Holoflow

Ultra high throughput image processing for laser doppler holography applied to retinal imaging.

Features

TODO

Project layout

holoflow
|   .clang-format
|   CMakeLists.txt
|   CMakePresets.json
|
+---bench/
|   |   CMakeLists.txt
|   +---curaii/      CMakeLists.txt  ...
|   +---holofile/    CMakeLists.txt  ...
|   +---holoflow/    CMakeLists.txt  ...
|   \---holovibes/   CMakeLists.txt  ...
|
+---cmake/
|       ProjectOptions.cmake
|
+---doc/
|       CMakeLists.txt
|
+---external/
|       CMakeLists.txt
|
+---src/
|   |   CMakeLists.txt
|   +---curaii/
|   |   |   CMakeLists.txt
|   |   +---include/curaii/*.hh
|   |   \---src/*.cc *.cu
|   +---holofile/
|   |   |   CMakeLists.txt
|   |   +---include/holofile/*.hh
|   |   \---src/*.cc
|   +---holoflow/
|   |   |   CMakeLists.txt
|   |   +---include/holoflow/*.hh
|   |   \---src/*.cc *.cu
|   \---holovibes/
|       |   CMakeLists.txt
|       \---src/
|           main.cc  ...
|
\---test/
    |   CMakeLists.txt
    +---curaii/      CMakeLists.txt  ...
    +---holofile/    CMakeLists.txt  ...
    +---holoflow/    CMakeLists.txt  ...
    \---holovibes/   CMakeLists.txt  ...

Prerequisites

• Windows 10/11 x64
• MSVC (Visual Studio Build Tools 2022) and SDK
• CMake >= 3.24 usually comes with VS
• Ninja (Multi-Config) usually comes with VS
• CUDA Toolkit (13.0+ recommended)
• x64 Native Tools Command Prompt (for running all commands)
• Python >= 3.10
• Git
• Qt >= 6.5 with Qt Graphs package enabled during a custom installation. Set Qt6_DIR env var to your Qt installation path, e.g. C:\Qt\6.5.2\msvc2019_64\lib\cmake\Qt6, add C:\Qt\6.5.2\msvc2019_64\bin to your PATH
• Intel oneAPI Base Toolkit add C:\Program Files (x86)\Intel\oneAPI\mkl\latest\bin and C:\Program Files (x86)\Intel\oneAPI\compiler\latest\bin to your PATH
• Node.js (both node and npm in your PATH)
• quicktype install via npm install -g quicktype

Python dependencies

The python dependencies are listed in requirements.txt. The recommended way to set up the Python environment is by using a virtual environment. You can create and activate a virtual environment using the following commands:

# Create a virtual environment
python -m venv .venv

# Activate the virtual environment
.\.venv\Scripts\activate.bat

After activating the virtual environment, you can install the required Python packages using:

pip install -r requirements.txt

Configure

Ninja Multi-Config is used. One configure step, many build configs.

cmake --preset msvc-multi

Common cache variables

• PROJECT_CUDA_ARCHS (string list, default 75;86;89;90)
• ENABLE_TESTING (ON/OFF)
• ENABLE_BENCHMARKS (ON/OFF)
• ENABLE_DOCUMENTATION (ON/OFF)
• ENABLE_FETCHCONTENT (ON/OFF)
• ENABLE_WARNINGS (ON/OFF)
• ENABLE_WARNINGS_AS_ERRORS (ON/OFF)
• ENABLE_IPO (ON/OFF)

Set at configure time:

cmake --preset msvc-multi -DPROJECT_CUDA_ARCHS="86;89" -DENABLE_DOCUMENTATION=ON

Build

cmake --build --preset build-Debug   -j
cmake --build --preset build-Release -j

Artifacts appear under build/msvc-multi/.

Run

The main application is holovibes.

# Example
build\msvc-multi\Release\holovibes.exe --help

Test

The individual tests can be run from cmd:

build\msvc-multi\Debug\holoflow_test.exe

Package

This project uses CMake, CPack, and the NSIS installer generator to produce a Windows installer (.exe) that contains the compiled application and all required Qt runtime libraries.

Prerequisites

Before packaging, make sure these following tools are installed :

• NSIS

Command

To generate the installer, run:

cmake --build --preset build-Release --target package -j

It will generate the installer inside the build\msvc-multi\ folder.

Benchmarks

TODO

Documentation

This project’s documentation is built using MkDocs and organized into a structured set of Markdown (.md) files.

Link to the documentation.

Build and Run

Before building or serving the documentation, ensure that all required Python dependencies are installed. If not, you can refer to the Python dependencies section of the README.

Make sure you are working inside the project’s virtual environment. If it is not already activated, you can activate it with:

.\.env\Scripts\activate

Navigate to the documentation directory, which contains the mkdocs.yml configuration file:

cd doc\mkdocs

You must run all MkDocs commands from the directory where the mkdocs.yml file is located.

You can now start the MkDocs development server:

mkdocs serve

This command will launch a local web server where you can preview the documentation during development.

Generate JSON schema

The JSON schemas are generated using the json-schema-for-humans dependency. They are used to display the settings associated of each node.

To generate a new schema, you must first create the corresponding xxx_settings.json file inside the src/holovibes/schemas/tasks/ directory.

Once the file is created, run the following command:

generate-schema-doc src\holovibes\schemas\tasks\node_type\xxx_settings.json doc\mkdocs\docs\schemas\node_type\xxx_settings.md --config template_name=md

You must run this command in Python Virtual Environment

Dependency management

• FetchContent: enabled by ENABLE_FETCHCONTENT=ON. Dependencies declared in external/CMakeLists.txt.

Git

This project uses Git for version control. Make sure to have Git installed and configured on your system. This project follows the Conventional Commits specification. This project comes with pre-commit hooks to enforce coding standards. You can enable these hooks by running:

pre-commit install

License

This project is licensed under the Apache License 2.0. See LICENSE for details.