[Insight-users] SignedMaurerDistanceMapImageFilter performance

Mon Jul 2 12:15:06 EDT 2012

Hi  Dženan and Bradley,

I use Control+F5 normally. and it's a Professional version of Visual Studio
9 (2008)

I've made a minimum test scenario to remove any possible interferences from
other libraries/dependencies. This one only links against ITK, and still
times are arrount 13-14 segs.
By the way switching to ITK 4.0 did not improve my numbers :(

cmake_minimum_required(VERSION 2.6)
project(dmap)
find_package(ITK REQUIRED)
include(${ITK_USE_FILE})
add_executable(dmap main.cxx)
target_link_libraries(dmap  ${ITK_LIBRARIES})

#include <itkTimeProbe.h>
#include <itkImage.h>
#include <itkImageFileReader.h>
#include <itkSignedMaurerDistanceMapImageFilter.h>

int main(int argc, char *argv[])
{
typedef itk::Image<unsigned char,3> ITKImg;
typedef itk::ImageFileReader<ITKImg> Reader;
Reader::Pointer reader = Reader::New();
reader->SetFileName("C:/Users/sergio.vera/Documents/MATLAB/images/CTAbdomenThr1800.mha");
reader->Update();
std::cout << "Image readed!\n ";
itk::TimeProbe timer;
timer.Start();
typedef itk::SignedMaurerDistanceMapImageFilter <ITKImg, ITKImg>
DistanceMapper;
DistanceMapper::Pointer distanceMapper = DistanceMapper::New();
distanceMapper->SetUseImageSpacing(true);
distanceMapper->SetSquaredDistance(false);
distanceMapper->SetInsideIsPositive(false);
distanceMapper->SetInput(reader->GetOutput());
distanceMapper->SetNumberOfThreads(2);
distanceMapper->Update();
 timer.Stop();
std::cout << "Time Spent: " << timer.GetMeanTime() << "\n";
  return EXIT_SUCCESS;
}

On Mon, Jul 2, 2012 at 6:02 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>wrote:

> 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
>
>
>
>

-- 
Sergio Vera

 Alma IT Systems
 C/ Vilana, 4B, 4º 1ª
 08022 Barcelona
 T. (+34) 932 380 592
 www.alma3d.com
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