release notes for 9.2.0

.clang-format

@@ -1,7 +0,0 @@
-BasedOnStyle: LLVM
-IndentWidth: 4
-
-UseTab: Never
-ColumnLimit: 80
-AlignConsecutiveAssignments: false 
-AlignConsecutiveMacros: true

.clang-tidy

@@ -1,42 +0,0 @@
----
-Checks:          '*, 
-                    -altera-*,
-                    -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,
-                    -readability-identifier-length,
-                    -cppcoreguidelines-pro-bounds-constant-array-index,
-                    -cppcoreguidelines-pro-type-reinterpret-cast,
-                    -llvm-header-guard,
-                    -modernize-use-nodiscard,
-                    -misc-non-private-member-variables-in-classes,
-                    -readability-static-accessed-through-instance,
-                    -readability-braces-around-statements,
-                    -readability-isolate-declaration,
-                    -readability-implicit-bool-conversion,
-                    -readability-identifier-length,
-                    -readability-identifier-naming,
-                    -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,
-                    -llvmlibc-*'
-
-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 }
-...

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,42 +0,0 @@
----
-name: Bug Report
-about: Create a report to help us improve 
-title: New Bug Report
-labels: action - Bug, priority - Unclassified, status - Pending
-template: bug_report.md
----
-<!-- Preview changes before submitting -->
-<!-- Please fill out everything with an *, as this report will be discarded otherwise -->
-<!-- This is a comment, the syntax is a bit different from c++ or bash -->
-
-##### *Distribution: 
-<!-- RHEL7, RHEL6, Fedora, etc -->
-
-
-##### *Detector type: 
-<!-- If applicable, Eiger, Jungfrau, Mythen3, Gotthard2, Gotthard, Moench, ChipTestBoard -->
-
-##### *Software Package Version: 
-<!-- developer, 4.2.0, 4.1.1, etc -->
-
-##### Priority:
-<!-- Super Low, Low, Medium, High, Super High -->
-
-##### *Describe the bug
-<!--  A clear and concise description of what the bug is -->
-
-##### Expected behavior
-<!--  A clear and concise description of what you expected to happen. -->
-
-##### To Reproduce
-<!--  Steps to reproduce the behavior: -->
-<!--  1. Go to '...' -->
-<!--  2. Click on '....' -->
-<!--  3. Scroll down to '....' -->
-<!--  4. See error -->
-
-##### Screenshots
-<!--  If applicable, add screenshots to help explain your problem. -->
-
-##### Additional context
-<!--  Add any other context about the problem here. -->

.github/ISSUE_TEMPLATE/change_request.md

@@ -1,28 +0,0 @@
----
-name: Change Request
-about: Suggest a change to an existing feature
-title: New Change Request
-labels: action - Change, priority - Unclassified, status - Pending
-template: change_request.md
----
-<!-- Preview changes before submitting -->
-<!-- Please fill out everything with an *, as this report will be discarded otherwise -->
-<!-- This is a comment, the syntax is a bit different from c++ or bash -->
-
-##### *Detector type: 
-<!-- If applicable, Eiger, Jungfrau, Mythen3, Gotthard2, Gotthard, Moench, ChipTestBoard -->
-
-##### *Software Package Version: 
-<!-- developer, 4.2.0, 4.1.1, etc -->
-
-##### Priority:
-<!-- Super Low, Low, Medium, High, Super High -->
-
-##### *State the change request:
-<!--  A clear and concise description of what the change is to an existing feature -->
-
-##### Is your change request related to a problem. Please describe:
-<!-- A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] -->
-
-##### Additional context:
-<!--  Add any other context about the feature here -->

.github/ISSUE_TEMPLATE/config.yml

@@ -1 +0,0 @@
-blank_issues_enabled: false

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,34 +0,0 @@
----
-name: Feature Request
-about: Suggest a feature, documentation or submit a question
-title: New Feature Request
-labels: action - Enhancement, priority - Unclassified, status - Pending
-template: feature_request.md
----
-<!-- Preview changes before submitting -->
-<!-- Please fill out everything with an *, as this report will be discarded otherwise -->
-<!-- This is a comment, the syntax is a bit different from c++ or bash -->
-
-##### *Detector type: 
-<!-- If applicable, Eiger, Jungfrau, Mythen3, Gotthard2, Gotthard, Moench, ChipTestBoard -->
-
-##### *Software Package Version: 
-<!-- developer, 4.2.0, 4.1.1, etc -->
-
-##### Priority:
-<!-- Super Low, Low, Medium, High, Super High -->
-
-##### *State the feature:
-<!--  A clear and concise description of what the feature is -->
-
-##### Is your feature request related to a problem. Please describe:
-<!-- A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] -->
-
-##### Describe the solution you'd like:
-<!-- A clear and concise description of what you want to happen -->
-
-##### Describe alternatives you've considered:
-<!-- A clear and concise description of any alternative solutions or features you've considered -->
-
-##### Additional context:
-<!--  Add any other context about the feature here -->

.github/workflows/cmake.yaml

@@ -1,47 +0,0 @@
-name: Native CMake Build
-
-on: [push, pull_request]
-
-env:
-  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
-  BUILD_TYPE: Debug
-
-jobs:
-  build:
-    # The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
-    # You can convert this to a matrix build if you need cross-platform coverage.
-    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
-    runs-on: ubuntu-latest
-    name: Configure and build using cmake
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.12
-          cache: 'pip'
-      - run: pip install pytest numpy
-
-      - uses: awalsh128/cache-apt-pkgs-action@latest
-        with:
-          packages: libhdf5-dev qtbase5-dev qt5-qmake libqt5svg5-dev libpng-dev libtiff-dev
-          version: 1.0
-
-      - name: Configure CMake
-        # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
-        # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
-        run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -DSLS_USE_TESTS=ON -DSLS_USE_HDF5=ON -DSLS_USE_GUI=ON -DSLS_USE_MOENCH=ON -DSLS_USE_PYTHON=ON
-
-      - name: Build
-        # Build your program with the given configuration
-        run: cmake --build ${{github.workspace}}/build -j4 --config ${{env.BUILD_TYPE}}
-
-      - name: C++ unit tests
-        working-directory: ${{github.workspace}}/build
-        run: ctest -C ${{env.BUILD_TYPE}} -j1
-
-      - name: Python unit tests
-        working-directory: ${{github.workspace}}/build/bin
-        run: |
-          python -m pytest ${{github.workspace}}/python/tests
-
-

.github/workflows/conda_library.yaml

@@ -1,42 +0,0 @@
-name: Build slsdetlib
-
-on: [pull_request]
-
-jobs:
-  build:
-    strategy:
-      fail-fast: false
-      matrix:
-        platform: [ubuntu-latest, ] # macos-12, windows-2019]
-        python-version: ["3.12",]
-
-    runs-on: ${{ matrix.platform }}
-
-    # The setup-miniconda action needs this to activate miniconda
-    defaults:
-      run:
-        shell: "bash -l {0}"
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Get conda
-        uses: conda-incubator/setup-miniconda@v3.0.4
-        with:
-          python-version: ${{ matrix.python-version }}
-          channels: conda-forge
-
-      - name: Prepare
-        run: conda install conda-build conda-verify pytest anaconda-client
-
-      - name: Disable upload
-        run: conda config --set anaconda_upload no
-
-      - name: Build
-        run: conda build conda-recipes/main-library --output-folder build_output
-
-      - name: Upload all Conda packages
-        uses: actions/upload-artifact@v4
-        with:
-          name: conda-packages
-          path: build_output/**  # Uploads all packages

.github/workflows/conda_python.yaml

@@ -1,42 +0,0 @@
-name: slsdet
-
-on: [pull_request]
-
-jobs:
-  build:
-    strategy:
-      fail-fast: false
-      matrix:
-        platform: [ubuntu-latest, ] # macos-12, windows-2019]
-        python-version: ["3.12",]
-
-    runs-on: ${{ matrix.platform }}
-
-    # The setup-miniconda action needs this to activate miniconda
-    defaults:
-      run:
-        shell: "bash -l {0}"
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Get conda
-        uses: conda-incubator/setup-miniconda@v3.0.4
-        with:
-          python-version: ${{ matrix.python-version }}
-          channels: conda-forge
-
-      - name: Prepare
-        run: conda install conda-build conda-verify pytest anaconda-client
-
-      - name: Disable upload
-        run: conda config --set anaconda_upload no
-
-      - name: Build
-        run: conda build conda-recipes/python-client --output-folder build_output
-
-      - name: Upload all Conda packages
-        uses: actions/upload-artifact@v4
-        with:
-          name: conda-packages
-          path: build_output/**  # Uploads all packages

.gitignore

@@ -1,23 +1,8 @@
 .cproject
 .project
-bin/
 .settings
 *.aux
 *.log
 *.out
 *.toc
-*.o
-*.so
-.*
-build/
-RELEASE.txt
-Testing/
-
-ctbDict.cpp
-ctbDict.h
-
-
-
-*.pyc
-*/__pycache__/*
 

.travis.yml

@@ -1,38 +0,0 @@
-sudo: false
-
-language: cpp
-
-os: linux
-
-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 $HOME/miniconda
-  - source "$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 -q conda
-  - conda info -a
-
-  # Useful for debugging any issues with conda
-  - conda create -q -n testenv conda-build anaconda-client conda-verify
-  - conda activate testenv
-  - conda-build .
-
-script:
- - CTEST_OUTPUT_ON_FAILURE=1 ctest -j 2
-
-
-deploy:
-  provider: script
-  script: find $HOME/miniconda/envs/testenv/conda-bld/${TRAVIS_OS_NAME}-64 -name "*.tar.bz2" -exec anaconda -v --show-traceback -t $CONDA_TOKEN upload --force {} \;
-  on:
-    branch: developer
-    tags: true
-

CMakeLists.txt

@@ -1,389 +0,0 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
-cmake_minimum_required(VERSION 3.15)
-project(slsDetectorPackage)
-
-# Read VERSION file into project version
-set(VERSION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/VERSION")
-file(READ "${VERSION_FILE}" VERSION_CONTENT)
-string(STRIP "${VERSION_CONTENT}" PROJECT_VERSION_STRING)
-set(PROJECT_VERSION ${PROJECT_VERSION_STRING})
-
-# Pass it to the compiler
-add_compile_definitions(SLS_DET_VERSION="${PROJECT_VERSION}")
-
-set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
-
-cmake_policy(SET CMP0074 NEW)
-
-if (${CMAKE_VERSION} VERSION_GREATER "3.24")
-    cmake_policy(SET CMP0135 NEW) #Fetch content download timestamp
-endif()
-include(cmake/project_version.cmake)
-include(cmake/SlsAddFlag.cmake)
-
-
-
-# Using FetchContent to get libzmq
-include(FetchContent)
-option(SLS_FETCH_ZMQ_FROM_GITHUB "Fetch zmq from github" OFF)
-option(SLS_FETCH_PYBIND11_FROM_GITHUB "Fetch pybind11 from github" OFF)
-
-
-
-# Allow FetchContent_Populate to be called with a single argument
-# otherwise deprecated warning is issued
-# Note: From cmake 3.28 we can pass EXCLUDE_FROM_ALL to FetchContent_Declare
-# and avoid direct use of Populate
-if (${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.30")
-    cmake_policy(SET CMP0169 OLD) 
-endif()
-
-# Patch libzmq to set minimum cmake version to 3.15 to avoid warnings
-# with newer cmake versions
-# Patch is applied in the FetchContent_Declare
-set(SLS_LIBZMQ_VERSION "4.3.4")
-
-
-if(SLS_FETCH_ZMQ_FROM_GITHUB)
-    # Opt in to pull down a zmq version from github instead of
-    # using the bundled version
-    FetchContent_Declare(
-        libzmq
-        GIT_REPOSITORY https://github.com/zeromq/libzmq.git
-        GIT_TAG        v${SLS_LIBZMQ_VERSION}
-        PATCH_COMMAND ${CMAKE_COMMAND} -E chdir <SOURCE_DIR> patch -p1 < ${CMAKE_CURRENT_SOURCE_DIR}/libs/libzmq/libzmq_cmake_version.patch
-        UPDATE_DISCONNECTED 1
-    )
-else()
-    # Standard behaviour use libzmq included in this repo (libs/libzmq)
-    FetchContent_Declare(
-        libzmq
-        URL ${CMAKE_CURRENT_SOURCE_DIR}/libs/libzmq/libzmq-${SLS_LIBZMQ_VERSION}.tar.gz
-        URL_HASH MD5=cc20b769ac10afa352e5ed2769bb23b3
-        PATCH_COMMAND ${CMAKE_COMMAND} -E chdir <SOURCE_DIR> patch -p1 < ${CMAKE_CURRENT_SOURCE_DIR}/libs/libzmq/libzmq_cmake_version.patch
-        UPDATE_DISCONNECTED 1
-    )
-endif()
-
-# Disable unwanted options from libzmq
-set(BUILD_TESTS OFF CACHE BOOL "Switch off libzmq test build")
-set(BUILD_SHARED OFF CACHE BOOL "Switch off libzmq shared libs")
-set(WITH_PERF_TOOL OFF CACHE BOOL "")
-set(ENABLE_CPACK OFF CACHE BOOL "")
-set(ENABLE_CLANG OFF CACHE BOOL "")
-set(ENABLE_CURVE OFF CACHE BOOL "")
-set(ENABLE_DRAFTS OFF CACHE BOOL "")
-set(ENABLE_PRECOMPILED OFF CACHE BOOL "")
-set(WITH_DOC OFF CACHE BOOL "")
-set(WITH_DOCS OFF CACHE BOOL "")
-
- 
-
-# Using GetProperties and Populate to be able to exclude zmq
-# from install (not possible with FetchContent_MakeAvailable(libzmq))
-FetchContent_GetProperties(libzmq)
-if(NOT libzmq_POPULATED)
-  FetchContent_Populate(libzmq)
-  add_subdirectory(${libzmq_SOURCE_DIR} ${libzmq_BINARY_DIR} EXCLUDE_FROM_ALL)
-endif()
-
-
-
-include(GNUInstallDirs)
-
-# If conda build, always set lib dir to 'lib'
-if($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 "${PROJECT_NAME_LOWER}-targets")
-set(namespace "sls::")
-
-set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
-
-
-# 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)
-endif()
-
-
-
-option(SLS_USE_HDF5 "HDF5 File format" OFF)
-option(SLS_BUILD_SHARED_LIBRARIES "Build shared libaries" ON)
-option(SLS_USE_TEXTCLIENT "Text Client" ON)
-option(SLS_USE_DETECTOR "Detector libs" ON)
-option(SLS_USE_RECEIVER "Receiver" ON)
-option(SLS_USE_RECEIVER_BINARIES "Receiver binaries" 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_INSTALL_PYTHONEXT "Install the python extension in the install tree under CMAKE_INSTALL_PREFIX/python/" OFF)
-option(SLS_USE_CTBGUI "ctb GUI" OFF)
-option(SLS_BUILD_DOCS "docs" OFF)
-option(SLS_BUILD_EXAMPLES "examples" OFF)
-option(SLS_TUNE_LOCAL "tune to local machine" OFF)
-option(SLS_DEVEL_HEADERS "install headers for devel" OFF)
-option(SLS_USE_MOENCH "compile zmq and post processing for Moench" OFF)
-option(SLS_USE_JUNGFRAU "compile post processing for Jungfrau" OFF)
-
-#Convenience option to switch off defaults when building Moench binaries only
-option(SLS_BUILD_ONLY_MOENCH "compile only Moench" OFF)
-if(SLS_BUILD_ONLY_MOENCH)
-    message(STATUS "Build MOENCH binaries only!")
-    set(SLS_BUILD_SHARED_LIBRARIES OFF CACHE BOOL "Disabled for MOENCH_ONLY" FORCE)
-    set(SLS_USE_TEXTCLIENT OFF CACHE BOOL "Disabled for MOENCH_ONLY" FORCE)
-    set(SLS_USE_DETECTOR OFF CACHE BOOL "Disabled for MOENCH_ONLY" FORCE)
-    set(SLS_USE_RECEIVER OFF CACHE BOOL "Disabled for MOENCH_ONLY" FORCE)
-    set(SLS_USE_RECEIVER_BINARIES OFF CACHE BOOL "Disabled for MOENCH_ONLY" FORCE)
-    set(SLS_USE_MOENCH ON CACHE BOOL "Enable" FORCE)
-endif()
-
-#Convenience option to switch off defaults when building Jungfrau binaries only
-option(SLS_BUILD_ONLY_JUNGFRAU "compile only Jungfrau" OFF)
-if(SLS_BUILD_ONLY_JUNGFRAU)
-    message(STATUS "Build JUNGFRAU binaries only!")
-    set(SLS_BUILD_SHARED_LIBRARIES OFF CACHE BOOL "Disabled for JUNGFRAU_ONLY" FORCE)
-    set(SLS_USE_TEXTCLIENT OFF CACHE BOOL "Disabled for JUNGFRAU_ONLY" FORCE)
-    set(SLS_USE_DETECTOR OFF CACHE BOOL "Disabled for JUNGFRAU_ONLY" FORCE)
-    set(SLS_USE_RECEIVER OFF CACHE BOOL "Disabled for JUNGFRAU_ONLY" FORCE)
-    set(SLS_USE_RECEIVER_BINARIES OFF CACHE BOOL "Disabled for JUNGFRAU_ONLY" FORCE)
-    set(SLS_USE_JUNGFRAU ON CACHE BOOL "Enable" FORCE)
-endif()
-
-
-option(SLS_EXT_BUILD "external build of part of the project" OFF)
-if(SLS_EXT_BUILD)
-    message(STATUS "External build using already installed libraries")
-    set(SLS_BUILD_SHARED_LIBRARIES OFF CACHE BOOL "Should already exist" FORCE)
-    set(SLS_USE_TEXTCLIENT OFF CACHE BOOL "Should already exist" FORCE)
-    set(SLS_USE_DETECTOR OFF CACHE BOOL "Should already exist" FORCE)
-    set(SLS_USE_RECEIVER OFF CACHE BOOL "Should already exist" FORCE)
-    set(SLS_USE_RECEIVER_BINARIES OFF CACHE BOOL "Should already exist" FORCE)
-    set(SLS_MASTER_PROJECT OFF CACHE BOOL "No master proj in case of extbuild" FORCE) 
-endif()
-
-#Maybe have an option guarding this?
-set(SLS_INTERNAL_RAPIDJSON_DIR ${CMAKE_CURRENT_SOURCE_DIR}/libs/rapidjson)
-
-set(SLS_INTERNAL_QWT_DIR ${CMAKE_CURRENT_SOURCE_DIR}/libs/qwt-6.1.5)
-
-set(ClangFormat_EXCLUDE_PATTERNS    "build/" 
-                                    "libs/" 
-                                    "slsDetectorCalibration/" 
-                                    "manual/"
-                                    "python/"
-                                    "sample/"
-                                    ${CMAKE_BINARY_DIR})
-find_package(ClangFormat)
-
-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()
-
-
-#Enable LTO if available
-include(CheckIPOSupported)
-check_ipo_supported(RESULT SLS_LTO_AVAILABLE)
-if((CMAKE_BUILD_TYPE STREQUAL "Release") AND SLS_LTO_AVAILABLE)
-    message(STATUS "Building with link time optimization")
-else()
-    message(STATUS "Building without link time optimization")
-endif()
-
-
-if(SLS_EXT_BUILD)
-    # Find ourself in case of external build
-    find_package(slsDetectorPackage ${PROJECT_VERSION} REQUIRED)
-endif()
-
-
-
-# slsProjectOptions and slsProjectWarnings are used
-# to control options for the libraries
-if(NOT TARGET slsProjectOptions)
-    add_library(slsProjectOptions INTERFACE)
-   target_compile_features(slsProjectOptions INTERFACE cxx_std_11)
-endif()
-
-if (NOT TARGET slsProjectWarnings)
-    add_library(slsProjectWarnings INTERFACE)
-    target_compile_options(slsProjectWarnings INTERFACE 
-        -Wall
-        -Wextra
-        -Wno-unused-parameter
-        # -Wold-style-cast
-        -Wnon-virtual-dtor
-        -Woverloaded-virtual
-        -Wdouble-promotion
-        -Wformat=2
-        -Wredundant-decls
-        # -Wconversion
-        -Wvla
-        -Wdouble-promotion
-        -Werror=return-type
-    )
-    # Add or disable warnings depending on if the compiler supports them 
-    # The function checks internally and sets HAS_warning-name
-    sls_enable_cxx_warning("-Wnull-dereference")
-    sls_enable_cxx_warning("-Wduplicated-cond")
-    sls_disable_cxx_warning("-Wclass-memaccess")
-
-    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5 AND "${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
-            target_compile_options(slsProjectWarnings INTERFACE 
-                                                -Wno-missing-field-initializers)
-    endif()
-
-
-endif()
-
-
-if (NOT TARGET slsProjectCSettings)
-    #Settings for C code
-    add_library(slsProjectCSettings INTERFACE)
-    target_compile_options(slsProjectCSettings INTERFACE 
-                                                -std=gnu99 #fixed
-                                                -Wall
-                                                -Wextra
-                                                -Wno-unused-parameter
-                                                -Wdouble-promotion
-                                                -Wformat=2
-                                                -Wredundant-decls
-                                                -Wdouble-promotion
-                                                -Werror=return-type
-                                                -Wno-format-overflow 
-                                                -Wno-format-truncation
-                                    )
-    sls_disable_c_warning("-Wstringop-truncation")
-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 -fno-omit-frame-pointer)
-    #target_link_libraries(slsProjectOptions INTERFACE -fsanitize=thread)
-endif()
-
-
-if(SLS_TUNE_LOCAL)
-    target_compile_options(slsProjectOptions INTERFACE -mtune=native -march=native)
-endif()
-
-
-if(SLS_MASTER_PROJECT)
-install(TARGETS slsProjectOptions slsProjectWarnings 
-    EXPORT "${TARGETS_EXPORT_NAME}"
-    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-    ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-    PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
-)
-endif()
-
-set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-set(CMAKE_INSTALL_RPATH $ORIGIN)
-set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
-
-if (SLS_USE_TESTS)
-    enable_testing()
-    add_subdirectory(tests)
-endif(SLS_USE_TESTS)
-
-
-if(NOT SLS_EXT_BUILD)
-    add_subdirectory(slsSupportLib)
-endif()
-
-if (SLS_USE_DETECTOR OR SLS_USE_TEXTCLIENT)
-    add_subdirectory(slsDetectorSoftware)
-endif ()
-
-if (SLS_USE_RECEIVER)
-    add_subdirectory(slsReceiverSoftware) 
-endif (SLS_USE_RECEIVER)
-
-if (SLS_USE_GUI)   
-    add_subdirectory(libs/qwt)  
-    add_subdirectory(slsDetectorGui)
-endif (SLS_USE_GUI)
-
-if (SLS_USE_SIMULATOR)
-    add_subdirectory(slsDetectorServers)
-endif (SLS_USE_SIMULATOR)
-
-if (SLS_USE_INTEGRATION_TESTS)
-    add_subdirectory(integrationTests)
-endif (SLS_USE_INTEGRATION_TESTS)
-
-if (SLS_USE_PYTHON)
-    find_package (Python 3.8 COMPONENTS Interpreter Development)
-    if(SLS_FETCH_PYBIND11_FROM_GITHUB)
-        FetchContent_Declare(
-            pybind11
-            GIT_REPOSITORY https://github.com/pybind/pybind11
-            GIT_TAG        v2.13.6
-        )
-
-    else()
-    # https://github.com/pybind/pybind11/releases
-        FetchContent_Declare(
-            pybind11
-            URL ${CMAKE_CURRENT_SOURCE_DIR}/libs/pybind11/v2.13.6.tar.gz
-            URL_HASH MD5=a04dead9c83edae6d84e2e343da7feeb
-        )
-    endif()
-    FetchContent_MakeAvailable(pybind11)
-
-    add_subdirectory(python)
-endif(SLS_USE_PYTHON)
-
-if (SLS_USE_CTBGUI)
-    add_subdirectory(pyctbgui)
-endif(SLS_USE_CTBGUI)
-
-# Workaround for file note being copied to build directory
-# when issuing a python -m build
-# TODO! Proper fix
-if(EXISTS ".clang-tidy")
-    configure_file(.clang-tidy  
-        ${CMAKE_BINARY_DIR}/.clang-tidy  
-    )
-endif()
-
-
-if (SLS_BUILD_EXAMPLES)
-    add_subdirectory(sample)
-endif(SLS_BUILD_EXAMPLES)
-
-if(SLS_BUILD_DOCS)
-    add_subdirectory(docs)
-endif(SLS_BUILD_DOCS)
-
-if(SLS_USE_MOENCH)
-    add_subdirectory(slsDetectorCalibration/tiffio)
-    add_subdirectory(slsDetectorCalibration/moenchExecutables)
-endif(SLS_USE_MOENCH)
-
-if(SLS_USE_JUNGFRAU)
-    add_subdirectory(slsDetectorCalibration/tiffio)
-    add_subdirectory(slsDetectorCalibration/jungfrauExecutables)
-endif(SLS_USE_JUNGFRAU)
-
-if(SLS_MASTER_PROJECT)
-    set(CMAKE_INSTALL_DIR "share/cmake/${PROJECT_NAME}")
-    set(PROJECT_LIBRARIES slsSupportShared slsDetectorShared slsReceiverShared)
-    include(cmake/package_config.cmake)
-endif()

COPYING

@@ -1,17 +0,0 @@
-The SLS Detector Package is provided under:
-
-	SPDX-License-Identifier: LGPL-3.0-or-later
-
-Being under the terms of the GNU Lesser General Public License version 3 or later, 
-according with:
-
-	LICENSES/LGPL-3.0
-
-Source code under the Apache 2.0 License have the SPDX Identifier and are 
-according with:
-
-	LICENSES/ThirdParty/Apache-2.0
-
-All contributions to the SLS Detector Package are subject to this COPYING file.
-
-

LICENSES/GPL-3.0

@@ -1,688 +0,0 @@
-Valid-License-Identifier: GPL-3.0
-Valid-License-Identifier: GPL-3.0+
-SPDX-URL: https://spdx.org/licenses/GPL-3.0-or-later.html
-Usage-Guide:
-  To use this license in source code, put one of the following SPDX
-  tag/value pairs into a comment according to the placement
-  guidelines in the licensing rules documentation.
-  For 'GNU Library General Public License (LGPL) version 3.0 only' use:
-    SPDX-License-Identifier: GPL-3.0
-  For 'GNU Library General Public License (LGPL) version 3.0 or any later
-  version' use:
-    SPDX-License-Identifier: GPL-3.0-or-later
-License-Text:
-
-                    GNU GENERAL PUBLIC LICENSE
-                       Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
-                            Preamble
-
-  The GNU General Public License is a free, copyleft license for
-software and other kinds of works.
-
-  The licenses for most software and other practical works are designed
-to take away your freedom to share and change the works.  By contrast,
-the GNU General Public License is intended to guarantee your freedom to
-share and change all versions of a program--to make sure it remains free
-software for all its users.  We, the Free Software Foundation, use the
-GNU General Public License for most of our software; it applies also to
-any other work released this way by its authors.  You can apply it to
-your programs, too.
-
-  When we speak of free software, we are referring to freedom, not
-price.  Our General Public Licenses are designed to make sure that you
-have the freedom to distribute copies of free software (and charge for
-them if you wish), that you receive source code or can get it if you
-want it, that you can change the software or use pieces of it in new
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-you modify it: responsibilities to respect the freedom of others.
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-<https://www.gnu.org/licenses/why-not-lgpl.html>.

LICENSES/LGPL-3.0

@@ -1,179 +0,0 @@
-Valid-License-Identifier: LGPL-3.0
-Valid-License-Identifier: LGPL-3.0+
-SPDX-URL: https://spdx.org/licenses/LGPL-3.0-or-later.html
-Usage-Guide:
-  To use this license in source code, put one of the following SPDX
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-    SPDX-License-Identifier: LGPL-3.0-or-later
-License-Text:
-
-                   GNU LESSER GENERAL PUBLIC LICENSE
-                       Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
- Everyone is permitted to copy and distribute verbatim copies
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-
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-  This version of the GNU Lesser General Public License incorporates
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-Library.

LICENSES/Third Party/Apache-2.0

@@ -1,210 +0,0 @@
-Valid-License-Identifier: Apache-2.0
-SPDX-URL: https://spdx.org/licenses/Apache-2.0.html
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-  To use this license in source code, put one of the following SPDX
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-   limitations under the License.

README.md

@@ -1,281 +0,0 @@
-## Dependencies
-Before building from source make sure that you have the [software wiki](https://slsdetectorgroup.github.io/devdoc/dependencies.html) installed. If installing using conda, conda will manage the dependencies. Avoid also installing packages with pip. 
-
-## Documentaion
-Detailed documentation including installation can be found in the [software wiki](https://slsdetectorgroup.github.io/devdoc/index.html).
-
-Different releases can be found on the [official site](https://www.psi.ch/en/lxn/software-releases).
-
-Firmware compatiblity can be found in [firmware page](https://github.com/slsdetectorgroup/slsDetectorFirmware)
-
-## Installation
-
-### 1. Install binaries using conda
-Conda is not only useful to manage python environments but can also
-be used as a user space package manager. Dates in the tag (for eg. 2020.07.23.dev0) 
-are from the developer branch. Please use released tags for stability.
-
-We have three different packages available:
-* **slsdetlib** shared libraries and command line utilities 
-* **slsdetgui** GUI
-* **slsdet** Python bindings
-
-```
-#Add channels for dependencies and our library
-conda config --add channels conda-forge
-conda config --add channels slsdetectorgroup
-conda config --set channel_priority strict
-
-#create and activate an environment with our library
-#replace 6.1.1 with the required tag
-conda create -n myenv slsdetlib=6.1.1
-conda activate myenv
-
-#ready to use
-sls_detector_get exptime
-etc ...
-```
-
-```
-# List available versions
-# lib and binaries
-conda search slsdetlib
-# python
-conda search slsdet
-# gui
-conda search slsdetgui
-```
-
-## 2. Build from source
-
-### 2.1 Download Source Code from github
-```
-git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch 7.0.0
-```
-
-> **Note:** For v6.x.x of slsDetectorPackage and older, refer [pybind11 notes on cloning](#Pybind-and-Zeromq).
-
-
-### 2.2 Build from source
-
-
-### Build using CMake
-
-```
-# outside slsDetecorPackage folder
-mkdir build && cd build
-
-# configure & generate Makefiles using cmake
-# by listing all your options (alternately use ccmake described below)
-# cmake3 for some systems
-cmake ../slsDetectorPackage -DCMAKE_INSTALL_PREFIX=/your/install/path
-
-# compiled to the build/bin directory
-make -j12 #or whatever number of cores you are using to build
-
-# install headers and libs in /your/install/path directory
-make install
-```
-
-Instead of the cmake command, one can use ccmake to get a list of options to configure and generate Makefiles at ease.
-
-
-```
-# ccmake3 for some systems
-ccmake ..
- 
-# choose the options
-# first press [c] - configure (unil you see [g])
-# then press [g] - generate
-```
-
-|Example cmake options|Comment|
-|---|---|
-| -DSLS_USE_PYTHON=ON            | Python                                 |   
-| -DPython_FIND_VIRTUALENV=ONLY  | Python from only the conda env         | 
-| -DSLS_USE_GUI=ON               | GUI                                    |
-| -DSLS_USE_HDF5=ON              | HDF5                                   |
-| -DSLS_USE_SIMULATOR=ON         | Simulator                              |
-
-> **Note:** For v7.x.x of slsDetectorPackage and older, refer [zeromq notes for cmake option to hint library location](#Pybind-and-Zeromq).
-
-### Build using in-built cmk.sh script
-
-```
-The binaries are generated in slsDetectorPackage/build/bin directory.
-
-Usage: $0 [-b] [-c] [-d <HDF5 directory>] [-e] [-g] [-h] [-i]
-[-j <Number of threads>] [-k <CMake command>] [-l <Install directory>]
-[-m] [-n] [-p] [-r] [-s] [-t] [-u] [-z]
--[no option]: only make
--b: Builds/Rebuilds CMake files normal mode
--c: Clean
--d: HDF5 Custom Directory
--e: Debug mode
--g: Build/Rebuilds gui
--h: Builds/Rebuilds Cmake files with HDF5 package
--i: Builds tests
--j: Number of threads to compile through
--k: CMake command
--l: Install directory
--m: Manuals
--n: Manuals without compiling doxygen (only rst)
--p: Builds/Rebuilds Python API
--r: Build/Rebuilds only receiver
--s: Simulator
--t: Build/Rebuilds only text client
--u: Chip Test Gui
--z: Moench zmq processor
-
-
-# display all options
-./cmk.sh -?
-
-# new build and compile in parallel (recommended basic option):
-./cmk.sh -cbj5
-
-# new build, python and compile in parallel:
-./cmk.sh -cbpj5
-
-#For rebuilding only certain sections
-./cmk.sh -tg #only text client and gui
-./cmk.sh -r #only receiver
-```
-
-> **Note:** For v7.x.x of slsDetectorPackage and older, refer [zeromq notes for cmk script option to hint library location](#Pybind-and-Zeromq).
-
-### Build on old distributions
-
-If your linux distribution doesn't come with a C++11 compiler (gcc>4.8) then 
-it's possible to install a newer gcc using conda and build the slsDetectorPackage
-using this compiler
-
-```
-#Create an environment with the dependencies
-conda create -n myenv gxx_linux-64 cmake zmq
-conda activate myenv
-
-# outside slsDetecorPackage folder
-mkdir build && cd build
-cmake ../slsDetectorPackage -DCMAKE_PREFIX_PATH=$CONDA_PREFIX
-make -j12
-```
-
-> **Note:** For v7.x.x of slsDetectorPackage and older, refer [zeromq notes for dependencies for conda](#Pybind-and-Zeromq).
-
-
-### Build slsDetectorGui (Qt5)
-
-1. Using pre-built binary on conda
-```
-conda create -n myenv slsdetgui=7.0.0
-conda activate myenv
-```
-
-2. Using system installation on RHEL7
-```
-yum install qt5-qtbase-devel.x86_64
-yum install qt5-qtsvg-devel.x86_64 
-```
-
-3. Using system installation on RHEL8
-```
-yum install qt5-qtbase-devel.x86_64
-yum install qt5-qtsvg-devel.x86_64 
-yum install expat-devel.x86_64
-```
-
-4. Using conda
-```
-#Add channels for dependencies and our library
-conda config --add channels conda-forge
-conda config --add channels slsdetectorgroup
-conda config --set channel_priority strict
-
-# create environment to compile
-# on rhel7
-conda create -n slsgui zeromq gxx_linux-64 gxx_linux-64 mesa-libgl-devel-cos6-x86_64 qt
-# on fedora or newer systems
-conda create -n slsgui zeromq qt
-
-# when using conda compilers, would also need libgl, but no need for it on fedora unless maybe using it with ROOT
-
-# activate environment
-conda activate slsgui
-
-# compile with cmake outside slsDetecorPackage folder
-mkdir build && cd build
-cmake ../slsDetectorPackage -DSLS_USE_GUI=ON
-make -j12
-
-# or compile with cmk.sh
-cd slsDetectorPackage
-./cmk.sh -cbgj9
-```
-
-> **Note:** For v7.x.x of slsDetectorPackage and older, refer [zeromq notes for dependencies for conda](#Pybind-and-Zeromq).
-
-### Build documentation from package
-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 
-
-```
-conda create -n myenv python=3.12 sphinx sphinx_rtd_theme breathe doxygen numpy
-```
-
-```
-# using cmake or ccmake to enable DSLS_BUILD_DOCS
-# outside slsDetecorPackage folder
-mkdir build && cd build
-cmake ../slsDetectorPackage -DSLS_BUILD_DOCS=ON
-
-make docs # generate API docs and build Sphinx RST
-make rst # rst only, saves time in case the API did not change
-```
-
-
-
-## Pybind and Zeromq
-
-### Pybind11 for Python
-**v8.0.0+**:
-pybind11 is built
-* by default from tar file in repo (libs/pybind/v2.1x.0.tar.gz)
-* or use advanced option SLS_FETCH_PYBIND11_FROM_GITHUB [link].
-   * v9.0.0+: pybind11 (v2.13.6)
-   * v8.x.x : pybind11 (v2.11.0)
-
-**v7.x.x**:
-pybind11 packaged into ‘libs/pybind’. No longer a submodule. No need for “recursive” or “submodule update”.
-
-**Older versions**:
-pybind11 is a submodule. Must be cloned using “recursive” and updated when switching between versions using the following commands.
-
-```
-# Note: Only for v6.x.x versions and older
-
-# clone using recursive to get pybind11 submodule
-git clone --recursive https://github.com/slsdetectorgroup/slsDetectorPackage.git
-
-# update submodule when switching between releases
-cd slsDetectorPackage
-git submodule update --init
-```
-
-### Zeromq
-**v8.0.0+**:
-zeromq (v4.3.4) is built
-* by default from tar file in repo (libs/libzmq/libzmq-4.3.4.tar.gz)
-* or use advanced option SLS_FETCH_ZMQ_FROM_GITHUB [link].
-
-**v7.x.x and older**:
-zeromq-devel must be installed and one can hint its location using
-* cmake option:’-DZeroMQ_HINT=/usr/lib64’ or
-* option ‘-q’ in cmk.sh script: : ./cmk.sh -cbj5 -q /usr/lib64
-* ‘zeromq’ dependency added when installing using conda
-
-
-## Support
-    dhanya.thattil@psi.ch
-    erik.frojdh@psi.ch

VERSION

@@ -1 +0,0 @@
-0.0.0

bash_autocomplete.sh

@@ -1 +0,0 @@
-slsDetectorSoftware/generator/autocomplete/bash_autocomplete.sh

cmake/Catch.cmake

@@ -1,175 +0,0 @@
-# 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

@@ -1,78 +0,0 @@
-# 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/FindCBF.cmake

@@ -1,11 +0,0 @@
-FIND_PATH (CBF_INCLUDE_DIR
-    ${CBF_DIR}/include
-    ${CBF_DIR}/include/cbflib
-)
-FIND_LIBRARY (CBF_LIBRARY
-    NAMES cbf
-    HINTS ${CBF_DIR}/lib
-)
-INCLUDE ( FindPackageHandleStandardArgs )
-FIND_PACKAGE_HANDLE_STANDARD_ARGS (CBF DEFAULT_MSG CBF_LIBRARY CBF_INCLUDE_DIR )
-

cmake/FindClangFormat.cmake

@@ -1,39 +0,0 @@
-# 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/FindROOT.cmake

@@ -1,167 +0,0 @@
-# - Finds ROOT instalation
-# This module sets up ROOT information 
-# It defines:
-# ROOT_FOUND          If the ROOT is found
-# ROOT_INCLUDE_DIR    PATH to the include directory
-# ROOT_LIBRARIES      Most common libraries
-# ROOT_GUI_LIBRARIES  Most common libraries + GUI
-# ROOT_LIBRARY_DIR    PATH to the library directory 
-
-
-find_program(ROOT_CONFIG_EXECUTABLE root-config
-  PATHS $ENV{ROOTSYS}/bin)
-
-if(NOT ROOT_CONFIG_EXECUTABLE)
-  set(ROOT_FOUND FALSE)
-else()    
-  set(ROOT_FOUND TRUE)
-
-  execute_process(
-    COMMAND ${ROOT_CONFIG_EXECUTABLE} --prefix 
-    OUTPUT_VARIABLE ROOTSYS 
-    OUTPUT_STRIP_TRAILING_WHITESPACE)
-
-  execute_process(
-    COMMAND ${ROOT_CONFIG_EXECUTABLE} --version 
-    OUTPUT_VARIABLE ROOT_VERSION
-    OUTPUT_STRIP_TRAILING_WHITESPACE)
-
-  execute_process(
-    COMMAND ${ROOT_CONFIG_EXECUTABLE} --incdir
-    OUTPUT_VARIABLE ROOT_INCLUDE_DIR
-    OUTPUT_STRIP_TRAILING_WHITESPACE)
-
-  execute_process(
-    COMMAND ${ROOT_CONFIG_EXECUTABLE} --libs
-    OUTPUT_VARIABLE ROOT_LIBRARIES
-    OUTPUT_STRIP_TRAILING_WHITESPACE)
-
-  execute_process(
-    COMMAND ${ROOT_CONFIG_EXECUTABLE} --glibs
-    OUTPUT_VARIABLE ROOT_GUI_LIBRARIES
-    OUTPUT_STRIP_TRAILING_WHITESPACE)
-
-  #set(ROOT_LIBRARIES ${ROOT_LIBRARIES} -lThread -lMinuit -lHtml -lVMC -lEG -lGeom -lTreePlayer -lXMLIO -lProof)
-  #set(ROOT_LIBRARIES ${ROOT_LIBRARIES} -lProofPlayer -lMLP -lSpectrum -lEve -lRGL -lGed -lXMLParser -lPhysics)
-  set(ROOT_LIBRARY_DIR ${ROOTSYS}/lib)
-
-  # Make variables changeble to the advanced user
-  mark_as_advanced(ROOT_CONFIG_EXECUTABLE)
-
-  if(NOT ROOT_FIND_QUIETLY)
-    message(STATUS "Found ROOT ${ROOT_VERSION} in ${ROOTSYS}")
-  endif()
-endif()
-
-
-include(CMakeParseArguments)
-find_program(ROOTCINT_EXECUTABLE rootcint PATHS $ENV{ROOTSYS}/bin)
-find_program(GENREFLEX_EXECUTABLE genreflex PATHS $ENV{ROOTSYS}/bin)
-find_package(GCCXML)
-
-#----------------------------------------------------------------------------
-# function ROOT_GENERATE_DICTIONARY( dictionary   
-#                                    header1 header2 ... 
-#                                    LINKDEF linkdef1 ... 
-#                                    OPTIONS opt1...)
-function(ROOT_GENERATE_DICTIONARY dictionary)
-  CMAKE_PARSE_ARGUMENTS(ARG "" "" "LINKDEF;OPTIONS" "" ${ARGN})
-  #---Get the list of header files-------------------------
-  set(headerfiles)
-  foreach(fp ${ARG_UNPARSED_ARGUMENTS})
-    file(GLOB files ${fp})
-    if(files)
-      foreach(f ${files})
-        if(NOT f MATCHES LinkDef)
-          set(headerfiles ${headerfiles} ${f})
-        endif()
-      endforeach()
-    else()
-      set(headerfiles ${headerfiles} ${fp})
-    endif()
-  endforeach()
-  #---Get the list of include directories------------------
-  get_directory_property(incdirs INCLUDE_DIRECTORIES)
-  set(includedirs) 
-  foreach( d ${incdirs})    
-   set(includedirs ${includedirs} -I${d})
-  endforeach()
-  #---Get LinkDef.h file------------------------------------
-  set(linkdefs)
-  foreach( f ${ARG_LINKDEF})
-    if( IS_ABSOLUTE ${f})
-      set(linkdefs ${linkdefs} ${f})
-    else() 
-      if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/inc/${f})
-        set(linkdefs ${linkdefs} ${CMAKE_CURRENT_SOURCE_DIR}/inc/${f})
-      else()
-        set(linkdefs ${linkdefs} ${CMAKE_CURRENT_SOURCE_DIR}/${f})
-      endif()
-    endif()
-  endforeach()
-  #---call rootcint------------------------------------------
-  add_custom_command(OUTPUT ${dictionary}.cxx ${dictionary}.h
-                     COMMAND ${ROOTCINT_EXECUTABLE} -cint -f  ${dictionary}.cxx 
-                                          -c ${ARG_OPTIONS} ${includedirs} ${headerfiles} ${linkdefs} 
-                     DEPENDS ${headerfiles} ${linkdefs})
-endfunction()
-
-#----------------------------------------------------------------------------
-# function REFLEX_GENERATE_DICTIONARY(dictionary   
-#                                     header1 header2 ... 
-#                                     SELECTION selectionfile ... 
-#                                     OPTIONS opt1...)
-function(REFLEX_GENERATE_DICTIONARY dictionary)  
-  CMAKE_PARSE_ARGUMENTS(ARG "" "" "SELECTION;OPTIONS" "" ${ARGN})
-  #---Get the list of header files-------------------------
-  set(headerfiles)
-  foreach(fp ${ARG_UNPARSED_ARGUMENTS})
-    file(GLOB files ${fp})
-    if(files)
-      foreach(f ${files})
-        set(headerfiles ${headerfiles} ${f})
-      endforeach()
-    else()
-      set(headerfiles ${headerfiles} ${fp})
-    endif()
-  endforeach()
-  #---Get Selection file------------------------------------
-  if(IS_ABSOLUTE ${ARG_SELECTION})
-    set(selectionfile ${ARG_SELECTION})
-  else() 
-    set(selectionfile ${CMAKE_CURRENT_SOURCE_DIR}/${ARG_SELECTION})
-  endif()
-  #---Get the list of include directories------------------
-  get_directory_property(incdirs INCLUDE_DIRECTORIES)
-  set(includedirs) 
-  foreach( d ${incdirs})    
-    set(includedirs ${includedirs} -I${d})
-  endforeach()
-  #---Get preprocessor definitions--------------------------
-  get_directory_property(defs COMPILE_DEFINITIONS)
-  foreach( d ${defs})    
-   set(definitions ${definitions} -D${d})
-  endforeach()
-  #---Nanes and others---------------------------------------
-  set(gensrcdict ${dictionary}.cpp)
-  if(MSVC)
-    set(gccxmlopts "--gccxmlopt=\"--gccxml-compiler cl\"")
-  else()
-    #set(gccxmlopts "--gccxmlopt=\'--gccxml-cxxflags -m64 \'")
-    set(gccxmlopts)
-  endif()  
-  #set(rootmapname ${dictionary}Dict.rootmap)
-  #set(rootmapopts --rootmap=${rootmapname} --rootmap-lib=${libprefix}${dictionary}Dict)
-  #---Check GCCXML and get path-----------------------------
-  if(GCCXML)
-    get_filename_component(gccxmlpath ${GCCXML} PATH)
-  else()
-    message(WARNING "GCCXML not found. Install and setup your environment to find 'gccxml' executable")
-  endif()
-  #---Actual command----------------------------------------
-  add_custom_command(OUTPUT ${gensrcdict} ${rootmapname}     
-                     COMMAND ${GENREFLEX_EXECUTABLE} ${headerfiles} -o ${gensrcdict} ${gccxmlopts} ${rootmapopts} --select=${selectionfile}
-                             --gccxmlpath=${gccxmlpath} ${ARG_OPTIONS} ${includedirs} ${definitions}
-                     DEPENDS ${headerfiles} ${selectionfile})
-endfunction()
-  

cmake/FindSphinx.cmake

@@ -1,11 +0,0 @@
-#Look for an executable called sphinx-build
-find_program(SPHINX_EXECUTABLE
-             NAMES sphinx-build sphinx-build-3.6
-             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/ParseAndAddCatchTests.cmake

@@ -1,203 +0,0 @@
-#==================================================================================================#
-#  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/SlsAddFlag.cmake

@@ -1,64 +0,0 @@
-include(CheckCXXCompilerFlag)
-include(CheckCCompilerFlag)
-
-
-function(enable_cxx_warning flag target)
-    string(REPLACE "-W" "HAS_" flag_name ${flag})
-    check_cxx_compiler_flag(${flag} ${flag_name})
-    if(${flag_name})
-        target_compile_options(${target} INTERFACE ${flag})
-        message(STATUS "Adding: ${flag} to ${target}")
-    else()
-        message(STATUS "Flag: ${flag} not supported")
-    endif()
-endfunction()
-
-function(enable_c_warning flag target)
-    string(REPLACE "-W" "HAS_" flag_name ${flag})
-    check_c_compiler_flag(${flag} ${flag_name})
-    if(${flag_name})
-        target_compile_options(${target} INTERFACE ${flag})
-        message(STATUS "Adding: ${flag} to ${target}")
-    else()
-        message(STATUS "Flag: ${flag} not supported")
-    endif()
-endfunction()
-
-
-function(disable_cxx_warning flag target)
-    string(REPLACE "-W" "HAS_" flag_name ${flag})
-    check_cxx_compiler_flag(${flag} ${flag_name})
-
-    if(${flag_name})
-        string(REPLACE "-W" "-Wno-" neg_flag ${flag})
-        message(STATUS "Adding: ${neg_flag} to ${target}")
-        target_compile_options(${target} INTERFACE ${neg_flag})
-    else()
-        message(STATUS "Warning: ${flag} not supported no need to disable")
-    endif()
-endfunction()
-
-function(disable_c_warning flag target)
-    string(REPLACE "-W" "HAS_" flag_name ${flag})
-    check_c_compiler_flag(${flag} ${flag_name})
-    if(${flag_name})
-        string(REPLACE "-W" "-Wno-" neg_flag ${flag})
-        message(STATUS "Adding: ${neg_flag} to ${target}")
-        target_compile_options(${target} INTERFACE ${neg_flag})
-    else()
-        message(STATUS "Warning: ${flag} not supported no need to disable")
-    endif()
-endfunction()
-
-
-function(sls_disable_c_warning flag)
-    disable_c_warning(${flag} slsProjectCSettings)
-endfunction()
-
-function(sls_enable_cxx_warning flag)
-    enable_cxx_warning(${flag} slsProjectWarnings)
-endfunction()
-
-function(sls_disable_cxx_warning flag)
-    disable_cxx_warning(${flag} slsProjectWarnings)
-endfunction()

cmake/clang-format.cmake

@@ -1,47 +0,0 @@
-# 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

@@ -1,35 +0,0 @@
-# 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

@@ -1,26 +0,0 @@
-# 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@")
-
-
-find_dependency(Threads)
-
-# Add optional dependencies here
-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

@@ -1,14 +0,0 @@
-#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

@@ -1,154 +0,0 @@
-#
-# 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

@@ -1,34 +0,0 @@
-#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

@@ -1,339 +0,0 @@
-#!/bin/bash
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
-CMAKE="cmake3"
-BUILDDIR="build"
-INSTALLDIR=""
-HDF5DIR="/opt/hdf5v1.10.0"
-HDF5=0
-COMPILERTHREADS=0
-TEXTCLIENT=0
-RECEIVER=0
-GUI=0
-DEBUG=0
-PYTHON=0
-TESTS=0
-SIMULATOR=0
-CTBGUI=0
-MANUALS=0
-MANUALS_ONLY_RST=0
-MOENCHZMQ=0
-
-
-CLEAN=0
-REBUILD=0
-CMAKE_PRE=""
-CMAKE_POST=""
-
-usage() { echo -e "
-Usage: $0 [-b] [-c] [-d <HDF5 directory>] [-e] [-g] [-h] [-i] [-j <Number of threads>] [-k <CMake command>] [-l <Install directory>] [-m] [-n] [-p] [-r] [-s] [-t] [-u] [-z]  
- -[no option]: only make
- -b: Builds/Rebuilds CMake files normal mode
- -c: Clean
- -d: HDF5 Custom Directory
- -e: Debug mode
- -g: Build/Rebuilds gui
- -h: Builds/Rebuilds Cmake files with HDF5 package
- -i: Builds tests
- -j: Number of threads to compile through
- -k: CMake command
- -l: Install directory
- -m: Manuals
- -n: Manuals without compiling doxygen (only rst)
- -p: Builds/Rebuilds Python API
- -r: Build/Rebuilds only receiver
- -s: Simulator
- -t: Build/Rebuilds only text client
- -u: Chip Test Gui
- -z: Moench zmq processor
-
-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
-
-For make clean;make:
-./cmk.sh -c
-
-For using hdf5 without default dir /opt/hdf5v1.10.0:
-./cmk.sh -h
-
-For using hdf5 without custom dir /blabla:
-./cmk.sh -h -d /blabla
-
-For rebuilding cmake without hdf5 (Use this if you had previously run with hdf5 and now you dont want it)
-./cmk.sh -b
-
-For using multiple cores to compile faster:
-(all these options work)
-./cmk.sh -j9
-./cmk.sh -cj9 #with clean
-./cmk.sh -hj9 #with hdf5
-./cmk.sh -j9 -h #with hdf
-
-For rebuilding only certain sections
-./cmk.sh -tg #only text client and gui
-./cmk.sh -r #only receiver
- 
- " ; exit 1; }
-
-while getopts ":bcd:eghij:k:l:mnpq:rstuz" opt ; do
-	case $opt in
-	b) 
-		echo "Building of CMake files Required"
-		REBUILD=1
-		;;
-	c) 
-		echo "Clean Required"
-		CLEAN=1
-		;;
-	d) 
-		echo "New HDF5 directory: $OPTARG" 
-		HDF5DIR=$OPTARG
-		;;
-	e)
-		echo "Compiling Options: Debug" 
-		DEBUG=1
-		;;  
-	g) 
-		echo "Compiling Options: GUI" 
-		GUI=1
-		REBUILD=1
-		;; 
-	h) 
-		echo "Building of CMake files with HDF5 option Required"
-		HDF5=1
-		REBUILD=1
-		;;
-	i)
-		echo "Compiling Options: Tests" 
-		TESTS=1
-		;;   
-	j) 
-		echo "Number of compiler threads: $OPTARG" 
-		COMPILERTHREADS=$OPTARG
-		;;
-	k)
-		echo "CMake command: $OPTARG"
-		CMAKE="$OPTARG"
-		;;
-	l)
-		echo "CMake install directory: $OPTARG"
-		INSTALLDIR="$OPTARG"
-		;;
-	m)	
-		echo "Compiling Manuals"
-		MANUALS=1
-		;;
-	n)	
-		echo "Compiling Manuals (Only RST)"
-		MANUALS_ONLY_RST=1
-		;;
-	p)
-    	echo "Compiling Options: Python" 
-		PYTHON=1
-		REBUILD=1
-		;;   
-	r) 
-		echo "Compiling Options: Receiver" 
-		RECEIVER=1
-		REBUILD=1
-		;;      
-	s)
-		echo "Compiling Options: Simulator" 
-		SIMULATOR=1
-		;; 
-	t) 
-    	echo "Compiling Options: Text Client" 
-		TEXTCLIENT=1
-		REBUILD=1
-		;;
-	u)
-		echo "Compiling Options: Chip Test Gui"
-		CTBGUI=1
-		;;
-	z)	
-		echo "Compiling Moench Zmq Processor"
-		MOENCHZMQ=1
-		;;
-  \?)
-    echo "Invalid option: -$OPTARG" 
-		usage
-    exit 1
-   	;;
-  :)
-    echo "Option -$OPTARG requires an argument."
-		usage
-    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 "
-	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 -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 [ $GUI -eq 1 ]; then
-        CMAKE_POST+=" -DSLS_USE_GUI=ON "
-        echo "Enabling Compile Option: GUI"
-    fi
-fi
-
-
-
-
-
-#build dir doesnt exist
-if [ ! -d "$BUILDDIR" ] ; then
-	echo "No Build Directory. Building of Cmake files required"
-	mkdir $BUILDDIR;
-	REBUILD=1
-else
-	#rebuild not requested, but no makefile
-	if [ $REBUILD -eq 0 ] && [ ! -f "$BUILDDIR/Makefile" ] ; then
-		echo "No Makefile. Building of Cmake files required"
-		REBUILD=1
-	fi
-fi
-
-#Debug
-if [ $DEBUG -eq 1 ]; then
-#	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 
-
-#Moench zmq processor
-if [ $MOENCHZMQ -eq 1 ]; then
-	CMAKE_POST+=" -DSLS_USE_MOENCH=ON "
-	echo "Moench Zmq Processor Option enabled"
-fi 
-
-#Chip Test Gui
-if [ $CTBGUI -eq 1 ]; then
-	CMAKE_POST+=" -DSLS_USE_CTBGUI=ON "
-	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_POST+=" -DCMAKE_INSTALL_PREFIX="$HDF5DIR
-	CMAKE_POST+=" -DSLS_USE_HDF5=ON "
-#normal mode rebuild
-else
-	CMAKE_POST+=" -DSLS_USE_HDF5=OFF "
-fi
-
-
-#install
-if [ -n "$INSTALLDIR" ]; then
-	CMAKE_POST+=" -DCMAKE_INSTALL_PREFIX=$INSTALLDIR"
-	CMAKE_POST+=" -DCMAKE_FIND_ROOT_PATH=$INSTALLDIR"
-fi
-
-
-#enter build dir
-#pushd $BUILDDIR;
-cd $BUILDDIR;
-echo "in "$PWD
-
-
-
-#cmake
-if [ $REBUILD -eq 1 ]; then
-	rm -f CMakeCache.txt
-	BUILDCOMMAND="$CMAKE_PRE $CMAKE $CMAKE_POST .."
-	echo $BUILDCOMMAND
-	eval $BUILDCOMMAND
-fi
-
-#make clean
-if [ $CLEAN -eq 1 ]; then
-	make clean;
-fi
-
-
-#make
-if [ $COMPILERTHREADS -gt 0 ]; then
-	if [ $MANUALS -eq 0 ] && [ $MANUALS_ONLY_RST -eq 0 ]; then
-		BUILDCOMMAND="make -j$COMPILERTHREADS"
-		echo $BUILDCOMMAND
-		eval $BUILDCOMMAND
-	else
-		if [ $MANUALS -eq 1 ]; then
-			BUILDCOMMAND="make docs -j$COMPILERTHREADS"
-			echo $BUILDCOMMAND
-			eval $BUILDCOMMAND
-		else
-			BUILDCOMMAND="make rst -j$COMPILERTHREADS"
-			echo $BUILDCOMMAND
-			eval $BUILDCOMMAND		
-		fi
-	fi 
-else
-	if [ $MANUALS -eq 0 ] && [ $MANUALS_ONLY_RST -eq 0 ]; then
-		echo "make"
-		make
-	else
-		if [ $MANUALS -eq 1 ]; then
-			echo "make docs"
-			make docs
-		else
-			echo "make rst"
-			make rst
-		fi
-	fi 
-fi
-
-
-#install
-if [ -n "$INSTALLDIR" ]; then
-	make install
-#	popd
-#	$CMAKE --build $BUILDDIR --target install
-fi
-
-
-
-
-

conda-recipes/main-library/build.sh

@@ -1,28 +0,0 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
-
-if [ ! -d "build" ]; then
-    mkdir build
-fi
-if [ ! -d "install" ]; then
-    mkdir install
-fi
-cd build
-cmake .. -G Ninja \
-      -DCMAKE_PREFIX_PATH=$CONDA_PREFIX \
-      -DCMAKE_INSTALL_PREFIX=install \
-      -DSLS_USE_TEXTCLIENT=ON \
-      -DSLS_USE_RECEIVER=ON \
-      -DSLS_USE_GUI=ON \
-      -DSLS_USE_MOENCH=ON\
-      -DSLS_USE_TESTS=ON \
-      -DSLS_USE_PYTHON=OFF \
-      -DCMAKE_BUILD_TYPE=Release \
-      -DSLS_USE_HDF5=OFF \
-     
-NCORES=$(getconf _NPROCESSORS_ONLN)
-echo "Building using: ${NCORES} cores"
-cmake --build . -- -j${NCORES}
-cmake --build . --target install
-
-CTEST_OUTPUT_ON_FAILURE=1 ctest -j 1

conda-recipes/main-library/conda_build_config.yaml

@@ -1,13 +0,0 @@
-
-c_compiler:
-  - gcc                        # [linux]
-
-c_stdlib:
-  - sysroot                    # [linux]
-
-cxx_compiler:
-  - gxx                        # [linux]
-
-
-c_stdlib_version:              # [linux]
-  - 2.17                       # [linux]

conda-recipes/main-library/copy_gui.sh

@@ -1,5 +0,0 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
-#Copy the GUI 
-mkdir -p $PREFIX/bin
-cp build/install/bin/slsDetectorGui $PREFIX/bin/.

conda-recipes/main-library/copy_lib.sh

@@ -1,24 +0,0 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
-
-mkdir -p $PREFIX/lib
-mkdir -p $PREFIX/bin
-mkdir -p $PREFIX/include/sls
-
-#Shared and static libraries
-cp build/install/lib/* $PREFIX/lib/
-
-#Binaries
-cp build/install/bin/sls_detector_acquire $PREFIX/bin/.
-cp build/install/bin/sls_detector_acquire_zmq $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/sls_detector $PREFIX/bin/.
-cp build/install/bin/slsReceiver $PREFIX/bin/.
-cp build/install/bin/slsMultiReceiver $PREFIX/bin/.
-cp build/install/bin/slsFrameSynchronizer $PREFIX/bin/.
-
-
-cp build/install/include/sls/* $PREFIX/include/sls
-cp -rv build/install/share $PREFIX

conda-recipes/main-library/copy_moench.sh

@@ -1,6 +0,0 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
-
-#Copy the Moench executables 
-mkdir -p $PREFIX/bin
-cp build/install/bin/moench* $PREFIX/bin/.

conda-recipes/main-library/meta.yaml

@@ -1,79 +0,0 @@
-package:
-  name: sls_detector_software
-  version: 2025.3.19
-
-
-source:
-  path: ../..
-
-build:
-  number: 0
-  binary_relocation: True
-  rpaths: 
-    - lib/
-
-requirements:
-  build:
-    - {{ compiler('c') }}
-    - {{ stdlib("c") }}
-    - {{ compiler('cxx') }}
-    - git
-    - cmake
-    - ninja
-    - qt 5.*
-
-  host:
-    - libstdcxx-ng
-    - libgcc-ng
-    - libgl-devel  # [linux]
-    - libtiff
-    - zlib
-
-  run:
-    - libstdcxx-ng
-    - libgcc-ng 
-
-
-outputs:
-  - name: slsdetlib
-    script: copy_lib.sh
-
-    requirements:
-      build:
-        - {{ compiler('c') }}
-        - {{ stdlib("c") }}
-        - {{ compiler('cxx') }}
-
-      run: 
-        - libstdcxx-ng
-        - libgcc-ng
-
-
-
-
-  - name: slsdetgui
-    script: copy_gui.sh
-    requirements:
-
-      build:
-        - {{ compiler('c') }}
-        - {{compiler('cxx')}}
-        - {{ pin_subpackage('slsdetlib', exact=True) }}
-
-      run:
-        - {{ pin_subpackage('slsdetlib', exact=True) }}
-        - qt 5.*
-
-
-  - name: moenchzmq
-    script: copy_moench.sh
-    requirements:
-
-      build:
-        - {{ compiler('c') }}
-        - {{compiler('cxx')}}
-        - {{ pin_subpackage('slsdetlib', exact=True) }}
-
-
-      run:
-        - {{ pin_subpackage('slsdetlib', exact=True) }}

conda-recipes/python-client/conda_build_config.yaml

@@ -1,16 +0,0 @@
-python:
-    - 3.11 
-    - 3.12
-    - 3.13
-
-c_compiler:
-  - gcc                        # [linux]
-
-c_stdlib:
-  - sysroot                    # [linux]
-
-cxx_compiler:
-  - gxx                        # [linux]
-
-c_stdlib_version:              # [linux]
-  - 2.17                       # [linux]

conda-recipes/python-client/meta.yaml

@@ -1,45 +0,0 @@
-package:
-  name: slsdet
-  version: 2025.3.19 #TODO! how to not duplicate this?
-
-source:
-  path: ../..
-
-build:
-  number: 0
-  script:
-    - unset CMAKE_GENERATOR && {{ PYTHON }} -m pip install . -vv  # [not win]
-
-requirements:
-  build:
-    - python {{python}}
-    - {{ compiler('c') }}
-    - {{ stdlib("c") }}
-    - {{ compiler('cxx') }}
-
-
-  host:
-    - cmake
-    - ninja
-    - python {{python}}
-    - pip
-    - scikit-build-core
-    - pybind11 >=2.13.0
-    - fmt
-    - zeromq
-    - nlohmann_json
-    - catch2
-
-  run:
-    - python {{python}}
-    - numpy
-
-
-test:
-  imports:
-    - slsdet
-
-
-about:
-  summary: An example project built with pybind11 and scikit-build.
-  # license_file: LICENSE

docs/CMakeLists.txt

@@ -1,111 +0,0 @@
-# SPDX-License-Identifier: LGPL-3.0-or-other
-# Copyright (C) 2021 Contributors to the SLS Detector Package
-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/pyPatternGenerator.rst
-  src/servers.rst
-  src/receiver_api.rst
-  src/result.rst
-  src/type_traits.rst
-  src/ToString.rst
-  src/examples.rst
-  src/pygettingstarted.rst
-  src/firmware.rst
-  src/serverupgrade.rst
-  src/virtualserver.rst
-  src/serverdefaults.rst
-  src/quick_start_guide.rst
-  src/troubleshooting.rst
-  src/pattern.rst
-  src/receivers.rst
-  src/slsreceiver.rst
-  src/udpheader.rst
-  src/udpconfig.rst
-  src/udpdetspec.rst
-  src/fileformat.rst
-  src/slsreceiverheaderformat.rst
-  src/masterfileattributes.rst
-  src/binaryfileformat.rst
-  src/hdf5fileformat.rst
-  src/zmqjsonheaderformat.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"
-  "${SPHINX_BUILD}/conf.py"
-  @ONLY)
-
-configure_file(
-  "${CMAKE_CURRENT_SOURCE_DIR}/gen_server_doc.py.in"
-  "${SPHINX_BUILD}/gen_server_doc.py"
-  @ONLY)
-
-  configure_file(
-  "${CMAKE_CURRENT_SOURCE_DIR}/static/extra.css"
-  "${SPHINX_BUILD}/static/css/extra.css"
-  @ONLY)
-
-add_custom_target(server_rst python gen_server_doc.py)  
-
-add_custom_target(docs
-              gendoc
-              COMMAND python gen_server_doc.py
-              COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYGEN_OUT}
-              COMMAND ${SPHINX_EXECUTABLE} -a -b html
-              -Dbreathe_projects.slsDetectorPackage=${CMAKE_CURRENT_BINARY_DIR}/xml
-              -c "${SPHINX_BUILD}"
-              ${SPHINX_BUILD}/src 
-              ${SPHINX_BUILD}/html
-              COMMENT "Generating documentation with Sphinx")
-
-add_custom_target(rst
-              COMMAND ${SPHINX_EXECUTABLE} -a -b html
-              -Dbreathe_projects.slsDetectorPackage=${CMAKE_CURRENT_BINARY_DIR}/xml
-              -c "${SPHINX_BUILD}"
-              ${SPHINX_BUILD}/src 
-              ${SPHINX_BUILD}/html
-              COMMENT "Generating documentation with Sphinx")
-

docs/conf.py.in

@@ -1,66 +0,0 @@
-# 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 = '2020, 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']
-
-
-def setup(app):
-    app.add_css_file('css/extra.css')  # may also be an URL

docs/gen_server_doc.py.in

@@ -1,86 +0,0 @@
-import os 
-import re
-from pathlib import Path
-def remove_comments(text):
-    def replacer(match):
-        s = match.group(0)
-        if s.startswith('/'):
-            return " " # note: a space and not an empty string
-        else:
-            return s
-    pattern = re.compile(
-        r'//.*?$|/\*.*?\*/|\'(?:\\.|[^\\\'])*\'|"(?:\\.|[^\\"])*"',
-        re.DOTALL | re.MULTILINE
-    )
-    return re.sub(pattern, replacer, text)
-
-
-# @CMAKE_CURRENT_BINARY_DIR@
-
-print('\n\n\n\n SERVER CSV')
-
-src = Path('@CMAKE_SOURCE_DIR@')/'slsDetectorServers/'
-detectors = ['Mythen3', 'Gotthard2', 'Eiger', 
-            'Jungfrau', 'Moench', 'Ctb']
-
-
-for det in detectors:
-    print(det)
-    in_fname = src/f'{det.lower()}DetectorServer/slsDetectorServer_defs.h'
-    #print(f'Reading: {in_fname}')
-    with open(in_fname) as f:
-        lines = f.read().replace('\\\n', '')
-        lines = lines.splitlines(keepends = True)
-
-    lines = [l.strip('#define').strip(' ') for l in lines if l.startswith('#define')]
-    output = []
-    signals = []
-    fields = ['Name,', 'Value', 'Comment']
-    excluded = ['DAC_NAMES', 'DEFAULT_DAC_VALS', 'CLK_NAMES', 'ONCHIP_DAC_NAMES']
-    header = f'{fields[0]:35}{fields[1]:35}\n'
-    output.append(header)
-    signals.append(header)
-    dac_names = []
-    dac_values = []
-    for line in lines:
-        name, *parts = line.split()
-        arg = ' '.join(parts)
-        value, *comments = arg.split('//') 
-        value = value.strip('() ')
-        # value = value.replace(', ', ' ')
-        value = value.replace('\"', '')
-        if name not in excluded:
-            name += ','
-            if name.startswith('SIGNAL_'):
-                signals.append(f'{name:35}{value}\n')
-            else:
-                output.append(f'{name:35}\"{value}\"\n')
-        elif name == 'DAC_NAMES':
-            dac_names = [v.strip(', ') for v in value.split()]
-            dac_names = [n+',' for n in dac_names]
-        elif name == 'DEFAULT_DAC_VALS':
-            dac_values = remove_comments(value).strip('{}; ')
-            dac_values = dac_values.replace(',', '').split()
-            dac_values = [v.strip('') for v in dac_values]
-
-    print(f"dac_names: {len(dac_names)}, dac_values={len(dac_values)}")
-    if len(dac_values) == 0:
-        dac_values = ['N/A']*len(dac_names)
-
-    
-
-    rstpath = Path('@CMAKE_SOURCE_DIR@')/'docs/src/'
-
-    out_fname = Path.cwd()/f'src/{det.lower()}.csv'
-    out_dac_fname = Path.cwd()/f'src/{det.lower()}-dacs.csv'
-    #print(f'Writing: {out_fname}')
-    with open(out_fname, 'w') as f:
-        f.writelines(output)
-
-    output = [f'{n:35}{v}\n' for n,v in zip(dac_names, dac_values)]
-    output.insert(0, header)
-
-    with open(out_dac_fname, 'w') as f:
-        f.writelines(output)
-
-print('END\n\n\n\n')

docs/html/angularCalibrationHowTo/WARNINGS

@@ -0,0 +1 @@
+No implementation found for style `graphicx'

docs/html/angularCalibrationHowTo/angularCalibrationHowTo.css

@@ -0,0 +1,30 @@
+/* Century Schoolbook font is very similar to Computer Modern Math: cmmi */
+.MATH    { font-family: "Century Schoolbook", serif; }
+.MATH I  { font-family: "Century Schoolbook", serif; font-style: italic }
+.BOLDMATH { font-family: "Century Schoolbook", serif; font-weight: bold }
+
+/* implement both fixed-size and relative sizes */
+SMALL.XTINY		{ font-size : xx-small }
+SMALL.TINY		{ font-size : x-small  }
+SMALL.SCRIPTSIZE	{ font-size : smaller  }
+SMALL.FOOTNOTESIZE	{ font-size : small    }
+SMALL.SMALL		{  }
+BIG.LARGE		{  }
+BIG.XLARGE		{ font-size : large    }
+BIG.XXLARGE		{ font-size : x-large  }
+BIG.HUGE		{ font-size : larger   }
+BIG.XHUGE		{ font-size : xx-large }
+
+/* heading styles */
+H1		{  }
+H2		{  }
+H3		{  }
+H4		{  }
+H5		{  }
+
+/* mathematics styles */
+DIV.displaymath		{ }	/* math displays */
+TD.eqno			{ }	/* equation-number cells */
+
+
+/* document-specific styles come next */

docs/html/angularCalibrationHowTo/angularCalibrationHowTo.html

@@ -0,0 +1,81 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2012 (1.2)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Angular calibration wizard manual</TITLE>
+<META NAME="description" CONTENT="Angular calibration wizard manual">
+<META NAME="keywords" CONTENT="angularCalibrationHowTo">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2012">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="angularCalibrationHowTo.css">
+
+<LINK REL="next" HREF="node1.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html6"
+  HREF="node1.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="next.png"></A> 
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="up_g.png"> 
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="prev_g.png">   
+<BR>
+<B> Next:</B> <A NAME="tex2html7"
+  HREF="node1.html">Introduction</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<P>
+
+<H1 ALIGN="CENTER">Angular calibration wizard manual</H1>
+<DIV>
+
+<P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
+<P ALIGN="CENTER"><STRONG>April 8, 2019</STRONG></P>
+</DIV>
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"></A>
+
+<UL>
+<LI><A NAME="tex2html8"
+  HREF="node1.html">Introduction</A>
+<LI><A NAME="tex2html9"
+  HREF="node2.html">Data acquisition</A>
+<UL>
+<LI><A NAME="tex2html10"
+  HREF="node2.html#SECTION00021000000000000000">Software</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html11"
+  HREF="node3.html">Data analysis</A>
+<UL>
+<LI><A NAME="tex2html12"
+  HREF="node3.html#SECTION00031000000000000000">Software</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html13"
+  HREF="node4.html">Setup calibration files</A>
+<LI><A NAME="tex2html14"
+  HREF="node5.html">About this document ...</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+Thattil Dhanya
+2019-04-08
+</ADDRESS>
+</BODY>
+</HTML>

docs/html/angularCalibrationHowTo/images.pl

@@ -0,0 +1,116 @@
+# LaTeX2HTML 2012 (1.2)
+# Associate images original text with physical files.
+
+
+$key = q/Theta_e;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="24" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img4.png"
+ ALT="$\Theta_e$">|; 
+
+$key = q/C_{center}^{i};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="53" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img7.png"
+ ALT="$C_{center}^{i}$">|; 
+
+$key = q/i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="10" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img3.png"
+ ALT="$i$">|; 
+
+$key = q/mu;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="14" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img11.png"
+ ALT="$\mu$">|; 
+
+$key = q/Theta_o^i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="24" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img6.png"
+ ALT="$\Theta_o^i$">|; 
+
+$key = q/includegraphics[width=textwidth]{enable_angcal.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="555" HEIGHT="603" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img14.png"
+ ALT="\includegraphics[width=\textwidth]{enable_angcal.eps}">|; 
+
+$key = q/p=50~mum;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="79" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img9.png"
+ ALT="$p=50&nbsp;\mu m$">|; 
+
+$key = q/C_{peak};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="43" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img2.png"
+ ALT="$C_{peak}$">|; 
+
+$key = q/_6;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="12" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img10.png"
+ ALT="$_6$">|; 
+
+$key = q/includegraphics[width=textwidth]{peakFit.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img17.png"
+ ALT="\includegraphics[width=\textwidth]{peakFit.eps}">|; 
+
+$key = q/pslashR^i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="38" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img13.png"
+ ALT="$p/R^i$">|; 
+
+$key = q/includegraphics[width=textwidth]{setupAngcal.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img16.png"
+ ALT="\includegraphics[width=\textwidth]{setupAngcal.eps}">|; 
+
+$key = q/includegraphics[width=textwidth]{angleFit.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img18.png"
+ ALT="\includegraphics[width=\textwidth]{angleFit.eps}">|; 
+
+$key = q/pm;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="17" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img12.png"
+ ALT="$\pm$">|; 
+
+$key = q/{displaymath}Theta_e=Theta_o^i-arctanBig(frac{pcdot(C_{peak}-C_{center}^i)}{R^i}Big),{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="291" HEIGHT="41" BORDER="0"
+ SRC="|."$dir".q|img5.png"
+ ALT="\begin{displaymath}
+\Theta_e=\Theta_o^i-\arctan\Big(\frac{p \cdot (C_{peak}-C_{center}^i)}{R^i}\Big),
+\end{displaymath}">|; 
+
+$key = q/theta;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img1.png"
+ ALT="$\theta$">|; 
+
+$key = q/R^i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="22" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img8.png"
+ ALT="$R^i$">|; 
+
+$key = q/includegraphics[width=textwidth]{position_scan.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="555" HEIGHT="603" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img15.png"
+ ALT="\includegraphics[width=\textwidth]{position_scan.eps}">|; 
+
+1;
+

docs/html/angularCalibrationHowTo/images.tex

@@ -0,0 +1,255 @@
+\batchmode
+\documentclass{article}
+\RequirePackage{ifthen}
+
+
+\usepackage{amssymb}
+\usepackage[dvips]{graphicx}
+\usepackage{verbatim}
+
+
+\usepackage[dvips]{color}
+
+
+\pagecolor[gray]{.7}
+
+\usepackage[]{inputenc}
+
+
+
+\makeatletter
+
+\makeatletter
+\count@=\the\catcode`\_ \catcode`\_=8 
+\newenvironment{tex2html_wrap}{}{}%
+\catcode`\<=12\catcode`\_=\count@
+\newcommand{\providedcommand}[1]{\expandafter\providecommand\csname #1\endcsname}%
+\newcommand{\renewedcommand}[1]{\expandafter\providecommand\csname #1\endcsname{}%
+  \expandafter\renewcommand\csname #1\endcsname}%
+\newcommand{\newedenvironment}[1]{\newenvironment{#1}{}{}\renewenvironment{#1}}%
+\let\newedcommand\renewedcommand
+\let\renewedenvironment\newedenvironment
+\makeatother
+\let\mathon=$
+\let\mathoff=$
+\ifx\AtBeginDocument\undefined \newcommand{\AtBeginDocument}[1]{}\fi
+\newbox\sizebox
+\setlength{\hoffset}{0pt}\setlength{\voffset}{0pt}
+\addtolength{\textheight}{\footskip}\setlength{\footskip}{0pt}
+\addtolength{\textheight}{\topmargin}\setlength{\topmargin}{0pt}
+\addtolength{\textheight}{\headheight}\setlength{\headheight}{0pt}
+\addtolength{\textheight}{\headsep}\setlength{\headsep}{0pt}
+\setlength{\textwidth}{349pt}
+\newwrite\lthtmlwrite
+\makeatletter
+\let\realnormalsize=\normalsize
+\global\topskip=2sp
+\def\preveqno{}\let\real@float=\@float \let\realend@float=\end@float
+\def\@float{\let\@savefreelist\@freelist\real@float}
+\def\liih@math{\ifmmode$\else\bad@math\fi}
+\def\end@float{\realend@float\global\let\@freelist\@savefreelist}
+\let\real@dbflt=\@dbflt \let\end@dblfloat=\end@float
+\let\@largefloatcheck=\relax
+\let\if@boxedmulticols=\iftrue
+\def\@dbflt{\let\@savefreelist\@freelist\real@dbflt}
+\def\adjustnormalsize{\def\normalsize{\mathsurround=0pt \realnormalsize
+ \parindent=0pt\abovedisplayskip=0pt\belowdisplayskip=0pt}%
+ \def\phantompar{\csname par\endcsname}\normalsize}%
+\def\lthtmltypeout#1{{\let\protect\string \immediate\write\lthtmlwrite{#1}}}%
+\newcommand\lthtmlhboxmathA{\adjustnormalsize\setbox\sizebox=\hbox\bgroup\kern.05em }%
+\newcommand\lthtmlhboxmathB{\adjustnormalsize\setbox\sizebox=\hbox to\hsize\bgroup\hfill }%
+\newcommand\lthtmlvboxmathA{\adjustnormalsize\setbox\sizebox=\vbox\bgroup %
+ \let\ifinner=\iffalse \let\)\liih@math }%
+\newcommand\lthtmlboxmathZ{\@next\next\@currlist{}{\def\next{\voidb@x}}%
+ \expandafter\box\next\egroup}%
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docs/html/angularCalibrationHowTo/index.html

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+<!--Converted with LaTeX2HTML 2012 (1.2)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Angular calibration wizard manual</TITLE>
+<META NAME="description" CONTENT="Angular calibration wizard manual">
+<META NAME="keywords" CONTENT="angularCalibrationHowTo">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
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+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="up_g.png"> 
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+<B> Next:</B> <A NAME="tex2html7"
+  HREF="node1.html">Introduction</A>
+<BR>
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+<!--End of Navigation Panel-->
+
+<P>
+
+<H1 ALIGN="CENTER">Angular calibration wizard manual</H1>
+<DIV>
+
+<P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
+<P ALIGN="CENTER"><STRONG>April 8, 2019</STRONG></P>
+</DIV>
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"></A>
+
+<UL>
+<LI><A NAME="tex2html8"
+  HREF="node1.html">Introduction</A>
+<LI><A NAME="tex2html9"
+  HREF="node2.html">Data acquisition</A>
+<UL>
+<LI><A NAME="tex2html10"
+  HREF="node2.html#SECTION00021000000000000000">Software</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html11"
+  HREF="node3.html">Data analysis</A>
+<UL>
+<LI><A NAME="tex2html12"
+  HREF="node3.html#SECTION00031000000000000000">Software</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html13"
+  HREF="node4.html">Setup calibration files</A>
+<LI><A NAME="tex2html14"
+  HREF="node5.html">About this document ...</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+Thattil Dhanya
+2019-04-08
+</ADDRESS>
+</BODY>
+</HTML>

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docs/html/angularCalibrationHowTo/labels.pl

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+

docs/html/angularCalibrationHowTo/node1.html

@@ -0,0 +1,180 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2012 (1.2)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Introduction</TITLE>
+<META NAME="description" CONTENT="Introduction">
+<META NAME="keywords" CONTENT="angularCalibrationHowTo">
+<META NAME="resource-type" CONTENT="document">
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+  HREF="angularCalibrationHowTo.html">Angular calibration wizard manual</A>
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+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00010000000000000000">
+Introduction</A>
+</H1>
+
+<P>
+In order to convert from strip number to 2<IMG
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="img1.png"
+ ALT="$\theta$">-angle, an accurate angular calibration of the detector must be performed (for details see the paper Bergamaschi, A. et al. (2010). J. Synchrotron Rad. 17, 653-668). 
+<BR>
+<P>
+For this purpose, a series of patterns of a powder standard with symmetric peaks (e.g. silicon) must acquired while shifting the detector by an angular step of the order of about 2% of the module size. During the measurement, a strong intensity peak (e.g. Si(111)) should pass through the field of view of every module such that it can be used as a reference angular position to perform the calibration of the modules position.
+<BR>
+<P>
+In a first step, the   peak is fitted with a Gaussian in order to determine its position <IMG
+ WIDTH="43" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img2.png"
+ ALT="$C_{peak}$"> in channel number for each of the acquired patterns.
+<BR>
+In a second step, for each module <IMG
+ WIDTH="10" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img3.png"
+ ALT="$i$">, the encoder position  <IMG
+ WIDTH="24" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img4.png"
+ ALT="$\Theta_e$"> is fitted as a function of the peak position  <IMG
+ WIDTH="43" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img2.png"
+ ALT="$C_{peak}$"> according to:
+<BR>
+<DIV ALIGN="RIGHT">
+
+<!-- MATH
+ \begin{equation}
+\Theta_e=\Theta_o^i-\arctan\Big(\frac{p \cdot (C_{peak}-C_{center}^i)}{R^i}\Big),
+\end{equation}
+ -->
+<TABLE WIDTH="100%" ALIGN="CENTER">
+<TR VALIGN="MIDDLE"><TD ALIGN="CENTER" NOWRAP><A NAME="eq:angcal"></A><IMG
+ WIDTH="291" HEIGHT="41" BORDER="0"
+ SRC="img5.png"
+ ALT="\begin{displaymath}
+\Theta_e=\Theta_o^i-\arctan\Big(\frac{p \cdot (C_{peak}-C_{center}^i)}{R^i}\Big),
+\end{displaymath}"></TD>
+<TD WIDTH=10 ALIGN="RIGHT">
+(1)</TD></TR>
+</TABLE>
+<BR CLEAR="ALL"></DIV><P></P>
+where the parameters <IMG
+ WIDTH="24" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="img6.png"
+ ALT="$\Theta_o^i$"> is the angular offset with respect to the diffractometer zero position, <!-- MATH
+ $C_{center}^{i}$
+ -->
+<IMG
+ WIDTH="53" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="img7.png"
+ ALT="$C_{center}^{i}$"> is the central channel  and <IMG
+ WIDTH="22" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img8.png"
+ ALT="$R^i$"> is the distance of the module <IMG
+ WIDTH="10" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img3.png"
+ ALT="$i$"> from the diffractometer center while <IMG
+ WIDTH="79" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img9.png"
+ ALT="$p=50~\mu m$"> is the strip pitch of the detector. 
+<BR>
+Finally, the global offset of the detector system is precisely determined by refining a silicon pattern at a well-defined energy (i.e., knowing the position of the peak).
+
+<P>
+The same function of equation&nbsp;<A HREF="#eq:angcal">1</A>, with the parameters obtained from the calibration, is used in order to convert from channel number to 2<IMG
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="img1.png"
+ ALT="$\theta$">-angle.
+
+<P>
+The parallax at the borders of the modules due to the thickness of the silicon sensor is a function of the X-ray energy (higher energy X-rays are absorbed deeper inside the sensor) and is of the order of 0.2&nbsp;mdeg at 12&nbsp;keV and 0.5&nbsp;mdeg at 30&nbsp;keV. 
+<BR>
+The differences in pixel size due to the different portion of solid angle covered by the strips on the border of the modules and  the higher efficiency due to the longer path of the X-rays in the sensor are removed by the flat field correction. This also normalizes additional differences in pixel size between channels which are also present because of mismatches in the strip sensor fabrication and in fluctuations of the channels threshold level.
+
+<P>
+Patterns acquired at different detector positions are generally merged together  in order to fill the gaps between the modules and correct possibly bad functioning channels. In this procedure the data from different positions which are closer than 4&nbsp;mdeg (the average pixel size) are averaged and the new position is set to the mean of the positions of the original points.
+
+<P>
+The position and width of the peaks results from a fit over several detector channels. Geometrical distortions might disturb this determination mainly because of errors in the angular calibration, fluctuations in the encoder position, variations between channels and parallax effects.
+<BR>
+The resolution in locating the peak center and determining its width and integrated intensity has been estimated by acquiring several patterns of a LaB<IMG
+ WIDTH="12" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img10.png"
+ ALT="$_6$"> sample in a 300&nbsp;<IMG
+ WIDTH="14" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img11.png"
+ ALT="$\mu$">m capillary with the detector shifted in 5&nbsp;mdeg steps between 30.4 and 36.5 degrees. The 16&nbsp;peaks acquired have been fitted with a Gaussian function plus background and the fluctuations on the fitted parameters have been calculated. The resulting average resolutions are  0.63<IMG
+ WIDTH="17" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img12.png"
+ ALT="$\pm$">0.06&nbsp;mdeg for the peak center and 0.22<IMG
+ WIDTH="17" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img12.png"
+ ALT="$\pm$">0.05&nbsp;mdeg for the peak Full-Width at Half-Maximum (FWHM) for an average peak FWHM of 27.0<IMG
+ WIDTH="17" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="img12.png"
+ ALT="$\pm$">2.5&nbsp;mdeg. 
+<BR>
+These results show that  the angular calibration allows a resolution in determining the peaks position and width which is appropriate for structural determination.
+
+<P>
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html23"
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+<TITLE>Data acquisition</TITLE>
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+
+<H1><A NAME="SECTION00020000000000000000">
+Data acquisition</A>
+</H1>
+
+<P>
+The angular calibration consists in acquiring a set of diffraction patterns of a well known powder standard (e.g. Silicon) at different encoder positions.  In order to facilitate the procedure, the sample should not emit fluorescent light and should present relatively symmetric peaks. 
+<BR>
+During the measurement, a strong intensity peak (e.g. Si(111)) should pass through the field of view of every module such that it can be used as a reference angular position to perform the calibration of the modules position. In general the highest peak will be used for the calibration, but this is not necessary in case there would be e.g. geometrical limitations for shifting the detector. 
+<BR><B>Do not forget to properly position the beam stopper if the detector is scanned in front of the direct beam.</B>
+<BR>
+The detector should be shifted of an angular step of the order of about 2% of the module size, such that about 50 patterns can contribute to the fitting of the 3 parameters necessary for the angular calibration.
+<BR>
+<P>
+All the angular calibration procedure should be acquired using a trimmed detector with the threshold set at half of the X-ray energy (Assuming no fluorescent element in the standard). A flat field should also be acquired in order to precisely correct the data, while the X-ray intensity should be kept lower than about 100&nbsp;kHz per strip in order to avoid the need for rate corrections.
+
+<P>
+A rough angular conversion file starting from a previous calibration or from the geometric characteristics of the mechanics is an advantage. The angular conversion file should contain a line for each module of the detector with its module number <IMG
+ WIDTH="10" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="img3.png"
+ ALT="$i$">, center  <!-- MATH
+ $C_{center}^{i}$
+ -->
+<IMG
+ WIDTH="53" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="img7.png"
+ ALT="$C_{center}^{i}$"> and error, conversion radius <IMG
+ WIDTH="38" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="img13.png"
+ ALT="$p/R^i$"> and error, offset <IMG
+ WIDTH="24" HEIGHT="36" ALIGN="MIDDLE" BORDER="0"
+ SRC="img6.png"
+ ALT="$\Theta_o^i$"> and error:
+<PRE>
+module 0 center 639.5 +- 0 conversion 6.56E-05 +- 0 offset 0 +- 0
+</PRE>
+Also the <I>global offset</I> value of the beamline should be approximately known i.e. the angular position of channel 0 of module 0 when the motor is set at 0. 
+<BR>
+All the documentation assumes that the detector is oriented in the same direction as the encoder position i.e. large channel number at higher angles (both per module and absolute). If this is not the case, the <I>angular direction</I> should be set to -1. 
+
+<P>
+
+<H2><A NAME="SECTION00021000000000000000">
+Software</A>
+</H2>
+
+<P>
+For the acquisition ot the data you need to install the slsDetector software package (please refere to separate documentation). The use of the GUI is optional and all operations can be performed also using the text client.
+<BR>
+<P>
+Please make sure that you have edited the 
+<BR><I>slsDetectorSoftware/usersFunctions/angleFunction.h</I> 
+<BR>
+in order to match the angular conversion for your geometry and 
+<BR><I>slsDetectorSoftware/usersFunctions/usersFunctions.cpp</I> 
+<BR>
+in order to be able to move the detector and read out its position by using the slsDetector software.
+
+<P>
+In the following the command to acquire a dataset for the angular calibration with an exposure time of 1&nbsp;s, and position shift 
+<PRE>
+#setup angular calibration log mode
+&gt; sls_detector_put angcallog 1 
+#set exposure time to 1s
+&gt; sls_detector_put exptime 1. 
+#setup threshold scan
+&gt; sls_detector_put scan0script position 
+#setup the precision for the scan variable in the file name
+&gt; sls_detector_put scan0prec 2 
+#set scan range between 20deg and -60deg, step of -0.1deg
+# (at 12.4 keV the Si(111) peak is at approx 19deg
+&gt; sls_detector_put scan0range 20 -60 -0.1 
+#acquire the data
+&gt; sls_detector_acquire
+#unset angular calibration log mode
+&gt; sls_detector_put angcallog 0
+</PRE>
+
+<P>
+With the GUI you can obtain the same results by clicking on the <I>Angular calibration</I> log button in the advanced tab (see figure&nbsp;<A HREF="#fig:guiangcallog">1</A>) and setting up the motor position scan in the Actions tab (see figure&nbsp;<A HREF="#fig:guiposscan">2</A>). The exposure time should also be set in the measurement tab.
+
+<P>
+Additional to the data files, the acquisition will produce a .angcal file containing an header and, for each step of the acquisition, the exect value of the motor position and the file name. 
+<BR>
+In case you forgot to enable the angcallog flag in the software, you can produce the file with the syntax as follows, assuming that you know the exact values of your encoder for each frame:
+<PRE>
+type Mythen
+maxmod 32
+nmod 32
+angconv /scratch/angcal20120422/ang.off
+globaloff 5.088
+fineoff 0.0
+angdir 1
+ffdir /scratch/angcal20120422/
+flatfield flatfield_E12keV_T6keV_0.raw
+badchannels /scratch/cal/bad.chans
+19.99998 angcal_S20.00_0
+19.90001 angcal_S19.90_0
+19.79999 angcal_S19.80_0
+19.70002 angcal_S19.70_0
+......
+</PRE>
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:guiangcallog"></A><A NAME="46"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 1:</STRONG>
+Acquisition GUI window to enable the angular calibration log.</CAPTION>
+<TR><TD><IMG
+ WIDTH="555" HEIGHT="603" ALIGN="BOTTOM" BORDER="0"
+ SRC="img14.png"
+ ALT="\includegraphics[width=\textwidth]{enable_angcal.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:guiposscan"></A><A NAME="51"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 2:</STRONG>
+Acquisition GUI window to setup the motor position scan.</CAPTION>
+<TR><TD><IMG
+ WIDTH="555" HEIGHT="603" ALIGN="BOTTOM" BORDER="0"
+ SRC="img15.png"
+ ALT="\includegraphics[width=\textwidth]{position_scan.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
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+<H1><A NAME="SECTION00030000000000000000">
+Data analysis</A>
+</H1>
+
+<P>
+The data analysis consists in fitting with a gaussian the selected peak of the powder pattern for each position in order to determine its position is channel number as a function of the encoder position. 
+<BR>
+In a second step, for each module, the channel vs. encoder curve is fitted in order to extrapolate the three parameters necessary for the angular conversion and the result is written to file
+
+<P>
+
+<H2><A NAME="SECTION00031000000000000000">
+Software</A>
+</H2>
+
+<P>
+The software used for the angular calibration data analysis is based on root (see http://root.cern.ch).
+<BR>
+This can be downloaded as binary or installed from sources. The version of the software should not play an important role, but up to now everything has been implemented and tested using version 5.20.
+
+<P>
+To start the data analysis simply launch:
+<PRE>
+&gt; ./angularCalibrationWizard
+</PRE>
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:setangcal"></A><A NAME="60"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 3:</STRONG>
+Overview of the nagular calibration dataset.</CAPTION>
+<TR><TD><IMG
+ WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
+ SRC="img16.png"
+ ALT="\includegraphics[width=\textwidth]{setupAngcal.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+To setup the angular calibration dataset, the .angcal file should be selected (or digited) and the load button should be pressed to confirm. The parameters of the angular calibration are then read to the file and the data loaded for a quick overview (see figure&nbsp;<A HREF="#fig:setangcal">3</A>).
+<BR>
+The software assumes that the data files (.raw) and the .encal file are in the same directory.
+<BR>
+A 2D color plot will show a rebinned overview of the dataset. The peak to be fitted should be visible as a high intensity diagonal line passing through all the channels.
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:peakfit"></A><A NAME="66"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 4:</STRONG>
+Preview of the fitting of the Si(111) peak for one of the detector positions.</CAPTION>
+<TR><TD><IMG
+ WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
+ SRC="img17.png"
+ ALT="\includegraphics[width=\textwidth]{peakFit.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+For a more detailed view of the data, one can select an angular calibration step from the combo box, select the plot mode (raw data or processed data as a function of channel number, processed angular converted data, flat field data, or again an overview of the whole dataset). 
+<BR>
+By (right) clicking close to the axis you are able to zoom in/out, set the scale to logarithmic etc.
+<BR>
+<P>
+If the bad channel list, angular conversion file or flat field file are changed compared to the acquisition, they can be reloaded by editing the correspondent text entries and pressing enter.
+
+<P>
+In particular, the angular converted data should be checked in order to view the position of the selected peak. In this case, the plot will be zoomed to the angular region slected in the minimum and maximum angle entries. By pressing fit, the fit of the peak in the selected angular range will be shown (see figure&nbsp;<A HREF="#fig:peakfit">4</A>).  It is useful to check that it works properly in several positions such that then the sequential fitting on all steps can give good results.
+
+<P>
+To automatically fit all positions simply press <I>Proceed to Modules Calibration</I> and wait until all steps are fitted. This can take sometime, depending on the number of steps.
+
+<P>
+
+<DIV ALIGN="CENTER"><A NAME="fig:anglefit"></A><A NAME="73"></A>
+<TABLE>
+<CAPTION ALIGN="BOTTOM"><STRONG>Figure 5:</STRONG>
+Window for fitting the angular calibration parameters of a module.</CAPTION>
+<TR><TD><IMG
+ WIDTH="555" HEIGHT="707" ALIGN="BOTTOM" BORDER="0"
+ SRC="img18.png"
+ ALT="\includegraphics[width=\textwidth]{angleFit.eps}"></TD></TR>
+</TABLE>
+</DIV>
+
+<P>
+In the module calibration window (see figure&nbsp;<A HREF="#fig:anglefit">5</A>), you will be able to fit the channel number to encoder position curve to estimate the three angular calibration parameters for each module.
+<BR>
+The entries show the angular calibration parameters used for approximate angular conversion in the previous step of the calibration. These can be edited and will be used as start parameters for the fit.
+By clicking on the check box next to the parameters, the selected parameter will be set and fixed during the fit. Often the center is used as a fix parameter.
+<BR>
+It is possible to navigate between modules by using the Previous and Next module buttons. To refit the current module (e.g. after changing one of the parameters) simply re-click on the module number.
+
+<P>
+After fitting all modules you can click on the <I>Write Angular Calibration</I> button, select the file name to write to and save the calibration angulat calibration data. Please note that the offset of module 0 will always be 0 and the other values will be rescaled to its value. Therefore the global offset of the steup will always need to be specified for a proper angular conversion unless the home of the encoder will not be redifined.
+
+<P>
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+<H1><A NAME="SECTION00040000000000000000">
+Setup calibration files</A>
+</H1>
+
+<P>
+To use the generated angular calibration files, using the text client:
+<PRE>
+sls_detector_put angconv /scratch/ang_new.off
+</PRE>
+while for the GUI the file name should be specified in the configuration file (works also for the text client).
+<BR><HR>
+<ADDRESS>
+Thattil Dhanya
+2019-04-08
+</ADDRESS>
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+This document was generated using the
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+/* Century Schoolbook font is very similar to Computer Modern Math: cmmi */
+.MATH    { font-family: "Century Schoolbook", serif; }
+.MATH I  { font-family: "Century Schoolbook", serif; font-style: italic }
+.BOLDMATH { font-family: "Century Schoolbook", serif; font-weight: bold }
+
+/* implement both fixed-size and relative sizes */
+SMALL.XTINY		{ font-size : xx-small }
+SMALL.TINY		{ font-size : x-small  }
+SMALL.SCRIPTSIZE	{ font-size : smaller  }
+SMALL.FOOTNOTESIZE	{ font-size : small    }
+SMALL.SMALL		{  }
+BIG.LARGE		{  }
+BIG.XLARGE		{ font-size : large    }
+BIG.XXLARGE		{ font-size : x-large  }
+BIG.HUGE		{ font-size : larger   }
+BIG.XHUGE		{ font-size : xx-large }
+
+/* heading styles */
+H1		{  }
+H2		{  }
+H3		{  }
+H4		{  }
+H5		{  }
+
+/* mathematics styles */
+DIV.displaymath		{ }	/* math displays */
+TD.eqno			{ }	/* equation-number cells */
+
+
+/* document-specific styles come next */

docs/html/energyCalibrationHowTo/energyCalibrationHowTo.html

@@ -0,0 +1,81 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2012 (1.2)
+original version by:  Nikos Drakos, CBLU, University of Leeds
+* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Energy calibration wizard manual</TITLE>
+<META NAME="description" CONTENT="Energy calibration wizard manual">
+<META NAME="keywords" CONTENT="energyCalibrationHowTo">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META NAME="Generator" CONTENT="LaTeX2HTML v2012">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="energyCalibrationHowTo.css">
+
+<LINK REL="next" HREF="node1.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html9"
+  HREF="node1.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="next.png"></A> 
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="up_g.png"> 
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="prev_g.png">   
+<BR>
+<B> Next:</B> <A NAME="tex2html10"
+  HREF="node1.html">Introduction</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<P>
+
+<H1 ALIGN="CENTER">Energy calibration wizard manual</H1>
+<DIV>
+
+<P ALIGN="CENTER"><STRONG>Anna Bergamaschi</STRONG></P>
+<P ALIGN="CENTER"><STRONG>April 8, 2019</STRONG></P>
+</DIV>
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"></A>
+
+<UL>
+<LI><A NAME="tex2html11"
+  HREF="node1.html">Introduction</A>
+<LI><A NAME="tex2html12"
+  HREF="node2.html">Data acquisition</A>
+<UL>
+<LI><A NAME="tex2html13"
+  HREF="node2.html#SECTION00021000000000000000">Software</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html14"
+  HREF="node3.html">Data analysis</A>
+<UL>
+<LI><A NAME="tex2html15"
+  HREF="node3.html#SECTION00031000000000000000">Software</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html16"
+  HREF="node4.html">Setup calibration files</A>
+<LI><A NAME="tex2html17"
+  HREF="node5.html">About this document ...</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+Thattil Dhanya
+2019-04-08
+</ADDRESS>
+</BODY>
+</HTML>

docs/html/energyCalibrationHowTo/images.pl

@@ -0,0 +1,252 @@
+# LaTeX2HTML 2012 (1.2)
+# Associate images original text with physical files.
+
+
+$key = q/CS=frac{N_S}{N_0};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="71" HEIGHT="38" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img32.png"
+ ALT="$CS=\frac{N_S}{N_0}$">|; 
+
+$key = q/O;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="17" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img25.png"
+ ALT="$O$">|; 
+
+$key = q/N_gamma;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="25" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img17.png"
+ ALT="$N_\gamma$">|; 
+
+$key = q/E_t;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="22" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img10.png"
+ ALT="$E_t$">|; 
+
+$key = q/includegraphics[width=textwidth]{calibrateModule.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="514" HEIGHT="654" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img40.png"
+ ALT="\includegraphics[width=\textwidth]{calibrateModule.eps}">|; 
+
+$key = q/{displaymath}N_n(E_t)simfrac{T}{tau_s}DBig(frac{-E_t}{ENC}Big).{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="169" HEIGHT="41" BORDER="0"
+ SRC="|."$dir".q|img23.png"
+ ALT="\begin{displaymath}
+N_n(E_t) \sim \frac{T}{\tau_s} D \Big(\frac{-E_t}{ENC} \Big).
+\end{displaymath}">|; 
+
+$key = q/tau_s;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="18" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img21.png"
+ ALT="$\tau_s$">|; 
+
+$key = q/V_t;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="19" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img27.png"
+ ALT="$V_t$">|; 
+
+$key = q/ENC;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="44" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img3.png"
+ ALT="$ENC$">|; 
+
+$key = q/includegraphics[width=textwidth]{fig8.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="556" HEIGHT="539" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img36.png"
+ ALT="\includegraphics[width=\textwidth]{fig8.eps}">|; 
+
+$key = q/N_n;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="26" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img16.png"
+ ALT="$N_n$">|; 
+
+$key = q/T;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="16" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img22.png"
+ ALT="$T$">|; 
+
+$key = q/E_0;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="23" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img1.png"
+ ALT="$E_0$">|; 
+
+$key = q/G;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="17" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img26.png"
+ ALT="$G$">|; 
+
+$key = q/{displaymath}N_gamma(E_t)=frac{N_0}{2}cdotBig(1+C_sfrac{E_0-2E_t}{E_0}Big)DBig(frac{E_0-E_t}{ENC}Big),{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="335" HEIGHT="41" BORDER="0"
+ SRC="|."$dir".q|img18.png"
+ ALT="\begin{displaymath}
+N_\gamma(E_t)=\frac{N_0}{2}\cdot\Big(1+C_s \frac{E_0-2E_t}{E_0}\Big)D \Big(\frac{E_0-E_t}{ENC} \Big),
+\end{displaymath}">|; 
+
+$key = q/includegraphics[width=textwidth]{GUI_ThresholdScan.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="555" HEIGHT="603" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img38.png"
+ ALT="\includegraphics[width=\textwidth]{GUI_ThresholdScan.eps}">|; 
+
+$key = q/N_0;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="24" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img2.png"
+ ALT="$N_0$">|; 
+
+$key = q/N_S;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="27" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img5.png"
+ ALT="$N_S$">|; 
+
+$key = q/O_i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="22" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img30.png"
+ ALT="$O_i$">|; 
+
+$key = q/E_f;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="25" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img7.png"
+ ALT="$E_f$">|; 
+
+$key = q/i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="10" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img29.png"
+ ALT="$i$">|; 
+
+$key = q/G_i;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="22" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img31.png"
+ ALT="$G_i$">|; 
+
+$key = q/includegraphics[width=textwidth]{fig7.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="556" HEIGHT="553" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img35.png"
+ ALT="\includegraphics[width=\textwidth]{fig7.eps}">|; 
+
+$key = q/D;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="18" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img13.png"
+ ALT="$D$">|; 
+
+$key = q/N_s=C_sN_0;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="83" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img20.png"
+ ALT="$N_s=C_s N_0$">|; 
+
+$key = q/E_0slash2;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="39" HEIGHT="32" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img8.png"
+ ALT="$E_0/2$">|; 
+
+$key = q/E_t=E_0slash2;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="78" HEIGHT="32" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img14.png"
+ ALT="$E_t=E_0/2$">|; 
+
+$key = q/includegraphics[width=textwidth]{fig4.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="556" HEIGHT="539" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img33.png"
+ ALT="\includegraphics[width=\textwidth]{fig4.eps}">|; 
+
+$key = q/includegraphics[width=textwidth]{GUI_Advanced.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="555" HEIGHT="603" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img37.png"
+ ALT="\includegraphics[width=\textwidth]{GUI_Advanced.eps}">|; 
+
+$key = q/includegraphics[width=textwidth]{addEnergy.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="514" HEIGHT="654" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img39.png"
+ ALT="\includegraphics[width=\textwidth]{addEnergy.eps}">|; 
+
+$key = q/C_s;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="23" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img19.png"
+ ALT="$C_s$">|; 
+
+$key = q/CS={begingroup{N_Sbegingroup{overN_0};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="24" HEIGHT="12" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img6.png"
+ ALT="$CS={\begingroupN_S\endgroup\over N_0}$">|; 
+
+$key = q/CS=;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="45" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img4.png"
+ ALT="$CS=$">|; 
+
+$key = q/e^-;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="23" HEIGHT="19" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img12.png"
+ ALT="$e^-$">|; 
+
+$key = q/includegraphics[width=textwidth]{fig5.eps};AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="556" HEIGHT="539" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img34.png"
+ ALT="\includegraphics[width=\textwidth]{fig5.eps}">|; 
+
+$key = q/{displaymath}V_{t}=O+GcdotE_t.{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="111" HEIGHT="26" BORDER="0"
+ SRC="|."$dir".q|img28.png"
+ ALT="\begin{displaymath}
+V_{t}=O+G \cdot E_t.
+\end{displaymath}">|; 
+
+$key = q/Sigma>3ENC;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="85" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img11.png"
+ ALT="$\Sigma &gt;3ENC$">|; 
+
+$key = q/N;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="19" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img15.png"
+ ALT="$N$">|; 
+
+$key = q/Sigma>3,ENC;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="88" HEIGHT="30" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img24.png"
+ ALT="$\Sigma&gt;3 ENC$">|; 
+
+$key = q/Deltasim;MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="35" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img9.png"
+ ALT="$\Delta \sim $">|; 
+
+1;
+

docs/html/energyCalibrationHowTo/images.tex

@@ -0,0 +1,391 @@
+\batchmode
+\documentclass{article}
+\RequirePackage{ifthen}
+
+
+\usepackage{amssymb}
+\usepackage[dvips]{graphicx}
+\usepackage{verbatim}
+
+
+\usepackage[dvips]{color}
+
+
+\pagecolor[gray]{.7}
+
+\usepackage[]{inputenc}
+
+
+
+\makeatletter
+
+\makeatletter
+\count@=\the\catcode`\_ \catcode`\_=8 
+\newenvironment{tex2html_wrap}{}{}%
+\catcode`\<=12\catcode`\_=\count@
+\newcommand{\providedcommand}[1]{\expandafter\providecommand\csname #1\endcsname}%
+\newcommand{\renewedcommand}[1]{\expandafter\providecommand\csname #1\endcsname{}%
+  \expandafter\renewcommand\csname #1\endcsname}%
+\newcommand{\newedenvironment}[1]{\newenvironment{#1}{}{}\renewenvironment{#1}}%
+\let\newedcommand\renewedcommand
+\let\renewedenvironment\newedenvironment
+\makeatother
+\let\mathon=$
+\let\mathoff=$
+\ifx\AtBeginDocument\undefined \newcommand{\AtBeginDocument}[1]{}\fi
+\newbox\sizebox
+\setlength{\hoffset}{0pt}\setlength{\voffset}{0pt}
+\addtolength{\textheight}{\footskip}\setlength{\footskip}{0pt}
+\addtolength{\textheight}{\topmargin}\setlength{\topmargin}{0pt}
+\addtolength{\textheight}{\headheight}\setlength{\headheight}{0pt}
+\addtolength{\textheight}{\headsep}\setlength{\headsep}{0pt}
+\setlength{\textwidth}{349pt}
+\newwrite\lthtmlwrite
+\makeatletter
+\let\realnormalsize=\normalsize
+\global\topskip=2sp
+\def\preveqno{}\let\real@float=\@float \let\realend@float=\end@float
+\def\@float{\let\@savefreelist\@freelist\real@float}
+\def\liih@math{\ifmmode$\else\bad@math\fi}
+\def\end@float{\realend@float\global\let\@freelist\@savefreelist}
+\let\real@dbflt=\@dbflt \let\end@dblfloat=\end@float
+\let\@largefloatcheck=\relax
+\let\if@boxedmulticols=\iftrue
+\def\@dbflt{\let\@savefreelist\@freelist\real@dbflt}
+\def\adjustnormalsize{\def\normalsize{\mathsurround=0pt \realnormalsize
+ \parindent=0pt\abovedisplayskip=0pt\belowdisplayskip=0pt}%
+ \def\phantompar{\csname par\endcsname}\normalsize}%
+\def\lthtmltypeout#1{{\let\protect\string \immediate\write\lthtmlwrite{#1}}}%
+\newcommand\lthtmlhboxmathA{\adjustnormalsize\setbox\sizebox=\hbox\bgroup\kern.05em }%
+\newcommand\lthtmlhboxmathB{\adjustnormalsize\setbox\sizebox=\hbox to\hsize\bgroup\hfill }%
+\newcommand\lthtmlvboxmathA{\adjustnormalsize\setbox\sizebox=\vbox\bgroup %
+ \let\ifinner=\iffalse \let\)\liih@math }%
+\newcommand\lthtmlboxmathZ{\@next\next\@currlist{}{\def\next{\voidb@x}}%
+ \expandafter\box\next\egroup}%
+\newcommand\lthtmlmathtype[1]{\gdef\lthtmlmathenv{#1}}%
+\newcommand\lthtmllogmath{\dimen0\ht\sizebox \advance\dimen0\dp\sizebox
+  \ifdim\dimen0>.95\vsize
+   \lthtmltypeout{%
+*** image for \lthtmlmathenv\space is too tall at \the\dimen0, reducing to .95 vsize ***}%
+   \ht\sizebox.95\vsize \dp\sizebox\z@ \fi
+  \lthtmltypeout{l2hSize %
+:\lthtmlmathenv:\the\ht\sizebox::\the\dp\sizebox::\the\wd\sizebox.\preveqno}}%
+\newcommand\lthtmlfigureA[1]{\let\@savefreelist\@freelist
+       \lthtmlmathtype{#1}\lthtmlvboxmathA}%
+\newcommand\lthtmlpictureA{\bgroup\catcode`\_=8 \lthtmlpictureB}%
+\newcommand\lthtmlpictureB[1]{\lthtmlmathtype{#1}\egroup
+       \let\@savefreelist\@freelist \lthtmlhboxmathB}%
+\newcommand\lthtmlpictureZ[1]{\hfill\lthtmlfigureZ}%
+\newcommand\lthtmlfigureZ{\lthtmlboxmathZ\lthtmllogmath\copy\sizebox
+       \global\let\@freelist\@savefreelist}%
+\newcommand\lthtmldisplayA{\bgroup\catcode`\_=8 \lthtmldisplayAi}%
+\newcommand\lthtmldisplayAi[1]{\lthtmlmathtype{#1}\egroup\lthtmlvboxmathA}%
+\newcommand\lthtmldisplayB[1]{\edef\preveqno{(\theequation)}%
+  \lthtmldisplayA{#1}\let\@eqnnum\relax}%
+\newcommand\lthtmldisplayZ{\lthtmlboxmathZ\lthtmllogmath\lthtmlsetmath}%
+\newcommand\lthtmlinlinemathA{\bgroup\catcode`\_=8 \lthtmlinlinemathB}
+\newcommand\lthtmlinlinemathB[1]{\lthtmlmathtype{#1}\egroup\lthtmlhboxmathA
+  \vrule height1.5ex width0pt }%
+\newcommand\lthtmlinlineA{\bgroup\catcode`\_=8 \lthtmlinlineB}%
+\newcommand\lthtmlinlineB[1]{\lthtmlmathtype{#1}\egroup\lthtmlhboxmathA}%
+\newcommand\lthtmlinlineZ{\egroup\expandafter\ifdim\dp\sizebox>0pt %
+  \expandafter\centerinlinemath\fi\lthtmllogmath\lthtmlsetinline}
+\newcommand\lthtmlinlinemathZ{\egroup\expandafter\ifdim\dp\sizebox>0pt %
+  \expandafter\centerinlinemath\fi\lthtmllogmath\lthtmlsetmath}
+\newcommand\lthtmlindisplaymathZ{\egroup %
+  \centerinlinemath\lthtmllogmath\lthtmlsetmath}
+\def\lthtmlsetinline{\hbox{\vrule width.1em \vtop{\vbox{%
+  \kern.1em\copy\sizebox}\ifdim\dp\sizebox>0pt\kern.1em\else\kern.3pt\fi
+  \ifdim\hsize>\wd\sizebox \hrule depth1pt\fi}}}
+\def\lthtmlsetmath{\hbox{\vrule width.1em\kern-.05em\vtop{\vbox{%
+  \kern.1em\kern0.8 pt\hbox{\hglue.17em\copy\sizebox\hglue0.8 pt}}\kern.3pt%
+  \ifdim\dp\sizebox>0pt\kern.1em\fi \kern0.8 pt%
+  \ifdim\hsize>\wd\sizebox \hrule depth1pt\fi}}}
+\def\centerinlinemath{%
+  \dimen1=\ifdim\ht\sizebox<\dp\sizebox \dp\sizebox\else\ht\sizebox\fi
+  \advance\dimen1by.5pt \vrule width0pt height\dimen1 depth\dimen1 
+ \dp\sizebox=\dimen1\ht\sizebox=\dimen1\relax}
+
+\def\lthtmlcheckvsize{\ifdim\ht\sizebox<\vsize 
+  \ifdim\wd\sizebox<\hsize\expandafter\hfill\fi \expandafter\vfill
+  \else\expandafter\vss\fi}%
+\providecommand{\selectlanguage}[1]{}%
+\makeatletter \tracingstats = 1 
+
+
+\begin{document}
+\pagestyle{empty}\thispagestyle{empty}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength hsize=\the\hsize}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength vsize=\the\vsize}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength hoffset=\the\hoffset}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength voffset=\the\voffset}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength topmargin=\the\topmargin}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength topskip=\the\topskip}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength headheight=\the\headheight}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength headsep=\the\headsep}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength parskip=\the\parskip}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength oddsidemargin=\the\oddsidemargin}\lthtmltypeout{}%
+\makeatletter
+\if@twoside\lthtmltypeout{latex2htmlLength evensidemargin=\the\evensidemargin}%
+\else\lthtmltypeout{latex2htmlLength evensidemargin=\the\oddsidemargin}\fi%
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+\setcounter{page}{1}
+\onecolumn
+
+% !!! IMAGES START HERE !!!
+
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+\lthtmlinlinemathZ
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+
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+\lthtmlinlinemathZ
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+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline490}%
+$\Delta \sim $%
+\lthtmlinlinemathZ
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+
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+$E_t$%
+\lthtmlinlinemathZ
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+\lthtmlinlinemathZ
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+
+\stepcounter{section}
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+$T$%
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+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath26}%
+\begin{displaymath}
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+
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+
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+\lthtmlinlinemathZ
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+
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+
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+$CS=\frac{N_S}{N_0}$%
+\lthtmlinlinemathZ
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+
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+
+\stepcounter{section}
+\stepcounter{subsection}
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+\includegraphics[width=\textwidth]{GUI_Advanced.eps}%
+\lthtmlpictureZ
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+
+{\newpage\clearpage
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+\includegraphics[width=\textwidth]{GUI_ThresholdScan.eps}%
+\lthtmlpictureZ
+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{section}
+\stepcounter{subsection}
+{\newpage\clearpage
+\lthtmlpictureA{tex2html_wrap605}%
+\includegraphics[width=\textwidth]{addEnergy.eps}%
+\lthtmlpictureZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlpictureA{tex2html_wrap609}%
+\includegraphics[width=\textwidth]{calibrateModule.eps}%
+\lthtmlpictureZ
+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{section}
+
+\end{document}