A rusty mutex watershed

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Project description

mwatershed

A rusty mutex watershed

  • Free software: MIT License

Installation

pip install git+https://github.com/pattonw/mwatershed

Features

  • A mutex watershed implementation for affinities
  • Should handle up to 6 dimensional arrays of fragments (7 dimensions if you include offsets in affinities) but only tested on 2 and 3 dimensions

Usage

components = mwatershed.agglom(
    affinities: NDArray[np.float64],
    offsets: list[list[int]],
    seeds: NDArray[np.uint64],
    edges: Optional[list[tuple[usize, usize, f64]]] = None,
)

where:

  • affinities is a k+1 dimensional array of non nan affinities with leading dimension having size n
  • offsets is a list of length n of offset tuples of k integers
  • seeds is a k dimensional array of fragment ids. Note seeds.shape must be equal to affinities.shape[1:]. Any entry not equal to 0 is guaranteed to stay that way, any entry equal to zero has no priors.
  • edges is a list of (u, v, aff) tuples to insert arbitrary extra affinities between fragment ids

Credits

This package was created with Cookiecutter and the pattonw/cookiecutter-rust-pypackage project template.

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