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Exports ome-ngff metadata #737

Merged
merged 9 commits into from
Jun 2, 2022
Merged

Exports ome-ngff metadata #737

merged 9 commits into from
Jun 2, 2022

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normanrz
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@normanrz normanrz commented May 25, 2022 •
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Description:

  • If a dataset has a Zarr layer, the OME-NGFF metadata as well as .zgroup structure will be written out.

Issues:

Todos:

Make sure to delete unnecessary points or to check all before merging:

  • Updated Changelog
  • Updated Documentation
  • Added / Updated Tests

@normanrz normanrz self-assigned this May 25, 2022
@normanrz normanrz requested a review from jstriebel May 27, 2022 18:55
jstriebel
jstriebel approved these changes Jun 1, 2022
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Nice, code LGTM 👍 I didn't test it myself, did you open the resulting dataset with a reader? Maybe it makes sense to include a test with https://github.com/ome/ome-zarr-py?

webknossos/tests/test_dataset.py
Comment on lines +41 to +42
MINIO_ROOT_USER = "ANTN35UAENTS5UIAEATD"
MINIO_ROOT_PASSWORD = "TtnuieannGt2rGuie2t8Tt7urarg5nauedRndrur"
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Password rotation :trollface:

@normanrz
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normanrz commented Jun 2, 2022

Maybe it makes sense to include a test with https://github.com/ome/ome-zarr-py?

I think that's too much trouble, because the libs brings many deps and doesn't easily work with our minio S3 etc. The OME format is fairly straight-forward. I added a validation based on the json schema.

jstriebel
jstriebel approved these changes Jun 2, 2022
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Awesome 👍

@bulldozer-boy bulldozer-boy bot merged commit 4ebefcb into master Jun 2, 2022
@bulldozer-boy bulldozer-boy bot deleted the ngff-export branch June 2, 2022 08:44
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