SBSGEMModule.cxx

#include <iostream>

#include "SBSGEMModule.h"
#include "TDatime.h"
#include "THaEvData.h"
#include "THaApparatus.h"
#include "THaRun.h"
#include "TRotation.h"
#include "TH1D.h"
#include "TH2D.h"
#include "TF1.h"
#include "TGraphErrors.h"
#include "TClonesArray.h"
#include <algorithm>
#include <iomanip>

using namespace std;
//using namespace SBSGEMModule;

//This should not be hard-coded, I think, but read in from the database (or perhaps not, if it never changes? For now we keep it hard-coded)
// const int APVMAP[128] = {1, 33, 65, 97, 9, 41, 73, 105, 17, 49, 81, 113, 25, 57, 89, 121, 3, 35, 67, 99, 11, 43, 75, 107, 19, 51, 83, 115, 27, 59, 91, 123, 5, 37, 69, 101, 13, 45, 77, 109, 21, 53, 85, 117, 29, 61, 93, 125, 7, 39, 71, 103, 15, 47, 79, 111, 23, 55, 87, 119, 31, 63, 95, 127, 0, 32, 64, 96, 8, 40, 72, 104, 16, 48, 80, 112, 24, 56, 88, 120, 2, 34, 66, 98, 10, 42, 74, 106, 18, 50, 82, 114, 26, 58, 90, 122, 4, 36, 68, 100, 12, 44, 76, 108, 20, 52, 84, 116, 28, 60, 92, 124, 6, 38, 70, 102, 14, 46, 78, 110, 22, 54, 86, 118, 30, 62, 94, 126};

SBSGEMModule::SBSGEMModule( const char *name, const char *description,
			    THaDetectorBase* parent ):
  THaSubDetector(name,description,parent)
{
  // FIXME:  To database
  //Set Default values for fZeroSuppress and fZeroSuppressRMS:
  fZeroSuppress    = kTRUE;
  fZeroSuppressRMS = 5.0; //threshold in units of RMS:

  fNegSignalStudy = kFALSE;

  fPedestalMode = kFALSE;
  fPedHistosInitialized = kFALSE;

  fSubtractPedBeforeCommonMode = false; //only affects the pedestal-mode analysis 
  
  //Default online zero suppression to FALSE: actually I wonder if it would be better to use this in 
  // Moved this to MPDModule, since this should be done during the decoding of the raw APV data:
  fOnlineZeroSuppression = kFALSE;

  fCommonModeFlag = 0; //"sorting" method
  fCommonModeOnlFlag = 3; // 3 = Danning method during GMn, 4 = Danning method during GEn
  //Default: discard highest and lowest 28 strips for "sorting method" common-mode calculation:
  fCommonModeNstripRejectHigh = 28; 
  fCommonModeNstripRejectLow = 28;

  fCommonModeNumIterations = 3;
  fCommonModeMinStripsInRange = 10;
  fMakeCommonModePlots = false;
  fCommonModePlotsInitialized = false;
  fCommonModePlots_DBoverride = false;

  fMakeEventInfoPlots = false;
  fEventInfoPlotsInitialized = false;
  
  fPedSubFlag = 1; //default to online ped subtraction, as that is the mode we will run in most of the time

  fTrigTime = 0.0;

  fMaxTrigTimeCorrection = 25.0;
  fTrigTimeSlope = 1.0; //slope of GEM time versus trig time correlation

  //Set default values for decode map parameters:
  fN_APV25_CHAN = 128;
  fN_MPD_TIME_SAMP = 6;
  fMPDMAP_ROW_SIZE = 9;

  //We should probably get rid of this as it's not used, only leads to confusion:
  fNumberOfChannelInFrame = 129;

  fSamplePeriod = 24.0; //nanoseconds:

  fSigma_hitshape = 0.0004; //0.4 mm; controls cluster-splitting algorithm
  // for( Int_t i = 0; i < N_MPD_TIME_SAMP; i++ ){
  //     fadc[i] = NULL;
  // }

  //Default clustering parameters:
  fThresholdSample = 50.0;
  fThresholdStripSum = 250.0;
  fThresholdClusterSum = 500.0;

  fThresholdSampleDeconv = 50.0;
  fThresholdDeconvADCMaxCombo = 75.0;
  fThresholdClusterSumDeconv = 150.0;
  
  fADCasymCut = 1.1;
  fTimeCutUVdiff = 30.0;
  fCorrCoeffCut = -1.1;
  fCorrCoeffCutDeconv = -1.1;

  fADCasymSigma = 0.06;
  fADCratioSigma = 0.1;
  fTimeCutUVsigma = 3.0; //ns

  fTimeCutUVdiffDeconv = 40.0; //ns
  fTimeCutUVsigmaDeconv = 7.0;

  fTimeCutUVdiffFit = 30.0;
  fTimeCutUVsigmaFit = 3.0;

  fFiltering_flag1D = 0; //"soft" cuts
  fFiltering_flag2D = 0; //"soft" cuts
  
  // default these offsets to zero: 
  fUStripOffset = 0.0;
  fVStripOffset = 0.0;
  
  fMakeEfficiencyPlots = true;
  fEfficiencyInitialized = false;

  // We want to change the default values for these dummy channels to accommodate up to 40 MPDs per VTP:
  // fChan_CM_flags = 512; //default to 512:
  // fChan_TimeStamp_low = 513;
  // fChan_TimeStamp_high = 514;
  // fChan_MPD_EventCount = 515;
  // fChan_MPD_Debug = 516;

  //Start dummy channels at 640 by default, to accommodate up to 40 MPDs per VTP crate
  fChan_CM_flags = 640; //default to 640 (so as not to step on up to 40 MPDs per VTP crate):
  fChan_TimeStamp_low = 641;
  fChan_TimeStamp_high = 642;
  fChan_MPD_EventCount = 643;
  fChan_MPD_Debug = 644;
  
  UInt_t MAXNSAMP_PER_APV = fN_APV25_CHAN * fN_MPD_TIME_SAMP;
  //arrays to hold raw data from one APV card:
  fStripAPV.resize( MAXNSAMP_PER_APV );
  fRawStripAPV.resize( MAXNSAMP_PER_APV );
  fRawADC_APV.resize( MAXNSAMP_PER_APV );
  fPedSubADC_APV.resize( MAXNSAMP_PER_APV );
  fCommonModeSubtractedADC_APV.resize( MAXNSAMP_PER_APV );

  fCM_online.resize( fN_MPD_TIME_SAMP );
  
  //default to 
  //fMAX2DHITS = 250000;
  fMAX2DHITS = 10000;

  fRMS_ConversionFactor = sqrt(fN_MPD_TIME_SAMP); //=2.45

  fIsMC = false; //need to set default value!

  fAPVmapping = SBSGEM::kUVA_XY; //default to UVA X/Y style APV mapping, but require this in the database::

  InitAPVMAP();

  fModuleGain = 1.0;
  //  std::cout << "SBSGEMModule constructor invoked, name = " << name << std::endl;

  //Number of sigmas for defining common-mode max for online zero suppression
  fCommonModeRange_nsigma = 5.0;

  fSuppressFirstLast = 0; // suppress strips peaking in first or last time sample by default:
  //fUseStripTimingCuts = false;

  fStripTau = 56.0; //ns, default value. Eventually load this from DB. This is not actually used as of yet.
  fUseStripTimingCuts = 0;
  fUseTSchi2cut = false;

  for( int axis=0; axis<2; axis++ ){
  
    fStripMaxTcut_central[axis] = 87.0; //ns
    fStripMaxTcut_width[axis] = 4.5; //sigmas
    fStripMaxTcut_sigma[axis] = 7.0; //ns, for purpose of "hit quality chi2" calculation
    
    fStripMaxTcut_central_deconv[axis] = 50.0; //ns
    fStripMaxTcut_width_deconv[axis] = 4.5; //number of sigmas
    fStripMaxTcut_sigma_deconv[axis] = 15.0; //ns 

    fStripMaxTcut_central_fit[axis] = 20.0; //ns
    fStripMaxTcut_width_fit[axis] = 4.5; //sigmas
    fStripMaxTcut_sigma_fit[axis] = 10.0; //ns

    fHitTimeMean[axis] = 87.0;
    fHitTimeSigma[axis] = 7.0;
    fHitTimeMeanDeconv[axis] = 50.0;
    fHitTimeSigmaDeconv[axis] = 15.0;
    fHitTimeMeanFit[axis] = 20.0;
    fHitTimeSigmaFit[axis] = 10.0;
  }

  fSigmaHitTimeAverageCorrected = 5.0; //ns
    
  fStripAddTcut_width = 50.0; //this one we keep in ns
  fStripAddCorrCoeffCut = 0.25;
  fStripTSchi2Cut = 10.0; //not yet clear what is a good value for this.

  
  
  fGoodStrip_TSfrac_mean.resize( fN_MPD_TIME_SAMP );
  fGoodStrip_TSfrac_sigma.resize( fN_MPD_TIME_SAMP );

  //Define some defaults for these:
  double fracmean_default[6] = {0.055, 0.135, 0.203, 0.224, 0.208, 0.174};
  double fracsigma_default[6] = {0.034, 0.039, 0.019, 0.021, 0.032, 0.035};

  for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
    if( isamp < fN_MPD_TIME_SAMP && isamp < 6 ){
      fGoodStrip_TSfrac_mean[isamp] = fracmean_default[isamp];
      fGoodStrip_TSfrac_sigma[isamp] = fracsigma_default[isamp];
    }
  }
  
  fPulseShapeInitialized = false;

  fMeasureCommonMode = true;
  fNeventsCommonModeLookBack = 15;

  fCorrectCommonMode = false;
  fCorrectCommonModeMinStrips = 20;
  fCorrectCommonMode_Nsigma = 5.0;

  fCommonModeBinWidth_Nsigma = 1.0; //Bin width +/- 1 sigma by default
  fCommonModeScanRange_Nsigma = 4.0; //Scan window +/- 4 sigma
  fCommonModeStepSize_Nsigma = 0.2; //sigma/5 for step size:

  fCommonModeDanningMethod_NsigmaCut = 3.0; //Default to 3 sigma

  fClusteringFlag = 0; //"standard" clustering based on sum of six time samples on a strip
  //fDeconvolutionFlag = 1; //Set "keep strip" flag based on deconvoluted ADC samples
  fDeconvolutionFlag = 0; //Default should be zero
  
  return;
}

SBSGEMModule::~SBSGEMModule() {
  // if( fStrip ){
  //     fadc0 = NULL;
  //     fadc1 = NULL;
  //     fadc2 = NULL;
  //     fadc3 = NULL;
  //     fadc4 = NULL;
  //     fadc5 = NULL;

  //     for( Int_t i = 0; i < N_MPD_TIME_SAMP; i++ ){
  //         delete fadc[i];
  //         fadc[i] = NULL;
  //     }
  //     delete fPedestal;
  //     fPedestal = NULL;
  //     delete fStrip;
  //     fStrip = NULL;
  // }

  delete fStripTimeFunc;

}

Int_t SBSGEMModule::ReadDatabase( const TDatime& date ){
  
  std::cout << "[SBSGEMModule::ReadDatabase]" << std::endl;
  
  Int_t status;

  FILE* file = OpenFile( date );
  if( !file ) return kFileError;

  std::vector<Double_t> rawpedu,rawpedv;
  std::vector<Double_t> rawrmsu,rawrmsv;

  //UShort_t layer;
  
  //I think we can set up the entire database parsing in one shot here (AJRP). Together with the call to ReadGeometry, this should define basically everything we need.
  //After loading, we will run some checks on the loaded information:
  //copying commented structure of DBRequest here for reference (see VarDef.h):
  // struct DBRequest {
  //   const char*      name;     // Key name
  //   void*            var;      // Pointer to data (default to Double*)
  //   VarType          type;     // (opt) data type (see VarType.h, default Double_t)
  //   UInt_t           nelem;    // (opt) number of array elements (0/1 = 1 or auto)
  //   Bool_t           optional; // (opt) If true, missing key is ok
  //   Int_t            search;   // (opt) Search for key along name tree
  //   const char*      descript; // (opt) Key description (if 0, same as name)
  // };

  // default these offsets to zero: 
  fUStripOffset = 0.0;
  fVStripOffset = 0.0;

  //std::cout << "Before loadDB, fCommonModePlotsInitialized = " << fCommonModePlotsInitialized << std::endl;

  int cmplots_flag = fMakeCommonModePlots ? 1 : 0;
  int zerosuppress_flag = fZeroSuppress ? 1 : 0;
  int negsignalstudy_flag = fNegSignalStudy ? 1 : 0;
  int onlinezerosuppress_flag = fOnlineZeroSuppression ? 1 : 0;

  int eventinfoplots_flag = fMakeEventInfoPlots ? 1 : 0;

  int usestriptimingcuts = fUseStripTimingCuts;
  int useTSchi2cut = fUseTSchi2cut ? 1 : 0;
  int suppressfirstlast = fSuppressFirstLast;
  int usecommonmoderollingaverage = fMeasureCommonMode ? 1 : 0;

  int correctcommonmode = fCorrectCommonMode ? 1 : 0;
  
  std::vector<double> TSfrac_mean_temp;
  std::vector<double> TSfrac_sigma_temp;

  //For parsing "strip" timing cuts:
  std::vector<double> t0_temp, tsigma_temp, tcut_temp;
  std::vector<double> t0_deconv_temp, tsigma_deconv_temp, tcut_deconv_temp;
  std::vector<double> t0_fit_temp, tsigma_fit_temp, tcut_fit_temp;

  //For parsing "hit" timing cuts:
  std::vector<double> t0hit_temp, tsigmahit_temp;
  std::vector<double> t0hit_deconv_temp, tsigmahit_deconv_temp;
  std::vector<double> t0hit_fit_temp, tsigmahit_fit_temp;
  
  const DBRequest request[] = {
    { "chanmap",        &fChanMapData,        kIntV, 0, 0, 0}, // mandatory: decode map info
    { "apvmap",         &fAPVmapping,    kUInt, 0, 1, 1}, //optional, allow search up the tree if all modules in a setup have the same APV mapping
    { "pedu",           &rawpedu,        kDoubleV, 0, 1, 0}, // optional raw pedestal info (u strips)
    { "pedv",           &rawpedv,        kDoubleV, 0, 1, 0}, // optional raw pedestal info (v strips)
    { "rmsu",           &rawrmsu,        kDoubleV, 0, 1, 0}, // optional pedestal rms info (u strips)
    { "rmsv",           &rawrmsv,        kDoubleV, 0, 1, 0}, // optional pedestal rms info (v strips)
    { "layer",          &fLayer,         kUShort, 0, 0, 0}, // mandatory: logical tracking layer must be specified for every module:
    { "nstripsu",       &fNstripsU,     kUInt, 0, 0, 1}, //mandatory: number of strips in module along U axis
    { "nstripsv",       &fNstripsV,     kUInt, 0, 0, 1}, //mandatory: number of strips in module along V axis
    { "uangle",         &fUAngle,       kDouble, 0, 0, 1}, //mandatory: Angle of "U" strips wrt X axis
    { "vangle",         &fVAngle,       kDouble, 0, 0, 1}, //mandatory: Angle of "V" strips wrt X axis
    { "uoffset",        &fUStripOffset, kDouble, 0, 1, 1}, //optional: position of first U strip
    { "voffset",        &fVStripOffset, kDouble, 0, 1, 1}, //optional: position of first V strip
    { "upitch",         &fUStripPitch,  kDouble, 0, 0, 1}, //mandatory: Pitch of U strips
    { "vpitch",         &fVStripPitch,  kDouble, 0, 0, 1}, //mandatory: Pitch of V strips
    { "ugain",          &fUgain,        kDoubleV, 0, 1, 0}, //(optional): Gain of U strips by APV card (ordered by strip position, NOT by order of appearance in decode map)
    { "vgain",          &fVgain,        kDoubleV, 0, 1, 0}, //(optional): Gain of V strips by APV card (ordered by strip position, NOT by order of appearance in decode map)
    { "modulegain",     &fModuleGain,   kDouble, 0, 1, 1},
    { "threshold_sample",  &fThresholdSample, kDouble, 0, 1, 1}, //(optional): threshold on max. ADC sample to keep strip (baseline-subtracted)
    { "threshold_stripsum", &fThresholdStripSum, kDouble, 0, 1, 1}, //(optional): threshold on sum of ADC samples on a strip (baseline-subtracted)
    { "threshold_clustersum", &fThresholdClusterSum, kDouble, 0, 1, 1}, //(optional): threshold on sum of all ADCs over all strips in a cluster (baseline-subtracted)
    { "threshold_sample_deconv", &fThresholdSampleDeconv, kDouble, 0, 1, 1 },
    { "threshold_maxcombo_deconv", &fThresholdDeconvADCMaxCombo, kDouble, 0, 1, 1 },
    { "threshold_clustersum_deconv", &fThresholdClusterSumDeconv, kDouble, 0, 1, 1 },
    { "ADCasym_cut", &fADCasymCut, kDouble, 0, 1, 1}, //(optional): filter 2D hits by ADC asymmetry, |Asym| < cut
    { "deltat_cut", &fTimeCutUVdiff, kDouble, 0, 1, 1}, //(optional): filter 2D hits by U/V time difference
    { "corrcoeff_cut", &fCorrCoeffCut, kDouble, 0, 1, 1},
    { "filterflag1D", &fFiltering_flag1D, kInt, 0, 1, 1},
    { "filterflag2D", &fFiltering_flag2D, kInt, 0, 1, 1},
    { "peakprominence_minsigma", &fThresh_2ndMax_nsigma, kDouble, 0, 1, 1}, //(optional): reject overlapping clusters with peak prominence less than this number of sigmas
    { "peakprominence_minfraction", &fThresh_2ndMax_fraction, kDouble, 0, 1, 1}, //(optional): reject overlapping clusters with peak prominence less than this fraction of height of nearby higher peak
    { "maxnu_charge", &fMaxNeighborsU_totalcharge, kUShort, 0, 1, 1}, //(optional): cluster size restriction along U for total charge calculation
    { "maxnv_charge", &fMaxNeighborsV_totalcharge, kUShort, 0, 1, 1}, //(optional): cluster size restriction along V for total charge calculation
    { "maxnu_pos", &fMaxNeighborsU_hitpos, kUShort, 0, 1, 1}, //(optional): cluster size restriction for position reconstruction
    { "maxnv_pos", &fMaxNeighborsV_hitpos, kUShort, 0, 1, 1}, //(optional): cluster size restriction for position reconstruction
    { "sigmahitshape", &fSigma_hitshape, kDouble, 0, 1, 1}, //(optional): width parameter for cluster-splitting algorithm
    { "zerosuppress", &zerosuppress_flag, kUInt, 0, 1, 1}, //(optional, search): toggle offline zero suppression (default = true).
    { "zerosuppress_nsigma", &fZeroSuppressRMS, kDouble, 0, 1, 1}, //(optional, search):
    { "do_neg_signal_study", &negsignalstudy_flag, kUInt, 0, 1, 1}, //(optional, search): toggle doing negative signal analysis
    { "onlinezerosuppress", &onlinezerosuppress_flag, kUInt, 0, 1, 1}, //(optional, search)
    { "commonmode_meanU", &fCommonModeMeanU, kDoubleV, 0, 1, 0}, //(optional, don't search)
    { "commonmode_meanV", &fCommonModeMeanV, kDoubleV, 0, 1, 0}, //(optional, don't search)
    { "commonmode_rmsU", &fCommonModeRMSU, kDoubleV, 0, 1, 0}, //(optional, don't search)
    { "commonmode_rmsV", &fCommonModeRMSV, kDoubleV, 0, 1, 0}, //(optional, don't search)
    { "commonmode_flag", &fCommonModeFlag, kInt, 0, 1, 1}, //optional, search up the tree
    { "commonmode_online_flag", &fCommonModeOnlFlag, kInt, 0, 1, 1}, //optional, search up the tree
    { "commonmode_nstriplo", &fCommonModeNstripRejectLow, kInt, 0, 1, 1}, //optional, search up the tree:
    { "commonmode_nstriphi", &fCommonModeNstripRejectHigh, kInt, 0, 1, 1}, //optional, search:
    { "commonmode_niter", &fCommonModeNumIterations, kInt, 0, 1, 1},
    { "commonmode_minstrips", &fCommonModeMinStripsInRange, kInt, 0, 1, 1},
    { "commonmode_range_nsigma", &fCommonModeRange_nsigma, kDouble, 0, 1, 1},
    { "commonmode_danning_nsigma_cut", &fCommonModeDanningMethod_NsigmaCut, kDouble, 0, 1, 1 },
    { "plot_common_mode", &cmplots_flag, kInt, 0, 1, 1},
    { "plot_event_info", &eventinfoplots_flag, kInt, 0, 1, 1},
    { "chan_cm_flags", &fChan_CM_flags, kUInt, 0, 1, 1}, //optional, search up the tree: must match the value in crate map!
    { "chan_timestamp_low", &fChan_TimeStamp_low, kUInt, 0, 1, 1},
    { "chan_timestamp_high", &fChan_TimeStamp_high, kUInt, 0, 1, 1},
    { "chan_event_count", &fChan_MPD_EventCount, kUInt, 0, 1, 1},
    { "pedsub_online", &fPedSubFlag, kInt, 0, 1, 1},
    { "max2Dhits", &fMAX2DHITS, kUInt, 0, 1, 1}, //optional, search up tree
    { "usestriptimingcut", &fUseStripTimingCuts, kInt, 0, 1, 1 },
    { "useTSchi2cut", &useTSchi2cut, kInt, 0, 1, 1 },
    { "maxstrip_t0", &t0_temp, kDoubleV, 0, 1, 1 },
    { "maxstrip_t0_deconv", &t0_deconv_temp, kDoubleV, 0, 1, 1 },
    { "maxstrip_t0_fit", &t0_fit_temp, kDoubleV, 0, 1, 1 },
    { "maxstrip_tcut", &tcut_temp, kDoubleV, 0, 1, 1 },
    { "maxstrip_tcut_deconv", &tcut_deconv_temp, kDoubleV, 0, 1, 1 },
    { "maxstrip_tcut_fit", &tcut_fit_temp, kDoubleV, 0, 1, 1 },
    { "maxstrip_tsigma", &tsigma_temp, kDoubleV, 0, 1, 1 },
    { "maxstrip_tsigma_deconv", &tsigma_deconv_temp, kDoubleV, 0, 1, 1 },
    { "maxstrip_tsigma_fit", &tsigma_fit_temp, kDoubleV, 0, 1, 1 },
    { "addstrip_tcut", &fStripAddTcut_width, kDouble, 0, 1, 1 },
    { "addstrip_ccor_cut", &fStripAddCorrCoeffCut, kDouble, 0, 1, 1 },
    { "goodstrip_TSfrac_mean", &TSfrac_mean_temp, kDoubleV, 0, 1, 1 },
    { "goodstrip_TSfrac_sigma", &TSfrac_sigma_temp, kDoubleV, 0, 1, 1 },
    { "suppressfirstlast", &suppressfirstlast, kInt, 0, 1, 1 },
    { "use_commonmode_rolling_average", &usecommonmoderollingaverage, kInt, 0, 1, 1 },
    { "commonmode_nevents_lookback", &fNeventsCommonModeLookBack, kUInt, 0, 1, 1 },
    { "correct_common_mode", &correctcommonmode, kInt, 0, 1, 1 },
    { "correct_common_mode_minstrips", &fCorrectCommonModeMinStrips, kUInt, 0, 1, 1 },
    { "correct_common_mode_nsigma", &fCorrectCommonMode_Nsigma, kDouble, 0, 1, 1 },
    { "commonmode_binwidth_nsigma", &fCommonModeBinWidth_Nsigma, kDouble, 0, 1, 1 },
    { "commonmode_scanrange_nsigma", &fCommonModeScanRange_Nsigma, kDouble, 0, 1, 1 },
    { "commonmode_stepsize_nsigma", &fCommonModeStepSize_Nsigma, kDouble, 0, 1, 1 },
    { "deconvolution_tau", &fStripTau, kDouble, 0, 1, 1 },
    { "CMbiasU", &fCMbiasU, kDoubleV, 0, 1, 1 },
    { "CMbiasV", &fCMbiasV, kDoubleV, 0, 1, 1 },
    { "clustering_flag", &fClusteringFlag, kInt, 0, 1, 1 },
    { "deconvolution_flag", &fDeconvolutionFlag, kInt, 0, 1, 1 },
    { "maxtrigtime_correction", &fMaxTrigTimeCorrection, kDouble, 0, 1, 1 },
    { "trigtime_slope", &fTrigTimeSlope, kDouble, 0, 1, 1 },
    { "ADCasym_sigma", &fADCasymSigma, kDouble, 0, 1, 1 },
    { "deltat_sigma", &fTimeCutUVsigma, kDouble, 0, 1, 1 },
    { "deltat_cut_deconv", &fTimeCutUVdiffDeconv, kDouble, 0, 1, 1 },
    { "deltat_sigma_deconv", &fTimeCutUVsigmaDeconv, kDouble, 0, 1, 1 },
    { "deltat_cut_fit", &fTimeCutUVdiffFit, kDouble, 0, 1, 1 },
    { "deltat_sigma_fit", &fTimeCutUVsigmaFit, kDouble, 0, 1, 1 },
    { "corrcoeff_cut_deconv", &fCorrCoeffCutDeconv, kDouble, 0, 1, 1 },
    { "ADCratio_sigma", &fADCratioSigma, kDouble, 0, 1, 1 },
    { "HitTimeMean", &t0hit_temp, kDoubleV, 0, 1, 1 },
    { "HitTimeSigma", &tsigmahit_temp, kDoubleV, 0, 1, 1 },
    { "HitTimeMeanDeconv", &t0hit_deconv_temp, kDoubleV, 0, 1, 1 },
    { "HitTimeSigmaDeconv", &tsigmahit_deconv_temp, kDoubleV, 0, 1, 1 },
    { "HitTimeMeanFit", &t0hit_fit_temp, kDoubleV, 0, 1, 1 },
    { "HitTimeSigmaFit", &tsigmahit_fit_temp, kDoubleV, 0, 1, 1 },
    { "sigma_tcorr", &fSigmaHitTimeAverageCorrected, kDouble, 0, 1, 1 },
    {0}
  };
  status = LoadDB( file, date, request, fPrefix, 1 ); //The "1" after fPrefix means search up the tree

  if( status != 0 ){
    fclose(file);
    return status;
  }

  if( !fCommonModePlots_DBoverride ) fMakeCommonModePlots = cmplots_flag != 0;
  fZeroSuppress = zerosuppress_flag != 0;
  fOnlineZeroSuppression = onlinezerosuppress_flag != 0;

  fNegSignalStudy = negsignalstudy_flag != 0;

  fMakeEventInfoPlots = eventinfoplots_flag != 0;

  //fUseStripTimingCuts = usestriptimingcuts != 0;
  fUseTSchi2cut = useTSchi2cut != 0;

  fSuppressFirstLast = suppressfirstlast; 

  //fMeasureCommonMode = usecommonmoderollingaverage != 0;
  fMeasureCommonMode = true; //we're not turning this off
  fCorrectCommonMode = correctcommonmode != 0;
  
  if( fUseTSchi2cut && TSfrac_mean_temp.size() == fN_MPD_TIME_SAMP && TSfrac_sigma_temp.size() == fN_MPD_TIME_SAMP ){
    fGoodStrip_TSfrac_mean = TSfrac_mean_temp;
    fGoodStrip_TSfrac_sigma = TSfrac_sigma_temp;
  }
  
  //  std::cout << "After loadDB, fCommonModePlotsInitialized = " << fCommonModePlotsInitialized << std::endl;
 
  if( /*fAPVmapping < SBSGEM::kINFN ||*/ fAPVmapping > SBSGEM::kMC ) {
    std::cout << "Warning in SBSGEMModule::Decode for module " << GetParent()->GetName() << "." << GetName() << ": invalid APV mapping choice, defaulting to UVA X/Y." << std::endl
	      << " Analysis results may be incorrect" << std::endl;
    fAPVmapping = SBSGEM::kUVA_XY;
  }
  
  //prevent the user from defining something silly for the common-mode stuff:
  fCommonModeNstripRejectLow = std::min( 50, std::max( 0, fCommonModeNstripRejectLow ) );
  fCommonModeNstripRejectHigh = std::min( 50, std::max( 0, fCommonModeNstripRejectHigh ) );
  fCommonModeNumIterations = std::min( 10, std::max( 2, fCommonModeNumIterations ) );
  fCommonModeMinStripsInRange = std::min( fN_APV25_CHAN-25, std::max(1, fCommonModeMinStripsInRange ) );

  double x = fSamplePeriod/fStripTau;
  
  fDeconv_weights[0] = exp( x - 1.0 )/x; //~1.32
  fDeconv_weights[1] = -2.0*exp(-1.0)/x; //~ -1.72
  fDeconv_weights[2] = exp(-1.0-x)/x; //0.56
  
  //std::cout << GetName() << " fThresholdStripSum " << fThresholdStripSum 
  //<< " fThresholdSample " << fThresholdSample << std::endl;
  
  if( fIsMC ){
    fCommonModeFlag = -1;
    fPedestalMode = false;
    fOnlineZeroSuppression = true;
    fAPVmapping = SBSGEM::kMC;
  }

  fPxU = cos( fUAngle * TMath::DegToRad() );
  fPyU = sin( fUAngle * TMath::DegToRad() );
  fPxV = cos( fVAngle * TMath::DegToRad() );
  fPyV = sin( fVAngle * TMath::DegToRad() );

  fAPVch_by_Ustrip.clear();
  fAPVch_by_Vstrip.clear();
  fMPDID_by_Ustrip.clear();
  fMPDID_by_Vstrip.clear();
  fADCch_by_Ustrip.clear();
  fADCch_by_Vstrip.clear();

  //Count APV cards by axis. Each APV card must have one decode map entry:
  fNAPVs_U = 0;
  fNAPVs_V = 0;

  fMPDmap.clear();
  
  Int_t nentry = fChanMapData.size()/fMPDMAP_ROW_SIZE;

  fCommonModeResultContainer_by_APV.resize( nentry );
  fCommonModeRollingAverage_by_APV.resize( nentry );
  fCommonModeRollingRMS_by_APV.resize( nentry );
  fNeventsRollingAverage_by_APV.resize( nentry );

  fCMbiasResultContainer_by_APV.resize( nentry );
  fCommonModeOnlineBiasRollingAverage_by_APV.resize( nentry );
  fCommonModeOnlineBiasRollingRMS_by_APV.resize( nentry );
  fNeventsOnlineBias_by_APV.resize( nentry );
  
  for( Int_t mapline = 0; mapline < nentry; mapline++ ){
    mpdmap_t thisdata;
    thisdata.crate  = fChanMapData[0+mapline*fMPDMAP_ROW_SIZE];
    thisdata.slot   = fChanMapData[1+mapline*fMPDMAP_ROW_SIZE];
    thisdata.mpd_id = fChanMapData[2+mapline*fMPDMAP_ROW_SIZE];
    thisdata.gem_id = fChanMapData[3+mapline*fMPDMAP_ROW_SIZE];
    thisdata.adc_id = fChanMapData[4+mapline*fMPDMAP_ROW_SIZE];
    thisdata.i2c    = fChanMapData[5+mapline*fMPDMAP_ROW_SIZE];
    thisdata.pos    = fChanMapData[6+mapline*fMPDMAP_ROW_SIZE];
    thisdata.invert = fChanMapData[7+mapline*fMPDMAP_ROW_SIZE];
    thisdata.axis   = fChanMapData[8+mapline*fMPDMAP_ROW_SIZE];
    thisdata.index  = mapline;

    //Populate relevant quantities mapped by strip index:
    for( int ich=0; ich<fN_APV25_CHAN; ich++ ){
      int strip = GetStripNumber( ich, thisdata.pos, thisdata.invert );
      if( thisdata.axis == SBSGEM::kUaxis ){
	fAPVch_by_Ustrip[strip] = ich;
	fMPDID_by_Ustrip[strip] = thisdata.mpd_id;
	fADCch_by_Ustrip[strip] = thisdata.adc_id;
      } else {
	fAPVch_by_Vstrip[strip] = ich;
	fMPDID_by_Vstrip[strip] = thisdata.mpd_id;
	fADCch_by_Vstrip[strip] = thisdata.adc_id;
      }
    }

    if( thisdata.axis == SBSGEM::kUaxis ){
      fNAPVs_U++;
    } else {
      fNAPVs_V++;
    }
    
    fMPDmap.push_back(thisdata);

    fEventCount_by_APV.push_back( 0 );

    fT0_by_APV.push_back( 0 );
    fTcoarse_by_APV.push_back( 0 );
    fTfine_by_APV.push_back( 0 );
    fTimeStamp_ns_by_APV.push_back( 0 );

    //fCommonModeRollingFirstEvent_by_APV[mapline] = 0.0;
    fCommonModeResultContainer_by_APV[mapline].resize( fNeventsCommonModeLookBack*fN_MPD_TIME_SAMP );
    fCommonModeRollingAverage_by_APV[mapline] = 0.0;
    fCommonModeRollingRMS_by_APV[mapline] = 10.0;
    fNeventsRollingAverage_by_APV[mapline] = 0; //Really will be the number of time samples = 6 * number of events

    fCMbiasResultContainer_by_APV[mapline].resize( fNeventsCommonModeLookBack*fN_MPD_TIME_SAMP );
    fCommonModeOnlineBiasRollingAverage_by_APV[mapline] = 0.0;
    fCommonModeOnlineBiasRollingRMS_by_APV[mapline] = 10.0;
    fNeventsOnlineBias_by_APV[mapline] = 0;
  }

  //if a different number of decode map entries is counted than the expectation based on the number of strips, 
  //e.g., because we commented out one or more decode map entries, then we go with the larger of the two numbers. 
  //This isn't perfectly idiot-proof, but prevents the kind of undefined behavior we want to avoid:
  //if( fNAPVs_U != fNstripsU/fN_APV25_CHAN ){
  fNAPVs_U = std::max( fNAPVs_U, fNstripsU/fN_APV25_CHAN );
    //}
  fNAPVs_V = std::max( fNAPVs_V, fNstripsV/fN_APV25_CHAN );


  //resize vectors that hold APV-card specific parameters:
  // fUgain.resize( fNAPVs_U );
  // fVgain.resize( fNAPVs_V );
  // fCommonModeMeanU.resize( fNAPVs_U );
  // fCommonModeMeanV.resize( fNAPVs_V );
  // fCommonModeRMSU.resize( fNAPVs_U );
  // fCommonModeRMSV.resize( fNAPVs_V );
  
  std::cout << fName << " mapped to " << nentry << " APV25 chips, module gain = " << fModuleGain << std::endl;
  
  //Geometry info is required to be present in the database for each module:
  Int_t err = ReadGeometry( file, date, true );
  if( err ) {
    fclose(file);
    return err;
  }

  //Initialize all pedestals to zero, RMS values to default:
  fPedestalU.clear();
  fPedestalU.resize( fNstripsU ); 

  fPedRMSU.clear();
  fPedRMSU.resize( fNstripsU );
  
  // std::cout << "got " << rawpedu.size() << " u pedestal mean values and " << rawrmsu.size() << " u pedestal rms values" << std::endl;
  // std::cout << "got " << rawpedv.size() << " v pedestal mean values and " << rawrmsv.size() << " v pedestal rms values" << std::endl;

  // for( int i=0; i<rawpedu.size(); i++ ){
  //   cout << i << ", " << rawpedu[i] << endl;
  // }
  
  for ( UInt_t istrip=0; istrip<fNstripsU; istrip++ ){
    fPedestalU[istrip] = 0.0;
    fPedRMSU[istrip] = 10.0; //placeholder to be replaced by value from database
    
    if( rawpedu.size() == fNstripsU ){
      fPedestalU[istrip] = rawpedu[istrip];
    }else if( rawpedu.size() == fNstripsU/128 ){
      fPedestalU[istrip] = rawpedu[istrip/128];
    }else if(!rawpedu.empty()){
      fPedestalU[istrip] = rawpedu[0];
    }

    if( rawrmsu.size() == fNstripsU ){
      fPedRMSU[istrip] = rawrmsu[istrip];
    }else if( rawrmsu.size() == fNstripsU/128 ){
      fPedRMSU[istrip] = rawrmsu[istrip/128];
    }else if(!rawrmsu.empty()){
      fPedRMSU[istrip] = rawrmsu[0];
    }
 
  }

  //Initialize all pedestals to zero, RMS values to default:
  fPedestalV.clear();
  fPedestalV.resize( fNstripsV ); 

  fPedRMSV.clear();
  fPedRMSV.resize( fNstripsV );
  
  for( UInt_t istrip=0; istrip<fNstripsV; istrip++ ){
    fPedestalV[istrip] = 0.0;
    fPedRMSV[istrip] = 10.0;

    if( rawpedv.size() == fNstripsV ){
      fPedestalV[istrip] = rawpedv[istrip];
    }else if( rawpedv.size() == fNstripsV/128 ){
      fPedestalV[istrip] = rawpedv[istrip/128];
    }else if(!rawpedv.empty()){
      fPedestalV[istrip] = rawpedv[0];
    }

    if( rawrmsv.size() == fNstripsV ){
      fPedRMSV[istrip] = rawrmsv[istrip];
    }else if( rawrmsv.size() == fNstripsV/128 ){
      fPedRMSV[istrip] = rawrmsv[istrip/128];
    }else if(!rawrmsv.empty()){
      fPedRMSV[istrip] = rawrmsv[0];
    } 
  }


  // //resize all the "decoded strip" arrays to their maximum possible values for this module:
  UInt_t nstripsmax = fNstripsU + fNstripsV;
  
  fStrip.resize( nstripsmax );
  fAxis.resize( nstripsmax );
  fADCsamples.resize( nstripsmax );
  fRawADCsamples.resize( nstripsmax );
  fADCsamples_deconv.resize( nstripsmax );
  //The lines below are problematic and unnecessary
  for( unsigned int istrip=0; istrip<nstripsmax; istrip++ ){
    fADCsamples[istrip].resize( fN_MPD_TIME_SAMP );
    fRawADCsamples[istrip].resize( fN_MPD_TIME_SAMP );
    fADCsamples_deconv[istrip].resize( fN_MPD_TIME_SAMP );
  }
  
  fADCsums.resize( nstripsmax );
  fADCsumsDeconv.resize( nstripsmax );
  fStripADCavg.resize( nstripsmax );
  fStripIsU.resize( nstripsmax );
  fStripIsV.resize( nstripsmax );
  fStripOnTrack.resize( nstripsmax );
  fStripIsNeg.resize( nstripsmax );
  fStripIsNegU.resize( nstripsmax );
  fStripIsNegV.resize( nstripsmax );
  fStripIsNegOnTrack.resize( nstripsmax );
  fStripIsNegOnTrackU.resize( nstripsmax );
  fStripIsNegOnTrackV.resize( nstripsmax );
  fStripRaw.resize( nstripsmax );
  fStripEvent.resize( nstripsmax );
  fStripCrate.resize( nstripsmax );
  fStripMPD.resize( nstripsmax );
  fStripADC_ID.resize( nstripsmax );
  fStripTrackIndex.resize( nstripsmax );
  fKeepStrip.resize( nstripsmax );
  fMaxSamp.resize( nstripsmax );
  fMaxSampDeconv.resize( nstripsmax );
  fMaxSampDeconvCombo.resize( nstripsmax );
  fADCmax.resize( nstripsmax );
  fADCmaxDeconv.resize( nstripsmax );
  fADCmaxDeconvCombo.resize( nstripsmax );
  fTmean.resize( nstripsmax );
  fTmeanDeconv.resize( nstripsmax );
  fTsigma.resize( nstripsmax );
  fStripTdiff.resize( nstripsmax );
  fStripTSchi2.resize( nstripsmax );
  fStripTSprob.resize( nstripsmax );
  fStripCorrCoeff.resize( nstripsmax );
  fStripTfit.resize( nstripsmax );
  fTcorr.resize( nstripsmax );
  //Storing these by individual strip is redundant but convenient:
  fStrip_ENABLE_CM.resize( nstripsmax );
  fStrip_CM_GOOD.resize( nstripsmax );
  fStrip_BUILD_ALL_SAMPLES.resize( nstripsmax );

  fStripUonTrack.resize( nstripsmax );
  fStripVonTrack.resize( nstripsmax );

  fADCsamples1D.resize( nstripsmax * fN_MPD_TIME_SAMP );
  fRawADCsamples1D.resize( nstripsmax * fN_MPD_TIME_SAMP );
  fADCsamplesDeconv1D.resize( nstripsmax * fN_MPD_TIME_SAMP );
 
  
  //default all common-mode mean and RMS values to 0 and 10 respectively if they were
  // NOT loaded from the DB and/or they are loaded with the wrong size:
  if( fCommonModeMeanU.size() != fNAPVs_U ){
    fCommonModeMeanU.resize( fNAPVs_U );
    for( unsigned int iAPV=0; iAPV<fNAPVs_U; iAPV++ ){
      fCommonModeMeanU[iAPV] = 0.0;
    }
  }

  if( fCommonModeRMSU.size() != fNAPVs_U ){
    fCommonModeRMSU.resize( fNAPVs_U );
    for( unsigned int iAPV=0; iAPV<fNAPVs_U; iAPV++ ){
      fCommonModeRMSU[iAPV] = 10.0;
    }
  }

  //default all common-mode mean and RMS values to 0 and 10 respectively if they were
  // NOT loaded from the DB and/or they were loaded with the wrong size:
  if( fCommonModeMeanV.size() != fNAPVs_V ){
    fCommonModeMeanV.resize( fNAPVs_V );
    for( unsigned int iAPV=0; iAPV<fNAPVs_V; iAPV++ ){
      fCommonModeMeanV[iAPV] = 0.0;
    }
  }

  if( fCommonModeRMSV.size() != fNAPVs_V ){
    fCommonModeRMSV.resize( fNAPVs_V );
    for( unsigned int iAPV=0; iAPV<fNAPVs_V; iAPV++ ){
      fCommonModeRMSV[iAPV] = 10.0;
    }
  }

  // Initialize default "CM correction bias" values to zero if they were not loaded from the DB:
  if( fCMbiasU.size() != fNAPVs_U ){
    fCMbiasU.resize( fNAPVs_U );
    for( unsigned int iAPV=0; iAPV<fNAPVs_U; iAPV++ ){
      fCMbiasU[iAPV] = 0.0;
    }
  }

  if( fCMbiasV.size() != fNAPVs_V ){
    fCMbiasV.resize( fNAPVs_V );
    for( unsigned int iAPV=0; iAPV<fNAPVs_V; iAPV++ ){
      fCMbiasV[iAPV] = 0.0;
    }
  }
  
  //default all gains to 1 if they were not loaded from the DB and/or if they were loaded with the 
  //wrong size: 
  if( fUgain.size() != fNAPVs_U ){
    fUgain.resize(fNAPVs_U);
    for( unsigned int iAPV=0; iAPV<fNAPVs_U; iAPV++ ){
      fUgain[iAPV] = 1.0;
    }
  }

  //Multiply in Module gain:
  for( unsigned int iAPV=0; iAPV<fNAPVs_U; iAPV++ ){
    fUgain[iAPV] *= fModuleGain;
  }
  

  if( fVgain.size() != fNAPVs_V ){
    fVgain.resize(fNAPVs_V);
    for( unsigned int iAPV=0; iAPV<fNAPVs_V; iAPV++ ){
      fVgain[iAPV] = 1.0;
    }
  }

  for( unsigned int iAPV=0; iAPV<fNAPVs_V; iAPV++ ){
    fVgain[iAPV] *= fModuleGain;
  }

  if( fPedestalMode ){
    fZeroSuppress = false;
    fOnlineZeroSuppression = false;
    //fPedSubFlag = 0;
  }

  //Add parsing of timing cut arguments now:

  //All timing cut arguments have default values so we can parse them individually:
  if( t0_temp.size() > 0 ){
    if( t0_temp.size() == 1 ){
      fStripMaxTcut_central[0] = fStripMaxTcut_central[1] = t0_temp[0];
    } else if( t0_temp.size() == 2 ){
      for( int axis=0; axis<2; axis++ ){
	fStripMaxTcut_central[axis] = t0_temp[axis];
      }
    } else {
      Error(Here("ReadDatabase"), "Incorrect number of values for max strip tcut center (must be 1 or 2). Fix database");
      return kInitError;
    }
  }

  if( tcut_temp.size() > 0 ){
    if( tcut_temp.size() == 1 ){
      fStripMaxTcut_width[0] = fStripMaxTcut_width[1] = tcut_temp[0];
    } else if( tcut_temp.size() == 2 ){
      for( int axis=0; axis<2; axis++ ){
	fStripMaxTcut_width[axis] = tcut_temp[axis];
      }
    } else {
      Error(Here("ReadDatabase"), "Incorrect number of values for max strip tcut width (must be 1 or 2). Fix database");
      return kInitError;
    }
  }

  if( tsigma_temp.size() > 0 ){
    if( tsigma_temp.size() == 1 ){
      fStripMaxTcut_sigma[0] = fStripMaxTcut_sigma[1] = tsigma_temp[0];
    } else if( tsigma_temp.size() == 2 ){
      for( int axis=0; axis<2; axis++ ){
	fStripMaxTcut_sigma[axis] = tsigma_temp[axis];
      }
    } else {
      Error(Here("ReadDatabase"), "Incorrect number of values for max strip tcut sigma (must be 1 or 2). Fix database");
      return kInitError;
    }
  }
  

  //Deconvoluted strip time cuts:
  //All timing cut arguments have default values so we can parse them individually:
  if( t0_deconv_temp.size() > 0 ){
    if( t0_deconv_temp.size() == 1 ){
      fStripMaxTcut_central_deconv[0] = fStripMaxTcut_central_deconv[1] = t0_deconv_temp[0];
    } else if( t0_deconv_temp.size() == 2 ){
      for( int axis=0; axis<2; axis++ ){
	fStripMaxTcut_central_deconv[axis] = t0_deconv_temp[axis];
      }
    } else {
      Error(Here("ReadDatabase"), "Incorrect number of values for max strip tcut center deconv (must be 1 or 2). Fix database");
      return kInitError;
    }
  }

  if( tcut_deconv_temp.size() > 0 ){
    if( tcut_deconv_temp.size() == 1 ){
      fStripMaxTcut_width_deconv[0] = fStripMaxTcut_width_deconv[1] = tcut_deconv_temp[0];
    } else if( tcut_deconv_temp.size() == 2 ){
      for( int axis=0; axis<2; axis++ ){
	fStripMaxTcut_width_deconv[axis] = tcut_deconv_temp[axis];
      }
    } else {
      Error(Here("ReadDatabase"), "Incorrect number of values for max strip tcut width (must be 1 or 2). Fix database");
      return kInitError;
    }
  }

  if( tsigma_deconv_temp.size() > 0 ){
    if( tsigma_deconv_temp.size() == 1 ){
      fStripMaxTcut_sigma_deconv[0] = fStripMaxTcut_sigma_deconv[1] = tsigma_deconv_temp[0];
    } else if( tsigma_deconv_temp.size() == 2 ){
      for( int axis=0; axis<2; axis++ ){
	fStripMaxTcut_sigma_deconv[axis] = tsigma_deconv_temp[axis];
      }
    } else {
      Error(Here("ReadDatabase"), "Incorrect number of values for max strip tcut center (must be 1 or 2). Fix database");
      return kInitError;
    }
  }
  
  //Fit strip time cuts:
  //All timing cut arguments have default values so we can parse them individually:
  if( t0_fit_temp.size() > 0 ){
    if( t0_fit_temp.size() == 1 ){
      fStripMaxTcut_central_fit[0] = fStripMaxTcut_central_fit[1] = t0_fit_temp[0];
    } else if( t0_fit_temp.size() == 2 ){
      for( int axis=0; axis<2; axis++ ){
	fStripMaxTcut_central_fit[axis] = t0_fit_temp[axis];
      }
    } else {
      Error(Here("ReadDatabase"), "Incorrect number of values for max strip tcut fit center (must be 1 or 2). Fix database");
      return kInitError;
    }
  }

  if( tcut_fit_temp.size() > 0 ){
    if( tcut_fit_temp.size() == 1 ){
      fStripMaxTcut_width_fit[0] = fStripMaxTcut_width_fit[1] = tcut_fit_temp[0];
    } else if( tcut_fit_temp.size() == 2 ){
      for( int axis=0; axis<2; axis++ ){
	fStripMaxTcut_width_fit[axis] = tcut_fit_temp[axis];
      }
    } else {
      Error(Here("ReadDatabase"), "Incorrect number of values for max strip tcut width (must be 1 or 2). Fix database");
      return kInitError;
    }
  }

  if( tsigma_fit_temp.size() > 0 ){
    if( tsigma_fit_temp.size() == 1 ){
      fStripMaxTcut_sigma_fit[0] = fStripMaxTcut_sigma_fit[1] = tsigma_fit_temp[0];
    } else if( tsigma_fit_temp.size() == 2 ){
      for( int axis=0; axis<2; axis++ ){
	fStripMaxTcut_sigma_fit[axis] = tsigma_fit_temp[axis];
      }
    } else {
      Error(Here("ReadDatabase"), "Incorrect number of values for max strip tcut center (must be 1 or 2). Fix database");
      return kInitError;
    }
  }

  //Parsing hit time mean and sigma: standard
  
  if( t0hit_temp.size() != 0 ){
    if( t0hit_temp.size() == 1 ){
      fHitTimeMean[1] = fHitTimeMean[0] = t0hit_temp[0];
    } else if( t0hit_temp.size() == 2 ){
      for( int axis=0; axis<2; axis++ ){
	fHitTimeMean[axis] = t0hit_temp[axis];
      }
    } else {
      Error(Here("ReadDatabase"), "Incorrect number of values for hit time mean (must be 1 or 2). Fix database");
      return kInitError;
    }
  }


  if( tsigmahit_temp.size() != 0 ){
    if( tsigmahit_temp.size() == 1 ){
      fHitTimeSigma[1] = fHitTimeSigma[0] = tsigmahit_temp[0];
    } else if( tsigmahit_temp.size() == 2 ){
      for( int axis=0; axis<2; axis++ ){
	fHitTimeSigma[axis] = tsigmahit_temp[axis];
      }
    } else {
      Error(Here("ReadDatabase"), "Incorrect number of values for hit time sigma (must be 1 or 2). Fix database");
      return kInitError;
    }
  }

  //Parsing hit time mean and sigma: deconvoluted:
  
  if( t0hit_deconv_temp.size() != 0 ){
    if( t0hit_deconv_temp.size() == 1 ){
      fHitTimeMeanDeconv[1] = fHitTimeMeanDeconv[0] = t0hit_deconv_temp[0];
    } else if( t0hit_deconv_temp.size() == 2 ){
      for( int axis=0; axis<2; axis++ ){
	fHitTimeMeanDeconv[axis] = t0hit_deconv_temp[axis];
      }
    } else {
      Error(Here("ReadDatabase"), "Incorrect number of values for hit time mean (must be 1 or 2). Fix database");
      return kInitError;
    }
  }


  if( tsigmahit_deconv_temp.size() != 0 ){
    if( tsigmahit_deconv_temp.size() == 1 ){
      fHitTimeSigmaDeconv[1] = fHitTimeSigmaDeconv[0] = tsigmahit_deconv_temp[0];
    } else if( tsigmahit_deconv_temp.size() == 2 ){
      for( int axis=0; axis<2; axis++ ){
	fHitTimeSigmaDeconv[axis] = tsigmahit_deconv_temp[axis];
      }
    } else {
      Error(Here("ReadDatabase"), "Incorrect number of values for hit time sigma (must be 1 or 2). Fix database");
      return kInitError;
    }
  }

  //cluster time mean and sigma parsing: fit times

  if( t0hit_fit_temp.size() != 0 ){
    if( t0hit_fit_temp.size() == 1 ){
      fHitTimeMeanFit[1] = fHitTimeMeanFit[0] = t0hit_fit_temp[0];
    } else if( t0hit_fit_temp.size() == 2 ){
      for( int axis=0; axis<2; axis++ ){
	fHitTimeMeanFit[axis] = t0hit_fit_temp[axis];
      }
    } else {
      Error(Here("ReadDatabase"), "Incorrect number of values for hit time mean (must be 1 or 2). Fix database");
      return kInitError;
    }
  }

  if( tsigmahit_fit_temp.size() != 0 ){
    if( tsigmahit_fit_temp.size() == 1 ){
      fHitTimeSigmaFit[1] = fHitTimeSigmaFit[0] = tsigmahit_fit_temp[0];
    } else if( tsigmahit_fit_temp.size() == 2 ){
      for( int axis=0; axis<2; axis++ ){
	fHitTimeSigmaFit[axis] = tsigmahit_fit_temp[axis];
      }
    } else {
      Error(Here("ReadDatabase"), "Incorrect number of values for hit time sigma (must be 1 or 2). Fix database");
      return kInitError;
    }
  }
  
  // for( UInt_t i = 0; i < rawped.size(); i++ ){
  //   if( (i % 2) == 1 ) continue;
  //   int idx = (int) rawped[i];
	
  //   if( idx < N_APV25_CHAN*nentry ){
  //     fPedestal[idx] = rawped[i+1];
  //   } else {
		
  //     std::cout << "[SBSGEMModule::ReadDatabase]  WARNING: " << " strip " << idx  << " listed but not enough strips in cratemap" << std::endl;
  //   }
  // }

  // for( UInt_t i = 0; i < rawrms.size(); i++ ){
  //   if( (i % 2) == 1 ) continue;
  //   int idx = (int) rawrms[i];
  //   if( idx < N_APV25_CHAN*nentry ){
  //     fRMS[idx] = rawrms[i+1];
  //   } else {
  //     std::cout << "[SBSGEMModule::ReadDatabase]  WARNING: " << " strip " << idx  << " listed but not enough strips in cratemap" << std::endl;
  //   }
  // }

  fclose(file);
  
  return 0;
}

Int_t SBSGEMModule::ReadGeometry( FILE *file, const TDatime &date, Bool_t required ){ //We start with a copy of THaDetectorBase::ReadGeometry and modify accordingly:
  // Read this detector's basic geometry information from the database.
  // Derived classes may override to read more advanced data.

  const char* const here = "ReadGeometry";

  vector<double> position, size, angles;
  Bool_t optional = !required;
  DBRequest request[] = {
    { "position", &position, kDoubleV, 0, optional, 0,
      "\"position\" (detector position [m])" },
    { "size",     &size,     kDoubleV, 0, optional, 1,
      "\"size\" (detector size [m])" },
    { "angle",    &angles,   kDoubleV, 0, true, 0,
      "\"angle\" (detector angles(s) [deg]" },
    { nullptr }
  };
  Int_t err = LoadDB( file, date, request );
  if( err )
    return kInitError;

  if( !position.empty() ) {
    if( position.size() != 3 ) {
      Error( Here(here), "Incorrect number of values = %u for "
	     "detector position. Must be exactly 3. Fix database.",
	     static_cast<unsigned int>(position.size()) );
      return 1;
    }
    fOrigin.SetXYZ( position[0], position[1], position[2] );
  }
  else
    fOrigin.SetXYZ(0,0,0);

  if( !size.empty() ) {
    if( size.size() != 3 ) {
      Error( Here(here), "Incorrect number of values = %u for "
	     "detector size. Must be exactly 3. Fix database.",
	     static_cast<unsigned int>(size.size()) );
      return 2;
    }
    if( size[0] == 0 || size[1] == 0 || size[2] == 0 ) {
      Error( Here(here), "Illegal zero detector dimension. Fix database." );
      return 3;
    }
    if( size[0] < 0 || size[1] < 0 || size[2] < 0 ) {
      Warning( Here(here), "Illegal negative value for detector dimension. "
	       "Taking absolute. Check database." );
    }
    fSize[0] = 0.5 * TMath::Abs(size[0]);
    fSize[1] = 0.5 * TMath::Abs(size[1]);
    fSize[2] = TMath::Abs(size[2]);
  }
  else
    fSize[0] = fSize[1] = fSize[2] = kBig;

  if( !angles.empty() ) {
    if( angles.size() != 1 && angles.size() != 3 ) {
      Error( Here(here), "Incorrect number of values = %u for "
	     "detector angle(s). Must be either 1 or 3. Fix database.",
	     static_cast<unsigned int>(angles.size()) );
      return 4;
    }
    // If one angle is given, it indicates a rotation about y, as before.
    // If three angles are given, they are interpreted as rotations about the X, Y, and Z axes, respectively:
    // 
    if( angles.size() == 1 ) {
      DefineAxes( angles[0] * TMath::DegToRad() );
    }
    else {
      TRotation RotTemp;

      // So let's review how to define the detector axes correctly.

      // THaDetectorBase::DetToTrackCoord(TVector3 p) returns returns p.X * fXax() + p.Y * fYax() + p.Z * fZax() + fOrigin
      // In the standalone code, we do Rot * (p) + fOrigin (essentially):
      // So in matrix form, when we do TRotation::RotateX(alpha), we get:

      // RotTemp * Point =  |  1    0            0         |    |  p.X()  |
      //                    |  0   cos(alpha) -sin(alpha)  | *  |  p.Y()  |
      //                    |  0   sin(alpha)  cos(alpha)  |    |  p.Z()  |
      // 
      // This definition ***appears**** to be consistent with the "sense" of the rotation as applied by the standalone code.
      // The detector axes are defined as the columns of the rotation matrix. We will have to test that it is working correctly, however:
      
      RotTemp.RotateX( angles[0] * TMath::DegToRad() );
      RotTemp.RotateY( angles[1] * TMath::DegToRad() );
      RotTemp.RotateZ( angles[2] * TMath::DegToRad() );
      
      fXax.SetXYZ( RotTemp.XX(), RotTemp.YX(), RotTemp.ZX() );
      fYax.SetXYZ( RotTemp.XY(), RotTemp.YY(), RotTemp.ZY() );
      fZax.SetXYZ( RotTemp.XZ(), RotTemp.YZ(), RotTemp.ZZ() );
    }
  } else
    DefineAxes(0);

  return 0;
}

    
Int_t SBSGEMModule::DefineVariables( EMode mode ) {
  if( mode == kDefine and fIsSetup ) return kOK;
  fIsSetup = ( mode == kDefine );

  //Int_t nstripsmax = fNstripsU + fNstripsV;
  
  
  VarDef varstrip[] = {
    { "strip.nstripsfired", "Number of strips fired", kUInt, 0, &fNstrips_hit_pos },
    { "strip.nstripsfired_neg", "Number of strips fired negative", kUInt, 0, &fNstrips_hit_neg },
    { "strip.nstrips_keep", "Number of fired strips passing basic timing cuts", kUInt, 0, &fNstrips_keep },
    { "strip.nstrips_keepU", "Number of U/X strips passing basic timing cuts", kUInt, 0, &fNstrips_keepU },
    { "strip.nstrips_keepV", "Number of V/Y strips passing basic timing cuts", kUInt, 0, &fNstrips_keepV },
    { "strip.nstrips_keep_lmax", "Number of strips passing local max thresholds and basic timing cuts", kUInt, 0, &fNstrips_keep_lmax },
    { "strip.nstrips_keep_lmaxU", "Number of U/X strips passing local max thresholds and basic timing cuts", kUInt, 0, &fNstrips_keep_lmaxU },
    { "strip.nstrips_keep_lmaxV", "Number of V/Y strips passing local max thresholds and basic timing cuts", kUInt, 0, &fNstrips_keep_lmaxV },
    { "strip.crate", "strip crate number", kUInt, 0, &(fStripCrate[0]), &fNstrips_hit },
    { "strip.mpd", "strip mpd number", kUInt, 0, &(fStripMPD[0]), &fNstrips_hit },
    { "strip.adc_id", "strip adc channel number", kUInt, 0, &(fStripADC_ID[0]), &fNstrips_hit },
    { "strip.istrip", "strip index", kUInt, 0, &(fStrip[0]), &fNstrips_hit },
    { "strip.IsU", "U strip?", kUInt, 0, &(fStripIsU[0]), &fNstrips_hit },
    { "strip.IsV", "V strip?", kUInt, 0, &(fStripIsV[0]), &fNstrips_hit },
    { "strip.ADCsamples", "ADC samples (index = isamp+Nsamples*istrip)", kDouble, 0, &(fADCsamples1D[0]), &fNdecoded_ADCsamples },
    { "strip.rawADCsamples", "raw ADC samples (no baseline subtraction)", kInt, 0, &(fRawADCsamples1D[0]), &fNdecoded_ADCsamples },
    { "strip.DeconvADCsamples", "Deconvoluted ADC samples (index = isamp+Nsamples*istrip)", kDouble, 0, &(fADCsamplesDeconv1D[0]), &fNdecoded_ADCsamples },
    { "strip.ADCsum", "Sum of ADC samples on a strip", kDouble, 0, &(fADCsums[0]), &fNstrips_hit },
    { "strip.DeconvADCsum", "Sum of deconvoluted ADC samples on a strip", kDouble, 0, &(fADCsumsDeconv[0]), &fNstrips_hit },
    { "strip.isampmax", "sample in which max ADC occurred on a strip", kUInt, 0, &(fMaxSamp[0]), &fNstrips_hit },
    { "strip.isampmaxDeconv", "sample in which max deconvoluted ADC occurred", kUInt, 0, &(fMaxSampDeconv[0]), &fNstrips_hit },
    { "strip.isampmaxDeconvCombo", "first of max. pair of deconvoluted samples", kUInt, 0, &(fMaxSampDeconvCombo[0]), &fNstrips_hit },
    { "strip.ADCmax", "Value of max ADC sample on a strip", kDouble, 0, &(fADCmax[0]), &fNstrips_hit },
    { "strip.DeconvADCmax", "Value of max deconvoluted ADC sample", kDouble, 0, &(fADCmaxDeconv[0]), &fNstrips_hit },
    { "strip.DeconvADCmaxCombo", "max sum of two adjacent deconv. samples", kDouble, 0, &(fADCmaxDeconvCombo[0]), &fNstrips_hit },
    { "strip.Tmean", "ADC-weighted mean strip time", kDouble, 0, &(fTmean[0]), &fNstrips_hit },
    { "strip.Tsigma", "ADC-weighted rms strip time", kDouble, 0, &(fTsigma[0]), &fNstrips_hit },
    { "strip.TmeanDeconv", "ADC-weighted mean deconvoluted strip time", kDouble, 0, &(fTmeanDeconv[0]), &fNstrips_hit },
    { "strip.Tcorr", "Corrected strip time", kDouble, 0, &(fTcorr[0]), &fNstrips_hit },
    { "strip.Tfit", "Fitted strip time", kDouble, 0, &(fStripTfit[0]), &fNstrips_hit },
    { "strip.Tdiff", "time diff. wrt max strip in cluster (or perhaps cluster tmean)", kDouble, 0, &(fStripTdiff[0]), &fNstrips_hit },
    { "strip.TSchi2", "chi2 of strip pulse shape (time samples) wrt average good strip pulse shape", kDouble, 0, &(fStripTSchi2[0]), &fNstrips_hit },
    { "strip.TSprob", "p-Value wrt average good strip pulse shape", kDouble, 0, &(fStripTSprob[0]), &fNstrips_hit },
    { "strip.CorrCoeff", "Correlation coefficient of strip wrt max strip on cluster (or perhaps cluster tmean)", kDouble, 0, &(fStripCorrCoeff[0]), &fNstrips_hit },
    { "strip.itrack", "Index of track containing this strip (-1 if not on any track)", kInt, 0, &(fStripTrackIndex[0]), &fNstrips_hit },
    { "strip.ontrack", "Is this strip on any track (0/1)?", kUInt, 0, &(fStripOnTrack[0]), &fNstrips_hit },
    { "strip.isnegative", "Is this strip passing negative zero suppression?", kUInt, 0, &(fStripIsNeg[0]), &fNstrips_hit },
    { "strip.isnegativeU", "Is this strip passing negative zero suppression on U axis?", kUInt, 0, &(fStripIsNegU[0]), &fNstrips_hit },
    { "strip.isnegativeV", "Is this strip passing negative zero suppression on V axis?", kUInt, 0, &(fStripIsNegV[0]), &fNstrips_hit },
    { "strip.isnegontrack", "Is this strip passing negative zero suppression on a track?", kUInt, 0, &(fStripIsNegOnTrack[0]), &fNstrips_hit },
    { "strip.isnegontrackU", "Is this strip passing negative zero suppression on a track on U axis?", kUInt, 0, &(fStripIsNegOnTrackU[0]), &fNstrips_hit },
    { "strip.isnegontrackV", "Is this strip passing negative zero suppression on a track on V axis?", kUInt, 0, &(fStripIsNegOnTrackV[0]), &fNstrips_hit },
    { "strip.ADCavg", "average of ADC samples on a strip", kDouble, 0, &(fStripADCavg[0]), &fNstrips_hit },
    { "strip.ENABLE_CM", "online common-mode enabled?", kUInt, 0, &(fStrip_ENABLE_CM[0]), &fNstrips_hit },
    { "strip.CM_GOOD", "common-mode out of range? (online failed)", kUInt, 0, &(fStrip_CM_GOOD[0]), &fNstrips_hit },
    { "strip.BUILD_ALL_SAMPLES", "online or offline zero suppression", kUInt, 0, &(fStrip_BUILD_ALL_SAMPLES[0]), &fNstrips_hit },
    { "strip.ontrackU", "U strip on track", kUInt, 0, &(fStripUonTrack[0]), &fNstrips_hit },
    { "strip.ontrackV", "V strip on track", kUInt, 0, &(fStripVonTrack[0]), &fNstrips_hit },
    { nullptr },
  };
  
  // //Raw strip info:
  // RVarDef varstrip[] = {
  //   { "nstripsfired",   "Number of strips fired",   "fNstrips_hit" },
  //   { "strip", "Strip index", "fStrip" },
  //   { "stripIsU", "U strip?", "fStripIsU"},
  //   { "stripIsV", "V strip?", "fStripIsV"},
  //   { "stripADCsamples", "ADC samples (index = isamp+Nsamples*istrip)", "fADCsamples1D" },
  //   { "striprawADCsamples", "raw ADC samples (no baseline subtraction)", "fRawADCsamples1D" },
  //   { "stripADCsum", "Sum of ADC samples on a strip", "fADCsums" },
  //   { "stripisampmax", "sample in which max ADC occurred on a strip", "fMaxSamp" },
  //   { "stripADCmax", "Value of max ADC sample on a strip", "fADCmax" },
  //   { "stripTmean", "ADC-weighted mean strip time", "fTmean" },
  //   { "stripTsigma", "ADC-weighted rms strip time", "fTsigma" },
  //   { "stripTcorr", "Corrected strip time", "fTcorr" },
  //   { "stripItrack", "Index of track containing this strip (-1 if not on any track)", "fStripTrackIndex" },
  //   { "stripADCavg", "average of ADC samples on a strip", "fStripADCavg" },
  //   { nullptr },
  // };


  Int_t ret = DefineVarsFromList( varstrip, mode );

  if( ret != kOK )
    return ret;

  //Note: for both 1D clusters and 2D hits,
  //we should add some of the new variables relating to deconvolution in these arrays, but
  //that should take a lower priority than the ones in SBSGEMSpectrometerTracker relating to hits that
  //end up on good tracks

  RVarDef varclust[] = {
    { "clust.nclustu",   "Number of clusters in u",   "fNclustU_pos" },
    { "clust.nclustu_neg",   "Number of clusters in u that are negative",   "fNclustU_neg" },
    { "clust.nclustu_tot", "Total number of U clusters found in total active area", "fNclustU_total" },
    { "clust.clustu_strips",   "u clusters strip multiplicity",   "fUclusters.nstrips" },
    { "clust.clustu_pos",   "u clusters position",   "fUclusters.hitpos_mean" },
    { "clust.clustu_adc",   "u clusters adc sum",   "fUclusters.clusterADCsum" },
    { "clust.clustu_time",   "u clusters time",   "fUclusters.t_mean" },
    { "clust.nclustv",   "Number of clusters in v",   "fNclustV_pos" },
    { "clust.nclustv_neg",   "Number of clusters in v that are negative",   "fNclustV_neg" },
    { "clust.nclustv_tot", "Total number of V clusters found in total active area", "fNclustV_total" },
    { "clust.clustv_strips",   "v clusters strip multiplicity",   "fVclusters.nstrips" },
    { "clust.clustv_pos",   "v clusters position",   "fVclusters.hitpos_mean" },
    { "clust.clustv_adc",   "v clusters adc sum",   "fVclusters.clusterADCsum" },
    { "clust.clustv_time",   "v clusters time",   "fVclusters.t_mean" },
    { "clust.isnegativeU",   "Is cluster negative?",   "fUclusters.isneg" },
    { "clust.isnegativeV",   "Is cluster negative?",   "fVclusters.isneg" },
    { "clust.isnegontrackU",   "Is cluster negative and on a track?",   "fUclusters.isnegontrack" },
    { "clust.isnegontrackV",   "Is cluster negative and on a track?",   "fVclusters.isnegontrack" },
    { nullptr },
  };

  ret = DefineVarsFromList( varclust, mode );

  if( ret != kOK )
    return ret;

  RVarDef varhits[] = {
    { "hit.nhits2d",   "Number of 2d hits",   "fN2Dhits" },
    { "hit.hitx",   "local X coordinate of hit",   "fHits.xhit" },
    { "hit.hity",   "local Y coordinate of hit",   "fHits.yhit" },
    { "hit.hitxg",   "transport X coordinate of hit",   "fHits.xghit" },
    { "hit.hityg",   "transport Y coordinate of hit",   "fHits.yghit" },
    { "hit.hitADCasym",   "hit ADC asymmetry (ADCU-ADCV)/2",   "fHits.ADCasym" },
    { "hit.hitADCavg",  "(ADCU+ADCV)/2", "fHits.Ehit" },
    { "hit.hitTdiff",   "hit time difference (u-v)",   "fHits.tdiff" },
    { "hit.hitTavg",   "average time of 2D hit", "fHits.thitcorr" },
    { "hit.hit_iuclust", "index in u cluster array", "fHits.iuclust" },
    { "hit.hit_ivclust", "index in v cluster array", "fHits.ivclust" },
    { "hit.ontrack", "hit is on track", "fHits.ontrack" },
    { nullptr },
  };

  ret = DefineVarsFromList( varhits, mode );

  RVarDef vartiming[] = {
    { "time.T0_by_APV", "Coarse MPD timestamp of first event", "fT0_by_APV" },
    { "time.Tref_coarse", "Reference coarse MPD time stamp for this event", "fTref_coarse" },
    { "time.Tcoarse_by_APV", "Coarse MPD timestamp by APV relative to Tref_coarse", "fTcoarse_by_APV" },
    { "time.Tfine_by_APV", "Fine MPD timestamp by APV", "fTfine_by_APV" },
    { "time.EventCount_by_APV", "MPD event counter by APV (these should all agree in any one event)", "fEventCount_by_APV" },
    { "time.T_ns_by_APV", "Time stamp in ns relative to coarse T_ref", "fTimeStamp_ns_by_APV" },
    { nullptr },
  };

  RVarDef varmisc[] = {
    {"ontrack", "Track passed through this module", "fTrackPassedThrough" },
    {"layer", "Layer number of this module", "fLayer" },
    { nullptr },
  };

  ret = DefineVarsFromList( vartiming, mode );
  ret = DefineVarsFromList( varmisc, mode );
  
  if( ret != kOK )
    return ret;

  return kOK;
    
}

void SBSGEMModule::Clear( Option_t* opt){ //we will want to clear out many more things too
  // Modify this a little bit so we only clear out the "hit counters", not necessarily the
  // arrays themselves, to make the decoding more efficient:

  THaSubDetector::Clear(opt);
  
  fNstrips_hit = 0;
  fNstrips_hitU = 0;
  fNstrips_hitV = 0;
  fNstrips_hitU_neg = 0;
  fNstrips_hitV_neg = 0;
  fNdecoded_ADCsamples = 0;
  fIsDecoded = false;

  fTrackPassedThrough = 0;

  //numbers of strips passing basic zero suppression thresholds and timing cuts:
  fNstrips_keep = 0;
  fNstrips_keepU = 0;
  fNstrips_keepV = 0;
  //numbers of strips passing basic zero suppression thresholds, timing cuts, and higher max. sample and strip sum thresholds for
  // local max:
  fNstrips_keep_lmax = 0;
  fNstrips_keep_lmaxU = 0;
  fNstrips_keep_lmaxV = 0;
  
  
  fNclustU = 0;
  fNclustV = 0;
  fNclustU_pos = 0;
  fNclustV_pos = 0;
  fNclustU_neg = 0;
  fNclustV_neg = 0;
  fNclustU_total = 0;
  fNclustV_total = 0;
  //later we may need to check whether this is a performance bottleneck:
  fUclusters.clear();
  fVclusters.clear();
  fN2Dhits = 0;
  //similar here:
  fHits.clear();

  fTrigTime = 0.0;
  
  fCM_online.assign(fN_MPD_TIME_SAMP,0.0);
  
  //fStripAxis.clear();
  // fADCsamples1D.clear();
  // fStripTrackIndex.clear();
  // fRawADCsamples1D.clear();

  // fStripIsU.clear();
  // fStripIsV.clear();
  // fStripADCavg.clear();
  
  // fUstripIndex.clear();
  // fVstripIndex.clear();
  // fStrip.clear();
  // fAxis.clear();
  // fADCsamples.clear();
  // fRawADCsamples.clear();
  // fADCsums.clear();
  // fKeepStrip.clear();
  // fMaxSamp.clear();
  // fADCmax.clear();
  // fTmean.clear();
  // fTsigma.clear();
  // fTcorr.clear();

  //THaSubDetector::Clear(opt);
}

Int_t   SBSGEMModule::Decode( const THaEvData& evdata ){
  //std::cout << "[SBSGEMModule::Decode " << fName << "]" << std::endl;
  
  //initialize generic "strip" counter to zero:
  fNstrips_hit = 0;
  fNstrips_hit_neg = 0;
  fNstrips_hit_pos = 0;
  //initialize "U" and "V" strip counters to zero:
  fNstrips_hitU = 0;
  fNstrips_hitV = 0;
  fNstrips_hitU_neg = 0;
  fNstrips_hitV_neg = 0;
  
  //UInt_t MAXNSAMP_PER_APV = fN_APV25_CHAN * fN_MPD_TIME_SAMP;

  //std::cout << "MAXNSAMP_PER_APV = " << MAXNSAMP_PER_APV << std::endl;

  //we could save some time on these allocations by making these data members of SBSGEMModule: these are probably expensive:

  //to avoid rewriting the other code below, declare references to the fixed-size arrays:
  vector<UInt_t> &Strip = fStripAPV;
  vector<UInt_t> &rawStrip = fRawStripAPV;
  vector<Int_t> &rawADC = fRawADC_APV;
  vector<Double_t> &pedsubADC = fPedSubADC_APV; //ped-subtracted, not necessarily common-mode subtracted
  vector<Double_t> &commonModeSubtractedADC = fCommonModeSubtractedADC_APV;

  
  
  
  //Now, how are we going to implement any kind of common-mode "sag" correction?
  // 1. It has to be optional
  // 2. It will probably require some new optional user-adjustable database parameters to control the behavior.
  // 3. We will want to keep track of the mean of the "sorting-method" common-mode calculation for the full-readout events; specifically a
  //    rolling average over the previous, say, 100 full readout events? Then the error of this calculation will be the RMS over 10.
  //    we can make the size of the "look-back" window user-adjustable. For a trigger rate of 3 kHz, 10,000 /100 = 100 = ~3 s of data taking
  // 4. For online zero-suppressed events, we want to check if the calculated common-mode is less than some number of standard deviations below the common-mode rolling mean, and if there is a sufficient number of strips with raw ADC within +/- some number of standard deviations of the rolling common-mode mean, then we re-calculate the common-mode and correct the ADC values accordingly before we pass them to the cluster-finding routines.
  
  //Do we need to loop on all APV cards? maybe not,
  int apvcounter=0;

  bool firstevcnt = true;
  UInt_t FirstEvCnt = 0;
  
  for (std::vector<mpdmap_t>::iterator it = fMPDmap.begin() ; it != fMPDmap.end(); ++it){
    //loop over all decode map entries associated with this module (each decode map entry is one APV card)
    Int_t effChan = it->mpd_id << 4 | it->adc_id; //left-shift mpd id by 4 bits and take the bitwise OR with ADC_id to uniquely identify the APV card.
    //mpd_id is not necessarily equal to slot, but that seems to be the convention in many cases
    // Find channel for this crate/slot
    
    // TO-DO: rewrite this "time stamp" part of the code more efficiently, by somehow pulling it outside the loop over APVs, since the time stamp is
    // really per-MPD, not per-APV. This is unnecessarily repeated analysis for up to 16 times per MPD.
    // Note that we don't use the information in the analysis in any way so far.
    // on the other hand, the decode map is organized by APV card, so it is difficult to imagine how we would restructure this part of the code
    // since otherwise we don't know which crate/slot to look in.
    // First get time stamp info:
    UInt_t nhits_timestamp_low = evdata.GetNumHits( it->crate, it->slot, fChan_TimeStamp_low );
    UInt_t nhits_timestamp_high = evdata.GetNumHits( it->crate, it->slot, fChan_TimeStamp_high );
    UInt_t nhits_event_count = evdata.GetNumHits( it->crate, it->slot, fChan_MPD_EventCount );

    //std::cout << "nhits_timestamp_low = " << nhits_timestamp_low << std::endl;
    
    if( nhits_timestamp_low > 0 && nhits_timestamp_high == nhits_timestamp_low && nhits_event_count == nhits_timestamp_low ){
      for( unsigned int ihit=0; ihit<nhits_timestamp_low; ihit++ ){
	unsigned int fiber = evdata.GetRawData( it->crate, it->slot, fChan_TimeStamp_low, ihit );
	if( fiber == it->mpd_id ){ //this is the channel we want: 
	  UInt_t Tlow = evdata.GetData( it->crate, it->slot, fChan_TimeStamp_low, ihit );
	  UInt_t Thigh = evdata.GetData( it->crate, it->slot, fChan_TimeStamp_high, ihit );
	  UInt_t EvCnt = evdata.GetData( it->crate, it->slot, fChan_MPD_EventCount, ihit );

	  //std::cout << "Tlow, Thigh, EvCnt = " << Tlow << ", " << Thigh << ", " << EvCnt << std::endl;

	  if( firstevcnt ){
	    FirstEvCnt = EvCnt;
	    firstevcnt = false;
	  }
	  
	  fEventCount_by_APV[apvcounter] = EvCnt;
										    
	  // Fine time stamp is in the first 8 bits of Tlow;
	  fTfine_by_APV[apvcounter] = Tlow & 0x000000FF;

	  if( fMakeEventInfoPlots && fEventInfoPlotsInitialized ){
	    hMPD_EventCount_Alignment->Fill( EvCnt - FirstEvCnt );
	    hMPD_EventCount_Alignment_vs_Fiber->Fill( fiber, EvCnt - FirstEvCnt );

	    hMPD_FineTimeStamp_vs_Fiber->Fill( fiber, fTfine_by_APV[apvcounter] * 4.0 );
	  }
	    
	  Long64_t Tcoarse = Thigh << 16 | ( Tlow << 8 );
	  double Tc = double(Tcoarse);
	  
	  if( EvCnt == 0 ) fT0_by_APV[apvcounter] = Tc;

	  //T ref is the coarse time stamp of the reference APV (the first one, in this case)
	  if( apvcounter == 0 ) fTref_coarse = Tc - fT0_by_APV[apvcounter];

	  //This SHOULD make fTcoarse_by_APV the Tcoarse RELATIVE to the
	  // "reference" APV
	  fTcoarse_by_APV[apvcounter] = Tc - fT0_by_APV[apvcounter] - fTref_coarse;

	  //We probably don't want to hard-code 24 ns and 4 ns here for the units of
	  //Tcoarse and Tfine, but this should be fine for initial checkout of decoding:
	  fTimeStamp_ns_by_APV[apvcounter] = 24.0 * fTcoarse_by_APV[apvcounter] + 4.0 * (fTfine_by_APV[apvcounter] % 6);

	  // std::cout << "fiber, apvcounter, EvCnt, Tcoarse, Tfine, time stamp ns = " << fiber << ", " <<  apvcounter << ", "
	  // 	    << fEventCount_by_APV[apvcounter] << ", " 
	  // 	    << Tcoarse << ", " << fTfine_by_APV[apvcounter] << ", "
	  // 	    << fTimeStamp_ns_by_APV[apvcounter] << std::endl;
							   
	  break;
	}	
      }
    }
    
    // Get common-mode flags, if applicable:
    // Default to the values from the database (or the default values):

    Bool_t CM_ENABLED = fCommonModeFlag != 0 && fCommonModeFlag != 1 && !fPedestalMode;
    Bool_t BUILD_ALL_SAMPLES = !fOnlineZeroSuppression;
    Bool_t CM_OUT_OF_RANGE = false;

    //Initialize default values based on the run "DAQ info":
    if(fCODA_BUILD_ALL_SAMPLES != -1){
      BUILD_ALL_SAMPLES = fCODA_BUILD_ALL_SAMPLES;
      fPedSubFlag = (fCODA_BUILD_ALL_SAMPLES == 0);
    }
    if(fCODA_CM_ENABLED != -1) CM_ENABLED = fCODA_CM_ENABLED;
 
    
    UInt_t cm_flags=4*CM_OUT_OF_RANGE + 2*CM_ENABLED + BUILD_ALL_SAMPLES;
    UInt_t nhits_cm_flag=evdata.GetNumHits( it->crate, it->slot, fChan_CM_flags );
    
    //bool cm_flags_found = false;
      
    if( nhits_cm_flag > 0 ){
      
      // If applicable, find the common-mode/zero-suppression settings loaded from the raw data for this APV:
      // In principle in the SSP/VTP event format, there should be exactly one "hit" per APV in this "channel":
      for( unsigned int ihit=0; ihit<nhits_cm_flag; ihit++ ){
        int chan_temp = evdata.GetRawData( it->crate, it->slot, fChan_CM_flags, ihit );
	if( chan_temp == effChan ){ //assume that this is only filled once per MPD per event, and exit the loop when we find this MPD:
	  // std::cout << "Before decoding cm flags, CM_ENABLED, BUILD_ALL_SAMPLES = " << CM_ENABLED << ", "
	  // 	    << BUILD_ALL_SAMPLES << std::endl;
	  cm_flags = evdata.GetData( it->crate, it->slot, fChan_CM_flags, ihit );
	  //cm_flags_found = true;
	  break;
	}
      }
    }

    
    

    //The proper logic of common-mode calculation/subtraction and zero suppression is as follows:
    // 1. If CM_ENABLED is true, we never calculate the common-mode ourselves, it has already been subtracted from the data:
    // 2. If BUILD_ALL_SAMPLES is false, then online zero suppression is enabled. We can, in addition, apply our own higher thresholds if we want:
    // 3. If CM_ENABLED is true, the pedestal has also been subtracted, so we don't subtract it again.
    // 4. If CM_ENABLED is false, we need to subtract the pedestals (maybe) AND calculate and subtract the common-mode:
    // 5. If BUILD_ALL_SAMPLES is false then CM_ENABLED had better be true!
    // 6. If CM_OUT_OF_RANGE is true then BUILD_ALL_SAMPLES must be true and CM_ENABLED
    //    must be false!
    
    CM_OUT_OF_RANGE = cm_flags/4;
    CM_ENABLED = cm_flags/2;
    BUILD_ALL_SAMPLES = cm_flags%2;

    // if( cm_flags_found ){
    //std::cout << "cm flag defaults overridden by raw data, effChan = " << effChan << ", CM_ENABLED = " << CM_ENABLED << ", BUILD_ALL_SAMPLES = " << BUILD_ALL_SAMPLES << std::endl;
    // }
    
    //cout<<BUILD_ALL_SAMPLES<<" "<<CM_ENABLED<<endl;
    //fOnlineZeroSuppression = !BUILD_ALL_SAMPLES;
    if( !BUILD_ALL_SAMPLES && !CM_ENABLED ) { //This should never happen: skip this APV card
      continue;
    }
    if( CM_OUT_OF_RANGE && !BUILD_ALL_SAMPLES ){ // this should also never happen: skip this APV card:
      continue;
    }

    if( CM_OUT_OF_RANGE && CM_ENABLED ){ //force CM_ENABLED to false if CM_OUT_OF_RANGE is true;
      //This should have already been done online:
      CM_ENABLED = false; 
    }

  
    
    //Int_t nchan = evdata.GetNumChan( it->crate, it->slot ); //this could be made faster

    SBSGEM::GEMaxis_t axis = it->axis == 0 ? SBSGEM::kUaxis : SBSGEM::kVaxis; 
    
    //printf("nchan = %d\n", nchan );

    //std::cout << "crate, slot, nchan = " << it->crate << ", " << it->slot << ", " << nchan << std::endl;

    //this is looping on all the 
    //for( Int_t ichan = 0; ichan < nchan; ++ichan ) { //this is looping over all the "channels" (APV cards) in the crate and slot containing this decode map entry/APV card:
    //Int_t chan = evdata.GetNextChan( it->crate, it->slot, ichan ); //"chan" here refers to one APV card 
      //std::cout << it->crate << " " << it->slot << " mpd_id ??? " << it->mpd_id << " " << chan << " " << effChan << std::endl;

      //if( chan != effChan ) continue; // 

    if( fIsMC ) {
      CM_ENABLED = true;
      BUILD_ALL_SAMPLES = false;
    }

    //Let's see if we can actually decode the MPD debug headers:
    UInt_t nhits_MPD_debug = 0;

    //Let's store here in temporary arrays the calculated common-mode values decoded from the MPD debug headers for events with online zero suppression:
    
    UInt_t CMcalc[fN_MPD_TIME_SAMP];
    Int_t CMcalc_signed[fN_MPD_TIME_SAMP];
    
  
    if( CM_ENABLED ){ //try to decode MPD debug headers and see if the results make any sense:
      nhits_MPD_debug = evdata.GetNumHits( it->crate, it->slot, fChan_MPD_Debug );
      
      if( nhits_MPD_debug > 0 ){ //we expect to get three words per APV card:
	UInt_t wcount=0;

	UInt_t MPDdebugwords[3];
	
	for( unsigned int ihit=0; ihit<nhits_MPD_debug; ihit++ ){
	  UInt_t chan_temp = evdata.GetRawData( it->crate, it->slot, fChan_MPD_Debug, ihit );
	  UInt_t word_temp = evdata.GetData( it->crate, it->slot, fChan_MPD_Debug, ihit );
	  if( chan_temp == effChan && wcount < 3 ){
	    MPDdebugwords[wcount++] = word_temp;
	  }
	  if( wcount == 3 ) break; //if we found all 3 MPD debug words for this channel, exit the loop

	}
	if( wcount == 3 ){ //Then let's decode the debug headers:
	  
	  for( unsigned int iw=0; iw<3; iw++ ){
	    CMcalc[2*iw] = ( MPDdebugwords[iw] & 0xFFF ) | ( ( MPDdebugwords[iw] & 0x1000 ) ? 0xFFFFF000 : 0x0 );
	    CMcalc[2*iw+1] = ( (MPDdebugwords[iw]>>13) & 0xFFF ) | ( ( (MPDdebugwords[iw]>>13) & 0x1000 ) ? 0xFFFFF000 : 0x0 );
	    CMcalc_signed[2*iw] = Int_t( CMcalc[2*iw] );
	    CMcalc_signed[2*iw+1] = Int_t( CMcalc[2*iw+1] );

	    fCM_online[2*iw] = double(CMcalc_signed[2*iw]);
	    fCM_online[2*iw+1] = double(CMcalc_signed[2*iw+1]);
	  }

	  //
	  // for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
	  //   std::cout << "MPD debug words for APV in (crate,slot,effChan)=(" << it->crate << ", " << it->slot << ", " << effChan << "): time sample " << isamp
	  // 	      << ", online calculated common-mode = " << CMcalc_signed[isamp] << std::endl;
	  // }
	}
      }
    }//End check if CM_ENABLED
    
    Int_t nsamp = evdata.GetNumHits( it->crate, it->slot, effChan );

   
    if( nsamp > 0 ){

      //      assert(nsamp%fN_MPD_TIME_SAMP==0); //this is making sure that the number of samples is equal to an integer multiple of the number of time samples per strip
      Int_t nstrips = nsamp/fN_MPD_TIME_SAMP; //number of strips fired on this APV card (should be exactly 128 if online zero suppression is NOT used):

      bool fullreadout = !CM_ENABLED && BUILD_ALL_SAMPLES && nstrips == fN_APV25_CHAN;
      // std::cout << "MPD ID, ADC channel, number of strips fired = " << it->mpd_id << ", "
      // 		<< it->adc_id << ", " << nstrips << std::endl;

      double commonMode[fN_MPD_TIME_SAMP];

      double CommonModeCorrection[fN_MPD_TIME_SAMP]; //possible correction to apply, initialize to zero:
      
      for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
	commonMode[isamp] = 0.0;
	CommonModeCorrection[isamp] = 0.0;
      }

      // Let's throw in the towel and always do a first loop over the data, despite a small loss of efficiency,
      // to populate the local arrays; otherwise this code is getting too confusing and bug-prone:
      // First loop over the hits: populate strip, raw strip, raw ADC, ped sub ADC and common-mode-subtracted aDC:
      for( int iraw=0; iraw<nsamp; iraw++ ){ //NOTE: iraw = isamp + fN_MPD_TIME_SAMP * istrip
	int strip = evdata.GetRawData( it->crate, it->slot, effChan, iraw );
	UInt_t decoded_rawADC = evdata.GetData( it->crate, it->slot, effChan, iraw );

	int isamp = iraw%fN_MPD_TIME_SAMP;
	  
	Int_t ADC = Int_t( decoded_rawADC );
	
	rawStrip[iraw] = strip;
	Strip[iraw] = GetStripNumber( strip, it->pos, it->invert );

	rawADC[iraw] = ADC;
	
	double ped = (axis == SBSGEM::kUaxis ) ? fPedestalU[Strip[iraw]] : fPedestalV[Strip[iraw]];

	// If pedestal subtraction was done online, don't do it again:
	// In pedestal mode, the DAQ should NOT have subtracted the pedestals,
	// but even if it did, it shouldn't affect the pedestal analysis to first order whether we subtract the pedestals or not:
	if( fPedSubFlag != 0 && !fPedestalMode && !fIsMC ) ped = 0.0;
	if( CM_ENABLED && !fIsMC ) {
	  ped = 0.0; //If this is true then the pedestal was DEFINITELY always calculated online:
	  //rawADC[iraw] += fCM_online[isamp] (not yet sure if we want to add back the online-CM) ;
	}
	  
	pedsubADC[iraw] = double(ADC) - ped;
	commonModeSubtractedADC[iraw] = double(ADC) - ped; 

	//the calculation of common mode in pedestal mode analysis differs from the
	// offline or online zero suppression analysis; here we use a simple average of all 128 channels:
	if( fPedestalMode ){
	  //do simple common-mode calculation involving the simple average of all 128 (ped-subtracted) ADC
	  //values   
	    
	  if( fSubtractPedBeforeCommonMode ){
	    commonMode[isamp] += pedsubADC[iraw]/double(fN_APV25_CHAN);
	  } else {
	    commonMode[isamp] += rawADC[iraw]/double(fN_APV25_CHAN);
	  }
	}
      }
      
      if( fullreadout ){ //then we need to calculate the common-mode:
	//declare temporary array to hold common mode values for this APV card and, if necessary, calculate them:

	
	//std::cout << "Common-mode calculation: " << std::endl;
	
	if( fMakeCommonModePlots || !fPedestalMode ) { // calculate both ways:

	  //vector<double> CM_danning_online_temp(fN_MPD_TIME_SAMP,0);
	  
	  for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
	    
	    //moved common-mode calculation to its own function:
	    
	    // Now: a question is should we modify the behavior/do added checks if
	    // CM_OUT_OF_RANGE is set? 
	  
	    if( fMakeCommonModePlots ){
	      //double cm_danning = GetCommonMode( isamp, 1, *it );
	      //experimental: Test histogramming method:
	      double cm_danning = GetCommonMode( isamp, 1, *it );
	      double cm_histo= GetCommonMode( isamp, 2, *it );
	      //if( !CM_OUT_OF_RANGE ) { // this is a hack so I only get debug printouts for good (full readout) events
	      //cm_histo = GetCommonMode( isamp, 2, *it );
	      // }	else {
	      //cm_histo = cm_danning;
	      //}
	      double cm_sorting = GetCommonMode( isamp, 0, *it );
	      double cm_danning_online = GetCommonMode( isamp, fCommonModeOnlFlag, *it );
	      //double cm_danning_offline = GetCommonMode( isamp, 4, *it, cm_danning_online ); //Artificially zero suppress this calculation to check the CM correction algorithm

	      fCM_online[isamp] = cm_danning_online;
	      
	      //If we are in this if-block, this is a full-readout event

	      //std::cout << "cm danning, sorting = " << cm_danning << ", " << cm_sorting << std::endl;
	      
	      if( !fPedestalMode ){
		switch( fCommonModeFlag ){
		case 2:
		  commonMode[isamp] = cm_histo;
		  break;
		case 1:
		default:
		  commonMode[isamp] = cm_danning;
		  break;
		case 0:
		  commonMode[isamp] = cm_sorting;
		  break;
		}
	      }

	      // //Common-mode correction needs to be moved to its own method:
	      
	      // //Calculate diagnostic plots for the CM correction algorithm
	      // double CM_meas = cm_danning_online;
	      // double CM_expect_mean, CM_expect_rms;
	      // if( fMeasureCommonMode && fNeventsRollingAverage_by_APV[apvcounter] >= std::min(UInt_t(100),fNeventsCommonModeLookBack*fN_MPD_TIME_SAMP) ){
	      // 	//If we have a critical mass of events in the rolling CM average for this to be a reliable estimate, use it: 
	      // 	CM_expect_mean = fCommonModeRollingAverage_by_APV[apvcounter];
	      // 	CM_expect_rms = fCommonModeRollingRMS_by_APV[apvcounter]; 
	      // } else { //use database value:
	      // 	UInt_t postemp = fMPDmap[apvcounter].pos;
	      // 	UInt_t axistemp = fMPDmap[apvcounter].axis;
		
	      // 	CM_expect_mean = (axistemp == SBSGEM::kUaxis) ? fCommonModeMeanU[postemp] : fCommonModeMeanV[postemp];
	      // 	CM_expect_rms = (axistemp == SBSGEM::kUaxis) ? fCommonModeRMSU[postemp] : fCommonModeRMSV[postemp];		
	      // }
	      
	      // //if( CM_meas < CM_expect_mean - fCorrectCommonMode_Nsigma * CM_expect_rms ){
	      // if(true){ // Lets try forcing every event to pass this first cut
	      // 	// The online common mode appears to have a large negative bias relative to the expectation. 
	      // 	// Try to correct the common-mode. To calculate the correction requires us to loop on all the strips on this APV that passed
	      // 	// online zero suppression.
	      // 	// The simplest approach is just to take a simple average of all the strips within +/- some number of standard deviations of the
	      // 	// *EXPECTED* common-mode mean, but this is a biased approach.
		
	      // 	UInt_t NstripsInRange = 0; 
		
	      // 	//Loop on all strips on this APV and calculate raw ADC values from 
	      // 	for(int istrip=0; istrip<nstrips; ++istrip ){
	      // 	  int iraw = isamp + fN_MPD_TIME_SAMP * istrip;
		  
	      // 	  int strip = evdata.GetRawData( it->crate, it->slot, effChan, iraw );
	      // 	  UInt_t decoded_rawADC = evdata.GetData( it->crate, it->slot, effChan, iraw );
		  
	      // 	  Int_t ADCtemp = pedsubADC[iraw];

	      // 	  double rmstemp = (axis == SBSGEM::kUaxis ) ? fPedRMSU[Strip[iraw]] : fPedRMSV[Strip[iraw]];

	      // 	  double strip_sum = 0;
	      // 	  for(int itsamp=0; itsamp < 6; itsamp++)
	      // 	    strip_sum += ADCtemp - cm_danning_online;
	      // 	  if(strip_sum/fN_MPD_TIME_SAMP < 3*rmstemp) continue;
		  
	      // 	  rawStrip[iraw] = strip;
	      // 	  Strip[iraw] = GetStripNumber( strip, it->pos, it->invert );
		  		  
	      // 	  rawADC[iraw] = ADCtemp;
	      // 	  pedsubADC[iraw] = double( rawADC[iraw] ); //this is the one that goes into the common-mode calculation
	      // 	  if( fabs( pedsubADC[iraw] - CM_expect_mean ) <= fCorrectCommonMode_Nsigma * CM_expect_rms ) NstripsInRange++;
	      // 	}
		
	      // 	if( NstripsInRange >= fCommonModeMinStripsInRange ){
	      // 	  //Correction to be ADDED to ADC value to get corrected value:
	      // 	  CommonModeCorrection[isamp] = CM_meas -  GetCommonMode( isamp, 4, *it, cm_danning_online, nstrips ) + 3*8.3*(1 - NstripsInRange*1.0 / 128); //add extra 3 sigma * (1 - occupancy) to correct for extra positive bias from zero suppression
		  
	      // 	} else {
	      // 	  CommonModeCorrection[isamp] = 0.0; //To be added to ADC value! 
	      // 	}
	      // }
	      
	    
	      
	      //commonMode[isamp] = fCommonModeFlag == 0 ? cm_sorting : cm_danning;

	      //commonMode[isamp] = cm_histo;
	      
	      double cm_mean;
	      
	      UInt_t iAPV = it->pos;
	      
	      // std::cout << "Filling common-mode histograms..." << std::endl;
	      
	      // std::cout << "iAPV, nAPVsU, nAPVsV, axis = " << iAPV << ", " << fNAPVs_U << ", "
	      // 		<< fNAPVs_V << ", " << axis << std::endl;
	      if(!CM_OUT_OF_RANGE || fPedestalMode){
	      if( axis == SBSGEM::kUaxis ){
		cm_mean = fCommonModeMeanU[iAPV];

		fCommonModeDistU->Fill( iAPV, commonMode[isamp] - cm_mean );
		fCommonModeDistU_Histo->Fill( iAPV, cm_histo - cm_mean );
		fCommonModeDistU_Sorting->Fill( iAPV, cm_sorting - cm_mean );
		fCommonModeDistU_Danning->Fill( iAPV, cm_danning - cm_mean );
		fCommonModeDiffU->Fill( iAPV, commonMode[isamp] - cm_danning_online );
		// Moving simulated common-mode corrections for full-readout events to a separate dedicated method
		// if(CommonModeCorrection[isamp] != 0.0) fCommonModeCorrectionU->Fill( iAPV, cm_sorting - (cm_danning_online - CommonModeCorrection[isamp]));
		// else fCommonModeNotCorrectionU->Fill( iAPV, cm_sorting - (cm_danning_online - CommonModeCorrection[isamp]));
	      } else {
		cm_mean = fCommonModeMeanV[iAPV];
		
		fCommonModeDistV->Fill( iAPV, commonMode[isamp] - cm_mean );
		fCommonModeDistV_Histo->Fill( iAPV, cm_histo - cm_mean );
		fCommonModeDistV_Sorting->Fill( iAPV, cm_sorting - cm_mean );
		fCommonModeDistV_Danning->Fill( iAPV, cm_danning - cm_mean );
		fCommonModeDiffV->Fill( iAPV, commonMode[isamp] - cm_danning_online );
		// Moving simulated common-mode corrections for full-readout events to a separate dedicated method
		// if(CommonModeCorrection[isamp] != 0.0) fCommonModeCorrectionV->Fill( iAPV, cm_sorting - (cm_danning_online - CommonModeCorrection[isamp]));
		// else fCommonModeNotCorrectionV->Fill( iAPV, cm_sorting - (cm_danning_online - CommonModeCorrection[isamp]));
	      }
	      }
	      //std::cout << "Done..." << std::endl;
	      
	    } else if( !fPedestalMode ) { //if not doing diagnostic plots, just calculate whichever way the user wanted:
	      
	      commonMode[isamp] = GetCommonMode( isamp, fCommonModeFlag, *it );

	      if( fCorrectCommonMode ){
		//always calculate online CM if doing corrections:
		fCM_online[isamp] = GetCommonMode( isamp, fCommonModeOnlFlag, *it ); 
	      }

	    }
	    //std::cout << "effChan, isamp, Common-mode = " << effChan << ", " << isamp << ", " << commonMode[isamp] << std::endl;

	    //Now handle rolling average common-mode calculation:
	    
	    //UpdateRollingCommonModeAverage(apvcounter,commonMode[isamp]);

	    if( !CM_OUT_OF_RANGE ){
	      UpdateRollingAverage( apvcounter, commonMode[isamp],
				    fCommonModeResultContainer_by_APV,
				    fCommonModeRollingAverage_by_APV,
				    fCommonModeRollingRMS_by_APV,
				    fNeventsRollingAverage_by_APV ); 
	    }
	  } //loop over time samples

	  if( fCorrectCommonMode ){ //For full readout events we are mainly interested in monitoring the "bias" of the ONLINE calculation,
	    // NOT correcting the offline calculation
	    for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
	      //Are we passing sufficient information for this purpose? Let's see:
	      UInt_t ngoodhits=0;

	      //std::cout << "Attempting common-mode correction for full-readout event sample " << isamp << "...";
	      
	      double Correction = GetCommonModeCorrection( isamp, *it, ngoodhits, fN_APV25_CHAN, true );

	      double bias = fCM_online[isamp] - Correction - commonMode[isamp];

	      if( Correction != 0. && !CM_OUT_OF_RANGE ){
		UpdateRollingAverage( apvcounter, bias,
				      fCMbiasResultContainer_by_APV,
				      fCommonModeOnlineBiasRollingAverage_by_APV,
				      fCommonModeOnlineBiasRollingRMS_by_APV,
				      fNeventsOnlineBias_by_APV );
	      }

	      //Correction += 2.0*bias*(1.0-double(ngoodhits)/double(fN_APV25_CHAN));
	      
	      //double Correction = 0.0;
	      
	      //std::cout << " done." << std::endl;
	      //We are subtracting the result of the CM correction from the data. 
	      
	      UInt_t iAPV = it->pos;

	      if( fMakeCommonModePlots ){
		if( Correction != 0. ){

		  double CMbiasDB = ( it->axis == SBSGEM::kUaxis ) ? fCMbiasU[iAPV] : fCMbiasV[iAPV];
		  double CMbias = CMbiasDB;
		  
		  if( fNeventsOnlineBias_by_APV[apvcounter] >= std::min( UInt_t(100), std::max(UInt_t(10), fN_MPD_TIME_SAMP * fNeventsCommonModeLookBack) ) ){
		    CMbias = fCommonModeOnlineBiasRollingAverage_by_APV[apvcounter]; 
		  }
		  
		  if( it->axis == SBSGEM::kUaxis ){
		    fCommonModeCorrectionU->Fill( iAPV, -Correction );
		    fCommonModeResidualBiasU->Fill( iAPV, fCM_online[isamp] -Correction - commonMode[isamp] );
		    fCommonModeResidualBias_vs_OccupancyU->Fill( double(ngoodhits)/double(fN_APV25_CHAN), fCM_online[isamp] - Correction - commonMode[isamp] );		    
		    fCommonModeResidualBiasU_corrected->Fill( iAPV, fCM_online[isamp] -Correction - commonMode[isamp] - 2.0*CMbias*(1.0-double(ngoodhits)/double(fN_APV25_CHAN)) );
		  } else {
		    fCommonModeCorrectionV->Fill( iAPV, -Correction );
		    fCommonModeResidualBiasV->Fill( iAPV, fCM_online[isamp] - Correction - commonMode[isamp] );
		    fCommonModeResidualBias_vs_OccupancyV->Fill( double(ngoodhits)/double(fN_APV25_CHAN), fCM_online[isamp] - Correction - commonMode[isamp] );
		    fCommonModeResidualBiasV_corrected->Fill( iAPV, fCM_online[isamp] -Correction - commonMode[isamp] - 2.0*CMbias*(1.0-double(ngoodhits)/double(fN_APV25_CHAN)) );
		  }
		} else {
		  if( it->axis == SBSGEM::kUaxis ){
		    fCommonModeDiffU_Uncorrected->Fill( iAPV, commonMode[isamp] - fCM_online[isamp] );
		  } else {
		    fCommonModeDiffV_Uncorrected->Fill( iAPV, commonMode[isamp] - fCM_online[isamp] );
		  }
		}
	      }
	    }
	  }
	  
	} //check if conditions are satisfied to require offline common-mode calculation
      
      } //End check !CM_ENABLED && BUILD_ALL_SAMPLES
      
    
      if( CM_ENABLED && fCorrectCommonMode ){
	// Under certain conditions we want to attempt to correct the ADC values for all strips on an APV card using either
	// the rolling average over a certain number of previous events, or the CM mean from the database.
	// There are two conditions that must be satisfied to attempt correcting the ADC values for an event:
	// 1) The online calculated CM must be more than some number of std. deviations below the "expected" CM according to the rolling average
	// 2) The number of strips with ADC values within some number of std. deviations of the "expected" CM must exceed some threshold to allow us to
	//    to obtain a new estimate of the "true" common-mode for that event
	// If both 1) and 2) are satisfied, then we will attempt a new common-mode calculation using the strips that passed zero suppression using the online common-mode calculation.
      
	for(int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){

	  UInt_t ngood=0;
	  UInt_t nhitstemp = UInt_t(nstrips);

	  //std::cout << "Attempting common-mode correction for online zero-suppressed event sample " << isamp << "...";
	  
	  CommonModeCorrection[isamp] = GetCommonModeCorrection( isamp, *it, ngood, nhitstemp );

	  if( CommonModeCorrection[isamp] != 0.0 ){ //if we are applying a correction, correct it for bias:
	    UInt_t iAPV = it->pos;
	    
	    double CMbiasDB = ( it->axis == SBSGEM::kUaxis ) ? fCMbiasU[iAPV] : fCMbiasV[iAPV];
	    
	    double CMbias = CMbiasDB;
	    
	    if( fNeventsOnlineBias_by_APV[apvcounter] >= std::min( UInt_t(100), std::max(UInt_t(10), fN_MPD_TIME_SAMP * fNeventsCommonModeLookBack) ) ){
	      CMbias = fCommonModeOnlineBiasRollingAverage_by_APV[apvcounter]; 
	    }

	    //bias is DEFINED as Online common-mode MINUS correction MINUS "true" common-mode:
	    //"correction" is DEFINED as Online common-mode MINUS "corrected common-mode" and is to be ADDED to the ADC values:

	    // bias = online CM - (online CM - corrected CM) - true CM = corrected CM - true CM
	    // --> true CM = corrected CM - bias
	    // corrected ADC = ADC + online CM - true CM = uncorrected ADC + [online CM - (corrected CM - bias)]
	    // = uncorrected ADC + [correction + bias]
	    // [...] = correction to be ADDED to ADC
	    // --> corrected correction = correction + bias
	    CommonModeCorrection[isamp] += 2.0*CMbias*(1.0-double(ngood)/double(fN_APV25_CHAN));
	    
	    //"TRUE" common-mode is equal to 
	    
	  }
	  //std::cout << " done." << std::endl;
	}
	  
      }
	
      
   
      //std::cout << "finished common mode " << std::endl;
      // Last loop over all the strips and samples in the data and populate/calculate global variables that are passed to track-finding:
      //Int_t ihit = 0;
    
      for( Int_t istrip = 0; istrip < nstrips; ++istrip ) {

	//The following loop is no longer necessary if we always do a loop over the data to populate the "local" hit arrays:
	// if( CM_ENABLED ){ //unless fIsMC is true, then both CM and pedestals were subtracted online:
	//   // then we skipped the first loop over the data; need to grab the actual data into our temporary arrays:
	//   // Technically, if we attempted to perform a common-mode correction above, then this loop is unnecessary, but
	//   // to avoid confusion and needless overcomplication, we keep it for now, and repeating this step is
	//   // harmless in any case:
	//   for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
	//     int iraw = isamp + fN_MPD_TIME_SAMP * istrip;
	//     int strip = evdata.GetRawData( it->crate, it->slot, effChan, iraw );
	//     int ADC = evdata.GetData( it->crate, it->slot, effChan, iraw );
	//     rawStrip[iraw] = strip;
	//     Strip[iraw] = GetStripNumber( strip, it->pos, it->invert );
	//     //no need to grab pedestal if CM_ENABLED is true:
	    
	//     double ped = 0;
	//     if(fIsMC) ped = (axis == SBSGEM::kUaxis ) ? fPedestalU[Strip[iraw]] : fPedestalV[Strip[iraw]];
	    
	//     rawADC[iraw] = Int_t(ADC);
	//     pedsubADC[iraw] = double(ADC) - ped;
	//     commonModeSubtractedADC[iraw] = double(ADC) - ped + CommonModeCorrection[isamp]; //common-mode correction will be zero unless a correction was calculated above:    
	//   }
	// }
      
	//Temporary vector to hold ped-subtracted ADC samples for this strip:
	std::vector<double> ADCtemp(fN_MPD_TIME_SAMP);
	std::vector<int> rawADCtemp(fN_MPD_TIME_SAMP);
	std::vector<Double_t> DeconvADCtemp(fN_MPD_TIME_SAMP,0.0);
	
	//sums over time samples
	double ADCsum_temp = 0.0;
	double maxADC = 0.0;
	double minADC = 10000.0;  //Negative pulse
	Int_t iSampMax = -1;
	Int_t iSampMin = -1;   //Negative pulse
	
	//crude timing calculations:
	double Tsum = 0.0;
	double T2sum = 0.0;

	//grab decoded strip number directly:
	int strip = Strip[fN_MPD_TIME_SAMP * istrip];
      
	//Pedestal has already been subtracted by the time we get herre, but let's grab anyway in case it's needed:
	
	//"pedtemp" is only used to fill pedestal histograms as of now:
	double pedtemp = ( axis == SBSGEM::kUaxis ) ? fPedestalU[strip] : fPedestalV[strip];

	if( fPedSubFlag != 0 && !fIsMC && !fPedestalMode ) pedtemp = 0.0;

	double rmstemp = ( axis == SBSGEM::kUaxis ) ? fPedRMSU[strip] : fPedRMSV[strip];
	double gaintemp = ( axis == SBSGEM::kUaxis ) ? fUgain[strip/fN_APV25_CHAN] : fVgain[strip/fN_APV25_CHAN]; //should probably not hard-code 128 here

	// std::cout << "pedestal temp, rms temp, nsigma cut, threshold, zero suppress, pedestal mode = " << pedtemp << ", " << rmstemp << ", " << fZeroSuppressRMS
	//   	  << ", " << fZeroSuppressRMS * rmstemp << ", " << fZeroSuppress << ", " << fPedestalMode << std::endl;
	
	//Now loop over the time samples:
	for( Int_t adc_samp = 0; adc_samp < fN_MPD_TIME_SAMP; adc_samp++ ){

	  int iraw = adc_samp + fN_MPD_TIME_SAMP * istrip;

	  //If applicable, subtract common-mode here:
	  
	  //We need to subtract the common-mode if it was calculated offline:
	  if( !CM_ENABLED && BUILD_ALL_SAMPLES && nstrips == fN_APV25_CHAN ){
	    
	    // std::cout << "isamp, commonMode = " << adc_samp << ", " << commonMode[adc_samp]
	    // 	      << std::endl;
	    commonModeSubtractedADC[ iraw ] = pedsubADC[ iraw ] - commonMode[adc_samp];
	  }

	  //We need to apply a common-mode correction if we calculated one:
	  if( fCorrectCommonMode ) commonModeSubtractedADC[ iraw ] += CommonModeCorrection[adc_samp];
	  
	  // Int_t ihit = adc_samp + fN_MPD_TIME_SAMP * istrip; //index in the "hit" array for this APV card:
	  // assert(ihit<nsamp);
	  
	  
	  //Int_t rawADC = evdata.GetData(it->crate, it->slot, chan, ihit);
	  Int_t RawADC = rawADC[iraw]; //this value has no corrections applied:
         
	  //cout << adc_samp << " " << istrip << " " << rawADC << " ";// << endl;
	  
	  //rawADCtemp.push_back( RawADC );
	  rawADCtemp[adc_samp] = RawADC; //raw only
	  
	  //The following value already has pedestal and common-mode subtracted (if applicable):
	  double ADCvalue = commonModeSubtractedADC[iraw]; //zero-suppress BEFORE we apply gain correction

	  // if( fPedestalMode ){ //If we are analyzing pedestal data, DON'T substract the pedestal
	  //   ADCvalue = commonModeSubtractedADC[adc_samp][istrip];
	  // }
	  //pedestal-subtracted ADC values:
	  //ADCtemp.push_back( ADCvalue );
	  ADCtemp[adc_samp] = ADCvalue; //common-mode AND pedestal subtracted
	  // fadc[adc_samp][fNch] =  evdata.GetData(it->crate, it->slot,
	  // 					 chan, isamp++) - fPedestal[strip];

	  ADCsum_temp += ADCvalue;
	  //cout << ADCvalue << " "<< endl;
	  if( iSampMax < 0 || ADCvalue > maxADC ){
	    maxADC = ADCvalue;
	    iSampMax = adc_samp;
	  }

	  ///// Used for negative pulse study
	  if( iSampMin < 0 || ADCvalue < minADC ){
	    minADC = ADCvalue;
	    iSampMin = adc_samp;
	  }

	  
	  //for crude strip timing, just take simple time bins at the center of each sample (we'll worry about trigger time words later):
	  double Tsamp = fSamplePeriod * ( adc_samp + 0.5 );
	  
	  Tsum += Tsamp * ADCvalue;
	  T2sum += pow(Tsamp,2) * ADCvalue;
	  
	  //assert( ((UInt_t) fNch) < fMPDmap.size()*fN_APV25_CHAN );
	  //assert( fNstrips_hit < fMPDmap.size()*fN_APV25_CHAN );
	}

	//after the temporary ADC samples are calculated we can calculate the temporary deconvoluted ADC samples:
	CalcDeconvolutedSamples( ADCtemp, DeconvADCtemp );
	//	assert(strip>=0); // Make sure we don't end up with negative strip numbers!
	// Zero suppression based on third time sample only?
	//Maybe better to do based on max ADC sample:

	// if( !CM_ENABLED && BUILD_ALL_SAMPLES ){
	//   std::cout << " before zero suppression: common-mode and pedestal-subtracted ADC sum: effChan, istrip, ADC sum = " 
	// 	    << effChan << ", " << istrip << ", " << ADCsum_temp << std::endl;
	// }

	//cout << ADCsum_temp << " >? " << fThresholdStripSum << "; " 
	//   << ADCsum_temp/double(fN_MPD_TIME_SAMP) << " >? " << fZeroSuppressRMS*rmstemp << "; " 
	//   << maxADC << " >? " << fZeroSuppressRMS*rmstemp 
	//   << "; " << fThresholdSample << endl;

	//fill pedestal diagnostic histograms if and only if we are in pedestal mode or plot common mode 
	// AND the CM_ENABLED is not set, meaning we did cm and ped subtraction offline
	
	if( (fPedestalMode || fMakeCommonModePlots) && !CM_ENABLED ){ 
	  int iAPV = strip/fN_APV25_CHAN;
	  
	  if( axis == SBSGEM::kUaxis ){
	    for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
	      // std::cout << "U axis: isamp, strip, rawADC, ADC, ped, commonmode = " << isamp << ", " << strip << ", "
	      // 	  << rawADCtemp[isamp] << ", " << ADCtemp[isamp] << ", " << pedtemp << ", " << commonMode[isamp] << std::endl;
	      
	      hrawADCs_by_stripU->Fill( strip, rawADCtemp[isamp] );
	      hpedestal_subtracted_ADCs_by_stripU->Fill( strip, ADCtemp[isamp] ); //common-mode AND ped-subtracted
	      hcommonmode_subtracted_ADCs_by_stripU->Fill( strip, ADCtemp[isamp] + pedtemp ); //common-mode subtraction only, no ped:
	      hpedestal_subtracted_rawADCs_by_stripU->Fill( strip, ADCtemp[isamp] + commonMode[isamp] ); //pedestal subtraction only, no common-mode

	      hpedestal_subtracted_rawADCsU->Fill( ADCtemp[isamp] + commonMode[isamp] ); //1D distribution of ped-subtracted ADCs w/o common-mode subtraction
	      hpedestal_subtracted_ADCsU->Fill( ADCtemp[isamp] ); //1D distribution of ped-and-common-mode subtracted ADCs

	      hcommonmode_mean_by_APV_U->Fill( iAPV, commonMode[isamp] );
	      // ( (TH2D*) (*hrawADCs_by_strip_sampleU)[isamp] )->Fill( strip, rawADCtemp[isamp] );
	      // //for this one, we add back in the pedestal:
	      // ( (TH2D*) (*hcommonmode_subtracted_ADCs_by_strip_sampleU)[isamp] )->Fill( strip, ADCtemp[isamp] + pedtemp );
	      // ( (TH2D*) (*hpedestal_subtracted_ADCs_by_strip_sampleU)[isamp] )->Fill( strip, ADCtemp[isamp] );

	      if( iSampMax != 0 ){
		hdeconv_ADCsU->Fill( DeconvADCtemp[isamp] );
	      }
	    }
	  } else {
	    for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
	      // std::cout << "V axis: isamp, strip, rawADC, ADC, ped, commonmode = " << isamp << ", " << strip << ", "
	      // 	  << rawADCtemp[isamp] << ", " << ADCtemp[isamp] << ", " << pedtemp << ", " << commonMode[isamp] << std::endl;
	      hrawADCs_by_stripV->Fill( strip, rawADCtemp[isamp] );
	      hpedestal_subtracted_ADCs_by_stripV->Fill( strip, ADCtemp[isamp] );
	      hcommonmode_subtracted_ADCs_by_stripV->Fill( strip, ADCtemp[isamp] + pedtemp );
	      hpedestal_subtracted_rawADCs_by_stripV->Fill( strip, ADCtemp[isamp] + commonMode[isamp] );

	      hpedestal_subtracted_rawADCsV->Fill( ADCtemp[isamp] + commonMode[isamp] );
	      hpedestal_subtracted_ADCsV->Fill( ADCtemp[isamp] );

		
	      hcommonmode_mean_by_APV_V->Fill( iAPV, commonMode[isamp] );

	      if( iSampMax != 0 ){
		hdeconv_ADCsV->Fill( DeconvADCtemp[isamp] );
	      }
	      // ( (TH2D*) (*hrawADCs_by_strip_sampleV)[isamp] )->Fill( strip, rawADCtemp[isamp] );
	      // ( (TH2D*) (*hcommonmode_subtracted_ADCs_by_strip_sampleV)[isamp] )->Fill( strip, ADCtemp[isamp] );
	      // ( (TH2D*) (*hpedestal_subtracted_ADCs_by_strip_sampleV)[isamp] )->Fill( strip, ADCtemp[isamp] - pedtemp );
	    }
	  }

	  // std::cout << "finished pedestal histograms..." << std::endl;
	    
	}
	
	//the ROOTgui multicrate uses a threshold on the AVERAGE ADC sample (not the MAX). To be consistent
	// with how the "Hit" root files are produced, let's use the same threshold;
	// this amounts to using a higher effective threshold than cutting on the max ADC sample would have been:
	//fThresholdStripSum is in many respects redundant with fZeroSuppressRMS
	if(!fZeroSuppress ||
	   ( ADCsum_temp/double(fN_MPD_TIME_SAMP) > fZeroSuppressRMS*rmstemp ) ){ //Default threshold is 5-sigma!
	  //Increment hit count and populate decoded data structures:
	  //cout<<ADCsum_temp/double(fN_MPD_TIME_SAMP)<<endl;
	  //threshold on the average ADC
	  
	  //Slight reorganization: compute Tmean and Tsigma before applying gain correction:
	  //(since these sums were computed using the uncorrected ADC samples)
	  double Tmean_temp = Tsum/ADCsum_temp; 
	  double Tsigma_temp = sqrt( T2sum/ADCsum_temp - pow( Tmean_temp,2) );

	  //NOW apply gain correction:
	  //Don't apply any gain correction if we are doing pedestal mode analysis:
	  if( !fPedestalMode ){ //only apply gain correction if we aren't in pedestal-mode:
	    for( Int_t isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
	      ADCtemp[isamp] *= gaintemp;
	      DeconvADCtemp[isamp] *= gaintemp;
	    }
	    maxADC *= gaintemp;
	    ADCsum_temp *= gaintemp;
	  }

	  
	  //  ADCsum_temp /= gaintemp;
	
	  
	  //fStrip.push_back( strip );
	  //fAxis.push_back( axis );

	  //std::cout << "strip, axis = " << strip << ", " << axis << std::endl;
	  
	  fStrip[fNstrips_hit] = strip;
	  fAxis[fNstrips_hit] = axis;
	  fStripRaw[fNstrips_hit] = rawStrip[fN_MPD_TIME_SAMP * istrip];
	  
	  fKeepStrip[fNstrips_hit] = true;
	  //fStripKeep[fNstrips_hit] = 1;
	  //	  fMaxSamp.push_back( iSampMax );
	  fMaxSamp[fNstrips_hit] = iSampMax;

	  //if( fSuppressFirstLast && (iSampMax == 0 || iSampMax+1 == fN_MPD_TIME_SAMP ) ){
	  // fSuppressFirstLast:
	  // 0 = allow peaking in first or last sample
	  // 1 = suppress peaking in first and last sample
	  // -1 = suppress peaking in first sample only (or other negative number)
	  // -2 = suppress peaking in last sample only:
	  if( fDeconvolutionFlag == 0 ){ //if "deconvolution flag" is non-zero, then set "keep strip" based on deconvoluted variables
	    if( fSuppressFirstLast != 0 ){
	      bool peakfirst = iSampMax == 0;
	      bool peaklast = iSampMax+1 == fN_MPD_TIME_SAMP;
	      
	      if( peakfirst ){
		if( fSuppressFirstLast > 0 || fSuppressFirstLast != -2 ){
		  fKeepStrip[fNstrips_hit] = false;
		}
	      } else if( peaklast ){
		if( fSuppressFirstLast > 0 || fSuppressFirstLast == -2 ){
		  fKeepStrip[fNstrips_hit] = false;
		}
	      }
	    }
	    
	    // if( fUseStripTimingCuts && fabs( Tmean_temp - fStripMaxTcut_central ) > fStripMaxTcut_width ){
	    //   fKeepStrip[fNstrips_hit] = false;
	    //   //fStripKeep[fNstrips_hit] = 0;
	    // }
	  } 

	  //std::cout << "axis, Int_t(axis) = " << axis << ", " << Int_t(axis) << std::endl;
	  //fStripAxis.push_back( Int_t(axis) );
	  // fADCsamples.push_back( ADCtemp ); //pedestal-subtracted
	  // fRawADCsamples.push_back( rawADCtemp ); //Raw
	  
	  double ADCsum_deconv = 0.0;
	  double maxdeconv=0.0;
	  int imaxdeconv=0;

	  double Tsum_deconv = 0.0;

	  double maxcombo = 0.0;
	  //std::vector<double> combostemp(fN_MPD_TIME_SAMP+1,0.0);
	  double combotemp = 0.0;
	  int imaxcombo=0;

	  //we don't need to repeat the calculation of deconvoluted samples. That was moved to its own helper method:
	  
	    
	  for( Int_t isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
	    fADCsamples[fNstrips_hit][isamp] = ADCtemp[isamp];
	    fRawADCsamples[fNstrips_hit][isamp] = rawADCtemp[isamp];

	    fADCsamples_deconv[fNstrips_hit][isamp] = DeconvADCtemp[isamp];

	    ADCsum_deconv += DeconvADCtemp[isamp];

	    if( isamp==0 ){
	      combotemp = DeconvADCtemp[isamp];
	      maxcombo = combotemp;
	      imaxcombo=isamp;
	    } else {
	      combotemp = DeconvADCtemp[isamp] + DeconvADCtemp[isamp-1];
	      if( combotemp > maxcombo ){
		maxcombo = combotemp;
		imaxcombo = isamp;
	      }
	    }
	    if( isamp == 5 ){
	      combotemp = DeconvADCtemp[isamp];
	      if( combotemp > maxcombo ){
		maxcombo = combotemp;
		imaxcombo = fN_MPD_TIME_SAMP;
	      }
	    }
	    
	    if( isamp == 0 || DeconvADCtemp[isamp] > maxdeconv ){
	      imaxdeconv = isamp;
	      maxdeconv = DeconvADCtemp[isamp];
	    }

	    Tsum_deconv += ( fSamplePeriod * (isamp + 0.5) ) * DeconvADCtemp[isamp];
	    
	    //fADCsamples1D.push_back( ADCtemp[isamp] );
	    //fRawADCsamples1D.push_back( rawADCtemp[isamp] );
	    fADCsamples1D[isamp + fN_MPD_TIME_SAMP * fNstrips_hit ] = ADCtemp[isamp];
	    fRawADCsamples1D[isamp + fN_MPD_TIME_SAMP * fNstrips_hit ] = rawADCtemp[isamp];
	    fADCsamplesDeconv1D[isamp + fN_MPD_TIME_SAMP * fNstrips_hit ] = fADCsamples_deconv[fNstrips_hit][isamp];
	    
	    if( fKeepStrip[fNstrips_hit] && hADCfrac_vs_timesample_allstrips != NULL ){
	      hADCfrac_vs_timesample_allstrips->Fill( isamp, ADCtemp[isamp]/ADCsum_temp );
	    }
	  }
	  
	  fADCsumsDeconv[fNstrips_hit] = ADCsum_deconv;
	  //fStripTrackIndex.push_back( -1 ); //This could be modified later based on tracking results
	  fStripTrackIndex[fNstrips_hit] = -1;
	  fStripOnTrack[fNstrips_hit] = 0;

	  //This block is only used for the negative signal studies
	  fStripIsNeg[fNstrips_hit] = 0;
	  fStripIsNegU[fNstrips_hit] = 0;
	  fStripIsNegV[fNstrips_hit] = 0;
	  fStripIsNegOnTrack[fNstrips_hit] = 0;
	  fStripIsNegOnTrackU[fNstrips_hit] = 0;
	  fStripIsNegOnTrackV[fNstrips_hit] = 0;

	  //These are used for saving numbers to a text file for event displays
	  fStripEvent[fNstrips_hit] = evdata.GetEvNum();
	  fStripCrate[fNstrips_hit] = it->crate;
	  fStripMPD[fNstrips_hit] = it->mpd_id;
	  fStripADC_ID[fNstrips_hit] = it->adc_id;
	  /// This block above is used for negative signal studies
	  
	  //	  fKeepStrip.push_back( true ); //keep all strips by default
	  
	  
	  //	  fADCmax.push_back( maxADC );
	  fADCmax[fNstrips_hit] = maxADC;
	  fADCmaxDeconv[fNstrips_hit] = maxdeconv;
	  fADCmaxDeconvCombo[fNstrips_hit] = maxcombo;

	  fMaxSampDeconv[fNstrips_hit] = imaxdeconv;
	  fMaxSampDeconvCombo[fNstrips_hit] = imaxcombo;

	  if( fDeconvolutionFlag != 0 ){
	    //rmstemp is the rms of the average of six time samples. To get individual sample noise, we take:
	    double sigma_1sample = rmstemp * fRMS_ConversionFactor; 

	    //5 * 8 * sqrt(6) ~= 100 
	    
	    if( maxcombo <= fZeroSuppressRMS * sigma_1sample ){
	      fKeepStrip[fNstrips_hit] = false;
	    }

	    if( fSuppressFirstLast != 0 && imaxcombo == 0 ){
	      fKeepStrip[fNstrips_hit] = false;
	    }
	  }
	  
	  fTmeanDeconv[fNstrips_hit] = Tsum_deconv/ADCsum_deconv - fTrigTimeSlope*fTrigTime;

	  // if( imaxcombo == 0 ){
	  //   fTmeanDeconv[fNstrips_hit] = 0.5*fSamplePeriod - fTrigTime;
	  // } else if( imaxcombo < fN_MPD_TIME_SAMP ){
	  //   int samp1 = imaxcombo-1;
	  //   int samp2 = imaxcombo;
	  //   double tsamp1 = (samp1 + 0.5) * fSamplePeriod - fTrigTime;
	  //   double tsamp2 = (samp2 + 0.5) * fSamplePeriod - fTrigTime;
	  //   double ADC1 = fADCsamples_deconv[fNstrips_hit][samp1];
	  //   double ADC2 = fADCsamples_deconv[fNstrips_hit][samp2];
	  //   fTmeanDeconv[fNstrips_hit] = ( tsamp1 * ADC1 + tsamp2 * ADC2 )/( ADC1 + ADC2 );
	  // } else {
	  //   fTmeanDeconv[fNstrips_hit] = 5.5*fSamplePeriod - fTrigTime;
	  // }
	  
	  //	  fTmean.push_back( Tsum/ADCsum_temp );
	  fTmean[fNstrips_hit] = Tmean_temp - fTrigTimeSlope*fTrigTime;
	  //  fTsigma.push_back( sqrt( T2sum/ADCsum_temp - pow( fTmean.back(), 2 ) ) );
	  fTsigma[fNstrips_hit] = Tsigma_temp;
	  //fTcorr.push_back( fTmean.back() ); //don't apply any corrections for now

	  fStripTSchi2[fNstrips_hit] = StripTSchi2(fNstrips_hit);
	  fStripTSprob[fNstrips_hit] = TMath::Prob( fStripTSchi2[fNstrips_hit], 6 );

	  if( fUseTSchi2cut && fStripTSchi2[fNstrips_hit] > fStripTSchi2Cut ){
	    fKeepStrip[fNstrips_hit] = false;
	  }
	  
	  fStripTdiff[fNstrips_hit] = -1000.; //This will become meaningful only at the clustering stage
	  fStripCorrCoeff[fNstrips_hit] = -1000.; //This will become meaningful only at the clustering stage
	  fTcorr[fNstrips_hit] = fTmean[fNstrips_hit];

	  fStripTfit[fNstrips_hit] = FitStripTime( fNstrips_hit, rmstemp*2.45 );
	  //fStripTfit[fNstrips_hit] = fTmean[fNstrips_hit];

	  fStrip_ENABLE_CM[fNstrips_hit] = CM_ENABLED;
	  fStrip_CM_GOOD[fNstrips_hit] = !CM_OUT_OF_RANGE;
	  fStrip_BUILD_ALL_SAMPLES[fNstrips_hit] = BUILD_ALL_SAMPLES;

	  //  fADCsums.push_back( ADCsum_temp ); //sum of all (pedestal-subtracted) samples
	  fADCsums[fNstrips_hit] = ADCsum_temp;
	  
	  //  fStripADCavg.push_back( ADCsum_temp/double(fN_MPD_TIME_SAMP) );
	  fStripADCavg[fNstrips_hit] = ADCsum_temp/double(fN_MPD_TIME_SAMP);
	  
	  UInt_t isU = (axis == SBSGEM::kUaxis) ? 1 : 0;
	  UInt_t isV = (axis == SBSGEM::kVaxis) ? 1 : 0;
	  //	  fStripIsU.push_back( isU );
	  //      fStripIsV.push_back( isV );
	  fStripIsU[fNstrips_hit] = isU;
	  fStripIsV[fNstrips_hit] = isV;

	  fStripUonTrack[fNstrips_hit] = 0;
	  fStripVonTrack[fNstrips_hit] = 0;
	  
	  fNstrips_hitU += isU;
	  fNstrips_hitV += isV;
	  
	  //	  if( axis == SBSGEM::kUaxis ) fUstripIndex[strip] = fNstrips_hit;
	  //      if( axis == SBSGEM::kVaxis ) fVstripIndex[strip] = fNstrips_hit;

	  //std::cout << "starting pedestal histograms..." << std::endl;

	  if( fKeepStrip[fNstrips_hit] ){
	    fNstrips_keep++;
	    fNstrips_keepU += isU;
	    fNstrips_keepV += isV;
	    if( fADCmax[fNstrips_hit] >= fThresholdSample && fADCsums[fNstrips_hit] >= fThresholdStripSum ){
	      fNstrips_keep_lmax++;
	      fNstrips_keep_lmaxU += isU;
	      fNstrips_keep_lmaxV += isV;
	    }
	    
	  }
	  
	  
	  fNstrips_hit++;
	  fNstrips_hit_pos++;
	
	  
	  
	} //check if passed zero suppression cuts

	/////// Negative pulse study, This is an exact copy of the loop above but instead stores the negative ADC info. "Keep" is set
	/////// to false regardless so these strips will not be used for any of the normal clustering and tracking algorithms. They 
	/////// are differentiated from positive strips by fStripIsNeg.
	if(ADCsum_temp/double(fN_MPD_TIME_SAMP) < -1.0*fZeroSuppressRMS*rmstemp && BUILD_ALL_SAMPLES && !CM_ENABLED && fNegSignalStudy ){
	  
	  //Increment hit count and populate decoded data structures:
	 
	  //threshold on the average ADC
	  
	  //Slight reorganization: compute Tmean and Tsigma before applying gain correction:
	  //(since these sums were computed using the uncorrected ADC samples)
	  double Tmean_temp = Tsum/ADCsum_temp; 
	  double Tsigma_temp = sqrt( -1.0*T2sum/ADCsum_temp - pow( Tmean_temp,2) );

	  //NOW apply gain correction:
	  //Don't apply any gain correction if we are doing pedestal mode analysis:
	  if( !fPedestalMode ){ //only apply gain correction if we aren't in pedestal-mode:
	    for( Int_t isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
	      ADCtemp[isamp] *= gaintemp;
	    }
	    minADC *= gaintemp;  //Use min ADC instead of max for negative signals
	    ADCsum_temp *= gaintemp;
	  }

	  //  ADCsum_temp /= gaintemp;
	
	  
	  //fStrip.push_back( strip );
	  //fAxis.push_back( axis );

	  //std::cout << "strip, axis = " << strip << ", " << axis << std::endl;
	  
	  fStrip[fNstrips_hit] = strip;
	  fAxis[fNstrips_hit] = axis;
	  fStripRaw[fNstrips_hit] = rawStrip[fN_MPD_TIME_SAMP * istrip];	  

	  //fStripKeep[fNstrips_hit] = 1;
	  //	  fMaxSamp.push_back( iSampMax );
	  fMaxSamp[fNstrips_hit] = iSampMin;

	  //if( fSuppressFirstLast && (iSampMax == 0 || iSampMax+1 == fN_MPD_TIME_SAMP ) ){
	  // fSuppressFirstLast:
	  // 0 = allow peaking in first or last sample
	  // 1 = suppress peaking in first and last sample
	  // -1 = suppress peaking in first sample only (or other negative number)
	  // -2 = suppress peaking in last sample only:	
	  if( fSuppressFirstLast != 0 ){
	    bool peakfirst = iSampMin == 0;
	    bool peaklast = iSampMin+1 == fN_MPD_TIME_SAMP;
	    
	    if( peakfirst ){
	      if( fSuppressFirstLast > 0 || fSuppressFirstLast != -2 ){
		fKeepStrip[fNstrips_hit] = false;
	      }
	    } else if( peaklast ){
	      if( fSuppressFirstLast > 0 || fSuppressFirstLast == -2 ){
		fKeepStrip[fNstrips_hit] = false;
	      }
	    }
	  }
	  

	  //if( fUseStripTimingCuts && fabs( Tmean_temp - fStripMaxTcut_central ) > fStripMaxTcut_width ){
	  //  fKeepStrip[fNstrips_hit] = false;
	  //}

	  //std::cout << "axis, Int_t(axis) = " << axis << ", " << Int_t(axis) << std::endl;
	  //fStripAxis.push_back( Int_t(axis) );
	  // fADCsamples.push_back( ADCtemp ); //pedestal-subtracted
	  // fRawADCsamples.push_back( rawADCtemp ); //Raw
	  for( Int_t isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
	    fADCsamples[fNstrips_hit][isamp] = ADCtemp[isamp];
	    fRawADCsamples[fNstrips_hit][isamp] = rawADCtemp[isamp];
	    
	    //fADCsamples1D.push_back( ADCtemp[isamp] );
	    //fRawADCsamples1D.push_back( rawADCtemp[isamp] );
	    fADCsamples1D[isamp + fN_MPD_TIME_SAMP * fNstrips_hit ] = ADCtemp[isamp];
	    fRawADCsamples1D[isamp + fN_MPD_TIME_SAMP * fNstrips_hit ] = rawADCtemp[isamp];

	    if( fKeepStrip[fNstrips_hit] && hADCfrac_vs_timesample_allstrips != NULL ){
	      hADCfrac_vs_timesample_allstrips->Fill( isamp, ADCtemp[isamp]/ADCsum_temp );
	    }
	  }
	  //fStripTrackIndex.push_back( -1 ); //This could be modified later based on tracking results
	  fStripTrackIndex[fNstrips_hit] = -1;
	  fStripOnTrack[fNstrips_hit] = 0;

	  //Variables used for negative signal studies
	  fStripIsNeg[fNstrips_hit] = 1;
	  fStripIsNegU[fNstrips_hit] = (axis == SBSGEM::kUaxis) ? 1 : 0;
	  fStripIsNegV[fNstrips_hit] = (axis == SBSGEM::kVaxis) ? 1 : 0;
	  fStripIsNegOnTrack[fNstrips_hit] = 0;
	  fStripIsNegOnTrackU[fNstrips_hit] = 0;
	  fStripIsNegOnTrackV[fNstrips_hit] = 0;

	  //These are used for saving numbers to a text file for event displays
	  fStripEvent[fNstrips_hit] = evdata.GetEvNum();
	  fStripCrate[fNstrips_hit] = it->crate;
	  fStripMPD[fNstrips_hit] = it->mpd_id;
	  fStripADC_ID[fNstrips_hit] = it->adc_id;
	  //Variables used for negative signal studies
	  

	  //	  fKeepStrip.push_back( true ); //keep all strips by default
	  
	  
	  //	  fADCmax.push_back( maxADC );
	  fADCmax[fNstrips_hit] = minADC;    //Use minADC instead for negative strips
	  //	  fTmean.push_back( Tsum/ADCsum_temp );
	  fTmean[fNstrips_hit] = Tmean_temp;
	  //  fTsigma.push_back( sqrt( T2sum/ADCsum_temp - pow( fTmean.back(), 2 ) ) );
	  fTsigma[fNstrips_hit] = Tsigma_temp;
	  //fTcorr.push_back( fTmean.back() ); //don't apply any corrections for now

	  fStripTSchi2[fNstrips_hit] = StripTSchi2(fNstrips_hit);

	  if( fUseTSchi2cut && fStripTSchi2[fNstrips_hit] > fStripTSchi2Cut ){
	    fKeepStrip[fNstrips_hit] = false;
	  }
	  
	  fStripTdiff[fNstrips_hit] = -1000.; //This will become meaningful only at the clustering stage
	  fStripCorrCoeff[fNstrips_hit] = -1000.; //This will become meaningful only at the clustering stage
	  fTcorr[fNstrips_hit] = fTmean[fNstrips_hit];

	  fStripTfit[fNstrips_hit] = FitStripTime( fNstrips_hit, rmstemp*2.45 );
	  //fStripTfit[fNstrips_hit] = fTmean[fNstrips_hit];

	  fStrip_ENABLE_CM[fNstrips_hit] = CM_ENABLED;
	  fStrip_CM_GOOD[fNstrips_hit] = !CM_OUT_OF_RANGE;
	  fStrip_BUILD_ALL_SAMPLES[fNstrips_hit] = BUILD_ALL_SAMPLES;
	  
	  //  fADCsums.push_back( ADCsum_temp ); //sum of all (pedestal-subtracted) samples
	  fADCsums[fNstrips_hit] = ADCsum_temp;
	  
	  //  fStripADCavg.push_back( ADCsum_temp/double(fN_MPD_TIME_SAMP) );
	  fStripADCavg[fNstrips_hit] = ADCsum_temp/double(fN_MPD_TIME_SAMP);
	  
	  UInt_t isU = (axis == SBSGEM::kUaxis) ? 1 : 0;
	  UInt_t isV = (axis == SBSGEM::kVaxis) ? 1 : 0;
	  //	  fStripIsU.push_back( isU );
	  //      fStripIsV.push_back( isV );
	  fStripIsU[fNstrips_hit] = isU;
	  fStripIsV[fNstrips_hit] = isV;

	  fStripUonTrack[fNstrips_hit] = 0;
	  fStripVonTrack[fNstrips_hit] = 0;
	  
	  fNstrips_hitU_neg += isU;
	  fNstrips_hitV_neg += isV;
	  
	  //	  if( axis == SBSGEM::kUaxis ) fUstripIndex[strip] = fNstrips_hit;
	  //      if( axis == SBSGEM::kVaxis ) fVstripIndex[strip] = fNstrips_hit;

	  //std::cout << "starting pedestal histograms..." << std::endl;

	  if( fKeepStrip[fNstrips_hit] ){
	    fNstrips_keep++;
	    fNstrips_keepU += isU;
	    fNstrips_keepV += isV;
	    if( fADCmax[fNstrips_hit] >= fThresholdSample && fADCsums[fNstrips_hit] >= fThresholdStripSum ){
	      fNstrips_keep_lmax++;
	      fNstrips_keep_lmaxU += isU;
	      fNstrips_keep_lmaxV += isV;
	    }
	    
	  }
	  
	  
	  fNstrips_hit++;
	  fNstrips_hit_neg++;

	  
	  

	}// end loop over negative zero suppression for full readout events

      } //end loop over strips on this APV card	
    } //end if( nsamp > 0 )
  
    apvcounter++;
  } //end loop on decode map entries for this module

  fNdecoded_ADCsamples = fNstrips_hit * fN_MPD_TIME_SAMP;
  
  //We will want to resize the 

  //resize all the "decoded strip" arrays to the actual number of fired strips:
  
  // fStrip.resize( fNstrips_hit );
  // fAxis.resize( fNstrips_hit );
  // fADCsamples.resize( fNstrips_hit );
  // fRawADCsamples.resize( fNstrips_hit );
  // for( int istrip=0; istrip<fNstrips_hit; istrip++ ){
  //   fADCsamples[istrip].resize( fN_MPD_TIME_SAMP );
  //   fRawADCsamples[istrip].resize( fN_MPD_TIME_SAMP );
  // }
  // fADCsums.resize( fNstrips_hit );
  // fStripADCavg.resize( fNstrips_hit );
  // fStripIsU.resize( fNstrips_hit );
  // fStripIsV.resize( fNstrips_hit );
  // fKeepStrip.resize( fNstrips_hit );
  // fMaxSamp.resize( fNstrips_hit );
  // fADCmax.resize( fNstrips_hit );
  // fTmean.resize( fNstrips_hit );
  // fTsigma.resize( fNstrips_hit );
  // fTcorr.resize( fNstrips_hit );

  // fADCsamples1D.resize( fNstrips_hit * fN_MPD_TIME_SAMP );
  // fRawADCsamples1D.resize( fNstrips_hit * fN_MPD_TIME_SAMP );
  // fStripTrackIndex.resize( fNstrips_hit );
  
  // No longer necessary:
  //fNstrips_hitU = fUstripIndex.size();
  //fNstrips_hitV = fVstripIndex.size();
  
  //std::cout << fName << " decoded, number of strips fired = " << fNstrips_hit << std::endl;

  fIsDecoded = true;
  
  return 0;
}

void SBSGEMModule::find_2Dhits(){ //version with no arguments calls 1D cluster finding with default (wide-open) track search constraints
  //these functions will fill the 1D cluster arrays:

  
  find_clusters_1D(SBSGEM::kUaxis); //u strips
  find_clusters_1D(SBSGEM::kVaxis); //v strips

  // find_clusters_1D_experimental(SBSGEM::kUaxis);
  // find_clusters_1D_experimental(SBSGEM::kVaxis);
  
  //Now make 2D clusters:

  if( fNclustU > 0 && fNclustV > 0 ){
  
    fxcmin = -1.e12;
    fxcmax = 1.e12;
    fycmin = -1.e12;
    fycmax = 1.e12;

    fill_2D_hit_arrays();

  }
}

void SBSGEMModule::find_2Dhits(TVector2 constraint_center, TVector2 constraint_width ){
  //constraint center and constraint width are assumed given in meters in "local" detector x,y coordinates.

  double ucenter = constraint_center.X() * fPxU + constraint_center.Y() * fPyU;
  double vcenter = constraint_center.X() * fPxV + constraint_center.Y() * fPyV;

  //To determine the constraint width along u/v, we need to transform the X/Y constraint widths, which define a rectangular region,
  //into U and V limits for 1D clustering:

  double umin,umax,vmin,vmax;

  double xmin = constraint_center.X() - constraint_width.X();
  double xmax = constraint_center.X() + constraint_width.X();
  double ymin = constraint_center.Y() - constraint_width.Y();
  double ymax = constraint_center.Y() + constraint_width.Y();

  //store these for later use:
  fxcmin = xmin;
  fxcmax = xmax;
  fycmin = ymin;
  fycmax = ymax;
  
  //check the four corners of the rectangle and compute the maximum values of u and v occuring at the four corners of the rectangular region:
  // NOTE: we will ALSO enforce the 2D search region in X and Y when we combine 1D U/V clusters into 2D X/Y hits, which, depending on the U/V strip orientation
  // can exclude some 2D hits that would have passed the U/V constraints defined by the corners of the X/Y rectangle, but been outside the X/Y constraint rectangle

  double u00 = xmin * fPxU + ymin * fPyU;
  double u01 = xmin * fPxU + ymax * fPyU;
  double u10 = xmax * fPxU + ymin * fPyU;
  double u11 = xmax * fPxU + ymax * fPyU;

  //this is some elegant-looking (compact) code, but perhaps algorithmically clunky:
  umin = std::min( u00, std::min(u01, std::min(u10, u11) ) );
  umax = std::max( u00, std::max(u01, std::max(u10, u11) ) );

  double v00 = xmin * fPxV + ymin * fPyV;
  double v01 = xmin * fPxV + ymax * fPyV;
  double v10 = xmax * fPxV + ymin * fPyV;
  double v11 = xmax * fPxV + ymax * fPyV;
  
  vmin = std::min( v00, std::min(v01, std::min(v10, v11) ) );
  vmax = std::max( v00, std::max(v01, std::max(v10, v11) ) );

  //The following routines will loop on all the strips and populate the 1D "cluster list" (vector<sbsgemcluster_t> )
  //Taking half the difference between max and min as the "width" is consistent with how it is used in
  // find_clusters_1D; i.e., the peak is required to be within |peak position - constraint center| <= constraint width
  find_clusters_1D(SBSGEM::kUaxis, ucenter, (umax-umin)/2.0 ); //U clusters
  find_clusters_1D(SBSGEM::kVaxis, vcenter, (vmax-vmin)/2.0 );  //V clusters

  //find_clusters_1D_experimental(SBSGEM::kUaxis, ucenter, (umax-umin)/2.0 );
  //find_clusters_1D_experimental(SBSGEM::kVaxis, vcenter, (vmax-vmin)/2.0 );
  
  //Now make 2D clusters

  if( fNclustU > 0 && fNclustV > 0 ){
    fill_2D_hit_arrays();
  }
}

//This will borrow a lot from the "standard" version:
void SBSGEMModule::find_clusters_1D_experimental( SBSGEM::GEMaxis_t axis, Double_t constraint_center, Double_t constraint_width ){
  if( !fIsDecoded ){
    cout << "find_clusters invoked before decoding for GEM Module " << GetName() << ", doing nothing" << endl;
    return;
  }

  UShort_t maxsep = ( axis == SBSGEM::kUaxis) ? fMaxNeighborsU_totalcharge : fMaxNeighborsV_totalcharge;
  UShort_t maxsepcoord = ( axis == SBSGEM::kUaxis ) ? fMaxNeighborsU_hitpos : fMaxNeighborsV_hitpos;
  UInt_t Nstrips = ( axis == SBSGEM::kUaxis ) ? fNstripsU : fNstripsV;
  Double_t pitch = ( axis == SBSGEM::kUaxis ) ? fUStripPitch : fVStripPitch;
  Double_t offset = (axis == SBSGEM::kUaxis) ? fUStripOffset : fVStripOffset;

  
  
  std::set<UShort_t> striplist;  //sorted list of ALL fired strips for 1D clustering
  std::map<UShort_t, UInt_t> hitindex; //key = strip ID, mapped value = index in decoded hit array, needed to access the other information efficiently
  std::map<UShort_t, Double_t> pedrms_strip;

  //this temporary array is unnecessary (I think)
  //std::vector<std::map<UShort_t,Double_t> > ADCsamples(fN_MPD_TIME_SAMP); //key = strip, mapped value is array ADC values by time sample:

  std::vector<sbsgemcluster_t> &clusters = (axis == SBSGEM::kUaxis ) ? fUclusters : fVclusters;

  UInt_t &nclust = ( axis == SBSGEM::kUaxis ) ? fNclustU : fNclustV; 
  UInt_t &nclust_pos = ( axis == SBSGEM::kUaxis ) ? fNclustU_pos : fNclustV_pos; 
  UInt_t &nclust_neg = ( axis == SBSGEM::kUaxis ) ? fNclustU_neg : fNclustV_neg; 
  UInt_t &nclust_tot = ( axis == SBSGEM::kUaxis ) ? fNclustU_total : fNclustV_total;

  nclust = 0;
  nclust_pos = 0;
  nclust_neg = 0;
  nclust_tot = 0;
  
  clusters.clear();

  //First we loop on all fired strips and populate the temporary arrays for clustering above:

  //All we need in this version are the sorted list of fired strips, the index in the hit array, and the pedestal RMS value for each strip:
  for( int ihit=0; ihit<fNstrips_hit; ihit++ ){
    if( fAxis[ihit] == axis && fKeepStrip[ihit] ){
      bool newstrip = (striplist.insert( fStrip[ihit] ) ).second;
      if( newstrip ){ //should always be true:
	hitindex[fStrip[ihit]] = ihit;
	pedrms_strip[fStrip[ihit]] = ( axis == SBSGEM::kUaxis ) ? fPedRMSU[fStrip[ihit]] : fPedRMSV[fStrip[ihit]];
      }
      
    } // check strip is along axis we are currently studying
  } //end loop over fired strips in this module

  std::vector<std::set<UShort_t> > localmaxima(fN_MPD_TIME_SAMP);
  std::vector<std::map<UShort_t,bool> > islocalmax(fN_MPD_TIME_SAMP);

  std::set<UShort_t> allmaxima; //list of all strips that are local maxima in one or more time samples
  std::map<UShort_t,UShort_t> timesamples_allmaxima; //list of time samples in which this strip is maximum:
  std::map<UShort_t,UShort_t> Nsamp_allmaxima; //NUMBER of time samples for which this strip is maximum
  std::map<UShort_t,std::map<UShort_t,sbsgemcluster_t> > protoclusters; //clustering results in individual time samples
  std::map<UShort_t,int> isampmax_allmaxima; //time sample for which the (cluster-summed) ADC value is maximum for a given strip.
  std::map<UShort_t,Double_t> ADCmax_allmaxima; // (cluster-summed
  
  //What properties do we want to store for "protoclusters"?
  //We can use the sbsgemcluster_t structure for the protoclusters because
  //they have all the basic variables we need (and some that won't make sense until we merge the time samples together):
  //std::vector<std::vector<sbsgemcluster_t> > protoclusters(fN_MPD_TIME_SAMP);
  
  //Now loop over all time samples and find all local maxima in each time sample; also erase "not prominent" peaks:
  
  for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
    localmaxima[isamp].clear();
    for( auto istrip : striplist ){
      islocalmax[isamp][istrip] = false;

      double ADCstrip = fADCsamples[hitindex[istrip]][isamp];
      double ADCleft = 0.0;
      double ADCright = 0.0;
      if( striplist.find( istrip + 1 ) != striplist.end() ){
	ADCright = fADCsamples[hitindex[istrip+1]][isamp];
      }
      if( striplist.find( istrip - 1) != striplist.end() ){
	ADCleft = fADCsamples[hitindex[istrip-1]][isamp];
      }

      if( ADCstrip >= ADCleft && ADCstrip >= ADCright && ADCstrip >= fThresholdSample ){
	islocalmax[isamp][istrip] = true;
	localmaxima[isamp].insert( istrip );
      }
    } //end loop over all fired strips:

    //std::cout << " Before peak erasing, time sample " << isamp << ", N local maxima = " << localmaxima[isamp].size() << std::endl;
    
    //now loop over all maxima and do "peak erasing":

    vector<int> peakstoerase; 

    int nerased_fraction=0, nerased_sigma=0;
    
    for( auto stripmax : localmaxima[isamp] ){
      double ADCmax = fADCsamples[hitindex[stripmax]][isamp];
      double prominence = ADCmax;
      int striplo = stripmax, striphi = stripmax;
      double ADCminright = ADCmax, ADCminleft = ADCmax;

      bool higherpeakleft = false, higherpeakright = false;
      int peakright = -1, peakleft = -1;

      double sigma_max = pedrms_strip[stripmax];
      
      while( striplist.find( striphi + 1 ) != striplist.end() ){
	striphi++;
	double ADCtest = fADCsamples[hitindex[striphi]][isamp];
	if( ADCtest < ADCminright && !higherpeakright ){
	  ADCminright = ADCtest;
	}
	if( islocalmax[isamp][striphi] && ADCtest > ADCmax ){ // then this peak is in a contiguous group with another higher peak to the right:
	  higherpeakright = true;
	  peakright = striphi;
	  break;
	}
      }

      while( striplist.find( striplo - 1 ) != striplist.end() ){
	striplo--;
	double ADCtest = fADCsamples[hitindex[striplo]][isamp];
	if( ADCtest < ADCminleft && !higherpeakleft ){
	  ADCminleft = ADCtest;
	}
	if( islocalmax[isamp][striplo] && ADCtest > ADCmax ){ // then this peak is in a contiguous group with another higher peak to the left:
	  higherpeakleft = true;
	  peakleft = striplo;
	  break;
	}
      }

      bool peak_close = false;
      if( !higherpeakleft ) ADCminleft = 0.0;
      if( !higherpeakright ) ADCminright = 0.0;

      double sigma = pedrms_strip[stripmax];

      if( higherpeakright || higherpeakleft ){ //this peak is contiguous with higher peaks on either the left or right or both:
	prominence = ADCmax - std::max( ADCminleft, ADCminright ); //subtract the higher of the two valleys to get the peak prominence
	if( higherpeakleft && std::abs( peakleft - stripmax ) <= 2*maxsep ) peak_close = true;
	if( higherpeakright && std::abs( peakright - stripmax ) <= 2*maxsep ) peak_close = true;

	if( peak_close && ( prominence < fThresh_2ndMax_nsigma * sigma  ||
			    prominence/ADCmax < fThresh_2ndMax_fraction ) ){
	  if( prominence < fThresh_2ndMax_nsigma * sigma ) nerased_sigma++;
	  if( prominence/ADCmax < fThresh_2ndMax_fraction ) nerased_fraction++;

	  // std::cout << "Warning: erasing strip " << stripmax << " from list of local maxima, prominence = " << prominence
	  // 	    << ", sigma = " << sigma << ", ADC max = " << ADCmax << ", prominence/ADCmax = " << prominence/ADCmax
	  // 	    << ", (peakleft,peakright)=(" << higherpeakleft << ", " << higherpeakright << ")" << std::endl;

	  // if( higherpeakleft ) std::cout << "Merged with higher peak at " << peakleft << ", separation = " << stripmax - peakleft << std::endl;
	  // if( higherpeakright ) std::cout << "Merged with higher peak at " << peakright << ", separation = " << peakright - stripmax << std::endl;
	  
	  peakstoerase.push_back( stripmax );
	}
      }
    } //end loop on local maxima for erasing "insignificant" peaks
    
    for( auto ipeak : peakstoerase ){
      localmaxima[isamp].erase( ipeak );
      islocalmax[isamp][ipeak] = false;
    }

    // std::cout << " After peak erasing, time sample " << isamp << ", N local maxima = " << localmaxima[isamp].size() << std::endl;
    // std::cout << " Npeaks erased (Nsigma, Nfraction)=(" << nerased_sigma << ", " << nerased_fraction << ")" << std::endl;

    //Each local maximum in a time sample is one "proto-cluster". We need to declare some kind of temporary local container
    //for these so that we can then merge all the time samples together after the fact:
    //NEXT: cluster formation and cluster splitting from remaining local maxima:
    
    for( auto stripmax : localmaxima[isamp] ){

      // std::cout << "time sample " << isamp << ", local max in strip " << stripmax << " starting clustering, maxsep = " << maxsep << std::endl;
      
      int striplo = stripmax;
      int striphi = stripmax;
      double ADCmax = fADCsamples[hitindex[stripmax]][isamp];

      bool found_neighbor_high = true, found_neighbor_low = true;

      while( found_neighbor_low ){
	found_neighbor_low = striplist.find( striplo - 1 ) != striplist.end() && stripmax - striplo < maxsep;

	if( found_neighbor_low ) striplo--;
      }

      while( found_neighbor_high ){
	found_neighbor_high = striplist.find( striphi + 1 ) != striplist.end() && striphi - stripmax < maxsep;

	if( found_neighbor_high ) striphi++;
      }
      
      int nstrips = striphi-striplo+1;

      //std::cout << "time sample " << isamp << ", local max in strip " << stripmax << ", nstrips = " << nstrips << std::endl;
      
      sbsgemcluster_t clusttemp;
      clusttemp.nstrips = nstrips;
      clusttemp.istriplo = striplo;
      clusttemp.istriphi = striphi;
      clusttemp.istripmax = stripmax;
      clusttemp.hitindex.resize(nstrips);
      clusttemp.stripADCsum.resize(nstrips);
      
      double ADCsum = 0.0;
      double sumx = 0.0, sumx2 = 0.0, sumwx = 0.0;

      map<int,double> splitfraction;
      vector<double> stripADC(nstrips);
      
      double maxpos = (stripmax + 0.5 - 0.5*Nstrips)*pitch + offset;

      for( int istrip=striplo; istrip<=striphi; istrip++ ){
	double sumweight = ADCmax/(1.0 + pow( (stripmax-istrip)*pitch/fSigma_hitshape, 2 ) );
	double maxweight = sumweight;
	//loop over nearby local maxima and calculate split fraction for each strip:
	for( int jstrip = striplo-maxsep; jstrip<=striphi+maxsep; jstrip++ ){
	  if( localmaxima[isamp].find( jstrip ) != localmaxima[isamp].end() && jstrip != stripmax && std::abs(jstrip-istrip)<maxsep ){
	    sumweight += fADCsamples[hitindex[jstrip]][isamp]/(1.0 + pow( (jstrip-istrip)*pitch/fSigma_hitshape, 2 ) );
	  }
	}

	splitfraction[istrip] = maxweight/sumweight; //Fraction of this strip ADC signal assigned to the current cluster
	stripADC[istrip-striplo] = fADCsamples[hitindex[istrip]][isamp]*splitfraction[istrip]; //not yet totally clear how we will use this information
	
	ADCsum += stripADC[istrip-striplo];

	double hitpos = (istrip + 0.5 - 0.5*Nstrips) * pitch + offset;
	
	if( std::abs( istrip - stripmax ) <= std::max(UShort_t(1),std::min(UShort_t(maxsepcoord),UShort_t(maxsep) ) ) ){
	  double ADCtemp = stripADC[istrip-striplo];
	  sumx += hitpos * ADCtemp;
	  sumx2 += pow(hitpos,2)*ADCtemp;
	  sumwx += ADCtemp;
	}
	clusttemp.hitindex[istrip-striplo] = hitindex[istrip];
	clusttemp.stripADCsum[istrip-striplo] = stripADC[istrip-striplo];
	
      } //end loop over strips in cluster

      
      clusttemp.hitpos_mean = sumx/sumwx;
      clusttemp.hitpos_sigma = sqrt(sumx2/sumwx - pow(clusttemp.hitpos_mean,2));
      clusttemp.clusterADCsum = ADCsum; //sum of all ADCs in the cluster in this time sample:

      bool newmax = (allmaxima.insert( stripmax ) ).second;
      if( newmax ){
	timesamples_allmaxima[stripmax] = 0;
	Nsamp_allmaxima[stripmax] = 0;
	ADCmax_allmaxima[stripmax] = ADCsum;
	isampmax_allmaxima[stripmax] = isamp;
	protoclusters[stripmax].clear();
      }

      protoclusters[stripmax][isamp] = clusttemp;
      timesamples_allmaxima[stripmax] |= BIT(isamp);
      Nsamp_allmaxima[stripmax]++;

      if( ADCsum > ADCmax_allmaxima[stripmax] ){
	ADCmax_allmaxima[stripmax] = ADCsum;
	isampmax_allmaxima[stripmax] = isamp;
      }
      
    } //end loop over local maxima of ADC in this time sample
  } //end loop over time samples

 
  //We need an algorithm to build the
  //clusters from the proto-clusters and to possibly do time-based splitting of clusters and/or to merge together overlapping clusters: 

  clusters.resize( allmaxima.size() );

  //std::cout << "Number of strips with local maximum in at least one time sample = " << allmaxima.size() << endl;
  
  //Loop on the list of all strips which are local maxima in at least one time sample: 
  // for( auto stripmax : allmaxima ){

  //   //First, calculate the upper and lower limits of CONSECUTIVE time samples in which this strip is maximum, and compute a "mean time" of these samples
  //   int samplo = isampmax_allmaxima[stripmax];
  //   int samphi = isampmax_allmaxima[stripmax];
    
  //   while( samphi + 1 < fN_MPD_TIME_SAMP ){
  //     if( TESTBIT( timesamples_allmaxima, samphi+1 ) ) samphi++;
  //   }

  //   while( samplo - 1 >= 0 ){
  //     if( TESTBIT( timesamples_allmaxima, samplo-1 ) ) samplo--;
  //   }

  //   int nsamp_consecutive = samphi-samplo + 1; //number of consecutive time samples in which this strip is a local maximum:

  //   double sumt = 0.0, sumwt = 0.0;

  //   for( int isamp=samplo; isamp<=samphi; isamp++ ){
  //     double ADCtemp = protoclusters[stripmax][isamp].clusterADCsum;
  //     double tsamp = (isamp+0.5)*fSamplePeriod;
  //     sumt +=  tsamp*ADCtemp;
  //     sumwt += ADCtemp;
  //   }
    
  //   if( nsamp_consecutive < fN_MPD_TIME_SAMP ){ 
      
  //   }
  // }

  for( auto stripmax : allmaxima ){
    if( Nsamp_allmaxima[stripmax] > 2 ){ // we want this strip to be a local max in at least three time samples (at this stage we aren't requiring them to be consecutive)
      
      sbsgemcluster_t fullcluster;

      fullcluster.ADCsamples.resize( fN_MPD_TIME_SAMP, 0.0 );
      fullcluster.DeconvADCsamples.resize( fN_MPD_TIME_SAMP, 0.0 );
	    
      fullcluster.istripmax = stripmax;
	    
      fullcluster.isampmax = isampmax_allmaxima[stripmax];
      fullcluster.isneg = false;
      fullcluster.isnegontrack = false;
      fullcluster.keep = true;
      fullcluster.isampmaxDeconv = 0; //will need to actually calculate these deconvoluted things later. for now initialize to zero to avoid seg. fault.
      fullcluster.icombomaxDeconv = 0;

      fullcluster.rawstrip = fStripRaw[hitindex[stripmax]];
      fullcluster.rawMPD = fStripMPD[hitindex[stripmax]];
      fullcluster.rawAPV = fStripADC_ID[hitindex[stripmax]];
      
      int ngoodsamp=0;
    
      double sumx=0.0, sumx2=0.0, sumwx=0.0;
      double sumt=0.0, sumt2=0.0, sumwt=0.0;
      //do one loop over all samples, figure out the maximum size:
      for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
	if( TESTBIT( timesamples_allmaxima[stripmax], isamp ) ){ //then this strip is a local maximum in this time sample:
	  sbsgemcluster_t &protocluster = protoclusters[stripmax][isamp];
	  if( ngoodsamp == 0 ){
	    //initialize the full cluster
	    fullcluster.istriplo = protocluster.istriplo;
	    fullcluster.istriphi = protocluster.istriphi;
	    fullcluster.nstrips = protocluster.nstrips;
	    fullcluster.clusterADCsum = protocluster.clusterADCsum;
	  } else {
	    if( protocluster.istriplo < fullcluster.istriplo ) fullcluster.istriplo = protocluster.istriplo;
	    if( protocluster.istriphi > fullcluster.istriphi ) fullcluster.istriphi = protocluster.istriphi;
	    fullcluster.clusterADCsum += protocluster.clusterADCsum;
	  }
	  fullcluster.nstrips = fullcluster.istriphi-fullcluster.istriplo + 1;
	  fullcluster.ADCsamples[isamp] = protocluster.clusterADCsum; //we'll come back to deconvoluted values later:
	  sumx += protocluster.clusterADCsum * protocluster.hitpos_mean;
	  sumx2 += protocluster.clusterADCsum * pow( protocluster.hitpos_mean, 2 );
	  sumwx += protocluster.clusterADCsum;

	  //Of course, the above calculation will be changing the definition of hitpos_sigma from what it was!

	  sumt += protocluster.clusterADCsum * (isamp+0.5)*fSamplePeriod;
	  sumt2 += protocluster.clusterADCsum * pow( (isamp+0.5)*fSamplePeriod, 2 );
	  sumwt += protocluster.clusterADCsum;
	  
	  ngoodsamp++;
	} else { //if this strip is not a maximum in this time sample, we zero out the ADC value.
	  fullcluster.ADCsamples[isamp] = 0.0;
	}
	fullcluster.DeconvADCsamples[isamp] = 0.0;
      }

      fullcluster.hitpos_mean = sumx/sumwx;
      fullcluster.hitpos_sigma = sqrt( sumx2/sumwx - pow(fullcluster.hitpos_mean,2) );
      fullcluster.t_mean = sumt/sumwt;
      fullcluster.t_sigma = sqrt(sumt2/sumwt - pow(fullcluster.t_mean,2) );
      
      //    fullcluster.
      //we need a second loop to calculate the strip specific cluster properties:

      fullcluster.stripADCsum.resize( fullcluster.nstrips, 0.0 );
      fullcluster.DeconvADCsum.resize( fullcluster.nstrips, 0.0 );
      fullcluster.hitindex.resize( fullcluster.nstrips, 0.0 );

      //initialize hitindex for fullcluster:
      for( int istrip=0; istrip<fullcluster.nstrips; istrip++ ){
	fullcluster.hitindex[istrip] = hitindex[fullcluster.istriplo+istrip];

	int stripidx_full = fullcluster.istriplo + istrip;
      
	//loop over time samples:
	for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
	  if( TESTBIT( timesamples_allmaxima[stripmax], isamp ) ){
	    sbsgemcluster_t &protocluster = protoclusters[stripmax][isamp];

	    if( stripidx_full >= protocluster.istriplo && stripidx_full <= protocluster.istriphi ){
	      int idxproto = stripidx_full - protocluster.istriplo;
	      fullcluster.stripADCsum[istrip] += protocluster.stripADCsum[idxproto];
	    }
	  }
	}
      }

      //Now implement tests to add the current cluster to the array:
      if( fullcluster.stripADCsum[fullcluster.istripmax-fullcluster.istriplo] >= fThresholdStripSum && fullcluster.nstrips >= 2 && fullcluster.clusterADCsum >= fThresholdClusterSum ){
	if( (fabs( fullcluster.t_mean - fStripMaxTcut_central[axis] ) <= fStripMaxTcut_width[axis]) || !fUseStripTimingCuts ){

	  nclust_tot++;
	  
	  if( fabs( fullcluster.hitpos_mean - constraint_center ) <= constraint_width ){
	    fullcluster.keep = true;
	    fullcluster.isneg = false;
	    fullcluster.isnegontrack = false;
	    clusters[nclust] = fullcluster;
	    nclust++;
	    nclust_pos++;
	  }
	  
	}
      }
      
    } //end check that current strip is maximum in at least three time samples
  } //end loop over strips with local maximum in any time sample

  //Fill cluster multiplicity and "hit rate" histograms:
  if( fMakeEfficiencyPlots && fEfficiencyInitialized
      && hClusterBasedOccupancyUstrips != nullptr
      && hClusterBasedOccupancyVstrips != nullptr
      && hClusterMultiplicityUstrips != nullptr
      && hClusterMultiplicityVstrips != nullptr ){
    
    //We are using units of kHz/cm^2 for our "rate" plot:
    //Timing window size = cut width:
    
    //The following is in ns, we want to convert to milliseconds, so need to DIVIDE by 1e6:
    double window = 2.*fStripMaxTcut_width[axis]; //later we can use a fancier definition:
    if( !fUseStripTimingCuts ) window = fN_MPD_TIME_SAMP * fSamplePeriod; //If we aren't using strip timing cuts we take the entire six-sample window as the time interval for "occupancy"
    //The following is in m^2, need to multiply by 1e4
    double area = GetXSize() * GetYSize();
    
    //window * area = ns * m^2 * 1e4 cm^2 /m^2 * 1e-6 ms/ns 
    double ratefac = window*area/100.0; // ms * cm^2
    
    if( axis == SBSGEM::kUaxis ){
      hClusterBasedOccupancyUstrips->Fill( double(nclust_tot)/ratefac );
      hClusterMultiplicityUstrips->Fill( double(nclust_tot) );
    } else {
      hClusterBasedOccupancyVstrips->Fill( double(nclust_tot)/ratefac );
      hClusterMultiplicityVstrips->Fill( double(nclust_tot) );
    }
  }
  
}



void SBSGEMModule::find_clusters_1D( SBSGEM::GEMaxis_t axis, Double_t constraint_center, Double_t constraint_width ){

  //Constraint center and constraint width are assumed to be given in "standard" Hall A units (meters) in module-local coordinates
  // (SPECIFICALLY: constraint center and constraint width are assumed to refer to the direction measured by the strips being considered here)
  //This method will generally only be called by the reconstruction methods of SBSGEMTrackerBase

  // cout << "constraint center, constraint width = " << constraint_center << ", " << constraint_width << endl;
  
  if( !fIsDecoded ){
    cout << "find_clusters invoked before decoding for GEM Module " << GetName() << ", doing nothing" << endl;
    return;
  }

  UShort_t maxsep = ( axis == SBSGEM::kUaxis ) ? fMaxNeighborsU_totalcharge : fMaxNeighborsV_totalcharge;
  UShort_t maxsepcoord = ( axis == SBSGEM::kUaxis ) ? fMaxNeighborsU_hitpos : fMaxNeighborsV_hitpos; 
  UInt_t Nstrips = ( axis == SBSGEM::kUaxis ) ? fNstripsU : fNstripsV;
  Double_t pitch = ( axis == SBSGEM::kUaxis ) ? fUStripPitch : fVStripPitch;
  Double_t offset = (axis == SBSGEM::kUaxis) ? fUStripOffset : fVStripOffset;
  
  //hopefully this compiles and works correctly:
  std::vector<sbsgemcluster_t> &clusters = (axis == SBSGEM::kUaxis ) ? fUclusters : fVclusters;

  UInt_t &nclust = ( axis == SBSGEM::kUaxis ) ? fNclustU : fNclustV; 
  UInt_t &nclust_pos = ( axis == SBSGEM::kUaxis ) ? fNclustU_pos : fNclustV_pos; 
  UInt_t &nclust_neg = ( axis == SBSGEM::kUaxis ) ? fNclustU_neg : fNclustV_neg; 
  UInt_t &nclust_tot = ( axis == SBSGEM::kUaxis ) ? fNclustU_total : fNclustV_total;
  
  nclust = 0;
  nclust_pos = 0;
  nclust_neg = 0;
  nclust_tot = 0;
 
  
  clusters.clear();
  
  std::set<UShort_t> striplist;  //sorted list of strips for 1D clustering
  std::map<UShort_t, UInt_t> hitindex; //key = strip ID, mapped value = index in decoded hit array, needed to access the other information efficiently:
  std::map<UShort_t, Double_t> pedrms_strip;
  std::map<UShort_t, Double_t> ADC_strip; // These are the (configuration-dependent) quantities we use for clustering. They depend on the values of fClusteringFlag and fSuppressFirstLast and fDeconvolution_flag
  std::map<UShort_t, Double_t> ADC_maxsamp; //
  std::map<UShort_t, Double_t> Tmean_strip; //strip mean time with first and/or last samples removed (if applicable)
  std::map<UShort_t, Double_t> Tmean_strip_deconv; //strip deconvoluted mean time
  std::map<UShort_t, Double_t> Tfit_strip; //strip "fit" time
  std::map<UShort_t, Double_t> Tsigma_strip; //strip rms time with first and/or last samples removed (if applicable)
  
  std::set<UShort_t> striplist_neg;  //same as above but for negative strips
  std::map<UShort_t, UInt_t> hitindex_neg;
  std::map<UShort_t, Double_t> pedrms_strip_neg;

  UShort_t FirstSampleCorrCoeff=0;
  UShort_t NsampCorrCoeff=fN_MPD_TIME_SAMP;

  // if( fSuppressFirstLast != 0 ){
  //   if( fSuppressFirstLast > 0 ){ //suppress first and last time samples
  //     FirstSampleCorrCoeff = 1;
  //     NsampCorrCoeff = fN_MPD_TIME_SAMP-2;
  //   } else if( fSuppressFirstLast == -2 ){ //exclude last time sample only:
  //     FirstSampleCorrCoeff = 0;
  //     NsampCorrCoeff = fN_MPD_TIME_SAMP-1;
  //   } else { //negative value other than -2: exclude first time sample only:
  //     FirstSampleCorrCoeff = 1;
  //     NsampCorrCoeff = fN_MPD_TIME_SAMP-1;
  //   }
  // }
  
  for( int ihit=0; ihit<fNstrips_hit; ihit++ ){
    //if( fAxis[ihit] == axis && fKeepStrip[ihit] ){
    if( fAxis[ihit] == axis ){ //Try only enforcing fKeepStrip on the cluster maximum:
    
      bool newstrip = (striplist.insert( fStrip[ihit] ) ).second;

      if( newstrip ){ //should always be true:
	hitindex[fStrip[ihit]] = ihit;
	if( axis == SBSGEM::kUaxis ){
	  pedrms_strip[fStrip[ihit]] = fPedRMSU[fStrip[ihit]];
	} else {
	  pedrms_strip[fStrip[ihit]] = fPedRMSV[fStrip[ihit]];
	}

	//Default behavior is that clustering is done using sums of ADC values over all time
	//samples on a strip:
	ADC_strip[fStrip[ihit]] = fADCsums[ihit];
	ADC_maxsamp[fStrip[ihit]] = fADCmax[ihit];
	Tmean_strip[fStrip[ihit]] = fTmean[ihit];
	Tmean_strip_deconv[fStrip[ihit]] = fTmeanDeconv[ihit];
	Tfit_strip[fStrip[ihit]] = fStripTfit[ihit];
	Tsigma_strip[fStrip[ihit]] = fTsigma[ihit];

	//fClusteringFlag =
	// 1. Use deconvoluted max. combo
	// 2. Use sum of the three time samples closest to maxstrip_t0

	if( fClusteringFlag == 1 ){ //Use deconvoluted max combo and max sample for clustering:
 	  ADC_strip[fStrip[ihit]] = fADCmaxDeconvCombo[ihit]; //deconvoluted max. two-sample combination
	  ADC_maxsamp[fStrip[ihit]] = fADCmaxDeconv[ihit];
	}
      }
    }
    //Also add strips for negative signal clustering if fNegSignalStudy is true
    if( fAxis[ihit] == axis && fStripIsNeg[ihit] && fStrip_BUILD_ALL_SAMPLES[ihit] && !fStrip_ENABLE_CM[ihit] && fNegSignalStudy){
      bool newstrip = (striplist_neg.insert( fStrip[ihit] ) ).second;
      
      if( newstrip ){ //should always be true:
	hitindex_neg[fStrip[ihit]] = ihit;
	if( axis == SBSGEM::kUaxis ){
	  pedrms_strip_neg[fStrip[ihit]] = fPedRMSU[fStrip[ihit]];
	} else {
	  pedrms_strip_neg[fStrip[ihit]] = fPedRMSV[fStrip[ihit]];
	}
      }
    }
  }

  std::set<UShort_t> localmaxima;
  std::map<UShort_t,bool> islocalmax;
  //std::map<UShort_t,bool> passed_constraint;
  
  
  for( std::set<UShort_t>::iterator i=striplist.begin(); i != striplist.end(); ++i ){
    int strip = *i;
    //int hitidx = hitindex[strip];
    islocalmax[strip] = false;

    //double sumstrip = fADCsums[hitindex[strip]];
    double sumstrip = ADC_strip[strip];  
    double sumleft = 0.0;
    double sumright = 0.0;

    
    if( striplist.find( strip - 1 ) != striplist.end() ){
      //sumleft = fADCsums[hitindex[strip-1]]; //if strip - 1 is found in strip list, hitindex is guaranteed to have been initialized above
      sumleft = ADC_strip[strip-1]; //if strip - 1 is found in strip list, hitindex is guaranteed to have been initialized above
    }
    if( striplist.find( strip + 1 ) != striplist.end() ){
      //sumright = fADCsums[hitindex[strip+1]];
      sumright = ADC_strip[strip+1];
    }

    double thresh_samp = fThresholdSample; 
    double thresh_strip = fThresholdStripSum;
    if( fClusteringFlag == 1 ){
      thresh_strip = fThresholdDeconvADCMaxCombo;
      thresh_samp = fThresholdSampleDeconv;
    }
    
    bool goodADC = sumstrip >= thresh_strip && ADC_maxsamp[strip] >= thresh_samp;
    if( goodADC && sumstrip >= sumleft && sumstrip >= sumright ){
	//	fADCmax[hitindex[strip]] >= fThresholdSample ){ //new local max:
      bool goodtime = true;

      double tstrip = Tmean_strip[strip];
      double t0 = fStripMaxTcut_central[axis];
      double tcut = fStripMaxTcut_width[axis];
      double tsigma = fStripMaxTcut_sigma[axis];

      //double t0 = 0.0; //now the mean value has been subtracted off.
      
      if( fUseStripTimingCuts == 2 && fClusteringFlag != 1 ){ //alternate timing cut based on strip "fitted" time
	tstrip = Tfit_strip[strip];
	t0 = fStripMaxTcut_central_fit[axis];
	tcut = fStripMaxTcut_width_fit[axis];
	tsigma = fStripMaxTcut_sigma_fit[axis]; 
      }
      
      if( fClusteringFlag == 1 ){
	tstrip = Tmean_strip_deconv[strip];
	t0 = fStripMaxTcut_central_deconv[axis];
	tcut = fStripMaxTcut_width_deconv[axis];
	tsigma = fStripMaxTcut_sigma_deconv[axis]; 
      }
      
      if( fUseStripTimingCuts != 0 && fabs( tstrip - t0 ) > tcut * tsigma ) goodtime = false;

      // if( !goodtime && fClusteringFlag == 1 ){
      // 	// if a strip fails the basic timing cut but has good deconvoluted ADC value, keep it
      // 	// anyway:
      // 	if( fADCmaxDeconvCombo[hitindex[strip]] >= fThresholdSample ){
      // 	  goodtime = true;
      // 	}
      // }

      if( goodtime && fKeepStrip[hitindex[strip]] ){
	islocalmax[strip] = true;
	localmaxima.insert( strip );
      }
    }
  } // end loop over list of strips along this axis:

  //cout << "before peak erasing, n local maxima = " << localmaxima.size() << endl;
  
  vector<int> peakstoerase; 

  //now calculate "prominence" for all peaks and erase "insignificant" peaks:

  for( std::set<UShort_t>::iterator i=localmaxima.begin(); i != localmaxima.end(); ++i ){
    int stripmax = *i;

    //double ADCmax = fADCsums[hitindex[stripmax]];
    double ADCmax = ADC_strip[stripmax];
    double prominence = ADCmax;

    int striplo = stripmax, striphi = stripmax;
    double ADCminright=ADCmax, ADCminleft=ADCmax;

    bool higherpeakright=false,higherpeakleft=false;
    int peakright = -1, peakleft = -1;

    while( striplist.find( striphi+1 ) != striplist.end() ){
      striphi++;

      //Double_t ADCtest = fADCsums[hitindex[striphi]];
      Double_t ADCtest = ADC_strip[striphi];
      
      if( ADCtest < ADCminright && !higherpeakright ){ //as long as we haven't yet found a higher peak to the right, this is the lowest point between the current maximum and the next higher peak to the right:
	ADCminright = ADCtest;
      }

      if( islocalmax[striphi] && ADCtest > ADCmax ){ //then this peak is in a contiguous group with another higher peak to the right:
	higherpeakright = true;
	peakright = striphi;
      }
    }

    while( striplist.find(striplo-1) != striplist.end() ){
      striplo--;
      //Double_t ADCtest = fADCsums[hitindex[striplo]];
      Double_t ADCtest = ADC_strip[striplo];
      if( ADCtest < ADCminleft && !higherpeakleft ){ //as long as we haven't yet found a higher peak to the left, this is the lowest point between the current maximum and the next higher peak to the left:
	ADCminleft = ADCtest;
      }

      if( islocalmax[striplo] && ADCtest > ADCmax ){ //then this peak is in a contiguous group with another higher peak to the left:
	higherpeakleft = true;
	peakleft = striplo;
      }
    }

    //    double sigma_sum = sqrt( double(fN_MPD_TIME_SAMP) )*fZeroSuppressRMS; //~25-50 ADC

    // the above calculation is not consistent with the intended usages of the above variables.
    // We should instead use the pedestal RMS value for the strip in question. The strip RMS values
    // represent the RMS of the AVERAGE of the samples. So the prominence threshold should be expressed in terms of the same thing to be consistent:
    double sigma_sum = double(fN_MPD_TIME_SAMP)*pedrms_strip[stripmax]; //Typically 60-70 ADC. Since pedrms_strip represents the rms of the sum of the ADC samples divided by the number of samples, to get the RMS of the sum, we need only multiply by the number of samples.
    //A 5-sigma threshold on this quantity would typically be about 300-350 ADC.

    if( fClusteringFlag == 1 ){ //What is the effect of deconvolution on noise? 
      // It turns out from looking at the width of the pedestal peak
      // in the deconvoluted ADCs from
      // full readout events that the noise in the deconvoluted samples
      // is about the same as the noise in the regular samples.
      // HOWEVER: in this case we aren't working with the sum of six samples. So we need to
      // modify "sigma" accordingly. We are generally working with the sum of two deconvoluted
      // samples. ASSUMING the deconvoluted sample width is the same as the individual
      // sample width, we have: 
      sigma_sum = pedrms_strip[stripmax] * fRMS_ConversionFactor;
    }
    bool peak_close = false;
    if( !higherpeakleft ) ADCminleft = 0.0;
    if( !higherpeakright ) ADCminright = 0.0;

    if( higherpeakright || higherpeakleft ){ //this peak is contiguous with higher peaks on either the left or right or both:
      prominence = ADCmax - std::max( ADCminleft, ADCminright ); //subtract the higher of the two valleys to get the prominence

      if( higherpeakleft && std::abs( peakleft - stripmax ) <= 2*maxsep ) peak_close = true;
      if( higherpeakright && std::abs( peakright - stripmax ) <= 2*maxsep ) peak_close = true;

      if( peak_close && (prominence < fThresh_2ndMax_nsigma * sigma_sum ||
			 prominence/ADCmax < fThresh_2ndMax_fraction ) ){
	peakstoerase.push_back( stripmax );
      }
    }
  }

  //Erase "insignificant" peaks (those in contiguous grouping with higher peak with prominence below thresholds):
  for(int ipeak : peakstoerase){
    localmaxima.erase( ipeak );
    islocalmax[ipeak] = false;
  }
  

  //cout << "After peak erasing, n local maxima = " << localmaxima.size() << endl;
  //for speed/efficiency, resize the cluster array to the theoretical maximum
  //and use operator[] rather than push_back:
  clusters.resize( localmaxima.size() );

  //nclust_tot = localmaxima.size();
  
  //Cluster formation and cluster splitting from remaining local maxima:
  for( auto i = localmaxima.begin(); i != localmaxima.end(); ++i ){
    int stripmax = *i;
    int striplo = stripmax;
    int striphi = stripmax;
    //double ADCmax = fADCsums[hitindex[stripmax]];
    double ADCmax = ADC_strip[stripmax];
    
    bool found_neighbor_low = true;

    //double Tfit = 

    
    
    //while( striplist.find( striplo-1 ) != striplist.end() &&
    //	   stripmax - striplo < maxsep ){
    while( found_neighbor_low ){
      
      found_neighbor_low = striplist.find( striplo - 1 ) != striplist.end() && stripmax - striplo < maxsep;

      double Tdiff = fTmean[hitindex[striplo-1]] - fTmean[hitindex[stripmax]];
      
      
      if( fUseStripTimingCuts == 2 && fClusteringFlag == 0 ){ //Use "fitted" strip time instead:
	Tdiff = fStripTfit[hitindex[striplo-1]] - fStripTfit[hitindex[stripmax]];
      }
      if( fClusteringFlag == 1 ){
	Tdiff = fTmeanDeconv[hitindex[striplo-1]] - fTmeanDeconv[hitindex[stripmax]];
      }

      double Ccoeff = CorrCoeff( NsampCorrCoeff, fADCsamples[hitindex[striplo-1]], fADCsamples[hitindex[stripmax]], FirstSampleCorrCoeff );
      //double Tdiff_deconv = 
      
      //correlation coefficient of the deconvoluted samples:
      double Ccoeff_deconv = CorrCoeff( fN_MPD_TIME_SAMP, fADCsamples_deconv[hitindex[striplo-1]], fADCsamples_deconv[hitindex[stripmax]] );

      if( fUseStripTimingCuts != 0 && fabs(Tdiff) > fStripAddTcut_width ) found_neighbor_low = false;
      //Apply ONE cut on corr. coeff.; either regular or deconvoluted samples:
      //if( fClusteringFlag == 1 && std::abs( fMaxSampDeconvCombo[hitindex[striplo-1]]-fMaxSampDeconvCombo[hitindex[stripmax]] ) > 1 ) found_neighbor_low = false;
      
      double Ccoeff_test = fClusteringFlag == 1 ? Ccoeff_deconv : Ccoeff;

      if( Ccoeff_test < fStripAddCorrCoeffCut ) found_neighbor_low = false;
      
      
      if( found_neighbor_low ) striplo--;
    }

    // while( striplist.find( striphi+1 ) != striplist.end() &&
    // 	   striphi - stripmax < maxsep ){
    //   striphi++;
    // }

    bool found_neighbor_high = true;
    
    //while( striplist.find( striplo-1 ) != striplist.end() &&
    //	   stripmax - striplo < maxsep ){
    while( found_neighbor_high ){
      
      found_neighbor_high = striplist.find( striphi + 1 ) != striplist.end() && striphi - stripmax < maxsep;

      double Tdiff = fTmean[hitindex[striphi+1]] - fTmean[hitindex[stripmax]];

      if( fUseStripTimingCuts == 2 && fClusteringFlag == 0 ){ //Use "fitted" strip time instead:
	Tdiff = fStripTfit[hitindex[striphi+1]] - fStripTfit[hitindex[stripmax]];
      }
      if( fClusteringFlag == 1 ){
	Tdiff = fTmeanDeconv[hitindex[striphi+1]] - fTmeanDeconv[hitindex[stripmax]];
      }
      
      double Ccoeff = CorrCoeff( NsampCorrCoeff, fADCsamples[hitindex[striphi+1]], fADCsamples[hitindex[stripmax]], FirstSampleCorrCoeff );
      //double Tdiff_deconv = fTmeanDeconv[hitindex[striphi+1]] - fTmeanDeconv[hitindex[stripmax]];
      
      //correlation coefficient of the deconvoluted samples:
      double Ccoeff_deconv = CorrCoeff( fN_MPD_TIME_SAMP, fADCsamples_deconv[hitindex[striphi+1]], fADCsamples_deconv[hitindex[stripmax]] );

      if( fUseStripTimingCuts != 0 && fabs(Tdiff) > fStripAddTcut_width ) found_neighbor_high = false;
      //if( fClusteringFlag == 1 && std::abs( fMaxSampDeconvCombo[hitindex[striphi+1]]-fMaxSampDeconvCombo[hitindex[stripmax]] ) > 1 ) found_neighbor_high = false;
      
      
      double Ccoeff_test = fClusteringFlag == 1 ? Ccoeff_deconv : Ccoeff;

      if( Ccoeff_test < fStripAddCorrCoeffCut ) found_neighbor_high = false;
      
      // if( fDeconvolutionFlag != 0 ){
      // 	Ccoeff = CorrCoeff( fN_MPD_TIME_SAMP, fADCsamples_deconv[hitindex[striplo-1]], fADCsamples_deconv[hitindex[stripmax]] );
      // }

      //if the greater of the two correlation coefficients (shaped samples vs. deconvoluted samples) is too low, don't add this strip:
     
	

      //If either the strip time difference with the max. strip or the Correlation coefficient with the max strip
      //fails the cuts, stop growing the cluster in this direction
      
      if( found_neighbor_high ) striphi++;
    }
    
    int nstrips = striphi-striplo+1;

    double sumx = 0.0, sumx2 = 0.0, sumADC = 0.0, sumt = 0.0, sumt2 = 0.0;
    double sumwx = 0.0;
    double sumtdeconv = 0.0;
    double sumADCdeconv = 0.0;
    //double sumADCdeconv_combo = 0.0;
    
    map<int,double> splitfraction;
    vector<double> stripADCsum(nstrips);

    double maxpos = (stripmax + 0.5 - 0.5*Nstrips) * pitch + offset;

    //If peak position falls inside the "track search region" constraint, add a new cluster: 
    //if( fabs( maxpos - constraint_center ) <= constraint_width ){
    //Move constraint check to later so we can filter the "total cluster multiplicity" by basic quality criteria:
    //This MIGHT slow down analysis at higher occupancies, but we'll have to see how noticeable it is:
    
    //create a cluster, but don't add it to the 1D cluster array unless it passes the track search region constraint:
    sbsgemcluster_t clusttemp;
    clusttemp.nstrips = nstrips;
    clusttemp.istriplo = striplo;
    clusttemp.istriphi = striphi;
    clusttemp.istripmax = stripmax;
    clusttemp.ADCsamples.resize(fN_MPD_TIME_SAMP);
    clusttemp.DeconvADCsamples.resize( fN_MPD_TIME_SAMP, 0.0 );
    clusttemp.stripADCsum.clear();
    clusttemp.DeconvADCsum.clear();
    clusttemp.hitindex.clear();
    clusttemp.rawstrip = fStripRaw[hitindex[stripmax]];
    clusttemp.rawMPD = fStripMPD[hitindex[stripmax]];
    clusttemp.rawAPV = fStripADC_ID[hitindex[stripmax]];

    for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){ //initialize cluster-summed ADC samples to zero:
      clusttemp.ADCsamples[isamp] = 0.0;
      clusttemp.DeconvADCsamples[isamp] = 0.0;
    }
      
    for( int istrip=striplo; istrip<=striphi; istrip++ ){
      //int nmax_strip = 1;

      //calculate "split fraction" for each strip in the cluster:
      double sumweight = ADCmax/(1.0 + pow( (stripmax-istrip)*pitch/fSigma_hitshape, 2 ) );
      double maxweight = sumweight;
      for( int jstrip=istrip-maxsep; jstrip<=istrip+maxsep; jstrip++ ){
	if( localmaxima.find( jstrip ) != localmaxima.end() && jstrip != stripmax ){
	  sumweight += ADC_strip[jstrip]/( 1.0 + pow( (jstrip-istrip)*pitch/fSigma_hitshape, 2 ) );
	}
      }
   
      splitfraction[istrip] = maxweight/sumweight;

      double hitpos = (istrip + 0.5 - 0.5*Nstrips) * pitch + offset; //local hit position along direction measured by these strips
      double ADCstrip = ADC_strip[istrip] * splitfraction[istrip];
      //double tstrip = fTmean[hitindex[istrip]];
      double tstrip = Tmean_strip[istrip];

      //    double tstrip_deconv = fTmeanDeconv[hitindex[istrip]];
      double tstrip_deconv = Tmean_strip_deconv[istrip];
      double ADCstrip_deconv = fADCsumsDeconv[hitindex[istrip]]*splitfraction[istrip];
      
      for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
	clusttemp.ADCsamples[isamp] += fADCsamples[hitindex[istrip]][isamp]*splitfraction[istrip];
	clusttemp.DeconvADCsamples[isamp] += fADCsamples_deconv[hitindex[istrip]][isamp]*splitfraction[istrip];
      }
      
      //clusttemp.stripADCsum.push_back( ADCstrip );
      clusttemp.stripADCsum.push_back( fADCsums[hitindex[istrip]]*splitfraction[istrip] );
      clusttemp.DeconvADCsum.push_back( ADCstrip_deconv );
      
      clusttemp.hitindex.push_back( hitindex[istrip] ); //do we use this anywhere? Yes, it is good to keep track of this if we want to access raw strip info later on 
				       //sumADC += ADCstrip;
      sumADC += fADCsums[hitindex[istrip]]*splitfraction[istrip];
				       
      sumADCdeconv += ADCstrip_deconv;
      //sumADCdeconv_combo += fADCmaxDeconvCombo[hitindex[istrip]]*splitfraction[istrip];
      
      if( std::abs( istrip - stripmax ) <= std::max(UShort_t(1),std::min(maxsepcoord,maxsep)) ){ 
	sumx += hitpos * ADCstrip;
	sumx2 += pow(hitpos,2) * ADCstrip;
	sumwx += ADCstrip;
	//use same strip cuts for cluster timing determination as for position reconstruction: may revisit later:
	sumt += tstrip * ADCstrip;
	sumt2 += pow(tstrip,2) * ADCstrip;
	sumtdeconv += tstrip_deconv * ADCstrip;
      } 
    }
    clusttemp.isampmaxDeconv = 0;
    clusttemp.icombomaxDeconv = 0;
    clusttemp.isampmax = 0; //figure out time sample in which peak of cluster-summed ADC values occurs:
    double maxADC = 0.0;
    double maxADC_deconv = 0.0;
    double maxADCcombo_deconv = 0.0;
    
    for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
      if( isamp == 0 || clusttemp.ADCsamples[isamp] > maxADC ){
	maxADC = clusttemp.ADCsamples[isamp];
	clusttemp.isampmax = isamp;
      }

      if( isamp == 0 || clusttemp.DeconvADCsamples[isamp] > maxADC_deconv ){
	maxADC_deconv = clusttemp.DeconvADCsamples[isamp];
	clusttemp.isampmaxDeconv = isamp;
      }

      double combotemp = clusttemp.DeconvADCsamples[isamp];
      if( isamp == 0 ){
	clusttemp.icombomaxDeconv = 0;
	maxADCcombo_deconv = combotemp;
      } else {
	combotemp += clusttemp.DeconvADCsamples[isamp-1];
	if( combotemp > maxADCcombo_deconv ){
	  maxADCcombo_deconv = combotemp;
	  clusttemp.icombomaxDeconv = isamp; 
	}
      }
      if( isamp + 1 == fN_MPD_TIME_SAMP && clusttemp.DeconvADCsamples[isamp] > maxADCcombo_deconv ){
	maxADCcombo_deconv = clusttemp.DeconvADCsamples[isamp];
	clusttemp.icombomaxDeconv = fN_MPD_TIME_SAMP;
      }	
    }
    
    clusttemp.hitpos_mean = sumx / sumwx;
    clusttemp.hitpos_sigma = sqrt( sumx2/sumwx - pow(clusttemp.hitpos_mean,2) );
    clusttemp.clusterADCsum = sumADC;
    clusttemp.clusterADCsumDeconv = sumADCdeconv;
    clusttemp.clusterADCsumDeconvMaxCombo = maxADCcombo_deconv;
    clusttemp.t_mean = sumt / sumwx;
    clusttemp.t_sigma = sqrt( sumt2 / sumwx - pow(clusttemp.t_mean,2) );

    clusttemp.t_mean_deconv = sumtdeconv/sumwx;

    FitClusterTime( clusttemp );

    //clusttemp.t_mean_fit -= fStripMaxTcut_central_fit[axis];
    
    //initialize "keep" flag for all 1D clusters to true:
    clusttemp.keep = true;
      
    clusttemp.isneg = false; //This is used for negative strip analysis
    clusttemp.isnegontrack = false; //This is used for negative strip analysis

      // In the standalone we don't apply an independent threshold on the cluster sum in the context of 1D cluster-finding:
      // if( sumADC >= fThresholdClusterSum ){
      // if( axis == SBSGEM::kVaxis ){
      // 	fVclusters.push_back( clusttemp );
      // 	fNclustV++;
      // } else {
      // 	fUclusters.push_back( clusttemp );
      // 	fNclustU++;
      // }
    if( sumADC >= fThresholdClusterSum && clusttemp.nstrips >= 2 ){ //Increment "total cluster multiplicity"
      nclust_tot++;
    }
    
    //Hopefully this works correctly:
    if( fabs( clusttemp.hitpos_mean - constraint_center ) <= constraint_width ){

      //Fit max strip time for hits in constraint region:
      // double Tfit = FitStripTime( hitindex[stripmax], 20.0 );
      // fStripTfit[hitindex[stripmax]] = Tfit;

      
      // if( fabs( Tfit - 25.0 ) < 10.0 ){ //Experimental, crude hack for testing:
      
      clusters[nclust] = clusttemp;
      nclust++;
      nclust_pos++;
	//}

	// std::cout << "found cluster, (axis, istripmax, nstrips, ADCsum, hit pos (mm) )=(" << axis << ", " << clusttemp.istripmax << ", "
	// 	  << clusttemp.nstrips << ", " << clusttemp.clusterADCsum
	// 	  << ", " << clusttemp.hitpos_mean*1000.0 << ")" << std::endl;
	
      //}
    } //Check if peak is inside track search region constraint
  } //end loop on local maxima

  //Fill cluster multiplicity and "hit rate" histograms:
  if( fMakeEfficiencyPlots && fEfficiencyInitialized
      && hClusterBasedOccupancyUstrips != nullptr
      && hClusterBasedOccupancyVstrips != nullptr
      && hClusterMultiplicityUstrips != nullptr
      && hClusterMultiplicityVstrips != nullptr ){
    
    //We are using units of kHz/cm^2 for our "rate" plot:
    //Timing window size = cut width:
    
    //The following is in ns, we want to convert to milliseconds, so need to DIVIDE by 1e6:
    double window = fStripMaxTcut_width[axis]; //later we can use a fancier definition:
    if( !fUseStripTimingCuts ) window = fN_MPD_TIME_SAMP * fSamplePeriod/2.0; //If we aren't using strip timing cuts we take the entire six-sample window as the time interval for "occupancy"
    //The following is in m^2, need to multiply by 1e4
    double area = GetXSize() * GetYSize();
    
    //window * area = ns * m^2 * 1e4 cm^2 /m^2 * 1e-6 ms/ns 
    double ratefac = 2.0*window*area/100.0; // ms * cm^2
    
    if( axis == SBSGEM::kUaxis ){
      hClusterBasedOccupancyUstrips->Fill( double(nclust_tot)/ratefac );
      hClusterMultiplicityUstrips->Fill( double(nclust_tot) );
    } else {
      hClusterBasedOccupancyVstrips->Fill( double(nclust_tot)/ratefac );
      hClusterMultiplicityVstrips->Fill( double(nclust_tot) );
    }
  }
  
  //clusters.resize(nclust); //just to make sure no pathological behavior later on

  //std::cout << "number of clusters found = " << nclust << std::endl;
  
  filter_1Dhits(axis);
  // filter_1Dhits(SBSGEM::kVaxis);


  ////// Below is an exact copy of the parts above but clusters negative strips instead. This works by adding -1 factors
  ////// whenever we need the ADC value. Then at the end when saving the cluster information we flip the ADC back 
  ////// negative again. 
  localmaxima.clear();
  islocalmax.clear();
  
  //Do clustering again but for negative strips
  for( std::set<UShort_t>::iterator i=striplist_neg.begin(); i != striplist_neg.end(); ++i ){
    int strip = *i;
    //int hitidx = hitindex_neg[strip];
    islocalmax[strip] = false;

    double sumstrip = -1*fADCsums[hitindex_neg[strip]]; //Add -1 factor
    double sumleft = 0.0;
    double sumright = 0.0;
    
    
    if( striplist_neg.find( strip - 1 ) != striplist_neg.end() ){
      sumleft = -1*fADCsums[hitindex_neg[strip-1]]; //if strip - 1 is found in strip list, hitindex_neg is guaranteed to have been initialized above
    }
    if( striplist_neg.find( strip + 1 ) != striplist_neg.end() ){
      sumright = -1*fADCsums[hitindex_neg[strip+1]];
    }

    //apply additional thresholds on max. sample and strip sum for local maxima:
    //If a strip is not a local max, the threshold is just 5sigma above the noise 
    //from decoding
    //-1 factor added in if statuement
    if( sumstrip >= sumleft && sumstrip >= sumright && 
	sumstrip >= fThresholdStripSum &&
	-1*fADCmax[hitindex_neg[strip]] >= fThresholdSample ){ //new local max:
      islocalmax[strip] = true;
      localmaxima.insert( strip );      
    } 
  } // end loop over list of strips along this axis:

  //  cout << "before peak erasing, n local maxima = " << localmaxima.size() << endl;
  
  peakstoerase.clear(); 

  //now calculate "prominence" for all peaks and erase "insignificant" peaks:

  for( std::set<UShort_t>::iterator i=localmaxima.begin(); i != localmaxima.end(); ++i ){
    int stripmax = *i;

    //Added -1 factor
    double ADCmax = -1*fADCsums[hitindex_neg[stripmax]];
    double prominence = -1*ADCmax;

    int striplo = stripmax, striphi = stripmax;
    double ADCminright=ADCmax, ADCminleft=ADCmax;

    bool higherpeakright=false,higherpeakleft=false;
    int peakright = -1, peakleft = -1;

    while( striplist_neg.find( striphi+1 ) != striplist_neg.end() ){
      striphi++;

      Double_t ADCtest = -1*fADCsums[hitindex_neg[striphi]]; //Added -1 factor
      
      if( ADCtest < ADCminright && !higherpeakright ){ //as long as we haven't yet found a higher peak to the right, this is the lowest point between the current maximum and the next higher peak to the right:
	ADCminright = ADCtest;
      }

      if( islocalmax[striphi] && ADCtest > ADCmax ){ //then this peak is in a contiguous group with another higher peak to the right:
	higherpeakright = true;
	peakright = striphi;
      }
    }

    while( striplist_neg.find(striplo-1) != striplist_neg.end() ){
      striplo--;
      Double_t ADCtest = -1*fADCsums[hitindex_neg[striplo]]; //Added -q factor
      if( ADCtest < ADCminleft && !higherpeakleft ){ //as long as we haven't yet found a higher peak to the left, this is the lowest point between the current maximum and the next higher peak to the left:
	ADCminleft = ADCtest;
      }

      if( islocalmax[striplo] && ADCtest > ADCmax ){ //then this peak is in a contiguous group with another higher peak to the left:
	higherpeakleft = true;
	peakleft = striplo;
      }
    }

    //    double sigma_sum = sqrt( double(fN_MPD_TIME_SAMP) )*fZeroSuppressRMS; //~25-50 ADC

    // the above calculation is not consistent with the intended usages of the above variables.
    // We should instead use the pedestal RMS value for the strip in question. The strip RMS values
    // represent the RMS of the AVERAGE of the samples. So the prominence threshold should be expressed in terms of the same thing to be consistent:
    double sigma_sum = double(fN_MPD_TIME_SAMP)*pedrms_strip_neg[stripmax]; //Typically 60-70 ADC. Since pedrms_strip represents the rms of the sum of the ADC samples divided by the number of samples, to get the RMS of the sum, we need only multiply by the number of samples.
    //A 5-sigma threshold on this quantity would typically be about 300-350 ADC.
    
    bool peak_close = false;
    if( !higherpeakleft ) ADCminleft = 0.0;
    if( !higherpeakright ) ADCminright = 0.0;

    if( higherpeakright || higherpeakleft ){ //this peak is contiguous with higher peaks on either the left or right or both:
      prominence = ADCmax - std::max( ADCminleft, ADCminright ); //subtract the higher of the two valleys to get the prominence

      if( higherpeakleft && std::abs( peakleft - stripmax ) <= 2*maxsep ) peak_close = true;
      if( higherpeakright && std::abs( peakright - stripmax ) <= 2*maxsep ) peak_close = true;

      if( peak_close && (prominence < fThresh_2ndMax_nsigma * sigma_sum ||
			 prominence/ADCmax < fThresh_2ndMax_fraction ) ){
	peakstoerase.push_back( stripmax );
      }
    }
  }

  //Erase "insignificant" peaks (those in contiguous grouping with higher peak with prominence below thresholds):
  for(int ipeak : peakstoerase){
    localmaxima.erase( ipeak );
    islocalmax[ipeak] = false;
  }
  

  //cout << "After peak erasing, n local maxima = " << localmaxima.size() << endl;
  //for speed/efficiency, resize the cluster array to the theoretical maximum
  //and use operator[] rather than push_back:
  //The clusters array will have negative and positive clusters. So we add the 
  //maximum negative clusters (localmaxima.size()) with the positive clusters
  //found earlier (nclust).
  clusters.resize( localmaxima.size() + nclust);
  
  //Cluster formation and cluster splitting from remaining local maxima:
  for( auto i = localmaxima.begin(); i != localmaxima.end(); ++i ){
    int stripmax = *i;
    int striplo = stripmax;
    int striphi = stripmax;
    double ADCmax = -1*fADCsums[hitindex_neg[stripmax]]; //added -1 factor
    
    bool found_neighbor_low = true;
    
    //while( striplist_neg.find( striplo-1 ) != striplist_neg.end() &&
    //	   stripmax - striplo < maxsep ){
    while( found_neighbor_low ){
      
      found_neighbor_low = striplist_neg.find( striplo - 1 ) != striplist_neg.end() && stripmax - striplo < maxsep;

      if( found_neighbor_low && fUseStripTimingCuts ){
	//check time difference and correlation coefficient of the candidate strip
	//with the max strip:
	double Tdiff = fTmean[hitindex_neg[striplo-1]] - fTmean[hitindex_neg[stripmax]];
	if( fabs(Tdiff) > fStripAddTcut_width ) found_neighbor_low = false;
	double Ccoeff = CorrCoeff( fN_MPD_TIME_SAMP, fADCsamples[hitindex_neg[striplo-1]], fADCsamples[hitindex_neg[stripmax]] );
	if( Ccoeff < fStripAddCorrCoeffCut ) found_neighbor_low = false;
      }

      //If either the strip time difference with the max. strip or the Correlation coefficient with the max strip
      //fails the cuts, stop growing the cluster in this direction
      
      if( found_neighbor_low ) striplo--;
    }

    // while( striplist_neg.find( striphi+1 ) != striplist_neg.end() &&
    // 	   striphi - stripmax < maxsep ){
    //   striphi++;
    // }

    bool found_neighbor_high = true;
    
    while( found_neighbor_high ){
      
      found_neighbor_high = striplist_neg.find( striphi + 1 ) != striplist_neg.end() && striphi - stripmax < maxsep;

      if( found_neighbor_high && fUseStripTimingCuts ){
	//check time difference and correlation coefficient of the candidate strip
	//with the max strip:
	double Tdiff = fTmean[hitindex_neg[striphi+1]] - fTmean[hitindex_neg[stripmax]];
	if( fabs(Tdiff) > fStripAddTcut_width ) found_neighbor_high = false;
	double Ccoeff = CorrCoeff( fN_MPD_TIME_SAMP, fADCsamples[hitindex_neg[striphi+1]], fADCsamples[hitindex_neg[stripmax]] );
	if( Ccoeff < fStripAddCorrCoeffCut ) found_neighbor_high = false;
      }

      //If either the strip time difference with the max. strip or the Correlation coefficient with the max strip
      //fails the cuts, stop growing the cluster in this direction
      
      if( found_neighbor_high ) striphi++;
    }
    
    int nstrips = striphi-striplo+1;

    double sumx = 0.0, sumx2 = 0.0, sumADC = 0.0, sumt = 0.0, sumt2 = 0.0;
    double sumwx = 0.0;

    map<int,double> splitfraction;
    vector<double> stripADCsum(nstrips);

    double maxpos = (stripmax + 0.5 - 0.5*Nstrips) * pitch + offset;

    //If peak position falls inside the "track search region" constraint, add a new cluster: 
    if( fabs( maxpos - constraint_center ) <= constraint_width ){
      
      //create a cluster, but don't add it to the 1D cluster array unless it passes the track search region constraint:
      sbsgemcluster_t clusttemp;
      clusttemp.nstrips = nstrips;
      clusttemp.istriplo = striplo;
      clusttemp.istriphi = striphi;
      clusttemp.istripmax = stripmax;
      clusttemp.ADCsamples.resize(fN_MPD_TIME_SAMP);
      clusttemp.stripADCsum.clear();
      clusttemp.hitindex.clear();
      clusttemp.rawstrip = fStripRaw[hitindex_neg[stripmax]];
      clusttemp.rawMPD = fStripMPD[hitindex_neg[stripmax]];
      clusttemp.rawAPV = fStripADC_ID[hitindex_neg[stripmax]];
      
      for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){ //initialize cluster-summed ADC samples to zero:
	clusttemp.ADCsamples[isamp] = 0.0;
      }
      
      for( int istrip=striplo; istrip<=striphi; istrip++ ){
	//int nmax_strip = 1;
	double sumweight = ADCmax/(1.0 + pow( (stripmax-istrip)*pitch/fSigma_hitshape, 2 ) );
	double maxweight = sumweight;
	
	for( int jstrip=istrip-maxsep; jstrip<=istrip+maxsep; jstrip++ ){
	  if( localmaxima.find( jstrip ) != localmaxima.end() && jstrip != stripmax ){
	    sumweight += -1*fADCsums[hitindex_neg[jstrip]]/( 1.0 + pow( (jstrip-istrip)*pitch/fSigma_hitshape, 2 ) ); //Added -1 factor
	  }
	}
   
	splitfraction[istrip] = maxweight/sumweight;
	
	double hitpos = (istrip + 0.5 - 0.5*Nstrips) * pitch + offset; //local hit position along direction measured by these strips
	double ADCstrip = fADCsums[hitindex_neg[istrip]] * splitfraction[istrip];
	double tstrip = fTmean[hitindex_neg[istrip]];
	
	for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
	  //Do not add -1 factor. We are now saving the negative cluster information
	  clusttemp.ADCsamples[isamp] += fADCsamples[hitindex_neg[istrip]][isamp]*splitfraction[istrip]; 
	}

	clusttemp.stripADCsum.push_back( ADCstrip );

	clusttemp.hitindex.push_back( hitindex_neg[istrip] ); //do we use this anywhere? Yes, it is good to keep track of this if we want to access raw strip info later on 
	
	sumADC += ADCstrip;
	
	//The variables below do not change if the ADC is negative or positive so we leave them alone
	if( std::abs( istrip - stripmax ) <= std::max(UShort_t(1),std::min(maxsepcoord,maxsep)) ){ 
	  sumx += hitpos * ADCstrip;
	  sumx2 += pow(hitpos,2) * ADCstrip;
	  sumwx += ADCstrip;
	  //use same strip cuts for cluster timing determination as for position reconstruction: may revisit later:
	  sumt += tstrip * ADCstrip;
	  sumt2 += pow(tstrip,2) * ADCstrip;
	} 
      }

      clusttemp.isampmax = 0; //figure out time sample in which peak of cluster-summed ADC values occurs:
      double minADC = 10000;
      for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
	if( isamp == 0 || clusttemp.ADCsamples[isamp] < minADC ){
	  minADC = clusttemp.ADCsamples[isamp];
	  clusttemp.isampmax = isamp;
	}
      }
      
      clusttemp.hitpos_mean = sumx / sumwx;
      clusttemp.hitpos_sigma = sqrt( sumx2/sumwx - pow(clusttemp.hitpos_mean,2) );
      clusttemp.clusterADCsum = sumADC;
      clusttemp.t_mean = sumt / sumwx;
      clusttemp.t_sigma = sqrt( sumt2 / sumwx - pow(clusttemp.t_mean,2) );
      
      //initialize "keep" flag to false for negative strips:
      clusttemp.keep = false;
      
      clusttemp.isneg = true; //This is used for negative strip analysis
      clusttemp.isnegontrack = false; //This is used for negative strip analysis      

      // In the standalone we don't apply an independent threshold on the cluster sum in the context of 1D cluster-finding:
      // if( sumADC >= fThresholdClusterSum ){
      // if( axis == SBSGEM::kVaxis ){
      // 	fVclusters.push_back( clusttemp );
      // 	fNclustV++;
      // } else {
      // 	fUclusters.push_back( clusttemp );
      // 	fNclustU++;
      // }

      
      //Hopefully this works correctly:
      clusters[nclust] = clusttemp;
      nclust++;
      nclust_neg++;      

	// std::cout << "found cluster, (axis, istripmax, nstrips, ADCsum, hit pos (mm) )=(" << axis << ", " << clusttemp.istripmax << ", "
	// 	  << clusttemp.nstrips << ", " << clusttemp.clusterADCsum
	// 	  << ", " << clusttemp.hitpos_mean*1000.0 << ")" << std::endl;
	
      //}
    } //Check if peak is inside track search region constraint
  } //end loop on local maxima
  
  clusters.resize(nclust); //just to make sure no pathological behavior later on
 

}

void SBSGEMModule::fill_2D_hit_arrays(){
  //Clear out the 2D hit array to get rid of any leftover junk from prior events:
  //fHits.clear();
  fN2Dhits = 0;

  //fHits.resize( fNclustU * fNclustV );
  //fHits.clear();
  fHits.resize( std::min( fNclustU*fNclustV, fMAX2DHITS ) );

  //if( fNclustU * fNclustV > fMAX2DHITS ){
  //   std::cout << "Warning in SBSGEMModule::fill_2D_hit_arrays(): 
  // }

  int nsamp_corr = fN_MPD_TIME_SAMP;
  int firstsamp_corr = 0;

  //the following commented lines are experimental:
  // if( fSuppressFirstLast > 0 ){
  //   nsamp_corr = fN_MPD_TIME_SAMP-2;
  //   firstsamp_corr = 1;
  // }
  // if( fSuppressFirstLast < 0 ){
  //   nsamp_corr = fN_MPD_TIME_SAMP-1;
  //   firstsamp_corr = (fSuppressFirstLast == -2 ? 0 : 1);
  // }
  
  //This routine is simple: just form all possible 2D hits from combining one "U" cluster with one "V" cluster. Here we assume that find_clusters_1D has already
  //been called, if that is NOT the case, then this routine will just do nothing:
  bool maxhits_exceeded = false;

  for( UInt_t iu=0; iu<fNclustU; iu++ ){
    for( UInt_t iv=0; iv<fNclustV; iv++ ){

      if( fUclusters[iu].keep && fVclusters[iv].keep ){
	//Initialize sums for computing cluster and strip correlation coefficients:
	sbsgemhit_t hittemp; // declare a temporary "hit" object:

	//copying overhead, might be inefficient:
	//sbsgemcluster_t uclusttemp = fUclusters[iu];
	//sbsgemcluster_t vclusttemp = fVclusters[iv];
      
	//Initialize "keep" to true:
	hittemp.keep = true;
	hittemp.highquality = false;
	hittemp.ontrack = false;
	hittemp.trackidx = -1;
	hittemp.iuclust = iu;
	hittemp.ivclust = iv;
      
	hittemp.uhit = fUclusters[iu].hitpos_mean;
	hittemp.vhit = fVclusters[iv].hitpos_mean;

	double pos_maxstripu = ( fUclusters[iu].istripmax + 0.5 - 0.5*fNstripsU ) * fUStripPitch + fUStripOffset;
	double pos_maxstripv = ( fVclusters[iv].istripmax + 0.5 - 0.5*fNstripsV ) * fVStripPitch + fVStripOffset;

	//"Cluster moments" defined as differences between reconstructed hit position and center of strip with max. signal in the cluster:
	hittemp.umom = (hittemp.uhit - pos_maxstripu)/fUStripPitch;
	hittemp.vmom = (hittemp.vhit - pos_maxstripv)/fVStripPitch;
      
	TVector2 UVtemp(hittemp.uhit,hittemp.vhit);
	TVector2 XYtemp = UVtoXY( UVtemp );

	hittemp.xhit = XYtemp.X();
	hittemp.yhit = XYtemp.Y();

	
	
	//Check if candidate 2D hit is inside the constraint region before doing anything else:
	if( fxcmin <= hittemp.xhit && hittemp.xhit <= fxcmax &&
	    fycmin <= hittemp.yhit && hittemp.yhit <= fycmax &&
	    IsInActiveArea( hittemp.xhit, hittemp.yhit ) ){
    
	  hittemp.thit = 0.5*(fUclusters[iu].t_mean + fVclusters[iv].t_mean);
	  hittemp.Ehit = 0.5*(fUclusters[iu].clusterADCsum + fVclusters[iv].clusterADCsum);
	
	  hittemp.thitcorr = hittemp.thit; //don't apply any corrections on thit yet
	
	  //Next up is to calculate "global" hit coordinates (actually coordinates in "tracker-local" system)
	  //DetToTrackCoord is a utility function defined in THaDetectorBase
	  TVector3 hitpos_global = DetToTrackCoord( hittemp.xhit, hittemp.yhit );
	
	  // Unclear whether it is actually necessary to store these variables, but we also probably want to avoid 
	  // repeated calls to THaDetectorBase::DetToTrackCoord, so let's keep these for now:
	  hittemp.xghit = hitpos_global.X();
	  hittemp.yghit = hitpos_global.Y();
	  hittemp.zghit = hitpos_global.Z();
	
	  hittemp.ADCasym = ( fUclusters[iu].clusterADCsum - fVclusters[iv].clusterADCsum )/( 2.0*hittemp.Ehit );

	  hittemp.ADCasymDeconv = (fUclusters[iu].clusterADCsumDeconvMaxCombo-fVclusters[iv].clusterADCsumDeconvMaxCombo)/(fUclusters[iu].clusterADCsumDeconvMaxCombo+fVclusters[iv].clusterADCsumDeconvMaxCombo);

	  hittemp.EhitDeconv = 0.5*(fUclusters[iu].clusterADCsumDeconvMaxCombo+fVclusters[iv].clusterADCsumDeconvMaxCombo);
	  
	  hittemp.tdiff = fUclusters[iu].t_mean - fVclusters[iv].t_mean - (fHitTimeMean[0]-fHitTimeMean[1]);
	  hittemp.tdiffDeconv = fUclusters[iu].t_mean_deconv - fVclusters[iv].t_mean_deconv - (fHitTimeMeanDeconv[0]-fHitTimeMeanDeconv[1]);
	  hittemp.thitDeconv = 0.5*(fUclusters[iu].t_mean_deconv + fVclusters[iv].t_mean_deconv);
	  
	  //Calculate correlation coefficients:
	  hittemp.corrcoeff_clust = CorrCoeff( nsamp_corr, fUclusters[iu].ADCsamples, fVclusters[iv].ADCsamples, firstsamp_corr );
	
	  //compute index of strip with max ADC sum within cluster strip array:
	  UInt_t ustripidx = fUclusters[iu].istripmax-fUclusters[iu].istriplo; //
	  UInt_t vstripidx = fVclusters[iv].istripmax-fVclusters[iv].istriplo; //
	
	  //compute index of strip with max ADC sum within decoded hit array:
	  UInt_t uhitidx = fUclusters[iu].hitindex[ustripidx];
	  UInt_t vhitidx = fVclusters[iv].hitindex[vstripidx];
	
	  hittemp.corrcoeff_strip = CorrCoeff( nsamp_corr, fADCsamples[uhitidx], fADCsamples[vhitidx], firstsamp_corr );

	  hittemp.corrcoeff_clust_deconv = CorrCoeff( fN_MPD_TIME_SAMP, fUclusters[iu].DeconvADCsamples, fVclusters[iv].DeconvADCsamples );
	  hittemp.corrcoeff_strip_deconv = CorrCoeff( fN_MPD_TIME_SAMP, fADCsamples_deconv[uhitidx], fADCsamples_deconv[vhitidx] );
	  //these lines redundant with the lines above (3860-3862):
	  // hittemp.ADCasymDeconv = (fUclusters[iu].clusterADCsumDeconvMaxCombo - fVclusters[iv].clusterADCsumDeconvMaxCombo)/
	  //   (fUclusters[iu].clusterADCsumDeconvMaxCombo + fVclusters[iv].clusterADCsumDeconvMaxCombo);
	  // hittemp.EhitDeconv = 0.5 * (fUclusters[iu].clusterADCsumDeconvMaxCombo + fVclusters[iv].clusterADCsumDeconvMaxCombo);

	  hittemp.thitFit = 0.5*( fUclusters[iu].t_mean_fit + fVclusters[iv].t_mean_fit );
	  hittemp.tdiffFit = fUclusters[iu].t_mean_fit - fVclusters[iv].t_mean_fit - (fHitTimeMeanFit[0]-fHitTimeMeanFit[1]);
	  
	  //A "high-quality" hit is one that passes filtering criteria for either "standard" or deconvoluted information:
	  
	  double asym = hittemp.ADCasym;
	  double ccor = hittemp.corrcoeff_clust;
	  double ADCsum = hittemp.Ehit;
	  double deltat = hittemp.tdiff;
	  double thit = hittemp.thit;
	  double ADC_thresh = fThresholdClusterSum;
	  double ccor_cut = fCorrCoeffCut;
	  //Do we want to hard-code the number of sigmas in the "high-quality" designation?
	  // --> Yes: if we want to make it wider or narrower, we can adjust the sigma
	  // or the cut value in the database. 
	  // Go with the larger of 3.5sigma or cut from DB
	  double dtcut = std::max( 3.5 * fTimeCutUVsigma, fTimeCutUVdiff );
	  double t0 = 0.5*(fHitTimeMean[0]+fHitTimeMean[1]);
	  double tcut = 3.5*0.5*(fHitTimeSigma[0]+fHitTimeSigma[1]);
	  
	  
	  if( fClusteringFlag == 1 ){
	    asym = hittemp.ADCasymDeconv;
	    ccor = hittemp.corrcoeff_clust_deconv;
	    ADCsum = hittemp.EhitDeconv;
	    deltat = hittemp.tdiffDeconv;
	    thit = hittemp.thitDeconv;
	    ADC_thresh = fThresholdClusterSumDeconv;
	    ccor_cut = fCorrCoeffCutDeconv;
	    dtcut = std::max( 3.5*fTimeCutUVsigmaDeconv, fTimeCutUVdiffDeconv );
	    t0 = 0.5*(fHitTimeMeanDeconv[0]+fHitTimeMeanDeconv[1]);
	    tcut = 3.5*0.5*(fHitTimeSigmaDeconv[0]+fHitTimeSigmaDeconv[1]);
	  }

	  if( fClusteringFlag == 0 && fUseStripTimingCuts == 2 ){
	    thit = hittemp.thitFit;
	    t0 = 0.5*(fHitTimeMeanFit[0]+fHitTimeMeanFit[1]);
	    dtcut = std::max( 3.5*fTimeCutUVsigmaFit, fTimeCutUVdiffFit );
	    tcut = 3.5*0.5*(fHitTimeSigmaFit[0]+fHitTimeSigmaFit[1]);
	  }

	  double asymcut = std::max( 4.5*fADCasymSigma, fADCasymCut );
	  
	  hittemp.highquality = fabs(asym) <= asymcut &&
	    fUclusters[iu].nstrips > 1 && fVclusters[iv].nstrips > 1 &&
	    ADCsum >= ADC_thresh && ccor >= ccor_cut &&
	    fabs(deltat)<=dtcut && fabs(thit-t0)<=tcut;

	  //hittemp.highquality = true;

	  hittemp.thitcorr = thit - t0;
	  
	  // hittemp.highquality = fabs(hittemp.ADCasym)<=fADCasymCut && 
	  //   fUclusters[iu].nstrips > 1 && fVclusters[iv].nstrips > 1 && 
	  //   fUclusters[iu].clusterADCsum >= fThresholdClusterSum && 
	  //   fVclusters[iv].clusterADCsum >= fThresholdClusterSum && 
	  //   hittemp.corrcoeff_clust >= fCorrCoeffCut &&
	  //   hittemp.corrcoeff_strip >= fCorrCoeffCut && 
	  //   fabs( hittemp.tdiff ) <= fTimeCutUVdiff*fTimeCutUVsigma &&
	  //   fabs( hittemp.ADCasymDeconv ) <= fADCasymCut &&
	  //   hittemp.corrcoeff_clust_deconv >= fCorrCoeffCutDeconv &&
	  //   hittemp.corrcoeff_strip_deconv >= fCorrCoeffCutDeconv;

       
	  
	  //cutting on deconvoluted ADC quantities could be dangerous before further study...

	  bool add_hit = true;
	  //we need special handling if we want to use single-strip clusters: 
	  if( fUclusters[iu].nstrips == 1 || fVclusters[iv].nstrips == 1 ){
	    //If EITHER of these clusters is only single-strip, it must pass more stringent requirements to use as a 2D hit candidate:
	    //To use single-strip clusters, we will REQUIRE good timing, ADC asymmetry, and correlation coefficient cuts:
	    add_hit = fabs(asym) <= asymcut && ccor >= ccor_cut && fabs(deltat)<=dtcut && fabs(thit-t0)<=tcut;
	    // if( fabs(hittemp.ADCasym) <= fADCasymCut && fabs( hittemp.tdiff ) <= fTimeCutUVdiff*fTimeCutUVsigma &&
	    // 	hittemp.corrcoeff_strip >= fCorrCoeffCut && hittemp.corrcoeff_clust >= fCorrCoeffCut && fabs( hittemp.ADCasymDeconv ) <= fADCasymCut &&
	    // 	hittemp.corrcoeff_clust_deconv >= fCorrCoeffCutDeconv &&
	    // 	hittemp.corrcoeff_strip_deconv >= fCorrCoeffCutDeconv ){
	    //   add_hit = true;
	    // }
	  }

	  //add_hit = true;
	  
	  //Okay, that should be everything. Now add it to the 2D hit array:
	  //fHits.push_back( hittemp );
	  if( add_hit && fN2Dhits < fMAX2DHITS ) {
	    fHits[fN2Dhits++] = hittemp; //should be faster than push_back();
	  } else if( add_hit ){ //
	    maxhits_exceeded = true;
	  }
	  //fN2Dhits++;
	} //end check that 2D point is inside track search region
      } //end check that both U and V clusters passed filtering criteria:
    } //end loop over "V" clusters
  } //end loop over "U" clusters

  if( maxhits_exceeded ){
    std::cout << "Warning in [SBSGEMModule::fill_2D_hit_arrays()]: good 2D hit candidates exceeded user maximum of " << fMAX2DHITS << " for module " << GetName() << ", 2D hit list truncated" << std::endl;
  }

  fHits.resize( fN2Dhits );
  
  filter_2Dhits();
  
}

void    SBSGEMModule::Print( Option_t* opt) const{
  return;
}

Int_t   SBSGEMModule::Begin( THaRunBase* r){ //Does nothing
  //Here we can create some histograms that will be written to the ROOT file:
  //This is a natural place to do the hit maps/efficiency maps:
  fZeroSuppress = fZeroSuppress && !fPedestalMode; 
  fCODA_BUILD_ALL_SAMPLES = r->GetDAQInfo("VTP_MPDRO_BUILD_ALL_SAMPLES") == "1";
  fCODA_CM_ENABLED = r->GetDAQInfo("VTP_MPDRO_ENABLE_CM") == "1";
    
  if(r->GetDAQInfo("VTP_MPDRO_ENABLE_CM").empty()){
    fCODA_BUILD_ALL_SAMPLES = -1;
    fCODA_CM_ENABLED = -1;
  }

  //pulled these lines out of the if-block below to avoid code duplication:
  TString appname = (static_cast<THaDetector *>(GetParent()) )->GetApparatus()->GetName();
  appname.ReplaceAll(".","_");
  appname += "_";
  TString detname = GetParent()->GetName();
  detname.Prepend(appname);
  detname.ReplaceAll(".","_");
  detname += "_";
  detname += GetName();
  

  if( fMakeEventInfoPlots && !fEventInfoPlotsInitialized ){
    fEventInfoPlotsInitialized = true;
    
    hMPD_EventCount_Alignment = new TH1D(TString::Format("h%s_MPD_EvCntAlign",detname.Data() ), TString::Format("MPD event count diffs, module %s; MPD event count offsets", detname.Data() ), 201, -100.5,100.5 );

    //We should really get the range for the fibers histogram from the MPDmap but we are lazy:
    
    hMPD_EventCount_Alignment_vs_Fiber = new TH2D(TString::Format("h%s_MPD_EvCntAlign_vs_fiber",detname.Data() ), "; fiber ; MPD event count diff",
						  33,-0.5,32.5, 201,-100.5,100.5);

    hMPD_FineTimeStamp_vs_Fiber = new TH2D(TString::Format("h%s_MPD_FineTimeStamp_vs_fiber",detname.Data() ), "; fiber ; MPD fine time stamp (ns)",
					   33,-0.5,32.5,256, -0.5, 1023.5);
  }
  
  if( fMakeEfficiencyPlots && !fEfficiencyInitialized ){
    fEfficiencyInitialized = true;

    int nbinsx1D = int( round( 1.02*GetXSize() /fBinSize_efficiency1D ) );
    int nbinsy1D = int( round( 1.02*GetYSize() /fBinSize_efficiency1D ) );
    int nbinsx2D = int( round( 1.02*GetXSize() /fBinSize_efficiency2D ) );
    int nbinsy2D = int( round( 1.02*GetYSize() /fBinSize_efficiency2D ) );
    
    fhdidhitx = new TH1D( TString::Format( "hdidhitx_%s", detname.Data() ), "Local x of hits on good tracks;  x (m)", nbinsx1D, -0.51*GetXSize(), 0.51*GetXSize() );
    fhdidhity = new TH1D( TString::Format( "hdidhity_%s", detname.Data() ), "Local y of hits on good tracks;  y (m)", nbinsy1D, -0.51*GetYSize(), 0.51*GetYSize() );
    fhdidhitxy = new TH2D( TString::Format( "hdidhitxy_%s", detname.Data() ), "x vs y of hits on good tracks; y (m); x (m)",
			   nbinsy2D, -0.51*GetYSize(), 0.51*GetYSize(),
			   nbinsx2D, -0.51*GetXSize(), 0.51*GetXSize() );

    fhshouldhitx = new TH1D( TString::Format( "hshouldhitx_%s", detname.Data() ), "x of good track passing through (m); x (m)", nbinsx1D, -0.51*GetXSize(), 0.51*GetXSize() );
    fhshouldhity = new TH1D( TString::Format( "hshouldhity_%s", detname.Data() ), "y of good track passing through (m); y (m)", nbinsy1D, -0.51*GetYSize(), 0.51*GetYSize() );
    fhshouldhitxy = new TH2D( TString::Format( "hshouldhitxy_%s", detname.Data() ), "x vs y of good track passing through (m); y(m); x(m",
			      nbinsy2D, -0.51*GetYSize(), 0.51*GetYSize(),
			      nbinsx2D, -0.51*GetXSize(), 0.51*GetXSize() );

    //We want to plot number of clusters/event/time;
    // Let's use area units of cm^2, and time units of milliseconds; so that one cluster/cm^2/ms = 1,000 clusters/cm^2/s
    // Since "expected" rates are in the range of up to 500 kHz/cm^2/s, we might set the limits of the histogram to something like 0-500 (kHz/cm^2) 								
    hClusterBasedOccupancyUstrips = new TH1D( TString::Format( "hClusterBasedOccupancy_%s_U", detname.Data() ), TString::Format( "U strips; Hit rate (kHz/cm^2) ;"), 250, 0.0, 500.0 );
    hClusterBasedOccupancyVstrips = new TH1D( TString::Format( "hClusterBasedOccupancy_%s_V", detname.Data() ), TString::Format( "V strips; Hit rate (kHz/cm^2) ;"), 250, 0.0, 500.0 );

    hClusterMultiplicityUstrips = new TH1D( TString::Format("hClusterMultiplicity_%s_U", detname.Data() ), TString::Format( "U/X strips; Total number of clusters/event;"), 501,-0.5,500.5);
    hClusterMultiplicityVstrips = new TH1D( TString::Format("hClusterMultiplicity_%s_V", detname.Data() ), TString::Format( "V/Y strips; Total number of clusters/event;"), 501,-0.5,500.5);
    
    fEfficiencyInitialized = true;
  }

  if( (fPedestalMode || fMakeCommonModePlots) && !fPedHistosInitialized ){ //make pedestal histograms:

    //Procedure:
    // 1. Analyze pedestal data with no pedestals supplied from the database.
    // 2. Extract "coarse" strip offsets from raw ADC histograms (i.e., common-mode means)
    // 3. Extract "fine" strip offsets from common-mode-subtracted histograms 
    // 3. Add "coarse" strip offsets (common-mode means) back into "common-mode subtracted" ADC 

    //U strips:
    hpedrmsU_distribution = new TH1D( TString::Format( "hpedrmsU_distribution_%s", detname.Data() ), "Pedestal RMS distribution, U strips; Ped. RMS", 200, 0, 100 );
    hpedmeanU_distribution = new TH1D( TString::Format( "hpedmeanU_distribution_%s", detname.Data() ), "Pedestal mean distribution, U strips; Ped. mean", 250, -250, 250 );
    hpedrmsU_by_strip = new TH1D( TString::Format( "hpedrmsU_by_strip_%s", detname.Data() ), "Pedestal rms U by strip; strip; ped. RMS", fNstripsU, -0.5, fNstripsU - 0.5 );
    hpedmeanU_by_strip = new TH1D( TString::Format( "hpedmeanU_by_strip_%s", detname.Data() ), "Pedestal mean U by strip; strip; ped. mean", fNstripsU, -0.5, fNstripsU - 0.5 );

    //V strips:
    hpedrmsV_distribution = new TH1D( TString::Format( "hpedrmsV_distribution_%s", detname.Data() ), "Pedestal RMS distribution, V strips; Ped. RMS", 200, 0, 100 );
    hpedmeanV_distribution = new TH1D( TString::Format( "hpedmeanV_distribution_%s", detname.Data() ), "Pedestal mean distribution, V strips; Ped. mean", 250, -250, 250 );
    hpedrmsV_by_strip = new TH1D( TString::Format( "hpedrmsV_by_strip_%s", detname.Data() ), "Pedestal rms V by strip; strip; Ped. RMS", fNstripsV, -0.5, fNstripsV - 0.5 );
    hpedmeanV_by_strip = new TH1D( TString::Format( "hpedmeanV_by_strip_%s", detname.Data() ), "Pedestal mean V by strip; strip; Ped. mean", fNstripsV, -0.5, fNstripsV - 0.5 );

    if( !fPedestalMode ){ //fill the above histograms with the pedestal info loaded from the database:
      for( UInt_t istrip = 0; istrip<fNstripsU; istrip++ ){
	hpedmeanU_distribution->Fill( fPedestalU[istrip] );
	hpedrmsU_distribution->Fill( fPedRMSU[istrip] );
	hpedmeanU_by_strip->SetBinContent( istrip+1, fPedestalU[istrip] );
	hpedrmsU_by_strip->SetBinContent( istrip+1, fPedRMSU[istrip] );	
      }

      for( UInt_t istrip=0; istrip<fNstripsV; istrip++ ){
	hpedmeanV_distribution->Fill( fPedestalV[istrip] );
	hpedrmsV_distribution->Fill( fPedRMSV[istrip] );
	hpedmeanV_by_strip->SetBinContent( istrip+1, fPedestalV[istrip] );
	hpedrmsV_by_strip->SetBinContent( istrip+1, fPedRMSV[istrip] );
      }
      
    }
    
    
    hrawADCs_by_stripU = new TH2D( TString::Format( "hrawADCs_by_stripU_%s", detname.Data() ), "Raw ADCs by U strip number, no corrections; U/X strip; Raw ADC",
				   fNstripsU, -0.5, fNstripsU-0.5,
				   512, -0.5, 4095.5 );
    hrawADCs_by_stripV = new TH2D( TString::Format( "hrawADCs_by_stripV_%s", detname.Data() ), "Raw ADCs by V strip number, no corrections; V/Y strip; Raw ADC",
				   fNstripsV, -0.5, fNstripsV-0.5,
				   512, -0.5, 4095.5 );

    hcommonmode_subtracted_ADCs_by_stripU = new TH2D( TString::Format( "hpedestalU_%s", detname.Data() ), "ADCs by U strip number, w/common mode correction, no ped. subtraction; U/X strip; ADC - Common-mode",
						      fNstripsU, -0.5, fNstripsU-0.5,
						      500, -500.0, 500.0 );
    hcommonmode_subtracted_ADCs_by_stripV = new TH2D( TString::Format( "hpedestalV_%s", detname.Data() ), "ADCs by V strip number, w/common mode correction, no ped. subtraction; V/Y strip; ADC - Common-mode",
						      fNstripsV, -0.5, fNstripsV-0.5,
						      500, -500.0, 500.0 );

    hpedestal_subtracted_ADCs_by_stripU = new TH2D( TString::Format( "hADCpedsubU_%s", detname.Data() ), "Pedestal and common-mode subtracted ADCs by U strip number; U/X strip; ADC - Common-mode - pedestal",
						    fNstripsU, -0.5, fNstripsU-0.5,
						    500,-500.,4500. );
    hpedestal_subtracted_ADCs_by_stripV = new TH2D( TString::Format( "hADCpedsubV_%s", detname.Data() ), "Pedestal and common-mode subtracted ADCs by V strip number; V/Y strip; ADC - Common-mode - pedestal",
						    fNstripsV, -0.5, fNstripsV-0.5,
						    500,-500.,4500. );

    hpedestal_subtracted_rawADCs_by_stripU = new TH2D( TString::Format( "hrawADCpedsubU_%s", detname.Data() ), "ADCs by U strip, ped-subtracted, no common-mode correction; U/X strip; ADC - pedestal",
						       fNstripsU, -0.5, fNstripsU-0.5,
						       500,-500.,4500. );
    hpedestal_subtracted_rawADCs_by_stripV = new TH2D( TString::Format( "hrawADCpedsubV_%s", detname.Data() ), "ADCs by V strip, ped-subtracted, no common-mode correction; V/Y strip; ADC - pedestal",
						       fNstripsV, -0.5, fNstripsV-0.5,
						       500,-500.,4500. );

    hpedestal_subtracted_rawADCsU = new TH1D( TString::Format( "hrawADCpedsubU_allstrips_%s", detname.Data() ), "distribution of ped-subtracted U strip ADCs w/o common-mode correction; ADC - pedestal",
					      1250, -500.,4500. );
    hpedestal_subtracted_rawADCsV = new TH1D( TString::Format( "hrawADCpedsubV_allstrips_%s", detname.Data() ), "distribution of ped-subtracted V strip ADCs w/o common-mode correction; ADC - pedestal",
					      1250, -500.,4500. );

    hpedestal_subtracted_ADCsU = new TH1D( TString::Format( "hADCpedsubU_allstrips_%s", detname.Data() ), "ped-subtracted U strip ADCs w/common-mode correction; ADC - Common-mode - pedestal",
					      1250, -500.,4500. );
    hpedestal_subtracted_ADCsV = new TH1D( TString::Format( "hADCpedsubV_allstrips_%s", detname.Data() ), "ped-subtracted V strip ADCs w/common-mode correction; ADC - Common-mode - pedestal",
					      1250, -500.,4500. );

    hdeconv_ADCsU = new TH1D( TString::Format( "hADCdeconvU_allstrips_%s", detname.Data() ), "Full readout events; Deconvoluted ADCs", 1250,-500.,4500. );

    hdeconv_ADCsV = new TH1D( TString::Format( "hADCdeconvV_allstrips_%s", detname.Data() ), "Full readout events; Deconvoluted ADCs", 1250,-500.,4500. );
    
    UInt_t nAPVs_U = fNstripsU/fN_APV25_CHAN;
    hcommonmode_mean_by_APV_U = new TH2D( TString::Format( "hCommonModeMean_by_APV_U_%s", detname.Data() ), "distribution of common-mode means for U strip pedestal data; APV card; Common-mode",
					  nAPVs_U, -0.5, nAPVs_U-0.5,  
					  1024, -0.5, 4095.5 );
    UInt_t nAPVs_V = fNstripsV/fN_APV25_CHAN;
    hcommonmode_mean_by_APV_V = new TH2D( TString::Format( "hCommonModeMean_by_APV_V_%s", detname.Data() ), "distribution of common-mode means for V strip pedestal data; APV card; Common-mode",
					  nAPVs_V, -0.5, nAPVs_V-0.5,
					  1024, -0.5, 4095.5 );

    fPedHistosInitialized = true;
    
    // Uncomment these later if you want them:
    // hrawADCs_by_strip_sampleU = new TClonesArray( "TH2D", fN_MPD_TIME_SAMP );
    // hrawADCs_by_strip_sampleV = new TClonesArray( "TH2D", fN_MPD_TIME_SAMP );

    // hcommonmode_subtracted_ADCs_by_strip_sampleU = new TClonesArray( "TH2D", fN_MPD_TIME_SAMP );
    // hcommonmode_subtracted_ADCs_by_strip_sampleV = new TClonesArray( "TH2D", fN_MPD_TIME_SAMP );

    // hpedestal_subtracted_ADCs_by_strip_sampleU = new TClonesArray( "TH2D", fN_MPD_TIME_SAMP );
    // hpedestal_subtracted_ADCs_by_strip_sampleV = new TClonesArray( "TH2D", fN_MPD_TIME_SAMP );
    
    // for( int isamp = 0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
    //   new( (*hrawADCs_by_strip_sampleU)[isamp] ) TH2D( histname.Format( "hrawADCU_%s_sample%d", detname.Data(), isamp ), "Raw U ADCs by strip and sample",
    // 						       fNstripsU, -0.5, fNstripsU-0.5,
    // 						       1024, -0.5, 4095.5 );
    //   new( (*hrawADCs_by_strip_sampleV)[isamp] ) TH2D( histname.Format( "hrawADCV_%s_sample%d", detname.Data(), isamp ), "Raw V ADCs by strip and sample",
    // 						       fNstripsV, -0.5, fNstripsV-0.5,
    // 						       1024, -0.5, 4095.5 );

    //   new( (*hcommonmode_subtracted_ADCs_by_strip_sampleU)[isamp] ) TH2D( histname.Format( "hpedestalU_%s_sample%d", detname.Data(), isamp ), "Pedestals by strip and sample",
    // 									  fNstripsU, -0.5, fNstripsU-0.5,
    // 									  1500, -500.0, 1000.0 );
    //   new( (*hcommonmode_subtracted_ADCs_by_strip_sampleV)[isamp] ) TH2D( histname.Format( "hpedestalV_%s_sample%d", detname.Data(), isamp ), "Pedestals by strip and sample",
    // 									  fNstripsV, -0.5, fNstripsV-0.5,
    // 									  1500, -500.0, 1000.0 );

    //   new( (*hpedestal_subtracted_ADCs_by_strip_sampleU)[isamp] ) TH2D( histname.Format( "hADCpedsubU_%s_sample%d", detname.Data(), isamp ), "Pedestal-subtracted ADCs by strip and sample",
    // 									fNstripsU, -0.5, fNstripsU-0.5,
    // 									1000, -500.0, 500.0 );
    //   new( (*hpedestal_subtracted_ADCs_by_strip_sampleV)[isamp] ) TH2D( histname.Format( "hADCpedsubV_%s_sample%d", detname.Data(), isamp ), "Pedestal-subtracted ADCs by strip and sample",
    // 									fNstripsV, -0.5, fNstripsV-0.5,
    // 									1000, -500.0, 500.0 );
      
    // }
    
  }

  //std::cout << "fCommonModePlotsInitialized = " << fCommonModePlotsInitialized << std::endl;
  if( fMakeCommonModePlots && !fCommonModePlotsInitialized ){

    //std::cout << "SBSGEMModule::Begin: making common-mode histograms for module " << GetName() << std::endl;
    //U strips:
   
    fCommonModeDistU = new TH2D( TString::Format( "hcommonmodeU_%s", detname.Data() ), "U/X strips common-mode (user); APV card; Common-mode - Common-mode mean (user)", fNAPVs_U, -0.5, fNAPVs_U-0.5, 500, -200.0,200.0 );

    fCommonModeDistU_Histo = new TH2D( TString::Format( "hcommonmodeU_histo_%s", detname.Data() ), "U/X strips common-mode (user); APV card; Common-mode - Common-mode mean (Histogram)", fNAPVs_U, -0.5, fNAPVs_U-0.5, 500, -200.0,200.0 );
    
    
    fCommonModeDistU_Sorting = new TH2D( TString::Format( "hcommonmodeU_sorting_%s", detname.Data() ), "U/X strips common-mode (Sorting); APV card; Common-mode (Sorting) - Common-mode mean", fNAPVs_U, -0.5, fNAPVs_U-0.5, 500, -200.0,200.0 );
    
    
    fCommonModeDistU_Danning = new TH2D( TString::Format( "hcommonmodeU_danning_%s", detname.Data() ), "U/X strips common-mode (Danning); APV card; Common-mode (Danning) - Common-mode mean", fNAPVs_U, -0.5, fNAPVs_U-0.5, 500, -200.0,200.0 );
    
   
    fCommonModeDiffU = new TH2D( TString::Format( "hcommonmodeU_diff_%s", detname.Data() ), "U/X strips (all events); APV card; Common-mode (User) - Common-mode (Danning online)", fNAPVs_U, -0.5, fNAPVs_U-0.5, 200, -100.0, 100.0 );

    fCommonModeDiffU_Uncorrected = new TH2D( TString::Format( "hcommonmodeU_diff_uncorrected_%s", detname.Data() ), "U/X strips (uncorrected events only); APV card; CM (User) - CM (Danning online)", fNAPVs_U, -0.5, fNAPVs_U-0.5, 200, -100.0, 100.0 );
    
    fCommonModeCorrectionU = new TH2D( TString::Format( "hcommonmodeU_corr_%s", detname.Data() ), "U/X strips; APV card; applied CM correction", fNAPVs_U, -0.5, fNAPVs_U-0.5, 200, -100.0, 100.0 );
    
    //fCommonModeNotCorrectionU = new TH2D( TString::Format( "hcommonmodeU_notcorr_%s", detname.Data() ), "U/X strips; APV card; CM Sorting - CM Danning without Correction", fNAPVs_U, -0.5, fNAPVs_U-0.5, 250, -100.0, 100.0 );
    fCommonModeResidualBiasU = new TH2D( TString::Format( "hcommonmodeU_bias_%s", detname.Data() ), "U/X strips; APV card; residual bias (corr. - true)", fNAPVs_U, -0.5, fNAPVs_U-0.5, 200, -100, 100 );

    fCommonModeResidualBiasU_corrected = new TH2D( TString::Format( "hcommonmodeU_bias_corrected_%s", detname.Data() ), "U/X strips; APV card; residual bias (corr. - true)", fNAPVs_U, -0.5, fNAPVs_U-0.5, 200, -100, 100 );

    fCommonModeResidualBias_vs_OccupancyU = new TH2D( TString::Format( "hcommonmodeU_bias_vs_occupancy_%s", detname.Data() ), "U/X strips; APV in-range occupancy; residual bias (corr. - true)", 100, 0.0, 1.0, 200, -100, 100 );

    //V strips:
    fCommonModeDistV = new TH2D( TString::Format( "hcommonmodeV_%s", detname.Data() ), "V/Y strips common-mode (user); APV card; Common-mode - Common-mode mean (user)", fNAPVs_V, -0.5, fNAPVs_V-0.5, 500, -200.0,200.0 );

    fCommonModeDistV_Histo = new TH2D( TString::Format( "hcommonmodeV_histo_%s", detname.Data() ), "V/Y strips common-mode (user); APV card; Common-mode - Common-mode mean (Histogram)", fNAPVs_V, -0.5, fNAPVs_V-0.5, 500, -200.0,200.0 );
    
    fCommonModeDistV_Sorting = new TH2D( TString::Format( "hcommonmodeV_sorting_%s", detname.Data() ), "V/Y strips common-mode (Sorting); APV card; Common-mode (Sorting) - Common-mode mean", fNAPVs_V, -0.5, fNAPVs_V-0.5, 500, -200.0,200.0 );
    
    
    fCommonModeDistV_Danning = new TH2D( TString::Format( "hcommonmodeV_danning_%s", detname.Data() ), "V/Y strips common-mode (Danning); APV card; Common-mode (Danning) - Common-mode mean", fNAPVs_V, -0.5, fNAPVs_V-0.5, 500, -200.0,200.0 );
    
    
    fCommonModeDiffV = new TH2D( TString::Format( "hcommonmodeV_diff_%s", detname.Data() ), "V/Y strips (all events); APV card; Common-mode (User) - Common-mode (Danning online)", fNAPVs_V, -0.5, fNAPVs_V-0.5, 200, -100.0,100.0 );

    fCommonModeDiffV_Uncorrected = new TH2D( TString::Format( "hcommonmodeV_diff_uncorrected_%s", detname.Data() ), "V/Y strips (uncorrected events only); APV card; CM (User) - CM (Danning online)", fNAPVs_V, -0.5, fNAPVs_V-0.5, 200, -100.0, 100.0 );
    
    fCommonModeCorrectionV = new TH2D( TString::Format( "hcommonmodeV_corr_%s", detname.Data() ), "V/Y strips; APV card; applied CM correction", fNAPVs_V, -0.5, fNAPVs_V-0.5, 200, -100.0, 100.0 );

    fCommonModeResidualBiasV = new TH2D( TString::Format( "hcommonmodeV_bias_%s", detname.Data() ), "V/Y strips; APV card; residual bias (corr. - true)", fNAPVs_V, -0.5, fNAPVs_V-0.5, 200, -100, 100 );

    fCommonModeResidualBiasV_corrected = new TH2D( TString::Format( "hcommonmodeV_bias_corrected_%s", detname.Data() ), "V/Y strips; APV card; residual bias (corr. - true)", fNAPVs_V, -0.5, fNAPVs_V-0.5, 200, -100, 100 );

    fCommonModeResidualBias_vs_OccupancyV = new TH2D( TString::Format( "hcommonmodeV_bias_vs_occupancy_%s", detname.Data() ), "V/Y strips; APV in-range occupancy; residual bias (corr. - true)", 100, 0.0, 1.0, 200, -100, 100 );
    
    //fCommonModeNotCorrectionV = new TH2D( TString::Format( "hcommonmodeV_notcorr_%s", detname.Data() ), "V/Y strips; APV card; CM Sorting - CM Danning without Correction", fNAPVs_V, -0.5, fNAPVs_V-0.5, 250, -100.0, 100.0 );

    // fCommonModeDistU->Print();
    // fCommonModeDistU_Sorting->Print();
    // fCommonModeDistU_Danning->Print();
    // fCommonModeDiffU->Print();

    // fCommonModeDistV->Print();
    // fCommonModeDistV_Sorting->Print();
    // fCommonModeDistV_Danning->Print();
    // fCommonModeDiffV->Print();
    fCommonModePlotsInitialized = true;
  }

  //The following histograms we more or less always want: 
  if( !fPulseShapeInitialized ){
    hADCfrac_vs_timesample_allstrips = new TH2D( TString::Format( "h%s_ADCfrac_vs_timesample_all", detname.Data() ), "All strips ; Time sample ; ADC_{i}/ADCsum", fN_MPD_TIME_SAMP, -0.5, fN_MPD_TIME_SAMP-0.5, 200, 0.0, 1.0 );
    hADCfrac_vs_timesample_goodstrips = new TH2D( TString::Format( "h%s_ADCfrac_vs_timesample_good", detname.Data() ), "Strips on good tracks ; Time sample ; ADC_{i}/ADCsum", fN_MPD_TIME_SAMP, -0.5, fN_MPD_TIME_SAMP-0.5, 200, 0.0, 1.0 );
		
    hADCfrac_vs_timesample_maxstrip = new TH2D( TString::Format( "h%s_ADCfrac_vs_timesample_max", detname.Data() ), "Max strip in cluster on track; Time sample ; ADC_{i}/ADCsum", fN_MPD_TIME_SAMP, -0.5, fN_MPD_TIME_SAMP-0.5, 200, 0.0, 1.0 );

    fPulseShapeInitialized = true;
  }

  //  std::cout << "fCommonModePlotsInitialized = " << fCommonModePlotsInitialized << std::endl;
    
  //if( !fStripTimeFunc ){
  fStripTimeFunc = new TF1( TString::Format("StripPulseShape_%s",detname.Data() ),
			    "std::max([3],[3]+[0]*exp(1.0)*(x-[1])/[2]*exp(-(x-[1])/[2]))",0.,fN_MPD_TIME_SAMP * fSamplePeriod );
  //  }

  return 0;
}

void SBSGEMModule::PrintPedestals( std::ofstream &dbfile_CM, std::ofstream &daqfile_ped, std::ofstream &daqfile_CM ){
  //The first argument is a file in the format expected by the database,
  //The second argument is a file in the format expected by the DAQ:

  //Step 1: we need to extract pedestal mean and rms by channel, and also grab
  // "common-mode min" and "common-mode max" values:
  // we can simply use the existing arrays to store the values:

  std::cout << "[SBSGEMModule::PrintPedestals]: module " << GetName() << std::endl;

  hpedmeanU_distribution->Reset();
  hpedmeanV_distribution->Reset();
  hpedrmsU_distribution->Reset();
  hpedrmsV_distribution->Reset();

  hpedmeanU_by_strip->Reset();
  hpedmeanV_by_strip->Reset();
  hpedrmsU_by_strip->Reset();
  hpedrmsV_by_strip->Reset();
  
  //start with pedestals;
  for( UInt_t iu = 0; iu<fNstripsU; iu++ ){
    TH1D *htemp = hcommonmode_subtracted_ADCs_by_stripU->ProjectionY( "htemp", iu+1,iu+1 );
    
    fPedestalU[iu] = htemp->GetMean();

    //htemp here represents the individual sample noise width, but the threshold is applied on the average of the six (or other number) time samples:
    // sigma(average) = sigma(1 sample)/sqrt(number of samples):
    fPedRMSU[iu] = htemp->GetRMS() / sqrt( double( fN_MPD_TIME_SAMP ) ); 

    hpedmeanU_distribution->Fill( fPedestalU[iu] );
    hpedrmsU_distribution->Fill( fPedRMSU[iu] );

    hpedmeanU_by_strip->SetBinContent( iu+1, fPedestalU[iu] );
    hpedrmsU_by_strip->SetBinContent( iu+1, fPedRMSU[iu] );
    
    htemp->Delete();
  }

  for( UInt_t iv = 0; iv<fNstripsV; iv++ ){
    TH1D *htemp = hcommonmode_subtracted_ADCs_by_stripV->ProjectionY( "htemp", iv+1, iv+1 );
    fPedestalV[iv] = htemp->GetMean();
    fPedRMSV[iv] = htemp->GetRMS() / sqrt( double( fN_MPD_TIME_SAMP ) );

    hpedmeanV_distribution->Fill( fPedestalV[iv] );
    hpedrmsV_distribution->Fill( fPedRMSV[iv] );

    hpedmeanV_by_strip->SetBinContent( iv+1, fPedestalV[iv] );
    hpedrmsV_by_strip->SetBinContent( iv+1, fPedRMSV[iv] );
    
    htemp->Delete();
  }

  
  
  TString appname = static_cast<THaDetector *>(GetParent())->GetApparatus()->GetName();
  TString detname = GetParent()->GetName();
  TString modname = GetName();
  
  TString header;
  /* We use the pedestal daq file for the DB, so this code is not needed
  header.Form( "%s.%s.%s.pedu = ", appname.Data(), detname.Data(), modname.Data() );
  dbfile << std::endl << header << std::endl;
  for( UInt_t iu=0; iu<fNstripsU; iu++ ){
    TString sentry;
    sentry.Form( "  %15.5g ", fPedestalU[iu] );
    dbfile << sentry;
    if( (iu+1)%16 == 0 ) dbfile << std::endl;
  }

  dbfile << std::endl;
  
  header.Form( "%s.%s.%s.rmsu = ", appname.Data(), detname.Data(), modname.Data() );
  dbfile << std::endl << header << std::endl;

  for( UInt_t iu=0; iu<fNstripsU; iu++ ){
    TString sentry;
    sentry.Form( "  %15.5g ", fPedRMSU[iu] );
    dbfile << sentry;
    if( (iu+1)%16 == 0 ) dbfile << std::endl;
  }

  dbfile << std::endl;

  header.Form( "%s.%s.%s.pedv = ", appname.Data(), detname.Data(), modname.Data() );
  dbfile << std::endl << header << std::endl;
  for( UInt_t iv=0; iv<fNstripsV; iv++ ){
    TString sentry;
    sentry.Form( "  %15.5g ", fPedestalV[iv] );
    dbfile << sentry;
    if( (iv+1)%16 == 0 ) dbfile << std::endl;
  }

  dbfile << std::endl;
  
  header.Form( "%s.%s.%s.rmsv = ", appname.Data(), detname.Data(), modname.Data() );
  dbfile << std::endl << header << std::endl;

  for( UInt_t iv=0; iv<fNstripsV; iv++ ){
    TString sentry;
    sentry.Form( "  %15.5g ", fPedRMSV[iv] );
    dbfile << sentry;
    if( (iv+1)%16 == 0 ) dbfile << std::endl;
  }

  dbfile << std::endl;
  */
  //TO DO: common-mode mean, min, and max by APV card:

  
  
  int nAPVsU = fNstripsU/fN_APV25_CHAN;
  int nAPVsV = fNstripsV/fN_APV25_CHAN;
  std::vector<double> commonmode_meanU(nAPVsU), commonmode_rmsU(nAPVsU);
  std::vector<double> commonmode_meanV(nAPVsV), commonmode_rmsV(nAPVsV);

  
  for( int iAPV = 0; iAPV<nAPVsU; iAPV++ ){
    TH1D *htemp = hcommonmode_mean_by_APV_U->ProjectionY("htemp", iAPV+1, iAPV+1 );

    commonmode_meanU[iAPV] = htemp->GetMean();
    commonmode_rmsU[iAPV] = htemp->GetRMS();
  }
  /* Moving to new format for CM DB file, but keeping this commented out for reference
  header.Form( "%s.%s.%s.commonmode_meanU = ", appname.Data(), detname.Data(), modname.Data() );

  dbfile_CM << std::endl << header << std::endl;
  for( int iAPV = 0; iAPV<nAPVsU; iAPV++ ){
    TString sentry;
    sentry.Form( "  %15.5g ", commonmode_meanU[iAPV] );
    dbfile_CM << sentry;

    if( (iAPV+1) % 16 == 0 ) dbfile_CM << std::endl;
  }

  header.Form( "%s.%s.%s.commonmode_rmsU = ", appname.Data(), detname.Data(), modname.Data() );

  dbfile_CM << std::endl << header << std::endl;
  for( int iAPV = 0; iAPV<nAPVsU; iAPV++ ){
    TString sentry;
    sentry.Form( "  %15.5g ", commonmode_rmsU[iAPV] );
    dbfile_CM << sentry;

    if( (iAPV+1) % 16 == 0 ) dbfile_CM << std::endl;
  }
  */
  
  for( int iAPV = 0; iAPV<nAPVsV; iAPV++ ){
    TH1D *htemp = hcommonmode_mean_by_APV_V->ProjectionY("htemp", iAPV+1, iAPV+1 );

    commonmode_meanV[iAPV] = htemp->GetMean();
    commonmode_rmsV[iAPV] = htemp->GetRMS();
  }
  /*Moving to new format for CM DB file, but keeping this commented out for reference
  header.Form( "%s.%s.%s.commonmode_meanV = ", appname.Data(), detname.Data(), modname.Data() );

  dbfile_CM << std::endl << header << std::endl;
  for( int iAPV = 0; iAPV<nAPVsV; iAPV++ ){
    TString sentry;
    sentry.Form( "  %15.5g ", commonmode_meanV[iAPV] );
    dbfile_CM << sentry;

    if( (iAPV+1) % 16 == 0 ) dbfile_CM << std::endl;
  }

  header.Form( "%s.%s.%s.commonmode_rmsV = ", appname.Data(), detname.Data(), modname.Data() );

  dbfile_CM << std::endl << header << std::endl;
  for( int iAPV = 0; iAPV<nAPVsV; iAPV++ ){
    TString sentry;
    sentry.Form( "  %15.5g ", commonmode_rmsV[iAPV] );
    dbfile_CM << sentry;

    if( (iAPV+1) % 16 == 0 ) dbfile_CM << std::endl;
  }
  

  dbfile_CM << std::endl << std::endl;
  */
  //That takes care of the database file. For the "DAQ" file, we need to organize things by APV card. For this we can loop over the MPDmap:
  
  for( auto iapv = fMPDmap.begin(); iapv != fMPDmap.end(); iapv++ ){
    int crate = iapv->crate;
    int slot = iapv->slot;
    int mpd = iapv->mpd_id;
    int adc_ch = iapv->adc_id;
    int pos = iapv->pos;
    int invert = iapv->invert;
    int axis = iapv->axis;

    
    daqfile_ped << "APV "
	    << std::setw(16) << crate 
	    << std::setw(16) << slot 
	    << std::setw(16) << mpd
	    << std::setw(16) << adc_ch
	    << std::endl;
    
    //Then loop over the strips:
    for( int ich=0; ich<fN_APV25_CHAN; ich++ ){
      int strip = GetStripNumber( ich, pos, invert );
      double pedmean = (axis == SBSGEM::kUaxis ) ? fPedestalU[strip] : fPedestalV[strip];
      double pedrms = (axis == SBSGEM::kUaxis ) ? fPedRMSU[strip] : fPedRMSV[strip];

      daqfile_ped << std::setw(16) << ich
	      << std::setw(16) << std::setprecision(4) << pedmean
	      << std::setw(16) << std::setprecision(4) << pedrms
	      << std::endl;
    }

    double cm_mean = (axis == SBSGEM::kUaxis ) ? commonmode_meanU[ pos ] : commonmode_meanV[ pos ];
    double cm_rms = (axis == SBSGEM::kUaxis ) ? commonmode_rmsU[ pos ] : commonmode_rmsV[ pos ];

    //std::cout << "module " << GetName() << ", common-mode range number of sigmas = " << fCommonModeRange_nsigma  << std::endl;
    
    double cm_min = cm_mean - fCommonModeRange_nsigma * cm_rms;
    
    double cm_max = cm_mean + fCommonModeRange_nsigma * cm_rms;

    //daq CM file needs a CM min and max and integers
    daqfile_CM << std::setw(12) << crate 
		<< std::setw(12) << slot
		<< std::setw(12) << mpd
		<< std::setw(12) << adc_ch
		<< std::setw(12) << int( cm_min )
		<< std::setw(12) << int( cm_max )
		<< std::endl;
		
    //DB CM file prefers the CM mean and RMS and doubles
    dbfile_CM << std::setw(12) << crate 
		      << std::setw(12) << slot
		      << std::setw(12) << mpd
		      << std::setw(12) << adc_ch
		      << std::setw(12) << Form("%15.5g", cm_mean)
		      << std::setw(12) << Form("%15.5g", cm_rms)
		      << std::endl;
    
  }
}

Int_t   SBSGEMModule::End( THaRunBase* r){ //Calculates efficiencies and writes hit maps and efficiency histograms and/or pedestal info to ROOT file:
  if( fMakeEventInfoPlots && fEventInfoPlotsInitialized ){
    hMPD_EventCount_Alignment->Write(0,kOverwrite);
    hMPD_EventCount_Alignment_vs_Fiber->Write(0,kOverwrite);
    hMPD_FineTimeStamp_vs_Fiber->Write(0,kOverwrite);
  }
  
  
  if( fMakeEfficiencyPlots ){
    //Create the track-based efficiency histograms at the end of the run:
    TString histname;
    TString appname = (static_cast<THaDetector *>(GetParent()) )->GetApparatus()->GetName();
    appname.ReplaceAll(".","_");
    appname += "_";
    TString detname = GetParent()->GetName();
    detname.Prepend(appname);
    detname.ReplaceAll(".","_");
    detname += "_";
    detname += GetName();
  
    if( fhdidhitx != NULL && fhshouldhitx != NULL ){ //Create efficiency histograms and write to the ROOT file:
      TH1D *hefficiency_vs_x = new TH1D(*fhdidhitx);
      hefficiency_vs_x->SetName( histname.Format( "hefficiency_vs_x_%s", detname.Data() ) );
      hefficiency_vs_x->SetTitle( histname.Format( "Track-based efficiency vs x, module %s; x(m) ; Efficiency", GetName() ) );
      hefficiency_vs_x->Divide( fhshouldhitx );
      hefficiency_vs_x->Write( 0, kOverwrite );
      hefficiency_vs_x->Delete();
    }

    if( fhdidhity != NULL && fhshouldhity != NULL ){ //Create efficiency histograms and write to the ROOT file:
      TH1D *hefficiency_vs_y = new TH1D(*fhdidhity);
      hefficiency_vs_y->SetName( histname.Format( "hefficiency_vs_y_%s", detname.Data() ) );
      hefficiency_vs_y->SetTitle( histname.Format( "Track-based efficiency vs y, module %s; y(m); Efficiency", GetName() ) );
      hefficiency_vs_y->Divide( fhshouldhity );
      hefficiency_vs_y->Write( 0, kOverwrite);
      hefficiency_vs_y->Delete();
    }

    if( fhdidhitxy != NULL && fhshouldhitxy != NULL ){ //Create efficiency histograms and write to the ROOT file:
      TH2D *hefficiency_vs_xy = new TH2D(*fhdidhitxy);
      hefficiency_vs_xy->SetName( histname.Format( "hefficiency_vs_xy_%s", detname.Data() ) );
      hefficiency_vs_xy->SetTitle( histname.Format( "Track-based efficiency vs x and y, module %s; y(m); x(m)", GetName() ) );
      hefficiency_vs_xy->Divide( fhshouldhitxy );
      hefficiency_vs_xy->Write( 0, kOverwrite );
      hefficiency_vs_xy->Delete();
    }
  
    if( fhdidhitx != NULL  ) fhdidhitx->Write(fhdidhitx->GetName(), kOverwrite );
    if( fhdidhity != NULL  ) fhdidhity->Write(fhdidhity->GetName(), kOverwrite );
    if( fhdidhitxy != NULL  ) fhdidhitxy->Write(fhdidhitxy->GetName(), kOverwrite );

    if( fhshouldhitx != NULL  ) fhshouldhitx->Write(fhshouldhitx->GetName(), kOverwrite );
    if( fhshouldhity != NULL  ) fhshouldhity->Write(fhshouldhity->GetName(), kOverwrite );
    if( fhshouldhitxy != NULL  ) fhshouldhitxy->Write(fhshouldhitxy->GetName(), kOverwrite );

    if( hClusterBasedOccupancyUstrips != nullptr ) hClusterBasedOccupancyUstrips->Write( hClusterBasedOccupancyUstrips->GetName(), kOverwrite );
    if( hClusterBasedOccupancyVstrips != nullptr ) hClusterBasedOccupancyVstrips->Write( hClusterBasedOccupancyVstrips->GetName(), kOverwrite );
    if( hClusterMultiplicityUstrips != nullptr ) hClusterMultiplicityUstrips->Write( hClusterMultiplicityUstrips->GetName(), kOverwrite );
    if( hClusterMultiplicityVstrips != nullptr ) hClusterMultiplicityVstrips->Write( hClusterMultiplicityVstrips->GetName(), kOverwrite );
  }

  if( fPedestalMode || fMakeCommonModePlots ){ //write out pedestal histograms, print out pedestals in the format needed for both database and DAQ:

    //The channel map and pedestal information are specific to a GEM module.
    //But we want ONE database file and ONE DAQ file for the entire tracker.
    //So probably the best way to proceed is to have the  
    hpedrmsU_distribution->Write(0,kOverwrite);
    hpedmeanU_distribution->Write(0,kOverwrite);
    hpedrmsV_distribution->Write(0,kOverwrite);
    hpedmeanV_distribution->Write(0,kOverwrite);

    hpedrmsU_by_strip->Write(0,kOverwrite);
    hpedmeanU_by_strip->Write(0,kOverwrite);
    hpedrmsV_by_strip->Write(0,kOverwrite);
    hpedmeanV_by_strip->Write(0,kOverwrite);
    
    hrawADCs_by_stripU->Write(0,kOverwrite);
    hrawADCs_by_stripV->Write(0,kOverwrite);
    hcommonmode_subtracted_ADCs_by_stripU->Write(0,kOverwrite);
    hcommonmode_subtracted_ADCs_by_stripV->Write(0,kOverwrite);
    hpedestal_subtracted_ADCs_by_stripU->Write(0,kOverwrite);
    hpedestal_subtracted_ADCs_by_stripV->Write(0,kOverwrite);
    hpedestal_subtracted_rawADCs_by_stripU->Write(0,kOverwrite);
    hpedestal_subtracted_rawADCs_by_stripV->Write(0,kOverwrite);

    hpedestal_subtracted_rawADCsU->Write(0,kOverwrite);
    hpedestal_subtracted_rawADCsV->Write(0,kOverwrite);
    hpedestal_subtracted_ADCsU->Write(0,kOverwrite);
    hpedestal_subtracted_ADCsV->Write(0,kOverwrite);

    hdeconv_ADCsU->Write(0,kOverwrite);
    hdeconv_ADCsV->Write(0,kOverwrite);
    
    hcommonmode_mean_by_APV_U->Write(0,kOverwrite);
    hcommonmode_mean_by_APV_V->Write(0,kOverwrite);

    // hrawADCs_by_strip_sampleU->Write();
    // hrawADCs_by_strip_sampleV->Write();
    // hcommonmode_subtracted_ADCs_by_strip_sampleU->Write();
    // hcommonmode_subtracted_ADCs_by_strip_sampleV->Write();
    // hpedestal_subtracted_ADCs_by_strip_sampleU->Write();
    // hpedestal_subtracted_ADCs_by_strip_sampleV->Write();
  }

  if ( fMakeCommonModePlots ){
    fCommonModeDistU->Write(0,kOverwrite);
    fCommonModeDistU_Histo->Write(0,kOverwrite);
    fCommonModeDistU_Sorting->Write(0,kOverwrite);
    fCommonModeDistU_Danning->Write(0,kOverwrite);
    fCommonModeDiffU->Write(0,kOverwrite);
    fCommonModeDiffU_Uncorrected->Write(0,kOverwrite);
    fCommonModeCorrectionU->Write(0,kOverwrite);
    fCommonModeResidualBiasU->Write(0,kOverwrite);
    fCommonModeResidualBiasU_corrected->Write(0,kOverwrite);
    fCommonModeResidualBias_vs_OccupancyU->Write(0,kOverwrite);
    //fCommonModeNotCorrectionU->Write(0,kOverwrite);

    fCommonModeDistV->Write(0,kOverwrite);
    fCommonModeDistV_Histo->Write(0,kOverwrite);
    fCommonModeDistV_Sorting->Write(0,kOverwrite);
    fCommonModeDistV_Danning->Write(0,kOverwrite);
    fCommonModeDiffV->Write(0,kOverwrite);
    fCommonModeDiffV_Uncorrected->Write(0,kOverwrite);
    fCommonModeCorrectionV->Write(0,kOverwrite);
    fCommonModeResidualBiasV->Write(0,kOverwrite);
    fCommonModeResidualBiasV_corrected->Write(0,kOverwrite);
    fCommonModeResidualBias_vs_OccupancyV->Write(0,kOverwrite);
    //fCommonModeNotCorrectionV->Write(0,kOverwrite);
  }
    
  if( fPulseShapeInitialized ){
    hADCfrac_vs_timesample_allstrips->Write(0,kOverwrite);
    hADCfrac_vs_timesample_goodstrips->Write(0,kOverwrite);
    hADCfrac_vs_timesample_maxstrip->Write(0,kOverwrite);
  }

  //if( fStripTimeFunc ) 

  //delete fStripTimeFunc;

  return 0;
}

//utility method to calculate correlation coefficient of U and V samples: 
Double_t SBSGEMModule::CorrCoeff( int nsamples, const std::vector<double> &Usamples, const std::vector<double> &Vsamples, int firstsample ){
  Double_t sumu=0.0, sumv=0.0, sumu2=0.0, sumv2=0.0, sumuv=0.0;

  if ( (int)Usamples.size() < firstsample+nsamples || (int)Vsamples.size() < firstsample+nsamples ){
    return -10.0; //nonsense value, correlation coefficient by definition is -1 < c < 1
  }
  
  for( int isamp=firstsample; isamp<firstsample+nsamples; isamp++ ){
    sumu += Usamples[isamp];
    sumv += Vsamples[isamp];
    sumu2 += pow(Usamples[isamp],2);
    sumv2 += pow(Vsamples[isamp],2);
    sumuv += Usamples[isamp]*Vsamples[isamp];
  }

  double nSAMP = double(nsamples);
  double mu = sumu/nSAMP;
  double mv = sumv/nSAMP;
  double varu = sumu2/nSAMP - pow(mu,2);
  double varv = sumv2/nSAMP - pow(mv,2);
  double sigu = sqrt(varu);
  double sigv = sqrt(varv);

  return (sumuv - nSAMP*mu*mv)/(nSAMP*sigu*sigv);
  
}

TVector2 SBSGEMModule::UVtoXY( TVector2 UV ){
  double det = fPxU*fPyV - fPyU*fPxV;

  double Utemp = UV.X();
  double Vtemp = UV.Y();
  
  double Xtemp = (fPyV*Utemp - fPyU*Vtemp)/det;
  double Ytemp = (fPxU*Vtemp - fPxV*Utemp)/det;

  return TVector2(Xtemp,Ytemp);
}

TVector2 SBSGEMModule::XYtoUV( TVector2 XY ){
  double Xtemp = XY.X();
  double Ytemp = XY.Y();

  double Utemp = Xtemp*fPxU + Ytemp*fPyU;
  double Vtemp = Xtemp*fPxV + Ytemp*fPyV;

  return TVector2(Utemp,Vtemp);
}

Int_t SBSGEMModule::GetStripNumber( UInt_t rawstrip, UInt_t pos, UInt_t invert ){
  Int_t RstripNb = APVMAP[fAPVmapping][rawstrip];
  RstripNb = RstripNb + (127-2*RstripNb)*invert;
  Int_t RstripPos = RstripNb + 128*pos;

  if( fIsMC ){
    return rawstrip + 128*pos;
  }
  
  return RstripPos;
}

void SBSGEMModule::filter_1Dhits(SBSGEM::GEMaxis_t axis){
  
  if( fFiltering_flag1D < 0 ) return; //flag < 0 means don't filter 1D clusters at all
  // flag = 0 means use a "soft" filter (only reject if at least one other cluster passed)
  // flag > 0 means use a "hard" filter (reject failing clusters no matter what)
  //First filter on cluster ADC sum:
  int ngood = 0;
  int nclust = (axis == SBSGEM::kUaxis) ? fNclustU : fNclustV; 
  
  std::vector<sbsgemcluster_t> &clusters =  (axis == SBSGEM::kUaxis) ? fUclusters : fVclusters;

  double threshold = fThresholdClusterSum;
  if( fClusteringFlag == 1 ) threshold = fThresholdClusterSumDeconv;
  
  bool passed[nclust];
  
  for( int ipass=0; ipass<2; ipass++ ){
    if( ipass == 0 ) ngood = 0;
    for( int icl=0; icl<nclust; icl++ ){

      double clustersum = clusters[icl].clusterADCsum;
      if( fClusteringFlag == 1 ) clustersum = clusters[icl].clusterADCsumDeconvMaxCombo;
      //On the first pass, determine which clusters passed the criterion and count the number of good clusters:
      if( ipass == 0 ){
	passed[icl] = clusters[icl].keep && clustersum >= threshold;
	if( passed[icl] ) ngood++;
      }

      //on the second pass, if at least one good cluster was found passing the criterion, we set "keep" for all others to false:
      if( ipass == 1 && !passed[icl] && (ngood > 0 || fFiltering_flag1D > 0 ) ){
	clusters[icl].keep = false;
      }
    }
  }

  //Second, filter on cluster size (we may not actually want to filter on cluster size at this stage):
  ngood = 0;

  for( int ipass=0; ipass<2; ipass++ ){
    if( ipass == 0 ) ngood = 0;

    for( int icl=0; icl<nclust; icl++ ){
      if( ipass == 0 ){
	passed[icl] = clusters[icl].keep && clusters[icl].nstrips >= 2;
	if( passed[icl] ) ngood++;
      }

      if( ipass == 1 && !passed[icl] && (ngood > 0 || fFiltering_flag1D > 0 ) ){
	clusters[icl].keep = false;
      }
    }
  }
    
  
  
  
}

void SBSGEMModule::filter_2Dhits(){
  //Here we will initially filter only based on time U/V time difference, ADC asymmetry, and perhaps correlation coefficient:

  if( fFiltering_flag2D < 0 ) return;

  double tcut = fTimeCutUVdiff;
  double ccor_cut = fCorrCoeffCut;
  double asym_cut = fADCasymCut;
  if( fClusteringFlag == 1 ){
    tcut = fTimeCutUVdiffDeconv;
    ccor_cut = fCorrCoeffCutDeconv;
    // asym_cut = fADCasymCut
  }
  if( fUseStripTimingCuts == 2 && fClusteringFlag != 1 ){
    tcut = fTimeCutUVdiffFit;
  }
  
  //First U/V time difference:
  bool passed[fN2Dhits];
  int ngood = 0;
  for( UInt_t ipass=0; ipass<2; ipass++ ){
    if( ipass == 0 ) ngood = 0;
    for( UInt_t ihit=0; ihit<fN2Dhits; ihit++ ){
      double dt = fHits[ihit].tdiff;
      if( fClusteringFlag == 1 ) dt = fHits[ihit].tdiffDeconv;
      if( fUseStripTimingCuts == 2 && fClusteringFlag != 1 ) dt = fHits[ihit].tdiffFit;
      
      if( ipass == 0 ){
	passed[ihit] = fHits[ihit].keep && fabs( dt ) <= tcut;
	if( passed[ihit] ) ngood++;
      }

      if( ipass == 1 && !passed[ihit] && ( ngood > 0 || fFiltering_flag2D > 0 ) ){
	fHits[ihit].keep = false;
      }
    }
  }

  //Second: Cluster Correlation Coefficient:
  ngood = 0;
  for( UInt_t ipass=0; ipass<2; ipass++ ){
    if( ipass == 0 ) ngood = 0;
    for( UInt_t ihit=0; ihit<fN2Dhits; ihit++ ){
      double ccor = fHits[ihit].corrcoeff_clust;
      if( fClusteringFlag == 1 ) ccor = fHits[ihit].corrcoeff_clust_deconv;
      
      if( ipass == 0 ){
	passed[ihit] = fHits[ihit].keep && ccor >= ccor_cut;
	if( passed[ihit] ) ngood++;
      }

      if( ipass == 1 && !passed[ihit] && ( ngood > 0 || fFiltering_flag2D > 0 ) ){
	fHits[ihit].keep = false;
      }
    }
  }
  
  //Third: ADC asymmetry:
  ngood = 0;
  for( UInt_t ipass=0; ipass<2; ipass++ ){
    if( ipass == 0 ) ngood = 0;
    for( UInt_t ihit=0; ihit<fN2Dhits; ihit++ ){
      double asym = fHits[ihit].ADCasym;
      if( fClusteringFlag == 1 ) asym = fHits[ihit].ADCasymDeconv;
      if( ipass == 0 ){
	passed[ihit] = fHits[ihit].keep && fabs( asym ) <= asym_cut;
	if( passed[ihit] ) ngood++;
      }

      if( ipass == 1 && !passed[ihit] && ( ngood > 0 || fFiltering_flag2D > 0 ) ){
	fHits[ihit].keep = false;
      }
    }
  }

}

double SBSGEMModule::GetCommonMode( UInt_t isamp, Int_t flag, const mpdmap_t &apvinfo, UInt_t nhits ){ 
  if( isamp > fN_MPD_TIME_SAMP ) return 0;

  //unsigned int index = apvinfo.index;
  
  if( flag == 0 ){ //Sorting method: doesn't actually use the apv info:
    //int ngoodhits=0;
    vector<double> sortedADCs(nhits);

    

    if( nhits < fCommonModeNstripRejectLow + fCommonModeNstripRejectHigh + fCommonModeMinStripsInRange ){
      Error(Here("SBSGEMModule::GetCommonMode()"), "Sorting-method common-mode calculation requested with nhits %d less than minimum %d required", nhits, fCommonModeNstripRejectLow + fCommonModeNstripRejectHigh + fCommonModeMinStripsInRange );

      exit(-1);
    }
    
    for( int ihit=0; ihit<nhits; ihit++ ){
      int iraw = isamp + fN_MPD_TIME_SAMP * ihit;

      sortedADCs[ihit] = fPedSubADC_APV[ iraw ];
    }
	    
    std::sort( sortedADCs.begin(), sortedADCs.end() );
	    
    //   commonMode[isamp] = 0.0;
    double cm_temp = 0.0;
    int stripcount=0;

    for( int k=fCommonModeNstripRejectLow; k<nhits-fCommonModeNstripRejectHigh; k++ ){
      cm_temp += sortedADCs[k];
      stripcount++;
    }

    return  cm_temp/double(stripcount);
  } else if( flag == 2 ) { //Histogramming method (experimental):
    
    int iAPV = apvinfo.pos;
    double cm_mean = ( apvinfo.axis == SBSGEM::kUaxis ) ? fCommonModeMeanU[iAPV] : fCommonModeMeanV[iAPV];
    double cm_rms = ( apvinfo.axis == SBSGEM::kUaxis ) ? fCommonModeRMSU[iAPV] : fCommonModeRMSV[iAPV];

    //for now these are unused. Comment out to suppress compiler warning.
    double DBmean = cm_mean;
    double DBrms = cm_rms;
    
    // Not sure if we SHOULD update cm_mean and cm_rms in this context because then the logic can become somewhat circular/self-referential:
    if( fMeasureCommonMode && fNeventsRollingAverage_by_APV[apvinfo.index] >= std::min(UInt_t(100), fN_MPD_TIME_SAMP*fNeventsCommonModeLookBack ) ){
      cm_mean = fCommonModeRollingAverage_by_APV[apvinfo.index];
      cm_rms = std::max(0.2*DBrms, std::min(5.0*DBrms,fCommonModeRollingRMS_by_APV[apvinfo.index]));
    }

    cm_rms = DBrms;
    
    //bin width/stepsize = 8 with these settings:
    double stepsize = cm_rms*fCommonModeStepSize_Nsigma; //Default is 0.2 = rms/5
    double binwidth = cm_rms*fCommonModeBinWidth_Nsigma; //Default is +/- 2 sigma, bin width / step size = 20 with these settings

    //this will actually include all ADCs within +/- (ScanRange + BinWidth) sigma of the mean since range is bin center +/- 1*RMS.
    double scan_min = cm_mean - fCommonModeScanRange_Nsigma*cm_rms; 
    double scan_max = cm_mean + fCommonModeScanRange_Nsigma*cm_rms;

    int nbins= int( (scan_max - scan_min)/stepsize ); //20 * RMS / (RMS/4) = 80

    // std::cout << "histogramming cm: (scan min, scan max, step size, bin width, nbins)=("
    // 	      << scan_min << ", " << scan_max << ", " << stepsize << ", " << binwidth << ", " << nbins << ")" << std::endl;
    
    //NOTE: The largest number of bins that could contain any given sample is binwidth/stepsize = 20 with default settings:
    
    if(stepsize == 0) return GetCommonMode( isamp, 0, apvinfo );
    
    if(stepsize == 0) cout<<"SBSGEMModule::GetCommonMode() ERROR Histogramming has zeros"<<endl;
    //Construct std::vectors and explicitly zero-initialize them:
    std::vector<int> bincounts(nbins+1,0);
    std::vector<double> binADCsum(nbins+1,0.0);
    std::vector<double> binADCsum2(nbins+1,0.0);
    
    int ibinmax=-1;
    int maxcounts=0;
    //Now loop on all the strips and fill the histogram: 
    //for( int ihit=0; ihit<fN_APV25_CHAN; ihit++ ){
    for( int ihit=0; ihit<nhits; ihit++ ){
      double ADC = fPedSubADC_APV[ isamp + fN_MPD_TIME_SAMP * ihit ];
      //calculate the lowest bin containing this ADC value. 
      int nearestbin = std::max(0,std::min(nbins-1, int(round( (ADC - scan_min)/stepsize ) ) ) );

      int binlow = nearestbin;
      int binhigh = nearestbin+1;
      
      while( binlow >= 0 && fabs( ADC - (scan_min + binlow*stepsize) ) <= binwidth ){
	bincounts[binlow]++;
	binADCsum[binlow] += ADC;
	binADCsum2[binlow] += pow(ADC,2);

	if( ibinmax < 0 || bincounts[binlow] > maxcounts ){
	  ibinmax = binlow;
	  maxcounts = bincounts[binlow];
	}
	binlow--;
      }

      while( binhigh <= nbins && fabs( ADC - (scan_min + binhigh*stepsize) ) <= binwidth ){
	bincounts[binhigh]++;
	binADCsum[binhigh] += ADC;
	binADCsum2[binhigh] += pow(ADC,2);
	if( ibinmax < 0 || bincounts[binhigh] > maxcounts ){
	  ibinmax = binhigh;
	  maxcounts = bincounts[binhigh];
	}
	binhigh++;
      }
    }

    
    // for( int ibin=0; ibin<nbins; ibin++ ){
    //   if( bincounts[ibin] > 0 ){
    // 	double binAVG = binADCsum[ibin]/double(bincounts[ibin]);
    // 	double binRMS = sqrt( binADCsum2[ibin]/double(bincounts[ibin])-pow(binAVG,2) );
    //   }
    // }
    
    if( ibinmax >= 0 && maxcounts >= fCommonModeMinStripsInRange ){
      return binADCsum[ibinmax]/double(bincounts[ibinmax]);
    } else { //Fall back on sorting method:
      return GetCommonMode( isamp, 0, apvinfo );
    }
    
  } else if( flag == 3 ) { //Online Danning method with cm min set to 0 used during GMn
    int iAPV = apvinfo.pos;
    double cm_mean = ( apvinfo.axis == SBSGEM::kUaxis ) ? fCommonModeMeanU[iAPV] : fCommonModeMeanV[iAPV];
    double cm_rms = ( apvinfo.axis == SBSGEM::kUaxis ) ? fCommonModeRMSU[iAPV] : fCommonModeRMSV[iAPV];
    
    double CM_1 = 0;
    double CM_2 = 0;
    int n_keep = 0;
    
    for( int ihit=0; ihit<nhits; ihit++ ){
      int iraw=isamp + fN_MPD_TIME_SAMP * ihit;
      
      double ADCtemp = fPedSubADC_APV[iraw];
      
      if(ADCtemp > 0 && ADCtemp < cm_mean + 5*cm_rms){
	CM_1 += ADCtemp;
	n_keep++;
      }
    }
    
    CM_1 /= n_keep;
    n_keep = 0;
    
    
    for( int ihit=0; ihit<nhits; ihit++ ){
      int iraw=isamp + fN_MPD_TIME_SAMP * ihit;
      
      double ADCtemp = fPedSubADC_APV[iraw];
      double rmstemp = ( apvinfo.axis == SBSGEM::kUaxis ) ? fPedRMSU[fStripAPV[iraw]] : fPedRMSV[fStripAPV[iraw]];
      
      if(ADCtemp > 0 && ADCtemp < CM_1 + 3*rmstemp){
	CM_2 += ADCtemp;
	n_keep++;
      }
    }
    
    return CM_2/n_keep;
    
    
  } else if( flag == 4 ) { //Online Danning method for GEn
    int iAPV = apvinfo.pos;
    double cm_mean = ( apvinfo.axis == SBSGEM::kUaxis ) ? fCommonModeMeanU[iAPV] : fCommonModeMeanV[iAPV];
    double cm_rms = ( apvinfo.axis == SBSGEM::kUaxis ) ? fCommonModeRMSU[iAPV] : fCommonModeRMSV[iAPV];
    
    
      
    double cm_temp = 0.0;


    
    for( int iter=0; iter<3; iter++ ){

      double cm_min = cm_mean - fCommonModeRange_nsigma*cm_rms;
      double cm_max = cm_mean + fCommonModeRange_nsigma*cm_rms;
      double sumADCinrange = 0.0;
      int n_keep = 0;

      
      for( int ihit=0; ihit<nhits; ihit++ ){
	int iraw=isamp + fN_MPD_TIME_SAMP * ihit;
	
	double ADCtemp = fPedSubADC_APV[iraw];
	double rmstemp = ( apvinfo.axis == SBSGEM::kUaxis ) ? fPedRMSU[fStripAPV[iraw]] : fPedRMSV[fStripAPV[iraw]];
	
	if(iter != 0){
	  cm_min = cm_temp - fCommonModeDanningMethod_NsigmaCut*2.5*rmstemp;
	  cm_max = cm_temp + fCommonModeDanningMethod_NsigmaCut*2.5*rmstemp;
	}

	if( ADCtemp >= cm_min && ADCtemp <= cm_max ){
	  n_keep++;
	  sumADCinrange += ADCtemp;

	}
      }
   
      cm_temp = sumADCinrange / n_keep;
    }
   
    
    return cm_temp;
            
    } else { //"offline" Danning method (default): requires apv info for cm-mean and cm-rms values:
    int iAPV = apvinfo.pos;
    double cm_mean = ( apvinfo.axis == SBSGEM::kUaxis ) ? fCommonModeMeanU[iAPV] : fCommonModeMeanV[iAPV];
    double cm_rms = ( apvinfo.axis == SBSGEM::kUaxis ) ? fCommonModeRMSU[iAPV] : fCommonModeRMSV[iAPV];
   
    // Not sure if we should update cm_mean and cm_rms in this context because then the logic can become somewhat circular/self-referential:
    if( fMeasureCommonMode && fNeventsRollingAverage_by_APV[apvinfo.index] >= std::min(UInt_t(100), fN_MPD_TIME_SAMP*fNeventsCommonModeLookBack ) ){
      cm_mean = fCommonModeRollingAverage_by_APV[apvinfo.index];
      cm_rms = fCommonModeRollingRMS_by_APV[apvinfo.index];
    }
    
    
    //TODO: allow to use a different parameter than the one used for
    // zero-suppression:
    double cm_min = cm_mean - fCommonModeDanningMethod_NsigmaCut*cm_rms;
    double cm_max = cm_mean + fCommonModeDanningMethod_NsigmaCut*cm_rms;

    double cm_temp = 0.0;
    
    for( int iter=0; iter<fCommonModeNumIterations; iter++ ){
      int nstripsinrange=0;
      double sumADCinrange=0.0;
      //double sum2ADCinrange=0.0;
      //for( int ihit=0; ihit<fN_APV25_CHAN; ihit++ ){
      for( int ihit=0; ihit<nhits; ihit++ ){
	int iraw=isamp + fN_MPD_TIME_SAMP * ihit;
	
	double ADCtemp = fPedSubADC_APV[iraw];
	
	//on iterations after the first iteration, reject strips with signals above nsigma * pedrms:
	double rmstemp = ( apvinfo.axis == SBSGEM::kUaxis ) ? fPedRMSU[fStripAPV[iraw]] : fPedRMSV[fStripAPV[iraw]];

	// if(flag == 4){  //This is used for diagnostic plots where we "pretend" the data is zero suppressed //moving this to another method
	//   double strip_sum = 0;
	//   for(int itsamp=0; itsamp < fN_MPD_TIME_SAMP; itsamp++)
	//     strip_sum += ADCtemp - CM_online;
	//   if(strip_sum/fN_MPD_TIME_SAMP < 3*rmstemp) continue;
	// }

	double mintemp = cm_min;
	double maxtemp = cm_max;
	
	if( iter > 0 ) {
	  maxtemp = cm_temp + fCommonModeDanningMethod_NsigmaCut*rmstemp*fRMS_ConversionFactor; //2.45 = sqrt(6), don't want to calculate sqrt every time
	  //mintemp = 0.0;
	  mintemp = cm_temp - fCommonModeDanningMethod_NsigmaCut*rmstemp*fRMS_ConversionFactor;
	}
	
	if( ADCtemp >= mintemp && ADCtemp <= maxtemp ){
	  nstripsinrange++;
	  sumADCinrange += ADCtemp;
	  //sum2ADCinrange += pow(ADCtemp,2);
	}
      }
      
      //double rmsinrange = cm_rms;
      
      //TO-DO: don't hard-code the minimum strip count. 
      
      if( nstripsinrange >= fCommonModeMinStripsInRange ){ //require minimum 10 strips in range:
	cm_temp = sumADCinrange/double(nstripsinrange);
	//rmsinrange = sqrt( sum2ADCinrange/double(nstripsinrange) - pow(commonMode[isamp],2) );
	//cm_max = commonMode[isamp] + fZeroSuppressRMS*std::min( rmsinrange, cm_rms );
      } else if( iter==0 ){ //not enough strips on FIRST iteration, use mean from sorting-method:
	// std::cout << "Warning: fewer than ten strips in range on first iteration for common-mode calculation, crate, slot, MPD, ADC, cm_min, cm_max, n strips in range, cm_mean = "
	// 	  << apvinfo.crate << ", " << apvinfo.slot << ", " << apvinfo.mpd_id << ", " << apvinfo.adc_id << ", "
	// 	  << cm_min << ", " << cm_max << ", " << nstripsinrange << ", "
	// 	  << cm_mean << ", defaulting to sorting method" << std::endl;

	return GetCommonMode( isamp, 0, apvinfo );
      }

      // std::cout << "iteration " << iter << ": isamp, crate, slot, mpd, adc, cm_mean, cm_min, cm_max, nstrips in range, cm calc, cm sorting method = " << isamp << ", "
      // 		<< apvinfo.crate << ", " << apvinfo.slot << ", " << apvinfo.mpd_id << ", " << apvinfo.adc_id << ", "
      // 		<< cm_mean << ", " << cm_min << ", " << cm_max << ", " << nstripsinrange << ", " << cm_temp << ", "
      // 		<< GetCommonMode( isamp, 0, apvinfo ) << std::endl;
    } //loop over iterations for "Danning method" CM calculation

    //std::cout << std::endl;
    
    return cm_temp;
  }
}

void SBSGEMModule::fill_ADCfrac_vs_time_sample_goodstrip( Int_t hitindex, bool ismax ){
  if( hitindex < 0 || hitindex >= fNstrips_hit ) return;
  if( hADCfrac_vs_timesample_goodstrips == NULL ) return;
  if( hADCfrac_vs_timesample_maxstrip == NULL ) return;

  for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
    hADCfrac_vs_timesample_goodstrips->Fill( isamp, fADCsamples[hitindex][isamp]/fADCsums[hitindex] );
    if( ismax ){
      hADCfrac_vs_timesample_maxstrip->Fill( isamp, fADCsamples[hitindex][isamp]/fADCsums[hitindex] );
    }
  }
}

//This function calculates the chi2 of a vector of time samples with respect to the "Good Strip" averages:
double SBSGEMModule::StripTSchi2( int hitindex ){
  if( hitindex < 0 || hitindex > fNstrips_hit ) return -1.;
  double chi2 = 0.0;
  double t0 = fStripMaxTcut_central[fAxis[hitindex]] - fStripTau;

  double sigma = (fAxis[hitindex] == SBSGEM::kUaxis) ? fPedRMSU[fStrip[hitindex]] : fPedRMSV[fStrip[hitindex]] * fRMS_ConversionFactor; 

  //NOTE: the "ped RMS" is the RMS of the average of six time samples, so we multiply by "RMS conversion factor" (sqrt(6)) to get the sigma
  // for individual ADC samples
  
  for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
    double tsamp = (isamp + 0.5)*fSamplePeriod;
    //chi2 += pow( (fADCsamples[hitindex][isamp] / fADCsums[hitindex] - fGoodStrip_TSfrac_mean[isamp])/fGoodStrip_TSfrac_sigma[isamp], 2 );
    chi2 += pow( (fADCsamples[hitindex][isamp] - fADCmax[hitindex] * std::max(0.0, (tsamp-t0)/fStripTau * exp( 1.0 - (tsamp-t0)/fStripTau) ) )/sigma, 2 ); 
  }
  return chi2;
}

//Experimental, not used for now:
double SBSGEMModule::FitStripTime( int striphitindex, double RMS ){
  if( striphitindex < 0 || striphitindex > fNstrips_hit ) return -1000.0;

  std::vector<Double_t> &ADC = fADCsamples[striphitindex];

  return CalcFitTime( ADC, RMS );
  
}

//common code for calculating strip and cluster fit times:
double SBSGEMModule::CalcFitTime( const std::vector<Double_t> &ADC, double RMS ){

  double ndeconv[fN_MPD_TIME_SAMP-1];
  double dndeconv[fN_MPD_TIME_SAMP-1];
  double weight[fN_MPD_TIME_SAMP-1];
  double Tdeconv[fN_MPD_TIME_SAMP-1]; //estimate of signal start time based on ndeconv.
  double dTdeconv[fN_MPD_TIME_SAMP-1];
  
  //Grab pedestal RMS to estimate weights in strip mean time calculation:
  
  //Double_t pedrms = ( fAxis[striphitindex] == SBSGEM::kUaxis ) ? fPedRMSU[fStrip[striphitindex]] : fPedRMSV[fStrip[striphitindex]];

  Double_t xdeconv = fSamplePeriod/fStripTau;
  Double_t exdeconv = exp(xdeconv);

  // n = 1.0/(r * exdeconv - 1.0);
  // dn = -1.0 / (r * exdeconv - 1)^2 * exdeconv * dr = -exdeconv * n^2 * dr
  // dr = r * sqrt( (dADCi/ADCi,2) + pow(dADC_{i+1}/ADC_{i+1},2))

  //dADC = sigma 
  double sigma = RMS;

  double Tsum = 0.0, Tsum2=0.0;
  double sumw2 = 0.0;
  
  for( int isamp=0; isamp<fN_MPD_TIME_SAMP-1; isamp++ ){
    ndeconv[isamp] = ADC[isamp]/(ADC[isamp+1]*exdeconv - ADC[isamp]); //estimated number of samples before current sample that the signal started

    double r = ADC[isamp+1]/ADC[isamp];
    double dr2 = r*r * sigma * sigma * ( pow( ADC[isamp], -2 ) + pow( ADC[isamp+1], -2 ) );
    dndeconv[isamp] = exdeconv * pow(ndeconv[isamp],2) * sqrt(dr2);

    Tdeconv[isamp] = ( isamp + 0.5 - ndeconv[isamp] ) * fSamplePeriod;
    dTdeconv[isamp] = dndeconv[isamp] * fSamplePeriod;

    double weight = pow(dTdeconv[isamp],-2);
    
    //weight = 1.0;
    
    //if( ndeconv[isamp] >= 0.0 ){
    // if( true ){
    Tsum += Tdeconv[isamp] * weight;
    Tsum2 += pow(Tdeconv[isamp],2) * weight;
    sumw2 += weight;
      //}
  }

  //if( true ){
  //if( true ){
  return Tsum / sumw2 - fTrigTimeSlope * fTrigTime;
  //} 
}

void SBSGEMModule::InitAPVMAP(){
  APVMAP[SBSGEM::kINFN].resize(fN_APV25_CHAN);
  APVMAP[SBSGEM::kUVA_XY].resize(fN_APV25_CHAN);
  APVMAP[SBSGEM::kUVA_UV].resize(fN_APV25_CHAN);
  APVMAP[SBSGEM::kMC].resize(fN_APV25_CHAN);

  for( UInt_t i=0; i<fN_APV25_CHAN; i++ ){
    Int_t strip1 = 32*(i%4) + 8*(i/4) - 31*(i/16);
    Int_t strip2 = strip1 + 1 + strip1 % 4 - 5 * ( ( strip1/4 ) % 2 );
    Int_t strip3 = ( strip2 % 2 == 0 ) ? strip2/2 + 32 : ( (strip2<64) ? (63 - strip2)/2 : 127 + (65-strip2)/2 ); 
    APVMAP[SBSGEM::kINFN][i] = strip1; 
    APVMAP[SBSGEM::kUVA_XY][i] = strip2;
    APVMAP[SBSGEM::kUVA_UV][i] = strip3;
    APVMAP[SBSGEM::kMC][i] = i;
  }

  //Print out to test:
  // //std::cout << "INFN X/Y APV mapping: " << std::endl;
  // for( UInt_t i=0; i<fN_APV25_CHAN; i++ ){
  //   std::cout << std::setw(8) << APVMAP[SBSGEM::kINFN][i] << ", ";
  //   if( (i+1) % 10 == 0 ) std::cout << endl;
  // }
  // std::cout << endl;


  // //Print out to test:
  // std::cout << "UVA X/Y APV mapping: " << std::endl;
  // for( UInt_t i=0; i<fN_APV25_CHAN; i++ ){
  //   std::cout << std::setw(8) << APVMAP[SBSGEM::kUVA_XY][i] << ", ";
  //   if( (i+1) % 10 == 0 ) std::cout << endl;
  // }
  // std::cout << endl;

  // //Print out to test:
  // std::cout << "UVA U/V APV mapping: " << std::endl;
  // for( UInt_t i=0; i<fN_APV25_CHAN; i++ ){
  //   std::cout << std::setw(8) << APVMAP[SBSGEM::kUVA_UV][i] << ", ";
  //   if( (i+1) % 10 == 0 ) std::cout << endl;
  // }
  // std::cout << endl;
  
}

void SBSGEMModule::UpdateRollingCommonModeAverage( int iapv, double CM_sample ){
  //This gets called for each time sample for each APV or each full readout event or whenever BUILD_ALL_SAMPLES is true and CM_ENABLED is false:
  //There are two cases to handle:
  // 1) before the container is full, meaning less than fN_MPD_TIME_SAMP*fNeventsCommonModeLookBack have been added. In this case we increment everything.
  // 2) after the container is full, meaning the earliest sample needs to roll off the average and one new sample has to be added at the end.
  
  UInt_t N = fNeventsRollingAverage_by_APV[iapv];
  UInt_t Nmax = fN_MPD_TIME_SAMP*fNeventsCommonModeLookBack;
  
  double sum, sum2;

  // For now "pos" and "axis" are unused. Comment out to suppress compiler warning:
  // UInt_t pos = fMPDmap[iapv].pos;
  // UInt_t axis = fMPDmap[iapv].axis;

  // For now these are unused. Comment out to suppress compiler warning:
  // double cm_mean_from_DB = (axis == SBSGEM::kUaxis) ? fCommonModeMeanU[pos] : fCommonModeMeanV[pos];
  // double cm_rms_from_DB = (axis == SBSGEM::kUaxis) ? fCommonModeRMSU[pos] : fCommonModeRMSV[pos];   
  
  //std::cout << "Updating rolling average common mode from full readout events for module " << GetName() << " iapv = " << iapv << std::endl;
  
  if( N < Nmax ){
    //before reaching the size of the look back window, we just add the common-mode samples onto the end of the array

    fCommonModeResultContainer_by_APV[iapv][N] = CM_sample;

    if( N == 0 ){ //First sample, initialize all sums/averages:
      fCommonModeRollingAverage_by_APV[iapv] = CM_sample;
      fCommonModeRollingRMS_by_APV[iapv] = 0.0;
      sum = CM_sample;
      sum2 = pow(CM_sample,2);
    } else { //Second and subsequent samples: increment sums, recalculate
      double oldavg = fCommonModeRollingAverage_by_APV[iapv];
      double oldrms = fCommonModeRollingRMS_by_APV[iapv];
      
      sum = N*oldavg + CM_sample;
      sum2 = N * (pow(oldrms,2) + pow(oldavg,2)) + pow(CM_sample,2);

      double newavg = sum/double(N+1);
      double newrms = sqrt( sum2/double(N+1) - pow(newavg,2) );

      fCommonModeRollingAverage_by_APV[iapv] = newavg;
      fCommonModeRollingRMS_by_APV[iapv] = newrms;
    }

    // std::cout << "(N, average, rms)=(" << N << ", " << fCommonModeRollingAverage_by_APV[iapv]
    // 	      << ", " << fCommonModeRollingRMS_by_APV[iapv] << ")" << std::endl;
    fNeventsRollingAverage_by_APV[iapv] = N+1;
  
  } else {
      
    //grab the earliest sample in the rolling average:
    double oldfirstsample = fCommonModeResultContainer_by_APV[iapv].front();
    
    //The net result of the following two operations should be to keep the container size the same:
    fCommonModeResultContainer_by_APV[iapv].pop_front(); //remove oldest sample
    fCommonModeResultContainer_by_APV[iapv].push_back( CM_sample ); //Insert newest sample at the end
    //we only need to update the calculation for the fact that the
    //earliest sample rolled off and a new sample was added: 
    double oldavg = fCommonModeRollingAverage_by_APV[iapv];
    double oldsum = oldavg * Nmax;

    double oldrms = fCommonModeRollingRMS_by_APV[iapv];
    // RMS^2 = sum^2/N - avg^2 --> sum^2 = N * (RMS^2 + avg^2)
    double oldsum2 = Nmax * ( pow(oldrms,2) + pow(oldavg,2) );

    //double lastsample = fCommonModeResultContainer_by_APV[iapv].back();
    double lastsample = CM_sample;
    
    double newsum = oldsum - oldfirstsample + lastsample;
    double newsum2 = oldsum2 - pow(oldfirstsample,2) + pow(lastsample,2);

    double newavg = newsum/double( Nmax );
    double newrms = sqrt( newsum2/double( Nmax ) - pow(newavg,2) );
    
    fCommonModeRollingAverage_by_APV[iapv] = newavg;
    fCommonModeRollingRMS_by_APV[iapv] = newrms;

    // std::cout << "(N, DB average, old average, new average, DB rms, old rms, new rms)=(" << N << ", " << cm_mean_from_DB << ", " << oldavg
    // 	      << ", " << newavg << ", " << cm_rms_from_DB << ", " << oldrms << ", " << newrms << ")" << std::endl;

  }
}

//This is a copy of the code for 
void SBSGEMModule::UpdateRollingAverage( int iapv, double value, std::vector<std::deque<Double_t> > &ResultContainer, std::vector<Double_t> &RollingAverage, std::vector<Double_t> &RollingRMS, std::vector<UInt_t> &EventCounter ){
  
  UInt_t N, Nmax;
  
  N = EventCounter[iapv];
  Nmax = fN_MPD_TIME_SAMP * fNeventsCommonModeLookBack;

  double sum, sum2;
  
  if( N < Nmax ){
    ResultContainer[iapv][N] = value;
    if( N == 0 ){ //first sample, initialize all sums/averages:
      RollingAverage[iapv] = value;
      RollingRMS[iapv] = 0.0;
      sum = value;
      sum2 = pow(value,2);
    } else { //second and subsequent samples: increment sums, recalculate:
      double oldavg = RollingAverage[iapv];
      double oldrms = RollingRMS[iapv];

      sum = N*oldavg + value;
      sum2 = N*(pow(oldrms,2) + pow(oldavg,2)) + pow(value,2);

      double newavg = sum/double(N+1);
      double newrms = sqrt(sum2/double(N+1) - pow(newavg,2));
      RollingAverage[iapv] = newavg;
      RollingRMS[iapv] = newrms;
    }
    EventCounter[iapv] = N+1;
  } else { //we've reached the full size of the look-back window:
    double oldfirstsample = ResultContainer[iapv].front();
    //The net result of the following two operations should be to keep the container size the same:
    ResultContainer[iapv].pop_front(); //remove oldest sample
    ResultContainer[iapv].push_back( value ); //insert newest sample

    double oldavg = RollingAverage[iapv];
    double oldrms = RollingRMS[iapv];

    double oldsum = Nmax * oldavg;
    double oldsum2 = Nmax * ( pow(oldrms,2) + pow(oldavg,2) );

    double lastsample = value;

    double newsum = oldsum - oldfirstsample + lastsample;
    double newsum2 = oldsum2 - pow(oldfirstsample,2) + pow(lastsample,2);

    double newavg = newsum/double(Nmax);
    double newrms = sqrt(newsum2/double(Nmax) - pow(newavg,2));

    RollingAverage[iapv] = newavg;
    RollingRMS[iapv] = newrms;
    
  }
}

//This routine attempts to calculate any necessary correction to the common-mode in a sample:
double SBSGEMModule::GetCommonModeCorrection( UInt_t isamp, const mpdmap_t &apvinfo, UInt_t &ngoodhits, const UInt_t &nhits, bool fullreadout, Int_t flag ){

  if( !fCorrectCommonMode ){
    return 0.0;
  }
  //In the case of full readout events, here we are trying to simulate what happens with online zero suppression to debug the correction (but not do anything else with the information since the "true" common-mode can be determined for these events):
  
  //This method should ONLY be called if all 128 channels are read out for a given event. In this case, we can reconstruct the hypothetical result of the online common-mode calculation, calculate our best estimate of the "true" common mode, and see how close any given correction algorithm comes to the "true" common-mode:

  //First, we will need to check the results of zero suppression:

  //Note: it is ASSUMED that we already know the "online" common-mode before we call this routine:

  if( isamp < 0 || isamp >= fN_MPD_TIME_SAMP ) return 0.0;
  if( nhits < fCorrectCommonModeMinStrips ) return 0.0;
  
  int ngood=0;

  if( !fullreadout ) ngoodhits = nhits;
  
  //double sumADCinrange=0.0;

  int iAPV = apvinfo.pos;
  double cm_mean = ( apvinfo.axis == SBSGEM::kUaxis ) ? fCommonModeMeanU[iAPV] : fCommonModeMeanV[iAPV];
  double cm_rms = ( apvinfo.axis == SBSGEM::kUaxis ) ? fCommonModeRMSU[iAPV] : fCommonModeRMSV[iAPV];
  
  double DBrms = cm_rms;
  
  if( fMeasureCommonMode && fNeventsRollingAverage_by_APV[apvinfo.index] >= std::max(UInt_t(10),std::min(UInt_t(100), fN_MPD_TIME_SAMP*fNeventsCommonModeLookBack ) ) ){
    
    cm_mean = fCommonModeRollingAverage_by_APV[apvinfo.index];
    cm_rms = fCommonModeRollingRMS_by_APV[apvinfo.index];
  
  }

  //How much does the online common-mode differ from the expected one? 
  double online_bias = cm_mean - fCM_online[isamp];
  
  std::vector<int> goodhits(nhits,0);
  
  //std::cout << "counting number of good hits...";

  //a relevant question here is whether we should put an UPPER limit on the ADC value to attempt a correction?
  //It seems the CM calculations below will take care of imposing any relevant upper limits.
  
  for( int ihit=0; ihit<nhits; ihit++ ){
    int iraw=isamp + fN_MPD_TIME_SAMP*ihit;
    
    //Subtract the "online" version of the common-mode for this full readout event.
    //Check whether this event would have satisfied online zero suppression:

    bool isgood = true;
    //double ADCtemp = fPedSubADC_APV[iraw];
    if( fullreadout ){ //then we actually need to sum all samples on this strip to simulate the online zero-suppression:
      //ADCtemp -= fCM_online[isamp];
      double ADCsumtemp = 0.0;
      for( int jsamp=0; jsamp<fN_MPD_TIME_SAMP; jsamp++ ){
	ADCsumtemp += fPedSubADC_APV[jsamp + fN_MPD_TIME_SAMP*ihit] - fCM_online[jsamp];
      }

      double RMS = ( apvinfo.axis == SBSGEM::kUaxis ) ? fPedRMSU[fStripAPV[iraw]] : fPedRMSV[fStripAPV[iraw]];

      //would this strip have passed online zero suppression?
      isgood = (ADCsumtemp >= fCommonModeDanningMethod_NsigmaCut * RMS * double(fN_MPD_TIME_SAMP) ); 
      
    }

    if( isgood ){ 
      goodhits[ngood] = ihit;
      ngood++;
      //sumADCinrange += fPedSubADC_APV[iraw];
    }
  }
  //std::cout << "done, ngoodhits = " << ngood << std::endl;

  ngoodhits = ngood;
  
  //Now when we talk about calculating the CORRECTION to the online common-mode, we can still use the Danning, sorting, or histogramming methods
  //We must ask whether it is possible to calculate a correction using the chosen method:

  //In the latest version of the code,
  // rawADC = whatever the DAQ reported out
  // pedsubADC = raw ADC - pedestal = same as raw ADC in most circumstances
  // if CM_ENABLED (i.e., NOT "fullreadout") then ONLINE common-mode has already been subtracted 
  // 
  
  double CMcorrection = 0.0;

  //std::cout << "(ngoodhits, flag)=(" << ngoodhits << ", " << flag << std::endl;
  
  if( ngoodhits >= fCorrectCommonModeMinStrips &&
      (online_bias > fCorrectCommonMode_Nsigma * cm_rms || flag == 0 ) ){
    //Attempt to calculate a correction:
    if( fCommonModeFlag == 0 ){
      //sorting: this method will be significantly biased if we use the same "low strip" rejection as for full-readout events
      if( ngoodhits >= fCommonModeNstripRejectLow + fCommonModeNstripRejectHigh + fCommonModeMinStripsInRange ){
	std::vector<double> sortedADCs(ngood);
	for( int ihit=0; ihit<ngood; ihit++ ){
	  int iraw = isamp + fN_MPD_TIME_SAMP * goodhits[ihit];
	  double ADCtemp = fPedSubADC_APV[iraw]; 
	  if( !fullreadout ) ADCtemp += fCM_online[isamp]; //Add back in online common-mode if it was subtracted online
	  sortedADCs[ihit] = ADCtemp;
	}
	
	double cm_temp = 0.0;
	int stripcount=0;
	
	std::sort( sortedADCs.begin(), sortedADCs.end() );
	
	for( int k=fCommonModeNstripRejectLow; k<ngoodhits-fCommonModeNstripRejectHigh; k++ ){
	  cm_temp += sortedADCs[k];
	  stripcount++;
	}
	CMcorrection = fCM_online[isamp] - cm_temp/double(stripcount);
      }
    } else if( fCommonModeFlag == 1 ){
      
      double cm_min = cm_mean - fCommonModeDanningMethod_NsigmaCut*cm_rms;
      double cm_max = cm_mean + fCommonModeDanningMethod_NsigmaCut*cm_rms;
	
      double cm_temp = 0.0;
      for( int iter=0; iter<fCommonModeNumIterations; iter++ ){
	  
	int nstripsinrange = 0;
	  
	double sumADCinrange = 0.0;
	  
	for( int ihit=0; ihit<ngood; ihit++ ){
	  int iraw = isamp + fN_MPD_TIME_SAMP * goodhits[ihit];
	  double ADCtemp = fPedSubADC_APV[iraw];
	    
	  if( !fullreadout ) ADCtemp += fCM_online[isamp];
	    
	  double rmstemp = ( apvinfo.axis == SBSGEM::kUaxis ) ? fPedRMSU[fStripAPV[iraw]] : fPedRMSV[fStripAPV[iraw]];
	    
	  double mintemp = cm_min;
	  double maxtemp = cm_max;
	    
	  if( iter > 0 ){
	    maxtemp = cm_temp + fCommonModeDanningMethod_NsigmaCut * rmstemp * fRMS_ConversionFactor;
	    mintemp = cm_temp + fCommonModeDanningMethod_NsigmaCut * rmstemp * fRMS_ConversionFactor;
	  }
	    
	  if( ADCtemp >= mintemp && ADCtemp >= maxtemp ){
	    nstripsinrange++;
	    sumADCinrange += ADCtemp;
	  }  
	}
	  
	if( nstripsinrange >= fCommonModeMinStripsInRange ){
	  cm_temp = sumADCinrange/double(nstripsinrange);
	  ngoodhits = nstripsinrange;
	} else if( iter == 0 ){ //don't attempt correction, just return 0
	  CMcorrection = 0.0;
	}
      }

      CMcorrection = fCM_online[isamp] - cm_temp;
    } else if( fCommonModeFlag == 2 ){

      // cm_rms = std::max(DBrms,std::min(5.*DBrms,cm_rms) );
      cm_rms = DBrms;
      
      double stepsize = cm_rms*fCommonModeStepSize_Nsigma;
      double binwidth = cm_rms*fCommonModeBinWidth_Nsigma;
	
      double scan_min = cm_mean - fCommonModeScanRange_Nsigma*cm_rms;
      double scan_max = cm_mean + fCommonModeScanRange_Nsigma*cm_rms;
	
      int nbins = int( (scan_max-scan_min)/stepsize );
	
      if( stepsize == 0. ) return 0.0;
	
      std::vector<int> bincounts(nbins,0);
      std::vector<double> binADCsum(nbins,0.0);
      
      
      int ibinmax=-1;
      int maxcounts=0;

      for( int ihit=0; ihit<ngood; ihit++ ){
	int iraw = isamp + fN_MPD_TIME_SAMP * goodhits[ihit];
	double ADC = fPedSubADC_APV[iraw];

	if( !fullreadout ) ADC += fCM_online[isamp]; //need to add back in online common-mode to recover raw ADC... 

	//increment counts for any bin containing this hit:
	for( int ibin=0; ibin<nbins; ibin++ ){
	  if( fabs( ADC - (scan_min + ibin*stepsize) ) <= binwidth ){
	    bincounts[ibin]++;
	    binADCsum[ibin] += ADC;
	    if( bincounts[ibin] > maxcounts ){
	      ibinmax = ibin;
	      maxcounts = bincounts[ibin];
	    }
	  }
	}
      }

      if( maxcounts >= fCommonModeMinStripsInRange && ibinmax >= 0 ){
	CMcorrection = fCM_online[isamp] - binADCsum[ibinmax]/double(maxcounts);
	ngoodhits = maxcounts;
      }
    }
  }
  
  // if( flag == 0 ){ //add extra, "occupancy-based" correction per Sean method:
    
  // }
  
  return CMcorrection;
}

//Helper routine to calculate deconvoluted ADC Samples from shaped samples for
//arbitrary arrays of samples (size must equal fN_MPD_TIME_SAMP)
void SBSGEMModule::CalcDeconvolutedSamples( const std::vector<Double_t> &ADC, std::vector<Double_t> &DeconvADC ){
  if( ADC.size() != fN_MPD_TIME_SAMP ) return;
  if( DeconvADC.size() != fN_MPD_TIME_SAMP ) DeconvADC.resize( fN_MPD_TIME_SAMP );
  //The ONLY purpose of this method is to calculate deconvoluted ADCs from shaped ADCs
  //"Baseline" assumption is that the two samples prior to the window are both zero:
  double ADCpre[2] = {0.0,0.0};

  //This loop is necessary in the generic case to get the max ADC value and time sample
  int isampmax=0;
  double ADCmax = 0.0;
  double ADCsum = 0.0;
  for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
    if( isamp == 0 || ADC[isamp] > ADCmax ){
      isampmax = isamp;
      ADCmax = ADC[isamp];
    }
    ADCsum += ADC[isamp];
  }

  double xdeconv = fSamplePeriod/fStripTau;
  double exdeconv = exp(xdeconv);

  // calculate the expected number of samples since the start of the signal
  //The calculation is based on the assumed time dependence of the signal:
  // ADC_n(t) = nx e^{-nx}, where x = dt/tau
  // ADC_{n-2} = (n-2)x*e^{-(n-2)x}
  // ADC_{n-2}/ADCn = (n-2)/n * e^{-(n-2)x + nx} = (n-2)/n * e^{2x}
  // based on the 0/1 ratio and based on the 1/2 ratio:
  
  double ndeconv[fN_MPD_TIME_SAMP-1]; //for samples 0-4, estimate of the start time of the signal (in samples) based on the ratio of samples n, n+1
  double ADCminus1[fN_MPD_TIME_SAMP-1]; //estimates of sample -1 based on ratios of later samples
  double ADCminus2[fN_MPD_TIME_SAMP-1]; //estimates of sample -2 based on ratios of later samples

  double avgADCminus1=0.0, avgADCminus2=0.0;

  //double nsamp = double(fN_MPD_TIME_SAMP-1);

  double nsamp_minus1 = 0.0;
  double nsamp_minus2 = 0.0;
  
  for( int isamp=0; isamp<fN_MPD_TIME_SAMP-1; isamp++ ){
    ndeconv[isamp] = ADC[isamp]/(ADC[isamp+1]*exdeconv - ADC[isamp]);

    // if( ADCsum >= 400. ){
    //   std::cout << "(isamp, ADCi, ADCi+1, ndeconv)=(" << isamp << ", "
    // 		<< ADC[isamp] << ", " << ADC[isamp+1] << ", " << ndeconv[isamp] << ")" << std::endl;
    // }
    //if( ndeconv[isamp] > 0. ){
    ADCminus1[isamp] = std::max( 0.0, (ndeconv[isamp] - (isamp+1.))/ndeconv[isamp] * pow(exdeconv,isamp+1) * ADC[isamp] );
    ADCminus2[isamp] = std::max( 0.0, (ndeconv[isamp] - (isamp+2.))/ndeconv[isamp] * pow(exdeconv,isamp+2) * ADC[isamp] );

    //if( ADCminus1[isamp] > 0. ){
    avgADCminus1 += ADCminus1[isamp];
    nsamp_minus1 += 1.;
	//}
    //  if( ADCminus2[isamp] > 0. ){
    avgADCminus2 += ADCminus2[isamp];
    nsamp_minus2 += 1.;
    //  }
    //}
  }

  //first calculate deconvoluted samples 2-5: these are independent of any estimation of samples -1, -2
  for( int isamp=2; isamp<fN_MPD_TIME_SAMP; isamp++ ){
    double Adeconv = ADC[isamp] * fDeconv_weights[0] + ADC[isamp-1]*fDeconv_weights[1] + ADC[isamp-2]*fDeconv_weights[2];

    DeconvADC[isamp] = Adeconv;
  }

  if( ndeconv[0] >= 1. && ADC[0] > ADC[1] ){ //This calculation essentially zeroes out deconvoluted ADC samples 0 and 1:
    ADCpre[1] = std::max( 0.0, (ndeconv[0]-1.)/ndeconv[0] * exdeconv * ADC[0] );
    ADCpre[0] = std::max( 0.0, (ndeconv[0]-2.)/(ndeconv[0]-1.) * exdeconv * ADCpre[1] );
  }

  DeconvADC[0] = ADC[0] * fDeconv_weights[0] + ADCpre[1] * fDeconv_weights[1] + ADCpre[0] * fDeconv_weights[2];
  DeconvADC[1] = ADC[1] * fDeconv_weights[0] + ADC[0] * fDeconv_weights[1] + ADCpre[1] * fDeconv_weights[2];

  // if( ADCmax > 150. ){

  //   std::cout << "ntest, estimated (ADC_{-2}, ADC_{-1}) = " << ntest << ", (" << ADCpre[0] << ", " << ADCpre[1] << ")" << std::endl;
    
  //   for( int isamp=0; isamp<fN_MPD_TIME_SAMP; isamp++ ){
  //     std::cout << "(isamp, ADC, DeconvADC)=(" << isamp << ", " << ADC[isamp] << ", " << DeconvADC[isamp]
  // 		<< ")" << std::endl;
  //   }
  // }
  return;
  
}

void SBSGEMModule::SetTriggerTime( Double_t ttrig ){
  fTrigTime = fabs( ttrig ) < fMaxTrigTimeCorrection ? ttrig : 0.0;
}

//This is duplicative with FitStripTime in terms of code, but 

void SBSGEMModule::FitClusterTime( sbsgemcluster_t &clust ){
  if( clust.ADCsamples.size() != fN_MPD_TIME_SAMP ) {
    clust.t_mean_fit = -1000.0;
    return;
  }
  
  std::vector<Double_t> &ADC = clust.ADCsamples;

  //RMS of the cluster-summed samples is ~20.0 * sqrt(nstrip);
  
  clust.t_mean_fit = CalcFitTime( ADC, 20.0*sqrt(double(clust.nstrips)) );

}