processing bogs down

[John Alexander-7]

Hi, I am not sure if this is a java or imageJ issue.

I am running Suse 10.2 (64-bit) and the imageJ 1.39j (but what I am
about to describe has been an issue with previous versions too).

I was using Java 1.5 and recently switched to java 1.6 - same thing.

Basically, whenever I do an operation, like simply renaming a window,
imageJ pauses for a few seconds.  This happens with many many such
simple things. Another example is highlighting a ROI and clicking 'm' to
measure - the first time I do that after opening imageJ - there is a
very long pause.  But then all subsequent attempts are fast (not the
case with renaming a window, that always takes a few seconds).

Can anyone offer advice on how to track these problems down?  I do a lot
of image analysis and these little slow downs accumulate to a lot of
time ...

John

[Gabriel Landini]

On Friday 07 December 2007 16:03:24 John Alexander wrote:
> I am running Suse 10.2 (64-bit) and the imageJ 1.39j.
> Basically, whenever I do an operation, like simply renaming a window,
> imageJ pauses for a few seconds.

Yes, this drove me mad for weeks trying to find out what it was.
I haven't tried the build 08 of java 1.6, but I tried the previous ones.

Wayne discovered that this is a problem of Java, not IJ.
The solutions:

1. Continue using Java 1.5 (or 1.7, but in 1.7 the images get locked for some
reason so it is unusable at this moment).

2. Use Gnome instead of KDE

3. Use KDE, but let ImageJ use the Motif toolkit  with the option:

-Dawt.toolkit=sun.awt.motif.MToolkit

It looks awful, but works OK.

I hope it helps.

Gabriel

[John Alexander-7]

Well - interesting news ...

I have ImageJ 1.39j and java 1.6.0

here is the script I WAS using

java -Xmx1536m -Dawt.toolkit=sun.awt.motif.MToolkit -jar ij.jar

but was experiencing the problems I described. (I am using KDE too)


so - I tried removing the Motif toolkit and used this script

java -Xmx1536m -jar ij.jar


and now everything is lightning fast!

I verified this by immediately re-running the old script and things
bogged down again ...



I would be glad to provide more detailed information about my system if
it will help track down the problem for others ...

but for me - it seems that it runs BETTER without the Motif toolkit ...


John



Gabriel Landini wrote:

> On Friday 07 December 2007 16:03:24 John Alexander wrote:
>> I am running Suse 10.2 (64-bit) and the imageJ 1.39j.
>> Basically, whenever I do an operation, like simply renaming a window,
>> imageJ pauses for a few seconds.
>
> Yes, this drove me mad for weeks trying to find out what it was.
> I haven't tried the build 08 of java 1.6, but I tried the previous ones.
>
> Wayne discovered that this is a problem of Java, not IJ.
> The solutions:
>
> 1. Continue using Java 1.5 (or 1.7, but in 1.7 the images get locked for some
> reason so it is unusable at this moment).
>
> 2. Use Gnome instead of KDE
>
> 3. Use KDE, but let ImageJ use the Motif toolkit  with the option:
>
> -Dawt.toolkit=sun.awt.motif.MToolkit
>
> It looks awful, but works OK.
>
> I hope it helps.
>
> Gabriel
>

--
John K. Alexander, Ph.D.
Post-Doctoral Fellow
William Green Laboratory
University of Chicago
Dept. Neurobiology, Pharmacology, and Physiology
947 East 58th Street
Abott Hall 402
Chicago, IL 60637
(off) 773-702-9386
(fax) 773-702-3774
[hidden email]

[Gabriel Landini]

On Friday 07 December 2007 16:39:16 John Alexander wrote:
> Well - interesting news ...
> I have ImageJ 1.39j and java 1.6.0

Which release version 1.6.0_? (latest is b08).

> here is the script I WAS using
>
> java -Xmx1536m -Dawt.toolkit=sun.awt.motif.MToolkit -jar ij.jar
> but was experiencing the problems I described. (I am using KDE too)
>
> so - I tried removing the Motif toolkit and used this script
>
> java -Xmx1536m -jar ij.jar
>
> and now everything is lightning fast!

Hm...  maybe a different issue. Good that it works for you.

The delays I am talking about happen when I call any function that shows a
dialog (for example the Process>Math dialog) AND there are several images
open.
For example, load the MRI sample stack, convert stack to images, select one
image and use the Process>Math (which has a dialog) to multiply the image by
any value. I get a 3-5 sec delay. The more images, the longer the dealy. :-/

Do you get that too?

It was reportedly sorted in 1.7, but I cannot make IJ work (Locked image
errors everywhere).

Cheers,

Gabriel

[John Alexander-7]

That is exactly the problem I have (had :D) too - anything with a dialog
was slow.

./jre/bin/java -version

java version "1.6.0"
Java(TM) SE Runtime Environment (build 1.6.0-b105)
Java HotSpot(TM) Client VM (build 1.6.0-b105, mixed mode, sharing)



Gabriel Landini wrote:

> On Friday 07 December 2007 16:39:16 John Alexander wrote:
>> Well - interesting news ...
>> I have ImageJ 1.39j and java 1.6.0
>
> Which release version 1.6.0_? (latest is b08).
>
>> here is the script I WAS using
>>
>> java -Xmx1536m -Dawt.toolkit=sun.awt.motif.MToolkit -jar ij.jar
>> but was experiencing the problems I described. (I am using KDE too)
>>
>> so - I tried removing the Motif toolkit and used this script
>>
>> java -Xmx1536m -jar ij.jar
>>
>> and now everything is lightning fast!
>
> Hm...  maybe a different issue. Good that it works for you.
>
> The delays I am talking about happen when I call any function that shows a
> dialog (for example the Process>Math dialog) AND there are several images
> open.
> For example, load the MRI sample stack, convert stack to images, select one
> image and use the Process>Math (which has a dialog) to multiply the image by
> any value. I get a 3-5 sec delay. The more images, the longer the dealy. :-/
>
> Do you get that too?
>
> It was reportedly sorted in 1.7, but I cannot make IJ work (Locked image
> errors everywhere).
>
> Cheers,
>
> Gabriel
>

--
John K. Alexander, Ph.D.
Post-Doctoral Fellow
William Green Laboratory
University of Chicago
Dept. Neurobiology, Pharmacology, and Physiology
947 East 58th Street
Abott Hall 402
Chicago, IL 60637
(off) 773-702-9386
(fax) 773-702-3774
[hidden email]

[Gabriel Landini]

On Friday 07 December 2007 17:06:59 John Alexander wrote:
> That is exactly the problem I have (had :D) too - anything with a dialog
> was slow.
>
> ./jre/bin/java -version
>
> java version "1.6.0"
> Java(TM) SE Runtime Environment (build 1.6.0-b105)
> Java HotSpot(TM) Client VM (build 1.6.0-b105, mixed mode, sharing)

I think that you have an older beta version of 1.6.
According to this:
http://download.java.net/jdk6/archive/b105/index.html
it was released on Nov 29 2006.

If you upgrade to one of the latest releases here:
http://download.java.net/jdk6/binaries/
you will get the bug I mentioned that it is cured (what a paradox!) with the
Motif toolkit.

I have installed:
java version "1.6.0_02-ea"
Java(TM) SE Runtime Environment (build 1.6.0_02-ea-b02)
Java HotSpot(TM) Client VM (build 1.6.0_02-ea-b02, mixed mode, sharing)

and it still gives me a hassle with the dialogs.
I tried 1.6.0_05 and it was the same.

Now that I found b105 I might try that one again.

Regards,

Gabriel

[Gabriel Landini]

John,
Can you direct me to where you downloaded Java 1.6.0-b105 for linux, please?
I cannot find the binaries, only the source at the sun site.

Thanks,

Gabriel

PS: 1.6.0_10 still has the bug I described.