Failed to redact item. 65449

[markemus]

I got this error trying to redact the label image for the CMU-1.tiff (renamed to .ndpi) test image from Openslide.

https://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu/

Any idea why this is? These should be proper ndpi images, I've used them (with the rename) in other programs without running into issues.

[markemus]

I get the same error when trying to redact a text field or even when redacting nothing at all.

[manthey]

I don't know what error you are getting.

tiff and ndpi aren't equivalent -- our software shouldn't care what they are named, but renaming a tiff as an ndpi or doing the reverse seems confusing (ndpi is almost a tiff file, but breaks the tiff specification in important ways).

[markemus]

It does break the format, but these are supposed to be ndpi and I believe they actually are. We've been able to use them to develop for ndpi in the past so I'm pretty confident that they are proper ndpi files. You can see some of the weirdness if you look at them in tiffinfo (with or without the rename).

But do you have ndpi test files that will work with this software?

[manthey]

You linked to ndpi files (not tiff). The CMU tests files also have tiff versions (which aren't ndpi). Yes, we have test files -- you'll see them listed in the https://github.com/DigitalSlideArchive/DSA-WSI-DeID/blob/master/tests/datastore.py. They get downloaded when you run the tests.

[markemus]

If you download the test files on the Openslide site you'll see they actually come with the .tiff extension :) but it doesn't matter. Thanks for the help finding your own test files.

How can I run the tests from within docker? I don't have all the dependencies installed locally.

EDIT: I tried 'docker exec -it wsi_deid_girder_1 sh' and then running pytest, but pytest wasn't installed and pip3 couldn't reach the repository.