Out of available memory? Help!

[Jonathan Thomas-2]

(cliffs at bottom)

I am currently trying to use ImageJ to do image segmentation on some ~11MB
RGB images.  The images load fine into ImageJ, but if I attempt to do any
filtering on them ImageJ throws this error:

<Out of memory>
<All available memory (63MB) has been>
<used. Instructions for making more>
<available can be found in the "Memory" >
<sections of the installation notes at>
<http://rsb.info.nih.gov/ij/docs/install/>
>>>>>>>>>>>>>>>>>>>>>>>>>>>

I then poked through the options and raised the memory alotted to 500MB,
closed ImageJ and reopened it attempted the same operation and got an
identical error.  Even mentioning 63MB.  Note that the default was not 63
MB nor was the max memory set anywhere near 63MB after I changed it.


So I came here, and I see people recommending changing the command given
to the executable, so I checked my ImageJ.cfg and it reads:

.
C:\Program Files\Java\j2re1.4.2_03\bin\javaw.exe
-Xmx500m -cp ij.jar ij.ImageJ

In a previous thread someone mentioned a similar problem and modifying
this line fixed the problem but I believe that java should have plenty of
memory the way I have it configured.

So that's my problem, I'd appreciate any help you guys can give me.

If you have read this far here is some more information that may be
helpful:

2.99Ghz Pentium D
2GB Ram

ImageJ 1.36b
Java 1.5.0_06
About ImageJ displays 55MB of 500MB (11%) while the error message is still
in the log.

The java is on this machine, while the ImageJ is being run from a network
drive.  The same error arrizes when I run ImageJ as an applet from the NIH
page.

I have contacted the sys admin and he assures me that there is no
constraint put on memory used by a user, with the exception of the
physical memory on the machine and what is being used by other software.

Software running in the background or not has no effect on the error
message.

I have replicated this error on 2 machines, each using their own local
java but the same ImageJ off the same network drive.  I have also
replicated it running ImageJ as an applet on both machines.

Curiously when I look at the size of the image in windows it is listed as
11MB, but ImageJ claims it's 27MB.  (perhaps this is extra space for a
buffer?)  One image is 2915x2456 pixel tiff.  The others are similar.  All
tiffs, all RGB, all produce the same error.

If you have made it this far I truly commend you.  Thank you for the
attention and here's a quote for your efforts.

"'That is indisputable,' was the answer, 'but in this country it is a good
thing to kill an admiral from time to time to encourage the others.'"
-Voltaire (François-Marie Arouet), Candide

Thank you for any help you can give me.
-Stumped in StonyBrook





finally cliffnotes:
1. ImageJ throws an out of memory error when I try to analyze some large
tiff images
2. The machine has plenty of memory and so does java.
3. Solutions to similar problems from this listserv do not help.
4. Recent software, reproducible.
5. HELP!
6. quote for your efforts, thanks!

[Lucas, Falk /BDF HAM]

Hi,

we have encountered this issue too and found an solution, but only for some of our machines...

We had an early version (1.31) on hte machines and I set up an script for just overwriting hte old version with a new one, which results in the same error message you get.
Solution: Delete the ImagJ Folder completly and install/copy the current version again.
However, if your account (on a PC) is  just associated with the user group (minimum rights), this message can still be there. We never encountered the message  if the user is in the main user or admin group.

Falk  

-----Ursprüngliche Nachricht-----
Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von Jonathan Thomas
Gesendet: Mittwoch, 1. November 2006 23:23
An: [hidden email]
Betreff: Out of available memory? Help!

(cliffs at bottom)

I am currently trying to use ImageJ to do image segmentation on some ~11MB RGB images.  The images load fine into ImageJ, but if I attempt to do any filtering on them ImageJ throws this error:

<Out of memory>
<All available memory (63MB) has been>
<used. Instructions for making more>
<available can be found in the "Memory" > <sections of the installation notes at> <http://rsb.info.nih.gov/ij/docs/install/>
>>>>>>>>>>>>>>>>>>>>>>>>>>>

I then poked through the options and raised the memory alotted to 500MB, closed ImageJ and reopened it attempted the same operation and got an identical error.  Even mentioning 63MB.  Note that the default was not 63 MB nor was the max memory set anywhere near 63MB after I changed it.


So I came here, and I see people recommending changing the command given to the executable, so I checked my ImageJ.cfg and it reads:

.
C:\Program Files\Java\j2re1.4.2_03\bin\javaw.exe
-Xmx500m -cp ij.jar ij.ImageJ

In a previous thread someone mentioned a similar problem and modifying this line fixed the problem but I believe that java should have plenty of memory the way I have it configured.

So that's my problem, I'd appreciate any help you guys can give me.

If you have read this far here is some more information that may be
helpful:

2.99Ghz Pentium D
2GB Ram

ImageJ 1.36b
Java 1.5.0_06
About ImageJ displays 55MB of 500MB (11%) while the error message is still in the log.

The java is on this machine, while the ImageJ is being run from a network drive.  The same error arrizes when I run ImageJ as an applet from the NIH page.

I have contacted the sys admin and he assures me that there is no constraint put on memory used by a user, with the exception of the physical memory on the machine and what is being used by other software.

Software running in the background or not has no effect on the error message.

I have replicated this error on 2 machines, each using their own local java but the same ImageJ off the same network drive.  I have also replicated it running ImageJ as an applet on both machines.

Curiously when I look at the size of the image in windows it is listed as 11MB, but ImageJ claims it's 27MB.  (perhaps this is extra space for a
buffer?)  One image is 2915x2456 pixel tiff.  The others are similar.  All tiffs, all RGB, all produce the same error.

If you have made it this far I truly commend you.  Thank you for the attention and here's a quote for your efforts.

"'That is indisputable,' was the answer, 'but in this country it is a good thing to kill an admiral from time to time to encourage the others.'"
-Voltaire (François-Marie Arouet), Candide

Thank you for any help you can give me.
-Stumped in StonyBrook





finally cliffnotes:
1. ImageJ throws an out of memory error when I try to analyze some large tiff images 2. The machine has plenty of memory and so does java.
3. Solutions to similar problems from this listserv do not help.
4. Recent software, reproducible.
5. HELP!
6. quote for your efforts, thanks!

_____________________  Confidentiality  _____________________

This electronic transmission is strictly confidential and intended
solely for the addressee.  It may contain information which is covered
by legal, professional or other privilege.  If you are not the intended
addressee, you must not disclose, copy or take any action in reliance
of this transmission.  If you have received this transmission in error,
please notify us and delete the received data as soon as possible.

This footnote also confirms that this email message has been swept
for the presence of computer viruses.
_______________________________________________________

[Michael Weber-4]

Hi,

it usually works for us if we:

- define the amount of RAM in the config (~75% of system memory)
- have this amount of RAM free (double check with the task manager, if
you're a Windows user)
- use the newest Java version
- run only one instance of ImageJ

Maybe this helps.

cheers,
Michael


Lucas, Falk /BDF HAM schrieb:

> Hi,
>
> we have encountered this issue too and found an solution, but only for some of our machines...
>
> We had an early version (1.31) on hte machines and I set up an script for just overwriting hte old version with a new one, which results in the same error message you get.
> Solution: Delete the ImagJ Folder completly and install/copy the current version again.
> However, if your account (on a PC) is  just associated with the user group (minimum rights), this message can still be there. We never encountered the message  if the user is in the main user or admin group.
>
> Falk  
>
> -----Ursprüngliche Nachricht-----
> Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von Jonathan Thomas
> Gesendet: Mittwoch, 1. November 2006 23:23
> An: [hidden email]
> Betreff: Out of available memory? Help!
>
> (cliffs at bottom)
>
> I am currently trying to use ImageJ to do image segmentation on some ~11MB RGB images.  The images load fine into ImageJ, but if I attempt to do any filtering on them ImageJ throws this error:
>
> <Out of memory>
> <All available memory (63MB) has been>
> <used. Instructions for making more>
> <available can be found in the "Memory" > <sections of the installation notes at> <http://rsb.info.nih.gov/ij/docs/install/>
>
> I then poked through the options and raised the memory alotted to 500MB, closed ImageJ and reopened it attempted the same operation and got an identical error.  Even mentioning 63MB.  Note that the default was not 63 MB nor was the max memory set anywhere near 63MB after I changed it.
>
>
> So I came here, and I see people recommending changing the command given to the executable, so I checked my ImageJ.cfg and it reads:
>
> .
> C:\Program Files\Java\j2re1.4.2_03\bin\javaw.exe
> -Xmx500m -cp ij.jar ij.ImageJ
>
> In a previous thread someone mentioned a similar problem and modifying this line fixed the problem but I believe that java should have plenty of memory the way I have it configured.
>
> So that's my problem, I'd appreciate any help you guys can give me.
>
> If you have read this far here is some more information that may be
> helpful:
>
> 2.99Ghz Pentium D
> 2GB Ram
>
> ImageJ 1.36b
> Java 1.5.0_06
> About ImageJ displays 55MB of 500MB (11%) while the error message is still in the log.
>
> The java is on this machine, while the ImageJ is being run from a network drive.  The same error arrizes when I run ImageJ as an applet from the NIH page.
>
> I have contacted the sys admin and he assures me that there is no constraint put on memory used by a user, with the exception of the physical memory on the machine and what is being used by other software.
>
> Software running in the background or not has no effect on the error message.
>
> I have replicated this error on 2 machines, each using their own local java but the same ImageJ off the same network drive.  I have also replicated it running ImageJ as an applet on both machines.
>
> Curiously when I look at the size of the image in windows it is listed as 11MB, but ImageJ claims it's 27MB.  (perhaps this is extra space for a
> buffer?)  One image is 2915x2456 pixel tiff.  The others are similar.  All tiffs, all RGB, all produce the same error.
>
> If you have made it this far I truly commend you.  Thank you for the attention and here's a quote for your efforts.
>
> "'That is indisputable,' was the answer, 'but in this country it is a good thing to kill an admiral from time to time to encourage the others.'"
> -Voltaire (François-Marie Arouet), Candide
>
> Thank you for any help you can give me.
> -Stumped in StonyBrook
>
>
>
>
>
> finally cliffnotes:
> 1. ImageJ throws an out of memory error when I try to analyze some large tiff images 2. The machine has plenty of memory and so does java.
> 3. Solutions to similar problems from this listserv do not help.
> 4. Recent software, reproducible.
> 5. HELP!
> 6. quote for your efforts, thanks!
>
> _____________________  Confidentiality  _____________________
>
> This electronic transmission is strictly confidential and intended
> solely for the addressee.  It may contain information which is covered
> by legal, professional or other privilege.  If you are not the intended
> addressee, you must not disclose, copy or take any action in reliance
> of this transmission.  If you have received this transmission in error,
> please notify us and delete the received data as soon as possible.
>
> This footnote also confirms that this email message has been swept
> for the presence of computer viruses.
> _______________________________________________________

[Harry Parker]

I had a similar problem when running ImageJ locally on my Windows PC.

I had renamed ImageJ to something like "ImageJv1.3" to allow myself mutiple versions for testing.
It appeared to work well in every respect, EXCEPT it did not read the config file memory allocation option!

Changing the name back to "ImageJ" fixed the problem.

I found that I could do what I wanted to do by renaming links to the ImageJ versions in different directories.

Did you rename ImageJ?
 
--  
Harry Parker  
Senior Systems Engineer  
Dialog Imaging Systems, Inc.

----- Original Message ----
From: Jonathan Thomas <[hidden email]>
To: [hidden email]
Sent: Wednesday, November 1, 2006 5:23:24 PM
Subject: Out of available memory? Help!

(cliffs at bottom)

I am currently trying to use ImageJ to do image segmentation on some ~11MB
RGB images.  The images load fine into ImageJ, but if I attempt to do any
filtering on them ImageJ throws this error:

<Out of memory>
<All available memory (63MB) has been>
<used. Instructions for making more>
<available can be found in the "Memory" >
<sections of the installation notes at>
<http://rsb.info.nih.gov/ij/docs/install/>
>>>>>>>>>>>>>>>>>>>>>>>>>>>

I then poked through the options and raised the memory alotted to 500MB,
closed ImageJ and reopened it attempted the same operation and got an
identical error.  Even mentioning 63MB.  Note that the default was not 63
MB nor was the max memory set anywhere near 63MB after I changed it.


So I came here, and I see people recommending changing the command given
to the executable, so I checked my ImageJ.cfg and it reads:

.
C:\Program Files\Java\j2re1.4.2_03\bin\javaw.exe
-Xmx500m -cp ij.jar ij.ImageJ

In a previous thread someone mentioned a similar problem and modifying
this line fixed the problem but I believe that java should have plenty of
memory the way I have it configured.

So that's my problem, I'd appreciate any help you guys can give me.

If you have read this far here is some more information that may be
helpful:

2.99Ghz Pentium D
2GB Ram

ImageJ 1.36b
Java 1.5.0_06
About ImageJ displays 55MB of 500MB (11%) while the error message is still
in the log.

The java is on this machine, while the ImageJ is being run from a network
drive.  The same error arrizes when I run ImageJ as an applet from the NIH
page.

I have contacted the sys admin and he assures me that there is no
constraint put on memory used by a user, with the exception of the
physical memory on the machine and what is being used by other software.

Software running in the background or not has no effect on the error
message.

I have replicated this error on 2 machines, each using their own local
java but the same ImageJ off the same network drive.  I have also
replicated it running ImageJ as an applet on both machines.

Curiously when I look at the size of the image in windows it is listed as
11MB, but ImageJ claims it's 27MB.  (perhaps this is extra space for a
buffer?)  One image is 2915x2456 pixel tiff.  The others are similar.  All
tiffs, all RGB, all produce the same error.

If you have made it this far I truly commend you.  Thank you for the
attention and here's a quote for your efforts.

"'That is indisputable,' was the answer, 'but in this country it is a good
thing to kill an admiral from time to time to encourage the others.'"
-Voltaire (François-Marie Arouet), Candide

Thank you for any help you can give me.
-Stumped in StonyBrook





finally cliffnotes:
1. ImageJ throws an out of memory error when I try to analyze some large
tiff images
2. The machine has plenty of memory and so does java.
3. Solutions to similar problems from this listserv do not help.
4. Recent software, reproducible.
5. HELP!
6. quote for your efforts, thanks!

[Wayne Rasband]

How do you run ImageJ? Double-clicking on ij.jar instead of on
ImageJ.exe would cause this problem. Java programs are limited to 64MB
when you run them by double clicking on their JAR file.

A 2915x2456 color image does require 27MB of memory. To do the
calculations, open a text window (shift-n), paste in the following line

     round(2915*2456*4/(1024*1024)) + " MB"

and press ctrl-r (Run Macro).

-wayne

> (cliffs at bottom)
>
> I am currently trying to use ImageJ to do image segmentation on some
> ~11MB
> RGB images.  The images load fine into ImageJ, but if I attempt to do
> any
> filtering on them ImageJ throws this error:
>
> <Out of memory>
> <All available memory (63MB) has been>
> <used. Instructions for making more>
> <available can be found in the "Memory" >
> <sections of the installation notes at>
> <http://rsb.info.nih.gov/ij/docs/install/>
> >>>>>>>>>>>>>>>>>>>>>>>>>>>
>
> I then poked through the options and raised the memory alotted to
> 500MB,
> closed ImageJ and reopened it attempted the same operation and got an
> identical error.  Even mentioning 63MB.  Note that the default was not
> 63
> MB nor was the max memory set anywhere near 63MB after I changed it.
>
>
> So I came here, and I see people recommending changing the command
> given
> to the executable, so I checked my ImageJ.cfg and it reads:
>
> .
> C:\Program Files\Java\j2re1.4.2_03\bin\javaw.exe
> -Xmx500m -cp ij.jar ij.ImageJ
>
> In a previous thread someone mentioned a similar problem and modifying
> this line fixed the problem but I believe that java should have plenty
> of
> memory the way I have it configured.
>
> So that's my problem, I'd appreciate any help you guys can give me.
>
> If you have read this far here is some more information that may be
> helpful:
>
> 2.99Ghz Pentium D
> 2GB Ram
>
> ImageJ 1.36b
> Java 1.5.0_06
> About ImageJ displays 55MB of 500MB (11%) while the error message is
> still
> in the log.
>
> The java is on this machine, while the ImageJ is being run from a
> network
> drive.  The same error arrizes when I run ImageJ as an applet from the
> NIH
> page.
>
> I have contacted the sys admin and he assures me that there is no
> constraint put on memory used by a user, with the exception of the
> physical memory on the machine and what is being used by other
> software.
>
> Software running in the background or not has no effect on the error
> message.
>
> I have replicated this error on 2 machines, each using their own local
> java but the same ImageJ off the same network drive.  I have also
> replicated it running ImageJ as an applet on both machines.
>
> Curiously when I look at the size of the image in windows it is listed
> as
> 11MB, but ImageJ claims it's 27MB.  (perhaps this is extra space for a
> buffer?)  One image is 2915x2456 pixel tiff.  The others are similar.  
> All
> tiffs, all RGB, all produce the same error.
>
> If you have made it this far I truly commend you.  Thank you for the
> attention and here's a quote for your efforts.
>
> "'That is indisputable,' was the answer, 'but in this country it is a
> good
> thing to kill an admiral from time to time to encourage the others.'"
> -Voltaire (François-Marie Arouet), Candide
>
> Thank you for any help you can give me.
> -Stumped in StonyBrook
>
>
>
>
>
> finally cliffnotes:
> 1. ImageJ throws an out of memory error when I try to analyze some
> large
> tiff images
> 2. The machine has plenty of memory and so does java.
> 3. Solutions to similar problems from this listserv do not help.
> 4. Recent software, reproducible.
> 5. HELP!
> 6. quote for your efforts, thanks!

[Jonathan Thomas-2]

Thanks!  That solved the problem.  I was running it from the .jar.  As far
as the memory usage the 27MB must be correct.  Windows must be doing some
compression or some such.  Either way, thank you very much for the help.

-Jon


On 11/2/06, Wayne Rasband <[hidden email]> wrote:

>
> How do you run ImageJ? Double-clicking on ij.jar instead of on
> ImageJ.exe would cause this problem. Java programs are limited to 64MB
> when you run them by double clicking on their JAR file.
>
> A 2915x2456 color image does require 27MB of memory. To do the
> calculations, open a text window (shift-n), paste in the following line
>
>     round(2915*2456*4/(1024*1024)) + " MB"
>
> and press ctrl-r (Run Macro).
>
> -wayne
>
> > (cliffs at bottom)
> >
> > I am currently trying to use ImageJ to do image segmentation on some
> > ~11MB
> > RGB images.  The images load fine into ImageJ, but if I attempt to do
> > any
> > filtering on them ImageJ throws this error:
> >
> > <Out of memory>
> > <All available memory (63MB) has been>
> > <used. Instructions for making more>
> > <available can be found in the "Memory" >
> > <sections of the installation notes at>
> > <http://rsb.info.nih.gov/ij/docs/install/>
> > >>>>>>>>>>>>>>>>>>>>>>>>>>>
> >
> > I then poked through the options and raised the memory alotted to
> > 500MB,
> > closed ImageJ and reopened it attempted the same operation and got an
> > identical error.  Even mentioning 63MB.  Note that the default was not
> > 63
> > MB nor was the max memory set anywhere near 63MB after I changed it.
> >
> >
> > So I came here, and I see people recommending changing the command
> > given
> > to the executable, so I checked my ImageJ.cfg and it reads:
> >
> > .
> > C:\Program Files\Java\j2re1.4.2_03\bin\javaw.exe
> > -Xmx500m -cp ij.jar ij.ImageJ
> >
> > In a previous thread someone mentioned a similar problem and modifying
> > this line fixed the problem but I believe that java should have plenty
> > of
> > memory the way I have it configured.
> >
> > So that's my problem, I'd appreciate any help you guys can give me.
> >
> > If you have read this far here is some more information that may be
> > helpful:
> >
> > 2.99Ghz Pentium D
> > 2GB Ram
> >
> > ImageJ 1.36b
> > Java 1.5.0_06
> > About ImageJ displays 55MB of 500MB (11%) while the error message is
> > still
> > in the log.
> >
> > The java is on this machine, while the ImageJ is being run from a
> > network
> > drive.  The same error arrizes when I run ImageJ as an applet from the
> > NIH
> > page.
> >
> > I have contacted the sys admin and he assures me that there is no
> > constraint put on memory used by a user, with the exception of the
> > physical memory on the machine and what is being used by other
> > software.
> >
> > Software running in the background or not has no effect on the error
> > message.
> >
> > I have replicated this error on 2 machines, each using their own local
> > java but the same ImageJ off the same network drive.  I have also
> > replicated it running ImageJ as an applet on both machines.
> >
> > Curiously when I look at the size of the image in windows it is listed
> > as
> > 11MB, but ImageJ claims it's 27MB.  (perhaps this is extra space for a
> > buffer?)  One image is 2915x2456 pixel tiff.  The others are similar.
> > All
> > tiffs, all RGB, all produce the same error.
> >
> > If you have made it this far I truly commend you.  Thank you for the
> > attention and here's a quote for your efforts.
> >
> > "'That is indisputable,' was the answer, 'but in this country it is a
> > good
> > thing to kill an admiral from time to time to encourage the others.'"
> > -Voltaire (François-Marie Arouet), Candide
> >
> > Thank you for any help you can give me.
> > -Stumped in StonyBrook
> >
> >
> >
> >
> >
> > finally cliffnotes:
> > 1. ImageJ throws an out of memory error when I try to analyze some
> > large
> > tiff images
> > 2. The machine has plenty of memory and so does java.
> > 3. Solutions to similar problems from this listserv do not help.
> > 4. Recent software, reproducible.
> > 5. HELP!
> > 6. quote for your efforts, thanks!
>