just for fast feedback which might help you: i have a very simple pipeline that crashes the newest trunk build r20120705134759 (CellProfiler_2.0.0_win64_r20120705134759.exe). It seems the corresponding pipeline for the current official CP2 (version r11710) doesn’t crash.
error module seems to be: cellprofiler.cpmath._cpmorphology2.pyd
not crashing r11710 .cp (7.17 KB)
crashing trunk build r20120705134759.cp (8.11 KB)
In the IdentifyPrimaryObject the ‘size of smoothing filter’ was 0. Now after changing to ‘automatically calculate size of smoothing filter’ the program doesn’t crash anymore. Cheers, Jonathan
I’ve managed to replicate this error and have posted a bug report: github.com/CellProfiler/CellProfiler/issues/352. Thanks for the feedback!
You win the prize here - I had some code in “fill_labeled_holes” that assumed that there would be less than 64K hole-candidates in the image. Your noisy image (not your fault) must have been generating a random pattern after thresholding which broke the assumption. I should never have written the code that way to begin with - should be fixed in the upcoming trunk build.
Nice, concise, repeatable bug report - please feel free to send us more of the same (but I’m hoping it takes you a while before you find the next one).
This issue has been resolved in CellProfiler 2.1 and later, new releases of which can now be downloaded from http://cellprofiler.org.