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mobie / mobie.github.io

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Add optional channel property to ome.zarr image sources. #99

Closed tibuch closed 1 year ago

tibuch commented 1 year ago

Updates the source.schema.json such that the following call in mobie-utils-python works:

add_source_to_dataset(join(mobie_project_folder, dataset_name), "image", "C05", file_format="ome.zarr", 
                     image_metadata_path=join("/home/tibuch/Data/MolecularDevices/Test-set/zarr-files/MIP-4P-4sub.zarr/C/5/0/"),
                     channel=0)

Otherwise I get an error with channel not being allowed by the schema.

constantinpape commented 1 year ago

Hmm, it's weird that this change fixes the schema error. It should not even evaluate the bdv.ome.zarr schema, since you're specifying the ome.zarr schema (which is separate, and the only one for which we currently support the channel attribute). Does MoBIE work as expected after you make this change?

tibuch commented 1 year ago

~Oh, this is a stupid copy-paste error. In my local copy I added it to ome.zarr and not bdv.ome.zarr. Will update the PR in a sec.~

Okay, I think I am using old schemas locally. Must have a closer look again.

tibuch commented 1 year ago

Okay, my bad sorry. I just deleted the existing schemas and it pulled the new ones and everything works as it should!