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

[Kristian Kjærgaard]

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