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Possible to handle arbitrary fsmaps? #402
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This issue has been mentioned on Image.sc Forum. There might be relevant details there: |
I'm not aware that we've discussed or planned this, but thanks for the suggestion. It looks worth considering. Looking at your code, I can't see where It would also help to understand the proposed usage a bit better if you were to separate your code into one script for writing the data and one for reading, to show what info needs to be saved in order to read the data. |
Sorry, fixed.
ome_zarr.io.ZarrLocation accepts a zarr.storage.FSStore as input and zarr's documentation says this is a wrapper of fsspec.FSMap which is what I was trying to input. But I can't seem to generate FSStore from a reference dict or JSON or a FSMap directly... However it looks like with zarr v3 the zarr.storage module is drastically changing, including removing FSStore. I'll need to dig into it more. Hopefully these changes are good for ome-zarr-py and good for my proposed use case. |
With the move to zarr-python 3.x, my hope is that we can accept any base Store as opposed to needing the explicit FSStore as with v2. |
Yes, I was looking at using |
Alternatively, maybe ome-zarr-py should simply use "Implicit Store Creation" https://github.com/zarr-developers/zarr-python/blob/main/docs/guide/storage.rst#implicit-store-creation and always create a group when we do |
Quite possibly.
Not necessarily.
Hmmm.... I was definitely using that in the challenge Python code. |
I've used kerchunk and fsspec to create a reference file system of a full plate of raw tiff images and I was hoping to visualize them in napari using
napari-ome-zarr
. Is this ability currently possible, on the roadmap, or not planned?The main benefit of this approach is that I only have to generate the referential json and don't have to read and write everything to a zarr file, which also duplicates the data as I don't like deleting raw data. I can tile the arrays in memory and add them to napari but I would lose out on any other benefits that the plugin provides now or in the future, such as surfacing metadata.
Example code:
As a first step I should probably validate my NGFF metadata is in fact valid. Related to this I think it would be a good idea to refactor
ome_zarr.writer
so that metadata can be easily generated outside of actually writing it (i.e. surface and rename functions like _validate_plate_rows_columns to produce metadata dicts or dataclasses).The text was updated successfully, but these errors were encountered: