From c9269d0f21dcd082be2489ca07bc2d186cc34f69 Mon Sep 17 00:00:00 2001
From: Dhanya Maliakal <dhanya.maliakal@psi.ch>
Date: Mon, 16 Mar 2015 17:53:54 +0100
Subject: [PATCH 1/4] included a cstring include for compilation in
 slsReceiverData.h

---
 slsDetectorCalibration/slsReceiverData.h | 1 +
 1 file changed, 1 insertion(+)

diff --git a/slsDetectorCalibration/slsReceiverData.h b/slsDetectorCalibration/slsReceiverData.h
index e07a757fd..51e371434 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> {

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 2/4] 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 3/4] 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 4/4] 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));
+  };
 
    /**