updated all servers

Trim

.clang-format

@@ -2,5 +2,6 @@ BasedOnStyle: LLVM
 IndentWidth: 4
 
 UseTab: Never
-ColumnLimit: 0
-AlignConsecutiveAssignments: false 
+ColumnLimit: 80
+AlignConsecutiveAssignments: false 
+AlignConsecutiveMacros: true

.clang-tidy

@@ -1,7 +1,34 @@
 ---
-Checks:          '*, -google-runtime-references, -hicpp-no-array-decay, -cppcoreguidelines-pro-bounds-array-to-pointer-decay, -cppcoreguidelines-pro-bounds-pointer-arithmetic, -fuchsia*,-readability-else-after-return,-readability-avoid-const-params-in-decls,-hicpp-signed-bitwise,-cppcoreguidelines-pro-bounds-constant-array-index,-llvm-header-guard,-readability-static-accessed-through-instance,-google-readability-todo'
-WarningsAsErrors: '*'
-HeaderFilterRegex: '.*'
+Checks:          '*, 
+                    -android-cloexec-fopen,
+                    -cppcoreguidelines-pro-bounds-array-to-pointer-decay, 
+                    -cppcoreguidelines-pro-bounds-pointer-arithmetic, 
+                    -fuchsia*,
+                    -readability-else-after-return,
+                    -readability-avoid-const-params-in-decls,
+                    -cppcoreguidelines-pro-bounds-constant-array-index,
+                    -cppcoreguidelines-pro-type-reinterpret-cast,
+                    -llvm-header-guard,
+                    -readability-static-accessed-through-instance,
+                    -readability-braces-around-statements,
+                    -hicpp-signed-bitwise,
+                    -hicpp-no-array-decay, 
+                    -hicpp-braces-around-statements,
+                    -google-runtime-references, 
+                    -google-readability-todo, 
+                    -google-readability-braces-around-statements,
+                    -modernize-use-trailing-return-type,
+                    -readability-isolate-declaration'
+
+HeaderFilterRegex: \.h
 AnalyzeTemporaryDtors: false
 FormatStyle:     none
+CheckOptions:
+  - { key: readability-identifier-naming.NamespaceCase,       value: lower_case }
+ # - { key: readability-identifier-naming.FunctionCase,        value: lower_case }
+  - { key: readability-identifier-naming.ClassCase,           value: CamelCase  }
+ # - { key: readability-identifier-naming.MethodCase,          value: CamelCase  }
+ # - { key: readability-identifier-naming.StructCase,          value: CamelCase  }
+ # - { key: readability-identifier-naming.VariableCase,        value: lower_case }
+  - { key: readability-identifier-naming.GlobalConstantCase,  value: UPPER_CASE }
 ...

.gitignore

@@ -6,6 +6,18 @@ bin/
 *.log
 *.out
 *.toc
+*.o
+*.so
+.*
 build
-docs/
 RELEASE.txt
+Testing/
+
+ctbDict.cpp
+ctbDict.h
+
+
+
+*.pyc
+*/__pycache__/*
+

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "python/pybind11"]
+	path = libs/pybind11
+	url = https://github.com/pybind/pybind11.git

.travis.yml

@@ -2,44 +2,37 @@ sudo: false
 
 language: cpp
 
-matrix:
-  include:
-    - os: linux
-      env: CONDA_PY=3.6
+os: linux
 
-dist: trusty
+dist: bionic
 
 install:
   - sudo apt-get update
   - ldd --version
   - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
   - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
+  - source "$HOME/miniconda/etc/profile.d/conda.sh"
   - rm -f miniconda.sh
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
   - conda config --add channels conda-forge
   - conda config --add channels slsdetectorgroup
-  - conda update conda
-  - conda update --all
-  - conda install conda-build anaconda-client
-
-  # Useful for debugging any issues with conda
+  - conda update -q conda
   - conda info -a
 
-
-  # Replace dep1 dep2 ... with your dependencies
-  - conda create -q -n test-environment python=$CONDA_PY
-  - source activate test-environment
+  # Useful for debugging any issues with conda
+  - conda create -q -n testenv conda-build anaconda-client conda-verify
+  - conda activate testenv
   - conda-build .
 
 script:
- - echo "No test scripts to be run!"
+ - CTEST_OUTPUT_ON_FAILURE=1 ctest -j 2
 
 
 deploy:
   provider: script
-  script: find $HOME/miniconda/conda-bld/${TRAVIS_OS_NAME}-64 -name "*.tar.bz2" -exec anaconda -t $CONDA_TOKEN upload --force {} \;
+  script: find $HOME/miniconda/envs/testenv/conda-bld/${TRAVIS_OS_NAME}-64 -name "*.tar.bz2" -exec anaconda -t $CONDA_TOKEN upload --force {} \;
   on:
-    branch: 4.0.1-rc
+    branch: developer
+    tags: true
 

CMakeLists.txt

@@ -1,76 +1,238 @@
-cmake_minimum_required(VERSION 2.8)
+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)
+
+# Include additional modules that are used unconditionally
+include(GNUInstallDirs)
+
+# If conda build, always set lib dir to 'lib'
+if($ENV{CONDA_BUILD})
+  set(CMAKE_INSTALL_LIBDIR "lib")
+endif()
+
+# Set lower / upper case project names
+string(TOUPPER "${PROJECT_NAME}" PROJECT_NAME_UPPER)
+string(TOLOWER "${PROJECT_NAME}" PROJECT_NAME_LOWER)
+
+# Set targets export name (used by slsDetectorPackage and dependencies)
+set(TARGETS_EXPORT_NAME "${PROJECT_NAME_LOWER}-targets")
+#set(namespace "${PROJECT_NAME}::")
+
 set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
-set (CALIBRATE OFF)
+
 
 # Check if project is being used directly or via add_subdirectory
 set(SLS_MASTER_PROJECT OFF)
 if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
-	set(SLS_MASTER_PROJECT ON)
+    set(SLS_MASTER_PROJECT ON)
 endif()
 
 option (SLS_USE_HDF5 "HDF5 File format" OFF)
-option (SLS_USE_TEXTCLIENT "Text Client" OFF)
-option (SLS_USE_RECEIVER "Receiver" OFF)
+option (SLS_USE_TEXTCLIENT "Text Client" ON)
+option (SLS_USE_RECEIVER "Receiver" ON)
 option (SLS_USE_GUI "GUI" OFF)
+option (SLS_USE_SIMULATOR "Simulator" OFF)
+option (SLS_USE_TESTS "TESTS" OFF)
+option (SLS_USE_INTEGRATION_TESTS "Integration Tests" OFF)
+option(SLS_USE_SANITIZER "Sanitizers for debugging" OFF)
+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)
+
+# 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)
 
 
-#Flags to always be used
-# -Wno-unused-parameter should eventually be removes
-# -Wno-overloaded-virtual TODO! remove warnings in refactor
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Wno-overloaded-virtual -Wno-unused-parameter -std=c++98")
-
-if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
-    # clang does not support -Wno-misleading-indentation 
-    # add any special clang flags
-elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
-    if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 6.0)
-        set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -Wno-misleading-indentation")
+# 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)
+  message(STATUS "No build type selected, default to Release")
+  set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Build type (default Release)" FORCE)
 endif()
 
 
-find_package(Qt4)
-find_package(Qwt 6)
-find_package(CBF)
-find_package(Doxygen)
-# find_package(PNG REQUIRED)
+#Add two fake libraries to manage options
+add_library(slsProjectOptions INTERFACE)
+add_library(slsProjectWarnings INTERFACE)
+target_compile_features(slsProjectOptions INTERFACE cxx_std_11)
+target_compile_options(slsProjectWarnings INTERFACE 
+                                            -Wall
+                                            -Wextra
+                                            -Wno-unused-parameter #Needs to be slowly mitigated
+                                            # -Wold-style-cast
+                                            -Wnon-virtual-dtor
+                                            -Woverloaded-virtual
+                                            -Wdouble-promotion
+                                            -Wformat=2
+                                            -Wredundant-decls
+                                            # -Wconversion
+                                            -Wdouble-promotion
+                                            -Werror=return-type
 
-if (SLS_USE_HDF5)
-	find_package(HDF5 1.10 COMPONENTS CXX)
-endif (SLS_USE_HDF5)
+                                 )
+
+
+#Testing for minimum version for compilers
+if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 3.2)
+        message(FATAL_ERROR "Clang version must be at least 3.2!")
+    endif()
+    target_compile_options(slsProjectWarnings INTERFACE -Wshadow) #Clag does not warn on constructor
+elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.8)
+            message(FATAL_ERROR "GCC version must be at least 4.8!")
+    endif()
+
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5)
+            target_compile_options(slsProjectWarnings INTERFACE 
+                                             -Wno-missing-field-initializers)
+    endif()
+    
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 6.0)
+        target_compile_options(slsProjectWarnings INTERFACE 
+                                                -Wno-misleading-indentation # mostly in rapidjson remove using clang format
+                                                -Wduplicated-cond
+                                                -Wnull-dereference )
+
+    endif()
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 8.0)
+        target_compile_options(slsProjectWarnings INTERFACE 
+                                                -Wno-class-memaccess )
+
+    endif()
+endif()
+
+
+if(SLS_USE_SANITIZER)
+    target_compile_options(slsProjectOptions INTERFACE -fsanitize=address,undefined -fno-omit-frame-pointer)
+    target_link_libraries(slsProjectOptions INTERFACE -fsanitize=address,undefined)
+    # target_compile_options(slsProjectOptions INTERFACE -fsanitize=thread)
+    # 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
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/libs/rapidjson>  
+)
+
+# Install fake the libraries
+install(TARGETS slsProjectOptions slsProjectWarnings rapidjson
+    EXPORT "${TARGETS_EXPORT_NAME}"
+    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+)
 
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+set(CMAKE_INSTALL_RPATH $ORIGIN)
+# set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
+set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
 
-set(CMAKE_INSTALL_RPATH "$ORIGIN")
-set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
 
 
+find_package(ZeroMQ 4 REQUIRED)
+
+if (SLS_USE_TESTS)
+    enable_testing()
+    add_subdirectory(tests)
+endif(SLS_USE_TESTS)
+
+
+
+
+# Common functionallity to detector and receiver
+add_subdirectory(slsSupportLib)
+
 if (SLS_USE_TEXTCLIENT)
-       add_subdirectory(slsDetectorSoftware)
+    add_subdirectory(slsDetectorSoftware)
 endif (SLS_USE_TEXTCLIENT)
 
+
 if (SLS_USE_RECEIVER)
-       add_subdirectory(slsReceiverSoftware)
-       add_subdirectory(manual/manual-api)    
+    if (SLS_USE_HDF5)
+        find_package(HDF5 1.10 COMPONENTS CXX REQUIRED)
+    endif (SLS_USE_HDF5)
+    add_subdirectory(slsReceiverSoftware) 
 endif (SLS_USE_RECEIVER)
-               
-               
+
 if (SLS_USE_GUI)   
-       if (QT4_FOUND AND QWT_FOUND)
-       add_subdirectory(slsDetectorGui)
-       endif()
+    find_package(Qt4 REQUIRED)
+    find_package(Qwt 6.1 REQUIRED)
+    if (QT4_FOUND AND QWT_FOUND)
+        add_subdirectory(slsDetectorGui)
+    endif()
 endif (SLS_USE_GUI)
 
-if (SLS_MASTER_PROJECT)
-	# Set targets export name (otherwise set by upstream project)
-	set(TARGETS_EXPORT_NAME "slsdetector-targets")
-endif (SLS_MASTER_PROJECT)
+if (SLS_USE_SIMULATOR)
+    add_subdirectory(slsDetectorServers)
+endif (SLS_USE_SIMULATOR)
 
-if (CALIBRATE)
-    if (DEFINED ENV{ROOTSYS})
-        find_package(ROOT)
-        if (ROOT_FOUND)
-            add_subdirectory(calibrationWizards)
-        endif()
-    endif()
-endif(CALIBRATE)
+if (SLS_USE_INTEGRATION_TESTS)
+    add_subdirectory(integrationTests)
+endif (SLS_USE_INTEGRATION_TESTS)
+
+if (SLS_USE_PYTHON)
+    set(PYBIND11_CPP_STANDARD -std=c++11)
+    add_subdirectory(libs/pybind11)
+    add_subdirectory(python)
+endif(SLS_USE_PYTHON)
+
+if (SLS_USE_CTBGUI)
+    add_subdirectory(ctbGui)
+endif(SLS_USE_CTBGUI)
+
+configure_file( .clang-tidy  
+    ${CMAKE_BINARY_DIR}/.clang-tidy  
+)
+
+if (SLS_BUILD_EXAMPLES)
+    add_subdirectory(sample)
+endif(SLS_BUILD_EXAMPLES)
+
+if(SLS_BUILD_DOCS)
+    add_subdirectory(docs)
+endif(SLS_BUILD_DOCS)
+
+if(SLS_MASTER_PROJECT)
+    # Set install dir CMake packages
+    set(CMAKE_INSTALL_DIR "share/cmake/${PROJECT_NAME}")
+    # Set the list of exported targets
+    set(PROJECT_LIBRARIES slsSupportLib slsDetectorShared slsReceiverShared)
+    # Generate and install package config file and version
+    include(cmake/package_config.cmake)
+endif()

Makefile

@@ -1,235 +0,0 @@
-# do not change below this line#
-
-# Include common definitions
-include Makefile.include
-
-INSTALLROOT	?=	$(PWD)
-BINDIR	?=	$(INSTALLROOT)/bin
-DOCDIR	?=	$(INSTALLROOT)/manual/docs
-LIBDIR	?=	$(INSTALLROOT)/bin
-INCDIR	?=	$(INSTALLROOT)/include
-DETAILDOC	?=	$(INSTALLROOT)/docs
- 
-WD				=	$(shell pwd)
-LIBRARYDIR		=	$(WD)/slsDetectorSoftware
-LIBRARYRXRDIR 		= 	$(WD)/slsReceiverSoftware
-CLIENTDIR		=	$(LIBRARYDIR)/slsDetectorClient
-GUIDIR			=	$(WD)/slsDetectorGui
-RECEIVERDIR		=	$(LIBRARYRXRDIR)
-CALWIZDIR		=	$(WD)/calibrationWizards
-MANDIR			=	$(WD)/manual
-CALIBDIR		=	$(WD)/slsDetectorCalibration
-MANAPIDIR		=	$(MANDIR)/manual-api
-
-TABSPACE		:=	"\t"
-
- 
-INCLUDES=-I. -I$(LIBRARYDIR)/commonFiles -I$(LIBRARYDIR)/slsDetector -I$(LIBRARYDIR)/usersFunctions -I$(LIBRARYDIR)/multiSlsDetector -I$(LIBRARYDIR)/slsDetectorUtils -I$(LIBRARYDIR)/slsDetectorCommand -I$(LIBRARYDIR)/slsDetectorAnalysis -I$(LIBRARYDIR)/slsReceiverInterface  -I$(LIBRARYRXRDIR)/include -I$(LIBRARYDIR)/threadFiles -I$(LIBRARYDIR)/sharedMemory -I$(ASM)
-
-INCLUDESRXR += -I. -I$(LIBRARYRXRDIR)/include -I$(CALIBDIR) -I$(ASM) 
-#LIBFLAGRXR += 
-
-$(info )
-$(info #######################################)
-$(info #   In slsDetectorsPackage Makefile   #)
-$(info #######################################)
-$(info )
-
-
-.PHONY: all nonstatic static lib libreceiver textclient receiver gui stextclient sreceiver
-
-#all: lib textclient  receiver gui 
-all: textclient  receiver gui 
-
-nonstatic: lib libreceiver textclient receiver  gui 
-
-static: lib  libreceiver stextclient sreceiver gui 
-
-
-lib:
-	cd $(LIBRARYDIR) && $(MAKE) FLAGS='$(FLAGS)' DESTDIR='$(LIBDIR)' LIBRARYDIR='$(LIBRARYDIR)' LIBS='$(LDFLAGDET)' INCLUDES='$(INCLUDES)' LIBDIR='$(LIBDIR)'
-
-libreceiver:
-	cd $(LIBRARYRXRDIR) && $(MAKE) FLAGS='$(FLAGS)' DESTDIR='$(LIBDIR)' LIBS='$(LDFLAGRXR)' INCLUDES='$(INCLUDESRXR)' LIBDIR='$(LIBDIR)'
-
-
-stextclient: slsDetectorClient_static
-
-slsDetectorClient: textclient
-
-slsDetectorClient_static: #lib
-	cd  $(CLIENTDIR) && $(MAKE) static_clients FLAGS='$(FLAGS)' DESTDIR='$(BINDIR)' LIBRARYDIR='$(LIBRARYDIR)' LIBS='$(LDFLAGDET)' INCLUDES='$(INCLUDES)' LIBDIR='$(LIBDIR)'
-	@echo ""
-	@echo "#######################################"
-	@echo "# Back in slsDetectorPackage Makefile #"
-	@echo "#######################################"
-	@echo ""
-		
-textclient: #lib
-	cd  $(CLIENTDIR) && $(MAKE) FLAGS='$(FLAGS)' DESTDIR='$(BINDIR)'  LIBRARYDIR='$(LIBRARYDIR)' LIBS='$(LDFLAGDET)' INCLUDES='$(INCLUDES)' LIBDIR='$(LIBDIR)'
-	@echo ""
-	@echo "#######################################"
-	@echo "# Back in slsDetectorPackage Makefile #"
-	@echo "#######################################"
-	@echo ""
-	
-slsReceiver: receiver
-
-slsReceiver_static: receiver
-
-receiver: #libreceiver
-#	cd  $(RECEIVERDIR) && $(MAKE) receiver FLAGS='$(FLAGS)' DESTDIR='$(BINDIR)'  LIBS='$(LDFLAGRXR)' INCLUDES='$(INCLUDESRXR)' LIBDIR='$(LIBDIR)'
-	cd  $(RECEIVERDIR) && $(MAKE) FLAGS='$(FLAGS)' DESTDIR='$(BINDIR)'  LIBS='$(LDFLAGRXR)' INCLUDES='$(INCLUDESRXR)' LIBDIR='$(LIBDIR)'
-	cd  $(MANAPIDIR) && $(MAKE) slsMultiReceiver
-	@echo ""
-	@echo "#######################################"
-	@echo "# Back in slsDetectorPackage Makefile #"
-	@echo "#######################################"
-	@echo ""
-		
-sreceiver: #libreceiver
-	cd  $(RECEIVERDIR) && $(MAKE)  static_receiver FLAGS='$(FLAGS)' DESTDIR='$(BINDIR)'  LIBS='$(LDFLAGRXR)' INCLUDES='$(INCLUDESRXR)' LIBDIR='$(LIBDIR)'
-	@echo ""
-	@echo "#######################################"
-	@echo "# Back in slsDetectorPackage Makefile #"
-	@echo "#######################################"
-	@echo ""
-
-slsDetectorGUI: #lib
-	cd  $(GUIDIR) && $(MAKE) DESTDIR='$(BINDIR)' LIBRARYDIR='$(LIBRARYDIR)' INCLUDES='$(INCLUDES)' LDFLAGDET='$(LDFLAGDETONLY)' LIBDIR='$(LIBDIR)'
-	@echo ""
-	@echo "#######################################"
-	@echo "# Back in slsDetectorPackage Makefile #"
-	@echo "#######################################"
-	@echo ""
-	
-calWiz: 
-	cd  $(CALWIZDIR) && $(MAKE)  DESTDIR=$(BINDIR) #FLAGS=$(FLAGS)  LDFLAGDET=$(LDFLAGDET) INCLUDES=$(INCLUDES)
-
-
-
-gui: slsDetectorGUI
-
-
-doc:
-	$(shell test -d $(DOCDIR) || mkdir -p $(DOCDIR))
-	cd manual && make all DESTDIR=$(DOCDIR)
-
-htmldoc:
-	make doc
-	$(shell test -d $(DOCDIR) || mkdir -p $(DOCDIR))
-	cd manual && make html DESTDIR=$(DOCDIR)
-	
-detaildoc: createdocs docspdf docshtml removedocs
-
-createdocs: $(LIBRARYDIR)/doxy.config
-	doxygen $(LIBRARYDIR)/doxy.config	
-
-docspdf: 
-	cd slsDetectorPackageDocs/latex && make 
-	$(shell test -d $(DETAILDOC) || mkdir -p $(DETAILDOC))
-	$(shell test -d $(DETAILDOC)/pdf || mkdir -p $(DETAILDOC)/pdf)
-	mv slsDetectorPackageDocs/latex/refman.pdf $(DETAILDOC)/pdf/slsDetectorPackageDocs.pdf
-
-docshtml: 
-	$(shell test -d $(DETAILDOC) || mkdir -p $(DETAILDOC))
-	$(shell test -d $(DETAILDOC)/html || mkdir -p $(DETAILDOC)/html)
-	$(shell test -d $(DETAILDOC)/html/slsDetectorPackageDocs && rm -r $(DETAILDOC)/html/slsDetectorPackageDocs)
-	mv slsDetectorPackageDocs/html $(DETAILDOC)/html/slsDetectorPackageDocs
-	
-removedocs:
-	rm -rf 	slsDetectorPackageDocs;
-
-
-clean:
-	cd $(BINDIR) && rm -rf sls_detector_* slsDetectorGui slsReceiver angularCalibrationWizard energyCalibrationWizard 
-	cd $(LIBDIR) && rm -rf libSlsDetector.so libSlsDetector.a libSlsReceiver.so libSlsReceiver.a 
-	cd $(LIBRARYDIR) && $(MAKE) clean 
-	cd $(LIBRARYRXRDIR) && $(MAKE) clean 
-	cd $(CLIENTDIR) && $(MAKE) clean
-	cd $(GUIDIR) && $(MAKE) clean
-	cd $(CALWIZDIR) && $(MAKE) clean
-	cd manual && $(MAKE) clean
-	cd $(DOCDIR) && rm -rf * 
-	rm -rf 	slsDetectorPackageDocs;
-	rm -rf $(DETAILDOC)
-	rm -rf $(MANAPIDIR)/slsMultiReceiver
-
-
-#install_lib: 
-#	cd $(LIBRARYDIR) && $(MAKE) install DESTDIR=$(LIBDIR) INCLUDES=$(INCLUDES)
-#	cd $(LIBRARYDIR) && $(MAKE) install_inc DESTDIR=$(INCDIR)
-
-mythen_virtual:
-	cd $(LIBRARYDIR) && $(MAKE) mythenVirtualServer DESTDIR=$(BINDIR)
-
-
-gotthard_virtual:
-	cd $(LIBRARYDIR) && $(MAKE) gotthardVirtualServer DESTDIR=$(BINDIR)
-
-
-install_client: textclient slsReceiver
-
-install_gui: gui
-
-confinstall:
-	make conf;\
-	make install
-
-install_lib: 
-	make lib;\
-	make libreceiver; \
-	make textclient; \
-	make slsReceiver; \
-	make doc; \
-	make htmldoc; \
-	cd $(LIBRARYDIR) && $(MAKE) install_inc DESTDIR=$(INCDIR); \
-	cd $(LIBRARYRXRDIR) && $(MAKE) install_inc DESTDIR=$(INCDIR);
-
-install: 
-	make install_lib; \
-	make gui; \
-	make calWiz; \
-	cd $(LIBRARYDIR) && $(MAKE) install_inc DESTDIR=$(INCDIR);\
-	cd $(LIBRARYRXRDIR) && $(MAKE) install_inc DESTDIR=$(INCDIR);
-
-conf:
-	set -e; \
-	. ./configure; \
-	@echo "INSTALLROOT is $(INSTALLROOT)"
-	@echo "BINDIR is $(BINDIR)"
-	@echo "LIBDIR is $(LIBDIR)"
-	@echo "INCDIR is $(INCDIR)"
-	@echo "DOCDIR is $(DOCDIR)"
-
-
-help:
-	@echo "Targets:"
-	@echo "make all 		compile library,  text clients, data reciever"
-	@echo "make lib 		compile library"
-	@echo "make libreceiver 		compile receiver library"
-	@echo "make textclient		compile the slsDetectorClient dynamically linking the libraries"
-	@echo "make stextclient 		compile slsDetectorClient statically linking the libraries"
-	@echo "make receiver		compile the slsReciever dynamically linking the libraries"
-	@echo "make sreceiver		compile the slsReciever statically linking the libraries"
-	@echo "make gui			compile slsDetectorGUI - requires a working Qt4 and Qwt installation"
-	@echo "make calWiz 		compile the calibration wizards - requires a working Root installation"
-	@echo "make doc			compile pdf documentation"
-	@echo "make htmldoc		compile html (and pdf) documentation"
-	@echo "make install_lib         installs the libraries, the text clients, the documentation and the includes for the API"
-	@echo "make install             installs all software, including the gui, the cal wizards and the includes for the API"
-	@echo "make confinstall         installs all software, including the gui, the cal wizards and the includes for the API, prompting for the install paths"
-	@echo "make clean              	remove object files and executables"
-	@echo "make help               	lists possible targets"
-	@echo ""
-	@echo ""
-	@echo "Makefile variables"
-	@echo "DEBUG=1,2		 set debug level to 1 (VERBOSE) or 2 (VERYVERBOSE)"
-	@echo ""
-	@echo ""
-	@echo "Variables -  to change them run <source configure> :"
-	@echo "INSTALLROOT=<yourdir>:    installation root di	r, default $PWD"
-	@echo "BINDIR=<yourbin>:         binary installation dir below INSTALLROOT, default bin"
-	@echo "LIBDIR=<yourlib>:         library installation dir below INSTALLROOT, default lib"
-	@echo "INCDIR=<yourincludes>:    header installation dir below INSTALLROOT, default include"
-	@echo "DOCDIR=<yourdoc>:         documentation installation dir below INSTALLROOT, default doc"

Makefile.include

@@ -1,58 +0,0 @@
-##############################################################
-# Generic 
-##############################################################
-
-CC = g++
-CXX = $(CC)
-ASM=$(shell echo "/lib/modules/`uname -r`/build/include")
-LDFLAGDETONLY = -L$(LIBDIR)  -Wl,-rpath=$(LIBDIR) -lSlsDetector 
-LDFLAGDET = -L$(LIBDIR)  -Wl,-rpath=$(LIBDIR) -lSlsDetector -L/usr/lib64/ -pthread
-LDFLAGRXR = -L$(LIBDIR)  -Wl,-rpath=$(LIBDIR) -lSlsReceiver -L/usr/lib64/ -pthread
-FLAGS= -Wall  -pthread  #-DEIGER_DEBUG2
-# -DVERBOSE 
-
-# Setting up the verbose flags
-ifeq ($(DEBUG),1)
-     FLAGS = -Wall -DVERBOSE
-endif
-ifeq ($(DEBUG),2)
-     FLAGS = -Wall -DVERYVERBOSE
-endif
-
-##############################################################
-# HDF5 specific. Set this to yes, if you want to compile
-# HDF5 code: in this case, you need HDF5 libraries
-##############################################################   
-
-HDF5 = no
-HDF5_DIR = /opt/hdf5v1.10.0
-
-ifeq ($(HDF5),yes)
-	LDFLAGRXR = -L$(LIBDIR) -Wl,-rpath=$(LIBDIR) -lSlsReceiver -L$(HDF5_DIR)/lib  -Wl,-rpath=$(HDF5_DIR)/lib -lhdf5 -lhdf5_cpp -lsz -lz -DHDF5C -L/usr/lib64/ -pthread
-	INCLUDESRXR = -I$(HDF5_DIR)/include
-endif	
-
-
-##############################################################
-# ROOTSLS specific. Set this to yes, if you want to compile
-# ROOTSLS code: in this case, you need also root libraries
-##############################################################   
-
-ROOTSLS = no
-
-ROOTFLAGS = $(shell root-config --cflags --glibs) -DMYROOT1   #-DALLFILE_DEBUG #-DMYROOT1 
-
-ifeq ($(ROOTSLS),yes)
-     LDFLAGRXR = -L$(LIBDIR) -lSlsReceiver $(ROOTFLAGS) -DROOTSLS
-endif
-
-
-define colorecho
-      @tput setaf 6
-      @echo $1
-      @tput sgr0
-endef
-
-
-
-

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
 ```

RELEASE.txt

@@ -1,205 +1,2 @@
-SLS Detector Package 4.0.1 released on 08.02.2018 (Bug Fix Release)
-===================================================================
-
-
-This document describes the differences between 4.0.1 and 4.0.0 releases.   
-    
-    CONTENTS
-    --------
-    1.  Topics Concerning
-    2.  Resolved Issues
-    3.  Known Issues
-    4.  Firmware Requirements
-    5.  Download, Documentation & Support
-    
-
-
-1. Topics Concerning
-====================
-
-    - Jungfrau server (new firmware mapped)
-    - Eiger server (measuredPeriod, reg)
-    - Gotthard server(ADC channel shift, ROI, 25um slave packets)
-    - Receiver (padding, releasing resources segfault, gappixels)
-    - Users class (detectorSize, ROI, versions, status)
-    - API (config error, ROI)
-    - Compile (Options prefix, static libraries, Makefile for API)
-    - Gui (multi module)
-
-
-
-2. Resolved Issues
-==================          
-
-    Detector Server
-    ---------------
-    
-    1.  (Jungfrau): Latest Jungfrau firmware release mapped.
-    
-    2.  (Eiger): Measured subperiod initially wrapped around 4.29s. Now, upto 42.9s.
-        
-        Advanced command "reg" was writing only to right FPGA. 
-    
-    3.  (Gotthard 25/50um): Since Gotthard only sends packet numbers, one had to 
-        remember to take even number of images in ROI mode, if they wanted to 
-        switch back to non ROI mode.
-        This is fixed now, but temporary fix involves sending an image during 
-        configuration, which will not be captured by the receiver. Hence, it takes
-        longer to configure. Permanent fix will require a firmware update.
-           
-        The detector output is shifted by 1 for every 32 channels. This is fixed now.
-        
-        
-    Receiver
-    --------
-    
-    1.  Receiver padding was enabled only if deactivated padding was also enabled.
-        Receiver padding enable and receiver deactivated padding enable are independent now.
-        
-    2.  Starting and stopping receiver without listening resulted in seg faults.
-    
-    3.  Gappixels in receiver bug fix.
-        
-        
-    Client
-    ------
-            
-    1.  (Users class): DetectorSize modified to set/get ROI if ROI is only 1 in number.
-    
-        Allowed setting/getting ROI at single detector level via API. 
-        (ROI for Gotthard only). Added them to the users class as setROI and getROI.
-        
-        Retrieving versions at module level is possible now.
-        
-        Added "stopped" as status in getRunStatus list.
-    
-    2.  (API): Incorrect mac address in config file will set error flag in API and not just
-        print the error.
-        
-        ROI possible at module level.
-         
-    
-    Compile
-    -------
-    
-    1.	CMake options now have a prefix 'SLS_'.
-
-    2.  Static libraries removed.
-    
-    2.  slsDetectorPackage/manual/manual-api/Makefile modified to use libraries
-        from slsDetectorPackage/bin as the main Makefile copies the libraries there. 
-        No effect when using CMakeFiles.
-    
-
-    Gui
-    ---
-        
-    1.  Adding multiple detectors in x and y direction incremented number of detectors
-        in y direction incorrectly. Effect seen only in GUI (segfault) if 
-        detsizechan has multi detectors in both direction. Fixed.
-        
-        
-        
-3. Known Issues
-===============
-    
-    Detector Specific 
-    -----------------
-    
-    1.  (Gotthard 25 um): Slave misses or captures an extra frame. Occurs irregularly.
-    
-    2.  (Gotthard 25/50um): Using ROI (2 chips, 256 channels) missses last pixel
-        of that ADC.
-    
-    
-    
-4. Firmware Requirements
-========================
-
-        Gotthard
-        ========   
-        Minimum compatible version  : 11.01.2013
-        Latest compatible version   : 08.02.2018 (50um and 25um Master)
-                                      09.02.2018 (25 um Slave) 
-        Eiger
-        =====  
-        Minimum compatible version  : 22
-        Latest compatible version   : 22
-        
-        Jungfrau
-        ========       
-        Minimum compatible version  : 26.02.2018
-        Latest compatible version   : 06.12.2018
-
-        
-        Detector Upgrade
-        ================
-        Gotthard    Cannot be upgraded remotely. Requires programming via USB blaster
-        Eiger       Can be upgraded remotely via bit files
-        Jungfrau    Can be upgraded remotely using sls_detector_put programfpga <pof>
-        
-        Instructions available at
-        https://www.psi.ch/detectors/installation-instructions
-        under Detector Upgrade -> [Detector Type] -> Firmware. 
-        
-         
-    Please refer to the link below for more details on the firmware versions.
-    https://www.psi.ch/detectors/firmware.
-    
-    
-        
-5. Download, Documentation & Support
-====================================
-
-    Download
-    --------
-    
-    The Source Code (Default C++ API):
-         https://github.com/slsdetectorgroup/slsDetectorPackage
-         
-    The Conda Lib Package:
-        https://github.com/slsdetectorgroup/sls_detector_lib
-        
-    The Conda GUI Package:
-        https://github.com/slsdetectorgroup/sls_detector_gui    
-        
-    The Python Interface (including the package):
-        https://github.com/slsdetectorgroup/sls_detector
-    
-    
-    Documentation
-    -------------
-    
-    Manual (HTML & PDF):
-        https://www.psi.ch/detectors/documentation
-        slsDetectorPackage/manual/docs/
-        
-    Command Line Documentation:
-        manual/docs/html/slsDetectorClientDocs/index.html
-        manual/docs/pdf/slsDetectorClientDocs.pdf
-        
-    C++ API Documentation:
-        manual/docs/html/slsDetectorUsersDocs/index.html
-        manual/docs/pdf/slsDetectorUsersDocs.pdf
-        
-    C++ API Example:
-        manual/manual-api/mainClient.cpp
-        manual/manual-api/mainReceiver.cpp
-        
-    Python API Documentation:
-        https://slsdetectorgroup.github.io/sls_detector/
-        
-    Further Documentation:
-        https://www.psi.ch/detectors/users-support
-        
-    
-    Support
-    -------
-
-    General Software related:
-        dhanya.thattil@psi.ch
-        anna.bergamaschi@psi.ch
-        
-    Python related:
-        erik.frojdh@psi.ch
-
+Draft
+- dr 4, 8, 16 in eiger -> speed 0, 32 stays same (speed 1)

cleansharedmemory.sh

@@ -1 +0,0 @@
-rm /dev/shm/slsDetectorPackage*;

cmake/Catch.cmake

@@ -0,0 +1,175 @@
+# Distributed under the OSI-approved BSD 3-Clause License.  See accompanying
+# file Copyright.txt or https://cmake.org/licensing for details.
+
+#[=======================================================================[.rst:
+Catch
+-----
+
+This module defines a function to help use the Catch test framework.
+
+The :command:`catch_discover_tests` discovers tests by asking the compiled test
+executable to enumerate its tests.  This does not require CMake to be re-run
+when tests change.  However, it may not work in a cross-compiling environment,
+and setting test properties is less convenient.
+
+This command is intended to replace use of :command:`add_test` to register
+tests, and will create a separate CTest test for each Catch test case.  Note
+that this is in some cases less efficient, as common set-up and tear-down logic
+cannot be shared by multiple test cases executing in the same instance.
+However, it provides more fine-grained pass/fail information to CTest, which is
+usually considered as more beneficial.  By default, the CTest test name is the
+same as the Catch name; see also ``TEST_PREFIX`` and ``TEST_SUFFIX``.
+
+.. command:: catch_discover_tests
+
+  Automatically add tests with CTest by querying the compiled test executable
+  for available tests::
+
+    catch_discover_tests(target
+                         [TEST_SPEC arg1...]
+                         [EXTRA_ARGS arg1...]
+                         [WORKING_DIRECTORY dir]
+                         [TEST_PREFIX prefix]
+                         [TEST_SUFFIX suffix]
+                         [PROPERTIES name1 value1...]
+                         [TEST_LIST var]
+    )
+
+  ``catch_discover_tests`` sets up a post-build command on the test executable
+  that generates the list of tests by parsing the output from running the test
+  with the ``--list-test-names-only`` argument.  This ensures that the full
+  list of tests is obtained.  Since test discovery occurs at build time, it is
+  not necessary to re-run CMake when the list of tests changes.
+  However, it requires that :prop_tgt:`CROSSCOMPILING_EMULATOR` is properly set
+  in order to function in a cross-compiling environment.
+
+  Additionally, setting properties on tests is somewhat less convenient, since
+  the tests are not available at CMake time.  Additional test properties may be
+  assigned to the set of tests as a whole using the ``PROPERTIES`` option.  If
+  more fine-grained test control is needed, custom content may be provided
+  through an external CTest script using the :prop_dir:`TEST_INCLUDE_FILES`
+  directory property.  The set of discovered tests is made accessible to such a
+  script via the ``<target>_TESTS`` variable.
+
+  The options are:
+
+  ``target``
+    Specifies the Catch executable, which must be a known CMake executable
+    target.  CMake will substitute the location of the built executable when
+    running the test.
+
+  ``TEST_SPEC arg1...``
+    Specifies test cases, wildcarded test cases, tags and tag expressions to
+    pass to the Catch executable with the ``--list-test-names-only`` argument.
+
+  ``EXTRA_ARGS arg1...``
+    Any extra arguments to pass on the command line to each test case.
+
+  ``WORKING_DIRECTORY dir``
+    Specifies the directory in which to run the discovered test cases.  If this
+    option is not provided, the current binary directory is used.
+
+  ``TEST_PREFIX prefix``
+    Specifies a ``prefix`` to be prepended to the name of each discovered test
+    case.  This can be useful when the same test executable is being used in
+    multiple calls to ``catch_discover_tests()`` but with different
+    ``TEST_SPEC`` or ``EXTRA_ARGS``.
+
+  ``TEST_SUFFIX suffix``
+    Similar to ``TEST_PREFIX`` except the ``suffix`` is appended to the name of
+    every discovered test case.  Both ``TEST_PREFIX`` and ``TEST_SUFFIX`` may
+    be specified.
+
+  ``PROPERTIES name1 value1...``
+    Specifies additional properties to be set on all tests discovered by this
+    invocation of ``catch_discover_tests``.
+
+  ``TEST_LIST var``
+    Make the list of tests available in the variable ``var``, rather than the
+    default ``<target>_TESTS``.  This can be useful when the same test
+    executable is being used in multiple calls to ``catch_discover_tests()``.
+    Note that this variable is only available in CTest.
+
+#]=======================================================================]
+
+#------------------------------------------------------------------------------
+function(catch_discover_tests TARGET)
+  cmake_parse_arguments(
+    ""
+    ""
+    "TEST_PREFIX;TEST_SUFFIX;WORKING_DIRECTORY;TEST_LIST"
+    "TEST_SPEC;EXTRA_ARGS;PROPERTIES"
+    ${ARGN}
+  )
+
+  if(NOT _WORKING_DIRECTORY)
+    set(_WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
+  endif()
+  if(NOT _TEST_LIST)
+    set(_TEST_LIST ${TARGET}_TESTS)
+  endif()
+
+  ## Generate a unique name based on the extra arguments
+  string(SHA1 args_hash "${_TEST_SPEC} ${_EXTRA_ARGS}")
+  string(SUBSTRING ${args_hash} 0 7 args_hash)
+
+  # Define rule to generate test list for aforementioned test executable
+  set(ctest_include_file "${CMAKE_CURRENT_BINARY_DIR}/${TARGET}_include-${args_hash}.cmake")
+  set(ctest_tests_file "${CMAKE_CURRENT_BINARY_DIR}/${TARGET}_tests-${args_hash}.cmake")
+  get_property(crosscompiling_emulator
+    TARGET ${TARGET}
+    PROPERTY CROSSCOMPILING_EMULATOR
+  )
+  add_custom_command(
+    TARGET ${TARGET} POST_BUILD
+    BYPRODUCTS "${ctest_tests_file}"
+    COMMAND "${CMAKE_COMMAND}"
+            -D "TEST_TARGET=${TARGET}"
+            -D "TEST_EXECUTABLE=$<TARGET_FILE:${TARGET}>"
+            -D "TEST_EXECUTOR=${crosscompiling_emulator}"
+            -D "TEST_WORKING_DIR=${_WORKING_DIRECTORY}"
+            -D "TEST_SPEC=${_TEST_SPEC}"
+            -D "TEST_EXTRA_ARGS=${_EXTRA_ARGS}"
+            -D "TEST_PROPERTIES=${_PROPERTIES}"
+            -D "TEST_PREFIX=${_TEST_PREFIX}"
+            -D "TEST_SUFFIX=${_TEST_SUFFIX}"
+            -D "TEST_LIST=${_TEST_LIST}"
+            -D "CTEST_FILE=${ctest_tests_file}"
+            -P "${_CATCH_DISCOVER_TESTS_SCRIPT}"
+    VERBATIM
+  )
+
+  file(WRITE "${ctest_include_file}"
+    "if(EXISTS \"${ctest_tests_file}\")\n"
+    "  include(\"${ctest_tests_file}\")\n"
+    "else()\n"
+    "  add_test(${TARGET}_NOT_BUILT-${args_hash} ${TARGET}_NOT_BUILT-${args_hash})\n"
+    "endif()\n"
+  )
+
+  if(NOT ${CMAKE_VERSION} VERSION_LESS "3.10.0") 
+    # Add discovered tests to directory TEST_INCLUDE_FILES
+    set_property(DIRECTORY
+      APPEND PROPERTY TEST_INCLUDE_FILES "${ctest_include_file}"
+    )
+  else()
+    # Add discovered tests as directory TEST_INCLUDE_FILE if possible
+    get_property(test_include_file_set DIRECTORY PROPERTY TEST_INCLUDE_FILE SET)
+    if (NOT ${test_include_file_set})
+      set_property(DIRECTORY
+        PROPERTY TEST_INCLUDE_FILE "${ctest_include_file}"
+      )
+    else()
+      message(FATAL_ERROR
+        "Cannot set more than one TEST_INCLUDE_FILE"
+      )
+    endif()
+  endif()
+
+endfunction()
+
+###############################################################################
+
+set(_CATCH_DISCOVER_TESTS_SCRIPT
+  ${CMAKE_CURRENT_LIST_DIR}/CatchAddTests.cmake
+)

cmake/CatchAddTests.cmake

@@ -0,0 +1,78 @@
+# Distributed under the OSI-approved BSD 3-Clause License.  See accompanying
+# file Copyright.txt or https://cmake.org/licensing for details.
+
+set(prefix "${TEST_PREFIX}")
+set(suffix "${TEST_SUFFIX}")
+set(spec ${TEST_SPEC})
+set(extra_args ${TEST_EXTRA_ARGS})
+set(properties ${TEST_PROPERTIES})
+set(script)
+set(suite)
+set(tests)
+
+function(add_command NAME)
+  set(_args "")
+  foreach(_arg ${ARGN})
+    if(_arg MATCHES "[^-./:a-zA-Z0-9_]")
+      set(_args "${_args} [==[${_arg}]==]") # form a bracket_argument
+    else()
+      set(_args "${_args} ${_arg}")
+    endif()
+  endforeach()
+  set(script "${script}${NAME}(${_args})\n" PARENT_SCOPE)
+endfunction()
+
+# Run test executable to get list of available tests
+if(NOT EXISTS "${TEST_EXECUTABLE}")
+  message(FATAL_ERROR
+    "Specified test executable '${TEST_EXECUTABLE}' does not exist"
+  )
+endif()
+execute_process(
+  COMMAND ${TEST_EXECUTOR} "${TEST_EXECUTABLE}" ${spec} --list-test-names-only
+  OUTPUT_VARIABLE output
+  RESULT_VARIABLE result
+)
+# Catch --list-test-names-only reports the number of tests, so 0 is... surprising
+if(${result} EQUAL 0)
+  message(WARNING
+    "Test executable '${TEST_EXECUTABLE}' contains no tests!\n"
+  )
+elseif(${result} LESS 0)
+  message(FATAL_ERROR
+    "Error running test executable '${TEST_EXECUTABLE}':\n"
+    "  Result: ${result}\n"
+    "  Output: ${output}\n"
+  )
+endif()
+
+string(REPLACE "\n" ";" output "${output}")
+
+# Parse output
+foreach(line ${output})
+  set(test ${line})
+  # use escape commas to handle properly test cases with commans inside the name
+  string(REPLACE "," "\\," test_name ${test})
+  # ...and add to script
+  add_command(add_test
+    "${prefix}${test}${suffix}"
+    ${TEST_EXECUTOR}
+    "${TEST_EXECUTABLE}"
+    "${test_name}"
+    ${extra_args}
+  )
+  add_command(set_tests_properties
+    "${prefix}${test}${suffix}"
+    PROPERTIES
+    WORKING_DIRECTORY "${TEST_WORKING_DIR}"
+    ${properties}
+  )
+  list(APPEND tests "${prefix}${test}${suffix}")
+endforeach()
+
+# Create a list of all discovered tests, which users may use to e.g. set
+# properties on the tests
+add_command(set ${TEST_LIST} ${tests})
+
+# Write CTest script
+file(WRITE "${CTEST_FILE}" "${script}")

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/FindSphinx.cmake

@@ -0,0 +1,11 @@
+#Look for an executable called sphinx-build
+find_program(SPHINX_EXECUTABLE
+             NAMES sphinx-build
+             DOC "Path to sphinx-build executable")
+ 
+include(FindPackageHandleStandardArgs)
+ 
+#Handle standard arguments to find_package like REQUIRED and QUIET
+find_package_handle_standard_args(Sphinx
+                                  "Failed to find sphinx-build executable"
+                                  SPHINX_EXECUTABLE)

cmake/FindZeroMQ.cmake

@@ -0,0 +1,112 @@
+
+# This file is originally from https://github.com/zeromq/azmq and distributed 
+# under Boost Software Lincese 1.0
+# Boost Software License - Version 1.0 - August 17th, 2003
+
+# Permission is hereby granted, free of charge, to any person or organization
+# obtaining a copy of the software and accompanying documentation covered by
+# this license (the "Software") to use, reproduce, display, distribute,
+# execute, and transmit the Software, and to prepare derivative works of the
+# Software, and to permit third-parties to whom the Software is furnished to
+# do so, all subject to the following:
+
+# The copyright notices in the Software and this entire statement, including
+# the above license grant, this restriction and the following disclaimer,
+# must be included in all copies of the Software, in whole or in part, and
+# all derivative works of the Software, unless such copies or derivative
+# works are solely in the form of machine-executable object code generated by
+# a source language processor.
+
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+# SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+# FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+# ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+# --------------------------------------------------------------------------------
+
+# Find ZeroMQ Headers/Libs
+
+# Variables
+# ZMQ_ROOT - set this to a location where ZeroMQ may be found
+#
+# ZeroMQ_FOUND - True of ZeroMQ found
+# ZeroMQ_INCLUDE_DIRS - Location of ZeroMQ includes
+# ZeroMQ_LIBRARIES - ZeroMQ libraries
+
+include(FindPackageHandleStandardArgs)
+
+if (NOT ZMQ_ROOT)
+    set(ZMQ_ROOT "$ENV{ZMQ_ROOT}")
+endif()
+
+if (NOT ZMQ_ROOT)
+    find_path(_ZeroMQ_ROOT NAMES include/zmq.h)
+else()
+    set(_ZeroMQ_ROOT "${ZMQ_ROOT}")
+endif()
+
+find_path(ZeroMQ_INCLUDE_DIRS NAMES zmq.h HINTS ${_ZeroMQ_ROOT}/include)
+
+if (ZeroMQ_INCLUDE_DIRS)
+    set(_ZeroMQ_H ${ZeroMQ_INCLUDE_DIRS}/zmq.h)
+
+    function(_zmqver_EXTRACT _ZeroMQ_VER_COMPONENT _ZeroMQ_VER_OUTPUT)
+        set(CMAKE_MATCH_1 "0")
+        set(_ZeroMQ_expr "^[ \\t]*#define[ \\t]+${_ZeroMQ_VER_COMPONENT}[ \\t]+([0-9]+)$")
+        file(STRINGS "${_ZeroMQ_H}" _ZeroMQ_ver REGEX "${_ZeroMQ_expr}")
+        string(REGEX MATCH "${_ZeroMQ_expr}" ZeroMQ_ver "${_ZeroMQ_ver}")
+        set(${_ZeroMQ_VER_OUTPUT} "${CMAKE_MATCH_1}" PARENT_SCOPE)
+    endfunction()
+
+    _zmqver_EXTRACT("ZMQ_VERSION_MAJOR" ZeroMQ_VERSION_MAJOR)
+    _zmqver_EXTRACT("ZMQ_VERSION_MINOR" ZeroMQ_VERSION_MINOR)
+    _zmqver_EXTRACT("ZMQ_VERSION_PATCH" ZeroMQ_VERSION_PATCH)
+
+    message(STATUS "ZeroMQ version: ${ZeroMQ_VERSION_MAJOR}.${ZeroMQ_VERSION_MINOR}.${ZeroMQ_VERSION_PATCH}")
+
+    # We should provide version to find_package_handle_standard_args in the same format as it was requested,
+    # otherwise it can't check whether version matches exactly.
+    if (ZeroMQ_FIND_VERSION_COUNT GREATER 2)
+        set(ZeroMQ_VERSION "${ZeroMQ_VERSION_MAJOR}.${ZeroMQ_VERSION_MINOR}.${ZeroMQ_VERSION_PATCH}")
+    else()
+        # User has requested ZeroMQ version without patch part => user is not interested in specific patch =>
+        # any patch should be an exact match.
+        set(ZeroMQ_VERSION "${ZeroMQ_VERSION_MAJOR}.${ZeroMQ_VERSION_MINOR}")
+    endif()
+
+    if (NOT ${CMAKE_CXX_PLATFORM_ID} STREQUAL "Windows")
+        find_library(ZeroMQ_LIBRARIES NAMES zmq HINTS ${_ZeroMQ_ROOT}/lib)
+    else()
+        find_library(
+            ZeroMQ_LIBRARY_RELEASE
+            NAMES
+                libzmq
+                "libzmq-${CMAKE_VS_PLATFORM_TOOLSET}-mt-${ZeroMQ_VERSION_MAJOR}_${ZeroMQ_VERSION_MINOR}_${ZeroMQ_VERSION_PATCH}"
+            HINTS
+                ${_ZeroMQ_ROOT}/lib
+            )
+
+        find_library(
+            ZeroMQ_LIBRARY_DEBUG
+            NAMES
+                libzmq_d
+                "libzmq-${CMAKE_VS_PLATFORM_TOOLSET}-mt-gd-${ZeroMQ_VERSION_MAJOR}_${ZeroMQ_VERSION_MINOR}_${ZeroMQ_VERSION_PATCH}"
+            HINTS
+                ${_ZeroMQ_ROOT}/lib)
+
+        # On Windows we have to use corresponding version (i.e. Release or Debug) of ZeroMQ because of `errno` CRT global variable
+        # See more at http://www.drdobbs.com/avoiding-the-visual-c-runtime-library/184416623
+        set(ZeroMQ_LIBRARIES optimized "${ZeroMQ_LIBRARY_RELEASE}" debug "${ZeroMQ_LIBRARY_DEBUG}")
+    endif()
+endif()
+
+find_package_handle_standard_args(ZeroMQ FOUND_VAR ZeroMQ_FOUND
+    REQUIRED_VARS ZeroMQ_INCLUDE_DIRS ZeroMQ_LIBRARIES
+    VERSION_VAR ZeroMQ_VERSION)
+
+if (ZeroMQ_FOUND)
+    mark_as_advanced(ZeroMQ_INCLUDE_DIRS ZeroMQ_LIBRARIES ZeroMQ_VERSION
+        ZeroMQ_VERSION_MAJOR ZeroMQ_VERSION_MINOR ZeroMQ_VERSION_PATCH)
+endif()

cmake/ParseAndAddCatchTests.cmake

@@ -0,0 +1,203 @@
+#==================================================================================================#
+#  supported macros                                                                                #
+#    - TEST_CASE,                                                                                  #
+#    - SCENARIO,                                                                                   #
+#    - TEST_CASE_METHOD,                                                                           #
+#    - CATCH_TEST_CASE,                                                                            #
+#    - CATCH_SCENARIO,                                                                             #
+#    - CATCH_TEST_CASE_METHOD.                                                                     #
+#                                                                                                  #
+#  Usage                                                                                           #
+# 1. make sure this module is in the path or add this otherwise:                                   #
+#    set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake.modules/")              #
+# 2. make sure that you've enabled testing option for the project by the call:                     #
+#    enable_testing()                                                                              #
+# 3. add the lines to the script for testing target (sample CMakeLists.txt):                       #
+#        project(testing_target)                                                                   #
+#        set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake.modules/")          #
+#        enable_testing()                                                                          #
+#                                                                                                  #
+#        find_path(CATCH_INCLUDE_DIR "catch.hpp")                                                  #
+#        include_directories(${INCLUDE_DIRECTORIES} ${CATCH_INCLUDE_DIR})                          #
+#                                                                                                  #
+#        file(GLOB SOURCE_FILES "*.cpp")                                                           #
+#        add_executable(${PROJECT_NAME} ${SOURCE_FILES})                                           #
+#                                                                                                  #
+#        include(ParseAndAddCatchTests)                                                            #
+#        ParseAndAddCatchTests(${PROJECT_NAME})                                                    #
+#                                                                                                  #
+# The following variables affect the behavior of the script:                                       #
+#                                                                                                  #
+#    PARSE_CATCH_TESTS_VERBOSE (Default OFF)                                                       #
+#    -- enables debug messages                                                                     #
+#    PARSE_CATCH_TESTS_NO_HIDDEN_TESTS (Default OFF)                                               #
+#    -- excludes tests marked with [!hide], [.] or [.foo] tags                                     #
+#    PARSE_CATCH_TESTS_ADD_FIXTURE_IN_TEST_NAME (Default ON)                                       #
+#    -- adds fixture class name to the test name                                                   #
+#    PARSE_CATCH_TESTS_ADD_TARGET_IN_TEST_NAME (Default ON)                                        #
+#    -- adds cmake target name to the test name                                                    #
+#    PARSE_CATCH_TESTS_ADD_TO_CONFIGURE_DEPENDS (Default OFF)                                      #
+#    -- causes CMake to rerun when file with tests changes so that new tests will be discovered    #
+#                                                                                                  #
+# One can also set (locally) the optional variable OptionalCatchTestLauncher to precise the way    #
+# a test should be run. For instance to use test MPI, one can write                                #
+#     set(OptionalCatchTestLauncher ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${NUMPROC})                 #
+# just before calling this ParseAndAddCatchTests function                                          #
+#                                                                                                  #
+#==================================================================================================#
+
+cmake_minimum_required(VERSION 2.8.8)
+
+option(PARSE_CATCH_TESTS_VERBOSE "Print Catch to CTest parser debug messages" OFF)
+option(PARSE_CATCH_TESTS_NO_HIDDEN_TESTS "Exclude tests with [!hide], [.] or [.foo] tags" OFF)
+option(PARSE_CATCH_TESTS_ADD_FIXTURE_IN_TEST_NAME "Add fixture class name to the test name" ON)
+option(PARSE_CATCH_TESTS_ADD_TARGET_IN_TEST_NAME "Add target name to the test name" ON)
+option(PARSE_CATCH_TESTS_ADD_TO_CONFIGURE_DEPENDS "Add test file to CMAKE_CONFIGURE_DEPENDS property" OFF)
+
+function(PrintDebugMessage)
+    if(PARSE_CATCH_TESTS_VERBOSE)
+            message(STATUS "ParseAndAddCatchTests: ${ARGV}")
+    endif()
+endfunction()
+
+# This removes the contents between
+#  - block comments (i.e. /* ... */)
+#  - full line comments (i.e. // ... )
+# contents have been read into '${CppCode}'.
+# !keep partial line comments
+function(RemoveComments CppCode)
+  string(ASCII 2 CMakeBeginBlockComment)
+  string(ASCII 3 CMakeEndBlockComment)
+  string(REGEX REPLACE "/\\*" "${CMakeBeginBlockComment}" ${CppCode} "${${CppCode}}")
+  string(REGEX REPLACE "\\*/" "${CMakeEndBlockComment}" ${CppCode} "${${CppCode}}")
+  string(REGEX REPLACE "${CMakeBeginBlockComment}[^${CMakeEndBlockComment}]*${CMakeEndBlockComment}" "" ${CppCode} "${${CppCode}}")
+  string(REGEX REPLACE "\n[ \t]*//+[^\n]+" "\n" ${CppCode} "${${CppCode}}")
+
+  set(${CppCode} "${${CppCode}}" PARENT_SCOPE)
+endfunction()
+
+# Worker function
+function(ParseFile SourceFile TestTarget)
+    # According to CMake docs EXISTS behavior is well-defined only for full paths.
+    get_filename_component(SourceFile ${SourceFile} ABSOLUTE)
+    if(NOT EXISTS ${SourceFile})
+        message(WARNING "Cannot find source file: ${SourceFile}")
+        return()
+    endif()
+    PrintDebugMessage("parsing ${SourceFile}")
+    file(STRINGS ${SourceFile} Contents NEWLINE_CONSUME)
+
+    # Remove block and fullline comments
+    RemoveComments(Contents)
+
+    # Find definition of test names
+    string(REGEX MATCHALL "[ \t]*(CATCH_)?(TEST_CASE_METHOD|SCENARIO|TEST_CASE)[ \t]*\\([^\)]+\\)+[ \t\n]*{+[ \t]*(//[^\n]*[Tt][Ii][Mm][Ee][Oo][Uu][Tt][ \t]*[0-9]+)*" Tests "${Contents}")
+
+    if(PARSE_CATCH_TESTS_ADD_TO_CONFIGURE_DEPENDS AND Tests)
+      PrintDebugMessage("Adding ${SourceFile} to CMAKE_CONFIGURE_DEPENDS property")
+      set_property(
+        DIRECTORY
+        APPEND
+        PROPERTY CMAKE_CONFIGURE_DEPENDS ${SourceFile}
+      )
+    endif()
+
+    foreach(TestName ${Tests})
+        # Strip newlines
+        string(REGEX REPLACE "\\\\\n|\n" "" TestName "${TestName}")
+
+        # Get test type and fixture if applicable
+        string(REGEX MATCH "(CATCH_)?(TEST_CASE_METHOD|SCENARIO|TEST_CASE)[ \t]*\\([^,^\"]*" TestTypeAndFixture "${TestName}")
+        string(REGEX MATCH "(CATCH_)?(TEST_CASE_METHOD|SCENARIO|TEST_CASE)" TestType "${TestTypeAndFixture}")
+        string(REGEX REPLACE "${TestType}\\([ \t]*" "" TestFixture "${TestTypeAndFixture}")
+
+        # Get string parts of test definition
+        string(REGEX MATCHALL "\"+([^\\^\"]|\\\\\")+\"+" TestStrings "${TestName}")
+
+        # Strip wrapping quotation marks
+        string(REGEX REPLACE "^\"(.*)\"$" "\\1" TestStrings "${TestStrings}")
+        string(REPLACE "\";\"" ";" TestStrings "${TestStrings}")
+
+        # Validate that a test name and tags have been provided
+        list(LENGTH TestStrings TestStringsLength)
+        if(TestStringsLength GREATER 2 OR TestStringsLength LESS 1)
+            message(FATAL_ERROR "You must provide a valid test name and tags for all tests in ${SourceFile}")
+        endif()
+
+        # Assign name and tags
+        list(GET TestStrings 0 Name)
+        if("${TestType}" STREQUAL "SCENARIO")
+            set(Name "Scenario: ${Name}")
+        endif()
+        if(PARSE_CATCH_TESTS_ADD_FIXTURE_IN_TEST_NAME AND TestFixture)
+            set(CTestName "${TestFixture}:${Name}")
+        else()
+            set(CTestName "${Name}")
+        endif()
+        if(PARSE_CATCH_TESTS_ADD_TARGET_IN_TEST_NAME)
+            set(CTestName "${TestTarget}:${CTestName}")
+        endif()
+        # add target to labels to enable running all tests added from this target
+        set(Labels ${TestTarget})
+        if(TestStringsLength EQUAL 2)
+            list(GET TestStrings 1 Tags)
+            string(TOLOWER "${Tags}" Tags)
+            # remove target from labels if the test is hidden
+            if("${Tags}" MATCHES ".*\\[!?(hide|\\.)\\].*")
+                list(REMOVE_ITEM Labels ${TestTarget})
+            endif()
+            string(REPLACE "]" ";" Tags "${Tags}")
+            string(REPLACE "[" "" Tags "${Tags}")
+        else()
+          # unset tags variable from previous loop
+          unset(Tags)
+        endif()
+
+        list(APPEND Labels ${Tags})
+
+        list(FIND Labels "!hide" IndexOfHideLabel)
+        set(HiddenTagFound OFF)
+        foreach(label ${Labels})
+            string(REGEX MATCH "^!hide|^\\." result ${label})
+            if(result)
+                set(HiddenTagFound ON)
+                break()
+            endif(result)
+        endforeach(label)
+        if(PARSE_CATCH_TESTS_NO_HIDDEN_TESTS AND ${HiddenTagFound} AND ${CMAKE_VERSION} VERSION_LESS "3.9")
+            PrintDebugMessage("Skipping test \"${CTestName}\" as it has [!hide], [.] or [.foo] label")
+        else()
+            PrintDebugMessage("Adding test \"${CTestName}\"")
+            if(Labels)
+                PrintDebugMessage("Setting labels to ${Labels}")
+            endif()
+
+            # Escape commas in the test spec
+            string(REPLACE "," "\\," Name ${Name})
+
+            # Add the test and set its properties
+            add_test(NAME "\"${CTestName}\"" COMMAND ${OptionalCatchTestLauncher} ${TestTarget} ${Name} ${AdditionalCatchParameters})
+            # Old CMake versions do not document VERSION_GREATER_EQUAL, so we use VERSION_GREATER with 3.8 instead
+            if(PARSE_CATCH_TESTS_NO_HIDDEN_TESTS AND ${HiddenTagFound} AND ${CMAKE_VERSION} VERSION_GREATER "3.8")
+                PrintDebugMessage("Setting DISABLED test property")
+                set_tests_properties("\"${CTestName}\"" PROPERTIES DISABLED ON)
+            else()
+                set_tests_properties("\"${CTestName}\"" PROPERTIES FAIL_REGULAR_EXPRESSION "No tests ran"
+                                                        LABELS "${Labels}")
+            endif()
+        endif()
+
+
+    endforeach()
+endfunction()
+
+# entry point
+function(ParseAndAddCatchTests TestTarget)
+    PrintDebugMessage("Started parsing ${TestTarget}")
+    get_target_property(SourceFiles ${TestTarget} SOURCES)
+    PrintDebugMessage("Found the following sources: ${SourceFiles}")
+    foreach(SourceFile ${SourceFiles})
+        ParseFile(${SourceFile} ${TestTarget})
+    endforeach()
+    PrintDebugMessage("Finished parsing ${TestTarget}")
+endfunction()

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

@@ -0,0 +1,34 @@
+# This cmake code creates the configuration that is found and used by
+# find_package() of another cmake project
+
+# get lower and upper case project name for the configuration files
+
+# configure and install the configuration files
+include(CMakePackageConfigHelpers)
+
+configure_package_config_file(
+  "${CMAKE_SOURCE_DIR}/cmake/project-config.cmake.in"
+  "${PROJECT_BINARY_DIR}/${PROJECT_NAME_LOWER}-config.cmake"
+  INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME_LOWER}
+  PATH_VARS CMAKE_INSTALL_DIR)
+
+write_basic_package_version_file(
+  "${PROJECT_BINARY_DIR}/${PROJECT_NAME_LOWER}-config-version.cmake"
+  VERSION ${PROJECT_VERSION}
+  COMPATIBILITY SameMajorVersion
+)
+
+install(FILES
+  "${PROJECT_BINARY_DIR}/${PROJECT_NAME_LOWER}-config.cmake"
+  "${PROJECT_BINARY_DIR}/${PROJECT_NAME_LOWER}-config-version.cmake"
+  COMPONENT devel
+  DESTINATION ${CMAKE_INSTALL_DIR}
+)
+
+if (PROJECT_LIBRARIES OR PROJECT_STATIC_LIBRARIES)
+  install(
+    EXPORT "${TARGETS_EXPORT_NAME}"
+    FILE ${PROJECT_NAME_LOWER}-targets.cmake
+    DESTINATION ${CMAKE_INSTALL_DIR}
+    )
+endif ()

cmake/project-config.cmake.in

@@ -0,0 +1,24 @@
+# Config file for @PROJECT_NAME_LOWER@
+#
+# It defines the following variables:
+#
+# @PROJECT_NAME_UPPER@_INCLUDE_DIRS     - include directory
+# @PROJECT_NAME_UPPER@_LIBRARIES        - all dynamic libraries
+# @PROJECT_NAME_UPPER@_STATIC_LIBRARIES - all static libraries
+
+@PACKAGE_INIT@
+
+include(CMakeFindDependencyMacro)
+
+set(SLS_USE_HDF5 "@SLS_USE_HDF5@")
+
+# Add optional dependencies here
+find_dependency(Threads)
+if (SLS_USE_HDF5)
+    find_dependency(HDF5)
+endif ()
+
+set_and_check(@PROJECT_NAME_UPPER@_CMAKE_INCLUDE_DIRS "@PACKAGE_CMAKE_INSTALL_DIR@")
+
+include("${CMAKE_CURRENT_LIST_DIR}/@TARGETS_EXPORT_NAME@.cmake")
+check_required_components("@PROJECT_NAME@")

cmake/project_version.cc.in

@@ -0,0 +1,14 @@
+#include "project_version.h"
+/// project version as major.minor.patch string
+const char* @PROJECT_NAME@_runtime_project_version(){ return "@PROJECT_VERSION@"; }
+/// package version as string, possibly with git commit: v1.2.3+4+g56789abc
+const char* @PROJECT_NAME@_runtime_package_version(){ return "@PACKAGE_VERSION@"; }
+/// project version as integer: major * 10000 + minor * 100 + patch
+int @PROJECT_NAME@_runtime_version_int()  { return @PROJECT_VERSION_INT@; }
+/// project version as integer: major
+int @PROJECT_NAME@_runtime_version_major(){ return @PACKAGE_VERSION_MAJOR@; }
+/// project version as integer: minor
+int @PROJECT_NAME@_runtime_version_minor(){ return @PACKAGE_VERSION_MINOR@; }
+/// project version as integer: patch
+int @PROJECT_NAME@_runtime_version_patch(){ return @PACKAGE_VERSION_PATCH@; }
+

cmake/project_version.cmake

@@ -0,0 +1,154 @@
+#
+# Sets PROJECT_VERSION and PACKAGE_VERSION
+#
+
+# Don't set PROJECT_VERSION to empty string when no VERSION is given to project() command.
+#if(POLICY CMP0048)
+#  cmake_policy(SET CMP0048 OLD)
+#endif()
+
+# Split a version number into separate components
+# version the version number to split
+# major variable name to store the major version in
+# minor variable name to store the minor version in
+# patch variable name to store the patch version in
+# extra variable name to store a version suffix in
+function(version_split version major minor patch extra)
+    string(REGEX MATCH "([0-9]+)\\.([0-9]+)\\.([0-9]+)(.*)?" version_valid ${version})
+    if(version_valid)
+        string(REGEX REPLACE "([0-9]+)\\.([0-9]+)\\.([0-9]+)(.*)?" "\\1;\\2;\\3;\\4" VERSION_MATCHES ${version})
+        list(GET VERSION_MATCHES 0 version_major)
+        set(${major} ${version_major} PARENT_SCOPE)
+        list(GET VERSION_MATCHES 1 version_minor)
+        set(${minor} ${version_minor} PARENT_SCOPE)
+        list(GET VERSION_MATCHES 2 version_patch)
+        set(${patch} ${version_patch} PARENT_SCOPE)
+        list(GET VERSION_MATCHES 3 version_extra)
+        set(${extra} ${version_extra} PARENT_SCOPE)
+    else(version_valid)
+        message(AUTHOR_WARNING "Bad version ${version}; falling back to 0 (have you made an initial release?)")
+        set(${major} "0" PARENT_SCOPE)
+        set(${minor} "0" PARENT_SCOPE)
+        set(${patch} "0" PARENT_SCOPE)
+        set(${extra} "" PARENT_SCOPE)
+    endif(version_valid)
+endfunction(version_split)
+
+##############################
+# get PROJECT_VERSION from git
+##############################
+find_program(GIT_CMD git)
+mark_as_advanced(GIT_CMD)
+if (GIT_CMD)
+    execute_process(COMMAND ${GIT_CMD} rev-parse --show-toplevel
+            WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+            OUTPUT_VARIABLE GIT_TOPLEVEL
+            ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+endif()
+if (GIT_CMD AND NOT "${GIT_TOPLEVEL}" STREQUAL "")
+    execute_process(COMMAND ${GIT_CMD} rev-parse --short HEAD
+            WORKING_DIRECTORY ${GIT_TOPLEVEL}
+            OUTPUT_VARIABLE GIT_SHA1
+            OUTPUT_STRIP_TRAILING_WHITESPACE)
+    #message(STATUS "GIT_SHA1: " ${GIT_SHA1})
+    execute_process(COMMAND ${GIT_CMD} describe --match "*[0-9].[0-9]*" HEAD
+            WORKING_DIRECTORY ${GIT_TOPLEVEL}
+            OUTPUT_VARIABLE GIT_DESCRIBE
+            ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+    #message(STATUS "GIT_DESCRIBE: " ${GIT_DESCRIBE})
+
+    # if (GIT_DESCRIBE)
+    #     string(REGEX REPLACE "v?([0-9.]+).*" "\\1" GIT_VERSION ${GIT_DESCRIBE})
+    #     message(STATUS "GIT_VERSION: " ${GIT_VERSION})
+
+    #     # as package version we use the full version from git describe: 1.7.1+7+ge324c81
+    #     if (GIT_DESCRIBE MATCHES ".*-g.*")
+    #         # convert a git describe string to usable debian version, e.g. v1.7.1-7-ge324c81 to 1.7.1+7+ge324c81
+    #         string(REGEX REPLACE "v?([0-9]*.[0-9.]*).*-([0-9]*)-([a-g0-9]*)" "\\1+\\2+\\3" GIT_FULL_VERSION ${GIT_DESCRIBE})
+    #     else()
+    #         # current HEAD is git tag (i.e. releaase), directly use the version
+    #         set(GIT_FULL_VERSION ${GIT_VERSION})
+    #     endif()
+    # else ()
+    #     # no (suitable) tag found
+    #     set(GIT_VERSION "0.0.0")
+    #     # get number of commits in repo
+    #     execute_process(COMMAND ${GIT_CMD} rev-list --count HEAD
+    #             WORKING_DIRECTORY ${GIT_TOPLEVEL}
+    #             OUTPUT_VARIABLE GIT_COMMIT_COUNT
+    #             OUTPUT_STRIP_TRAILING_WHITESPACE)
+    #     set(GIT_FULL_VERSION 0.0.0+${GIT_COMMIT_COUNT}+g${GIT_SHA1})
+    # endif ()
+endif ()
+
+# get version from package.xml if it exists
+if (EXISTS "${PROJECT_SOURCE_DIR}/package.xml")
+    file(STRINGS "${PROJECT_SOURCE_DIR}/package.xml" PACKAGE_XML_VERSION_LINE REGEX <version>[0-9.]*</version>)
+    string(REGEX REPLACE .*<version>\([0-9.]*\)</version>.* \\1 PACKAGE_XML_VERSION "${PACKAGE_XML_VERSION_LINE}")
+    MESSAGE(STATUS "PACKAGE_XML_VERSION: " ${PACKAGE_XML_VERSION})
+endif ()
+
+# set version (if not already manually specified)
+# check versions from different sources and set actually used version
+if (NOT PROJECT_VERSION)
+    # set PROJECT_VERSION to MAJOR.MINOR.PATCH
+    # PACKAGE_VERSION can have extra info
+    if (GIT_VERSION)
+        set(PROJECT_VERSION ${GIT_VERSION})
+        set(PACKAGE_VERSION ${GIT_FULL_VERSION})
+    elseif (PACKAGE_XML_VERSION)
+        set(PROJECT_VERSION ${PACKAGE_XML_VERSION})
+        set(PACKAGE_VERSION ${PROJECT_VERSION})
+    else ()
+        message(WARNING "PROJECT_VERSION not set. Defaulting to 0.0.0")
+        set(PROJECT_VERSION "0.0.0")
+    endif ()
+endif ()
+# if (NOT PACKAGE_VERSION)
+    # message(WARNING "PACKAGE_VERSION not set! Falling back to (${PROJECT_VERSION})")
+    set(PACKAGE_VERSION ${PROJECT_VERSION})
+# endif ()
+
+# warn if versions don't match
+if (GIT_VERSION AND NOT GIT_VERSION MATCHES ${PROJECT_VERSION})
+    message(WARNING "Version from git (${GIT_VERSION}) doesn't match PROJECT_VERSION (${PROJECT_VERSION})")
+endif()
+if (PACKAGE_XML_VERSION AND NOT PACKAGE_XML_VERSION MATCHES ${PROJECT_VERSION})
+    message(WARNING "Version from package.xml (${PACKAGE_XML_VERSION}) doesn't match PROJECT_VERSION (${PROJECT_VERSION})")
+endif()
+
+message(STATUS "PROJECT_VERSION: " ${PROJECT_VERSION})
+message(STATUS "PACKAGE_VERSION: " ${PACKAGE_VERSION})
+
+
+version_split(${PROJECT_VERSION} PACKAGE_VERSION_MAJOR PACKAGE_VERSION_MINOR PACKAGE_VERSION_PATCH extra)
+#message(STATUS "PACKAGE_VERSION_MAJOR: " ${PACKAGE_VERSION_MAJOR})
+#message(STATUS "PACKAGE_VERSION_MINOR: " ${PACKAGE_VERSION_MINOR})
+#message(STATUS "PACKAGE_VERSION_PATCH: " ${PACKAGE_VERSION_PATCH})
+
+# generate an integer version number: major * 10000 + minor * 100 + patch
+math(EXPR PROJECT_VERSION_INT "${PACKAGE_VERSION_MAJOR} * 10000 + ${PACKAGE_VERSION_MINOR} * 100 + ${PACKAGE_VERSION_PATCH}")
+
+# make PROJECT_VERSION available as define in the project source
+#add_definitions(-DPROJECT_VERSION="${PROJECT_VERSION}")
+#add_definitions(-DPROJECT_VERSION_INT=${PROJECT_VERSION_INT})
+#add_definitions(-DPACKAGE_VERSION="${PACKAGE_VERSION}")
+#add_definitions(-DPACKAGE_VERSION_MAJOR=${PACKAGE_VERSION_MAJOR})
+#add_definitions(-DPACKAGE_VERSION_MINOR=${PACKAGE_VERSION_MINOR})
+#add_definitions(-DPACKAGE_VERSION_PATCH=${PACKAGE_VERSION_PATCH})
+
+# set ABI version to major.minor, which will be used for the SOVERSION
+set(abiversion "${PACKAGE_VERSION_MAJOR}.${PACKAGE_VERSION_MINOR}")
+
+# generate a version.h file in the binary output dir, don't forget to install it...
+string(TOUPPER "${PROJECT_NAME}" PROJECT_NAME_UPPER)
+
+# These files provide compile-time and runtime version information about your project.
+# To offer the version info to the users of your library, you need to
+# adapt the following lines in your respective CMakeLists.txt:
+#   add_library(<yourlibraryname> SHARED <your code files> ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}/project_version.cc)
+#   install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}/project_version.h COMPONENT dev DESTINATION include/<your-include-dir>)
+# To use it within your library or tests you need to add the include directory:
+# > target_include_directories(yourtarget PUBLIC ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME})
+configure_file(${CMAKE_CURRENT_LIST_DIR}/project_version.h.in  ${PROJECT_NAME}/project_version.h @ONLY)
+configure_file(${CMAKE_CURRENT_LIST_DIR}/project_version.cc.in ${PROJECT_NAME}/project_version.cc @ONLY)

cmake/project_version.h.in

@@ -0,0 +1,34 @@
+#ifndef @PROJECT_NAME_UPPER@_VERSION_H_
+#define @PROJECT_NAME_UPPER@_VERSION_H_
+
+/// project version as major.minor.patch string
+#define @PROJECT_NAME_UPPER@_VERSION "@PROJECT_VERSION@"
+/// project version as integer: major * 10000 + minor * 100 + patch
+#define @PROJECT_NAME_UPPER@_VERSION_INT @PROJECT_VERSION_INT@
+#define @PROJECT_NAME_UPPER@_VERSION_MAJOR @PACKAGE_VERSION_MAJOR@
+#define @PROJECT_NAME_UPPER@_VERSION_MINOR @PACKAGE_VERSION_MINOR@
+#define @PROJECT_NAME_UPPER@_VERSION_PATCH @PACKAGE_VERSION_PATCH@
+/// package version as string, possibly with git commit: v1.2.3+4+g56789abc
+#define @PROJECT_NAME_UPPER@_PACKAGE_VERSION "@PACKAGE_VERSION@"
+
+///runtime versions, where the above values are linked into a lib and therefore reflect the version
+///of the library itself (not the version of the header at compile time of the user code)
+const char* @PROJECT_NAME@_runtime_project_version();
+const char* @PROJECT_NAME@_runtime_package_version();
+int @PROJECT_NAME@_runtime_version_int();
+int @PROJECT_NAME@_runtime_version_major();
+int @PROJECT_NAME@_runtime_version_minor();
+int @PROJECT_NAME@_runtime_version_patch();
+
+///Check consistency of runtime vs compile-time version number. I.e. the header used
+///for compilation was from the same version as the linked library.
+inline bool @PROJECT_NAME@_check_version_consistency(bool major_minor_only)
+{
+  return @PROJECT_NAME@_runtime_version_major() == @PROJECT_NAME_UPPER@_VERSION_MAJOR &&
+         @PROJECT_NAME@_runtime_version_minor() == @PROJECT_NAME_UPPER@_VERSION_MINOR &&
+         (major_minor_only ||
+          @PROJECT_NAME@_runtime_version_patch() == @PROJECT_NAME_UPPER@_VERSION_PATCH);
+}
+
+
+#endif

cmk.sh

@@ -7,6 +7,11 @@ TEXTCLIENT=0
 RECEIVER=0
 GUI=0
 DEBUG=0
+PYTHON=0
+TESTS=0
+SIMULATOR=0
+CTBGUI=0
+MANUALS=0
 
 
 CLEAN=0
@@ -15,17 +20,28 @@ CMAKE_PRE=""
 CMAKE_POST=""
 
 usage() { echo -e "
-Usage: $0 [-c] [-b] [-h] [-d <HDF5 directory>] [-j]
+Usage: $0 [-c] [-b] [-p] [e] [t] [r] [g] [s] [u] [i] [m] [-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
+ -m: Manuals
+
+Rebuild when you switch to a new build and compile in parallel:
+./cmk.sh -bj5
+
+Rebuild python
+./cmk.sh -p
  
 For only make:
 ./cmk.sh
@@ -55,12 +71,17 @@ For rebuilding only certain sections
  
  " ; exit 1; }
 
-while getopts ":bchd:j:trge" opt ; do
+while getopts ":bpchd:j:trgeisum" opt ; do
 	case $opt in
 	b) 
 		echo "Building of CMake files Required"
 		REBUILD=1
 		;;
+	p)
+    	echo "Compiling Options: Python" 
+		PYTHON=1
+		REBUILD=1
+		;;   
 	c) 
 		echo "Clean Required"
 		CLEAN=1
@@ -96,42 +117,61 @@ while getopts ":bchd:j:trge" opt ; do
 	e)
 		echo "Compiling Options: Debug" 
 		DEBUG=1
-		;;    
-    \?)
-     	echo "Invalid option: -$OPTARG" 
+		;;   
+	i)
+		echo "Compiling Options: Tests" 
+		TESTS=1
+		;;   
+	s)
+		echo "Compiling Options: Simulator" 
+		SIMULATOR=1
+		;; 
+	m)	
+		echo "Compiling Manuals"
+		MANUALS=1
+		;;
+	u)
+		echo "Compiling Options: Chip Test Gui"
+		CTBGUI=1
+		;;
+  \?)
+    echo "Invalid option: -$OPTARG" 
 		usage
-      	exit 1
-      	;;
-    :)
-      	echo "Option -$OPTARG requires an argument."
+    exit 1
+   	;;
+  :)
+    echo "Option -$OPTARG requires an argument."
 		usage
-      	exit 1
-      	;;	
+    exit 1
+    ;;	
 	esac
 done
 
 
-
-
+#python
+if [ $PYTHON -eq 1 ]; then
+	CMAKE_POST+=" -DSLS_USE_PYTHON=ON "
+	echo "Enabling Compile Option: Python"
+fi
 
 
 if [ $TEXTCLIENT -eq 0 ] && [ $RECEIVER -eq 0 ]  && [ $GUI -eq 0 ]; then
-       CMAKE_POST+=" -DSLS_USE_TEXTCLIENT=ON -DSLS_USE_RECEIVER=ON -DSLS_USE_GUI=ON "
-       echo "Compile Option: TextClient, Receiver and GUI"
+	#CMAKE_POST+=" -DSLS_USE_TEXTCLIENT=ON -DSLS_USE_RECEIVER=ON -DSLS_USE_GUI=ON "
+	CMAKE_POST+=" -DSLS_USE_TEXTCLIENT=ON -DSLS_USE_RECEIVER=ON -DSLS_USE_GUI=OFF "
+    echo "Enabling Compile Option: TextClient, Receiver and GUI"
 else 
-       if [ $TEXTCLIENT -eq 1 ]; then
-              CMAKE_POST+=" -DSLS_USE_TEXTCLIENT=ON "
-               echo "Compile Option: TextClient"
-       fi
-       if [ $RECEIVER -eq 1 ]; then
-               CMAKE_POST+=" -DSLS_USE_RECEIVER=ON "
-               echo "Compile Option: Receiver"
-       fi
-                               
-       if [ $GUI -eq 1 ]; then
-               CMAKE_POST+=" -DSLS_USE_GUI=ON "
-               echo "Compile Option: GUI"
-       fi
+    if [ $TEXTCLIENT -eq 1 ]; then
+        CMAKE_POST+=" -DSLS_USE_TEXTCLIENT=ON -DSLS_USE_RECEIVER=OFF "
+        echo "Enabling Compile Option: TextClient"
+    fi
+    if [ $RECEIVER -eq 1 ]; then
+        CMAKE_POST+=" -DSLS_USE_RECEIVER=ON "
+        echo "Enabling Compile Option: Receiver"
+    fi              
+    if [ $GUI -eq 1 ]; then
+        CMAKE_POST+=" -DSLS_USE_GUI=ON "
+        echo "Enabling Compile Option: GUI"
+    fi
 fi
 
 
@@ -153,14 +193,40 @@ fi
 
 #Debug
 if [ $DEBUG -eq 1 ]; then
-	CMAKE_POST+=" -DCMAKE_BUILD_TYPE=Debug "
+#	CMAKE_POST+=" -DCMAKE_BUILD_TYPE=Debug "
+	CMAKE_POST+=" -DCMAKE_BUILD_TYPE=Debug -DSLS_USE_SANITIZER=ON "
 	echo "Debug Option enabled"
 fi 
 
+#Simulator
+if [ $SIMULATOR -eq 1 ]; then
+	CMAKE_POST+=" -DSLS_USE_SIMULATOR=ON "
+	echo "Simulator Option enabled"
+fi 
+
+#Manuals
+if [ $MANUALS -eq 1 ]; then
+	CMAKE_POST+=" -DSLS_BUILD_DOCS=ON "
+	echo "Manuals Option enabled"
+fi 
+
+#Chip Test Gui
+if [ $CTBGUI -eq 1 ]; then
+	CMAKE_POST+=" -DSLS_USE_CTBGUI=ON "
+	echo "CTB Gui Option enabled"
+fi 
+
+#Tests
+if [ $TESTS -eq 1 ]; then
+	CMAKE_POST+=" -DSLS_USE_TESTS=ON -DSLS_USE_INTEGRATION_TESTS=ON"
+	echo "Tests Option enabled"
+fi 
+
 
 #hdf5 rebuild
 if [ $HDF5 -eq 1 ]; then
-	CMAKE_PRE+="HDF5_ROOT="$HDF5DIR
+#	CMAKE_PRE+="HDF5_ROOT="$HDF5DIR
+	CMAKE_POST+=" -DCMAKE_INSTALL_PREFIX="$HDF5DIR
 	CMAKE_POST+=" -DSLS_USE_HDF5=ON "
 #normal mode rebuild
 else
@@ -177,7 +243,7 @@ echo "in "$PWD
 #cmake
 if [ $REBUILD -eq 1 ]; then
 	rm -f CMakeCache.txt
-	BUILDCOMMAND="$CMAKE_PRE cmake $CMAKE_POST .."
+	BUILDCOMMAND="$CMAKE_PRE cmake3 $CMAKE_POST .."
 	echo $BUILDCOMMAND
 	eval $BUILDCOMMAND
 fi
@@ -197,6 +263,9 @@ else
 	make
 fi
 
+if [ $MANUALS -eq 1 ]; then
+	make docs
+fi 
 
 
 

commitVersions.sh

@@ -1,15 +0,0 @@
-sh updateSvnVersion.sh
-
-cd slsDetectorGui
-git commit -a -m "updating versions"
-git push origin developer:developer
-
-cd ../slsDetectorSoftware
-git commit -a -m "updating versions"
-git push origin developer:developer
-
-cd ../slsReceiverSoftware
-git commit -a -m "updating versions"
-git push origin developer:developer
-
-cd ..

conda-recepie/build.sh

@@ -1,3 +1,4 @@
+
 mkdir build
 mkdir install
 cd build
@@ -7,9 +8,13 @@ cmake .. \
       -DSLS_USE_TEXTCLIENT=ON \
       -DSLS_USE_RECEIVER=ON \
       -DSLS_USE_GUI=ON \
+      -DSLS_USE_TESTS=ON \
+      -DSLS_USE_PYTHON=OFF \
       -DCMAKE_BUILD_TYPE=Release \
       -DSLS_USE_HDF5=OFF\
      
 
 cmake --build . -- -j10
-cmake --build . --target install
+cmake --build . --target install
+
+CTEST_OUTPUT_ON_FAILURE=1 ctest -j 2

conda-recepie/build_pylib.sh

@@ -0,0 +1,4 @@
+
+echo "|<-------- starting python build"
+cd python
+${PYTHON} setup.py install

conda-recepie/conda_build_config.yaml

@@ -0,0 +1,7 @@
+python:
+    - 3.6
+    - 3.7
+    - 3.8
+    
+numpy: 
+    - 1.17

conda-recepie/copy_ctbgui.sh

@@ -0,0 +1,9 @@
+mkdir $PREFIX/lib
+mkdir $PREFIX/bin
+mkdir $PREFIX/include
+
+
+
+cp build/bin/ctbGui $PREFIX/bin/.
+cp build/bin/libctbRootLib.so $PREFIX/lib/.
+

conda-recepie/copy_gui.sh

@@ -0,0 +1,3 @@
+#Copy the GUI 
+mkdir $PREFIX/bin
+cp build/bin/slsDetectorGui $PREFIX/bin/.

conda-recepie/copy_lib.sh

@@ -0,0 +1,24 @@
+
+mkdir $PREFIX/lib
+mkdir $PREFIX/bin
+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/install/lib/* $PREFIX/lib/
+
+#Binaries
+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/.
+
+
+cp build/install/include/* $PREFIX/include/
+cp -r build/install/share/ $PREFIX/share

conda-recepie/meta.yaml

@@ -1,13 +1,14 @@
 
 package:
   name: sls_detector_software
-  version: 4.0.1
+  version: {{ environ.get('GIT_DESCRIBE_TAG', '') }}
 
 source:
   - path: ..
 
 build:
   number: 0
+  binary_relocation: True
   rpaths:
     - lib/
 
@@ -17,9 +18,8 @@ requirements:
     - {{compiler('cxx')}}
     - cmake
     - qwt 6.*
-    - qt=4.8.7=7
-    - zeromq=4.2.5=hfc679d8_5
-    - pyzmq
+    - qt 4.8.*
+    - zeromq
     - xorg-libx11
     - xorg-libice
     - xorg-libxext
@@ -30,14 +30,14 @@ requirements:
     - {{ cdt('mesa-libgl-devel') }}      # [linux]
     - {{ cdt('mesa-libegl-devel') }}     # [linux]
     - {{ cdt('mesa-dri-drivers') }}      # [linux]
-    - {{ cdt('libselinux') }}      # [linux]
+    - {{ cdt('libselinux') }}            # [linux]
     - {{ cdt('libxdamage') }}            # [linux]
     - {{ cdt('libxxf86vm') }}            # [linux]
 
   host:
     - libstdcxx-ng
     - libgcc-ng
-    - libpng >=1.6.32,<1.6.35
+    - zeromq
     - xorg-libx11
     - xorg-libice
     - xorg-libxext
@@ -47,43 +47,52 @@ requirements:
     - xorg-libxfixes
 
   run:
+    - zeromq
     - libstdcxx-ng
     - libgcc-ng 
 
+
 outputs:
-  - name: sls_detector_lib
-    version: 4.0.1
+  - name: slsdetlib
     script: copy_lib.sh
+
+    requirements:
+      run: 
+        - libstdcxx-ng
+        - libgcc-ng
+        - zeromq
+
+  - name: slsdet
+
+    script: build_pylib.sh
+
     requirements:
       build:
+        - python
         - {{ compiler('c') }}
         - {{compiler('cxx')}}
-  - name: sls_detector_gui
-    version: 4.0.1
+        - {{ pin_subpackage('slsdetlib', exact=True) }}
+        - setuptools
+
+      host:
+        - python
+
+      run:
+        - libstdcxx-ng
+        - libgcc-ng
+        - python
+        - numpy
+        - {{ pin_subpackage('slsdetlib', exact=True) }}
+
+
+    test:
+      imports:
+        - slsdet
+
+  - name: slsdetgui
     script: copy_gui.sh
     requirements:
-      build:
-      - {{ compiler('c') }}
-      - {{compiler('cxx')}}
-      - cmake
-      - qwt 6.*
-      - qt=4.8.7=7
-      - zeromq=4.2.5=hfc679d8_5
-      - pyzmq
-      - xorg-libx11
-      - xorg-libice
-      - xorg-libxext
-      - xorg-libsm
-      - xorg-libxau
-      - xorg-libxrender
-      - xorg-libxfixes
-      - {{ cdt('mesa-libgl-devel') }}      # [linux]
-      - {{ cdt('mesa-libegl-devel') }}     # [linux]
-      - {{ cdt('mesa-dri-drivers') }}      # [linux]
-      - {{ cdt('libselinux') }}      # [linux]
-      - {{ cdt('libxdamage') }}            # [linux]
-      - {{ cdt('libxxf86vm') }}            # [linux]
       run:
-        - sls_detector_lib=4.0.1
+        - {{ pin_subpackage('slsdetlib', exact=True) }}
         - qwt 6.*
-        - qt=4.8.7=7
+        - qt 4.8.*

conda-recepie/run_test.sh

@@ -0,0 +1 @@
+ctest -j2

configure

@@ -1,58 +0,0 @@
-##!/bin/bash
-
-: ${INSTALLROOT=$PWD}
-read -p "Installation directory [default:\"$INSTALLROOT\"]:" -e t3
-if [ -z "$t3" ]
-then
-echo
-else
-	INSTALLROOT=$t3
-fi
-echo "INSTALLROOT will be  \"$INSTALLROOT\""	
-export INSTALLROOT
-
-: ${BINDIR="bin"}
-read -p "Binaries directory [default:\"$BINDIR\"]:" -e t4
-if [ -z "$t4" ]
-then
-	BINDIR=$INSTALLROOT/$BINDIR
-else
-	BINDIR=$INSTALLROOT/$t4
-fi
-echo "BINDIR will be  \"$BINDIR\""	
-export BINDIR
-
-: ${LIBDIR="bin"}
-read -p "Libraries directory [default:\"$LIBDIR\"]:" -e t5
-if [ -z "$t5" ]
-then
-	LIBDIR=$INSTALLROOT/$LIBDIR
-else
-	LIBDIR=$INSTALLROOT/$t5
-fi	
-echo "LIBDIR will be  \"$LIBDIR\""	
-export LIBDIR
-
-:  ${INCDIR="include"}
-read -p "Includes directory [default:\"$INCDIR\"]:" -e t6
-if [ -z "$t6" ]
-then
-	INCDIR=$INSTALLROOT/$INCDIR
-else
-	INCDIR=$INSTALLROOT/$t6
-fi	
-echo "INCDIR will be  \"$INCDIR\""	
-export INCDIR
-
-:  ${DOCDIR="doc"}
-read -p "Documentation directory [default:\"$DOCDIR\"]:" -e t7
-if [ -z "$t7" ]
-then
-	DOCDIR=$INSTALLROOT/$DOCDIR
-else	
-	DOCDIR=$INSTALLROOT/$t7
-fi
-echo "DOCDIR will be  \"$DOCDIR\""
-export DOCDIR
-
-

ctbGui/CMakeLists.txt

@@ -0,0 +1,89 @@
+
+
+find_package(ROOT CONFIG REQUIRED  COMPONENTS Core Gui)
+find_package(TIFF REQUIRED)
+
+target_include_directories(ROOT::Core INTERFACE "${ROOT_INCLUDE_DIRS}")
+add_library(ROOT::Flags_CXX IMPORTED INTERFACE)
+separate_arguments(ROOT_CXX_FLAGS)
+target_compile_options(ROOT::Flags_CXX INTERFACE ${ROOT_CXX_FLAGS})
+separate_arguments(ROOT_DEFINITIONS)
+target_compile_definitions(ROOT::Flags_CXX INTERFACE ${ROOT_DEFINITIONS})
+
+# This fixes a bug in the linker flags
+string(REPLACE "-L " "-L" ROOT_EXE_LINKER_FLAGS "${ROOT_EXE_LINKER_FLAGS}")
+separate_arguments(ROOT_EXE_LINKER_FLAGS)
+
+# Stuck into using old property method due to separate -L and -l arguments
+# (A full path to -l is better!)
+set_property(TARGET ROOT::Flags_CXX PROPERTY
+    INTERFACE_LINK_LIBRARIES ${ROOT_EXE_LINKER_FLAGS})
+set_property(TARGET ROOT::Core PROPERTY
+    INTERFACE_INCLUDE_DIRECTORIES "${ROOT_INCLUDE_DIRS}")
+
+
+add_executable(ctbGui 
+    ctbGui.cpp 
+    ctbMain.cpp
+    ctbDacs.cpp
+    ctbPowers.cpp
+    ctbSlowAdcs.cpp
+    ctbSignals.cpp
+    ctbAdcs.cpp
+    ctbPattern.cpp
+    ctbAcquisition.cpp
+    ${CMAKE_SOURCE_DIR}/slsDetectorCalibration/tiffIO.cpp
+)
+
+
+#TODO! Replace with target
+target_include_directories(ctbGui PRIVATE 
+    ${CMAKE_SOURCE_DIR}/slsDetectorCalibration/dataStructures
+    ${CMAKE_SOURCE_DIR}/slsDetectorCalibration/interpolations
+    ${CMAKE_SOURCE_DIR}/slsDetectorCalibration/
+)
+
+# Headders needed for ROOT dictionary generation
+set( HEADERS
+    ctbDefs.h
+    ctbMain.h 
+    ctbDacs.h   
+    ctbPattern.h  
+    ctbSignals.h  
+    ctbAdcs.h 
+    ctbAcquisition.h 
+    ctbPowers.h   
+    ctbSlowAdcs.h
+)
+
+#set(ROOT_INCLUDE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
+
+# ROOT dictionary generation 
+include("${ROOT_DIR}/modules/RootNewMacros.cmake")
+root_generate_dictionary(ctbDict ${HEADERS} LINKDEF ctbLinkDef.h)
+add_library(ctbRootLib SHARED ctbDict.cxx)
+target_include_directories(ctbRootLib PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+target_link_libraries(ctbRootLib PUBLIC 
+    ROOT::Core 
+    slsDetectorShared
+    slsSupportLib
+    ${ROOT_LIBRARIES} 
+    ${ROOT_EXE_LINKER_FLAGS}
+)
+
+set_target_properties(
+    ctbRootLib PROPERTIES
+    LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin
+)
+
+target_link_libraries(ctbGui PUBLIC 
+    slsDetectorShared
+    slsSupportLib
+    ctbRootLib
+    ${TIFF_LIBRARIES}
+)
+
+set_target_properties(ctbGui PROPERTIES
+    RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin
+
+)

ctbGui/Makefile.root5

@@ -0,0 +1,44 @@
+
+
+INCS=ctbMain.h ctbDacs.h   ctbPattern.h  ctbSignals.h  ctbAdcs.h ctbAcquisition.h ctbPowers.h   ctbSlowAdcs.h 
+SRC= $(INCS:.h=.cpp) ctbDict.cpp 
+LINKDEF=ctbLinkDef.h 
+ZMQLIB=../slsReceiverSoftware/include
+LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
+
+INCDIR=-I../slsReceiverSoftware/include/ -I../slsDetectorSoftware/include/ -I../slsSupportLib/include/  -I../slsDetectorCalibration -I../slsDetectorCalibration/dataStructures  -I$(CBFLIBDIR)/include  -I../slsDetectorCalibration/interpolations
+LDFLAG=-L../build/bin -lSlsDetector -lSlsSupport  -L/usr/lib64/ -lpthread -lm  -lstdc++  -lzmq -pthread -lrt  -ltiff -L$(ZMQLIB) -L$(CBFLIBDIR)/lib/ -std=c++11
+#
+MAIN=ctbGui.cpp
+
+DESTDIR?=../build/bin
+
+
+OBJS = $(SRC:.cpp=.o) $(MAIN:.cpp=.o)
+
+all: $(DESTDIR)/ctbGui
+
+
+doc:
+	cd manual && make DESTDIR=$(DESTDIR)
+
+htmldoc:
+	cd manual && make html DESTDIR=$(DESTDIR)
+
+ctbDict.cpp: $(INCS)  $(LINKDEF)
+	rootcint -f ctbDict.cpp -c $(INCS) $(LINKDEF)	
+
+%.o : %.cpp 
+	echo $@
+	g++ -DMYROOT `root-config --cflags --glibs` -lMinuit -DCTB $(LDFLAG)  -o $@ -c $< $(INCDIR)
+#$(CXX) -o $@ -c $< $(INCLUDES) $(DFLAGS) -fPIC  $(EPICSFLAGS) -lpthread #$(FLAGS)
+
+
+
+$(DESTDIR)/ctbGui: $(OBJS) $(LINKDEF) 
+	g++ -DMYROOT `root-config --cflags --glibs` -lMinuit -DCTB $(LDFLAG) -o ctbGui $(INCDIR) $(OBJS)  ../slsDetectorCalibration/tiffIO.cpp
+	mv ctbGui $(DESTDIR)	
+
+clean:
+	rm -f $(DESTDIR)/ctbGui *.o ctbDict.* $(OBJS)
+

ctbGui/Makefile.root6

@@ -0,0 +1,46 @@
+
+
+INCS=ctbMain.h ctbDacs.h   ctbPattern.h  ctbSignals.h  ctbAdcs.h ctbAcquisition.h ctbPowers.h   ctbSlowAdcs.h  
+SRC= $(INCS:.h=.cpp) ctbDict.cpp 
+LINKDEF=ctbLinkDef.h 
+#ctbActions.h 
+ZMQLIB=../slsReceiverSoftware/include
+LIBRARYCBF=$(CBFLIBDIR)/lib/*.o
+
+INCDIR=-I../slsReceiverSoftware/include/ -I../slsDetectorSoftware/include/ -I../slsSupportLib/include/  -I../slsDetectorCalibration -I../slsDetectorCalibration/dataStructures  -I$(CBFLIBDIR)/include  -I../slsDetectorCalibration/interpolations
+
+LDFLAG=-L../build/bin -lSlsDetector -lSlsSupport  -L/usr/lib64/ -lpthread -lm  -lstdc++  -lzmq -pthread -lrt  -ltiff -L$(ZMQLIB) -L$(CBFLIBDIR)/lib/ -std=c++11
+#
+MAIN=ctbGui.cpp
+
+DESTDIR?=../build/bin
+
+
+OBJS = $(SRC:.cpp=.o) $(MAIN:.cpp=.o)
+
+all: $(DESTDIR)/ctbGui
+
+
+doc:
+	cd manual && make DESTDIR=$(DESTDIR)
+
+htmldoc:
+	cd manual && make html DESTDIR=$(DESTDIR)
+
+ctbDict.cpp: $(INCS)  $(LINKDEF)
+	rootcling -f ctbDict.cpp -c $(INCS) $(LINKDEF)	
+
+%.o : %.cpp 
+	echo $@
+	g++ -DMYROOT `source root-config --cflags --glibs` -lMinuit -DCTB $(LDFLAG)  -o $@ -c $< $(INCDIR)
+#$(CXX) -o $@ -c $< $(INCLUDES) $(DFLAGS) -fPIC  $(EPICSFLAGS) -lpthread #$(FLAGS)
+
+
+
+$(DESTDIR)/ctbGui: $(OBJS) $(LINKDEF) 
+	g++ -DMYROOT `source root-config --cflags --glibs` -lMinuit -DCTB $(LDFLAG) -o ctbGui $(INCDIR) $(OBJS)  ../slsDetectorCalibration/tiffIO.cpp
+	mv ctbGui $(DESTDIR)	
+
+clean:
+	rm -f $(DESTDIR)/ctbGui *.o ctbDict.* $(OBJS)
+

ctbGui/ctbAcquisition.h

@@ -0,0 +1,246 @@
+#ifndef CTBACQUISITION_H
+#define CTBACQUISITION_H
+#include  <TGFrame.h>
+
+#include "ctbAdcs.h"
+#include "ctbSignals.h"
+#include "ctbPattern.h"
+class TGTextEntry;
+class TGLabel;
+class TGNumberEntry;
+class TGCheckButton;
+class TThread;
+class TGraph;
+class TMultiGraph;
+class THStack;
+class TGButtonGroup;
+class TGRadioButton;
+class TGComboBox;
+class TTimer;
+class TCanvas;
+class TH2F;
+class TH1F;
+class TGLabel;
+class TGTextButton;
+
+namespace sls
+{
+   class Detector;
+};
+class detectorData;
+
+template <class dataType> class slsDetectorData;
+
+class singlePhotonDetector;
+//class singlePhotonDetector;
+class commonModeSubtraction;
+
+#include <string>
+#include <stdint.h>
+using namespace std;
+
+class ctbAcquisition : public TGGroupFrame {
+
+
+  enum {DESERIALIZER, MOENCH04, MOENCH02, MOENCH03, IMAGE32B, IMAGE16B, ADCSAR2, MYTHEN301, MYTHEN302};
+
+
+ private:
+  TGTextEntry *eOutdir;
+  TGTextEntry *eFname;
+  TGNumberEntry *eFindex;
+  TGCheckButton *cFileSave;
+
+
+  TGNumberEntry *eSerOff;
+  TGNumberEntry *eDynRange;
+  TGNumberEntry *eNumCount;
+
+
+  TGNumberEntry *ePixX;
+  TGNumberEntry *ePixY;
+
+  TGNumberEntry *eFitADC;
+  TGNumberEntry *eBitPlot;
+  TGNumberEntry *eMinRaw;
+  TGNumberEntry *eMaxRaw;
+  TGNumberEntry *eMinPedSub;
+  TGNumberEntry *eMaxPedSub;
+  TGCheckButton *cMinMaxRaw;
+  TGCheckButton *cMinMaxPedSub;
+
+
+
+
+  TGNumberEntry *eMeasurements;
+
+
+
+  TGTextButton *bStatus;
+  // TGTextButton 
+  TGCheckButton *cCompile;
+  TGTextButton *cLoad;
+  //  TGCheckButton *cRun;
+  
+  TThread *acqThread;
+
+
+  THStack *adcStack;
+  THStack *bitStack;
+  THStack *countsStack;
+
+
+  TH1F *adcHisto[NADCS];
+  TH1F *countsHisto[NADCS];
+ 
+  TH1F *bitHisto[NSIGNALS];
+  float bitOffset[NSIGNALS];
+  
+  // int enableFlag[NADCS+4];
+  int roMode;
+
+  int dBitOffset;
+
+
+
+  TH1F *adcFit;
+  TH1F *bitPlot;
+  TH1F *countsFit;
+
+
+
+  TH2F *h2DMapAn; // for 2D detectors
+  TH2F *h2DMapDig; // for 2D detectors
+  TH1F *h1DMap; //for 1D detectors
+
+  //  TH2F *h2Scan; // for 2D detectors
+  // TMultiGraph *mgAdcs;
+  // TH1I *plotAdc[NADCS];
+
+
+  sls::Detector* myDet;
+  
+  int plotFlag[NADCS];
+  int bitPlotFlag[NSIGNALS];
+  
+  int ip;
+  // int nChannels;
+  // int chanEnable;
+  //int nADCs;
+
+  std::vector <int> dbitlist;
+  std::vector <int> adclist;
+
+  TGButtonGroup *bgPlot;// = new TGVButtonGroup(main_frame);
+  TGRadioButton *rbPlotOff;
+  TGRadioButton *rbWaveform;
+  TGRadioButton *rbDistribution;
+  TGRadioButton *rb2D;
+  //  TGRadioButton *rbScan;
+  TGComboBox *cbDetType;
+  TGCheckButton *cbGetPedestal;
+  TGCheckButton *cbSubtractPedestal;
+  TGCheckButton *cbCommonMode;
+  TGTextButton *bResetPedestal;
+
+  TGLabel *lClickX;
+  TGLabel *lClickY;
+  TGLabel *lClickValue;
+
+
+  TCanvas *myCanvas;
+  TTimer *plotTimer;
+
+  char patternFile[10000];
+  char patternCompiler[10000];
+  
+  int globalPlot;
+  int adcPlot;
+  int dbitPlot;
+  int tenG;
+
+  int nAnalogSamples, nDigitalSamples;
+  // int iScanStep;
+
+  slsDetectorData<uint16_t> *dataStructure;
+  singlePhotonDetector *photonFinder;
+    //singlePhotonDetector *photonFinder;
+  commonModeSubtraction *commonMode;
+  int cmSub;
+
+  int stop;
+
+  uint64_t dBitMask;
+
+  int deserializer;
+
+ public:
+   ctbAcquisition(TGVerticalFrame*,  sls::Detector*);
+   void setOutdir();
+   void setFname();
+   void setMeasurements();
+   void setFsave(Bool_t);
+   void changePlot(Int_t);
+   void changeDetector(Int_t);
+   void changePlot();
+   void changeDetector();
+   void setFindex();
+   void Draw();
+   void setCanvas(TCanvas*);
+
+   void toggleAcquisition();
+   void loadPattern();
+   static void* ThreadHandle(void *arg);
+   void update();
+   void acquisitionFinished();
+   //  string getParameters();
+
+   void setGraph (int i ,int en, Pixel_t col);
+   void setBitGraph (int i ,int en, Pixel_t col);
+   void startAcquisition();
+   static   void progressCallback(double,void*);
+   static void dataCallback(detectorData*, long unsigned int, unsigned int,  void*);
+   int StopFlag;
+   
+   int plotData(detectorData*, int);
+
+   void setPatternFile(const char* t);
+
+   void setPatternCompiler(const char* t);
+
+   void setAnalogSamples(int);
+   void setDigitalSamples(int);
+   
+   void setADCEnable(Int_t);
+   void setDbitEnable(Int_t);
+   void setReadoutMode(int);
+   void updateChans();
+
+   void resetPedestal();
+
+   void ToggleCommonMode(Bool_t);
+   void TogglePedSub(Bool_t);
+   void ChangeHistoLimitsPedSub(Long_t );
+   void ChangeHistoLimitsRaw(Long_t);
+   void ChangeHistoLimitsPedSub( );
+   void ChangeHistoLimitsRaw();
+   void ChangeHistoLimitsPedSub(Bool_t );
+   void ChangeHistoLimitsRaw(Bool_t);
+   
+
+   void ChangeSerialOffset();
+   void ChangeSerialOffset(Long_t);
+   void ChangeNumberOfChannels();
+   void ChangeNumberOfChannels(Long_t);
+   void ChangeDynamicRange();
+   void ChangeDynamicRange(Long_t);
+   void ChangeImagePixels();
+   void ChangeImagePixels(Long_t);
+
+   void canvasClicked();
+   void FitADC();
+   void plotBit();
+   ClassDef(ctbAcquisition,0)
+};
+
+#endif

ctbGui/ctbAdcs.cpp

@@ -0,0 +1,614 @@
+#include <TApplication.h>
+#include <TGClient.h>
+#include <TCanvas.h>
+#include <TF1.h>
+#include <TRandom.h>
+#include <TGButton.h>
+#include <TRootEmbeddedCanvas.h>
+#include <TGButtonGroup.h>
+#include <TGNumberEntry.h>
+#include <TGLabel.h>
+#include <TList.h>
+#include <TGFileDialog.h>
+#include <TGComboBox.h>
+#include <TH2F.h>
+#include <TColor.h>
+#include <TH1F.h>
+#include <TGraphErrors.h>
+#include <TGColorSelect.h>
+#include <THStack.h>
+#include <TGTab.h>
+
+#include <stdio.h>
+#include <iostream>
+#include <fstream>
+
+#include "ctbAdcs.h"
+#include "ctbDefs.h"
+#include "Detector.h"
+
+using namespace std;
+
+
+
+ctbAdc::ctbAdc(TGVerticalFrame *page, int i, sls::Detector *det)
+  : TGHorizontalFrame(page, 800,800), id(i), myDet(det) {
+
+  TGHorizontalFrame *hframe=this;
+  char tit[100];
+
+   page->AddFrame(hframe,new TGLayoutHints(kLHintsTop | kLHintsExpandX , 1,1,1,1));
+   hframe->MapWindow();
+
+
+   
+
+
+   sprintf(tit, "ADC%d", id);
+
+   sAdcLabel= new TGLabel(hframe, tit);
+   hframe->AddFrame(sAdcLabel,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 1, 1, 1, 1));
+   sAdcLabel->MapWindow();
+   sAdcLabel->SetTextJustify(kTextLeft);
+
+
+
+   
+   
+
+   sAdcInvert= new TGCheckButton(hframe, "Inv");
+   hframe->AddFrame( sAdcInvert,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 1, 1, 1, 1));
+   sAdcInvert->MapWindow();
+   sAdcInvert->Connect("Toggled(Bool_t)","ctbAdc",this,"ToggledInvert(Bool_t)");
+
+
+   sAdcEnable= new TGCheckButton(hframe, "En");
+   hframe->AddFrame( sAdcEnable,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 1, 1, 1, 1));
+   sAdcEnable->MapWindow();
+   // sAdcEnable->SetOn(kTRUE);
+   // sAdcEnable->SetEnabled(kFALSE);
+   sAdcEnable->Connect("Toggled(Bool_t)","ctbAdc",this,"ToggledEnable(Bool_t)");
+
+
+
+   sAdcPlot= new TGCheckButton(hframe, "Plot");
+   hframe->AddFrame( sAdcPlot,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 1, 1, 1, 1));
+   sAdcPlot->MapWindow();
+
+
+   sAdcPlot->Connect("Toggled(Bool_t)","ctbAdc",this,"ToggledPlot(Bool_t)");
+
+
+
+   fColorSel = new TGColorSelect(hframe, id+1, 0);
+
+   fColorSel->Connect("ColorSelected(Pixel_t)","ctbAdc",this,"ColorChanged(Pixel_t)");
+   hframe->AddFrame(fColorSel, new TGLayoutHints(kLHintsTop |
+                          kLHintsLeft, 2, 0, 2, 2));
+   
+
+   fColorSel->SetColor(TColor::Number2Pixel(id+1));
+   //   sprintf(tit,"adc%d",id);
+//    gADC=new TGraph();
+//    gADC->SetName(tit);
+//    gADC->SetLineColor(id+1);
+//    gADC->SetMarkerColor(id+1);
+   
+   
+
+};
+Pixel_t ctbAdc::getColor(){
+  return fColorSel->GetColor();
+}
+Bool_t ctbAdc::getEnabled(){
+  return getPlot();
+}
+Bool_t ctbAdc::getPlot(){
+  return sAdcPlot->IsOn();
+}
+Bool_t ctbAdc::getInverted(){
+  return sAdcInvert->IsOn();
+}
+
+Bool_t ctbAdc::getEnable(){
+  return sAdcEnable->IsOn();
+}
+
+
+
+void ctbAdc::setInverted(Bool_t b){
+  //  cout << id << "set enabled " << b << endl;
+  if (b)
+    sAdcInvert->SetOn(kTRUE,kTRUE);
+  else
+    sAdcInvert->SetOn(kFALSE,kTRUE);
+    
+}
+
+
+void ctbAdc::setEnable(Bool_t b){
+  //  cout << id << "set enabled " << b << endl;
+  if (b)
+    sAdcEnable->SetOn(kTRUE,kFALSE);
+  else
+    sAdcEnable->SetOn(kFALSE,kFALSE);
+    
+}
+
+
+
+
+
+void ctbAdc::setAdcAlias(char *tit, int plot, int color) {
+  if (tit)
+    sAdcLabel->SetText(tit);
+  if (plot>0)
+    sAdcPlot->SetOn(kTRUE,kTRUE);
+  else if (plot==0)
+    sAdcPlot->SetOn(kFALSE,kTRUE);
+  if (color>=0)
+    fColorSel->SetColor(color);
+  fColorSel->SetEnabled(sAdcPlot->IsOn());
+}
+
+
+string ctbAdc::getAdcAlias() {
+
+  char line[1000];
+  sprintf(line,"ADC%d %s %d %lx\n",id,sAdcLabel->GetText()->Data(),sAdcPlot->IsOn(),fColorSel->GetColor());
+  return string(line);
+}
+
+void ctbAdc::update() {
+
+  
+  //Emit("ToggledAdcEnable(Int_t)", id);
+  
+}
+
+
+void ctbAdc::ToggledPlot(Bool_t b){
+
+  //  Long_t mask=b<<id;
+  //  ToggledAdcPlot(mask);
+  cout << "Colsel " << id << " enable " << b << endl;
+  if (b)
+    fColorSel->SetEnabled(kTRUE);
+  else
+    fColorSel->SetEnabled(kFALSE);
+    
+  // fColorSel->SetEnabled(sAdcPlot->IsOn());
+  Emit("ToggledAdcPlot(Int_t)", id);
+  
+}
+
+
+
+void ctbAdc::ToggledInvert(Bool_t b){
+
+    
+  // fColorSel->SetEnabled(sAdcPlot->IsOn());
+  Emit("ToggledAdcInvert(Int_t)", id);
+  
+}
+
+
+
+void ctbAdc::ToggledEnable(Bool_t b){
+
+    
+  fColorSel->SetEnabled(sAdcPlot->IsOn());
+  Emit("ToggledAdcEnable(Int_t)", id);
+  
+}
+
+
+
+
+
+
+void ctbAdc::ColorChanged(Pixel_t) {
+  
+  Emit("ToggledAdcPlot(Int_t)", id);
+
+}
+
+void ctbAdc::ToggledAdcPlot(Int_t b){
+
+  
+  Emit("ToggledAdcPlot(Int_t)", id);
+
+}
+
+void ctbAdc::ToggledAdcInvert(Int_t b){
+
+  
+  Emit("ToggledAdcInvert(Int_t)", id);
+
+}
+
+void ctbAdc::ToggledAdcEnable(Int_t b){
+
+  
+  Emit("ToggledAdcEnable(Int_t)", id);
+
+}
+
+
+
+
+void ctbAdc::setEnabled(Bool_t b){
+  //  cout << id << "set enabled " << b << endl;
+  if (b)
+    sAdcPlot->SetOn(kTRUE,kFALSE);
+  else
+    sAdcPlot->SetOn(kFALSE,kFALSE);
+    
+}
+
+
+
+void ctbAdc::setPlot(Bool_t b){
+  //  cout << id << "set enabled " << b << endl;
+  if (b)
+    sAdcPlot->SetOn(kTRUE,kTRUE);
+  else
+    sAdcPlot->SetOn(kFALSE,kTRUE);
+    
+  
+}
+
+
+
+
+
+
+
+ctbAdcs::ctbAdcs(TGVerticalFrame *page, sls::Detector *det)
+  : TGGroupFrame(page,"Adcs",kVerticalFrame), myDet(det) {
+
+
+  SetTitlePos(TGGroupFrame::kLeft);
+  page->AddFrame(this,new TGLayoutHints( kLHintsTop | kLHintsExpandX , 10,10,10,10));
+  MapWindow();
+  
+
+ 
+  TGHorizontalFrame* hframe=new TGHorizontalFrame(this, 800,800);
+  AddFrame(hframe,new TGLayoutHints(kLHintsTop | kLHintsExpandX , 1,1,1,1));
+  hframe->MapWindow();
+
+
+
+
+  int idac=0;
+
+
+
+
+ 
+  TGHorizontalFrame* hhframe=new TGHorizontalFrame(this, 800,800);
+  AddFrame(hhframe,new TGLayoutHints(kLHintsTop | kLHintsExpandX , 1,1,1,1));
+  hhframe->MapWindow();
+
+  TGVerticalFrame *vframe;
+
+
+
+
+  for (idac=0; idac<NADCS; idac++) {
+    if (idac%16==0) {
+
+
+    vframe=new TGVerticalFrame(hhframe, 400,800);
+     hhframe->AddFrame(vframe,new TGLayoutHints(kLHintsTop | kLHintsExpandX , 1,1,1,1));
+    vframe->MapWindow();
+   
+  
+
+    }
+
+    sAdc[idac]=new ctbAdc(vframe,idac,myDet);
+
+    
+    sAdc[idac]->Connect("ToggledAdcPlot(Int_t)","ctbAdcs",this,"ToggledAdcPlot(Int_t)");
+    sAdc[idac]->Connect("ToggledAdcInvert(Int_t)","ctbAdcs",this,"ToggledAdcInvert(Int_t)");
+    sAdc[idac]->Connect("ToggledAdcEnable(Int_t)","ctbAdcs",this,"ToggledAdcEnable(Int_t)");
+
+  }
+
+  hframe=new TGHorizontalFrame(this, 800,800);
+  AddFrame(hframe,new TGLayoutHints(kLHintsTop | kLHintsExpandX , 1,1,1,1));
+  hframe->MapWindow();
+
+
+    bCheckHalf[0]=new TGTextButton(hframe, "All 0-15");
+    hframe->AddFrame(bCheckHalf[0],new TGLayoutHints(kLHintsTop |  kLHintsExpandX, 5, 5, 5, 5));
+    bCheckHalf[0]->MapWindow();
+    bCheckHalf[0]->Connect("Clicked()","ctbAdcs",this,"CheckHalf0()");
+
+
+    bRemoveHalf[0]=new TGTextButton(hframe, "None 0-15");
+    hframe->AddFrame(bRemoveHalf[0],new TGLayoutHints(kLHintsBottom |  kLHintsExpandX, 5, 5, 5, 5));
+    bRemoveHalf[0]->MapWindow();
+    bRemoveHalf[0]->Connect("Clicked()","ctbAdcs",this,"RemoveHalf0()");
+
+
+    bCheckHalf[1]=new TGTextButton(hframe, "All 16-23");
+    hframe->AddFrame(bCheckHalf[1],new TGLayoutHints(kLHintsTop |  kLHintsExpandX, 5, 5, 5, 5));
+    bCheckHalf[1]->MapWindow();
+    bCheckHalf[1]->Connect("Clicked()","ctbAdcs",this,"CheckHalf1()");
+    //  bCheckAll->Connect("Clicked()","ctbAdcs",this,"CheckAll()");
+
+
+    bRemoveHalf[1]=new TGTextButton(hframe, "None 16-23");
+    hframe->AddFrame(bRemoveHalf[1],new TGLayoutHints(kLHintsBottom |  kLHintsExpandX, 5, 5, 5, 5));
+    bRemoveHalf[1]->MapWindow();
+    bRemoveHalf[1]->Connect("Clicked()","ctbAdcs",this,"RemoveHalf1()");
+    // bRemoveAll->Connect("Clicked()","ctbAdcs",this,"RemoveAll()");
+
+
+
+
+  hframe=new TGHorizontalFrame(this, 800,800);
+  AddFrame(hframe,new TGLayoutHints(kLHintsTop | kLHintsExpandX , 1,1,1,1));
+  hframe->MapWindow();
+
+
+    bCheckAll=new TGTextButton(hframe, "All");
+    hframe->AddFrame(bCheckAll,new TGLayoutHints(kLHintsTop |  kLHintsExpandX, 5, 5, 5, 5));
+    bCheckAll->MapWindow();
+    bCheckAll->Connect("Clicked()","ctbAdcs",this,"CheckAll()");
+
+
+    bRemoveAll=new TGTextButton(hframe, "None");
+    hframe->AddFrame(bRemoveAll,new TGLayoutHints(kLHintsBottom |  kLHintsExpandX, 5, 5, 5, 5));
+    bRemoveAll->MapWindow();
+    bRemoveAll->Connect("Clicked()","ctbAdcs",this,"RemoveAll()");
+
+
+
+  hframe=new TGHorizontalFrame(this, 800,50);
+ AddFrame(hframe,new TGLayoutHints(kLHintsTop | kLHintsExpandX , 1,1,1,1));
+  hframe->MapWindow();
+
+
+  TGLabel *label= new TGLabel(hframe, "Inversion mask: ");
+   hframe->AddFrame(label,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 1, 1, 1, 1));
+   label->MapWindow();
+   label->SetTextJustify(kTextLeft);
+
+
+   eInversionMask = new TGNumberEntry(hframe, 0, 16,999, TGNumberFormat::kNESHex,
+                                               TGNumberFormat::kNEANonNegative, 
+                                               TGNumberFormat::kNELNoLimits);
+
+  hframe->AddFrame(eInversionMask,new TGLayoutHints(kLHintsTop |  kLHintsExpandX, 1, 1, 1, 1));
+   eInversionMask->MapWindow();
+   eInversionMask->Resize(150,30);
+   eInversionMask->SetState(kFALSE);
+
+
+  hframe=new TGHorizontalFrame(this, 800,50);
+ AddFrame(hframe,new TGLayoutHints(kLHintsTop | kLHintsExpandX , 1,1,1,1));
+  hframe->MapWindow();
+
+
+ label= new TGLabel(hframe, "Enable mask: ");
+   hframe->AddFrame(label,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 1, 1, 1, 1));
+   label->MapWindow();
+   label->SetTextJustify(kTextLeft);
+
+
+   eEnableMask = new TGNumberEntry(hframe, 0, 16,999, TGNumberFormat::kNESHex,
+                                               TGNumberFormat::kNEANonNegative, 
+                                               TGNumberFormat::kNELNoLimits);
+
+   hframe->AddFrame(eEnableMask,new TGLayoutHints(kLHintsTop |  kLHintsExpandX, 1, 1, 1, 1));
+   eEnableMask->MapWindow();
+   eEnableMask->Resize(150,30);
+   eEnableMask->SetState(kFALSE);
+
+}
+
+
+int ctbAdcs::setEnable(int reg) {
+
+  try {
+    if (reg > -1) {
+      myDet->setADCEnableMask(reg);
+    }
+    auto retval = myDet->getADCEnableMask().tsquash("Different values");
+    eEnableMask->SetHexNumber(retval);
+    return retval;
+  } CATCH_DISPLAY ("Could not set/get adc enablemask.", "ctbAdcs::setEnable")
+  
+  return -1;
+}
+
+int ctbAdcs::setInvert(int reg) {
+
+  try {
+    if (reg > -1) {
+      myDet->setADCInvert(reg);
+    }
+    auto retval = myDet->getADCInvert().tsquash("Different values");
+    eInversionMask->SetHexNumber(retval);
+    return retval;
+  } CATCH_DISPLAY ("Could not set/get adc enablemask.", "ctbAdcs::setEnable")
+  
+  return -1;
+}
+
+
+
+void ctbAdcs::update() {
+  Int_t invreg;
+  Int_t disreg;
+
+  disreg=setEnable();
+  invreg=setInvert();
+  
+  for (int is=0; is<NADCS; is++) {
+    sAdc[is]->setAdcAlias(NULL,-1,-1);
+    if (invreg & (1<<is) )
+      sAdc[is]->setInverted(kTRUE);
+    else
+      sAdc[is]->setInverted(kFALSE);
+
+    if (disreg & (1<<is) )
+      sAdc[is]->setEnable(kTRUE);
+    else
+      sAdc[is]->setEnable(kFALSE);
+  }
+  
+   Emit("AdcEnable(Int_t)", disreg);
+
+}
+string ctbAdcs::getAdcParameters() {
+    ostringstream line;
+  line << "reg "<< hex  << setInvert() << "# ADC invert reg" << dec << endl;
+  line << "reg "<< hex  << setEnable() << " # ADC enable reg"<< dec <<  endl;
+  return line.str();
+
+}
+
+
+void ctbAdcs::CheckAll() {
+  for (int is=0; is<NADCS; is++){
+    sAdc[is]->setPlot(kTRUE);
+  }
+}
+
+
+void ctbAdcs::RemoveAll() {
+  for (int is=0; is<NADCS; is++) {
+    sAdc[is]->setPlot(kFALSE);
+  }
+}
+
+
+
+void ctbAdcs::CheckHalf0() {
+  for (int is=0; is<NADCS/2; is++) {
+    sAdc[is]->setPlot(kTRUE);
+  }
+}
+
+
+void ctbAdcs::RemoveHalf0() {
+  for (int is=0; is<NADCS/2; is++){
+    sAdc[is]->setPlot(kFALSE);
+  }
+}
+
+void ctbAdcs::CheckHalf1() {
+  for (int is=NADCS/2; is<NADCS; is++){
+    sAdc[is]->setPlot(kTRUE);
+  }
+}
+
+
+void ctbAdcs::RemoveHalf1() {
+  for (int is=NADCS/2; is<NADCS; is++){
+    sAdc[is]->setPlot(kFALSE);
+  }
+}
+
+
+int ctbAdcs::setAdcAlias(string line) {
+
+  int is=-1, plot=0, color=-1;
+  char tit[100];
+  int narg=sscanf(line.c_str(),"ADC%d %s %d %x",&is,tit,&plot, &color);
+  if (narg<2)
+    return -1;
+  if (narg!=3)
+    color=-1;
+  if (is>=0 && is<NADCS) {
+    sAdc[is]->setAdcAlias(tit,plot,color);
+  }
+  return is;
+
+}
+
+string ctbAdcs::getAdcAlias() {
+
+  ostringstream line;
+
+  for (int is=0; is<NADCS; is++)
+    line << sAdc[is]->getAdcAlias();
+
+  return line.str();
+}
+
+
+void ctbAdcs::ToggledAdcPlot(Int_t b){
+
+  
+  Emit("ToggledAdcPlot(Int_t)", b);
+
+}
+
+void ctbAdcs::AdcEnable(Int_t b){
+   Emit("AdcEnable(Int_t)", b);
+}
+
+
+void ctbAdcs::ToggledAdcEnable(Int_t b){
+
+   Int_t oreg=setEnable();
+   Int_t m=1<<b;
+  
+   if (sAdc[b]->getEnable())
+     oreg|=m;
+   else
+     oreg&=~m;
+
+   setEnable(oreg);
+  
+   Emit("AdcEnable(Int_t)", oreg);
+}
+
+
+void ctbAdcs::ToggledAdcInvert(Int_t b){
+
+   Int_t oreg=setInvert();
+   Int_t m=1<<b;
+  
+
+   if (sAdc[b]->getInverted())
+     oreg|=m;
+   else
+     oreg&=~m;
+  
+   setInvert(oreg);
+}
+
+
+
+
+
+Pixel_t ctbAdcs::getColor(int i){
+  if (i>=0 && i<NADCS)
+    return sAdc[i]->getColor();
+  return static_cast<Pixel_t>(-1);
+}
+
+Bool_t ctbAdcs::getEnabled(int i){
+  if (i>=0 && i<NADCS)
+    return sAdc[i]->getEnabled();
+  return static_cast<Bool_t>(-1);
+}
+
+Bool_t ctbAdcs::getEnable(int i){
+  if (i>=0 && i<NADCS)
+    return sAdc[i]->getEnable();
+  return static_cast<Bool_t>(-1);
+}
+
+Bool_t ctbAdcs::getPlot(int i){
+  if (i>=0 && i<NADCS)
+    return sAdc[i]->getPlot();
+  return static_cast<Bool_t>(-1);
+}

ctbGui/ctbAdcs.h

@@ -0,0 +1,155 @@
+
+
+
+#ifndef CTBADCS_H
+#define CTBADCS_H
+#include  <TGFrame.h>
+
+
+#define NADCS 32
+
+class TRootEmbeddedCanvas;
+class TGButtonGroup;
+class TGVerticalFrame;
+class TGHorizontalFrame;
+class TGTextEntry;
+class TGLabel;
+class TGNumberEntry;
+class TH2F;
+class TGComboBox;
+class TGCheckButton;
+class TGColorSelect;
+class TColor;
+
+class   THStack;
+class   TGraphErrors;
+class  TGTextButton;
+class  TGTab;
+
+class TGraph;
+
+namespace sls
+{
+   class Detector;
+};
+
+#include <string>
+using namespace std;
+
+class ctbAdc : public TGHorizontalFrame {
+
+
+ private:
+  
+
+   TGLabel *sAdcLabel;
+   TGCheckButton *sAdcEnable;
+   TGCheckButton *sAdcPlot;
+   TGCheckButton *sAdcInvert;
+
+   TGColorSelect  *fColorSel;
+
+   //  TGraph *gADC;
+
+   int id;
+   sls::Detector *myDet;
+   
+ public:
+   ctbAdc(TGVerticalFrame *page, int i, sls::Detector *det);
+
+
+   void setAdcAlias(char *tit, int plot, int color);
+   string getAdcAlias();
+   void ToggledAdcPlot(Int_t b);
+   void ToggledAdcEnable(Int_t b);
+   void ToggledAdcInvert(Int_t b);
+
+
+   void ToggledPlot(Bool_t b);
+   void ToggledEnable(Bool_t b);
+   void ToggledInvert(Bool_t b);
+   void ColorChanged(Pixel_t);
+   void setEnabled(Bool_t b);
+   Bool_t getEnabled();
+   // TGraph *getGraph();
+   void update();
+
+   Pixel_t getColor();
+   
+   Bool_t getEnable();
+   void setEnable(Bool_t);
+   void setPlot(Bool_t);
+   Bool_t getInverted();
+   Bool_t getPlot();
+   void setInverted(Bool_t);
+
+   ClassDef(ctbAdc,0)
+     };
+
+
+
+class ctbAdcs : public TGGroupFrame {
+private:
+  
+  ctbAdc *sAdc[NADCS];
+   sls::Detector *myDet;
+
+   
+  TGTextButton *bCheckAll;
+  TGTextButton *bRemoveAll;
+  TGTextButton *bCheckHalf[2];
+  TGTextButton *bRemoveHalf[2];
+  TGNumberEntry *eInversionMask;
+  TGNumberEntry *eEnableMask;
+
+
+/*   TGTextButton *bPlotSelected; */
+/*   TGNumberEntry *eMinX; */
+/*   TGNumberEntry *eMaxX; */
+/*   TGNumberEntry *eMinY; */
+/*   TGNumberEntry *eMaxY; */
+  
+  
+
+/*   TGTextButton *bGetPixel; */
+/*   TGNumberEntry *ePixelX; */
+/*   TGNumberEntry *ePixelY; */
+/*   TGLabel *lPixelValue; */
+
+public:
+
+   ctbAdcs(TGVerticalFrame *page, sls::Detector *det);
+   int setAdcAlias(string line);
+   string getAdcAlias();
+   string getAdcParameters();
+   void ToggledAdcPlot(Int_t);
+   void ToggledAdcInvert(Int_t);
+   void ToggledAdcEnable(Int_t);
+   void AdcEnable(Int_t b);
+   //   TGraph *getGraph(int i);
+   void CheckAll();
+   void RemoveAll();
+   void update();
+
+   int setInvert(int reg=-1);
+   int setEnable(int reg=-1);
+
+
+   Pixel_t getColor(int i);
+   Bool_t getEnabled(int i);
+   Bool_t getPlot(int i);
+   Bool_t getEnable(int i);
+
+   void CheckHalf0();
+   void RemoveHalf0();
+   
+   void CheckHalf1();
+   void RemoveHalf1();
+   
+
+   ClassDef(ctbAdcs,0)
+};
+
+#endif
+
+

ctbGui/ctbDacs.cpp

@@ -0,0 +1,233 @@
+
+#include <stdio.h>
+#include <iostream>
+#include <fstream>
+
+#include <TGTextEntry.h>
+#include <TGLabel.h>
+#include <TGNumberEntry.h>
+#include <TGButton.h>
+
+#include "ctbDacs.h"
+#include "ctbDefs.h"
+#include "Detector.h"
+#include "sls_detector_defs.h"
+
+using namespace std;
+
+
+ctbDac::ctbDac(TGGroupFrame *page, int idac, sls::Detector *det) : TGHorizontalFrame(page, 800,50) , id(idac), myDet(det) {
+
+    TGHorizontalFrame *hframe=this;
+
+    page->AddFrame(hframe,new TGLayoutHints(kLHintsTop | kLHintsExpandX , 1,1,1,1));
+    MapWindow();
+
+    char tit[100];
+    
+
+   sprintf(tit, "DAC %d:",idac);
+
+   dacsLabel= new TGCheckButton(hframe, tit);// new TGLabel(hframe, tit);
+   dacsLabel->SetOn(kTRUE, kTRUE);
+   
+   dacsLabel->Connect("Toggled(Bool_t)","ctbDac",this,"setOn(Bool_t)");
+
+
+   hframe->AddFrame(dacsLabel,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 5, 5, 5, 5));
+   dacsLabel->MapWindow();
+   dacsLabel->SetTextJustify(kTextLeft);
+
+  
+   dacsEntry = new TGNumberEntry(hframe, 0, 9,999, TGNumberFormat::kNESInteger,
+                                               TGNumberFormat::kNEANonNegative, 
+                                               TGNumberFormat::kNELLimitMinMax,
+                                               0, 65535);
+
+  hframe->AddFrame(dacsEntry,new TGLayoutHints(kLHintsTop |  kLHintsExpandX, 5, 5, 5, 5));
+   dacsEntry->MapWindow();
+   dacsEntry->Resize(150,30);
+
+
+   dacsUnit= new TGCheckButton(hframe, "mV");
+   // if (idac!=slsDetectorDefs::ADC_VPP) {
+     hframe->AddFrame( dacsUnit,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 5, 5, 5, 5));
+     dacsUnit->MapWindow();
+     if (idac==slsDetectorDefs::ADC_VPP) {
+       dacsUnit->SetEnabled(kFALSE);
+       hframe->HideFrame(dacsUnit);
+       dacsUnit->MapWindow();
+       cout << "hiding!" << endl;
+     }
+     if (idac==slsDetectorDefs::HIGH_VOLTAGE) {
+       dacsUnit->SetText("V"); 
+       dacsUnit->SetOn(kTRUE,kTRUE);
+       dacsUnit->SetEnabled(kFALSE);
+     }
+     //}
+
+
+
+   sprintf(tit, "xxx");
+   dacsValue= new TGLabel(hframe, tit);
+   hframe->AddFrame( dacsValue,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 5, 5, 5, 5));
+   dacsValue->MapWindow();
+   dacsValue->SetTextJustify(kTextLeft);
+
+   TGTextEntry *e=dacsEntry->TGNumberEntry::GetNumberEntry();
+   e->Connect("ReturnPressed()","ctbDac",this,"setValue()");
+   // e->Connect("ValueSet(Long_t)","ctbDac",this,"setValue(Long_t)");
+   dacsEntry->Connect("ValueSet(Long_t)","ctbDac",this,"setValue(Long_t)");
+   //  cout << "(((((((((((((((((((((((((((((((" << dacsEntry->GetListOfSignals()->At(0)->IsA() << endl;
+   
+
+}
+
+
+
+int ctbDac::setLabel(char *tit, int mv) {
+  if(tit)
+    dacsLabel->SetText(tit);
+  if (mv==1)
+    dacsUnit->SetOn(kTRUE,kTRUE);
+  else if (mv==0)
+    dacsUnit->SetOn(kFALSE,kTRUE);
+  // else if (mv==2) {
+  //   ;}
+  // else if  (mv==3)
+  //   ; 
+  return id;
+
+}
+
+string ctbDac::getLabel() {
+  ostringstream line;
+  line << dacsLabel->GetText() << " " <<  dacsUnit->IsOn() << endl;
+   //  line << "DAC" << dec << id << " " <<  dacsUnit->IsOn() << endl;
+  return line.str();
+
+}
+
+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 {
+    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();
+}
+
+void ctbDac::setOn(Bool_t b) {
+  //  cout << "setting dac! "<< id << endl;
+  if ( dacsLabel->IsOn()) {
+    setValue();
+  } else {
+    try {
+      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();
+}
+
+int ctbDac::getValue() { 
+  try {
+    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) {
+      dacsLabel->SetOn(kTRUE);
+    } else {
+      dacsLabel->SetOn(kFALSE);
+    }
+    return val;
+  } CATCH_DISPLAY ("Could not get dac " + to_string(id) + ".", "ctbDac::getValue")
+  
+  return -1;
+}
+
+
+ctbDacs::ctbDacs(TGVerticalFrame *page, sls::Detector *det)   : TGGroupFrame(page,"DACs",kVerticalFrame) , myDet(det){
+
+  SetTitlePos(TGGroupFrame::kLeft);
+  page->AddFrame(this,new TGLayoutHints( kLHintsTop | kLHintsExpandX , 10,10,10,10));
+  MapWindow();
+  
+  // cout << "window mapped " << endl;
+
+  for (int idac=0; idac<NDACS; idac++) {
+
+     dacs[idac]=new ctbDac(this, idac, myDet);
+
+  }
+  dacs[NDACS]=new ctbDac(this, slsDetectorDefs::ADC_VPP, myDet);
+  dacs[NDACS+1]=new ctbDac(this, slsDetectorDefs::HIGH_VOLTAGE, myDet);
+  dacs[NDACS]->setLabel((char*)"ADC Vpp",2); 
+  dacs[NDACS+1]->setLabel((char*)"High Voltage",3); 
+}
+
+
+int ctbDacs::setDacAlias(string line) {
+  int is=-1, mv=0;
+  char tit[100];
+  int narg=sscanf(line.c_str(),"DAC%d %s %d",&is,tit,&mv);
+  if (narg<2)
+    return -1;
+  if (is>=0 && is<NDACS) 
+    dacs[is]->setLabel(tit,mv);
+  return is;
+
+}
+
+string ctbDacs::getDacAlias() {
+  ostringstream line;
+
+  for (int i=0; i<NDACS; i++)
+    line << dacs[i]->getLabel() << endl;
+  return line.str();
+}
+
+
+
+
+
+string ctbDacs::getDacParameters() {
+  ostringstream line;
+
+  for (int i=0; i<NDACS; i++) {
+    //line << "dacs:" << i << " " << dacs[i]->getValue << endl;
+    line << "dac:" << i << " " << dacs[i]->getValue() << endl;
+  } 
+  return line.str();
+}
+
+
+
+void  ctbDacs::update() {
+  for (int idac=0; idac<NDACS+1; idac++) {
+    dacs[idac]->getValue();
+  }
+}

ctbGui/ctbDacs.h

@@ -0,0 +1,75 @@
+
+
+#ifndef CTBDACS_H
+#define CTBDACS_H
+#include  <TGFrame.h>
+
+
+#define NDACS 18
+//#define NDACS 16
+
+
+class TGTextEntry;
+class TGLabel;
+class TGNumberEntry;
+class TGCheckButton;
+
+
+namespace sls
+{
+   class Detector;
+};
+
+#include <string>
+using namespace std;
+
+
+class ctbDac : public TGHorizontalFrame {
+
+
+ protected:
+  // TGLabel *dacsLabel;
+   TGNumberEntry *dacsEntry;
+   TGCheckButton *dacsUnit;
+   TGCheckButton *dacsLabel;
+   TGLabel *dacsValue;
+   int id;
+
+   sls::Detector* myDet;
+ public:
+   ctbDac(TGGroupFrame*, int , sls::Detector*);
+   void setValue();
+   void setValue(Long_t);
+   int getValue();
+   void setOn(Bool_t);
+   
+   int setLabel(char *tit, int mv);
+   string getLabel();
+int getMoenchDacId();
+
+
+   ClassDef(ctbDac,0)
+};
+
+class ctbDacs : public TGGroupFrame {
+private:
+  
+   ctbDac *dacs[NDACS+2];
+
+   sls::Detector* myDet;
+
+public:
+   ctbDacs(TGVerticalFrame *page, sls::Detector*);
+
+   int setDacAlias(string line);
+   // int setDacAlias(string line);
+   string getDacAlias();
+   string getDacParameters();
+
+   void update();
+
+   ClassDef(ctbDacs,0)
+};
+
+#endif
+

ctbGui/ctbDefs.h

@@ -0,0 +1,84 @@
+#pragma once
+
+#include <string>
+#include <stdexcept>
+#include <chrono>
+
+//#include "sls_detector_exceptions.h"
+//#include "ansi.h"
+#define RED    	 	"\x1b[31m"
+#define RESET   	"\x1b[0m"
+#define BOLD    	"\x1b[1m"
+#define cprintf(code, format, ...) printf(code format RESET, ##__VA_ARGS__)
+
+
+#define CATCH_DISPLAY(m, s) catch(...) { ctbDefs::DisplayExceptions(m, s); }
+#define CATCH_HANDLE(...) catch(...) { ctbDefs::HandleExceptions(__VA_ARGS__); }
+
+class ctbDefs {
+  public:
+    /**
+     * Empty Constructor
+     */
+    ctbDefs(){};
+
+    // convert double seconds to chrono ns
+    static std::chrono::nanoseconds ConvertDoubleStoChronoNS(double timeS) {
+        using std::chrono::duration;
+        using std::chrono::duration_cast;
+        using std::chrono::nanoseconds; 
+        return duration_cast<nanoseconds>(duration<double>(timeS));
+    }
+
+    // convert chrono ns to doubel s
+    static double ConvertChronoNStoDoubleS(std::chrono::nanoseconds timeNs) {
+        using std::chrono::duration;
+        using std::chrono::duration_cast;    
+        return duration_cast<duration<double>>(timeNs).count();
+    }
+
+    static void DisplayExceptions(std::string emsg, std::string src) {
+        try {
+            throw;
+        } /* catch (const sls::SocketError &e) {
+            throw;
+        } catch (const sls::SharedMemoryError &e) {
+            throw;
+        } */catch (const std::exception &e) {
+            ExceptionMessage(emsg, e.what(), src);
+        }
+    };
+
+    template <class CT> struct NonDeduced { using type = CT; };
+    template <class S, typename RT, typename... CT>
+    static void HandleExceptions(const std::string emsg, const std::string src, S* s,
+                                    RT (S::*somefunc)(CT...),
+                                    typename NonDeduced<CT>::type... Args) {
+        try {
+            throw;
+        } /*catch (const sls::SocketError &e) {
+            throw;
+        } catch (const sls::SharedMemoryError &e) {
+            throw;
+        } */catch (const std::exception &e) {
+
+            ExceptionMessage(emsg, e.what(), src);
+            (s->*somefunc)(Args...);
+        }
+    };
+
+    static void ExceptionMessage(std::string message, 
+                    std::string exceptionMessage,
+                    std::string source) {
+        // because sls_detector_exceptions cannot be included
+      if (exceptionMessage.find("hared memory") != std::string::npos) {
+            throw;
+        }
+      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/ctbGui.cpp

@@ -0,0 +1,157 @@
+#include <TApplication.h>
+#include <TColor.h>
+
+#include <TStyle.h>
+#include <TROOT.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <iostream>
+#include <fstream>
+#include <string>
+
+#include "Detector.h"
+#include "sls_detector_defs.h"
+//#include "sls_receiver_defs.h"
+#include "ctbMain.h"
+#include "ctbDefs.h"
+using namespace std;
+
+
+int main(int argc, char **argv) {
+
+
+  string afname, cfname, pfname;
+  int id=0;
+
+  int af=0, cf=0, pf=0;
+
+
+  cout << " *** " << argc << endl;
+  for (int ia=0; ia<argc; ia++) {
+    if (strcmp(argv[ia],"-alias")==0) {
+      if (ia+1<argc) {
+	afname=argv[ia+1];
+	ia++;
+	af=1;
+      }
+
+    } else if  (strcmp(argv[ia],"-config")==0) {
+      if (ia+1<argc) {
+	cfname=argv[ia+1];
+	ia++;
+	cf=1;
+      }
+
+
+    } else if  (strcmp(argv[ia],"-par")==0) {
+      if (ia+1<argc) {
+  pfname=argv[ia+1];
+	ia++;
+  pf=1;
+      }
+
+
+    } else if  (strcmp(argv[ia],"-id")==0) {
+      if (ia+1<argc) {
+	id=atoi(argv[ia+1]);
+	ia++;
+      }
+    } 
+  }
+  
+
+  cout << " *** "  << endl;
+  sls::Detector *myDet = nullptr;
+  try {
+    /****** Create detector ****************/
+    myDet=new sls::Detector(id);
+    cout << "Created multi detector id " << id << endl;
+
+    if (cf) {
+      myDet->loadConfig(cfname);
+      cout << "Config file loaded successfully" << endl;
+    } else {
+      cout << "No config file specified" << endl;
+    }
+    cout << "hostname " << myDet->getHostname() << endl;
+    
+    if (pf) {
+      myDet->loadParameters(pfname);
+      cout << "Loaded parameter file successfully" << endl;
+    } else{
+      cout  << "No parameter file specified" << endl;
+    }
+  } CATCH_DISPLAY ("Could not create detector/ load config/parameters.", "ctbGui::main")
+
+  /***********Create GUI stuff *******************/
+   TApplication theApp("App",&argc,argv);
+
+
+ gStyle->SetDrawBorder(0);
+  gStyle->SetCanvasColor(kWhite);
+  gStyle->SetCanvasDefH(800);
+  gStyle->SetCanvasDefW(800);
+  gStyle->SetCanvasBorderMode(0);
+  gStyle->SetPadBorderMode(0);
+  gStyle->SetPaintTextFormat("5.2f");
+  gStyle->SetLineWidth(2);
+  gStyle->SetTextSize(1.1);
+  gStyle->SetLabelSize(0.04,"xy");
+  gStyle->SetTitleSize(0.05,"xy");
+  gStyle->SetTitleOffset(1.0,"x");
+  gStyle->SetTitleOffset(1.1,"y");
+  gStyle->SetPadTopMargin(0.15);
+  gStyle->SetPadRightMargin(0.15);
+  gStyle->SetPadBottomMargin(0.15);
+  gStyle->SetPadLeftMargin(0.15);
+  gStyle->SetLegendBorderSize(1);
+  gStyle->SetFrameBorderMode(0);
+  gStyle->SetFrameFillColor(kWhite);
+  // gStyle->SetLegendFillColor(kWhite);
+  gStyle->SetTitleFillColor(kWhite);
+  gStyle->SetFillColor(kWhite);
+  gStyle->SetStatFontSize(0.03);
+  gStyle->SetStatBorderSize(1);
+  gStyle->SetStatFormat("6.4g");
+  gStyle->SetStatX(0.95);
+  gStyle->SetStatY(0.95);
+  gStyle->SetStatW(0.2);
+  gStyle->SetStatH(0.2);
+  gStyle->SetTitleX(0.1);
+  gStyle->SetTitleY(0.95);
+  gStyle->SetTitleBorderSize(0);
+  gStyle->SetTitleFontSize(0.05);
+  gROOT->SetStyle("Default");
+
+
+  TColor::InitializeColors();
+  const Int_t NRGBs = 5;
+  const Int_t NCont = 90;
+
+  Double_t stops[NRGBs] = { 0.00, 0.34, 0.61, 0.84, 1.00 };
+  Double_t red[NRGBs]   = { 0.00, 0.00, 0.87, 1.00, 0.51 };
+  Double_t green[NRGBs] = { 0.00, 0.81, 1.00, 0.20, 0.00 };
+  Double_t blue[NRGBs]  = { 0.51, 1.00, 0.12, 0.00, 0.00 };
+  TColor::CreateGradientColorTable(NRGBs, stops, red, green, blue, NCont);
+  gStyle->SetNumberContours(NCont);
+
+
+  gROOT->ForceStyle();
+  ctbMain *mf=new ctbMain(gClient->GetRoot(), myDet);
+
+  cout << " *** " << argc << endl;
+  for (int ia=0; ia<argc; ia++)
+    cout << argv[ia] << endl;
+  
+
+  cout << " *** "  << endl;
+  
+  if (af)
+    mf->loadAlias(afname);
+  else
+    cout << "no alias specified" << endl;
+
+   theApp.Run();
+
+   return 0;
+}

ctbGui/ctbLinkDef.h

@@ -0,0 +1,15 @@
+#pragma link C++ class ctbMain;
+#pragma link C++ class ctbDacs;
+#pragma link C++ class ctbDac;
+#pragma link C++ class ctbSignals;
+#pragma link C++ class ctbSignal;
+#pragma link C++ class ctbAdc;
+#pragma link C++ class ctbAdcs;
+#pragma link C++ class ctbLoop;
+#pragma link C++ class ctbWait;
+#pragma link C++ class ctbPattern;
+#pragma link C++ class ctbAcquisition;
+#pragma link C++ class ctbPower;
+#pragma link C++ class ctbPowers;
+#pragma link C++ class ctbSlowAdc;
+#pragma link C++ class ctbSlowAdcs;

ctbGui/ctbMain.cpp

@@ -0,0 +1,586 @@
+#include <TApplication.h>
+#include <TGClient.h>
+#include <TCanvas.h>
+#include <TF1.h>
+#include <TRandom.h>
+#include <TGButton.h>
+#include <TRootEmbeddedCanvas.h>
+#include <TGButtonGroup.h>
+#include <TGNumberEntry.h>
+#include <TGLabel.h>
+#include <TList.h>
+#include <TGFileDialog.h>
+#include <TGComboBox.h>
+#include <TH2F.h>
+#include <TColor.h>
+#include <TH1F.h>
+#include <TGraphErrors.h>
+#include <THStack.h>
+#include <TGTab.h>
+#include <TApplication.h>
+#include <TGCanvas.h>
+#include <stdlib.h>
+
+#include <TGMenu.h>
+#include <TGDockableFrame.h>
+//#include <TGMenuBar.h>
+//#include <TGPopupMenu.h>
+
+
+
+
+#include <stdio.h>
+#include <iostream>
+#include <fstream>
+#include <string>
+
+#include "Detector.h"
+#include "ctbDefs.h"
+#include "ctbMain.h"
+#include "ctbDacs.h"
+#include "ctbSlowAdcs.h"
+#include "ctbPowers.h"
+#include "ctbSignals.h"
+#include "ctbPattern.h"
+#include "ctbAdcs.h"
+#include "ctbAcquisition.h"
+//#include "ctbActions.h"
+
+using namespace std;
+
+
+
+ctbMain::ctbMain(const TGWindow *p, sls::Detector *det)
+  : TGMainFrame(p,800,800), pwrs(NULL), senses(NULL) {
+
+  myDet=det;
+
+  Connect("CloseWindow()", "ctbMain", this, "CloseWindow()");
+
+
+
+
+
+//   fMenuDock = new TGDockableFrame(this);
+//   AddFrame(fMenuDock, new TGLayoutHints(kLHintsExpandX, 0, 0, 1, 0));
+//   fMenuDock->SetWindowName("GuiTest Menu");
+
+  fMenuBarLayout = new TGLayoutHints(kLHintsTop | kLHintsExpandX);
+  fMenuBarItemLayout = new TGLayoutHints(kLHintsTop | kLHintsLeft, 0, 4, 0, 0);
+  fMenuBarHelpLayout = new TGLayoutHints(kLHintsTop | kLHintsRight);
+
+  fMenuFile = new TGPopupMenu(gClient->GetRoot());
+  int im=0;
+
+   fMenuFile->AddEntry("Open Alias", im++);
+   fMenuFile->AddEntry("Save Alias", im++);
+   fMenuFile->AddSeparator();
+   fMenuFile->AddEntry("Open Parameters", im++);
+   fMenuFile->AddEntry("Save Parameters", im++);
+   fMenuFile->AddSeparator();
+   fMenuFile->AddEntry("Open Configuration", im++);
+   fMenuFile->AddEntry("Save Configuration", im++);
+   fMenuFile->AddSeparator();
+   fMenuFile->AddEntry("Open Pattern", im++);
+   fMenuFile->AddEntry("Save Pattern", im++);
+   fMenuFile->AddSeparator();
+   fMenuFile->AddEntry("Exit", im++);
+
+    fMenuFile->Connect("Activated(Int_t)", "ctbMain", this,
+                       "HandleMenu(Int_t)");
+ 
+
+    i_dacs=-1;
+    i_pwrs=-1;
+    i_senses=-1;
+    i_sig=-1;
+    i_adcs=-1;
+    i_pat=-1;
+    i_acq=-1;
+
+    int i_page=0;
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+  TGVerticalFrame *vframe=new TGVerticalFrame(this, 800,1200); //main frame
+
+
+
+   fMenuBar = new TGMenuBar(vframe, 1, 1, kHorizontalFrame);
+   fMenuBar->AddPopup("&File", fMenuFile, fMenuBarItemLayout);
+//    fMenuBar->AddPopup("&Test", fMenuTest, fMenuBarItemLayout);
+//    fMenuBar->AddPopup("&View", fMenuView, fMenuBarItemLayout);
+//    fMenuBar->AddPopup("&Help", fMenuHelp, fMenuBarHelpLayout);
+
+   vframe->AddFrame(fMenuBar, fMenuBarLayout);
+
+  TGHorizontalFrame* hpage=new TGHorizontalFrame(vframe, 800,1200); //horizontal frame. Inside there should be the tab and the canvas
+  mtab=new TGTab(hpage, 1500, 1200); //tab!
+  //  page=new TGVerticalFrame(mtab, 1500,1200);
+
+  cout << "DACS" << endl;
+
+  TGCompositeFrame *tf = mtab->AddTab("DACs");
+  TGVerticalFrame *page=new TGVerticalFrame(tf, 1500,1200);
+  tf->AddFrame(page, new TGLayoutHints(kLHintsExpandX | kLHintsExpandY, 10,10,10,1));
+  dacs=new ctbDacs(page, myDet);
+  i_dacs=i_page++;
+  
+
+  cout << "power " << endl;
+  tf = mtab->AddTab("Power Supplies");
+  page=new TGVerticalFrame(tf, 1500,1200);
+  tf->AddFrame(page, new TGLayoutHints(kLHintsExpandX | kLHintsExpandY, 10,10,10,1));
+  pwrs=new ctbPowers(page, myDet);
+
+  i_pwrs=i_page++;
+
+  cout << "sense " << endl;
+  tf = mtab->AddTab("Sense");
+  page=new TGVerticalFrame(tf, 1500,1200);
+  tf->AddFrame(page, new TGLayoutHints(kLHintsExpandX | kLHintsExpandY, 10,10,10,1));
+  senses=new ctbSlowAdcs(page, myDet);
+
+  i_senses=i_page++;
+
+
+ 
+  cout << "signals " << endl;
+  tf = mtab->AddTab("Signals");
+  page=new TGVerticalFrame(tf, 1500,1200);
+  tf->AddFrame(page, new TGLayoutHints(kLHintsExpandX | kLHintsExpandY, 10,10,10,1));
+  sig=new ctbSignals(page, myDet);
+  sig->Connect("ToggledSignalPlot(Int_t)","ctbMain",this,"setSignalPlot(Int_t)");
+
+  i_sig=i_page++;
+
+  cout << "adcs " << endl;
+  tf = mtab->AddTab("ADCs");
+  page=new TGVerticalFrame(tf, 1500,1200);
+  tf->AddFrame(page, new TGLayoutHints(kLHintsExpandX | kLHintsExpandY, 10,10,10,1));
+  adcs=new ctbAdcs(page, myDet);
+  adcs->Connect("ToggledAdcPlot(Int_t)","ctbMain",this,"setADCPlot(Int_t)");
+  adcs->Connect("AdcEnable(Int_t)","ctbMain",this,"setADCEnable(Int_t)");
+  i_adcs=i_page++;
+
+
+  cout << "pattern" << endl;
+
+  tf = mtab->AddTab("Pattern");
+  page=new TGVerticalFrame(tf, 1500,1200);
+  tf->AddFrame(page, new TGLayoutHints(kLHintsExpandX | kLHintsExpandY, 10,10,10,1));
+  pat=new ctbPattern(page, myDet);
+  pat->Connect("patternFileChanged(const char*)","ctbMain",this,"setPatternFile(const char*)");
+  pat->Connect("patternCompilerChanged(const char*)","ctbMain",this,"setPatternCompiler(const char*)");
+  pat->Connect("analogSamplesChanged(const int)","ctbMain",this,"setAnalogSamples(int)");
+  pat->Connect("digitalSamplesChanged(const int)","ctbMain",this,"setDigitalSamples(int)");
+  pat->Connect("readoutModeChanged(int)","ctbMain",this,"setReadoutMode(int)");
+
+  i_pat=i_page++;
+
+  cout << "acquisition" << endl;
+
+  tf = mtab->AddTab("Acquisition");
+  page=new TGVerticalFrame(tf, 1500,1200);
+  tf->AddFrame(page, new TGLayoutHints(kLHintsExpandX | kLHintsExpandY, 10,10,10,1));
+  acq=new ctbAcquisition(page, myDet);
+
+
+  i_acq=i_page++;
+
+
+  // cout << "actions" << endl;
+  // tf = mtab->AddTab("Actions");
+  // page=new TGVerticalFrame(tf, 1500,1200);
+  // tf->AddFrame(page, new TGLayoutHints(kLHintsExpandX | kLHintsExpandY, 10,10,10,1));
+  // actions=new ctbActions(page, myDet);
+
+
+  // i_actions=i_page++;
+
+
+
+   cout << "tabs finished" << endl;
+
+  hpage->AddFrame(mtab,new TGLayoutHints(kLHintsExpandX | kLHintsExpandY, 10,10,10,1));
+
+  vframe->AddFrame(hpage,new TGLayoutHints(kLHintsExpandX | kLHintsExpandY, 10,10,10,1));
+  
+  AddFrame(vframe,new TGLayoutHints(kLHintsExpandX | kLHintsExpandY, 10,10,10,1));
+  vframe->MapWindow();
+  hpage->MapWindow();
+  mtab->MapWindow();
+  page->MapWindow();
+
+  // Sets window name and shows the main frame
+   cout << "dockabel" << endl;
+   TGDockableFrame *fdock=new TGDockableFrame(hpage);
+   hpage->AddFrame(fdock, new TGLayoutHints(kLHintsBottom | kLHintsCenterX | kLHintsExpandX | kLHintsExpandY, 10,10,10,10));
+   fdock->MapWindow();
+
+   cout << "canvas" << endl;
+//    // Creates widgets of the example
+
+
+   fEcanvas = new TRootEmbeddedCanvas ("Ecanvas",fdock,800,800);//hpage,800,800);
+   //fEcanvas = new TRootEmbeddedCanvas ("Ecanvas",this,800,800);//hpage,800,800);
+  // fEcanvas->Resize();
+  //  fEcanvas->GetCanvas()->Update();
+  //AddFrame(fEcanvas, new TGLayoutHints(kLHintsBottom | kLHintsCenterX | kLHintsExpandX | kLHintsExpandY, 10,10,10,10));
+
+  // // hpage->
+  fdock->AddFrame(fEcanvas, new TGLayoutHints(kLHintsBottom | kLHintsCenterX | kLHintsExpandX | kLHintsExpandY, 10,10,10,10));
+
+
+  fEcanvas->MapWindow();
+
+  acq->setCanvas(getCanvas());
+
+
+
+  hpage->MapSubwindows();
+   mtab->Connect("Selected(Int_t)","ctbMain",this,"tabSelected(Int_t)");
+
+
+
+   cout << "connect mtab" << endl;
+
+  try{  
+   setReadoutMode(pat->getReadoutMode());  
+  } CATCH_DISPLAY ("Could not get readout flags", "ctbPattern::getReadoutMode")
+
+   setADCEnable(adcs->setEnable());
+   setAnalogSamples(pat->getAnalogSamples());
+   setDigitalSamples(pat->getDigitalSamples());
+   
+   tabSelected(0);
+
+   SetWindowName("CTB Gui");
+   MapSubwindows();
+   Resize(1500,1200);
+
+   MapWindow();
+}
+
+void ctbMain::CloseWindow() {
+   gApplication->Terminate();
+}
+
+TCanvas* ctbMain::getCanvas() {
+  return fEcanvas->GetCanvas();
+}
+
+
+
+void ctbMain::HandleMenu(Int_t id)
+{
+   // Handle menu items.
+   
+  
+ 
+
+   switch (id) {
+
+   case 0:   // fMenuFile->AddEntry("Open Alias", im++);
+     cout << "Open Alias" << endl;
+         {
+             static TString dir(".");
+             TGFileInfo fi;
+             //fi.fFileTypes = filetypes;
+             fi.fIniDir    = StrDup(dir);
+             printf("fIniDir = %s\n", fi.fIniDir);
+             new TGFileDialog(gClient->GetRoot(), this, kFDOpen, &fi);
+             printf("Open file: %s (dir: %s)\n", fi.fFilename, fi.fIniDir);
+	     // dir = fi.fIniDir;
+	     if (fi.fFilename)
+	       loadAlias(fi.fFilename);
+          }
+         break;
+
+   case 1: // fMenuFile->AddEntry("Save Alias", im++);
+     cout << "Save Alias" << endl;
+         {
+             static TString dir(".");
+             TGFileInfo fi;
+             //fi.fFileTypes = filetypes;
+             fi.fIniDir    = StrDup(dir);
+             printf("fIniDir = %s\n", fi.fIniDir);
+             new TGFileDialog(gClient->GetRoot(), this, kFDSave, &fi);
+             printf("Save file: %s (dir: %s)\n", fi.fFilename, fi.fIniDir);
+	     // dir = fi.fIniDir;
+	     if (fi.fFilename)
+	       saveAlias(fi.fFilename);
+          }
+         break;
+   case 2: //fMenuFile->AddEntry("Open Parameters", im++);
+     cout << "Open Parameters" << endl;
+         {
+             static TString dir(".");
+             TGFileInfo fi;
+             //fi.fFileTypes = filetypes;
+             fi.fIniDir    = StrDup(dir);
+             printf("fIniDir = %s\n", fi.fIniDir);
+             new TGFileDialog(gClient->GetRoot(), this, kFDOpen, &fi);
+             printf("Open file: %s (dir: %s)\n", fi.fFilename, fi.fIniDir);
+	     // dir = fi.fIniDir;
+	     if (fi.fFilename)
+	       loadParameters(fi.fFilename);
+          }
+         break;
+
+   case 3: // fMenuFile->AddEntry("Open Configuration", im++);
+     cout << "Open configuration" << endl;
+         {
+             static TString dir(".");
+             TGFileInfo fi;
+             //fi.fFileTypes = filetypes;
+             fi.fIniDir    = StrDup(dir);
+             printf("fIniDir = %s\n", fi.fIniDir);
+             new TGFileDialog(gClient->GetRoot(), this, kFDOpen, &fi);
+             printf("Open file: %s (dir: %s)\n", fi.fFilename, fi.fIniDir);
+	     // dir = fi.fIniDir;
+	     if (fi.fFilename)
+	       loadConfiguration(fi.fFilename);
+          }
+         break;
+ 
+   case 4: //fMenuFile->AddEntry("Open Pattern", im++);
+     cout << "Open pattern" << endl;
+         {
+             static TString dir(".");
+             TGFileInfo fi;
+             //fi.fFileTypes = filetypes;
+             fi.fIniDir    = StrDup(dir);
+             printf("fIniDir = %s\n", fi.fIniDir);
+             new TGFileDialog(gClient->GetRoot(), this, kFDOpen, &fi);
+             printf("Open file: %s (dir: %s)\n", fi.fFilename, fi.fIniDir);
+	     // dir = fi.fIniDir;
+	     if (fi.fFilename)
+	       loadParameters(fi.fFilename);
+          }
+     break;
+
+   case 5:   //fMenuFile->AddEntry("Save Pattern", im++);
+     cout << "Save pattern" << endl;
+         {
+             static TString dir(".");
+             TGFileInfo fi;
+             //fi.fFileTypes = filetypes;
+             fi.fIniDir    = StrDup(dir);
+             printf("fIniDir = %s\n", fi.fIniDir);
+             new TGFileDialog(gClient->GetRoot(), this, kFDSave, &fi);
+             printf("Open file: %s (dir: %s)\n", fi.fFilename, fi.fIniDir);
+	     // dir = fi.fIniDir;
+	     if (fi.fFilename)
+	       savePattern(fi.fFilename);
+          }
+         break;
+
+   case 6: //  fMenuFile->AddEntry("Exit", im++);
+     CloseWindow();
+
+      default:
+         printf("Menu item %d selected\n", id);
+         break;
+   }
+}
+
+
+
+int  ctbMain::setADCPlot(Int_t i) {
+
+  //  cout << "ADC " << i << " plot or color toggled" << endl;
+  //  acq->setGraph(i,adcs->getGraph(i));
+  acq->setGraph(i,adcs->getEnabled(i),adcs->getColor(i));
+  return -1;
+}
+
+
+int  ctbMain::setSignalPlot(Int_t i) {
+
+  //  cout << "ADC " << i << " plot or color toggled" << endl;
+  //  acq->setGraph(i,adcs->getGraph(i));
+  acq->setBitGraph(i,sig->getPlot(i),sig->getColor(i));
+  return -1;
+}
+
+
+
+void  ctbMain::loadConfiguration(string fname) {
+  try{
+    myDet->loadConfig(fname);
+  } CATCH_DISPLAY ("Could not load config.", "ctbMain::loadConfiguration")
+}
+
+void  ctbMain::loadParameters(string fname) {
+  try{
+    myDet->loadParameters(fname);
+  } CATCH_DISPLAY ("Could not load parameters.", "ctbMain::loadParameters")
+}
+
+void  ctbMain::savePattern(string fname) {
+  try{
+    myDet->savePattern(fname);
+  } CATCH_DISPLAY ("Could not save pattern.", "ctbMain::savePattern")
+}
+
+
+
+int  ctbMain::loadAlias(string fname) {
+
+
+  string line;
+  char aaaa[1000];
+  int i;
+  ifstream myfile (fname.c_str());
+  if (myfile.is_open())
+  {
+    while ( getline (myfile,line) )
+    {
+      // cout << line ;
+      if (sscanf(line.c_str(),"BIT%d",&i)>0) {
+	//cout << "*******" << line<< endl;
+	sig->setSignalAlias(line);
+      // cout << line ;
+      } else if (sscanf(line.c_str(),"DAC%d",&i)>0) {
+	dacs->setDacAlias(line);
+	//	cout << "+++++++++" << line<< endl;
+      } else if (sscanf(line.c_str(),"ADC%d",&i)>0) {
+	adcs->setAdcAlias(line);
+	//	cout << "---------" << line<< endl;
+      }      //  else
+      //	cout << "<<<<<<<" << line << endl;
+      else if (sscanf(line.c_str(),"PAT%s",aaaa)>0) {
+	pat->setPatternAlias(line);
+	//	cout << "---------" << line<< endl;
+      }	else if (sscanf(line.c_str(),"V%s",aaaa)>0) {
+	    if (pwrs)	pwrs->setPwrAlias(line);
+	//	cout << "+++++++++" << line<< endl;
+      } else if (sscanf(line.c_str(),"SENSE%d",&i)>0) {
+	if (senses) senses->setSlowAdcAlias(line);
+	//	cout << "+++++++++" << line<< endl;
+      } 
+      
+    }
+    myfile.close();
+  }
+
+  else cout << "Unable to open file"; 
+
+  return 0;
+
+}
+
+
+
+
+
+int  ctbMain::saveAlias(string fname) {
+
+
+  string line;
+  ofstream myfile (fname.c_str());
+  if (myfile.is_open())
+  {
+    //while ( getline (myfile,line) )
+    // {
+      // cout << line ;
+      //if (sscanf(line.c_str(),"BIT%d",&i)>0) {
+	//cout << "*******" << line<< endl;
+    myfile << sig->getSignalAlias();
+      // cout << line ;
+    //  } else if (sscanf(line.c_str(),"DAC%d",&i)>0) {
+    myfile << dacs->getDacAlias();
+    if (pwrs) myfile << pwrs->getPwrAlias();
+    if (senses) myfile << senses->getSlowAdcAlias();
+	//	cout << "+++++++++" << line<< endl;
+    //  } else if (sscanf(line.c_str(),"ADC%d",&i)>0) {
+    myfile << adcs->getAdcAlias();
+	//	cout << "---------" << line<< endl;
+    //  }      //  else
+      //	cout << "<<<<<<<" << line << endl;
+    myfile << pat->getPatternAlias();
+      
+    //}
+    myfile.close();
+  }
+
+  else cout << "Unable to open file"; 
+
+  return 0;
+
+}
+
+
+
+
+
+
+
+
+
+
+
+void ctbMain::tabSelected(Int_t i) {
+
+  //  cout << "Selected tab " << i << endl;
+  // cout << "Current tab is " <<  mtab->GetCurrent() << endl;
+
+  if (i==i_dacs) dacs->update();
+  else if (i==i_pwrs) pwrs->update();
+  else if (i==i_senses) ;//senses->update();
+ else if (i==i_sig) sig->update();
+ else if (i==i_adcs) adcs->update();
+ else if (i==i_pat) pat->update();
+ else if (i==i_acq) acq->update();
+ else if (i==i_acq) acq->update();
+  // else if (i==i_actions) actions->update();
+ else cout << "Unknown tab " << i << endl;
+ 
+
+}
+
+void ctbMain::setPatternFile(const char* t) {
+  acq->setPatternFile(t);
+
+}
+
+void ctbMain::setPatternCompiler(const char* t) {
+  acq->setPatternCompiler(t);
+
+
+}
+
+void ctbMain::setAnalogSamples(const int n) {
+  acq->setAnalogSamples(n);
+
+
+}
+
+void ctbMain::setDigitalSamples(const int n) {
+  acq->setDigitalSamples(n);
+
+
+}
+
+void ctbMain::setReadoutMode(int flags) {
+  acq->setReadoutMode(flags);
+}
+
+void ctbMain::setADCEnable(Int_t reg){
+  acq->setADCEnable(reg);
+}

ctbGui/ctbMain.h

@@ -0,0 +1,128 @@
+#ifndef CTBMAIN_H
+#define CTBMAIN_H
+#include <TGFrame.h>
+
+
+class TRootEmbeddedCanvas;
+class TGButtonGroup;
+class TGVerticalFrame;
+class TGHorizontalFrame;
+class TGTextEntry;
+class TGLabel;
+class TGNumberEntry;
+class TH2F;
+class TGComboBox;
+class TGCheckButton;
+
+class   THStack;
+class   TGraphErrors;
+class  TGTextButton;
+class  TGTab;
+
+class   TGMenuBar;
+class   TGPopupMenu;
+class   TGDockableFrame;
+class TGLayoutHints;
+class TGCanvas;
+class TCanvas;
+
+class   ctbDacs;
+class   ctbSlowAdcs;
+class   ctbPowers;
+
+ 
+class  ctbSignals;
+
+namespace sls
+{
+   class Detector;
+};
+
+class  ctbPattern;
+class  ctbAdcs;
+class  ctbAcquisition;
+//class  ctbActions;
+
+#include <string>
+using namespace std;
+
+class ctbMain : public TGMainFrame { 
+private:
+
+
+  sls::Detector *myDet;
+
+
+
+   TRootEmbeddedCanvas *fEcanvas;
+   TRootEmbeddedCanvas *fModulecanvas;
+   TGButtonGroup *br;
+   
+   TGTab *mtab;
+
+   
+   ctbDacs *dacs;
+   int i_dacs;
+
+   ctbPowers *pwrs;
+   int i_pwrs;
+
+   ctbSlowAdcs *senses;
+   int i_senses;
+
+ 
+  ctbSignals *sig;
+  int i_sig;
+
+
+  ctbAdcs *adcs;
+  int i_adcs;
+  
+
+  ctbPattern *pat;
+  int i_pat;
+
+  ctbAcquisition *acq;
+  int i_acq;
+
+  // ctbActions *actions;
+  int i_actions;
+
+   TGDockableFrame    *fMenuDock;
+
+   TGMenuBar          *fMenuBar;
+   TGPopupMenu        *fMenuFile, *fMenuTest, *fMenuView, *fMenuHelp;
+   TGPopupMenu        *fCascadeMenu, *fCascade1Menu, *fCascade2Menu;
+   TGPopupMenu        *fMenuNew1, *fMenuNew2;
+   TGLayoutHints      *fMenuBarLayout, *fMenuBarItemLayout, *fMenuBarHelpLayout;
+   TGCanvas *myCanvas;
+
+
+public:
+   ctbMain(const TGWindow *p, sls::Detector *det);
+
+
+   int  loadAlias(string fname);
+   int  saveAlias(string fname);
+   void  loadParameters(string fname);
+   void  savePattern(string fname);
+   void  loadConfiguration(string fname);
+   void tabSelected(Int_t);
+   int setADCPlot(Int_t);
+   int setSignalPlot(Int_t);
+   void CloseWindow();
+
+   void setPatternFile(const char* t);
+
+   void setPatternCompiler(const char* t);
+   void setAnalogSamples(const int);
+   void setDigitalSamples(const int);
+   void setReadoutMode(int);
+   void setADCEnable(Int_t);
+
+   void HandleMenu(Int_t);
+   TCanvas* getCanvas();
+   ClassDef(ctbMain,0)
+};
+
+#endif

ctbGui/ctbPattern.h

@@ -0,0 +1,179 @@
+#ifndef CTBPATTERN_H
+#define CTBPATTERN_H
+#include  <TGFrame.h>
+
+
+#define NLOOPS 3
+#define NWAITS 3
+#define NADCS 32
+#define PATLEN 1024
+
+class TRootEmbeddedCanvas;
+class TGButtonGroup;
+class TGVerticalFrame;
+class TGHorizontalFrame;
+class TGTextEntry;
+class TGLabel;
+class TGNumberEntry;
+class TH2F;
+class TGComboBox;
+class TGCheckButton;
+class TGTextEntry;
+class TGCheckButton;
+
+class   THStack;
+class   TGraphErrors;
+class energyCalibration;
+class  TGTextButton;
+class  TGTab;
+
+namespace sls
+{
+   class Detector;
+};
+
+
+#include <string>
+using namespace std;
+
+
+
+class ctbLoop : public TGHorizontalFrame {
+ 
+
+ private:
+
+   TGNumberEntry *eLoopStartAddr; 
+   TGNumberEntry *eLoopStopAddr; 
+   TGNumberEntry *eLoopNumber; 
+
+   int id;
+
+   sls::Detector *myDet;
+
+ public:
+   ctbLoop(TGGroupFrame *page, int i,sls::Detector *det);
+   
+   void setNLoops();
+   void update();
+
+   ClassDef(ctbLoop,0)
+     };
+
+class ctbWait : public TGHorizontalFrame {
+ 
+
+ private:
+
+   TGNumberEntry *eWaitAddr; 
+   TGNumberEntry *eWaitTime; 
+
+   int id;
+
+   sls::Detector *myDet;
+
+ public:
+   ctbWait(TGGroupFrame *page, int i,sls::Detector *det);
+   
+   void setWaitTime();
+   void update();
+
+   ClassDef(ctbWait,0)
+     };
+
+
+
+
+
+
+
+class ctbPattern : public TGGroupFrame {
+private:
+   
+
+   TGNumberEntry *eAdcClkFreq;
+   TGNumberEntry *eRunClkFreq;
+   TGNumberEntry *eDBitClkFreq;
+   TGNumberEntry *eAdcClkPhase;
+   TGNumberEntry *eDBitClkPhase;
+   //TGNumberEntry *eRunClkPhase;
+
+   TGNumberEntry *eStartAddr;
+   TGNumberEntry *eStopAddr;
+   TGNumberEntry *eFrames;
+   TGNumberEntry *ePeriod;
+   TGNumberEntry *eTriggers;
+   // TGNumberEntry *eMeasurements;
+   TGNumberEntry *eAdcPipeline;
+   TGNumberEntry *eDBitPipeline;
+   
+   ctbLoop *eLoop[NLOOPS];
+   ctbWait *eWait[NWAITS];
+
+   TGTextEntry *patternCompiler;
+   TGTextEntry *patternFile;
+   
+   TGTextButton *browseCompiler;
+   TGTextButton *browseFile;
+   
+
+   TGNumberEntry *eAnalogSamples;
+   TGNumberEntry *eDigitalSamples;
+
+  TGCheckButton *cbAnalog;
+  TGCheckButton *cbDigital;
+  
+   char pat[PATLEN*8];
+
+   sls::Detector *myDet;
+
+public:
+
+   ctbPattern(TGVerticalFrame *page, sls::Detector *det);
+
+   void update();
+   void setAdcFreq();
+   void setRunFreq();
+   void setDBitFreq();
+   void setAdcPhase();
+   void setDBitPhase();
+   // void setRunPhase();
+   void setAdcPipeline();
+   void setDBitPipeline();
+   void setFrames();
+   void setTriggers();
+   // void setMeasurements();
+   void setPeriod();
+
+   
+   void chooseCompiler();
+   void choosePattern();
+
+   string getCompiler();
+   string getPatternFile();
+   
+   void setPatternAlias(string);
+   string getPatternAlias();
+
+
+   int getAnalogSamples();
+   void  setAnalogSamples();
+   int getDigitalSamples();
+   void  setDigitalSamples();
+   void  setReadoutMode(Bool_t);
+   int  getReadoutMode();
+
+
+   void setFile();
+   void setCompiler();
+   void patternFileChanged(const char*);
+   void patternCompilerChanged(const char*);
+   void analogSamplesChanged(const int t);
+   void digitalSamplesChanged(const int t);
+   void readoutModeChanged(int);
+
+
+   ClassDef(ctbPattern,0)
+};
+
+#endif

ctbGui/ctbPowers.cpp

@@ -0,0 +1,223 @@
+#include  <TGFrame.h>
+
+
+#include <TGButtonGroup.h>
+#include <TGNumberEntry.h>
+#include <TGLabel.h>
+#include <TList.h>
+
+#include <stdio.h>
+#include <iostream>
+#include <fstream>
+
+#include "ctbDefs.h"
+#include "ctbDacs.h"
+#include "ctbPowers.h"
+#include "Detector.h"
+#include "sls_detector_defs.h"
+
+using namespace std;
+
+
+
+ctbPower::ctbPower(TGGroupFrame* f, int i,  sls::Detector* d)
+  : ctbDac(f, i, d) 
+{
+  cout << "****************************************************************power " << i << endl;
+     dacsUnit->SetOn(kTRUE); 
+     dacsUnit->SetEnabled(kFALSE);
+
+     switch(i) {
+     case slsDetectorDefs::V_POWER_IO: 
+     	 dacsLabel->SetText("VIO"); 
+     	 break; 
+     case slsDetectorDefs::V_POWER_A: 
+     	 dacsLabel->SetText("VA"); 
+     	 break;  
+     case slsDetectorDefs::V_POWER_B: 
+     	 dacsLabel->SetText("VB"); 
+     	 break;   
+     case slsDetectorDefs::V_POWER_C: 
+     	 dacsLabel->SetText("VC");
+     	 break;    
+     case slsDetectorDefs::V_POWER_D: 
+     	 dacsLabel->SetText("VD");
+     	 break;      
+     case slsDetectorDefs::V_POWER_CHIP: 
+     	 dacsLabel->SetText("VCHIP"); 
+     	 dacsLabel->SetEnabled(kFALSE);
+     	 break;    
+     default: 
+     	 dacsLabel->SetText("Bad index"); 
+     	 break; 
+     };
+     
+
+     TGTextEntry *e=dacsEntry->TGNumberEntry::GetNumberEntry();
+     e->Disconnect 	("ReturnPressed()");
+     e->Disconnect 	("ValueSet(Long_t)");
+     
+     e->Connect("ReturnPressed()","ctbPower",this,"setValue()");
+     dacsEntry->Connect("ValueSet(Long_t)","ctbPower",this,"setValue(Long_t)");
+ };
+
+
+string ctbPower::getLabel() {
+
+  ostringstream line;
+  switch (id) {
+     case slsDetectorDefs::V_POWER_IO: 
+	 line << "VIO"; 
+	 break; 
+     case slsDetectorDefs::V_POWER_A: 
+	 line << "VA"; 
+	 break;  
+     case slsDetectorDefs::V_POWER_B: 
+	 line << "VB"; 
+	 break;   
+     case slsDetectorDefs::V_POWER_C: 
+	 line << "VC"; 
+	 break;    
+     case slsDetectorDefs::V_POWER_D: 
+	 line << "VD"; 
+	 break;      
+     case slsDetectorDefs::V_POWER_CHIP: 
+	 line << "VCHIP"; 
+	 break;    
+     default:  
+	 line << "VBAD"; 
+	 break; 
+
+  }
+  line << " " <<  dacsLabel->GetText() << endl;
+  return line.str();
+}
+
+void ctbPower::setValue(Long_t a) {ctbPower::setValue();}
+
+void ctbPower::setValue() {
+  cout << "***************************Setting power " << dacsEntry->GetIntNumber() << " " << id << " " << 1 << endl;
+ 
+  try {
+    myDet->setVoltage(static_cast<slsDetectorDefs::dacIndex>(id), dacsEntry->GetIntNumber());
+  } CATCH_DISPLAY ("Could not set power " + to_string(id) + ".", "ctbPower::setValue")
+
+  getValue();
+}
+
+
+int ctbPower::getValue() {
+  try {
+
+  int val = myDet->getVoltage(static_cast<slsDetectorDefs::dacIndex>(id)).tsquash("Different values");
+  cout << "****************************Getting power " << val << " " << id << " " << 1 << endl;
+
+  dacsValue->SetText(to_string(val).c_str());
+  if (val > 0) {
+    if (id != static_cast<int>(slsDetectorDefs::V_POWER_CHIP))
+      dacsLabel->SetOn(kTRUE);
+  } else {
+    dacsLabel->SetOn(kFALSE);
+  }
+
+  return val;
+
+  } CATCH_DISPLAY ("Could not get power " + to_string(id) + ".", "ctbPower::getValue") 
+
+  return -1;
+}
+
+
+
+ctbPowers::ctbPowers(TGVerticalFrame* page, sls::Detector* det)   : TGGroupFrame(page,"Power Supplies",kVerticalFrame) , myDet(det){
+
+
+  SetTitlePos(TGGroupFrame::kLeft);
+  page->AddFrame(this,new TGLayoutHints( kLHintsTop | kLHintsExpandX , 10,10,10,10));
+  MapWindow();
+  
+  // cout << "window mapped " << endl;
+
+  for (int idac=0; idac<NPOWERS; idac++) {
+     dacs[idac]=new ctbPower(this, slsDetectorDefs::V_POWER_A+idac, myDet);
+
+  }
+}
+
+
+int ctbPowers::setPwrAlias(string line) {
+
+  int is=-1;
+  char tit[100];
+
+  if (sscanf(line.c_str(),"VA %s",tit)) {
+    dacs[0]->setLabel(tit,1);
+    is=0;
+  }
+
+  if (sscanf(line.c_str(),"VB %s",tit)) {
+    dacs[1]->setLabel(tit,1);
+    is=1;
+  }
+
+  if (sscanf(line.c_str(),"VC %s",tit)) {
+    dacs[2]->setLabel(tit,1);
+    is=2;
+  }
+
+  if (sscanf(line.c_str(),"VD %s",tit)) {
+    dacs[3]->setLabel(tit,1);
+    is=3;
+  }
+
+  if (sscanf(line.c_str(),"VIO %s",tit)) {
+    dacs[4]->setLabel(tit,1);
+    is=4;
+  }
+
+  if (sscanf(line.c_str(),"VCHIP %s",tit)) {
+    dacs[5]->setLabel(tit,1);
+    is=5;
+  }
+    
+  return is;
+
+}
+
+string ctbPowers::getPwrAlias() {
+
+  ostringstream line;
+
+  for (int i=0; i<NPOWERS; i++)
+    line << dacs[i]->getLabel() << endl;
+  return line.str();
+
+}
+
+
+
+
+string ctbPowers::getPwrParameters() {
+
+  ostringstream line;
+  line << "v_a" << " " << dacs[0]->getValue() << " mv" << endl;
+  line << "v_b" << " " << dacs[1]->getValue() << " mv" << endl;
+  line << "v_c" << " " << dacs[2]->getValue() << " mv" << endl;
+  line << "v_d" << " " << dacs[3]->getValue() << " mv" << endl;
+  line << "v_io" << " " << dacs[4]->getValue() << " mv" << endl;
+  line << "v_chip" << " " << dacs[5]->getValue() << " mv" << endl;
+  // for (int i=0; i<POWERS; i++) {
+  //   //line << "dacs:" << i << " " << dacs[i]->getValue << endl;
+  //   line << "dac:" << i << " " << dacs[i]->getValue() << endl;
+  // } 
+  return line.str();
+}
+
+
+
+void  ctbPowers::update() {
+  for (int idac=0; idac<NPOWERS; idac++) {
+    dacs[idac]->getValue();
+
+  }
+}

ctbGui/ctbPowers.h

@@ -0,0 +1,67 @@
+#ifndef CTBPOWERS_H
+#define CTBPOWERS_H
+
+#include  <TGFrame.h>
+
+#define NPOWERS 6
+
+
+
+class TGTextEntry;
+class TGLabel;
+class TGNumberEntry;
+class TGCheckButton;
+
+
+
+
+namespace sls
+{
+   class Detector;
+};
+
+#include <string>
+using namespace std;
+
+
+class ctbPower : public ctbDac {
+
+  
+
+
+ public:
+
+  ctbPower(TGGroupFrame* f, int i, sls::Detector* d);
+
+    string getLabel();
+
+    int getValue();
+    void setValue();
+    void setValue(Long_t);
+
+   ClassDef(ctbPower,0)
+};
+
+
+class ctbPowers : public TGGroupFrame 
+{
+ private:
+  
+   ctbPower *dacs[NPOWERS]; 
+
+   sls::Detector* myDet; 
+
+public:
+   //ctbPowers();
+    ctbPowers(TGVerticalFrame*, sls::Detector*);
+
+    int setPwrAlias(string); 
+    string getPwrAlias(); 
+    string getPwrParameters(); 
+
+    void update(); 
+
+    ClassDef(ctbPowers,0)
+};
+
+#endif

ctbGui/ctbSignals.cpp

@@ -0,0 +1,541 @@
+#include <TApplication.h>
+#include <TGClient.h>
+#include <TCanvas.h>
+#include <TF1.h>
+#include <TRandom.h>
+#include <TGButton.h>
+#include <TRootEmbeddedCanvas.h>
+#include <TGButtonGroup.h>
+#include <TGNumberEntry.h>
+#include <TGLabel.h>
+#include <TList.h>
+#include <TGFileDialog.h>
+#include <TGComboBox.h>
+#include <TH2F.h>
+#include <TColor.h>
+#include <TH1F.h>
+#include <TGraphErrors.h>
+#include <THStack.h>
+#include <TGTab.h>
+
+#include <stdio.h>
+#include <iostream>
+#include <fstream>
+#include <TGButton.h>
+#include <TRootEmbeddedCanvas.h>
+#include <TGButtonGroup.h>
+#include <TGNumberEntry.h>
+#include <TGLabel.h>
+#include <stdio.h>
+#include <iostream>
+#include <fstream>
+#include <TColor.h>
+#include <TGColorSelect.h>
+
+
+#include "ctbSignals.h"
+#include "ctbDefs.h"
+#include "Detector.h"
+
+using namespace std;
+
+
+
+//#define DEFAULTFN "run_0.encal"
+
+
+ctbSignal::ctbSignal(TGFrame *page, int i,  sls::Detector *det)
+  : TGHorizontalFrame(page, 800,50), myDet(det), id(i), hsig(NULL) {
+
+
+  TGHorizontalFrame *hframe=this;
+  char tit[100];
+
+
+   
+   sprintf(tit, "BIT%d ",id);
+
+   sLabel= new TGLabel(hframe, tit);
+   hframe->AddFrame( sLabel,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 1, 1, 1, 1));
+   sLabel->MapWindow();
+   sLabel->SetTextJustify(kTextLeft);
+
+
+
+   sOutput= new TGCheckButton(hframe, "Out");
+   hframe->AddFrame( sOutput,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 1, 1, 1, 1));
+   sOutput->MapWindow();
+
+ 
+   sOutput->Connect("Toggled(Bool_t)","ctbSignal",this,"ToggledOutput(Bool_t)");
+
+   sDbitList= new TGCheckButton(hframe, "DB List");
+   hframe->AddFrame( sDbitList,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 1, 1, 1, 1));
+   sDbitList->MapWindow();
+
+   sDbitList->Connect("Toggled(Bool_t)","ctbSignal",this,"ToggledDbitList(Bool_t)");
+
+
+   sPlot= new TGCheckButton(hframe, "Plot");
+   hframe->AddFrame( sPlot,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 1, 1, 1, 1));
+   sPlot->MapWindow();
+
+   sPlot->Connect("Toggled(Bool_t)","ctbSignal",this,"ToggledPlot(Bool_t)");
+   
+   fColorSel = new TGColorSelect(hframe, id+1, 0);
+   fColorSel->Connect("ColorSelected(Pixel_t)","ctbSignal",this,"ColorChanged(Pixel_t)");
+   hframe->AddFrame(fColorSel, new TGLayoutHints(kLHintsTop |
+                          kLHintsLeft, 2, 0, 2, 2));
+   
+
+   fColorSel->SetColor(TColor::Number2Pixel(id+1));
+
+   
+   ToggledOutput(kFALSE);
+
+  
+   ToggledPlot(kFALSE);
+
+  //  if (id==63) {
+//      sOutput->SetOn(kTRUE);
+//      sOutput->SetEnabled(kFALSE);
+//    }
+// #ifdef CTB
+//    if (id==62) {
+//      sOutput->SetOn(kTRUE);
+//      sOutput->SetEnabled(kFALSE);
+//    }
+
+//    // if (id>=32 && id<48)
+//    //   fixOutput(1);
+//    // else if (id>=48 && id<64)
+//    //   fixOutput(0);
+
+// #endif
+}
+int ctbSignal::setSignalAlias(char *tit, int plot, int col) {
+
+  if (tit)
+    sLabel->SetText(tit);
+
+  if (plot>0) {
+      sPlot->SetOn(kTRUE,kTRUE); 
+  } else if (plot==0)
+      sPlot->SetOn(kFALSE,kTRUE);
+    
+  if (col>=0)
+    fColorSel->SetColor(col);//TColor::Number2Pixel(col+1));
+
+  fColorSel->SetEnabled(sPlot->IsOn());
+  return 0;
+
+}
+
+string ctbSignal::getSignalAlias() {
+  
+
+  ostringstream oss;
+  oss << "BIT" << dec << id << " " << sLabel->GetText()->Data() << " " << sPlot->IsOn() << hex << " " << fColorSel->GetColor() << endl;
+  return oss.str();
+
+
+
+
+}
+int ctbSignal::setOutput(Long64_t r) {
+
+
+  //  cout << hex << r << dec <<endl;
+
+  Long64_t mask=((Long64_t)1<<id);
+
+  if (r&mask)
+      sOutput->SetOn(kTRUE,kTRUE);
+  else 
+      sOutput->SetOn(kFALSE,kTRUE);
+    
+  return sOutput->IsOn();
+
+}
+
+int ctbSignal::fixOutput(int i) {
+
+  if (i) {
+    sPlot->SetOn(kFALSE);
+    //sClock->SetOn(kFALSE,kTRUE);
+    sOutput->SetOn(kTRUE);
+    //   sPlot->SetEnabled(kFALSE);
+    //  sClock->SetEnabled(kTRUE);
+  } else {
+    sOutput->SetOn(kFALSE,kTRUE);
+    //  sClock->SetOn(kFALSE);  
+    // sClock->SetEnabled(kFALSE);
+    sPlot->SetEnabled(kTRUE);
+  }
+  sOutput->SetEnabled(kFALSE);
+  return 0;
+
+}
+
+int ctbSignal::setDbitList(Long64_t r) {
+
+  if (r)
+      sDbitList->SetOn(kTRUE,kFALSE);
+  else 
+      sDbitList->SetOn(kFALSE,kFALSE);
+    
+  return sDbitList->IsOn();
+
+}
+
+int ctbSignal::isDbitList() { return sDbitList->IsOn();}
+int ctbSignal::isOutput() { return sOutput->IsOn();}
+int ctbSignal::isPlot() { return sPlot->IsOn();}
+Pixel_t ctbSignal::getColor(){return fColorSel->GetColor();}
+
+void ctbSignal::ToggledOutput(Bool_t b) {
+  ToggledSignalOutput(id);
+  if (b) {
+    // sClock->SetEnabled(kTRUE);
+    sPlot->SetOn(kFALSE);
+    // sPlot->SetEnabled(kFALSE);
+    fColorSel->SetEnabled(kFALSE);
+  } else {
+    // sClock->SetEnabled(kFALSE);
+    // sClock->SetOn(kFALSE);
+    sPlot->SetEnabled(kTRUE);
+    if ( sPlot->IsOn())
+      fColorSel->SetEnabled(kFALSE);
+    else
+      fColorSel->SetEnabled(kTRUE);
+  }
+
+
+}
+
+void ctbSignal::ToggledDbitList(Bool_t b){
+  Long_t mask=id;
+  ToggledSignalDbitList(mask);
+}
+
+
+void ctbSignal::ToggledPlot(Bool_t b){
+  Long_t mask=b<<id;
+  ToggledSignalPlot(mask);
+  fColorSel->SetEnabled(b);
+}
+
+void ctbSignal::ColorChanged(Pixel_t p){
+  ToggledSignalPlot(id);
+}
+
+
+void ctbSignal::ToggledSignalOutput(Int_t b) {
+  cout << "Toggle signal " << id << " " << b  << " " <<  sOutput->IsOn() <<endl;;
+  Emit("ToggledSignalOutput(Int_t)", id);
+}
+
+void ctbSignal::ToggledSignalDbitList(Int_t b){
+  cout << "Toggle dbitlist " << id << " " << b << endl;;
+  Emit("ToggledSignalDbitList(Int_t)", id);
+}
+
+void ctbSignal::ToggledSignalPlot(Int_t b){
+  Emit("ToggledSignalPlot(Int_t)", id);
+}
+
+
+ctbSignals::ctbSignals(TGVerticalFrame *page, sls::Detector *det)
+  : TGGroupFrame(page,"IO Signals",kVerticalFrame), myDet(det) {
+
+
+  SetTitlePos(TGGroupFrame::kLeft);
+  page->AddFrame(this,new TGLayoutHints( kLHintsTop | kLHintsExpandX , 10,10,10,10));
+  MapWindow();
+  
+
+  TGHorizontalFrame *hframe;
+ 
+  TGHorizontalFrame* hhframe=new TGHorizontalFrame(this, 800,800);
+  AddFrame(hhframe,new TGLayoutHints(kLHintsTop | kLHintsExpandX , 1,1,1,1));
+  hhframe->MapWindow();
+
+  TGVerticalFrame *vframe;
+
+
+
+
+  int idac=0;
+  for (idac=0; idac<NSIGNALS; idac++) {
+    if (idac%((NSIGNALS+2)/2)==0) {
+    vframe=new TGVerticalFrame(hhframe, 400,800);
+     hhframe->AddFrame(vframe,new TGLayoutHints(kLHintsTop | kLHintsExpandX , 1,1,1,1));
+    vframe->MapWindow();
+    }
+
+
+    signals[idac]=new ctbSignal(vframe,idac,myDet);
+    signals[idac]->Connect("ToggledSignalOutput(Int_t)","ctbSignals",this,"ToggledOutReg(Int_t)");
+    signals[idac]->Connect("ToggledSignalDbitList(Int_t)","ctbSignals",this,"ToggledDbitList(Int_t)");
+    signals[idac]->Connect("ToggledSignalPlot(Int_t)","ctbSignals",this,"ToggledPlot(Int_t)");
+ 
+    vframe->AddFrame(signals[idac],new TGLayoutHints(kLHintsTop | kLHintsExpandX , 1,1,1,1));
+    signals[idac]->MapWindow();
+
+
+  }
+
+  hframe=new TGHorizontalFrame(vframe, 800,50);
+  vframe->AddFrame(hframe,new TGLayoutHints(kLHintsTop | kLHintsExpandX , 1,1,1,1));
+  hframe->MapWindow();
+
+
+  TGLabel *label= new TGLabel(hframe, "IO Control Register: ");
+   hframe->AddFrame(label,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 1, 1, 1, 1));
+   label->MapWindow();
+   label->SetTextJustify(kTextLeft);
+
+
+   eIOCntrlRegister = new TGNumberEntry(hframe, 0, 16,999, TGNumberFormat::kNESHex,
+                                               TGNumberFormat::kNEANonNegative, 
+                                               TGNumberFormat::kNELNoLimits);
+
+  hframe->AddFrame(eIOCntrlRegister,new TGLayoutHints(kLHintsTop |  kLHintsExpandX, 1, 1, 1, 1));
+   eIOCntrlRegister->MapWindow();
+   eIOCntrlRegister->Resize(150,30);
+
+
+
+
+    hframe=new TGHorizontalFrame(vframe, 800,50);
+    vframe->AddFrame(hframe,new TGLayoutHints(kLHintsTop | kLHintsExpandX , 1,1,1,1));
+    hframe->MapWindow();
+   
+
+   label= new TGLabel(hframe, "DBit Offset: ");
+   hframe->AddFrame(label,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 1, 1, 1, 1));
+   label->MapWindow();
+   label->SetTextJustify(kTextLeft);
+
+
+   eDbitOffset = new TGNumberEntry(hframe, 0, 9,999, TGNumberFormat::kNESInteger,
+                                               TGNumberFormat::kNEANonNegative, 
+                                               TGNumberFormat::kNELNoLimits);
+
+  hframe->AddFrame(eDbitOffset,new TGLayoutHints(kLHintsTop |  kLHintsExpandX, 1, 1, 1, 1));
+   eDbitOffset->MapWindow();
+   eDbitOffset->Resize(150,30);
+   
+ 
+  TGTextEntry *e= eDbitOffset->TGNumberEntry::GetNumberEntry();
+    e->Connect("ReturnPressed()","ctbSignals",this,"setDbitOffset()");
+
+    e->Connect("ValueSet(Long_t)","ctbSignals",this,"setDbitOffset(Long_t)");
+}
+
+
+
+
+int ctbSignals::setSignalAlias(string line) {
+
+  int is=-1, plot=0, col=-1;
+  char tit[100];
+  int narg=sscanf(line.c_str(),"BIT%d %s %d %d",&is,tit,&plot,&col);
+  if (narg<2)
+    return -1;
+  if (is>=0 && is<NIOSIGNALS) {
+    signals[is]->setSignalAlias(tit,plot,col);
+  }
+  return is;
+
+}
+
+string ctbSignals::getSignalAlias() {
+
+  ostringstream oss;
+  for (int is=0; is<NIOSIGNALS; is++)
+    oss << signals[is]->getSignalAlias() << endl;
+
+
+    return oss.str();
+
+}
+
+
+void ctbSignals::update() {
+  try {
+
+    Long64_t oreg = static_cast<Long64_t>(myDet->getPatternIOControl().tsquash("Different values"));
+    cout << hex << oreg << dec << endl;
+
+    for (int idac=0; idac<NIOSIGNALS; idac++) {
+      signals[idac]->setOutput(oreg);
+    }
+
+  } CATCH_DISPLAY ("Could not get patternIOcontrol.", "ctbSignals::update")
+
+  if (myDet->getDetectorType().squash() == slsDetectorDefs::MOENCH) {
+    // enable all
+    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);
+        } 
+      }
+      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")
+  }
+}
+
+
+string ctbSignals::getSignalParameters() {
+
+  try {
+
+    auto val = myDet->getPatternIOControl().tsquash("Different values");
+    ostringstream line;
+    line <<  "patioctrl " << hex << val << dec << endl;
+    return line.str();
+
+  } CATCH_DISPLAY ("Could not get patternIOcontrol.", "ctbSignals::getSignalParameters")
+
+  return ("");
+}
+
+void ctbSignals::ToggledOutReg(Int_t mask) {
+  try {
+
+    Long64_t oreg = static_cast<Long64_t>(myDet->getPatternIOControl().tsquash("Different values"));
+    Long64_t m=((Long64_t)1)<<mask;
+    cout << dec << sizeof(Long64_t) << " " << mask << " " << hex << m << " ioreg " << oreg;
+
+    if (signals[mask]->isOutput()) {
+      cout <<  " or " << m ;
+      oreg|=m;
+    } else {
+      cout <<  " not " << ~m ;
+      oreg&=~m;
+    }
+    cout <<  " after " << oreg << endl;
+
+    myDet->setPatternIOControl(static_cast<uint64_t>(oreg));
+    oreg = static_cast<Long64_t>(myDet->getPatternIOControl().tsquash("Different values"));
+    cout << dec << sizeof(Long64_t) << " " << mask << " " << hex << m << " ioreg " << oreg << endl;
+
+    eIOCntrlRegister->SetText(to_string(oreg).c_str());
+
+  } CATCH_DISPLAY ("Could not get/set patternIOcontrol.", "ctbSignals::ToggledOutReg")
+
+}
+
+
+
+void ctbSignals::ToggledDbitList(Int_t mask){
+  try {
+
+    auto dbitlist = myDet->getRxDbitList().tsquash("Different values");
+
+    // anyway all enabled
+    if ((dbitlist.empty()) && (signals[mask]->isDbitList())) {
+      ;
+    } 
+    // set the dbitlist
+    else  {
+      std::vector <int> new_dbitlist;
+      for (int is=0; is<64; is++) {
+        if (signals[is]->isDbitList()){ 
+          new_dbitlist.push_back(is);
+          cout << is << " " << new_dbitlist.size() - 1 << endl;
+        }
+      }
+      if (new_dbitlist.size() > 64) 
+        new_dbitlist.clear();
+      myDet->setRxDbitList(new_dbitlist);
+      // get list again
+      dbitlist = myDet->getRxDbitList().tsquash("Different values");
+    }
+    
+    // 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);
+      }
+      // enable selected
+      for (const auto &value : dbitlist)  {
+        signals[value]->setDbitList(1);
+      }
+    }
+
+  } CATCH_DISPLAY ("Could not get/set receiver dbit list.", "ctbSignals::ToggledDbitList")
+}
+
+
+
+
+void ctbSignals::ToggledPlot(Int_t b) {
+  
+  Emit("ToggledSignalPlot(Int_t)", b);
+
+}
+
+
+void ctbSignals::ToggledSignalPlot(Int_t b) {
+  
+  Emit("ToggledSignalPlot(Int_t)", b);
+
+}
+
+
+Pixel_t ctbSignals::getColor(int i){
+  if (i>=0 && i<NSIGNALS) 
+    return signals[i]->getColor();
+  return static_cast<Pixel_t>(-1);
+}
+
+int ctbSignals::getPlot(int i){
+  if (i>=0 && i<NSIGNALS) 
+    return signals[i]->isPlot();
+  return -1;
+};
+
+void ctbSignals::setDbitOffset(Long_t) {
+  setDbitOffset();
+}
+
+void ctbSignals::setDbitOffset(){
+  try {
+    myDet->setRxDbitOffset(eDbitOffset->GetNumber());
+  } CATCH_DISPLAY ("Could not set receiver dbit offset.", "ctbSignals::setDbitOffset")
+}

ctbGui/ctbSignals.h

@@ -0,0 +1,121 @@
+#ifndef CTBSIGNALS_H
+#define CTBSIGNALS_H
+#include  <TGFrame.h>
+
+
+#define NSIGNALS 64
+
+#define NIOSIGNALS 64 //for moench board was 52
+
+
+#define ADCLATCH 63
+#define DIGSIGLATCH 62
+
+
+
+
+class TGTextEntry;
+class TGLabel;
+class TGNumberEntry;
+class TGCheckButton;
+class TH1I;
+class  TGTextButton;
+class TGColorSelect;
+
+
+
+class TGNumberEntry;
+namespace sls
+{
+   class Detector;
+};
+class ctbSignal;
+
+#include <string>
+using namespace std;
+
+class ctbSignal : public TGHorizontalFrame {
+
+  // RQ_OBJECT("ctbSignal")
+
+private:
+
+   TGLabel *sLabel;
+   TGCheckButton *sOutput;
+   TGCheckButton *sDbitList;
+   TGCheckButton *sPlot;
+   TGLabel *sValue;
+   TGNumberEntry *sEntry;
+   TGColorSelect *fColorSel;
+
+   sls::Detector *myDet;
+   Int_t id;
+
+   TH1I *hsig;
+
+public:
+
+   ctbSignal(TGFrame *page, int i, sls::Detector *det);
+   int setSignalAlias(char *tit, int plot, int col);
+   string getSignalAlias();
+
+   TH1I *getPlot() {return hsig;};
+   int setOutput(Long64_t);
+   int fixOutput(int);
+   int setDbitList(Long64_t);
+
+   void ToggledOutput(Bool_t); 
+   void ToggledDbitList(Bool_t); 
+   void ToggledPlot(Bool_t); 
+   void ColorChanged(Pixel_t); 
+
+   int isDbitList();
+   int isOutput();
+   int isPlot();
+   Pixel_t getColor();
+
+
+   void ToggledSignalOutput(Int_t); //*SIGNAL*
+   void ToggledSignalDbitList(Int_t); //*SIGNAL*
+   void ToggledSignalPlot(Int_t); //*SIGNAL*
+
+
+
+   ClassDef(ctbSignal,0)
+};
+
+class ctbSignals : public TGGroupFrame {
+private:
+ 
+  ctbSignal *signals[NSIGNALS];
+
+  TGNumberEntry *eIOCntrlRegister;
+  TGNumberEntry *eDbitOffset;
+
+  sls::Detector *myDet;
+
+public:
+  ctbSignals(TGVerticalFrame *page, sls::Detector *det);
+   int setSignalAlias(string line);
+   string getSignalAlias();
+
+   int getPlot(int);
+   Pixel_t getColor(int);
+   
+   void update();
+   // void saveParameters();
+   string getSignalParameters();
+
+   //void setDbitList(Int_t);
+   void setDbitOffset(Long_t);
+   void setDbitOffset();
+
+   void ToggledOutReg(Int_t);
+   void ToggledDbitList(Int_t);
+   void ToggledPlot(Int_t);
+   void ToggledSignalPlot(Int_t); //*SIGNAL*
+
+   ClassDef(ctbSignals,0)
+};
+
+#endif

ctbGui/ctbSlowAdcs.cpp

@@ -0,0 +1,182 @@
+
+#include <stdio.h>
+#include <iostream>
+#include <fstream>
+
+#include <TGTextEntry.h>
+#include <TGLabel.h>
+#include <TGNumberEntry.h>
+#include <TGButton.h>
+
+#include "ctbSlowAdcs.h"
+#include "ctbDefs.h"
+#include "Detector.h"
+#include "sls_detector_defs.h"
+
+using namespace std;
+
+
+
+
+ctbSlowAdc::ctbSlowAdc(TGGroupFrame *page, int idac, sls::Detector *det) : TGHorizontalFrame(page, 800,50) , id(idac), myDet(det) {
+
+
+    TGHorizontalFrame *hframe=this;
+
+    page->AddFrame(hframe,new TGLayoutHints(kLHintsTop | kLHintsExpandX , 1,1,1,1));
+    MapWindow();
+
+    char tit[100];
+    
+
+   sprintf(tit, "SENSE %d:",idac-1000);
+
+   dacsLabel= new TGLabel(hframe, tit);// new TGLabel(hframe, tit);
+   
+ 
+
+   hframe->AddFrame(dacsLabel,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 5, 5, 5, 5));
+   dacsLabel->MapWindow();
+   dacsLabel->SetTextJustify(kTextLeft);
+
+  
+
+
+   sprintf(tit, "xxx");
+   dacsValue= new TGLabel(hframe, tit);
+   hframe->AddFrame( dacsValue,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 5, 5, 5, 5));
+   dacsValue->MapWindow();
+   dacsValue->SetTextJustify(kTextLeft);
+
+   
+
+   TGTextButton *b= new TGTextButton(hframe, "Update");
+   hframe->AddFrame( b,new TGLayoutHints(kLHintsTop | kLHintsLeft| kLHintsExpandX, 5, 5, 5, 5));
+   b->MapWindow();
+   b->SetTextJustify(kTextLeft);
+
+   b->Connect("Clicked()","ctbSlowAdc",this,"getValue()");
+}
+
+
+
+int ctbSlowAdc::setLabel(char *tit) {
+  if(tit)
+    dacsLabel->SetText(tit);
+
+  return id;
+
+}
+
+string ctbSlowAdc::getLabel() {
+  ostringstream line;
+  line << dacsLabel->GetText() <<  endl;
+
+   //  line << "DAC" << dec << id << " " <<  dacsUnit->IsOn() << endl;
+
+  return line.str();
+}
+
+
+
+int ctbSlowAdc::getValue() {
+  try {
+    std::string s;
+
+    // temp
+    if (id == static_cast<int>(slsDetectorDefs::SLOW_ADC_TEMP)) {
+
+      int val = myDet->getTemperature(static_cast<slsDetectorDefs::dacIndex>(id)).tsquash("Different values");
+      cout << "slow adc temp" << " " << val << endl;
+
+      s = to_string(val) + " " + to_string(0x00b0) + "C";//<2F>C
+      dacsValue->SetText(s.c_str());
+      return val;
+    } 
+    
+    // mv
+    else {
+
+      int val = myDet->getSlowADC(static_cast<slsDetectorDefs::dacIndex>(id)).tsquash("Different values");
+      cout << "slow adc " << id << " " << val << endl;
+      
+      s = to_string(val) + " mV"; 
+      dacsValue->SetText(s.c_str());
+      return val;
+    }
+
+  } CATCH_DISPLAY ("Could not get slow dac " + to_string(id) + ".", "ctbSlowAdc::getValue")
+
+  return -1;
+}
+
+
+
+
+
+
+
+ctbSlowAdcs::ctbSlowAdcs(TGVerticalFrame *page, sls::Detector *det)   : TGGroupFrame(page,"Sense",kVerticalFrame) , myDet(det){
+
+  SetTitlePos(TGGroupFrame::kLeft);
+  page->AddFrame(this,new TGLayoutHints( kLHintsTop | kLHintsExpandX , 10,10,10,10));
+  MapWindow();
+  
+  // cout << "window mapped " << endl;
+
+ 
+  for (int idac=0; idac<NSLOWADCS + 1; idac++) {
+
+     adcs[idac]=new ctbSlowAdc(this, idac+1000, myDet);
+
+  }
+  adcs[NSLOWADCS]->setLabel((char*)"Temperature"); 
+}
+
+
+
+
+int ctbSlowAdcs::setSlowAdcAlias(string line) {
+
+  int is=-1, mv=0;
+  char tit[100];
+  int narg=sscanf(line.c_str(),"SENSE%d %s %d",&is,tit,&mv);
+  if (narg<2)
+    return -1;
+  if (is>=0 && is<NSLOWADCS) 
+    adcs[is]->setLabel(tit);
+  return is;
+
+}
+
+string ctbSlowAdcs::getSlowAdcAlias() {
+
+  ostringstream line;
+
+  for (int i=0; i<NSLOWADCS; i++)
+    line << adcs[i]->getLabel() << endl;
+  return line.str();
+}
+
+
+
+
+string ctbSlowAdcs::getAdcParameters() {
+
+  ostringstream line;
+
+  for (int i=0; i<NSLOWADCS; i++) {
+    //line << "dacs:" << i << " " << dacs[i]->getValue << endl;
+    line << "adc:" << i << " " << adcs[i]->getValue() << endl;
+  }    
+  line << "adc:-1" << adcs[NSLOWADCS]->getValue() << endl;
+  return line.str();
+}
+
+
+
+void  ctbSlowAdcs::update() {
+  for (int idac=0; idac<NSLOWADCS+1; idac++) {
+    adcs[idac]->getValue();
+  }
+}

ctbGui/ctbSlowAdcs.h

@@ -0,0 +1,78 @@
+
+
+#ifndef CTBSLOWADCS_H
+#define CTBSLOWADCS_H
+#include  <TGFrame.h>
+
+
+//#define NDACS 16
+#define NSLOWADCS 8
+
+
+
+
+class TGTextEntry;
+class TGLabel;
+class TGNumberEntry;
+class TGCheckButton;
+class TGTextButton;
+
+
+
+namespace sls
+{
+   class Detector;
+};
+
+#include <string>
+using namespace std;
+
+class ctbSlowAdc : public TGHorizontalFrame {
+
+
+ protected:
+  // TGLabel *dacsLabel;
+  // TGNumberEntry *dacsEntry;
+  // TGCheckButton *dacsUnit;
+   TGLabel *dacsLabel;
+   TGLabel *dacsValue;
+   int id;
+
+   sls::Detector* myDet;
+ public:
+   ctbSlowAdc(TGGroupFrame*, int , sls::Detector*);
+   int getValue();
+   
+   int setLabel(char *tit);
+   string getLabel();
+
+
+
+   ClassDef(ctbSlowAdc,0)
+};
+
+
+class ctbSlowAdcs : public TGGroupFrame {
+private:
+  
+
+
+   ctbSlowAdc *adcs[NSLOWADCS+1];
+
+   sls::Detector* myDet;
+
+public:
+   ctbSlowAdcs(TGVerticalFrame *page, sls::Detector*);
+
+   int setSlowAdcAlias(string line);
+   // int setDacAlias(string line);
+   string getSlowAdcAlias();
+   string getAdcParameters();
+
+   void update();
+
+   ClassDef(ctbSlowAdcs,0)
+};
+
+#endif
+

ctbGui/patternGenerator/deserializer.cpp

@@ -0,0 +1,110 @@
+
+#include <stdlib.h>  
+#include <stdint.h>  
+#include <string.h>  
+#include <sys/utsname.h>   
+#include <sys/types.h>
+#include <unistd.h>  
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <errno.h>
+#include <math.h>
+#include <fcntl.h>
+#include <stdarg.h>
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+
+int main(int argc, char *argv[]) {
+
+  int iarg;
+  char fname[10000];
+  uint64_t word;
+  int val[64];
+  int bit[64];
+  FILE *fdin;
+  
+  int nb=2;
+  int off=0;
+  int ioff=0;
+  int dr=24;
+  int idr=0;
+  int ib=0;
+  int iw=0;
+  bit[0]=19;
+  bit[1]=8;
+  //  for (iarg=0; iarg<argc; iarg++) printf("%d %s\n",iarg, argv[iarg]);
+  
+  if (argc<2) printf("Error: usage is %s fname [dr off  b0 b1 bn]\n");
+  
+  if (argc>2) dr=atoi(argv[2]);
+  if (argc>3) off=atoi(argv[3]);
+  if (argc>4) {
+  for (ib=0; ib<64; ib++) {
+    if (argc>4+ib) {
+      bit[ib]=atoi(argv[4+ib]);
+      nb++;
+    }
+  }
+  
+  }
+  
+  idr=0;
+  for (ib=0; ib<nb; ib++) {
+    val[ib]=0;
+  }
+  
+  
+  fdin=fopen(argv[1],"rb");
+  if (fdin==NULL) {
+    printf("Cannot open input file %s for reading\n",argv[1]);
+    return 200;
+  } 
+  
+  while (fread((void*)&word, 8, 1, fdin)) {
+    //   printf("%llx\n",word);
+    if (ioff<off) ioff++;
+    else {
+      
+      for (ib=0; ib<nb; ib++) {
+	if (word&(1<<bit[ib])) 	  val[ib]|=(1<<idr);
+      }
+      idr++;
+      if (idr==dr) {
+	idr=0;
+	fprintf(stdout,"%d\t",iw++);
+	for (ib=0; ib<nb; ib++) {
+#ifdef HEX
+	  fprintf(stdout,"%08llx\t",val[ib]);
+#else
+	  fprintf(stdout,"%lld\t",val[ib]);
+	  
+#endif
+	  
+	  val[ib]=0;
+	}
+	fprintf(stdout,"\n");
+      }
+      
+    }
+
+  }
+  if (idr!=0) {
+    fprintf(stdout,"%d\t",iw++);
+    for (ib=0; ib<nb; ib++) {
+#ifdef HEX
+	  fprintf(stdout,"%08llx\t",val[ib]);
+#else
+	  fprintf(stdout,"%lld\t",val[ib]);
+	  
+#endif
+	  
+	  val[ib]=0;
+    }
+    fprintf(stdout,"\n");
+  }
+
+  fclose(fdin);
+
+  return 0;
+}

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

ctbGui/patternGenerator/generator.c

@@ -126,11 +126,26 @@ void setwaittime(int iloop, uint64_t t) {
 void pw(){
   if (iaddr<MAXWORDS)
     PAT[iaddr]= pat;
-  fprintf(fd,"patword %04x %016llx\n",iaddr, pat);
+  fprintf(fd,"patword 0x%04x 0x%016llx\n",iaddr, pat);
   iaddr++;
   if (iaddr>=MAXWORDS) printf("ERROR: too many word in the pattern (%d instead of %d)!",iaddr, MAXWORDS);
 }
 
+int parseCommand(int clk, int cmdbit, int cmd, int length) {
+  int ibit;
+  clearbit(clk);
+  for (ibit=0; ibit<length; ibit++) {
+    if (cmd&(1>>ibit))
+      setbit(cmdbit);
+    else
+      clearbit(cmdbit);
+    pw();
+    /******/
+    setbit(clk);
+    pw();
+    /******/
+  }
+};
 
 
 
@@ -139,18 +154,18 @@ main(void) {
   fd=fopen(OUTFILE,"w");
 #include INFILE
 
-  fprintf(fd,"patioctrl %016llx\n",iopat);
-  fprintf(fd,"patclkctrl %016llx\n",clkpat);
-  fprintf(fd,"patlimits %04x %04x\n",start, stop);
+  fprintf(fd,"patioctrl 0x%016llx\n",iopat);
+  fprintf(fd,"patclkctrl 0x%016llx\n",clkpat);
+  fprintf(fd,"patlimits 0x%04x 0x%04x\n",start, stop);
 
   for (iloop=0; iloop<MAXLOOPS; iloop++) {
-    fprintf(fd,"patloop%d %04x %04x\n",iloop, startloopaddr[iloop], stoploopaddr[iloop]);
+    fprintf(fd,"patloop%d 0x%04x 0x%04x\n",iloop, startloopaddr[iloop], stoploopaddr[iloop]);
     if ( startloopaddr[iloop]<0 || stoploopaddr[iloop]<= startloopaddr[iloop]) nloop[iloop]=0;
     fprintf(fd,"patnloop%d %d\n",iloop, nloop[iloop]);
   }
 
   for (iloop=0; iloop<MAXTIMERS; iloop++) {
-    fprintf(fd,"patwait%d %04x\n",iloop, waitaddr[iloop]);
+    fprintf(fd,"patwait%d 0x%04x\n",iloop, waitaddr[iloop]);
     if (waitaddr[iloop]<0) waittime[iloop]=0;
     fprintf(fd,"patwaittime%d %lld\n",iloop, waittime[iloop]);
   }

docs/CMakeLists.txt

@@ -0,0 +1,69 @@
+find_package(Doxygen REQUIRED)
+find_package(Sphinx REQUIRED)
+
+
+
+
+# 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)
+
+#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/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")
+
+

docs/conf.py.in

@@ -0,0 +1,62 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# 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('.'))
+sys.path.insert(0, os.path.abspath('../bin/'))
+#sys.path.insert(0, '/home/l_frojdh/sls/build/bin')
+#sys.path.insert(0, @CMAKE_CURRENT_BINARY_DIR@)
+print(sys.path)
+
+# -- Project information -----------------------------------------------------
+
+project = 'slsDetectorPackage'
+copyright = '2019, PSD Detector Group'
+author = 'PSD Detector Group'
+version = '@PROJECT_VERSION@'
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['breathe',
+              'sphinx_rtd_theme',
+              'sphinx.ext.autodoc',
+              'sphinx.ext.napoleon',
+             ]
+
+breathe_default_project = "slsDetectorPackage"
+napoleon_use_ivar = True
+
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- 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"
+
+# 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']

docs/src/ToString.rst

@@ -0,0 +1,6 @@
+ToString
+==============
+
+String conversion
+
+.. doxygenfile:: ToString.h

docs/src/commandline.rst

@@ -0,0 +1,16 @@
+Command line interface
+==============================================
+
+Usage
+-------------
+
+Commands can be uses either with sls_detector_get or sls_detector_put
+
+.. code-block::
+
+    sls_detector_get vrf
+
+Commands
+-----------
+
+.. include:: ../commands.rst

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/container_utils.rst

@@ -0,0 +1,14 @@
+ContainerUtils
+==================
+
+Helper functions to handle standard container compliant 
+containers. Supports array, vector, sls::Result etc.
+
+While not a part of the public API we aim not to change this
+interface too much. However, we don't give the same strong
+guarantees as for Detector etc. 
+
+Any reoccurring container operation should probably be added to
+this file.  
+
+.. doxygenfile:: container_utils.h

docs/src/dependencies.rst

@@ -0,0 +1,53 @@
+Dependencies
+=========================
+
+While we value few dependencies some libraries are required in 
+order to not have to reinvent the wheel. Due to the state of package
+management in C++ we decided to bundle some of them with our source
+code. These are found in the libs/ directory. 
+
+-----------------------
+Core
+-----------------------
+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 > 3.12 
+ * C++11 compatible compiler. (We test with gcc and clang)
+ * ZeroMQ version 4
+
+-----------------------
+GUI
+-----------------------
+
+The GUI is currently using Qt4 but watch out for an upgrade to 5. 
+
+ * Qt 4.8
+ * Qwt 6.1
+
+-----------------------
+Python bindings
+-----------------------
+
+ * Python > 3.6
+ * pybind11 (packaged in libs/)
+
+
+-----------------------
+Documentation
+-----------------------
+
+The documentation that you are reading now is built with 
+
+ * Doxygen (to extract C++ classes etc.)
+ * Breathe (Sphinx plugin to handle doxygen xml)
+ * Sphinx 
+
+-----------------------
+Packaged in libs/
+-----------------------
+
+ * catch2 (unit testing)
+ * rapidjson (streaming from receiver)
+ * pybind11 (python bindings)  

docs/src/detector.rst

@@ -0,0 +1,16 @@
+Detector
+==============================================
+
+The sls::Detector is the new public API to control 
+detectors from C++. This API is also used internally
+for the Python bindings and the command line interface. 
+If a receiver has been configured this is also controlled
+through this class.
+
+Most, if not all, functions are called in parallel
+and the return value is a thin std::vector wrapper 
+containing results from all modules. (Result<T>)
+
+.. doxygenclass:: sls::Detector
+   :members:
+   :undoc-members:

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

@@ -0,0 +1,54 @@
+/**
+ * Utility program to generate input files for the command line
+ * documentation. Uses the string returned from sls_detector_help cmd
+ *
+ */
+#include <fstream>
+#include <iostream>
+#include <sstream>
+#include <string>
+#include <vector>
+
+#include "CmdProxy.h"
+#include "Detector.h"
+#include "sls_detector_defs.h"
+
+std::string replace_all(const std::string &src, const std::string &from,
+                        const std::string &to) {
+
+    std::string results;
+    std::string::const_iterator end = src.end();
+    std::string::const_iterator current = src.begin();
+    std::string::const_iterator next =
+        std::search(current, end, from.begin(), from.end());
+    while (next != end) {
+        results.append(current, next);
+        results.append(to);
+        current = next + from.size();
+        next = std::search(current, end, from.begin(), from.end());
+    }
+    results.append(current, next);
+    return results;
+}
+
+int main() {
+
+    std::cout << "Generating command line documentation!\n";
+
+    sls::CmdProxy proxy(nullptr);
+    auto commands = proxy.GetProxyCommands();
+
+    std::ofstream fs("commands.rst");
+    fs << ".. glossary::\n";
+
+    for (const auto &cmd : commands) {
+        std::ostringstream os;
+        proxy.Call(cmd, {}, -1, slsDetectorDefs::HELP_ACTION, os);
+
+        auto tmp = os.str().erase(0, cmd.size());
+        auto usage = tmp.substr(0, tmp.find_first_of('\n'));
+        tmp.erase(0, usage.size());
+        auto help = replace_all(tmp, "\n\t", "\n\t\t");
+        fs << '\t' << cmd << usage << help << "\n";
+    }
+}

docs/src/index.rst

@@ -0,0 +1,57 @@
+.. slsDetectorPackage documentation master file, created by
+   sphinx-quickstart on Mon Jul 29 17:38:15 2019.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+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
+    :maxdepth: 2
+
+    detector
+    result
+    receiver
+    examples
+
+.. toctree::
+    :caption: Python API
+    :maxdepth: 2
+
+    pydetector
+    pyenums
+    pyexamples
+
+.. toctree::
+    :caption: Command line
+    :maxdepth: 2
+
+    commandline  
+
+.. toctree::
+    :caption: Developer
+
+    container_utils
+    type_traits
+    ToString
+
+.. Indices and tables
+.. ==================
+
+.. * :ref:`genindex`
+.. * :ref:`modindex`
+.. * :ref:`search`

docs/src/installation.rst

@@ -0,0 +1,69 @@
+
+Installation
+==============================================
+
+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

@@ -0,0 +1,9 @@
+Detector
+=====================================================
+
+.. py:currentmodule:: slsdet
+
+.. autoclass:: Detector
+    :members:  
+    :undoc-members:
+    :show-inheritance:

docs/src/pyenums.rst

@@ -0,0 +1,12 @@
+Enums
+===========
+
+These enums are defined in slsDetectorDefs in the C++ package and 
+exposed to Python through pybind11.
+
+.. py:currentmodule:: sls_detector
+
+.. autoclass:: runStatus
+    :members:  
+    :undoc-members:
+    :show-inheritance:

docs/src/pyexamples.rst

@@ -0,0 +1,143 @@
+Examples
+================
+
+Some short hints on how to use the detector
+
+------------------------
+Simple threshold scan
+------------------------
+
+Assuming you have set up your detector with exposure time, period, enabled
+file writing etc.
+
+.. code-block:: python
+ 
+    from slsdet import Eiger
+
+    d = Eiger()
+    threshold = range(0, 2000, 200)
+    for th in threshold:
+        d.vthreshold = th
+        d.acquire()
+    
+
+If we want to control the shutter of for example, the big X-ray box we can add
+this line in our code. It then opens the shutter just before the measurement
+and closes is afterwards.
+    
+::
+
+    with xrf_shutter_open(box, 'Fe'):
+        for th in threshold:
+            d.vthreshold = th
+            d.acquire()
+        
+        
+-----------------------
+Reading temperatures
+-----------------------       
+
+::
+
+    d.temp
+    >>
+    temp_fpga     :  43.19°C,  51.83°C
+    temp_fpgaext  :  38.50°C,  38.50°C
+    temp_10ge     :  39.50°C,  39.50°C
+    temp_dcdc     :  42.50°C,  42.50°C
+    temp_sodl     :  39.50°C,  40.50°C
+    temp_sodr     :  39.50°C,  40.50°C
+    temp_fpgafl   :  40.87°C,  37.61°C
+    temp_fpgafr   :  34.51°C,  35.63°C
+    
+    d.temp.fpga
+    >> temp_fpga     :  40.84°C,  39.31°C
+    
+    t = d.temp.fpga[0]
+    t
+    >> 40.551
+    
+    t = d.temp.fpga[:]
+    t
+    >> [40.566, 39.128]
+
+
+-----------------------
+Non blocking acquire
+-----------------------
+
+There are mainly two ways to achieve a non blocking acquire when calling from the Python API. One is to manually start
+the detector and the second one is to launch the normal acquire from a different process. Depending on your measurement
+it might also be better to run the other task in a seperate process and use acq in the main thread.
+But lets start looking at the at the manual way:
+
+::
+
+    import time
+    from sls_detector import Eiger
+    d = Eiger()
+
+    n = 10
+    t = 1
+
+    d.exposure_time = t
+    d.n_frames = n
+    d.reset_frames_caught()
+
+    #Start the measurement
+    t0 = time.time()
+    d.start_receiver()
+    d.start_detector()
+
+    #Wait for the detector to be ready or do other important stuff
+    time.sleep(t*n)
+
+    #check if the detector is ready otherwise wait a bit longer
+    while d.status != 'idle':
+        time.sleep(0.1)
+
+    #Stop the receiver after we got the frames
+    #Detector is already idle so we don't need to stop it
+    d.stop_receiver()
+
+    lost = d.frames_caught - n
+    print(f'{n} frames of {t}s took {time.time()-t0:{.3}}s with {lost} frames lost ')
+
+    #Reset to not interfere with a potential next measurement
+    d.reset_frames_caught()
+
+Instead launching d.acq() from a different process is a bit easier since the control of receiver and detector
+is handled in the acq call. However, you need to join the process used otherwise a lot of zombie processes would
+hang around until the main process exits.
+
+::
+
+    import time
+    from multiprocessing import Process
+    from sls_detector import Eiger
+
+    def acquire():
+        """
+        Create a new Eiger object that still referes to the same actual detector
+        and same shared memory. Then launch acq.
+        """
+        detector = Eiger()
+        detector.acq()
+
+    #This is the detector we use throughout the session
+    d = Eiger()
+
+    #Process to run acquire
+    p = Process(target=acquire)
+
+    #Start the thread and short sleep to allow the acq to start
+    p.start()
+    time.sleep(0.01)
+
+    #Do some other work
+    while d.busy is True:
+        print(d.busy)
+        time.sleep(0.1)
+
+    #Join the process
+    p.join()

docs/src/receiver.rst

@@ -0,0 +1,6 @@
+Receiver
+==============================================
+
+.. doxygenclass:: slsReceiver
+   :members:
+..    :undoc-members:

docs/src/result.rst

@@ -0,0 +1,4 @@
+Result
+==============================================
+
+.. doxygenfile:: Result.h

docs/src/type_traits.rst

@@ -0,0 +1,7 @@
+TypeTraits
+==============
+
+Template meta functions in the same spirit as type_traits
+from the standard library.
+
+.. doxygenfile:: TypeTraits.h

examples/ang.off

@@ -1,24 +0,0 @@
- module 0 center 6.395E+02 +- 0.00E+00 conversion 6.5660E-05 +- 7.10E-09 offset 0.00000 +- 0.00015 
- module 1 center 6.395E+02 +- 0.00E+00 conversion 6.5650E-05 +- 7.09E-09 offset 5.00211 +- 0.00015 
- module 2 center 6.395E+02 +- 0.00E+00 conversion 6.5625E-05 +- 7.09E-09 offset 10.00733 +- 0.00015 
- module 3 center 6.395E+02 +- 0.00E+00 conversion 6.5618E-05 +- 7.09E-09 offset 15.00742 +- 0.00015 
- module 4 center 6.395E+02 +- 0.00E+00 conversion 6.5642E-05 +- 7.15E-09 offset 20.00620 +- 0.00015 
- module 5 center 6.395E+02 +- 0.00E+00 conversion 6.5612E-05 +- 7.09E-09 offset 25.00281 +- 0.00015 
- module 6 center 6.395E+02 +- 0.00E+00 conversion 6.5623E-05 +- 6.93E-09 offset 30.00704 +- 0.00015 
- module 7 center 6.395E+02 +- 0.00E+00 conversion 6.5605E-05 +- 7.10E-09 offset 34.99715 +- 0.00015 
- module 8 center 6.395E+02 +- 0.00E+00 conversion 6.5643E-05 +- 7.21E-09 offset 39.99533 +- 0.00015 
- module 9 center 6.395E+02 +- 0.00E+00 conversion 6.5638E-05 +- 7.09E-09 offset 44.99969 +- 0.00015 
- module 10 center 6.395E+02 +- 0.00E+00 conversion 6.5638E-05 +- 6.94E-09 offset 49.99859 +- 0.00015 
- module 11 center 6.395E+02 +- 0.00E+00 conversion 6.5644E-05 +- 7.10E-09 offset 54.99499 +- 0.00015 
- module 12 center 6.395E+02 +- 0.00E+00 conversion 6.5618E-05 +- 7.09E-09 offset 59.99120 +- 0.00015 
- module 13 center 6.395E+02 +- 0.00E+00 conversion 6.5607E-05 +- 7.11E-09 offset 64.98880 +- 0.00015 
- module 14 center 6.395E+02 +- 0.00E+00 conversion 6.5609E-05 +- 7.09E-09 offset 69.98205 +- 0.00015 
- module 15 center 6.395E+02 +- 0.00E+00 conversion 6.5611E-05 +- 7.09E-09 offset 74.98379 +- 0.00015 
- module 16 center 6.395E+02 +- 0.00E+00 conversion 6.5619E-05 +- 4.72E-09 offset 79.98559 +- 0.00015 
- module 17 center 6.395E+02 +- 0.00E+00 conversion 6.5604E-05 +- 7.09E-09 offset 84.98376 +- 0.00015 
- module 18 center 6.395E+02 +- 0.00E+00 conversion 6.5605E-05 +- 7.09E-09 offset 89.98307 +- 0.00015 
- module 19 center 6.395E+02 +- 0.00E+00 conversion 6.5616E-05 +- 7.09E-09 offset 94.98907 +- 0.00015 
- module 20 center 6.395E+02 +- 0.00E+00 conversion 6.5634E-05 +- 7.08E-09 offset 99.97965 +- 0.00015 
- module 21 center 6.395E+02 +- 0.00E+00 conversion 6.5608E-05 +- 4.16E-09 offset 104.99732 +- 0.00016 
- module 22 center 6.395E+02 +- 0.00E+00 conversion 6.5608E-05 +- 7.09E-09 offset 109.98646 +- 0.00015 
- module 23 center 6.395E+02 +- 0.00E+00 conversion 6.5649E-05 +- 7.09E-09 offset 114.98765 +- 0.00015 

examples/bad.chans

@@ -1,5 +0,0 @@
-15
-1528
-5000
-6513
-

examples/config_gen_script/generic_example.config

@@ -0,0 +1,39 @@
+hostname hostname1+hostname2+hostname3+hostname55+
+header_var1 wow
+header_var2 great
+header_var3 very nice
+
+0:counter1 100
+0:counter2 1024
+0:counter3 1500
+0:forallmodules val_mod1
+0:constant1 const1
+0:constant2 const2
+0:constant3 const3 /path/to/something
+
+1:counter1 101
+1:counter2 1036
+1:counter3 1503
+1:forallmodules val_mod2
+1:constant1 const1
+1:constant2 const2
+1:constant3 const3 /path/to/something
+
+2:counter1 102
+2:counter2 1048
+2:counter3 1506
+2:forallmodules val_mod3
+2:constant1 const1
+2:constant2 const2
+2:constant3 const3 /path/to/something
+
+3:counter1 103
+3:counter2 1060
+3:counter3 1509
+3:forallmodules val_mod4
+3:constant1 const1
+3:constant2 const2
+3:constant3 const3 /path/to/something
+
+footer1 foot1
+footer2 somethingelseathebottom

examples/config_gen_script/generic_example.config_gen

@@ -0,0 +1,47 @@
+#!/bin/bash
+
+# local variables
+a_variable=/path/to/something
+
+# HOSTNAMES is special
+# Beside of the hostname line it also defines the amount of modules
+# for the body part
+# take care for the last space
+HOSTNAMES="hostname1 hostname2 hostname3 hostname55 "
+
+## header contains constant values at the beginning of the file
+header=(
+header_var1="wow"
+header_var2="great"
+header_var3="very nice"
+)
+
+## the body part is for each half module
+# counters will count automatically
+# the number behind ':' indicates the incrementation value
+
+counters=(
+counter1="100:1"
+counter2="1024:12"
+counter3="1500:3"
+)
+
+# constant values
+constants=(
+constant1="const1"
+constant2="const2"
+constant3="const3 ${a_variable}"
+)
+
+# lists contains space separated lists each value for each half module
+lists=(
+forallmodules="val_mod1 val_mod2 val_mod3 val_mod4"
+)
+
+
+## footer contains constant values for the end of the file
+footer=(
+footer1=foot1
+footer2=somethingelseathebottom
+)
+

examples/gotthard2_veto_photon.txt

@@ -0,0 +1,132 @@
+#G1 Energy #G2 Energy
+300	7000
+
+#G0 pedestal    G1 pedestal    G2 pedestal    G0 gain    G1 gain    G2 gain (for every channel) ADU
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
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+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
+100        100        100        10        1        0.1
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examples/gotthard_setup.det

@@ -8,7 +8,7 @@ period 0.000024984
 delay 0.999999968
 gates 1
 frames 300000.000000000
-cycles 1.000000000
+triggers 1.000000000
 timing auto
 fineoff 0.000000
 startscript none

examples/gotthard_two.config

@@ -0,0 +1,57 @@
+detsizechan 2560 1
+
+hostname bchip074+bchip075+
+
+
+0:extsig:0 trigger_in_rising_edge
+0:rx_tcpport 1954
+0:rx_udpport 50001
+0:vhighvoltage 0
+
+1:extsig:0 trigger_in_rising_edge
+1:rx_tcpport 1955
+1:rx_udpport 50002
+1:vhighvoltage 0
+
+##############################################################################
+#########
+######### Uncomment this part to use the gotthard25umZmq process
+#########
+##############################################################################
+
+# #replace my_receiver_hostname with the hostname of IP of the machine where the receiver runs
+#0:rx_zmqip my_receiver_hostname 
+#0:rx_zmqport 30003
+# #replace my_client_hostname with the hostname of IP of the machine where the client/GUI or softIOC runs
+#0:zmqip my_client_hostname 
+#0:zmqport  40003
+
+# #replace my_receiver_hostname with the hostname of IP of the machine where the receiver runs
+#1:rx_zmqip my_receiver_hostname 
+#1:rx_zmqport 30004
+# #replace my_client_hostname with the hostname of IP of the machine where the client/GUI or softIOC runs
+#1:zmqip  my_client_hostname 
+#1:zmqport  40004
+
+##############################################################################
+#########
+######### until here
+#########
+##############################################################################
+
+
+r_readfreq 1
+rx_datastream 1
+
+#replace my_receiver_hostname with the hostname of 1Gb IP of the machine where the receiver runs
+rx_hostname my_receiver_hostname
+rx_datastream 1
+outdir /tmp/
+
+
+settings veryhighgain
+exptime 0.000005
+period 0.0001
+
+vhighvoltage 90
+

examples/howto_gotthard_twomodules.txt

@@ -0,0 +1,13 @@
+Turn on the two receivers:
+slsReceiver -t1954 &
+slsReceiver -t1955 &
+
+Switch on the photon conversion on the receiver machine (replace my_receiver_hostname):
+gotthard25umZmq my_receiver_hostname 30003 my_receiver_hostname 40003 &
+
+Run the configuration file:
+sls_detector_put config bchip2modules.config 
+
+
+Start your measurements using the command line, the slsDetectorGui or the EPICS driver
+

examples/jctb_moench03_T1.config

@@ -0,0 +1,501 @@
+initialchecks 0
+#############################################
+### edit with hostname or IP address of your detector 
+############################################
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+dbitclk 40
+
+
+
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+patclkctrl 0000000000000000
+patlimits 0000 018c
+patloop0 013a 016b
+patnloop0 199
+patloop1 0400 0400
+patnloop1 0
+patloop2 0400 0400
+patnloop2 0
+patwait0 00aa
+patwaittime0 10000
+patwait1 0400
+patwaittime1 0
+patwait2 0400
+patwaittime2 0
+
+
+#0:rx_tcpport 1977
+
+#############################################
+### 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
+
+rx_datastream 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
+adcinvert 4a342593
+#0xb5cbda6c
+asamples 5000
+dsamples 0
+adcphase 30 deg
+adcpipeline 14
+adcreg 14 40
+
+
+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

examples/jungfrau.config

@@ -1,15 +1,16 @@
-hostname bchip038+
+hostname localhost
 
 0:rx_udpport 50004
-0:rx_udpip 10.1.1.100
-0:detectorip 10.1.1.10
-rx_hostname pcmoench01
+0:rx_udpip 172.24.8.84
+0:detectorip 172.24.8.254
+rx_hostname localhost
 
-powerchip 1
+#powerchip 1
+#vhighvoltage 200
 
 #extsig:0 trigger_in_rising_edge
 #timing trigger
 
-outdir /external_pool/jungfrau_data/softwaretest
+outdir /tmp/slsdetector
 
 

examples/jungfrau_two.config

@@ -17,6 +17,7 @@ hostname bchip048+bchip052+
 rx_hostname pcmoench01
 
 powerchip 1
+vhighvoltage 200
 #extsig:0 trigger_in_rising_edge
 #timing trigger
 

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
+
+