scverse / scverse/spatialdata

Extent calculation doesn't account for radius of Points

Open
#693 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

bug 🚨 method: transforms 🔃
Dominant language
Python
Stars
394
Forks
95
Avg merge
4d 3h
Merged PRs (30d)
7

Description

Just fixed https://github.com/scverse/spatialdata-plot/pull/334 and noticed that the extent calculation does not account for the radius of points. In the first version of this picture we calculated this within spatialdata-plot but that has since moved upstream. It's realistically not super noticeable if these are small, but f.e. in our test case it stands out:

image

Can be mitigated through the pad_extent parameter in sdata.pl.show(), but figured I'd report anyway.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by tracing the extent calculation used by sdata.pl.show(), focusing on how point radius is represented after the calculation moved upstream. Compare the computed extent with the displayed test case and verify that the resulting bounds include point radii.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.