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Hi Lawrence,
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<div class="">It does look like it is related to the file size of the converted file. Setting a compression codec should reduce the required size and might allow for easier conversion. </div>
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<div class="">For example using:</div>
<div class="">bfconvert -compression JPEG-2000 /path/to/originalFile.svs /path/to/convertedFile.ome.tiff</div>
<div class="">bfconvert -compression LZW /path/to/originalFile.svs /path/to/convertedFile.ome.tiff</div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<div class="">On 5 Nov 2018, at 20:19, Tarbox, Lawrence <<a href="mailto:LRTarbox@uams.edu" class="">LRTarbox@uams.edu</a>> wrote:</div>
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I am using 5.9.2, from 3 Sept 2018.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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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 class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<b class="">From:</b><span class="Apple-converted-space"> </span>ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" class="">ome-users-bounces@lists.openmicroscopy.org.uk</a>><span class="Apple-converted-space"> </span><b class="">On
Behalf Of<span class="Apple-converted-space"> </span></b>David Gault (Staff)<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, November 5, 2018 7:10 AM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-users] Error when converting large .svs or .vsi images<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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Hi Lawrence,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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That error looks as though the buffer has been unable to successfully increase its limit for some reason.<o:p class=""></o:p></div>
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What size are the original files you are trying to convert? Also what version of Bio-Formats are you currently using?<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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With Thanks,<o:p class=""></o:p></div>
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David Gault<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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On 2 Nov 2018, at 15:21, Tarbox, Lawrence <<a href="mailto:LRTarbox@uams.edu" style="color: purple; text-decoration: underline;" class="">LRTarbox@uams.edu</a>> wrote:<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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In converting large .svs or .vsi images, I get the following error:<o:p class=""></o:p></div>
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<o:p class=""></o:p></div>
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/home/ltarbox/CIR-scans<o:p class=""></o:p></div>
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54680.svs<o:p class=""></o:p></div>
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SVSReader initializing 54680.svs<o:p class=""></o:p></div>
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Reading IFDs<o:p class=""></o:p></div>
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Populating metadata<o:p class=""></o:p></div>
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Populating OME metadata<o:p class=""></o:p></div>
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[Aperio SVS] -> /home/ltarbox/CIR-scans/out/WSI-2_S%s.ome.tif [OME-TIFF]<o:p class=""></o:p></div>
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Switching to BigTIFF (by file size)<o:p class=""></o:p></div>
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Tile size = 256 x 256<o:p class=""></o:p></div>
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Exception in thread "main" java.lang.IllegalArgumentException<o:p class=""></o:p></div>
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at java.nio.Buffer.limit(Buffer.java:275)<o:p class=""></o:p></div>
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at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:636)<o:p class=""></o:p></div>
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at loci.common.NIOFileHandle.writeSetup(NIOFileHandle.java:642)<o:p class=""></o:p></div>
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at loci.common.NIOFileHandle.write(NIOFileHandle.java:505)<o:p class=""></o:p></div>
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at loci.common.NIOFileHandle.write(NIOFileHandle.java:499)<o:p class=""></o:p></div>
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at loci.common.NIOFileHandle.write(NIOFileHandle.java:487)<o:p class=""></o:p></div>
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at loci.common.RandomAccessOutputStream.write(RandomAccessOutputStream.java:217)<o:p class=""></o:p></div>
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at loci.formats.tiff.TiffSaver.writeIFDStrips(TiffSaver.java:987)<o:p class=""></o:p></div>
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at loci.formats.tiff.TiffSaver.writeImageIFD(TiffSaver.java:451)<o:p class=""></o:p></div>
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at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:401)<o:p class=""></o:p></div>
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at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:277)<o:p class=""></o:p></div>
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at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:275)<o:p class=""></o:p></div>
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at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:218)<o:p class=""></o:p></div>
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at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:748)<o:p class=""></o:p></div>
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at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:634)<o:p class=""></o:p></div>
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at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:563)<o:p class=""></o:p></div>
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at loci.formats.tools.ImageConverter.main(ImageConverter.java:884)<o:p class=""></o:p></div>
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Smaller images convert fine.<span class="apple-converted-space"> </span><o:p class=""></o:p></div>
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I tripled the memory size (to 40 GB), but it stll fails<o:p class=""></o:p></div>
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Ideas?<o:p class=""></o:p></div>
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<span style="color: rgb(68, 114, 196);" class=""> </span><o:p class=""></o:p></div>
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<div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class=""><span style="color: rgb(68, 114, 196);" class="">Lawrence Tarbox, Ph.D., Dept. of Biomedical Informatics, Univ. of Arkansas for Medical Sciences</span></i><o:p class=""></o:p></div>
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<i class=""><span style="color: rgb(68, 114, 196);" class=""><a href="mailto:LTarbox@uams.edu" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">mailto:LTarbox@uams.edu</span></a><span class="apple-converted-space"> </span>+1.314.681-2752</span></i><o:p class=""></o:p></div>
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