Create cmake-multi-platform.yml

.github/workflows/cmake-multi-platform.yml

@@ -0,0 +1,77 @@
+# This starter workflow is for a CMake project running on multiple platforms. There is a different starter workflow if you just want a single platform.
+# See: https://github.com/actions/starter-workflows/blob/main/ci/cmake-single-platform.yml
+name: CMake on multiple platforms
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      # Set fail-fast to false to ensure that feedback is delivered for all matrix combinations. Consider changing this to true when your workflow is stable.
+      fail-fast: false
+
+      # Set up a matrix to run the following 3 configurations:
+      # 1. <Windows, Release, latest MSVC compiler toolchain on the default runner image, default generator>
+      # 2. <Linux, Release, latest GCC compiler toolchain on the default runner image, default generator>
+      # 3. <Linux, Release, latest Clang compiler toolchain on the default runner image, default generator>
+      #
+      # To add more build types (Release, Debug, RelWithDebInfo, etc.) customize the build_type list.
+      matrix:
+        os: [ubuntu-latest]
+        build_type: [Release]
+        c_compiler: [gcc, clang]
+        include:
+          - os: ubuntu-latest
+            c_compiler: gcc
+            cpp_compiler: g++
+            # define the standard C++ version to use
+            env:
+              CXX_STANDARD: 20
+          - os: ubuntu-latest
+            c_compiler: clang
+            cpp_compiler: clang++
+            # define the standard C++ version to use
+            env:
+              CXX_STANDARD: 20
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set reusable strings
+      # Turn repeated input strings (such as the build output directory) into step outputs. These step outputs can be used throughout the workflow file.
+      id: strings
+      shell: bash
+      run: |
+        echo "build-output-dir=${{ github.workspace }}/build" >> "$GITHUB_OUTPUT"
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get -y install libxrandr-dev libhdf5-serial-dev libxinerama-dev libxcursor-dev libxi-dev libgl1-mesa-dev
+
+
+    - name: Configure CMake
+      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
+      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
+      run: >
+        cmake -B ${{ steps.strings.outputs.build-output-dir }}
+        -DCMAKE_CXX_COMPILER=${{ matrix.cpp_compiler }}
+        -DCMAKE_C_COMPILER=${{ matrix.c_compiler }}
+        -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}
+        -S ${{ github.workspace }}
+
+    - name: Build
+      # Build your program with the given configuration. Note that --config is needed because the default Windows generator is a multi-config generator (Visual Studio generator).
+      run: cmake --build ${{ steps.strings.outputs.build-output-dir }} --config ${{ matrix.build_type }}
+
+    - name: Test
+      working-directory: ${{ steps.strings.outputs.build-output-dir }}
+      # Execute tests defined by the CMake configuration. Note that --build-config is needed because the default Windows generator is a multi-config generator (Visual Studio generator).
+      # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
+      run: ctest --build-config ${{ matrix.build_type }}

.github/workflows/deploy-documentation.yml

@@ -0,0 +1,64 @@
+# Sample workflow for building and deploying a VitePress site to GitHub Pages
+#
+name: Deploy VitePress site to Pages
+
+on:
+  # Runs on pushes targeting the `main` branch. Change this to `master` if you're
+  # using the `master` branch as the default branch.
+  push:
+    branches: [main]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: pages
+  cancel-in-progress: false
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # Not needed if lastUpdated is not enabled
+      # - uses: pnpm/action-setup@v3 # Uncomment this if you're using pnpm
+      # - uses: oven-sh/setup-bun@v1 # Uncomment this if you're using Bun
+      - name: Setup Node
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+          cache: npm # or pnpm / yarn
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+      - name: Install dependencies
+        run: npm ci # or pnpm install / yarn install / bun install
+      - name: Build with VitePress
+        run: npm run docs:build # or pnpm docs:build / yarn docs:build / bun run docs:build
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/.vitepress/dist
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    needs: build
+    runs-on: ubuntu-latest
+    name: Deploy
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

CMakeLists.txt

@@ -7,16 +7,15 @@ project(opensaft
 	LANGUAGES CXX)
 
 set(CMAKE_CXX_STANDARD 20)
-set(CMAKE_CXX_STANDARD_REQUIRED true)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
 
 if (NOT CMAKE_BUILD_TYPE)
 	set(CMAKE_BUILD_TYPE RelWithDebInfo)
 endif()
-message(STATUS "CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE}")
-
 
 option(OPENSAFT_CUDA_SUPPORT "Enable CUDA support" OFF)
 option(OPENSAFT_TESTING "Build unit tests" ON)
+option(OPENSAFT_GUI "build graphical user interface alongside" OFF)
 
 # prepare for cuda compilation
 if (OPENSAFT_CUDA_SUPPORT)
@@ -37,55 +36,71 @@ set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS}; -x cu -rdc=true -ftz=false -prec-div=tru
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/modules/")
 
 # find dependencies (most of them are handled through FetchContent)
-find_package(ImGUI REQUIRED)
-find_package(glfw3 REQUIRED)
-find_package(OpenGL REQUIRED)
-find_package(SDL2 REQUIRED)
 find_library(H5CPP_LIB hdf5_cpp)
 find_library(H5_LIB hdf5) # todo this sounds fishy that
-find_package(ImPlot REQUIRED)
-find_package(ImGUIFileDialog REQUIRED)
-find_package(CVolume REQUIRED)
-find_package(Backward REQUIRED)
 
 # main library holding the backbone of the application
 add_library(opensaft STATIC "")
 
 add_subdirectory(src/)
 
 target_link_libraries(opensaft PUBLIC
-	${ImGUI_LIBRARIES}
-	${implot_LIBRARIES}
-	${GLFW_LIBRARIES}
-	${cvolume_LIBRARIES}
-	${ImGUIFileDialog_LIBRARIES}
-	${backward_LIBRARIES}
 )
 
 target_include_directories(opensaft PUBLIC
 	${CMAKE_SOURCE_DIR}/src
-	${ImGUI_INCLUDE_DIR}
-	${ImPlot_INCLUDE_DIR}
-	${ImGUIFileDialog_INCLUDE_DIR}
-	${OPENGL_INCLUDE_DIRS}
-	${GLFW3_INCLUDE_DIR}
-	${cvolume_INCLUDE_DIR}
-	${backward_INCLUDE_DIR}
 )
 
+if (OPENSAFT_GUI)
+
+	add_library(opensaft-gui)
+
+	find_package(ImGUI REQUIRED)
+	find_package(GLFW REQUIRED)
+	find_package(OpenGL REQUIRED)
+	find_package(ImPlot REQUIRED)
+	find_package(ImGUIFileDialog REQUIRED)
+	find_package(Backward REQUIRED)
+
+
+	target_link_libraries(opensaft-gui PUBLIC
+		${ImGUI_LIBRARIES}
+		${implot_LIBRARIES}
+		${GLFW_LIBRARIES}
+		${cvolume_LIBRARIES}
+		${ImGUIFileDialog_LIBRARIES}
+		${backward_LIBRARIES}
+	)
+
+	target_include_directories(opensaft PUBLIC
+		${CMAKE_SOURCE_DIR}/src
+		${ImGUI_INCLUDE_DIR}
+		${ImPlot_INCLUDE_DIR}
+		${ImGUIFileDialog_INCLUDE_DIR}
+		${OPENGL_INCLUDE_DIRS}
+		${GLFW3_INCLUDE_DIR}
+		${cvolume_INCLUDE_DIR}
+		${backward_INCLUDE_DIR}
+	)
+
+
+	# add an executable for the main graphical user interface
+	add_executable(OpensaftGui src/main.cpp)
+	if (OPENSAFT_CUDA_SUPPORT)
+		set_property(TARGET OpensaftGui PROPERTY CUDA_SEPARABLE_COMPILATION ON)
+		set_property(TARGET OpensaftGui PROPERTY CUDA_ARCHITECTURES 50 75 86)
+	endif()
+	target_link_libraries(OpensaftGui PUBLIC opensaft-gui)
+
+	install(TARGETS OpensaftGui DESTINATION bin)
+
+endif (OPENSAFT_GUI)
+
 
 find_library(TERM_LIB curses)
 
 if (OPENSAFT_TESTING)
 	add_subdirectory(tests)
 endif()
 
-# add an executable for the main graphical user interface
-add_executable(main_exp src/main.cpp)
-if (OPENSAFT_CUDA_SUPPORT)
-	set_property(TARGET main_exp PROPERTY CUDA_SEPARABLE_COMPILATION ON)
-	set_property(TARGET main_exp PROPERTY CUDA_ARCHITECTURES 50 75 86)
-endif()
-target_link_libraries(main_exp PUBLIC opensaft)
 
-install(TARGETS main_exp DESTINATION bin)

README.md

@@ -1,5 +1,9 @@
 # opensaft
 
+::: warning
+This project is currently under development and not yet ready for use. Please check back later.
+:::
+
 Volumetric synthetic aperture focusing technique (SAFT) for acoustic resolution optoacoustic microscopy and (soon) scanning acoustic microscopy.
 
 This repository contains an implementation of the synthetic aperture focsuing technique purely written in C++ and CUDA. You need a CUDA capable device and Linux installed on your PC to run the fast GPU version of it. A "slow" CPU version is implemented as well. Installation instructions will soon be provided for ArchLinux as well as dataset specifications.
@@ -21,17 +25,18 @@ Required packages:
 - a capable C++ compiler which can be consumed by `CMake`
 - `CUDA` for GPU acceleration (can be disabled, not required)
 - `hdf5` for dataset import and export
+- `libxrandr`, `libxinerama`, `libxcursor`, `libxi`, `libgl1-mesa-dev`: used for GUI framework
 
 Package installation command ArchLinux:
 
 ```bash
-pacman -S hdf5
+pacman -S hdf5 libxrandr libxinerama
 ```
 
 Package installation command Ubuntu:
 
 ```bash
-apt-get install libhdf5-serial-dev
+apt-get install libhdf5-serial-dev libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libgl1-mesa-dev
 ```
 
 Many other dependencies are directly managed through CMake based on `FetchContent`.
@@ -62,12 +67,26 @@ SAFT induces a strong absorption bias over depth. Absorbance "reconstructed" at
 
 The documentation should be running with `vitepress` and is compiled into a static website that is also published to github pages. All documentation is written in markdown and can be found in the doc folder.
 
-To run the documentation locally, run the following commands:
+If this is the first time that you have a look at the documentation, you need to run
+
+```bash
+npm install
+```
+
+Afterwards, to display the documentation run
 
 ```bash
 npm run docs:dev
 ```
 
+To build the static website, run
+
+```bash
+npm run docs:build
+```
+
+The documentation is published on every merge to `main` to [github pages](https://hofmannu.github.io/opensaft/).
+
 ## Literature
 
 - J. Turner et al.: Improved optoacoustic microscopy through three-dimensional spatial impulse response synthetic aperture focusing technique in Optics Letters 39 (12), pp. 3390 - 3393 (2014), [10.1364/OL.39.003390](https://doi.org/10.1364/OL.39.003390)

cmake/modules/FindBackward.cmake

@@ -1,13 +1,14 @@
 include(FetchContent)
 
-FetchContent_Declare(backward
-    GIT_REPOSITORY https://github.com/bombela/backward-cpp
-    GIT_TAG master  # or a version tag, such as v1.6
-    SYSTEM          # optional, the Backward include directory will be treated as system directory
+FetchContent_Declare(
+  backward
+  GIT_REPOSITORY https://github.com/bombela/backward-cpp
+  GIT_TAG master  # or a version tag, such as v1.6
+  SYSTEM          # optional, the Backward include directory will be treated as system directory
 )
 
 FetchContent_GetProperties(backward)
-if(NOT backward_POPULATED)
+if (NOT backward_POPULATED)
   FetchContent_Populate(backward)
   add_subdirectory(${backward_SOURCE_DIR} ${backward_BINARY_DIR})
 endif()

cmake/modules/FindCatch2.cmake

@@ -9,7 +9,7 @@ FetchContent_Declare(
 )
 
 FetchContent_GetProperties(catch2)
-if(NOT catch2_POPULATED)
+if (NOT catch2_POPULATED)
   FetchContent_Populate(catch2)
   add_subdirectory(${catch2_SOURCE_DIR} ${catch2_BINARY_DIR})
 endif()

cmake/modules/FindImGUI.cmake

@@ -45,7 +45,7 @@ if (NOT imgui_POPULATED)
 	# glfw3_LIBRARIES is empty
 	target_link_libraries(ImGUI_target
 	PRIVATE
-		${glfw3_LIBRARIES}
+		${glfw_LIBRARIES}
 		${OPENGL_LIBRARIES}
 	)