pyisyntax

A Python library for working with pathology images in the iSyntax file format, powered by libisyntax.

Installation

$ pip install pyisyntax

Usage

Read and display a region of the WSI via Pillow.

from isyntax import ISyntax
import PIL.Image

with ISyntax.open("my_file.isyntax") as isyntax:
    # Read pixels from the specified region into a numpy array
    pixels = isyntax.read_region(500, 500, 400, 200, level=4)
    # Convert numpy array into a PIL image
    pil_image = PIL.Image.fromarray(pixels)
    # Show the image
    pil_image.show()

Extract and save the associated macro image.

from isyntax import ISyntax

with ISyntax.open("my_file.isyntax") as isyntax:
    # The macro image will be returned as compressed JPEG data.
    jpeg_data = isyntax.read_macro_image_jpeg()
    # This JPEG data can be written directly to a file.
    with open("macro_image.jpg", "wb") as f:
        f.write(jpeg_data)
    # Alternatively, you could decompress the data using Pillow:
    # pil_image = PIL.Image.open(io.BytesIO(jpeg_data), formats=["JPEG"])

Development

Dependency management

To set up a development environment from the lock file:

1. Ensure that you have uv installed.
2. Create the virtual environment:

   $ uv sync --frozen
   

To modify pyisyntax project dependencies:

1. Edit dependencies in pyproject.toml.
2. Update the lock file using uv:

   $ uv lock
   

Cutting a new release

1. Ensure that tests are passing and everything is ready for release.
2. Create and push a Git tag:

   $ git tag v0.1.6
   $ git push --tags
   

3. Download the artifacts from GitHub Actions, which will include the source distribution tarball and binary wheels.
4. Create a new release on GitHub from the tagged commit and upload the packages as attachments to the release.
5. Also upload the packages to PyPI using Twine:

   $ uv run twine upload pyisyntax-*.tar.gz pyisyntax-*.whl
   

6. Bump the version number in pyproject.toml and create a commit, signalling the start of development on the next version.

These files should also be added to a GitHub release.