bioformats2raw.layout #112
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Pushed some schema fun, @will-moore, if you want to take a look. I need to force push away the commits from #110 but I'll hold off on that a bit. |
I think the latest commit is missing |
Thanks. Pushed.
Compared to the debate? |
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Now that #110 is merged, can you merge |
Done, @will-moore |
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Pushed a statement about the recent realization that we want this layout for previous versions as opposed to upcoming versions. There might be a function in bikeshed along the lines of "applicable-to-version" that we may want to make use of. |
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Likely a last call for comments here. I'm going to move on to the various PRs:
Note: https://github.com/ome/ome-zarr-metadata will not be used for this release. |
While trying to get the `bioformats2raw.layout` specification (ome/ngff#112) this raised its head again. Following the discussion in ome/ome-model#158 changing the size checks to `40` passes. fix: ome/bioformats#3810 fix: ome/napari-ome-zarr#47 (comment)
* Update Hex40 definition While trying to get the `bioformats2raw.layout` specification (ome/ngff#112) this raised its head again. Following the discussion in ome/ome-model#158 changing the size checks to `40` passes. fix: ome/bioformats#3810 fix: ome/napari-ome-zarr#47 (comment) * Bump to min_length=40
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Noticed a couple of small typos while reading latest comments from @sbesson.
Co-authored-by: Melissa Linkert <[email protected]> Co-authored-by: Sébastien Besson <[email protected]>
Yes. I'll do once all edits are made (Hopefully this morning). |
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From my POV, I think we are ready to move forward with this PR as well as the bioformats2raw PR itself. Python I think will follow relatively quickly and then we'll look into Javascript. @tischi: do you think there is interest in trying to add this to MoBIE now? or wait for the non-transitional version? |
I would be interested adding this to the |
latest/index.bs
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| - If "OME/METADATA.ome.xml" or the "series" attribute do not exist: | ||
| - existing "plate" metadata will take precedence if it exists, or |
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Does will here actually mean MUST?
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Hmmm.... I think that's right, but what I was trying to get across is that "the next statement only holds when "plate" isn't defined". Is that the same thing as the MUST?
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or more simply:
- If "OME/METADATA.ome.xml" or the "series" attribute do not exist and "plate" metadata is not defined
?
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I think what bothers me in the logic is that the "plate MUST take precedence" applies much higher, e.g. even if the XML exists. Let me try to break all the clauses apart.
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Pushed this proposal for feedback, @melissalinkert:
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Primary question from my side is if it's actually:
Matching "series" metadata (as described next) SHOULD be provided ...
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Latest version is definitely clearer, thank you. I think Matching "series" metadata (as described next) SHOULD be provided makes sense, but I don't have strong objections to MAY.
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If we're unsure, I'll err on the side of the stricter SHOULD and then we can downgrade it later.
bioformats2raw.layout SHA: 449fbca Reason: push, by @joshmoore Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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This pull request has been mentioned on Image.sc Forum. There might be relevant details there: https://forum.image.sc/t/intermission-ome-ngff-0-4-1-bioformats2raw-0-5-0-et-al/72214/1 |
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This pull request has been mentioned on Image.sc Forum. There might be relevant details there: https://forum.image.sc/t/using-bioformats2raw-for-creating-ome-zarr-scale-format-string/72716/6 |
First update for supporting bioformats2raw output as described in #104. Introduces the concept of "transitional" metadata to allow readers to start supporting extensions that have grown in the community before they are added here.
Draft previwable under: http://api.csswg.org/bikeshed/?url=https://raw.githubusercontent.com/joshmoore/ngff/bf2raw/latest/index.bs#bf2raw
Note: currently builds on top of #110 to prevent conflicts.