patchworks 0.11.20__tar.gz → 0.11.21__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {patchworks-0.11.20 → patchworks-0.11.21}/.github/workflows/release.yml +0 -14
- {patchworks-0.11.20 → patchworks-0.11.21}/PKG-INFO +2 -2
- {patchworks-0.11.20 → patchworks-0.11.21}/pyproject.toml +1 -1
- {patchworks-0.11.20 → patchworks-0.11.21}/tests/test_relations.py +6 -2
- {patchworks-0.11.20 → patchworks-0.11.21}/.github/workflows/docs.yml +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/.github/workflows/lint.yml +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/.gitignore +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/.markdownlint-cli2.yaml +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/LICENSE +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/README.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/cliff.toml +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/chunks.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/cluster.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/io.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/merge_tile_labels.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/plugins/cellpose.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/plugins/napari.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/plugins/ome_zarr.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/relabel.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/api/tile_process.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/assets/logo.png +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/cellpose_2d.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/cellpose_2d.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/cellpose_3d.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/cellpose_3d.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/custom.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/custom_method.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/standalone_merge.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/stardist.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/examples/stardist_2d.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/getting_started.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/guide/gpu_distributed.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/guide/merging.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/guide/ome_zarr_napari.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/guide/performance.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/guide/pitfalls.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/guide/skip_empty.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/guide/snakemake.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/guide/tiling.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/docs/index.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/mkdocs.yml +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/__init__.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/_chunks.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/_cluster.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/_core.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/_distributed.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/_io.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/_merge.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/_relabel.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/_relations.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/plugins/__init__.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/plugins/cellpose.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/plugins/napari.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/src/patchworks/plugins/ome_zarr.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/tests/test_core.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/tests/test_distributed.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/tests/test_napari.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/tests/test_ome_zarr.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/README.md +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/Snakefile +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/config/config.yaml +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/config/config_cyto.yaml +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/config/config_nuclei.yaml +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/config/multi.yaml +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/pixi.toml +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/profile/slurm/config.yaml +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/rules/common.smk +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/rules/convert.smk +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/rules/merge.smk +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/rules/segment.smk +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/scripts/_pw.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/scripts/convert.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/scripts/fetch_model.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/scripts/merge.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/scripts/prepare_tiles.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/scripts/run_multi.py +0 -0
- {patchworks-0.11.20 → patchworks-0.11.21}/workflow/scripts/segment_tile.py +0 -0
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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# Rebuild the org-wide pdoc apidocs site so it picks up the new version.
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apidocs:
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needs: release
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runs-on: ubuntu-latest
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steps:
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- name: Trigger imcf.github.io apidocs rebuild
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uses: peter-evans/repository-dispatch@v3
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with:
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# Fine-grained PAT with "Contents: write" on imcf/imcf.github.io,
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# stored as the APIDOCS_DISPATCH_TOKEN secret in this repo.
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token: ${{ secrets.APIDOCS_DISPATCH_TOKEN }}
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repository: imcf/imcf.github.io
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event-type: dispatch-event
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@@ -1,10 +1,10 @@
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Metadata-Version: 2.4
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Name: patchworks
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Version: 0.11.
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Version: 0.11.21
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Summary: Tiled processing of arbitrarily large images with globally consistent labels
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Project-URL: Homepage, https://github.com/imcf/patchworks
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Project-URL: Issues, https://github.com/imcf/patchworks/issues
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Author:
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Author-email: Laurent Guerard <laurent.guerard@unibas.ch>
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License: GPL-3.0-only
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License-File: LICENSE
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Keywords: bioimage,chunked,dask,image processing,segmentation,tiling,zarr
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description = "Tiled processing of arbitrarily large images with globally consistent labels"
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readme = "README.md"
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license = { text = "GPL-3.0-only" }
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authors = [{ name = "
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authors = [{ name = "Laurent Guerard", email = "laurent.guerard@unibas.ch" }]
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keywords = [
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"image processing",
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"tiling",
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@@ -17,7 +17,9 @@ def test_label_relations_majority_overlap():
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b[0:2, 6:8] = 21 # 4 voxels overlap with label 2 -> tie, but let's skew it
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b[0:2, 6:7] = 20 # tip the tie: label 20 now has 6 voxels vs 21's 2
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table = label_relations(
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table = label_relations(
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da.from_array(a, chunks=(2, 5)), da.from_array(b, chunks=(2, 5))
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)
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assert table[1]["match"] == 10
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assert table[1]["overlap_voxels"] == 4
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a[0, 0] = 1
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b = np.zeros((2, 2), dtype=np.int32) # all background, no overlap anywhere
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table = label_relations(
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table = label_relations(
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da.from_array(a, chunks=(2, 2)), da.from_array(b, chunks=(2, 2))
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)
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assert table == {}
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