[ome-users] ImageJ plugin in 4.4-RC2

[Harri Jäälinoja]

Hi Will,

thanks, this helped, Insight opens and I can login to OMERO. Sorry, I 
was just confused about how to install the plugin.

So basically this is another way to distribute/install the Insight 
client? I had the idea the plugin would somehow allow you to select 
images from OMERO for processing.

Hmm, now if I try to download a project or a dataset or a single image 
from Insight, the "Download" item I get by right-clicking on the 
file-tree on the left is not active. I wonder why?

Thanks,
Harri


On 12/07/12 13:19, Will Moore wrote:
> 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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>