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Task #9338 (closed)

Opened 12 years ago

Closed 12 years ago

Last modified 12 years ago

Bug: ImageJ open Image

Reported by: wmoore Owned by: jburel
Priority: major Milestone: OMERO-4.4.4
Component: Insight Version: n.a.
Keywords: n.a. Cc: ux@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2012-08-14 (2)

Description

Not sure if we "ever" want to display the standard Insight image viewer when running as an ImageJ plugin? But I guess the current behaviour is that we should "always" open Images in ImageJ?

Currently, the standard Insight image viewer opens when I:

  • click on an image in the Dataset Table view
  • click on an Image result from running a script
  • click on an Image link (E.g. in another Image description)

Change History (12)

comment:1 Changed 12 years ago by jburel

  • Cc ux@… added
  • Remaining Time set to 0.25
  • Sprint set to 2012-08-14 (2)

Default behaviour should be: open in imageJ when we run insight as a plugin.
This is true for some actions but not for all as pointed out.

comment:2 Changed 12 years ago by jburel

  • Status changed from new to accepted

comment:3 Changed 12 years ago by jburel

  • Remaining Time changed from 0.25 to 0
  • Resolution set to fixed
  • Status changed from accepted to closed

see 81e405edeecb407880b165aadf14ec0a63051db0 jburel/bugs-sprint2

comment:4 Changed 12 years ago by saloynton

In viewing the image result of channel offset, combine images, and images from ROI's I am still seeing the image open in OMERO not imagej. Has this been covered in clicking on an Image result from running a script in the update?

comment:5 Changed 12 years ago by jburel

  • Resolution fixed deleted
  • Status changed from closed to reopened

It should have been covered. Are the other cases working?

Last edited 12 years ago by jburel (previous) (diff)

comment:6 Changed 12 years ago by jburel

  • Resolution set to fixed
  • Status changed from reopened to closed

Open imageJ viewer for script output see 9e5ec20c43a20eca15570bd3acd3c07a9c59bd9b

comment:7 Changed 12 years ago by saloynton

I have had the following exception from clicking on the image CFPNEAT01_R3D.dv in Project

  • ProjectB_1/imagesToBeAnnotated_1

I am logged in as user-6 in the read-only1 group

I have checked the same image in Insight without the imagej plugin and I do not see such an exception but I have not been able to open the image via clicking on the id. 

loci.formats.FormatException: Could not find Image with ID=212 in group 'null'.
	at loci.ome.io.OmeroReader.initFile(OmeroReader.java:317)
	at loci.formats.FormatReader.setId(FormatReader.java:1105)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
	at loci.plugins.in.Importer.run(Importer.java:79)
	at loci.plugins.LociImporter.run(LociImporter.java:81)
	at ij.IJ.runUserPlugIn(IJ.java:185)
	at ij.IJ.runPlugIn(IJ.java:152)
	at ij.IJ.runPlugIn(IJ.java:141)
	at org.openmicroscopy.shoola.env.ui.TaskBarManager.runAsImageJ(TaskBarManager.java:390)
	at org.openmicroscopy.shoola.env.ui.TaskBarManager.handleViewInPluginEvent(TaskBarManager.java:410)
	at org.openmicroscopy.shoola.env.ui.TaskBarManager.eventFired(TaskBarManager.java:1033)
	at org.openmicroscopy.shoola.env.event.EventBusImpl.dispatch(EventBusImpl.java:91)
	at org.openmicroscopy.shoola.env.event.EventBusImpl.post(EventBusImpl.java:222)
	at org.openmicroscopy.shoola.agents.metadata.editor.PropertiesUI.propertyChange(PropertiesUI.java:1518)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:339)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:276)
	at java.awt.Component.firePropertyChange(Component.java:8248)
	at org.openmicroscopy.shoola.util.ui.omeeditpane.OMEWikiComponent.onSelection(OMEWikiComponent.java:354)
	at org.openmicroscopy.shoola.util.ui.omeeditpane.OMEEditPane.actionPerformed(OMEEditPane.java:170)
	at javax.swing.Timer.fireActionPerformed(Timer.java:291)
	at javax.swing.Timer$DoPostEvent.run(Timer.java:221)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:682)
	at java.awt.EventQueue.access$000(EventQueue.java:85)
	at java.awt.EventQueue$1.run(EventQueue.java:643)
	at java.awt.EventQueue$1.run(EventQueue.java:641)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:652)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
loci.formats.FormatException: Could not find Image with ID=212 in group 'null'.
	at loci.ome.io.OmeroReader.initFile(OmeroReader.java:317)
	at loci.formats.FormatReader.setId(FormatReader.java:1105)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
	at loci.plugins.in.Importer.run(Importer.java:79)
	at loci.plugins.LociImporter.run(LociImporter.java:81)
	at ij.IJ.runUserPlugIn(IJ.java:185)
	at ij.IJ.runPlugIn(IJ.java:152)
	at ij.IJ.runPlugIn(IJ.java:141)
	at org.openmicroscopy.shoola.env.ui.TaskBarManager.runAsImageJ(TaskBarManager.java:390)
	at org.openmicroscopy.shoola.env.ui.TaskBarManager.handleViewInPluginEvent(TaskBarManager.java:410)
	at org.openmicroscopy.shoola.env.ui.TaskBarManager.eventFired(TaskBarManager.java:1033)
	at org.openmicroscopy.shoola.env.event.EventBusImpl.dispatch(EventBusImpl.java:91)
	at org.openmicroscopy.shoola.env.event.EventBusImpl.post(EventBusImpl.java:222)
	at org.openmicroscopy.shoola.agents.metadata.editor.PropertiesUI.propertyChange(PropertiesUI.java:1518)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:339)
	at java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:276)
	at java.awt.Component.firePropertyChange(Component.java:8248)
	at org.openmicroscopy.shoola.util.ui.omeeditpane.OMEWikiComponent.onSelection(OMEWikiComponent.java:354)
	at org.openmicroscopy.shoola.util.ui.omeeditpane.OMEEditPane.actionPerformed(OMEEditPane.java:170)
	at javax.swing.Timer.fireActionPerformed(Timer.java:291)
	at javax.swing.Timer$DoPostEvent.run(Timer.java:221)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:682)
	at java.awt.EventQueue.access$000(EventQueue.java:85)
	at java.awt.EventQueue$1.run(EventQueue.java:643)
	at java.awt.EventQueue$1.run(EventQueue.java:641)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:652)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

comment:8 Changed 12 years ago by saloynton

Testing the fix for:

  • clicking on an Image result from running a script works as expected with the new build OMERO.insight-4.4.1-70-45311e4-ice33-b126.

comment:9 Changed 12 years ago by jburel

The image is not owned by the user and does not seem to be in that group. So that is a different problem/limitation. Scott could you open a new ticket for that?

comment:10 Changed 12 years ago by saloynton

New ticket created #9460 for this separate issue.

comment:11 Changed 12 years ago by jburel <j.burel@…>

(In [81e405edeecb407880b165aadf14ec0a63051db0/ome.git] on branch develop) Make the loci viewer the default when run as IJ plugin (see #9338)

comment:12 Changed 12 years ago by jburel <j.burel@…>

(In [9e5ec20c43a20eca15570bd3acd3c07a9c59bd9b/ome.git] on branch develop) Open imageJ viewer by default from script output (see #9338)

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