[Docs] tracking issue for issues with the documentation

[psobolewskiPhD]

Documentation issues for 0.0.19 release docs, as viewed on June 1, 2024

Overview, installation are fine.

How do I section:

• interactively position a render plane issue: https://github.com/napari-threedee/napari-threedee/issues/205
  • major: there is no sample to load, either need to add it or re-work the example, e.g. using https://napari-threedee.github.io/generated/gallery/plugin/point_annotator_plugin/
• interactively position points issue: https://github.com/napari-threedee/napari-threedee/issues/206
• interactively position layers issue: https://github.com/napari-threedee/napari-threedee/issues/207
• annotate points in 3D issue: https://github.com/napari-threedee/napari-threedee/issues/208
  • major: Points layer is missing, the script needs to be updated
• annotate spheres in 3D issue: https://github.com/napari-threedee/napari-threedee/issues/209
  • major: extra plane layer in viewer versus the images, Points layer with different name
• annotate splines in 3D issue: https://github.com/napari-threedee/napari-threedee/issues/210
  • major: name is path now, no advance index in widget
• add ambient occlusion to a surface: everything is fine! 🎉
• paint labels on arbitrary planes issue: https://github.com/napari-threedee/napari-threedee/issues/211

Segmentation tutorial:

• 3D segmentation issue: https://github.com/napari-threedee/napari-threedee/issues/214
  • minor: installation instructions issue (pyqt needs to be installed, pydantic issue)

Explanations:

• Core concepts
  • Out-dated image, I think the copy is OK? PR to update: https://github.com/napari-threedee/napari-threedee/pull/229
• Manipulators
  • post https://github.com/napari-threedee/napari-threedee/pull/168 manipulators are in world coords.
  • _initial_rotator_normals and initial_rotator_normals doesn't exist anymore?
  • PR to update: https://github.com/napari-threedee/napari-threedee/pull/230

Annotations:

• Overview
  • spline is now Path
• Input/Output
  • There is no reader or writer anymore, should document the new way from https://github.com/napari-threedee/napari-threedee/pull/96
• the 3 specifications: I'm not sure if they need updating, seem ok, just Spline may need to be renamed Path?

Examples Gallery:

• top level ToC item Gallery for napari-threedee just points to homepage, should be removed? I made a fix: https://github.com/napari-threedee/napari-threedee/pull/226
• Library examples:
  • may be worth to have two approaches here for each case, the QtWidget ones, like https://napari-threedee.github.io/generated/gallery/library/render_plane_manipulator_library/ and then pure programmatic access rather than spawning the widget, like https://napari-threedee.github.io/generated/gallery/library/point_annotator_library/
    • see also: https://github.com/napari-threedee/napari-threedee/issues/154
    • surface annotator doesn't show anything and alt-click gives traceback: ValueError: operands could not be broadcast together with shapes (0,) (4,)
• Plugin examples:
  • all work, except for:
    • Plane point annotator (plugin): as noted above, it does not have a Points layer, adding one in the GUI requires close/reopen widget, as the dropdown is not updated. Fix as part of: https://github.com/napari-threedee/napari-threedee/pull/222
  • camera spline control could benefit from a how to?
  • surface annotator could benefit from a How to? Not clear how to use, but alt-clicks give traceback ValueError: operands could not be broadcast together with shapes (0,) (4,)

[psobolewskiPhD]

For all the How to, i'd like the same copy for the "open the example" in Instructions, point 1. How does this sound? (with a proper link to the proper Gallery page)

To run this example, download the script from the Examples Gallery page; the link is at the bottom. Ensure the location is somewhere memorable. Or, if you've cloned this repository, the script can be found at napari-threedee/docs/examples/plugin/. Ensure you have the appropriate virtual environment active, change directories to the script location, and then you can execute the script using:

python <name of script>