Change error in spherefitted curvature to a warning

[haesleinhuepf]

I'm wondering if the tools would be easier to use if we suppressed this error and replaced it with a warning. This could be done here:

https://github.com/haesleinhuepf/napari-process-points-and-surfaces/blob/a6c9113b4860917cbf6beb2b6c535e9ecced1d25/napari_process_points_and_surfaces/_quantification.py#L247-L254

By writing something like:

     except Exception: 
         curvature[idx] = np.nan 
         residues[idx] = np.nan

 if np.nan in curvature: 
     warnings.warn(f"The chosen curvature radius ({radius})" 
                       "was too small to calculate curvatures. Increase "  
                       "the radius to silence this warning.") 

[haesleinhuepf]

Hi Johannes @jo-mueller ,

I'm wondering what's your opinion here. I tried the above implementation in a branch and you can find an example notebook here. Read the last columns of the two tables there carefully. As far as I can see, the proposed code-change will enable us to use the function in more scenarios, because only some values are NaNs and no error happens.

Let me know what you think! Thanks!

Best, Robert

[jo-mueller]

Hi @haesleinhuepf ,

I think that's very reasonable to do. The NaNs are also already accounted for in the cluster plotter so I wouldn't expect them to do much harm. Also, I like using the mesh average size as a way to standardize the measurement!

[haesleinhuepf]

Thanks for the feedback @jo-mueller !

Also, I like using the mesh average size as a way to standardize the measurement!

Yeah, I also like it. Unfortunately, this doesn't allow inter-sample comparison. I'll open another issue for this.