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

[Melissa Linkert]

Hi Felix,

> cropping on import did the trick. Thanks.

Glad to hear it.

> What baffles me though is that even if I only take an ROI that corresponds to approximately 1/8 of the high-resolution series and save it as a tiff, the resulting file is about as big as the original ndpi file. When I use JPEG-200 compression, the resulting output is about 1/3 of the size of the original file (which is still bigger, since I only have 1/8 of the original pixels).
> Also the compressed images take forever to load again.
> 
> So I am curious how the people from Hamamatsu actually do it???

NDPI files use JPEG compression, so the JPEG-2000-compressed size of a
tile won't be a direct comparison.  In a limited test, saving a tile as
a TIFF with JPEG compression should provide a compressed size similar to
that of the tile in the original NDPI file.

Regards,
-Melissa

On Sat, Mar 21, 2015 at 04:34:08PM +0000, MEYENHOFER Felix wrote:
> Hi Melissa
> 
> cropping on import did the trick. Thanks.
> 
> What baffles me though is that even if I only take an ROI that corresponds to approximately 1/8 of the high-resolution series and save it as a tiff, the resulting file is about as big as the original ndpi file. When I use JPEG-200 compression, the resulting output is about 1/3 of the size of the original file (which is still bigger, since I only have 1/8 of the original pixels).
> Also the compressed images take forever to load again.
> 
> So I am curious how the people from Hamamatsu actually do it???
> 
> Best, 
> 
> Felix
> 
> 
> > On 18 Mar 2015, at 18:54 , Melissa Linkert <melissa at glencoesoftware.com> wrote:
> > 
> > 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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>