[ome-users] Negative position error with bfconvert

[Frank Pennekamp]

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)
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users