[ome-users] BioFormats (5.0.2) can't handle very large NDPI files

[Philippe Mailly]

Hi Kristian,

Did you try the NDPITools from Christophe Deroulers it use BigTiff 
librairies then handle very larges ndpi files.
http://www.imnc.in2p3.fr/pagesperso/deroulers/software/ndpitools/

Regards

Philippe

Le 09/06/2014 20:15, Melissa Linkert a écrit :
> Hi Kristian,
>
>> I have a few very large (>4GB) NDPI files from a HAMAMATSU scanner.
>> The scanned slides are sometimes very large (like blood smears) and
>> scanned in three or five layers.
>>
>> In BioFormats 5.0.2 with bftools, running "showinf -nopix 65.ndpi", I get
> *snip*
>
>> The problem seems to be related to integer overflow. I think,
>> however, that a solution isn't as simple as changing ints to longs
>> (I tried, didn't work).
>>
>> I have five sample files at http://micro.sdu.dk/media/bioformats -
>> 66.ndpi and 67.ndpi works; 65.ndpi, 68.ndpi, and 69.ndpi don't work.
> Thank you for reporting this problem.  The issue definitely does have to
> do with file size - anything larger than 4GB will not be readable as
> .ndpi files do not follow the BigTIFF specification.  I have filed a
> ticket for this on our issue tracking system:
>
> http://trac.openmicroscopy.org.uk/ome/ticket/12367
>
> and would expect this to be working in the next release.
>
> Regards,
> -Melissa
>
> On Wed, Jun 04, 2014 at 11:17:11AM +0200, Kristian Kjærgaard wrote:
>> Dear fellow users
>>
>> I have a few very large (>4GB) NDPI files from a HAMAMATSU scanner.
>> The scanned slides are sometimes very large (like blood smears) and
>> scanned in three or five layers.
>>
>> In BioFormats 5.0.2 with bftools, running "showinf -nopix 65.ndpi", I get
>>
>> Checking file format [Hamamatsu NDPI]
>> Initializing reader
>> NDPIReader initializing 65.ndpi
>> Reading IFDs
>> Populating metadata
>> Exception in thread "main" java.lang.IllegalArgumentException:
>> Negative position
>>          at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:675)
>>          at loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:131)
>>          at loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:116)
>>          at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:551)
>>          at loci.common.NIOFileHandle.seek(NIOFileHandle.java:273)
>>          at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:154)
>>          at loci.formats.tiff.TiffParser.getIFDValue(TiffParser.java:479)
>>          at loci.formats.tiff.TiffParser.fillInIFD(TiffParser.java:460)
>>          at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:451)
>>          at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:540)
>>          at loci.formats.in.NDPIReader.initFile(NDPIReader.java:269)
>>          at loci.formats.FormatReader.setId(FormatReader.java:1315)
>>          at loci.formats.ImageReader.setId(ImageReader.java:753)
>>          at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569)
>>          at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:992)
>>          at loci.formats.tools.ImageInfo.main(ImageInfo.java:1074)
>>
>> The problem seems to be related to integer overflow. I think,
>> however, that a solution isn't as simple as changing ints to longs
>> (I tried, didn't work).
>>
>> I have five sample files at http://micro.sdu.dk/media/bioformats -
>> 66.ndpi and 67.ndpi works; 65.ndpi, 68.ndpi, and 69.ndpi don't work.
>>
>> I may be able to provide more samples if needed.
>>
>> - Kristian Kjærgaard, BSc.med, happy user of BioFormats
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