ome / omero-cli-render

OMERO command-line tool for rendering
https://www.openmicroscopy.org/omero/
GNU General Public License v2.0
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Add support for defaultZ/defaultT #16

Closed sbesson closed 5 years ago

sbesson commented 5 years ago

As noticed as part of the work on https://github.com/IDR/idr0044-mcdole-tardislightsheet/pull/4, the render plugin YML format does not support the OMERO defaultZ/defaultT values.

For some datasets being able to both retrieve and set these values would be extremely valuable. I assume this might be represented as new top-level keys in the YML/JSON format

sbesson commented 5 years ago

As we might converge towards a version 2 of the YML format (https://github.com/ome/omero-cli-render/pull/15#discussion_r248330683), we might as well use the occasion and decision how we are going to represent these concepts in the YML rendering files.

Immediate options coming to mind are z/defaultz/defaultZ and t/defaultt/defaultT, depending on the compromise between short names, matching the OMERO names and keeping every key lowercase. An example would probably look as follows

---
version: 2
z: 5
t: 1
channels:
  1:
    color: "FF0000"
    label: "Red"
    start: 1
    end: 255
    active: True

/cc @dominikl

jburel commented 5 years ago

It is probably time to go back to the discussion about the url formatting for the web viewer since it is exactly the same thing here i.e. what is the best/efficient way to specify rendering settings. Entries like reverse lut will be needed too. and even taking it a step further see https://github.com/ome/omero-iviewer/issues/219

Let's try to unify so all apps "support" the same configuration

sbesson commented 5 years ago

Definitely :+100 for trying and unify/converge on our way to pass/return rendering settings . Also worth including the JSON representation returned by imgData https://docs.openmicroscopy.org/omero/5.4.9/developers/Web/WebGateway.html#imgdata as part of this discussion.

Practically, note we might need to have these features implemented in the upcoming weeks as some upcoming IDR studies might require setting defaultZ/defaultT. What are the next steps to start this discussion ? Should we start listing all representations across the various components and discuss them one by one?

jburel commented 5 years ago

defaultZ and defaultT won't be a problem to introduce I am thinking more about the rest since it will come. Let's go over the various apps after the storm has passed Already in the configuration we have a mix of rendering settings and channel metadata (label)

sbesson commented 5 years ago

Discussed with @dominikl @francesw and @pwalczysko. As some of the images in idr0050 would benefit from setting defaultZ. @dominikl and myself will be looking at extending the render format to support z/t as additional keys.