TrakEM Mipmap regeneration slow

Posted by Ashwin on Jul 11, 2013; 4:35pm
URL: http://imagej.273.s1.nabble.com/TrakEM-Mipmap-regeneration-slow-tp5003921.html

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