Posted by
ctrueden on
Mar 25, 2015; 8:21pm
URL: http://imagej.273.s1.nabble.com/Running-scripts-with-an-open-Virtual-Hyperstack-tp5012163p5012175.html
Hi Greg,
> this is the stack dump right after opening the virtual stack
Thank you very much for that vital information. It identified a serious bug
in ImageJ2, which I believe is now fixed.
Would you mind testing it? You can find the relevant JAR files here:
http://curtis.imagej.net/2015-03-25-bad-syncing/Place the two JAR files in your ImageJ installation's jars folder, and
delete the previous versions.
Two major changes of note:
1) The new imagej-common hopefully fixes the crazy RAM flooding.
2) The new imagej-legacy fully eliminates the "Enable ImageJ2 data
structures" option so that users are not bitten by problems relating to it
in the future. Developers who need this feature can instead now set the
"imagej.legacy.sync" system property, if they want to test it.
Please let us know how it goes; I am optimistic that these changes will
greatly improve matters.
We plan to upload these fixes to the ImageJ update site by end of day
tomorrow, unless you report back with continued (or worse) problems.
Regards,
Curtis
On Wed, Mar 25, 2015 at 11:15 AM, Greg <
[hidden email]> wrote:
> Hi Curtis,
>
> ya you are right, it might actually not related to scripts/plugins at all I
> think, this was just the first action I undertook after opening the virtual
> stack. That totally explains that slugginess ! The ImageJ2 datastructure
> option is and was disabled.
>
> So this is the stack dump right after opening the virtual stack, ca. 1.2Gb
> are used by Fiji at this moment:
>
>
http://pastebin.com/ex1yG6JM>
> The next dump is (hopefully) right in the moment when the RAM is filled
> rather quickly (around 8Gb at that very moment), this time to initiate the
> RAM flood I just started the script manager (without trying to run an empty
> script):
>
>
http://pastebin.com/LucCkLcA>
> After that, every [next slice] fills up the RAM a little more right now it
> is at 14.2Gb (the input file is 7Gb):
>
>
http://pastebin.com/BmiEketC>
> In the end Fiji is now almost unresponsive and filled 18Gb of my physical
> RAM (I got 32). Even when I close the virtual hyperstack, there are still
> 18Gb used as indicated by the activity Monitor from Mac OS 10.10:
>
>
http://pastebin.com/jApGDHs2>
> Please tell me if you need anything else, I am running ImageJ 149p as Fiji.
> Thanks for your help !
>
> Best,
> Greg
>
>
>
>
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