Question regarding returning files with no masks found

[GloriaAlvarado]

Hi,

I may have missed a command for this in the read the docs, and if so I apologize. I am having an issue where I run omnipose on a large image set via the command line and if an image does not have anything to segment, omnipose stops running. I get the error "AttributeError: 'NoneType' object has no attribute 'shape'". However, if I use the GUI to segment the same image that caused the error I can get an output that is empty, as in it is all recognized as background. Is there an argument I can add to my command line that will spit out empty mask files when needed?

Thank you,
Gloria

[kevinjohncutler]

@GloriaAlvarado Sorry about that, look's like that's an artifact of the npy output that you get without the --no_npy flag. I'll push a fix soon, but in the meantime, you can use that flag to avoid the error.

[GloriaAlvarado]

Hi!
Thanks for such a quick reply, I greatly appreciate it. Would you happen to have any additional advice on this if I said I was already using the --_no_npy flag?

-Gloria