#include "MLogManip.h"

/*****************************************************************

 CALLISTO -- CALibrate LIght Signals and Time Offsets

 datafile:
    A data file written by the fadctrl, e.g.
    20170727_006.fits.fz or
    00000015.003_D_MonteCarlo019_Events.fits.fz

 drsfile:
    Usually the third of the three .drs.fits files from a
    DRS calibration sequence, e.g. 20170727_004.drs.fits

 drstime:
    An input file with the constants for the DRS timing calibration
    [Not used right now, keep it 0]

 delays:
    A file with the delays of the individual channels
    [Not available right now, keep it 0]

 outpath:
    The path to which the output files are written


 To run the macro from the command line (assuming you are in a directory
 Mars/build where you have built your Mars environment) you can do

    root ../hawc/callisto.C\(\"20191002_018.fits.fz\",\"20191002_013.drs.fits\"\)

 or from within root

    [0] .x ../hawc/callisto.C("20191002_018.fits.fz", "20191002_013.drs.fits")

******************************************************************/
int callisto(const char *datafile, const char *drsfile,  bool ismc,
             const char *outpath=".")
{
    // ======================================================

    const char *drstime = 0;
    const char *delays  = 0;

    // ======================================================

    // true:  Display correctly mapped pixels in the camera displays
    //        but the value-vs-index plot is in software/spiral indices
    // false: Display pixels in hardware/linear indices,
    //        but the order is the camera display is distorted.
    //        false is assumed automatically for files with the ISMC flag set.
    bool usemap = true;

    // mapping file (found in Mars/hawc)
    const char *mmap = usemap ? "../hawc/FAMOUSmap170719.txt": NULL;

    //const char *pulse_template = "template-pulse.root";

    // Define a list of defect pixels here (software index)
    // They get interpolated from their neighbors
    // (if there are at least three valid neighbors)
    // The bahaviour can be altered in the corresponding task
    // (MBadPixelsTreat)
    MBadPixelsCam badpixels;
    badpixels.InitSize(64);
    badpixels[61].SetUnsuitable(MBadPixelsPix::kUnsuitable);
    badpixels[62].SetUnsuitable(MBadPixelsPix::kUnsuitable);
    badpixels[63].SetUnsuitable(MBadPixelsPix::kUnsuitable);

    // Range in which the pulse extraction searches for the
    // pulse (in samples).
    const int first_slice = 250;
    const int last_slice  = 330;

    // Calibration constant (for the moment a single constant to
    // convert the extracted charge to photo-electrons)
    //double scale = 1./22.553;//0.2;
    double scale = 1./17.557;

    // Three pixels have a slightly different gain
    // so there signal must be attenuated
    // THIS ONLY HAS TO BE USED FOR DATA WITH THE RESISTORS IN PLACE!!
    MArrayD calib(64);
    calib.Reset(1);
    if (!ismc)
    {
        calib[33] = 1./0.82;
        calib[37] = 1./0.82;
        calib[43] = 1./0.82;
    }

    // ------------------------------------------------------

    Long_t max = 0;  // All

    // ======================================================

    // Check if the requested mapping file is available
    if (mmap && gSystem->AccessPathName(mmap, kFileExists))
    {
        gLog << err << "ERROR - Cannot access mapping file '" << mmap << "'" << endl;
        return 11;
    }

    // -------------------------------------------------------

    // Check if the requested DRS time calibration constants are available
    MDrsCalibrationTime timecam;
    if (drstime && !timecam.ReadFits(drstime))
    {
        gLog << err << "ERROR - Could not get MDrsCalibrationTime from " << drstime << endl;
        return 21;
    }

    if (delays)
    {
        TGraph g(delays);
        if (g.GetN()!=1440)
        {
            gLog << err << "Error reading file " << delays << endl;
            return 22;
        }

        timecam.SetDelays(g);
    }

    // ------------------------------------------------------

    // Check and read the channel delays
    if (drstime && delays)
    {
        TGraph g(delays);
        if (g.GetN()!=1440)
        {
            gLog << err << "Error reading file " << delays << endl;
            return 41;
        }

        timecam.SetDelays(g);
    }

    // -------------------------------------------------------

    // Check and read the DRS calibration constants
    MDrsCalibration drscalib300;
    if (drsfile && !drscalib300.ReadFits(drsfile))
        return 31;

    // ======================================================

    gLog.Separator("Callisto");
    gLog << all;
    gLog << "Data file: " << datafile << '\n';
    if (drsfile)
        gLog << "DRS Calib: " << drsfile  << '\n';
    if (drstime)
        gLog << "DRS Time:  " << drstime  << '\n';
    if (delays)
        gLog << "Delays:    " << delays   << '\n';
    gLog << "Outpath:   " << outpath  << '\n';
    gLog << endl;

    // ------------------------------------------------------

    gStyle->SetOptFit(kTRUE);

    // ===================================================================

    gLog << endl;
    gLog.Separator("Calibrating data");

    // Instantiate the list of tasks
    MTaskList tlist5;

    // Instantiate the list of data containers
    MParList plist5;
    plist5.AddToList(&tlist5);
    plist5.AddToList(&badpixels);
    if (drsfile)
        plist5.AddToList(&drscalib300);
    if (drstime)
        plist5.AddToList(&timecam);

    // Instantiate the camera geometry
    MGeomCamFAMOUS geom;
    plist5.AddToList(&geom);

    // Instantiate the status display
    MStatusDisplay *d = new MStatusDisplay;

    // Instantiate the event loop
    MEvtLoop loop5("CalibratingData");
    loop5.SetDisplay(d);
    loop5.SetParList(&plist5);

    // ------------------ Setup the tasks ---------------

    MDirIter files(datafile);

    // Instantiate the reading task
    // You can use
    //    read5.AddFiles("*.fits.fz")
    // for example to read more than one file at once
    MRawFitsRead read5;
    read5.AddFiles(files);
    if (mmap)
        read5.LoadMap(mmap);

    // Instantiate the histogram to be filled with the rates
    MH3 hrate("MRawRunHeader.GetFileID", "int(MRawEvtHeader.GetTriggerID)&0xff00");
    hrate.SetWeight("1./TMath::Max(MRawRunHeader.GetRunLength,1.)");
    hrate.SetName("Rate");
    hrate.SetTitle("Event rate [Hz];File Id;Trigger Type;");
    hrate.InitLabels(MH3::kLabelsXY);
    hrate.DefineLabelY(    0, "Data"); // What if TriggerID==0 already???
    hrate.DefineLabelY(0x100, "Cal");
    hrate.DefineLabelY(0x400, "Ped");
    // hrate.DefaultLabelY("ERROR");

    // Instantiate the task to fill therate histogram
    MFillH fill5a(&hrate);

    // Instantiate the task to ensure proper sizing of all containers
    MGeomApply apply5;

    // Instantiate the task to apply the drs calibration constants
    MDrsCalibApply drsapply5;
    drsapply5.SetMaxNumPrevEvents(0); // Switched off step-correction -> crashes due to the requirement of N*9 ch

    // Instantiate the filter to select only physics events
    MFDataPhrase filterdat("(int(MRawEvtHeader.GetTriggerID)&0xff00)==0", "SelectDat");

    // ---
/*
    MExtractTimeAndChargeSpline extractor5dat;
    extractor5dat.SetRange(first_slice, last_slice);
    extractor5dat.SetRiseTimeHiGain(rise_time_dat);
    extractor5dat.SetFallTimeHiGain(fall_time_dat);
    extractor5dat.SetHeightTm(heighttm);
    extractor5dat.SetChargeType(type);
    extractor5dat.SetSaturationLimit(600000);
    extractor5dat.SetNoiseCalculation(kFALSE);
*/

    // Instantiate the digital filter (weighted sliding average) to clean the data
    // Note that the weights are not adapted yet to HAWC's Eye
    // A better filter might be worth to think about
    MFilterData filterdata1;

    // Instatiate task to extract the maximum of the pulse (correspondins to
    // a weighted integral) and the position of the leading edge between
    // first_slice and last_slice as charge and arrival time
    MExtractFACT extractor5dat("ExtractPulse");
    extractor5dat.SetRange(first_slice, last_slice);
    extractor5dat.SetNoiseCalculation(kFALSE);

    // Instantiate task which applies the calibration constants
    MCalibrateFact conv5;
    conv5.SetScale(scale);
    conv5.SetCalibConst(calib);

    // Instantiate task which applies the DRS time calibration
    MCalibrateDrsTimes calctm5;
    calctm5.SetNameUncalibrated("UncalibratedTimes");

    // Instantiate task to interpolate bad pixels
    MBadPixelsTreat treat5;
    treat5.SetProcessPedestalRun(kFALSE);
    treat5.SetProcessPedestalEvt(kFALSE);

    // Instantiate histograms to display charges
    MHCamEvent evt5b(0, "ExtSig",   "Extracted signal;;S [mV#cdot sl]");
    MHCamEvent evt5c(0, "CalSig",   "Calibrated and interpolated signal;;S [~phe]");
    MHCamEvent evt5d(4, "ExtSigTm", "Extracted time;;T [sl]");
    MHCamEvent evt5e(6, "CalSigTm", "Calibrated and interpolated time;;T [ns]");

    // Instantiate task to fill those histograms
    MFillH fill5b(&evt5b, "MExtractedSignalCam", "FillExtSig");
    MFillH fill5c(&evt5c, "MSignalCam",          "FillCalSig");
    MFillH fill5d(&evt5d, "MArrivalTimeCam",     "FillExtTm");
    MFillH fill5e(&evt5e, "MSignalCam",          "FillCalTm");

    // Setup those histograms to fit a gaussian to the distribution
    fill5c.SetDrawOption("gaus");
    fill5d.SetDrawOption("gaus");
    fill5e.SetDrawOption("gaus");

    // Instantiate the task to apply the software trigger
    MSoftwareTriggerCalc swtrig;

    // This is an alternative if more than one file should be read in a single loop
    // In this case the output file name of each file is created with this rule
    // from the input file name. Note that the filename of the output file
    // with the status display must then be explicitly given.
    //
    //const TString fname(Form("s/([0-9]+_[0-9]+)[.]fits([.][fg]z)?$/%s\\/$1_C.root/",
    //                         MJob::Esc(outpath).Data()));
    //MWriteRootFile write5(2, fname, "RECREATE", "Calibrated Data");

    /*
    // Convert the name of the input file to the name of the output file
    TString fname = gSystem->ConcatFileName(outpath, gSystem->BaseName(datafile));
    fname.ReplaceAll(".fits.gz", ".root");
    fname.ReplaceAll(".fits.fz", ".root");
    fname.ReplaceAll(".fits",    ".root");
    fname.ReplaceAll("_D_",      "_C_");

    gSystem->ExpandPathName(fname);
    */

    const TString rule(Form("s/([0-9]+)([._])([0-9]+)(_[DPC])?([_].*)?([.]fits([.]fz)?)$/%s\\/$1$2$3_Y$5.root/",
                            MJob:: Esc(outpath).Data()));

    // Instantitate the writing task and setup the writing
    MWriteRootFile write5(2, rule, "RECREATE", "Calibrated Data");
    write5.AddContainer("MSignalCam",      "Events");
    write5.AddContainer("MRawEvtHeader",   "Events");
    write5.AddContainer("MSoftwareTrigger","Events");
    write5.AddContainer("MRawRunHeader",   "RunHeaders");
    write5.AddContainer("MGeomCam",        "RunHeaders");

    write5.AddContainer("MMcCorsikaRunHeader", "RunHeaders", kFALSE);
    write5.AddContainer("MCorsikaRunHeader",   "RunHeaders", kFALSE);
    write5.AddContainer("MMcRunHeader",        "RunHeaders", kFALSE);
    write5.AddContainer("MCorsikaEvtHeader",   "Events", kFALSE);
    write5.AddContainer("MMcEvt",              "Events", kFALSE);
    write5.AddContainer("IncidentAngle",       "Events", kFALSE);
    write5.AddContainer("MPointingPos",        "Events", kFALSE);
    write5.AddContainer("MSimSourcePos",       "Events", kFALSE);
    write5.AddContainer("MTime",               "Events", kFALSE);
    write5.AddContainer("MRawBoardsFACT",      "Events", kFALSE);
    write5.AddContainer("MSrcPosCam",          "Events", kFALSE);

    // ------------------ Setup histograms and fill tasks ----------------

    // Instantitate the task list and setp the list
    MTaskList tlist5dat;
    tlist5dat.AddToList(&fill5b);
    tlist5dat.AddToList(&fill5c);
    tlist5dat.AddToList(&fill5d);
    tlist5dat.AddToList(&fill5e);
    tlist5dat.SetFilter(&filterdat);

    tlist5.AddToList(&read5);
    tlist5.AddToList(&apply5);
    tlist5.AddToList(&drsapply5);
    tlist5.AddToList(&fill5a);
    tlist5.AddToList(&swtrig);
    tlist5.AddToList(&filterdata1);
    tlist5.AddToList(&extractor5dat);
    tlist5.AddToList(&calctm5);
    tlist5.AddToList(&conv5);
    tlist5.AddToList(&treat5);
    tlist5.AddToList(&filterdat);
    tlist5.AddToList(&tlist5dat);
    tlist5.AddToList(&write5);

    // run the eventloop
    if (!loop5.Eventloop(max))
        return 18;

    // Check if the display was closed (deleted) by the user
    if (!loop5.GetDisplay())
        return 19;

    // ============================================================

    TString fname = write5.GetFileName();
    fname.ReplaceAll(".root", "-display.root");

    // Write the status display to the file
    TString title = "--  Calibrated signal [";
    title += datafile;
    title += "] --";
    d->SetTitle(title, kFALSE);

    d->SaveAsRoot(fname);

    return 0;
}