Unable to exit ImageJ

[Sven Boekhoff]

Hi.
I'm using ImageJ 1.45f on Ubuntu Linux 11.04.

When I:
1) open the "About ImageJ"-window,
2) draw a filled rectangle on it,
3) try to close the "About ImageJ"-window,
4) answer the question "Save changes to 'About ImageJ'" with "yes", "no"
or "Cancel",

the window does not close and I can't exit ImageJ anymore.

WHY?


I tested two java Versions that installed on my computer, by switching
between them with: "sudo update-alternatives --config java".

java version "1.6.0_22"
OpenJDK Runtime Environment (IcedTea6 1.10.1) (6b22-1.10.1-0ubuntu1)
OpenJDK 64-Bit Server VM (build 20.0-b11, mixed mode)

and

java version "1.6.0_24"
Java(TM) SE Runtime Environment (build 1.6.0_24-b07)
Java HotSpot(TM) 64-Bit Server VM (build 19.1-b02, mixed mode)


Does anyone have a solution?

Sven

[Gabriel Landini]

On Sunday 01 May 2011, Sven Boekhoff wrote:
> the window does not close and I can't exit ImageJ anymore.

I can run ImageJ and Fiji in kubuntu 11.04 without problems so far.

If you have the Desktop Effects enabled, try disabling them to see if that is
the reason.

Cheers

Gabriel

[Gluender-4]

Good day Sven,

thanks for reporting this important issue!
:-)

No problem here with MacOS.

>Hi.
>I'm using ImageJ 1.45f on Ubuntu Linux 11.04.
>
>When I:
>1) open the "About ImageJ"-window,
>2) draw a filled rectangle on it,
>3) try to close the "About ImageJ"-window,
>4) answer the question "Save changes to 'About ImageJ'" with "yes",
>"no" or "Cancel",
>
>the window does not close and I can't exit ImageJ anymore.

Interesting.

>WHY?

Labor day effect?

>I tested two java Versions that installed on my computer, by
>switching between them with: "sudo update-alternatives --config
>java".
>
>java version "1.6.0_22"
>OpenJDK Runtime Environment (IcedTea6 1.10.1) (6b22-1.10.1-0ubuntu1)
>OpenJDK 64-Bit Server VM (build 20.0-b11, mixed mode)
>
>and
>
>java version "1.6.0_24"
>Java(TM) SE Runtime Environment (build 1.6.0_24-b07)
>Java HotSpot(TM) 64-Bit Server VM (build 19.1-b02, mixed mode)
>
>Does anyone have a solution?

I guess you need to modify the About window quite often, hence it is
an important issue, right?

Sorry, no idea for a solution.

>Sven

Regards

Herbie

[Carnë Draug]

On 1 May 2011 17:22, Sven Boekhoff <[hidden email]> wrote:

> Hi.
> I'm using ImageJ 1.45f on Ubuntu Linux 11.04.
>
> When I:
> 1) open the "About ImageJ"-window,
> 2) draw a filled rectangle on it,
> 3) try to close the "About ImageJ"-window,
> 4) answer the question "Save changes to 'About ImageJ'" with "yes", "no" or
> "Cancel",
>
> the window does not close and I can't exit ImageJ anymore.

This seems very similar to the bugs. But they were supposedly fixed.

Debian Bug report #600997 imagej: cannot quit imagej when an image was changed
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=600997

Debian Bug report #592381 imagej: refuses to close unless everything
is saved before
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=592381

Bug #661545 on imagej - imagej refuses to quit
https://bugs.launchpad.net/ubuntu/+source/imagej/+bug/661545


On 1 May 2011 17:59, Gabriel Landini <[hidden email]> wrote:
> On Sunday 01 May 2011, Sven Boekhoff wrote:
>> the window does not close and I can't exit ImageJ anymore.
>
> I can run ImageJ and Fiji in kubuntu 11.04 without problems so far.

Did you install ImageJ from the Ubuntu repositories or from the ImageJ website?

Carnë Draug

[Sven Boekhoff]

Hi Carnë.

Now I'm again using the version from the Ubuntu repository (imagej
(1.44i-1) unstable; urgency=low). Before, I was using a manually updated
version.

It seems that in the 1.44 version the problem was solved. The Ubuntu
changelog for the package ImageJ says:
   * New upstream release (Closes: #601020).
     - Solves a bug that prevented to quit (Closes: #600997, LP: 661545).
But when I download an new jar file via the update plugin, it does not
work afterwards. Would be nice if the bug will be also fixed in the
newer versions.

Sven


On 01.05.2011 19:40, Carnë Draug wrote:

> On 1 May 2011 17:22, Sven Boekhoff<[hidden email]>  wrote:
>> Hi.
>> I'm using ImageJ 1.45f on Ubuntu Linux 11.04.
>>
>> When I:
>> 1) open the "About ImageJ"-window,
>> 2) draw a filled rectangle on it,
>> 3) try to close the "About ImageJ"-window,
>> 4) answer the question "Save changes to 'About ImageJ'" with "yes", "no" or
>> "Cancel",
>>
>> the window does not close and I can't exit ImageJ anymore.
>
> This seems very similar to the bugs. But they were supposedly fixed.
>
> Debian Bug report #600997 imagej: cannot quit imagej when an image was changed
> http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=600997
>
> Debian Bug report #592381 imagej: refuses to close unless everything
> is saved before
> http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=592381
>
> Bug #661545 on imagej - imagej refuses to quit
> https://bugs.launchpad.net/ubuntu/+source/imagej/+bug/661545
>
>
> On 1 May 2011 17:59, Gabriel Landini<[hidden email]>  wrote:
>> On Sunday 01 May 2011, Sven Boekhoff wrote:
>>> the window does not close and I can't exit ImageJ anymore.
>>
>> I can run ImageJ and Fiji in kubuntu 11.04 without problems so far.
>
> Did you install ImageJ from the Ubuntu repositories or from the ImageJ website?
>
> Carnë Draug

[Gabriel Landini]

On Sunday 01 May 2011, you wrote:

> Now I'm again using the version from the Ubuntu repository (imagej
> (1.44i-1) unstable; urgency=low). Before, I was using a manually updated
> version.
>
> It seems that in the 1.44 version the problem was solved. The Ubuntu
> changelog for the package ImageJ says:
>    * New upstream release (Closes: #601020).
>      - Solves a bug that prevented to quit (Closes: #600997, LP: 661545).
> But when I download an new jar file via the update plugin, it does not
> work afterwards. Would be nice if the bug will be also fixed in the
> newer versions.

I cannot replicate it in either opensuse or kubuntu, so I suspect that this is
something else in your setup.

Did you switch the desktop effects off as originally suggested, to see if that
resolves it?

Did you try the local install of IJ instead? (I see no advantage of installing
it system wide in a single user machine).

Gabriel

[Carnë Draug]

2011/5/1 Sven Boekhoff <[hidden email]>:

> Hi Carnë.
>
> Now I'm again using the version from the Ubuntu repository (imagej (1.44i-1)
> unstable; urgency=low). Before, I was using a manually updated version.
>
> It seems that in the 1.44 version the problem was solved. The Ubuntu
> changelog for the package ImageJ says:
>  * New upstream release (Closes: #601020).
>    - Solves a bug that prevented to quit (Closes: #600997, LP: 661545).
> But when I download an new jar file via the update plugin, it does not work
> afterwards. Would be nice if the bug will be also fixed in the newer
> versions.

There's a reason it's recommended to install things from the
repositories only. Also, sometimes to make things work they apply
patches to code they receive from upstream. This is something that
some people criticize but that's how it is.

That said, all the bugs were reported to be related to the java used
and it's weird that you have it with both OpenJDK and Oracle's Java.
Also, how did you update ImageJ? If I try to update the ImageJ that
was installed from the repository I get "no write access to
/usr/share/java/". Did you run ImageJ with sudo?

I'm using the same version available for Ubuntu 11.04 (but on Debian)
but haven't updated it, since I haven't needed to.

Carnë

[Sven Boekhoff]

To update manually, i started imagej with sudo (in a terminal window:
"sudo imagej").
Maybe you try if you have the same problem afterwards.
If yes, you can easily overwrite the updated version by reinstalling
imagej via synaptic.

Sven




Am 02.05.11 12:22, schrieb Carnë Draug:

> 2011/5/1 Sven Boekhoff<[hidden email]>:
>> Hi Carnë.
>>
>> Now I'm again using the version from the Ubuntu repository (imagej (1.44i-1)
>> unstable; urgency=low). Before, I was using a manually updated version.
>>
>> It seems that in the 1.44 version the problem was solved. The Ubuntu
>> changelog for the package ImageJ says:
>>   * New upstream release (Closes: #601020).
>>     - Solves a bug that prevented to quit (Closes: #600997, LP: 661545).
>> But when I download an new jar file via the update plugin, it does not work
>> afterwards. Would be nice if the bug will be also fixed in the newer
>> versions.
> There's a reason it's recommended to install things from the
> repositories only. Also, sometimes to make things work they apply
> patches to code they receive from upstream. This is something that
> some people criticize but that's how it is.
>
> That said, all the bugs were reported to be related to the java used
> and it's weird that you have it with both OpenJDK and Oracle's Java.
> Also, how did you update ImageJ? If I try to update the ImageJ that
> was installed from the repository I get "no write access to
> /usr/share/java/". Did you run ImageJ with sudo?
>
> I'm using the same version available for Ubuntu 11.04 (but on Debian)
> but haven't updated it, since I haven't needed to.
>
> Carnë

[Carnë Draug]

On 2 May 2011 14:54, Sven Boekhoff <[hidden email]> wrote:
> To update manually, i started imagej with sudo (in a terminal window: "sudo
> imagej").
> Maybe you try if you have the same problem afterwards.
> If yes, you can easily overwrite the updated version by reinstalling imagej
> via synaptic.

Yes. After upgrading this way, the bug returns for me as well. No idea
how to fix it.

Carnë

[Carnë Draug]

I have the fix but the mailing list does not allow me to send a patch
file. There's a line on the file ij/gui/YesNoCancelDialog.java that
after being removed fix this issue.

The patch had been applied to Debian (and therefore to Ubuntu), but
never found its way upstream for some reason.

Carnë Draug

[Gabriel Landini]

On Monday 02 May 2011, you wrote:
> I have the fix but the mailing list does not allow me to send a patch
> file. There's a line on the file ij/gui/YesNoCancelDialog.java that
> after being removed fix this issue.

I had a look at this in the net and it is a bug in open-jdk, not ImageJ.
So even if this gets fixed, the same call might be present in other parts of
IJ and in mabye in other plugins, so I wonder if this will be the end of the
problem.

A better alternative until open-jdk fixes it would be to install sun-java
package instead of open-jdk.
The sun java package is in the "Canonical partners" repository. So it is only
a couple of clicks away.

Gabriel

[Carnë Draug]

On 2 May 2011 17:20, Gabriel Landini <[hidden email]> wrote:
> I had a look at this in the net and it is a bug in open-jdk, not ImageJ.
> So even if this gets fixed, the same call might be present in other parts of
> IJ and in mabye in other plugins, so I wonder if this will be the end of the
> problem.

Yes, I agree with you. But they also say that the offending line is
actually useless (I wouldn't know as I don't write Java).

> A better alternative until open-jdk fixes it would be to install sun-java
> package instead of open-jdk.
> The sun java package is in the "Canonical partners" repository. So it is only
> a couple of clicks away.

Supposedly OpenJDK-7 has this fixed already but isn't in the repos yet.

About using Sun's java, many things are just a click away, but that
doesn't make them right and Oracle's java is not free.

Also, Sven Boekhoff (the bug reporter) says that he tried with both
java and the bug didn't go away. This is unexpected.

Carnë Draug

[Rasband, Wayne (NIH/NIMH) [E]]

On May 1, 2011, at 12:22 PM, Sven Boekhoff wrote:

> Hi.
> I'm using ImageJ 1.45f on Ubuntu Linux 11.04.
>
> When I:
> 1) open the "About ImageJ"-window,
> 2) draw a filled rectangle on it,
> 3) try to close the "About ImageJ"-window,
> 4) answer the question "Save changes to 'About ImageJ'" with "yes", "no"
> or "Cancel",
>
> the window does not close and I can't exit ImageJ anymore.
>
> WHY?
>
> I tested two java Versions that installed on my computer, by switching
> between them with: "sudo update-alternatives --config java".
>
> java version "1.6.0_22"
> OpenJDK Runtime Environment (IcedTea6 1.10.1) (6b22-1.10.1-0ubuntu1)
> OpenJDK 64-Bit Server VM (build 20.0-b11, mixed mode)
>
> and
>
> java version "1.6.0_24"
> Java(TM) SE Runtime Environment (build 1.6.0_24-b07)
> Java HotSpot(TM) 64-Bit Server VM (build 19.1-b02, mixed mode)
>
>
> Does anyone have a solution?

This OpenJDK related bug is fixed in ImageJ 1.45g. The fix removes line 75 ["setVisible(false);"] from ij/gui/YesNoCancelDialog.java.

-wayne

[Carnë Draug]

On 3 May 2011 05:18, Rasband, Wayne (NIH/NIMH) [E]
<[hidden email]> wrote:
> This OpenJDK related bug is fixed in ImageJ 1.45g. The fix removes line 75 ["setVisible(false);"] from ij/gui/YesNoCancelDialog.java.

Thank you Wayne for dealing with this so quickly.

Carnë Draug