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bioformats2raw.layout #112

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merged 32 commits into from
Sep 28, 2022
Merged

bioformats2raw.layout #112

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d7c0556
First draft of bioformats2raw.layout
joshmoore Apr 7, 2022
8ee02d1
Add layout example
joshmoore Apr 8, 2022
ee15455
Improve wording of "SHOULD parse multiple images", thanks to Ilan
joshmoore Apr 20, 2022
c8e98e4
Clarify contents of METADATA.ome.xml, thanks to Melissa
joshmoore Apr 20, 2022
6403d88
Add schema & test for bf2raw metadata
joshmoore Apr 21, 2022
890e8a2
Add missing schema file
joshmoore Apr 21, 2022
b099281
Merge 'origin/main' into bf2raw
joshmoore May 3, 2022
2b67a36
Add applicable versions statement
joshmoore May 11, 2022
31d34c3
Update text with suggestions
joshmoore May 30, 2022
3173303
Merge 'origin/main' into bf2raw
joshmoore May 30, 2022
d44a066
Add bf2raw examples config
joshmoore May 30, 2022
7574d22
Add test to find missing configs
joshmoore May 30, 2022
ff5d7ec
Split subitems to pass linting
joshmoore May 30, 2022
e2119e5
Add graphical layout representation
joshmoore May 30, 2022
4fcc045
Fix missing whitespace
joshmoore May 30, 2022
57acc23
Add "series" attribute in "OME" group under bioformats2raw.layout
melissalinkert Jul 5, 2022
5eca169
Update the MUST/SHOULD semantics
joshmoore Jul 18, 2022
cf4e04c
Fix doubly indented bullets
joshmoore Sep 14, 2022
89c322d
Make minimum spec a link
joshmoore Sep 14, 2022
3691437
Add no-toc sections
joshmoore Sep 14, 2022
499caee
Re-arrange and add more text
joshmoore Sep 14, 2022
c7582e5
Make changes based on feedback from Will
joshmoore Sep 15, 2022
399b70b
Add bf2raw plate example
joshmoore Sep 15, 2022
740a11b
Add schema for ome series
joshmoore Sep 15, 2022
1f91482
Apply suggestions from code review
joshmoore Sep 19, 2022
861227b
Apply to v0.4 only
joshmoore Sep 22, 2022
8e612ef
Re-iterate plate precedence without OME/METADATA.ome.xml
joshmoore Sep 22, 2022
a0919be
Backport latest/bf2raw to 0.4
joshmoore Sep 22, 2022
5971927
Re-word the 'series' section
joshmoore Sep 22, 2022
88fd042
Make plate/series link a "SHOULD"
joshmoore Sep 22, 2022
7b7c43f
Add 'transitional' to 'omero' spec
joshmoore Sep 26, 2022
106c301
Add 0.4.1 changelog
joshmoore Sep 26, 2022
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7 changes: 4 additions & 3 deletions latest/index.bs
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Expand Up @@ -315,10 +315,11 @@ Conforming groups:
Additionally:
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- If "OME/METADATA.ome.xml" is present, "OME" MUST be a Zarr group which:
- MAY contain a "series" attribute.
- "series" MUST be a list of string objects, each of which is a path to an image group.
- The order of the paths MUST match the order of the "Image" elements in "OME/METADATA.ome.xml".
- MAY contain a "series" attribute. If so:
- "series" MUST be a list of string objects, each of which is a path to an image group.
- The order of the paths MUST match the order of the "Image" elements in "OME/METADATA.ome.xml".
- 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.

- separate "multiscales" images MUST be stored in consecutively numbered groups starting from 0 (i.e. "0/", "1/", "2/", "3/", ...).
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- Every "multiscales" group MUST represent exactly one OME-XML "Image" in the same order as either the series index or the group numbers.

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