Add hole filling option to mask2stl

[crnh]

Add --fill-holes flag to fill holes in the binary mask before converting it to a mesh.
I also added basic tests for the results of mask2stl.

[Copilot]

Pull request overview

Adds an optional hole-filling step to the mask2stl conversion pipeline and introduces basic integration tests (using committed test data) to validate mesh output, alongside some Ruff configuration refactoring.

Changes:

• Add fill_holes_in_mask() and a --fill-holes/-f CLI flag to optionally fill holes in binary masks before meshing.
• Add integration tests and _data fixtures to compare generated meshes against expected STL outputs.
• Introduce ruff_defaults.toml and wire it into pyproject.toml; update README with the new CLI option.

Reviewed changes

Copilot reviewed 6 out of 11 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/stl2mask/mask2stl.py	Implements hole-filling + CLI flag wiring; updates mask2stl signature.
tests/test_mask2stl.py	Adds mesh-based integration tests and updates existing unit tests for new parameter.
tests/conftest.py	Adds a data_path fixture for locating tests/_data.
tests/_data/sphere.nii.gz	Adds binary mask fixture for sphere conversion tests.
tests/_data/hollow_sphere.nii.gz	Adds binary mask fixture for hollow-sphere conversion tests.
README.md	Documents --fill-holes option.
ruff_defaults.toml	Adds shared Ruff defaults/config presets.
pyproject.toml	Configures Ruff to extend ruff_defaults.toml and adds a Hatch static-analysis env.

Comments suppressed due to low confidence (2)

src/stl2mask/mask2stl.py:44

• fill_holes_in_mask computes foreground_value by converting the whole image to a NumPy view and taking .max(), which adds another full pass over the volume. Since mask2stl already computes mask_values for validation, consider reusing mask_values.max() (or passing the foreground value in) to avoid the extra scan when --fill-holes is enabled.

    foreground_value = float(sitk.GetArrayViewFromImage(mask).max())

    return sitk.BinaryFillhole(mask, fullyConnected=False, foregroundValue=foreground_value)

tests/test_mask2stl.py:275

• The comment says hole filling is enabled, but the call passes fill_holes=False. Please fix the comment (or the argument) so the test intent matches the behavior being exercised.

    # Convert the mask to STL with hole filling enabled
    mask2stl_module.mask2stl(mask_path=mask_path, image_path=None, output_path=output_path, fill_holes=False)

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[jwmbeenakker]

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