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

[Curtis Rueden]

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
>
>
>
>
>
>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
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>
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