Cpp multi example (#84)

- Small modifications to the ProducerConsumerQueue to allow for storage
in a vector
- Example showing multi threading in C++ using queues
- fixes for python bindings

---------

Co-authored-by: Bechir <bechir.brahem420@gmail.com>
Co-authored-by: Bechir Braham <bachbrahem@gmail.com>

.clang-format

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

.clang-tidy

@@ -1,35 +1,50 @@
-
 ---
-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-*'
+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
+HeaderFilterRegex: '*.hpp'
+ImplementationFileExtensions: [cpp]
+AnalyzeTemporaryDtors: false
+WarningsAsErrors: '*,
+-bugprone-implicit-widening-of-multiplication-result'
 FormatStyle:     none
 CheckOptions:
   - { key: readability-identifier-naming.NamespaceCase,       value: lower_case }

.clang-uml

@@ -0,0 +1,103 @@
+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

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

.gitattributes

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

.gitea/workflows/cmake_build.yml

@@ -1,58 +0,0 @@
-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

@@ -1,36 +0,0 @@
-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

@@ -1,31 +0,0 @@
-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

@@ -1,42 +0,0 @@
-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

@@ -1,41 +0,0 @@
-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

@@ -1,69 +0,0 @@
-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

@@ -1,64 +0,0 @@
-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

@@ -0,0 +1,98 @@
+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

@@ -0,0 +1,33 @@
+# 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

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

.ipynb_checkpoints/Untitled-checkpoint.ipynb

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

CMakeLists.txt

@@ -1,32 +1,17 @@
-cmake_minimum_required(VERSION 3.15)
+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)
 
 project(aare 
+    VERSION 0.1
     DESCRIPTION "Data processing library for PSI detectors"
     HOMEPAGE_URL "https://github.com/slsdetectorgroup/aare"
     LANGUAGES C CXX 
 )
 
-# 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 CMP0135 NEW)
 cmake_policy(SET CMP0079 NEW)
 
 include(GNUInstallDirs)
@@ -34,37 +19,23 @@ 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}")
 
-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_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)
 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_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(AARE_FETCH_LMFIT "Use FetchContent to download lmfit" ON)
+option(ENABLE_DRAFTS "Enable zmq drafts (depends on gnutls or nss)" OFF)
 
 
-#Convenience option to use system libraries only (no FetchContent)
+#Convenience option to use system libraries
 option(AARE_SYSTEM_LIBRARIES "Use system libraries" OFF)
 if(AARE_SYSTEM_LIBRARIES)
     message(STATUS "Build using system libraries")
@@ -73,100 +44,19 @@ 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::logERROR)
 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_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 ${ZMQ_PATCH_COMMAND}
-        UPDATE_DISCONNECTED 1
     )
-    # Disable unwanted options from libzmq
-    set(BUILD_TESTS OFF CACHE BOOL "Switch off libzmq test build")
-    set(BUILD_SHARED OFF CACHE BOOL "Switch off libzmq shared libs")
-    set(WITH_PERF_TOOL OFF CACHE BOOL "")
-    set(ENABLE_CPACK OFF CACHE BOOL "")
-    set(ENABLE_CLANG OFF CACHE BOOL "")
-    set(ENABLE_CURVE OFF CACHE BOOL "")
-    set(ENABLE_DRAFTS OFF CACHE BOOL "")
-
     # TODO! Verify that this is what we want to do in aare
     # Using GetProperties and Populate to be able to exclude zmq
     # from install (not possible with FetchContent_MakeAvailable(libzmq))
@@ -175,6 +65,7 @@ if(AARE_FETCH_ZMQ)
         FetchContent_Populate(libzmq)
         add_subdirectory(${libzmq_SOURCE_DIR} ${libzmq_BINARY_DIR} EXCLUDE_FROM_ALL)
     endif()
+
 else()
     find_package(ZeroMQ 4 REQUIRED)
 endif()
@@ -189,71 +80,16 @@ 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 #
 #################
@@ -295,208 +131,94 @@ 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
+    )
+
+    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()
 
-# 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(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()
+
+
+
+
+
 
 if(AARE_TESTS)
     enable_testing()
     add_subdirectory(tests)
-    target_compile_definitions(tests PRIVATE AARE_TESTS)
 endif()
 
-###------------------------------------------------------------------------------MAIN LIBRARY
-###------------------------------------------------------------------------------------------
+add_subdirectory(src)
 
-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/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/DetectorGeometry.hpp
-    include/aare/JungfrauDataFile.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
+
+#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(SourceFiles
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/CtbRawFile.cpp
-    ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.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/DetectorGeometry.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
-)
-
-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_TESTS)
-    target_compile_definitions(aare_core PRIVATE AARE_TESTS)
-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/decode.test.cpp
-            ${CMAKE_CURRENT_SOURCE_DIR}/src/Dtype.test.cpp
-            ${CMAKE_CURRENT_SOURCE_DIR}/src/Frame.test.cpp
-            ${CMAKE_CURRENT_SOURCE_DIR}/src/DetectorGeometry.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
-
-        )
-    target_sources(tests PRIVATE ${TestSources} )
-endif()
+add_subdirectory(examples)
 
 
 
-###------------------------------------------------------------------------------------------
-###------------------------------------------------------------------------------------------
-
-
-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(
@@ -525,14 +247,9 @@ 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

@@ -0,0 +1,17 @@
+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

@@ -0,0 +1,688 @@
+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
+make it effectively proprietary.  To prevent this, the GPL assures that
+patents cannot be used to render the program non-free.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                       TERMS AND CONDITIONS
+
+  0. Definitions.
+
+  "This License" refers to version 3 of the GNU General Public License.
+
+  "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
+  "The Program" refers to any copyrightable work licensed under this
+License.  Each licensee is addressed as "you".  "Licensees" and
+"recipients" may be individuals or organizations.
+
+  To "modify" a work means to copy from or adapt all or part of the work
+in a fashion requiring copyright permission, other than the making of an
+exact copy.  The resulting work is called a "modified version" of the
+earlier work or a work "based on" the earlier work.
+
+  A "covered work" means either the unmodified Program or a work based
+on the Program.
+
+  To "propagate" a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for
+infringement under applicable copyright law, except executing it on a
+computer or modifying a private copy.  Propagation includes copying,
+distribution (with or without modification), making available to the
+public, and in some countries other activities as well.
+
+  To "convey" a work means any kind of propagation that enables other
+parties to make or receive copies.  Mere interaction with a user through
+a computer network, with no transfer of a copy, is not conveying.
+
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+  "Additional permissions" are terms that supplement the terms of this
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+Additional permissions that are applicable to the entire Program shall
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+
+  Nothing in this License shall be construed as excluding or limiting
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+  12. No Surrender of Others' Freedom.
+
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+  13. Use with the GNU Affero General Public License.
+
+  Notwithstanding any other provision of this License, you have
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+  14. Revised Versions of this License.
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+  If the Program specifies that a proxy can decide which future
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+  17. Interpretation of Sections 15 and 16.
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+  If the disclaimer of warranty and limitation of liability provided
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+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
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+free software which everyone can redistribute and change under these terms.
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+  To do so, attach the following notices to the program.  It is safest
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+    <one line to give the program's name and a brief idea of what it does.>
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+
+    This program is distributed in the hope that it will be useful,
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+Also add information on how to contact you by electronic and paper mail.
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+    <program>  Copyright (C) <year>  <name of author>
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+
+The hypothetical commands `show w' and `show c' should show the appropriate
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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
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+may consider it more useful to permit linking proprietary applications with
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+Public License instead of this License.  But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.

LICENSES/LGPL-3.0

@@ -0,0 +1,179 @@
+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:
+    SPDX-License-Identifier: LGPL-3.0
+  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.
+
+
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LICENSES/Third Party/Apache-2.0

@@ -0,0 +1,210 @@
+Valid-License-Identifier: Apache-2.0
+SPDX-URL: https://spdx.org/licenses/Apache-2.0.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.
+    SPDX-License-Identifier: Apache-2.0
+License-Text:
+
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README.md

@@ -2,70 +2,76 @@
 Data analysis library for PSI hybrid detectors
 
 
-## Build and install
 
-Prerequisites
-- cmake >= 3.14
-- C++17 compiler (gcc >= 8)
-- python >= 3.10
 
-### Development install (for Python)
+## 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**
 
 ```bash
-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 
+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
 ```
 
-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')
+**2. Launch the slsReceiver**
+```bash
+bin/slsReceiver
 ```
 
-To run form other folders either add the path to your conda environment using conda-build or add it to your PYTHONPATH
+**3. Launch the virtual server**
+```bash
+bin/jungfrauDetectorServer_virtual
+```
 
-
-### Install using conda/mamba
+**4 Configure the detector simulator**
 
 ```bash
-#enable your env first!
-conda install aare=2024.10.29.dev0 -c slsdetectorgroup
+#sample config file is in etc/ in the aare repo
+sls_detector_put config etc/virtual_jf.config
+
+#Now you can take images using sls_detector_acquire
+sls_detector_acquire
 ```
 
-### Install to a custom location and use in your project
-
-Working example in: https://github.com/slsdetectorgroup/aare-examples
-
+**5. Run the zmq example**
 ```bash
-#build and install aare 
-git clone git@github.com:slsdetectorgroup/aare.git --branch=v1 #or using http...
-mkdir build
-cd build
+examples/zmq_example
 
-#configure using cmake
-cmake ../aare -DCMAKE_INSTALL_PREFIX=/where/to/put/aare
+#Will print the headers fof the frames received
 
-#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
 ```
 
-### Local build of conda pkgs
 
+## Test the zmq processing replaying data
+
+To be implemented
+
+## generate documentation
 ```bash
-conda build . --variants="{python: [3.11, 3.12, 3.13]}"
+# for doxygen documentation
+doxygen .doxygen.config 
+
+# for automatically generated plant uml diagrams
+clang-uml
+
+
+
+
+
 ```

RELEASE.md

@@ -1,22 +0,0 @@
-# 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

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

aare-environment.yml

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

benchmarks/CMakeLists.txt

@@ -1,27 +0,0 @@
-
-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

@@ -1,70 +0,0 @@
-#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

@@ -1,132 +0,0 @@
-#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

@@ -0,0 +1 @@
+

cmake/FindSphinx.cmake

@@ -1,11 +0,0 @@
-#Look for an executable called sphinx-build
-find_program(SPHINX_EXECUTABLE
-             NAMES sphinx-build sphinx-build-3.6
-             DOC "Path to sphinx-build executable")
- 
-include(FindPackageHandleStandardArgs)
- 
-#Handle standard arguments to find_package like REQUIRED and QUIET
-find_package_handle_standard_args(Sphinx
-                                  "Failed to find sphinx-build executable"
-                                  SPHINX_EXECUTABLE)

cmake/helpers.cmake

@@ -4,43 +4,3 @@ 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

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

cmake/project-config.cmake.in

@@ -1,28 +0,0 @@
-# Config file for @PROJECT_NAME_LOWER@
-#
-# It defines the following variables:
-#
-# @PROJECT_NAME_UPPER@_INCLUDE_DIRS     - include directory
-# @PROJECT_NAME_UPPER@_LIBRARIES        - all dynamic libraries
-# @PROJECT_NAME_UPPER@_STATIC_LIBRARIES - all static libraries
-
-@PACKAGE_INIT@
-
-include(CMakeFindDependencyMacro)
-
-set(SLS_USE_HDF5 "@SLS_USE_HDF5@")
-
-# 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

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

conda-recipe/meta.yaml

@@ -1,50 +0,0 @@
-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

@@ -0,0 +1,53 @@
+{
+    "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

@@ -0,0 +1,53 @@
+{
+    "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

@@ -0,0 +1,47 @@
+{
+    "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

@@ -0,0 +1,47 @@
+{
+    "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

@@ -0,0 +1,50 @@
+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

@@ -0,0 +1,87 @@
+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

@@ -0,0 +1,40 @@
+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

@@ -0,0 +1,40 @@
+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

@@ -0,0 +1,58 @@
+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

@@ -0,0 +1,55 @@
+{
+    "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

@@ -0,0 +1,57 @@
+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

@@ -0,0 +1,40 @@
+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

@@ -0,0 +1,12 @@
+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

@@ -0,0 +1,62 @@
+###
+### 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

@@ -1,56 +0,0 @@
-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

@@ -0,0 +1,8 @@
+# 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

@@ -1,63 +0,0 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
-# http://www.sphinx-doc.org/en/master/config
-
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-import os
-import sys
-sys.path.insert(0, os.path.abspath('..'))
-
-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

@@ -0,0 +1,141 @@
+@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

@@ -0,0 +1,95 @@
+@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

@@ -0,0 +1,267 @@
+@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

@@ -0,0 +1,200 @@
+@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

@@ -0,0 +1,136 @@
+@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