Re: ImageJ hangs

[Vladimir Hegyi]

Hi all,
in the last weeks I noticed that my (until now perfectly running) ImageJ
hangs when I want to close more then 3-4 windows with images (one by one).
There is all the time the message "cancel" "save as" "OK" but the Java is
not responding. This behaviour is on my 2 computers, Java is 1.5.0_06 or
1.5.0_03 respectively.
Did somebody noticed similar behaviour?
Any suggestion will be apreciated.
Vlado

Assoc.Prof.Vladimir Hegyi,MD,PhD.
Dept. of Pediatric Dermatovenerology
School of Medicine
Comenius University
Limbova 1
833 40 Bratislava
Slovak Republic
e-mail: [hidden email]
www.dermatology.sk

[Wayne Rasband]

> in the last weeks I noticed that my (until now perfectly
> running) ImageJ hangs when I want to close more then 3-4
> windows with images (one by one). There is all the time the
> message "cancel" "save as" "OK" but the Java is not
> responding. This behaviour is on my 2 computers, Java is
> 1.5.0_06 or 1.5.0_03 respectively.

This sounds like a thread deadlock. It would help if you could generate
a thread dump and send it to me ([hidden email]).

The method used to generate a thread dump differs depending on the
platform:

Windows:
     Press Ctrl-Break in the command console. This requires that
     you either start ImageJ from the command line or edit the
     second line of ImageJ.cfg and change "javaw.exe" to "java.exe".

Mac OS X:
     Open a Terminal window and find the process id of the Java
     VM running ImageJ by entering "ps -ax". Then generate a
     thread dump by sending the QUIT signal to this process by
     entering "kill -QUIT process_id". The output will be sent to
     the /Applications/Utilities/Console window.

Linux (or MAC OS X):
     Press Ctrl-\ in the terminal window you used to start ImageJ.

-wayne

[vytas-2]

This may the same thing or related. For the last few IJ versions, trying to
quit ImageJ with several image windows open will commonly cause the
software to hang, requiring cntl-alt-del to kill javaw.exe. Typically the
"save changes to image" dialog becomes unresponsive (save, don't save,
cancel buttons do nillo) and program is locked (dialog box can be moved,
however). I have had several other users report the same thing. Unmodified
images do close correctly, perhaps it's a case where multiple mods must be
reconciled...
(latest case is IJ1.35p using java1.3.1 in XP) Using java1.5.0 a quit did
clear/close after 20 images with 2 mods, but hung if there were 20 images
with 4mods.

At 04:13 PM 2/14/2006, you wrote:

>>in the last weeks I noticed that my (until now perfectly
>>running) ImageJ hangs when I want to close more then 3-4
>>windows with images (one by one). There is all the time the
>>message "cancel" "save as" "OK" but the Java is not
>>responding. This behaviour is on my 2 computers, Java is
>>1.5.0_06 or 1.5.0_03 respectively.
>
>This sounds like a thread deadlock. It would help if you could generate a
>thread dump and send it to me ([hidden email]).
>
>The method used to generate a thread dump differs depending on the platform:
>
>Windows:
>     Press Ctrl-Break in the command console. This requires that
>     you either start ImageJ from the command line or edit the
>     second line of ImageJ.cfg and change "javaw.exe" to "java.exe".
>
>Mac OS X:
>     Open a Terminal window and find the process id of the Java
>     VM running ImageJ by entering "ps -ax". Then generate a
>     thread dump by sending the QUIT signal to this process by
>     entering "kill -QUIT process_id". The output will be sent to
>     the /Applications/Utilities/Console window.
>
>Linux (or MAC OS X):
>     Press Ctrl-\ in the terminal window you used to start ImageJ.
>
>-wayne
>
>

Vytas Bindokas, Ph.D.
Research Assoc. / Assoc. Prof.,
Director, BSD Light Microscopy Core Facility
Dept Neurobiol Pharmacol Physiol MC0926
947 E 58th Street
The University of Chicago
Chicago IL 60637
Room 1007 (CLSC)

773-702-4875

email [hidden email]
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[Gabriel Landini]

> This sounds like a thread deadlock.

I may be very wrong, but I have the feeling that when I tried to close IJ with
many images that have been edited, sometimes I have ended up trying to click
the wrong dialog (and so it seemed to be not responding).
Could this be the same thing?

Cheers,

Gabriel

[Wayne Rasband]

 > This may the same thing or related. For the last few IJ
 > versions, trying to quit ImageJ with several image windows
 > open will commonly cause the software to hang, requiring
 > cntl-alt-del to kill javaw.exe. Typically the "save changes
 > to image" dialog becomes unresponsive (save, don't save,
 > cancel buttons do nillo) and program is locked (dialog box
 > can be moved, however).

ImageJ 1.35q closes images when quitting on a separate thread instead
of on the event dispatch thread. This should help prevent thread
deadlocks ("hangs") when quitting with images open.

-wayne

[MESSAOUDI Cédric]

Hi,


I have a problem with ImageJ when saving very large stack (1024*1024*700 32
bits real).

When I save these images in ImageJ with the command "File>save as" there is
no problem.
When I save in one of my plugins using a FileSaver and the function
saveAsTiffStack(path) there is a problem. I can't open the file after
because of "negative seek offset"

When looking inside TiffEncoder it seems that the stackSize
(1024*1024*700*4) is bigger than the maximum value of an int and then
"loops" to negative value.

Is there a possibility to correct this problem in TiffEncoder?
Which function is called when saving with the menu in ImageJ?

Thanks
Cédric

[Wayne Rasband]

ImageJ 1.35r, due next week, will be able to save stacks larger than
2GB in TIFF format. It will also save stacks larger than 4GB but only
ImageJ will be able to open them since the TIFF standard does not
support files greater than 4GB.

-wayne

> I have a problem with ImageJ when saving very large stack
> (1024*1024*700 32 bits real).
>
> When I save these images in ImageJ with the command
> "File>save as" there is no problem. When I save in one of my
> plugins using a FileSaver and the function
> saveAsTiffStack(path) there is a problem. I can't open the
> file after because of "negative seek offset"
>
> When looking inside TiffEncoder it seems that the stackSize
> (1024*1024*700*4) is bigger than the maximum value of an int
> and then "loops" to negative value.
>
> Is there a possibility to correct this problem in
> TiffEncoder? Which function is called when saving with the
> menu in ImageJ?
>
> Thanks Cédric
>