bioformats2raw.layout #112

joshmoore · 2022-04-07T14:06:16Z

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.

latest/index.bs

see: ome#104 (comment)

latest/index.bs

joshmoore · 2022-04-21T10:14:48Z

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.

sbesson · 2022-04-21T11:40:28Z

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 !

joshmoore · 2022-04-21T13:45:56Z

I think the latest commit is missing bf2raw.schema.

Thanks. Pushed.

Unbearable suspense ! :)

Compared to the debate?

will-moore · 2022-04-27T09:12:18Z

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

joshmoore · 2022-05-03T11:02:41Z

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

Done, @will-moore

latest/tests/test_validation.py

joshmoore · 2022-05-11T10:41:59Z

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.

latest/index.bs

latest/tests/test_validation.py

joshmoore · 2022-09-15T09:36:02Z

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

sbesson

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?

latest/index.bs

melissalinkert

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

latest/index.bs

Co-authored-by: Melissa Linkert <melissa@glencoesoftware.com> Co-authored-by: Sébastien Besson <seb.besson@gmail.com>

joshmoore · 2022-09-22T06:20:45Z

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).

joshmoore · 2022-09-22T06:51:47Z

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?

tischi · 2022-09-22T09:03:40Z

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.

melissalinkert

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

melissalinkert · 2022-09-22T15:54:01Z

latest/index.bs

 - If "OME/METADATA.ome.xml" or the "series" attribute do not exist:
+    - existing "plate" metadata will take precedence if it exists, or


Does will here actually mean MUST?

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?

or more simply:

- If "OME/METADATA.ome.xml" or the "series" attribute do not exist and "plate" metadata is not defined

?

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.

Pushed this proposal for feedback, @melissalinkert:

Primary question from my side is if it's actually:

Matching "series" metadata (as described next) SHOULD be provided ...

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.

If we're unsure, I'll err on the side of the stricter SHOULD and then we can downgrade it later.

latest/index.bs

0.4/index.bs

@joshmoore

bioformats2raw.layout SHA: 449fbca Reason: push, by @joshmoore Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

imagesc-bot · 2022-09-28T18:25:02Z

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

imagesc-bot · 2022-10-13T10:59:36Z

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

@thewtex

bioformats2raw.layout SHA: 449fbca Reason: push, by @thewtex Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

First draft of bioformats2raw.layout

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will-moore reviewed Apr 7, 2022

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joshmoore mentioned this pull request Apr 7, 2022

Multi-file images do not import correctly if nested in a .zarr folder ome/ZarrReader#25

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Add layout example

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joshmoore mentioned this pull request Apr 8, 2022

OME Metadata Support #104

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melissalinkert reviewed Apr 13, 2022

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joshmoore added 2 commits April 20, 2022 08:26

Improve wording of "SHOULD parse multiple images", thanks to Ilan

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see: ome#104 (comment)

Clarify contents of METADATA.ome.xml, thanks to Melissa

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will-moore reviewed Apr 20, 2022

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Add schema & test for bf2raw metadata

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joshmoore added this to the 0.5 milestone Apr 21, 2022

Add missing schema file

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This was referenced Apr 29, 2022

ZarrReader: Add support for OME-XML from bf2raw ome/ZarrReader#31

Merged

ENH: Add ConvertPyImageJ example spatial-image/multiscale-spatial-image#23

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Merge 'origin/main' into bf2raw

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will-moore mentioned this pull request May 9, 2022

Collection thumbs hms-dbmi/vizarr#125

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sbesson reviewed May 9, 2022

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Proposal: consolidate JSON schema tests using keys #116

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will-moore mentioned this pull request May 10, 2022

Support bioformats2raw layout hms-dbmi/vizarr#149

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Add applicable versions statement

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sbesson reviewed May 16, 2022

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joshmoore added 3 commits May 30, 2022 12:32

Update text with suggestions

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Merge 'origin/main' into bf2raw

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Add bf2raw examples config

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joshmoore mentioned this pull request Sep 15, 2022

bioformats2raw metadata support ome/ome-zarr-py#174

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5 tasks

Add schema for ome series

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joshmoore mentioned this pull request Sep 15, 2022

fix: Update Hex40 definition tlambert03/ome-types#146

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Apply suggestions from code review

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Co-authored-by: Melissa Linkert <melissa@glencoesoftware.com> Co-authored-by: Sébastien Besson <seb.besson@gmail.com>

joshmoore added 3 commits September 22, 2022 08:24

Apply to v0.4 only

861227b

Re-iterate plate precedence without OME/METADATA.ome.xml

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Backport latest/bf2raw to 0.4

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melissalinkert reviewed Sep 22, 2022

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Re-word the 'series' section

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Make plate/series link a "SHOULD"

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sbesson approved these changes Sep 26, 2022

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joshmoore added 2 commits September 26, 2022 15:17

Add 'transitional' to 'omero' spec

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Add 0.4.1 changelog

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joshmoore mentioned this pull request Sep 26, 2022

Bioformats layout ome/ome-ngff-validator#13

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joshmoore merged commit 449fbca into ome:main Sep 28, 2022

joshmoore deleted the bf2raw branch September 28, 2022 18:20

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bioformats2raw.layout #112

bioformats2raw.layout #112

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imagesc-bot commented Oct 13, 2022

		- If "OME/METADATA.ome.xml" or the "series" attribute do not exist:
		- existing "plate" metadata will take precedence if it exists, or

bioformats2raw.layout #112

bioformats2raw.layout #112

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