ReadRun.cc

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#include "ReadRun.h"
 
ReadRun::ReadRun(int last_bin_file, int first_bin_file) {
 
    cout << "\ninitializing ..." << endl;
 
    if (last_bin_file > 0) {
        cout << "will read " << last_bin_file - first_bin_file << " .bin files from file number " 
            << first_bin_file << " to file number " << last_bin_file << endl;
    }
    if (first_bin_file > 0) discard_original_eventnr = true;
 
    ROOT::EnableImplicitMT();
    TH1::AddDirectory(kFALSE);
    // init counters
    nwf = 0;
    PrintChargeSpectrum_cnt = 0;
    PlotChannelAverages_cnt = 0;
    PrintWFProjection_cnt = 0;
    PlotWFHeatmaps_cnt = 0;
    LastBinFileToRead = last_bin_file;
    FirstBinFileToRead = first_bin_file;
 
    root_out = new TFile(); // init results file
}
 
void ReadRun::ReadFile(string path, bool change_polarity, int change_sign_from_to_ch_num, string out_file_name, bool debug, long long max_nevents_to_read) {
    if (max_nevents_to_read <= 0) max_nevents_to_read = static_cast<long long>(1e9);
    rundata.reserve(1'000'000);                     // reserve space for 1M waveforms
    if (path.back() != '/') path += '/';
    data_path = path;
    
    // save results to root file
    if (out_file_name.empty()) out_file_name = "out.root";
    printf("+++ saving analysis results in '%s' ...\n\n", out_file_name.c_str());
    root_out = TFile::Open(out_file_name.c_str(), "recreate");
 
    // invert channels
    auto polarity_map = PolarityMap(change_polarity, change_sign_from_to_ch_num);
 
    // verbosity
    bool debug_header = debug;
    bool debug_data = debug;
 
    unsigned short output_channel;
    unsigned int output_event;
    unsigned short output_nbchannels;
    unsigned short read_channels = 0;
 
    //Start reading the raw data from .bin files.
    stringstream inFileList;
    inFileList << Helpers::ListFiles(path.c_str(), ".bin"); //all *.bin* files in folder path
    if (debug) cout << inFileList.str() << endl;
    string fileName;
    int file_counter = 0;
    int wfcounter = 0;
    int event_counter = 0;
 
    // file loop
    while (inFileList >> fileName) {
        // read only fraction/batch of the .bin files for testing or to reduce memory usage
        if (FirstBinFileToRead > 0 && FirstBinFileToRead < LastBinFileToRead && file_counter < FirstBinFileToRead) continue;
        if (LastBinFileToRead > 0 && file_counter > LastBinFileToRead) break;
 
        fileName = path + fileName;
        ifstream input_file(fileName.c_str(), ios::binary | ios::in);
 
        bool has_measurement = false;
 
        if (!input_file.is_open()) {
            printf("*** failed to open '%s'\n", fileName.c_str());
            continue;
        }
 
        if (file_counter < 10 || file_counter % 10 == 0 || debug) printf("+++ reading '%s' ...\n", fileName.c_str());
 
        // Header
        string header_line;
        // HEADER 1 //
        //
        // "=== DATA FILE SAVED WITH SOFTWARE VERSION: V?.??.? ==="
        //
        getline(input_file, header_line, '\n');
 
        if (debug_header) printf("%s\n", header_line.data());
        assert(header_line[0] == '=');
 
        size_t header_version_first = header_line.find_last_of('V');
        size_t header_version_last = header_line.find_first_of(' ', header_version_first);
        string software_version = header_line.substr(header_version_first, header_version_last - header_version_first);
        if (debug_header) printf("    |- data version = '%s'\n", software_version.data());
        // convert software version
        software_version.erase(0, 1);
        int v_major, v_minor, v_patch;
        istringstream software_version_iss(software_version);
        char dot_;
        software_version_iss >> v_major >> dot_ >> v_minor >> dot_ >> v_patch;
 
        // HEADER 2 //
        // "=== WAVECATCHER SYSTEM OF TYPE ?? WITH ?? CHANNELS AND GAIN: ??? ==="
        getline(input_file, header_line, '\n');
 
        if (debug_header) printf("%s\n", header_line.data());
        assert(header_line[0] == '=');
 
        // HEADER 3 //
        // === Rate coincidence masks ... === Posttrig in ns for SamBlock ... ===
        getline(input_file, header_line, '\n');
 
        if (debug_header) printf("%s\n", header_line.data());
        assert(header_line[0] == '=');
 
        // HEADER 4 //
        // V2.9.13: === DATA SAMPLES [1024] in Volts == NB OF CHANNELS ACQUIRED: 64 == Sampling Period: 312.5 ps == INL Correction: 1
        // V2.9.15: === DATA SAMPLES [1024] in Volts == NB OF CHANNELS ACQUIRED: 64 == Sampling Period: 312.5 ps == INL Correction: 1 == MEASUREMENTS: 0 ===
        getline(input_file, header_line, '\n');
 
        if (debug_header) printf("%s\n", header_line.data());
        assert(header_line[0] == '=');
 
        size_t nsamples_first = 1 + header_line.find_last_of('[');
        size_t nsamples_last = header_line.find_first_of(']', nsamples_first);
        string nsamples_str = header_line.substr(nsamples_first, nsamples_last - nsamples_first);
 
        binNumber = atoi(nsamples_str.data());
        if (debug_header) printf("    |- data sample  = %d\n", binNumber);
        if (file_counter == 0 && binNumber != 1024) {
            cout << "\nWARNING: Measurement has " << binNumber << " samples, which is non-standard. Please report any bugs!" << endl;
            cout << "If this was not intentional check the WaveCatcher settings!" << endl;
        }
        size_t waveform_bytes = static_cast<size_t>(binNumber) * sizeof(short);
        vector<short> waveform(binNumber);
        vector<float> waveform_f(binNumber);
 
        if (file_counter == 0) amplValuessum.resize(nChannelsWC, vector<float>(binNumber, 0.));
 
        size_t nchannels_first = 10 + header_line.find("ACQUIRED: ", nsamples_first);
        size_t nchannels_last = header_line.find_first_of(' ', nchannels_first);
        string nchannels_str = header_line.substr(nchannels_first, nchannels_last - nchannels_first);
 
        nchannels = atoi(nchannels_str.data());
        if (debug_header) printf("    |- nchannels    = %d\n", nchannels);
 
        size_t sp_first = 8 + header_line.find("Period:");
        size_t sp_last = header_line.find(" ps");
        float sampling_period = atof(header_line.substr(sp_first, sp_last - sp_first).data());
        if (debug_header) printf("sampling period  = %f ps\n", sampling_period);
        SP = sampling_period * 1e-3;
        SP_inv = 1/SP;
 
        // compatibility with older WC software versions
        if (v_major ==2 && v_minor == 9 && v_patch <= 13) {
            // V2.9.13 has always measurement stored (everything is set to 0 when disabled!)
            has_measurement = true; 
        }
        else {
            size_t has_measurement_first = 14 + header_line.find("MEASUREMENTS: ", nsamples_first);
            size_t has_measurement_last = header_line.find_first_of(' ', has_measurement_first);
            string has_measurement_str = header_line.substr(has_measurement_first, has_measurement_last - has_measurement_first);
            has_measurement = atoi(has_measurement_str.data());
        }
 
        if (debug_header) printf("    `- measurement  = %d\n", has_measurement);
 
        // end of header reader
 
        event_data an_event;
 
        while (input_file.read((char*)(&an_event), sizeof(an_event))) {
            //event loop
            if (debug_data) printf("%03d has %d channels\n", an_event.EventNumber, an_event.nchannelstored);
 
            output_event = an_event.EventNumber;
            output_nbchannels = an_event.nchannelstored;
 
            if (debug_data && output_event % 200 == 0) printf("EventNr: %d, nCh: %d\n", output_event, output_nbchannels);
            if (output_nbchannels > nChannelsWC) {
                cout << "ERROR:\nThe number of channels in the data is " << output_nbchannels 
                    << ", which is larger than the maximum allowed number of channels which is set to " << nChannelsWC 
                    << "\nPlease set the parameter nChannelsWC=" << output_nbchannels << endl;
            }
 
            // do analysis only for limited range of channels to reduce memory usage for large datasets with many channels and many events
            int start_at_ch = 0;
            if (start_read_at_channel < output_nbchannels && start_read_at_channel >= 0) start_at_ch = start_read_at_channel;
            int end_at_ch = output_nbchannels - 1;
            if (end_read_at_channel == -1 && start_read_at_channel != -1) end_read_at_channel = start_read_at_channel;
            else if (end_read_at_channel < output_nbchannels && end_read_at_channel >= 0) end_at_ch = end_read_at_channel;
            read_channels = end_at_ch - start_at_ch + 1;
 
            if (event_counter == 0) cout << "\nstart at ch " << start_at_ch << " end at ch " << end_at_ch << endl;
 
            for (int ch = 0; ch < output_nbchannels; ++ch) { // channel loop
                channel_data_with_measurement a_channel_data;
                channel_data_without_measurement a_channel_data_without_measurement;
                
                if (has_measurement) { // read with 'channel_data_with_measurement' struct
                    input_file.read((char*)(&a_channel_data), sizeof(channel_data_with_measurement));
                }
                else { // read with 'channel_data_without_measurement' struct
                    input_file.read((char*)(&a_channel_data_without_measurement), sizeof(channel_data_without_measurement));
 
                    // copy the content
                    a_channel_data.channel = a_channel_data_without_measurement.channel;
                    a_channel_data.EventIDsamIndex = a_channel_data_without_measurement.EventIDsamIndex;
                    a_channel_data.FirstCellToPlotsamIndex = a_channel_data_without_measurement.FirstCellToPlotsamIndex;
                }
 
                output_channel = a_channel_data.channel;
                if (debug_data) cout << "- reading channel " << output_channel << endl;
                
                // read waveform
                input_file.read((char*)waveform.data(), waveform_bytes);
 
                //---------------------------------------------------------------------------------------------------------------
                if (ch >= start_at_ch && ch <= end_at_ch) {
                    if (event_counter == 0) active_channels.push_back(static_cast<int>(output_channel));
 
                    float factor = DAQ_factor;
                    if (polarity_map[static_cast<int>(output_channel)]) factor = -factor;
 
                    // loop to fill waveform histograms
                    for (int i = 0; i < binNumber; i++) {
                        waveform_f[i] = static_cast<float>(waveform[i]) * factor;
                        amplValuessum[static_cast<int>(output_channel)][i] += waveform_f[i];
                    }
                    rundata.push_back(waveform_f);
 
                    // baseline correction
                    if (Using_BaselineCorrection_in_file_loop) {
                        CorrectBaseline_function(rundata[wfcounter], tCutg, tCutEndg, wfcounter);
                    }
 
                    wfcounter++;
                }//--------------------------------------------------------------------------------------------------------------
 
            } // for ch
 
            skip_event.push_back(false);
            if (!discard_original_eventnr) eventnr_storage.push_back(output_event); // Stores the current WaveCatcher event number
            else eventnr_storage.push_back(event_counter);
            event_counter++;
            if (event_counter >= max_nevents_to_read) {
                cout << "Stopped reading events after max_nevents_to_read=" << max_nevents_to_read << endl;
                break;
            }
        } // while an_event
 
        input_file.close();
        file_counter++;
    } // for file_id
 
    // in case there are empty channels, nchannels is the number of channels which contain data
    nchannels = read_channels;
 
    // get bins where the sum spectrum has its maximum for runs with fixed trigger delay and fixed 
    // integration window relative to the max of the sum spectrum (not working for DC measurement)
    for (int ch = 0; ch < nChannelsWC; ch++) {
        if (Helpers::Contains(active_channels, ch)) {
            float max_val = -9.e99;
            int i_max = 0;
            for (int i = 0; i < binNumber; i++) {
                if (amplValuessum[ch][i] > max_val) {
                    max_val = amplValuessum[ch][i];
                    i_max = i;
                }
            }
            maxSumBin.push_back(i_max);
        }
    }
 
    nevents = event_counter;
    nwf = wfcounter;
 
    printf("Finished reading %d files containing %d events with %d channels.\n\n", file_counter, nevents, nchannels);
}
 
ReadRun::~ReadRun() {
    // plot_active_channels.clear();
    rundata.clear();
    if (root_out->IsOpen()) root_out->Close();
    cout << "\nAnalysis completed." << endl;
}
 
void ReadRun::PlotChannelSums(bool smooth, bool normalize, double shift, double sigma, int smooth_method) {
 
    double* xv = getx<double>(shift);
    auto mgsums = new TMultiGraph();
    mgsums->SetTitle("channel sums; t [ns]; amplitude [mV]");
    if (normalize) mgsums->SetTitle("channel sums; t [ns]; amplitude [arb.]");
 
    double max_val = 0., min_val = 0.;
    int color = 0;
 
    for (int i = 0; i < nchannels; i++) {
        if (PlotChannel(i)) {
            color++;
            double* yv = new double[binNumber];
            for (int k = 0; k < binNumber; k++) yv[k] = static_cast<double>(amplValuessum[active_channels[i]][k]);
 
            if (smooth) Filters::SmoothArray(yv, binNumber, sigma, smooth_method);
 
            TGraph* gr = new TGraph(binNumber, xv, yv);
            delete[] yv;
 
            double tmp_min = TMath::MinElement(gr->GetN(), gr->GetY());
            if (tmp_min < min_val) min_val = tmp_min;
            double tmp_max = TMath::MaxElement(gr->GetN(), gr->GetY());
            if (tmp_max > max_val) max_val = tmp_max;
            if (normalize) {
                double i_tmp_max = (tmp_max != 0) ? 1. / tmp_max : 1.;
                for (int j = 0; j < gr->GetN(); j++) gr->SetPointY(j, gr->GetPointY(j) * i_tmp_max);
            }
 
            TString name(Form("channel_%02d", active_channels[i]));
            TString title(Form("Channel %d", active_channels[i]));
            gr->SetName(name.Data());
            gr->SetTitle(title.Data());
            gr->SetLineColor(Helpers::rcolor(color));
            gr->SetMarkerColor(Helpers::rcolor(color));
            mgsums->Add(gr);
        }
    }
    delete[] xv;
 
    auto sumc = new TCanvas("Sums", "", 600, 400);
    mgsums->Draw("AL");
    if (normalize) mgsums->GetYaxis()->SetRangeUser(-0.2, 1);
    else mgsums->GetYaxis()->SetRangeUser(min_val, max_val);
    sumc->BuildLegend(0.85, 0.70, .99, .95);
    sumc->SetGrid();
    root_out->WriteObject(mgsums, "channelsums");
    root_out->WriteObject(sumc, "channelsums_c");
}
 
void ReadRun::PlotChannelAverages(bool normalize) {
    float* xv = getx<float>();
    
    auto mgav = new TMultiGraph();
    mgav->SetTitle("channel averages; t [ns]; amplitude [mV]");
    if (normalize) mgav->SetTitle("channel averages; t[ns]; amplitude[arb.]");
 
    float max_val = 0., min_val = 0.;
    int color = 0;
 
    for (int i = 0; i < nchannels; i++) {
        if (PlotChannel(i)) {
            color++;
            float* yv = new float[binNumber]();
 
            for (int j = 0; j < nevents; j++) {
                if (!SkipEvent(j, i)) {
                    for (int k = 0; k < binNumber; k++) yv[k] += rundata[GetWaveformIndex(j, i)][k];
                }
            }
 
            float norm = max(1.f, static_cast<float>(Nevents_good(i)));
            for (int k = 0; k < binNumber; k++) yv[k] /= norm;
 
            auto gr = new TGraph(binNumber, xv, yv);
            delete[] yv;
 
            double tmp_min = TMath::MinElement(gr->GetN(), gr->GetY());
            if (tmp_min < min_val) min_val = tmp_min;
            double tmp_max = TMath::MaxElement(gr->GetN(), gr->GetY());
            if (tmp_max > max_val) max_val = tmp_max;
            if (normalize) {
                double i_tmp_max = (tmp_max != 0) ? 1. / tmp_max : 1.;
                for (int j = 0; j < gr->GetN(); j++) gr->SetPointY(j, gr->GetPointY(j) * i_tmp_max);
            }
 
            TString name(Form("channel_%02d", active_channels[i]));
            TString title(Form("Channel %d", active_channels[i]));
            gr->SetName(name.Data());
            gr->SetTitle(title.Data());
            gr->SetLineColor(Helpers::rcolor(color));
            gr->SetMarkerColor(Helpers::rcolor(color));
            mgav->Add(gr);
        }
    }
    delete[] xv;
 
    string cname("Averages_" + to_string(PlotChannelAverages_cnt++));
    auto avc = new TCanvas(cname.c_str(), cname.c_str(), 600, 400);
    mgav->Draw("AL");
    if (normalize) mgav->GetYaxis()->SetRangeUser(-0.2, 1);
    else mgav->GetYaxis()->SetRangeUser(min_val, max_val);
    avc->BuildLegend(0.85, 0.70, .99, .95);
    avc->SetGrid();
    root_out->WriteObject(mgav, ("channelaverages" + to_string(PlotChannelAverages_cnt)).c_str());
    root_out->WriteObject(avc, ("channelaverages_c" + to_string(PlotChannelAverages_cnt)).c_str());
}
 
 
TH2F* ReadRun::WFHeatmapChannel(int channel_index, float ymin, float ymax, int n_bins_y) {
 
    TString name(Form("channel__%02d", active_channels[channel_index]));
    TH2F* h2 = new TH2F(name.Data(), name.Data(), binNumber, 0, SP * static_cast<float>(binNumber), n_bins_y, ymin, ymax);
    h2->GetXaxis()->SetTitle("t [ns]");
    h2->GetYaxis()->SetTitle("I [arb.]");
    h2->GetZaxis()->SetTitle("entries");
 
    auto xv = getx<float>();
    // create temporary histo per thread
    int n_threads = omp_get_max_threads();
    vector<TH2F*> h2_thread(n_threads);
    for (int t = 0; t < n_threads; ++t) {
        h2_thread[t] = new TH2F("", "", binNumber, 0, SP * static_cast<float>(binNumber), n_bins_y, ymin, ymax);
    }
 
    #pragma omp parallel
    {
        int t_id = omp_get_thread_num();
        TH2F* hlocal = h2_thread[t_id];
 
        #pragma omp for
        for (int j = 0; j < nevents; ++j) {
            if (!SkipEvent(j, channel_index)) {
                int wf_index = GetWaveformIndex(j, channel_index);
                for (int i = 0; i < binNumber; ++i) {
                    hlocal->Fill(xv[i], rundata[wf_index][i]);
                }
            }
        }
    }
 
    //merge
    for (int t = 0; t < n_threads; ++t) {
        h2->Add(h2_thread[t]);
        delete h2_thread[t];
    }
 
    delete[] xv;
    return h2;
}
 
void ReadRun::PlotWFHeatmaps(float ymin, float ymax, int n_bins_y, string z_opt, float z_max, EColorPalette palette) {
 
    gStyle->SetOptStat(0);
    string name("waveforms_heatmap_" + to_string(PlotWFHeatmaps_cnt++));
    auto wfhm_c = new TCanvas(name.c_str(), name.c_str(), 600, 400);
    Helpers::SplitCanvas(wfhm_c, active_channels, plot_active_channels);
 
    // create histograms in parallel
    map<int, shared_future<TH2F*>> h2_future;
    for (int i = 0; i < nchannels; ++i) {
        if (PlotChannel(i)) {
            h2_future[i] = async(launch::async, [this, i, ymin, ymax, n_bins_y]() {
                return WFHeatmapChannel(i, ymin, ymax, n_bins_y);
            });
        }
    }
 
    // plot histograms
    int current_canvas = 0;
    for (int i = 0; i < nchannels; ++i) {
        if (PlotChannel(i)) {
            wfhm_c->cd(++current_canvas);
 
            gPad->SetTopMargin(.1);
            gPad->SetBottomMargin(.1);
            gPad->SetLeftMargin(.15);
            gPad->SetRightMargin(.15);
            gStyle->SetPalette(palette);
 
            auto h2 = h2_future[i].get();
 
            h2->SetContour(99);
            h2->SetStats(0);
            if (z_opt == "COLZ0") h2->Draw("COLZ0");
            else h2->Draw("CONT4Z");
 
            if (z_opt == "log") {
                gPad->SetLogz();
                if (z_max > 1) h2->GetZaxis()->SetRangeUser(1, z_max);
            }
            else if (z_max > 0) h2->GetZaxis()->SetRangeUser(0, z_max);
        }
    }
 
    wfhm_c->Update();
    root_out->WriteObject(wfhm_c, name.c_str());
}
 
void ReadRun::SmoothAll(double sigma, int method) {
    cout << "Smoothing all non-skipped waveforms..." << endl;
 
    #pragma omp parallel for
    for (int j = 0; j < nwf; j++) {
        if (!SkipEvent(GetCurrentEvent(j), GetCurrentChannel(j))) {
            vector<double> tmp_(rundata[j].begin(), rundata[j].end());
            double* tmp_wf = tmp_.data();
 
            Filters::SmoothArray(tmp_wf, binNumber, sigma, method, SP);
            for (int i = 0; i < binNumber; ++i) rundata[j][i] = static_cast<float>(tmp_[i]);
        }
    }
}
 
void ReadRun::SmoothAll(double sigma, string method) {
    cout << "\nSmoothing all non-skipped waveforms:" << endl;
 
    #pragma omp parallel for
    for (int j = 0; j < nwf; j++) {
        if (!SkipEvent(GetCurrentEvent(j), GetCurrentChannel(j))) {
            vector<double> tmp_(rundata[j].begin(), rundata[j].end());
            double* tmp_wf = tmp_.data();
 
            Filters::SmoothArray(tmp_wf, binNumber, sigma, method, SP);
            for (int i = 0; i < binNumber; ++i) rundata[j][i] = static_cast<float>(tmp_[i]);
        }
    }
}
 
void ReadRun::FilterAll(double sigma1, double sigma2, double factor) {
    cout << "\nFiltering all waveforms..." << endl;
 
    #pragma omp parallel for
    for (int j = 0; j < nwf; j++) {
        vector<double> tmp_(rundata[j].begin(), rundata[j].end());
        double* tmp_wf = tmp_.data();
 
        if (factor > 0 && factor <= 1) Filters::ResponseFilter(tmp_wf, binNumber, sigma1, sigma2, factor, SP);
        else Filters::SecondOrderUnderdampedFilter(tmp_wf, binNumber, sigma1, sigma2, abs(factor), SP);
        for (int i = 0; i < binNumber; ++i) rundata[j][i] = static_cast<float>(tmp_[i]);
    }
}
 
void ReadRun::ShiftAllToAverageCF() {
    cout << "\nShifting all waveforms to the average constant fraction time for each channel:" << endl;
 
    //call GetTimingCFD() in case it was not initialized
    if (static_cast<int>(timing_results.size()) == 0) GetTimingCFD();
 
    double* timing_mean = new double[nchannels]();
 
    for (int j = 0; j < nwf; j++) {
        int curr_ch = GetCurrentChannel(j);
        if (!SkipEvent(GetCurrentEvent(j), curr_ch)) timing_mean[curr_ch] += timing_results[j][0];
    }
 
    int* timing_mean_n = new int[nchannels];
    for (int i = 0; i < nchannels; i++) {
        double i_norm = 1. / max(1., static_cast<double>(Nevents_good(i)));
        timing_mean_n[i] = static_cast<int>(round(timing_mean[i] * i_norm));
    }
    delete[] timing_mean;
 
    #pragma omp parallel for
    for (int j = 0; j < nwf; j++) {
        int curr_ch = GetCurrentChannel(j);
        if (!SkipEvent(GetCurrentEvent(j), curr_ch)) {
            int shift = static_cast<int>(timing_results[j][0]) - timing_mean_n[curr_ch];
            shift = shift % binNumber;
            if (shift < 0) shift += binNumber;
            rotate(rundata[j].begin(), rundata[j].begin() + shift, rundata[j].end());
        }
    }
    delete[] timing_mean_n;
}
 
void ReadRun::CorrectBaseline(float tCut, float tCutEnd) {
    checkData(true);
 
    cout << "\nPerforming simple baseline correction in fixed time window."
        << "This method is only suitable for measurements without dark counts!" << endl;
    tCutg = tCut;
    tCutEndg = tCutEnd;
    if (nwf == 0) {
        Using_BaselineCorrection_in_file_loop = true;
    }
    else {
        cout << "Baseline correction (" << nwf << " waveforms):" << endl;
        baseline_correction_result.resize(nwf, vector<float>(4));
 
        #pragma omp parallel for
        for (int j = 0; j < nwf; j++) {
            CorrectBaseline_function(rundata[j], tCut, tCutEnd, j);
        }
    }
}
 
void ReadRun::CorrectBaseline_function(vector<float>& waveform, float tCut, float tCutEnd, int waveform_index) {
    int iCut, iCutEnd;
    float corr = 0;
 
    iCut = TimeToIndex(tCut);
 
    if (tCutEnd <= 0) { //
        for (int i=0; i<=iCut; i++) corr += waveform[i];
        corr /= static_cast<float>(iCut);
    }
    else {
        iCutEnd = TimeToIndex(tCutEnd);
        for (int i=iCut; i<=iCutEnd; i++) corr += waveform[i]; 
        corr /= static_cast<float>(iCutEnd - iCut + 1);
    }
 
    // write corrected values to histograms
    if (tCut >= 0) {
        for (int i = 0; i < binNumber; i++) waveform[i] -= corr;
    }
 
    if (!Using_BaselineCorrection_in_file_loop) {
        baseline_correction_result[waveform_index][0] = corr;
        baseline_correction_result[waveform_index][1] = 0;
        baseline_correction_result[waveform_index][2] = tCut;
        baseline_correction_result[waveform_index][3] = tCutEnd;
    }
}
 
void ReadRun::CorrectBaselineMinSlopeRMS(vector<float> window, double sigma, int smooth_method) {
    checkData(true);
 
    cout << "\nBaseline correction (minimum slope variation method, " << nwf << " waveforms):" << endl;
    if (window.empty()) cout << "\nWarning: Window not set in CorrectBaselineMinSlopeRMS. Will use default values." << endl;
    if (sigma != 0.) cout << "\nNotification: Using smoothing in CorrectBaselineMinSlopeRMS." << endl;
 
    int nbins_average = !window.empty() ? TimeToIndex(window[0]) : TimeToIndex(50.);
    int start_search_at = static_cast<int>(window.size()) > 1 ? TimeToIndex(window[1]) : 0;
    int end_search_at = static_cast<int>(window.size()) > 2 ? TimeToIndex(window[2]) : binNumber - 1;
 
    int end_search_loop_at = end_search_at - start_search_at - nbins_average;
 
    // if no valid static search window is specified, it will be dynamic from 0 ns up to 8 ns before the global maximum
    bool search_relative_to_local_max = false;
    int min_distance_from_max = TimeToIndex(8.);
    if (start_search_at < 0) {
        search_relative_to_local_max = true;
        start_search_at = 0;
        cout << "\nNotification: Using dynamic search window in CorrectBaselineMinSlopeRMS." << endl;
    }
 
    int nbins_search = end_search_at - start_search_at;
 
    baseline_correction_result.resize(nwf, vector<float>(6));
 
    #pragma omp parallel for
    for (int j = 0; j < nwf; j++) {
        float minchange = 1.e99;
        float sum = 0, sumsum = 0, change = 0, minsumsq = 0, sqsum = 0, minsqsum = 0, corr = 0;
        int iintwindowstart = 0, imax = 0;
        int nbins_search_ = nbins_search;
        int end_search_at_ = end_search_at;
        int end_search_loop_at_ = end_search_loop_at;
 
        if (search_relative_to_local_max) {
            imax = GetIntWindow(rundata[j], 0, 0, nbins_search_ + min_distance_from_max, end_search_at_)[1];
            end_search_at_ = imax - min_distance_from_max;
            nbins_search_ = end_search_at_; // starts at 0
            end_search_loop_at_ = nbins_search_ - nbins_average;
        }
 
        double* yvals = Helpers::gety(rundata[j], start_search_at, end_search_at_);
        // smoothing suppresses variations in slope due to noise, so the method is potentially more sensitive to excluding peaks
        if (sigma > 0) Filters::SmoothArray(yvals, nbins_search_, sigma, smooth_method);
        //calculate slope
        nbins_search_--;
        double* slope = new double[nbins_search_];
        double* slope_sq = new double[nbins_search_];
        for (int i = 0; i < nbins_search_; i++) {
            slope[i] = yvals[i + 1] - yvals[i];
            slope_sq[i] = slope[i] * slope[i];
            if (i < nbins_average) { // init
                sum += slope[i];
                sqsum += slope_sq[i];
            }
        }
        delete[] yvals;
 
        //find window for correction
        for (int i = 0; i < end_search_loop_at_; i++) {
            sumsum = sum * sum;
            change = sqsum + sumsum;
 
            if (change < minchange) {
                minchange = change;
                iintwindowstart = i + start_search_at;
                minsumsq = sumsum;
                minsqsum = sqsum;
            }
 
            sum -= slope[i];
            sum += slope[i + nbins_average];
            sqsum -= slope_sq[i];
            sqsum += slope_sq[i + nbins_average];
        }
        delete[] slope;
        delete[] slope_sq;
 
        // do correction
        for (int i=iintwindowstart; i<=iintwindowstart + nbins_average; i++) corr += rundata[j][i];
        corr /= static_cast<float>(nbins_average + 1);
        for (int i = 0; i < binNumber; i++) rundata[j][i] -= corr;
 
        baseline_correction_result[j][0] = corr;
        baseline_correction_result[j][1] = minchange;
        baseline_correction_result[j][2] = IndexToTime(iintwindowstart);
        baseline_correction_result[j][3] = IndexToTime(iintwindowstart + nbins_average);
        baseline_correction_result[j][4] = minsumsq;
        baseline_correction_result[j][5] = minsqsum;
    }
}
 
void ReadRun::CorrectBaselineMinSlopeRMS(int nIntegrationWindow, bool smooth, double sigma, int max_bin_for_baseline, int start_at, int smooth_method) {
    cout << "WARNING: This is a deprecated version of CorrectBaselineMinSlopeRMS. "
        << "It will be removed in future releases. Parameter bool smooth=" << smooth << " will be ignored." << endl;
    vector<float> window;
    window.push_back(IndexToTime(nIntegrationWindow));
    window.push_back(IndexToTime(start_at));
    window.push_back(IndexToTime(max_bin_for_baseline));
    CorrectBaselineMinSlopeRMS(window, sigma, smooth_method);
}
 
void ReadRun::CorrectBaselineMinSlopeRMS(vector<float> window, double sigma, int smooth_method, int increment) {
    (void)increment;
    cout << "WARNING: This is a deprecated version of CorrectBaselineMinSlopeRMS. "
        << "It will be removed in future releases. Parameter increment=" << increment << " will be ignored." << endl;
    CorrectBaselineMinSlopeRMS(window, sigma, smooth_method);
}
 
void ReadRun::CorrectBaselineMin(vector<float> window, double sigma, int smooth_method) {
    checkData(true);
 
    cout << "\nBaseline correction (minimal sum method, " << nwf << " waveforms):" << endl;
    if (window.empty()) cout << "\nWarning: Window not set in CorrectBaselineMin. Will use default values." << endl;
    if (sigma != 0.) cout << "\nNotification: Using smoothing in CorrectBaselineMin." << endl;
 
    int nbins_average = !window.empty() ? TimeToIndex(window[0]) : TimeToIndex(10.);
    int start_search_at = static_cast<int>(window.size()) > 1 ? TimeToIndex(window[1]) : 0;
    int end_search_at = static_cast<int>(window.size()) > 2 ? TimeToIndex(window[2]) : binNumber - 1;
 
    int end_search_loop_at = end_search_at - start_search_at - nbins_average;
 
    // if no valid static search window is specified, it will be dynamic from 0 ns up to 8 ns before the global maximum
    bool search_relative_to_local_max = false;
    int min_distance_from_max = TimeToIndex(8.);
    if (start_search_at < 0 || end_search_loop_at < 0) {
        search_relative_to_local_max = true;
        start_search_at = 0;
        cout << "\nNotification: Using dynamic search window in CorrectBaselineMin." << endl;
    }
 
    int nbins_search = end_search_at - start_search_at;
 
    baseline_correction_result.resize(nwf, vector<float>(4));
 
    #pragma omp parallel for
    for (int j = 0; j < nwf; j++) {
        float minchange = 1e9;
        float sum = 0, corr = 0;
        int iintwindowstart = 0, imax = 0;
        int nbins_search_ = nbins_search;
        int end_search_at_ = end_search_at;
        int end_search_loop_at_ = end_search_loop_at;
 
        if (search_relative_to_local_max) {
            imax = GetIntWindow(rundata[j], 0, 0, nbins_search_ + min_distance_from_max, end_search_at_)[1];
            end_search_at_ = imax - min_distance_from_max;
            nbins_search_ = end_search_at_;
            end_search_loop_at_ = nbins_search_ - nbins_average;
        }
 
        double* yvals = Helpers::gety(rundata[j], start_search_at, end_search_at_);
        // smoothing suppresses variations in slope due to noise, so the method is potentially more sensitive to excluding peaks
        if (sigma > 0) Filters::SmoothArray(yvals, nbins_search_, sigma, smooth_method);
        //find window for correction
        for (int i = 0; i < nbins_average; i++) sum += yvals[i]; // init
        for (int i = 0; i < end_search_loop_at_; i++) {
            if (sum < minchange) {
                minchange = sum;
                iintwindowstart = i + start_search_at;
            }
 
            sum -= yvals[i];
            sum += yvals[i + nbins_average];
        }
        delete[] yvals;
        
        // do correction
        for (int i=iintwindowstart; i<=iintwindowstart + nbins_average; i++) corr += rundata[j][i];
        corr /= static_cast<float>(nbins_average + 1);
        for (int i = 0; i < binNumber; i++) rundata[j][i] -= corr;
 
        baseline_correction_result[j][0] = corr;
        baseline_correction_result[j][1] = minchange;
        baseline_correction_result[j][2] = IndexToTime(iintwindowstart);
        baseline_correction_result[j][3] = IndexToTime(iintwindowstart + nbins_average);
    }
}
 
void ReadRun::CorrectBaselineMin(int nIntegrationWindow, double sigma, int max_bin_for_baseline, int start_at, int smooth_method) {
    cout << "WARNING: This is a deprecated version of CorrectBaselineMin. It will be removed in future releases." << endl;
    vector<float> window;
    window.push_back(IndexToTime(nIntegrationWindow));
    window.push_back(IndexToTime(start_at));
    window.push_back(IndexToTime(max_bin_for_baseline));
    CorrectBaselineMin(window, sigma, smooth_method);
}
 
void ReadRun::CorrectBaselineMin(vector<float> window, double sigma, int smooth_method, int increment) {
    (void)increment;
    cout << "WARNING: This is a deprecated version of CorrectBaselineMin. It will be removed in future releases." << endl;
    CorrectBaselineMin(window, sigma, smooth_method);
}
 
TH1F* ReadRun::WFProjectionChannel(int channel_index, int from_n, int to_n, float rangestart, float rangeend, int nbins) {
    from_n = CheckBoundsX(from_n);
    to_n = CheckBoundsX(to_n);
 
    TString name(Form("channel__%02d", active_channels[channel_index]));
    auto h1 = new TH1F(name.Data(), name.Data(), nbins, rangestart, rangeend);
    
    for (int j = 0; j < nevents; j++) {
        if (!SkipEvent(j, channel_index)) {
            for (int i = from_n; i <= to_n; i++) h1->Fill(rundata[GetWaveformIndex(j, channel_index)][i]);
        }
    }
    return h1;
}
 
void ReadRun::PrintWFProjection(float from, float to, float rangestart, float rangeend, int nbins) {
    gStyle->SetOptFit(111);
    float default_rangestart = -10;
    float default_rangeend = 20;
    if (default_rangestart > rangestart) default_rangestart = rangestart;
    if (default_rangeend < rangeend) default_rangeend = rangeend;
    int default_nbins = static_cast<int>((default_rangeend - default_rangestart) * nbins / (rangeend - rangestart));
 
    string ctitle("WFProjection" + to_string(PrintWFProjection_cnt++));
    auto wf_projection_c = new TCanvas(ctitle.c_str(), ctitle.c_str(), 600, 400);
    Helpers::SplitCanvas(wf_projection_c, active_channels, plot_active_channels);
    int current_canvas = 0;
 
    int from_n = TimeToIndex(from);
    int to_n = TimeToIndex(to);
 
    for (int i = 0; i < nchannels; i++) {
        if (PlotChannel(i)) {
            wf_projection_c->cd(++current_canvas);
 
            auto his = WFProjectionChannel(i, from_n, to_n, default_rangestart, default_rangeend, default_nbins);
            his->GetYaxis()->SetTitle("#Entries");
            his->GetXaxis()->SetTitle("amplitude in mV");
            TString name(Form("WFProjection channel_%02d_%d", active_channels[i], PrintWFProjection_cnt));
            his->Draw();
            his->Fit("gaus", "M", "same");
            root_out->WriteObject(his, name.Data());
        }
    }
 
    Helpers::SetRangeCanvas(wf_projection_c, rangestart, rangeend);
    root_out->WriteObject(wf_projection_c, ("WFProjections" + to_string(PrintWFProjection_cnt)).c_str());
}
 
TH1F* ReadRun::BaselineCorrectionResults(int channel_index, int which, float rangestart, float rangeend, int nbins) {
    if (baseline_correction_result.empty() || static_cast<int>(baseline_correction_result[0].size()) < which - 1) {
        cout << "\nError: baseline_correction_result empty. Call baseline correction first." << endl;
    }
    TString name(Form("channel__%02d", active_channels[channel_index]));
    auto h1 = new TH1F(name.Data(), name.Data(), nbins, rangestart, rangeend);
 
    float average_baseline = 0.;
    int counter = 0;
    for (int j = 0; j < nevents; j++) {
        if (!SkipEvent(j, channel_index)) {
            float current_baseline = baseline_correction_result[GetWaveformIndex(j, channel_index)][which];
            average_baseline += current_baseline;
            counter++;
            h1->Fill(current_baseline);
        }
    }
    cout << "Mean baseline ch" << active_channels[channel_index] << ": " << average_baseline / max(1.f, static_cast<float>(counter)) << endl;
    return h1;
}
 
void ReadRun::PrintBaselineCorrectionResults(float rangestart, float rangeend, int nbins) {
    checkData();
    gStyle->SetOptFit(111);
    float default_rangestart = -10;
    float default_rangeend = 20;
    if (default_rangestart > rangestart) default_rangestart = rangestart;
    if (default_rangeend < rangeend) default_rangeend = rangeend;
    int default_nbins = static_cast<int>((default_rangeend - default_rangestart) * nbins / (rangeend - rangestart));
 
    string ctitle;
    ctitle = "Correction values in mV";
    auto blc_res_c = new TCanvas(ctitle.c_str(), ctitle.c_str(), 600, 400);
    Helpers::SplitCanvas(blc_res_c, active_channels, plot_active_channels);
    int current_canvas = 0;
 
    for (int i = 0; i < nchannels; i++) {
        if (PlotChannel(i)) {
            blc_res_c->cd(++current_canvas);
 
            auto his = BaselineCorrectionResults(i, 0, default_rangestart, default_rangeend, default_nbins);
            his->GetYaxis()->SetTitle("#Entries");
            his->GetXaxis()->SetTitle(ctitle.c_str());
            his->Draw();
            his->Fit("gaus", "WWM", "same");
        }
    }
    Helpers::SetRangeCanvas(blc_res_c, rangestart, rangeend);
    root_out->WriteObject(blc_res_c, ctitle.c_str());
}
 
void ReadRun::GetTimingCFD(float cf_r, float start_at_t, float end_at_t, double sigma, bool find_CF_from_start, int smooth_method, bool use_spline, bool verbose) {
 
    int start_at = CheckBoundsX(TimeToIndex(start_at_t));
    int end_at = CheckBoundsX(TimeToIndex(end_at_t));
    int n_range = end_at - start_at;
    
    if (cf_r <= 0) cf_r = 1;
    cout << "\nGet timing at " << (cf_r > 0 && cf_r <= 1 ? "CF=" : "threshold=");
    printf("%.2f between %.2f ns and %.2f ns (%d waveforms):\n", cf_r, start_at_t, end_at_t, nwf);
 
    timing_results.resize(nwf, vector<float>(8));
 
    double* xvals = new double[n_range]; // x values for spline interpolation
    for (int k = 0; k < n_range; k++) xvals[k] = static_cast<double>(k) + .5;
    
    #pragma omp parallel for
    for (int j = 0; j < nwf; j++) {
        double* yvals = Helpers::gety(rundata[j], start_at, end_at); // get range where to search for CFD for timing
        
        // smoothing to suppress noise, will also change timing so use with care!
        if (sigma > 0.) Filters::SmoothArray(yvals, n_range, sigma, smooth_method);
 
        double* max_ptr = max_element(yvals, yvals + n_range);
        float max_val = *max_ptr;
        int n_max = static_cast<int>(max_ptr - yvals);
 
        float cf = (cf_r <= 1) ? cf_r * max_val : cf_r;
 
        int i = 0;
        if (!find_CF_from_start) {
            i = n_max;
            while (i > 0 && yvals[i] > cf) i--;
        }
        else {
            i = 0;
            while (i < n_max && yvals[i] < cf) i++;
            i--;
        }
 
        float interpol_bin = 0.;
        pair<float, bool> lin_interpol_res = {0, false};
        if (i==0) {
            if (verbose) cout << "WARNING: CFD failed for Ch" << GetCurrentChannel(j) << ", event " << GetCurrentEvent(j) << endl;
        }
        else {
            // do interpolation for cf
            lin_interpol_res = LinearInterpolation(cf, static_cast<float>(i), static_cast<float>(i + 1), yvals[i], yvals[i + 1]);
            // go to center of bin
            interpol_bin = lin_interpol_res.first + .5;
 
            if (use_spline) { // use spline interpolation with tolerance epsilon*bin_size
                double epsilon = 1e-4;
                double x_low = interpol_bin - .5;
                double x_high = interpol_bin + .5;
 
                TSpline5* wfspl = 0;
                wfspl = new TSpline5("wf_spline", xvals, yvals, n_range, "b1e1b2e2", 0., 0., 0., 0.);
 
                // using bisection method: halving search window until cf is less than epsilon bins from spline value
                while (x_high - x_low > epsilon) {
                    double x_mid = (x_low + x_high) * 0.5;
                    double f_mid = wfspl->Eval(x_mid);
                    if (f_mid == cf) break;
 
                    if (f_mid > cf) x_high = x_mid;
                    else x_low = x_mid;
                }
                interpol_bin = (x_low + x_high) * 0.5;
                delete wfspl;
            }
        }
        timing_results[j][0] = interpol_bin;                                            // the bin we looked for
        timing_results[j][1] = (interpol_bin + static_cast<float>(start_at)) * SP;      // cfd-time we looked for
        timing_results[j][2] = max_val;                                                 // maximum value
        timing_results[j][3] = n_max;                                                   // bin of maximum
        timing_results[j][4] = cf;                                                      // constant fraction
        timing_results[j][5] = IndexToTime(start_at);                                   // starting time
        timing_results[j][6] = IndexToTime(end_at);                                     // end time
        timing_results[j][7] = static_cast<float>(lin_interpol_res.second);             // flag will be 1 if linear interpolation worked
        delete[] yvals;
    }
    delete[] xvals;
}
 
void ReadRun::SkipEventsTimeDiffCut(int first_channel_abs, int second_channel_abs, double time_diff_min, double time_diff_max, bool verbose) {
 
    cout << "\n Removing events if the event-wise time difference between the main peaks in ch"
        << first_channel_abs << " and ch" << second_channel_abs << " is <" << setprecision(2)
        << time_diff_min << " ns or >" << time_diff_max << " ns" << endl;
 
    int counter = 0;
    int first_channel = GetChannelIndex(first_channel_abs);
    int second_channel = GetChannelIndex(second_channel_abs);
 
    // call GetTimingCFD() in case it was not initialized
    if (static_cast<int>(timing_results.size()) == 0) GetTimingCFD();
 
    // loop through events, calculate timing difference between channels and compare with cuts
    #pragma omp parallel for reduction(+:counter)
    for (int j = 0; j < nevents; j++) {
        if (!SkipEvent(j, first_channel) && !SkipEvent(j, second_channel)) {
            const int ind_first = GetWaveformIndex(j, first_channel);
            const int ind_second = GetWaveformIndex(j, second_channel);
            if (max(ind_first, ind_second) >= static_cast<int>(timing_results.size())) continue;
 
            float time_diff = timing_results[ind_first][1] - timing_results[ind_second][1];
 
            if (time_diff < time_diff_min || time_diff > time_diff_max) {
                int currevent = eventnr_storage[j];
                if (verbose) cout << "\nevent:\t" << currevent << "\tchannels:\t" << first_channel_abs << " & " << second_channel_abs << "\ttime diff:\t" << time_diff;
                skip_event[j] = true;
                counter++;
            }
        }
    }
    cout << "\t" << counter << " events will be cut out of " << nevents << endl;
}
 
 
void ReadRun::SkipEventsPerChannel(vector<float> thresholds, float rangestart, float rangeend, bool verbose) { // merge with IntegralFilter()?
 
    if (thresholds.empty()) cout << "\nError: thresholds is empty";
    while (thresholds.size() <= active_channels.size()) thresholds.push_back(thresholds[0]);
 
    cout << "\n Removing events with individual amplitude threshold per channel:" << endl;
    int counter = 0;
    int n_thrshld = static_cast<int>(thresholds.size());
 
    int bin_start = CheckBoundsX(TimeToIndex(rangestart));
    int bin_end = CheckBoundsX(TimeToIndex(rangeend));
 
    #pragma omp parallel for reduction(+:counter)
    for (int j = 0; j < nwf; j++) {
        int current_event = GetCurrentEvent(j);
        int current_channel = GetCurrentChannel(j);
        if (current_event >= 0 && !SkipEvent(current_event, current_channel)) {
            if (current_channel < n_thrshld) {
                const float current_threshold = thresholds[current_channel];
                if (current_threshold == 0.) continue;
 
                auto max_it = max_element(rundata[j].begin() + bin_start, rundata[j].begin() + bin_end);
                auto min_it = min_element(rundata[j].begin() + bin_start, rundata[j].begin() + bin_end);
 
                float max_val = (max_it != rundata[j].end()) ? *max_it : 0.;
                float min_val = (min_it != rundata[j].end()) ? *min_it : 0.;
 
                
                if ((current_threshold > 0  && max_val > current_threshold) || 
                    (current_threshold < 0 && min_val < current_threshold)) {
 
                    int currevent = eventnr_storage[current_event];
                    if (verbose) cout << "\nevent:\t" << currevent << "\tchannel:\t" << active_channels[current_channel] << "\tthreshold\t" << current_threshold;
                    skip_event[current_event] = true;
                    counter++;
                }
            }
        }
    }
 
    cout << "\t" << counter << " events will be cut out of " << nevents << endl;
}
 
void ReadRun::IntegralFilter(vector<float> thresholds, vector<bool> g_thr, float windowlow, float windowhi, float start, float end, bool use_AND_condition , bool verbose) {
 
    if (thresholds.empty() || g_thr.empty()) cout << "\nERROR: thresholds or g_thr are empty in ReadRun::IntegralFilter().";
    while (thresholds.size() <= active_channels.size()) { thresholds.push_back(thresholds[0]); }
    while (g_thr.size() <= active_channels.size()) { g_thr.push_back(g_thr[0]); }
 
    cout << "\n\nRemoving events with individual integral threshold per channel:" << endl;
    int counter = 0;
    int n_thresholds = static_cast<int>(thresholds.size());
 
    #pragma omp parallel for reduction(+:counter)
    for (int j = 0; j < nwf; j++) {
        int currevent_counter = GetCurrentEvent(j);
        if (currevent_counter < 0) continue;
        
        if ((use_AND_condition && skip_event[currevent_counter]) || !skip_event[currevent_counter]) {
            int current_channel = GetCurrentChannel(j);
            if (current_channel >= n_thresholds) continue;
            
            float current_threshold = thresholds[current_channel];
            if (current_threshold == 0.) continue;
 
            auto integral = GetPeakIntegral(rundata[j], windowlow, windowhi, start, end, current_channel);
 
            int currevent = eventnr_storage[currevent_counter];
            // skip if above/below thresholds
            if ((g_thr[current_channel] && integral > current_threshold) || (!g_thr[current_channel] && integral < current_threshold)) {
                if (!skip_event[currevent_counter]) {
                    if (verbose) cout << "Event:\t" << currevent << "\tchannel:\t" << active_channels[current_channel] << "\tthreshold\t" << thresholds[current_channel] << "\tintegral:\t" << integral << endl;
                    skip_event[currevent_counter] = true;
                    // go to last wf of current event
                    while (GetCurrentEvent(++j) == currevent_counter); 
                    j--;
                    counter++;
                }
            }
            else if (use_AND_condition) { // don't skip if not
                skip_event[currevent_counter] = false;
                if (verbose) cout << "Event:\t" << currevent << "\tchannel:\t" << active_channels[current_channel] << "\thas been flagged good by integral:\t" << integral << endl;
                counter--;
            }
        }
    }
    cout << counter << " additional events will be cut out of " << nevents << " (" << static_cast<float>(100*counter/nevents) << "%)" << endl;
}
 
void ReadRun::PrintSkippedEvents() {
    int counter = 0;
    stringstream buffer;
    for (int j = 0; j < static_cast<int>(skip_event.size()); j++) {
        if (skip_event[j]) {
            int currevent = eventnr_storage[j];
            buffer << "Event:\t" << currevent << endl;
            counter++;
        }
    }
    cout << buffer.str().c_str();
    cout << "Total number of skipped events:\t" << counter << "\tout of:\t" << nevents << endl;
}
 
void ReadRun::UnskipAll() {
    const int skip_event_size = static_cast<int>(skip_event.size());
    for (int j = 0; j < skip_event_size; j++) skip_event[j] = false;
    cout << "\n\nAll event cuts were removed" << endl;
}
 
bool ReadRun::SkipEvent(int event_index, int channel_index) {
    (void)channel_index; // avoid unused parameter warning
    if (event_index >= static_cast<int>(skip_event.size()) || event_index < 0) return true;
    else return skip_event[event_index];
}
 
int ReadRun::Nevents_good(int channel_index) {
    int nevents_good = 0;
    for (int i = 0; i < nevents; i++) if (!SkipEvent(i, channel_index)) nevents_good++;
    return nevents_good;
}
 
// functions for charge spectrum
 
array<int, 3> ReadRun::GetIntWindow(TH1F* his, float windowlow, float windowhi, float start, float end, int channel) {
 
    int istart, iend;
    array<int, 3> foundindices = {0, 0, 0};
 
    if (start < 0 || end < 0) {                         // fixed integration window relative to maximum of sum spectrum for each channel
        foundindices[1] = his->GetXaxis()->FindBin(his->GetXaxis()->GetBinCenter(maxSumBin[channel]) - windowlow);
        foundindices[2] = his->GetXaxis()->FindBin(his->GetXaxis()->GetBinCenter(maxSumBin[channel]) + windowhi);
    }
    else if (windowlow == start && windowhi == end) {   // fixed integration window for all channels
        foundindices[1] = his->GetXaxis()->FindBin(windowlow);
        foundindices[2] = his->GetXaxis()->FindBin(windowhi);
    }
    else {                                              // fixed integration window relative to maximum of each individual waveform
        istart = his->GetXaxis()->FindBin(start);
        iend = his->GetXaxis()->FindBin(end);
        foundindices[0] = istart;
 
        if (istart < 1 || iend > his->GetNbinsX()) {
            cout << "\nError: Start=" << istart << " or end=" << iend << " of GetIntWindow() out of range. Fix integration window." << endl;
        }
 
        float max_val = -9.e99;
        float curr_val = 0;
        for (int i = istart; i < iend; i++) {
            curr_val = his->GetBinContent(i);
            if (curr_val > max_val) {
                max_val = curr_val;
                foundindices[0] = i;
            }
        }
 
        foundindices[1] = his->GetXaxis()->FindBin(his->GetXaxis()->GetBinCenter(foundindices[0]) - windowlow);
        foundindices[2] = his->GetXaxis()->FindBin(his->GetXaxis()->GetBinCenter(foundindices[0]) + windowhi);
    }
    return foundindices;
}
 
array<int, 3> ReadRun::GetIntWindow(const vector<float>& waveform, float windowlow, float windowhi, float start, float end, int channel) {
 
    array<int, 3> foundindices = {0, 0, 0};
 
    if (start < 0 || end < 0) {                         // fixed integration window relative to maximum of sum spectrum for each channel
        foundindices[1] = maxSumBin[channel] - TimeToIndex(windowlow);
        foundindices[2] = maxSumBin[channel] + TimeToIndex(windowhi);
    }
    else if (windowlow == start && windowhi == end) {   // fixed integration window for all channels
        foundindices[1] = TimeToIndex(windowlow);
        foundindices[2] = TimeToIndex(windowlow);
    }
    else {                                              // fixed integration window relative to maximum of each individual waveform
        int istart = TimeToIndex(start);
        int iend = TimeToIndex(end);
        foundindices[0] = istart;
 
        auto max_it = max_element(waveform.begin() + istart, waveform.begin() + iend);
        foundindices[0] = static_cast<int>(distance(waveform.begin(), max_it));
 
        float t_max = IndexToTime(foundindices[0]) + SP * 0.5; // time at center of maximum bin
        foundindices[1] = TimeToIndex(t_max - windowlow);
        foundindices[2] = TimeToIndex(t_max + windowhi);
    }
    return foundindices;
}
 
array<int, 3> ReadRun::GetIntWindow(const vector<float>& waveform, int windowlow, int windowhi, int start, int end, int channel) {
 
    array<int, 3> foundindices = {0, 0, 0};
 
    if (start < 0 || end < 0) {                         // fixed integration window relative to maximum of sum spectrum for each channel
        foundindices[1] = maxSumBin[channel] - windowlow;
        foundindices[2] = maxSumBin[channel] + windowhi;
    }
    else if (windowlow == start && windowhi == end) {   // fixed integration window for all channels
        foundindices[1] = windowlow;
        foundindices[2] = windowlow;
    }
    else {                                              // fixed integration window relative to maximum of each individual waveform
        int istart = CheckBoundsX(start);
        int iend = CheckBoundsX(end);
        foundindices[0] = istart;
 
        auto max_it = max_element(waveform.begin() + istart, waveform.begin() + iend);
        foundindices[0] = static_cast<int>(distance(waveform.begin(), max_it));
 
        foundindices[1] = CheckBoundsX(foundindices[0] - windowlow);
        foundindices[2] = CheckBoundsX(foundindices[0] + windowhi);
    }
    return foundindices;
}
 
float ReadRun::GetPeakIntegral(TH1F* his, float windowlow, float windowhi, float start, float end, int channel_index) {
    auto windowind = GetIntWindow(his, windowlow, windowhi, start, end, channel_index); // find integration window
    string integral_option(""); // For amplitude -> unit[mV].
    if (windowind[1] != windowind[2]) integral_option = "width"; // 'width' (bin width) for integral -> unit[mV x ns].
    float integral = his->Integral(windowind[1], windowind[2], integral_option.c_str());
    return integral;
}
 
float ReadRun::GetPeakIntegral(const vector<float>& waveform, float windowlow, float windowhi, float start, float end, int channel_index) {
    auto windowind = GetIntWindow(waveform, windowlow, windowhi, start, end, channel_index);    // find integration window
    float integral = 0;
    for (int i = windowind[1]; i <= windowind[2]; ++i) integral += waveform[i];                 // sum -> unit[mV].
    if (windowind[1] != windowind[2]) integral *= SP;                                           // integral -> unit[mV x ns].
    return integral;
}
 
void ReadRun::PrintChargeSpectrumWF(float windowlow, float windowhi, float start, float end, int eventnr, float ymin, float ymax, float xmin, float xmax) {
 
    gStyle->SetOptStat(0);
    TString name(Form("waveforms_event__%05d", eventnr));
    auto intwinc = new TCanvas(name.Data(), name.Data(), 600, 400);
    Helpers::SplitCanvas(intwinc, active_channels, plot_active_channels);
    int event_index = GetEventIndex(eventnr);
    
    int current_canvas = 0;
    for (int i = 0; i < nchannels; i++) {
        if (PlotChannel(i)) {
            intwinc->cd(++current_canvas);
 
            auto his = Getwf(i, event_index);
            int wf_index = GetWaveformIndex(event_index, i);
 
            // drawing and formatting
            gPad->SetTopMargin(.01);
            int last_canvas = nchannels;
            if (!plot_active_channels.empty()) last_canvas = static_cast<int>(plot_active_channels.size());
            if (current_canvas == 1 && last_canvas < 4) gPad->SetLeftMargin(.15);
            if (current_canvas % 4 == 0 || current_canvas == last_canvas) gPad->SetRightMargin(.01);
            his->Draw("HIST");
            his->SetStats(0);
 
            if (wf_index !=  -1) {
                // create lines to indicate the integration window
                auto windowind = GetIntWindow(his, windowlow, windowhi, start, end, i);
                TLine* low = new TLine(his->GetXaxis()->GetBinCenter(windowind[1]), -5, his->GetXaxis()->GetBinCenter(windowind[1]), 10);
                low->SetLineColor(2);
                TLine* hi = new TLine(his->GetXaxis()->GetBinCenter(windowind[2]), -2, his->GetXaxis()->GetBinCenter(windowind[2]), 3);
                hi->SetLineColor(2);
                TLine* zero = new TLine(0, 0, 320, 0); // draw line at x=0 to check if baseline correction worked
                zero->SetLineColor(1);
 
                low->Draw("same");
                hi->Draw("same");
                zero->Draw("same");         
 
                // draw baseline and CFD parameters
                if (wf_index < static_cast<int>(baseline_correction_result.size())) {
                    TLine* baselinel = new TLine(baseline_correction_result[wf_index][2], -1, baseline_correction_result[wf_index][2], 1);
                    baselinel->SetLineColor(6);
                    baselinel->SetLineWidth(2);
                    TLine* baselineh = new TLine(baseline_correction_result[wf_index][3], -1, baseline_correction_result[wf_index][3], 1);
                    baselineh->SetLineColor(6);
                    baselineh->SetLineWidth(2);
                    TLine* baseline = new TLine(baseline_correction_result[wf_index][2], 0, baseline_correction_result[wf_index][3], 0);
                    baseline->SetLineColor(6);
                    TLine* correction_value = new TLine(baseline_correction_result[wf_index][2], baseline_correction_result[wf_index][0], baseline_correction_result[wf_index][3], baseline_correction_result[wf_index][0]);
                    correction_value->SetLineColor(2);
 
                    baselinel->Draw("same");
                    baselineh->Draw("same");
                    baseline->Draw("same");
                    correction_value->Draw("same");
                }
                
                if (wf_index < static_cast<int>(timing_results.size())) {
                    TLine* timing = new TLine(timing_results[wf_index][1], -10, timing_results[wf_index][1], 100);
                    timing->SetLineColor(9);
                    timing->SetLineWidth(2);
                    timing->Draw("same");
                }
            }
 
            if (ymin != 0. && ymax != 0.) his->GetYaxis()->SetRangeUser(ymin, ymax); // fix y range for better comparison 
            if (xmin != 0. && xmax != 0.) his->GetXaxis()->SetRangeUser(xmin, xmax);
        }
    }
    intwinc->Update();
 
    root_out->WriteObject(intwinc, name.Data());
}
 
float* ReadRun::ChargeList(int channel_index, float windowlow, float windowhi, float start, float end, bool negative_vals) {
    float* charge_list = new float[nevents]();
 
    #pragma omp parallel for
    for (int j = 0; j < nevents; j++) {
        int wf_index = GetWaveformIndex(j, channel_index);
        if (wf_index == -1) {
            charge_list[j] = -999.;
            continue;
        }
 
        charge_list[j] = GetPeakIntegral(rundata[wf_index], windowlow, windowhi, start, end, channel_index);
        if (!negative_vals && charge_list[j] < 0.) charge_list[j] = 0.;
    }
    return charge_list;
}
 
void ReadRun::SaveChargeLists(float windowlow, float windowhi, float start, float end, bool negative_vals) {
    float* event_list = new float[nevents];
    for (int i = 0; i < nevents; i++) event_list[i] = static_cast<float>(i);
 
    auto charge_list_mg = new TMultiGraph();
    if (windowlow + windowhi > 0.) charge_list_mg->SetTitle("event-wise integrals; Event number; integral [mV#timesns]");
    else charge_list_mg->SetTitle("event-wise amplitudes; Event number; amplitude [mV]");
    int color = 0;
 
    for (int i = 0; i < nchannels; i++) {
        if (PlotChannel(i)) {
            color++;
            TString name(Form("charge_list_ch_%02d", active_channels[i]));
            float* charge_list = ChargeList(i, windowlow, windowhi, start, end, negative_vals);
            TGraph* charge_list_graph = new TGraph(nevents, event_list, charge_list);
            charge_list_graph->SetLineWidth(0);
            charge_list_graph->SetMarkerStyle(2);
            charge_list_graph->SetMarkerColor(Helpers::rcolor(color));
            charge_list_graph->SetTitle(name.Data());
 
            //remove skipped events
            for (int j = 0; j < nevents; j++) {
                if (skip_event[j]) charge_list_graph->RemovePoint(j);
            }
 
            charge_list_mg->Add(charge_list_graph);
            root_out->WriteObject(charge_list_graph, name.Data());
            delete[] charge_list;
        }
    }
    root_out->WriteObject(charge_list_mg, "all_charge_lists");
    delete[] event_list;
}
 
void ReadRun::ChargeCorrelation(float windowlow, float windowhi, float start, float end, float rangestart, float rangeend, int nbins, int channel1, int channel2, bool ignore_skipped_events) {
    gStyle->SetOptStat(1111);
    stringstream name;
    name << "charge_correlation_ch" << channel1 << "_ch" << channel2;
    stringstream title;
    if (windowlow + windowhi > 0.) title << ";integral ch" << channel1 << " in mV#timesns;integral ch" << channel2 << " in mV#timesns;Entries";
    else title << ";amplitude ch" << channel1 << " in mV;amplitude ch" << channel2 << " in mV;Entries";
 
    auto charge_corr_canvas = new TCanvas(name.str().c_str(), "canvas", 600, 600);
    charge_corr_canvas->SetRightMargin(0.15);
 
    float* charge1 = ChargeList(GetChannelIndex(channel1), windowlow, windowhi, start, end);
    float* charge2 = ChargeList(GetChannelIndex(channel2), windowlow, windowhi, start, end);
 
    auto charge_corr = new TH2F(name.str().c_str(), title.str().c_str(), nbins, rangestart, rangeend, nbins, rangestart, rangeend);
    
    for (int i = 0; i < nevents; i++) {
        if (charge1[i] == -999. || charge2[i] == -999.) continue; // skip if data is missing for one of the channels
        if (!ignore_skipped_events || !skip_event[i]) charge_corr->Fill(charge1[i], charge2[i]);
    }
 
    charge_corr->Draw("colz");
    root_out->WriteObject(charge_corr, name.str().c_str());
 
    charge_corr_canvas->Update();
    charge_corr_canvas->SetGrid();
    // move stat box out of the way (causing problems since May 23?)
    //TPaveStats* stat_box = (TPaveStats*)charge_corr->FindObject("stats"); 
    //stat_box->SetX1NDC(0.6); 
    //stat_box->SetX2NDC(0.85);
    charge_corr->SetStats(0);
    charge_corr_canvas->Modified();
    name << "_c";
    root_out->WriteObject(charge_corr_canvas, name.str().c_str());
    delete[] charge1;
    delete[] charge2;
}
 
TH1F* ReadRun::ChargeSpectrum(int channel_index, float windowlow, float windowhi, float start, float end, float rangestart, float rangeend, int nbins) {
    TString name(Form("channel__%02d", active_channels[channel_index]));
    auto h1 = new TH1F(name.Data(), name.Data(), nbins, rangestart, rangeend);
 
    float pedestal = 0;
    float gain = 1;
    if (channel_index < static_cast<int>(PrintChargeSpectrum_cal.size())) {
        if (PrintChargeSpectrum_cal[channel_index][0] != 0) gain = PrintChargeSpectrum_cal[channel_index][0];
        if (PrintChargeSpectrum_cal[channel_index][1] != 1) pedestal = PrintChargeSpectrum_cal[channel_index][1];
    }
    float i_gain = 1. / gain;
 
    // create temporary histo per thread
    vector<TH1F*> h1_thread;
    int n_threads = omp_get_max_threads();
    h1_thread.resize(n_threads);
    for (int t = 0; t < n_threads; ++t) h1_thread[t] = new TH1F("", "", nbins, rangestart, rangeend);
 
    #pragma omp parallel
    {
        int t_id = omp_get_thread_num();
        TH1F* hlocal = h1_thread[t_id];
 
        #pragma omp for
        for (int j = 0; j < nevents; ++j) {
            if (!SkipEvent(j, channel_index)) {
                float integral_value = GetPeakIntegral(rundata[GetWaveformIndex(j, channel_index)], windowlow, windowhi, start, end, channel_index);
                hlocal->Fill((integral_value - pedestal) * i_gain);
            }
        }
    }
    // merge
    for (auto htmp : h1_thread) {
        h1->Add(htmp);
        delete htmp;
    }
    return h1;
}
 
void ReadRun::PrintChargeSpectrum(float windowlow, float windowhi, float start, float end, float rangestart, float rangeend, int nbins, float fitrangestart, float fitrangeend, int max_channel_nr_to_fit, int which_fitf, bool use_log_y) {
    // print ReadRun::ChargeSpectrum for all channels optimized for SiPM signals
    checkData();
    cout << "Creating charge spectrum ..." << endl;
    
    gStyle->SetOptStat("ne");
    gStyle->SetOptFit(1111);
 
    if (fitrangestart == 0.)    fitrangestart = rangestart;
    if (fitrangeend == 0.)      fitrangeend = rangeend;
 
    string ctitle("\"charge\" spectra" + to_string(PrintChargeSpectrum_cnt++));
    auto chargec = new TCanvas(ctitle.c_str(), ctitle.c_str(), 600, 400);
    Helpers::SplitCanvas(chargec, active_channels, plot_active_channels);
    int current_canvas = 0;
 
    float default_rangestart = -2000;
    float default_rangeend = 30000;
    if (default_rangestart > rangestart) default_rangestart = rangestart;
    if (default_rangeend < rangeend) default_rangeend = rangeend;
    int default_nbins = static_cast<int>((default_rangeend - default_rangestart) * nbins / (rangeend - rangestart));
 
    // create histograms in parallel
    map<int, shared_future<TH1F*>> h1_future;
    for (int i = 0; i < nchannels; ++i) {
        if (PlotChannel(i)) {
            h1_future[i] = async(launch::async, [this, i, windowlow, windowhi, start, end, default_rangestart, default_rangeend, default_nbins]() {
                return ChargeSpectrum(i, windowlow, windowhi, start, end, default_rangestart, default_rangeend, default_nbins);
            });
        }
    }
 
    for (int i = 0; i < nchannels; i++) {
        if (PlotChannel(i)) {
            chargec->cd(++current_canvas);
 
            auto his = h1_future[i].get();
            his->GetYaxis()->SetTitle("#Entries");
            if (windowlow + windowhi > 0.) his->GetXaxis()->SetTitle("Integral in mV#timesns");
            else his->GetXaxis()->SetTitle("Amplitude in mV");
            
            if (i < static_cast<int>(PrintChargeSpectrum_cal.size()) && PrintChargeSpectrum_cal[i][0] != 1) {
                cout << "Charge spectrum for channel index " << i << " will be normalized using a gain of "
                    << PrintChargeSpectrum_cal[i][0] << " and a pedestal value of " << PrintChargeSpectrum_cal[i][1] << endl;
                his->GetXaxis()->SetTitle("Number of photoelectrons");
            }
 
            //store the mean integral of each channel --> used for correction factors of phi_ew analysis
            mean_integral.push_back(his->GetMean());
 
            //fitting
            if (i < max_channel_nr_to_fit) {
                if (which_fitf == 0) {}
                else if (which_fitf == 1) { // landau gauss convolution for large number of photons
                    Fitf_langaus fitf;
                    int n_par = 4;
                    TF1* f = new TF1("fitf_langaus", fitf, fitrangestart, fitrangeend, n_par); f->SetLineColor(3); f->SetNpx(1000);
 
                    f->SetParName(0, "Width");              f->SetParameter(0, 35);
                    f->SetParName(1, "MPV");                f->SetParameter(1, 1000);
                    f->SetParName(2, "Area");               f->SetParameter(2, 10000);
                    f->SetParName(3, "#sigma_{Gauss}");     f->SetParameter(3, 100);
 
                    if (!PrintChargeSpectrum_pars.empty()) for (int j = 0; j < min(4, static_cast<int>(PrintChargeSpectrum_pars.size())); j++) f->SetParameter(j, PrintChargeSpectrum_pars[j]);
 
                    if (i < max_channel_nr_to_fit) {
                        cout << "\n\n---------------------- Fit for channel " << active_channels[i] << " ----------------------\n";
                        TFitResultPtr fresults = his->Fit(f, "LRS");
                        fit_results.push_back(fresults);
                    }
                }
                else if (which_fitf == 2) { // if pedestal is biased because of peak finder algorithm
                    Fitf_biased fitf;
                    int n_par = 9;
                    TF1* f = new TF1("fitf_biased", fitf, fitrangestart, fitrangeend, n_par); f->SetLineColor(3); f->SetNpx(1000);
 
                    f->SetParName(0, "N_{0}");              f->SetParameter(0, his->Integral());
                    f->SetParName(1, "#mu");                f->SetParameter(1, 2.);
                    f->SetParName(2, "#lambda");            f->SetParameter(2, .04);
                    f->SetParName(3, "#sigma_{0}");         f->SetParameter(3, 2.1);
                    f->SetParName(4, "#sigma_{1}");         f->SetParameter(4, 3.4); //f->SetParLimits(4, 1.e-9, 1.e3);
                    f->SetParName(5, "Gain");               f->SetParameter(5, 30.); //f->FixParameter(5, 10.);
                    f->SetParName(6, "Pedestal");           f->SetParameter(6, 2.);
                    f->SetParName(7, "norm_{0}");           f->SetParameter(7, 0.7);
                    f->SetParName(8, "x_{0}");              f->SetParameter(8, 5.);
 
                    if (!PrintChargeSpectrum_pars.empty()) for (int j = 0; j < min(n_par, static_cast<int>(PrintChargeSpectrum_pars.size())); j++) f->SetParameter(j, PrintChargeSpectrum_pars[j]);
 
                    if (i < max_channel_nr_to_fit) {
                        cout << "\n\n---------------------- Fit for channel " << active_channels[i] << " ----------------------\n";
                        TFitResultPtr fresults = his->Fit(f, "LRS");
                        fit_results.push_back(fresults);
                    }
 
                    // get number of excess events in the pedestal in the fit region. To get the absolute number of excess events the full pedestal needs to be inside of the fit range (fitrangestart, fitrangeend)
                    //double excessEventsInPedestal = f->Integral(fitrangestart, fitrangeend)/.3125;
                    //f->SetParameter(7, 1.);
                    //excessEventsInPedestal -= f->Integral(fitrangestart, fitrangeend)/.3125;
                    //cout << "\nNumber of excess events in the pedestal within the fit range:\t" << excessEventsInPedestal << "\n\n";
                }
                else if (which_fitf == 3) { // SiPM fit function with exponential delayed after pulsing
                    Fitf_full fitf;
                    int n_par = 9;
                    TF1* f = new TF1("fitf", fitf, fitrangestart, fitrangeend, n_par); f->SetLineColor(3); f->SetNpx(1000);
 
                    f->SetParName(0, "N_{0}");              f->SetParameter(0, his->Integral());
                    f->SetParName(1, "#mu");                f->SetParameter(1, 2.);
                    f->SetParName(2, "#lambda");            f->SetParameter(2, .04);
                    f->SetParName(3, "#sigma_{0}");         f->SetParameter(3, 2.1);
                    f->SetParName(4, "#sigma_{1}");         f->SetParameter(4, 3.4);
                    f->SetParName(5, "Gain");               f->SetParameter(5, 30.); //f->FixParameter(5, 40.);
                    f->SetParName(6, "Pedestal");           f->SetParameter(6, 2.);
                    f->SetParName(7, "#alpha");             f->SetParameter(7, .1); //f->FixParameter(7, .2);
                    f->SetParName(8, "#beta");              f->SetParameter(8, 80.); //f->FixParameter(8, 80);
 
                    if (!PrintChargeSpectrum_pars.empty()) for (int j = 0; j < min(n_par, static_cast<int>(PrintChargeSpectrum_pars.size())); j++) f->SetParameter(j, PrintChargeSpectrum_pars[j]);
 
                    if (i < max_channel_nr_to_fit) {
                        cout << "\n\n---------------------- Fit for channel " << active_channels[i] << " ----------------------\n";
                        TFitResultPtr fresults = his->Fit(f, "LRS");
                        fit_results.push_back(fresults);
                    }
                }
                else if (which_fitf == 4) { // ideal PMT fit function
                    Fitf_PMT_ideal fitf;
                    int n_par = 4;
                    TF1* f = new TF1("fitf", fitf, fitrangestart, fitrangeend, n_par); f->SetLineColor(3); f->SetNpx(1000);
 
                    f->SetParName(0, "N_{0}");              f->SetParameter(0, his->Integral());
                    f->SetParName(1, "#mu");                f->SetParameter(1, 1.);
                    f->SetParName(2, "#sigma");             f->SetParameter(2, 5.);
                    f->SetParName(3, "gain");               f->SetParameter(3, 10.);
 
                    if (!PrintChargeSpectrum_pars.empty()) for (int j = 0; j < min(n_par, static_cast<int>(PrintChargeSpectrum_pars.size())); j++) f->SetParameter(j, PrintChargeSpectrum_pars[j]);
 
                    if (i < max_channel_nr_to_fit) {
                        cout << "\n\n---------------------- Fit for channel " << active_channels[i] << " ----------------------\n";
                        TFitResultPtr fresults = his->Fit(f, "LRS");
                        fit_results.push_back(fresults);
                    }
                }
                else if (which_fitf == 5) { // PMT fit function
                    Fitf_PMT fitf;
                    int n_par = 8;
                    TF1* f = new TF1("fitf", fitf, fitrangestart, fitrangeend, n_par); f->SetLineColor(3); f->SetNpx(1000);
 
                    f->SetParName(0, "N_{0}");              f->SetParameter(0, his->Integral());
                    f->SetParName(1, "w");                  f->SetParameter(1, .05);    f->SetParLimits(1, 1.e-99, 4.e-1); //probability for type II BG
                    f->SetParName(2, "#alpha");             f->SetParameter(2, .05);    f->SetParLimits(2, 1.e-99, 5.e-2); //coefficient of exponential decrease of typ II BG
                    f->SetParName(3, "#sigma_{0}");         f->SetParameter(3, 5.);     f->SetParLimits(3, 1.e-9, 1.e3);
                    f->SetParName(4, "Q_{0}");              f->SetParameter(4, 0.);
                    f->SetParName(5, "#mu");                f->SetParameter(5, 1.);
                    f->SetParName(6, "#sigma_{1}");         f->SetParameter(6, 5.);     f->SetParLimits(6, 1.e-9, 1.e3);
                    f->SetParName(7, "Q_{1}");              f->SetParameter(7, 10.);
 
                    if (!PrintChargeSpectrum_pars.empty()) for (int j = 0; j < min(n_par, static_cast<int>(PrintChargeSpectrum_pars.size())); j++) f->SetParameter(j, PrintChargeSpectrum_pars[j]);
 
                    if (i < max_channel_nr_to_fit) {
                        cout << "\n\n---------------------- Fit for channel " << active_channels[i] << " ----------------------\n";
                        TFitResultPtr fresults = his->Fit(f, "LRS");
                        fit_results.push_back(fresults);
                    }
                }
                else if (which_fitf == 6) { // PMT fit function with biased pedestal
                    Fitf_PMT_pedestal fitf;
                    int n_par = 9;
                    TF1* f = new TF1("fitf", fitf, fitrangestart, fitrangeend, n_par); f->SetLineColor(3); f->SetNpx(1000);
 
                    f->SetParName(0, "A");                  f->SetParameter(0, his->Integral());
                    f->SetParName(1, "w");                  f->SetParameter(1, .05);    f->SetParLimits(1, 1.e-9, 4.e-1);   //probability for type II BG
                    f->SetParName(2, "#alpha");             f->SetParameter(2, .05);    f->SetParLimits(2, 1.e-9, 5.e-2);   //coefficient of exponential decrease of typ II BG
                    f->SetParName(3, "#sigma_{0}");         f->SetParameter(3, 5.);     f->SetParLimits(3, 1.e-9, 1.e3);
                    f->SetParName(4, "Q_{0}");              f->SetParameter(4, 0.);     f->SetParLimits(4, -1.e2, 1.e2);
                    f->SetParName(5, "#mu");                f->SetParameter(5, 1.);     f->SetParLimits(5, 1.e-9, 1.e2);
                    f->SetParName(6, "#sigma_{1}");         f->SetParameter(6, 5.);     f->SetParLimits(6, 1.e-9, 1.e3);
                    f->SetParName(7, "Q_{1}");              f->SetParameter(7, 10.);    f->SetParLimits(7, 1.e-9, 1.e9);
                    f->SetParName(8, "A_{0}");              f->SetParameter(8, 1.);     f->SetParLimits(8, 1.e-9, 1.e1);
 
                    if (!PrintChargeSpectrum_pars.empty()) for (int j = 0; j < min(n_par, static_cast<int>(PrintChargeSpectrum_pars.size())); j++) f->SetParameter(j, PrintChargeSpectrum_pars[j]);
 
                    if (i < max_channel_nr_to_fit) {
                        cout << "\n\n---------------------- Fit for channel " << active_channels[i] << " ----------------------\n";
                        TFitResultPtr fresults = his->Fit(f, "LRS");
                        fit_results.push_back(fresults);
                    }
                }
                else if (which_fitf == 7) { // default SiPM fit function + dark count spectrum (for lots of false triggers)
                    Fitf_plus_DC fitf;
                    int n_par = 9;
                    TF1* f = new TF1("fitf", fitf, fitrangestart, fitrangeend, n_par); f->SetLineColor(3); f->SetNpx(1000);
 
                    f->SetParName(0, "A");                  f->SetParameter(0, his->Integral());
                    f->SetParName(1, "w");                  f->SetParameter(1, .05);    f->SetParLimits(1, 1.e-9, 4.e-1);   //probability for type II BG
                    f->SetParName(2, "#alpha");             f->SetParameter(2, .05);    f->SetParLimits(2, 1.e-9, 5.e-2);   //coefficient of exponential decrease of typ II BG
                    f->SetParName(3, "#sigma_{0}");         f->SetParameter(3, 5.);     f->SetParLimits(3, 1.e-9, 1.e3);
                    f->SetParName(4, "Q_{0}");              f->SetParameter(4, 0.);     f->SetParLimits(4, -1.e2, 1.e2);
                    f->SetParName(5, "#mu");                f->SetParameter(5, 1.);     f->SetParLimits(5, 1.e-9, 1.e2);
                    f->SetParName(6, "#sigma_{1}");         f->SetParameter(6, 5.);     f->SetParLimits(6, 1.e-9, 1.e3);
                    f->SetParName(7, "#mu_darkcount");      f->SetParameter(7, .1);     f->SetParLimits(7, 1.e-9, 1.);
                    f->SetParName(8, "N_{0}_darkcount");    f->SetParameter(8, .05);    f->SetParLimits(8, 1.e-9, .3);
 
                    if (!PrintChargeSpectrum_pars.empty()) for (int j = 0; j < min(n_par, static_cast<int>(PrintChargeSpectrum_pars.size())); j++) f->SetParameter(j, PrintChargeSpectrum_pars[j]);
 
                    if (i < max_channel_nr_to_fit) {
                        cout << "\n\n---------------------- Fit for channel " << active_channels[i] << " ----------------------\n";
                        TFitResultPtr fresults = his->Fit(f, "LRS");
                        fit_results.push_back(fresults);
                    }
                }
                else { // default SiPM fit function
                    Fitf fitf;
                    int n_par = 7;
                    TF1* f = new TF1("fitf", fitf, fitrangestart, fitrangeend, n_par); f->SetLineColor(3); f->SetNpx(1000);
 
                    f->SetParName(0, "N_{0}");              f->SetParameter(0, his->Integral());
                    f->SetParName(1, "#mu");                f->SetParameter(1, 2.);
                    f->SetParName(2, "#lambda");            f->SetParameter(2, .04);
                    f->SetParName(3, "#sigma_{0}");         f->SetParameter(3, 2.1);
                    f->SetParName(4, "#sigma_{1}");         f->SetParameter(4, 3.4);
                    f->SetParName(5, "Gain");               f->SetParameter(5, 30.); //f->FixParameter(5, 40.);
                    f->SetParName(6, "Pedestal");           f->SetParameter(6, 2.);
 
                    if (!PrintChargeSpectrum_pars.empty()) for (int j = 0; j < min(n_par, static_cast<int>(PrintChargeSpectrum_pars.size())); j++) f->SetParameter(j, PrintChargeSpectrum_pars[j]);
 
                    if (i < max_channel_nr_to_fit) {
                        cout << "\n\n---------------------- Fit for channel " << active_channels[i] << " ----------------------\n";
                        TFitResultPtr fresults = his->Fit(f, "LRS");
                        fit_results.push_back(fresults);
                    }
                }
            }
            TString name(Form("ChargeSpectrum channel_%02d_%d", active_channels[i], PrintChargeSpectrum_cnt));
            root_out->WriteObject(his, name.Data());
            his->Draw();
            if (use_log_y) gPad->SetLogy();
        }
    }
 
    Helpers::SetRangeCanvas(chargec, rangestart, rangeend);
    root_out->WriteObject(chargec, ("ChargeSpectra" + to_string(PrintChargeSpectrum_cnt)).c_str());
}
 
void ReadRun::PrintDCR(float windowlow, float windowhi, float rangestart, float rangeend, double threshold) {
 
    string unit(" mV");
    if (windowlow + windowhi > 0.) unit = " mV*ns";
 
    for (int i = 0; i < nchannels; i++) {
        if (PlotChannel(i)) {
            auto his = ChargeSpectrum(i, windowlow, windowhi, rangestart, rangeend, rangestart, rangeend, 500);
 
            stringstream lonamerate;
            lonamerate << "<0.5 pe=" << threshold << unit << " -> " << his->Integral(his->GetXaxis()->FindBin(rangestart), his->GetXaxis()->FindBin(threshold)) / his->GetEntries() / (1.e-3 * (rangeend - rangestart)) << " MHz";
            cout << "\n" << lonamerate.str().c_str() << endl;
 
            stringstream hinamerate;
            hinamerate << ">0.5 pe=" << threshold << unit << " -> " << his->Integral(his->GetXaxis()->FindBin(threshold) + 1, his->GetXaxis()->FindBin(rangeend)) / his->GetEntries() / (1.e-3 * (rangeend - rangestart)) << " MHz";
            cout << "\n" << hinamerate.str().c_str() << endl;
        }
    }
}
 
TH1F* ReadRun::TimeDist(int channel_index, float from, float to, float rangestart, float rangeend, int nbins, int which, float cf_r) {
    int from_n = TimeToIndex(from);
    int to_n = TimeToIndex(to);
 
    TString name(Form("timedist_ch%02d", active_channels[channel_index]));
    auto h1 = new TH1F(name.Data(), name.Data(), nbins, rangestart, rangeend);
    
    for (int j = 0; j < nevents; j++) {
        if (!SkipEvent(j, channel_index)) {
            int wf_index = GetWaveformIndex(j, channel_index);
            int max_n = GetIntWindow(rundata[wf_index], 0, 0, from_n, to_n)[0];
            float max_val = rundata[wf_index][max_n];
 
            if (which == 0) { // time of maximum 
                h1->Fill(max_val);
            }
            else if (which == 1) { // time of 50% CFD
                do {
                    max_n--;
                } while (rundata[wf_index][max_n] >= cf_r * max_val && max_n >= from_n);
                max_n++;
 
                h1->Fill(LinearInterpolation(cf_r * max_val, IndexToTime(max_n - 1), IndexToTime(max_n), rundata[wf_index][max_n - 1], rundata[wf_index][max_n]).first);
            }
            else { // 10%-90% rise time
                // search backwards from maximum
                int n10 = -1;
                int n90 = -1;
                do {
                    max_n--;
                    if (n10 == -1 && rundata[wf_index][max_n] >= .1 * max_val && rundata[wf_index][max_n - 1] <= .1 * max_val) n10 = max_n;
                    if (n90 == -1 && rundata[wf_index][max_n] >= .9 * max_val && rundata[wf_index][max_n - 1] <= .9 * max_val) n90 = max_n;
                } while (rundata[wf_index][max_n] <= max_val && max_n > from_n);
 
                float t10 = LinearInterpolation(.1 * max_val, IndexToTime(n10 - 1), IndexToTime(n10), IndexToTime(n10 - 1), IndexToTime(n10)).first;
                float t90 = LinearInterpolation(.9 * max_val, IndexToTime(n90 - 1), IndexToTime(n90), IndexToTime(n90 - 1), IndexToTime(n90)).first;
 
                h1->Fill(t90 - t10);
            }
        }
    }
    if (which == 1) h1->Fit("gaus", "WWM", "same");
    return h1;
}
 
void ReadRun::PrintTimeDist(float from, float to, float rangestart, float rangeend, int nbins, int which, float cf_r) {
    gStyle->SetOptStat(1111); // 11 is title + entries
 
    auto time_dist_c = new TCanvas("timing of maximum", "timing of maximum", 600, 400);
    Helpers::SplitCanvas(time_dist_c, active_channels, plot_active_channels);
 
    int current_canvas = 0;
 
    for (int i = 0; i < nchannels; i++) {
        if (PlotChannel(i)) {
            time_dist_c->cd(++current_canvas);
 
            auto his = TimeDist(i, from, to, rangestart, rangeend, nbins, which, cf_r);
            his->GetYaxis()->SetTitle("#Entries");
            his->GetXaxis()->SetTitle("time [ns]");
            his->Draw();
            stringstream name; name << "t_{max} for " << from << "<t<" << to << " ns";
            his->SetTitle(name.str().c_str());
 
            TString name_save(Form("TimeDist channel_%02d", active_channels[i]));
            root_out->WriteObject(his, name_save.Data());
        }
    }
 
    time_dist_c->Update();
    root_out->WriteObject(time_dist_c, "TimeDist");
}
 
TGraph2D* ReadRun::MaxDist(int channel_index, float from, float to) {
    // find maximum amplitude for a given channel in time window [from, to] and return 3d histogram with the number of bins nbinsy,z
 
    TString name(Form("maxdist_ch%02d", active_channels[channel_index]));
    TGraph2D* g3d = new TGraph2D((binNumber + 2) * nevents);
    g3d->SetTitle("waveforms; t [ns]; max. amplitude [mv]; amplitude [mV]");
    g3d->SetMarkerStyle(7);
    double* xvals = getx<double>();
 
    for (int j = 0; j < nevents; j++) {
        if (!SkipEvent(j, channel_index)) {
            int wf_index = GetWaveformIndex(j, channel_index);
 
            int bin_from = TimeToIndex(from);
            int bin_to = TimeToIndex(to);
            double max_val = rundata[wf_index][bin_from];
            for (int i = bin_from; i <= bin_to; ++i) {
                double val = rundata[wf_index][i];
                if (val > max_val) max_val = val;
            }
            
            for (int i = 0; i < binNumber; i++) g3d->SetPoint(j * binNumber + i, xvals[i], max_val, rundata[wf_index][i]);
        }
    }
    delete[] xvals;
    root_out->WriteObject(g3d, name.Data());
    return g3d;
}
 
 
void ReadRun::PrintMaxDist(float from, float to) {
 
    auto max_dist_c = new TCanvas("wf grouped by maximum", "wf grouped by maximum", 600, 400);
    Helpers::SplitCanvas(max_dist_c, active_channels, plot_active_channels);
 
    int current_canvas = 0;
 
    for (int i = 0; i < nchannels; i++) {
        if (PlotChannel(i)) {
            max_dist_c->cd(++current_canvas);
            auto g3d = MaxDist(i, from, to);
            g3d->Draw("AP");
        }
    }
    max_dist_c->Update();
    root_out->WriteObject(max_dist_c, "MaxDist");
}
 
TH1F* ReadRun::His_GetTimingCFD(int channel_index, float rangestart, float rangeend, int nbins) {
 
    if (nbins == -999) nbins = static_cast<int>((rangeend - rangestart) * SP_inv);
 
    TString name(Form("GetTimingCFD_ch%02d", active_channels[channel_index]));
    auto his = new TH1F(name.Data(), name.Data(), nbins, rangestart, rangeend);
    for (int j = 0; j < nevents; j++) {
        if (!SkipEvent(j, channel_index)) his->Fill(timing_results[GetWaveformIndex(j, channel_index)][1]);
    }
    return his;
}
 
void ReadRun::Print_GetTimingCFD(float rangestart, float rangeend, int do_fit, int nbins, string fitoption, bool set_errors) {
 
    // call GetTimingCFD() in case it was not initialized
    if (static_cast<int>(timing_results.size()) == 0) GetTimingCFD();
 
    gStyle->SetOptStat(1111);
    gStyle->SetOptFit(111);
 
    auto timing_cfd_c = new TCanvas("timing of cfd", "timing of cfd", 600, 400);
    Helpers::SplitCanvas(timing_cfd_c, active_channels, plot_active_channels);
    int current_canvas = 0;
 
    for (int i = 0; i < nchannels; i++) {
        if (PlotChannel(i)) {
            timing_cfd_c->cd(++current_canvas);
 
            auto his = His_GetTimingCFD(i, rangestart, rangeend, nbins);
            his->GetYaxis()->SetTitle("#Entries");
            his->GetXaxis()->SetTitle("time [ns]");
 
            if (set_errors) {
                int end = his->GetNbinsX();
                for (int k = 1; k <= end; k++) {
                    if (his->GetBinContent(k) < 2) his->SetBinError(k, 1);
                    else his->SetBinError(k, sqrt(his->GetBinContent(k)));
                }
            }
 
            his->Draw();
 
            if (do_fit == 1) {
                TFitResultPtr fresults = his->Fit("gaus", fitoption.c_str(), "same");
                timing_fit_results.push_back(fresults);
            }
 
            TString name_save(Form("Timing_cfd_channel_%02d", active_channels[i]));
            root_out->WriteObject(his, name_save.Data());
        }
    }
 
    timing_cfd_c->Update();
    root_out->WriteObject(timing_cfd_c, "TimingCFD");
}
 
TH1F* ReadRun::His_GetTimingCFD_diff(vector<int> channels1, vector<int> channels2, float rangestart, float rangeend, int nbins) {
 
    if (nbins == -999) nbins = static_cast<int>((rangeend - rangestart) * SP_inv);
 
    stringstream name;
    name << "GetTimingCFD_diff <";
 
    // find channel indices and assemble title
    int counter = 0;
    for (int& entry : channels2) {
        if (counter > 0) name << "&";
        auto chin2 = find(active_channels.begin(), active_channels.end(), entry);
        if (chin2 != active_channels.end()) {
            name << "ch" << entry;
            entry = chin2 - active_channels.begin();
        }
        else cout << "\n\n ERROR: channels2 = " << entry << " does not exist in data. Check parameters for Print_GetTimingCFD_diff()\n\n";
        counter++;
    }
    name << ">-<";
    counter = 0;
 
    for (int& entry : channels1) {
        if (counter > 0) name << "&";
        auto chin1 = find(active_channels.begin(), active_channels.end(), entry);
        if (chin1 != active_channels.end()) {
            name << "ch" << entry;
            entry = chin1 - active_channels.begin();
        }
        else cout << "\n\n ERROR: channels1 = " << entry << " does not exist in data. Check parameters for Print_GetTimingCFD_diff()\n\n";
        counter++;
    }
    name << ">";
 
    // fill histogram
    auto his = new TH1F(name.str().c_str(), name.str().c_str(), nbins, rangestart, rangeend);
    for (int j = 0; j < nevents; j++) {
        if (!SkipEvent(j)) {
            float mean1 = 0., mean2 = 0., cnt1 = 0., cnt2 = 0.;
            for (int i : channels1) {
                int wf_index = GetWaveformIndex(j, i);
                if (wf_index >= 0) {
                    mean1 += timing_results[GetWaveformIndex(j, i)][1];
                    cnt1 += 1.;
                }
            }
            for (int i : channels2) {
                int wf_index = GetWaveformIndex(j, i);
                if (wf_index >= 0) {
                    mean2 += timing_results[GetWaveformIndex(j, i)][1];
                    cnt2 += 1.;
                }
            }
 
            if (cnt1 != 0. && cnt2 !=0.) his->Fill(mean2 / cnt2 - mean1 / cnt1);
        }
    }
 
    return his;
}
 
void ReadRun::Print_GetTimingCFD_diff(vector<int> channels1, vector<int> channels2, float rangestart, float rangeend, int do_fit, int nbins, float fitrangestart, float fitrangeend, string fitoption, bool set_errors) {
 
    // call GetTimingCFD() in case it was not initialized
    if (static_cast<int>(timing_results.size()) == 0) GetTimingCFD();
 
    if (fitrangestart == -999) {
        fitrangestart = rangestart;
        fitrangeend = rangeend;
    }
 
    //gStyle->SetOptStat(1111);
    gStyle->SetOptFit(111);
 
    auto timing_cfd_d_c = new TCanvas("timing of cfd diff", "timing of cfd diff", 600, 400);
 
    auto his = His_GetTimingCFD_diff(channels1, channels2, rangestart, rangeend, nbins);
    his->GetYaxis()->SetTitle("#Entries");
    his->GetXaxis()->SetTitle("time [ns]");
 
    if (set_errors) {
        int end = his->GetNbinsX();
        for (int i = 1; i <= end; i++) {
            if (his->GetBinContent(i) < 2) his->SetBinError(i, 1);
            else his->SetBinError(i, sqrt(his->GetBinContent(i)));
        }
    }
 
    his->Draw();
 
    double skewness = his->GetSkewness();
    
    if (do_fit == 1 || (do_fit == 2 && abs(skewness) < .15)) {
        // gauss (default)
        TFitResultPtr fresults = his->Fit("gaus", fitoption.c_str(), "same", fitrangestart, fitrangeend);
        timing_fit_results.push_back(fresults);
        if (do_fit == 2) cout << "\nWARNING: Print_GetTimingCFD_diff\nFITTING GAUSS INSTEAD OF GAUSS x EXP CONVOLUTION BC SYMMETRY" << endl;
    }
    else if (do_fit == 2) {
        // gauss x exp convolution (effective delay from random light path and/or self-absorption and reemission)
        Fitf_exp_gauss fitf_exp_gauss;
        auto expgconv = new TF1("exp x gauss convolution", fitf_exp_gauss, fitrangestart, fitrangeend, 4);
        expgconv->SetNpx(5000);
 
        // this parameter describes the sigma from different light paths 
        // and/or the effective decay time constant for self-absorption and reemission
        expgconv->SetParName(0, "#tau_{eff}");      expgconv->SetParameter(0, skewness);
        if (skewness > 0) expgconv->SetParLimits(0, .15, 5.);
        else expgconv->SetParLimits(0, -5., -.15);
        //expgconv->FixParameter(0, 1.55);
 
        expgconv->SetParName(1, "#sigma_{gaus}");       expgconv->SetParameter(1, his->GetStdDev());
        expgconv->SetParLimits(1, 1e-1, 7.);    //expgconv->FixParameter(1, .7);
 
        expgconv->SetParName(2, "t_{0}");       expgconv->SetParameter(2, his->GetMean());
        expgconv->SetParLimits(2, fitrangestart, fitrangeend);  //expgconv->FixParameter(2, 6.6);
 
        expgconv->SetParName(3, "norm");        expgconv->SetParameter(3, his->Integral("width"));
        expgconv->SetParLimits(3, 1., 1e8);     //expgconv->FixParameter(3, 105.5);
 
        TFitResultPtr fresults = his->Fit(expgconv, "SR", "same");
        timing_fit_results.push_back(fresults);
 
        // for the phi_ew-analysis: print out the time value of the maximum of the best fit --> used to determine timing cuts
        float t_of_maximum = expgconv->GetMaximumX(-5, 5);
        cout << "Maximum of the fit is at t=" << t_of_maximum << " ns and the ";
 
        double max_val = expgconv->GetMaximum();
        double fwhm_x1 = expgconv->GetX(max_val * 0.5, fitrangestart, fitrangeend);
        double fwhm_x2 = expgconv->GetX(max_val * 0.5, fwhm_x1 + 1e-3, fitrangeend);
        double fwhm = fwhm_x2 - fwhm_x1;
        auto fwhm_line = new TLine(fwhm_x1, max_val/2, fwhm_x2, max_val/2);
        fwhm_line->SetLineColor(2); fwhm_line->SetLineWidth(2);
        fwhm_line->Draw("same");
        cout << "FWHM=" << fwhm << " ns" << endl;
 
        // TLatex l;
        // l.SetTextSize(0.025);
        // l.DrawLatex(t_of_maximum/(rangeend - rangestart), 0.4, Form("FWHM = %.2f ns", fwhm));
 
        auto mean = new TLine(expgconv->GetParameter(2), 1e-2, expgconv->GetParameter(2), his->GetMaximum());
        mean->SetLineColor(1); mean->SetLineWidth(2);
        mean->Draw("same");
    }
    else if (do_fit == 3) {
        // sum of two gaussians (one as background estimate)
        auto two_gauss = new TF1("two gaussians", "gaus(0)+gaus(3)", rangestart, rangeend);
        two_gauss->SetTitle("Sum of two gauss");
        float posmax = his->GetXaxis()->GetBinCenter(his->GetMaximumBin());
        two_gauss->SetParameters(his->Integral("width"), posmax, 0.35, his->Integral("width") * 0.03, posmax, 2);
        two_gauss->SetParName(0, "norm_{peak}");        two_gauss->SetParName(1, "#mu_{peak}");         two_gauss->SetParName(2, "#sigma_{peak}");          two_gauss->SetParLimits(2, 1e-9, 1e2);
        two_gauss->SetParName(3, "norm_{background}");  two_gauss->SetParName(4, "#mu_{background}");   two_gauss->SetParName(5, "#sigma_{background}");    two_gauss->SetParLimits(5, 1e-9, 1e2);
        TFitResultPtr fresults = his->Fit(two_gauss, fitoption.c_str(), "same", fitrangestart, fitrangeend);
        timing_fit_results.push_back(fresults);
    }
 
    root_out->WriteObject(his, his->GetTitle());
    timing_cfd_d_c->Update();
    root_out->WriteObject(timing_cfd_d_c, "TimingCFD_diff");
}
 
 
 
 
 
 
TH1F* ReadRun::Getwf(int wfindex) {
    int channel = GetCurrentChannel(wfindex);
    int event_nr = GetCurrentEvent(wfindex);
    TString name(Form("ch%02d_%05d", channel, event_nr));
    TString title(Form("ch%d, event %d;t [ns];U [mV]", channel, event_nr));
    auto his = new TH1F(name.Data(), title.Data(), binNumber, 0, static_cast<float>(binNumber) * SP);
    for (int i = 1; i <= binNumber; i++) his->SetBinContent(i, rundata[wfindex][i - 1]);
    return his;
}
 
TH1F* ReadRun::Getwf(int channelnr, int eventnr, int color) {
    TString name(Form("ch%02d_%05d", channelnr, eventnr));
    TString title(Form("ch%d, event %d;t [ns];U [mV]", channelnr, eventnr));
    auto his = new TH1F(name.Data(), title.Data(), binNumber, 0, static_cast<float>(binNumber) * SP);
    for (int i = 1; i <= binNumber; i++) his->SetBinContent(i, rundata[eventnr * nchannels + channelnr][i - 1]);
    his->SetLineColor(color);
    his->SetMarkerColor(color);
    return his;
}
 
template<typename T>
T* ReadRun::getx(double shift) {
    T* xvals = new T[binNumber];
    for (int i = 0; i < binNumber; ++i) {
        xvals[i] = static_cast<T>(SP) * (static_cast<T>(i) + 0.5) + shift;
    }
    return xvals;
}
template double* ReadRun::getx<double>(double);
template float* ReadRun::getx<float>(double);
 
 
double* ReadRun::gety(int waveform_index) {
    double* waveform = new double[binNumber];
    for (int i = 0; i < binNumber; i++) waveform[i] = static_cast<double>(rundata[waveform_index][i]);
    return waveform;
}
 
double* ReadRun::gety(int channelnr, int eventnr) {
    double* waveform = new double[binNumber];
    int wf_index = GetWaveformIndex(eventnr, channelnr);
    for (int i = 0; i < binNumber; i++) waveform[i] = static_cast<double>(rundata[wf_index][i]);
    return waveform;
}
 
int ReadRun::GetWaveformIndex(int eventnr, int channel_index) {
    return max(0, min(nwf - 1, eventnr * nchannels + channel_index));
}
 
int ReadRun::GetEventIndex(unsigned int eventnr) {
    auto event_pos = find(eventnr_storage.begin(), eventnr_storage.end(), eventnr);
    if (event_pos == eventnr_storage.end()) {
        cout << "WARNING: Event number " << eventnr << " for GetEventIndex() does not exist in data.\n"
            << "Please check the events in the data or set discard_original_eventnr = true before calling ReadFile()." << endl;
        
        if (static_cast<int>(eventnr) < nevents) {
            eventnr = eventnr_storage[eventnr];
            event_pos = find(eventnr_storage.begin(), eventnr_storage.end(), eventnr);
            cout << "Found event number " << eventnr << " in data and will use it." << endl;
        }
    }
    return static_cast<int>(distance(eventnr_storage.begin(), event_pos));
}
 
int ReadRun::GetChannelIndex(int channel_number) {
    int channel_index = -1;
    for (int i = 0; i < static_cast<int>(active_channels.size()); i++) {
        if (active_channels[i] == channel_number) channel_index = i;
    }
    if (channel_index == -1) {
        cout << "\n\n\tERROR: channel " << channel_number << " does not exist in data. Will continue with first channel\n\n";
        channel_index = 0;
    }
    return channel_index;
}
 
int ReadRun::GetCurrentChannel(int waveform_index) {
    return (waveform_index - nchannels * floor(waveform_index / nchannels));
}
 
int ReadRun::GetCurrentEvent(int waveform_index) {
    return floor(waveform_index / nchannels);
}
 
bool ReadRun::PlotChannel(int i) {
    if (plot_active_channels.empty() || Helpers::Contains(plot_active_channels, active_channels[i])) return true;
    else return false;
}
 
pair<float, bool> ReadRun::LinearInterpolation(float ym, float x1, float x2, float y1, float y2, bool verbose) {
    if (y1 == y2) return {(x1 + x2) * 0.5, false};
    else if ((y1 > ym && y2 > ym) || (y1 < ym && y2 < ym)) {
        if (verbose){
            cout << "\nError in LinearInterpolation: Value ym=" << ym << " out of range (" << y1 << "|" << y2 << ")." << endl;
            cout << "Will return x1. Increase window for search." << endl;
        }
        return {x1, false};
    }
    else return {x1 + (ym - y1) * (x2 - x1) / (y2 - y1), true};
}
 
vector<bool> ReadRun::PolarityMap(bool change_polarity, int change_sign_from_to_ch_num) {
    vector<bool> pol(nChannelsWC, false);
    if (!change_polarity) {
        return pol;
    }
    else if (!switch_polarity_for_channels.empty()) {
        for (int current_channel=0; current_channel<nChannelsWC; current_channel++) {
            if (Helpers::Contains(switch_polarity_for_channels, current_channel)) {
                pol[current_channel] = true;
            }
        }
        return pol;
    }
    else {
        for (int current_channel=0; current_channel<nChannelsWC; current_channel++) {
            if ((current_channel >= change_sign_from_to_ch_num) || 
                (change_sign_from_to_ch_num < 0 && current_channel <= abs(change_sign_from_to_ch_num))) {
                pol[current_channel] = true;
            }
        }
        return pol;
    }
}
 
int ReadRun::CheckBoundsX(int index) {
    return min(max(0, index), binNumber - 1);
}
 
int ReadRun::TimeToIndex(float time) {
    return CheckBoundsX(static_cast<int>(time * SP_inv));
}
 
float ReadRun::IndexToTime(int bin_index) {
    return static_cast<float>(CheckBoundsX(bin_index)) * SP;
}