Re: TrakEM Mipmap regeneration slow
Posted by
Albert Cardona-2 on
Jul 11, 2013; 5:21pm
URL: http://imagej.273.s1.nabble.com/TrakEM-Mipmap-regeneration-slow-tp5003921p5003922.html
2013/7/11 Ashwin <
[hidden email]>
> Hi,
>
> I am attempting to regenerate mipmaps for a large EM data-set and seem to
> be
> running into problems with the mipmap generation.
>
> Once the images are imported into TrakEM2 (with enable mipmap turned off),
> I
> begin aligning the sections (with enable mipmap turned on). In the log
> window, I notice that TrakEM2 has submitted to generate mipmaps for all
> images that its trying to extract features form.
>
> Here I can follow the mipmap regeneration, the problem that I notice is
> that
> the mipmap creation and saving times increase progressively, to the point
> that it takes ~20 min to regenerate mipmaps from 1 tile.
>
> I use the following strategy to regenerate mipmaps;
>
> Strategy A: your data consists of large images (over 4000x4000).
> Right-click
> on the TrakEM2 display and choose "Project - Properties...", and set the
> mipmap threads to 1. Now, mipmaps will be regenerated for one single image
> at a time, using 12 threads (given 12 cores) for computing the Gaussians.
>
> my comp specs; 24 processors, 140G memory.
> here is how I call Fiji; ./ImageJ-linux64 -Xms55g -Xmx55g -Xincgc
> -XX:MaxPermSize=256m -XX:PermSize=256m
> -XX:NewRatio=5 -XX:CMSTriggerRatio=50 -XX:+UseCompressedOops --
>
> I am not sure if I am doing this right or not, but I would like to be able
> to do this faster.
>
> Any help or suggestions are welcome.
>
> Thanks,
> Ashwin
>
>
Ashwin,
1. what are the type and dimensions of your images?
2. CompressedOops won't work when allocating over 31 GB of heap.
3. What operating system?
Albert
--
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