[ome-users] Negative position error with bfconvert

[Melissa Linkert]

Hi Frank,

> thanks for  the quick response. I understand now why it's not
> working. As you suggested, bigtiffs work indeed fine with the whole
> video!

Glad to hear it!

> I have tried what you suggested about time points, but it is
> splitting now each frame into a single file. Would be nice to have
> chunks of, say, 500 frames in one avi file and then as many avi
> files as needed. Is there a way of specifying this? Otherwise I can
> just use a shell script looping over the file and extracting
> non-overlapping ranges....

Unfortunately, no, there isn't a way of doing that as a single command.
Using the '-range' option in a loop should work, though - if not, please
let us know.

Regards,
-Melissa


On Thu, Apr 02, 2015 at 08:49:50PM +0200, Frank Pennekamp wrote:
> Dear Melissa,
> 
> thanks for  the quick response. I understand now why it's not
> working. As you suggested, bigtiffs work indeed fine with the whole
> video!
> 
> I have tried what you suggested about time points, but it is
> splitting now each frame into a single file. Would be nice to have
> chunks of, say, 500 frames in one avi file and then as many avi
> files as needed. Is there a way of specifying this? Otherwise I can
> just use a shell script looping over the file and extracting
> non-overlapping ranges....
> 
> Thanks again and all the best,
> 
>     Frank
> 
> On 02/04/2015 16:33, Melissa Linkert wrote:
> >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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