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

[David Gault (Staff)]

Hi Kouichi,

Thank you for testing and confirming that this conflict is present. In the short term for Bio-Formats 5.7.3 we have updated the documentation for the JAI Image IO component and the MATLAB user information to highlight this issue and advice removing the conflicting jars just as you have suggested.

https://docs.openmicroscopy.org/bio-formats/5.7.3/developers/components.html#forks-jai
https://docs.openmicroscopy.org/bio-formats/5.7.3/users/matlab/index.html

With Thanks,
David Gault

On 11 Jan 2018, at 17:46, Kouichi Nakamura <kouichi.nakamura at pharm.ox.ac.uk<mailto:kouichi.nakamura at pharm.ox.ac.uk>> wrote:

To whom it may concern,

I've tried out newer Bioformats MATLAB toolbox 5.7.3 on MATLAB R2017b, but the same bug is still there. This is to draw your attention.

As Sebastien Besson suggested earlier, `C:\Program Files\MATLAB\R2017b\java\jarext\tika-app.jar` appears to be the culprit. After renaming `tika-app.jar` to `tika-app.jar_` and relaunching MATLAB, I was able to open a `.jp2` file on R2017b successfully.


Best regards,

Kouichi



Warning: "bioformats_package.jar" is already specified on static java
path.
> In javaclasspath>local_validate_dynamic_path (line 290)
  In javaclasspath>local_javapath (line 187)
  In javaclasspath (line 124)
  In javaaddpath (line 71)
  In bfCheckJavaPath (line 57)
  In bfopen (line 99)
  In BFImage (line 99)
Reading series #1
    .Error using bfGetPlane (line 78)
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 (line 150)
        arr = bfGetPlane(r, i, varargin{:});
Error in BFImage (line 99)
            obj.Data = bfopen(filename);
78  plane = r.openBytes(...



--
Kouichi C. Nakamura, PhD
Senior Postdoctoral Neuroscientist
MRC Brain Network Dynamics Unit
University of Oxford
Mansfield Road, Oxford OX1 3TH, United Kingdom
+44-1865-271582 (office)
http://www.mrcbndu.ox.ac.uk/people/dr-kouichi-c-nakamura
kouichi.c.nakamura at gmail.com
kouichi.nakamura at pharm.ox.ac.uk

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