Python code to read/write .annotation files from Halo. Can export as .geojson for further analysis.
Example 1 : Move rectangles to a different layer and save as .annotation.
Example 2 : Check if annotations have holes in them and save as .geojson.
Example 3 : Show the wkt representation of the shapely polygon.
Example 4 : Create a .annotation file from coordinates.
Available at readthedocs.
pip install pyhaloxml
The matching of negative to positive regions now needs to be done by the user after loading the data. The examples have been updated. This needed to happen because negative regions can be unmatched in Halo. This would cause errors when loading.
- Clone the repository
pip install --no-build-isolation --editable .[dev]- These tools are used in this project:
- ruff : Code formatting and linting
- bumpver : Automatic versioning
- pytest : Testing
- mypy : Type checking
- numpydoc : Checking docstring style
- isort : Sorting imports
- The xml is relatively simple. There are Annotations and an annotation contains regions.
- Regions can be either positive or negative. However regions in an annotation are not hierarchical. So there is no telling what negative region should go with what positive region.
- This package expects a negative region to be fully enclosed by one positive region. The matching is done by taking a single point that is inside or on the border of the negative region and checking if it is inside a positive region.