[GOAL] Support Range Annotations

[droumis]

Summary and Links

• annotation (lead: @hoxbro)
• Use holonote for roi/annotation management
• Potential extension: UI integration into the Bokeh toolbar.

Relevant Workflows

• ephys viewer
• eeg viewer
• spike raster

Inspiration:

• MNE timespan annotations.. Our 1D annotations should be able to cover the functionality on this tutorial.
• CaImAn spatial annotation (contours) renderer
• SpatialData package polygon annotations

Requirements

• Add/remove individual annotations
  • Add
    • Programmatically
    • UI:
      • Drag inside the data-view to create annotations with the description currently selected, or If there is none selected, can add a new description for the yet uncategorized annotations.
      • editing the table
  • Remove
    • Programmatically
    • UI:
      • right-clicking on an individual annotation, or all selected, for an option to remove
      • editing the table
• Edit individual annotation range
  • Programmatically
  • UI:
    • dragging them or their boundaries
    • editing the table (ideally with optional dial widgets in each value cell)
    • auto merge overlapping annotation ranges of same description
• Add/remove/edit description (aka tag / label)
  • Edit the description of one single annotation or all annotations of the currently selected kind
  • Remove description removes all annotations of the input or selected description
  • ability to assign multiple descriptions to the same annotated range
    Styling
  • Auto-color-code any annotations based on description
• Labels on annotations OR some way to easily derive a legend/color-key from the annotation table
  • 
    Behavior
• Synchronized annotations across a HoloViews container (overlay, layout)
  • example: annotations need to be linked across eeg-viewer and its minimap
    • 
• Synchronized annotations across plots in different notebook cells
• Shift-select of multiple annotations (for batch actions)
• Live-updating table UI of annotation - (ID, dimN-start, dimN-end, description(s))
  • Ideally as a click & type-editable tabulator-like pane
• Often, the duration of annotations for a given description will be consistent (e.g. 1 second), so we need some way to create annotations just based on start/onset and a defined duration
• Here is an example of how annotations are stored for MNE.. it contains original time then onset, duration, and description fields

# MNE-Annotations
# orig_time : 2009-08-12 16:15:00
# onset, duration, description
0.0,4.2,T0
4.2,4.1,T2
8.3,4.2,T0
12.5,4.1,T1
16.6,4.2,T0
20.8,4.1,T1
24.9,4.2,T0