CDCalibrator.cc

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#include "CDCalibrator.hh"
 
MiniballCDCalibrator::MiniballCDCalibrator( std::shared_ptr<MiniballSettings> myset ){
 
    // First get the settings
    set = myset;
    
    // No calibration file by default
    overwrite_cal = false;
    
    // No input file at the start by default
    flag_input_file = false;
    
    // Progress bar starts as false
    _prog_ = false;
 
    // Start at MBS event 0
    preveventid = 0;
 
    // ------------------------------- //
    // Initialise variables and flags  //
    // ------------------------------- //
    build_window = set->GetEventWindow();
 
    // Intialise the hist list
    histlist = new TList();
 
}
 
void MiniballCDCalibrator::StartFile(){
 
    // Call for every new file
    // Reset counters etc.
    
    time_prev       = 0;
    time_min        = 0;
    time_max        = 0;
    time_first      = 0;
 
}
 
void MiniballCDCalibrator::SetInputFile( std::vector<std::string> input_file_names ) {
 
    input_tree = new TChain( "mb_sort" );
    mbsinfo_tree = new TChain( "mbsinfo" );
    for( unsigned int i = 0; i < input_file_names.size(); i++ ) {
 
        input_tree->Add( input_file_names[i].data() );
        mbsinfo_tree->Add( input_file_names[i].data() );
 
    }
 
    flag_input_file = true;
 
    input_tree->SetBranchAddress( "data", &in_data );
    mbsinfo_tree->SetBranchAddress( "mbsinfo", &mbs_info );
    mbsinfo_tree->BuildIndex("GetEventID()");
 
    return;
 
}
 
void MiniballCDCalibrator::SetInputFile( std::string input_file_name ) {
 
    // Open next Root input file.
    input_file = new TFile( input_file_name.data(), "read" );
    if( input_file->IsZombie() ) {
        
        std::cout << "Cannot open " << input_file_name << std::endl;
        return;
        
    }
    
    flag_input_file = true;
    
    // Set the input tree
    SetInputTree( (TTree*)input_file->Get("mb_sort") );
    SetMBSInfoTree( (TTree*)input_file->Get("mbsinfo") );
    StartFile();
 
    return;
    
}
 
void MiniballCDCalibrator::SetInputTree( TTree *user_tree ){
 
    // Find the tree and set branch addresses
    input_tree = (TChain*)user_tree;
    in_data = nullptr;
    input_tree->SetBranchAddress( "data", &in_data );
 
    return;
    
}
 
void MiniballCDCalibrator::SetMBSInfoTree( TTree *user_tree ){
 
    // Find the tree and set branch addresses
    mbsinfo_tree = (TChain*)user_tree;
    mbs_info = nullptr;
    mbsinfo_tree->SetBranchAddress( "mbsinfo", &mbs_info );
 
    return;
 
}
 
void MiniballCDCalibrator::SetOutput( std::string output_file_name, bool cWrite ) {
 
    // ------------------------------------------------------------------------ //
    // Create output file and create events tree
    // ------------------------------------------------------------------------ //
    output_file = new TFile( output_file_name.data(), "recreate" );
 
    // Hisograms in separate function
    MakeHists();
 
    // Output the calibration coefficients
    std::string cal_file_name = output_file_name.substr( 0, output_file_name.find_last_of(".") );
    cal_file_name += ".cal";
    output_cal.open( cal_file_name.data(), std::ios::trunc );
 
    // Write once at the start if in spy
    if( cWrite ) output_file->Write();
 
}
 
void MiniballCDCalibrator::Initialise(){
 
    
    flag_close_event = false;
    event_open = false;
 
    hit_ctr = 0;
    
    std::vector<float>().swap(cd_en_list);
    std::vector<unsigned int>().swap(cd_Q_list);
    std::vector<unsigned long long>().swap(cd_ts_list);
    std::vector<unsigned char>().swap(cd_det_list);
    std::vector<unsigned char>().swap(cd_sec_list);
    std::vector<unsigned char>().swap(cd_side_list);
    std::vector<unsigned char>().swap(cd_strip_list);
    
    return;
    
}
 
 
void MiniballCDCalibrator::MakeHists(){
 
    std::string hname, htitle;
 
    // ------------- //
    // CD histograms //
    // ------------- //
    cd_pen_nen.resize( set->GetNumberOfCDDetectors() );
    cd_nen_pen.resize( set->GetNumberOfCDDetectors() );
    cd_pen_nQ.resize( set->GetNumberOfCDDetectors() );
    cd_nQ_pQ.resize( set->GetNumberOfCDDetectors() );
 
    // Get sizes and scales
    double maxQ = 1073741824;
    unsigned int Qbins = 8192;
 
    if( set->GetNumberOfCaenAdcModules() > 0 ) {
        maxQ = 4096;
        Qbins = 4096;
    }
 
    else if( set->GetNumberOfFebexSfps() > 1 &&
            set->GetNumberOfFebexBoards() > 0 &&
            set->GetNumberOfFebexChannels() > 0 ) {
 
        if( cal->FebexType( 1, 0, 0 ) == "Qshort" ) {
            maxQ = 65536;
        }
    }
 
    for( unsigned int i = 0; i < set->GetNumberOfCDDetectors(); ++i ) {
        
        cd_pen_nen[i].resize( set->GetNumberOfCDSectors() );
        cd_nen_pen[i].resize( set->GetNumberOfCDSectors() );
        cd_pen_nQ[i].resize( set->GetNumberOfCDSectors() );
        cd_nQ_pQ[i].resize( set->GetNumberOfCDSectors() );
 
        for( unsigned int j = 0; j < set->GetNumberOfCDSectors(); ++j ) {
 
            cd_nen_pen[i][j].resize( set->GetNumberOfCDPStrips() );
            cd_nQ_pQ[i][j].resize( set->GetNumberOfCDPStrips() );
 
            for( unsigned int k = 0; k < set->GetNumberOfCDPStrips(); ++k ) {
 
                hname  = "cd_" + std::to_string(i) + "_" + std::to_string(j);
                hname  += "_nen_" + std::to_string(ptag) + "_pen_" + std::to_string(k);
                htitle  = "CD n-side energy vs p-side energy for detector " + std::to_string(i);
                htitle += ", sector " + std::to_string(j) + ", pid " + std::to_string(k);
                htitle += ", nid " + std::to_string(ntag);
                htitle += ";n-side energy (keV);p-side energy (keV);Counts";
                cd_nen_pen[i][j][k] = new TH2F( hname.data(), htitle.data(),
                                               4000, 0, 2000e3, 4000, 0, 2000e3 );
                histlist->Add(cd_nen_pen[i][j][k]);
 
                hname  = "cd_" + std::to_string(i) + "_" + std::to_string(j);
                hname  += "_nQ_" + std::to_string(ptag) + "_pQ_" + std::to_string(k);
                htitle  = "CD n-side energy vs p-side raw charge for detector " + std::to_string(i);
                htitle += ", sector " + std::to_string(j) + ", pid " + std::to_string(k);
                htitle += ", nid " + std::to_string(ntag);
                htitle += ";n-side raw charge (ADC units);p-side raw charge (ADC units);Counts";
                cd_nQ_pQ[i][j][k] = new TH2F( hname.data(), htitle.data(),
                                              Qbins, 0, maxQ, Qbins, 0, maxQ );
                histlist->Add(cd_nQ_pQ[i][j][k]);
 
            } // k
 
            cd_pen_nen[i][j].resize( set->GetNumberOfCDNStrips() );
            cd_pen_nQ[i][j].resize( set->GetNumberOfCDNStrips() );
 
            for( unsigned int k = 0; k < set->GetNumberOfCDNStrips(); ++k ) {
 
                hname  = "cd_" + std::to_string(i) + "_" + std::to_string(j);
                hname  += "_pen_" + std::to_string(ptag) + "_nen_" + std::to_string(k);
                htitle  = "CD p-side energy vs n-side energy for detector " + std::to_string(i);
                htitle += ", sector " + std::to_string(j) + ", pid " + std::to_string(ptag);
                htitle += ", nid " + std::to_string(k);
                htitle += ";p-side energy (keV);n-side energy (keV);Counts";
                cd_pen_nen[i][j][k] = new TH2F( hname.data(), htitle.data(),
                                               4000, 0, 2000e3, 4000, 0, 2000e3 );
                histlist->Add(cd_pen_nen[i][j][k]);
 
                hname  = "cd_" + std::to_string(i) + "_" + std::to_string(j);
                hname  += "_pen_" + std::to_string(ptag) + "_nQ_" + std::to_string(k);
                htitle  = "CD p-side energy vs n-side raw charge for detector " + std::to_string(i);
                htitle += ", sector " + std::to_string(j) + ", pid " + std::to_string(ptag);
                htitle += ", nid " + std::to_string(k);
                htitle += ";p-side energy (keV);n-side raw charge (ADC units);Counts";
                cd_pen_nQ[i][j][k] = new TH2F( hname.data(), htitle.data(),
                                              4000, 0, 2000e3, Qbins, 0, maxQ );
                histlist->Add(cd_pen_nQ[i][j][k]);
 
            } // k
 
        } // j
 
    } // i
    
    
    // flag to denote that hists are ready (used for spy)
    hists_ready = true;
 
    return;
    
}
 
// Reset histograms in the DataSpy
void MiniballCDCalibrator::ResetHists(){
 
    // Loop over the hist list
    TIter next( histlist->MakeIterator() );
    while( TObject *obj = next() ) {
 
        if( obj->InheritsFrom( "TH2" ) )
            ( (TH2*)obj )->Reset("ICESM");
        else if( obj->InheritsFrom( "TH1" ) )
            ( (TH1*)obj )->Reset("ICESM");
 
    }
 
    return;
 
}
 
bool MiniballCDCalibrator::FindCDChannels( int det, int sec, int side, int strip, int &adc, int &ch ) {
 
    // Loop over ADCs
    for( unsigned int m = 0; m < set->GetNumberOfCaenAdcModules(); ++m ) {
 
        // Loop over channels
        for( unsigned int c = 0; c < set->GetNumberOfCaenAdcChannels(); ++c ) {
 
            // Check that it's a CD
            if( !set->IsCD(m,c) ) continue;
 
            // Check we have the correct CD detector
            if( set->GetCDDetector(m,c) != det ) continue;
 
            // Check we have the correct sector
            if( set->GetCDSector(m,c) != sec ) continue;
 
            // Check we have an P side (==0)
            if( set->GetCDSide(m,c) != side ) continue;
 
            // Check we have the correct strip
            if( set->GetCDStrip(m,c) != strip ) continue;
 
            // Then we got the right channel
            adc = m;
            ch = c;
            return true;
 
        } // c
 
    } // m
 
    std::cerr << "CD strip not found, det=" << det << ", sec=" << sec;
    std::cerr << ", side=" << side << ", strip=" << strip << std::endl;
    return false;
 
}
 
bool MiniballCDCalibrator::FindCDChannels( int det, int sec, int side, int strip, int &sfp, int &board, int &ch ) {
 
    // Loop over SFPs
    for( unsigned int s = 0; s < set->GetNumberOfFebexSfps(); ++s ) {
 
        // Loop over boards
        for( unsigned int m = 0; m < set->GetNumberOfFebexBoards(); ++m ) {
 
            // Loop over channels
            for( unsigned int c = 0; c < set->GetNumberOfFebexChannels(); ++c ) {
 
                // Check that it's a CD
                if( !set->IsCD(s,m,c) ) continue;
 
                // Check we have the correct CD detector
                if( set->GetCDDetector(s,m,c) != det ) continue;
 
                // Check we have the correct sector
                if( set->GetCDSector(s,m,c) != sec ) continue;
 
                // Check we have the right side
                if( set->GetCDSide(s,m,c) != side ) continue;
 
                // Check we have the correct strip
                if( set->GetCDStrip(s,m,c) != strip ) continue;
 
                // Then we got the right channel
                sfp = s;
                board = m;
                ch = c;
                return true;
 
            } // c
 
        } // m
 
    } // s
 
    std::cerr << "CD strip not found, det=" << det << ", sec=" << sec;
    std::cerr << ", side=" << side << ", strip=" << strip << std::endl;
    return false;
 
}
 
void MiniballCDCalibrator::CalibratePsides() {
 
    // Check if we have old or new DAQ
    bool oldDAQ = false;
    if( set->GetNumberOfCaenAdcModules() > 0 )
        oldDAQ = true;
 
    // Create a TF1 for the linear fit
    auto pfit = std::make_unique<TF1>( "pfit", "[0]+[1]*x", 0, 1e9 );
 
    // Some canvases to check fits
    gErrorIgnoreLevel = kError;
    std::vector<std::vector<std::unique_ptr<TCanvas>>> canv;
    canv.resize( set->GetNumberOfCDDetectors() );
 
    // Loop over detectors
    for( unsigned int i = 0; i < set->GetNumberOfCDDetectors(); ++i ) {
 
        canv[i].resize( set->GetNumberOfCDSectors() );
 
        // Loop over the sectors
        for( unsigned int j = 0; j < set->GetNumberOfCDSectors(); ++j ) {
 
            std::string cname = "cdcal_p_" + std::to_string(i) + "_" + std::to_string(j);
            canv[i][j] = std::make_unique<TCanvas>( cname.data(), cname.data(), 800, 1000 );
 
            // Loop over all the strips
            for( unsigned int k = 0; k < set->GetNumberOfCDPStrips(); ++k ) {
 
                // Get the right histogram to do the fit
                auto res = cd_nQ_pQ[i][j][k]->Fit( pfit.get(), "QWL" );
                if( res != 0 ) continue;
                double fit_gain = ngain / pfit->GetParameter(1);
                double fit_offset = noffset - pfit->GetParameter(0) * fit_gain;
 
                // If we have the n-side tag, set the gain and offset
                if( k == ptag ) {
                    std::cout << "!! This is the p-side tag channel, cross-check check the parameters below !!" << std::endl;
                    pgain = fit_gain;
                    poffset = fit_offset;
                }
 
                // Get the output names for the calibration file
                std::string cal_base;
                std::string modchstr;
                int fsfp, fmod, fch;
                if( oldDAQ ) {
 
                    // Search for the correct ADC and channel combination
                    cal_base = "adc_";
                    if( !FindCDChannels( i, j, 0, k, fmod, fch ) )
                       continue;
                    modchstr = std::to_string(fmod) + "_" + std::to_string(fch);
 
                } // old DAQ
 
                else {
 
                    // Search for the correct ADC and channel combination
                    cal_base = "febex_";
                    if( !FindCDChannels( i, j, 0, k, fsfp, fmod, fch ) )
                        continue;
                    modchstr  = std::to_string(fsfp) + "_" + std::to_string(fmod);
                    modchstr += "_" + std::to_string(fch);
 
                } // new DAQ
 
                // Add gain and offset
                std::string gainstr = cal_base + modchstr + ".Gain: " + std::to_string( fit_gain );
                std::string offsetstr = cal_base + modchstr + ".Offset: " + std::to_string( fit_offset );
 
                // Write them to the file
                std::cout << gainstr << std::endl;
                std::cout << offsetstr << std::endl;
                output_cal << gainstr << std::endl;
                output_cal << offsetstr << std::endl;
 
                // Print to a file
                std::string pdfname = cname + ".pdf";
                if( k == 0 && set->GetNumberOfCDPStrips() != 1 )
                    pdfname += "(";
                else if( k > 0 && k == set->GetNumberOfCDPStrips() - 1 )
                    pdfname += ")";
                canv[i][j]->Print( pdfname.data(), "pdf" );
 
            } // k
 
        } // j
 
    } // i
 
    // Reset warning level
    gErrorIgnoreLevel = kInfo;
 
    return;
 
}
 
void MiniballCDCalibrator::CalibrateNsides() {
 
    // Check if we have old or new DAQ
    bool oldDAQ = false;
    if( set->GetNumberOfCaenAdcModules() > 0 )
        oldDAQ = true;
 
    // Create a TF1 for the linear fit
    auto nfit = std::make_unique<TF1>( "nfit", "[0]+[1]*x", 0, 1e9 );
 
    // Some canvases to check fits
    gErrorIgnoreLevel = kError;
    std::vector<std::vector<std::unique_ptr<TCanvas>>> canv;
    canv.resize( set->GetNumberOfCDDetectors() );
 
    // Loop over detectors
    for( unsigned int i = 0; i < set->GetNumberOfCDDetectors(); ++i ) {
 
        canv[i].resize( set->GetNumberOfCDSectors() );
 
        // Loop over the sectors
        for( unsigned int j = 0; j < set->GetNumberOfCDSectors(); ++j ) {
 
            std::string cname = "cdcal_n_" + std::to_string(i) + "_" + std::to_string(j);
            canv[i][j] = std::make_unique<TCanvas>( cname.data(), cname.data(), 800, 1000 );
 
            // Loop over all the strips
            for( unsigned int k = 0; k < set->GetNumberOfCDNStrips(); ++k ) {
 
                // Get the right histogram to do the fit
                auto res = cd_pen_nQ[i][j][k]->Fit( nfit.get(), "QWL" );
                if( res != 0 ) continue;
                double fit_gain = 1.0 / nfit->GetParameter(1);
                double fit_offset = -1.0 * nfit->GetParameter(0) * fit_gain;
                //double fit_gain = 1.0;
                //double fit_offset = 0.0;
 
                // If we have the n-side tag, set the gain and offset
                if( k == ntag ) {
                    ngain = fit_gain;
                    noffset = fit_offset;
                }
 
                // Get the output names for the calibration file
                std::string cal_base;
                std::string modchstr;
                int fsfp, fmod, fch;
                if( oldDAQ ) {
 
                    // Search for the correct ADC and channel combination
                    cal_base = "adc_";
                    if( !FindCDChannels( i, j, 1, k, fmod, fch ) )
                       continue;
                    modchstr = std::to_string(fmod) + "_" + std::to_string(fch);
 
                } // old DAQ
 
                else {
                    
                    // Search for the correct ADC and channel combination
                    cal_base = "febex_";
                    if( !FindCDChannels( i, j, 1, k, fsfp, fmod, fch ) )
                        continue;
                    modchstr  = std::to_string(fsfp) + "_" + std::to_string(fmod);
                    modchstr += "_" + std::to_string(fch);
                    
                } // new DAQ
 
                // Add gain and offset
                std::string gainstr = cal_base + modchstr + ".Gain: " + std::to_string( fit_gain );
                std::string offsetstr = cal_base + modchstr + ".Offset: " + std::to_string( fit_offset );
 
                // Write them to the file
                std::cout << gainstr << std::endl;
                std::cout << offsetstr << std::endl;
                output_cal << gainstr << std::endl;
                output_cal << offsetstr << std::endl;
 
                // Print to a file
                std::string pdfname = cname + ".pdf";
                if( k == 0 && set->GetNumberOfCDNStrips() != 1 )
                    pdfname += "(";
                else if( k > 0 && k == set->GetNumberOfCDNStrips() - 1 )
                    pdfname += ")";
                canv[i][j]->Print( pdfname.data(), "pdf" );
 
            } // k
 
        } // j
 
    } // i
 
    // Reset warning level
    gErrorIgnoreLevel = kInfo;
 
    return;
 
}
 
void MiniballCDCalibrator::FillPixelHists() {
 
    // Variables for the finder algorithm
    std::vector<unsigned char> pindex;
    std::vector<unsigned char> nindex;
 
    // Loop over each detector and sector
    for( unsigned int i = 0; i < set->GetNumberOfCDDetectors(); ++i ){
 
        for( unsigned int j = 0; j < set->GetNumberOfCDSectors(); ++j ){
 
            // Reset variables for a new detector element
            pindex.clear();
            nindex.clear();
            std::vector<unsigned char>().swap(pindex);
            std::vector<unsigned char>().swap(nindex);
 
            // Calculate p/n side multiplicities and get indicies
            for( unsigned int k = 0; k < cd_en_list.size(); ++k ){
 
                // Test that we have the correct detector and quadrant
                if( i != cd_det_list.at(k) || j != cd_sec_list.at(k) )
                    continue;
 
                // Check max energy and push back the multiplicity
                if( cd_side_list.at(k) == 0 )
                    pindex.push_back(k);
 
                else if( cd_side_list.at(k) == 1 )
                    nindex.push_back(k);
 
            } // k: all CD events
 
            // Keep only multiplicity 1v1 events
            if( pindex.size() != 1 || nindex.size() != 1 )
                continue;
 
            // Fill the hit in the right pixel
            int pid = cd_strip_list[pindex[0]];
            int nid = cd_strip_list[nindex[0]];
            double pen = cd_en_list[pindex[0]];
            double nen = cd_en_list[nindex[0]];
            unsigned int pQ = cd_Q_list[pindex[0]];
            unsigned int nQ = cd_Q_list[nindex[0]];
 
            // skip events with very diiferent energies
            if( nQ / pQ > 1.5 || pQ / nQ > 1.5 ) continue;
 
            // For p-side tags
            if( pid == ptag ) {
 
                cd_pen_nen[i][j][nid]->Fill( pen, nen );
                cd_pen_nQ[i][j][nid]->Fill( pen, nQ );
                
            }
            
            // For n-side tags
            if( nid == ntag ) {
 
                cd_nen_pen[i][j][pid]->Fill( nen, pen );
                cd_nQ_pQ[i][j][pid]->Fill( nQ, pQ );
 
            }
 
        } // j
 
    } // i
 
 
}
 
unsigned long MiniballCDCalibrator::FillHists() {
 
 
    if( input_tree->LoadTree(0) < 0 ){
        
        std::cout << " CD Calibrator: nothing to do" << std::endl;
        return 0;
        
    }
    
    // Get ready and go
    Initialise();
    n_entries = input_tree->GetEntries();
    n_mbs_entries = mbsinfo_tree->GetEntries();
 
    std::cout << " CD Calibrator: number of entries in input tree = ";
    std::cout << n_entries << std::endl;
 
    std::cout << "\tnumber of MBS Events/triggers in input tree = ";
    std::cout << n_mbs_entries << std::endl;
    
    // ------------------------------------------------------------------------ //
    // Main loop over TTree to find events
    // ------------------------------------------------------------------------ //
    for( unsigned long i = 0; i < n_entries; ++i ) {
        
        // First event, yes please!
        if( i == 0 ){
 
            input_tree->GetEntry(i);
            myeventid = in_data->GetEventID();
            myeventtime = in_data->GetTime();
 
            // Try to get the MBS info event with the index
            if( mbsinfo_tree->GetEntryWithIndex( myeventid ) < 0 &&
                n_mbs_entries > 0 ) {
 
                // Look for the matches MBS Info event if we didn't match automatically
                for( unsigned long j = 0; j < n_mbs_entries; ++j ){
 
                    mbsinfo_tree->GetEntry(j);
                    if( mbs_info->GetEventID() == myeventid ) {
                        myeventtime = mbs_info->GetTime();
                        break;
                    }
 
                    // Panic if we failed!
                    if( j+1 == n_mbs_entries ) {
                        std::cerr << "Didn't find matching MBS Event IDs at start of the file: ";
                        std::cerr << myeventid << std::endl;
                    }
 
                }
 
            }
 
            //std::cout << "MBS Trigger time = " << myeventtime << std::endl;
 
        }
 
        // Get the time of the event
        if( set->GetMbsEventMode() ) {
        
            myhittime = in_data->GetTime();
            mytime = myeventtime + myhittime;
            
        }
        
        else mytime = in_data->GetTime();
        
        // check time stamp monotonically increases in time-ordered mode!
        if( time_prev > mytime && !set->GetMbsEventMode() ) {
            
            std::cout << "Out of order event in ";
            std::cout << input_tree->GetName() << std::endl;
            
        }
            
        // check event id is increasing in MBS event ordered mode
        if( preveventid > myeventid && set->GetMbsEventMode() ) {
 
            std::cout << "Out of order MBS event " << myeventid;
            std::cout << " < " << preveventid << std::endl;
 
        }
 
        // record time of this event
        time_prev = mytime;
        
        // assume this is above threshold initially
        mythres = true;
 
        // ------------------------------------------ //
        // Find FEBEX data
        // ------------------------------------------ //
        if( in_data->IsFebex() ) {
            
            // Get the data
            febex_data = in_data->GetFebexData();
            mysfp = febex_data->GetSfp();
            myboard = febex_data->GetBoard();
            mych = febex_data->GetChannel();
            mypileup = febex_data->IsPileup();
            myclipped = febex_data->IsClipped();
 
            // Update calibration always for CD calibrator
            unsigned int adc_tmp_value;
            if( cal->FebexType( mysfp, myboard, mych ) == "Qshort" )
                adc_tmp_value = febex_data->GetQshort();
            else if( cal->FebexType( mysfp, myboard, mych ) == "Qint" )
                adc_tmp_value = febex_data->GetQint();
            else adc_tmp_value = febex_data->GetQshort();
 
            myenergy = cal->FebexEnergy( mysfp, myboard, mych, adc_tmp_value );
 
            if( adc_tmp_value > cal->FebexThreshold( mysfp, myboard, mych ) )
                mythres = true;
            else mythres = false;
 
            // Is it a particle from the CD?
            if( set->IsCD( mysfp, myboard, mych ) && mythres ) {
 
                // Increment counts and open the event
                hit_ctr++;
 
                // Clipped rejection and pileup rejection
                if( ( !myclipped || !set->GetClippedRejection() ) &&
                   ( !mypileup || !set->GetPileupRejection() ) ) {
 
                    event_open = true;
                    cd_en_list.push_back( myenergy );
                    cd_Q_list.push_back( adc_tmp_value );
                    cd_ts_list.push_back( mytime );
                    cd_det_list.push_back( set->GetCDDetector( mysfp, myboard, mych ) );
                    cd_sec_list.push_back( set->GetCDSector( mysfp, myboard, mych ) );
                    cd_side_list.push_back( set->GetCDSide( mysfp, myboard, mych ) );
                    cd_strip_list.push_back( set->GetCDStrip( mysfp, myboard, mych ) );
 
                }
 
            }
 
        }
        
        // ------------------------------------------ //
        // Find ADC data
        // ------------------------------------------ //
        if( in_data->IsAdc() ) {
            
            // Get the data
            adc_data = in_data->GetAdcData();
            myadc = adc_data->GetModule();
            mych = adc_data->GetChannel();
            myclipped = adc_data->IsClipped();
 
            // Update calibration always for CD calibrator
            unsigned int adc_tmp_value = adc_data->GetQshort();
            myenergy = cal->AdcEnergy( myadc, mych, adc_tmp_value );
 
            if( adc_tmp_value > cal->AdcThreshold( myadc, mych ) )
                mythres = true;
            else mythres = false;
 
            // Is it a particle from the CD?
            if( set->IsCD( myadc, mych ) && mythres ) {
                
                // Increment counts and open the event
                hit_ctr++;
                
                if( !myclipped || !set->GetClippedRejection() ) {
 
                    event_open = true;
                    cd_en_list.push_back( myenergy );
                    cd_Q_list.push_back( adc_tmp_value );
                    cd_ts_list.push_back( mytime );
                    cd_det_list.push_back( set->GetCDDetector( myadc, mych ) );
                    cd_sec_list.push_back( set->GetCDSector( myadc, mych ) );
                    cd_side_list.push_back( set->GetCDSide( myadc, mych ) );
                    cd_strip_list.push_back( set->GetCDStrip( myadc, mych ) );
                    
                }
                
            }
            
        }
 
        // Sort out the timing for the event window
        // but only if it isn't an info event, i.e only for real data
        if( !in_data->IsInfo() ) {
            
            // if this is first datum included in Event
            if( hit_ctr == 1 && mythres ) {
                
                time_min    = mytime;
                time_max    = mytime;
                time_first  = mytime;
                
            }
            
            // Update min and max
            if( mytime > time_max ) time_max = mytime;
            else if( mytime < time_min ) time_min = mytime;
            
        } // not info data
 
        //------------------------------
        //  check if last datum from this event and do some cleanup
        //------------------------------
        
        if( input_tree->GetEntry(i+1) ) {
            
            // Get the next MBS event ID
            preveventid = myeventid;
            myeventid = in_data->GetEventID();
 
            // If the next MBS event ID is the same, carry on
            // If not, we have to go look for the next trigger time
            if( myeventid != preveventid ) {
 
                // Close the event
                flag_close_event = true;
 
                // And find the next MBS event ID
                if( mbsinfo_tree->GetEntryWithIndex( myeventid ) < 0 &&
                    n_mbs_entries > 0 ) {
 
                    std::cerr << "MBS Event " << myeventid << " not found by index, looking up manually" << std::endl;
 
                    // Look for the matches MBS Info event if we didn't match automatically
                    for( unsigned long j = 0; j < n_mbs_entries; ++j ){
 
                        mbsinfo_tree->GetEntry(j);
                        if( mbs_info->GetEventID() == myeventid ) {
                            myeventtime = mbs_info->GetTime();
                            break;
                        }
 
                        // Panic if we failed!
                        if( j+1 == n_mbs_entries ) {
                            std::cerr << "Didn't find matching MBS Event IDs at start of the file: ";
                            std::cerr << myeventid << std::endl;
                        }
                    }
 
                }
 
                else myeventtime = mbs_info->GetTime();
 
            }
 
            // BELOW IS THE TIME-ORDERED METHOD!
 
            // Get the time of the next event
            if( set->GetMbsEventMode() ) {
            
                myhittime = in_data->GetTime();
                mytime = myeventtime + myhittime;
                
            }
            
            else mytime = in_data->GetTime();
 
            // Calculate time diff
            time_diff = mytime - time_first;
 
            // window = time_stamp_first + time_window
            if( time_diff > build_window )
                flag_close_event = true; // set flag to close this event
 
            // we've gone on to the next file in the chain
            else if( time_diff < 0 )
                flag_close_event = true; // set flag to close this event
                
        } // if next entry beyond time window: close event!
        
        
        //----------------------------
        // if close this event or last entry
        //----------------------------
        if( flag_close_event || (i+1) == n_entries ) {
 
            //--------------------------------------------------
            // clear values of arrays to store intermediate info
            //--------------------------------------------------
            FillPixelHists();
            Initialise();
            
        } // if close event && hit_ctr > 0
        
        // Progress bar
        bool update_progress = false;
        if( n_entries < 200 )
            update_progress = true;
        else if( i % (n_entries/100) == 0 || i+1 == n_entries )
            update_progress = true;
        
        if( update_progress ) {
 
            // Percent complete
            float percent = (float)(i+1)*100.0/(float)n_entries;
 
            // Progress bar in GUI
            if( _prog_ ) {
                
                prog->SetPosition( percent );
                gSystem->ProcessEvents();
                
            }
 
            // Progress bar in terminal
            std::cout << " " << std::setw(6) << std::setprecision(4);
            std::cout << percent << "%    \r";
            std::cout.flush();
 
        }       
        
    } // End of main loop over TTree to process raw FEBEX data entries (for n_entries)
 
 
    //--------------------------
    // Do the fitting to get calibration coefficients
    //--------------------------
 
    std::cout << "\n\nUsing p-side strip " << (int)ptag << " as reference for calibrating n-sides" << std::endl;
    CalibrateNsides();
    std::cout << "\n\nUsing n-side strip " << (int)ntag << " as reference for calibrating p-sides" << std::endl;
    CalibratePsides();
 
    //--------------------------
    // Clean up
    //--------------------------
 
    std::cout << "\n MiniballCDCalibrator finished..." << std::endl;
 
    return n_entries;
    
}