Harmonize artifical dataset creation
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- Python
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Description
Is your feature request related to a problem? Please describe.
There are multiple artificial dataset creation functions. It should be clear which ones are most useful and when.
Describe the solution you'd like
Merge or document the different artificial dataset implementations. Ideally, the default one and the benchmarking one are merged and the ones from libraries using SpatialData can reuse some functionality to make more specific artificial datasets.
Additional context
Here is a list of some implementations:
- spatialdata.datasets.blobs
- default basic option, slow and limited in use
- https://github.com/scverse/spatialdata/blob/main/src/spatialdata/datasets.py
- from benchmarks.utils import make_blobs
- SOPA blobs
- https://github.com/gustaveroussy/sopa/blob/f1f5a99ee7f5a9489e511241a3a62bb520ec9860/sopa/utils/data.py#L188
- more irregular cell shapes, genes from list
- Harpy cluster_blobs
- https://github.com/saeyslab/harpy/blob/main/src/sparrow/datasets/cluster_blobs.py
- multisample, multichannel, ground truth cell type annotation
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 comparing spatialdata.datasets.blobs in src/spatialdata/datasets.py with benchmarks/utils.py and the linked SOPA and Harpy implementations. Identify the overlapping capabilities and differences, then clarify whether the expected outcome is a shared dataset API, merged implementations, documentation, or some combination; completion criteria are not defined in the issue.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100