[ome-users] question

[Melissa Linkert]

Hi Martin,

> I'm using the bfGetReader and the bfopen functions to analyzie
> HIS.files in Matlab (R2011b). Everything is working perfectly as
> long as the file is relatively small (approx. 700 MB). However, as
> soon as I try to read larger files (approx. 10 GB) Matlab gives me
> the following error:
> 
> "Error using loci.formats.ChannelSeparator/setId
> Java exception occurred:
> java.lang.NegativeArraySizeException
> 	at loci.formats.in.HISReader.initFile(HISReader.java:125)
> 	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.ChannelFiller.setId(ChannelFiller.java:259)
> 	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569)
> 	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270)"
> 
> Everything runs smoothly up to this line: r.setId(id) (last line of
> the bfGETReader function), whereby the id is just the path of the
> HIS-file.
> 
> Increasing the Java heap space did not help!

Thank you for reporting this problem.  This is something that we will
need to fix in Bio-Formats, but unfortunately none of the files that we
have is large enough to reproduce the error.

Would you be willing to send one of the files that does not open?
As the file will be too large for our QA system, I will send alternate
upload instructions in a private email.

Regards,
-Melissa

On Fri, Jan 16, 2015 at 09:42:14AM +0100, martin.kaiser at physiologie.uni-heidelberg.de wrote:
> Dear all,
> 
> I'm using the bfGetReader and the bfopen functions to analyzie
> HIS.files in Matlab (R2011b). Everything is working perfectly as
> long as the file is relatively small (approx. 700 MB). However, as
> soon as I try to read larger files (approx. 10 GB) Matlab gives me
> the following error:
> 
> "Error using loci.formats.ChannelSeparator/setId
> Java exception occurred:
> java.lang.NegativeArraySizeException
> 	at loci.formats.in.HISReader.initFile(HISReader.java:125)
> 	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.ChannelFiller.setId(ChannelFiller.java:259)
> 	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569)
> 	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270)"
> 
> Everything runs smoothly up to this line: r.setId(id) (last line of
> the bfGETReader function), whereby the id is just the path of the
> HIS-file.
> 
> Increasing the Java heap space did not help!
> 
> Does anyone have an idea how to solve the problem?
> 
> Thanks very much in advance!
> 
> 
> cheers
> 
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