[ome-users] ImageConverter: Big image to OME-TIFF fails

[Melissa Linkert]

Hi Matthias,

> Conversion of big images (series >= 4096 x 4096 pixel) to OME-TIFFs
> using LOCI Tools 4.4.8 and bfconvert/ImageConverter always fails
> with the following exception:
> 
> bfconvert -series 0 CMU-2.svs test.ome.tiff
> CMU-2.svs
> SVSReader initializing CMU-2.svs
> Reading IFDs
> Populating metadata
> Populating OME metadata
> [Aperio SVS] -> test.ome.tiff [OME-TIFF]
> Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1
>     at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:204)
>     at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:591)
>     at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:535)
>     at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:481)
>     at loci.formats.tools.ImageConverter.main(ImageConverter.java:667)
> 
> A SVS test image of OpenSlide was used in the case above. However,
> the exception is thrown for other big image formats too. I tried
> using the latest trunk build but the exception remains.

Thank you for the bug report.  We are reviewing a fix for this now:

https://github.com/openmicroscopy/bioformats/pull/711

If you have any feedback on that fix, it would be most welcome -
otherwise, I would expect it to be included in the upcoming 4.4.9
release.

Regards,
-Melissa


On Mon, Sep 30, 2013 at 11:04:02AM +0200, Matthias Baldauf wrote:
> Hello all,
> 
> Conversion of big images (series >= 4096 x 4096 pixel) to OME-TIFFs
> using LOCI Tools 4.4.8 and bfconvert/ImageConverter always fails
> with the following exception:
> 
> bfconvert -series 0 CMU-2.svs test.ome.tiff
> CMU-2.svs
> SVSReader initializing CMU-2.svs
> Reading IFDs
> Populating metadata
> Populating OME metadata
> [Aperio SVS] -> test.ome.tiff [OME-TIFF]
> Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1
>     at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:204)
>     at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:591)
>     at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:535)
>     at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:481)
>     at loci.formats.tools.ImageConverter.main(ImageConverter.java:667)
> 
> A SVS test image of OpenSlide was used in the case above. However,
> the exception is thrown for other big image formats too. I tried
> using the latest trunk build but the exception remains.
> 
> May I ask you to have a look at it?
> Thank you in advance.
> 
> Regards,
> Matthias
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users