Cannot aggregate Labels2DModel by ShapesModel
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 394
- Forks
- 95
- Avg merge
- 4d 3h
- Merged PRs (30d)
- 7
Description
Hi @LucaMarconato ! I got an error when I use aggregate() to aggregate a label layer by a shape layer.
Here is my code:
The label layer in codex_sdata was created by code below:
segmentation = iio.imread(data_dir / '3-D2_segmentation_borders.tiff')
labels = { 'labels': sd.models.Labels2DModel.parse(segmentation, dims=("y", "x")) }
sdata = sd.SpatialData(table=table, labels=labels, images=images)
In addition, following the conclusion of last Thursday's community meeting, I sent you an email with the subject 'Inquiry Regarding CODEX Data and High-Resolution Visium Image Alignment.' It contained attachments with the test data and scripts I provided. I wanted to confirm whether you received that email?
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 by reproducing the reported aggregate() operation using the Labels2DModel.parse(segmentation, dims=("y", "x")) setup and the label and shape layers shown in the issue. Inspect the resulting error and determine what is needed for aggregation to complete successfully; done means a Labels2DModel can be aggregated by a ShapesModel without the reported failure.
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
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100