ome / ome/ngff

OMERO schema is inconsistent with description

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Python
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Description

In v0.5.2 of the specification, the description of the OMERO metadata is inconsistent with the schema definition.

Specifically, the description says

Each dictionary in "channels" MUST contain the field "color", which is a string of 6 hexadecimal digits specifying the color of the channel in RGB format. Each dictionary in "channels" MUST contain the field "window", which is a dictionary describing the windowing of the channel.

but the schema does not label window or color as required properties.

This is strongly related to #192 which seems to be half complete because the schema was updated in https://github.com/ome/ngff/pull/202 but the description update was not merged in #297.

I believe that ome/ngff-spec as of the latest commit also has this inconsistency.

To clarify, the issue here is the inconsistency and not what parts of the OMERO metadata should be required (though as someone that often thinks about visualization, I appreciate the presence of color and window when possible!). Therefore, I created a new issue to be be resolved instead of adding this as a comment to #192 or #297.

I think resolving #192 should resolve this issue too, perhaps by merging #297.

Also, I apologize if my permarefs are not quite accurate or if this issue should be created in ome/ngff-spec. I became a little lost in the various repos and submodules.

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Compare the OMERO metadata description in index.bs around the referenced section with the required properties in schemas/image.schema. Read the history of #192, #297, and the referenced schema update to understand the intended resolution. Done means the specification text and schema agree about whether color and window are required.

Written by the indexing model from the issue text.

Assessment

Domain
documentation
Issue type
Documentation
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
38/100

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