Automatically set volume step to 1 on newly opened segmentations

[Elaine Meng]

Most of the time, click-drag with segmentation cursor in slice view doesn't put anything in the current segmentation model, or at least there is no blob shown in the 3D view. I realized that it is even more likely if you haven't recently changed which slice is shown (e.g. used the slider below the slice). If you just start the 4x4 view and don't move any sliders, then none of the segmentation-cursor drags create a surface, at least in my hands.

[Zach Pearson]

Change the step to '1'

[Elaine Meng]

Even if I manually change step size to 1, that only shows it in the 3D view.  Need to additionally show it in the slice view or else impossible to edit (e.g. erase parts).

[Zach Pearson]

I see what you mean. I've tried displaying segmentations in the 2D views a couple of ways: first, using the segmentation colors command to color the 2D slices by the segmentation. This sort of works, but is hard to update programmatically. Second, I tried another extreme abuse of ChimeraX's rendering engine to try to get it to blend the 2D texture of the segmentation with the 2D texture of the orthoplanes. That sort of worked again, but it's extremely fragile and tends to make graphics panic and stop working.

Looking again at the way 3D slicer accomplishes its 2D segmentation illustrations, they look like what ChimeraX calls overlays to me, so that's the next avenue I'm going to try.

[Zach Pearson]

Overlays are working great. 3 bugs to work out before merge:

• 3d segmentations still need to have step 1 set automatically
• need to figure out why you have to change the 2d view's current slice to see the segmentation overlay update (this only happens once then it updates automatically)
• the axial view is upside down

[Zach Pearson]

OK, should be fixed in tomorrow's build. Now whenever we create a new segmentation we call volume.new_region to set the step to 1 automatically.

You no longer have to jiggle the slices to get the new segmentation's overlay to start updating.

The axial view is no longer reversed.