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

[David Gault (Staff)]

Hi Kouichi,

We have been trying to reproduce this issue with the sample file you provided. After testing across different platforms and versions we have so far been unable to do so.
What would be helpful for our investigation would be to find out exactly where the J2K classes are being loaded from in MATLAB.

This can be done by creating a MATLAB function 'whereisjavaclassloadingfrom’ which can be found at this link https://github.com/dgault/bioformats/blob/a75a1f84a389a395529a876fed38b1ed384b88fb/components/formats-gpl/matlab/whereisjavaclassloadingfrom.m

This can then be run with the following commands to find the version and location of the class:

whereisjavaclassloadingfrom('com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader')
whereisjavaclassloadingfrom('com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState’)

This should output results similar to below:
Version: 9.3.0.713579 (R2017b)
Class:       com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
ClassLoader: sun.misc.Launcher$AppClassLoader at c387f44
URL:         jar:file:/path/to/bioformats_package.jar!/com/sun/media/imageioimpl/plugins/jpeg2000/J2KImageReader.class


With Thanks,
David Gault

On 25 Oct 2017, at 23:30, Kouichi C. Nakamura <kouichi.c.nakamura at gmail.com<mailto:kouichi.c.nakamura at gmail.com>> wrote:


Hi David,

I tried deployment of javaclassoath.txt to the folder, but I got a warning and then error message.

Best,

Kouichi


Warning: "bioformats_package.jar" is already specified on static java path.

Reading series #1



Error using bfGetPlane<matlab:matlab.internal.language.introspective.errorDocCallback%28%27bfGetPlane%27,%20%27D:%5CDropbox%5CPrivate_Dropbox%5Cmatlab_toolbox%5Cbfmatlab%5CbfGetPlane.m%27,%2078%29> (line 78<matlab:%20opentoline%28%27D:%5CDropbox%5CPrivate_Dropbox%5Cmatlab_toolbox%5Cbfmatlab%5CbfGetPlane.m%27,78,0%29>)
Java exception occurred:
java.lang.RuntimeException: 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:729)
at com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState.<init>(J2KReadState.java:241)
at com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader.readRaster(J2KImageReader.java:551)
at ome.codecs.services.JAIIIOServiceImpl.readRaster(JAIIIOServiceImpl.java:177)
at ome.codecs.JPEG2000Codec.decompress(JPEG2000Codec.java:296)
at ome.codecs.JPEG2000Codec.decompress(JPEG2000Codec.java:267)
at loci.formats.codec.WrappedCodec.decompress(WrappedCodec.java:132)
at loci.formats.codec.JPEG2000Codec.decompress(JPEG2000Codec.java:63)
at loci.formats.in.JPEG2000Reader.openBytes(JPEG2000Reader.java:182)
at loci.formats.ImageReader.openBytes(ImageReader.java:457)
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:148)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:159)
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<matlab:matlab.internal.language.introspective.errorDocCallback%28%27bfopen%27,%20%27D:%5CDropbox%5CPrivate_Dropbox%5Cmatlab_toolbox%5Cbfmatlab%5Cbfopen.m%27,%20150%29> (line 150<matlab:%20opentoline%28%27D:%5CDropbox%5CPrivate_Dropbox%5Cmatlab_toolbox%5Cbfmatlab%5Cbfopen.m%27,150,0%29>)
arr = bfGetPlane(r, i, varargin{:});

 .

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