added photon counter no thread

cmk.sh

@@ -60,6 +60,7 @@ while getopts ":bchd:j:trge" opt ; do
 	b) 
 		echo "Building of CMake files Required"
 		REBUILD=1
+		CLEAN=1
 		;;
 	c) 
 		echo "Clean Required"
@@ -69,6 +70,7 @@ while getopts ":bchd:j:trge" opt ; do
 		echo "Building of CMake files with HDF5 option Required"
 		HDF5=1
 		REBUILD=1
+		CLEAN=1
 		;;
 	d) 
 		echo "New HDF5 directory: $OPTARG" 
@@ -82,16 +84,19 @@ while getopts ":bchd:j:trge" opt ; do
     	echo "Compiling Options: Text Client" 
 		TEXTCLIENT=1
 		REBUILD=1
+		CLEAN=1
 		;;      
 	r) 
 		echo "Compiling Options: Receiver" 
 		RECEIVER=1
 		REBUILD=1
+		CLEAN=1
 		;;      
 	g) 
 		echo "Compiling Options: GUI" 
 		GUI=1
 		REBUILD=1
+		CLEAN=1
 		;;  
 	e)
 		echo "Compiling Options: Debug" 

examples/moench03_T1_lab.config

@@ -1,4 +1,4 @@
-hostname bchip085+
+hostname bchip071+
 
 patword 0000 0000000000000000
 patword 0001 0000000000000000
@@ -416,28 +416,37 @@ patwaittime2 0
 
 
 ####mcp2011
-#0:rx_udpip 10.1.1.102
+0:rx_tcpport 1954
+0:rx_udpport 32411
+####gui listening to 
+zmqport 50001
+####data streaming out of
+rx_zmqport 50003
+
+#zmqip 129.129.202.86
+#0:rx_udpip 10.1.2.117
+#0:detectorip 10.1.2.19
+#rx_zmqip 10.1.2.117
+#0:rx_hostname mpc2608
+
+zmqip 129.129.202.98
+0:rx_udpip 10.1.1.102
+0:detectorip 10.1.1.19
+rx_zmqip 10.1.1.102
+0:rx_hostname mpc2011
+
+####pcmoench01
+#0:rx_tcpport 1977
+#0:rx_udpip 10.1.1.100
 #0:detectorip 10.1.1.19
 #0:rx_udpport 32410
-####gui listening to 
-#zmqip 129.129.202.131
-#zmqport 30001
-####data streaming out of
-#rx_zmqip 10.1.2.103
-#rx_zmqport 30003
-#0:rx_hostname mpc2011
-
-####mx-test-1
-0:rx_udpip 10.1.1.100
-0:detectorip 10.1.1.19
-0:rx_udpport 32410
 ####gui listening to (on receiver pc)
-zmqip 129.129.202.92
-zmqport 30001
+#zmqip 129.129.202.92
+#zmqport 50001
 ####data streaming out of
-rx_zmqip 10.1.1.100
-rx_zmqport 30003
-0:rx_hostname pcmoench01
+#rx_zmqip 10.1.1.100
+#rx_zmqport 50003
+#0:rx_hostname mx-test-1
 
 
 
@@ -474,16 +483,17 @@ adcphase 90
 adcpipeline 15
 adcreg 14 40
 powerchip 1
-vhighvoltage 90
+vhighvoltage 200
 period 0.005
 
 
 
 
+r_discardpolicy discardpartial
 
 
 frames 100
 period 0.1
-outdir /scratch/
+outdir /mnt/moench_data/scratch/
 enablefwrite 0
 

slsDetectorCalibration/.gitignore

@@ -1,2 +0,0 @@
-*.o
-*.*~

slsDetectorCalibration/MovingStat.h

@@ -33,16 +33,17 @@ class MovingStat
         {
 	  if (m>=0) m_n = m;  else m_n = n; 
 	  m_newM=val*m_n; 
+	  // cout << "set " << val << " " << m << " " << m_n << " " << m_newM << endl;
 	  SetRMS(rms);
         }
-		/**
+	/**
 	   clears the moving average number of samples parameter, mean and standard deviation
 	*/
         void SetRMS(double rms)
         {
 	  if (rms<=0) {
 	    m_newM2=m_newM*m_newM/n;
-	    m_n=0;
+	    //m_n=0;
 	  } else {
 	    if (m_n>0)
 	      m_newM2=(m_n*rms*rms+m_newM*m_newM/m_n);
@@ -120,6 +121,7 @@ class MovingStat
 	 */
         inline double Mean() const
         {
+	  //  cout << "get " <<  m_n << " " << m_newM << " " << m_newM/m_n << endl;
             return (m_n > 0) ? m_newM/m_n : 0.0;
         }
 

slsDetectorCalibration/analogDetector.h

@@ -6,7 +6,8 @@
 #include <pthread.h>
 #include "slsDetectorData.h"
 #include "pedestalSubtraction.h"
-#include "commonModeSubtraction.h"
+#include "commonModeSubtractionNew.h"
+#include "ghostSummation.h"
 #include "tiffIO.h"
 #include "slsInterpolation.h"
 
@@ -61,16 +62,16 @@ template <class dataType> class analogDetector {
   
 
  analogDetector(slsDetectorData<dataType> *d, int sign=1, 
-		commonModeSubtraction *cm=NULL, int nped=1000, int nnx=-1, int nny=-1, double *gm=NULL) : det(d), nx(nnx), ny(nny), stat(NULL), cmSub(cm),  iframe(-1), dataSign(sign), gmap(gm), id(0) {
+		commonModeSubtraction *cm=NULL, int nped=1000, int nnx=-1, int nny=-1, double *gm=NULL, ghostSummation<dataType> *gs=NULL) : det(d), nx(nnx), ny(nny), stat(NULL), cmSub(cm), dataSign(sign), iframe(-1), gmap(gm), ghSum(gs), id(0) {
     
     if (det)
       det->getDetectorSize(nx,ny);
     
-    stat=new pedestalSubtraction*[ny];
+    stat=new pedestalSubtraction[ny*nx];
     for (int i=0; i<ny; i++) {
-      stat[i]=new pedestalSubtraction[nx];
+      // stat[i]=new pedestalSubtraction[nx];
       for (int ix=0; ix<nx; ix++) {
-	stat[i][ix].SetNPedestals(nped);
+	stat[i*nx+ix].SetNPedestals(nped);
       }
     }
     image=new int[nx*ny];
@@ -94,7 +95,7 @@ template <class dataType> class analogDetector {
   /**
      destructor. Deletes the pdestalSubtraction array and the image
   */
-  virtual ~analogDetector() {for (int i=0; i<ny; i++) delete [] stat[i]; delete [] stat; delete [] image;
+  virtual ~analogDetector() {for (int i=0; i<ny; i++) delete [] stat;  delete [] image;
 #ifdef ROOTSPECTRUM
     delete hs;
 #ifdef ROOTCLUST
@@ -118,7 +119,7 @@ template <class dataType> class analogDetector {
     dataSign=orig->dataSign;
     iframe=orig->iframe;
     gmap=orig->gmap;
-    cmSub=orig->cmSub;
+    //  cmSub=orig->cmSub;
     id=orig->id;
     xmin=orig->xmin;
     xmax=orig->xmax;
@@ -130,16 +131,13 @@ template <class dataType> class analogDetector {
     myFile=orig->myFile;
     
 
-    stat=new pedestalSubtraction*[ny];
-    for (int i=0; i<ny; i++) {
-      stat[i]=new pedestalSubtraction[nx];
-    }
+    stat=new pedestalSubtraction[ny*nx];
     
     int nped=orig->SetNPedestals();
     //cout << nped << " " << orig->getPedestal(ix,iy) << orig->getPedestalRMS(ix,iy) << endl;
     for (int iy=0; iy<ny; iy++) {
       for (int ix=0; ix<nx; ix++) {
-	stat[iy][ix].SetNPedestals(nped);
+	stat[iy*nx+ix].SetNPedestals(nped);
 	setPedestal(ix,iy,orig->getPedestal(ix,iy),orig->getPedestalRMS(ix,iy),orig->GetNPedestals(ix,iy));
       }
     }
@@ -153,7 +151,16 @@ template <class dataType> class analogDetector {
      hs9=(TH2F*)(orig->hs9)->Clone();//new TH2F("hs","hs",(orig->hs)-getNbins,-500,9500,nx*ny,-0.5,nx*ny-0.5); 
 #endif
 #endif
-
+     if (orig->cmSub) {
+       cmSub=(orig->cmSub)->Clone();
+       cout <<"cloning cm" << endl;
+     }
+     else cmSub=NULL;
+     if (orig->ghSum) {
+       ghSum=(orig->ghSum)->Clone();
+       cout <<"cloning gs" << endl;
+     }
+     else ghSum=NULL;
   }
 
 
@@ -189,7 +196,7 @@ template <class dataType> class analogDetector {
      \param nns reference to number of subpixels for interpolating detector, will always be 1 in this case
      \returns number of pixels of the detector image
    */
-  virtual int getImageSize(int &nnx, int &nny, int &nns){nnx=nx; nny=ny; nns=1; return nx*ny;}; 
+  virtual int getImageSize(int &nnx, int &nny, int &nnsx, int &nnsy){nnx=nx; nny=ny; nnsx=1; nnsy=1; return nx*ny;}; 
  /**
      Returns data size of the detector image matrix
      \param nnx reference to pixel size in x
@@ -216,14 +223,18 @@ template <class dataType> class analogDetector {
      \returns pointer to current gain map is file reading succeeded, NULL is file reading didn't work.
   */
   double *readGainMap(const char * imgname) {
-    uint32 nnx, nny;
-    float *gm=ReadFromTiff( imgname, nny, nnx);
+    uint32 unnx, unny;
+    int nnx, nny;
+    float *gm=ReadFromTiff( imgname, unny, unnx);
+    nnx=unnx;
+    nny=unny;
     if (gm) {
       if (gmap) delete [] gmap; 
       gmap=new double[nnx*nny];
-	for (int iy=0; iy<nny; iy++) {
-      for (int ix=0; ix<nnx; ix++) {
+      for (int iy=0; iy<nny; iy++) {
+	for (int ix=0; ix<nnx; ix++) {
 	  gmap[iy*nnx+ix]=gm[iy*nnx+ix];
+	  // cout << gmap[iy*nnx+ix] << " " ;
 	}
       }
       return gmap;
@@ -258,7 +269,7 @@ template <class dataType> class analogDetector {
     iframe=-1; 
     for (int iy=0; iy<ny; iy++) 
       for (int ix=0; ix<nx; ix++) {
-	stat[iy][ix].Clear(); 
+	stat[iy*nx+ix].Clear(); 
 	image[iy*nx+ix]=0;
       }
     if (cmSub) cmSub->Clear(); 
@@ -275,6 +286,14 @@ template <class dataType> class analogDetector {
   
   /** resets the commonModeSubtraction and increases the frame index */
   virtual void newFrame(){iframe++; if (cmSub) cmSub->newFrame();};
+
+  /** resets the commonModeSubtraction and increases the frame index */
+  virtual void newFrame(char *data){
+    iframe++; 
+    if (cmSub) cmSub->newFrame(); 
+    calcGhost(data); 
+    //    cout << getId() << " Calc ghost " <<  getGhost(15,15) << endl;
+      };
   
 
     /** sets the commonModeSubtraction algorithm to be used 
@@ -289,6 +308,11 @@ template <class dataType> class analogDetector {
     commonModeSubtraction *getCommonModeSubtraction() {return cmSub;};
 
 
+    ghostSummation<dataType> *getGhostSummation(){return ghSum;};
+    ghostSummation<dataType> *setGhostSummation(ghostSummation<dataType> *gs){ghSum=gs; return ghSum;}; 
+
+
+
     /**
        sets the sign of the data
        \param sign 1 means positive values for photons, -1 negative, 0 gets
@@ -304,12 +328,18 @@ template <class dataType> class analogDetector {
        \param iy pixel y coordinate
        \param cm 1 adds the value to common mod, 0 skips it. Defaults to 0. - not properly implemented
     */
-    virtual void addToPedestal(double val, int ix, int iy=0, int cm=0){ 
+    virtual void addToPedestal(double val, int ix, int iy, int cm=0){ 
       if (ix>=0 && ix<nx && iy>=0 && iy<ny) { 
+	
+	//	cout << val << " " ;
 	if (cmSub && cm>0)  { 
 	  val-=	getCommonMode(ix, iy);
 	}
-	stat[iy][ix].addToPedestal(val); 
+	//	cout << val << " " ;
+	val+=getGhost(ix,iy);
+	//	cout << val ;
+	//	cout << endl;
+	stat[iy*nx+ix].addToPedestal(val); 
 	/* if (cmSub && cm>0)  { */
 	/*   if (det) if (det->isGood(ix, iy)==0) return; */
 	/*   cmSub->addToCommonMode(val, ix, iy); */
@@ -318,29 +348,47 @@ template <class dataType> class analogDetector {
     }
     
     double getCommonMode(int ix, int iy) {
-      if (cmSub) return cmSub->getCommonMode(ix, iy);
-      else return 0;
+      if (cmSub) {
+	return cmSub->getCommonMode(ix, iy);
+      }
+      return 0;
     }
 
 
     virtual void addToCommonMode(char *data){ 
+      // cout << "+"<< getId() << endl;
       if (cmSub) {
+	//cout << "*" << endl;
 	  for (int iy=ymin; iy<ymax; iy++) { 
 	for (int ix=xmin; ix<xmax; ix++) {
 	    // if (getNumpedestals(ix,iy)>0) 
-	    if (det->isGood(ix,iy))
+	  //  if (det->isGood(ix,iy)) {
 	      addToCommonMode(data, ix, iy);
-	  }
+	      //  cout << ":";
+	      // }
 	}
+	  }
 	//cout << "cm " << getCommonMode(0,0) << " " << getCommonMode(1,0) << endl;
       }
     }      
+
     virtual void addToCommonMode(char *data, int ix, int iy=0){ 
+      //  cout <<".";
       if (cmSub) {
+	//cout <<":";
 	if (det) if (det->isGood(ix, iy)==0) return;
 	if (getNumpedestals(ix,iy)>0){
-	    cmSub->addToCommonMode(subtractPedestal(data,ix,iy,0), ix, iy);
-	    // cout << ix << " " <<subtractPedestal(data,ix,iy,0)  << endl;
+	  double val;
+	  if (det) {
+	  /* if (det->getChannel(data, ix, iy)>=0x3fff) */
+	  /*   cout << ix << " " << iy << " " << det->getChannel(data, ix, iy) <<endl; */
+	    val= (dataSign*det->getValue(data, ix, iy)-getPedestal(ix,iy,0));
+	  }	else
+	    val= (((double*)data)[iy*nx+ix]-getPedestal(ix,iy));
+	  	val+=getGhost(ix,iy);
+	
+	  cmSub->addToCommonMode(val, ix, iy);
+	  //cout << ":";
 	}
       }
     }      
@@ -351,12 +399,13 @@ template <class dataType> class analogDetector {
        \param cm 0 (default) without common mode subtraction, 1 with common mode subtraction (if defined)
        \returns pedestal value
     */
-    virtual double getPedestal(int ix, int iy, int cm=0){
-      if (ix>=0 && ix<nx && iy>=0 && iy<ny) 
-	if (cmSub && cm>0) 
-	  return stat[iy][ix].getPedestal()+getCommonMode(ix,iy); 
-	else return stat[iy][ix].getPedestal(); 
-      else return -1;
+    virtual double getPedestal (int ix, int iy, int cm=0){
+      if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
+	if (cmSub && cm>0) {
+	  return stat[iy*nx+ix].getPedestal()+getCommonMode(ix,iy); 
+	  
+	}     	else return stat[iy*nx+ix].getPedestal(); 
+      } else return -1;
     };
 
 
@@ -367,15 +416,22 @@ template <class dataType> class analogDetector {
        \returns pedestal rms
     */
     virtual double getPedestalRMS(int ix, int iy){
-      if (ix>=0 && ix<nx && iy>=0 && iy<ny) 
-	return stat[iy][ix].getPedestalRMS();
-      else return -1;
+      double g=1;
+      if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
+	if (gmap) {
+	  g=gmap[iy*nx+ix];
+	  if (g==0) g=-1.;
+	}
+      
+	return stat[iy*nx+ix].getPedestalRMS()/g;//divide by gain?
+      }
+      return -1;
     };
 
      virtual int getNumpedestals(int ix, int iy){
       if (ix>=0 && ix<nx && iy>=0 && iy<ny) 
-	return stat[iy][ix].getNumpedestals();
-      else return -1;
+	return stat[iy*nx+ix].getNumpedestals();
+      return -1;
     };
     /**
        gets  pedestal (and common mode)
@@ -385,12 +441,13 @@ template <class dataType> class analogDetector {
        \returns pedestal value
     */
     virtual double* getPedestal(double *ped){
-      if (ped==NULL)
+      if (ped==NULL) {
 	ped=new double[nx*ny];
-	for (int iy=0; iy<ny; iy++) {
-      for (int ix=0; ix<nx; ix++) {
-	  ped[iy*nx+ix]=stat[iy][ix].getPedestal();
-	  //cout << ped[iy*nx+ix] << " " ;
+      }
+      for (int iy=0; iy<ny; iy++) {
+	for (int ix=0; ix<nx; ix++) {
+	  ped[iy*nx+ix]=stat[iy*nx+ix].getPedestal();
+	    //cout << ped[iy*nx+ix] << " " ;
 	}
       }
       return ped;
@@ -403,11 +460,12 @@ template <class dataType> class analogDetector {
        \returns pedestal rms
     */
     virtual double* getPedestalRMS(double *ped=NULL){
-      if (ped==NULL)
+      if (ped==NULL) {
 	ped=new double[nx*ny];
-	for (int iy=0; iy<ny; iy++) {
-      for (int ix=0; ix<nx; ix++) {
-	  ped[iy*nx+ix]=stat[iy][ix].getPedestalRMS();
+      }
+      for (int iy=0; iy<ny; iy++) {
+	for (int ix=0; ix<nx; ix++) {
+	  ped[iy*nx+ix]=stat[iy*nx+ix].getPedestalRMS();
 	}
       }
       return ped;
@@ -433,7 +491,7 @@ template <class dataType> class analogDetector {
        \param rms rms to be set if any, defaults to 0
        \param m number of pedestal samples to be set or the moving stat structure is any, defaults to 0
     */
-    virtual void setPedestal(int ix, int iy, double val, double rms=0, int m=-1){if (ix>=0 && ix<nx && iy>=0 && iy<ny) stat[iy][ix].setPedestal(val,rms, m);};
+    virtual void setPedestal(int ix, int iy, double val, double rms=0, int m=-1){if (ix>=0 && ix<nx && iy>=0 && iy<ny) stat[iy*nx+ix].setPedestal(val,rms, m);};
     
   /**
        sets  pedestal
@@ -445,13 +503,14 @@ template <class dataType> class analogDetector {
     */
     virtual void setPedestal(double *ped, double *rms=NULL, int m=-1){
       double rr=0;
-	for (int iy=ymin; iy<ymax; iy++) {
-      for (int ix=xmin; ix<xmax; ix++) {
+      for (int iy=ymin; iy<ymax; iy++) {
+	for (int ix=xmin; ix<xmax; ix++) {
 	  if (rms) rr=rms[iy*nx+ix];
-	  stat[iy][ix].setPedestal(ped[iy*nx+ix],rr, m);
+	  stat[iy*nx+ix].setPedestal(ped[iy*nx+ix],rr, m);
+	  //  cout << ix << " " << iy << " " << ped[iy*nx+ix] << " " << stat[iy*nx+ix].getPedestal() << endl;
 	};
       };
-
+      
     }
     
 
@@ -464,7 +523,7 @@ template <class dataType> class analogDetector {
        \param iy pixel y coordinate
        \param rms value to set
     */
-    virtual void setPedestalRMS(int ix, int iy, double rms=0){if (ix>=0 && ix<nx && iy>=0 && iy<ny) stat[iy][ix].setPedestalRMS(rms);};
+    virtual void setPedestalRMS(int ix, int iy, double rms=0){if (ix>=0 && ix<nx && iy>=0 && iy<ny) stat[iy*nx+ix].setPedestalRMS(rms);};
     
 
 
@@ -476,13 +535,30 @@ template <class dataType> class analogDetector {
  virtual void setPedestalRMS(double *rms){
 	for (int iy=ymin; iy<ymax; iy++) {
       for (int ix=xmin; ix<xmax; ix++) {
-	  stat[iy][ix].setPedestalRMS(rms[iy*nx+ix]);
+	  stat[iy*nx+ix].setPedestalRMS(rms[iy*nx+ix]);
 	};
       };
 
     }
     
+ virtual void calcGhost(char *data, int ix, int iy=1) {
+   if (ghSum) {
+     ghSum->calcGhost(data, ix, iy);
+   }
+     
+};
 
+ virtual void calcGhost(char *data){if (ghSum) {
+     ghSum->calcGhost(data);
+     
+     //  cout << getId() << " @ " << ghSum->getXTalk() << " " <<  ghSum->getGhost(15,15) << endl;
+   }
+     
+
+};
+
+
+ virtual double getGhost(int ix, int iy) {if (ghSum) return ghSum->getGhost(ix, iy); return 0;};
 
      /**
        write 32bit tiff file with detector image data
@@ -549,9 +625,9 @@ template <class dataType> class analogDetector {
       for (int iy=0; iy<ny; iy++) {
     for (int ix=0; ix<nx; ix++) {
 	/* if (cmSub)  */
-	/*     gm[iy*nx+ix]=stat[iy][ix].getPedestal()-cmSub->getCommonMode(); */
+	/*     gm[iy*nx+ix]=stat[iy*nx+ix].getPedestal()-cmSub->getCommonMode(); */
 	/* else */
-	  gm[iy*nx+ix]=stat[iy][ix].getPedestal();
+	  gm[iy*nx+ix]=stat[iy*nx+ix].getPedestal();
 #ifdef ROOTSPECTRUM
 	  hmap->SetBinContent(ix+1, iy+1,gm[iy*nx+ix]);
 #endif
@@ -595,13 +671,13 @@ template <class dataType> class analogDetector {
     if (gm) {
 	for (int iy=0; iy<nny; iy++) {
       for (int ix=0; ix<nnx; ix++) {
-	  stat[iy][ix].setPedestal(gm[iy*nx+ix],-1,-1);
+	  stat[iy*nx+ix].setPedestal(gm[iy*nx+ix],-1,-1);
 	}
       }
       delete [] gm;
       return 1;
     }
-    return NULL;
+    return 0;
   }
   
  /**
@@ -626,7 +702,7 @@ template <class dataType> class analogDetector {
       delete [] gm;
       return 1;
     }
-    return NULL;
+    return 0;
   }
   
    
@@ -646,7 +722,7 @@ template <class dataType> class analogDetector {
       gm=new float[nx*ny];
 	for (int iy=0; iy<ny; iy++) {
       for (int ix=0; ix<nx; ix++) {
-	    gm[iy*nx+ix]=stat[iy][ix].getPedestalRMS();
+	    gm[iy*nx+ix]=stat[iy*nx+ix].getPedestalRMS();
 	}
       }
       ret=WriteToTiff(gm, imgname, ny, nx);  
@@ -668,7 +744,7 @@ template <class dataType> class analogDetector {
     if (gm) {
 	for (int iy=0; iy<nny; iy++) {
       for (int ix=0; ix<nnx; ix++) {
-	  stat[iy][ix].setPedestalRMS(gm[iy*nx+ix]);
+	  stat[iy*nx+ix].setPedestalRMS(gm[iy*nx+ix]);
 	}
       }
       delete [] gm;
@@ -690,19 +766,24 @@ template <class dataType> class analogDetector {
     
     virtual void addToPedestal(char *data, int cm=0) {
       
-      //    cout << "add to pedestal " << endl;
-      newFrame();
+      // cout << "add to pedestal " << endl;
+      newFrame(data);
       
-      if (cmSub) {
+      //calcGhost(data);
+
+
+      if (cmSub && cm) {
+	//	cout <<",";
 	addToCommonMode(data);
-      }
+      } 
             
       //cout << xmin << " " << xmax << endl;
       // cout << ymin << " " << ymax << endl;
-	for (int iy=ymin; iy<ymax; iy++) {
-      for (int ix=xmin; ix<xmax; ix++) {
+      for (int iy=ymin; iy<ymax; iy++) {
+	for (int ix=xmin; ix<xmax; ix++) {
 	  if (det->isGood(ix,iy)) {
-	    addToPedestal(data,ix,iy,1);
+	    // addToPedestal(data,ix,iy,1);
+	    addToPedestal(data,ix,iy,cm);
 	  //if (ix==10 && iy==10) 
 	  // cout <<ix << " " << iy << " " << getPedestal(ix,iy)<< endl;
 #ifdef ROOTSPECTRUM 
@@ -782,7 +863,7 @@ template <class dataType> class analogDetector {
     */
 
 
-    virtual void addToPedestal(char *data, int ix, int iy=0, int cm=0) {
+    virtual void addToPedestal(char *data, int ix, int iy, int cm=0) {
       
       
       double val;
@@ -792,12 +873,13 @@ template <class dataType> class analogDetector {
 	  val=dataSign*det->getValue(data, ix, iy);
 	else
 	  val=((double*)data)[iy*nx+ix];
-	
+	//	cout << val << endl;
 	 /* if (ix==10 && iy==10)  */
 	 /*     cout << ix << " " << iy << " " << val ;  */
 	  /* if (ix==100 && iy==100) */
 	  /*   cout << ix << " " << iy << " " << val; */
 	addToPedestal(val,ix,iy);
+	//	cout << val << endl;
 	  /* if (ix==10 && iy==10)  */
 	  /*   cout <<" " << getPedestal(ix,iy)<< endl; */
 	  /* if (ix==100 && iy==100) */
@@ -818,15 +900,17 @@ template <class dataType> class analogDetector {
       
     virtual  int *subtractPedestal(char *data, int *val=NULL, int cm=0) {
       
-      newFrame();
+      newFrame(data);
       
       if (val==NULL)
 	val=image;//new double[nx*ny];
       
-	for (int iy=ymin; iy<ymax; iy++) {
-      for (int ix=xmin; ix<xmax; ix++) {
-	    if (det->isGood(ix,iy))
-	      val[iy*nx+ix]+=subtractPedestal(data, ix, iy,cm);
+      //calcGhost(data);
+
+      for (int iy=ymin; iy<ymax; iy++) {
+	for (int ix=xmin; ix<xmax; ix++) {
+	  if (det->isGood(ix,iy))
+	    val[iy*nx+ix]+=subtractPedestal(data, ix, iy,cm);
 	}
       }
       return  val;
@@ -847,18 +931,25 @@ template <class dataType> class analogDetector {
 
    virtual  double subtractPedestal(char *data, int ix, int iy=0, int cm=0) {
      double g=1.;
-     double val;
+     double val =0;
       if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
 	if (gmap) {
 	  g=gmap[iy*nx+ix];
 	  if (g==0) g=-1.;
 	}
 
-	if (det)
+	if (det) {
+	  /* if (det->getChannel(data, ix, iy)>=0x3fff) */
+	  /*   cout << ix << " " << iy << " " << det->getChannel(data, ix, iy) <<endl; */
 	  val= (dataSign*det->getValue(data, ix, iy)-getPedestal(ix,iy,cm))/g;
-	else
+	}	else
 	  val= (((double*)data)[iy*nx+ix]-getPedestal(ix,iy))/g;
-    
+	
+	//if (val>=0.5*thr)
+	// cout << val << " " << (dataSign*det->getValue(data, ix, iy)-getPedestal(ix,iy,cm)) << " " << g << " ";
+
+	val+=getGhost(ix,iy)/g;
+
 #ifdef ROOTSPECTRUM
 	hs->Fill(val,(iy-ymin)*(xmax-xmin)+(ix-xmin));
 #ifdef ROOTCLUST
@@ -890,6 +981,7 @@ template <class dataType> class analogDetector {
 #endif
 	return val;
       }	  
+      return val;
    };
       
 
@@ -917,8 +1009,7 @@ template <class dataType> class analogDetector {
      int nph=0;
      double v;
      if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
-       v=subtractPedestal(data,ix,iy);
-
+       v=subtractPedestal(data,ix,iy,1);
 /*        // cout << v << " " ; */
 /* #ifdef ROOTSPECTRUM */
 /*        // cout << (iy-ymin)*(xmax-xmin)+(ix-xmin) << endl; */
@@ -927,8 +1018,14 @@ template <class dataType> class analogDetector {
        if (thr>0) {
 	 v+=0.5*thr;
 	 nph=v/thr;
-	 if (nph>0)
+	 
+	 /* if (ix ==10 && iy<20) */
+	 /*   cout << det->getValue(data,ix,iy) << " " << stat[iy*nx+ix].getPedestal() << " " << getCommonMode(ix,iy) << " " << getPedestal(ix,iy,0)<< " "  << getPedestal(ix,iy,1) << endl; */
+	 // cout << subtractPedestal(data,ix,iy,0) << " " << subtractPedestal(data,ix,iy,1) << " " << nph << endl;
+	 if (nph>0) {
+	   //cout << " " << nph << endl;
 	   return nph;
+	 }
 	 return 0;
        } 
        return v;
@@ -944,15 +1041,16 @@ template <class dataType> class analogDetector {
    */
      int *getNPhotons(char *data,  int *nph=NULL) {
        
-       double val;
+       //double val;
        if (nph==NULL)
 	 nph=image;
-       newFrame();
+       
+       newFrame(data);
 
+       //calcGhost(data);
        addToCommonMode(data);
-
-	 for (int iy=ymin; iy<ymax; iy++) {
-       for (int ix=xmin; ix<xmax; ix++) {
+       for (int iy=ymin; iy<ymax; iy++) {
+	 for (int ix=xmin; ix<xmax; ix++) {
 	   if (det->isGood(ix,iy))
 	     nph[iy*nx+ix]+=getNPhotons(data, ix, iy);
 	 }
@@ -999,8 +1097,8 @@ template <class dataType> class analogDetector {
       if (i>0) 
 	  for (iy=0; iy<ny; iy++) 
 	for (ix=0; ix<nx; ix++) 
-	    stat[iy][ix].SetNPedestals(i); 
-      return stat[0][0].SetNPedestals();
+	    stat[iy*nx+ix].SetNPedestals(i); 
+      return stat[0].SetNPedestals();
     };
 
  /** gets number of samples for moving average pedestal calculation
@@ -1008,7 +1106,7 @@ template <class dataType> class analogDetector {
     */
     int GetNPedestals(int ix, int iy) {
       if  (ix>=0 &&  ix<nx && iy>=0 && iy<ny) 
-	return stat[iy][ix].GetNPedestals(); 
+	return stat[iy*nx+ix].GetNPedestals(); 
       else
 	return -1;
     };
@@ -1030,13 +1128,16 @@ template <class dataType> class analogDetector {
       if (ymi<0) ymi=ymin;
       if (yma<0) yma=ymax;
       
-	for (int iy=ymi; iy<yma; iy++)
-      for (int ix=xmi; ix<xma; ix++)
+      newFrame(data);
+      //calcGhost(data);
+      addToCommonMode(data);
+      for (int iy=ymi; iy<yma; iy++)
+	for (int ix=xmi; ix<xma; ix++)
 	  if (det->isGood(ix,iy)) {
 	    if (ix>=0 && ix<nx && iy>=0 && iy<ny) 
 	      val+=getNPhotons(data, ix, iy);
 	  }
-
+      
       return val;
       
     };
@@ -1054,7 +1155,7 @@ template <class dataType> class analogDetector {
       switch(fMode) {
       case ePedestal:
 	//cout << "analog ped " << endl;
-	addToPedestal(data);
+	addToPedestal(data,1);
 	break;
       default:
 	//	cout << "analog " << endl;
@@ -1133,11 +1234,12 @@ FILE *getFilePointer(){return myFile;};
     slsDetectorData<dataType> *det; /**< slsDetectorData to be used */
     int nx; /**< Size of the detector in x direction */
     int ny; /**< Size of the detector in y direction */
-    pedestalSubtraction **stat; /**< pedestalSubtraction class */
+    pedestalSubtraction *stat; /**< pedestalSubtraction class */
     commonModeSubtraction *cmSub;/**< commonModeSubtraction class */
     int dataSign; /**< sign of the data i.e. 1 if photon is positive, -1 if negative */
     int iframe;  /**< frame number (not from file but incremented within the dataset every time newFrame is called */
     double *gmap;
+    ghostSummation<dataType> *ghSum;/**< ghostSummation class */
     int *image;
     int id;
     //int xmin, xmax, ymin, ymax;  int xmin; /**< minimum x of the region of interest */

slsDetectorCalibration/commonModeSubtractionNew.h

@@ -14,7 +14,7 @@ class commonModeSubtraction {
       \param iroi number of regions on which one can calculate the common mode separately. Defaults to 1 i.e. whole detector
 
   */
- commonModeSubtraction(int iroi=1, int ns=3) : nROI(iroi), nsigma(ns)  {
+ commonModeSubtraction(int iroi=1, int ns=3) : nsigma(ns), nROI(iroi)  {
     mean=new double[nROI];  
     mean2=new double[nROI]; 
     nCm=new double[nROI];
@@ -23,6 +23,13 @@ class commonModeSubtraction {
     /** destructor - deletes the moving average(s) and the sum of pedestals calculator(s) */
     virtual ~commonModeSubtraction() {delete [] mean; delete [] mean2; delete [] nCm;};
     
+    /* commonModeSubtraction(commonModeSubtraction *cs) { */
+    /*   if (cs) new commonModeSubtraction(cs->getNRoi(), cs->nsigma); */
+    /* } */
+    
+    virtual commonModeSubtraction *Clone() {
+      return new commonModeSubtraction(this->nROI, this->nsigma);
+    }
 
     /** clears the moving average and the sum of pedestals calculation - virtual func*/
     virtual void  Clear(){
@@ -34,6 +41,7 @@ class commonModeSubtraction {
     
     /** 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(){
+      //cout << "Reset CM" << endl;
       for (int i=0; i<nROI; i++) {
 	//	if (nCm[i]>0) cmStat[i].Calc(cmPed[i]/nCm[i]); 
 	nCm[i]=0; 
@@ -52,7 +60,10 @@ class commonModeSubtraction {
       // if (iroi==0) val=100;
       // else val=-100;
       // if (isc>=0 && isc<nROI) {
+      //	cout << ix << " " << iy << " " << iroi << endl;
+      //if (ix==15 && iy==15) cout << "=" << val << endl;
       if (iroi>=0 && iroi<nROI) {
+	//	cout << ix << " " << iy << " " << iroi << endl;
 	mean[iroi]+=val; 
 	mean2[iroi]+=val*val; 
 	nCm[iroi]++;
@@ -70,9 +81,10 @@ class commonModeSubtraction {
       /* 	return 100; */
       /* else */
       /* 	return -100; */
-
+      // cout << "*" << ix << " " << iy << " " << iroi << " " << mean[iroi] << " " << nCm[iroi]<< endl;
+      // if (ix==15 && iy==15) cout << "-" << mean[iroi]/nCm[iroi] << endl;
       if (iroi>=0 && iroi<nROI) {
-	if (nCm[iroi]>0) 
+	if (nCm[iroi]>0)  
 	  return mean[iroi]/nCm[iroi]; 
       }
       return 0;
@@ -96,8 +108,7 @@ class commonModeSubtraction {
 	gets the common mode ROI for pixel ix, iy -should be overloaded!
      */
     virtual int getROI(int ix, int iy){ (void) ix; (void) iy; return 0;};
-
-
+    int getNRoi(){return nROI;};
 
  protected:
   double *mean; /**<array of moving average of the pedestal average per region of interest */

slsDetectorCalibration/dataStructures/Mythen3_01_jctbData.h

@@ -45,7 +45,7 @@ class mythen3_01_jctbData : public slsDetectorData<short unsigned int> {
 
  virtual short unsigned int* mythen03_frame(char *ptr, int dr=24,  int nch=64*3, int off=5) {
    // off=0;
-    int iarg;
+    //int iarg;
     int64_t word, *wp;
     short unsigned int* val=new short unsigned int[nch];
     int bit[64];

slsDetectorCalibration/dataStructures/Mythen3_02_jctbData.h

@@ -49,7 +49,7 @@ class mythen3_02_jctbData : public mythen3_01_jctbData {
 
  virtual short unsigned int* mythen03_frame(char *ptr, int dr=24,  int nch=64*3, int off=5) {
    // off=0;
-    int iarg;
+    //int iarg;
     int64_t word, *wp;
     short unsigned int* val=new short unsigned int[nch];
     int bit[64];
@@ -57,7 +57,7 @@ class mythen3_02_jctbData : public mythen3_01_jctbData {
     int ioff=0;
     int idr=0;
     int ib=0;
-    int ich=0;
+    //int ich=0;
     int ii=0;
     int iw=0;
     bit[0]=17;//19;

slsDetectorCalibration/dataStructures/deserializer.h

@@ -0,0 +1,171 @@
+#ifndef DESERIALIZER_H
+#define DESERIALIZER_H
+#include <vector>
+
+class deserializer : public slsDetectorData<int> {
+
+
+ public:
+
+
+ deserializer( std::vector <int> dbl, int nch=64*3,int dr=24, int off=2): slsDetectorData<int>(nch,1,nch*dr*8+off*8,NULL,NULL,NULL), dynamicRange(dr), serialOffset(off), frameNumber(0), numberOfCounters(nch), dbitlist(dbl) {};
+
+ deserializer( std::vector <int> dbl, int nch,int dr, int off, int ds): slsDetectorData<int>(nch,1,ds,NULL,NULL,NULL), dynamicRange(dr), serialOffset(off), frameNumber(0), numberOfCounters(nch),  dbitlist(dbl) {};
+
+  virtual void getPixel(int ip, int &x, int &y) {x=-1; y=-1;};
+  
+  virtual int getChannel(char *data, int ix, int iy=0) {
+    int ret=-1;
+    if (ix>=0 && ix<numberOfCounters) {
+      int *val=deserializeAll(data,dbitlist,dynamicRange,numberOfCounters,serialOffset); 
+      ret=val[ix];
+      delete [] val;
+    }
+    return ret;
+  };
+  
+  virtual int getFrameNumber(char *buff) {return frameNumber;};
+ 
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize) {
+    ndata=dsize;
+    return data;
+  }
+  
+ virtual char *readNextFrame(ifstream &filebin) {
+    char *data=NULL;
+    if (filebin.is_open()) {
+      data=new char[dataSize];
+      filebin.read(data,dataSize);
+    }
+    return data;
+  }
+ 
+ virtual int **getData(char *ptr, int dsize=-1) {
+   int **val;
+   val=new int*[1];
+   val[0]=deserializeAll(ptr,dbitlist,dynamicRange,nx,serialOffset);
+   return val;
+   
+ }
+ 
+
+ static int* deserializeAll(char *ptr, std::vector <int> dbl, int dr=24,  int nch=64*3, int off=5) {
+   // off=0;
+   //int iarg;
+   int64_t word, *wp;
+   int* val=new int[nch];
+   int ioff=0;
+   int idr=0;
+   int ib=0;
+   int iw=0;
+   int ii=0;
+   int ich;
+   int nb=dbl.size();
+   idr=0;
+   for (ib=0; ib<nch; ib++) {
+     val[ib]=0;
+   }
+   wp=(int64_t*)ptr;
+   
+   for (iw=0; iw<nch/nb; iw) {
+     word=*wp;;
+     if (ioff<off) {
+       ioff++;
+       // cout <<"*";
+     }  else {
+       //if (idr<16) {
+       ib=0;
+	for (const auto &bit : dbl) {
+	  ich=iw+nch/nb*(ib);
+	  if (word&(1<<bit) && ich<nch)  {
+	    //cout << "+" ;
+	    val[ich]|=(1<<idr);
+	  }  //else { 
+	  //cout << "-" ; 
+	  //}
+	  ib++;
+	}
+	
+     }
+     
+     idr++; 
+     if (idr==dr) {
+       idr=0;
+	//  cout << dec << " " << iw << " " << val[iw] << " " << val[iw+nch/2] << endl;
+       cout <<dec << iw<<endl;
+       iw++;
+     }//end if()
+     
+      //end else()
+     wp+=1;
+     ii++;
+   }//end for
+   
+    
+    return val;
+ }
+
+ static int* deserializeList(char *ptr, std::vector <int> dbl, int dr=24,  int nch=64*3, int off=5) {
+   // off=0;
+   //int iarg;
+  // int64_t word;
+   int* val=new int[nch];
+   //int ioff=0;
+   int idr=0;
+   int ib=0;
+   int iw=0;
+   int ii=0;
+   int ich;
+   int nb=dbl.size();
+
+   char *dval;
+
+   idr=0;
+   for (ib=0; ib<nch; ib++) {
+     val[ib]=0;
+   }
+   dval=ptr;
+   
+   ib=0;
+   ich=0;
+   for (const auto &bit : dbl) {
+     //ioff=off;
+     idr=0;
+     for (iw=0; iw<(nch*dr/nb)/8; iw++) {
+       val[ich]|=(*dval)<<idr;
+       idr+=8;
+       dval++;
+       if (idr>=dr) {
+	 idr=0;
+	 ich++;
+       }	
+     }
+     ii++;
+     ib++;
+   }//end for
+   
+    
+    return val;
+ }
+
+ virtual int setFrameNumber(int f=0) {if (f>=0) frameNumber=f; return frameNumber; };
+ virtual int setDynamicRange(int d=-1) {if (d>0 && d<=24) dynamicRange=d; return dynamicRange;};
+ virtual int setSerialOffset(int d=-1) {if (d>=0) serialOffset=d; return serialOffset;};
+ virtual int setNumberOfCounters(int d=-1) {if (d>=0) numberOfCounters=d; return numberOfCounters;};
+ virtual  std::vector <int> setDBitList(std::vector <int> dbl) {dbitlist=dbl; return dbitlist;};
+ virtual  std::vector <int> getDBitList() {return dbitlist;};
+ 
+ 
+ private:
+ 
+ int dynamicRange;
+ int serialOffset;
+ int frameNumber;
+ int numberOfCounters;
+ std::vector <int> dbitlist;
+   
+
+ 
+};
+
+#endif

slsDetectorCalibration/dataStructures/eigerHalfModuleData.h

@@ -1,470 +0,0 @@
-#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(bool t, bool l, int dr, int tg, int psize, int dsize, int npf, int x, int y, double c=0):
-		slsReceiverData<uint32_t>(x, y, npf, psize),
-		top(t), left(l),
-		dynamicRange(dr), tenGiga(tg),
-		packetSize(psize), onepacketdataSize(dsize), numberofPacketsPerFrame(npf),
-		xtalk(c),
-		header_t(0), footer_t(0){
-
-
-		int **dMap;
-		uint32_t **dMask;
-
-		dMap=new int*[ny];
-		dMask=new uint32_t*[ny];
-
-
-		for (int i = 0; i < ny; i++) {
-			dMap[i] = new int[nx];
-			dMask[i] = new uint32_t[nx];
-		}
-
-		//Map
-		int totalNumberOfBytes = numberofPacketsPerFrame * packetSize;
-		int iPacket = 8;
-		int iData = 0;
-		int increment = (dynamicRange/8);
-		int ic_increment = 1;
-		if (dynamicRange == 4) {
-			increment = 1;
-			ic_increment = 2;
-		}
-
-		if(top){
-			for (int ir=0; ir<ny; ir++) {
-				for (int ic=0; ic<nx; ic = ic + ic_increment) {
-					dMap[ir][ic]  = iPacket;
-					iPacket += increment;
-					iData += increment;
-					//increment header
-					if(iData >= onepacketdataSize){
-						iPacket += 16;
-						iData = 0;
-					}
-
-				}
-			}
-		}
-
-		//bottom
-		else{
-			iData = 0;
-			int numbytesperline;
-			switch(dynamicRange){
-				case 4: numbytesperline = 256; break;
-				case 8:	numbytesperline = 512; break;
-				case 16:numbytesperline = 1024; break;
-				case 32:numbytesperline = 2048; break;
-			}
-			iPacket = totalNumberOfBytes - numbytesperline - 8;
-			if((dynamicRange == 32) && (!tenGiga))
-					iPacket -= 16;
-
-			for (int ir=0; ir<ny; ir++) {
-				for (int ic=0; ic<nx; ic = ic + ic_increment) {
-					dMap[ir][ic]  = iPacket;
-					iPacket += increment;
-					iData += increment;
-					//--------------------32 bit 1giga -------------------
-					if((dynamicRange == 32) && (!tenGiga)){
-						if(iData == numbytesperline){
-							iPacket -= (numbytesperline*2 + 16*3);
-							iData = 0;
-						}
-						if(iData == onepacketdataSize){
-							iPacket += 16;
-						}
-					}//------------end of 32 bit -------------------------
-					else if((iData % numbytesperline) == 0){
-						iPacket -= (numbytesperline*2);
-						if(iData == onepacketdataSize){
-							iPacket -= 16;
-							iData = 0;
-						}
-					}
-					//---------------------------------------------------
-				}
-			}
-		}
-
-
-
-
-		//Mask
-		for(int ir=0; ir<ny; ++ir)
-			for(int ic=0; ic<nx; ++ic)
-				dMask[ir][ic] = 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){
-		footer_t = (eiger_packet_footer_t*)(buff + onepacketdataSize + sizeof(eiger_packet_header_t));
-		return ((uint32_t)(*( (uint64_t*) footer_t)));
-	};
-
-
-
-
-
-	/** gets the packets number
-     	 \param buff pointer to the memory
-     	 \returns packet number
-	 */
-	int getPacketNumber(char *buff){
-		footer_t = (eiger_packet_footer_t*)(buff + onepacketdataSize + sizeof(eiger_packet_header_t));
-		return(*( (uint16_t*) footer_t->packetnum));
-	};
-
-
-
-	/**
-    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 getChannelwithMissingPackets(data, ix, iy);
-		else
-			return getChannelwithMissingPackets(data, ix, iy)-xtalk * getChannelwithMissingPackets(data, ix-1, iy);
-	};
-
-
-	/**
-
-	     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
-	     \returns data for the selected channel, with inversion if required
-
-	 */
-
-	virtual int getChannelwithMissingPackets(char *data, int ix, int iy) {
-		uint32_t m=0, n = 0;
-		int linesperpacket,newix, newiy,origX;
-
-
-		//cout <<"ix:"<<ix<<" nx:"<<nx<<" iy:"<<iy<<" 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];
-
-
-			//pixelpos1d = (nx * iy + ix);
-
-			switch(dynamicRange){
-			case 4: 	if(tenGiga) linesperpacket=16;	else linesperpacket=4;break;
-			case 8: 	if(tenGiga) linesperpacket=8; 	else linesperpacket=2;break;
-			case 16: 	if(tenGiga) linesperpacket=4; 	else linesperpacket=1;break;
-			case 32:	if(tenGiga) linesperpacket=2; 	else linesperpacket=1;break;
-			}
-
-
-
-			//each byte is shared by 2 pixels for 4 bit mode
-			origX = ix;
-			if((dynamicRange == 4) && (ix%2))
-				ix--;
-
-
-
-			// ------check if missing packet, get to pixel at start of packet-----------------
-
-			//to get the starting of a packet (except 1g 32 bit)
-			newix = 0;
-			// 0.5 Lines per packet for 1g 32 bit
-			if(dynamicRange == 32 && !tenGiga)
-				newix = ix - (ix%256);
-
-			//iy divided by linesperpacket depending on bitmode
-			if(!(iy%linesperpacket))
-				newiy = iy;
-			else
-				newiy = (iy - (iy%linesperpacket));
-
-			header_t = (eiger_packet_header_t*)((char*)(data +(dataMap[newiy][newix]-8)));
-			uint16_t identifier = (uint16_t)*( (uint16_t*) header_t->missingpacket);
-
-			if(identifier==deactivatedPacketValue){
-				//	cprintf(RED,"deactivated packet\n");
-				return -2;
-			}
-			// -----END OF CHECK -------------------------------------------------------------
-
-
-		}else{
-			cprintf(RED,"outside limits\n");
-			return -99;
-		}
-
-		//get proper data
-		n = ((uint32_t)(*((uint32_t*)(((char*)data)+(dataMap[iy][ix])))));
-
-		//each byte is shared by 2 pixels for 4 bit mode
-		if(dynamicRange == 4){
-			if(ix != origX)
-				return ((n & 0xf0)>>4)^m;
-			return (n & 0xf)^m;
-		}
-		else if(dynamicRange == 8)	return (n & 0xff)^m;
-		else if(dynamicRange == 16)	return (n & 0xffff)^m;
-		else				return (n & 0xffffffff)^m;
-
-
-	};
-
-
-	/** 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;}
-
-	void getChannelArray(double* data, char* buffer){
-		for(int iy = 0; iy < ny; iy++){
-			for(int ix = 0; ix < nx; ix++){
-				data[iy*nx+ix] = getValue((char*)buffer,ix,iy);
-				//cprintf(BLUE,"%d,%d :%f\n",ix,iy,value);
-			}
-		}
-	}
-
-
-	int* decodeData(int *datain) {
-
-		int dataBytes = numberofPacketsPerFrame * onepacketdataSize;
-		int nch = nx*ny;
-		int* dataout = new int [nch];
-		char *ptr=(char*)datain;
-		char iptr;
-
-		const int bytesize=8;
-		int ival=0;
-		int  ipos=0, ichan=0, ibyte;
-
-		switch (dynamicRange) {
-		case 4:
-			for (ibyte=0; ibyte<dataBytes; ++ibyte) {//for every byte (1 pixel = 1/2 byte)
-				iptr=ptr[ibyte]&0xff;				//???? a byte mask
-				for (ipos=0; ipos<2; ++ipos) {		//loop over the 8bit (twice)
-					ival=(iptr>>(ipos*4))&0xf;		//pick the right 4bit
-					dataout[ichan]=ival;
-					ichan++;
-				}
-			}
-			break;
-		case 8:
-			for (ichan=0; ichan<dataBytes; ++ichan) {//for every pixel (1 pixel = 1 byte)
-				ival=ptr[ichan]&0xff;				//????? a byte mask
-				dataout[ichan]=ival;
-			}
-			break;
-		case 16:
-			for (ichan=0; ichan<nch; ++ichan) { 	//for every pixel
-				ival=0;
-				for (ibyte=0; ibyte<2; ++ibyte) { 	//for each byte (concatenate 2 bytes to get 16 bit value)
-					iptr=ptr[ichan*2+ibyte];
-					ival|=((iptr<<(ibyte*bytesize))&(0xff<<(ibyte*bytesize)));
-				}
-				dataout[ichan]=ival;
-			}
-			break;
-		default:
-													//for every 32 bit (every element in datain array)
-			for (ichan=0; ichan<nch; ++ichan) { 	//for every pixel
-				ival=datain[ichan]&0xffffff;
-				dataout[ichan]=ival;
-			}
-		}
-
-
-
-		return dataout;
-
-	};
-
-
-	int* readNextFrameOnlyData(ifstream &filebin, int& fnum) {
-		int framesize = numberofPacketsPerFrame * onepacketdataSize;
-
-		int* data = new int[framesize/(sizeof(int))];
-		char *packet=new char[packetSize];
-		fnum = -1;
-		int pn=-1;
-		int dataoffset = 0;
-
-		if (filebin.is_open()) {
-
-			while (filebin.read(packet,packetSize)) {
-
-				fnum = getFrameNumber(packet); //cout << "fn:"<<fn<<endl;
-				pn = getPacketNumber(packet); //cout << "pn:"<<pn<<endl;
-
-				memcpy(((char*)data)+dataoffset,packet+DATA_PACKET_HEADER_SIZE,onepacketdataSize);
-				dataoffset+=onepacketdataSize;
-				if(pn == numberofPacketsPerFrame)
-					break;
-			}
-		}
-
-		delete [] packet;
-		if(!dataoffset){
-			delete [] data;
-			return NULL;
-		}
-
-		return data;
-
-	}
-	/*
-	when u get packet form next frames
-	//to remember the position to read next frame
-	filebin.seekg (position, filebin.beg);
-	position = filebin.tellg();
-
-	*/
-
-	int *readNextFramewithMissingPackets(ifstream &filebin, int& fnum) {
-
-		int* data = new int[(numberofPacketsPerFrame * onepacketdataSize)/(sizeof(int))];
-		char *packet=new char[packetSize];
-		fnum = -1;
-		int pnum = 0;
-		int fn = -1;
-		int pn =-1;
-		int dataoffset = 0;
-		int missingpackets;
-
-
-		if (filebin.is_open()) {
-
-			while (filebin.read(packet,packetSize)) {
-
-				fn = getFrameNumber(packet); //cout << "fn:"<<fn<<endl;
-				pn = getPacketNumber(packet); //cout << "pn:"<<pn<<endl;
-
-				//first packet
-				if(fnum == -1){
-					fnum = fn;
-				}
-				//next frame packet
-				else if (fnum != fn){
-					//set file reading to the last frame's packet in file
-					filebin.seekg(-packetSize, ios::cur);//filebin.beg
-					break;
-				}
-
-				//missing packets
-				missingpackets = pn - pnum - 1;
-				if(missingpackets){
-					memset(((char*)data)+dataoffset,0xFF,missingpackets*onepacketdataSize);
-					dataoffset+=(missingpackets*onepacketdataSize);
-					pnum+=missingpackets;
-				}
-
-				memcpy(((char*)data)+dataoffset,packet+DATA_PACKET_HEADER_SIZE,onepacketdataSize);
-				dataoffset+=onepacketdataSize;
-				pnum++;
-				if(pnum == numberofPacketsPerFrame)
-					break;
-
-			}
-		}
-
-		delete [] packet;
-		if(!pnum){
-			delete [] data;
-			return NULL;
-		}
-
-		//missing packets (added here to also catch end of file)
-		missingpackets = numberofPacketsPerFrame - pnum;
-		if(missingpackets){
-			memset(((char*)data)+dataoffset,0xFF,missingpackets*onepacketdataSize);
-			dataoffset+=(missingpackets*onepacketdataSize);
-		}
-
-		return data;
-	}
-
-
-
-private:
-	/** Missing Packet identifier value */
-	const static uint16_t deactivatedPacketValue = 0xFEFE;
-
-	const static int DATA_PACKET_HEADER_SIZE = 8;
-	const bool top;
-	const bool left;
-	const int dynamicRange;
-	const bool tenGiga;
-	const int packetSize;
-	const int onepacketdataSize;
-	const int numberofPacketsPerFrame;
-	double xtalk; /**<output buffer crosstalk correction parameter */
-
-
-	/** structure of an eiger packet*/
-	typedef struct{
-		unsigned char subframenum[4];
-		unsigned char missingpacket[2];
-		unsigned char portnum[1];
-		unsigned char dynamicrange[1];
-	} eiger_packet_header_t;
-
-	typedef struct{
-		unsigned char framenum[6];
-		unsigned char packetnum[2];
-	} eiger_packet_footer_t;
-
-	eiger_packet_header_t* header_t;
-	eiger_packet_footer_t* footer_t;
-};
-
-
-
-
-#endif

slsDetectorCalibration/dataStructures/gotthardModuleData.h

@@ -1,148 +0,0 @@
-#ifndef GOTTHARDMODULEDATA_H
-#define  GOTTHARDMODULEDATA_H
-#include "slsReceiverData.h"
-
-
-
-
-
-#define FRAMEMASK 0xFFFFFFFE
-#define PACKETMASK 1
-#define FRAMEOFFSET 0x1
-
-
-class gotthardModuleData : public slsReceiverData<uint16_t> {
-public:
-
-
-
-
-	/**
-     Implements the slsReceiverData structure for the gotthard read out by a module i.e. using the slsReceiver
-     (1x1280 pixels, 2 packets 1286 large etc.)
-     \param c crosstalk parameter for the output buffer
-
-	 */
-
-
-	gotthardModuleData(double c=0): slsReceiverData<uint16_t>(xpixels, ypixels, npackets, buffersize), xtalk(c) {
-
-		uint16_t **dMask;
-		int **dMap;
-		int ix, iy;
-		int initial_offset = 2;
-		int offset = initial_offset;
-
-		dMask=new uint16_t*[ypixels];
-		dMap=new int*[ypixels];
-		for (int i = 0; i < ypixels; i++) {
-			dMap[i] = new int[xpixels];
-			dMask[i] = new uint16_t[xpixels];
-		}
-
-		for(ix=0; ix<ypixels; ++ix)
-			for(iy=0; iy<xpixels; ++iy)
-				dMask[ix][iy] = 0x0;
-
-		for(ix=0; ix<ypixels; ++ix){
-			if(ix == (ypixels/2)){
-				offset += initial_offset;//2
-				offset++;
-			}
-			for(iy=0; iy<xpixels; ++iy){
-				dMap[ix][iy] = offset;
-				offset++;
-			}
-		}
-
-		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){
-		int np=(*(int*)buff);
-		//gotthards frame header must be incremented
-		++np;
-		//packet index should be 1 or 2
-		return ((np&FRAMEMASK)>>FRAMEOFFSET);
-	};
-
-
-
-	/**
-     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){
-		int np=(*(int*)buff);
-		//gotthards frame header must be incremented
-		++np;
-		//packet index should be 1 or 2
-		return ((np&PACKETMASK)+1);
-	};
-
-
-	/**
-    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) {
-		//check how it is for gotthard
-	    if (xtalk==0)
-	      return  slsDetectorData<uint16_t>::getValue(data, ix, iy);
-	    else
-	      return slsDetectorData<uint16_t>::getValue(data, ix, iy)-xtalk*slsDetectorData<uint16_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 = 1280;
-	const static int ypixels = 1;
-	const static int npackets = 2;
-	const static int buffersize = 1286;
-};
-
-
-
-
-
-#endif

slsDetectorCalibration/dataStructures/gotthardModuleDataNew.h

@@ -1,170 +0,0 @@
-#ifndef GOTTHARDMODULEDATANEW_H
-#define  GOTTHARDMODULEDATANEW_H
-#include "slsDetectorData.h"
-
-
-
-
-
-    typedef struct {
-        uint64_t frameNumber;    /**< is the frame number */
-        uint32_t expLength;        /**< is the subframe number (32 bit eiger) or real time exposure time in 100ns (others) */
-        uint32_t packetNumber;    /**< is the packet number */
-        uint64_t bunchId;        /**< is the bunch id from beamline */
-        uint64_t timestamp;        /**< is the time stamp with 10 MHz clock */
-        uint16_t modId;            /**< is the unique module id (unique even for left, right, top, bottom) */
-        uint16_t xCoord;        /**< is the x coordinate in the complete detector system */
-        uint16_t yCoord;        /**< is the y coordinate in the complete detector system */
-        uint16_t zCoord;        /**< is the z coordinate in the complete detector system */
-        uint32_t debug;            /**< is for debugging purposes */
-        uint16_t roundRNumber;    /**< is the round robin set number */
-        uint8_t detType;        /**< is the detector type see :: detectorType */
-        uint8_t version;        /**< is the version number of this structure format */
-    } sls_detector_header;
-
-
-
-
-
-
-
-
-class gotthardModuleDataNew : public slsDetectorData<uint16_t> {
-
- private:
-  
-  int iframe;
-  const int offset;
-
-
-public:
-
-
-
-	/**
-     Implements the slsReceiverData structure for the gotthard read out by a module i.e. using the slsReceiver
-     (1x1280 pixels, 2 packets 1286 large etc.)
-     \param c crosstalk parameter for the output buffer
-
-	 */
-
-
-    gotthardModuleDataNew(int off=24*2, int nch=1280): slsDetectorData<uint16_t>(nch, 1, nch*2+off), offset(off) {
-
-		uint16_t **dMask;
-		int **dMap;
-		int ix, iy;
-		int ypixels=1;
-		int xpixels=nch;
-
-		dMask=new uint16_t*[1];
-		dMap=new int*[1];
-		dMap[0] = new int[nch];
-		dMask[0] = new uint16_t[nch];
-
-		for(int ix=0; ix<xpixels; ix++) {
-		  dMap[0][ix] = 2*ix+offset; 
-		  dMask[0][ix] = 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){if (offset>=sizeof(sls_detector_header)) return ((sls_detector_header*)buff)->frameNumber; return iframe;};//*((int*)(buff+5))&0xffffff;};   
-
-
-
-	/**
-     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){if (offset>=sizeof(sls_detector_header))return ((sls_detector_header*)buff)->packetNumber;};
-
-
-
-
-  /**
-
-     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 
-     
-  */
-  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
-    if (dsize<dataSize) ndata=dsize;
-    else ndata=dataSize;
-    return data;
-
-  }
-
-  virtual char *readNextFrame(ifstream &filebin) {
-    int ff=-1, np=-1;
-    return readNextFrame(filebin, ff, np);
-  };
-
-  virtual char *readNextFrame(ifstream &filebin, int &ff) {
-    int np=-1;
-    return readNextFrame(filebin, ff, np);
-  };
-
-  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
-	  char *data=new char[dataSize];
-	  char *d=readNextFrame(filebin, ff, np, data);
-	  if (d==NULL) {delete [] data; data=NULL;}
-	  return data;
-  }
-
-
-
-
-  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
-	  char *retval=0;
-	  int  nd;
-	  int fnum = -1;
-	  np=0;
-	  int  pn;
-	  
-	  //  cout << dataSize << endl;
-	  if (ff>=0)
-	    fnum=ff;
-
-	  if (filebin.is_open()) {
-	    if (filebin.read(data, dataSize) ){
-	      ff=getFrameNumber(data);
-	      np=getPacketNumber(data);
-	      return data;
-	    }
-	  }
-	    return NULL;
-	    
-	    
-	  
-  };
-
-  
-
-
-};
-
-
-
-
-
-#endif

slsDetectorCalibration/dataStructures/jungfrau02Data.h

@@ -1,156 +0,0 @@
-#ifndef JUNGFRAU02DATA_H
-#define JUNGFRAU02DATA_H
-
-#include "chiptestBoardData.h"
-
-
-
-class jungfrau02Data : public chiptestBoardData {
- public:
-
-/* test :) */
-
-
-  /**
-     Implements the chiptestBoardData structure for the jungfrau02 prototype 
-     (48x48 pixels, ADC2 for analog output, 2 more ADCs used for readout of digital bits, pixel offset configurable.)
-     \param c crosstalk parameter for the output buffer
-
-  */
-  
-
-  jungfrau02Data(int nadc, int offset, double c=0): chiptestBoardData(48, 48, nadc, offset), 
-    xtalk(c) {
-
-
-
-
-    uint16_t **dMask;
-    int **dMap;
-
-
-
-    dMask=new uint16_t*[48];
-    dMap=new int*[48];
-    for (int i = 0; i < 48; i++) {
-      dMap[i] = new int[48];
-      dMask[i] = new uint16_t[48];
-    }
-
-
-    for (int iy=0; iy<48; iy++) {
-      for (int ix=0; ix<48; ix++) {
-	
-	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);
-    }
-
-
-
-  };
-    
-   /**
-
-     Returns the value of the selected channel for the given dataset. Since the ADC is only 14bit wide, only bit 0-13 are occupied. If the gain bits are read out, they are returned in bit 14-15.
-     \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
-     \returns data for the selected channel, with inversion if required
-
-  */
- 
- virtual uint16_t getChannel(char *data, int ix, int iy=0) { 
-    uint16_t 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]; 
-          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;
-	  if (*((uint16_t*)(data)+dataMap[iy][ix]+2)>8000) //exchange if gainBits==2 is returned!
-		d|=(1<<14); // gain bit 1
-	  if (*((uint16_t*)(data)+dataMap[iy][ix]+1)>8000) //exchange if gainBits==2 is returned!
-		d|=(1<<15); // gain bit 0
-	  
-        }
-
-    }  
-    return d^m;
-  };
-
-  /**
-    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;
-    uint16_t d=getChannel(data, ix, iy);
-    // cout << d << " " << (d&0x3fff) << endl;
-    if (xtalk==0 || ix==0)
-      return  (double)(getChannel(data, ix, iy)&0x3fff);
-    else
-      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
-      \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 */
-
-
-};
-
-
-
-#endif

slsDetectorCalibration/dataStructures/jungfrau10ModuleData.h

@@ -1,217 +0,0 @@
-#ifndef JUNGFRAU10MODULEDATA_H
-#define  JUNGFRAU10MODULEBDATA_H
-#include "slsDetectorData.h"
-
-
-
-class jungfrau10ModuleData : public slsDetectorData<uint16_t> {
-
- private:
-
-     typedef struct {
-        uint64_t frameNumber;    /**< is the frame number */
-        uint32_t expLength;        /**< is the subframe number (32 bit eiger) or real time exposure time in 100ns (others) */
-        uint32_t packetNumber;    /**< is the packet number */
-        uint64_t bunchId;        /**< is the bunch id from beamline */
-        uint64_t timestamp;        /**< is the time stamp with 10 MHz clock */
-        uint16_t modId;            /**< is the unique module id (unique even for left, right, top, bottom) */
-        uint16_t xCoord;        /**< is the x coordinate in the complete detector system */
-        uint16_t yCoord;        /**< is the y coordinate in the complete detector system */
-        uint16_t zCoord;        /**< is the z coordinate in the complete detector system */
-        uint32_t debug;            /**< is for debugging purposes */
-        uint16_t roundRNumber;    /**< is the round robin set number */
-        uint8_t detType;        /**< is the detector type see :: detectorType */
-        uint8_t version;        /**< is the version number of this structure format */
-    } sls_detector_header;
-
-
-  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, 256*256*8*2+48, NULL, NULL, NULL) , iframe(0) {
-
-    
-   
-    int row, col;
-
-    int isample;
-    int iadc;
-    int ix, iy;
-
-    int ichip;
-
-    // cout << sizeof(uint16_t) << endl;
-    int ip=0;
-    for (int iy=0; iy<256*2; iy++) {
-      for (int ix=0; ix<256*4; ix++){
-	dataMap[iy][ix]=ip*2+48;
-	ip++;
-      }
-    }
-      
-
-    /* for (iadc=0; iadc<nadc; iadc++) { */
-    /*   ichip=iadc/4; */
-
-    /*   for (int i=0; i<sc_width*sc_height; i++) { */
-
-/* 	if (ichip%2==0) { */
-/* 	  row=sc_height+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; */
-/* 	} */
-	  
-
-	
-/* /\* 	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; */
-
-      /* 	} */
-      /* } */
-
-    //  }
-
-    
-    
-  };
-  
-  
-
-     /**
-
-     Returns the frame number for the given dataset. Purely virtual func.
-     \param buff pointer to the dataset
-     \returns frame number
-
-  */
-
-
-  int getFrameNumber(return (sls_detector_header*)buff)->frameNumber;};   
-
-  /**
-
-     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
-
-  */
-  virtual char *readNextFrame(ifstream &filebin) {
-    int ff=-1, np=-1;
-    return readNextFrame(filebin, ff, np);
-  };
-
-  virtual char *readNextFrame(ifstream &filebin, int &ff) {
-    int np=-1;
-    return readNextFrame(filebin, ff, np);
-  };
-
-  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
-	  char *data=new char[dataSize];
-	  char *d=readNextFrame(filebin, ff, np, data);
-	  if (d==NULL) {delete [] data; data=NULL;}
-	  return data;
-  }
-
-
-  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
-    // 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; */
-    /* }; */
-
- char *retval=0;
-	  int  nd;
-	  int fnum = -1;
-	  np=0;
-	  int  pn;
-	  
-	  //  cout << dataSize << endl;
-	  if (ff>=0)
-	    fnum=ff;
-
-	  if (filebin.is_open()) {
-	    if (filebin.read(data, dataSize) ){
-	      ff=getFrameNumber(data);
-	      np=getPacketNumber(data);
-	      return data;
-	    }
-	  }
-	    return NULL;
-	    
-  
-
-};
-
-
-
-#endif

slsDetectorCalibration/dataStructures/moench02Ctb10GbData.h

@@ -1,246 +0,0 @@
-#ifndef MOENCH02CTB10GBDATA_H
-#define  MOENCH02CTB10GBDATA_H
-#include <stdio.h>
-#include "slsDetectorData.h"
-#include "slsReceiverData.h"
-
-
-class moench02Ctb10GbData : public slsReceiverData<uint16_t> {
-
- private:
-  
-  int iframe;
-  // int *xmap, *ymap;
-  int nadc;
-  int sc_width;
-  int sc_height;
-
-  int maplength;
-
-
-
- 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
-
-  */
-  
-
- moench02Ctb10GbData(int ns=6400): slsReceiverData<uint16_t>(160, 160, 50, 8208) , nadc(4), sc_width(40), sc_height(160) {
-
-    
-    int adc_nr[4]={120,0,80,40};
-    int row, col;
-
-    int isample;
-    int iadc;
-    int ix, iy;
-    int i;
-    int npackets=50;
-    maplength = 8208*npackets;
-    //this->setDataSize(maplength);
-    /* maplength=this->getDataSize()/2; */
-    
-    for (int ip=0; ip<npackets; ip++) {
-      for (int is=0; is<128; is++) {
-
-	for (iadc=0; iadc<nadc; iadc++) {
-	  i=128*ip+is;
-	  if (i<sc_width*sc_height) {
-	    col=adc_nr[iadc]+(i%sc_width);
-	    row=i/sc_width;
-	    dataMap[row][col]=(32*i+iadc+2)*2+16*(ip+1);
-	    if (dataMap[row][col]<0 || dataMap[row][col]>=8208*npackets) {
-	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;	  
-	    }
-	  
-	  }
-	}
-      }
-    }
-    int ibyte;
-    int ii=0;
-
-    for (int ipacket=0; ipacket<npackets; ipacket++) {
-      for (int ibyte=0;  ibyte< 8208/2; ibyte++) {
-	i=ipacket*8208/2+ibyte;
-	if(ibyte<8){
-	  xmap[i]=-1;
-	  ymap[i]=-1;
-	}else{
-	  isample=ii/32;
-	  iadc=ii%32;
-	  ix=isample%sc_width;
-	  iy=isample/sc_width;
-	  if(iadc>=2 && iadc<=5){
-	    xmap[i]=adc_nr[iadc-2]+ix;
-	    ymap[i]=iy;
-	  }else{
-	    xmap[i]=-1;
-	    ymap[i]=-1;
-	  }
-	  ii++;
-	}
-      }//end loop on bytes
-    }//end loop on packets
-
-    iframe=0;
-    cout << "data struct created" << endl;
-  };
-    
-  void getPixel(int ip, int &x, int &y) {
-    if(ip>=0 && ip<maplength){
-      x=xmap[ip]; 
-      y=ymap[ip];
-    }else{
-      cerr<<"WRONG ARRAY LENGTH"<<endl;
-      cerr<<"Trying to access the "<<ip<<"-th element"<<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){return *((int*)buff)&0xffffffff;};  
-  /* virtual  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;
-
-  */
-  int getPacketNumber(char *buff){return ((*(((int*)(buff+4))))&0xff)+1;};  
-  /**
-
-     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 
-
-  */
-  //virtual  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
-
-  */
-  /* virtual 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; */
-  /* }; */
-  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
-    char *data=new char[packetSize*nPackets];
-    char *retval=0;
-    int nd;
-    np=0;
-    int  pn;
-    char aa[8224]={0};
-    char *packet=(char *)aa;
-    int  fnum = -1;
-    if (ff>=0)
-      fnum=ff;
-
-    if (filebin.is_open()) {
-
-
-      cout << "+";
-
-      while(filebin.read((char*)packet, 8208)){
-	      
-	pn=getPacketNumber(packet);
-	if (fnum<0)
-	  fnum= getFrameNumber(packet);
-	
-
-	if (fnum>=0) {
-	  if (getFrameNumber(packet) !=fnum) { 
-	    
-	    if (np==0){
-	      cout << "-";
-	      delete [] data;
-	      return NULL;
-	    } else
-	      filebin.seekg(-8208,ios_base::cur);
-	    return data;
-	  }
-	
-	  memcpy(data+(pn-1)*packetSize, packet, packetSize);
-
-	  np++;
-	  if (np==nPackets)
-	    break;
-	  if (pn==nPackets)
-	    break;
-	}
-      }	    
-    }else{
-      cerr<<filebin<<" not open!!!"<<endl;
-      return NULL;
-    }
-	  
-    if (np==0){
-      cout << "?";
-      delete [] data;
-      return NULL;
-    }// else if (np<nPackets)
-    //  cout << "Frame " << fnum << " lost "  << nPackets-np << " packets " << endl;
-
-    
-    return data;
-	  
-  };
-
-
-
-  virtual char *readNextFrame(ifstream &filebin) {
-    int fnum=-1, np;
-    return readNextFrame(filebin, fnum, np);
-  };
-
-  
-
-};
-
-
-
-#endif

slsDetectorCalibration/dataStructures/moench02CtbDataDGS.h

@@ -1,187 +0,0 @@
-#ifndef MOENCH02CTBDATADGS_H
-#define  MOENCH02CTBDATADGS_H
-#include "slsDetectorData.h"
-
-
-
-class moench02CtbData : public slsDetectorData<uint16_t> {
-
- private:
-  
-  int iframe;
-  // int *xmap, *ymap;
-  //int nadc;
-  int sc_width;
-  int sc_height;
-
-  int maplength;
-
-
-
- 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
-
-  */
-  
-
- moench02CtbDataDGS(int ns=6400): slsDetectorData<uint16_t>(160, 160, ns*(2*32+8), NULL, NULL) ,  sc_width(40), sc_height(160) {
-
-    
-    int adc_off[4]={40,0,120,80};
-    int adc_nr[4]={8,10,20,23};
-    int row, col;
-
-    int isample;
-    int iadc, iiadc;
-    int ix, iy;
-    maplength=this->getDataSize()/2;
-    //cout << maplength << endl;
-
-    for (iiadc=0; iiadc<4; iiadc++) {
-      
-      iadc=adc_nr[iiadc];
-      //cout << iiadc << endl;
-      for (int i=0; i<sc_width*sc_height; i++) {
-	col=adc_off[iiadc]+(i%sc_width);
-	row=i/sc_width;
-	dataMap[row][col]=(32*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<maplength; i++) {
-      //cout << i << endl;
-      isample=i/32;
-      iiadc=i%32;
-      iadc=-1;
-      for (int iii=0; iii<4; iii++) {
-	if (iiadc==adc_nr[iii]) iadc=iii;
-      }
-      ix=isample%sc_width;
-      iy=isample/sc_width;
-      if(iadc>=0){
-	xmap[i]=adc_off[iadc]+ix;
-	ymap[i]=iy;
-      }else{
-	xmap[i]=-1;
-	ymap[i]=-1;
-      }
-    }
-    iframe=0;
-    cout << "data struct created" << endl;
-  };
-  
-  void getPixel(int ip, int &x, int &y) {
-    if(ip>=0 && ip<maplength){
-      x=xmap[ip]; 
-      y=ymap[ip];
-    }/*else{
-      cerr<<"WRONG ARRAY LENGTH"<<endl;
-      cerr<<"Trying to access the "<<ip<<"-th element"<<endl;
-      }*/
-
-  };
-  
-  /**
-     Returns the gain for the selected pixel (at the moemnt only 3rd supercolumn)
-     \param buff pointer to the dataset
-     \param ix x coordinate 
-     \param iy y coordinate
-     \returns gain value
-   */
-
-  int getGain(char *buff, int ix, int iy) {
-    int isample=iy*sc_width+iy;
-    if (ix<sc_width) return 0; //first supercolumn no gain switching - could return the static gain if wished
-    if (ix<2*sc_width) return 0; //second supercolumn no gain switching  - could return the static gain if wished
-    if (ix<3*sc_width){ 
-      if(*((long*)(buff+(32*2*isample+8*(isample-1)))&(1>>31)) return 1;
-      return 0;
-    }
-    return 0; //not yet implemented for 4th supercolumn
-  }
-
-
-     /**
-
-     Returns the frame number for the given dataset. Purely virtual func.
-     \param buff pointer to the dataset
-     \returns frame number
-
-  */
-
-
-    virtual  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 
-
-  */
-    virtual  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
-
-  */
-    virtual 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/2 << "-" << endl;
-	  //for (int i=0; i<ib/2; i++)
-	  //cout << i << " " << afifo_cont[i] << endl;
-	  return (char*)afifo_cont;
-	} else {
-	  delete [] afifo_cont;
-	  return NULL;
-	}
-      }     
-      return NULL;
-    };
-
-
-  
-
-};
-
-
-
-#endif

slsDetectorCalibration/dataStructures/moench02ModuleData.h

@@ -1,137 +0,0 @@
-#ifndef MOENCH02MODULEDATA_H
-#define  MOENCH02MODULEDATA_H
-#include "slsReceiverData.h"
-
-
-
-class moench02ModuleData : public slsReceiverData<uint16_t> {
- 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
-
-  */
-  
-
-  moench02ModuleData(double c=0): slsReceiverData<uint16_t>(160, 160, 40, 1286), 
-    xtalk(c) {
-
-
-
-
-    uint16_t **dMask;
-    int **dMap;
-    int ix, iy;
-
-
-
-    dMask=new uint16_t*[160];
-    dMap=new int*[160];
-    for (int i = 0; i < 160; i++) {
-      dMap[i] = new int[160];
-      dMask[i] = new uint16_t[160];
-    }
-
-    for (int isc=0; isc<4; isc++) {
-      for (int ip=0; ip<10; ip++) {
-
-	for (int ir=0; ir<16; ir++) {
-	  for (int ic=0; ic<40; ic++) {
-
-	    ix=isc*40+ic;
-	    iy=ip*16+ir;
-
-	    dMap[iy][ix]=1286*(isc*10+ip)+2*ir*40+2*ic+4; 
-	    // cout << ix << " " << iy << " " << dMap[ix][iy] << endl;
-	  }
-	}
-      }
-    }
-
-    for (ix=0; ix<120; ix++) {
-      for (iy=0; iy<160; iy++)
-	dMask[iy][ix]=0x3fff;
-    }
-    for (ix=120; ix<160; ix++) {
-      for (iy=0; iy<160; iy++)
-	dMask[iy][ix]=0x0;
-    }
-
-
-    setDataMap(dMap);
-    setDataMask(dMask);
-
-
-    
-
-  };
-    
-  
-  
-  /**
-     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){
-    int np=(*(int*)buff)&0xff;
-    if (np==0)
-      np=40;
-    return np;
-  };
-
-
-  /**
-    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 || ix%40==0)
-      return  slsDetectorData<uint16_t>::getValue(data, ix, iy);
-    else
-      return slsDetectorData<uint16_t>::getValue(data, ix, iy)-xtalk*slsDetectorData<uint16_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 */
-
-
-};
-
-
-
-#endif

slsDetectorCalibration/dataStructures/moench03Ctb10GbData.h

@@ -1,285 +0,0 @@
-#ifndef MOENCH03CTB10GBDATA_H
-#define  MOENCH03CTB10GBDATA_H
-#include "slsReceiverData.h"
-
-
-
-class moench03Ctb10GbData : public slsReceiverData<uint16_t> {
- 
- protected:
-  
-  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
-
-  */
-  
-
-  //  moench03Ctb10GbData(int ns=5000): slsDetectorData<uint16_t>(400, 400, 8208*40, NULL, NULL) , nadc(32), sc_width(25), sc_height(200) {
- moench03Ctb10GbData(int ns=5000): slsReceiverData<uint16_t>(400, 400, 40, 8208), nadc(32), sc_width(25), sc_height(200) {
-
-    int adc_nr[32]={200,225,250,275,300,325,350,375,\
-		    0,25,50,75,100,125,150,175,\
-		    175,150,125,100,75,50,25,0,\
-		    375,350,325,300,275,250,225,200};
-    int row, col;
-
-    int isample;
-    int iadc;
-    int ix, iy;
-    
-    int npackets=40;
-    int i;
-
-
-    for (int ip=0; ip<npackets; ip++) {
-      for (int is=0; is<128; is++) {
-
-	for (iadc=0; iadc<nadc; iadc++) {
-	  i=128*ip+is;
-	  if (i<sc_width*sc_height) {
-	    //  for (int i=0; i<sc_width*sc_height; i++) {
-	    col=adc_nr[iadc]+(i%sc_width);
-	    if (iadc<16) {
-	      row=199-i/sc_width;
-	    } else {
-	      row=200+i/sc_width;
-	    }
-	    dataMap[row][col]=(nadc*i+iadc)*2+16*(ip+1);
-	    if (dataMap[row][col]<0 || dataMap[row][col]>=8208*40)
-	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
-	  }
-	}
-      }
-    }
-
-    int ipacket;
-    int ibyte;
-    int ii=0;
-    for (int ipacket=0; ipacket<npackets; ipacket++) {
-      for (int ibyte=0;  ibyte< 8208/2; ibyte++) {
-	i=ipacket*8208/2+ibyte;
-	if (ibyte<8) {
-	//header!
-	  xmap[i]=-1;
-	  ymap[i]=-1;
-	} else {
-	  // ii=ibyte+128*32*ipacket;
-	  isample=ii/nadc;
-	  iadc=ii%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;
-	  }
-	  
-	ii++;
-	}
-      }
-    }
-    
-
-    
-    
-    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){return *((int*)buff)&0xffffffff;};   
-
-  /**
-
-     Returns the packet number for the given dataset. purely virtual func
-     \param buff pointer to the dataset
-     \returns packet number number
-
-
-
-  */
-  int getPacketNumber(char *buff){return ((*(((int*)(buff+4))))&0xff)+1;};   
-
-/*    /\** */
-
-/*      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  */
-
-/*   *\/ */
-/*     virtual  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 */
-
-/*   *\/ */
-/*     virtual 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; */
-/*     }; */
-
-
-  virtual char *readNextFrame(ifstream &filebin, int& fnum, char *data=NULL) {
-    int dd=0;
-    if (data==NULL) {
-      data=new char[packetSize*nPackets];
-      dd=1;
-    }
-      char *retval=0;
-      int np=0, nd;
-      fnum = -1;
-      int  pn;
-      char aa[8224];
-      char *packet=(char *)aa;
-      int place;
-      
-      if (filebin.is_open()) {
-
-
-
-        place=filebin.tellg();
-        while(filebin.read((char*)packet, 8208) && np<nPackets){
-          pn=getPacketNumber(packet);
-          if (pn==1 && fnum<0)
-	    fnum= getFrameNumber(packet);
-          
-	  //	  cout <<getFrameNumber(packet)<< " fn: " << fnum << "\t pn: " << pn << " np " << np << endl;
-          if (fnum>=0) {
-	    if (getFrameNumber(packet) !=fnum) {
-	      cout << "-"<<endl;
-	      filebin.seekg(place);
-	      if (np==0){
-		if (dd)
-		  delete [] data;
-		return NULL;
-	      } else {
-		return data;
-	      }
-	    }
-        
-	    memcpy(data+(pn-1)*packetSize, packet, packetSize);
-	    np++;
-	    if (np==nPackets)
-	      return data;
-        
-          }
-          place=filebin.tellg();
-        }
-        
-      }
-
-	      
-      if (np==0){
-	cout << "-"<<endl;
-        filebin.seekg(place);
-	if (dd)
-	  delete [] data;
-        return NULL;
-      }
-
-      //filebin.seekg(place);
-      return data;
-    };
-
-/*   	virtual char *readNextFrame(ifstream &filebin, int& fnum) { */
-/* 	  char *data=new char[packetSize*nPackets]; */
-/* 	  char *retval=0; */
-/* 	  int np=0, nd; */
-/* 	  fnum = -1; */
-/* 	  int  pn; */
-/* 	  char aa[8224]; */
-/* 	  char *packet=(char *)aa; */
-
-/* 	  if (filebin.is_open()) { */
-
-
-
-
-/* 	    while(filebin.read((char*)packet, 8208) && np<nPackets){ */
-/* 	      pn=getPacketNumber(packet); */
-	      
-/* 	      if (pn==1 && fnum<0) */
-/* 		fnum= getFrameNumber(packet); */
-	      
-/* 	      // cout << "fn: " << fnum << "\t pn: " << pn << endl; */
-/* 	      if (fnum>=0) { */
-/* 		if (getFrameNumber(packet) !=fnum) {  */
-		  
-/* 		  if (np==0){ */
-/* 		    delete [] data; */
-/* 		    return NULL; */
-/* 		  } else */
-/* 		    return data; */
-/* 		} */
-		
-/* 		memcpy(data+(pn-1)*packetSize, packet, packetSize); */
-/* 		np++; */
-		
-/* 	      } */
-/* 	    } */
-	    
-/* 	  } */
-
-/* 	  if (np==0){ */
-/* 	    delete [] data; */
-/* 	    return NULL; */
-/* 	  } */
-
-/* 	}; */
-
-int getPacketNumber(int x, int y) {return dataMap[y][x]/8208;};
-
-
-};
-
-
-
-
-#endif

slsDetectorCalibration/dataStructures/moench03T1ReceiverDataNew.h

@@ -2,7 +2,7 @@
 #define  MOENCH03T1RECDATANEW_H
 #include "slsDetectorData.h"
 
-#define VERSION_V2
+//#define VERSION_V2
     /**
         @short  structure for a Detector Packet or Image Header
         @li frameNumber is the frame number
@@ -33,7 +33,7 @@
         uint16_t roundRNumber;    /**< is the round robin set number */
         uint8_t detType;        /**< is the detector type see :: detectorType */
         uint8_t version;        /**< is the version number of this structure format */
-#ifdef VERSION_V2
+#ifndef VERSION_V1
       uint64_t packetCaught[8];        /**< is the version number of this structure format */
 #endif
 
@@ -77,9 +77,9 @@ class moench03T1ReceiverDataNew : public slsDetectorData<uint16_t> {
 
     int row, col;
 
-    int isample;
+    // int isample;
     int iadc;
-    int ix, iy;
+    // int ix, iy;
     
      int npackets=40;
     int i;
@@ -99,43 +99,46 @@ class moench03T1ReceiverDataNew : public slsDetectorData<uint16_t> {
 	    } else {
 	      row=200+i/sc_width;
 	    }
-	    dataMap[row][col]=sizeof(sls_detector_header)+(nadc*i+iadc)*2;//+16*(ip+1);
-	    if (dataMap[row][col]<0 || dataMap[row][col]>=nSamples*2*32)
-	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	    dataMap[row*nx+col]=sizeof(sls_detector_header)+(nadc*i+iadc)*2;//+16*(ip+1);
+#ifdef HIGHZ
+	    dataMask[row*nx+col]=0x3fff;
+#endif
+	    if (dataMap[row*nx+col]<0 || dataMap[row*nx+col]>=nSamples*2*32)
+	      cout << "Error: pointer " << dataMap[row*nx+col] << " out of range "<< endl;
 	  }
 	}
       }
     }
 
-    int ipacket;
-    int ibyte;
-    int ii=0;
-    for (ibyte=0; ibyte<sizeof(sls_detector_header)/2; ibyte++){
-      xmap[ibyte]=-1;
-      ymap[ibyte]=-1;
-    }
-    int off=sizeof(sls_detector_header)/2;
-    for (ipacket=0; ipacket<npackets; ipacket++) {
-      for (ibyte=0;  ibyte< 8192/2; ibyte++) {
-	i=ipacket*8208/2+ibyte;
-	  isample=ii/nadc;
-	  if (isample<nSamples) {
-	  iadc=ii%nadc;
-	  adc4 = (int)iadc/4;
-	  ix=isample%sc_width;
-	  iy=isample/sc_width;
-	  if (adc4%2==0) {
-	    xmap[i+off]=adc_nr[iadc]+ix;
-	    ymap[i+off]=ny/2-1-iy;
-	  } else {
-	    xmap[i+off]=adc_nr[iadc]+ix;
-	    ymap[i+off]=ny/2+iy;
-	  }
-	  }
-	ii++;
-	//	}
-      }
-    }
+    // int ipacket;
+    // int ibyte;
+    // int ii=0;
+    // for (ibyte=0; ibyte<sizeof(sls_detector_header)/2; ibyte++){
+    //   xmap[ibyte]=-1;
+    //   ymap[ibyte]=-1;
+    // }
+    // int off=sizeof(sls_detector_header)/2;
+    // for (ipacket=0; ipacket<npackets; ipacket++) {
+    //   for (ibyte=0;  ibyte< 8192/2; ibyte++) {
+    // 	i=ipacket*8208/2+ibyte;
+    // 	  isample=ii/nadc;
+    // 	  if (isample<nSamples) {
+    // 	  iadc=ii%nadc;
+    // 	  adc4 = (int)iadc/4;
+    // 	  ix=isample%sc_width;
+    // 	  iy=isample/sc_width;
+    // 	  if (adc4%2==0) {
+    // 	    xmap[i+off]=adc_nr[iadc]+ix;
+    // 	    ymap[i+off]=ny/2-1-iy;
+    // 	  } else {
+    // 	    xmap[i+off]=adc_nr[iadc]+ix;
+    // 	    ymap[i+off]=ny/2+iy;
+    // 	  }
+    // 	  }
+    // 	ii++;
+    // 	//	}
+    //   }
+    // }
     
     iframe=0;
     //  cout << "data struct created" << endl;
@@ -237,15 +240,15 @@ class moench03T1ReceiverDataNew : public slsDetectorData<uint16_t> {
 
 
   virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
-	  char *retval=0;
-	  int  nd;
-	  int fnum = -1;
-	  np=0;
-	  int  pn;
+    //char *retval=0;
+    //	  int  nd;
+    //int fnum = -1;
+    //	  np=0;
+	  //	  int  pn;
 	  
 	  //  cout << dataSize << endl;
-	  if (ff>=0)
-	    fnum=ff;
+    //	  if (ff>=0)
+    //	    fnum=ff;
 
 	  if (filebin.is_open()) {
 	    if (filebin.read(data, dataSize) ){

slsDetectorCalibration/dataStructures/moench03T1ReceiverDataNewRect.h

@@ -34,6 +34,9 @@
         uint16_t roundRNumber;    /**< is the round robin set number */
         uint8_t detType;        /**< is the detector type see :: detectorType */
         uint8_t version;        /**< is the version number of this structure format */
+#ifndef VERSION_V1
+      uint64_t packetCaught[8];        /**< is the version number of this structure format */
+#endif
     } sls_detector_header;
 
 

slsDetectorCalibration/dataStructures/moench03T1ReorderedData.h

@@ -0,0 +1,176 @@
+#ifndef MOENCH03T1REORDERED_H
+#define  MOENCH03T1REORDERED_H
+#include "slsDetectorData.h"
+
+
+class moench03T1ReorderedData : public slsDetectorData<uint16_t> {
+ 
+ private:
+  
+ 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
+
+	fwrite(&ff, 8, 1,of);//write detector frame number
+	fwrite(&ifr, 8, 1,of);//write datset frame number
+	fwrite(data,2,NX*NY,of);//write reordered data
+  */
+ moench03T1ReorderedData(): slsDetectorData<uint16_t>(400, 400, 2*400*400+2*8) {
+    for (int iy=0; iy<400; iy++)
+      for (int ix=0; ix<400; ix++)
+	dataMap[iy][ix]=2*8+2*(iy*400+ix);
+    
+    int ibyte;
+    for (ibyte=0; ibyte<8; ibyte++){
+      xmap[ibyte]=-1;
+      ymap[ibyte]=-1;
+    }
+    for (ibyte=0; ibyte<400*400; ibyte++){
+      xmap[ibyte+8]=ibyte%400;
+      ymap[ibyte+8]=ibyte/400;
+    }
+    
+    //  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
+
+  */
+
+/* class jfrau_packet_header_t { */
+/*  public: */
+/* 	unsigned char reserved[4]; */
+/* 	unsigned char packetNumber[1]; */
+/* 	unsigned char frameNumber[3]; */
+/* 	unsigned char bunchid[8]; */
+/* }; */
+
+
+
+  int getFrameNumber(char *buff){return *((int*)buff);};
+
+/*    /\** */
+
+/*      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  */
+
+/*   *\/ */
+/*     virtual  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 */
+
+/*   *\/ */
+/*     virtual 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; */
+/*     }; */
+
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[dataSize];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+	  char *retval=0;
+	  int  nd;
+	  int fnum = -1;
+	  np=0;
+	  int  pn;
+	  
+	  if (ff>=0)
+	    fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, dataSize) ){
+	      ff=getFrameNumber(data);
+	      np=40;
+	      return data;
+	    }
+	  }
+	  return NULL;
+	    
+	    
+	  
+  };
+
+
+
+  /**
+
+     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 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<dataSize) ndata=dsize;
+    else ndata=dataSize;
+    return data;
+
+  }
+
+
+
+  //int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+
+};
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/moench03T1ZmqDataNew.h

@@ -60,9 +60,12 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
 	    } else {
 	      row=200+i/sc_width;
 	    }
-	    dataMap[row][col]=(nadc*i+iadc)*2+offset;//+16*(ip+1);
-	    if (dataMap[row][col]<0 || dataMap[row][col]>=dataSize)
-	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	    dataMap[row*nx+col]=(nadc*i+iadc)*2+offset;//+16*(ip+1);
+#ifdef HIGHZ
+	    dataMask[row*nx+col]=0x3fff;
+#endif
+	    if (dataMap[row*nx+col]<0 || dataMap[row*nx+col]>=dataSize)
+	      cout << "Error: pointer " << dataMap[row*nx+col] << " out of range "<< endl;
 	  }
 	}
       }
@@ -71,8 +74,8 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
     
     int ii=0;
     
-    for (i=0; i<  dataSize; i++) {
-      if (i<offset) {
+    for (i=0; i<  dataSize/2; i++) {
+      if (i<offset/2) {
     	//header! */
     	xmap[i]=-1;
     	ymap[i]=-1;
@@ -201,15 +204,15 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
 
 
   virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
-	  char *retval=0;
-	  int  nd;
-	  int fnum = -1;
+	  /* char *retval=0; */
+	  /* int  nd; */
+	  /* int fnum = -1; */
 	  np=0;
-	  int  pn;
+	  /* int  pn; */
 	  
 
-	  if (ff>=0)
-	    fnum=ff;
+	  /* if (ff>=0) */
+	  /*   fnum=ff; */
 
 	  if (filebin.is_open()) {
 	    if (filebin.read(data, 32*2*nSamples) ){
@@ -218,7 +221,7 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
 	      return data;
 	    }
 	  }
-	    return NULL;
+	  return NULL;
 	    
 	    
 	  

slsDetectorCalibration/dataStructures/moench03T1ZmqDataNewRect.h

@@ -1,10 +1,12 @@
-#ifndef MOENCH03CTB10GBT1DATA_H
-#define  MOENCH03CTB10GBT1DATA_H
-#include "slsReceiverData.h"
+#ifndef MOENCH03T1ZMQNEWRECT_H
+#define  MOENCH03T1ZMQNEWRECT_H
+#include "slsDetectorData.h"
+
+#define VERT 1
 
 
 
-class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
+class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
  
  private:
   
@@ -12,9 +14,12 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
   int nadc;
   int sc_width;
   int sc_height;
- public:
+  const int nSamples;
+  const int offset;
 
 
+ public:
+
 
 
   /**
@@ -23,9 +28,16 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
      \param c crosstalk parameter for the output buffer
 
   */
-   moench03Ctb10GbT1Data(int ns=5000): slsReceiverData<uint16_t>(400, 400, 40, 8208), nadc(32), sc_width(25), sc_height(200) {
-
+#ifdef HOR
+ moench03T1ZmqDataNew(int ns=5000): slsDetectorData<uint16_t>(800, 200, ns*2*32), nSamples(ns), offset(sizeof(int)) {
+#endif
+#ifdef VERT
+   moench03T1ZmqDataNew(int ns=5000): slsDetectorData<uint16_t>(200, 800, ns*2*32), nSamples(ns), offset(sizeof(int)) {
+#endif
 
+    int nadc=32;
+    int sc_width=25;
+    int sc_height=200;
 
     int adc_nr[32]={300,325,350,375,300,325,350,375,		\
     		    200,225,250,275,200,225,250,275,\
@@ -34,13 +46,21 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
 
     int row, col;
 
-    int isample;
+    // int isample;
     int iadc;
     int ix, iy;
     
-    int npackets=40;
+     int npackets=40;
     int i;
     int adc4(0);
+    int pix;
+
+
+    int off=0;
+#ifdef OFF_1
+    off=1;
+#endif
+    cout << "This is a MOENCH with rectangular pixels!" << endl;
 
     for (int ip=0; ip<npackets; ip++) {
       for (int is=0; is<128; is++) {
@@ -56,46 +76,67 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
 	    } else {
 	      row=200+i/sc_width;
 	    }
-	    dataMap[row][col]=(nadc*i+iadc)*2+16*(ip+1);
-	    if (dataMap[row][col]<0 || dataMap[row][col]>=8208*40)
-	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	    pix=(nadc*i+iadc)*2+offset;//+16*(ip+1);
+	    if (pix<0 || pix>=nSamples*2*32)
+	      cout << "Error: pointer " << pix << " out of range "<< endl;
+	    ix=col;
+	    iy=row;
+	    //col and row have to do with data sequence
+	    //ix and iy have to do with implant position
+#ifdef HOR
+	    if (row%2==off) {
+	      ix=2*col;
+	      iy=row/2;
+	    } else {
+	      ix=2*col+1;
+	      iy=row/2;
+	    }
+#endif
+
+#ifdef VERT
+	    if (col%2==off) {
+	      ix=col/2;
+	      iy=row*2+1;
+	    } else {
+	      ix=col/2;
+	      iy=row*2;
+	    }
+#endif
+	    dataMap[iy*nx+ix]=pix;
 	  }
 	}
       }
     }
 
-    int ipacket;
-    int ibyte;
-    int ii=0;
-    for (int ipacket=0; ipacket<npackets; ipacket++) {
-      for (int ibyte=0;  ibyte< 8208/2; ibyte++) {
-	i=ipacket*8208/2+ibyte;
-	if (ibyte<8) {
-	//header!
-	  xmap[i]=-1;
-	  ymap[i]=-1;
-	} else {
-	  // ii=ibyte+128*32*ipacket;
-	  isample=ii/nadc;
-	  iadc=ii%nadc;
-	  adc4 = (int)iadc/4;
-	  ix=isample%sc_width;
-	  iy=isample/sc_width;
-	  if (adc4%2==0) {
-	    xmap[i]=adc_nr[iadc]+ix;
-	    ymap[i]=ny/2-1-iy;
-	  } else {
-	    xmap[i]=adc_nr[iadc]+ix;
-	    ymap[i]=ny/2+iy;
-	  }
-	  
-	ii++;
-	}
-      }
-    }
-    
-
-    
+    /* int ipacket; */
+    /* int ibyte; */
+    /* int ii=0; */
+    /* for (ibyte=0; ibyte<sizeof(sls_detector_header)/2; ibyte++){ */
+    /*   xmap[ibyte]=-1; */
+    /*   ymap[ibyte]=-1; */
+    /* } */
+    /* int off=sizeof(sls_detector_header)/2; */
+    /* for (ipacket=0; ipacket<npackets; ipacket++) { */
+    /*   for (ibyte=0;  ibyte< 8192/2; ibyte++) { */
+    /* 	i=ipacket*8208/2+ibyte; */
+    /* 	  isample=ii/nadc; */
+    /* 	  if (isample<nSamples) { */
+    /* 	  iadc=ii%nadc; */
+    /* 	  adc4 = (int)iadc/4; */
+    /* 	  ix=isample%sc_width; */
+    /* 	  iy=isample/sc_width; */
+    /* 	  if (adc4%2==0) { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2-1-iy; */
+    /* 	  } else { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2+iy; */
+    /* 	  } */
+    /* 	  } */
+    /* 	ii++; */
+    /* 	//	} */
+    /*   } */
+    /* } */
     
     iframe=0;
     //  cout << "data struct created" << endl;
@@ -121,8 +162,7 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
 
 
 
-  // int getFrameNumber(char *buff){return *((int*)buff)&0xffffffff;}; 
-   int getFrameNumber(char *buff){return *((int*)(buff+5))&0xffffff;};   
+  int getFrameNumber(char *buff){return *((int*)buff);};//*((int*)(buff+5))&0xffffff;};   
 
   /**
 
@@ -133,7 +173,7 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
 
 
   */
-  int getPacketNumber(char *buff){return ((*(((int*)(buff+4))))&0xff)+1;};   
+  int getPacketNumber(char *buff){return 0;}//((*(((int*)(buff+4))))&0xff)+1;};   
 
 /*    /\** */
 
@@ -188,79 +228,63 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
   };
 
   virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
-	  char *data=new char[packetSize*nPackets];
+	  char *data=new char[32*2*nSamples];
 	  char *d=readNextFrame(filebin, ff, np, data);
 	  if (d==NULL) {delete [] data; data=NULL;}
 	  return data;
-
   }
 
+
+
+
   virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
-	  char *retval=0;
-	  int  nd;
-	  int fnum = -1;
+	  /* char *retval=0; */
+	  /* int  nd; */
+	  /* int fnum = -1; */
 	  np=0;
-	  int  pn, po=0;
-	  char aa[8224];
-	  char *packet=(char *)aa;
-	  //  cout << packetSize*nPackets << endl;
-	  if (ff>=0)
-	    fnum=ff;
+	  /* int  pn; */
+	  
+
+	  /* if (ff>=0) */
+	  /*   fnum=ff; */
 
 	  if (filebin.is_open()) {
-
-
-
-
-	    while(filebin.read((char*)packet, 8208) ){
-	      pn=getPacketNumber(packet);
-	      
-	      if (fnum<0)
-		fnum= getFrameNumber(packet);
-	      
-	      //   cout << "fn: " << fnum << "\t pn: " << pn << endl;
-	      if (fnum>=0) {
-		if (getFrameNumber(packet) !=fnum || pn<po) { 
-		  
-		  if (np==0){
-		    // delete [] data;
-		    return NULL;
-		  } else
-		    filebin.seekg(-8208,ios_base::cur);
-		  po =pn;
-		    return data;
-		}
-		if (pn>nPackets) {
-		  cout << "Bad packet number " << pn << endl;
-		}
-
-		memcpy(data+(pn-1)*packetSize, packet, packetSize);
-		np++;
-		po =pn;
-
-		if (np==nPackets)
-		  break;
-
-		if (pn==nPackets)
-		  break;
-		
-	      }
+	    if (filebin.read(data, 32*2*nSamples) ){
+	      // iframe++;
+	      //ff=iframe;
+	      return data;
 	    }
+	  }
+	  return NULL;
+	    
 	    
-	  }
-
-	  if (np==0){
-	    // delete [] data;
-	    return NULL;
-	  }
-
-	  ff=fnum;
-	  return data;
 	  
   };
 
 
 
+  /**
+
+     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 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<32*2*nSamples) ndata=dsize;
+    else ndata=32*2*nSamples;
+    return data;
+
+  }
+  
+
+
+
+
+
+  // virtual int setFrameNumber(int ff){iframe=ff};
 
 
 
@@ -271,13 +295,7 @@ class moench03Ctb10GbT1Data : public slsReceiverData<uint16_t> {
 
 
 
-
-
-
-
-
-int getPacketNumber(int x, int y) {return dataMap[y][x]/8208;};
-
+int getPacketNumber(int x, int y) {return 0;};
 
 };
 
@@ -285,3 +303,4 @@ int getPacketNumber(int x, int y) {return dataMap[y][x]/8208;};
 
 
 #endif
+

slsDetectorCalibration/dataStructures/moench03TCtb10GbData.h

@@ -1,285 +0,0 @@
-#ifndef MOENCH03TCTB10GBDATA_H
-#define  MOENCH03TCTB10GBDATA_H
-#include "moench03Ctb10GbData.h"
-
-
-
-class moench03TCtb10GbData : public moench03Ctb10GbData { //slsReceiverData<uint16_t> {
- 
-
- 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
-
-  */
-  
-
-  //  moench03TCtb10GbData(int ns=5000): slsDetectorData<uint16_t>(400, 400, 8208*40, NULL, NULL) , nadc(32), sc_width(25), sc_height(200) {
- moench03TCtb10GbData(int ns=5000): moench03Ctb10GbData(ns) {//slsReceiverData<uint16_t>(400, 400, 40, 8208), nadc(32), sc_width(25), sc_height(200) {
-    // cout <<"constructor"<< endl;
-      // nadc=32;
-    int adc_nr[32]={300,325,350,375,300,325,350,375,		\
-		    200,225,250,275,200,225,250,275,\
-		    100,125,150,175,100,125,150,175,\
-		    0,25,50,75,0,25,50,75};
-    int row, col;
-
-    int isample;
-    int iadc;
-    int ix, iy;
-    
-    int npackets=40;
-    int i;
-    int adc4(0);
-
-    for (int ip=0; ip<npackets; ip++) {
-      for (int is=0; is<128; is++) {
-
-	for (iadc=0; iadc<nadc; iadc++) {
-	  i=128*ip+is;
-	  //cout << i << endl;
-	   adc4=(int)iadc/4;
-	  if (i<sc_width*sc_height) {
-	    //  for (int i=0; i<sc_width*sc_height; i++) {
-	    col=adc_nr[iadc]+(i%sc_width);
-	    if (adc4%2==0) {
-	      // if (iadc<(nadc/2)) {
-	      row=199-i/sc_width; 	            
-	    } else {
-	      row=200+i/sc_width;
-	    }
-	    dataMap[row][col]=(nadc*i+iadc)*2+16*(ip+1);
-	    if (dataMap[row][col]<0 || dataMap[row][col]>=8208*40)
-	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
-	  }
-	}
-      }
-    }
-    //  cout <<"map"<< endl;
-    int ipacket;
-    int ibyte;
-    int ii=0;
-    for (int ipacket=0; ipacket<npackets; ipacket++) {
-      for (int ibyte=0;  ibyte< 8208/2; ibyte++) {
-    	i=ipacket*8208/2+ibyte;
-    	//	cout << i << " ";
-    	if (ibyte<8) {
-    	//header!
-    	  xmap[i]=-1;
-    	  ymap[i]=-1;
-    	} else {
-    	  // ii=ibyte+128*32*ipacket;
-    	  // cout << nadc << endl;
-    	  isample=ii/nadc;
-    	  iadc=ii%nadc;
-	
-    	  adc4 = (int)iadc/4;
-
-    	  ix=isample%sc_width;
-    	  iy=isample/sc_width;
-    	  //  cout << isample << " " << iadc << " " << ix << " " << iy ;//<< endl;
-    	  if (adc4%2==0) {//iadc<(nadc/2)) {
-    	  //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;
-    	  }
-	  
-    	ii++;
-    	}
-      }
-    }
-    
-
-    
-    /* int ipacket; */
-    /* int ibyte; */
-    /* int ii=0; */
-    
-    /* for (int ipacket=0; ipacket<npackets; ipacket++) { */
-    /*   for (int ibyte=0;  ibyte< 8208/2; ibyte++) { */
-    /* 	i=ipacket*8208/2+ibyte; */
-    /* 	cout << i << endl; */
-    /* 	if (ibyte<8) { */
-    /* 	//header! */
-    /* 	  xmap[i]=-1; */
-    /* 	  ymap[i]=-1; */
-    /* 	} else { */
-    /* 	  ii=ibyte+128*32*ipacket; */
-    /* 	  isample=ii/nadc; */
-    /* 	  iadc=ii%nadc; */
-    /* 	  adc4 = (int)iadc/4; */
-
-    /* 	  ix=isample%sc_width; */
-    /* 	  iy=isample/sc_width; */
-    /* 	  if (adc4%2==0) { */
-    /* 	    xmap[i]=adc_nr[iadc]+ix; */
-    /* 	    ymap[i]=ny/2-1-iy; */
-
-
-
-    /* 	  } else { */
-    /* 	    xmap[i]=adc_nr[iadc]+ix; */
-    /* 	    ymap[i]=ny/2+iy; */
-
-    /* 	  } */
-	  
-    /* 	ii++; */
-    /* 	} */
-    /*   } */
-    /* } */
-    
-
-    
-    //  cout <<"done"<< endl;
-    
-    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){return *((int*)buff)&0xffffffff;};    */
-
-/*   /\** */
-
-/*      Returns the packet number for the given dataset. purely virtual func */
-/*      \param buff pointer to the dataset */
-/*      \returns packet number number */
-
-
-
-/*   *\/ */
-/*   int getPacketNumber(char *buff){return ((*(((int*)(buff+4))))&0xff)+1;};    */
-
-/* /\*    /\\** *\/ */
-
-/* /\*      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  *\/ */
-
-/* /\*   *\\/ *\/ */
-/* /\*     virtual  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 *\/ */
-
-/* /\*   *\\/ *\/ */
-/* /\*     virtual 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; *\/ */
-/* /\*     }; *\/ */
-
-
-/*   virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) { */
-/* 	  char *data=new char[packetSize*nPackets]; */
-/* 	  char *retval=0; */
-/* 	  int nd; */
-/* 	  np=0; */
-/* 	  int  pn; */
-/* 	  char aa[8224]={0}; */
-/* 	  char *packet=(char *)aa; */
-/* 	  int  fnum = -1; */
-	  
-/* 	  if (ff>=0) */
-/* 	    fnum=ff; */
-
-/* 	  if (filebin.is_open()) { */
-
-
-/* 	    cout << "+"; */
-
-/* 	    while(filebin.read((char*)packet, 8208)){ */
-	      
-/* 	      pn=getPacketNumber(packet); */
-	      
-/* 	      if (fnum<0) */
-/* 		fnum= getFrameNumber(packet); */
-	      
-/* 	      if (fnum>=0) { */
-/* 		if (getFrameNumber(packet) !=fnum) {  */
-		  
-/* 		  if (np==0){ */
-/* 		    cout << "-"; */
-/* 		    delete [] data; */
-/* 		    return NULL; */
-/* 		  } else */
-/* 		    filebin.seekg(-8208,ios_base::cur); */
-
-/* 		    return data; */
-/* 		} */
-		
-/* 		memcpy(data+(pn-1)*packetSize, packet, packetSize); */
-/* 		np++; */
-/* 		if (np==nPackets) */
-/* 		  break; */
-/* 		if (pn==nPackets) */
-/* 		  break; */
-/* 	      } */
-/* 	    } */
-	    
-/* 	  } */
-	  
-/* 	  if (np==0){ */
-/* 	    cout << "?"; */
-/* 	    delete [] data; */
-/* 	    return NULL; */
-/* 	  }// else if (np<nPackets) */
-/* 	    //  cout << "Frame " << fnum << " lost "  << nPackets-np << " packets " << endl; */
-
-/* 	  return data; */
-	  
-/* 	}; */
-
-/* int getPacketNumber(int x, int y) {return dataMap[y][x]/8208;}; */
-
-/*   	virtual char *readNextFrame(ifstream &filebin) { */
-/* 	  int fnum=-1, np; */
-/* 	  return readNextFrame(filebin, fnum, np); */
-/* 	}; */
-
-};
-
-
-
-
-#endif

slsDetectorCalibration/dataStructures/moench04CtbReceiver10GbData.h

@@ -0,0 +1,294 @@
+#ifndef MOENCH04REC10GBDATA_H
+#define  MOENCH04REC10GBDATA_H
+#include "slsDetectorData.h"
+
+//#define VERSION_V2
+    /**
+        @short  structure for a Detector Packet or Image Header
+        @li frameNumber is the frame number
+        @li expLength is the subframe number (32 bit eiger) or real time exposure time in 100ns (others)
+        @li packetNumber is the packet number
+        @li bunchId is the bunch id from beamline
+        @li timestamp is the time stamp with 10 MHz clock
+        @li modId is the unique module id (unique even for left, right, top, bottom)
+        @li xCoord is the x coordinate in the complete detector system
+        @li yCoord is the y coordinate in the complete detector system
+        @li zCoord is the z coordinate in the complete detector system
+        @li debug is for debugging purposes
+        @li roundRNumber is the round robin set number
+        @li detType is the detector type see :: detectorType
+        @li version is the version number of this structure format
+    */
+    typedef struct {
+        uint64_t frameNumber;    /**< is the frame number */
+        uint32_t expLength;        /**< is the subframe number (32 bit eiger) or real time exposure time in 100ns (others) */
+        uint32_t packetNumber;    /**< is the packet number */
+        uint64_t bunchId;        /**< is the bunch id from beamline */
+        uint64_t timestamp;        /**< is the time stamp with 10 MHz clock */
+        uint16_t modId;            /**< is the unique module id (unique even for left, right, top, bottom) */
+        uint16_t xCoord;        /**< is the x coordinate in the complete detector system */
+        uint16_t yCoord;        /**< is the y coordinate in the complete detector system */
+        uint16_t zCoord;        /**< is the z coordinate in the complete detector system */
+        uint32_t debug;            /**< is for debugging purposes */
+        uint16_t roundRNumber;    /**< is the round robin set number */
+        uint8_t detType;        /**< is the detector type see :: detectorType */
+        uint8_t version;        /**< is the version number of this structure format */
+      uint64_t packetCaught[8];        /**< is the version number of this structure format */
+
+    } sls_detector_header;
+
+
+
+
+class moench04CtbReceiver10GbData : public slsDetectorData<uint16_t> {
+ 
+ private:
+  
+  int iframe;
+  int nadc;
+  int sc_width;
+  int sc_height;
+  const int aSamples;
+  const int dSamples;
+
+
+ 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
+
+  */
+ moench04CtbReceiver10GbData(int nas=5000, int nds=0): slsDetectorData<uint16_t>(400, 400, nas*2*32+sizeof(sls_detector_header)+nds*8), aSamples(nas), dSamples(nds) {
+
+    int nadc=32;
+    int sc_width=25;
+    int sc_height=200;
+
+    int adc_nr[32]={9, 8,11,10,13,12,15,14,1,0,3,2,5,4,7,6,23,22,21,20,19,18,17,16,31,30,29,28,27,26,25,24 };
+
+    int row, col;
+
+    int isample;
+    int iadc;
+    int ix, iy;
+    
+     int npackets=40;
+    int i;
+    int adc4(0);
+
+    for (int ip=0; ip<npackets; ip++) {
+      for (int is=0; is<128; is++) {
+
+	for (iadc=0; iadc<nadc; iadc++) {
+	  i=128*ip+is;
+	  adc4=(int)iadc/4;
+	  if (i<sc_width*sc_height) {
+	    //  for (int i=0; i<sc_width*sc_height; i++) {
+	    col=(adc_nr[iadc]%16)*sc_width+(i%sc_width);
+	    // if (adc4%2==0) {
+	    if (iadc/16>0) {
+	      row=199-i/sc_width;
+	    } else {
+	      row=200+i/sc_width;
+	    }
+	    if (nds>0)
+	      dataMap[row][col]=sizeof(sls_detector_header)+((nadc+4)*i+iadc)*2;//+16*(ip+1); 
+	    else
+	    dataMap[row][col]=sizeof(sls_detector_header)+(nadc*i+iadc)*2;//+16*(ip+1);
+	    if (dataMap[row][col]<0 || dataMap[row][col]>=aSamples*2*32)
+	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	  }
+	}
+      }
+    }
+
+    int ipacket;
+    int ibyte;
+    int ii=0;
+    for (ibyte=0; ibyte<sizeof(sls_detector_header)/2; ibyte++){
+      xmap[ibyte]=-1;
+      ymap[ibyte]=-1;
+    }
+    /* int off=sizeof(sls_detector_header)/2; */
+    
+    /*   for (ibyte=0;  ibyte<dataSize; ibyte++) { */
+
+
+    /* for (ipacket=0; ipacket<npackets; ipacket++) { */
+    /*   for (ibyte=0;  ibyte< 8192/2; ibyte++) { */
+    /* 	i=ipacket*8208/2+ibyte; */
+    /* 	  isample=ii/nadc; */
+    /* 	  if (isample<nSamples) { */
+    /* 	  iadc=ii%nadc; */
+    /* 	  adc4 = (int)iadc/4; */
+    /* 	  ix=isample%sc_width; */
+    /* 	  iy=isample/sc_width; */
+    /* 	  if (adc4%2==0) { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2-1-iy; */
+    /* 	  } else { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2+iy; */
+    /* 	  } */
+    /* 	  } */
+    /* 	ii++; */
+    /* 	//	} */
+    /*   } */
+    /* } */
+    
+    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
+
+  */
+
+/* class jfrau_packet_header_t { */
+/*  public: */
+/* 	unsigned char reserved[4]; */
+/* 	unsigned char packetNumber[1]; */
+/* 	unsigned char frameNumber[3]; */
+/* 	unsigned char bunchid[8]; */
+/* }; */
+
+
+
+  int getFrameNumber(char *buff){return ((sls_detector_header*)buff)->frameNumber;};//*((int*)(buff+5))&0xffffff;};   
+
+  /**
+
+     Returns the packet number for the given dataset. purely virtual func
+     \param buff pointer to the dataset
+     \returns packet number number
+
+
+
+  */
+  int getPacketNumber(char *buff){return ((sls_detector_header*)buff)->packetNumber;}//((*(((int*)(buff+4))))&0xff)+1;};   
+
+/*    /\** */
+
+/*      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  */
+
+/*   *\/ */
+/*     virtual  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 */
+
+/*   *\/ */
+/*     virtual 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; */
+/*     }; */
+
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[dataSize];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+	  char *retval=0;
+	  int  nd;
+	  int fnum = -1;
+	  np=0;
+	  int  pn;
+	  
+	  //  cout << dataSize << endl;
+	  if (ff>=0)
+	    fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, dataSize) ){
+	      ff=getFrameNumber(data);
+	      np=getPacketNumber(data);
+	      return data;
+	    }
+	  }
+	    return NULL;
+	    
+	    
+	  
+  };
+
+
+
+  /**
+
+     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 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<dataSize) ndata=dsize;
+    else ndata=dataSize;
+    return data;
+
+  }
+
+
+
+  //int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+
+};
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/moench04CtbReceiverData.h

@@ -1,7 +1,8 @@
-#ifndef MOENCH03T1ZMQDATA_H
-#define  MOENCH03T1ZMQDATA_H
+#ifndef MOENCH04RECDATA_H
+#define  MOENCH04RECDATA_H
 #include "slsDetectorData.h"
 
+//#define VERSION_V2
     /**
         @short  structure for a Detector Packet or Image Header
         @li frameNumber is the frame number
@@ -32,12 +33,14 @@
         uint16_t roundRNumber;    /**< is the round robin set number */
         uint8_t detType;        /**< is the detector type see :: detectorType */
         uint8_t version;        /**< is the version number of this structure format */
+      uint64_t packetCaught[8];        /**< is the version number of this structure format */
+
     } sls_detector_header;
 
 
 
 
-class moench03T1ReceiverData : public slsDetectorData<uint16_t> {
+class moench04CtbReceiverData : public slsDetectorData<uint16_t> {
  
  private:
   
@@ -45,8 +48,8 @@ class moench03T1ReceiverData : public slsDetectorData<uint16_t> {
   int nadc;
   int sc_width;
   int sc_height;
-  const int nPackets; /**<number of UDP packets constituting one frame */
-  const int packetSize; /**< size of a udp packet */
+  const int aSamples;
+  const int dSamples;
 
 
  public:
@@ -60,16 +63,13 @@ class moench03T1ReceiverData : public slsDetectorData<uint16_t> {
      \param c crosstalk parameter for the output buffer
 
   */
-    moench03T1ReceiverData(int npackets=40, int ps=8192): slsDetectorData<uint16_t>(400, 400, ps*npackets+sizeof(sls_detector_header)), packetSize(ps), nPackets(npackets) {
+ moench04CtbReceiverData(int nas=5000, int nds=0): slsDetectorData<uint16_t>(400, 400, nas*2*32+sizeof(sls_detector_header)+nds*8), aSamples(nas), dSamples(nds) {
 
     int nadc=32;
     int sc_width=25;
     int sc_height=200;
 
-    int adc_nr[32]={300,325,350,375,300,325,350,375,		\
-    		    200,225,250,275,200,225,250,275,\
-    		    100,125,150,175,100,125,150,175,\
-    		    0,25,50,75,0,25,50,75};
+    int adc_nr[32]={9, 8,11,10,13,12,15,14,1,0,3,2,5,4,7,6,23,22,21,20,19,18,17,16,31,30,29,28,27,26,25,24 };
 
     int row, col;
 
@@ -77,7 +77,7 @@ class moench03T1ReceiverData : public slsDetectorData<uint16_t> {
     int iadc;
     int ix, iy;
     
-    // int npackets=40;
+     int npackets=40;
     int i;
     int adc4(0);
 
@@ -89,14 +89,15 @@ class moench03T1ReceiverData : public slsDetectorData<uint16_t> {
 	  adc4=(int)iadc/4;
 	  if (i<sc_width*sc_height) {
 	    //  for (int i=0; i<sc_width*sc_height; i++) {
-	    col=adc_nr[iadc]+(i%sc_width);
-	    if (adc4%2==0) {
+	    col=(adc_nr[iadc]%16)*sc_width+(i%sc_width);
+	    // if (adc4%2==0) {
+	    if (iadc/16>0) {
 	      row=199-i/sc_width;
 	    } else {
 	      row=200+i/sc_width;
 	    }
 	    dataMap[row][col]=sizeof(sls_detector_header)+(nadc*i+iadc)*2;//+16*(ip+1);
-	    if (dataMap[row][col]<0 || dataMap[row][col]>=8192*40)
+	    if (dataMap[row][col]<0 || dataMap[row][col]>=aSamples*2*32)
 	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
 	  }
 	}
@@ -110,27 +111,32 @@ class moench03T1ReceiverData : public slsDetectorData<uint16_t> {
       xmap[ibyte]=-1;
       ymap[ibyte]=-1;
     }
-    int off=sizeof(sls_detector_header)/2;
-    for (ipacket=0; ipacket<npackets; ipacket++) {
-      for (ibyte=0;  ibyte< 8192/2; ibyte++) {
-	i=ipacket*8208/2+ibyte;
-	  isample=ii/nadc;
-	  iadc=ii%nadc;
-	  adc4 = (int)iadc/4;
-	  ix=isample%sc_width;
-	  iy=isample/sc_width;
-	  if (adc4%2==0) {
-	    xmap[i+off]=adc_nr[iadc]+ix;
-	    ymap[i+off]=ny/2-1-iy;
-	  } else {
-	    xmap[i+off]=adc_nr[iadc]+ix;
-	    ymap[i+off]=ny/2+iy;
-	  }
-	  
-	ii++;
-	//	}
-      }
-    }
+    /* int off=sizeof(sls_detector_header)/2; */
+    
+    /*   for (ibyte=0;  ibyte<dataSize; ibyte++) { */
+
+
+    /* for (ipacket=0; ipacket<npackets; ipacket++) { */
+    /*   for (ibyte=0;  ibyte< 8192/2; ibyte++) { */
+    /* 	i=ipacket*8208/2+ibyte; */
+    /* 	  isample=ii/nadc; */
+    /* 	  if (isample<nSamples) { */
+    /* 	  iadc=ii%nadc; */
+    /* 	  adc4 = (int)iadc/4; */
+    /* 	  ix=isample%sc_width; */
+    /* 	  iy=isample/sc_width; */
+    /* 	  if (adc4%2==0) { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2-1-iy; */
+    /* 	  } else { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2+iy; */
+    /* 	  } */
+    /* 	  } */
+    /* 	ii++; */
+    /* 	//	} */
+    /*   } */
+    /* } */
     
     iframe=0;
     //  cout << "data struct created" << endl;
@@ -167,7 +173,7 @@ class moench03T1ReceiverData : public slsDetectorData<uint16_t> {
 
 
   */
-  int getPacketNumber(char *buff){((sls_detector_header*)buff)->packetNumber;}//((*(((int*)(buff+4))))&0xff)+1;};   
+  int getPacketNumber(char *buff){return ((sls_detector_header*)buff)->packetNumber;}//((*(((int*)(buff+4))))&0xff)+1;};   
 
 /*    /\** */
 
@@ -275,7 +281,7 @@ class moench03T1ReceiverData : public slsDetectorData<uint16_t> {
 
 
 
-int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+  //int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
 
 };
 

slsDetectorCalibration/dataStructures/moench04CtbZmq10GbData.h

@@ -0,0 +1,290 @@
+#ifndef MOENCH04ZMQ10GBDATA_H
+#define  MOENCH04ZMQ10GBDATA_H
+#include "slsDetectorData.h"
+
+
+
+
+class moench04CtbZmq10GbData : public slsDetectorData<uint16_t> {
+ 
+ private:
+  
+  int iframe;
+  int nadc;
+  int sc_width;
+  int sc_height;
+  const int aSamples;
+  const int dSamples;
+
+
+ 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
+
+  */
+  //moench04CtbZmq10GbData(int nas=5000, int nds=0): slsDetectorData<uint16_t>(400, 400, nas*2*32+nds*8), aSamples(nas), dSamples(nds), nadc(32), sc_width(25), sc_height(200) {
+ moench04CtbZmq10GbData(int nas=5000, int nds=0): slsDetectorData<uint16_t>(400, 400, (nas > 0) && (nds>0) ? max(nas,nds)*(32*2+8) : nas*32*2+nds*8), nadc(32), sc_width(25), sc_height(200), aSamples(nas), dSamples(nds) {
+
+    /* int ds; */
+    /* if (nas && nds) */
+    /*   if (nds>nas) */
+    /* 	ds=nds*(32*2+8); */
+    /*   else */
+    /* 	ds=nas*(32*2+8); */
+    /* else */
+    /*   ds=nas*32*2+nds*8; */
+
+    /* new slsDetectorData<uint16_t>(400, 400, ds); */
+
+    int adc_nr[32]={9, 8,11,10,13,12,15,14,1,0,3,2,5,4,7,6,23,22,21,20,19,18,17,16,31,30,29,28,27,26,25,24 };
+
+    int row, col;
+
+    //int isample;
+    int iadc;
+   // int ix, iy;
+    
+    // int npackets=40;
+    int i;
+    //int adc4(0);
+
+      for (int is=0; is<aSamples; is++) {
+	
+	for (iadc=0; iadc<nadc; iadc++) {
+	  i=is;
+	  //	  adc4=(int)iadc/4;
+	  if (i<sc_width*sc_height) {
+	    //  for (int i=0; i<sc_width*sc_height; i++) {
+	    col=(adc_nr[iadc]%16)*sc_width+(i%sc_width);
+	    // if (adc4%2==0) {
+	    if (iadc<16) {
+	      row=199-i/sc_width;
+	    } else {
+	      row=200+i/sc_width;
+	    }
+	    if (nds>0)
+	      dataMap[row][col]=((nadc+4)*i+iadc)*2;//+16*(ip+1);
+	    else
+	      dataMap[row][col]=(nadc*i+iadc)*2;//+16*(ip+1);
+	    if (dataMap[row][col]<0 || dataMap[row][col]>=aSamples*2*32)
+	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	  }
+	}
+      }
+  
+
+    /* for (ibyte=0; ibyte<sizeof(sls_detector_header)/2; ibyte++){ */
+    /*   xmap[ibyte]=-1; */
+    /*   ymap[ibyte]=-1; */
+    /* } */
+    /* int off=sizeof(sls_detector_header)/2; */
+    
+    /*   for (ibyte=0;  ibyte<dataSize; ibyte++) { */
+
+
+    /* for (ipacket=0; ipacket<npackets; ipacket++) { */
+    /*   for (ibyte=0;  ibyte< 8192/2; ibyte++) { */
+    /* 	i=ipacket*8208/2+ibyte; */
+    /* 	  isample=ii/nadc; */
+    /* 	  if (isample<nSamples) { */
+    /* 	  iadc=ii%nadc; */
+    /* 	  adc4 = (int)iadc/4; */
+    /* 	  ix=isample%sc_width; */
+    /* 	  iy=isample/sc_width; */
+    /* 	  if (adc4%2==0) { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2-1-iy; */
+    /* 	  } else { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2+iy; */
+    /* 	  } */
+    /* 	  } */
+    /* 	ii++; */
+    /* 	//	} */
+    /*   } */
+    /* } */
+    
+    iframe=0;
+    //  cout << "data struct created" << endl;
+  }
+    
+  int getGain(char *data, int x, int y) {
+   // int aoff=aSamples*2*32;
+    int irow;
+    int isc=x/sc_width;
+    int icol=x%sc_width;
+    if (y<200) irow=sc_height-1-y;
+    else {
+      irow=y-sc_height;
+      isc++;
+    }
+    int ibit[32]={-1,-1,-1,-1,-1,-1,1,3,5,7,-1,-1,-1,-1,-1,-1,62,60,58,56,54,52,50,48,63,61,59,57,55,53,51,49};
+    int isample=irow*sc_width+icol;
+   
+    uint64_t sample;
+    char *ptr;
+    if (isc<0 || isc>=32) return 0;
+    if (ibit[isc]<0 || ibit[isc]>=64) return 0;
+    if (dSamples>isample) {
+      ptr=data+32*(isample+1)+8*isample;
+      sample=*((uint64_t*)ptr);
+    cout << isc << " " << ibit[isc] << " " << isample << hex << sample << dec << endl;
+    if (sample & (1<<ibit[isc]))
+      return 1;
+    else
+      return 0;
+    } else
+      return 0;
+  }
+
+     /**
+
+     Returns the frame number for the given dataset. Purely virtual func.
+     \param buff pointer to the dataset
+     \returns frame number
+
+  */
+
+/* class jfrau_packet_header_t { */
+/*  public: */
+/* 	unsigned char reserved[4]; */
+/* 	unsigned char packetNumber[1]; */
+/* 	unsigned char frameNumber[3]; */
+/* 	unsigned char bunchid[8]; */
+/* }; */
+
+
+
+  int getFrameNumber(char *buff){return iframe;};//((sls_detector_header*)buff)->frameNumber;};//*((int*)(buff+5))&0xffffff;};   
+
+  /**
+
+     Returns the packet number for the given dataset. purely virtual func
+     \param buff pointer to the dataset
+     \returns packet number number
+
+
+
+  */
+  //int getPacketNumber(char *buff){return ((sls_detector_header*)buff)->packetNumber;}//((*(((int*)(buff+4))))&0xff)+1;};   
+
+/*    /\** */
+
+/*      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  */
+
+/*   *\/ */
+/*     virtual  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 */
+
+/*   *\/ */
+/*     virtual 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; */
+/*     }; */
+
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[dataSize];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+	 // char *retval=0;
+	 // int  nd;
+	 // int fnum = -1;
+	  np=0;
+	  //int  pn;
+	  
+	  //  cout << dataSize << endl;
+	  if (ff>=0)
+	   // fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, dataSize) ){
+	      ff=getFrameNumber(data);
+	      //     np=getPacketNumber(data);
+	      return data;
+	    }
+	  }
+	    return NULL;
+	    
+	    
+	  
+  };
+
+
+
+  /**
+
+     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 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<dataSize) ndata=dsize;
+    else ndata=dataSize;
+    return data;
+
+  }
+
+
+
+  //int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+
+};
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/moench04CtbZmqData.h

@@ -0,0 +1,276 @@
+#ifndef MOENCH04ZMQDATA_H
+#define  MOENCH04ZMQDATA_H
+#include "slsDetectorData.h"
+
+
+
+
+class moench04CtbZmqData : public slsDetectorData<uint16_t> {
+ 
+ private:
+  
+  int iframe;
+  int nadc;
+  int sc_width;
+  int sc_height;
+  const int aSamples;
+  const int dSamples;
+
+
+ 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
+
+  */
+ moench04CtbZmqData(int nas=5000, int nds=0): slsDetectorData<uint16_t>(400, 400, nas*2*32+nds*8), nadc(32), sc_width(25), sc_height(200), aSamples(nas), dSamples(nds) {
+    
+
+    int adc_nr[32]={9, 8,11,10,13,12,15,14,1,0,3,2,5,4,7,6,23,22,21,20,19,18,17,16,31,30,29,28,27,26,25,24 };
+
+    int row, col;
+
+    //int isample;
+    int iadc;
+    //int ix, iy;
+    
+    // int npackets=40;
+    int i;
+    //int adc4(0);
+
+      for (int is=0; is<aSamples; is++) {
+	
+	for (iadc=0; iadc<nadc; iadc++) {
+	  i=is;
+	  //	  adc4=(int)iadc/4;
+	  if (i<sc_width*sc_height) {
+	    //  for (int i=0; i<sc_width*sc_height; i++) {
+	    col=(adc_nr[iadc]%16)*sc_width+(i%sc_width);
+	    // if (adc4%2==0) {
+	    if (iadc<16) {
+	      row=199-i/sc_width;
+	    } else {
+	      row=200+i/sc_width;
+	    }
+	    dataMap[row][col]=(nadc*i+iadc)*2;//+16*(ip+1);
+	    if (dataMap[row][col]<0 || dataMap[row][col]>=aSamples*2*32)
+	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	  }
+	}
+      }
+  
+
+    /* for (ibyte=0; ibyte<sizeof(sls_detector_header)/2; ibyte++){ */
+    /*   xmap[ibyte]=-1; */
+    /*   ymap[ibyte]=-1; */
+    /* } */
+    /* int off=sizeof(sls_detector_header)/2; */
+    
+    /*   for (ibyte=0;  ibyte<dataSize; ibyte++) { */
+
+
+    /* for (ipacket=0; ipacket<npackets; ipacket++) { */
+    /*   for (ibyte=0;  ibyte< 8192/2; ibyte++) { */
+    /* 	i=ipacket*8208/2+ibyte; */
+    /* 	  isample=ii/nadc; */
+    /* 	  if (isample<nSamples) { */
+    /* 	  iadc=ii%nadc; */
+    /* 	  adc4 = (int)iadc/4; */
+    /* 	  ix=isample%sc_width; */
+    /* 	  iy=isample/sc_width; */
+    /* 	  if (adc4%2==0) { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2-1-iy; */
+    /* 	  } else { */
+    /* 	    xmap[i+off]=adc_nr[iadc]+ix; */
+    /* 	    ymap[i+off]=ny/2+iy; */
+    /* 	  } */
+    /* 	  } */
+    /* 	ii++; */
+    /* 	//	} */
+    /*   } */
+    /* } */
+    
+    iframe=0;
+    //  cout << "data struct created" << endl;
+  }
+    
+  int getGain(char *data, int x, int y) {
+    int aoff=aSamples*2*32;
+    int irow;
+    int isc=x/sc_width;
+    int icol=x%sc_width;
+    if (y<200) irow=sc_height-1-y;
+    else {
+      irow=y-sc_height;
+      isc++;
+    }
+    int ibit[32]={-1,-1,-1,-1,-1,-1,1,3,5,7,-1,-1,-1,-1,-1,-1,62,60,58,56,54,52,50,48,63,61,59,57,55,53,51,49};
+    int isample=irow*sc_width+icol;
+   
+    uint64_t sample;
+    char *ptr;
+    if (isc<0 || isc>=32) return 0;
+    if (ibit[isc]<0 || ibit[isc]>=64) return 0;
+    if (dSamples>isample) {
+      ptr=data+aoff+8*isample;
+      sample=*((uint64_t*)ptr);
+    cout << isc << " " << ibit[isc] << " " << isample << hex << sample << dec << endl;
+    if (sample & (1<<ibit[isc]))
+      return 1;
+    else
+      return 0;
+    } else
+      return 0;
+  }
+
+     /**
+
+     Returns the frame number for the given dataset. Purely virtual func.
+     \param buff pointer to the dataset
+     \returns frame number
+
+  */
+
+/* class jfrau_packet_header_t { */
+/*  public: */
+/* 	unsigned char reserved[4]; */
+/* 	unsigned char packetNumber[1]; */
+/* 	unsigned char frameNumber[3]; */
+/* 	unsigned char bunchid[8]; */
+/* }; */
+
+
+
+  int getFrameNumber(char *buff){return iframe;};//((sls_detector_header*)buff)->frameNumber;};//*((int*)(buff+5))&0xffffff;};   
+
+  /**
+
+     Returns the packet number for the given dataset. purely virtual func
+     \param buff pointer to the dataset
+     \returns packet number number
+
+
+
+  */
+  //int getPacketNumber(char *buff){return ((sls_detector_header*)buff)->packetNumber;}//((*(((int*)(buff+4))))&0xff)+1;};   
+
+/*    /\** */
+
+/*      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  */
+
+/*   *\/ */
+/*     virtual  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 */
+
+/*   *\/ */
+/*     virtual 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; */
+/*     }; */
+
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[dataSize];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+	 // char *retval=0;
+	  //int  nd;
+	  //int fnum = -1;
+	  np=0;
+	  //int  pn;
+	  
+	  //  cout << dataSize << endl;
+	  if (ff>=0)
+	   // fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, dataSize) ){
+	      ff=getFrameNumber(data);
+	      //     np=getPacketNumber(data);
+	      return data;
+	    }
+	  }
+	    return NULL;
+	    
+	    
+	  
+  };
+
+
+
+  /**
+
+     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 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<dataSize) ndata=dsize;
+    else ndata=dataSize;
+    return data;
+
+  }
+
+
+
+  //int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+
+};
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/slsDetectorData.h

@@ -15,9 +15,9 @@ class slsDetectorData {
   const int nx; /**< Number of pixels in the x direction */
   const int ny; /**< Number of pixels in the y direction */
   int dataSize; /**<size of the data constituting one frame */
-  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 *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;
   
@@ -37,35 +37,25 @@ class slsDetectorData {
   \param dROI Array of size nx*ny. The elements are 1s if the channel is good or in the ROI, 0 is bad or out of the ROI. NULL (default) means all 1s. 
   
   */
- slsDetectorData(int npx, int npy, int dsize, int **dMap=NULL, dataType **dMask=NULL, int **dROI=NULL): nx(npx), ny(npy), dataSize(dsize) {
+ 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[dsize/sizeof(dataType)];
-    ymap=new int[dsize/sizeof(dataType)];
+   int el=dsize/sizeof(dataType);
+    xmap=new int[el];
+    ymap=new int[el];
     
 
     //  if (dataMask==NULL) {
-    dataMask=new dataType*[ny];
-    for(int i = 0; i < ny; i++) {
-      dataMask[i] = new dataType[nx];
-    }
+    dataMask=new dataType[ny*nx];
     // }
     
     // if (dataMap==NULL) {
-    dataMap=new int*[ny];
-    for(int i = 0; i < ny; i++) {
-      dataMap[i] = new int[nx];
-      }
+    dataMap=new int[ny*nx];
     // }
     // if (dataROIMask==NULL) {
-    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;
-    }
+    dataROIMask=new int [ny*nx];
     // }
-    for (int ip=0; ip<dsize/sizeof(dataType); ip++){
+  
+    for (int ip=0; ip<el; ip++){
       xmap[ip]=-1;
       ymap[ip]=-1;
       }
@@ -77,11 +67,6 @@ class slsDetectorData {
   };
   
   virtual ~slsDetectorData() {
-    for(int i = 0; i < ny; i++) {
-      delete [] dataMap[i];
-      delete [] dataMask[i];
-      delete [] dataROIMask[i];
-    }
     delete [] dataMap;
     delete [] dataMask;
     delete [] dataROIMask;
@@ -94,14 +79,14 @@ class slsDetectorData {
      defines the data map (as offset) - no error checking if datasize and offsets are compatible!
      \param dMap array of size nx*ny storing the pointers to the data in the dataset (as offset). If NULL (default),the data are arranged as if read out row by row (dataMap[iy][ix]=(iy*nx+ix)*sizeof(dataType);)
   */
-  void setDataMap(int **dMap=NULL) {
+  void setDataMap(int *dMap=NULL) {
     
     int ip=0;
     int ix, iy;
     if (dMap==NULL) {
       for (iy=0; iy<ny; iy++) {
 	for (ix=0; ix<nx; ix++) {
-		dataMap[iy][ix]=(iy*nx+ix)*sizeof(dataType);
+		dataMap[iy*nx+ix]=(iy*nx+ix)*sizeof(dataType);
 	}
       }
     } else {
@@ -109,7 +94,7 @@ class slsDetectorData {
       for (iy=0; iy<ny; iy++){
 			 // cout << iy << endl;
 	for (ix=0; ix<nx; ix++) {
-	  dataMap[iy][ix]=dMap[iy][ix];
+	  dataMap[iy*nx+ix]=dMap[iy*nx+ix];
 	  // cout << ix << " " << iy << endl;
 	  /*ip=dataMap[ix][iy]/sizeof(dataType);
 	    xmap[ip]=ix;
@@ -119,7 +104,7 @@ class slsDetectorData {
     }
     for (iy=0; iy<ny; iy++){
       for (ix=0; ix<nx; ix++) {
-	ip=dataMap[iy][ix]/sizeof(dataType);
+	ip=dataMap[iy*nx+ix]/sizeof(dataType);
 	xmap[ip]=ix;
 	ymap[ip]=iy;
       }
@@ -135,17 +120,17 @@ class slsDetectorData {
      \param dMask 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)
 
   */
-  void setDataMask(dataType **dMask=NULL){
+  void setDataMask(dataType *dMask=NULL){
     
     if (dMask!=NULL) {
       
       for (int iy=0; iy<ny; iy++)
 	 for (int ix=0; ix<nx; ix++)
-	   dataMask[iy][ix]=dMask[iy][ix];
+	   dataMask[iy*nx+ix]=dMask[iy*nx+ix];
     } else {
       for (int iy=0; iy<ny; iy++)
 	for (int ix=0; ix<nx; ix++)
-	  dataMask[iy][ix]=0;
+	  dataMask[iy*nx+ix]=0;
     }
   };
   /**
@@ -153,18 +138,18 @@ class slsDetectorData {
      \param dROI Array of size nx*ny. The lements are 1s if the channel is good or in the ROI, 0 is bad or out of the ROI. NULL (default) means all 1s. 
      
   */
-  void setDataROIMask(int **dROI=NULL){
+  void setDataROIMask(int *dROI=NULL){
     
     if (dROI!=NULL) {
       
       for (int iy=0; iy<ny; iy++)
 	for (int ix=0; ix<nx; ix++)
-	   dataROIMask[iy][ix]=dROI[iy][ix];
+	   dataROIMask[iy*nx+ix]=dROI[iy*nx+ix];
     } else {
       
       for (int iy=0; iy<ny; iy++)
 	for (int ix=0; ix<nx; ix++)
-	   dataROIMask[iy][ix]=1;
+	   dataROIMask[iy*nx+ix]=1;
       
     }
     
@@ -178,14 +163,14 @@ class slsDetectorData {
      \param i 1 if pixel is good (or in the roi), 0 if bad
      \returns 1 if pixel is good, 0 if it's bad, -1 if pixel is out of range
   */
-  int setGood(int ix, int iy, int i=1) {  if (ix>=0 && ix<nx && iy>=0 && iy<ny) dataROIMask[iy][ix]=i; return isGood(ix,iy);};
+  int setGood(int ix, int iy, int i=1) {  if (ix>=0 && ix<nx && iy>=0 && iy<ny) dataROIMask[iy*nx+ix]=i; return isGood(ix,iy);};
   /**
      Define bad channel or roi mask for a single channel
      \param ix channel x coordinate
      \param iy channel y coordinate (1 for strips)
      \returns 1 if pixel is good, 0 if it's bad, -1 if pixel is out of range
   */
-  int isGood(int ix, int iy) {  if (ix>=0 && ix<nx && iy>=0 && iy<ny) return dataROIMask[iy][ix]; else return -1;};
+  int isGood(int ix, int iy) {  if (ix>=0 && ix<nx && iy>=0 && iy<ny) return dataROIMask[iy*nx+ix]; else return -1;};
   
   /**
      Returns detector size in x,y
@@ -204,38 +189,33 @@ class slsDetectorData {
   
   virtual void getPixel(int ip, int &x, int &y) {x=xmap[ip]; y=ymap[ip];};
   
-  virtual dataType **getData(char *ptr, int dsize=-1) {
-    
-    dataType **data;
+  virtual dataType *getData(char *ptr, int dsize=-1) {
+    int el=dsize/sizeof(dataType);
+    dataType  *data;
     int ix,iy;
-    data=new dataType*[ny];
-    for(int i = 0; i < ny; i++) {
-      data[i]=new dataType[nx];
-    }
+    data=new dataType[ny*nx];
     if (dsize<=0 || dsize>dataSize) dsize=dataSize;
-    for (int ip=0; ip<(dsize/sizeof(dataType)); ip++) {
+    for (int ip=0; ip<(el); ip++) {
       getPixel(ip,ix,iy);
       if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
-	data[iy][ix]=getChannel(ptr,ix,iy);
+	data[iy*nx+ix]=getChannel(ptr,ix,iy);
       }
     }
     return data;
     
   };
   
-  virtual double **getImage(char *ptr, int dsize=-1) {
+  virtual double *getImage(char *ptr, int dsize=-1) {
     
-    double **data;
+    double *data;
     int ix,iy;
-    data=new double*[ny];
-    for(int i = 0; i < ny; i++) {
-      data[i]=new double[nx];
-    }
+    data=new double[ny*nx];
+    int el=dsize/sizeof(dataType);
     if (dsize<=0 || dsize>dataSize) dsize=dataSize;
-    for (int ip=0; ip<(dsize/sizeof(dataType)); ip++) {
+    for (int ip=0; ip<el; ip++) {
       getPixel(ip,ix,iy);
       if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
-	data[iy][ix]=getValue(ptr,ix,iy);
+	data[iy*nx+ix]=getValue(ptr,ix,iy);
       }
     }
     return data;
@@ -251,16 +231,19 @@ class slsDetectorData {
 
   */
   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) {
+    dataType m=0, d=0, *p;
+    if (ix>=0 && ix<nx && iy>=0 && iy<ny && dataMap[iy*nx+ix]>=0 && dataMap[iy*nx+ix]<dataSize) {
       // cout << ix << " " << iy << " " ;
       //cout << dataMap[ix][iy] << " " << (void*)data << " " << dataSize<< endl;
-      m=dataMask[iy][ix];
-      d=*((dataType*)(data+dataMap[iy][ix]));
+      m=dataMask[iy*nx+ix];
+      p=(dataType*)(data+dataMap[iy*nx+ix]);
+      d=*p;
     }  
     return d^m;
   };
 
+  virtual int getGain(char *data, int ix, int iy=0){return 0;};
+
   /**
 
      Returns the value of the selected channel for the given dataset. Virtual function, can be overloaded.

slsDetectorCalibration/energyCalibration.cpp

@@ -1,534 +0,0 @@
-#include "energyCalibration.h"
-
-#ifdef __CINT
-#define MYROOT
-#endif
-
-
-#ifdef MYROOT
-#include <TMath.h>
-#include <TH1F.h>
-#include <TH2F.h>
-#include <TGraphErrors.h>
-#endif
-
-#include <iostream>
-
-#define max(a,b) ((a) > (b) ? (a) : (b))
-#define min(a,b) ((a) < (b) ? (a) : (b))
-#define ELEM_SWAP(a,b) { register int t=(a);(a)=(b);(b)=t; }
-
-
-using namespace std;
-
-#ifdef MYROOT
-
-Double_t energyCalibrationFunctions::pedestal(Double_t *x, Double_t *par) { 
-    return par[0]-par[1]*sign*x[0];                                      
-}
-
-
-Double_t energyCalibrationFunctions::gaussChargeSharing(Double_t *x, Double_t *par) { 
-  Double_t f, arg=0;
-  if (par[3]!=0) arg=sign*(x[0]-par[2])/par[3];
-    f=TMath::Exp(-1*arg*arg/2.); 
-    f=f+par[5]/2.*(TMath::Erfc(arg/(TMath::Sqrt(2.)))); 
-    return par[4]*f+pedestal(x,par);                                       
-}
-
-Double_t energyCalibrationFunctions::gaussChargeSharingPixel(Double_t *x, Double_t *par) { 
-  Double_t f;
-  if (par[3]<=0 || par[2]*(*x)<=0 || par[5]<0 || par[4]<=0) return 0;
-
-  Double_t pp[3];
-
-  pp[0]=0;
-  pp[1]=par[2];
-  pp[2]=par[3];
-  
-
-  f=(par[5]-par[6]*(TMath::Log(*x/par[2])))*erfBox(x,pp);
-  f+=par[4]*TMath::Gaus(*x, par[2], par[3], kTRUE);
-  return f+pedestal(x,par);                                       
-}
-
-Double_t energyCalibrationFunctions::erfBox(Double_t *z, Double_t *par) {
-
-  
-  
-  Double_t m=par[0];
-  Double_t M=par[1];
-  
-  if (par[0]>par[1]) {
-    m=par[1];
-    M=par[0];
-  }
-  
-  if (m==M)
-    return 0;
-
-
-  if (par[2]<=0) {
-    if (*z>=m && *z<=M)
-      return 1./(M-m);
-    else
-      return 0;
-
-  }
-
-  return (TMath::Erfc((z[0]-M)/par[2])-TMath::Erfc((z[0]-m)/par[2]))*0.5/(M-m);
-
-}
-
-
-// basic erf function
-Double_t energyCalibrationFunctions::erfFunction(Double_t *x, Double_t *par) {	
-  double arg=0;
-  if (par[1]!=0) arg=(par[0]-x[0])/par[1];
-  return ((par[2]/2.*(1+TMath::Erf(sign*arg/(TMath::Sqrt(2))))));  
-};
-  
-
-Double_t energyCalibrationFunctions::erfFunctionChargeSharing(Double_t *x, Double_t *par) {	       
-  Double_t f;		
-  
-  f=erfFunction(x, par+2)*(1+par[5]*(par[2]-x[0]))+par[0]-par[1]*x[0]*sign;		
-  return f;								
-};
-  
-  
-Double_t energyCalibrationFunctions::erfFuncFluo(Double_t *x, Double_t *par) {
-  Double_t f;							       
-  f=erfFunctionChargeSharing(x, par)+erfFunction(x, par+6)*(1+par[9]*(par[6]-x[0])); 
-  return f;							
-};
-#endif
-
-double energyCalibrationFunctions::median(double *x, int n){
-  // sorts x into xmed array and returns median 
-  // n is number of values already in the xmed array
-  double xmed[n];
-  int k,i,j;
-
-  for (i=0; i<n; i++) {
-    k=0;
-    for (j=0; j<n; j++) {
-      if(*(x+i)>*(x+j))
-	k++;
-      if (*(x+i)==*(x+j)) {
-	if (i>j) 
-	  k++;
-      }
-    }
-    xmed[k]=*(x+i);
-  }
-  k=n/2;
-  return xmed[k];
-}
-
-
-int energyCalibrationFunctions::quick_select(int arr[], int n){
-    int low, high ;
-    int median;
-    int middle, ll, hh;
-
-    low = 0 ; high = n-1 ; median = (low + high) / 2;
-    for (;;) {
-        if (high <= low) /* One element only */
-            return arr[median] ;
-
-        if (high == low + 1) {  /* Two elements only */
-            if (arr[low] > arr[high])
-                ELEM_SWAP(arr[low], arr[high]) ;
-            return arr[median] ;
-        }
-
-    /* Find median of low, middle and high items; swap into position low */
-    middle = (low + high) / 2;
-    if (arr[middle] > arr[high])    ELEM_SWAP(arr[middle], arr[high]) ;
-    if (arr[low] > arr[high])       ELEM_SWAP(arr[low], arr[high]) ;
-    if (arr[middle] > arr[low])     ELEM_SWAP(arr[middle], arr[low]) ;
-
-    /* Swap low item (now in position middle) into position (low+1) */
-    ELEM_SWAP(arr[middle], arr[low+1]) ;
-
-    /* Nibble from each end towards middle, swapping items when stuck */
-    ll = low + 1;
-    hh = high;
-    for (;;) {
-        do ll++; while (arr[low] > arr[ll]) ;
-        do hh--; while (arr[hh]  > arr[low]) ;
-
-        if (hh < ll)
-        break;
-
-        ELEM_SWAP(arr[ll], arr[hh]) ;
-    }
-
-    /* Swap middle item (in position low) back into correct position */
-    ELEM_SWAP(arr[low], arr[hh]) ;
-
-    /* Re-set active partition */
-    if (hh <= median)
-        low = ll;
-        if (hh >= median)
-        high = hh - 1;
-    }
-}
-
-int energyCalibrationFunctions::kth_smallest(int *a, int n, int k){
-    register int i,j,l,m ;
-    register double x ;
-
-    l=0 ; m=n-1 ;
-    while (l<m) {
-        x=a[k] ;
-        i=l ;
-        j=m ;
-        do {
-            while (a[i]<x) i++ ;
-            while (x<a[j]) j-- ;
-            if (i<=j) {
-                ELEM_SWAP(a[i],a[j]) ;
-                i++ ; j-- ;
-            }
-        } while (i<=j) ;
-        if (j<k) l=i ;
-        if (k<i) m=j ;
-    }
-    return a[k] ;
-}
-
-
-
-#ifdef MYROOT
-Double_t energyCalibrationFunctions::spectrum(Double_t *x, Double_t *par) {
-  return gaussChargeSharing(x,par);	
-}
-
-Double_t energyCalibrationFunctions::spectrumPixel(Double_t *x, Double_t *par) {
-  return gaussChargeSharingPixel(x,par);	
-}
-
-
-Double_t energyCalibrationFunctions::scurve(Double_t *x, Double_t *par) {
-  return erfFunctionChargeSharing(x,par);
-}
-
-
-Double_t energyCalibrationFunctions::scurveFluo(Double_t *x, Double_t *par) {
-  return erfFuncFluo(x,par);						
-}
-#endif
-
-energyCalibration::energyCalibration() : 
-#ifdef MYROOT	
-					 fit_min(-1),	
-					 fit_max(-1),	
-					 bg_offset(-1),	
-					 bg_slope(-1),	
-					 flex(-1),
-					 noise(-1),
-					 ampl(-1),
-					 cs_slope(-1),
-					 fscurve(NULL),
-					 fspectrum(NULL),
-#endif
-					 funcs(NULL),
-					 plot_flag(1), // fit parameters output to screen
-					 cs_flag(1)
-{
-
-#ifdef MYROOT	
-  funcs=new energyCalibrationFunctions();
-  
-  fscurve=new TF1("fscurve",funcs,&energyCalibrationFunctions::scurve,0,1000,6,"energyCalibrationFunctions","scurve");	
-  fscurve->SetParNames("Background Offset","Background Slope","Inflection Point","Noise RMS", "Number of Photons","Charge Sharing Slope");
-
-  fspectrum=new TF1("fspectrum",funcs,&energyCalibrationFunctions::spectrum,0,1000,6,"energyCalibrationFunctions","spectrum");	
-  fspectrum->SetParNames("Background Pedestal","Background slope", "Peak position","Noise RMS", "Number of Photons","Charge Sharing Pedestal");
-
-  fspixel=new TF1("fspixel",funcs,&energyCalibrationFunctions::spectrumPixel,0,1000,7,"energyCalibrationFunctions","spectrumPixel");	
-  fspixel->SetParNames("Background Pedestal","Background slope", "Peak position","Noise RMS", "Number of Photons","Charge Sharing Pedestal","Corner");
-
-#endif
-
-
-}
-
-
-
-void energyCalibration::fixParameter(int ip, Double_t val){
-  
-  fscurve->FixParameter(ip, val);
-  fspectrum->FixParameter(ip, val);
-}
-
-
-void energyCalibration::releaseParameter(int ip){
-
-  fscurve->ReleaseParameter(ip);
-  fspectrum->ReleaseParameter(ip);
-}
-
-
-
-
-
-
-
-energyCalibration::~energyCalibration(){ 
-#ifdef MYROOT
-  delete fscurve;
-  delete fspectrum;
-#endif
-  
-}
-
-#ifdef MYROOT
-
-
-
-
-
-TH1F* energyCalibration::createMedianHistogram(TH2F* h2, int ch0, int nch, int direction) {
-
-  if (h2==NULL || nch==0)
-    return NULL;
-
-  double *x=new double[nch];
-  TH1F *h1=NULL;
-  
-  double val=-1;
-
-  if (direction==0) {
-    h1=new TH1F("median","Median",h2->GetYaxis()->GetNbins(),h2->GetYaxis()->GetXmin(),h2->GetYaxis()->GetXmax());
-    for (int ib=0; ib<h1->GetXaxis()->GetNbins(); ib++) {
-      for (int ich=0; ich<nch; ich++) {
-	x[ich]=h2->GetBinContent(ch0+ich+1,ib+1);
-      }
-      val=energyCalibrationFunctions::median(x, nch);
-      h1->SetBinContent(ib+1,val);
-    }
-  } else if (direction==1) {   
-    h1=new TH1F("median","Median",h2->GetXaxis()->GetNbins(),h2->GetXaxis()->GetXmin(),h2->GetXaxis()->GetXmax());
-    for (int ib=0; ib<h1->GetYaxis()->GetNbins(); ib++) {
-      for (int ich=0; ich<nch; ich++) {
-	x[ich]=h2->GetBinContent(ib+1,ch0+ich+1);
-      }
-      val=energyCalibrationFunctions::median(x, nch);
-      h1->SetBinContent(ib+1,val);
-    }
-  }
-  delete [] x;
-
-  return h1;
-
-}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-void energyCalibration::setStartParameters(Double_t *par){	
-  bg_offset=par[0];						
-  bg_slope=par[1];						
-  flex=par[2];							
-  noise=par[3];							
-  ampl=par[4];							
-  cs_slope=par[5];						
-}
-
-
-void energyCalibration::getStartParameters(Double_t *par){	
-  par[0]=bg_offset;
-  par[1]=bg_slope;
-  par[2]=flex;
-  par[3]=noise;
-  par[4]=ampl;				
-  par[5]=cs_slope;				
-}
-
-#endif
-int energyCalibration::setChargeSharing(int p) {
-  if (p>=0) {
-    cs_flag=p; 
-#ifdef MYROOT  
-    if (p) {
-      fscurve->ReleaseParameter(5);
-      fspectrum->ReleaseParameter(1);
-    } else {
-      fscurve->FixParameter(5,0);
-      fspectrum->FixParameter(1,0);
-    }
-#endif
-  } 
-  
-  return cs_flag;
-}
-
- 
-#ifdef MYROOT  
-void energyCalibration::initFitFunction(TF1 *fun, TH1 *h1) {
-
- Double_t min=fit_min, max=fit_max; 
-
- Double_t mypar[6];
-  
- if (max==-1) 
-    max=h1->GetXaxis()->GetXmax();
- 
-  if (min==-1) 
-    min=h1->GetXaxis()->GetXmin();
-
-  
-  if (bg_offset==-1)
-    mypar[0]=0;
-  else
-    mypar[0]=bg_offset;
-
-
-  if (bg_slope==-1)
-    mypar[1]=0;
-  else
-    mypar[1]=bg_slope;
-
-
-  if (flex==-1)
-    mypar[2]=(min+max)/2.;
-  else
-    mypar[2]=flex;
-
-
-  if (noise==-1)
-    mypar[3]=0.1;
-  else
-    mypar[3]=noise;
-
-  if (ampl==-1)
-    mypar[4]=h1->GetBinContent(h1->GetXaxis()->FindBin(0.5*(max+min)));
-  else
-    mypar[4]=ampl;
-
-  if (cs_slope==-1)
-    mypar[5]=0;
-  else
-    mypar[5]=cs_slope;
- 
-  fun->SetParameters(mypar);
-
-  fun->SetRange(min,max);
-
-}
-
-
-TF1* energyCalibration::fitFunction(TF1 *fun, TH1 *h1, Double_t *mypar, Double_t *emypar) {
-
-
-  TF1* fitfun;
-
-  char fname[100];
-
-  strcpy(fname, fun->GetName());
-
-  if (plot_flag) {
-    h1->Fit(fname,"R0Q");
-  } else
-    h1->Fit(fname,"R0Q");
-
-
-  fitfun= h1->GetFunction(fname);
-  fitfun->GetParameters(mypar);
-  for (int ip=0; ip<6; ip++) {
-    emypar[ip]=fitfun->GetParError(ip);
-  }
-  return fitfun;
-}
-
-TF1* energyCalibration::fitSCurve(TH1 *h1, Double_t *mypar, Double_t *emypar) {
-  initFitFunction(fscurve,h1);
-  return fitFunction(fscurve, h1, mypar, emypar);
-}
-
-
-
-
-
-TF1* energyCalibration::fitSpectrum(TH1 *h1, Double_t *mypar, Double_t *emypar) {
-  initFitFunction(fspectrum,h1);
-  return fitFunction(fspectrum, h1, mypar, emypar);
-}
-
-
-
-TF1* energyCalibration::fitSpectrumPixel(TH1 *h1, Double_t *mypar, Double_t *emypar) {
-  initFitFunction(fspixel,h1);
-  return fitFunction(fspixel, h1, mypar, emypar);
-}
-
-
-
-TGraphErrors* energyCalibration::linearCalibration(int nscan, Double_t *en, Double_t *een, Double_t *fl, Double_t *efl, Double_t &gain, Double_t &off, Double_t &egain, Double_t &eoff) { 
- 
-  TGraphErrors *gr;
- 
-  Double_t  mypar[2];
- 
-  gr = new TGraphErrors(nscan,en,fl,een,efl);
-
-  if (plot_flag) {
-    gr->Fit("pol1");
-    gr->SetMarkerStyle(20);
-  } else
-    gr->Fit("pol1","0Q");
-        
-  TF1 *fitfun= gr->GetFunction("pol1"); 
-  fitfun->GetParameters(mypar);
-
-  egain=fitfun->GetParError(1);
-  eoff=fitfun->GetParError(0);
-
-  gain=funcs->setScanSign()*mypar[1];
-  
-  off=mypar[0]; 
-  
-  return gr;
-}
-
-
-TGraphErrors* energyCalibration::calibrate(int nscan, Double_t *en, Double_t *een, TH1F **h1, Double_t &gain, Double_t &off, Double_t &egain, Double_t &eoff, int integral) {
-
-  TH1F *h;
-
-  Double_t mypar[6], emypar[6];
-  Double_t fl[nscan], efl[nscan];
-  
-
-  for (int ien=0; ien<nscan; ien++) {
-    h=h1[ien];
-    if (integral)
-      fitSCurve(h,mypar,emypar);
-    else
-      fitSpectrum(h,mypar,emypar);
-
-    fl[ien]=mypar[2];
-    efl[ien]=emypar[2];
-  }
-  return linearCalibration(nscan,en,een,fl,efl,gain,off, egain, eoff);
-
-}
-
-#endif
-
-
-
-

slsDetectorCalibration/ghostSummation.h

@@ -0,0 +1,65 @@
+#ifndef GHOSTSUMMATION_H
+#define GHOSTSUMMATION_H
+
+#include <cmath>
+#include "slsDetectorData.h"
+
+template <class dataType> class ghostSummation {
+
+  /** @short virtual calss to handle ghosting*/ 
+
+ public:
+  
+  /** constructor
+      \param xt crosstalk
+  */
+  ghostSummation(slsDetectorData<dataType> *d, double xt) : xtalk(xt),det(d), nx(1), ny(1)  {
+    if (det)
+      det->getDetectorSize(nx,ny);
+    ghost=new double[nx*ny];
+  };
+
+  ghostSummation(ghostSummation *orig) {
+    xtalk=orig->xtalk; 
+    det=orig->det;
+    nx=1;
+    ny=1;
+    det->getDetectorSize(nx,ny);
+    ghost=new double[nx*ny];
+    
+  }
+  ~ghostSummation() {delete [] ghost;};
+
+  virtual ghostSummation *Clone() {
+    return new ghostSummation(this);
+  }
+
+  double getXTalk(){return xtalk;};
+  void setXTalk(double g) {xtalk=g;};
+
+  virtual double calcGhost(char *data, int ix, int iy=1){ghost[iy*nx+ix]=0; return 0;};
+
+  virtual void calcGhost(char *data){
+    for (int iy=0; iy<ny; iy++)
+      for (int ix=0; ix<nx; ix++)
+	ghost[iy*nx+ix]=calcGhost(data, ix, iy);
+  }
+
+  virtual double getGhost(int ix, int iy) {
+    if (ix<0 || ix>=nx || iy<0 || iy>=ny) return 0;
+    return ghost[iy*nx+ix];
+  }
+
+ protected:
+    double xtalk;
+    slsDetectorData<dataType> *det;
+    double *ghost;
+    int nx, ny;
+
+};
+
+
+
+
+
+#endif

slsDetectorCalibration/gotthardDoubleModuleCommonModeSubtractionNew.h

@@ -1,30 +0,0 @@
-#ifndef GOTTHARDDOUBLECOMMONMODESUBTRACTION_H
-#define GOTTHARDDOUBLECOMMONMODESUBTRACTION_H
-
-
-#include "commonModeSubtractionNew.h"
-
-class gotthardDoubleModuleCommonModeSubtraction : public commonModeSubtraction {
-
-  /** @short class to calculate the common mode of the pedestals based on an approximated moving average*/ 
-
- public:
-  
-  /** constructor
-      \param nn number of samples for the moving average to calculate the average common mode
-      \param iroi number of regions on which one can calculate the common mode separately. Defaults to 1 i.e. whole detector
-
-  */
- gotthardDoubleModuleCommonModeSubtraction(int ns=3) : commonModeSubtraction(2, ns) {};
-
-    /** 
-	gets the common mode ROI for pixel ix, iy 
-     */
-  virtual int getROI(int ix, int iy){return ix%2;};
-
-
-};
-
-
-
-#endif

slsDetectorCalibration/gotthardExecutables/Makefile.onTheFly

@@ -1,22 +0,0 @@
-
-CBFLIBDIR=/afs/psi.ch/project/sls_det_software/CBFlib-0.9.5
-LIBRARYCBF=$(CBFLIBDIR)/lib/*.o ../tiffIO.cpp
-ZMQLIB=../../slsReceiverSoftware/include
-INCDIR=-I.. -I../../slsReceiverSoftware/include -I$(CBFLIBDIR)/include/ -I. -I../interpolations  -I../dataStructures
-LIBHDF5=-L$(CBFLIBDIR)/lib/ -lhdf5
-LDFLAG= -L/usr/lib64/ -lpthread
-#-L../../bin 
-MAIN=gotthard25umZmqAnalysis.C
-
-#DESTDIR?=../bin
-
-all: gotthard25umOnTheFlyAnalysis gotthard25umZmq
-
-gotthard25umOnTheFlyAnalysis:  $(MAIN)  $(INCS) clean
-			   g++ -o gotthard25umOnTheAnalysis  $(MAIN)  -lm -ltiff -lstdc++ $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) 
-
-gotthard25umZmq:  $(MAIN)  $(INCS) clean
-			   g++ -o gotthard25umZmq  $(MAIN)  -lm -ltiff -lstdc++ $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DZMQ  -L$(ZMQLIB) -lzmq
-
-clean:
-	rm -f gotthard25umOnTheFlyAnalysis

slsDetectorCalibration/gotthardExecutables/bchip2modules_pc8829.config

@@ -0,0 +1,40 @@
+detsizechan 2560 1
+
+hostname bchip074+bchip075+
+#hostname bchip092+bchip093+
+
+settingsdir settingsdir/gotthard
+angdir 1.000000
+caldir settingsdir/gotthard
+
+0:extsig:0 trigger_in_rising_edge
+0:rx_tcpport 1954
+0:rx_udpport 50001
+0:vhighvoltage 0
+
+#0:rx_zmqip pc8829
+#0:rx_zmqport 30003
+#0:zmqip pc8829
+#0:zmqport  40003
+
+1:extsig:0 trigger_in_rising_edge
+1:rx_tcpport 1955
+1:rx_udpport 50002
+#1:detectorip 10.1.1.52
+1:vhighvoltage 0
+
+#1:rx_zmqip pc8829
+#1:rx_zmqport 30004
+#1:zmqip pc8829
+#1:zmqport  40004
+
+
+r_readfreq 1
+rx_datastream 1
+
+#rx_udpip 10.1.1.100
+rx_hostname pc8498
+rx_datastream 1
+outdir /tmp/
+angconv none
+threaded 1

slsDetectorCalibration/gotthardExecutables/gotthard25umZmqAnalysis.C

@@ -1,517 +0,0 @@
-#include "sls_receiver_defs.h"
-//#ifdef ZMQ
-#include "ZmqSocket.h"
-//#endif
-#include <vector>
-#include <string>
-#include <sstream>
-#include <iomanip>
-#include <fstream>
-#include <stdio.h>
-//#include <deque>
-//#include <list>
-//#include <queue>
-#include <fstream>
-#include <cstring>
-
-//#define BCHIP074_BCHIP075
-
-#include "gotthardModuleDataNew.h"
-#include "gotthardDoubleModuleDataNew.h"
-#include "gotthardDoubleModuleCommonModeSubtractionNew.h"
-
-#include "singlePhotonDetector.h"
-//#include "interpolatingDetector.h"
-//#include "linearInterpolation.h"
-#include "multiThreadedAnalogDetector.h"
-
-#include <ctime>
-
-#define NC 1280
-#define NR 1
-
-//#include "tiffIO.h"
-
-
-
-
-
-#define SLS_DETECTOR_JSON_HEADER_VERSION 0x2
-int main(int argc, char *argv[]){
-  //void *gotthardProcessFrame() {
-
-
-
-  int fifosize=1000;
-  int nthreads=1;
-  int nph, nph1;
-  int etabins=550;
-  double etamin=-1, etamax=2;
-  int nsubpix=1;
-  float *etah=new float[etabins*etabins];
-  int *heta, *himage;
-  int offset=48;
-  #ifdef ZMQ
-  offset=0;
-  #endif
-  #ifndef ZMQ
-  offset=48;
-  #endif
- 
-  //commonModeSubtraction *cm=NULL;
-
-  gotthardDoubleModuleCommonModeSubtraction *cm=new gotthardDoubleModuleCommonModeSubtraction();
-  gotthardModuleDataNew *decoder=new   gotthardModuleDataNew();
-  gotthardDoubleModuleDataNew *det=new   gotthardDoubleModuleDataNew(offset);
-  singlePhotonDetector *filter=new singlePhotonDetector(det,3, 5, 1, cm, 1000, 100);
-  // analogDetector<uint16_t> *filter=new analogDetector<uint16_t>(det, 1, cm, 1000);
-  // analogDetector<uint16_t> *filter_nocm=new analogDetector<uint16_t>(det, 1, NULL, 1000);
-  filter->setROI(0,2560,0,1);
-  char *buff;//[2*(48+1280*2)];
-  char *buff0;
-  char *buff1;
-  multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
-  mt->setFrameMode(eFrame);
-  // mt->setFrameMode(eFrame);
-  // mt->setFrameMode(ePedestal);
-  mt->StartThreads();
-  mt->popFree(buff);
-  buff0=buff;
-  buff1=buff+offset*2+1280*2;
-  int photons[1280*2];
-  int nf=0;
-  int ok=0;
-  std::time_t end_time;
-  //int16_t dout[1280*2];
-  int iFrame=-1;
-  int np=-1;
-  nph=0;
-  nph1=0;
-  //int np;
-  int iph;
-  int data_ready=1;
-  int *image;
-
-
-
-	int length;
-	int nnx, nny,nns;
-	int nix, niy,nis;
-	// infinite loop
-	int ix, iy, isx, isy;
-
-  filter->getImageSize(nnx, nny,nns);
-  int16_t *dout=new int16_t [nnx*nny];
-
-
-
-#ifdef ZMQ
-	if (argc < 3 ) {
-	  cprintf(RED, "Help: %s [receive socket ip] [receive starting port number] [send_socket ip] [send starting port number]\n",argv[0]);
-		return EXIT_FAILURE;
-	}
-
-	// receive parameters
-	bool send = false;
-	  char* socketip=argv[1];
-	uint32_t portnum = atoi(argv[2]);
-	int size = nnx*nny*2;
-
-	// send parameters if any
-	char* socketip2 = 0;
-	uint32_t portnum2 = 0;
-	if (argc > 3) {
-		send = true;
-		socketip2 = argv[3];
-		portnum2 = atoi(argv[4]);
-	}
-	cout << "\nrx socket ip : " << socketip <<
-	  "\nrx port num  : " <<  portnum ;
-	if (send) {
-	  cout << "\nsd socket ip : " << socketip2 <<
-	    "\nsd port num  : " <<  portnum2;
-	}
-	cout << endl;
-
-
-
-	// receive socket
-	  ZmqSocket* zmqsocket0 = new ZmqSocket(socketip,portnum); 
-	if (zmqsocket0->IsError()) {
-	  cprintf(RED, "Error: Could not create Zmq socket on port %d with ip %s\n", portnum, socketip);
-	  delete zmqsocket0;
-	  return EXIT_FAILURE;
-	}
-
-	  ZmqSocket* zmqsocket1 = new ZmqSocket(socketip,portnum+1); 
-	if (zmqsocket1->IsError()) {
-	  cprintf(RED, "Error: Could not create Zmq socket on port %d with ip %s\n", portnum+1, socketip);
-	  delete zmqsocket1;
-	  delete zmqsocket0;
-	  return EXIT_FAILURE;
-	}
-
-
-	zmqsocket0->Connect();
-	printf("Zmq Client 0 at %s\n", zmqsocket0->GetZmqServerAddress());
-	zmqsocket1->Connect();
-	printf("Zmq Client 1 at %s\n", zmqsocket1->GetZmqServerAddress());
-
-	// send socket
-	ZmqSocket* zmqsocket2 = 0;
-	ZmqSocket* zmqsocket3 = 0;
-	if (send) {
-	  zmqsocket2 = new ZmqSocket(portnum2, socketip2);
-	  if (zmqsocket2->IsError()) {
-	    bprintf(RED, "Error: Could not create Zmq socket server on port %d and ip %s\n",  portnum2, socketip2);
-	    delete zmqsocket2;
-	    delete zmqsocket1;
-	    delete zmqsocket0;
-	    return EXIT_FAILURE;
-	  }
-	  
-	  zmqsocket3 = new ZmqSocket(portnum2+1, socketip2);
-	  if (zmqsocket3->IsError()) {
-	    bprintf(RED, "Error: Could not create Zmq socket server on port %d and ip %s\n",  portnum2+1, socketip2);
-	    delete zmqsocket3;
-	    delete zmqsocket2;
-	    delete zmqsocket1;
-	    delete zmqsocket0;
-	    return EXIT_FAILURE;
-	  }
-	  
-	  zmqsocket2->Connect();
-	  printf("Zmq Server 0 started at %s\n", zmqsocket2->GetZmqServerAddress());
-	  zmqsocket3->Connect();
-	  printf("Zmq Server 1 started at %s\n", zmqsocket3->GetZmqServerAddress());
-	}
-
-
-
-
-
-
-
-	uint64_t acqIndex1 = -1;
-	uint64_t frameIndex1 = -1;
-	uint32_t subframeIndex1 = -1;
-	uint64_t fileindex1 = -1;
-	string filename1 = "";
-
-	uint64_t acqIndex0 = -1;
-	uint64_t frameIndex0 = -1;
-	uint32_t subframeIndex0 = -1;
-	uint64_t fileindex0 = -1;
-	string filename0 = "";
-
-
-	int eoa0=0;
-	int eoa1=0;
-
-
-
-
-
-  #endif
-
-
-
-
-
-
-
-
-
-
-
-
-	char ofname[10000];
-	char fn0[10000], fn1[10000];
-	FILE *fout=NULL;
-	FILE *fclust=NULL;
-	for (int i=0; i<nnx; i++)
-	  dout[i]=0;
-	char fname0[10000], fname1[10000];
-	int irun;
-
-#ifndef ZMQ
-
-	char ff[10000];
-  if (argc < 6 ) {
-    cprintf(RED, "Help: %s [indir] [fformat] [runmin] [runmax] [out file format]\n",argv[0]);
-    return EXIT_FAILURE;
-  }
-  char *indir=argv[1];
-  char *fformat=argv[2];
-  int runmin=atoi(argv[3]);
-  int runmax=atoi(argv[4]);
-  char *outdir=argv[5];
-  sprintf(ff,"%s/%s",indir,fformat);
-  // strcpy(fformat,"/external_pool/gotthard_data/datadir_gotthardI/bchip074075/20170731/Xray/xray_15kV_200uA_5us_d%d_f000000000000_0.raw");
-  // sprintf(fname0,fformat,0,0);
-  // sprintf(fname1,fformat,1,1);
-  
-  ifstream filebin0,filebin1;
-  for (irun=runmin; irun<runmax; irun++) {
-
-    sprintf(fname0,ff,0,irun);
-    sprintf(fname1,ff,1,irun);
-    sprintf(ofname,outdir,irun);
-
-    filebin0.open((const char *)(fname0), ios::in | ios::binary);
-    filebin1.open((const char *)(fname1), ios::in | ios::binary);
-    if (filebin0.is_open() && filebin1.is_open()) {
-      cout << "Opened file " << fname0<< endl;
-      cout << "Opened file " << fname1<< endl;
-      nf=0;
-      iFrame=-1;
-      while ((decoder->readNextFrame(filebin0, iFrame, np, buff0)) && (decoder->readNextFrame(filebin1, iFrame, np, buff1))) {
-#endif
-
-
-
-
-
-#ifdef ZMQ
-
-	int end_of_acquisition;
-	while(1) {
-	  end_of_acquisition=0;
-	  eoa0=0;
-	  eoa1=0;
-	  
-	  //  cout << "Receive header " << nf << endl;
-	  if (!zmqsocket0->ReceiveHeader(0, acqIndex0, frameIndex0, subframeIndex0, filename0, fileindex0)) {
-	    
-	    //   cout << "************************************************************************** packet0!*****************************"<< endl;
-	    eoa0=1;
-	    end_of_acquisition++;
-	  } 
-	  if (!zmqsocket1->ReceiveHeader(0, acqIndex1, frameIndex1, subframeIndex1, filename1, fileindex1)) {
-	    //cout << "************************************************************************** packet1!*****************************"<< endl;
-	    eoa1=1;
-	    end_of_acquisition++;
-	  }
-
-
-
-
-
-	  //	  if ((!zmqsocket0->ReceiveHeader(0, acqIndex0, frameIndex0, subframeIndex0, filename0, fileindex0)) && (!zmqsocket1->ReceiveHeader(0, acqIndex1, frameIndex1, subframeIndex1, filename1, fileindex1))){
-	  if (end_of_acquisition==0) {
-	    
-	    if (acqIndex0!=acqIndex1)
-	      cout << "different acquisition indexes " << acqIndex0 << " and " << acqIndex1 << endl;
-	    if (frameIndex0!=frameIndex1)
-	      cout << "different frame indexes " << frameIndex0 << " and " << frameIndex1 << endl;
-	    
-	    
-	    while (frameIndex0<frameIndex1) {
-	      cout << "aligning det 0 " << endl; 
-	      length = zmqsocket0->ReceiveData(0, buff0, size/2);
-	      if (!zmqsocket0->ReceiveHeader(0, acqIndex0, frameIndex0, subframeIndex0, filename0, fileindex0)) {
-		end_of_acquisition++;
-		eoa0=1;
-		break;
-	      } 
-	    }
-	    
-	    while (frameIndex1<frameIndex0) {
-	      cout << "aligning det 1 " << endl; 
-	      length = zmqsocket1->ReceiveData(0, buff1, size/2);
-	      if (!zmqsocket1->ReceiveHeader(0, acqIndex1, frameIndex1, subframeIndex1, filename1, fileindex1)) {
-		end_of_acquisition++;
-		eoa1=1;
-		break;
-	      } 
-	    }
-	  }
-
-
-
-	  if (eoa0!=eoa1) {
-
-	    while (eoa0<1) {
-	      length = zmqsocket0->ReceiveData(0, buff0, size/2);
-	      if (!zmqsocket0->ReceiveHeader(0, acqIndex0, frameIndex0, subframeIndex0, filename0, fileindex0)) {
-		end_of_acquisition++;
-		eoa0=1;
-	      }
-	    }
-
-
-	    while (eoa1<1) {
-	      length = zmqsocket1->ReceiveData(0, buff1, size/2);
-	      if (!zmqsocket1->ReceiveHeader(0, acqIndex1, frameIndex1, subframeIndex1, filename1, fileindex1)) {
-		end_of_acquisition++;
-		eoa1=1;
-	      }
-	    }
-	  }
-
-	  
-
-
-
-	  
-	  if (end_of_acquisition) {
-	    // cout << "************************************************************************** END OF FRAME" << end_of_acquisition << " !*****************************"<< endl;
-	    //  return 0;
-	    
-	    sprintf(ofname,"%s_%d.ph",fn0,irun);
-	    while (mt->isBusy()) {;}
-	    image=filter->getImage();
-	    if (image) {
-	      fout=fopen(ofname,"w");
-	      cout << nf << "*****************" << endl;
-	      for (int i=0; i<2560; i++) {
-		fprintf(fout,"%d %d\n",i,image[i]);
-		dout[i]=image[i];
-		if (dout[i]<0)
-		   dout[i]=0;
-	      }
-	      fclose(fout);
-	    }
-	    
-
-	    if (send) {
-	      
-	      zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fn0, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
-	      zmqsocket3->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fn1, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
-	      
-	      zmqsocket2->SendData((char*)dout,size/2);
-	      zmqsocket3->SendData(((char*)dout)+size/2,size/2);
-	      //    	//	cprintf(GREEN, "Sent Data\n");
-
-	      
-	      zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-	      zmqsocket3->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-	    }
-	    
-	    
-	    //mt->setFrameMode(eFrame);
-	    filter->clearImage();
-	    // std::time(&end_time);
-	    // cout << std::ctime(&end_time) << " " << nf <<   endl;
-	    fclose(fclust);
-	    fclust=NULL;
-	    
-	    
-	    
-	    continue; 
-	  }
-	  
-	  if (fclust==NULL) {
-
-	    strcpy(fn0,filename0.c_str());
-	    strcpy(fn1,filename1.c_str());
-	    sprintf(ofname,"%s_%d.clust",fn0,irun);
-	    fclust=fopen(ofname,"w");
-	    while (mt->isBusy()) {;}
-	    mt->setFilePointer(fclust);
-	  }
-
-	  // strcpy(fn0,filename0.c_str());
-	  // strcpy(fn1,filename1.c_str());
-	  
-	  //	  cout << "Receive data " << nf << endl;
-	  length = zmqsocket0->ReceiveData(0, buff0, size/2);
-	  length += zmqsocket1->ReceiveData(0, buff1, size/2);  
-	  
-	  irun=fileindex0;
-	  
-	  
-	    
-	    // //  if (nf>100)
-	    // //  mt->setFrameMode(eFrame);
-	    // //filter->clearImage();
-
-
-#endif
-
-
-	mt->pushData(buff);
-	mt->nextThread();
-	// cout << "==" << nf << endl;
-
-	    // while (mt->isBusy()) {;}
-	    // image=filter->getImage();
-	    // if (image) {
-	    //   for (int i=0; i<2560; i++) {
-	    // 	//	if (i<512)
-	
-	    // 	//  	fprintf(fout,"%d %d\n",i,image[i]);
-	    //   	dout[i]=filter->subtractPedestal(buff,i,0,1);//image[i];//filter->getPedestal(i,0);//
-	    // 	if (dout[i]<0)
-	    // 	   dout[i]=0;
-	    // 	//	cout << i << " " << image[i] << " " << dout[i] << endl;
-	    //   }
-	    // }
-
-
-	    // if (send) {
-	    // 	strcpy(fname0,filename0.c_str());
-	    // 	strcpy(fname1,filename1.c_str());
-	    // 	//  zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,16,fileindex,400,400,400*400, acqIndex,frameIndex,fname, acqIndex, 0,0,0,0,0,0,0,0,0,0,0,1);
-	    // 	zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fname0, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
-	    // 	zmqsocket3->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fname1, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
-		
-	    // 	zmqsocket2->SendData((char*)dout,size/2);
-	    // 	zmqsocket3->SendData(((char*)dout)+size/2,size/2);
-	    // 	//	cprintf(GREEN, "Sent Data\n");
-
-
-	    // 	// zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-	    // 	// zmqsocket3->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-
-	    // 	//	cprintf(RED, "Received %d frames\n", nf);
-
-	    // }
-	    
-
-	mt->popFree(buff);
-	buff0=buff;
-	buff1=buff+offset*2+1280*2;
-	  
-
-
-	nf++;
-	
-
-
-
-#ifndef ZMQ
-
-
-	 
-
-	  while (mt->isBusy()) {;}
-	  image=filter->getImage();
-	  if (image) {
-	      fout=fopen(ofname,"w");
-	      //cout << nf << "*****************" << endl;
-	      for (int i=0; i<512; i++) {
-		fprintf(fout,"%d %d\n",i,image[i]);
-	      }
-	      fclose(fout);
-	  }
-	  filter->clearImage();
-      
-
-
-	  iFrame=-1;
-      }
-      
-      filebin0.close();
-      filebin1.close();
-    }
-    else
-      cout << "Could not open file " << fname0<< " or " << fname1 <<  endl;
-#endif
-
-    }
-  return NULL;
-
-
-
-}

slsDetectorCalibration/gotthardExecutables/howto_gotthatd_twomodules.txt

@@ -0,0 +1,14 @@
+slsReceiver --rx_tcpport 1954 &
+slsReceiver --rx_tcpport 1955 &
+
+./gotthard25umZmq pc8829 30003 129.129.202.98 40003 &
+slsDetectorGui -f examples/bchip2modules_pc8829.config &
+
+
+sls_detector_put settings veryhighgain
+sls_detector_put exptime 0.000005
+sls_detector_put period 0.01
+
+
+sls_detector_put vhighvoltage 90
+

slsDetectorCalibration/interpolatingDetector.h

@@ -46,11 +46,16 @@ class interpolatingDetector : public singlePhotonDetector {
 		       int sign=1, 
 		       commonModeSubtraction *cm=NULL,
 		       int nped=1000, 
-		       int nd=100, int nnx=-1, int nny=-1) : 
-  singlePhotonDetector(d, 3,nsigma,sign, cm, nped, nd, nnx, nny) , interp(inte), id(0)  {
+		       int nd=100, int nnx=-1, int nny=-1, double *gm=NULL, ghostSummation<uint16_t> *gs=NULL) : 
+  singlePhotonDetector(d, 3,nsigma,sign, cm, nped, nd, nnx, nny, gm, gs) , interp(inte), id(0)  {
     //cout << "**"<< xmin << " " << xmax << " " << ymin << " " << ymax << endl;
     fi=new pthread_mutex_t ;
+    
 
+    if (pthread_mutex_init(fi, NULL) != 0)
+    {
+        printf("\n mutex init failed\n");
+    }
 };
   
   
@@ -107,11 +112,11 @@ class interpolatingDetector : public singlePhotonDetector {
       singlePhotonDetector::clearImage();
   };
 
-  int getImageSize(int &nnx, int &nny, int &ns) {
+  int getImageSize(int &nnx, int &nny, int &nsx, int &nsy) {
     if (interp) 
-      return interp->getImageSize(nnx, nny, ns); 
+      return interp->getImageSize(nnx, nny, nsx, nsy); 
     else 
-      return analogDetector<uint16_t>::getImageSize(nnx, nny, ns);
+      return analogDetector<uint16_t>::getImageSize(nnx, nny, nsx, nsy);
   };
 
 
@@ -139,8 +144,8 @@ class interpolatingDetector : public singlePhotonDetector {
     nph=addFrame(data,val,0); 
     if (interp)
       return interp->getInterpolatedImage();
-    else
-      singlePhotonDetector::getImage();
+    //else
+    return singlePhotonDetector::getImage();
       //return NULL;
   };
   
@@ -233,7 +238,7 @@ int addFrame(char *data,  int *ph=NULL, int ff=0) {
     };
     
     virtual slsInterpolation *setInterpolation(slsInterpolation *ii){
-      int ok; 
+      // int ok; 
       interp=ii; 
       /*  pthread_mutex_lock(fi);
       if (interp)
@@ -251,6 +256,7 @@ int addFrame(char *data,  int *ph=NULL, int ff=0) {
     }
 
     virtual int getNSubPixels(){ if (interp) return interp->getNSubPixels(); else return 1;}
+
     virtual int setNSubPixels(int ns)  { 
       if (interp) {
 	pthread_mutex_lock(fi); 

slsDetectorCalibration/interpolations/eta2InterpolationBase.h

@@ -13,7 +13,7 @@
 class eta2InterpolationBase : public virtual etaInterpolationBase {
   
  public:
- eta2InterpolationBase(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) :  etaInterpolationBase(nx,ny, ns, nb, emin, emax) {
+ eta2InterpolationBase(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) :  etaInterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax) {
     
     /* if (etamin>=etamax) { */
     /*   etamin=-1; */
@@ -33,11 +33,11 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
   {
     double sDum[2][2];
     double tot, totquad;
-    double etax,etay;
+    double etax=0,etay=0;
     
     int corner;
     corner=calcQuad(data, tot, totquad, sDum); 
-    if (nSubPixels>2) 
+    if (nSubPixelsX>2 || nSubPixelsY>2) 
       calcEta(totquad, sDum, etax, etay); 
     getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
 
@@ -49,11 +49,11 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
   {
     double sDum[2][2];
     double tot, totquad;
-    double etax,etay;
+    double etax=0,etay=0;
     
     int corner;
     corner=calcQuad(data, tot, totquad, sDum); 
-    if (nSubPixels>2) 
+    if (nSubPixelsX>2 || nSubPixelsY>2  ) 
       calcEta(totquad, sDum, etax, etay); 
     getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
 
@@ -71,7 +71,7 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
   virtual void getInterpolatedPosition(int x, int y, double totquad,int quad,double *cl,double &int_x, double &int_y) {
     
      double cc[2][2];
-     int xoff, yoff;
+     int xoff=0, yoff=0;
      switch (quad) {
      case BOTTOM_LEFT:
        xoff=0;
@@ -92,14 +92,15 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
      default:
        ;
      } 
-     double etax, etay;
-     if (nSubPixels>2) { 
+     double etax=0, etay=0;
+     if (nSubPixelsX>2 || nSubPixelsY>2) { 
        cc[0][0]=cl[xoff+3*yoff];
        cc[1][0]=cl[xoff+3*(yoff+1)];
        cc[0][1]=cl[xoff+1+3*yoff];
        cc[1][1]=cl[xoff+1+3*(yoff+1)];
        calcEta(totquad,cc,etax,etay);
      }
+     
      return getInterpolatedPosition(x,y,etax, etay,quad,int_x,int_y);
 
   }
@@ -109,7 +110,7 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
   virtual void getInterpolatedPosition(int x, int y, double totquad,int quad,int *cl,double &int_x, double &int_y) {
     
      double cc[2][2];
-     int xoff, yoff;
+     int xoff=0, yoff=0;
      
      switch (quad) {
      case BOTTOM_LEFT:
@@ -131,8 +132,8 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
      default:
        ;
      } 
-     double etax, etay;
-     if (nSubPixels>2) { 
+     double etax=0, etay=0;
+     if (nSubPixelsX>2 || nSubPixelsY>2) { 
        cc[0][0]=cl[xoff+3*yoff];
        cc[1][0]=cl[xoff+3*(yoff+1)];
        cc[0][1]=cl[xoff+1+3*yoff];
@@ -181,31 +182,31 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
       }
     
 
-     if (nSubPixels>2) { 
+     if (nSubPixelsX>2 || nSubPixelsY>2 ) { 
 
-       ex=(etax-etamin)/etastep;
-       ey=(etay-etamin)/etastep;
+       ex=(etax-etamin)/etastepX;
+       ey=(etay-etamin)/etastepY;
        if (ex<0) {
 	 cout << "x*"<< ex << endl;
 	 ex=0;
        } 
-       if (ex>=nbeta) {
+       if (ex>=nbetaX) {
 	 cout << "x?"<< ex << endl;
-	 ex=nbeta-1;
+	 ex=nbetaX-1;
        }
        if (ey<0) {
-	 cout << "y*"<< ey << endl;
+	 cout << "y*"<< ey << " " << nbetaY << endl;
 	 ey=0;
        } 
-       if (ey>=nbeta) {
-	 cout << "y?"<< ey << endl;
-	 ey=nbeta-1;
+       if (ey>=nbetaY) {
+	 cout << "y?"<< ey << " " << nbetaY << endl;
+	 ey=nbetaY-1;
        }
     
     
    
-       xpos_eta=(((double)hhx[(ey*nbeta+ex)]))+dX ;///((double)nSubPixels);
-       ypos_eta=(((double)hhy[(ey*nbeta+ex)]))+dY ;///((double)nSubPixels);
+       xpos_eta=(((double)hhx[(ey*nbetaX+ex)]))+dX ;///((double)nSubPixels);
+       ypos_eta=(((double)hhy[(ey*nbetaX+ex)]))+dY ;///((double)nSubPixels);
        
      } else {
        xpos_eta=0.5*dX+0.25;
@@ -222,7 +223,7 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
   
   virtual int addToFlatField(double totquad,int quad,int *cl,double &etax, double &etay) {
      double cc[2][2];
-     int xoff, yoff;
+     int xoff=0, yoff=0;
      
      switch (quad) {
      case BOTTOM_LEFT:
@@ -260,7 +261,7 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
 
    virtual int addToFlatField(double totquad,int quad,double *cl,double &etax, double &etay) {
      double cc[2][2];
-     int xoff, yoff;
+     int xoff=0, yoff=0;
      
      switch (quad) {
      case BOTTOM_LEFT:
@@ -308,11 +309,12 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
   virtual int addToFlatField(double *cluster, double &etax, double &etay){
     double sDum[2][2];
     double tot, totquad;
-    int corner;
-    corner=calcQuad(cluster, tot, totquad, sDum); 
+    // int corner;
+    //corner=
+    calcQuad(cluster, tot, totquad, sDum); 
     
-    double xpos_eta,ypos_eta;
-    double dX,dY;
+    //double xpos_eta,ypos_eta;
+    //double dX,dY;
   
     
     calcEta(totquad, sDum, etax, etay); 
@@ -324,11 +326,12 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
   virtual int addToFlatField(int *cluster, double &etax, double &etay){
     double sDum[2][2];
     double tot, totquad;
-    int corner;
-    corner=calcQuad(cluster, tot, totquad, sDum); 
+    //int corner;
+    //corner=
+    calcQuad(cluster, tot, totquad, sDum); 
     
-    double xpos_eta,ypos_eta;
-    double dX,dY;
+    // double xpos_eta,ypos_eta;
+    //double dX,dY;
   
     
     calcEta(totquad, sDum, etax, etay); 
@@ -344,10 +347,10 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
 #endif
 #ifndef MYROOT1
     int ex,ey; 
-    ex=(etax-etamin)/etastep;
-    ey=(etay-etamin)/etastep;
-    if (ey<nbeta && ex<nbeta && ex>=0 && ey>=0)
-      heta[ey*nbeta+ex]++; 
+    ex=(etax-etamin)/etastepX;
+    ey=(etay-etamin)/etastepY;
+    if (ey<nbetaY && ex<nbetaX && ex>=0 && ey>=0)
+      heta[ey*nbetaX+ex]++; 
 #endif
     return 0;    
   };
@@ -357,22 +360,22 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
    // cout << "ff" << endl;
    calcDiff(1, hhx, hhy); //get flat
    double avg=0;
-   for (ipx=0; ipx<nSubPixels; ipx++)
-     for (ipy=0; ipy<nSubPixels; ipy++)
-       avg+=flat[ipx+ipy*nSubPixels];
-   avg/=nSubPixels*nSubPixels;
+   for (ipx=0; ipx<nSubPixelsX; ipx++)
+     for (ipy=0; ipy<nSubPixelsY; ipy++)
+       avg+=flat[ipx+ipy*nSubPixelsX];
+   avg/=nSubPixelsY*nSubPixelsX;
 
-   for (int ibx=0 ; ibx<nSubPixels*nPixelsX; ibx++) {
-     ipx=ibx%nSubPixels-nSubPixels/2;
-       if (ipx<0) ipx=nSubPixels+ipx;
-     for (int iby=0 ; iby<nSubPixels*nPixelsY; iby++) {
-       ipy=iby%nSubPixels-nSubPixels/2;
-     if (ipy<0) ipy=nSubPixels+ipy;
+   for (int ibx=0 ; ibx<nSubPixelsX*nPixelsX; ibx++) {
+     ipx=ibx%nSubPixelsX-nSubPixelsX/2;
+       if (ipx<0) ipx=nSubPixelsX+ipx;
+     for (int iby=0 ; iby<nSubPixelsY*nPixelsY; iby++) {
+       ipy=iby%nSubPixelsY-nSubPixelsY/2;
+     if (ipy<0) ipy=nSubPixelsY+ipy;
      // cout << ipx << " " << ipy << " " << ibx << " " << iby << endl;
-     if (flat[ipx+ipy*nSubPixels]>0)
-       hintcorr[ibx+iby*nSubPixels*nPixelsX]=hint[ibx+iby*nSubPixels*nPixelsX]*(avg/flat[ipx+ipy*nSubPixels]);
+     if (flat[ipx+ipy*nSubPixelsX]>0)
+       hintcorr[ibx+iby*nSubPixelsX*nPixelsX]=hint[ibx+iby*nSubPixelsX*nPixelsX]*(avg/flat[ipx+ipy*nSubPixelsX]);
      else
-       hintcorr[ibx+iby*nSubPixels*nPixelsX]=hint[ibx+iby*nSubPixels*nPixelsX];
+       hintcorr[ibx+iby*nSubPixelsX*nPixelsX]=hint[ibx+iby*nSubPixelsX*nPixelsX];
 
 
      }

slsDetectorCalibration/interpolations/eta3InterpolationBase.h

@@ -13,35 +13,12 @@
 class eta3InterpolationBase : public virtual etaInterpolationBase  {
   
  public:
- eta3InterpolationBase(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationBase(nx, ny, ns, nb, emin, emax) {
+ eta3InterpolationBase(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) : etaInterpolationBase(nx, ny, ns, nsy, nb, nby, emin, emax) {
     //  cout << "e3ib " << nb << " " << emin << " " << emax << endl; 
     /* if (nbeta<=0) { */
     /*   nbeta=nSubPixels*10;    */
     /* } */
-    if (etamin>=etamax) {
-      etamin=-1;
-      etamax=1; 
-    }
-    
-    etastep=(etamax-etamin)/nbeta;
-#ifdef MYROOT1
-    delete heta;
-    delete hhx;
-    delete hhy;
-    heta=new TH2D("heta","heta",nbeta,etamin,etamax,nbeta,etamin,etamax);
-    hhx=new TH2D("hhx","hhx",nbeta,etamin,etamax,nbeta,etamin,etamax);
-    hhy=new TH2D("hhy","hhy",nbeta,etamin,etamax,nbeta,etamin,etamax);
-#endif
-#ifndef MYROOT1
-    /* delete [] heta; */
-    /* delete [] hhx; */
-    /* delete [] hhy; */
-
-    /* heta=new int[nbeta*nbeta]; */
-    /* hhx=new float[nbeta*nbeta]; */
-    /* hhy=new float[nbeta*nbeta]; */
-    
-#endif
+  
     //   cout << nbeta << " " << etamin << " " << etamax << endl;
 };
   
@@ -59,10 +36,10 @@ class eta3InterpolationBase : public virtual etaInterpolationBase  {
   //////////// /*It return position hit for the event in input */ //////////////
   virtual void getInterpolatedPosition(int x, int y, int *data, double &int_x, double &int_y)
   {
-   double tot, totquad;
+   double tot;
     double etax,etay;
     
-    int corner=calcEta3(data,etax,etay, totquad);
+    int corner=calcEta3(data,etax,etay, tot);
     
     getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
 
@@ -72,11 +49,11 @@ class eta3InterpolationBase : public virtual etaInterpolationBase  {
 
   virtual void getInterpolatedPosition(int x, int y, double *data, double &int_x, double &int_y)
   {
-    double sDum[2][2];
-    double tot, totquad;
+    //double sDum[2][2];
+    double tot;
     double etax,etay;
     
-    int corner=calcEta3(data,etax,etay, totquad);
+    int corner=calcEta3(data,etax,etay, tot);
     
     getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
 
@@ -88,7 +65,7 @@ class eta3InterpolationBase : public virtual etaInterpolationBase  {
     
   
     double etax, etay;
-     if (nSubPixels>2) { 
+     if (nSubPixelsX>2 || nSubPixelsY>2 ) { 
        calcEta3(cl,etax,etay, totquad);
      } 
      return getInterpolatedPosition(x,y,etax, etay,quad,int_x,int_y);
@@ -101,7 +78,7 @@ class eta3InterpolationBase : public virtual etaInterpolationBase  {
     
     
      double etax, etay;
-     if (nSubPixels>2) { 
+     if (nSubPixelsX>2 || nSubPixelsY>2 ) { 
        calcEta3(cl,etax,etay, totquad);
      }
      return getInterpolatedPosition(x,y,etax, etay,quad,int_x,int_y);
@@ -117,38 +94,38 @@ class eta3InterpolationBase : public virtual etaInterpolationBase  {
     double xpos_eta=0,ypos_eta=0;
     int ex,ey;
 
-     if (nSubPixels>2) { 
+     if (nSubPixelsX>2 || nSubPixelsY>2 ) { 
 
 #ifdef MYROOT1
-    xpos_eta=(hhx->GetBinContent(hhx->GetXaxis()->FindBin(etax),hhy->GetYaxis()->FindBin(etay)))/((double)nSubPixels);
-    ypos_eta=(hhy->GetBinContent(hhx->GetXaxis()->FindBin(etax),hhy->GetYaxis()->FindBin(etay)))/((double)nSubPixels);
+    xpos_eta=(hhx->GetBinContent(hhx->GetXaxis()->FindBin(etax),hhy->GetYaxis()->FindBin(etay)))/((double)nSubPixelsX);
+    ypos_eta=(hhy->GetBinContent(hhx->GetXaxis()->FindBin(etax),hhy->GetYaxis()->FindBin(etay)))/((double)nSubPixelsY);
 #endif
 #ifndef MYROOT1
-    ex=(etax-etamin)/etastep;
-    ey=(etay-etamin)/etastep;
+    ex=(etax-etamin)/etastepX;
+    ey=(etay-etamin)/etastepY;
     if (ex<0) {
       /* cout << etax << " " << etamin << " "; */
       /*  cout << "3x*"<< ex << endl; */
       ex=0;
 	} 
-    if (ex>=nbeta) {
+    if (ex>=nbetaX) {
       /* cout << etax << " " << etamin << " "; */
       /* cout << "3x?"<< ex << endl; */
-      ex=nbeta-1;
+      ex=nbetaX-1;
     }
     if (ey<0) {
       /* cout << etay << " " << etamin << " "; */
       /* cout << "3y*"<< ey << endl; */
       ey=0;
 	} 
-    if (ey>=nbeta) {
+    if (ey>=nbetaY) {
       /* cout << etay << " " << etamin << " "; */
       /* cout << "3y?"<< ey << endl; */
-      ey=nbeta-1;
+      ey=nbetaY-1;
       
     }
-    xpos_eta=(((double)hhx[(ey*nbeta+ex)]));///((double)nSubPixels);
-    ypos_eta=(((double)hhy[(ey*nbeta+ex)]));///((double)nSubPixels);
+    xpos_eta=(((double)hhx[(ey*nbetaX+ex)]));///((double)nSubPixels);
+    ypos_eta=(((double)hhy[(ey*nbetaX+ex)]));///((double)nSubPixels);
 
 #endif
    
@@ -265,10 +242,10 @@ class eta3InterpolationBase : public virtual etaInterpolationBase  {
 #endif
 #ifndef MYROOT1
     int ex,ey; 
-    ex=(etax-etamin)/etastep;
-    ey=(etay-etamin)/etastep;
-    if (ey<nbeta && ex<nbeta && ex>=0 && ey>=0)
-      heta[ey*nbeta+ex]++; 
+    ex=(etax-etamin)/etastepX;
+    ey=(etay-etamin)/etastepY;
+    if (ey<nbetaY && ex<nbetaX && ex>=0 && ey>=0)
+      heta[ey*nbetaX+ex]++; 
 #endif
     return 0;    
   };

slsDetectorCalibration/interpolations/etaInterpolationBase.h

@@ -7,7 +7,7 @@
 #include <TH2D.h>
 #include <TH2F.h>
 #endif
-
+#include <cmath> 
 #include "slsInterpolation.h"
 #include "tiffIO.h"
 
@@ -15,44 +15,51 @@ class etaInterpolationBase : public slsInterpolation {
   
  public:
  
- etaInterpolationBase(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : slsInterpolation(nx,ny,ns), hhx(NULL), hhy(NULL), heta(NULL), nbeta(nb), etamin(emin), etamax(emax) {
+ etaInterpolationBase(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) : slsInterpolation(nx,ny,ns,nsy), hhx(NULL), hhy(NULL), heta(NULL), nbetaX(nb), nbetaY(nby), etamin(emin), etamax(emax) {
     // cout << "eb " << nb << " " << emin << " " << emax << endl;  
     // cout << nb << " " << etamin << " " << etamax << endl;
-    if (nbeta<=0) {
+    if (nbetaX<=0) {
       //cout << "aaa:" <<endl;
-      nbeta=nSubPixels*10;
+      nbetaX=nSubPixelsX*10;
+    } 
+    if (nbetaY<=0) {
+      //cout << "aaa:" <<endl;
+      nbetaY=nSubPixelsY*10;
     }
     if (etamin>=etamax) {
       etamin=-1;
       etamax=2;
     }
-    etastep=(etamax-etamin)/nbeta;
-    heta=new int[nbeta*nbeta];
-    hhx=new float[nbeta*nbeta];
-    hhy=new float[nbeta*nbeta];
+    etastepX=(etamax-etamin)/nbetaX;
+    etastepY=(etamax-etamin)/nbetaY;
+    heta=new int[nbetaX*nbetaY];
+    hhx=new float[nbetaX*nbetaY];
+    hhy=new float[nbetaX*nbetaY];
     rangeMin=etamin;
     rangeMax=etamax;
-    flat= new double[nSubPixels*nSubPixels];
-    hintcorr=new int [nSubPixels*nSubPixels*nPixelsX*nPixelsY];
+    flat= new double[nSubPixelsX*nSubPixelsY];
+    hintcorr=new int [nSubPixelsX*nSubPixelsY*nPixelsX*nPixelsY];
     
   };
   
  etaInterpolationBase(etaInterpolationBase *orig): slsInterpolation(orig){
-   nbeta=orig->nbeta;
+   nbetaX=orig->nbetaX;
+   nbetaY=orig->nbetaY;
    etamin=orig->etamin;
    etamax=orig->etamax;
    rangeMin=orig->rangeMin;
    rangeMax=orig->rangeMax;
 
 
-    etastep=(etamax-etamin)/nbeta;
-    heta=new int[nbeta*nbeta];
-    memcpy(heta,orig->heta,nbeta*nbeta*sizeof(int));
-    hhx=new float[nbeta*nbeta];
-    memcpy(hhx,orig->hhx,nbeta*nbeta*sizeof(float));
-    hhy=new float[nbeta*nbeta];
-    memcpy(hhy,orig->hhy,nbeta*nbeta*sizeof(float));
-    hintcorr=new int [nSubPixels*nSubPixels*nPixelsX*nPixelsY];
+    etastepX=(etamax-etamin)/nbetaX;
+    etastepY=(etamax-etamin)/nbetaY;
+    heta=new int[nbetaX*nbetaY];
+    memcpy(heta,orig->heta,nbetaX*nbetaY*sizeof(int));
+    hhx=new float[nbetaX*nbetaY];
+    memcpy(hhx,orig->hhx,nbetaX*nbetaY*sizeof(float));
+    hhy=new float[nbetaX*nbetaY];
+    memcpy(hhy,orig->hhy,nbetaX*nbetaY*sizeof(float));
+    hintcorr=new int [nSubPixelsX*nSubPixelsY*nPixelsX*nPixelsY];
 
  };
 
@@ -61,7 +68,7 @@ class etaInterpolationBase : public slsInterpolation {
 
 
   virtual void resetFlatField() {
-    for (int ibx=0; ibx<nbeta*nbeta; ibx++) {
+    for (int ibx=0; ibx<nbetaX*nbetaY; ibx++) {
       heta[ibx]=0;
       hhx[ibx]=0;
       hhy[ibx]=0;
@@ -70,13 +77,16 @@ class etaInterpolationBase : public slsInterpolation {
 
   };
     
-  int *setEta(int *h, int nb=-1, double emin=1, double emax=0)
+  int *setEta(int *h, int nb=-1, int nby=-1, double emin=1, double emax=0)
   {  
     if (h) {
       if (heta) delete [] heta;
       heta=h;
-      nbeta=nb;
-      if (nb<=0) nbeta=nSubPixels*10;
+      nbetaX=nb;
+      nbetaY=nby;
+      if (nbetaX<=0) nbetaX=nSubPixelsX*10;
+      if (nbetaY<=0) nbetaY=nSubPixelsY*10;
+      
       etamin=emin;
       etamax=emax;
       if (etamin>=etamax) {
@@ -85,22 +95,24 @@ class etaInterpolationBase : public slsInterpolation {
       }
       rangeMin=etamin;
       rangeMax=etamax;
-      etastep=(etamax-etamin)/nbeta;
+      etastepX=(etamax-etamin)/nbetaX;
+      etastepY=(etamax-etamin)/nbetaY;
     }
     return heta;
   };
   
-   int *setFlatField(int *h, int nb=-1, double emin=1, double emax=0)
+   int *setFlatField(int *h, int nb=-1, int nby=-1, double emin=1, double emax=0)
   {  
-    return setEta(h, nb, emin, emax);
+    return setEta(h, nb, nby, emin, emax);
   };
 
 
 
   int *getFlatField(){return setEta(NULL);};
   
-  int *getFlatField(int &nb, double &emin, double &emax){
-    nb=nbeta; 
+  int *getFlatField(int &nb, int &nby, double &emin, double &emax){
+    nb=nbetaX; 
+    nby=nbetaY; 
     emin=etamin; 
     emax=etamax; 
     return getFlatField();
@@ -109,13 +121,13 @@ class etaInterpolationBase : public slsInterpolation {
   
   void *writeFlatField(const char * imgname) {
     float *gm=NULL;
-    gm=new float[nbeta*nbeta];
-    for (int ix=0; ix<nbeta; ix++) {
-      for (int iy=0; iy<nbeta; iy++) {
-	gm[iy*nbeta+ix]=heta[iy*nbeta+ix];
+    gm=new float[nbetaX*nbetaY];
+    for (int ix=0; ix<nbetaX; ix++) {
+      for (int iy=0; iy<nbetaY; iy++) {
+	gm[iy*nbetaX+ix]=heta[iy*nbetaX+ix];
       }
     } 
-    WriteToTiff(gm, imgname, nbeta, nbeta);   
+    WriteToTiff(gm, imgname, nbetaX, nbetaY);   
     delete [] gm;
     return NULL; 
   };
@@ -129,16 +141,18 @@ class etaInterpolationBase : public slsInterpolation {
       etamax=2;
     }
     
-    etastep=(etamax-etamin)/nbeta;
+    etastepX=(etamax-etamin)/nbetaX;
+    etastepY=(etamax-etamin)/nbetaY;
     uint32 nnx;
     uint32 nny;
     float *gm=ReadFromTiff(imgname, nnx, nny);
-    if (nnx!=nny) {
-      cout << "different number of bins in x " << nnx << "  and y " << nny<< " !"<< endl;
-      cout << "Aborting read"<< endl;
-      return 0;
-    }
-    nbeta=nnx;
+    /* if (nnx!=nny) { */
+    /*   cout << "different number of bins in x " << nnx << "  and y " << nny<< " !"<< endl; */
+    /*   cout << "Aborting read"<< endl; */
+    /*   return 0; */
+    /* } */
+    nbetaX=nnx;
+    nbetaY=nny;
     if (gm) {
       if (heta) {
 	delete [] heta;
@@ -146,13 +160,13 @@ class etaInterpolationBase : public slsInterpolation {
 	delete [] hhy;
       }
       
-      heta=new int[nbeta*nbeta];
-      hhx=new float[nbeta*nbeta];
-      hhy=new float[nbeta*nbeta];
+      heta=new int[nbetaX*nbetaY];
+      hhx=new float[nbetaX*nbetaY];
+      hhy=new float[nbetaX*nbetaY];
       
-      for (int ix=0; ix<nbeta; ix++) {
-	for (int iy=0; iy<nbeta; iy++) {
-	  heta[iy*nbeta+ix]=gm[iy*nbeta+ix];
+      for (int ix=0; ix<nbetaX; ix++) {
+	for (int iy=0; iy<nbetaY; iy++) {
+	  heta[iy*nbetaX+ix]=gm[iy*nbetaX+ix];
 	}
       }
       delete [] gm;
@@ -178,10 +192,10 @@ float *gethhx()
     };
   virtual int addToFlatField(double etax, double etay){
     int ex,ey; 
-    ex=(etax-etamin)/etastep;
-    ey=(etay-etamin)/etastep;
-    if (ey<nbeta && ex<nbeta && ex>=0 && ey>=0)
-      heta[ey*nbeta+ex]++; 
+    ex=(etax-etamin)/etastepX;
+    ey=(etay-etamin)/etastepY;
+    if (ey<nbetaY && ex<nbetaX && ex>=0 && ey>=0)
+      heta[ey*nbetaX+ex]++; 
     return 0;    
   };
   
@@ -190,85 +204,85 @@ float *gethhx()
 
 
   void debugSaveAll(int ind=0) {
-    int ib, ibx, iby;
+    int  ibx, iby;
    char tit[10000];
    
    float tot_eta=0;
 
-  float *etah=new float[nbeta*nbeta];
-  int etabins=nbeta;
+  float *etah=new float[nbetaX*nbetaY];
+  // int etabins=nbeta;
   int ibb=0;
 
-  for (int ii=0; ii<etabins*etabins; ii++) {
+  for (int ii=0; ii<nbetaX*nbetaY; ii++) {
    
       etah[ii]=heta[ii];
       tot_eta+=heta[ii];
   }
-  sprintf(tit,"/scratch/eta.tiff",ind);
-  WriteToTiff(etah, tit, etabins, etabins);
+  sprintf(tit,"/scratch/eta_%d.tiff",ind);
+  WriteToTiff(etah, tit, nbetaX, nbetaY);
 
 
-  for (int ii=0; ii<etabins*etabins; ii++) {
-    ibb=(hhx[ii]*nSubPixels);
+  for (int ii=0; ii<nbetaX*nbetaY; ii++) {
+    ibb=(hhx[ii]*nSubPixelsX);
     etah[ii]=ibb;
   }
   sprintf(tit,"/scratch/eta_hhx_%d.tiff",ind);
-  WriteToTiff(etah, tit, etabins, etabins);
+  WriteToTiff(etah, tit, nbetaX, nbetaY);
 	  
-  for (int ii=0; ii<etabins*etabins; ii++) {
-    ibb=hhy[ii]*nSubPixels;
+  for (int ii=0; ii<nbetaX*nbetaY; ii++) {
+    ibb=hhy[ii]*nSubPixelsY;
     etah[ii]=ibb;
   }
   sprintf(tit,"/scratch/eta_hhy_%d.tiff",ind);
-  WriteToTiff(etah, tit, etabins, etabins);
+  WriteToTiff(etah, tit, nbetaX, nbetaY);
 	  
   
-  float *ftest=new float[nSubPixels*nSubPixels];
+  float *ftest=new float[nSubPixelsX*nSubPixelsY];
 
-  for (int ib=0; ib<nSubPixels*nSubPixels; ib++) ftest[ib]=0;
+  for (int ib=0; ib<nSubPixelsX*nSubPixelsY; ib++) ftest[ib]=0;
   
 
   //int ibx=0, iby=0;
   
-  for (int ii=0; ii<nbeta*nbeta; ii++) {
+  for (int ii=0; ii<nbetaX*nbetaY; ii++) {
     
-    ibx=nSubPixels*hhx[ii];
-    iby=nSubPixels*hhy[ii];
+    ibx=nSubPixelsX*hhx[ii];
+    iby=nSubPixelsY*hhy[ii];
     if (ibx<0) ibx=0;
     if (iby<0) iby=0;
-    if (ibx>=nSubPixels) ibx=nSubPixels-1;
-    if (iby>=nSubPixels) iby=nSubPixels-1;
+    if (ibx>=nSubPixelsX) ibx=nSubPixelsX-1;
+    if (iby>=nSubPixelsY) iby=nSubPixelsY-1;
     
 
-    if (ibx>=0 && ibx<nSubPixels && iby>=0 && iby<nSubPixels) {
+    if (ibx>=0 && ibx<nSubPixelsX && iby>=0 && iby<nSubPixelsY) {
       //
       // if (ibx>0 && iby>0) cout << ibx << " " << iby << " " << ii << endl;
-      ftest[ibx+iby*nSubPixels]+=heta[ii];
+      ftest[ibx+iby*nSubPixelsX]+=heta[ii];
     } else
       cout << "Bad interpolation "<< ii << " " << ibx << " " << iby<< endl; 
-
+    
   }
 
   sprintf(tit,"/scratch/ftest_%d.tiff",ind);
-  WriteToTiff(ftest, tit, nSubPixels, nSubPixels);
+  WriteToTiff(ftest, tit, nSubPixelsX, nSubPixelsY);
 
   //int ibx=0, iby=0;
-  tot_eta/=nSubPixels*nSubPixels;
+  tot_eta/=nSubPixelsX*nSubPixelsY;
   int nbad=0;
-  for (int ii=0; ii<etabins*etabins; ii++) {
-    ibx=nSubPixels*hhx[ii];
-    iby=nSubPixels*hhy[ii];
-    if (ftest[ibx+iby*nSubPixels]<tot_eta*0.5) {
+  for (int ii=0; ii<nbetaX*nbetaY; ii++) {
+    ibx=nSubPixelsX*hhx[ii];
+    iby=nSubPixelsY*hhy[ii];
+    if (ftest[ibx+iby*nSubPixelsX]<tot_eta*0.5) {
       etah[ii]=1;
       nbad++;
-    } else if(ftest[ibx+iby*nSubPixels]>tot_eta*2.){
+    } else if(ftest[ibx+iby*nSubPixelsX]>tot_eta*2.){
       etah[ii]=2;
       nbad++;
     } else
       etah[ii]=0;
   }
   sprintf(tit,"/scratch/eta_bad_%d.tiff",ind);
-  WriteToTiff(etah, tit, etabins, etabins);
+  WriteToTiff(etah, tit, nbetaX, nbetaY);
   // cout << "Index: " << ind << "\t Bad bins: "<< nbad << endl;
   //int ibx=0, iby=0;
 
@@ -284,48 +298,46 @@ float *gethhx()
   double calcDiff(double avg, float *hx, float *hy) {
     //double p_tot=0;
     double diff=0, d;
-    double bsize=1./nSubPixels;
+    //double bsize=1./nSubPixels;
     int nbad=0;
-    double p_tot_x[nSubPixels], p_tot_y[nSubPixels], p_tot[nSubPixels*nSubPixels];
-    double maxdiff=0, mindiff=avg*nSubPixels*nSubPixels;
+    double p_tot_x[nSubPixelsX], p_tot_y[nSubPixelsY], p_tot[nSubPixelsX*nSubPixelsY];
+    double maxdiff=0, mindiff=avg*nSubPixelsX*nSubPixelsY;
    
     int ipx, ipy;
-    for (ipy=0; ipy<nSubPixels; ipy++) {
-      for (ipx=0; ipx<nSubPixels; ipx++) {
-	p_tot[ipx+ipy*nSubPixels]=0;
+    for (ipy=0; ipy<nSubPixelsY; ipy++) {
+      for (ipx=0; ipx<nSubPixelsX; ipx++) {
+	p_tot[ipx+ipy*nSubPixelsX]=0;
       }
       p_tot_y[ipy]=0;
       p_tot_x[ipy]=0;
     }
    
-    for (int ibx=0; ibx<nbeta; ibx++) {
-      for (int iby=0; iby<nbeta; iby++) {
-	ipx=hx[ibx+iby*nbeta]*nSubPixels;
+    for (int ibx=0; ibx<nbetaX; ibx++) {
+      for (int iby=0; iby<nbetaY; iby++) {
+	ipx=hx[ibx+iby*nbetaX]*nSubPixelsX;
 	if (ipx<0) ipx=0;
-	if (ipx>=nSubPixels) ipx=nSubPixels-1;
+	if (ipx>=nSubPixelsX) ipx=nSubPixelsX-1;
 	
-	ipy=hy[ibx+iby*nbeta]*nSubPixels;
+	ipy=hy[ibx+iby*nbetaX]*nSubPixelsY;
 	if (ipy<0) ipy=0;
-	if (ipy>=nSubPixels) ipy=nSubPixels-1;
+	if (ipy>=nSubPixelsY) ipy=nSubPixelsY-1;
 	
-	p_tot[ipx+ipy*nSubPixels]+=heta[ibx+iby*nbeta];
-	p_tot_y[ipy]+=heta[ibx+iby*nbeta];
-	p_tot_x[ipx]+=heta[ibx+iby*nbeta];
-	
-
+	p_tot[ipx+ipy*nSubPixelsX]+=heta[ibx+iby*nbetaX];
+	p_tot_y[ipy]+=heta[ibx+iby*nbetaX];
+	p_tot_x[ipx]+=heta[ibx+iby*nbetaX];
       }
     }
     
     
     //  cout << endl << endl;
-    for (ipy=0; ipy<nSubPixels; ipy++) { 
+    for (ipy=0; ipy<nSubPixelsY; ipy++) { 
      cout.width(5);
      //flat_y[ipy]=p_tot_y[ipy];//avg/nSubPixels;
-      for (ipx=0; ipx<nSubPixels; ipx++) {
+      for (ipx=0; ipx<nSubPixelsX; ipx++) {
 
 	//	flat_x[ipx]=p_tot_x[ipx];///avg/nSubPixels;
-	flat[ipx+nSubPixels*ipy]=p_tot[ipx+nSubPixels*ipy];///avg;
-	d=p_tot[ipx+nSubPixels*ipy]-avg;
+	flat[ipx+nSubPixelsX*ipy]=p_tot[ipx+nSubPixelsX*ipy];///avg;
+	d=p_tot[ipx+nSubPixelsX*ipy]-avg;
 	if (d<0) d*=-1.;
 	if (d>5*sqrt(avg) )
 	  nbad++;
@@ -351,11 +363,11 @@ float *gethhx()
     return sqrt(diff);
   }
   
-  int *heta;
   float *hhx;
   float *hhy;
-  int nbeta;
-  double etamin, etamax, etastep;
+  int *heta;
+  int nbetaX, nbetaY;
+  double etamin, etamax, etastepX, etastepY;
   double rangeMin, rangeMax;
 
 

slsDetectorCalibration/interpolations/etaInterpolationPosXY.h

@@ -9,7 +9,7 @@
 
 class etaInterpolationPosXY : public virtual etaInterpolationBase{
  public:
- etaInterpolationPosXY(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny,ns, nb, emin,emax){
+ etaInterpolationPosXY(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax){
     //  cout << "epxy " << nb << " " << emin << " " << emax << endl; cout << nbeta << " " << etamin << " " << etamax << endl; 
   };
 
@@ -24,122 +24,136 @@ class etaInterpolationPosXY : public virtual etaInterpolationBase{
   virtual void prepareInterpolation(int &ok)
   {
    ok=1;  
-#ifdef MYROOT1   
-   if (hhx) delete hhx;
-   if (hhy) delete hhy;
-
-   hhx=new TH2D("hhx","hhx",heta->GetNbinsX(),heta->GetXaxis()->GetXmin(),heta->GetXaxis()->GetXmax(), heta->GetNbinsY(),heta->GetYaxis()->GetXmin(),heta->GetYaxis()->GetXmax()); 
-   hhy=new TH2D("hhy","hhy",heta->GetNbinsX(),heta->GetXaxis()->GetXmin(),heta->GetXaxis()->GetXmax(), heta->GetNbinsY(),heta->GetYaxis()->GetXmin(),heta->GetYaxis()->GetXmax()); 
-   
-#endif
 
 
    ///*Eta Distribution Rebinning*///
-   double bsize=1./nSubPixels; //precision
+   // double bsize=1./nSubPixels; //precision
    // cout<<"nPixelsX = "<<nPixelsX<<" nPixelsY = "<<nPixelsY<<" nSubPixels = "<<nSubPixels<<endl;
    double tot_eta=0;
    double tot_eta_x=0;
    double tot_eta_y=0;
-   for (int ip=0; ip<nbeta*nbeta; ip++)
+   for (int ip=0; ip<nbetaX*nbetaY; ip++)
      tot_eta+=heta[ip];
    cout << "total eta entries is :"<< tot_eta << endl;   
    if (tot_eta<=0) {ok=0; return;};
 
 
-   double hx[nbeta]; //profile x
-   double hy[nbeta]; //profile y
-   double hix[nbeta]; //integral of projection x
-   double hiy[nbeta]; //integral of projection y
-   int ii=0;
+   double hx[nbetaX]; //profile x
+   double hy[nbetaY]; //profile y
+   double hix[nbetaX]; //integral of projection x
+   double hiy[nbetaY]; //integral of projection y
+   //  int ii=0;
    double etax, etay;
-   for (int ib=0; ib<nbeta; ib++) {
+   for (int ib=0; ib<nbetaX; ib++) {
 
-     tot_eta_x=0;
-     tot_eta_y=0;
+   
+     //tot_eta_y=0;
 
-     for (int iby=0; iby<nbeta; iby++) {
-       etax=etamin+iby*etastep;
+     for (int iby=0; iby<nbetaY; iby++) {
+       etay=etamin+iby*etastepY;
        //cout << etax << endl;
-       if (etax>=0 && etax<=1)
-	 hx[iby]=heta[iby+ib*nbeta];
-       else {
-	 hx[iby]=0;
-       }
+     
        // tot_eta_x+=hx[iby];
-       if (etax>=0 && etax<=1)
-	 hy[iby]=heta[ib+iby*nbeta];
+       if (etay>=0 && etay<=1)
+	 hy[iby]=heta[ib+iby*nbetaX];
        else
 	 hy[iby]=0;
        // tot_eta_y+=hy[iby];
      }
 
-     hix[0]=hx[0];
+   
      hiy[0]=hy[0];
 
-     for (int iby=1; iby<nbeta; iby++) {
-       hix[iby]=hix[iby-1]+hx[iby];
+     for (int iby=1; iby<nbetaY; iby++) {
        hiy[iby]=hiy[iby-1]+hy[iby];
      }
 
-     ii=0;
-     tot_eta_x=hix[nbeta-1]+1;
-     tot_eta_y=hiy[nbeta-1]+1;
+     tot_eta_y=hiy[nbetaY-1]+1;
      
-     for (int ibx=0; ibx<nbeta; ibx++) {
-       if (tot_eta_x<=0) {
-	 hhx[ibx+ib*nbeta]=-1;
-	 //ii=(ibx)/nbeta;
-       } else //if (hix[ibx]>(ii+1)*tot_eta_x*bsize) 
-	 { 
-	   //if (hix[ibx]>tot_eta_x*(ii+1)/nSubPixels) ii++;
-	   hhx[ibx+ib*nbeta]=hix[ibx]/tot_eta_x;
-	 }
-     }
-     /* if (ii!=(nSubPixels-1)) */
-     /*   cout << ib << " x " <<  tot_eta_x << " " << (ii+1)*tot_eta_x*bsize << " " << ii << " " << hix[nbeta-1]<< endl; */
-     
-     ii=0;
-     
-     for (int ibx=0; ibx<nbeta; ibx++) {
+     for (int iby=0; iby<nbetaY; iby++) {
        if (tot_eta_y<=0) {
-	 hhy[ib+ibx*nbeta]=-1;
+	 hhy[ib+iby*nbetaX]=-1;
 	 //ii=(ibx*nSubPixels)/nbeta;
        } else {   
 	 //if (hiy[ibx]>tot_eta_y*(ii+1)/nSubPixels) ii++;
-	 hhy[ib+ibx*nbeta]=hiy[ibx]/tot_eta_y;
+	 hhy[ib+iby*nbetaX]=hiy[iby]/tot_eta_y;
        }
      }
    }
 
 
+
+   for (int ib=0; ib<nbetaY; ib++) {
+
+     for (int ibx=0; ibx<nbetaX; ibx++) {
+       etax=etamin+ibx*etastepX;
+       //cout << etax << endl;
+       if (etax>=0 && etax<=1)
+	 hx[ibx]=heta[ibx+ib*nbetaX];
+       else {
+	 hx[ibx]=0;
+       }
+     }
+     hix[0]=hx[0];
+       
+     for (int ibx=1; ibx<nbetaX; ibx++) {
+       hix[ibx]=hix[ibx-1]+hx[ibx];
+     }
+
+  
+     tot_eta_x=hix[nbetaX-1]+1;
+     
+     for (int ibx=0; ibx<nbetaX; ibx++) {
+       if (tot_eta_x<=0) {
+	 hhx[ibx+ib*nbetaX]=-1;
+       } 
+       else { 
+	 hhx[ibx+ib*nbetaX]=hix[ibx]/tot_eta_x;
+       }
+     }
+     
+
+     
+     for (int ibx=0; ibx<nbetaX; ibx++) {
+       if (tot_eta_x<=0) {
+	 hhx[ibx+ib*nbetaX]=-1;
+       } else	 { 
+	 //if (hix[ibx]>tot_eta_x*(ii+1)/nSubPixels) ii++;
+	 hhx[ibx+ib*nbetaX]=hix[ibx]/tot_eta_x;
+       }
+     }
+     
+   }
+
+     
    int ibx, iby, ib; 
    
    iby=0;
-   while (hhx[iby*nbeta+nbeta/2]<0) iby++;
+   while (hhx[iby*nbetaY+nbetaY/2]<0) iby++;
    for (ib=0; ib<iby;ib++) {
-     for (ibx=0; ibx<nbeta;ibx++)
-       hhx[ibx+nbeta*ib]=hhx[ibx+nbeta*iby];
+     for (ibx=0; ibx<nbetaX;ibx++)
+       hhx[ibx+nbetaX*ib]=hhx[ibx+nbetaX*iby];
    }
-   iby=nbeta-1;
+   iby=nbetaY-1;
    
-   while (hhx[iby*nbeta+nbeta/2]<0) iby--;
-   for (ib=iby+1; ib<nbeta;ib++) {
-     for (ibx=0; ibx<nbeta;ibx++)
-       hhx[ibx+nbeta*ib]=hhx[ibx+nbeta*iby];
+   while (hhx[iby*nbetaY+nbetaY/2]<0) iby--;
+   for (ib=iby+1; ib<nbetaY;ib++) {
+     for (ibx=0; ibx<nbetaX;ibx++)
+       hhx[ibx+nbetaX*ib]=hhx[ibx+nbetaX*iby];
    }
    
    iby=0;
-   while (hhy[nbeta/2*nbeta+iby]<0) iby++;
+   while (hhy[nbetaX/2*nbetaX+iby]<0) iby++;
    for (ib=0; ib<iby;ib++) {
-     for (ibx=0; ibx<nbeta;ibx++)
-       hhy[ib+nbeta*ibx]=hhy[iby+nbeta*ibx];
+     for (ibx=0; ibx<nbetaY;ibx++)
+       hhy[ib+nbetaX*ibx]=hhy[iby+nbetaX*ibx];
    }
-   iby=nbeta-1;
+   iby=nbetaX-1;
    
-   while (hhy[nbeta/2*nbeta+iby]<0) iby--;
-   for (ib=iby+1; ib<nbeta;ib++) {
-     for (ibx=0; ibx<nbeta;ibx++)
-       hhy[ib+nbeta*ibx]=hhy[iby+nbeta*ibx];
+   while (hhy[nbetaX/2*nbetaX+iby]<0) iby--;
+   for (ib=iby+1; ib<nbetaX;ib++) {
+     for (ibx=0; ibx<nbetaY;ibx++)
+       hhy[ib+nbetaX*ibx]=hhy[iby+nbetaX*ibx];
    }
 
 
@@ -156,9 +170,16 @@ class etaInterpolationPosXY : public virtual etaInterpolationBase{
 
 };
 
+
+
+
+
+
+
+
 class eta2InterpolationPosXY : public virtual eta2InterpolationBase, public virtual etaInterpolationPosXY {
  public:
- eta2InterpolationPosXY(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny,ns, nb, emin,emax),eta2InterpolationBase(nx,ny,ns, nb, emin,emax),etaInterpolationPosXY(nx,ny,ns, nb, emin,emax){
+ eta2InterpolationPosXY(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax),eta2InterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax),etaInterpolationPosXY(nx,ny, ns, nsy, nb, nby, emin, emax){
     //  cout << "e2pxy " << nb << " " << emin << " " << emax << endl; 
   };
  
@@ -172,8 +193,8 @@ class eta2InterpolationPosXY : public virtual eta2InterpolationBase, public virt
 
 class eta3InterpolationPosXY : public virtual eta3InterpolationBase, public virtual etaInterpolationPosXY {
  public:
- eta3InterpolationPosXY(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny,ns, nb, emin,emax),eta3InterpolationBase(nx,ny,ns, nb, emin,emax), etaInterpolationPosXY(nx,ny,ns, nb, emin,emax){
-      cout << "e3pxy " << nbeta << " " << etamin << " " << etamax << " " << nSubPixels<< endl;  
+ eta3InterpolationPosXY(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax),eta3InterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax), etaInterpolationPosXY(nx,ny, ns, nsy, nb, nby, emin, emax){
+    //   cout << "e3pxy " << nbeta << " " << etamin << " " << etamax << " " << nSubPixels<< endl;  
   };
 
  eta3InterpolationPosXY(eta3InterpolationPosXY *orig): etaInterpolationBase(orig), etaInterpolationPosXY(orig)  {};

slsDetectorCalibration/interpolations/etaVEL/etaVELInterpolation.h~

@@ -0,0 +1,52 @@
+#ifndef INTERPOLATION_ETAVEL_H
+#define INTERPOLATION_ETAVEL_H
+
+#include <slsInterpolation.h>
+#include "EtaVEL.h"
+#include "TH2F.h"
+//#include "EtaVEL.cpp"
+//class EtaVEL;
+
+class  interpolation_EtaVEL: public slsInterpolation {
+
+ public:
+  interpolation_EtaVEL(int nx=40, int ny=160, int ns=25, double etamin=-0.02, double etamax=1.02, int p=0);
+  ~interpolation_EtaVEL();
+ 
+ 
+  //create eta distribution, eta rebinnining etc.
+  //returns flat field image
+  void prepareInterpolation(int &ok){prepareInterpolation(ok,10000);};
+  void prepareInterpolation(int &ok, int maxit);
+
+  //create interpolated image
+  //returns interpolated image
+  
+  //return position inside the pixel for the given photon
+  void getInterpolatedPosition(Int_t x, Int_t y, Double_t *data, Double_t &int_x, Double_t &int_y);
+  void getInterpolatedBin(Double_t *cluster, Int_t &int_x, Int_t &int_y);
+ 
+
+
+  int addToFlatField(Double_t *cluster, Double_t &etax, Double_t &etay);
+  int addToFlatField(Double_t etax, Double_t etay);
+  int setPlot(int p=-1) {if (p>=0) plot=p; return plot;};
+  int WriteH(){newEta->Write("newEta"); heta->Write("heta");};
+  EtaVEL *setEta(EtaVEL *ev){if (ev) {delete newEta; newEta=ev;} return newEta;};
+  TH2F *setEta(TH2F *ev){if (ev) {delete heta; heta=ev;} return heta;};
+  void iterate();
+  void DrawH();
+  double getChiSq(){return newEta->getChiSq();};
+ 
+
+
+ protected:
+  EtaVEL *newEta;
+  TH2F *heta;
+  int plot;
+
+  //  ClassDefNV(interpolation_EtaVEL,1);
+  // #pragma link C++ class interpolation_EtaVEL-;
+};
+
+#endif

slsDetectorCalibration/interpolations/slsInterpolation.h

@@ -29,19 +29,21 @@ class slsInterpolation
 {
 
  public:
- slsInterpolation(int nx=400, int ny=400, int ns=25) :nPixelsX(nx), nPixelsY(ny),  nSubPixels(ns), id(0) {
+ slsInterpolation(int nx=400, int ny=400, int ns=25, int nsy=-1) :nPixelsX(nx), nPixelsY(ny),  nSubPixelsX(ns), nSubPixelsY(nsy),id(0) {
    
- hint=new int[ns*nx*ns*ny];
+    if (nSubPixelsY<=0) nSubPixelsY=nSubPixelsX;
+    hint=new int[nSubPixelsX*nx*nSubPixelsY*ny];
 
 };
   
  slsInterpolation(slsInterpolation *orig){
    nPixelsX=orig->nPixelsX;
    nPixelsY=orig->nPixelsY;
-   nSubPixels=orig->nSubPixels;
+   nSubPixelsX=orig->nSubPixelsX;
+   nSubPixelsY=orig->nSubPixelsY;
    
-   hint=new int[nSubPixels*nPixelsX*nSubPixels*nPixelsY];
-   memcpy(hint, orig->hint,nSubPixels*nPixelsX*nSubPixels*nPixelsY*sizeof(int));
+   hint=new int[nSubPixelsX*nPixelsX*nSubPixelsY*nPixelsY];
+   memcpy(hint, orig->hint,nSubPixelsX*nPixelsX*nSubPixelsY*nPixelsY*sizeof(int));
  
  };
 
@@ -51,23 +53,37 @@ class slsInterpolation
    return new slsInterpolation(this);
    }*/
 
-  int getNSubPixels() {return nSubPixels;};
+  int getNSubPixelsX() {return nSubPixelsX;};
+  int getNSubPixelsY() {return nSubPixelsY;};
+  int getNSubPixels() {if (nSubPixelsX==nSubPixelsY) return nSubPixelsX; else return 0;};
+  void getNSubPixels(int &nsx, int &nsy) {nsx=nSubPixelsX; nsy=nsx=nSubPixelsY;}
 
-
-  int setNSubPixels(int ns)   {
-    if (ns>0 && ns!=nSubPixels) {
+  void setNSubPixels(int ns, int nsy=-1)   {
+   
       delete [] hint;
-      nSubPixels=ns;
-      hint=new int[nSubPixels*nPixelsX*nSubPixels*nPixelsY];
-    }
-    return nSubPixels;
+      nSubPixelsX=ns;
+      if (nsy>0)  nSubPixelsY=nsy;
+      else nSubPixelsY=ns;
+      
+      hint=new int[nSubPixelsX*nPixelsX*nSubPixelsY*nPixelsY];
+      
+      //return nSubPixels;
   }
 
-  int getImageSize(int &nnx, int &nny, int &ns) {
-    nnx=nSubPixels*nPixelsX;
-    nny=nSubPixels*nPixelsY;
-    ns=nSubPixels;
-    return nSubPixels*nSubPixels*nPixelsX*nPixelsY;
+  
+
+
+  int getImageSize(int &nnx, int &nny, int &nsx, int &nsy) {
+    nnx=nSubPixelsX*nPixelsX;
+    nny=nSubPixelsY*nPixelsY;
+    nsx=nSubPixelsX;
+    nsy=nSubPixelsY;
+    return nSubPixelsX*nSubPixelsY*nPixelsX*nPixelsY;
+  };
+  
+
+  int getImageSize() {
+    return nSubPixelsX*nSubPixelsY*nPixelsX*nPixelsY;
   };
   
   
@@ -92,14 +108,14 @@ class slsInterpolation
     //cout << "!" <<endl;
     float *gm=NULL;
     int *dummy=getInterpolatedImage();
-    gm=new float[ nSubPixels*  nSubPixels* nPixelsX*nPixelsY];
+    gm=new float[ nSubPixelsX*  nSubPixelsY* nPixelsX*nPixelsY];
     if (gm) {
-      for (int ix=0; ix<nPixelsX*nSubPixels; ix++) {
-	for (int iy=0; iy<nPixelsY*nSubPixels; iy++) {
-	  gm[iy*nPixelsX*nSubPixels+ix]=dummy[iy*nPixelsX*nSubPixels+ix];
+      for (int ix=0; ix<nPixelsX*nSubPixelsX; ix++) {
+	for (int iy=0; iy<nPixelsY*nSubPixelsY; iy++) {
+	  gm[iy*nPixelsX*nSubPixelsX+ix]=dummy[iy*nPixelsX*nSubPixelsX+ix];
 	}
       }
-      WriteToTiff(gm, imgname,nSubPixels* nPixelsX ,nSubPixels* nPixelsY); 
+      WriteToTiff(gm, imgname,nSubPixelsY* nPixelsX ,nSubPixelsY* nPixelsY); 
       delete [] gm;
     } else cout << "Could not allocate float image " << endl;
     return NULL;    
@@ -120,9 +136,9 @@ class slsInterpolation
   virtual void clearInterpolatedImage() {
 
 
-      for (int ix=0; ix<nPixelsX*nSubPixels; ix++) {
-	for (int iy=0; iy<nPixelsY*nSubPixels; iy++) {
-	  hint[iy*nPixelsX*nSubPixels+ix]=0;
+      for (int ix=0; ix<nPixelsX*nSubPixelsX; ix++) {
+	for (int iy=0; iy<nPixelsY*nSubPixelsY; iy++) {
+	  hint[iy*nPixelsX*nSubPixelsX+ix]=0;
 	}
       }
 
@@ -133,11 +149,11 @@ class slsInterpolation
 
 
   virtual int *addToImage(double int_x, double int_y){ 
-    int iy=((double)nSubPixels)*int_y; 
-    int ix=((double)nSubPixels)*int_x; 
-     if (ix>=0 && ix<(nPixelsX*nSubPixels) && iy<(nSubPixels*nPixelsY) && iy>=0 ){
+    int iy=((double)nSubPixelsY)*int_y; 
+    int ix=((double)nSubPixelsX)*int_x; 
+     if (ix>=0 && ix<(nPixelsX*nSubPixelsX) && iy<(nSubPixelsY*nPixelsY) && iy>=0 ){
        // cout << int_x << " " << int_y << " " << "  " << ix << " " << iy << " " << ix+iy*nPixelsX*nSubPixels << " " << hint[ix+iy*nPixelsX*nSubPixels];
-       (*(hint+ix+iy*nPixelsX*nSubPixels))+=1; 
+       (*(hint+ix+iy*nPixelsX*nSubPixelsX))+=1; 
        // cout << " " << hint[ix+iy*nPixelsX*nSubPixels] << endl;
      }// else
       // cout << "bad! "<< int_x << " " << int_y << " " << "  " << ix << " " << iy << " " << ix+iy*nPixelsX*nSubPixels << endl;
@@ -156,7 +172,7 @@ class slsInterpolation
   virtual int *setFlatField(int *h, int nb=-1, double emin=-1, double emax=-1){return NULL;}; 
   virtual void *writeFlatField(const char * imgname){return NULL;};
   virtual void *readFlatField(const char * imgname, int nb=-1, double emin=1, double emax=0){return NULL;};
- virtual int *getFlatField(int &nb, double &emin, double &emax){nb=0; emin=0; emax=0; return getFlatField();}; 
+  virtual int *getFlatField(int &nb, int &nby, double &emin, double &emax){nb=0; nby=0; emin=0; emax=0; return getFlatField();}; 
 
  virtual void resetFlatField()=0;
 
@@ -180,11 +196,12 @@ class slsInterpolation
     /* cluster[2]=cl+6; */
     
     sum=0;
+    int xoff=0, yoff=0;
+#ifndef WRITE_QUAD 
     double sumBL=0;
     double sumTL=0;
     double sumBR=0;
     double sumTR=0;
-    int xoff=0, yoff=0;
     for (int ix=0; ix<3; ix++) {
       for (int iy=0; iy<3; iy++) {
 	sum+=cl[ix+3*iy];
@@ -204,34 +221,95 @@ class slsInterpolation
 
     
     if(sumTL  >= totquad){
-      /* sDum[0][0] = cluster[1][0]; sDum[1][0] = cluster[2][0]; */
-      /* sDum[0][1] = cluster[1][1]; sDum[1][1] = cluster[2][1]; */
-      
+/* #ifdef WRITE_QUAD */
+/*       /\* sDum[0][0] = cluster[1][0]; sDum[1][0] = cluster[2][0]; *\/ */
+/*       /\* sDum[0][1] = cluster[1][1]; sDum[1][1] = cluster[2][1]; *\/ */
+/*       if (sumTL  ==sum) { */
+/* #endif */
       corner = TOP_LEFT;
       totquad=sumTL;
       xoff=0;
       yoff=1;
+/* #ifdef WRITE_QUAD */
+/*       } */
+/* #endif */
     } 
 
     if(sumBR  >= totquad){
       /* sDum[0][0] = cluster[0][1]; sDum[1][0] = cluster[1][1]; */
       /* sDum[0][1] = cluster[0][2]; sDum[1][1] = cluster[1][2]; */
       
+/* #ifdef WRITE_QUAD */
+/*       /\* sDum[0][0] = cluster[1][0]; sDum[1][0] = cluster[2][0]; *\/ */
+/*       /\* sDum[0][1] = cluster[1][1]; sDum[1][1] = cluster[2][1]; *\/ */
+/*       if (sumBR   ==sum) { */
+/* #endif */
+      corner = BOTTOM_RIGHT;
       xoff=1;
       yoff=0;
-      corner = BOTTOM_RIGHT;
       totquad=sumBR;
+/* #ifdef WRITE_QUAD */
+/*       } */
+/* #endif */
     }
     
     if(sumTR  >= totquad){
+/* #ifdef WRITE_QUAD */
+/*       /\* sDum[0][0] = cluster[1][0]; sDum[1][0] = cluster[2][0]; *\/ */
+/*       /\* sDum[0][1] = cluster[1][1]; sDum[1][1] = cluster[2][1]; *\/ */
+/*       if (sumTR ==sum) { */
+/* #endif */
       xoff=1;
       yoff=1;
       /* sDum[0][0] = cluster[1][1]; sDum[1][0] = cluster[2][1]; */
       /* sDum[0][1] = cluster[1][2]; sDum[1][1] = cluster[2][2]; */
       corner = TOP_RIGHT;
       totquad=sumTR;
+/* #ifdef WRITE_QUAD */
+/*       } */
+/* #endif */
     }
+ 
+#endif    
+#ifdef WRITE_QUAD    
+   
+    double sumB=0;
+    double sumT=0;
+    double sumR=0;
+    double sumL=0;
+
+    for (int ix=0; ix<3; ix++) {
+      for (int iy=0; iy<3; iy++) {
+	sum+=cl[ix+3*iy];
+	if (ix<1 ) sumL+=cl[ix+iy*3];
+	if (ix>1) sumR+=cl[ix+iy*3];
+	if (iy<1) sumB=cl[ix+iy*3];
+	if (iy>1) sumT+=cl[ix+iy*3];
+      }
+    } 
     
+    totquad=sum;
+    if ( sumT==0 && sumR==0) {
+        corner = BOTTOM_LEFT;
+	xoff=0;
+	yoff=0;
+    } else if ( sumB==0 && sumR==0 ) {
+        corner = TOP_LEFT;
+      xoff=0;
+      yoff=1;
+    } else if ( sumT==0 && sumL==0) {
+      corner = BOTTOM_RIGHT;
+      xoff=1;
+      yoff=0;
+    } else if ( sumB==0 && sumL==0) {
+      xoff=1;
+      yoff=1;
+      corner = TOP_RIGHT;
+    } else
+      printf("** bad 2x2 cluster!\n");
+
+#endif
+
 
     for (int ix=0; ix<2; ix++) {
       for (int iy=0; iy<2; iy++) {
@@ -495,7 +573,7 @@ class slsInterpolation
 
  protected:
   int nPixelsX, nPixelsY;
-  int nSubPixels;
+  int nSubPixelsX, nSubPixelsY;
   int id;
   int *hint;
 };

slsDetectorCalibration/moench03CommonMode.h

@@ -1,44 +1,60 @@
 #ifndef MOENCH03COMMONMODE_H
 #define MOENCH03COMMONMODE_H
 
-#include "commonModeSubtraction.h"
+#include "commonModeSubtractionNew.h"
 
-class moench03CommonMode : public commonModeSubtraction {
+class commonModeSubtractionColumn:  public commonModeSubtraction{
+public:
+ commonModeSubtractionColumn(int nr=200) : commonModeSubtraction(800), rows(nr) {};
+  virtual int getROI(int ix, int iy){return ix+(iy/200)*400;};
+  
+   virtual void addToCommonMode(double val, int ix=0, int iy=0) {
+     if (iy<rows || iy>399-rows) {
+       int iroi=getROI(ix,iy);
+       // cout << iy << " " << ix << " " << iroi ;
+       if (iroi>=0 && iroi<nROI) {
+	 mean[iroi]+=val; 
+	 mean2[iroi]+=val*val; 
+	 nCm[iroi]++;
+	 if (nCm[iroi]>rows) cout << "Too many pixels added " << nCm[iroi] << endl;
+	 /* if (ix==10 && iy<20) */
+	 /*   cout << " ** "<<val << " " << mean[iroi] << " " << nCm[iroi] << " " << getCommonMode(ix, iy) << endl; */
+       }
+     }
+    };
+
+  virtual  commonModeSubtractionColumn *Clone() {
+      return new  commonModeSubtractionColumn(this->rows);
+    }
+
+ private:
+  int rows;
+};
+
+
+class commonModeSubtractionSuperColumn:  public commonModeSubtraction{
+public:
+commonModeSubtractionSuperColumn() : commonModeSubtraction(32) {};
+  virtual int getROI(int ix, int iy){  return ix/25+(iy/200)*16;};
+};
+
+
+class commonModeSubtractionHalf:  public commonModeSubtraction{
+public:
+commonModeSubtractionHalf() : commonModeSubtraction(2) {};
+  virtual int getROI(int ix, int iy){  (void) ix; return iy/200;};
+};
+
+
+class moench03CommonMode : public commonModeSubtractionColumn {
   /** @short class to calculate the common mode noise for moench02 i.e. on 4 supercolumns separately */
  public:
   /** constructor -  initalizes a commonModeSubtraction with 4 different regions of interest 
       \param nn number of samples for the moving average
   */
-  moench03CommonMode(int nn=1000) : commonModeSubtraction(nn,32){} ;
+  moench03CommonMode(int nr=20) : commonModeSubtractionColumn(nr){} ;
     
 
-    /** add value to common mode as a function of the pixel value, subdividing the region of interest in the 4 supercolumns of 40 columns each;
-	\param val value to add to the common mode
-	\param ix pixel coordinate in the x direction
-	\param iy pixel coordinate in the y direction
-    */
-    virtual void addToCommonMode(double val, int ix=0, int iy=0) {
-      // (void) iy;  
-      int isc=ix/25+(iy/200)*16;
-      if (isc>=0 && isc<nROI) {
-	cmPed[isc]+=val; 
-	nCm[isc]++;
-      }
-    };
-     /**returns common mode value as a function of the pixel value, subdividing the region of interest in the 4 supercolumns of 40 columns each;
-	\param ix pixel coordinate in the x direction
-	\param iy pixel coordinate in the y direction
-	\returns common mode value
-    */
-    virtual double getCommonMode(int ix=0, int iy=0) {
-      (void) iy;
-      int isc=ix/25+(iy/200)*16;
-      if (isc>=0 && isc<nROI) { 
-	if (nCm[isc]>0) return cmPed[isc]/nCm[isc]-cmStat[isc].Mean(); 
-      }
-      return 0;
-    };
-
 };
 
 

slsDetectorCalibration/moench03GhostSummation.h

@@ -0,0 +1,64 @@
+#ifndef MOENCH03GHOSTSUMMATION_H
+#define MOENCH03GHOSTSUMMATION_H
+
+#include "ghostSummation.h"
+
+class moench03GhostSummation : public ghostSummation<uint16_t> {
+
+  /** @short virtual calss to handle ghosting*/ 
+
+ public:
+  
+  /** constructor
+      \param xt crosstalk
+  */
+ moench03GhostSummation(slsDetectorData<uint16_t> *d, double xt=0.0004) : ghostSummation<uint16_t>(d, xt)  {}
+  
+  virtual void calcGhost(char *data){
+    for (int iy=0; iy<200; iy++){
+      for (int ix=0; ix<25; ix++){
+	calcGhost(data,ix,iy);
+      }
+    }
+  };
+
+ moench03GhostSummation(moench03GhostSummation *orig) : ghostSummation(orig) {
+  }
+
+  virtual  moench03GhostSummation *Clone() {
+    return new  moench03GhostSummation(this);
+  }
+
+  virtual double calcGhost(char *data, int x, int y=0){
+    int ix=x%25;
+    int iy=y;
+    if (y>=200) iy=399-y;
+    if (iy<0 || ix<0) return 0;
+    double val=0;
+    val=0;
+    for (int isc=0; isc<16; isc++) {
+      val+=det->getChannel(data,ix+25*isc,iy);
+      //  cout << val << " " ;
+      val+=det->getChannel(data,ix+25*isc,399-iy);
+      //  cout << val << " " ;
+    }
+    ghost[iy*nx+ix]=xtalk*val;
+    // if (ix==15 && iy==15) cout << ":" << ghost[iy*nx+ix] << " " << val << endl; 
+    return ghost[iy*nx+ix];
+  };
+
+
+  virtual double getGhost(int ix, int iy) {
+    if (iy >=0 && iy<200) return ghost[iy*nx+(ix%25)]; 
+    if (iy<400) return ghost[(399-iy)*nx+(ix%25)];
+    return 0;
+  };
+
+
+};
+
+
+
+
+
+#endif

slsDetectorCalibration/moenchCommonMode.h

@@ -1,7 +1,7 @@
 #ifndef MOENCHCOMMONMODE_H
 #define MOENCHCOMMONMODE_H
 
-#include "commonModeSubtraction.h"
+#include "commonModeSubtractionNew.h"
 
 class moenchCommonMode : public commonModeSubtraction {
   /** @short class to calculate the common mode noise for moench02 i.e. on 4 supercolumns separately */
@@ -9,35 +9,36 @@ class moenchCommonMode : public commonModeSubtraction {
   /** constructor -  initalizes a commonModeSubtraction with 4 different regions of interest 
       \param nn number of samples for the moving average
   */
-  moenchCommonMode(int nn=1000) : commonModeSubtraction(nn,4){} ;
+
+  moenchCommonMode(int nn=0) : commonModeSubtraction(0){} ;
     
 
-    /** add value to common mode as a function of the pixel value, subdividing the region of interest in the 4 supercolumns of 40 columns each;
-	\param val value to add to the common mode
-	\param ix pixel coordinate in the x direction
-	\param iy pixel coordinate in the y direction
-    */
-    virtual void addToCommonMode(double val, int ix=0, int iy=0) {
-      (void) iy;  
-      int isc=ix/40;
-      if (isc>=0 && isc<nROI) {
-	cmPed[isc]+=val; 
-	nCm[isc]++;
-      }
-    };
-     /**returns common mode value as a function of the pixel value, subdividing the region of interest in the 4 supercolumns of 40 columns each;
-	\param ix pixel coordinate in the x direction
-	\param iy pixel coordinate in the y direction
-	\returns common mode value
-    */
-    virtual double getCommonMode(int ix=0, int iy=0) {
-      (void) iy;
-      int isc=ix/40;
-      if (isc>=0 && isc<nROI) { 
-	if (nCm[isc]>0) return cmPed[isc]/nCm[isc]-cmStat[isc].Mean(); 
-      }
-      return 0;
-    };
+    /* /\** add value to common mode as a function of the pixel value, subdividing the region of interest in the 4 supercolumns of 40 columns each; */
+    /* 	\param val value to add to the common mode */
+    /* 	\param ix pixel coordinate in the x direction */
+    /* 	\param iy pixel coordinate in the y direction */
+    /* *\/ */
+    /* virtual void addToCommonMode(double val, int ix=0, int iy=0) { */
+    /*   (void) iy;   */
+    /*   int isc=ix/40; */
+    /*   if (isc>=0 && isc<nROI) { */
+    /* 	cmPed[isc]+=val;  */
+    /* 	nCm[isc]++; */
+    /*   } */
+    /* }; */
+    /*  /\**returns common mode value as a function of the pixel value, subdividing the region of interest in the 4 supercolumns of 40 columns each; */
+    /* 	\param ix pixel coordinate in the x direction */
+    /* 	\param iy pixel coordinate in the y direction */
+    /* 	\returns common mode value */
+    /* *\/ */
+    /* virtual double getCommonMode(int ix=0, int iy=0) { */
+    /*   (void) iy; */
+    /*   int isc=ix/40; */
+    /*   if (isc>=0 && isc<nROI) {  */
+    /* 	if (nCm[isc]>0) return cmPed[isc]/nCm[isc]-cmStat[isc].Mean();  */
+    /*   } */
+    /*   return 0; */
+    /* }; */
 
 };
 

slsDetectorCalibration/moenchExecutables/Makefile.cluster_finder

@@ -1,39 +1,61 @@
+#module add CBFlib/0.9.5
+INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures -I../../slsReceiverSoftware/include/
 
-CBFLIBDIR= /afs/psi.ch/project/sls_det_software/CBFlib-0.9.5/
-#ZMQLIB=../slsReceiverSoftware/include
-#LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
-INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures -I../../slsReceiverSoftware/include -I$(CBFLIBDIR)/include/ 
-#LIBHDF5=
-LDFLAG= ../tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++ -L.  -pthread -lrt -L$(CBFLIBDIR)/lib/   -ltiff 
-#-L$(ZMQLIB) -lzmq
-#-L../../bin 
+LDFLAG= ../tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++   -pthread -lrt    -ltiff  -std=c++11 -Wall  -O3
+#-g3 
+#-fsanitize=thread -fno-omit-frame-pointer
+#-fsanitize=address,undefined,
 MAIN=moench03ClusterFinder.cpp
-#-lhdf5
-#DESTDIR?=../bin
 
-all: moenchClusterFinder moenchMakeEta moenchInterpolation moenchNoInterpolation moenchPhotonCounter moenchAnalog
+
+all: moenchClusterFinder moenchMakeEta moenchMakeEta3 moenchInterpolation moenchInterpolation3 moenchNoInterpolation moenchPhotonCounter moenchAnalog moenchPhotonCounterNoThread  moenchAnalogNoThread 
 
 
 
-moenchClusterFinder:  $(MAIN)  $(INCS) clean
-			 g++ -o moenchClusterFinder  $(MAIN)  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DOLDDATA #-DNEWRECEIVER 
+moenchClusterFinder:  moench03ClusterFinder.cpp  $(INCS) clean
+			 g++ -o moenchClusterFinder  moench03ClusterFinder.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL  -DNEWRECEIVER 
 
-moenchMakeEta:  moench03MakeEta.cpp  $(INCS) clean
-			 g++ -o moenchMakeEta moench03MakeEta.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL
+
+moenchClusterFinderHighZ:  moench03ClusterFinder.cpp  $(INCS) clean
+			 g++ -o moenchClusterFinderHighZ  moench03ClusterFinder.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL  -DNEWRECEIVER -DHIGHZ 
+
+
+
+
+moenchMakeEta:  moench03Interpolation.cpp  $(INCS) clean
+			 g++ -o moenchMakeEta moench03Interpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DFF
+
+moenchMakeEta3:  moench03Interpolation.cpp  $(INCS) clean
+			 g++ -o moenchMakeEta3 moench03Interpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DFF -DETA3
 
 moenchInterpolation:  moench03Interpolation.cpp  $(INCS) clean
-			 g++ -o moenchInterpolation moench03Interpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL 
+			 g++ -o moenchInterpolation moench03Interpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  
+
+moenchInterpolation3:  moench03Interpolation.cpp  $(INCS) clean
+			 g++ -o moenchInterpolation3 moench03Interpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DETA3
 
 moenchNoInterpolation:  moench03NoInterpolation.cpp  $(INCS) clean
-			 g++ -o moenchNoInterpolation moench03NoInterpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL
+			 g++ -o moenchNoInterpolation moench03NoInterpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) 
 
 moenchPhotonCounter: moenchPhotonCounter.cpp   $(INCS) clean
-			 g++ -o moenchPhotonCounter  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DNEWRECEIVER
+			 g++ -o moenchPhotonCounter  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER
 
 moenchAnalog: moenchPhotonCounter.cpp  $(INCS) clean
-			 g++ -o moenchAnalog  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DNEWRECEIVER -DANALOG
+			 g++ -o moenchAnalog  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DANALOG
+
+moenchPhotonCounterHighZ: moenchPhotonCounter.cpp   $(INCS) clean
+			 g++ -o moenchPhotonCounterHighZ  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DHIGHZ
+
+moenchAnalogHighZ: moenchPhotonCounter.cpp  $(INCS) clean
+			 g++ -o moenchAnalogHighZ  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DANALOG -DHIGHZ
+
+moenchAnalogNoThread : moenchPhotonCounterNoThread.cpp  $(INCS) clean
+			 g++ -o moenchAnalogNoThread   moenchPhotonCounterNoThread.cpp  $(LDFLAG) $(INCDIR)   -DNEWRECEIVER -DANALOG 
+
+moenchPhotonCounterNoThread : moenchPhotonCounterNoThread.cpp   $(INCS) clean
+			 g++ -o moenchPhotonCounterNoThread   moenchPhotonCounterNoThread.cpp  $(LDFLAG) $(INCDIR) $  -DNEWRECEIVER 
 
 clean: 	
-	rm -f  moenchClusterFinder moenchMakeEta moenchInterpolation moenchNoInterpolation moenchPhotonCounter
+	rm -f  moenchClusterFinder moenchMakeEta moenchInterpolation moenchNoInterpolation moenchPhotonCounter moenchAnalog moenchPhotonCounterNoThread  moenchAnalogNoThread 
 
 

slsDetectorCalibration/moenchExecutables/Makefile.cluster_finder_rect_rh7

@@ -0,0 +1,46 @@
+
+#CBFLIBDIR= /afs/psi.ch/project/sls_det_software/CBFlib-0.9.5/
+#ZMQLIB=../slsReceiverSoftware/include
+#LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
+INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures -I../../slsReceiverSoftware/include 
+#-I$(CBFLIBDIR)/include/ 
+#LIBHDF5=
+LDFLAG= ../tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++ -L.  -pthread -lrt   -ltiff 
+#-L$(ZMQLIB) -lzmq -L$(CBFLIBDIR)/lib/ 
+#-L../../bin 
+MAIN=moench03ClusterFinder.cpp
+#-lhdf5
+#DESTDIR?=../bin
+
+all: moenchClusterFinderRect moenchMakeEtaRect moenchInterpolationRect moenchNoInterpolationRect moenchPhotonCounterRect moenchAnalogRect moenchMakeEtaRect1 moenchInterpolationRect1 
+
+
+
+moenchClusterFinderRect:  moench03ClusterFinder.cpp  $(INCS) clean
+			 g++ -o moenchClusterFinderRect  moench03ClusterFinder.cpp $(LDFLAG) $(INCDIR) -DSAVE_ALL  -DNEWRECEIVER -DRECT 
+
+moenchMakeEtaRect:  moench03Interpolation.cpp  $(INCS) clean
+			 g++ -o moenchMakeEtaRect moench03Interpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DFF -DRECT
+
+moenchInterpolationRect:  moench03Interpolation.cpp  $(INCS) clean
+			 g++ -o moenchInterpolationRect moench03Interpolation.cpp    $(LDFLAG) $(INCDIR)   -DRECT
+
+moenchNoInterpolationRect:  moench03NoInterpolation.cpp  $(INCS) clean
+			 g++ -o moenchNoInterpolationRect moench03NoInterpolation.cpp    $(LDFLAG) $(INCDIR)  -DRECT
+
+moenchPhotonCounterRect: moenchPhotonCounter.cpp   $(INCS) clean
+			 g++ -o moenchPhotonCounterRect  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $  -DNEWRECEIVER -DRECT
+
+moenchAnalogRect: moenchPhotonCounter.cpp  $(INCS) clean
+			 g++ -o moenchAnalogRect  moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR)   -DNEWRECEIVER -DANALOG -DRECT
+
+moenchMakeEtaRect1:  moench03Interpolation.cpp  $(INCS) clean
+			 g++ -o moenchMakeEtaRect1 moench03Interpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DFF -DRECT -DRECT1
+
+moenchInterpolationRect1:  moench03Interpolation.cpp  $(INCS) clean
+			 g++ -o moenchInterpolationRect1 moench03Interpolation.cpp    $(LDFLAG) $(INCDIR)   -DRECT  -DRECT1
+
+clean: 	
+	rm -f  moenchClusterFinderRect moenchMakeEtaRect moenchInterpolationRect moenchNoInterpolationRect moenchPhotonCounterRect moenchAnalogRect
+
+

slsDetectorCalibration/moenchExecutables/Makefile.cluster_finder_sl6

@@ -1,10 +1,15 @@
-#module add CBFlib/0.9.5
-INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures -I../../slsReceiverSoftware/include 
-
-LDFLAG= ../tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++   -pthread -lrt    -ltiff -O3
 
+CBFLIBDIR= /afs/psi.ch/project/sls_det_software/CBFlib-0.9.5/
+#ZMQLIB=../slsReceiverSoftware/include
+#LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
+INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures -I../../slsReceiverSoftware/include -I$(CBFLIBDIR)/include/ 
+#LIBHDF5=
+LDFLAG= ../tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++ -L.  -pthread -lrt -L$(CBFLIBDIR)/lib/   -ltiff 
+#-L$(ZMQLIB) -lzmq
+#-L../../bin 
 MAIN=moench03ClusterFinder.cpp
-
+#-lhdf5
+#DESTDIR?=../bin
 
 all: moenchClusterFinder moenchMakeEta moenchInterpolation moenchNoInterpolation moenchPhotonCounter moenchAnalog
 

slsDetectorCalibration/moenchExecutables/Makefile.moench

@@ -1,20 +0,0 @@
-
-CBFLIBDIR=/afs/psi.ch/project/sls_det_software/CBFlib-0.9.5
-LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
-INCDIR=-IslsDetectorCalibration -I../slsReceiverSoftware/include -I$(CBFLIBDIR)/include/ -I. -IetaVEL
-LIBHDF5=-L$(CBFLIBDIR)/lib/ -lhdf5
-LDFLAG= -L/usr/lib64/ -lpthread
-#-L../../bin 
-MAIN=moench03OnTheFlyAnalysis.C
-
-#DESTDIR?=../bin
-
-all: moench03OnTheFlyAnalysis
-
-
-
-moench03OnTheFlyAnalysis:  $(MAIN)  $(INCS) clean
-			   g++ -o moench03OnTheFlyAnalysis  $(MAIN)  -lm -ltiff -lstdc++ $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL
-
-clean:
-	rm -f moench03OnTheFlyAnalysis

slsDetectorCalibration/moenchExecutables/Makefile.moench_eta

@@ -1,23 +0,0 @@
-
-CBFLIBDIR= /home/l_msdetect/CBFlib-0.9.5
-ZMQLIB=../slsReceiverSoftware/include
-LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
-INCDIR=-IslsDetectorCalibration -I../slsReceiverSoftware/include -I$(CBFLIBDIR)/include/ -I. 
-#-IetaVEL
-LIBHDF5=
-LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++ -L. -lzmq -pthread -lrt -L$(CBFLIBDIR)/lib/ -lhdf5 -ltiff -L$(ZMQLIB)
-#-L../../bin 
-MAIN=moench03ClusterFinder.cpp
-
-#DESTDIR?=../bin
-
-all: moench03ClusterFinder
-
-
-
-moench03ClusterFinder:  $(MAIN)  $(INCS) clean
-			 g++ -o moenchClusterFinder  $(MAIN)  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) tiffIO.cpp -DSAVE_ALL
-
-clean: 	
-	rm -f  moench03ClusterFinder
-

slsDetectorCalibration/moenchExecutables/Makefile.moench_zmq_rh7

@@ -1,17 +0,0 @@
-
-ZMQLIB=../../slsReceiverSoftware/include
-INCDIR= -I$(ZMQLIB)  -I. -I../dataStructures ../tiffIO.cpp -I../ -I../interpolations/
-LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++  -lzmq -pthread -lrt -ltiff -L$(ZMQLIB)  -O3 -g
-#-L../../bin -lhdf5  -L.
-
-#DESTDIR?=../bin
-
-all:  moenchZmqProcess
-
-moenchZmqProcess:  moenchZmqProcess.cpp   clean
-		      g++ -o moenchZmqProcess  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP
-
-clean: 	
-	rm -f  moenchZmqProcess  
-
-

slsDetectorCalibration/moenchExecutables/Makefile.moench_zmq_sl6

@@ -1,12 +1,8 @@
-
-CBFLIBDIR=/afs/psi.ch/project/sls_det_software/CBFlib-0.9.5
+CBFLIBDIR= /afs/psi.ch/project/sls_det_software/CBFlib-0.9.5/
 ZMQLIB=../../slsReceiverSoftware/include
-LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
-INCDIR=-I../../slsReceiverSoftware/include -I$(CBFLIBDIR)/include/ -I. -I../dataStructures ../tiffIO.cpp -I../ -I../interpolations/
-LIBHDF5=
-#-I../interpolations/etaVEL 
-LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++ -L. -lzmq -pthread -lrt -lhdf5 -ltiff -L$(ZMQLIB) -L$(CBFLIBDIR)/lib/ -O3 
-#-L../../bin 
+INCDIR= -I$(ZMQLIB)  -I. -I../dataStructures ../tiffIO.cpp -I../ -I../interpolations/  -I$(CBFLIBDIR)/include/
+LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++  -lzmq -pthread -lrt  -lrt -L$(CBFLIBDIR)/lib/ -ltiff -L$(ZMQLIB)  -O3 
+#-L../../bin -lhdf5  -L.
 
 #DESTDIR?=../bin
 
@@ -14,7 +10,7 @@ aaa: moenchZmqProcess
 
 all: moenchZmqClusterFinder moenchZmqInterpolating moenchZmqAnalog
 
-moenchZmqProcess:  moenchZmqProcess.cpp  $(INCS) clean
+moenchZmqProcess:  moenchZmqProcess.cpp   clean
 		      g++ -o moenchZmqProcess  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ
 
 moenchZmqInterpolating:  $(MAIN)  $(INCS) clean

slsDetectorCalibration/moenchExecutables/Makefile.phoenix

@@ -1,24 +0,0 @@
-
-CBFLIBDIR= /afs/psi.ch/project/sls_det_software/CBFlib-0.9.5/
-#ZMQLIB=../slsReceiverSoftware/include
-LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
-INCDIR=-I..  -I. -I../interpolations -I../interpolations/etaVEL -I../../slsReceiverSoftware/include -I$(CBFLIBDIR)/include/  ../tiffIO.cpp -I../dataStructures
-#LIBHDF5=
-LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++ -L.  -pthread -lrt -L$(CBFLIBDIR)/lib/   -ltiff -lhdf5
-#-L$(ZMQLIB) -lzmq
-#-L../../bin 
-MAIN=moench03ClusterFinderPhoenix.cpp
-#
-#DESTDIR?=../bin
-
-all: moenchClusterFinderPhoenix 
-#moenchMakeEtaPhoenix moenchInterpolationPhoenix
-
-
-
-moenchClusterFinderPhoenix:  $(MAIN)  $(INCS) clean
-			 g++ -o moenchClusterFinderPhoenix  $(MAIN)  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)
-
-clean: 	
-	rm -f  moenchClusterFinderPhoenix 
-

slsDetectorCalibration/moenchExecutables/Makefile.reoder_image

@@ -1,22 +0,0 @@
-
-CBFLIBDIR= /afs/psi.ch/project/sls_det_software/CBFlib-0.9.5/
-#ZMQLIB=../slsReceiverSoftware/include
-INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures -I../../slsReceiverSoftware/include -I$(CBFLIBDIR)/include/ 
-LDFLAG= ../tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++ -L.  -pthread -lrt -L$(CBFLIBDIR)/lib/   -ltiff 
-MAIN=moench03ReorderImage.cpp
-
-all: moenchReorderImage moenchClusterFinder
-
-
-
-moenchReorderImage:  $(MAIN)  $(INCS) clean
-			 g++ -o moenchReorderImage  $(MAIN)  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DNEWRECEIVER 
-
-moenchClusterFinder: moench03ClusterFinder.cpp
-			 g++ -o moenchClusterFinder  $(MAIN)  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DNEWRECEIVER 
-
-
-clean: 	
-	rm -f  moenchReorderImage moenchClusterFinder
-
-

slsDetectorCalibration/moenchExecutables/Makefile.tiff_to_th2f

@@ -1,27 +0,0 @@
-#INCSROOT= receiverGui.h 
-#INCS= $(INCSROOT) moench03_receiver.h 
-#LINKDEF=receiverGuiLinkDef.h 
-
-#CBFLIBDIR= /afs/psi.ch/project/sls_det_software/CBFlib-0.9.5/
-#ZMQLIB=../slsReceiverSoftware/include
-#LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
-INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures -I../../slsReceiverSoftware/include -I$(ROOTSYS)/include
-#-I$(CBFLIBDIR)/include/ 
-#LIBHDF5=
-LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++ -L.  -pthread -lrt  -ltiff 
-#-L$(CBFLIBDIR)/lib/ -lhdf5 
-
-MAIN=tiff_to_th2f.cpp 
-
-
-all: tiff_to_th2f 
-
-
-
-tiff_to_th2f: $(MAIN)  $(INCS) 
-	      	
-	   g++ -o tiff_to_th2f  $(MAIN) `root-config --cflags --glibs` -lMinuit -lm -ltiff -lstdc++ $(LDFLAG) $(INCDIR)  ../tiffIO.cpp 
-#$(LIBRARYCBF)  $(LIBHDF5)
-clean: 	
-	rm -f tiff_to_th2f
-

slsDetectorCalibration/moenchExecutables/Makefile.zmq

@@ -0,0 +1,24 @@
+
+INCDIR=   -I. -I../dataStructures ../tiffIO.cpp -I../ -I../interpolations/ -I../../slsDetectorSoftware/commonFiles/ -I../../slsReceiverSoftware/include/
+LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++  -lzmq -pthread -lrt -ltiff   -O3 -g -std=c++11 -Wall
+#-L../../bin -lhdf5  -L.
+
+#DESTDIR?=../bin
+
+all:  moenchZmqProcess moenchZmqProcessHighZ moenchZmqProcessRect
+
+moenchZmqProcess:  moenchZmqProcess.cpp   clean
+		      g++ -o moenchZmqProcess  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP
+moenchZmqProcessRect:  moenchZmqProcess.cpp   clean
+		      g++ -o moenchZmqProcessRect  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP -DRECT
+		      
+moenchZmqProcessHighZ:  moenchZmqProcess.cpp   clean
+		      g++ -o moenchZmqProcessHighZ  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP -DHIGHZ
+
+
+
+clean: 	
+	rm -f  moenchZmqProcess  moenchZmqProcessHighZ
+
+
+

slsDetectorCalibration/moenchExecutables/moench03ClusterFinder.cpp

@@ -1,6 +1,7 @@
 //#include "ansi.h"
 #include <iostream>
 
+// bin/moenchClusterFinder moench03_25022020 moench_fluo_outputs flat_27keV_d0_f000000%d00000_1 0 10
 
 //#include "moench03T1ZmqData.h"
 #ifdef NEWRECEIVER
@@ -22,6 +23,10 @@
 #include "moench03Ctb10GbT1Data.h"
 #endif 
 
+#ifdef REORDERED
+#include "moench03T1ReorderedData.h"
+#endif
+
 // #include "interpolatingDetector.h"
 //#include "etaInterpolationPosXY.h"
 // #include "linearInterpolation.h"
@@ -29,7 +34,9 @@
 #include "multiThreadedAnalogDetector.h"
 #include "singlePhotonDetector.h"
 //#include "interpolatingDetector.h"
-
+ 
+#include <string>
+#include <sstream>  
 #include <stdio.h>
 #include <map>
 #include <fstream>
@@ -46,20 +53,20 @@ int main(int argc, char *argv[]) {
     cout << "Usage is " << argv[0] << "indir outdir fname runmin runmax " << endl;
     return 1;
   }
-  int p=10000;
+  //int p=10000;
   int fifosize=1000;
-  int nthreads=24;
-  int nsubpix=25;
-  int etabins=nsubpix*10;
-  double etamin=-1, etamax=2;
+  int nthreads=16;
+  //int nsubpix=25;
+  //int etabins=nsubpix*10;
+  //double etamin=-1, etamax=2;
   int csize=3;
   int nx=400, ny=400;
-  int save=1;
+  //int save=1;
   int nsigma=5;
   int nped=1000;
-  int ndark=100;
-  int ok;
-  int iprog=0;
+  //int ndark=100;
+  //int ok;
+  //int iprog=0;
 
 
 
@@ -83,6 +90,14 @@ int main(int argc, char *argv[]) {
   cout << "OLD RECEIVER DATA!"<<endl;
 #endif
 
+#ifdef REORDERED
+  moench03T1ReorderedData *decoder=new  moench03T1ReorderedData();
+  cout << "REORDERED DATA!"<<endl;
+#endif
+
+
+  decoder->getDetectorSize(nx,ny);
+  cout << "nx " << nx << " ny " << ny << endl;
 
   //moench03T1ZmqData *decoder=new  moench03T1ZmqData();
   singlePhotonDetector *filter=new singlePhotonDetector(decoder,csize, nsigma, 1, 0, nped, 200);
@@ -96,9 +111,9 @@ int main(int argc, char *argv[]) {
   // cout << "filter "<< endl;
   
 
-  int size = 327680;////atoi(argv[3]);
+  //int size = 327680;////atoi(argv[3]);
   
-  int* image;
+  //int* image;
 	//int* image =new int[327680/sizeof(int)];
   filter->newDataSet();
 
@@ -108,21 +123,21 @@ int main(int argc, char *argv[]) {
   cout << " data size is " << dsize;
   
 
-  char data[dsize];
+  //char data[dsize];
 
   ifstream filebin;
-  char *indir=argv[1];
-  char *outdir=argv[2];
-  char *fformat=argv[3];
+  string indir=string(argv[1]);
+  string outdir=string(argv[2]);
+  string fformat=string(argv[3]);
   int runmin=atoi(argv[4]);
   int runmax=atoi(argv[5]);
   
-  char fname[10000];
-  char outfname[10000];
-  char imgfname[10000];
-  char pedfname[10000];
+  string fname;
+  string outfname;
+  string imgfname;
+  //char pedfname[10000];
   //  strcpy(pedfname,argv[6]);
-  char fn[10000];
+  char  fn[10000];
   
   std::time_t end_time;
 
@@ -136,12 +151,6 @@ int main(int argc, char *argv[]) {
   cout << std::ctime(&end_time) <<   endl;
  
 
-
-
-
-
-
-
   char* buff;
   multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
 
@@ -158,17 +167,26 @@ int main(int argc, char *argv[]) {
  
 
   for (int irun=runmin; irun<runmax; irun++) {
-    sprintf(fn,fformat,irun);
-    sprintf(fname,"%s/%s.raw",indir,fn);
-    sprintf(outfname,"%s/%s.clust",outdir,fn);
-    sprintf(imgfname,"%s/%s.tiff",outdir,fn);
+    sprintf(fn,fformat.c_str(),irun);
+    fname=indir+"/"+string(fn)+".raw";
+    //sprintf(fname,"%s/%s.raw",indir,fn);
+#ifndef WRITE_QUAD
+    outfname=outdir+string(fn)+".clust";
+    //sprintf(outfname,"%s/%s.clust",outdir,fn);
+#endif
+#ifdef WRITE_QUAD
+    outfname=outdir+string(fn)+".clust2";
+    //    sprintf(outfname,"%s/%s.clust2",outdir,fn);
+#endif
+    imgfname=outdir+string(fn)+".tiff";
+    //sprintf(imgfname,"%s/%s.tiff",outdir,fn);
     std::time(&end_time);
     cout << std::ctime(&end_time) <<    endl;
     cout <<  fname << " " << outfname << " " << imgfname <<  endl;
-    filebin.open((const char *)(fname), ios::in | ios::binary);
+    filebin.open(fname.c_str(), ios::in | ios::binary);
     //      //open file
     if (filebin.is_open()){
-      of=fopen(outfname,"w");
+      of=fopen(outfname.c_str(),"w");
       if (of) {
   	mt->setFilePointer(of);
 	//	cout << "file pointer set " << endl;
@@ -183,16 +201,24 @@ int main(int argc, char *argv[]) {
 	//	cout << "*"<<ifr++<<"*"<<ff<< endl;
 	//	cout << ff << " " << np << endl;
   	//         //push
-	mt->pushData(buff);
-  // 	//         //pop
-	mt->nextThread();
-  // // 		//	cout << " " << (void*)buff;
-	mt->popFree(buff);
-	ifr++;
-	if (ifr%10000==0) cout << ifr << " " << ff << endl;
+	// for (int ix=0; ix<400; ix++)
+	//   for (int iy=0; iy<400; iy++) {
+	//     if (decoder->getChannel(buff, ix, iy)<3000 || decoder->getChannel(buff, ix, iy)>8000) {
+	//       cout <<  ifr << " " << ff << " " << ix << " " << iy << " " << decoder->getChannel(buff, ix, iy) << endl ;
+	//     }
+	//   }
+	if (np==40) {
+	  mt->pushData(buff);
+	  // 	//         //pop
+	  mt->nextThread();
+	  // // 		//	cout << " " << (void*)buff;
+	  mt->popFree(buff);
+	  ifr++;
+	  if (ifr%10000==0) cout << ifr << " " << ff << endl;
+	}
 	ff=-1;
       }
-        cout << "--" << endl;
+      cout << "--" << endl;
       filebin.close();	 
       //      //close file 
       //     //join threads
@@ -200,7 +226,7 @@ int main(int argc, char *argv[]) {
       if (of)
   	fclose(of);
       
-      mt->writeImage(imgfname);
+      mt->writeImage(imgfname.c_str());
       mt->clearImage();
    
       std::time(&end_time);

slsDetectorCalibration/moenchExecutables/moench03ClusterFinderPhoenix.cpp

@@ -1,201 +0,0 @@
-//#include "ansi.h"
-#include <iostream>
-
-//#include "moench03T1ZmqData.h"
-//#include "moench03T1ReceiverData.h"
-
-#include "moench03Ctb10GbT1Data.h"
-
-// #include "interpolatingDetector.h"
-//#include "etaInterpolationPosXY.h"
-// #include "linearInterpolation.h"
-// #include "noInterpolation.h"
-#include "multiThreadedAnalogDetector.h"
-#include "singlePhotonDetector.h"
-//#include "interpolatingDetector.h"
-
-#include <stdio.h>
-#include <map>
-#include <fstream>
-#include <sys/stat.h>
-
-#include <ctime>
-using namespace std;
-
-
-int main(int argc, char *argv[]) {
-
-
-  if (argc<6) {
-    cout << "Usage is " << argv[0] << "indir outdir fname runmin runmax " << endl;
-    return 0;
-  }
-  int ii=0;
-  int p=10000;
-  int fifosize=1000;
-  int nthreads=5;
-  int nsubpix=25;
-  int etabins=nsubpix*10;
-  double etamin=-1, etamax=2;
-  int csize=3;
-  int nx=400, ny=400;
-  int save=1;
-  int nsigma=5;
-  int nped=1000;
-  int ndark=100;
-  int ok;
-  int iprog=0;
-  moench03Ctb10GbT1Data *decoder=new  moench03Ctb10GbT1Data();
-  cout << "decoder" << endl;
-  //moench03T1ReceiverData *decoder=new  moench03T1ReceiverData();
-  //moench03T1ZmqData *decoder=new  moench03T1ZmqData();
-  singlePhotonDetector *filter=new singlePhotonDetector(decoder,csize, nsigma, 1, 0, nped, 100);
-  //  char tit[10000];
-  cout << "filter" << endl;
-
-
-
-
-  // filter->readPedestals("/scratch/ped_100.tiff");
-  // interp->readFlatField("/scratch/eta_100.tiff",etamin,etamax);
-  // cout << "filter "<< endl;
-  
-
-  int size = 327680;////atoi(argv[3]);
-  
-  int* image;
-	//int* image =new int[327680/sizeof(int)];
-  filter->newDataSet();
-
-  cout << "dataset" << endl;
-
-  int ff, np;
-  int dsize=decoder->getDataSize();
-  cout << " data size is " << dsize << endl;
-  
-
-  char data[dsize];
-
-  ifstream filebin;
-  char *indir=argv[1];
-  cout << "input directory is " << indir << endl;
-  char *outdir=argv[2];
-  cout << "output directory is " << outdir << endl;
-  char *fformat=argv[3];
-  cout << "fileformat is " << fformat << endl;
-  int runmin=atoi(argv[4]);
-  cout << "runmin : " << runmin << endl;
-  int runmax=atoi(argv[5]);
-  cout << "runmax : " << runmax << endl;
-  
-  char fname[10000];
-  char outfname[10000];
-  char imgfname[10000];
-  char pedfname[10000];
-  char fn[10000];
-  
-  std::time_t end_time;
-
-  FILE *of=NULL;
-  
-  
-  cout << "time " << endl;
-  std::time(&end_time);
-  cout << std::ctime(&end_time) <<   endl;
-  filter->setFrameMode(eFrame);
-	//  mt->setFrameMode(ePedestal);
- 
-
-  // for (int ix=0; ix<400; ix++)
-  //   for (int iy=0; iy<400; iy++)
-  //     cout << ix << " " << iy << " " << filter->getPedestal(ix,iy) << " " << filter->getPedestalRMS(ix,iy) << endl;
-
-
-  char* buff;
-  cout << "aa " << endl;
-  multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
-  cout << "mt " << endl;
-  
-  // mt->setFrameMode(eFrame); //need to find a way to switch between flat and frames!
-  // mt->prepareInterpolation(ok);
-  mt->setFrameMode(eFrame);
-  mt->StartThreads();
-  mt->popFree(buff);
-  
-
-  
-  int ifr=0;
-  // //loop on files
-  // mt->setFrameMode(eFrame);
-  //mt->setFrameMode(eFlat);
-  
-  
-  
-  
-  
-  for (int irun=runmin; irun<runmax; irun++) {
-    sprintf(fn,fformat,irun);
-    sprintf(fname,"%s/%s.raw",indir,fn);
-    sprintf(outfname,"%s/%s.clust",outdir,fn);
-    sprintf(imgfname,"%s/%s.tiff",outdir,fn);
-    std::time(&end_time);
-    cout << std::ctime(&end_time) <<    endl;
-    cout <<  fname << " " << outfname << " " << imgfname <<  endl;
-    filebin.open((const char *)(fname), ios::in | ios::binary);
-    //      //open file
-    if (filebin.is_open()){
-      of=fopen(outfname,"w");
-      if (of) {
-  	mt->setFilePointer(of);
-	//	cout << "file pointer set " << endl;
-      } else {
-  	cout << "Could not open "<< outfname << " for writing " << endl;
-  	mt->setFilePointer(NULL);
-  	return 1;
-      }
-      //     //while read frame 
-      ff=-1;
-      while (decoder->readNextFrame(filebin, ff, np,buff)) {
-	//cout << "*"<<ifr++<<"*"<<ff<< endl;
-	//cout << ff << " " << np << endl;
-  	//         //push
-  		mt->pushData(buff);
-  // 	//         //pop
-  		mt->nextThread();
-  // // 		//	cout << " " << (void*)buff;
-   		mt->popFree(buff);
-	
-		ff=-1;
-		ii++;
-		if (ii%10000==0) {
-
-		  cout << ii << endl;
-
-		  while (mt->isBusy()) {;}//wait until all data are processed from the queues
-		  mt->writeImage("/scratch/tmp.tiff");
-      		}
-      }
-      //  cout << "--" << endl;
-      filebin.close();	 
-      //      //close file 
-      //     //join threads
-      while (mt->isBusy()) {;}//wait until all data are processed from the queues
-      if (of)
-  	fclose(of);
-      
-      mt->writeImage(imgfname);
-      mt->clearImage();
-   
-      std::time(&end_time);
-      cout << std::ctime(&end_time) <<   endl;
-
-    } else 
-     cout << "Could not open "<< fname << " for reading " << endl;
-      
-    
-  }
-    
-
-  return 0;
-}
-

slsDetectorCalibration/moenchExecutables/moench03CodedApertureColor.cpp

@@ -0,0 +1,245 @@
+
+#include "ansi.h"
+#include <iostream>
+#include <math.h>
+
+//#include "moench03T1ZmqData.h"
+//#define DOUBLE_SPH
+//#define MANYFILES
+
+#ifdef DOUBLE_SPH
+#include "single_photon_hit_double.h"
+#endif
+
+#ifndef DOUBLE_SPH
+#include "single_photon_hit.h"
+#endif
+
+//#include "etaInterpolationPosXY.h"
+#include "slsInterpolation.h"
+#include "Stat.h"
+//#include "etaInterpolationRandomBins.h"
+using namespace std;
+#define NC 400
+#define NR 400
+#define MAX_EBINS 100
+
+int main(int argc, char *argv[]) {
+
+  if (argc<7) {
+    cout << "Wrong usage! Should be: "<< argv[0] << " infile  outfile runmin runmax cmin cmax nb" << endl;
+    return 1;
+  }
+  
+  int iarg=4;
+  char infname[10000];
+  char fname[10000];
+  char outfname[10000];
+
+  float img[NC*NR];
+  iarg=3;
+
+  int runmin=atoi(argv[iarg++]);
+  int runmax=atoi(argv[iarg++]); 
+  cout << "Run min: " << runmin << endl;
+  cout << "Run max: " << runmax << endl;
+  
+
+  float cmin=atof(argv[iarg++]);
+  float cmax=atof(argv[iarg++]);
+  cout << "Energy min: " << cmin << endl;
+  cout << "Energy max: " << cmax << endl;
+  int n_ebins=1;
+  if (argc>iarg)
+    n_ebins=atoi(argv[iarg++]);
+  //int etabins=500;
+  int etabins=1000;//nsubpix*2*100;
+  double etamin=-1, etamax=2;
+  //double etamin=-0.1, etamax=1.1;
+  double eta3min=-2, eta3max=2;
+  int quad;
+  double sum, totquad;
+  double sDum[2][2];
+  double etax, etay, int_x, int_y;
+  double eta3x, eta3y, int3_x, int3_y, noint_x, noint_y;
+  int ok;
+  int f0=-1;
+  int ix, iy, isx, isy;
+  int nframes=0, lastframe=-1;
+  double d_x, d_y, res=5, xx, yy;
+  int nph=0, badph=0, totph=0;
+    FILE *f=NULL;
+
+    single_photon_hit cl(3,3);
+
+
+    int iebin=0;
+    double eb_size=(cmax-cmin)/n_ebins;
+
+    Stat *statsX=new Stat[(n_ebins+1)*NC*NR];
+    Stat *statsY=new Stat[(n_ebins+1)*NC*NR];
+    
+
+    int irun;
+    for (irun=runmin; irun<runmax; irun++) {
+      sprintf(infname,argv[1],irun);
+ 
+      f=fopen(infname,"r");
+      if (f) {
+	cout << infname << endl;
+	nframes=0;
+	f0=-1;
+
+	while (cl.read(f)) {
+	  totph++;
+	  if (lastframe!=cl.iframe) {
+	    lastframe=cl.iframe;
+	    // cout << cl.iframe << endl;
+	    // f0=cl.iframe;
+	    if (nframes==0) f0=lastframe;
+	    nframes++;
+	  }
+	  slsInterpolation::calcEta(cl.get_cluster(), etax, etay, sum, totquad, sDum);
+	  if (sum>cmin && totquad/sum>0.8 && totquad/sum<1.2 && sum<cmax ) {
+	    nph++;
+	    iebin=(sum-cmin)/eb_size;
+	    if (iebin>=0 && iebin<n_ebins && cl.x>=0 && cl.x<NC && cl.y>=0 && cl.y<NR) {
+	      statsX[iebin+cl.x*(n_ebins+1)+cl.y*(NC*(n_ebins+1))].Push(etax);
+	      statsY[iebin+cl.x*(n_ebins+1)+cl.y*(NC*(n_ebins+1))].Push(etay);  
+	      statsX[n_ebins+cl.x*(n_ebins+1)+cl.y*(NC*(n_ebins+1))].Push(etax);
+	      statsY[n_ebins+cl.x*(n_ebins+1)+cl.y*(NC*(n_ebins+1))].Push(etay);  
+	    }
+	    
+	    if (nph%1000000==0) cout << nph << endl;
+	   
+	  }
+	} 
+	fclose(f);
+      } else
+	  cout << "could not open file " << infname << endl;
+    
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_abs_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsX[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].NumDataValues();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_etameanX_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsX[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].Mean();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_etarmsX_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsX[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].StandardDeviation();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_etameanY_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsY[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].Mean();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_etarmsY_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsY[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].StandardDeviation();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+
+
+      
+
+    }
+
+
+
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_abs_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsX[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].NumDataValues();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_etameanX_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsX[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].Mean();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_etarmsX_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsX[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].StandardDeviation();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+      
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_etameanY_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsY[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].Mean();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+      for (int ien=0; ien<n_ebins+1; ien++) {
+	sprintf(outfname,"%s_etarmsY_energy%d.tiff",argv[2],ien);
+	for (int iy=0; iy<NR; iy++) {
+	  for (int ix=0; ix<NC; ix++) {
+	    img[ix+NC*iy]= statsY[ien+ix*(n_ebins+1)+iy*(NC*(n_ebins+1))].StandardDeviation();
+	  }
+	}
+	WriteToTiff(img, outfname, NR, NC);
+      }
+      
+      
+
+
+    cout << "Filled " << nph << " (/"<< totph <<") " << endl; 
+    return 0;
+}
+

slsDetectorCalibration/moenchExecutables/moench03Interpolation.cpp

@@ -5,7 +5,7 @@
 //#include "moench03T1ZmqData.h"
 //#define DOUBLE_SPH
 //#define MANYFILES
-
+//#define WRITE_QUAD
 #ifdef DOUBLE_SPH
 #include "single_photon_hit_double.h"
 #endif
@@ -14,13 +14,21 @@
 #include "single_photon_hit.h"
 #endif
 
-//#include "etaInterpolationPosXY.h"
+#include "etaInterpolationPosXY.h"
 #include "noInterpolation.h"
-#include "etaInterpolationCleverAdaptiveBins.h"
+//#include "etaInterpolationCleverAdaptiveBins.h"
 //#include "etaInterpolationRandomBins.h"
 using namespace std;
+#ifndef RECT
 #define NC 400
 #define NR 400
+#endif
+#ifdef RECT
+#define NC 200
+#define NR 800
+#endif
+
+
 #define MAX_ITERATIONS (nSubPixels*100)
 
 #define XTALK
@@ -42,9 +50,9 @@ int main(int argc, char *argv[]) {
 #endif
   int iarg=4;
   char infname[10000];
-  char fname[10000];
   char outfname[10000];
 #ifndef FF
+  char fname[10000];
   iarg=4;
 #endif
 
@@ -66,22 +74,42 @@ int main(int argc, char *argv[]) {
   cout << "Energy min: " << cmin << endl;
   cout << "Energy max: " << cmax << endl;
   //int etabins=500;
+#ifndef NOINTERPOLATION
   int etabins=1000;//nsubpix*2*100;
+  int etabinsY=etabins;//nsubpix*2*100;
+
   double etamin=-1, etamax=2;
   //double etamin=-0.1, etamax=1.1;
-  double eta3min=-2, eta3max=2;
+ 
+  double etax=0, etay=0; 
+#ifndef FF
+  double int_x, int_y;
+  //  double d_x, d_y, res=5, xx, yy;
+  int ok;
+#endif
+#ifdef ETA3
+  etamin=-2;
+  etamax=2;
+#endif
+#endif
+  //#ifndef FF
   int quad;
+  //#endif
   double sum, totquad;
   double sDum[2][2];
-  double etax, etay, int_x, int_y;
-  double eta3x, eta3y, int3_x, int3_y, noint_x, noint_y;
-  int ok;
+
+#ifdef NOINTERPOLATION
+#ifndef FF
+  double noint_x, noint_y;
+#endif
+#endif
   int f0=-1;
   int ix, iy, isx, isy;
   int nframes=0, lastframe=-1;
-  double d_x, d_y, res=5, xx, yy;
-  int nph=0, badph=0, totph=0;
-    FILE *f=NULL;
+
+  //badph=0,
+  int nph=0,  totph=0;
+  FILE *f=NULL;
 
 #ifdef DOUBLE_SPH
     single_photon_hit_double cl(3,3);
@@ -90,23 +118,38 @@ int main(int argc, char *argv[]) {
 #ifndef DOUBLE_SPH
     single_photon_hit cl(3,3);
 #endif
-
     int nSubPixels=nsubpix;
+    int nSubPixelsY=nsubpix;
+#ifdef RECT1
+//     nSubPixels=2; //might make more sense using 2?
+//     etabins=100;
+    
+    
+    float *rectimg=new float[NC*NR*nSubPixelsY];;
+#endif
+// #endif
 #ifndef NOINTERPOLATION
-   eta2InterpolationPosXY *interp=new eta2InterpolationPosXY(NC, NR, nsubpix, etabins, etamin, etamax);
+#ifndef ETA3
+    eta2InterpolationPosXY *interp=new eta2InterpolationPosXY(NC, NR, nSubPixels, nSubPixelsY, etabins, etabinsY, etamin, etamax);
+#endif
+#ifdef ETA3
+    eta3InterpolationPosXY *interp=new eta3InterpolationPosXY(NC, NR, nSubPixels, nSubPixelsY, etabins, etabinsY, etamin, etamax);
+#endif
+
    //eta2InterpolationCleverAdaptiveBins *interp=new eta2InterpolationCleverAdaptiveBins(NC, NR, nsubpix, etabins, etamin, etamax);  
 #endif
 #ifdef NOINTERPOLATION
-    noInterpolation *interp=new noInterpolation(NC, NR, nsubpix);  
+    noInterpolation *interp=new noInterpolation(NC, NR, nsubpix, nSubPixelsY);  
 #endif
 
 
  
 #ifndef FF
+    int *img;
 #ifndef NOINTERPOLATION
     cout << "read ff " << argv[2] << endl;
     sprintf(fname,"%s",argv[2]);
-    interp->readFlatField(fname);
+    interp->readFlatField(fname, etamin, etamax);
     interp->prepareInterpolation(ok);//, MAX_ITERATIONS);
 #endif
     // return 0;
@@ -115,13 +158,12 @@ int main(int argc, char *argv[]) {
     cout << "Will write eta file " << argv[2] << endl;
 #endif
 
-    int *img;
-    float *totimg=new float[NC*NR*nsubpix*nsubpix];
+    float *totimg=new float[NC*NR*nSubPixels*nSubPixelsY];
     for (ix=0; ix<NC; ix++) {
       for (iy=0; iy<NR; iy++) {
-	for (isx=0; isx<nsubpix; isx++) {
-	  for (isy=0; isy<nsubpix; isy++) {
-	    totimg[ix*nsubpix+isx+(iy*nsubpix+isy)*(NC*nsubpix)]=0;
+	for (isx=0; isx<nSubPixels; isx++) {
+	  for (isy=0; isy<nSubPixelsY; isy++) {
+	    totimg[ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels)]=0;
 	      }
 	}
       }
@@ -148,37 +190,56 @@ int main(int argc, char *argv[]) {
 	  totph++;
 	  if (lastframe!=cl.iframe) {
 	    lastframe=cl.iframe;
-	    // cout << cl.iframe << endl;
-	    // f0=cl.iframe;
 	    if (nframes==0) f0=lastframe;
 	    nframes++;
 	  }
-	  //quad=interp->calcQuad(cl.get_cluster(), sum, totquad, sDum);
+	  //#ifndef FF
+#ifndef ETA3
 	  quad=interp->calcEta(cl.get_cluster(), etax, etay, sum, totquad, sDum);
+#endif
+#ifdef ETA3
+	  quad=interp->calcEta3(cl.get_cluster(), etax, etay, sum);
+	  totquad=sum;
+#endif
+	  //#endif
+// #ifdef FF
+// #ifndef ETA3
+// 	  interp->calcEta(cl.get_cluster(), etax, etay, sum, totquad, sDum);
+// #endif
+// #endif
+	  
 	    if (sum>cmin && totquad/sum>0.8 && totquad/sum<1.2 && sum<cmax ) {
-	    nph++;
+	      nph++;
 	    //  if (sum>200 && sum<580) {
 	    //  interp->getInterpolatedPosition(cl.x,cl.y, totquad,quad,cl.get_cluster(),int_x, int_y);
 // #ifdef SOLEIL
 // 	    if (cl.x>210 && cl.x<240 && cl.y>210 && cl.y<240) {
 // #endif
+	    if (cl.x<0 || cl.y<0 || cl.x>NC || cl.y>NR) {
+	      if (cl.x<-1 || cl.y<-1 || cl.x>NC+1 || cl.y>NR+1) {
+		cout <<"**************"<< endl;
+		cout << cl.x << " " << cl.y << " " << sum << endl;
+		cl.print();
+		cout <<"**************"<< endl;
+	      }
+	    } else  {
 #ifndef FF
-	    // interp->getInterpolatedPosition(cl.x,cl.y, cl.get_cluster(),int_x, int_y);  
-	    interp->getInterpolatedPosition(cl.x,cl.y, etax, etay, quad,int_x, int_y);
+	      // interp->getInterpolatedPosition(cl.x,cl.y, cl.get_cluster(),int_x, int_y);  
+	      interp->getInterpolatedPosition(cl.x,cl.y, etax, etay, quad,int_x, int_y);
 	      // cout <<"**************"<< endl;
 	      // cout << cl.x << " " << cl.y << " " << sum << endl;
 	      // cl.print();
 	      // cout << int_x << " " << int_y << endl;
 	      // cout <<"**************"<< endl;
 	    //  if (etax!=0 && etay!=0 && etax!=1 && etay!=1)
-	    interp->addToImage(int_x, int_y);
-	    if (int_x<0 || int_y<0 || int_x>400 || int_y>400) {
-	      cout <<"**************"<< endl;
-	      cout << cl.x << " " << cl.y << " " << sum << endl;
-	      cl.print();
-	      cout << int_x << " " << int_y << endl;
-	      cout <<"**************"<< endl;
-	    }
+	      if (int_x<-1 || int_y<-1 || int_x>NC+1 || int_y>NR+1) {
+		cout <<"**************"<< endl;
+		cout << cl.x << " " << cl.y << " " << sum << endl;
+		cl.print();
+		cout << int_x << " " << int_y << endl;
+		cout <<"**************"<< endl;
+	      } else
+		interp->addToImage(int_x, int_y);
 #endif
 #ifdef FF
 	    //	interp->addToFlatField(cl.get_cluster(), etax, etay);
@@ -190,6 +251,7 @@ int main(int argc, char *argv[]) {
 	    //  if (etax==0 || etay==0) cout << cl.x << " " << cl.y << endl;
 	     
 #endif
+	    }
 // #ifdef SOLEIL
 // 	    }
 // #endif
@@ -215,28 +277,63 @@ int main(int argc, char *argv[]) {
 #endif
 	
 #ifndef FF
+#ifndef RECT1
 	interp->writeInterpolatedImage(outfname); 
-
+#endif
 	img=interp->getInterpolatedImage();
 	for (ix=0; ix<NC; ix++) {
-	  for (iy=0; iy<NR; iy++) {
-	    for (isx=0; isx<nsubpix; isx++) {
-	      for (isy=0; isy<nsubpix; isy++) {
-		totimg[ix*nsubpix+isx+(iy*nsubpix+isy)*(NC*nsubpix)]+=img[ix*nsubpix+isx+(iy*nsubpix+isy)*(NC*nsubpix)];
+	  for (iy=0; iy<NR; iy++) {	
+	     
+	      for (isx=0; isx<nSubPixels; isx++) {
+	      for (isy=0; isy<nSubPixelsY; isy++) {
+		totimg[ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels)]+=img[ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels)];
+#ifdef RECT1
+		if (isx==0) 
+		  rectimg[ix+(iy*nSubPixelsY+isy)*(NC)]=img[ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels)];
+		else
+		  rectimg[ix+(iy*nSubPixelsY+isy)*(NC)]+=img[ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels)];
+
+#endif
 		}
 	    }
 	  }
 	}
-	cout << "Read " << nframes << " frames (first frame: " << f0 << " last frame: " << lastframe << " delta:" << lastframe-f0 << ") nph="<< nph <<endl;
+	
+#ifdef RECT1
+	WriteToTiff(rectimg, outfname,NC,NR*nSubPixelsY);
+#endif
 	interp->clearInterpolatedImage();
 #endif
+	cout << "Read " << nframes << " frames (first frame: " << f0 << " last frame: " << lastframe << " delta:" << lastframe-f0 << ") nph="<< nph <<endl;
 	
       } else
 	cout << "could not open file " << infname << endl;
     }
 #ifndef FF
     sprintf(outfname,argv[3],11111);
-    WriteToTiff(totimg, outfname,NC*nsubpix,NR*nsubpix);
+    
+#ifndef RECT1
+    WriteToTiff(totimg, outfname,NC*nSubPixels,NR*nSubPixelsY);
+#endif
+#ifdef RECT1
+	img=interp->getInterpolatedImage();
+	for (ix=0; ix<NC; ix++) {
+	  for (iy=0; iy<NR; iy++) {	
+	     
+	      for (isx=0; isx<nSubPixels; isx++) {
+	      for (isy=0; isy<nSubPixelsY; isy++) {
+		if (isx==0) 
+		  rectimg[ix+(iy*nSubPixelsY+isy)*(NC)]=totimg[ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels)];
+		else
+		  rectimg[ix+(iy*nSubPixelsY+isy)*(NC)]+=totimg[ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels)];
+		}
+	    }
+	  }
+	}
+	WriteToTiff(rectimg, outfname,NC,NR*nSubPixelsY);
+	
+#endif
+    
 #endif 
     
 #ifdef FF

slsDetectorCalibration/moenchExecutables/moench03InterpolationColor.cpp

@@ -1,269 +0,0 @@
-
-#include "ansi.h"
-#include <iostream>
-
-//#include "moench03T1ZmqData.h"
-//#define DOUBLE_SPH
-//#define MANYFILES
-
-#ifdef DOUBLE_SPH
-#include "single_photon_hit_double.h"
-#endif
-
-#ifndef DOUBLE_SPH
-#include "single_photon_hit.h"
-#endif
-
-//#include "etaInterpolationPosXY.h"
-#include "noInterpolation.h"
-#include "etaInterpolationCleverAdaptiveBins.h"
-//#include "etaInterpolationRandomBins.h"
-using namespace std;
-#define NC 400
-#define NR 400
-#define MAX_ITERATIONS (nSubPixels*100)
-#define MAX_EBINS 100
-#define XTALK
-
-int main(int argc, char *argv[]) {
-
-#ifndef FF
-  if (argc<9) {
-    cout << "Wrong usage! Should be: "<< argv[0] << " infile  etafile outfile runmin runmax ns cmin cmax" << endl;
-    return 1;
-  }
-#endif
-  
-#ifdef FF
-  if (argc<7) {
-    cout << "Wrong usage! Should be: "<< argv[0] << " infile  etafile runmin runmax cmin cmax" << endl;
-    return 1;
-  }
-#endif
-  int iarg=4;
-  char infname[10000];
-  char fname[10000];
-  char outfname[10000];
-#ifndef FF
-  iarg=4;
-#endif
-
-#ifdef FF
-  iarg=3;
-#endif
-  int runmin=atoi(argv[iarg++]);
-  int runmax=atoi(argv[iarg++]); 
-  cout << "Run min: " << runmin << endl;
-  cout << "Run max: " << runmax << endl;
-  
-  int nsubpix=4;
-#ifndef FF
-  nsubpix=atoi(argv[iarg++]);
-  cout << "Subpix: " << nsubpix << endl;
-#endif
-  float cmin=atof(argv[iarg++]);
-  float cmax=atof(argv[iarg++]);
-  cout << "Energy min: " << cmin << endl;
-  cout << "Energy max: " << cmax << endl;
-  int n_ebins=1;
-  if (argc>iarg)
-    n_ebins=atoi(argv[iarg++]);
-  //int etabins=500;
-  int etabins=1000;//nsubpix*2*100;
-  double etamin=-1, etamax=2;
-  //double etamin=-0.1, etamax=1.1;
-  double eta3min=-2, eta3max=2;
-  int quad;
-  double sum, totquad;
-  double sDum[2][2];
-  double etax, etay, int_x, int_y;
-  double eta3x, eta3y, int3_x, int3_y, noint_x, noint_y;
-  int ok;
-  int f0=-1;
-  int ix, iy, isx, isy;
-  int nframes=0, lastframe=-1;
-  double d_x, d_y, res=5, xx, yy;
-  int nph=0, badph=0, totph=0;
-    FILE *f=NULL;
-
-#ifdef DOUBLE_SPH
-    single_photon_hit_double cl(3,3);
-#endif
-
-#ifndef DOUBLE_SPH
-    single_photon_hit cl(3,3);
-#endif
-
-    int nSubPixels=nsubpix;
-
-    int iebin=0;
-    double eb_size=(cmax-cmin)/n_ebins;
-#ifndef NOINTERPOLATION
-    //  eta2InterpolationPosXY *interp[MAX_EBINS];
-    eta2InterpolationCleverAdaptiveBins *interp[MAX_EBINS];
-    for (int i=0; i< n_ebins; i++) {
-      //interp[i]=new eta2InterpolationPosXY(NC, NR, nsubpix, etabins, etamin, etamax);
-      interp[i]=new eta2InterpolationCleverAdaptiveBins(NC, NR, nsubpix, etabins, etamin, etamax);  
-    }
-#endif
-#ifdef NOINTERPOLATION
-    noInterpolation *interp=new noInterpolation(NC, NR, nsubpix);  
-#endif
-
-
- 
-#ifndef FF
-#ifndef NOINTERPOLATION
-    cout << "read ff " << argv[2] << endl; 
-    for (int i=0; i< n_ebins; i++) {
-      sprintf(fname,argv[2],i);
-      interp[i]->readFlatField(fname);
-      interp[i]->prepareInterpolation(ok);//, MAX_ITERATIONS);
-    }
-#endif
-    // return 0;
-#endif
-#ifdef FF
-    cout << "Will write eta file " << argv[2] << endl;
-#endif
-
-    int *img;
-    float *totimg=new float[NC*NR*nsubpix*nsubpix];
-    for (ix=0; ix<NC; ix++) {
-      for (iy=0; iy<NR; iy++) {
-	for (isx=0; isx<nsubpix; isx++) {
-	  for (isy=0; isy<nsubpix; isy++) {
-	    totimg[ix*nsubpix+isx+(iy*nsubpix+isy)*(NC*nsubpix)]=0;
-	      }
-	}
-      }
-    }
-
-#ifdef FF
-      sprintf(outfname,argv[2]);
-#endif     
-
-    int irun;
-    for (irun=runmin; irun<runmax; irun++) {
-      sprintf(infname,argv[1],irun);
-#ifndef FF
-      sprintf(outfname,argv[3],irun);
-#endif
- 
-      f=fopen(infname,"r");
-      if (f) {
-	cout << infname << endl;
-	nframes=0;
-	f0=-1;
-
-	while (cl.read(f)) {
-	  totph++;
-	  if (lastframe!=cl.iframe) {
-	    lastframe=cl.iframe;
-	    // cout << cl.iframe << endl;
-	    // f0=cl.iframe;
-	    if (nframes==0) f0=lastframe;
-	    nframes++;
-	  }
-	  //quad=interp->calcQuad(cl.get_cluster(), sum, totquad, sDum);
-	  quad=interp[0]->calcEta(cl.get_cluster(), etax, etay, sum, totquad, sDum);
-	  if (sum>cmin && totquad/sum>0.8 && totquad/sum<1.2 && sum<cmax ) {
-	    nph++;
-	    iebin=(sum-cmin)/eb_size;
-	    if (iebin>=0 && iebin<n_ebins) {
-	    //  if (sum>200 && sum<580) {
-	    //  interp->getInterpolatedPosition(cl.x,cl.y, totquad,quad,cl.get_cluster(),int_x, int_y);
-// #ifdef SOLEIL
-// 	    if (cl.x>210 && cl.x<240 && cl.y>210 && cl.y<240) {
-// #endif
-#ifndef FF
-	    // interp->getInterpolatedPosition(cl.x,cl.y, cl.get_cluster(),int_x, int_y);  
-	    interp[iebin]->getInterpolatedPosition(cl.x,cl.y, etax, etay, quad,int_x, int_y);
-	      // cout <<"**************"<< endl;
-	      // cout << cl.x << " " << cl.y << " " << sum << endl;
-	      // cl.print();
-	      // cout << int_x << " " << int_y << endl;
-	      // cout <<"**************"<< endl;
-	    if (etax!=0 && etay!=0 && etax!=1 && etay!=1)
-	      interp[iebin]->addToImage(int_x, int_y);
-#endif
-#ifdef FF
-	    //	interp->addToFlatField(cl.get_cluster(), etax, etay);
-#ifdef UCL
-	    if (cl.x>50)
-#endif
-	      if (etax!=0 && etay!=0 && etax!=1 && etay!=1)
-		interp[iebin]->addToFlatField(etax, etay);
-	    //  if (etax==0 || etay==0) cout << cl.x << " " << cl.y << endl;
-	     
-#endif
-// #ifdef SOLEIL
-// 	    }
-// #endif
-	    
-	    if (nph%1000000==0) cout << nph << endl;
-	    if (nph%10000000==0) { 
-#ifndef FF
-	      for (int i=0; i<n_ebins; i++) {
-		sprintf(outfname,argv[3],i);
-		interp[i]->writeInterpolatedImage(outfname);
-	      }
-#endif
-#ifdef FF 
-	      for (int i=0; i<n_ebins; i++) {
-		sprintf(outfname,argv[2],i);
-		cout << outfname << " " << argv[2] << " " << i << endl;
-		interp[i]->writeFlatField(outfname);
-	      }
-#endif
-	      
-	    }
-	    }
-	    
-	  } 
-	  
-	}
-	fclose(f);
-#ifdef FF
-	for (int i=0; i<n_ebins; i++) {
-	  sprintf(outfname,argv[2],i);
-	  cout << outfname << " " << argv[2] << " " << i << endl;
-	  interp[i]->writeFlatField(outfname);
-	}
-#endif
-	
-#ifndef FF 
-	      for (int i=0; i<n_ebins; i++) {
-		sprintf(outfname,argv[3],i,irun);
-		interp[i]->writeInterpolatedImage(outfname);
-		img=interp[i]->getInterpolatedImage();
-		for (ix=0; ix<NC; ix++) {
-		  for (iy=0; iy<NR; iy++) {
-		    for (isx=0; isx<nsubpix; isx++) {
-		      for (isy=0; isy<nsubpix; isy++) {
-			totimg[ix*nsubpix+isx+(iy*nsubpix+isy)*(NC*nsubpix)]+=img[ix*nsubpix+isx+(iy*nsubpix+isy)*(NC*nsubpix)];
-		      }
-		    }
-		  }
-		}
-		//interp[i]->clearInterpolatedImage();
-	      }
-	      cout << "Read " << nframes << " frames (first frame: " << f0 << " last frame: " << lastframe << " delta:" << lastframe-f0 << ")"<<endl;
-#endif
-	
-      } else
-	cout << "could not open file " << infname << endl;
-    }
-#ifndef FF
-    sprintf(outfname,argv[3], 11111);
-    WriteToTiff(totimg, outfname,NC*nsubpix,NR*nsubpix);
-#endif 
-    
-#ifdef FF
-	interp[iebin]->writeFlatField(outfname);
-#endif
-
-    cout << "Filled " << nph << " (/"<< totph <<") " << endl; 
-    return 0;
-}
-

slsDetectorCalibration/moenchExecutables/moench03MakeEta.cpp

@@ -1,114 +0,0 @@
-
-#include "ansi.h"
-#include <iostream>
-
-#include "moench03T1ZmqData.h"
-#include "single_photon_hit.h"
-
- #include "etaInterpolationPosXY.h"
-
-using namespace std;
-#define NC 400
-#define NR 400
-
-#define XTALK
-
-int main(int argc, char *argv[]) {
-/**
- * trial.o [socket ip] [starting port number] [outfname]
- *
- */
-  int nsubpix=10;
-  int etabins=nsubpix*100;
-  double etamin=-1, etamax=2;
-  double eta3min=-2, eta3max=2;
-  int quad;
-  double sum, totquad;
-  double sDum[2][2];
-  char fname[10000];
-  double etax, etay;
-  int runmin, runmax;
-    single_photon_hit cl(3,3);
-int iph=0;
- 
-  if (argc<7) {
-    cout << "Wrong usage! Should be: "<< argv[0] << " infile " << " outfile runmin runmax cmin cmax" << endl;
-    return 1;
-  }
-
-  eta2InterpolationPosXY *interp2=new eta2InterpolationPosXY(NR, NC, nsubpix, etabins, etamin, etamax);
-  cout << "###########"<< endl;
-  eta3InterpolationPosXY *interp3=new eta3InterpolationPosXY(NR, NC, nsubpix, etabins, eta3min, eta3max);
-  // cout << eta3min << " " << eta3max << endl;
-  runmin=atoi(argv[3]);
-  runmax=atoi(argv[4]);
-  double cmin=atof(argv[5]); //200
-  double cmax=atof(argv[6]); //3000
-  
-#ifdef XTALK
-  int old_val[3][3];
-  int new_val[3][3];
-  double xcorr=0.04;
-  
-  // int ix=0;
-#endif
-
-    FILE *f;
-    for (int i=runmin; i<runmax; i++) {
-	sprintf(fname,argv[1],i);
-      f=fopen(fname,"r");
-      if (f) {
-	cout << "*" << endl;
-	while (cl.read(f)) {
-#ifdef XTALK
-	  if ((cl.x+1)%25!=0) {
-	  for (int ix=-1; ix<2; ix++) {
-	    for (int iy=-1; iy<2; iy++) {
-	      old_val[iy+1][ix+1]=cl.get_data(ix,iy);
-	      if (ix>=0) {
-		new_val[iy+1][ix+1]=old_val[iy+1][ix+1]-old_val[iy+1][ix]*xcorr;
-		cl.set_data(new_val[iy+1][ix+1],ix,iy);
-	      }
-	    }
-	  }
-	  }
-#endif
-	   quad=interp2->calcQuad(cl.get_cluster(), sum, totquad, sDum);
-	   
-	    if (sum>cmin && totquad/sum>0.8 && totquad/sum<1.2 && totquad<cmax && quad<cmax) {
-	      /* Cross talk corrections !!! */
-	      //	for (int ix=0; ix<2; ix++) {
-	  
-
-	      interp2->addToFlatField(cl.get_cluster(),etax, etay);
-	      // if (etax>0.49 && etax<0.51 && etay>0.49 && etay<0.51 ) {
-	      // 	cout << cl.y << " " << cl.x << " " << quad << " "<< totquad << " " <<sum << endl;
-
-	      // } 
-	      interp3->addToFlatField(cl.get_cluster(),etax, etay);
-	      iph++;
-	      if (iph%1000000==0) cout << iph << endl;
-	      if (iph%100000000==0) { 
-		sprintf(fname,"%s_eta2.tiff",argv[2]);
-		interp2->writeFlatField(fname);
-		sprintf(fname,"%s_eta3.tiff",argv[2]);
-		interp3->writeFlatField(fname);
-	      }
-	      // if (iph>1E8) break;
-	    }
-	    //	  }
-	  
-	}
-	fclose(f);
-	
-      }
-      else cout << "could not open file " << fname << endl;
-    }
-    
-    sprintf(fname,"%s_eta2.tiff",argv[2]);
-	interp2->writeFlatField(fname);
-    sprintf(fname,"%s_eta3.tiff",argv[2]);
-	interp3->writeFlatField(fname);
-    return 0;
-}
-

slsDetectorCalibration/moenchExecutables/moench03NoInterpolation.cpp

@@ -2,7 +2,6 @@
 #include "ansi.h"
 #include <iostream>
 
-#include "moench03T1ZmqData.h"
 #include "single_photon_hit.h"
 
 #include "noInterpolation.h"
@@ -19,7 +18,7 @@ int main(int argc, char *argv[]) {
  */
 
   if (argc<7) {
-    cout << "Wrong usage! Should be: "<< argv[0] << " infile " << " etafile outfile runmin runmax ns" << endl;
+    cout << "Wrong usage! Should be: "<< argv[0] << " infile " << " outfile runmin runmax ns" << endl;
     return 1;
   }
 
@@ -29,13 +28,14 @@ int main(int argc, char *argv[]) {
   int runmax=atoi(argv[5]);
   int nsubpix=atoi(argv[6]);
   
-  int etabins=1000;//nsubpix*2*100;
-  double etamin=-1, etamax=2;
+  //  int etabins=1000;//nsubpix*2*100;
+  // double etamin=-1, etamax=2;
   int quad;
   double sum, totquad;
   double sDum[2][2];
-  double etax, etay, int_x, int_y;
-  int ok;
+  //double etax, etay,
+  double int_x, int_y;
+  //int ok;
 
   int ix, iy, isx, isy;
 

slsDetectorCalibration/moenchExecutables/moench03ReorderImage.cpp

@@ -1,163 +0,0 @@
-//#include "ansi.h"
-#include <iostream>
-
-
-
-//#include "moench03T1ZmqData.h"
-
-#include "moench03T1ReceiverDataNew.h"
-
-// #include "interpolatingDetector.h"
-//#include "etaInterpolationPosXY.h"
-// #include "linearInterpolation.h"
-// #include "noInterpolation.h"
-//#include "interpolatingDetector.h"
-
-#include <stdio.h>
-#include <map>
-#include <fstream>
-#include <sys/stat.h>
-
-#include <cstdlib>
-
-#include <ctime>
-using namespace std;
-
-#define NX 400 //number of x pixels
-#define NY 400 //number of y pixels
-
-int main(int argc, char *argv[]) {
-
-
-  if (argc<6) {
-    cout << "Usage is " << argv[0] << "indir outdir fname runmin runmax " << endl;
-    return 1;
-  }
-  int p=10000;
-  int fifosize=1000;
-  int nthreads=8;
-  int nsubpix=25;
-  int etabins=nsubpix*10;
-  double etamin=-1, etamax=2;
-  int csize=3;
-  int nx=400, ny=400;
-  int save=1;
-  int nsigma=5;
-  int nped=1000;
-  int ndark=100;
-  int ok;
-  int iprog=0;
-
-
-
-
-  moench03T1ReceiverDataNew *decoder=new  moench03T1ReceiverDataNew();
-
-
-  uint16_t data[NY*NX];
-
-
-  int size = 327680;////atoi(argv[3]);
-  
-  int* image;
-
-  int ff, np;
-  int dsize=decoder->getDataSize();
-  
-
-  //char data[dsize];
-
-  ifstream filebin;
-  char *indir=argv[1];
-  char *outdir=argv[2];
-  char *fformat=argv[3];
-  int runmin=atoi(argv[4]);
-  int runmax=atoi(argv[5]);
-  
-  char fname[10000];
-  char outfname[10000];
-  char imgfname[10000];
-  char pedfname[10000];
-  //  strcpy(pedfname,argv[6]);
-  char fn[10000];
-  
-  std::time_t end_time;
-
-  FILE *of=NULL;
-  cout << "input directory is " << indir << endl;
-  cout << "output directory is " << outdir << endl;
-  cout << "fileformat is " << fformat << endl;
-  
-
-  std::time(&end_time);
-  cout << std::ctime(&end_time) <<   endl;
- 
-
-
-
-
-
-
-  char* buff;
-
- 
-
-
-  int ifr=0;
- 
-
-  for (int irun=runmin; irun<runmax; irun++) {
-    sprintf(fn,fformat,irun);
-    sprintf(fname,"%s/%s.raw",indir,fn);
-    sprintf(outfname,"%s/%s_image.raw",outdir,fn);
-    std::time(&end_time);
-    cout << std::ctime(&end_time) <<    endl;
-    cout <<  fname << " " << outfname << " " << imgfname <<  endl;
-    filebin.open((const char *)(fname), ios::in | ios::binary);
-    //      //open file
-    if (filebin.is_open()){
-      of=fopen(outfname,"w");
-      if (of) {
-	;
-      } else {
-  	cout << "Could not open "<< outfname << " for writing " << endl;
-  	return 1;
-      }
-      //     //while read frame 
-      ff=-1;
-      while (decoder->readNextFrame(filebin, ff, np,buff)) {
-	for (int ix=0; ix<400; ix++)
-	  for (int iy=0; iy<400; iy++)
-	    data[iy*NX+ix]=decoder->getChannel(buff,ix,iy);
-	
-	ifr++;
-
-	fwrite(&ff, 8, 1,of);//write detector frame number
-	fwrite(&ifr, 8, 1,of);//write datset frame number
-	fwrite(data,2,NX*NY,of);//write reordered data
-
-	if (ifr%10000==0) cout << ifr << " " << ff << endl;
-	ff=-1;
-
-      }
-        cout << "--" << endl;
-      filebin.close();	 
-      //      //close file 
-      //     //join threads
-  
-      if (of)
-  	fclose(of);
-      
-      std::time(&end_time);
-      cout << std::ctime(&end_time) <<   endl;
-
-    } else 
-     cout << "Could not open "<< fname << " for reading " << endl;
-      
-    
-  }
-    
-
-  return 0;
-}
-

slsDetectorCalibration/moenchExecutables/moenchAnalog.cpp

@@ -1,242 +0,0 @@
-//#include "ansi.h"
-#include <iostream>
-
-
-
-//#include "moench03T1ZmqData.h"
-#ifdef NEWRECEIVER
-#include "moench03T1ReceiverDataNew.h"
-#endif
-#ifdef CSAXS_FP
-#include "moench03T1ReceiverData.h"
-#endif 
-#ifdef OLDDATA
-#include "moench03Ctb10GbT1Data.h"
-#endif 
-
-// #include "interpolatingDetector.h"
-//#include "etaInterpolationPosXY.h"
-// #include "linearInterpolation.h"
-// #include "noInterpolation.h"
-#include "multiThreadedAnalogDetector.h"
-#include "singlePhotonDetector.h"
-//#include "interpolatingDetector.h"
-
-#include <stdio.h>
-#include <map>
-#include <fstream>
-#include <sys/stat.h>
-
-#include <ctime>
-using namespace std;
-
-
-int main(int argc, char *argv[]) {
-
-
-  if (argc<4) {
-    cout << "Usage is " << argv[0] << "indir outdir fname [pedfile] [threshold]" << endl;
-    return 1;
-  }
-  int p=10000;
-  int fifosize=1000;
-  int nthreads=8;
-  int nsubpix=25;
-  int etabins=nsubpix*10;
-  double etamin=-1, etamax=2;
-  int csize=3;
-  int nx=400, ny=400;
-  int save=1;
-  int nsigma=5;
-  int nped=1000;
-  int ndark=100;
-  int ok;
-  int iprog=0;
-
-
-
-#ifdef NEWRECEIVER
-  moench03T1ReceiverDataNew *decoder=new  moench03T1ReceiverDataNew();
-  cout << "RECEIVER DATA WITH ONE HEADER!"<<endl;
-#endif
-
-#ifdef CSAXS_FP
-  moench03T1ReceiverData *decoder=new  moench03T1ReceiverData();
-  cout << "RECEIVER DATA WITH ALL HEADERS!"<<endl;
-#endif
-
-#ifdef OLDDATA
-  moench03Ctb10GbT1Data *decoder=new  moench03Ctb10GbT1Data();
-  cout << "OLD RECEIVER DATA!"<<endl;
-#endif
-
-#ifndef ANALOG
-  //moench03T1ZmqData *decoder=new  moench03T1ZmqData();
-  singlePhotonDetector *filter=new singlePhotonDetector(decoder,csize, nsigma, 1, 0, nped, 200);
-  //  char tit[10000];
-  cout << "filter " << endl;
-#endif
-
-#ifdef ANALOG
-  //moench03T1ZmqData *decoder=new  moench03T1ZmqData();
-  analogDetector<uint16_t> *filter=new analogDetector<uint16_t>(decoder, 1, 0, nped);
-  //  char tit[10000];
-  cout << "filter " << endl;
-#endif
-
-
-
-  // filter->readPedestals("/scratch/ped_100.tiff");
-  // interp->readFlatField("/scratch/eta_100.tiff",etamin,etamax);
-  // cout << "filter "<< endl;
-  
-
-  int size = 327680;////atoi(argv[3]);
-  
-  int* image;
-	//int* image =new int[327680/sizeof(int)];
-  filter->newDataSet();
-
-
-  int ff, np;
-  int dsize=decoder->getDataSize();
-  cout << " data size is " << dsize;
-  
-
-  char data[dsize];
-
-  ifstream filebin;
-  char *indir=argv[1];
-  char *outdir=argv[2];
-  char *fformat=argv[3];
-  char *pedfile=NULL;
-  if (argc>=5) {
-    pedfile=argv[4];
-  }
-  double thr=0;
-  if (argc>=6) {
-    thr=atoi(argv[5]);
-  }
-  
-
-  char fname[10000];
-  char imgfname[10000];
-  //  strcpy(pedfname,argv[6]);
-  char fn[10000];
-  
-  std::time_t end_time;
-
-  FILE *of=NULL;
-  cout << "input directory is " << indir << endl;
-  cout << "output directory is " << outdir << endl;
-  cout << "input file is " << fformat << endl;
-  if (pedfile)
-    cout << "pedestal file is " << pedfile << endl;
-  if (thr>0) {
-    cout << "threshold is " << thr << endl;
-    filter->setThreshold(thr);
-  }
-
-  filter->setROI(0,150,0,150);
-
-  std::time(&end_time);
-  cout << std::ctime(&end_time) <<   endl;
- 
-
-
-
-
-
-
-
-  char* buff;
-  multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
-
- 
-  mt->StartThreads();
-  mt->popFree(buff);
-
-
-  cout << "mt " << endl;
-
-  int ifr=0;
- 
-
-
-
-
-
-
-
-
-
-  for (int irun=0; irun<2; irun++) {
-    if (irun>0) {
-      mt->setFrameMode(eFrame);
-      // sprintf(fn,fformat,irun);
-      sprintf(fname,"%s/%s.raw",indir,fformat);
-    //  sprintf(outfname,"%s/%s.clust",outdir,fn);
-      sprintf(imgfname,"%s/%s.tiff",outdir,fformat);
-    } else {
-      mt->setFrameMode(ePedestal);
-      // sprintf(fn,fformat,irun);
-      sprintf(fname,"%s/%s.raw",indir,pedfile);
-    //  sprintf(outfname,"%s/%s.clust",outdir,fn);
-      // sprintf(imgfname,"%s/%s.tiff",outdir,fn);
-    }
-    cout << fname << endl;
-    std::time(&end_time);
-    cout << std::ctime(&end_time) <<    endl;
-    //  cout <<  fname << " " << outfname << " " << imgfname <<  endl;
-    filebin.open((const char *)(fname), ios::in | ios::binary);
-    //      //open file
-    if (filebin.is_open()){
-      // of=fopen(outfname,"w");
-      // if (of) {
-      // 	mt->setFilePointer(of);
-      // 	//	cout << "file pointer set " << endl;
-      // } else {
-      // 	cout << "Could not open "<< outfname << " for writing " << endl;
-      // 	mt->setFilePointer(NULL);
-      // 	return 1;
-      // }
-      //     //while read frame 
-      ff=-1;
-      while (decoder->readNextFrame(filebin, ff, np,buff)) {
-	//	cout << "*"<<ifr++<<"*"<<ff<< endl;
-	//	cout << ff << " " << np << endl;
-  	//         //push
-	mt->pushData(buff);
-  // 	//         //pop
-	mt->nextThread();
-  // // 		//	cout << " " << (void*)buff;
-	mt->popFree(buff);
-	ifr++;
-	if (ifr%10000==0) cout << ifr << " " << ff << endl;
-	ff=-1;
-      }
-      cout << "--" << endl;
-      filebin.close();	 
-      //      //close file 
-      //     //join threads
-      while (mt->isBusy()) {;}//wait until all data are processed from the queues
-      // if (of)
-      // 	fclose(of);
-      if (irun>0) {
-	cout << "Writing tiff to " << imgfname << endl;
-	mt->writeImage(imgfname);
-	//	mt->clearImage();
-      }
-      std::time(&end_time);
-      cout << std::ctime(&end_time) <<   endl;
-
-    } else 
-     cout << "Could not open "<< fname << " for reading " << endl;
-      
-    
-   }
-    
-
-  return 0;
-}
-

slsDetectorCalibration/moenchExecutables/moenchPhotonCounter.cpp

@@ -1,7 +1,12 @@
 //#include "ansi.h"
 #include <iostream>
+#define CORR
 
+#define C_GHOST 0.0004
 
+#define CM_ROWS 50
+
+//#define VERSION_V1
 
 //#include "moench03T1ZmqData.h"
 #ifdef NEWRECEIVER
@@ -27,15 +32,18 @@
 //#include "etaInterpolationPosXY.h"
 // #include "linearInterpolation.h"
 // #include "noInterpolation.h"
-#include "multiThreadedAnalogDetector.h"
+#include "multiThreadedCountingDetector.h"
+//#include "multiThreadedAnalogDetector.h"
 #include "singlePhotonDetector.h"
+#include "moench03GhostSummation.h"
+#include "moench03CommonMode.h"
 //#include "interpolatingDetector.h"
 
 #include <stdio.h>
 #include <map>
 #include <fstream>
 #include <sys/stat.h>
-
+#include <dirent.h>
 #include <ctime>
 using namespace std;
 
@@ -44,25 +52,25 @@ int main(int argc, char *argv[]) {
 
 
   if (argc<4) {
-    cout << "Usage is " << argv[0] << "indir outdir fname [runmin] [runmax] [pedfile] [threshold] [nframes] [xmin xmax ymin ymax]" << endl;
+    cout << "Usage is " << argv[0] << "indir outdir fname [runmin] [runmax] [pedfile] [threshold] [nframes] [xmin xmax ymin ymax] [gainmap]" << endl;
     cout << "threshold <0 means analog; threshold=0 means cluster finder; threshold>0 means photon counting" << endl;
     cout << "nframes <0 means sum everything; nframes=0 means one file per run; nframes>0 means one file every nframes" << endl;
     return 1;
   }
 
-  int p=10000;
+  //int p=10000;
   int fifosize=1000;
-  int nthreads=8;
-  int nsubpix=25;
-  int etabins=nsubpix*10;
-  double etamin=-1, etamax=2;
+  int nthreads=10;
+  //int nsubpix=25;
+  //int etabins=nsubpix*10;
+  //double etamin=-1, etamax=2;
   int csize=3;
-  int save=1;
+  //int save=1;
   int nsigma=5;
-  int nped=1000;
-  int ndark=100;
-  int ok;
-  int iprog=0;
+  int nped=10000;
+  //int ndark=100;
+  //int ok;
+  //int iprog=0;
 
   int cf=0;
 
@@ -88,21 +96,24 @@ int main(int argc, char *argv[]) {
 
   decoder->getDetectorSize(nx,ny);
 
-  singlePhotonDetector *filter=new singlePhotonDetector(decoder,csize, nsigma, 1, 0, nped, 200);
+  int ncol_cm=CM_ROWS;
+  double xt_ghost=C_GHOST;
+  moench03CommonMode *cm=NULL;
+  moench03GhostSummation *gs;
+  double *gainmap=NULL;
+  //float *gm;
 
-  int size = 327680;////atoi(argv[3]);
+
+
+  //int size = 327680;////atoi(argv[3]);
   
-  int* image;
+  //int* image;
 	//int* image =new int[327680/sizeof(int)];
-  filter->newDataSet();
-
 
   int ff, np;
-  int dsize=decoder->getDataSize();
   //cout << " data size is " << dsize;
   
 
-  char data[dsize];
 
   ifstream filebin;
   char *indir=argv[1];
@@ -129,7 +140,7 @@ int main(int argc, char *argv[]) {
   double thr1=1;
 
   if (argc>=8) {
-    thr=atoi(argv[7]);
+    thr=atof(argv[7]);
   }
   
 
@@ -147,6 +158,12 @@ int main(int argc, char *argv[]) {
   }
 
   
+  char *gainfname=NULL;
+  if (argc>13) {
+    gainfname=argv[13];
+    cout << "Gain map file name is: " << gainfname << endl;
+  }
+
   
 
 
@@ -154,7 +171,7 @@ int main(int argc, char *argv[]) {
   char fname[10000];
   char imgfname[10000];
   char cfname[10000];
-  char fn[10000];
+  //char fn[10000];
   
   std::time_t end_time;
 
@@ -166,25 +183,74 @@ int main(int argc, char *argv[]) {
   cout << "runmax is " << runmax << endl;
   if (pedfile)
     cout << "pedestal file is " << pedfile << endl;
+ if (thr>0) 
+    cout << "threshold is " << thr << endl;
+ uint32 unnx, unny;
+ int  nnx, nny;
+ //double *gmap;
+
+  // if (gainfname) {
+  //   gm=ReadFromTiff(gainfname, nny, nnx);
+  //   if (gm && nnx==nx && nny==ny) {
+  //     gmap=new double[nx*ny];
+  //     for (int i=0; i<nx*ny; i++) {
+  // 	gmap[i]=gm[i];
+  //     }
+  //     delete gm;
+  //   } else
+  //     cout << "Could not open gain map " << gainfname << endl;
+  // }
+
+#ifdef CORR
+ cout << "Applying common mode  " << ncol_cm << endl;
+  cm=new moench03CommonMode(ncol_cm);
+  
+
+  cout << "Applying ghost corrections " << xt_ghost << endl;
+  gs=new moench03GhostSummation(decoder, xt_ghost);
+#endif
+
+  singlePhotonDetector *filter=new singlePhotonDetector(decoder,csize, nsigma, 1, cm, nped, 200, -1, -1, gainmap, gs);
+
+  if (gainfname) {
+
+    if (filter->readGainMap(gainfname))
+      cout << "using gain map " << gainfname << endl;
+    else
+      cout << "Could not open gain map " << gainfname << endl;
+  } else
+    thr=0.15*thr;
+  filter->newDataSet();
+  //int dsize=decoder->getDataSize();
+
+
+  //char data[dsize];
+
+
+
+
+
   //#ifndef ANALOG
   if (thr>0) {
     cout << "threshold is " << thr << endl;
+    //#ifndef ANALOG
     filter->setThreshold(thr);
+    //#endif
+      cf=0;
+
   } else
     cf=1;
   //#endif
 
 
   filter->setROI(xmin,xmax,ymin,ymax);
-#ifdef SOLEIL
-  filter->setROI(150,210,170,230);
-  nframes=-1;
-#endif
   std::time(&end_time);
   cout << std::ctime(&end_time) <<   endl;
 
   char* buff;
-  multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
+
+  // multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
+ multiThreadedCountingDetector *mt=new multiThreadedCountingDetector(filter,nthreads,fifosize);
 #ifndef ANALOG
     mt->setDetectorMode(ePhotonCounting);
     cout << "Counting!" << endl;
@@ -197,81 +263,105 @@ int main(int argc, char *argv[]) {
       mt->setDetectorMode(eAnalog);
       cout << "Analog!" << endl;
       cf=0;
-// #ifdef ANALOG
-//       thr1=thr;
+      //thr1=thr;
 #endif  
       //  }
   
   mt->StartThreads();
   mt->popFree(buff);
 
-
+  DIR *dir;
+  struct dirent *ent;
+ 
   //  cout << "mt " << endl;
 
   int ifr=0;
- 
 
+  double ped[nx*ny];//, *ped1;
 
 
   if (pedfile) {
-    cout << "PEDESTAL " ;
-    sprintf(fname,"%s.raw",pedfile);
-    cout << fname << endl ;
-    sprintf(imgfname,"%s/pedestals.tiff",outdir,fformat);
-    std::time(&end_time);
-    cout << "aaa" << std::ctime(&end_time) <<   endl;
 
+    cout << "PEDESTAL " << endl;
+    sprintf(imgfname,"%s/pedestals.tiff",outdir);
 
-    mt->setFrameMode(ePedestal);
-      // sprintf(fn,fformat,irun);
-    filebin.open((const char *)(fname), ios::in | ios::binary);
-    //      //open file
-    if (filebin.is_open()){
-      ff=-1;
-      while (decoder->readNextFrame(filebin, ff, np,buff)) {
-	mt->pushData(buff);
-	mt->nextThread();
-	mt->popFree(buff);
-	ifr++;
-	if (ifr%10000==0) 
-	  cout << ifr << " " << ff << " " << np << endl;
-	ff=-1;
-      }
-      filebin.close();	 
-      while (mt->isBusy()) {;}
-      mt->writePedestal(imgfname);
+    if (string(pedfile).find(".tif")==std::string::npos){
+      sprintf(fname,"%s.raw",pedfile);
+      cout << fname << endl ;
       std::time(&end_time);
-      cout << std::ctime(&end_time) <<   endl;
+      cout << "aaa" << std::ctime(&end_time) <<   endl;
       
+      
+      mt->setFrameMode(ePedestal);
+      // sprintf(fn,fformat,irun);
+      filebin.open((const char *)(fname), ios::in | ios::binary);
+      //      //open file
+      if (filebin.is_open()){
+	ff=-1;
+	while (decoder->readNextFrame(filebin, ff, np,buff)) {
+	  if (np==40) {
+	    mt->pushData(buff);
+	    mt->nextThread();
+	    mt->popFree(buff);
+	    ifr++;
+	    if (ifr%10000==0) 
+	      cout << ifr << " " << ff << " " << np << endl;
+	  } else
+	    cout << ifr << " " << ff << " " << np << endl;
+	  ff=-1;
+	}
+	filebin.close();	 
+	while (mt->isBusy()) {;}
+	
       } else 
-	cout << "Could not open "<< fname << " for reading " << endl;
+	cout << "Could not open pedestal file "<< fname << " for reading " << endl;
+    } else {
+      float *pp=ReadFromTiff(pedfile, unny, unnx);
+      nny=unny;
+      nnx=unnx;
+      if (pp && nnx==nx && nny==ny) {
+	for (int i=0; i<nx*ny; i++) {
+	  ped[i]=pp[i];
+	}
+	delete [] pp;
+	mt->setPedestal(ped);
+	// ped1=mt->getPedestal();
+	
+	// for (int i=0; i<nx*ny; i++) {
+
+	//   cout << ped[i]<<"/"<<ped1[i] << " " ;
+	// }
+	cout << "Pedestal set from tiff file " << pedfile << endl;
+      } else {
+	cout << "Could not open pedestal tiff file "<< pedfile << " for reading " << endl;
+      }
+    }
+    mt->writePedestal(imgfname);
+    std::time(&end_time);
+    cout << std::ctime(&end_time) <<   endl;
   }
   
 
+
   ifr=0;
   int ifile=0;
-  
+  char ext[100];
+  mt->setFrameMode(eFrame);
   for (int irun=runmin; irun<=runmax; irun++) {
     cout << "DATA " ;
-    mt->setFrameMode(eFrame);
     // sprintf(fn,fformat,irun);
-    sprintf(ffname,"%s/%s.raw",indir,fformat);
-    sprintf(fname,ffname,irun);
-    sprintf(ffname,"%s/%s.tiff",outdir,fformat);
-    sprintf(imgfname,ffname,irun);
-    sprintf(ffname,"%s/%s.clust",outdir,fformat);
-    sprintf(cfname,ffname,irun);
-    cout << fname << " " ;
+    sprintf(ext,"_%d.raw",irun);
+
+    
+    sprintf(imgfname,"%s/%s_%d.tiff",outdir,fformat,irun);
+    // sprintf(imgfname,ffname,irun);
+    sprintf(cfname,"%s/%s_%d.clust",outdir,fformat, irun);
+    //sprintf(cfname,ffname,irun);
+    cout << cfname << " " ;
     cout << imgfname << endl;
-    std::time(&end_time);
-    cout << std::ctime(&end_time) <<    endl;
-    //  cout <<  fname << " " << outfname << " " << imgfname <<  endl;
-    filebin.open((const char *)(fname), ios::in | ios::binary);
-    //      //open file
-    ifile=0;
-    if (filebin.is_open()){
-      if (thr<=0) {
-	if (cf) {
+
+    
+    if (thr<=0 && cf!=0) { //cluster finder
 	  if (of==NULL) {
 	    of=fopen(cfname,"w");
 	    if (of) {
@@ -283,65 +373,106 @@ int main(int argc, char *argv[]) {
 	      return 1;
 	    }
 	  }
-	}
       }
-      //     //while read frame 
-      ff=-1;
-      ifr=0;
-      while (decoder->readNextFrame(filebin, ff, np,buff)) {
-	//	cout << "*"<<ifr++<<"*"<<ff<< endl;
-	//	cout << ff << " " << np << endl;
-  	//         //push
-	mt->pushData(buff);
-  // 	//         //pop
-	mt->nextThread();
-  // // 		//	cout << " " << (void*)buff;
-	mt->popFree(buff);
-	ifr++;
-	if (ifr%1000==0) cout << ifr << " " << ff << endl;
-	if (nframes>0) {
-	  if (ifr%nframes==0) {
-	    //The name has an additional "_fXXXXX" at the end, where "XXXXX" is the initial frame number of the image (0,1000,2000...)
-	    
-	    sprintf(ffname,"%s/%s_f%05d.tiff",outdir,fformat,ifile);
-	    sprintf(imgfname,ffname,irun);
-	    //cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
-	    mt->writeImage(imgfname, thr1);
-	    mt->clearImage();
-	    ifile++;
-	  }
-	}
+    
+  if ((dir = opendir (indir)) != NULL) {
+    /* print all the files and directories within directory */
+    while ((ent = readdir (dir)) != NULL) {
+      // printf ("----------- %s\n", ent->d_name);
+      //	printf ("************** %s", ent->d_name);
+      //	cout << string(ent->d_name).find(fformat) << endl;
+      if (string(ent->d_name).find(string(fformat)+"_d0_f0")==0) {
+	//  printf ("+++++++++++++++ %s\n", ent->d_name);
+	if (string(ent->d_name).find(ext)!= string::npos) {
+	  //printf ("**************8 %s\n", ent->d_name);
+	  sprintf(fname,"%s/%s",indir,ent->d_name);
+    //sprintf(fname,ffname,irun);
+	  cout << fname << endl;
 
-	ff=-1;
+	  std::time(&end_time);
+	  cout << std::ctime(&end_time) <<    endl;
+	  //  cout <<  fname << " " << outfname << " " << imgfname <<  endl;
+	  filebin.open((const char *)(fname), ios::in | ios::binary);
+	  //      //open file
+	  ifile=0;
+	  if (filebin.is_open()){
+	    //     //while read frame 
+	    ff=-1;
+	    ifr=0;
+	    while (decoder->readNextFrame(filebin, ff, np,buff)) {
+	      if (np==40) {
+		mt->pushData(buff);
+		mt->nextThread();
+		mt->popFree(buff);
+		ifr++;
+		if (ifr%10000==0) cout << ifr << " " << ff << endl;
+		if (nframes>0) {
+		  while (mt->isBusy()) {;}
+		  if (ifr%nframes==0) {
+		    //The name has an additional "_fXXXXX" at the end, where "XXXXX" is the initial frame number of the image (0,1000,2000...)		    
+		    sprintf(ffname,"%s/%s_f%05d.tiff",outdir,fformat,ifile);
+		    sprintf(imgfname,ffname,irun);
+		    //cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
+		    mt->writeImage(imgfname, thr1);
+		    mt->clearImage();
+		    ifile++;
+		  }
+		}
+	      }
+	      ff=-1;
+	    }
+	    filebin.close();	 
+	  } else 
+	    cout << "Could not open "<< fname << " for reading " << endl;
+	}	
       }
-      cout << "--" << endl;
-      filebin.close();	 
-      //      //close file 
-      //     //join threads
-      while (mt->isBusy()) {;}
-      if (nframes>=0) {
-	if (nframes>0) {
-	    sprintf(ffname,"%s/%s_f%05d.tiff",outdir,fformat,ifile);
-	    sprintf(imgfname,ffname,irun);
-	}
-	sprintf(ffname,"%s/%s.tiff",outdir,fformat);
+
+
+    }  
+    while (mt->isBusy()) {;}
+    if (nframes>=0) {
+      if (nframes>0) {
+	sprintf(ffname,"%s/%s_f%05d.tiff",outdir,fformat,ifile);
 	sprintf(imgfname,ffname,irun);
-	cout << "Writing tiff to " << imgfname << " " << thr1 <<endl;
-	mt->writeImage(imgfname, thr1);
-	mt->clearImage();
-	if (of) {
-	  fclose(of);
-	  of=NULL;
-	  mt->setFilePointer(NULL);
-	}
-      }	
-      std::time(&end_time);
-      cout << std::ctime(&end_time) <<   endl;
-    } else 
-      cout << "Could not open "<< fname << " for reading " << endl;
+      } else {
+	sprintf(imgfname,"%s/%s_%d.tiff",outdir,fformat,irun);
+	//sprintf(imgfname,ffname,irun);
+      }
+      cout << "Writing tiff to " << imgfname << " " << ifr <<endl;
+      mt->writeImage(imgfname, thr1);
+      mt->clearImage();
+      if (of) {
+	fclose(of);
+	of=NULL;
+	mt->setFilePointer(NULL);
+      }
+    }	
+    std::time(&end_time);
+    cout << std::ctime(&end_time) <<   endl;
+      
+    closedir (dir);
+  } else {
+    /* could not open directory */
+    cout << "could not open directory " << indir << endl;
   }
 
+  }
+  
+  if (nframes<0){
+    sprintf(ffname,"%s/%s.tiff",outdir,fformat);
+    strcpy(imgfname,ffname);
+    cout << "Writing tiff to " << imgfname << " " << ifr <<endl;
+    mt->writeImage(imgfname, thr1);
+  }
+  
+  
+  sprintf(imgfname,"%s/%s_ped.tiff",outdir,fformat);
+  mt->writePedestal(imgfname);
+  sprintf(imgfname,"%s/%s_noise.tiff",outdir,fformat);
+  mt->writePedestalRMS(imgfname);
 
+  
+  
   return 0;
 }
 

slsDetectorCalibration/moenchExecutables/moenchPhotonCounterNoThread.cpp

@@ -0,0 +1,527 @@
+//#include "ansi.h"
+#include <iostream>
+//#define CORR
+#define NOTHREAD
+
+#define C_GHOST 0.0004
+
+#define CM_ROWS 50
+
+//#define VERSION_V1
+
+//#include "moench03T1ZmqData.h"
+#ifdef NEWRECEIVER
+#ifndef RECT
+#include "moench03T1ReceiverDataNew.h"
+#endif
+
+#ifdef RECT
+#include "moench03T1ReceiverDataNewRect.h"
+#endif
+
+#endif
+
+
+#ifdef CSAXS_FP
+#include "moench03T1ReceiverData.h"
+#endif 
+#ifdef OLDDATA
+#include "moench03Ctb10GbT1Data.h"
+#endif 
+
+// #include "interpolatingDetector.h"
+//#include "etaInterpolationPosXY.h"
+// #include "linearInterpolation.h"
+// #include "noInterpolation.h"
+#include "multiThreadedCountingDetector.h"
+//#include "multiThreadedAnalogDetector.h"
+#include "singlePhotonDetector.h"
+#include "moench03GhostSummation.h"
+#include "moench03CommonMode.h"
+//#include "interpolatingDetector.h"
+
+#include <stdio.h>
+#include <map>
+#include <fstream>
+#include <sys/stat.h>
+#include <dirent.h>
+#include <ctime>
+using namespace std;
+
+
+int main(int argc, char *argv[]) {
+
+
+  if (argc<4) {
+    cout << "Usage is " << argv[0] << "indir outdir fname [runmin] [runmax] [pedfile] [threshold] [nframes] [xmin xmax ymin ymax] [gainmap]" << endl;
+    cout << "threshold <0 means analog; threshold=0 means cluster finder; threshold>0 means photon counting" << endl;
+    cout << "nframes <0 means sum everything; nframes=0 means one file per run; nframes>0 means one file every nframes" << endl;
+    return 1;
+  }
+
+  //int p=10000;
+  int fifosize=1000;
+  int nthreads=10;
+  //int nsubpix=25;
+  //int etabins=nsubpix*10;
+  //double etamin=-1, etamax=2;
+  int csize=3;
+  //int save=1;
+  int nsigma=5;
+  int nped=10000;
+  //int ndark=100;
+  //int ok;
+  //int iprog=0;
+
+  int cf=0;
+
+#ifdef NEWRECEIVER
+#ifdef RECT
+  cout << "Should be rectangular!" <<endl;
+#endif
+  moench03T1ReceiverDataNew *decoder=new  moench03T1ReceiverDataNew();
+  cout << "RECEIVER DATA WITH ONE HEADER!"<<endl;
+#endif
+
+#ifdef CSAXS_FP
+  moench03T1ReceiverData *decoder=new  moench03T1ReceiverData();
+  cout << "RECEIVER DATA WITH ALL HEADERS!"<<endl;
+#endif
+
+#ifdef OLDDATA
+  moench03Ctb10GbT1Data *decoder=new  moench03Ctb10GbT1Data();
+  cout << "OLD RECEIVER DATA!"<<endl;
+#endif
+
+  int nx=400, ny=400;
+
+  decoder->getDetectorSize(nx,ny);
+
+  int ncol_cm=CM_ROWS;
+  double xt_ghost=C_GHOST;
+  moench03CommonMode *cm=NULL;
+  moench03GhostSummation *gs;
+  double *gainmap=NULL;
+  //float *gm;
+
+
+
+  //int size = 327680;////atoi(argv[3]);
+  
+  //int* image;
+	//int* image =new int[327680/sizeof(int)];
+
+  int ff, np;
+  //cout << " data size is " << dsize;
+  
+
+
+  ifstream filebin;
+  char *indir=argv[1];
+  char *outdir=argv[2];
+  char *fformat=argv[3];
+  int runmin=0;
+  
+  // cout << "argc is " << argc << endl;
+ if (argc>=5) {
+   runmin=atoi(argv[4]);
+  }
+
+ int runmax=runmin;
+
+ if (argc>=6) {
+   runmax=atoi(argv[5]);
+  }
+
+  char *pedfile=NULL;
+  if (argc>=7) {
+    pedfile=argv[6];
+  }
+  double thr=0;
+  double thr1=1;
+
+  if (argc>=8) {
+    thr=atof(argv[7]);
+  }
+  
+
+  int nframes=0;
+  
+  if (argc>=9) {
+    nframes=atoi(argv[8]);
+  }
+  int xmin=0, xmax=nx, ymin=0, ymax=ny;
+  if (argc>=13) {
+    xmin=atoi(argv[9]);
+    xmax=atoi(argv[10]);
+    ymin=atoi(argv[11]);
+    ymax=atoi(argv[12]);
+  }
+
+  
+  char *gainfname=NULL;
+  if (argc>13) {
+    gainfname=argv[13];
+    cout << "Gain map file name is: " << gainfname << endl;
+  }
+
+  
+
+
+  char ffname[10000];
+  char fname[10000];
+  char imgfname[10000];
+  char cfname[10000];
+  //char fn[10000];
+  
+  std::time_t end_time;
+
+  FILE *of=NULL;
+  cout << "input directory is " << indir << endl;
+  cout << "output directory is " << outdir << endl;
+  cout << "input file is " << fformat << endl;
+  cout << "runmin is " << runmin << endl;
+  cout << "runmax is " << runmax << endl;
+  if (pedfile)
+    cout << "pedestal file is " << pedfile << endl;
+ if (thr>0) 
+    cout << "threshold is " << thr << endl;
+ uint32 unnx, unny;
+ int  nnx, nny;
+ //double *gmap;
+
+  // if (gainfname) {
+  //   gm=ReadFromTiff(gainfname, nny, nnx);
+  //   if (gm && nnx==nx && nny==ny) {
+  //     gmap=new double[nx*ny];
+  //     for (int i=0; i<nx*ny; i++) {
+  // 	gmap[i]=gm[i];
+  //     }
+  //     delete gm;
+  //   } else
+  //     cout << "Could not open gain map " << gainfname << endl;
+  // }
+
+#ifdef CORR
+ cout << "Applying common mode  " << ncol_cm << endl;
+  cm=new moench03CommonMode(ncol_cm);
+  
+
+  cout << "Applying ghost corrections " << xt_ghost << endl;
+  gs=new moench03GhostSummation(decoder, xt_ghost);
+#endif
+
+  singlePhotonDetector *filter=new singlePhotonDetector(decoder,csize, nsigma, 1, cm, nped, 200, -1, -1, gainmap, gs);
+
+  if (gainfname) {
+
+    if (filter->readGainMap(gainfname))
+      cout << "using gain map " << gainfname << endl;
+    else
+      cout << "Could not open gain map " << gainfname << endl;
+  } else
+    thr=0.15*thr;
+  filter->newDataSet();
+  //int dsize=decoder->getDataSize();
+
+
+  //char data[dsize];
+
+
+
+
+
+  //#ifndef ANALOG
+  if (thr>0) {
+    cout << "threshold is " << thr << endl;
+    //#ifndef ANALOG
+    filter->setThreshold(thr);
+    //#endif
+      cf=0;
+
+  } else
+    cf=1;
+  //#endif
+
+
+  filter->setROI(xmin,xmax,ymin,ymax);
+  std::time(&end_time);
+  cout << std::ctime(&end_time) <<   endl;
+
+  char* buff;
+
+  // multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
+#ifndef NOTHREAD
+ multiThreadedCountingDetector *mt=new multiThreadedCountingDetector(filter,nthreads,fifosize);
+#endif
+#ifdef NOTHREAD
+ singlePhotonDetector *mt=filter;
+#endif
+
+#ifndef ANALOG
+    mt->setDetectorMode(ePhotonCounting);
+    cout << "Counting!" << endl;
+  if (thr>0) {
+    cf=0;
+  } 
+#endif
+//{
+#ifdef ANALOG
+      mt->setDetectorMode(eAnalog);
+      cout << "Analog!" << endl;
+      cf=0;
+      //thr1=thr;
+#endif  
+      //  }
+#ifndef NOTHREAD 
+  mt->StartThreads();
+  mt->popFree(buff);
+#endif
+
+  DIR *dir;
+  struct dirent *ent;
+ 
+  //  cout << "mt " << endl;
+
+  int ifr=0;
+
+  double ped[nx*ny];//, *ped1;
+
+
+  if (pedfile) {
+
+    cout << "PEDESTAL " << endl;
+    sprintf(imgfname,"%s/pedestals.tiff",outdir);
+
+    if (string(pedfile).find(".tif")==std::string::npos){
+      sprintf(fname,"%s.raw",pedfile);
+      cout << fname << endl ;
+      std::time(&end_time);
+      cout << "aaa" << std::ctime(&end_time) <<   endl;
+      
+      
+      mt->setFrameMode(ePedestal);
+      // sprintf(fn,fformat,irun);
+      filebin.open((const char *)(fname), ios::in | ios::binary);
+      //      //open file
+      if (filebin.is_open()){
+	ff=-1;
+	while (decoder->readNextFrame(filebin, ff, np,buff)) {
+	  if (np==40) {
+#ifdef NOTHREAD
+	    mt->processData(buff);
+#endif
+#ifndef NOTHREAD
+	    mt->pushData(buff);
+	    mt->nextThread();
+	    mt->popFree(buff);
+#endif
+	    ifr++;
+	    if (ifr%10000==0) 
+	      cout << ifr << " " << ff << " " << np << endl;
+	  } else
+	    cout << ifr << " " << ff << " " << np << endl;
+	  ff=-1;
+	}
+	filebin.close();
+#ifndef NOTHREAD	 
+	while (mt->isBusy()) {;}
+#endif
+	
+      } else 
+	cout << "Could not open pedestal file "<< fname << " for reading " << endl;
+    } else {
+      float *pp=ReadFromTiff(pedfile, unny, unnx);
+      nny=unny;
+      nnx=unnx;
+      if (pp && nnx==nx && nny==ny) {
+	for (int i=0; i<nx*ny; i++) {
+	  ped[i]=pp[i];
+	}
+	delete [] pp;
+	mt->setPedestal(ped);
+	// ped1=mt->getPedestal();
+	
+	// for (int i=0; i<nx*ny; i++) {
+
+	//   cout << ped[i]<<"/"<<ped1[i] << " " ;
+	// }
+	cout << "Pedestal set from tiff file " << pedfile << endl;
+      } else {
+	cout << "Could not open pedestal tiff file "<< pedfile << " for reading " << endl;
+      }
+    }
+#ifdef NOTHREAD
+    mt->writePedestals(imgfname);
+#endif
+#ifndef NOTHREAD
+    mt->writePedestal(imgfname);
+#endif
+    std::time(&end_time);
+    cout << std::ctime(&end_time) <<   endl;
+  }
+  
+
+
+  ifr=0;
+  int ifile=0;
+  char ext[100];
+  mt->setFrameMode(eFrame);
+  for (int irun=runmin; irun<=runmax; irun++) {
+    cout << "DATA " ;
+    // sprintf(fn,fformat,irun);
+    sprintf(ext,"_%d.raw",irun);
+
+    
+    sprintf(imgfname,"%s/%s_%d.tiff",outdir,fformat,irun);
+    // sprintf(imgfname,ffname,irun);
+    sprintf(cfname,"%s/%s_%d.clust",outdir,fformat, irun);
+    //sprintf(cfname,ffname,irun);
+    cout << cfname << " " ;
+    cout << imgfname << endl;
+
+    
+    if (thr<=0 && cf!=0) { //cluster finder
+	  if (of==NULL) {
+	    of=fopen(cfname,"w");
+	    if (of) {
+	    mt->setFilePointer(of);
+	    cout << "file pointer set " << endl;
+	    } else {
+	      cout << "Could not open "<< cfname << " for writing " << endl;
+	      mt->setFilePointer(NULL);
+	      return 1;
+	    }
+	  }
+      }
+    
+  if ((dir = opendir (indir)) != NULL) {
+    /* print all the files and directories within directory */
+    while ((ent = readdir (dir)) != NULL) {
+      // printf ("----------- %s\n", ent->d_name);
+      //	printf ("************** %s", ent->d_name);
+      //	cout << string(ent->d_name).find(fformat) << endl;
+      if (string(ent->d_name).find(string(fformat)+"_d0_f0")==0) {
+	//  printf ("+++++++++++++++ %s\n", ent->d_name);
+	if (string(ent->d_name).find(ext)!= string::npos) {
+	  //printf ("**************8 %s\n", ent->d_name);
+	  sprintf(fname,"%s/%s",indir,ent->d_name);
+    //sprintf(fname,ffname,irun);
+	  cout << fname << endl;
+
+	  std::time(&end_time);
+	  cout << std::ctime(&end_time) <<    endl;
+	  //  cout <<  fname << " " << outfname << " " << imgfname <<  endl;
+	  filebin.open((const char *)(fname), ios::in | ios::binary);
+	  //      //open file
+	  ifile=0;
+	  if (filebin.is_open()){
+	    //     //while read frame 
+	    ff=-1;
+	    ifr=0;
+	    while (decoder->readNextFrame(filebin, ff, np,buff)) {
+	      if (np==40) {
+#ifdef NOTHREAD
+		mt->processData(buff);
+#endif
+#ifndef NOTHREAD
+		mt->pushData(buff);
+		mt->nextThread();
+		mt->popFree(buff);
+#endif
+		ifr++;
+		if (ifr%10000==0) cout << ifr << " " << ff << endl;
+		if (nframes>0) {
+#ifndef NOTHREAD
+		  while (mt->isBusy()) {;}
+#endif
+		  if (ifr%nframes==0) {
+		    //The name has an additional "_fXXXXX" at the end, where "XXXXX" is the initial frame number of the image (0,1000,2000...)		    
+		    sprintf(ffname,"%s/%s_f%05d.tiff",outdir,fformat,ifile);
+		    sprintf(imgfname,ffname,irun);
+		    //cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
+#ifdef NOTHREAD
+		    mt->writeImage(imgfname);
+#endif
+#ifndef NOTHREAD
+		    mt->writeImage(imgfname, thr1);
+#endif
+		    mt->clearImage();
+		    ifile++;
+		  }
+		}
+	      }
+	      ff=-1;
+	    }
+	    filebin.close();	 
+	  } else 
+	    cout << "Could not open "<< fname << " for reading " << endl;
+	}	
+      }
+
+
+    } 
+#ifndef NOTHREAD 
+    while (mt->isBusy()) {;}
+#endif
+    if (nframes>=0) {
+      if (nframes>0) {
+	sprintf(ffname,"%s/%s_f%05d.tiff",outdir,fformat,ifile);
+	sprintf(imgfname,ffname,irun);
+      } else {
+	sprintf(imgfname,"%s/%s_%d.tiff",outdir,fformat,irun);
+	//sprintf(imgfname,ffname,irun);
+      }
+      cout << "Writing tiff to " << imgfname << " " << ifr <<endl;
+#ifdef NOTHREAD
+		    mt->writeImage(imgfname);
+#endif
+#ifndef NOTHREAD
+		    mt->writeImage(imgfname, thr1);
+#endif
+      mt->clearImage();
+      if (of) {
+	fclose(of);
+	of=NULL;
+	mt->setFilePointer(NULL);
+      }
+    }	
+    std::time(&end_time);
+    cout << std::ctime(&end_time) <<   endl;
+      
+    closedir (dir);
+  } else {
+    /* could not open directory */
+    cout << "could not open directory " << indir << endl;
+  }
+
+  }
+  
+  if (nframes<0){
+    sprintf(ffname,"%s/%s.tiff",outdir,fformat);
+    strcpy(imgfname,ffname);
+    cout << "Writing tiff to " << imgfname << " " << ifr <<endl;
+#ifdef NOTHREAD
+		    mt->writeImage(imgfname);
+#endif
+#ifndef NOTHREAD
+		    mt->writeImage(imgfname, thr1);
+#endif
+  }
+  
+  
+  sprintf(imgfname,"%s/%s_ped.tiff",outdir,fformat);
+#ifdef NOTHREAD
+    mt->writePedestals(imgfname);
+#endif
+#ifndef NOTHREAD
+    mt->writePedestal(imgfname);
+#endif
+  sprintf(imgfname,"%s/%s_noise.tiff",outdir,fformat);
+  mt->writePedestalRMS(imgfname);
+
+  
+  
+  return 0;
+}
+

slsDetectorCalibration/moenchExecutables/moenchZmqAnalog.cpp

@@ -1,394 +0,0 @@
-//#define ROOTSPECTRUM
-
-#include "multiThreadedAnalogDetector.h"
-
-#include "sls_receiver_defs.h"
-#include "ZmqSocket.h"
-#include "moench03T1ZmqDataNew.h"
-
-#ifdef ROOTSPECTRUM
-#include <TPaveText.h> 
-#include <TLegend.h> 
-#include <TF1.h> 
-#include <TGraphErrors.h> 
-#include <TH2F.h> 
-#include <TASImage.h> 
-#include <TImage.h> 
-#include <TFile.h> 
-#endif
-
-#include <vector> 
-#include <string> 
-#include <sstream> 
-#include <iomanip> 
-#include <fstream> 
-#include "tiffIO.h"
-
-#include<iostream>
-
-//#include "analogDetector.h"
-#include "singlePhotonDetector.h"
-#include "ansi.h"
-#include <iostream>
-using namespace std;
-
-
-#define SLS_DETECTOR_JSON_HEADER_VERSION 0x2
-
-
-int main(int argc, char *argv[]) {
-/**
- * trial.o [socket ip] [starting port number] [send_socket ip] [send port number]
- *
- */
-  int fifosize=1000;
-  int nthreads=20;
-  char* buff;
-  char tit[10000];
-	// help
-	if (argc < 3 ) {
-		cprintf(RED, "Help: ./trial [receive socket ip] [receive starting port number] [send_socket ip] [send starting port number]\n");
-		return EXIT_FAILURE;
-	}
-
-	// receive parameters
-	bool send = false;
-	  char* socketip=argv[1];
-	uint32_t portnum = atoi(argv[2]);
-	int size = 32*2*5000;//atoi(argv[3]);
-
-	// send parameters if any
-	char* socketip2 = 0;
-	uint32_t portnum2 = 0;
-	if (argc > 3) {
-		send = true;
-		socketip2 = argv[3];
-		portnum2 = atoi(argv[4]);
-	}
-	cout << "\nrx socket ip : " << socketip <<
-			"\nrx port num  : " <<  portnum ;
-	if (send) {
-		cout << "\nsd socket ip : " << socketip2 <<
-				"\nsd port num  : " <<  portnum2;
-	}
-	cout << endl;
-
-	//slsDetectorData *det=new moench03T1ZmqDataNew(); 
-	 moench03T1ZmqDataNew *det=new moench03T1ZmqDataNew(); 
-	 analogDetector<uint16_t> *filter=new analogDetector<uint16_t>(det,1,NULL,1000);
-	 //singlePhotonDetector *filter=new singlePhotonDetector(det,3, 5, 1, 0, 1000, 10);
-	 //filter->setROI(250, 400, 30, 150);
-	 float threshold=1;
-	if (argc > 5) {
-	  threshold=atof(argv[5]);
-	 filter->setThreshold(threshold);
-	  cout << "Threshold set to " << threshold << endl;
-	}
-
-	int nnx, nny, nns;
-	int imsize=filter->getImageSize(nnx,nny,nns);
-
-  multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
-
-
-
-  // mt->prepareInterpolation(ok);
-  mt->StartThreads();
-  mt->popFree(buff);
-
-
-
-	  cout << "det " << endl;
-	int16_t dout[400*400];
-	double ddark[400*400];
-	  cout << "dout " << endl;
-
-	// receive socket
-	  ZmqSocket* zmqsocket = new ZmqSocket(socketip,portnum); 
-#ifdef ROOTSPECTRUM
-	  TH2F *h2=NULL;
-	  TH2F *hmap=NULL;
-	  TFile *froot=NULL;
-
-	  h2=new TH2F("hs","hs",500,-500,500,400*400,-0.5,400*400-0.5);
-	  hmap=new TH2F("hmap","hmap",400,-0.5,400-0.5,400,-0.5,400-0.5);
-#endif
-	  cout << "zmq1 " << endl;
-	  
-	if (zmqsocket->IsError()) {
-		cprintf(RED, "Error: Could not create Zmq socket on port %d with ip %s\n", portnum, socketip);
-		delete zmqsocket;
-		return EXIT_FAILURE;
-	}
-	zmqsocket->Connect();
-	printf("Zmq Client at %s\n", zmqsocket->GetZmqServerAddress());
-
-	// send socket
-	ZmqSocket* zmqsocket2 = 0;
-	  cout << "zmq2 " << endl;
-	if (send) {
-		zmqsocket2 = new ZmqSocket(portnum2, socketip2);
-		if (zmqsocket2->IsError()) {
-			bprintf(RED, "Error: Could not create Zmq socket server on port %d and ip %s\n",  portnum2, socketip2);
-			delete zmqsocket2;
-			delete zmqsocket;
-			return EXIT_FAILURE;
-		}
-		zmqsocket2->Connect();
-		printf("Zmq Server started at %s\n", zmqsocket2->GetZmqServerAddress());
-		//	zmqsocket2->Disconnect();
-	}
-
-
-	// header variables
-	uint64_t acqIndex = -1;
-	uint64_t frameIndex = -1;
-	uint32_t subframeIndex = -1;
-	uint64_t fileindex = -1;
-	string filename = "";
-	//char* image = new char[size];
-	//int* image = new int[(size/sizeof(int))]();
-
-	int *nph;//[400*400];
-	int iframe=0;
-	char rootfname[10000];
-		    
-	char fname[10000];
-	char ff[10000];
-	int fi;
-	int length;
-	char newped=-1, ped=-1, dat=-1, isdark=-1;
-	
-	double *peds;
-	int *im;
-	int fnumber;
-	float *gm=new float[400*400];
-	// infinite loop
-	while(1) {
-	  
-
-	  //	  cout << "+++++++++++++++++++++++++++++++LOOP" << endl;
-		// get header, (if dummy, fail is on parse error or end of acquisition)
-	  if (!zmqsocket->ReceiveHeader(0, acqIndex, frameIndex, subframeIndex, filename, fileindex)){
-	    //	  if (!zmqsocket->ReceiveHeader(0, acqIndex, frameIndex, subframeIndex, filename, fileindex)) {
-			cprintf(RED, "Got Dummy\n");
-			while (mt->isBusy()) {;}//wait until all data are processed from the queues
-			if (dat==1) {
-			  
-			  sprintf(tit,"%s_%lld.tiff",filename.c_str(),fi);
-			  cout << tit << endl;
-			  im=mt->getImage(nnx,nny,nns);
-			  if (isdark) cout << "getting dark "<< endl;
-			  else cout << "subtracting dark"<< endl;
-			  if (gm) {
-			    for (int ii=0; ii<400*400; ii++) {
-			      //      if (image[ix]>0) cout << ix << " " << image[ix]<< endl;
-			      if (isdark) {
-				ddark[ii]=(double)im[ii]/((double)iframe);
-				if (ddark[ii]>0) cout << "*" ;
-				gm[ii]=im[ii];
-				if (send) dout[ii]=im[ii];
-			      } else {
-				gm[ii]=im[ii];//-ddark[ii]*iframe;
-				if (gm[ii]<0) gm[ii]=0;
-				if (send) dout[ii]=gm[ii];
-			      }
-			      //cout << endl;
-			      
-			    }
-			    cout << endl;
-			    //cout << "image " << nnx << " " << nny << endl;
-			    WriteToTiff(gm,tit ,nnx, nny); 
-			    // delete [] gm;
-			  } else cout << "Could not allocate float image " << endl;
-     
-
-
-			} else {
-
-			  sprintf(tit,"%s_%lld.tiff",filename.c_str(),fi);
-			  cout << tit << endl;
-			  mt->writePedestal(tit);
-
-			}
-
-			// mt->writeImage(tit);
-			//  cout << "wrote" << endl;
-	
-	 
-	 
-
-
-
-
-	 
-			  if (send) {
-			  if (dat==1) {
-			    //im=mt->getImage(nnx,nny,nns);
-			    
-			    //if (im)
-			    //  cout << "got image" << endl;
-			    //else
-			    //  cout << "could not get image" << endl;
-			    
-
-			    //for (int ii=0; ii<400*400; ii++) {
-			      //if (im[ii]>0)
-			      //cout << im[ii] << endl;
-			      //  if (im[ii]>=0)
-			      
-			    // if (isdark) {
-				//ddark[ii]=im[ii];
-			    //	dout[ii]=im[ii];
-			    // } else {
-			    //	dout[ii]=im[ii]-ddark[ii];
-			    //	if (dout[ii]<0) dout[ii]=0;
-			    // }
-			      // else
-			      //	dout[ii]=0;
-				//else
-				//dout[ii]=0;
-			      // cout << im[ii] << " " << dout[ii] << endl;
-			    //  }
-			    //for (int iiy=49; iiy<52; iiy++)
-			    //  for (int iix=80; iix<83; iix++)
-			    //	dout[iiy*400+iix]=0;
-			    ;
-			  } else {
-			    peds=mt->getPedestal();
-			    //  sprintf(tit,"%s_%lld.tiff",filename.c_str(),fi);
-			    //cout << tit << endl;
-			    //mt->writePedestal(tit);
-			    if (peds)
-			      cout << "got peds" << endl;
-			    else
-			      cout << "could not get peds" << endl;
-			    for (int ii=0; ii<400*400; ii++) {
-			      dout[ii]=peds[ii];
-			      // if (ii%400==10 && ii/400==10)
-			      // 	cout << ii/400 << " " << ii%400 << " " << peds[ii] << " " << dout[ii] << endl; 
-			      // if (ii%400==100 && ii/400==100)
-			      // 	cout << ii/400 << " " << ii%400 << " " << peds[ii] << " " << dout[ii] << endl; 
-			    }
-
-			  }
-
-			    
-		// zmqsocket2 = new ZmqSocket(portnum2, socketip2);
-		// if (zmqsocket2->IsError()) {
-		// 	bprintf(RED, "Error: Could not create Zmq socket server on port %d and ip %s\n",  portnum2, socketip2);
-		// 	delete zmqsocket2;
-		// 	delete zmqsocket;
-		// 	return EXIT_FAILURE;
-		// }
-		// zmqsocket2->Connect();
-		// printf("Zmq Server started at %s\n", zmqsocket2->GetZmqServerAddress());
-			  //zmqsocket2->Connect();
-
-	
-			  zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,ff, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
-			  
-			  
-			  zmqsocket2->SendData((char*)dout,length);
-			  cprintf(GREEN, "Sent Data %d \n",length);
-			  
-			  zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-			  cprintf(RED, "Sent Dummy\n");
-			  //	zmqsocket2->Disconnect();
-
-			  // delete zmqsocket2;
-			  }
-			  cout << "Acquired "<< iframe << " frames " << endl;
-			  iframe=0;
-			  newped=-1;
-			  ped=-1;
-			  dat=-1;
-			  mt->clearImage();
-			  isdark=0;
-			  continue; //continue to not get out
-	  }
-	  //	cprintf(GREEN, "Got Header \n");
-
-	  strcpy(ff,filename.c_str());
-	  fi=fileindex;
-	  //isdark=0;
-	  if (newped<0) {
-	    if (filename.find("newped")!=std::string::npos) {
-	      cout << "NEWPED" << endl;
-	      if (newped<=0) {
-		newped=1;
-		ped=1;
-		while (mt->isBusy()) {;}
-		mt->newDataSet(); //resets pedestal
-		mt->setFrameMode(ePedestal);
-		cout << "New data set"<< endl;
-	      }
-	    } else {
-	      newped=0;
-	    }
-	  }
-	  if (ped<0) { 
-	    if (filename.find("ped")!=std::string::npos) {
-	      ped=1;
-	      dat=0;
-	      while (mt->isBusy()) {;}
-	      mt->setFrameMode(ePedestal);
-	      cout << "pedestal!"<< endl;
-	    } else {
-	      ped=0;
-	      dat=1;	
-	      while (mt->isBusy()) {;}
-	      mt->setFrameMode(eFrame);
-	      cout << "data!"<< endl;
-	      if (filename.find("dark")!=std::string::npos) {
-		isdark=1;
-		cout << "this is a dark image" << endl;
-	      }
-	      
-	    }
-	  }
-	  
-		// get data
-	  length = zmqsocket->ReceiveData(0, buff, size);
-		//	cprintf(GREEN, "Got Data\n");
-
-		//processing with image
-		//...
-		//	if (iframe<10) {
-		// filter->addToPedestal(image);
-		//} else {
-		//SLOW!!!
-		//***
-		//filter->getNPhotons(image);
-		//nph=filter->getImage();
-		//filter->addToPedestal(image);
-		//*****
-	 
-		//	cprintf(BLUE, "Data processed\n");
-	  
-
-		mt->pushData(buff);
-		mt->nextThread();
-		//	cout << " " << (void*)buff;
-		mt->popFree(buff);
-		
-	  
-	  
-		//stream data from socket 2
-		  
-	  iframe++;
-	}
-	
-	//	}// exiting infinite loop
-	
-
-	
-	delete zmqsocket;
-	if (send)
-	  delete zmqsocket2;
-	
-
-	cout<<"Goodbye"<<  endl;
-	return 0;
-}
-

slsDetectorCalibration/moenchExecutables/moenchZmqClusterFinder.cpp

@@ -1,402 +0,0 @@
-#include "sls_receiver_defs.h"
-#include "ZmqSocket.h"
-#include "moench03T1ZmqDataNew.h"
-#include <vector> 
-#include <string> 
-#include <sstream> 
-#include <iomanip> 
-#include <fstream> 
-#include "tiffIO.h"
-
-
-//#define NEWZMQ
-#ifdef NEWZMQ
-#include <rapidjson/document.h> //json header in zmq stream
-#endif
-
-#include<iostream>
-
-//#include "analogDetector.h"
-#include "singlePhotonDetector.h"
-#include "multiThreadedAnalogDetector.h"
-#include "ansi.h"
-#include <iostream>
-using namespace std;
-
-
-#define SLS_DETECTOR_JSON_HEADER_VERSION 0x2
-
-
-int main(int argc, char *argv[]) {
-/**
- * trial.o [socket ip] [starting port number] [send_socket ip] [send port number]
- *
- */
-  FILE *of=NULL;
-  int fifosize=1000;
-  int nthreads=20;
-	// help
-  if (argc < 3 ) {
-    cprintf(RED, "Help: ./trial [receive socket ip] [receive starting port number] [send_socket ip] [send starting port number]\n");
-    return EXIT_FAILURE;
-  }
-  
-  // receive parameters
-  bool send = false;
-  char* socketip=argv[1];
-  uint32_t portnum = atoi(argv[2]);
-  int maxSize = 32*2*8192;//5000;//atoi(argv[3]);
-  int size= 32*2*5000;
-  int multisize=size;
-  // send parameters if any
-  char* socketip2 = 0;
-  uint32_t portnum2 = 0;
-  if (argc > 3) {
-	  send = true;
-	  socketip2 = argv[3];
-	  portnum2 = atoi(argv[4]);
-  }
-  cout << "\nrx socket ip : " << socketip <<
-    "\nrx port num  : " <<  portnum ;
-  if (send) {
-    cout << "\nsd socket ip : " << socketip2 <<
-      "\nsd port num  : " <<  portnum2;
-  }
-  cout << endl;
-  
-  //slsDetectorData *det=new moench03T1ZmqDataNew(); 
-  moench03T1ZmqDataNew *det=new moench03T1ZmqDataNew(); 
-  //analogDetector<uint16_t> *filter=new analogDetector<uint16_t>(det,1,NULL,1000);
-  singlePhotonDetector *filter=new singlePhotonDetector(det,3, 5, 1, 0, 1000, 10);
-  
-
-  char* buff;
-  multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
-  mt->setFrameMode(eFrame);
-  mt->StartThreads();
-  mt->popFree(buff);
-  
-  
-  ZmqSocket* zmqsocket=NULL;
-
-#ifdef NEWZMQ
-  // receive socket
-  try{
-#endif
-    
-    zmqsocket = new ZmqSocket(socketip,portnum); 
-    
-
-#ifdef NEWZMQ
-	  }  catch (...) {
-		cprintf(RED, "Error: Could not create Zmq socket on port %d with ip %s\n", portnum, socketip);
-		delete zmqsocket;
-		return EXIT_FAILURE;
-        }
-#endif
-
-#ifndef NEWZMQ	  
-	if (zmqsocket->IsError()) {
-		cprintf(RED, "Error: Could not create Zmq socket on port %d with ip %s\n", portnum, socketip);
-		delete zmqsocket;
-		return EXIT_FAILURE;
-	}
-#endif
-	if (zmqsocket->Connect()) {
-	  cprintf(RED, "Error: Could not connect to socket  %s\n",
-		  zmqsocket->GetZmqServerAddress());
-	  delete zmqsocket;
-	  return EXIT_FAILURE;
-	} else 
-	  printf("Zmq Client at %s\n", zmqsocket->GetZmqServerAddress());
-	
-	// send socket
-	ZmqSocket* zmqsocket2 = 0;
-	  cout << "zmq2 " << endl;
-	if (send) {
-#ifdef NEWZMQ
-	// receive socket
-	  try{
-#endif
-		zmqsocket2 = new ZmqSocket(portnum2, socketip2);
-
-
-
-#ifdef NEWZMQ
-	  }  catch (...) {
-			cprintf(RED, "Error: Could not create Zmq socket server on port %d and ip %s\n",  portnum2, socketip2);
-			delete zmqsocket2;
-			delete zmqsocket;
-			return EXIT_FAILURE;
-	  }
-#endif
-
-#ifndef NEWZMQ	  
-		if (zmqsocket2->IsError()) {
-			cprintf(RED, "Error: Could not create Zmq socket server on port %d and ip %s\n",  portnum2, socketip2);
-			delete zmqsocket2;
-			delete zmqsocket;
-			return EXIT_FAILURE;
-		}
-#endif	
-		if (zmqsocket2->Connect()) {
-		  cprintf(RED, "Error: Could not connect to socket  %s\n",
-					zmqsocket2->GetZmqServerAddress());
-		delete zmqsocket2;
-		return EXIT_FAILURE;
-	} else 
-		  printf("Zmq Client at %s\n", zmqsocket2->GetZmqServerAddress());
-
-	}
-
-
-	// header variables
-	uint64_t acqIndex = -1;
-	uint64_t frameIndex = -1;
-	uint32_t subFrameIndex = -1;
-	uint64_t fileindex = -1;
-	string filename = "";
-	//	char* image = new char[size];
-	//int* image = new int[(size/sizeof(int))]();
-	uint32_t flippedDataX = -1;
-	int *nph;
-	int iframe=0;
-	char ofname[10000];
-		    
-	char fname[10000];
-	int length;
-	int *detimage;
-	int nnx, nny,nns;
-	uint32_t imageSize = 0, nPixelsX = 0, nPixelsY = 0, dynamicRange = 0;
-	filter->getImageSize(nnx, nny,nns);
-	int16_t *dout=new int16_t [nnx*nny];
-	// infinite loop
-	uint32_t packetNumber = 0;
-	uint64_t bunchId = 0;
-	uint64_t timestamp = 0;
-	int16_t modId = 0;
-	uint16_t xCoord = 0;
-	uint16_t yCoord = 0;
-	uint16_t zCoord = 0;
-	uint32_t debug = 0;
-	uint32_t dr = 16;
-	uint16_t roundRNumber = 0;
-	uint8_t detType = 0;
-	uint8_t version = 0;
-	int* flippedData = 0;
-	char* additionalJsonHeader = 0;
-
-	uint32_t threshold=0;
-	
-	uint32_t xmin=0, xmax=400, ymin=0, ymax=400;
-	
-	string frameMode_s, detectorMode_s;
-
-	int emin, emax;
-
-
-	int newFrame=1;
-
-	while(1) {
-
-
-	  //  cout << "+++++++++++++++++++++++++++++++LOOP" << endl;
-		// get header, (if dummy, fail is on parse error or end of acquisition)
-#ifndef NEWZMQ	
-	  if (!zmqsocket->ReceiveHeader(0, acqIndex, frameIndex, subframeIndex, filename, fileindex)){
-#endif
-
-#ifdef NEWZMQ	
-	    rapidjson::Document doc;
-	    if (!zmqsocket->ReceiveHeader(0, doc, SLS_DETECTOR_JSON_HEADER_VERSION)) {
-	      zmqsocket->CloseHeaderMessage();
-
-#endif
-	    //	  if (!zmqsocket->ReceiveHeader(0, acqIndex, frameIndex, subframeIndex, filename, fileindex)) {
-	    cprintf(RED, "Got Dummy\n");
-
-
-
-
-	    while (mt->isBusy()) {;}//wait until all data are processed from the queues
-			
-	    
-	    detimage=mt->getImage(nnx,nny,nns);
-	    for (int ix=0; ix<nnx; ix++) {
-	      for (int iy=0; iy<nny; iy++) {
-		dout[iy*nnx+ix]=detimage[iy*nnx+ix];
-	      }
-	    }
-
-	    if (send) {
-	      strcpy(fname,filename.c_str());
-#ifdef NEWZMQ	
-	      //zmqsocket2->SendHeaderData (0, false, SLS_DETECTOR_JSON_HEADER_VERSION, dynamicRange, fileindex,
-	      //			  nnx, nny, nns*dynamicRange/8,acqIndex, frameIndex, fname, acqIndex, subFrameIndex, packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, flippedData, additionalJsonHeader);
-	
-	      zmqsocket2->SendHeaderData (0, false, SLS_DETECTOR_JSON_HEADER_VERSION, dr, fileindex,
-					  nnx, nny, nns*dr/8,acqIndex, frameIndex, fname, acqIndex, subFrameIndex, packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, flippedData, additionalJsonHeader);
-					   				   
-#endif
-
-#ifndef NEWZMQ
-	        zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fname, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
-#endif
-	     
-	      zmqsocket2->SendData((char*)dout,length);
-	      cprintf(GREEN, "Sent Data\n");
-	    }
-	    
-	    
-	    // stream dummy  to socket2 to signal end of acquisition
-	    if (send) {
-	      zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-	      cprintf(RED, "Sent Dummy\n");
-	    }
-	    mt->clearImage();
-	    if (of) {
-	      fclose(of);
-	      of=NULL;
-	    }
-	    
-	    newFrame=1;
-	    continue; //continue to not get out
-	  }
-
-#ifdef NEWZMQ
-	    if (newFrame) {
-	      //  acqIndex, frameIndex, subframeIndex, filename, fileindex
-	      size       = doc["size"].GetUint();
-	      multisize  = size;// * zmqsocket->size();
-	      dynamicRange  = doc["bitmode"].GetUint();
-	      nPixelsX = doc["shape"][0].GetUint();
-	      nPixelsY = doc["shape"][1].GetUint();
-	      filename        = doc["fname"].GetString();
-	      acqIndex = doc["acqIndex"].GetUint64();
-	      frameIndex       = doc["fIndex"].GetUint64();
-	      fileindex        = doc["fileIndex"].GetUint64();
-	      subFrameIndex    = doc["expLength"].GetUint();
-	      xCoord                  = doc["xCoord"].GetUint();
-	      yCoord                  = doc["yCoord"].GetUint();
-	      zCoord                  = doc["zCoord"].GetUint();
-	      flippedDataX=doc["flippedDataX"].GetUint();
-	      packetNumber=doc["packetNumber"].GetUint();
-	      bunchId=doc["bunchId"].GetUint();
-	      timestamp=doc["timestamp"].GetUint();
-	      modId=doc["modId"].GetUint();
-	      debug=doc["debug"].GetUint();
-	      roundRNumber=doc["roundRNumber"].GetUint();
-	      detType=doc["detType"].GetUint();
-	      version=doc["version"].GetUint();
-
-
-
-	      cprintf(BLUE, "Header Info:\n"
-		      "size: %u\n"
-		      "multisize: %u\n"
-		      "dynamicRange: %u\n"
-		      "nPixelsX: %u\n"
-		      "nPixelsY: %u\n"
-		      "currentFileName: %s\n"
-		      "currentAcquisitionIndex: %lu\n"
-		      "currentFrameIndex: %lu\n"
-		      "currentFileIndex: %lu\n"
-		      "currentSubFrameIndex: %u\n"
-		      "xCoordX: %u\n"
-		      "yCoordY: %u\n"
-		      "zCoordZ: %u\n"
-		      "flippedDataX: %u\n"
-		      "packetNumber: %u\n"
-		      "bunchId: %u\n"
-		      "timestamp: %u\n"
-		      "modId: %u\n"
-		      "debug: %u\n"
-		      "roundRNumber: %u\n"
-		      "detType: %u\n"
-		      "version: %u\n",
-		      size, multisize, dynamicRange, nPixelsX, nPixelsY,
-		      filename.c_str(), acqIndex,
-		      frameIndex, fileindex, subFrameIndex,
-		      xCoord, yCoord,zCoord,
-		      flippedDataX, packetNumber, bunchId, timestamp, modId, debug, roundRNumber, detType, version);
-
-
-	      if (doc.HasMember("threshold")) {
-		version=doc["threshold"].GetUint();
-	
-	      }
-
-	      if (doc.HasMember("roi")) {
-		xmin=doc["roi"][0].GetUint();
-		xmax=doc["roi"][1].GetUint();
-		ymin=doc["roi"][2].GetUint();
-		ymax=doc["roi"][3].GetUint();	
-
-	      }
-	      
-	      if (doc.HasMember("frameMode")) {
-		frameMode_s=doc["frameMode"].GetString();
-
-	      }
-	      
-	      if (doc.HasMember("detectorMode")) {
-		detectorMode_s=doc["detectorMode"].GetString();
-
-	      }
-	      
-	      if (doc.HasMember("energyRange")) {
-		emin=doc["energyRange"][0].GetUint();
-		emax=doc["energyRange"][0].GetUint();
-
-	      }
-	      
-	      
-	      if (doc.HasMember("dynamicRange")) {
-		dr=doc["dynamicRange"].GetUint();
-	      }
-	      
-	      if (doc.HasMember("nSubPixels")) {
-		nsubPixels=doc["nSubPixels"].GetUint();
-	      }
-	      
-	      
-
-	      newFrame=0;
-	      zmqsocket->CloseHeaderMessage();
-	    }
-#endif
-
-	  if (of==NULL) {
-	    sprintf(ofname,"%s_%d.clust",filename.c_str(),fileindex);
-	    of=fopen(ofname,"w");
-	    if (of) {
-	      mt->setFilePointer(of);
-	    }else {
-	      cout << "Could not open "<< ofname << " for writing " << endl;
-	      mt->setFilePointer(NULL);
-	    }
-	  }
-	  
-	  // get data
-	  length = zmqsocket->ReceiveData(0, buff, size);
-	  mt->pushData(buff);
-	  mt->nextThread();
-	  mt->popFree(buff);
-	  
-	
-	  
-	  
-	  iframe++;
-	}	// exiting infinite loop
-
-
-
-	delete zmqsocket;
-	if (send)
-	  delete zmqsocket2;
-
-	
-	cout<<"Goodbye"<<  endl;
-	return 0;
-}
-

slsDetectorCalibration/moenchExecutables/moenchZmqInterpolating.cpp

@@ -1,292 +0,0 @@
-#include "sls_receiver_defs.h"
-#include "ZmqSocket.h"
-#include "moench03T1ZmqDataNew.h"
-#include <vector> 
-#include <string> 
-#include <sstream> 
-#include <iomanip> 
-#include <fstream> 
-#include "tiffIO.h"
-
-#include<iostream>
-
-//#include "analogDetector.h"
-#include "interpolatingDetector.h"
-#include "linearInterpolation.h"
-#include "multiThreadedAnalogDetector.h"
-#include "ansi.h"
-#include <iostream>
-using namespace std;
-
-
-#define SLS_DETECTOR_JSON_HEADER_VERSION 0x2
-
-
-
-
-int main(int argc, char *argv[]) {
-/**
- * trial.o [socket ip] [starting port number] [send_socket ip] [send port number]
- *
- */
-
-  int nthreads=20;
-  int nsigma=5;
-  int xmin=0;
-  int xmax=400;
-  int ymin=0;
-  int ymax=400;
-  int nsubpixels=2;
-
-
-  FILE *of=NULL;
-  int fifosize=1000;
-  int int_ready=0;
-  int ok;
-  // help
-  if (argc < 3 ) {
-    cprintf(RED, "Help: %s [receive socket ip] [receive starting port number] [send_socket ip] [send starting port number] [nsubpixels] [nthreads] [nsigma] [xmin xmax ymin ymax]\n", argv[0]);
-    return EXIT_FAILURE;
-  }
-
-  char* socketip2 = 0;
-  uint32_t portnum2 = 0;
-	// receive parameters
-  int size = 32*2*5000;//atoi(argv[3]);
-  bool send = false;
-
-
-
-  char* socketip=argv[1];
-  uint32_t portnum = atoi(argv[2]);
-  if (argc > 3) {
-    send = true;
-    socketip2 = argv[3];
-    portnum2 = atoi(argv[4]);
-  }
-  if (argc > 5) {
-    nsubpixels=atoi(argv[5]);
-  }
-  if (argc>6) {
-    nthreads=atoi(argv[6]);
-  }
-  if (argc>7) {
-    nsigma=atoi(argv[7]);
-  }
-  if (argc>11) {
-    xmin=atoi(argv[8]);
-    xmax=atoi(argv[8]);
-    ymin=atoi(argv[10]);
-    ymax=atoi(argv[11]);
-  }
-
-  cout << "\nrx socket ip : " << socketip <<
-    "\nrx port num  : " <<  portnum ;
-  if (send) {
-    cout << "\nsd socket ip : " << socketip2 <<
-      "\nsd port num  : " <<  portnum2;
-	}
-  cout << endl;
-
-  //slsDetectorData *det=new moench03T1ZmqDataNew(); 
-  int npx, npy;
-  moench03T1ZmqDataNew *det=new moench03T1ZmqDataNew(); 
-  det->getDetectorSize(npx, npy);
-  linearInterpolation *interp=new linearInterpolation(npx,npy,nsubpixels);
-  interpolatingDetector *filter=new interpolatingDetector(det,interp, nsigma, 1, 0, 1000, 100,npx,npy);
-  cout << "Setting noise cut to " << nsigma << " sigma"<< endl;
-  filter->setROI(xmin,xmax,ymin,ymax);
-  cout << "Setting ROI to "<< xmin << " " << xmax << " " << ymin << " " << ymax << endl;
-  
-  char* buff;
-  multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
-	  int frameMode=eFrame;
-	  mt->setFrameMode(frameMode);
-	  mt->StartThreads();
-	  mt->popFree(buff);
-
-
-	  
-
-
-	// receive socket
-	  ZmqSocket* zmqsocket = new ZmqSocket(socketip,portnum); 
-	if (zmqsocket->IsError()) {
-		cprintf(RED, "Error: Could not create Zmq socket on port %d with ip %s\n", portnum, socketip);
-		delete zmqsocket;
-		return EXIT_FAILURE;
-	}
-	zmqsocket->Connect();
-	printf("Zmq Client at %s\n", zmqsocket->GetZmqServerAddress());
-
-	// send socket
-	ZmqSocket* zmqsocket2 = 0;
-	if (send) {
-		zmqsocket2 = new ZmqSocket(portnum2, socketip2);
-		if (zmqsocket2->IsError()) {
-			bprintf(RED, "Error: Could not create Zmq socket server on port %d and ip %s\n",  portnum2, socketip2);
-			delete zmqsocket2;
-			delete zmqsocket;
-			return EXIT_FAILURE;
-		}
-		zmqsocket2->Connect();
-		printf("Zmq Server started at %s\n", zmqsocket2->GetZmqServerAddress());
-	}
-
-
-	// header variables
-	uint64_t acqIndex = -1;
-	uint64_t frameIndex = -1;
-	uint32_t subframeIndex = -1;
-	uint64_t fileindex = -1;
-	string filename = "";
-	char ffname[10000];
-	int ffindex;
-
-	char* image = new char[size];
-	//int* image = new int[(size/sizeof(int))]();
-
-	int *nph;
-	int iframe=0;
-	char ofname[10000];
-		    
-	char fname[10000];
-	int length;
-	int *detimage;
-	int nnx, nny,nns;
-	int nix, niy,nis;
-	filter->getImageSize(nnx, nny,nns);
-	int16_t *dout=new int16_t [nnx*nny];
-	// infinite loop
-	int ix, iy, isx, isy;
-	while(1) {
-
-
-	  //  cout << "+++++++++++++++++++++++++++++++LOOP" << endl;
-		// get header, (if dummy, fail is on parse error or end of acquisition)
-	  if (!zmqsocket->ReceiveHeader(0, acqIndex, frameIndex, subframeIndex, filename, fileindex)){
-	    //	  if (!zmqsocket->ReceiveHeader(0, acqIndex, frameIndex, subframeIndex, filename, fileindex)) {
-	    // cprintf(RED, "Got Dummy\n");
-	    while (mt->isBusy()) {;}//wait until all data are processed from the queues
-	    if (frameMode==ePedestal) {	
-	      detped=mt->getPedestal();
- 	      if (detped) {
-		
- 		for (ix=0; ix<400; ix++) {
- 		  for (iy=0; iy<400; iy++) {
- 		    dout[iy*400+ix]+=detped[iy*400+ix];
-		  }
-		}
-	      }
-
-	    } else {	      
- 	      detimage=mt->getImage(nix,niy,nis);
- 	      if (detimage) {
- 		for (ix=0; ix<nix/nis; ix++) {
-                   for (iy=0; iy<niy/nis; iy++) {
-                     dout[iy*(nix/nis)+ix]=0;
- 		  }
- 		}
- 		for (ix=0; ix<nix; ix++) {
- 		  for (iy=0; iy<niy; iy++) {
- 		    dout[(iy/nis)*(nix/nis)+(ix/nis)]+=detimage[iy*nix+ix];
-		  }
-		}
-	      }
-	    }
-	  	    
-	     
-	   
-	   
-	    if (send) {
-	      strcpy(fname,filename.c_str());
-	      //  zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,16,fileindex,400,400,400*400, acqIndex,frameIndex,fname, acqIndex, 0,0,0,0,0,0,0,0,0,0,0,1);
-	      zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fname, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
-	      
-	      zmqsocket2->SendData((char*)dout,length);
-	      cprintf(GREEN, "Sent Data\n");
-	    }
-	    
-	    sprintf(ofname,"%s_%d.tiff",ffname,ffindex);
-	    if (frameMode==eFlat)
-	      mt->writeFlatField(ofname); 
-	    else if (frameMode==ePedestal)
-	      mt->writePedestal(ofname);
-	    else
-	      mt->writeImage(ofname); 
-	    
-	  
-	    // stream dummy  to socket2 to signal end of acquisition
-	    if (send) {
-	      zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-	      // cprintf(RED, "Sent Dummy\n");
-	      cprintf(RED, "Received %d frames\n", iframe);
-	    }
-	    mt->clearImage();
-	    if (of) {
-	      fclose(of);
-	      of=NULL;
-	    }
-	    iframe=0;
-	    continue; //continue to not get out
-	  }
-
-
-	  if (of==NULL) {  
-	    while (mt->isBusy()) {;}
-	    sprintf(ofname,"%s_%d.clust",filename.c_str(),fileindex);
-	    of=fopen(ofname,"w");
-	    if (of) {
-	      mt->setFilePointer(of);
-	    }else {
-	      cout << "Could not open "<< ofname << " for writing " << endl;
-	      mt->setFilePointer(NULL);
-	    }
-	    ffindex=fileindex;
-	    strcpy(ffname,filename.c_str());
-	    if (filename.find("flat")!=std::string::npos) {
-	      cout << "add to ff" << endl;
-	      frameMode=eFlat;//ePedestal;
-	      int_ready=0;
-	      
-	    } else if  (filename.find("newped")!=std::string::npos) {
-	      frameMode=ePedestal;
-	      cout << "new pedestal" << endl;
-	      
-	      mt->newDataSet();
-	    } else if  (filename.find("ped")!=std::string::npos){ 
-	      frameMode=ePedestal;
-	      cout << "pedestal" << endl;
-	    } else { 
-	      frameMode=eFrame;
-	      cout << "data" << endl;
-	      if (int_ready==0) {
-		mt->prepareInterpolation(ok);
-		cout << "prepare interpolation " << endl;
-		int_ready=1;
-	      }
-	    }
-	   
-	    mt->setFrameMode(frameMode);
-	  }
-	  
-	  // get data
-	  length = zmqsocket->ReceiveData(0, buff, size);
-	  mt->pushData(buff);
-	  mt->nextThread();
-	  mt->popFree(buff);
-	  
-	  iframe++;
-	}	// exiting infinite loop
-
-
-
-	delete zmqsocket;
-	if (send)
-	  delete zmqsocket2;
-
-	
-	//	cout<<"Goodbye"<<  endl;
-	return 0;
-}
-

slsDetectorCalibration/moenchExecutables/moenchZmqProcess.cpp

@@ -1,8 +1,20 @@
-#define WRITE_QUAD
+//#define WRITE_QUAD
+#define MOENCH_BRANCH
 
-#include "sls_receiver_defs.h"
+#define C_GHOST 0.0004
+
+#define CM_ROWS 20
+
+#include "sls_detector_defs.h"
 #include "ZmqSocket.h"
+#ifndef RECT
 #include "moench03T1ZmqDataNew.h"
+#endif
+#ifdef RECT
+#include "moench03T1ZmqDataNewRect.h"
+#endif
+#include "moench03GhostSummation.h"
+#include "moench03CommonMode.h"
 #include <vector> 
 #include <string> 
 #include <sstream> 
@@ -10,10 +22,7 @@
 #include <fstream> 
 #include "tiffIO.h"
 
-//#define NEWZMQ
-#ifdef NEWZMQ
 #include <rapidjson/document.h> //json header in zmq stream
-#endif
 
 #include<iostream>
 
@@ -45,11 +54,14 @@ int main(int argc, char *argv[]) {
  */
   FILE *of=NULL;
   int fifosize=5000;
-  int etabins=1000;//nsubpix*2*100;
+  int etabins=1000, etabinsy=1000;//nsubpix*2*100;
   double etamin=-1, etamax=2;
+  int nSubPixelsX=2;
+  //	int emin, emax;
+  int nSubPixelsY=2;
 	// help
   if (argc < 3 ) {
-    cprintf(RED, "Help: ./trial [receive socket ip] [receive starting port number] [send_socket ip] [send starting port number] [nthreads] [nsubpix] [etafile]\n");
+    cprintf(RED, "Help: ./trial [receive socket ip] [receive starting port number] [send_socket ip] [send starting port number] [nthreads] [nsubpix] [gainmap]  [etafile]\n");
     return EXIT_FAILURE;  
   }
   
@@ -61,6 +73,7 @@ int main(int argc, char *argv[]) {
   char* socketip2 = 0;
   uint32_t portnum2 = 0;
 
+  uint32_t nSigma=5;
 
   int ok;
 
@@ -86,17 +99,26 @@ int main(int argc, char *argv[]) {
     nthreads=atoi(argv[5]);
 
   cout << "Number of threads is: " << nthreads << endl;
-  int nSubPixels=2;
-  if (argc>6)
-    nSubPixels=atoi(argv[6]);
-  cout << "Number of subpixels is: " << nSubPixels << endl;
-  
-  char *etafname=NULL;
+  if (argc>6) {
+    nSubPixelsX=atoi(argv[6]);
+    nSubPixelsY=nSubPixelsX;
+#ifdef RECT
+    nSubPixelsX=2;
+#endif
+  }
+  cout << "Number of subpixels is: " << nSubPixelsX << " " <<  nSubPixelsY << endl;
+
+  char *gainfname=NULL;
   if (argc>7) {
-    etafname=argv[7];
-    cout << "Eta file name is: " << etafname << endl;
+    gainfname=argv[7];
+    cout << "Gain map file name is: " << gainfname << endl;
   }
 
+  char *etafname=NULL;
+  if (argc>8) {
+    etafname=argv[8];
+    cout << "Eta file name is: " << etafname << endl;
+  }
 
   //slsDetectorData *det=new moench03T1ZmqDataNew(); 
   moench03T1ZmqDataNew *det=new moench03T1ZmqDataNew(); 
@@ -104,32 +126,64 @@ int main(int argc, char *argv[]) {
   int npx, npy;
   det->getDetectorSize(npx, npy);
 
-
+  int send_something=0;
 
 
   int maxSize = npx*npy*2;//32*2*8192;//5000;//atoi(argv[3]);
   int size= maxSize;//32*2*5000;
-  int multisize=size;
-  int dataSize=size;
+  //int multisize=size;
+  //int dataSize=size;
 
   char dummybuff[size];
+  
+
+  int ncol_cm=CM_ROWS;
+  double xt_ghost=C_GHOST;
+  moench03CommonMode *cm=NULL;
+  moench03GhostSummation *gs=NULL;
+#ifdef CORR
+  gs=new moench03GhostSummation(det, xt_ghost);
+  cm=new moench03CommonMode(ncol_cm);
+#endif
+  double *gainmap=NULL;
+  float *gm;
+  double *gmap=NULL;
+
+  uint32_t nnnx, nnny;
+  if (gainfname) {
+    gm=ReadFromTiff(gainfname, nnny, nnnx);
+    if (gm && nnnx==(uint)npx && nnny==(uint)npy) {
+      gmap=new double[npx*npy];
+      for (int i=0; i<npx*npy; i++) {
+	gmap[i]=gm[i];
+      }
+      delete [] gm;
+    } else
+      cout << "Could not open gain map " << gainfname << endl;
+  }
+
+
+
+
+
+
 
 
 
   //analogDetector<uint16_t> *filter=new analogDetector<uint16_t>(det,1,NULL,1000);
 #ifndef INTERP
-  singlePhotonDetector *filter=new singlePhotonDetector(det,3, 5, 1, 0, 1000, 10);
+  singlePhotonDetector *filter=new singlePhotonDetector(det,3, nSigma, 1, cm, 1000, 10, -1, -1, gainmap, gs);
 
     multiThreadedCountingDetector *mt=new multiThreadedCountingDetector(filter,nthreads,fifosize);
 
     // multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
 #endif
 #ifdef INTERP
-  eta2InterpolationPosXY *interp=new eta2InterpolationPosXY(npx, npy, nSubPixels, etabins, etamin, etamax);
+    eta2InterpolationPosXY *interp=new eta2InterpolationPosXY(npx, npy, nSubPixelsX,nSubPixelsY, etabins,  etabinsy, etamin, etamax);
 
   if (etafname) interp->readFlatField(etafname);
 
-  interpolatingDetector *filter=new interpolatingDetector(det,interp, 5, 1, 0, 1000, 10);
+  interpolatingDetector *filter=new interpolatingDetector(det,interp, nSigma, 1, cm,  1000, 10, -1, -1, gainmap, gs);
   multiThreadedInterpolatingDetector *mt=new multiThreadedInterpolatingDetector(filter,nthreads,fifosize);
 #endif
 
@@ -220,21 +274,32 @@ int main(int argc, char *argv[]) {
 	// header variables
 	uint64_t acqIndex = -1;
 	uint64_t frameIndex = -1;
-	uint32_t subFrameIndex = -1;
+#ifdef MOENCH_BRANCH
+ 	uint32_t subFrameIndex = -1;
+	int* flippedData = 0;
+#endif
+	
+	uint64_t subframes=0;
+	//uint64_t  isubframe=0;
+	uint64_t  insubframe=0;
+	double subnorm=1;
+	uint64_t  f0=-1, nsubframes=0, nnsubframe=0;
+
 	uint64_t fileindex = -1;
 	string filename = "";
 	//	char* image = new char[size];
 	//int* image = new int[(size/sizeof(int))]();
-	uint32_t flippedDataX = -1;
-	int *nph;
+	//uint32_t flippedDataX = -1;
+	//int *nph;
 	int iframe=0;
 	char ofname[10000];
 		    
-	char fname[10000];
-	int length;
-	int *detimage;
-	int nnx, nny,nns;
-	uint32_t imageSize = 0, nPixelsX = 0, nPixelsY = 0, dynamicRange = 0;
+	string fname;
+	//	int length;
+	int *detimage=NULL;
+	int nnx, nny,nnsx, nnsy;
+	//uint32_t imageSize = 0, nPixelsX = 0, nPixelsY = 0, 
+	//uint32_t  dynamicRange = 0;
 	// infinite loop
 	uint32_t packetNumber = 0;
 	uint64_t bunchId = 0;
@@ -248,11 +313,10 @@ int main(int argc, char *argv[]) {
 	//int16_t *dout;//=new int16_t [nnx*nny];
 	uint32_t dr = 32;
 	int32_t *dout=NULL;//=new int32_t [nnx*nny];
-	uint32_t nSigma=5;
+	float *doutf=NULL;//=new int32_t [nnx*nny];
 	uint16_t roundRNumber = 0;
 	uint8_t detType = 0;
 	uint8_t version = 0;
-	int* flippedData = 0;
 	char* additionalJsonHeader = 0;
 
 	int32_t threshold=0;
@@ -261,18 +325,17 @@ int main(int argc, char *argv[]) {
 	
 	string frameMode_s, detectorMode_s, intMode_s;
 
-	int emin, emax;
-	int resetFlat=0;
-	int resetPed=0;
-	int nsubPixels=1;
-	int isPedestal;
-	int isFlat=0;
+	//	int resetFlat=0;
+	//int resetPed=0;
+	//	int nsubPixels=1;
+	//int isPedestal=0;
+	//int isFlat=0;
 	int newFrame=1;
-	detectorMode dMode;
-	frameMode fMode;
+	detectorMode dMode=eAnalog;
+	frameMode fMode=eFrame;
 	double *ped;
 
-	filter->getImageSize(nnx, nny,nns);
+	filter->getImageSize(nnx, nny,nnsx, nnsy);
 
 	
 
@@ -301,8 +364,9 @@ int main(int argc, char *argv[]) {
 
 
 	    while (mt->isBusy()) {;}//wait until all data are processed from the queues
-	    
+	    usleep(1000);
 	    if (of) {
+	      mt->setFilePointer(NULL);
 	      fclose(of);
 	      of=NULL;
 	    }
@@ -313,35 +377,70 @@ int main(int argc, char *argv[]) {
 	      cprintf(RED, "Sent Dummy\n");
 	    }
 	    } else {
-	    if (fMode==ePedestal) {
-	      sprintf(ofname,"%s_%d_ped.tiff",fname,fileindex);
-	      mt->writePedestal(ofname);
-	       cout << "Writing pedestal to " << ofname << endl;
-	    }
+	      send_something=0;
+	      if (fMode==ePedestal) {
+		sprintf(ofname,"%s_%ld_ped.tiff",fname.c_str(),fileindex);
+		mt->writePedestal(ofname);
+		cout << "Writing pedestal to " << ofname << endl;
+		send_something=1;
+	      }
 #ifdef INTERP
-	    else if  (fMode==eFlat) {
-	      mt->prepareInterpolation(ok);
-	      sprintf(ofname,"%s_%d_eta.tiff",fname,fileindex);
-	      mt->writeFlatField(ofname);
-	       cout << "Writing eta to " << ofname << endl;
-	    }
+	      else if  (fMode==eFlat) {
+		mt->prepareInterpolation(ok);
+		sprintf(ofname,"%s_%ld_eta.tiff",fname.c_str(),fileindex);
+		mt->writeFlatField(ofname);
+		cout << "Writing eta to " << ofname << endl;
+		send_something=1;
+	      }
 #endif
-	    else {
-	      sprintf(ofname,"%s_%d.tiff",fname,fileindex);
-	      mt->writeImage(ofname);
-	       cout << "Writing image to " << ofname << endl;
-	    }
-	    //  cout << nns*nnx*nny*nns*dr/8 << " " << length << endl;
+	      else {
+		if (subframes>0 ) { 
+		  if (insubframe>0) {
+		    sprintf(ofname,"%s_sf%ld_%ld.tiff",fname.c_str(),nnsubframe,fileindex);
+		    //		  mt->writeImage(ofname);
+		    doutf= new float[nnx*nny];
+		    if (subframes>0 && insubframe!=subframes && insubframe>0)
+		      subnorm=((double)subframes)/((double)insubframe);
+		    else
+		      subnorm=1.;
+		    for (int ix=0; ix<nnx*nny; ix++) {
+		    doutf[ix]=detimage[ix]*subnorm;
+		    if (doutf[ix]<0) doutf[ix]=0;
+		    }
+	    
+		    cout << "Writing image to " << ofname << endl;
+		    
+		    WriteToTiff(doutf,ofname ,nnx, nny); 
+		    
+		    if (doutf)
+		      delete [] doutf;
+		    doutf=NULL;
+		    
+		    nsubframes++;
+		    insubframe=0;
+		    send_something=1;
+		  }
+		} else {
+		  sprintf(ofname,"%s_%ld.tiff",fname.c_str(),fileindex);
+		  mt->writeImage(ofname);
+		  send_something=1;
+		}
+		
+		cout << "Writing image to " << ofname << endl;
+	      }
+	      //  cout << nns*nnx*nny*nns*dr/8 << " " << length << endl;
 
 	    if (send) {
-
+	      
 	    if (fMode==ePedestal) {   
 	      cprintf(MAGENTA,"Get pedestal!\n");
-	      nns=1;
+	      nnsx=1;
+	      nnsy=1;
+	      
 	      nnx=npx;
 	      nny=npy;
 	      //dout= new int16_t[nnx*nny*nns*nns];
-	      dout= new int32_t[nnx*nny*nns*nns];
+	      dout= new int32_t[nnx*nny*nnsx*nnsy];
 	      // cout << "get pedestal " << endl;
 	      ped=mt->getPedestal();
 	      // cout << "got pedestal " << endl;
@@ -355,11 +454,11 @@ int main(int argc, char *argv[]) {
 	    }
 #ifdef INTERP
 	    else if  (fMode==eFlat) {
-	       int nb;
-	      double emi, ema;
-	       int *ff=mt->getFlatField(nb, emi, ema);
+	      int nb, nby;
+	       double emi=0, ema=1;
+	       int *ff=mt->getFlatField(nb, nby, emi, ema);
 	       nnx=nb;
-	       nny=nb;
+	       nny=nby;
 	       dout= new int32_t[nb*nb];
 	       for (int ix=0; ix<nb*nb; ix++) {
 	     	dout[ix]=ff[ix];
@@ -367,15 +466,19 @@ int main(int argc, char *argv[]) {
 	     }
 #endif
 	    else {
-	      detimage=mt->getImage(nnx,nny,nns);
+	      detimage=mt->getImage(nnx,nny,nnsx, nnsy);
 	      cprintf(MAGENTA,"Get image!\n");
-	      cout << nnx << " " << nny << " " << nns << endl;
+	      cout << nnx << " " << nny << " " << nnsx << " " << nnsy << endl;
 	      // nns=1;
 	      // nnx=npx;
 	      // nny=npy;
 	      // nnx=nnx*nns;
 	      //nny=nny*nns;
 	      dout= new int32_t[nnx*nny];
+	      if (subframes>0 && insubframe!=subframes && insubframe>0)
+		subnorm=((double)subframes)/((double)insubframe);
+	      else
+		subnorm=1.;
 	      for (int ix=0; ix<nnx*nny; ix++) {
 		// for (int iy=0; iy<nny*nns; iy++) {
 		 //  for (int isx=0; isx<nns; isx++) {
@@ -387,34 +490,41 @@ int main(int argc, char *argv[]) {
 		    
 		//   }
 		// }
-		  dout[ix]=detimage[ix];
+		  dout[ix]=detimage[ix]*subnorm;
 		  if (dout[ix]<0) dout[ix]=0;
 		  //   cout << ix << " " << dout[ix] << endl;
 		  // }
 	      }
 	    }
+	    //if ((insubframe>0 && subframes>0) || (subframes<=0) ){
 
-
-
-#ifdef NEWZMQ	
-	    cout << "Sending image size " << nnx << " " << nny << endl;
-	      zmqsocket2->SendHeaderData (0, false, SLS_DETECTOR_JSON_HEADER_VERSION, dr, fileindex, nnx, nny, nnx*nny*dr/8,acqIndex, frameIndex, fname, acqIndex, subFrameIndex, packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, flippedData, additionalJsonHeader);
-					   				   
+	    if(send_something) {
+#ifndef DEVELOPER
+#ifndef MOENCH_BRANCH
+	      zmqsocket2->SendHeaderData (0, false, SLS_DETECTOR_JSON_HEADER_VERSION, dr, fileindex, 0,0, nnx, nny, nnx*nny*dr/8,acqIndex, frameIndex, fname.c_str(), acqIndex,0 , packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, 0,0, additionalJsonHeader);
 #endif
-
-#ifndef NEWZMQ
-	        zmqsocket2->SendHeaderData(0, false, SLS_DETECTOR_JSON_HEADER_VERSION,0,0,0,0,0, 0,0,fname, 0, 0,0,0,0,0,0,0,0,0,0,0,1);
 #endif
-		
-		zmqsocket2->SendData((char*)dout,nnx*nny*dr/8);
-		cprintf(GREEN, "Sent Data\n");
-		
-		zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-		cprintf(RED, "Sent Dummy\n");
-		if (dout)
-		  delete [] dout;
-		dout=NULL;
-
+	      
+#ifdef DEVELOPER
+	      zmqsocket2->SendHeaderData (0, false,SLS_DETECTOR_JSON_HEADER_VERSION , dr, fileindex, 0,0,nnx,nny,nnx*nny*dr/8,acqIndex, frameIndex, fname.c_str(),acqIndex,0 , packetNumber,bunchId, timestamp, modId,xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, 0,0, 0,additionalJsonHeader);
+#endif	
+#ifdef MOENCH_BRANCH
+	   
+	      zmqsocket2->SendHeaderData (0, false, SLS_DETECTOR_JSON_HEADER_VERSION, dr, fileindex, nnx, nny, nnx*nny*dr/8,acqIndex, frameIndex, fname.c_str(), acqIndex, subFrameIndex, packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, flippedData, additionalJsonHeader);
+#endif		
+	      
+			
+	      
+	      zmqsocket2->SendData((char*)dout,nnx*nny*dr/8);
+	      cprintf(GREEN, "Sent Data\n");
+	    }
+	    
+	    zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
+	    cprintf(RED, "Sent Dummy\n");
+	    if (dout)
+	      delete [] dout;
+	    dout=NULL;
+	    
 	    }
 	    }
 
@@ -427,8 +537,8 @@ int main(int argc, char *argv[]) {
 	      //   auto meas_duration = duration_cast<microseconds>( t2 - t0 ).count();
 	      //   auto real_duration = duration_cast<microseconds>( t2 - t1 ).count();
 	    
-	    cout << "Measurement lasted " << difftime(end,begin) << endl;
-	    cout << "Processing lasted " << difftime(finished,begin) << endl;
+	      // cout << "Measurement lasted " << difftime(end,begin) << endl;
+	      //cout << "Processing lasted " << difftime(finished,begin) << endl;
 	    continue; //continue to not get out
 
 
@@ -443,7 +553,7 @@ int main(int argc, char *argv[]) {
 	      //  acqIndex, frameIndex, subframeIndex, filename, fileindex
 	      size       = doc["size"].GetUint();
 	      // multisize  = size;// * zmqsocket->size();
-	      dynamicRange  = doc["bitmode"].GetUint();
+	      // dynamicRange  = doc["bitmode"].GetUint();
 	      //  nPixelsX = doc["shape"][0].GetUint();
 	      // nPixelsY = doc["shape"][1].GetUint();
 	      filename        = doc["fname"].GetString();
@@ -460,10 +570,10 @@ int main(int argc, char *argv[]) {
 	      //detType=doc["detType"].GetUint();
 	      //version=doc["version"].GetUint();
 
-	      dataSize=size;
-
-	      strcpy(fname,filename.c_str());
+	      //dataSize=size;
 
+	      //strcpy(fname,filename.c_str());
+	      fname=filename;
 	      // cprintf(BLUE, "Header Info:\n"
 	      // 	      "size: %u\n"
 	      // 	      "multisize: %u\n"
@@ -494,8 +604,8 @@ int main(int argc, char *argv[]) {
 	      // 	      flippedDataX, packetNumber, bunchId, timestamp, modId, debug, roundRNumber, detType, version);
 	      
 	      /* Analog detector commands */
-	      isPedestal=0;
-	      isFlat=0;
+	      //isPedestal=0;
+	      //isFlat=0;
 	      fMode=eFrame;
 	      frameMode_s="frame";
 	      cprintf(MAGENTA, "Frame mode: ");
@@ -504,28 +614,28 @@ int main(int argc, char *argv[]) {
 		  frameMode_s=doc["frameMode"].GetString();
 		  if (frameMode_s == "pedestal"){
 		    fMode=ePedestal;
-		    isPedestal=1;
+		    //isPedestal=1;
 		  } else if (frameMode_s == "newPedestal"){
 		    mt->newDataSet(); //resets pedestal  
 		    // cprintf(MAGENTA, "Resetting pedestal\n");
 		    fMode=ePedestal;
-		    isPedestal=1;
+		    //isPedestal=1;
 		  }
 #ifdef INTERP 
 		  else if (frameMode_s == "flatfield") {
 		     fMode=eFlat;
-		     isFlat=1;
+		     //isFlat=1;
 		   } else if (frameMode_s == "newFlatfield") {
 		     mt->resetFlatField();
-		     isFlat=1;
+		     //isFlat=1;
 		     cprintf(MAGENTA, "Resetting flatfield\n");
 		     fMode=eFlat;
 		   }
 #endif
 		  else {
 		    fMode=eFrame;
-		    isPedestal=0;
-		    isFlat=0;
+		    //isPedestal=0;
+		    //isFlat=0;
 		    fMode=eFrame;
 		    frameMode_s="frame";
 		  }
@@ -648,6 +758,21 @@ int main(int argc, char *argv[]) {
 	      // 	mt->setNSubPixels(nSubPixels);
 	      // }
 	      
+	      // threshold=0;
+	      cprintf(MAGENTA, "Subframes: ");
+	      subframes=0;
+	      //isubframe=0;
+	      insubframe=0;
+	      subnorm=1;
+	      f0=0;
+	      nnsubframe=0;
+	      if (doc.HasMember("subframes")) {	
+		if (doc["subframes"].IsInt()) {
+		  subframes=doc["subframes"].GetInt();
+		}
+	      }	
+	      cprintf(MAGENTA, "%ld\n", subframes);
+
 	      
 	      newFrame=0;
 	      /* zmqsocket->CloseHeaderMessage();*/
@@ -657,7 +782,12 @@ int main(int argc, char *argv[]) {
 	    // cout << "file" << endl;
 	    //  cout << "data " << endl;
 	  if (of==NULL) {
-	    sprintf(ofname,"%s_%d.clust",filename.c_str(),fileindex);
+#ifdef WRITE_QUAD
+	    sprintf(ofname,"%s_%ld.clust2",filename.c_str(),fileindex);
+#endif
+#ifndef WRITE_QUAD
+	    sprintf(ofname,"%s_%ld.clust",filename.c_str(),fileindex);
+#endif
 	    of=fopen(ofname,"w");
 	    if (of) {
 	      mt->setFilePointer(of);
@@ -666,31 +796,109 @@ int main(int argc, char *argv[]) {
 	      mt->setFilePointer(NULL);
 	    }
 	  }
+
 	  
 
 	  // cout << "data" << endl;
 	  // get data
 	  // acqIndex = doc["acqIndex"].GetUint64();
+
 	  frameIndex       = doc["fIndex"].GetUint64();
+
 	  // subFrameIndex    = doc["expLength"].GetUint();
 
 	  //  bunchId=doc["bunchId"].GetUint();
 	  //  timestamp=doc["timestamp"].GetUint();
-	      packetNumber=doc["packetNumber"].GetUint();
-	      // cout << acqIndex << " " << frameIndex << " " << subFrameIndex << " "<< bunchId << " " << timestamp << " " << packetNumber << endl;
-	      if (packetNumber>=40) {
-		//*((int*)buff)=frameIndex;
-		memcpy(buff,&frameIndex,sizeof(int));
-		length = zmqsocket->ReceiveData(0, buff+sizeof(int), size);
-		mt->pushData(buff);
-		mt->nextThread();
-		mt->popFree(buff);
-	      } else {
-		cprintf(RED, "Incomplete frame: received only %d packet\n", packetNumber);
-		length = zmqsocket->ReceiveData(0, dummybuff, size);
+	  packetNumber=doc["packetNumber"].GetUint();
+	  // cout << acqIndex << " " << frameIndex << " " << subFrameIndex << " "<< bunchId << " " << timestamp << " " << packetNumber << endl;
+	  if (packetNumber>0) {
+	    //*((int*)buff)=frameIndex;
+	    if (insubframe==0) f0=frameIndex;
+	    memcpy(buff,&frameIndex,sizeof(int));
+	    //length = 
+	    zmqsocket->ReceiveData(0, buff+sizeof(int), size);
+	    mt->pushData(buff);
+	    mt->nextThread();
+	    mt->popFree(buff);
+	    insubframe++;
+	    nsubframes=frameIndex+1-f0;
+	  } else {
+	    cprintf(RED, "Empty frame %d\n", frameIndex);
+	    //length = 
+	    zmqsocket->ReceiveData(0, dummybuff, size);
+	  }
+	  
+
+
+
+	  if (subframes>0 && insubframe>=subframes && fMode==eFrame) {
+	    while (mt->isBusy()) {;}//wait until all data are processed from the queues
+	    detimage=mt->getImage(nnx,nny,nnsx, nnsy);
+	    cprintf(MAGENTA,"Get image!\n");
+	    dout= new int32_t[nnx*nny];
+	    doutf= new float[nnx*nny];
+	    if (subframes>0 && insubframe!=subframes && insubframe>0)
+	      subnorm=((double)subframes)/((double)insubframe);
+	    else
+	      subnorm=1.;
+	    for (int ix=0; ix<nnx*nny; ix++) {
+	      dout[ix]=detimage[ix]*subnorm;
+	      if (dout[ix]<0) dout[ix]=0;
+	      doutf[ix]=dout[ix];
+	    }
+	    sprintf(ofname,"%s_sf%ld_%ld.tiff",fname.c_str(),nnsubframe,fileindex);
+	    
+	    cout << "Writing image to " << ofname << endl;
+
+	    WriteToTiff(doutf,ofname ,nnx, nny); 
+	    nsubframes++;
+	    insubframe=0;
+	    nnsubframe++;
+
+
+#ifndef DEVELOPER
+#ifndef MOENCH_BRANCH
+	    zmqsocket2->SendHeaderData (0, false, SLS_DETECTOR_JSON_HEADER_VERSION, dr, fileindex, 0,0, nnx, nny, nnx*nny*dr/8,acqIndex, frameIndex, fname.c_str(), acqIndex,0 , packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, 0,0, additionalJsonHeader);
+#endif
+#endif
+
+#ifdef DEVELOPER
+	    zmqsocket2->SendHeaderData (0, false,SLS_DETECTOR_JSON_HEADER_VERSION , dr, fileindex, 0,0,nnx,nny,nnx*nny*dr/8,acqIndex, frameIndex, fname.c_str(),acqIndex,0 , packetNumber,bunchId, timestamp, modId,xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, 0,0, 0,additionalJsonHeader);
+#endif	
+#ifdef MOENCH_BRANCH
+	   
+	    zmqsocket2->SendHeaderData (0, false, SLS_DETECTOR_JSON_HEADER_VERSION, dr, fileindex, nnx, nny, nnx*nny*dr/8,acqIndex, frameIndex, fname.c_str(), acqIndex, subFrameIndex, packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, flippedData, additionalJsonHeader);
+#endif		
+	       
+	    
+
+	    zmqsocket2->SendData((char*)dout,nnx*nny*dr/8);
+	    cprintf(GREEN, "Sent subdata\n");
+		
+
+	    if (dout)
+	      delete [] dout;
+	    dout=NULL;
+
+	    if (doutf)
+	      delete [] doutf;
+	    doutf=NULL;
+	    
+	    mt->clearImage();
+	    
+	  }
+
+		 
+
+
+
+
+
 
-	      }
 	
+	      
+
+
 	  
 	  
 	  iframe++;

slsDetectorCalibration/moenchExecutables/tiff_to_th2f.cpp

@@ -1,57 +0,0 @@
-#include <TPaveText.h> 
-#include <TLegend.h> 
-#include <TF1.h> 
-#include <TGraphErrors.h> 
-#include <TH2F.h> 
-#include <TASImage.h> 
-#include <TImage.h> 
-#include <TFile.h> 
-#include <vector> 
-#include <string> 
-#include <sstream> 
-#include <iomanip> 
-#include <fstream> 
-#include "tiffIO.h"
-
-#include<iostream>
-
-using namespace std;
-
-
-int main(int argc, char *argv[]) {
-/**
- * trial.o [socket ip] [starting port number] [outfname]
- *
- */
-
-  if (argc<3) {
-    cout << "Wrong usage! Should be: "<< argv[0] << " infile " << " outfile " << endl;
-    return 1;
-  }
-
-  uint32  nx, ny;
-  
-  float *data=ReadFromTiff(argv[1],nx, ny);
-
-  TH2F *h2=NULL;
-  if (data) {
-    TFile *fout=new TFile(argv[2],"RECREATE");
-    if (fout) {
-      h2=new TH2F("h2",argv[1],nx,0,nx,ny,0, ny);
-      for (int ix=0; ix<nx ; ix++) {
-	for (int iy=0; iy<ny ; iy++) {
-	  
-	  h2->SetBinContent(ix+1, iy+1, data[ix+iy*nx]);
-	}
-      }
-      h2->Write();
-      fout->Close();
-    }
-    delete [] data;
-  }
-    
-
- 
-  return 0;
-}
-

slsDetectorCalibration/multiThreadedAnalogDetector.h

@@ -32,11 +32,11 @@ class threadedAnalogDetector
 {
 public:
   threadedAnalogDetector(analogDetector<uint16_t> *d, int fs=10000) {
-    char *mem, *mm;
+    char *mm;//*mem, 
     det=d;
     fifoFree=new CircularFifo<char>(fs);
     fifoData=new CircularFifo<char>(fs);
-   
+    // mem==NULL;
     /* mem=(char*)calloc(fs, det->getDataSize()); */
     /* if (mem) */
     /*   memset(mem,0, fs*det->getDataSize()); */
@@ -46,6 +46,7 @@ public:
       //  mm=mem+i*det->getDataSize();
       // cout << i << endl;
       mm=(char*)calloc(1, det->getDataSize());
+     
       if (mm) { 
 	//memset(mm,0, det->getDataSize());
 	fifoFree->push(mm);
@@ -60,7 +61,8 @@ public:
     fMode=eFrame;
     ff=NULL;
   }
-  
+
+
 
   virtual int setFrameMode(int fm) {
     if (fm>=0) {
@@ -93,14 +95,17 @@ public:
   virtual int *getImage() {
     return det->getImage();
   }
-  virtual int getImageSize(int &nnx, int &nny, int &ns) {return det->getImageSize(nnx, nny, ns);};
+  virtual int getImageSize(int &nnx, int &nny, int &nsx,int &nsy) {return det->getImageSize(nnx, nny, nsx, nsy);};
   virtual int getDetectorSize(int &nnx, int &nny) {return det->getDetectorSize(nnx, nny);};
 
-  ~threadedAnalogDetector() {StopThread(); free(mem); delete fifoFree; delete fifoData;}
+  virtual ~threadedAnalogDetector() {StopThread();  delete fifoFree; delete fifoData;}
 
    /** Returns true if the thread was successfully started, false if there was an error starting the thread */
    virtual bool StartThread()
-   { stop=0; 
+   { stop=0;  
+     cout << "Detector number " << det->getId() << endl; 
+     cout << "common mode is " << det->getCommonModeSubtraction()<< endl;
+     cout << "ghost summation is " << det->getGhostSummation()<< endl;
      return (pthread_create(&_thread, NULL, processData, this) == 0);
    }
 
@@ -111,14 +116,20 @@ public:
    
 
    virtual bool pushData(char* &ptr) {
-     fifoData->push(ptr);
+     return fifoData->push(ptr);
    }
 
    virtual bool popFree(char* &ptr) {
-     fifoFree->pop(ptr);
+     return fifoFree->pop(ptr);
    }
 
-   virtual int isBusy() {return busy;}
+   virtual int isBusy() {
+     if (fifoData->isEmpty()) 
+       busy=0; 
+     else 
+       busy=1; 
+     return busy;
+   }
    
    //protected:
    /** Implement this method in your subclass with the code you want your thread to run. */
@@ -182,23 +193,26 @@ FILE *getFilePointer(){return det->getFilePointer();};
 
    void *writeFlatField(const char * imgname) {
      slsInterpolation *interp=(det)->getInterpolation();
-     cout << "interp " << interp << endl;
+     //cout << "interp " << interp << endl;
      if (interp)  {
        cout << imgname << endl;
-       interp->writeFlatField(imgname);
+       return interp->writeFlatField(imgname);
      }
+     return NULL;
    }
+
    void *readFlatField(const char * imgname, int nb=-1, double emin=1, double emax=0){
      slsInterpolation *interp=(det)->getInterpolation();
      if (interp)  
-       interp->readFlatField(imgname, nb, emin, emax);
+       return interp->readFlatField(imgname, nb, emin, emax);
+     return NULL;
    }
 
-   virtual int *getFlatField(int &nb, double emi, double ema){
+   virtual int *getFlatField(int &nb, int &nby, double emi, double ema){
      slsInterpolation *interp=(det)->getInterpolation();
      int *ff=NULL;
      if (interp) { 
-       ff=interp->getFlatField(nb,emi,ema);
+       ff=interp->getFlatField(nb,nby,emi,ema);
      }     
      return ff;
    }
@@ -213,10 +227,11 @@ FILE *getFilePointer(){return det->getFilePointer();};
    }
 
 
-   virtual int setNSubPixels(int ns)  { 
+   virtual void setNSubPixels(int ns, int nsy=-1) {
      slsInterpolation *interp=(det)->getInterpolation();
-     if (interp)  return interp->setNSubPixels(ns);
-     else return 1;};
+     if (interp) interp->setNSubPixels(ns, nsy);
+     //else return 1;
+   };
 
 
    virtual slsInterpolation *setInterpolation(slsInterpolation *f){
@@ -228,7 +243,6 @@ protected:
    int dMode;
    int *dataSize;
    pthread_t _thread;
-   char *mem;
    CircularFifo<char> *fifoFree;
    CircularFifo<char> *fifoData;
    int stop;
@@ -242,13 +256,13 @@ protected:
    }
 
    void * processData() {
-     busy=1;
+     // busy=1;
      while (!stop) {
        if (fifoData->isEmpty()) {
-	 busy=0;
+	 // busy=0;
 	 usleep(100);
        } else {
-	 busy=1;
+	 // busy=1;
 	 fifoData->pop(data); //blocking!
 	 det->processData(data);
 	 fifoFree->push(data); 
@@ -292,44 +306,55 @@ public:
     StopThreads();
     for (int i=0; i<nThreads; i++) 
       delete dets[i]; 
-    for (int i=1; i<nThreads; i++) 
-      delete dd[i];
+    /* for (int i=1; i<nThreads; i++)  */
+    /*   delete dd[i]; */
     //delete [] image;
   }
 
 
-  virtual int setFrameMode(int fm) { int ret; for (int i=0; i<nThreads; i++) {  ret=dets[i]->setFrameMode(fm);} return ret;};
-  virtual double setThreshold(int fm) { double ret; for (int i=0; i<nThreads; i++) ret=dets[i]->setThreshold(fm); return ret;};
-  virtual int setDetectorMode(int dm) { int ret; for (int i=0; i<nThreads; i++) ret=dets[i]->setDetectorMode(dm); return ret;};
+  virtual int setFrameMode(int fm) { int ret=dets[0]->setFrameMode(fm); for (int i=1; i<nThreads; i++) { dets[i]->setFrameMode(fm);} return ret;};
+  virtual double setThreshold(int fm) { double ret=dets[0]->setThreshold(fm); for (int i=1; i<nThreads; i++) dets[i]->setThreshold(fm); return ret;};
+  virtual int setDetectorMode(int dm) { int ret=dets[0]->setDetectorMode(dm);; for (int i=1; i<nThreads; i++) dets[i]->setDetectorMode(dm); return ret;};
   virtual void setROI(int xmin, int xmax, int ymin, int ymax) { for (int i=0; i<nThreads; i++) dets[i]->setROI(xmin, xmax,ymin,ymax);};
   
    
   virtual void newDataSet(){for (int i=0; i<nThreads; i++) dets[i]->newDataSet();};
   
-  virtual int *getImage(int &nnx, int &nny, int &ns) {
+  virtual int *getImage(int &nnx, int &nny, int &ns, int &nsy) {
     int *img;
+    cout << "get image "<< image << endl;
     // int nnx, nny, ns; 
     // int nnx, nny, ns;
-    int nn=dets[0]->getImageSize(nnx, nny,ns);
+    int nn=dets[0]->getImageSize(nnx, nny,ns, nsy);
     if (image) {
-      delete image;
+      cout << "del image "<< image << endl;
+      delete [] image;
       image=NULL;
     }
     image=new int[nn];
+    cout << "new image" << image << endl;
     //int nn=dets[0]->getImageSize(nnx, nny, ns);
     //for (i=0; i<nn; i++) image[i]=0;
-    
-    for (int ii=0; ii<nThreads; ii++) {
-      //cout << ii << " " << nn << " " << nnx << " " << nny << " " << ns << endl;
-      img=dets[ii]->getImage();
-      for (int i=0; i<nn; i++) {
-	if (ii==0)
-	  image[i]=img[i];
-	else
-	  image[i]+=img[i];
-	//if (img[i])	  cout << "det " << ii << " pix " << i << " val " <<  img[i] << " " << image[i] << endl;
+    if (image) {
+      for (int ii=0; ii<nThreads; ii++) {
+	cout << ii << " " << nn << " " << nnx << " " << nny << " " << nsy << endl;
+	img=dets[ii]->getImage();
+	for (int i=0; i<nn; i++) {
+	  if (ii==0)
+	  //	  if (img[i]>0)
+	    image[i]=img[i];
+	  // else
+	  //  image[i]=0;
+	  else	//if (img[i]>0)
+	    image[i]+=img[i];
+	  /***
+	      gdb runtime error
+	      ../multiThreadedAnalogDetector.h:349:14: runtime error: signed integer overflow: -1094794611 + -1094795013 cannot be rep
+	  **/
+	  //if (img[i])	  cout << "det " << ii << " pix " << i << " val " <<  img[i] << " " << image[i] << endl;
+	}
+	
       }
-    
     }
     return image;
     
@@ -352,26 +377,32 @@ public:
 /*        dets[ii]->writeImage(tit); */
 /*      } */
 /* #endif */
-     int nnx, nny, ns;
-     getImage(nnx, nny, ns);
+    cout << "write image" << endl;
+    int nnx, nny, ns, nsy;
+    getImage(nnx, nny, ns, nsy);
      //int nnx, nny, ns;
-     int nn=dets[0]->getImageSize(nnx, nny, ns);
-     float *gm=new float[nn];
-     if (gm) {
-       for (int ix=0; ix<nn; ix++) {
-	 if (t)
-	   gm[ix]=(image[ix])/t;
-	 else
-	   gm[ix]=image[ix];
-	   
-	 //if (image[ix]>0 && ix/nnx<350) cout << ix/nnx << " " << ix%nnx << " " << image[ix]<< " " << gm[ix] << endl;
-       }
-       //cout << "image " << nnx << " " << nny << endl;
-       WriteToTiff(gm,imgname ,nnx, nny); 
-       delete [] gm;
-     } else cout << "Could not allocate float image " << endl;
-     return NULL;
-   }
+    int nn=dets[0]->getImageSize(nnx, nny, ns, nsy);
+    float *gm=new float[nn];
+    if (gm) {
+      for (int ix=0; ix<nn; ix++) {
+	if (t) {
+	  if (image[ix]<0) 
+	    gm[ix]=0;
+	  else
+	    gm[ix]=(image[ix])/t;
+	} else
+	  gm[ix]=image[ix];
+
+	//if (image[ix]>0 && ix/nnx<350) cout << ix/nnx << " " << ix%nnx << " " << image[ix]<< " " << gm[ix] << endl;
+      }
+      cout << "image " << nnx << " " << nny << endl;
+      WriteToTiff(gm,imgname ,nnx, nny); 
+      cout << imgname << endl;
+      delete [] gm;
+       cout << "del" << endl;
+    } else cout << "Could not allocate float image " << endl;
+    return NULL;
+  }
   
 
   virtual void StartThreads() { 
@@ -402,12 +433,12 @@ public:
   
    
    virtual bool pushData(char* &ptr) {
-     dets[ithread]->pushData(ptr);
+     return dets[ithread]->pushData(ptr);
    }
 
    virtual bool popFree(char* &ptr) {
      //  cout << ithread << endl;
-     dets[ithread]->popFree(ptr);
+     return dets[ithread]->popFree(ptr);
    }
    
    virtual int nextThread() {
@@ -448,6 +479,37 @@ public:
     return ped;
   };
    
+  virtual double *getPedestalRMS(){
+    int nx, ny;
+    dets[0]->getDetectorSize(nx,ny);
+    double *rms=new double[nx*ny];
+    double *p0=new double[nx*ny];
+    
+    for (int i=0; i<nThreads; i++) {
+      //inte=(slsInterpolation*)dets[i]->getInterpolation(nb,emi,ema);
+      //  cout << i << endl;
+      p0=dets[i]->getPedestalRMS(p0);
+      if (p0) {
+	if (i==0) {
+
+	for (int ib=0; ib<nx*ny; ib++) {
+	  rms[ib]=p0[ib]/((double)nThreads);
+	  //  cout << p0[ib] << " ";
+	}
+	} else {
+	for (int ib=0; ib<nx*ny; ib++) {
+	  rms[ib]+=p0[ib]/((double)nThreads);
+	  //  cout << p0[ib] << " ";
+	}
+	}
+      }
+	
+    } 
+    delete [] p0;
+    return rms;
+  };
+   
+   
    
    virtual double *setPedestal(double *h=NULL){
      //int nb=0;
@@ -484,23 +546,44 @@ public:
 
    };
 
-
-  virtual void *readPedestal(const char * imgname, int nb=-1, double emin=1, double emax=0){
+   virtual void *writePedestalRMS(const char * imgname){     
     
      int nx, ny;
      dets[0]->getDetectorSize(nx,ny);
+   
+      double *rms=getPedestalRMS();
+      float *gm=new float[nx*ny];
+      if (gm) {
+       for (int ix=0; ix<nx*ny; ix++) {
+	 gm[ix]=rms[ix];
+       }    
+       WriteToTiff(gm,imgname ,nx, ny); 
+       delete [] gm;
+       delete [] rms;
+     } else cout << "Could not allocate float image " << endl;
+    
+    return NULL;
+
+   };
+
+
+  virtual void *readPedestal(const char * imgname, int nb=-1, double emin=1, double emax=0){
+    
+    int nx, ny;
+    dets[0]->getDetectorSize(nx,ny);
     uint32 nnx;
     uint32 nny;
     float *gm=ReadFromTiff(imgname, nnx, nny);
     if (ped) delete [] ped;
-    if (nnx>nx) nx=nnx;
-    if (nny>ny) ny=nny;
+    if (nnx>(uint)nx) nx=nnx;
+    if (nny>(uint)ny) ny=nny;
     ped=new double[nx*ny];
     
     for (int ix=0; ix<nx*ny; ix++) {
       ped[ix]=gm[ix];
     }
     delete [] gm;
+    
     return setPedestal();
     
   };
@@ -539,7 +622,7 @@ public:
   int *ff;
   double *ped;
   pthread_mutex_t fmutex;
-};
+  };
 
 #endif
 

slsDetectorCalibration/multiThreadedCountingDetector.h

@@ -25,7 +25,7 @@ class multiThreadedCountingDetector : public multiThreadedAnalogDetector
 public:
  multiThreadedCountingDetector(singlePhotonDetector *d, int n, int fs=1000) : multiThreadedAnalogDetector(d,n,fs) { };
 
-  virtual double setNSigma(double n) {double ret; for (int i=0; i<nThreads; i++) ret=(dets[i])->setNSigma(n); return ret;};
+  virtual double setNSigma(double n) {double ret=(dets[0])->setNSigma(n); for (int i=1; i<nThreads; i++) (dets[i])->setNSigma(n); return ret;};
   virtual void setEnergyRange(double emi, double ema) {for (int i=0; i<nThreads; i++) (dets[i])->setEnergyRange(emi,ema);};
   
 };

slsDetectorCalibration/multiThreadedInterpolatingDetector.h

@@ -28,8 +28,8 @@ public:
      return (dets[0])->getFlatField();
    }
    
-   virtual int *getFlatField(int &nb, double emi, double ema){
-     return (dets[0])->getFlatField(nb,emi,ema);
+   virtual int *getFlatField(int &nb, int &nby, double emi, double ema){
+     return (dets[0])->getFlatField(nb,nby,emi,ema);
    }
    
    virtual int *setFlatField(int *h=NULL, int nb=-1, double emin=1, double emax=0){
@@ -37,16 +37,16 @@ public:
    }; 
 
    void *writeFlatField(const char * imgname){
-     dets[0]->writeFlatField(imgname);
+     return dets[0]->writeFlatField(imgname);
    };
 
 
   void *readFlatField(const char * imgname, int nb=-1, double emin=1, double emax=0){
-    (dets[0])->readFlatField(imgname, nb, emin, emax);
+    return (dets[0])->readFlatField(imgname, nb, emin, emax);
   };
   
 
-   virtual int setNSubPixels(int ns)  { return (dets[0])->setNSubPixels(ns);};
+   /* virtual int setNSubPixels(int ns)  { return (dets[0])->setNSubPixels(ns);}; */
 
    virtual void resetFlatField() {(dets[0])->resetFlatField();};
    
@@ -56,7 +56,7 @@ public:
     \returns current file pointer
 */
    virtual slsInterpolation *setInterpolation(slsInterpolation *f){
-     int ok;
+     //int ok;
      for (int i=0; i<nThreads; i++)  
        (dets[i])->setInterpolation(f);
      return  (dets[0])->getInterpolation();
@@ -69,15 +69,15 @@ public:
 
 
 
-  virtual int *getImage(int &nnx, int &nny, int &ns) {
-    if (getInterpolation()==NULL) return multiThreadedAnalogDetector::getImage(nnx,nny,ns);
+   virtual int *getImage(int &nnx, int &nny, int &nsx, int &nsy) {
+     if (getInterpolation()==NULL) return multiThreadedAnalogDetector::getImage(nnx,nny,nsx, nsy);
     //if one interpolates, the whole image is stored in detector 0;
     int *img;
     // int nnx, nny, ns; 
     // int nnx, nny, ns;
-    int nn=dets[0]->getImageSize(nnx, nny,ns);
+    int nn=dets[0]->getImageSize(nnx, nny,nsx, nsy);
     if (image) {
-      delete image;
+      delete [] image;
       image=NULL;
     }
     image=new int[nn];    

slsDetectorCalibration/singlePhotonDetector.h

@@ -4,7 +4,7 @@
 #include "analogDetector.h" 
 
 #include "single_photon_hit.h"
-
+#include <mutex> 
 
 
 //#define MYROOT1
@@ -58,17 +58,14 @@ public analogDetector<uint16_t> {
 		      int sign=1,
 		      commonModeSubtraction *cm=NULL,
 		      int nped=1000,
-		      int nd=100, int nnx=-1, int nny=-1, double *gm=NULL) : analogDetector<uint16_t>(d, sign, cm, nped, nnx, nny, gm),   nDark(nd), eventMask(NULL),nSigma (nsigma), clusterSize(csize), clusterSizeY(csize), clusters(NULL),   quad(UNDEFINED_QUADRANT), tot(0), quadTot(0), eMin(-1), eMax(-1) {
+		      int nd=100, int nnx=-1, int nny=-1, double *gm=NULL, ghostSummation<uint16_t> *gs=NULL) : analogDetector<uint16_t>(d, sign, cm, nped, nnx, nny, gm, gs),   nDark(nd), eventMask(NULL),nSigma (nsigma), eMin(-1), eMax(-1), clusterSize(csize), clusterSizeY(csize), clusters(NULL),   quad(UNDEFINED_QUADRANT), tot(0), quadTot(0)  {
     
     
     
-    
-    fm=new pthread_mutex_t ;
+   fm=new mutex;
+   // fm=new pthread_mutex_t ;
 
-    eventMask=new eventType*[ny];
-    for (int i=0; i<ny; i++) {
-      eventMask[i]=new eventType[nx];
-    }
+    eventMask=new eventType[ny*nx];
     
     if (ny==1)
       clusterSizeY=1;
@@ -84,7 +81,7 @@ public analogDetector<uint16_t> {
     /**
        destructor. Deletes the cluster structure, the pdestalSubtraction and the image array
     */
-  virtual ~singlePhotonDetector() {delete [] clusters; for (int i=0; i<ny; i++) delete [] eventMask[i]; delete [] eventMask; };
+  virtual ~singlePhotonDetector() {delete [] clusters; for (int i=0; i<ny; i++)  delete [] eventMask; };
 
     
   
@@ -99,10 +96,7 @@ public analogDetector<uint16_t> {
     nDark=orig->nDark;
     myFile=orig->myFile;
     
-    eventMask=new eventType*[ny];
-    for (int i=0; i<ny; i++) {
-      eventMask[i]=new eventType[nx];
-    }
+    eventMask=new eventType[ny*nx];
     eMin=orig->eMin;
     eMax=orig->eMax;
     
@@ -117,6 +111,9 @@ public analogDetector<uint16_t> {
     
     setClusterSize(clusterSize);
     fm=orig->fm;
+    //setMutex(orig->fm);
+
+
     
     quad=UNDEFINED_QUADRANT;
     tot=0;
@@ -182,14 +179,14 @@ public analogDetector<uint16_t> {
 	nph=image;
       //nph=new int[nx*ny];
       
-      double rest[ny][nx];
-      int cy=(clusterSizeY+1)/2; //quad size
-      int cs=(clusterSize+1)/2; //quad size
+      double rest[ny*nx];
+      //int cy=(clusterSizeY+1)/2; //quad size
+      //int cs=(clusterSize+1)/2; //quad size
       
-      int ccs=clusterSize; //cluster size
-      int ccy=clusterSizeY; //cluster size
+      //int ccs=clusterSize; //cluster size
+      //int ccy=clusterSizeY; //cluster size
       
-      double g=1.;
+      //double g=1.;
 
       
       double tthr=thr, tthr1, tthr2;
@@ -201,10 +198,10 @@ public analogDetector<uint16_t> {
       if (cmSub) cm=1;
 
       if (thr>0) {
-	cy=1;
-	cs=1;
-	ccs=1;
-	ccy=1;
+	//cy=1;
+	//cs=1;
+	//ccs=1;
+	//ccy=1;
       }
       if (iframe<nDark) { 
 	//	cout << "ped " << iframe << endl;
@@ -213,24 +210,24 @@ public analogDetector<uint16_t> {
 	return nph;
       }	else {
 	if (thr>0) {
-	  newFrame();
+	  newFrame(data);
 	  if (cmSub) {
 	    cout << "add to common mode?"<< endl;
 	    addToCommonMode(data);
 	  }
-	    for (int iy=ymin; iy<ymax; iy++) {
-	  for (int ix=xmin; ix<xmax; ix++) {
+	  for (int iy=ymin; iy<ymax; iy++) {
+	    for (int ix=xmin; ix<xmax; ix++) {
 	      if (det->isGood(ix,iy)) {
 		val=subtractPedestal(data,ix,iy, cm);
 		
 		nn=analogDetector<uint16_t>::getNPhotons(data,ix,iy);//val/thr;//
 		if (nn>0) {
 		  nph[ix+nx*iy]+=nn;
-		  rest[iy][ix]=(val-nn*thr);//?+0.5*thr
+		  rest[iy*nx+ix]=(val-nn*thr);//?+0.5*thr
 		  nphFrame+=nn;
 		  nphTot+=nn;
 		} else 
-		  rest[iy][ix]=val;
+		  rest[iy*nx+ix]=val;
 		
 	      }
 	    }
@@ -240,7 +237,7 @@ public analogDetector<uint16_t> {
 	for (int ix=xmin; ix<xmax; ix++) {
 	    
 	    if (det->isGood(ix,iy)) {
-	      eventMask[iy][ix]=PEDESTAL;
+	      eventMask[iy*nx+ix]=PEDESTAL;
 	      max=0;
 	      tl=0;
 	      tr=0;
@@ -249,15 +246,15 @@ public analogDetector<uint16_t> {
 	      tot=0;
 	      quadTot=0;
 	      
-	      if (rest[iy][ix]>0.25*thr) {
-		eventMask[iy][ix]=NEIGHBOUR;
+	      if (rest[iy*nx+ix]>0.25*thr) {
+		eventMask[iy*nx+ix]=NEIGHBOUR;
 		for (int ir=-(clusterSizeY/2); ir<(clusterSizeY/2)+1; ir++) {
 		  for (int ic=-(clusterSize/2); ic<(clusterSize/2)+1; ic++) {
 		    if ((iy+ir)>=0 && (iy+ir)<ny && (ix+ic)>=0 && (ix+ic)<nx) {
-		      //clusters->set_data(rest[iy+ir][ix+ic], ic, ir);
+		      //clusters->set_data(rest[(iy+ir)*nx+ix+ic], ic, ir);
 		    
 		      
-		      v=rest[iy+ir][ix+ic];//clusters->get_data(ic,ir);
+		      v=rest[(iy+ir)*nx+ix+ic];//clusters->get_data(ic,ir);
 		      tot+=v;
 		      
 		      if (ir<=0 && ic<=0)
@@ -276,8 +273,9 @@ public analogDetector<uint16_t> {
 		      //}
 		    }
 		  }
+		}
 		
-		if (rest[iy][ix]>=max) { 
+		if (rest[iy*nx+ix]>=max) { 
 		  if (bl>=br && bl>=tl && bl>=tr) {
 		    quad=BOTTOM_LEFT;
 		    quadTot=bl;
@@ -289,9 +287,9 @@ public analogDetector<uint16_t> {
 		    quadTot=tl;
 		  } else if   (tr>=bl && tr>=tl && tr>=br) {
 		    quad=TOP_RIGHT;
-		  quadTot=tr;
+		    quadTot=tr;
 		  }
-		 
+		  
 		  if (nSigma==0) {
 		    tthr=thr;
 		    tthr1=thr;
@@ -312,9 +310,9 @@ public analogDetector<uint16_t> {
 		  }
 		  
 		  if (tot>tthr1 || quadTot>tthr2 || max>tthr) {
-		    eventMask[iy][ix]=PHOTON;
+		    eventMask[iy*nx+ix]=PHOTON;
 		    nph[ix+nx*iy]++;
-		    rest[iy][ix]-=thr;
+		    rest[iy*nx+ix]-=thr;
 		    nphFrame++;
 		    nphTot++;
 		    
@@ -322,9 +320,8 @@ public analogDetector<uint16_t> {
 		}
 	      }
 	    }
-	  }
-		}
 	}
+	  }
 	} else return getClusters(data, nph);
       }
       return NULL;
@@ -346,12 +343,12 @@ int *getClusters(char *data,  int *ph=NULL) {
 
  
   int nph=0;
-  double val[ny][nx];
+  double val[ny*nx];
   int cy=(clusterSizeY+1)/2;
   int cs=(clusterSize+1)/2;
-  int ir, ic;
-  
-  double max=0, tl=0, tr=0, bl=0,br=0, *v, vv;
+  //int ir, ic;
+  int iframe=det->getFrameNumber(data);
+  double max=0, tl=0, tr=0, bl=0,br=0, *v;
   int cm=0;
   int good=1;
   if (cmSub) cm=1;
@@ -362,16 +359,16 @@ int *getClusters(char *data,  int *ph=NULL) {
     addToPedestal(data);
     return 0;
   }
-  newFrame();
+  newFrame(data);
 
 
   
-  if (cm)
+  if (cm) {
     addToCommonMode(data);
+  }
 
-
-    for (int iy=ymin; iy<ymax; iy++) {
-  for (int ix=xmin; ix<xmax; ix++) {
+  for (int iy=ymin; iy<ymax; iy++) {
+    for (int ix=xmin; ix<xmax; ix++) {
       if (det->isGood(ix,iy)) {
 	max=0;
 	tl=0;
@@ -384,7 +381,7 @@ int *getClusters(char *data,  int *ph=NULL) {
 	
       
 	
-	eventMask[iy][ix]=PEDESTAL;
+	eventMask[iy*nx+ix]=PEDESTAL;
 	
 	
 	(clusters+nph)->rms=getPedestalRMS(ix,iy);
@@ -394,35 +391,40 @@ int *getClusters(char *data,  int *ph=NULL) {
 	for (int ir=-(clusterSizeY/2); ir<(clusterSizeY/2)+1; ir++) {
 	  for (int ic=-(clusterSize/2); ic<(clusterSize/2)+1; ic++) {
 	    
-	    if ((iy+ir)>=iy && (iy+ir)<ny && (ix+ic)>=ix && (ix+ic)<nx) {
-	      val[iy+ir][ix+ic]=subtractPedestal(data,ix+ic,iy+ir, cm);
-	    }
-	    
-	    v=&(val[iy+ir][ix+ic]);
-	    tot+=*v;
-	    if (ir<=0 && ic<=0)
-	      bl+=*v;
-	    if (ir<=0 && ic>=0)
-	      br+=*v;
-	    if (ir>=0 && ic<=0)
-	      tl+=*v;
-	    if (ir>=0 && ic>=0)
-	      tr+=*v;
-	    if (*v>max) {
-	      max=*v;
-	    }
+	    if ((iy+ir)>=0 &&  (iy+ir)<ny && (ix+ic)>=0 && (ix+ic)<nx) {
+	      if ((iy+ir)>=iy &&(ix+ic)>=ix)
+		val[(iy+ir)*nx+ix+ic]=subtractPedestal(data,ix+ic,iy+ir, cm);
+	      
+	      (clusters+nph)->set_data(val[(iy+ir)*nx+ix+ic],ic,ir);
+	      
+	      v=&(val[(iy+ir)*nx+ix+ic]);
+	      tot+=*v;
+	      if (ir<=0 && ic<=0)
+		bl+=*v;
+	      if (ir<=0 && ic>=0)
+		br+=*v;
+	      if (ir>=0 && ic<=0)
+		tl+=*v;
+	      if (ir>=0 && ic>=0)
+		tr+=*v;
+	      if (*v>max) {
+		max=*v;
+	      }
 	    
 	    
-	    if (ir==0 && ic==0) {
-	      if (*v<-nSigma*(clusters+nph)->rms)
-		eventMask[iy][ix]=NEGATIVE_PEDESTAL;
-	      else if (*v>nSigma*(clusters+nph)->rms)
-		eventMask[iy][ix]=PHOTON;
-	    }
-	    
+	      if (ir==0 && ic==0) {
+		if (*v<-nSigma*(clusters+nph)->rms)
+		  eventMask[iy*nx+ix]=NEGATIVE_PEDESTAL;
+		else if (*v>nSigma*(clusters+nph)->rms)
+		  eventMask[iy*nx+ix]=PHOTON;
+	      }
+	      
+	    } else
+	      (clusters+nph)->set_data(0,ic,ir);
+	      
 	  }
 	}
-	if (eventMask[iy][ix]==PHOTON && val[iy][ix]<max) 
+	if (eventMask[iy*nx+ix]==PHOTON && val[iy*nx+ix]<max) 
 	  continue;
 	
 	if (bl>=br && bl>=tl && bl>=tr) {
@@ -430,7 +432,7 @@ int *getClusters(char *data,  int *ph=NULL) {
 	  (clusters+nph)->quadTot=bl;
 	} else if (br>=bl && br>=tl && br>=tr) {
 	  (clusters+nph)->quad=BOTTOM_RIGHT;
-	(clusters+nph)->quadTot=br;
+	  (clusters+nph)->quadTot=br;
 	} else if (tl>=br && tl>=bl && tl>=tr) {
 	  (clusters+nph)->quad=TOP_LEFT;
 	  (clusters+nph)->quadTot=tl;
@@ -438,34 +440,36 @@ int *getClusters(char *data,  int *ph=NULL) {
 	  (clusters+nph)->quad=TOP_RIGHT;
 	  (clusters+nph)->quadTot=tr;
 	}
-      
+	
 	if (max>nSigma*(clusters+nph)->rms || tot>sqrt(clusterSizeY*clusterSize)*nSigma*(clusters+nph)->rms || ((clusters+nph)->quadTot)>sqrt(cy*cs)*nSigma*(clusters+nph)->rms) {
-	  if (val[iy][ix]>=max) {
-	  eventMask[iy][ix]=PHOTON_MAX;
-	  (clusters+nph)->tot=tot;
-	  (clusters+nph)->x=ix;
-	  (clusters+nph)->y=iy;
-	  //	  (clusters+nph)->iframe=det->getFrameNumber(data);
-	  // cout << det->getFrameNumber(data) << " " << (clusters+nph)->iframe << endl;
-	  (clusters+nph)->ped=getPedestal(ix,iy,0);
-	  for (int ir=-(clusterSizeY/2); ir<(clusterSizeY/2)+1; ir++) {
-	    for (int ic=-(clusterSize/2); ic<(clusterSize/2)+1; ic++) {
-	      (clusters+nph)->set_data(val[iy+ir][ix+ic],ic,ir);
+	  if (val[iy*nx+ix]>=max) {
+	    eventMask[iy*nx+ix]=PHOTON_MAX;
+	    //   (clusters+nph)->tot=tot;
+	    (clusters+nph)->x=ix;
+	    (clusters+nph)->y=iy;
+	    (clusters+nph)->iframe=iframe;
+	    // cout << det->getFrameNumber(data) << " " << (clusters+nph)->iframe << endl;
+	    //   (clusters+nph)->ped=getPedestal(ix,iy,0);
+	    // for (int ir=-(clusterSizeY/2); ir<(clusterSizeY/2)+1; ir++) {
+	    //   for (int ic=-(clusterSize/2); ic<(clusterSize/2)+1; ic++) {
+	    // 	if ((iy+ir)>=0 && (iy+ir)<ny && (ix+ic)>=0 && (ix+ic)<nx)
+	    // 	  (clusters+nph)->set_data(val[(iy+ir)*nx+ix+ic],ic,ir);
+	    // 	else
+	    // 	  (clusters+nph)->set_data(0,ic,ir);
+		  
+	    //   }
+	    // }
+	    good=1;
+	    if (eMin>0 && tot<eMin) good=0;
+	    if (eMax>0 && tot>eMax) good=0;
+	    if (good) {
+	      nph++;
+	      image[iy*nx+ix]++;
 	    }
-	  }
-	  good=1;
-	  if (eMin>0 && tot<eMin) good=0;
-	  if (eMax>0 && tot>eMax) good=0;
-	  if (good) {
-	    nph++;
-	    image[iy*nx+ix]++;
-	  }
-	  
-
 	  } else {
-	    eventMask[iy][ix]=PHOTON;
+	    eventMask[iy*nx+ix]=PHOTON;
 	  }
-	} else if (eventMask[iy][ix]==PEDESTAL) {
+	} else if (eventMask[iy*nx+ix]==PEDESTAL) {
 	  addToPedestal(data,ix,iy,cm);
 	}
       }
@@ -474,8 +478,9 @@ int *getClusters(char *data,  int *ph=NULL) {
   nphFrame=nph;
   nphTot+=nph;
   //cout << nphFrame << endl;
-  //  cout <<"**********************************"<< det->getFrameNumber(data) << " " << nphFrame << endl;
-  writeClusters(det->getFrameNumber(data));
+  if (iframe%10000==0)
+    cout <<"**********************************"<< iframe << " " << nphFrame << endl;
+  writeClusters(iframe);
   return  image;
   
 };
@@ -517,7 +522,7 @@ int *getClusters(char *data,  int *ph=NULL) {
 	\param ir y coordinate (center is (0,0))
 	\returns event mask enum for the given pixel
     */
-    eventType getEventMask(int ic, int ir=0){return eventMask[ir][ic];};
+    eventType getEventMask(int ic, int ir=0){return eventMask[ir*nx+ic];};
  
 
 #ifdef MYROOT1
@@ -566,7 +571,9 @@ int *getClusters(char *data,  int *ph=NULL) {
 /*       if (fwrite((void*)&fn, 1,  sizeof(int), f))  */
 /* 	if (fwrite((void*)&nph, 1,  sizeof(int), f))  */
 /* #endif    */
-	  for (int i=0; i<nph; i++) (cl+i)->write(f);
+      if (f)
+	for (int i=0; i<nph; i++) (cl+i)->write(f);
+
 };
  void writeClusters(FILE *f, int fn=0){
    writeClusters(f,clusters,nphFrame, fn);
@@ -576,12 +583,15 @@ int *getClusters(char *data,  int *ph=NULL) {
  void writeClusters(int fn){
    if (myFile) {  
      //cout << "++" << endl;  
-     pthread_mutex_lock(fm);
-     //   cout <<"**********************************"<< fn << " " << nphFrame << endl;
+     //pthread_mutex_lock(fm);
+     fm->lock();
+     //  cout <<id << " **********************************"<< fn << " " << nphFrame << endl;
      writeClusters(myFile,clusters,nphFrame, fn);
      // for (int i=0; i<nphFrame; i++) 
      //  (clusters+i)->write(myFile);
-     pthread_mutex_unlock(fm); 
+     // cout << "--" << endl; 
+     fm->unlock();
+     //pthread_mutex_unlock(fm); 
      //cout << "--" << endl; 
    } 
  };
@@ -592,7 +602,7 @@ int *getClusters(char *data,  int *ph=NULL) {
       switch(fMode) {
       case ePedestal:
 	//cout <<"spc add to ped " << endl;
-	addToPedestal(data);
+	addToPedestal(data,1);
 	break;
       default:
 	switch (dMode) {
@@ -613,12 +623,13 @@ int *getClusters(char *data,  int *ph=NULL) {
     void setEnergyRange(double emi, double ema){eMin=emi; eMax=ema;};
     void getEnergyRange(double &emi, double &ema){emi=eMin; ema=eMax;};
 
-    void setMutex(pthread_mutex_t *m){fm=m;};
+  //   void setMutex(pthread_mutex_t *m){fm=m;};
+     void setMutex(mutex *m){fm=m;};
 
  protected:
 
     int nDark; /**< number of frames to be used at the beginning of the dataset to calculate pedestal without applying photon discrimination */
-    eventType **eventMask; /**< matrix of event type or each pixel */
+    eventType *eventMask; /**< matrix of event type or each pixel */
     double nSigma; /**< number of sigma parameter for photon discrimination */
     double eMin, eMax;
     int clusterSize; /**< cluster size in the x direction */
@@ -631,8 +642,8 @@ int *getClusters(char *data,  int *ph=NULL) {
     int nphTot;
     int nphFrame;
 
-    pthread_mutex_t *fm;
-
+  // pthread_mutex_t *fm;
+  mutex *fm;
     };
 
 

slsDetectorCalibration/single_photon_hit.h

@@ -44,8 +44,8 @@ class single_photon_hit {
       //#endif  
 #ifndef WRITE_QUAD
       //printf("no quad ");
-    if (fwrite((void*)&x, 2,  sizeof(int16_t), myFile)) 
-      return fwrite((void*)data, 1, dx*dy*sizeof(int), myFile);
+    if (fwrite((void*)&x,  sizeof(int16_t), 2, myFile)) 
+      return fwrite((void*)data, sizeof(int),dx*dy,  myFile);
 #endif 
 #ifdef WRITE_QUAD
     // printf("quad ");
@@ -91,8 +91,8 @@ class single_photon_hit {
     default:
       ;
     }
-    if (fwrite((void*)&x, 2,  sizeof(int16_t), myFile)) 
-      return fwrite((void*)qq, 1, 4*sizeof(int), myFile);
+    if (fwrite((void*)&x,  sizeof(int16_t), 2, myFile)) 
+      return fwrite((void*)qq,  sizeof(int), 4, myFile);
 #endif
     return 0;
   };   
@@ -110,20 +110,20 @@ class single_photon_hit {
 #ifndef WRITE_QUAD
       // printf( "no quad \n");
     if (fread((void*)&x, 2,  sizeof(int16_t), myFile))  
-      return fread((void*)data, 1, dx*dy*sizeof(int), myFile);
+      return fread((void*)data,sizeof(int),  dx*dy, myFile);
 #endif 
 #ifdef WRITE_QUAD
     int qq[4];
     // printf( "quad \n");
-    if (fread((void*)&x, 2,  sizeof(int16_t), myFile))  
-      if (fread((void*)qq, 1, 4*sizeof(int), myFile)) {
+    if (fread((void*)&x,  sizeof(int16_t), 2, myFile))  
+      if (fread((void*)qq, sizeof(int), 4, myFile)) {
 
 	quad=TOP_RIGHT;
 	int mm=qq[0];
 	for (int i=1; i<4; i++) {
-	  if (qq[i]<mm) {
+	  if (qq[i]>mm) {
 	    switch (i) {
-	    case 1: 
+	    case 1:
 	      quad=TOP_LEFT;
 	      break;
 	    case 2:
@@ -135,7 +135,7 @@ class single_photon_hit {
 	    default:
 	      ;
 	    }
-
+	    mm=qq[i];
 	  }
 
 	}
@@ -210,9 +210,12 @@ class single_photon_hit {
   };
 
   void print() {
-
-    int ix, iy;
+#ifdef WRITE_QUAD
     
+    printf("Q");
+#endif
+   // int ix, iy;
+    printf("*** %d %d %d\n",iframe, x, y);
     for (int iy=0; iy<dy; iy++) {
       for (int ix=0; ix<dx; ix++) {
 	printf("%d \t",data[ix+iy*dx]);
@@ -220,7 +223,7 @@ class single_photon_hit {
       }
     printf("\n");
     }
-
+    printf("***\n");
   }
 
 

slsDetectorCalibration/single_photon_hit_double.h

@@ -1,98 +0,0 @@
-#ifndef SINGLE_PHOTON_HIT_H
-#define SINGLE_PHOTON_HIT_H
-#include <stdio.h>
-#include <stdint.h>
-
-typedef  double double32_t;
-typedef  float float32_t;
-typedef  int int32_t;
-
-#ifndef DEF_QUAD
-#define DEF_QUAD
-  enum quadrant {
-    TOP_LEFT=0,
-    TOP_RIGHT=1,
-    BOTTOM_LEFT=2,
-    BOTTOM_RIGHT=3,
-    UNDEFINED_QUADRANT=-1
-  };
-#endif
-
-
-class single_photon_hit_double {
-
-  /** @short Structure for a single photon hit */
-
- public: 
-  /** constructor, instantiates the data array  -- all class elements are public!
-      \param nx cluster size in x direction
-      \param ny cluster size in y direction (defaults to 1 for 1D detectors)
-  */
-  single_photon_hit_double(int nx=3, int ny=3): dx(nx), dy(ny) {
-    data=new double[dx*dy];
-  };
-
-  ~single_photon_hit_double(){delete [] data;};  /**< destructor, deletes the data array */
-
-  /** binary write to file of all elements of the structure, except size of the cluster
-      \param myFile file descriptor
-  */
-  size_t write(FILE *myFile) {
-    //fwrite((void*)this, 1, 3*sizeof(int)+4*sizeof(double)+sizeof(quad), myFile); 
-    if (fwrite((void*)this, 1, sizeof(int)+2*sizeof(int), myFile)) 
-      return fwrite((void*)data, 1, dx*dy*sizeof(double), myFile);
-    return 0;
-  };   
-  
-  /** 
-      binary read from file of all elements of the structure, except size of the cluster. The structure is then filled with those args
-      \param myFile file descriptor
-  */
-  size_t read(FILE *myFile) {
-    //fread((void*)this, 1,  3*sizeof(int)+4*sizeof(double)+sizeof(quad), myFile); 
-    
-    if (fread((void*)this, 1,  sizeof(int)+2*sizeof(int), myFile))  
-      return fread((void*)data, 1, dx*dy*sizeof(double), myFile);
-    return 0;
-  };
-
-    /** 
-	assign the value to the element of the cluster matrix, with relative coordinates where the center of the cluster is (0,0)
-	\param v value to be set
-	\param ix coordinate x within the cluster (center is (0,0))
-	\param iy coordinate y within the cluster (center is (0,0))
-  */
-  void set_data(double v, int ix, int iy=0){data[(iy+dy/2)*dx+ix+dx/2]=v;};
-
-  void set_cluster_size(int nx, int ny) {
-  
-  if (nx>0) dx=nx; if (ny>0) dy=ny; delete [] data; data=new double[dx*dy];
-  };
-  void get_cluster_size(int &nx, int &ny) {nx=dx; ny=dy;};
-  void get_pixel(int &x1, int &y1) {x1=x; y1=y;};
-
-    /** 
-	gets the value to the element of the cluster matrix, with relative coordinates where the center of the cluster is (0,0)
-	\param ix coordinate x within the cluster (center is (0,0))
-	\param iy coordinate y within the cluster (center is (0,0))
-	\returns value of the cluster element
-  */
-  double get_data(int ix, int iy=0){return data[(iy+dy/2)*dx+ix+dx/2];};
-  double *get_cluster() {return data;};
-
-  int	iframe; 	        /**< frame number */
-  int 	x; 			/**< x-coordinate of the center of hit */
-  int	y; 			/**< x-coordinate of the center of hit */
-  double	rms; 		/**< noise of central pixel l -- at some point it can be removed*/
-  double 	ped; 		/**< pedestal of the central pixel -- at some point it can be removed*/
-   double tot; /**< sum of the 3x3 cluster */
-   quadrant quad; /**< quadrant where the photon is located */
-   double quadTot; /**< sum of the maximum 2x2cluster */ 
-  int dx;	                /**< size of data cluster in x */
-  int dy;                 /**< size of data cluster in y */  
-  double *data;		        /**< pointer to data */
-};
-
-
-
-#endif

slsDetectorCalibration/single_photon_hit_old.h

@@ -1,93 +0,0 @@
-#ifndef SINGLE_PHOTON_HIT_H
-#define SINGLE_PHOTON_HIT_H
-#include <stdio.h>
-#include <stdint.h>
-
-typedef  double double32_t;
-typedef  float float32_t;
-typedef  int int32_t;
-
-#ifndef DEF_QUAD
-#define DEF_QUAD
-  enum quadrant {
-    TOP_LEFT=0,
-    TOP_RIGHT=1,
-    BOTTOM_LEFT=2,
-    BOTTOM_RIGHT=3,
-    UNDEFINED_QUADRANT=-1
-  };
-#endif
-
-
-class single_photon_hit {
-
-  /** @short Structure for a single photon hit */
-
- public: 
-  /** constructor, instantiates the data array  -- all class elements are public!
-      \param nx cluster size in x direction
-      \param ny cluster size in y direction (defaults to 1 for 1D detectors)
-  */
-  single_photon_hit(int nx=3, int ny=3): dx(nx), dy(ny) {data=new int[dx*dy];};
-
-  ~single_photon_hit(){delete [] data;};  /**< destructor, deletes the data array */
-
-  /** binary write to file of all elements of the structure, except size of the cluster
-      \param myFile file descriptor
-  */
-  size_t write(FILE *myFile) {
-    //fwrite((void*)this, 1, 3*sizeof(int)+4*sizeof(double)+sizeof(quad), myFile); 
-    if (fwrite((void*)this, 1, sizeof(int)+2*sizeof(int16_t), myFile)) 
-      return fwrite((void*)data, 1, dx*dy*sizeof(int), myFile);
-    return 0;
-  };   
-  
-  /** 
-      binary read from file of all elements of the structure, except size of the cluster. The structure is then filled with those args
-      \param myFile file descriptor
-  */
-  size_t read(FILE *myFile) {
-    //fread((void*)this, 1,  3*sizeof(int)+4*sizeof(double)+sizeof(quad), myFile); 
-    
-    if (fread((void*)this, 1,  sizeof(int)+2*sizeof(int16_t), myFile))  
-      return fread((void*)data, 1, dx*dy*sizeof(int), myFile);
-    return 0;
-  };
-
-    /** 
-	assign the value to the element of the cluster matrix, with relative coordinates where the center of the cluster is (0,0)
-	\param v value to be set
-	\param ix coordinate x within the cluster (center is (0,0))
-	\param iy coordinate y within the cluster (center is (0,0))
-  */
-  void set_data(double v, int ix, int iy=0){data[(iy+dy/2)*dx+ix+dx/2]=v;};
-
-  void set_cluster_size(int nx, int ny) {if (nx>0) dx=nx; if (ny>0) dy=ny; delete [] data; data=new int[dx*dy];};
-  void get_cluster_size(int &nx, int &ny) {nx=dx; ny=dy;};
-  void get_pixel(int &x1, int &y1) {x1=x; y1=y;};
-
-    /** 
-	gets the value to the element of the cluster matrix, with relative coordinates where the center of the cluster is (0,0)
-	\param ix coordinate x within the cluster (center is (0,0))
-	\param iy coordinate y within the cluster (center is (0,0))
-	\returns value of the cluster element
-  */
-  double get_data(int ix, int iy=0){return data[(iy+dy/2)*dx+ix+dx/2];};
-  int *get_cluster() {return data;};
-
-  int	iframe; 	        /**< frame number */
-  int16_t 	x; 			/**< x-coordinate of the center of hit */
-  int16_t	y; 			/**< x-coordinate of the center of hit */
-  double	rms; 		/**< noise of central pixel l -- at some point it can be removed*/
-  double 	ped; 		/**< pedestal of the central pixel -- at some point it can be removed*/
-   double tot; /**< sum of the 3x3 cluster */
-   quadrant quad; /**< quadrant where the photon is located */
-   double quadTot; /**< sum of the maximum 2x2cluster */ 
-  int dx;	                /**< size of data cluster in x */
-  int dy;                 /**< size of data cluster in y */  
-  int *data;		        /**< pointer to data */
-};
-
-
-
-#endif

slsDetectorCalibration/slsDetectorCalibration.doxy

@@ -1,103 +0,0 @@
-# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in 
-# documentation are documented, even if no documentation was available. 
-# Private class members and static file members will be hidden unless 
-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
-
-EXTRACT_ALL            = YES
-
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class 
-# will be included in the documentation.
-
-EXTRACT_PRIVATE        = NO
-
-
-
-# If the EXTRACT_STATIC tag is set to YES all static members of a file 
-# will be included in the documentation.
-
-EXTRACT_STATIC         = YES
-
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs) 
-# defined locally in source files will be included in the documentation.
-# If set to NO only classes defined in header files are included.
-
-EXTRACT_LOCAL_CLASSES  = YES
-
-# This flag is only useful for Objective-C code. When set to YES local
-# methods, which are defined in the implementation section but not in
-# the interface are included in the documentation.
-# If set to NO (the default) only methods in the interface are included.
-
-EXTRACT_LOCAL_METHODS  = YES
-
-# If this flag is set to YES, the members of anonymous namespaces will be
-# extracted and appear in the documentation as a namespace called
-# 'anonymous_namespace{file}', where file will be replaced with the base
-# name of the file that contains the anonymous namespace. By default
-# anonymous namespace are hidden.
-
-EXTRACT_ANON_NSPACES   = NO
-
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
-# undocumented members of documented classes, files or namespaces.
-# If set to NO (the default) these members will be included in the
-# various overviews, but no documentation section is generated.
-# This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_MEMBERS     = NO
-
-# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
-# undocumented classes that are normally visible in the class hierarchy.
-# If set to NO (the default) these classes will be included in the various
-# overviews. This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_CLASSES     = NO
-
-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
-# friend (class|struct|union) declarations.
-# If set to NO (the default) these declarations will be included in the
-# documentation.
-
-HIDE_FRIEND_COMPOUNDS  = NO
-
-INTERNAL_DOCS = NO
-
-SHOW_INCLUDE_FILES = NO
-
-SHOW_FILES = NO
-
-SHOW_NAMESPACES = NO
-
-COMPACT_LATEX = YES
-
-PAPER_TYPE = a4
-
-PDF_HYPERLINKS = YES
-
-USE_PDFLATEX = YES
-
-LATEX_HIDE_INDICES = YES
-
-PREDEFINED           = __cplusplus
-
-INPUT		= analogDetector.h \
-		pedestalSubtraction.h \ 
-		MovingStat.h  \
-		singlePhotonDetector.h  \
-		interpolatingDetector.h tiffIO.h \
-		single_photon_hit.h \
-		dataStructures/slsDetectorData.h \
-		commonModeSubtraction.h \			 
-		RunningStat.h \
-		interpolations/etaInterpolationBase.h \
-		interpolations/slsInterpolation.h \
-		interpolations/etaInterpolationPosXY.h \
-		interpolations/linearInterpolation.h \
-		interpolations/noInterpolation.h \
-		interpolations/etaInterpolationGlobal.h \
-		multiThreadedAnalogDetector.h 
-				
-			
-OUTPUT_DIRECTORY = slsDetectorCalibrationDocs
-
-#moench03Ctb10GbT1Data.h moench03TCtbData.h moench03T1CtbData.h moench03CtbData.h moench03Ctb10GbData.h moench03TCtb10GbData.h Mythen3_01_jctbData.h adcSar2_jctbData.h eigerHalfModuleData.h energyCalibration.h slsReceiverData.h gotthardModuleData.h gotthardShortModuleData.h jungfrau02Data.h jungfrau10ModuleData.h moench02Ctb10GbData.h moench02CtbData.h moench02ModuleData.h moench03CommonMode.h moenchCommonMode.h chiptestBoardData.h interpolation/etaVEL/interpolation_EtaVEL.h interpolation/etaVEL/EtaVEL.h etaVEL/iterativeEtaInterpolation.h dataStructures/moench03T1ZmqData.h	

slsDetectorCalibration/tiffIO.cpp

@@ -4,20 +4,20 @@
 #include<iostream>
 using namespace std;
 // #undef cbf_failnez 
-// #define cbf_failnez(x)				\
-//   {						\
-//   int err;	        			\
-//   err = (x);					\
-//   if (err) {						\
-//   fprintf(stderr,"\nCBFlib fatal error %x \n",err);	\
-//   exit(-1);						\
-//   }							\
+// #define cbf_failnez(x)				
+//   {						
+//   int err;	        			
+//   err = (x);					
+//   if (err) {						
+//   fprintf(stderr,"\nCBFlib fatal error %x \n",err);	
+//   exit(-1);						
+//   }							
 //   }
 
-void *WriteToTiff(float * imgData, const char * imgname, int nrow, int ncol){
+void *WriteToTiff(float * imgData, const char * imgname, int ncol, int nrow){
   int sampleperpixel=1;
   // unsigned char * buff=NULL;
-  tsize_t linebytes;
+  //tsize_t linebytes;
   // cout << "--" <<endl;
   TIFF * tif = TIFFOpen(imgname,"w");
   if (tif) {
@@ -30,7 +30,7 @@ void *WriteToTiff(float * imgData, const char * imgname, int nrow, int ncol){
     TIFFSetField(tif, TIFFTAG_PHOTOMETRIC, PHOTOMETRIC_MINISBLACK);
     TIFFSetField(tif, TIFFTAG_SAMPLEFORMAT, SAMPLEFORMAT_IEEEFP);
     
-    linebytes = sampleperpixel*ncol;
+    //linebytes = sampleperpixel*ncol;
     TIFFSetField(tif, TIFFTAG_ROWSPERSTRIP, TIFFDefaultStripSize(tif, ncol*sampleperpixel));
     for(int irow=0; irow<nrow; irow++){
       TIFFWriteScanline(tif,&imgData[irow*ncol],irow,0);
@@ -43,14 +43,14 @@ void *WriteToTiff(float * imgData, const char * imgname, int nrow, int ncol){
   return NULL;
 };
 
-float *ReadFromTiff( const char * imgname, uint32 &nrow, uint32 &ncol){
+float *ReadFromTiff( const char * imgname, uint32 &ncol, uint32 &nrow){
   // unsigned char * buff=NULL;
 
   TIFF * tif = TIFFOpen(imgname,"r");
   if (tif){
         uint32 bps;
 	uint32 sampleperpixel=1;
-  tsize_t linebytes;
+  //tsize_t linebytes;
 
  uint32 imagelength;
 
@@ -61,9 +61,9 @@ float *ReadFromTiff( const char * imgname, uint32 &nrow, uint32 &ncol){
     TIFFGetField(tif, TIFFTAG_IMAGELENGTH, &imagelength);
 
     float * imgData=new float[ncol*nrow];
-    linebytes = sampleperpixel*ncol;
+    //linebytes = sampleperpixel*ncol;
     //  TIFFSetField(tif, TIFFTAG_ROWSPERSTRIP, TIFFDefaultStripSize(tif, ncol*sampleperpixel));
-    for(int irow=0; irow<nrow; irow++){
+    for(uint32 irow=0; irow<nrow; irow++){
       //tiffreadscanline(tif, buf, row);
       TIFFReadScanline(tif,&imgData[irow*ncol],irow);
     }

slsDetectorSoftware/commonFiles/sls_detector_defs.h

@@ -195,7 +195,7 @@ enum networkParameter {
 /**
     type of action performed (for text client)
 */
-enum {GET_ACTION, PUT_ACTION, READOUT_ACTION, HELP_ACTION};
+ enum {GET_ACTION, PUT_ACTION, READOUT_ACTION, HELP_ACTION, PROCESS_ACTION};
 
 /** online flags enum \sa setOnline*/
 enum {GET_ONLINE_FLAG=-1, /**< returns wether the detector is in online or offline state */

slsDetectorSoftware/jctbDetectorServer/Makefile

@@ -6,7 +6,7 @@
 CROSS  = bfin-uclinux-
 CC    = $(CROSS)gcc
 
-CFLAGS += -Wall -DMOENCHD -DMCB_FUNCS -DDACS_INT  -DDEBUG -DV1 -DCTB 
+CFLAGS += -Wall -DMOENCHD -DMCB_FUNCS -DDACS_INT  -DDEBUG -DV1 -DCTB -DOLDVERSION
 
 
 PROGS= 	 jctbDetectorServer 

slsDetectorSoftware/jctbDetectorServer/gitInfo.txt

@@ -1,9 +1,9 @@
 Path: slsDetectorsPackage/slsDetectorSoftware/jctbDetectorServer 
 URL: origin git@github.com:slsdetectorgroup/slsDetectorPackage.git 
 Repository Root: origin git@github.com:slsdetectorgroup/slsDetectorPackage.git 
-Repsitory UUID: 9e5ec6a57bf206fe9384260fc4040867a9bbd71c 
-Revision: 33 
-Branch: developer 
-Last Changed Author: Erik_Frojdh 
-Last Changed Rev: 4065 
-Last Changed Date: 2019-01-30 17:38:35.000000002 +0100 ./firmware_funcs.c
+Repsitory UUID: 53ba22dbc40d17c8ca77647d4ca2edad230f9f8a 
+Revision: 34 
+Branch: moench 
+Last Changed Author: Anna_Bergamaschi 
+Last Changed Rev: 4088 
+Last Changed Date: 2020-02-19 12:03:18.000000002 +0100 ./Makefile

slsDetectorSoftware/jctbDetectorServer/gitInfoMoench.h

@@ -1,6 +1,6 @@
 #define GITURL "git@github.com:slsdetectorgroup/slsDetectorPackage.git"
-#define GITREPUUID "9e5ec6a57bf206fe9384260fc4040867a9bbd71c"
-#define GITAUTH "Erik_Frojdh"
-#define GITREV 0x4065
-#define GITDATE 0x20190130
-#define GITBRANCH "developer"
+#define GITREPUUID "53ba22dbc40d17c8ca77647d4ca2edad230f9f8a"
+#define GITAUTH "Anna_Bergamaschi"
+#define GITREV 0x4088
+#define GITDATE 0x20200219
+#define GITBRANCH "moench"

slsDetectorSoftware/multiSlsDetector/multiSlsDetector.cpp

@@ -4952,6 +4952,9 @@ int multiSlsDetector::createReceivingDataSockets(const bool destroy) {
 		cout << "Destroyed Receiving Data Socket(s)" << endl;
 		return OK;
 	}
+	if (client_downstream) {
+		return OK;
+	}
 
 	cprintf(MAGENTA, "Going to create data sockets\n");
 

slsDetectorSoftware/multiSlsDetector/multiSlsDetectorClient.h

@@ -8,10 +8,14 @@
 
 
 #include <stdlib.h>
+int progressCallback(double f,void* arg) { cout << f << "%"<< endl;  return 0;};
+int dummyAcquisitionFinished(double prog,int status,void* p){cout <<"Acquisition finished callback! " << prog << " " << status << endl; return 0;};
+int dummyMeasurementFinished(int im,int findex,void* p){cout <<"Measurement finished callback! " << im << " " << findex << endl; return 0;};
 
-
-int dummyCallback(detectorData* d, int p,void*) {
-	cout << "got data "	<< p <<  endl;
+//int (*)(detectorData*, int, int, void*)
+int dummyCallback(detectorData*, int p , int p1, void*) {
+	cout << p 	 <<  endl;
+	
 	return 0;
 };
 
@@ -25,7 +29,8 @@ public:
 		bool verify = true, update = true;										\
 		int del = 0;					      									\
 		char cmd[100] = "";														\
-
+	       
+		
 		if (action==slsDetectorDefs::PUT_ACTION && argc<2) {					\
 			cout << "Wrong usage - should be: "<< argv[0] <<					\
 			"[id-][pos:]channel arg" << endl;									\
@@ -41,7 +46,9 @@ public:
 			return;																\
 		};																		\
 
-		if (action==slsDetectorDefs::READOUT_ACTION)  {							\
+		
+		
+		if (action==slsDetectorDefs::READOUT_ACTION || action==slsDetectorDefs::PROCESS_ACTION)  {							\
 			id = 0;																\
 			pos = -1;															\
 			if (argc) {															\
@@ -125,6 +132,18 @@ public:
 			del=1;																\
 		}																		\
 
+
+		if (action==slsDetectorDefs::PROCESS_ACTION) {
+	
+
+		  /* myDetector->registerAcquisitionFinishedCallback(&dummyAcquisitionFinished,NULL); */
+		  /* myDetector->registerMeasurementFinishedCallback(&dummyMeasurementFinished,NULL); */
+		  action=slsDetectorDefs::READOUT_ACTION;
+		  myDetector->registerDataCallback(&dummyCallback, NULL);
+		 
+		  // myDetector->registerProgressCallback(&progressCallback, NULL);
+		}
+
 		// call multi detector command line
 		myCmd=new multiSlsDetectorCommand(myDetector);							\
 		try {																	\
@@ -142,9 +161,9 @@ public:
 		}																		\
 		if (action!=slsDetectorDefs::READOUT_ACTION) { 							\
 			cout << argv[0] << " " ;											\
-		}																		\
+		}						\
 		cout << answer<< endl;													\
-		delete myCmd;															\
+		delete myCmd;						\
 		if (del) delete myDetector;												\
 	};
 

slsDetectorSoftware/slsDetector/slsDetector.cpp

@@ -3242,13 +3242,13 @@ string slsDetector::getSettingsDir() {
 	return std::string(thisDetector->settingsDir);
 }
 string slsDetector::setSettingsDir(string s) {
-	sprintf(thisDetector->settingsDir, s.c_str()); return thisDetector->settingsDir;
+	sprintf(thisDetector->settingsDir, "%s", s.c_str()); return thisDetector->settingsDir;
 }
 string slsDetector::getCalDir() {
 	return thisDetector->calDir;
 }
 string slsDetector::setCalDir(string s) {
-	sprintf(thisDetector->calDir, s.c_str()); return thisDetector->calDir;
+	sprintf(thisDetector->calDir, "%s", s.c_str()); return thisDetector->calDir;
 }
 
 
@@ -4110,10 +4110,13 @@ int slsDetector::configureMAC() {
 		//converting IPaddress to hex
 		stringstream ss(arg[0]);
 		char cword[50]="";
-		bzero(cword, 50);
+		memset(cword, 0, sizeof(cword));
 		string s;
 		while (getline(ss, s, '.')) {
-			sprintf(cword,"%s%02x",cword,atoi(s.c_str()));
+			char temp[20]="";
+			memset(temp, 0, sizeof(temp));
+			sprintf(temp,"%02x",atoi(s.c_str()));
+			strcat(cword, temp);
 		}
 		bzero(arg[0], 50);
 		strcpy(arg[0],cword);
@@ -4126,12 +4129,12 @@ int slsDetector::configureMAC() {
 		//converting MACaddress to hex
 		stringstream ss(arg[1]);
 		char cword[50]="";
-		bzero(cword, 50);
+		memset(cword, 0, sizeof(cword));
 		string s;
 		while (getline(ss, s, ':')) {
-			sprintf(cword,"%s%s",cword,s.c_str());
+			strcat(cword, s.c_str());
 		}
-		bzero(arg[1], 50);
+		memset(arg[1], 0, sizeof(arg[1]));
 		strcpy(arg[1],cword);
 #ifdef VERBOSE
 		std::cout<<"receiver mac:"<<arg[1]<<"."<<std::endl;
@@ -4145,12 +4148,12 @@ int slsDetector::configureMAC() {
 	{
 		stringstream ss(arg[3]);
 		char cword[50]="";
-		bzero(cword, 50);
+		memset(cword, 0, sizeof(cword));
 		string s;
 		while (getline(ss, s, ':')) {
-			sprintf(cword,"%s%s",cword,s.c_str());
+			strcat(cword, s.c_str());
 		}
-		bzero(arg[3], 50);
+		memset(arg[3], 0, sizeof(arg[3]));
 		strcpy(arg[3],cword);
 #ifdef VERBOSE
 		std::cout<<"detecotor mac:"<<arg[3]<<"."<<std::endl;
@@ -4161,12 +4164,15 @@ int slsDetector::configureMAC() {
 		//converting IPaddress to hex
 		stringstream ss(arg[4]);
 		char cword[50]="";
-		bzero(cword, 50);
+		memset(cword, 0, sizeof(cword));
 		string s;
 		while (getline(ss, s, '.')) {
-			sprintf(cword,"%s%02x",cword,atoi(s.c_str()));
+			char temp[20]="";
+			memset(temp, 0, sizeof(temp));
+			sprintf(temp,"%02x",atoi(s.c_str()));
+			strcat(cword, temp);
 		}
-		bzero(arg[4], 50);
+		memset(arg[4], 0, sizeof(arg[4]));
 		strcpy(arg[4],cword);
 #ifdef VERBOSE
 		std::cout<<"detector ip:"<<arg[4]<<"."<<std::endl;
@@ -4426,7 +4432,7 @@ int64_t slsDetector::getTimeLeft(timerIndex index, int imod) {
 
 
 	int fnum=F_GET_TIME_LEFT;
-	int64_t retval;
+	int64_t retval = FAIL;
 	char mess[MAX_STR_LENGTH]="";
 	int ret=OK;
 
@@ -6051,8 +6057,10 @@ int slsDetector::setUDPConnection() {
 				std::cout << "could not configure mac" << endl;
 			}
 		}
-	}else
+	}else{
 		ret=FAIL;
+		setErrorMask((getErrorMask())|(COULD_NOT_CONFIGURE_MAC));
+	}
 #ifdef VERBOSE
 	printReceiverConfiguration();
 #endif

slsDetectorSoftware/slsDetector/slsDetectorBase.h

@@ -846,6 +846,7 @@ virtual int enableDataStreamingFromReceiver(int enable=-1)=0;
     case RUNNING:      return std::string("running");\
     case TRANSMITTING:      return std::string("data");	\
     case  RUN_FINISHED:      return std::string("finished");	\
+    case STOPPED:           return std::string("stopped");  \
     default:       return std::string("idle");		\
     }};
 

slsDetectorSoftware/slsDetector/slsDetectorUtils.cpp

@@ -64,9 +64,12 @@ int  slsDetectorUtils::acquire(int delflag){
 	if(!receiver){
 		setDetectorIndex(-1);
 	}
-
+	
+	pthread_mutex_lock(&mg);
 	int nc=setTimer(CYCLES_NUMBER,-1);
 	int nf=setTimer(FRAME_NUMBER,-1);
+	pthread_mutex_unlock(&mg);
+
 	if (nc==0) nc=1;
 	if (nf==0) nf=1;
 	int multiframe = nc*nf;

slsDetectorSoftware/slsDetectorAnalysis/fileIO.h

@@ -93,7 +93,7 @@ class fileIO :  public fileIOStatic, public virtual slsDetectorBase  {
   */
   virtual std::string setFilePath(std::string s) {
     pthread_mutex_lock(&mf);
-    sprintf(filePath, s.c_str()); 
+    sprintf(filePath, "%s", s.c_str()); 
     pthread_mutex_unlock(&mf); 
     return std::string(filePath);
   };

slsDetectorSoftware/slsDetectorClient/CMakeLists.txt

@@ -54,6 +54,20 @@ set_target_properties(sls_detector_acquire PROPERTIES
     COMPILE_DEFINITIONS READOUT=1
 )
 
+add_executable(sls_detector_process
+    ${SOURCES}
+)
+target_link_libraries(sls_detector_process
+   slsDetectorShared
+   pthread
+   zmq
+   rt
+)
+set_target_properties(sls_detector_process PROPERTIES 
+    RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin
+    COMPILE_DEFINITIONS PROCESS=1
+)
+
 add_executable(sls_detector_help
     ${SOURCES}
 )

slsDetectorSoftware/slsDetectorClient/Makefile

@@ -24,7 +24,7 @@ all: clients
 
 nonstatic: clients
 
-clients: builddir lib $(DESTDIR)/sls_detector_put $(DESTDIR)/sls_detector_get $(DESTDIR)/sls_detector_acquire $(DESTDIR)/sls_detector_help
+clients: builddir lib $(DESTDIR)/sls_detector_put $(DESTDIR)/sls_detector_get $(DESTDIR)/sls_detector_acquire $(DESTDIR)/sls_detector_help $(DESTDIR)/sls_detector_process
 
 static_clients: builddir lib $(DESTDIR)/ssls_detector_put $(DESTDIR)/ssls_detector_get $(DESTDIR)/ssls_detector_acquire $(DESTDIR)/ssls_detector_help
 
@@ -89,6 +89,13 @@ $(DESTDIR)/sls_detector_acquire: $(SRC_CLNT) $(DESTDIR)/libSlsDetector.so $(DEST
 	$(CXX) -o $(BIN)/sls_detector_acquire $(SRC_CLNT)   $(FLAGS)  $(INCLUDES) -DREADOUT  $(LIBS) $(LDFLAG)
 	$(shell test -d $(DESTDIR) || mkdir -p $(DESTDIR))
 
+$(DESTDIR)/sls_detector_process: $(SRC_CLNT) $(DESTDIR)/libSlsDetector.so $(DESTDIR)/libSlsDetector.a
+	$(call colorecho,"#######################################")
+	$(call colorecho,"#    Compiling sls_detector_process   #")
+	$(call colorecho,"#######################################")
+	$(CXX) -o $(BIN)/sls_detector_process $(SRC_CLNT)   $(FLAGS)  $(INCLUDES) -DREADOUT  $(LIBS) $(LDFLAG) -DPROCESS
+	$(shell test -d $(DESTDIR) || mkdir -p $(DESTDIR))
+
 $(DESTDIR)/sls_detector_help: $(SRC_CLNT) $(DESTDIR)/libSlsDetector.so $(DESTDIR)/libSlsDetector.a
 	$(call colorecho,"#######################################")
 	$(call colorecho,"#      Compiling sls_detector_help    #")

slsDetectorSoftware/slsDetectorClient/sls_detector_client.cpp

@@ -4,6 +4,10 @@
 
 #include <stdlib.h>
 using namespace std;
+#ifdef PROCESS
+
+#endif
+
 
 int main(int argc, char *argv[])
   
@@ -15,31 +19,37 @@ int main(int argc, char *argv[])
 			return 0;
 		}
 	}
-
+	int action=slsDetectorDefs::HELP_ACTION;
 #ifdef PUT
-  int action=slsDetectorDefs::PUT_ACTION;
+  action=slsDetectorDefs::PUT_ACTION;
 #endif
     
 #ifdef GET
-  int action=slsDetectorDefs::GET_ACTION;
+  action=slsDetectorDefs::GET_ACTION;
 #endif
     
 
 #ifdef READOUT
-  int action=slsDetectorDefs::READOUT_ACTION;
+  action=slsDetectorDefs::READOUT_ACTION;
+#endif
+  
+#ifdef PROCESS
+ action=slsDetectorDefs::PROCESS_ACTION;
 #endif
     
 
 #ifdef HELP
-  int action=slsDetectorDefs::HELP_ACTION;
+ action=slsDetectorDefs::HELP_ACTION;
 #endif
 
   multiSlsDetectorClient *cl;
   if (argc>1)
     cl=new multiSlsDetectorClient(argc-1, argv+1, action);
-  else
+  else {
     cl=new multiSlsDetectorClient(argc-1, argv, action);
 
+
+  }
   delete cl;
 }
 

slsDetectorSoftware/threadFiles/ThreadPool.cpp

@@ -151,6 +151,7 @@ void* ThreadPool::execute_thread(){
 int ThreadPool::add_task(Task* task){
 	if(m_pool_size == 1){
 		(*task)();
+		delete task;
 		return 0;
 	}
 	m_task_mutex.lock();

slsReceiverSoftware/CMakeLists.txt

@@ -106,4 +106,4 @@ install(TARGETS slsReceiverShared slsReceiverStatic slsReceiver
         
  
 install(FILES ${ZMQ_STATIC_ARCHIVE}
-DESTINATION lib)       
+DESTINATION lib)     

slsReceiverSoftware/Makefile

@@ -62,6 +62,7 @@ else
 	$(CXX) -o $@ -c $< $(INCLUDES) $(DFLAGS) -fPIC  $(EPICSFLAGS) $(LDFLAGRXR) -pthread $(FLAGS) $(LIBZMQ)  -lrt 
 endif
 
+
 versioning: 
 	$(call colorecho,`./updateGitVersion.sh`)