1 - Add cmake for jungfrauExecutables rawdataprocess (#717)

* Fix ROI mapping

* intial draft of cmake for jungfrau executables Makefile.rawdataprocess

* added the cmake file

* missed Makefile

* added libfmt

* Fix some compiler warnings


---------

Co-authored-by: vhinger182 <hinger_v@hv_home_lt1.localdomain>
Co-authored-by: Dhanya Thattil <dhanya.thattil@psi.ch>

CMakeLists.txt

@@ -55,6 +55,7 @@ option(SLS_BUILD_EXAMPLES "examples" OFF)
 option(SLS_TUNE_LOCAL "tune to local machine" OFF)
 option(SLS_DEVEL_HEADERS "install headers for devel" OFF)
 option(SLS_USE_MOENCH "compile zmq and post processing for Moench" OFF)
+option(SLS_USE_JUNGFRAU "compile post processing for Jungfrau" OFF)
 
 #Convenience option to switch off defaults when building Moench binaries only
 option(SLS_BUILD_ONLY_MOENCH "compile only Moench" OFF)
@@ -68,6 +69,18 @@ if(SLS_BUILD_ONLY_MOENCH)
     set(SLS_USE_MOENCH ON CACHE BOOL "Enable" FORCE)
 endif()
 
+#Convenience option to switch off defaults when building Jungfrau binaries only
+option(SLS_BUILD_ONLY_JUNGFRAU "compile only Jungfrau" OFF)
+if(SLS_BUILD_ONLY_JUNGFRAU)
+    message(STATUS "Build JUNGFRAU binaries only!")
+    set(SLS_BUILD_SHARED_LIBRARIES OFF CACHE BOOL "Disabled for JUNGFRAU_ONLY" FORCE)
+    set(SLS_USE_TEXTCLIENT OFF CACHE BOOL "Disabled for JUNGFRAU_ONLY" FORCE)
+    set(SLS_USE_DETECTOR OFF CACHE BOOL "Disabled for JUNGFRAU_ONLY" FORCE)
+    set(SLS_USE_RECEIVER OFF CACHE BOOL "Disabled for JUNGFRAU_ONLY" FORCE)
+    set(SLS_USE_RECEIVER_BINARIES OFF CACHE BOOL "Disabled for JUNGFRAU_ONLY" FORCE)
+    set(SLS_USE_JUNGFRAU ON CACHE BOOL "Enable" FORCE)
+endif()
+
 
 option(SLS_EXT_BUILD "external build of part of the project" OFF)
 if(SLS_EXT_BUILD)
@@ -264,6 +277,11 @@ if(SLS_USE_MOENCH)
     add_subdirectory(slsDetectorCalibration/moenchExecutables)
 endif(SLS_USE_MOENCH)
 
+if(SLS_USE_JUNGFRAU)
+    add_subdirectory(slsDetectorCalibration/tiffio)
+    add_subdirectory(slsDetectorCalibration/jungfrauExecutables)
+endif(SLS_USE_JUNGFRAU)
+
 if(SLS_MASTER_PROJECT)
     set(CMAKE_INSTALL_DIR "share/cmake/${PROJECT_NAME}")
     set(PROJECT_LIBRARIES slsSupportShared slsDetectorShared slsReceiverShared)

slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsDataSingleChip.h

@@ -69,7 +69,7 @@ class jungfrauLGADStrixelsDataSingleChip : public slsDetectorData<uint16_t> {
     int mchip;
 
     void remapGroup( const int group ) {
-      int ix, iy;
+      int ix, iy=0;
       int x0, y0, x1, y1, shifty;
       int multiplicator;
 
@@ -261,15 +261,15 @@ class jungfrauLGADStrixelsDataSingleChip : public slsDetectorData<uint16_t> {
     };
 
     char *readNextFrame(std::ifstream &filebin, int &ff, int &np,char *data) {
-        char *retval = 0;
+      //char *retval = 0;
-        int nd;
+      //int nd;
-        int fnum = -1;
+      //int fnum = -1;
         np = 0;
-        int pn;
+        //int pn;
 
         //  cout << dataSize << endl;
         if (ff >= 0)
-            fnum = ff;
+	  // fnum = ff;
 
         if (filebin.is_open()) {
             if (filebin.read(data, dataSize)) {

slsDetectorCalibration/dataStructures/jungfrauLGADStrixelsData_new.h

@@ -193,7 +193,7 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
 
     void remapGroup(const int group) {
         int multiplicator = getMultiplicator(group);
-        int shiftx;
+        //int shiftx;
         int ix, iy = 0;
 
         setMappingShifts(group);
@@ -236,6 +236,9 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
         } else if (ymax <= c6g1_yend - bond_shift_y) {
             group = 1;
             mchip = 6;
+        } else { //to fix compiler warning
+	  group = -1;
+	  mchip = -1;
 	}
         int multiplicator = getMultiplicator(group);
         setMappingShifts(group);
@@ -315,14 +318,13 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
         } else {
 
             mchip = 1;
-            remapGroup(1);
+	    for (int group=1; group!=4; ++group)
-            remapGroup(2);
+	      remapGroup(group);
-            remapGroup(3);
 
             mchip = 6;
-            remapGroup(1);
+	    for (int group=1; group!=4; ++group)
-            remapGroup(2);
+	      remapGroup(group);
-            remapGroup(3);
+
         }
 
         iframe = 0;
@@ -353,10 +355,9 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
 
     int getFrameNumber(char *buff) {
 #ifdef ALDO                                      // VH
-        return ((header *)buff)->bunchNumber; // VH
+        return ((jf_header *)buff)->bunchNumber; // VH
-#else                                         // VH
-        return ((header *)buff)->detHeader.frameNumber;
 #endif                                           // VH
+        return ((header *)buff)->detHeader.frameNumber;
     };
 
     /**
@@ -374,9 +375,8 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
         // 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
+        return ((header *)buff)->detHeader.packetNumber;
     };
 
     char *readNextFrame(std::ifstream &filebin) {
@@ -400,15 +400,15 @@ class jungfrauLGADStrixelsData : public slsDetectorData<uint16_t> {
     };
 
     char *readNextFrame(std::ifstream &filebin, int &ff, int &np, char *data) {
-        char *retval = 0;
+      //char *retval = 0;
-        int nd;
+      //int nd;
-        int fnum = -1;
+      //int fnum = -1;
         np = 0;
-        int pn;
+        //int pn;
 
         // std::cout << dataSize << std::endl;
         if (ff >= 0)
-            fnum = ff;
+          //  fnum = ff;
 
         if (filebin.is_open()) {
             if (filebin.read(data, dataSize)) {

slsDetectorCalibration/dataStructures/jungfrauModuleData.h

@@ -142,15 +142,15 @@ class jungfrauModuleData : public slsDetectorData<uint16_t> {
     };
 
     char *readNextFrame(ifstream &filebin, int &ff, int &np,char *data) {
-        char *retval = 0;
+      //char *retval = 0;
-        int nd;
+      //int nd;
-        int fnum = -1;
+      //int fnum = -1;
         np = 0;
-        int pn;
+        //int pn;
 
         //  cout << dataSize << endl;
         if (ff >= 0)
-            fnum = ff;
+	  //fnum = ff;
 
         if (filebin.is_open()) {
             if (filebin.read(data, dataSize)) {

slsDetectorCalibration/dataStructures/jungfrauStrixelsHalfModuleOldDesign.h

@@ -227,15 +227,15 @@ class jungfrauStrixelsHalfModuleOldDesign : public slsDetectorData<uint16_t> {
     };
 
     char *readNextFrame(std::ifstream &filebin, int &ff, int &np,char *data) {
-        char *retval = 0;
+      //char *retval = 0;
-        int nd;
+      //int nd;
-        int fnum = -1;
+      //int fnum = -1;
         np = 0;
-        int pn;
+        //int pn;
 
         //  cout << dataSize << endl;
         if (ff >= 0)
-            fnum = ff;
+	  //fnum = ff;
 
         if (filebin.is_open()) {
             if (filebin.read(data, dataSize)) {

slsDetectorCalibration/jungfrauExecutables/CMakeLists.txt

@@ -0,0 +1,101 @@
+# SPDX-License-Identifier: LGPL-3.0-or-other
+# Copyright (C) 2021 Contributors to the SLS Detector Package
+
+
+# Initial draft for Makefile.rawdataprocess
+
+set(JUNGFRAU_EXECUTABLES)
+
+find_package(fmt REQUIRED)
+
+# jungfrauRawDataProcess
+add_executable(jungfrauRawDataProcess jungfrauRawDataProcess.cpp)
+target_compile_definitions(jungfrauRawDataProcess PRIVATE MODULE)
+list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcess)
+
+# jungfrauRawDataProcessStrx
+add_executable(jungfrauRawDataProcessStrx jungfrauRawDataProcess.cpp)
+target_compile_definitions(jungfrauRawDataProcessStrx PRIVATE JFSTRX)
+list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcessStrx)
+
+
+# jungfrauRawDataProcessStrxChip1
+add_executable(jungfrauRawDataProcessStrxChip1 jungfrauRawDataProcess.cpp)
+target_compile_definitions(jungfrauRawDataProcessStrxChip1 PRIVATE JFSTRXCHIP1)
+list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcessStrxChip1)
+
+# jungfrauRawDataProcessStrxChip6
+add_executable(jungfrauRawDataProcessStrxChip6 jungfrauRawDataProcess.cpp)
+target_compile_definitions(jungfrauRawDataProcessStrxChip6 PRIVATE JFSTRXCHIP6)
+list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcessStrxChip6)
+
+# jungfrauRawDataProcessStrxChip1Aldo
+add_executable(jungfrauRawDataProcessStrxChip1Aldo jungfrauRawDataProcess.cpp)
+target_compile_definitions(jungfrauRawDataProcessStrxChip1Aldo PRIVATE JFSTRXCHIP1 ALDO)
+list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcessStrxChip1Aldo)
+
+# jungfrauRawDataProcessStrxChip6Aldo
+add_executable(jungfrauRawDataProcessStrxChip6Aldo jungfrauRawDataProcess.cpp)
+target_compile_definitions(jungfrauRawDataProcessStrxChip6Aldo PRIVATE JFSTRXCHIP6 ALDO)
+list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcessStrxChip6Aldo)
+
+# jungfrauRawDataProcessStrxAldo
+add_executable(jungfrauRawDataProcessStrxAldo jungfrauRawDataProcess.cpp)
+target_compile_definitions(jungfrauRawDataProcessStrxAldo PRIVATE JFSTRX ALDO)
+list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcessStrxAldo)
+
+# jungfrauRawDataProcessStrxOld
+add_executable(jungfrauRawDataProcessStrxOld jungfrauRawDataProcess.cpp)
+target_compile_definitions(jungfrauRawDataProcessStrxOld PRIVATE JFSTRXOLD)
+list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcessStrxOld)
+
+# jungfrauRawDataProcessStrxOldAldo
+add_executable(jungfrauRawDataProcessStrxOldAldo jungfrauRawDataProcess.cpp)
+target_compile_definitions(jungfrauRawDataProcessStrxOldAldo PRIVATE JFSTRXOLD ALDO)
+list(APPEND JUNGFRAU_EXECUTABLES jungfrauRawDataProcessStrxOldAldo)
+
+
+# others to be added if needed (might already be there in Makefile.cluster_finder TO BE CHECKED)
+
+
+
+
+foreach(exe ${JUNGFRAU_EXECUTABLES})
+    #TODO! At a later stage clean up include dirs and have a proper lib
+    target_include_directories(${exe} PRIVATE 
+        ../ 
+        ../interpolations
+        ../dataStructures 
+        ../interpolations/etaVEL
+        ../../slsSupportLib/include/
+        ../../slsReceiverSoftware/include/
+        ../tiffio/include
+        ${fmt_INCLUDE_DIRS}
+    )
+
+    target_link_libraries(${exe} 
+        PUBLIC
+        slsSupportStatic
+        pthread 
+        tiffio
+        fmt::fmt
+          #-L/usr/lib64/
+        #-lm  -lstdc++  -lrt
+
+        PRIVATE
+        slsProjectWarnings
+        slsProjectOptions
+    )
+
+
+    set_target_properties(${exe}  PROPERTIES 
+        RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin
+    )
+    if((CMAKE_BUILD_TYPE STREQUAL "Release") AND SLS_LTO_AVAILABLE)
+        set_property(TARGET ${exe} PROPERTY INTERPROCEDURAL_OPTIMIZATION True)
+    endif()
+
+    
+endforeach(exe ${JUNGFRAU_EXECUTABLES})
+
+install(TARGETS ${JUNGFRAU_EXECUTABLES} DESTINATION bin)

slsDetectorCalibration/jungfrauExecutables/Makefile.rawdataprocess

@@ -1,6 +1,8 @@
 # SPDX-License-Identifier: LGPL-3.0-or-other
 # Copyright (C) 2021 Contributors to the SLS Detector Package
 #module add CBFlib/0.9.5
+
+
 INCDIR=-I. -I../ -I../interpolations  -I../interpolations/etaVEL  -I../dataStructures  -I../../slsSupportLib/include/ -I../../slsReceiverSoftware/include/ -I../tiffio/include
 
 LDFLAG= ../tiffio/src/tiffIO.cpp -L/usr/lib64/ -lpthread -lm  -lstdc++   -pthread -lrt    -ltiff -O3  -std=c++11
@@ -11,64 +13,65 @@ MAIN=jungfrauClusterFinder.cpp
 all: jungfrauRawDataProcess
 
 jungfrauRawDataProcess:  jungfrauRawDataProcess.cpp  $(INCS) clean
-			 g++ -o jungfrauRawDataProcess  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL  -DMODULE
+			 g++ -o jungfrauRawDataProcess  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR)   -DMODULE
 
 jungfrauRawDataProcessStrx:  jungfrauRawDataProcess.cpp  $(INCS) clean
-			 g++ -o jungfrauRawDataProcessStrx  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DJFSTRX
+			 g++ -o jungfrauRawDataProcessStrx  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR)  -DJFSTRX
 
 jungfrauRawDataProcessStrxChip1:  jungfrauRawDataProcess.cpp  $(INCS) clean
-			 g++ -o jungfrauRawDataProcessStrxChip1  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DJFSTRXCHIP1
+			 g++ -o jungfrauRawDataProcessStrxChip1  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR)  -DJFSTRXCHIP1
 
 jungfrauRawDataProcessStrxChip6:  jungfrauRawDataProcess.cpp  $(INCS) clean
-			 g++ -o jungfrauRawDataProcessStrxChip6  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DJFSTRXCHIP6
+			 g++ -o jungfrauRawDataProcessStrxChip6  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR)  -DJFSTRXCHIP6
 
 jungfrauRawDataProcessStrxChip1Aldo:  jungfrauRawDataProcess.cpp  $(INCS) clean
-			 g++ -o jungfrauRawDataProcessStrxChip1Aldo  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DJFSTRXCHIP1 -DALDO
+			 g++ -o jungfrauRawDataProcessStrxChip1Aldo  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR)  -DJFSTRXCHIP1 -DALDO
 
 jungfrauRawDataProcessStrxChip6Aldo:  jungfrauRawDataProcess.cpp  $(INCS) clean
-			 g++ -o jungfrauRawDataProcessStrxChip6Aldo  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DJFSTRXCHIP6 -DALDO
+			 g++ -o jungfrauRawDataProcessStrxChip6Aldo  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR)  -DJFSTRXCHIP6 -DALDO
 
 jungfrauRawDataProcessStrxAldo:  jungfrauRawDataProcess.cpp  $(INCS) clean
-			 g++ -o jungfrauRawDataProcessStrxAldo  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DJFSTRX -DALDO
+			 g++ -o jungfrauRawDataProcessStrxAldo  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR)  -DJFSTRX -DALDO
 
 jungfrauRawDataProcessStrxOld:  jungfrauRawDataProcess.cpp  $(INCS) clean
-			 g++ -o jungfrauRawDataProcessStrxOld  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DJFSTRXOLD 
+			 g++ -o jungfrauRawDataProcessStrxOld  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR)  -DJFSTRXOLD 
 
 jungfrauRawDataProcessStrxOldAldo:  jungfrauRawDataProcess.cpp  $(INCS) clean
-			 g++ -o jungfrauRawDataProcessStrxOldAldo  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL -DJFSTRXOLD -DALDO
+			 g++ -o jungfrauRawDataProcessStrxOldAldo  jungfrauRawDataProcess.cpp $(LDFLAG) $(INCDIR)  -DJFSTRXOLD -DALDO
 
 
 
 jungfrauClusterFinder:  jungfrauClusterFinder.cpp  $(INCS) clean
-			 g++ -o jungfrauClusterFinder  jungfrauClusterFinder.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL  
+			 g++ -o jungfrauClusterFinder  jungfrauClusterFinder.cpp $(LDFLAG) $(INCDIR)   
 
 
 jungfrauClusterFinderHighZ:  jungfrauClusterFinder.cpp  $(INCS) clean
-			 g++ -o jungfrauClusterFinderHighZ  jungfrauClusterFinder.cpp $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DSAVE_ALL  -DHIGHZ 
+			 g++ -o jungfrauClusterFinderHighZ  jungfrauClusterFinder.cpp $(LDFLAG) $(INCDIR)   -DHIGHZ 
-
 
 
 
+# doesnt compile
 jungfrauMakeEta:  jungfrauInterpolation.cpp  $(INCS) clean
-			 g++ -o jungfrauMakeEta jungfrauInterpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) -DFF
+			 g++ -o jungfrauMakeEta jungfrauInterpolation.cpp    $(LDFLAG) $(INCDIR)  -DFF 
 
 jungfrauInterpolation:  jungfrauInterpolation.cpp  $(INCS) clean
-			 g++ -o jungfrauInterpolation jungfrauInterpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  
+			 g++ -o jungfrauInterpolation jungfrauInterpolation.cpp    $(LDFLAG) $(INCDIR)   
 
-jungfrauNoInterpolation:  jungfrauNoInterpolation.cpp  $(INCS) clean
+# cpp doesnt exist
-			 g++ -o jungfrauNoInterpolation jungfrauNoInterpolation.cpp    $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF) 
+#jungfrauNoInterpolation:  jungfrauNoInterpolation.cpp  $(INCS) clean
+#			 g++ -o jungfrauNoInterpolation jungfrauNoInterpolation.cpp    $(LDFLAG) $(INCDIR)  
 
 jungfrauPhotonCounter: jungfrauPhotonCounter.cpp   $(INCS) clean
-			 g++ -o jungfrauPhotonCounter  jungfrauPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER
+			 g++ -o jungfrauPhotonCounter  jungfrauPhotonCounter.cpp  $(LDFLAG) $(INCDIR)   -DNEWRECEIVER
 
 jungfrauAnalog: jungfrauPhotonCounter.cpp  $(INCS) clean
-			 g++ -o jungfrauAnalog  jungfrauPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DANALOG
+			 g++ -o jungfrauAnalog  jungfrauPhotonCounter.cpp  $(LDFLAG) $(INCDIR)   -DNEWRECEIVER -DANALOG
 
 jungfrauPhotonCounterHighZ: jungfrauPhotonCounter.cpp   $(INCS) clean
-			 g++ -o jungfrauPhotonCounterHighZ  jungfrauPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DHIGHZ
+			 g++ -o jungfrauPhotonCounterHighZ  jungfrauPhotonCounter.cpp  $(LDFLAG) $(INCDIR)   -DNEWRECEIVER -DHIGHZ
 
 jungfrauAnalogHighZ: jungfrauPhotonCounter.cpp  $(INCS) clean
-			 g++ -o jungfrauAnalogHighZ  jungfrauPhotonCounter.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWRECEIVER -DANALOG -DHIGHZ
+			 g++ -o jungfrauAnalogHighZ  jungfrauPhotonCounter.cpp  $(LDFLAG) $(INCDIR)   -DNEWRECEIVER -DANALOG -DHIGHZ
 
 clean: 	
 	rm -f  jungfrauClusterFinder jungfrauMakeEta jungfrauInterpolation jungfrauNoInterpolation jungfrauPhotonCounter jungfrauAnalog

slsDetectorCalibration/jungfrauExecutables/jungfrauRawDataProcess.cpp

@@ -39,7 +39,7 @@
 #include <sys/stat.h>
 
 #include <ctime>
-// using namespace std;
+#include <fmt/core.h>
 
 int main(int argc, char *argv[]) {