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fix: particle centres include shifts; skip filament objects - #161
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Shifts. copick's particle centre is location + t, with t the translation of the pick's transform; the datasets cropped at the location alone, so every pick carrying a shift (RELION imports with origins, refined poses) was extracted off-centre. CopickDataset, SimpleCopickDataset and MinimalCopickDataset now crop at location + t, as does the background exclusion and slab fitting from picks. Filaments. Picks of an object declared a filament (copick's is_filament, or metadata["copick"]["filament"] on copick < 1.28) sample one continuous structure rather than separate particles, so they are no longer a particle class by default. They still keep background samples away. New options on all three datasets: include_filaments=False and object_names=None (train on these objects only; picks of the others also keep background away). The background sample count still follows the training particles. Cache files carry the object selection in their name (_objs-all, _objs-<hash>, _fil), so caches built before this change, or for another selection, are not reused. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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) ## Summary `v2.0` twin of #161, cherry-picked. The description and the reasoning are in #161; in short: - **Shifts:** particle crops are taken at `location + t`, the particle centre, not at `location`. That covers `CopickDataset`, `SimpleCopickDataset`, `MinimalCopickDataset`, the background exclusion and slab fitting. - **Filaments:** filament objects are no longer a particle class by default, and their picks still keep background samples away. The new options are `include_filaments` and `object_names`. - **Caches:** cache names carry the object selection, so caches cropped without shifts are not reused. **Cherry-pick:** two conflicts, both import lines. `v2.0`'s `copick_torch/dataset.py` and `minimal_dataset.py` already import `from .storage import get_level_array`; both imports are kept. Two tests needed `v2.0`'s storage layer: - `test_pick_selection` now patches `storage.get_level_array`, which `MinimalCopickDataset` uses on `v2.0`, instead of `zarr.open`. - The pick stubs in `test_slab_shape_lookup_does_not_read_array_payload` carry an identity `transformation`, as every copick point does, since slab fitting now takes each centre as `location + t`. **Depends on** copick/copick-pipeliner#4 reaching users first, as #161 does: pick sets it stored earlier carry their position in `t` as well. ## Tests - Full suite on `v2.0`'s lock: 99 passed (`v2.0` itself: 87; the 12 new ones come from #161's `test_pick_selection`). - Lint is clean with the repo's pinned ruff 0.3.4 and black 24.3.0. 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
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🤖 I have created a release *beep* *boop* --- ## [1.2.1](copick-torch-v1.2.0...copick-torch-v1.2.1) (2026-10-06) ### 🐞 Bug Fixes * bump actions/setup-python from 6 to 7 ([#133](#133)) ([d3640f1](d3640f1)) * bump chanzuckerberg/github-actions from 6.29.4 to 6.32.0 ([#135](#135)) ([057024b](057024b)) * bump chanzuckerberg/github-actions from 6.32.0 to 6.35.0 ([#143](#143)) ([27e28ac](27e28ac)) * bump chanzuckerberg/github-actions from 6.35.0 to 6.41.2 ([#160](#160)) ([4813bf1](4813bf1)) * bump dask from 2026.3.0 to 2026.7.1 ([#145](#145)) ([2e0b09d](2e0b09d)) * bump matplotlib from 3.10.9 to 3.11.1 ([#148](#148)) ([0870732](0870732)) * bump monai from 1.5.2 to 1.6.0 ([#112](#112)) ([c6a70c4](c6a70c4)) * bump pandas from 3.0.4 to 3.0.5 ([#144](#144)) ([9e615a1](9e615a1)) * bump ruff from 0.15.20 to 0.15.21 ([#129](#129)) ([a6bd111](a6bd111)) * bump scikit-learn from 1.8.0 to 1.9.0 ([#131](#131)) ([1f3c8a6](1f3c8a6)) * bump simpleitk from 2.5.3 to 2.5.6 ([#147](#147)) ([ce1911d](ce1911d)) * bump torchvision from 0.26.0 to 0.28.0 ([#128](#128)) ([e3cac53](e3cac53)) * bump tox from 4.56.1 to 4.56.4 ([#130](#130)) ([d463215](d463215)) * particle centres include shifts; skip filament objects ([#161](#161)) ([2acedb1](2acedb1)) --- Merging this PR will release copick-torch on PyPI. Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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Summary
Shifts. copick's particle centre is
location + t, wheretis the pick transform's translation. The datasets cropped atlocationalone, so every pick carrying a shift was extracted off-centre: for example, RELION imports with origins, or refined poses. Now crops are taken atlocation + tin:CopickDataset,SimpleCopickDatasetandMinimalCopickDataset;Filaments. Picks along a filament sample one continuous structure, not separate particles.
is_filament, ormetadata["copick"]["filament"]on copick < 1.28, see feat: filament objects, pick identity, and RELION/EM pick geometry fixes copick#479) are no longer a particle class by default.include_filaments=False, andobject_names=Noneto train on those objects only. Picks of excluded objects also keep background away.Caches. Cache files carry the object selection in their name (
_objs-all,_objs-<hash>,_fil). Caches built before this change, which were cropped without shifts, or for another selection, are not reused.test_dataset_cachingexpectations are updated accordingly.Depends on copick/copick-pipeliner#4 reaching users first. Pick sets it stored earlier carry their position in
tas well, and would now be cropped at twice their position.Tests
New
tests/test_pick_selection.py:t;include_filaments,object_names);The touched set passes (49 tests:
test_pick_selection,test_background_sampling,test_simple_dataset,test_minimal_dataset,test_dataset_caching,test_slab_fitting,test_copick_dataset).Not addressed here, noted for a follow-up:
MinimalCopickDataset._sample_background_pointsdraws in voxels, compares against particle coordinates in Å, and then extracts the result as Å.🤖 Generated with Claude Code