How to tell if pcv.find_objects() didn't find any contours?

[Tronheim]

I would like to handle an exception in an automated phenotyping system when no objects have been found. It is not clear to me what would find_objects return in that case that I could use for verification that there are no contours detected.

[nfahlgren]

Hi @Tronheim, great question. There are at least two approaches, depending on what works best for you.

When pcv.find_objects does not find any contours, it returns an empty list (contours is otherwise a list of contours) and None (hierarchy). So you could check the length of the contours list, set up a conditional on whether contours is True/False (not empty/empty), etc.

Alternatively, I think a somewhat more robust approach is to check later in the workflow. This is because pcv.find_objects may find contours that end up getting filtered out by pcv.roi_objects later. Or in other words, find_objects is only empty when no contours are found (no background) but roi_objects is empty when no plant is found within the ROI, even if there are background contours.

When you run pcv.roi_objects the last of the four return values is area of the remaining object(s) and I typically put a conditional check on the rest of the workflow that only continues it when area > 0, for example: https://plantcv.readthedocs.io/en/stable/tutorials/arabidopsis_multi_plant_tutorial/

[Tronheim]

Thanks @nfahlgren . I changed from contour list length to r_roi_object area and that fixed my problem.