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

[David Gault (Staff)]

Hi Lawrence,

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.

For example using:
bfconvert -compression JPEG-2000 /path/to/originalFile.svs /path/to/convertedFile.ome.tiff
bfconvert -compression LZW /path/to/originalFile.svs /path/to/convertedFile.ome.tiff

With Thanks,
David Gault

On 5 Nov 2018, at 20:19, Tarbox, Lawrence <LRTarbox at uams.edu<mailto:LRTarbox at uams.edu>> wrote:

I am using 5.9.2, from 3 Sept 2018.

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.

From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> On Behalf Of David Gault (Staff)
Sent: Monday, November 5, 2018 7:10 AM
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] Error when converting large .svs or .vsi images

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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