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bioformats2raw.layout #112

Merged
merged 32 commits into from
Sep 28, 2022
Merged

bioformats2raw.layout #112

merged 32 commits into from
Sep 28, 2022

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joshmoore
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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

Screen Shot 2022-04-07 at 16 04 04

Note: currently builds on top of #110 to prevent conflicts.

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@joshmoore joshmoore mentioned this pull request Apr 8, 2022
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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.

@joshmoore joshmoore added this to the 0.5 milestone Apr 21, 2022
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sbesson commented Apr 21, 2022

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 bf2raw.schema. Unbearable suspense !

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I think the latest commit is missing bf2raw.schema.

Thanks. Pushed.

Unbearable suspense ! :)

Compared to the debate?

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Now that #110 is merged, can you merge main into here so that the diffs are cleaner?

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can you merge main into here so that the diffs are cleaner?

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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joshmoore added a commit to joshmoore/ome-types that referenced this pull request Sep 15, 2022
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)
tlambert03 pushed a commit to tlambert03/ome-types that referenced this pull request Sep 16, 2022
* 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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A few comments. I think the PR includes the bulk of the rules describing the bioformats2raw layout and its associated metadata. Is the proposal still to port this transitional metadata specification only to the current stable 0.4 specification?

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Noticed a couple of small typos while reading latest comments from @sbesson.

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Co-authored-by: Melissa Linkert <[email protected]>
Co-authored-by: Sébastien Besson <[email protected]>
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Is the proposal still to port this transitional metadata specification only to the current stable 0.4 specification?

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.

cc: @melissalinkert @sbesson

@tischi: do you think there is interest in trying to add this to MoBIE now? or wait for the non-transitional version?

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tischi commented Sep 22, 2022

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 hackathon package in mobie-io.

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Apart from one small clarification, I think this is fine to merge.

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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:

Screen Shot 2022-09-22 at 19 40 56

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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.

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@joshmoore joshmoore merged commit 449fbca into ome:main Sep 28, 2022
@joshmoore joshmoore deleted the bf2raw branch September 28, 2022 18:20
github-actions bot added a commit that referenced this pull request Sep 28, 2022
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

github-actions bot added a commit to thewtex/ngff that referenced this pull request Oct 20, 2022
bioformats2raw.layout

SHA: 449fbca
Reason: push, by @thewtex

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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6 participants