Index: /trunk/MagicSoft/Mars/mtemp/mifae/programs/Makefile
===================================================================
--- /trunk/MagicSoft/Mars/mtemp/mifae/programs/Makefile	(revision 4393)
+++ /trunk/MagicSoft/Mars/mtemp/mifae/programs/Makefile	(revision 4394)
@@ -18,5 +18,5 @@
 include ../../../Makefile.conf.general
 
-PROGRAMS = makeHillas psffit falseSource srcPos optimizeCuts
+PROGRAMS = makeHillas psffit falseSource srcPos optimizeCuts calib controlPlot
 SOLIB    = $(MARSSYS)/libmars.so
 
@@ -43,5 +43,6 @@
 	   -I../../../mcamera \
 	   -I../../../mhist \
-	   -I../../../mastro
+	   -I../../../mastro \
+           -I../../../mtemp
 
 all: $(PROGRAMS)
Index: /trunk/MagicSoft/Mars/mtemp/mifae/programs/calib.cc
===================================================================
--- /trunk/MagicSoft/Mars/mtemp/mifae/programs/calib.cc	(revision 4394)
+++ /trunk/MagicSoft/Mars/mtemp/mifae/programs/calib.cc	(revision 4394)
@@ -0,0 +1,312 @@
+/*********************************/
+/* Compute the hillas parameters */
+/*********************************/
+
+#include "TString.h"
+#include "TArrayS.h"
+
+#include "MParList.h"
+#include "MTaskList.h"
+#include "MPedestalCam.h"
+#include "MBadPixelsCam.h"
+#include "MBadPixelsTreat.h"
+#include "MReadMarsFile.h"
+#include "MGeomApply.h"
+#include "MPedCalcPedRun.h"
+#include "MEvtLoop.h"
+#include "MGeomCamMagic.h"
+#include "MExtractedSignalCam.h"
+#include "MCalibrationChargeCam.h"
+#include "MCalibrationQECam.h"
+#include "MCalibrationQEPix.h"
+#include "MHCalibrationChargeCam.h"
+#include "MHCalibrationRelTimeCam.h"
+#include "MExtractor.h"
+#include "MExtractFixedWindow.h"
+#include "MExtractSlidingWindow.h"
+#include "MExtractSignal.h"
+#include "MCalibrationChargeCalc.h"
+#include "MFCosmics.h"
+#include "MContinue.h"
+#include "MLog.h"
+#include "MCerPhotEvt.h"
+#include "MPedPhotCam.h"
+#include "MCalibrate.h"
+#include "MPedPhotCalc.h"
+#include "MHillas.h"
+#include "MNewImagePar.h"
+#include "MRawRunHeader.h"
+#include "MSrcPosCam.h"
+#include "MBlindPixelCalc.h"
+#include "MImgCleanStd.h"
+#include "MHillasSrcCalc.h"
+#include "MHillasCalc.h"
+#include "MArrivalTimeCam.h"
+#include "MArrivalTimeCalc2.h"
+#include "MIslands.h"
+#include "MIslandCalc.h"
+#include "MIslandClean.h"
+#include "MWriteRootFile.h"
+#include "MArgs.h"
+#include "MRunIter.h"
+#include "MJPedestal.h"
+#include "MJCalibration.h"
+#include "MHillasDisplay.h"
+#include "MF.h"
+#include "MContinue.h"
+
+#include "TApplication.h"
+
+#include <iostream>
+#include <fstream>
+#include <stdlib.h>
+
+using namespace std;
+
+Bool_t readDatacards(TString& filename);
+void calib();
+
+// initial and final time slices to be used in signal extraction
+const Byte_t hifirst = 1;
+const Byte_t hilast  = 14;
+const Byte_t lofirst = 3;
+const Byte_t lolast  = 14;
+
+// declaration of variables read from datacards
+TString  outname;
+TString  idirname;
+TString  filter;
+TString  psfilename("makehillas.ps");
+MRunIter caliter;
+MRunIter pediter;
+MRunIter datiter;
+UInt_t   display   = 0;
+ULong_t  nmaxevents= 999999999;
+Short_t  calflag   = 1;
+Float_t  lcore     = 3.0;
+Float_t  ltail     = 1.5;
+Int_t    islflag   = 0;
+Float_t  lnew      = 40;
+Int_t    kmethod   = 1;
+Int_t    kalgorithm = 1;
+Int_t    nfiles    = 0;
+
+const TString defaultcard="makehillas.datacard";
+/*************************************************************/
+static void Usage()
+{
+  gLog <<endl;
+  gLog << "Usage is:" << endl;
+  gLog << "   calib [-h] [-?] <datacards>" << endl << endl;
+  gLog << "     <datacards>: datacards file name (dafault input.datacards)" << endl;
+  gLog << "     -?/-h: This help" << endl << endl;
+}
+/*************************************************************/
+int main(int argc, char **argv)
+{
+  // create a TApplication to be able to 
+  TApplication app("Application",0,0);
+
+  // evaluate arguments
+  MArgs arg(argc, argv);
+  if (arg.HasOnly("-?") || arg.HasOnly("-h") || arg.HasOnly("--help"))
+    {
+      Usage();
+      return -1;
+    }
+
+  TString datacard  = arg.GetArgumentStr(0);
+  if(!datacard.Length())
+    datacard = defaultcard;
+
+  if(!readDatacards(datacard))
+    {
+      cout << "Error reading datacards. Stoping" << endl;
+      return -1;
+    }
+
+  calib();
+}
+
+/*************************************************************/
+void calib()
+{
+  // Set the general tasks/containers
+  MExtractFixedWindow    extractor;
+  extractor.SetRange(hifirst,hilast,lofirst,lolast);
+ 
+  //  MExtractSlidingWindow    extractor;
+  // extractor.SetRange(hifirst,hilast,lofirst,lolast);
+  // extractor.SetWindowSize(2,2);
+  
+  MGeomCamMagic       geomcam;
+  MGeomApply          geomapl;
+
+  /************************************/
+  /* FIRST LOOP: PEDESTAL COMPUTATION */
+  /************************************/
+
+  // If you want to exclude pixels from the beginning, read 
+  // an ascii-file with the corr. pixel numbers (see MBadPixelsCam)  
+  //badcam.AsciiRead("badpixels.dat");
+
+  MJPedestal pedloop;
+  pedloop.SetInput(&pediter);
+  pedloop.SetExtractor(&extractor);
+  //  pedloop.SetBadPixels(badcam);
+
+  if (!pedloop.Process())
+    return;
+
+  /*****************************/
+  /* SECOND LOOP: CALIBRATION  */
+  /*****************************/        
+
+  MJCalibration calloop;
+
+  calloop.SetExtractor(&extractor);
+  calloop.SetInput(&caliter);
+  calloop.SetBadPixels(pedloop.GetBadPixels());
+  if(calflag==2)
+    calloop.SetUseBlindPixel();
+
+  if(calflag>0)
+    if (!calloop.Process(pedloop.GetPedestalCam()))
+      return;
+
+  Float_t meanCharge[577];
+  Float_t meanSigma[577];
+  Float_t meanFADC2Phe[577];
+  Float_t meanFADCtoPh[577];
+  Float_t prob[577];
+  ofstream fout;
+
+  fout.open(outname);
+
+  for (Int_t i=0; i<577; i++)
+    {
+      meanCharge[i] = 0;
+      MCalibrationChargePix calpix = (MCalibrationChargePix&)(calloop.GetCalibrationCam())[i];
+      MCalibrationQEPix qepix = ( MCalibrationQEPix&)(calloop.GetQECam())[i];
+      meanCharge[i] = calpix.GetMean();
+      meanSigma[i] = calpix.GetSigma();
+      meanFADC2Phe[i]=calpix.GetMeanConvFADC2Phe();
+      meanFADCtoPh[i]=calpix.GetMeanConvFADC2Phe()/qepix.GetQECascadesFFactor(0);
+      prob[i]=calpix.GetProb();
+      fout << i << '\t' << meanCharge[i] << '\t' << meanSigma[i]<< '\t' << meanFADC2Phe[i]<< '\t' <<meanFADCtoPh[i]<< '\t' <<prob[i]<< '\t' <<(Int_t)calpix.IsHiGainSaturation()<<endl;
+    }
+
+  fout.close();
+
+  return;
+
+}
+//-------------------------------------------------------------------------------
+
+Bool_t readDatacards(TString& filename)
+{
+  ifstream ifun(filename.Data());
+  if(!ifun)
+    {
+      cout << "File " << filename << " not found" << endl;
+      return kFALSE;
+    }
+
+  TString word;
+  
+  while(ifun >> word)
+    {
+      // skip comments
+      if(word[0]=='/' && word[1]=='/')
+	{
+	  while(ifun.get()!='\n'); // skip line
+	  continue;
+	}
+
+      // input file directory
+      if(strcmp(word.Data(),"IDIR")==0)
+	{
+	  if(idirname.Length())
+	    cout << "readDataCards Warning: overriding input directory file name" << endl;
+	  ifun >> idirname;
+	}
+
+      // pedestal runs
+      if(strcmp(word.Data(),"PRUNS")==0)
+	{
+	  if(pediter.GetNumRuns())
+	    cout << "readDataCards Warning: adding pedestal runs to the existing list" << endl;
+	  ifun >> word;
+	  pediter.AddRuns(word.Data(),idirname.Data());
+	}
+
+      // calibration runs
+      if(strcmp(word.Data(),"CRUNS")==0)
+	{
+	  if(caliter.GetNumRuns())
+	    cout << "readDataCards Warning: adding calibration runs to the existing list" << endl;
+	  ifun >> word;
+	  caliter.AddRuns(word.Data(),idirname.Data());
+	}
+
+      // output file name
+      if(strcmp(word.Data(),"OUTFILE")==0)
+	{
+	  if(outname.Length())
+	    cout << "readDataCards Warning: overriding output file name" << endl;
+	  ifun >> outname;
+	}
+
+      // calibration flag
+      if(strcmp(word.Data(),"CALFLAG")==0)
+	ifun >> calflag;
+
+
+    }
+
+  pediter.Reset();
+  caliter.Reset();
+  datiter.Reset();
+  TString pfile;
+
+  // Dump read values
+  cout << "************************************************" << endl;
+  cout << "* Datacards read from file " << filename << endl;
+  cout << "************************************************" << endl;
+  cout << "Pedestal file (s): "  << endl;
+  while(!(pfile=pediter.Next()).IsNull())
+    cout << pfile << endl;
+  cout << "Calibration file (s): "  << endl;
+  while(!(pfile=caliter.Next()).IsNull())
+    cout << pfile << endl;
+  cout << "Output file name: " << outname << endl;
+  cout << "Calibration: ";
+  if(calflag==0)    
+    cout << "Pixel area proportional intercalibration" << endl;
+  else if(calflag==-1)    
+    cout << "No calibration whatsoever" << endl;
+  else if(calflag==1)
+    cout << "Default calibration" << endl;
+  else if(calflag==11)
+    cout << "Default calibration + bad pixels interpolation" << endl;
+  
+  if(!pediter.GetNumEntries())
+    {
+      cout << "No pedestal file name specified" << endl;
+      return kFALSE;
+    }
+  if(!caliter.GetNumEntries() && calflag>0)
+    {
+      cout << "No calibration file name specified" << endl;
+      return kFALSE;
+    }
+  if(!outname.Length())
+    {
+      cout << "No output file name specified" << endl;
+      return kFALSE;
+    }
+
+
+  return kTRUE;
+}
+
Index: /trunk/MagicSoft/Mars/mtemp/mifae/programs/calib.datacard
===================================================================
--- /trunk/MagicSoft/Mars/mtemp/mifae/programs/calib.datacard	(revision 4394)
+++ /trunk/MagicSoft/Mars/mtemp/mifae/programs/calib.datacard	(revision 4394)
@@ -0,0 +1,32 @@
+/////////////////////////////////////////////////////////
+// Data card template for calib executable             //
+//                                                     //
+// *** Compulsory cards are:                           //
+// PRUNS, CRUNS, DRUNS, OUTFILE                        //
+//                                                     //
+// the rest are optional                               //
+// *** Do NEVER add a datacard with no value after it  //
+/////////////////////////////////////////////////////////
+
+
+// data file directory
+IDIR /nfs/magic/CCdata/rootdata/Mrk421/Period016/2004_04_22/
+
+// Pedestal (PRUNS), calibration (CRUNS)
+PRUNS 30150
+CRUNS 30148
+
+// output file name
+OUTFILE ./prueba.root
+
+// calibration flag:
+// -1: kDummy
+//  0: kNone
+//  1: kDefault (F factor)
+//  2: kDefault (Blind Pixels)
+// 11: kDefault + bad pixel interpolation
+CALFLAG 1
+
+
+
+