[ome-users] ImageJ plugin in 4.4-RC2

[Will Moore]

Hi Harri,

You say "Something happens..." but it's still not working (stack trace), right?

I just downloaded and updated Fiji, then downloaded hudson.openmicroscopy.org.uk/job/OMERO-trunk/lastSuccessfulBuild/artifact/src/target/OMERO.insight-ij-4.4.0-RC2-217-a46c0f5-ice33-b3030.zip
and put the entire OMERO.ij-4.4.0-RC2-217-a46c0f5-ice33-b3030 folder into the Fiji plugins folder.

This worked fine for me,

 Hope that helps,

  Will. 




On 12 Jul 2012, at 10:12, Harri Jäälinoja wrote:

> 
>>> http://hudson.openmicroscopy.org.uk/job/OMERO-trunk/3028/artifact/src/targ
>>> et/OMERO.insight-ij-4.4.0-RC2-188-da0c55d-ice33-b3028.zip
>>> 
>>> You'll still need the new loci_tools.jar.
>> 
>> And ome-io.jar installed in the ImageJ/Plugins folder in order to work.
>> 
> 
> 
> Hi,
> 
> I first reinstalled Fiji, to be sure, and updated it. Then:
> 
> hajaalin at dh2-bll10-06:~$ cp Downloads/OMERO.ij-4.4.0-RC2-188-da0c55d-ice33-b3028/omero_ij.jar Fiji.app/plugins/
> hajaalin at dh2-bll10-06:~$ cp Downloads/OMERO.ij-4.4.0-RC2-188-da0c55d-ice33-b3028/libs/ome-io.jar Fiji.app/plugins/
> 
> hajaalin at dh2-bll10-06:~$ wget http://hudson.openmicroscopy.org.uk/view/Bio-Formats/job/BIOFORMATS-trunk/lastSuccessfulBuild/artifact/artifacts/loci_tools.jar
> hajaalin at dh2-bll10-06:~$ mv loci_tools.jar Fiji.app/plugins/
> 
> hajaalin at dh2-bll10-06:~$ Fiji.app/fiji-linux64
> Re-executing with correct library lookup path (/home/hajaalin/Fiji.app/lib/linux64)
> 
> 
> Now the OMERO plugin menu item is different, says "Connect to OMERO". When I select it, nothing happens.
> 
> Then I looked at the jar files in Downloads/OMERO.ij-4.4.0-RC2-188-da0c55d-ice33-b3028/libs/, and I noticed that for example TableLayout.jar and JHotDraw.jar are not in Fiji.app/plugins or Fiji.app/
> 
> To be sure (or maybe to overdo), I did like this:
> hajaalin at dh2-bll10-06:~$ cp Downloads/OMERO.ij-4.4.0-RC2-188-da0c55d-ice33-b3028/libs/* Fiji.app/plugins/
> 
> Now something happens when I select OMERO plugin, so maybe it's a matter of getting the jars right?
> 
> Cheers,
> Harri
> 
> 
> java.lang.reflect.InvocationTargetException
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> 	at java.lang.reflect.Method.invoke(Method.java:597)
> 	at ij.Command.runPlugIn(Command.java:146)
> 	at ij.Command.runCommand(Command.java:95)
> 	at ij.Executer.run(Executer.java:64)
> 	at java.lang.Thread.run(Thread.java:662)
> Caused by: java.lang.RuntimeException: Failed to intialize the Container in test mode.
> 	at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:414)
> 	at org.openmicroscopy.shoola.MainIJPlugin.run(MainIJPlugin.java:160)
> 	at ij.IJ.runUserPlugIn(IJ.java:185)
> 	at ij.IJ.runPlugIn(IJ.java:152)
> 	... 8 more
> Caused by: org.openmicroscopy.shoola.env.init.StartupException: Unable to load Container configuration
> 	at org.openmicroscopy.shoola.env.init.ContainerConfigInit.execute(ContainerConfigInit.java:100)
> 	at org.openmicroscopy.shoola.env.init.Initializer.doInit(Initializer.java:255)
> 	at org.openmicroscopy.shoola.env.Container.startupInPluginMode(Container.java:409)
> 	... 11 more
> Caused by: org.openmicroscopy.shoola.env.config.ConfigException: An error occurred while attempting to process /home/hajaalin/Fiji.app/plugins/config/container.xml. (/home/hajaalin/Fiji.app/plugins/config/container.xml (No such file or directory))
> 	at org.openmicroscopy.shoola.env.config.Parser.rethrow(Parser.java:105)
> 	at org.openmicroscopy.shoola.env.config.Parser.parse(Parser.java:173)
> 	at org.openmicroscopy.shoola.env.config.RegistryFactory.fillFromFile(RegistryFactory.java:102)
> 	at org.openmicroscopy.shoola.env.init.ContainerConfigInit.execute(ContainerConfigInit.java:84)
> 	... 13 more
> Caused by: java.io.FileNotFoundException: /home/hajaalin/Fiji.app/plugins/config/container.xml (No such file or directory)
> 	at java.io.FileInputStream.open(Native Method)
> 	at java.io.FileInputStream.<init>(FileInputStream.java:106)
> 	at java.io.FileInputStream.<init>(FileInputStream.java:66)
> 	at org.openmicroscopy.shoola.util.file.IOUtil.readConfigFile(IOUtil.java:262)
> 	at org.openmicroscopy.shoola.env.config.Parser.parse(Parser.java:156)
> 	... 15 more
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