[ome-users] Error processing VSI image with OMER0 4.4.7

[Elizabeth Moran]

Hi Curtis:
Thank you for your fast response!

The files are slightly over 500 Mb
 du -h C00010/
585M	C00010/_C00010-H01_/stack10002
585M	C00010/_C00010-H01_
561M	C00010/_C00010-H02_/stack10002
561M	C00010/_C00010-H02_
1.2G	C00010/

Is there another option for getting them to you?

Many thanks and best wishes,
--Liz


On May 23, 2013, at 3:56 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> Hi Liz,
> 
> > I can supply two non-working VSI images if you can provide the
> > location and FTP information.
> 
> If the files are less than 500 MB each, you can upload them to:
>     http://qa.openmicroscopy.org.uk/qa/upload/
> 
> Thanks,
> Curtis
> 
> 
> On Thu, May 23, 2013 at 2:40 PM, Elizabeth Moran <emoran550 at gmail.com> wrote:
> Hello:
> 
> We are using the BioFormats libraries to convert VSI images into tiled jpgs for display by the Zoomify viewer, and we are getting an "Attempting to read beyond end of file" error for two of the VSI images.  This error was addressed in Ticket: http://trac.openmicroscopy.org.uk/ome/ticket/10611 but, after installing OMERO 4.4.7 on April 30, we are still getting the same or a similar error for two of our VSI images.
> 
> 
> Error message:
> ImageSourceFactory - Error constructing Image Source for /home/moran/C00010/C00010-H01.vsi
> java.lang.reflect.InvocationTargetException
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
> at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
> at edu.isi.misd.image.gateway.conversion.ImageSourceFactory.getImageSource(ImageSourceFactory.java:126)
> at edu.isi.misd.image.gateway.conversion.ConvertImageToZoomifyTiles.<init>(ConvertImageToZoomifyTiles.java:83)
> at edu.isi.misd.image.gateway.conversion.ConvertImageToZoomifyTiles.main(ConvertImageToZoomifyTiles.java:51)
> Caused by: java.io.EOFException: Attempting to read beyond end of file.
> at loci.common.NIOFileHandle.readInt(NIOFileHandle.java:331)
> at loci.common.RandomAccessInputStream.readInt(RandomAccessInputStream.java:373)
> at loci.formats.in.CellSensReader.parseETSFile(CellSensReader.java:614)
> at loci.formats.in.CellSensReader.initFile(CellSensReader.java:413)
> at loci.formats.FormatReader.setId(FormatReader.java:1183)
> at loci.formats.ImageReader.setId(ImageReader.java:727)
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
> at edu.isi.misd.image.gateway.conversion.loci.LociImageSource.<init>(LociImageSource.java:196)
> at edu.isi.misd.image.gateway.conversion.loci.LociImageSource.<init>(LociImageSource.java:102)
> ... 7 more
> Caused by: java.nio.BufferUnderflowException
> at java.nio.Buffer.nextGetIndex(Buffer.java:497)
> at java.nio.HeapByteBuffer.getInt(HeapByteBuffer.java:355)
> at loci.common.NIOFileHandle.readInt(NIOFileHandle.java:329)
> ... 15 more
> 
> I can supply two non-working VSI images if you can provide the location and FTP information.
> 
> If you need any further information from me, please don't hesitate to ask.
> 
> Many thanks and best wishes,
> --Liz
> 
> Elizabeth Moran
> Senior Technical Writer/ Business Analyst
> emoran550 at gmail.com
> 
> 
> 
> 
> 
> 
> 
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> 

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