Add "no size marker detected" fatal error message to pcv.report_size_marker
?
#1638
Labels
enhancement
Enhancements to existing features
pcv.report_size_marker
?
#1638
Is your feature request related to a problem? Please describe.
We generally recommend that color cards be utilized as size markers for scaling pixel measurements, but report size marker is still an option. It's a helpful wrapper for cases where someone doesn't have a color card, which is true of microscopy images for example. If no size marker object is detected under the current parameters, a rather unhelpful error message is triggered in the middle of the function.
Describe the solution you'd like
I propose we detect the lack of
marker_contour
orroi_mask
upstream of this step in the function, and give an informative error message. Also maybe plotmarker_bin
overlaid on the input image as a debug to help adjust threshold up or down.Describe alternatives you've considered
Warning message and add "size marker found" observation/return? Continues on with analysis workflow to extract data but those datapoints are unscalable later on and could get filtered out.
Additional context
The text was updated successfully, but these errors were encountered: