Error NamesAndTypes Java Attribute Error 'mssage'

Usage & Issues
#1

Hi All,

I am trying to run a simple pipeline that resizes images and am having trouble getting past the metadata extraction.

My images files seem to be placed in the appropriate groups after metadata extraction step; however, when going to the NamesAndTypes step I receive the following error:

==

Error

Error while processing NamesAndTypes:
(Worker) AttributeError: ‘JavaException’ object has no attribute ‘message’

Do you want to stop processing?

==

I am running the latest version of CellProfiler with the latest version of Java available for OS X Catalina.

Any help would be greatly appreciated.

Ryan

#2

Hi @rmcqui1

Would you be able to confirm which version of CellProfiler you’re running? It also might help if you could upload a copy of the pipeline and a sample image set so that we can take a look.

#3

Hi @DStirling

Thanks for your replay. I am using CellProfiler 4.0.7 in OS X Catalina 10.15.17.

I am using a small subset of the sample data obtained by Bray et. al. available on github here:

Attached is the illumination pipeline I am using.

The metadata key I am currently using is:

^(?P<Plate>.*)_(?P<well>.*)_s(?P<site>[0-9])_w(?P<wavelength>[0-9])

Illum_Pipeline.cpproj (8.6 MB)

#4

Thanks for uploading that, the pipeline seems to be working just fine on my end so I’m not sure what’s happening there. Could you perhaps have an image missing or duplicated?

#5

Thanks for looking into this! When I went to check for duplicates I found that some of the images in my working directory got corrupted somehow. I redownloaded them and now the problem is solved! I’ll remember to check this first next time.

Thanks again.

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