Plugin is not working on the Fiji 1.53t version

[Mailfert]

Dear all,
the lugin does not work on my latest FiJi version.
Could you help me please?

[mkitti]

The plugin seems to be an old version.

[ctrueden]

@mkitti Yes, but it may be that the current state of the Java-8 update site is not functional, due to skew in Fiji 2.9.0? I will be uploading the latest Fiji release (2.13.1) this week, and will look into this as part of my updates.

[mkitti]

ncsa.hdf.hdf5lib is a really old prefix.

[ctrueden]

@mkitti This plugin was updated to use the newer JHDF5 19.04 API with 9385408, which happened about 9 months ago. That change became part of HDF5_Vibez v1.1.1, which is part of Fiji 2.9.0, and is currently shipped on the Java-8 update site.

@Mailfert Is your Fiji up-to-date? Try running Help → Update... and installing the latest updates. You should have HDF5_Vibez 1.1.1 or newer in your plugins folder; if not, that would explain the error you are seeing.

[peterhpark]

I have the same issue with the latest fiji. Both my Fiji and the plug-in were updated to the latest versions... Any solutions?

[shiaway]

Is there any solution to this yet? I am also getting the same issue with version 2.16.0:

(Fiji Is Just) ImageJ 2.16.0/1.54g; Java 1.8.0_322 [64-bit]; Mac OS X 10.16; 94MB of 7221MB (1%)

java.lang.NoClassDefFoundError: ncsa/hdf/hdf5lib/exceptions/HDF5Exception
at java.lang.Class.getDeclaredConstructors0(Native Method)
at java.lang.Class.privateGetDeclaredConstructors(Class.java:2671)
at java.lang.Class.getConstructor0(Class.java:3075)
at java.lang.Class.newInstance(Class.java:412)
at ij.IJ.runUserPlugIn(IJ.java:242)
at ij.IJ.runPlugIn(IJ.java:210)
at ij.Executer.runCommand(Executer.java:152)
at ij.Executer.run(Executer.java:70)
at java.lang.Thread.run(Thread.java:750)
Caused by: java.lang.ClassNotFoundException: ncsa.hdf.hdf5lib.exceptions.HDF5Exception
at java.net.URLClassLoader.findClass(URLClassLoader.java:387)
at java.lang.ClassLoader.loadClass(ClassLoader.java:419)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
at java.lang.ClassLoader.loadClass(ClassLoader.java:352)
... 9 more

[mkitti]

HDF5 Vibez 1.1.1 depends on jhdf5 19.04 as of this commit 9385408

These should now refer to hdf.hdf5lib.exceptions.HDF5Exception and not NCSA.
https://sissource.ethz.ch/sispub/jhdf5/-/blob/master/source/java/hdf/hdf5lib/exceptions/HDF5Exception.java?ref_type=heads

There must be an old copy somewhere. If you cannot find it, I suggest downloading a new copy of FIJI from https://fiji.sc/ .

[mkitti]

In the Fiji.app folder there should be a plugins/HDF5_Vibez-1.1.1.jar file. That should be the only one version of HDF_Vibez there.

[mkitti]

Also in the Fiji.app folder there should be jars/jhdf5-19.04.1.jar

If you have the jar command available, you can inspect that it refers to

% jar tvf jhdf5-19.04.1.jar | grep HDF5Exception.class
   594 Mon Jul 25 20:49:22 EDT 2022 hdf/hdf5lib/exceptions/HDF5Exception.class

If you have the unzip command available, you can also do a similar inspection.

% unzip -l jhdf5-19.04.1.jar | grep HDF5Exception.class
      594  07-25-2022 20:49   hdf/hdf5lib/exceptions/HDF5Exception.class