From 2afa620a97fd9e6e879b9278f675ffb9f1f5f6da Mon Sep 17 00:00:00 2001
From: Anna Bergamaschi <anna.bergamaschi@psi.ch>
Date: Tue, 16 Jun 2020 13:52:36 +0200
Subject: [PATCH] pedestal and data structures moved from 2D to 1D array; fixed
 bug with the file pointer in the zmq process

---
 slsDetectorCalibration/analogDetector.h       |  61 ++++-----
 .../moench03T1ReceiverDataNew.h               |   8 +-
 .../dataStructures/moench03T1ZmqDataNew.h     |   8 +-
 .../dataStructures/moench03T1ZmqDataNewRect.h |   2 +-
 .../dataStructures/slsDetectorData.h          |  82 ++++-------
 .../interpolatingDetector.h                   |   5 +
 .../moenchExecutables/moenchZmqProcess.cpp    |   7 +-
 slsDetectorCalibration/singlePhotonDetector.h | 128 +++++++++---------
 slsReceiverSoftware/CMakeLists.txt            |  18 +--
 slsReceiverSoftware/Makefile                  |   1 +
 10 files changed, 149 insertions(+), 171 deletions(-)

diff --git a/slsDetectorCalibration/analogDetector.h b/slsDetectorCalibration/analogDetector.h
index 9f372ea06..21cb87be2 100644
--- a/slsDetectorCalibration/analogDetector.h
+++ b/slsDetectorCalibration/analogDetector.h
@@ -67,11 +67,11 @@ template <class dataType> class analogDetector {
     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];
@@ -95,7 +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
@@ -131,16 +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));
       }
     }
@@ -272,7 +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(); 
@@ -342,7 +339,7 @@ template <class dataType> class analogDetector {
 	val+=getGhost(ix,iy);
 	//	cout << val ;
 	//	cout << endl;
-	stat[iy][ix].addToPedestal(val); 
+	stat[iy*nx+ix].addToPedestal(val); 
 	/* if (cmSub && cm>0)  { */
 	/*   if (det) if (det->isGood(ix, iy)==0) return; */
 	/*   cmSub->addToCommonMode(val, ix, iy); */
@@ -405,9 +402,9 @@ template <class dataType> class analogDetector {
     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); 
+	  return stat[iy*nx+ix].getPedestal()+getCommonMode(ix,iy); 
 	  
-	}     	else return stat[iy][ix].getPedestal(); 
+	}     	else return stat[iy*nx+ix].getPedestal(); 
       } else return -1;
     };
 
@@ -426,14 +423,14 @@ template <class dataType> class analogDetector {
 	  if (g==0) g=-1.;
 	}
       
-	return stat[iy][ix].getPedestalRMS()/g;//divide by gain?
+	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();
+	return stat[iy*nx+ix].getNumpedestals();
       return -1;
     };
     /**
@@ -449,7 +446,7 @@ template <class dataType> class analogDetector {
       }
       for (int iy=0; iy<ny; iy++) {
 	for (int ix=0; ix<nx; ix++) {
-	  ped[iy*nx+ix]=stat[iy][ix].getPedestal();
+	  ped[iy*nx+ix]=stat[iy*nx+ix].getPedestal();
 	    //cout << ped[iy*nx+ix] << " " ;
 	}
       }
@@ -468,7 +465,7 @@ template <class dataType> class analogDetector {
       }
       for (int iy=0; iy<ny; iy++) {
 	for (int ix=0; ix<nx; ix++) {
-	  ped[iy*nx+ix]=stat[iy][ix].getPedestalRMS();
+	  ped[iy*nx+ix]=stat[iy*nx+ix].getPedestalRMS();
 	}
       }
       return ped;
@@ -494,7 +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
@@ -509,8 +506,8 @@ template <class dataType> class analogDetector {
       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);
-	  //  cout << ix << " " << iy << " " << ped[iy*nx+ix] << " " << stat[iy][ix].getPedestal() << endl;
+	  stat[iy*nx+ix].setPedestal(ped[iy*nx+ix],rr, m);
+	  //  cout << ix << " " << iy << " " << ped[iy*nx+ix] << " " << stat[iy*nx+ix].getPedestal() << endl;
 	};
       };
       
@@ -526,7 +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);};
     
 
 
@@ -538,7 +535,7 @@ 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]);
 	};
       };
 
@@ -628,9 +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
@@ -674,7 +671,7 @@ template <class dataType> class analogDetector {
     if (gm) {
 	for (int iy=0; iy<nny; iy++) {
       for (int ix=0; ix<nnx; ix++) {
-	  stat[iy][ix].setPedestal(gm[iy*nx+ix],-1,-1);
+	  stat[iy*nx+ix].setPedestal(gm[iy*nx+ix],-1,-1);
 	}
       }
       delete [] gm;
@@ -725,7 +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);  
@@ -747,7 +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;
@@ -1023,7 +1020,7 @@ template <class dataType> class analogDetector {
 	 nph=v/thr;
 	 
 	 /* if (ix ==10 && iy<20) */
-	 /*   cout << det->getValue(data,ix,iy) << " " << stat[iy][ix].getPedestal() << " " << getCommonMode(ix,iy) << " " << getPedestal(ix,iy,0)<< " "  << getPedestal(ix,iy,1) << endl; */
+	 /*   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;
@@ -1100,8 +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
@@ -1109,7 +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;
     };
@@ -1237,7 +1234,7 @@ 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 */
diff --git a/slsDetectorCalibration/dataStructures/moench03T1ReceiverDataNew.h b/slsDetectorCalibration/dataStructures/moench03T1ReceiverDataNew.h
index 62fe17db0..a0ce0c3aa 100644
--- a/slsDetectorCalibration/dataStructures/moench03T1ReceiverDataNew.h
+++ b/slsDetectorCalibration/dataStructures/moench03T1ReceiverDataNew.h
@@ -99,12 +99,12 @@ 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);
+	    dataMap[row*nx+col]=sizeof(sls_detector_header)+(nadc*i+iadc)*2;//+16*(ip+1);
 #ifdef HIGHZ
-	    dataMask[row][col]=0x3fff;
+	    dataMask[row*nx+col]=0x3fff;
 #endif
-	    if (dataMap[row][col]<0 || dataMap[row][col]>=nSamples*2*32)
-	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	    if (dataMap[row*nx+col]<0 || dataMap[row*nx+col]>=nSamples*2*32)
+	      cout << "Error: pointer " << dataMap[row*nx+col] << " out of range "<< endl;
 	  }
 	}
       }
diff --git a/slsDetectorCalibration/dataStructures/moench03T1ZmqDataNew.h b/slsDetectorCalibration/dataStructures/moench03T1ZmqDataNew.h
index 268ec027a..bf359279b 100644
--- a/slsDetectorCalibration/dataStructures/moench03T1ZmqDataNew.h
+++ b/slsDetectorCalibration/dataStructures/moench03T1ZmqDataNew.h
@@ -60,12 +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);
+	    dataMap[row*nx+col]=(nadc*i+iadc)*2+offset;//+16*(ip+1);
 #ifdef HIGHZ
-	    dataMask[row][col]=0x3fff;
+	    dataMask[row*nx+col]=0x3fff;
 #endif
-	    if (dataMap[row][col]<0 || dataMap[row][col]>=dataSize)
-	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	    if (dataMap[row*nx+col]<0 || dataMap[row*nx+col]>=dataSize)
+	      cout << "Error: pointer " << dataMap[row*nx+col] << " out of range "<< endl;
 	  }
 	}
       }
diff --git a/slsDetectorCalibration/dataStructures/moench03T1ZmqDataNewRect.h b/slsDetectorCalibration/dataStructures/moench03T1ZmqDataNewRect.h
index ac7b3cc0e..dcaf687d4 100644
--- a/slsDetectorCalibration/dataStructures/moench03T1ZmqDataNewRect.h
+++ b/slsDetectorCalibration/dataStructures/moench03T1ZmqDataNewRect.h
@@ -102,7 +102,7 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
 	      iy=row*2;
 	    }
 #endif
-	    dataMap[iy][ix]=pix;
+	    dataMap[iy*nx+ix]=pix;
 	  }
 	}
       }
diff --git a/slsDetectorCalibration/dataStructures/slsDetectorData.h b/slsDetectorCalibration/dataStructures/slsDetectorData.h
index 7b49392be..b36d3ee31 100644
--- a/slsDetectorCalibration/dataStructures/slsDetectorData.h
+++ b/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;
   
@@ -37,7 +37,7 @@ 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) {
     
    int el=dsize/sizeof(dataType);
     xmap=new int[el];
@@ -45,25 +45,14 @@ class slsDetectorData {
     
 
     //  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<el; ip++){
@@ -78,11 +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;
@@ -95,14 +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 {
@@ -110,7 +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;
@@ -120,7 +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;
       }
@@ -136,17 +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;
     }
   };
   /**
@@ -154,18 +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;
       
     }
     
@@ -179,14 +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
@@ -205,39 +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) {
+  virtual dataType *getData(char *ptr, int dsize=-1) {
     int el=dsize/sizeof(dataType);
-    dataType **data;
+    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<(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<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;
@@ -254,11 +232,11 @@ class slsDetectorData {
   */
   virtual dataType getChannel(char *data, int ix, int iy=0) {
     dataType m=0, d=0, *p;
-    if (ix>=0 && ix<nx && iy>=0 && iy<ny && dataMap[iy][ix]>=0 && dataMap[iy][ix]<dataSize) {
+    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];
-      p=(dataType*)(data+dataMap[iy][ix]);
+      m=dataMask[iy*nx+ix];
+      p=(dataType*)(data+dataMap[iy*nx+ix]);
       d=*p;
     }  
     return d^m;
diff --git a/slsDetectorCalibration/interpolatingDetector.h b/slsDetectorCalibration/interpolatingDetector.h
index 973bd57ed..d40603def 100644
--- a/slsDetectorCalibration/interpolatingDetector.h
+++ b/slsDetectorCalibration/interpolatingDetector.h
@@ -50,7 +50,12 @@ class interpolatingDetector : public singlePhotonDetector {
   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");
+    }
 };
   
   
diff --git a/slsDetectorCalibration/moenchExecutables/moenchZmqProcess.cpp b/slsDetectorCalibration/moenchExecutables/moenchZmqProcess.cpp
index 277da4d3f..2d7784f07 100644
--- a/slsDetectorCalibration/moenchExecutables/moenchZmqProcess.cpp
+++ b/slsDetectorCalibration/moenchExecutables/moenchZmqProcess.cpp
@@ -364,8 +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;
 	    }
@@ -536,8 +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
 
 
diff --git a/slsDetectorCalibration/singlePhotonDetector.h b/slsDetectorCalibration/singlePhotonDetector.h
index b07e48658..7a6956e21 100644
--- a/slsDetectorCalibration/singlePhotonDetector.h
+++ b/slsDetectorCalibration/singlePhotonDetector.h
@@ -65,10 +65,7 @@ public analogDetector<uint16_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;
     
@@ -185,7 +179,7 @@ public analogDetector<uint16_t> {
 	nph=image;
       //nph=new int[nx*ny];
       
-      double rest[ny][nx];
+      double rest[ny*nx];
       //int cy=(clusterSizeY+1)/2; //quad size
       //int cs=(clusterSize+1)/2; //quad size
       
@@ -221,19 +215,19 @@ public analogDetector<uint16_t> {
 	    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;
 		
 	      }
 	    }
@@ -243,7 +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;
@@ -252,15 +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)
@@ -279,8 +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;
@@ -292,9 +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;
@@ -315,9 +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++;
 		    
@@ -325,9 +320,8 @@ public analogDetector<uint16_t> {
 		}
 	      }
 	    }
-	  }
-		}
 	}
+	  }
 	} else return getClusters(data, nph);
       }
       return NULL;
@@ -349,7 +343,7 @@ 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;
@@ -387,7 +381,7 @@ int *getClusters(char *data,  int *ph=NULL) {
 	
       
 	
-	eventMask[iy][ix]=PEDESTAL;
+	eventMask[iy*nx+ix]=PEDESTAL;
 	
 	
 	(clusters+nph)->rms=getPedestalRMS(ix,iy);
@@ -399,38 +393,38 @@ int *getClusters(char *data,  int *ph=NULL) {
 	    
 	    if ((iy+ir)>=0 &&  (iy+ir)<ny && (ix+ic)>=0 && (ix+ic)<nx) {
 	      if ((iy+ir)>=iy &&(ix+ic)>=ix)
-		val[iy+ir][ix+ic]=subtractPedestal(data,ix+ic,iy+ir, cm);
-
-	      (clusters+nph)->set_data(val[iy+ir][ix+ic],ic,ir);
-	  
-	    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;
-	    }
+		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);
+	      (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) {
@@ -438,7 +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;
@@ -446,20 +440,20 @@ 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;
+	  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;
+	    // 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][ix+ic],ic,ir);
+	    // 	  (clusters+nph)->set_data(val[(iy+ir)*nx+ix+ic],ic,ir);
 	    // 	else
 	    // 	  (clusters+nph)->set_data(0,ic,ir);
 		  
@@ -472,12 +466,10 @@ int *getClusters(char *data,  int *ph=NULL) {
 	      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);
 	}
       }
@@ -530,7 +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
@@ -579,7 +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);
@@ -635,7 +629,7 @@ int *getClusters(char *data,  int *ph=NULL) {
  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 */
diff --git a/slsReceiverSoftware/CMakeLists.txt b/slsReceiverSoftware/CMakeLists.txt
index 7fdc5d042..9c1a6a343 100644
--- a/slsReceiverSoftware/CMakeLists.txt
+++ b/slsReceiverSoftware/CMakeLists.txt
@@ -41,12 +41,12 @@ include_directories(
     include
 )
 
-add_library(zmq STATIC IMPORTED GLOBAL)
+#add_library(zmq STATIC IMPORTED GLOBAL)
 
-set(ZMQ_STATIC_ARCHIVE ${CMAKE_CURRENT_SOURCE_DIR}/include/libzmq.a)
-set_target_properties(zmq PROPERTIES
-    IMPORTED_LOCATION ${ZMQ_STATIC_ARCHIVE}
-)
+#set(ZMQ_STATIC_ARCHIVE ${CMAKE_CURRENT_SOURCE_DIR}/include/libzmq.a)
+#set_target_properties(zmq PROPERTIES
+#    IMPORTED_LOCATION ${ZMQ_STATIC_ARCHIVE}
+#)
 
 add_library(slsReceiverStatic STATIC
     ${SOURCES}
@@ -88,7 +88,7 @@ set_target_properties(slsReceiver PROPERTIES
 target_link_libraries(slsReceiver
     slsReceiverShared
     pthread
-    zmq
+#    zmq
     rt
 )
 
@@ -105,5 +105,7 @@ install(TARGETS slsReceiverShared slsReceiverStatic slsReceiver
         PUBLIC_HEADER DESTINATION include)
         
  
-install(FILES ${ZMQ_STATIC_ARCHIVE}
-DESTINATION lib)       
\ No newline at end of file
+#install(FILES ${ZMQ_STATIC_ARCHIVE}
+#DESTINATION lib)     
+install(FILES 
+DESTINATION lib)         
\ No newline at end of file
diff --git a/slsReceiverSoftware/Makefile b/slsReceiverSoftware/Makefile
index 655d0c1dc..142b3b465 100644
--- a/slsReceiverSoftware/Makefile
+++ b/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`)