Bookmarks no longer colour correctly

[K-Meech]

Bookmarks e.g. https://github.com/mobie/platybrowser-datasets/blob/master/data/1.0.1/misc/bookmarks/manuscript_bookmarks.json#L553 no longer colour correctly. They still add extra tables / recognise the column, but don't apply the selected lut.

@constantinpape - could you possibly try changing 'glasbey' to 'Glasbey' in the bookmark? (I can't edit files on the arendt share so it's a bit hard for me to check)

[constantinpape]

That would be incosistent though, we use lower case for all the colors. Anyway, I gave you permissions for /g/arendt/EM_6dpf_segmentation/platy-browser-data/data/1.0.1/misc so you should be able to change it locally to test now.

[K-Meech]

I just tested this quickly on the arendt share, and changing it to upper case fixes the issue for me. Upper case is also how the luts are stated here: https://github.com/tischi/imagej-utils/blob/master/src/main/java/de/embl/cba/tables/color/ColoringLuts.java I imagine this means a number of bookmarks are affected this way...

[constantinpape]

Thanks for checking!

https://github.com/tischi/imagej-utils/blob/master/src/main/java/de/embl/cba/tables/color/ColoringLuts.java I imagine this means a number of bookmarks are affected this way...

Hmm, this means that the definition of colors in java and in the jsons got out of sync at some point. I don't really know why, because we agreed to have all the colors in the jsons lower capital at some point, e.g. glasbey or randomFromGlasbey.

Also, the colors in the images.json are specified this way, so I am a bit confused why this is inconsistent with the bookmarks.

Anyway, I can change this but we should make sure beforehand that everything is consistent.

[tischi]

I think we said lower case for the Bookmarks indeed. Let me check why that could have changed...

[tischi]

@K-Meech I guess this is only for the fancy olors, like Glasbey and not for simple colours like white and magenta, right?

[tischi]

Can you guys provide me with an example Bookmark in the platybrowser that I can use for testing. I have to do something else now but will fix it after lunch.

[constantinpape]

You just need a bookmark with glasbey in "color by column", right? Then take "Figure 5C: Gene clustering full body".

[constantinpape]

Just to add to the incosistencies with colormaps: The randomFromGlasbey we use for prospr doesn't work anymore, see #69.

(Smaller case glasbey in images.json still works though: the colormap for the cell segmentation is correctly displayed https://github.com/mobie/platybrowser-datasets/blob/master/data/1.0.1/images/images.json#L2608)

[tischi]

"Figure 5C: Gene clustering full body"

This works again with this change:

        if ( metadata.color != null )
        {
            // within MoBIE the convention is Captial first letter:
            // see class ColoringLuts
            metadata.color = WordUtils.capitalize( metadata.color );
        }