"Allocating 30MB, press ESC to abort"

[aget]

Hi, this sign pop up when i am instruct imagej to to 3D fast filter of a image stack (512x512x161). It wont go further. Could anyone help me?

[Thomas Boudier]

Hi,

It looks like ImageJ tries to get memory space to create the filtered
stack (Wayne has to confirm). I have to mention that on 1 or 2 cores
computers 3D filtering on such data can be quite long if you use large
radii. The 3D filtering use extensive parallelization and then are more
adapted to computers with large numbers of cores (6-12).

Thomas


Le 06/09/2012 00:37, aget a écrit :

> Hi, this sign pop up when i am instruct imagej to to 3D fast filter of a
> image stack (512x512x161). It wont go further. Could anyone help me?
>
>
>
> --
> View this message in context: http://imagej.1557.n6.nabble.com/Allocating-30MB-press-ESC-to-abort-tp4999954.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
   /**********************************************************/
      Thomas Boudier, MCU Université Pierre et Marie Curie,
      Modélisation Cellulaire et Imagerie Biologique (EE1),
      IFR 83, Bat B 7ème étage, porte 723, Campus Jussieu.
      Tel : [phone]   Fax : [phone]
/*******************************************************/

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[oojeyboojey]

Have you already increased the maximum memory?

Edit -> Options -> Memory and Threads

Apologies if you've already done this, but it's something I encountered when I started analysing large stacks!

[aget]

Thanks guys, i have a RAM of 4GB, in imagej, the Maximus memory is 2495MB, parallel threads for stack is 2. Everytime, when i use the 3D fast filter, it takes long time (5min) waiting for allocation of memory. What is the difference if i use filtering>3D median, compared to plugin> 3D>faster filter? It seems to prevent the problem of allocating memory. Thanks

[Thomas Boudier]

Hi,

Actually it is the same algorithm for 3D filters in ImageJ (except 3D
Gaussian) and FastFilters3D. Maybe the memory allocation is not done
exactly the same way (but it should ;-) ).

Thomas


Le 06/09/2012 13:49, aget a écrit :

> Thanks guys, i have a RAM of 4GB, in imagej, the Maximus memory is 2495MB,
> parallel threads for stack is 2. Everytime, when i use the 3D fast filter,
> it takes long time (5min) waiting for allocation of memory. What is the
> difference if i use filtering>3D median, compared to plugin>  3D>faster
> filter? It seems to prevent the problem of allocating memory. Thanks
>
>
>
> --
> View this message in context: http://imagej.1557.n6.nabble.com/Allocating-30MB-press-ESC-to-abort-tp4999954p4999962.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
   /**********************************************************/
      Thomas Boudier, MCU Université Pierre et Marie Curie,
      Modélisation Cellulaire et Imagerie Biologique (EE1),
      IFR 83, Bat B 7ème étage, porte 723, Campus Jussieu.
      Tel : [phone]   Fax : [phone]
/*******************************************************/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html