Repository navigation
STAMP v0.11.0 release - #58
Merged
Merged
Conversation
- Modified classify/extract.py to drop subvolumes from memory after extraction.
- Added schemas/subvolumes.py to define a schema for Subvolumes to allow lazy particle access instead of reading all into memory. - Modified tests/unit/test_schemas.py to add tests for subvolume schema.
- Modified classify/extract.py to return Subvolumes instance rather than actual subvolumes. - Modified tests/unit/test_classify.py to fix test suite following refactor.
- Modified classify/features.py to stream feature extraction from Subvolumes instance.
- Modified classify/align.py to batch cluster alignment using Subvolumes instance.
- Modified classify/average.py to batch class averaging using a Subvolumes instance.
- Modified commands/classify.py to use Subvolumes-based batching throughout classification.
- Modified tests/unit/test_classify.py to fix unit tests broken due to refactoring. - Modified tests/integration/test_classify_command.py to add tests for chunking.
Merge pull request #57 from holsam/memory-optimisation
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Changelog
classifyto use chunked processing: Use chunked processing for classification #57