scverse / scverse/spatialdata

Keep polygon interior during vectorization

Open
#920 1 comment 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

needs: triage priority: medium
Dominant language
Python
Stars
394
Forks
95
Avg merge
4d 3h
Merged PRs (30d)
7

Description

There is a minor issue in spatialdata._core.operations.vectorize._vectorize_mask

The interior is removed when we have a mask with an interior, for instance this one:

import numpy as np

mask = np.zeros((100, 100), dtype=np.uint8)
mask[10:90, 10:90] = 1
mask[40:60, 40:60] = 0
mask[45:55, 45:55] = 1

Image

Instead, it will create three polygons nested inside each other. A good behavior should be one of the following:

  • one polygon with an interior, and another polygon (for the small square)
  • or one multipolygon composed of the two above polygons

I'm not sure if it's very easy to fix. I'll investigate later.

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 in spatialdata._core.operations.vectorize._vectorize_mask and reproduce the issue with the nested-square NumPy mask shown in the report. Inspect the vectorization result and its polygon relationships; done means the outer polygon retains its interior while the small square remains a separate polygon or part of a multipolygon.

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
68/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.