Index: trunk/MagicSoft/Mars/mjobs/MJCalibration.cc
===================================================================
--- trunk/MagicSoft/Mars/mjobs/MJCalibration.cc	(revision 3054)
+++ trunk/MagicSoft/Mars/mjobs/MJCalibration.cc	(revision 3055)
@@ -52,4 +52,5 @@
 #include "MGeomApply.h"
 #include "MExtractSignal.h"
+#include "MExtractSignal2.h"
 #include "MCalibrationCalc.h"
 
@@ -58,5 +59,4 @@
 
 ClassImp(MJCalibration);
-
 using namespace std;
 
@@ -69,83 +69,100 @@
 void MJCalibration::DrawProjection(MHCamera *obj1, Int_t fit) const
 {
-    TH1D *obj2 = (TH1D*)obj1->Projection();
-    obj2->Draw();
-    obj2->SetBit(kCanDelete);
-
-    const Double_t min   = obj2->GetBinCenter(obj2->GetXaxis()->GetFirst());
-    const Double_t max   = obj2->GetBinCenter(obj2->GetXaxis()->GetLast());
-    const Double_t integ = obj2->Integral("width")/2.5;
-    const Double_t mean  = obj2->GetMean();
-    const Double_t rms   = obj2->GetRMS();
-    const Double_t width = max-min;
-
-    TF1 *f=0;
-    switch (fit)
-    {
-    case 0:
-        f = new TF1("sgaus", "gaus(0)", min, max);
-        f->SetLineColor(kYellow);
-        f->SetBit(kCanDelete);
-        f->SetParNames("Area", "#mu", "#sigma");
-        f->SetParameters(integ/rms, mean, rms);
-        f->SetParLimits(0, 0,   integ);
-        f->SetParLimits(1, min, max);
-        f->SetParLimits(2, 0,   width/1.5);
-
-        obj2->Fit(f, "QLR");
-        break;
-
+
+  TH1D *obj2 = (TH1D*)obj1->Projection();
+  obj2->Draw();
+  obj2->SetBit(kCanDelete);
+  
+  const Double_t min   = obj2->GetBinCenter(obj2->GetXaxis()->GetFirst());
+  const Double_t max   = obj2->GetBinCenter(obj2->GetXaxis()->GetLast());
+  const Double_t integ = obj2->Integral("width")/2.5;
+  const Double_t mean  = obj2->GetMean();
+  const Double_t rms   = obj2->GetRMS();
+  const Double_t width = max-min;
+  
+  const TString dgausformula = "([0]-[3])/[2]*exp(-0.5*(x-[1])*(x-[1])/[2]/[2])"
+                               "+[3]/[5]*exp(-0.5*(x-[4])*(x-[4])/[5]/[5])";
+
+  const TString tgausformula = "([0]-[3]-[6])/[2]*exp(-0.5*(x-[1])*(x-[1])/[2]/[2])"
+                               "+[3]/[5]*exp(-0.5*(x-[4])*(x-[4])/[5]/[5])"
+                               "+[6]/[8]*exp(-0.5*(x-[7])*(x-[7])/[8]/[8])";
+  TF1 *f=0;
+  switch (fit)
+    {
     case 1:
-        f = new TF1("dgaus", "gaus(0)+gaus(3)", min, max);
-        f->SetLineColor(kYellow);
-        f->SetBit(kCanDelete);
-        f->SetParNames("A1", "#mu1", "#sigma1", "A2", "#mu2", "#sigma2");
-        f->SetParameters(integ/width, max-width/6, width/4, integ/width, min+width/6, width/4);
-        f->SetParLimits(0, 0,   integ);
-        f->SetParLimits(1, min, max);
-        f->SetParLimits(2, 0,   width/3);
-        f->SetParLimits(3, 0,   integ);
-        f->SetParLimits(4, min, max);
-        f->SetParLimits(5, 0,   width/3);
-
-        obj2->Fit(f, "QLR");
-        break;
-
+      f = new TF1("sgaus", "gaus(0)", min, max);
+      f->SetLineColor(kYellow);
+      f->SetBit(kCanDelete);
+      f->SetParNames("Area", "#mu", "#sigma");
+      f->SetParameters(integ/rms, mean, rms);
+      f->SetParLimits(0, 0,   integ);
+      f->SetParLimits(1, min, max);
+      f->SetParLimits(2, 0,   width/1.5);
+      
+      obj2->Fit(f, "QLR");
+      break;
+      
     case 2:
-        f = new TF1("tgaus", "gaus(0)+gaus(3)+gaus(6)", min, max);
-        f->SetLineColor(kYellow);
-        f->SetBit(kCanDelete);
-        f->SetParNames("A1", "#mu1", "#sigma1", "A2", "#mu2", "#sigma2", "A3", "#mu3", "#sigma3");
-        f->SetParameters(integ/width, max-width/6, width/4, integ/width, min+width/6, width/4, integ/width,min+width/6, width/2);
-        f->SetParLimits(0, 0,   integ);
-        f->SetParLimits(1, min, max);
-        f->SetParLimits(2, 0,   width/4);
-        f->SetParLimits(3, 0,   integ);
-        f->SetParLimits(4, min, max);
-        f->SetParLimits(5, 0,   width/4);
-        f->SetParLimits(6, 0,   integ);
-        f->SetParLimits(7, min, max);
-        f->SetParLimits(8, 0,   width/2);
-
-        obj2->Fit(f, "QLR");
-        break;
-
+      f = new TF1("dgaus",dgausformula.Data(),min,max);
+      f->SetLineColor(kYellow);
+      f->SetBit(kCanDelete);
+      f->SetParNames("A_{tot}", "#mu1", "#sigma1", "A2", "#mu2", "#sigma2");
+      f->SetParameters(integ,(min+mean)/2.,width/4.,
+                       integ/width/2.,(max+mean)/2.,width/4.);
+      // The left-sided Gauss 
+      f->SetParLimits(0,integ-1.5      , integ+1.5);
+      f->SetParLimits(1,min+(width/10.), mean);
+      f->SetParLimits(2,0              , width/2.);
+      // The right-sided Gauss 
+      f->SetParLimits(3,0   , integ);
+      f->SetParLimits(4,mean, max-(width/10.));
+      f->SetParLimits(5,0   , width/2.);
+      obj2->Fit(f,"QLRM");
+      break;
+      
     case 3:
-        obj2->Fit("pol0", "Q");
-        obj2->GetFunction("pol0")->SetLineColor(kYellow);
-        break;
-
+      f = new TF1("tgaus",tgausformula.Data(),min,max);
+      f->SetLineColor(kYellow);
+      f->SetBit(kCanDelete);
+      f->SetParNames("A_{tot}","#mu_{1}","#sigma_{1}",
+                     "A_{2}","#mu_{2}","#sigma_{2}",
+                     "A_{3}","#mu_{3}","#sigma_{3}");
+      f->SetParameters(integ,(min+mean)/2,width/4.,
+                       integ/width/3.,(max+mean)/2.,width/4.,
+                       integ/width/3.,mean,width/2.);
+      // The left-sided Gauss 
+      f->SetParLimits(0,integ-1.5,integ+1.5);
+      f->SetParLimits(1,min+(width/10.),mean);
+      f->SetParLimits(2,width/15.,width/2.);
+      // The right-sided Gauss 
+      f->SetParLimits(3,0.,integ);
+      f->SetParLimits(4,mean,max-(width/10.));
+      f->SetParLimits(5,width/15.,width/2.);
+      // The Gauss describing the outliers
+      f->SetParLimits(6,0.,integ);
+      f->SetParLimits(7,min,max);
+      f->SetParLimits(8,width/4.,width/1.5);
+      obj2->Fit(f,"QLRM");
+      break;
+
+    case 4:
+      obj2->Fit("pol0", "Q");
+      obj2->GetFunction("pol0")->SetLineColor(kYellow);
+      break;
+      
     case 9:
-        break;
-
+      break;
+        
     default:
-        obj2->Fit("gaus", "Q");
-        obj2->GetFunction("gaus")->SetLineColor(kYellow);
-        break;
-    }
-}
-
-void MJCalibration::CamDraw(TCanvas &c, Int_t x, Int_t y, MHCamera &cam1, Int_t fit)
-{
+      obj2->Fit("gaus", "Q");
+      obj2->GetFunction("gaus")->SetLineColor(kYellow);
+      break;
+    }
+}
+
+void MJCalibration::CamDraw(TCanvas &c, const Int_t x, const Int_t y, const MHCamera &cam1, const Int_t fit)
+{
+
+
     c.cd(x);
     gPad->SetBorderMode(0);
@@ -157,16 +174,12 @@
     obj1->Draw();
 
-    c.cd(x+2*y);
-    gPad->SetBorderMode(0);
-    DrawProjection(obj1, fit);
-
-    // tbretz: Using gStyle in this context is totally useless!
-    //const Float_t he = gStyle->GetStatH();
-    //const Float_t wi = gStyle->GetStatH();
-    //gStyle->SetStatH(0.4);
-    //gStyle->SetStatW(0.25);
-    //gStyle->SetStatH(he);
-    //gStyle->SetStatW(wi);
-}
+    if (fit)
+      {
+        c.cd(x+2*y);
+        gPad->SetBorderMode(0);
+        DrawProjection(obj1, fit);
+      }
+}
+
 
 void MJCalibration::DisplayResult(MParList &plist)
@@ -190,118 +203,158 @@
 
     // Create histograms to display
-    MHCamera disp1 (geomcam, "Cal;Charge",        "Fitted Mean Charges");
-    MHCamera disp3 (geomcam, "Cal;SigmaCharge",   "Sigma of Fitted Charges");
-    MHCamera disp5 (geomcam, "Cal;FitProb",       "Probability of Fit");
-    /*
-     MHCamera disp6 (geomcam, "Cal;Time",          "Arrival Times");
-     MHCamera disp7 (geomcam, "Cal;SigmaTime",     "Sigma of Arrival Times");
-     MHCamera disp8 (geomcam, "Cal;TimeChiSquare", "Chi Square of Time Fit");
-     */
-//    MHCamera disp9 (geomcam, "Cal;Ped",           "Pedestals");
-//    MHCamera disp10(geomcam, "Cal;PedRms",        "Pedestal RMS");
-//    MHCamera disp11(geomcam, "Cal;RSigma",         "Reduced Sigmas");
-    MHCamera disp12(geomcam, "Cal;FFactorPhe",     "Nr. of Phe's (F-Factor Method)");
-    MHCamera disp13(geomcam, "Cal;FFactorConv",    "Conversion Factor (F-Factor Method)");
-    MHCamera disp14(geomcam, "Cal;BlindPixPhe",    "Nr. of Photons inside plexiglass (Blind Pixel Method)");
-    MHCamera disp15(geomcam, "Cal;BlindPixConv",   "Conversion Factor (Blind Pixel Method)");
-//    MHCamera disp16(geomcam, "Cal;RSigma/Charge",  "Reduced Sigma per Charge");
-
-    disp1.SetCamContent(fCalibrationCam, 0);
-    disp1.SetCamError(fCalibrationCam, 1);
-
-    disp3.SetCamContent(fCalibrationCam, 2);
-    disp3.SetCamError(fCalibrationCam, 3);
-
-    disp5.SetCamContent(fCalibrationCam, 4);
-
-    /*
-    disp6.SetCamContent(fCalibrationCam, 5);
-    disp6.SetCamError(fCalibrationCam, 6);
-    disp7.SetCamContent(fCalibrationCam, 6);
-    disp8.SetCamContent(fCalibrationCam, 7);
-    */
-/*
-    disp9.SetCamContent(calcam, 8);
-    disp9.SetCamError(calcam, 9);
-    disp10.SetCamContent(calcam, 9);
-    disp11.SetCamContent(fCalibrationCam, 10);
- */
-    disp12.SetCamContent(fCalibrationCam, 11);
-    disp12.SetCamError(fCalibrationCam, 12);
-    disp13.SetCamContent(fCalibrationCam, 13);
-    disp13.SetCamError(fCalibrationCam, 14);
-
-    disp14.SetCamContent(fCalibrationCam, 15);
-    disp15.SetCamContent(fCalibrationCam, 16);
- //   disp16.SetCamContent(fCalibrationCam, 17);
+    MHCamera disp1  (geomcam, "Cal;Charge",         "Fitted Mean Charges");
+    MHCamera disp2  (geomcam, "Cal;SigmaCharge",    "Sigma of Fitted Charges");
+    MHCamera disp3  (geomcam, "Cal;FitProb",        "Probability of Fit");
+    MHCamera disp4  (geomcam, "Cal;RSigma",         "Reduced Sigmas");
+    MHCamera disp5  (geomcam, "Cal;RSigma/Charge",  "Reduced Sigma per Charge");
+    MHCamera disp6  (geomcam, "Cal;FFactorPhe",     "Nr. of Phe's (F-Factor Method)");
+    MHCamera disp7  (geomcam, "Cal;FFactorConv",    "Conversion Factor (F-Factor Method)");
+    MHCamera disp8  (geomcam, "Cal;FFactorFFactor", "Total F-Factor (F-Factor Method)");
+    MHCamera disp9  (geomcam, "Cal;BlindPixPh",     "Nr. of Photons inside plexiglass (Blind Pixel Method)");
+    MHCamera disp10 (geomcam, "Cal;BlindPixConv",   "Conversion Factor (Blind Pixel Method)");
+    MHCamera disp11 (geomcam, "Cal;BlindPixFFactor","Total F-Factor (Blind Pixel Method)");
+    MHCamera disp12 (geomcam, "Cal;PINDiodePh",     "Nr. of Photons outside plexiglass (PIN Diode Method)");
+    MHCamera disp13 (geomcam, "Cal;PINDiodeConv",   "Conversion Factor (PIN Diode Method)");
+    MHCamera disp14 (geomcam, "Cal;PINDiodeFFactor","Total F-Factor (PIN Diode Method)");
+    MHCamera disp15 (geomcam, "Cal;Excluded",       "Pixels previously excluded");
+    MHCamera disp16 (geomcam, "Cal;NotFitted",      "Pixels that could not be fitted");
+    MHCamera disp17 (geomcam, "Cal;NotFitValid",    "Pixels with not valid fit results");
+    MHCamera disp18 (geomcam, "Cal;Oscillating",    "Oscillating Pixels");
+    MHCamera disp19 (geomcam, "Cal;Saturation",     "Pixels with saturated Hi Gain");
+
+
+    // Fitted charge means and sigmas
+    disp1.SetCamContent(fCalibrationCam,  0);
+    disp1.SetCamError(  fCalibrationCam,  1);
+    disp2.SetCamContent(fCalibrationCam,  2);
+    disp2.SetCamError(  fCalibrationCam,  3);
+    // Fit probabilities
+    disp3.SetCamContent(fCalibrationCam,  4);
+
+    // Reduced Sigmas and reduced sigmas per charge
+    disp4.SetCamContent(fCalibrationCam,  5);
+    disp4.SetCamError(  fCalibrationCam,  6);
+    disp5.SetCamContent(fCalibrationCam,  7);
+    disp5.SetCamError(  fCalibrationCam,  8);
+
+    // F-Factor Method
+    disp6.SetCamContent(fCalibrationCam,  9);
+    disp6.SetCamError(  fCalibrationCam, 10);
+    disp7.SetCamContent(fCalibrationCam, 11);
+    disp7.SetCamError(  fCalibrationCam, 12);
+    disp8.SetCamContent(fCalibrationCam, 13);
+    disp8.SetCamError(  fCalibrationCam, 14);
+
+    /// Blind Pixel Method
+    disp9.SetCamContent(fCalibrationCam, 15);
+    disp9.SetCamError(  fCalibrationCam, 16);
+    disp10.SetCamContent(fCalibrationCam,17);
+    disp10.SetCamError(  fCalibrationCam,18);
+    disp11.SetCamContent(fCalibrationCam,19);
+    disp11.SetCamError(  fCalibrationCam,20);
+
+    // PIN Diode Method
+    disp12.SetCamContent(fCalibrationCam,21);
+    disp12.SetCamError(  fCalibrationCam,22);
+    disp13.SetCamContent(fCalibrationCam,23);
+    disp13.SetCamError(  fCalibrationCam,24);
+    disp14.SetCamContent(fCalibrationCam,25);
+    disp14.SetCamError(  fCalibrationCam,26);
+
+    // Pixels with defects
+    disp15.SetCamContent(fCalibrationCam,27);
+    disp16.SetCamContent(fCalibrationCam,28);
+    disp17.SetCamContent(fCalibrationCam,29);
+    disp18.SetCamContent(fCalibrationCam,30);
+
+    // Lo Gain calibration
+    disp19.SetCamContent(fCalibrationCam,31);
+
 
     disp1.SetYTitle("Charge [FADC units]");
-    disp3.SetYTitle("\\sigma_{Charge} [FADC units]");
-    disp5.SetYTitle("P_{Charge} [1]");
-    /*
-     disp6.SetYTitle("Arr. Time [FADC slice Nr.]");
-     disp7.SetYTitle("\\sigma_{Time} [FADC slices]");
-     disp8.SetYTitle("\\chi^{2}_{Time} [1]");
-    disp9.SetYTitle("Ped [FADC Counts ]");
-    disp10.SetYTitle("RMS_{Ped} [FADC Counts ]");
-    disp11.SetYTitle("\\sqrt{\\sigma^{2}_{Charge} - RMS^{2}_{Ped}} [FADC units]");
-     */
-    disp12.SetYTitle("Nr. Photo-Electrons [1]");
-    disp13.SetYTitle("Conversion Factor [PhE/FADC Count]");
-    disp14.SetYTitle("Nr. Photons [1]");
-    disp15.SetYTitle("Conversion Factor [Phot/FADC Count]");
-//    disp16.SetYTitle("Reduced Sigma / Charge [1]");
+    disp2.SetYTitle("\\sigma_{Charge} [FADC units]");
+    disp3.SetYTitle("P_{Charge} [1]");
+
+    disp4.SetYTitle("\\sqrt{\\sigma^{2}_{Charge} - RMS^{2}_{Ped}} [FADC Counts]");
+    disp5.SetYTitle("Reduced Sigma / Mean Charge [1]");
+
+    disp6.SetYTitle("Nr. Photo-Electrons [1]");
+    disp7.SetYTitle("Conversion Factor [PhE/FADC Count]");
+    disp8.SetYTitle("\\sqrt{N_{PhE}}*\\sigma_{Charge}/\\mu_{Charge} [1]");
+
+    disp9.SetYTitle("Nr. Photons [1]");
+    disp10.SetYTitle("Conversion Factor [Phot/FADC Count]");
+    disp11.SetYTitle("\\sqrt{N_{Ph}}*\\sigma_{Charge}/\\mu_{Charge} [1]");
+
+    disp12.SetYTitle("Nr. Photons [1]");
+    disp13.SetYTitle("Conversion Factor [Phot/FADC Count]");
+    disp14.SetYTitle("\\sqrt{N_{Ph}}*\\sigma_{Charge}/\\mu_{Charge} [1]");
+
+    disp15.SetYTitle("[1]");
+    disp16.SetYTitle("[1]");
+    disp17.SetYTitle("[1]");
+    disp18.SetYTitle("[1]");
 
     gStyle->SetOptStat(1111);
     gStyle->SetOptFit();
 
-    TCanvas &c1 = fDisplay->AddTab("FitCharge");
+    // Charges
+    TCanvas &c1 = fDisplay->AddTab("Fit.Charge");
     c1.Divide(2, 3);
 
-    CamDraw(c1, 1, 2, disp1, 1);
-    CamDraw(c1, 2, 2, disp3, 2);
+    CamDraw(c1, 1, 2, disp1, 2);
+    CamDraw(c1, 2, 2, disp2, 2);
 
     // Fit Probability
-    TCanvas &c2 = fDisplay->AddTab("FitProb");
+    TCanvas &c2 = fDisplay->AddTab("Fit.Prob");
     c2.Divide(1,3);
 
-    CamDraw(c2, 1, 1, disp5, 3);
-/*
-    // Times
-    TCanvas &c3 = fDisplay->AddTab("FitTimes");
-    c3.Divide(3,3);
-
-    CamDraw(c3, 1, 3, disp6, 1);
-    CamDraw(c3, 2, 3, disp7, 0);
-    CamDraw(c3, 3, 3, disp8, 0);
-
-    // Pedestals
-    TCanvas &c4 = d3->AddTab("Pedestals");
-    c4.Divide(2,3);
-
-    CamDraw(c4, 1, 2, disp9,  0);
-    CamDraw(c4, 2, 2, disp10, 1);
+    CamDraw(c2, 1, 1, disp3, 4);
 
     // Reduced Sigmas
-    TCanvas &c5 = fDisplay->AddTab("RedSigma");
-    c5.Divide(2,3);
-
-    CamDraw(c5, 1, 2, disp11, 2);
-    CamDraw(c5, 2, 2, disp16, 2);
-    */
+    TCanvas &c3 = fDisplay->AddTab("Red.Sigma");
+    c3.Divide(2,3);
+
+    CamDraw(c3, 1, 2, disp4, 2);
+    CamDraw(c3, 2, 2, disp5, 2);
 
     // F-Factor Method
-    TCanvas &c6 = fDisplay->AddTab("F-Factor");
-    c6.Divide(2,3);
-
-    CamDraw(c6, 1, 2, disp12, 1);
-    CamDraw(c6, 2, 2, disp13, 1);
+    TCanvas &c4 = fDisplay->AddTab("F-Factor");
+    c4.Divide(3,3);
+
+    CamDraw(c4, 1, 3, disp6, 2);
+    CamDraw(c4, 2, 3, disp7, 2);
+    CamDraw(c4, 3, 3, disp8, 2);
 
     // Blind Pixel Method
-    TCanvas &c7 = fDisplay->AddTab("BlindPix");
-    c7.Divide(2, 3);
-
-    CamDraw(c7, 1, 2, disp14, 9);
-    CamDraw(c7, 2, 2, disp15, 1);
+    TCanvas &c5 = fDisplay->AddTab("BlindPix");
+    c5.Divide(3, 3);
+
+    CamDraw(c5, 1, 3, disp9,  9);
+    CamDraw(c5, 2, 3, disp10, 2);
+    CamDraw(c5, 3, 3, disp11, 2);
+
+    // PIN Diode Method
+    TCanvas &c6 = fDisplay->AddTab("PINDiode");
+    c6.Divide(3,3);
+
+    CamDraw(c6, 1, 3, disp12, 9);
+    CamDraw(c6, 2, 3, disp13, 2);
+    CamDraw(c6, 3, 3, disp14, 2);
+
+    // Defects
+    TCanvas &c7 = fDisplay->AddTab("Defects");
+    c7.Divide(4,2);
+
+    CamDraw(c7, 1, 4, disp15, 0);
+    CamDraw(c7, 2, 4, disp16, 0);
+    CamDraw(c7, 3, 4, disp17, 0);
+    CamDraw(c7, 4, 4, disp18, 0);
+
+    // Lo Gain Calibration
+    TCanvas &c8 = fDisplay->AddTab("LowGain");
+    c8.Divide(1,3);
+
+    CamDraw(c8, 1, 4, disp19, 0);
 
 }
@@ -413,5 +466,5 @@
 
     MGeomApply       apply;
-    MExtractSignal   extract;
+    MExtractSignal2  extract;
     MCalibrationCalc calcalc;
 
