[ome-users] Fwd: java.lang.illegalArgumentException: Array size too large

[Melissa Linkert]

Hi Felix,

> I am trying to open an ndpi-file of about 90MB. And I get the following exception:
> 
> 
> (Fiji Is Just) ImageJ 2.0.0-rc-25/1.49p; Java 1.6.0_65 [64-bit]; Mac OS X 10.10.2; 37MB of 5011MB (<1%)
> 
> java.lang.IllegalArgumentException: Array size too large: 82560 x 29440 x 1
> 	at loci.common.DataTools.safeMultiply32(DataTools.java:854)
*snip*
> Here’s a link to the file
> https://dl.dropboxusercontent.com/u/18607042/hamamatsu_slide-scanner-example.ndpi
> 
> The image can be imported with OMERO.importer. However fiji or icy have the same problem if I want to open the series with the highest resolution.
> I tried running imageJ with java8 too, to see if it was a java array problem…
> 
> I was using the bio-formats version 5.0.7
> 
> Is this a java of a loci problem?

ImageJ/Fiji/Icy are limited to 2GB of pixel data in each image.  You
will need to select the "Crop on import" option in the "Bio-Formats
Import Options" window to open smaller sections of the image at a time.
OMERO handles large images like this by working with small tiles at a
time behind the scenes, which is why the file imports into OMERO without
an error.

If the "Crop on import" option doesn't work, please let us know.

Regards,
-Melissa

On Wed, Mar 18, 2015 at 11:47:55AM +0000, MEYENHOFER Felix wrote:
> 
> Hi
> 
> I am trying to open an ndpi-file of about 90MB. And I get the following exception:
> 
> 
> (Fiji Is Just) ImageJ 2.0.0-rc-25/1.49p; Java 1.6.0_65 [64-bit]; Mac OS X 10.10.2; 37MB of 5011MB (<1%)
> 
> java.lang.IllegalArgumentException: Array size too large: 82560 x 29440 x 1
> 	at loci.common.DataTools.safeMultiply32(DataTools.java:854)
> 	at loci.common.DataTools.allocate(DataTools.java:828)
> 	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:153)
> 	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:313)
> 	at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:243)
> 	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:313)
> 	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:313)
> 	at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:190)
> 	at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:87)
> 	at loci.plugins.util.ImageProcessorSource.getObject(ImageProcessorSource.java:74)
> 	at loci.formats.cache.Cache.recache(Cache.java:208)
> 	at loci.formats.cache.Cache.recache(Cache.java:228)
> 	at loci.formats.cache.Cache.<init>(Cache.java:92)
> 	at loci.plugins.util.BFVirtualStack.<init>(BFVirtualStack.java:123)
> 	at loci.plugins.in.ImagePlusReader.createVirtualStack(ImagePlusReader.java:331)
> 	at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:276)
> 	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:199)
> 	at ij.IJ.runPlugIn(IJ.java:163)
> 	at ij.Executer.runCommand(Executer.java:131)
> 	at ij.Executer.run(Executer.java:64)
> 	at java.lang.Thread.run(Thread.java:695)
> 
> 
> Here’s a link to the file
> https://dl.dropboxusercontent.com/u/18607042/hamamatsu_slide-scanner-example.ndpi
> 
> The image can be imported with OMERO.importer. However fiji or icy have the same problem if I want to open the series with the highest resolution.
> I tried running imageJ with java8 too, to see if it was a java array problem…
> 
> I was using the bio-formats version 5.0.7
> 
> Is this a java of a loci problem?
> 
> Best regards, 
> 
> 
> -------------------------------------
> Felix Meyenhofer
> University of Fribourg
> Departement of Medicine - Anatomy
> 1, Rte. Albert Gockel
> CH-1700 Fribourg 
> 
> Tel:  +41 26 300 85 45
> Web:  www.unifr.ch/anatomy
>      www.unifr.ch/bioimage
> -------------------------------------
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