Open ohkio opened 1 month ago
Ah, there's something fishy here:
java.lang.InterruptedException: The pool has been closed
I need to try to use kheops like you, headless in pyimagej. Maybe this is what triggers the issue. Have you tried directly in ImageJ / Fiji ? Can you potentially share a small example tiff you use in case the problem is data specific ?
Can you please try with this initialisation ?
import imagej
ij = imagej.init(['ch.epfl.biop:ijp-kheops:0.5.0'])
And then, if you want to keep 'stitching' to still specify the kheops version ?
(I couldn't reproduce your issue in pyimagej launching Kheops the way you did)
I observed a similar behaviour recently. Most probably it is because your original file is not calibrated. You can directly fix this by calling kheops and specifying the pixel size and using the checkbox 'override pixel size' in the kheops command. Alternatively you have a put a calibration in the original file to convert
Hello ijp-kheops team! I'm helping out a team close to me with slide digitization, I'm trying to incorporate this library into a script and workflow. I'm starting with a sequence of tiff images that have been stitched together using the Imagej stitching algorithm. My setup is on a dell laptop, kubuntu os, installed pyimagej using mamba, and I am trying to call the kheops command on a single stitched plane, not the whole set of images. I have been working at the problem for a while and am having trouble determining where the issue is happening. This is the log+error that I get when I run the code:
Here's the way that I called the function:
and here's how I initialized Imagej
Again, I've already got the stitching part to work so I know that my setup is decent, but any insights you can offer around what might be happening with the kheops part would be much appreciated.
Thank you!