Out of memory

[Iva Dobrovic]

Hello people,

I am knew with ImageJ. I am measuring a scanned plant material and using only the simple utilities of the program. Today it doesn't want to work and the message "out of memory" pumps up after every few measures!?
What should I do? Did anybody else had that problem?
Thx,

Iva

Iva Dobrovic, Ph.D. student
Department of Botany
Faculty of Science
University of Zagreb
Rooseveltov trg 6
HR-10000 Zagreb
Croatia
tel/fax: [phone]
gsm: [phone]
e-mail: [hidden email]

[Morgiane Richard]

Hi Iva,
 
I am not specialist in Java peogramming but very used to see that kind of message with C; in general, this is because I have not allocated enough memory to an array, or have not closed a file I am writing in and reading.
 
I do not know if it can help...
 
Morgiane

________________________________

From: ImageJ Interest Group on behalf of Iva Dobrovic
Sent: Fri 21/10/2005 12:48
To: [hidden email]
Subject: Out of memory



Hello people,

I am knew with ImageJ. I am measuring a scanned plant material and using only the simple utilities of the program. Today it doesn't want to work and the message "out of memory" pumps up after every few measures!?
What should I do? Did anybody else had that problem?
Thx,

Iva

Iva Dobrovic, Ph.D. student
Department of Botany
Faculty of Science
University of Zagreb
Rooseveltov trg 6
HR-10000 Zagreb
Croatia
tel/fax: [phone]
gsm: [phone]
e-mail: [hidden email]

[Andreas Jahnen]

Hello Iva,

this is because Java has only a specific amount of Memory available. You
can set the memory available for a Java app with  -Xmx512M for example to
512 MByte.

The command

java -Xmx512M -jar ij.jar

should help you......

Andreas


--------------------------------------------
Andreas Jahnen                                   Ingenieur de Recherche
--------------------------------------------
e-mail: [hidden email]      CRP Henri Tudor
http://www.santec.lu                        29, Avenue John F. Kennedy
phone: +352 - 42 59 91 - 250        L-1855 Luxembourg
--------------------------------------------

ImageJ Interest Group <[hidden email]> wrote on 21.10.2005 13:48:12:

> Hello people,
>
> I am knew with ImageJ. I am measuring a scanned plant material and
> using only the simple utilities of the program. Today it doesn't
> want to work and the message "out of memory" pumps up after every
> few measures!?
> What should I do? Did anybody else had that problem?
> Thx,
>
> Iva
>
> Iva Dobrovic, Ph.D. student
> Department of Botany
> Faculty of Science
> University of Zagreb
> Rooseveltov trg 6
> HR-10000 Zagreb
> Croatia
> tel/fax: [phone]
> gsm: [phone]
> e-mail: [hidden email]

[Jon Harman]

Hi,

I have written a plugin to ImageJ.  I'd like to give visitors to my web
site the chance to test it.  So I'd like to let them start ImageJ as an
applet, open up some images stored on the site and use the plugin.  Is
there any way to do this without requiring users to jump over hoops with
internet security settings?  Do I need to somehow "sign" my version of
ij.jar?


Thanks for any help

[Wayne Rasband]

> I have written a plugin to ImageJ.  I'd like to give
> visitors to my web site the chance to test it.  So I'd like
> to let them start ImageJ as an applet, open up some images
> stored on the site and use the plugin.  Is there any way to
> do this without requiring users to jump over hoops with
> internet security settings?  Do I need to somehow "sign" my
> version of ij.jar?

You will have to add the plugin to ij.jar and add a command that runs
it to IJ_props.txt. The plugin can open images on the website it is
loaded from. You do not need to "sign" the applet. Tony Parker has
example applets that run plugins and open images at
"http://www.med.harvard.edu/JPNM/ij/applets/".

-wayne

[Jon Harman]

Thanks, I've got it working.  Here is a link to my site:www.dstretch.com
<http://www.dstretch.com/>
The plugin seems to be pretty touchy.  On a PC running XP it would crash
the ImageJ applet using jre1.4.2, but works using jre 1.5.0_5.  I have
no clue as to why, as a plugin to the program ImageJ it works fine using
jre 1.4.2.  I used the latest jar for ImageJ 135e.

Jon


Wayne Rasband wrote:

>> I have written a plugin to ImageJ.  I'd like to give
>> visitors to my web site the chance to test it.  So I'd like
>> to let them start ImageJ as an applet, open up some images
>> stored on the site and use the plugin.  Is there any way to
>> do this without requiring users to jump over hoops with
>> internet security settings?  Do I need to somehow "sign" my
>> version of ij.jar?
>
>
> You will have to add the plugin to ij.jar and add a command that runs
> it to IJ_props.txt. The plugin can open images on the website it is
> loaded from. You do not need to "sign" the applet. Tony Parker has
> example applets that run plugins and open images at
> "http://www.med.harvard.edu/JPNM/ij/applets/".
>
> -wayne
>

[Michael Herron]

Dumb question:  What IS an applet and why would someone want to use
ImageJ that way??

I know there are good reasons, I am just curious.

On Oct 22, 2005, at 1:22 PM, Jon Harman wrote:

> Thanks, I've got it working.  Here is a link to my
> site:www.dstretch.com <http://www.dstretch.com/>
> The plugin seems to be pretty touchy.  On a PC running XP it would
> crash the ImageJ applet using jre1.4.2, but works using jre 1.5.0_5.  
> I have no clue as to why, as a plugin to the program ImageJ it works
> fine using jre 1.4.2.  I used the latest jar for ImageJ 135e.
>
> Jon
>
>
>

Michael J. Herron,  U of MN, Dept. of Entomology
   [hidden email]
      612-624-3688 (office) 612-625-5299 (FAX)

[Puneet Kishor]

On Oct 22, 2005, at 2:06 PM, Michael Herron wrote:

> Dumb question:  What IS an applet and why would someone want to use
> ImageJ that way??
>
> I know there are good reasons, I am just curious.

an applet is a program that gets downloaded from the web, and runs
within your browser. You might want to run a program as an applet so
web users can use your program.

>
> On Oct 22, 2005, at 1:22 PM, Jon Harman wrote:
>
>> Thanks, I've got it working.  Here is a link to my
>> site:www.dstretch.com <http://www.dstretch.com/>
>> The plugin seems to be pretty touchy.  On a PC running XP it would
>> crash the ImageJ applet using jre1.4.2, but works using jre 1.5.0_5.  
>> I have no clue as to why, as a plugin to the program ImageJ it works
>> fine using jre 1.4.2.  I used the latest jar for ImageJ 135e.
>>
>> Jon
>>
>>
>>
>
> Michael J. Herron,  U of MN, Dept. of Entomology
>   [hidden email]
>      612-624-3688 (office) 612-625-5299 (FAX)
>

--
Puneet Kishor

[Jeff Linn]

So how would I set up an applet so it could access macros and a  
specific ROI.  How about setting it up so that a web user could  
process their own images and store them in a local directory??

Jeff Linn


On Oct 22, 2005, at 10:18 AM, Puneet Kishor wrote:

> On Oct 22, 2005, at 2:06 PM, Michael Herron wrote:
>
>
>> Dumb question:  What IS an applet and why would someone want to  
>> use ImageJ that way??
>>
>> I know there are good reasons, I am just curious.
>>
>
> an applet is a program that gets downloaded from the web, and runs  
> within your browser. You might want to run a program as an applet  
> so web users can use your program.
>
>
>
>
>>
>> On Oct 22, 2005, at 1:22 PM, Jon Harman wrote:
>>
>>
>>> Thanks, I've got it working.  Here is a link to my  
>>> site:www.dstretch.com <http://www.dstretch.com/>
>>> The plugin seems to be pretty touchy.  On a PC running XP it  
>>> would crash the ImageJ applet using jre1.4.2, but works using jre  
>>> 1.5.0_5.  I have no clue as to why, as a plugin to the program  
>>> ImageJ it works fine using jre 1.4.2.  I used the latest jar for  
>>> ImageJ 135e.
>>>
>>> Jon
>>>
>>>
>>>
>>>
>>
>> Michael J. Herron,  U of MN, Dept. of Entomology
>>   [hidden email]
>>      612-624-3688 (office) 612-625-5299 (FAX)
>>
>>
> --
> Puneet Kishor
>

"Philosophy is a battle against the bewitchment of our intelligence  
by means of language." Ludwig Wittgenstein

[Prodanov, D. (FYS)]

Hi Iva,

Perhaps your image is too large?  Check the DPI setting of the scanner
and if not absolutely necessary decrease it.

best
D Prodanov

[leo durosemont]

> I use ImageJ to view medical CTs, MRIs, and X-ray images.  Is there a
> way for there to be automatic contrast & brightness selector for the
> different image types ...
   
  Hi Jason,
   
  You can use a macro like this one :
                    Sincerely, Leo.
   
  // edit these arrays as needed
var w=newArray(1800,400,80,2500,260);
var l=newArray(-600,50,35,450,65);
var t=newArray("1-Lung","2-Abd Soft Tissue","3-Brain","4-Bone","5-Spine Soft Tissue");

macro "WL Tool - C059T0a09WTaa09L" {
}

macro "WL Tool Selected" {
restorePreviousTool();
Dialog.create("Choose...");
Dialog.addChoice("Tissue",t);
Dialog.show();
choice=Dialog.getChoice();
n=substring(choice,0,indexOf(choice,"-"));
setMinAndMax(l[n]-(w[n]/2),l[n]+(w[n]/2));
}



                       
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