[Suggestion] Allow strings for method when constructing multiscale Image2DModel
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- Dominant language
- Python
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Description
When constructing an Image2DModel, the following code will work:
from multiscale_spatial_image.to_multiscale.to_multiscale import Methods
sdata.images['my_image'] = sd.models.Image2DModel.parse(
imarr,
dims=['c','y','x'],
c_coords=['DAPI','ATP1A1/CD45/E-Cadherin','18S','alphaSMA/Vimentin'],
scale_factors=[2,2,2,2,2,2,2,2],
method=Methods.XARRAY_COARSEN, chunks=(1,256,256),
)
However, the following code will work (as of v0.4.0), but not produce a multiscale image:
sdata.images['my_image'] = sd.models.Image2DModel.parse(
imarr,
dims=['c','y','x'],
c_coords=['DAPI','ATP1A1/CD45/E-Cadherin','18S','alphaSMA/Vimentin'],
scale_factors=[2,2,2,2,2,2,2,2],
method='xarray_coarsen', chunks=(1,256,256),
)
Based on the documentation, it would be nice if the second method worked. Thanks!
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 at Image2DModel.parse and inspect how the documented Methods.XARRAY_COARSEN value is handled compared with the string "xarray_coarsen". Confirm that passing the string selects the same multiscale method and produces a multiscale image, then add or update coverage if the repository provides a relevant test entry point.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100