[ome-users] Negative position error with bfconvert

[Melissa Linkert]

Hi Frank,

> I use the bio-formats command line tools (version 5.1.0) to convert
> large cxd files (> 60GB) into avi files. However, the processing
> stops after about 500 planes with an error message
> java.lang.IllegalArgumentException: Negative position. This threads
> was the only related information I could find and suggest its maybe
> a bug. Any suggestions how to circumvent this problem?

Standard .avi files cannot be larger than 2GB.  If using .avi files is necessary,
you might try splitting each timepoint or Z section into a separate
file, e.g.:

$ bfconvert 20150331_jg_para_didin_trials00001.cxd out_Z%z.avi

or:

$ bfconvert 20150331_jg_para_didin_trials00001.cxd out_T%t.avi

(see
http://www.openmicroscopy.org/site/support/bio-formats5.1/users/comlinetools/conversion.html)

To have all of the planes in a single file, you will need to convert to
BigTIFF instead:

$ bfconvert -bigtiff 20150331_jg_para_didin_trials00001.cxd out.tiff

Regards,
-Melissa

On Thu, Apr 02, 2015 at 02:26:00PM +0200, Frank Pennekamp wrote:
> Dear all,
> 
> I use the bio-formats command line tools (version 5.1.0) to convert
> large cxd files (> 60GB) into avi files. However, the processing
> stops after about 500 planes with an error message
> java.lang.IllegalArgumentException: Negative position. This threads
> was the only related information I could find and suggest its maybe
> a bug. Any suggestions how to circumvent this problem?
> 
> Many thanks,
> 
>    Frank
> 
> 
> 
> Please find the terminal output here:
> ieu0825-petchey:1 - raw Frank$
> /Users/Frank/Documents/Postdoc/Software/bftools/bfconvert
> 20150331_jg_para_didin_trials00001.cxd out.avi
> 20150331_jg_para_didin_trials00001.cxd
> PCIReader initializing 20150331_jg_para_didin_trials00001.cxd
> [Compix Simple-PCI] -> out.avi [Audio Video Interleave]
>     Converted 16/18000 planes (0%)
>     Converted 37/18000 planes (0%)
>     Converted 57/18000 planes (0%)
>     Converted 78/18000 planes (0%)
>     Converted 98/18000 planes (0%)
>     Converted 107/18000 planes (0%)
>     Converted 122/18000 planes (0%)
>     Converted 137/18000 planes (0%)
>     Converted 152/18000 planes (0%)
>     Converted 167/18000 planes (0%)
>     Converted 182/18000 planes (1%)
>     Converted 196/18000 planes (1%)
>     Converted 210/18000 planes (1%)
>     Converted 224/18000 planes (1%)
>     Converted 238/18000 planes (1%)
>     Converted 252/18000 planes (1%)
>     Converted 266/18000 planes (1%)
>     Converted 280/18000 planes (1%)
>     Converted 294/18000 planes (1%)
>     Converted 307/18000 planes (1%)
>     Converted 320/18000 planes (1%)
>     Converted 333/18000 planes (1%)
>     Converted 346/18000 planes (1%)
>     Converted 359/18000 planes (1%)
>     Converted 372/18000 planes (2%)
>     Converted 384/18000 planes (2%)
>     Converted 401/18000 planes (2%)
>     Converted 417/18000 planes (2%)
>     Converted 433/18000 planes (2%)
>     Converted 450/18000 planes (2%)
>     Converted 467/18000 planes (2%)
>     Converted 483/18000 planes (2%)
>     Converted 495/18000 planes (2%)
>     Converted 507/18000 planes (2%)
> Exception in thread "main" java.lang.IllegalArgumentException:
> Negative position
>     at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:600)
>     at loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:127)
>     at loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:112)
>     at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:600)
>     at loci.common.NIOFileHandle.seek(NIOFileHandle.java:291)
>     at loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:174)
>     at loci.formats.out.AVIWriter.setId(AVIWriter.java:257)
>     at loci.formats.ImageWriter.setId(ImageWriter.java:433)
>     at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:521)
>     at loci.formats.tools.ImageConverter.main(ImageConverter.java:822)
> 
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