Update modules to use markups instead of annotations

[lassoan]

Annotations module, which provides vtkMRMLAnnotationROI and vtkMRMLAnnotationRuler nodes have been deprecated since April 2021 and will be removed in Slicer-5.4 stable version early next year.
Since some modules in this extension use annotation nodes, these modules need to be updated to use markups nodes before the end of this year.

This section of the migration guide should help with implementing the changes and any questions can be asked at the Remove Annotations module topic in the Slicer forum.

Impacted module:
GelDosimetryAnalysis\GelDosimetryAnalysis.py

[cpinter]

I checked the code and saw that it is fairly easy to enable using markups instead of annotations in this extension.

However, so many other things have changed in Slicer that in order to make it fully (and conveniently) functional again, more work would be needed. For example the DICOM browser now opens inside the main Slicer window and the user needs to switch back and forth. Also, the line profile plot (this is related to the ruler/line issue) does not appear in the view for some reason. My assessment, however, is that instead of just fixing the plot view, much more work would be needed to make this extension actually usable again in the latest Slicer (my guess is a whole week for me). It would include making it guidelet-style instead of slicelet.

[lassoan]

If you don't think you'll have time to maintain the extension then you can describe in the documentation what Slicer version is needed to use it and remove it from the extension index for the current Slicer version. If someone wants to use the extension with a more recent Slicer version then the necessary updates can be done and the extension can be added back to the extensions index.