[Insight-users] SignedMaurerDistanceMapImageFilter performance

[Bradley Lowekamp]

Would you by any chance be using an express Visual Studio version? Those compiler are missing a fair amount of optimization. I have not compared the difference myself though.

Brad

On Jul 2, 2012, at 11:38 AM, Sergio Vera wrote:

> Hello Bradley
> 
> Thanks for your script
> 
> I've tried your script and the timings are coherent with yours (although my desktop is slower than your laptop :) )
> 
> The average time it took to execute SignedMaurerDistanceMap was 5.3353600223 seconds. 
> The average time it took to execute SignedMaurerDistanceMap was 6.62535580948 seconds. 
> The average time it took to execute SignedMaurerDistanceMap was 6.90300935124 seconds. 
> 
> I've modified it to read my image (it's only 300k but it seems too big for the list) and the results are definitely lower than 13 seconds, closer to the 7 seconds from Mevislab's ITK....
> 
> The average time it took to execute SignedMaurerDistanceMap was 8.87152283895 seconds. 
> The average time it took to execute SignedMaurerDistanceMap was 9.38857726434 seconds. 
> The average time it took to execute SignedMaurerDistanceMap was 9.54250972999 seconds. 
> 
> Indeed it is strange that my code runs slower :( My executable being compiled in release mode, compiler flags are /02 and Visual studio is clearly put in release. Also, when I launch the debug version the distance map time is 114 seconds. However I'm not sure why it tools so long to compute the distance map..
> 
> Thanks
> 
> On Mon, Jul 2, 2012 at 4:07 PM, Bradley Lowekamp <blowekamp at mail.nih.gov> wrote:
> Hello Sergio,
> 
> But are you compiling your program also in release mode? The filter is not part of the ITK code in the library, because it is a templated filter, it will be compiled in your application, so that is where it matters if you are in Release or debug mode.
> 
> I wrote the following little SimpleITK python script, which uses the latest ITK 4.2rc04:
> 
> import SimpleITK as sitk
> import os
> from timeit import Timer
> 
> repeat = 10
> 
> img = sitk.Image( [512,512,110], sitk.sitkUInt8 )
> img[255,255,55 ] = 1
> 
> filter = sitk.SignedMaurerDistanceMapImageFilter()
> 
> print "Defaults:"
> print filter
> 
> t = Timer( lambda: filter.Execute( img ) )
> 
> print "The average time it took to execute", filter.GetName(), "was",  min(t.repeat( repeat=repeat,number=1 )), "seconds. "
> 
> filter.InsideIsPositiveOff()
> filter.SquaredDistanceOff()
> filter.UseImageSpacingOn();
> 
> t = Timer( lambda: filter.Execute( img ) )
> 
> print "The average time it took to execute", filter.GetName(), "was",  min(t.repeat( repeat=repeat,number=1 )), "seconds. "
> 
> t = Timer( lambda: filter.Execute( ~img ) )
> 
> print "The average time it took to execute", filter.GetName(), "was",  min(t.repeat( repeat=repeat,number=1 )), "seconds. "
> 
> Your large image didn't come attached, so I just created a trivial on to run performance. This is my results in my i7 laptop:
> 
> Defaults:
> itk::simple::SignedMaurerDistanceMapImageFilter
>   InsideIsPositive: 0
>   SquaredDistance: 1
>   UseImageSpacing: 0
> 
> The average time it took to execute SignedMaurerDistanceMap was 2.05940294266 seconds.
> The average time it took to execute SignedMaurerDistanceMap was 2.61217999458 seconds.
> The average time it took to execute SignedMaurerDistanceMap was 2.7291328907 seconds.
> 
> 
> As I was running this multiple times, I appear to be getting a variation of ~.5 seconds due to what I am assuming is the temperature of my CPU, and intel's TuboBoost.
> 
> Additionally, it's not clear which timings are using only one thread and which are using more. So I also ran the test with only one thread:
> 
> The average time it took to execute SignedMaurerDistanceMap was 8.77108097076 seconds.
> The average time it took to execute SignedMaurerDistanceMap was 9.40146708488 seconds.
> The average time it took to execute SignedMaurerDistanceMap was 9.63690400124 seconds.
> 
> I tend to agree with Bill, there is something funny about how you compiled it.
> 
> Brad
> 
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> 
> 
> -- 
> Sergio Vera
> 
>  Alma IT Systems
>  C/ Vilana, 4B, 4º 1ª
>  08022 Barcelona
>  T. (+34) 932 380 592
>  www.alma3d.com

========================================================
Bradley Lowekamp  
Medical Science and Computing for
Office of High Performance Computing and Communications
National Library of Medicine 
blowekamp at mail.nih.gov



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