segment folder function not working for dev_mc branch.

[Abraham George Smith]

A problem has been reported with segment folder not working in the dev_mc branch.

Looks like the following is causing the issue:

segment_folder.py", line 87, in segment_folder
assert seg_classes[0][0] == 'Background'
AssertionError

I will work on first reproducing this issue and then working on a solution (it's probably quite simple to fix).

[Abraham George Smith]

I now ran into a problem where images can be 'too small' as they are smaller than the automatically found patch size on the server.

/trainer/model_utils.py", line 264, in segment_3d
assert image.shape[2] >= in_tile_shape[2], f"{image.shape[2]},{in_tile_shape[2]}"
AssertionError: 212,244

I need to update the server to handle images smaller than the default patch size.

[Abraham George Smith]

Now solved (I believe) with 1f8e287
and 400149a
Waiting on feedback from user testers.

[Abraham George Smith]

I noticed that the segment folder progress bar does not update. I will work on a fix.

[Abraham George Smith]

Segment folder progress bar now fixed to work for multiclass output with the following commit:

3e4aa16

[Abraham George Smith]

It worked with my own tests and I haven't received any more complaints from the users so I will close this for now.