label properties

[will-moore]

Adds properties to labels .zattrs exported from OMERO.

See functionality tests below. But first question is probably what we want to name these properties and if we want them included by default or only with a cli argument?

        "properties": [
            {
                "label-value": 1,
                "omero:roiId": 212825,
                "omero:shapeId": 390575
            },

To Test - need an Image or Plate with masks

• omero zarr export Image or Plate
• omero zarr masks (same Image or Plate)
• Open the image/labels/0/.zattrs in a text editor to see properties.
• And/or napari path/to/image with ome-zarr-py at Add support for label properties in zattrs and plugin ome-zarr-py#61 installed should display properties when you mouse-over a mask.

[joshmoore]

One minor question, otherwise, 👍

[joshmoore]

If we assume that omero: is a "safe"-prefix for the moment, i.e. we can do what we want there, then probably the only question I have is the naming of the text field. @DragaDoncila proposed class in ome/ome-zarr-py#61. @will-moore, from your POV, would we post-process text into class where appropriate? Should it then be omero:text?

[will-moore]

I don't think we have to specify that this text came from OMERO in order to understand it. Similar to color - it might have come from OMERO, but we don't really care - we just want to know that the label has a color (or some text).
But these properties don't have defined keys in the spec (like flexible key-value pairs in OMERO) so I think we're "safe" to do what we want, without any prefix?
On the other hand I guess there's no harm to record the state that OMERO masks were in at the time of export, so I'm happy to use omero:text. I think class was just an example, rather than a reserved word?

[joshmoore]

Otherwise, tested via:

$ omero hql --style=plain "select distinct s.textValue, s.roi.id from Shape s where s.roi.image.id = 5514374" --limit=-1 | tee rois.csv
$ omero zarr masks Image:5514374 --label-map=rois.csv
$ cat 5514374.zarr/labels/Chromosomes/.zattrs  | jq '.["image-label"]["properties"][0]'
{
  "label-value": 1,
  "omero:roiId": 1369051,
  "omero:shapeId": 1369067,
  "text": "Chromosomes"
}

[will-moore]

That last commit is needed if we want to stitch together multiple Images + Labels, e.g. into a Plate as at ome/ome-zarr-py@4306bbb
and was used in my demo last week.

I noticed from that code, that (even before this change) we are only exporting 1 properties dict per ROI, not per shape. So if there are multiple Shapes per ROI, the omero:text value and omero:shapeId exported will simply be from the last one. This comes from the decision previously to have all 'shapes' exported with the same mask_value so that they are all displayed with the same color in napari (with 'auto' color mode). However, we could achieve the same thing by specifying a 'color' value in the labels metadata.

[joshmoore]

This sounds correct since we only support a UNION interpretation of shapes within a single ROI.

[joshmoore]

Ran successfully together with gh-53 after solving the merge conflict on Plate:2551. Waiting for labels to upload to visually verify.