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 bchip020+
+hostname bchip071+
 
 patword 0000 0000000000000000
 patword 0001 0000000000000000
@@ -417,18 +417,23 @@ patwaittime2 0
 
 ####mcp2011
 0:rx_tcpport 1954
-0:rx_udpip 10.1.1.102
-0:detectorip 10.1.1.19
 0:rx_udpport 32411
 ####gui listening to 
-zmqip 129.129.202.106
 zmqport 50001
 ####data streaming out of
-rx_zmqip 10.1.2.103
 rx_zmqport 50003
 
-0:rx_hostname mpc2011
+#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
@@ -478,16 +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/MovingStat.h

@@ -31,7 +31,7 @@ class MovingStat
 	*/
         void Set(double val, double rms=0, int m=-1)
         {
-	  if (m>0) m_n = m;  else m_n = n; 
+	  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);

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));
       }
     }
@@ -199,7 +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
@@ -226,8 +223,11 @@ 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];
@@ -269,7 +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(); 
@@ -339,7 +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); */
@@ -402,9 +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;
     };
 
@@ -423,14 +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;
     };
     /**
@@ -441,11 +441,12 @@ 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();
+	  ped[iy*nx+ix]=stat[iy*nx+ix].getPedestal();
 	    //cout << ped[iy*nx+ix] << " " ;
 	}
       }
@@ -459,11 +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;
@@ -489,7 +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
@@ -504,8 +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;
 	};
       };
       
@@ -521,7 +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);};
     
 
 
@@ -533,7 +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]);
 	};
       };
 
@@ -623,9 +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
@@ -669,7 +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;
@@ -720,7 +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);  
@@ -742,7 +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;
@@ -1018,7 +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;
@@ -1095,8 +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
@@ -1104,7 +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;
     };
@@ -1232,7 +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 */

slsDetectorCalibration/dataStructures/moench03T1ReceiverDataNew.h

@@ -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;
@@ -99,46 +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);
+	    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;
 	  }
 	}
       }
     }
 
-    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;
@@ -240,15 +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/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;
 	  }
 	}
       }
@@ -74,8 +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;

slsDetectorCalibration/dataStructures/moench03T1ZmqDataNewRect.h

@@ -46,7 +46,7 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
 
     int row, col;
 
-    int isample;
+    // int isample;
     int iadc;
     int ix, iy;
     
@@ -102,7 +102,7 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
 	      iy=row*2;
 	    }
 #endif
-	    dataMap[iy][ix]=pix;
+	    dataMap[iy*nx+ix]=pix;
 	  }
 	}
       }

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;
@@ -251,12 +231,13 @@ 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;
   };

slsDetectorCalibration/ghostSummation.h

@@ -13,7 +13,7 @@ template <class dataType> class ghostSummation {
   /** constructor
       \param xt crosstalk
   */
- ghostSummation(slsDetectorData<dataType> *d, double xt) : xtalk(xt),det(d)  {
+  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];
@@ -22,6 +22,9 @@ template <class dataType> class ghostSummation {
   ghostSummation(ghostSummation *orig) {
     xtalk=orig->xtalk; 
     det=orig->det;
+    nx=1;
+    ny=1;
+    det->getDetectorSize(nx,ny);
     ghost=new double[nx*ny];
     
   }

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");
+    }
 };
   
   
@@ -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);
   };
 
 
@@ -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

@@ -0,0 +1,406 @@
+#ifndef ETA2_INTERPOLATION_BASE_H
+#define ETA2_INTERPOLATION_BASE_H
+
+#ifdef MYROOT1
+#include <TObject.h>
+#include <TTree.h>
+#include <TH2D.h>
+#include <TH2F.h>
+#endif
+
+#include "etaInterpolationBase.h"
+
+class eta2InterpolationBase : public virtual etaInterpolationBase {
+  
+ public:
+ 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; */
+    /*   etamax=2;  */
+    /*   //  cout << ":" <<endl; */
+    /* } */
+    /* etastep=(etamax-etamin)/nbeta; */
+    
+  };
+  
+ eta2InterpolationBase(eta2InterpolationBase *orig): etaInterpolationBase(orig){ };
+
+ 
+  //////////////////////////////////////////////////////////////////////////////
+  //////////// /*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 sDum[2][2];
+    double tot, totquad;
+    double etax=0,etay=0;
+    
+    int corner;
+    corner=calcQuad(data, tot, totquad, sDum); 
+    if (nSubPixelsX>2 || nSubPixelsY>2) 
+      calcEta(totquad, sDum, etax, etay); 
+    getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
+
+    return;
+  };
+  
+
+  virtual void getInterpolatedPosition(int x, int y, double *data, double &int_x, double &int_y)
+  {
+    double sDum[2][2];
+    double tot, totquad;
+    double etax=0,etay=0;
+    
+    int corner;
+    corner=calcQuad(data, tot, totquad, sDum); 
+    if (nSubPixelsX>2 || nSubPixelsY>2  ) 
+      calcEta(totquad, sDum, etax, etay); 
+    getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
+
+    return;
+  };
+  
+
+
+
+
+
+
+
+
+  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=0, yoff=0;
+     switch (quad) {
+     case BOTTOM_LEFT:
+       xoff=0;
+       yoff=0;
+       break;
+     case BOTTOM_RIGHT:
+       xoff=1;
+       yoff=0;
+       break;
+     case TOP_LEFT:
+       xoff=0;
+       yoff=1;
+       break;
+     case TOP_RIGHT:
+       xoff=1;
+       yoff=1;
+       break;
+     default:
+       ;
+     } 
+     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);
+
+  }
+
+
+
+  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=0, yoff=0;
+     
+     switch (quad) {
+     case BOTTOM_LEFT:
+       xoff=0;
+       yoff=0;
+       break;
+     case BOTTOM_RIGHT:
+       xoff=1;
+       yoff=0;
+       break;
+     case TOP_LEFT:
+       xoff=0;
+       yoff=1;
+       break;
+     case TOP_RIGHT:
+       xoff=1;
+       yoff=1;
+       break;
+     default:
+       ;
+     } 
+     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*(xoff+1)];
+       calcEta(totquad,cc,etax,etay);
+     }
+     return getInterpolatedPosition(x,y,etax, etay,quad,int_x,int_y);
+
+  }
+
+
+
+
+
+
+  virtual void getInterpolatedPosition(int x, int y, double etax, double etay, int corner, double &int_x, double &int_y)
+  {
+
+
+    double xpos_eta=0,ypos_eta=0;
+    double dX,dY;
+    int ex,ey;
+    switch (corner)
+      {
+      case TOP_LEFT:
+	dX=-1.;
+	dY=0;
+	break;
+      case TOP_RIGHT:
+	;
+	dX=0;
+	dY=0;
+	break;
+      case BOTTOM_LEFT:
+	dX=-1.;
+	dY=-1.;
+	break;
+      case BOTTOM_RIGHT:
+	dX=0;
+	dY=-1.;
+	break;
+      default:
+	cout << "bad quadrant" << endl;
+	dX=0.; 
+	dY=0.;
+      }
+    
+
+     if (nSubPixelsX>2 || nSubPixelsY>2 ) { 
+
+       ex=(etax-etamin)/etastepX;
+       ey=(etay-etamin)/etastepY;
+       if (ex<0) {
+	 cout << "x*"<< ex << endl;
+	 ex=0;
+       } 
+       if (ex>=nbetaX) {
+	 cout << "x?"<< ex << endl;
+	 ex=nbetaX-1;
+       }
+       if (ey<0) {
+	 cout << "y*"<< ey << " " << nbetaY << endl;
+	 ey=0;
+       } 
+       if (ey>=nbetaY) {
+	 cout << "y?"<< ey << " " << nbetaY << endl;
+	 ey=nbetaY-1;
+       }
+    
+    
+   
+       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;
+       ypos_eta=0.5*dY+0.25;
+     }
+     
+     int_x=((double)x) + xpos_eta+0.5;
+     int_y=((double)y) +  ypos_eta+0.5;
+     
+
+  }
+  
+
+  
+  virtual int addToFlatField(double totquad,int quad,int *cl,double &etax, double &etay) {
+     double cc[2][2];
+     int xoff=0, yoff=0;
+     
+     switch (quad) {
+     case BOTTOM_LEFT:
+       xoff=0;
+       yoff=0;
+       break;
+     case BOTTOM_RIGHT:
+       xoff=1;
+       yoff=0;
+       break;
+     case TOP_LEFT:
+       xoff=0;
+       yoff=1;
+       break;
+     case TOP_RIGHT:
+       xoff=1;
+       yoff=1;
+       break;
+     default:
+       ;
+     } 
+     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)];
+     
+     //calcMyEta(totquad,quad,cl,etax, etay);
+     calcEta(totquad, cc,etax, etay);
+
+     //     cout <<"******"<< etax << " " << etay << endl;
+
+
+     return addToFlatField(etax,etay);
+   }
+
+   virtual int addToFlatField(double totquad,int quad,double *cl,double &etax, double &etay) {
+     double cc[2][2];
+     int xoff=0, yoff=0;
+     
+     switch (quad) {
+     case BOTTOM_LEFT:
+       xoff=0;
+       yoff=0;
+       break;
+     case BOTTOM_RIGHT:
+       xoff=1;
+       yoff=0;
+       break;
+     case TOP_LEFT:
+       xoff=0;
+       yoff=1;
+       break;
+     case TOP_RIGHT:
+       xoff=1;
+       yoff=1;
+       break;
+     default:
+       ;
+     } 
+     cc[0][0]=cl[xoff+3*yoff];
+     cc[1][0]=cl[(yoff+1)*3+xoff];
+     cc[0][1]=cl[yoff*3+xoff+1];
+     cc[1][1]=cl[(yoff+1)*3+xoff+1];
+     
+      /* cout << cl[0] << " " << cl[1] << " " << cl[2] << endl;   */
+      /* cout << cl[3] << " " << cl[4] << " " << cl[5] << endl;   */
+      /* cout << cl[6] << " " << cl[7] << " " << cl[8] << endl;   */
+      /* cout <<"******"<<totquad << " " << quad << endl;  */
+      /* cout << cc[0][0]<< " " << cc[0][1] << endl;  */
+      /* cout << cc[1][0]<< " " << cc[1][1] << endl;  */
+     //calcMyEta(totquad,quad,cl,etax, etay);
+     calcEta(totquad, cc,etax, etay);
+
+     //     cout <<"******"<< etax << " " << etay << endl;
+
+
+     return addToFlatField(etax,etay);
+   }
+
+
+
+  //////////////////////////////////////////////////////////////////////////////////////
+  virtual int addToFlatField(double *cluster, double &etax, double &etay){
+    double sDum[2][2];
+    double tot, totquad;
+    // int corner;
+    //corner=
+    calcQuad(cluster, tot, totquad, sDum); 
+    
+    //double xpos_eta,ypos_eta;
+    //double dX,dY;
+  
+    
+    calcEta(totquad, sDum, etax, etay); 
+   
+    return addToFlatField(etax,etay);
+
+    };
+
+  virtual int addToFlatField(int *cluster, double &etax, double &etay){
+    double sDum[2][2];
+    double tot, totquad;
+    //int corner;
+    //corner=
+    calcQuad(cluster, tot, totquad, sDum); 
+    
+    // double xpos_eta,ypos_eta;
+    //double dX,dY;
+  
+    
+    calcEta(totquad, sDum, etax, etay); 
+   
+    return addToFlatField(etax,etay);
+
+    };
+
+
+  virtual int addToFlatField(double etax, double etay){
+#ifdef MYROOT1
+    heta->Fill(etax,etay);
+#endif
+#ifndef MYROOT1
+    int ex,ey; 
+    ex=(etax-etamin)/etastepX;
+    ey=(etay-etamin)/etastepY;
+    if (ey<nbetaY && ex<nbetaX && ex>=0 && ey>=0)
+      heta[ey*nbetaX+ex]++; 
+#endif
+    return 0;    
+  };
+
+ virtual int *getInterpolatedImage(){
+   int ipx, ipy;
+   // cout << "ff" << endl;
+   calcDiff(1, hhx, hhy); //get flat
+   double avg=0;
+   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<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*nSubPixelsX]>0)
+       hintcorr[ibx+iby*nSubPixelsX*nPixelsX]=hint[ibx+iby*nSubPixelsX*nPixelsX]*(avg/flat[ipx+ipy*nSubPixelsX]);
+     else
+       hintcorr[ibx+iby*nSubPixelsX*nPixelsX]=hint[ibx+iby*nSubPixelsX*nPixelsX];
+
+
+     }
+   }
+
+
+
+    return hintcorr;
+  };
+
+/*  protected: */
+  
+/* #ifdef MYROOT1 */
+/*   TH2D *heta; */
+/*   TH2D *hhx; */
+/*   TH2D *hhy; */
+/* #endif */
+/* #ifndef MYROOT1 */
+/*   int *heta; */
+/*   float *hhx; */
+/*   float *hhy; */
+/* #endif */
+/*   int nbeta; */
+/*   double etamin, etamax, etastep; */
+
+};
+
+#endif

slsDetectorCalibration/interpolations/eta3InterpolationBase.h

@@ -0,0 +1,271 @@
+#ifndef ETA3_INTERPOLATION_BASE_H
+#define ETA3_INTERPOLATION_BASE_H
+
+#ifdef MYROOT1
+#include <TObject.h>
+#include <TTree.h>
+#include <TH2D.h>
+#include <TH2F.h>
+#endif
+
+#include "etaInterpolationBase.h"
+
+class eta3InterpolationBase : public virtual etaInterpolationBase  {
+  
+ public:
+ 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;    */
+    /* } */
+  
+    //   cout << nbeta << " " << etamin << " " << etamax << endl;
+};
+  
+ eta3InterpolationBase(eta3InterpolationBase *orig): etaInterpolationBase(orig){ };
+
+  /* virtual eta3InterpolationBase* Clone()=0; */
+  
+  
+
+  
+  // virtual void prepareInterpolation(int &ok){};
+ 
+
+  //////////////////////////////////////////////////////////////////////////////
+  //////////// /*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;
+    double etax,etay;
+    
+    int corner=calcEta3(data,etax,etay, tot);
+    
+    getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
+
+    return;
+  };
+  
+
+  virtual void getInterpolatedPosition(int x, int y, double *data, double &int_x, double &int_y)
+  {
+    //double sDum[2][2];
+    double tot;
+    double etax,etay;
+    
+    int corner=calcEta3(data,etax,etay, tot);
+    
+    getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
+
+    return;
+  };
+  
+
+  virtual void getInterpolatedPosition(int x, int y, double totquad,int quad,double *cl,double &int_x, double &int_y) {
+    
+  
+    double etax, etay;
+     if (nSubPixelsX>2 || nSubPixelsY>2 ) { 
+       calcEta3(cl,etax,etay, totquad);
+     } 
+     return getInterpolatedPosition(x,y,etax, etay,quad,int_x,int_y);
+
+  }
+
+
+
+  virtual void getInterpolatedPosition(int x, int y, double totquad,int quad,int *cl,double &int_x, double &int_y) {
+    
+    
+     double etax, etay;
+     if (nSubPixelsX>2 || nSubPixelsY>2 ) { 
+       calcEta3(cl,etax,etay, totquad);
+     }
+     return getInterpolatedPosition(x,y,etax, etay,quad,int_x,int_y);
+
+  }
+
+
+
+  virtual void getInterpolatedPosition(int x, int y, double etax, double etay, int corner, double &int_x, double &int_y)
+  {
+
+
+    double xpos_eta=0,ypos_eta=0;
+    int ex,ey;
+
+     if (nSubPixelsX>2 || nSubPixelsY>2 ) { 
+
+#ifdef MYROOT1
+    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)/etastepX;
+    ey=(etay-etamin)/etastepY;
+    if (ex<0) {
+      /* cout << etax << " " << etamin << " "; */
+      /*  cout << "3x*"<< ex << endl; */
+      ex=0;
+	} 
+    if (ex>=nbetaX) {
+      /* cout << etax << " " << etamin << " "; */
+      /* cout << "3x?"<< ex << endl; */
+      ex=nbetaX-1;
+    }
+    if (ey<0) {
+      /* cout << etay << " " << etamin << " "; */
+      /* cout << "3y*"<< ey << endl; */
+      ey=0;
+	} 
+    if (ey>=nbetaY) {
+      /* cout << etay << " " << etamin << " "; */
+      /* cout << "3y?"<< ey << endl; */
+      ey=nbetaY-1;
+      
+    }
+    xpos_eta=(((double)hhx[(ey*nbetaX+ex)]));///((double)nSubPixels);
+    ypos_eta=(((double)hhy[(ey*nbetaX+ex)]));///((double)nSubPixels);
+
+#endif
+   
+     } else {
+         switch (corner) {
+     case BOTTOM_LEFT:
+       xpos_eta=-0.25;
+       ypos_eta=-0.25;
+       break;
+     case BOTTOM_RIGHT:
+       xpos_eta=0.25;
+       ypos_eta=-0.25;
+       break;
+     case TOP_LEFT:
+       xpos_eta=-0.25;
+       ypos_eta=0.25;
+       break;
+     case TOP_RIGHT:
+       xpos_eta=0.25;
+       ypos_eta=0.25;
+       break;
+     default:
+       xpos_eta=0;
+       ypos_eta=0;
+     } 
+	 
+     }
+    int_x=((double)x) + xpos_eta;
+    int_y=((double)y) + ypos_eta;
+     // int_x=5. + xpos_eta;
+     //  int_y=5. + ypos_eta;
+    
+
+  }
+
+
+
+
+
+
+/*   ///////////////////////////////////////////////////////////////////////////////////////////////// */
+/*    virtual void getPositionETA3(int x, int y, double *data, double &int_x, double &int_y) */
+/*    { */
+/*     double sDum[2][2]; */
+/*     double tot, totquad; */
+/*     double eta3x,eta3y; */
+/*     double ex,ey; */
+    
+/*     calcQuad(data, tot, totquad, sDum);  */
+/*     calcEta3(data,eta3x, eta3y,tot);  */
+    
+/*     double xpos_eta,ypos_eta; */
+    
+/* #ifdef MYROOT1 */
+/*     xpos_eta=((hhx->GetBinContent(hhx->GetXaxis()->FindBin(eta3x),hhy->GetYaxis()->FindBin(eta3y))))/((double)nSubPixels); */
+/*     ypos_eta=((hhy->GetBinContent(hhx->GetXaxis()->FindBin(eta3x),hhy->GetYaxis()->FindBin(eta3y))))/((double)nSubPixels); */
+    
+/* #endif */
+/* #ifndef MYROOT1 */
+/*     ex=(eta3x-etamin)/etastep; */
+/*     ey=(eta3y-etamin)/etastep; */
+    
+/*     if (ex<0) ex=0; */
+/*     if (ex>=nbeta) ex=nbeta-1; */
+/*     if (ey<0) ey=0; */
+/*     if (ey>=nbeta) ey=nbeta-1; */
+
+/*     xpos_eta=(((double)hhx[(int)(ey*nbeta+ex)]))/((double)nSubPixels); */
+/*     ypos_eta=(((double)hhy[(int)(ey*nbeta+ex)]))/((double)nSubPixels); */
+/* #endif */
+    
+/*     int_x=((double)x) + xpos_eta; */
+/*     int_y=((double)y) + ypos_eta; */
+    
+/*     return; */
+/*   }; */
+  
+   virtual int addToFlatField(double totquad,int quad,int *cl,double &etax, double &etay) {
+   
+     calcEta3(cl, etax, etay, totquad);
+     return addToFlatField(etax,etay);
+   }
+
+   virtual int addToFlatField(double totquad,int quad,double *cl,double &etax, double &etay) {
+    
+
+     calcEta3(cl, etax, etay, totquad);
+     return addToFlatField(etax,etay);
+   }
+
+
+
+  //////////////////////////////////////////////////////////////////////////////////////
+  virtual int addToFlatField(double *cluster, double &etax, double &etay){
+    double totquad;
+     calcEta3(cluster, etax, etay, totquad);
+    return addToFlatField(etax,etay);
+
+    };
+
+  virtual int addToFlatField(int *cluster, double &etax, double &etay){
+  
+    double totquad;
+   
+     calcEta3(cluster, etax, etay, totquad);
+    return addToFlatField(etax,etay);
+
+    };
+
+
+  virtual int addToFlatField(double etax, double etay){
+#ifdef MYROOT1
+    heta->Fill(etax,etay);
+#endif
+#ifndef MYROOT1
+    int ex,ey; 
+    ex=(etax-etamin)/etastepX;
+    ey=(etay-etamin)/etastepY;
+    if (ey<nbetaY && ex<nbetaX && ex>=0 && ey>=0)
+      heta[ey*nbetaX+ex]++; 
+#endif
+    return 0;    
+  };
+  
+  
+/*  protected: */
+  
+/* #ifdef MYROOT1 */
+/*   TH2D *heta; */
+/*   TH2D *hhx; */
+/*   TH2D *hhy; */
+/* #endif */
+/* #ifndef MYROOT1 */
+/*   int *heta; */
+/*   float *hhx; */
+/*   float *hhy; */
+/* #endif */
+/*   int nbeta; */
+/*   double etamin, etamax, etastep; */
+
+};
+
+#endif

slsDetectorCalibration/interpolations/etaInterpolationBase.h

@@ -12,19 +12,6 @@
 #include "tiffIO.h"
 
 class etaInterpolationBase : public slsInterpolation {
-
- protected:
-  float *hhx;
-  float *hhy;
-  int *heta;
-  int nbetaX, nbetaY;
-  double etamin, etamax, etastepX, etastepY;
-  double rangeMin, rangeMax;
-  
-  
-  
-  double *flat;
-  int *hintcorr;
   
  public:
  
@@ -203,10 +190,19 @@ float *gethhx()
     // hhy->Scale((double)nSubPixels);
     return hhy;
     };
-
-
+  virtual int addToFlatField(double etax, double etay){
+    int ex,ey; 
+    ex=(etax-etamin)/etastepX;
+    ey=(etay-etamin)/etastepY;
+    if (ey<nbetaY && ex<nbetaX && ex>=0 && ey>=0)
+      heta[ey*nbetaX+ex]++; 
+    return 0;    
+  };
   
   
+  // virtual void prepareInterpolation(int &ok)=0;
+
+
   void debugSaveAll(int ind=0) {
     int  ibx, iby;
    char tit[10000];
@@ -227,15 +223,15 @@ float *gethhx()
 
 
   for (int ii=0; ii<nbetaX*nbetaY; ii++) {
-    //ibb=hhx[ii];//*nSubPixelsX);
-    etah[ii]=hhx[ii];
+    ibb=(hhx[ii]*nSubPixelsX);
+    etah[ii]=ibb;
   }
   sprintf(tit,"/scratch/eta_hhx_%d.tiff",ind);
   WriteToTiff(etah, tit, nbetaX, nbetaY);
 	  
   for (int ii=0; ii<nbetaX*nbetaY; ii++) {
-    //ibb=hhy[ii];//*nSubPixelsY;
-    etah[ii]=hhy[ii];
+    ibb=hhy[ii]*nSubPixelsY;
+    etah[ii]=ibb;
   }
   sprintf(tit,"/scratch/eta_hhy_%d.tiff",ind);
   WriteToTiff(etah, tit, nbetaX, nbetaY);
@@ -295,37 +291,6 @@ float *gethhx()
 
   }
 
-  virtual int *getInterpolatedImage(){ 
-  
-   /* int ipx, ipy; */
-   /* // cout << "ff" << endl; */
-   /* calcDiff(1, hhx, hhy); //get flat */
-   /* double avg=0; */
-   /* 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<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*nSubPixelsX]>0) */
-   /*     hintcorr[ibx+iby*nSubPixelsX*nPixelsX]=hint[ibx+iby*nSubPixelsX*nPixelsX]*(avg/flat[ipx+ipy*nSubPixelsX]); */
-   /*   else */
-   /*     hintcorr[ibx+iby*nSubPixelsX*nPixelsX]=hint[ibx+iby*nSubPixelsX*nPixelsX]; */
-   /*   } */
-   /* } */
-
-
-      return hint;
-  /*   return hintcorr; */
-   }; 
-
-
 
  protected:
   
@@ -398,575 +363,19 @@ float *gethhx()
     return sqrt(diff);
   }
   
+  float *hhx;
+  float *hhy;
+  int *heta;
+  int nbetaX, nbetaY;
+  double etamin, etamax, etastepX, etastepY;
+  double rangeMin, rangeMax;
+
+
+
+  double *flat;
+  int *hintcorr;
+  
 
 };
 
-
-
-
-class eta2InterpolationBase : public virtual etaInterpolationBase {
-  
- public:
- 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) {
-    
-   
-    
-  };
-  
- eta2InterpolationBase(eta2InterpolationBase *orig): etaInterpolationBase(orig){ };
-
- 
-  //////////////////////////////////////////////////////////////////////////////
-  //////////// /*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 sDum[2][2];
-    double tot, totquad;
-    double etax=0,etay=0;
-    
-    int corner;
-    corner=calcQuad(data, tot, totquad, sDum); 
-    if (nSubPixelsX>2 || nSubPixelsY>2) 
-      calcEta(totquad, sDum, etax, etay); 
-    getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
-
-    return;
-  };
-  
-
-  virtual void getInterpolatedPosition(int x, int y, double *data, double &int_x, double &int_y)
-  {
-    double sDum[2][2];
-    double tot, totquad;
-    double etax=0,etay=0;
-    
-    int corner;
-    corner=calcQuad(data, tot, totquad, sDum); 
-    if (nSubPixelsX>2 || nSubPixelsY>2  ) 
-      calcEta(totquad, sDum, etax, etay); 
-    getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
-
-    return;
-  };
-  
-  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=0, yoff=0;
-     switch (quad) {
-     case BOTTOM_LEFT:
-       xoff=0;
-       yoff=0;
-       break;
-     case BOTTOM_RIGHT:
-       xoff=1;
-       yoff=0;
-       break;
-     case TOP_LEFT:
-       xoff=0;
-       yoff=1;
-       break;
-     case TOP_RIGHT:
-       xoff=1;
-       yoff=1;
-       break;
-     default:
-       ;
-     } 
-     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);
-
-  }
-
-
-
-  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=0, yoff=0;
-     
-     switch (quad) {
-     case BOTTOM_LEFT:
-       xoff=0;
-       yoff=0;
-       break;
-     case BOTTOM_RIGHT:
-       xoff=1;
-       yoff=0;
-       break;
-     case TOP_LEFT:
-       xoff=0;
-       yoff=1;
-       break;
-     case TOP_RIGHT:
-       xoff=1;
-       yoff=1;
-       break;
-     default:
-       ;
-     } 
-     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*(xoff+1)];
-       calcEta(totquad,cc,etax,etay);
-     }
-     return getInterpolatedPosition(x,y,etax, etay,quad,int_x,int_y);
-
-  }
-
-  virtual void getInterpolatedPosition(int x, int y, double etax, double etay, int corner, double &int_x, double &int_y)
-  {
-
-
-    double xpos_eta=0,ypos_eta=0;
-    double dX,dY;
-    int ex,ey;
-    switch (corner)
-      {
-      case TOP_LEFT:
-	dX=-1.;
-	dY=0;
-	break;
-      case TOP_RIGHT:
-	;
-	dX=0;
-	dY=0;
-	break;
-      case BOTTOM_LEFT:
-	dX=-1.;
-	dY=-1.;
-	break;
-      case BOTTOM_RIGHT:
-	dX=0;
-	dY=-1.;
-	break;
-      default:
-	cout << "bad quadrant" << endl;
-	dX=0.; 
-	dY=0.;
-      }
-    
-
-     if (nSubPixelsX>2 || nSubPixelsY>2 ) { 
-
-       ex=(etax-etamin)/etastepX;
-       ey=(etay-etamin)/etastepY;
-       if (ex<0) {
-	 cout << "x*"<< ex << endl;
-	 ex=0;
-       } 
-       if (ex>=nbetaX) {
-	 cout << "x?"<< ex << endl;
-	 ex=nbetaX-1;
-       }
-       if (ey<0) {
-	 cout << "y*"<< ey << " " << nbetaY << endl;
-	 ey=0;
-       } 
-       if (ey>=nbetaY) {
-	 cout << "y?"<< ey << " " << nbetaY << endl;
-	 ey=nbetaY-1;
-       }
-    
-    
-   
-       xpos_eta=(((double)hhx[(ey*nbetaX+ex)]));
-       ypos_eta=(((double)hhy[(ey*nbetaX+ex)]));
-       
-       
-     if (xpos_eta<0 || xpos_eta>1)
-       xpos_eta=-100;
-     else
-       xpos_eta+=dX ;///((double)nSubPixels);
-
-     if (ypos_eta<0 || ypos_eta>1)
-       ypos_eta=-100;
-     else
-       ypos_eta+=dY ;///((double)nSubPixels);
-       
-     } else {
-       xpos_eta=0.5*dX+0.25;
-       ypos_eta=0.5*dY+0.25;
-     }
-     
-  
-     if (xpos_eta<-1)
-       int_x=-100;
-     else
-       int_x=((double)x) + xpos_eta+0.5;
-
-     if (ypos_eta<-1)
-       int_y=-100;
-     else 
-       int_y=((double)y) +  ypos_eta+0.5;
-           
-    
-     
-
-  }
-  
-
-  
-  virtual int addToFlatField(double totquad,int quad,int *cl,double &etax, double &etay) {
-     double cc[2][2];
-     int xoff=0, yoff=0;
-     
-     switch (quad) {
-     case BOTTOM_LEFT:
-       xoff=0;
-       yoff=0;
-       break;
-     case BOTTOM_RIGHT:
-       xoff=1;
-       yoff=0;
-       break;
-     case TOP_LEFT:
-       xoff=0;
-       yoff=1;
-       break;
-     case TOP_RIGHT:
-       xoff=1;
-       yoff=1;
-       break;
-     default:
-       ;
-     } 
-     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)];
-     
-     //calcMyEta(totquad,quad,cl,etax, etay);
-     calcEta(totquad, cc,etax, etay);
-
-     //     cout <<"******"<< etax << " " << etay << endl;
-
-
-     return addToFlatField(etax,etay);
-   }
-
-   virtual int addToFlatField(double totquad,int quad,double *cl,double &etax, double &etay) {
-     double cc[2][2];
-     int xoff=0, yoff=0;
-     
-     switch (quad) {
-     case BOTTOM_LEFT:
-       xoff=0;
-       yoff=0;
-       break;
-     case BOTTOM_RIGHT:
-       xoff=1;
-       yoff=0;
-       break;
-     case TOP_LEFT:
-       xoff=0;
-       yoff=1;
-       break;
-     case TOP_RIGHT:
-       xoff=1;
-       yoff=1;
-       break;
-     default:
-       ;
-     } 
-     cc[0][0]=cl[xoff+3*yoff];
-     cc[1][0]=cl[(yoff+1)*3+xoff];
-     cc[0][1]=cl[yoff*3+xoff+1];
-     cc[1][1]=cl[(yoff+1)*3+xoff+1];
-     
-      /* cout << cl[0] << " " << cl[1] << " " << cl[2] << endl;   */
-      /* cout << cl[3] << " " << cl[4] << " " << cl[5] << endl;   */
-      /* cout << cl[6] << " " << cl[7] << " " << cl[8] << endl;   */
-      /* cout <<"******"<<totquad << " " << quad << endl;  */
-      /* cout << cc[0][0]<< " " << cc[0][1] << endl;  */
-      /* cout << cc[1][0]<< " " << cc[1][1] << endl;  */
-     //calcMyEta(totquad,quad,cl,etax, etay);
-     calcEta(totquad, cc,etax, etay);
-
-     //     cout <<"******"<< etax << " " << etay << endl;
-
-
-     return addToFlatField(etax,etay);
-   }
-
-
-
-  //////////////////////////////////////////////////////////////////////////////////////
-  virtual int addToFlatField(double *cluster, double &etax, double &etay){
-    double sDum[2][2];
-    double tot, totquad;
-    // int corner;
-    //corner=
-    calcQuad(cluster, tot, totquad, sDum); 
-    
-    //double xpos_eta,ypos_eta;
-    //double dX,dY;
-  
-    
-    calcEta(totquad, sDum, etax, etay); 
-   
-    return addToFlatField(etax,etay);
-
-    };
-
-  virtual int addToFlatField(int *cluster, double &etax, double &etay){
-    double sDum[2][2];
-    double tot, totquad;
-    //int corner;
-    //corner=
-    calcQuad(cluster, tot, totquad, sDum); 
-    
-    // double xpos_eta,ypos_eta;
-    //double dX,dY;
-  
-    
-    calcEta(totquad, sDum, etax, etay); 
-   
-    return addToFlatField(etax,etay);
-
-    };
-
-
-  virtual int addToFlatField(double etax, double etay){
-#ifdef MYROOT1
-    heta->Fill(etax,etay);
-#endif
-#ifndef MYROOT1
-    int ex,ey;
-    ex=(etax-etamin)/etastepX;
-    ey=(etay-etamin)/etastepY;
-    if (ey<nbetaY && ex<nbetaX && ex>=0 && ey>=0)
-      heta[ey*nbetaX+ex]++;
-#endif
-    return 0;
-  };
-
-};
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-class eta3InterpolationBase : public virtual etaInterpolationBase  {
-  
- public:
- 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; 
-  
-};
-  
- eta3InterpolationBase(eta3InterpolationBase *orig): etaInterpolationBase(orig){ };
-
-
-  //////////////////////////////////////////////////////////////////////////////
-  //////////// /*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;
-    double etax,etay;
-    
-    int corner=calcEta3(data,etax,etay, tot);
-    
-    getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
-
-    return;
-  };
-  
-
-  virtual void getInterpolatedPosition(int x, int y, double *data, double &int_x, double &int_y)
-  {
-    //double sDum[2][2];
-    double tot;
-    double etax,etay;
-    
-    int corner=calcEta3(data,etax,etay, tot);
-    
-    getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
-
-    return;
-  };
-  
-
-  virtual void getInterpolatedPosition(int x, int y, double totquad,int quad,double *cl,double &int_x, double &int_y) {
-    
-  
-    double etax, etay;
-     if (nSubPixelsX>2 || nSubPixelsY>2 ) { 
-       calcEta3(cl,etax,etay, totquad);
-     } 
-     return getInterpolatedPosition(x,y,etax, etay,quad,int_x,int_y);
-
-  }
-
-
-
-  virtual void getInterpolatedPosition(int x, int y, double totquad,int quad,int *cl,double &int_x, double &int_y) {
-    
-    
-     double etax, etay;
-     if (nSubPixelsX>2 || nSubPixelsY>2 ) { 
-       calcEta3(cl,etax,etay, totquad);
-     }
-     return getInterpolatedPosition(x,y,etax, etay,quad,int_x,int_y);
-
-  }
-
-
-
-  virtual void getInterpolatedPosition(int x, int y, double etax, double etay, int corner, double &int_x, double &int_y)
-  {
-
-
-    //cout << "**";
-    double xpos_eta=0,ypos_eta=0;
-    int ex,ey;
-
-     if (nSubPixelsX>2 || nSubPixelsY>2 ) { 
-
-#ifdef MYROOT1
-    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)/etastepX;
-    ey=(etay-etamin)/etastepY;
-    if (ex<0) {
-      /* cout << etax << " " << etamin << " "; */
-      /*  cout << "3x*"<< ex << endl; */
-      ex=0;
-	} 
-    if (ex>=nbetaX) {
-      /* cout << etax << " " << etamin << " "; */
-      /* cout << "3x?"<< ex << endl; */
-      ex=nbetaX-1;
-    }
-    if (ey<0) {
-      /* cout << etay << " " << etamin << " "; */
-      /* cout << "3y*"<< ey << endl; */
-      ey=0;
-	} 
-    if (ey>=nbetaY) {
-      /* cout << etay << " " << etamin << " "; */
-      /* cout << "3y?"<< ey << endl; */
-      ey=nbetaY-1;
-      
-    }
-    xpos_eta=(((double)hhx[(ey*nbetaX+ex)]));///((double)nSubPixels);
-    ypos_eta=(((double)hhy[(ey*nbetaX+ex)]));///((double)nSubPixels);
-
-#endif
-   
-     } else {
-       switch (corner) {
-       case BOTTOM_LEFT:
-	 xpos_eta=-0.25;
-	 ypos_eta=-0.25;
-	 break;
-       case BOTTOM_RIGHT:
-	 xpos_eta=0.25;
-	 ypos_eta=-0.25;
-	 break;
-       case TOP_LEFT:
-	 xpos_eta=-0.25;
-	 ypos_eta=0.25;
-	 break;
-       case TOP_RIGHT:
-	 xpos_eta=0.25;
-	 ypos_eta=0.25;
-	 break;
-       default:
-	 xpos_eta=0;
-	 ypos_eta=0;
-       } 
-       
-     }
-     /* if (xpos_eta<0 || xpos_eta>1) */
-     /*   int_x=-1; */
-     /* else */
-       int_x=((double)x) + xpos_eta;
-     /* if (ypos_eta<0 || ypos_eta>1) */
-     /*   int_y=-1; */
-     /* else */
-       int_y=((double)y) + ypos_eta;
-     // int_x=5. + xpos_eta;
-     //  int_y=5. + ypos_eta;
-    
-
-  }
-
-  
-   virtual int addToFlatField(double totquad,int quad,int *cl,double &etax, double &etay) {
-   
-     calcEta3(cl, etax, etay, totquad);
-     return addToFlatField(etax,etay);
-   }
-
-   virtual int addToFlatField(double totquad,int quad,double *cl,double &etax, double &etay) {
-    
-
-     calcEta3(cl, etax, etay, totquad);
-     return addToFlatField(etax,etay);
-   }
-
-
-
-  //////////////////////////////////////////////////////////////////////////////////////
-  virtual int addToFlatField(double *cluster, double &etax, double &etay){
-    double totquad;
-     calcEta3(cluster, etax, etay, totquad);
-    return addToFlatField(etax,etay);
-
-    };
-
-  virtual int addToFlatField(int *cluster, double &etax, double &etay){
-  
-    double totquad;
-   
-     calcEta3(cluster, etax, etay, totquad);
-    return addToFlatField(etax,etay);
-
-    };
-
-  
-
-  virtual int addToFlatField(double etax, double etay){
-#ifdef MYROOT1
-    heta->Fill(etax,etay);
-#endif
-#ifndef MYROOT1
-    int ex,ey;
-    ex=(etax-etamin)/etastepX;
-    ey=(etay-etamin)/etastepY;
-    if (ey<nbetaY && ex<nbetaX && ex>=0 && ey>=0)
-      heta[ey*nbetaX+ex]++;
-#endif
-    return 0;
-  };
-  
-  
-};
-
 #endif

slsDetectorCalibration/interpolations/etaInterpolationGlobal.h

@@ -4,12 +4,12 @@
 
 #include "etaInterpolationBase.h"
 
-class etaInterpolationGlobal : public virtual etaInterpolationBase {
+class etaInterpolationGlobal : public etaInterpolationBase{
  public:
- etaInterpolationGlobal(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){};
-  
+ globalEtaInterpolation(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){};
   
 
+
   virtual void prepareInterpolation(int &ok)
   {
    ok=1;  
@@ -24,106 +24,62 @@ class etaInterpolationGlobal : public virtual etaInterpolationBase {
 
 
    ///*Eta Distribution Rebinning*///
-   // double bsizeX=1./nSubPixelsX; //precision
+   double bsize=1./nSubPixels; //precision
    // cout<<"nPixelsX = "<<nPixelsX<<" nPixelsY = "<<nPixelsY<<" nSubPixels = "<<nSubPixels<<endl;
    double tot_eta=0;
-   for (int ip=0; ip<nbetaX*nbetaY; ip++)
+   for (int ip=0; ip<nbeta*nbeta; ip++)
      tot_eta+=heta[ip];
    cout << "total eta entries is :"<< tot_eta << endl;   
    if (tot_eta<=0) {ok=0; return;};
 
 
-   double hx[nbetaX]; //projection x
-   double hy[nbetaY]; //projection y
+   double hx[nbeta]; //projection x
+   double hy[nbeta]; //projection y
 
-   for (int ibx=0; ibx<nbetaX; ibx++) { hx[ibx]=0;}
-
-     for (int iby=0; iby<nbetaY; iby++) { hy[iby]=0;}
-
-   for (int ibx=0; ibx<nbetaX; ibx++) {
-     for (int iby=0; iby<nbetaY; iby++) {
-       hx[ibx]=hx[ibx]+heta[ibx+iby*nbetaX];
-       hy[iby]=hy[iby]+heta[ibx+iby*nbetaX];
+   for (int ibx=0; ibx<nbeta; ibx++) {
+     for (int iby=0; iby<nbeta; iby++) {
+       hx[ibx]=hx[ibx]+heta[ibx+iby*nbeta];
+       hy[iby]=hx[iby]+heta[ibx+iby*nbeta];
      }
    }
-  double hix[nbetaX]; //integral of projection x
-  double hiy[nbetaY]; //integral of projection y
+  double hix[nbeta]; //integral of projection x
+  double hiy[nbeta]; //integral of projection y
   hix[0]=hx[0];
   hiy[0]=hy[0];
   
-  for (int ib=1; ib<nbetaX; ib++) {
+  for (int ib=1; ib<nbeta; ib++) {
     hix[ib]=hix[ib-1]+hx[ib];
+    hiy[ib]=hiy[ib-1]+hx[ib];
   }
 
-  for (int ib=1; ib<nbetaY; ib++) {
-    hiy[ib]=hiy[ib-1]+hy[ib];
-  }
-  double tot_x=hix[nbetaX-1]+1;
-  double tot_y=hiy[nbetaY-1]+1;
   int ib=0;
-
-  for (int ibx=0; ibx<nbetaX; ibx++) {
-    //     if (hix[ibx]>(ib+1)*tot_eta*bsize) ib++;
-    for (int iby=0; iby<nbetaY; iby++) {
-
-      if (tot_x>0)
-	hhx[ibx+iby*nbetaX]=hix[ibx]/tot_x; 
-      else
-	hhx[ibx+iby*nbetaX]=-1; 
-      
-      if (tot_y>0)
-       hhy[ibx+iby*nbetaX]=hiy[iby]/tot_y;  
-      else
-	hhy[ibx+iby*nbetaX]=-1; 
+   for (int ibx=0; ibx<nbeta; ibx++) {
+     if (hix[ibx]>(ib+1)*tot_eta*bsize) ib++;
+     for (int iby=0; iby<nbeta; iby++) {
+#ifdef MYROOT1  
+       hhx->SetBinContent(ibx+1,iby+1,ib);
+#endif
+#ifndef MYROOT1  
+       hhx[ibx+iby*nbeta]=ib; 
+#endif
+     }
+   }
+   ib=0;
+   for (int iby=0; iby<nbeta; iby++) {
+     if (hiy[iby]>(ib+1)*tot_eta*bsize) ib++;
+     for (int ibx=0; ibx<nbeta; ibx++) {
+#ifdef MYROOT1 
+       hhy->SetBinContent(ibx+1,iby+1,ib); 
+#endif
+#ifndef MYROOT1  
+       hhy[ibx+iby*nbeta]=ib; 
+#endif
      }
    }
-/*    ib=0; */
-/*    for (int iby=0; iby<nbeta; iby++) { */
-/*      if (hiy[iby]>(ib+1)*tot_eta*bsize) ib++; */
-/*      for (int ibx=0; ibx<nbeta; ibx++) { */
-/* #ifdef MYROOT1  */
-/*        hhy->SetBinContent(ibx+1,iby+1,ib);  */
-/* #endif */
-/* #ifndef MYROOT1   */
-/*        hhy[ibx+iby*nbeta]=ib;  */
-/* #endif */
-/*      } */
-/*    } */
 
    return ;
   };
-  
- etaInterpolationGlobal(etaInterpolationGlobal *orig): etaInterpolationBase(orig)  {};
 
 };
 
-
-//etaInterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax),
-
-class eta2InterpolationGlobal : public virtual eta2InterpolationBase, public virtual etaInterpolationGlobal {
-  
- public:
- eta2InterpolationGlobal(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) : eta2InterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax), etaInterpolationGlobal(nx,ny, ns, nsy, nb, nby, emin, emax){
-    cout << "e2pxy " << nbetaX << " " << nbetaY << etamin << " " << etamax << " " << nSubPixelsX<< " " << nSubPixelsY << endl;  
-  };
- 
- eta2InterpolationGlobal(eta2InterpolationGlobal *orig): etaInterpolationBase(orig), etaInterpolationGlobal(orig)  {};
-
-  virtual eta2InterpolationGlobal* Clone() { return new eta2InterpolationGlobal(this);};
-
-};
-
-//etaInterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax),
-
-class eta3InterpolationGlobal : public virtual eta3InterpolationBase, public virtual etaInterpolationGlobal {
- public:
- eta3InterpolationGlobal(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) :  eta3InterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax), etaInterpolationGlobal(nx,ny, ns, nsy, nb, nby, emin, emax){
-    cout << "e3pxy " << nbetaX << " " << nbetaY << etamin << " " << etamax << " " << nSubPixelsX<< " " << nSubPixelsY << endl;  
-  };
-
- eta3InterpolationGlobal(eta3InterpolationGlobal *orig): etaInterpolationBase(orig), etaInterpolationGlobal(orig)  {};
-
-  virtual eta3InterpolationGlobal* Clone() {return new eta3InterpolationGlobal(this);};
-};
-
 #endif

slsDetectorCalibration/interpolations/etaInterpolationPosXY.h

@@ -4,6 +4,8 @@
 
 //#include "tiffIO.h"
 #include "etaInterpolationBase.h"
+#include "eta2InterpolationBase.h"
+#include "eta3InterpolationBase.h"
 
 class etaInterpolationPosXY : public virtual etaInterpolationBase{
  public:
@@ -42,8 +44,9 @@ class etaInterpolationPosXY : public virtual etaInterpolationBase{
    double hiy[nbetaY]; //integral of projection y
    //  int ii=0;
    double etax, etay;
-   
    for (int ib=0; ib<nbetaX; ib++) {
+
+   
      //tot_eta_y=0;
 
      for (int iby=0; iby<nbetaY; iby++) {
@@ -51,10 +54,10 @@ class etaInterpolationPosXY : public virtual etaInterpolationBase{
        //cout << etax << endl;
      
        // tot_eta_x+=hx[iby];
-       //  if (etay>=0 && etay<=1)
+       if (etay>=0 && etay<=1)
 	 hy[iby]=heta[ib+iby*nbetaX];
-	 // else
-	 //	 hy[iby]=0;
+       else
+	 hy[iby]=0;
        // tot_eta_y+=hy[iby];
      }
 
@@ -68,7 +71,7 @@ class etaInterpolationPosXY : public virtual etaInterpolationBase{
      tot_eta_y=hiy[nbetaY-1]+1;
      
      for (int iby=0; iby<nbetaY; iby++) {
-       if (tot_eta_y<=1) {
+       if (tot_eta_y<=0) {
 	 hhy[ib+iby*nbetaX]=-1;
 	 //ii=(ibx*nSubPixels)/nbeta;
        } else {   
@@ -77,7 +80,7 @@ class etaInterpolationPosXY : public virtual etaInterpolationBase{
        }
      }
    }
-   cout << "hhy filled " << endl;
+
 
 
    for (int ib=0; ib<nbetaY; ib++) {
@@ -85,11 +88,11 @@ class etaInterpolationPosXY : public virtual etaInterpolationBase{
      for (int ibx=0; ibx<nbetaX; ibx++) {
        etax=etamin+ibx*etastepX;
        //cout << etax << endl;
-       //   if (etax>=0 && etax<=1)
+       if (etax>=0 && etax<=1)
 	 hx[ibx]=heta[ibx+ib*nbetaX];
-	 //  else {
-	 //	 hx[ibx]=0;
-	 // }
+       else {
+	 hx[ibx]=0;
+       }
      }
      hix[0]=hx[0];
        
@@ -101,7 +104,7 @@ class etaInterpolationPosXY : public virtual etaInterpolationBase{
      tot_eta_x=hix[nbetaX-1]+1;
      
      for (int ibx=0; ibx<nbetaX; ibx++) {
-       if (tot_eta_x<=1) {
+       if (tot_eta_x<=0) {
 	 hhx[ibx+ib*nbetaX]=-1;
        } 
        else { 
@@ -119,49 +122,40 @@ class etaInterpolationPosXY : public virtual etaInterpolationBase{
 	 hhx[ibx+ib*nbetaX]=hix[ibx]/tot_eta_x;
        }
      }
-  }
+     
+   }
 
      
-   /* cout << "hhx filled " << endl; */
-   /* int ibx, iby, ib; */
+   int ibx, iby, ib; 
    
-   /* iby=0; */
-   /* while (hhx[iby*nbetaY+nbetaY/2]<0 && iby<nbetaY/2) iby++; */
-   /* for (ib=0; ib<iby;ib++) { */
-   /*   for (ibx=0; ibx<nbetaX;ibx++) */
-   /*     hhx[ibx+nbetaX*ib]=hhx[ibx+nbetaX*iby]; */
-   /* } */
+   iby=0;
+   while (hhx[iby*nbetaY+nbetaY/2]<0) iby++;
+   for (ib=0; ib<iby;ib++) {
+     for (ibx=0; ibx<nbetaX;ibx++)
+       hhx[ibx+nbetaX*ib]=hhx[ibx+nbetaX*iby];
+   }
+   iby=nbetaY-1;
    
-   /* cout << "hhx  low optimized" << endl; */
-
-   /* iby=nbetaY-1; */
-   /* while (hhx[iby*nbetaY+nbetaY/2]<0 && iby>0) 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];
+   }
    
-   /* for (ib=iby+1; ib<nbetaY;ib++) { */
-   /*   for (ibx=0; ibx<nbetaX;ibx++){ */
-   /*     cout << iby << " " << ib << " " << ibx << " " << ibx+nbetaX*ib << " " << ibx+nbetaX*iby << " " << nbetaX*nbetaY << endl; */
-   /*     hhx[ibx+nbetaX*ib]=hhx[ibx+nbetaX*iby]; */
-   /* 	 } */
-   /* } */
+   iby=0;
+   while (hhy[nbetaX/2*nbetaX+iby]<0) iby++;
+   for (ib=0; ib<iby;ib++) {
+     for (ibx=0; ibx<nbetaY;ibx++)
+       hhy[ib+nbetaX*ibx]=hhy[iby+nbetaX*ibx];
+   }
+   iby=nbetaX-1;
    
-   /* cout << "hhx  high optimized" << endl; */
+   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];
+   }
 
-   /* iby=0; */
-   /* while (hhy[nbetaX/2*nbetaX+iby]<0 && iby<nbetaX) iby++; */
-   /* for (ib=0; ib<iby;ib++) { */
-   /*   for (ibx=0; ibx<nbetaY;ibx++) */
-   /*     hhy[ib+nbetaX*ibx]=hhy[iby+nbetaX*ibx]; */
-   /* } */
-   /* cout << "hhy  low optimized" << endl; */
-
-   /* iby=nbetaX-1; */
-   /* while (hhy[nbetaX/2*nbetaX+iby]<0 && iby>) iby--; */
-   /* for (ib=iby+1; ib<nbetaX;ib++) { */
-   /*   for (ibx=0; ibx<nbetaY;ibx++) */
-   /*     hhy[ib+nbetaX*ibx]=hhy[iby+nbetaX*ibx]; */
-   /* } */
-
-   /* cout << "hhy  high optimized" << endl; */
 
 
      
@@ -186,7 +180,7 @@ 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 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 " << nbetaX << " " << nbetaY << etamin << " " << etamax << " " << nSubPixelsX<< " " << nSubPixelsY << endl;  
+    //  cout << "e2pxy " << nb << " " << emin << " " << emax << endl; 
   };
  
  eta2InterpolationPosXY(eta2InterpolationPosXY *orig): etaInterpolationBase(orig), etaInterpolationPosXY(orig)  {};
@@ -195,12 +189,12 @@ 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 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 " << nbetaX << " " << nbetaY << etamin << " " << etamax << " " << nSubPixelsX<< " " << nSubPixelsY << 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/slsInterpolation.h

@@ -94,7 +94,10 @@ class slsInterpolation
   //create interpolated image
   //returns interpolated image
   virtual int *getInterpolatedImage(){
-    //cout << "?" <<endl;
+    //  cout << "return interpolated image " << endl;
+    /* for (int i=0; i<nSubPixels*  nSubPixels* nPixelsX*nPixelsY; i++) { */
+    /*   cout << i << " " << hint[i] << endl; */
+    /* } */
     return hint;
   };
 
@@ -102,21 +105,17 @@ class slsInterpolation
 
     
   void *writeInterpolatedImage(const char * imgname) {
-    float *gm=NULL;
     //cout << "!" <<endl;
+    float *gm=NULL;
     int *dummy=getInterpolatedImage();
-    cout << "got interpolated image " << endl;
     gm=new float[ nSubPixelsX*  nSubPixelsY* nPixelsX*nPixelsY];
-    cout << "created dummy " << endl;
     if (gm) {
       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];
-	  //  cout << "++" << ix << " " << iy << " " << iy*nPixelsX*nSubPixelsX+ix << endl;
 	}
       }
-      WriteToTiff(gm, imgname,nSubPixelsX* nPixelsX ,nSubPixelsY* nPixelsY); 
-      // cout << "wrote to tiff " << endl;
+      WriteToTiff(gm, imgname,nSubPixelsY* nPixelsX ,nSubPixelsY* nPixelsY); 
       delete [] gm;
     } else cout << "Could not allocate float image " << endl;
     return NULL;    
@@ -173,7 +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;
 
@@ -189,7 +188,6 @@ class slsInterpolation
     
 
   static int calcQuad(double *cl, double &sum, double &totquad, double sDum[2][2]){
-    //cout << "2";
     
     int corner = UNDEFINED_QUADRANT;
     /* double *cluster[3]; */
@@ -198,11 +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];
@@ -222,34 +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++) {
@@ -370,7 +430,6 @@ class slsInterpolation
 
 
   static int calcEta3(double *cl, double &etax, double &etay, double &sum) {
-    // cout << "3";
     double l=0,r=0,t=0,b=0, val;
     sum=0;
     //  int quad;
@@ -378,10 +437,10 @@ class slsInterpolation
       for (int iy=0; iy<3; iy++) {
 	val=cl[ix+3*iy];
 	sum+=val;
-	if (ix==0) l+=val;
-	if (ix==2) r+=val;
-	if (iy==0) b+=val;
-	if (iy==2) t+=val;
+	if (iy==0) l+=val;
+	if (iy==2) r+=val;
+	if (ix==0) b+=val;
+	if (ix==2) t+=val;
       }
     }
     if (sum>0) {

slsDetectorCalibration/moenchExecutables/Makefile.cluster_finder

@@ -1,12 +1,14 @@
 #module add CBFlib/0.9.5
-INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures  -I../../slsSupportLib/include/ -I../../slsReceiverSoftware/include/
-
-LDFLAG= ../tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++   -pthread -lrt    -ltiff -O3  -std=c++11
+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  -std=c++11 -Wall  -O3
+#-g3 
+#-fsanitize=thread -fno-omit-frame-pointer
+#-fsanitize=address,undefined,
 MAIN=moench03ClusterFinder.cpp
 
 
-all: moenchClusterFinder moenchMakeEta moenchInterpolation moenchNoInterpolation moenchPhotonCounter moenchAnalog
+all: moenchClusterFinder moenchMakeEta moenchMakeEta3 moenchInterpolation moenchInterpolation3 moenchNoInterpolation moenchPhotonCounter moenchAnalog moenchPhotonCounterNoThread  moenchAnalogNoThread 
 
 
 
@@ -23,9 +25,15 @@ moenchClusterFinderHighZ:  moench03ClusterFinder.cpp  $(INCS) clean
 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)  
 
+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) 
 
@@ -41,7 +49,13 @@ moenchPhotonCounterHighZ: moenchPhotonCounter.cpp   $(INCS) clean
 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 moenchAnalog
+	rm -f  moenchClusterFinder moenchMakeEta moenchInterpolation moenchNoInterpolation moenchPhotonCounter moenchAnalog moenchPhotonCounterNoThread  moenchAnalogNoThread 
 
 

slsDetectorCalibration/moenchExecutables/Makefile.cluster_finder_rect_rh7

@@ -12,12 +12,12 @@ MAIN=moench03ClusterFinder.cpp
 #-lhdf5
 #DESTDIR?=../bin
 
-all: moenchClusterFinderRect moenchMakeEtaRect moenchInterpolationRect moenchNoInterpolationRect moenchPhotonCounterRect moenchAnalogRect
+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
+			 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
@@ -34,6 +34,12 @@ moenchPhotonCounterRect: moenchPhotonCounter.cpp   $(INCS) clean
 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_rh7

@@ -1,40 +0,0 @@
-
-#CBFLIBDIR= /afs/psi.ch/project/sls_det_software/CBFlib-0.9.5/
-#ZMQLIB=../slsReceiverSoftware/include
-#LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
-INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures -I../../slsReceiverSoftware/include 
-#-I$(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: moenchClusterFinder moenchMakeEta  moenchInterpolation  moenchNoInterpolation  moenchPhotonCounter  moenchAnalog 
-
-
-
-moenchClusterFinder :  moench03ClusterFinder.cpp  $(INCS) clean
-			 g++ -o moenchClusterFinder   moench03ClusterFinder.cpp $(LDFLAG) $(INCDIR) -DSAVE_ALL  -DNEWRECEIVER -DWRITE_QUAD
-
-moenchMakeEta :  moench03Interpolation.cpp  $(INCS) clean
-			 g++ -o moenchMakeEta  moench03Interpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DFF -DWRITE_QUAD
-
-moenchInterpolation :  moench03Interpolation.cpp  $(INCS) clean
-			 g++ -o moenchInterpolation  moench03Interpolation.cpp    $(LDFLAG) $(INCDIR)  -DWRITE_QUAD
-
-moenchNoInterpolation :  moench03NoInterpolation.cpp  $(INCS) clean
-			 g++ -o moenchNoInterpolation  moench03NoInterpolation.cpp    $(LDFLAG) $(INCDIR)  -DWRITE_QUAD
-
-moenchPhotonCounter : moenchPhotonCounter.cpp   $(INCS) clean
-			 g++ -o moenchPhotonCounter   moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $  -DNEWRECEIVER -DWRITE_QUAD
-
-moenchAnalog : moenchPhotonCounter.cpp  $(INCS) clean
-			 g++ -o moenchAnalog   moenchPhotonCounter.cpp  $(LDFLAG) $(INCDIR)   -DNEWRECEIVER -DANALOG -DWRITE_QUAD
-
-clean: 	
-	rm -f  moenchClusterFinder  moenchMakeEta  moenchInterpolation  moenchNoInterpolation  moenchPhotonCounter  moenchAnalog 
-
-

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
@@ -33,7 +34,9 @@
 #include "multiThreadedAnalogDetector.h"
 #include "singlePhotonDetector.h"
 //#include "interpolatingDetector.h"
-
+ 
+#include <string>
+#include <sstream>  
 #include <stdio.h>
 #include <map>
 #include <fstream>
@@ -50,20 +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=1;
-  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 nsigma=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;
 
 
 
@@ -108,9 +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();
 
@@ -120,21 +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;
 
@@ -148,12 +151,6 @@ int main(int argc, char *argv[]) {
   cout << std::ctime(&end_time) <<   endl;
  
 
-
-
-
-
-
-
   char* buff;
   multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
 
@@ -170,17 +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;
@@ -212,7 +218,7 @@ int main(int argc, char *argv[]) {
 	}
 	ff=-1;
       }
-        cout << "--" << endl;
+      cout << "--" << endl;
       filebin.close();	 
       //      //close file 
       //     //join threads
@@ -220,7 +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/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
@@ -14,12 +14,7 @@
 #include "single_photon_hit.h"
 #endif
 
-#ifdef RECT
-#include "etaInterpolationGlobal.h"
-#endif
-#ifndef RECT
 #include "etaInterpolationPosXY.h"
-#endif
 #include "noInterpolation.h"
 //#include "etaInterpolationCleverAdaptiveBins.h"
 //#include "etaInterpolationRandomBins.h"
@@ -41,7 +36,6 @@ using namespace std;
 int main(int argc, char *argv[]) {
 
 #ifndef FF
-  cout << "INTERPOLATING" << endl;
   if (argc<9) {
     cout << "Wrong usage! Should be: "<< argv[0] << " infile  etafile outfile runmin runmax ns cmin cmax" << endl;
     return 1;
@@ -49,7 +43,6 @@ int main(int argc, char *argv[]) {
 #endif
   
 #ifdef FF
-  cout << "CALC ETA" << endl;
   if (argc<7) {
     cout << "Wrong usage! Should be: "<< argv[0] << " infile  etafile runmin runmax cmin cmax" << endl;
     return 1;
@@ -57,9 +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
 
@@ -81,26 +74,42 @@ int main(int argc, char *argv[]) {
   cout << "Energy min: " << cmin << endl;
   cout << "Energy max: " << cmax << endl;
   //int etabins=500;
-  int etabins=999;//nsubpix*2*100;
+#ifndef NOINTERPOLATION
+  int etabins=1000;//nsubpix*2*100;
   int etabinsY=etabins;//nsubpix*2*100;
-  double etamin=0, etamax=1;
+
+  double etamin=-1, etamax=2;
   //double etamin=-0.1, etamax=1.1;
-  double eta3min=-1, eta3max=1;
+ 
+  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;
 
-
-    char fff[10000];
+  //badph=0,
+  int nph=0,  totph=0;
+  FILE *f=NULL;
 
 #ifdef DOUBLE_SPH
     single_photon_hit_double cl(3,3);
@@ -111,24 +120,23 @@ int main(int argc, char *argv[]) {
 #endif
     int nSubPixels=nsubpix;
     int nSubPixelsY=nsubpix;
-#ifdef RECT
-    nSubPixels=5; //might make more sense using 2?
-    // etabins=5;
+#ifdef RECT1
+//     nSubPixels=2; //might make more sense using 2?
+//     etabins=100;
+    
+    
+    float *rectimg=new float[NC*NR*nSubPixelsY];;
 #endif
+// #endif
 #ifndef NOINTERPOLATION
-    etaInterpolationBase *interp;
-#ifndef RECT
-    interp=new eta2InterpolationPosXY(NC, NR, nSubPixels, nSubPixelsY, etabins, etabinsY, etamin, etamax);
-   //eta2InterpolationCleverAdaptiveBins *interp=new eta2InterpolationCleverAdaptiveBins(NC, NR, nsubpix, etabins, etamin, etamax);  
+#ifndef ETA3
+    eta2InterpolationPosXY *interp=new eta2InterpolationPosXY(NC, NR, nSubPixels, nSubPixelsY, etabins, etabinsY, etamin, etamax);
 #endif
-#ifdef RECT
-    interp=new eta2InterpolationGlobal(NC, NR, nSubPixels, nSubPixelsY, etabins, etabinsY, eta3min, eta3max);
- 
-    //  eta3InterpolationPosXY *interpOdd=new eta3InterpolationPosXY(NC, NR, nSubPixels, nSubPixelsY, etabins, etabinsY, eta3min, eta3max);
-   //eta2InterpolationCleverAdaptiveBins *interp=new eta2InterpolationCleverAdaptiveBins(NC, NR, nsubpix, etabins, etamin, etamax);  
- 
+#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, nSubPixelsY);  
@@ -137,24 +145,12 @@ int main(int argc, char *argv[]) {
 
  
 #ifndef FF
+    int *img;
 #ifndef NOINTERPOLATION
     cout << "read ff " << argv[2] << endl;
     sprintf(fname,"%s",argv[2]);
-    //#ifndef RECT
     interp->readFlatField(fname, etamin, etamax);
     interp->prepareInterpolation(ok);//, MAX_ITERATIONS);
-    interp->debugSaveAll(0);
-    //#endif
-// #ifdef RECT
-//     sprintf(fff,"%s.even",fname);
-//     interpEven->readFlatField(fff, etamin, etamax);
-//     interpEven->prepareInterpolation(ok);, MAX_ITERATIONS);
-//     interpEven->debugSaveAll(1);
-//     sprintf(fff,"%s.odd",fname);
-//     interpOdd->readFlatField(fff, etamin, etamax);
-//     interpOdd->prepareInterpolation(ok);, MAX_ITERATIONS);
-//     interpOdd->debugSaveAll(2);
-// #endif
 #endif
     // return 0;
 #endif
@@ -162,7 +158,6 @@ int main(int argc, char *argv[]) {
     cout << "Will write eta file " << argv[2] << endl;
 #endif
 
-    int *img;
     float *totimg=new float[NC*NR*nSubPixels*nSubPixelsY];
     for (ix=0; ix<NC; ix++) {
       for (iy=0; iy<NR; iy++) {
@@ -177,9 +172,6 @@ int main(int argc, char *argv[]) {
 #ifdef FF
       sprintf(outfname,argv[2]);
 #endif     
- 
-
-      int tl=0, tr=0, bl=0, br=0;
 
     int irun;
     for (irun=runmin; irun<runmax; irun++) {
@@ -201,80 +193,76 @@ int main(int argc, char *argv[]) {
 	    if (nframes==0) f0=lastframe;
 	    nframes++;
 	  }
-#ifdef RECT
-	  //	  quad=interp->calcEta3(cl.get_cluster(), etax, etay, sum);  
+	  //#ifndef FF
+#ifndef ETA3
 	  quad=interp->calcEta(cl.get_cluster(), etax, etay, sum, totquad, sDum);
-	  // if (cl.y%2==0)
-	  //   if (etay>0)
-	  //     interp=interpEven;
-	  //   else
-	  //     interp=interpOdd;
-	  // else
-	  //   if (etay>0)
-	  //     interp=interpOdd;
-	  //   else
-	  //     interp=interpEven;
+#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
 	  
-#endif
-
-#ifndef RECT
-	  quad=interp->calcEta(cl.get_cluster(), etax, etay, sum, totquad, sDum);
-
-	
-#endif
-	  switch(quad) {
-	  case TOP_LEFT:
-	    tl++;
-	    break;
-	  case TOP_RIGHT:
-	    tr++;
-	    break;
-	  case BOTTOM_LEFT:
-	    bl++;
-	    break;
-	  case BOTTOM_RIGHT:
-	    br++;
-	    break;
-	  }
-	  //  if (sum>cmin && totquad/sum>0.8 && totquad/sum<1.2 && sum<cmax ) {
-	  if (sum>cmin &&  sum<cmax ) {
+	    if (sum>cmin && totquad/sum>0.8 && totquad/sum<1.2 && sum<cmax ) {
 	      nph++;
-#ifndef FF 
+	    //  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->addToImage(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)
+	      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);
+// #ifdef UCL
+// 	    if (cl.x>50)
+// #endif
+// 	    if (etax!=0 && etay!=0 && etax!=1 && etay!=1)
 	      interp->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
-	      
-	      cout << "writing interpolated iamge" << endl;
-	      //#ifndef RECT
-	interp->writeInterpolatedImage(outfname); 
-	//#endif
-// #ifdef RECT
-// 	sprintf(fff,"%s.even",outfname);
-// 	interpEven->writeInterpolatedImage(fff); 
-// 	sprintf(fff,"%s.odd",outfname);
-// 	interpOdd->writeInterpolatedImage(fff); 
-// #endif
-		cout << "done" << endl;
+		interp->writeInterpolatedImage(outfname);
 #endif
 #ifdef FF 
-		cout << "writing eta" << endl;
-		//#ifndef RECT
-	interp->writeFlatField(outfname);
-	//#endif
-// #ifdef RECT
-// 	sprintf(fff,"%s.even",outfname);
-// 	interpEven->writeFlatField(fff);
-// 	sprintf(fff,"%s.odd",outfname);
-// 	interpOdd->writeFlatField(fff);
-// #endif
-		cout << "done" << endl;
+		interp->writeFlatField(outfname);
 #endif
 		
 		}
@@ -285,84 +273,71 @@ int main(int argc, char *argv[]) {
 	  
 	fclose(f);
 #ifdef FF
-	//#ifndef RECT
 	interp->writeFlatField(outfname);
-// #endif
-// #ifdef RECT
-// 	sprintf(fff,"%s.even",outfname);
-// 	interpEven->writeFlatField(outfname);
-// 	sprintf(fff,"%s.odd",outfname);
-// 	interpOdd->writeFlatField(outfname);
-// #endif
 #endif
 	
 #ifndef FF
-	  //#ifndef RECT
+#ifndef RECT1
 	interp->writeInterpolatedImage(outfname); 
-// #endif
-// #ifdef RECT
-// 	sprintf(fff,"%s.even",outfname);
-// 	interpEven->writeInterpolatedImage(fff); 
-// 	sprintf(fff,"%s.odd",outfname);
-// 	interpOdd->writeInterpolatedImage(fff); 
-// #endif
-
-//#ifdef RECT
-	  //interp=interpEven;
-	//#endif
+#endif
 	img=interp->getInterpolatedImage();
 	for (ix=0; ix<NC; ix++) {
-	  for (iy=0; iy<NR; iy++) {
-	    for (isx=0; isx<nSubPixels; isx++) {
+	  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)];
-		//	cout << "--" << ix << " " << iy <<" " << ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels) << endl;
+#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;
-	cout << "Top-Left=" << tl << " " << " Top-Right=" << tr << " Bottom-Left="<< bl << " Bottom-Right=" << br << endl;
-	interp->clearInterpolatedImage();
-// #ifdef RECT
-
-// 	interp=interpOdd;
-// 	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++) {
-// 		totimg[ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels)]+=img[ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels)];
-// 		//	cout << "--" << ix << " " << iy <<" " << ix*nSubPixels+isx+(iy*nSubPixelsY+isy)*(NC*nSubPixels) << endl;
-// 		}
-// 	    }
-// 	  }
-// 	}
-
-// 	interp->clearInterpolatedImage();
-// #endif
-
-
+	
+#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);
+    
+#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
-    //#ifndef RECT
 	interp->writeFlatField(outfname);
-	//#endif
-// #ifdef RECT
-// 	sprintf(fff,"%s.even",outfname);
-// 	interpEven->writeFlatField(fff);
-// 	sprintf(fff,"%s.odd",outfname);
-// 	interpOdd->writeFlatField(fff);
-// #endif
 #endif
 
     cout << "Filled " << nph << " (/"<< totph <<") " << endl; 

slsDetectorCalibration/moenchExecutables/moench03NoInterpolation.cpp

@@ -18,7 +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;
   }
 
@@ -28,13 +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/moenchPhotonCounter.cpp

@@ -43,7 +43,7 @@
 #include <map>
 #include <fstream>
 #include <sys/stat.h>
-
+#include <dirent.h>
 #include <ctime>
 using namespace std;
 
@@ -58,19 +58,19 @@ int main(int argc, char *argv[]) {
     return 1;
   }
 
-  int p=10000;
+  //int p=10000;
   int fifosize=1000;
   int nthreads=10;
-  int nsubpix=25;
-  int etabins=nsubpix*10;
-  double etamin=-1, etamax=2;
+  //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=10000;
-  int ndark=100;
-  int ok;
-  int iprog=0;
+  //int ndark=100;
+  //int ok;
+  //int iprog=0;
 
   int cf=0;
 
@@ -101,13 +101,13 @@ int main(int argc, char *argv[]) {
   moench03CommonMode *cm=NULL;
   moench03GhostSummation *gs;
   double *gainmap=NULL;
-  float *gm;
+  //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)];
 
   int ff, np;
@@ -171,7 +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;
 
@@ -185,9 +185,9 @@ int main(int argc, char *argv[]) {
     cout << "pedestal file is " << pedfile << endl;
  if (thr>0) 
     cout << "threshold is " << thr << endl;
- 
- uint32 nnx, nny;
- double *gmap;
+ uint32 unnx, unny;
+ int  nnx, nny;
+ //double *gmap;
 
   // if (gainfname) {
   //   gm=ReadFromTiff(gainfname, nny, nnx);
@@ -221,10 +221,10 @@ int main(int argc, char *argv[]) {
   } else
     thr=0.15*thr;
   filter->newDataSet();
-  int dsize=decoder->getDataSize();
+  //int dsize=decoder->getDataSize();
 
 
-  char data[dsize];
+  //char data[dsize];
 
 
 
@@ -270,12 +270,14 @@ int main(int argc, char *argv[]) {
   mt->StartThreads();
   mt->popFree(buff);
 
-
+  DIR *dir;
+  struct dirent *ent;
+ 
   //  cout << "mt " << endl;
 
   int ifr=0;
 
-  double ped[nx*ny], *ped1;
+  double ped[nx*ny];//, *ped1;
 
 
   if (pedfile) {
@@ -302,7 +304,7 @@ int main(int argc, char *argv[]) {
 	    mt->nextThread();
 	    mt->popFree(buff);
 	    ifr++;
-	    if (ifr%100==0) 
+	    if (ifr%10000==0) 
 	      cout << ifr << " " << ff << " " << np << endl;
 	  } else
 	    cout << ifr << " " << ff << " " << np << endl;
@@ -314,7 +316,9 @@ int main(int argc, char *argv[]) {
       } else 
 	cout << "Could not open pedestal file "<< fname << " for reading " << endl;
     } else {
-      float *pp=ReadFromTiff(pedfile, nny, nnx);
+      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];
@@ -341,28 +345,23 @@ int main(int argc, char *argv[]) {
 
   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(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 && cf!=0) { //cluster finder
+
+    
+    if (thr<=0 && cf!=0) { //cluster finder
 	  if (of==NULL) {
 	    of=fopen(cfname,"w");
 	    if (of) {
@@ -375,77 +374,105 @@ int main(int argc, char *argv[]) {
 	    }
 	  }
       }
-      //     //while read frame 
-      ff=-1;
-      ifr=0;
-      while (decoder->readNextFrame(filebin, ff, np,buff)) {
-	if (np==40) {
-	//	cout << "*"<<ifr++<<"*"<<ff<< endl;
-	//	cout << ff << " " << np << endl;
-  	//         //push
-	  mt->pushData(buff);
-	  // 	//         //pop
-	  mt->nextThread();
-	  // // 		//	cout << " " << (void*)buff;
-	  mt->popFree(buff);
+    
+  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;
 
-
-
-
-	  ifr++;
-	  if (ifr%100==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++;
+	  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;
 	    }
-	  }
-	} else
-	  cout << ifr << " " << ff << " " << np << endl;
-	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);
-	} else {
-	  sprintf(ffname,"%s/%s.tiff",outdir,fformat);
-	  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;
+
+
+    }  
+    while (mt->isBusy()) {;}
+    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;
+      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 << " " << thr1 <<endl;
+    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/moenchZmqProcess.cpp

@@ -1,4 +1,4 @@
-#define WRITE_QUAD
+//#define WRITE_QUAD
 #define MOENCH_BRANCH
 
 #define C_GHOST 0.0004
@@ -54,10 +54,11 @@ 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 nSubPixels=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] [gainmap]  [etafile]\n");
@@ -98,10 +99,14 @@ int main(int argc, char *argv[]) {
     nthreads=atoi(argv[5]);
 
   cout << "Number of threads is: " << nthreads << endl;
-  if (argc>6)
-    nSubPixels=atoi(argv[6]);
-  cout << "Number of subpixels is: " << nSubPixels << endl;
-  
+  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) {
@@ -134,8 +139,12 @@ int main(int argc, char *argv[]) {
 
   int ncol_cm=CM_ROWS;
   double xt_ghost=C_GHOST;
-  moench03CommonMode *cm=new moench03CommonMode(ncol_cm);
-  moench03GhostSummation *gs=new moench03GhostSummation(det, xt_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;
@@ -170,7 +179,7 @@ int main(int argc, char *argv[]) {
     // 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);
 
@@ -285,10 +294,10 @@ int main(int argc, char *argv[]) {
 	int iframe=0;
 	char ofname[10000];
 		    
-	char fname[10000];
+	string fname;
 	//	int length;
 	int *detimage=NULL;
-	int nnx, nny,nns;
+	int nnx, nny,nnsx, nnsy;
 	//uint32_t imageSize = 0, nPixelsX = 0, nPixelsY = 0, 
 	//uint32_t  dynamicRange = 0;
 	// infinite loop
@@ -326,7 +335,7 @@ int main(int argc, char *argv[]) {
 	frameMode fMode=eFrame;
 	double *ped;
 
-	filter->getImageSize(nnx, nny,nns);
+	filter->getImageSize(nnx, nny,nnsx, nnsy);
 
 	
 
@@ -355,8 +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;
 	    }
@@ -369,7 +379,7 @@ int main(int argc, char *argv[]) {
 	    } else {
 	      send_something=0;
 	      if (fMode==ePedestal) {
-		sprintf(ofname,"%s_%ld_ped.tiff",fname,fileindex);
+		sprintf(ofname,"%s_%ld_ped.tiff",fname.c_str(),fileindex);
 		mt->writePedestal(ofname);
 		cout << "Writing pedestal to " << ofname << endl;
 		send_something=1;
@@ -377,7 +387,7 @@ int main(int argc, char *argv[]) {
 #ifdef INTERP
 	      else if  (fMode==eFlat) {
 		mt->prepareInterpolation(ok);
-		sprintf(ofname,"%s_%ld_eta.tiff",fname,fileindex);
+		sprintf(ofname,"%s_%ld_eta.tiff",fname.c_str(),fileindex);
 		mt->writeFlatField(ofname);
 		cout << "Writing eta to " << ofname << endl;
 		send_something=1;
@@ -386,7 +396,7 @@ int main(int argc, char *argv[]) {
 	      else {
 		if (subframes>0 ) { 
 		  if (insubframe>0) {
-		    sprintf(ofname,"%s_sf%ld_%ld.tiff",fname,nnsubframe,fileindex);
+		    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)
@@ -411,7 +421,7 @@ int main(int argc, char *argv[]) {
 		    send_something=1;
 		  }
 		} else {
-		  sprintf(ofname,"%s_%ld.tiff",fname,fileindex);
+		  sprintf(ofname,"%s_%ld.tiff",fname.c_str(),fileindex);
 		  mt->writeImage(ofname);
 		  send_something=1;
 		}
@@ -424,11 +434,13 @@ int main(int argc, char *argv[]) {
 	      
 	    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;
@@ -442,11 +454,11 @@ int main(int argc, char *argv[]) {
 	    }
 #ifdef INTERP
 	    else if  (fMode==eFlat) {
-	       int nb;
+	      int nb, nby;
 	       double emi=0, ema=1;
-	       int *ff=mt->getFlatField(nb, emi, ema);
+	       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];
@@ -454,9 +466,9 @@ 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;
@@ -489,16 +501,16 @@ int main(int argc, char *argv[]) {
 	    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, acqIndex,0 , packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, 0,0, additionalJsonHeader);
+	      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,acqIndex,0 , packetNumber,bunchId, timestamp, modId,xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, 0,0, 0,additionalJsonHeader);
+	      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, 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, 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		
 	      
 			
@@ -525,8 +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
 
 
@@ -560,8 +572,8 @@ int main(int argc, char *argv[]) {
 
 	      //dataSize=size;
 
-	      strcpy(fname,filename.c_str());
-
+	      //strcpy(fname,filename.c_str());
+	      fname=filename;
 	      // cprintf(BLUE, "Header Info:\n"
 	      // 	      "size: %u\n"
 	      // 	      "multisize: %u\n"
@@ -799,7 +811,7 @@ int main(int argc, char *argv[]) {
 	  //  timestamp=doc["timestamp"].GetUint();
 	  packetNumber=doc["packetNumber"].GetUint();
 	  // cout << acqIndex << " " << frameIndex << " " << subFrameIndex << " "<< bunchId << " " << timestamp << " " << packetNumber << endl;
-	  if (packetNumber>=40) {
+	  if (packetNumber>0) {
 	    //*((int*)buff)=frameIndex;
 	    if (insubframe==0) f0=frameIndex;
 	    memcpy(buff,&frameIndex,sizeof(int));
@@ -811,7 +823,7 @@ int main(int argc, char *argv[]) {
 	    insubframe++;
 	    nsubframes=frameIndex+1-f0;
 	  } else {
-	    cprintf(RED, "Incomplete frame: received only %d packet\n", packetNumber);
+	    cprintf(RED, "Empty frame %d\n", frameIndex);
 	    //length = 
 	    zmqsocket->ReceiveData(0, dummybuff, size);
 	  }
@@ -821,7 +833,7 @@ int main(int argc, char *argv[]) {
 
 	  if (subframes>0 && insubframe>=subframes && fMode==eFrame) {
 	    while (mt->isBusy()) {;}//wait until all data are processed from the queues
-	    detimage=mt->getImage(nnx,nny,nns);
+	    detimage=mt->getImage(nnx,nny,nnsx, nnsy);
 	    cprintf(MAGENTA,"Get image!\n");
 	    dout= new int32_t[nnx*nny];
 	    doutf= new float[nnx*nny];
@@ -834,7 +846,7 @@ int main(int argc, char *argv[]) {
 	      if (dout[ix]<0) dout[ix]=0;
 	      doutf[ix]=dout[ix];
 	    }
-	    sprintf(ofname,"%s_sf%ld_%ld.tiff",fname,nnsubframe,fileindex);
+	    sprintf(ofname,"%s_sf%ld_%ld.tiff",fname.c_str(),nnsubframe,fileindex);
 	    
 	    cout << "Writing image to " << ofname << endl;
 
@@ -846,16 +858,16 @@ int main(int argc, char *argv[]) {
 
 #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, acqIndex,0 , packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, 0,0, additionalJsonHeader);
+	    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,acqIndex,0 , packetNumber,bunchId, timestamp, modId,xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, 0,0, 0,additionalJsonHeader);
+	    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, 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, 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		
 	       
 	    

slsDetectorCalibration/multiThreadedAnalogDetector.h

@@ -95,7 +95,7 @@ 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);};
 
   virtual ~threadedAnalogDetector() {StopThread();  delete fifoFree; delete fifoData;}
@@ -208,11 +208,11 @@ FILE *getFilePointer(){return det->getFilePointer();};
      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;
    }
@@ -320,33 +320,41 @@ public:
    
   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)
+    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];
-	//if (img[i])	  cout << "det " << ii << " pix " << i << " val " <<  img[i] << " " << image[i] << endl;
+	  // 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;
     
@@ -369,29 +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) {
-	   if (image[ix]<0) 
-	     gm[ix]=0;
-	   else
-	     gm[ix]=(image[ix])/t;
-	 } else
-	   gm[ix]=image[ix];
+    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); 
-       delete [] gm;
-     } else cout << "Could not allocate float image " << endl;
-     return NULL;
-   }
+	//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() { 
@@ -468,6 +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;
@@ -504,6 +546,26 @@ public:
 
    };
 
+   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){
     
@@ -560,7 +622,7 @@ public:
   int *ff;
   double *ped;
   pthread_mutex_t fmutex;
-};
+  };
 
 #endif
 

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){
@@ -46,7 +46,7 @@ public:
   };
   
 
-   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();};
    
@@ -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
@@ -62,13 +62,10 @@ public analogDetector<uint16_t> {
     
     
     
-    
-    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;
@@ -182,7 +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
       
@@ -218,19 +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;
 		
 	      }
 	    }
@@ -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;
@@ -346,11 +343,11 @@ 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;
-  
+  int iframe=det->getFrameNumber(data);
   double max=0, tl=0, tr=0, bl=0,br=0, *v;
   int cm=0;
   int good=1;
@@ -366,12 +363,12 @@ int *getClusters(char *data,  int *ph=NULL) {
 
 
   
-  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; 
    } 
  };
@@ -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;
   };   
@@ -110,53 +110,53 @@ 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) { */
-	/*     switch (i) { */
-	/*     case 1:  */
-	/*       quad=TOP_LEFT; */
-	/*       break; */
-	/*     case 2: */
-	/*       quad=BOTTOM_RIGHT; */
-	/*       break; */
-	/*     case 3: */
-	/*       quad=BOTTOM_LEFT; */
-	/*       break; */
-	/*     default: */
-	/*       ; */
-	/*     } */
+	int mm=qq[0];
+	for (int i=1; i<4; i++) {
+	  if (qq[i]>mm) {
+	    switch (i) {
+	    case 1:
+	      quad=TOP_LEFT;
+	      break;
+	    case 2:
+	      quad=BOTTOM_RIGHT;
+	      break;
+	    case 3:
+	      quad=BOTTOM_LEFT;
+	      break;
+	    default:
+	      ;
+	    }
+	    mm=qq[i];
+	  }
 
-	/*   } */
-
-	/* } */
+	}
 
 
-    /* switch(quad) { */
-    /* case TOP_LEFT: */
-    /*   data[0]=0; */
-    /*   data[1]=0; */
-    /*   data[2]=0; */
-    /*   data[3]=qq[0]; */
-    /*   data[4]=qq[1]; */
-    /*   data[5]=0; */
-    /*   data[6]=qq[2]; */
-    /*   data[7]=qq[3]; */
-    /*   data[8]=0; */
-    /*   x=x+1; */
-    /*   y=y; */
-    /*   break; */
+    switch(quad) {
+    case TOP_LEFT:
+      data[0]=0;
+      data[1]=0;
+      data[2]=0;
+      data[3]=qq[0];
+      data[4]=qq[1];
+      data[5]=0;
+      data[6]=qq[2];
+      data[7]=qq[3];
+      data[8]=0;
+      x=x+1;
+      y=y;
+      break;
       
-    /* case TOP_RIGHT: */
+    case TOP_RIGHT:
       data[0]=0;
       data[1]=0;
       data[2]=0;
@@ -168,40 +168,40 @@ class single_photon_hit {
       data[8]=qq[3];
       x=x;
       y=y;
-     /*  break; */
+      break;
 
 
-    /* case BOTTOM_LEFT: */
-    /*   data[0]=qq[0]; */
-    /*   data[1]=qq[1]; */
-    /*   data[2]=0; */
-    /*   data[3]=qq[2]; */
-    /*   data[4]=qq[3]; */
-    /*   data[5]=0; */
-    /*   data[6]=0; */
-    /*   data[7]=0; */
-    /*   data[8]=0; */
-    /*   x=x+1; */
-    /*   y=y+1; */
-    /*   break; */
-    /* case BOTTOM_RIGHT: */
-    /*   data[0]=0; */
-    /*   data[1]=qq[0]; */
-    /*   data[2]=qq[1]; */
-    /*   data[3]=0; */
-    /*   data[4]=qq[2]; */
-    /*   data[5]=qq[3]; */
-    /*   data[6]=0; */
-    /*   data[7]=0; */
-    /*   data[8]=0; */
-    /*   x=x; */
-    /*   y=y+1; */
-    /*   break; */
+    case BOTTOM_LEFT:
+      data[0]=qq[0];
+      data[1]=qq[1];
+      data[2]=0;
+      data[3]=qq[2];
+      data[4]=qq[3];
+      data[5]=0;
+      data[6]=0;
+      data[7]=0;
+      data[8]=0;
+      x=x+1;
+      y=y+1;
+      break;
+    case BOTTOM_RIGHT:
+      data[0]=0;
+      data[1]=qq[0];
+      data[2]=qq[1];
+      data[3]=0;
+      data[4]=qq[2];
+      data[5]=qq[3];
+      data[6]=0;
+      data[7]=0;
+      data[8]=0;
+      x=x;
+      y=y+1;
+      break;
 
 
-    /* default: */
-    /*   ; */
-    /* } */
+    default:
+      ;
+    }
     return 1;
       }
 #endif
@@ -210,7 +210,10 @@ class single_photon_hit {
   };
 
   void print() {
-
+#ifdef WRITE_QUAD
+    
+    printf("Q");
+#endif
    // int ix, iy;
     printf("*** %d %d %d\n",iframe, x, y);
     for (int iy=0; iy<dy; iy++) {

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/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/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`)
 

slsReceiverSoftware/include/DataStreamer.h

@@ -206,7 +206,7 @@ class DataStreamer : private virtual slsReceiverDefs, public ThreadObject {
 	uint64_t firstMeasurementIndex;
 
 	/* File name to stream */
-	char fileNametoStream[MAX_STR_LENGTH];
+	std::string fileNametoStream;
 
 	/** Complete buffer used for roi, eg. shortGotthard */
 	char* completeBuffer;

slsReceiverSoftware/include/ZmqSocket.h

@@ -56,8 +56,10 @@ public:
 		 (ConvertInternetAddresstoIpString(result, ip, MAX_STR_LENGTH)))
 		    throw std::exception();
 
+		std::string sip(ip);
+
 		// construct address
-		sprintf (sockfd.serverAddress, "tcp://%s:%d", ip, portno);
+		sprintf (sockfd.serverAddress, "tcp://%s:%d", sip.c_str(), portno);
 #ifdef VERBOSE
 		cprintf(BLUE,"address:%s\n",sockfd.serverAddress);
 #endif
@@ -245,7 +247,7 @@ public:
 	 */
 	int SendHeaderData ( int index, bool dummy, uint32_t jsonversion, uint32_t dynamicrange = 0, uint64_t fileIndex = 0,
 			uint32_t npixelsx = 0, uint32_t npixelsy = 0, uint32_t imageSize = 0,
-			uint64_t acqIndex = 0, uint64_t fIndex = 0, char* fname = NULL,
+			uint64_t acqIndex = 0, uint64_t fIndex = 0, std::string fname = "",
 			uint64_t frameNumber = 0, uint32_t expLength = 0, uint32_t packetNumber = 0,
 			uint64_t bunchId = 0, uint64_t timestamp = 0,
 			uint16_t modId = 0, uint16_t row = 0, uint16_t column = 0, uint16_t reserved = 0,
@@ -286,9 +288,9 @@ public:
 		        "\"flippedDataX\":%u"
 
 				;//"}\n";
-		int length = sprintf(buf, jsonHeaderFormat,
+		sprintf(buf, jsonHeaderFormat,
 				jsonversion, dynamicrange, fileIndex, npixelsx, npixelsy, imageSize,
-				acqIndex, fIndex, (fname == NULL)? "":fname, dummy?0:1,
+				acqIndex, fIndex, fname.c_str(), dummy?0:1,
 
 				        frameNumber, expLength, packetNumber, bunchId, timestamp,
 						modId, row, column, reserved, debug, roundRNumber,
@@ -298,10 +300,12 @@ public:
 						((flippedData == 0 ) ? 0 :flippedData[0])
 		);
 		if (additionalJsonHeader && strlen(additionalJsonHeader)) {
-		    length = sprintf(buf, "%s, %s}\n", buf, additionalJsonHeader);
-		} else {
-		    length = sprintf(buf, "%s}\n", buf);
+		    strcat(buf, ", ");
+		    strcat(buf, additionalJsonHeader);
 		}
+		strcat(buf,"}\n");
+		int length = strlen(buf);
+		
 
 #ifdef VERBOSE
 		//if(!index)

slsReceiverSoftware/include/receiver_defs.h

@@ -21,7 +21,7 @@
 #define FILE_BUFFER_SIZE        		(16*1024*1024) //16mb
 
 //fifo
-#define FIFO_HEADER_NUMBYTES			4
+#define FIFO_HEADER_NUMBYTES			8
 
 
 //hdf5

slsReceiverSoftware/src/DataProcessor.cpp

@@ -146,7 +146,7 @@ void DataProcessor::ResetParametersforNewMeasurement(){
 		delete [] tempBuffer;
 		tempBuffer = 0;
 	}
-	if (*gapPixelsEnable >= 0) {
+	if (*gapPixelsEnable) {
 		tempBuffer = new char[generalData->imageSize];
 		memset(tempBuffer, 0, generalData->imageSize);
 	}

slsReceiverSoftware/src/DataStreamer.cpp

@@ -40,7 +40,6 @@ DataStreamer::DataStreamer(int ind, Fifo*& f, uint32_t* dr, std::vector<ROI>* r,
 
     FILE_LOG(logDEBUG) << "DataStreamer " << ind << " created";
 
-	memset(fileNametoStream, 0, MAX_STR_LENGTH);
 }
 
 
@@ -83,7 +82,7 @@ void DataStreamer::ResetParametersforNewMeasurement(char* fname){
     runningFlag = false;
 	firstMeasurementIndex = 0;
 	measurementStartedFlag = false;
-	strcpy(fileNametoStream, fname);
+	fileNametoStream.assign(fname);
 	if (completeBuffer) {
 		delete [] completeBuffer;
 		completeBuffer = 0;

slsReceiverSoftware/src/Listener.cpp

@@ -64,9 +64,11 @@ Listener::Listener(int ind, detectorType dtype, Fifo*& f, runStatus* s,
 
 
 Listener::~Listener() {
-	if (udpSocket) delete udpSocket;
-	sem_post(&semaphore_socket);
-    sem_destroy(&semaphore_socket);
+	if (udpSocket)   {
+		delete udpSocket;
+		sem_post(&semaphore_socket);
+    	sem_destroy(&semaphore_socket);
+	}
 	if (carryOverPacket) delete [] carryOverPacket;
 	if (listeningPacket) delete [] listeningPacket;
 	ThreadObject::DestroyThread();
@@ -228,7 +230,9 @@ void Listener::ShutDownUDPSocket() {
 		FILE_LOG(logINFO) << "Shut down of UDP port " << *udpPortNumber;
 		fflush(stdout);
 		//delete socket at stoplistening
-	    sem_wait(&semaphore_socket);
+		if (runningFlag) {
+			sem_wait(&semaphore_socket);
+		}
         delete udpSocket;
         udpSocket = 0;
 	    sem_destroy(&semaphore_socket);

slsReceiverSoftware/src/main.cpp

@@ -16,12 +16,13 @@
 #include <sys/wait.h>	//wait
 #include <unistd.h> 	//usleep
 #include <syscall.h>
+#include <semaphore.h>
 
+sem_t semaphore;
 
-bool keeprunning;
 
 void sigInterruptHandler(int p){
-	keeprunning = false;
+	sem_post(&semaphore);
 }
 
 /*
@@ -65,7 +66,7 @@ void GetData(char* metadata, char* datapointer, uint32_t datasize, void* p){
 
 int main(int argc, char *argv[]) {
 
-	keeprunning = true;
+	sem_init(&semaphore,1,0);
 	cprintf(BLUE,"Created [ Tid: %ld ]\n", (long)syscall(SYS_gettid));
 
 	// Catch signal SIGINT to close files and call destructors properly
@@ -148,8 +149,8 @@ int main(int argc, char *argv[]) {
 
 	FILE_LOG(logINFO) << "Ready ... ";
 	cprintf(RESET, "\n[ Press \'Ctrl+c\' to exit ]\n");
-	while(keeprunning)
-		pause();
+	sem_wait(&semaphore);
+	sem_destroy(&semaphore);
 
 	delete receiver;
 	cprintf(BLUE,"Exiting [ Tid: %ld ]\n", (long)syscall(SYS_gettid));