minor fixes

* changed to pure virtual methods for Clone and setClusterSize

* added std::

* added moench to the github actions build

.github/workflows/cmake.yml

@@ -0,0 +1,38 @@
+name: CMake
+
+on: [push, pull_request]
+
+env:
+  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  BUILD_TYPE: Debug
+
+jobs:
+  build:
+    # The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
+    # You can convert this to a matrix build if you need cross-platform coverage.
+    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+    runs-on: ubuntu-latest
+    name: Configure and build using cmake
+    steps:
+      - uses: actions/checkout@v3
+      - uses: awalsh128/cache-apt-pkgs-action@latest
+        with:
+          packages: libzmq3-dev libhdf5-dev qtbase5-dev qt5-qmake libqt5svg5-dev
+          version: 1.0
+
+      - name: Configure CMake
+        # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
+        # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
+        run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -DSLS_USE_TESTS=ON -DSLS_USE_HDF5=ON -DSLS_USE_GUI=ON -DSLS_USE_MOENCH=ON
+
+      - name: Build
+        # Build your program with the given configuration
+        run: cmake --build ${{github.workspace}}/build -j2 --config ${{env.BUILD_TYPE}}
+
+      - name: Test
+        working-directory: ${{github.workspace}}/build
+        # Execute tests defined by the CMake configuration.
+        # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
+        run: ctest -C ${{env.BUILD_TYPE}} -j1
+
+

slsDetectorCalibration/analogDetector.h

@@ -220,7 +220,7 @@ template <class dataType> class analogDetector {
        clone. Must be virtual!
        \returns a clone of the original analog detector
      */
-    virtual analogDetector *Clone() { return new analogDetector(this); }
+    virtual analogDetector *Clone() = 0;
 
     /**
        Gives an id to the structure. For debugging purposes in case of
@@ -298,8 +298,8 @@ template <class dataType> class analogDetector {
             if (gmap)
                 delete[] gmap;
             gmap = new double[nnx * nny];
-            for (iy = 0; iy < nny; ++iy) {
-                for (ix = 0; ix < nnx; ++ix) {
+            for (iy = 0; iy < static_cast<int>(nny); ++iy) {
+                for (ix = 0; ix < static_cast<int>(nnx); ++ix) {
                     gmap[iy * nnx + ix] = gm[iy * nnx + ix];
                     // cout << gmap[iy*nnx+ix] << " " ;
                 }
@@ -866,7 +866,7 @@ template <class dataType> class analogDetector {
             for (ix = xmin; ix < xmax; ++ix) {
                 if (det->isGood(ix, iy)) {
                     // addToPedestal(data,ix,iy,1);
-                    addToPedestal(data, ix, iy, 0);
+                    addToPedestal(data, ix, iy, cm);
                     /* if (ix==50 && iy==50) */
                     /*   cout<< "*ped* " << id << " " << ix << " " << iy << " "
                      * << det->getChannel(data,ix,iy) << " " <<
@@ -1097,7 +1097,7 @@ template <class dataType> class analogDetector {
         return thr;
     };
 
-    virtual int setClusterSize(int n = -1) { return 0;     };
+    virtual int setClusterSize(int n = -1) = 0;
 
     /**
        gets threshold value for conversion into number of photons

slsDetectorCalibration/commonModeSubtractionNew.h

@@ -100,10 +100,7 @@ class commonModeSubtraction {
         if (iroi >= 0 && iroi < nROI) {
             if (nCm[iroi] > 0)
                 return mean[iroi] / nCm[iroi];
-	    else
-	      std::cout << ix << " " << iy << " no data in cm " << iroi << std::endl; 
-        } else
-	  std::cout << ix << " " << iy << " bad roi " << iroi << std::endl; 
+        }
         return 0;
     };
 
@@ -120,8 +117,6 @@ class commonModeSubtraction {
                 return sqrt(mean2[iroi] / nCm[iroi] -
                             (mean[iroi] / nCm[iroi]) *
                                 (mean[iroi] / nCm[iroi]));
-	    else
-	      std::cout << ix << " " << iy << " no data in cm " << iroi << std::endl; 
         }
         return 0;
     };

slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsData.h

@@ -57,21 +57,33 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
        1286 large etc.) \param c crosstalk parameter for the output buffer
 
     */
+
+    int groupmap[512*5][1024/5];
+
+ 
     jungfrauLGADStrixelsData()
         : slsDetectorData<uint16_t>(1024/5, 512*5,
                                     512 * 1024 * 2 + sizeof(header)) {
-      cout << "aaa" << endl;
+      //      cout << "aaa" << endl;
 #ifdef ALDO //VH
       cout<< "using reduced jf_header" << endl; //VH
 #endif //VH
         for (int ix = 0; ix < 1024/5; ix++) {
             for (int iy = 0; iy < 512*5; iy++) {
 	      dataMap[iy][ix] = sizeof(header);//+ ( 1024 * 5 + 300) * 2; //somewhere on the guardring of the LGAD
+	      groupmap[iy][ix]=-1;
 #ifdef HIGHZ
                 dataMask[iy][ix] = 0x3fff;
 #endif
             }
         }
+        
+	int x0=256+10, x1=256+246;
+	int y0=10, y1=256-10;
+	int ix,iy;
+	int ox=0, oy=0, ooy=0;
+	ox=2;//0; //original value is 0
+	cout << "G0" << endl;
 
 	//chip1
 	/*
@@ -90,10 +102,11 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
 	ox=0;
 	for (int ipx=x0; ipx<x1; ipx++) {
 	  for (int ipy=y0; ipy<y0+54; ipy++) { //y0+54 excludes the last row (in chip coordinates), should be y0+55 to include all rows
-	    ix=(ipx-x0+ox)/3;
 	    iy=(ipx-x0+ox)%3+(ipy-y0+oy)*3+ooy;
+	    ix=(ipx-x0+ox)/3;
 	    dataMap[iy][ix] = sizeof(header) + (1024 * ipy + ipx) * 2;
-	     //  cout << ipx << " " << ipy << " " << ix << " " << iy << endl;
+	    groupmap[iy][ix]=0;
+	    //  cout << ipx << " " << ipy << " " << ix << " " << iy << endl;
 	  }
 	}
 
@@ -101,12 +114,13 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
 	//3 square pixels in x on the left
 	oy=-54;
 	ooy=54*3;
-	ox=3;
+	ox=2;//; //original value is 3
 	for (int ipx=x0; ipx<x1; ipx++) {
 	  for (int ipy=y0+54; ipy<y0+64+54; ipy++) { //I think y0+54 catches the last row of group1! Should be y0+55 if we want to include all rows? And y0+55+64
 	    ix=(ipx-x0+ox)/5;
 	    iy=(ipx-x0+ox)%5+(ipy-y0+oy)*5+ooy;
 	    dataMap[iy][ix] = sizeof(header) + (1024 * ipy + ipx) * 2;
+	    groupmap[iy][ix]=1;
 	  }
 	}
 	
@@ -120,6 +134,7 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
 	    ix=(ipx-x0+ox)/4;
 	    iy=(ipx-x0+ox)%4+(ipy-y0+oy)*4+ooy;
 	    dataMap[iy][ix] = sizeof(header) + (1024 * ipy + ipx) * 2;
+	    groupmap[iy][ix]=2;
 	  }
 	}
 	
@@ -143,8 +158,8 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
 	    ix=(ipx-x0+ox)/4;
 	    iy=(ipx-x0+ox)%4+(ipy-y0+oy)*4+ooy;
 	    dataMap[iy][ix] = sizeof(header) + (1024 * ipy + ipx) * 2;
-	    //if (ipx==x0)
-	    //  cout << ipx << " " << ipy << " " << ix << " " << iy << endl;
+	    //if (ipx==x0)    cout << ipx << " " << ipy << " " << ix << " " << iy << endl;
+	    groupmap[iy][ix]=2;
 	  }
 	}
 
@@ -158,6 +173,7 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
 	    ix=(ipx-x0+ox)/5;
 	    iy=(ipx-x0+ox)%5+(ipy-y0+oy)*5+ooy;
 	    dataMap[iy][ix] = sizeof(header) + (1024 * ipy + ipx) * 2;
+	    groupmap[iy][ix]=1;
 	  }
 	}
 	
@@ -171,6 +187,7 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
 	    ix=(ipx-x0+ox)/3;
 	    iy=(ipx-x0+ox)%3+(ipy-y0+oy)*3+ooy;
 	    dataMap[iy][ix] = sizeof(header) + (1024 * ipy + ipx) * 2;
+	    groupmap[iy][ix]=0;
 	  }
 	}
 	

slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsData_new.h

@@ -0,0 +1,336 @@
+// SPDX-License-Identifier: LGPL-3.0-or-other
+// Copyright (C) 2021 Contributors to the SLS Detector Package
+#ifndef JUNGFRAULGADSTRIXELSDATA_H
+#define JUNGFRAULGADSTRIXELSDATA_H
+#ifdef CINT
+#include "sls/sls_detector_defs_CINT.h"
+#else
+#include "sls/sls_detector_defs.h"
+#endif
+#include "slsDetectorData.h"
+
+//#define VERSION_V2
+/**
+    @short  structure for a Detector Packet or Image Header
+    @li frameNumber is the frame number
+    @li expLength is the subframe number (32 bit eiger) or real time exposure
+   time in 100ns (others)
+    @li packetNumber is the packet number
+    @li bunchId is the bunch id from beamline
+    @li timestamp is the time stamp with 10 MHz clock
+    @li modId is the unique module id (unique even for left, right, top, bottom)
+    @li xCoord is the x coordinate in the complete detector system
+    @li yCoord is the y coordinate in the complete detector system
+    @li zCoord is the z coordinate in the complete detector system
+    @li debug is for debugging purposes
+    @li roundRNumber is the round robin set number
+    @li detType is the detector type see :: detectorType
+    @li version is the version number of this structure format
+*/
+
+namespace strixelSingleChip {
+  constexpr int nc_rawimg = 1024; //for full images  //256;
+  constexpr int nr_rawimg = 512; 
+  constexpr int nr_chip = 256;
+  constexpr int gr = 9;
+
+  //Group 1: 25um pitch, groups of 3, 1 column of square pixels
+  constexpr int g1_ncols{ (nc_rawimg-(2*gr)-1)/3 }; //79
+  constexpr int g1_nrows{ ( (nr_chip/4)-gr )*3 }; //165
+  
+  //Group 2: 15um pitch, groups of 5, 3 columns of square pixels
+  constexpr int g2_ncols{ (nc_rawimg-(2*gr)-3)/5 }; //47
+  constexpr int g2_nrows{ (nr_chip/4)*5 }; //320
+  
+  //Group 3: 18.75um pitch, groups of 4, 2 columns of square pixels (double the size of the other groups)
+  constexpr int g3_ncols{ (nc_rawimg-(2*gr)-2)/4 }; //59
+  constexpr int g3_nrows{ ( ((nr_chip/4)*2)-gr )*4 }; //476
+
+  constexpr int nc_strixel = 2*gr + 1 + g1_ncols; //group 1 is the "longest" group in x and has one extra square pixel
+  constexpr int nr_strixel = 2*gr + g1_nrows + g2_nrows + g3_nrows;
+
+
+
+}
+
+typedef struct {
+    uint64_t bunchNumber; /**< is the frame number */
+    uint64_t pre;         /**< something */
+
+} jf_header; //Aldo's header
+
+
+using namespace strixelSingleChip; 
+   
+class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
+
+  private:
+    int iframe;
+    int mchip;
+    int chip_x0;
+    int chip_y0;
+
+    void remapGroup( const int group ) {
+      int ix, iy=0;
+      int x0, y0, x1, y1, shifty;
+      int multiplicator;
+      int shiftx;
+      switch (group) {
+      default:
+      case 1:
+	multiplicator = 3;
+	break;
+      case 2:
+	multiplicator = 5;
+	break;
+      case 3:
+	multiplicator = 4;
+	break;
+      }
+
+       if ( mchip == 1 ) {
+        
+	chip_x0=256;
+	chip_y0=1;  //because of bump bonding issues(+1 row)  on M408 
+	
+	switch (group) {
+	default:
+	case 1:
+	  x0 = 10+chip_x0;  //9 gr + 1 sq pixel 
+	  x1 = 246+chip_x0;
+	  y0 = 9+chip_y0;
+	  y1 = 64+chip_y0;
+	  shifty = 0;
+	  break;
+	case 2:
+	  x0 = 12+chip_x0;
+	  x1 = 247+chip_x0;
+	  y0 = 64+chip_y0;
+	  y1 = 128+chip_y0;
+	  shifty = g1_nrows;
+	  break;
+	case 3:
+	  x0 = 11+chip_x0;
+	  x1 = 247+chip_x0;
+	  y0 = 128+chip_y0;
+	  y1 = 247+chip_y0;
+	  shifty = g2_nrows+g1_nrows;
+	  break;
+	}
+      }
+
+      if ( mchip == 6 ) {
+
+	chip_x0=512;
+	chip_y0=255;  //should be 256 but is 255 because of bump bonding issues (+1 row) on M408
+	
+	switch (group) {
+	default:
+	case 1:
+
+	  x0 = 9+chip_x0;  //9 gr sq pixel 
+	  x1 = 246+chip_x0;
+	  y0 = 192+chip_y0;
+	  y1 = 244+chip_y0;
+
+	  shifty = g1_nrows+2*g2_nrows+2*g3_nrows;
+	  break;
+
+	case 2:
+	  
+	  x0 = 9+chip_x0;
+	  x1 = 244+chip_x0;
+	  y0 = 128+chip_y0;
+	  y1 = 191+chip_y0;
+	  
+
+	  shifty = g1_nrows+g2_nrows+2*g3_nrows;;
+	  break;
+	case 3:
+
+	  x0 = 9+chip_x0;
+	  x1 = 244+chip_x0;
+	  y0 = 9+chip_y0;
+	  y1 = 127+chip_y0;
+	  shifty =g1_nrows+g2_nrows+g3_nrows;
+
+	  break;
+	}
+      }
+     
+      //remapping loop
+      for ( int ipy=y0; ipy<=y1;ipy++) {
+	for ( int ipx=x0; ipx<=x1; ipx++ ) {
+
+	  ix = int ((ipx-x0)/multiplicator);
+	  for ( int m=0; m<multiplicator;m++ ) {
+	    if ( (ipx-x0)%multiplicator==m ) iy=(ipy-y0)*multiplicator +m + shifty;
+	  
+
+	  }
+	  
+	  //	  if (iy< 40)	  cout << iy << "  " << ix <<endl;
+	  	  dataMap[iy][ix] = sizeof(header) + (nc_rawimg * ipy + ipx) * 2;
+	  	  groupmap[iy][ix]=group-1;
+	}
+      } 
+
+    }
+
+  public:
+
+    int groupmap[512*5][1024/3];
+
+    using header = sls::defs::sls_receiver_header;
+
+    
+    jungfrauLGADStrixelsData()
+      : slsDetectorData<uint16_t>( /*nc_strixel*/g1_ncols, /*nr_strixel*/ 2*g1_nrows+2*g2_nrows+2*g3_nrows,
+				   g1_ncols*  (2*g1_nrows+2*g2_nrows+2*g3_nrows) * 2 + sizeof(header) ) {
+      std::cout << "Jungfrau strixels 2X single chip with full module data " << std::endl;
+
+      
+
+      
+      //Fill all strixels with dummy values
+      for (int ix = 0; ix != g1_ncols; ++ix) {
+	for (int iy = 0; iy != 2*g1_nrows+2*g2_nrows+2*g3_nrows; ++iy) {
+	  dataMap[iy][ix] = sizeof(header);
+
+	}
+      }
+
+      cout << "sizeofheader = "<<sizeof(header)<<endl;
+std::cout << "Jungfrau strixels 2X single chip with full module data " << std::endl;
+
+      mchip = 1;
+      remapGroup(1);
+  
+
+      remapGroup(2);
+      remapGroup(3);
+
+      mchip = 6;
+      remapGroup(1);
+      remapGroup(2);
+      remapGroup(3);
+	
+      iframe = 0;
+      std::cout << "data struct created" << std::endl;
+    };
+
+    /**
+       Returns the value of the selected channel for the given dataset as
+       double. \param data pointer to the dataset (including headers etc) \param
+       ix pixel number in the x direction \param iy pixel number in the y
+       direction \returns data for the selected channel, with inversion if
+       required as double
+
+    */
+    virtual double getValue(char *data, int ix, int iy = 0) {
+
+        uint16_t val = getChannel(data, ix, iy) & 0x3fff;
+        return val;
+    };
+
+    /**
+
+    Returns the frame number for the given dataset. Purely virtual func.
+    \param buff pointer to the dataset
+    \returns frame number
+
+    */
+
+
+    int getFrameNumber(char *buff) {
+#ifdef ALDO //VH
+      return ((header *)buff)->bunchNumber; //VH
+#else //VH
+      return ((header *)buff)->detHeader.frameNumber;
+#endif //VH
+    };
+
+    /**
+
+       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) {
+#ifdef ALDO //VH
+      //uint32_t fakePacketNumber = 1000;
+      //return fakePacketNumber; //VH //TODO: Keep in mind in case of bugs! //This is definitely bad!
+      return 1000;
+#else //VH
+      return ((header *)buff)->detHeader.packetNumber;
+#endif //VH
+    };
+
+   
+
+    char *readNextFrame(std::ifstream &filebin) {
+        int ff = -1, np = -1;
+        return readNextFrame(filebin, ff, np);
+    };
+
+    char *readNextFrame(std::ifstream &filebin, int &ff) {
+        int np = -1;
+        return readNextFrame(filebin, ff, np);
+    };
+
+    char *readNextFrame(std::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;
+    };
+
+    char *readNextFrame(std::ifstream &filebin, int &ff, int &np,char *data) {
+        char *retval = 0;
+        int nd;
+        int fnum = -1;
+        np = 0;
+        int pn;
+
+        //  cout << dataSize << endl;
+        if (ff >= 0)
+            fnum = ff;
+
+        if (filebin.is_open()) {
+            if (filebin.read(data, dataSize)) {
+                ff = getFrameNumber(data);
+                np = getPacketNumber(data);
+                return data;
+            }
+        }
+        return NULL;
+    };
+
+    /*    Loops over a memory slot until a complete frame is found (i.e. all */
+    /*    packets 0 to nPackets, same frame number). purely virtual func \param */
+    /*    data pointer to the memory to be analyzed \param ndata reference to the */
+    /*    amount of data found for the frame, in case the frame is incomplete at */
+    /*    the end of the memory slot \param dsize size of the memory slot to be */
+    /*    analyzed \returns pointer to the beginning of the last good frame (might */
+    /*    be incomplete if ndata smaller than dataSize), or NULL if no frame is */
+    /*    found */
+
+    /* *\/ */
+    virtual char *findNextFrame(char *data, int &ndata, int dsize) {
+        if (dsize < dataSize)
+            ndata = dsize;
+        else
+            ndata = dataSize;
+        return data;
+    };
+
+    // int getPacketNumber(int x, int y) {return dataMap[y][x]/packetSize;};
+};
+
+#endif

slsDetectorCalibration/dataStructures/jungfrauModuleData.h

@@ -3,7 +3,6 @@
 #ifndef JUNGFRAUMODULEDATA_H
 #define JUNGFRAUMODULEDATA_H
 #include "slsDetectorData.h"
-#include "sls/sls_detector_defs.h"
 
 //#define VERSION_V2
 /**
@@ -42,15 +41,8 @@ class jungfrauModuleData : public slsDetectorData<uint16_t> {
        1286 large etc.) \param c crosstalk parameter for the output buffer
 
    */
-   
-#ifdef ALDO //VH
-    using header = jf_header; //VH
-#else //VH
-    using header = sls::defs::sls_receiver_header;
-#endif //VH
-
 #ifndef ZMQ
-#define off sizeof(header)
+#define off sizeof(jf_header)
 #endif
 #ifdef ZMQ
 #define off 0
@@ -110,13 +102,9 @@ class jungfrauModuleData : public slsDetectorData<uint16_t> {
     /* 	unsigned char frameNumber[3]; */
     /* 	unsigned char bunchid[8]; */
     /* }; */
-    
+
     int getFrameNumber(char *buff) {
-    #ifdef ALDO
-    return ((header *)buff)->bunchNumber; 
-    #else 
-    return ((header *)buff)->detHeader.frameNumber;
-    #endif 
+        return ((jf_header *)buff)->bunchNumber;
     };
   
     /**

slsDetectorCalibration/dataStructures/moench04CtbZmq10GbData.h

@@ -54,28 +54,28 @@ class moench04CtbZmq10GbData : public slsDetectorData<uint16_t> {
 #endif
 #endif
 
-      cout << "off is " << off << endl;
+    cout << "off is " << off << endl;
 	  
-	  if (off>0)
+	if (off>0)
 	    cout << "M04 RAW DATA NEW " << endl;
-	  else
+	else
 	    cout << "M04 ZMQ DATA NEW " << endl;
 	    
-            int adc_nr[32] = {9,  8,  11, 10, 13, 12, 15, 14, 1,  0,  3,
-                              2,  5,  4,  7,  6,  23, 22, 21, 20, 19, 18,
-                              17, 16, 31, 30, 29, 28, 27, 26, 25, 24};
+    int adc_nr[32] = {9,  8,  11, 10, 13, 12, 15, 14, 1,  0,  3,
+                        2,  5,  4,  7,  6,  23, 22, 21, 20, 19, 18,
+                        17, 16, 31, 30, 29, 28, 27, 26, 25, 24};
 
-           
+    
 
-            int row, col;
+    int row, col;
 
-            // int isample;
-            int iadc;
-            // int ix, iy;
+    // int isample;
+    int iadc;
+    // int ix, iy;
 
-            // int npackets=40;
-            int i;
-            // int adc4(0);
+    // int npackets=40;
+    int i;
+    // int adc4(0);
 
             for (int is = 0; is < aSamples; is++) {
 

slsDetectorCalibration/dataStructures/slsDetectorData.h

@@ -12,8 +12,7 @@ template <class dataType> 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) */
@@ -25,6 +24,9 @@ template <class dataType> class slsDetectorData {
     int isOrdered;
 
   public:
+
+    int **dataMap; /**< Array of size nx*ny storing the pointers to the data in
+                      the dataset (as offset)*/
     /**
     General slsDetectors data structure. Works for data acquired using the
     slsDetectorReceiver. Can be generalized to other detectors (many virtual
@@ -196,19 +198,18 @@ template <typename dataType> slsDetectorData<dataType>::~slsDetectorData() {
 template <typename dataType>
 void slsDetectorData<dataType>::setDataMap(int **dMap) {
 
-    int ip = 0;
-    int ix, iy;
+    // int ip = 0;
     if (dMap == NULL) {
-        for (iy = 0; iy < ny; iy++) {
-            for (ix = 0; ix < nx; ix++) {
+        for (int iy = 0; iy < ny; iy++) {
+            for (int ix = 0; ix < nx; ix++) {
                 dataMap[iy][ix] = (iy * nx + ix) * sizeof(dataType);
             }
         }
     } else {
         // cout << "set dmap "<< dataMap << " " << dMap << endl;
-        for (iy = 0; iy < ny; iy++) {
+        for (int iy = 0; iy < ny; iy++) {
             // cout << iy << endl;
-            for (ix = 0; ix < nx; ix++) {
+            for (int ix = 0; ix < nx; ix++) {
                 dataMap[iy][ix] = dMap[iy][ix];
                 // cout << ix << " " << iy << endl;
                 /*ip=dataMap[ix][iy]/sizeof(dataType);
@@ -218,8 +219,8 @@ void slsDetectorData<dataType>::setDataMap(int **dMap) {
         }
     }
     /* //commented this part because it causes out-of-bound issues if nx or ny are larger than dataMap bounds (single-chip readout of strixel with groups of different pitches) VH 2023-02-24
-    for (iy = 0; iy < ny; iy++) {
-        for (ix = 0; ix < nx; ix++) {
+    for (int iy = 0; iy < ny; iy++) {
+        for (int ix = 0; ix < nx; ix++) {
             ip = dataMap[iy][ix] / sizeof(dataType);
             xmap[ip] = ix;
             ymap[ip] = iy;
@@ -291,7 +292,6 @@ template <typename dataType>
 dataType **slsDetectorData<dataType>::getData(char *ptr, int dsize) {
     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];
@@ -301,6 +301,7 @@ dataType **slsDetectorData<dataType>::getData(char *ptr, int dsize) {
         dsize = dataSize;
 
     for (int ip = 0; ip < (el); ip++) {
+        int ix, iy;
         getPixel(ip, ix, iy);
         if (ix >= 0 && ix < nx && iy >= 0 && iy < ny) {
             // data[iy][ix]=getChannel(ptr,ix,iy);

slsDetectorCalibration/interpolations/eta2InterpolationBase.h

@@ -23,7 +23,7 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
               /* if (etamin>=etamax) { */
               /*   etamin=-1; */
               /*   etamax=2;  */
-              /*   //  cout << ":" <<endl; */
+              /*   //  std::cout << ":" <<endl; */
               /* } */
               /* etastep=(etamax-etamin)/nbeta; */
 
@@ -164,7 +164,7 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
             dY = -1.;
             break;
         default:
-            cout << "bad quadrant" << endl;
+            std::cout << "bad quadrant" << std::endl;
             dX = 0.;
             dY = 0.;
         }
@@ -174,19 +174,19 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
             ex = (etax - etamin) / etastepX;
             ey = (etay - etamin) / etastepY;
             if (ex < 0) {
-                cout << "x*" << ex << endl;
+                std::cout << "x*" << ex << std::endl;
                 ex = 0;
             }
             if (ex >= nbetaX) {
-                cout << "x?" << ex << endl;
+                std::cout << "x?" << ex << std::endl;
                 ex = nbetaX - 1;
             }
             if (ey < 0) {
-                cout << "y*" << ey << " " << nbetaY << endl;
+                std::cout << "y*" << ey << " " << nbetaY << std::endl;
                 ey = 0;
             }
             if (ey >= nbetaY) {
-                cout << "y?" << ey << " " << nbetaY << endl;
+                std::cout << "y?" << ey << " " << nbetaY << std::endl;
                 ey = nbetaY - 1;
             }
 
@@ -236,7 +236,7 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
         // calcMyEta(totquad,quad,cl,etax, etay);
         calcEta(totquad, cc, etax, etay);
 
-        //     cout <<"******"<< etax << " " << etay << endl;
+        //     std::cout <<"******"<< etax << " " << etay << std::endl;
 
         return addToFlatFieldDistribution(etax, etay);
     }
@@ -270,16 +270,16 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
     /*     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;  *\/ */
+    /*     /\* std::cout << cl[0] << " " << cl[1] << " " << cl[2] << std::endl;   *\/ */
+    /*     /\* std::cout << cl[3] << " " << cl[4] << " " << cl[5] << std::endl;   *\/ */
+    /*     /\* std::cout << cl[6] << " " << cl[7] << " " << cl[8] << std::endl;   *\/ */
+    /*     /\* std::cout <<"******"<<totquad << " " << quad << std::endl;  *\/ */
+    /*     /\* std::cout << cc[0][0]<< " " << cc[0][1] << std::endl;  *\/ */
+    /*     /\* std::cout << cc[1][0]<< " " << cc[1][1] << std::endl;  *\/ */
     /*     // calcMyEta(totquad,quad,cl,etax, etay); */
     /*     calcEta(totquad, cc, etax, etay); */
 
-    /*     //     cout <<"******"<< etax << " " << etay << endl; */
+    /*     //     std::cout <<"******"<< etax << " " << etay << std::endl; */
 
     /*     return addToFlatFieldDistribution(etax, etay); */
     /* } */
@@ -331,7 +331,7 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
 
     virtual int *getInterpolatedImage() {
         int ipx, ipy;
-        // cout << "ff" << endl;
+        // std::cout << "ff" << std::endl;
         calcDiff(1, hhx, hhy); // get flat
         double avg = 0;
         for (ipx = 0; ipx < nSubPixelsX; ipx++)
@@ -347,8 +347,8 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
                 ipy = iby % nSubPixelsY - nSubPixelsY / 2;
                 if (ipy < 0)
                     ipy = nSubPixelsY + ipy;
-                // cout << ipx << " " << ipy << " " << ibx << " " << iby <<
-                // endl;
+                // std::cout << ipx << " " << ipy << " " << ibx << " " << iby <<
+                // std::endl;
                 if (flat[ipx + ipy * nSubPixelsX] > 0)
                     hintcorr[ibx + iby * nSubPixelsX * nPixelsX] =
                         hint[ibx + iby * nSubPixelsX * nPixelsX] *

slsDetectorCalibration/interpolations/etaInterpolationBase.h

@@ -21,14 +21,14 @@ class etaInterpolationBase : public slsInterpolation {
                          double emax = 0)
         : slsInterpolation(nx, ny, ns, nsy), hhx(NULL), hhy(NULL), heta(NULL),
           nbetaX(nb), nbetaY(nby), etamin(emin), etamax(emax) {
-        // cout << "eb " << nb << " " << emin << " " << emax << endl;
-        // cout << nb << " " << etamin << " " << etamax << endl;
+        // std::cout << "eb " << nb << " " << emin << " " << emax << std::endl;
+        // std::cout << nb << " " << etamin << " " << etamax << std::endl;
         if (nbetaX <= 0) {
-            // cout << "aaa:" <<endl;
+            // std::cout << "aaa:" <<endl;
             nbetaX = nSubPixelsX * 10;
         }
         if (nbetaY <= 0) {
-            // cout << "aaa:" <<endl;
+            // std::cout << "aaa:" <<endl;
             nbetaY = nSubPixelsY * 10;
         }
         if (etamin >= etamax) {
@@ -145,9 +145,9 @@ class etaInterpolationBase : public slsInterpolation {
         uint32_t nny;
         float *gm = ReadFromTiff(imgname, nnx, nny);
         /* if (nnx!=nny) { */
-        /*   cout << "different number of bins in x " << nnx << "  and y " <<
-         * nny<< " !"<< endl; */
-        /*   cout << "Aborting read"<< endl; */
+        /*   std::cout << "different number of bins in x " << nnx << "  and y " <<
+         * nny<< " !"<< std::endl; */
+        /*   std::cout << "Aborting read"<< std::endl; */
         /*   return 0; */
         /* } */
         nbetaX = nnx;
@@ -254,12 +254,12 @@ class etaInterpolationBase : public slsInterpolation {
             if (ibx >= 0 && ibx < nSubPixelsX && iby >= 0 &&
                 iby < nSubPixelsY) {
                 //
-                // if (ibx>0 && iby>0) cout << ibx << " " << iby << " " << ii <<
-                // endl;
+                // if (ibx>0 && iby>0) std::cout << ibx << " " << iby << " " << ii <<
+                // std::endl;
                 ftest[ibx + iby * nSubPixelsX] += heta[ii];
             } else
-                cout << "Bad interpolation " << ii << " " << ibx << " " << iby
-                     << endl;
+                std::cout << "Bad interpolation " << ii << " " << ibx << " " << iby
+                     << std::endl;
         }
 
         sprintf(tit, "/scratch/ftest_%d.tiff", ind);
@@ -282,7 +282,7 @@ class etaInterpolationBase : public slsInterpolation {
         }
         sprintf(tit, "/scratch/eta_bad_%d.tiff", ind);
         WriteToTiff(etah, tit, nbetaX, nbetaY);
-        // cout << "Index: " << ind << "\t Bad bins: "<< nbad << endl;
+        // std::cout << "Index: " << ind << "\t Bad bins: "<< nbad << std::endl;
         // int ibx=0, iby=0;
 
         delete[] ftest;
@@ -330,9 +330,9 @@ class etaInterpolationBase : public slsInterpolation {
             }
         }
 
-        //  cout << endl << endl;
+        //  std::cout << std::endl << std::endl;
         for (ipy = 0; ipy < nSubPixelsY; ipy++) {
-            cout.width(5);
+            std::cout.width(5);
             // flat_y[ipy]=p_tot_y[ipy];//avg/nSubPixels;
             for (ipx = 0; ipx < nSubPixelsX; ipx++) {
 
@@ -353,19 +353,19 @@ class etaInterpolationBase : public slsInterpolation {
                 //"   ";
             }
 
-            /* cout << "** "  << setprecision(4) <<  flat_y[ipy]; */
-            // cout << "\n";
+            /* std::cout << "** "  << setprecision(4) <<  flat_y[ipy]; */
+            // std::cout << "\n";
         }
-        /* cout << "**" << endl; cout.width(5); */
+        /* std::cout << "**" << std::endl; std::cout.width(5); */
         /* for (ipx=0; ipx<nSubPixels; ipx++) { */
-        /*   cout  << setprecision(4) <<  flat_x[ipx] << " "; */
+        /*   std::cout  << setprecision(4) <<  flat_x[ipx] << " "; */
         /* } */
-        // cout << "**" << endl; cout.width(5);
-        // cout << "Min diff: " << mindiff/sqrt(avg) << " Max diff: " <<
-        // maxdiff/sqrt(avg) << " Nbad: " << nbad << endl;
+        // std::cout << "**" << std::endl; std::cout.width(5);
+        // std::cout << "Min diff: " << mindiff/sqrt(avg) << " Max diff: " <<
+        // maxdiff/sqrt(avg) << " Nbad: " << nbad << std::endl;
 
-        //   cout << "Bad pixels: " <<
-        //   100.*(float)nbad/((float)(nSubPixels*nSubPixels)) << " %" << endl;
+        //   std::cout << "Bad pixels: " <<
+        //   100.*(float)nbad/((float)(nSubPixels*nSubPixels)) << " %" << std::endl;
         delete[] p_tot_x;
         delete[] p_tot_y;
         delete[] p_tot;

slsDetectorCalibration/interpolations/etaInterpolationPosXY.h

@@ -14,8 +14,8 @@ class etaInterpolationPosXY : public virtual etaInterpolationBase {
                           int nb = -1, int nby = -1, double emin = 1,
                           double emax = 0)
         : etaInterpolationBase(nx, ny, ns, nsy, nb, nby, emin, emax){
-              //  cout << "epxy " << nb << " " << emin << " " << emax << endl;
-              //  cout << nbeta << " " << etamin << " " << etamax << endl;
+              //  std::cout << "epxy " << nb << " " << emin << " " << emax << std::endl;
+              //  std::cout << nbeta << " " << etamin << " " << etamax << std::endl;
           };
 
     etaInterpolationPosXY(etaInterpolationPosXY *orig)
@@ -32,14 +32,14 @@ class etaInterpolationPosXY : public virtual etaInterpolationBase {
 
         ///*Eta Distribution Rebinning*///
         // double bsize=1./nSubPixels; //precision
-        // cout<<"nPixelsX = "<<nPixelsX<<" nPixelsY = "<<nPixelsY<<" nSubPixels
+        // std::cout<<"nPixelsX = "<<nPixelsX<<" nPixelsY = "<<nPixelsY<<" nSubPixels
         // = "<<nSubPixels<<endl;
         double tot_eta = 0;
         double tot_eta_x = 0;
         double tot_eta_y = 0;
         for (int ip = 0; ip < nbetaX * nbetaY; ip++)
             tot_eta += heta[ip];
-        cout << "total eta entries is :" << tot_eta << endl;
+        std::cout << "total eta entries is :" << tot_eta << std::endl;
         if (tot_eta <= 0) {
             ok = 0;
             return;
@@ -57,7 +57,7 @@ class etaInterpolationPosXY : public virtual etaInterpolationBase {
 
             for (int iby = 0; iby < nbetaY; iby++) {
                 etay = etamin + iby * etastepY;
-                // cout << etax << endl;
+                // std::cout << etax << std::endl;
 
                 // tot_eta_x+=hx[iby];
                 if (etay >= 0 && etay <= 1)
@@ -90,7 +90,7 @@ class etaInterpolationPosXY : public virtual etaInterpolationBase {
 
             for (int ibx = 0; ibx < nbetaX; ibx++) {
                 etax = etamin + ibx * etastepX;
-                // cout << etax << endl;
+                // std::cout << etax << std::endl;
                 if (etax >= 0 && etax <= 1)
                     hx[ibx] = heta[ibx + ib * nbetaX];
                 else {
@@ -178,7 +178,7 @@ class eta2InterpolationPosXY : public virtual eta2InterpolationBase,
         : etaInterpolationBase(nx, ny, ns, nsy, nb, nby, emin, emax),
           eta2InterpolationBase(nx, ny, ns, nsy, nb, nby, emin, emax),
           etaInterpolationPosXY(nx, ny, ns, nsy, nb, nby, emin, emax){
-              //  cout << "e2pxy " << nb << " " << emin << " " << emax << endl;
+              //  std::cout << "e2pxy " << nb << " " << emin << " " << emax << std::endl;
           };
 
     eta2InterpolationPosXY(eta2InterpolationPosXY *orig)
@@ -198,8 +198,8 @@ class eta3InterpolationPosXY : public virtual eta3InterpolationBase,
         : 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;
+              //   std::cout << "e3pxy " << nbeta << " " << etamin << " " << etamax
+              //   << " " << nSubPixels<< std::endl;
           };
 
     eta3InterpolationPosXY(eta3InterpolationPosXY *orig)

slsDetectorCalibration/interpolations/slsInterpolation.h

@@ -27,8 +27,6 @@ enum quadrant {
 //#ifdef MYROOT1
 //: public TObject
 //#endif
-using namespace std;
-
 class slsInterpolation {
 
   public:

slsDetectorCalibration/jungfrauCommonMode.h

@@ -1,58 +0,0 @@
-// SPDX-License-Identifier: LGPL-3.0-or-other
-// Copyright (C) 2021 Contributors to the SLS Detector Package
-#ifndef COMMONMODEJF_H
-#define COMMONMODEJF_H
-
-#include "commonModeSubtractionNew.h"
-
-class commonModeSubtractionSuperColumnJF : public commonModeSubtraction {
-  public:
-    commonModeSubtractionSuperColumnJF()
-        : commonModeSubtraction(32){};
-    virtual int getROI(int ix, int iy) { int top=iy/256; int sc=ix/64; return sc+top*16; };
-/*
-    virtual void addToCommonMode(double val, int ix = 0, int iy = 0) {
-            int iroi = getROI(ix, iy);
-            // cout << iy << " " << ix << " " << iroi ;
-            if (iroi >= 0 && iroi < nROI) {
-                mean[iroi] += val;
-                mean2[iroi] += val * val;
-                nCm[iroi]++;
-                if (nCm[iroi] > 64*256)
-                    std::cout << "Too many pixels added " << nCm[iroi] << std::endl;
-           
-        }
-    };
-*/
-    virtual commonModeSubtractionSuperColumnJF *Clone() {
-        return new commonModeSubtractionSuperColumnJF();
-    };
-};
-
-
-class commonModeSubtractionChip : public commonModeSubtraction {
-  public:
-    commonModeSubtractionChip()
-        : commonModeSubtraction(8){};
-    virtual int getROI(int ix, int iy) { int top=iy/256; int sc=ix/256; return sc+top*4; };
-/*
-    virtual void addToCommonMode(double val, int ix = 0, int iy = 0) {
-            int iroi = getROI(ix, iy);
-            // cout << iy << " " << ix << " " << iroi ;
-            if (iroi >= 0 && iroi < nROI) {
-                mean[iroi] += val;
-                mean2[iroi] += val * val;
-                nCm[iroi]++;
-                if (nCm[iroi] > 64*256)
-                    std::cout << "Too many pixels added " << nCm[iroi] << std::endl;
-           
-        }
-    };
-*/
-    virtual commonModeSubtractionChip *Clone() {
-        return new commonModeSubtractionChip();
-    };
-};
-
-
-#endif

slsDetectorCalibration/jungfrauExecutables/Makefile

@@ -0,0 +1 @@
+Makefile.zmqrootdisp

slsDetectorCalibration/jungfrauExecutables/Makefile.zmqrootdisp

@@ -18,7 +18,7 @@ LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++  -lzmq -pthread -lrt -ltiff   -O3
 
 default: onlinedisp_zmq
 
-onlinedisp_zmq: onlinedisp_zmq.cpp onlinedisp_zmq.h 
+onlinedisp_zmq: onlinedisp_zmq.cpp onlinedisp_zmq.h ../dataStructures/jungfrauLGADStrixelsData_new.h
 # flags from root-config --cflags --glibs
 	g++ -o onlinedisp_zmq onlinedisp_zmq.cpp  -I. -I$(ROOTSYS)/include -Wall -g -lm  -L. -lzmq -pthread -lrt -L$(ROOTSYS)/lib -lGui -lCore  -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix  -lPhysics -lMathCore -lThread -m64 $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) 
 

slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp

@@ -2,12 +2,8 @@
 // Copyright (C) 2021 Contributors to the SLS Detector Package
 //#include "sls/ansi.h"
 #include <iostream>
-
-//enable common mode subtraction
-#define CMS
-//disable common mode subtraction
-//#undef CMS
 #undef CORR
+
 #define C_GHOST 0.0004
 
 #define CM_ROWS 50
@@ -40,17 +36,15 @@
 #include <map>
 #include <stdio.h>
 #include <sys/stat.h>
-//#include "commonModeSubtractionNew.h"
-#include "jungfrauCommonMode.h"
 
 #include <ctime>
 using namespace std;
 
 int main(int argc, char *argv[]) {
 
-    if (argc < 6) {
+    if (argc < 5) {
         cout << "Usage is " << argv[0]
-             << " indir outdir fname(no extension) fextension csize [runmin] [runmax] [pedfile (raw or tiff)] [threshold]"
+             << "indir outdir fname(no extension) fextension [runmin] [runmax] [pedfile (raw or tiff)] [threshold] "
                 "[nframes] [xmin xmax ymin ymax] [gainmap]"
              << endl;
         cout << "threshold <0 means analog; threshold=0 means cluster finder; "
@@ -59,12 +53,11 @@ int main(int argc, char *argv[]) {
         cout << "nframes <0 means sum everything; nframes=0 means one file per "
                 "run; nframes>0 means one file every nframes"
              << endl;
-
         return 1;
     }
 
     int fifosize = 1000;
-    int nthreads = 1;
+    int nthreads = 10;
     int csize = 3; //3
     int nsigma = 5;
     int nped = 10000;
@@ -74,12 +67,10 @@ int main(int argc, char *argv[]) {
 
 #if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 && !defined JFSTRXCHIP6
 #ifndef MODULE
-    cout << "This is a JF single chip!" <<endl;
     jungfrauHighZSingleChipData *decoder = new jungfrauHighZSingleChipData();
     int nx = 256, ny = 256;
 #endif
 #ifdef MODULE
-    cout << "This is a JF module!" <<endl;
     jungfrauModuleData *decoder = new jungfrauModuleData();
     int nx = 1024, ny = 512;
 #endif
@@ -89,7 +80,7 @@ int main(int argc, char *argv[]) {
     cout << "Jungfrau strixel full module readout" << endl;
     jungfrauLGADStrixelsData *decoder = new jungfrauLGADStrixelsData();
     int nx = 1024/5, ny = 512*5;
-#endif 
+#endif
 #ifdef JFSTRXCHIP1
     std::cout << "Jungfrau strixel LGAD single chip 1" << std::endl;
     jungfrauLGADStrixelsDataSingleChip *decoder = new jungfrauLGADStrixelsDataSingleChip(1);
@@ -108,9 +99,20 @@ int main(int argc, char *argv[]) {
 
 
     decoder->getDetectorSize(nx, ny);
-    
+
+
+
+
+
     cout << "Detector size is " << nx << " " << ny << endl;
 
+
+
+
+
+
+
+
     double *gainmap = NULL;
     //float *gm;
 
@@ -122,48 +124,47 @@ int main(int argc, char *argv[]) {
     char *outdir = argv[2];
     char *fformat = argv[3];
     char *fext = argv[4];
-    sscanf(argv[5], "%d", &csize);
     int runmin = 0;
 
     // cout << "argc is " << argc << endl;
-    if (argc >= 7) {
-        runmin = atoi(argv[6]);
+    if (argc >= 6) {
+        runmin = atoi(argv[5]);
     }
 
     int runmax = runmin;
 
-    if (argc >= 8) {
-        runmax = atoi(argv[7]);
+    if (argc >= 7) {
+        runmax = atoi(argv[6]);
     }
 
     char *pedfile = NULL;
-    if (argc >= 9) {
-        pedfile = argv[8];
+    if (argc >= 8) {
+        pedfile = argv[7];
     }
     double thr = 0;
     double thr1 = 1;
 
-    if (argc >= 10) {
-        thr = atof(argv[9]);
+    if (argc >= 9) {
+        thr = atof(argv[8]);
     }
 
     int nframes = 0;
 
-    if (argc >= 11) {
-        nframes = atoi(argv[10]);
+    if (argc >= 10) {
+        nframes = atoi(argv[9]);
     }
 
     int xmin = 0, xmax = nx, ymin = 0, ymax = ny;
-    if (argc >= 15) {
-        xmin = atoi(argv[11]);
-        xmax = atoi(argv[12]);
-        ymin = atoi(argv[13]);
-        ymax = atoi(argv[14]);
+    if (argc >= 14) {
+        xmin = atoi(argv[10]);
+        xmax = atoi(argv[11]);
+        ymin = atoi(argv[12]);
+        ymax = atoi(argv[13]);
     }
 
     char *gainfname = NULL;
-    if (argc > 15) {
-        gainfname = argv[15];
+    if (argc > 14) {
+        gainfname = argv[14];
         cout << "Gain map file name is: " << gainfname << endl;
     }
 
@@ -187,13 +188,9 @@ int main(int argc, char *argv[]) {
     cout << "Nframes is " << nframes << endl;
 
     uint32_t nnx, nny;
-    commonModeSubtraction *cm = NULL;
-#ifdef CMS
-    cm = new commonModeSubtractionChip();//commonModeSubtraction(1,5);//commonModeSubtractionSuperColumnJF();
-    std::cout << "Enabled common mode subtraction" << std::endl;
-#endif
+
     singlePhotonDetector *filter = new singlePhotonDetector(
-        decoder, 3, nsigma, 1, cm, nped, 200, -1, -1, gainmap, NULL);
+        decoder, 3, nsigma, 1, NULL, nped, 200, -1, -1, gainmap, NULL);
 
     if (gainfname) {
 
@@ -253,14 +250,13 @@ int main(int argc, char *argv[]) {
     double *ped=new double[nx * ny];//, *ped1;
 
     int pos,pos1;
-    int ipixX=351, ipixY=331;
 
     if (pedfile) {
 
-      if (string(pedfile).find(".raw") != std::string::npos) {
+      if (string(pedfile).find(".dat") != std::string::npos) {
 	pos1=string(pedfile).rfind("/");
 	strcpy(froot,pedfile+pos1);
-	pos=string(froot).find(".raw");
+	pos=string(froot).find(".dat");
 	froot[pos]='\0';
       }
 
@@ -281,43 +277,19 @@ int main(int argc, char *argv[]) {
                 ff = -1;
                 while (decoder->readNextFrame(filebin, ff, np, buff)) {
 		  // if (np == 40) {
-		  // if ((ifr+1) % 100 == 0) {
-		  //   cout << " ****" << decoder->getValue(buff,20,20);// << endl;
-		  // }
+		  if ((ifr+1) % 100 == 0) {
+		    cout << " ****" << decoder->getValue(buff,20,20);// << endl;
+		  }
                         mt->pushData(buff);
-
-
-			// while (mt->isBusy()) 
-			//   ;
-			//if ((ifr+1) % 100 == 0)
-
-			// double pix=0,ped=0,sub=0,cmp=0, sub0=0;
-
-			// for (int ix=-1; ix<2; ix++) {
-			//   for (int iy=-1; iy<2; iy++) {
-			//     pix+=decoder->getValue(buff, ipixX+ix, ipixY+iy);
-			//     sub+=filter->subtractPedestal(buff, ipixX+ix, ipixY+iy, 1);
-			//     sub0+=filter->subtractPedestal(buff, ipixX+ix, ipixY+iy, 0);
-			//     ped+=filter->getPedestal(ipixX+ix, ipixY+iy);
-			//     cmp+=filter->getCommonMode(ipixX+ix, ipixY+iy);
-			//   }
-			// }
-
-			// cout << pix << " " << sub << " " sub0 << " " << ped << " " << cmp  << endl;
-
-
                         mt->nextThread();
                         mt->popFree(buff);
                         ifr++;
-                        // if (ifr % 100 == 0) {
-			//   cout << " ****" << ifr << " " << ff << " " << np << endl;
-			// } 
-
-			//else
+                        if (ifr % 100 == 0) {
+			  cout << " ****" << ifr << " " << ff << " " << np << endl;
+			} //else
                         //cout << ifr << " " << ff << " " << np << endl;
-			// if (ifr>=1000)
-			//   break;
-			
+			if (ifr>=1000)
+			  break;
                     ff = -1;
                 }
                 filebin.close();
@@ -398,25 +370,7 @@ int main(int argc, char *argv[]) {
 		  if ((ifr+1) % 100 == 0) {
 		    cout << " ****" << decoder->getValue(buff,20,20);// << endl;
 		  }
-                    mt->pushData(buff);	
-
-
-		    // while (mt->isBusy()) 
-
-			// double pix=0,ped=0,sub=0,cmp=0, sub0=0;
-
-			// for (int ix=-1; ix<2; ix++) {
-			//   for (int iy=-1; iy<2; iy++) {
-			//     pix+=decoder->getValue(buff, ipixX+ix, ipixY+iy);
-			//     sub+=filter->subtractPedestal(buff, ipixX+ix, ipixY+iy, 1);
-			//     sub0+=filter->subtractPedestal(buff, ipixX+ix, ipixY+iy, 0);
-			//     ped+=filter->getPedestal(ipixX+ix, ipixY+iy);
-			//     cmp+=filter->getCommonMode(ipixX+ix, ipixY+iy);
-			//   }
-			// }
-
-			// cout << pix << " " << sub << " " sub0 << " " << ped << " " << cmp  << endl;
-
+                    mt->pushData(buff);
                     // 	//         //pop
                     mt->nextThread();
                     mt->popFree(buff);

slsDetectorCalibration/jungfrauExecutables/onlinedisp_zmq.cpp

@@ -7,17 +7,23 @@ sls::zmqHeader zHeader;
 #define NPRO 50
 #define NPRI 50
 
-//#define JFSTRX
+#define JFSTRX
 #ifdef JFSTRX
-#include "jungfrauLGADStrixelsData.h"
-#else
-#include "jungfrauModuleData.h"
+#include "jungfrauLGADStrixelsData_new.h"
+#include "sls/sls_detector_defs.h"
+#include "slsDetectorData.h"
+using header = sls::defs::sls_receiver_header;
 #endif
 
 
-
 int main(int argc, char* argv[]) 
 {
+
+
+
+
+
+
   goout=1;
   hasallpede=false;
   dophotonmap=true;  if ((argc<3)) {printf("USAGE: command photon_energy_(peakinADC) [rx_ip]  [port] \n"); return -1  ;}
@@ -43,9 +49,19 @@ int main(int argc, char* argv[])
 #ifdef JFSTRX
     cout << "JFSTRX" << endl;
     jungfrauLGADStrixelsData *decoder = new jungfrauLGADStrixelsData();
-    nx = 1024/5; ny= 512*5;
+
+    decoder->getDetectorSize(nx,ny);
+
+    
+    
+
+    cout<<    decoder->dataMap[22][22] <<endl;
+
+
 #else
     nx = 1024; ny= 512;
+
+
 #endif
 
 
@@ -57,7 +73,7 @@ int main(int argc, char* argv[])
  
   HDraw_every=20;
   fixranges=false;
-
+  int group;
   
   hchptr = (short*) malloc(NCH*sizeof(short)); 
 
@@ -80,29 +96,85 @@ int main(int argc, char* argv[])
   char hname[100];
 
 
+#ifdef JFSTRX
+  int nxx=79; int nyy=165;
+  his1000= new TH2F("his1000","2d, chip 1 group 1 (25um) pede corr.",nxx,-0.5,nxx-0.5,nyy,-0.5,nyy-0.5);
+  his1060= new TH2F("his1060","2d,  chip 6 group 1 (25um) pede corr.",nxx,-0.5,nxx-0.5,nyy,-0.5,nyy-0.5);
+  nxx=47; nyy=320; //320;
+  his1001= new TH2F("his1001","2d, chip 1 group 2 (15um) pede corr.",nxx,-0.5,nxx-0.5,nyy,-0.5,nyy-0.5);
+  his1061= new TH2F("his1061","2d, chip 6 group 2 (15um) pede corr.",nxx,-0.5,nxx-0.5,nyy,-0.5,nyy-0.5);
+  nxx=59; nyy=476; //476;
+  his1002= new TH2F("his1002","2d, chip 1 group 3 (18.75um) pede corr.",nxx,-0.5,nxx-0.5,nyy,-0.5,nyy-0.5);
+  his1062= new TH2F("his1002","2d, chip 6 group 3 (18.75um) pede corr.",nxx,-0.5,nxx-0.5,nyy,-0.5,nyy-0.5);
 
+  his1000->SetOption("colz");
+  his1001->SetOption("colz");
+  his1002->SetOption("colz");
+  his1060->SetOption("colz");
+  his1061->SetOption("colz");
+  his1062->SetOption("colz");
+
+#else
   his1000= new TH2F("his1000","2d , ev. pede corrected",nx,-0.5,nx-0.5,ny,-0.5,ny-0.5);
   his1000->SetOption("colz");
+#endif
+
   his2000= new TH2F("his2000","2d gain ",nx,-0.5,nx-0.5,ny,-0.5,ny-0.5);
   his2000->GetZaxis()->SetRangeUser(0,4);
 
   if (dophotonmap) {
-    his3000= new TH2F("his3000"," photon map  ",nx,-0.5,nx-0.5,ny,-0.5,ny-0.5);
+    his3000= new TH2F("his3000"," photon map  ",1024,-0.5,1024-0.5,512,-0.5,512-0.5);
   }
   else {
-    his3000= new TH2F("his3000"," raw adc  ",nx,-0.5,nx-0.5,ny,-0.5,ny-0.5);
+    his3000= new TH2F("his3000"," raw adc  ",1024,-0.5,1024-0.5,512,-0.5,512-0.5);
   }
  
-  his4500= new TH2F("his45000","L vs R",101,-50,500,101,-50,500);
+  his4500= new TH2F("his4500","T vs B",101,-500,MAX_POS,101,-500,MAX_POS);
   hchip=new TH1I*[8];
+#ifdef JFSTRX
+  for (i=0;i<8;i++) {
+    if(i<3)
+      sprintf(hname,"%d_hchip1group%d",i,i+1);
+    else if (i>4)
+      sprintf(hname,"%d_hchip6group%d",i, i-4);
+    else
+      sprintf(hname,"%d_",i);
+    hchip[i] = new TH1I(hname,hname,NBIN,MIN_POS,MAX_POS);
+  }
+#else
   for (i=0;i<8;i++) {
     sprintf(hname,"hchip%d",i);
     hchip[i] = new TH1I(hname,hname,NBIN,MIN_POS,MAX_POS);
   }
+#endif
 
   cout <<"end of histo booking" <<endl;
   if  (A2==NULL)  A2 = new TCanvas("A2","Plotting Canvas gain",150,10,500,250);
-  if  (A3==NULL)  A3 = new TCanvas("A3","Plotting Canvas ADC",150,360,1200,550);
+  if  (A3==NULL)  {
+#ifdef JFSTRX
+    A3 = new TCanvas("A3","Plotting Canvas ADC",150,360,1200,750);
+    p1 = new TPad("p1","p1",0.01,0.5,0.49,1.);
+    p1->Draw();
+    p2 = new TPad("p2","p2",0.51,0.75,0.99,0.97);
+    p2->Draw();
+    p3 = new TPad("p3","p3",0.01,0.25,0.49,0.47);
+    p3->Draw();
+    p4 = new TPad("p4","p4",0.51,0.53,0.99,0.75);
+    p4->Draw();
+    p5 = new TPad("p5","p5",0.01,0.03,0.49,0.25);
+    p5->Draw();
+    p6 = new TPad("p6","p6",0.51,0.,0.99,0.5);
+    p6->Draw();
+    //A3->Divide(2,3);
+
+    // TVirtualPad* g=A3->cd(1);
+    // g->SetCanvasSize( g->GetWw(), 2*g->GetWw());
+    //  g=A3->cd(6);
+    // g->SetCanvasSize( g->GetWw(), 2*g->GetWw());
+#else
+    A3 = new TCanvas("A3","Plotting Canvas ADC",150,360,1200,550);
+#endif
+    }
   if  (A4==NULL)  A4 = new TCanvas("A4","Plotting Canvas PHs",750,300,1000,800);
   A4->Clear();
   A4->Divide(4,2,0.005,0.005);
@@ -131,7 +203,14 @@ int main(int argc, char* argv[])
     }
 
     {
-
+     
+       
+      memcpy(&croi, &zHeader.detSpec1, 8);  
+      ROIxmin=croi.xmin;
+      ROIxmax=croi.xmax;
+      ROIymin=croi.ymin;
+      ROIymax=croi.ymax;
+      cout<<" ROIymin "<<  ROIymin<<endl;
       framesinstream++;
       running++;
      
@@ -143,7 +222,19 @@ int main(int argc, char* argv[])
  
       npacket=0;
       if  (show2Ds)  {
+#ifdef JFSTRX
 	his1000->Reset(); 
+	his1001->Reset(); 
+	his1002->Reset();
+	his1060->Reset(); 
+	his1061->Reset(); 
+	his1062->Reset();
+#else
+
+	his1000->Reset(); 
+#endif
+
+
 	his2000->Reset(); 
 	if (!dophotonmap) his3000->Reset(); //FOR RAW ADC DISPLAY 
       }
@@ -187,10 +278,28 @@ int main(int argc, char* argv[])
 	  if (fill1Ds) {
 	    if (((i%1024)<1004)&&((i%1024)>20)&&((i/1024)>20)) { //skip the pix near guardring for PH plots
 	      ichip= i/(256*256*4)*4+((i/256)%4)  ;
-	   
+#ifdef JFSTRX
+	      int new_ichip=0;
+	      //exclude border rows of each group
+	      if (ichip==1) {
+		if (i<=(1024*(64-2))) new_ichip=0; //chip 1 group 1
+		if (i>(1024*(64+6))&&(i<=(1024*(64*2-4)))) new_ichip=1; //chip 1 group 2
+		if (i>(1024*(64*2+5))) new_ichip=2; //chip 1 group 3
+	      }
+
+	      if (ichip==6) {
+		if (i<=(1024*(256+2*64-5))) new_ichip=7; //chip 6 group 3
+		if (i>(1024*(256+2*64+4))&&(i<=(1024*(256+64*3-6)))) new_ichip=6; //chip 6 group 2
+		if (i>(1024*(256+64*3-4))) new_ichip=5; //chip 6 group 1
+	      }
+
+	      hchip[new_ichip]->Fill(adcpedecorr,1);
+
+#else	   
 	      hchip[ichip]->Fill(adcpedecorr,1);
+#endif
 	    
-	      if (((i%256)<253)&&((i%256)>2)) his4500->Fill(adcpedecorrold,adcpedecorr,1);
+	      //	      if (((i%256)<253)&&((i%256)>2)) his4500->Fill(adcpedecorrold,adcpedecorr,1);
 	      adcpedecorrold=adcpedecorr;
 	    
 	    
@@ -200,33 +309,110 @@ int main(int argc, char* argv[])
 
 	
 
-	  if ((show2Ds)) {
-	    factor=2.0;
-	    value=adcpedecorr;
-	    if ((i%256==0)||(i%256==255)) value=int(value/factor);
-	    if ((i/1024==255)||(i/1024==256)||(i/1024==767)||(i/1024==768)) value=int(value/factor);
-
-	    his1000->Fill(float(i%1024),float(int (i/1024)),value);
-
-	    if (!dophotonmap) his3000->Fill(float(i%1024),float(int (i/1024)) ,adcvalue);
 	  
-	    his2000->Fill(float(i%1024),float(int (i/1024)) ,gain);
-
-	    value=(int)(hchptr[i]);
-	 
-	    if ((i%256==0)||(i%256==255)) value=int(value/factor);
-	    if ((i/1024==255)||(i/1024==256)||(i/1024==767)||(i/1024==768)) value=int(value/factor);
-	    if (dophotonmap) his3000->Fill(float(i%1024),float(int (i/1024)),float(value));
-
-	  }
 	}//   for (i=0 ;i<NCH-0;i++)
+
+
+	if ((show2Ds)) {
+	  for (ipx=0;ipx<nx;ipx++){
+	    for (ipy=0;ipy<ny;ipy++){
+	    // for (ipx=0;ipx<nx;ipx++){
+#ifdef JFSTRX
+
+	      //cout<<i<< " cdcsdcvsvcsc  " << group << "  " << (decoder->dataMap[ipy][ipx])/2 << endl; 
+	      i=int (((decoder->dataMap[ipy][ipx])-sizeof(header)) /2);
+	      group=(decoder->groupmap[ipy][ipx]);
+	     
+	      //     cout<<i<< "  "<<ipx<<"  "<<ipy<< "  " << group <<endl; 
+
+  
+
+
+#else	      
+	      i=ipx+ipy*1024;
+#endif
+
+
+
+		value= ((image_data[i]) & 0x3fff) -fpeded[i];
+#ifndef JFSTRX
+		if ((i%256==0)||(i%256==255)) value=int(value/factor);
+		if ((i/1024==255)||(i/1024==256)||(i/1024==767)||(i/1024==768)) value=int(value/factor);
+#endif
+
+		//	        his1000->Fill(float(ipx),float(ipy),value);
+		//	if ((ipy>165)&&(ipy<320+165)){ his1000->Fill(float(ipx)*5/3.0,float(ipy),value);}
+		//	else  { his1000->Fill(float(ipx),float(ipy),value);}
+
+#ifdef JFSTRX
+		static const int mc1g1y_start = 0;
+		static const int mc1g2y_start = g1_nrows;
+		static const int mc1g3y_start = g1_nrows+g2_nrows;
+
+		static const int mc6g3y_start = g1_nrows+g2_nrows+g3_nrows;
+		static const int mc6g2y_start = mc6g3y_start + g3_nrows;
+		static const int mc6g1y_start = mc6g3y_start  + g3_nrows + g2_nrows;
+
+		if (group==0) {
+		  if (ipy<165){
+		    his1000->Fill(float(ipx),float(ipy-mc1g1y_start),value);}
+		  if (ipy>=mc6g1y_start){
+		    his1060->Fill(float(ipx),float(ipy-mc6g1y_start),value);}
+		}
+		if (group==1) {
+		  if (ipy<(165+320)){ 
+		    his1001->Fill(float(ipx),float(ipy-mc1g2y_start),value);}
+		  if ( (ipy>=mc6g2y_start) && (ipy<mc6g1y_start) ){his4500->Fill(value,oldvalue,1.0);
+		    oldvalue=value;
+		    his1061->Fill(float(ipx),float(ipy-mc6g2y_start),value);}
+		}
+		if (group==2) {
+		  if (ipy<(165+320+476))
+		    his1002->Fill(float(ipx),float(ipy-mc1g3y_start),value);
+		  if ( (ipy>=mc6g3y_start) && (ipy<mc6g2y_start) )
+		    his1062->Fill(float(ipx),float(ipy-mc6g3y_start),value);
+		}
+	 
+#else
+
+	his1000->Fill(float(ipx),float(ipy),value);
+	
+
+
+#endif
+
+	
+
+	his2000->Fill(float(ipx),float(ipy) ,gain);
+
+		// if (!dophotonmap)his3000->Fill(float(ipx),float(ipy) ,value);
+		// value=(int)(hchptr[i]);
+		// if (dophotonmap) his3000->Fill(float(ipx),float(ipy),float(value));
+		
+	    }// for ipx
+	  } //for ipy
+
+	  for (ipx=0;ipx<1024;ipx++){
+	    for (ipy=0;ipy<512;ipy++){
+	      i=ipx+ipy*1024;
+	      value= ((image_data[i]) & 0x3fff) -fpeded[i];
+	      if (!dophotonmap)his3000->Fill(float(ipx),float(ipy) ,value);
+	      value=(int)(hchptr[i]);
+	      if (dophotonmap) his3000->Fill(float(ipx),float(ipy),float(value));
+	    }
+	  }
+
+	}// endo of show2d 
+	   	  	  
+
+
       }// /end of do something 
    
 
 
       if   ((show2Ds)) {
 
-	for (ipx=0;ipx<NCH;ipx++) hchptr[(ipx)]=0;
+	for (i=0;i<NCH;i++) hchptr[(i)]=0;
 
 
 
@@ -419,10 +605,31 @@ void SetRanges() {
 
 void axisreset(){
   fixranges=false;
+#ifdef JFSTRX
+  his1000->GetXaxis()->UnZoom();
+  his1000->GetYaxis()->UnZoom();
+  his1000->GetZaxis()->UnZoom();
+  his1001->GetXaxis()->UnZoom();
+  his1001->GetYaxis()->UnZoom();
+  his1001->GetZaxis()->UnZoom();
+  his1002->GetXaxis()->UnZoom();
+  his1002->GetYaxis()->UnZoom();
+  his1002->GetZaxis()->UnZoom();
+  his1060->GetXaxis()->UnZoom();
+  his1060->GetYaxis()->UnZoom();
+  his1060->GetZaxis()->UnZoom();
+  his1061->GetXaxis()->UnZoom();
+  his1061->GetYaxis()->UnZoom();
+  his1061->GetZaxis()->UnZoom();
+  his1062->GetXaxis()->UnZoom();
+  his1062->GetYaxis()->UnZoom();
+  his1062->GetZaxis()->UnZoom();
+#else
   his1000->GetXaxis()->UnZoom();
 
   his1000->GetYaxis()->UnZoom();
   his1000->GetZaxis()->UnZoom();
+#endif
   his2000->GetXaxis()->UnZoom();
   his2000->GetYaxis()->UnZoom();
 
@@ -540,7 +747,6 @@ void Plot1DHistos(void){
 
 void Plot2DHistos(void){
   gStyle->SetOptStat(0);
-  A3->cd();
 
   //  if (bw_flag) LoadPaletteBW(1.0);
 
@@ -553,8 +759,24 @@ void Plot2DHistos(void){
   }
 
   his1000->SetMinimum(-200);
-  his1000->Draw();
 
+#ifdef JFSTRX
+  p5->cd();
+  his1000->Draw("colz");
+  p3->cd();
+  his1001->Draw("colz");
+  p1->cd();
+  his1002->Draw("colz");
+  p2->cd();
+  his1060->Draw("colz");
+  p4->cd();
+  his1061->Draw("colz");
+  p6->cd();
+  his1062->Draw("colz");
+#else
+  A3->cd();
+  his1000->Draw("colz");
+#endif
   A3->Update();
   A2->cd();
   // if (bw_flag)  LoadPaletteFalse();
@@ -565,9 +787,16 @@ void Plot2DHistos(void){
   A2->Update(); 
   A5->cd();
 
-  his3000->GetXaxis()->SetRange(his1000->GetXaxis()->GetFirst(),his1000->GetXaxis()->GetLast());
-  his3000->GetYaxis()->SetRange(his1000->GetYaxis()->GetFirst(),his1000->GetYaxis()->GetLast());
+  //his3000->GetXaxis()->SetRange(his1000->GetXaxis()->GetFirst(),his1000->GetXaxis()->GetLast());
+  //his3000->GetYaxis()->SetRange(his1000->GetYaxis()->GetFirst(),his1000->GetYaxis()->GetLast());
   his3000->Draw("colz");
+
+  box = new TBox(ROIxmin,ROIymin,ROIxmax,ROIymax);
+  box->SetLineColor(kRed);
+  
+  box->SetFillStyle(0);
+  box->SetLineWidth(2);
+  box->Draw();
   A5->Update();
  
   A6->cd();

slsDetectorCalibration/jungfrauExecutables/onlinedisp_zmq.h

@@ -56,6 +56,7 @@ using namespace sls;
 #include "TMath.h"
 #include "TFile.h"
 #include "TStyle.h"
+#include "TBox.h"
 #include "TSystem.h"
 #include "TTimer.h"
 #include "TProfile.h"
@@ -81,7 +82,7 @@ using namespace sls;
 #define OFFSET 0
 #define NBIN 500  
 #define MIN_POS  -500.5   // 400.5   
-#define MAX_POS 3499.5   //-100.5
+#define MAX_POS 8499.5   //-100.5
 
 
 #define NCH 524288
@@ -92,7 +93,7 @@ int portnum;
 FILE * sfilefd;
 
 short* hchptr; // photon counted map "histogram"
-int value;
+int value,oldvalue;
 float factor=1.84;
 int npacket=0;
 int totalnpacket=0;
@@ -105,6 +106,7 @@ struct hostent      *server;
  
 int i=0;
 int ipx=0;
+int ipy=0;
 bool haveconnection;
 
 
@@ -112,6 +114,12 @@ TStyle *gStyle;
 TApplication* rootapp;
 TCanvas *A2;
 TCanvas *A3;
+TPad *p1;
+TPad *p2;
+TPad *p3;
+TPad *p4;
+TPad *p5;
+TPad *p6;
 TCanvas *A4;
 TCanvas *A5;
 TCanvas *A6;
@@ -139,6 +147,18 @@ bool fill1Ds;
 bool pede_flag;
 bool dophotonmap;
 
+      typedef struct {
+        uint16_t xmin;
+     	uint16_t xmax;
+     	uint16_t ymin;
+     	uint16_t ymax;
+      } receriverRoi_compact;   
+     receriverRoi_compact croi;
+TBox *box;
+uint16_t ROIxmin;
+uint16_t ROIxmax;
+uint16_t ROIymin;
+uint16_t ROIymax;     
 int nx, ny;
 int nframes;
 int goout;
@@ -154,7 +174,8 @@ int frameIndex_old;
 char pedefilename[128];
 int  framenum,bunchid;
 
-TH2F* his1000;
+TH2F* his1000;TH2F* his1001;TH2F* his1002;
+TH2F* his1060;TH2F* his1061;TH2F* his1062;
 TH2F* his2000;
 TH2F* his3000;
 TH2F* his4500;

slsDetectorCalibration/moenchExecutables/moench03NoInterpolation.cpp

@@ -30,13 +30,14 @@ 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/moenchRawDataProcess.cpp

@@ -86,17 +86,10 @@ int main(int argc, char *argv[]) {
     
 #endif
 
-
-    int nx = 400, ny = 400;
-
+    //Read detector size from decoder
+    int nx , ny;
     decoder->getDetectorSize(nx, ny);
-#ifdef CORR
-    int ncol_cm = CM_ROWS;
-    double xt_ghost = C_GHOST;
-#endif
-    moench03CommonMode *cm = NULL;
-    moench03GhostSummation *gs;
-    double *gainmap = NULL;
+
     //float *gm;
 
     int ff, np;
@@ -171,8 +164,15 @@ int main(int argc, char *argv[]) {
 
     uint32_t nnx, nny;
 
+
+    moench03CommonMode *cm = nullptr;
+    moench03GhostSummation *gs = nullptr;
+    double *gainmap = nullptr;
+
 #ifdef CORR
-    cout << "Applying common mode  " << ncol_cm << endl;
+    int ncol_cm = CM_ROWS;
+    double xt_ghost = C_GHOST;
+    std::cout << "Applying common mode  " << ncol_cm << endl;
     cm = new moench03CommonMode(ncol_cm);
 
     // cout << "Applying ghost corrections " << xt_ghost << endl;

slsDetectorCalibration/singlePhotonDetector.h

@@ -396,14 +396,14 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
             return 0;
         }
         newFrame(data);
-	/*
+
         if (cmSub) {
             addToCommonMode(data);
             cm = 1;
         }
-	*/
+
         double *val = new double[ny * nx];
-	cm=0;
+
         for (iy = ymin; iy < ymax; ++iy) {
             for (ix = xmin; ix < xmax; ++ix) {
                 if (det->isGood(ix, iy) == 0)
@@ -547,50 +547,12 @@ class singlePhotonDetector : public analogDetector<uint16_t> {
 
                 } else if (ee == PEDESTAL) {
                     addToPedestal(data, ix, iy, cm);
-		    if (cmSub) {
-		      addToCommonMode(data, ix, iy);
-		    }
                 } /*else {
                     eventMask[iy][ix]=PHOTON;
                     }*/
                   // eventMask[iy][ix]=ee;
             }
         }
-	
-	if (cmSub) {
-	  
-	  double cmv=0;
-	  for (int iph=0; iph<nph; iph++) {
-	    ix=(clusters + iph)->x ;
-	    iy=(clusters + nph)->y;
-	    
-	    for (ir = -(clusterSizeY / 2); ir < (clusterSizeY / 2) + 1;
-		 ir++) {
-	      for (ic = -(clusterSize / 2);
-		   ic < (clusterSize / 2) + 1; ic++) {
-		if ((iy + ir) >= 0 && (iy + ir) < ny &&
-		    (ix + ic) >= 0 && (ix + ic) < nx) {
-		  
-		  cmv=getCommonMode(ix+ic, iy+ir);
-		  //if (ir==0 && ic==0)
-		    //cout << cmv << endl;
-		  (clusters + iph)
-		    ->set_data((clusters + iph)
-		    ->get_data(ic,ir)-cmv, ic,ir);
-		}
-		
-	      }
-	      
-	    }
-	    
-	  }
-	  
-	  
-	}
-	
-
-	
-
 
         nphFrame = nph;
         nphTot += nph;

slsDetectorCalibration/tiffio/src/tiffIO.cpp

@@ -3,8 +3,7 @@
 
 #include "sls/tiffIO.h"
 #include <iostream>
-#include "/usr/include/tiffio.h"
-//#include <tiffio.h>
+#include <tiffio.h>
 
 void *WriteToTiff(float *imgData, const char *imgname, int ncol, int nrow) {
     constexpr uint32_t sampleperpixel = 1;

slsDetectorServers/ctbDetectorServer/slsDetectorFunctionList.c

@@ -332,7 +332,7 @@ void getServerVersion(char *version) { strcpy(version, APICTB); }
 
 uint64_t getFirmwareVersion() {
 #ifdef VIRTUAL
-    return 0;
+    return REQRD_FRMWR_VRSN;
 #endif
     return ((bus_r(FPGA_VERSION_REG) & FPGA_VERSION_BRD_RVSN_MSK) >>
             FPGA_VERSION_BRD_RVSN_OFST);

slsDetectorServers/gotthard2DetectorServer/slsDetectorFunctionList.c

@@ -256,7 +256,7 @@ void getServerVersion(char *version) { strcpy(version, APIGOTTHARD2); }
 
 u_int64_t getFirmwareVersion() {
 #ifdef VIRTUAL
-    return 0;
+    return REQRD_FRMWRE_VRSN;
 #endif
     return ((bus_r(FPGA_VERSION_REG) & FPGA_COMPILATION_DATE_MSK) >>
             FPGA_COMPILATION_DATE_OFST);

slsDetectorServers/gotthardDetectorServer/slsDetectorFunctionList.c

@@ -275,7 +275,7 @@ void getServerVersion(char *version) { strcpy(version, APIGOTTHARD); }
 
 u_int64_t getFirmwareVersion() {
 #ifdef VIRTUAL
-    return 0;
+    return 1;
 #endif
     return ((bus_r(FPGA_VERSION_REG) & FPGA_VERSION_MSK) >> FPGA_VERSION_OFST);
 }

slsDetectorServers/jungfrauDetectorServer/slsDetectorFunctionList.c

@@ -266,7 +266,7 @@ void getServerVersion(char *version) { strcpy(version, APIJUNGFRAU); }
 
 u_int64_t getFirmwareVersion() {
 #ifdef VIRTUAL
-    return 0;
+    return REQRD_FRMWRE_VRSN;
 #endif
     return ((bus_r(FPGA_VERSION_REG) & FPGA_COMPILATION_DATE_MSK) >>
             FPGA_COMPILATION_DATE_OFST);

slsDetectorServers/moenchDetectorServer/slsDetectorFunctionList.c

@@ -270,7 +270,8 @@ void getServerVersion(char *version) { strcpy(version, APIMOENCH); }
 
 u_int64_t getFirmwareVersion() {
 #ifdef VIRTUAL
-    return 0;
+    return (isHardwareVersion_1_0() ? REQRD_FRMWRE_VRSN
+                                    : REQRD_FRMWRE_VRSN_BOARD2);
 #endif
     return ((bus_r(FPGA_VERSION_REG) & FPGA_COMPILATION_DATE_MSK) >>
             FPGA_COMPILATION_DATE_OFST);

slsDetectorServers/mythen3DetectorServer/slsDetectorFunctionList.c

@@ -250,7 +250,7 @@ void getServerVersion(char *version) { strcpy(version, APIMYTHEN3); }
 
 u_int64_t getFirmwareVersion() {
 #ifdef VIRTUAL
-    return 0;
+    return REQRD_FRMWRE_VRSN;
 #endif
     return ((bus_r(FPGA_VERSION_REG) & FPGA_COMPILATION_DATE_MSK) >>
             FPGA_COMPILATION_DATE_OFST);