constexpr

* gotthard config file path using readlink

* gotthard2

* eiger

* eieger, mnythen3, moench

* binaries in

* moved readlink to a common function

* binaries in

.clang-format

@@ -3,4 +3,5 @@ IndentWidth: 4
 
 UseTab: Never
 ColumnLimit: 80
-AlignConsecutiveAssignments: false 
+AlignConsecutiveAssignments: false 
+AlignConsecutiveMacros: true

.clang-tidy

@@ -17,7 +17,8 @@ Checks:          '*,
                     -google-runtime-references, 
                     -google-readability-todo, 
                     -google-readability-braces-around-statements,
-                    -modernize-use-trailing-return-type'
+                    -modernize-use-trailing-return-type,
+                    -readability-isolate-declaration'
 
 HeaderFilterRegex: \.h
 AnalyzeTemporaryDtors: false

.travis.yml

@@ -4,12 +4,6 @@ language: cpp
 
 os: linux
 
-# env: 
-#   matrix: 
-#      - CONDA_PY="3.7"
-
-
-
 dist: bionic
 
 install:
@@ -39,5 +33,6 @@ deploy:
   provider: script
   script: find $HOME/miniconda/envs/testenv/conda-bld/${TRAVIS_OS_NAME}-64 -name "*.tar.bz2" -exec anaconda -t $CONDA_TOKEN upload --force {} \;
   on:
-    branch: udp
+    branch: developer
+    tags: true
 

CMakeLists.txt

@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.12)
 project(slsDetectorPackage)
 set(PROJECT_VERSION 5.0.0)
 include(CheckIPOSupported)
-
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
 
 cmake_policy(SET CMP0074 NEW)
 include(cmake/project_version.cmake)
@@ -44,6 +44,36 @@ option(SLS_USE_PYTHON "Python bindings" OFF)
 option(SLS_USE_CTBGUI "ctb GUI" OFF)
 option(SLS_BUILD_DOCS "docs" OFF)
 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)
+
+# set(ClangFormat_BIN_NAME clang-format)
+set(ClangFormat_EXCLUDE_PATTERNS  "build/" 
+                                    "libs/" 
+                                    "slsDetectorCalibration/" 
+                                    "ctbGui/" 
+                                    "manual/"
+                                    "python/"
+                                    "sample/"
+                                    ${CMAKE_BINARY_DIR})
+find_package(ClangFormat)
+
+#Enable LTO if available
+check_ipo_supported(RESULT SLS_LTO_AVAILABLE)
+
+
+# Use ld.gold if it is available and isn't disabled explicitly
+option(SLS_USE_LD_GOLD "Use GNU gold linker" ON)
+if (SLS_USE_LD_GOLD)
+    execute_process(COMMAND ${CMAKE_C_COMPILER} -fuse-ld=gold -Wl,--version ERROR_QUIET OUTPUT_VARIABLE LD_VERSION)
+    if ("${LD_VERSION}" MATCHES "GNU gold")
+        set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fuse-ld=gold")
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fuse-ld=gold")
+    else ()
+        message(WARNING "GNU gold linker isn't available, using the default system linker.")
+    endif ()
+endif ()
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
 if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
@@ -111,6 +141,11 @@ if(SLS_USE_SANITIZER)
     # target_link_libraries(slsProjectOptions INTERFACE -fsanitize=thread)
 endif()
 
+if(SLS_TUNE_LOCAL)
+    target_compile_options(slsProjectOptions INTERFACE -mtune=native -march=native)
+endif()
+
+
 #rapidjson
 add_library(rapidjson INTERFACE)
 target_include_directories(rapidjson INTERFACE
@@ -159,7 +194,7 @@ endif (SLS_USE_RECEIVER)
 
 if (SLS_USE_GUI)   
     find_package(Qt4 REQUIRED)
-    find_package(Qwt 6 REQUIRED)
+    find_package(Qwt 6.1 REQUIRED)
     if (QT4_FOUND AND QWT_FOUND)
         add_subdirectory(slsDetectorGui)
     endif()
@@ -196,10 +231,13 @@ if(SLS_BUILD_DOCS)
 endif(SLS_BUILD_DOCS)
 
 
+if(SLS_USE_MOENCH)
+    add_subdirectory(slsDetectorCalibration/moenchExecutables)
+endif(SLS_USE_MOENCH)
 
 if(SLS_MASTER_PROJECT)
     # Set install dir CMake packages
-    set(CMAKE_INSTALL_DIR ${CMAKE_INSTALL_DATADIR}/cmake/sls)
+    set(CMAKE_INSTALL_DIR "share/cmake/${PROJECT_NAME}")
     # Set the list of exported targets
     set(PROJECT_LIBRARIES slsSupportLib slsDetectorShared slsReceiverShared)
     # Generate and install package config file and version

README.md

@@ -2,90 +2,67 @@
 Detailed documentation can be found on the [official site.](https://www.psi.ch/detectors/users-support)
 
 ### Binaries
-Documentation to obtain the binaries via the conda package is available for [lib](https://github.com/slsdetectorgroup/sls_detector_lib) and [gui](https://github.com/slsdetectorgroup/sls_detector_gui)
+Binaries for the slsDetectorPackage are available through conda. 
+```
+#Add conda channels
+conda config --add channels conda-forge
+conda config --add channels slsdetectorgroup
+
+conda install slsdetlib   #only shared lib and command line
+conda install slsdet      #python bindings (includes slsdetlib)
+conda install slsdetgui   #gui (includes qt4)
+
+#Install specific version
+conda install slsdet=2020.03.02.dev0 #developer version from 3 March 2020
+
+```
 
 ### Source code
-One can also obtain the source code from this repository and compile while realizing the setup dependencies as required.
+One can also obtain the source code from this repository and compile.
 ```
 git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git
 
 ```
-#### Setup dependencies 
-* Gui Client <br>
-Requirements: Qt 4.8 and Qwt 6.0
-```
-    export QTDIR=/usr/local/Trolltech/
-    export QWTDIR=/usr/local/qwt-6.0.1/
-```
-If either of them does not exist, the GUI client will not be built.
+#### Dependencies 
+* Lib: c++11 compiler (gcc=>4.8), ZeroMQ 4
+* Gui: Qt 4.8 and Qwt 6.0
+* Calibration wizards and ctbGUI: ROOT
+* Optional: HDF5
 
-* Advanced user Calibration wizards<br>
-Requirements: ROOT
-```
-    export ROOTSYS=/usr/local/root-5.34
-```
 
 #### Compilation 
 
-Compiling can be done in two ways.
+Compiling can be done in two ways. Either with the convenience script
+cmk.sh or directly with cmake for more control.
 
 **1. Compile using script cmk.sh**<br>
 
 After compiling, the libraries and executables will be found in `slsDetectorPackage/build/bin` directory<br>
 
-Usage: [-c] [-b] [-h] [-d HDF5 directory] [-j]<br>
- * -[no option]: only make<br>
- * -c: Clean<br>
- * -b: Builds/Rebuilds CMake files normal mode<br>
- * -h: Builds/Rebuilds Cmake files with HDF5 package<br>
- * -d: HDF5 Custom Directory<br>
- * -t: Build/Rebuilds only text client<br>
- * -r: Build/Rebuilds only receiver<br>
- * -g: Build/Rebuilds only gui<br>
- * -j: Number of threads to compile through<br>
- * -e: Debug mode
- 
-Basic Option:
-./cmk.sh -b
- 
-For only make:
-./cmk.sh
-
-For make clean;make:
-./cmk.sh -c
-
-For using hdf5 without custom dir /blabla:
-./cmk.sh -h -d /blabla
-
-For rebuilding cmake without hdf5 
-./cmk.sh -b
-
-For using multiple cores to compile faster:
-./cmk.sh -j9<br>
-
-
-For rebuilding only certain sections<br>
-./cmk.sh -tg #only text client and gui<br>
-./cmk.sh -r #only receiver<br>
-
+Usage: [-c] [-b] [-p] [e] [t] [r] [g] [s] [u] [i] [-h] [-d <HDF5 directory>] [-j] <Number of threads>
+ -[no option]: only make
+ -c: Clean
+ -b: Builds/Rebuilds CMake files normal mode
+ -p: Builds/Rebuilds Python API
+ -h: Builds/Rebuilds Cmake files with HDF5 package
+ -d: HDF5 Custom Directory
+ -t: Build/Rebuilds only text client
+ -r: Build/Rebuilds only receiver
+ -g: Build/Rebuilds only gui
+ -s: Simulator
+ -u: Chip Test Gui
+ -j: Number of threads to compile through
+ -e: Debug mode
+ -i: Builds tests
+  
+eg. Rebuild when you switch to a new build and compile in parallel:
+./cmk.sh -bj5
 
 **2. Compile without script**<br>
-Use cmake to create out-of-source builds, by creating a build folder parallel to source directory.
+Use cmake to create out-of-source builds, by creating a build folder parallel to source directory. This would create a debug build with address sanitizers.
 ```
-    $ cd ..
-    $ mkdir slsDetectorPackage-build
-    $ cd slsDetectorPackage-build
-    $ cmake ../slsDetectorPackage  -DCMAKE_BUILD_TYPE=Debug -DSLS_USE_HDF5=OFF 
-    $ make
-```
-
-Use the following as an example to compile statically and using specific hdf5 folder
-```
-    $ HDF5_ROOT=/opt/hdf5v1.10.0 cmake ../slsDetectorPackage -DCMAKE_BUILD_TYPE=Debug -DSLS_USE_HDF5=ON
- ```  
-After compiling, the libraries and executables will be found at `bin` directory
-```
-    $ ls bin/
-    gui_client  libSlsDetector.a  libSlsDetector.so  libSlsReceiver.a  libSlsReceiver.so
-    sls_detector_acquire  sls_detector_get  slsDetectorGui  sls_detector_help  sls_detector_put  slsReceiver slsMultiReceiver
+    $ mkdir build
+    $ cd build
+    $ cmake ../slsDetectorPackage  -DCMAKE_BUILD_TYPE=Debug -DSLS_USE_SANITIZER=ON
+    $ make -j12 #or whatever number of threads wanted
 ```

cmake/FindClangFormat.cmake

@@ -0,0 +1,39 @@
+# Find Clang format
+if(NOT ClangFormat_BIN_NAME)
+	set(ClangFormat_BIN_NAME clang-format)
+endif()
+
+# if custom path check there first
+if(ClangFormat_ROOT_DIR)
+    find_program(ClangFormat_BIN 
+        NAMES
+        ${ClangFormat_BIN_NAME}
+        PATHS
+        "${ClangFormat_ROOT_DIR}"
+        NO_DEFAULT_PATH)
+endif()
+
+find_program(ClangFormat_BIN NAMES ${ClangFormat_BIN_NAME})
+
+include(FindPackageHandleStandardArgs)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(
+    ClangFormat
+    DEFAULT_MSG 
+    ClangFormat_BIN)
+
+mark_as_advanced(
+    ClangFormat_BIN)
+
+if(ClangFormat_FOUND)
+    exec_program(${ClangFormat_BIN} ${CMAKE_CURRENT_SOURCE_DIR} ARGS --version OUTPUT_VARIABLE CLANG_VERSION_TEXT)
+    string(REGEX MATCH "([0-9]+)\\.[0-9]+\\.[0-9]+" CLANG_VERSION ${CLANG_VERSION_TEXT})
+    if((${CLANG_VERSION} GREATER "9") OR (${CLANG_VERSION} EQUAL "9"))
+        # A CMake script to find all source files and setup clang-format targets for them
+        message(STATUS "found clang-format \"${CLANG_VERSION}\" adding formatting targets")
+        include(clang-format)
+    else()
+        message(STATUS "clang-format version \"${CLANG_VERSION}\" found but need at least 9. Not setting up format targets")
+    endif()
+else()
+    message(STATUS "clang-format not found. Not setting up format targets")
+endif()

cmake/clang-format.cmake

@@ -0,0 +1,47 @@
+# A CMake script to find all source files and setup clang-format targets for them
+
+# Find all source files
+set(ClangFormat_CXX_FILE_EXTENSIONS ${ClangFormat_CXX_FILE_EXTENSIONS} *.cpp *.h *.cxx *.hxx *.hpp *.cc *.ipp *.c)
+file(GLOB_RECURSE ALL_SOURCE_FILES ${ClangFormat_CXX_FILE_EXTENSIONS})
+
+# Don't include some common build folders
+set(ClangFormat_EXCLUDE_PATTERNS ${ClangFormat_EXCLUDE_PATTERNS} "/CMakeFiles/" "cmake")
+
+# get all project files file
+foreach (SOURCE_FILE ${ALL_SOURCE_FILES}) 
+    foreach (EXCLUDE_PATTERN ${ClangFormat_EXCLUDE_PATTERNS})
+        string(FIND ${SOURCE_FILE} ${EXCLUDE_PATTERN} EXCLUDE_FOUND) 
+        if (NOT ${EXCLUDE_FOUND} EQUAL -1) 
+            list(REMOVE_ITEM ALL_SOURCE_FILES ${SOURCE_FILE})
+        endif () 
+    endforeach ()
+endforeach ()
+
+#target for formatting soruce files
+add_custom_target(format
+    COMMENT "Running clang-format to change files"
+    COMMAND ${ClangFormat_BIN}
+    -style=file
+    -i
+    ${ALL_SOURCE_FILES}
+)
+
+
+#target to check format on source files 
+add_custom_target(format-check
+    COMMENT "Checking clang-format changes"
+    # Use ! to negate the result for correct output
+    COMMAND !
+    ${ClangFormat_BIN}
+    -style=file
+    -output-replacements-xml
+    ${ALL_SOURCE_FILES}
+    | grep -q "replacement offset" 
+)
+
+# debug to check which file will be formatted
+add_custom_target(
+    listformatfiles
+    COMMAND
+    echo ${ALL_SOURCE_FILES}
+)

cmake/package_config.cmake

@@ -15,17 +15,20 @@ configure_package_config_file(
 write_basic_package_version_file(
   "${PROJECT_BINARY_DIR}/${PROJECT_NAME_LOWER}-config-version.cmake"
   VERSION ${PROJECT_VERSION}
-  COMPATIBILITY SameMajorVersion)
+  COMPATIBILITY SameMajorVersion
+)
 
 install(FILES
   "${PROJECT_BINARY_DIR}/${PROJECT_NAME_LOWER}-config.cmake"
   "${PROJECT_BINARY_DIR}/${PROJECT_NAME_LOWER}-config-version.cmake"
   COMPONENT devel
-  DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME_LOWER})
+  DESTINATION ${CMAKE_INSTALL_DIR}
+)
 
 if (PROJECT_LIBRARIES OR PROJECT_STATIC_LIBRARIES)
   install(
     EXPORT "${TARGETS_EXPORT_NAME}"
     FILE ${PROJECT_NAME_LOWER}-targets.cmake
-    DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME_LOWER})
+    DESTINATION ${CMAKE_INSTALL_DIR}
+    )
 endif ()

cmk.sh

@@ -11,6 +11,8 @@ PYTHON=0
 TESTS=0
 SIMULATOR=0
 CTBGUI=0
+MANUALS=0
+MOENCHZMQ=0
 
 
 CLEAN=0
@@ -19,7 +21,7 @@ CMAKE_PRE=""
 CMAKE_POST=""
 
 usage() { echo -e "
-Usage: $0 [-c] [-b] [-p] [e] [t] [r] [g] [s] [u] [i] [-h] [-d <HDF5 directory>] [-j] <Number of threads>
+Usage: $0 [-c] [-b] [-p] [e] [t] [r] [g] [s] [u] [i] [m] [-h] [z] [-d <HDF5 directory>] [-j] <Number of threads>
  -[no option]: only make
  -c: Clean
  -b: Builds/Rebuilds CMake files normal mode
@@ -34,6 +36,8 @@ Usage: $0 [-c] [-b] [-p] [e] [t] [r] [g] [s] [u] [i] [-h] [-d <HDF5 directory>]
  -j: Number of threads to compile through
  -e: Debug mode
  -i: Builds tests
+ -m: Manuals
+ -z: Moench zmq processor
 
 Rebuild when you switch to a new build and compile in parallel:
 ./cmk.sh -bj5
@@ -69,7 +73,7 @@ For rebuilding only certain sections
  
  " ; exit 1; }
 
-while getopts ":bpchd:j:trgeisu" opt ; do
+while getopts ":bpchd:j:trgeisumz" opt ; do
 	case $opt in
 	b) 
 		echo "Building of CMake files Required"
@@ -124,6 +128,14 @@ while getopts ":bpchd:j:trgeisu" opt ; do
 		echo "Compiling Options: Simulator" 
 		SIMULATOR=1
 		;; 
+	m)	
+		echo "Compiling Manuals"
+		MANUALS=1
+		;;
+	z)	
+		echo "Compiling Moench Zmq Processor"
+		MOENCHZMQ=1
+		;;
 	u)
 		echo "Compiling Options: Chip Test Gui"
 		CTBGUI=1
@@ -187,8 +199,8 @@ fi
 
 #Debug
 if [ $DEBUG -eq 1 ]; then
-	CMAKE_POST+=" -DCMAKE_BUILD_TYPE=Debug "
-# CMAKE_POST+=" -DCMAKE_BUILD_TYPE=Debug -DSLS_USE_SANITIZER=ON "
+#	CMAKE_POST+=" -DCMAKE_BUILD_TYPE=Debug "
+	CMAKE_POST+=" -DCMAKE_BUILD_TYPE=Debug -DSLS_USE_SANITIZER=ON "
 	echo "Debug Option enabled"
 fi 
 
@@ -198,6 +210,18 @@ if [ $SIMULATOR -eq 1 ]; then
 	echo "Simulator Option enabled"
 fi 
 
+#Manuals
+if [ $MANUALS -eq 1 ]; then
+	CMAKE_POST+=" -DSLS_BUILD_DOCS=ON "
+	echo "Manuals Option enabled"
+fi 
+
+#Moench zmq processor
+if [ $MOENCHZMQ -eq 1 ]; then
+	CMAKE_POST+=" -DSLS_USE_MOENCH=ON "
+	echo "Moench Zmq Processor Option enabled"
+fi 
+
 #Chip Test Gui
 if [ $CTBGUI -eq 1 ]; then
 	CMAKE_POST+=" -DSLS_USE_CTBGUI=ON "
@@ -247,8 +271,18 @@ if [ $COMPILERTHREADS -gt 0 ]; then
 	BUILDCOMMAND="make -j$COMPILERTHREADS"
 	echo $BUILDCOMMAND
 	eval $BUILDCOMMAND
+	if [ $MANUALS -eq 1 ]; then
+		BUILDCOMMAND="make docs -j$COMPILERTHREADS"
+		echo $BUILDCOMMAND
+		eval $BUILDCOMMAND
+	fi 
 else
+	echo "make"
 	make
+	if [ $MANUALS -eq 1 ]; then
+		echo "make docs"
+		make docs
+	fi 
 fi
 
 

conda-recepie/copy_lib.sh

@@ -5,18 +5,20 @@ mkdir $PREFIX/include
 mkdir $PREFIX/include/slsDetectorPackage
 
 #Shared and static libraries
-cp build/bin/libSlsDetector.so $PREFIX/lib/.
-cp build/bin/libSlsReceiver.so $PREFIX/lib/.
-cp build/bin/libSlsSupport.so $PREFIX/lib/.
+# cp build/bin/libSlsDetector.so $PREFIX/lib/.
+# cp build/bin/libSlsReceiver.so $PREFIX/lib/.
+# cp build/bin/libSlsSupport.so $PREFIX/lib/.
+
+cp build/install/lib/* $PREFIX/lib/
 
 #Binaries
-cp build/bin/sls_detector_acquire $PREFIX/bin/.
-cp build/bin/sls_detector_get $PREFIX/bin/.
-cp build/bin/sls_detector_put $PREFIX/bin/.
-cp build/bin/sls_detector_help $PREFIX/bin/.
-cp build/bin/slsReceiver $PREFIX/bin/.
-cp build/bin/slsMultiReceiver $PREFIX/bin/.
+cp build/install/bin/sls_detector_acquire $PREFIX/bin/.
+cp build/install/bin/sls_detector_get $PREFIX/bin/.
+cp build/install/bin/sls_detector_put $PREFIX/bin/.
+cp build/install/bin/sls_detector_help $PREFIX/bin/.
+cp build/install/bin/slsReceiver $PREFIX/bin/.
+cp build/install/bin/slsMultiReceiver $PREFIX/bin/.
 
-#Which headers do we need for development??
-cp build/install/include/* $PREFIX/include/slsDetectorPackage/
-# cp include/some_lib.h $PREFIX/include/.
+
+cp build/install/include/* $PREFIX/include/
+cp -r build/install/share/ $PREFIX/share

conda-recepie/meta.yaml

@@ -1,13 +1,13 @@
 
 package:
   name: sls_detector_software
-  version: "udp"
+  version: {{ environ.get('GIT_DESCRIBE_TAG', '') }}
 
 source:
   - path: ..
 
 build:
-  number: 1
+  number: 0
   binary_relocation: True
   rpaths:
     - lib/
@@ -37,6 +37,7 @@ requirements:
   host:
     - libstdcxx-ng
     - libgcc-ng
+    - zeromq
     - xorg-libx11
     - xorg-libice
     - xorg-libxext
@@ -46,6 +47,7 @@ requirements:
     - xorg-libxfixes
 
   run:
+    - zeromq
     - libstdcxx-ng
     - libgcc-ng 
 

ctbGui/ctbAcquisition.cpp

@@ -29,9 +29,10 @@
 #include "sls_detector_defs.h"
 #include "ctbMain.h"
 #include "moench03CtbData.h" 
-#include "moench03TCtbData.h" 
-#include "moench03T1CtbData.h" 
+//#include "moench03TCtbData.h" 
+//#include "moench03T1CtbData.h" 
 #include "moench03CommonMode.h" 
+#include "moench03T1ZmqDataNew.h" 
 #include "moench02CtbData.h" 
 //#include "jungfrau10ModuleData.h" 
 #include "moenchCommonMode.h" 
@@ -43,6 +44,9 @@
 #include "moench04CtbZmq10GbData.h"
 #include "deserializer.h"
 #include "detectorData.h"
+#include "imageZmq16bit.h"
+#include "imageZmq32bit.h"
+
 
 using namespace std;
 
@@ -232,7 +236,10 @@ hframe=new TGHorizontalFrame(this, 800,50);
   cbDetType->AddEntry("MOENCH02", MOENCH02);
   cbDetType->AddEntry("MOENCH04", MOENCH04);
   // cbDetType->AddEntry("JUNGFRAU1.0", 2);
-  //cbDetType->AddEntry("MOENCH03 T", iiii++);
+  cbDetType->AddEntry("MOENCH03",MOENCH03);
+  cbDetType->AddEntry("IMAGE32BIT",IMAGE32B);
+  cbDetType->AddEntry("IMAGE16BIT",IMAGE16B);
+
   //cbDetType->AddEntry("MOENCH03", iiii++);
   // cbDetType->AddEntry("MYTHEN3 0.1", MYTHEN301);
   // cbDetType->AddEntry("ADCSAR2", ADCSAR2);
@@ -271,7 +278,7 @@ hframe=new TGHorizontalFrame(this, 800,50);
 
 
 
-    cout << "off "<< endl;
+  //  cout << "off "<< endl;
 
 
   hframe=new TGHorizontalFrame(this, 800,50);
@@ -290,8 +297,8 @@ hframe=new TGHorizontalFrame(this, 800,50);
                                                TGNumberFormat::kNEANonNegative, 
 			     TGNumberFormat::kNELLimitMinMax,0,16535);
    hframe->AddFrame(eSerOff,new TGLayoutHints(kLHintsTop |  kLHintsExpandX, 1, 1, 1, 1));
-   eSerOff->MapWindow();;
-   eSerOff->SetNumber(5);
+   eSerOff->MapWindow();
+   eSerOff->SetNumber(0);
    e= eSerOff->TGNumberEntry::GetNumberEntry();
    eSerOff->Connect("ValueSet(Long_t)","ctbAcquisition",this,"ChangeSerialOffset(Long_t)");
    e->Connect("ReturnPressed()","ctbAcquisition",this,"ChangeSerialOffset()");
@@ -337,6 +344,53 @@ hframe=new TGHorizontalFrame(this, 800,50);
    
 
 
+  hframe=new TGHorizontalFrame(this, 800,50);
+  AddFrame(hframe,new TGLayoutHints(kLHintsTop | kLHintsExpandX , 10,10,10,10));
+  hframe->MapWindow();
+    
+ 
+
+  label=new TGLabel(hframe,"Image Pixels");
+  hframe->AddFrame(label,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 5, 5, 5, 5));
+  label->MapWindow();
+  label->SetTextJustify(kTextLeft);
+
+
+  label=new TGLabel(hframe,"X: ");
+  hframe->AddFrame(label,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 5, 5, 5, 5));
+  label->MapWindow();
+  label->SetTextJustify(kTextRight);
+
+
+  ePixX=new TGNumberEntry(hframe, 0, 9,999, TGNumberFormat::kNESInteger,
+                                               TGNumberFormat::kNEANonNegative, 
+			     TGNumberFormat::kNELLimitMinMax,0,16535);
+   hframe->AddFrame(ePixX,new TGLayoutHints(kLHintsTop |  kLHintsExpandX, 1, 1, 1, 1));
+   ePixX->MapWindow();
+   ePixX->SetNumber(400);
+   e= ePixX->TGNumberEntry::GetNumberEntry();
+   ePixX->Connect("ValueSet(Long_t)","ctbAcquisition",this,"ChangeImagePixels(Long_t)");
+   e->Connect("ReturnPressed()","ctbAcquisition",this,"ChangeImagePixels()");
+
+
+
+  label=new TGLabel(hframe,"Y: ");
+  hframe->AddFrame(label,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 5, 5, 5, 5));
+  label->MapWindow();
+  label->SetTextJustify(kTextRight);
+
+
+  ePixY=new TGNumberEntry(hframe, 0, 9,999, TGNumberFormat::kNESInteger,
+                                               TGNumberFormat::kNEANonNegative, 
+			     TGNumberFormat::kNELLimitMinMax,0,16535);
+   hframe->AddFrame(ePixY,new TGLayoutHints(kLHintsTop |  kLHintsExpandX, 1, 1, 1, 1));
+   ePixY->MapWindow();
+   ePixY->SetNumber(400);
+   e= ePixY->TGNumberEntry::GetNumberEntry();
+   ePixY->Connect("ValueSet(Long_t)","ctbAcquisition",this,"ChangeImagePixels(Long_t)");
+   e->Connect("ReturnPressed()","ctbAcquisition",this,"ChangeImagePixels()");
+
+
 
 
   hframe=new TGHorizontalFrame(this, 800,50);
@@ -609,8 +663,10 @@ hframe=new TGHorizontalFrame(this, 800,50);
   cout <<"Registering data callback" << endl;
   try {
     myDet->registerDataCallback(&dataCallback, (void*)this);
-  } CATCH_DISPLAY ("Could not get register call back.", "ctbAcquisition::ctbAcquisition")
-
+  } CATCH_DISPLAY ("Could not get register call back.", "ctbAcquisition::ctbAcquisition") 
+      try {
+	myDet->setRxZmqDataStream(true); 
+      } CATCH_DISPLAY ("Could not get set RxZmqDataStream.", "ctbAcquisition::ctbAcquisition") 
   cout <<"Done" << endl;
   
     //  mgAdcs=new TMultiGraph();
@@ -832,7 +888,7 @@ sample1 (dbit0 + dbit1 +...)if (cmd == "rx_dbitlist") {
 
   //  cout <<"global plot is " << globalPlot << endl;
   // cout << "*******************************************" <<endl;
-  // cout <<"------Plot: "<<  index << " prog:" << data->progressIndex << " npoints:" << data->npoints << " npy: " << data->npy << " " << data->fileName << " bytes: " << data->databytes << " dr:"<< data->dynamicRange << " fi: " << data ->fileIndex <<  endl;
+   cout <<"------Plot: "<<  index << " prog:" << data->progressIndex << " nx:" << data->nx << " ny: " << data->ny << " " << data->fileName << " bytes: " << data->databytes << " dr:"<< data->dynamicRange << " fi: " << data ->fileIndex <<  endl;
   if (globalPlot || cbGetPedestal->IsOn()) {
     //#ifdef TESTADC
     //  cout <<"------"<<  index << " " << ip << " " << data->npoints << endl;
@@ -859,6 +915,11 @@ sample1 (dbit0 + dbit1 +...)if (cmd == "rx_dbitlist") {
     nx=eNumCount->GetIntNumber();
     dr=eDynRange->GetIntNumber();
     soff=eSerOff->GetIntNumber();
+    // cout <<"deserializer: " << endl;
+    // cout << "Number of chans:\t" << nx << endl;
+    // cout << "Serial Offset:\t" << soff << endl;
+    // cout << "Dynamic range:\t" << dr << endl;
+    
   }
 
   i=0;
@@ -923,7 +984,8 @@ sample1 (dbit0 + dbit1 +...)if (cmd == "rx_dbitlist") {
       for (int y=0; y<ny; y++) {
 	ped=0;
 	aval=dataStructure->getValue(data->data,x,y);
-      
+	//aval=dataStructure->getChannel(data->data,x,y);
+	cout << x << " " <<y << " "<< aval << endl;
 	if (cbGetPedestal->IsOn()) {
 	  if (photonFinder) {
 	    photonFinder->addToPedestal(aval,x,y);
@@ -1094,8 +1156,20 @@ void ctbAcquisition::Draw(){
 void ctbAcquisition::changePlot(){
   if (rbPlotOff->IsOn()) {
     adcPlot=0;
-    dbitPlot=0;
+    dbitPlot=0;   
+    try {
+      myDet->registerDataCallback(nullptr, this);  
+    } CATCH_DISPLAY ("Could not get unregister call back.", "ctbAcquisition::ctbAcquisition")   
+    try {
+      myDet->setRxZmqDataStream(false); 
+    } CATCH_DISPLAY ("Could not get unset RxZmqDataStream.", "ctbAcquisition::ctbAcquisition") 
   } else {
+  try {
+    myDet->registerDataCallback(&dataCallback, (void*)this);
+  } CATCH_DISPLAY ("Could not get register call back.", "ctbAcquisition::ctbAcquisition")   
+    try {
+      myDet->setRxZmqDataStream(true); 
+    } CATCH_DISPLAY ("Could not get set RxZmqDataStream.", "ctbAcquisition::ctbAcquisition") 
     adcPlot=0;
     dbitPlot=0;
     for (int ii=0; ii<NADCS; ii++)
@@ -1200,6 +1274,9 @@ void ctbAcquisition::changeDetector(){
    eNumCount->SetState(kFALSE);
   eDynRange->SetState(kFALSE);
   eSerOff->SetState(kFALSE);
+  ePixX->SetState(kFALSE);
+  ePixY->SetState(kFALSE);
+    
   deserializer=0;
   if (rb2D->IsOn() ) {//|| rbScan->IsOn()
     switch  (cbDetType->GetSelected()) {
@@ -1210,7 +1287,6 @@ void ctbAcquisition::changeDetector(){
       // commonMode=new moench03CommonMode();
       break;
      case MOENCH04:
-
       try {
         auto retval = myDet->getTenGiga().tsquash("Different values");
         if (retval) {
@@ -1223,6 +1299,54 @@ void ctbAcquisition::changeDetector(){
        cout << "MOENCH 0.4!" << endl;
        commonMode=new moench03CommonMode();
       break;
+     case MOENCH03:
+       //try {
+	// auto retval = myDet->getTenGiga().tsquash("Different values");
+	// if (retval) {
+          dataStructure=new moench03T1ZmqDataNew(nAnalogSamples); 
+        // } else {
+        //   dataStructure=new moench04CtbZmqData(nAnalogSamples, nDigitalSamples); 
+        // }
+	  //} CATCH_DISPLAY ("Could not get ten giga enable.", "ctbAcquisition::changeDetector")
+
+       cout << "MOENCH 0.3! USE JUNGFRAU MODULE!" << endl;
+       commonMode=new moench03CommonMode();
+      break;
+       case IMAGE32B:
+       //try {
+       	// auto retval = myDet->getTenGiga().tsquash("Different values");
+       	// if (retval) {
+       	// if (deserializer) {
+       	   ePixX->SetState(kTRUE);
+       	   ePixY->SetState(kTRUE);
+       	   // }
+       	 dataStructure=new imageZmq32bit(ePixX->GetIntNumber(),ePixY->GetIntNumber()); 
+        // } else {
+        //   dataStructure=new moench04CtbZmqData(nAnalogSamples, nDigitalSamples); 
+        // }
+       	  //} CATCH_DISPLAY ("Could not get ten giga enable.", "ctbAcquisition::changeDetector")
+
+       	 cout << "Image 32bit, no channel shuffling" << endl;
+       commonMode=NULL;
+       break;
+   
+       case IMAGE16B:
+       //try {
+	// auto retval = myDet->getTenGiga().tsquash("Different values");
+	// if (retval) {
+	// if (deserializer) {
+	   ePixX->SetState(kTRUE);
+	   ePixY->SetState(kTRUE);
+	   // }
+	 dataStructure=new imageZmq16bit(ePixX->GetIntNumber(),ePixY->GetIntNumber()); 
+        // } else {
+        //   dataStructure=new moench04CtbZmqData(nAnalogSamples, nDigitalSamples); 
+        // }
+	  //} CATCH_DISPLAY ("Could not get ten giga enable.", "ctbAcquisition::changeDetector")
+
+	 cout << "Image 16bit, no channel shuffling" << endl;
+       commonMode=NULL;
+       break;
    
     // case 1:
     //   cout << "************** T!!!!!!!!!!" << endl;
@@ -1286,6 +1410,7 @@ void ctbAcquisition::changeDetector(){
 	photonFinder=new singlePhotonDetector(dataStructure,csize,nsigma,1,cm); //sign is positive - should correct with ADC mask, no common mode 
 	//photonFinder=new singlePhotonDetector(dataStructure,csize,nsigma,1,cm); //sign is positive - should correct with ADC mask, no common mode
 	dataStructure->getDetectorSize(nx,ny);
+	
       }
       if (deserializer) {
 	ny=1;
@@ -1511,20 +1636,23 @@ void ctbAcquisition::update() {
 
    if (dataStructure) {
      cout << cbDetType->GetSelected()<< endl;
-    if (cbDetType->GetSelected()==MYTHEN301 || cbDetType->GetSelected()==MYTHEN302){
-      cout << "settings deserialiation parameters for MYTHEN" << endl;
-      mythen3_01_jctbData* ms=(mythen3_01_jctbData*)dataStructure;
-      eSerOff->SetNumber( ms->setSerialOffset(-1));
-      eDynRange->SetNumber( ms->setDynamicRange(-1));
-      eNumCount->SetNumber( ms->setNumberOfCounters(-1));
-    }
+    // if (cbDetType->GetSelected()==MYTHEN301 || cbDetType->GetSelected()==MYTHEN302){
+    //   cout << "settings deserialiation parameters for MYTHEN" << endl;
+    //   mythen3_01_jctbData* ms=(mythen3_01_jctbData*)dataStructure;
+    //   eSerOff->SetNumber( ms->setSerialOffset(-1));
+    //   eDynRange->SetNumber( ms->setDynamicRange(-1));
+    //   eNumCount->SetNumber( ms->setNumberOfCounters(-1));
+    // }
     
    }
 
-  try {
-    dBitOffset = myDet->getRxDbitOffset().tsquash("Different values");
-  } CATCH_DISPLAY ("Could not get receiver dbit offset", "ctbAcquisition::update")
-
+  if (myDet->getDetectorType().squash() == slsDetectorDefs::MOENCH) {
+    dBitOffset = 0;
+  } else {
+    try {
+      dBitOffset = myDet->getRxDbitOffset().tsquash("Different values");
+    } CATCH_DISPLAY ("Could not get receiver dbit offset", "ctbAcquisition::update")
+  }
   try {
     tenG = myDet->getTenGiga().tsquash("Different values");
   } CATCH_DISPLAY ("Could not get ten giga enable", "ctbAcquisition::update")
@@ -1610,9 +1738,13 @@ void ctbAcquisition::toggleAcquisition() {
     setDigitalSamples(retval);
   } CATCH_DISPLAY ("Could not get number of digital samples", "ctbAcquisition::toggleAcquisition")
   
+  if (myDet->getDetectorType().squash() == slsDetectorDefs::MOENCH) {
+    dBitOffset = 0;
+  } else {
   try {
-    dBitOffset = myDet->getRxDbitOffset().tsquash("Different values");
-  } CATCH_DISPLAY ("Could not get receiver dbit offset", "ctbAcquisition::toggleAcquisition")
+      dBitOffset = myDet->getRxDbitOffset().tsquash("Different values");
+    } CATCH_DISPLAY ("Could not get receiver dbit offset", "ctbAcquisition::toggleAcquisition")
+  }
 
   try {
     roMode = static_cast<int>(myDet->getReadoutMode().tsquash("Different values"));
@@ -1849,14 +1981,18 @@ void ctbAcquisition::setDbitEnable(Int_t reg){
 void ctbAcquisition::updateChans() {
 
   // dbit list
-  try { 
-    auto retval = myDet->getRxDbitList().tsquash("Different values");
+  if (myDet->getDetectorType().squash() == slsDetectorDefs::MOENCH) {
     dbitlist.clear();
-    if (!retval.empty()) {
-      for (const auto &value : retval) 
-        dbitlist.push_back(value);
-    }
-  } CATCH_DISPLAY ("Could not get receiver dbit list.", "ctbAcquisition::updateChans")
+  } else {
+    try {
+      auto retval = myDet->getRxDbitList().tsquash("Different values");
+      dbitlist.clear();
+      if (!retval.empty()) {
+        for (const auto &value : retval) 
+          dbitlist.push_back(value);
+      }
+    } CATCH_DISPLAY ("Could not get receiver dbit list.", "ctbAcquisition::updateChans")
+  }
 
   // adc mask
   try { 
@@ -1977,20 +2113,22 @@ void ctbAcquisition::ChangeNumberOfChannels(Long_t a){
 
 
 void ctbAcquisition::ChangeSerialOffset(){
+  changeDetector();
   // if (dataStructure) {
 
-  //   //  cout << cbDetType->GetSelected()<< endl;
-  //   // if (cbDetType->GetSelected()==MYTHEN301 || cbDetType->GetSelected()==MYTHEN302 ){
-  //   //   cout << "settings offsets for MYTHEN" << endl;
-  //   //   mythen3_01_jctbData* ms=(mythen3_01_jctbData*)dataStructure;
-  //   //   ms->setSerialOffset(eSerOff->GetIntNumber());
+  //    cout << cbDetType->GetSelected()<< endl;
+  //   if (cbDetType->GetSelected()==MYTHEN301 || cbDetType->GetSelected()==MYTHEN302 ){
+  //     cout << "settings offsets for MYTHEN" << endl;
+  //     mythen3_01_jctbData* ms=(mythen3_01_jctbData*)dataStructure;
+  //     ms->setSerialOffset(eSerOff->GetIntNumber());
       
-  //   // }
+  //   }
   // }
 };
 
 
 void ctbAcquisition::ChangeDynamicRange(){
+  changeDetector();
   // if (dataStructure) {
 
   //    cout << cbDetType->GetSelected()<< endl;
@@ -2004,6 +2142,7 @@ void ctbAcquisition::ChangeDynamicRange(){
 };
 
 void ctbAcquisition::ChangeNumberOfChannels(){
+  changeDetector();
   // if (dataStructure) {
   //    cout << cbDetType->GetSelected()<< endl;
   //   if (cbDetType->GetSelected()==MYTHEN301 || cbDetType->GetSelected()==MYTHEN302){
@@ -2017,6 +2156,24 @@ void ctbAcquisition::ChangeNumberOfChannels(){
     changePlot();
 };
 
+void ctbAcquisition::ChangeImagePixels(Long_t a){
+  ChangeImagePixels();
+};
+
+void ctbAcquisition::ChangeImagePixels(){
+  changeDetector();
+  // if (dataStructure) {
+  //    cout << cbDetType->GetSelected()<< endl;
+  //   if (cbDetType->GetSelected()==MYTHEN301 || cbDetType->GetSelected()==MYTHEN302){
+  //     cout << "settings number of channels for MYTHEN" << endl;
+  //     mythen3_01_jctbData* ms=(mythen3_01_jctbData*)dataStructure;
+  //     ms->setNumberOfCounters(eNumCount->GetIntNumber());
+      
+  //   }
+  // }
+  // if (deserializer)
+  //  changePlot();
+};
 
 
 void ctbAcquisition::ChangeHistoLimitsPedSub(Long_t a){

ctbGui/ctbAcquisition.h

@@ -42,7 +42,7 @@ using namespace std;
 class ctbAcquisition : public TGGroupFrame {
 
 
-  enum {DESERIALIZER, MOENCH04, MOENCH02, ADCSAR2, MYTHEN301, MYTHEN302};
+  enum {DESERIALIZER, MOENCH04, MOENCH02, MOENCH03, IMAGE32B, IMAGE16B, ADCSAR2, MYTHEN301, MYTHEN302};
 
 
  private:
@@ -57,6 +57,9 @@ class ctbAcquisition : public TGGroupFrame {
   TGNumberEntry *eNumCount;
 
 
+  TGNumberEntry *ePixX;
+  TGNumberEntry *ePixY;
+
   TGNumberEntry *eFitADC;
   TGNumberEntry *eBitPlot;
   TGNumberEntry *eMinRaw;
@@ -231,7 +234,8 @@ class ctbAcquisition : public TGGroupFrame {
    void ChangeNumberOfChannels(Long_t);
    void ChangeDynamicRange();
    void ChangeDynamicRange(Long_t);
-
+   void ChangeImagePixels();
+   void ChangeImagePixels(Long_t);
 
    void canvasClicked();
    void FitADC();

ctbGui/ctbDacs.cpp

@@ -108,15 +108,26 @@ string ctbDac::getLabel() {
 
 }
 
+int ctbDac::getMoenchDacId() {
+  slsDetectorDefs::dacIndex moenchDacIndices[8] = {slsDetectorDefs::VBP_COLBUF, slsDetectorDefs::VIPRE, slsDetectorDefs::VIN_CM, slsDetectorDefs::VB_SDA, slsDetectorDefs::VCASC_SFP, slsDetectorDefs::VOUT_CM, slsDetectorDefs::VIPRE_CDS, slsDetectorDefs::IBIAS_SFP}; 
+
+  if (id >= 8) {
+    return id;
+  }
+  return static_cast<int>(moenchDacIndices[id]);
+}
 
 void ctbDac::setValue(Long_t a) {setValue();}
 
 void ctbDac::setValue() {
-
   cout << "setting dac! "<< id << " value " << dacsEntry->GetIntNumber() << " units " << dacsUnit->IsOn() << endl;
 
   try {
-    myDet->setDAC(static_cast<slsDetectorDefs::dacIndex>(id), dacsEntry->GetIntNumber(), dacsUnit->IsOn()); 
+    int sid = id;
+    if (myDet->getDetectorType().squash() == slsDetectorDefs::MOENCH) {
+      sid = getMoenchDacId();
+    }
+    myDet->setDAC(static_cast<slsDetectorDefs::dacIndex>(sid), dacsEntry->GetIntNumber(), dacsUnit->IsOn()); 
   } CATCH_DISPLAY ("Could not set dac " + to_string(id) + ".", "ctbDac::setValue")
 
   getValue();
@@ -128,7 +139,11 @@ void ctbDac::setOn(Bool_t b) {
     setValue();
   } else {
     try {
-      myDet->setDAC(static_cast<slsDetectorDefs::dacIndex>(id), -100, false);
+      int sid = id;
+      if (myDet->getDetectorType().squash() == slsDetectorDefs::MOENCH) {
+	sid = getMoenchDacId();
+      }
+      myDet->setDAC(static_cast<slsDetectorDefs::dacIndex>(sid), -100, false);
     } CATCH_DISPLAY ("Could not power off dac " + to_string(id) + ".", "ctbDac::setOn")
   }
   getValue();
@@ -136,7 +151,11 @@ void ctbDac::setOn(Bool_t b) {
 
 int ctbDac::getValue() { 
   try {
-    int val = myDet->getDAC(static_cast<slsDetectorDefs::dacIndex>(id), dacsUnit->IsOn()).tsquash("Different values"); 
+    int sid = id;
+    if (myDet->getDetectorType().squash() == slsDetectorDefs::MOENCH) {
+      sid = getMoenchDacId();
+    }
+    int val = myDet->getDAC(static_cast<slsDetectorDefs::dacIndex>(sid), dacsUnit->IsOn()).tsquash("Different values"); 
     cout << "dac " << id << " " << val << endl;
     dacsValue->SetText(to_string(val).c_str());
     if (val >= 0) {

ctbGui/ctbDacs.h

@@ -45,7 +45,7 @@ class ctbDac : public TGHorizontalFrame {
    
    int setLabel(char *tit, int mv);
    string getLabel();
-
+int getMoenchDacId();
 
 
    ClassDef(ctbDac,0)
@@ -54,8 +54,6 @@ class ctbDac : public TGHorizontalFrame {
 class ctbDacs : public TGGroupFrame {
 private:
   
-
-
    ctbDac *dacs[NDACS+2];
 
    sls::Detector* myDet;

ctbGui/ctbDefs.h

@@ -71,14 +71,14 @@ class ctbDefs {
                     std::string exceptionMessage,
                     std::string source) {
         // because sls_detector_exceptions cannot be included
-        if (exceptionMessage.find("hared memory")) {
+      if (exceptionMessage.find("hared memory") != std::string::npos) {
             throw;
         }
-        if (exceptionMessage.find("annot connect")) {
+      if (exceptionMessage.find("annot connect") != std::string::npos) {
             throw;
         }
         cprintf(RED, "Warning (%s): %s [Caught Exception: %s]\n", source.c_str(), message.c_str(), exceptionMessage.c_str());
         //return Message(qDefs::WARNING, message + std::string("\nCaught exception:\n") + exceptionMessage, source);
     }; 
 
-};
+};

ctbGui/ctbMain.cpp

@@ -259,8 +259,10 @@ ctbMain::ctbMain(const TGWindow *p, sls::Detector *det)
 
    cout << "connect mtab" << endl;
 
-   
-   setReadoutMode(pat->getReadoutMode());
+  try{  
+   setReadoutMode(pat->getReadoutMode());  
+  } CATCH_DISPLAY ("Could not get readout flags", "ctbPattern::getReadoutMode")
+
    setADCEnable(adcs->setEnable());
    setAnalogSamples(pat->getAnalogSamples());
    setDigitalSamples(pat->getDigitalSamples());

ctbGui/ctbPattern.cpp

@@ -1035,33 +1035,42 @@ void ctbPattern::readoutModeChanged(int flags) {
 
 }
 
-int ctbPattern::getReadoutMode() {
-  try{
-    auto retval = myDet->getReadoutMode().tsquash("Different values");
-    switch(retval) {
-      case slsDetectorDefs::ANALOG_AND_DIGITAL:
-        cout << "analog and digital" << endl;
-        cbAnalog->SetOn(kTRUE);
-        cbDigital->SetOn(kTRUE);
-        break;
-      case slsDetectorDefs::DIGITAL_ONLY:
-        cout << "digital only" << endl;
-        cbAnalog->SetOn(kFALSE);
-        cbDigital->SetOn(kTRUE);
-        break;
-      case slsDetectorDefs::ANALOG_ONLY:
-        cout << "analog only" << endl;
-        cbAnalog->SetOn(kTRUE);
-        cbDigital->SetOn(kFALSE);    
-        break;
-      default:
-        throw("unknown readout flag");
-    }
+int ctbPattern::getReadoutMode() {  
+ int retval=slsDetectorDefs::ANALOG_ONLY;
+    
+ if (myDet->getDetectorType().squash() == slsDetectorDefs::CHIPTESTBOARD) {
+   try{
+     retval = myDet->getReadoutMode().tsquash("Different values");
+   } CATCH_DISPLAY ("Could not get readout flags", "ctbPattern::getReadoutMode")
+      
+   switch(retval) {
+   case slsDetectorDefs::ANALOG_AND_DIGITAL:
+     cout << "analog and digital" << endl;
+     cbAnalog->SetOn(kTRUE);
+     cbDigital->SetOn(kTRUE);
+     break;
+   case slsDetectorDefs::DIGITAL_ONLY:
+     cout << "digital only" << endl;
+     cbAnalog->SetOn(kFALSE);
+     cbDigital->SetOn(kTRUE);
+     break;
+   case slsDetectorDefs::ANALOG_ONLY:
+     cout << "analog only" << endl;
+     cbAnalog->SetOn(kTRUE);
+     cbDigital->SetOn(kFALSE);    
+     break;
+   default:
+     throw("unknown readout flag");
+   }
+ } else {
+   cbAnalog->SetOn(kTRUE);
+   cbDigital->SetOn(kFALSE);    
+ }
+    
     Emit("readoutModeChanged(int)",static_cast<int>(retval));
     return retval;
-  } CATCH_DISPLAY ("Could not get readout flags", "ctbPattern::getReadoutMode")
-
-  return -1;
+ 
+ 
 }
 
 int ctbPattern::getAnalogSamples() {
@@ -1075,13 +1084,17 @@ int ctbPattern::getAnalogSamples() {
   return -1;
 }
    
-int ctbPattern::getDigitalSamples() {
-  try{
-    auto retval = myDet->getNumberOfDigitalSamples().tsquash("Different values");
-    eDigitalSamples->SetNumber((Double_t)retval);
-    Emit("digitalSamplesChanged(const int)", eDigitalSamples->GetNumber());
-    return eDigitalSamples->GetNumber();
-  } CATCH_DISPLAY ("Could not get number of triggers.", "ctbPattern::update")
+int ctbPattern::getDigitalSamples() { 
+  int retval=0;
+  if (myDet->getDetectorType().squash() == slsDetectorDefs::CHIPTESTBOARD) {
+    try{
+      auto retval = myDet->getNumberOfDigitalSamples().tsquash("Different values"); 
+    } CATCH_DISPLAY ("Could not get number of digital samples.", "ctbPattern::getDigitalSamples")
+	}
+  eDigitalSamples->SetNumber((Double_t)retval);
+  Emit("digitalSamplesChanged(const int)", eDigitalSamples->GetNumber());
+  return eDigitalSamples->GetNumber();
+ 
 
   return -1;
 }

ctbGui/ctbSignals.cpp

@@ -374,33 +374,43 @@ void ctbSignals::update() {
 
   } CATCH_DISPLAY ("Could not get patternIOcontrol.", "ctbSignals::update")
 
-  try {
-
-    auto dbitlist = myDet->getRxDbitList().tsquash("Different values");
+  if (myDet->getDetectorType().squash() == slsDetectorDefs::MOENCH) {
     // enable all
-    if (dbitlist.empty()) {
-      for (int is=0; is<64; is++) {
-        signals[is]->setDbitList(1);
-      } 
-    }
-    else {
-      // disable all
-      for (int is=0; is<64; is++) {
-        signals[is]->setDbitList(0);
+    for (int is=0; is<64; is++) {
+      signals[is]->setDbitList(1);
+    } 
+    eDbitOffset->SetNumber(0);
+  } 
+  
+  // ctb
+  else {
+    try {
+
+      auto dbitlist = myDet->getRxDbitList().tsquash("Different values");
+      // enable all
+      if (dbitlist.empty()) {
+        for (int is=0; is<64; is++) {
+          signals[is]->setDbitList(1);
+        } 
       }
-      // enable selected
-      for (const auto &value : dbitlist)  {
-        signals[value]->setDbitList(1);
+      else {
+        // disable all
+        for (int is=0; is<64; is++) {
+          signals[is]->setDbitList(0);
+        }
+        // enable selected
+        for (const auto &value : dbitlist)  {
+          signals[value]->setDbitList(1);
+        }
       }
-    }
 
-  } CATCH_DISPLAY ("Could not get receiver dbit list.", "ctbSignals::update")
-
-  try {
-    auto val = myDet->getRxDbitOffset().tsquash("Different values");
-    eDbitOffset->SetNumber(val);
-  } CATCH_DISPLAY ("Could not get receiver dbit offset.", "ctbSignals::update")
+    } CATCH_DISPLAY ("Could not get receiver dbit list.", "ctbSignals::update")
 
+    try {
+      auto val = myDet->getRxDbitOffset().tsquash("Different values");
+      eDbitOffset->SetNumber(val);
+    } CATCH_DISPLAY ("Could not get receiver dbit offset.", "ctbSignals::update")
+  }
 }
 
 

ctbGui/patternGenerator/generate.sh

@@ -21,6 +21,7 @@ if [ -f "$infile" ]
 then
 gcc -DINFILE="\"$infile\"" -DOUTFILE="\"$outfile\""  -DOUTFILEBIN="\"$outfilebin\"" -o $exe generator.c ; 
 echo compiling
+echo gcc -DINFILE="\"$infile\"" -DOUTFILE="\"$outfile\""  -DOUTFILEBIN="\"$outfilebin\"" -o $exe generator.c ; 
 $exe ; 
 echo cleaning
 rm $exe

docs/CMakeLists.txt

@@ -1,69 +1,75 @@
-find_package(Doxygen)
-find_package(Sphinx)
+find_package(Doxygen REQUIRED)
+find_package(Sphinx REQUIRED)
 
 
-if (DOXYGEN_FOUND AND SPHINX_FOUND)
-    message(${CMAKE_PROJECT_SORURCE_DIR}/slsDetectorSoftware/src)
-    # Utility to generate command line documentation
-    add_executable(gendoc src/gendoc.cpp)
-    # This is a bit hacky, but better than exposing stuff? 
-    target_include_directories(gendoc PRIVATE ${PROJECT_SOURCE_DIR}/slsDetectorSoftware/src)
-    target_link_libraries(gendoc PRIVATE
-      slsDetectorShared
-    )
-    set_target_properties(gendoc PROPERTIES 
-      RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin
-    )
 
-    
-    
 
-    #Doxygen
-    set(DOXYGEN_IN ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in)
-    set(DOXYGEN_OUT ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile)
-    configure_file(${DOXYGEN_IN} ${DOXYGEN_OUT} @ONLY)
+# Utility to generate command line documentation
+add_executable(gendoc src/gendoc.cpp)
+# This is a bit hacky, but better than exposing stuff? 
+target_include_directories(gendoc PRIVATE ${PROJECT_SOURCE_DIR}/slsDetectorSoftware/src)
+target_link_libraries(gendoc PRIVATE
+  slsDetectorShared
+)
+set_target_properties(gendoc PROPERTIES 
+  RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin
+)
 
-    #Sphinx
-    set(SPHINX_SOURCE ${CMAKE_CURRENT_SOURCE_DIR}/src)
-    set(SPHINX_BUILD ${CMAKE_CURRENT_BINARY_DIR})
 
-    set(SPHINX_SOURCE_FILES
-      src/commandline.rst
-      src/container_utils.rst
-      src/dependencies.rst
-      src/detector.rst
-      src/index.rst
-      src/installation.rst
-      src/pydetector.rst
-      src/pyenums.rst
-      src/pyexamples.rst
-      src/receiver.rst
-      src/result.rst
-      src/type_traits.rst
-      src/ToString.rst
-      
-    )
 
-    foreach(filename ${SPHINX_SOURCE_FILES})
-      configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${filename} 
-                    "${SPHINX_BUILD}/${filename}")
-    endforeach(filename ${SPHINX_SOURCE_FILES})
 
-    configure_file(
-        "${CMAKE_CURRENT_SOURCE_DIR}/conf.py.in"
-        "${SPHINX_BUILD}/conf.py"
-        @ONLY)
+#Doxygen
+set(DOXYGEN_IN ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in)
+set(DOXYGEN_OUT ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile)
+configure_file(${DOXYGEN_IN} ${DOXYGEN_OUT} @ONLY)
 
-    add_custom_target(docs
-                    gendoc
-                    COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYGEN_OUT}
-                    COMMAND ${SPHINX_EXECUTABLE} -a -b html
-                    -Dbreathe_projects.slsDetectorPackage=${CMAKE_CURRENT_BINARY_DIR}/xml
-                    -c "${SPHINX_BUILD}"
-                    ${SPHINX_BUILD}/src 
-                    ${SPHINX_BUILD}/html
-                    COMMENT "Generating documentation with Sphinx")
+#Sphinx
+set(SPHINX_SOURCE ${CMAKE_CURRENT_SOURCE_DIR}/src)
+set(SPHINX_BUILD ${CMAKE_CURRENT_BINARY_DIR})
 
-else (DOXYGEN_FOUND AND SPHINX_FOUND)
-  message("Doxygen and Sphinx are needed to build documentation")
-endif (DOXYGEN_FOUND AND SPHINX_FOUND)
+set(SPHINX_SOURCE_FILES
+  src/commandline.rst
+  src/container_utils.rst
+  src/consuming.rst
+  src/dependencies.rst
+  src/detector.rst
+  src/index.rst
+  src/installation.rst
+  src/pydetector.rst
+  src/pyenums.rst
+  src/pyexamples.rst
+  src/receiver.rst
+  src/result.rst
+  src/type_traits.rst
+  src/ToString.rst
+  src/examples.rst
+  
+)
+
+foreach(filename ${SPHINX_SOURCE_FILES})
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${filename} 
+              "${SPHINX_BUILD}/${filename}")
+endforeach(filename ${SPHINX_SOURCE_FILES})
+
+configure_file(
+  "${CMAKE_CURRENT_SOURCE_DIR}/conf.py.in"
+  "${SPHINX_BUILD}/conf.py"
+  @ONLY)
+
+add_custom_target(docs
+              gendoc
+              COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYGEN_OUT}
+              COMMAND ${SPHINX_EXECUTABLE} -a -b html
+              -Dbreathe_projects.slsDetectorPackage=${CMAKE_CURRENT_BINARY_DIR}/xml
+              -c "${SPHINX_BUILD}"
+              ${SPHINX_BUILD}/src 
+              ${SPHINX_BUILD}/html
+              COMMENT "Generating documentation with Sphinx")
+
+add_custom_target(rst
+              COMMAND ${SPHINX_EXECUTABLE} -a -b html
+              -Dbreathe_projects.slsDetectorPackage=${CMAKE_CURRENT_BINARY_DIR}/xml
+              -c "${SPHINX_BUILD}"
+              ${SPHINX_BUILD}/src 
+              ${SPHINX_BUILD}/html
+              COMMENT "Generating documentation with Sphinx")

docs/conf.py.in

@@ -21,7 +21,7 @@ print(sys.path)
 # -- Project information -----------------------------------------------------
 
 project = 'slsDetectorPackage'
-copyright = '2019, PSD Detector Group'
+copyright = '2020, PSD Detector Group'
 author = 'PSD Detector Group'
 version = '@PROJECT_VERSION@'
 

docs/src/consuming.rst

@@ -0,0 +1,116 @@
+Consuming slsDetectorPackage
+===============================
+
+Depending on how you want to build your integration with 
+slsDetectorPackage there are a few different ways to 
+consume our package. The recommended way is to use one of the 
+CMake approaches. 
+
+
+
+CMake: slsDetectorPackage as submodule in your project
+---------------------------------------
+
+If you are using CMake to build your integration and want to build everything
+in one go, we support adding slsDetectorPackage as a subfolder in your cmake project. 
+
+A minimal CMakeLists.txt could look like this: 
+
+.. code-block:: cmake
+
+    project(myDetectorIntegration)
+    cmake_minimum_required(VERSION 3.12)
+    add_subdirectory(slsDetectorPackage)
+
+    #Add your executable
+    add_executable(example main.cpp)
+    target_compile_features(example PRIVATE cxx_std_11)
+
+    #Link towards slsDetectorShared
+    target_link_libraries(example slsDetectorShared)
+
+A fully working example can be found at:
+
+https://github.com/slsdetectorgroup/cmake-subfolder-example
+
+
+CMake: find_package(slsDetectorPackage)
+------------------------------------------
+
+If you have compiled and installed slsDetectorPackage we also support
+find_package in CMake. If installed in a system wide location no path
+should be needed, otherwise specify cmake prefix path. 
+
+.. code-block:: cmake 
+
+    cmake_minimum_required(VERSION 3.12)
+    project(myintegration)
+
+    find_package(slsDetectorPackage 5.0 REQUIRED)
+    add_executable(example main.cpp)
+    target_link_libraries(example slsDetectorShared)
+
+
+Then assuming the slsDetectorPackage is installed in /path/to/sls/install
+you should be able to configure and build your project in this way. 
+
+.. code-block:: bash
+
+    cmake ../path/to/your/source -DCMAKE_PREFIX_PATH=/path/to/sls/install
+    make
+
+
+A minimal example is available at: https://github.com/slsdetectorgroup/minimal-cmake
+
+
+CMake: find_package and conda
+----------------------------------
+
+.. note::
+
+    conda can also be used for installing dependencies such as zmq, Qt4 etc. 
+
+find_package(slsDetectorPackage) also works if you have installed slsDetectorPackage using conda.
+The only difference is that you point CMake to $CONDA_PREFIX 
+
+
+.. code-block:: bash
+
+    #assuming myenv contains slsdetlib
+    conda activate myenv
+    cmake ../path/to/your/source -DCMAKE_PREFIX_PATH=$CONDA_PREFIX
+    make
+
+Depending on your system compiler you might also have to install gxx_linux-64 to compiled.
+
+No tools minimal approach
+-----------------------------
+
+While not recommended it is still possible to specify the include and library paths
+manually when invoking g++. This can sometimes be handy for a quick try. 
+
+.. code-block:: cpp
+
+    #include "Detector.h"
+    #include <iostream>
+    int main(){
+
+        sls::Detector det;
+
+        //Get all values and print them
+        std::cout << "Hostname: " << det.getHostname() << "\n";
+        std::cout << "Type: " << det.getDetectorType() << "\n";
+        std::cout << "Udp ip: " << det.getSourceUDPIP() << "\n";
+
+
+        //Get mac addr 
+        const int module = 0;
+        auto mac = det.getSourceUDPMAC()[module];
+        std::cout << "Mac addr of module "<< module <<  " is " <<  mac.str() << '\n'; 
+
+    }     
+
+
+.. code-block:: bash
+
+    g++ -I/install/path/include/  -L/install/path/lib64/ myapp.cpp -lSlsDetector -lSlsSupport -Wl,-rpath=../install/path/lib64

docs/src/dependencies.rst

@@ -13,7 +13,7 @@ To use the basic building blocks, meaning sls_detector_get/put and
 the shared libraries these are needed: 
 
  * Linux, preferably recent kernel (currently no cross platform support)
- * CMake > 3.9 
+ * CMake > 3.12 
  * C++11 compatible compiler. (We test with gcc and clang)
  * ZeroMQ version 4
 
@@ -24,7 +24,7 @@ GUI
 The GUI is currently using Qt4 but watch out for an upgrade to 5. 
 
  * Qt 4.8
- * Qwt 6
+ * Qwt 6.1
 
 -----------------------
 Python bindings

docs/src/examples.rst

@@ -0,0 +1,115 @@
+
+
+
+Examples
+===========
+
+Setup 
+------------
+
+The examples here assume that you have compiled and installed slsDetectorPackage
+to ~/sls/install and that the option for SLS_USE_SIMULATOR was enabled. This also builds
+the virtual detector servers that we will be using for testing. 
+
+We also add ~/sls/detector/install/bin to the path for convenience. 
+
+Compile examples
+-------------------
+
+The source code of the examples is available at:
+https://github.com/slsdetectorgroup/api-examples
+
+
+.. code-block:: bash
+
+    git clone https://github.com/slsdetectorgroup/api-examples.git
+    mkdir build && cd build
+    cmake ../api-examples -DCMAKE_PREFIX_PATH=~/sls/detector/install
+    make
+
+Below follows a short description of what is included in the examples.
+
+
+Running a config file [e1]
+-----------------------------
+
+
+.. code-block:: cpp
+
+    #include "Detector.h"
+    ...
+    sls::Detector det;
+    det.loadConfig("path/to/config/file.config");
+
+
+
+To configure the connection between PC and detector the easiest 
+is to run a config file. For this example we first launch a virtual Jungfrau server and
+then set up the detector. 
+
+**Launch a virtual detector server**
+
+.. code-block:: bash
+
+    jungfrauDetectorServer_virtual
+
+This launches a virtual Jungfrau detector server. As default is uses port 1952 and 1953
+for communication over TCP. Most commands go on 1952 and only stop and status on 1953. 
+
+**Run example to configure**
+
+.. code-block:: bash
+
+    ./e1-config one_det_no_receiver.config
+    - 12:01:06.371 INFO: Shared memory deleted /slsDetectorPackage_multi_0_sls_0
+    - 12:01:06.371 INFO: Shared memory deleted /slsDetectorPackage_multi_0
+    - 12:01:06.372 INFO: Shared memory created /slsDetectorPackage_multi_0
+    - 12:01:06.376 INFO: Loading configuration file: one_det_no_receiver.config
+    - 12:01:06.376 INFO: Adding detector localhost
+    - 12:01:06.377 INFO: Shared memory created /slsDetectorPackage_multi_0_sls_0
+    - 12:01:06.377 INFO: Checking Detector Version Compatibility
+    - 12:01:06.378 INFO: Detector connecting - updating!
+    hostname [localhost]
+
+
+    Jungfrau detector with 1 modules configured
+
+
+Using the return type sls::Result [e2]
+-----------------------------------------
+
+Since many our detectors have multiple modules we cannot return
+a single value when reading from the Detector. Hostname, Ip and also
+for example exposure time can differ between modules. 
+
+Therefore we return Result<T> which is a thin wrapper around
+std::vector. 
+
+.. code-block:: cpp
+
+    sls::Result<int> res1{1, 1, 1};
+    std::cout << "res1: " << res1 << '\n';
+    res1.squash();
+    res1.squash(-1);
+
+
+
+Setting exposure time [e3]
+-----------------------------------------
+
+For setting times, like exposure time, period, delay etc. 
+we use std::chrono::duration. 
+
+Example 3 shows how to set and read exposure time as well
+as converting to floating point. 
+
+.. code-block:: cpp
+
+    #include "Detector.h"
+    #include <chrono>
+    ...
+    std::chrono::microseconds t0{500};
+    det.setExptime(t0);
+
+
+

docs/src/gendoc.cpp

@@ -1,7 +1,7 @@
-/** 
- * Utility program to generate input files for the command line 
+/**
+ * Utility program to generate input files for the command line
  * documentation. Uses the string returned from sls_detector_help cmd
- * 
+ *
  */
 #include <fstream>
 #include <iostream>
@@ -9,7 +9,6 @@
 #include <string>
 #include <vector>
 
-
 #include "CmdProxy.h"
 #include "Detector.h"
 #include "sls_detector_defs.h"
@@ -52,5 +51,4 @@ int main() {
         auto help = replace_all(tmp, "\n\t", "\n\t\t");
         fs << '\t' << cmd << usage << help << "\n";
     }
-
 }

docs/src/index.rst

@@ -6,12 +6,18 @@
 Welcome to slsDetectorPackage's documentation!
 ==============================================
 
+.. note :: 
+
+    This is the documentation for the latest development version of slsDetectorPackage
+    For documentation on current and previous releases visit the official page: https://www.psi.ch/en/detectors/documentation
+
 .. toctree::
     :maxdepth: 1
     :caption: Installation:
 
     installation
     dependencies
+    consuming
    
 .. toctree::
     :caption: C++ API
@@ -20,6 +26,7 @@ Welcome to slsDetectorPackage's documentation!
     detector
     result
     receiver
+    examples
 
 .. toctree::
     :caption: Python API

docs/src/installation.rst

@@ -2,4 +2,68 @@
 Installation
 ==============================================
 
-get the source etc.
+Build from source using CMake
+---------------------------------
+
+.. note :: 
+
+    The default branch of our git repository is developer. It contains the 
+    latest development version. It is expected to compile and work but 
+    features might be added or tweaked. In some cases the API might also change
+    without being communicated. If absolute stability of the API is needed please
+    use one of the release versions. 
+
+.. code-block:: bash
+
+    git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git
+    mkdir build && cd build
+    cmake ../slsDetectorPackage -DCMAKE_INSTALL_PREFIX=/your/install/path
+    make -j12
+    make install
+
+Install binaries using conda
+--------------------------------
+
+.. code-block:: bash
+
+    #Add channels for dependencies and our library
+    conda config --add channels conda-forge
+    conda config --add channels slsdetectorgroup
+    conda config --set channel_priority strict
+
+    #cerate an environment with our library, then activate
+    conda create -n myenv slsdetlib=2020.03.18.dev2
+    codna activate myenv
+
+    #ready to use
+    sls_detector_get exptime
+    etc ...
+
+
+
+Build from source on old distributions
+-----------------------------------------
+
+If your linux distribution doesn't come with a C++11 compiler (gcc>4.8) then 
+it's possible to install a newer gcc using conda and build the slsDetectorPackage
+using this compiler
+
+.. code-block:: bash
+
+    #Create an environment with the dependencies
+    conda create -n myenv gxx_linux-64 cmake zmq
+    conda activate myenv
+    cmake ../slsDetectorPackage -DCMAKE_PREFIX_PATH=$CONDA_PREFIX
+    make -j12
+
+
+Build this documentation
+-------------------------------
+
+The documentation for the slsDetectorPackage is build using a combination 
+of Doxygen, Sphinx and Breathe. The easiest way to install the dependencies
+is to use conda 
+
+.. code-block:: bash
+
+    conda create -n myenv python sphinx sphinx_rtd_theme

docs/src/pydetector.rst

@@ -1,9 +1,9 @@
 Detector
 =====================================================
 
-.. py:currentmodule:: sls_detector
+.. py:currentmodule:: slsdet
 
-.. autoclass:: ExperimentalDetector
+.. autoclass:: Detector
     :members:  
     :undoc-members:
     :show-inheritance:

docs/src/pyenums.rst

@@ -4,7 +4,7 @@ Enums
 These enums are defined in slsDetectorDefs in the C++ package and 
 exposed to Python through pybind11.
 
-.. py:currentmodule:: sls_detector
+.. py:currentmodule:: slsdet
 
 .. autoclass:: runStatus
     :members:  

docs/src/pyexamples.rst

@@ -74,7 +74,7 @@ But lets start looking at the at the manual way:
 ::
 
     import time
-    from sls_detector import Eiger
+    from slsdet import Eiger
     d = Eiger()
 
     n = 10
@@ -114,7 +114,7 @@ hang around until the main process exits.
 
     import time
     from multiprocessing import Process
-    from sls_detector import Eiger
+    from slsdet import Eiger
 
     def acquire():
         """

examples/gotthard_II.config

@@ -0,0 +1,29 @@
+hostname strip3
+
+udp_srcip 10.1.1.184
+udp_dstip 10.1.1.107
+
+udp_dstport2 50084
+udp_srcip2 10.1.1.185
+udp_dstip2 10.1.1.107
+
+rx_hostname pc12365:1954
+#udp_dstmac 3c:fd:fe:d2:a4:25
+fpath  /tmp
+fname run
+fwrite 0
+
+bursts 10
+frames 2700
+burstperiod 100ms
+
+numinterfaces 2
+veto 1
+
+#fixing data looks
+# Sampling pipeline 1 clk
+reg 0x120 0x00000010
+clkphase 1 135 deg
+
+
+

examples/jctb_moench03_T1.config

@@ -1,4 +1,14 @@
-hostname bchip085+
+initialchecks 0
+#############################################
+### edit with hostname or IP address of your detector 
+############################################
+hostname bchip181+
+runclk 40
+adcclk 20
+dbitclk 40
+
+
+
 
 patword 0000 0000000000000000
 patword 0001 0000000000000000
@@ -408,84 +418,84 @@ patnloop1 0
 patloop2 0400 0400
 patnloop2 0
 patwait0 00aa
-patwaittime0 40000
+patwaittime0 10000
 patwait1 0400
 patwaittime1 0
 patwait2 0400
 patwaittime2 0
 
 
-####mcp2011
-#0:rx_udpip 10.1.1.102
-#0:detectorip 10.1.1.19
-#0:rx_udpport 32410
-####gui listening to 
-#zmqip 129.129.202.131
-#zmqport 30001
-####data streaming out of
-#rx_zmqip 10.1.2.103
-#rx_zmqport 30003
-#0:rx_hostname mpc2011
+#0:rx_tcpport 1977
 
-####mx-test-1
-0:rx_udpip 10.1.1.100
-0:detectorip 10.1.1.19
-0:rx_udpport 32410
-####gui listening to (on receiver pc)
-zmqip 129.129.202.92
-zmqport 30001
-####data streaming out of
-rx_zmqip 10.1.1.100
-rx_zmqport 30003
-0:rx_hostname pcmoench01
+#############################################
+### edit with 10 Gbs IP of your server
+############################################
+0:udp_dstip 10.1.1.102
+#0:udp_dstip 129.129.202.136
+#############################################
+### edit with any number in the subnet of your server (first 3 numbers as above)
+############################################
+0:udp_srcip 10.1.1.19
+#0:udp_srcip 129.129.202.13
+
+0:udp_dstport 33410
+#############################################
+### edit with 10 Gbs IP of your server
+############################################
+#zmqip 129.129.202.110
+#rx_zmqip 10.1.1.102
+#rx_zmqport 30001
+#############################################
+### edit with 1 Gbs IP of PC where you will run the GUI
+############################################
+#zmqip 129.129.202.110
+#zmqport 50001
 
 
+#############################################
+### edit with hostname or 1Gbs IP address of your server
+############################################
+rx_hostname mpc2011
 
+tengiga 1
 
-
-
-
-
-
-
-
-#turn on datastream from commandline
 rx_datastream 1
-
-r_readfreq 1
-
-#0:configuremac -1
-rx_datastream 1
-
-r_readfreq 1
+rx_readfreq 1
 
 
-dac:6 800
-dac:0 1300
-dac:4 1428
-dac:1 1000
-dac:7 900
-dac:3 680
-dac:2 1400
-dac:5 1200
+dac 6 800
+dac 0 1300
+dac 4 1428
+dac 1 1000
+dac 7 900
+dac 3 680
+dac 2 1400
+dac 5 1200
 adcinvert 4a342593
-samples 5000
-adcphase 90
-adcpipeline 15
+#0xb5cbda6c
+asamples 5000
+dsamples 0
+adcphase 30 deg
+adcpipeline 14
 adcreg 14 40
-powerchip 1
+
+
+frames 1000
+period 0.001
+#############################################
+### edit with directory you want to write to
+############################################
+fpath /tmp/
+fwrite 0
+
+romode analog
+#rx_jsonaddheader frameMode
+rx_jsonpara frameMode newpedestal
+#rx_jsonaddheader detectorMode
+rx_jsonpara detectorMode analog
+#flags newpedestal
+#flags analog
+
+reg 0x5e 0x00010000
+#powerchip 1
 vhighvoltage 90
-period 0.005
-
-
-
-
-
-
-frames 100
-period 0.1
-outdir /scratch/
-enablefwrite 0
-
-
-

examples/moench03_T1.config

@@ -0,0 +1,63 @@
+initialchecks 0
+#############################################
+### edit with hostname or IP address of your detector 
+############################################
+hostname bchip181+
+
+#############################################
+### edit with hostname or 1Gbs IP address of your server
+############################################
+rx_hostname mpc2011
+
+rx_tcpport 1954
+#############################################
+### edit with 10 Gbs IP of your server
+############################################
+udp_dstip 10.1.1.102
+#############################################
+### edit with any number in the subnet of your server (first 3 numbers as above)
+############################################
+udp_srcip 10.1.1.19
+udp_dstport 32411
+
+#############################################
+### edit with 10 Gbs IP of your server
+############################################
+rx_zmqip 10.1.1.102
+rx_zmqport 50003
+#############################################
+### edit with 1 Gbs IP of PC where you will run the GUI
+############################################
+zmqip 129.129.202.136
+zmqport 50001
+
+
+
+
+tengiga 1
+rx_datastream 1
+
+
+
+frames 100000
+period 0.0006
+#############################################
+### edit with directory you want to write to
+############################################
+fpath /mnt/moench_data/scratch/
+fwrite 0
+rx_datastream 1
+
+rx_jsonpara frameMode frame
+rx_jsonpara detectorMode counting
+rx_discardpolicy discardpartial
+
+
+adcpipeline 15
+
+powerchip 1
+vhighvoltage 90
+
+#adcreg 0x14 0x40
+
+

integrationTests/test-eigerIntegration.cpp

@@ -1,5 +1,5 @@
-#include "catch.hpp"
 #include "DetectorImpl.h"
+#include "catch.hpp"
 #include "string_utils.h"
 #include "tests/globals.h"
 #include <iostream>

integrationTests/test-integrationDectector.cpp

@@ -2,9 +2,9 @@
 #include "catch.hpp"
 
 #include "ClientSocket.h"
-#include "logger.h"
 #include "DetectorImpl.h"
-#include "slsDetector.h"
+#include "Module.h"
+#include "logger.h"
 #include "sls_detector_defs.h"
 
 #include "Timer.h"
@@ -23,10 +23,10 @@
 // extern dt type;
 
 TEST_CASE("Single detector no receiver", "[.integration][.single]") {
-    auto t = slsDetector::getTypeFromDetector(test::hostname);
+    auto t = Module::getTypeFromDetector(test::hostname);
     CHECK(t == test::type);
 
-    slsDetector d(t);
+    Module d(t);
     CHECK(d.getDetectorTypeAsEnum() == t);
     CHECK(d.getDetectorTypeAsString() == test::detector_type);
 
@@ -51,7 +51,7 @@ TEST_CASE("Set control port then create a new object with this control port",
     int new_cport = 1993;
     int new_sport = 2000;
     {
-        slsDetector d(test::type);
+        Module d(test::type);
         d.setHostname(test::hostname);
         CHECK(d.getControlPort() == old_cport);
         d.setControlPort(new_cport);
@@ -60,7 +60,7 @@ TEST_CASE("Set control port then create a new object with this control port",
         d.freeSharedMemory();
     }
     {
-        slsDetector d(test::type);
+        Module d(test::type);
         d.setHostname(test::hostname);
         d.setControlPort(new_cport);
         d.setStopPort(new_sport);
@@ -73,24 +73,23 @@ TEST_CASE("Set control port then create a new object with this control port",
         d.freeSharedMemory();
     }
 
-    slsDetector d(test::type);
+    Module d(test::type);
     d.setHostname(test::hostname);
     CHECK(d.getStopPort() == DEFAULT_PORTNO + 1);
     d.freeSharedMemory();
 }
 
-
 TEST_CASE("single EIGER detector no receiver basic set and get",
           "[.integration][eiger]") {
     // TODO! this test should take command line arguments for config
     SingleDetectorConfig c;
 
     // Read type by connecting to the detector
-    auto type = slsDetector::getTypeFromDetector(c.hostname);
+    auto type = Module::getTypeFromDetector(c.hostname);
     CHECK(type == c.type_enum);
 
-    // Create slsDetector of said type and set hostname and detector online
-    slsDetector d(type);
+    // Create Module of said type and set hostname and detector online
+    Module d(type);
     CHECK(d.getDetectorTypeAsEnum() == type);
     CHECK(d.getDetectorTypeAsString() == c.type_string);
 
@@ -130,10 +129,8 @@ TEST_CASE("single EIGER detector no receiver basic set and get",
     d.freeSharedMemory();
 }
 
-
-
 TEST_CASE("Locking mechanism and last ip", "[.integration][.single]") {
-    slsDetector d(test::type);
+    Module d(test::type);
     d.setHostname(test::hostname);
 
     // Check that detector server is unlocked then lock
@@ -154,13 +151,12 @@ TEST_CASE("Locking mechanism and last ip", "[.integration][.single]") {
     d.freeSharedMemory();
 }
 
-TEST_CASE("Set settings", "[.integration][.single]"){
-    slsDetector d(test::type);
+TEST_CASE("Set settings", "[.integration][.single]") {
+    Module d(test::type);
     d.setHostname(test::hostname);
     CHECK(d.setSettings(defs::STANDARD) == defs::STANDARD);
 }
 
-
 TEST_CASE("Timer functions", "[.integration][cli]") {
     // FRAME_NUMBER, /**< number of real time frames: total number of
     // acquisitions is number or frames*number of triggers */ ACQUISITION_TIME,
@@ -185,7 +181,7 @@ TEST_CASE("Timer functions", "[.integration][cli]") {
     // MEASURED_SUBPERIOD,	/**< measured subperiod */
     // MAX_TIMERS
 
-    slsDetector d(test::type);
+    Module d(test::type);
     d.setHostname(test::hostname);
 
     // Number of frames
@@ -204,8 +200,7 @@ TEST_CASE("Timer functions", "[.integration][cli]") {
     if (test::type != dt::EIGER) {
         auto delay = 10000;
         d.setDelayAfterTrigger(delay);
-        CHECK(d.getDelayAfterTrigger() ==
-              delay);
+        CHECK(d.getDelayAfterTrigger() == delay);
     }
 
     auto triggers = 2;
@@ -218,16 +213,15 @@ TEST_CASE("Timer functions", "[.integration][cli]") {
         CHECK(d.getSubExptime() == subtime);
     }
     // for (int i =0; i!=frames; ++i)
-        d.startAndReadAll();
+    d.startAndReadAll();
 
     d.freeSharedMemory();
-
 }
 
 // TEST_CASE("Aquire", "[.integration][eiger]"){
 //     SingleDetectorConfig c;
-//     auto type = slsDetector::getTypeFromDetector(c.hostname);
-//     slsDetector d(type);
+//     auto type = Module::getTypeFromDetector(c.hostname);
+//     Module d(type);
 //     d.setHostname(c.hostname);
 
 //     auto period = 1000000000;
@@ -382,8 +376,8 @@ TEST_CASE("Chiptestboard Loading Patterns", "[.ctbintegration]") {
     }
 }
 
-
-TEST_CASE("Chiptestboard Dbit offset, list, sampling, advinvert", "[.ctbintegration][dbit]") {
+TEST_CASE("Chiptestboard Dbit offset, list, sampling, advinvert",
+          "[.ctbintegration][dbit]") {
     SingleDetectorConfig c;
 
     // pick up multi detector from shm id 0
@@ -403,27 +397,27 @@ TEST_CASE("Chiptestboard Dbit offset, list, sampling, advinvert", "[.ctbintegrat
 
     // dbit list
 
-    std::vector <int> list = m.getReceiverDbitList();
+    std::vector<int> list = m.getReceiverDbitList();
     list.clear();
     for (int i = 0; i < 10; ++i)
         list.push_back(i);
     m.setReceiverDbitList(list);
-    
+
     CHECK(m.getReceiverDbitList().size() == 10);
 
     list.push_back(64);
     CHECK_THROWS_AS(m.setReceiverDbitList(list), sls::RuntimeError);
-    CHECK_THROWS_WITH(m.setReceiverDbitList(list), 
-        Catch::Matchers::Contains("be between 0 and 63"));
+    CHECK_THROWS_WITH(m.setReceiverDbitList(list),
+                      Catch::Matchers::Contains("be between 0 and 63"));
 
     list.clear();
     for (int i = 0; i < 65; ++i)
         list.push_back(i);
     CHECK(list.size() == 65);
-    CHECK_THROWS_WITH(m.setReceiverDbitList(list),  
-        Catch::Matchers::Contains("be greater than 64"));
+    CHECK_THROWS_WITH(m.setReceiverDbitList(list),
+                      Catch::Matchers::Contains("be greater than 64"));
 
-    list.clear(); 
+    list.clear();
     m.setReceiverDbitList(list);
     CHECK(m.getReceiverDbitList().empty());
 
@@ -441,8 +435,8 @@ TEST_CASE("Chiptestboard Dbit offset, list, sampling, advinvert", "[.ctbintegrat
     m.setExternalSamplingSource(62);
     CHECK(m.getExternalSamplingSource() == 62);
     CHECK_THROWS_WITH(m.setExternalSamplingSource(64),
-         Catch::Matchers::Contains("be 0-63"));
-    CHECK(m.getExternalSamplingSource() == 62); 
+                      Catch::Matchers::Contains("be 0-63"));
+    CHECK(m.getExternalSamplingSource() == 62);
     m.setExternalSampling(1);
     CHECK(m.getExternalSampling() == 1);
     m.setExternalSampling(0);
@@ -450,20 +444,23 @@ TEST_CASE("Chiptestboard Dbit offset, list, sampling, advinvert", "[.ctbintegrat
     m.setExternalSampling(1);
     CHECK(m.getExternalSampling() == 1);
     CHECK(m.readRegister(0x7b) == 0x1003E);
-    
 }
 
-TEST_CASE("Eiger or Jungfrau startingfnum", "[.eigerintegration][.jungfrauintegration][startingfnum]") {
+TEST_CASE("Eiger or Jungfrau startingfnum",
+          "[.eigerintegration][.jungfrauintegration][startingfnum]") {
     SingleDetectorConfig c;
 
     // pick up multi detector from shm id 0
     DetectorImpl m(0);
 
     // ensure ctb detector type, hostname and online
-    REQUIRE(((m.getDetectorTypeAsEnum() == slsDetectorDefs::detectorType::EIGER) || (m.getDetectorTypeAsEnum() == slsDetectorDefs::detectorType::JUNGFRAU)));
+    REQUIRE(
+        ((m.getDetectorTypeAsEnum() == slsDetectorDefs::detectorType::EIGER) ||
+         (m.getDetectorTypeAsEnum() ==
+          slsDetectorDefs::detectorType::JUNGFRAU)));
     REQUIRE(m.getHostname() == c.hostname);
 
-     CHECK(m.setNumberOfFrames(1) == 1);
+    CHECK(m.setNumberOfFrames(1) == 1);
 
     // starting fnum
     uint64_t val = 8;
@@ -498,7 +495,8 @@ TEST_CASE("Eiger readnlines", "[.eigerintegration][readnlines]") {
     DetectorImpl m(0);
 
     // ensure detector type, hostname
-    REQUIRE((m.getDetectorTypeAsEnum() == slsDetectorDefs::detectorType::EIGER));
+    REQUIRE(
+        (m.getDetectorTypeAsEnum() == slsDetectorDefs::detectorType::EIGER));
     REQUIRE(m.getHostname() == c.hostname);
 
     m.setDynamicRange(16);
@@ -507,7 +505,7 @@ TEST_CASE("Eiger readnlines", "[.eigerintegration][readnlines]") {
     CHECK(m.getReadNLines() == 256);
     m.setReadNLines(1);
     CHECK(m.getReadNLines() == 1);
-        
+
     m.setDynamicRange(8);
     m.setReadNLines(256);
     CHECK(m.getReadNLines() == 256);

integrationTests/test-integrationMulti.cpp

@@ -1,5 +1,5 @@
-#include "catch.hpp"
 #include "DetectorImpl.h"
+#include "catch.hpp"
 #include "string_utils.h"
 #include "tests/globals.h"
 #include <iostream>
@@ -24,8 +24,6 @@ TEST_CASE("Initialize a multi detector", "[.integration][.multi]") {
     d.freeSharedMemory();
 }
 
-
-
 TEST_CASE("Set and read timers", "[.integration][.multi]") {
 
     DetectorImpl d(0, true, true);
@@ -57,7 +55,6 @@ TEST_CASE("Set and read timers", "[.integration][.multi]") {
     // PROGRESS, /**< fraction of measurement elapsed - only get! */
     // MEASUREMENTS_NUMBER,
 
-
     // FRAMES_FROM_START,
     // FRAMES_FROM_START_PG,
     // SAMPLES,
@@ -78,7 +75,6 @@ TEST_CASE("Set and read timers", "[.integration][.multi]") {
         CHECK(d.setSubFrameExposureDeadTime(-1) == Approx(subframe_deadtime));
     }
 
-    
     if (test::type == dt::EIGER) {
         // 32bit is needed for subframe exposure
         d.setDynamicRange(32);

manual/manual-client/Eiger_short.tex

@@ -176,6 +176,7 @@ One can configure all the detector settings in a parameter file {\tt{setup.det}}
 \begin{verbatim}
 sls_detector_put 0-parameters setup.det
 \end{verbatim}
+Note that the parameter file for any realease before 4.1.1 has not the possibility to understand parameters to be set differently for different half modules, i.e.  {\tt{0:txndelay\_left xxxxx},\tt{1:txndelay\_left yyyyy}}. 
 
 In the case of \E, the proper bias voltage of the sensor has to be setup, i.e. the {\tt{setup.det}} file needs to contain the line {\tt{vhighvoltage 150}}. Other detector functionality, which are rarely changed can be setup here. 
 Other important settings that are configured in the {\tt{setup.det}} file are:
@@ -359,16 +360,16 @@ In the case of REAL CONTINUOUS readout, i.e. continuous acquire and readout from
 \hline 
 1 &  32 &  \textbf{128} & 7820 & \\
 \hline 
-10 & 4 & \textbf{10240} & 98 & 105/128\\
+10 & 4 & \textbf{7813} & 98 & 105/128\\
 \hline 
-10 & 8 & \textbf{5120} & 196 & 210/250\\
+10 & 8 & \textbf{4000} & 196 & 210/250\\
 \hline
-10 & 16 & \textbf{2560} & 391 & 420/490\\  
+10 & 16 & \textbf{2000} & 391 & 420/490\\  
 \hline 
-10 & 32 & \textbf{1280} & 782 & 840/977\\  
+10 & 32 & \textbf{1023} & 782 & 840/977\\  
 \hline 
 \end{tabular}
-\caption{Frame rate limits for the CONTINUOS streaming out of images, i.e. the data rate out is just below 1Gb/s or 10Gb/s. 1280~Hz for 32-bit, 10GbE is obtained from the 10GbE limitation. The maximum achievable frame rate is 977~Hz.} 
+\caption{Frame rate limits for the CONTINUOS streaming out of images, i.e. the data rate out is just below 1Gb/s or 10Gb/s. 1023~Hz for 32-bit, 10GbE is obtained from the 10GbE limitation. The maximum achievable frame rate is 977~Hz.} 
 \label{tcont}\end{table}
  Note that in the {\tt{continuous}} flag mode, some buffering is still done on the memories, so a higher frame rate than the proper real continuous one can be achieved. Still, this extra buffering is possible till the memories are not saturated. The number of images that can be stored on the DDR2 on board memories are listed in table~\ref{timgs}.
 \begin{table}
@@ -609,18 +610,19 @@ The detector can be setup such to receive external triggers. Connect a LEMO sign
 \begin{verbatim}
 sls_detector_put 0-timing [auto/trigger/burst_trigger/gating]
 sls_detector_put 0-frames x
-sls_detector_put 0-triggers y
+sls_detector_put 0-cycles y
 sls_detector_acquire 0-
 \end{verbatim}
 No timeout is expected between the start of the acquisition and the arrival of the first trigger. 
 
 Here are the implemented options so far:
 \begin{itemize}
-\item {\tt{auto}} is the software controlled acquisition (does not use triggers), where {\tt{exptime}} and {\tt{period}} have to be set. Set number of triggers (i.e. triggers) to 1 using {\tt{triggers}}. Set number of frames using {\tt{frames}}.
-\item {\tt{trigger}} 1 frame taken for 1 trigger. Your {\tt{frames}} needs to be  1 always, {\tt{triggers}} can be changed and defines how many triggers are considered.  {\tt{exptime}} needs to be set. In the GUI this is called trigger exposure series.  
-\item {\tt{burst\_trigger}} gets only 1 trigger, but allows to take many frames. With {\tt{frames}} one can change the number of frames. {\tt{triggers}} needs to be 1.  {\tt{exptime}} and {\tt{period}} have to be set. In the gui it is called trigger readout.
-\item{\tt{gating}} allows to get a frame only when the trigger pulse is gating. Note that in this case the exp time and period only depend on the gating signal. {\tt{triggers}} allows to select how many gates to consider.  Set number of frames to 1 using {\tt{frames}}. IMPORTANT: Up to firmware 23, the last subframe is oblige to finish being taken, despite the gate signal going down. This will be configurable from later fw and software version. Also, in gating mode, due to timimg of the state machine, you need to leave 500~$\mu$s deadtime between the end on an acquisition and the next. This is as the state machine is unable to check for changes in the status in the first 500~$\mu$s. ATTENTION: if you are in 16 bit mode and you are applying online rate corrections, as now the exptime is generated by the trigger, you might not have correct rate corrections. If you know what the exposure time is in the gating signal, then you can set the {\tt{exptime}} once and the rate corrections will be correct. In 32 bit mode, it does not matter as the rate corrections depends on the {\tt{subexptime}} which is software set independently from the gate exptime.
+\item {\tt{auto}} is the software controlled acquisition (does not use triggers), where {\tt{exptime}} and {\tt{period}} have to be set. Set number of cycles (i.e. triggers) to 1 using {\tt{cycles}}. Set number of frames using {\tt{frames}}.
+\item {\tt{trigger}} 1 frame taken for 1 trigger. Your {\tt{frames}} needs to be  1 always, {\tt{cycles}} can be changed and defines how many triggers are considered.  {\tt{exptime}} needs to be set. In the GUI this is called trigger exposure series.  
+\item {\tt{burst\_trigger}} gets only 1 trigger, but allows to take many frames. With {\tt{frames}} one can change the number of frames. {\tt{cycles}} needs to be 1.  {\tt{exptime}} and {\tt{period}} have to be set. In the gui it is called trigger readout.
+\item{\tt{gating}} allows to get a frame only when the trigger pulse is gating. Note that in this case the exp time and period only depend on the gating signal. {\tt{cycles}} allows to select how many gates to consider.  Set number of frames to 1 using {\tt{frames}}. IMPORTANT: Up to firmware 23, the last subframe is oblige to finish being taken, despite the gate signal going down. This will be configurable from later fw and software version. Also, in gating mode, due to timimg of the state machine, you need to leave 500~$\mu$s deadtime between the end on an acquisition and the next. This is as the state machine is unable to check for changes in the status in the first 500~$\mu$s. ATTENTION: if you are in 16 bit mode and you are applying online rate corrections, as now the exptime is generated by the trigger, you might not have correct rate corrections. If you know what the exposure time is in the gating signal, then you can set the {\tt{exptime}} once and the rate corrections will be correct. In 32 bit mode, it does not matter as the rate corrections depends on the {\tt{subexptime}} which is software set independently from the gate exptime.
 
+ATTENTION: From release 4.1.1 with the {\tt{trigger}} option it is possible to have software triggers as a debugging tool (instead of the hardware trigger signal. One should start the acquisition (with the blocking {\tt{sls\_detector\_acquire}} if wanted and with another client one can send the softare trigger {\tt{sls\_detector\_put status trigger}}. This option allows for example to perform a motor scan (moving a motor in between single images) and still writing all images to the same file. 
 When using 32-bit mode, by default the acquisition ends the last complete subframe that was started when still the acquisition time was valid. This has been chosen as many people wants to know the exact acquisition time for when the detector was taking data and also, if {\tt{ratecorr}} are active, the last subframe will be correctly corrected, while otherwise it will be corrected with a wrong subdeadtime. 
 However, from 4.1.0, in gating mode, an option to immediately terminate the subframe when the gate signal goes down it is implemented to stop the acquisition at the same time.  This option is {\tt{./sls\_detector\_put interruptsubframe 1}} while the default option is {\tt{./sls\_detector\_put interruptsubframe 0}}.  
 
@@ -628,13 +630,13 @@ However, from 4.1.0, in gating mode, an option to immediately terminate the subf
 
 Hardware-wise, the ENABLE OUT signal outputs when the chips are really acquiring. This means that the single subframes will be output in 32 bit mode. The TRIGGER OUT outputs the sum-up-signal at the moment (which is useless). This will be changed in the future to output the envelop of the enable signal. 
 
-We are planning to change some functionality, i.e. unify the {\tt{trigger}} and {\tt{burst\_trigger}} trigger modes and make both {\tt{frames}} and {\tt{triggers}} configurable at the same time.
+We are planning to change some functionality, i.e. unify the {\tt{trigger}} and {\tt{burst\_trigger}} trigger modes and make both {\tt{frames}} and {\tt{cycles}} configurable at the same time.
 
 There is the possibility to use {\tt{timing trigger/burst\_trigger}} and send software single commands to fake the trigger. This is done with:
 \begin{verbatim}
 sls_detector_put 0-timing [trigger/burst_trigger]
 sls_detector_put 0-frames x
-sls_detector_put 0-triggers y
+sls_detector_put 0-cycles y
 sls_detector_status trigger
 \end{verbatim}
  Note that this functionality is very (!) useful if you need to do something between and acquisition and the next. This can be used to do a fast threshold scan for example. See section~\ref{sec:fastthresholdscan}.
@@ -715,7 +717,7 @@ If \textbf{dr} is 32 and \textbf{clkdivider} is not 2, whatever the detector get
 Here is a list of parameters that should be reset:
 \begin{enumerate}
 \item  \textbf{resetframescaught} should be reset to zero after every acquisition taken with {\tt{receiver start}},{\tt{status start}},{\tt{receiver stop}}. If the acquisition is taken with {\tt{sls\_detector\_acquire}}, there is no need to reset this.
-\item After changing the {\tt{timing}} mode of the detector, one should reset to '1' the unused value, in that specific timing mode, between \textbf{frames} and \textbf{triggers}. See section~\ref{triggering} for how to use the timing. At the present moment the detector will acquire more frames than planned if the variable not used between \textbf{frames} and \textbf{triggers} is not reset. In future releases, the unused variable will be ignored. Still resetting is a good practice.
+\item After changing the {\tt{timing}} mode of the detector, one should reset to '1' the unused value, in that specific timing mode, between \textbf{frames} and \textbf{cycles}. See section~\ref{triggering} for how to use the timing. At the present moment the detector will acquire more frames than planned if the variable not used between \textbf{frames} and \textbf{cycles} is not reset. In future releases, the unused variable will be ignored. Still resetting is a good practice.
       
 \end{enumerate}
 
@@ -988,13 +990,14 @@ Packets Caught Mask        : 64 bytes
 Note that if one wants to  reconstruct the real time the detector was acquiring in 32 bit (autosumming mode), one would have to multiply the SubExptime (ns) for the SubFrame Number. 
 
 \subsection{Offline image reconstruction}
-The offline image reconstruction{\tt{slsImageReconstruction}} is not part of the package anymore. The code is still available doing \\
-{\tt{git clone git@git.psi.ch:sls\_detectors\_software/sls\_image\_reconstruction.git slsImageReconstruction}}.
-Checkout the {\tt{developer}} branch if in a 3.1.X release, the {\tt{v4.0.0}} branch if in 4.0.X release, or the {\tt{v4.1}} branch if in 4.1.X release of the {\tt{slsDetector}} code.
+The offline image reconstruction{\tt{slsImageReconstruction}} is not part of the package anymore. However, it can be retrieved from \\
+{\tt{git clone https://github.com/slsdetectorgroup/slsImageReconstruction.git slsImageReconstruction}}.\\
+Checkout the {\tt{v3.1}} branch if in a 3.1.X release, the {\tt{v4.0.0}} branch if in 4.0.X release, or the {\tt{v4.1}} branch if in 4.1.X release of the {\tt{slsDetector}} code. There is a {\tt{developer}} branch that has newer updates but needs to be tested.
 
-Three possible conversions are possible: into \textbf{cbf}, \textbf{hdf5} and \textbf{root} format. The detector writes 4 raw files per receiver. An offline image reconstruction executable has been written to collate the possible files together and produce output files. By default an interpolation between the values of the large pixels is performed. Gap pixels between modules are also inserted.
+Three possible conversions are possible: into \textbf{cbf}, \textbf{hdf5}. \textbf{tiff} and  \textbf{root} format. The detector writes 2 raw files per receiver. An offline image reconstruction executable has been written to collate the possible files together and produce output files. By default an interpolation between the values of the large pixels is performed. Gap pixels between modules are also inserted.
 
-Note that the number of images per file in the 3.1.X release is hardcoded and needs to match whatever you are using in {\tt{slsDetectorsPackage/slsReceiverSoftware/include/sls\_receiver\_defs.h}}:
+Note that the number of images per file in the 3.1.X release is hardcoded and needs to match whatever you are using in \\
+{\tt{slsDetectorsPackage/slsReceiverSoftware/include/sls\_receiver\_defs.h}}:
 \begin{verbatim}
 #define EIGER_MAX_FRAMES_PER_FILE	2000
 \end{verbatim}
@@ -1043,11 +1046,12 @@ cbfMaker9M [file_name_with_dir]
 contain the hardcoded geometry for the 1.5M (3 modules horizontal on the long side), the 1.5M OMNY geometry (3 modules next to each other on the long side) and for the 9M at cSAXS: 6(short side)$\times$3 (long side) modules.\\ 
 Missing packets in a frame and border pixels ($\times 2$ and $\times 4$ are given with value $-1$ at the present time.
 
+From the new {{v4.1.1}} all the define that you see below need only to be modified in the Makefile.
+
 Make sure the following options are uncommented in the {\tt{slsImageReconstruction/src/main\_csaxs.cpp}} file. 
 \begin{verbatim}
 #define MYCBF
-##following line only if you need to process with 
-##BUBBLE (Material Science / uXAS beamlines).
+##following line only if you need to process with BUBBLE
 #define MSHeader 
 \end{verbatim}
 Compile it with: 
@@ -1096,6 +1100,10 @@ To use it any geometry:\\
 eg.
 {\tt image /scratch/run\_63\_d0\_f000000000000\_3.raw  3072 512 1 2 ``Eiger'' 0}.\\
 
+With new new software, the new options to run the cbfMaker/hdf5Maker executablesare: 
+
+./hdf5Maker -f [filename] -d [outdirname] -x [npix\_x] -y [npix\_y] -v  (v flags that longedge is vertical, no argument) -n [name\_of\_hdf5\_dataset] -m (mask\_hot\_pixels, need to be in file maskpix.txt in the samedir as executable, no argument) -g [0,no filling/1,division/2,interpolation/3,interpolate,alternative]  
+
 \subsection{Read temperatures/HV from boards}
 
 With an updated kernel on the linux boards (ask to the SLS detector group for specifications), it is possible to monitor the temperature on the boards: 
@@ -1257,7 +1265,7 @@ We have also been requested if we could speed up the threshold scan. At the mome
 ./sls_detector_put enablefwrite 0
 ./sls_detector_put resetframescaught 0 
 ./sls_detector_put index 0
-./sls_detector_put triggers 21
+./sls_detector_put cycles 21
 ./sls_detector_put receiver start
 ./sls_detector_put status start 
 for i in $(seq 0 20); 
@@ -1515,8 +1523,8 @@ frames number
 where {\tt{number}} is a string to be interpreted as an integer.
 
 \item \begin{verbatim}
-sls_detector_get triggers
-triggers number 
+sls_detector_get cycles
+cycles number 
 \end{verbatim}
 where {\tt{number}} is a string to be interpreted as an integer.
 

python/CMakeLists.txt

@@ -12,6 +12,7 @@ target_link_libraries(_slsdet PUBLIC
                         slsDetectorShared
                         slsReceiverShared
                         slsSupportLib
+                        ${ZeroMQ_LIBRARIES}
                         )  
 
 

python/api-tests/test_detector.py

@@ -0,0 +1,82 @@
+import pytest
+import datetime as dt
+from slsdet import Detector, timingMode, detectorType
+
+not_eiger = pytest.mark.skipif(
+    Detector().type == detectorType.EIGER, reason="Does not work for eiger"
+)
+
+
+@pytest.fixture
+def det():
+    from slsdet import Detector
+
+    return Detector()
+
+
+def test_frames(det):
+    for n in [1, 100, 3245, 10000]:
+        det.frames = n
+        assert det.frames == n
+    det.frames = 1
+
+
+def test_triggers(det):
+    for n in [1, 100, 3245, 10000]:
+        det.triggers = n
+        assert det.triggers == n
+    det.triggers = 1
+
+
+def test_exptime(det):
+    det.exptime = 1
+    assert det.exptime == 1
+    det.exptime = dt.timedelta(milliseconds=10)
+    assert det.exptime == 0.01
+    det.exptime = 1
+
+
+def test_period(det):
+    det.period = 3.2
+    assert det.period == 3.2
+
+    p = dt.timedelta(microseconds=1020)
+    det.period = p
+    assert det.period == 0.001020
+    r = det.getPeriod()
+    assert r[0] == p
+    det.period = 0
+    assert det.period == 0
+
+
+def test_lock(det):
+    for l in [True, False]:
+        det.lock = l
+        assert det.lock == l
+
+
+def test_timing(det):
+    # auto and trigger is available for all det
+    for m in [timingMode.TRIGGER_EXPOSURE, timingMode.AUTO_TIMING]:
+        det.timing = m
+        assert det.timing == m
+
+@not_eiger
+def test_delay(det):
+    det.delay = 1
+    assert det.delay == 1
+
+    t  = dt.timedelta(microseconds=1)
+    det.delay = t
+    assert det.delay == t.total_seconds()
+
+    r = det.getDelayAfterTrigger()[0]
+    assert r == t
+
+    det.delay = 0
+    assert det.delay == 0
+
+
+@not_eiger
+def test_delayl(det):
+    assert det.delayl == 0

python/api-tests/test_jungfrau.py

@@ -0,0 +1,89 @@
+import pytest
+import datetime as dt
+from slsdet import Detector, detectorType
+
+"""
+These tests are designed to work the API and catch
+any changes in behavior or naming. Tests are expected
+to pass with a virtual detector or a real one
+
+"""
+
+
+@pytest.fixture
+def jf():
+    from slsdet import Jungfrau
+    return Jungfrau()
+
+
+jungfrautest = pytest.mark.skipif(
+    Detector().type != detectorType.JUNGFRAU, reason="Only valid for Jungfrau"
+)
+
+
+@jungfrautest
+def test_storagecells(jf):
+    for i in range(16):
+        jf.storagecells = i
+        assert jf.storagecells == i
+    jf.storagecells = 0  # default
+
+@jungfrautest
+def test_storagecell_start(jf):
+    for i in range(16):
+        jf.storagecell_start = i
+        assert jf.storagecell_start == i
+    jf.storagecells = 15  # default
+
+@jungfrautest
+def test_storagecell_delay(jf):
+    for t in [0.001, 0.0002, 0.0013]:
+        jf.storagecell_delay = t
+        assert jf.storagecell_delay == t
+    jf.storagecell_delay = 0  # default
+
+@jungfrautest
+def test_temp_event(jf):
+    # hard to test with virtual server
+    assert jf.temp_event == 0
+
+@jungfrautest
+def test_temp_threshold(jf):
+    for th in [0, 10, 43, 72]:
+        jf.temp_threshold = th
+        assert jf.temp_threshold == th
+    jf.temp_threshold = 0
+
+@jungfrautest
+def test_auto_comp_disable(jf):
+    for v in [True, False]:
+        jf.auto_comp_disable = v
+        assert jf.auto_comp_disable == v
+
+@jungfrautest
+def test_numinterfaces(jf):
+    for n in [2, 1]:
+        jf.numinterfaces = n
+        assert jf.numinterfaces == n
+
+@jungfrautest
+def test_dr(jf):
+    assert jf.dr == 16
+
+@jungfrautest
+def test_temp_control(jf):
+    for v in [True, False]:
+        jf.temp_control = v
+        assert jf.temp_control == v
+
+@jungfrautest
+def test_startingfnum(jf):
+    for n in [10, 127, 43321, 1]:
+        jf.startingfnum = n
+        assert jf.startingfnum == n
+
+@jungfrautest
+def test_selinterface(jf):
+    for i in [1, 0]:
+        jf.selinterface = i
+        assert jf.selinterface == i

python/scripts/basic.py

@@ -3,9 +3,9 @@ import sys
 import numpy as np
 sys.path.append(os.path.join(os.getcwd(), 'bin'))
 
-from sls_detector import Detector, Mythen3, Eiger, Jungfrau, DetectorDacs, Dac, Ctb
-from sls_detector import dacIndex, readoutMode
-from sls_detector.lookup import view, find
+from slsdet import Detector, Mythen3, Eiger, Jungfrau, DetectorDacs, Dac, Ctb
+from slsdet import dacIndex, readoutMode
+from slsdet.lookup import view, find
 
 d = Detector()
 # e = Eiger()

python/scripts/cmd_python.py

@@ -4,17 +4,18 @@ out = subprocess.run(['g', 'list'], stdout = subprocess.PIPE, encoding=locale.ge
 cmd = out.stdout.splitlines()
 cmd.pop(0)
 
-from sls_detector import Detector, Eiger, Ctb
+from slsdet import Detector, Eiger, Ctb
 
 pycmd = dir(Detector)+dir(Eiger)+dir(Ctb)
 
+#Add commands that we should not expect as direct commands in python
 pycmd += ['vrf', 'vtr', 'vrs', 'vtgstv', 'vsvn', 'vtrim',
 'vsvp', 'vth1', 'vth2', 'vth3', 'vshaper', 'vshaperneg', 'rxb_rb',
 'rxb_lb', 'vref_prech', 'vref_rstore', 'vref_cds',
 'vpreamp', 'vref_comp', 'vref_comp_fe vref_ds', 'vref_h_adc', 
 'vref_l_adc', 'iodelay', 'list', 'vref_ds', 'vis', 'vpl', 
 'vref_comp_fe', 'vph', 'vout_cm', 'vcp', 'vcn', 'vcmp_ll', 'vcmp_lr'
-, 'vcmp_rl', 'vcmp_rr']
+, 'vcmp_rl', 'vcmp_rr', 'daclist', 'dacvalues', 'vcal', 'vcas']
 
 missing = []
 for c in cmd:

python/scripts/generate_enums.py

@@ -11,6 +11,10 @@ import subprocess
 
 from parse import remove_comments
 
+def single_line_enum(line):
+    sub = line[line.find('{')+1:line.find('}')]
+    return sub.strip().split(',')
+
 def extract_enums(lines):
     line_iter = iter(lines)
     enums = {}
@@ -18,19 +22,26 @@ def extract_enums(lines):
         m = re.search("(?<=enum )\w+(?= {)", line)
         if m:
             enum_name = m.group()
-            # print(enum_name)
+            print(enum_name)
+            # print(line)
             fields = []
-            while True:
-                l  = next(line_iter)
-                if '};' in l:
-                    break
-                m = re.search("\w+", l)
-                try:
-                    # print('\t', m.group())
-                    fields.append(m.group())
 
-                except:
-                    pass
+            #deal with single line enums
+            if '};' in line:
+                fields = single_line_enum(line)
+            else:
+                #deal with multi line enums
+                while True:
+                    l  = next(line_iter)
+                    if '};' in l:
+                        break
+                    m = re.search("\w+", l)
+                    try:
+                        # print('\t', m.group())
+                        fields.append(m.group())
+
+                    except:
+                        pass
             enums[enum_name] = fields
     return enums
 

python/scripts/generate_functions.py

@@ -13,12 +13,18 @@ import argparse
 
 from parse import system_include_paths
 
-default_build_path = "/home/l_frojdh/sls/build/" 
+default_build_path = "/home/l_frojdh/sls/build/"
 fpath = "../../slsDetectorSoftware/src/Detector.cpp"
 
 
 parser = argparse.ArgumentParser()
-parser.add_argument("-p", "--build_path", help="Path to the build database", type = str, default=default_build_path)
+parser.add_argument(
+    "-p",
+    "--build_path",
+    help="Path to the build database",
+    type=str,
+    default=default_build_path,
+)
 cargs = parser.parse_args()
 
 db = cindex.CompilationDatabase.fromDirectory(cargs.build_path)
@@ -26,7 +32,7 @@ index = cindex.Index.create()
 args = db.getCompileCommands(fpath)
 args = list(iter(args).__next__().arguments)[0:-1]
 args = args + "-x c++ --std=c++11".split()
-syspath = system_include_paths('clang++')
+syspath = system_include_paths("clang++")
 incargs = ["-I" + inc for inc in syspath]
 args = args + incargs
 
@@ -39,6 +45,9 @@ ag = []
 
 lines = []
 
+ag2 = []
+
+cn = []
 
 def get_arguments(node):
     args = [a.type.spelling for a in node.get_arguments()]
@@ -46,9 +55,25 @@ def get_arguments(node):
         "py::arg() = Positions{}" if item == "sls::Positions" else "py::arg()"
         for item in args
     ]
-    args = ', '.join(args)
+    args = ", ".join(args)
     if args:
-        args = f', {args}'
+        args = f", {args}"
+    return args
+
+
+def get_fdec(node):
+    args = [a.type.spelling for a in node.get_arguments()]
+    if node.result_type.spelling:
+        return_type = node.result_type.spelling
+    else:
+        return_type = 'void'
+    
+    if node.is_const_method():
+        const = 'const'
+    else:
+        const = ''
+    args = ", ".join(args)
+    args = f'({return_type}(Detector::*)({args}){const})'
     return args
 
 
@@ -62,23 +87,37 @@ def visit(node):
                 ):
                     m.append(child)
                     args = get_arguments(child)
-                    lines.append(f'.def(\"{child.spelling}\", &Detector::{child.spelling}{args})')
+                    fs = get_fdec(child)
+                    lines.append(
+                        f'.def("{child.spelling}",{fs} &Detector::{child.spelling}{args})'
+                    )
+                    cn.append(child)
     for child in node.get_children():
         visit(child)
 
+        # .def("setRxHostname",
+        #      (void (Detector::*)(const std::string &, Positions)) &
+        #          Detector::setRxHostname,
+        #      py::arg(), py::arg() = Positions{})
+        # .def("setRxHostname",
+        #      (void (Detector::*)(const std::vector<std::string> &)) &
+        #          Detector::setRxHostname,
+        #      py::arg())
+
 
 visit(tu.cursor)
 
 
-with open('../src/detector_in.cpp') as f:
+with open("../src/detector_in.cpp") as f:
     data = f.read()
-s = ''.join(lines)
-s += ';'
-text = data.replace('[[FUNCTIONS]]', s)
-warning = '/* WARINING This file is auto generated any edits might be overwritten without warning */\n\n'
-with open('../src/detector.cpp', 'w') as f:
+s = "".join(lines)
+s += ";"
+text = data.replace("[[FUNCTIONS]]", s)
+warning = "/* WARINING This file is auto generated any edits might be overwritten without warning */\n\n"
+with open("../src/detector.cpp", "w") as f:
     f.write(warning)
     f.write(text)
 
 # run clang format on the output
-subprocess.run(['clang-format', '../src/detector.cpp', '-i'])
+subprocess.run(["clang-format", "../src/detector.cpp", "-i"])
+

python/scripts/list_tested_cmd.py

@@ -1,11 +1,19 @@
+"""
+Utility to find and list which command line functions have tests and
+where the tests are located
+"""
+#local import for for parsing c++
 import parse
-from pathlib import Path
+
+#General python stuff
 import os
 import locale
 import argparse
-path  = Path('../../slsDetectorSoftware/tests/')
 import subprocess
+from pathlib import Path
 
+#Realative path from this dir
+path  = Path('../../slsDetectorSoftware/tests/')
 parser = argparse.ArgumentParser()
 parser.add_argument("-s", "--startswith", help="for filter", type = str, default=None)
 args = parser.parse_args()
@@ -15,15 +23,12 @@ tested = []
 for fname in files:
     with open(path/fname) as f:
         data = f.read()
-
     data = parse.remove_comments(data)
     data = data.splitlines()
-
-
     for line in data:
         if 'TEST_CASE' in line or 'SECTION' in line:
             cmd = line.split("\"")[1]
-            tested.append(cmd)
+            tested.append([cmd, fname])
 
 out = subprocess.run(['g', 'list'], stdout = subprocess.PIPE, encoding=locale.getpreferredencoding())
 all_cmd = out.stdout.splitlines()
@@ -33,18 +38,18 @@ all_cmd.pop(0)
 
 if args.startswith is not None:
     all_cmd = [cmd for cmd in all_cmd if cmd.startswith(args.startswith)]
-    tested = [cmd for cmd in tested if cmd.startswith(args.startswith)]
+    tested = [cmd for cmd in tested if cmd[0].startswith(args.startswith)]
 
+tn = [cmd[0] for cmd in tested]
 
-
-not_tested = [cmd for cmd in all_cmd if cmd not in tested]
-misnamed = [cmd for cmd in tested if cmd not in all_cmd]
-tested = [cmd for cmd in tested if cmd in all_cmd]
+not_tested = [cmd for cmd in all_cmd if cmd not in tn]
+misnamed = [cmd for cmd in tn if cmd not in all_cmd]
+tested = [cmd for cmd in tested if cmd[0] in all_cmd]
 
 
 print("\nThe following commands are tested:")
 for cmd in tested:
-    print(cmd)
+    print(f'{cmd[0]:>18} : {cmd[1]}')
 
 print("\nThe following commands are NOT tested:")
 for cmd in not_tested:

python/setup.py

@@ -1,5 +1,5 @@
 """
-Setup file for sls_detector
+Setup file for slsdet
 Build upon the pybind11 example found here: https://github.com/pybind/python_example
 """
 from setuptools import setup, Extension, find_packages
@@ -8,7 +8,7 @@ import sys
 import setuptools
 import os
 
-__version__ = 'udp'
+__version__ = os.environ.get('GIT_DESCRIBE_TAG', 'developer')
 
 
 def get_conda_path():
@@ -45,7 +45,7 @@ ext_modules = [
             # get_pybind_include(),
             # get_pybind_include(user=True),
             os.path.join('../libs/pybind11/include'),
-            os.path.join(get_conda_path(), 'include/slsDetectorPackage'),
+            os.path.join(get_conda_path(), 'include'),
 
         ],
         libraries=['SlsDetector', 'SlsReceiver', 'zmq'],

python/slsdet/detector.py

@@ -1,23 +1,29 @@
 from _slsdet import CppDetectorApi
 from _slsdet import slsDetectorDefs
+from _slsdet import IpAddr, MacAddr
 
 runStatus = slsDetectorDefs.runStatus
+timingMode = slsDetectorDefs.timingMode
 speedLevel = slsDetectorDefs.speedLevel
 dacIndex = slsDetectorDefs.dacIndex
+detectorType = slsDetectorDefs.detectorType
 
 from .utils import element_if_equal, all_equal, get_set_bits, list_to_bitmask
-from .utils import Geometry, to_geo, element
+from .utils import Geometry, to_geo, element, reduce_time, is_iterable
+from . import utils as ut
 from .registers import Register, Adc_register
 import datetime as dt
 
 from functools import wraps
 from collections import namedtuple
+import socket
+
 
 def freeze(cls):
     cls._frozen = False
 
     def frozensetattr(self, key, value):
-        if self._frozen and not hasattr(self, key):
+        if self._frozen and not key in dir(self):
             raise AttributeError(
                 "Class {} is frozen. Cannot set {} = {}".format(
                     cls.__name__, key, value
@@ -57,23 +63,16 @@ class Detector(CppDetectorApi):
         self._register = Register(self)
         self._adc_register = Adc_register(self)
 
-
-
     # CONFIGURATION
     def __len__(self):
         return self.size()
 
     def __repr__(self):
-            return '{}(id = {})'.format(self.__class__.__name__,
-                                        self.getShmId())
-
+        return "{}(id = {})".format(self.__class__.__name__, self.getShmId())
 
     def free(self):
         self.freeSharedMemory()
 
-
-
-
     @property
     def config(self):
         return NotImplementedError("config is set only")
@@ -109,7 +108,7 @@ class Detector(CppDetectorApi):
 
     @property
     def server_version(self):
-        #TODO! handle hex print
+        # TODO! handle hex print
         return element_if_equal(self.getDetectorServerVersion())
 
     @property
@@ -130,7 +129,7 @@ class Detector(CppDetectorApi):
 
     @dr.setter
     def dr(self, dr):
-        self.setDynamicRange(dr)    
+        self.setDynamicRange(dr)
 
     @property
     def module_geometry(self):
@@ -161,65 +160,54 @@ class Detector(CppDetectorApi):
     def frames(self, n_frames):
         self.setNumberOfFrames(n_frames)
 
+    @property
+    def triggers(self):
+        return element_if_equal(self.getNumberOfTriggers())
+
+    @triggers.setter
+    def triggers(self, n_triggers):
+        self.setNumberOfTriggers(n_triggers)
 
     @property
     def exptime(self):
-        res = self.getExptime()
-        return element_if_equal([it.total_seconds() for it in res])
+        if self.type == detectorType.MYTHEN3:
+            res = self.getExptimeForAllGates()
+        else:
+            res = self.getExptime()
+        return reduce_time(res)
 
     @exptime.setter
     def exptime(self, t):
-        if isinstance(t, dt.timedelta):
-            self.setExptime(t)
-        else:
-            self.setExptime(dt.timedelta(seconds=t))
-
-    @property
-    def subexptime(self):
-        res = self.getSubExptime()
-        return element_if_equal([it.total_seconds() for it in res])
-
-    @subexptime.setter
-    def subexptime(self, t):
-        if isinstance(t, dt.timedelta):
-            self.setSubExptime(t)
-        else:
-            self.setSubExptime(dt.timedelta(seconds=t))
-
-    @property
-    def subdeadtime(self):
-        res = self.getSubDeadTime()
-        return element_if_equal([it.total_seconds() for it in res])
-
-    @subdeadtime.setter
-    def subdeadtime(self, t):
-        if isinstance(t, dt.timedelta):
-            self.setSubDeadTime(t)
-        else:
-            self.setSubDeadTime(dt.timedelta(seconds=t))
-
+        self.setExptime(t)
 
     @property
     def period(self):
         res = self.getPeriod()
-        return element_if_equal([it.total_seconds() for it in res])
+        return reduce_time(res)
 
     @period.setter
     def period(self, t):
-        if isinstance(t, dt.timedelta):
-            self.setPeriod(t)
-        else:
-            self.setPeriod(dt.timedelta(seconds=t))
+        self.setPeriod(t)
 
-    
+    @property
+    @element
+    def delay(self):
+        return ut.reduce_time(self.getDelayAfterTrigger())
 
-    
-  
+    @delay.setter
+    def delay(self, t):
+        self.setDelayAfterTrigger(t)
+
+    @property
+    @element
+    def delayl(self):
+        return ut.reduce_time(self.getDelayAfterTriggerLeft())
+
+   
     # Time
     @property
     def rx_framescaught(self):
         return element_if_equal(self.getFramesCaught())
-    
 
     @property
     def startingfnum(self):
@@ -228,10 +216,7 @@ class Detector(CppDetectorApi):
     @startingfnum.setter
     def startingfnum(self, value):
         self.setStartingFrameNumber(value)
-
-
-
-     #TODO! add txdelay
+    # TODO! add txdelay
 
     @property
     def use_receiver(self):
@@ -297,14 +282,21 @@ class Detector(CppDetectorApi):
     @property
     def rx_lastclient(self):
         return element_if_equal(self.getRxLastClientIP())
+    # FILE
 
+    @property
+    @element
+    def numinterfaces(self):
+        return self.getNumberofUDPInterfaces()
 
-    #FILE
+    @numinterfaces.setter
+    def numinterfaces(self, value):
+        self.setNumberofUDPInterfaces(value)
 
     @property
     def fformat(self):
         return element_if_equal(self.getFileFormat())
-    
+
     @fformat.setter
     def fformat(self, format):
         self.setFileFormat(format)
@@ -415,14 +407,15 @@ class Detector(CppDetectorApi):
     def zmqip(self, ip):
         self.setClientZmqIp(ip)
 
-
     @property
     def udp_dstip(self):
         return element_if_equal(self.getDestinationUDPIP())
 
     @udp_dstip.setter
     def udp_dstip(self, ip):
-        self.getDestinationUDPIP(ip)
+        if ip == "auto":
+            ip = socket.gethostbyname(self.rx_hostname)
+        self.setDestinationUDPIP(IpAddr(ip))
 
     @property
     def udp_dstip2(self):
@@ -430,7 +423,9 @@ class Detector(CppDetectorApi):
 
     @udp_dstip2.setter
     def udp_dstip2(self, ip):
-        self.getDestinationUDPIP2(ip)
+        if ip == "auto":
+            ip = socket.gethostbyname(self.rx_hostname)
+        self.setDestinationUDPIP2(IpAddr(ip))
 
     @property
     def udp_dstmac(self):
@@ -438,7 +433,7 @@ class Detector(CppDetectorApi):
 
     @udp_dstmac.setter
     def udp_dstmac(self, mac):
-        self.getDestinationUDPMAC2(mac)
+        self.setDestinationUDPMAC(MacAddr(mac))
 
     @property
     def udp_dstmac2(self):
@@ -446,8 +441,7 @@ class Detector(CppDetectorApi):
 
     @udp_dstmac2.setter
     def udp_dstmac2(self, mac):
-        self.getDestinationUDPMAC2(mac)
-
+        self.setDestinationUDPMAC2(MacAddr(mac))
 
     @property
     def udp_srcip(self):
@@ -455,7 +449,7 @@ class Detector(CppDetectorApi):
 
     @udp_srcip.setter
     def udp_srcip(self, ip):
-        self.setSourceUDPIP(ip)
+        self.setSourceUDPIP(IpAddr(ip))
 
     @property
     def udp_srcip2(self):
@@ -487,7 +481,7 @@ class Detector(CppDetectorApi):
 
     @src_udpmac.setter
     def src_udpmac(self, mac):
-        self.setSourceUDPMAC(mac)
+        self.setSourceUDPMAC(MacAddr(mac))
 
     @property
     def src_udpip2(self):
@@ -495,7 +489,7 @@ class Detector(CppDetectorApi):
 
     @src_udpip2.setter
     def src_udpip2(self, ip):
-        self.setSourceUDPIP(ip)
+        self.setSourceUDPIP(IpAddr(ip))
 
     @property
     def src_udpip(self):
@@ -503,8 +497,7 @@ class Detector(CppDetectorApi):
 
     @src_udpip.setter
     def src_udpip(self, ip):
-        self.setSourceUDPIP(ip)
-
+        self.setSourceUDPIP(IpAddr(ip))
 
     @property
     def src_udpmac2(self):
@@ -512,7 +505,7 @@ class Detector(CppDetectorApi):
 
     @src_udpmac2.setter
     def src_udpmac2(self, mac):
-        self.setSourceUDPMAC2(mac)
+        self.setSourceUDPMAC2(MacAddr(mac))
 
     @property
     def vhighvoltage(self):
@@ -542,8 +535,6 @@ class Detector(CppDetectorApi):
     def rx_status(self):
         return element_if_equal(self.getReceiverStatus())
 
-
-
     @property
     def rx_udpsocksize(self):
         return element_if_equal(self.getRxUDPSocketBufferSize())
@@ -558,7 +549,7 @@ class Detector(CppDetectorApi):
 
     @property
     def trimbits(self):
-        return NotImplementedError('trimbits are set only')
+        return NotImplementedError("trimbits are set only")
 
     @trimbits.setter
     def trimbits(self, fname):
@@ -592,7 +583,6 @@ class Detector(CppDetectorApi):
     def adcreg(self):
         return self._adc_register
 
-
     @property
     def led(self):
         return element_if_equal(self.getLEDEnable())
@@ -633,11 +623,11 @@ class Detector(CppDetectorApi):
 
     @property
     def timing(self):
-        return element_if_equal(self.getTimingMode()) 
+        return element_if_equal(self.getTimingMode())
 
     @timing.setter
     def timing(self, mode):
-        self.setTimingMode(mode) 
+        self.setTimingMode(mode)
 
     @property
     def trimen(self):
@@ -649,9 +639,7 @@ class Detector(CppDetectorApi):
 
     @property
     def vthreshold(self):
-        return element_if_equal(self.getDAC(dacIndex.THRESHOLD))
-
-    
+        return element_if_equal(self.getDAC(dacIndex.VTHRESHOLD, False))
 
     @property
     def type(self):
@@ -665,10 +653,27 @@ class Detector(CppDetectorApi):
     def rx_missingpackets(self):
         return element_if_equal(self.getNumMissingPackets())
 
-
     """
     Some Eiger stuff, does this have to be here or can we move it to subclass?
     """
+    @property
+    def subexptime(self):
+        res = self.getSubExptime()
+        return reduce_time(res)
+
+    @subexptime.setter
+    def subexptime(self, t):
+        self.setSubExptime(t)
+
+    @property
+    def subdeadtime(self):
+        res = self.getSubDeadTime()
+        reduce_time(res)
+
+    @subdeadtime.setter
+    def subdeadtime(self, t):
+        self.setSubDeadTime(t)
+
     @property
     def partialreset(self):
         return element_if_equal(self.getPartialReset())
@@ -680,7 +685,7 @@ class Detector(CppDetectorApi):
     @property
     def tengiga(self):
         return element_if_equal(self.getTenGiga())
-    
+
     @tengiga.setter
     def tengiga(self, value):
         self.setTenGiga(value)
@@ -728,19 +733,116 @@ class Detector(CppDetectorApi):
         return element_if_equal([it.total_seconds() for it in res])
 
 
-    @property
-    def storeinram(self):
-        return element_if_equal(self.getStoreInRamMode())
+    """
+    Jungfrau specific
+    """
 
-    @storeinram.setter
-    def storeinram(self, value):
-        self.setStoreInRamMode(value)
+    @property
+    @element
+    def auto_comp_disable(self):
+        return self.getAutoCompDisable()
+
+    @auto_comp_disable.setter
+    def auto_comp_disable(self, value):
+        self.setAutoCompDisable(value)
+
+    @property
+    @element
+    def storagecells(self):
+        return self.getNumberOfAdditionalStorageCells()
+
+    @storagecells.setter
+    def storagecells(self, n_cells):
+        self.setNumberOfAdditionalStorageCells(n_cells)
+
+    @property
+    @element
+    def storagecell_start(self):
+        return self.getStorageCellStart()
+
+    @storagecell_start.setter
+    def storagecell_start(self, value):
+        self.setStorageCellStart(value)
+
+    @property
+    @element
+    def storagecell_delay(self):
+        return ut.reduce_time(self.getStorageCellDelay())
+
+    @storagecell_delay.setter
+    def storagecell_delay(self, t):
+        self.setStorageCellDelay(t)
+
+    @property
+    @element
+    def temp_threshold(self):
+        return self.getThresholdTemperature()
+
+    @temp_threshold.setter
+    def temp_threshold(self, value):
+        self.setThresholdTemperature(value)
+
+    @property
+    @element
+    def temp_event(self):
+        return self.getTemperatureEvent()
+
+    @temp_event.setter
+    def temp_event(self, value):
+        if value != 0:
+            raise ValueError("Value needs to be 0 for reset. Setting not allowed")
+        self.resetTemperatureEvent()
+
+    @property
+    @element
+    def temp_control(self):
+        return self.getTemperatureControl()
+
+    @temp_control.setter
+    def temp_control(self, value):
+        self.setTemperatureControl(value)
+
+
+    @property
+    @element
+    def selinterface(self):
+        return self.getSelectedUDPInterface()
+
+    @selinterface.setter
+    def selinterface(self, i):
+        self.selectUDPInterface(i)
+
+    """
+    Gotthard2
+    """
+
+    @property
+    @element
+    def veto(self):
+        return self.getVeto()
+
+    @veto.setter
+    def veto(self, value):
+        self.setVeto(value)
 
 
     """
     Mythen3 specific
     """
 
+    @property
+    def gatedelay(self):
+        return reduce_time(self.getGateDelayForAllGates())
+
+    @gatedelay.setter
+    def gatedelay(self, value):
+        if is_iterable(value):
+            if len(value) == 3:
+                for i, v in enumerate(value):
+                    self.setGateDelay(i, v)
+        else:
+            self.setGateDelay(-1, value)
+
     @property
     def counters(self):
         mask = self.getCounterMask()
@@ -750,11 +852,10 @@ class Detector(CppDetectorApi):
         else:
             return [get_set_bits(m) for m in mask]
 
-
     @counters.setter
     def counters(self, values):
         self.setCounterMask(list_to_bitmask(values))
-        
+
     """
     CTB stuff 
     """
@@ -802,7 +903,7 @@ class Detector(CppDetectorApi):
     @property
     def dbitclk(self):
         return element_if_equal(self.getDBITClock())
-    
+
     @dbitclk.setter
     def dbitclk(self, value):
         self.setDBITClock(value)
@@ -842,7 +943,7 @@ class Detector(CppDetectorApi):
     @property
     def adcphase(self):
         return element_if_equal(self.getADCPhase())
-    
+
     @adcphase.setter
     def adcphase(self, value):
         self.setADCPhase(value)
@@ -866,21 +967,13 @@ class Detector(CppDetectorApi):
     @property
     def syncclk(self):
         return element_if_equal(self.getSYNCClock())
-    
+
     @property
     def pattern(self):
-        #TODO! Clean fix
+        # TODO! Clean fix
         print("Set only")
         return 0
 
-    @property
-    def patclkctrl(self):
-        return element_if_equal(self.getPatternClockControl())
-
-    @patclkctrl.setter
-    def patclkctrl(self, mask):
-        self.setPatternClockControl(mask)
-
     # patioctrl
     @property
     def patioctrl(self):
@@ -958,7 +1051,6 @@ class Detector(CppDetectorApi):
     def patwaittime2(self, nclk):
         self.setPatternWaitTime(2, nclk)
 
-
     @property
     def patloop0(self):
         return element_if_equal(self.getPatternLoopAddresses(0))
@@ -1007,7 +1099,6 @@ class Detector(CppDetectorApi):
     def patnloop2(self, n):
         self.setPatternLoopCycles(2, n)
 
-
     @property
     @element
     def v_a(self):
@@ -1085,4 +1176,4 @@ class Detector(CppDetectorApi):
     @property
     @element
     def im_io(self):
-        return self.getMeasuredCurrent(dacIndex.I_POWER_IO)
+        return self.getMeasuredCurrent(dacIndex.I_POWER_IO)

python/slsdet/eiger.py

@@ -60,23 +60,23 @@ class EigerDacs(DetectorDacs):
     """
     Eiger specific dacs
     """
-    _dacs = [('vsvp',    dacIndex.SVP,0, 4000,    0),
-             ('vtr',     dacIndex.VTR,0, 4000, 2500),
-             ('vrf',     dacIndex.VRF,0, 4000, 3300),
-             ('vrs',     dacIndex.VRS,0, 4000, 1400),
-             ('vsvn',    dacIndex.SVN,0, 4000, 4000),
-             ('vtgstv',  dacIndex.VTGSTV,0, 4000, 2556),
-             ('vcmp_ll', dacIndex.VCMP_LL,0, 4000, 1500),
-             ('vcmp_lr', dacIndex.VCMP_LR,0, 4000, 1500),
-             ('vcall',   dacIndex.CAL,0, 4000, 4000),
-             ('vcmp_rl', dacIndex.VCMP_RL,0, 4000, 1500),
-             ('rxb_rb',  dacIndex.RXB_RB,0, 4000, 1100),
-             ('rxb_lb',  dacIndex.RXB_LB,0, 4000, 1100),
-             ('vcmp_rr', dacIndex.VCMP_RR,0, 4000, 1500),
-             ('vcp',     dacIndex.VCP,0, 4000,  200),
-             ('vcn',     dacIndex.VCN,0, 4000, 2000),
-             ('vis',     dacIndex.VIS,0, 4000, 1550),
-             ('iodelay', dacIndex.IO_DELAY,0, 4000,  660)]
+    _dacs = [('vsvp',     dacIndex.VSVP,0, 4000,    0),
+             ('vtrim',    dacIndex.VTRIM,0, 4000, 2500),
+             ('vrpreamp', dacIndex.VRPREAMP,0, 4000, 3300),
+             ('vrshaper', dacIndex.VRSHAPER,0, 4000, 1400),
+             ('vsvn',     dacIndex.VSVN,0, 4000, 4000),
+             ('vtgstv',   dacIndex.VTGSTV,0, 4000, 2556),
+             ('vcmp_ll',  dacIndex.VCMP_LL,0, 4000, 1500),
+             ('vcmp_lr',  dacIndex.VCMP_LR,0, 4000, 1500),
+             ('vcal',    dacIndex.VCAL,0, 4000, 4000),
+             ('vcmp_rl',  dacIndex.VCMP_RL,0, 4000, 1500),
+             ('rxb_rb',   dacIndex.RXB_RB,0, 4000, 1100),
+             ('rxb_lb',   dacIndex.RXB_LB,0, 4000, 1100),
+             ('vcmp_rr',  dacIndex.VCMP_RR,0, 4000, 1500),
+             ('vcp',      dacIndex.VCP,0, 4000,  200),
+             ('vcn',      dacIndex.VCN,0, 4000, 2000),
+             ('vishaper', dacIndex.VISHAPER,0, 4000, 1550),
+             ('iodelay',  dacIndex.IO_DELAY,0, 4000,  660)]
     _dacnames = [_d[0] for _d in _dacs]
 
 # # noinspection PyProtectedMember

python/slsdet/lookup.py

@@ -1,9 +1,9 @@
 from .detector import Detector
 
-def view(name):
-    names =  find(name)
+def view(name, det = Detector):
+    names =  find(name, det)
     for n in names:
         print(n)
 
-def find(name):
-    return [n for n in dir(Detector) if name in n]
+def find(name, det = Detector):
+    return [n for n in dir(det) if name.lower() in n.lower()]

python/slsdet/mythen3.py

@@ -13,49 +13,32 @@ import _slsdet
 dacIndex = _slsdet.slsDetectorDefs.dacIndex
 from .detector_property import DetectorProperty
 
-# vcassh 1200, 
-# vth2 2800, 
-# vshaper 1280, 
-# vshaperneg 2800, 
-# vipre_out 1220, 
-# vth3 2800, 
-# vth1 2800, 
-# vicin 1708, 
-# vcas 1800, 
-# vpreamp 1100, 
-# vpl 1100, 
-# vipre 2624, 
-# viinsh 1708, 
-# vph 1712, 
-# vtrim 2800, 
-# vdcsh 800
-
 
 # @freeze
 class Mythen3Dacs(DetectorDacs):
     """
     Jungfrau specific DACs
     """
-    _dacs = [('vcassh',     dacIndex.CASSH,     0, 4000, 1220),
+    _dacs = [('vcassh',     dacIndex.VCASSH,     0, 4000, 1220),
              ('vth2',       dacIndex.VTH2,      0, 4000, 2800),
-             ('vshaper',    dacIndex.SHAPER1,   0, 4000, 1280),
-             ('vshaperneg', dacIndex.SHAPER2,   0, 4000, 2800),
+             ('vrshaper',   dacIndex.VRSHAPER,   0, 4000, 1280),
+             ('vrshaper_n', dacIndex.VRSHAPER_N,   0, 4000, 2800),
              ('vipre_out',  dacIndex.VIPRE_OUT, 0, 4000, 1220),
              ('vth3',       dacIndex.VTH3,      0, 4000, 2800),
-             ('vth1',       dacIndex.THRESHOLD,      0, 4000,  2800),
+             ('vth1',       dacIndex.VTH1,      0, 4000,  2800),
              ('vicin',      dacIndex.VICIN,     0, 4000,  1708),
-             ('vcas',       dacIndex.CAS,       0, 4000,  1800),
-             ('vpreamp',    dacIndex.PREAMP,    0, 4000,  1100),
-             ('vpl',        dacIndex.VPL,       0, 4000,  1100),
+             ('vcas',       dacIndex.VCAS,       0, 4000,  1800),
+             ('vrpreamp',    dacIndex.VRPREAMP,    0, 4000,  1100),
+             ('vcal_n',     dacIndex.VCAL_N,       0, 4000,  1100),
              ('vipre',      dacIndex.VIPRE,     0, 4000,  2624),
-             ('viinsh',     dacIndex.VIINSH,    0, 4000,  1708),
-             ('vph',    dacIndex.CALIBRATION_PULSE,    0, 4000,  1712),
-             ('vtrim',    dacIndex.TRIMBIT_SIZE,    0, 4000,  2800),
-             ('vdcsh',    dacIndex.VDCSH,    0, 4000,  800),
+             ('vishaper',   dacIndex.VISHAPER,    0, 4000,  1708),
+             ('vcal_p',     dacIndex.VCAL_P,    0, 4000,  1712),
+             ('vtrim',      dacIndex.VTRIM,    0, 4000,  2800),
+             ('vdcsh',      dacIndex.VDCSH,    0, 4000,  800),
             ]
     _dacnames = [_d[0] for _d in _dacs]
 
-
+#vthreshold??
 
 
 @freeze

python/slsdet/utils.py

@@ -7,10 +7,17 @@ but not directly used in controlling the detector
 from collections import namedtuple
 import _slsdet #C++ lib
 import functools
-
+import datetime as dt
 
 Geometry = namedtuple('Geometry', ['x', 'y'])
 
+def is_iterable(item):
+    try: 
+        iter(item)
+    except TypeError:
+        return False
+    return True
+
 def get_set_bits(mask):
     """
     Return a list of the set bits in a python integer
@@ -41,6 +48,9 @@ def all_equal(mylist):
 
 def element_if_equal(mylist):
     """If all elements are equal return only one element"""
+    if not is_iterable(mylist):
+        return mylist
+        
     if all_equal(mylist):
         if len(mylist) == 0:
             return None
@@ -49,6 +59,15 @@ def element_if_equal(mylist):
     else:
         return mylist
 
+def reduce_time(mylist):
+    res = element_if_equal(element_if_equal(mylist))
+    if isinstance(res, dt.timedelta):
+        return res.total_seconds()
+    elif isinstance(res[0], list):
+        return [[item.total_seconds() for item in subl] for subl in res]
+    else:
+        return [r.total_seconds() for r in res]
+
 def element(func):
     """
     Wrapper to return either list or element
@@ -69,3 +88,8 @@ def eiger_register_to_time(register):
     exponent = register & 0b111
     return clocks*10**exponent / 100e6
 
+def make_timedelta(t):
+    if isinstance(t, dt.timedelta):
+           return t
+    else:
+        return dt.timedelta(seconds=t)

python/sphinx/Makefile

@@ -1,20 +0,0 @@
-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = python -msphinx
-SPHINXPROJ    = sls_detector_tools
-SOURCEDIR     = .
-BUILDDIR      = _build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

python/sphinx/code_quality.rst

@@ -1,134 +0,0 @@
-Code quality
-=============================
-
-For usability and reliability of the software the code needs to be high quality. For this
-project it means meeting the four criteria described below. Any addition should pass all of 
-them. 
-
-
---------------------------------
-Look, read and feel like Python
---------------------------------
-
-When using classes and functions from the 
-package it should feel like you are using Python tools and be forces
-to write C++ style code with Python syntax.
-
-::
-	
-    with xray_box.shutter_open():
-        for th in threshold:
-            d.vthreshold = th
-            d.acq()
-
-should be preferred over
-
-::
-
-    N = len(threshold)
-    xray_box.open_shutter()
-    for i in range(N):
-        d.dacs.set_dac('vthreshold', threshold[i])
-        d.acq()
-    xray_box.close_shutter()
-    
-even if the difference might seem small.
-
---------------------
-Have documentation
---------------------
-
-Classes and functions should be documented with doc-strings
-in the source code. Preferably with examples. The syntax to be used
-is numpy-sphinx.
-
-::
-
-    def function(arg):
-        """
-        This is a function that does something
-        
-        Parameters
-        ----------
-        arg: int
-            An argument
-            
-        Returns
-        --------
-        value: double
-            Returns a value
-            
-        """
-        return np.sin(arg+np.pi)
-
----------------------------------
-Pass static analysis with pylint
----------------------------------
-
-Yes, anything less than 9/10 just means that you are lazy. If 
-there is a good reason why to diverge, then we can always 
-add an exception.
-
-Currently the following additions are made:
-
- * good-names: x, y, ax, im etc. 
- * function arguments 10
- * Whitelist: numpy, _sls
-
-
-
------------------------
-Tested code
------------------------
-
-Last but not least... *actually last just because of the long list included.*
-All code that goes in should have adequate tests. If a new function does not
-have a minimum of one test it does not get added.
- 
-**Unit-tests with pytest and mocker**
-
-::
-
-    ----------- coverage: platform linux, python 3.6.4-final-0 -----------
-    Name                         Stmts   Miss  Cover
-    ------------------------------------------------
-    sls_detector/__init__.py         4      0   100%
-    sls_detector/decorators.py      14      3    79%
-    sls_detector/detector.py       461    115    75%
-    sls_detector/eiger.py          150     64    57%
-    sls_detector/errors.py           7      0   100%
-    sls_detector/jungfrau.py        59     26    56%
-    ------------------------------------------------
-    TOTAL                          695    208    70%
-
-
-    ========= 78 passed in 0.60 seconds =========
-
-
-    
-**Simple integration tests**
-
-These tests require a detector connected. Performs simple tasks like setting 
-exposure time and reading back to double check the value
-
-::
-
-    ----------- coverage: platform linux, python 3.6.4-final-0 -----------
-    Name                         Stmts   Miss  Cover
-    ------------------------------------------------
-    sls_detector/__init__.py         4      0   100%
-    sls_detector/decorators.py      14      0   100%
-    sls_detector/detector.py       461    103    78%
-    sls_detector/eiger.py          150     20    87%
-    sls_detector/errors.py           7      0   100%
-    sls_detector/jungfrau.py        59     26    56%
-    ------------------------------------------------
-    TOTAL                          695    149    79%
-
-
-    ========= 67 passed, 1 skipped in 16.66 seconds =========
-
-**Complex integration test**
-
-Typical measurements. Might require X-rays. Tests are usually evaluated from 
-plots

python/sphinx/command_line.rst

@@ -1,370 +0,0 @@
-Command line to Python
-=========================
-
-If you are already familiar with the command line interface to the
-slsDetectorSoftware here is a quick reference translating to Python commands
-
-
- .. note ::
-
-     Commands labeled Mythen only  or Gotthard only are currently not implemented in the
-     Python class. If you need this functionallity please contact the SLS Detector Group
-
-.. py:currentmodule:: sls_detector
-
-.. |ro| replace:: *(read only)*
-.. |free| replace:: :py:func:`Detector.free_shared_memory`
-.. |sub| replace:: :py:attr:`Detector.sub_exposure_time`
-.. |mg| replace:: Mythen and Gotthard only
-.. |g| replace:: Gotthard only
-.. |m| replace:: Mythen only
-.. |msp| replace:: :py:attr:`Detector.measured_subperiod`
-.. |new_chiptest| replace:: New chip test board only
-.. |chiptest| replace:: Chip test board only
-.. |dr| replace::  :py:attr:`Detector.dynamic_range`
-.. |j| replace:: Jungfrau only
-.. |te| replace:: :py:attr:`Detector.trimmed_energies`
-.. |temp_fpgaext| replace:: :py:attr:`Detector.temp`.fpgaext
-.. |epa| replace:: :py:func:`Eiger.pulse_all_pixels`
-.. |rfc| replace:: :py:func:`Detector.reset_frames_caught`
-.. |rfi| replace:: :py:attr:`Detector.receiver_frame_index`
-.. |ron| replace:: :py:attr:`Detector.receiver_online`
-.. |flipy| replace:: :py:attr:`Detector.flipped_data_y`
-.. |flipx| replace:: :py:attr:`Detector.flipped_data_x`
-.. |adcr| replace:: :py:func:`DetectorApi.writeAdcRegister`
-.. |sb| replace:: :py:func:`DetectorApi.setBitInRegister`
-.. |cb| replace:: :py:func:`DetectorApi.clearBitInRegister`
-.. |tempth| replace:: :py:attr:`Jungfrau.temperature_threshold`
-.. |tempev| replace:: :py:attr:`Jungfrau.temperature_event`
-.. |tempco| replace:: :py:attr:`Jungfrau.temperature_control`
-.. |depr| replace:: *Deprecated/Internal*
-.. |nimp| replace:: *Not implemented*
-.. |rudp| replace:: :py:attr:`Detector.rx_realudpsocksize`
-.. |lci| replace:: :py:attr:`Detector.last_client_ip`
-.. |rlci| replace:: :py:attr:`Detector.receiver_last_client_ip`
-.. |fdp| replace:: :py:attr:`Detector.frame_discard_policy`
-.. |apic| replace:: :py:attr:`Detector.api_compatibility`
-
-
-------------------------
-Commands
-------------------------
-
-===================== ===================================== ================== =========
-Command               Python                                Implementation     Tests
-===================== ===================================== ================== =========
-sls_detector_acquire  :py:func:`Detector.acq`                OK                 OK
-test                  |depr|                                 \-                 \-
-help                  help(Detector.acq)                     \-                 \-
-exitserver            |depr|                                 \-                 \-
-exitreceiver          |depr|                                 \-                 \-
-flippeddatay          |flipy|                                OK                 \-
-digitest              |depr|                                 \-                 \-
-bustest               |depr|                                 \-                 \-
-digibittest           Which detector?                        \-                 \-
-reg                   :py:attr:`Detector.register`           OK                 \-
-adcreg                |adcr|                                 OK                 \-
-setbit                |sb|                                   OK                 \-
-clearbit              |cb|                                   OK                 \-
-getbit                |nimp|                                 \-                 \-
-r_compression         Not implemented in receiver            \-                 \-
-acquire               :py:func:`Detector.acq`                OK                 \-
-busy                  :py:attr:`Detector.busy`               OK                 Partial
-status                :py:attr:`Detector.status`             OK |ro|            \-
-status start          :py:func:`Detector.start_detector`     OK                 \-
-status stop           :py:func:`Detector.stop_detector`      OK                 \-
-data                  |depr|                                 \-                 \-
-frame                 |depr|                                 \-                 \-
-readctr               |g|                                    \-                 \-
-resetctr              |g|                                    \-                 \-
-resmat                :py:attr:`Eiger.eiger_matrix_reset`    OK                 OK
-free                  |free|                                 OK                 \-
-hostname              :py:attr:`Detector.hostname`           OK                 OK
-add                   |nimp|                                 \-                 \-
-replace               |nimp|                                 \-                 \-
-user                  |nimp|                                 \-                 \-
-master                |nimp|                                 \-                 \-
-sync                  Which detector?                        \-                 \-
-online                :py:attr:`Detector.online`             OK                 \-
-checkonline           |nimp|                                 \-                 \-
-activate              :py:attr:`Eiger.active`                \-                 \-
-nmod                  :py:attr:`Detector.n_modules`          OK                 \-
-maxmod                |depr|                                 \-                 \-
-dr                    |dr|                                   OK                 OK
-roi                   |g|                                    \-                 \-
-detsizechan           :py:attr:`Detector.image_size`         OK                 \-
-roimask               |nimp|                                 \-                 \-
-flippeddatax          |flipx|                                OK                 \-
-tengiga               :py:attr:`Eiger.tengiga`               OK                 \-
-gappixels             :py:attr:`Eiger.add_gappixels`         OK                 \-
-flags                 :py:attr:`Detector.flags`              OK                 \-
-extsig                |mg|                                   \-                 \-
-programfpga           |j|                                    \-                 \-
-resetfpga             |j|                                    \-                 \-
-powerchip             :py:attr:`Jungfrau.powerchip`          \-                 \-
-led                   |nimp|                                 \-                 \-
-auto_comp_disable     |j|                                    \-                 \-
-pulse                 Used in |epa|                          OK                 \-
-pulsenmove            Used in |epa|                          OK                 \- 
-pulsechip             :py:func:`Eiger.pulse_chip`            OK                 \-
-checkdetversion       |apic|                                 \-                 \-
-checkrecversion       |apic|                                 \-                 \-
-moduleversion         |m|                                    \-                 \-
-detectornumber        :py:attr:`Detector.detector_number`    OK                 \-
-modulenumber          |m|                                    \-                 \-
-detectorversion       :py:attr:`Detector.firmware_version`   OK                 OK
-softwareversion       :py:attr:`Detector.server_version`     \-                 \-
-thisversion           :py:attr:`Detector.client_version`     Reads date         \-
-receiverversion       :py:attr:`Detector.receiver_version`   Reads date         \-
-timing                :py:attr:`Detector.timing_mode`        OK                 \-
-exptime               :py:attr:`Detector.exposure_time`      OK                 OK
-subexptime            |sub|                                  OK                 OK
-period                :py:attr:`Detector.period`             OK                 OK
-subdeadtime           :py:attr:`Eiger.sub_deadtime`          OK                 OK
-delay                 :py:attr:`Jungfrau.delay`              OK                 \-
-gates                 :py:attr:`Jungfrau.n_gates`            OK                 \-
-frames                :py:attr:`Detector.n_frames`           OK                 OK
-cycles                :py:attr:`Detector.n_cycles`           OK                 \-
-probes                :py:attr:`Jungfrau.n_probes`           OK                 \-
-measurements          :py:attr:`Detector.n_measurements`     OK                 \-
-samples               Chip test board only (new?)            \-                 \-
-storagecells          :py:attr:`Jungfrau.n_storagecells`     OK                 \-
-storagecell_start     :py:attr:`Jungfrau.storagecell_start`  OK                 \-
-exptimel              |mg|                                   \-                 \-
-periodl               |mg|                                   \-                 \-
-delayl                |mg|                                   \-                 \-
-gatesl                |mg|                                   \-                 \-
-framesl               |mg|                                   \-                 \-
-cyclesl               |mg|                                   \-                 \-
-probesl               |mg|                                   \-                 \-
-now                   |nimp|                                 \-                 \-
-timestamp             |m|                                    \-                 \-
-nframes               |nimp|                                 \-                 \-
-measuredperiod        :py:attr:`Detector.measured_period`    OK                 \-
-measuredsubperiod     |msp|                                  \-                 \-
-clkdivider            :py:attr:`Detector.readout_clock`      OK                 OK
-setlength             |m|                                    \-                 \-
-waitstates            |m|                                    \-                 \-
-totdivider            |m|                                    \-                 \-
-totdutycycle          |m|                                    \-                 \-
-phasestep             |g|                                    \-                 \-
-oversampling          |new_chiptest|                         \-                 \-
-adcclk                |new_chiptest|                         \-                 \-
-adcphase              |new_chiptest|                         \-                 \-
-adcpipeline           |new_chiptest|                         \-                 \-
-dbitclk               |new_chiptest|                         \-                 \-
-dbitphase             |new_chiptest|                         \-                 \-
-dbitpipeline          |new_chiptest|                         \-                 \-
-config                :py:func:`Detector.load_config`        OK                 \-
-rx_printconfig        |nimp|                                 \-                 \-
-parameters            :py:func:`Detector.load_parameters`    OK                 \-
-setup                 |nimp|                                 \-                 \-
-flatfield             |nimp|                                 \-                 \-
-ffdir                 |nimp|                                 \-                 \-
-ratecorr              :py:attr:`Detector.rate_correction`    OK                 \-
-badchannels           |nimp|                                 \-                 \-
-angconv               |m|                                    \-                 \-
-globaloff             |nimp|                                 \-                 \-
-fineoff               |nimp|                                 \-                 \-
-binsize               |nimp|                                 \-                 \-
-angdir                |nimp|                                 \-                 \-
-moveflag              |nimp|                                 \-                 \-
-samplex               |nimp|                                 \-                 \-
-sampley               |nimp|                                 \-                 \-
-threaded              :py:attr:`Detector.threaded`           OK                 \-
-darkimage             |nimp|                                 \-                 \-
-gainimage             |nimp|                                 \-                 \-
-settingsdir           :py:attr:`Detector.settings_path`      OK                 \-
-trimdir               |nimp|                                 \-                 \-
-caldir                |nimp|                                 \-                 \-
-trimen                :py:attr:`Detector.trimmed_energies`   OK                 \-
-settings              :py:attr:`Detector.settings`           OK                 \-
-threshold             :py:attr:`Detector.threshold`          OK                 \-
-thresholdnotb         |nimp|                                 \-                 \-
-trimbits              :py:func:`Detector.load_trimbits`      OK                 \-
-trim                  |nimp|                                 \-                 \-
-trimval               :py:attr:`Detector.trimbits`           OK                 OK
-pedestal              |nimp|                                 \-                 \-
-vthreshold            :py:attr:`Detector.vthreshold`         OK                 \-
-vcalibration          |nimp|                                 \-                 \-
-vtrimbit              |nimp|                                 \-                 \-
-vpreamp               |nimp|                                 \-                 \-
-vshaper1              |nimp|                                 \-                 \-
-vshaper2              |nimp|                                 \-                 \-
-vhighvoltage          :py:attr:`Detector.high_voltage`       OK                 \-
-vapower               |nimp|                                 \-                 \-
-vddpower              |nimp|                                 \-                 \-
-vshpower              |nimp|                                 \-                 \-
-viopower              |nimp|                                 \-                 \-
-vref_ds               :py:attr:`Jungfrau.dacs.vref_ds`       OK                 \-
-vcascn_pb             |nimp|                                 \-                 \-
-vcascp_pb             |nimp|                                 \-                 \-
-vout_cm               |nimp|                                 \-                 \-
-vcasc_out             |nimp|                                 \-                 \-
-vin_cm                |nimp|                                 \-                 \-
-vref_comp             |nimp|                                 \-                 \-
-ib_test_c             |nimp|                                 \-                 \-
-dac0                  |nimp|                                 \-                 \-
-dac1                  |nimp|                                 \-                 \-
-dac2                  |nimp|                                 \-                 \-
-dac3                  |nimp|                                 \-                 \-
-dac4                  |nimp|                                 \-                 \-
-dac5                  |nimp|                                 \-                 \-
-dac6                  |nimp|                                 \-                 \-
-dac7                  |nimp|                                 \-                 \-
-vsvp                  :py:attr:`Eiger.dacs.vsvp`             OK                 \-
-vsvn                  :py:attr:`Eiger.dacs.vsvn`             OK                 \- 
-vtr                   :py:attr:`Eiger.dacs.vtr`              OK                 \-
-vrf                   :py:attr:`Eiger.dacs.vrf`              OK                 \-
-vrs                   :py:attr:`Eiger.dacs.vrs`              OK                 \-
-vtgstv                :py:attr:`Eiger.dacs.vtgstv`           OK                 \-
-vcmp_ll               :py:attr:`Eiger.dacs.vcmp_ll`          OK                 \-
-vcmp_ll               :py:attr:`Eiger.dacs.vcmp_ll`          OK                 \-
-vcall                 :py:attr:`Eiger.dacs.vcall`            OK                 \-
-vcmp_rl               :py:attr:`Eiger.dacs.vcmp_rl`          OK                 \-
-vcmp_rr               :py:attr:`Eiger.dacs.vcmp_rr`          OK                 \-
-rxb_rb                :py:attr:`Eiger.dacs.rxb_rb`           OK                 \-
-rxb_lb                :py:attr:`Eiger.dacs.rxb_lb`           OK                 \-
-vcp                   :py:attr:`Eiger.dacs.vcp`              OK                 \-
-vcn                   :py:attr:`Eiger.dacs.vcn`              OK                 \-
-vis                   :py:attr:`Eiger.dacs.vis`              OK                 \-
-iodelay               :py:attr:`Eiger.dacs.iodelay`          OK                 \-
-dac                   |nimp|                                 \-                 \-
-adcvpp                |nimp|                                 \-                 \-
-v_a                   |nimp|                                 \-                 \-
-v_b                   |nimp|                                 \-                 \- 
-v_c                   |nimp|                                 \-                 \-  
-v_d                   |nimp|                                 \-                 \- 
-v_io                  |nimp|                                 \-                 \- 
-v_chip                |nimp|                                 \-                 \- 
-v_limit               |nimp|                                 \-                 \- 
-vIpre                 |nimp|                                 \-                 \- 
-VcdSh                 |nimp|                                 \-                 \- 
-Vth1                  |nimp|                                 \-                 \- 
-Vth2                  |nimp|                                 \-                 \- 
-Vth3                  |nimp|                                 \-                 \- 
-VPL                   |nimp|                                 \-                 \- 
-Vtrim                 |nimp|                                 \-                 \- 
-vIbias                |nimp|                                 \-                 \- 
-vIinSh                |nimp|                                 \-                 \- 
-cas                   |nimp|                                 \-                 \- 
-casSh                 |nimp|                                 \-                 \- 
-vIbiasSh              |nimp|                                 \-                 \- 
-vIcin                 |nimp|                                 \-                 \- 
-vIpreOut              |nimp|                                 \-                 \- 
-temp_adc              |nimp|                                 \-                 \- 
-temp_fpga             :py:attr:`Detector.temp`.fpga          OK                 \- 
-temp_fpgaext          |temp_fpgaext|                         OK                 \- 
-temp_10ge             :py:attr:`Detector.temp`.t10ge         OK                 \- 
-temp_dcdc             :py:attr:`Detector.temp`.dcdc          OK                 \- 
-temp_sodl             :py:attr:`Detector.temp`.sodl          OK                 \- 
-temp_sodr             :py:attr:`Detector.temp`.sodr          OK                 \- 
-adc                   |nimp|                                 \-                 \- 
-temp_fpgafl           :py:attr:`Detector.temp`.fpgafl        OK                 \- 
-temp_fpgafr           :py:attr:`Detector.temp`.fpgafr        OK                 \- 
-i_a                   |nimp|                                 \-                 \-        
-i_b                   |nimp|                                 \-                 \-        
-i_c                   |nimp|                                 \-                 \-        
-i_d                   |nimp|                                 \-                 \-        
-i_io                  |nimp|                                 \-                 \-        
-vm_a                  |nimp|                                 \-                 \-        
-vm_b                  |nimp|                                 \-                 \-        
-vm_c                  |nimp|                                 \-                 \-        
-vm_d                  |nimp|                                 \-                 \-        
-vm_io                 |nimp|                                 \-                 \-        
-temp_threshold        |tempth|                               \-                 \-                        
-temp_control          |tempco|                               \-                 \-  
-temp_event            |tempev|                               \-                 \-  
-outdir                :py:attr:`Detector.file_path`          OK                 OK
-fname                 :py:attr:`Detector.file_name`          OK                 OK
-index                 :py:attr:`Detector.file_index`         OK                 OK
-enablefwrite          :py:attr:`Detector.file_write`         OK                 OK
-overwrite             :py:attr:`Detector.file_overwrite`     OK                 \-
-currentfname          |nimp|                                 \-                 \-      
-fileformat            :py:attr:`Detector.file_format`        OK                 \-
-positions             |depr|                                 \-                 \-
-startscript           |depr|                                 \-                 \-
-startscriptpar        |depr|                                 \-                 \-
-stopscript            |depr|                                 \-                 \-
-stopscriptpar         |depr|                                 \-                 \-
-scriptbefore          |depr|                                 \-                 \-
-scriptbeforepar       |depr|                                 \-                 \-
-scriptafter           |depr|                                 \-                 \-
-scriptafterpar        |depr|                                 \-                 \-
-headerafter           |depr|                                 \-                 \-
-headerbefore          |depr|                                 \-                 \-
-headerbeforepar       |depr|                                 \-                 \-
-headerafterpar        |depr|                                 \-                 \-
-encallog              |depr|                                 \-                 \-
-angcallog             |depr|                                 \-                 \-
-scan0script           |depr|                                 \-                 \-
-scan0par              |depr|                                 \-                 \-
-scan0prec             |depr|                                 \-                 \-
-scan0steps            |depr|                                 \-                 \-
-scan0range            |depr|                                 \-                 \-
-scan1script           |depr|                                 \-                 \-
-scan1par              |depr|                                 \-                 \-
-scan1prec             |depr|                                 \-                 \-
-scan1steps            |depr|                                 \-                 \-
-scan1range            |depr|                                 \-                 \-
-rx_hostname           :py:attr:`Detector.rx_hostname`        OK                 \-
-rx_udpip              :py:attr:`Detector.rx_udpip`           OK                 \-
-rx_udpmac             :py:attr:`Detector.rx_udpmac`          OK                 \-
-rx_udpport            :py:attr:`Detector.rx_udpport`         OK                 \-
-rx_udpport2           :py:attr:`Detector.rx_udpport`         OK                 \-
-rx_udpsocksize        :py:attr:`Detector.rx_udpsocksize`     OK                 \-
-rx_realudpsocksize    |rudp|                                 OK
-detectormac           :py:attr:`Detector.detector_mac`       OK                 \-
-detectorip            :py:attr:`Detector.detector_ip`        OK                 \-
-txndelay_left         :py:attr:`Eiger.delay`.left            OK                 \-
-txndelay_right        :py:attr:`Eiger.delay`.right           OK                 \-
-txndelay_frame        :py:attr:`Eiger.delay`.frame           OK                 \-
-flowcontrol_10g       :py:attr:`Eiger.flowcontrol_10g`       OK                 \-
-zmqport               :py:attr:`Detector.client_zmqport`     Read               \- 
-rx_zmqport            :py:attr:`Detector.rx_zmqport`         Read               \-
-rx_datastream         :py:attr:`Detector.rx_datastream`      OK                 \-
-zmqip                 :py:attr:`Detector.client_zmqip`       OK                 \- 
-rx_zmqip              :py:attr:`Detector.rx_zmqip`           Read               \-
-rx_jsonaddheader      :py:attr:`Detector.rx_jsonaddheader`   OK                 \- 
-configuremac          :py:attr:`Detector.config_network`     OK                 \-
-rx_tcpport            :py:attr:`Detector.rx_tcpport`    
-port                  |nimp|                                 \-                 \- 
-stopport              |nimp|                                 \-                 \- 
-lock                  :py:attr:`Detector.lock`               OK                 \-
-lastclient            :py:attr:`Detector.last_client_ip`     OK                 \-
-receiver start        :py:func:`Detector.start_receiver`     OK                 \-   
-receiver stop         :py:func:`Detector.stop_receiver`      \-                 \-  
-r_online              |ron|                                  OK                 \-
-r_checkonline         |nimp|                                 \-                 \-   
-framescaught          :py:attr:`Detector.frames_caught`      OK                 \-
-resetframescaught     |rfc|                                  OK                 \-
-frameindex            |rfi|                                  OK                 \-
-r_lock                :py:attr:`Detector.lock_receiver`      OK                 \-
-r_lastclient          |rlci|                                 OK                 \-
-r_readfreq            |nimp|                                 \-                 \- 
-rx_fifodepth          :py:attr:`Detector.rx_fifodepth`       OK                 \-
-r_silent              |nimp|                                 \-                 \- 
-r_framesperfile       :py:attr:`Detector.n_frames_per_file`  OK                 \-
-r_discardpolicy       |fdp|                                  OK                 \-
-r_padding             :py:attr:`Detector.file_padding`       OK                 \-
-adcinvert             |chiptest|                             \-                 \-
-adcdisable            |chiptest|                             \-                 \-
-pattern               |chiptest|                             \-                 \-
-patword               |chiptest|                             \-                 \-
-patioctrl             |chiptest|                             \-                 \-
-patclkctrl            |chiptest|                             \-                 \-
-patlimits             |chiptest|                             \-                 \-
-patloop0              |chiptest|                             \-                 \-
-patnloop0             |chiptest|                             \-                 \-
-patwait0              |chiptest|                             \-                 \-
-patwaittime0          |chiptest|                             \-                 \-
-patloop1              |chiptest|                             \-                 \-
-patnloop1             |chiptest|                             \-                 \-
-patwait1              |chiptest|                             \-                 \-
-patwaittime1          |chiptest|                             \-                 \-
-patloop2              |chiptest|                             \-                 \-
-patnloop2             |chiptest|                             \-                 \-
-patwait2              |chiptest|                             \-                 \-
-patwaittime2          |chiptest|                             \-                 \-
-dut_clk               |chiptest|                             \-                 \-
-===================== ===================================== ================== =========   

python/sphinx/conf.py

@@ -1,178 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-#
-# sls_detector_tools documentation build configuration file, created by
-# sphinx-quickstart on Wed Nov  1 10:17:29 2017.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-import os
-import sys
-sys.path.insert(0, os.path.abspath('..'))
-
-
-# -- General configuration ------------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#
-# needs_sphinx = '1.0'
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = ['sphinx.ext.autodoc',
-              'sphinx.ext.doctest',
-              'sphinx.ext.coverage',
-              'sphinx.ext.mathjax',
-              'sphinx.ext.viewcode',
-              'sphinx.ext.napoleon',
-              'sphinx.ext.todo',
-              'sphinx.ext.autosummary']
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-#
-# source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = 'sls_detector'
-copyright = '2019, Sls Detector Group'
-author = 'Erik Frojdh'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = '4.0.1'
-# The full version, including alpha/beta/rc tags.
-release = '4.0.1'
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = None
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-# If true, `todo` and `todoList` produce output, else they produce nothing.
-todo_include_todos = True
-
-
-# -- Options for HTML output ----------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = "sphinx_rtd_theme"
-
-# Theme options are theme-specific and customize the look and feel of a theme
-# further.  For a list of options available for each theme, see the
-# documentation.
-#
-# html_theme_options = {}
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-# Custom sidebar templates, must be a dictionary that maps document names
-# to template names.
-#
-# This is required for the alabaster theme
-# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
-html_sidebars = {
-    '**': [
-        'about.html',
-        'navigation.html',
-        'relations.html',  # needs 'show_related': True theme option to display
-        'searchbox.html',
-        'donate.html',
-    ]
-}
-
-
-# -- Options for HTMLHelp output ------------------------------------------
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'sls_detector_doc'
-napoleon_use_ivar = True
-
-# -- Options for LaTeX output ---------------------------------------------
-
-latex_elements = {
-    # The paper size ('letterpaper' or 'a4paper').
-    #
-    # 'papersize': 'letterpaper',
-
-    # The font size ('10pt', '11pt' or '12pt').
-    #
-    # 'pointsize': '10pt',
-
-    # Additional stuff for the LaTeX preamble.
-    #
-    # 'preamble': '',
-
-    # Latex figure (float) alignment
-    #
-    # 'figure_align': 'htbp',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title,
-#  author, documentclass [howto, manual, or own class]).
-latex_documents = [
-    (master_doc, 'sls_detector.tex', 'sls_detector Documentation',
-     'Erik Frojdh', 'manual'),
-]
-
-
-# -- Options for manual page output ---------------------------------------
-
-# One entry per manual page. List of tuples
-# (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'sls_detector_tools', 'sls_detector_tools Documentation',
-     [author], 1)
-]
-
-
-# -- Options for Texinfo output -------------------------------------------
-
-# Grouping the document tree into Texinfo files. List of tuples
-# (source start file, target name, title, author,
-#  dir menu entry, description, category)
-texinfo_documents = [
-    (master_doc, 'py_sls', 'py_sls Documentation',
-     author, 'py_sls', 'One line description of project.',
-     'Miscellaneous'),
-]
-
-

python/sphinx/cpp_api.rst

@@ -1,12 +0,0 @@
-C++ API
-=====================================================
-
-
-.. py:currentmodule:: _slsdet
-
-.. autoclass:: DetectorApi
-    :members:  
-    :undoc-members:
-
-
-

python/sphinx/error-handling.rst

@@ -1,67 +0,0 @@
-Error handling
-=========================
-
-
-Check input in Python
-----------------------
-
-As far as possible we try to check the input on the Python side
-before calling the slsDeteectorsSoftware. Errors should not pass
-silently but raise an exception
-
-::
-
-    #Trimbit range for Eiger is 0-63
-    detector.trimbits = 98
-    (...)
-    ValueError: Trimbit setting 98 is  outside of range:0-63
-    
-Errors in slsDetectorsSoftware
--------------------------------
-
-The slsDetectorsSoftware uses a mask to record errors from the different
-detectors. If an error is found we raise a RuntimeError at the end of the 
-call using the error message from slsDetectorsSoftware
-
-.. todo ::
-
-    Implement this for all functions
-
-::
-
-    detector.settings = 'bananas'
-    (...)
-    RuntimeError: Detector 0:
-    Could not set settings.
-    Detector 1:
-    Could not set settings.
-    Detector 2:
-    Could not set settings.
-    
-    
-Using decorators
--------------------
-
-Using decorators we can reset the error mask before the command and then 
-check it after the command
-
-.. code-block:: python
-
-    #add decorator to check the error mask
-    @error_handling
-    def some_function():
-        a = 1+1
-        return a
-
-Communication with the detector is usually the biggest overhead so 
-this does not impact performance. 
-
-::
-
-    %timeit d.exposure_time
-    >> 1.52 ms ± 5.42 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)
-
-    %timeit d.decorated_exposure_time
-    >> 1.53 ms ± 3.18 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)
-
-

python/sphinx/getting_started.rst

@@ -1,122 +0,0 @@
-Getting started
-================
-
-
-------------------------
-Setting up the detector
-------------------------
-        
-All configuration of the detector can either be done from the Python
-API (including loading config file) or externally. The detector setup is
-discovered from the shared memory when launching a new script. Because the
-detector usually should remain online longer than a specific script it is
-recommended to run the receivers seperate.
-        
----------------------------------
-Setting and getting attributes
----------------------------------        
-
-Most of the detector and software setting are implemented as attributes
-in the Detector class. When something is assigned it is also set 
-in the detector and when the attribute is called using dot notation it
-it looked up from the detector.
-
-::
-
-    #Currently Eiger and Jungfrau but Detector should work for all
-    from sls_detector import Eiger()
-    d = Eiger()
-    
-    d.file_write = True
-    d.vthreshold = 1500
-    
-    d.frame_index
-    >> 12
-    
-    d.file_name
-    >> 'run'
-    
----------------------------------
-Working with DACs
----------------------------------  
-
-The following examples assumes an Eiger500k detector. But the same syntax
-works for other detector sizes and models.
-
-::
-
-    d.dacs
-    >>
-    ========== DACS =========
-    vsvp      :     0,     0
-    vtr       :  4000,  4000
-    vrf       :  2000,  2300
-    vrs       :  1400,  1400
-    vsvn      :  4000,  4000
-    vtgstv    :  2556,  2556
-    vcmp_ll   :  1500,  1500
-    vcmp_lr   :  1500,  1500
-    vcall     :  3500,  3600
-    vcmp_rl   :  1500,  1500
-    rxb_rb    :  1100,  1100
-    rxb_lb    :  1100,  1100
-    vcmp_rr   :  1500,  1500
-    vcp       :  1500,  1500
-    vcn       :  2000,  2000
-    vis       :  1550,  1550
-    iodelay   :   660,   660
-    
-    #Read dac values to a variable
-    vrf = d.dacs.vrf[:]
-    
-    #Set a dac in a module
-    d.dacs.vrf[0] = 1500
-    d.dacs.vrf[0]
-    >> 1500
-    
-    #Set vrf to the same value in all moduels
-    d.dacs.vrf = 1500
-    
-    #Set a dac using an iterable
-    d.dacs.vrf = [1500, 1600]
-    d.dacs.vrf
-    >> vrf       :  1500,  1600
-    
-    #Set dacs iterating on index and values
-    d.dacs.vrf[0,1] = 1300,1400
-
-
----------------------------------
-Operating multiple detectors
----------------------------------
-
-Operating multiple detectors is supported by assigning an id when creating the object. If no id is
-set it defaults to 0.
-
-::
-
-    d0 = Eiger() #id is now 0
-    d1 = Jungfrau(1)
-
-    #Or explicitly
-    d1 = Jungfrau(id = 0)
-
-The detectors now operate independently of each other but can be synchronized using a hardware trigger.
-
-::
-
-    from sls_detector import Eiger
-
-    d0 = Eiger(0)
-    d1 = Eiger(1)
-
-    d0.load_config('/some/path/T45.config')
-    d1.load_config('/some/path/T62.config')
-
-    d0.n_frames = 1
-    d0.exposure_time = 1
-    d0.timing_mode = 'trigger'
-
-    d1.n_frames = 5
-    d1.exposure_time = 0.2
-    d1.timing_mode = 'trigger'

python/sphinx/index.rst

@@ -1,30 +0,0 @@
-sls_detector - Python interface for the slsDetectorsPackage
-==============================================================
-
-sls_detector provide Python bindings to the slsDetectorsPackage using mainly the 
-DetectorImpl API. This module contains two parts, a compiled C module to
-expose the API and a Python class to offer a more Pythonic interface.
-
-
-.. toctree::
-   :maxdepth: 3
-   :caption: Contents:
-
-   installation
-   getting_started
-   code_quality
-   command_line
-   examples
-   error-handling
-   
-   sls_detector
-   cpp_api
-
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

python/sphinx/installation.rst

@@ -1,90 +0,0 @@
-Installation
-=========================
-
-The easiest way to install the Python API and the slsDetectorPackage is using conda. But other
-methods are also available. 
-
----------------------
-Install using conda
----------------------
-If you don't have it installed get the latest version of `Miniconda`_
-
-.. _Miniconda: https://conda.io/miniconda.html
-
-::
-
-    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-    sh Miniconda3-latest-Linux-x86_64.sh
-
-
-Install sls_detector and sls_detector_lib using:
-
-::
-
-    #Add conda channels
-    conda config --add channels conda-forge
-    conda config --add channels slsdetectorgroup
-
-    #Install latest version
-    conda install sls_detector
-
-    #Install specific version
-    conda install sls_detector=3.0.1
-
-------------------------------
-Local build using conda-build
-------------------------------
-
-Needs the `sls_detector_lib`_ installed  in order to automatically find headers
-and shared libraries. Make sure that the branch of sls_detector matches the lib 
-version installed. 
-
-.. _sls_detector_lib: https://github.com/slsdetectorgroup/sls_detector_lib
-
-::
-
-    #Clone source code
-    git clone https://github.com/slsdetectorgroup/sls_detector.git
-
-    #Checkout the branch needed
-    git checkout 3.0.1
-
-    #Build and install the local version
-    conda-build sls_detector
-    conda install --use-local sls_detector
-
-
------------------------
-Developer build
------------------------
-
-IF you if you are developing and are making constant changes to the code it's a bit cumbersome
-to build with conda and install. Then an easier way is to build the C/C++ parts in the package
-directory and temporary add this to the path
-
-::
-
-    #in path/to/sls_detector
-    python setup.py build_ext --inplace
-
-Then in your Python script
-
-::
-
-    import sys
-    sys.path.append('/path/to/sls_detector')
-    from sls_detector import Detector
-
-
-
---------------
-Prerequisites
---------------
-
-All dependencies are manged trough conda but for a stand alone build you would need
-
- * gcc 4.8+
- * Qwt 6
- * Qt 4.8
- * numpy
- * slsDetectorPackage

python/sphinx/makedocs.sh

@@ -1,6 +0,0 @@
-make clean
-make html
-rm -rf ../docs/
-mv  _build/html/ ../docs/
-touch ../docs/.nojekyll
-rm -rf _build

python/sphinx/modules.rst

@@ -1,8 +0,0 @@
-sls_detector
-==================
-
-.. toctree::
-   :maxdepth: 4
-
-   sls_detector
-   

python/sphinx/sls_detector.rst

@@ -1,33 +0,0 @@
-Python classes
-=====================================================
-
-
-.. py:currentmodule:: sls_detector
-    
-Detector
-----------
-
-.. autoclass:: Detector
-    :members:  
-    :undoc-members:
-    :show-inheritance:
-
-
-
-Eiger
--------
-
-.. autoclass:: Eiger
-    :members:  
-    :undoc-members:
-    :show-inheritance:
-
-    
-    
-Jungfrau
-----------
-    
-.. autoclass:: Jungfrau
-    :members:  
-    :undoc-members:
-    :show-inheritance:

python/src/detector_in.cpp

@@ -8,10 +8,17 @@
 #include "network_utils.h"
 #include "sls_detector_defs.h"
 #include "typecaster.h"
+
+#include "TimeHelper.h"
+#include <array>
+#include <chrono>
 namespace py = pybind11;
 void init_det(py::module &m) {
     using sls::Detector;
     using sls::Positions;
+    using sls::Result;
+    using sls::defs;
+    using sls::ns;
     
     py::class_<Detector> CppDetectorApi(m, "CppDetectorApi");
     CppDetectorApi

python/src/enums.cpp

@@ -17,8 +17,6 @@ void init_enums(py::module &m) {
     xy.def_readwrite("y", &slsDetectorDefs::xy::y);
 
     py::enum_<slsDetectorDefs::detectorType>(Defs, "detectorType")
-        .value("GET_DETECTOR_TYPE",
-               slsDetectorDefs::detectorType::GET_DETECTOR_TYPE)
         .value("GENERIC", slsDetectorDefs::detectorType::GENERIC)
         .value("EIGER", slsDetectorDefs::detectorType::EIGER)
         .value("GOTTHARD", slsDetectorDefs::detectorType::GOTTHARD)
@@ -40,8 +38,6 @@ void init_enums(py::module &m) {
         .export_values();
 
     py::enum_<slsDetectorDefs::frameDiscardPolicy>(Defs, "frameDiscardPolicy")
-        .value("GET_FRAME_DISCARD_POLICY",
-               slsDetectorDefs::frameDiscardPolicy::GET_FRAME_DISCARD_POLICY)
         .value("NO_DISCARD", slsDetectorDefs::frameDiscardPolicy::NO_DISCARD)
         .value("DISCARD_EMPTY_FRAMES",
                slsDetectorDefs::frameDiscardPolicy::DISCARD_EMPTY_FRAMES)
@@ -52,72 +48,76 @@ void init_enums(py::module &m) {
         .export_values();
 
     py::enum_<slsDetectorDefs::fileFormat>(Defs, "fileFormat")
-        .value("GET_FILE_FORMAT", slsDetectorDefs::fileFormat::GET_FILE_FORMAT)
         .value("BINARY", slsDetectorDefs::fileFormat::BINARY)
-        .value("HDF5", slsDetectorDefs::fileFormat::HDF5)
-        .value("NUM_FILE_FORMATS",
+        .value(" HDF5", slsDetectorDefs::fileFormat::HDF5)
+        .value(" NUM_FILE_FORMATS",
                slsDetectorDefs::fileFormat::NUM_FILE_FORMATS)
         .export_values();
 
     py::enum_<slsDetectorDefs::dimension>(Defs, "dimension")
         .value("X", slsDetectorDefs::dimension::X)
-        .value("Y", slsDetectorDefs::dimension::Y)
+        .value(" Y", slsDetectorDefs::dimension::Y)
         .export_values();
 
     py::enum_<slsDetectorDefs::externalSignalFlag>(Defs, "externalSignalFlag")
-        .value("GET_EXTERNAL_SIGNAL_FLAG",
-               slsDetectorDefs::externalSignalFlag::GET_EXTERNAL_SIGNAL_FLAG)
-        .value("SIGNAL_OFF", slsDetectorDefs::externalSignalFlag::SIGNAL_OFF)
-        .value("GATE_IN_ACTIVE_HIGH",
-               slsDetectorDefs::externalSignalFlag::GATE_IN_ACTIVE_HIGH)
-        .value("GATE_IN_ACTIVE_LOW",
-               slsDetectorDefs::externalSignalFlag::GATE_IN_ACTIVE_LOW)
         .value("TRIGGER_IN_RISING_EDGE",
                slsDetectorDefs::externalSignalFlag::TRIGGER_IN_RISING_EDGE)
         .value("TRIGGER_IN_FALLING_EDGE",
                slsDetectorDefs::externalSignalFlag::TRIGGER_IN_FALLING_EDGE)
-        .value("RO_TRIGGER_IN_RISING_EDGE",
-               slsDetectorDefs::externalSignalFlag::RO_TRIGGER_IN_RISING_EDGE)
-        .value("RO_TRIGGER_IN_FALLING_EDGE",
-               slsDetectorDefs::externalSignalFlag::RO_TRIGGER_IN_FALLING_EDGE)
-        .value("GATE_OUT_ACTIVE_HIGH",
-               slsDetectorDefs::externalSignalFlag::GATE_OUT_ACTIVE_HIGH)
-        .value("GATE_OUT_ACTIVE_LOW",
-               slsDetectorDefs::externalSignalFlag::GATE_OUT_ACTIVE_LOW)
-        .value("TRIGGER_OUT_RISING_EDGE",
-               slsDetectorDefs::externalSignalFlag::TRIGGER_OUT_RISING_EDGE)
-        .value("TRIGGER_OUT_FALLING_EDGE",
-               slsDetectorDefs::externalSignalFlag::TRIGGER_OUT_FALLING_EDGE)
-        .value("RO_TRIGGER_OUT_RISING_EDGE",
-               slsDetectorDefs::externalSignalFlag::RO_TRIGGER_OUT_RISING_EDGE)
-        .value("RO_TRIGGER_OUT_FALLING_EDGE",
-               slsDetectorDefs::externalSignalFlag::RO_TRIGGER_OUT_FALLING_EDGE)
-        .value("OUTPUT_LOW", slsDetectorDefs::externalSignalFlag::OUTPUT_LOW)
-        .value("OUTPUT_HIGH", slsDetectorDefs::externalSignalFlag::OUTPUT_HIGH)
-        .value(
-            "MASTER_SLAVE_SYNCHRONIZATION",
-            slsDetectorDefs::externalSignalFlag::MASTER_SLAVE_SYNCHRONIZATION)
+        .value("INVERSION_ON",
+               slsDetectorDefs::externalSignalFlag::INVERSION_ON)
+        .value("INVERSION_OFF",
+               slsDetectorDefs::externalSignalFlag::INVERSION_OFF)
         .export_values();
 
     py::enum_<slsDetectorDefs::timingMode>(Defs, "timingMode")
-        .value("GET_TIMING_MODE", slsDetectorDefs::timingMode::GET_TIMING_MODE)
         .value("AUTO_TIMING", slsDetectorDefs::timingMode::AUTO_TIMING)
         .value("TRIGGER_EXPOSURE",
                slsDetectorDefs::timingMode::TRIGGER_EXPOSURE)
         .value("GATED", slsDetectorDefs::timingMode::GATED)
         .value("BURST_TRIGGER", slsDetectorDefs::timingMode::BURST_TRIGGER)
+        .value("TRIGGER_GATED", slsDetectorDefs::timingMode::TRIGGER_GATED)
+        .value("NUM_TIMING_MODES",
+               slsDetectorDefs::timingMode::NUM_TIMING_MODES)
         .export_values();
 
     py::enum_<slsDetectorDefs::dacIndex>(Defs, "dacIndex")
-        .value("THRESHOLD", slsDetectorDefs::dacIndex::THRESHOLD)
-        .value("CALIBRATION_PULSE",
-               slsDetectorDefs::dacIndex::CALIBRATION_PULSE)
-        .value("TRIMBIT_SIZE", slsDetectorDefs::dacIndex::TRIMBIT_SIZE)
-        .value("PREAMP", slsDetectorDefs::dacIndex::PREAMP)
-        .value("SHAPER1", slsDetectorDefs::dacIndex::SHAPER1)
-        .value("SHAPER2", slsDetectorDefs::dacIndex::SHAPER2)
-        .value("TEMPERATURE_ADC", slsDetectorDefs::dacIndex::TEMPERATURE_ADC)
-        .value("TEMPERATURE_FPGA", slsDetectorDefs::dacIndex::TEMPERATURE_FPGA)
+        .value("DAC_0", slsDetectorDefs::dacIndex::DAC_0)
+        .value("DAC_1", slsDetectorDefs::dacIndex::DAC_1)
+        .value("DAC_2", slsDetectorDefs::dacIndex::DAC_2)
+        .value("DAC_3", slsDetectorDefs::dacIndex::DAC_3)
+        .value("DAC_4", slsDetectorDefs::dacIndex::DAC_4)
+        .value("DAC_5", slsDetectorDefs::dacIndex::DAC_5)
+        .value("DAC_6", slsDetectorDefs::dacIndex::DAC_6)
+        .value("DAC_7", slsDetectorDefs::dacIndex::DAC_7)
+        .value("DAC_8", slsDetectorDefs::dacIndex::DAC_8)
+        .value("DAC_9", slsDetectorDefs::dacIndex::DAC_9)
+        .value("DAC_10", slsDetectorDefs::dacIndex::DAC_10)
+        .value("DAC_11", slsDetectorDefs::dacIndex::DAC_11)
+        .value("DAC_12", slsDetectorDefs::dacIndex::DAC_12)
+        .value("DAC_13", slsDetectorDefs::dacIndex::DAC_13)
+        .value("DAC_14", slsDetectorDefs::dacIndex::DAC_14)
+        .value("DAC_15", slsDetectorDefs::dacIndex::DAC_15)
+        .value("DAC_16", slsDetectorDefs::dacIndex::DAC_16)
+        .value("DAC_17", slsDetectorDefs::dacIndex::DAC_17)
+        .value("VSVP", slsDetectorDefs::dacIndex::VSVP)
+        .value("VTRIM", slsDetectorDefs::dacIndex::VTRIM)
+        .value("VRPREAMP", slsDetectorDefs::dacIndex::VRPREAMP)
+        .value("VRSHAPER", slsDetectorDefs::dacIndex::VRSHAPER)
+        .value("VSVN", slsDetectorDefs::dacIndex::VSVN)
+        .value("VTGSTV", slsDetectorDefs::dacIndex::VTGSTV)
+        .value("VCMP_LL", slsDetectorDefs::dacIndex::VCMP_LL)
+        .value("VCMP_LR", slsDetectorDefs::dacIndex::VCMP_LR)
+        .value("VCAL", slsDetectorDefs::dacIndex::VCAL)
+        .value("VCMP_RL", slsDetectorDefs::dacIndex::VCMP_RL)
+        .value("RXB_RB", slsDetectorDefs::dacIndex::RXB_RB)
+        .value("RXB_LB", slsDetectorDefs::dacIndex::RXB_LB)
+        .value("VCMP_RR", slsDetectorDefs::dacIndex::VCMP_RR)
+        .value("VCP", slsDetectorDefs::dacIndex::VCP)
+        .value("VCN", slsDetectorDefs::dacIndex::VCN)
+        .value("VISHAPER", slsDetectorDefs::dacIndex::VISHAPER)
+        .value("VTHRESHOLD", slsDetectorDefs::dacIndex::VTHRESHOLD)
+        .value("IO_DELAY", slsDetectorDefs::dacIndex::IO_DELAY)
         .value("VREF_DS", slsDetectorDefs::dacIndex::VREF_DS)
         .value("VCASCN_PB", slsDetectorDefs::dacIndex::VCASCN_PB)
         .value("VCASCP_PB", slsDetectorDefs::dacIndex::VCASCP_PB)
@@ -126,25 +126,46 @@ void init_enums(py::module &m) {
         .value("VIN_CM", slsDetectorDefs::dacIndex::VIN_CM)
         .value("VREF_COMP", slsDetectorDefs::dacIndex::VREF_COMP)
         .value("IB_TESTC", slsDetectorDefs::dacIndex::IB_TESTC)
-        .value("SVP", slsDetectorDefs::dacIndex::SVP)
-        .value("SVN", slsDetectorDefs::dacIndex::SVN)
-        .value("VTR", slsDetectorDefs::dacIndex::VTR)
-        .value("VRF", slsDetectorDefs::dacIndex::VRF)
-        .value("VRS", slsDetectorDefs::dacIndex::VRS)
-        .value("VTGSTV", slsDetectorDefs::dacIndex::VTGSTV)
-        .value("VCMP_LL", slsDetectorDefs::dacIndex::VCMP_LL)
-        .value("VCMP_LR", slsDetectorDefs::dacIndex::VCMP_LR)
-        .value("CAL", slsDetectorDefs::dacIndex::CAL)
-        .value("VCMP_RL", slsDetectorDefs::dacIndex::VCMP_RL)
-        .value("VCMP_RR", slsDetectorDefs::dacIndex::VCMP_RR)
-        .value("RXB_RB", slsDetectorDefs::dacIndex::RXB_RB)
-        .value("RXB_LB", slsDetectorDefs::dacIndex::RXB_LB)
-        .value("VCP", slsDetectorDefs::dacIndex::VCP)
-        .value("VCN", slsDetectorDefs::dacIndex::VCN)
-        .value("VIS", slsDetectorDefs::dacIndex::VIS)
-        .value("IO_DELAY", slsDetectorDefs::dacIndex::IO_DELAY)
+        .value("VB_COMP", slsDetectorDefs::dacIndex::VB_COMP)
+        .value("VDD_PROT", slsDetectorDefs::dacIndex::VDD_PROT)
+        .value("VIN_COM", slsDetectorDefs::dacIndex::VIN_COM)
+        .value("VREF_PRECH", slsDetectorDefs::dacIndex::VREF_PRECH)
+        .value("VB_PIXBUF", slsDetectorDefs::dacIndex::VB_PIXBUF)
+        .value("VB_DS", slsDetectorDefs::dacIndex::VB_DS)
+        .value("VREF_H_ADC", slsDetectorDefs::dacIndex::VREF_H_ADC)
+        .value("VB_COMP_FE", slsDetectorDefs::dacIndex::VB_COMP_FE)
+        .value("VB_COMP_ADC", slsDetectorDefs::dacIndex::VB_COMP_ADC)
+        .value("VCOM_CDS", slsDetectorDefs::dacIndex::VCOM_CDS)
+        .value("VREF_RSTORE", slsDetectorDefs::dacIndex::VREF_RSTORE)
+        .value("VB_OPA_1ST", slsDetectorDefs::dacIndex::VB_OPA_1ST)
+        .value("VREF_COMP_FE", slsDetectorDefs::dacIndex::VREF_COMP_FE)
+        .value("VCOM_ADC1", slsDetectorDefs::dacIndex::VCOM_ADC1)
+        .value("VREF_L_ADC", slsDetectorDefs::dacIndex::VREF_L_ADC)
+        .value("VREF_CDS", slsDetectorDefs::dacIndex::VREF_CDS)
+        .value("VB_CS", slsDetectorDefs::dacIndex::VB_CS)
+        .value("VB_OPA_FD", slsDetectorDefs::dacIndex::VB_OPA_FD)
+        .value("VCOM_ADC2", slsDetectorDefs::dacIndex::VCOM_ADC2)
+        .value("VCASSH", slsDetectorDefs::dacIndex::VCASSH)
+        .value("VTH2", slsDetectorDefs::dacIndex::VTH2)
+        .value("VRSHAPER_N", slsDetectorDefs::dacIndex::VRSHAPER_N)
+        .value("VIPRE_OUT", slsDetectorDefs::dacIndex::VIPRE_OUT)
+        .value("VTH3", slsDetectorDefs::dacIndex::VTH3)
+        .value("VTH1", slsDetectorDefs::dacIndex::VTH1)
+        .value("VICIN", slsDetectorDefs::dacIndex::VICIN)
+        .value("VCAS", slsDetectorDefs::dacIndex::VCAS)
+        .value("VCAL_N", slsDetectorDefs::dacIndex::VCAL_N)
+        .value("VIPRE", slsDetectorDefs::dacIndex::VIPRE)
+        .value("VCAL_P", slsDetectorDefs::dacIndex::VCAL_P)
+        .value("VDCSH", slsDetectorDefs::dacIndex::VDCSH)
+        .value("VBP_COLBUF", slsDetectorDefs::dacIndex::VBP_COLBUF)
+        .value("VB_SDA", slsDetectorDefs::dacIndex::VB_SDA)
+        .value("VCASC_SFP", slsDetectorDefs::dacIndex::VCASC_SFP)
+        .value("VIPRE_CDS", slsDetectorDefs::dacIndex::VIPRE_CDS)
+        .value("IBIAS_SFP", slsDetectorDefs::dacIndex::IBIAS_SFP)
         .value("ADC_VPP", slsDetectorDefs::dacIndex::ADC_VPP)
         .value("HIGH_VOLTAGE", slsDetectorDefs::dacIndex::HIGH_VOLTAGE)
+        .value("TEMPERATURE_ADC", slsDetectorDefs::dacIndex::TEMPERATURE_ADC)
+        .value("TEMPERATURE_FPGA", slsDetectorDefs::dacIndex::TEMPERATURE_FPGA)
         .value("TEMPERATURE_FPGAEXT",
                slsDetectorDefs::dacIndex::TEMPERATURE_FPGAEXT)
         .value("TEMPERATURE_10GE", slsDetectorDefs::dacIndex::TEMPERATURE_10GE)
@@ -155,35 +176,6 @@ void init_enums(py::module &m) {
                slsDetectorDefs::dacIndex::TEMPERATURE_FPGA2)
         .value("TEMPERATURE_FPGA3",
                slsDetectorDefs::dacIndex::TEMPERATURE_FPGA3)
-        .value("VIPRE", slsDetectorDefs::dacIndex::VIPRE)
-        .value("VIINSH", slsDetectorDefs::dacIndex::VIINSH)
-        .value("VDCSH", slsDetectorDefs::dacIndex::VDCSH)
-        .value("VTH2", slsDetectorDefs::dacIndex::VTH2)
-        .value("VPL", slsDetectorDefs::dacIndex::VPL)
-        .value("VTH3", slsDetectorDefs::dacIndex::VTH3)
-        .value("CASSH", slsDetectorDefs::dacIndex::CASSH)
-        .value("CAS", slsDetectorDefs::dacIndex::CAS)
-        .value("VICIN", slsDetectorDefs::dacIndex::VICIN)
-        .value("VIPRE_OUT", slsDetectorDefs::dacIndex::VIPRE_OUT)
-        .value("VREF_H_ADC", slsDetectorDefs::dacIndex::VREF_H_ADC)
-        .value("VB_COMP_FE", slsDetectorDefs::dacIndex::VB_COMP_FE)
-        .value("VB_COMP_ADC", slsDetectorDefs::dacIndex::VB_COMP_ADC)
-        .value("VCOM_CDS", slsDetectorDefs::dacIndex::VCOM_CDS)
-        .value("VREF_RSTORE", slsDetectorDefs::dacIndex::VREF_RSTORE)
-        .value("VB_OPA_1ST", slsDetectorDefs::dacIndex::VB_OPA_1ST)
-        .value("VREF_COMP_FE", slsDetectorDefs::dacIndex::VREF_COMP_FE)
-        .value("VCOM_ADC1", slsDetectorDefs::dacIndex::VCOM_ADC1)
-        .value("VREF_PRECH", slsDetectorDefs::dacIndex::VREF_PRECH)
-        .value("VREF_L_ADC", slsDetectorDefs::dacIndex::VREF_L_ADC)
-        .value("VREF_CDS", slsDetectorDefs::dacIndex::VREF_CDS)
-        .value("VB_CS", slsDetectorDefs::dacIndex::VB_CS)
-        .value("VB_OPA_FD", slsDetectorDefs::dacIndex::VB_OPA_FD)
-        .value("VCOM_ADC2", slsDetectorDefs::dacIndex::VCOM_ADC2)
-        .value("VB_DS", slsDetectorDefs::dacIndex::VB_DS)
-        .value("VB_COMP", slsDetectorDefs::dacIndex::VB_COMP)
-        .value("VB_PIXBUF", slsDetectorDefs::dacIndex::VB_PIXBUF)
-        .value("VIN_COM", slsDetectorDefs::dacIndex::VIN_COM)
-        .value("VDD_PROT", slsDetectorDefs::dacIndex::VDD_PROT)
         .value("V_POWER_A", slsDetectorDefs::dacIndex::V_POWER_A)
         .value("V_POWER_B", slsDetectorDefs::dacIndex::V_POWER_B)
         .value("V_POWER_C", slsDetectorDefs::dacIndex::V_POWER_C)
@@ -208,7 +200,6 @@ void init_enums(py::module &m) {
         .export_values();
 
     py::enum_<slsDetectorDefs::detectorSettings>(Defs, "detectorSettings")
-        .value("GET_SETTINGS", slsDetectorDefs::detectorSettings::GET_SETTINGS)
         .value("STANDARD", slsDetectorDefs::detectorSettings::STANDARD)
         .value("FAST", slsDetectorDefs::detectorSettings::FAST)
         .value("HIGHGAIN", slsDetectorDefs::detectorSettings::HIGHGAIN)
@@ -224,6 +215,18 @@ void init_enums(py::module &m) {
         .value("FORCESWITCHG2",
                slsDetectorDefs::detectorSettings::FORCESWITCHG2)
         .value("VERYLOWGAIN", slsDetectorDefs::detectorSettings::VERYLOWGAIN)
+        .value("G1_HIGHGAIN", slsDetectorDefs::detectorSettings::G1_HIGHGAIN)
+        .value("G1_LOWGAIN", slsDetectorDefs::detectorSettings::G1_LOWGAIN)
+        .value("G2_HIGHCAP_HIGHGAIN",
+               slsDetectorDefs::detectorSettings::G2_HIGHCAP_HIGHGAIN)
+        .value("G2_HIGHCAP_LOWGAIN",
+               slsDetectorDefs::detectorSettings::G2_HIGHCAP_LOWGAIN)
+        .value("G2_LOWCAP_HIGHGAIN",
+               slsDetectorDefs::detectorSettings::G2_LOWCAP_HIGHGAIN)
+        .value("G2_LOWCAP_LOWGAIN",
+               slsDetectorDefs::detectorSettings::G2_LOWCAP_LOWGAIN)
+        .value("G4_HIGHGAIN", slsDetectorDefs::detectorSettings::G4_HIGHGAIN)
+        .value("G4_LOWGAIN", slsDetectorDefs::detectorSettings::G4_LOWGAIN)
         .value("UNDEFINED", slsDetectorDefs::detectorSettings::UNDEFINED)
         .value("UNINITIALIZED",
                slsDetectorDefs::detectorSettings::UNINITIALIZED)
@@ -231,57 +234,55 @@ void init_enums(py::module &m) {
 
     py::enum_<slsDetectorDefs::clockIndex>(Defs, "clockIndex")
         .value("ADC_CLOCK", slsDetectorDefs::clockIndex::ADC_CLOCK)
-        .value("DBIT_CLOCK", slsDetectorDefs::clockIndex::DBIT_CLOCK)
-        .value("RUN_CLOCK", slsDetectorDefs::clockIndex::RUN_CLOCK)
-        .value("SYNC_CLOCK", slsDetectorDefs::clockIndex::SYNC_CLOCK)
+        .value(" DBIT_CLOCK", slsDetectorDefs::clockIndex::DBIT_CLOCK)
+        .value(" RUN_CLOCK", slsDetectorDefs::clockIndex::RUN_CLOCK)
+        .value(" SYNC_CLOCK", slsDetectorDefs::clockIndex::SYNC_CLOCK)
         .export_values();
 
     py::enum_<slsDetectorDefs::readoutMode>(Defs, "readoutMode")
         .value("ANALOG_ONLY", slsDetectorDefs::readoutMode::ANALOG_ONLY)
-        .value("DIGITAL_ONLY", slsDetectorDefs::readoutMode::DIGITAL_ONLY)
-        .value("ANALOG_AND_DIGITAL",
+        .value(" DIGITAL_ONLY", slsDetectorDefs::readoutMode::DIGITAL_ONLY)
+        .value(" ANALOG_AND_DIGITAL",
                slsDetectorDefs::readoutMode::ANALOG_AND_DIGITAL)
         .export_values();
 
     py::enum_<slsDetectorDefs::speedLevel>(Defs, "speedLevel")
         .value("FULL_SPEED", slsDetectorDefs::speedLevel::FULL_SPEED)
-        .value("HALF_SPEED", slsDetectorDefs::speedLevel::HALF_SPEED)
-        .value("QUARTER_SPEED", slsDetectorDefs::speedLevel::QUARTER_SPEED)
-        .export_values();
-
-    py::enum_<slsDetectorDefs::portType>(Defs, "portType")
-        .value("CONTROL_PORT", slsDetectorDefs::portType::CONTROL_PORT)
-        .value("STOP_PORT", slsDetectorDefs::portType::STOP_PORT)
-        .value("DATA_PORT", slsDetectorDefs::portType::DATA_PORT)
+        .value(" HALF_SPEED", slsDetectorDefs::speedLevel::HALF_SPEED)
+        .value(" QUARTER_SPEED", slsDetectorDefs::speedLevel::QUARTER_SPEED)
         .export_values();
 
     py::enum_<slsDetectorDefs::masterFlags>(Defs, "masterFlags")
-        .value("GET_MASTER", slsDetectorDefs::masterFlags::GET_MASTER)
         .value("NO_MASTER", slsDetectorDefs::masterFlags::NO_MASTER)
-        .value("IS_MASTER", slsDetectorDefs::masterFlags::IS_MASTER)
-        .value("IS_SLAVE", slsDetectorDefs::masterFlags::IS_SLAVE)
+        .value(" IS_MASTER", slsDetectorDefs::masterFlags::IS_MASTER)
+        .value(" IS_SLAVE", slsDetectorDefs::masterFlags::IS_SLAVE)
         .export_values();
 
     py::enum_<slsDetectorDefs::frameModeType>(Defs, "frameModeType")
-        .value("GET_FRAME_MODE", slsDetectorDefs::frameModeType::GET_FRAME_MODE)
         .value("PEDESTAL", slsDetectorDefs::frameModeType::PEDESTAL)
-        .value("NEW_PEDESTAL", slsDetectorDefs::frameModeType::NEW_PEDESTAL)
-        .value("FLATFIELD", slsDetectorDefs::frameModeType::FLATFIELD)
-        .value("NEW_FLATFIELD", slsDetectorDefs::frameModeType::NEW_FLATFIELD)
+        .value(" NEW_PEDESTAL", slsDetectorDefs::frameModeType::NEW_PEDESTAL)
+        .value(" FLATFIELD", slsDetectorDefs::frameModeType::FLATFIELD)
+        .value(" NEW_FLATFIELD", slsDetectorDefs::frameModeType::NEW_FLATFIELD)
         .export_values();
 
     py::enum_<slsDetectorDefs::detectorModeType>(Defs, "detectorModeType")
-        .value("GET_DETECTOR_MODE",
-               slsDetectorDefs::detectorModeType::GET_DETECTOR_MODE)
         .value("COUNTING", slsDetectorDefs::detectorModeType::COUNTING)
-        .value("INTERPOLATING",
+        .value(" INTERPOLATING",
                slsDetectorDefs::detectorModeType::INTERPOLATING)
-        .value("ANALOG", slsDetectorDefs::detectorModeType::ANALOG)
+        .value(" ANALOG", slsDetectorDefs::detectorModeType::ANALOG)
         .export_values();
 
     py::enum_<slsDetectorDefs::burstMode>(Defs, "burstMode")
         .value("BURST_OFF", slsDetectorDefs::burstMode::BURST_OFF)
         .value("BURST_INTERNAL", slsDetectorDefs::burstMode::BURST_INTERNAL)
         .value("BURST_EXTERNAL", slsDetectorDefs::burstMode::BURST_EXTERNAL)
+        .value("NUM_BURST_MODES", slsDetectorDefs::burstMode::NUM_BURST_MODES)
+        .export_values();
+
+    py::enum_<slsDetectorDefs::timingSourceType>(Defs, "timingSourceType")
+        .value("TIMING_INTERNAL",
+               slsDetectorDefs::timingSourceType::TIMING_INTERNAL)
+        .value(" TIMING_EXTERNAL",
+               slsDetectorDefs::timingSourceType::TIMING_EXTERNAL)
         .export_values();
 }

python/src/network.cpp

@@ -15,10 +15,11 @@ using sls::IpAddr;
 using sls::MacAddr;
 void init_network(py::module &m) {
 
-    py::class_ <IpAddr> IpAddr(m, "IpAddr");
-    IpAddr.def(py::init())
+    py::class_ <IpAddr>(m, "IpAddr")
+    .def(py::init())
     .def(py::init<const std::string&>())
     .def(py::init<uint32_t>())
+    .def(py::init<const IpAddr&>())
     .def("hex", &IpAddr::hex)
     .def("uint32", &IpAddr::uint32)
     .def(py::self == py::self)
@@ -26,10 +27,11 @@ void init_network(py::module &m) {
     .def("str", &IpAddr::str);
 
 
-    py::class_ <MacAddr> MacAddr(m, "MacAddr");
-    MacAddr.def(py::init())
+    py::class_ <MacAddr>(m, "MacAddr")
+    .def(py::init())
     .def(py::init<const std::string&>())
     .def(py::init<uint64_t>())
+    .def(py::init<const MacAddr&>())
     .def("hex", &MacAddr::hex)
     .def(py::self == py::self)
     .def("uint64", &MacAddr::uint64)

python/unit-tests/test_utils.py

@@ -5,7 +5,28 @@ Testing functions from utils.py
 """
 
 import pytest
-from sls_detector.utils import *
+from slsdet.utils import *
+import datetime as dt
+
+def test_iterable():
+    assert is_iterable(5) == False
+    assert is_iterable('abc') == True
+    assert is_iterable([]) == True
+    assert is_iterable(5.9) == False
+
+def test_reduce_time_to_single_value_from_list():
+    t = 3*[dt.timedelta(seconds = 1)]
+    assert reduce_time(t) == 1
+
+def test_reduce_time_to_single_value_from_list_of_lists():
+    t = 3*[dt.timedelta(seconds = 3.3)]
+    tt = 5*t
+    assert reduce_time(tt) == 3.3
+
+def test_reduce_time_when_sublist_is_different():
+    t = [dt.timedelta(seconds = 1), dt.timedelta(seconds = 2), dt.timedelta(seconds = 1)]
+    tt = [t for i in range(4)]
+    assert reduce_time(tt) == [1,2,1]
 
 
 def test_convert_zero():
@@ -59,4 +80,17 @@ def test_list_to_mask():
     assert(list_to_bitmask([0]) == 1)
     assert(list_to_bitmask([1]) == 2)
     assert(list_to_bitmask([3]) == 8)
-    assert(list_to_bitmask([1,1,1]) == 2)
+    assert(list_to_bitmask([1,1,1]) == 2)
+
+
+def test_make_timedelta_from_double():
+    t = 1.7
+    r = make_timedelta(t)
+    assert t == r.total_seconds()
+    assert r == dt.timedelta(seconds=t)
+
+def test_make_timedelta_from_timedelta():
+    t = dt.timedelta(minutes=1)
+    r = make_timedelta(t)
+    assert 60 == r.total_seconds()
+    assert r == dt.timedelta(minutes=1)

sample/CMakeLists.txt

@@ -1,36 +1,35 @@
-add_executable(a api.cpp)
-target_link_libraries(a 
-    slsDetectorShared
+add_executable(using_logger using_logger.cpp)
+target_link_libraries(using_logger 
     slsSupportLib
     pthread
     rt
 )  
 
-set_target_properties(a PROPERTIES
+set_target_properties(using_logger PROPERTIES
     RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin
 )
 
 
-add_executable(result useResult.cpp)
-target_link_libraries(result 
-    slsDetectorShared
-)  
+# add_executable(result useResult.cpp)
+# target_link_libraries(result 
+#     slsDetectorShared
+# )  
 
-set_target_properties(result PROPERTIES
-    RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin
-)
+# set_target_properties(result PROPERTIES
+#     RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin
+# )
 
-add_executable(udp udp.cpp)
-target_link_libraries(udp 
-    slsDetectorShared
-    slsSupportLib
-    pthread
-    rt
-    fmt
-)  
+# add_executable(udp udp.cpp)
+# target_link_libraries(udp 
+#     slsDetectorShared
+#     slsSupportLib
+#     pthread
+#     rt
+#     fmt
+# )  
 
-set_target_properties(udp PROPERTIES
-    RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin
-)
+# set_target_properties(udp PROPERTIES
+#     RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin
+# )
 
 

sample/using_logger.cpp

@@ -0,0 +1,42 @@
+#include "logger.h"
+#include <iostream>
+#include <chrono>
+int main() {
+
+    //compare old and new
+    std::cout << "Compare output between old and new:\n";
+    LOG(logINFO) << "Some info message";
+    LOG(logERROR) << "This is an error";
+    LOG(logWARNING) << "While this is only a warning";
+
+    //Logging level can be configure at runtime
+    std::cout << "\n\n";
+    std::cout << "The default macro controlled level is: "
+              << sls::Logger::ToString(LOG_MAX_REPORTING_LEVEL) << '\n';
+    
+    sls::Logger::ReportingLevel() = logERROR;
+    LOG(logINFO) << "Now this is not written";
+    LOG(logWARNING) << "and also not this";
+
+    sls::Logger::ReportingLevel() = logINFO;
+    LOG(logINFO) << "But now we can see it";
+
+
+    //The output can be redirected to another buffer 
+    std::ostringstream local;
+    auto clog_buff = std::clog.rdbuf();
+    std::clog.rdbuf(local.rdbuf());
+
+    LOG(logINFOBLUE) << "A message";
+    LOG(logWARNING) << "And another one";
+
+    std::clog.rdbuf(clog_buff); // restore
+
+    std::cout << "local buf:\n" << local.str(); 
+
+    LOG(logINFO) << "After reset we should print directly";
+    LOG(logINFOBLUE) << "some infoBLUE text";
+    LOG(logINFOGREEN) << "some infoGREEN text";
+    LOG(logINFORED) << "some infoRED text";
+
+}

slsDetectorCalibration/MovingStat.h

@@ -14,27 +14,27 @@ class MovingStat
       /** constructor
 	  \param nn number of samples  parameter to be used
       */
-      MovingStat(int nn=1000) : n(nn), m_n(0) {}
-
+    MovingStat(int nn) : n(nn), m_n(0), m_newM(0),m_newM2(0)  {}
+      //  void setPointers(double *me, double *va) {mean=me; var=va;}
 	/**
 	   clears the moving average number of samples parameter, mean and standard deviation
 	*/
-        void Clear()
-        {
+      void Clear()
+      {
 	  m_n = 0; 
 	  m_newM=0; 
 	  m_newM2=0;
-        }
+      }
 
 	/**
 	   clears the moving average number of samples parameter, mean and standard deviation
 	*/
         void Set(double val, double rms=0, int m=-1)
         {
-	  if (m>0) m_n = m;  else m_n = n; 
+	  if (m>=0) m_n = m;  else m_n = n; 
 	  m_newM=val*m_n; 
-	  // cout << "set " << val << " " << m << " " << m_n << " " << m_newM << endl;
 	  SetRMS(rms);
+	  // cout << "set " << val << " " << m << " " << m_n << " " << m_newM << endl;
         }
 	/**
 	   clears the moving average number of samples parameter, mean and standard deviation
@@ -42,12 +42,15 @@ class MovingStat
         void SetRMS(double rms)
         {
 	  if (rms<=0) {
-	    m_newM2=m_newM*m_newM/n;
+	    if (m_n>0)
+	      m_newM2=m_newM*m_newM/m_n;
+	    else
+	      m_newM2=0;
 	    //m_n=0;
 	  } else {
-	    if (m_n>0)
+	    if (m_n>0) {
 	      m_newM2=(m_n*rms*rms+m_newM*m_newM/m_n);
-	    else {
+	    } else {
 	      m_newM2=(m_n*rms*rms+m_newM*m_newM/n);
 	      m_n=0;
 	    }
@@ -102,13 +105,14 @@ class MovingStat
 	      m_newM = x;
 	      m_newM2 = x*x;
 	      m_n++;
-            }             else             {
-                m_newM = m_newM + x - m_newM/m_n;
-		m_newM2 = m_newM2 + x*x - m_newM2/m_n;
-            }
-
+            }             
+	  else             {
+	    m_newM = m_newM + x - m_newM/m_n;
+	    m_newM2 = m_newM2 + x*x - m_newM2/m_n;
+	  }
+	  
         }
-
+	
 	/** returns the current number of elements of the moving average
 	    \returns  returns the current number of elements of the moving average
 	 */
@@ -122,7 +126,9 @@ class MovingStat
         inline double Mean() const
         {
 	  //  cout << "get " <<  m_n << " " << m_newM << " " << m_newM/m_n << endl;
-            return (m_n > 0) ? m_newM/m_n : 0.0;
+	 
+	  
+	    return (m_n > 0) ? m_newM/m_n : 0.0;
         }
 
 	/** returns the squared mean, 0 if no elements are inside
@@ -138,7 +144,7 @@ class MovingStat
 	 */
         inline double Variance() const
         {
-	  return ( (m_n > 1) ? (M2()-Mean()*Mean()) : 0.0 );
+	  return (m_n > 0) ? m_newM2/m_n-m_newM/m_n*m_newM/m_n : 0.0;
         }
 
 	/** returns the standard deviation, 0 if no elements are inside
@@ -146,7 +152,8 @@ class MovingStat
 	 */
         inline double StandardDeviation() const
         {
-	  return ( (Variance() > 0) ? sqrt( Variance() ) : -1 );
+	  
+	  return sqrt(Variance());//
         }
 
     private:

slsDetectorCalibration/analogDetector.h

@@ -68,10 +68,15 @@ template <class dataType> class analogDetector {
       det->getDetectorSize(nx,ny);
     
     stat=new pedestalSubtraction*[ny];
+    /* pedMean=new double*[ny]; */
+    /* pedVariance=new double*[ny]; */
     for (int i=0; i<ny; i++) {
       stat[i]=new pedestalSubtraction[nx];
-      for (int ix=0; ix<nx; ix++) {
+      /* pedMean[i]=new double[nx]; */
+      /* pedVariance[i]=new double[nx]; */
+      for (ix=0; ix<nx; ++ix) {
 	stat[i][ix].SetNPedestals(nped);
+	/* stat[i][ix].setPointers(&(pedMean[iy][ix]),&(pedVariance[iy][ix])); */
       }
     }
     image=new int[nx*ny];
@@ -95,7 +100,16 @@ template <class dataType> class analogDetector {
   /**
      destructor. Deletes the pdestalSubtraction array and the image
   */
-  virtual ~analogDetector() {for (int i=0; i<ny; i++) delete [] stat[i]; delete [] stat; delete [] image;
+  virtual ~analogDetector() {
+    for (int i=0; i<ny; i++) {
+      delete [] stat[i]; 
+      /* delete [] pedMean[i];  */
+      /* delete [] pedVariance[i]; */
+    }; 
+    /* delete [] pedMean;  */
+    /* delete [] pedVariance; */ 
+    delete [] stat; 
+    delete [] image;
 #ifdef ROOTSPECTRUM
     delete hs;
 #ifdef ROOTCLUST
@@ -132,16 +146,23 @@ template <class dataType> class analogDetector {
     
 
     stat=new pedestalSubtraction*[ny];
+    /* pedMean=new double*[ny]; */
+    /* pedVariance=new double*[ny]; */
     for (int i=0; i<ny; i++) {
       stat[i]=new pedestalSubtraction[nx];
+      /* pedMean[i]=new double[nx]; */
+      /* pedVariance[i]=new double[nx]; */
     }
     
     int nped=orig->SetNPedestals();
     //cout << nped << " " << orig->getPedestal(ix,iy) << orig->getPedestalRMS(ix,iy) << endl;
-    for (int iy=0; iy<ny; iy++) {
-      for (int ix=0; ix<nx; ix++) {
+    for (iy=0; iy<ny; ++iy) {
+      for (ix=0; ix<nx; ++ix) {
+	//stat[iy][ix].setPointers(&(pedMean[iy][ix]),&(pedVariance[iy][ix]));
 	stat[iy][ix].SetNPedestals(nped);
 	setPedestal(ix,iy,orig->getPedestal(ix,iy),orig->getPedestalRMS(ix,iy),orig->GetNPedestals(ix,iy));
+	/* if (ix==50 && iy==50)  */
+	/*   cout << "clone ped " <<  " " << ix << " " << iy << " " << getPedestal(ix,iy) << " " << getPedestalRMS(ix,iy)<< " " << GetNPedestals(ix,iy) << endl; */
       }
     }
     image=new int[nx*ny];
@@ -199,7 +220,7 @@ template <class dataType> class analogDetector {
      \param nns reference to number of subpixels for interpolating detector, will always be 1 in this case
      \returns number of pixels of the detector image
    */
-  virtual int getImageSize(int &nnx, int &nny, int &nns){nnx=nx; nny=ny; nns=1; return nx*ny;}; 
+  virtual int getImageSize(int &nnx, int &nny, int &nnsx, int &nnsy){nnx=nx; nny=ny; nnsx=1; nnsy=1; return nx*ny;}; 
  /**
      Returns data size of the detector image matrix
      \param nnx reference to pixel size in x
@@ -231,8 +252,8 @@ template <class dataType> class analogDetector {
     if (gm) {
       if (gmap) delete [] gmap; 
       gmap=new double[nnx*nny];
-      for (int iy=0; iy<nny; iy++) {
-	for (int ix=0; ix<nnx; ix++) {
+      for (iy=0; iy<nny; ++iy) {
+	for (ix=0; ix<nnx; ++ix) {
 	  gmap[iy*nnx+ix]=gm[iy*nnx+ix];
 	  // cout << gmap[iy*nnx+ix] << " " ;
 	}
@@ -251,8 +272,8 @@ template <class dataType> class analogDetector {
     void *ret;
     if (gmap)  {
       gm=new float[nx*ny];
-	for (int iy=0; iy<ny; iy++) {
-      for (int ix=0; ix<nx; ix++) {
+      for (iy=0; iy<ny; ++iy) {
+	for (ix=0; ix<nx; ++ix) {
 	  gm[iy*nx+ix]=gmap[iy*nx+ix];
 	}
       }
@@ -267,8 +288,8 @@ template <class dataType> class analogDetector {
     
   virtual void newDataSet(){
     iframe=-1; 
-    for (int iy=0; iy<ny; iy++) 
-      for (int ix=0; ix<nx; ix++) {
+    for (iy=0; iy<ny; ++iy) 
+      for (ix=0; ix<nx; ++ix) {
 	stat[iy][ix].Clear(); 
 	image[iy*nx+ix]=0;
       }
@@ -285,15 +306,17 @@ template <class dataType> class analogDetector {
   };  
   
   /** resets the commonModeSubtraction and increases the frame index */
-  virtual void newFrame(){iframe++; if (cmSub) cmSub->newFrame();};
+  virtual void newFrame(){iframe++; if (cmSub) cmSub->newFrame(); det->newFrame();};
 
   /** resets the commonModeSubtraction and increases the frame index */
   virtual void newFrame(char *data){
     iframe++; 
     if (cmSub) cmSub->newFrame(); 
+    det->newFrame();
+    // det->getData(data);
     calcGhost(data); 
     //    cout << getId() << " Calc ghost " <<  getGhost(15,15) << endl;
-      };
+  };
   
 
     /** sets the commonModeSubtraction algorithm to be used 
@@ -359,8 +382,8 @@ template <class dataType> class analogDetector {
       // cout << "+"<< getId() << endl;
       if (cmSub) {
 	//cout << "*" << endl;
-	  for (int iy=ymin; iy<ymax; iy++) { 
-	for (int ix=xmin; ix<xmax; ix++) {
+	for (iy=ymin; iy<ymax; ++iy) { 
+	  for (ix=xmin; ix<xmax; ++ix) {
 	    // if (getNumpedestals(ix,iy)>0) 
 	  //  if (det->isGood(ix,iy)) {
 	      addToCommonMode(data, ix, iy);
@@ -403,8 +426,10 @@ template <class dataType> class analogDetector {
       if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
 	if (cmSub && cm>0) {
 	  return stat[iy][ix].getPedestal()+getCommonMode(ix,iy); 
-	  
-	}     	else return stat[iy][ix].getPedestal(); 
+	  //return pedMean[iy][ix]+getCommonMode(ix,iy); 
+	} 
+	//return pedMean[iy][ix];
+	return stat[iy][ix].getPedestal(); 
       } else return -1;
     };
 
@@ -422,7 +447,7 @@ template <class dataType> class analogDetector {
 	  g=gmap[iy*nx+ix];
 	  if (g==0) g=-1.;
 	}
-      
+	//	return sqrt(pedVariance[iy][ix])/g;
 	return stat[iy][ix].getPedestalRMS()/g;//divide by gain?
       }
       return -1;
@@ -441,10 +466,11 @@ template <class dataType> class analogDetector {
        \returns pedestal value
     */
     virtual double* getPedestal(double *ped){
-      if (ped==NULL)
+      if (ped==NULL) {
 	ped=new double[nx*ny];
-      for (int iy=0; iy<ny; iy++) {
-	for (int ix=0; ix<nx; ix++) {
+      }
+      for (iy=0; iy<ny; ++iy) {
+	for (ix=0; ix<nx; ++ix) {
 	  ped[iy*nx+ix]=stat[iy][ix].getPedestal();
 	    //cout << ped[iy*nx+ix] << " " ;
 	}
@@ -459,10 +485,11 @@ template <class dataType> class analogDetector {
        \returns pedestal rms
     */
     virtual double* getPedestalRMS(double *ped=NULL){
-      if (ped==NULL)
+      if (ped==NULL) {
 	ped=new double[nx*ny];
-	for (int iy=0; iy<ny; iy++) {
-      for (int ix=0; ix<nx; ix++) {
+      }
+      for (iy=0; iy<ny; ++iy) {
+	for (ix=0; ix<nx; ++ix) {
 	  ped[iy*nx+ix]=stat[iy][ix].getPedestalRMS();
 	}
       }
@@ -501,8 +528,8 @@ template <class dataType> class analogDetector {
     */
     virtual void setPedestal(double *ped, double *rms=NULL, int m=-1){
       double rr=0;
-      for (int iy=ymin; iy<ymax; iy++) {
-	for (int ix=xmin; ix<xmax; ix++) {
+      for (iy=ymin; iy<ymax; ++iy) {
+	for (ix=xmin; ix<xmax; ++ix) {
 	  if (rms) rr=rms[iy*nx+ix];
 	  stat[iy][ix].setPedestal(ped[iy*nx+ix],rr, m);
 	  //  cout << ix << " " << iy << " " << ped[iy*nx+ix] << " " << stat[iy][ix].getPedestal() << endl;
@@ -531,8 +558,8 @@ template <class dataType> class analogDetector {
        \param rms pointer to array of pedestal rms
     */
  virtual void setPedestalRMS(double *rms){
-	for (int iy=ymin; iy<ymax; iy++) {
-      for (int ix=xmin; ix<xmax; ix++) {
+   for (iy=ymin; iy<ymax; ++iy) {
+     for (ix=xmin; ix<xmax; ++ix) {
 	  stat[iy][ix].setPedestalRMS(rms[iy*nx+ix]);
 	};
       };
@@ -572,8 +599,8 @@ template <class dataType> class analogDetector {
 
 #endif
       gm=new float[nx*ny];
-	for (int iy=0; iy<ny; iy++) {
-      for (int ix=0; ix<nx; ix++) {
+      for (iy=0; iy<ny; ++iy) {
+	for (ix=0; ix<nx; ++ix) {
 	    gm[iy*nx+ix]=image[iy*nx+ix];
 #ifdef ROOTSPECTRUM
 	    hmap->SetBinContent(ix+1, iy+1,image[iy*nx+ix]);
@@ -620,8 +647,8 @@ template <class dataType> class analogDetector {
       TH2F *hmap=new TH2F("hmap","hmap",nx, -0.5,nx-0.5, ny, -0.5, ny-0.5);
 
 #endif
-      for (int iy=0; iy<ny; iy++) {
-    for (int ix=0; ix<nx; ix++) {
+      for (iy=0; iy<ny; ++iy) {
+	for (ix=0; ix<nx; ++ix) {
 	/* if (cmSub)  */
 	/*     gm[iy*nx+ix]=stat[iy][ix].getPedestal()-cmSub->getCommonMode(); */
 	/* else */
@@ -667,15 +694,15 @@ template <class dataType> class analogDetector {
 
 
     if (gm) {
-	for (int iy=0; iy<nny; iy++) {
-      for (int ix=0; ix<nnx; ix++) {
+      for (iy=0; iy<nny; ++iy) {
+	for (ix=0; ix<nnx; ++ix) {
 	  stat[iy][ix].setPedestal(gm[iy*nx+ix],-1,-1);
 	}
       }
       delete [] gm;
       return 1;
     }
-    return NULL;
+    return 0;
   }
   
  /**
@@ -692,15 +719,15 @@ template <class dataType> class analogDetector {
 
 
     if (gm) {
-	for (int iy=0; iy<nny; iy++) {
-      for (int ix=0; ix<nnx; ix++) {
+      for (iy=0; iy<nny; ++iy) {
+	for (ix=0; ix<nnx; ++ix) {
 	  image[iy*nx+ix]=gm[iy*nx+ix];
 	}
       }
       delete [] gm;
       return 1;
     }
-    return NULL;
+    return 0;
   }
   
    
@@ -718,9 +745,9 @@ template <class dataType> class analogDetector {
     float *gm=NULL;
     void *ret;
       gm=new float[nx*ny];
-	for (int iy=0; iy<ny; iy++) {
-      for (int ix=0; ix<nx; ix++) {
-	    gm[iy*nx+ix]=stat[iy][ix].getPedestalRMS();
+      for (iy=0; iy<ny; ++iy) {
+	for (ix=0; ix<nx; ++ix) {
+	  gm[iy*nx+ix]=stat[iy][ix].getPedestalRMS();
 	}
       }
       ret=WriteToTiff(gm, imgname, ny, nx);  
@@ -740,8 +767,8 @@ template <class dataType> class analogDetector {
     if (nnx>nx) nnx=nx;
     if (nny>ny) nny=ny;
     if (gm) {
-	for (int iy=0; iy<nny; iy++) {
-      for (int ix=0; ix<nnx; ix++) {
+      for (iy=0; iy<nny; ++iy) {
+	for (ix=0; ix<nnx; ++ix) {
 	  stat[iy][ix].setPedestalRMS(gm[iy*nx+ix]);
 	}
       }
@@ -777,11 +804,13 @@ template <class dataType> class analogDetector {
             
       //cout << xmin << " " << xmax << endl;
       // cout << ymin << " " << ymax << endl;
-      for (int iy=ymin; iy<ymax; iy++) {
-	for (int ix=xmin; ix<xmax; ix++) {
+      for (iy=ymin; iy<ymax; ++iy) {
+	for (ix=xmin; ix<xmax; ++ix) {
 	  if (det->isGood(ix,iy)) {
 	    // addToPedestal(data,ix,iy,1);
 	    addToPedestal(data,ix,iy,cm);
+	/* if (ix==50 && iy==50) */
+	/*   cout<< "*ped* " << id << " " << ix << " " << iy << " " << det->getChannel(data,ix,iy) << " " << stat[iy][ix].getPedestal() << " " <<  stat[iy][ix].getPedestalRMS() <<" " << stat[iy][ix]. GetNPedestals() << endl; */
 	  //if (ix==10 && iy==10) 
 	  // cout <<ix << " " << iy << " " << getPedestal(ix,iy)<< endl;
 #ifdef ROOTSPECTRUM 
@@ -905,8 +934,8 @@ template <class dataType> class analogDetector {
       
       //calcGhost(data);
 
-      for (int iy=ymin; iy<ymax; iy++) {
-	for (int ix=xmin; ix<xmax; ix++) {
+      for (iy=ymin; iy<ymax; ++iy) {
+	for (ix=xmin; ix<xmax; ++ix) {
 	  if (det->isGood(ix,iy))
 	    val[iy*nx+ix]+=subtractPedestal(data, ix, iy,cm);
 	}
@@ -952,8 +981,8 @@ template <class dataType> class analogDetector {
 	hs->Fill(val,(iy-ymin)*(xmax-xmin)+(ix-xmin));
 #ifdef ROOTCLUST
 	double v3=0,v5=0,v7=0,v9=0;
-	for (int iix=-4; iix<5; iix++)
-	  for (int iiy=-4; iiy<5; iiy++) {
+	for (int iix=-4; iix<5; i++ix)
+	  for (int iiy=-4; iiy<5; i++iy) {
 	    if (det)
 	      val= (dataSign*det->getValue(data, ix+iix, iy+iiy)-getPedestal(ix+iix,iy+iiy,cm))/g;
 	    else
@@ -1047,8 +1076,8 @@ template <class dataType> class analogDetector {
 
        //calcGhost(data);
        addToCommonMode(data);
-       for (int iy=ymin; iy<ymax; iy++) {
-	 for (int ix=xmin; ix<xmax; ix++) {
+       for (iy=ymin; iy<ymax; ++iy) {
+	 for (ix=xmin; ix<xmax; ++ix) {
 	   if (det->isGood(ix,iy))
 	     nph[iy*nx+ix]+=getNPhotons(data, ix, iy);
 	 }
@@ -1062,8 +1091,8 @@ template <class dataType> class analogDetector {
      
     */
    virtual void clearImage(){  
-       for (int iy=0; iy<ny; iy++) { 
-     for (int ix=0; ix<nx; ix++) {
+       for (iy=0; iy<ny; ++iy) { 
+     for (ix=0; ix<nx; ++ix) {
 	 image[iy*nx+ix]=0;
        }
      }
@@ -1093,8 +1122,8 @@ template <class dataType> class analogDetector {
     int SetNPedestals(int i=-1) {
       int ix=0, iy=0; 
       if (i>0) 
-	  for (iy=0; iy<ny; iy++) 
-	for (ix=0; ix<nx; ix++) 
+	  for (iy=0; iy<ny; ++iy) 
+	for (ix=0; ix<nx; ++ix) 
 	    stat[iy][ix].SetNPedestals(i); 
       return stat[0][0].SetNPedestals();
     };
@@ -1129,8 +1158,8 @@ template <class dataType> class analogDetector {
       newFrame(data);
       //calcGhost(data);
       addToCommonMode(data);
-      for (int iy=ymi; iy<yma; iy++)
-	for (int ix=xmi; ix<xma; ix++)
+      for (iy=ymi; iy<yma; ++iy)
+	for (ix=xmi; ix<xma; ++ix)
 	  if (det->isGood(ix,iy)) {
 	    if (ix>=0 && ix<nx && iy>=0 && iy<ny) 
 	      val+=getNPhotons(data, ix, iy);
@@ -1233,6 +1262,8 @@ FILE *getFilePointer(){return myFile;};
     int nx; /**< Size of the detector in x direction */
     int ny; /**< Size of the detector in y direction */
     pedestalSubtraction **stat; /**< pedestalSubtraction class */
+    /* double **pedMean; /\**< pedestalSubtraction class *\/ */
+    /* double **pedVariance; /\**< pedestalSubtraction class *\/ */
     commonModeSubtraction *cmSub;/**< commonModeSubtraction class */
     int dataSign; /**< sign of the data i.e. 1 if photon is positive, -1 if negative */
     int iframe;  /**< frame number (not from file but incremented within the dataset every time newFrame is called */
@@ -1250,6 +1281,7 @@ FILE *getFilePointer(){return myFile;};
     frameMode fMode; /**< current detector frame mode */
     detectorMode dMode; /**< current detector frame mode */
     FILE *myFile; /**< file pointer to write to */
+    int ix, iy;
 #ifdef ROOTSPECTRUM
     TH2F *hs;
 #ifdef ROOTCLUST

slsDetectorCalibration/dataStructures/deserializer.h

@@ -1,6 +1,7 @@
 #ifndef DESERIALIZER_H
 #define DESERIALIZER_H
 #include <vector>
+#include "slsDetectorData.h"
 
 class deserializer : public slsDetectorData<int> {
 
@@ -52,7 +53,13 @@ class deserializer : public slsDetectorData<int> {
  static int* deserializeAll(char *ptr, std::vector <int> dbl, int dr=24,  int nch=64*3, int off=5) {
    // off=0;
    //int iarg;
-   int64_t word, *wp;
+
+
+    cout <<"** deserializer: " << endl;
+    cout << "** Number of chans:\t" << nch << endl;
+    cout << "** Serial Offset:\t" << off << endl;
+    cout << "** Dynamic range:\t" << dr << endl;
+    int64_t word, *wp, ww,one=1, bit ;
    int* val=new int[nch];
    int ioff=0;
    int idr=0;
@@ -66,39 +73,62 @@ class deserializer : public slsDetectorData<int> {
      val[ib]=0;
    }
    wp=(int64_t*)ptr;
+
+   int nw=nch/nb;
+
+   cout << "** Number of bits:\t" << nb << endl;
+   cout << "** Samples:\t" << nw << endl;
+    
+  for (ib=0; ib<nb; ib++) {
+    cout << dbl[ib] << " " ;
+  }
+  cout << endl;
    
-   for (iw=0; iw<nch/nb; iw) {
+  for (ib=0; ib<nch; ib++) {
+    val[ib]=0;
+  }
+   
+   for (iw=0; iw<nw; iw) {
      word=*wp;;
      if (ioff<off) {
        ioff++;
        // cout <<"*";
      }  else {
        //if (idr<16) {
-       ib=0;
-	for (const auto &bit : dbl) {
-	  ich=iw+nch/nb*(ib);
-	  if (word&(1<<bit) && ich<nch)  {
+       //ib=0; 
+       // cout << hex << "*************" << word << endl;
+      for (ib=0; ib<nb; ib++) {
+	//	for (const auto &bit : dbl) {
+	  ich=iw+nch*ib/nb;
+	  /* if (ich>1060) */
+	  /* cout << iw << " " << idr << " " << ib << " " << bit << " " << ich << " " << val[ich] << " **  " ; */ 
+	  bit=dbl[ib];
+	  ww=one<<bit;
+	  if (word&(ww) && ich<nch)  {
 	    //cout << "+" ;
 	    val[ich]|=(1<<idr);
-	  }  //else { 
+	  }
+	  /* if (ich>1060) */
+	  /*   cout << val[ich]  << " " << hex << word << " " << ww << " " << (word&(ww)) << dec <<endl; */
+	  /* //else {  */
 	  //cout << "-" ; 
 	  //}
-	  ib++;
+	  //ib++;
 	}
 	
+      idr++; 
      }
      
-     idr++; 
      if (idr==dr) {
        idr=0;
 	//  cout << dec << " " << iw << " " << val[iw] << " " << val[iw+nch/2] << endl;
-       cout <<dec << iw<<endl;
+       // cout <<dec << iw<<endl;
        iw++;
      }//end if()
      
       //end else()
      wp+=1;
-     ii++;
+     // ii++;
    }//end for
    
     
@@ -117,7 +147,7 @@ class deserializer : public slsDetectorData<int> {
    int ii=0;
    int ich;
    int nb=dbl.size();
-
+   int bit;
    char *dval;
 
    idr=0;
@@ -127,8 +157,13 @@ class deserializer : public slsDetectorData<int> {
    dval=ptr;
    
    ib=0;
-   ich=0;
-   for (const auto &bit : dbl) {
+   ich=0; 
+     for (ib=0; ib<nb; ib++) {
+       //	for (const auto &bit : dbl) {
+
+       /* if (ich>1060) */
+       /* cout << iw << " " << idr << " " << ib << " " << bit << " " << ich << " " << val[ich] << " **  " ; */ 
+       bit=dbl[ib];
      //ioff=off;
      idr=0;
      for (iw=0; iw<(nch*dr/nb)/8; iw++) {
@@ -141,7 +176,7 @@ class deserializer : public slsDetectorData<int> {
        }	
      }
      ii++;
-     ib++;
+     // ib++;
    }//end for
    
     

slsDetectorCalibration/dataStructures/imageZmq16bit.h

@@ -0,0 +1,125 @@
+#ifndef IMAGEZMQ16BIT_H
+#define  IMAGEZMQ16BIT_H
+#include "slsDetectorData.h"
+
+
+class imageZmq16bit : public slsDetectorData<uint16_t> {
+ 
+ private:
+  
+  // int iframe;
+ public:
+
+
+
+
+  /**
+     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
+     (160x160 pixels, 40 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+  */
+  // moench03T1ZmqDataNew(int ns=5000): slsDetectorData<uint16_t>(400, 400, ns*32*2+sizeof(int)), nSamples(ns), offset(sizeof(int)), xtalk(0.00021) {
+ imageZmq16bit(int nnx=400, int nny=400): slsDetectorData<uint16_t>(nnx, nny, 2*nnx*nny) {
+    cout << "* " << nx << " " << ny << endl;
+    int is=0;
+    for (int row=0; row<ny; row++){
+      for(int col=0;col<nx;col++){
+	dataMap[row][col]=is*2;
+	is++;  
+      }
+    }
+ 
+
+  };
+
+  virtual double getValue(char *data, int ix, int iy=0) {
+   
+    cout << ix << " " << ix <<  dataMap[iy][ix] << 2*nx*ny << " "<< endl;
+    uint16_t val=getChannel(data, ix, iy)&0x3fff;
+    return val;
+  };
+
+
+  int getFrameNumber(char *buff){return *((int*)buff);};//*((int*)(buff+5))&0xffffff;};   
+
+ 
+  int getPacketNumber(char *buff){return 0;}//((*(((int*)(buff+4))))&0xff)+1;};   
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[2*nx*ny];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+    //char *retval=0;
+    //	  int  nd;
+    //int fnum = -1;
+	  np=0;
+	  //	  int  pn;
+	  
+
+	  //  if (ff>=0)
+	  //  fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, 2*nx*ny) ){
+	      // iframe++;
+	      //ff=iframe;
+	      return data;
+	    }
+	  }
+	    return NULL;
+	    
+	    
+	  
+  };
+
+
+
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<2*nx*ny) ndata=dsize;
+    else ndata=2*nx*ny;
+    return data;
+
+  }
+  
+
+
+
+
+
+  // virtual int setFrameNumber(int ff){iframe=ff};
+
+
+
+
+
+
+
+
+
+
+int getPacketNumber(int x, int y) {return 0;};
+
+};
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/imageZmq32bit.h

@@ -0,0 +1,125 @@
+#ifndef IMAGEZMQ32BIT_H
+#define  IMAGEZMQ32BIT_H
+#include "slsDetectorData.h"
+
+
+class imageZmq32bit : public slsDetectorData<uint16_t> {
+ 
+ private:
+  
+  // int iframe;
+ public:
+
+
+
+
+  /**
+     Implements the slsReceiverData structure for the moench02 prototype read out by a module i.e. using the slsReceiver
+     (160x160 pixels, 40 packets 1286 large etc.)
+     \param c crosstalk parameter for the output buffer
+
+  */
+  // moench03T1ZmqDataNew(int ns=5000): slsDetectorData<uint16_t>(400, 400, ns*32*2+sizeof(int)), nSamples(ns), offset(sizeof(int)), xtalk(0.00021) {
+ imageZmq32bit(int nnx=400, int nny=400): slsDetectorData<uint16_t>(nnx, nny, sizeof(uint32_t)*nnx*nny) {
+    cout << "* " << nx << " " << ny << endl;
+    int is=0;
+    for (int row=0; row<ny; row++){
+      for(int col=0;col<nx;col++){
+	dataMap[row][col]=is*sizeof(uint32_t);
+	is++;  
+      }
+    }
+ 
+
+  };
+
+  /* virtual double getValue(char *data, int ix, int iy=0) { */
+   
+  /*   //cout << ix << " " << ix <<  dataMap[iy][ix] << 2*nx*ny << " "<< endl; */
+  /*   uint16_t val=getChannel(data, ix, iy); */
+  /*   return val; */
+  /* }; */
+
+
+  int getFrameNumber(char *buff){return *((int*)buff);};//*((int*)(buff+5))&0xffffff;};   
+
+ 
+  int getPacketNumber(char *buff){return 0;}//((*(((int*)(buff+4))))&0xff)+1;};   
+
+  virtual char *readNextFrame(ifstream &filebin) {
+    int ff=-1, np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int &ff) {
+    int np=-1;
+    return readNextFrame(filebin, ff, np);
+  };
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np) {
+	  char *data=new char[2*nx*ny];
+	  char *d=readNextFrame(filebin, ff, np, data);
+	  if (d==NULL) {delete [] data; data=NULL;}
+	  return data;
+  }
+
+
+
+
+  virtual char *readNextFrame(ifstream &filebin, int& ff, int &np, char *data) {
+    //char *retval=0;
+    //	  int  nd;
+    //int fnum = -1;
+	  np=0;
+	  //	  int  pn;
+	  
+
+	  //  if (ff>=0)
+	  //  fnum=ff;
+
+	  if (filebin.is_open()) {
+	    if (filebin.read(data, 2*nx*ny) ){
+	      // iframe++;
+	      //ff=iframe;
+	      return data;
+	    }
+	  }
+	    return NULL;
+	    
+	    
+	  
+  };
+
+
+
+  virtual  char *findNextFrame(char *data, int &ndata, int dsize){
+    if (dsize<2*nx*ny) ndata=dsize;
+    else ndata=2*nx*ny;
+    return data;
+
+  }
+  
+
+
+
+
+
+  // virtual int setFrameNumber(int ff){iframe=ff};
+
+
+
+
+
+
+
+
+
+
+int getPacketNumber(int x, int y) {return 0;};
+
+};
+
+
+
+
+#endif

slsDetectorCalibration/dataStructures/moench03T1ZmqDataNew.h

@@ -28,7 +28,8 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
      \param c crosstalk parameter for the output buffer
 
   */
- moench03T1ZmqDataNew(int ns=5000): slsDetectorData<uint16_t>(400, 400, ns*32*2+sizeof(int)), nSamples(ns), offset(sizeof(int)), xtalk(0.00021) {
+  // moench03T1ZmqDataNew(int ns=5000): slsDetectorData<uint16_t>(400, 400, ns*32*2+sizeof(int)), nSamples(ns), offset(sizeof(int)), xtalk(0.00021) {
+ moench03T1ZmqDataNew(int ns=5000, int oo=0): slsDetectorData<uint16_t>(400, 400, ns*32*2+oo), nSamples(ns), offset(oo), xtalk(0.00021) {
 
     int nadc=32;
     int sc_width=25;
@@ -137,6 +138,7 @@ class moench03T1ZmqDataNew : public slsDetectorData<uint16_t> {
     /* vout+=0.0008*val-6224; */
     /* return vout; //(double)getChannel(data, ix, iy);
      */
+    // cout << ix << " "<< iy << " " << dataMap[iy][ix] << endl;
     return ((double)getChannel(data, ix, iy))+xtalk*getGhost(iy,iy);
   };
 

slsDetectorCalibration/dataStructures/moench04CtbZmq10GbData.h

@@ -44,6 +44,28 @@ class moench04CtbZmq10GbData : public slsDetectorData<uint16_t> {
 
     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 };
 
+    /* 
+       iadc=ptr%32
+       isample=ptr/32
+
+       col=(adc_nr[iadc]%16)*25+isample%25
+       if (adc_nr[iadc]<16)
+       row=199-isample/25;
+       else
+       row=200+isample/25
+
+
+       adc0 col(9*25..10*25-1) row(199..0)
+       adc1 col(8*25..9*25-1)  row(199..0)
+       adc2 col(11*25..12*25-1) row(199..0)
+       adc3 col(10*25..11*25-1) row(199..0)
+       adc4 col(13*25..14*25-1) row(199..0)
+       adc5 col(12*25..13*25-1) row(199..0)
+       adc6 col(15*25..16*25-1) row(199..0)
+       adc7 col(14*25..15*25-1) row(199..0)
+       adc8 col(1*25..2*25-1) row(199..0)
+     */
+
     int row, col;
 
     //int isample;
@@ -134,7 +156,7 @@ class moench04CtbZmq10GbData : public slsDetectorData<uint16_t> {
     if (dSamples>isample) {
       ptr=data+32*(isample+1)+8*isample;
       sample=*((uint64_t*)ptr);
-    cout << isc << " " << ibit[isc] << " " << isample << hex << sample << dec << endl;
+      // cout << isc << " " << ibit[isc] << " " << isample << hex << sample << dec << endl;
     if (sample & (1<<ibit[isc]))
       return 1;
     else

slsDetectorCalibration/dataStructures/moench04CtbZmqData.h

@@ -120,7 +120,7 @@ class moench04CtbZmqData : public slsDetectorData<uint16_t> {
     if (dSamples>isample) {
       ptr=data+aoff+8*isample;
       sample=*((uint64_t*)ptr);
-    cout << isc << " " << ibit[isc] << " " << isample << hex << sample << dec << endl;
+      // cout << isc << " " << ibit[isc] << " " << isample << hex << sample << dec << endl;
     if (sample & (1<<ibit[isc]))
       return 1;
     else

slsDetectorCalibration/dataStructures/slsDetectorData.h

@@ -20,6 +20,8 @@ class slsDetectorData {
   int **dataROIMask; /**< Array of size nx*ny 1 if channel is good (or in the ROI), 0 if bad channel (or out of ROI)   */
   int *xmap;
   int *ymap;
+  dataType **orderedData; 
+  int isOrdered;
   
  public:
   
@@ -37,35 +39,29 @@ class slsDetectorData {
   \param dROI Array of size nx*ny. The elements are 1s if the channel is good or in the ROI, 0 is bad or out of the ROI. NULL (default) means all 1s. 
   
   */
- slsDetectorData(int npx, int npy, int dsize, int **dMap=NULL, dataType **dMask=NULL, int **dROI=NULL): nx(npx), ny(npy), dataSize(dsize) {
+ slsDetectorData(int npx, int npy, int dsize, int **dMap=NULL, dataType **dMask=NULL, int **dROI=NULL): nx(npx), ny(npy), dataSize(dsize), orderedData(NULL), isOrdered(0) {
     
-    
-    xmap=new int[dsize/sizeof(dataType)];
-    ymap=new int[dsize/sizeof(dataType)];
+   int el=dsize/sizeof(dataType);
+    xmap=new int[el];
+    ymap=new int[el];
     
 
-    //  if (dataMask==NULL) {
-    dataMask=new dataType*[ny];
-    for(int i = 0; i < ny; i++) {
-      dataMask[i] = new dataType[nx];
-    }
-    // }
     
-    // if (dataMap==NULL) {
+    orderedData=new dataType*[ny];
     dataMap=new int*[ny];
-    for(int i = 0; i < ny; i++) {
-      dataMap[i] = new int[nx];
-      }
-    // }
-    // if (dataROIMask==NULL) {
+    dataMask=new dataType*[ny];
     dataROIMask=new int*[ny];
     for(int i = 0; i < ny; i++) {
+      dataMap[i] = new int[nx];
+      orderedData[i]=new dataType[nx];
+      dataMask[i] = new dataType[nx];
       dataROIMask[i] = new int[nx];
       for (int j=0; j<nx; j++)
 	dataROIMask[i][j]=1;
-    }
-    // }
-    for (int ip=0; ip<dsize/sizeof(dataType); ip++){
+    
+    }    
+  
+    for (int ip=0; ip<el; ip++){
       xmap[ip]=-1;
       ymap[ip]=-1;
       }
@@ -74,22 +70,24 @@ class slsDetectorData {
     setDataMask(dMask);
     setDataROIMask(dROI);
     
-  };
+  }
   
   virtual ~slsDetectorData() {
     for(int i = 0; i < ny; i++) {
       delete [] dataMap[i];
       delete [] dataMask[i];
       delete [] dataROIMask[i];
+      delete [] orderedData[i];
     }
     delete [] dataMap;
     delete [] dataMask;
     delete [] dataROIMask;
+    delete [] orderedData;
     delete [] xmap;
     delete [] ymap;
   };
   
-  
+  virtual int getPointer(int ix,int iy) {return dataMap[iy][ix];};
   /**
      defines the data map (as offset) - no error checking if datasize and offsets are compatible!
      \param dMap array of size nx*ny storing the pointers to the data in the dataset (as offset). If NULL (default),the data are arranged as if read out row by row (dataMap[iy][ix]=(iy*nx+ix)*sizeof(dataType);)
@@ -202,27 +200,32 @@ class slsDetectorData {
   int setDataSize(int d) {dataSize=d; return dataSize;};
 
   
-  virtual void getPixel(int ip, int &x, int &y) {x=xmap[ip]; y=ymap[ip];};
+virtual void getPixel(int ip, int &x, int &y) {x=xmap[ip]; y=ymap[ip];};
   
-  virtual dataType **getData(char *ptr, int dsize=-1) {
-    
-    dataType **data;
+virtual dataType **getData(char *ptr, int dsize=-1) {
+    int el=dsize/sizeof(dataType);
+    //dataType **data;
     int ix,iy;
-    data=new dataType*[ny];
-    for(int i = 0; i < ny; i++) {
-      data[i]=new dataType[nx];
-    }
+    //data=new dataType*[ny];
+    //for(int i = 0; i < ny; i++) {
+    //  data[i]=new dataType[nx];
+    //}
+     isOrdered=0;
     if (dsize<=0 || dsize>dataSize) dsize=dataSize;
-    for (int ip=0; ip<(dsize/sizeof(dataType)); ip++) {
+
+    for (int ip=0; ip<(el); ip++) {
       getPixel(ip,ix,iy);
       if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
-	data[iy][ix]=getChannel(ptr,ix,iy);
+	//data[iy][ix]=getChannel(ptr,ix,iy);
+	orderedData[iy][ix]=*(ptr+ip);//getChannel(ptr,ix,iy);
       }
     }
-    return data;
-    
-  };
-  
+    isOrdered=1;
+    return orderedData;
+}
+
+ void newFrame(){isOrdered=0;};
+
   virtual double **getImage(char *ptr, int dsize=-1) {
     
     double **data;
@@ -231,15 +234,15 @@ class slsDetectorData {
     for(int i = 0; i < ny; i++) {
       data[i]=new double[nx];
     }
+    int el=dsize/sizeof(dataType);
     if (dsize<=0 || dsize>dataSize) dsize=dataSize;
-    for (int ip=0; ip<(dsize/sizeof(dataType)); ip++) {
+    for (int ip=0; ip<el; ip++) {
       getPixel(ip,ix,iy);
       if (ix>=0 && ix<nx && iy>=0 && iy<ny) {
 	data[iy][ix]=getValue(ptr,ix,iy);
       }
     }
-    return data;
-    
+    return data;   
   };
   
   /** 
@@ -256,7 +259,10 @@ class slsDetectorData {
       // cout << ix << " " << iy << " " ;
       //cout << dataMap[ix][iy] << " " << (void*)data << " " << dataSize<< endl;
       m=dataMask[iy][ix];
-      d=*((dataType*)(data+dataMap[iy][ix]));
+        if (isOrdered==0)
+	  d=*((dataType*)(data+getPointer(ix,iy)));
+      else
+	d=orderedData[iy][ix];
     }  
     return d^m;
   };

slsDetectorCalibration/ghostSummation.h

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

slsDetectorCalibration/interpolatingDetector.h

@@ -107,11 +107,11 @@ class interpolatingDetector : public singlePhotonDetector {
       singlePhotonDetector::clearImage();
   };
 
-  int getImageSize(int &nnx, int &nny, int &ns) {
+  int getImageSize(int &nnx, int &nny, int &nsx, int &nsy) {
     if (interp) 
-      return interp->getImageSize(nnx, nny, ns); 
+      return interp->getImageSize(nnx, nny, nsx, nsy); 
     else 
-      return analogDetector<uint16_t>::getImageSize(nnx, nny, ns);
+      return analogDetector<uint16_t>::getImageSize(nnx, nny, nsx, nsy);
   };
 
 
@@ -251,6 +251,7 @@ int addFrame(char *data,  int *ph=NULL, int ff=0) {
     }
 
     virtual int getNSubPixels(){ if (interp) return interp->getNSubPixels(); else return 1;}
+
     virtual int setNSubPixels(int ns)  { 
       if (interp) {
 	pthread_mutex_lock(fi); 

slsDetectorCalibration/interpolations/eta2InterpolationBase.h

@@ -13,7 +13,7 @@
 class eta2InterpolationBase : public virtual etaInterpolationBase {
   
  public:
- eta2InterpolationBase(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) :  etaInterpolationBase(nx,ny, ns, nb, emin, emax) {
+ eta2InterpolationBase(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) :  etaInterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax) {
     
     /* if (etamin>=etamax) { */
     /*   etamin=-1; */
@@ -37,7 +37,7 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
     
     int corner;
     corner=calcQuad(data, tot, totquad, sDum); 
-    if (nSubPixels>2) 
+    if (nSubPixelsX>2 || nSubPixelsY>2) 
       calcEta(totquad, sDum, etax, etay); 
     getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
 
@@ -53,7 +53,7 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
     
     int corner;
     corner=calcQuad(data, tot, totquad, sDum); 
-    if (nSubPixels>2) 
+    if (nSubPixelsX>2 || nSubPixelsY>2  ) 
       calcEta(totquad, sDum, etax, etay); 
     getInterpolatedPosition(x,y,etax,etay,corner,int_x,int_y);
 
@@ -93,7 +93,7 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
        ;
      } 
      double etax=0, etay=0;
-     if (nSubPixels>2) { 
+     if (nSubPixelsX>2 || nSubPixelsY>2) { 
        cc[0][0]=cl[xoff+3*yoff];
        cc[1][0]=cl[xoff+3*(yoff+1)];
        cc[0][1]=cl[xoff+1+3*yoff];
@@ -133,7 +133,7 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
        ;
      } 
      double etax=0, etay=0;
-     if (nSubPixels>2) { 
+     if (nSubPixelsX>2 || nSubPixelsY>2) { 
        cc[0][0]=cl[xoff+3*yoff];
        cc[1][0]=cl[xoff+3*(yoff+1)];
        cc[0][1]=cl[xoff+1+3*yoff];
@@ -182,31 +182,31 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
       }
     
 
-     if (nSubPixels>2) { 
+     if (nSubPixelsX>2 || nSubPixelsY>2 ) { 
 
-       ex=(etax-etamin)/etastep;
-       ey=(etay-etamin)/etastep;
+       ex=(etax-etamin)/etastepX;
+       ey=(etay-etamin)/etastepY;
        if (ex<0) {
 	 cout << "x*"<< ex << endl;
 	 ex=0;
        } 
-       if (ex>=nbeta) {
+       if (ex>=nbetaX) {
 	 cout << "x?"<< ex << endl;
-	 ex=nbeta-1;
+	 ex=nbetaX-1;
        }
        if (ey<0) {
-	 cout << "y*"<< ey << endl;
+	 cout << "y*"<< ey << " " << nbetaY << endl;
 	 ey=0;
        } 
-       if (ey>=nbeta) {
-	 cout << "y?"<< ey << endl;
-	 ey=nbeta-1;
+       if (ey>=nbetaY) {
+	 cout << "y?"<< ey << " " << nbetaY << endl;
+	 ey=nbetaY-1;
        }
     
     
    
-       xpos_eta=(((double)hhx[(ey*nbeta+ex)]))+dX ;///((double)nSubPixels);
-       ypos_eta=(((double)hhy[(ey*nbeta+ex)]))+dY ;///((double)nSubPixels);
+       xpos_eta=(((double)hhx[(ey*nbetaX+ex)]))+dX ;///((double)nSubPixels);
+       ypos_eta=(((double)hhy[(ey*nbetaX+ex)]))+dY ;///((double)nSubPixels);
        
      } else {
        xpos_eta=0.5*dX+0.25;
@@ -347,10 +347,10 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
 #endif
 #ifndef MYROOT1
     int ex,ey; 
-    ex=(etax-etamin)/etastep;
-    ey=(etay-etamin)/etastep;
-    if (ey<nbeta && ex<nbeta && ex>=0 && ey>=0)
-      heta[ey*nbeta+ex]++; 
+    ex=(etax-etamin)/etastepX;
+    ey=(etay-etamin)/etastepY;
+    if (ey<nbetaY && ex<nbetaX && ex>=0 && ey>=0)
+      heta[ey*nbetaX+ex]++; 
 #endif
     return 0;    
   };
@@ -360,22 +360,22 @@ class eta2InterpolationBase : public virtual etaInterpolationBase {
    // cout << "ff" << endl;
    calcDiff(1, hhx, hhy); //get flat
    double avg=0;
-   for (ipx=0; ipx<nSubPixels; ipx++)
-     for (ipy=0; ipy<nSubPixels; ipy++)
-       avg+=flat[ipx+ipy*nSubPixels];
-   avg/=nSubPixels*nSubPixels;
+   for (ipx=0; ipx<nSubPixelsX; ipx++)
+     for (ipy=0; ipy<nSubPixelsY; ipy++)
+       avg+=flat[ipx+ipy*nSubPixelsX];
+   avg/=nSubPixelsY*nSubPixelsX;
 
-   for (int ibx=0 ; ibx<nSubPixels*nPixelsX; ibx++) {
-     ipx=ibx%nSubPixels-nSubPixels/2;
-       if (ipx<0) ipx=nSubPixels+ipx;
-     for (int iby=0 ; iby<nSubPixels*nPixelsY; iby++) {
-       ipy=iby%nSubPixels-nSubPixels/2;
-     if (ipy<0) ipy=nSubPixels+ipy;
+   for (int ibx=0 ; ibx<nSubPixelsX*nPixelsX; ibx++) {
+     ipx=ibx%nSubPixelsX-nSubPixelsX/2;
+       if (ipx<0) ipx=nSubPixelsX+ipx;
+     for (int iby=0 ; iby<nSubPixelsY*nPixelsY; iby++) {
+       ipy=iby%nSubPixelsY-nSubPixelsY/2;
+     if (ipy<0) ipy=nSubPixelsY+ipy;
      // cout << ipx << " " << ipy << " " << ibx << " " << iby << endl;
-     if (flat[ipx+ipy*nSubPixels]>0)
-       hintcorr[ibx+iby*nSubPixels*nPixelsX]=hint[ibx+iby*nSubPixels*nPixelsX]*(avg/flat[ipx+ipy*nSubPixels]);
+     if (flat[ipx+ipy*nSubPixelsX]>0)
+       hintcorr[ibx+iby*nSubPixelsX*nPixelsX]=hint[ibx+iby*nSubPixelsX*nPixelsX]*(avg/flat[ipx+ipy*nSubPixelsX]);
      else
-       hintcorr[ibx+iby*nSubPixels*nPixelsX]=hint[ibx+iby*nSubPixels*nPixelsX];
+       hintcorr[ibx+iby*nSubPixelsX*nPixelsX]=hint[ibx+iby*nSubPixelsX*nPixelsX];
 
 
      }

slsDetectorCalibration/interpolations/eta3InterpolationBase.h

@@ -13,35 +13,12 @@
 class eta3InterpolationBase : public virtual etaInterpolationBase  {
   
  public:
- eta3InterpolationBase(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationBase(nx, ny, ns, nb, emin, emax) {
+ eta3InterpolationBase(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) : etaInterpolationBase(nx, ny, ns, nsy, nb, nby, emin, emax) {
     //  cout << "e3ib " << nb << " " << emin << " " << emax << endl; 
     /* if (nbeta<=0) { */
     /*   nbeta=nSubPixels*10;    */
     /* } */
-    if (etamin>=etamax) {
-      etamin=-1;
-      etamax=1; 
-    }
-    
-    etastep=(etamax-etamin)/nbeta;
-#ifdef MYROOT1
-    delete heta;
-    delete hhx;
-    delete hhy;
-    heta=new TH2D("heta","heta",nbeta,etamin,etamax,nbeta,etamin,etamax);
-    hhx=new TH2D("hhx","hhx",nbeta,etamin,etamax,nbeta,etamin,etamax);
-    hhy=new TH2D("hhy","hhy",nbeta,etamin,etamax,nbeta,etamin,etamax);
-#endif
-#ifndef MYROOT1
-    /* delete [] heta; */
-    /* delete [] hhx; */
-    /* delete [] hhy; */
-
-    /* heta=new int[nbeta*nbeta]; */
-    /* hhx=new float[nbeta*nbeta]; */
-    /* hhy=new float[nbeta*nbeta]; */
-    
-#endif
+  
     //   cout << nbeta << " " << etamin << " " << etamax << endl;
 };
   
@@ -88,7 +65,7 @@ class eta3InterpolationBase : public virtual etaInterpolationBase  {
     
   
     double etax, etay;
-     if (nSubPixels>2) { 
+     if (nSubPixelsX>2 || nSubPixelsY>2 ) { 
        calcEta3(cl,etax,etay, totquad);
      } 
      return getInterpolatedPosition(x,y,etax, etay,quad,int_x,int_y);
@@ -101,7 +78,7 @@ class eta3InterpolationBase : public virtual etaInterpolationBase  {
     
     
      double etax, etay;
-     if (nSubPixels>2) { 
+     if (nSubPixelsX>2 || nSubPixelsY>2 ) { 
        calcEta3(cl,etax,etay, totquad);
      }
      return getInterpolatedPosition(x,y,etax, etay,quad,int_x,int_y);
@@ -117,38 +94,38 @@ class eta3InterpolationBase : public virtual etaInterpolationBase  {
     double xpos_eta=0,ypos_eta=0;
     int ex,ey;
 
-     if (nSubPixels>2) { 
+     if (nSubPixelsX>2 || nSubPixelsY>2 ) { 
 
 #ifdef MYROOT1
-    xpos_eta=(hhx->GetBinContent(hhx->GetXaxis()->FindBin(etax),hhy->GetYaxis()->FindBin(etay)))/((double)nSubPixels);
-    ypos_eta=(hhy->GetBinContent(hhx->GetXaxis()->FindBin(etax),hhy->GetYaxis()->FindBin(etay)))/((double)nSubPixels);
+    xpos_eta=(hhx->GetBinContent(hhx->GetXaxis()->FindBin(etax),hhy->GetYaxis()->FindBin(etay)))/((double)nSubPixelsX);
+    ypos_eta=(hhy->GetBinContent(hhx->GetXaxis()->FindBin(etax),hhy->GetYaxis()->FindBin(etay)))/((double)nSubPixelsY);
 #endif
 #ifndef MYROOT1
-    ex=(etax-etamin)/etastep;
-    ey=(etay-etamin)/etastep;
+    ex=(etax-etamin)/etastepX;
+    ey=(etay-etamin)/etastepY;
     if (ex<0) {
       /* cout << etax << " " << etamin << " "; */
       /*  cout << "3x*"<< ex << endl; */
       ex=0;
 	} 
-    if (ex>=nbeta) {
+    if (ex>=nbetaX) {
       /* cout << etax << " " << etamin << " "; */
       /* cout << "3x?"<< ex << endl; */
-      ex=nbeta-1;
+      ex=nbetaX-1;
     }
     if (ey<0) {
       /* cout << etay << " " << etamin << " "; */
       /* cout << "3y*"<< ey << endl; */
       ey=0;
 	} 
-    if (ey>=nbeta) {
+    if (ey>=nbetaY) {
       /* cout << etay << " " << etamin << " "; */
       /* cout << "3y?"<< ey << endl; */
-      ey=nbeta-1;
+      ey=nbetaY-1;
       
     }
-    xpos_eta=(((double)hhx[(ey*nbeta+ex)]));///((double)nSubPixels);
-    ypos_eta=(((double)hhy[(ey*nbeta+ex)]));///((double)nSubPixels);
+    xpos_eta=(((double)hhx[(ey*nbetaX+ex)]));///((double)nSubPixels);
+    ypos_eta=(((double)hhy[(ey*nbetaX+ex)]));///((double)nSubPixels);
 
 #endif
    
@@ -265,10 +242,10 @@ class eta3InterpolationBase : public virtual etaInterpolationBase  {
 #endif
 #ifndef MYROOT1
     int ex,ey; 
-    ex=(etax-etamin)/etastep;
-    ey=(etay-etamin)/etastep;
-    if (ey<nbeta && ex<nbeta && ex>=0 && ey>=0)
-      heta[ey*nbeta+ex]++; 
+    ex=(etax-etamin)/etastepX;
+    ey=(etay-etamin)/etastepY;
+    if (ey<nbetaY && ex<nbetaX && ex>=0 && ey>=0)
+      heta[ey*nbetaX+ex]++; 
 #endif
     return 0;    
   };

slsDetectorCalibration/interpolations/etaInterpolationBase.h

@@ -7,7 +7,7 @@
 #include <TH2D.h>
 #include <TH2F.h>
 #endif
-
+#include <cmath> 
 #include "slsInterpolation.h"
 #include "tiffIO.h"
 
@@ -15,44 +15,51 @@ class etaInterpolationBase : public slsInterpolation {
   
  public:
  
- etaInterpolationBase(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : slsInterpolation(nx,ny,ns), hhx(NULL), hhy(NULL), heta(NULL), nbeta(nb), etamin(emin), etamax(emax) {
+ etaInterpolationBase(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, 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;
-    if (nbeta<=0) {
+    if (nbetaX<=0) {
       //cout << "aaa:" <<endl;
-      nbeta=nSubPixels*10;
+      nbetaX=nSubPixelsX*10;
+    } 
+    if (nbetaY<=0) {
+      //cout << "aaa:" <<endl;
+      nbetaY=nSubPixelsY*10;
     }
     if (etamin>=etamax) {
       etamin=-1;
       etamax=2;
     }
-    etastep=(etamax-etamin)/nbeta;
-    heta=new int[nbeta*nbeta];
-    hhx=new float[nbeta*nbeta];
-    hhy=new float[nbeta*nbeta];
+    etastepX=(etamax-etamin)/nbetaX;
+    etastepY=(etamax-etamin)/nbetaY;
+    heta=new int[nbetaX*nbetaY];
+    hhx=new float[nbetaX*nbetaY];
+    hhy=new float[nbetaX*nbetaY];
     rangeMin=etamin;
     rangeMax=etamax;
-    flat= new double[nSubPixels*nSubPixels];
-    hintcorr=new int [nSubPixels*nSubPixels*nPixelsX*nPixelsY];
+    flat= new double[nSubPixelsX*nSubPixelsY];
+    hintcorr=new int [nSubPixelsX*nSubPixelsY*nPixelsX*nPixelsY];
     
   };
   
  etaInterpolationBase(etaInterpolationBase *orig): slsInterpolation(orig){
-   nbeta=orig->nbeta;
+   nbetaX=orig->nbetaX;
+   nbetaY=orig->nbetaY;
    etamin=orig->etamin;
    etamax=orig->etamax;
    rangeMin=orig->rangeMin;
    rangeMax=orig->rangeMax;
 
 
-    etastep=(etamax-etamin)/nbeta;
-    heta=new int[nbeta*nbeta];
-    memcpy(heta,orig->heta,nbeta*nbeta*sizeof(int));
-    hhx=new float[nbeta*nbeta];
-    memcpy(hhx,orig->hhx,nbeta*nbeta*sizeof(float));
-    hhy=new float[nbeta*nbeta];
-    memcpy(hhy,orig->hhy,nbeta*nbeta*sizeof(float));
-    hintcorr=new int [nSubPixels*nSubPixels*nPixelsX*nPixelsY];
+    etastepX=(etamax-etamin)/nbetaX;
+    etastepY=(etamax-etamin)/nbetaY;
+    heta=new int[nbetaX*nbetaY];
+    memcpy(heta,orig->heta,nbetaX*nbetaY*sizeof(int));
+    hhx=new float[nbetaX*nbetaY];
+    memcpy(hhx,orig->hhx,nbetaX*nbetaY*sizeof(float));
+    hhy=new float[nbetaX*nbetaY];
+    memcpy(hhy,orig->hhy,nbetaX*nbetaY*sizeof(float));
+    hintcorr=new int [nSubPixelsX*nSubPixelsY*nPixelsX*nPixelsY];
 
  };
 
@@ -61,7 +68,7 @@ class etaInterpolationBase : public slsInterpolation {
 
 
   virtual void resetFlatField() {
-    for (int ibx=0; ibx<nbeta*nbeta; ibx++) {
+    for (int ibx=0; ibx<nbetaX*nbetaY; ibx++) {
       heta[ibx]=0;
       hhx[ibx]=0;
       hhy[ibx]=0;
@@ -70,13 +77,16 @@ class etaInterpolationBase : public slsInterpolation {
 
   };
     
-  int *setEta(int *h, int nb=-1, double emin=1, double emax=0)
+  int *setEta(int *h, int nb=-1, int nby=-1, double emin=1, double emax=0)
   {  
     if (h) {
       if (heta) delete [] heta;
       heta=h;
-      nbeta=nb;
-      if (nb<=0) nbeta=nSubPixels*10;
+      nbetaX=nb;
+      nbetaY=nby;
+      if (nbetaX<=0) nbetaX=nSubPixelsX*10;
+      if (nbetaY<=0) nbetaY=nSubPixelsY*10;
+      
       etamin=emin;
       etamax=emax;
       if (etamin>=etamax) {
@@ -85,22 +95,24 @@ class etaInterpolationBase : public slsInterpolation {
       }
       rangeMin=etamin;
       rangeMax=etamax;
-      etastep=(etamax-etamin)/nbeta;
+      etastepX=(etamax-etamin)/nbetaX;
+      etastepY=(etamax-etamin)/nbetaY;
     }
     return heta;
   };
   
-   int *setFlatField(int *h, int nb=-1, double emin=1, double emax=0)
+   int *setFlatField(int *h, int nb=-1, int nby=-1, double emin=1, double emax=0)
   {  
-    return setEta(h, nb, emin, emax);
+    return setEta(h, nb, nby, emin, emax);
   };
 
 
 
   int *getFlatField(){return setEta(NULL);};
   
-  int *getFlatField(int &nb, double &emin, double &emax){
-    nb=nbeta; 
+  int *getFlatField(int &nb, int &nby, double &emin, double &emax){
+    nb=nbetaX; 
+    nby=nbetaY; 
     emin=etamin; 
     emax=etamax; 
     return getFlatField();
@@ -109,13 +121,13 @@ class etaInterpolationBase : public slsInterpolation {
   
   void *writeFlatField(const char * imgname) {
     float *gm=NULL;
-    gm=new float[nbeta*nbeta];
-    for (int ix=0; ix<nbeta; ix++) {
-      for (int iy=0; iy<nbeta; iy++) {
-	gm[iy*nbeta+ix]=heta[iy*nbeta+ix];
+    gm=new float[nbetaX*nbetaY];
+    for (int ix=0; ix<nbetaX; ix++) {
+      for (int iy=0; iy<nbetaY; iy++) {
+	gm[iy*nbetaX+ix]=heta[iy*nbetaX+ix];
       }
     } 
-    WriteToTiff(gm, imgname, nbeta, nbeta);   
+    WriteToTiff(gm, imgname, nbetaX, nbetaY);   
     delete [] gm;
     return NULL; 
   };
@@ -129,16 +141,18 @@ class etaInterpolationBase : public slsInterpolation {
       etamax=2;
     }
     
-    etastep=(etamax-etamin)/nbeta;
+    etastepX=(etamax-etamin)/nbetaX;
+    etastepY=(etamax-etamin)/nbetaY;
     uint32 nnx;
     uint32 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;
-      return 0;
-    }
-    nbeta=nnx;
+    /* if (nnx!=nny) { */
+    /*   cout << "different number of bins in x " << nnx << "  and y " << nny<< " !"<< endl; */
+    /*   cout << "Aborting read"<< endl; */
+    /*   return 0; */
+    /* } */
+    nbetaX=nnx;
+    nbetaY=nny;
     if (gm) {
       if (heta) {
 	delete [] heta;
@@ -146,13 +160,13 @@ class etaInterpolationBase : public slsInterpolation {
 	delete [] hhy;
       }
       
-      heta=new int[nbeta*nbeta];
-      hhx=new float[nbeta*nbeta];
-      hhy=new float[nbeta*nbeta];
+      heta=new int[nbetaX*nbetaY];
+      hhx=new float[nbetaX*nbetaY];
+      hhy=new float[nbetaX*nbetaY];
       
-      for (int ix=0; ix<nbeta; ix++) {
-	for (int iy=0; iy<nbeta; iy++) {
-	  heta[iy*nbeta+ix]=gm[iy*nbeta+ix];
+      for (int ix=0; ix<nbetaX; ix++) {
+	for (int iy=0; iy<nbetaY; iy++) {
+	  heta[iy*nbetaX+ix]=gm[iy*nbetaX+ix];
 	}
       }
       delete [] gm;
@@ -178,10 +192,10 @@ float *gethhx()
     };
   virtual int addToFlatField(double etax, double etay){
     int ex,ey; 
-    ex=(etax-etamin)/etastep;
-    ey=(etay-etamin)/etastep;
-    if (ey<nbeta && ex<nbeta && ex>=0 && ey>=0)
-      heta[ey*nbeta+ex]++; 
+    ex=(etax-etamin)/etastepX;
+    ey=(etay-etamin)/etastepY;
+    if (ey<nbetaY && ex<nbetaX && ex>=0 && ey>=0)
+      heta[ey*nbetaX+ex]++; 
     return 0;    
   };
   
@@ -195,80 +209,80 @@ float *gethhx()
    
    float tot_eta=0;
 
-  float *etah=new float[nbeta*nbeta];
-  int etabins=nbeta;
+  float *etah=new float[nbetaX*nbetaY];
+  // int etabins=nbeta;
   int ibb=0;
 
-  for (int ii=0; ii<etabins*etabins; ii++) {
+  for (int ii=0; ii<nbetaX*nbetaY; ii++) {
    
       etah[ii]=heta[ii];
       tot_eta+=heta[ii];
   }
   sprintf(tit,"/scratch/eta_%d.tiff",ind);
-  WriteToTiff(etah, tit, etabins, etabins);
+  WriteToTiff(etah, tit, nbetaX, nbetaY);
 
 
-  for (int ii=0; ii<etabins*etabins; ii++) {
-    ibb=(hhx[ii]*nSubPixels);
+  for (int ii=0; ii<nbetaX*nbetaY; ii++) {
+    ibb=(hhx[ii]*nSubPixelsX);
     etah[ii]=ibb;
   }
   sprintf(tit,"/scratch/eta_hhx_%d.tiff",ind);
-  WriteToTiff(etah, tit, etabins, etabins);
+  WriteToTiff(etah, tit, nbetaX, nbetaY);
 	  
-  for (int ii=0; ii<etabins*etabins; ii++) {
-    ibb=hhy[ii]*nSubPixels;
+  for (int ii=0; ii<nbetaX*nbetaY; ii++) {
+    ibb=hhy[ii]*nSubPixelsY;
     etah[ii]=ibb;
   }
   sprintf(tit,"/scratch/eta_hhy_%d.tiff",ind);
-  WriteToTiff(etah, tit, etabins, etabins);
+  WriteToTiff(etah, tit, nbetaX, nbetaY);
 	  
   
-  float *ftest=new float[nSubPixels*nSubPixels];
+  float *ftest=new float[nSubPixelsX*nSubPixelsY];
 
-  for (int ib=0; ib<nSubPixels*nSubPixels; ib++) ftest[ib]=0;
+  for (int ib=0; ib<nSubPixelsX*nSubPixelsY; ib++) ftest[ib]=0;
   
 
   //int ibx=0, iby=0;
   
-  for (int ii=0; ii<nbeta*nbeta; ii++) {
+  for (int ii=0; ii<nbetaX*nbetaY; ii++) {
     
-    ibx=nSubPixels*hhx[ii];
-    iby=nSubPixels*hhy[ii];
+    ibx=nSubPixelsX*hhx[ii];
+    iby=nSubPixelsY*hhy[ii];
     if (ibx<0) ibx=0;
     if (iby<0) iby=0;
-    if (ibx>=nSubPixels) ibx=nSubPixels-1;
-    if (iby>=nSubPixels) iby=nSubPixels-1;
+    if (ibx>=nSubPixelsX) ibx=nSubPixelsX-1;
+    if (iby>=nSubPixelsY) iby=nSubPixelsY-1;
     
 
-    if (ibx>=0 && ibx<nSubPixels && iby>=0 && iby<nSubPixels) {
+    if (ibx>=0 && ibx<nSubPixelsX && iby>=0 && iby<nSubPixelsY) {
       //
       // if (ibx>0 && iby>0) cout << ibx << " " << iby << " " << ii << endl;
-      ftest[ibx+iby*nSubPixels]+=heta[ii];
+      ftest[ibx+iby*nSubPixelsX]+=heta[ii];
     } else
       cout << "Bad interpolation "<< ii << " " << ibx << " " << iby<< endl; 
-
+    
   }
 
   sprintf(tit,"/scratch/ftest_%d.tiff",ind);
-  WriteToTiff(ftest, tit, nSubPixels, nSubPixels);
+  WriteToTiff(ftest, tit, nSubPixelsX, nSubPixelsY);
 
   //int ibx=0, iby=0;
-  tot_eta/=nSubPixels*nSubPixels;
+  tot_eta/=nSubPixelsX*nSubPixelsY;
   int nbad=0;
-  for (int ii=0; ii<etabins*etabins; ii++) {
-    ibx=nSubPixels*hhx[ii];
-    iby=nSubPixels*hhy[ii];
-    if (ftest[ibx+iby*nSubPixels]<tot_eta*0.5) {
+  for (int ii=0; ii<nbetaX*nbetaY; ii++) {
+    ibx=nSubPixelsX*hhx[ii];
+    iby=nSubPixelsY*hhy[ii];
+    if (ftest[ibx+iby*nSubPixelsX]<tot_eta*0.5) {
       etah[ii]=1;
       nbad++;
-    } else if(ftest[ibx+iby*nSubPixels]>tot_eta*2.){
+    } else if(ftest[ibx+iby*nSubPixelsX]>tot_eta*2.){
       etah[ii]=2;
       nbad++;
     } else
       etah[ii]=0;
   }
   sprintf(tit,"/scratch/eta_bad_%d.tiff",ind);
-  WriteToTiff(etah, tit, etabins, etabins);
+  WriteToTiff(etah, tit, nbetaX, nbetaY);
   // cout << "Index: " << ind << "\t Bad bins: "<< nbad << endl;
   //int ibx=0, iby=0;
 
@@ -286,46 +300,44 @@ float *gethhx()
     double diff=0, d;
     //double bsize=1./nSubPixels;
     int nbad=0;
-    double p_tot_x[nSubPixels], p_tot_y[nSubPixels], p_tot[nSubPixels*nSubPixels];
-    double maxdiff=0, mindiff=avg*nSubPixels*nSubPixels;
+    double p_tot_x[nSubPixelsX], p_tot_y[nSubPixelsY], p_tot[nSubPixelsX*nSubPixelsY];
+    double maxdiff=0, mindiff=avg*nSubPixelsX*nSubPixelsY;
    
     int ipx, ipy;
-    for (ipy=0; ipy<nSubPixels; ipy++) {
-      for (ipx=0; ipx<nSubPixels; ipx++) {
-	p_tot[ipx+ipy*nSubPixels]=0;
+    for (ipy=0; ipy<nSubPixelsY; ipy++) {
+      for (ipx=0; ipx<nSubPixelsX; ipx++) {
+	p_tot[ipx+ipy*nSubPixelsX]=0;
       }
       p_tot_y[ipy]=0;
       p_tot_x[ipy]=0;
     }
    
-    for (int ibx=0; ibx<nbeta; ibx++) {
-      for (int iby=0; iby<nbeta; iby++) {
-	ipx=hx[ibx+iby*nbeta]*nSubPixels;
+    for (int ibx=0; ibx<nbetaX; ibx++) {
+      for (int iby=0; iby<nbetaY; iby++) {
+	ipx=hx[ibx+iby*nbetaX]*nSubPixelsX;
 	if (ipx<0) ipx=0;
-	if (ipx>=nSubPixels) ipx=nSubPixels-1;
+	if (ipx>=nSubPixelsX) ipx=nSubPixelsX-1;
 	
-	ipy=hy[ibx+iby*nbeta]*nSubPixels;
+	ipy=hy[ibx+iby*nbetaX]*nSubPixelsY;
 	if (ipy<0) ipy=0;
-	if (ipy>=nSubPixels) ipy=nSubPixels-1;
+	if (ipy>=nSubPixelsY) ipy=nSubPixelsY-1;
 	
-	p_tot[ipx+ipy*nSubPixels]+=heta[ibx+iby*nbeta];
-	p_tot_y[ipy]+=heta[ibx+iby*nbeta];
-	p_tot_x[ipx]+=heta[ibx+iby*nbeta];
-	
-
+	p_tot[ipx+ipy*nSubPixelsX]+=heta[ibx+iby*nbetaX];
+	p_tot_y[ipy]+=heta[ibx+iby*nbetaX];
+	p_tot_x[ipx]+=heta[ibx+iby*nbetaX];
       }
     }
     
     
     //  cout << endl << endl;
-    for (ipy=0; ipy<nSubPixels; ipy++) { 
+    for (ipy=0; ipy<nSubPixelsY; ipy++) { 
      cout.width(5);
      //flat_y[ipy]=p_tot_y[ipy];//avg/nSubPixels;
-      for (ipx=0; ipx<nSubPixels; ipx++) {
+      for (ipx=0; ipx<nSubPixelsX; ipx++) {
 
 	//	flat_x[ipx]=p_tot_x[ipx];///avg/nSubPixels;
-	flat[ipx+nSubPixels*ipy]=p_tot[ipx+nSubPixels*ipy];///avg;
-	d=p_tot[ipx+nSubPixels*ipy]-avg;
+	flat[ipx+nSubPixelsX*ipy]=p_tot[ipx+nSubPixelsX*ipy];///avg;
+	d=p_tot[ipx+nSubPixelsX*ipy]-avg;
 	if (d<0) d*=-1.;
 	if (d>5*sqrt(avg) )
 	  nbad++;
@@ -354,8 +366,8 @@ float *gethhx()
   float *hhx;
   float *hhy;
   int *heta;
-  int nbeta;
-  double etamin, etamax, etastep;
+  int nbetaX, nbetaY;
+  double etamin, etamax, etastepX, etastepY;
   double rangeMin, rangeMax;
 
 

slsDetectorCalibration/interpolations/etaInterpolationPosXY.h

@@ -9,7 +9,7 @@
 
 class etaInterpolationPosXY : public virtual etaInterpolationBase{
  public:
- etaInterpolationPosXY(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny,ns, nb, emin,emax){
+ etaInterpolationPosXY(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax){
     //  cout << "epxy " << nb << " " << emin << " " << emax << endl; cout << nbeta << " " << etamin << " " << etamax << endl; 
   };
 
@@ -24,14 +24,6 @@ class etaInterpolationPosXY : public virtual etaInterpolationBase{
   virtual void prepareInterpolation(int &ok)
   {
    ok=1;  
-#ifdef MYROOT1   
-   if (hhx) delete hhx;
-   if (hhy) delete hhy;
-
-   hhx=new TH2D("hhx","hhx",heta->GetNbinsX(),heta->GetXaxis()->GetXmin(),heta->GetXaxis()->GetXmax(), heta->GetNbinsY(),heta->GetYaxis()->GetXmin(),heta->GetYaxis()->GetXmax()); 
-   hhy=new TH2D("hhy","hhy",heta->GetNbinsX(),heta->GetXaxis()->GetXmin(),heta->GetXaxis()->GetXmax(), heta->GetNbinsY(),heta->GetYaxis()->GetXmin(),heta->GetYaxis()->GetXmax()); 
-   
-#endif
 
 
    ///*Eta Distribution Rebinning*///
@@ -40,106 +32,128 @@ class etaInterpolationPosXY : public virtual etaInterpolationBase{
    double tot_eta=0;
    double tot_eta_x=0;
    double tot_eta_y=0;
-   for (int ip=0; ip<nbeta*nbeta; ip++)
+   for (int ip=0; ip<nbetaX*nbetaY; ip++)
      tot_eta+=heta[ip];
    cout << "total eta entries is :"<< tot_eta << endl;   
    if (tot_eta<=0) {ok=0; return;};
 
 
-   double hx[nbeta]; //profile x
-   double hy[nbeta]; //profile y
-   double hix[nbeta]; //integral of projection x
-   double hiy[nbeta]; //integral of projection y
+   double hx[nbetaX]; //profile x
+   double hy[nbetaY]; //profile y
+   double hix[nbetaX]; //integral of projection x
+   double hiy[nbetaY]; //integral of projection y
    //  int ii=0;
-   double etax;//, etay;
-   for (int ib=0; ib<nbeta; ib++) {
+   double etax, etay;
+   for (int ib=0; ib<nbetaX; ib++) {
 
-     tot_eta_x=0;
-     tot_eta_y=0;
+   
+     //tot_eta_y=0;
 
-     for (int iby=0; iby<nbeta; iby++) {
-       etax=etamin+iby*etastep;
+     for (int iby=0; iby<nbetaY; iby++) {
+       etay=etamin+iby*etastepY;
        //cout << etax << endl;
-       if (etax>=0 && etax<=1)
-	 hx[iby]=heta[iby+ib*nbeta];
-       else {
-	 hx[iby]=0;
-       }
+     
        // tot_eta_x+=hx[iby];
-       if (etax>=0 && etax<=1)
-	 hy[iby]=heta[ib+iby*nbeta];
+       if (etay>=0 && etay<=1)
+	 hy[iby]=heta[ib+iby*nbetaX];
        else
 	 hy[iby]=0;
        // tot_eta_y+=hy[iby];
      }
 
-     hix[0]=hx[0];
+   
      hiy[0]=hy[0];
 
-     for (int iby=1; iby<nbeta; iby++) {
-       hix[iby]=hix[iby-1]+hx[iby];
+     for (int iby=1; iby<nbetaY; iby++) {
        hiy[iby]=hiy[iby-1]+hy[iby];
      }
 
-     // ii=0;
-     tot_eta_x=hix[nbeta-1]+1;
-     tot_eta_y=hiy[nbeta-1]+1;
+     tot_eta_y=hiy[nbetaY-1]+1;
      
-     for (int ibx=0; ibx<nbeta; ibx++) {
-       if (tot_eta_x<=0) {
-	 hhx[ibx+ib*nbeta]=-1;
-	 //ii=(ibx)/nbeta;
-       } else //if (hix[ibx]>(ii+1)*tot_eta_x*bsize) 
-	 { 
-	   //if (hix[ibx]>tot_eta_x*(ii+1)/nSubPixels) ii++;
-	   hhx[ibx+ib*nbeta]=hix[ibx]/tot_eta_x;
-	 }
-     }
-     /* if (ii!=(nSubPixels-1)) */
-     /*   cout << ib << " x " <<  tot_eta_x << " " << (ii+1)*tot_eta_x*bsize << " " << ii << " " << hix[nbeta-1]<< endl; */
-     
-     //ii=0;
-     
-     for (int ibx=0; ibx<nbeta; ibx++) {
+     for (int iby=0; iby<nbetaY; iby++) {
        if (tot_eta_y<=0) {
-	 hhy[ib+ibx*nbeta]=-1;
+	 hhy[ib+iby*nbetaX]=-1;
 	 //ii=(ibx*nSubPixels)/nbeta;
        } else {   
 	 //if (hiy[ibx]>tot_eta_y*(ii+1)/nSubPixels) ii++;
-	 hhy[ib+ibx*nbeta]=hiy[ibx]/tot_eta_y;
+	 hhy[ib+iby*nbetaX]=hiy[iby]/tot_eta_y;
        }
      }
    }
 
 
+
+   for (int ib=0; ib<nbetaY; ib++) {
+
+     for (int ibx=0; ibx<nbetaX; ibx++) {
+       etax=etamin+ibx*etastepX;
+       //cout << etax << endl;
+       if (etax>=0 && etax<=1)
+	 hx[ibx]=heta[ibx+ib*nbetaX];
+       else {
+	 hx[ibx]=0;
+       }
+     }
+     hix[0]=hx[0];
+       
+     for (int ibx=1; ibx<nbetaX; ibx++) {
+       hix[ibx]=hix[ibx-1]+hx[ibx];
+     }
+
+  
+     tot_eta_x=hix[nbetaX-1]+1;
+     
+     for (int ibx=0; ibx<nbetaX; ibx++) {
+       if (tot_eta_x<=0) {
+	 hhx[ibx+ib*nbetaX]=-1;
+       } 
+       else { 
+	 hhx[ibx+ib*nbetaX]=hix[ibx]/tot_eta_x;
+       }
+     }
+     
+
+     
+     for (int ibx=0; ibx<nbetaX; ibx++) {
+       if (tot_eta_x<=0) {
+	 hhx[ibx+ib*nbetaX]=-1;
+       } else	 { 
+	 //if (hix[ibx]>tot_eta_x*(ii+1)/nSubPixels) ii++;
+	 hhx[ibx+ib*nbetaX]=hix[ibx]/tot_eta_x;
+       }
+     }
+     
+   }
+
+     
    int ibx, iby, ib; 
    
    iby=0;
-   while (hhx[iby*nbeta+nbeta/2]<0) iby++;
+   while (hhx[iby*nbetaY+nbetaY/2]<0) iby++;
    for (ib=0; ib<iby;ib++) {
-     for (ibx=0; ibx<nbeta;ibx++)
-       hhx[ibx+nbeta*ib]=hhx[ibx+nbeta*iby];
+     for (ibx=0; ibx<nbetaX;ibx++)
+       hhx[ibx+nbetaX*ib]=hhx[ibx+nbetaX*iby];
    }
-   iby=nbeta-1;
+   iby=nbetaY-1;
    
-   while (hhx[iby*nbeta+nbeta/2]<0) iby--;
-   for (ib=iby+1; ib<nbeta;ib++) {
-     for (ibx=0; ibx<nbeta;ibx++)
-       hhx[ibx+nbeta*ib]=hhx[ibx+nbeta*iby];
+   while (hhx[iby*nbetaY+nbetaY/2]<0) iby--;
+   for (ib=iby+1; ib<nbetaY;ib++) {
+     for (ibx=0; ibx<nbetaX;ibx++)
+       hhx[ibx+nbetaX*ib]=hhx[ibx+nbetaX*iby];
    }
    
    iby=0;
-   while (hhy[nbeta/2*nbeta+iby]<0) iby++;
+   while (hhy[nbetaX/2*nbetaX+iby]<0) iby++;
    for (ib=0; ib<iby;ib++) {
-     for (ibx=0; ibx<nbeta;ibx++)
-       hhy[ib+nbeta*ibx]=hhy[iby+nbeta*ibx];
+     for (ibx=0; ibx<nbetaY;ibx++)
+       hhy[ib+nbetaX*ibx]=hhy[iby+nbetaX*ibx];
    }
-   iby=nbeta-1;
+   iby=nbetaX-1;
    
-   while (hhy[nbeta/2*nbeta+iby]<0) iby--;
-   for (ib=iby+1; ib<nbeta;ib++) {
-     for (ibx=0; ibx<nbeta;ibx++)
-       hhy[ib+nbeta*ibx]=hhy[iby+nbeta*ibx];
+   while (hhy[nbetaX/2*nbetaX+iby]<0) iby--;
+   for (ib=iby+1; ib<nbetaX;ib++) {
+     for (ibx=0; ibx<nbetaY;ibx++)
+       hhy[ib+nbetaX*ibx]=hhy[iby+nbetaX*ibx];
    }
 
 
@@ -156,9 +170,16 @@ class etaInterpolationPosXY : public virtual etaInterpolationBase{
 
 };
 
+
+
+
+
+
+
+
 class eta2InterpolationPosXY : public virtual eta2InterpolationBase, public virtual etaInterpolationPosXY {
  public:
- eta2InterpolationPosXY(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny,ns, nb, emin,emax),eta2InterpolationBase(nx,ny,ns, nb, emin,emax),etaInterpolationPosXY(nx,ny,ns, nb, emin,emax){
+ eta2InterpolationPosXY(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax),eta2InterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax),etaInterpolationPosXY(nx,ny, ns, nsy, nb, nby, emin, emax){
     //  cout << "e2pxy " << nb << " " << emin << " " << emax << endl; 
   };
  
@@ -172,8 +193,8 @@ class eta2InterpolationPosXY : public virtual eta2InterpolationBase, public virt
 
 class eta3InterpolationPosXY : public virtual eta3InterpolationBase, public virtual etaInterpolationPosXY {
  public:
- eta3InterpolationPosXY(int nx=400, int ny=400, int ns=25, int nb=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny,ns, nb, emin,emax),eta3InterpolationBase(nx,ny,ns, nb, emin,emax), etaInterpolationPosXY(nx,ny,ns, nb, emin,emax){
-      cout << "e3pxy " << nbeta << " " << etamin << " " << etamax << " " << nSubPixels<< endl;  
+ eta3InterpolationPosXY(int nx=400, int ny=400, int ns=25, int nsy=25, int nb=-1, int nby=-1, double emin=1, double emax=0) : etaInterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax),eta3InterpolationBase(nx,ny, ns, nsy, nb, nby, emin, emax), etaInterpolationPosXY(nx,ny, ns, nsy, nb, nby, emin, emax){
+    //   cout << "e3pxy " << nbeta << " " << etamin << " " << etamax << " " << nSubPixels<< endl;  
   };
 
  eta3InterpolationPosXY(eta3InterpolationPosXY *orig): etaInterpolationBase(orig), etaInterpolationPosXY(orig)  {};

slsDetectorCalibration/interpolations/slsInterpolation.h

@@ -29,19 +29,21 @@ class slsInterpolation
 {
 
  public:
- slsInterpolation(int nx=400, int ny=400, int ns=25) :nPixelsX(nx), nPixelsY(ny),  nSubPixels(ns), id(0) {
+ slsInterpolation(int nx=400, int ny=400, int ns=25, int nsy=-1) :nPixelsX(nx), nPixelsY(ny),  nSubPixelsX(ns), nSubPixelsY(nsy),id(0) {
    
- hint=new int[ns*nx*ns*ny];
+    if (nSubPixelsY<=0) nSubPixelsY=nSubPixelsX;
+    hint=new int[nSubPixelsX*nx*nSubPixelsY*ny];
 
 };
   
  slsInterpolation(slsInterpolation *orig){
    nPixelsX=orig->nPixelsX;
    nPixelsY=orig->nPixelsY;
-   nSubPixels=orig->nSubPixels;
+   nSubPixelsX=orig->nSubPixelsX;
+   nSubPixelsY=orig->nSubPixelsY;
    
-   hint=new int[nSubPixels*nPixelsX*nSubPixels*nPixelsY];
-   memcpy(hint, orig->hint,nSubPixels*nPixelsX*nSubPixels*nPixelsY*sizeof(int));
+   hint=new int[nSubPixelsX*nPixelsX*nSubPixelsY*nPixelsY];
+   memcpy(hint, orig->hint,nSubPixelsX*nPixelsX*nSubPixelsY*nPixelsY*sizeof(int));
  
  };
 
@@ -51,23 +53,37 @@ class slsInterpolation
    return new slsInterpolation(this);
    }*/
 
-  int getNSubPixels() {return nSubPixels;};
+  int getNSubPixelsX() {return nSubPixelsX;};
+  int getNSubPixelsY() {return nSubPixelsY;};
+  int getNSubPixels() {if (nSubPixelsX==nSubPixelsY) return nSubPixelsX; else return 0;};
+  void getNSubPixels(int &nsx, int &nsy) {nsx=nSubPixelsX; nsy=nsx=nSubPixelsY;}
 
-
-  int setNSubPixels(int ns)   {
-    if (ns>0 && ns!=nSubPixels) {
+  void setNSubPixels(int ns, int nsy=-1)   {
+   
       delete [] hint;
-      nSubPixels=ns;
-      hint=new int[nSubPixels*nPixelsX*nSubPixels*nPixelsY];
-    }
-    return nSubPixels;
+      nSubPixelsX=ns;
+      if (nsy>0)  nSubPixelsY=nsy;
+      else nSubPixelsY=ns;
+      
+      hint=new int[nSubPixelsX*nPixelsX*nSubPixelsY*nPixelsY];
+      
+      //return nSubPixels;
   }
 
-  int getImageSize(int &nnx, int &nny, int &ns) {
-    nnx=nSubPixels*nPixelsX;
-    nny=nSubPixels*nPixelsY;
-    ns=nSubPixels;
-    return nSubPixels*nSubPixels*nPixelsX*nPixelsY;
+  
+
+
+  int getImageSize(int &nnx, int &nny, int &nsx, int &nsy) {
+    nnx=nSubPixelsX*nPixelsX;
+    nny=nSubPixelsY*nPixelsY;
+    nsx=nSubPixelsX;
+    nsy=nSubPixelsY;
+    return nSubPixelsX*nSubPixelsY*nPixelsX*nPixelsY;
+  };
+  
+
+  int getImageSize() {
+    return nSubPixelsX*nSubPixelsY*nPixelsX*nPixelsY;
   };
   
   
@@ -92,14 +108,14 @@ class slsInterpolation
     //cout << "!" <<endl;
     float *gm=NULL;
     int *dummy=getInterpolatedImage();
-    gm=new float[ nSubPixels*  nSubPixels* nPixelsX*nPixelsY];
+    gm=new float[ nSubPixelsX*  nSubPixelsY* nPixelsX*nPixelsY];
     if (gm) {
-      for (int ix=0; ix<nPixelsX*nSubPixels; ix++) {
-	for (int iy=0; iy<nPixelsY*nSubPixels; iy++) {
-	  gm[iy*nPixelsX*nSubPixels+ix]=dummy[iy*nPixelsX*nSubPixels+ix];
+      for (int ix=0; ix<nPixelsX*nSubPixelsX; ix++) {
+	for (int iy=0; iy<nPixelsY*nSubPixelsY; iy++) {
+	  gm[iy*nPixelsX*nSubPixelsX+ix]=dummy[iy*nPixelsX*nSubPixelsX+ix];
 	}
       }
-      WriteToTiff(gm, imgname,nSubPixels* nPixelsX ,nSubPixels* nPixelsY); 
+      WriteToTiff(gm, imgname,nSubPixelsY* nPixelsX ,nSubPixelsY* nPixelsY); 
       delete [] gm;
     } else cout << "Could not allocate float image " << endl;
     return NULL;    
@@ -120,9 +136,9 @@ class slsInterpolation
   virtual void clearInterpolatedImage() {
 
 
-      for (int ix=0; ix<nPixelsX*nSubPixels; ix++) {
-	for (int iy=0; iy<nPixelsY*nSubPixels; iy++) {
-	  hint[iy*nPixelsX*nSubPixels+ix]=0;
+      for (int ix=0; ix<nPixelsX*nSubPixelsX; ix++) {
+	for (int iy=0; iy<nPixelsY*nSubPixelsY; iy++) {
+	  hint[iy*nPixelsX*nSubPixelsX+ix]=0;
 	}
       }
 
@@ -133,11 +149,11 @@ class slsInterpolation
 
 
   virtual int *addToImage(double int_x, double int_y){ 
-    int iy=((double)nSubPixels)*int_y; 
-    int ix=((double)nSubPixels)*int_x; 
-     if (ix>=0 && ix<(nPixelsX*nSubPixels) && iy<(nSubPixels*nPixelsY) && iy>=0 ){
+    int iy=((double)nSubPixelsY)*int_y; 
+    int ix=((double)nSubPixelsX)*int_x; 
+     if (ix>=0 && ix<(nPixelsX*nSubPixelsX) && iy<(nSubPixelsY*nPixelsY) && iy>=0 ){
        // cout << int_x << " " << int_y << " " << "  " << ix << " " << iy << " " << ix+iy*nPixelsX*nSubPixels << " " << hint[ix+iy*nPixelsX*nSubPixels];
-       (*(hint+ix+iy*nPixelsX*nSubPixels))+=1; 
+       (*(hint+ix+iy*nPixelsX*nSubPixelsX))+=1; 
        // cout << " " << hint[ix+iy*nPixelsX*nSubPixels] << endl;
      }// else
       // cout << "bad! "<< int_x << " " << int_y << " " << "  " << ix << " " << iy << " " << ix+iy*nPixelsX*nSubPixels << endl;
@@ -180,11 +196,12 @@ class slsInterpolation
     /* cluster[2]=cl+6; */
     
     sum=0;
+    int xoff=0, yoff=0;
+#ifndef WRITE_QUAD 
     double sumBL=0;
     double sumTL=0;
     double sumBR=0;
     double sumTR=0;
-    int xoff=0, yoff=0;
     for (int ix=0; ix<3; ix++) {
       for (int iy=0; iy<3; iy++) {
 	sum+=cl[ix+3*iy];
@@ -204,34 +221,95 @@ class slsInterpolation
 
     
     if(sumTL  >= totquad){
-      /* sDum[0][0] = cluster[1][0]; sDum[1][0] = cluster[2][0]; */
-      /* sDum[0][1] = cluster[1][1]; sDum[1][1] = cluster[2][1]; */
-      
+/* #ifdef WRITE_QUAD */
+/*       /\* sDum[0][0] = cluster[1][0]; sDum[1][0] = cluster[2][0]; *\/ */
+/*       /\* sDum[0][1] = cluster[1][1]; sDum[1][1] = cluster[2][1]; *\/ */
+/*       if (sumTL  ==sum) { */
+/* #endif */
       corner = TOP_LEFT;
       totquad=sumTL;
       xoff=0;
       yoff=1;
+/* #ifdef WRITE_QUAD */
+/*       } */
+/* #endif */
     } 
 
     if(sumBR  >= totquad){
       /* sDum[0][0] = cluster[0][1]; sDum[1][0] = cluster[1][1]; */
       /* sDum[0][1] = cluster[0][2]; sDum[1][1] = cluster[1][2]; */
       
+/* #ifdef WRITE_QUAD */
+/*       /\* sDum[0][0] = cluster[1][0]; sDum[1][0] = cluster[2][0]; *\/ */
+/*       /\* sDum[0][1] = cluster[1][1]; sDum[1][1] = cluster[2][1]; *\/ */
+/*       if (sumBR   ==sum) { */
+/* #endif */
+      corner = BOTTOM_RIGHT;
       xoff=1;
       yoff=0;
-      corner = BOTTOM_RIGHT;
       totquad=sumBR;
+/* #ifdef WRITE_QUAD */
+/*       } */
+/* #endif */
     }
     
     if(sumTR  >= totquad){
+/* #ifdef WRITE_QUAD */
+/*       /\* sDum[0][0] = cluster[1][0]; sDum[1][0] = cluster[2][0]; *\/ */
+/*       /\* sDum[0][1] = cluster[1][1]; sDum[1][1] = cluster[2][1]; *\/ */
+/*       if (sumTR ==sum) { */
+/* #endif */
       xoff=1;
       yoff=1;
       /* sDum[0][0] = cluster[1][1]; sDum[1][0] = cluster[2][1]; */
       /* sDum[0][1] = cluster[1][2]; sDum[1][1] = cluster[2][2]; */
       corner = TOP_RIGHT;
       totquad=sumTR;
+/* #ifdef WRITE_QUAD */
+/*       } */
+/* #endif */
     }
+ 
+#endif    
+#ifdef WRITE_QUAD    
+   
+    double sumB=0;
+    double sumT=0;
+    double sumR=0;
+    double sumL=0;
+
+    for (int ix=0; ix<3; ix++) {
+      for (int iy=0; iy<3; iy++) {
+	sum+=cl[ix+3*iy];
+	if (ix<1 ) sumL+=cl[ix+iy*3];
+	if (ix>1) sumR+=cl[ix+iy*3];
+	if (iy<1) sumB=cl[ix+iy*3];
+	if (iy>1) sumT+=cl[ix+iy*3];
+      }
+    } 
     
+    totquad=sum;
+    if ( sumT==0 && sumR==0) {
+        corner = BOTTOM_LEFT;
+	xoff=0;
+	yoff=0;
+    } else if ( sumB==0 && sumR==0 ) {
+        corner = TOP_LEFT;
+      xoff=0;
+      yoff=1;
+    } else if ( sumT==0 && sumL==0) {
+      corner = BOTTOM_RIGHT;
+      xoff=1;
+      yoff=0;
+    } else if ( sumB==0 && sumL==0) {
+      xoff=1;
+      yoff=1;
+      corner = TOP_RIGHT;
+    } else
+      printf("** bad 2x2 cluster!\n");
+
+#endif
+
 
     for (int ix=0; ix<2; ix++) {
       for (int iy=0; iy<2; iy++) {
@@ -495,7 +573,7 @@ class slsInterpolation
 
  protected:
   int nPixelsX, nPixelsY;
-  int nSubPixels;
+  int nSubPixelsX, nSubPixelsY;
   int id;
   int *hint;
 };

slsDetectorCalibration/moenchExecutables/CMakeLists.txt

@@ -0,0 +1,39 @@
+
+
+#Moench ZMQ
+add_executable(moenchZmqProcess moenchZmqProcess.cpp ../tiffIO.cpp)
+add_compile_definitions(moenchZmqProcess NEWZMQ INTERP)
+
+#Moench04 ZMQ
+add_executable(moench04ZmqProcess moenchZmqProcess.cpp ../tiffIO.cpp)
+add_compile_definitions(moenchZmqProcess NEWZMQ INTERP MOENCH04)
+
+
+#Both executables should have the same includes and output dirs
+set(MOENCH_EXECUTABLES "moenchZmqProcess" "moench04ZmqProcess")
+
+foreach(exe ${MOENCH_EXECUTABLES})
+    #TODO! At a later stage clean up include dirs and have a proper lib
+    target_include_directories(${exe} PRIVATE 
+        ../ 
+        ../dataStructures 
+        ../interpolations
+        ../../slsReceiverSoftware/include/
+    )
+
+    target_link_libraries(${exe} 
+        PUBLIC
+        slsSupportLib 
+        ${ZeroMQ_LIBRARIES} 
+        pthread 
+        tiff
+
+        PRIVATE
+        slsProjectWarnings
+    )
+
+
+    set_target_properties(${exe}  PROPERTIES 
+        RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin
+    )
+endforeach(exe ${MOENCH_EXECUTABLES})

slsDetectorCalibration/moenchExecutables/Makefile.zmq

@@ -1,14 +1,21 @@
 
-INCDIR=   -I. -I../dataStructures ../tiffIO.cpp -I../ -I../interpolations/ -I../../slsSupportLib/include/ -I../../slsReceiverSoftware/include/
-LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++  -lzmq -pthread -lrt -ltiff   -O3 -g -std=c++11 -Wall
+INCDIR=   -I. -I../dataStructures ../tiffIO.cpp -I../ -I../interpolations/ -I../../slsSupportLib/include/ -I../../slsReceiverSoftware/include/ -I../../libs/rapidjson/
+LDFLAG= -L/usr/lib64/ -lpthread -lm  -lstdc++  -lzmq -pthread -lrt -ltiff   -O3  -std=c++11 -Wall -L../../build/bin/ -lSlsSupport
 #-L../../bin -lhdf5  -L.
 
 #DESTDIR?=../bin
 
-all:  moenchZmqProcess
+all:  moenchZmqProcess moenchZmq04Process
+ #moenchZmqProcessCtbGui
 
 moenchZmqProcess:  moenchZmqProcess.cpp   clean
-		      g++ -o moenchZmqProcess  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP
+		      g++ -o moenchZmqProcess  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP 
+
+moenchZmq04Process:  moenchZmqProcess.cpp   clean
+		      g++ -o moench04ZmqProcess  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP -DMOENCH04 
+
+#moenchZmqProcessCtbGui:  moenchZmqProcess.cpp   clean
+#		      g++ -o moenchZmqProcessCtbGui  moenchZmqProcess.cpp  $(LDFLAG) $(INCDIR) $(LIBHDF5) $(LIBRARYCBF)  -DNEWZMQ -DINTERP -DCTBGUI
 
 clean: 	
 	rm -f  moenchZmqProcess  

slsDetectorCalibration/moenchExecutables/moench03Interpolation.cpp

@@ -16,7 +16,8 @@
 
 //#include "etaInterpolationPosXY.h"
 #include "noInterpolation.h"
-#include "etaInterpolationCleverAdaptiveBins.h"
+#include "etaInterpolationPosXY.h"
+//#include "etaInterpolationCleverAdaptiveBins.h"
 //#include "etaInterpolationRandomBins.h"
 using namespace std;
 #define NC 400

slsDetectorCalibration/moenchExecutables/moenchPhotonCounter.cpp

@@ -149,6 +149,7 @@ int main(int argc, char *argv[]) {
   if (argc>=9) {
     nframes=atoi(argv[8]);
   }
+
   int xmin=0, xmax=nx, ymin=0, ymax=ny;
   if (argc>=13) {
     xmin=atoi(argv[9]);
@@ -185,6 +186,7 @@ int main(int argc, char *argv[]) {
     cout << "pedestal file is " << pedfile << endl;
  if (thr>0) 
     cout << "threshold is " << thr << endl;
+ cout << "Nframes is " << nframes << endl;
  
  uint32 nnx, nny;
  double *gmap;

slsDetectorCalibration/moenchExecutables/moenchZmqProcess.cpp

@@ -1,13 +1,24 @@
-#define WRITE_QUAD
+//#define WRITE_QUAD
 #define DEVELOPER
-
+#undef CORR
 #define C_GHOST 0.0004
 
 #define CM_ROWS 20
 
 #include "sls_detector_defs.h"
 #include "ZmqSocket.h"
+#ifndef RECT
+#ifndef MOENCH04
 #include "moench03T1ZmqDataNew.h"
+#endif
+#ifdef MOENCH04
+#include "moench04CtbZmq10GbData.h"
+#endif
+
+#endif
+#ifdef RECT
+#include "moench03T1ZmqDataNewRect.h"
+#endif
 #include "moench03GhostSummation.h"
 #include "moench03CommonMode.h"
 #include <vector> 
@@ -31,12 +42,12 @@
 #include "ansi.h"
 #include <iostream>
 
-//#include <chrono>
+#include <chrono>
 #include <ctime> // time_t
 #include <cstdio>
 
 using namespace std;
-//using namespace std::chrono;
+using namespace std::chrono;
 
 //#define SLS_DETECTOR_JSON_HEADER_VERSION 0x2
 
@@ -49,10 +60,11 @@ int main(int argc, char *argv[]) {
  */
   FILE *of=NULL;
   int fifosize=5000;
-  int etabins=1000;//nsubpix*2*100;
+  int etabins=1000, etabinsy=1000;//nsubpix*2*100;
   double etamin=-1, etamax=2;
-  int nSubPixels=2;
+  int nSubPixelsX=2;
   //	int emin, emax;
+  int nSubPixelsY=2;
 	// help
   if (argc < 3 ) {
     cprintf(RED, "Help: ./trial [receive socket ip] [receive starting port number] [send_socket ip] [send starting port number] [nthreads] [nsubpix] [gainmap]  [etafile]\n");
@@ -67,13 +79,20 @@ int main(int argc, char *argv[]) {
   char* socketip2 = 0;
   uint32_t portnum2 = 0;
 
+  zmqHeader zHeader, outHeader;
+  zHeader.jsonversion = SLS_DETECTOR_JSON_HEADER_VERSION;
+  outHeader.jsonversion = SLS_DETECTOR_JSON_HEADER_VERSION;
+
   uint32_t nSigma=5;
 
   int ok;
 
-  // high_resolution_clock::time_point t1;
-  // high_resolution_clock::time_point t2 ;
-  time_t begin,end,finished;
+  high_resolution_clock::time_point t1;
+  high_resolution_clock::time_point t2 ;
+    std::chrono::steady_clock::time_point begin,end,finished;
+      //time_t begin,end,finished;
+  int rms=0;
+  
 
 
   if (argc > 4) {
@@ -93,10 +112,14 @@ int main(int argc, char *argv[]) {
     nthreads=atoi(argv[5]);
 
   cout << "Number of threads is: " << nthreads << endl;
-  if (argc>6)
-    nSubPixels=atoi(argv[6]);
-  cout << "Number of subpixels is: " << nSubPixels << endl;
-  
+  if (argc>6) {
+    nSubPixelsX=atoi(argv[6]);
+    nSubPixelsY=nSubPixelsX;
+#ifdef RECT
+    nSubPixelsX=2;
+#endif
+  }
+  cout << "Number of subpixels is: " << nSubPixelsX << " " <<  nSubPixelsY << endl;
 
   char *gainfname=NULL;
   if (argc>7) {
@@ -111,12 +134,17 @@ int main(int argc, char *argv[]) {
   }
 
   //slsDetectorData *det=new moench03T1ZmqDataNew(); 
+#ifndef MOENCH04
   moench03T1ZmqDataNew *det=new moench03T1ZmqDataNew(); 
+#endif
+#ifdef MOENCH04
+  moench04CtbZmq10GbData *det=new moench04CtbZmq10GbData(); 
+#endif
   cout << endl << " det" <<endl;
   int npx, npy;
   det->getDetectorSize(npx, npy);
 
-
+  int send_something=0;
 
 
   int maxSize = npx*npy*2;//32*2*8192;//5000;//atoi(argv[3]);
@@ -127,10 +155,16 @@ int main(int argc, char *argv[]) {
   char dummybuff[size];
   
 
-  int ncol_cm=CM_ROWS;
-  double xt_ghost=C_GHOST;
-  moench03CommonMode *cm=new moench03CommonMode(ncol_cm);
-  moench03GhostSummation *gs=new moench03GhostSummation(det, xt_ghost);
+  moench03CommonMode *cm=NULL;
+  moench03GhostSummation *gs=NULL;
+#ifdef CORR
+  
+  //int ncol_cm=CM_ROWS;
+  //double xt_ghost=C_GHOST;
+
+  cm=new moench03CommonMode(CM_ROWS);
+  gs=new moench03GhostSummation(det, C_GHOST);
+#endif
   double *gainmap=NULL;
   float *gm;
   double *gmap=NULL;
@@ -158,14 +192,14 @@ int main(int argc, char *argv[]) {
 
   //analogDetector<uint16_t> *filter=new analogDetector<uint16_t>(det,1,NULL,1000);
 #ifndef INTERP
-  singlePhotonDetector *filter=new singlePhotonDetector(det,3, nSigma, 1, cm, 1000, 10, -1, -1, gainmap, gs);
+  singlePhotonDetector *filter=new singlePhotonDetector(det,3, nSigma, 1, cm, 1000, 100, -1, -1, gainmap, gs);
 
     multiThreadedCountingDetector *mt=new multiThreadedCountingDetector(filter,nthreads,fifosize);
 
     // multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
 #endif
 #ifdef INTERP
-  eta2InterpolationPosXY *interp=new eta2InterpolationPosXY(npx, npy, nSubPixels, etabins, etamin, etamax);
+    eta2InterpolationPosXY *interp=new eta2InterpolationPosXY(npx, npy, nSubPixelsX,nSubPixelsY, etabins,  etabinsy, etamin, etamax);
 
   if (etafname) interp->readFlatField(etafname);
 
@@ -211,7 +245,7 @@ int main(int argc, char *argv[]) {
 	  delete zmqsocket;
 	  return EXIT_FAILURE;
 	} else 
-	  printf("Zmq Client at %s\n", zmqsocket->GetZmqServerAddress());
+	  printf("Zmq Client at %s\n", zmqsocket->GetZmqServerAddress().c_str());
 	
 	// send socket
 	ZmqSocket* zmqsocket2 = 0;
@@ -260,7 +294,17 @@ int main(int argc, char *argv[]) {
 	// header variables
 	uint64_t acqIndex = -1;
 	uint64_t frameIndex = -1;
-	//uint32_t subFrameIndex = -1;
+#ifdef MOENCH_BRANCH
+ 	uint32_t subFrameIndex = -1;
+	int* flippedData = 0;
+#endif
+	
+	uint64_t subframes=0;
+	//uint64_t  isubframe=0;
+	uint64_t  insubframe=0;
+	double subnorm=1;
+	uint64_t  f0=-1, nsubframes=0, nnsubframe=0;
+
 	uint64_t fileindex = -1;
 	string filename = "";
 	//	char* image = new char[size];
@@ -270,10 +314,10 @@ int main(int argc, char *argv[]) {
 	int iframe=0;
 	char ofname[10000];
 		    
-	char fname[10000];
+	string fname;
 	//	int length;
-	int *detimage;
-	int nnx, nny,nns;
+	int *detimage=NULL;
+	int nnx, nny,nnsx, nnsy;
 	//uint32_t imageSize = 0, nPixelsX = 0, nPixelsY = 0, 
 	//uint32_t  dynamicRange = 0;
 	// infinite loop
@@ -281,19 +325,20 @@ int main(int argc, char *argv[]) {
 	uint64_t bunchId = 0;
 	uint64_t timestamp = 0;
 	int16_t modId = 0;
+	uint32_t expLength=0;
 	uint16_t xCoord = 0;
 	uint16_t yCoord = 0;
-	uint16_t zCoord = 0;
+	//uint16_t zCoord = 0;
 	uint32_t debug = 0;
 	//uint32_t dr = 16;
 	//int16_t *dout;//=new int16_t [nnx*nny];
 	uint32_t dr = 32;
 	int32_t *dout=NULL;//=new int32_t [nnx*nny];
+	float *doutf=NULL;//=new int32_t [nnx*nny];
 	uint16_t roundRNumber = 0;
 	uint8_t detType = 0;
 	uint8_t version = 0;
-	//	int* flippedData = 0;
-	char* additionalJsonHeader = 0;
+	string additionalJsonHeader="" ;
 
 	int32_t threshold=0;
 	
@@ -311,9 +356,10 @@ int main(int argc, char *argv[]) {
 	frameMode fMode=eFrame;
 	double *ped;
 
-	filter->getImageSize(nnx, nny,nns);
+	filter->getImageSize(nnx, nny,nnsx, nnsy);
 
 	
+	std::map<std::string, std::string> addJsonHeader;
 
 
 
@@ -323,21 +369,21 @@ int main(int argc, char *argv[]) {
 
 	  //  cout << "+++++++++++++++++++++++++++++++LOOP" << endl;
 		// get header, (if dummy, fail is on parse error or end of acquisition)
-#ifndef NEWZMQ	
-	  if (!zmqsocket->ReceiveHeader(0, acqIndex, frameIndex, subframeIndex, filename, fileindex)){
-#endif
 
-#ifdef NEWZMQ	
-	    rapidjson::Document doc;
-	    if (!zmqsocket->ReceiveHeader(0, doc, SLS_DETECTOR_JSON_HEADER_VERSION)) {
+
+
+	  //  rapidjson::Document doc;
+	    if (!zmqsocket->ReceiveHeader(0, zHeader, SLS_DETECTOR_JSON_HEADER_VERSION)) {
 	      /* zmqsocket->CloseHeaderMessage();*/
 
-#endif
 	    //	  if (!zmqsocket->ReceiveHeader(0, acqIndex, frameIndex, subframeIndex, filename, fileindex)) {
-	      //  cprintf(RED, "Got Dummy\n");
+	       cprintf(RED, "Got Dummy\n");
 	      //   t1=high_resolution_clock::now();
-	      time(&end);
+	       //time(&end);
+	       //cout << "Measurement lasted " << difftime(end,begin) << endl;
 
+	       end = std::chrono::steady_clock::now();
+	       cout << "Measurement lasted " << (end-begin).count()*0.000001 << " ms" << endl;
 
 	    while (mt->isBusy()) {;}//wait until all data are processed from the queues
 	    
@@ -348,39 +394,83 @@ int main(int argc, char *argv[]) {
 	    if (newFrame>0) {
 	      cprintf(RED,"DIDn't receive any data!\n");
 	    if (send) { 
-	      zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
+	      
+	      //zHeader.data = false;
+	      outHeader.data=false;
+	      //  zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
+	      zmqsocket2->SendHeader(0,outHeader);
 	      cprintf(RED, "Sent Dummy\n");
 	    }
 	    } else {
-	    if (fMode==ePedestal) {
-	      sprintf(ofname,"%s_%ld_ped.tiff",fname,fileindex);
-	      mt->writePedestal(ofname);
-	       cout << "Writing pedestal to " << ofname << endl;
-	    }
+	      send_something=0;
+	      if (fMode==ePedestal) {
+		sprintf(ofname,"%s_%ld_ped.tiff",fname.c_str(),fileindex);
+		mt->writePedestal(ofname);
+		cout << "Writing pedestal to " << ofname << endl;
+		if (rms){
+		  sprintf(ofname,"%s_%ld_var.tiff",fname.c_str(),fileindex);
+		  mt->writePedestalRMS(ofname);
+		  
+		} 
+		send_something=1;
+	      }
 #ifdef INTERP
-	    else if  (fMode==eFlat) {
-	      mt->prepareInterpolation(ok);
-	      sprintf(ofname,"%s_%ld_eta.tiff",fname,fileindex);
-	      mt->writeFlatField(ofname);
-	       cout << "Writing eta to " << ofname << endl;
-	    }
+	      else if  (fMode==eFlat) {
+		mt->prepareInterpolation(ok);
+		sprintf(ofname,"%s_%ld_eta.tiff",fname.c_str(),fileindex);
+		mt->writeFlatField(ofname);
+		cout << "Writing eta to " << ofname << endl;
+		send_something=1;
+	      }
 #endif
-	    else {
-	      sprintf(ofname,"%s_%ld.tiff",fname,fileindex);
-	      mt->writeImage(ofname);
-	       cout << "Writing image to " << ofname << endl;
-	    }
-	    //  cout << nns*nnx*nny*nns*dr/8 << " " << length << endl;
+	      else {
+		if (subframes>0 ) { 
+		  if (insubframe>0) {
+		    sprintf(ofname,"%s_sf%ld_%ld.tiff",fname.c_str(),nnsubframe,fileindex);
+		    //		  mt->writeImage(ofname);
+		    doutf= new float[nnx*nny];
+		    if (subframes>0 && insubframe!=subframes && insubframe>0)
+		      subnorm=((double)subframes)/((double)insubframe);
+		    else
+		      subnorm=1.;
+		    for (int ix=0; ix<nnx*nny; ix++) {
+		    doutf[ix]=detimage[ix]*subnorm;
+		    if (doutf[ix]<0) doutf[ix]=0;
+		    }
+	    
+		    cout << "Writing image to " << ofname << endl;
+		    
+		    WriteToTiff(doutf,ofname ,nnx, nny); 
+		    
+		    if (doutf)
+		      delete [] doutf;
+		    doutf=NULL;
+		    
+		    nsubframes++;
+		    insubframe=0;
+		    send_something=1;
+		  }
+		} else {
+		  sprintf(ofname,"%s_%ld.tiff",fname.c_str(),fileindex);
+		  mt->writeImage(ofname);
+		  send_something=1;
+		}
+		
+		cout << "Writing image to " << ofname << endl;
+	      }
+	      //  cout << nns*nnx*nny*nns*dr/8 << " " << length << endl;
 
 	    if (send) {
-
+	      
 	    if (fMode==ePedestal) {   
 	      cprintf(MAGENTA,"Get pedestal!\n");
-	      nns=1;
+	      nnsx=1;
+	      nnsy=1;
+	      
 	      nnx=npx;
 	      nny=npy;
 	      //dout= new int16_t[nnx*nny*nns*nns];
-	      dout= new int32_t[nnx*nny*nns*nns];
+	      dout= new int32_t[nnx*nny*nnsx*nnsy];
 	      // cout << "get pedestal " << endl;
 	      ped=mt->getPedestal();
 	      // cout << "got pedestal " << endl;
@@ -406,15 +496,19 @@ int main(int argc, char *argv[]) {
 	     }
 #endif
 	    else {
-	      detimage=mt->getImage(nnx,nny,nns);
+	      detimage=mt->getImage(nnx,nny,nnsx, nnsy);
 	      cprintf(MAGENTA,"Get image!\n");
-	      cout << nnx << " " << nny << " " << nns << endl;
+	      cout << nnx << " " << nny << " " << nnsx << " " << nnsy << endl;
 	      // nns=1;
 	      // nnx=npx;
 	      // nny=npy;
 	      // nnx=nnx*nns;
 	      //nny=nny*nns;
 	      dout= new int32_t[nnx*nny];
+	      if (subframes>0 && insubframe!=subframes && insubframe>0)
+		subnorm=((double)subframes)/((double)insubframe);
+	      else
+		subnorm=1.;
 	      for (int ix=0; ix<nnx*nny; ix++) {
 		// for (int iy=0; iy<nny*nns; iy++) {
 		 //  for (int isx=0; isx<nns; isx++) {
@@ -426,125 +520,157 @@ int main(int argc, char *argv[]) {
 		    
 		//   }
 		// }
-		  dout[ix]=detimage[ix];
+		  dout[ix]=detimage[ix]*subnorm;
 		  if (dout[ix]<0) dout[ix]=0;
 		  //   cout << ix << " " << dout[ix] << endl;
 		  // }
 	      }
 	    }
+	    //if ((insubframe>0 && subframes>0) || (subframes<=0) ){
 
-
-	    //// int SendHeaderData ( int index, bool dummy, uint32_t jsonversion, uint32_t dynamicrange = 0, uint64_t fileIndex = 0,
-	      // 		uint32_t ndetx = 0, uint32_t ndety = 0, uint32_t npixelsx = 0, uint32_t npixelsy = 0, uint32_t imageSize = 0,
-	      // 		uint64_t acqIndex = 0, uint64_t fIndex = 0, const char* fname = NULL,
-	      // 		uint64_t frameNumber = 0, uint32_t expLength = 0, uint32_t packetNumber = 0,
-	      // 		uint64_t bunchId = 0, uint64_t timestamp = 0,
-	      // 		uint16_t modId = 0, uint16_t row = 0, uint16_t column = 0, uint16_t reserved = 0,
-	      // 		uint32_t debug = 0, uint16_t roundRNumber = 0,
-	      // 		uint8_t detType = 0, uint8_t version = 0, int gapPixelsEnable = 0, int flippedDataX = 0,
-	      // 		char* additionalJsonHeader = 0) {
-
-
-
-	    //  cout << "Sending image size " << nnx << " " << nny << endl;
-
-#ifndef DEVELOPER
-#ifndef MOENCH_BRANCH
-	    zmqsocket2->SendHeaderData (0, false, SLS_DETECTOR_JSON_HEADER_VERSION, dr, fileindex, 0,0, nnx, nny, nnx*nny*dr/8,acqIndex, frameIndex, fname, acqIndex,0 , packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, 0,0, additionalJsonHeader);
-#endif
-#endif
-
-#ifdef DEVELOPER
-	    zmqsocket2->SendHeaderData (0, false,SLS_DETECTOR_JSON_HEADER_VERSION , dr, fileindex, 0,0,nnx,nny,nnx*nny*dr/8,acqIndex, frameIndex, fname,acqIndex,0 , packetNumber,bunchId, timestamp, modId,xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, 0,0, 0,additionalJsonHeader);
-#endif	
-#ifdef MOENCH_BRANCH
-	    /*
- int SendHeaderData ( int index, bool dummy, uint32_t jsonversion, uint32_t dynamicrange = 0, uint64_t fileIndex = 0,
-                        uint32_t npixelsx = 0, uint32_t npixelsy = 0, uint32_t imageSize = 0,
-                        uint64_t acqIndex = 0, uint64_t fIndex = 0, char* fname = NULL,
-                        uint64_t frameNumber = 0, uint32_t expLength = 0, uint32_t packetNumber = 0,
-                        uint64_t bunchId = 0, uint64_t timestamp = 0,
-                        uint16_t modId = 0, uint16_t row = 0, uint16_t column = 0, uint16_t reserved = 0,
-                        uint32_t debug = 0, uint16_t roundRNumber = 0,
-                        uint8_t detType = 0, uint8_t version = 0, int* flippedData = 0,
-                        char* additionalJsonHeader = 0) {
-int ZmqSocket::SendHeaderData(int 0, bool false, uint32_t SLS_DETECTOR_JSON_HEADER_VERSION , uint32_t dr, uint64_t fileindex, uint32_t 0, uint32_t 0, uint32_t, uint64_t, uint64_t, char*, uint64_t, uint32_t, uint32_t, uint64_t, uint64_t, uint16_t, uint16_t, uint16_t, uint16_t, uint32_t, uint16_t, uint8_t, uint8_t, int*, char*)
-
-	     */
-	    //zmqsocket2->SendHeaderData (0, false,SLS_DETECTOR_JSON_HEADER_VERSION , dr, fileindex, 0,0,nnx,nny,nnx*nny*dr/8,acqIndex, frameIndex, fname,acqIndex,0 , packetNumber,bunchId, timestamp, modId,xCoord, yCoord, zCoord,debug, roundRNumber, detType, version);//, 0,additionalJsonHeader);
-	    zmqsocket2->SendHeaderData (0, false, SLS_DETECTOR_JSON_HEADER_VERSION, dr, fileindex, nnx, nny, nnx*nny*dr/8,acqIndex, frameIndex, fname, acqIndex, subFrameIndex, packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, flippedData, additionalJsonHeader);
-
-	    /* old 
-	       zmqsocket2->SendHeaderData (0, false, SLS_DETECTOR_JSON_HEADER_VERSION, dr, fileindex, nnx, nny, nnx*nny*dr/8,acqIndex, frameIndex, fname, acqIndex, subFrameIndex, packetNumber,bunchId, timestamp, modId, xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, flippedData, additionalJsonHeader);
-	    */
-	    /*
-
-
-	      new
-	      zmqsocket2->SendHeaderData (0, false,SLS_DETECTOR_JSON_HEADER_VERSION , dr, fileindex, 0,0,nnx,nny,nnx*nny*dr/8,acqIndex, frameIndex, fname,acqIndex,0 , packetNumber,bunchId, timestamp, modId,xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, 0,additionalJsonHeader);
-	     */
-#endif		
-	       
-			
-
-		zmqsocket2->SendData((char*)dout,nnx*nny*dr/8);
-		cprintf(GREEN, "Sent Data\n");
-		
-		zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
-		cprintf(RED, "Sent Dummy\n");
-		if (dout)
-		  delete [] dout;
-		dout=NULL;
-
+	    if(send_something) {
+	   
+	      //  zmqsocket2->SendHeaderData (0, false,SLS_DETECTOR_JSON_HEADER_VERSION , dr, fileindex, 1,1,nnx,nny,nnx*nny*dr/8,acqIndex, frameIndex, fname,acqIndex,0 , packetNumber,bunchId, timestamp, modId,xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, 0,0, 0,&additionalJsonHeader);   
+	      
+	      outHeader.data=true;
+	      outHeader.dynamicRange=dr;
+	      outHeader.fileIndex=fileindex;
+	      outHeader.ndetx=1;
+	      outHeader.ndety=1;
+	      outHeader.npixelsx=nnx;
+	      outHeader.npixelsy=nny;
+	      outHeader.imageSize=nnx*nny*dr/8;
+	      outHeader.acqIndex=acqIndex;
+	      outHeader.frameIndex=frameIndex;
+	      outHeader.fname=fname;
+	      outHeader.frameNumber=acqIndex;
+	      outHeader.expLength=expLength;
+	      outHeader.packetNumber=packetNumber;
+	      outHeader.bunchId=bunchId;
+	      outHeader.timestamp=timestamp;
+	      outHeader.modId=modId;
+	      outHeader.row=xCoord;
+	      outHeader.column=yCoord;
+	      outHeader.debug=debug;
+	      outHeader.roundRNumber=roundRNumber;
+	      outHeader.detType=detType;
+	      outHeader.version=version;
+	      
+	      zmqsocket2->SendHeader(0,outHeader);
+	      zmqsocket2->SendData((char*)dout,nnx*nny*dr/8);
+	      cprintf(GREEN, "Sent Data\n");
+	    }
+	    outHeader.data=false;
+	    zmqsocket2->SendHeader(0,outHeader);
+	    // zmqsocket2->SendHeaderData(0, true, SLS_DETECTOR_JSON_HEADER_VERSION);
+	    cprintf(RED, "Sent Dummy\n");
+	    if (dout)
+	      delete [] dout;
+	    dout=NULL;
+	    
 	    }
 	    }
 
 	    mt->clearImage();
 	    
 	    newFrame=1;
-	    //t2 = high_resolution_clock::now();
 	    
-	      time(&finished);
-	      //   auto meas_duration = duration_cast<microseconds>( t2 - t0 ).count();
-	      //   auto real_duration = duration_cast<microseconds>( t2 - t1 ).count();
 	    
-	    cout << "Measurement lasted " << difftime(end,begin) << endl;
-	    cout << "Processing lasted " << difftime(finished,begin) << endl;
+	    //time(&finished);
+	    //cout << "Processing lasted " << difftime(finished,begin) << endl;
+	    
+	       finished = std::chrono::steady_clock::now();
+	       cout << "Processing lasted " << (finished-begin).count()*0.000001 << " ms" << endl;
+#ifdef OPTIMIZE
+	    return 0;
+#endif
 	    continue; //continue to not get out
 
 
 	    }
 
-#ifdef NEWZMQ
+	    //#ifdef NEWZMQ
 	    if (newFrame) {
-	      time(&begin);
-	      // t0 = high_resolution_clock::now();
-	      //cout <<"new frame" << endl;
+	      begin = std::chrono::steady_clock::now();
+   
+	      size       = zHeader.imageSize;//doc["size"].GetUint();
+	      
+	      // dynamicRange  = zheader.dynamicRange; //doc["bitmode"].GetUint();
+	      // nPixelsX = zHeader.npixelsx; //doc["shape"][0].GetUint();
+	      // nPixelsY = zHeader.npixelsy;// doc["shape"][1].GetUint();
+	      filename        = zHeader.fname;//doc["fname"].GetString();
+	      acqIndex = zHeader.acqIndex; //doc["acqIndex"].GetUint64();
+		// frameIndex       = zHeader.frameIndex;//doc["fIndex"].GetUint64();
+	      fileindex        = zHeader.fileIndex;//doc["fileIndex"].GetUint64();
+	      expLength   = zHeader.expLength;//doc["expLength"].GetUint();
+	      packetNumber=zHeader.packetNumber;//doc["packetNumber"].GetUint();
+	      bunchId=zHeader.bunchId;//doc["bunchId"].GetUint();
+	      timestamp=zHeader.timestamp;//doc["timestamp"].GetUint();
+	      modId=zHeader.modId;//doc["modId"].GetUint();
+	      debug=zHeader.debug;//doc["debug"].GetUint();
+	      //  roundRNumber=r.roundRNumber;//doc["roundRNumber"].GetUint();
+	      detType=zHeader.detType;//doc["detType"].GetUint();
+	      version=zHeader.version;//doc["version"].GetUint();
+	      /*document["bitmode"].GetUint(); zHeader.dynamicRange
 
-	      //  acqIndex, frameIndex, subframeIndex, filename, fileindex
-	      size       = doc["size"].GetUint();
-	      // multisize  = size;// * zmqsocket->size();
-	      // dynamicRange  = doc["bitmode"].GetUint();
-	      //  nPixelsX = doc["shape"][0].GetUint();
-	      // nPixelsY = doc["shape"][1].GetUint();
-	      filename        = doc["fname"].GetString();
-	      //acqIndex = doc["acqIndex"].GetUint64();
-	      //frameIndex       = doc["fIndex"].GetUint64();
-	      fileindex        = doc["fileIndex"].GetUint64();
-	      //subFrameIndex    = doc["expLength"].GetUint();
-	      //packetNumber=doc["packetNumber"].GetUint();
-	      //bunchId=doc["bunchId"].GetUint();
-	      //timestamp=doc["timestamp"].GetUint();
-	      //modId=doc["modId"].GetUint();
-	      //debug=doc["debug"].GetUint();
-	      //roundRNumber=doc["roundRNumber"].GetUint();
-	      //detType=doc["detType"].GetUint();
-	      //version=doc["version"].GetUint();
+document["fileIndex"].GetUint64(); zHeader.fileIndex
 
+document["detshape"][0].GetUint();
+zHeader.ndetx
+
+document["detshape"][1].GetUint();
+zHeader.ndety
+
+document["shape"][0].GetUint();
+zHeader.npixelsx
+
+document["shape"][1].GetUint();
+zHeader.npixelsy
+
+document["size"].GetUint(); zHeader.imageSize
+
+document["acqIndex"].GetUint64(); zHeader.acqIndex
+
+document["frameIndex"].GetUint64(); zHeader.frameIndex
+
+document["fname"].GetString(); zHeader.fname
+
+document["frameNumber"].GetUint64(); zHeader.frameNumber
+
+document["expLength"].GetUint(); zHeader.expLength
+
+document["packetNumber"].GetUint(); zHeader.packetNumber
+
+document["bunchId"].GetUint64(); zHeader.bunchId
+
+document["timestamp"].GetUint64(); zHeader.timestamp
+
+document["modId"].GetUint(); zHeader.modId
+
+document["row"].GetUint(); zHeader.row
+
+document["column"].GetUint(); zHeader.column
+
+document["reserved"].GetUint(); zHeader.reserved
+
+document["debug"].GetUint(); zHeader.debug
+
+document["roundRNumber"].GetUint(); zHeader.roundRNumber
+
+document["detType"].GetUint(); zHeader.detType
+
+document["version"].GetUint(); zHeader.version
+
+document["flippedDataX"].GetUint(); zHeader.flippedDataX
+
+document["quad"].GetUint(); zHeader.quad
+
+document["completeImage"].GetUint(); zHeader.completeImage
+	      */
 	      //dataSize=size;
 
-	      strcpy(fname,filename.c_str());
-
+	      //strcpy(fname,filename.c_str());
+	      fname=filename;
 	      // cprintf(BLUE, "Header Info:\n"
 	      // 	      "size: %u\n"
 	      // 	      "multisize: %u\n"
@@ -574,15 +700,19 @@ int ZmqSocket::SendHeaderData(int 0, bool false, uint32_t SLS_DETECTOR_JSON_HEAD
 	      // 	      xCoord, yCoord,zCoord,
 	      // 	      flippedDataX, packetNumber, bunchId, timestamp, modId, debug, roundRNumber, detType, version);
 	      
+	      addJsonHeader=zHeader.addJsonHeader;
+
 	      /* Analog detector commands */
 	      //isPedestal=0;
 	      //isFlat=0;
+	      rms=0;
 	      fMode=eFrame;
 	      frameMode_s="frame";
 	      cprintf(MAGENTA, "Frame mode: ");
-	      if (doc.HasMember("frameMode")) {
-		if (doc["frameMode"].IsString()) {
-		  frameMode_s=doc["frameMode"].GetString();
+	      //	      if (doc.HasMember("frameMode")) {
+	      if (addJsonHeader.find("frameMode")!= addJsonHeader.end()) { 
+		//	if (doc["frameMode"].IsString()) {
+		frameMode_s=addJsonHeader.at("frameMode");//doc["frameMode"].GetString();
 		  if (frameMode_s == "pedestal"){
 		    fMode=ePedestal;
 		    //isPedestal=1;
@@ -591,6 +721,12 @@ int ZmqSocket::SendHeaderData(int 0, bool false, uint32_t SLS_DETECTOR_JSON_HEAD
 		    // cprintf(MAGENTA, "Resetting pedestal\n");
 		    fMode=ePedestal;
 		    //isPedestal=1;
+		  } else if (frameMode_s == "variance"){
+		    mt->newDataSet(); //resets pedestal  
+		    // cprintf(MAGENTA, "Resetting pedestal\n");
+		    fMode=ePedestal;
+		    //isPedestal=1;
+		    rms=1;
 		  }
 #ifdef INTERP 
 		  else if (frameMode_s == "flatfield") {
@@ -602,7 +738,7 @@ int ZmqSocket::SendHeaderData(int 0, bool false, uint32_t SLS_DETECTOR_JSON_HEAD
 		     cprintf(MAGENTA, "Resetting flatfield\n");
 		     fMode=eFlat;
 		   }
-#endif
+		  //#endif
 		  else {
 		    fMode=eFrame;
 		    //isPedestal=0;
@@ -610,19 +746,23 @@ int ZmqSocket::SendHeaderData(int 0, bool false, uint32_t SLS_DETECTOR_JSON_HEAD
 		    fMode=eFrame;
 		    frameMode_s="frame";
 		  }
-		}
+		  //}
 	      }
 	      cprintf(MAGENTA, "%s\n" , frameMode_s.c_str());
 	      mt->setFrameMode(fMode);
 
 	      // threshold=0;
-	      cprintf(MAGENTA, "Threshold: ");
-	      if (doc.HasMember("threshold")) {	
-		if (doc["threshold"].IsInt()) {
-		  threshold=doc["threshold"].GetInt();
-		  mt->setThreshold(threshold);
-		}
-	      }	
+	      cprintf(MAGENTA, "Threshold: "); 
+	      if (addJsonHeader.find("threshold")!= addJsonHeader.end()) {
+		istringstream(addJsonHeader.at("threshold")) >>threshold;
+		//		threshold=atoi(addJsonHeader.at("threshold").c_str());//doc["frameMode"].GetString();
+	      }
+	      //if (doc.HasMember("threshold")) {	
+	      //if (doc["threshold"].IsInt()) {
+	      //  threshold=doc["threshold"].GetInt();
+	      mt->setThreshold(threshold);
+	      //	}
+	      // }	
 	      cprintf(MAGENTA, "%d\n", threshold);
 
 	      xmin=0;
@@ -630,40 +770,47 @@ int ZmqSocket::SendHeaderData(int 0, bool false, uint32_t SLS_DETECTOR_JSON_HEAD
 	      ymin=0;
 	      ymax=npy;
 	      cprintf(MAGENTA, "ROI: ");
-	      if (doc.HasMember("roi")) {
-		if (doc["roi"].IsArray()) {
-		  if (doc["roi"].Size() > 0 )
-		    if (doc["roi"][0].IsInt())
-		      xmin=doc["roi"][0].GetInt();
+	      
+	      if (addJsonHeader.find("roi")!= addJsonHeader.end()) {
+		istringstream(addJsonHeader.at("roi")) >> xmin >> xmax >> ymin >> ymax ;
+		//  if (doc.HasMember("roi")) {
+		//if (doc["roi"].IsArray()) {
+		// if (doc["roi"].Size() > 0 )
+		//  if (doc["roi"][0].IsInt())
+		   //    xmin=doc["roi"][0].GetInt();
 		  
-		  if (doc["roi"].Size() > 1 )
-		    if (doc["roi"][1].IsInt())
-		      xmax=doc["roi"][1].GetInt();
+		//   if (doc["roi"].Size() > 1 )
+		//     if (doc["roi"][1].IsInt())
+		//       xmax=doc["roi"][1].GetInt();
 
-		  if (doc["roi"].Size() > 2 )
-		    if (doc["roi"][2].IsInt())
-		      ymin=doc["roi"][2].GetInt();
+		//   if (doc["roi"].Size() > 2 )
+		//     if (doc["roi"][2].IsInt())
+		//       ymin=doc["roi"][2].GetInt();
 		  
-		  if (doc["roi"].Size() > 3 )
-		    if (doc["roi"][3].IsInt())
-		      ymax=doc["roi"][3].GetInt();
-		}
+		//   if (doc["roi"].Size() > 3 )
+		//     if (doc["roi"][3].IsInt())
+		//       ymax=doc["roi"][3].GetInt();
+		// }
 	      }
 
 	      cprintf(MAGENTA, "%d %d %d %d\n", xmin, xmax, ymin, ymax);
 	      mt->setROI(xmin, xmax, ymin, ymax);	
-	
-	      if (doc.HasMember("dynamicRange")) {
-		dr=doc["dynamicRange"].GetUint();
+	      if (addJsonHeader.find("dynamicRange")!= addJsonHeader.end()) {
+		istringstream(addJsonHeader.at("dynamicRange")) >> dr ;
 		dr=32;
 	      }
+	      // if (doc.HasMember("dynamicRange")) {
+	      // 	dr=doc["dynamicRange"].GetUint();
+	      // 	dr=32;
+	      // }
 
 	      dMode=eAnalog;
 	      detectorMode_s="analog";
-	      cprintf(MAGENTA, "Detector mode: ");
-	      if (doc.HasMember("detectorMode")) {
-		if (doc["detectorMode"].IsString()) {
-		    detectorMode_s=doc["detectorMode"].GetString();
+	      cprintf(MAGENTA, "Detector mode: ");	  
+		if (addJsonHeader.find("detectorMode")!= addJsonHeader.end()) {;
+		  //if (doc.HasMember("detectorMode")) {
+		  //if (doc["detectorMode"].IsString()) {
+		  detectorMode_s=addJsonHeader.at("detectorMode");//=doc["detectorMode"].GetString();
 #ifdef INTERP
 		    if (detectorMode_s == "interpolating"){
 		      dMode=eInterpolating;
@@ -681,7 +828,7 @@ int ZmqSocket::SendHeaderData(int 0, bool false, uint32_t SLS_DETECTOR_JSON_HEAD
 		      mt->setInterpolation(NULL);
 #endif
 		    }
-		  }
+		    // }
 		  
 	      }
 
@@ -729,6 +876,21 @@ int ZmqSocket::SendHeaderData(int 0, bool false, uint32_t SLS_DETECTOR_JSON_HEAD
 	      // 	mt->setNSubPixels(nSubPixels);
 	      // }
 	      
+	      // threshold=0;
+	      // cprintf(MAGENTA, "Subframes: ");
+	      // subframes=0;
+	      // //isubframe=0;
+	      // insubframe=0;
+	      // subnorm=1;
+	      // f0=0;
+	      // nnsubframe=0;
+	      // if (doc.HasMember("subframes")) {	
+	      // 	if (doc["subframes"].IsInt()) {
+	      // 	  subframes=doc["subframes"].GetInt();
+	      // 	}
+	      // }	
+	      // cprintf(MAGENTA, "%ld\n", subframes);
+
 	      
 	      newFrame=0;
 	      /* zmqsocket->CloseHeaderMessage();*/
@@ -752,33 +914,98 @@ int ZmqSocket::SendHeaderData(int 0, bool false, uint32_t SLS_DETECTOR_JSON_HEAD
 	      mt->setFilePointer(NULL);
 	    }
 	  }
+
 	  
 
 	  // cout << "data" << endl;
 	  // get data
 	  // acqIndex = doc["acqIndex"].GetUint64();
-	  frameIndex       = doc["fIndex"].GetUint64();
+
+	  frameIndex       = zHeader.frameIndex;////doc["fIndex"].GetUint64();
+
 	  // subFrameIndex    = doc["expLength"].GetUint();
 
 	  //  bunchId=doc["bunchId"].GetUint();
 	  //  timestamp=doc["timestamp"].GetUint();
-	      packetNumber=doc["packetNumber"].GetUint();
-	      // cout << acqIndex << " " << frameIndex << " " << subFrameIndex << " "<< bunchId << " " << timestamp << " " << packetNumber << endl;
-	      if (packetNumber>=40) {
-		//*((int*)buff)=frameIndex;
-		memcpy(buff,&frameIndex,sizeof(int));
-		//length = 
-		zmqsocket->ReceiveData(0, buff+sizeof(int), size);
-		mt->pushData(buff);
-		mt->nextThread();
-		mt->popFree(buff);
-	      } else {
-		cprintf(RED, "Incomplete frame: received only %d packet\n", packetNumber);
-		//length = 
-		  zmqsocket->ReceiveData(0, dummybuff, size);
+	  packetNumber=zHeader.packetNumber; //doc["packetNumber"].GetUint();
+	  // cout << acqIndex << " " << frameIndex << " " << subFrameIndex << " "<< bunchId << " " << timestamp << " " << packetNumber << endl;
+	  //cprintf(GREEN, "frame\n");
+	  if (packetNumber>=40) {
+	    //*((int*)buff)=frameIndex;
+	    if (insubframe==0) f0=frameIndex;
+	    memcpy(buff,&frameIndex,sizeof(int));
+	    //length = 
+	    zmqsocket->ReceiveData(0, buff+sizeof(int), size);
+	    mt->pushData(buff);
+	    mt->nextThread();
+	    mt->popFree(buff);
+	    insubframe++;
+	    nsubframes=frameIndex+1-f0;
+	  } else {
+	    cprintf(RED, "Incomplete frame: received only %d packet\n", packetNumber);
+	    //length = 
+	    zmqsocket->ReceiveData(0, dummybuff, size);
+	  }
+	  
+
+
+
+	  if (subframes>0 && insubframe>=subframes && fMode==eFrame) {
+	    while (mt->isBusy()) {;}//wait until all data are processed from the queues
+	    detimage=mt->getImage(nnx,nny,nnsx, nnsy);
+	    cprintf(MAGENTA,"Get image!\n");
+	    dout= new int32_t[nnx*nny];
+	    doutf= new float[nnx*nny];
+	    if (subframes>0 && insubframe!=subframes && insubframe>0)
+	      subnorm=((double)subframes)/((double)insubframe);
+	    else
+	      subnorm=1.;
+	    for (int ix=0; ix<nnx*nny; ix++) {
+	      dout[ix]=detimage[ix]*subnorm;
+	      if (dout[ix]<0) dout[ix]=0;
+	      doutf[ix]=dout[ix];
+	    }
+	    sprintf(ofname,"%s_sf%ld_%ld.tiff",fname.c_str(),nnsubframe,fileindex);
+	    
+	    cout << "Writing image to " << ofname << endl;
+
+	    WriteToTiff(doutf,ofname ,nnx, nny); 
+	    nsubframes++;
+	    insubframe=0;
+	    nnsubframe++;
+
+
+	    
+	    //   zmqsocket2->SendHeaderData (0, false,SLS_DETECTOR_JSON_HEADER_VERSION , dr, fileindex, 1,1,nnx,nny,nnx*nny*dr/8,acqIndex, frameIndex, fname,acqIndex,0 , packetNumber,bunchId, timestamp, modId,xCoord, yCoord, zCoord,debug, roundRNumber, detType, version, 0,0, 0,&additionalJsonHeader);
+	    zHeader.data = true;
+	    zmqsocket2->SendHeader(0,zHeader);
+	    zmqsocket2->SendData((char*)dout,nnx*nny*dr/8);
+	    cprintf(GREEN, "Sent subdata\n");
+		
+
+	    if (dout)
+	      delete [] dout;
+	    dout=NULL;
+
+	    if (doutf)
+	      delete [] doutf;
+	    doutf=NULL;
+	    
+	    mt->clearImage();
+	    
+	  }
+
+		 
+
+
+
+
+
 
-	      }
 	
+	      
+
+
 	  
 	  
 	  iframe++;

slsDetectorCalibration/multiThreadedAnalogDetector.h

@@ -95,7 +95,7 @@ public:
   virtual int *getImage() {
     return det->getImage();
   }
-  virtual int getImageSize(int &nnx, int &nny, int &ns) {return det->getImageSize(nnx, nny, ns);};
+  virtual int getImageSize(int &nnx, int &nny, int &ns, int &nsy) {return det->getImageSize(nnx, nny, ns, nsy);};
   virtual int getDetectorSize(int &nnx, int &nny) {return det->getDetectorSize(nnx, nny);};
 
   virtual ~threadedAnalogDetector() {StopThread();  delete fifoFree; delete fifoData;}
@@ -123,7 +123,7 @@ public:
      return fifoFree->pop(ptr);
    }
 
-   virtual int isBusy() {return busy;}
+   virtual int isBusy() {if (fifoData->isEmpty() && busy==0) return 0; else return 1;}
    
    //protected:
    /** Implement this method in your subclass with the code you want your thread to run. */
@@ -221,10 +221,10 @@ FILE *getFilePointer(){return det->getFilePointer();};
    }
 
 
-   virtual int setNSubPixels(int ns)  { 
+  virtual int setNSubPixels(int ns, int nsy)  { 
      slsInterpolation *interp=(det)->getInterpolation();
-     if (interp)  return interp->setNSubPixels(ns);
-     else return 1;};
+     if (interp)  interp->setNSubPixels(ns, nsy);
+     return 1;};
 
 
    virtual slsInterpolation *setInterpolation(slsInterpolation *f){
@@ -249,7 +249,7 @@ protected:
    }
 
    void * processData() {
-     busy=1;
+     //  busy=1;
      while (!stop) {
        if (fifoData->isEmpty()) {
 	 busy=0;
@@ -259,6 +259,7 @@ protected:
 	 fifoData->pop(data); //blocking!
 	 det->processData(data);
 	 fifoFree->push(data); 
+	 //busy=0;
        }
      }
      return NULL;
@@ -313,13 +314,13 @@ public:
    
   virtual void newDataSet(){for (int i=0; i<nThreads; i++) dets[i]->newDataSet();};
   
-  virtual int *getImage(int &nnx, int &nny, int &ns) {
+  virtual int *getImage(int &nnx, int &nny, int &ns, int &nsy) {
     int *img;
     // int nnx, nny, ns; 
     // int nnx, nny, ns;
-    int nn=dets[0]->getImageSize(nnx, nny,ns);
+    int nn=dets[0]->getImageSize(nnx, nny,ns, nsy);
     if (image) {
-      delete image;
+      delete [] image;
       image=NULL;
     }
     image=new int[nn];
@@ -362,10 +363,10 @@ public:
 /*        dets[ii]->writeImage(tit); */
 /*      } */
 /* #endif */
-     int nnx, nny, ns;
-     getImage(nnx, nny, ns);
+    int nnx, nny, ns, nsy;
+    getImage(nnx, nny, ns,nsy);
      //int nnx, nny, ns;
-     int nn=dets[0]->getImageSize(nnx, nny, ns);
+    int nn=dets[0]->getImageSize(nnx, nny, ns, nsy);
      float *gm=new float[nn];
      if (gm) {
        for (int ix=0; ix<nn; ix++) {
@@ -461,6 +462,50 @@ public:
     return ped;
   };
    
+  
+  virtual double *getPedestalRMS(){
+    int nx, ny;
+    dets[0]->getDetectorSize(nx,ny);
+    // if (ped) delete [] ped;
+    double *rms=new double[nx*ny];
+    double *p0=new double[nx*ny];
+    
+    for (int i=0; i<nThreads; i++) {
+      //inte=(slsInterpolation*)dets[i]->getInterpolation(nb,emi,ema);
+      //  cout << i << endl;
+      p0=dets[i]->getPedestalRMS(p0);
+      if (p0) {
+	if (i==0) {
+	  
+	  for (int ib=0; ib<nx*ny; ib++) {
+	    rms[ib]=p0[ib]*p0[ib]/((double)nThreads);
+	  //  cout << p0[ib] << " ";
+	}
+	} else {
+	for (int ib=0; ib<nx*ny; ib++) {
+	  rms[ib]+=p0[ib]*p0[ib]/((double)nThreads);
+	  //  cout << p0[ib] << " ";
+	}
+	}
+      }
+	
+    }
+    delete [] p0;
+    
+    /* for (int ib=0; ib<nx*ny; ib++) { */
+    /*   if (rms[ib]>0) */
+    /* 	rms[ib]=sqrt(ped[ib]); */
+    /*   else */
+    /* 	rms[ib]=0; */
+    /* } */
+
+
+    return rms;
+  };
+   
+  
+
+
    
    virtual double *setPedestal(double *h=NULL){
      //int nb=0;
@@ -498,6 +543,27 @@ public:
    };
 
 
+   virtual void *writePedestalRMS(const char * imgname){     
+    
+     int nx, ny;
+     dets[0]->getDetectorSize(nx,ny);
+   
+      double *rms=getPedestalRMS();
+      float *gm=new float[nx*ny];
+      if (gm) {
+       for (int ix=0; ix<nx*ny; ix++) {
+	 gm[ix]=rms[ix];
+       }    
+       WriteToTiff(gm,imgname ,nx, ny); 
+       delete [] gm;
+       delete [] rms;
+     } else cout << "Could not allocate float image " << endl;
+    
+    return NULL;
+
+   };
+
+
   virtual void *readPedestal(const char * imgname, int nb=-1, double emin=1, double emax=0){
     
     int nx, ny;

slsDetectorCalibration/multiThreadedInterpolatingDetector.h

@@ -46,7 +46,7 @@ public:
   };
   
 
-   virtual int setNSubPixels(int ns)  { return (dets[0])->setNSubPixels(ns);};
+   /* virtual int setNSubPixels(int ns)  { return (dets[0])->setNSubPixels(ns);}; */
 
    virtual void resetFlatField() {(dets[0])->resetFlatField();};
    
@@ -69,13 +69,13 @@ public:
 
 
 
-  virtual int *getImage(int &nnx, int &nny, int &ns) {
-    if (getInterpolation()==NULL) return multiThreadedAnalogDetector::getImage(nnx,nny,ns);
+   virtual int *getImage(int &nnx, int &nny, int &nsx, int &nsy) {
+     if (getInterpolation()==NULL) return multiThreadedAnalogDetector::getImage(nnx,nny,nsx, nsy);
     //if one interpolates, the whole image is stored in detector 0;
     int *img;
     // int nnx, nny, ns; 
     // int nnx, nny, ns;
-    int nn=dets[0]->getImageSize(nnx, nny,ns);
+    int nn=dets[0]->getImageSize(nnx, nny,nsx, nsy);
     if (image) {
       delete image;
       image=NULL;

slsDetectorCalibration/pedestalSubtraction.h

@@ -10,7 +10,7 @@ class pedestalSubtraction  {
       \param nn number of samples to calculate the moving average (defaults to 1000)
   */
   pedestalSubtraction (int nn=1000) : stat(nn) {};
-    
+  /* void setPointers(double *me, double *va) {mean=me; var=va; stat.setPointers(mean, var);}; */
     /** virtual destructorr 
      */
     virtual ~pedestalSubtraction() {};

slsDetectorCalibration/singlePhotonDetector.h

@@ -50,7 +50,6 @@ public analogDetector<uint16_t> {
 
 
   */
-  
 
  singlePhotonDetector(slsDetectorData<uint16_t> *d,
 		      int csize=3,
@@ -58,7 +57,7 @@ public analogDetector<uint16_t> {
 		      int sign=1,
 		      commonModeSubtraction *cm=NULL,
 		      int nped=1000,
-		      int nd=100, int nnx=-1, int nny=-1, double *gm=NULL, ghostSummation<uint16_t> *gs=NULL) : analogDetector<uint16_t>(d, sign, cm, nped, nnx, nny, gm, gs),   nDark(nd), eventMask(NULL),nSigma (nsigma), eMin(-1), eMax(-1), clusterSize(csize), clusterSizeY(csize), clusters(NULL),   quad(UNDEFINED_QUADRANT), tot(0), quadTot(0)  {
+		      int nd=100, int nnx=-1, int nny=-1, double *gm=NULL, ghostSummation<uint16_t> *gs=NULL) : analogDetector<uint16_t>(d, sign, cm, nped, nnx, nny, gm, gs),   nDark(nd), eventMask(NULL),nSigma (nsigma), eMin(-1), eMax(-1), clusterSize(csize), clusterSizeY(csize), c2(1),c3(1), clusters(NULL),   quad(UNDEFINED_QUADRANT), tot(0), quadTot(0)  {
     
     
     
@@ -66,13 +65,18 @@ public analogDetector<uint16_t> {
     fm=new pthread_mutex_t ;
 
     eventMask=new eventType*[ny];
+    //  val=new double*[ny];
     for (int i=0; i<ny; i++) {
       eventMask[i]=new eventType[nx];
+      // val[i]=new double[nx];
     }
     
     if (ny==1)
       clusterSizeY=1;
 
+  
+    c2=sqrt((clusterSizeY+1)/2* (clusterSize+1)/2);
+    c3=sqrt(clusterSizeY*clusterSize);
     // cluster=new single_photon_hit(clusterSize,clusterSizeY);
     clusters=new single_photon_hit[nx*ny];
    
@@ -100,8 +104,10 @@ public analogDetector<uint16_t> {
     myFile=orig->myFile;
     
     eventMask=new eventType*[ny];
+    // val=new double*[ny];
     for (int i=0; i<ny; i++) {
       eventMask[i]=new eventType[nx];
+      // val[i]=new double[nx];
     }
     eMin=orig->eMin;
     eMax=orig->eMax;
@@ -111,6 +117,10 @@ public analogDetector<uint16_t> {
     clusterSize=orig->clusterSize;
     clusterSizeY=orig->clusterSizeY;
     // cluster=new single_photon_hit(clusterSize,clusterSizeY);
+
+    c2=sqrt((clusterSizeY+1)/2* (clusterSize+1)/2);
+    c3=sqrt(clusterSizeY*clusterSize);
+
     clusters=new single_photon_hit[nx*ny];
 
     // cluster=clusters;
@@ -124,7 +134,9 @@ public analogDetector<uint16_t> {
     gmap=orig->gmap;
     nphTot=0;
     nphFrame=0;
-
+    nphTot=0;
+    nphFrame=0;
+    
   }
   
 
@@ -196,7 +208,6 @@ public analogDetector<uint16_t> {
       int nn=0;
       double max=0, tl=0, tr=0, bl=0,br=0, v;
       double rms=0;
-      
       int cm=0;
       if (cmSub) cm=1;
 
@@ -218,8 +229,8 @@ public analogDetector<uint16_t> {
 	    cout << "add to common mode?"<< endl;
 	    addToCommonMode(data);
 	  }
-	    for (int iy=ymin; iy<ymax; iy++) {
-	  for (int ix=xmin; ix<xmax; ix++) {
+	    for (iy=ymin; iy<ymax; ++iy) {
+	  for (ix=xmin; ix<xmax; ++ix) {
 	      if (det->isGood(ix,iy)) {
 		val=subtractPedestal(data,ix,iy, cm);
 		
@@ -236,8 +247,8 @@ public analogDetector<uint16_t> {
 	    }
 	  }
 	  
-	  for (int iy=ymin; iy<ymax; iy++) {
-	for (int ix=xmin; ix<xmax; ix++) {
+	  for (iy=ymin; iy<ymax; ++iy) {
+	for (ix=xmin; ix<xmax; ++ix) {
 	    
 	    if (det->isGood(ix,iy)) {
 	      eventMask[iy][ix]=PEDESTAL;
@@ -346,18 +357,23 @@ int *getClusters(char *data,  int *ph=NULL) {
 
  
   int nph=0;
-  double val[ny][nx];
-  int cy=(clusterSizeY+1)/2;
-  int cs=(clusterSize+1)/2;
+  // const int cy=(clusterSizeY+1)/2;
+  //const int cs=(clusterSize+1)/2;
+
   //int ir, ic;
-  
+  eventType ee;
   double max=0, tl=0, tr=0, bl=0,br=0, *v;
   int cm=0;
   int good=1;
-  if (cmSub) cm=1;
+  int ir, ic;
+  // double quadTot;
+  //quadrant quad;
+  double rms;
+  //if (cmSub) cm=1;
+      double val[ny][nx];
   if (ph==NULL)
     ph=image;
-
+  
   if (iframe<nDark) {
     addToPedestal(data);
     return 0;
@@ -366,13 +382,15 @@ int *getClusters(char *data,  int *ph=NULL) {
 
 
   
-  if (cm)
+  if (cmSub) {
     addToCommonMode(data);
+    cm=1;
+  }
 
+  for (iy=ymin; iy<ymax; ++iy) {
+    for (ix=xmin; ix<xmax; ++ix) {
+      if (det->isGood(ix,iy)==0) continue; 
 
-    for (int iy=ymin; iy<ymax; iy++) {
-  for (int ix=xmin; ix<xmax; ix++) {
-      if (det->isGood(ix,iy)) {
 	max=0;
 	tl=0;
 	tr=0;
@@ -384,97 +402,120 @@ int *getClusters(char *data,  int *ph=NULL) {
 	
       
 	
-	eventMask[iy][ix]=PEDESTAL;
+	//eventMask[iy][ix]
+	  ee=PEDESTAL;
 	
 	
-	(clusters+nph)->rms=getPedestalRMS(ix,iy);
+	  rms=getPedestalRMS(ix,iy);
 	// cluster=clusters+nph;
 	
-      
-	for (int ir=-(clusterSizeY/2); ir<(clusterSizeY/2)+1; ir++) {
-	  for (int ic=-(clusterSize/2); ic<(clusterSize/2)+1; ic++) {
+	  // cout << ix << " " << iy << endl;
+	for (ir=-(clusterSizeY/2); ir<(clusterSizeY/2)+1; ir++) {
+	  for (ic=-(clusterSize/2); ic<(clusterSize/2)+1; ic++) {
 	    
 	    if ((iy+ir)>=iy && (iy+ir)<ny && (ix+ic)>=ix && (ix+ic)<nx) {
 	      val[iy+ir][ix+ic]=subtractPedestal(data,ix+ic,iy+ir, cm);
+	      v=&(val[iy+ir][ix+ic]);
+	      tot+=*v;
+	      if (ir<=0 && ic<=0)
+		bl+=*v;
+	      if (ir<=0 && ic>=0)
+		br+=*v;
+	      if (ir>=0 && ic<=0)
+		tl+=*v;
+	      if (ir>=0 && ic>=0)
+		tr+=*v;
+	      if (*v>max) {
+		max=*v;
+	      }
+	   
 	    }
 	    
-	    v=&(val[iy+ir][ix+ic]);
-	    tot+=*v;
-	    if (ir<=0 && ic<=0)
-	      bl+=*v;
-	    if (ir<=0 && ic>=0)
-	      br+=*v;
-	    if (ir>=0 && ic<=0)
-	      tl+=*v;
-	    if (ir>=0 && ic>=0)
-	      tr+=*v;
-	    if (*v>max) {
-	      max=*v;
-	    }
-	    
-	    
-	    if (ir==0 && ic==0) {
-	      if (*v<-nSigma*(clusters+nph)->rms)
-		eventMask[iy][ix]=NEGATIVE_PEDESTAL;
-	      else if (*v>nSigma*(clusters+nph)->rms)
-		eventMask[iy][ix]=PHOTON;
-	    }
 	    
 	  }
 	}
-	if (eventMask[iy][ix]==PHOTON && val[iy][ix]<max) 
-	  continue;
-	
-	if (bl>=br && bl>=tl && bl>=tr) {
-	  (clusters+nph)->quad=BOTTOM_LEFT;
-	  (clusters+nph)->quadTot=bl;
-	} else if (br>=bl && br>=tl && br>=tr) {
-	  (clusters+nph)->quad=BOTTOM_RIGHT;
-	(clusters+nph)->quadTot=br;
-	} else if (tl>=br && tl>=bl && tl>=tr) {
-	  (clusters+nph)->quad=TOP_LEFT;
-	  (clusters+nph)->quadTot=tl;
-	} else if   (tr>=bl && tr>=tl && tr>=br) {
-	  (clusters+nph)->quad=TOP_RIGHT;
-	  (clusters+nph)->quadTot=tr;
+	/* if (ix==50 && iy==50) */
+	/*   cout << id << " " << ix << " " << iy << " " << det->getValue(data,ix,iy)<< " "  << val[iy][ix] << " " << getPedestal(ix,iy) << " " << rms << endl;  */
+	if (val[iy][ix]<-nSigma*rms){
+	  ee=NEGATIVE_PEDESTAL;
+	  continue;    
+	} 
+	if (max>nSigma*rms){
+	  //	  cout << "ph1 " << max << " " << nSigma*rms << endl;
+	  ee=PHOTON;
+	  if (val[iy][ix]<max)
+	    continue;
 	}
-      
-	if (max>nSigma*(clusters+nph)->rms || tot>sqrt(clusterSizeY*clusterSize)*nSigma*(clusters+nph)->rms || ((clusters+nph)->quadTot)>sqrt(cy*cs)*nSigma*(clusters+nph)->rms) {
-	  if (val[iy][ix]>=max) {
-	  eventMask[iy][ix]=PHOTON_MAX;
-	  (clusters+nph)->tot=tot;
-	  (clusters+nph)->x=ix;
-	  (clusters+nph)->y=iy;
-	  //	  (clusters+nph)->iframe=det->getFrameNumber(data);
-	  // cout << det->getFrameNumber(data) << " " << (clusters+nph)->iframe << endl;
-	  (clusters+nph)->ped=getPedestal(ix,iy,0);
-	  for (int ir=-(clusterSizeY/2); ir<(clusterSizeY/2)+1; ir++) {
-	    for (int ic=-(clusterSize/2); ic<(clusterSize/2)+1; ic++) {
-	      (clusters+nph)->set_data(val[iy+ir][ix+ic],ic,ir);
+	else if (tot>c3*nSigma*rms) {
+	  //	  cout << "ph3 " << tot << " " << c3*nSigma*rms << endl;
+	  ee=PHOTON;
+	}
+#ifndef WRITE_QUAD
+	else {
+#endif
+	    quad=BOTTOM_RIGHT;
+	    quadTot=br;
+	    if (bl>=quadTot) {
+	      quad=BOTTOM_LEFT;
+	      quadTot=bl;
+	    }
+	    if (tl>=quadTot) {
+	      quad=TOP_LEFT;
+	      quadTot=tl;
+	    }
+	    if (tr>=quadTot) {
+	      quad=TOP_RIGHT;
+	      quadTot=tr;
+	    }
+	    
+	    if (quadTot>c2*nSigma*rms) {
+	      //   cout << "ph2 " << quadTot << " " << c2*nSigma*rms << endl;
+	      ee=PHOTON;
 	    }
-	  }
-	  good=1;
-	  if (eMin>0 && tot<eMin) good=0;
-	  if (eMax>0 && tot>eMax) good=0;
-	  if (good) {
-	    nph++;
-	    image[iy*nx+ix]++;
-	  }
 	  
-
-	  } else {
-	    eventMask[iy][ix]=PHOTON;
-	  }
-	} else if (eventMask[iy][ix]==PEDESTAL) {
-	  addToPedestal(data,ix,iy,cm);
+#ifndef WRITE_QUAD
 	}
+#endif
+	if (ee==PHOTON && val[iy][ix]==max) {
+	  ee=PHOTON_MAX;
+	  // cout << "**" <<id<< " " << iframe << " "  << nDark << " "   << ix << " " << iy << " " << rms << " " << max << " " << quadTot << " " << tot << endl;
+      	  (clusters+nph)->tot=tot;
+      	  (clusters+nph)->x=ix;
+      	  (clusters+nph)->y=iy;
+      	  (clusters+nph)->quad=quad;
+      	  (clusters+nph)->quadTot=quadTot;
+      	  //(clusters+nph)->rms=rms;
+      	  //	  (clusters+nph)->iframe=det->getFrameNumber(data);
+      	  // cout << det->getFrameNumber(data) << " " << (clusters+nph)->iframe << endl;
+      	  //  (clusters+nph)->ped=getPedestal(ix,iy,0);
+	  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) 
+		(clusters+nph)->set_data(val[iy+ir][ix+ic],ic,ir);
+	    }
       }
-    }
+      good=1;
+      if (eMin>0 && tot<eMin) good=0;
+      if (eMax>0 && tot>eMax) good=0;
+      if (good) {
+	nph++;
+	image[iy*nx+ix]++;
+      }
+      
+      
+	} else if (ee==PEDESTAL) {
+	  addToPedestal(data,ix,iy,cm);
+	} /*else {
+	    eventMask[iy][ix]=PHOTON;
+	    }*/
+	//eventMask[iy][ix]=ee;
   }
+}
+  
   nphFrame=nph;
   nphTot+=nph;
   //cout << nphFrame << endl;
-  //  cout <<"**********************************"<< det->getFrameNumber(data) << " " << nphFrame << endl;
+  //cout <<id << " **********************************"<< iframe << " " << det->getFrameNumber(data) << " " << nphFrame << endl;
   writeClusters(det->getFrameNumber(data));
   return  image;
   
@@ -561,13 +602,20 @@ int *getClusters(char *data,  int *ph=NULL) {
 */
 
     static void writeClusters(FILE *f, single_photon_hit *cl, int nph, int fn=0){
-  
-/* #ifndef OLDFORMAT   */
-/*       if (fwrite((void*)&fn, 1,  sizeof(int), f))  */
-/* 	if (fwrite((void*)&nph, 1,  sizeof(int), f))  */
-/* #endif    */
-	  for (int i=0; i<nph; i++) (cl+i)->write(f);
-};
+      if (nph>0) {
+#ifndef OLDFORMAT   
+	if (fwrite((void*)&fn, 1,  sizeof(int), f))  
+	  if (fwrite((void*)&nph, 1,  sizeof(int), f))  
+#endif    
+	    for (int i=0; i<nph; i++) (cl+i)->write(f);
+      }
+    };
+      
+
+
+
+
+
  void writeClusters(FILE *f, int fn=0){
    writeClusters(f,clusters,nphFrame, fn);
   //for (int i=0; i<nphFrame; i++) 
@@ -623,6 +671,7 @@ int *getClusters(char *data,  int *ph=NULL) {
     double eMin, eMax;
     int clusterSize; /**< cluster size in the x direction */
     int clusterSizeY; /**< cluster size in the y direction i.e. 1 for strips, clusterSize for pixels */
+    double c2, c3;
     //  single_photon_hit *cluster; /**< single photon hit data structure */
     single_photon_hit *clusters; /**< single photon hit data structure */
     quadrant quad; /**< quadrant where the photon is located */
@@ -631,6 +680,7 @@ int *getClusters(char *data,  int *ph=NULL) {
     int nphTot;
     int nphFrame;
 
+    //    double **val;
     pthread_mutex_t *fm;
 
     };

slsDetectorCalibration/single_photon_hit.h

@@ -36,19 +36,17 @@ class single_photon_hit {
       \param myFile file descriptor
   */
   size_t write(FILE *myFile) {
-    //fwrite((void*)this, 1, 3*sizeof(int)+4*sizeof(double)+sizeof(quad), myFile); 
-    
-    // if (fwrite((void*)this, 1, sizeof(int)+2*sizeof(int16_t), myFile))
-    //#ifdef OLDFORMAT 
+    //fwrite((void*)this, 1, 3*sizeof(int)+4*sizeof(double)+sizeof(quad), myFile);  // if (fwrite((void*)this, 1, sizeof(int)+2*sizeof(int16_t), myFile))
+#ifdef OLDFORMAT 
     if (fwrite((void*)&iframe, 1,  sizeof(int), myFile)) {};
-      //#endif  
+#endif  
 #ifndef WRITE_QUAD
       //printf("no quad ");
-    if (fwrite((void*)&x, 2,  sizeof(int16_t), myFile)) 
-      return fwrite((void*)data, 1, dx*dy*sizeof(int), myFile);
+    if (fwrite((void*)&x, sizeof(int16_t), 2, myFile)) 
+      return fwrite((void*)data, sizeof(int), dx*dy, myFile);
 #endif 
 #ifdef WRITE_QUAD
-    // printf("quad ");
+    //  printf("quad ");
     int qq[4];
     switch(quad) {
     case TOP_LEFT:
@@ -91,8 +89,8 @@ class single_photon_hit {
     default:
       ;
     }
-    if (fwrite((void*)&x, 2,  sizeof(int16_t), myFile)) 
-      return fwrite((void*)qq, 1, 4*sizeof(int), myFile);
+     if (fwrite((void*)&x,   sizeof(int16_t), 2, myFile)) 
+      return fwrite((void*)qq, sizeof(int), 4, myFile);
 #endif
     return 0;
   };   
@@ -104,19 +102,19 @@ class single_photon_hit {
   size_t read(FILE *myFile) {
     //fread((void*)this, 1,  3*sizeof(int)+4*sizeof(double)+sizeof(quad), myFile); 
     
-    //#ifdef OLDFORMAT 
+#ifdef OLDFORMAT 
     if (fread((void*)&iframe, 1,  sizeof(int), myFile))  {}
-      //#endif   
+#endif   
 #ifndef WRITE_QUAD
       // printf( "no quad \n");
-    if (fread((void*)&x, 2,  sizeof(int16_t), myFile))  
-      return fread((void*)data, 1, dx*dy*sizeof(int), myFile);
+    if (fread((void*)&x,  sizeof(int16_t),2, myFile))  
+      return fread((void*)data, sizeof(int), dx*dy,myFile);
 #endif 
 #ifdef WRITE_QUAD
     int qq[4];
-    // printf( "quad \n");
-    if (fread((void*)&x, 2,  sizeof(int16_t), myFile))  
-      if (fread((void*)qq, 1, 4*sizeof(int), myFile)) {
+    printf( "quad \n");
+    if (fread((void*)&x, sizeof(int16_t), 2,  myFile))  
+      if (fread((void*)qq, sizeof(int), 4, myFile)) {
 
 	quad=TOP_RIGHT;
 	/*	int mm=qq[0]; */
@@ -216,7 +214,6 @@ class single_photon_hit {
     for (int iy=0; iy<dy; iy++) {
       for (int ix=0; ix<dx; ix++) {
 	printf("%d \t",data[ix+iy*dx]);
-
       }
     printf("\n");
     }
@@ -246,15 +243,15 @@ class single_photon_hit {
   int *get_cluster() {return data;};
 
   int	iframe; 	        /**< frame number */
-  int16_t 	x; 			/**< x-coordinate of the center of hit */
-  int16_t	y; 			/**< x-coordinate of the center of hit */
   double	rms; 		/**< noise of central pixel l -- at some point it can be removed*/
   double 	ped; 		/**< pedestal of the central pixel -- at some point it can be removed*/
    double tot; /**< sum of the 3x3 cluster */
    quadrant quad; /**< quadrant where the photon is located */
    double quadTot; /**< sum of the maximum 2x2cluster */ 
   int dx;	                /**< size of data cluster in x */
-  int dy;                 /**< size of data cluster in y */  
+  int dy;                 /**< size of data cluster in y */ 
+  int16_t 	x; 			/**< x-coordinate of the center of hit */
+  int16_t	y; 			/**< x-coordinate of the center of hit */ 
   int *data;		        /**< pointer to data */
 };