<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Curtis:</div>Thank you for your fast response!<div><br></div><div>The files are slightly over 500 Mb</div><div><div> du -h C00010/</div><div>585M<span class="Apple-tab-span" style="white-space:pre"> </span>C00010/_C00010-H01_/stack10002</div><div>585M<span class="Apple-tab-span" style="white-space:pre"> </span>C00010/_C00010-H01_</div><div>561M<span class="Apple-tab-span" style="white-space:pre"> </span>C00010/_C00010-H02_/stack10002</div><div>561M<span class="Apple-tab-span" style="white-space:pre"> </span>C00010/_C00010-H02_</div><div>1.2G<span class="Apple-tab-span" style="white-space:pre"> </span>C00010/</div></div><div><br></div><div>Is there another option for getting them to you?</div><div><br></div><div>Many thanks and best wishes,</div><div>--Liz</div><div><br></div><div>
<br><div><div>On May 23, 2013, at 3:56 PM, Curtis Rueden <<a href="mailto:ctrueden@wisc.edu">ctrueden@wisc.edu</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Hi Liz,<div><br></div><div><div>> I can supply two non-working VSI images if you can provide the</div><div>> location and FTP information.</div></div><div><br></div><div style="">If the files are less than 500 MB each, you can upload them to:</div>
<div style=""> <a href="http://qa.openmicroscopy.org.uk/qa/upload/">http://qa.openmicroscopy.org.uk/qa/upload/</a></div><div style=""><br></div><div style="">Thanks,</div><div style="">Curtis</div></div><div class="gmail_extra"><br>
<br><div class="gmail_quote">On Thu, May 23, 2013 at 2:40 PM, Elizabeth Moran <span dir="ltr"><<a href="mailto:emoran550@gmail.com" target="_blank">emoran550@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello:<br>
<br>
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: <a href="http://trac.openmicroscopy.org.uk/ome/ticket/10611" target="_blank">http://trac.openmicroscopy.org.uk/ome/ticket/10611</a> 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.<br>
<br>
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Error message:<br>
ImageSourceFactory - Error constructing Image Source for /home/moran/C00010/C00010-H01.vsi<br>
java.lang.reflect.InvocationTargetException<br>
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)<br>
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)<br>
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)<br>
at java.lang.reflect.Constructor.newInstance(Constructor.java:532)<br>
at edu.isi.misd.image.gateway.conversion.ImageSourceFactory.getImageSource(ImageSourceFactory.java:126)<br>
at edu.isi.misd.image.gateway.conversion.ConvertImageToZoomifyTiles.<init>(ConvertImageToZoomifyTiles.java:83)<br>
at edu.isi.misd.image.gateway.conversion.ConvertImageToZoomifyTiles.main(ConvertImageToZoomifyTiles.java:51)<br>
Caused by: java.io.EOFException: Attempting to read beyond end of file.<br>
at loci.common.NIOFileHandle.readInt(NIOFileHandle.java:331)<br>
at loci.common.RandomAccessInputStream.readInt(RandomAccessInputStream.java:373)<br>
at loci.formats.in.CellSensReader.parseETSFile(CellSensReader.java:614)<br>
at loci.formats.in.CellSensReader.initFile(CellSensReader.java:413)<br>
at loci.formats.FormatReader.setId(FormatReader.java:1183)<br>
at loci.formats.ImageReader.setId(ImageReader.java:727)<br>
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)<br>
at edu.isi.misd.image.gateway.conversion.loci.LociImageSource.<init>(LociImageSource.java:196)<br>
at edu.isi.misd.image.gateway.conversion.loci.LociImageSource.<init>(LociImageSource.java:102)<br>
... 7 more<br>
Caused by: java.nio.BufferUnderflowException<br>
at java.nio.Buffer.nextGetIndex(Buffer.java:497)<br>
at java.nio.HeapByteBuffer.getInt(HeapByteBuffer.java:355)<br>
at loci.common.NIOFileHandle.readInt(NIOFileHandle.java:329)<br>
... 15 more<br>
<br>
I can supply two non-working VSI images if you can provide the location and FTP information.<br>
<br>
If you need any further information from me, please don't hesitate to ask.<br>
<br>
Many thanks and best wishes,<br>
--Liz<br>
<br>
Elizabeth Moran<br>
Senior Technical Writer/ Business Analyst<br>
<a href="mailto:emoran550@gmail.com">emoran550@gmail.com</a><br>
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