scverse / scverse/spatialdata

Invalid shapes during vectorization

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element: shapes ▲ method: vectorize ◃ needs: triage priority: medium
Dominant language
Python
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394
Forks
95
Avg merge
4d 3h
Merged PRs (30d)
7

Description

shapely.make_valid should be run on every shape after vectorization. It will fix the "polygons with holes"

See example here

Contributor guide

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First steps

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  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 reproducing the invalid polygon case from the linked polygons_test.ipynb, then trace the vectorization entry point in spatialdata. Check how vectorized shapes are returned and add coverage for polygons with holes. Done means every shape produced by vectorization has been passed through shapely.make_valid and the example no longer produces invalid shapes.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Active
Clarity
Mostly clear
Newbie friendliness
65/100

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