Posted by
Stephan Saalfeld on
Jul 11, 2013; 6:49pm
URL: http://imagej.273.s1.nabble.com/TrakEM-Mipmap-regeneration-slow-tp5003921p5003926.html
Hi Ashwin,
please change, under Project>Project Properties, Image resizing mode to
Area downsampling
this avoids Gaussian downsampling, saves memory and is a lot faster
while still appropriate in quality. If you can spare some diskspace,
change mipmap format to
rag
Mipmaps will now generate ~100x faster, including disk access this can
still make up to 10x speedup, memory demands are generally lower.
The other behavior I don't get but I have noticed similar hickups
before. Try this Beanshell script to regenerate the mipmaps:
https://github.com/axtimwalde/fiji-scripts/blob/master/TrakEM2/updatemipmaps.bshChange line 39 to 0 to start from first layer. Consider to update some
ranges of layers and save in between when dealing with large projects.
Best,
Stephan
On Thu, 2013-07-11 at 09:35 -0700, Ashwin wrote:
> 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
>
>
>
>
>
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