Jungfrau stuff updated

git-svn-id: file:///afs/psi.ch/project/sls_det_software/svn/slsDetectorCalibration@48 113b152e-814d-439b-b186-022a431db7b5

slsDetectorCalibration/chiptestBoardData.h

@@ -62,7 +62,7 @@ class chiptestBoardData : public slsDetectorData<uint16_t> {
     if (filebin.is_open()) {
      if (filebin.read((char*)&afifo_length,sizeof(uint32_t))) {
 	setDataSize(afifo_length*nAdc*sizeof(uint16_t));
-	afifo_cont=new uint16_t[afifo_length];
+	afifo_cont=new uint16_t[afifo_length*nAdc];
  	if (filebin.read((char*)afifo_cont,afifo_length*sizeof(uint16_t)*nAdc)) {
 		iframe++;
 		return (char*)afifo_cont;

slsDetectorCalibration/commonModeSubtraction.h

@@ -31,7 +31,7 @@ class commonModeSubtraction {
 	cmPed[i]=0;
       }};
     
-    /** adds the average of pedestals to the  moving average and reienitialize the calculation of the sum of pedestals for all ROIs. - virtual func*/
+    /** adds the average of pedestals to the moving average and reinitializes the calculation of the sum of pedestals for all ROIs. - virtual func*/
     virtual void  newFrame(){
       for (int i=0; i<nROI; i++) {
 	if (nCm[i]>0) cmStat[i].Calc(cmPed[i]/nCm[i]);  

slsDetectorCalibration/energyCalibration.cpp

@@ -235,7 +235,7 @@ energyCalibration::energyCalibration() :
 					 fspectrum(NULL),
 #endif
 					 funcs(NULL),
-					 plot_flag(1),
+					 plot_flag(1), // fit parameters output to screen
 					 cs_flag(1)
 {
 
@@ -441,7 +441,7 @@ TF1* energyCalibration::fitFunction(TF1 *fun, TH1 *h1, Double_t *mypar, Double_t
   strcpy(fname, fun->GetName());
 
   if (plot_flag) {
-    h1->Fit(fname,"R");
+    h1->Fit(fname,"R0Q");
   } else
     h1->Fit(fname,"R0Q");
 
@@ -526,4 +526,4 @@ TGraphErrors* energyCalibration::calibrate(int nscan, Double_t *en, Double_t *ee
 
 
 
-
+Fit data is empty

slsDetectorCalibration/jungfrau02Data.h

@@ -41,19 +41,22 @@ class jungfrau02Data : public chiptestBoardData {
     for (int iy=0; iy<48; iy++) {
       for (int ix=0; ix<48; ix++) {
 	
-	dMap[iy][ix]=offset+(iy*48+ix)*nAdc;
+	dMap[ix][iy]=offset+(iy*48+ix)*nAdc;//dMap[iy][ix]=offset+(iy*48+ix)*nAdc;
 	// cout << ix << " " << iy << " " << dMap[ix][iy] << endl;
       }
     }
 
+    cout << (0,0) << " " << dMap[0][0] << endl;
+    cout << (47,47) << " " << dMap[47][47] << endl;
+	
+
     for (int ix=0; ix<48; ix++) {
       for (int iy=0; iy<48; iy++)
 	dMask[iy][ix]=0x0; 
-    }
 
     setDataMap(dMap);
     setDataMask(dMask);
-
+    }
 
 
 
@@ -76,11 +79,11 @@ class jungfrau02Data : public chiptestBoardData {
           d=*(((uint16_t*)(data))+dataMap[iy][ix]); 
       // cout << ix << " " << iy << " " << (uint16_t*)data << " " << ((uint16_t*)(data))+dataMap[iy][ix] << " " << d << endl;
 	if (nAdc==3) {
-	  cout << "Gain bit!" << endl;
+	  //cout << "Gain bit!" << endl;
-	  if (*((uint16_t*)(data)+dataMap[iy][ix]+1)>8000)
+	  if (*((uint16_t*)(data)+dataMap[iy][ix]+2)>8000) //exchange if gainBits==2 is returned!
-		d|=(1<<14); // set gain bit 0
+		d|=(1<<14); // gain bit 1
-	  if (*((uint16_t*)(data)+dataMap[iy][ix]+2)>8000)
+	  if (*((uint16_t*)(data)+dataMap[iy][ix]+1)>8000) //exchange if gainBits==2 is returned!
-		d|=(1<<15); // set gain bit 1
+		d|=(1<<15); // gain bit 0
 	  
         }
 
@@ -106,6 +109,20 @@ class jungfrau02Data : public chiptestBoardData {
       return  (double)(getChannel(data, ix, iy)&0x3fff)-xtalk* (double)(getChannel(data, ix, iy)&0x3fff);
   };
   
+  /**
+    returns the gain bit value, i.e. returns 0 if(GB0==0 && GB1==0), returns 1 if(GB0==1 && GB1==0), returns 3 if(GB0==1 && GB1==1), if it returns 2 -> the gain bits are read out the wrong way around (i.e. GB0 and GB1 have to be reversed!)
+     \param data pointer to the memory
+     \param ix coordinate in the x direction
+     \param iy coordinate in the y direction
+     \returns gain bits as int
+  */
+  int getGainBits(char *data, int ix, int iy=0) { 
+  	uint16_t d=getChannel(data, ix, iy);
+  	return ((d&0xc000)>>14); 
+  };
+  //*/
+ 
+
   
 
   /** sets the output buffer crosstalk correction parameter

slsDetectorCalibration/jungfrauReadData.C

@@ -15,12 +15,12 @@
 //#include <queue>
 #include <fstream>
 #include "jungfrau02Data.h"
-#include "moenchCommonMode.h"
 #include "jungfrau02CommonMode.h"
 #include "singlePhotonDetector.h"
 
 //#include "MovingStat.h"
 
+
 using namespace std;
 
 #define NC 48
@@ -49,18 +49,37 @@ Loops over data file to find single photons, fills the tree (and writes it to fi
   \param xmax maximum x coordinate
   \param ymin minimum y coordinate
   \param ymax maximum y coordinate
-  \param cmsub  enable commonmode subtraction -> Currently, CM subtraction is not implemented for Jungfrau!
+  \param cmsub  enable commonmode subtraction 
   \param hitfinder if 0: performs pedestal subtraction, not hit finding; if 1: performs both pedestal subtraction and hit finding
+  \param fcal -> calibration file, which contains 7 columns per pixel; 1) pixel #, 2) cal. offset G0, 3) cal. slope G0, 4) cal. offset G1, 5) cal. slope G1, 6) cal. offset G2, 7) cal. slope G2
   \returns pointer to histo stack with cluster spectra
 */
 
 
-THStack *jungfrauReadData(char *fformat, char *tit, int runmin, int runmax, int nbins=1500, int hmin=-500, int hmax=1000, int sign=1, double hc=0, int xmin=1, int xmax=NC-1, int ymin=1, int ymax=NR-1, int cmsub=0, int hitfinder=1) {
+THStack *jungfrauReadData(char *fformat, char *tit, int runmin, int runmax, int nbins=1500, int hmin=-500, int hmax=1000, int sign=1, double hc=0, int xmin=1, int xmax=NC-1, int ymin=1, int ymax=NR-1, int cmsub=0, int hitfinder=1){
 
-  jungfrau02Data *decoder=new jungfrau02Data(1,0,0);
+  // read in calibration file
-  jungfrau02CommonMode *cmSub=NULL;//moenchCommonMode *cmSub=NULL; //
+  ifstream calfile("/mnt/slitnas/datadir_jungfrau02/analysis_tests/CalibrationParametersTest_fake.txt");
-//   if (cmsub)
+  if (calfile.is_open()==0){cout << "Unable to open calibration file!" << endl;}
-//     cmSub=new moenchCommonMode();
+  int pix;
+  double of0,sl0,of1,sl1,of2,sl2;
+  double of_0[NC*NR], of_1[NC*NR], of_2[NC*NR], sl_0[NC*NR], sl_1[NC*NR], sl_2[NC*NR];
+  while (calfile >> pix >> of0 >> sl0 >> of1 >> sl1 >> of2 >> sl2){ 
+    	of_0[pix]=of0;
+    	sl_0[pix]=sl0;
+    	of_1[pix]=of1;
+    	sl_1[pix]=sl1;
+    	of_2[pix]=of2;
+    	sl_2[pix]=sl2; //if(pix==200) cout << "sl_2[200] " << sl_2[200] << endl;
+  }
+  calfile.close();
+  
+  double adc_value, num_photon;
+
+  jungfrau02Data *decoder=new jungfrau02Data(1,0,0);//(3,0,0); // (adc,offset,crosstalk) //(1,0,0) //(3,0,0) for readout of GB
+  jungfrau02CommonMode *cmSub=NULL;
+   if (cmsub)
+     cmSub=new jungfrau02CommonMode();
 
   int nph=0;
   int iev=0;
@@ -85,10 +104,12 @@ THStack *jungfrauReadData(char *fformat, char *tit, int runmin, int runmax, int
   THStack *hs=new THStack("hs",fformat);
 
 
-
   TH2F *h1=new TH2F("h1",tit,nbins,hmin-0.5,hmax-0.5,NC*NR,-0.5,NC*NR-0.5);
   hs->Add(h1);
   
+  
+ 
+
   if (hitfinder) {
     h2=new TH2F("h2",tit,nbins,hmin-0.5,hmax-0.5,NC*NR,-0.5,NC*NR-0.5);
     h3=new TH2F("h3",tit,nbins,hmin-0.5,hmax-0.5,NC*NR,-0.5,NC*NR-0.5);
@@ -101,7 +122,6 @@ THStack *jungfrauReadData(char *fformat, char *tit, int runmin, int runmax, int
   }
 
   
-  
   ifstream filebin;
 
 
@@ -143,7 +163,7 @@ THStack *jungfrauReadData(char *fformat, char *tit, int runmin, int runmax, int
   filter->newDataSet();
 
 
-  for (int irun=runmin; irun<=runmax; irun++){ //{for (int irun=runmin; irun<runmax; irun++) {
+  for (int irun=runmin; irun<=runmax; irun++){ 
     sprintf(fname,fformat,irun);
     cout << "file name " << fname << endl;
     filebin.open((const char *)(fname), ios::in | ios::binary);
@@ -173,19 +193,25 @@ THStack *jungfrauReadData(char *fformat, char *tit, int runmin, int runmax, int
 
 
 	  thisEvent=filter->getEventType(buff, ix, iy, cmsub);
+	  int gainBits=decoder->getGainBits(buff,ix,iy); // get gain bits
 
 #ifdef MY_DEBUG
 	  if (hitfinder) {
 	    if (iev%1000==0)
-	      he->SetBinContent(ix+1-xmin, iy+1-ymin, (int)thisEvent);
+	     //he->SetBinContent(ix+1-xmin, iy+1-ymin, (int)thisEvent); // show single photon hits // original
-	    
+	     //he->SetBinContent(ix+1-xmin, iy+1-ymin, cmSub->getCommonMode(ix,iy)); //show common mode!
+ 	     he->SetBinContent(iy+1-ymin, ix+1-xmin, (int)gainBits); //show gain bits   
+             //he->SetBinContent(ix+1-xmin, iy+1-ymin, (int)gainBits); // rows and columns reversed!!! 
 	  }
 #endif	  
 	  
-	  if (nf>1000) {
+	  if (nf>1000) { // only start filing data after 1000 frames
 
 	    //   h1->Fill(decoder->getValue(buff,ix,iy), iy+NR*ix);
 	    h1->Fill(filter->getClusterTotal(1), iy+NR*ix);
+
+            
+ 
 	    if (hitfinder) {
 	      
 	      if (thisEvent==PHOTON_MAX ) {

slsDetectorCalibration/pedestalSubtraction.h

@@ -21,7 +21,7 @@ class pedestalSubtraction  {
     /** adds the element to the moving average 
 	\param val value to be added
     */
-    virtual void addToPedestal(double val){ stat.Calc(val);};
+    virtual void addToPedestal(double val){stat.Calc(val);};
 
   /** returns the average value of the pedestal
       \returns mean of the moving average

slsDetectorCalibration/readJungfrauData.C

@@ -1,13 +1,19 @@
 { // script to run Jungfrau data analysis
 
-  gROOT->ProcessLine(".L jungfrauReadData.C+");
+  gROOT->ProcessLine(".L jungfrauReadData.C++");//");
 
   TFile *fout; 		// output file
   THStack *hs2N; 	// collection of objects
 
-  fout=new TFile("/mnt/slitnas/datadir_jungfrau02/20140131_analysis/test/outfile.root","RECREATE"); // careful "RECREATE" will OVERWRITE!
+  fout=new TFile("/mnt/slitnas/datadir_jungfrau02/jungfrau_Trieste_2014/TriesteBeam2014/Analysis/D4_M1_HG_2000clk_CD986_CMsub.root","RECREATE"); // 
+    
+  //hs2N=jungfrauReadData("/mnt/slitnas/datadir_jungfrau02/20140131_BeamSLS/datadir_310114/21keV_10us_HIGHG0_CDS550_%d.bin","tit",0,75,1500,-500,2500,1,0.,1,47,1,47,1,1); //1,1); 
+  
+ //hs2N=jungfrauReadData("/mnt/slitnas/datadir_jungfrau02/20140228_GainBits/GSdata_laser_%d.bin","tit",0,5,1500,-500,2500,1,0.,1,47,1,47,0,1);//,"/mnt/slitnas/datadir_jungfrau02/analysis_tests/CalibrationParametersTest_fake.txt"); //1,1); // data set test GB -> set (3,0,0) in junfrauReadData.C
+
+  hs2N=jungfrauReadData("/mnt/slitnas/datadir_jungfrau02/jungfrau_Trieste_2014/Trieste_20140314/HG_20keV_CDS986_2000clk_%d.bin","tit",0,201,3000,-499.5,2500.5,1,0.,1,47,1,47,1,1);
+//,"/mnt/slitnas/datadir_jungfrau02/analysis_tests/CalibrationParametersTest_fake.txt"); //1,1); // data set test GB -> set (3,0,0) in junfrauReadData.C
 
-  hs2N=jungfrauReadData("/mnt/slitnas/datadir_jungfrau02/20140131_BeamSLS/datadir_310114/18keV_10us_HIGHG0_CDS550_%d.bin","tit",0,10,1500,-500,2500,1,0.,1,47,1,47,1,1); //0,1);
   //hs2N->SetName("cds_g4");
   //hs2N->SetTitle("cds_g4");
 
@@ -16,11 +22,10 @@
  (TH2F*)(hs2N->GetHists()->At(2))->Write();
  (TH2F*)(hs2N->GetHists()->At(3))->Write();
  (TH2F*)(hs2N->GetHists()->At(4))->Write();
+ //(TH2F*)(hs2N->GetHists()->At(5))->Write();
+ //(TH2F*)(hs2N->GetHists()->At(6))->Write();
 
-
+  //fout->Close(); // uncomment
-  fout->Close();
-
-
 
 }
 

slsDetectorCalibration/slsDetectorData.h

@@ -44,6 +44,8 @@ class slsDetectorData {
     dataROIMask=new int*[ny];
     for(int i = 0; i < ny; i++) {
       dataROIMask[i] = new int[nx];
+      for (int j=0; j<nx; j++)
+	 dataROIMask[i][j]=1;
     }
     
     setDataMap(dMap);