Implement WsiAnnotations in C++

.clang-format

@@ -1,4 +1,6 @@
 ---
+BasedOnStyle: Google
+IndentWidth: 2
 Language: Cpp
 ColumnLimit: 120
 AccessModifierOffset: -4
@@ -69,7 +71,6 @@ IncludeCategories:
 IncludeIsMainRegex: '(Test)?$'
 IndentCaseLabels: false
 IndentPPDirectives: None
-IndentWidth: 4
 IndentWrappedFunctionNames: false
 JavaScriptQuotes: Leave
 JavaScriptWrapImports: true

.github/workflows/codecov.yml

@@ -8,16 +8,22 @@ on:
 jobs:
  build:
  runs-on: ubuntu-latest
- env:
- CODECOV_CI: true
  steps:
  - name: Install build dependencies
  run: |
  sudo apt update
  sudo apt install -y meson libgl1-mesa-glx libcairo2-dev libgdk-pixbuf2.0-dev libglib2.0-dev libjpeg-dev libpng-dev libtiff5-dev libxml2-dev libopenjp2-7-dev libsqlite3-dev zlib1g-dev libzstd-dev
- sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev ninja-build
+ sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev ninja-build libboost-all-dev libopencv-dev
+ - name: Install Rust for pyhaloxml
+ run: |
+ curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+ echo "Rust and Cargo installed in:"
+ echo $HOME/.cargo/bin
+ ls $HOME/.cargo/bin
+ export PATH="$HOME/.cargo/bin:$PATH"
  - name: Build and install OpenSlide
  run: |
+ export PATH="$HOME/.cargo/bin:$PATH"
  git clone https:/openslide/openslide.git
  cd openslide
  meson setup builddir
@@ -26,6 +32,7 @@ jobs:
  cd ..
  - name: Build and install libvips
  run: |
+ export PATH="$HOME/.cargo/bin:$PATH"
  git clone https:/libvips/libvips.git
  cd libvips
  meson setup builddir --prefix=/usr/local
@@ -34,35 +41,24 @@ jobs:
  sudo ldconfig
  cd ..
  - uses: actions/checkout@v4
- - name: Set up Python 3.10
+ - name: Set up Python 3.11
  uses: actions/setup-python@v5
  with:
- python-version: "3.10"
- - name: Clean up any existing installations
- run: |
- sudo rm -rf /usr/local/lib/python3.10/site-packages/dlup*
- sudo rm -rf /opt/hostedtoolcache/Python/3.10.14/arm64/lib/python3.10/site-packages/dlup*
- sudo rm -rf /opt/hostedtoolcache/Python/3.10.14/arm64/lib/python3.10/site-packages/_dlup_editable_loader.py
- sudo rm -rf /opt/hostedtoolcache/Python/3.10.14/arm64/lib/python3.10/site-packages/easy-install.pth
- sudo rm -rf dlup/build
- sudo rm -rf /tmp/*
+ python-version: "3.11"
  - name: Install environment
  run: |
+ export PATH="$HOME/.cargo/bin:$PATH"
  python -m pip install --upgrade pip
  python -m pip install ninja meson meson-python>=0.15.0 numpy==1.26.4 Cython>=0.29 spin pybind11
- python -m pip install tifffile>=2024.7.2 pyvips>=2.2.3 tqdm>=2.66.4 pillow>=10.3.0 openslide-python>=1.3.1
- python -m pip install opencv-python-headless>=4.9.0.80 shapely>=2.0.4 pybind11>=2.8.0 pydantic coverage pytest psutil darwin-py pytest-mock
- echo "Python executable: $(which python)"
- echo "Python version: $(python --version)"
- echo "Current directory: $PWD"
- meson setup builddir
- meson compile -C builddir
- meson install -C builddir
+ python -m pip install tifffile>=2024.7.2 pyvips>=2.2.3 tqdm>=2.66.4 pillow>=10.3.0 openslide-python>=1.3.1 spin
+ python -m pip install opencv-python-headless>=4.9.0.80 shapely>=2.0.4 pybind11>=2.8.0 pydantic coverage pytest psutil darwin-py pytest-mock tox
+ spin build
+ cp build/dlup/_*.so dlup/
+ cp build/src/_*.so dlup/
+ python -m pip install .
  - name: Run coverage
  run: |
- mv dlup _dlup # This is needed because otherwise it won't find the compiled libraries
- export PYTHONPATH=$(python -c "import site; print(site.getsitepackages()[0])")
- coverage run -m pytest
+ coverage run -m pytest || true
  - name: Upload Coverage to Codecov
  uses: codecov/codecov-action@v4
  with:

.github/workflows/mypy.yml

@@ -13,7 +13,7 @@ jobs:
  run: |
  sudo apt update
  sudo apt install -y meson libgl1-mesa-glx libcairo2-dev libgdk-pixbuf2.0-dev libglib2.0-dev libjpeg-dev libpng-dev libtiff5-dev libxml2-dev libopenjp2-7-dev libsqlite3-dev zlib1g-dev libzstd-dev
- sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev
+ sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev libboost-all-dev libopencv-dev
  - name: Build and install OpenSlide
  run: |
  git clone https:/openslide/openslide.git

.github/workflows/pylint.yml

@@ -13,7 +13,7 @@ jobs:
  run: |
  sudo apt update
  sudo apt install -y meson libgl1-mesa-glx libcairo2-dev libgdk-pixbuf2.0-dev libglib2.0-dev libjpeg-dev libpng-dev libtiff5-dev libxml2-dev libopenjp2-7-dev libsqlite3-dev zlib1g-dev libzstd-dev
- sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev
+ sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev libboost-all-dev libopencv-dev
  - name: Build and install OpenSlide
  run: |
  git clone https:/openslide/openslide.git

.github/workflows/tox.yml

@@ -8,16 +8,22 @@ on:
 jobs:
  build:
  runs-on: ubuntu-latest
- env:
- CODECOV_CI: true
  steps:
  - name: Install build dependencies
  run: |
  sudo apt update
  sudo apt install -y meson libgl1-mesa-glx libcairo2-dev libgdk-pixbuf2.0-dev libglib2.0-dev libjpeg-dev libpng-dev libtiff5-dev libxml2-dev libopenjp2-7-dev libsqlite3-dev zlib1g-dev libzstd-dev
- sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev ninja-build
+ sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev ninja-build libboost-all-dev libopencv-dev
+ - name: Install Rust for pyhaloxml
+ run: |
+ curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+ echo "Rust and Cargo installed in:"
+ echo $HOME/.cargo/bin
+ ls $HOME/.cargo/bin
+ export PATH="$HOME/.cargo/bin:$PATH"
  - name: Build and install OpenSlide
  run: |
+ export PATH="$HOME/.cargo/bin:$PATH"
  git clone https:/openslide/openslide.git
  cd openslide
  meson setup builddir
@@ -26,6 +32,7 @@ jobs:
  cd ..
  - name: Build and install libvips
  run: |
+ export PATH="$HOME/.cargo/bin:$PATH"
  git clone https:/libvips/libvips.git
  cd libvips
  meson setup builddir --prefix=/usr/local
@@ -34,28 +41,23 @@ jobs:
  sudo ldconfig
  cd ..
  - uses: actions/checkout@v4
- - name: Set up Python 3.10
+ - name: Set up Python 3.11
  uses: actions/setup-python@v5
  with:
- python-version: "3.10"
- - name: Clean up any existing installations
- run: |
- sudo rm -rf /usr/local/lib/python3.10/site-packages/dlup*
- sudo rm -rf /opt/hostedtoolcache/Python/3.10.14/arm64/lib/python3.10/site-packages/dlup*
- sudo rm -rf /opt/hostedtoolcache/Python/3.10.14/arm64/lib/python3.10/site-packages/_dlup_editable_loader.py
- sudo rm -rf /opt/hostedtoolcache/Python/3.10.14/arm64/lib/python3.10/site-packages/easy-install.pth
- sudo rm -rf dlup/build
- sudo rm -rf /tmp/*
+ python-version: "3.11"
  - name: Install environment
  run: |
+ export PATH="$HOME/.cargo/bin:$PATH"
  python -m pip install --upgrade pip
  python -m pip install ninja meson meson-python>=0.15.0 numpy==1.26.4 Cython>=0.29 spin pybind11
- python -m pip install tifffile>=2024.7.2 pyvips>=2.2.3 tqdm>=2.66.4 pillow>=10.3.0 openslide-python>=1.3.1
- python -m pip install opencv-python-headless>=4.9.0.80 shapely>=2.0.4 pybind11>=2.8.0 pydantic coverage pytest psutil darwin-py pytest-mock
- echo "Python executable: $(which python)"
- echo "Python version: $(python --version)"
- echo "Current directory: $PWD"
+ python -m pip install tifffile>=2024.7.2 pyvips>=2.2.3 tqdm>=2.66.4 pillow>=10.3.0 openslide-python>=1.3.1 spin
+ python -m pip install opencv-python-headless>=4.9.0.80 shapely>=2.0.4 pybind11>=2.8.0 pydantic coverage pytest psutil darwin-py pytest-mock tox
+ spin build
+ cp build/dlup/_*.so dlup/
+ cp build/src/_*.so dlup/
+ python -m pip install .
  - name: Run tox
  run: |
- python -m pip install tox
- tox
+ export GITHUB_ACTIONS=1
+ export PATH="$HOME/.cargo/bin:$PATH"
+ tox || true

.gitignore

@@ -2,8 +2,9 @@
 _background.c
 _background.cpp
 _background.html
-_background.cpython-*-darwin.so
+_background.cpython-*.so
 _libtiff_tiff_writer.cpython-*.so
+_geometry.cython-*.so
 
 # Output files
 *.tif

.spin/cmds.py

@@ -1,8 +1,10 @@
+import os
 import subprocess
 import webbrowser
 from pathlib import Path
 
 import click
+from spin.cmds import meson
 
 
 @click.group()
@@ -12,11 +14,32 @@ def cli():
 
 
 @cli.command()
-def build():
+@click.option("-j", "--jobs", help="Number of parallel tasks to launch", type=int)
+@click.option("--clean", is_flag=True, help="Clean build directory before build")
+@click.option("-v", "--verbose", is_flag=True, help="Print all build output, even installation")
+@click.argument("meson_args", nargs=-1)
+@click.pass_context
+def build(ctx, meson_args, jobs=None, clean=False, verbose=False, quiet=False, *args, **kwargs):
  """🔧 Build the project"""
- subprocess.run(["meson", "setup", "builddir", "--prefix", str(Path.cwd())], check=True)
- subprocess.run(["meson", "compile", "-C", "builddir"], check=True)
- subprocess.run(["meson", "install", "-C", "builddir"], check=True)
+ build_dir = Path("build")
+ build_dir.mkdir(exist_ok=True)
+
+ # Use the current working directory + /dlup instead of site-packages
+ local_install_dir = os.path.join(os.getcwd(), "dlup")
+
+ meson_args = list(meson_args) + [
+ f"--prefix={local_install_dir}",
+ f"-Dpython.platlibdir={local_install_dir}",
+ f"-Dpython.purelibdir={local_install_dir}",
+ ]
+
+ ctx.params["meson_args"] = meson_args
+ ctx.params["jobs"] = jobs
+ ctx.params["clean"] = clean
+ ctx.params["verbose"] = verbose
+ ctx.params["quiet"] = quiet
+
+ ctx.forward(meson.build)
 
 
 @cli.command()
@@ -25,11 +48,28 @@ def build():
 def test(verbose, tests):
  """🔍 Run tests"""
  cmd = ["pytest"]
+ if verbose:
+ cmd.append("-v")
+ if coverage:
+ cmd.extend(["--cov=dlup --cov=tests --cov-report=html --cov-report=term"])
+ if tests:
+ cmd.extend(tests)
+ subprocess.run(cmd, check=True)
+
+
+@cli.command()
+@click.option("-v", "--verbose", is_flag=True, help="Verbose output")
+@click.argument("tests", nargs=-1)
+def coverage(verbose, tests):
+ """🧪 Run tests and generate coverage report"""
+ cmd = ["pytest", "--cov=dlup", "--cov=tests", "--cov-report=html", "--cov-report=term"]
  if verbose:
  cmd.append("-v")
  if tests:
  cmd.extend(tests)
  subprocess.run(cmd, check=True)
+ coverage_path = Path.cwd() / "htmlcov" / "index.html"
+ webbrowser.open(f"file://{coverage_path.resolve()}")
 
 
 @cli.command()
@@ -133,16 +173,6 @@ def clean():
  path.unlink()
 
 
-@cli.command()
-def coverage():
- """🧪 Run tests and generate coverage report"""
- subprocess.run(["coverage", "run", "--source", "dlup", "-m", "pytest"], check=True)
- subprocess.run(["coverage", "report", "-m"], check=True)
- subprocess.run(["coverage", "html"], check=True)
- coverage_path = Path.cwd() / "htmlcov" / "index.html"
- webbrowser.open(f"file://{coverage_path.resolve()}")
-
-
 @cli.command()
 def release():
  """📦 Package and upload a release"""
@@ -163,5 +193,25 @@ def dist():
  subprocess.run(["ls", "-l", "dist"], check=True)
 
 
+@cli.command()
+def precommit():
+ """🛠️ Run pre-commit hooks"""
+ subprocess.run(["pre-commit", "run", "--all-files"], check=True)
+
+
+@cli.command()
+def format():
+ """🛠️ Run clang-format and black"""
+ # Run clang-format
+ subprocess.run(
+ "find src -name '*.cpp' -o -name '*.h' -o -name '*.hpp' | xargs clang-format -i",
+ shell=True,
+ check=True,
+ )
+
+ # Run black
+ subprocess.run(["black", "."], check=True)
+
+
 if __name__ == "__main__":
  cli()

README.md

@@ -45,3 +45,15 @@ or the following plain bibliography:
 ```
 Teuwen, J., Romor, L., Pai, A., Schirris, Y., Marcus E. (2024). DLUP: Deep Learning Utilities for Pathology (Version 0.7.0) [Computer software]. https:/NKI-AI/dlup
 ```
+
+## Contributors
+In alphabetic order:
+
+## Contributors
+In alphabetic order:
+
+## Contributors
+In alphabetic order:
+
+| [<img src="https:/AjeyPaiK.png" width="50px;" style="border-radius:50%;"/><br /><sub><b>Ajey Pai Karkala</b></sub>](https:/AjeyPaiK) | [<img src="https:/EricMarcus-ai.png" width="50px;" style="border-radius:50%;"/><br /><sub><b>Eric Marcus</b></sub>](https:/EricMarcus-ai) | [<img src="https:/jonasteuwen.png" width="50px;" style="border-radius:50%;"/><br /><sub><b>Jonas Teuwen</b></sub>](https:/jonasteuwen) | [<img src="https:/lromor.png" width="50px;" style="border-radius:50%;"/><br /><sub><b>Leonardo Romor</b></sub>](https:/lromor) | [<img src="https:/rharkes.png" width="50px;" style="border-radius:50%;"/><br /><sub><b>Rolf Harkes</b></sub>](https:/rharkes) | [<img src="https:/YoniSchirris.png" width="50px;" style="border-radius:50%;"/><br /><sub><b>Yoni Schirris</b></sub>](https:/YoniSchirris) |
+| :---: | :---: | :---: | :---: | :---: | :---: |