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Bug 379 - Since the automatic uptade of today (I did it this morning) my installed plugin Perkin ElmerPan is not working anymore. It loads the images but it does not open the image window anymore. Yesterday worked just fine and today after the fiji update is not...
Since the automatic uptade of today (I did it this morning) my installed plug...
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2011-11-04 12:57 CDT by Claudio Collinet
Modified: 2011-11-04 19:01 CDT
1 user (show)

See Also:

Description Claudio Collinet 2011-11-04 12:57:05 CDT
[Enter details of the problem or bug and how to reproduce it here.]

Information about your version of Java - this information is useful for the Fiji developers:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: Up-to-date

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\PROGRA~1\Fiji.app/java/win64/jdk1.6.0_24/jre
  fiji.dir => C:\PROGRA~1\Fiji.app

Information about the version of each plugin:

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Comment 1 Johannes Schindelin 2011-11-04 15:33:04 CDT
Hi Claudio,

this is unfortunately awfully little information to go on... if I were still at the MPI I could now walk to your computer and extract more details :-(

> Since the automatic uptade of today (I did it this morning) my installed
> plugin Perkin ElmerPan is not working anymore. It loads the images but it
> does not open the image window anymore. Yesterday worked just fine and today
> after the fiji update is not working anymore.

Is there any way to get at this plugin and your procedure to be able to reproduce the problem?

If not, could you start Fiji from the command line (http://fiji.sc/Command_Line_Debugging) with the --console option? Hopefully there is more information there which I'd like to ask you to paste into an additional comment of this ticket.
Comment 2 Claudio Collinet 2011-11-04 17:00:47 CDT
(In reply to comment #1)
> Hi Claudio,
> 
> this is unfortunately awfully little information to go on... if I were still at
> the MPI I could now walk to your computer and extract more details :-(
> 
> > Since the automatic uptade of today (I did it this morning) my installed
> > plugin Perkin ElmerPan is not working anymore. It loads the images but it
> > does not open the image window anymore. Yesterday worked just fine and today
> > after the fiji update is not working anymore.
> 
> Is there any way to get at this plugin and your procedure to be able to
> reproduce the problem?
> 
> If not, could you start Fiji from the command line
> (http://fiji.sc/Command_Line_Debugging) with the --console option? Hopefully
> there is more information there which I'd like to ask you to paste into an
> additional comment of this ticket.
> 
Hi Johannes,
nice to hear from you. Unfortunately, even if you were still at MPI-CBG you could not have come to my PC because I am no longer there...
Concerning the problem, I stated fiji from the command line as you suggested and here below is what appears (in the command line) when I try to do what I described before it does not work:

C:\Users\collinet>cd C:\Program Files\Fiji.app

C:\Program Files\Fiji.app>fiji-win64 --console

C:\Program Files\Fiji.app>Exception in thread "AWT-EventQueue-0" java.lang.Illeg
alArgumentException: Must be IndexColorModel
        at ij.process.ImageProcessor.setColorModel(ImageProcessor.java:146)
        at i5d.Image5D.restoreChannelProperties(Image5D.java:1547)
        at i5d.Image5D.setDisplayMode(Image5D.java:819)
        at i5d.Image5D.<init>(Image5D.java:257)
        at i5d.Image5D.<init>(Image5D.java:173)
        at i5d.Image5D.<init>(Image5D.java:154)
        at i5d.Image5D.<init>(Image5D.java:165)
        at PerkinElmerOpener.image5D(PerkinElmerOpener.java:716)
        at PerkinElmerPanel.PEopen(PerkinElmerPanel.java:225)
        at PerkinElmerPanel$PEpanel$PEopen.actionPerformed(PerkinElmerPanel.java
:53)
        at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:19
95)
        at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.jav
a:2318)
        at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel
.java:387)
        at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242
)
        at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonL
istener.java:236)
        at java.awt.Component.processMouseEvent(Component.java:6289)
        at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
        at java.awt.Component.processEvent(Component.java:6054)
        at java.awt.Container.processEvent(Container.java:2041)
        at java.awt.Component.dispatchEventImpl(Component.java:4652)
        at java.awt.Container.dispatchEventImpl(Container.java:2099)
        at java.awt.Component.dispatchEvent(Component.java:4482)
        at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577
)
        at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)

        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
        at java.awt.Container.dispatchEventImpl(Container.java:2085)
        at java.awt.Window.dispatchEventImpl(Window.java:2478)
        at java.awt.Component.dispatchEvent(Component.java:4482)
        at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644)
        at java.awt.EventQueue.access$000(EventQueue.java:85)
        at java.awt.EventQueue$1.run(EventQueue.java:603)
        at java.awt.EventQueue$1.run(EventQueue.java:601)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo
ntrolContext.java:87)
        at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo
ntrolContext.java:98)
        at java.awt.EventQueue$2.run(EventQueue.java:617)
        at java.awt.EventQueue$2.run(EventQueue.java:615)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo
ntrolContext.java:87)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:614)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThre
ad.java:269)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.
java:184)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre
ad.java:174)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)

        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)

        at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

I can also explain to you how to reproduce the problem on your machine and I could pass you some of the images I need to open (just let me know how)

The plugin I am using is the Perkin ElmerPan.jar version 1.2.0 which you can download at the website http://www.embl.de/almf/almf_services/services/downloads/PE_plugin/
With this I do File>Import>Perkin Elmer
there is a window appearing onto which I select the command "Open" and I then select the fist image of an image series contained into a folder (that I can pass you). Normally, a log message window appears along with a window with images. Right now I can see the log message window, you can see that it is loading files but the image window never appears afterwards.
Let me know how to proceed and if you need any more detail.
Best
Claudio
Comment 3 Claudio Collinet 2011-11-04 17:01:07 CDT
(In reply to comment #1)
> Hi Claudio,
> 
> this is unfortunately awfully little information to go on... if I were still at
> the MPI I could now walk to your computer and extract more details :-(
> 
> > Since the automatic uptade of today (I did it this morning) my installed
> > plugin Perkin ElmerPan is not working anymore. It loads the images but it
> > does not open the image window anymore. Yesterday worked just fine and today
> > after the fiji update is not working anymore.
> 
> Is there any way to get at this plugin and your procedure to be able to
> reproduce the problem?
> 
> If not, could you start Fiji from the command line
> (http://fiji.sc/Command_Line_Debugging) with the --console option? Hopefully
> there is more information there which I'd like to ask you to paste into an
> additional comment of this ticket.
> 
Hi Johannes,
nice to hear from you. Unfortunately, even if you were still at MPI-CBG you could not have come to my PC because I am no longer there...
Concerning the problem, I stated fiji from the command line as you suggested and here below is what appears (in the command line) when I try to do what I described before it does not work:

C:\Users\collinet>cd C:\Program Files\Fiji.app

C:\Program Files\Fiji.app>fiji-win64 --console

C:\Program Files\Fiji.app>Exception in thread "AWT-EventQueue-0" java.lang.Illeg
alArgumentException: Must be IndexColorModel
        at ij.process.ImageProcessor.setColorModel(ImageProcessor.java:146)
        at i5d.Image5D.restoreChannelProperties(Image5D.java:1547)
        at i5d.Image5D.setDisplayMode(Image5D.java:819)
        at i5d.Image5D.<init>(Image5D.java:257)
        at i5d.Image5D.<init>(Image5D.java:173)
        at i5d.Image5D.<init>(Image5D.java:154)
        at i5d.Image5D.<init>(Image5D.java:165)
        at PerkinElmerOpener.image5D(PerkinElmerOpener.java:716)
        at PerkinElmerPanel.PEopen(PerkinElmerPanel.java:225)
        at PerkinElmerPanel$PEpanel$PEopen.actionPerformed(PerkinElmerPanel.java
:53)
        at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:19
95)
        at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.jav
a:2318)
        at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel
.java:387)
        at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242
)
        at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonL
istener.java:236)
        at java.awt.Component.processMouseEvent(Component.java:6289)
        at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
        at java.awt.Component.processEvent(Component.java:6054)
        at java.awt.Container.processEvent(Container.java:2041)
        at java.awt.Component.dispatchEventImpl(Component.java:4652)
        at java.awt.Container.dispatchEventImpl(Container.java:2099)
        at java.awt.Component.dispatchEvent(Component.java:4482)
        at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577
)
        at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)

        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
        at java.awt.Container.dispatchEventImpl(Container.java:2085)
        at java.awt.Window.dispatchEventImpl(Window.java:2478)
        at java.awt.Component.dispatchEvent(Component.java:4482)
        at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644)
        at java.awt.EventQueue.access$000(EventQueue.java:85)
        at java.awt.EventQueue$1.run(EventQueue.java:603)
        at java.awt.EventQueue$1.run(EventQueue.java:601)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo
ntrolContext.java:87)
        at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo
ntrolContext.java:98)
        at java.awt.EventQueue$2.run(EventQueue.java:617)
        at java.awt.EventQueue$2.run(EventQueue.java:615)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo
ntrolContext.java:87)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:614)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThre
ad.java:269)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.
java:184)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre
ad.java:174)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)

        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)

        at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

I can also explain to you how to reproduce the problem on your machine and I could pass you some of the images I need to open (just let me know how)

The plugin I am using is the Perkin ElmerPan.jar version 1.2.0 which you can download at the website http://www.embl.de/almf/almf_services/services/downloads/PE_plugin/
With this I do File>Import>Perkin Elmer
there is a window appearing onto which I select the command "Open" and I then select the fist image of an image series contained into a folder (that I can pass you). Normally, a log message window appears along with a window with images. Right now I can see the log message window, you can see that it is loading files but the image window never appears afterwards.
Let me know how to proceed and if you need any more detail.
Best
Claudio
Comment 4 Curtis Rueden 2011-11-04 17:07:20 CDT
Thanks for the additional information, Claudio. From the stack trace, it looks like a bug in Image5D. I am investigating now.
Comment 5 Claudio Collinet 2011-11-04 17:09:30 CDT
(In reply to comment #4)
> Thanks for the additional information, Claudio. From the stack trace, it looks
> like a bug in Image5D. I am investigating now.
> 
This makes a lot of sense because this plugin requires Image5D.

Comment 6 Curtis Rueden 2011-11-04 17:36:36 CDT
I pushed a new Image5D to the updater, which I hope fixes the problem. Could you please try updating Fiji and let me know if it works for you now?
Comment 7 Claudio Collinet 2011-11-04 18:57:56 CDT
(In reply to comment #6)
> I pushed a new Image5D to the updater, which I hope fixes the problem. Could
> you please try updating Fiji and let me know if it works for you now?
> 

Hi Curtis,
it works now. Thanks a lot!
Claudio
Comment 8 Johannes Schindelin 2011-11-04 19:01:04 CDT
Fantastic! Thanks all.
Comment 9 Claudio Collinet 2012-09-04 15:56:40 CDT
The original summary for this bug was longer than 255 characters, and so it was truncated when Bugzilla was upgraded. The original summary was:

Since the automatic uptade of today (I did it this morning) my installed plugin Perkin ElmerPan is not working anymore. It loads the images but it does not open the image window anymore. Yesterday worked just fine and today after the fiji update is not working anymore.