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Re: Running scripts with an open Virtual Hyperstack

Posted by ctrueden on Mar 25, 2015; 3:15pm
URL: http://imagej.273.s1.nabble.com/Running-scripts-with-an-open-Virtual-Hyperstack-tp5012163p5012167.html

Hi Greg,

> you just have to try to run an empty (!) script from the script editor
> to see all your RAM eaten up.

Firstly, I suggest checking:

  Edit > Options > ImageJ2

And ensure that "Enable ImageJ2 data structures" is _unchecked_.

There is a known issue with IJ1<->IJ2 image syncing where virtual stacks
can indeed be erroneously expanded to non-virtual images.

This option being enabled would also explain some of the sluggishness you
previously reported.

If that doesn't work, then I suggest you follow the directions at:
  http://imagej.net/Debugging#Debugging_JVM_hangs

To diagnose what exactly is happening to fill up all the RAM. In short, try
pressing Shift+\ (Plugins > Debug > Dump Stack) to open up a window with
information about what ImageJ is doing during the problematic operation.

You can then copy/paste the Stack Dump text (using e.g. pastebin.com or
gist.github.com) and send a link to the mailing list, so that developers
can investigate the issue.

Regards,
Curtis

On Wed, Mar 25, 2015 at 8:51 AM, Greg <[hidden email]> wrote:

> Hi,
>
> today I witnessed a rather odd behavior of Fiji when trying to run my
> jython
> scripts on a opened virtual hyperstack. So basically it took ages to run my
> script so I stripped it down to the point, where I realized that you just
> have to try to run an empty (!) script from the script editor to see all
> your RAM eaten up. I tested that for jython and javascript.
>
> So what I did:
>
> opened a 7gb ome.tiff with Bio Formats Importer in virtual hyperstack mode
> opened the script editor via file -> new -> script
> choosed python/java script as language
> pressed run on the empty(!) script
>
> What I see:
>
> When monitoring the RAM, I see it gets filled rather quickly by Fiji up to
> the size of 9.5Gb. For bigger input files more RAM gets 'used' accordingly.
> So for files exceeding my physical amount of Memory Fiji becomes
> unresponsive rather quickly. I experienced the same behavior for nd2 files.
>
> Is there a way to cirmumvent this ? I guess Fiji tries to load the whole
> image stack despite having chosen 'virtual stack' in the first place ?
>
> Best,
> Greg
>
>
>
>
> --
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> Sent from the ImageJ mailing list archive at Nabble.com.
>
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>

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