ebi_oct

oct_analysis is a Python library for the processing of image data for optical methods (foremost optical coherence tomography (OCT)).

Installation¶

pip install oct_analysis

Features¶

The oct_analysis python package includes various functions for:

• Unpacking *.oct files and loading tiff files as numpy array
• Preprocessing functions to identify and remove objects/boundaries
• Image segmentation and binarization
• Post-processing funtions for the calcuation and saving of structural parameters from the imaging stacks

Usage¶

The documentation can be found in https://oct-analysis.readthedocs.io/en/latest/index.html

Examples for the usage of the functions are described in https://github.com/AndreasNetsch/oct_analysis/tree/main/examples

from oct_analysis import (
    read_tiff,
    select_tiff_folder,
    convert_to_8bit,
    find_substratum,
    voxel_count,
    find_max_zero,
    untilt,
    generate_Height_Map
)

Collaboration and Development¶

Setup¶

1. Clone the repository:

git clone https://github.com/AndreasNetsch/oct_analysis.git
cd oct_analysis

2. Create a virtual environment and install development dependencies:

python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate
pip install -e ".[dev]"

Testing¶

Run tests with pytest:

pytest

Code Formatting and Linting¶

This project uses pre-commit hooks to ensure code quality. After installing the development dependencies, set up the pre-commit hooks:

pre-commit install

This will automatically format your code with Black and check it with Flake8 before each commit. You can also run the hooks manually:

pre-commit run --all-files

Building the package¶

python -m build

Documentation¶

This project uses Sphinx for documentation. To build the documentation locally:

cd docs
make html

The generated documentation will be available in docs/build/html/index.html.

ReadTheDocs Integration¶

The documentation is also configured to be built automatically on ReadTheDocs. To set it up:

1. Push your code to GitHub
2. Sign up for a ReadTheDocs account
3. Import your repository on ReadTheDocs
4. ReadTheDocs will automatically build and host the documentation

You can customize the build process by modifying .readthedocs.yml and the Sphinx configuration files in the docs directory.

CI/CD¶

This project uses GitHub Actions for:

• Running tests on multiple Python versions
• Linting the code
• Building and publishing the package to PyPI when a new version tag is pushed

Creating Releases¶

The CI/CD pipeline is configured to automatically build and publish the package to PyPI when a new version tag is pushed to the repository. This process ensures that only properly versioned, tagged releases get published.

To create and publish a new release:

1. Update the version number in setup.py
2. Commit your changes:

   git add setup.py
   git commit -m "Bump version to x.y.z"

3. Create a new version tag (tag name must start with "v"):

   git tag vx.y.z

4. Push the tag to GitHub:

   git push origin vx.y.z

Once the tag is pushed, GitHub Actions will:

1. Run all tests on multiple Python versions
2. If tests pass, build the package
3. Publish the package to PyPI using the configured PyPI API token

Note: Make sure you've added a PYPI_API_TOKEN secret to your GitHub repository settings under "Settings > Secrets and Variables > Actions" before triggering a release.

License¶

MIT License