[ome-users] Large SVS file convertion problem

[Jianjiong Gao]

Hi Melissa,

Thank you so much for the quick reply! This is very helpful. I was
able to convert SVS to OME-TIFF (w/o JPEG compression). But when I
turn on JPEG compression, it always gave me the following exception.

Exception in thread "main" java.awt.image.RasterFormatException: Data
array too small (should be 65535 but is 21845 )
	at sun.awt.image.IntegerComponentRaster.verify(IntegerComponentRaster.java:643)
	at sun.awt.image.IntegerComponentRaster.<init>(IntegerComponentRaster.java:194)
	at sun.awt.image.IntegerInterleavedRaster.<init>(IntegerInterleavedRaster.java:111)
	at sun.awt.image.IntegerInterleavedRaster.<init>(IntegerInterleavedRaster.java:78)
	at java.awt.image.Raster.createWritableRaster(Raster.java:994)
	at loci.formats.gui.AWTImageTools.constructImage(AWTImageTools.java:702)
	at loci.formats.gui.AWTImageTools.constructImage(AWTImageTools.java:653)
	at loci.formats.gui.AWTImageTools.makeRGBImage(AWTImageTools.java:591)
	at loci.formats.gui.AWTImageTools.makeImage(AWTImageTools.java:207)
	at loci.formats.gui.AWTImageTools.makeImage(AWTImageTools.java:494)
	at loci.formats.codec.JPEGCodec.compress(JPEGCodec.java:85)
	at loci.formats.tiff.TiffCompression.compress(TiffCompression.java:328)
	at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:371)
	at loci.formats.tiff.TiffSaver.writeImage(TiffSaver.java:265)
	at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:191)
	at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:197)
	at loci.formats.tools.ImageConverter.convertTilePlane(ImageConverter.java:569)
	at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:513)
	at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:459)
	at loci.formats.tools.ImageConverter.main(ImageConverter.java:645)

An example svs file is http://goo.gl/JBZhL

Do you think it is a problem with the svs file or some potential bug
in the tool?

Thanks again and best regards!
-JJ



On Thu, Oct 25, 2012 at 7:14 PM, Melissa Linkert
<melissa at glencoesoftware.com> wrote:
> Hi,
>
>> Lately, I am using the Bio-Formats/bfconvert to convert SVS to JPEG.
>> Some of the SVS files are really big and I got the follow exception:
>>
>> Exception in thread "main" loci.formats.FormatException: Image plane
>> too large. Only 2GB of data can be extracted at one time. You can
>> workaround the problem by opening the plane in tiles; for further
>> details, see: http://www.openmicroscopy.org/site/support/faq/bio-formats/i-see-an-outofmemory-or-negativearraysize-error-message-when-attempting-to-open-an-svs-or-jpeg-2000-file.-what-does-this-mean
>>
>> Is there any easy solution for this problem? Do I have to crop a large
>> image into smaller pieces first? Is there any way to stitch them
>> together after converting?
>
> Bio-Formats does not support saving images with more than 2 GB of pixel
> data into a single JPEG file.  You will need to save smaller tiles into
> separate JPEG files, like this:
>
>   $ bfconvert -crop 0,0,4096,4096 input.svs output.jpg
>
> where '0,0,4096,4096' is the X coordinate, Y coordinate, width, and
> height of the tile to be saved.
>
> However, you could convert to an OME-TIFF file (with or without JPEG
> compression) instead, and then there is no need to save individual tiles or
> stitch them back together.  This command should save the entire image
> into a single file (with JPEG compression):
>
>   $ bfconvert -compression JPEG input.svs output.ome.tiff
>
> Regards,
> -Melissa
>
> On Thu, Oct 25, 2012 at 03:26:12PM -0400, Jianjiong Gao wrote:
>> Hello,
>>
>> First of all, thanks for maintaining such a great resource!
>>
>> Lately, I am using the Bio-Formats/bfconvert to convert SVS to JPEG.
>> Some of the SVS files are really big and I got the follow exception:
>>
>> Exception in thread "main" loci.formats.FormatException: Image plane
>> too large. Only 2GB of data can be extracted at one time. You can
>> workaround the problem by opening the plane in tiles; for further
>> details, see: http://www.openmicroscopy.org/site/support/faq/bio-formats/i-see-an-outofmemory-or-negativearraysize-error-message-when-attempting-to-open-an-svs-or-jpeg-2000-file.-what-does-this-mean
>>
>> Is there any easy solution for this problem? Do I have to crop a large
>> image into smaller pieces first? Is there any way to stitch them
>> together after converting?
>>
>> Thank you!
>> -JJ
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
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