From 985b4d71b409c021a60eab8fdf987e7f72a5f069 Mon Sep 17 00:00:00 2001
From: Anna Bergamaschi <anna.bergamaschi@psi.ch>
Date: Thu, 5 Mar 2015 13:04:31 +0100
Subject: [PATCH 01/13] Added jungfrau1.0 data structure (bad) and added xmap,
 ymap and getPixel method to the slsDetectorData base class

---
 slsDetectorCalibration/jungfrau10ModuleData.h | 154 ++++++++++++++++++
 slsDetectorCalibration/moench02CtbData.h      |   4 +-
 slsDetectorCalibration/moench03CtbData.h      |   7 +-
 slsDetectorCalibration/moench03ReadData.C     |  57 +++----
 slsDetectorCalibration/readMoench03Data.C     |  36 ++--
 slsDetectorCalibration/slsDetectorData.h      |  30 +++-
 6 files changed, 230 insertions(+), 58 deletions(-)
 create mode 100644 slsDetectorCalibration/jungfrau10ModuleData.h

diff --git a/slsDetectorCalibration/jungfrau10ModuleData.h b/slsDetectorCalibration/jungfrau10ModuleData.h
new file mode 100644
index 000000000..a107f5058
--- /dev/null
+++ b/slsDetectorCalibration/jungfrau10ModuleData.h
@@ -0,0 +1,154 @@
+#ifndef JUNGFRAU10MODULEDATA_H
+#define  JUNGFRAU10MODULEBDATA_H
+#include "slsDetectorData.h"
+
+
+
+class jungfrau10ModuleData : public slsDetectorData<uint16_t> {
+
+ private:
+  
+  int iframe;
+  int nadc;
+  int sc_width;
+  int sc_height;
+ public:
+
+
+
+
+  /**
+     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
+     (160x160 pixels, 40 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+  */
+  
+
+  jungfrau10ModuleData(int ns=16384): slsDetectorData<uint16_t>(256*4, 256*2, ns*2*32, NULL, NULL) , nadc(32), sc_width(64), sc_height(256) {
+
+    
+   
+    int row, col;
+
+    int isample;
+    int iadc;
+    int ix, iy;
+
+    
+
+    cout << nx << " " << ny << " " << dataSize << endl;
+
+    for (iadc=0; iadc<nadc; iadc++) {
+      for (int i=0; i<sc_width*sc_height; i++) {
+	if (iadc<nadc/2) {
+	  row=sc_height+i/sc_width;
+	  col=iadc*sc_width+(i%sc_width);
+	} else {
+	  row=sc_height-1-i/sc_width;
+	  col=(ny-1)-(iadc-16)*sc_width-(i%sc_width);
+	}
+	dataMap[row][col]=(nadc*i+iadc)*2;
+	if (dataMap[row][col]<0 || dataMap[row][col]>=dataSize)
+	   cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	  
+      }
+
+    }
+    for (int i=0; i<nx*ny; i++) {
+      isample=i/nadc;
+      iadc=i%nadc;
+      ix=isample%sc_width;
+      iy=isample/sc_width;
+      if (iadc<(nadc/2)) {
+	xmap[i]=iadc*sc_width+ix;//adc_nr[iadc]+ix;
+	ymap[i]=ny/2+iy;
+      } else {
+	xmap[i]=(ny-1)-(iadc-16)*sc_width-ix;//adc_nr[iadc]+ix;
+	ymap[i]=ny/2-1-iy;
+      }
+
+
+    }
+
+
+
+    
+    
+    iframe=0;
+    //  cout << "data struct created" << endl;
+  };
+  
+  
+
+     /**
+
+     Returns the frame number for the given dataset. Purely virtual func.
+     \param buff pointer to the dataset
+     \returns frame number
+
+  */
+
+
+  int getFrameNumber(char *buff){(void)buff; return iframe;};   
+
+  /**
+
+     Returns the packet number for the given dataset. purely virtual func
+     \param buff pointer to the dataset
+     \returns packet number number
+
+
+  virtual int getPacketNumber(char *buff)=0;
+
+  */
+
+   /**
+
+     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
+     \param data pointer to the memory to be analyzed
+     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
+     \param dsize size of the memory slot to be analyzed
+     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
+
+  */
+   char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;};
+
+
+   /**
+
+     Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors! 
+     \param filebin input file stream (binary)
+     \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete
+
+  */
+   char *readNextFrame(ifstream &filebin){
+      //	int afifo_length=0;  
+      uint16_t *afifo_cont; 
+      int ib=0;
+      if (filebin.is_open()) {
+	afifo_cont=new uint16_t[dataSize/2];
+ 	while (filebin.read(((char*)afifo_cont)+ib,2)) {
+	  ib+=2;
+	  if (ib==dataSize) break;
+	}
+	if (ib>0) {
+	  iframe++;
+	  // cout << ib << "-" << endl;
+	  return (char*)afifo_cont;
+	} else {
+	  delete [] afifo_cont;
+	  return NULL;
+	}
+      }     
+      return NULL;
+    };
+
+
+  
+
+};
+
+
+
+#endif
diff --git a/slsDetectorCalibration/moench02CtbData.h b/slsDetectorCalibration/moench02CtbData.h
index 03ffd4ac5..37bf8304d 100644
--- a/slsDetectorCalibration/moench02CtbData.h
+++ b/slsDetectorCalibration/moench02CtbData.h
@@ -47,9 +47,11 @@ class moench02CtbData : public slsDetectorData<uint16_t> {
 	col=adc_nr[iadc]+(i%sc_width);
 	row=i/sc_width;
 	dataMap[row][col]=(32*i+iadc)*2;
-	if (dataMap[row][col]<0 || dataMap[row][col]>=2*160*160)
+	if (dataMap[row][col]<0 || dataMap[row][col]>=dataSize) {
 	  cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
 	  
+	}
+	  
       }
     }
     for (int i=0; i<nx*ny; i++) {
diff --git a/slsDetectorCalibration/moench03CtbData.h b/slsDetectorCalibration/moench03CtbData.h
index 30bebed23..7ad309942 100644
--- a/slsDetectorCalibration/moench03CtbData.h
+++ b/slsDetectorCalibration/moench03CtbData.h
@@ -9,7 +9,6 @@ class moench03CtbData : public slsDetectorData<uint16_t> {
  private:
   
   int iframe;
-  int *xmap, *ymap;
   int nadc;
   int sc_width;
   int sc_height;
@@ -39,8 +38,6 @@ class moench03CtbData : public slsDetectorData<uint16_t> {
     int iadc;
     int ix, iy;
 
-    xmap=new int[nx*ny];
-    ymap=new int[nx*ny];
     
 
 
@@ -83,8 +80,6 @@ class moench03CtbData : public slsDetectorData<uint16_t> {
     //  cout << "data struct created" << endl;
   };
     
-    void getPixel(int ip, int &x, int &y) {if (ip>=0 && ip<nx*ny) {x=xmap[ip]; y=ymap[ip];}};
-  
 
      /**
 
@@ -139,7 +134,7 @@ class moench03CtbData : public slsDetectorData<uint16_t> {
 	}
 	if (ib>0) {
 	  iframe++;
-	  cout << ib << "-" << endl;
+	  // cout << ib << "-" << endl;
 	  return (char*)afifo_cont;
 	} else {
 	  delete [] afifo_cont;
diff --git a/slsDetectorCalibration/moench03ReadData.C b/slsDetectorCalibration/moench03ReadData.C
index a2f268aff..c54a7655e 100644
--- a/slsDetectorCalibration/moench03ReadData.C
+++ b/slsDetectorCalibration/moench03ReadData.C
@@ -27,7 +27,7 @@ using namespace std;
 #define NR 400
 
 
-#define MY_DEBUG 1
+//#define MY_DEBUG 1
 
 #ifdef MY_DEBUG
 #include <TCanvas.h>
@@ -47,7 +47,7 @@ TH2F *readImage(ifstream &filebin,   TH2F *h2=NULL, TH2F *hped=NULL) {
       h2=new TH2F("h2","",400,0,400,400,0,400);
       h2->SetStats(kFALSE);
     }
-    cout << "." << endl;
+    //  cout << "." << endl;
     for (int ix=0; ix<400; ix++) {
       for (int iy=0; iy<400; iy++) {
 	//	cout <<  decoder->getDataSize() << " " << decoder->getValue(buff,ix,iy)<< endl;
@@ -77,7 +77,7 @@ TH2F *readImage(char *fname, int iframe=0, TH2F *hped=NULL) {
     if (hh==NULL) break;
     hh=readImage(filebin, h2, hped );
     if (hh)
-      cout << "="<< endl;
+      ;// cout << "="<< endl;
     else {
       delete h2;
       return NULL;
@@ -114,7 +114,7 @@ TH2F *calcPedestal(char *fformat, int runmin, int runmax){
 	}
       }
       delete [] buff;
-      cout << "="<< endl;
+      //cout << "="<< endl;
       ii++;
     }
     if (filebin.is_open())
@@ -146,8 +146,6 @@ Loops over data file to find single photons, fills the tree (and writes it to fi
   \param nbins  number of bins for spectrum hists
   \param hmin histo minimum for spectrum hists
   \param hmax histo maximum for spectrum hists
-  \param sign sign of the spectrum to find hits
-  \param hc readout correlation coefficient with previous pixel
   \param xmin minimum x coordinate
   \param xmax maximum x coordinate
   \param ymin minimum y coordinate
@@ -156,8 +154,10 @@ Loops over data file to find single photons, fills the tree (and writes it to fi
   \returns pointer to histo stack with cluster spectra
 */
 
-THStack *moench03ReadData(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 *moench03ReadData(char *fformat, char *tit, int runmin, int runmax, int nbins=1500, int hmin=-500, int hmax=1000,  int xmin=1, int xmax=NC-1, int ymin=1, int ymax=NR-1, int cmsub=0, int hitfinder=1) {
+  double hc=0;
+  int sign=1;
+
   moench03CtbData *decoder=new moench03CtbData();
   cout << "decoder allocated " << endl;
 
@@ -173,7 +173,7 @@ THStack *moench03ReadData(char *fformat, char *tit, int runmin, int runmax, int
    int iev=0;
   int nph=0;
 
-  singlePhotonDetector<uint16_t> *filter=new singlePhotonDetector<uint16_t>(decoder, 3, 5, sign, cmSub, 10, 100);
+  singlePhotonDetector<uint16_t> *filter=new singlePhotonDetector<uint16_t>(decoder, 3, 5, sign, cmSub, 100, 10);
   cout << "filter allocated " << endl;
 
   char *buff;
@@ -270,11 +270,8 @@ THStack *moench03ReadData(char *fformat, char *tit, int runmin, int runmax, int
     nph=0;
     while ((buff=decoder->readNextFrame(filebin))) {
       
+      filter->newFrame();
 
-      if (hitfinder) {
-	filter->newFrame();
-
-	//calculate pedestals and common modes
 	if (cmsub) {
 	//	cout << "cm" << endl;
 	  for (ix=xmin-1; ix<xmax+1; ix++)
@@ -282,25 +279,26 @@ THStack *moench03ReadData(char *fformat, char *tit, int runmin, int runmax, int
 	      thisEvent=filter->getEventType(buff, ix, iy,0);
 	    }
 	}
-      }
+      // if (hitfinder) {
+
+      // 	//calculate pedestals and common modes
+      // }
 
       //   cout << "new frame " << endl;
 
       for (ix=xmin-1; ix<xmax+1; ix++)
 	for (iy=ymin-1; iy<ymax+1; iy++) {
 	  //	  cout << ix << " " << iy << endl;
-	  thisEvent=filter->getEventType(buff, ix, iy, cmsub);
-
-#ifdef MY_DEBUG
-	  if (hitfinder) {
-	    //  if (iev%10==0)
-	      he->SetBinContent(ix+1-xmin, iy+1-ymin, (int)thisEvent);
-	  }
-#endif	  
-	  
+	    thisEvent=filter->getEventType(buff, ix, iy, cmsub);
 	  //  if (nf>10) {
 	    h1->Fill(filter->getClusterTotal(1), iy+NR*ix);
-	    if (hitfinder) {
+
+#ifdef MY_DEBUG
+	    //  if (iev%10==0)
+	    he->SetBinContent(ix+1-xmin, iy+1-ymin, (int)thisEvent);
+#endif	  
+	  
+	  if (hitfinder) {
 	      
 	      if (thisEvent==PHOTON_MAX ) {
 		nph++;
@@ -315,7 +313,10 @@ THStack *moench03ReadData(char *fformat, char *tit, int runmin, int runmax, int
 	      }
 	  
 	    
-	    }
+	  } // else {
+	  //   filter->addToPedestal(decoder->getValue(buff,ix,iy, cmsub));
+	    
+	  // }
 	    
 
 	    // }
@@ -323,7 +324,7 @@ THStack *moench03ReadData(char *fformat, char *tit, int runmin, int runmax, int
 	  //////////////////////////////////////////////////////////
     
 #ifdef MY_DEBUG
-      cout << iev << " " << h1->GetEntries() << " " << h2->GetEntries() << endl;
+      //    cout << iev << " " << h1->GetEntries() << " " << h2->GetEntries() << endl;
 //       if (iev%10==0) {
 // 	myC->Modified();
 // 	myC->Update();
@@ -338,10 +339,10 @@ THStack *moench03ReadData(char *fformat, char *tit, int runmin, int runmax, int
 #endif		    
       nf++;
       
-      cout << "=" ;
+      // cout << "=" ;
       delete [] buff;
     }
-    cout << nph << endl;
+    //  cout << nph << endl;
     if (filebin.is_open())
     filebin.close();	  
     else
diff --git a/slsDetectorCalibration/readMoench03Data.C b/slsDetectorCalibration/readMoench03Data.C
index 2bf22e111..8bbee83b3 100644
--- a/slsDetectorCalibration/readMoench03Data.C
+++ b/slsDetectorCalibration/readMoench03Data.C
@@ -12,31 +12,31 @@ void readMoench03Data(char *tit, int sign=1){
   TFile *fout;
   THStack *hs;
 
-  sprintf(fname,"/scratch/roberto/photons.root");
+  sprintf(fname,"/mnt/moenchnas/big_moench_xbox_20150223/Mo.root");
   fout=new TFile(fname,"RECREATE");
 
-  sprintf(fname,"/scratch/roberto/run_%%d.raw");
+  sprintf(fname,"/mnt/moenchnas/big_moench_xbox_20150223/Mo_f0_%%d.raw");
 
-  hs=moench03ReadData(fname,"photons",136,1135,1500,-500,2500,1,0.,1,399,1,399, 0,1); 
-//   cout << "returned" << endl;
-//   hs->SetName(tit);
-//   hs->SetTitle(tit);
-//   cout << "name/title set" << endl;
+  hs=moench03ReadData(fname,"Mo",25133,25187,1500,-500,2500,1,399,1,399, 0,1); 
+  cout << "returned" << endl;
+  hs->SetName(tit);
+  hs->SetTitle(tit);
+  cout << "name/title set" << endl;
   
   
-//   if (hs->GetHists()) {
-//     for (int i=0; i<3; i++) {
-//       if (hs->GetHists()->At(i)) {
-// 	cout << i << " " ;
-// 	(TH2F*)(hs->GetHists()->At(i))->Write();
-//       }
-//     } 
-//     cout << " histos written " << endl;
-//   } else
-//     cout << "no hists in stack " << endl;
+  if (hs->GetHists()) {
+    for (int i=0; i<3; i++) {
+      if (hs->GetHists()->At(i)) {
+	cout << i << " " ;
+	(TH2F*)(hs->GetHists()->At(i))->Write();
+      }
+    } 
+    cout << " histos written " << endl;
+  } else
+    cout << "no hists in stack " << endl;
   
 
-//   fout->Close();
+  fout->Close();
 
 
 
diff --git a/slsDetectorCalibration/slsDetectorData.h b/slsDetectorCalibration/slsDetectorData.h
index 8240a7484..b433960f3 100644
--- a/slsDetectorCalibration/slsDetectorData.h
+++ b/slsDetectorCalibration/slsDetectorData.h
@@ -19,6 +19,8 @@ class slsDetectorData {
   dataType **dataMask; /**< Array of size nx*ny storing the polarity of the data in the dataset (should be 0 if no inversion is required, 0xffffffff is inversion is required) */
   int **dataROIMask; /**< Array of size nx*ny 1 if channel is good (or in the ROI), 0 if bad channel (or out of ROI)   */
 
+  int *xmap;
+  int *ymap;
 
  public:
 
@@ -56,6 +58,16 @@ class slsDetectorData {
 	 dataROIMask[i][j]=1;
     }
     
+
+    
+    xmap=new int[dataSize/sizeof(dataType)];
+    ymap=new int[dataSize/sizeof(dataType)];
+
+    for (int i=0 ; i<dataSize/sizeof(dataType); i++) {
+      xmap[i]=-1;
+      ymap[i]=-1;
+    }
+    
     setDataMap(dMap);
     setDataMask(dMask);
     setDataROIMask(dROI);
@@ -64,17 +76,20 @@ class slsDetectorData {
 
   virtual ~slsDetectorData() {
     for(int i = 0; i < ny; i++) {
-    delete [] dataMap[i];
-    delete [] dataMask[i];
-    delete [] dataROIMask[i];
+      delete [] dataMap[i];
+      delete [] dataMask[i];
+      delete [] dataROIMask[i];
     }
     delete [] dataMap;
     delete [] dataMask;
     delete [] dataROIMask;
+    delete [] xmap;
+    delete [] ymap;
   }
 
-  virtual void getPixel(int ip, int &x, int &y) {x=ip; y=0;};
 
+  virtual void getPixel(int ip, int &x, int &y) {if (ip>=0 && ip<dataSize) {x=xmap[ip]; y=ymap[ip];} else {x=-1; y=-1;};};
+  
 
 
   /**
@@ -89,14 +104,19 @@ class slsDetectorData {
 
     if (dMap==NULL) {
       for (int iy=0; iy<ny; iy++)
-	 for (int ix=0; ix<nx; ix++)
+	for (int ix=0; ix<nx; ix++) {
 	   dataMap[iy][ix]=(iy*nx+ix)*sizeof(dataType);
+	}
     } else {
       cout << "set dmap "<< dataMap << " " << dMap << endl;
       for (int iy=0; iy<ny; iy++)
 	for (int ix=0; ix<nx; ix++) {
 	   dataMap[iy][ix]=dMap[iy][ix];
 	   cout << ix << " " << iy << endl;
+	   if (dMap[iy][ix]<dataSize) {
+	     xmap[dMap[iy][ix]/sizeof(dataType)]=ix;
+	     ymap[dMap[iy][ix]/sizeof(dataType)]=iy;
+	   }
 	}
     }
     

From 9b11df1c31e58a7a884326a9788929e16b8dab3b Mon Sep 17 00:00:00 2001
From: Dhanya Maliakal <dhanya.maliakal@psi.ch>
Date: Tue, 24 Mar 2015 10:42:22 +0100
Subject: [PATCH 02/13] a trial version of eiger mapping data

---
 slsDetectorCalibration/eigerHalfModuleData.h | 172 +++++++++++++++++++
 slsDetectorCalibration/slsDetectorData.h     |  38 ++++
 2 files changed, 210 insertions(+)
 create mode 100644 slsDetectorCalibration/eigerHalfModuleData.h

diff --git a/slsDetectorCalibration/eigerHalfModuleData.h b/slsDetectorCalibration/eigerHalfModuleData.h
new file mode 100644
index 000000000..9257c173b
--- /dev/null
+++ b/slsDetectorCalibration/eigerHalfModuleData.h
@@ -0,0 +1,172 @@
+#ifndef EIGERMODULEDATA_H
+#define  EIGERMODULEDATA_H
+#include "slsReceiverData.h"
+
+
+
+class eigerHalfModuleData : public slsReceiverData<uint32_t> {
+public:
+
+
+
+
+	/**
+     Implements the slsReceiverData structure for the eiger prototype read out by a half module i.e. using the slsReceiver
+     (256*256 pixels, 512 packets for 16 bit mode, 256 for 8, 128 for 4, 1024 for 32, 1040  etc.)
+     \param d dynamic range
+     \param c crosstalk parameter for the output buffer
+
+	 */
+
+
+	eigerHalfModuleData(int np, int dr, int t, int bsize, int dsize, double c=0): slsReceiverData<uint32_t>(xpixels, ypixels, nPackets, bsize),
+	xtalk(c), nPackets(np), dynamicRange(dr), bufferSize(bsize), dataSize(dsize){
+
+
+		int **dMap;
+		uint32_t **dMask;
+		int ix, iy;
+
+		dMap=new int*[ypixels];
+		dMask=new uint32_t*[ypixels];
+
+
+		for (int i = 0; i < ypixels; i++) {
+			dMap[i] = new int[xpixels];
+			dMask[i] = new uint32_t[xpixels];
+		}
+
+		//Map
+		int totalNumberOfBytes = 1040 * dynamicRange * 16 *2; //for both 1g and 10g
+		int iPacket1 = 8;
+		int iPacket2 = (totalNumberOfBytes/2) + 8;
+		int iData1 = 0, iData2 = 0;
+		int iPort;
+
+		for (int ir=0; ir<ypixels; ir++) {
+			for (int ic=0; ic<xpixels; ic++) {
+				iPort = ic / (xpixels/2);
+				if(!iPort){
+					dMap[ir][ic]  = iPacket1;
+					iPacket1 += (dynamicRange / 8);
+					iData1 +=(dynamicRange / 8);
+					if(iData1 >= dataSize){
+						iPacket1 += 16;
+						iData1 = 0;
+					}
+				}else{
+					dMap[ir][ic]  = iPacket2;
+					iPacket2 += (dynamicRange / 8);
+					iData2 +=(dynamicRange / 8);
+					if(iData2 >= dataSize){
+						iPacket2 += 16;
+						iData2 = 0;
+					}
+				}
+			}
+		}
+
+
+
+
+		//Mask
+		for(ix=0; ix<ypixels; ++ix)
+			for(iy=0; iy<xpixels; ++iy)
+				dMask[ix][iy] = 0x0;
+
+		setDataMap(dMap);
+		setDataMask(dMask);
+
+
+
+
+	};
+
+
+	/** Returns the frame number for the given dataset.
+	     \param buff pointer to the dataset
+	     \returns frame number
+	 */
+	int getFrameNumber(char *buff){
+		return htonl(*(unsigned int*)((eiger_image_header *)((char*)(buff)))->fnum);
+	};
+
+
+	/** gets the packets number (last packet is labelled with 0 and is replaced with 40)
+     	 \param buff pointer to the memory
+     	 \returns packet number
+	 */
+	int getPacketNumber(char *buff){
+		return htonl(*(unsigned int*)((eiger_packet_header *)((char*)(buff)))->num2);
+	};
+
+
+	/**
+    returns the pixel value as double correcting for the output buffer crosstalk
+     \param data pointer to the memory
+     \param ix coordinate in the x direction
+     \param iy coordinate in the y direction
+     \returns channel value as double
+
+	 */
+	double getValue(char *data, int ix, int iy=0) {
+		//  cout << "##" << (void*)data << " " << ix << " " <<iy << endl;
+		if (xtalk==0)
+			  return slsDetectorData<uint32_t>::getValue(data, ix, iy);
+		else
+			return slsDetectorData<uint32_t>::getValue(data, ix, iy)-xtalk*slsDetectorData<uint32_t>::getValue(data, ix-1, iy);
+	};
+
+
+
+	/** sets the output buffer crosstalk correction parameter
+      \param c output buffer crosstalk correction parameter to be set
+      \returns current value for the output buffer crosstalk correction parameter
+
+	 */
+	double setXTalk(double c) {xtalk=c; return xtalk;}
+
+
+	/** gets the output buffer crosstalk parameter
+      \returns current value for the output buffer crosstalk correction parameter
+	 */
+	double getXTalk() {return xtalk;}
+
+
+
+
+
+
+
+private:
+
+	double xtalk; /**<output buffer crosstalk correction parameter */
+
+	const static int xpixels = 1024;
+	const static int ypixels = 256;
+	const int bufferSize;
+	const int dataSize;
+	const int nPackets;
+	const int dynamicRange;
+
+
+	/** structure of an eiger image header*/
+	typedef struct
+	{
+		unsigned char header_before[20];
+		unsigned char  fnum[4];
+		unsigned char  header_after[24];
+	} eiger_image_header;
+
+	/** structure of an eiger image header*/
+	typedef struct
+	{
+		unsigned char num1[4];
+		unsigned char num2[4];
+	} eiger_packet_header;
+
+};
+
+
+
+#endif
diff --git a/slsDetectorCalibration/slsDetectorData.h b/slsDetectorCalibration/slsDetectorData.h
index 8240a7484..26efa53af 100644
--- a/slsDetectorCalibration/slsDetectorData.h
+++ b/slsDetectorCalibration/slsDetectorData.h
@@ -197,6 +197,32 @@ class slsDetectorData {
     return d^m;
   };
 
+
+  /**
+
+     Returns the value of the selected channel for the given dataset. Virtual function, can be overloaded.
+     \param data pointer to the dataset (including headers etc)
+     \param ix pixel number in the x direction
+     \param iy pixel number in the y direction
+     \param dr dynamic range
+     \returns data for the selected channel, with inversion if required
+
+  */
+  virtual dataType getChannel(char *data, int ix, int iy, int dr) {
+    dataType m=0, d=0;
+    uint64_t* s;
+    if (ix>=0 && ix<nx && iy>=0 && iy<ny && dataMap[iy][ix]>=0 && dataMap[iy][ix]<dataSize) {
+      m=dataMask[iy][ix];
+
+      int k = (((ix * iy + iy) * (dr / 8)) % 8);//which byte (1 to 8)
+      int index = (8 - k) * 8;
+      s = be64toh(((uint64_t)(*(((uint64_t*)data)+(dataMap[iy][ix]-index)))));
+
+      d=*((dataType*)(s+(k*8)));
+    }
+    return d^m;
+  };
+
   /**
 
      Returns the value of the selected channel for the given dataset as double.
@@ -208,6 +234,18 @@ class slsDetectorData {
   */
   virtual double getValue(char *data, int ix, int iy=0) {return (double)getChannel(data, ix, iy);};
 
+  /**
+
+     Returns the value of the selected channel for the given dataset as double.
+     \param data pointer to the dataset (including headers etc)
+     \param ix pixel number in the x direction
+     \param iy pixel number in the y direction
+     \param dr dynamic range
+     \returns data for the selected channel, with inversion if required as double
+
+  */
+  virtual double getValue(char *data, int ix, int iy, int dr) {return (double)getChannel(data, ix, iy, dr);};
+
    /**
 
      Returns the frame number for the given dataset. Purely virtual func.

From 7924989fb1bac543c9704e2c74d89669fb69b5ba Mon Sep 17 00:00:00 2001
From: Dhanya Maliakal <dhanya.maliakal@psi.ch>
Date: Wed, 25 Mar 2015 15:14:03 +0100
Subject: [PATCH 03/13] some more changes for eiger mapping

---
 slsDetectorCalibration/eigerHalfModuleData.h |  5 +-
 slsDetectorCalibration/slsDetectorData.h     | 50 +++++++++++++-------
 slsDetectorCalibration/slsReceiverData.h     |  3 +-
 3 files changed, 38 insertions(+), 20 deletions(-)

diff --git a/slsDetectorCalibration/eigerHalfModuleData.h b/slsDetectorCalibration/eigerHalfModuleData.h
index 9257c173b..555edee54 100644
--- a/slsDetectorCalibration/eigerHalfModuleData.h
+++ b/slsDetectorCalibration/eigerHalfModuleData.h
@@ -19,8 +19,8 @@ public:
 	 */
 
 
-	eigerHalfModuleData(int np, int dr, int t, int bsize, int dsize, double c=0): slsReceiverData<uint32_t>(xpixels, ypixels, nPackets, bsize),
-	xtalk(c), nPackets(np), dynamicRange(dr), bufferSize(bsize), dataSize(dsize){
+	eigerHalfModuleData(int dr, int np, int bsize, int dsize, double c=0): slsReceiverData<uint32_t>(xpixels, ypixels, np, bsize),
+	xtalk(c), dynamicRange(dr), bufferSize(bsize), dataSize(dsize){
 
 
 		int **dMap;
@@ -146,7 +146,6 @@ private:
 	const static int ypixels = 256;
 	const int bufferSize;
 	const int dataSize;
-	const int nPackets;
 	const int dynamicRange;
 
 
diff --git a/slsDetectorCalibration/slsDetectorData.h b/slsDetectorCalibration/slsDetectorData.h
index 26efa53af..d76310d21 100644
--- a/slsDetectorCalibration/slsDetectorData.h
+++ b/slsDetectorCalibration/slsDetectorData.h
@@ -87,19 +87,21 @@ class slsDetectorData {
   void setDataMap(int **dMap=NULL) {
 
 
-    if (dMap==NULL) {
-      for (int iy=0; iy<ny; iy++)
-	 for (int ix=0; ix<nx; ix++)
-	   dataMap[iy][ix]=(iy*nx+ix)*sizeof(dataType);
-    } else {
-      cout << "set dmap "<< dataMap << " " << dMap << endl;
-      for (int iy=0; iy<ny; iy++)
-	for (int ix=0; ix<nx; ix++) {
-	   dataMap[iy][ix]=dMap[iy][ix];
-	   cout << ix << " " << iy << endl;
-	}
-    }
-    
+	  if (dMap==NULL) {
+		  for (int iy=0; iy<ny; iy++)
+			  for (int ix=0; ix<nx; ix++)
+				  dataMap[iy][ix]=(iy*nx+ix)*sizeof(dataType);
+	  } else {
+		  cout << "set dmap "<< dataMap << " " << dMap << endl;
+		  for (int iy=0; iy<ny; iy++){
+			 // cout << iy << endl;
+			  for (int ix=0; ix<nx; ix++) {
+				  dataMap[iy][ix]=dMap[iy][ix];
+				 // cout << ix << " " << iy << endl;
+			  }
+		  }
+	  }
+	  cout << "nx:" <<nx << " ny:" << ny << endl;
   };
 
 
@@ -210,17 +212,33 @@ class slsDetectorData {
   */
   virtual dataType getChannel(char *data, int ix, int iy, int dr) {
     dataType m=0, d=0;
+    uint8_t d1=0;
+    uint8_t d2=0;
+    uint16_t d3=0;
+    uint32_t d4=0;
+    uint64_t t;
     uint64_t* s;
+    s= &t;
     if (ix>=0 && ix<nx && iy>=0 && iy<ny && dataMap[iy][ix]>=0 && dataMap[iy][ix]<dataSize) {
       m=dataMask[iy][ix];
-
+/*
       int k = (((ix * iy + iy) * (dr / 8)) % 8);//which byte (1 to 8)
       int index = (8 - k) * 8;
-      s = be64toh(((uint64_t)(*(((uint64_t*)data)+(dataMap[iy][ix]-index)))));
+      t = be64toh(((uint64_t)(*(((uint64_t*)data)+(dataMap[iy][ix]-index)))));
 
       d=*((dataType*)(s+(k*8)));
+      */
+      d=*((dataType*)(data+dataMap[iy][ix]));
     }
-    return d^m;
+    if(dr == 4)
+    	return d^0xf0;
+    else if(dr == 8)
+    	return d^d2;
+    else if(dr == 16)
+       	return d^d3;
+    else
+       	return d^d4;
+    //return d^m;
   };
 
   /**
diff --git a/slsDetectorCalibration/slsReceiverData.h b/slsDetectorCalibration/slsReceiverData.h
index 51e371434..4781cb36e 100644
--- a/slsDetectorCalibration/slsReceiverData.h
+++ b/slsDetectorCalibration/slsReceiverData.h
@@ -90,7 +90,7 @@ public:
 			dd+=packetSize;
 			np++;
 			// cout << pnum << " " << fn << " " << np << " " << dd << " " << dsize << endl;
-			if (np==nPackets)
+			if (np==nPackets){
 				if (pnum==nPackets) {
 					// cout << "Frame found!" << endl;
 					break;
@@ -98,6 +98,7 @@ public:
 					cout << "Too many packets for this frame! "<< fnum << " " << pnum << endl;
 					retval=NULL;
 				}
+			}
 		}
 		if (np<nPackets) {
 			if (np>0)

From 70c98a663de9c01088a55fea85f908aaaab92085 Mon Sep 17 00:00:00 2001
From: Dhanya Maliakal <dhanya.maliakal@psi.ch>
Date: Fri, 27 Mar 2015 17:42:23 +0100
Subject: [PATCH 04/13] eiger mapping done

---
 slsDetectorCalibration/eigerHalfModuleData.h |  7 +-
 slsDetectorCalibration/slsDetectorData.h     | 72 ++++++++++++--------
 2 files changed, 45 insertions(+), 34 deletions(-)

diff --git a/slsDetectorCalibration/eigerHalfModuleData.h b/slsDetectorCalibration/eigerHalfModuleData.h
index 555edee54..1c878af8c 100644
--- a/slsDetectorCalibration/eigerHalfModuleData.h
+++ b/slsDetectorCalibration/eigerHalfModuleData.h
@@ -25,7 +25,6 @@ public:
 
 		int **dMap;
 		uint32_t **dMask;
-		int ix, iy;
 
 		dMap=new int*[ypixels];
 		dMask=new uint32_t*[ypixels];
@@ -70,9 +69,9 @@ public:
 
 
 		//Mask
-		for(ix=0; ix<ypixels; ++ix)
-			for(iy=0; iy<xpixels; ++iy)
-				dMask[ix][iy] = 0x0;
+		for(int ir=0; ir<ypixels; ++ir)
+			for(int ic=0; ic<xpixels; ++ic)
+				dMask[ir][ic] = 0x0;
 
 		setDataMap(dMap);
 		setDataMask(dMask);
diff --git a/slsDetectorCalibration/slsDetectorData.h b/slsDetectorCalibration/slsDetectorData.h
index d76310d21..04ddc43d5 100644
--- a/slsDetectorCalibration/slsDetectorData.h
+++ b/slsDetectorCalibration/slsDetectorData.h
@@ -92,7 +92,7 @@ class slsDetectorData {
 			  for (int ix=0; ix<nx; ix++)
 				  dataMap[iy][ix]=(iy*nx+ix)*sizeof(dataType);
 	  } else {
-		  cout << "set dmap "<< dataMap << " " << dMap << endl;
+		  //cout << "set dmap "<< dataMap << " " << dMap << endl;
 		  for (int iy=0; iy<ny; iy++){
 			 // cout << iy << endl;
 			  for (int ix=0; ix<nx; ix++) {
@@ -101,7 +101,7 @@ class slsDetectorData {
 			  }
 		  }
 	  }
-	  cout << "nx:" <<nx << " ny:" << ny << endl;
+	 // cout << "nx:" <<nx << " ny:" << ny << endl;
   };
 
 
@@ -211,34 +211,44 @@ class slsDetectorData {
 
   */
   virtual dataType getChannel(char *data, int ix, int iy, int dr) {
-    dataType m=0, d=0;
-    uint8_t d1=0;
-    uint8_t d2=0;
-    uint16_t d3=0;
-    uint32_t d4=0;
-    uint64_t t;
-    uint64_t* s;
-    s= &t;
-    if (ix>=0 && ix<nx && iy>=0 && iy<ny && dataMap[iy][ix]>=0 && dataMap[iy][ix]<dataSize) {
-      m=dataMask[iy][ix];
-/*
-      int k = (((ix * iy + iy) * (dr / 8)) % 8);//which byte (1 to 8)
-      int index = (8 - k) * 8;
-      t = be64toh(((uint64_t)(*(((uint64_t*)data)+(dataMap[iy][ix]-index)))));
+	  dataType m=0, d=0;
+	  uint64_t t;
+	  int numBytes,divFactor,newix,pixelval;
 
-      d=*((dataType*)(s+(k*8)));
-      */
-      d=*((dataType*)(data+dataMap[iy][ix]));
-    }
-    if(dr == 4)
-    	return d^0xf0;
-    else if(dr == 8)
-    	return d^d2;
-    else if(dr == 16)
-       	return d^d3;
-    else
-       	return d^d4;
-    //return d^m;
+
+	  if (ix>=0 && ix<nx && iy>=0 && iy<ny && dataMap[iy][ix]>=0 && dataMap[iy][ix]<dataSize) {
+		  m=dataMask[iy][ix];
+
+		  numBytes = (nx * iy + ix);
+		  divFactor=2;
+		  if(dr == 4) divFactor = 16;
+		  else if (dr == 8) divFactor = 8;
+		  else if (dr == 16) divFactor = 4;
+
+		  pixelval = numBytes % divFactor;
+		  newix = ix - pixelval;
+
+		  //cout <<"pixelval:"<<pixelval<<" newix:"<<newix<<endl;
+		  //cout <<"64:"<< hex<<((uint64_t)(*((uint64_t*)(((char*)data)+(dataMap[iy][newix])))))<<endl;
+		  t = (be64toh((uint64_t)(*((uint64_t*)(((char*)data)+(dataMap[iy][newix]))))));
+		  //cout<<"t:"<<t<<endl;
+
+	  }else
+		  cprintf(RED,"outside limits\n");
+
+	  if(dr == 4)
+		  //uint8_t value =  t >> (pixelval*4); cout <<"value:"<< value << endl;
+		  return ((t >> (pixelval*4)) & 0xf)^m;
+	  else if(dr == 8)
+		  //uint8_t value =  t >> (pixelval*8); cout <<"value:"<< value << endl;
+		  return ((t >> (pixelval*8)) & 0xff)^m;
+	  else if(dr == 16){
+		  //uint16_t value =  t >> (pixelval*16); cout <<"value:"<< value << endl;
+		  return ((t >> (pixelval*16)) & 0xffff)^m;
+	  }else{
+		  //uint32_t value =  t >> (pixelval*32); cout <<"value:"<< value << endl;
+		  return ((t >> (pixelval*32)) & 0xffffffff)^m;
+	  }
   };
 
   /**
@@ -262,7 +272,9 @@ class slsDetectorData {
      \returns data for the selected channel, with inversion if required as double
 
   */
-  virtual double getValue(char *data, int ix, int iy, int dr) {return (double)getChannel(data, ix, iy, dr);};
+  virtual double getValue(char *data, int ix, int iy, int dr) {
+	  return ((double)getChannel(data, ix, iy, dr));
+  };
 
    /**
 

From 5e59c86d7249b599e5b208c85e3ebde1d7284f1a Mon Sep 17 00:00:00 2001
From: Anna Bergamaschi <anna.bergamaschi@psi.ch>
Date: Tue, 31 Mar 2015 14:41:06 +0200
Subject: [PATCH 05/13] Jungfrau10ModuleData modified

---
 slsDetectorCalibration/jungfrau10ModuleData.h | 61 ++++++++++---------
 slsDetectorCalibration/moench02CtbData.h      | 22 -------
 slsDetectorCalibration/slsDetectorData.h      | 28 ++++++---
 3 files changed, 50 insertions(+), 61 deletions(-)

diff --git a/slsDetectorCalibration/jungfrau10ModuleData.h b/slsDetectorCalibration/jungfrau10ModuleData.h
index a107f5058..39db07216 100644
--- a/slsDetectorCalibration/jungfrau10ModuleData.h
+++ b/slsDetectorCalibration/jungfrau10ModuleData.h
@@ -25,7 +25,7 @@ class jungfrau10ModuleData : public slsDetectorData<uint16_t> {
   */
   
 
-  jungfrau10ModuleData(int ns=16384): slsDetectorData<uint16_t>(256*4, 256*2, ns*2*32, NULL, NULL) , nadc(32), sc_width(64), sc_height(256) {
+ jungfrau10ModuleData(int ns=16384): slsDetectorData<uint16_t>(256*4, 256*2, 256*256*8*2, NULL, NULL, NULL) , iframe(0), nadc(32), sc_width(64), sc_height(256) {
 
     
    
@@ -35,48 +35,49 @@ class jungfrau10ModuleData : public slsDetectorData<uint16_t> {
     int iadc;
     int ix, iy;
 
-    
+    int ichip;
 
-    cout << nx << " " << ny << " " << dataSize << endl;
+    // cout << sizeof(uint16_t) << endl;
 
     for (iadc=0; iadc<nadc; iadc++) {
+      ichip=iadc/4;
+
       for (int i=0; i<sc_width*sc_height; i++) {
-	if (iadc<nadc/2) {
+
+	if (ichip%2==0) {
 	  row=sc_height+i/sc_width;
-	  col=iadc*sc_width+(i%sc_width);
-	} else {
-	  row=sc_height-1-i/sc_width;
-	  col=(ny-1)-(iadc-16)*sc_width-(i%sc_width);
+	  col=(ichip/2)*256+iadc%4*sc_width+(i%sc_width);
+	} else { 
+	  row=sc_height-1-i/sc_width; 
+	  col=((ichip/2)*256+iadc%4*sc_width)+sc_width-(i%sc_width)-1;
 	}
-	dataMap[row][col]=(nadc*i+iadc)*2;
-	if (dataMap[row][col]<0 || dataMap[row][col]>=dataSize)
-	   cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
 	  
+
+	
+/* 	if (iadc<nadc/2) { */
+/* 	  row=sc_height+i/sc_width; */
+/* 	  col=iadc*sc_width+(i%sc_width); */
+/* 	} else { */
+/* 	  row=sc_height-1-i/sc_width; */
+/* 	  col=(nx-1)-((iadc-16)*sc_width)-(i%sc_width); */
+/* 	} */
+	if (row<0 || row>=ny ||  col<0 || col>=nx) {
+	    cout << "Wrong row, column " << row << " " << col << " " << iadc << " " << i << endl;
+	} else
+	  dataMap[row][col]=(nadc*i+iadc)*2;
+	if (dataMap[row][col]<0 || dataMap[row][col]>=dataSize)
+	   cout << "Error: pointer " << dataMap[row][col] << " out of range " << row << " " << col  <<" " << iadc << " " << i << endl;
+	else {
+	  xmap[nadc*i+iadc]=col;
+	  ymap[nadc*i+iadc]=row;
+
+	}
       }
 
     }
-    for (int i=0; i<nx*ny; i++) {
-      isample=i/nadc;
-      iadc=i%nadc;
-      ix=isample%sc_width;
-      iy=isample/sc_width;
-      if (iadc<(nadc/2)) {
-	xmap[i]=iadc*sc_width+ix;//adc_nr[iadc]+ix;
-	ymap[i]=ny/2+iy;
-      } else {
-	xmap[i]=(ny-1)-(iadc-16)*sc_width-ix;//adc_nr[iadc]+ix;
-	ymap[i]=ny/2-1-iy;
-      }
-
-
-    }
-
-
 
     
     
-    iframe=0;
-    //  cout << "data struct created" << endl;
   };
   
   
diff --git a/slsDetectorCalibration/moench02CtbData.h b/slsDetectorCalibration/moench02CtbData.h
index 37bf8304d..b2860a3f3 100644
--- a/slsDetectorCalibration/moench02CtbData.h
+++ b/slsDetectorCalibration/moench02CtbData.h
@@ -36,9 +36,6 @@ class moench02CtbData : public slsDetectorData<uint16_t> {
     int iadc;
     int ix, iy;
 
-    xmap=new int[nx*ny];
-    ymap=new int[nx*ny];
-    
 
 
 
@@ -54,25 +51,6 @@ class moench02CtbData : public slsDetectorData<uint16_t> {
 	  
       }
     }
-    for (int i=0; i<nx*ny; i++) {
-      isample=i/32;
-      iadc=i%nadc;
-      ix=isample%sc_width;
-      iy=isample/sc_width;
-      if (iadc<(nadc/2)) {
-	xmap[i]=adc_nr[iadc]+ix;
-	ymap[i]=ny/2-1-iy;
-      } else {
-	xmap[i]=adc_nr[iadc]+ix;
-	ymap[i]=ny/2+iy;
-      }
-
-
-    }
-
-
-
-    
     
     iframe=0;
     //  cout << "data struct created" << endl;
diff --git a/slsDetectorCalibration/slsDetectorData.h b/slsDetectorCalibration/slsDetectorData.h
index b433960f3..0030091d7 100644
--- a/slsDetectorCalibration/slsDetectorData.h
+++ b/slsDetectorCalibration/slsDetectorData.h
@@ -41,6 +41,8 @@ class slsDetectorData {
   slsDetectorData(int npx, int npy, int dsize, int **dMap=NULL, dataType **dMask=NULL, int **dROI=NULL): nx(npx), ny(npy), dataSize(dsize) {
 
    
+    cout << "data size  is " <<  dataSize << endl;
+    cout << "detector size  is " <<  nx << " " << ny << endl;
 
     dataMask=new dataType*[ny];
     for(int i = 0; i < ny; i++) {
@@ -58,7 +60,7 @@ class slsDetectorData {
 	 dataROIMask[i][j]=1;
     }
     
-
+    cout << "map size is " <<  dataSize/sizeof(dataType) << endl;
     
     xmap=new int[dataSize/sizeof(dataType)];
     ymap=new int[dataSize/sizeof(dataType)];
@@ -75,16 +77,24 @@ class slsDetectorData {
   };
 
   virtual ~slsDetectorData() {
+    //  cout <<"delete xmap, ymap" << endl;
+    delete[] xmap;
+    delete[] ymap;
+
+    // cout <<"delete first d" << endl;
     for(int i = 0; i < ny; i++) {
-      delete [] dataMap[i];
-      delete [] dataMask[i];
-      delete [] dataROIMask[i];
+      // cout <<"delete data mask "<< i << endl;
+      delete[] dataMask[i];
+      // cout <<"delete data roi "<< i << endl;
+      delete[] dataROIMask[i];
+      // cout <<"delete data map "<< i << endl;
+      delete[] dataMap[i];
     }
-    delete [] dataMap;
-    delete [] dataMask;
-    delete [] dataROIMask;
-    delete [] xmap;
-    delete [] ymap;
+
+    // cout <<"delete second d" << endl;
+    delete[] dataMap;
+    delete[] dataMask;
+    delete[] dataROIMask;
   }
 
 

From 3c363d82e8566038edee641c607da7623e6c1311 Mon Sep 17 00:00:00 2001
From: Anna Bergamaschi <anna.bergamaschi@psi.ch>
Date: Tue, 31 Mar 2015 14:45:45 +0200
Subject: [PATCH 06/13] messing up while updating and merging

---
 slsDetectorCalibration/slsDetectorData.h | 84 ++++++++++++++++++++++++
 slsDetectorCalibration/slsReceiverData.h |  4 +-
 2 files changed, 87 insertions(+), 1 deletion(-)

diff --git a/slsDetectorCalibration/slsDetectorData.h b/slsDetectorCalibration/slsDetectorData.h
index 0030091d7..4f696ae29 100644
--- a/slsDetectorCalibration/slsDetectorData.h
+++ b/slsDetectorCalibration/slsDetectorData.h
@@ -112,6 +112,7 @@ class slsDetectorData {
   void setDataMap(int **dMap=NULL) {
 
 
+<<<<<<< HEAD
     if (dMap==NULL) {
       for (int iy=0; iy<ny; iy++)
 	for (int ix=0; ix<nx; ix++) {
@@ -130,6 +131,23 @@ class slsDetectorData {
 	}
     }
     
+=======
+	  if (dMap==NULL) {
+		  for (int iy=0; iy<ny; iy++)
+			  for (int ix=0; ix<nx; ix++)
+				  dataMap[iy][ix]=(iy*nx+ix)*sizeof(dataType);
+	  } else {
+		  //cout << "set dmap "<< dataMap << " " << dMap << endl;
+		  for (int iy=0; iy<ny; iy++){
+			 // cout << iy << endl;
+			  for (int ix=0; ix<nx; ix++) {
+				  dataMap[iy][ix]=dMap[iy][ix];
+				 // cout << ix << " " << iy << endl;
+			  }
+		  }
+	  }
+	 // cout << "nx:" <<nx << " ny:" << ny << endl;
+>>>>>>> 7ef3348d521f1a704f974b05dd763cd65253dd98
   };
 
 
@@ -227,6 +245,58 @@ class slsDetectorData {
     return d^m;
   };
 
+
+  /**
+
+     Returns the value of the selected channel for the given dataset. Virtual function, can be overloaded.
+     \param data pointer to the dataset (including headers etc)
+     \param ix pixel number in the x direction
+     \param iy pixel number in the y direction
+     \param dr dynamic range
+     \returns data for the selected channel, with inversion if required
+
+  */
+  virtual dataType getChannel(char *data, int ix, int iy, int dr) {
+	  dataType m=0, d=0;
+	  uint64_t t;
+	  int numBytes,divFactor,newix,pixelval;
+
+
+	  if (ix>=0 && ix<nx && iy>=0 && iy<ny && dataMap[iy][ix]>=0 && dataMap[iy][ix]<dataSize) {
+		  m=dataMask[iy][ix];
+
+		  numBytes = (nx * iy + ix);
+		  divFactor=2;
+		  if(dr == 4) divFactor = 16;
+		  else if (dr == 8) divFactor = 8;
+		  else if (dr == 16) divFactor = 4;
+
+		  pixelval = numBytes % divFactor;
+		  newix = ix - pixelval;
+
+		  //cout <<"pixelval:"<<pixelval<<" newix:"<<newix<<endl;
+		  //cout <<"64:"<< hex<<((uint64_t)(*((uint64_t*)(((char*)data)+(dataMap[iy][newix])))))<<endl;
+		  t = (be64toh((uint64_t)(*((uint64_t*)(((char*)data)+(dataMap[iy][newix]))))));
+		  //cout<<"t:"<<t<<endl;
+
+	  }else
+		  cprintf(RED,"outside limits\n");
+
+	  if(dr == 4)
+		  //uint8_t value =  t >> (pixelval*4); cout <<"value:"<< value << endl;
+		  return ((t >> (pixelval*4)) & 0xf)^m;
+	  else if(dr == 8)
+		  //uint8_t value =  t >> (pixelval*8); cout <<"value:"<< value << endl;
+		  return ((t >> (pixelval*8)) & 0xff)^m;
+	  else if(dr == 16){
+		  //uint16_t value =  t >> (pixelval*16); cout <<"value:"<< value << endl;
+		  return ((t >> (pixelval*16)) & 0xffff)^m;
+	  }else{
+		  //uint32_t value =  t >> (pixelval*32); cout <<"value:"<< value << endl;
+		  return ((t >> (pixelval*32)) & 0xffffffff)^m;
+	  }
+  };
+
   /**
 
      Returns the value of the selected channel for the given dataset as double.
@@ -238,6 +308,20 @@ class slsDetectorData {
   */
   virtual double getValue(char *data, int ix, int iy=0) {return (double)getChannel(data, ix, iy);};
 
+  /**
+
+     Returns the value of the selected channel for the given dataset as double.
+     \param data pointer to the dataset (including headers etc)
+     \param ix pixel number in the x direction
+     \param iy pixel number in the y direction
+     \param dr dynamic range
+     \returns data for the selected channel, with inversion if required as double
+
+  */
+  virtual double getValue(char *data, int ix, int iy, int dr) {
+	  return ((double)getChannel(data, ix, iy, dr));
+  };
+
    /**
 
      Returns the frame number for the given dataset. Purely virtual func.
diff --git a/slsDetectorCalibration/slsReceiverData.h b/slsDetectorCalibration/slsReceiverData.h
index e07a757fd..4781cb36e 100644
--- a/slsDetectorCalibration/slsReceiverData.h
+++ b/slsDetectorCalibration/slsReceiverData.h
@@ -2,6 +2,7 @@
 #define  SLSRECEIVERDATA_H
 
 #include "slsDetectorData.h"
+#include <cstring>
 
 template <class dataType>
 class slsReceiverData : public slsDetectorData<dataType> {
@@ -89,7 +90,7 @@ public:
 			dd+=packetSize;
 			np++;
 			// cout << pnum << " " << fn << " " << np << " " << dd << " " << dsize << endl;
-			if (np==nPackets)
+			if (np==nPackets){
 				if (pnum==nPackets) {
 					// cout << "Frame found!" << endl;
 					break;
@@ -97,6 +98,7 @@ public:
 					cout << "Too many packets for this frame! "<< fnum << " " << pnum << endl;
 					retval=NULL;
 				}
+			}
 		}
 		if (np<nPackets) {
 			if (np>0)

From 48d672b918cd04af35535fc87c582c4ccec11d47 Mon Sep 17 00:00:00 2001
From: Anna Bergamaschi <anna.bergamaschi@psi.ch>
Date: Tue, 31 Mar 2015 15:07:53 +0200
Subject: [PATCH 07/13] Moved eiger related stuff from slsDetectorData to
 eigerHalfModule data, added xmap and ymap to slsDetectorData calss

---
 slsDetectorCalibration/eigerHalfModuleData.h | 57 ++++++++++++++++++
 slsDetectorCalibration/slsDetectorData.h     | 62 +++-----------------
 2 files changed, 65 insertions(+), 54 deletions(-)

diff --git a/slsDetectorCalibration/eigerHalfModuleData.h b/slsDetectorCalibration/eigerHalfModuleData.h
index 1c878af8c..f81426bde 100644
--- a/slsDetectorCalibration/eigerHalfModuleData.h
+++ b/slsDetectorCalibration/eigerHalfModuleData.h
@@ -81,6 +81,57 @@ public:
 
 	};
 
+  /**
+
+     Returns the value of the selected channel for the given dataset. Virtual function, can be overloaded.
+     \param data pointer to the dataset (including headers etc)
+     \param ix pixel number in the x direction
+     \param iy pixel number in the y direction
+     \param dr dynamic range
+     \returns data for the selected channel, with inversion if required
+
+  */
+  virtual dataType getChannel(char *data, int ix, int iy=0, int dr=0) {
+	  dataType m=0, d=0;
+	  uint64_t t;
+	  int numBytes,divFactor,newix,pixelval;
+
+
+	  if (ix>=0 && ix<nx && iy>=0 && iy<ny && dataMap[iy][ix]>=0 && dataMap[iy][ix]<dataSize) {
+		  m=dataMask[iy][ix];
+
+		  numBytes = (nx * iy + ix);
+		  divFactor=2;
+		  if(dr == 4) divFactor = 16;
+		  else if (dr == 8) divFactor = 8;
+		  else if (dr == 16) divFactor = 4;
+
+		  pixelval = numBytes % divFactor;
+		  newix = ix - pixelval;
+
+		  //cout <<"pixelval:"<<pixelval<<" newix:"<<newix<<endl;
+		  //cout <<"64:"<< hex<<((uint64_t)(*((uint64_t*)(((char*)data)+(dataMap[iy][newix])))))<<endl;
+		  t = (be64toh((uint64_t)(*((uint64_t*)(((char*)data)+(dataMap[iy][newix]))))));
+		  //cout<<"t:"<<t<<endl;
+
+	  }else
+		  cprintf(RED,"outside limits\n");
+
+	  if(dr == 4)
+		  //uint8_t value =  t >> (pixelval*4); cout <<"value:"<< value << endl;
+		  return ((t >> (pixelval*4)) & 0xf)^m;
+	  else if(dr == 8)
+		  //uint8_t value =  t >> (pixelval*8); cout <<"value:"<< value << endl;
+		  return ((t >> (pixelval*8)) & 0xff)^m;
+	  else if(dr == 16){
+		  //uint16_t value =  t >> (pixelval*16); cout <<"value:"<< value << endl;
+		  return ((t >> (pixelval*16)) & 0xffff)^m;
+	  }else{
+		  //uint32_t value =  t >> (pixelval*32); cout <<"value:"<< value << endl;
+		  return ((t >> (pixelval*32)) & 0xffffffff)^m;
+	  }
+  };
+
 
 	/** Returns the frame number for the given dataset.
 	     \param buff pointer to the dataset
@@ -91,6 +142,12 @@ public:
 	};
 
 
+	
+
+
+
+
+
 	/** gets the packets number (last packet is labelled with 0 and is replaced with 40)
      	 \param buff pointer to the memory
      	 \returns packet number
diff --git a/slsDetectorCalibration/slsDetectorData.h b/slsDetectorCalibration/slsDetectorData.h
index 04ddc43d5..f5e42022c 100644
--- a/slsDetectorCalibration/slsDetectorData.h
+++ b/slsDetectorCalibration/slsDetectorData.h
@@ -18,7 +18,8 @@ class slsDetectorData {
   int **dataMap; /**< Array of size nx*ny storing the pointers to the data in the dataset (as offset)*/
   dataType **dataMask; /**< Array of size nx*ny storing the polarity of the data in the dataset (should be 0 if no inversion is required, 0xffffffff is inversion is required) */
   int **dataROIMask; /**< Array of size nx*ny 1 if channel is good (or in the ROI), 0 if bad channel (or out of ROI)   */
-
+ int *xmap;
+ int *ymap;
 
  public:
 
@@ -55,7 +56,9 @@ class slsDetectorData {
       for (int j=0; j<nx; j++)
 	 dataROIMask[i][j]=1;
     }
-    
+    xmap=new int[dsize];
+    ymap=new int[dsize];
+
     setDataMap(dMap);
     setDataMask(dMask);
     setDataROIMask(dROI);
@@ -71,6 +74,8 @@ class slsDetectorData {
     delete [] dataMap;
     delete [] dataMask;
     delete [] dataROIMask;
+    delete [] xmap;
+    delete [] ymap;
   }
 
   virtual void getPixel(int ip, int &x, int &y) {x=ip; y=0;};
@@ -190,7 +195,7 @@ class slsDetectorData {
   */
 
 
-  virtual dataType getChannel(char *data, int ix, int iy=0) {
+  virtual dataType getChannel(char *data, int ix, int iy=0, int dr=0) {
     dataType m=0, d=0;
     if (ix>=0 && ix<nx && iy>=0 && iy<ny && dataMap[iy][ix]>=0 && dataMap[iy][ix]<dataSize) {
       m=dataMask[iy][ix];
@@ -200,57 +205,6 @@ class slsDetectorData {
   };
 
 
-  /**
-
-     Returns the value of the selected channel for the given dataset. Virtual function, can be overloaded.
-     \param data pointer to the dataset (including headers etc)
-     \param ix pixel number in the x direction
-     \param iy pixel number in the y direction
-     \param dr dynamic range
-     \returns data for the selected channel, with inversion if required
-
-  */
-  virtual dataType getChannel(char *data, int ix, int iy, int dr) {
-	  dataType m=0, d=0;
-	  uint64_t t;
-	  int numBytes,divFactor,newix,pixelval;
-
-
-	  if (ix>=0 && ix<nx && iy>=0 && iy<ny && dataMap[iy][ix]>=0 && dataMap[iy][ix]<dataSize) {
-		  m=dataMask[iy][ix];
-
-		  numBytes = (nx * iy + ix);
-		  divFactor=2;
-		  if(dr == 4) divFactor = 16;
-		  else if (dr == 8) divFactor = 8;
-		  else if (dr == 16) divFactor = 4;
-
-		  pixelval = numBytes % divFactor;
-		  newix = ix - pixelval;
-
-		  //cout <<"pixelval:"<<pixelval<<" newix:"<<newix<<endl;
-		  //cout <<"64:"<< hex<<((uint64_t)(*((uint64_t*)(((char*)data)+(dataMap[iy][newix])))))<<endl;
-		  t = (be64toh((uint64_t)(*((uint64_t*)(((char*)data)+(dataMap[iy][newix]))))));
-		  //cout<<"t:"<<t<<endl;
-
-	  }else
-		  cprintf(RED,"outside limits\n");
-
-	  if(dr == 4)
-		  //uint8_t value =  t >> (pixelval*4); cout <<"value:"<< value << endl;
-		  return ((t >> (pixelval*4)) & 0xf)^m;
-	  else if(dr == 8)
-		  //uint8_t value =  t >> (pixelval*8); cout <<"value:"<< value << endl;
-		  return ((t >> (pixelval*8)) & 0xff)^m;
-	  else if(dr == 16){
-		  //uint16_t value =  t >> (pixelval*16); cout <<"value:"<< value << endl;
-		  return ((t >> (pixelval*16)) & 0xffff)^m;
-	  }else{
-		  //uint32_t value =  t >> (pixelval*32); cout <<"value:"<< value << endl;
-		  return ((t >> (pixelval*32)) & 0xffffffff)^m;
-	  }
-  };
-
   /**
 
      Returns the value of the selected channel for the given dataset as double.

From 904462b582324458c751db0e5628d9261d957414 Mon Sep 17 00:00:00 2001
From: Anna Bergamaschi <anna.bergamaschi@psi.ch>
Date: Wed, 1 Apr 2015 13:04:27 +0200
Subject: [PATCH 08/13] xmap, ymap added again to slsDetectorData

---
 slsDetectorCalibration/slsDetectorData.h | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/slsDetectorCalibration/slsDetectorData.h b/slsDetectorCalibration/slsDetectorData.h
index f5e42022c..643adad9a 100644
--- a/slsDetectorCalibration/slsDetectorData.h
+++ b/slsDetectorCalibration/slsDetectorData.h
@@ -40,6 +40,8 @@ class slsDetectorData {
   slsDetectorData(int npx, int npy, int dsize, int **dMap=NULL, dataType **dMask=NULL, int **dROI=NULL): nx(npx), ny(npy), dataSize(dsize) {
 
    
+    xmap=new int[nx*ny];
+    ymap=new int[nx*ny];
 
     dataMask=new dataType*[ny];
     for(int i = 0; i < ny; i++) {
@@ -56,8 +58,8 @@ class slsDetectorData {
       for (int j=0; j<nx; j++)
 	 dataROIMask[i][j]=1;
     }
-    xmap=new int[dsize];
-    ymap=new int[dsize];
+
+
 
     setDataMap(dMap);
     setDataMask(dMask);
@@ -78,7 +80,7 @@ class slsDetectorData {
     delete [] ymap;
   }
 
-  virtual void getPixel(int ip, int &x, int &y) {x=ip; y=0;};
+  virtual void getPixel(int ip, int &x, int &y) {x=xmap[ip]; y=ymap[ip];};
 
 
 
@@ -90,7 +92,7 @@ class slsDetectorData {
 
 
   void setDataMap(int **dMap=NULL) {
-
+    int ip;
 
 	  if (dMap==NULL) {
 		  for (int iy=0; iy<ny; iy++)
@@ -103,6 +105,9 @@ class slsDetectorData {
 			  for (int ix=0; ix<nx; ix++) {
 				  dataMap[iy][ix]=dMap[iy][ix];
 				 // cout << ix << " " << iy << endl;
+				  ip=dataMap[ix][iy]/sizeof(dataType);
+				  xmap[ip]=ix;
+				  ymap[ip]=iy;
 			  }
 		  }
 	  }

From 1f6c5c26b4d40be7d423a72f5e350d8ff018946d Mon Sep 17 00:00:00 2001
From: Dhanya Maliakal <dhanya.maliakal@psi.ch>
Date: Tue, 14 Apr 2015 17:13:09 +0200
Subject: [PATCH 09/13] eiger mapping for 32 bit done

---
 slsDetectorCalibration/eigerHalfModuleData.h | 112 ++++++++++++++-----
 slsDetectorCalibration/slsDetectorData.h     |  10 +-
 slsDetectorCalibration/slsReceiverData.h     |   2 +-
 3 files changed, 87 insertions(+), 37 deletions(-)

diff --git a/slsDetectorCalibration/eigerHalfModuleData.h b/slsDetectorCalibration/eigerHalfModuleData.h
index 1c878af8c..553e9dbd3 100644
--- a/slsDetectorCalibration/eigerHalfModuleData.h
+++ b/slsDetectorCalibration/eigerHalfModuleData.h
@@ -19,8 +19,8 @@ public:
 	 */
 
 
-	eigerHalfModuleData(int dr, int np, int bsize, int dsize, double c=0): slsReceiverData<uint32_t>(xpixels, ypixels, np, bsize),
-	xtalk(c), dynamicRange(dr), bufferSize(bsize), dataSize(dsize){
+	eigerHalfModuleData(int dr, int np, int bsize, int dsize, bool top, double c=0): slsReceiverData<uint32_t>(xpixels, ypixels, np, bsize),
+	xtalk(c), bufferSize(bsize), dataSize(dsize), dynamicRange(dr), numberOfPackets(np){
 
 
 		int **dMap;
@@ -42,29 +42,60 @@ public:
 		int iData1 = 0, iData2 = 0;
 		int iPort;
 
-		for (int ir=0; ir<ypixels; ir++) {
-			for (int ic=0; ic<xpixels; ic++) {
-				iPort = ic / (xpixels/2);
-				if(!iPort){
-					dMap[ir][ic]  = iPacket1;
-					iPacket1 += (dynamicRange / 8);
-					iData1 +=(dynamicRange / 8);
-					if(iData1 >= dataSize){
-						iPacket1 += 16;
-						iData1 = 0;
-					}
-				}else{
-					dMap[ir][ic]  = iPacket2;
-					iPacket2 += (dynamicRange / 8);
-					iData2 +=(dynamicRange / 8);
-					if(iData2 >= dataSize){
-						iPacket2 += 16;
-						iData2 = 0;
+
+		if(top){
+			for (int ir=0; ir<ypixels; ir++) {
+				for (int ic=0; ic<xpixels; ic++) {
+					iPort = ic / (xpixels/2);
+					if(!iPort){
+						dMap[ir][ic]  = iPacket1;
+						iPacket1 += (dynamicRange / 8);
+						iData1 +=(dynamicRange / 8);
+						if(iData1 >= dataSize){
+							iPacket1 += 16;
+							iData1 = 0;
+						}
+					}else{
+						dMap[ir][ic]  = iPacket2;
+						iPacket2 += (dynamicRange / 8);
+						iData2 +=(dynamicRange / 8);
+						if(iData2 >= dataSize){
+							iPacket2 += 16;
+							iData2 = 0;
+						}
 					}
 				}
 			}
 		}
 
+/*
+		else{
+			iPacket1 = (totalNumberOfBytes/2) - 1040 - 8;
+			iPacket2 = totalNumberOfBytes - 1040 - 8;
+			for (int ir=0; ir<ypixels; ir++) {
+				for (int ic=0; ic<xpixels; ic++) {
+					iPort = ic / (xpixels/2);
+					if(!iPort){
+						dMap[ir][ic]  = iPacket1;
+						iPacket1 += (dynamicRange / 8);//increment now but decrement before by 1024 before and after
+						iData1 +=(dynamicRange / 8);
+						if(iData1 >= dataSize){
+							iPacket1 += 16;
+							iData1 = 0;
+						}
+					}else{
+						dMap[ir][ic]  = iPacket2;
+						iPacket2 += (dynamicRange / 8);
+						iData2 +=(dynamicRange / 8);
+						if(iData2 >= dataSize){
+							iPacket2 += 16;
+							iData2 = 0;
+						}
+					}
+				}
+			}
+		}
+*/
 
 
 
@@ -87,7 +118,7 @@ public:
 	     \returns frame number
 	 */
 	int getFrameNumber(char *buff){
-		return htonl(*(unsigned int*)((eiger_image_header *)((char*)(buff)))->fnum);
+		return(*(unsigned int*)(((eiger_packet_header *)((char*)buff))->num1));
 	};
 
 
@@ -96,7 +127,31 @@ public:
      	 \returns packet number
 	 */
 	int getPacketNumber(char *buff){
-		return htonl(*(unsigned int*)((eiger_packet_header *)((char*)(buff)))->num2);
+		/*other way roud if its a bottom*/
+
+#ifdef VERY_DEBUG
+		cprintf(RED, "\n0x%x - %d - %d",
+			(*(uint8_t*)(((eiger_packet_header *)((char*)(buff)))->num3)),
+			(*(uint8_t*)(((eiger_packet_header *)((char*)(buff)))->num4)),
+			(*(uint16_t*)(((eiger_packet_header *)((char*)(buff)))->num2)));
+#endif
+		//32 bit packet number written in num2
+		if(dynamicRange == 32){
+			//both ports have same packet numbers, so reconstruct
+			if((*(uint8_t*)(((eiger_packet_header *)((char*)buff))->num3))){
+				return ((*(uint16_t*)(((eiger_packet_header *)((char*)buff))->num2))+(numberOfPackets/2) +1);
+			}else{
+				return ((*(uint16_t*)(((eiger_packet_header *)((char*)buff))->num2))+1);
+			}
+		}
+		else{
+			//both ports have same packet numbers, so reconstruct
+			if((*(uint8_t*)(((eiger_packet_header *)((char*)buff))->num3))){
+				return ((*(uint8_t*)(((eiger_packet_header *)((char*)buff))->num4))+(numberOfPackets/2) +1);
+			}else{
+				return ((*(uint8_t*)(((eiger_packet_header *)((char*)buff))->num4))+1);
+			}
+		}
 	};
 
 
@@ -146,21 +201,16 @@ private:
 	const int bufferSize;
 	const int dataSize;
 	const int dynamicRange;
+	const int numberOfPackets;
 
 
-	/** structure of an eiger image header*/
-	typedef struct
-	{
-		unsigned char header_before[20];
-		unsigned char  fnum[4];
-		unsigned char  header_after[24];
-	} eiger_image_header;
-
 	/** structure of an eiger image header*/
 	typedef struct
 	{
 		unsigned char num1[4];
-		unsigned char num2[4];
+		unsigned char num2[2];
+		unsigned char num3[1];
+		unsigned char num4[1];
 	} eiger_packet_header;
 
 };
diff --git a/slsDetectorCalibration/slsDetectorData.h b/slsDetectorCalibration/slsDetectorData.h
index 04ddc43d5..cb364bc04 100644
--- a/slsDetectorCalibration/slsDetectorData.h
+++ b/slsDetectorCalibration/slsDetectorData.h
@@ -211,14 +211,14 @@ class slsDetectorData {
 
   */
   virtual dataType getChannel(char *data, int ix, int iy, int dr) {
-	  dataType m=0, d=0;
+	  dataType m=0;
 	  uint64_t t;
 	  int numBytes,divFactor,newix,pixelval;
 
 
 	  if (ix>=0 && ix<nx && iy>=0 && iy<ny && dataMap[iy][ix]>=0 && dataMap[iy][ix]<dataSize) {
 		  m=dataMask[iy][ix];
-
+		  //cout <<"ix:"<<dec<<ix<<" iy:"<<iy<<endl;
 		  numBytes = (nx * iy + ix);
 		  divFactor=2;
 		  if(dr == 4) divFactor = 16;
@@ -228,10 +228,10 @@ class slsDetectorData {
 		  pixelval = numBytes % divFactor;
 		  newix = ix - pixelval;
 
-		  //cout <<"pixelval:"<<pixelval<<" newix:"<<newix<<endl;
-		  //cout <<"64:"<< hex<<((uint64_t)(*((uint64_t*)(((char*)data)+(dataMap[iy][newix])))))<<endl;
+		  //cout <<"pixelval:"<<dec <<pixelval<<" newix:"<<newix<<endl;
+		 // cout <<"64:"<< hex<<((uint64_t)(*((uint64_t*)(((char*)data)+(dataMap[iy][newix])))))<<endl;
 		  t = (be64toh((uint64_t)(*((uint64_t*)(((char*)data)+(dataMap[iy][newix]))))));
-		  //cout<<"t:"<<t<<endl;
+		 // cout<<"t:"<<hex<<t<<endl;
 
 	  }else
 		  cprintf(RED,"outside limits\n");
diff --git a/slsDetectorCalibration/slsReceiverData.h b/slsDetectorCalibration/slsReceiverData.h
index 4781cb36e..15d324ef6 100644
--- a/slsDetectorCalibration/slsReceiverData.h
+++ b/slsDetectorCalibration/slsReceiverData.h
@@ -67,7 +67,7 @@ public:
 		while (dd<=(dsize-packetSize)) {
 			pnum=getPacketNumber(p);
 			fn=getFrameNumber(p);
-
+			//cout <<"pnum:"<<pnum<<" fn:"<<fn<<"\t";
 
 			if (pnum<1 || pnum>nPackets) {
 				cout << "Bad packet number " << pnum << " frame "<< fn << endl;

From 5731ead4cba1d4ce9a11e9b03bfb9d23c823eff2 Mon Sep 17 00:00:00 2001
From: Dhanya Maliakal <dhanya.maliakal@psi.ch>
Date: Wed, 15 Apr 2015 14:38:32 +0200
Subject: [PATCH 10/13] eiger top mapping done. bottom doesnt work

---
 slsDetectorCalibration/eigerHalfModuleData.h | 63 +++++++++++++++-----
 1 file changed, 48 insertions(+), 15 deletions(-)

diff --git a/slsDetectorCalibration/eigerHalfModuleData.h b/slsDetectorCalibration/eigerHalfModuleData.h
index 553e9dbd3..34ee0f7de 100644
--- a/slsDetectorCalibration/eigerHalfModuleData.h
+++ b/slsDetectorCalibration/eigerHalfModuleData.h
@@ -20,7 +20,7 @@ public:
 
 
 	eigerHalfModuleData(int dr, int np, int bsize, int dsize, bool top, double c=0): slsReceiverData<uint32_t>(xpixels, ypixels, np, bsize),
-	xtalk(c), bufferSize(bsize), dataSize(dsize), dynamicRange(dr), numberOfPackets(np){
+	xtalk(c), bufferSize(bsize), dataSize(dsize), dynamicRange(dr), numberOfPackets(np), top(top){
 
 
 		int **dMap;
@@ -40,6 +40,7 @@ public:
 		int iPacket1 = 8;
 		int iPacket2 = (totalNumberOfBytes/2) + 8;
 		int iData1 = 0, iData2 = 0;
+		/*int iData=0*/
 		int iPort;
 
 
@@ -51,6 +52,7 @@ public:
 						dMap[ir][ic]  = iPacket1;
 						iPacket1 += (dynamicRange / 8);
 						iData1 +=(dynamicRange / 8);
+						//increment header
 						if(iData1 >= dataSize){
 							iPacket1 += 16;
 							iData1 = 0;
@@ -59,28 +61,38 @@ public:
 						dMap[ir][ic]  = iPacket2;
 						iPacket2 += (dynamicRange / 8);
 						iData2 +=(dynamicRange / 8);
+						//increment header
 						if(iData2 >= dataSize){
 							iPacket2 += 16;
 							iData2 = 0;
 						}
 					}
+					/*iData +=(dynamicRange / 8);
+					//increment header
+					if(iData1 >= dataSize){
+						iPacket1 += 16;
+						iData1 = 0;
+					}*/
 				}
 			}
 		}
 
-/*
+
 		else{
-			iPacket1 = (totalNumberOfBytes/2) - 1040 - 8;
-			iPacket2 = totalNumberOfBytes - 1040 - 8;
+			/*int iData=0;*/
+			iData1 = 0; iData2 = 0;
+			iPacket1 = (totalNumberOfBytes/2) - bufferSize - 8;
+			iPacket2 = totalNumberOfBytes - bufferSize - 8;
 			for (int ir=0; ir<ypixels; ir++) {
 				for (int ic=0; ic<xpixels; ic++) {
 					iPort = ic / (xpixels/2);
 					if(!iPort){
 						dMap[ir][ic]  = iPacket1;
-						iPacket1 += (dynamicRange / 8);//increment now but decrement before by 1024 before and after
+						iPacket1 += (dynamicRange / 8);
 						iData1 +=(dynamicRange / 8);
 						if(iData1 >= dataSize){
-							iPacket1 += 16;
+							iPacket1 -= (dataSize*2);
+							iPacket1 -= 16;
 							iData1 = 0;
 						}
 					}else{
@@ -88,14 +100,24 @@ public:
 						iPacket2 += (dynamicRange / 8);
 						iData2 +=(dynamicRange / 8);
 						if(iData2 >= dataSize){
-							iPacket2 += 16;
+							iPacket2 -= (dataSize*2);
+							iPacket2 -= 16;
 							iData2 = 0;
 						}
 					}
+					/*iData +=(dynamicRange / 8);
+					//increment header
+					if(iData >= dataSize){
+						iPacket1 -= (bufferSize*2);
+						iPacket2 -= (bufferSize*2);
+						iPacket1 += 16;
+						iPacket2 += 16;
+						iData = 0;
+					}*/
 				}
 			}
 		}
-*/
+
 
 
 
@@ -127,8 +149,6 @@ public:
      	 \returns packet number
 	 */
 	int getPacketNumber(char *buff){
-		/*other way roud if its a bottom*/
-
 #ifdef VERY_DEBUG
 		cprintf(RED, "\n0x%x - %d - %d",
 			(*(uint8_t*)(((eiger_packet_header *)((char*)(buff)))->num3)),
@@ -137,19 +157,31 @@ public:
 #endif
 		//32 bit packet number written in num2
 		if(dynamicRange == 32){
-			//both ports have same packet numbers, so reconstruct
+			//both ports have same packet numbers, so reconstruct, ports interchanged for bottom
 			if((*(uint8_t*)(((eiger_packet_header *)((char*)buff))->num3))){
-				return ((*(uint16_t*)(((eiger_packet_header *)((char*)buff))->num2))+(numberOfPackets/2) +1);
+				if (top)
+					return ((*(uint16_t*)(((eiger_packet_header *)((char*)buff))->num2))+(numberOfPackets/2) +1);
+				else
+					return ((*(uint16_t*)(((eiger_packet_header *)((char*)buff))->num2))+1);
 			}else{
-				return ((*(uint16_t*)(((eiger_packet_header *)((char*)buff))->num2))+1);
+				if (top)
+					return ((*(uint16_t*)(((eiger_packet_header *)((char*)buff))->num2))+1);
+				else
+					return ((*(uint16_t*)(((eiger_packet_header *)((char*)buff))->num2))+(numberOfPackets/2) +1);
 			}
 		}
 		else{
 			//both ports have same packet numbers, so reconstruct
 			if((*(uint8_t*)(((eiger_packet_header *)((char*)buff))->num3))){
-				return ((*(uint8_t*)(((eiger_packet_header *)((char*)buff))->num4))+(numberOfPackets/2) +1);
+				if (top)
+					return ((*(uint8_t*)(((eiger_packet_header *)((char*)buff))->num4))+(numberOfPackets/2) +1);
+				else
+					return ((*(uint8_t*)(((eiger_packet_header *)((char*)buff))->num4))+1);
 			}else{
-				return ((*(uint8_t*)(((eiger_packet_header *)((char*)buff))->num4))+1);
+				if (top)
+					return ((*(uint8_t*)(((eiger_packet_header *)((char*)buff))->num4))+1);
+				else
+					return ((*(uint8_t*)(((eiger_packet_header *)((char*)buff))->num4))+(numberOfPackets/2) +1);
 			}
 		}
 	};
@@ -202,6 +234,7 @@ private:
 	const int dataSize;
 	const int dynamicRange;
 	const int numberOfPackets;
+	bool top;
 
 
 	/** structure of an eiger image header*/

From 83a766914f62124f52f7c1c8540e11f0824677b2 Mon Sep 17 00:00:00 2001
From: Dhanya Maliakal <dhanya.maliakal@psi.ch>
Date: Wed, 15 Apr 2015 14:48:27 +0200
Subject: [PATCH 11/13] not necessary merge

---
 slsDetectorCalibration/slsDetectorData.h | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/slsDetectorCalibration/slsDetectorData.h b/slsDetectorCalibration/slsDetectorData.h
index 0316b8ec6..d5f567595 100644
--- a/slsDetectorCalibration/slsDetectorData.h
+++ b/slsDetectorCalibration/slsDetectorData.h
@@ -211,8 +211,6 @@ class slsDetectorData {
 
 
   /**
-
-<<<<<<< HEAD
      Returns the value of the selected channel for the given dataset. Virtual function, can be overloaded.
      \param data pointer to the dataset (including headers etc)
      \param ix pixel number in the x direction
@@ -263,9 +261,6 @@ class slsDetectorData {
   };
 
   /**
-
-=======
->>>>>>> b3dac953736499019603c2201df6e7eb45cc890c
      Returns the value of the selected channel for the given dataset as double.
      \param data pointer to the dataset (including headers etc)
      \param ix pixel number in the x direction

From 0c2bd83e968ea7b161629b8f3d524c399a12287e Mon Sep 17 00:00:00 2001
From: Dhanya Maliakal <dhanya.maliakal@psi.ch>
Date: Wed, 15 Apr 2015 15:49:52 +0200
Subject: [PATCH 12/13] moved getchannel back to slsdetectordata as it doesnt
 work for eiger

---
 slsDetectorCalibration/eigerHalfModuleData.h | 47 --------------------
 slsDetectorCalibration/slsDetectorData.h     | 18 +++++---
 2 files changed, 11 insertions(+), 54 deletions(-)

diff --git a/slsDetectorCalibration/eigerHalfModuleData.h b/slsDetectorCalibration/eigerHalfModuleData.h
index 74e81d7b9..f6b301d82 100644
--- a/slsDetectorCalibration/eigerHalfModuleData.h
+++ b/slsDetectorCalibration/eigerHalfModuleData.h
@@ -134,56 +134,9 @@ public:
 
 	};
 
-  /**
-
-     Returns the value of the selected channel for the given dataset. Virtual function, can be overloaded.
-     \param data pointer to the dataset (including headers etc)
-     \param ix pixel number in the x direction
-     \param iy pixel number in the y direction
-     \param dr dynamic range
-     \returns data for the selected channel, with inversion if required
-
-  */
-  virtual dataType getChannel(char *data, int ix, int iy=0, int dr=0) {
-	  dataType m=0, d=0;
-	  uint64_t t;
-	  int numBytes,divFactor,newix,pixelval;
 
 
-	  if (ix>=0 && ix<nx && iy>=0 && iy<ny && dataMap[iy][ix]>=0 && dataMap[iy][ix]<dataSize) {
-		  m=dataMask[iy][ix];
 
-		  numBytes = (nx * iy + ix);
-		  divFactor=2;
-		  if(dr == 4) divFactor = 16;
-		  else if (dr == 8) divFactor = 8;
-		  else if (dr == 16) divFactor = 4;
-
-		  pixelval = numBytes % divFactor;
-		  newix = ix - pixelval;
-
-		  //cout <<"pixelval:"<<pixelval<<" newix:"<<newix<<endl;
-		  //cout <<"64:"<< hex<<((uint64_t)(*((uint64_t*)(((char*)data)+(dataMap[iy][newix])))))<<endl;
-		  t = (be64toh((uint64_t)(*((uint64_t*)(((char*)data)+(dataMap[iy][newix]))))));
-		  //cout<<"t:"<<t<<endl;
-
-	  }else
-		  cprintf(RED,"outside limits\n");
-
-	  if(dr == 4)
-		  //uint8_t value =  t >> (pixelval*4); cout <<"value:"<< value << endl;
-		  return ((t >> (pixelval*4)) & 0xf)^m;
-	  else if(dr == 8)
-		  //uint8_t value =  t >> (pixelval*8); cout <<"value:"<< value << endl;
-		  return ((t >> (pixelval*8)) & 0xff)^m;
-	  else if(dr == 16){
-		  //uint16_t value =  t >> (pixelval*16); cout <<"value:"<< value << endl;
-		  return ((t >> (pixelval*16)) & 0xffff)^m;
-	  }else{
-		  //uint32_t value =  t >> (pixelval*32); cout <<"value:"<< value << endl;
-		  return ((t >> (pixelval*32)) & 0xffffffff)^m;
-	  }
-  };
 
 
 	/** Returns the frame number for the given dataset.
diff --git a/slsDetectorCalibration/slsDetectorData.h b/slsDetectorCalibration/slsDetectorData.h
index d5f567595..c9637aa5a 100644
--- a/slsDetectorCalibration/slsDetectorData.h
+++ b/slsDetectorCalibration/slsDetectorData.h
@@ -105,9 +105,9 @@ class slsDetectorData {
 			  for (int ix=0; ix<nx; ix++) {
 				  dataMap[iy][ix]=dMap[iy][ix];
 				 // cout << ix << " " << iy << endl;
-				  ip=dataMap[ix][iy]/sizeof(dataType);
+				 /*ip=dataMap[ix][iy]/sizeof(dataType);
 				  xmap[ip]=ix;
-				  ymap[ip]=iy;
+				  ymap[ip]=iy;Annaa*/
 			  }
 		  }
 	  }
@@ -200,7 +200,7 @@ class slsDetectorData {
   */
 
 
-  virtual dataType getChannel(char *data, int ix, int iy=0, int dr=0) {
+  virtual dataType getChannel(char *data, int ix, int iy=0) {
     dataType m=0, d=0;
     if (ix>=0 && ix<nx && iy>=0 && iy<ny && dataMap[iy][ix]>=0 && dataMap[iy][ix]<dataSize) {
       m=dataMask[iy][ix];
@@ -210,7 +210,10 @@ class slsDetectorData {
   };
 
 
+
+
   /**
+
      Returns the value of the selected channel for the given dataset. Virtual function, can be overloaded.
      \param data pointer to the dataset (including headers etc)
      \param ix pixel number in the x direction
@@ -219,6 +222,7 @@ class slsDetectorData {
      \returns data for the selected channel, with inversion if required
 
   */
+
   virtual dataType getChannel(char *data, int ix, int iy, int dr) {
 	  dataType m=0;
 	  uint64_t t;
@@ -227,7 +231,7 @@ class slsDetectorData {
 
 	  if (ix>=0 && ix<nx && iy>=0 && iy<ny && dataMap[iy][ix]>=0 && dataMap[iy][ix]<dataSize) {
 		  m=dataMask[iy][ix];
-		  //cout <<"ix:"<<dec<<ix<<" iy:"<<iy<<endl;
+
 		  numBytes = (nx * iy + ix);
 		  divFactor=2;
 		  if(dr == 4) divFactor = 16;
@@ -237,10 +241,10 @@ class slsDetectorData {
 		  pixelval = numBytes % divFactor;
 		  newix = ix - pixelval;
 
-		  //cout <<"pixelval:"<<dec <<pixelval<<" newix:"<<newix<<endl;
-		 // cout <<"64:"<< hex<<((uint64_t)(*((uint64_t*)(((char*)data)+(dataMap[iy][newix])))))<<endl;
+		  //cout <<"pixelval:"<<pixelval<<" newix:"<<newix<<endl;
+		  //cout <<"64:"<< hex<<((uint64_t)(*((uint64_t*)(((char*)data)+(dataMap[iy][newix])))))<<endl;
 		  t = (be64toh((uint64_t)(*((uint64_t*)(((char*)data)+(dataMap[iy][newix]))))));
-		 // cout<<"t:"<<hex<<t<<endl;
+		  //cout<<"t:"<<t<<endl;
 
 	  }else
 		  cprintf(RED,"outside limits\n");

From bbcd984df0f7c893a6ddd9f585cfa9548e88e0ee Mon Sep 17 00:00:00 2001
From: Dhanya Maliakal <dhanya.maliakal@psi.ch>
Date: Tue, 19 May 2015 10:12:57 +0200
Subject: [PATCH 13/13] mapping of bottom and top for all bit modes work

---
 slsDetectorCalibration/eigerHalfModuleData.h | 108 ++++++++++++-------
 slsDetectorCalibration/slsDetectorData.h     |   2 +-
 2 files changed, 69 insertions(+), 41 deletions(-)

diff --git a/slsDetectorCalibration/eigerHalfModuleData.h b/slsDetectorCalibration/eigerHalfModuleData.h
index f6b301d82..381456a54 100644
--- a/slsDetectorCalibration/eigerHalfModuleData.h
+++ b/slsDetectorCalibration/eigerHalfModuleData.h
@@ -40,18 +40,23 @@ public:
 		int iPacket1 = 8;
 		int iPacket2 = (totalNumberOfBytes/2) + 8;
 		int iData1 = 0, iData2 = 0;
-		/*int iData=0*/
+		int increment = (dynamicRange/8);
+		int ic_increment = 1;
+		if (dynamicRange == 4) {
+			increment = 1;
+			ic_increment = 2;
+		}
 		int iPort;
 
 
 		if(top){
 			for (int ir=0; ir<ypixels; ir++) {
-				for (int ic=0; ic<xpixels; ic++) {
+				for (int ic=0; ic<xpixels; ic = ic + ic_increment) {
 					iPort = ic / (xpixels/2);
 					if(!iPort){
 						dMap[ir][ic]  = iPacket1;
-						iPacket1 += (dynamicRange / 8);
-						iData1 +=(dynamicRange / 8);
+						iPacket1 += increment;
+						iData1 += increment;
 						//increment header
 						if(iData1 >= dataSize){
 							iPacket1 += 16;
@@ -59,61 +64,84 @@ public:
 						}
 					}else{
 						dMap[ir][ic]  = iPacket2;
-						iPacket2 += (dynamicRange / 8);
-						iData2 +=(dynamicRange / 8);
+						iPacket2 += increment;
+						iData2 += increment;
 						//increment header
 						if(iData2 >= dataSize){
 							iPacket2 += 16;
 							iData2 = 0;
 						}
 					}
-					/*iData +=(dynamicRange / 8);
-					//increment header
-					if(iData1 >= dataSize){
-						iPacket1 += 16;
-						iData1 = 0;
-					}*/
 				}
 			}
 		}
 
 
+		//bottom
 		else{
-			/*int iData=0;*/
 			iData1 = 0; iData2 = 0;
-			iPacket1 = (totalNumberOfBytes/2) - bufferSize - 8;
-			iPacket2 = totalNumberOfBytes - bufferSize - 8;
+			int numbytesperlineperport = 1024;
+			if (dynamicRange == 8)
+				numbytesperlineperport = 512;
+			else if (dynamicRange == 4)
+				numbytesperlineperport = 256;
+			else if (dynamicRange == 32)
+				numbytesperlineperport = 2048;
+
+
+
+			iPacket1 = (totalNumberOfBytes/2) - numbytesperlineperport - 8;
+			iPacket2 = totalNumberOfBytes - numbytesperlineperport - 8;
+			if (dynamicRange == 32){
+				iPacket1 -= 16;
+				iPacket2 -= 16;
+			}
+
 			for (int ir=0; ir<ypixels; ir++) {
-				for (int ic=0; ic<xpixels; ic++) {
+				for (int ic=0; ic<xpixels; ic = ic + ic_increment) {
 					iPort = ic / (xpixels/2);
 					if(!iPort){
 						dMap[ir][ic]  = iPacket1;
-						iPacket1 += (dynamicRange / 8);
-						iData1 +=(dynamicRange / 8);
-						if(iData1 >= dataSize){
-							iPacket1 -= (dataSize*2);
-							iPacket1 -= 16;
-							iData1 = 0;
-						}
-					}else{
-						dMap[ir][ic]  = iPacket2;
-						iPacket2 += (dynamicRange / 8);
-						iData2 +=(dynamicRange / 8);
-						if(iData2 >= dataSize){
-							iPacket2 -= (dataSize*2);
-							iPacket2 -= 16;
-							iData2 = 0;
+						iPacket1 += increment;
+						iData1 += increment;
+						if(dynamicRange == 32){
+							if(iData1 == numbytesperlineperport){
+								iPacket1 -= (numbytesperlineperport*2 + 16*3);
+								iData1 = 0;
+							}
+							if(iData1 == dataSize){
+								iPacket1 += 16;
+							}
+						}else if((iData1 % numbytesperlineperport) == 0){
+							iPacket1 -= (numbytesperlineperport*2);
+							if(iData1 == dataSize){
+								iPacket1 -= 16;
+								iData1 = 0;
+							}
+
+						}
+					}
+					//other port
+					else{
+						dMap[ir][ic]  = iPacket2;
+						iPacket2 += increment;
+						iData2 += increment;
+						if(dynamicRange == 32){
+							if(iData2 == numbytesperlineperport){
+								iPacket2 -= (numbytesperlineperport*2 + 16*3);
+								iData2 = 0;
+							}
+							if(iData2 == dataSize){
+								iPacket2 += 16;
+							}
+						}else if((iData2 % numbytesperlineperport) == 0){
+							iPacket2 -= (numbytesperlineperport*2);
+							if(iData2 == dataSize){
+								iPacket2 -= 16;
+								iData2 = 0;
+							}
 						}
 					}
-					/*iData +=(dynamicRange / 8);
-					//increment header
-					if(iData >= dataSize){
-						iPacket1 -= (bufferSize*2);
-						iPacket2 -= (bufferSize*2);
-						iPacket1 += 16;
-						iPacket2 += 16;
-						iData = 0;
-					}*/
 				}
 			}
 		}
diff --git a/slsDetectorCalibration/slsDetectorData.h b/slsDetectorCalibration/slsDetectorData.h
index c9637aa5a..b130b7aa2 100644
--- a/slsDetectorCalibration/slsDetectorData.h
+++ b/slsDetectorCalibration/slsDetectorData.h
@@ -228,7 +228,7 @@ class slsDetectorData {
 	  uint64_t t;
 	  int numBytes,divFactor,newix,pixelval;
 
-
+//cout <<"ix:"<<ix<<" nx:"<<nx<<" iy:"<<ny<<" ny:"<<ny<<" datamap[iy][ix]:"<< dataMap[iy][ix] <<"datasize:"<< dataSize <<endl;
 	  if (ix>=0 && ix<nx && iy>=0 && iy<ny && dataMap[iy][ix]>=0 && dataMap[iy][ix]<dataSize) {
 		  m=dataMask[iy][ix];