Posted by
Mark Hiner on
Dec 03, 2015; 1:35pm
URL: http://imagej.273.s1.nabble.com/handling-very-large-images-tp5015116p5015117.html
Hi Aryeh,
> but I did not find it in the FAQ after following the link.
Looks like it moved to the "Troubleshooting" section of the help pages:
http://imagej.net/Troubleshooting#NegativeArraySizeException> Again, no image has appeared even after about 20 minutes.
For situations like this you can try manually taking stack traces[1] to get
an idea of where it's getting stuck. If you check where the program is at 5
minutes and compare at 20 minutes you can get an idea of whether you have
hit an actual deadlock or are still processing. If you're up for it, this
is also a good use case for attaching a debugger to ImageJ[2] - then you
can truly see what's going on.
[1]
http://imagej.net/Troubleshooting#If_ImageJ_freezes_or_hangs[2]
http://imagej.net/Debugging#Attaching_to_ImageJ_instancesOn Thu, Dec 3, 2015 at 6:34 AM, Aryeh Weiss <
[hidden email]> wrote:
> I have a very large image (25x30 images, each is 1600x1200 pixels) that I
> want to load into imagej.
>
> This produces the java.lang.NegativeArraySizeException that was discussed
> in the following thread:
>
> imagej.1557.x6.nabble.com/Montage-java-lang-NegativeArraySizeException-td5014201.html
>
> In this thread, Curtis refers to a FAQ entry
>
http://imagej.net/FAQ#I_got_a_NegativeArraySizeException._What_caused_it.3F> but I did not find it in the FAQ after following the link.
>
> This image is not a stack, so I cannot use virtual stack.
> I tried to use the crop on import option, and asked for a 12000x12000
> section.
> It started off ok , and reported that it is verifying the cropping.
> Memory monitor reported that about 6.7GB were being used.
> It ran for about 45 minutes, and then finally threw the
> NegativeArraySizeException.
>
> Now I am trying it with a 5000x5000 crop, which should be no problem to
> load. memory monitor claims
> 6.4 GB are in use. Again, no image has appeared even after about 20
> minutes.
>
> Is there a work around to load it?
> Alternatively, is there a way to subsample it?
>
> --aryeh
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph: 972-3-5317638
> FAX: 972-3-7384051
>
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
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