supervoxel-splitter

Pluggable supervoxel-splitting algorithms behind a uniform Splitter interface.

What it does

Given a 3-D foreground mask, source seeds, and sink seeds, return a labeled volume that partitions the foreground into a source side and a sink side. Useful for proofreading workflows that need to split a single supervoxel without touching the rest of the segmentation.

The package ships multiple techniques behind the same Splitter protocol:

• GeodesicSplitter — anisotropic geodesic carve via an EDT-derived speed field. Default technique; preserves the neck-aware behavior used in PyChunkedGraph today.
• WatershedSplitter — seeded watershed on the distance transform.
• NoopSplitter — reference implementation; documents the protocol shape for downstream plugin authors (e.g. a learned splitter).

Install

Requires Python 3.14 or newer.

pip install supervoxel-splitter           # core
pip install "supervoxel-splitter[fast]"   # adds dijkstra3d as the geodesic backend

The uniform interface

Every splitter satisfies the same Splitter protocol. Technique-specific knobs live on the constructor; split() itself stays clean.

from supervoxel_splitter import GeodesicSplitter

splitter = GeodesicSplitter(backend="dj3d")
result = splitter.split(
    mask=foreground_3d_bool,
    sources=src_seeds_xyz,
    sinks=snk_seeds_xyz,
    voxel_size=(4.0, 4.0, 40.0),
)

# result.labels: uint8 in {0, SOURCE, SINK, STRAY}
# result.side_of_label: {SOURCE: 1, SINK: 2}
# result.diagnostics: per-stage timings, label counts, etc.

Plugin authors implement the protocol structurally — no base class to inherit:

class MyLearnedSplitter:
    def __init__(self, *, model_path):
        ...
    def split(self, mask, sources, sinks, *,
              voxel_size=(1.0, 1.0, 1.0),
              vol_order="xyz", vox_order="xyz", seed_order="xyz"):
        ...
        return SplitResult(...)

assert isinstance(MyLearnedSplitter(model_path="..."), Splitter)

Boundary

The package knows nothing about ChunkedGraph, BigTable, IDs, or edges. It takes voxels in and gives labels back. New-ID minting, edge updates, and persistence are the consumer's responsibility.

Status

v0.1.0 covers GeodesicSplitter. WatershedSplitter and NoopSplitter ship as small reference impls demonstrating the protocol; production-quality parity with geodesic is out of scope for v0.1.0.

Release

Published to PyPI by a one-click workflow — no manual tag or version edit.

• Release: Actions → CI → Run workflow → choose part (major/minor/patch), or gh workflow run test.yml -f part=patch. It computes the next version from the latest vX.Y.Z tag, tags it, builds, and publishes to PyPI (OIDC trusted publishing).
• Preview: dry-run=true prints the next version without tagging or publishing.

The version is derived from the git tag by setuptools_scm; there is no version literal to bump.

License

MIT.