Blockwise assign to organelles#61
Merged
Merged
Conversation
Rewrite assign_to_organelles to process data blockwise instead of loading the entire organelle volume into memory. Groups COMs by chunk, loads only blocks that contain COMs (with padding for n-nearest queries), and uses a margin check to guarantee correctness without block-edge artifacts. Supports dask parallelism via ComputeConfigMixin. Also add N5ArrayMetadata fallback in zarr_io.open_dataset for zarr 3.x which dropped native N5 support.
zarr.open_array in zarr 3.x defaults to v3 format even inside v2 containers, creating mixed-format containers that Neuroglancer can't read (it inherits the format from the root group). Now prepare_ds passes zarr_format=root.metadata.zarr_format so arrays match their container.
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #61 +/- ##
==========================================
+ Coverage 82.22% 82.27% +0.05%
==========================================
Files 26 26
Lines 3341 3475 +134
==========================================
+ Hits 2747 2859 +112
- Misses 594 616 +22 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
mostly to make assign-to-organelles work blockwise instead of loading all data in in one go