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imageJ instability?

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Winnok H. De Vos

imageJ instability?

Dear all,

Lately I have been experiencing some stability problems with imageJ which seem
to worsen. When I duplicate or crop a couple of images or run other commands
that create a new window it quite often causes imageJ to crash, ie the window
remains white and I have no other option but to close imageJ using a complete
process closing. I have tried changing the memory settings but this has no
influence whatsoever. I also tried reinstalling imageJ but this didn't prove
succesfull either. Has anybody encountered such instability? How can I resolve
this issue?
Many thanks in advance.
Kind regards,
winnok

--
assistent prof. P. Van Oostveldt
Dep. Moleculaire Biotechnologie
Fac. Toegepaste Landbouwwetenschappen, Ugent
Coupure links 653
9000 Gent
tel. (0032) 09/264.59.71

Harry Parker

Re: imageJ instability?

Hi all,

On my Windows system, the only lockup issue I've seen is when closing ImageJ with 2 or more images open.
This happens most often after I've used one of my custom filter plugins. What happens is the "Save changes to ...?" dialog comes up empty (buttons but no text in window). Then I must use the task manager to abort ImageJ. Its not consistent, so I think its some kind of thread deadlock related problem. It doesn't happen when I'm in Debug Mode. (The Heisenberg Uncertainty Principle applied to software?)

--
Harry Parker
Senior Systems Engineer
Digital Imaging Systems, Inc.

----- Original Message ----
From: Winnok De Vos <[hidden email]>
To: [hidden email]
Sent: Friday, May 18, 2007 1:43:05 PM
Subject: imageJ instability?

Dear all,

Lately I have been experiencing some stability problems with imageJ which seem
to worsen. When I duplicate or crop a couple of images or run other commands
that create a new window it quite often causes imageJ to crash, ie the window
remains white and I have no other option but to close imageJ using a complete
process closing. I have tried changing the memory settings but this has no
influence whatsoever. I also tried reinstalling imageJ but this didn't prove
succesfull either. Has anybody encountered such instability? How can I resolve
this issue?
Many thanks in advance.
Kind regards,
winnok

--
assistent prof. P. Van Oostveldt
Dep. Moleculaire Biotechnologie
Fac. Toegepaste Landbouwwetenschappen, Ugent
Coupure links 653
9000 Gent
tel. (0032) 09/264.59.71

____________________________________________________________________________________Get the free Yahoo! toolbar and rest assured with the added security of spyware protection.
http://new.toolbar.yahoo.com/toolbar/features/norton/index.php

Winnok H. De Vos

Re: imageJ instability?

In reply to this post by Winnok H. De Vos

Dear Wayne,

I'm using the most recent version (I think), ImageJ 1.38r on Java 1.5.0_06
and use 750mb of 1gb available working memory.
I do work with the WCIF imageJ bundle but update the jar file regularly from
your site. I had encountered this problem already with previous versions,
but it is getting more pronounced lately. So I don't think it is related to
the version. I am also having a similar problem as Harry Parker, ie crashing
while closing with multiple windows opened.
I will try debug mode. Is there something else I can try?
Many thanks in advance.
Kind regards,

winnok

______
ir. Winnok De Vos
Research Assistant

dep. Molecular Biotechnology
Faculty of Bioscience Engineering
Ghent University
Coupure links 653
9000 Ghent
Belgium

tel 0032.(0)9.264.59.71
fax 0032.(0)9.264.62.19
www.molecularbiotechnology.ugent.be
----- Original Message -----
From: "Rasband Wayne" <[hidden email]>
To: <[hidden email]>
Sent: Monday, May 21, 2007 4:16 PM
Subject: Re: imageJ instability?

> Dear Dr. Oostveldt,
>
> Which version of ImageJ are you using and which version of Java? You can
> get this information using the Help>About ImageJ command. Does the
> unstability go away if you revert to a previous version of ImageJ? You
> can get previous versions at <http://rsb.info.nih.gov/ij/ download/jars/>.
>
> Best regards,
>
> -wayne
>
>
> On May 18, 2007, at 1:43 PM, Winnok De Vos wrote:
>
>> Dear all,
>>
>> Lately I have been experiencing some stability problems with imageJ
>> which seem
>> to worsen. When I duplicate or crop a couple of images or run other
>> commands
>> that create a new window it quite often causes imageJ to crash, ie the
>> window
>> remains white and I have no other option but to close imageJ using a
>> complete
>> process closing. I have tried changing the memory settings but this has
>> no
>> influence whatsoever. I also tried reinstalling imageJ but this didn't
>> prove
>> succesfull either. Has anybody encountered such instability? How can I
>> resolve
>> this issue?
>> Many thanks in advance.
>> Kind regards,
>> winnok
>>
>> --
>> assistent prof. P. Van Oostveldt
>> Dep. Moleculaire Biotechnologie
>> Fac. Toegepaste Landbouwwetenschappen, Ugent
>> Coupure links 653
>> 9000 Gent
>> tel. (0032) 09/264.59.71
>

Dan Hsu

Re: imageJ instability?

Winnok

You didn't mention which OS, so am assuming your are running Win XP (SP2?).

I had experienced unmanageable instability, and after some analyses of types
of files and functions being used on ImageJ, moving to other PCs, fresh
installs of ImageJ & XP, etc. decided that this package was probably NOT at
fault, but was showing some conflict with another program(s). This was
ImageJ ~1.8m/n. After much online searching I found some discussion about
program instability and downloaded ShellExView to view which extensions were
open in the OS, and by trial-and-error deactivated Adobe Illustrator (v 10)
icon handler and thumbnail, as well as Acrobat (v 6) extensions.

Amazing how peaceful it now is!!! Try this program (freeware), if you are on
XP, and best wishes to undisturbed analyses.
www.nirsoft.net
Dan

on 5/21/07 8:21 AM, winnok ugent at [hidden email] wrote:

> Dear Wayne,
>
> I'm using the most recent version (I think), ImageJ 1.38r on Java 1.5.0_06
> and use 750mb of 1gb available working memory.
> I do work with the WCIF imageJ bundle but update the jar file regularly from
> your site. I had encountered this problem already with previous versions,
> but it is getting more pronounced lately. So I don't think it is related to
> the version. I am also having a similar problem as Harry Parker, ie crashing
> while closing with multiple windows opened.
> I will try debug mode. Is there something else I can try?
> Many thanks in advance.
> Kind regards,
>
> winnok
>
> ______
> ir. Winnok De Vos
> Research Assistant
>
> dep. Molecular Biotechnology
> Faculty of Bioscience Engineering
> Ghent University
> Coupure links 653
> 9000 Ghent
> Belgium
>
> tel 0032.(0)9.264.59.71
> fax 0032.(0)9.264.62.19
> www.molecularbiotechnology.ugent.be

Winnok H. De Vos

Re: imageJ instability?

Thanks very much Dan! I'll verify this and figure out soon enough whether it
indeed depends on something similar.
regards,

winnok
______
ir. Winnok De Vos
Research Assistant

dep. Molecular Biotechnology
Faculty of Bioscience Engineering
Ghent University
Coupure links 653
9000 Ghent
Belgium

tel 0032.(0)9.264.59.71
fax 0032.(0)9.264.62.19
www.molecularbiotechnology.ugent.be
----- Original Message -----
From: "Dan Hsu" <[hidden email]>
To: <[hidden email]>
Sent: Monday, May 21, 2007 7:32 PM
Subject: Re: imageJ instability?

> Winnok
>
> You didn't mention which OS, so am assuming your are running Win XP
> (SP2?).
>
> I had experienced unmanageable instability, and after some analyses of
> types
> of files and functions being used on ImageJ, moving to other PCs, fresh
> installs of ImageJ & XP, etc. decided that this package was probably NOT
> at
> fault, but was showing some conflict with another program(s). This was
> ImageJ ~1.8m/n. After much online searching I found some discussion about
> program instability and downloaded ShellExView to view which extensions
> were
> open in the OS, and by trial-and-error deactivated Adobe Illustrator (v
> 10)
> icon handler and thumbnail, as well as Acrobat (v 6) extensions.
>
> Amazing how peaceful it now is!!! Try this program (freeware), if you are
> on
> XP, and best wishes to undisturbed analyses.
> www.nirsoft.net
> Dan
>
>
> on 5/21/07 8:21 AM, winnok ugent at [hidden email] wrote:
>
>> Dear Wayne,
>>
>> I'm using the most recent version (I think), ImageJ 1.38r on Java
>> 1.5.0_06
>> and use 750mb of 1gb available working memory.
>> I do work with the WCIF imageJ bundle but update the jar file regularly
>> from
>> your site. I had encountered this problem already with previous versions,
>> but it is getting more pronounced lately. So I don't think it is related
>> to
>> the version. I am also having a similar problem as Harry Parker, ie
>> crashing
>> while closing with multiple windows opened.
>> I will try debug mode. Is there something else I can try?
>> Many thanks in advance.
>> Kind regards,
>>
>> winnok
>>
>> ______
>> ir. Winnok De Vos
>> Research Assistant
>>
>> dep. Molecular Biotechnology
>> Faculty of Bioscience Engineering
>> Ghent University
>> Coupure links 653
>> 9000 Ghent
>> Belgium
>>
>> tel 0032.(0)9.264.59.71
>> fax 0032.(0)9.264.62.19
>> www.molecularbiotechnology.ugent.be
>

ctrueden

Re: imageJ instability?

In reply to this post by Harry Parker

Hi Harry & Winnok,

Winnok De Vos wrote:
> I will try debug mode. Is there something else I can try?

Harry Parker wrote:
> Its not consistent, so I think its some kind of thread deadlock related problem.

If you are feeling investigative, one thing you can do is obtain a
full stack trace. How to do so depends on your operating system. On
Windows (version bundled with JRE):

Click Start, All Programs, Accessories, Command Prompt. In the window, type:

C:\Documents and Settings\curtis>cd "C:\Program Files\ImageJ"
C:\Program Files\ImageJ>jre\bin\java -mx256m -jar ij.jar

Perform the operations that cause the deadlock (if it doesn't happen,
just close the program and try again). Then click the Command Prompt
window and press Ctrl+Pause (for Mac and Linux, the combo is Ctrl+\).
You should see a whole bunch of text, similar to:

Full thread dump Java HotSpot(TM) Client VM (1.5.0_09-b01 mixed mode):

"DestroyJavaVM" prio=6 tid=0x000354a0 nid=0xdf4 waiting on condition [0x00000000
..0x0007fae8]

"SocketListener" prio=6 tid=0x16e83980 nid=0x758 runnable [0x1715f000..0x1715fd6
8]
at java.net.PlainSocketImpl.socketAccept(Native Method)
...................

You can right-click, choose "Mark", select all the text, press enter,
then paste it into an email message. This information can be useful
for showing lines of code within ImageJ (if any) where the program is
stuck. It can also report certain kinds of deadlocks.

-Curtis

On 5/21/07, Harry Parker <[hidden email]> wrote:

> Hi all,
>
> On my Windows system, the only lockup issue I've seen is when closing ImageJ with 2 or more images open.
> This happens most often after I've used one of my custom filter plugins. What happens is the "Save changes to ...?" dialog comes up empty (buttons but no text in window). Then I must use the task manager to abort ImageJ. Its not consistent, so I think its some kind of thread deadlock related problem. It doesn't happen when I'm in Debug Mode. (The Heisenberg Uncertainty Principle applied to software?)
>
> --
> Harry Parker
> Senior Systems Engineer
> Digital Imaging Systems, Inc.
>
> ----- Original Message ----
> From: Winnok De Vos <[hidden email]>
> To: [hidden email]
> Sent: Friday, May 18, 2007 1:43:05 PM
> Subject: imageJ instability?
>
> Dear all,
>
> Lately I have been experiencing some stability problems with imageJ which seem
> to worsen. When I duplicate or crop a couple of images or run other commands
> that create a new window it quite often causes imageJ to crash, ie the window
> remains white and I have no other option but to close imageJ using a complete
> process closing. I have tried changing the memory settings but this has no
> influence whatsoever. I also tried reinstalling imageJ but this didn't prove
> succesfull either. Has anybody encountered such instability? How can I resolve
> this issue?
> Many thanks in advance.
> Kind regards,
> winnok
>
> --
> assistent prof. P. Van Oostveldt
> Dep. Moleculaire Biotechnologie
> Fac. Toegepaste Landbouwwetenschappen, Ugent
> Coupure links 653
> 9000 Gent
> tel. (0032) 09/264.59.71
>
>
>
>
>
>
> ____________________________________________________________________________________Get the free Yahoo! toolbar and rest assured with the added security of spyware protection.
> http://new.toolbar.yahoo.com/toolbar/features/norton/index.php
>

Winnok H. De Vos

Re: imageJ instability?

Hello Curtis,
I tried selectively disabling certain extensions with ShellExView but,
unfortunately, without eliminating of the problem.
I ran the command promt and followed Curtis' instructions. I ran "Duplicate"
till it blocked and got the following messages with one deadlock detected. I
also ran a custom macro till it blocked and got a different error. I included
both command promt prints.
Does the following make sense to you ?
Thanks in advance.
Regards,
winnok

1.When duplicating:

"
C:\Documents and Settings\winnok de vos>cd "C:\Program Files\ImageJ

C:\Program Files\ImageJ>jre\bin\java -mx256m -jar ij.jar
Full thread dump Java HotSpot(TM) Client VM (1.5.0_06-b05 mixed mode):

"SliceSelector" prio=4 tid=0x1728d2b0 nid=0x53c in Object.wait()
[0x1853f000..0x
1853fd68]
at java.lang.Object.wait(Native Method)
- waiting on <0x02b3ada8> (a ij.gui.StackWindow)
at java.lang.Object.wait(Unknown Source)
at ij.gui.StackWindow.run(StackWindow.java:94)
- locked <0x02b3ada8> (a ij.gui.StackWindow)
at java.lang.Thread.run(Unknown Source)

"Duplicate..." prio=4 tid=0x16eb98f8 nid=0x11c waiting for monitor
entry [0x183b
f000..0x183bf9e8]
at ij.WindowManager.removeWindow(WindowManager.java:252)
- waiting to lock <0x12fffdc0> (a java.lang.Class)
at ij.gui.ImageWindow.close(ImageWindow.java:311)
at ij.gui.StackWindow.close(StackWindow.java:67)
at ij.gui.ImageWindow.<init>(ImageWindow.java:102)
at ij.gui.StackWindow.<init>(StackWindow.java:20)
at OpenStackWindow.<init>(OpenStackWindow.java:28)
at OpenImage5DAdapter.makeOpenWindow(OpenImage5DAdapter.java:32)
at Sync_Windows.buildWindowList(Sync_Windows.java:698)
at Sync_Windows.updateWindowList(Sync_Windows.java:828)
at Sync_Windows.imageOpened(Sync_Windows.java:657)
at ij.ImagePlus.notifyListeners(ImagePlus.java:1581)
- locked <0x02b25e50> (a ij.ImagePlus)
at ij.ImagePlus.show(ImagePlus.java:361)
at ij.ImagePlus.show(ImagePlus.java:321)
at ij.plugin.filter.Duplicater.duplicate(Duplicater.java:48)
at ij.plugin.filter.Duplicater.run(Duplicater.java:19)
at ij.IJ.runFilterPlugIn(IJ.java:218)
at ij.IJ.runPlugIn(IJ.java:132)
at ij.Executer.runCommand(Executer.java:95)
at ij.Executer.run(Executer.java:49)
at java.lang.Thread.run(Unknown Source)

"SliceSelector" prio=4 tid=0x17249aa8 nid=0x2c4 in Object.wait()
[0x1849f000..0x
1849fa68]
at java.lang.Object.wait(Native Method)
- waiting on <0x049dd270> (a OpenStackWindow)
at java.lang.Object.wait(Unknown Source)
at ij.gui.StackWindow.run(StackWindow.java:94)
- locked <0x049dd270> (a OpenStackWindow)
at java.lang.Thread.run(Unknown Source)

"SliceSelector" prio=4 tid=0x17249920 nid=0xa8c in Object.wait()
[0x183ff000..0x
183ffbe8]
at java.lang.Object.wait(Native Method)
- waiting on <0x04910d00> (a OpenStackWindow)
at java.lang.Object.wait(Unknown Source)
at ij.gui.StackWindow.run(StackWindow.java:94)
- locked <0x04910d00> (a OpenStackWindow)
at java.lang.Thread.run(Unknown Source)

"SliceSelector" prio=4 tid=0x171efeb8 nid=0xde4 in Object.wait()
[0x1837f000..0x
1837fd68]
at java.lang.Object.wait(Native Method)
- waiting on <0x04757410> (a OpenStackWindow)
at java.lang.Object.wait(Unknown Source)
at ij.gui.StackWindow.run(StackWindow.java:94)
- locked <0x04757410> (a OpenStackWindow)
at java.lang.Thread.run(Unknown Source)

"ThresholdAdjuster" prio=4 tid=0x16f0c5a8 nid=0xac in Object.wait()
[0x1808f000.
.0x1808fa68]
at java.lang.Object.wait(Native Method)
- waiting on <0x04456550> (a ij.plugin.frame.ThresholdAdjuster)
at java.lang.Object.wait(Unknown Source)
at ij.plugin.frame.ThresholdAdjuster.run(ThresholdAdjuster.java:530)
- locked <0x04456550> (a ij.plugin.frame.ThresholdAdjuster)
at java.lang.Thread.run(Unknown Source)

"SliceSelector" prio=4 tid=0x1728f008 nid=0xb6c in Object.wait()
[0x17f0f000..0x
17f0fae8]
at java.lang.Object.wait(Native Method)
- waiting on <0x04456778> (a OpenStackWindow)
at java.lang.Object.wait(Unknown Source)
at ij.gui.StackWindow.run(StackWindow.java:94)
- locked <0x04456778> (a OpenStackWindow)
at java.lang.Thread.run(Unknown Source)

"SliceSelector" prio=4 tid=0x16dbca40 nid=0xbec in Object.wait()
[0x17fef000..0x
17fefb68]
at java.lang.Object.wait(Native Method)
- waiting on <0x04456970> (a OpenStackWindow)
at java.lang.Object.wait(Unknown Source)
at ij.gui.StackWindow.run(StackWindow.java:94)
- locked <0x04456970> (a OpenStackWindow)
at java.lang.Thread.run(Unknown Source)

"TimerQueue" daemon prio=6 tid=0x16edc2e0 nid=0xe2c in Object.wait()
[0x17ebf000
..0x17ebfa68]
at java.lang.Object.wait(Native Method)
- waiting on <0x0407eb98> (a javax.swing.TimerQueue)
at javax.swing.TimerQueue.run(Unknown Source)
- locked <0x0407eb98> (a javax.swing.TimerQueue)
at java.lang.Thread.run(Unknown Source)

"DestroyJavaVM" prio=6 tid=0x000360f0 nid=0xfd0 waiting on condition
[0x00000000
..0x0007fae8]

"SocketListener" prio=6 tid=0x16ef0df0 nid=0xdb8 runnable
[0x1761f000..0x1761fae
8]
at java.net.PlainSocketImpl.socketAccept(Native Method)
at java.net.PlainSocketImpl.accept(Unknown Source)
- locked <0x03fa3868> (a java.net.SocksSocketImpl)
at java.net.ServerSocket.implAccept(Unknown Source)
at java.net.ServerSocket.accept(Unknown Source)
at ij.SocketListener.run(SocketListener.java:31)
at java.lang.Thread.run(Unknown Source)

"AWT-EventQueue-0" prio=6 tid=0x16db4008 nid=0x850 waiting for monitor
entry [0x
170cf000..0x170cfc68]
at ij.ImagePlus.trimProcessor(ImagePlus.java:591)
- waiting to lock <0x02b25e50> (a ij.ImagePlus)
at ij.WindowManager.setCurrentWindow(WindowManager.java:37)
- locked <0x12fffdc0> (a java.lang.Class)
at ij.gui.ImageWindow.focusGained(ImageWindow.java:407)
at java.awt.Component.processFocusEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Window.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.KeyboardFocusManager.redispatchEvent(Unknown Source)
at
java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(Unknown Sour
ce)
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.SequencedEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)

at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)

"AWT-Windows" daemon prio=6 tid=0x16d6a198 nid=0xc84 runnable
[0x1702f000..0x170
2fce8]
at sun.awt.windows.WToolkit.eventLoop(Native Method)
at sun.awt.windows.WToolkit.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

"AWT-Shutdown" prio=6 tid=0x16d4e398 nid=0x678 in Object.wait()
[0x16fef000..0x1
6fefd68]
at java.lang.Object.wait(Native Method)
- waiting on <0x03eb01b0> (a java.lang.Object)
at java.lang.Object.wait(Unknown Source)
at sun.awt.AWTAutoShutdown.run(Unknown Source)
- locked <0x03eb01b0> (a java.lang.Object)
at java.lang.Thread.run(Unknown Source)

"Java2D Disposer" daemon prio=10 tid=0x16d81bf0 nid=0xdd8 in
Object.wait() [0x16
faf000..0x16faf9e8]
at java.lang.Object.wait(Native Method)
at java.lang.ref.ReferenceQueue.remove(Unknown Source)
- locked <0x03eb0238> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(Unknown Source)
at sun.java2d.Disposer.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

"Low Memory Detector" daemon prio=6 tid=0x00a91970 nid=0x9ec runnable
[0x0000000
0..0x00000000]

"CompilerThread0" daemon prio=10 tid=0x00a90540 nid=0xe8 waiting on
condition [0
x00000000..0x16c8f8cc]

"Signal Dispatcher" daemon prio=10 tid=0x00a8f8c0 nid=0xd38 waiting on
condition
[0x00000000..0x00000000]

"Finalizer" daemon prio=8 tid=0x00a869e0 nid=0xfe8 in Object.wait()
[0x16c0f000.
.0x16c0fc68]
at java.lang.Object.wait(Native Method)
at java.lang.ref.ReferenceQueue.remove(Unknown Source)
- locked <0x03e9b9e0> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(Unknown Source)
at java.lang.ref.Finalizer$FinalizerThread.run(Unknown Source)

"Reference Handler" daemon prio=10 tid=0x00a85548 nid=0xe68 in
Object.wait() [0x
16bcf000..0x16bcfce8]
at java.lang.Object.wait(Native Method)
- waiting on <0x03e9ba60> (a java.lang.ref.Reference$Lock)
at java.lang.Object.wait(Unknown Source)
at java.lang.ref.Reference$ReferenceHandler.run(Unknown Source)
- locked <0x03e9ba60> (a java.lang.ref.Reference$Lock)

"VM Thread" prio=10 tid=0x00a813a8 nid=0xabc runnable

"VM Periodic Task Thread" prio=10 tid=0x00a92b50 nid=0x8a4 waiting on
condition

Found one Java-level deadlock:
=============================
"Duplicate...":
waiting to lock monitor 0x00a86354 (object 0x12fffdc0, a java.lang.Class),
which is held by "AWT-EventQueue-0"
"AWT-EventQueue-0":
waiting to lock monitor 0x00a86374 (object 0x02b25e50, a ij.ImagePlus),
which is held by "Duplicate..."

Java stack information for the threads listed above:
===================================================
"Duplicate...":
at ij.WindowManager.removeWindow(WindowManager.java:252)
- waiting to lock <0x12fffdc0> (a java.lang.Class)
at ij.gui.ImageWindow.close(ImageWindow.java:311)
at ij.gui.StackWindow.close(StackWindow.java:67)
at ij.gui.ImageWindow.<init>(ImageWindow.java:102)
at ij.gui.StackWindow.<init>(StackWindow.java:20)
at OpenStackWindow.<init>(OpenStackWindow.java:28)
at OpenImage5DAdapter.makeOpenWindow(OpenImage5DAdapter.java:32)
at Sync_Windows.buildWindowList(Sync_Windows.java:698)
at Sync_Windows.updateWindowList(Sync_Windows.java:828)
at Sync_Windows.imageOpened(Sync_Windows.java:657)
at ij.ImagePlus.notifyListeners(ImagePlus.java:1581)
- locked <0x02b25e50> (a ij.ImagePlus)
at ij.ImagePlus.show(ImagePlus.java:361)
at ij.ImagePlus.show(ImagePlus.java:321)
at ij.plugin.filter.Duplicater.duplicate(Duplicater.java:48)
at ij.plugin.filter.Duplicater.run(Duplicater.java:19)
at ij.IJ.runFilterPlugIn(IJ.java:218)
at ij.IJ.runPlugIn(IJ.java:132)
at ij.Executer.runCommand(Executer.java:95)
at ij.Executer.run(Executer.java:49)
at java.lang.Thread.run(Unknown Source)
"AWT-EventQueue-0":
at ij.ImagePlus.trimProcessor(ImagePlus.java:591)
- waiting to lock <0x02b25e50> (a ij.ImagePlus)
at ij.WindowManager.setCurrentWindow(WindowManager.java:37)
- locked <0x12fffdc0> (a java.lang.Class)
at ij.gui.ImageWindow.focusGained(ImageWindow.java:407)
at java.awt.Component.processFocusEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Window.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.KeyboardFocusManager.redispatchEvent(Unknown Source)
at
java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(Unknown Sour
ce)
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.SequencedEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)

at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)

Found 1 deadlock.
"

2. When running the macro

"

C:\Documents and Settings\winnok de vos>cd "C:\Program Files\ImageJ

C:\Program Files\ImageJ>jre\bin\java -mx256m -jar ij.jar
Full thread dump Java HotSpot(TM) Client VM (1.5.0_06-b05 mixed mode):

"SliceSelector" prio=4 tid=0x1728d2b0 nid=0x53c in Object.wait()
[0x1853f000..0x
1853fd68]
at java.lang.Object.wait(Native Method)
- waiting on <0x02b3ada8> (a ij.gui.StackWindow)
at java.lang.Object.wait(Unknown Source)
at ij.gui.StackWindow.run(StackWindow.java:94)
- locked <0x02b3ada8> (a ij.gui.StackWindow)
at java.lang.Thread.run(Unknown Source)

"Duplicate..." prio=4 tid=0x16eb98f8 nid=0x11c waiting for monitor
entry [0x183b
f000..0x183bf9e8]
at ij.WindowManager.removeWindow(WindowManager.java:252)
- waiting to lock <0x12fffdc0> (a java.lang.Class)
at ij.gui.ImageWindow.close(ImageWindow.java:311)
at ij.gui.StackWindow.close(StackWindow.java:67)
at ij.gui.ImageWindow.<init>(ImageWindow.java:102)
at ij.gui.StackWindow.<init>(StackWindow.java:20)
at OpenStackWindow.<init>(OpenStackWindow.java:28)
at OpenImage5DAdapter.makeOpenWindow(OpenImage5DAdapter.java:32)
at Sync_Windows.buildWindowList(Sync_Windows.java:698)
at Sync_Windows.updateWindowList(Sync_Windows.java:828)
at Sync_Windows.imageOpened(Sync_Windows.java:657)
at ij.ImagePlus.notifyListeners(ImagePlus.java:1581)
- locked <0x02b25e50> (a ij.ImagePlus)
at ij.ImagePlus.show(ImagePlus.java:361)
at ij.ImagePlus.show(ImagePlus.java:321)
at ij.plugin.filter.Duplicater.duplicate(Duplicater.java:48)
at ij.plugin.filter.Duplicater.run(Duplicater.java:19)
at ij.IJ.runFilterPlugIn(IJ.java:218)
at ij.IJ.runPlugIn(IJ.java:132)
at ij.Executer.runCommand(Executer.java:95)
at ij.Executer.run(Executer.java:49)
at java.lang.Thread.run(Unknown Source)

"SliceSelector" prio=4 tid=0x17249aa8 nid=0x2c4 in Object.wait()
[0x1849f000..0x
1849fa68]
at java.lang.Object.wait(Native Method)
- waiting on <0x049dd270> (a OpenStackWindow)
at java.lang.Object.wait(Unknown Source)
at ij.gui.StackWindow.run(StackWindow.java:94)
- locked <0x049dd270> (a OpenStackWindow)
at java.lang.Thread.run(Unknown Source)

"SliceSelector" prio=4 tid=0x17249920 nid=0xa8c in Object.wait()
[0x183ff000..0x
183ffbe8]
at java.lang.Object.wait(Native Method)
- waiting on <0x04910d00> (a OpenStackWindow)
at java.lang.Object.wait(Unknown Source)
at ij.gui.StackWindow.run(StackWindow.java:94)
- locked <0x04910d00> (a OpenStackWindow)
at java.lang.Thread.run(Unknown Source)

"SliceSelector" prio=4 tid=0x171efeb8 nid=0xde4 in Object.wait()
[0x1837f000..0x
1837fd68]
at java.lang.Object.wait(Native Method)
- waiting on <0x04757410> (a OpenStackWindow)
at java.lang.Object.wait(Unknown Source)
at ij.gui.StackWindow.run(StackWindow.java:94)
- locked <0x04757410> (a OpenStackWindow)
at java.lang.Thread.run(Unknown Source)

"ThresholdAdjuster" prio=4 tid=0x16f0c5a8 nid=0xac in Object.wait()
[0x1808f000.
.0x1808fa68]
at java.lang.Object.wait(Native Method)
- waiting on <0x04456550> (a ij.plugin.frame.ThresholdAdjuster)
at java.lang.Object.wait(Unknown Source)
at ij.plugin.frame.ThresholdAdjuster.run(ThresholdAdjuster.java:530)
- locked <0x04456550> (a ij.plugin.frame.ThresholdAdjuster)
at java.lang.Thread.run(Unknown Source)

"SliceSelector" prio=4 tid=0x1728f008 nid=0xb6c in Object.wait()
[0x17f0f000..0x
17f0fae8]
at java.lang.Object.wait(Native Method)
- waiting on <0x04456778> (a OpenStackWindow)
at java.lang.Object.wait(Unknown Source)
at ij.gui.StackWindow.run(StackWindow.java:94)
- locked <0x04456778> (a OpenStackWindow)
at java.lang.Thread.run(Unknown Source)

"SliceSelector" prio=4 tid=0x16dbca40 nid=0xbec in Object.wait()
[0x17fef000..0x
17fefb68]
at java.lang.Object.wait(Native Method)
- waiting on <0x04456970> (a OpenStackWindow)
at java.lang.Object.wait(Unknown Source)
at ij.gui.StackWindow.run(StackWindow.java:94)
- locked <0x04456970> (a OpenStackWindow)
at java.lang.Thread.run(Unknown Source)

"TimerQueue" daemon prio=6 tid=0x16edc2e0 nid=0xe2c in Object.wait()
[0x17ebf000
..0x17ebfa68]
at java.lang.Object.wait(Native Method)
- waiting on <0x0407eb98> (a javax.swing.TimerQueue)
at javax.swing.TimerQueue.run(Unknown Source)
- locked <0x0407eb98> (a javax.swing.TimerQueue)
at java.lang.Thread.run(Unknown Source)

"DestroyJavaVM" prio=6 tid=0x000360f0 nid=0xfd0 waiting on condition
[0x00000000
..0x0007fae8]

"SocketListener" prio=6 tid=0x16ef0df0 nid=0xdb8 runnable
[0x1761f000..0x1761fae
8]
at java.net.PlainSocketImpl.socketAccept(Native Method)
at java.net.PlainSocketImpl.accept(Unknown Source)
- locked <0x03fa3868> (a java.net.SocksSocketImpl)
at java.net.ServerSocket.implAccept(Unknown Source)
at java.net.ServerSocket.accept(Unknown Source)
at ij.SocketListener.run(SocketListener.java:31)
at java.lang.Thread.run(Unknown Source)

"AWT-EventQueue-0" prio=6 tid=0x16db4008 nid=0x850 waiting for monitor
entry [0x
170cf000..0x170cfc68]
at ij.ImagePlus.trimProcessor(ImagePlus.java:591)
- waiting to lock <0x02b25e50> (a ij.ImagePlus)
at ij.WindowManager.setCurrentWindow(WindowManager.java:37)
- locked <0x12fffdc0> (a java.lang.Class)
at ij.gui.ImageWindow.focusGained(ImageWindow.java:407)
at java.awt.Component.processFocusEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Window.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.KeyboardFocusManager.redispatchEvent(Unknown Source)
at
java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(Unknown Sour
ce)
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.SequencedEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)

at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)

"AWT-Windows" daemon prio=6 tid=0x16d6a198 nid=0xc84 runnable
[0x1702f000..0x170
2fce8]
at sun.awt.windows.WToolkit.eventLoop(Native Method)
at sun.awt.windows.WToolkit.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

"AWT-Shutdown" prio=6 tid=0x16d4e398 nid=0x678 in Object.wait()
[0x16fef000..0x1
6fefd68]
at java.lang.Object.wait(Native Method)
- waiting on <0x03eb01b0> (a java.lang.Object)
at java.lang.Object.wait(Unknown Source)
at sun.awt.AWTAutoShutdown.run(Unknown Source)
- locked <0x03eb01b0> (a java.lang.Object)
at java.lang.Thread.run(Unknown Source)

"Java2D Disposer" daemon prio=10 tid=0x16d81bf0 nid=0xdd8 in
Object.wait() [0x16
faf000..0x16faf9e8]
at java.lang.Object.wait(Native Method)
at java.lang.ref.ReferenceQueue.remove(Unknown Source)
- locked <0x03eb0238> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(Unknown Source)
at sun.java2d.Disposer.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

"Low Memory Detector" daemon prio=6 tid=0x00a91970 nid=0x9ec runnable
[0x0000000
0..0x00000000]

"CompilerThread0" daemon prio=10 tid=0x00a90540 nid=0xe8 waiting on
condition [0
x00000000..0x16c8f8cc]

"Signal Dispatcher" daemon prio=10 tid=0x00a8f8c0 nid=0xd38 waiting on
condition
[0x00000000..0x00000000]

"Finalizer" daemon prio=8 tid=0x00a869e0 nid=0xfe8 in Object.wait()
[0x16c0f000.
.0x16c0fc68]
at java.lang.Object.wait(Native Method)
at java.lang.ref.ReferenceQueue.remove(Unknown Source)
- locked <0x03e9b9e0> (a java.lang.ref.ReferenceQueue$Lock)
at java.lang.ref.ReferenceQueue.remove(Unknown Source)
at java.lang.ref.Finalizer$FinalizerThread.run(Unknown Source)

"Reference Handler" daemon prio=10 tid=0x00a85548 nid=0xe68 in
Object.wait() [0x
16bcf000..0x16bcfce8]
at java.lang.Object.wait(Native Method)
- waiting on <0x03e9ba60> (a java.lang.ref.Reference$Lock)
at java.lang.Object.wait(Unknown Source)
at java.lang.ref.Reference$ReferenceHandler.run(Unknown Source)
- locked <0x03e9ba60> (a java.lang.ref.Reference$Lock)

"VM Thread" prio=10 tid=0x00a813a8 nid=0xabc runnable

"VM Periodic Task Thread" prio=10 tid=0x00a92b50 nid=0x8a4 waiting on
condition

Found one Java-level deadlock:
=============================
"Duplicate...":
waiting to lock monitor 0x00a86354 (object 0x12fffdc0, a java.lang.Class),
which is held by "AWT-EventQueue-0"
"AWT-EventQueue-0":
waiting to lock monitor 0x00a86374 (object 0x02b25e50, a ij.ImagePlus),
which is held by "Duplicate..."

Java stack information for the threads listed above:
===================================================
"Duplicate...":
at ij.WindowManager.removeWindow(WindowManager.java:252)
- waiting to lock <0x12fffdc0> (a java.lang.Class)
at ij.gui.ImageWindow.close(ImageWindow.java:311)
at ij.gui.StackWindow.close(StackWindow.java:67)
at ij.gui.ImageWindow.<init>(ImageWindow.java:102)
at ij.gui.StackWindow.<init>(StackWindow.java:20)
at OpenStackWindow.<init>(OpenStackWindow.java:28)
at OpenImage5DAdapter.makeOpenWindow(OpenImage5DAdapter.java:32)
at Sync_Windows.buildWindowList(Sync_Windows.java:698)
at Sync_Windows.updateWindowList(Sync_Windows.java:828)
at Sync_Windows.imageOpened(Sync_Windows.java:657)
at ij.ImagePlus.notifyListeners(ImagePlus.java:1581)
- locked <0x02b25e50> (a ij.ImagePlus)
at ij.ImagePlus.show(ImagePlus.java:361)
at ij.ImagePlus.show(ImagePlus.java:321)
at ij.plugin.filter.Duplicater.duplicate(Duplicater.java:48)
at ij.plugin.filter.Duplicater.run(Duplicater.java:19)
at ij.IJ.runFilterPlugIn(IJ.java:218)
at ij.IJ.runPlugIn(IJ.java:132)
at ij.Executer.runCommand(Executer.java:95)
at ij.Executer.run(Executer.java:49)
at java.lang.Thread.run(Unknown Source)
"AWT-EventQueue-0":
at ij.ImagePlus.trimProcessor(ImagePlus.java:591)
- waiting to lock <0x02b25e50> (a ij.ImagePlus)
at ij.WindowManager.setCurrentWindow(WindowManager.java:37)
- locked <0x12fffdc0> (a java.lang.Class)
at ij.gui.ImageWindow.focusGained(ImageWindow.java:407)
at java.awt.Component.processFocusEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Window.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.KeyboardFocusManager.redispatchEvent(Unknown Source)
at
java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(Unknown Sour
ce)
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.SequencedEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at
java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown Source)

at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)

Found 1 deadlock.

Quoting Curtis Rueden <[hidden email]>:

> Hi Harry & Winnok,
>
> Winnok De Vos wrote:
>> I will try debug mode. Is there something else I can try?
>
> Harry Parker wrote:
>> Its not consistent, so I think its some kind of thread deadlock
>> related problem.
>
> If you are feeling investigative, one thing you can do is obtain a
> full stack trace. How to do so depends on your operating system. On
> Windows (version bundled with JRE):
>
> Click Start, All Programs, Accessories, Command Prompt. In the window, type:
>
> C:\Documents and Settings\curtis>cd "C:\Program Files\ImageJ"
> C:\Program Files\ImageJ>jre\bin\java -mx256m -jar ij.jar
>
> Perform the operations that cause the deadlock (if it doesn't happen,
> just close the program and try again). Then click the Command Prompt
> window and press Ctrl+Pause (for Mac and Linux, the combo is Ctrl+\).
> You should see a whole bunch of text, similar to:
>
> Full thread dump Java HotSpot(TM) Client VM (1.5.0_09-b01 mixed mode):
>
> "DestroyJavaVM" prio=6 tid=0x000354a0 nid=0xdf4 waiting on condition
> [0x00000000
> ..0x0007fae8]
>
> "SocketListener" prio=6 tid=0x16e83980 nid=0x758 runnable
> [0x1715f000..0x1715fd6
> 8]
> at java.net.PlainSocketImpl.socketAccept(Native Method)
> ...................
>
> You can right-click, choose "Mark", select all the text, press enter,
> then paste it into an email message. This information can be useful
> for showing lines of code within ImageJ (if any) where the program is
> stuck. It can also report certain kinds of deadlocks.
>
> -Curtis
>
> On 5/21/07, Harry Parker <[hidden email]> wrote:
>> Hi all,
>>
>> On my Windows system, the only lockup issue I've seen is when
>> closing ImageJ with 2 or more images open.
>> This happens most often after I've used one of my custom filter
>> plugins. What happens is the "Save changes to ...?" dialog comes up
>> empty (buttons but no text in window). Then I must use the task
>> manager to abort ImageJ. Its not consistent, so I think its some
>> kind of thread deadlock related problem. It doesn't happen when I'm
>> in Debug Mode. (The Heisenberg Uncertainty Principle applied to
>> software?)
>>
>> --
>> Harry Parker
>> Senior Systems Engineer
>> Digital Imaging Systems, Inc.
>>
>> ----- Original Message ----
>> From: Winnok De Vos <[hidden email]>
>> To: [hidden email]
>> Sent: Friday, May 18, 2007 1:43:05 PM
>> Subject: imageJ instability?
>>
>> Dear all,
>>
>> Lately I have been experiencing some stability problems with imageJ
>> which seem
>> to worsen. When I duplicate or crop a couple of images or run other commands
>> that create a new window it quite often causes imageJ to crash, ie
>> the window
>> remains white and I have no other option but to close imageJ using a
>> complete
>> process closing. I have tried changing the memory settings but this has no
>> influence whatsoever. I also tried reinstalling imageJ but this didn't prove
>> succesfull either. Has anybody encountered such instability? How can
>> I resolve
>> this issue?
>> Many thanks in advance.
>> Kind regards,
>> winnok
>>
>> --
>> assistent prof. P. Van Oostveldt
>> Dep. Moleculaire Biotechnologie
>> Fac. Toegepaste Landbouwwetenschappen, Ugent
>> Coupure links 653
>> 9000 Gent
>> tel. (0032) 09/264.59.71
>>
>>
>>
>>
>>
>>
>> ____________________________________________________________________________________Get the free Yahoo! toolbar and rest assured with the added security of spyware
>> protection.
>> http://new.toolbar.yahoo.com/toolbar/features/norton/index.php
>>
>

--
assistent prof. P. Van Oostveldt
Dep. Moleculaire Biotechnologie
Fac. Toegepaste Landbouwwetenschappen, Ugent
Coupure links 653
9000 Gent
tel. (0032) 09/264.59.71

Wayne Rasband

Re: imageJ instability?

In reply to this post by Winnok H. De Vos

ImageJ 1.38s, now available at <http://rsb.info.nih.gov/ij/notes.html>,
fixes bugs that could cause ImageJ to hang when using plugins that
implement the ImageListener interface (e.g., Sync Windows), or when
quitting ImageJ with open unsaved images.

-wayne

On May 18, 2007, at 1:43 PM, Winnok De Vos wrote:

> Dear all,
>
> Lately I have been experiencing some stability problems with imageJ
> which seem
> to worsen. When I duplicate or crop a couple of images or run other
> commands
> that create a new window it quite often causes imageJ to crash, ie the
> window
> remains white and I have no other option but to close imageJ using a
> complete
> process closing. I have tried changing the memory settings but this
> has no
> influence whatsoever. I also tried reinstalling imageJ but this didn't
> prove
> succesfull either. Has anybody encountered such instability? How can I
> resolve
> this issue?
> Many thanks in advance.
> Kind regards,
> winnok
>
> --
> assistent prof. P. Van Oostveldt
> Dep. Moleculaire Biotechnologie
> Fac. Toegepaste Landbouwwetenschappen, Ugent
> Coupure links 653
> 9000 Gent
> tel. (0032) 09/264.59.71
>

Harry Parker

Re: imageJ instability?

In reply to this post by Winnok H. De Vos

Thanks, Curtis, for the debugging technique.
I've attached the stack trace created just as you described, except I used an external Java, 1.6.
Hope this helps.

--
Harry Parker
Senior Systems Engineer
Digital Imaging Systems, Inc.

----- Original Message ----
From: Curtis Rueden <[hidden email]>
To: [hidden email]
Sent: Monday, May 21, 2007 2:28:23 PM
Subject: Re: imageJ instability?

Hi Harry & Winnok,

Winnok De Vos wrote:
> I will try debug mode. Is there something else I can try?

Harry Parker wrote:
> Its not consistent, so I think its some kind of thread deadlock related problem.

If you are feeling investigative, one thing you can do is obtain a
full stack trace. How to do so depends on your operating system. On
Windows (version bundled with JRE):

Click Start, All Programs, Accessories, Command Prompt. In the window, type:

C:\Documents and Settings\curtis>cd "C:\Program Files\ImageJ"
C:\Program Files\ImageJ>jre\bin\java -mx256m -jar ij.jar

Perform the operations that cause the deadlock (if it doesn't happen,
just close the program and try again). Then click the Command Prompt
window and press Ctrl+Pause (for Mac and Linux, the combo is Ctrl+\).
You should see a whole bunch of text, similar to:

Full thread dump Java HotSpot(TM) Client VM (1.5.0_09-b01 mixed mode):

"DestroyJavaVM" prio=6 tid=0x000354a0 nid=0xdf4 waiting on condition [0x00000000
..0x0007fae8]

"SocketListener" prio=6 tid=0x16e83980 nid=0x758 runnable [0x1715f000..0x1715fd6
8]
at java.net.PlainSocketImpl.socketAccept(Native Method)
...................

You can right-click, choose "Mark", select all the text, press enter,
then paste it into an email message. This information can be useful
for showing lines of code within ImageJ (if any) where the program is
stuck. It can also report certain kinds of deadlocks.

-Curtis

On 5/21/07, Harry Parker <[hidden email]> wrote:

____________________________________________________________________________________Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos & more.
http://mobile.yahoo.com/go?refer=1GNXIC

=?utf-8?q?HParker=5FImageJ=5Flockup=5Fstacktrace.txt?= (9K) Download Attachment

Harry Parker

Re: imageJ instability?

In reply to this post by Winnok H. De Vos

Hi Wayne,

I just tried your latest, 1.38t, for a few times and could not get it to hang.

So based on that quick test, I think its fixed.

Thanks.

--
Harry Parker
Senior Systems Engineer
Digital Imaging Systems, Inc.

----- Original Message ----
From: Wayne Rasband <[hidden email]>
To: Harry Parker <[hidden email]>
Sent: Friday, May 25, 2007 4:13:00 PM
Subject: Re: imageJ instability?

Dear Harry,

Are you using ImageJ 1.38s or later? It has fixes that prevent some
ImageJ lockups.

Thanks,

-wayne

On May 25, 2007, at 3:41 PM, Harry Parker wrote:

> Thanks, Curtis, for the debugging technique.
> I've attached the stack trace created just as you described, except I
> used an external Java, 1.6.
> Hope this helps.
>
> --
> Harry Parker
> Senior Systems Engineer
> Digital Imaging Systems, Inc.
>
> ----- Original Message ----
> From: Curtis Rueden <[hidden email]>
> To: [hidden email]
> Sent: Monday, May 21, 2007 2:28:23 PM
> Subject: Re: imageJ instability?
>
> Hi Harry & Winnok,
>
> Winnok De Vos wrote:
>> I will try debug mode. Is there something else I can try?
>
> Harry Parker wrote:
>> Its not consistent, so I think its some kind of thread deadlock
>> related problem.
>
> If you are feeling investigative, one thing you can do is obtain a
> full stack trace. How to do so depends on your operating system. On
> Windows (version bundled with JRE):
>
> Click Start, All Programs, Accessories, Command Prompt. In the window,
> type:
>
> C:\Documents and Settings\curtis>cd "C:\Program Files\ImageJ"
> C:\Program Files\ImageJ>jre\bin\java -mx256m -jar ij.jar
>
> Perform the operations that cause the deadlock (if it doesn't happen,
> just close the program and try again). Then click the Command Prompt
> window and press Ctrl+Pause (for Mac and Linux, the combo is Ctrl+\).
> You should see a whole bunch of text, similar to:
>
> Full thread dump Java HotSpot(TM) Client VM (1.5.0_09-b01 mixed mode):
>
> "DestroyJavaVM" prio=6 tid=0x000354a0 nid=0xdf4 waiting on condition
> [0x00000000
> ..0x0007fae8]
>
> "SocketListener" prio=6 tid=0x16e83980 nid=0x758 runnable
> [0x1715f000..0x1715fd6
> 8]
> at java.net.PlainSocketImpl.socketAccept(Native Method)
> ...................
>
> You can right-click, choose "Mark", select all the text, press enter,
> then paste it into an email message. This information can be useful
> for showing lines of code within ImageJ (if any) where the program is
> stuck. It can also report certain kinds of deadlocks.
>
> -Curtis
>
> On 5/21/07, Harry Parker <[hidden email]> wrote:
>> Hi all,
>>
>> On my Windows system, the only lockup issue I've seen is when closing
>> ImageJ with 2 or more images open.
>> This happens most often after I've used one of my custom filter
>> plugins. What happens is the "Save changes to ...?" dialog comes up
>> empty (buttons but no text in window). Then I must use the task
>> manager to abort ImageJ. Its not consistent, so I think its some kind
>> of thread deadlock related problem. It doesn't happen when I'm in
>> Debug Mode. (The Heisenberg Uncertainty Principle applied to
>> software?)
>>
>> --
>> Harry Parker
>> Senior Systems Engineer
>> Digital Imaging Systems, Inc.
>>
>> ----- Original Message ----
>> From: Winnok De Vos <[hidden email]>
>> To: [hidden email]
>> Sent: Friday, May 18, 2007 1:43:05 PM
>> Subject: imageJ instability?
>>
>> Dear all,
>>
>> Lately I have been experiencing some stability problems with imageJ
>> which seem
>> to worsen. When I duplicate or crop a couple of images or run other
>> commands
>> that create a new window it quite often causes imageJ to crash, ie
>> the window
>> remains white and I have no other option but to close imageJ using a
>> complete
>> process closing. I have tried changing the memory settings but this
>> has no
>> influence whatsoever. I also tried reinstalling imageJ but this
>> didn't prove
>> succesfull either. Has anybody encountered such instability? How can
>> I resolve
>> this issue?
>> Many thanks in advance.
>> Kind regards,
>> winnok
>>
>> --
>> assistent prof. P. Van Oostveldt
>> Dep. Moleculaire Biotechnologie
>> Fac. Toegepaste Landbouwwetenschappen, Ugent
>> Coupure links 653
>> 9000 Gent
>> tel. (0032) 09/264.59.71
>>
>>
>>
>>
>>
>>
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