[ome-users] java.lang.illegalArgumentException: Negative position error reporting

[MEYENHOFER Felix]

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
-------------------------------------

> On 19 Dec 2014, at 15:18 , Roger Leigh <rleigh at dundee.ac.uk> wrote:
> 
> On 18/12/14 20:50, Jeong, Young J. (MU-Student) wrote:
>> ​​Hello to whom it may concern,
>> 
>> 
>> I have initially posted this on imageJ group user page and someone
>> commented this error may be due to bugs... So here is what I did and
>> what I got afterward.
>> 
>> 
>>  I recently have started to figure out how to use imageJ to analyze the
>> uCT scans of bone geometry. The size of raw file is quite large, which
>> is about 16GB. Because of lare size of the file, it gives me an error
>> with memory issue. So what I have tried next is to open up file by
>> specifying the range of images. The size of file is 2048x2048; 2016
>> planes. It shows me an image when I have selected 1(Z begin)-250(Z End)
>> with 1 for Z step. The problem arise when I have tried to select beyond
>> 250 and it gives me following messages.
>> 
>> The file I am opening is ct.img.hdr file and this scan was done by
>> inveon uCT scan. The disc image file (.ct) is ~16GB
> 
> 
> Looking at the stacktrace you provided, this looks like it's an issue
> with the Inveon reader.  Melissa Linkert has opened a pull request for
> the proposed fix here:
> 
>  https://github.com/openmicroscopy/bioformats/pull/1502
> 
> If you would like to test this with your data, you can try out a build
> of this branch.  Alternatively, it should be backported to 5.0 for the
> next 5.0.x release, and this will be available as a Fiji update shortly
> after.
> 
> 
> Kind regards,
> Roger
> 
> --
> Dr Roger Leigh -- Open Microscopy Environment
> Wellcome Trust Centre for Gene Regulation and Expression,
> College of Life Sciences, University of Dundee, Dow Street,
> Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
> 
> The University of Dundee is a registered Scottish Charity, No: SC015096
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