Avoid using Labels.color

[zoccoler]

With napari 0.4.19, this warnings pops up after manually selecting a cluster

FutureWarning: Labels.color is deprecated since 0.4.19 and will be removed in 0.5.0, please set Labels.colormap directly with an instance of napari.utils.colormaps.DirectLabelColormap instead.!

It may be solved by replacing at least this line, this line and this line with something like:

layer_in_viewer.colormap= self.visualized_layer.colormap

and

"colormap": DirectLabelColormap(color_dict=cmap_dict),

This needs to be tested.

[gboscagli]

Hi all,
I know I'm probably a bit off-topic. I'm encountering the same Warning message using another Napari plugin (Napari-SpatialData). I have napari v.0.4.19.post1. My data points in Napari are not colored, they remain uniformely grey. To your knowledge, is there a way to set the colormap on-the-fly or some other adjustments I can do? From #308 I saw that this remains an issue in Napari >=0.5.0.

[zoccoler]

Hi all, I know I'm probably a bit off-topic. I'm encountering the same Warning message using another Napari plugin (Napari-SpatialData). I have napari v.0.4.19.post1. My data points in Napari are not colored, they remain uniformely grey. To your knowledge, is there a way to set the colormap on-the-fly or some other adjustments I can do? From #308 I saw that this remains an issue in Napari >=0.5.0.

Hi @gboscagli !
This issue is because the Labels layer in napari>=0.5.0 does not have a .color attribute anymore. The napari developers left a deprecation warning so that plugin developers could update their plugins in case they were using that attribute.
In your case, it would be best to create the issue directly in the Napari-SpatialData plugin, so that developers there can work on the issue on their code.

[gboscagli]

Hi @gboscagli ! This issue is because the Labels layer in napari>=0.5.0 does not have a .color attribute anymore. The napari developers left a deprecation warning so that plugin developers could update their plugins in case they were using that attribute. In your case, it would be best to create the issue directly in the Napari-SpatialData plugin, so that developers there can work on the issue on their code.

That's what I did, I'm in contact with Napari-SpatialData developers and they indeed confirmed it's on the roadmap. By the way, I updated Napari to 0.5.0 and the problem remains, so in the case of SpatialData it's probably matter of internal metadata.

Thanks for the response!

[zoccoler]

Fixed via #308