Add preliminary implementation for SAM2

[anwai98]

This PR adds preliminary (and super dirty) integration of SAM2 to our annotator.

As the current status:

• 2d works super smooth (all features from our current UI more or less) - and it's ready to test.
• For 3d, I have a few tiny puzzles to join, then it'll be ready. I'll ping @Marei33 once there's more progress here.

Also, keeping @constantinpape and @caroteu in loop!

[anwai98]

Additional TODOs spotted:

• Remove "s" keybinding for the 3d annotator tool

EDIT: Naaaah, we are trying to bring single slice segmentation back! ;)

[anwai98]

Another comment: I figured out the error for 3d annotator (finally) I'll debug it quickly and try to fix it!

[anwai98]

It's fixed now! @constantinpape

Can you give it a shot? (by pulling the latest state here and https://github.com/computational-cell-analytics/SAM2_Experiments/pull/43)

[constantinpape]

I gave it a try and it seems to work better now but is still not very stable.

What I tried:

• Add a single point and segment in 3D via Segment All Slices
• This worked (but takes quite long on CPU). The result is not great, but ok enough.
• Add a second negative point.
• It fails, see the traceback below.

ValueError                                Traceback (most recent call last)
File ~/Work/my_projects/micro-sam/micro_sam/sam_annotator/_widgets.py:1737, in SegmentNDWidget.__call__(self=<micro_sam.sam_annotator._widgets.SegmentNDWidget object>)
   1735     return self._run_tracking()
   1736 else:
-> 1737     return self._run_volumetric_segmentation()
        self = <micro_sam.sam_annotator._widgets.SegmentNDWidget object at 0x7fca95b12570>
File ~/Work/my_projects/micro-sam/micro_sam/sam_annotator/_widgets.py:1720, in SegmentNDWidget._run_volumetric_segmentation(self=<micro_sam.sam_annotator._widgets.SegmentNDWidget object>)
   1717     self._viewer.layers["current_object"].data = seg
   1718     self._viewer.layers["current_object"].refresh()
-> 1720 seg = volumetric_segmentation_impl()
   1721 self._viewer.layers["current_object"].data = seg
   1722 self._viewer.layers["current_object"].refresh()

File ~/Work/my_projects/micro-sam/micro_sam/sam_annotator/_widgets.py:1690, in SegmentNDWidget._run_volumetric_segmentation.<locals>.volumetric_segmentation_impl()
   1685 z_values_boxes = np.concatenate(
   1686     [box[:1, 0] for box in box_prompts.data]
   1687 ) if box_prompts.data else np.zeros(0, dtype="int")
   1689 # TODO: Make this modular.
-> 1690 if z_values:
        z_values = array([7., 7.])   1691     frame_id = z_values[0]
   1692 else:

ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

[constantinpape]

I also tried with a box prompt first -- the result looked much better, but trying to add more prompts fails with a similar error as before.