Merge branch 'developer' into jf_json_rxroi

* jf pedestal fix: touch enable bit last

slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsData_new.h

@@ -28,6 +28,10 @@
     @li version is the version number of this structure format
 */
 
+#include <algorithm>
+#include <numeric>
+#include <tuple>
+
 namespace strixelSingleChip {
 constexpr int nc_rawimg = 1024; // for full images  //256;
 constexpr int nr_rawimg = 512;
@@ -77,7 +81,7 @@ constexpr int c6g1_ystart = c6g2_yend + 1;        // 448
 constexpr int c6g1_yend = c6g2_yend + 64 - gr;    // 502
 
 // y shift due to faulty bonding (relevant for M408)
-constexpr int bond_shift_y = 1; // CHANGE IF YOU CHANGE MODULE!
+constexpr int bond_shift_y = 0; // CHANGE IF YOU CHANGE MODULE!
 
 } // namespace strixelSingleChip
 
@@ -97,6 +101,13 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
     int chip_x0;
     int chip_y0;
     int x0, y0, x1, y1, shifty;
+    struct {
+      uint16_t xmin;
+      uint16_t xmax;
+      uint16_t ymin;
+      uint16_t ymax;
+      int nc;
+    } globalROI;
 
     int getMultiplicator(const int group) {
         int multiplicator;
@@ -215,9 +226,113 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
         }
     }
 
-    void remapROI(uint16_t xmin, uint16_t xmax, uint16_t ymin, uint16_t ymax) {
+
+    std::tuple< uint16_t, uint16_t, uint16_t, uint16_t > adjustROItoLimits(uint16_t xmin,
+									   uint16_t xmax,
+									   uint16_t ymin,
+									   uint16_t ymax,
+									   uint16_t lim_roi_xmin,
+									   uint16_t lim_roi_xmax,
+									   uint16_t lim_roi_ymin,
+									   uint16_t lim_roi_ymax) {
+      uint16_t xmin_roi, xmax_roi, ymin_roi, ymax_roi;
+      if ( xmin < lim_roi_xmin)
+        xmin_roi = lim_roi_xmin;
+      else
+        xmin_roi = xmin;
+      if ( xmax > lim_roi_xmax )
+        xmax_roi = lim_roi_xmax;
+      else
+        xmax_roi = xmax;
+      if ( ymin < lim_roi_ymin )
+        ymin_roi = lim_roi_ymin;
+      else
+        ymin_roi = ymin;
+      if ( ymax > lim_roi_ymax )
+        ymax_roi = lim_roi_ymax;
+      else
+        ymax_roi = ymax;
+      return std::make_tuple(xmin_roi, xmax_roi, ymin_roi, ymax_roi);
+    }
+
+    std::vector < std::tuple< int, int, uint16_t, uint16_t, uint16_t, uint16_t > > mapSubROIs(uint16_t xmin,
+											      uint16_t xmax,
+											      uint16_t ymin,
+											      uint16_t ymax) {
+      bool chip_1_1 = false;
+      bool chip_1_2 = false;
+      bool chip_1_3 = false;
+      bool chip_6_1 = false;
+      bool chip_6_2 = false;
+      bool chip_6_3 = false;
+
+      for ( int x=xmin; x!=xmax+1; ++x ) {
+	for ( int y=ymin; y!=ymax; ++y ) {
+	  if ( c1g1_xstart<=x && x<=c1_xend && (c1g1_ystart+bond_shift_y)<=y && y<=(c1g1_yend+bond_shift_y) )
+	    chip_1_1 = true;
+	  if ( c1g2_xstart<=x && x<=c1_xend && (c1g2_ystart+bond_shift_y)<=y && y<=(c1g2_yend+bond_shift_y) )
+	    chip_1_2 = true;
+	  if ( c1g3_xstart<=x && x<=c1_xend && (c1g3_ystart+bond_shift_y)<=y && y<=(c1g3_yend+bond_shift_y) )
+	    chip_1_3 = true;
+	  if ( c6_xstart<=x && x<=c6g1_xend && (c6g1_ystart-bond_shift_y)<=y && y<=(c6g1_yend-bond_shift_y) )
+	    chip_6_1 = true;
+	  if ( c6_xstart<=x && x<=c6g2_xend && (c6g2_ystart-bond_shift_y)<=y && y<=(c6g2_yend-bond_shift_y) )
+	    chip_6_2 = true;
+	  if ( c6_xstart<=x && x<=c6g3_xend && (c6g3_ystart-bond_shift_y)<=y && y<=(c6g3_yend-bond_shift_y) )
+	    chip_6_3 = true;
+	}
+      }
+
+      uint16_t xmin_roi{}, xmax_roi{}, ymin_roi{}, ymax_roi{};
+       //[ chip, group, xmin, xmax, ymin, ymax ]
+      std::vector < std::tuple< int, int, uint16_t, uint16_t, uint16_t, uint16_t > > rois{};
+
+      if (chip_1_1) {
+	std::tie( xmin_roi, xmax_roi, ymin_roi, ymax_roi ) =
+	  adjustROItoLimits( xmin, xmax, ymin, ymax,
+			     c1g1_xstart, c1_xend, 0, c1g1_yend+bond_shift_y );
+	rois.push_back( std::make_tuple( 1, 1, xmin_roi, xmax_roi, ymin_roi, ymax_roi ) );
+      }
+      if (chip_1_2) {
+	std::tie( xmin_roi, xmax_roi, ymin_roi, ymax_roi ) =
+	  adjustROItoLimits( xmin, xmax, ymin, ymax,
+			     c1g2_xstart, c1_xend, c1g2_ystart+bond_shift_y, c1g2_yend+bond_shift_y );
+	rois.push_back( std::make_tuple( 1, 2, xmin_roi, xmax_roi, ymin_roi, ymax_roi ) );
+      }
+      if (chip_1_3) {
+	std::tie( xmin_roi, xmax_roi, ymin_roi, ymax_roi ) =
+	  adjustROItoLimits( xmin, xmax, ymin, ymax,
+			     c1g3_xstart, c1_xend, c1g3_ystart+bond_shift_y, c1g3_yend+bond_shift_y );
+	rois.push_back( std::make_tuple( 1, 3, xmin_roi, xmax_roi, ymin_roi, ymax_roi ) );
+      }
+      if (chip_6_3) {
+	std::tie( xmin_roi, xmax_roi, ymin_roi, ymax_roi ) =
+	  adjustROItoLimits( xmin, xmax, ymin, ymax,
+			     c6_xstart, c6g3_xend, c6g3_ystart-bond_shift_y, c6g3_yend-bond_shift_y );
+	rois.push_back( std::make_tuple( 6, 3, xmin_roi, xmax_roi, ymin_roi, ymax_roi ) );
+      }
+      if (chip_6_2) {
+	std::tie( xmin_roi, xmax_roi, ymin_roi, ymax_roi ) =
+	  adjustROItoLimits( xmin, xmax, ymin, ymax,
+			     c6_xstart, c6g2_xend, c6g2_ystart-bond_shift_y, c6g2_yend-bond_shift_y );
+	rois.push_back( std::make_tuple( 6, 2, xmin_roi, xmax_roi, ymin_roi, ymax_roi ) );
+      }
+      if (chip_6_1) {
+	std::tie( xmin_roi, xmax_roi, ymin_roi, ymax_roi ) =
+	  adjustROItoLimits( xmin, xmax, ymin, ymax,
+			     c6_xstart, c6g1_xend, c6g1_ystart-bond_shift_y, 511 );
+	rois.push_back( std::make_tuple( 6, 1, xmin_roi, xmax_roi, ymin_roi, ymax_roi ) );
+      }
+
+      return rois;
+
+    }
+
+    void remapROI(std::tuple< int, int, uint16_t, uint16_t, uint16_t, uint16_t > roi) {
         // determine group and chip selected by ROI
-        int group;
+      int group, xmin, xmax, ymin, ymax;
+	std::tie( mchip, group, xmin, xmax, ymin, ymax ) = roi;
+	/*
         if (ymax <= c1g1_yend + bond_shift_y) {
             group = 1;
             mchip = 1;
@@ -243,18 +358,17 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
 	  group = -1;
 	  mchip = -1;
 	}
+	*/
         int multiplicator = getMultiplicator(group);
         setMappingShifts(group);
 
-        std::cout << "chip: " << mchip << ", group: " << group << ", m: " << multiplicator
+        std::cout << "remapping chip: " << mchip << ", group: " << group << ", m: " << multiplicator
                   << ", x0: " << x0 << ", x1: " << x1 << ", y0: " << y0
                   << ", y1: " << y1 << std::endl;
-
+	std::cout << "Adjusted roi: [" << xmin << ", " << xmax << ", " << ymin << ", " << ymax << "]" << std::endl;
-        // get ROI raw image number of columns
-        int nc_roi = xmax - xmin + 1;
-        std::cout << "nc_roi = " << nc_roi << std::endl;
 
         // make sure loop bounds are correct
+	/*
         if (y0 < ymin)
             std::cout << "Error ymin" << std::endl;
         if (y1 > ymax)
@@ -264,6 +378,7 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
             std::cout << "Error xmin" << std::endl;
         if (x1 > xmax)
             std::cout << "Error xmax" << std::endl;
+	*/
 
         // remapping loop
         int ix, iy = 0;
@@ -277,8 +392,10 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
                 }
 
                 //	  if (iy< 40)	  cout << iy << "  " << ix <<endl;
-                dataMap[iy][ix] =
+		if ( ipx>=xmin && ipx<=xmax && ipy>=ymin && ipy <=ymax )
-                    sizeof(header) + (nc_roi * (ipy - ymin) + (ipx - xmin)) * 2;
+		  dataMap[iy][ix] =
+                    sizeof(header) + (globalROI.nc * (ipy - globalROI.ymin) + (ipx - globalROI.xmin)) * 2;
+		else dataMap[iy][ix] = sizeof(header);
                 groupmap[iy][ix] = group - 1;
             }
         }
@@ -307,16 +424,31 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
             }
         }
 
+	globalROI.xmin = xmin;
+	globalROI.xmax = xmax;
+	globalROI.ymin = ymin;
+	globalROI.ymax = ymax;
+
         std::cout << "sizeofheader = " << sizeof(header) << std::endl;
         std::cout << "Jungfrau strixels 2X single chip with full module data "
                   << std::endl;
 
         if (xmin < xmax && ymin < ymax) {
 
-            dataSize =
+	  // get ROI raw image number of columns
-                (xmax - xmin + 1) * (ymax - ymin + 1) * 2 + sizeof(header);
+	  globalROI.nc = xmax - xmin + 1;
-            std::cout << "datasize " << dataSize << std::endl;
+	  std::cout << "nc_roi = " << globalROI.nc << std::endl;
-            remapROI(xmin, xmax, ymin, ymax);
+	  
+	  dataSize =
+	    (xmax - xmin + 1) * (ymax - ymin + 1) * 2 + sizeof(header);
+	  std::cout << "datasize " << dataSize << std::endl;
+
+	  //[ chip, group, xmin, xmax, ymin, ymax ]
+	  auto rois = mapSubROIs(xmin, xmax, ymin, ymax);
+	  //function to fill vector of rois from globalROI
+
+	  for ( auto roi : rois )
+	    remapROI(roi);
 
         } else {
 

slsDetectorCalibration/dataStructures/jungfrauModuleData.h

@@ -3,6 +3,7 @@
 #ifndef JUNGFRAUMODULEDATA_H
 #define JUNGFRAUMODULEDATA_H
 #include <cstdint>
+#include "sls/sls_detector_defs.h"
 #include "slsDetectorData.h"
 
 //#define VERSION_V2
@@ -27,7 +28,7 @@ typedef struct {
     uint64_t bunchNumber; /**< is the frame number */
     uint64_t pre;         /**< something */
 
-} jf_header;
+} jf_header; //Aldo's header!
 
 using namespace std;  
 class jungfrauModuleData : public slsDetectorData<uint16_t> {
@@ -42,20 +43,56 @@ class jungfrauModuleData : public slsDetectorData<uint16_t> {
        1286 large etc.) \param c crosstalk parameter for the output buffer
 
    */
+
+#ifdef ALDO
+    using header = jf_header;
+#else
+    using header = sls::defs::sls_receiver_header;
+#endif
+
 #ifndef ZMQ
-#define off sizeof(jf_header)
+#define off sizeof(header)
 #endif
 #ifdef ZMQ
 #define off 0
 #endif
 
 
-    jungfrauModuleData()
+ jungfrauModuleData(uint16_t xmin=0, uint16_t xmax=0,
+		    uint16_t ymin=0, uint16_t ymax=0)
         : slsDetectorData<uint16_t>(1024, 512,
                                     1024* 512 * 2 + off) {
-  
+
-        for (int ix = 0; ix < 1024; ix++) {
+      for (int ix = 0; ix != 1024; ++ix) {
-            for (int iy = 0; iy < 512; iy++) {
+	for (int iy = 0; iy != 512; ++iy) {
+	  dataMap[iy][ix] = off;
+	}
+      }
+
+      if (xmin < xmax && ymin < ymax) {
+
+	int nc_roi = xmax - xmin + 1;
+	int nr_roi = ymax - ymin + 1;
+	std::cout << "nc_roi = " << nc_roi << std::endl;
+	std::cout << "nr_roi = " << nr_roi << std::endl;
+	  
+	dataSize =
+	  (xmax - xmin + 1) * (ymax - ymin + 1) * 2 + off;
+	std::cout << "datasize " << dataSize << std::endl;
+
+	for (int ix = xmin; ix < xmax+1; ++ix) {
+            for (int iy = ymin; iy < ymax+1; ++iy) {
+                dataMap[iy][ix] = off + (nc_roi * iy + ix) * 2;
+#ifdef HIGHZ
+                dataMask[iy][ix] = 0x3fff;
+#endif
+            }
+        }
+
+      } else {
+	  
+        for (int ix = 0; ix < 1024; ++ix) {
+            for (int iy = 0; iy < 512; ++iy) {
                 dataMap[iy][ix] = off + (1024 * iy + ix) * 2;
 #ifdef HIGHZ
                 dataMask[iy][ix] = 0x3fff;
@@ -63,7 +100,7 @@ class jungfrauModuleData : public slsDetectorData<uint16_t> {
             }
         }
 
-
+      }
 
 
         iframe = 0;
@@ -150,7 +187,7 @@ class jungfrauModuleData : public slsDetectorData<uint16_t> {
         //int pn;
 
         //  cout << dataSize << endl;
-        if (ff >= 0)
+        //if (ff >= 0)
 	  //fnum = ff;
 
         if (filebin.is_open()) {

slsDetectorCalibration/jungfrauExecutables/CMakeLists.txt

@@ -7,6 +7,7 @@
 set(JUNGFRAU_EXECUTABLES)
 
 find_package(fmt REQUIRED)
+find_package(nlohmann_json 3.11.2 REQUIRED)
 
 # jungfrauRawDataProcess
 add_executable(jungfrauRawDataProcess jungfrauRawDataProcess.cpp)
@@ -79,6 +80,7 @@ foreach(exe ${JUNGFRAU_EXECUTABLES})
         pthread 
         tiffio
         fmt::fmt
+	nlohmann_json::nlohmann_json
           #-L/usr/lib64/
         #-lm  -lstdc++  -lrt
 

slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp

@@ -41,6 +41,9 @@
 #include <ctime>
 #include <fmt/core.h>
 
+#include <nlohmann/json.hpp>
+using json = nlohmann::json;
+
 
 std::string getRootString( const std::string& filepath ) {
   size_t pos1 = filepath.find_last_of("/");
@@ -61,20 +64,24 @@ std::string getRootString( const std::string& filepath ) {
 std::string createFileName( const std::string& dir, const std::string& fprefix="run", const std::string& fsuffix="", const std::string& fext="raw", int aindex=0, int mindex=0, int findex=0, int outfilecounter=-1 ) {
   if (outfilecounter >= 0)
     return fmt::format("{:s}/{:s}_d{:d}_f{:d}_{:d}_f{:05d}.{:s}", dir, fprefix, mindex, findex, aindex, outfilecounter, fext);
-  else if (fsuffix.length()!=0)
+  else if (fsuffix.length()!=0) {
-    return fmt::format("{:s}/{:s}_{:s}.{:s}", dir, fprefix, fsuffix, fext);
+    if (fsuffix == "master")
+      return fmt::format("{:s}/{:s}_master_{:d}.{:s}", dir, fprefix, aindex, fext);
+    else
+      return fmt::format("{:s}/{:s}_{:s}.{:s}", dir, fprefix, fsuffix, fext);
+  }
   else
     return fmt::format("{:s}/{:s}_d{:d}_f{:d}_{:d}.{:s}", dir, fprefix, mindex, findex, aindex, fext);
 }
 
 int main(int argc, char *argv[]) {
 
-    if (argc < 5) {
+    if (argc < 6) {
         std::cout
             << "Usage is " << argv[0]
-            << "indir outdir fprefix(excluding slsDetector standard suffixes and extension) fextension "
+            << "indir outdir [fprefix(excluding slsDetector standard suffixes and extension)] [fextension] "
-               "[runmin] [runmax] [pedfile (raw or tiff)] [threshold] "
+	       "[fmin] [fmax] [runmin] [runmax] [pedfile (raw or tiff)] [threshold] "
-               "[nframes] [xmin xmax ymin ymax] [gainmap]"
+               "[nframes] [xmin xmax ymin ymax] [optional: bool read rxroi from data file header] [gainmap]"
             << std::endl;
         std::cout
             << "threshold <0 means analog; threshold=0 means cluster finder; "
@@ -106,36 +113,71 @@ int main(int argc, char *argv[]) {
     std::string outdir(argv[2]);
     std::string fprefix(argv[3]);
     std::string fext(argv[4]);
+
+    int fmin = 0;
+    if (argc >= 6)
+        fmin = atoi(argv[5]);
+    int fmax = fmin;
+    if (argc >= 7)
+        fmax = atoi(argv[6]);
+
     int runmin = 0;
-
     // cout << "argc is " << argc << endl;
-    if (argc >= 6) {
+    if (argc >= 8) {
-        runmin = atoi(argv[5]);
+        runmin = atoi(argv[7]);
     }
-
     int runmax = runmin;
-
+    if (argc >= 9) {
-    if (argc >= 7) {
+        runmax = atoi(argv[8]);
-        runmax = atoi(argv[6]);
     }
 
     std::string pedfilename{};
-    if (argc >= 8) {
+    if (argc >= 10) {
-        pedfilename = argv[7];
+        pedfilename = argv[9];
     }
     double thr = 0;
     double thr1 = 1;
 
-    if (argc >= 9) {
+    if (argc >= 11) {
-        thr = atof(argv[8]);
+        thr = atof(argv[10]);
     }
 
     int nframes = 0;
 
-    if (argc >= 10) {
+    if (argc >= 12) {
-        nframes = atoi(argv[9]);
+        nframes = atoi(argv[11]);
     }
+
+    bool readrxroifromdatafile = false;
+    if (argc >= 17)
+      readrxroifromdatafile = atoi(argv[16]);
     
+    // Receiver ROI
+    uint16_t rxroi_xmin = 0;
+    uint16_t rxroi_xmax = 0;
+    uint16_t rxroi_ymin = 0;
+    uint16_t rxroi_ymax = 0;
+
+    { //protective scope so ifstream gets destroyed properly
+
+      auto jsonmastername = createFileName( indir, fprefix, "master", "json", runmin );
+      std::cout << "json master file " << jsonmastername << std::endl;
+      std::ifstream masterfile(jsonmastername); //, ios::in | ios::binary);
+      if (masterfile.is_open()) {
+	json j;
+	masterfile >> j;
+	rxroi_xmin = j["Receiver Roi"]["xmin"];
+	rxroi_xmax = j["Receiver Roi"]["xmax"];
+	rxroi_ymin = j["Receiver Roi"]["ymin"];
+	rxroi_ymax = j["Receiver Roi"]["ymax"];
+	masterfile.close();
+	std::cout << "Read Receiver ROI [" << rxroi_xmin << ", " << rxroi_xmax << ", "
+		  << rxroi_ymin << ", " << rxroi_ymax << "] from json master file" << std::endl;
+      } else 
+	std::cout << "Could not open master file " << jsonmastername << std::endl;
+    
+    }
+
     // Define decoders...
 #if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 &&           \
     !defined JFSTRXCHIP6
@@ -144,56 +186,52 @@ int main(int argc, char *argv[]) {
     int nx = 256, ny = 256;
 #endif
 #ifdef MODULE
-    jungfrauModuleData *decoder = new jungfrauModuleData();
+    jungfrauModuleData *decoder = new jungfrauModuleData(rxroi_xmin, rxroi_xmax, rxroi_ymin, rxroi_ymax);
     int nx = 1024, ny = 512;
 #endif
 #endif
 
 #ifdef JFSTRX
     cout << "Jungfrau strixel full module readout" << endl;
-    // ROI
-    uint16_t xxmin = 0;
-    uint16_t xxmax = 0;
-    uint16_t yymin = 0;
-    uint16_t yymax = 0;
 
 #ifndef ALDO
-    { //THIS SCOPE IS IMPORTANT! (To ensure proper destruction of ifstream)
+    if (readrxroifromdatafile)
-      using header = sls::defs::sls_receiver_header;
+      { //THIS SCOPE IS IMPORTANT! (To ensure proper destruction of ifstream)
-      // check if there is a roi in the header
+	using header = sls::defs::sls_receiver_header;
-      typedef struct {
+	// check if there is a roi in the header
-        uint16_t xmin;
+	typedef struct {
-        uint16_t xmax;
+	  uint16_t xmin;
-        uint16_t ymin;
+	  uint16_t xmax;
-        uint16_t ymax;
+	  uint16_t ymin;
-      } receiverRoi_compact;
+	  uint16_t ymax;
-      receiverRoi_compact croi;
+	} receiverRoi_compact;
-      std::string fsuffix{};
+	receiverRoi_compact croi;
-      auto filename = createFileName( indir, fprefix, fsuffix, fext, runmin );
+	std::string fsuffix{};
-      std::cout << "Reading header of file " << filename << " to check for ROI "
+	auto filename = createFileName( indir, fprefix, fsuffix, fext, runmin );
-		<< std::endl;
+	std::cout << "Reading header of file " << filename << " to check for ROI "
-      ifstream firstfile(filename, ios::in | ios::binary);
+		  << std::endl;
-      if (firstfile.is_open()) {
+	ifstream firstfile(filename, ios::in | ios::binary);
-        header hbuffer;
+	if (firstfile.is_open()) {
-        std::cout << "sizeof(header) = " << sizeof(header) << std::endl;
+	  header hbuffer;
-        if (firstfile.read((char *)&hbuffer, sizeof(header))) {
+	  std::cout << "sizeof(header) = " << sizeof(header) << std::endl;
-	  memcpy(&croi, &hbuffer.detHeader.detSpec1, 8);
+	  if (firstfile.read((char *)&hbuffer, sizeof(header))) {
-	  std::cout << "Read ROI [" << croi.xmin << ", " << croi.xmax << ", "
+	    memcpy(&croi, &hbuffer.detHeader.detSpec1, 8);
-		    << croi.ymin << ", " << croi.ymax << "]" << std::endl;
+	    std::cout << "Read ROI [" << croi.xmin << ", " << croi.xmax << ", "
-	  xxmin = croi.xmin;
+		      << croi.ymin << ", " << croi.ymax << "]" << std::endl;
-	  xxmax = croi.xmax;
+	    rxroi_xmin = croi.xmin;
-	  yymin = croi.ymin;
+	    rxroi_xmax = croi.xmax;
-	  yymax = croi.ymax;
+	    rxroi_ymin = croi.ymin;
-        } else
+	    rxroi_ymax = croi.ymax;
-	  std::cout << "reading error" << std::endl;
+	  } else
-        firstfile.close();
+	    std::cout << "reading error" << std::endl;
-      } else
+	  firstfile.close();
-        std::cout << "Could not open " << filename << " for reading " << std::endl;
+	} else
-    } //end of protective scope
+	  std::cout << "Could not open " << filename << " for reading " << std::endl;
+      } //end of protective scope
 #endif
 
     jungfrauLGADStrixelsData *decoder =
-        new jungfrauLGADStrixelsData(xxmin, xxmax, yymin, yymax);
+      new jungfrauLGADStrixelsData(rxroi_xmin, rxroi_xmax, rxroi_ymin, rxroi_ymax);
     int nx = 1024 / 3, ny = 512 * 5;
 #endif
 #ifdef JFSTRXCHIP1
@@ -218,19 +256,20 @@ int main(int argc, char *argv[]) {
     decoder->getDetectorSize(nx, ny);
     std::cout << "Detector size is " << nx << " " << ny << std::endl;
 
-    int xmin = 0, xmax = nx, ymin = 0, ymax = ny;
+    //Cluster finder ROI
-    if (argc >= 14) {
+    int xmin = 0, xmax = nx-1, ymin = 0, ymax = ny-1;
-        xmin = atoi(argv[10]);
+    if (argc >= 16) {
-        xmax = atoi(argv[11]);
+        xmin = atoi(argv[12]);
-        ymin = atoi(argv[12]);
+        xmax = atoi(argv[13]);
-        ymax = atoi(argv[13]);
+        ymin = atoi(argv[14]);
+        ymax = atoi(argv[15]);
     }
-    std::cout << xmin << " " << xmax << " " << ymin << " " << ymax << " "
+    std::cout << "Cluster finder ROI: [" << xmin << ", " << xmax << ", " << ymin << ", " << ymax << "]"
               << std::endl;
 
     char *gainfname = NULL;
-    if (argc > 14) {
+    if (argc > 17) {
-        gainfname = argv[14];
+        gainfname = argv[17];
         std::cout << "Gain map file name is: " << gainfname << std::endl;
     }
 
@@ -239,6 +278,8 @@ int main(int argc, char *argv[]) {
     std::cout << "input directory is " << indir << std::endl;
     std::cout << "output directory is " << outdir << std::endl;
     std::cout << "input file prefix is " << fprefix << std::endl;
+    std::cout << "fmin is " << fmin << std::endl;
+    std::cout << "fmax is " << fmax << std::endl;
     std::cout << "runmin is " << runmin << std::endl;
     std::cout << "runmax is " << runmax << std::endl;
     if (pedfilename.length()!=0)
@@ -319,7 +360,7 @@ int main(int argc, char *argv[]) {
 
 	  mt->setFrameMode(ePedestal);
 
-	  ifstream pedefile(fname, ios::in | ios::binary);
+	  std::ifstream pedefile(fname, ios::in | ios::binary);
 	  //      //open file
 	  if (pedefile.is_open()) {
 	    std::cout << "bbbb " << std::ctime(&end_time) << std::endl;
@@ -380,26 +421,27 @@ int main(int argc, char *argv[]) {
     }
 
     ifr = 0;
-    int ifile = 0;
+    int ioutfile = 0;
 
     mt->setFrameMode(eFrame);
 
     FILE *of = NULL;
     
-    for (int irun = runmin; irun <= runmax; irun++) {
+    for (int irun = runmin; irun <= runmax; ++irun) {
+      for (int ifile = fmin; ifile <= fmax; ++ifile) {
         std::cout << "DATA ";
 	std::string fsuffix{};
-	auto fname = createFileName( indir, fprefix, fsuffix, fext, irun );
+	auto fname = createFileName( indir, fprefix, fsuffix, fext, irun, 0, ifile );
-	auto imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun );
+	auto imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, ifile );
-	auto cfname = createFileName( outdir, fprefix, fsuffix, "clust", irun );
+	auto cfname = createFileName( outdir, fprefix, fsuffix, "clust", irun, 0, ifile );
         std::cout << fname << " ";
         std::cout << imgfname << std::endl;
         std::time(&end_time);
         std::cout << std::ctime(&end_time) << std::endl;
         //  std::cout <<  fname << " " << outfname << " " << imgfname <<  std::endl;
-        ifstream filebin(fname, ios::in | ios::binary);
+	std::ifstream filebin(fname, ios::in | ios::binary);
         //      //open file
-        ifile = 0;
+        ioutfile = 0;
         if (filebin.is_open()) {
             if (thr <= 0 && cf != 0) { // cluster finder
                 if (of == NULL) {
@@ -436,10 +478,10 @@ int main(int argc, char *argv[]) {
                     std::cout << " " << ifr << " " << ff << std::endl;
                 if (nframes > 0) {
                     if (ifr % nframes == 0) {
-		      imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ifile );
+		      imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ioutfile );
 		      mt->writeImage(imgfname.c_str(), thr1);
                         mt->clearImage();
-                        ifile++;
+                        ioutfile++;
                     }
                 }
                 // } else
@@ -453,7 +495,7 @@ int main(int argc, char *argv[]) {
             }
             if (nframes >= 0) {
                 if (nframes > 0)
-		  imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ifile );
+		  imgfname = createFileName( outdir, fprefix, fsuffix, "tiff", irun, 0, 0, ioutfile );
                 std::cout << "Writing tiff to " << imgfname << " " << thr1
                           << std::endl;
                 mt->writeImage(imgfname.c_str(), thr1);
@@ -469,9 +511,10 @@ int main(int argc, char *argv[]) {
         } else
             std::cout << "Could not open " << fname << " for reading "
                       << std::endl;
+      }
     }
     if (nframes < 0) {
-      auto imgfname = createFileName( outdir, fprefix, "sum", "tiff", -1, 0, 0, -1 );
+      auto imgfname = createFileName( outdir, fprefix, "sum", "tiff", runmin, 0, fmin, -1 );
         std::cout << "Writing tiff to " << imgfname << " " << thr1 << std::endl;
         mt->writeImage(imgfname.c_str(), thr1);
     }

slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess_filetxt.cpp

@@ -41,6 +41,9 @@
 #include <ctime>
 #include <fmt/core.h>
 
+#include <nlohmann/json.hpp>
+using json = nlohmann::json;
+
 
 std::string getRootString( const std::string& filepath ) {
   size_t pos1;
@@ -71,11 +74,11 @@ std::string createFileName( const std::string& dir, const std::string& fprefix="
 //NOTE THAT THE DATA FILES HAVE TO BE IN THE RIGHT ORDER SO THAT PEDESTAL TRACKING WORKS!
 int main(int argc, char *argv[]) {
 
-    if (argc < 10) {
+    if (argc < 11) {
         std::cout
             << "Usage is " << argv[0]
-            << " filestxt outdir [pedfile (raw or tiff)] [xmin xmax ymin ymax] "
+            << " filestxt outdir [json master] [pedfile (raw or tiff)] [xmin xmax ymin ymax] "
-               "[threshold] [nframes] "
+               "[threshold] [nframes] [optional: bool read rxroi from data file header]"
 	       "NOTE THAT THE DATA FILES HAVE TO BE IN THE RIGHT ORDER SO THAT PEDESTAL TRACKING WORKS! "
             << std::endl;
         std::cout
@@ -105,19 +108,19 @@ int main(int argc, char *argv[]) {
 
     const std::string txtfilename(argv[1]);
     const std::string outdir(argv[2]);
-    const std::string pedfilename(argv[3]);
+    const std::string jsonmastername(argv[3]);
-
+    const std::string pedfilename(argv[4]);
-    int xmin = atoi(argv[4]);
-    int xmax = atoi(argv[5]);
-    int ymin = atoi(argv[6]);
-    int ymax = atoi(argv[7]);
 
     double thr = 0;
     double thr1 = 1;
-    thr = atof(argv[8]);
+    thr = atof(argv[9]);
 
     int nframes = 0;
-    nframes = atoi(argv[9]);
+    nframes = atoi(argv[10]);
+
+    bool readrxroifromdatafile = false;
+    if (argc > 11)
+      readrxroifromdatafile = atoi(argv[11]);
 
     //Get vector of filenames from input txt-file
     std::vector<std::string> filenames{};
@@ -146,7 +149,31 @@ int main(int argc, char *argv[]) {
     }
 
     std::cout << "###############" << std::endl;
-    
+
+    // Receiver ROI
+    uint16_t rxroi_xmin = 0;
+    uint16_t rxroi_xmax = 0;
+    uint16_t rxroi_ymin = 0;
+    uint16_t rxroi_ymax = 0;
+
+    { //protective scope so ifstream gets destroyed properly
+
+      std::ifstream masterfile(jsonmastername); //, ios::in | ios::binary);
+      if (masterfile.is_open()) {
+	json j;
+	masterfile >> j;
+	rxroi_xmin = j["Receiver Roi"]["xmin"];
+	rxroi_xmax = j["Receiver Roi"]["xmax"];
+	rxroi_ymin = j["Receiver Roi"]["ymin"];
+	rxroi_ymax = j["Receiver Roi"]["ymax"];
+	masterfile.close();
+	std::cout << "Read rxROI [" << rxroi_xmin << ", " << rxroi_xmax << ", "
+		      << rxroi_ymin << ", " << rxroi_ymax << "]" << std::endl;
+      } else 
+	std::cout << "Could not open master file " << jsonmastername << std::endl;
+      
+    }
+
     // Define decoders...
 #if !defined JFSTRX && !defined JFSTRXOLD && !defined JFSTRXCHIP1 &&           \
     !defined JFSTRXCHIP6
@@ -162,48 +189,44 @@ int main(int argc, char *argv[]) {
 
 #ifdef JFSTRX
     cout << "Jungfrau strixel full module readout" << endl;
-    // ROI
-    uint16_t xxmin = 0;
-    uint16_t xxmax = 0;
-    uint16_t yymin = 0;
-    uint16_t yymax = 0;
 
 #ifndef ALDO
-    { //THIS SCOPE IS IMPORTANT! (To ensure proper destruction of ifstream)
+    if (readrxroifromdatafile)
-      using header = sls::defs::sls_receiver_header;
+      { //THIS SCOPE IS IMPORTANT! (To ensure proper destruction of ifstream)
-      // check if there is a roi in the header
+	using header = sls::defs::sls_receiver_header;
-      typedef struct {
+	// check if there is a roi in the header
-        uint16_t xmin;
+	typedef struct {
-        uint16_t xmax;
+	  uint16_t xmin;
-        uint16_t ymin;
+	  uint16_t xmax;
-        uint16_t ymax;
+	  uint16_t ymin;
-      } receiverRoi_compact;
+	  uint16_t ymax;
-      receiverRoi_compact croi;
+	} receiverRoi_compact;
-      //std::string filepath(argv[9]); //This is a problem if the input files have different ROIs!
+	receiverRoi_compact croi;
-      std::cout << "Reading header of file " << filenames[0] << " to check for ROI "
+	//std::string filepath(argv[9]); //This is a problem if the input files have different ROIs!
-		<< std::endl;
+	std::cout << "Reading header of file " << filenames[0] << " to check for ROI "
-      ifstream firstfile(filenames[0], ios::in | ios::binary);
+		  << std::endl;
-      if (firstfile.is_open()) {
+	std::ifstream firstfile( filenames[0], ios::in | ios::binary);
-        header hbuffer;
+	if (firstfile.is_open()) {
-        std::cout << "sizeof(header) = " << sizeof(header) << std::endl;
+	  header hbuffer;
-        if (firstfile.read((char *)&hbuffer, sizeof(header))) {
+	  std::cout << "sizeof(header) = " << sizeof(header) << std::endl;
-	  memcpy(&croi, &hbuffer.detHeader.detSpec1, 8);
+	  if (firstfile.read((char *)&hbuffer, sizeof(header))) {
-	  std::cout << "Read ROI [" << croi.xmin << ", " << croi.xmax << ", "
+	    memcpy(&croi, &hbuffer.detHeader.detSpec1, 8);
-		    << croi.ymin << ", " << croi.ymax << "]" << std::endl;
+	    std::cout << "Read ROI [" << croi.xmin << ", " << croi.xmax << ", "
-	  xxmin = croi.xmin;
+		      << croi.ymin << ", " << croi.ymax << "]" << std::endl;
-	  xxmax = croi.xmax;
+	    rxroi_xmin = croi.xmin;
-	  yymin = croi.ymin;
+	    rxroi_xmax = croi.xmax;
-	  yymax = croi.ymax;
+	    rxroi_ymin = croi.ymin;
-        } else
+	    rxroi_ymax = croi.ymax;
-	  std::cout << "reading error" << std::endl;
+	  } else
-        firstfile.close();
+	    std::cout << "reading error" << std::endl;
-      } else
+	  firstfile.close();
-        std::cout << "Could not open " << filenames[0] << " for reading " << std::endl;
+	} else
-    } //end of protective scope
+	  std::cout << "Could not open " << filenames[0] << " for reading " << std::endl;
+      } //end of protective scope
 #endif
 
     jungfrauLGADStrixelsData *decoder =
-        new jungfrauLGADStrixelsData(xxmin, xxmax, yymin, yymax);
+        new jungfrauLGADStrixelsData(rxroi_xmin, rxroi_xmax, rxroi_ymin, rxroi_ymax);
     int nx = 1024 / 3, ny = 512 * 5;
 #endif
 #ifdef JFSTRXCHIP1
@@ -228,7 +251,16 @@ int main(int argc, char *argv[]) {
     decoder->getDetectorSize(nx, ny);
     std::cout << "Detector size is " << nx << " " << ny << std::endl;
 
+    //Cluster finder ROI
+    int xmin = 0, xmax = nx-1, ymin = 0, ymax = ny-1;
+    xmin = atoi(argv[5]);
+    xmax = atoi(argv[6]);
+    ymin = atoi(argv[7]);
+    ymax = atoi(argv[8]);
+    std::cout << "Cluster finder ROI: [" << xmin << ", " << xmax << ", " << ymin << ", " << ymax << "]"
+              << std::endl;
 
+    /* old
     if ( xmin == xmax ) {
       xmin = 0;
       xmax = nx;
@@ -239,6 +271,7 @@ int main(int argc, char *argv[]) {
     }
     std::cout << xmin << " " << xmax << " " << ymin << " " << ymax << " "
               << std::endl;
+    */
 
     /*
     char *gainfname = NULL;
@@ -410,7 +443,7 @@ int main(int argc, char *argv[]) {
       std::time(&end_time);
       std::cout << std::ctime(&end_time) << std::endl;
 
-      ifstream filebin(filenames[ifile], ios::in | ios::binary);
+      std::ifstream filebin(filenames[ifile], ios::in | ios::binary);
       //      //open file
       ioutfile = 0;
       if (filebin.is_open()) {

slsDetectorGui/src/qDrawPlot.cpp

@@ -193,6 +193,7 @@ void qDrawPlot::SetupPlots() {
     gainplot2d = new SlsQt2DPlot(boxPlot, true);
     gainplot2d->SetData(nPixelsX, -0.5, nPixelsX - 0.5, nPixelsY, -0.5,
                         nPixelsY - 0.5, gainData);
+    gainplot2d->Update();
     gainplot2d->hide();
     connect(plot2d, SIGNAL(PlotZoomedSignal(const QRectF &)), this,
             SLOT(Zoom2DGainPlot(const QRectF &)));
@@ -1009,6 +1010,7 @@ void qDrawPlot::Update2dPlot() {
     if (isGainDataExtracted) {
         gainplot2d->SetData(nPixelsX, -0.5, nPixelsX - 0.5, nPixelsY, -0.5,
                             nPixelsY - 0.5, gainData);
+        gainplot2d->Update();
         if (!gainplot2d->isVisible()) {
             gainplot2d->setFixedWidth(plot2d->width() /
                                       qDefs::DATA_GAIN_PLOT_RATIO);

slsDetectorServers/gotthard2DetectorServer/slsDetectorFunctionList.c

@@ -3323,6 +3323,27 @@ void *start_timer(void *arg) {
                 break;
             }
 
+            // change gain and data for every frame
+            {
+                const int nchannels = NCHIP * NCHAN;
+                int gainVal = 0;
+                for (int i = 0; i < nchannels; ++i) {
+                    if ((i % nchannels) < 400) {
+                        gainVal = 1 + frameNr;
+                    } else if ((i % nchannels) < 800) {
+                        gainVal = 2 + frameNr;
+                    } else {
+                        gainVal = 3 + frameNr;
+                    }
+                    int dataVal =
+                        *((uint16_t *)(imageData + i * sizeof(uint16_t)));
+                    dataVal += frameNr;
+                    int channelVal =
+                        (dataVal & ~GAIN_VAL_MSK) | (gainVal << GAIN_VAL_OFST);
+                    *((uint16_t *)(imageData + i * sizeof(uint16_t))) =
+                        (uint16_t)channelVal;
+                }
+            }
             // sleep for exposure time
             struct timespec begin, end;
             clock_gettime(CLOCK_REALTIME, &begin);

slsDetectorServers/jungfrauDetectorServer/slsDetectorFunctionList.c

@@ -2552,8 +2552,7 @@ void setPedestalMode(int enable, uint8_t frames, uint16_t loops) {
     if (enable) {
         LOG(logINFOBLUE, ("Enabling pedestal mode [frames: %hhu, loops: %hu]\n",
                           frames, loops));
-        // enable
+
-        bus_w(addr, bus_r(addr) | PEDESTAL_MODE_ENBLE_MSK);
         // frames
         bus_w(addr, bus_r(addr) & ~PEDESTAL_MODE_LNGTH_MSK);
         bus_w(addr, bus_r(addr) | ((frames << PEDESTAL_MODE_LNGTH_OFST) &
@@ -2562,6 +2561,8 @@ void setPedestalMode(int enable, uint8_t frames, uint16_t loops) {
         bus_w(addr, bus_r(addr) & ~PEDESTAL_MODE_ITRTNS_MSK);
         bus_w(addr, bus_r(addr) | ((loops << PEDESTAL_MODE_ITRTNS_OFST) &
                                    PEDESTAL_MODE_ITRTNS_MSK));
+        // enable
+        bus_w(addr, bus_r(addr) | PEDESTAL_MODE_ENBLE_MSK);
 
         // if it was switched off before, remember the #frames and #triggers
         if (prevPedestalEnable == 0) {
@@ -2726,6 +2727,7 @@ void *start_timer(void *arg) {
             if (i % pixelsPerPacket == 0) {
                 ++dataVal;
             }
+
             if ((i % 1024) < 300) {
                 gainVal = 1;
             } else if ((i % 1024) < 600) {
@@ -2766,6 +2768,28 @@ void *start_timer(void *arg) {
             clock_gettime(CLOCK_REALTIME, &begin);
             usleep(expUs);
 
+            // change gain and data for every frame
+            {
+                const int npixels = (NCHAN * NCHIP);
+                for (int i = 0; i < npixels; ++i) {
+                    int gainVal = 0;
+                    if ((i % 1024) < 300) {
+                        gainVal = 1 + iframes;
+                    } else if ((i % 1024) < 600) {
+                        gainVal = 2 + iframes;
+                    } else {
+                        gainVal = 3 + iframes;
+                    }
+                    int dataVal =
+                        *((uint16_t *)(imageData + i * sizeof(uint16_t)));
+                    dataVal += iframes;
+                    int pixelVal =
+                        (dataVal & ~GAIN_VAL_MSK) | (gainVal << GAIN_VAL_OFST);
+                    *((uint16_t *)(imageData + i * sizeof(uint16_t))) =
+                        (uint16_t)pixelVal;
+                }
+            }
+
             int srcOffset = 0;
             int srcOffset2 = DATA_BYTES / 2;
             int row0 = (numInterfaces == 1 ? detPos[1] : detPos[3]);