());
    }
    else
    {
      hitsPerCryHistEEP->SetBinContent(hashedIndex+1,cryCalib.timingEvents.size());
      hitsPerCryMapEEP->Fill(x,y,cryCalib.timingEvents.size());
    }
    
    // Make timing calibs
    double p1 = cryCalib.mean;
    double p1err = cryCalib.meanE;
    //cout << "cry ieta: " << ieta << " cry iphi: " << iphi << " p1: " << p1 << " p1err: " << p1err << endl;
    if(cryCalib.timingEvents.size() < 10)
    {
      fileStreamProb << "Cry (only " << cryCalib.timingEvents.size() << " events) was calibrated to avg: " << det.zside() << ", "
                                                                                        << x <<", " << y << ", hash: "
                                                                        << hashedIndex
                                                                          << "\t Calib: " << p1 << "\t Error: " << p1err << std::endl;
      hashesToCalibrateToAvg.push_back(hashedIndex);
      continue;
    }
    // Make it so we can add calib to reco time
    p1*=-1;
    if(p1err < 0.5 && p1err > 0)
    {
      fileStream << "EE\t" << hashedIndex << "\t" << p1 << "\t\t" << p1err << endl;
      if(det.zside() < 0)
      {
        calibHistEEM->Fill(p1);
        //calibMapEEMFlip->Fill(y-85,x+1,p1);
        calibMapEEM->Fill(x,y,p1);
        //calibMapEEMPhase->Fill(x+1,y-85,p1/25-floor(p1/25));
        //errorOnMeanVsNumEvtsHist->Fill(times.size(),p1err);
      }
      else
      {
        calibHistEEP->Fill(p1);
        //calibMapEEPFlip->Fill(y-85,x+1,p1);
        calibMapEEP->Fill(x,y,p1);
        //calibMapEEPPhase->Fill(x+1,y-85,p1/25-floor(p1/25));
        //errorOnMeanVsNumEvtsHist->Fill(times.size(),p1err);
      }
      cryCalibAvg+=p1;
      ++numCrysCalibrated;
      //Store in timeCalibration container
      EcalTimeCalibConstant tcConstant = p1;
      EcalTimeCalibError tcError = p1err;
      uint32_t rawId = EEDetId::unhashIndex(hashedIndex);
      timeCalibConstants[rawId] = tcConstant;
      timeCalibErrors[rawId] = tcError;
    }
    else
    {
      //std::cout << "Cry: " << y <<", " << x << ", hash: " << itr->first
      //  << "\t Calib: " << p1 << "\t Error: " << p1err << std::endl;
      fileStreamProb << "Cry was calibrated to avg: " << x <<", " << y << ", hash: " << hashedIndex
        << "\t Calib: " << p1 << "\t Error: " << p1err << std::endl;
    }

    sigmaHistEE->Fill(cryCalib.stdDev);
    if(det.zside() < 0)
    {
      //calibsVsErrorsEEM->Fill(p1err, p1 > 0 ? p1 : -1*p1);
      calibErrorHistEEM->Fill(p1err);
      calibErrorMapEEM->Fill(x,y,p1err);
      sigmaMapEEM->Fill(x,y,cryCalib.stdDev);
    }
    else
    {
      //calibsVsErrorsEEP->Fill(p1err, p1 > 0 ? p1 : -1*p1);
      calibErrorHistEEP->Fill(p1err);
      calibErrorMapEEP->Fill(x,y,p1err);
      sigmaMapEEP->Fill(x,y,cryCalib.stdDev);
    }
  }
  
  fileStream.close();
  fileStreamProb.close();
  // Calc average
  if(numCrysCalibrated > 0)
    cryCalibAvg/=numCrysCalibrated;
  cryCalibAvg-= 2.0833; // Global phase shift
  // calibrate uncalibratable crys
  for(vector<int>::const_iterator hashItr = hashesToCalibrateToAvg.begin();
      hashItr != hashesToCalibrateToAvg.end(); ++hashItr)
  {
    //Store in timeCalibration container
    EcalTimeCalibConstant tcConstant = cryCalibAvg;
    EcalTimeCalibError tcError = 999;
    uint32_t rawId = EEDetId::unhashIndex(*hashItr);
    timeCalibConstants[rawId] = tcConstant;
    timeCalibErrors[rawId] = tcError;
  }

  //Write XML files
  cout << "Writing XML files." << endl;
  EcalCondHeader header;
  header.method_="testmethod";
  header.version_="testversion";
  header.datasource_="testdata";
  header.since_=123;
  header.tag_="testtag";
  header.date_="Mar 24 1973";
  string timeCalibFile = "EcalTimeCalibsEE.xml";
  string timeCalibErrFile = "EcalTimeCalibErrorsEE.xml";
  // Hack to prevent seg fault
  EcalTimeCalibConstant tcConstant = 0;
  EcalTimeCalibError tcError = 0;
  uint32_t rawId = EBDetId::unhashIndex(0);
  timeCalibConstants[rawId] = tcConstant;
  timeCalibErrors[rawId] = tcError;
  // End hack
  EcalTimeCalibConstantsXMLTranslator::writeXML(timeCalibFile,header,timeCalibConstants);
  EcalTimeCalibErrorsXMLTranslator::writeXML(timeCalibErrFile,header,timeCalibErrors);

  cout << "Writing histograms." << endl;
  outfile->cd();
  calibHistEEM->SetXTitle("timingCalib [ns]");
  calibHistEEM->Write();
  calibHistEEP->SetXTitle("timingCalib [ns]");
  calibHistEEP->Write();
  calibErrorHistEEP->SetXTitle("uncertainty on mean [ns]");
  calibErrorHistEEP->Write();
  calibErrorHistEEM->SetXTitle("uncertainty on mean [ns]");
  calibErrorHistEEM->Write();
  calibErrorMapEEP->Write();
  calibErrorMapEEM->Write();
  sigmaHistEE->Write();
  sigmaMapEEM->Write();
  sigmaMapEEP->Write();

  //can->Print("calibs1D.png");
  //cout << "Writing calibVsErrors" << endl;
  //calibsVsErrors->SetYTitle("AbsCalibConst");
  //calibsVsErrors->SetXTitle("calibConstError");
  //calibsVsErrors->Write();

  //Move empty bins out of the way
  int nxbins = calibMapEEM->GetNbinsX();
  int nybins = calibMapEEM->GetNbinsY();
  for(int i=0;i<=(nxbins+2)*(nybins+2); ++i)
  {
    double binentsM = calibMapEEM->GetBinContent(i);
    if(binentsM==0)
    {
      calibMapEEM->SetBinContent(i,-1000);
    }
    double binentsP = calibMapEEP->GetBinContent(i);
    if(binentsP==0)
    {
      calibMapEEP->SetBinContent(i,-1000);
    }
  }
  calibMapEEM->SetXTitle("ix");
  calibMapEEM->SetYTitle("iy");
  calibMapEEM->Write();
  calibMapEEP->SetXTitle("ix");
  calibMapEEP->SetYTitle("iy");
  calibMapEEP->Write();

  //calibSigmaHist->SetXTitle("#sigma_{cryTime} [ns]");
  //calibSigmaHist->Write();
  
  // Old hist, commented Jun 15 2009
  //avgAmpVsSigmaTHist->SetXTitle("#sigma_{cryTime} [ns]");
  //avgAmpVsSigmaTHist->SetYTitle("Avg. amp. [adc]");
  //avgAmpVsSigmaTHist->Write();
 
  //errorOnMeanVsNumEvtsHist->SetXTitle("Events");
  //errorOnMeanVsNumEvtsHist->SetYTitle("Error_on_mean [ns]");
  //TProfile* theProf = (TProfile*) errorOnMeanVsNumEvtsHist->ProfileX();
  //TF1* myFit = new TF1("myFit","[0]/sqrt(x)+[1]",0,50);
  //myFit->SetRange(0,50);
  ////theProf->Fit("myFit");
  //theProf->Write();
  //errorOnMeanVsNumEvtsHist->Write();
  //
  //chiSquaredEachEventHist->Write();
  //chiSquaredVsAmpEachEventHist->SetXTitle("amplitude [ADC]");
  //chiSquaredVsAmpEachEventHist->SetYTitle("#Chi^{2}");
  //chiSquaredVsAmpEachEventHist->Write();
  //chiSquaredHighMap->SetXTitle("iphi");
  //chiSquaredHighMap->SetYTitle("ieta");
  //chiSquaredHighMap->Write();
  //chiSquaredTotalHist->Write();
  //chiSquaredSingleOverTotalHist->Write();

  expectedStatPresHistEEM->Write();
  expectedStatPresVsObservedMeanErrHistEEM->Write();
  expectedStatPresEachEventHistEEM->Write();
  expectedStatPresHistEEP->Write();
  expectedStatPresVsObservedMeanErrHistEEP->Write();
  expectedStatPresEachEventHistEEP->Write();
  //ampEachEventHist->Write();
  //numPointsErasedHist->Write();
  hitsPerCryHistEEP->Write();
  hitsPerCryMapEEP->Write();
  hitsPerCryHistEEM->Write();
  hitsPerCryMapEEM->Write();
  ampProfileEEP->Write();
  ampProfileMapEEP->Write();
  ampProfileEEM->Write();
  ampProfileMapEEM->Write();
  
  //cout << "All done!  Close input." << endl;
  //f->Close();
  //cout << "Close output and quit!" << endl;
  outfile->Close();
  cout << "done." << endl;
}
int main(int argc,  char * argv[])
{
  // Binary to view the hits per crystal maps of a TTree
  // Also prints out information on run range of the TTree and number of: hits, entries, and consecutive duplicate hits with amplitude above 26 (47) in EB (EE) and |t| < 5 (7) ns
  // Duplicate hits require the same time, amplitude, time error and in the barrel also the same swiss cross noise. Some duplicates are expected by random chance when enough hits are present in the input tree
  // To view for instance the occupancy EB map produced by this binary, open root and type .x occupancyEB.C
  // Jared Turkewitz
  // Usage: MakeEcalTimingTreePlots <TTree input file>

  char* infile = argv[1];
  if(!infile)
  {
    std::cout << "Missing input file." << std::endl;
    return -1;
  }

  EcalTimeTreeContent treeVars_;

  TFile* myFile = new TFile(infile);
  TTree *myInputTree_ = (TTree*)myFile->Get("EcalTimeAnalysis");

  float lastCryTimesEB[EBDetId::kSizeForDenseIndexing];
  for(int i=0; i<EBDetId::kSizeForDenseIndexing;++i)
    lastCryTimesEB[i] = 0;
  float lastCryAmpsEB[EBDetId::kSizeForDenseIndexing];
  for(int i=0; i<EBDetId::kSizeForDenseIndexing;++i)
    lastCryAmpsEB[i] = 0;
  float lastCrySwissCrossEB[EBDetId::kSizeForDenseIndexing];
  for(int i=0; i<EBDetId::kSizeForDenseIndexing;++i)
    lastCrySwissCrossEB[i] = 0;
  float lastCryTimeErrorEB[EBDetId::kSizeForDenseIndexing];
  for(int i=0; i<EBDetId::kSizeForDenseIndexing;++i)
    lastCryTimeErrorEB[i] = 0;

  float lastCryTimesEE[EEDetId::kSizeForDenseIndexing];
  for(int i=0; i<EEDetId::kSizeForDenseIndexing;++i)
    lastCryTimesEE[i] = 0;
  float lastCryAmpsEE[EEDetId::kSizeForDenseIndexing];
  for(int i=0; i<EEDetId::kSizeForDenseIndexing;++i)
    lastCryAmpsEE[i] = 0;
  float lastCryTimeErrorEE[EEDetId::kSizeForDenseIndexing];
  for(int i=0; i<EEDetId::kSizeForDenseIndexing;++i)
    lastCryTimeErrorEE[i] = 0;

  float hitCounterPerCrystalEB[EBDetId::kSizeForDenseIndexing];
  for(int i=0; i<EBDetId::kSizeForDenseIndexing;++i)
    hitCounterPerCrystalEB[i] = 0;
  float hitCounterPerCrystalEE[EEDetId::kSizeForDenseIndexing];
  for(int i=0; i<EEDetId::kSizeForDenseIndexing;++i)
    hitCounterPerCrystalEE[i] = 0;
  
  int runFirst = 999999;
  int runLast = 0;
  
  TCanvas* canvas = new TCanvas();
  TH2F* occupancyEB = new TH2F("hitsPerCryMapEB","Hits used in each crystal;i#phi;i#eta",360,1.,361.,171,-85,86);
  TH2F* occupancyEBNoDuplicates = new TH2F("occupancyEBNoDuplicates","occupancyEBNoDuplicates",360,1,361,171,-85,86); 
  TH2F* duplicatesEB = new TH2F("duplicatesEB","duplicatesEB",360,1,361,171,-85,86);
  TH2F* occupancyEEM = new TH2F("hitsPerCryMapEEM","Hits per cry EEM;ix;iy",100,1,101,100,1,101);
  TH2F* occupancyEEP = new TH2F("hitsPerCryMapEEP","Hits per cry EEP;ix;iy",100,1,101,100,1,101);

  setBranchAddresses(myInputTree_,treeVars_);
  int hitCounterEBAll = 0;
  int duplicateCounterEBAll = 0;
  int hitCounterEEAll = 0;
  int duplicateCounterEEAll = 0;
  int nEntries = myInputTree_->GetEntries();
  for(int entry = 0; entry < nEntries; ++entry)
  {
    myInputTree_->GetEntry(entry);
    // Loop over the clusters in the event
    for(int bCluster=0; bCluster < treeVars_.nClusters; bCluster++)
    {
      for(int cryInBC=0; cryInBC < treeVars_.nXtalsInCluster[bCluster]; cryInBC++)
      {
        int hashedIndex = treeVars_.xtalInBCHashedIndex[bCluster][cryInBC];
        float cryTime = treeVars_.xtalInBCTime[bCluster][cryInBC];
        float cryTimeError = treeVars_.xtalInBCTimeErr[bCluster][cryInBC];
        float cryAmp = treeVars_.xtalInBCAmplitudeADC[bCluster][cryInBC];
        float crySwissCrossNoise = treeVars_.xtalInBCSwissCross[bCluster][cryInBC];

	int runNumber = treeVars_.runId;
	if (runNumber < runFirst)
	{
	  runFirst = runNumber;
	}
	if (runNumber > runLast)
	{
	  runLast = runNumber;
	}
	
        if(treeVars_.xtalInBCIEta[bCluster][0] != -999999)
        {
	  EBDetId det = EBDetId::unhashIndex(hashedIndex);
          if(det==EBDetId()) // make sure DetId is valid
	  {
            continue;
          }
          int ieta = det.ieta();
          int iphi = det.iphi();

          // RecHit cuts
          bool keepHit = cryAmp >= 26
            && crySwissCrossNoise < 0.95
	    && cryTime >= -5
	    && cryTime <= 5;
          if(!keepHit)
            continue;
	  hitCounterEBAll++;
          hitCounterPerCrystalEB[hashedIndex]++;

          if(cryTime==lastCryTimesEB[hashedIndex] && cryAmp==lastCryAmpsEB[hashedIndex] && crySwissCrossNoise == lastCrySwissCrossEB[hashedIndex] && cryTimeError==lastCryTimeErrorEB[hashedIndex])
          {
            duplicateCounterEBAll++;
          }
          occupancyEB->Fill(iphi,ieta);
          if(cryTime!=lastCryTimesEB[hashedIndex])
            occupancyEBNoDuplicates->Fill(iphi,ieta);

          if(cryTime==lastCryTimesEB[hashedIndex])
	  {
	     duplicatesEB->Fill(iphi,ieta);
	  }
          //Store information on previous hit for duplicate checking
          lastCryTimesEB[hashedIndex] = cryTime;
	  lastCryAmpsEB[hashedIndex] = cryAmp;
	  lastCrySwissCrossEB[hashedIndex] = crySwissCrossNoise;
	  lastCryTimeErrorEB[hashedIndex] = cryTimeError;
        }
	else
       	{

	  EEDetId det = EEDetId::unhashIndex(hashedIndex);
	  if(det==EEDetId()) // make sure DetId is valid
	    continue; 

	  int ix = det.ix();
	  int iy = det.iy();
	  int zside = det.zside();

          bool keepHit = cryAmp >= 47 
	    && cryTime >= -7
	    && cryTime <= 7;
          if(!keepHit)
            continue;
          hitCounterPerCrystalEE[hashedIndex]++;
	  hitCounterEEAll++;
          if(cryTime==lastCryTimesEE[hashedIndex] && cryAmp==lastCryAmpsEE[hashedIndex] && cryTimeError==lastCryTimeErrorEE[hashedIndex])
          {
            duplicateCounterEEAll++;
          }
	  if(zside == -1)
            occupancyEEM->Fill(ix,iy);
	  if(zside == 1)
            occupancyEEP->Fill(ix,iy);

          //Store information on previous hit for duplicate checking
          lastCryTimesEE[hashedIndex] = cryTime;
	  lastCryAmpsEE[hashedIndex] = cryAmp;
	  lastCryTimeErrorEE[hashedIndex] = cryTimeError;
        }
      }
    }
  }
  if(runFirst > runLast)
  {
    std::cout << "No runs in the tree!" << std::endl;
  }
  std::cout << "Run Range: " << runFirst << "-" << runLast << std::endl;
  std::cout << "nEntries: " << nEntries << std::endl;  
  std::cout << "hitCounterEBAll: " << hitCounterEBAll << " duplicateCounterEBAll: " << duplicateCounterEBAll << std::endl;
  std::cout << "hitCounterEEAll: " << hitCounterEEAll << " duplicateCounterEEAll: " << duplicateCounterEEAll << std::endl;
  int nXtalsUnder10HitsEB = 0;
  for(int i=0; i<EBDetId::kSizeForDenseIndexing;++i)
    if(hitCounterPerCrystalEB[i] <= 10)
    {
      nXtalsUnder10HitsEB++; 
    } 
  int nXtalsUnder10HitsEE = 0;
  for(int i=0; i<EEDetId::kSizeForDenseIndexing;++i)
    if(hitCounterPerCrystalEE[i] <= 10)
    {
      nXtalsUnder10HitsEE++; 
    } 

  int nXtalsWithZeroHitsEB = 0;
  for(int i=0; i<EBDetId::kSizeForDenseIndexing;++i)
    if(hitCounterPerCrystalEB[i] == 0)
    {
      nXtalsWithZeroHitsEB++; 
    } 
  int nXtalsWithZeroHitsEE = 0;
  for(int i=0; i<EEDetId::kSizeForDenseIndexing;++i)
    if(hitCounterPerCrystalEE[i] == 0)
    {
      nXtalsWithZeroHitsEE++; 
    } 

  std::cout << "nXtalsWithZeroHitsEB: " << nXtalsWithZeroHitsEB << std::endl;
  std::cout << "nXtalsUnder10HitsEB: " << nXtalsUnder10HitsEB << std::endl;
  std::cout << "nXtalsWithZeroHitsEE: " << nXtalsWithZeroHitsEE << std::endl;
  std::cout << "nXtalsUnder10HitsEE: " << nXtalsUnder10HitsEE << std::endl;
  
  canvas->cd();
  occupancyEB->Draw("colz");
  canvas->Print("occupancyEB.C");

  occupancyEEM->Draw("colz");
  canvas->Print("occupancyEEM.C");

  occupancyEEP->Draw("colz");
  canvas->Print("occupancyEEP.C");

  occupancyEBNoDuplicates->Draw("colz");
  canvas->Print("occupancyEBNoDuplicates.C");
  
  duplicatesEB->Draw("colz");
  canvas->Print("duplicatesEB.C");
}