[Insight-users] erosion performance for binary images
Richard Beare
richard.beare at gmail.com
Mon Jun 8 19:43:57 EDT 2009
Hi,
Sorry about that - I still have work to do so I haven't put the latest
version on IJ.
Note that this is still using general purpose parabolic erode and
dilate. I anticipate further improvements when a fully customized
distance transform version is completed.
Also note that it should give you as an exact a sphere as possible,
even if voxels aren't isotropic.
On Mon, Jun 8, 2009 at 11:29 PM, <M.Staring at lumc.nl> wrote:
> Hi Richard,
>
> I just found your multi-threaded version of the parabolic morphology package
> (the IJ version was not your latest version):
>
> Box radius: 1
> Elapsed time parabolic (multi-threaded): 1.469s.
> Box radius: 2
> Elapsed time parabolic (multi-threaded): 1.313s.
> Box radius: 4
> Elapsed time parabolic (multi-threaded): 1.328s.
> Box radius: 8
> Elapsed time parabolic (multi-threaded): 1.375s.
> Box radius: 16
> Elapsed time parabolic (multi-threaded): 1.375s.
> Box radius: 32
> Elapsed time parabolic (multi-threaded): 1.515s.
> on my quad-core machine.
>
> I guess I can stop looking around for the fastest binary erosion filter :-)
>
> Great work,
>
> Marius
>
> ________________________________
> From: insight-users-bounces at itk.org [mailto:insight-users-bounces at itk.org]
> On Behalf Of M.Staring at lumc.nl
> Sent: Monday, June 08, 2009 12:46 PM
> To: gaetan.lehmann at jouy.inra.fr
> Cc: insight-users at itk.org
> Subject: Re: [Insight-users] erosion performance for binary images
>
> Hi Gaetan and Richard,
>
> I can confirm the performance dependence on pixel type (compare box.us.txt
> with box.uc.txt for unsigned short and char). For my problem it's ok to use
> unsigned char (and also to use a box structure element).
>
> Thank you guys for sharing your implementations of the binary contour +
> iterative filter and the parabolic morphology code. I added both of them to
> my little test program, see erosion2.zip. On my pc (WinXP, SP3, 32 bit,
> Intel Core 2 Quad Q6600 @ 2.4 GHz, 4 GB RAM) I get the following numbers:
>
> Box radius: 1
> Elapsed time erosion VHGW (multi-threaded): 14.719s.
> Elapsed time contour iterative (multi-threaded): 0.688s.
> Elapsed time parabolic (single-threaded): 5.094s.
> Box radius: 2
> Elapsed time erosion VHGW (multi-threaded): 19.235s.
> Elapsed time contour iterative (multi-threaded): 1.297s.
> Elapsed time parabolic (single-threaded): 5.094s.
> Box radius: 4
> Elapsed time erosion VHGW (multi-threaded): 14.968s.
> Elapsed time contour iterative (multi-threaded): 2.61s.
> Elapsed time parabolic (single-threaded): 5.141s.
> Box radius: 8
> Elapsed time erosion VHGW (multi-threaded): 36.89s.
> Elapsed time contour iterative (multi-threaded): 5.125s.
> Elapsed time parabolic (single-threaded): 5.188s.
> Box radius: 16
> Elapsed time erosion VHGW (multi-threaded): 20.328s.
> Elapsed time contour iterative (multi-threaded): 10.188s.
> Elapsed time parabolic (single-threaded): 5.312s.
> Box radius: 32
> Elapsed time erosion VHGW (multi-threaded): 30.391s.
> Elapsed time contour iterative (multi-threaded): 19.953s.
> Elapsed time parabolic (single-threaded): 5.765s.
>
> So, erosion based on the binary contours is very fast and the fastest up
> till a radius of 8. After that the parabolic morphology algorithm takes over
> with a very constant run time of about 5s!
>
> Richard, for the parabolic morphology algorithm I had to set:
>
> parabolic->SetScale( radii[ i ]*radii[ i ]/2 + 1 );
>
> to get identical results compared with my baseline algorithm (BinaryErode),
> instead of simply setting parabolic->SetScale( radii[ i ] ), like with the
> other filters. Does this make sense to you?
>
> Thanks again for all your feedback and sharing of this code!
>
> Regards,
>
> Marius
>
> ________________________________
> From: Gaëtan Lehmann [mailto:gaetan.lehmann at jouy.inra.fr]
> Sent: Sunday, June 07, 2009 8:50 PM
> To: Staring, M. (LKEB)
> Cc: insight-users at itk.org
> Subject: Re: [Insight-users] erosion performance for binary images
>
>
> Hi Marius,
>
> I was a bit surprised by the bad results with the anchor morphology -
> it seems to be caused by the pixel type used. Using unsigned char
> instead of unsigned short give those results for me:
>
> [glehmann at gbook src]$ ./test ../post_zoom_mask.mhd
> Box radius: 1
> Elapsed time erosion_binary: 8.67705s.
> Elapsed time erosion VHGW: 17.9855s.
> Elapsed time erosion Anchor: 26.9067s.
> Box radius: 2
> Elapsed time erosion_binary: 9.60058s.
> Elapsed time erosion VHGW: 19.3998s.
> Elapsed time erosion Anchor: 27.9886s.
> Box radius: 4
> Elapsed time erosion_binary: 12.2166s.
> Elapsed time erosion VHGW: 20.6566s.
> Elapsed time erosion Anchor: 28.6419s.
> Box radius: 8
> Elapsed time erosion_binary: 20.2531s.
> Elapsed time erosion VHGW: 20.6925s.
> Elapsed time erosion Anchor: 30.2072s.
> Box radius: 16
> Elapsed time erosion_binary: 50.8547s.
> Elapsed time erosion VHGW: 22.6839s.
> Elapsed time erosion Anchor: 31.6612s.
> Box radius: 32
> Elapsed time erosion_binary: 156.725s.
> Elapsed time erosion VHGW: 27.783s.
> Elapsed time erosion Anchor: 36.0459s.
>
> I guess we have to investigate what can do that…
>
> I've also implemented an erosion based on BinaryContourImageFilter.
> The contour filter is applied several times to get the same results as
> above. You can get the code at
>
> http://voxel.jouy.inra.fr/darcs/contrib-itk/fof/iterative.cxx
> http://voxel.jouy.inra.fr/darcs/contrib-itk/fof/itkIterativeImageFilter.h
> http://voxel.jouy.inra.fr/darcs/contrib-itk/fof/itkIterativeImageFilter.txx
>
> Here are the execution times for the same box sizes as above:
>
> 0.988033
> 1.69216
> 3.10681
> 6.00902
> 12.9424
> 27.6227
>
> That implementation is faster than all the other filters, up to a
> radius of 32 :-)
> It is much limited also, because it works only with binary images, and
> the same size on all the dimensions of the radius.
>
> All the measures where made on a macbook air with a core 2 duo at 1.8
> GHz, gcc 4.0.1, ITK 3.14, and built in Release mode.
>
> More input to come with separable implementations :-)
>
> Thanks for your feedbacks!
>
> Gaëtan
>
>
>
>
>
> Le 5 juin 09 à 18:46, <M.Staring at lumc.nl> <M.Staring at lumc.nl> a écrit :
>
>> Hi Dan and Gaetan,
>>
>> First of all: thanks for your feedback.
>>
>> I forgot about the importance of the specific choice of the kernel.
>> That makes sense of course. In my test code I used the line
>>
>> erosionFilter->SetRadius( radii[ i ] );
>>
>> and assumed it would be give a ball. Now I use:
>>
>> erosionFilter-
>> >SetKernel( itk::FlatStructuringElement<Dimension>::Box( radius ) );
>> or
>> erosionFilter-
>> >SetKernel( itk::FlatStructuringElement<Dimension>::Ball( radius ) );
>>
>> Then the VHGW filter indeed did not run for the Ball, because it is
>> not decomposable.
>>
>> The new performance results for ball and box are in the attachments.
>> For the box the binary erode still seems to be faster up till a
>> radius of 8, after which the VHGW takes over. The latter is not
>> constant for increasing radius though.
>>
>> I added the source code in the zip, so you can reproduce the
>> results. You can also find the binary image on which I did the test
>> in the zip.
>>
>> From: Gaëtan Lehmann [mailto:gaetan.lehmann at jouy.inra.fr]
>> The algorithm used in BinaryErodeImageFilter can't be easily
>> constrained to a zone, and so it is difficult to multithread it.
>> If you want to perform an erosion with a radius of 1 (on all the
>> dimension), BinaryContourImageFilter followed by a SubtractImageFilter
>> would be a lot faster (really) especially on a multicore system, as
>> they are both multithreaded. Some timings are available in section 3
>> of http://insight-journal.com/download/viewpdf/217/2
>>
>> I just assumed it would be, since there were multi-threaded versions
>> for grayscale images. But it's an entirely different algorithm I
>> guess.
>> Regards,
>> Marius
>> <erosion.zip><ball.txt><box.txt>
>
> --
> Gaëtan Lehmann
> Biologie du Développement et de la Reproduction
> INRA de Jouy-en-Josas (France)
> tel: +33 1 34 65 29 66 fax: 01 34 65 29 09
> http://voxel.jouy.inra.fr http://www.itk.org
> http://www.mandriva.org http://www.bepo.fr
>
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