mwatershed
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:
affinitiesis ak+1dimensional array of nonnanaffinities with leading dimension having sizenoffsetsis a list of lengthnof offset tuples ofkintegersseedsis akdimensional array of fragment ids. Noteseeds.shapemust be equal toaffinities.shape[1:]. Any entry not equal to 0 is guaranteed to stay that way, any entry equal to zero has no priors.edgesis 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)
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Release files / mwatershed-0.6.1-cp315-cp315-win_amd64.whl
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Release files / mwatershed-0.6.1-cp315-cp315-musllinux_1_2_x86_64.whl
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Release files / mwatershed-0.6.1-cp315-cp315-musllinux_1_2_aarch64.whl
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Release files / mwatershed-0.6.1-cp315-cp315-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
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| Size | 421.4 kB |
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Release files / mwatershed-0.6.1-cp315-cp315-manylinux2014_s390x.manylinux_2_17_s390x.whl
| Download URL | mwatershed-0.6.1-cp315-cp315-manylinux2014_s390x.manylinux_2_17_s390x.whl |
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| Size | 460.4 kB |
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Release files / mwatershed-0.6.1-cp315-cp315-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
| Download URL | mwatershed-0.6.1-cp315-cp315-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl |
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| Size | 577.8 kB |
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Release files / mwatershed-0.6.1-cp315-cp315-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
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| Size | 413.2 kB |
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Release files / mwatershed-0.6.1-cp314-cp314t-musllinux_1_2_x86_64.whl
| Download URL | mwatershed-0.6.1-cp314-cp314t-musllinux_1_2_x86_64.whl |
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Release files / mwatershed-0.6.1-cp314-cp314t-musllinux_1_2_aarch64.whl
| Download URL | mwatershed-0.6.1-cp314-cp314t-musllinux_1_2_aarch64.whl |
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Release files / mwatershed-0.6.1-cp314-cp314t-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
| Download URL | mwatershed-0.6.1-cp314-cp314t-manylinux2014_x86_64.manylinux_2_17_x86_64.whl |
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Release files / mwatershed-0.6.1-cp314-cp314t-manylinux2014_s390x.manylinux_2_17_s390x.whl
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Release files / mwatershed-0.6.1-cp314-cp314t-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
| Download URL | mwatershed-0.6.1-cp314-cp314t-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl |
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Release files / mwatershed-0.6.1-cp314-cp314t-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
| Download URL | mwatershed-0.6.1-cp314-cp314t-manylinux2014_aarch64.manylinux_2_17_aarch64.whl |
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Release files / mwatershed-0.6.1-cp314-cp314-win_amd64.whl
| Download URL | mwatershed-0.6.1-cp314-cp314-win_amd64.whl |
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Release files / mwatershed-0.6.1-cp314-cp314-musllinux_1_2_x86_64.whl
| Download URL | mwatershed-0.6.1-cp314-cp314-musllinux_1_2_x86_64.whl |
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Release files / mwatershed-0.6.1-cp314-cp314-musllinux_1_2_aarch64.whl
| Download URL | mwatershed-0.6.1-cp314-cp314-musllinux_1_2_aarch64.whl |
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Release files / mwatershed-0.6.1-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
| Download URL | mwatershed-0.6.1-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.whl |
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| Size | 421.2 kB |
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Release files / mwatershed-0.6.1-cp314-cp314-manylinux2014_s390x.manylinux_2_17_s390x.whl
| Download URL | mwatershed-0.6.1-cp314-cp314-manylinux2014_s390x.manylinux_2_17_s390x.whl |
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| Size | 460.5 kB |
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Release files / mwatershed-0.6.1-cp314-cp314-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
| Download URL | mwatershed-0.6.1-cp314-cp314-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl |
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| Size | 577.7 kB |
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Release files / mwatershed-0.6.1-cp314-cp314-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
| Download URL | mwatershed-0.6.1-cp314-cp314-manylinux2014_aarch64.manylinux_2_17_aarch64.whl |
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| Size | 413.1 kB |
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Release files / mwatershed-0.6.1-cp314-cp314-macosx_11_0_arm64.whl
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Release files / mwatershed-0.6.1-cp314-cp314-macosx_10_12_x86_64.whl
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Release files / mwatershed-0.6.1-cp313-cp313-win_amd64.whl
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Release files / mwatershed-0.6.1-cp313-cp313-musllinux_1_2_aarch64.whl
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Release files / mwatershed-0.6.1-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
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Release files / mwatershed-0.6.1-cp313-cp313-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
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Release files / mwatershed-0.6.1-cp313-cp313-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
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Release files / mwatershed-0.6.1-cp313-cp313-macosx_11_0_arm64.whl
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Release files / mwatershed-0.6.1-cp313-cp313-macosx_10_12_x86_64.whl
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Release files / mwatershed-0.6.1-cp312-cp312-win_amd64.whl
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Release files / mwatershed-0.6.1-cp312-cp312-musllinux_1_2_x86_64.whl
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Release files / mwatershed-0.6.1-cp312-cp312-musllinux_1_2_aarch64.whl
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Release files / mwatershed-0.6.1-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
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Release files / mwatershed-0.6.1-cp312-cp312-manylinux2014_s390x.manylinux_2_17_s390x.whl
| Download URL | mwatershed-0.6.1-cp312-cp312-manylinux2014_s390x.manylinux_2_17_s390x.whl |
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Release files / mwatershed-0.6.1-cp312-cp312-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
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Release files / mwatershed-0.6.1-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
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Release files / mwatershed-0.6.1-cp312-cp312-macosx_11_0_arm64.whl
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Release files / mwatershed-0.6.1-cp312-cp312-macosx_10_12_x86_64.whl
| Download URL | mwatershed-0.6.1-cp312-cp312-macosx_10_12_x86_64.whl |
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Release files / mwatershed-0.6.1-cp311-cp311-win_amd64.whl
| Download URL | mwatershed-0.6.1-cp311-cp311-win_amd64.whl |
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Release files / mwatershed-0.6.1-cp311-cp311-musllinux_1_2_x86_64.whl
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| Size | 630.0 kB |
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Release files / mwatershed-0.6.1-cp311-cp311-musllinux_1_2_aarch64.whl
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Release files / mwatershed-0.6.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl
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Release files / mwatershed-0.6.1-cp311-cp311-manylinux2014_s390x.manylinux_2_17_s390x.whl
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Release files / mwatershed-0.6.1-cp311-cp311-manylinux2014_ppc64le.manylinux_2_17_ppc64le.whl
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| Size | 580.2 kB |
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Release files / mwatershed-0.6.1-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.whl
| Download URL | mwatershed-0.6.1-cp311-cp311-manylinux2014_aarch64.manylinux_2_17_aarch64.whl |
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| Size | 416.7 kB |
| Tags | CPython 3.11 Linux glibc 2.17+ ARM64 |
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Release files / mwatershed-0.6.1-cp311-cp311-macosx_11_0_arm64.whl
| Download URL | mwatershed-0.6.1-cp311-cp311-macosx_11_0_arm64.whl |
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| Size | 381.3 kB |
| Tags | CPython 3.11 macOS 11.0+ ARM64 |
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Release files / mwatershed-0.6.1-cp311-cp311-macosx_10_12_x86_64.whl
| Download URL | mwatershed-0.6.1-cp311-cp311-macosx_10_12_x86_64.whl |
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| Size | 384.1 kB |
| Tags | CPython 3.11 macOS 10.12+ x86-64 |
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No |
| Uploaded via |
uv/0.13.7 {"installer":{"name":"uv","version":"0.13.7","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
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Security for mwatershed 0.6.1
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