Posted by
Olivier Burri on
Jul 23, 2013; 9:08am
URL: http://imagej.273.s1.nabble.com/Out-of-Memory-Problems-tp5004033p5004090.html
Dear Johannes,
Thanks for the email and the info.
I've tried loading a large dataset over and over through a macro (Load, close loop) after updating Fiji
And I still get the out of memory error.
Here it is, let me know if there's anything else you need.
Best
Oli
(Fiji Is Just) ImageJ 1.48a; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 18404MB of 18411MB (99%)
java.lang.OutOfMemoryError: Java heap space
at loci.common.DataTools.makeDataArray(DataTools.java:574)
at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:215)
at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)
at loci.plugins.in.Importer.readPixels(Importer.java:150)
at loci.plugins.in.Importer.run(Importer.java:89)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:196)
at ij.IJ.runPlugIn(IJ.java:160)
at ij.IJ.runPlugIn(IJ.java:149)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
at ij.IJ.runUserPlugIn(IJ.java:196)
at ij.IJ.runPlugIn(IJ.java:160)
at ij.IJ.runPlugIn(IJ.java:149)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:438)
at ij.io.Opener.openImage(Opener.java:310)
at ij.io.Opener.openImage(Opener.java:333)
at ij.io.Opener.open(Opener.java:143)
at ij.io.Opener.openAndAddToRecent(Opener.java:246)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
at java.lang.Thread.run(Thread.java:662)
Olivier Burri
Engineer - Image Processing
& Software Development
EPFL - SV - PTECH - PTBIOP
-----Original Message-----
From: Johannes Schindelin [mailto:
[hidden email]]
Sent: lundi 22 juillet 2013 18:15
To: Burri Olivier
Cc:
[hidden email]
Subject: Re: Out of Memory Problems
Hi Olivier,
On Mon, 22 Jul 2013, Burri Olivier wrote:
> Thanks for the info, I downloaded the "Life Line" version
It was Curtis' brilliant idea to force me to provide that version. I cannot thank him enough!
> 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.
I investigated and am almost certain to have solved the issue with this:
https://github.com/imagej/imagej/commit/849c2b9aI also uploaded a new ij-legacy.jar from the fixed version.
May I ask you to update Fiji and test again?
Thanks,
Johannes
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