[BUG] Drawing breaks due to `cv2.findContours` handling

[mrariden]

When drawing, sometimes multiple contours are found for a single mask, but the code expects to encounter only a single contour.

For example:

cellpose/cellpose/gui/gui.py

Lines 1574 to 1575 in 94ae120

	contours = cv2.findContours(mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_NONE)
	pvc, pvr = contours[-2][0][:,0].T

and

cellpose/cellpose/gui/gui.py

Lines 1589 to 1591 in 94ae120

	contours = cv2.findContours(mask, cv2.RETR_EXTERNAL,
	cv2.CHAIN_APPROX_NONE)
	pvc, pvr = contours[-2][0][:,0].T

and in 3d GUI:

cellpose/cellpose/gui/gui3d.py

Lines 292 to 294 in 94ae120

	contours = cv2.findContours(mask, cv2.RETR_EXTERNAL,
	cv2.CHAIN_APPROX_NONE)
	pvc, pvr = contours[-2][0].squeeze().T

and here:

cellpose/cellpose/gui/gui3d.py

Lines 308 to 310 in 94ae120

	contours = cv2.findContours(mask, cv2.RETR_EXTERNAL,
	cv2.CHAIN_APPROX_NONE)
	pvc, pvr = contours[-2][0].squeeze().T

and also in merge_cells():

cellpose/cellpose/gui/gui.py

Lines 1318 to 1320 in 94ae120

	contours = cv2.findContours(mask, cv2.RETR_EXTERNAL,
	cv2.CHAIN_APPROX_NONE)
	pvc, pvr = contours[-2][0].squeeze().T

This error manifests when there is a small hole in a mask that is being overlapped that is right on the edge of a mask, (see image below). Presumabely there are also other edge cases when this occurs. No errors are ever seen because the add_mask() functions are called in the overriden Qt virtual methods (keyPressEvent, mouseClickEvent) which is, apparently by design.

Example breaking mask (mask is on the left with a single missing interior pixel):

Two changes should be made:

1. Handle the edge case for when multiple contours are found.
2. Implement more robust drawing logic that will allow drawing to fail gracefully.

[mrariden]

This only appears to be a problem in the 3d GUI. Slicing out the problematic plane and using the 2D gui doesn't break

tiny_stack.tif

tiny_stack_masks.tif