added data structure for moench03 rectangual pixels module 019

slsDetectorCalibration/dataStructures/moench03T1ReceiverDataNewRect.h

@@ -0,0 +1,321 @@
+#ifndef MOENCH03T1RECDATANEWRECT_H
+#define  MOENCH03T1RECDATANEWRECT_H
+#include "slsDetectorData.h"
+
+#define VERT 1
+
+    /**
+        @short  structure for a Detector Packet or Image Header
+        @li frameNumber is the frame number
+        @li expLength is the subframe number (32 bit eiger) or real time exposure time in 100ns (others)
+        @li packetNumber is the packet number
+        @li bunchId is the bunch id from beamline
+        @li timestamp is the time stamp with 10 MHz clock
+        @li modId is the unique module id (unique even for left, right, top, bottom)
+        @li xCoord is the x coordinate in the complete detector system
+        @li yCoord is the y coordinate in the complete detector system
+        @li zCoord is the z coordinate in the complete detector system
+        @li debug is for debugging purposes
+        @li roundRNumber is the round robin set number
+        @li detType is the detector type see :: detectorType
+        @li version is the version number of this structure format
+    */
+    typedef struct {
+        uint64_t frameNumber;    /**< is the frame number */
+        uint32_t expLength;        /**< is the subframe number (32 bit eiger) or real time exposure time in 100ns (others) */
+        uint32_t packetNumber;    /**< is the packet number */
+        uint64_t bunchId;        /**< is the bunch id from beamline */
+        uint64_t timestamp;        /**< is the time stamp with 10 MHz clock */
+        uint16_t modId;            /**< is the unique module id (unique even for left, right, top, bottom) */
+        uint16_t xCoord;        /**< is the x coordinate in the complete detector system */
+        uint16_t yCoord;        /**< is the y coordinate in the complete detector system */
+        uint16_t zCoord;        /**< is the z coordinate in the complete detector system */
+        uint32_t debug;            /**< is for debugging purposes */
+        uint16_t roundRNumber;    /**< is the round robin set number */
+        uint8_t detType;        /**< is the detector type see :: detectorType */
+        uint8_t version;        /**< is the version number of this structure format */
+    } sls_detector_header;
+
+
+
+
+class moench03T1ReceiverDataNew : public slsDetectorData<uint16_t> {
+ 
+ private:
+  
+  int iframe;
+  int nadc;
+  int sc_width;
+  int sc_height;
+  const int nSamples;
+
+
+ public:
+
+
+
+
+  /**
+     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
+     (160x160 pixels, 40 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+  */
+#ifdef HOR
+    moench03T1ReceiverDataNew(int ns=5000): slsDetectorData<uint16_t>(800, 200, ns*2*32+sizeof(sls_detector_header)), nSamples(ns) {
+#endif
+#ifdef VERT
+    moench03T1ReceiverDataNew(int ns=5000): slsDetectorData<uint16_t>(200, 800, ns*2*32+sizeof(sls_detector_header)), nSamples(ns) {
+#endif
+    int nadc=32;
+    int sc_width=25;
+    int sc_height=200;
+
+    int adc_nr[32]={300,325,350,375,300,325,350,375,		\
+    		    200,225,250,275,200,225,250,275,\
+    		    100,125,150,175,100,125,150,175,\
+    		    0,25,50,75,0,25,50,75};
+
+    int row, col;
+
+    int isample;
+    int iadc;
+    int ix, iy;
+    
+     int npackets=40;
+    int i;
+    int adc4(0);
+    int pix;
+
+
+    int off=0;
+#ifdef OFF_1
+    off=1;
+#endif
+    cout << "This is a MOENCH with rectangular pixels!" << endl;
+
+    for (int ip=0; ip<npackets; ip++) {
+      for (int is=0; is<128; is++) {
+
+	for (iadc=0; iadc<nadc; iadc++) {
+	  i=128*ip+is;
+	  adc4=(int)iadc/4;
+	  if (i<sc_width*sc_height) {
+	    //  for (int i=0; i<sc_width*sc_height; i++) {
+	    col=adc_nr[iadc]+(i%sc_width);
+	    if (adc4%2==0) {
+	      row=199-i/sc_width;
+	    } else {
+	      row=200+i/sc_width;
+	    }
+	    pix=sizeof(sls_detector_header)+(nadc*i+iadc)*2;//+16*(ip+1);
+	    if (pix<0 || pix>=nSamples*2*32+sizeof(sls_detector_header))
+	      cout << "Error: pointer " << dataMap[row][col] << " out of range "<< endl;
+	    ix=col;
+	    iy=row;
+#ifdef HOR
+	    if (row%2==off) {
+	      ix=2*col;
+	      iy=row/2;
+	    } else {
+	      ix=2*col+1;
+	      iy=row/2;
+	    }
+#endif
+
+#ifdef VERT
+	    if (col%2==off) {
+	      ix=col/2;
+	      iy=row*2+1;
+	    } else {
+	      ix=col/2;
+	      iy=row*2;
+	    }
+#endif
+	    dataMap[iy][ix]=pix;
+	  }
+	}
+      }
+    }
+
+    /* 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;
+  };
+    
+
+
+     /**
+
+     Returns the frame number for the given dataset. Purely virtual func.
+     \param buff pointer to the dataset
+     \returns frame number
+
+  */
+
+/* class jfrau_packet_header_t { */
+/*  public: */
+/* 	unsigned char reserved[4]; */
+/* 	unsigned char packetNumber[1]; */
+/* 	unsigned char frameNumber[3]; */
+/* 	unsigned char bunchid[8]; */
+/* }; */
+
+
+
+  int getFrameNumber(char *buff){return ((sls_detector_header*)buff)->frameNumber;};//*((int*)(buff+5))&0xffffff;};   
+
+  /**
+
+     Returns the packet number for the given dataset. purely virtual func
+     \param buff pointer to the dataset
+     \returns packet number number
+
+
+
+  */
+  int getPacketNumber(char *buff){return ((sls_detector_header*)buff)->packetNumber;}//((*(((int*)(buff+4))))&0xff)+1;};   
+
+/*    /\** */
+
+/*      Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func */
+/*      \param data pointer to the memory to be analyzed */
+/*      \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot */
+/*      \param dsize size of the memory slot to be analyzed */
+/*      \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found  */
+
+/*   *\/ */
+/*     virtual  char *findNextFrame(char *data, int &ndata, int dsize){ndata=dsize; setDataSize(dsize);  return data;}; */
+
+
+/*    /\** */
+
+/*      Loops over a file stream until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). Can be overloaded for different kind of detectors!  */
+/*      \param filebin input file stream (binary) */
+/*      \returns pointer to the begin of the last good frame, NULL if no frame is found or last frame is incomplete */
+
+/*   *\/ */
+/*     virtual char *readNextFrame(ifstream &filebin){ */
+/*       //	int afifo_length=0;   */
+/*       uint16_t *afifo_cont;  */
+/*       int ib=0; */
+/*       if (filebin.is_open()) { */
+/* 	afifo_cont=new uint16_t[dataSize/2]; */
+/*  	while (filebin.read(((char*)afifo_cont)+ib,2)) { */
+/* 	  ib+=2; */
+/* 	  if (ib==dataSize) break; */
+/* 	} */
+/* 	if (ib>0) { */
+/* 	  iframe++; */
+/* 	  // cout << ib << "-" << endl; */
+/* 	  return (char*)afifo_cont; */
+/* 	} else { */
+/* 	  delete [] afifo_cont; */
+/* 	  return NULL; */
+/* 	} */
+/*       }      */
+/*       return NULL; */
+/*     }; */
+
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[dataSize];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+	  char *retval=0;
+	  int  nd;
+	  int fnum = -1;
+	  np=0;
+	  int  pn;
+	  
+	  //  cout << dataSize << endl;
+	  if (ff>=0)
+	    fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, dataSize) ){
+	      ff=getFrameNumber(data);
+	      np=getPacketNumber(data);
+	      return data;
+	    }
+	  }
+	    return NULL;
+	    
+	    
+	  
+  };
+
+
+
+  /**
+
+     Loops over a memory slot until a complete frame is found (i.e. all packets 0 to nPackets, same frame number). purely virtual func
+     \param data pointer to the memory to be analyzed
+     \param ndata reference to the amount of data found for the frame, in case the frame is incomplete at the end of the memory slot
+     \param dsize size of the memory slot to be analyzed
+     \returns pointer to the beginning of the last good frame (might be incomplete if ndata smaller than dataSize), or NULL if no frame is found 
+     
+  */
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<dataSize) ndata=dsize;
+    else ndata=dataSize;
+    return data;
+
+  }
+
+
+
+  //int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+
+};
+
+
+
+
+#endif

slsDetectorCalibration/moenchExecutables/moench03ClusterFinder.cpp

@@ -2,11 +2,19 @@
 #include <iostream>
 
 
-
 //#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 
@@ -58,6 +66,9 @@ int main(int argc, char *argv[]) {
 
 
 #ifdef NEWRECEIVER
+#ifdef RECT
+  cout << "Should be rectangular!" <<endl;
+#endif
   moench03T1ReceiverDataNew *decoder=new  moench03T1ReceiverDataNew();
   cout << "RECEIVER DATA WITH ONE HEADER!"<<endl;
 #endif
@@ -135,6 +146,7 @@ int main(int argc, char *argv[]) {
   multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
 
  
+  mt->setDetectorMode(ePhotonCounting);
   mt->setFrameMode(eFrame);
   mt->StartThreads();
   mt->popFree(buff);

slsDetectorCalibration/moenchExecutables/moenchPhotonCounter.cpp

@@ -5,8 +5,17 @@
 
 //#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 
@@ -48,7 +57,6 @@ int main(int argc, char *argv[]) {
   int etabins=nsubpix*10;
   double etamin=-1, etamax=2;
   int csize=3;
-  int nx=400, ny=400;
   int save=1;
   int nsigma=5;
   int nped=1000;
@@ -56,9 +64,12 @@ int main(int argc, char *argv[]) {
   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
@@ -73,6 +84,10 @@ int main(int argc, char *argv[]) {
   cout << "OLD RECEIVER DATA!"<<endl;
 #endif
 
+  int nx=400, ny=400;
+
+  decoder->getDetectorSize(nx,ny);
+
   singlePhotonDetector *filter=new singlePhotonDetector(decoder,csize, nsigma, 1, 0, nped, 200);
 
   int size = 327680;////atoi(argv[3]);
@@ -111,7 +126,7 @@ int main(int argc, char *argv[]) {
     pedfile=argv[6];
   }
   double thr=0;
-  double thr1=0;
+  double thr1=1;
 
   if (argc>=8) {
     thr=atoi(argv[7]);
@@ -123,7 +138,7 @@ int main(int argc, char *argv[]) {
   if (argc>=9) {
     nframes=atoi(argv[8]);
   }
-  int xmin=0, xmax=400, ymin=0, ymax=400;
+  int xmin=0, xmax=nx, ymin=0, ymax=ny;
   if (argc>=13) {
     xmin=atoi(argv[9]);
     xmax=atoi(argv[10]);
@@ -151,12 +166,13 @@ int main(int argc, char *argv[]) {
   cout << "runmax is " << runmax << endl;
   if (pedfile)
     cout << "pedestal file is " << pedfile << endl;
-#ifndef ANALOG
+  //#ifndef ANALOG
   if (thr>0) {
     cout << "threshold is " << thr << endl;
     filter->setThreshold(thr);
-  }
+  } else
-#endif
+    cf=1;
+  //#endif
 
 
   filter->setROI(xmin,xmax,ymin,ymax);
@@ -170,24 +186,27 @@ int main(int argc, char *argv[]) {
   char* buff;
   multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
 #ifndef ANALOG
-  if (thr>=0) {
     mt->setDetectorMode(ePhotonCounting);
     cout << "Counting!" << endl;
-  } else
+  if (thr>0) {
+    cf=0;
+  } 
 #endif
-    {
+//{
+#ifdef ANALOG
       mt->setDetectorMode(eAnalog);
       cout << "Analog!" << endl;
-#ifdef ANALOG
+      cf=0;
-      thr1=thr;
+// #ifdef ANALOG
+//       thr1=thr;
 #endif  
-    }
+      //  }
   
   mt->StartThreads();
   mt->popFree(buff);
 
 
-  cout << "mt " << endl;
+  //  cout << "mt " << endl;
 
   int ifr=0;
  
@@ -252,15 +271,17 @@ int main(int argc, char *argv[]) {
     ifile=0;
     if (filebin.is_open()){
       if (thr<=0) {
-	if (of==NULL) {
+	if (cf) {
-	  of=fopen(cfname,"w");
+	  if (of==NULL) {
-	  if (of) {
+	    of=fopen(cfname,"w");
+	    if (of) {
 	    mt->setFilePointer(of);
 	    cout << "file pointer set " << endl;
-	  } else {
+	    } else {
-	    cout << "Could not open "<< cfname << " for writing " << endl;
+	      cout << "Could not open "<< cfname << " for writing " << endl;
-	    mt->setFilePointer(NULL);
+	      mt->setFilePointer(NULL);
-	    return 1;
+	      return 1;
+	    }
 	  }
 	}
       }
@@ -284,7 +305,7 @@ int main(int argc, char *argv[]) {
 	    
 	    sprintf(ffname,"%s/%s_f%05d.tiff",outdir,fformat,ifile);
 	    sprintf(imgfname,ffname,irun);
-	    cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
+	    //cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
 	    mt->writeImage(imgfname, thr1);
 	    mt->clearImage();
 	    ifile++;

slsDetectorCalibration/multiThreadedAnalogDetector.h

@@ -145,9 +145,9 @@ FILE *getFilePointer(){return det->getFilePointer();};
 
 
   virtual void prepareInterpolation(int &ok){
-      slsInterpolation *interp=((interpolatingDetector*)det)->getInterpolation();
+       slsInterpolation *interp=det->getInterpolation(); 
-      if (interp) 
+       if (interp)  
-       interp->prepareInterpolation(ok);
+        interp->prepareInterpolation(ok); 
    }
 
    virtual int *getFlatField(){