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

[Elizabeth Moran]

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