Contour missing

[WuJunxu]

Thanks for your great work! While I tried to get the unique contour by calling the function omnipose.core.get_contour(), I got contour missing.

contour_map, contour_list, unique_L = omnipose.core.get_contour(msk, affinity_graph, coords, cardinal_only=1)

The white region in mask is the background, and the missing contour is in the transition of bg and fg. The missing contour present bellow (red rectangle region):

mask	boundary	contour

[kevinjohncutler]

@WuJunxu that is interesting! It also looks like it is not properly returning the contours between masks. They should be pairs of closed loops (indexed from 0 to N-1 where N is the number of pixels on the contour) but only one side of each interface is getting a contour. Also the edges of the image are not recognized as part of the contour. I'll have to look up my code for using this function, as it was more for internal development. Stay tuned.

[kevinjohncutler]

@WuJunxu could you share this example mask when you get the chance?

[kevinjohncutler]

Here is a link to a new docs page I have added to demo the use of the contour function: https://omnipose.readthedocs.io/contours.html

[kevinjohncutler]

@WuJunxu closing now, please reopen if the example code does not resolve your issue. Thanks!