Make dataset compose voxel-size-aware

[fm3]

When composing layers from datasets with different voxel sizes, finds a common voxel size and adapts the mags accordingly.

Using the existing functionality from dataset explorers also in compose.

Steps to test:

• Compose datasets with differing voxel sizes. Example: A dataset with 8,8,8 nm voxel size and a dataset with 64,64,64 nm voxel size are composed. The first layer should then have the mags 1,2,4,8,... and the second 8,16,32,64,...

Issues:

• fixes Compose doesn't take voxel sizes into account #8879

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• Added changelog entry (create a $PR_NUMBER.md file in unreleased_changes or use ./tools/create-changelog-entry.py)
• Considered common edge cases
• Needs datastore update after deployment

[coderabbitai]

📝 Walkthrough

Walkthrough

ComposeService now derives and propagates voxel sizes from layers, adapting layers and voxel size when no transformations are present. It extends ExploreLayerUtils to access adaptation. getLayerFromComposeLayer returns both layer and voxel size. DataSource construction uses the derived voxel size. adaptLayersAndVoxelSize visibility is reduced to protected.

Changes

Cohort / File(s)	Summary
Compose workflow and voxel-size propagation app/models/dataset/ComposeService.scala	- Import ExploreLayerUtils and extend it - Change getLayerFromComposeLayer to return (StaticLayer, VoxelSize) - During createDatasource, derive layers and voxelSize from inputs; if no transforms, call adaptLayersAndVoxelSize; otherwise use composeRequest.voxelSize - Build DataSource with derived voxelSize
Utility visibility tightening webknossos-datastore/app/com/scalableminds/webknossos/datastore/explore/ExploreLayerUtils.scala	- Change adaptLayersAndVoxelSize visibility from public to protected; signature otherwise unchanged

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~25 minutes

Poem

I twitch my ears at scales so fine,
Voxels align—oh what a sign!
Layers hop in measured size,
No more guesses, no disguise.
With guarded tools and careful art,
We compose as one—a perfect start. 🐇✨

Pre-merge checks and finishing touches

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title Check	✅ Passed	Title concisely and accurately summarizes the main functional change—making dataset composition voxel-size-aware—matching the code modifications to ComposeService and ExploreLayerUtils for voxel-size adaptation.
Linked Issues Check	✅ Passed	The pull request implements the core objectives from #8879 by extending ComposeService with ExploreLayerUtils and invoking adaptLayersAndVoxelSize to compute a shared voxel size and adjust layer magnifications when composing datasets of differing resolutions, thereby replacing the previous identity transform behavior.
Out of Scope Changes Check	✅ Passed	All modified files are within the compose and dataset explorer codepaths and solely introduce voxel-size adaptation logic without altering unrelated functionality, so no out-of-scope changes are present.
Description Check	✅ Passed	The description directly addresses adapting voxel sizes when composing layers, matching the implemented changes and linked issue resolution by describing functional behavior and test steps.
Docstring Coverage	✅ Passed	No functions found in the changes. Docstring coverage check skipped.

✨ Finishing touches

🧪 Generate unit tests

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch compose-voxel-size-aware

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📜 Recent review details

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Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 9ba3843 and 640503f.

📒 Files selected for processing (1)

• app/models/dataset/ComposeService.scala (5 hunks)

🧰 Additional context used

🧬 Code graph analysis (1)

app/models/dataset/ComposeService.scala (2)

webknossos-datastore/app/com/scalableminds/webknossos/datastore/explore/ExploreLayerUtils.scala (1)

• adaptLayersAndVoxelSize (21-32)

util/src/main/scala/com/scalableminds/util/tools/Fox.scala (1)

• successful (53-56)

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (3)

• GitHub Check: build-smoketest-push
• GitHub Check: backend-tests
• GitHub Check: frontend-tests

🔇 Additional comments (5)

app/models/dataset/ComposeService.scala (5)

6-6: LGTM!

The import is necessary for extending ExploreLayerUtils and accessing adaptLayersAndVoxelSize.

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38-41: LGTM!

Extending ExploreLayerUtils provides access to adaptLayersAndVoxelSize, reusing existing functionality as intended.

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58-77: LGTM!

The method now returns both the layer and its voxel size, enabling voxel-size-aware composition by propagating the source dataset's scale.

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102-108: LGTM with dependency on conditional logic.

The DataSource construction correctly uses the derived voxelSize. However, ensure that the voxel size derivation in the conditional logic above (lines 97-101) is correct for all cases, especially when transformations are present.

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97-101: Validate fallback voxelSize when transformations are present
The code bypasses adaptLayersAndVoxelSize whenever any layer has transformations and uses composeRequest.voxelSize directly. Confirm that under those transforms all source layers’ voxel sizes remain compatible with the requested voxelSize—or else derive the target voxelSize from the transformed layers or explicitly document that callers must supply a matching voxelSize.

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[fm3]

@normanrz do you happen to have some real-world test data for this? I tested with a constructed example and it looked ok, but I think some real test data would be helpful. I’m also not sure if this voxel-size auto-detection breaks composing datasets with incompatible voxel sizes, there are now assertions for that. But that feature might still be desired if you know affine transforms to get everything straight again.