[ome-users] Error when converting large .svs or .vsi images

[David Gault (Staff)]

Hi Lawrence,

That error looks as though the buffer has been unable to successfully increase its limit for some reason.
What size are the original files you are trying to convert? Also what version of Bio-Formats are you currently using?

With Thanks,
David Gault

On 2 Nov 2018, at 15:21, Tarbox, Lawrence <LRTarbox at uams.edu<mailto:LRTarbox at uams.edu>> wrote:

In converting large .svs or .vsi images, I get the following error:

/home/ltarbox/CIR-scans
54680.svs
SVSReader initializing 54680.svs
Reading IFDs
Populating metadata
Populating OME metadata
[Aperio SVS] -> /home/ltarbox/CIR-scans/out/WSI-2_S%s.ome.tif [OME-TIFF]
Switching to BigTIFF (by file size)
Tile size = 256 x 256
Exception in thread "main" java.lang.IllegalArgumentException
        at java.nio.Buffer.limit(Buffer.java:275)
        at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:636)
        at loci.common.NIOFileHandle.writeSetup(NIOFileHandle.java:642)
        at loci.common.NIOFileHandle.write(NIOFileHandle.java:505)
        at loci.common.NIOFileHandle.write(NIOFileHandle.java:499)
        at loci.common.NIOFileHandle.write(NIOFileHandle.java:487)
        at loci.common.RandomAccessOutputStream.write(RandomAccessOutputStream.java:217)
        at loci.formats.tiff.TiffSaver.writeIFDStrips(TiffSaver.java:987)
        at loci.formats.tiff.TiffSaver.writeImageIFD(TiffSaver.java:451)
        at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:401)
        at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:277)
        at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:275)
        at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:218)
        at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:748)
        at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:634)
        at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:563)
        at loci.formats.tools.ImageConverter.main(ImageConverter.java:884)

Smaller images convert fine.

I tripled the memory size (to 40 GB), but it stll fails

Ideas?

Lawrence Tarbox, Ph.D., Dept. of Biomedical Informatics, Univ. of Arkansas for Medical Sciences
mailto:LTarbox at uams.edu +1.314.681-2752

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