pef: Lazy metadata access#381
Merged
Merged
Conversation
…ion and eliminate pandas from validation hot path Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
gav-sturm
approved these changes
Feb 28, 2026
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
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Why:
open_ome_zarr()on HCS plates had a throughput regression caused by two things in the metadata parsing path:_first_pos_attr()usednext(group.groups())to find the first position's channel_names/axes, but zarr v3'sgroups()eagerly enumerates all children before yielding the first; scaling linearly with FOVs/well (0.2ms for 1 FOV, 259ms for 2500)unique_validator()built pandas DataFrames just to check field uniquenessChanges:
axesandchannel_nameslazy & cached viafunctools.cached_propertyonNGFFNode— they resolve on first access, not during__init__Plate, overrode both withcached_propertythat uses direct path access (self.zgroup[well_path][pos_name]) instead ofgroups()traversalunique_validator'smodel_dump()+ pandas DataFrame with a simplesetlength check, removed the pandas importBefore & After: on some test data