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<p class="MsoNormal">I am using 5.9.2, from 3 Sept 2018.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The file sizes that are not converting range from 1.7 GB to 4.2 GB. The .svs images that were smaller than about 1.3 GB converted without problem.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b>From:</b> ome-users <ome-users-bounces@lists.openmicroscopy.org.uk>
<b>On Behalf Of </b>David Gault (Staff)<br>
<b>Sent:</b> Monday, November 5, 2018 7:10 AM<br>
<b>To:</b> OME User Support List <ome-users@lists.openmicroscopy.org.uk><br>
<b>Subject:</b> Re: [ome-users] Error when converting large .svs or .vsi images<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Lawrence, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">That error looks as though the buffer has been unable to successfully increase its limit for some reason.<o:p></o:p></p>
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<p class="MsoNormal">What size are the original files you are trying to convert? Also what version of Bio-Formats are you currently using?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">With Thanks,<o:p></o:p></p>
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<p class="MsoNormal">David Gault<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 2 Nov 2018, at 15:21, Tarbox, Lawrence <<a href="mailto:LRTarbox@uams.edu">LRTarbox@uams.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">In converting large .svs or .vsi images, I get the following error:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">/home/ltarbox/CIR-scans<o:p></o:p></p>
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<p class="MsoNormal">54680.svs<o:p></o:p></p>
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<p class="MsoNormal">SVSReader initializing 54680.svs<o:p></o:p></p>
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<p class="MsoNormal">Reading IFDs<o:p></o:p></p>
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<p class="MsoNormal">Populating metadata<o:p></o:p></p>
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<p class="MsoNormal">Populating OME metadata<o:p></o:p></p>
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<p class="MsoNormal">[Aperio SVS] -> /home/ltarbox/CIR-scans/out/WSI-2_S%s.ome.tif [OME-TIFF]<o:p></o:p></p>
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<p class="MsoNormal">Switching to BigTIFF (by file size)<o:p></o:p></p>
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<p class="MsoNormal">Tile size = 256 x 256<o:p></o:p></p>
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<p class="MsoNormal">Exception in thread "main" java.lang.IllegalArgumentException<o:p></o:p></p>
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<p class="MsoNormal"> at java.nio.Buffer.limit(Buffer.java:275)<o:p></o:p></p>
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<p class="MsoNormal"> at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:636)<o:p></o:p></p>
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<p class="MsoNormal"> at loci.common.NIOFileHandle.writeSetup(NIOFileHandle.java:642)<o:p></o:p></p>
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<p class="MsoNormal"> at loci.common.NIOFileHandle.write(NIOFileHandle.java:505)<o:p></o:p></p>
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<p class="MsoNormal"> at loci.common.NIOFileHandle.write(NIOFileHandle.java:499)<o:p></o:p></p>
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<p class="MsoNormal"> at loci.common.NIOFileHandle.write(NIOFileHandle.java:487)<o:p></o:p></p>
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<p class="MsoNormal"> at loci.common.RandomAccessOutputStream.write(RandomAccessOutputStream.java:217)<o:p></o:p></p>
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<p class="MsoNormal"> at loci.formats.tiff.TiffSaver.writeIFDStrips(TiffSaver.java:987)<o:p></o:p></p>
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<p class="MsoNormal"> at loci.formats.tiff.TiffSaver.writeImageIFD(TiffSaver.java:451)<o:p></o:p></p>
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<p class="MsoNormal"> at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:401)<o:p></o:p></p>
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<p class="MsoNormal"> at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:277)<o:p></o:p></p>
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<p class="MsoNormal"> at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:275)<o:p></o:p></p>
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<p class="MsoNormal"> at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:218)<o:p></o:p></p>
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<p class="MsoNormal"> at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:748)<o:p></o:p></p>
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<p class="MsoNormal"> at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:634)<o:p></o:p></p>
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<p class="MsoNormal"> at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:563)<o:p></o:p></p>
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<p class="MsoNormal"> at loci.formats.tools.ImageConverter.main(ImageConverter.java:884)<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Smaller images convert fine.<span class="apple-converted-space"> </span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I tripled the memory size (to 40 GB), but it stll fails<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Ideas?<o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#4472C4"> </span><o:p></o:p></p>
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<p class="MsoNormal"><i><span style="color:#4472C4">Lawrence Tarbox, Ph.D., Dept. of Biomedical Informatics, Univ. of Arkansas for Medical Sciences</span></i><o:p></o:p></p>
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<p class="MsoNormal"><i><span style="color:#4472C4"><a href="mailto:LTarbox@uams.edu"><span style="color:#954F72">mailto:LTarbox@uams.edu</span></a><span class="apple-converted-space"> </span>+1.314.681-2752</span></i><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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