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mwatershed

pytest ruff cargo

pypi

A rusty mutex watershed

See docs here

Installation

pip install 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

Graphs as arrays

For a graph that already lives in numpy arrays, cluster_arrays runs the mutex watershed without building a Python object per edge:

nodes, labels = mwatershed.cluster_arrays(
    u, v, weights,            # one edge per position; positive attracts, else repels
    nodes=None,               # sorted unique node ids; default: those in the edges
    sorted=False,             # set if the edges are already in processing order
    prefix=None,              # (u, v, positive) hard decisions processed first
    linkage="abs_max",        # or any GASP linkage below
    cannot_link=True,
)

Node ids are arbitrary uint64. Edges are processed by descending |weight| with ties in input order, after the prefix edges, which are processed in their own order. The result is one label per entry of nodes: the smallest node id in that node's cluster, so the partition equals cluster on the same edges in the same order.

Linkage criteria (GASP)

agglom, cluster_edges and cluster_arrays accept a linkage argument that selects how the interaction between two clusters is computed from the affinities connecting them, following the GASP framework of Bailoni et al. (2022):

linkage Interaction between two clusters Known as
"abs_max" the connecting edge with the largest magnitude (default) Mutex watershed
"sum" sum of the connecting affinities GAEC / HCC-Sum
"mean" mean of the connecting affinities average linkage (HC-Avg / HCC-Avg)
"max" largest connecting affinity single linkage
"min" smallest connecting affinity complete linkage
components = mwatershed.agglom(affinities, offsets, linkage="mean")

Pairs of clusters are visited in order of decreasing interaction magnitude. An attractive pair is merged; a repulsive pair receives a cannot-link constraint when cannot_link=True (the default). Once every remaining pair is repulsive or constrained, the constraints are lifted and any pairs that are still attractive are merged. With "abs_max" the constraints never change the result, which is exactly the mutex watershed. Seeds and the edges argument always act as hard constraints regardless of the linkage.

The generic linkages use a contracted-graph priority queue and are several times slower than the dedicated mutex watershed path; see LINKAGE_REPORT.md for timings (cargo run --release --example benchmark_linkages) or run cargo bench for the Criterion comparison.

Metadata

Release files for mwatershed 0.6.1

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for mwatershed 0.6.1
File Size Uploaded Provenance Actions
mwatershed-0.6.1.tar.gz 63.8 kB Without provenance Details for mwatershed-0.6.1.tar.gz

Built distributions (wheels)

Table of built distributions (wheels) for mwatershed 0.6.1
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mwatershed-0.6.1-pp312-pypy312_pp80-musllinux_1_2_x86_64.whl PyPy 3.12 PyPy 3.12 8.0 Linux musl 1.2+ x86-64 Details for mwatershed-0.6.1-pp312-pypy312_pp80-musllinux_1_2_x86_64.whl
mwatershed-0.6.1-pp312-pypy312_pp80-musllinux_1_2_aarch64.whl PyPy 3.12 PyPy 3.12 8.0 Linux musl 1.2+ ARM64 Details for mwatershed-0.6.1-pp312-pypy312_pp80-musllinux_1_2_aarch64.whl
mwatershed-0.6.1-pp312-pypy312_pp80-manylinux2014_s390x.manylinux_2_17_s390x.whl PyPy 3.12 PyPy 3.12 8.0 Linux glibc 2.17+ IBM System/390x Details for mwatershed-0.6.1-pp312-pypy312_pp80-manylinux2014_s390x.manylinux_2_17_s390x.whl
mwatershed-0.6.1-pp312-pypy312_pp80-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl PyPy 3.12 PyPy 3.12 8.0 Linux glibc 2.17+ PowerPC 64-le Details for mwatershed-0.6.1-pp312-pypy312_pp80-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
mwatershed-0.6.1-pp312-pypy312_pp80-manylinux2014_aarch64.manylinux_2_17_aarch64.whl PyPy 3.12 PyPy 3.12 8.0 Linux glibc 2.17+ ARM64 Details for mwatershed-0.6.1-pp312-pypy312_pp80-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
mwatershed-0.6.1-pp311-pypy311_pp73-musllinux_1_2_x86_64.whl PyPy 3.11 PyPy 3.11 7.3 Linux musl 1.2+ x86-64 Details for mwatershed-0.6.1-pp311-pypy311_pp73-musllinux_1_2_x86_64.whl
mwatershed-0.6.1-pp311-pypy311_pp73-musllinux_1_2_aarch64.whl PyPy 3.11 PyPy 3.11 7.3 Linux musl 1.2+ ARM64 Details for mwatershed-0.6.1-pp311-pypy311_pp73-musllinux_1_2_aarch64.whl
mwatershed-0.6.1-pp311-pypy311_pp73-manylinux2014_x86_64.manylinux_2_17_x86_64.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ x86-64 Details for mwatershed-0.6.1-pp311-pypy311_pp73-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
mwatershed-0.6.1-pp311-pypy311_pp73-manylinux2014_s390x.manylinux_2_17_s390x.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ IBM System/390x Details for mwatershed-0.6.1-pp311-pypy311_pp73-manylinux2014_s390x.manylinux_2_17_s390x.whl
mwatershed-0.6.1-pp311-pypy311_pp73-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ PowerPC 64-le Details for mwatershed-0.6.1-pp311-pypy311_pp73-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
mwatershed-0.6.1-pp311-pypy311_pp73-manylinux2014_aarch64.manylinux_2_17_aarch64.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ ARM64 Details for mwatershed-0.6.1-pp311-pypy311_pp73-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
mwatershed-0.6.1-cp315-cp315t-musllinux_1_2_x86_64.whl CPython 3.15 CPython 3.15 free-threading Linux musl 1.2+ x86-64 Details for mwatershed-0.6.1-cp315-cp315t-musllinux_1_2_x86_64.whl
mwatershed-0.6.1-cp315-cp315t-musllinux_1_2_aarch64.whl CPython 3.15 CPython 3.15 free-threading Linux musl 1.2+ ARM64 Details for mwatershed-0.6.1-cp315-cp315t-musllinux_1_2_aarch64.whl
mwatershed-0.6.1-cp315-cp315t-manylinux2014_x86_64.manylinux_2_17_x86_64.whl CPython 3.15 CPython 3.15 free-threading Linux glibc 2.17+ x86-64 Details for mwatershed-0.6.1-cp315-cp315t-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
mwatershed-0.6.1-cp315-cp315t-manylinux2014_s390x.manylinux_2_17_s390x.whl CPython 3.15 CPython 3.15 free-threading Linux glibc 2.17+ IBM System/390x Details for mwatershed-0.6.1-cp315-cp315t-manylinux2014_s390x.manylinux_2_17_s390x.whl
mwatershed-0.6.1-cp315-cp315t-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl CPython 3.15 CPython 3.15 free-threading Linux glibc 2.17+ PowerPC 64-le Details for mwatershed-0.6.1-cp315-cp315t-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
mwatershed-0.6.1-cp315-cp315t-manylinux2014_aarch64.manylinux_2_17_aarch64.whl CPython 3.15 CPython 3.15 free-threading Linux glibc 2.17+ ARM64 Details for mwatershed-0.6.1-cp315-cp315t-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
mwatershed-0.6.1-cp315-cp315-win_amd64.whl CPython 3.15 CPython 3.15 Windows x86-64 Details for mwatershed-0.6.1-cp315-cp315-win_amd64.whl
mwatershed-0.6.1-cp315-cp315-musllinux_1_2_x86_64.whl CPython 3.15 CPython 3.15 Linux musl 1.2+ x86-64 Details for mwatershed-0.6.1-cp315-cp315-musllinux_1_2_x86_64.whl
mwatershed-0.6.1-cp315-cp315-musllinux_1_2_aarch64.whl CPython 3.15 CPython 3.15 Linux musl 1.2+ ARM64 Details for mwatershed-0.6.1-cp315-cp315-musllinux_1_2_aarch64.whl
mwatershed-0.6.1-cp315-cp315-manylinux2014_x86_64.manylinux_2_17_x86_64.whl CPython 3.15 CPython 3.15 Linux glibc 2.17+ x86-64 Details for mwatershed-0.6.1-cp315-cp315-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
mwatershed-0.6.1-cp315-cp315-manylinux2014_s390x.manylinux_2_17_s390x.whl CPython 3.15 CPython 3.15 Linux glibc 2.17+ IBM System/390x Details for mwatershed-0.6.1-cp315-cp315-manylinux2014_s390x.manylinux_2_17_s390x.whl
mwatershed-0.6.1-cp315-cp315-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl CPython 3.15 CPython 3.15 Linux glibc 2.17+ PowerPC 64-le Details for mwatershed-0.6.1-cp315-cp315-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
mwatershed-0.6.1-cp315-cp315-manylinux2014_aarch64.manylinux_2_17_aarch64.whl CPython 3.15 CPython 3.15 Linux glibc 2.17+ ARM64 Details for mwatershed-0.6.1-cp315-cp315-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
mwatershed-0.6.1-cp314-cp314t-musllinux_1_2_x86_64.whl CPython 3.14 CPython 3.14 free-threading Linux musl 1.2+ x86-64 Details for mwatershed-0.6.1-cp314-cp314t-musllinux_1_2_x86_64.whl
mwatershed-0.6.1-cp314-cp314t-musllinux_1_2_aarch64.whl CPython 3.14 CPython 3.14 free-threading Linux musl 1.2+ ARM64 Details for mwatershed-0.6.1-cp314-cp314t-musllinux_1_2_aarch64.whl
mwatershed-0.6.1-cp314-cp314t-manylinux2014_x86_64.manylinux_2_17_x86_64.whl CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ x86-64 Details for mwatershed-0.6.1-cp314-cp314t-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
mwatershed-0.6.1-cp314-cp314t-manylinux2014_s390x.manylinux_2_17_s390x.whl CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ IBM System/390x Details for mwatershed-0.6.1-cp314-cp314t-manylinux2014_s390x.manylinux_2_17_s390x.whl
mwatershed-0.6.1-cp314-cp314t-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ PowerPC 64-le Details for mwatershed-0.6.1-cp314-cp314t-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
mwatershed-0.6.1-cp314-cp314t-manylinux2014_aarch64.manylinux_2_17_aarch64.whl CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ ARM64 Details for mwatershed-0.6.1-cp314-cp314t-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
mwatershed-0.6.1-cp314-cp314-win_amd64.whl CPython 3.14 CPython 3.14 Windows x86-64 Details for mwatershed-0.6.1-cp314-cp314-win_amd64.whl
mwatershed-0.6.1-cp314-cp314-musllinux_1_2_x86_64.whl CPython 3.14 CPython 3.14 Linux musl 1.2+ x86-64 Details for mwatershed-0.6.1-cp314-cp314-musllinux_1_2_x86_64.whl
mwatershed-0.6.1-cp314-cp314-musllinux_1_2_aarch64.whl CPython 3.14 CPython 3.14 Linux musl 1.2+ ARM64 Details for mwatershed-0.6.1-cp314-cp314-musllinux_1_2_aarch64.whl
mwatershed-0.6.1-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ x86-64 Details for mwatershed-0.6.1-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
mwatershed-0.6.1-cp314-cp314-manylinux2014_s390x.manylinux_2_17_s390x.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ IBM System/390x Details for mwatershed-0.6.1-cp314-cp314-manylinux2014_s390x.manylinux_2_17_s390x.whl
mwatershed-0.6.1-cp314-cp314-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ PowerPC 64-le Details for mwatershed-0.6.1-cp314-cp314-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
mwatershed-0.6.1-cp314-cp314-manylinux2014_aarch64.manylinux_2_17_aarch64.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ ARM64 Details for mwatershed-0.6.1-cp314-cp314-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
mwatershed-0.6.1-cp314-cp314-macosx_11_0_arm64.whl CPython 3.14 CPython 3.14 macOS 11.0+ ARM64 Details for mwatershed-0.6.1-cp314-cp314-macosx_11_0_arm64.whl
mwatershed-0.6.1-cp314-cp314-macosx_10_12_x86_64.whl CPython 3.14 CPython 3.14 macOS 10.12+ x86-64 Details for mwatershed-0.6.1-cp314-cp314-macosx_10_12_x86_64.whl
mwatershed-0.6.1-cp313-cp313-win_amd64.whl CPython 3.13 CPython 3.13 Windows x86-64 Details for mwatershed-0.6.1-cp313-cp313-win_amd64.whl
mwatershed-0.6.1-cp313-cp313-musllinux_1_2_x86_64.whl CPython 3.13 CPython 3.13 Linux musl 1.2+ x86-64 Details for mwatershed-0.6.1-cp313-cp313-musllinux_1_2_x86_64.whl
mwatershed-0.6.1-cp313-cp313-musllinux_1_2_aarch64.whl CPython 3.13 CPython 3.13 Linux musl 1.2+ ARM64 Details for mwatershed-0.6.1-cp313-cp313-musllinux_1_2_aarch64.whl
mwatershed-0.6.1-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ x86-64 Details for mwatershed-0.6.1-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
mwatershed-0.6.1-cp313-cp313-manylinux2014_s390x.manylinux_2_17_s390x.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ IBM System/390x Details for mwatershed-0.6.1-cp313-cp313-manylinux2014_s390x.manylinux_2_17_s390x.whl
mwatershed-0.6.1-cp313-cp313-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ PowerPC 64-le Details for mwatershed-0.6.1-cp313-cp313-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
mwatershed-0.6.1-cp313-cp313-manylinux2014_aarch64.manylinux_2_17_aarch64.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ ARM64 Details for mwatershed-0.6.1-cp313-cp313-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
mwatershed-0.6.1-cp313-cp313-macosx_11_0_arm64.whl CPython 3.13 CPython 3.13 macOS 11.0+ ARM64 Details for mwatershed-0.6.1-cp313-cp313-macosx_11_0_arm64.whl
mwatershed-0.6.1-cp313-cp313-macosx_10_12_x86_64.whl CPython 3.13 CPython 3.13 macOS 10.12+ x86-64 Details for mwatershed-0.6.1-cp313-cp313-macosx_10_12_x86_64.whl
mwatershed-0.6.1-cp312-cp312-win_amd64.whl CPython 3.12 CPython 3.12 Windows x86-64 Details for mwatershed-0.6.1-cp312-cp312-win_amd64.whl
mwatershed-0.6.1-cp312-cp312-musllinux_1_2_x86_64.whl CPython 3.12 CPython 3.12 Linux musl 1.2+ x86-64 Details for mwatershed-0.6.1-cp312-cp312-musllinux_1_2_x86_64.whl
mwatershed-0.6.1-cp312-cp312-musllinux_1_2_aarch64.whl CPython 3.12 CPython 3.12 Linux musl 1.2+ ARM64 Details for mwatershed-0.6.1-cp312-cp312-musllinux_1_2_aarch64.whl
mwatershed-0.6.1-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ x86-64 Details for mwatershed-0.6.1-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
mwatershed-0.6.1-cp312-cp312-manylinux2014_s390x.manylinux_2_17_s390x.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ IBM System/390x Details for mwatershed-0.6.1-cp312-cp312-manylinux2014_s390x.manylinux_2_17_s390x.whl
mwatershed-0.6.1-cp312-cp312-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ PowerPC 64-le Details for mwatershed-0.6.1-cp312-cp312-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
mwatershed-0.6.1-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ ARM64 Details for mwatershed-0.6.1-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
mwatershed-0.6.1-cp312-cp312-macosx_11_0_arm64.whl CPython 3.12 CPython 3.12 macOS 11.0+ ARM64 Details for mwatershed-0.6.1-cp312-cp312-macosx_11_0_arm64.whl
mwatershed-0.6.1-cp312-cp312-macosx_10_12_x86_64.whl CPython 3.12 CPython 3.12 macOS 10.12+ x86-64 Details for mwatershed-0.6.1-cp312-cp312-macosx_10_12_x86_64.whl
mwatershed-0.6.1-cp311-cp311-win_amd64.whl CPython 3.11 CPython 3.11 Windows x86-64 Details for mwatershed-0.6.1-cp311-cp311-win_amd64.whl
mwatershed-0.6.1-cp311-cp311-musllinux_1_2_x86_64.whl CPython 3.11 CPython 3.11 Linux musl 1.2+ x86-64 Details for mwatershed-0.6.1-cp311-cp311-musllinux_1_2_x86_64.whl
mwatershed-0.6.1-cp311-cp311-musllinux_1_2_aarch64.whl CPython 3.11 CPython 3.11 Linux musl 1.2+ ARM64 Details for mwatershed-0.6.1-cp311-cp311-musllinux_1_2_aarch64.whl
mwatershed-0.6.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ x86-64 Details for mwatershed-0.6.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
mwatershed-0.6.1-cp311-cp311-manylinux2014_s390x.manylinux_2_17_s390x.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ IBM System/390x Details for mwatershed-0.6.1-cp311-cp311-manylinux2014_s390x.manylinux_2_17_s390x.whl
mwatershed-0.6.1-cp311-cp311-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ PowerPC 64-le Details for mwatershed-0.6.1-cp311-cp311-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
mwatershed-0.6.1-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ ARM64 Details for mwatershed-0.6.1-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
mwatershed-0.6.1-cp311-cp311-macosx_11_0_arm64.whl CPython 3.11 CPython 3.11 macOS 11.0+ ARM64 Details for mwatershed-0.6.1-cp311-cp311-macosx_11_0_arm64.whl
mwatershed-0.6.1-cp311-cp311-macosx_10_12_x86_64.whl CPython 3.11 CPython 3.11 macOS 10.12+ x86-64 Details for mwatershed-0.6.1-cp311-cp311-macosx_10_12_x86_64.whl

Total release size: 31.9 MB

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Release files / mwatershed-0.6.1-cp315-cp315-manylinux2014_aarch64.manylinux_2_17_aarch64.whl

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Release files / mwatershed-0.6.1-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.whl

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