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Hi Kouichi,
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<div class="">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. </div>
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<div class=""><a href="https://docs.openmicroscopy.org/bio-formats/5.7.3/developers/components.html#forks-jai" class="">https://docs.openmicroscopy.org/bio-formats/5.7.3/developers/components.html#forks-jai</a></div>
<div class=""><a href="https://docs.openmicroscopy.org/bio-formats/5.7.3/users/matlab/index.html" class="">https://docs.openmicroscopy.org/bio-formats/5.7.3/users/matlab/index.html</a></div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<blockquote type="cite" class="">
<div class="">On 11 Jan 2018, at 17:46, Kouichi Nakamura <<a href="mailto:kouichi.nakamura@pharm.ox.ac.uk" class="">kouichi.nakamura@pharm.ox.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">To whom it may concern,<br class="">
<br class="">
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.<br class="">
<br class="">
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.<br class="">
<br class="">
<br class="">
Best regards,<br class="">
<br class="">
Kouichi<br class="">
<br class="">
<br class="">
<br class="">
Warning: "bioformats_package.jar" is already specified on static java<br class="">
path.<br class="">
> In javaclasspath>local_validate_dynamic_path (line 290)<br class="">
In javaclasspath>local_javapath (line 187)<br class="">
In javaclasspath (line 124)<br class="">
In javaaddpath (line 71)<br class="">
In bfCheckJavaPath (line 57)<br class="">
In bfopen (line 99)<br class="">
In BFImage (line 99)<br class="">
Reading series #1<br class="">
.Error using bfGetPlane (line 78)<br class="">
Java exception occurred:<br class="">
java.lang.RuntimeException:<br class="">
jj2000.j2k.fileformat.reader.FileFormatReader.<init>(Ljj2000/j2k/io/RandomAccessIO;Lcom/sun/media/imageioimpl/plugins/jpeg2000/J2KMetadata;)V<br class="">
<br class="">
at<br class="">
com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState.initializeRead(J2KReadState.java:729)<br class="">
<br class="">
at<br class="">
com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState.<init>(J2KReadState.java:241)<br class="">
<br class="">
at<br class="">
com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader.readRaster(J2KImageReader.java:551)<br class="">
<br class="">
at<br class="">
ome.codecs.services.JAIIIOServiceImpl.readRaster(JAIIIOServiceImpl.java:177)<br class="">
<br class="">
at ome.codecs.JPEG2000Codec.decompress(JPEG2000Codec.java:296)<br class="">
<br class="">
at ome.codecs.JPEG2000Codec.decompress(JPEG2000Codec.java:267)<br class="">
<br class="">
at<br class="">
loci.formats.codec.WrappedCodec.decompress(WrappedCodec.java:132)<br class="">
<br class="">
at<br class="">
loci.formats.codec.JPEG2000Codec.decompress(JPEG2000Codec.java:63)<br class="">
<br class="">
at<br class="">
loci.formats.in.JPEG2000Reader.openBytes(JPEG2000Reader.java:182)<br class="">
<br class="">
at loci.formats.ImageReader.openBytes(ImageReader.java:457)<br class="">
<br class="">
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)<br class="">
<br class="">
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:148)<br class="">
<br class="">
at<br class="">
loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198)<br class="">
<br class="">
at<br class="">
loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:159)<br class="">
<br class="">
Caused by: java.lang.NoSuchMethodError:<br class="">
jj2000.j2k.fileformat.reader.FileFormatReader.<init>(Ljj2000/j2k/io/RandomAccessIO;Lcom/sun/media/imageioimpl/plugins/jpeg2000/J2KMetadata;)V<br class="">
<br class="">
at<br class="">
com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState.initializeRead(J2KReadState.java:450)<br class="">
<br class="">
... 13 more<br class="">
<br class="">
Error in bfopen (line 150)<br class="">
arr = bfGetPlane(r, i, varargin{:});<br class="">
Error in BFImage (line 99)<br class="">
obj.Data = bfopen(filename);<br class="">
78 plane = r.openBytes(...<br class="">
<br class="">
<br class="">
<br class="">
-- <br class="">
Kouichi C. Nakamura, PhD<br class="">
Senior Postdoctoral Neuroscientist<br class="">
MRC Brain Network Dynamics Unit<br class="">
University of Oxford<br class="">
Mansfield Road, Oxford OX1 3TH, United Kingdom<br class="">
+44-1865-271582 (office)<br class="">
<a href="http://www.mrcbndu.ox.ac.uk/people/dr-kouichi-c-nakamura" class="">http://www.mrcbndu.ox.ac.uk/people/dr-kouichi-c-nakamura</a><br class="">
kouichi.c.nakamura@gmail.com<br class="">
kouichi.nakamura@pharm.ox.ac.uk<br class="">
<br class="">
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ome-users@lists.openmicroscopy.org.uk<br class="">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br class="">
</div>
</blockquote>
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<br class="">
</div>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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