Jim,
I have not looked into the overhead of the pipeline..before. And this has not
been a major concern of mine for SimpleITK.
There part that does concern me is the needless overhead that in introduced by
SimpleITK itself. The overhead I am talking about here is the needless
reconstruction of the member function factory each time a SimpleITK filter is
created [1]. In the filters constructor a new factory is created and all the
instantiated functions are registered into the factory. This is really
pointless work and should not be done.
Ok, as I am writing this is has peaked my interest! So I just wrote a python
script which is attached. I created a 1x1 image and ran the
sitk::CastImageFilter. This one was chosen because it has by far the most
number of functions registered and is a more complicated I also ran the Square
filters. With a 1x1 sized image almost all of the work should be overhead and
not image processing. And these are my results:
$ ~/temp/sitkOverhead.py
With SITK function factory creation we are able to execute the cast filter
2145.70611073 per second.
With no SITK function factory creation we are able to execute the cast filter
4448.20061903 per second.
With SITK function factory creation we are able to execute the square filter
4135.92337362 per second.
With no SITK function factory creation we are able to execute the square filter
4579.52943668 per second.
And then for fun
$ export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
$ ~/temp/sitkOverhead.py
With SITK function factory creation we are able to execute the cast filter
3366.01247918 per second.
With no SITK function factory creation we are able to execute the cast filter
16825.8089362 per second.
With SITK function factory creation we are able to execute the square filter
13411.8373109 per second.
With no SITK function factory creation we are able to execute the square filter
15961.5489267 per second.
I ran this on my i7 laptop which defaults to 8 threads.
So to answer your questions:
No, I don't think there is significant overhead by the pipeline's update
sequence.
Up to 87% of the overhead execution time of the sitk::Cast is spent creating
the function factory and the creation threads.
Up to 70% of the overhead execution time is spent in the creation of threads.
Brad
[1]
https://github.com/SimpleITK/SimpleITK/blob/master/Code/BasicFilters/src/sitkCastImageFilter.cxx#L36
#! /usr/bin/env python
#
# This test script is designed to examine the amount of overhead in
# calling filters through SimpleITK. For additional analysis the
# enviromental variable "ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS" can be
# set to look at the overhead of threading.
#
import SimpleITK as sitk
from timeit import Timer
img = sitk.Image( 1, 1, sitk.sitkFloat32 )
repeat = 40
number = 2000
t = Timer( lambda: sitk.Cast( img, sitk.sitkUInt32 ) )
ffPerSec = number/min( t.repeat( repeat = repeat, number = number ) )
print "With SITK function factory creation we are able to execute the cast filter", ffPerSec, "per second."
cast = sitk.CastImageFilter()
cast.SetOutputPixelType( sitk.sitkUInt32 )
t = Timer( lambda: cast.Execute( img ) )
nffPerSec = number/min( t.repeat( repeat = repeat, number = number ) )
print "With no SITK function factory creation we are able to execute the cast filter", nffPerSec, "per second."
t = Timer( lambda: sitk.Square( img ) )
ffPerSec = number/min( t.repeat( repeat = repeat, number = number ) )
print "With SITK function factory creation we are able to execute the square filter", ffPerSec, "per second."
square = sitk.CastImageFilter()
t = Timer( lambda: square.Execute( img ) )
nffPerSec = number/min( t.repeat( repeat = repeat, number = number ) )
print "With no SITK function factory creation we are able to execute the square filter", nffPerSec, "per second."
On Oct 25, 2012, at 9:52 AM, "Miller, James V (GE Global Research)"
<[email protected]> wrote:
> Hey Brad,
>
> After the meeting on Monday, I starting wondering whether SimpleITK sees any
> appreciable overhead from the pipeline when Update() is called given each
> pipeline is only one filter long.
>
> Have you measured how much time SimpleITK spends chaining through the
> interpretative layer verses calling update verses actually running the
> filter? Would it make sense to add something to ITK to shortcut some of the
> pipeline checks?
>
> I wouldn't expect much overhead but I thought I would ask whether you had
> looked at it.
>
> Jim
>
> Jim Miller
> Senior Scientist
> GE Research
> Interventional and Therapy
>
> GE imagination at work
>
>
>
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