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showinf OutOfMemoryError
with large JPG file
#4175
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I was able to recreate the problem with showinf.bat from the bftools programs. I saw the problem go away when I increased the Java Max Heap size to 15g by setting a bftools environment variable BF_MAX_MEM: cmdprompt> set BF_MAX_MEM=15g The following are the commands to first show the problem and then display the image after setting BF_MAX_MEM to 15g cmdprompt> showinf ......\WORKSPACE\standalone\IHC45-10xLyz.jpg cmdprompt> set BF_MAX_MEM=15g cmdprompt> showinf ......\WORKSPACE\standalone\IHC45-10xLyz.jpg Reading core metadata Reading pixel data (0-0) Launching image viewer Reading global metadata Reading metadata The image then got displayed. I'm very new to bioformats,omero,showinf, etc so I'm not sure of your environment. So maybe try setting the environment variable to 15g and then try your commands. set BF_MAX_MEM=15g |
I do see BF_MAX_MEM mentioned in this doc: https://bio-formats.readthedocs.io/_/downloads/en/v6.13.0/pdf/ Also, doing a Google search on BF_MAX_MEM shows several discussions about using BF_MAX_MEM. |
Hi, thanks a lot @scuniff, I'm trying this today, and closing this following up |
We stumble had an error on a large jpeg image (6 624 x 40 653 px, 214 MB) when calling
showinf
(throughomero transfer prepare
)Here is the trace:
The file can be downloaded (till April 26th 2024, ping me here if you need it later) at that link:
https://filesender.renater.fr/?s=download&token=5052c708-6aeb-44b4-bae5-e570db81d985
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