Open Microscopy Environment

Hi all,

So the server here has been updated to 5.0.0.rc1 as well as the Imagej plugin.

I'm running Fiji from the package together with the OME-imagej plugin from package also.

When loading any image it hangs on populating metadata.

Here is the debug output:

Code: Select all

setKeyUp: -1
runPlugIn: org.openmicroscopy.shoola.MainIJPlugin
actionPerformed: time=1389288001296, java.awt.event.ActionEvent[ACTION_PERFORMED,cmd=Connect to OMERO,when=1389288001296,modifiers=] on menuitem0
runUserPlugIn: org.openmicroscopy.shoola.MainIJPlugin, arg=
Cannot listen to the Quit action of the menu.
setKeyUp: -1
runPlugIn: loci.plugins.LociImporter
runUserPlugIn: loci.plugins.LociImporter, arg=
LOCI: parse core options
LOCI: display option dialogs
LOCI: loci.plugins.in.UpgradeDialog: prompt
LOCI: loci.plugins.in.LocationDialog: skip
LOCI: loci.plugins.in.IdDialog: skip
LOCI: loci.plugins.in.MainDialog: prompt
LOCI: Cached networkup: true
LOCI: Cached networkup: true
LOCI: Cached networkup: true
LOCI: Cached networkup: true
err >Exception in thread "AWT-EventQueue-0" java.lang.NoSuchFieldError: core
err >   at loci.ome.io.OmeroReader.initFile(OmeroReader.java:337)
err >   at loci.formats.FormatReader.setId(FormatReader.java:1244)
err >   at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
err >   at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
err >   at loci.plugins.in.Importer.showDialogs(Importer.java:141)
err >   at loci.plugins.in.Importer.run(Importer.java:79)
err >   at loci.plugins.LociImporter.run(LociImporter.java:81)
err >   at ij.IJ.runUserPlugIn(IJ.java:196)
err >   at ij.IJ.runPlugIn(IJ.java:160)
err >   at ij.IJ.runPlugIn(IJ.java:149)
err >   at org.openmicroscopy.shoola.env.ui.TaskBarManager.runAsImageJ(TaskBarManager.java:346)
err >   at org.openmicroscopy.shoola.env.ui.TaskBarManager.handleViewInPluginEvent(TaskBarManager.java:366)
err >   at org.openmicroscopy.shoola.env.ui.TaskBarManager.eventFired(TaskBarManager.java:1031)
err >   at org.openmicroscopy.shoola.env.event.EventBusImpl.dispatch(EventBusImpl.java:91)
err >   at org.openmicroscopy.shoola.env.event.EventBusImpl.post(EventBusImpl.java:222)
err >   at org.openmicroscopy.shoola.agents.treeviewer.cmd.ViewInPluginCmd.execute(ViewInPluginCmd.java:85)
err >   at org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerComponent.browse(TreeViewerComponent.java:3357)
err >   at org.openmicroscopy.shoola.agents.treeviewer.browser.BrowserModel.browse(BrowserModel.java:708)
err >   at org.openmicroscopy.shoola.agents.treeviewer.browser.BrowserUI.onClick(BrowserUI.java:408)
err >   at org.openmicroscopy.shoola.agents.treeviewer.browser.BrowserUI.access$500(BrowserUI.java:119)
err >   at org.openmicroscopy.shoola.agents.treeviewer.browser.BrowserUI$1.mousePressed(BrowserUI.java:998)
err >   at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:263)
err >   at java.awt.Component.processMouseEvent(Component.java:6411)
err >   at javax.swing.JComponent.processMouseEvent(JComponent.java:3275)
err >   at java.awt.Component.processEvent(Component.java:6179)
err >   at java.awt.Container.processEvent(Container.java:2084)
err >   at java.awt.Component.dispatchEventImpl(Component.java:4776)
err >   at java.awt.Container.dispatchEventImpl(Container.java:2142)
err >   at java.awt.Component.dispatchEvent(Component.java:4604)
err >   at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4618)
err >   at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4276)
err >   at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4209)
err >   at java.awt.Container.dispatchEventImpl(Container.java:2128)
err >   at java.awt.Window.dispatchEventImpl(Window.java:2492)
err >   at java.awt.Component.dispatchEvent(Component.java:4604)
err >   at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:717)
err >   at java.awt.EventQueue.access$400(EventQueue.java:82)
err >   at java.awt.EventQueue$2.run(EventQueue.java:676)
err >   at java.awt.EventQueue$2.run(EventQueue.java:674)
err >   at java.security.AccessController.doPrivileged(Native Method)
err >   at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
err >   at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97)
err >   at java.awt.EventQueue$3.run(EventQueue.java:690)
err >   at java.awt.EventQueue$3.run(EventQueue.java:688)
err >   at java.security.AccessController.doPrivileged(Native Method)
err >   at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
err >   at java.awt.EventQueue.dispatchEvent(EventQueue.java:687)
err >   at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
err >   at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
err >   at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
err >   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
err >   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
err >   at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
setKeyDown: 157
keyPressed: code=157 (?), char="?" (65535), flags=?
keyTyped: char="s" (115), flags= 4 (?)
OME5_error.txt->OME5_error.txt


This looked similar to a previous problem where Fiji wouldn't run from the package but even with LOCI form OME5 website replaced I still get the error.

Let me know if there is anything else you might need.

Cheers,
Helio

This sounds like you've got some LOCI jars that are OMERO-4 (E.g. loci_tools.jar).

You need to follow instructions here http://fiji.sc/Bio-Formats#Daily_builds to update to BF-5.

Certainly with a clean Fiji install, this was sufficient, along with the OMERO-IJ-5 plugin in the plugins folder, to get it working.

Hope that helps,

Will.

Thanks Will.

Indeed a clean install of Fiji and OME-IJ-pl did the trick.

Cheers,
Helio