added test

Added a section on the ideas behind the library and also explaining the
branching strategy.

---------

Co-authored-by: Dhanya Thattil <dhanya.thattil@psi.ch>

.clang-format

@@ -2,6 +2,6 @@ BasedOnStyle: LLVM
 IndentWidth: 4
 
 UseTab: Never
-ColumnLimit: 120
+ColumnLimit: 80
 AlignConsecutiveAssignments: false 
 AlignConsecutiveMacros: true

.clang-tidy

@@ -1,50 +1,35 @@
----
-Checks: '*,
--abseil-*
--readability-magic-numbers,
--misc-include-cleaner,
--cppcoreguidelines-avoid-magic-numbers,
--cppcoreguidelines-owning-memory,
--bugprone-easily-swappable-parameters,
--cppcoreguidelines-non-private-member-variables-in-classes,
--cppcoreguidelines-special-member-functions,
--hicpp-special-member-functions,
--cert-err33-c,
--modernize-pass-by-value,
--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: '*.hpp'
-ImplementationFileExtensions: [cpp]
-AnalyzeTemporaryDtors: false
-WarningsAsErrors: '*,
--bugprone-implicit-widening-of-multiplication-result'
+---
+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: \.hpp
 FormatStyle:     none
 CheckOptions:
   - { key: readability-identifier-naming.NamespaceCase,       value: lower_case }

.clang-uml

@@ -1,103 +0,0 @@
-compilation_database_dir: ./build
-output_directory: docs/diagrams
-
-diagrams:
-  aare_class:
-    type: class
-    using_namespace: aare
-    include:
-      namespaces:
-        - aare
-    exclude:
-      element_types:
-        - enum
-      access:
-        - private
-        - protected
-        - public
-    glob:
-      - core/src/*.cpp
-      - file_io/src/*.cpp
-      - network_io/src/*.cpp
-      - utils/src/*.cpp
-
-  aare_class_simplified:
-    type: class
-    using_namespace: aare
-    include:
-      context:
-        - match:
-            radius: 1
-            pattern: aare::FileInterface
-        - match:
-            radius: 2
-            pattern: aare::ZmqSocket
-        - match:
-            radius: 2
-            pattern: aare::Frame
-      namespaces:
-        - aare
-    exclude:
-      elements:
-        - aare::xy
-      element_types:
-        - enum
-      access:
-        - private
-        - protected
-        - public
-    glob:
-      - core/src/*.cpp
-      - file_io/src/*.cpp
-      - network_io/src/*.cpp
-      - utils/src/*.cpp
-
-  # aare_package:
-  #   type: package
-  #   package_type: directory
-
-  #   include:
-  #     paths:
-  #       - core
-  #       - file_io
-  #       - network_io
-  #       - utils
-  #       - tests
-
-  file_io_class:
-    type: class
-    # generate_packages: true
-    # package_type: directory
-    include:
-      context:
-        - aare::FileInterface
-        - aare::File
-      namespaces:
-        - aare
-      # relationships:
-      #   - inheritance
-
-    glob:
-      - file_io/src/*.cpp
-
-  network_io_class:
-    type: class
-    include:
-      paths:
-        - network_io/include/aare/network_io/*.hpp
-        - core/include/aare/core/Frame.hpp
-      namespaces:
-        - aare
-    glob:
-      - network_io/src/*.cpp
-
-  core_class:
-    type: class
-    include:
-      paths:
-        - core/include/aare/core/*.hpp
-      namespaces:
-        - aare
-    glob:
-      - core/src/*.cpp
-

.env

@@ -1 +0,0 @@
-export AARE_ROOT_DIR="/home/bb/github/aare/"

.gitattributes

@@ -1 +0,0 @@
-*.ipynb -linguist-detectable

.gitea/workflows/cmake_build.yml

@@ -0,0 +1,58 @@
+name: Build the package using cmake then documentation
+
+on:
+  workflow_dispatch:
+
+    
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [ubuntu-latest, ] 
+        python-version: ["3.12", ] 
+
+    runs-on: ${{ matrix.platform }}
+
+
+    defaults:
+      run:
+        shell: "bash -l {0}"
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup dev env
+        run: |
+            sudo apt-get update
+            sudo apt-get -y install cmake gcc g++
+
+      - name: Get conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+          environment-file: etc/dev-env.yml
+          miniforge-version: latest
+          channels: conda-forge
+          conda-remove-defaults: "true"
+
+      - name: Build library 
+        run: |
+            mkdir build 
+            cd build 
+            cmake .. -DAARE_SYSTEM_LIBRARIES=ON -DAARE_DOCS=ON 
+            make -j 2 
+            make docs
+
+
+
+
+
+
+

.gitea/workflows/rh8-native.yml

@@ -0,0 +1,36 @@
+name: Build on RHEL8
+
+on:
+  push:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: "ubuntu-latest"
+    container:
+      image: gitea.psi.ch/images/rhel8-developer-gitea-actions
+    steps:
+      # workaround until actions/checkout@v4 is available for RH8
+      # - uses: actions/checkout@v4
+      - name: Clone repository
+        run: |
+          echo Cloning ${{ github.ref_name }}
+          git clone https://${{secrets.GITHUB_TOKEN}}@gitea.psi.ch/${{ github.repository }}.git --branch=${{ github.ref_name }} .
+
+
+      - name: Install dependencies
+        run: |
+          dnf install -y cmake python3.12 python3.12-devel python3.12-pip
+
+      - name: Build library 
+        run: |
+            mkdir build && cd build
+            cmake .. -DAARE_PYTHON_BINDINGS=ON -DAARE_TESTS=ON -DPython_FIND_VIRTUALENV=FIRST
+            make -j 2 
+
+      - name: C++ unit tests
+        working-directory: ${{gitea.workspace}}/build
+        run: ctest

.gitea/workflows/rh9-native.yml

@@ -0,0 +1,31 @@
+name: Build on RHEL9
+
+on:
+  push:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: "ubuntu-latest"
+    container:
+      image: gitea.psi.ch/images/rhel9-developer-gitea-actions
+    steps:
+      - uses: actions/checkout@v4
+
+
+      - name: Install dependencies
+        run: |
+          dnf install -y cmake python3.12 python3.12-devel python3.12-pip
+
+      - name: Build library 
+        run: |
+            mkdir build && cd build
+            cmake .. -DAARE_PYTHON_BINDINGS=ON -DAARE_TESTS=ON
+            make -j 2 
+
+      - name: C++ unit tests
+        working-directory: ${{gitea.workspace}}/build
+        run: ctest

.github/workflows/build_and_deploy_conda.yml

@@ -0,0 +1,42 @@
+name: Build pkgs and deploy if on main
+
+on:
+  release:
+      types:
+        - published
+
+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
+        with:
+          python-version: ${{ matrix.python-version }}
+          environment-file: etc/dev-env.yml
+          miniforge-version: latest
+          channels: conda-forge
+          conda-remove-defaults: "true"
+
+      - name: Enable upload
+        run: conda config --set anaconda_upload yes
+
+      - name: Build
+        env:
+          CONDA_TOKEN: ${{ secrets.CONDA_TOKEN }}
+        run: conda build conda-recipe --user slsdetectorgroup --token ${CONDA_TOKEN}
+

.github/workflows/build_conda.yml

@@ -0,0 +1,41 @@
+name: Build pkgs and deploy if on main
+
+on:
+  push:
+    branches:
+     - developer
+
+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
+        with:
+          python-version: ${{ matrix.python-version }}
+          environment-file: etc/dev-env.yml
+          miniforge-version: latest
+          channels: conda-forge
+          conda-remove-defaults: "true"
+
+  
+      - name: Disable upload
+        run: conda config --set anaconda_upload no
+
+      - name: Build
+        run: conda build conda-recipe 
+

.github/workflows/build_docs.yml

@@ -0,0 +1,69 @@
+name: Build the package using cmake then documentation
+
+on:
+  workflow_dispatch:
+  pull_request:
+  release:
+    types:
+      - published
+    
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [ubuntu-latest, ] 
+        python-version: ["3.12",]
+
+    runs-on: ${{ matrix.platform }}
+
+    defaults:
+      run:
+        shell: "bash -l {0}"
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Get conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+          environment-file: etc/dev-env.yml
+          miniforge-version: latest
+          channels: conda-forge
+          conda-remove-defaults: "true"
+
+      - name: Build library 
+        run: |
+            mkdir build 
+            cd build 
+            cmake .. -DAARE_SYSTEM_LIBRARIES=ON -DAARE_DOCS=ON 
+            make -j 2 
+            make docs
+
+      - name: Upload static files as artifact
+        id: deployment
+        uses: actions/upload-pages-artifact@v3 
+        with:
+         path: build/docs/html/
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    if: (github.event_name == 'release' && github.event.action == 'published') || (github.event_name == 'workflow_dispatch' )
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
+
+
+
+

.github/workflows/build_wheel.yml

@@ -0,0 +1,64 @@
+name: Build wheel
+
+on:
+    workflow_dispatch:
+    pull_request:
+    push:
+      branches:
+        - main
+    release:
+      types:
+        - published
+  
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest,]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build wheels
+        run: pipx run cibuildwheel==2.23.0
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+    
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Build sdist
+      run: pipx run build --sdist
+
+    - uses: actions/upload-artifact@v4
+      with:
+        name: cibw-sdist
+        path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+        id-token: write
+    if: github.event_name == 'release' && github.event.action == 'published'
+    # or, alternatively, upload to PyPI on every tag starting with 'v' (remove on: release above to use this)
+    # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    steps:
+        - uses: actions/download-artifact@v4
+          with:
+            # unpacks all CIBW artifacts into dist/
+            pattern: cibw-*
+            path: dist
+            merge-multiple: true
+
+        - uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/common-workflow.yml

@@ -1,98 +0,0 @@
-name: Build and run tests
-on: 
-  workflow_call:
-    inputs:
-      use-system-libraries: # the variable you can use in place of a matrix
-        required: true
-        type: string
-        default: OFF
-      build-type:
-        required: true
-        type: string
-        default: Debug
-      use-python-bindings:
-        required: true
-        type: string
-        default: OFF
-      os:
-        required: true
-        type: string
-        default: ubuntu-latest
-
-jobs:
-  build-and-test:
-    name: "Build and test[os: ${{ inputs.os }}, build-type: ${{ inputs.build-type }}, use-system-libraries: ${{ inputs.use-system-libraries }}, use-python-bindings: ${{ inputs.use-python-bindings }}]"
-    runs-on: ${{ inputs.os }}
-    steps:
-      - name: Dump GitHub context
-        env:
-          GITHUB_CONTEXT: ${{ toJson(github) }}
-          JOB_CONTEXT: ${{ toJson(job) }}
-          STEPS_CONTEXT: ${{ toJson(steps) }}
-          RUNNER_CONTEXT: ${{ toJson(runner) }}
-        run: |
-          echo "$GITHUB_CONTEXT"
-          echo "$JOB_CONTEXT"
-          echo "$STEPS_CONTEXT"
-          echo "$RUNNER_CONTEXT"
-          echo "The job_id is: $GITHUB_JOB"   # reference the default environment variables
-          echo "The id of this action is: $GITHUB_ACTION"   # reference the default environment variables
-          echo "The run id is: $GITHUB_RUN_ID"
-          echo "The GitHub Actor's username is: $GITHUB_ACTOR"
-          echo "GitHub SHA: $GITHUB_SHA"
-      
-      - name: print inputs
-        run: |
-          echo "use-system-libraries: ${{inputs.use-system-libraries}}"
-          echo "build-type: ${{inputs.build-type}}"
-          echo "use-python-bindings: ${{inputs.use-python-bindings}}"
-
-      - uses: actions/checkout@v4
-      - uses: mamba-org/setup-micromamba@v1
-        if: ${{ contains(inputs.use-system-libraries, 'ON')}}
-        with:
-          micromamba-version: '1.5.6-0' # any version from https://github.com/mamba-org/micromamba-releases
-          environment-file: aare-environment.yml
-          init-shell: bash
-          cache-environment: true
-          post-cleanup: 'all'
-        
-      - name: build
-        shell: bash -el {0}
-        run: |
-          mkdir build
-          cd build
-          cmake .. -DCMAKE_BUILD_TYPE=${{inputs.build-type}} -DAARE_PYTHON_BINDINGS=${{inputs.use-python-bindings}} -DAARE_SYSTEM_LIBRARIES=${{inputs.use-system-libraries}}
-          cmake --build . -j
-      - name: run tests
-        run: |
-          cd build/
-          ./run_tests
-        if: ${{ inputs.os != 'windows-latest' }}
-      - name: run tests
-        run: |
-          cd build/
-          dir
-          cd Debug/
-          dir
-          start run_tests.exe
-          # start /B /WAIT "run_tests.exe"
-        if: ${{ inputs.os == 'windows-latest' }}
-      - name: run examples
-        if: ${{ inputs.os != 'windows-latest' }}
-        # find all examples in build/examples and run them
-        run: |
-          pwd
-          export AARE_ROOT_DIR="$PWD"
-          ls build/examples/*_example
-          # examples to run
-          cd build/examples
-          examples=(raw_example json_example logger_example multiport_example mythen_example)
-          examples+=(numpy_read_example numpy_write_example)
-          for example in "${examples[@]}"; do
-            echo "Running example: $example"
-            ./$example
-          done
-
-
-

.github/workflows/config.yml

@@ -1,33 +0,0 @@
-# config file to run multiple jobs in parallel with matrix strategy
-name: Config Workflow
-
-on:
-  push:
-
-jobs:
-  build-and-test:
-    strategy:
-      # super important if you want to see all results, even if one fails
-      # fail-fast is true by default
-      fail-fast: false
-      matrix:
-        os: ["macos-latest", "ubuntu-latest", "windows-latest"]
-        build-type: ["Release", "Debug"]
-        use-system-libraries: ["ON", "OFF"]
-        use-python-bindings: ["OFF", "ON"]
-        exclude:
-          # excludes combinations that are not supported
-          - os: "windows-latest"
-            build-type: "Release" # TODO: fix this
-          - os: "windows-latest"
-            build-type: "Debug"
-            use-system-libraries: "ON" # different _ITERATOR_DEBUG_LEVEL for system libraries
-    
-    uses: ./.github/workflows/common-workflow.yml # calls the one above 
-    with:
-      use-system-libraries: ${{ matrix.use-system-libraries }}
-      build-type: ${{ matrix.build-type }}
-      use-python-bindings: ${{ matrix.use-python-bindings }}
-      os: ${{ matrix.os }}
-    secrets: inherit
-

.gitignore

@@ -1,6 +1,4 @@
-.vscode
-.env
-.env.dev
+install/
 .cproject
 .project
 bin/
@@ -11,10 +9,17 @@ bin/
 *.toc
 *.o
 *.so
-build/**
+.*
+build/
 RELEASE.txt
 Testing/
 
+ctbDict.cpp
+ctbDict.h
+
+wheelhouse/
+dist/
+
 *.pyc
 */__pycache__/*
 

.ipynb_checkpoints/Untitled-checkpoint.ipynb

@@ -1,6 +0,0 @@
-{
- "cells": [],
- "metadata": {},
- "nbformat": 4,
- "nbformat_minor": 5
-}

CMakeLists.txt

@@ -1,17 +1,32 @@
-cmake_minimum_required(VERSION 3.12)
-
-set(CMAKE_CXX_STANDARD 17) #TODO! Global or per target?
-set(CMAKE_CXX_STANDARD_REQUIRED ON)
-set(CMAKE_CXX_EXTENSIONS OFF)
+cmake_minimum_required(VERSION 3.15)
 
 project(aare 
-    VERSION 0.1
     DESCRIPTION "Data processing library for PSI detectors"
     HOMEPAGE_URL "https://github.com/slsdetectorgroup/aare"
     LANGUAGES C CXX 
 )
 
-cmake_policy(SET CMP0135 NEW)
+# 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})
+
+set(CMAKE_CXX_STANDARD 17) 
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+execute_process(
+        COMMAND git log -1 --format=%h
+        WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR}
+        OUTPUT_VARIABLE GIT_HASH
+        OUTPUT_STRIP_TRAILING_WHITESPACE
+        )
+message(STATUS "Building from git hash: ${GIT_HASH}")
+
+if (${CMAKE_VERSION} VERSION_GREATER "3.24")
+    cmake_policy(SET CMP0135 NEW) #Fetch content download timestamp
+endif()
 cmake_policy(SET CMP0079 NEW)
 
 include(GNUInstallDirs)
@@ -19,23 +34,38 @@ include(FetchContent)
 
 #Set default build type if none was specified
 include(cmake/helpers.cmake)
+
+
 default_build_type("Release")
+set_std_fs_lib()
+message(STATUS "Extra linking to fs lib:${STD_FS_LIB}")
 
-option(AARE_USE_WARNINGS "Enable warnings" ON)
-option(AARE_PYTHON_BINDINGS "Build python bindings" ON)
-option(AARE_TESTS "Build tests" ON)
-option(AARE_EXAMPLES "Build examples" ON)
+set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
+
+
+# General options
+option(AARE_PYTHON_BINDINGS "Build python bindings" OFF)
+option(AARE_TESTS "Build tests" OFF)
+option(AARE_BENCHMARKS "Build benchmarks" OFF)
+option(AARE_EXAMPLES "Build examples" OFF)
 option(AARE_IN_GITHUB_ACTIONS "Running in Github Actions" OFF)
+option(AARE_DOCS "Build documentation" OFF)
+option(AARE_VERBOSE "Verbose output" OFF)
+option(AARE_CUSTOM_ASSERT "Use custom assert" OFF)
+option(AARE_INSTALL_PYTHONEXT "Install the python extension in the install tree under CMAKE_INSTALL_PREFIX/aare/" OFF)
+option(AARE_HDF5 "Hdf5 File Format" OFF)
+option(AARE_ASAN "Enable AddressSanitizer" OFF)
 
+# Configure which of the dependencies to use FetchContent for
 option(AARE_FETCH_FMT "Use FetchContent to download fmt" ON)
 option(AARE_FETCH_PYBIND11 "Use FetchContent to download pybind11" ON)
 option(AARE_FETCH_CATCH "Use FetchContent to download catch2" ON)
 option(AARE_FETCH_JSON "Use FetchContent to download nlohmann::json" ON)
 option(AARE_FETCH_ZMQ "Use FetchContent to download libzmq" ON)
-option(ENABLE_DRAFTS "Enable zmq drafts (depends on gnutls or nss)" OFF)
+option(AARE_FETCH_LMFIT "Use FetchContent to download lmfit" ON)
 
 
-#Convenience option to use system libraries
+#Convenience option to use system libraries only (no FetchContent)
 option(AARE_SYSTEM_LIBRARIES "Use system libraries" OFF)
 if(AARE_SYSTEM_LIBRARIES)
     message(STATUS "Build using system libraries")
@@ -44,19 +74,100 @@ if(AARE_SYSTEM_LIBRARIES)
     set(AARE_FETCH_CATCH OFF CACHE BOOL "Disabled FetchContent for catch2" FORCE)
     set(AARE_FETCH_JSON OFF CACHE BOOL "Disabled FetchContent for nlohmann::json" FORCE)
     set(AARE_FETCH_ZMQ OFF CACHE BOOL "Disabled FetchContent for libzmq" FORCE)
-
+    # Still fetch lmfit when setting AARE_SYSTEM_LIBRARIES since this is not available
+    # on conda-forge
 endif()
 
+if(AARE_VERBOSE)
+    add_compile_definitions(AARE_VERBOSE)
+    add_compile_definitions(AARE_LOG_LEVEL=aare::logDEBUG5)
+else()
+    add_compile_definitions(AARE_LOG_LEVEL=aare::logINFOBLUE)
+endif()
+
+if(AARE_CUSTOM_ASSERT)
+    add_compile_definitions(AARE_CUSTOM_ASSERT)
+endif()
+
+if(AARE_BENCHMARKS)
+    add_subdirectory(benchmarks)
+endif()
+
+
 
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
-if(AARE_FETCH_ZMQ)
+if(AARE_FETCH_LMFIT)
+    #TODO! Should we fetch lmfit from the web or inlcude a tar.gz in the repo?
+    set(LMFIT_PATCH_COMMAND git apply ${CMAKE_CURRENT_SOURCE_DIR}/patches/lmfit.patch)
+
+    # For cmake < 3.28 we can't supply EXCLUDE_FROM_ALL to FetchContent_Declare
+    # so we need this workaround
+    if (${CMAKE_VERSION} VERSION_LESS "3.28")
+        FetchContent_Declare(
+            lmfit
+            GIT_REPOSITORY https://jugit.fz-juelich.de/mlz/lmfit.git
+            GIT_TAG        main
+            PATCH_COMMAND ${LMFIT_PATCH_COMMAND}
+            UPDATE_DISCONNECTED 1
+        )
+    else()
+        FetchContent_Declare(
+            lmfit
+            GIT_REPOSITORY https://jugit.fz-juelich.de/mlz/lmfit.git
+            GIT_TAG        main
+            PATCH_COMMAND ${LMFIT_PATCH_COMMAND}
+            UPDATE_DISCONNECTED 1
+            EXCLUDE_FROM_ALL 1
+        )
+    endif()
     
+
+    #Disable what we don't need from lmfit
+    set(BUILD_TESTING OFF CACHE BOOL "")
+    set(LMFIT_CPPTEST OFF CACHE BOOL "")
+    set(LIB_MAN OFF CACHE BOOL "")
+    set(LMFIT_CPPTEST OFF CACHE BOOL "")
+    set(BUILD_SHARED_LIBS OFF CACHE BOOL "")
+
+    if (${CMAKE_VERSION} VERSION_LESS "3.28")
+        if(NOT lmfit_POPULATED)
+            FetchContent_Populate(lmfit)
+            add_subdirectory(${lmfit_SOURCE_DIR} ${lmfit_BINARY_DIR} EXCLUDE_FROM_ALL)
+        endif()
+    else()
+        FetchContent_MakeAvailable(lmfit)
+    endif()
+    
+    set_property(TARGET lmfit PROPERTY POSITION_INDEPENDENT_CODE ON)
+else()
+    find_package(lmfit REQUIRED)
+endif()
+
+
+if(AARE_FETCH_ZMQ)
+    # Fetchcontent_Declare is deprecated need to find a way to update this
+    # for now setting the policy to old is enough
+    if (${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.30")
+        cmake_policy(SET CMP0169 OLD)
+    endif()
+    set(ZMQ_PATCH_COMMAND git apply ${CMAKE_CURRENT_SOURCE_DIR}/patches/libzmq_cmake_version.patch)
     FetchContent_Declare(
         libzmq
         GIT_REPOSITORY https://github.com/zeromq/libzmq.git
         GIT_TAG        v4.3.4
+        PATCH_COMMAND ${ZMQ_PATCH_COMMAND}
+        UPDATE_DISCONNECTED 1
     )
+    # Disable unwanted options from libzmq
+    set(BUILD_TESTS OFF CACHE BOOL "Switch off libzmq test build")
+    set(BUILD_SHARED OFF CACHE BOOL "Switch off libzmq shared libs")
+    set(WITH_PERF_TOOL OFF CACHE BOOL "")
+    set(ENABLE_CPACK OFF CACHE BOOL "")
+    set(ENABLE_CLANG OFF CACHE BOOL "")
+    set(ENABLE_CURVE OFF CACHE BOOL "")
+    set(ENABLE_DRAFTS OFF CACHE BOOL "")
+
     # TODO! Verify that this is what we want to do in aare
     # Using GetProperties and Populate to be able to exclude zmq
     # from install (not possible with FetchContent_MakeAvailable(libzmq))
@@ -65,7 +176,6 @@ if(AARE_FETCH_ZMQ)
         FetchContent_Populate(libzmq)
         add_subdirectory(${libzmq_SOURCE_DIR} ${libzmq_BINARY_DIR} EXCLUDE_FROM_ALL)
     endif()
-
 else()
     find_package(ZeroMQ 4 REQUIRED)
 endif()
@@ -80,16 +190,71 @@ if (AARE_FETCH_FMT)
             GIT_PROGRESS    TRUE
             USES_TERMINAL_DOWNLOAD TRUE
     )
+    set(FMT_INSTALL ON CACHE BOOL "")
+    # set(FMT_CMAKE_DIR "")
     FetchContent_MakeAvailable(fmt)
     set_property(TARGET fmt PROPERTY POSITION_INDEPENDENT_CODE ON)
+    install(TARGETS fmt 
+        EXPORT ${project}-targets
+        LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+        ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+        RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+        INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}   
+    )  
 else()
       find_package(fmt 6 REQUIRED)
 endif()
 
 
+if (AARE_FETCH_JSON)
+    FetchContent_Declare(
+        json 
+        URL https://github.com/nlohmann/json/releases/download/v3.11.3/json.tar.xz
+    )
+    set(JSON_Install ON CACHE BOOL "")
+    FetchContent_MakeAvailable(json)
+    set(NLOHMANN_JSON_TARGET_NAME nlohmann_json)
+    
+    install(
+        TARGETS nlohmann_json
+        EXPORT "${TARGETS_EXPORT_NAME}"
+    )
+    message(STATUS "target: ${NLOHMANN_JSON_TARGET_NAME}")
+else()
+    find_package(nlohmann_json 3.11.3 REQUIRED)
+endif()
+
+include(GNUInstallDirs)
+
+# If conda build, always set lib dir to 'lib'
+if($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 "${PROJECT_NAME_LOWER}-targets")
+set(namespace "aare::")
+
+set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
+
+# Check if project is being used directly or via add_subdirectory
+set(AARE_MASTER_PROJECT OFF)
+if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
+    set(AARE_MASTER_PROJECT ON)
+endif()
+
 add_library(aare_compiler_flags INTERFACE)
 target_compile_features(aare_compiler_flags INTERFACE cxx_std_17)
 
+if(AARE_PYTHON_BINDINGS)
+    add_subdirectory(python)
+endif()
+
 #################
 # MSVC specific #
 #################
@@ -131,69 +296,45 @@ if(CMAKE_BUILD_TYPE STREQUAL "Release")
     target_compile_options(aare_compiler_flags INTERFACE -O3)
 else()
     message(STATUS "Debug build")
-    target_compile_options(
-        aare_compiler_flags 
-        INTERFACE 
-            -Og 
-            -ggdb3 
-            # -D_GLIBCXX_DEBUG # causes errors with boost
-            -D_GLIBCXX_DEBUG_PEDANTIC
+endif()
+
+# Common flags for GCC and Clang
+target_compile_options(
+    aare_compiler_flags 
+    INTERFACE 
+        -Wall 
+        -Wextra 
+        -pedantic 
+        -Wshadow 
+        -Wold-style-cast
+        -Wnon-virtual-dtor
+        -Woverloaded-virtual
+        -Wdouble-promotion
+        -Wformat=2
+        -Wredundant-decls
+        -Wvla
+        -Wdouble-promotion
+        -Werror=return-type #important can cause segfault in optimzed builds
     )
 
-    if (NOT AARE_PYTHON_BINDINGS)
-        target_compile_options(
-            aare_compiler_flags
-            INTERFACE
-                -fdiagnostics-parseable-fixits
-                # -fdiagnostics-generate-patch 
-                -fdiagnostics-show-template-tree 
-                -fsanitize=address,undefined,pointer-compare 
-                -fno-sanitize-recover 
-                # -D_FORTIFY_SOURCE=2  # not needed for debug builds
-                # -fstack-protector  # cause errors wih folly? (ProducerConsumerQueue.hpp)
-                -fno-omit-frame-pointer
-        )
-    
-        target_link_libraries(
-            aare_compiler_flags
-            INTERFACE
-                -fdiagnostics-parseable-fixits
-                # -fdiagnostics-generate-patch 
-                -fdiagnostics-show-template-tree 
-                -fsanitize=address,undefined,pointer-compare 
-                -fno-sanitize-recover 
-                # -D_FORTIFY_SOURCE=2 
-                -fno-omit-frame-pointer
-        )
-    endif()
-
-endif()
-
-if(AARE_USE_WARNINGS)
-        target_compile_options(
-            aare_compiler_flags 
-            INTERFACE 
-                -Wall 
-                -Wextra 
-                -pedantic 
-                -Wshadow 
-                -Wnon-virtual-dtor
-                -Woverloaded-virtual
-                -Wdouble-promotion
-                -Wformat=2
-                -Wredundant-decls
-                -Wvla
-                -Wdouble-promotion
-                -Werror=return-type #important can cause segfault in optimzed builds
-            )
-endif()
-
-
-
 endif() #GCC/Clang specific
 
 
-
+if(AARE_ASAN)
+    message(STATUS "AddressSanitizer enabled")
+    target_compile_options(
+        aare_compiler_flags 
+        INTERFACE 
+            -fsanitize=address,undefined,pointer-compare 
+            -fno-omit-frame-pointer
+    )
+    target_link_libraries(
+        aare_compiler_flags 
+        INTERFACE 
+            -fsanitize=address,undefined,pointer-compare 
+            -fno-omit-frame-pointer
+    )
+endif()
 
 
 
@@ -204,22 +345,201 @@ if(AARE_TESTS)
     add_subdirectory(tests)
 endif()
 
-add_subdirectory(src)
+###------------------------------------------------------------------------------MAIN LIBRARY
+###------------------------------------------------------------------------------------------
 
-
-#Overall target to link to when using the library
-add_library(aare INTERFACE) 
-target_link_libraries(aare INTERFACE core file_io utils network_io processing aare_compiler_flags)
-target_include_directories(aare INTERFACE 
-    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
-    $<INSTALL_INTERFACE:include>
+set(PUBLICHEADERS
+    include/aare/ArrayExpr.hpp
+    include/aare/CalculateEta.hpp
+    include/aare/Cluster.hpp
+    include/aare/ClusterFinder.hpp
+    include/aare/ClusterFile.hpp
+    include/aare/CtbRawFile.hpp
+    include/aare/ClusterVector.hpp
+    include/aare/decode.hpp
+    include/aare/type_traits.hpp
+    include/aare/scan_parameters.hpp
+    include/aare/to_string.hpp
+    include/aare/string_utils.hpp
+    include/aare/defs.hpp
+    include/aare/Dtype.hpp
+    include/aare/File.hpp
+    include/aare/Fit.hpp
+    include/aare/FileInterface.hpp
+    include/aare/FilePtr.hpp
+    include/aare/Frame.hpp
+    include/aare/GainMap.hpp
+    include/aare/geo_helpers.hpp
+    include/aare/JungfrauDataFile.hpp
+    include/aare/logger.hpp
+    include/aare/NDArray.hpp
+    include/aare/NDView.hpp
+    include/aare/NumpyFile.hpp
+    include/aare/NumpyHelpers.hpp
+    include/aare/Pedestal.hpp
+    include/aare/PixelMap.hpp
+    include/aare/RawFile.hpp
+    include/aare/RawMasterFile.hpp
+    include/aare/RawSubFile.hpp
+    include/aare/VarClusterFinder.hpp
+    include/aare/utils/task.hpp
 )
 
-add_subdirectory(examples)
+
+set(SourceFiles
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/CtbRawFile.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/to_string.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/string_utils.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/Dtype.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/decode.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/Frame.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/File.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/FilePtr.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/Fit.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/geo_helpers.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/JungfrauDataFile.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyFile.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyHelpers.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/Interpolator.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/PixelMap.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/RawFile.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/RawSubFile.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/RawMasterFile.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/utils/task.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/utils/ifstream_helpers.cpp
+)
+
+# HDF5
+if (AARE_HDF5)
+    find_package(HDF5 1.10 COMPONENTS CXX REQUIRED)
+	    add_definitions( 
+	        ${HDF5_DEFINITIONS}
+	    )
+	    list (APPEND PUBLICHEADERS 
+            include/aare/Hdf5File.hpp
+            include/aare/Hdf5MasterFile.hpp
+	    )
+	    list (APPEND SourceFiles 
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/Hdf5File.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/Hdf5MasterFile.cpp
+	    )
+endif (AARE_HDF5)
+
+add_library(aare_core STATIC ${SourceFiles})
+target_include_directories(aare_core PUBLIC 
+    "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>" 
+    "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>" 
+)
+
+set(THREADS_PREFER_PTHREAD_FLAG ON)
+find_package(Threads REQUIRED)
+
+target_link_libraries(
+    aare_core 
+    PUBLIC 
+    fmt::fmt 
+    nlohmann_json::nlohmann_json 
+    ${STD_FS_LIB} # from helpers.cmake
+    PRIVATE 
+    aare_compiler_flags 
+    Threads::Threads
+    $<BUILD_INTERFACE:lmfit>
+
+)
+
+if (AARE_HDF5 AND HDF5_FOUND)
+    add_definitions(-DHDF5_FOUND)
+    target_link_libraries(aare_core PUBLIC 
+        ${HDF5_LIBRARIES}
+    )
+    target_include_directories(aare_core PUBLIC
+        ${HDF5_INCLUDE_DIRS}
+    )
+endif()
+
+set_target_properties(aare_core PROPERTIES
+    ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}
+    PUBLIC_HEADER "${PUBLICHEADERS}"
+)
+
+if (AARE_PYTHON_BINDINGS)
+    set_property(TARGET aare_core PROPERTY POSITION_INDEPENDENT_CODE ON)
+endif()
+
+if(AARE_TESTS)
+    set(TestSources
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/algorithm.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/to_string.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/scan_parameters.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/decode.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/Dtype.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/Frame.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/geo_helpers.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/RawMasterFile.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/NDArray.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/NDView.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterFinder.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterVector.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/Cluster.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/CalculateEta.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterFile.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/ClusterFinderMT.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/Pedestal.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/JungfrauDataFile.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyFile.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/NumpyHelpers.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/RawFile.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/RawSubFile.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/utils/task.test.cpp
+
+        )
+    if(HDF5_FOUND)
+        list (APPEND TestSources 
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/Hdf5MasterFile.test.cpp
+            ${CMAKE_CURRENT_SOURCE_DIR}/src/Hdf5File.test.cpp
+        )
+    endif() 
+    target_sources(tests PRIVATE ${TestSources} )
+endif()
 
 
 
 
+###------------------------------------------------------------------------------------------
+###------------------------------------------------------------------------------------------
+
+
+if(AARE_MASTER_PROJECT)
+    install(TARGETS aare_core aare_compiler_flags 
+        EXPORT "${TARGETS_EXPORT_NAME}"
+        LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+        ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+        PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/aare
+    )
+endif()
+
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+set(CMAKE_INSTALL_RPATH $ORIGIN)
+set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+
+
+# #Overall target to link to when using the library
+# add_library(aare INTERFACE) 
+# target_link_libraries(aare INTERFACE aare_core aare_compiler_flags)
+# target_include_directories(aare INTERFACE 
+#     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+#     $<INSTALL_INTERFACE:include>
+# )
+
+# add_subdirectory(examples)
+
+if(AARE_DOCS)
+    add_subdirectory(docs)
+endif()
+
+
 # custom target to run check formatting with clang-format
 add_custom_target(
     check-format
@@ -247,9 +567,14 @@ endif()
 
 add_custom_target(
     clang-tidy
-    COMMAND find \( -path "./src/*" -a -not -path "./src/python/*" -a \( -name "*.cpp"   -not -name "*.test.cpp"\)  \)    -not -name "CircularFifo.hpp" -not -name "ProducerConsumerQueue.hpp" -not -name "VariableSizeClusterFinder.hpp" | xargs -I {} -n 1 -P 10 bash -c "${CLANG_TIDY_COMMAND} --config-file=.clang-tidy -p build {}"
+    COMMAND find \( -path "./src/*" -a -not -path "./src/python/*" -a \( -name "*.cpp"   -not -name "*.test.cpp" \)  \)    -not -name "CircularFifo.hpp" -not -name "ProducerConsumerQueue.hpp" -not -name "VariableSizeClusterFinder.hpp" | xargs -I {} -n 1 -P 10 bash -c "${CLANG_TIDY_COMMAND} --config-file=.clang-tidy -p build {}"
     WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
     COMMENT "linting with clang-tidy"
     VERBATIM
 )
 
+if(AARE_MASTER_PROJECT)
+    set(CMAKE_INSTALL_DIR "share/cmake/${PROJECT_NAME}")
+    set(PROJECT_LIBRARIES aare-core aare-compiler-flags )
+    include(cmake/package_config.cmake)
+endif()

COPYING

@@ -1,17 +0,0 @@
-The Aare 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 Aare 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
-free programs, and that you know you can do these things.
-
-  To protect your rights, we need to prevent others from denying you
-these rights or asking you to surrender the rights.  Therefore, you have
-certain responsibilities if you distribute copies of the software, or if
-you modify it: responsibilities to respect the freedom of others.
-
-  For example, if you distribute copies of such a program, whether
-gratis or for a fee, you must pass on to the recipients the same
-freedoms that you received.  You must make sure that they, too, receive
-or can get the source code.  And you must show them these terms so they
-know their rights.
-
-  Developers that use the GNU GPL protect your rights with two steps:
-(1) assert copyright on the software, and (2) offer you this License
-giving you legal permission to copy, distribute and/or modify it.
-
-  For the developers' and authors' protection, the GPL clearly explains
-that there is no warranty for this free software.  For both users' and
-authors' sake, the GPL requires that modified versions be marked as
-changed, so that their problems will not be attributed erroneously to
-authors of previous versions.
-
-  Some devices are designed to deny users access to install or run
-modified versions of the software inside them, although the manufacturer
-can do so.  This is fundamentally incompatible with the aim of
-protecting users' freedom to change the software.  The systematic
-pattern of such abuse occurs in the area of products for individuals to
-use, which is precisely where it is most unacceptable.  Therefore, we
-have designed this version of the GPL to prohibit the practice for those
-products.  If such problems arise substantially in other domains, we
-stand ready to extend this provision to those domains in future versions
-of the GPL, as needed to protect the freedom of users.
-
-  Finally, every program is threatened constantly by software patents.
-States should not allow patents to restrict development and use of
-software on general-purpose computers, but in those that do, we wish to
-avoid the special danger that patents applied to a free program could
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-  You should also get your employer (if you work as a programmer) or school,
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-For more information on this, and how to apply and follow the GNU GPL, see
-<https://www.gnu.org/licenses/>.
-
-  The GNU General Public License does not permit incorporating your program
-into proprietary programs.  If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library.  If this is what you want to do, use the GNU Lesser General
-Public License instead of this License.  But first, please read
-<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
-  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:
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-  For 'GNU Library General Public License (LGPL) version 3.0 or any later
-  version' use:
-    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
- of this license document, but changing it is not allowed.
-
-
-  This version of the GNU Lesser General Public License incorporates
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LICENSES/Third Party/Apache-2.0

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README.md

@@ -2,76 +2,70 @@
 Data analysis library for PSI hybrid detectors
 
 
+## Build and install
 
+Prerequisites
+- cmake >= 3.14
+- C++17 compiler (gcc >= 8)
+- python >= 3.10
 
-## Folder structure 
-
-| Folder   | subfolder     | Content                             |
-|----------|---------------|-------------------------------------|
-| include/ |  aare/        | top level header/s                  |
-| core/    |    include/   | public headers for core             |
-|          | src/          | source files and non public headers |
-
-## file_io class diagram
-![file_io class diagram](./extra/uml/out/file_io/ClassDiagram.png)
-
-
-
-## Test the zmq socket with a detector simulator
- 
-**1. Download and build the slsDetectorPackage**
+### Development install (for Python)
 
 ```bash
-git clone https://github.com/slsdetectorgroup/slsDetectorPackage.git --branch=8.0.1 #or the desired branch
-cd slsDetectorPackage
-mkdir build && cd build
-cmake .. -DSLS_USE_SIMULATOR=ON
-make -j8 #or your number of cores
+git clone git@github.com:slsdetectorgroup/aare.git --branch=v1 #or using http...
+mkdir build
+cd build
+
+#configure using cmake
+cmake ../aare
+
+#build (replace 4 with the number of threads you want to use)
+make -j4 
 ```
 
-**2. Launch the slsReceiver**
-```bash
-bin/slsReceiver
+Now you can use the Python module from your build directory
+
+```python
+import aare
+f = aare.File('Some/File/I/Want_to_open_master_0.json')
 ```
 
-**3. Launch the virtual server**
+To run form other folders either add the path to your conda environment using conda-build or add it to your PYTHONPATH
+
+
+### Install using conda/mamba
+
 ```bash
-bin/jungfrauDetectorServer_virtual
+#enable your env first!
+conda install aare=2024.10.29.dev0 -c slsdetectorgroup
 ```
 
-**4 Configure the detector simulator**
+### Install to a custom location and use in your project
+
+Working example in: https://github.com/slsdetectorgroup/aare-examples
 
 ```bash
-#sample config file is in etc/ in the aare repo
-sls_detector_put config etc/virtual_jf.config
+#build and install aare 
+git clone git@github.com:slsdetectorgroup/aare.git --branch=v1 #or using http...
+mkdir build
+cd build
 
-#Now you can take images using sls_detector_acquire
-sls_detector_acquire
+#configure using cmake
+cmake ../aare -DCMAKE_INSTALL_PREFIX=/where/to/put/aare
+
+#build (replace 4 with the number of threads you want to use)
+make -j4 
+
+#install
+make install
+
+
+#Now configure your project
+ cmake .. -DCMAKE_PREFIX_PATH=SOME_PATH
 ```
 
-**5. Run the zmq example**
+### Local build of conda pkgs
+
 ```bash
-examples/zmq_example
-
-#Will print the headers fof the frames received
-
-```
-
-
-## Test the zmq processing replaying data
-
-To be implemented
-
-## generate documentation
-```bash
-# for doxygen documentation
-doxygen .doxygen.config 
-
-# for automatically generated plant uml diagrams
-clang-uml
-
-
-
-
-
+conda build . --variants="{python: [3.11, 3.12, 3.13]}"
 ```

RELEASE.md

@@ -0,0 +1,22 @@
+# Release notes
+
+
+### head
+
+Features:
+
+- Cluster finder now works with 5x5, 7x7 and 9x9 clusters
+
+
+### 2025.05.22
+
+Features:
+
+- Added scurve fitting
+
+Bugfixes:
+
+- Fixed crash when opening raw files with large number of data files
+
+
+

VERSION

@@ -0,0 +1 @@
+2025.5.22

aare-environment.yml

@@ -1,10 +0,0 @@
-name: aare
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - fmt
-  - pybind11
-  - nlohmann_json # should be removed
-  - catch2
-  - zeromq

benchmarks/CMakeLists.txt

@@ -0,0 +1,27 @@
+
+include(FetchContent)
+
+
+FetchContent_Declare(
+    benchmark
+    GIT_REPOSITORY https://github.com/google/benchmark.git
+    GIT_TAG        v1.8.3 # Change to the latest version if needed
+)
+
+# Ensure Google Benchmark is built correctly
+set(BENCHMARK_ENABLE_TESTING OFF CACHE BOOL "" FORCE)
+
+FetchContent_MakeAvailable(benchmark)
+
+add_executable(benchmarks)
+
+target_sources(benchmarks PRIVATE ndarray_benchmark.cpp calculateeta_benchmark.cpp)
+
+# Link Google Benchmark and other necessary libraries
+target_link_libraries(benchmarks PRIVATE benchmark::benchmark aare_core aare_compiler_flags)
+
+# Set output properties
+set_target_properties(benchmarks PROPERTIES
+    RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}
+    OUTPUT_NAME run_benchmarks
+)

benchmarks/calculateeta_benchmark.cpp

@@ -0,0 +1,70 @@
+#include "aare/CalculateEta.hpp"
+#include "aare/ClusterFile.hpp"
+#include <benchmark/benchmark.h>
+
+using namespace aare;
+
+class ClusterFixture : public benchmark::Fixture {
+  public:
+    Cluster<int, 2, 2> cluster_2x2{};
+    Cluster<int, 3, 3> cluster_3x3{};
+
+  private:
+    using benchmark::Fixture::SetUp;
+
+    void SetUp([[maybe_unused]] const benchmark::State &state) override {
+        int temp_data[4] = {1, 2, 3, 1};
+        std::copy(std::begin(temp_data), std::end(temp_data),
+                  std::begin(cluster_2x2.data));
+
+        cluster_2x2.x = 0;
+        cluster_2x2.y = 0;
+
+        int temp_data2[9] = {1, 2, 3, 1, 3, 4, 5, 1, 20};
+        std::copy(std::begin(temp_data2), std::end(temp_data2),
+                  std::begin(cluster_3x3.data));
+
+        cluster_3x3.x = 0;
+        cluster_3x3.y = 0;
+    }
+
+    // void TearDown(::benchmark::State& state) {
+    // }
+};
+
+BENCHMARK_F(ClusterFixture, Calculate2x2Eta)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        Eta2 eta = calculate_eta2(cluster_2x2);
+        benchmark::DoNotOptimize(eta);
+    }
+}
+
+// almost takes double the time
+BENCHMARK_F(ClusterFixture, CalculateGeneralEtaFor2x2Cluster)
+(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        Eta2 eta = calculate_eta2<int, 2, 2>(cluster_2x2);
+        benchmark::DoNotOptimize(eta);
+    }
+}
+
+BENCHMARK_F(ClusterFixture, Calculate3x3Eta)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        Eta2 eta = calculate_eta2(cluster_3x3);
+        benchmark::DoNotOptimize(eta);
+    }
+}
+
+// almost takes double the time
+BENCHMARK_F(ClusterFixture, CalculateGeneralEtaFor3x3Cluster)
+(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        Eta2 eta = calculate_eta2<int, 3, 3>(cluster_3x3);
+        benchmark::DoNotOptimize(eta);
+    }
+}
+// BENCHMARK_MAIN();

benchmarks/ndarray_benchmark.cpp

@@ -0,0 +1,132 @@
+#include "aare/NDArray.hpp"
+#include <benchmark/benchmark.h>
+
+using aare::NDArray;
+
+constexpr ssize_t size = 1024;
+class TwoArrays : public benchmark::Fixture {
+  public:
+    NDArray<int, 2> a{{size, size}, 0};
+    NDArray<int, 2> b{{size, size}, 0};
+    void SetUp(::benchmark::State &state) {
+        for (uint32_t i = 0; i < size; i++) {
+            for (uint32_t j = 0; j < size; j++) {
+                a(i, j) = i * j + 1;
+                b(i, j) = i * j + 1;
+            }
+        }
+    }
+
+    // void TearDown(::benchmark::State& state) {
+    // }
+};
+
+BENCHMARK_F(TwoArrays, AddWithOperator)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res = a + b;
+        benchmark::DoNotOptimize(res);
+    }
+}
+BENCHMARK_F(TwoArrays, AddWithIndex)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res(a.shape());
+        for (uint32_t i = 0; i < a.size(); i++) {
+            res(i) = a(i) + b(i);
+        }
+        benchmark::DoNotOptimize(res);
+    }
+}
+
+BENCHMARK_F(TwoArrays, SubtractWithOperator)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res = a - b;
+        benchmark::DoNotOptimize(res);
+    }
+}
+BENCHMARK_F(TwoArrays, SubtractWithIndex)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res(a.shape());
+        for (uint32_t i = 0; i < a.size(); i++) {
+            res(i) = a(i) - b(i);
+        }
+        benchmark::DoNotOptimize(res);
+    }
+}
+
+BENCHMARK_F(TwoArrays, MultiplyWithOperator)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res = a * b;
+        benchmark::DoNotOptimize(res);
+    }
+}
+BENCHMARK_F(TwoArrays, MultiplyWithIndex)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res(a.shape());
+        for (uint32_t i = 0; i < a.size(); i++) {
+            res(i) = a(i) * b(i);
+        }
+        benchmark::DoNotOptimize(res);
+    }
+}
+
+BENCHMARK_F(TwoArrays, DivideWithOperator)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res = a / b;
+        benchmark::DoNotOptimize(res);
+    }
+}
+BENCHMARK_F(TwoArrays, DivideWithIndex)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res(a.shape());
+        for (uint32_t i = 0; i < a.size(); i++) {
+            res(i) = a(i) / b(i);
+        }
+        benchmark::DoNotOptimize(res);
+    }
+}
+
+BENCHMARK_F(TwoArrays, FourAddWithOperator)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res = a + b + a + b;
+        benchmark::DoNotOptimize(res);
+    }
+}
+BENCHMARK_F(TwoArrays, FourAddWithIndex)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res(a.shape());
+        for (uint32_t i = 0; i < a.size(); i++) {
+            res(i) = a(i) + b(i) + a(i) + b(i);
+        }
+        benchmark::DoNotOptimize(res);
+    }
+}
+
+BENCHMARK_F(TwoArrays, MultiplyAddDivideWithOperator)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res = a * a + b / a;
+        benchmark::DoNotOptimize(res);
+    }
+}
+BENCHMARK_F(TwoArrays, MultiplyAddDivideWithIndex)(benchmark::State &st) {
+    for (auto _ : st) {
+        // This code gets timed
+        NDArray<int, 2> res(a.shape());
+        for (uint32_t i = 0; i < a.size(); i++) {
+            res(i) = a(i) * a(i) + b(i) / a(i);
+        }
+        benchmark::DoNotOptimize(res);
+    }
+}
+
+BENCHMARK_MAIN();

cmake/.gitignore

@@ -1 +0,0 @@
-

cmake/FindSphinx.cmake

@@ -0,0 +1,11 @@
+#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/helpers.cmake

@@ -4,3 +4,43 @@ if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
   set(CMAKE_BUILD_TYPE ${val} CACHE STRING "Build type (default ${val})" FORCE)
 endif()
 endfunction()
+
+function(set_std_fs_lib)
+# from pybind11
+# Check if we need to add -lstdc++fs or -lc++fs or nothing
+if(DEFINED CMAKE_CXX_STANDARD AND CMAKE_CXX_STANDARD LESS 17)
+  set(STD_FS_NO_LIB_NEEDED TRUE)
+elseif(MSVC)
+  set(STD_FS_NO_LIB_NEEDED TRUE)
+else()
+  file(
+    WRITE ${CMAKE_CURRENT_BINARY_DIR}/main.cpp
+    "#include <filesystem>\nint main(int argc, char ** argv) {\n  std::filesystem::path p(argv[0]);\n  return p.string().length();\n}"
+  )
+  try_compile(
+    STD_FS_NO_LIB_NEEDED ${CMAKE_CURRENT_BINARY_DIR}
+    SOURCES ${CMAKE_CURRENT_BINARY_DIR}/main.cpp
+    COMPILE_DEFINITIONS -std=c++17)
+  try_compile(
+    STD_FS_NEEDS_STDCXXFS ${CMAKE_CURRENT_BINARY_DIR}
+    SOURCES ${CMAKE_CURRENT_BINARY_DIR}/main.cpp
+    COMPILE_DEFINITIONS -std=c++17
+    LINK_LIBRARIES stdc++fs)
+  try_compile(
+    STD_FS_NEEDS_CXXFS ${CMAKE_CURRENT_BINARY_DIR}
+    SOURCES ${CMAKE_CURRENT_BINARY_DIR}/main.cpp
+    COMPILE_DEFINITIONS -std=c++17
+    LINK_LIBRARIES c++fs)
+endif()
+
+if(${STD_FS_NEEDS_STDCXXFS})
+  set(STD_FS_LIB stdc++fs PARENT_SCOPE)
+elseif(${STD_FS_NEEDS_CXXFS})
+  set(STD_FS_LIB c++fs PARENT_SCOPE)
+elseif(${STD_FS_NO_LIB_NEEDED})
+  set(STD_FS_LIB "" PARENT_SCOPE)
+else()
+  message(WARNING "Unknown C++17 compiler - not passing -lstdc++fs")
+  set(STD_FS_LIB "")
+endif()
+endfunction()

cmake/package_config.cmake

@@ -0,0 +1,35 @@
+# This cmake code creates the configuration that is found and used by
+# find_package() of another cmake project
+
+# get lower and upper case project name for the configuration files
+
+# configure and install the configuration files
+include(CMakePackageConfigHelpers)
+
+configure_package_config_file(
+  "${CMAKE_SOURCE_DIR}/cmake/project-config.cmake.in"
+  "${PROJECT_BINARY_DIR}/${PROJECT_NAME_LOWER}-config.cmake"
+  INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME_LOWER}
+  PATH_VARS CMAKE_INSTALL_DIR)
+
+write_basic_package_version_file(
+  "${PROJECT_BINARY_DIR}/${PROJECT_NAME_LOWER}-config-version.cmake"
+  VERSION ${PROJECT_VERSION}
+  COMPATIBILITY SameMajorVersion
+)
+
+install(FILES
+  "${PROJECT_BINARY_DIR}/${PROJECT_NAME_LOWER}-config.cmake"
+  "${PROJECT_BINARY_DIR}/${PROJECT_NAME_LOWER}-config-version.cmake"
+  COMPONENT devel
+  DESTINATION ${CMAKE_INSTALL_DIR}
+)
+
+
+if (PROJECT_LIBRARIES OR PROJECT_STATIC_LIBRARIES)
+  install(
+    EXPORT "${TARGETS_EXPORT_NAME}"
+    FILE ${PROJECT_NAME_LOWER}-targets.cmake
+    DESTINATION ${CMAKE_INSTALL_DIR}
+    )
+endif ()

cmake/project-config.cmake.in

@@ -0,0 +1,28 @@
+# 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@")
+
+# List dependencies
+find_dependency(Threads)
+find_dependency(fmt)
+find_dependency(nlohmann_json)
+
+# 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@")

conda-recipe/conda_build_config.yaml

@@ -0,0 +1,5 @@
+python:
+    - 3.11
+    - 3.12
+    - 3.13
+

conda-recipe/meta.yaml

@@ -0,0 +1,50 @@
+source:
+  path: ../
+
+{% set version = load_file_regex(load_file = 'VERSION', regex_pattern = '(\d+(?:\.\d+)*(?:[\+\w\.]+))').group(1) %}
+package:
+  name: aare
+  version: {{version}}
+
+source:
+  path: ..
+
+build:
+  number: 0
+  script:
+    - unset CMAKE_GENERATOR && {{ PYTHON }} -m pip install . -vv 
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - cmake
+    - ninja
+
+  host:
+    - python
+    - pip
+    - numpy=2.1
+    - scikit-build-core
+    - pybind11 >=2.13.0
+    - matplotlib # needed in host to solve the environment for run
+
+  run:
+    - python
+    - {{ pin_compatible('numpy') }}
+    - matplotlib
+    
+
+
+test:
+  imports:
+    - aare
+  requires:
+    - pytest
+    - boost-histogram 
+  source_files:
+    - python/tests
+  commands:
+    - python -m pytest python/tests
+
+about:
+  summary: Data analysis library for hybrid pixel detectors from PSI 

data/eiger/eiger_500k_16bit_master_0.json

@@ -1,53 +0,0 @@
-{
-    "Version": 7.2,
-    "Timestamp": "Tue Mar 26 17:24:02 2024",
-    "Detector Type": "Eiger",
-    "Timing Mode": "auto",
-    "Geometry": {
-        "x": 2,
-        "y": 2
-    },
-    "Image Size in bytes": 262144,
-    "Pixels": {
-        "x": 512,
-        "y": 256
-    },
-    "Max Frames Per File": 10000,
-    "Frame Discard Policy": "nodiscard",
-    "Frame Padding": 1,
-    "Scan Parameters": "[disabled]",
-    "Total Frames": 3,
-    "Receiver Roi": {
-        "xmin": 4294967295,
-        "xmax": 4294967295,
-        "ymin": 4294967295,
-        "ymax": 4294967295
-    },
-    "Dynamic Range": 16,
-    "Ten Giga": 0,
-    "Exptime": "5s",
-    "Period": "1s",
-    "Threshold Energy": -1,
-    "Sub Exptime": "2.62144ms",
-    "Sub Period": "2.62144ms",
-    "Quad": 0,
-    "Number of rows": 256,
-    "Rate Corrections": "[0, 0]",
-    "Frames in File": 3,
-    "Frame Header Format": {
-        "Frame Number": "8 bytes",
-        "SubFrame Number/ExpLength": "4 bytes",
-        "Packet Number": "4 bytes",
-        "Bunch ID": "8 bytes",
-        "Timestamp": "8 bytes",
-        "Module Id": "2 bytes",
-        "Row": "2 bytes",
-        "Column": "2 bytes",
-        "Reserved": "2 bytes",
-        "Debug": "4 bytes",
-        "Round Robin Number": "2 bytes",
-        "Detector Type": "1 byte",
-        "Header Version": "1 byte",
-        "Packets Caught Mask": "64 bytes"
-    }
-}

data/eiger/eiger_500k_32bit_master_0.json

@@ -1,53 +0,0 @@
-{
-    "Version": 7.2,
-    "Timestamp": "Tue Mar 26 17:24:34 2024",
-    "Detector Type": "Eiger",
-    "Timing Mode": "auto",
-    "Geometry": {
-        "x": 2,
-        "y": 2
-    },
-    "Image Size in bytes": 524288,
-    "Pixels": {
-        "x": 512,
-        "y": 256
-    },
-    "Max Frames Per File": 10000,
-    "Frame Discard Policy": "nodiscard",
-    "Frame Padding": 1,
-    "Scan Parameters": "[disabled]",
-    "Total Frames": 3,
-    "Receiver Roi": {
-        "xmin": 4294967295,
-        "xmax": 4294967295,
-        "ymin": 4294967295,
-        "ymax": 4294967295
-    },
-    "Dynamic Range": 32,
-    "Ten Giga": 0,
-    "Exptime": "5s",
-    "Period": "1s",
-    "Threshold Energy": -1,
-    "Sub Exptime": "2.62144ms",
-    "Sub Period": "2.62144ms",
-    "Quad": 0,
-    "Number of rows": 256,
-    "Rate Corrections": "[0, 0]",
-    "Frames in File": 3,
-    "Frame Header Format": {
-        "Frame Number": "8 bytes",
-        "SubFrame Number/ExpLength": "4 bytes",
-        "Packet Number": "4 bytes",
-        "Bunch ID": "8 bytes",
-        "Timestamp": "8 bytes",
-        "Module Id": "2 bytes",
-        "Row": "2 bytes",
-        "Column": "2 bytes",
-        "Reserved": "2 bytes",
-        "Debug": "4 bytes",
-        "Round Robin Number": "2 bytes",
-        "Detector Type": "1 byte",
-        "Header Version": "1 byte",
-        "Packets Caught Mask": "64 bytes"
-    }
-}

data/jungfrau/jungfrau_double_master_0.json

@@ -1,47 +0,0 @@
-{
-    "Version": 7.2,
-    "Timestamp": "Tue Feb 20 08:29:19 2024",
-    "Detector Type": "Jungfrau",
-    "Timing Mode": "auto",
-    "Geometry": {
-        "x": 1,
-        "y": 2
-    },
-    "Image Size in bytes": 524288,
-    "Pixels": {
-        "x": 1024,
-        "y": 256
-    },
-    "Max Frames Per File": 3,
-    "Frame Discard Policy": "nodiscard",
-    "Frame Padding": 1,
-    "Scan Parameters": "[disabled]",
-    "Total Frames": 10,
-    "Receiver Roi": {
-        "xmin": 4294967295,
-        "xmax": 4294967295,
-        "ymin": 4294967295,
-        "ymax": 4294967295
-    },
-    "Exptime": "10us",
-    "Period": "1ms",
-    "Number of UDP Interfaces": 2,
-    "Number of rows": 512,
-    "Frames in File": 10,
-    "Frame Header Format": {
-        "Frame Number": "8 bytes",
-        "SubFrame Number/ExpLength": "4 bytes",
-        "Packet Number": "4 bytes",
-        "Bunch ID": "8 bytes",
-        "Timestamp": "8 bytes",
-        "Module Id": "2 bytes",
-        "Row": "2 bytes",
-        "Column": "2 bytes",
-        "Reserved": "2 bytes",
-        "Debug": "4 bytes",
-        "Round Robin Number": "2 bytes",
-        "Detector Type": "1 byte",
-        "Header Version": "1 byte",
-        "Packets Caught Mask": "64 bytes"
-    }
-}

data/jungfrau/jungfrau_single_master_0.json

@@ -1,47 +0,0 @@
-{
-    "Version": 7.2,
-    "Timestamp": "Tue Feb 20 08:28:24 2024",
-    "Detector Type": "Jungfrau",
-    "Timing Mode": "auto",
-    "Geometry": {
-        "x": 1,
-        "y": 1
-    },
-    "Image Size in bytes": 1048576,
-    "Pixels": {
-        "x": 1024,
-        "y": 512
-    },
-    "Max Frames Per File": 3,
-    "Frame Discard Policy": "nodiscard",
-    "Frame Padding": 1,
-    "Scan Parameters": "[disabled]",
-    "Total Frames": 10,
-    "Receiver Roi": {
-        "xmin": 4294967295,
-        "xmax": 4294967295,
-        "ymin": 4294967295,
-        "ymax": 4294967295
-    },
-    "Exptime": "10us",
-    "Period": "1ms",
-    "Number of UDP Interfaces": 1,
-    "Number of rows": 512,
-    "Frames in File": 10,
-    "Frame Header Format": {
-        "Frame Number": "8 bytes",
-        "SubFrame Number/ExpLength": "4 bytes",
-        "Packet Number": "4 bytes",
-        "Bunch ID": "8 bytes",
-        "Timestamp": "8 bytes",
-        "Module Id": "2 bytes",
-        "Row": "2 bytes",
-        "Column": "2 bytes",
-        "Reserved": "2 bytes",
-        "Debug": "4 bytes",
-        "Round Robin Number": "2 bytes",
-        "Detector Type": "1 byte",
-        "Header Version": "1 byte",
-        "Packets Caught Mask": "64 bytes"
-    }
-}

data/jungfrau/read_frame.py

@@ -1,50 +0,0 @@
-import numpy as np
-import matplotlib.pyplot as plt
-plt.ion()
-
-header_dt = np.dtype(
-    [
-        ("Frame Number", "u8"),
-        ("SubFrame Number/ExpLength", "u4"),
-        ("Packet Number", "u4"),
-        ("Bunch ID", "u8"),
-        ("Timestamp", "u8"),
-        ("Module Id", "u2"),
-        ("Row", "u2"),
-        ("Column", "u2"),
-        ("Reserved", "u2"),
-        ("Debug", "u4"),
-        ("Round Robin Number", "u2"),
-        ("Detector Type", "u1"),
-        ("Header Version", "u1"),
-        ("Packets caught mask", "8u8")
-    ]
-)
-
-# Read three frames from a jungfrau file with a single interface
-rows = 1024
-cols = 512
-frames = 1
-
-data = np.zeros((frames,rows,cols), dtype = np.uint16)
-header = np.zeros(frames, dtype = header_dt)
-for frame in range(frames):
-    
-    file_name = '/tmp/raw_example_writing_master_'
-    print("Reading file:", file_name)
-    with open(file_name) as f:
-        for i in range(3 if file_id != 3 else 1):
-            header[i+file_id*3] = np.fromfile(f, dtype=header_dt, count = 1)
-            data[i+file_id*3] = np.fromfile(f, dtype=np.uint16,count = rows*cols).reshape(rows,cols)
-
-
-    # for i in range(frames if file_id != 3 else 1 ):
-    #     print("frame:",i)
-    #     print(header[i][0,0],data[i][0,1],data[i][1,0],data[i][rows-1,cols-1])
-    #     print("")
-
-
-print(header[1]["Frame Number"])
-#fig, ax = plt.subplots()
-#im = ax.imshow(data[0])
-#im.set_clim(2000,4000)

data/jungfrau/read_multiport.py

@@ -1,87 +0,0 @@
-import numpy as np
-
-header_dt = np.dtype(
-    [
-        ("Frame Number", "u8"),
-        ("SubFrame Number/ExpLength", "u4"),
-        ("Packet Number", "u4"),
-        ("Bunch ID", "u8"),
-        ("Timestamp", "u8"),
-        ("Module Id", "u2"),
-        ("Row", "u2"),
-        ("Column", "u2"),
-        ("Reserved", "u2"),
-        ("Debug", "u4"),
-        ("Round Robin Number", "u2"),
-        ("Detector Type", "u1"),
-        ("Header Version", "u1"),
-        ("Packets caught mask", "8u8")
-    ]
-)
-
-# Read three frames from a jungfrau file with a single interface
-
-frames = 10
-parts = 2
-frame_per_file = 3
-bytes_per_pixel = 2
-frame_cols = 1024
-frame_rows = 512
-
-part_cols = 1024
-part_rows = 256
-
-
-parts_data = np.zeros((frames,parts,part_rows,part_cols), dtype = np.uint16)
-data = np.zeros((frames,frame_rows,frame_cols), dtype = np.uint16)
-header = np.zeros((frames,parts), dtype = header_dt)
-
-
-
-# verify that all parts have the same frame number
-for frame in range(frames):
-    for part in range(parts):
-        file_name = f'jungfrau_double_d{part}_f{frame//frame_per_file}_{0}.raw'
-        with open(file_name) as f:
-            offset = (frame%frame_per_file)*(header_dt.itemsize+part_rows*part_cols*bytes_per_pixel)
-            # print(f"Reading file: {file_name} at offset {offset}")
-            header[frame,part] = np.fromfile(f, dtype=header_dt, count = 1,offset=offset)
-            # print(f"Frame {frame} part {part} frame number: {header[frame,part]['Frame Number']}")
-            if part > 0:
-                assert header[frame,part]['Frame Number'] == header[frame,0]['Frame Number']
-
-print("[X] All parts have the same frame number\n")
-
-
-for frame in range(frames):
-
-    for part in range(parts):
-        file_name = f'jungfrau_double_d{part}_f{frame//frame_per_file}_{0}.raw'
-        # print("Reading file:", file_name)
-        with open(file_name) as f:
-            offset = (frame%frame_per_file)*(header_dt.itemsize+part_rows*part_cols*bytes_per_pixel)
-            header[frame,part] = np.fromfile(f, dtype=header_dt, count = 1, offset=offset)
-            parts_data[frame,part] = np.fromfile(f, dtype=np.uint16,count = part_rows*part_cols).reshape(part_rows,part_cols)
-
-    
-    data[frame] = np.concatenate((parts_data[frame,0],parts_data[frame,1]),axis=0)
-
-
-
-pixel_0_0,pixel_0_1,pixel_1_0,pixel_255_1023,pixel_511_1023,= [],[],[],[],[]
-for frame in range(frames):
-    pixel_0_0.append(data[frame,0,0])
-    pixel_0_1.append(data[frame,0,1])
-    pixel_1_0.append(data[frame,1,0])
-    pixel_255_1023.append(data[frame,255,1023])
-    pixel_511_1023.append(data[frame,511,1023])
-print("upper left corner of each frame (pixel_0_0)")
-print(pixel_0_0)
-print("first pixel on new line of each frame (pixel_1_0)")
-print(pixel_1_0)
-print("second pixel of the first line of each frame (pixel_0_1)")
-print(pixel_0_1)
-print("first pixel of the second part on the last line of each frame (pixel_255_1023)")
-print(pixel_255_1023)
-print("lower right corner of each frame (pixel_511_1023)")
-print(pixel_511_1023)

data/moench/moench04_noise_200V_sto_both_100us_no_light_thresh_900_master_0.raw

@@ -1,40 +0,0 @@
-Version                    : 6.4
-TimeStamp                  : Wed Aug 31 09:08:49 2022
-
-Detector Type              : ChipTestBoard
-Timing Mode                : auto
-Geometry                   : [1, 1]
-Image Size                 : 360000 bytes
-Pixels                     : [96, 1]
-Max Frames Per File        : 20000
-Frame Discard Policy       : nodiscard
-Frame Padding              : 1
-Scan Parameters            : [disabled]
-Total Frames               : 100
-Exptime                    : 100us
-Period                     : 4ms
-Ten Giga                   : 1
-ADC Mask                   : 0xffffffff
-Analog Flag                : 1
-Analog Samples             : 5000
-Digital Flag               : 1
-Digital Samples            : 5000
-Dbit Offset                : 0
-Dbit Bitset                : 0
-Frames in File             : 100
-
-#Frame Header
-Frame Number               : 8 bytes
-SubFrame Number/ExpLength  : 4 bytes
-Packet Number              : 4 bytes
-Bunch ID                   : 8 bytes
-Timestamp                  : 8 bytes
-Module Id                  : 2 bytes
-Row                        : 2 bytes
-Column                     : 2 bytes
-Reserved                   : 2 bytes
-Debug                      : 4 bytes
-Round Robin Number         : 2 bytes
-Detector Type              : 1 byte
-Header Version             : 1 byte
-Packets Caught Mask        : 64 bytes

data/mythen/CORRECTED_scan242_master_3.raw

@@ -1,40 +0,0 @@
-Version                    : 6.2
-TimeStamp                  : Mon Sep 14 16:21:09 2020
-
-Detector Type              : Mythen3
-Timing Mode                : auto
-Geometry                   : [4, 1]
-Image Size                 : 5120 bytes
-Pixels                     : [1280, 1]
-Max Frames Per File        : 10000
-Frame Discard Policy       : nodiscard
-Frame Padding              : 1
-Scan Parameters            : [disabled]
-Total Frames               : 1
-Dynamic Range              : 32
-Ten Giga                   : 1
-Period                     : 0ns
-Counter Mask               : 0x1
-Exptime1                   : 0.2s
-Exptime2                   : 0.2s
-Exptime3                   : 0.2s
-GateDelay1                 : 0.1s
-GateDelay2                 : 0.1s
-GateDelay3                 : 0.1s
-Gates                      : 1
-
-#Frame Header
-Frame Number               : 8 bytes
-SubFrame Number/ExpLength  : 4 bytes
-Packet Number              : 4 bytes
-Bunch ID                   : 8 bytes
-Timestamp                  : 8 bytes
-Module Id                  : 2 bytes
-Row                        : 2 bytes
-Column                     : 2 bytes
-Reserved                   : 2 bytes
-Debug                      : 4 bytes
-Round Robin Number         : 2 bytes
-Detector Type              : 1 byte
-Header Version             : 1 byte
-Packets Caught Mask        : 64 bytes

data/mythen/correct_frame_numbers.py

@@ -1,58 +0,0 @@
-import numpy as np
-import shutil
-
-header_dt = np.dtype(
-    [
-        ("Frame Number", "u8"),
-        ("SubFrame Number/ExpLength", "u4"),
-        ("Packet Number", "u4"),
-        ("Bunch ID", "u8"),
-        ("Timestamp", "u8"),
-        ("Module Id", "u2"),
-        ("Row", "u2"),
-        ("Column", "u2"),
-        ("Reserved", "u2"),
-        ("Debug", "u4"),
-        ("Round Robin Number", "u2"),
-        ("Detector Type", "u1"),
-        ("Header Version", "u1"),
-        ("Packets caught mask", "8u8")
-    ]
-)
-
-# Read three frames from a jungfrau file with a single interface
-
-frames = 1
-parts = 4
-frame_per_file = 3
-bytes_per_pixel = 4
-frame_cols = 1
-frame_rows = 5120
-
-part_cols = 1280
-part_rows = 1
-
-header = np.zeros((frames,parts), dtype = header_dt)
-
-
-
-# verify that all parts have the same frame number
-frame = 0
-i = 55
-for part in range(parts):
-    file_name_r = f'scan242_d{part}_f{frame//frame_per_file}_{3}.raw'
-    file_name_w = f'CORRECTED_scan242_d{part}_f{frame//frame_per_file}_{3}.raw'
-    shutil.copyfile(file_name_r, file_name_w)
-
-    with open(file_name_r) as fr, open(file_name_w, 'r+b') as fw:
-        # get frame
-        offset = (frame%frame_per_file)*(header_dt.itemsize+part_rows*part_cols*bytes_per_pixel)
-        header[frame,part] = np.fromfile(fr, dtype=header_dt, count = 1,offset=offset)
-        # update frame number
-        header[frame,part]['Frame Number'] = i
-        fw.seek(offset)
-        header[frame,part].tofile(fw)
-
-
-print("[X] Done\n")
-

data/mythen/m3_master_0.json

@@ -1,55 +0,0 @@
-{
-    "Version": 7.1,
-    "Timestamp": "Wed Sep 21 13:48:10 2022",
-    "Detector Type": "Mythen3",
-    "Timing Mode": "auto",
-    "Geometry": {
-        "x": 1,
-        "y": 1
-    },
-    "Image Size in bytes": 15360,
-    "Pixels": {
-        "x": 3840,
-        "y": 1
-    },
-    "Max Frames Per File": 10000,
-    "Frame Discard Policy": "nodiscard",
-    "Frame Padding": 1,
-    "Scan Parameters": "[disabled]",
-    "Total Frames": 1,
-    "Receiver Roi": {
-        "xmin": 4294967295,
-        "xmax": 4294967295,
-        "ymin": 4294967295,
-        "ymax": 4294967295
-    },
-    "Dynamic Range": 32,
-    "Ten Giga": 1,
-    "Period": "2ms",
-    "Counter Mask": "0x7",
-    "Exptime1": "0.1s",
-    "Exptime2": "0.1s",
-    "Exptime3": "0.1s",
-    "GateDelay1": "0ns",
-    "GateDelay2": "0ns",
-    "GateDelay3": "0ns",
-    "Gates": 1,
-    "Threshold Energies": "[-1, -1, -1]",
-    "Frames in File": 1,
-    "Frame Header Format": {
-        "Frame Number": "8 bytes",
-        "SubFrame Number/ExpLength": "4 bytes",
-        "Packet Number": "4 bytes",
-        "Bunch ID": "8 bytes",
-        "Timestamp": "8 bytes",
-        "Module Id": "2 bytes",
-        "Row": "2 bytes",
-        "Column": "2 bytes",
-        "Reserved": "2 bytes",
-        "Debug": "4 bytes",
-        "Round Robin Number": "2 bytes",
-        "Detector Type": "1 byte",
-        "Header Version": "1 byte",
-        "Packets Caught Mask": "64 bytes"
-    }
-}

data/mythen/read_multiport.py

@@ -1,57 +0,0 @@
-import numpy as np
-
-header_dt = np.dtype(
-    [
-        ("Frame Number", "u8"),
-        ("SubFrame Number/ExpLength", "u4"),
-        ("Packet Number", "u4"),
-        ("Bunch ID", "u8"),
-        ("Timestamp", "u8"),
-        ("Module Id", "u2"),
-        ("Row", "u2"),
-        ("Column", "u2"),
-        ("Reserved", "u2"),
-        ("Debug", "u4"),
-        ("Round Robin Number", "u2"),
-        ("Detector Type", "u1"),
-        ("Header Version", "u1"),
-        ("Packets caught mask", "8u8")
-    ]
-)
-
-# Read three frames from a jungfrau file with a single interface
-
-frames = 1
-parts = 4
-frame_per_file = 3
-bytes_per_pixel = 4
-frame_cols = 1
-frame_rows = 5120
-
-part_cols = 1280
-part_rows = 1
-
-header = np.zeros((frames,parts), dtype = header_dt)
-
-
-
-# verify that all parts have the same frame number
-frame = 0
-sync = True
-for part in range(parts):
-    file_name = f'scan242_d{part}_f{frame//frame_per_file}_{3}.raw'
-    with open(file_name) as f:
-        offset = (frame%frame_per_file)*(header_dt.itemsize+part_rows*part_cols*bytes_per_pixel)
-        # print(f"Reading file: {file_name} at offset {offset}")
-        header[frame,part] = np.fromfile(f, dtype=header_dt, count = 1,offset=offset)
-        # print(f"Frame {frame} part {part} frame number: {header[frame,part]['Frame Number']}")
-        print(f"part {part} frame number: {header[frame,part]['Frame Number']}")
-        sync  = sync and (header[frame,part]['Frame Number'] == header[frame,0]['Frame Number'])
-
-
-if sync:
-    print("[X] subfiles have the same frame")
-else:
-    print("[X] subfiles do not have the same frame\n")
-
-

data/mythen/scan242_master_3.raw

@@ -1,40 +0,0 @@
-Version                    : 6.2
-TimeStamp                  : Mon Sep 14 16:21:09 2020
-
-Detector Type              : Mythen3
-Timing Mode                : auto
-Geometry                   : [4, 1]
-Image Size                 : 5120 bytes
-Pixels                     : [1280, 1]
-Max Frames Per File        : 10000
-Frame Discard Policy       : nodiscard
-Frame Padding              : 1
-Scan Parameters            : [disabled]
-Total Frames               : 1
-Dynamic Range              : 32
-Ten Giga                   : 1
-Period                     : 0ns
-Counter Mask               : 0x1
-Exptime1                   : 0.2s
-Exptime2                   : 0.2s
-Exptime3                   : 0.2s
-GateDelay1                 : 0.1s
-GateDelay2                 : 0.1s
-GateDelay3                 : 0.1s
-Gates                      : 1
-
-#Frame Header
-Frame Number               : 8 bytes
-SubFrame Number/ExpLength  : 4 bytes
-Packet Number              : 4 bytes
-Bunch ID                   : 8 bytes
-Timestamp                  : 8 bytes
-Module Id                  : 2 bytes
-Row                        : 2 bytes
-Column                     : 2 bytes
-Reserved                   : 2 bytes
-Debug                      : 4 bytes
-Round Robin Number         : 2 bytes
-Detector Type              : 1 byte
-Header Version             : 1 byte
-Packets Caught Mask        : 64 bytes

data/numpy/write_test_files.py

@@ -1,12 +0,0 @@
-import numpy as np
-
-
-arr = np.arange(10, dtype = np.int32)
-np.save('test_1d_int32.npy', arr)
-
-arr2 = np.zeros((3,2,5), dtype = np.float64)
-arr2[0,0,0] = 1.0
-arr2[0,0,1] = 2.0
-arr2[0,1,0] = 72.0
-arr2[2,0,4] = 63.0
-np.save('test_3d_double.npy', arr2)

data/scripts/verify_rawfile_writing.py

@@ -1,62 +0,0 @@
-###
-### Verify that the raw file written by the raw_example.cpp are correct
-###
-
-
-import numpy as np
-
-header_dt = np.dtype(
-    [
-        ("Frame Number", "u8"),
-        ("SubFrame Number/ExpLength", "u4"),
-        ("Packet Number", "u4"),
-        ("Bunch ID", "u8"),
-        ("Timestamp", "u8"),
-        ("Module Id", "u2"),
-        ("Row", "u2"),
-        ("Column", "u2"),
-        ("Reserved", "u2"),
-        ("Debug", "u4"),
-        ("Round Robin Number", "u2"),
-        ("Detector Type", "u1"),
-        ("Header Version", "u1"),
-        ("Packets caught mask", "8u8")
-    ]
-)
-
-frames = 1
-parts = 1
-frame_per_file = 3
-bytes_per_pixel = 2
-frame_cols = 512
-frame_rows = 1024
-
-part_cols = 512
-part_rows = 1024
-
-
-# parts_data = np.zeros((frames,parts,part_rows,part_cols), dtype = np.uint16)
-data = np.zeros((frames,frame_rows,frame_cols), dtype = np.uint16)
-header = np.zeros((frames,parts), dtype = header_dt)
-
-
-
-# verify that all parts have the same frame number
-for frame in range(frames):
-    for part in range(parts):
-        file_name = f'/tmp/raw_example_writing_d{part}_f{frame//frame_per_file}_{0}.raw'
-        with open(file_name) as f:
-            offset = (frame%frame_per_file)*(header_dt.itemsize+part_rows*part_cols*bytes_per_pixel)
-            # print(f"Reading file: {file_name} at offset {offset}")
-            header[frame,part] = np.fromfile(f, dtype=header_dt, count = 1,offset=offset)
-            # print(f"Frame {frame} part {part} frame number: {header[frame,part]['Frame Number']}")
-            data[frame] = np.fromfile(f, dtype=np.uint16,count = frame_rows*frame_cols).reshape(frame_rows,frame_cols)
-            
-
-for frame in range(frames):
-    for i,j in np.ndindex(data[frame].shape):
-        assert(data[frame][i,j] == i+j)
-
-print("[X] frame data is correct")
-        
-            

docs/CMakeLists.txt

@@ -0,0 +1,55 @@
+find_package(Doxygen REQUIRED)
+find_package(Sphinx REQUIRED)
+
+#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})
+
+
+file(GLOB SPHINX_SOURCE_FILES CONFIGURE_DEPENDS "src/*.rst")
+
+
+foreach(filename ${SPHINX_SOURCE_FILES})
+    get_filename_component(fname ${filename} NAME)
+    message(STATUS "Copying ${filename} to ${SPHINX_BUILD}/src/${fname}")
+    configure_file(${filename} "${SPHINX_BUILD}/src/${fname}")  
+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}/static/extra.css"
+    "${SPHINX_BUILD}/static/css/extra.css"
+    @ONLY
+)
+
+add_custom_target(
+    docs
+    COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYGEN_OUT}
+    COMMAND ${SPHINX_EXECUTABLE} -a -b html
+    -Dbreathe_projects.aare=${CMAKE_CURRENT_BINARY_DIR}/xml
+    -c "${SPHINX_BUILD}"
+    ${SPHINX_BUILD}/src 
+    ${SPHINX_BUILD}/html
+    COMMENT "Generating documentation with Sphinx"
+)
+
+add_custom_target(
+    rst
+    COMMAND ${SPHINX_EXECUTABLE} -a -b html
+    -Dbreathe_projects.aare=${CMAKE_CURRENT_BINARY_DIR}/xml
+    -c "${SPHINX_BUILD}"
+    ${SPHINX_BUILD}/src 
+    ${SPHINX_BUILD}/html
+    COMMENT "Generating documentation with Sphinx"
+)

docs/commands_multimodule.md

@@ -1,8 +0,0 @@
-# receive data from two zmqstreams
-```bash
-killall jungfrauDetectorServer_virtual
-jungfrauDetectorServer_virtual 
-jungfrauDetectorServer_virtual -p 1956
-slsMultiReceiver 1980 2 0
-sls_detector_put config etc/multimodule_virtual_jf.config
-```

docs/conf.py.in

@@ -0,0 +1,63 @@
+# 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('..'))
+
+print(sys.path)
+
+# -- Project information -----------------------------------------------------
+
+project = 'aare'
+copyright = '2024, CPS Detector Group'
+author = 'CPS 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.ext.autodoc',
+              'sphinx.ext.napoleon',
+             ]
+
+breathe_default_project = "aare"
+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 = "furo"
+
+# 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/diagrams/aare_class.puml

@@ -1,141 +0,0 @@
-@startuml
-class "NDView<T,ssize_t Ndim=2>" as C_0000853339819629793090
-class C_0000853339819629793090 {
-__
-}
-class "NDView<unsigned short,2L>" as C_0000800815410987673815
-class C_0000800815410987673815 {
-__
-}
-class "NDView<T,Ndim>" as C_0001549403386232143110
-class C_0001549403386232143110 {
-__
-}
-class "NDArray<bool,Ndim>" as C_0000823076622246857026
-class C_0000823076622246857026 {
-__
-}
-class "NDArray<V,Ndim>" as C_0002198222861307321825
-class C_0002198222861307321825 {
-__
-}
-class "NDArray<T,ssize_t Ndim=2>" as C_0001181947618035129503
-class C_0001181947618035129503 {
-__
-}
-class "sls_detector_header" as C_0001674535970515942906
-class C_0001674535970515942906 {
-__
-}
-class "xy" as C_0000162230005032830360
-class C_0000162230005032830360 {
-__
-}
-class "RawFileConfig" as C_0000511537329021463656
-class C_0000511537329021463656 {
-__
-}
-class "Frame" as C_0001608703618093824988
-class C_0001608703618093824988 {
-__
-}
-class "logger::Logger" as C_0001861698262135249810
-class C_0001861698262135249810 {
-__
-}
-class "ZmqHeader" as C_0000690012646166089557
-class C_0000690012646166089557 {
-__
-}
-class "ZmqSocket" as C_0000575290120620432482
-class C_0000575290120620432482 {
-__
-}
-class "ZmqFrame" as C_0001018278375791869829
-class C_0001018278375791869829 {
-__
-}
-class "network_io::NetworkError" as C_0001290043041844945927
-class C_0001290043041844945927 {
-__
-}
-class "ZmqSocketReceiver" as C_0001017868003595712218
-class C_0001017868003595712218 {
-__
-}
-class "ZmqSocketSender" as C_0002178845803227443176
-class C_0002178845803227443176 {
-__
-}
-class "DType" as C_0000703695317535186100
-class C_0000703695317535186100 {
-__
-}
-class "FileConfig" as C_0001694843161451381081
-class C_0001694843161451381081 {
-__
-}
-class "FileInterface" as C_0002122346448923803234
-class C_0002122346448923803234 {
-__
-}
-class "File" as C_0002007196654403438648
-class C_0002007196654403438648 {
-__
-}
-class "NumpyHeader" as C_0002287674849990076068
-class C_0002287674849990076068 {
-__
-}
-class "NumpyFile" as C_0001470720024404954003
-class C_0001470720024404954003 {
-__
-}
-class "SubFile" as C_0001884494008888210849
-class C_0001884494008888210849 {
-__
-}
-class "RawFile" as C_0001505206538021535080
-class C_0001505206538021535080 {
-__
-}
-C_0000800815410987673815 ..|> C_0000853339819629793090
-C_0001549403386232143110 ..|> C_0000853339819629793090
-C_0000823076622246857026 ..|> C_0001181947618035129503
-C_0002198222861307321825 ..|> C_0001181947618035129503
-C_0001181947618035129503 ..> C_0001549403386232143110
-C_0001181947618035129503 ..> C_0000823076622246857026
-C_0001181947618035129503 ..> C_0002198222861307321825
-C_0001018278375791869829 o-- C_0000690012646166089557 : +header
-C_0001018278375791869829 o-- C_0001608703618093824988 : +frame
-C_0001017868003595712218 ..> C_0001018278375791869829
-C_0001017868003595712218 ..> C_0000690012646166089557
-C_0000575290120620432482 <|-- C_0001017868003595712218
-C_0002178845803227443176 ..> C_0000690012646166089557
-C_0002178845803227443176 ..> C_0001018278375791869829
-C_0000575290120620432482 <|-- C_0002178845803227443176
-C_0001694843161451381081 o-- C_0000703695317535186100 : +dtype
-C_0001694843161451381081 o-- C_0000162230005032830360 : +geometry
-C_0002122346448923803234 ..> C_0001608703618093824988
-C_0002007196654403438648 ..> C_0001694843161451381081
-C_0002007196654403438648 ..> C_0001608703618093824988
-C_0002007196654403438648 --> C_0002122346448923803234 : -file_impl
-C_0002287674849990076068 o-- C_0000703695317535186100 : +dtype
-C_0001470720024404954003 ..> C_0001694843161451381081
-C_0001470720024404954003 ..> C_0001608703618093824988
-C_0001470720024404954003 ..> C_0000703695317535186100
-C_0001470720024404954003 o-- C_0002287674849990076068 : -m_header
-C_0002122346448923803234 <|-- C_0001470720024404954003
-C_0001884494008888210849 o-- C_0001884494008888210849 : #read_impl_map
-C_0001505206538021535080 ..> C_0001694843161451381081
-C_0001505206538021535080 ..> C_0001608703618093824988
-C_0001505206538021535080 ..> C_0001674535970515942906
-C_0001505206538021535080 --> C_0001884494008888210849 : -subfiles
-C_0001505206538021535080 o-- C_0000162230005032830360 : -geometry
-C_0001505206538021535080 o-- C_0000162230005032830360 : -positions
-C_0001505206538021535080 o-- C_0000511537329021463656 : -cfg
-C_0002122346448923803234 <|-- C_0001505206538021535080
-
-'Generated with clang-uml, version 0.5.1
-'LLVM version clang version 17.0.6 (Fedora 17.0.6-2.fc39)
-@enduml

docs/diagrams/aare_class_simplified.puml

@@ -1,95 +0,0 @@
-@startuml
-class "sls_detector_header" as C_0001674535970515942906
-class C_0001674535970515942906 {
-__
-}
-class "RawFileConfig" as C_0000511537329021463656
-class C_0000511537329021463656 {
-__
-}
-class "Frame" as C_0001608703618093824988
-class C_0001608703618093824988 {
-__
-}
-class "ZmqHeader" as C_0000690012646166089557
-class C_0000690012646166089557 {
-__
-}
-class "ZmqSocket" as C_0000575290120620432482
-class C_0000575290120620432482 {
-__
-}
-class "ZmqFrame" as C_0001018278375791869829
-class C_0001018278375791869829 {
-__
-}
-class "ZmqSocketReceiver" as C_0001017868003595712218
-class C_0001017868003595712218 {
-__
-}
-class "ZmqSocketSender" as C_0002178845803227443176
-class C_0002178845803227443176 {
-__
-}
-class "DType" as C_0000703695317535186100
-class C_0000703695317535186100 {
-__
-}
-class "FileConfig" as C_0001694843161451381081
-class C_0001694843161451381081 {
-__
-}
-class "FileInterface" as C_0002122346448923803234
-class C_0002122346448923803234 {
-__
-}
-class "File" as C_0002007196654403438648
-class C_0002007196654403438648 {
-__
-}
-class "NumpyHeader" as C_0002287674849990076068
-class C_0002287674849990076068 {
-__
-}
-class "NumpyFile" as C_0001470720024404954003
-class C_0001470720024404954003 {
-__
-}
-class "SubFile" as C_0001884494008888210849
-class C_0001884494008888210849 {
-__
-}
-class "RawFile" as C_0001505206538021535080
-class C_0001505206538021535080 {
-__
-}
-C_0001018278375791869829 o-- C_0000690012646166089557 : +header
-C_0001018278375791869829 o-- C_0001608703618093824988 : +frame
-C_0001017868003595712218 ..> C_0001018278375791869829
-C_0001017868003595712218 ..> C_0000690012646166089557
-C_0000575290120620432482 <|-- C_0001017868003595712218
-C_0002178845803227443176 ..> C_0000690012646166089557
-C_0002178845803227443176 ..> C_0001018278375791869829
-C_0000575290120620432482 <|-- C_0002178845803227443176
-C_0001694843161451381081 o-- C_0000703695317535186100 : +dtype
-C_0002122346448923803234 ..> C_0001608703618093824988
-C_0002007196654403438648 ..> C_0001694843161451381081
-C_0002007196654403438648 ..> C_0001608703618093824988
-C_0002007196654403438648 --> C_0002122346448923803234 : -file_impl
-C_0002287674849990076068 o-- C_0000703695317535186100 : +dtype
-C_0001470720024404954003 ..> C_0001694843161451381081
-C_0001470720024404954003 ..> C_0001608703618093824988
-C_0001470720024404954003 ..> C_0000703695317535186100
-C_0001470720024404954003 o-- C_0002287674849990076068 : -m_header
-C_0002122346448923803234 <|-- C_0001470720024404954003
-C_0001884494008888210849 o-- C_0001884494008888210849 : #read_impl_map
-C_0001505206538021535080 ..> C_0001694843161451381081
-C_0001505206538021535080 ..> C_0001608703618093824988
-C_0001505206538021535080 ..> C_0001674535970515942906
-C_0001505206538021535080 --> C_0001884494008888210849 : -subfiles
-C_0001505206538021535080 o-- C_0000511537329021463656 : -cfg
-C_0002122346448923803234 <|-- C_0001505206538021535080
-
-'Generated with clang-uml, version 0.5.1
-'LLVM version clang version 17.0.6 (Fedora 17.0.6-2.fc39)
-@enduml

docs/diagrams/core_class.puml

@@ -1,267 +0,0 @@
-@startuml
-class "aare::sls_detector_header" as C_0001674535970515942906
-class C_0001674535970515942906 {
-__
-+bunchId : uint64_t
-+column : uint16_t
-+debug : uint32_t
-+detType : uint8_t
-+expLength : uint32_t
-+frameNumber : uint64_t
-+modId : uint16_t
-+packetMask : uint8_t[64]
-+packetNumber : uint32_t
-+reserved : uint16_t
-+roundRNumber : uint16_t
-+row : uint16_t
-+timestamp : uint64_t
-+version : uint8_t
-}
-class "aare::xy" as C_0000162230005032830360
-class C_0000162230005032830360 {
-+operator!=(const xy & other) const : bool
-+operator==(const xy & other) const : bool
-__
-+col : int
-+row : int
-}
-enum "aare::DetectorType" as C_0000214432771357383463
-enum C_0000214432771357383463 {
-Jungfrau
-Eiger
-Mythen3
-Moench
-ChipTestBoard
-}
-enum "aare::TimingMode" as C_0000845115331155903292
-enum C_0000845115331155903292 {
-Auto
-Trigger
-}
-class "aare::RawFileConfig" as C_0000511537329021463656
-class C_0000511537329021463656 {
-+operator==(const RawFileConfig & other) const : bool
-__
-+module_gap_col : int
-+module_gap_row : int
-}
-enum "aare::endian" as C_0000190468130082798308
-enum C_0000190468130082798308 {
-little
-big
-native
-}
-class "aare::DType" as C_0000703695317535186100
-class C_0000703695317535186100 {
-+DType(const std::type_info & t) : void
-+DType(std::string_view sv) : void
-+DType(DType::TypeIndex ti) : void
-..
-+operator!=(const DType & other) const noexcept : bool
-+operator!=(const std::type_info & t) const : bool
-+operator==(const DType & other) const noexcept : bool
-+operator==(const std::type_info & t) const : bool
-..
-+bitdepth() const : uint8_t
-+str() const : std::string
-__
--m_type : TypeIndex
-}
-enum "aare::DType::TypeIndex" as C_0000575426556754591775
-enum C_0000575426556754591775 {
-INT8
-UINT8
-INT16
-UINT16
-INT32
-UINT32
-INT64
-UINT64
-FLOAT
-DOUBLE
-ERROR
-}
-class "aare::NDView<T,ssize_t Ndim=2>" as C_0000853339819629793090
-class C_0000853339819629793090 {
-+NDView() : void
-+NDView(T * buffer, std::array<ssize_t,Ndim> shape) : void
-+NDView(T * buffer, const std::vector<ssize_t> & shape) : void
-+NDView(const NDView<T,Ndim> &) = default : void
-+NDView(NDView<T,Ndim> &&) = default : void
-..
-+operator=(const NDView<T,Ndim> & other) : NDView<T,Ndim> &
-..
-+operator()(ssize_t i) : T &
-+operator()<Ix...>(Ix... index) : typename std::enable_if<sizeof...(Ix) == Ndim, T &>::type
-+operator()<Ix...>(Ix... index) const : typename std::enable_if<sizeof...(Ix) == Ndim, T &>::type
-+operator*=(const T val) : NDView<T,Ndim> &
-+operator+=(const T val) : NDView<T,Ndim> &
-+operator-=(const T val) : NDView<T,Ndim> &
-+operator/=(const T val) : NDView<T,Ndim> &
-+operator/=(const NDView<T,Ndim> & other) : NDView<T,Ndim> &
-+operator=(const T val) : NDView<T,Ndim> &
-+operator==(const NDView<T,Ndim> & other) const : bool
-+operator[](ssize_t i) : T &
-..
-+begin() : T *
-+data() : T *
--elemenwise<BinaryOperation>(T val, BinaryOperation op) : NDView<T, Ndim> &
--elemenwise<BinaryOperation>(const NDView<T,Ndim> & other, BinaryOperation op) : NDView<T, Ndim> &
-+end() : T *
-+shape() : auto &
-+shape(ssize_t i) const : auto
-+size() const : ssize_t
-__
--buffer_ : T *
--shape_ : std::array<ssize_t,Ndim>
--size_ : ssize_t
--strides_ : std::array<ssize_t,Ndim>
-}
-class "aare::NDView<unsigned short,2L>" as C_0000800815410987673815
-class C_0000800815410987673815 {
-+NDView() : void
-+NDView(unsigned short * buffer, std::array<ssize_t,2L> shape) : void
-+NDView(unsigned short * buffer, const std::vector<ssize_t> & shape) : void
-+NDView(const aare::NDView<uint16_t,2> &) = default : void
-+NDView(aare::NDView<uint16_t,2> &&) = default : void
-..
-+operator=(const aare::NDView<uint16_t,2> & other) : aare::NDView<uint16_t,2> &
-..
-+operator()(ssize_t i) : unsigned short &
-+operator()<Ix...>(Ix... index) : typename std::enable_if<sizeof...(Ix) == 2L, unsigned short &>::type
-+operator()<Ix...>(Ix... index) const : typename std::enable_if<sizeof...(Ix) == 2L, unsigned short &>::type
-+operator*=(const unsigned short val) : aare::NDView<uint16_t,2> &
-+operator+=(const unsigned short val) : aare::NDView<uint16_t,2> &
-+operator-=(const unsigned short val) : aare::NDView<uint16_t,2> &
-+operator/=(const unsigned short val) : aare::NDView<uint16_t,2> &
-+operator/=(const aare::NDView<uint16_t,2> & other) : aare::NDView<uint16_t,2> &
-+operator=(const unsigned short val) : aare::NDView<uint16_t,2> &
-+operator==(const aare::NDView<uint16_t,2> & other) const : bool
-+operator[](ssize_t i) : unsigned short &
-..
-+begin() : unsigned short *
-+data() : unsigned short *
--elemenwise<BinaryOperation>(unsigned short val, BinaryOperation op) : NDView<uint16_t, 2> &
--elemenwise<BinaryOperation>(const aare::NDView<uint16_t,2> & other, BinaryOperation op) : NDView<uint16_t, 2> &
-+end() : unsigned short *
-+shape() : std::array<ssize_t,2L> &
-+shape(ssize_t i) const : value_type
-+size() const : ssize_t
-__
--buffer_ : unsigned short *
--shape_ : std::array<ssize_t,2L>
--size_ : ssize_t
--strides_ : std::array<ssize_t,2L>
-}
-class "aare::NDView<T,Ndim>" as C_0001549403386232143110
-class C_0001549403386232143110 {
-__
-}
-class "aare::NDArray<bool,Ndim>" as C_0000823076622246857026
-class C_0000823076622246857026 {
-__
-}
-class "aare::NDArray<V,Ndim>" as C_0002198222861307321825
-class C_0002198222861307321825 {
-__
-}
-class "aare::NDArray<T,ssize_t Ndim=2>" as C_0001181947618035129503
-class C_0001181947618035129503 {
-+NDArray() : void
-+NDArray(std::array<ssize_t,Ndim> shape) : void
-+NDArray(std::array<ssize_t,Ndim> shape, T value) : void
-+NDArray(NDView<T,Ndim> span) : void
-+NDArray(NDArray<T,Ndim> && other) : void
-+NDArray(const NDArray<T,Ndim> & other) : void
-+~NDArray() : void
-..
-+operator=(NDArray<T,Ndim> && other) : NDArray<T,Ndim> &
-+operator=(const NDArray<T,Ndim> & other) : NDArray<T,Ndim> &
-..
-+operator!=(const NDArray<T,Ndim> & other) const : bool
-+operator&=(const T &) : NDArray<T,Ndim> &
-+operator()<Ix...>(Ix... index) const : typename std::enable_if<sizeof...(Ix) == Ndim, T &>::type
-+operator()<Ix...>(Ix... index) : typename std::enable_if<sizeof...(Ix) == Ndim, T &>::type
-+operator()(int i) const : const T &
-+operator()(int i) : T &
-+operator*(const NDArray<T,Ndim> & other) : NDArray<T,Ndim>
-+operator*(const T &) : NDArray<T,Ndim>
-+operator*=(const NDArray<T,Ndim> & other) : NDArray<T,Ndim> &
-+operator*=(const T &) : NDArray<T,Ndim> &
-+operator+(const NDArray<T,Ndim> & other) : NDArray<T,Ndim>
-+operator+(const T &) : NDArray<T,Ndim>
-+operator++() : NDArray<T,Ndim> &
-+operator+=(const NDArray<T,Ndim> & other) : NDArray<T,Ndim> &
-+operator+=(const T &) : NDArray<T,Ndim> &
-+operator-(const T &) : NDArray<T,Ndim>
-+operator-(const NDArray<T,Ndim> & other) : NDArray<T,Ndim>
-+operator-=(const T &) : NDArray<T,Ndim> &
-+operator-=(const NDArray<T,Ndim> & other) : NDArray<T,Ndim> &
-+operator/(const T &) : NDArray<T,Ndim>
-+operator/(const NDArray<T,Ndim> & other) : NDArray<T,Ndim>
-+operator/=(const T &) : NDArray<T,Ndim> &
-+operator/=<V>(const NDArray<V,Ndim> & other) : NDArray<T, Ndim> &
-+operator=(const T &) : NDArray<T,Ndim> &
-+operator==(const NDArray<T,Ndim> & other) const : bool
-+operator>(const NDArray<T,Ndim> & other) : NDArray<bool,Ndim>
-..
-+Print() : void
-+Print_all() : void
-+Print_some() : void
-+begin() : auto
-+buffer() : std::byte *
-+byte_strides() const noexcept : std::array<ssize_t,Ndim>
-+data() : T *
-+end() : auto
-+reset() : void
-+shape(ssize_t i) const noexcept : ssize_t
-+shape() const noexcept : std::array<ssize_t,Ndim>
-+size() const : ssize_t
-+span() const : NDView<T,Ndim>
-+sqrt() : void
-+strides() const noexcept : std::array<ssize_t,Ndim>
-+total_bytes() const : size_t
-+value<Ix...>(Ix... index) : typename std::enable_if<sizeof...(Ix) == Ndim, T>::type
-__
--data_ : T *
--shape_ : std::array<ssize_t,Ndim>
--size_ : ssize_t
--strides_ : std::array<ssize_t,Ndim>
-}
-class "aare::Frame" as C_0001608703618093824988
-class C_0001608703618093824988 {
-+Frame(ssize_t rows, ssize_t cols, ssize_t m_bitdepth) : void
-+Frame(std::byte * fp, ssize_t rows, ssize_t cols, ssize_t m_bitdepth) : void
-+Frame(Frame && other) : void
-+Frame(const Frame & other) : void
-+~Frame() : void
-..
-+operator=(Frame & other) : Frame &
-..
-+bitdepth() const : ssize_t
-+cols() const : ssize_t
-+data() const : std::byte *
-+get(int row, int col) : std::byte *
-+image<T>() : NDArray<T>
-+rows() const : ssize_t
-+set<T>(int row, int col, T data) : void
-+size() const : ssize_t
-+view<T>() : NDView<T>
-__
--m_bitdepth : ssize_t
--m_cols : ssize_t
--m_data : std::byte *
--m_rows : ssize_t
-}
-C_0000575426556754591775 --+ C_0000703695317535186100
-C_0000800815410987673815 ..|> C_0000853339819629793090
-C_0001549403386232143110 ..|> C_0000853339819629793090
-C_0000823076622246857026 ..|> C_0001181947618035129503
-C_0002198222861307321825 ..|> C_0001181947618035129503
-C_0001181947618035129503 ..> C_0001549403386232143110
-C_0001181947618035129503 ..> C_0000823076622246857026
-C_0001181947618035129503 ..> C_0002198222861307321825
-
-'Generated with clang-uml, version 0.5.1
-'LLVM version clang version 17.0.6 (Fedora 17.0.6-2.fc39)
-@enduml

docs/diagrams/file_io_class.puml

@@ -1,200 +0,0 @@
-@startuml
-enum "aare::DetectorType" as C_0000214432771357383463
-enum C_0000214432771357383463 {
-Jungfrau
-Eiger
-Mythen3
-Moench
-ChipTestBoard
-}
-class "aare::Frame" as C_0001608703618093824988
-class C_0001608703618093824988 {
-+Frame(ssize_t rows, ssize_t cols, ssize_t m_bitdepth) : void
-+Frame(std::byte * fp, ssize_t rows, ssize_t cols, ssize_t m_bitdepth) : void
-+Frame(Frame && other) : void
-+Frame(const Frame & other) : void
-+~Frame() : void
-..
-+operator=(Frame & other) : Frame &
-..
-+bitdepth() const : ssize_t
-+cols() const : ssize_t
-+data() const : std::byte *
-+get(int row, int col) : std::byte *
-+image<T>() : NDArray<T>
-+rows() const : ssize_t
-+set<T>(int row, int col, T data) : void
-+size() const : ssize_t
-+view<T>() : NDView<T>
-__
--m_bitdepth : ssize_t
--m_cols : ssize_t
--m_data : std::byte *
--m_rows : ssize_t
-}
-class "aare::FileConfig" as C_0001694843161451381081
-class C_0001694843161451381081 {
-+operator!=(const FileConfig & other) const : bool
-+operator==(const FileConfig & other) const : bool
-__
-+cols : uint64_t
-+dtype : aare::DType
-+geometry : xy
-+rows : uint64_t
-}
-abstract "aare::FileInterface" as C_0002122346448923803234
-abstract C_0002122346448923803234 {
-+~FileInterface() : void
-..
-{abstract} +bitdepth() const = 0 : ssize_t
-{abstract} +bytes_per_frame() = 0 : size_t
-{abstract} +cols() const = 0 : ssize_t
-{abstract} +frame_number(size_t frame_index) = 0 : size_t
-+iread(size_t frame_number) : Frame
-+iread(size_t frame_number, size_t n_frames) : std::vector<Frame>
-{abstract} +pixels() = 0 : size_t
-{abstract} +read() = 0 : Frame
-{abstract} +read(size_t n_frames) = 0 : std::vector<Frame>
-{abstract} +read_into(std::byte * image_buf) = 0 : void
-{abstract} +read_into(std::byte * image_buf, size_t n_frames) = 0 : void
-{abstract} +rows() const = 0 : ssize_t
-{abstract} +seek(size_t frame_number) = 0 : void
-{abstract} +tell() = 0 : size_t
-{abstract} +total_frames() const = 0 : size_t
-{abstract} +write(Frame & frame) = 0 : void
-__
-+current_frame : size_t
-+m_base_name : std::string
-+m_base_path : std::filesystem::path
-+m_bitdepth : ssize_t
-+m_cols : ssize_t
-+m_ext : std::string
-+m_findex : int
-+m_fname : std::filesystem::path
-+m_mode : std::string
-+m_rows : ssize_t
-+m_total_frames : size_t
-+m_type : DetectorType
-+max_frames_per_file : size_t
-+version : std::string
-}
-class "aare::File" as C_0002007196654403438648
-class C_0002007196654403438648 {
-+File(std::filesystem::path fname, std::string mode, FileConfig cfg = {}) : void
-+File(File && other) : void
-+~File() : void
-..
-+bitdepth() const : ssize_t
-+bytes_per_frame() : size_t
-+cols() const : ssize_t
-+frame_number(size_t frame_index) : size_t
-+iread(size_t frame_number) : Frame
-+pixels() : size_t
-+read() : Frame
-+read(size_t n_frames) : std::vector<Frame>
-+read_into(std::byte * image_buf) : void
-+read_into(std::byte * image_buf, size_t n_frames) : void
-+rows() const : ssize_t
-+seek(size_t frame_number) : void
-+tell() const : size_t
-+total_frames() const : size_t
-+write(Frame & frame) : void
-__
--file_impl : FileInterface *
-}
-class "aare::NumpyFile" as C_0001470720024404954003
-class C_0001470720024404954003 {
-+NumpyFile(const std::filesystem::path & fname, const std::string & mode = "r", FileConfig cfg = {}) : void
-+~NumpyFile() : void
-..
-+bitdepth() const : ssize_t
-+bytes_per_frame() : size_t
-+cols() const : ssize_t
-+dtype() const : DType
-+frame_number(size_t frame_index) : size_t
--get_frame(size_t frame_number) : Frame
--get_frame_into(size_t, std::byte *) : void
-+load<T,size_t NDim>() : NDArray<T, NDim>
--load_metadata() : void
-+pixels() : size_t
-+read() : Frame
-+read(size_t n_frames) : std::vector<Frame>
-+read_into(std::byte * image_buf, size_t n_frames) : void
-+read_into(std::byte * image_buf) : void
-+rows() const : ssize_t
-+seek(size_t frame_number) : void
-+shape() const : std::vector<size_t>
-+tell() : size_t
-+total_frames() const : size_t
-+write(Frame & frame) : void
-__
--current_frame : size_t
--fp : FILE *
--header_len : uint32_t
--header_len_size : uint8_t
--header_size : size_t
--initial_header_len : size_t
--m_header : NumpyHeader
--major_ver_ : uint8_t
--minor_ver_ : uint8_t
-}
-class "aare::RawFile" as C_0001505206538021535080
-class C_0001505206538021535080 {
-+RawFile(const std::filesystem::path & fname, const std::string & mode = "r", const FileConfig & cfg = {}) : void
-+~RawFile() : void
-..
-+bitdepth() const : ssize_t
-+bytes_per_frame() : size_t
-+cols() const : ssize_t
-+data_fname(int mod_id, int file_id) : std::filesystem::path
--find_geometry() : void
-+find_number_of_subfiles() : void
-+frame_number(size_t frame_index) : size_t
--get_frame(size_t frame_number) : Frame
--get_frame_into(size_t frame_number, std::byte * image_buf) : void
-{static} +is_master_file(std::filesystem::path fpath) : bool
-+master_fname() : std::filesystem::path
--open_subfiles() : void
--parse_fname() : void
--parse_json_metadata() : void
--parse_metadata() : void
--parse_raw_metadata() : void
-+pixels() : size_t
-+read(size_t n_frames) : std::vector<Frame>
-+read() : Frame
--read_header(const std::filesystem::path & fname) : sls_detector_header
-+read_into(std::byte * image_buf, size_t n_frames) : void
-+read_into(std::byte * image_buf) : void
-+rows() const : ssize_t
-+seek(size_t frame_number) : void
-+set_config(int row, int col) : void
-+tell() : size_t
-+total_frames() const : size_t
-+write(Frame & frame) : void
-__
--cfg : RawFileConfig
--geometry : xy
--n_subfile_parts : size_t
--n_subfiles : size_t
--positions : std::vector<xy>
--quad : bool
--subfile_cols : int
--subfile_rows : int
--subfiles : std::vector<std::vector<SubFile *>>
--timing_mode : TimingMode
-}
-C_0002122346448923803234 ..> C_0001608703618093824988
-C_0002122346448923803234 o-- C_0000214432771357383463 : +m_type
-C_0002007196654403438648 ..> C_0001694843161451381081
-C_0002007196654403438648 ..> C_0001608703618093824988
-C_0002007196654403438648 --> C_0002122346448923803234 : -file_impl
-C_0001470720024404954003 ..> C_0001694843161451381081
-C_0001470720024404954003 ..> C_0001608703618093824988
-C_0002122346448923803234 <|-- C_0001470720024404954003
-C_0001505206538021535080 ..> C_0001694843161451381081
-C_0001505206538021535080 ..> C_0001608703618093824988
-C_0002122346448923803234 <|-- C_0001505206538021535080
-
-'Generated with clang-uml, version 0.5.1
-'LLVM version clang version 17.0.6 (Fedora 17.0.6-2.fc39)
-@enduml

docs/diagrams/network_io_class.puml

@@ -1,136 +0,0 @@
-@startuml
-class "aare::Frame" as C_0001608703618093824988
-class C_0001608703618093824988 {
-+Frame(ssize_t rows, ssize_t cols, ssize_t m_bitdepth) : void
-+Frame(std::byte * fp, ssize_t rows, ssize_t cols, ssize_t m_bitdepth) : void
-+Frame(Frame && other) : void
-+Frame(const Frame & other) : void
-+~Frame() : void
-..
-+operator=(Frame & other) : Frame &
-..
-+bitdepth() const : ssize_t
-+cols() const : ssize_t
-+data() const : std::byte *
-+get(int row, int col) : std::byte *
-+image<T>() : NDArray<T>
-+rows() const : ssize_t
-+set<T>(int row, int col, T data) : void
-+size() const : ssize_t
-+view<T>() : NDView<T>
-__
--m_bitdepth : ssize_t
--m_cols : ssize_t
--m_data : std::byte *
--m_rows : ssize_t
-}
-class "aare::ZmqHeader" as C_0000690012646166089557
-class C_0000690012646166089557 {
-+operator==(const ZmqHeader & other) const : bool
-..
-+from_string(std::string & s) : void
-+to_string() const : std::string
-__
-+acqIndex : uint64_t
-+addJsonHeader : std::map<std::string,std::string>
-+column : uint16_t
-+completeImage : bool
-+data : bool
-+detSpec1 : uint64_t
-+detSpec2 : uint16_t
-+detSpec3 : uint32_t
-+detSpec4 : uint16_t
-+detType : uint8_t
-+dynamicRange : uint32_t
-+expLength : uint32_t
-+fileIndex : uint64_t
-+flipRows : int
-+fname : std::string
-+frameIndex : uint64_t
-+frameNumber : uint64_t
-+imageSize : uint32_t
-+jsonversion : uint32_t
-+modId : uint16_t
-+ndetx : uint32_t
-+ndety : uint32_t
-+npixelsx : uint32_t
-+npixelsy : uint32_t
-+packetNumber : uint32_t
-+progress : double
-+quad : uint32_t
-+row : uint16_t
-+rx_roi : std::array<int,4>
-+timestamp : uint64_t
-+version : uint8_t
-}
-class "aare::ZmqSocket" as C_0000575290120620432482
-class C_0000575290120620432482 {
-+ZmqSocket() = default : void
-+ZmqSocket(const ZmqSocket &) = deleted : void
-+ZmqSocket(ZmqSocket &&) = deleted : void
-+~ZmqSocket() : void
-..
-+operator=(const ZmqSocket &) = deleted : ZmqSocket
-..
-+disconnect() : void
-+set_potential_frame_size(size_t size) : void
-+set_timeout_ms(int n) : void
-+set_zmq_hwm(int hwm) : void
-__
-#m_context : void *
-#m_endpoint : std::string
-#m_header_buffer : char *
-{static} #m_max_header_size : const size_t
-#m_potential_frame_size : size_t
-#m_socket : void *
-#m_timeout_ms : int
-#m_zmq_hwm : int
-}
-class "aare::ZmqFrame" as C_0001018278375791869829
-class C_0001018278375791869829 {
-__
-+frame : Frame
-+header : ZmqHeader
-}
-class "aare::network_io::NetworkError" as C_0001290043041844945927
-class C_0001290043041844945927 {
-+NetworkError(const char * msg) : void
-+NetworkError(const std::string msg) : void
-..
-+what() const noexcept : const char *
-__
--m_msg : const char *
-}
-class "aare::ZmqSocketReceiver" as C_0001017868003595712218
-class C_0001017868003595712218 {
-+ZmqSocketReceiver(const std::string & endpoint) : void
-..
-+connect() : void
--receive_data(std::byte * data, size_t size) : int
--receive_header() : ZmqHeader
-+receive_n() : std::vector<ZmqFrame>
--receive_zmqframe() : ZmqFrame
-__
-}
-class "aare::ZmqSocketSender" as C_0002178845803227443176
-class C_0002178845803227443176 {
-+ZmqSocketSender(const std::string & endpoint) : void
-..
-+bind() : void
-+send(const ZmqHeader & header, const std::byte * data, size_t size) : size_t
-+send(const ZmqFrame & zmq_frame) : size_t
-+send(const std::vector<ZmqFrame> & zmq_frames) : size_t
-__
-}
-C_0001018278375791869829 o-- C_0000690012646166089557 : +header
-C_0001018278375791869829 o-- C_0001608703618093824988 : +frame
-C_0001017868003595712218 ..> C_0001018278375791869829
-C_0001017868003595712218 ..> C_0000690012646166089557
-C_0000575290120620432482 <|-- C_0001017868003595712218
-C_0002178845803227443176 ..> C_0000690012646166089557
-C_0002178845803227443176 ..> C_0001018278375791869829
-C_0000575290120620432482 <|-- C_0002178845803227443176
-
-'Generated with clang-uml, version 0.5.1
-'LLVM version clang version 17.0.6 (Fedora 17.0.6-2.fc39)
-@enduml