/* ======================================================================== *\
!
! *
! * This file is part of MARS, the MAGIC Analysis and Reconstruction
! * Software. It is distributed to you in the hope that it can be a useful
! * and timesaving tool in analysing Data of imaging Cerenkov telescopes.
! * It is distributed WITHOUT ANY WARRANTY.
! *
! * Permission to use, copy, modify and distribute this software and its
! * documentation for any purpose is hereby granted without fee,
! * provided that the above copyright notice appear in all copies and
! * that both that copyright notice and this permission notice appear
! * in supporting documentation. It is provided "as is" without express
! * or implied warranty.
! *
!
!
!   Author(s): Thomas Bretz, 1/2004 <mailto:tbretz@astro.uni-wuerzburg.de>
!              Markus Gaug, 02/2004 <mailto:markus@ifae.es>
!
!   Copyright: MAGIC Software Development, 2000-2004
!
!
\* ======================================================================== */
/////////////////////////////////////////////////////////////////////////////
//
//  MJCalibration
//
//  Do one calibration loop over serious of runs with the same pulser 
//  colour and the same intensity. The following containers (rectangular) and 
//  tasks (ellipses) are called to produce an MCalibrationChargeCam and to 
//  update the MCalibrationQECam: (MCalibrate is not called from this class)
//
//Begin_Html
/*
<img src="images/CalibClasses.gif">
*/
//End_Html
//
// Different signal extractors can be set with the command SetExtractor()
// Only extractors deriving from MExtractor can be set, default is MExtractSlidingWindow
//
// Different arrival time extractors can be set with the command SetTimeExtractor()
// Only extractors deriving from MExtractTime can be set, default is MExtractTimeSpline
//
// At the end of the eventloop, plots and results are displayed, depending on 
// the flags set (see DisplayResult()) 
// 
// If the flag SetFullDisplay() is set, all MHCameras will be displayed. 
// if the flag SetDataCheckDisplay() is set, only the most important ones are displayed 
// Otherwise, (default: SetNormalDisplay()), a good selection of plots is given
//
// If the flag SetDataCheck() is set, the calibration is used as in the data check at 
// La Palma, which mean especially running on raw data files.
// 
// The absolute light calibration devices Blind Pixel and PIN Diode can be switched on
// and off with the commands:
//
// - SetUseBlindPixel(Bool_t )
// - SetUsePINDiode(Bool_t )
//
// See also: MHCalibrationChargePix, MHCalibrationChargeCam, MHGausEvents
//           MHCalibrationChargeBlindPix, MHCalibrationChargePINDiode
//           MCalibrationChargePix, MCalibrationChargeCam, MCalibrationChargeCalc
//           MCalibrationChargeBlindPix, MCalibrationChargePINDiode,
//           MCalibrationQECam, MBadPixelsPix, MBadPixelsCam
//
// If the flag RelTimeCalibration() is set, a calibration of the relative arrival 
// times is also performed. The following containers (rectangular) and 
// tasks (ellipses) are called to produce an MCalibrationRelTimeCam used by  
// MCalibrateTime to correct timing offset between pixels: (MCalibrateTime is not 
// called from this class)
//
//Begin_Html
/*
<img src="images/RelTimeClasses.gif">
*/
//End_Html
//
// Different arrival time extractors can be set directly with the command SetTimeExtractor(MExtractor *)
//
// See also: MHCalibrationRelTimePix, MHCalibrationRelTimeCam, MHGausEvents
//           MCalibrationRelTimePix, MCalibrationRelTimeCam
//           MBadPixelsPix, MBadPixelsCam
//
/////////////////////////////////////////////////////////////////////////////
#include "MJCalibration.h"

#include <TFile.h>
#include <TStyle.h>
#include <TCanvas.h>
#include <TSystem.h>
#include <TLine.h>
#include <TLatex.h>
#include <TLegend.h>
#include <TRegexp.h>
#include <TPaveText.h>
#include <TPaveStats.h>

#include "MLog.h"
#include "MLogManip.h"

#include "MRunIter.h"
#include "MSequence.h"
#include "MParList.h"
#include "MTaskList.h"
#include "MEvtLoop.h"

#include "MHCamera.h"
#include "MGeomCam.h"

#include "MPedestalCam.h"
#include "MCalibrationCam.h"
#include "MCalibrationQECam.h"
#include "MCalibrationQEPix.h"
#include "MCalibrationChargeCam.h"
#include "MCalibrationChargePix.h"
#include "MCalibrationChargePINDiode.h"
#include "MCalibrationChargeBlindPix.h"
#include "MCalibrationChargeBlindCam.h"
#include "MCalibrationChargeBlindCamOneOldStyle.h"
#include "MCalibrationChargeBlindCamTwoNewStyle.h"
#include "MCalibrationChargeCalc.h"

#include "MHGausEvents.h"
#include "MHCalibrationCam.h"
#include "MHCalibrationChargeCam.h"
#include "MHCalibrationChargeBlindCam.h"
#include "MHCalibrationChargePINDiode.h"
#include "MHCalibrationRelTimeCam.h"
#include "MCalibrationRelTimeCam.h"
#include "MCalibrationRelTimeCalc.h"

#include "MReadMarsFile.h"
#include "MRawFileRead.h"
#include "MGeomApply.h"
#include "MTaskEnv.h"
#include "MBadPixelsMerge.h"
#include "MBadPixelsCam.h"
#include "MExtractTime.h"
#include "MExtractor.h"
#include "MExtractPINDiode.h"
#include "MExtractBlindPixel.h"
#include "MExtractSlidingWindow.h"
#include "MExtractTimeFastSpline.h"
#include "MFCosmics.h"
#include "MContinue.h"
#include "MFillH.h"

#include "MArrivalTimeCam.h"

#include "MStatusDisplay.h"

ClassImp(MJCalibration);

using namespace std;

const Int_t MJCalibration::gkIFAEBoxInaugurationRun       = 20113;
const Int_t MJCalibration::gkSecondBlindPixelInstallation = 31693;
const Int_t MJCalibration::gkThirdBlindPixelInstallation  = 99999;

const Double_t MJCalibration::fgConvFADC2PheMin           = 0.;
const Double_t MJCalibration::fgConvFADC2PheMax           = 1.5;
const Double_t MJCalibration::fgConvFADC2PhotMin          = 0.; 
const Double_t MJCalibration::fgConvFADC2PhotMax          = 10.; 
const Double_t MJCalibration::fgQEMin                     = 0.;
const Double_t MJCalibration::fgQEMax                     = 0.3;

const Float_t  MJCalibration::fgRefConvFADC2PheInner      = 0.14;       
const Float_t  MJCalibration::fgRefConvFADC2PheOuter      = 0.45;       
const Float_t  MJCalibration::fgRefConvFADC2PhotInner     = 0.8; 
const Float_t  MJCalibration::fgRefConvFADC2PhotOuter     = 3.8; 
const Float_t  MJCalibration::fgRefQEInner                = 0.18;            
const Float_t  MJCalibration::fgRefQEOuter                = 0.12;


// --------------------------------------------------------------------------
//
// Default constructor. 
//
// - Sets fRuns to 0, fExtractor to NULL, fTimeExtractor to NULL, fColor to kNONE, 
//   fDisplay to kNormalDisplay, fRelTime to kFALSE, fDataCheck to kFALSE, 
// - SetUseBlindPixel()
// - SetUsePINDiode()
//
MJCalibration::MJCalibration(const char *name, const char *title) 
    : fRuns(0), fExtractor(NULL), fTimeExtractor(NULL),
      fColor(MCalibrationCam::kNONE), fDisplayType(kNormalDisplay),
      fRelTimes(kFALSE), fDataCheck(kFALSE), fDebug(kFALSE)
{
    fName  = name  ? name  : "MJCalibration";
    fTitle = title ? title : "Tool to create the calibration constants for one calibration run";

    SetUseBlindPixel();
    SetUsePINDiode();
}

// --------------------------------------------------------------------------
//
// Display the results in MStatusDisplay: 
//
// - Add "Calibration" to the MStatusDisplay title
// - Retrieve the MGeomCam from MParList
// - Initialize the following MHCamera's:
//   1)  MCalibrationPix::GetMean()
//   2)  MCalibrationPix::Sigma()
//   3)  MCalibrationChargePix::GetRSigma()
//   4)  MCalibrationChargePix::GetRSigmaPerCharge()
//   5)  MCalibrationChargePix::GetPheFFactorMethod()
//   6)  MCalibrationChargePix::GetMeanConvFADC2Phe()
//   7)  MCalibrationChargePix::GetMeanFFactorFADC2Phot()
//   8)  MCalibrationQEPix::GetQECascadesFFactor()
//   9)  MCalibrationQEPix::GetQECascadesBlindPixel()
//   10) MCalibrationQEPix::GetQECascadesPINDiode()
//   11) MCalibrationQEPix::GetQECascadesCombined()
//   12) MCalibrationQEPix::IsAverageQEFFactorAvailable()
//   13) MCalibrationQEPix::IsAverageQEBlindPixelAvailable()
//   14) MCalibrationQEPix::IsAverageQEPINDiodeAvailable()
//   15) MCalibrationQEPix::IsAverageQECombinedAvailable()
//   16) MCalibrationChargePix::IsHiGainSaturation()
//   17) MCalibrationPix::GetHiLoMeansDivided()
//   18) MCalibrationPix::GetHiLoSigmasDivided()
//   19) MCalibrationChargePix::GetHiGainPickup()
//   20) MCalibrationChargePix::GetLoGainPickup()
//   21) MCalibrationChargePix::GetHiGainBlackout()
//   22) MCalibrationChargePix::GetLoGainBlackout()
//   23) MCalibrationPix::IsExcluded()
//   24) MBadPixelsPix::IsUnsuitable(MBadPixelsPix::kUnsuitableRun)
//   25) MBadPixelsPix::IsUnsuitable(MBadPixelsPix::kUnreliableRun)
//   26) MBadPixelsPix::IsUncalibrated(MBadPixelsPix::kHiGainOscillating)
//   27) MBadPixelsPix::IsUncalibrated(MBadPixelsPix::kLoGainOscillating)
//   28) MCalibrationChargePix::GetAbsTimeMean()
//   29) MCalibrationChargePix::GetAbsTimeRms()
//
// If the flag SetFullDisplay() is set, all MHCameras will be displayed. 
// if the flag SetDataCheckDisplay() is set, only the most important ones are displayed 
// and otherwise, (default: SetNormalDisplay()), a good selection of plots is given
//
void MJCalibration::DisplayResult(MParList &plist)
{

    if (!fDisplay)
        return;

    //
    // Update display
    //
    TString title = fDisplay->GetTitle();
    title += "--  Calibration ";
    title += fSequence.IsValid() ? Form("calib%06d", fSequence.GetSequence()) : (const char*)fRuns->GetRunsAsString();
    title += "  --";
    fDisplay->SetTitle(title);

    //
    // Get container from list
    //
    MGeomCam &geomcam = *(MGeomCam*)plist.FindObject("MGeomCam");

    // Create histograms to display
    MHCamera disp1 (geomcam, "Charge",            "Fitted Mean Signal (Charges)");
    MHCamera disp2 (geomcam, "SigmaCharge",       "Sigma of Fitted Signal");
    MHCamera disp3 (geomcam, "RSigma",            "Reduced Sigmas");
    MHCamera disp4 (geomcam, "RSigmaPerCharge",   "Reduced Sigma per Charge");
    MHCamera disp5 (geomcam, "NumPhes",           "Number Photo-electrons");
    MHCamera disp6 (geomcam, "ConvFADC2Phes",     "Conversion Factor to Phes");
    MHCamera disp7 (geomcam, "TotalFFactor",      "Total F-Factor(F-Factor Method)");
    MHCamera disp8 (geomcam, "CascadesQEFFactor", "Cascades QE (F-Factor Method)");
    MHCamera disp9 (geomcam, "CascadesQEBlindPix","Cascades QE (Blind Pixel Method)");
    MHCamera disp10(geomcam, "CascadesQEPINDiode","Cascades QE (PIN Diode Method)");
    MHCamera disp11(geomcam, "CascadesQECombined","Cascades QE (Combined Method)");
    MHCamera disp12(geomcam, "FFactorValid",      "Pixels with valid F-Factor calibration");
    MHCamera disp13(geomcam, "BlindPixelValid",   "Pixels with valid BlindPixel calibration");
    MHCamera disp14(geomcam, "PINdiodeValid",     "Pixels with valid PINDiode calibration");
    MHCamera disp15(geomcam, "CombinedValid",     "Pixels with valid Combined calibration");
    MHCamera disp16(geomcam, "Saturation",        "Pixels with saturated Hi Gain");
    MHCamera disp17(geomcam, "ConversionMeans",   "Conversion HiGain.vs.LoGain Means");
    MHCamera disp18(geomcam, "ConversionSigmas",  "Conversion HiGain.vs.LoGain Sigmas");
    MHCamera disp19(geomcam, "HiGainPickup",      "Number Pickup events Hi Gain");
    MHCamera disp20(geomcam, "LoGainPickup",      "Number Pickup events Lo Gain");
    MHCamera disp21(geomcam, "HiGainBlackout",    "Number Blackout events Hi Gain");
    MHCamera disp22(geomcam, "LoGainBlackout",    "Number Blackout events Lo Gain");
    MHCamera disp23(geomcam, "Excluded",          "Pixels previously excluded");
    MHCamera disp24(geomcam, "UnSuitable",        "Pixels not suited for further analysis");
    MHCamera disp25(geomcam, "UnReliable",        "Pixels not reliable for further analysis");
    MHCamera disp26(geomcam, "HiGainOscillating", "Oscillating Pixels High Gain");
    MHCamera disp27(geomcam, "LoGainOscillating", "Oscillating Pixels Low Gain");
    MHCamera disp28(geomcam, "AbsTimeMean",       "Abs. Arrival Times");
    MHCamera disp29(geomcam, "AbsTimeRms",        "RMS of Arrival Times");
    MHCamera disp30(geomcam, "MeanTime",          "Mean Rel. Arrival Times");
    MHCamera disp31(geomcam, "SigmaTime",         "Sigma Rel. Arrival Times");
    MHCamera disp32(geomcam, "TimeProb",          "Probability of Time Fit");
    MHCamera disp33(geomcam, "TimeNotFitValid",   "Pixels with not valid fit results");
    MHCamera disp34(geomcam, "TimeOscillating",   "Oscillating Pixels");
    MHCamera disp35(geomcam, "TotalConv",         "Conversion Factor to photons");

    // Fitted charge means and sigmas
    disp1.SetCamContent(fCalibrationCam,  0);
    disp1.SetCamError(  fCalibrationCam,  1);
    disp2.SetCamContent(fCalibrationCam,  2);
    disp2.SetCamError(  fCalibrationCam,  3);

    // Reduced Sigmas and reduced sigmas per charge
    disp3.SetCamContent(fCalibrationCam,  5);
    disp3.SetCamError(  fCalibrationCam,  6);
    disp4.SetCamContent(fCalibrationCam,  7);
    disp4.SetCamError(  fCalibrationCam,  8);

    // F-Factor Method
    disp5.SetCamContent(fCalibrationCam,  9);
    disp5.SetCamError(  fCalibrationCam, 10);
    disp6.SetCamContent(fCalibrationCam, 11);
    disp6.SetCamError(  fCalibrationCam, 12);
    disp7.SetCamContent(fCalibrationCam, 13);
    disp7.SetCamError(  fCalibrationCam, 14);

    // Quantum Efficiencies
    disp8.SetCamContent (fQECam, 0 );
    disp8.SetCamError   (fQECam, 1 );
    disp9.SetCamContent (fQECam, 2 );
    disp9.SetCamError   (fQECam, 3 );
    disp10.SetCamContent(fQECam, 4 );
    disp10.SetCamError  (fQECam, 5 );
    disp11.SetCamContent(fQECam, 6 );
    disp11.SetCamError  (fQECam, 7 );

    // Valid flags
    disp12.SetCamContent(fQECam, 8 );
    disp13.SetCamContent(fQECam, 9 );
    disp14.SetCamContent(fQECam, 10);
    disp15.SetCamContent(fQECam, 11);

    // Conversion Hi-Lo
    disp16.SetCamContent(fCalibrationCam, 25);
    disp17.SetCamContent(fCalibrationCam, 16);
    disp17.SetCamError  (fCalibrationCam, 17);
    disp18.SetCamContent(fCalibrationCam, 18);
    disp18.SetCamError  (fCalibrationCam, 19);

    // Pickup and Blackout
    disp19.SetCamContent(fCalibrationCam, 21);
    disp20.SetCamContent(fCalibrationCam, 22);
    disp21.SetCamContent(fCalibrationCam, 23);
    disp22.SetCamContent(fCalibrationCam, 24);

    // Pixels with defects
    disp23.SetCamContent(fCalibrationCam, 20);
    disp24.SetCamContent(fBadPixels, 6);
    disp25.SetCamContent(fBadPixels, 7);

    // Oscillations
    disp26.SetCamContent(fBadPixels, 10);
    disp27.SetCamContent(fBadPixels, 11);

    // Arrival Times
    disp28.SetCamContent(fCalibrationCam, 26);
    disp28.SetCamError(  fCalibrationCam, 27);
    disp29.SetCamContent(fCalibrationCam, 27);

    disp1.SetYTitle("Q [FADC counts]");
    disp2.SetYTitle("\\sigma_{Q} [FADC counts]");

    disp3.SetYTitle("\\sqrt{\\sigma^{2}_{Q} - RMS^{2}_{Ped}} [FADC Counts]");
    disp4.SetYTitle("Red.Sigma/<Q> [1]");

    disp5.SetYTitle("Photo-electons [1]");
    disp6.SetYTitle("Conv.Factor [PhE/FADC counts]");
    disp7.SetYTitle("Total F-Factor [1]");

    disp8.SetYTitle("QE [1]");
    disp9.SetYTitle("QE [1]");
    disp10.SetYTitle("QE [1]");
    disp11.SetYTitle("QE [1]");

    disp12.SetYTitle("[1]");
    disp13.SetYTitle("[1]");
    disp14.SetYTitle("[1]");
    disp15.SetYTitle("[1]");
    disp16.SetYTitle("[1]");

    disp17.SetYTitle("<Q>(High)/<Q>(Low) [1]");
    disp18.SetYTitle("\\sigma_{Q}(High)/\\sigma_{Q}(Low) [1]");

    disp19.SetYTitle("[1]");
    disp20.SetYTitle("[1]");
    disp21.SetYTitle("[1]");
    disp22.SetYTitle("[1]");
    //    disp23.SetYTitle("[1]");
    //    disp24.SetYTitle("[1]");
    //    disp25.SetYTitle("[1]");
    disp26.SetYTitle("[1]");
    disp27.SetYTitle("[1]");

    disp28.SetYTitle("Mean Abs. Time [FADC slice]");
    disp29.SetYTitle("RMS Abs. Time [FADC slices]");

    disp35.SetYTitle("Conv.Factor [Ph/FADC counts]");

    for (UInt_t i=0;i<geomcam.GetNumPixels();i++)
      {

        MCalibrationChargePix &pix = (MCalibrationChargePix&)fCalibrationCam[i];
        MCalibrationQEPix     &qe  = (MCalibrationQEPix&)    fQECam         [i];

        if (!pix.IsFFactorMethodValid())
          continue;

        const Float_t convphe  = pix.GetMeanConvFADC2Phe();
        const Float_t quaeff   = qe.GetQECascadesFFactor(0.);
        
        disp35.Fill(i,convphe/quaeff);
        disp35.SetUsed(i);
      }
    

    if (fRelTimes)
    {
        disp30.SetCamContent(fRelTimeCam,0);
        disp30.SetCamError(  fRelTimeCam,1);
        disp31.SetCamContent(fRelTimeCam,2);
        disp31.SetCamError(  fRelTimeCam,3);
        disp32.SetCamContent(fRelTimeCam,4);
        disp33.SetCamContent(fBadPixels,20);
        disp34.SetCamContent(fBadPixels,21);
    
        disp30.SetYTitle("Time Offset [FADC units]");
        disp31.SetYTitle("Timing resolution [FADC units]");
        disp32.SetYTitle("P_{Time} [1]");
        disp33.SetYTitle("[1]");
        disp34.SetYTitle("[1]");
    }


    
    if (fDisplayType == kDataCheckDisplay)
    {
      
      TCanvas &c1 = fDisplay->AddTab("Fit.Charge");
      c1.Divide(3, 3);
      
      //
      // MEAN CHARGES
      // 
      
      c1.cd(1);
      gPad->SetBorderMode(0);
      gPad->SetTicks();
      MHCamera *obj1=(MHCamera*)disp1.DrawCopy("hist");
      //
      // for the datacheck, fix the ranges!!
      //
      // obj1->SetMinimum(fgChargeMin);
      // obj1->SetMaximum(fgChargeMax);
      //
      // Set the datacheck sizes:
      //
      FixDataCheckHist((TH1D*)obj1);
      obj1->SetStats(kFALSE);
      //
      // set reference lines
      //
      //        DisplayReferenceLines(obj1,0);
      
      c1.cd(4);
      gPad->SetBorderMode(0);
      obj1->SetPrettyPalette();
      obj1->Draw();
      
      c1.cd(7);
      gPad->SetBorderMode(0);
      gPad->SetTicks();
      TH1D *obj2 = (TH1D*)obj1->Projection(obj1->GetName());
      obj2->Draw();
      obj2->SetBit(kCanDelete);
      obj2->Fit("gaus","Q");
      TF1 *fun2 = obj2->GetFunction("gaus");
      fun2->SetLineColor(kYellow);
      gPad->Modified();
      gPad->Update();      
      TPaveStats *st = (TPaveStats*)obj2->GetListOfFunctions()->FindObject("stats");
      st->SetY1NDC(0.55);
      st->SetY2NDC(0.89);
      st->SetX1NDC(0.65);
      st->SetX2NDC(0.99);
      gPad->Modified();
      gPad->Update();      
      //
      // Set the datacheck sizes:
      //
      FixDataCheckHist(obj2);
      obj2->SetStats(1);
      
      //
      // Display the outliers as dead and noisy pixels
      //
      DisplayOutliers(obj2,"low-ampl.","high-ampl.");
      TLatex flattex;
      flattex.SetTextSize(0.07);
      const Double_t minl = obj2->GetBinCenter(obj2->GetXaxis()->GetFirst());
      const Double_t maxl = obj2->GetBinCenter(obj2->GetXaxis()->GetLast());
      flattex.DrawLatex(minl+0.015*(maxl-minl),obj2->GetBinContent(obj2->GetMaximumBin())/1.35,
                        Form("Flatfield precision: %4.2f%%",
                             fun2->GetParameter(2)/fun2->GetParameter(1)*100.));
      
      //
      // REDUCED SIGMAS
      // 
      
      c1.cd(2);
      gPad->SetBorderMode(0);
      gPad->SetTicks();
      MHCamera *obj3=(MHCamera*)disp4.DrawCopy("hist");
      //
      // for the datacheck, fix the ranges!!
      //
      // obj3->SetMinimum(fgChargeMin);
      // obj3->SetMaximum(fgChargeMax);
      //
      // Set the datacheck sizes:
      //
      FixDataCheckHist((TH1D*)obj3);
      obj3->SetStats(kFALSE);
      //
      // set reference lines
      //
      //        DisplayReferenceLines(obj3,0);
      
      c1.cd(5);
      gPad->SetBorderMode(0);
      obj3->SetPrettyPalette();
      obj3->Draw();
      
      c1.cd(8);
      gPad->SetBorderMode(0);
      if (geomcam.InheritsFrom("MGeomCamMagic"))
        DisplayDoubleProject(&disp4, "dead", "noisy");
      
      //
      // PHOTO ELECTRONS
      // 
      
      c1.cd(3);
      gPad->SetBorderMode(0);
      gPad->SetTicks();
      MHCamera *obj4=(MHCamera*)disp5.DrawCopy("hist");
      //
      // for the datacheck, fix the ranges!!
      //
      // obj3->SetMinimum(fgChargeMin);
      // obj3->SetMaximum(fgChargeMax);
      //
      // Set the datacheck sizes:
      //
      FixDataCheckHist((TH1D*)obj4);
      obj4->SetStats(kFALSE);
      //
      // set reference lines
      //
      //        DisplayReferenceLines(obj3,0);
      
      c1.cd(6);
      gPad->SetBorderMode(0);
      obj4->SetPrettyPalette();
      obj4->Draw();
      
      c1.cd(9);
      gPad->SetBorderMode(0);
      if (geomcam.InheritsFrom("MGeomCamMagic"))
        DisplayDoubleProject(&disp5, "dead", "noisy");
      
      //
      // CONVERSION FACTORS
      // 

      TCanvas &c2 = fDisplay->AddTab("Conversion");
      c2.Divide(3,3);
      
      c2.cd(1);
      gPad->SetBorderMode(0);
      gPad->SetTicks();
      MHCamera *obj5=(MHCamera*)disp6.DrawCopy("hist");
      //
      // for the datacheck, fix the ranges!!
      //
      obj5->SetMinimum(fgConvFADC2PheMin);
      obj5->SetMaximum(fgConvFADC2PheMax);
      //
      // Set the datacheck sizes:
      //
      FixDataCheckHist((TH1D*)obj5);
      obj5->SetStats(kFALSE);
      //
      // set reference lines
      //
      DisplayReferenceLines(obj5,2);
      
      c2.cd(4);
      gPad->SetBorderMode(0);
      obj5->SetPrettyPalette();
      obj5->Draw();
      
      c2.cd(7);
      gPad->SetBorderMode(0);
      if (geomcam.InheritsFrom("MGeomCamMagic"))
        DisplayDoubleProject(&disp6, "noisy", "dead");
      
      //
      // QUANTUM EFFICIENCY
      //
      
      c2.cd(2);
      gPad->SetBorderMode(0);
      gPad->SetTicks();
      MHCamera *obj6=(MHCamera*)disp8.DrawCopy("hist");
      //
      // for the datacheck, fix the ranges!!
      //
      obj6->SetMinimum(fgQEMin);
      obj6->SetMaximum(fgQEMax);
      //
      // Set the datacheck sizes:
      //
      FixDataCheckHist((TH1D*)obj6);
      obj6->SetStats(kFALSE);
      //
      // set reference lines
      //
      DisplayReferenceLines(obj6,0);
      
      c2.cd(5);
      gPad->SetBorderMode(0);
      obj6->SetPrettyPalette();
      obj6->Draw();
      
      c2.cd(8);
      gPad->SetBorderMode(0);
      if (geomcam.InheritsFrom("MGeomCamMagic"))
        DisplayDoubleProject(&disp8, "noisy", "dead");
      
      //
      // CONVERSION FADC TO PHOTONS
      // 
      
      c2.cd(3);
      gPad->SetBorderMode(0);
      gPad->SetTicks();
      MHCamera *obj7=(MHCamera*)disp35.DrawCopy("hist");
      //
      // for the datacheck, fix the ranges!!
      //
      obj7->SetMinimum(fgConvFADC2PhotMin);
      obj7->SetMaximum(fgConvFADC2PhotMax);
      //
      // Set the datacheck sizes:
      //
      FixDataCheckHist((TH1D*)obj7);
      obj7->SetStats(kFALSE);
      //
      // set reference lines
      //
      DisplayReferenceLines(obj7,1);
      
      c2.cd(6);
      gPad->SetBorderMode(0);
      obj7->SetPrettyPalette();
      obj7->Draw();
      c2.cd(9);
      gPad->SetBorderMode(0);
      if (geomcam.InheritsFrom("MGeomCamMagic"))
        DisplayDoubleProject(&disp35, "noisy", "dead");

      //
      // UNSUITABLE PIXELS
      //
      TCanvas &c4 = fDisplay->AddTab("Defect");
      c4.Divide(2,2);
      
      c4.cd(1);
      gPad->SetBorderMode(0);
      gPad->SetTicks();
      MHCamera *obj8=(MHCamera*)disp24.DrawCopy("hist");
      //
      // for the datacheck, fix the ranges!!
      //
      const Double_t max = 11.;
      obj8->SetMinimum(0.);
      obj8->SetMaximum(11.);
      //
      // Set the datacheck sizes:
      //
      FixDataCheckHist((TH1D*)obj8);
      obj8->SetStats(kFALSE);

      gStyle->SetPalette(1);
      const Int_t numcol = gStyle->GetNumberOfColors()-3;
      
      TPaveText *pave = new TPaveText(0.0,0.0,0.99,0.99);
      pave->SetBit(kCanDelete);
      pave->ConvertNDCtoPad();
      pave->SetTextSize(0.05);
      pave->AddText("  ");
      TText *t1 = pave->AddText(Form("Signal smaller 3 Pedestal RMS:                 %3i pixels",
                                       CountBadPixels(&disp24,1)));
      t1->SetTextColor(gStyle->GetColorPalette(Int_t(1./max*numcol + 1.)));
      t1->SetTextAlign(12);
      TText *t2 = pave->AddText(Form("%s%3i%s","Signal Rel. error too large:                          ",
                                       CountBadPixels(&disp24,2)," pixels"));
      t2->SetTextColor(gStyle->GetColorPalette(Int_t(2./max*numcol + 1.)));
      t2->SetTextAlign(12);
      TText *t3 = pave->AddText(Form("Signal Sigma smaller than Pedestal RMS: %3i pixels",
                                       CountBadPixels(&disp24,3)));
      t3->SetTextColor(gStyle->GetColorPalette(Int_t(3./max*numcol + 1.)));
      t3->SetTextAlign(12);
      TText *t4 = pave->AddText(Form("Low Gain Saturation:                                   %3i pixels",
                                       CountBadPixels(&disp24,4)));
      t4->SetTextColor(gStyle->GetColorPalette(Int_t(4./max*numcol + 1.)));
      t4->SetTextAlign(12);
      TText *t5 = pave->AddText(Form("Mean Arr. Time In First Extraction Bin:      %3i pixels",
                                       CountBadPixels(&disp24,5)));
      t5->SetTextColor(gStyle->GetColorPalette(Int_t(5./max*numcol + 1.)));
      t5->SetTextAlign(12);
      TText *t6 = pave->AddText(Form("Mean Arr. Time In Last 2 Extraction Bins: %3i pixels",
                                       CountBadPixels(&disp24,6)));
      t6->SetTextColor(gStyle->GetColorPalette(Int_t(6./max*numcol + 1.)));
      t6->SetTextAlign(12);
      TText *t7 = pave->AddText(Form("Deviating Number of Photo-electrons:      %3i pixels",
                                       CountBadPixels(&disp24,7)));
      t7->SetTextColor(gStyle->GetColorPalette(Int_t(7./max*numcol + 1.)));
      t7->SetTextAlign(12);
      TText *t8 = pave->AddText(Form("Deviating global F-Factor:                         %3i pixels",
                                       CountBadPixels(&disp24,8)));
      t8->SetTextColor(gStyle->GetColorPalette(Int_t(8./max*numcol + 1.)));
      t8->SetTextAlign(12);
      TText *t9 = pave->AddText(Form("Deviating Number of Photons:                  %3i pixels",
                                       CountBadPixels(&disp24,9)));
      t9->SetTextColor(gStyle->GetColorPalette(Int_t(9./max*numcol + 1.)));
      t9->SetTextAlign(12);
      TText *t10= pave->AddText(Form("Previously Excluded:                                  %3i pixels",
                                       CountBadPixels(&disp24,10)));
      t10->SetTextColor(gStyle->GetColorPalette(Int_t(10./max*numcol + 1.)));
      t10->SetTextAlign(12);
      pave->Draw();

      c4.cd(3);
      gPad->SetBorderMode(0);
      obj8->Draw();
      obj8->SetPrettyPalette();

      //
      // UNRELIABLE PIXELS
      // 
      
      c4.cd(2);
      gPad->SetBorderMode(0);
      gPad->SetTicks();
      MHCamera *obj9=(MHCamera*)disp25.DrawCopy("hist");
      //
      // for the datacheck, fix the ranges!!
      //
      const Double_t max2 = 8.;
      obj9->SetMinimum(0.);
      obj9->SetMaximum(max2);
      //
      // Set the datacheck sizes:
      //
      FixDataCheckHist((TH1D*)obj9);
      obj9->SetStats(kFALSE);

      gStyle->SetPalette(1);
      
      TPaveText *pave2 = new TPaveText(0.0,0.0,0.99,0.99);
      pave2->SetBit(kCanDelete);
      pave2->ConvertNDCtoPad();
      pave2->SetTextSize(0.05);
      pave2->AddText("  ");
      TText *tt1 = pave2->AddText(Form("High Gain Signals could not be fitted:   %3i pixels",
                                       CountBadPixels(&disp25,1)));
      tt1->SetTextColor(gStyle->GetColorPalette(Int_t(1./max2*numcol + 1.)));
      tt1->SetTextAlign(12);
      TText *tt2 = pave2->AddText(Form("Low  Gain Signals could not be fitted:   %3i pixels",
                                       CountBadPixels(&disp25,2)));
      tt2->SetTextColor(gStyle->GetColorPalette(Int_t(2./max2*numcol + 1.)));
      tt2->SetTextAlign(12);
      TText *tt3 = pave2->AddText(Form("Relative Arr. Times could not be fitted:  %3i pixels",
                                       CountBadPixels(&disp25,3)));
      tt3->SetTextColor(gStyle->GetColorPalette(Int_t(3./max2*numcol + 1.)));
      tt3->SetTextAlign(12);
      TText *tt4 = pave2->AddText(Form("High Gain Signals Oscillation:               %3i pixels",
                                       CountBadPixels(&disp25,4)));
      tt4->SetTextColor(gStyle->GetColorPalette(Int_t(4./max2*numcol + 1.)));
      tt4->SetTextAlign(12);
      TText *tt5 = pave2->AddText(Form("Low  Gain Signals Oscillation:                %3i pixels",
                                       CountBadPixels(&disp25,5)));
      tt5->SetTextColor(gStyle->GetColorPalette(Int_t(5./max2*numcol + 1.)));
      tt5->SetTextAlign(12); 
      TText *tt6 = pave2->AddText(Form("Relative Arr. Times Oscillation:              %3i pixels",
                                       CountBadPixels(&disp25,6)));
      tt6->SetTextColor(gStyle->GetColorPalette(Int_t(6./max2*numcol + 1.)));
      tt6->SetTextAlign(12);
      pave2->Draw();

      c4.cd(4);
      gPad->SetBorderMode(0);
      obj9->SetPrettyPalette();
      obj9->Draw();

      if (fRelTimes)
        {
          // Rel. Times
          TCanvas &c5 = fDisplay->AddTab("Rel. Times");
          c5.Divide(2,4);
          
          disp30.CamDraw(c5, 1, 2, 2);
          disp31.CamDraw(c5, 2, 2, 2);
        }
      
      return;
    }
    
    if (fDisplayType == kNormalDisplay)
      {
        
        // Charges
        TCanvas &c11 = fDisplay->AddTab("Fit.Charge");
        c11.Divide(2, 4);
        
        disp1.CamDraw(c11, 1, 2, 5, 1);
        disp2.CamDraw(c11, 2, 2, 5, 1);
        
        // Reduced Sigmas
        TCanvas &c12 = fDisplay->AddTab("Red.Sigma");
        c12.Divide(2,4);
        
        disp3.CamDraw(c12, 1, 2, 5, 1);
        disp4.CamDraw(c12, 2, 2, 5, 1);
        
        //  F-Factor
        TCanvas &c13 = fDisplay->AddTab("Phe's");
        c13.Divide(3,4);
        
        disp5.CamDraw(c13, 1, 3, 5, 1);
        disp6.CamDraw(c13, 2, 3, 5, 1);
        disp7.CamDraw(c13, 3, 3, 5, 1);
        
        // QE's
        TCanvas &c14 = fDisplay->AddTab("QE's");
        c14.Divide(4,4);
        
        disp8.CamDraw(c14, 1, 4, 5, 1);
        disp9.CamDraw(c14, 2, 4, 5, 1);
        disp10.CamDraw(c14, 3, 4, 5, 1);
        disp11.CamDraw(c14, 4, 4, 5, 1);
        
        // Defects
        TCanvas &c15 = fDisplay->AddTab("Defect");
        //      c15.Divide(5,2);
        c15.Divide(4,2);
        
        /*
        disp23.CamDraw(c15, 1, 5, 0);
        disp24.CamDraw(c15, 2, 5, 0);
        disp25.CamDraw(c15, 3, 5, 0);
        disp26.CamDraw(c15, 4, 5, 0);
        disp27.CamDraw(c15, 5, 5, 0);
        */
        disp24.CamDraw(c15, 1, 4, 0);
        disp25.CamDraw(c15, 2, 4, 0);
        disp26.CamDraw(c15, 3, 4, 0);
        disp27.CamDraw(c15, 4, 4, 0);
        
        // Abs. Times
        TCanvas &c16 = fDisplay->AddTab("Abs. Times");
        c16.Divide(2,3);
        
        disp28.CamDraw(c16, 1, 2, 5);
        disp29.CamDraw(c16, 2, 2, 5);

        if (fRelTimes)
        {
            // Rel. Times
            TCanvas &c17 = fDisplay->AddTab("Rel. Times");
            c17.Divide(2,4);

            disp30.CamDraw(c17, 1, 2, 5, 1);
            disp31.CamDraw(c17, 2, 2, 5, 1);
        }
        
        return;
    }
    
    if (fDisplayType == kFullDisplay)
    {
        MHCalibrationCam *cam = (MHCalibrationCam*)plist.FindObject("MHCalibrationChargeCam");

        for (Int_t sector=1;sector<cam->GetAverageSectors();sector++)
        {
            cam->GetAverageHiGainSector(sector).DrawClone("all");
            cam->GetAverageLoGainSector(sector).DrawClone("all");
        }

        // Charges
        TCanvas &c21 = fDisplay->AddTab("Fit.Charge");
        c21.Divide(2, 4);

        disp1.CamDraw(c21, 1, 2, 2, 1);
        disp2.CamDraw(c21, 2, 2, 2, 1);

        // Reduced Sigmas
        TCanvas &c23 = fDisplay->AddTab("Red.Sigma");
        c23.Divide(2,4);

        disp3.CamDraw(c23, 1, 2, 2, 1);
        disp4.CamDraw(c23, 2, 2, 2, 1);

        //  F-Factor
        TCanvas &c24 = fDisplay->AddTab("Phe's");
        c24.Divide(3,5);
        
        disp5.CamDraw(c24, 1, 3, 2, 1, 1);
        disp6.CamDraw(c24, 2, 3, 2, 1, 1);
        disp7.CamDraw(c24, 3, 3, 2, 1, 1);
        
        // QE's
        TCanvas &c25 = fDisplay->AddTab("QE's");
        c25.Divide(4,5);
        
        disp8.CamDraw(c25, 1, 4, 2, 1, 1);
        disp9.CamDraw(c25, 2, 4, 2, 1, 1);
        disp10.CamDraw(c25, 3, 4, 2, 1, 1);
        disp11.CamDraw(c25, 4, 4, 2, 1, 1);
        
        // Validity
        TCanvas &c26 = fDisplay->AddTab("Valid");
        c26.Divide(4,2);
        
        disp12.CamDraw(c26, 1, 4, 0);
        disp13.CamDraw(c26, 2, 4, 0);
        disp14.CamDraw(c26, 3, 4, 0);
        disp15.CamDraw(c26, 4, 4, 0);
        
        // Other info
        TCanvas &c27 = fDisplay->AddTab("HiLoGain");
        c27.Divide(3,3);
        
        disp16.CamDraw(c27, 1, 3, 0);
        disp17.CamDraw(c27, 2, 3, 1);
        disp18.CamDraw(c27, 3, 3, 1);
        
        // Pickup
        TCanvas &c28 = fDisplay->AddTab("Pickup");
        c28.Divide(4,2);
        
        disp19.CamDraw(c28, 1, 4, 0);
        disp20.CamDraw(c28, 2, 4, 0);
        disp21.CamDraw(c28, 3, 4, 0);
        disp22.CamDraw(c28, 4, 4, 0);
        
        // Defects
        TCanvas &c29 = fDisplay->AddTab("Defect");
        //      c29.Divide(5,2);
        c29.Divide(4,2);
        
        disp24.CamDraw(c29, 1, 4, 0);
        disp25.CamDraw(c29, 2, 4, 0);
        disp26.CamDraw(c29, 3, 4, 0);
        disp27.CamDraw(c29, 4, 4, 0);
        
        // Abs. Times
        TCanvas &c30 = fDisplay->AddTab("Abs. Times");
        c30.Divide(2,3);
        
        disp28.CamDraw(c30, 1, 2, 2);
        disp29.CamDraw(c30, 2, 2, 1);

        if (fRelTimes)
        {
            // Rel. Times
            TCanvas &c31 = fDisplay->AddTab("Rel. Times");
            c31.Divide(3,5);
            
            disp30.CamDraw(c31, 1, 3, 2, 1, 1);
            disp31.CamDraw(c31, 2, 3, 2, 1, 1);
            disp32.CamDraw(c31, 3, 3, 4, 1, 1);

            // Time Defects
            TCanvas &c32 = fDisplay->AddTab("Time Def.");
            c32.Divide(2,2);
            
            disp33.CamDraw(c32, 1, 2, 0);
            disp34.CamDraw(c32, 2, 2, 0);

            MHCalibrationCam *cam = (MHCalibrationCam*)plist.FindObject("MHCalibrationRelTimeCam");
            
            for (Int_t sector=1;sector<cam->GetAverageSectors();sector++)
            {
                cam->GetAverageHiGainSector(sector).DrawClone("fourierevents");
                cam->GetAverageLoGainSector(sector).DrawClone("fourierevents");
            }

        }

        return;
    }
}
    

void  MJCalibration::DisplayReferenceLines(MHCamera *cam, const Int_t what) const
{

  const MGeomCam *geom = cam->GetGeometry();

  Double_t x = geom->InheritsFrom("MGeomCamMagic") ? 397 : cam->GetNbinsX() ;

  TLine line;
  line.SetLineStyle(kDashed);
  line.SetLineWidth(3);
  line.SetLineColor(kBlue);
  
  TLine *l1 = NULL;

  if (what == 0)
    l1 = line.DrawLine(0, fgRefQEInner, x, fgRefQEInner);      
  else if (what == 1)
    l1 = line.DrawLine(0, fgRefConvFADC2PhotInner, x, fgRefConvFADC2PhotInner);      
  else if (what == 2)
    l1 = line.DrawLine(0, fgRefConvFADC2PheInner, x, fgRefConvFADC2PheInner );
  
  if (geom->InheritsFrom("MGeomCamMagic"))
    {
      const Double_t x2 = cam->GetNbinsX();

      switch (what)
        {
        case 0:
          line.DrawLine(x2, fgRefQEOuter, 398, fgRefQEOuter);      
          break;
        case 1:
          line.DrawLine(x2, fgRefConvFADC2PhotOuter, 398, fgRefConvFADC2PhotOuter );      
          break;
        case 2:
          line.DrawLine(x2, fgRefConvFADC2PheOuter, 398, fgRefConvFADC2PheOuter);
          break;
        }
    }
  
  TLegend *leg = new TLegend(what ? 0.2 : 0.6,0.75,what ? 0.5 : 0.9 ,0.85);
  leg->SetBit(kCanDelete);
  leg->AddEntry(l1, "Reference","l");
  leg->Draw();
}

void  MJCalibration::DisplayOutliers(TH1D *hist, const char* whatsmall, const char* whatbig) const
{

  const Float_t mean  = hist->GetFunction("gaus")->GetParameter(1);
  const Float_t lolim = mean - 4.0*hist->GetFunction("gaus")->GetParameter(2);
  const Float_t uplim = mean + 4.0*hist->GetFunction("gaus")->GetParameter(2);
  const Stat_t  dead  = hist->Integral(0,hist->FindBin(lolim)-1);
  const Stat_t  noisy = hist->Integral(hist->FindBin(uplim)+1,hist->GetNbinsX()+1);

  const Double_t max = hist->GetBinContent(hist->GetMaximumBin());                                           
  
  const Double_t minl = hist->GetBinCenter(hist->GetXaxis()->GetFirst());
  const Double_t maxl = hist->GetBinCenter(hist->GetXaxis()->GetLast());

  TLatex deadtex;
  deadtex.SetTextSize(0.07);
  deadtex.DrawLatex(minl+0.015*(maxl-minl),max/1.1,
                    Form("%3i %s pixels",(Int_t)dead,whatsmall));

  TLatex noisytex;
  noisytex.SetTextSize(0.07);
  noisytex.DrawLatex(minl+0.015*(maxl-minl),max/1.2,
                     Form("%3i %s pixels",(Int_t)noisy,whatbig));

}

void MJCalibration::FixDataCheckHist(TH1D *hist) const 
{

    hist->SetDirectory(NULL);

    //
    // set the labels bigger
    //
    TAxis *xaxe = hist->GetXaxis();
    TAxis *yaxe = hist->GetYaxis();
    
    xaxe->CenterTitle();
    yaxe->CenterTitle();    
    xaxe->SetTitleSize(0.06);
    yaxe->SetTitleSize(0.06);    
    xaxe->SetTitleOffset(0.8);
    yaxe->SetTitleOffset(0.85);    
    xaxe->SetLabelSize(0.05);
    yaxe->SetLabelSize(0.05);    

}

const Int_t MJCalibration::CountBadPixels ( MHCamera *cam , const Int_t what ) const
{

  Int_t cnt = 0;

  for (UInt_t pix=0; pix<cam->GetNumPixels();pix++)
    if ((Int_t)cam->GetPixContent(pix) == what)
      cnt++;

  return cnt;
}


// --------------------------------------------------------------------------
//
// Find the colour of the pulsing LED:
// - If the run number is smaller than gkIFAEBoxInaugurationRun, take MCalibrationCam::kCT1
// - Otherwise find the colour out of the run name
// - If no colour is found, return kFALSE
// 
Bool_t MJCalibration::FindColor() 
{
    if (fColor != MCalibrationCam::kNONE)
      return kTRUE;

    if (fSequence.IsValid())
    {
        fColor = MCalibrationCam::kCT1;
        return kTRUE;
    }

    const UInt_t nruns = fRuns->GetNumRuns();
    if (nruns == 0)
        return kFALSE;

    fRuns->Reset();

    TString filenames;
    while (!(filenames=((MDirIter*)fRuns)->Next()).IsNull())
    {
        MCalibrationCam::PulserColor_t newcolor = MCalibrationCam::kNONE;

        TString number = filenames(TRegexp("[0-9]+_._.+[.]root$"));
        Int_t num = atoi(number.Data());

        if (num<gkIFAEBoxInaugurationRun)
            newcolor = MCalibrationCam::kCT1;

        switch (num)
        {
        case 26402:
            newcolor = MCalibrationCam::kBLUE;
            break;

        case 30090:
        case 20660:
        case 20661:
        case 26408:
        case 26409:
        case 26412:
        case 26568:
        case 26924:
            newcolor = MCalibrationCam::kGREEN;
            break;

        case 27474:
            newcolor = MCalibrationCam::kNONE;
            *fLog << "Sorry, run 27474 was taken with CLOSED LIDS. It should not be used! " << endl;
            return kFALSE;

        default:
            if (filenames.Contains("green",TString::kIgnoreCase))
                newcolor = MCalibrationCam::kGREEN;
            if (filenames.Contains("blue",TString::kIgnoreCase))
                newcolor = MCalibrationCam::kBLUE;
            if (filenames.Contains("uv",TString::kIgnoreCase))
                newcolor = MCalibrationCam::kUV;
            if (filenames.Contains("ct1",TString::kIgnoreCase))
                newcolor = MCalibrationCam::kCT1;
        }

        if (newcolor==MCalibrationCam::kNONE)
        {
            *fLog << err << "No color found for " << filenames << "... abort." << endl;
            return kFALSE;
        }

        if (fColor == MCalibrationCam::kNONE)
            fColor = newcolor;

        if (fColor != newcolor)
        {
            *fLog << err << "Color mismatch found in " << filenames << "... abort." << endl;
            return kFALSE;
        }
    }

    *fLog << inf << "Found color: ";
    switch (fColor)
    {
    case MCalibrationCam::kBLUE:  *fLog << "kBLUE";  break;
    case MCalibrationCam::kGREEN: *fLog << "kGREEN"; break;
    case MCalibrationCam::kUV:    *fLog << "kUV";    break;
    case MCalibrationCam::kCT1:   *fLog << "kCT1";   break;
    default:                      *fLog << "<none>"; break;
    }
    *fLog << endl;

    if (fColor!=MCalibrationCam::kNONE)
        return kTRUE;

    *fLog <<  "No colour found in: " << fRuns->GetRunsAsString() << "... abort." << endl;
    return kFALSE;
}

// --------------------------------------------------------------------------
//
// Retrieve the output file written by WriteResult()
// 
const char* MJCalibration::GetOutputFile() const
{
    if (fSequence.IsValid())
        return Form("%s/calib%06d.root", (const char*)fPathOut, fSequence.GetSequence());
    if (!fRuns)
        return "";

    return Form("%s/%s-F1.root", (const char*)fPathOut, (const char*)fRuns->GetRunsAsFileName());
}

Bool_t MJCalibration::IsUseBlindPixel() const 
{
    return TESTBIT(fDevices,kUseBlindPixel);
}

Bool_t MJCalibration::IsUsePINDiode() const 
{
    return TESTBIT(fDevices,kUsePINDiode);
}

// --------------------------------------------------------------------------
//
// MJCalibration allows to setup several option by a resource file:
//   MJCalibration.Display: full, datacheck, normal
//   MJCalibration.RelTimeCalibration: yes,no
//   MJCalibration.Datacheck: yes,no
//   MJCalibration.Debug: yes,no
//   MJCalibration.UseBlindPixel: yes,no
//   MJCalibration.UsePINDiode: yes,no
//
// For more details see the class description and the corresponding Getters
// 
Bool_t MJCalibration::CheckEnvLocal()
{
    TString col = GetEnv("Color", "");
    if (!col.IsNull())
    {
    }

    TString dis = GetEnv("Display", "");
    if (dis.BeginsWith("Full", TString::kIgnoreCase))
        SetFullDisplay();
    if (dis.BeginsWith("DataCheck", TString::kIgnoreCase))
        SetDataCheckDisplay();
    if (dis.BeginsWith("Normal", TString::kIgnoreCase))
        SetNormalDisplay();

    SetRelTimeCalibration(GetEnv("RelTimeCalibration", fRelTimes));
    SetDataCheck(GetEnv("Datacheck", fDataCheck));
    SetDebug(GetEnv("Debug", fDebug));
    SetUseBlindPixel(GetEnv("UseBlindPixel", IsUseBlindPixel()));
    SetUsePINDiode(GetEnv("UsePINDiode", IsUsePINDiode()));

    return kTRUE;
}

// --------------------------------------------------------------------------
//
// Call the ProcessFile(MPedestalCam)
// 
Bool_t MJCalibration::Process(MPedestalCam &pedcam)
{
    if (!ReadCalibrationCam())
        return ProcessFile(pedcam);

    return kTRUE;
}

void MJCalibration::InitBlindPixel(MExtractBlindPixel &blindext,
                                   MHCalibrationChargeBlindCam &blindcam)
{

  Int_t run = fSequence.IsValid() ? fSequence.GetLastRun() : fRuns->GetRuns()[fRuns->GetNumRuns()-1];
  
  //
  // Initialize the blind pixel. Unfortunately, there is a hardware difference
  // in the first blind pixel until run "gkSecondBlindPixelInstallation" and the
  // later setup. The first needs to use a filter because of the length of
  // spurious NSB photon signals. The latter get better along extracting the amplitude
  // from a small window.
  //
  if (run < gkSecondBlindPixelInstallation)
    {

      MCalibrationChargeBlindCamOneOldStyle blindresults;
      blindresults.Copy(fCalibrationBlindCam);

      blindext.SetExtractionType(MExtractBlindPixel::kIntegral);
      blindext.SetExtractionType(MExtractBlindPixel::kFilter);
      blindext.SetRange(10,19,0,6);
      blindext.SetNSBFilterLimit(70);
      blindcam.SetFitFunc( MHCalibrationChargeBlindPix::kEPoisson5 );
    }
  else if (run < gkThirdBlindPixelInstallation)
    {

      MCalibrationChargeBlindCamTwoNewStyle blindresults;
      blindresults.Copy(fCalibrationBlindCam);

      blindext.SetNumBlindPixels(blindresults.GetNumBlindPixels());
      for (UInt_t i=0;i<blindresults.GetNumBlindPixels();i++)
        blindext.SetBlindPixelIdx(blindresults[i].GetPixId(),i);

      blindext.SetExtractionType(MExtractBlindPixel::kAmplitude);
      blindext.SetExtractionType(MExtractBlindPixel::kFilter);
      blindext.SetRange(5,8,0,2);
      blindext.SetNSBFilterLimit(38);
      
    }
  else
    {
      *fLog << err << "Third blind pixel installation not yet completed, check your run number!!! " << endl;
    }
  
}

// --------------------------------------------------------------------------
//
// Execute the task list and the eventloop:
//
// - Check if there are fRuns, otherwise return
// - Check the colour of the files in fRuns (FindColor()), otherwise return
// - Check for consistency between run numbers and number of files
// - Add fRuns to MReadMarsFile
// - Put into MParList:
//   1) MPedestalCam          (pedcam)
//   2) MCalibrationQECam     (fQECam)
//   3) MCalibrationChargeCam (fCalibrationCam)
//   4) MCalibrationRelTimeCam (fRelTimeCam)   (only if flag fRelTimes is chosen)
//   5) MBadPixelsCam         (fBadPixels)
//   6) MCalibrationChargePINDiode
//   7) MCalibrationChargeBlindPix
// - Put into the MTaskList:
//   1)  MReadMarsFile
//   2)  MBadPixelsMerge
//   3)  MGeomApply
//   4)  MExtractor
//   5)  MExtractPINDiode
//   6)  MExtractBlindPixel
//   7)  MExtractTime (only if flag fRelTimes is chosen)
//   8)  MContinue(MFCosmics)
//   9)  MFillH("MHCalibrationChargePINDiode", "MExtractedSignalPINDiode")
//   10) MFillH("MHCalibrationChargeBlindCam", "MExtractedSignalBlindPixel")
//   11) MFillH("MHCalibrationChargeCam",      "MExtractedSignalCam")
//   12) MFillH("MHCalibrationChargeCam",      "MExtractedSignalCam")
//   13) MCalibrationChargeCalc
//   14) MFillH("MHCalibrationRelTimeCam",     "MArrivalTimeCam") (only if flag fRelTimes is chosen)
//   15) MCalibrationRelTimeCalc
// - Execute MEvtLoop
// - DisplayResult()
// - WriteResult()
//
Bool_t MJCalibration::ProcessFile(MPedestalCam &pedcam)
{
    if (!fSequence.IsValid())
    {
        if (!fRuns)
        {
            *fLog << err << "No Runs choosen... abort." << endl;
            return kFALSE;
        }

        if (fRuns->GetNumRuns() != fRuns->GetNumEntries())
        {
            *fLog << err << "Number of files found doesn't match number of runs... abort."
                << fRuns->GetNumRuns() << " vs. " << fRuns->GetNumEntries() << endl;
            return kFALSE;
        }
    }

    //if (!CheckEnv())
    //    return kFALSE;

    CheckEnv();

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

    *fLog << inf;
    fLog->Separator(GetDescriptor());

    if (!FindColor())
        return kFALSE;

    *fLog << "Calculate MCalibrationCam from ";
    if (fSequence.IsValid())
        *fLog << "Sequence #" << fSequence.GetSequence() << endl;
    else
        *fLog << "Runs " << fRuns->GetRunsAsString() << endl;
    *fLog << endl;

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

    // Setup Tasklist
    MParList plist;
    MTaskList tlist;
    plist.AddToList(&tlist);
    plist.AddToList(this); // take care of fDisplay!

    MReadMarsFile read("Events");
    MRawFileRead rawread(NULL);

    MDirIter iter;
    if (fSequence.IsValid())
    {
        const Int_t n0 = fSequence.SetupCalRuns(iter, fPathData);
        const Int_t n1 = fSequence.GetNumCalRuns();
        if (n0==0)
        {
            *fLog << err << "ERROR - No input files of sequence found!" << endl;
            return kFALSE;
        }
        if (n0!=n1)
        {
            *fLog << err << "ERROR - Number of files found (" << n0 << ") doesn't match number of files in sequence (" << n1 << ")" << endl;
            return kFALSE;
        }
    }

    if (fDataCheck)
    {
        rawread.AddFiles(fSequence.IsValid() ? iter : *fRuns);
        tlist.AddToList(&rawread);
    }
    else
    {
        read.DisableAutoScheme();
        read.AddFiles(fSequence.IsValid() ? iter : *fRuns);
        tlist.AddToList(&read);
    }

    MHCalibrationChargeCam      chargecam;
    MHCalibrationChargeBlindCam blindcam;

    plist.AddToList(&pedcam);
    plist.AddToList(&chargecam);
    plist.AddToList(&blindcam);
    plist.AddToList(&fBadPixels);
    plist.AddToList(&fQECam);
    plist.AddToList(&fCalibrationCam);
    plist.AddToList(&fCalibrationBlindCam);
    plist.AddToList(&fCalibrationPINDiode);
    plist.AddToList(&fRelTimeCam);

    MGeomApply               apply;
    MBadPixelsMerge          merge(&fBadPixels);
    MExtractPINDiode         pinext;
    MExtractBlindPixel       blindext;

    InitBlindPixel(blindext, blindcam);

    MExtractSlidingWindow    extract2;
    MExtractTimeFastSpline   timespline;
    MCalibrationChargeCalc   calcalc;
    MCalibrationRelTimeCalc  timecalc;

    if (!fSequence.IsValid())
    {
        calcalc.SetOutputPath(fPathOut);
        calcalc.SetOutputFile(Form("%s-ChargeCalibStat.txt",(const char*)fRuns->GetRunsAsFileName()));
    }

    if (fDebug)
    {
        chargecam.SetDebug();
        calcalc.SetDebug();
    }

    //
    // As long as there are no DM's, have to colour by hand
    //
    chargecam.SetColor    (fColor);
    calcalc.SetPulserColor(fColor);

    MFillH fillpin("MHCalibrationChargePINDiode", "MExtractedSignalPINDiode",   "FillPINDiode");
    MFillH fillbnd("MHCalibrationChargeBlindCam", "MExtractedSignalBlindPixel", "FillBlindCam");
    MFillH fillcam("MHCalibrationChargeCam",      "MExtractedSignalCam",        "FillChargeCam");
    MFillH filltme("MHCalibrationRelTimeCam",     "MArrivalTimeCam",            "FillRelTime");
    fillpin.SetNameTab("PINDiode");
    fillbnd.SetNameTab("BlindPix");
    fillcam.SetNameTab("Charge");
    filltme.SetNameTab("RelTimes");
  
    TString drawoption;

    if (fDisplayType == kDataCheckDisplay)
        drawoption += "datacheck";
    if (fDisplayType == kFullDisplay)
        drawoption += " all";

    fillcam.SetDrawOption(drawoption.Data());
    fillbnd.SetDrawOption(drawoption.Data());
    fillpin.SetDrawOption(drawoption.Data());
    filltme.SetDrawOption(drawoption.Data());

    //
    // Apply a filter against cosmics
    // (will have to be needed in the future
    // when the calibration hardware-trigger is working)
    //
    MFCosmics cosmics;
    MContinue cont(&cosmics);

    tlist.AddToList(&merge);
    tlist.AddToList(&apply);

    MTaskEnv taskenv("ExtractSignal");
    taskenv.SetDefault(fExtractor ? fExtractor : &extract2);

    tlist.AddToList(&taskenv);
    tlist.AddToList(&pinext);
    tlist.AddToList(&blindext);

    MTaskEnv taskenv2("ExtractTime");
    taskenv2.SetDefault(fTimeExtractor ? fTimeExtractor : &timespline);

    if (fRelTimes)
        tlist.AddToList(&taskenv2);

    if (fColor == MCalibrationCam::kCT1)
        tlist.AddToList(&cont);

    tlist.AddToList(&fillcam);

    if (fRelTimes)
    {
        tlist.AddToList(&filltme);
        tlist.AddToList(&timecalc);
    }

    if (IsUseBlindPixel())
      tlist.AddToList(&fillbnd);
    if (IsUsePINDiode())
      tlist.AddToList(&fillpin);

    tlist.AddToList(&calcalc);

    // Create and setup the eventloop
    MEvtLoop evtloop(fName);
    evtloop.SetParList(&plist);
    evtloop.SetDisplay(fDisplay);
    evtloop.SetLogStream(fLog);
    if (!SetupEnv(evtloop))
        return kFALSE;

    if (!taskenv.GetTask() && !taskenv2.GetTask())
    {
        *fLog << err << "ERROR - Neither ExtractSignal nor ExtractTime initialized or both '<dummy>'." << endl;
        return kFALSE;
    }

    if (!WriteTasks(taskenv.GetTask(), taskenv2.GetTask()))
        return kFALSE;

    // Execute first analysis
    if (!evtloop.Eventloop())
    {
        *fLog << err << GetDescriptor() << ": Failed." << endl;
        return kFALSE;
    }

    tlist.PrintStatistics();

    //
    // The next lines are necessary in order to avoid that
    // the last entry drawn by MFillH gets deleted again from
    // the display. No idea where this comes from...
    //
    // FIND THE REASON! THE NEXT CHANGE SOMEBODY DOES MIGHT RESULT
    // IN __YOUR__ WORKAROUN NOT WORKING IF IT IS NOT CLEANLY DONE!
    //
    // THE AUTHOR OF MFILLH SHOULD FIND THE REASON INSTEAD OF DELETING 
    // CODE WITHOUT INFORMING THE DATACHECK PEOPLE - SORRY, I SPENT 
    // TOO MANY DAYS TRYING TO FIND THIS REASON!
    //
    if (fDisplay)
    {
      if (IsUsePINDiode())
        {
          MHCalibrationChargePINDiode *pin =
            (MHCalibrationChargePINDiode*)plist.FindObject("MHCalibrationChargePINDiode");
          pin->DrawClone(Form("nonew %s",drawoption.Data()));
        }
      else if (IsUseBlindPixel())
        {
          MHCalibrationChargeBlindCam *cam =
            (MHCalibrationChargeBlindCam*)plist.FindObject("MHCalibrationChargeBlindCam");
          cam->DrawClone(Form("nonew %s",drawoption.Data()));
        }
      else if (fRelTimes)
        {
          MHCalibrationRelTimeCam *cam =
            (MHCalibrationRelTimeCam*)plist.FindObject("MHCalibrationRelTimeCam");
            cam->DrawClone(Form("nonew %s",drawoption.Data()));
        }
      else
        {
          MHCalibrationChargeCam *cam =
            (MHCalibrationChargeCam*)plist.FindObject("MHCalibrationChargeCam");
          cam->DrawClone(Form("nonew %s",drawoption.Data()));
        }
    }

    DisplayResult(plist);

    if (!WriteResult())
        return kFALSE;

    *fLog << all << GetDescriptor() << ": Done." << endl;

    return kTRUE;
}

// --------------------------------------------------------------------------
//
// Read the following containers from GetOutputFile()
// - MCalibrationChargeCam
// - MCalibrationQECam
// - MBadPixelsCam
//
Bool_t MJCalibration::ReadCalibrationCam()
{
  const TString fname = GetOutputFile();
  
  if (gSystem->AccessPathName(fname, kFileExists))
  {
      *fLog << err << "Input file " << fname << " doesn't exist." << endl;
      return kFALSE;
  }

  *fLog << inf << "Reading from file: " << fname << endl;

  TFile file(fname, "READ");
  if (fCalibrationCam.Read()<=0)
  {
      *fLog << err << "Unable to read MCalibrationChargeCam from " << fname << endl;
      return kFALSE;
  }

  if (fQECam.Read()<=0)
  {
      *fLog << err << "Unable to read MCalibrationQECam from " << fname << endl;
      return kFALSE;
  }


  if (file.FindKey("MCalibrationRelTimeCam"))
      if (fRelTimeCam.Read()<=0)
      {
          *fLog << err << "Unable to read MCalibrationRelTimeCam from " << fname << endl;
          return kFALSE;
      }

  if (file.FindKey("MBadPixelsCam"))
  {
      MBadPixelsCam bad;
      if (bad.Read()<=0)
      {
          *fLog << err << "Unable to read MBadPixelsCam from " << fname << endl;
          return kFALSE;
      }
      fBadPixels.Merge(bad);
  }

  if (fDisplay /*&& !fDisplay->GetCanvas("Pedestals")*/) // FIXME!
      fDisplay->Read();

  return kTRUE;
}


// --------------------------------------------------------------------------
//
// Set the useage of the Blind Pixel device 
// 
void MJCalibration::SetUseBlindPixel(const Bool_t b)
{
  b ? SETBIT(fDevices,kUseBlindPixel) : CLRBIT(fDevices,kUseBlindPixel);
}

// --------------------------------------------------------------------------
//
// Set the useage of the PIN Diode device 
// 
void MJCalibration::SetUsePINDiode(const Bool_t b)
{
  b ? SETBIT(fDevices,kUsePINDiode) : CLRBIT(fDevices,kUsePINDiode);
}

Bool_t MJCalibration::WriteEventloop(MEvtLoop &evtloop) const
{
    if (fPathOut.IsNull())
        return kTRUE;

    const TString oname(GetOutputFile());

    *fLog << inf << "Writing to file: " << oname << endl;

    TFile file(oname, fOverwrite?"RECREATE":"NEW", "File created by MJCalibration", 9);
    if (!file.IsOpen())
    {
        *fLog << err << "ERROR - Couldn't open file " << oname << " for writing..." << endl;
        return kFALSE;
    }

    if (evtloop.Write(fName)<=0)
    {
        *fLog << err << "Unable to write MEvtloop to " << oname << endl;
        return kFALSE;
    }

    return kTRUE;
}

Bool_t MJCalibration::WriteTasks(MTask *t1, MTask *t2) const
{
    if (fPathOut.IsNull())
        return kTRUE;

    const TString oname(GetOutputFile());

    *fLog << inf << "Writing to file: " << oname << endl;

    TFile file(oname, fOverwrite?"RECREATE":"NEW", "File created by MJCalibration", 9);
    if (!file.IsOpen())
    {
        *fLog << err << "ERROR - Couldn't open file " << oname << " for writing..." << endl;
        return kFALSE;
    }

    if (t1 && t1->Write()<=0)
    {
        *fLog << err << "Unable to write " << t1->GetName() << " to " << oname << endl;
        return kFALSE;
    }
    if (t2 && t2->Write()<=0)
    {
        *fLog << err << "Unable to write " << t2->GetName() << " to " << oname << endl;
        return kFALSE;
    }

    return kTRUE;
}

// --------------------------------------------------------------------------
//
// Write the result into the output file GetOutputFile(), if fOutputPath exists.
// 
// The following containers are written:
// - MStatusDisplay
// - MCalibrationChargeCam
// - MCalibrationChargeBlindPix
// - MCalibrationQECam
// - MBadPixelsCam
//
Bool_t MJCalibration::WriteResult()
{
    if (fPathOut.IsNull())
        return kTRUE;

    const TString oname(GetOutputFile());

    *fLog << inf << "Writing to file: " << oname << endl;

    TFile file(oname, "UPDATE", "File created by MJCalibration", 9);
    if (!file.IsOpen())
    {
        *fLog << err << "ERROR - Couldn't open file " << oname << " for writing..." << endl;
        return kFALSE;
    }

    *fLog << inf << " - MStatusDisplay..." << flush;
    if (fDisplay && fDisplay->Write()<=0)
    {
        *fLog << err << "Unable to write MStatusDisplay to " << oname << endl;
        return kFALSE;
    }
    *fLog << inf << "ok." << endl;

    *fLog << inf << " - MCalibrationChargeCam..." << flush;
    if (fCalibrationCam.Write()<=0)
    {
        *fLog << err << "Unable to write MCalibrationChargeCam to " << oname << endl;
        return kFALSE;
    }
    *fLog << inf << "ok." << endl;

    *fLog << inf << " - MCalibrationChargeBlindCam..." << flush;
    if (fCalibrationBlindCam.Write()<=0)
    {
        *fLog << err << "Unable to write MCalibrationChargeBlindCam to " << oname << endl;
        return kFALSE;
    }
    *fLog << inf << "ok." << endl;

    *fLog << inf << " - MCalibrationChargePINDiode..." << flush;
    if (fCalibrationPINDiode.Write()<=0)
    {
        *fLog << err << "Unable to write MCalibrationChargePINDiode to " << oname << endl;
        return kFALSE;
    }
    *fLog << inf << "ok." << endl;

    *fLog << inf << " - MCalibrationQECam..." << flush;
    if (fQECam.Write()<=0)
    {
        *fLog << err << "Unable to write MCalibrationQECam to " << oname << endl;
        return kFALSE;
    }
    *fLog << inf << "ok." << endl;

    *fLog << inf << " - MBadPixelsCam..." << flush;
    if (fBadPixels.Write()<=0)
    {
        *fLog << err << "Unable to write MBadPixelsCam to " << oname << endl;
        return kFALSE;
    }
    *fLog << inf << "ok." << endl;

    if (fRelTimes)
    {
        *fLog << inf << " - MCalibrationRelTimeCam..." << flush;
	if (fRelTimeCam.Write()<=0)
	{
	    *fLog << err << "Unable to write MCalibrationRelTimeCam to " << oname << endl;
	    return kFALSE;
	}
        *fLog << inf << "ok." << endl;
    }

    return kTRUE;

}

void MJCalibration::DisplayDoubleProject(MHCamera *cam, const char* whatsmall, const char* whatbig) const
{
  
  TArrayI inner(1);
  inner[0] = 0;
  
  TArrayI outer(1);
  outer[0] = 1;
          
  TArrayI s0(6);
  s0[0] = 6;
  s0[1] = 1;
  s0[2] = 2;
  s0[3] = 3;
  s0[4] = 4;
  s0[5] = 5;
  
  TArrayI s1(3);
  s1[0] = 6;
  s1[1] = 1;
  s1[2] = 2;
  
  TArrayI s2(3);
  s2[0] = 3;
  s2[1] = 4;
  s2[2] = 5;
  
  TVirtualPad *pad = gPad;
  pad->Divide(2,1);
  
  TH1D *inout[2];
  inout[0] = cam->ProjectionS(s0, inner, "Inner");
  inout[1] = cam->ProjectionS(s0, outer, "Outer");
  FixDataCheckHist(inout[0]);
  FixDataCheckHist(inout[1]);
  
  inout[0]->SetTitle(Form("%s %s",cam->GetTitle(),"Inner"));
  inout[1]->SetTitle(Form("%s %s",cam->GetTitle(),"Outer"));
  
  for (int i=0; i<2; i++)
    {
      pad->cd(i+1);
      gPad->SetBorderMode(0);
      gPad->SetTicks();
      
      inout[i]->SetDirectory(NULL);
      inout[i]->SetLineColor(kRed+i);
      inout[i]->SetBit(kCanDelete);
      inout[i]->Draw();
      inout[i]->Fit("gaus", "Q");
      gPad->Modified();
      gPad->Update();      
      TPaveStats *st = (TPaveStats*)inout[i]->GetListOfFunctions()->FindObject("stats");
      st->SetY1NDC(0.6);
      st->SetY2NDC(0.9);
      st->SetX1NDC(0.55);
      st->SetX2NDC(0.99);
      gPad->Modified();
      gPad->Update();      

      TLegend *leg2 = new TLegend(0.55,0.4,0.99,0.6);
      //
      // Display the outliers as dead and noisy pixels
      //
      DisplayOutliers(inout[i],whatsmall,whatbig);
      
      //
      // Display the two half of the camera separately
      //
      TH1D *half[2];
      half[0] = cam->ProjectionS(s1, i==0 ? inner : outer , "Sector 6-1-2");
      half[1] = cam->ProjectionS(s2, i==0 ? inner : outer , "Sector 3-4-5");
      
      for (int j=0; j<2; j++)
        {
          half[j]->SetLineColor(kRed+i+2*j+1);
          half[j]->SetDirectory(NULL);
          half[j]->SetBit(kCanDelete);
          half[j]->Draw("same");
          leg2->AddEntry(half[j], half[j]->GetName(), "l");
        }
      leg2->Draw();
    }
}