LISummarySorter.cxx

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// Program name: LISummarySorter.cxx     
//                                                                     
// Package: LISummary                    
//
// Coded by Jeff Hartnell Oct/2002 - Sep/2003  
//
// Based on code by: Rob Morse Feb/2002 
//                                                                   
// Purpose: To sort the raw LI summaries into the right electronics 
//          channel 
//                                                                    
// Contact: jeffrey.hartnell@physics.ox.ac.uk   

#include <fstream>
#include <string>
#include <cmath>

#include "TText.h"
#include "TPaveText.h"
#include "TCanvas.h"
#include "TPad.h"

#include "MessageService/MsgService.h"
#include "MessageService/MsgFormat.h"

#include "LISummary/LISummarySorter.h"

CVSID("$Id: LISummarySorter.cxx,v 1.46 2007/11/11 08:00:53 rhatcher Exp $");

//......................................................................

LISummarySorter::LISummarySorter()
{
  MSG("LISummarySorter",Msg::kDebug) 
    <<"Running LISummarySorter Constructor..."<<endl;

  //initialise data members
  ashtray=-1;
  badHitCounter=0;
  calibPoint=-1;
  calibType=-1;
  cerenkovCounter=0;
  chAdd=-1;
  channel=-1;
  chip=-1;
  commonModeCounter=0;//readoutType counter
  correlatedHit=-1;
  crate=-1;
  detectorType=-1;
  eastWest=-1;//0 is east, 1 is west 
  elecType=-1;
  farLed=-1;
  farPulserBox=-1;
  first_time=0;
  inRack=-1;//determines mux box in rack 0-7
  geoAdd=-1;
  goodHitCounter=0;
  led=-1;
  fMasterCh=-1;
  mean=-1.;
  fMinderCh=-1;
  nearLed=-1;
  nearPulserBox=-1;
  numEntries=-1;
  numericMuxBox=-1;
  outtree=0;//set pointer to tree to zero
  outputFile=0;
  fPe=-1;
  period=-1;
  pixel=-1;
  pinCounter=0;
  pinGain=-1;//0 is low, 1 is high gain
  pinInBox=-1;//0 is low gain (VA=0), 1 is high gain (VA=1)
  plane=-1;
  plexHandle=0;
  pulseHeight=-1;
  pulserBox=-1;
  pulses=-1;
  pulseWidth=-1;
  rackBay=-1;//determines which rack 0-15
  rackLevel=-1;//0 is top, 1 is bottom
  rawSummaryBlockCounter=0;
  rawSummaryCounter=0;
  readoutType=-1;
  rms=-1.;
  runNumber=-1;
  runNumberSub=-1;
  runType=-1;
  strip=-1;
  stripCounter=0;
  fStripEnd=-1;
  summaryCounter=0;
  timestamp=-1;
  timestampNanoSec=-1;
  timingFidCounter=0;
  tofCounter=0;
  triggerOrCounter=0;
  trigPmtCounter=0;
  unconnectedPixelCounter=0;
  unknownCounter=0;
  varc=-1;
  vfb=-1;
  vmm=-1;

  MSG("LISummarySorter",Msg::kDebug) 
    <<"Finished LISummarySorter Constructor"<<endl;
}

//......................................................................

LISummarySorter::~LISummarySorter()
{
  MSG("LISummarySorter",Msg::kDebug) 
    <<"Running LISummarySorter destructor..."<<endl;

  //get rid of memory leak right at the end
  if (plexHandle) delete plexHandle;

  MSG("LISummarySorter",Msg::kDebug) 
    <<"Finished LISummarySorter destructor"<<endl;
}

//......................................................................
  
void LISummarySorter::PrintRecoSummary()
{
  MSG("LISummarySorter",Msg::kVerbose)
    <<"Running PrintRecoSummary method..."<<endl;

  //print out summary of reconstruction information
  if (runNumber!=-1 && runNumberSub!=-1 && detectorType!=-1){
    Int_t totalHits=0;
    totalHits=
      unconnectedPixelCounter+
      unknownCounter+
      stripCounter+
      pinCounter+
      trigPmtCounter+
      commonModeCounter+
      triggerOrCounter+
      cerenkovCounter+
      tofCounter+
      timingFidCounter;
    
    MSG("LISummarySorter",Msg::kInfo) 
      <<endl 
      <<" ** Job Summary Information: **"<<endl
      <<"  Readout types processed:"<<endl
      <<"    kUnknown="<<unknownCounter<<endl      
      <<"    kScintStrip="<<stripCounter<<endl
      <<"    kUnconnectedPixel="<<unconnectedPixelCounter<<endl
      <<"    kPinDiode="<<pinCounter<<endl
      <<"    kFlashTrigPMT="<<trigPmtCounter<<endl
      <<"    kVACommonMode="<<commonModeCounter<<endl
      <<"    kTriggerOR="<<triggerOrCounter<<endl
      <<"    kCerenkov="<<cerenkovCounter<<endl
      <<"    kTOF="<<tofCounter<<endl
      <<"    kTimingFid="<<timingFidCounter<<endl
      <<"    Total hits="<<totalHits<<endl;
    
    if (totalHits!=0){

      MSG("LISummarySorter",Msg::kInfo) 
        <<endl
        <<"  Scintillator hits that were attributed to an LI pulse:" 
        <<endl
        <<"    Successful="<<goodHitCounter<<endl
        <<"    Failures="<<badHitCounter<<endl
        <<"    Sum of above=" 
        <<badHitCounter+goodHitCounter<<endl;
    
      //number of entries found for each pulser box
      totalHits=0;
      MSG("LISummarySorter",Msg::kInfo) 
        <<endl 
        <<"  Number of hits when a given pulser box was flashing:"<<endl;
      for (Int_t i=0;i<fLookup.NUMPULSERBOXES;i++){
        MSG("LISummarySorter",Msg::kInfo) 
          <<"    Pulser Box "<<i<<"=" 
          <<pulserBoxes[i]<<endl;
        totalHits+=pulserBoxes[i];
      }
      MSG("LISummarySorter",Msg::kInfo) 
        <<"    Total hits ="<<totalHits<<endl;
    
      //Plex results for pulser boxes
      totalHits=0;
      MSG("LISummarySorter",Msg::kInfo) 
        <<endl
        <<"  Plex results for pulser boxes:" 
        <<endl;
      for (Int_t i=0;i<fLookup.NUMPULSERBOXES;i++){
        MSG("LISummarySorter",Msg::kInfo) 
          <<"    Pulser Box "<<i<<"=" 
          <<plexPbCounter[i] 
          <<"    Opposite Pulser Box "<<i<<"=" 
          <<plexOppPbCounter[i] 
          <<endl;
        totalHits+=plexPbCounter[i];
      }
      MSG("LISummarySorter",Msg::kInfo) 
        <<"    Total hits ="<<totalHits<<endl;
    
      //number of entries found for each crate using plex
      totalHits=0;
      MSG("LISummarySorter",Msg::kInfo) 
        <<endl 
        <<"  Plex results for crates:"<<endl;
      for (Int_t i=0;i<fLookup.NUMCRATES;i++){
        MSG("LISummarySorter",Msg::kInfo) 
          <<"    Crate "<<i<<"=" 
          <<crates[i]<<endl;
        totalHits+=crates[i];
      }
      MSG("LISummarySorter",Msg::kInfo) 
        <<"  Total hits ="<<totalHits<<endl;
    
      //number of entries found for each led
      totalHits=0;
      MSG("LISummarySorter",Msg::kInfo) 
        <<endl<<"  Number of hits when a given led was flashing:"<<endl;
      for (Int_t i=0;i<fLookup.NUMLEDS;i++){
        MSG("LISummarySorter",Msg::kInfo) 
          <<"    led "<<i+1<<" = "<<leds[i]<<endl;
        totalHits+=leds[i];
      }
      MSG("LISummarySorter",Msg::kInfo) 
        <<"    Total hits = "<<totalHits<<endl;

      //number of reconstructed pins
      totalHits=0;
      MSG("LISummarySorter",Msg::kInfo) 
        <<endl<<"  Number of pins reconstructed:"<<endl;
      for (Int_t i=0;i<fLookup.NUMLEDS;i++){
        MSG("LISummarySorter",Msg::kInfo) 
          <<"    led "<<i+1<<" = "<<pinCounterReco[i]<<endl;
        totalHits+=pinCounterReco[i];
      }

      //change this bit for fpe problem
      MSG("LISummarySorter",Msg::kInfo) 
        <<"    Total reconstructed pins = "<<totalHits<<" of "
        <<pinCounter;
      if (pinCounter>0){
        MSG("LISummarySorter",Msg::kInfo) 
          <<" ("<<100.*totalHits/pinCounter<<"%)"<<endl;
      }
      else MSG("LISummarySorter",Msg::kInfo)<<endl;

      //number of summary blocks and summaries in those blocks    
      MSG("LISummarySorter",Msg::kInfo)  
        <<endl<<" Number of raw LI summary blocks found = "
        <<rawSummaryBlockCounter<<endl;     
      MSG("LISummarySorter",Msg::kInfo)   
        <<" Total number of raw LI summaries in above blocks = " 
        <<rawSummaryCounter<<endl; 
      MSG("LISummarySorter",Msg::kInfo)    
        <<" Average number of summaries per block = "  
        <<rawSummaryCounter/rawSummaryBlockCounter<<endl;  
    }//end of if totalHits

    MSG("LISummarySorter",Msg::kInfo) 
      <<endl<<" ** End of Job Summary Information: ** "<<endl; 
  }
  else {
    MSG("LISummarySorter",Msg::kInfo) 
      <<" ** No LI stream found in this file **"<<endl<<endl;
  }

  MSG("LISummarySorter",Msg::kVerbose) 
    <<"OutputData PrintRecoSummary finished"<<endl;
}

//......................................................................
  
void LISummarySorter::OutputData()
{
  MSG("LISummarySorter",Msg::kVerbose)
    <<"Running OutputData method..."<<endl;

  this->WriteFile(outputFile);
  this->CloseFile(outputFile);  

  MSG("LISummarySorter",Msg::kVerbose) 
    <<"OutputData method finished"<<endl;
}

//......................................................................
  
void LISummarySorter::PrintBlockInfo(string preString) const
{
  MSG("LISummarySorter",Msg::kVerbose)<<"PrintBlockInfo..."<<endl;

  if (time.GetSec()<1000){
    static Int_t numberMsg=0;
    if (numberMsg<10){
      MSG("LISummarySorter",Msg::kWarning) 
        <<"Number of seconds="<<time.GetSec()<<endl;
      if (numberMsg==9){
        MSG("LISummarySorter",Msg::kWarning) 
          <<endl
          <<"This is the last message of this type to be printed"
          <<endl;
      }
    }
    numberMsg++;
  }
  
  TDatime datime;
  datime.Set(time.GetSec());
  
  //play around with the formatting a little
  string sHour=Form("%d",datime.GetHour());
  string sMinute=Form("%d",datime.GetMinute());
  string sSecond=Form("%d",datime.GetSecond());
  string sMonth=Form("%d",datime.GetMonth());
  string sDay=Form("%d",datime.GetDay());
  if (datime.GetHour()<10) sHour="0"+sHour;
  if (datime.GetMinute()<10) sMinute="0"+sMinute;
  if (datime.GetSecond()<10) sSecond="0"+sSecond;
  if (datime.GetMonth()<10) sMonth="0"+sMonth;
  if (datime.GetDay()<10) sDay="0"+sDay;

  //protect from fpe
  Double_t pulseFreq=-1;
  if (period!=0) pulseFreq=ceil(1.0/(period*1.0e-5));
  string sPulseFreq=Form("%d",static_cast<Int_t>(pulseFreq));
  string sPeriod=Form("%d",static_cast<Int_t>(period));
  if (pulseFreq<0) sPulseFreq="??? (period="+sPeriod+")";

  MSG("LISummarySorter",Msg::kInfo) 
    <<preString 
    <<"PB="<<pulserBox 
    <<" Led="<<led
    <<" CP="<<calibPoint
    <<"/"<<calibType
    <<" PH="<<pulseHeight
    <<" PW="<<pulseWidth
    <<" PF="<<sPulseFreq
    <<" PN="<<pulses
    <<" at "<<sHour
    <<":"<<sMinute
    <<":"<<sSecond
    <<" on "<<datime.GetYear()
    <<"/"<<sMonth
    <<"/"<<sDay
    <<endl;

  MSG("LISummarySorter",Msg::kVerbose) 
    <<"PrintBlockInfo method finished"<<endl;
}

//......................................................................

void LISummarySorter::SetLIVariables(Int_t new_led,
                                     Int_t new_pulseHeight,
                                     Int_t new_pulseWidth,
                                     Int_t new_pulserBox,
                                     Int_t new_calibPoint,
                                     VldTimeStamp new_time, 
                                     Int_t new_calibType,
                                     Int_t new_pulses,
                                     Int_t new_period)
{
  //set summarySorters variables
  calibPoint=new_calibPoint;
  pulseHeight=new_pulseHeight;
  pulseWidth=new_pulseWidth;
  pulserBox=new_pulserBox;
  led=new_led;
  time=new_time;
  period=new_period;
  calibType=new_calibType;
  pulses=new_pulses; 
}

//......................................................................

Bool_t LISummarySorter::Update(Int_t new_led,
                             Int_t new_pulseHeight,
                             Int_t new_pulseWidth,
                             Int_t new_pulserBox,
                             Int_t new_calibPoint,
                             VldTimeStamp new_time, 
                             Int_t new_calibType,
                             Int_t new_pulses,
                             Int_t new_period)
{
  
  //this method gets called once for each raw summary block so
  //count the number of summary blocks here
  rawSummaryBlockCounter++;

  MSG("LISummarySorter",Msg::kVerbose)
    <<"Running LISummarySorter::Update method..."<<endl;

  if(led==-1){//it is initialised to -1

    MSG("LISummarySorter",Msg::kInfo) 
      <<"Initialising variables for LI settings in Update()"<<endl;
    
    //initialise the vector of LIChannels
    if (channels.size()==0){
      for (Int_t i=0;i<LILookup::NUMCRATES*LILookup::NUMCHADD;i++){
        channels.push_back(LIChannel());
      }
      MSG("LISummarySorter",Msg::kInfo) 
        <<"Vector of channels initialised to "
        <<LILookup::NUMCRATES*LILookup::NUMCHADD
        <<" (NUMCRATES="<<LILookup::NUMCRATES
        <<", NUMCHADD="<<LILookup::NUMCHADD<<")"
        <<endl; 
    }
    else{
      MSG("LISummarySorter",Msg::kInfo) 
        <<"Channels vector can't be initialised; already done!"<<endl;
    }

    this->SetLIVariables(new_led,new_pulseHeight,new_pulseWidth,
                         new_pulserBox,new_calibPoint,new_time,
                         new_calibType,new_pulses,new_period);
      
    this->PrintBlockInfo("First initialisation ");
    return false;//didn't update tree
  }
  // Write out data from previous led, pulse height, etc here
  else if(new_led!=led ||
          new_pulseHeight!=pulseHeight ||
          new_pulseWidth!=pulseWidth ||
          new_pulserBox!=pulserBox ||
          new_calibPoint!=calibPoint){

    //get an iterator to the map
    vector<LIChannel>::iterator chIt;
    chIt=channels.begin()-1;//so can increment straight away
    Int_t ch=-1;

    //loop over every possible channel
    while (chIt!=channels.end()){

      //increment the loop variables
      ch++;
      chIt++;
      MSG("LISummarySorterUltraVerbose",Msg::kVerbose) 
        <<"At beginning: Channel="<<ch<<endl;

      numEntries=channels[ch].GetNumEntries();      
      //check if channel was hit 
      if(numEntries==0) continue;

      //reset the variables and get the electronics info        
      this->ResetTreeVariables();
      this->GetElectronicsData(ch);

      //gather run statistics
      crates[crate]++;
      if (crate>fLookup.NUMCRATES || crate<0){
        MSG("LISummarySorter",Msg::kError) 
          <<"Crate out of range: crate="<<crate<<endl;
      }

      if (pulserBox<fLookup.NUMPULSERBOXES && pulserBox>=0 && 
          led<=fLookup.NUMLEDS && led>=1){
        pulserBoxes[pulserBox]++;
        leds[led-1]++;
      }
      else{
        static Int_t numberMsg=0;
        if (numberMsg<10){
          MSG("LISummarySorter",Msg::kError)
            <<"Pulser box or Led out of range: (PB,LED)=("<<pulserBox 
            <<","<<led<<")"<<endl;
          if (numberMsg==9){
            MSG("LISummarySorter",Msg::kError)
              <<endl
              <<"This is the last message of this type to be printed"
              <<endl;
          } 
        }
        numberMsg++;
      }

      //get readout type
      //      ReadoutType::Readout_t rt=plexHandle->
      //GetReadoutType(channels[ch]->GetChannelId());
      ReadoutType::Readout_t rt=plexHandle->
        GetReadoutType(chIt->GetChannelId());
      readoutType=static_cast<Int_t>(rt);//set tree variable
      MSG("LISummarySorter",Msg::kVerbose) 
        <<"rt="<<ReadoutType::AsString(rt)
        <<", mean="<<mean <<", rms="<<rms 
        <<", numEnt="<<numEntries 
        <<" "<<this->GetElecString()<<endl; 

      //check for dodgy channels
      if (rms==0 || numEntries==0 || mean==0){
        if (numEntries>10){
          if (readoutType==ReadoutType::kTOF ||
              readoutType==ReadoutType::kUnknown || 
              readoutType==ReadoutType::kTriggerOR){
            MSG("LISanityCheck",Msg::kVerbose) 
              <<" ** Channel with strange values: mean="<<mean 
              <<", rms="<<rms 
              <<", numEnt="<<numEntries 
              <<", rt="<<ReadoutType::AsString(rt)
              <<" "<<this->GetElecString()<<endl; 
          }
          else{
            //if (rms==0 && detectorType==Detector::kNear){
              //do nothing; too many of these with bad channels
            //}
            //else{
              MAXMSG("LISanityCheck",Msg::kInfo,50) 
                <<"Writing out bad channel: mean="
                <<(Int_t)mean 
                <<", rms="<<rms 
                <<", numEnt="<<numEntries 
                <<", rt="<<ReadoutType::AsString(rt)
                <<" "<<this->GetElecString()<<endl; 
              //}
          }
        }
      }

      //use the readout type to decide what to do
      //count the number of each type in file
      if (rt==ReadoutType::kUnknown){
        unknownCounter++;
      }
      else if (rt==ReadoutType::kUnconnectedPixel){
        unconnectedPixelCounter++;
      }
      else if (rt==ReadoutType::kScintStrip) {
        stripCounter++;

        //run the algorithm to correlate hits with flashes and 
        //determine the strip end
        this->ReconstructStripEnd(ch);

        //count hits that were attributed to an LI pulse        
        if (correlatedHit){
          goodHitCounter++;
        }
        else{
          badHitCounter++;
        }
      }//end of if
      else if (rt==ReadoutType::kPinDiode){
        pinCounter++;
        this->ReconstructPin(ch);
      }
      else if (rt==ReadoutType::kFlashTrigPMT){
        trigPmtCounter++;
        this->ReconstructTrigPmt();
      }
      else if (rt==ReadoutType::kVACommonMode){
        commonModeCounter++;
      }
      else if (rt==ReadoutType::kTriggerOR){
        triggerOrCounter++;
      }
      else if (rt==ReadoutType::kCerenkov){
        cerenkovCounter++;
      }
      else if (rt==ReadoutType::kTOF){
        tofCounter++;
      }
      else if (rt==ReadoutType::kTimingFid){
        timingFidCounter++;
      }
      else {
        MSG("LISummarySorter",Msg::kWarning) 
          <<"ReadoutType not defined:" 
          <<" rt="<<ReadoutType::AsString(rt)
          <<" "<<this->GetElecString()
          <<endl;
      }   
      //fill the tree with all the current data for this channel
      outtree->Fill();
    }//end of loop

    this->PrintBlockInfo("Wrote point: ");

    //reset all channels for next point
    for(UInt_t ch=0;ch<channels.size();ch++){
      channels[ch].Clean();       
    }

    //set the variables to be the new ones
    this->SetLIVariables(new_led,new_pulseHeight,new_pulseWidth,
                         new_pulserBox,new_calibPoint,new_time,
                         new_calibType,new_pulses,new_period);
    
    return true;//did update tree
  }//end of else if

  MSG("LISummarySorter",Msg::kVerbose)
    <<"Finished LISummarySorter::Update method..."<<endl;
  return false;//didn't update tree
}

//......................................................................
  
void LISummarySorter::ResetTreeVariables()
{
  //reset reconstructed tree variables
  //but not the LI pulser box settings

  //listed here for a checksum
  //   calibPoint=new_calibPoint;
  //   pulseHeight=new_pulseHeight;
  //   pulseWidth=new_pulseWidth;
  //   pulserBox=new_pulserBox;
  //   led=new_led;
  //   time=new_time;
  //   period=new_period;
  //   calibType=new_calibType;
  //   pulses=new_pulses;
  // 9 above but time is a struct and not directly in tree so only 8
    
  ashtray=-1;
  chAdd=-1;
  channel=-1;
  chip=-1;
  correlatedHit=0;
  crate=-1;

  //this only gets updated when you have a new led
  //so don't reset here
  //detectorType=-1;

  eastWest=-1;
  elecType=-1;
  farLed=-1;
  farPulserBox=-1;
  geoAdd=-1;
  inRack=-1;
  fMasterCh=-1;
  mean=-1.;
  fMinderCh=-1;
  nearLed=-1;
  nearPulserBox=-1;
  numEntries=-1;
  numericMuxBox=-1;
  fPe=-1;
  pixel=-1;
  pinGain=-1;
  pinInBox=-1;
  plane=-1;
  rackBay=-1;
  rackLevel=-1;
  readoutType=-1;
  rms=-1.;

  //these three only get updated when you have a new led etc
  //so don't reset here
  //runNumber=-1;
  //runNumberSub=-1;
  //runType=-1;

  strip=-1;
  fStripEnd=-1;
  summaryCounter=0;
  timestamp=-1;
  timestampNanoSec=-1;
  varc=-1;
  vfb=-1;
  vmm=-1;

  //38 variables above +fPe
  //+8 for pulser box settings
  //=46 altogether - same as number of branches in tree
}

//......................................................................

void LISummarySorter::PrintBigMessage() const
{ 
  MSG("LISummarySorter",Msg::kInfo) 
    <<"("<<pulserBox<<":"<<led<<")";
    
  if (elecType==ElecType::kVA){
    MSG("LISummarySorter",Msg::kInfo) 
      <<"VA("<<crate<<","<<varc<<","<<vmm<<","<<vfb
      <<","<<chip<<","<<channel<<")";
  }
  else if (elecType==ElecType::kQIE){
    MSG("LISummarySorter",Msg::kInfo) 
      <<"QIE("<<crate<<","<<geoAdd<<","<<fMasterCh<<","<<fMinderCh<<")";
  }
  
  MSG("LISummarySorter",Msg::kInfo) 
    <<", (m,r,n)=("<<mean<<","<<rms
    <<","<<numEntries<<"), cHit="<<correlatedHit
    <<", e/w="<<eastWest<<", rt="<<readoutType
    <<" (Pl;St)=("<<plane<<";"<<strip<<")"<<endl;
}

//......................................................................

string LISummarySorter::GetElecString() const 
{
  MSG("LISummarySorter",Msg::kVerbose) 
    <<"Running GetElecString method..."<<endl;

  string elecString="";
  string sCrate=Form("%d",crate);

  if (elecType==ElecType::kVA){
    string sVarc=Form("%d",varc);
    string sVmm=Form("%d",vmm);
    string sVfb=Form("%d",vfb);
    string sChip=Form("%d",chip);
    string sChannel=Form("%d",channel);
    string sElecType="VA";
    
    elecString=sElecType+
      "("+sCrate+","+sVarc+","+sVmm+","+sVfb+","+sChip+","+sChannel+")";
  }     
  else if (elecType==ElecType::kQIE){
    string sGeoAdd=Form("%d",geoAdd);
    string sMasterCh=Form("%d",fMasterCh);
    string sMinderCh=Form("%d",fMinderCh);
    string sElecType="QIE";
    
    elecString=sElecType+
      "("+sCrate+","+sGeoAdd+","+sMasterCh+","+sMinderCh+")";
  }
  return elecString;
}

//......................................................................

string LISummarySorter::GetElecString(RawChannelId rChId) const
{
  MSG("LISummarySorter",Msg::kVerbose) 
    <<"Running GetElecString method..."<<endl;

  string elecString="";
  string sCrate=Form("%d",rChId.GetCrate());
  string sElecType=ElecType::AsString(rChId.GetElecType());

  if (rChId.GetElecType()==ElecType::kVA){
    string sVarc=Form("%d",rChId.GetVarcId());
    string sVmm=Form("%d",rChId.GetVmm());
    string sVfb=Form("%d",rChId.GetVaAdcSel());
    string sChip=Form("%d",rChId.GetVaChip());
    string sChannel=Form("%d",rChId.GetVaChannel());

    elecString=sElecType+
      "("+sCrate+","+sVarc+","+sVmm+","+sVfb+","+sChip+","+sChannel+")";
  }     
  else if (rChId.GetElecType()==ElecType::kQIE){
    string sGeoAdd=Form("%d",rChId.GetGeographicAddress());
    string sMasterCh=Form("%d",rChId.GetMasterChannel());
    string sMinderCh=Form("%d",rChId.GetMinderChannel());
        
    elecString=sElecType+
      "("+sCrate+","+sGeoAdd+","+sMasterCh+","+sMinderCh+")";
  }
  return elecString;
}

//......................................................................

void LISummarySorter::GetElectronicsData(Int_t ch)
{
  //get the raw channel id to use below
  RawChannelId rChId=channels[ch].GetChannelId();

  //get generic electronics stuff
  elecType=rChId.GetElecType();
  crate=rChId.GetCrate();

  //fardet stuff
  chAdd=rChId.GetChAdd();
  varc=rChId.GetVarcId();
  vmm=rChId.GetVmm();
  vfb=rChId.GetVaAdcSel();
  chip=rChId.GetVaChip();
  channel=rChId.GetVaChannel();  

  //neardet stuff
  fMasterCh=rChId.GetMasterChannel();
  fMinderCh=rChId.GetMinderChannel();
  geoAdd=rChId.GetGeographicAddress();

  //not strictly electronics!
  timestamp=static_cast<Int_t>(time.GetSec());
  timestampNanoSec=time.GetNanoSec();
  mean=channels[ch].GetMean();
  rms=channels[ch].GetRms();
  numEntries=channels[ch].GetNumEntries();
  summaryCounter=channels[ch].GetSummaryCounter();
}

//......................................................................

void LISummarySorter::ReconstructStripEnd(Int_t ch)
{

  MSG("LISummarySorter",Msg::kDebug) 
    <<"Reconstructing strip end..."<<endl;

  //Get strip-end alternative list
  PlexSEIdAltL altlist = plexHandle->
    GetSEIdAltL(channels[ch].GetChannelId());
  
  //the plane is known from the rawchannel so get it here
  plane=altlist.GetPlane();  
  MSG("LISummarySorter",Msg::kVerbose)
    <<"New altlist: plane="<<plane<<endl;

  //check that the plane view is kX, kY, kU or kV before reconstructing
  PlaneView::PlaneView_t planeView=altlist.GetPlaneView();  
  if (planeView>PlaneView::kV){

    Msg::LogLevel_t msgLevel=Msg::kDebug;
    //if (planeView>7 || planeView<7) msgLevel=Msg::kVerbose;
    
    MSG("LISummarySorter",msgLevel) 
      <<"Plane="<<plane
      <<", PlaneView="<<PlaneView::AsString(planeView)
      <<", therefore not reconstructing this plane"<<endl;

    //if (planeView==7) this->PrintBigMessage();
    //I am seeing some unknown views on vmm 5 in various crates???

    return;//don't reconstruct planes with no LI
  }

  //variable to sanity check reconstruction
  Int_t loopCounter=0;
  //hold true strip end id
  PlexStripEndId tmpSeid;

  //loop over the alternative strips
  for (PlexSEIdAltL::iterator it=altlist.begin(); 
       it!=altlist.end();it++){

    //set default values for led and pin plex variables
    Int_t plexLedInBox=-1;
    Int_t plexPulserBox=-1;
    Int_t plexOppLedInBox=-1;
    Int_t plexOppPulserBox=-1;

    //get strip end and opposite strip end id
    PlexStripEndId SEId=(*it).GetSEId();
    PlexStripEndId oppSEId=SEId.GetOppositeSEId();

    //get the temporary pixel of this possible strip
    //it is always the same for FD but 4 diff possibilites for ND
    PlexPixelSpotId plexPixelSpotId=plexHandle->GetPixelSpotId
      ((*it).GetSEId());
    //pixel is the same for all altSE
    Int_t tmpPixel=plexPixelSpotId.GetPixel();

    //a bit of sanity checking
    loopCounter++;
    if ((loopCounter>1 && detectorType==Detector::kCalDet) || 
        (loopCounter>8 && detectorType==Detector::kFar) ||
        (loopCounter>4 && detectorType==Detector::kNear)){
      MSG("LISummarySorter",Msg::kWarning) 
        <<"SEIdAltList has > 1 entry, loopCounter="<<loopCounter
        <<", CH="<<correlatedHit
        <<", end="<<SEId.GetEnd()
        <<", led="<<led
        <<", pl="<<plane
        <<", "<<this->GetElecString()<<endl;
    }

    //get ledIds for strip end and opp strip end
    PlexLedId ledId=plexHandle->GetLedId(SEId);       
    PlexLedId oppLedId=plexHandle->GetLedId(oppSEId);

    //sanity check that ledid is valid
    if (!ledId.IsValid()){
      MAXMSG("LISummarySorter",Msg::kWarning,20) 
        <<"LedId not valid, jumping to next SEId"
        << ", L="<<led
        << ", PB="<<pulserBox
        << ", pl="<<plane
        << ", mean="<<mean
        << endl;
      continue;
    }   

    //get pulserbox info for both sides
    plexPulserBox=ledId.GetPulserBox();   
    plexOppPulserBox=oppLedId.GetPulserBox();
    
    //these are the same for all alternative SEs
    nearPulserBox=plexPulserBox;
    farPulserBox=plexOppPulserBox;
    
    //get led number for both sides
    plexLedInBox=ledId.GetLedInBox();
    plexOppLedInBox=oppLedId.GetLedInBox();
    
    //reconstruct the strip for xtalk hits at CalDet and at ND forward
    //section (ND spectrometer is ambiguous due to 4 pixels=1 channel)
    if ((detectorType==Detector::kCalDet) ||
        (detectorType==Detector::kNear && 
         plane<LILookup::FIRSTSPECTROMETERPLANE)){
      //this is unambiguous at CalDet, so do it here for ALL hits
      //i.e. do it for xtalk too
      nearLed=plexLedInBox;
      farLed=plexOppLedInBox;
      strip=SEId.GetStrip();
      fStripEnd=SEId.GetEnd();
      
      MAXMSG("LISummarySorter",Msg::kDebug,200) 
        <<"XTalk reco: PB="<<pulserBox
        <<", pl="<<plane
        <<", s="<<strip
        <<", mean="<<mean
        <<endl;
    }  

    //determine whether to continue or not
    //ignore noise hits in crates not being flashed
    //there is no more information that can be determined for them
    //18-Sep-04: moved below section to allocate strips to ND forward
    //section
    if (plexPulserBox!=pulserBox && 
        plexOppPulserBox!=pulserBox) continue;

    //if (led==18){
    MSG("LISummarySorter",Msg::kDebug) 
      <<"pxL="<<plexLedInBox
      <<", L="<<led
      <<", pxPB="<<plexPulserBox
      <<", pxOpPB="<<plexOppPulserBox
      <<", PB="<<pulserBox
      <<", pl="<<plane
      <<", s="<<strip
      <<", sPlex="<<SEId.GetStrip()
      <<", pix="<<tmpPixel
      <<", mean="<<mean
      <<endl;
    //}
    //determine if it's a correlated hit    
    if ((pulserBox==nearPulserBox && led==plexLedInBox) ||
        (pulserBox==farPulserBox && led==plexOppLedInBox)){

      //sanity check 
      if (((nearLed>0 || farLed>0) && 
           detectorType!=Detector::kCalDet && 
           (detectorType!=Detector::kNear &&
            plane>=LILookup::FIRSTSPECTROMETERPLANE)) || 
          correlatedHit==1){
        //only do the led check if detector is not CalDet
        //otherwise check that leds have not already been set
        MAXMSG("LISummarySorter",Msg::kWarning,50) 
          <<"Overwritten near or far led during strip reconstruction"
          <<", correlatedHit="<<correlatedHit<<endl
          <<"led="<<led
          <<", oldnL="<<nearLed<<", newnL="<<plexLedInBox
          <<", oldfL="<<farLed<<", newfL="<<plexOppLedInBox
          <<", oldSt="<<strip<<", newSt="<<SEId.GetStrip()
          <<", pix="<<tmpPixel<<", pl="<<plane
          <<" "<<this->GetElecString()<<endl;
      }
      
      //if (led==18){
      MSG("LISummarySorter",Msg::kDebug) 
        <<"Found CorrelatedHit"<<endl
        <<"led="<<led
        <<", oldnL="<<nearLed<<", newnL="<<plexLedInBox
        <<", oldfL="<<farLed<<", newfL="<<plexOppLedInBox
        <<", oldSt="<<strip<<", newSt="<<SEId.GetStrip()
        <<", pix="<<tmpPixel<<", pl="<<plane
        <<" "<<this->GetElecString()<<endl;
      //}
      //count entries for pulserboxes
      plexPbCounter[plexPulserBox]++;
      plexOppPbCounter[plexOppPulserBox]++;
      
      //set more variables
      correlatedHit=1;
      strip=SEId.GetStrip();
      fStripEnd=SEId.GetEnd();
      //Int_t oppStrip=oppSEId.GetStrip();//just used for message below
      nearLed=plexLedInBox;
      farLed=plexOppLedInBox;  
      //note that strip, se, nearL and farL get set twice for correlated
      //hits in CalDet, but so what!
      //Less complicated than checking if CalDet or not

      //save the reconstructed seid
      tmpSeid=SEId;
    }//end of if
    
    //use the led to determine which ashtray was being illuminated
    //only set the variable if the channel is in the crate 
    //(or opposite crate) that is being illuminated
    if (pulserBox==nearPulserBox || pulserBox==farPulserBox){
      ashtray=fLookup.Led2Ashtray(led,plane,detectorType);
    }
  }//end of for
  
  //reconstruct the pixel and mux box info
  //get pixel spot id for strip end
  PlexPixelSpotId plexPixelSpotId;
  if (tmpSeid.IsValid()){
    plexPixelSpotId=plexHandle->GetPixelSpotId(tmpSeid);
    pixel=plexPixelSpotId.GetPixel();
  }
  else{
    //if a stripend wasn't reconstructed then just use the first
    //strip end in the altlist to get the pixel
    //even though it will only be one of the possible four in the ND
    plexPixelSpotId=plexHandle->GetPixelSpotId
      ((*altlist.begin()).GetSEId());
    pixel=plexPixelSpotId.GetPixel();
  }
  //set all the mux box variables
  this->GetMuxBoxInfo(plexPixelSpotId);

  MSG("LISummarySorter",Msg::kVerbose) 
    <<"ReconstructStripEnd method finished"<<endl;
}

//......................................................................
  
Bool_t LISummarySorter::ReconstructPin(Int_t ch)
{

  MSG("LISummarySorter",Msg::kVerbose) 
    <<"Reconstructing Pin..."<<endl;

  PlexPinDiodeId plexPinDiodeId=plexHandle->
    GetPinDiodeId(channels[ch].GetChannelId());

  //check if pin diode id is valid          
  if (!plexPinDiodeId.IsValid()){
    MSG("LISummarySorter",Msg::kWarning)
      <<"PIN diode id not valid"
      <<", LED="<<led<<", PB="<<pulserBox<<", pl="<<plane
      <<", mean="<<mean<<endl;    
    MSG("LISummarySorter",Msg::kVerbose) 
      <<"ReconstructPin method finished"<<endl;
    return false;
  }

  //get led id associated with actual pin diode hit
  PlexLedId plexLedId=plexHandle->GetLedId(plexPinDiodeId);

  //check if led id associated with pin is valid
  if (!plexLedId.IsValid()){
    MSG("LISummarySorter",Msg::kVerbose)
      <<"LedId obtained from pin not valid = "<<plexLedId.AsString()
      <<" "<<this->GetElecString()<<endl;
    MSG("LISummarySorter",Msg::kVerbose) 
      <<"ReconstructPin method finished"<<endl;
    return false;
  }
  
  //set nearLed to be the led that the plex associates with the pin
  nearLed=plexLedId.GetLedInBox();
  farLed=-1;// there is no far led for a pin!
  //get pulserbox info
  nearPulserBox=plexLedId.GetPulserBox();
  //there is no far pulser box associated with a pin diode 
  //but get it anyway since it is just the opposite one
  farPulserBox=fLookup.GetOppPb(pulserBox,detectorType);
  
  //quick sanity check
  if ((nearLed<fLookup.FIRSTLED || nearLed>fLookup.LASTLED) && 
      detectorType==Detector::kFar){
    MSG("LISummarySorter",Msg::kWarning)
      <<"Strange values for led = "<<nearLed
      <<" "<<this->GetElecString()<<endl;
  }
  
  pinInBox=plexPinDiodeId.GetInBox();
  pinGain=plexPinDiodeId.GetGain();
  
  MSG("LISummarySorter",Msg::kVerbose)  
    <<"plexPinDiodeId="<<plexPinDiodeId.AsString() 
    <<", inBox="<<pinInBox 
    <<", pinGain="<<pinGain<<endl;
  
  //set all the mux box variables
  this->GetMuxBoxInfo(plexPinDiodeId);
  
  //generate a plex led id to then get the two possible pins
  PlexLedId ledId;
  if (detectorType==Detector::kFar){
    ledId=PlexLedId(Detector::kFar,pulserBox,led); 
  }
  else if (detectorType==Detector::kNear){
    ledId=PlexLedId(Detector::kNear,pulserBox,led); 
  }
  else if (detectorType==Detector::kCalDet){
    ledId=PlexLedId(Detector::kCalDet,pulserBox,led); 
  }
  else {
    MSG("LISummarySorter",Msg::kFatal)
      <<"Detector type not known = "<<detectorType<<endl;
  }
  
  if (!ledId.IsValid()){
    MSG("LISummarySorter",Msg::kWarning)
      <<"LedId not valid = "<<ledId.AsString()<<endl;
  }

  //create a pair to hold the two possible pin diode ids
  pair<PlexPinDiodeId,PlexPinDiodeId> plexPins=plexHandle->
    GetPinDiodeIds(ledId);
  
  //first is gain=1, second is gain=0
  MSG("LISummarySorter",Msg::kVerbose) 
    <<"first pin gain="<<plexPins.first.GetGain()
    <<", second pin gain="<<plexPins.second.GetGain()<<endl;
  
  //get the pin diode id of the current pin
  PlexPinDiodeId currentPinId=plexHandle->
    GetPinDiodeId(channels[ch].GetChannelId());

  //get the planes associated with the pin diode
  pair<Int_t,Int_t> pinPlanes=fLookup.GetPinDiodePlanes(currentPinId,
                                                        plexHandle);

  //set the plane to be the first
  //at FD this is ok since the shared pmt is not used
  //at CD you can work it out since you always return the lower plane
  plane=pinPlanes.first;

  MSG("LISummarySorter",Msg::kVerbose)
    <<"PIN diode's associated plane="<<plane<<endl;

  //get the raw channel id of the plex pin for this 
  //led and pulser box combination to then compare with the
  //raw channel id of the actual pin being reconstructed
  pair<RawChannelId,RawChannelId> rawChanIds;
  //get chan ids of pins 
  rawChanIds.first=plexHandle->GetRawChannelId(plexPins.first);
  rawChanIds.second=plexHandle->GetRawChannelId(plexPins.second);

  //compare chan id of first pin
  if (rawChanIds.first.IsSameChannel(channels[ch].GetChannelId())){
    MSG("LISummarySorter",Msg::kVerbose)
      <<"PIN reconstructed: First pin="
      <<plexPins.first.AsString()<<endl
      <<"                         pin="
      <<plexPinDiodeId.AsString()<<endl;
    correlatedHit=1;
    pinCounterReco[led-1]++;
  }
  else{//compare the second possibility
    if (rawChanIds.second.IsSameChannel(channels[ch].GetChannelId())){
      MSG("LISummarySorter",Msg::kVerbose) 
        <<"PIN reconstructed: Second pin="<<
        plexPins.second.AsString()<<endl
        <<"                          pin="<<
        plexPinDiodeId.AsString()<<endl;
      correlatedHit=1;
      pinCounterReco[led-1]++;
    }
  }

  //print out pin info of non-reconstructed pins
  if (correlatedHit!=1){
    MSG("LISummarySorter",Msg::kVerbose) 
      <<endl<<"PIN not reconstructed, noise hit"
      <<", pin="<<plexPinDiodeId.AsString()<<endl;
  }

  MSG("LISummarySorter",Msg::kVerbose) 
    <<"ReconstructPin method finished"<<endl;
  if (correlatedHit==1) return true;
  else return false;
}

//......................................................................

void LISummarySorter::ReconstructTrigPmt() 
{
  MSG("LISummarySorter",Msg::kVerbose) 
    <<"Reconstructing Trigger Pmt..."<<endl;

  if (channel==fLookup.Pb2TrigPmtChannel(pulserBox,detectorType)){
    nearPulserBox=pulserBox;
    //there is no far pulser box associated with a trig pmt hit
    //but get it anyway
    farPulserBox=fLookup.GetOppPb(pulserBox,detectorType);
    correlatedHit=1;
  }

  if (fLookup.Pb2TrigPmtChannel(pulserBox,detectorType)==-1){
    this->PrintBigMessage();
  }
  
  MSG("LISummarySorter",Msg::kVerbose)
    <<"ReconstructTrigPmt method finished"<<endl;
}

//......................................................................

void LISummarySorter::GetMuxBoxInfo(PlexPinDiodeId plexPinDiodeId) 
{
  MSG("LISummarySorter",Msg::kVerbose) 
    <<"Getting mux box info..."<<endl;

    rackBay=static_cast<Int_t>(plexPinDiodeId.GetRackBay());
    inRack=static_cast<Int_t>(plexPinDiodeId.GetInRack());
    numericMuxBox=static_cast<Int_t>
      (plexPinDiodeId.GetNumericMuxBox());
    const Char_t eastWestChar=plexPinDiodeId.GetEastWest();
    const Char_t rackLevelChar=plexPinDiodeId.GetRackLevel();
    string sEastWest=static_cast<string>(&eastWestChar);
    sEastWest=sEastWest[0];//sometimes has two characters
    string sRackLevel=static_cast<string>(&rackLevelChar);
    sRackLevel=sRackLevel[0];
    
    //translate eastWest string to an integer
    eastWest=fLookup.ConvertEastWest(sEastWest);
    if (eastWest==-1) {
      MSG("LISummarySorter",Msg::kWarning) 
        << "plexPinDiodeId="<<plexPinDiodeId.AsString()
        << ", eastWest="<<sEastWest
        << ", length="<<sEastWest.size()
        << ", 1st="<<sEastWest[0]
        << ", 2nd="<<sEastWest[1]
        << endl;
    }
         
    //translate rackLevel string to an integer
    rackLevel=fLookup.ConvertRackLevel(sRackLevel);
    if (rackLevel==-1){
      MSG("LISummarySorter",Msg::kWarning) 
        << "plexPinDiodeId="<<plexPinDiodeId.AsString()
        << ", rackLevel="<<sRackLevel 
        << ", length="<<sRackLevel.size()
        << ", 1st="<<sRackLevel[0]
        << ", 2nd="<<sRackLevel[1]
        << endl;
    }      

  MSG("LISummarySorter",Msg::kVerbose)
    <<"Finished getting mux box info"<<endl;
}

//......................................................................

void LISummarySorter::GetMuxBoxInfo(PlexPixelSpotId plexPixelSpotId) 
{
  MSG("LISummarySorter",Msg::kVerbose) 
    <<"Getting mux box info..."<<endl;

    rackBay=static_cast<Int_t>(plexPixelSpotId.GetRackBay());
    inRack=static_cast<Int_t>(plexPixelSpotId.GetInRack());
    numericMuxBox=static_cast<Int_t>
      (plexPixelSpotId.GetNumericMuxBox());
    const Char_t eastWestChar=plexPixelSpotId.GetEastWest();
    const Char_t rackLevelChar=plexPixelSpotId.GetRackLevel();
    string sEastWest=static_cast<string>(&eastWestChar);
    sEastWest=sEastWest[0];//sometimes has two characters
    string sRackLevel=static_cast<string>(&rackLevelChar);
    sRackLevel=sRackLevel[0];
    
    //translate eastwest string to an integer
    eastWest=fLookup.ConvertEastWest(sEastWest);
    if (eastWest==-1) {
      MSG("LISummarySorter",Msg::kWarning) 
        <<"plexPixelSpotId="<<plexPixelSpotId.AsString()
        <<", eastWest="<<sEastWest
        <<", length="<<sEastWest.size()
        <<", 1st="<<sEastWest[0]
        <<", 2nd="<<sEastWest[1]
        << endl;
    }
              
    //translate rackLevel string to an integer
    rackLevel=fLookup.ConvertRackLevel(sRackLevel);
    if (rackLevel==-1){
      MSG("LISummarySorter",Msg::kWarning) 
        <<"plexPixelSpotId="<<plexPixelSpotId.AsString()
        <<", rackLevel="<<sRackLevel 
        <<",size="<<sRackLevel.size()
        <<",1s="<<sRackLevel[0]
        <<",2s="<<sRackLevel[1]
        << endl;
    }      

  MSG("LISummarySorter",Msg::kVerbose)
    <<"Finished getting mux box info"<<endl;
}

//......................................................................

void LISummarySorter::AddEntry(RawChannelId channelId,
                               Float_t mean,
                               Float_t rms,
                               Int_t numEntries)
{
  //initialise the tree if the first time (also opens file)
  if (!outtree) this->InitialiseTree();

  Int_t ch=channelId.GetCrate()*fLookup.NUMCHADD+channelId.GetChAdd();
  
  MSG("LISummarySorterUltraVerbose",Msg::kVerbose) 
    <<"ch="<<ch<<", ChAdd="<<channelId.GetChAdd()<<endl;

  //set the channelId of the channel
  channels[ch].SetChannelId(channelId);
  
  //this is deliberately LIChannel type message
  MSG("LIChannel",Msg::kVerbose) 
    <<this->GetElecString(channels[ch].GetChannelId())<<endl;

  //do I really want to add zero channels????
  //maybe just add the channel once, so it appears in the tree?
  //probably just put everything in there!

  string msgPrefix="Used Summary w/ strange values ";

  //add the means and rms to the running total
  channels[ch].AddEntry(numEntries,mean,rms); 

  //do some sanity checking that there are no strange entries
  if (mean==0 || numEntries==0){
    //get the raw channel id to use below
    RawChannelId rChId=channels[ch].GetChannelId();
    
    //have to get the readout type since it wont have been set for the
    //first point
    if (plexHandle->GetReadoutType(channels[ch].GetChannelId())==
        ReadoutType::kTOF || 
        plexHandle->GetReadoutType(channels[ch].GetChannelId())==
        ReadoutType::kUnknown || 
        plexHandle->GetReadoutType(channels[ch].GetChannelId())==
        ReadoutType::kTriggerOR
        ){

      //these often have zero mean but finite num entries at caldet
      MAXMSG("LISanityCheck",Msg::kVerbose,50) 
        <<msgPrefix
        <<"numHits="<<numEntries
        <<", mean="<<static_cast<Int_t>(mean)
        <<", rms="<<static_cast<Int_t>(rms)
        <<", rt="<<ReadoutType::AsString(plexHandle->GetReadoutType
                                         (channels[ch].GetChannelId()))
        <<" "<<this->GetElecString(rChId)<<endl;
    }
    else{
      MAXMSG("LISanityCheck",Msg::kWarning,50) 
        <<msgPrefix
        <<"numHits="<<numEntries
        <<", mean="<<static_cast<Int_t>(mean)
        <<", rms="<<static_cast<Int_t>(rms)
        <<", rt="<<ReadoutType::AsString(plexHandle->GetReadoutType
                                         (channels[ch].GetChannelId()))
        <<" "<<this->GetElecString(rChId)<<endl;
    }
  }
  //check that there are no strange zero rms channels
  else if (rms==0){
    //get the raw channel id to use below
    RawChannelId rChId=channels[ch].GetChannelId();
    
    if (numEntries>=6){
      MAXMSG("LISanityCheck",Msg::kInfo,50) 
        <<msgPrefix
        <<"numHits="<<numEntries
        <<", adc="<<static_cast<Int_t>(mean)
        <<", rms="<<static_cast<Int_t>(rms)
        <<", rt="<<ReadoutType::AsString(plexHandle->GetReadoutType
                                         (channels[ch].GetChannelId()))
        <<" "<<this->GetElecString(rChId)<<endl;
    }
    else if (numEntries>=5){
      MAXMSG("LISanityCheck",Msg::kDebug,50) 
        <<msgPrefix
        <<"numHits="<<numEntries
        <<", mean="<<static_cast<Int_t>(mean)
        <<", rms="<<static_cast<Int_t>(rms)
        <<", rt="<<ReadoutType::AsString(plexHandle->GetReadoutType
                                         (channels[ch].GetChannelId()))
        <<" "<<this->GetElecString(rChId)<<endl;
    }
    else if (numEntries>=4){
      MAXMSG("LISanityCheck",Msg::kVerbose,50) 
        <<msgPrefix
        <<"numHits="<<numEntries
        <<", mean="<<static_cast<Int_t>(mean)
        <<", rms="<<static_cast<Int_t>(rms)
        <<", rt="<<ReadoutType::AsString(plexHandle->GetReadoutType
                                         (channels[ch].GetChannelId()))
        <<" "<<this->GetElecString(rChId)<<endl;
    }
  }
}

//......................................................................
 
void LISummarySorter::InitialiseTree()
{
  //open the file, doing this before the tree is created 
  //ensures tree is written to disk as it is created
  outputFile=this->OpenFile(runNumber,runNumberSub,detectorType);

  outtree = new TTree("li_tree","li_tree");
  
  //set tree branches  
  outtree->Branch("ashtray",&ashtray,"ashtray/I",32000);
  outtree->Branch("calibPoint",&calibPoint,"calibPoint/I",32000);
  outtree->Branch("calibType",&calibType,"calibType/I",32000);
  outtree->Branch("chAdd",&chAdd,"chAdd/I",32000);
  outtree->Branch("channel",&channel,"channel/I",32000);
  //
  outtree->Branch("chip",&chip,"chip/I",32000);
  outtree->Branch("correlatedHit",&correlatedHit,
                  "correlatedHit/I",32000);
  outtree->Branch("crate",&crate,"crate/I",32000);
  outtree->Branch("detectorType",&detectorType,"detectorType/I",32000); 
  outtree->Branch("eastWest",&eastWest,"eastWest/I",32000);
  //  
  outtree->Branch("elecType",&elecType,"elecType/I",32000);
  outtree->Branch("farLed",&farLed,"farLed/I",32000);
  outtree->Branch("farPulserBox",&farPulserBox,"farPulserBox/I",32000);
  outtree->Branch("geoAdd",&geoAdd,"geoAdd/I",32000);
  outtree->Branch("inRack",&inRack,"inRack/I",32000);
  //
  outtree->Branch("led",&led,"led/I",32000);
  outtree->Branch("masterCh",&fMasterCh,"masterCh/I",32000);
  outtree->Branch("mean",&mean,"mean/F",32000);
  outtree->Branch("minderCh",&fMinderCh,"minderCh/I",32000);
  outtree->Branch("nearLed",&nearLed,"nearLed/I",32000);
  //
  outtree->Branch("nearPulserBox",&nearPulserBox,
                  "nearPulserBox/I",32000);
  outtree->Branch("numEntries",&numEntries,"numEntries/I",32000);
  outtree->Branch("numericMuxBox",&numericMuxBox,
                  "numericMuxBox/I",32000);
  outtree->Branch("pe",&fPe,"pe/I",32000);

  outtree->Branch("period",&period,"period/I",32000);
  //
  outtree->Branch("pinGain",&pinGain,"pinGain/I",32000);
  outtree->Branch("pinInBox",&pinInBox,"pinInBox/I",32000);
  outtree->Branch("pixel",&pixel,"pixel/I",32000);
  outtree->Branch("plane",&plane,"plane/I",32000);
  outtree->Branch("pulseHeight",&pulseHeight,"pulseHeight/I",32000);
  //
  outtree->Branch("pulserBox",&pulserBox,"pulserBox/I",32000); 
  outtree->Branch("pulses",&pulses,"pulses/I",32000);
  outtree->Branch("pulseWidth",&pulseWidth,"pulseWidth/I",32000);
  outtree->Branch("rackBay",&rackBay,"rackBay/I",32000);
  outtree->Branch("rackLevel",&rackLevel,"rackLevel/I",32000);
  //
  outtree->Branch("readoutType",&readoutType,"readoutType/I",32000);
  outtree->Branch("rms",&rms,"rms/F",32000);
  outtree->Branch("runNumber",&runNumber,"runNumber/I",32000);
  outtree->Branch("runNumberSub",&runNumberSub,"runNumberSub/I",32000);
  outtree->Branch("runType",&runType,"runType/I",32000);
  //
  outtree->Branch("strip",&strip,"strip/I",32000);
  outtree->Branch("stripEnd",&fStripEnd,"stripEnd/I",32000);
  outtree->Branch("summaryCounter",&summaryCounter,
                  "summaryCounter/I",32000);
  outtree->Branch("timestamp",&timestamp,"timestamp/I",32000);
  outtree->Branch("varc",&varc,"varc/I",32000);
  //
  outtree->Branch("vfb",&vfb,"vfb/I",32000);
  outtree->Branch("vmm",&vmm,"vmm/I",32000);//this is branch number 47 
}

//......................................................................

TFile* LISummarySorter::OpenFile(Int_t runNumber,Int_t runNumberSub,
                                 Int_t detectorType)
{
  TFile *outputFile=0;

  string sRunNumber=Form("%d",runNumber);
  string sRunNumberSub=Form("%d",runNumberSub);
  string sDetector="";
  if (detectorType==static_cast<Int_t>(Detector::kFar)){
    sDetector="F";
  }
  else if (detectorType==static_cast<Int_t>(Detector::kNear)){
    sDetector="N"; 
  }
  else if (detectorType==static_cast<Int_t>(Detector::kCalDet)){
    sDetector="C"; 
  }
  else{
    sDetector="TypeNotKnown"; 
  }
  string sZeros="";
  string sZeros2="";

  if (runNumber>=0 && runNumber<10) sZeros="00000000";
  else if (runNumber>=10 && runNumber<100) sZeros="000000";
  else if (runNumber>=100 && runNumber<1000) sZeros="00000";
  else if (runNumber>=1000 && runNumber<10000) sZeros="0000";
  else if (runNumber>=10000 && runNumber<100000) sZeros="000";
  else if (runNumber>=100000 && runNumber<1000000) sZeros="00";
  else if (runNumber>=1000000 && runNumber<10000000) sZeros="0";
  else if (runNumber>=10000000 && runNumber<100000000) sZeros="";

  if (runNumberSub>=0 && runNumberSub<10) sZeros2="000";
  else if (runNumberSub>=10 && runNumberSub<100) sZeros2="00";
  else if (runNumberSub>=100 && runNumberSub<1000) sZeros2="0";
  else if (runNumberSub>=1000 && runNumberSub<10000) sZeros2="";

  string sFileName="LIData"+sDetector+sZeros+sRunNumber+"_"+
    sZeros2+sRunNumberSub+".root";

  //test if file already exists
  ifstream Test(sFileName.c_str());

  if(!Test){
    outputFile= new TFile(sFileName.c_str(),"NEW");
  }
  else {
    //Need new filename
    Int_t fred=1;
    while(Test) {
      Test.close();
      string sAppendage=Form("%d",fred);
      sFileName="LIData"+sDetector+sZeros+sRunNumber+"_"+
        sZeros2+sRunNumberSub+"_"+sAppendage+".root";
      Test.open(sFileName.c_str());
      fred++;
    }
    outputFile = new TFile(sFileName.c_str(),"NEW");
    outputFile->SetCompressionLevel(9);
  }
  MSG("LISummarySorter",Msg::kInfo) 
    <<" ** Output file opened: "<<sFileName<<" ** "<<endl;
  return outputFile;
}

//......................................................................

void LISummarySorter::WriteFile(TFile* outfile)
{
  if (outfile && outtree){
    MSG("LISummarySorter",Msg::kInfo)<<"Writing out tree..."<<endl;
    outfile->cd();
    outtree->Write();
    delete outtree;  
    MSG("LISummarySorter",Msg::kInfo) 
      <<"Tree written and deleted"<<endl;
  }
  else {
    MSG("LISummarySorter",Msg::kWarning)
      <<"Can't write out tree (outtree="<<outtree
      <<", outfile="<<outfile<<")"<<endl;
  }
}

//......................................................................

void LISummarySorter::CloseFile(TFile* outfile)
{
  if (outfile){
    MSG("LISummarySorter",Msg::kInfo)<<"Closing output file..."<<endl;
    outfile->Close();
    MSG("LISummarySorter",Msg::kInfo)<<"Output file closed"<<endl;
  }
  else{
    MSG("LISummarySorter",Msg::kWarning)
      <<"Can't close file: outfile="<<outfile<<endl;
  }
}

//......................................................................

void LISummarySorter::SetPlexHandle(VldContext vldC)
{
  MSG("LISummarySorter",Msg::kVerbose) 
    <<"Setting new validity context for plex handle..."<<endl;

  MSG("LISummarySorter",Msg::kDebug)
    <<"Input to SetPlexHandle() VldC="<<vldC.AsString()<<endl;
  
  if (vldC.GetTimeStamp().GetSec()==0){
    static Int_t numberMsg=0;
    if (numberMsg<2){
      MSG("LISummarySorter",Msg::kWarning)
        <<endl<<endl
        <<"************************* WARNING ********************"<<endl
        <<"* Number of seconds in summary block=0"<<endl
        <<"* Using RawDaqHeader timestamp to create"<<endl
        <<"* plex handle instead"<<endl
        <<"******************************************************"<<endl
        <<endl;
    }
    numberMsg++;

    const VldTimeStamp ts=fRawDaqVldCtx.GetTimeStamp();

    //print the timestamp if verbose
    if (MsgService::Instance()->IsActive("LISummarySorter",
                                         Msg::kVerbose)){
      MSG("LISummarySorter",Msg::kInfo) 
        <<"Using VldTimeStamp="<<endl;
      ts.Print();
    }
    
    VldContext hackedVldC(vldC.GetDetector(),SimFlag::kData,ts);
    
    MSG("LISummarySorter",Msg::kDebug) 
      <<"After setting plex handle using VldC="
      <<hackedVldC.AsString()<<endl; 
    
    //check if the validity context is valid then create the plex handle
    if (hackedVldC.IsValid()){

      //delete the plex handle if it already exists
      if (plexHandle){
        delete plexHandle;
      }
      //create a new plex handle
      plexHandle=new PlexHandle(hackedVldC); 
    }
    else{
      MSG("LISummarySorter",Msg::kFatal) 
        <<"Validity context not valid="<<vldC.AsString()<<endl;
      exit(1);
    }
  }
  else{ 
    //check if the validity context is valid then create the plex handle
    if (vldC.IsValid()){

      //delete the plex handle if it already exists
      if (plexHandle){
        delete plexHandle;
      }

      //create a new plex handle
      plexHandle=new PlexHandle(vldC); 
      
      //get validity range
      VldRange myVldRange=plexHandle->GetVldRange();
      MSG("LISummarySorter",Msg::kVerbose)
        <<"Range TimeStart="<<myVldRange.GetTimeStart().AsString()<<endl
        <<"Range TimeEnd="<<myVldRange.GetTimeEnd().AsString()<<endl
        <<"Compatible="<<myVldRange.IsCompatible(vldC)<<endl;
    }
    else{
      MSG("LISummarySorter",Msg::kFatal) 
        <<"Validity context not valid="<<vldC.AsString()<<endl;
      exit(1);
    }
  }
  
  MSG("LISummarySorter",Msg::kVerbose) 
    <<"Finished setting new validity context for plex handle"<<endl;
}

//......................................................................

void LISummarySorter::SetRawDaqVldCtx(VldContext vldC) 
{ 
  MSG("LISummarySorter",Msg::kVerbose)  
    <<"Setting RawDaqVldCtx"<<endl; 
 
  MSG("LISummarySorter",Msg::kDebug) 
    <<"Input to SetRawDaqVldCtx() VldC="<<vldC.AsString()<<endl; 
   
  //check if the validity context is valid 
  if (vldC.IsValid()){
    fRawDaqVldCtx=vldC;
  } 
  else{ 
    MSG("LISummarySorter",Msg::kWarning)  
      <<"Validity context not valid = "<<vldC.AsString()
      <<endl<<"Could not set fRawDaqVldCtx"<<endl; 
  } 
 
  MSG("LISummarySorter",Msg::kVerbose)  
    <<"Finished SetRawDaqVldCtx method"<<endl; 
} 

//......................................................................

void LISummarySorter::SetDetector(VldContext vldC) 
{ 
  MSG("LISummarySorter",Msg::kVerbose)  
    <<"Setting detector type..."<<endl; 
 
  MSG("LISummarySorter",Msg::kDebug) 
    <<"Argument of SetDetector: VldC="<<vldC.AsString()<<endl; 
   
  //check if the validity context is valid 
  if (vldC.IsValid()){

    detectorType=static_cast<Int_t>(vldC.GetDetector()); 
    MSG("LISummarySorter",Msg::kDebug) 
      <<"Detector Type "<<detectorType<<" found"<<endl;

    //set the detector specific variables only once
    static Bool_t detNotSet=true;
    if (detNotSet){
      fLookup.SetDetector(detectorType);
      detNotSet=false;
    }
  } 
  else{ 
    MSG("LISummarySorter",Msg::kWarning)  
      <<"Validity context not valid = "<<vldC.AsString()
      <<endl<<"Could not set detector type"<<endl; 
  } 
 
  MSG("LISummarySorter",Msg::kVerbose)  
    <<"Finished SetDetector method"<<endl; 
} 
 
//......................................................................

---