Densify tree ids when merging skeletons

[fm3]

URL of deployed dev instance (used for testing):

• https://skeletonmergedensifytreeids.webknossos.xyz

Steps to test:

• Create trees with large ids (e.g. via import agglomerate skeleton)
• Merge two such annotations
• Resulting tree ids should be compact.

Issues:

• fixes TreeIds grow too fast when merging annotations with agglomerate skeletons #8642

---

• Updated changelog
• Considered common edge cases

[coderabbitai]

📝 Walkthrough

Walkthrough

A new helper method was added to densify tree IDs in a sequence of trees, ensuring IDs are consecutive and start from 1. The mergeTrees function was updated to apply this densification to both source and target trees before merging, addressing issues with rapidly increasing tree IDs during annotation merges.

Changes

File(s)	Change Summary
CHANGELOG.unreleased.md	Added a line documenting the bug fix for errors when merging annotations with large tree IDs.
.../tracingstore/tracings/skeleton/TreeUtils.scala	Introduced densifyTreeIds (private); updated mergeTrees to densify tree IDs before merging and mapping trees.

Assessment against linked issues

Objective	Addressed	Explanation
Prevent tree IDs from growing too fast when merging annotations with agglomerate skeletons (#8642)	✅
Avoid potential int32 overflow by controlling tree ID growth during repeated merges (#8642)	✅

Poem

In the forest of code where tree IDs grew,
Rabbits hopped in, with a clever new view.
Densifying IDs, keeping numbers in line,
No more runaway growth—now everything’s fine!
With merges now tidy, the bugs hop away,
And the codebase feels lighter, hooray! 🐇🌳✨

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📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 736c9ef and 839f1cf.

📒 Files selected for processing (2)

• CHANGELOG.unreleased.md (1 hunks)
• webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/skeleton/TreeUtils.scala (1 hunks)

⏰ Context from checks skipped due to timeout of 90000ms (3)

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

🔇 Additional comments (4)

webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/skeleton/TreeUtils.scala (3)

36-39: Well-implemented densification function

The new densifyTreeIds helper method looks great. It elegantly sorts trees by ID and reassigns consecutive IDs starting from 1, which will ensure compact tree ID ranges after merging. The sorting preserves the relative ordering of trees, maintaining consistent behavior while solving the large ID issue.

---

45-47: Good application of densification to both tree sets

Applying densification to both source and target trees before merging is an excellent approach. This ensures that regardless of how sparse the original tree IDs might be, they'll be normalized to a compact range before the merge operation occurs, preventing potential issues with very large IDs.

---

49-56: Complete implementation of the merge logic with densified trees

The merge logic now properly works with the densified tree sets while maintaining the same functional behavior as before. By first densifying the trees and then applying the necessary ID mappings, you've ensured that the resulting merged tree collection will have compact, sequential IDs regardless of how large or sparse the original IDs were.

CHANGELOG.unreleased.md (1)

44-44: Clear and descriptive changelog entry

This changelog entry accurately describes the bug that was fixed and properly links to the PR. It clearly communicates to users that they no longer need to worry about errors when merging annotations with large tree IDs.

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[philippotto]

lgtm 👍