Faster version `aggregate()` method available
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 394
- Forks
- 95
- Avg merge
- 4d 3h
- Merged PRs (30d)
- 7
Description
While extending SOPA for Visium HD data, @quentinblampey encountered a performance bottleneck with aggregate() that he could improve using pure geopandas code. Since we use geopandas internally, this could be a bug of spatialdata that may be easy to fix.
Here is the SOPA code https://github.com/gustaveroussy/sopa/blob/master/sopa/segmentation/aggregation.py#L485.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the referenced SOPA implementation in sopa/segmentation/aggregation.py around line 485 and compare its aggregate() approach with spatialdata's implementation. Confirm that the faster approach preserves aggregate() results and measure an improvement on the Visium HD workload described in the issue.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data, performance
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Active
- Clarity
- Needs clarification
- Newbie friendliness
- 48/100