I am facing an intermittent error when trying to export fused images as tiffs (I see that someone else is struggling Problem in image fusion BigStitcher headless imageJ with fusion, but from the stack trace the error I am encountering appears unrelated).
When fusing/exporting images as Tif from a BigStitcher dataset using the option
Fused Image: Save as (compressed) TIFF stacks I encounter rejected tasks being submitted to the TreadPoolExecutor() object:
I have trouble recreating the conditions under which it worked (it seems to fail most of the time now).
- The error does not occur when I choose the output option to display the result in IJ.
- most other parameters (downsampling factor, bit depth) don’t seem to play a role if I toggle them individually.
- freshly downloaded and updated Fiji with only BigStitcher as an additional update site.
I have a feeling that the problem is not so much in BigStitcher per se, but in the underlying Tiff writing functions (several packages involved in the traceback) that split the write action into separate tasks that get submitted to the ThreadPoolExecutor.
I tried adjusting the maximum number of threads and the maximum amount of memory in the Fiji options to no avail. The system has a Core i9 CPU which has many cores and there are 128GB of RAM (don’t have the exact specs on hand atm) so I doubt it is a hardware limitation. In particular because it worked some of the time.
I googled the error message and although I found several stackoverflow posts I am none the wiser.
Any ideas ?