Posted by
ctrueden on
Jul 19, 2013; 5:29pm
URL: http://imagej.273.s1.nabble.com/Out-of-Memory-Problems-tp5004033p5004045.html
Hi Oli,
Thanks for the report.
> Has something changed in the way ImageJ/Fiji handles garbage cleanup?
Can you please test whether the problem occurs with the "Life-Line" version
of Fiji available for download from:
http://fiji.sc/DownloadsThis is the last version of Fiji before a recent update which began to
integrate some substantial changes. (Nothing specific to memory management,
but things that could conceivably affect it in some cases...)
Since it sounds like your macro does not use any Fiji-specific plugins, you
could also test with "vanilla" ImageJ 1.47 available from:
http://imagej.net/download.htmlIf the problem happens only with the latest Fiji, and not the Life-Line
version, it is probably due to those recent changes I mentioned, and we can
investigate further. Otherwise, I am not sure what is going on...
Regards,
Curtis
On Fri, Jul 19, 2013 at 8:08 AM, Burri Olivier <
[hidden email]>wrote:
> Hi all,
>
> We're running a simple script to resize extremely large images to a more
> manageable size for imageJ.
>
> The original image is in the vicinity of 40'000x40'000 pixels
>
> What the plugin does (In macro language)
> 1. Split the image in 4096x4096 chunks
> 2. Load a single chunk, resize it
> 3. Place this chunk in a stack
> 4. Close the loaded chunk and its scaled counterpart, leaving only the
> stack.
> 5. Repeat for all chunks
> 6. When done, make a montage of the stack.
>
> This used to work just fine, but on a recent trial, imageJ ran out of
> memory (We have 32 Gb on the system, most of which is allocated to the JVM
> and ImageJ sees and uses it).
>
> Normally we used no more than a few Gb per resize, but as we load the
> image, the memory usage goes way up (>10Gb) but still succeeds.
>
> However, when we run the script again, instead of reusing the previously
> allocated memory, it keeps rising until an out of memory error.
>
> We've tried just opening and closing the same image over and over and
> memory usage keeps climbing up to the Out of memory error as well,
> suggesting this does not come from the macro code itself.
>
>
> Has something changed in the way ImageJ/Fiji handles garbage cleanup?
>
> Thanks for any info!
>
> Oli
>
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