extracting sub matrix - time consuming

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lital
lital 2011-8-6
Hi, I need to perform a certain calculation on a sub matrix, then insert this sub matrix to another matrix. I'm using : to select the submatrix, problem is, it's very time consuming. After running the profiler i see that this two lines take 20+ seconds each (the lines run 1170 time). With 361*4*18 times this code should run I'm looking at several days of computations.
[x,y] = ndgrid(yup:ydown, xleft:xright);
exponent = (xpower(yup:ydown,xleft:xright).*ypower(yup:ydown,xleft:xright)).*exp(-(xc^2 + yc^2 - 2*xc*x- 2*yc*y)./(2*(sigma^2)));
mat(yup:ydown,xleft:xright) = mat(yup:ydown,xleft:xright)+ exponent;
xpower, ypower and mat are 1080*1920 matrices.
thanks!
  2 个评论
James Tursa
James Tursa 2011-8-6
A mex routine could avoid unnecessary intermediate data copies. Could you list the dimensions of *all* of your variables?
lital
lital 2011-8-6
x and y dimensions change at each run depending on xc and yc
my original needed calculation was:
[x,y] = ndgrid(1:1080, 1:1920);
gauss2d = gauss2d + exp(-((x-xc).^2 + (y-yc).^2)./(2*(sigma^2)));
where xc and yc are scalars that change at each run.
since there is no need for me to this calculation for the entire 1080*1920 matrix (as most of the gauss function will return 0) im only calculating the gauss2d function for a submatrix. (just to be sure i did run this line and it resulted in 300 sec.

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回答（1 个）

Sean de Wolski
Sean de Wolski 2011-8-6
  • Use bsxfun instead of ndgrid, it'll skip the expansions.
  • Do xc,yc and sigma change? If not, calculate them being multiplied by 2 (and squared for sigma) once, save that as a new variable.
  • Did you use the profiler to determine this line is the one slowing you down?
  • How much RAM do you have/are you on a 32 bit system, is it exceeded?
  2 个评论
lital
lital 2011-8-6
sigma does not change.
what changes in each run is x,y,xc,yc.
this code runs 1170 times for a frame and according to the profiler, the last two lines (without ndgrid) take more than 20 sec each to run for a frame.
i have 4 gb ram with a 64bit system and matlab works on 60-70% cpu according to the task manager.
Sean de Wolski
Sean de Wolski 2011-8-6
Look at using bsxfun for the multiplication (will speed up a bit probably) and remove ndgrid call. Are xc,yc scalar? If so this whole line exp process could be:
exp((-(xc^2+yc^2)+2*bsxfun(@plus,xc*((yup:ydown)'),yc*(xleft:xright)))./(TwoSigSquared))
Now no need for ndgrid which takes time and ram.
Calculate 2*sigma^2 once for a little gain (TwoSigSquared).

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