[ome-users] Bug report: Cannot open jp2 file created by StereoInvestigator

[Roger Leigh]

On 20/10/17 15:21, Kouichi C. Nakamura wrote:
> Dear Roger,
>
> I hope that you can read this (I'm not sure how this mailing list is
> organized).
>
> Thank you so much for your investigation. Following the instruction,
> I've increased the memory up to 2500m (see below), but still I cannot
> open the same file with the same error message. I've reinstalled
> bioformats toolbox 5.7.1. Any thoughts?

> Caused by: java.lang.NoSuchMethodError:
> jj2000.j2k.fileformat.reader.FileFormatReader.<init>(Ljj2000/j2k/io/RandomAccessIO;Lcom/sun/media/imageioimpl/plugins/jpeg2000/J2KMetadata;)V
>
>      at
> com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState.initializeRead(J2KReadState.java:450)
>
>      ... 13 more
>
> Error in bfopen (line 150)
>          arr = bfGetPlane(r, i, varargin{:});
> 78  plane = r.openBytes(...

Dear Kouichi,

We have checked opening your image internally with Matlab 2017a and it
opens correctly with this version of Matlab.

Our suspicion is that there may be other jars on your Java classpath
which might be conflicting with the Bio-Formats jar.  We would suggest
looking at what is on this path by running

   javaclasspath

This conflict might be caused by jars provided as part of Matlab, or it
might be other third-party jars, which also provide JPEG2000 decoding
support.  If the latter, I would suggest removing them temporarily while
you work with Bio-Formats so that you can open the image.  It would also
be useful to know which jars cause the problem so that we can
investigate removing the cause of the conflict in the future.


Kind regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096