Posted by
Cameron Nowell-2 on
Jul 22, 2013; 10:17pm
URL: http://imagej.273.s1.nabble.com/Out-of-Memory-Problems-tp5004033p5004082.html
Hi Guys,
I would like to add that the life line versions fixed similar memory overflow problems when running scripts on a couple of Macs here as well.
Cheers
Cam
Cameron J. Nowell
Research Facilities Manager
Monash Institute of Pharmaceutical Sciences
Monash University
399 Royal Parade
(Mail address: 381 Royal Parade)
Parkville, VIC, 3052
Australia
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-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Burri Olivier
Sent: Tuesday, 23 July 2013 12:43 AM
To:
[hidden email]
Subject: Re: Out of Memory Problems
Hi Curtis,
Thanks for the info, I downloaded the "Life Line" version In terms of loading images (Just .tif files) as well as for our macro, I see the problem disappears so it does seem like it might come from the latest installement of Fiji.
If you want more detailed info, please let me know!
Best
Oli
Olivier Burri
Engineer - Image Processing
& Software Development
EPFL - SV - PTECH - PTBIOP
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Curtis Rueden
Sent: vendredi 19 juillet 2013 19:29
To:
[hidden email]
Subject: Re: Out of Memory Problems
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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