[Insight-users] Noise simulation
Gaëtan Lehmann
gaetan.lehmann at jouy.inra.fr
Sat Jun 12 03:26:48 EDT 2010
I've added the code to let the user provide the minimum and maximum
value - yes, nothing but fast, but finally it's there :-)
Le 2 avr. 10 à 02:59, Kishore Mosaliganti a écrit :
> Thanks for the submission :). It was very helpful to my work.
great!
If you get a chance, please add a review on the insight journal :-)
Gaëtan
>
> Kishore
>
> On Thu, Apr 1, 2010 at 8:58 PM, Kishore Mosaliganti <kishoreraom at gmail.com
> > wrote:
> Sure, that will work well for everyone.
>
>
> Kishore
>
> 2010/4/1 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>
>
> Le 2 avr. 10 à 01:42, Kishore Mosaliganti a écrit :
>
> Hi Gaetan,
>
>
> Hi Kishore,
>
>
> I found that in the itkSaltAndPepperNoiseImageFilter, it would be
> more useful if the values m and M be computed from the minima and
> minima in the image.
>
> Currently, you are taking the pixel type maxima and minima which
> precludes the use of int or double or float pixel types in the image
> model with a narrow dynamic range of data.
>
> Does that sound reasonable ?
>
> That may not produce the expected behavior, because the maximum/
> minimum may not be the expected value. In the example image for
> example, the maximum is 200 (on purpose, to avoid saturating the
> pixel values when adding noise), but I do want a salt and pepper in
> the range [0 255].
>
> I had the same problem with the PSNR computation, where the maximum
> possible value of the pixel type should be used. To make it usable
> with pixel types which are not the ones used in the image format,
> the value used was measured as the maximum value in the image, but
> with that same example image, the value was not the expected one.
>
> In both cases, maybe the values should default to the maximum/
> minimum possible value, but be modifiable by the user with the usual
> Set/Get methods.
>
> Does it sound like reasonable option?
>
> Gaëtan
>
>
>
>
> Kishore
>
>
> 2010/4/1 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>
>
> Hi,
>
> Le 30 mars 10 à 17:40, Oleksandr Dzyubak a écrit :
>
> Hi Gaëtan,
>
> I have done my homework.
>
> 1) I studied the ITK header.
>
> InsightToolkit/Common/itkMersenneTwisterRandomVariateGenerator.h
>
> In that header the link to the inventors' web page
> www.math.keio.ac.jp/~matumoto/emt.html is dead.
> The correct and still alive one is below.
>
> http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/emt.html
>
> 2) I have also read the article by the inventors
> M. Matsumoto and T. Nishimura, "Mersenne Twister: A 623-
> dimensionally equidistributed uniform pseudorandom number
> generator", ACM Trans. on Modeling and Computer Simulation Vol. 8,
> No. 1, January pp.3-30 (1998).
>
> This classical article (along with others) can be downloaded from
> the Makoto Matsumoto's home page.
>
> http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/ARTICLES/
> earticles.html
>
> 3) From that article: "A new algorithm called Mersenne Twister
> is proposed for generating uniform pseudorandom numbers."
> Period is (2^ 19937) - 1, 632-dimensional equidistribution up to 32-
> bit accuracy.
> So the period is a such huge number
> that this generator could be considered as a "true random".
>
> Sounds good :-)
>
>
>
> 4) New debugged and updated release 2009/11/17 of the generator
> can be downloaded using link below.
>
> http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/index.html
>
>
> 5) I downloaded and tested the updated code version from the link
> you provided.
> http://mima2.jouy.inra.fr/darcs/contrib-itk/noise/
>
> a) Compiles -- fine.
> b) Works -- fantastic.
> c) Tested images are identical to those provided in the submission.
>
> Great!
>
>
>
> 6) Could you upload the revised version to the Insight Journal?
> I would be more than happy to write a review and
> recommend to add it to the ITK library.
>
>
> I just tried, but I'm still stuck at that stage http://insight-journal.com/submit/step10/59
> , as for the fftconv contrib.
> Julien, did you have a chance to look at that?
>
>
> Thanks for nice work,
>
> Thanks a lot for your very useful report and comments
>
> Gaëtan
>
>
>
> Alex
>
>
> Gaëtan Lehmann wrote:
>
> Le 29 mars 10 à 15:54, Oleksandr Dzyubak a écrit :
>
>
> Hi Gaëtan,
>
>
> Hi Alex,
>
> Whenever I try to send images using a regular email client,
> my emails get bounced. So I used the web page uploader
> from nabble.com to send the images. I hope you also got a copy.
> If not, below is the link to the images.
>
> http://old.nabble.com/Noise-simulation-to27990624.html#a28069421
>
> I'd say there is a small difference between the two images, but
> that's a random process :-)
>
>
> About median.cxx. In your submission you use it
> just as a denoiser to demonstrate that it works nice on, in
> particular, images
> with "salt-and-pepper", right?
>
> I included it to experiment a bit with PSNR calculator and
> denoising. That's really a not much useful program - I didn't event
> mentioned it in the paper!
>
>
> About the generator. How good is it? Is it random or chaotic?
> What is the cycle?
>
> I can't say at all. I simply modified the Mersenne Twister generator
> from ITK to make it thread safe.
> I actually don't have much skills in random generator.
>
>
> You say that the Gauss has been fixed.
> Is it possible the get the updated version?
>
>
> Sure! It is in the main development repository.
>
> http://mima2.jouy.inra.fr/darcs/contrib-itk/noise/
>
> I think I didn't say that you can use darcs to get it (http://www.darcs.net
> )
>
> darcs get http://mima2.jouy.inra.fr/darcs/contrib-itk/noise/
>
> Thanks,
>
> Gaëtan
>
>
> Thanks,
>
> Alex
>
> Gaëtan Lehmann wrote:
>
> Le 26 mars 10 à 16:27, Oleksandr Dzyubak a écrit :
>
> Hi Gaëtan,
>
> I downloaded the updated version from your repository that you
> provided.
> http://mima2.jouy.inra.fr/darcs/contrib-itk/noise/
>
> Below is the result of my tests.
>
> 1)
> The compilation was perfect.
>
> great :-)
>
>
> 2)
> dzyubak at helium: /Original_Images$ ./median cthead1.tif
> cthead1_median.png | grep " Number Of Threads"
>
> After Running the median program, I do see any difference
> between original and processed images.
> As I can see, in the median.cxx you just removed the neighborhood
> radius.
> What is the purpose of being that utility in the submission?
> Can't be the median.cxx just removed from the package?
>
>
> It does something here - by default, the radius is 1.
> Just try on the output of the salt and pepper filter :-)
>
> ./sp ../images/cthead1.tif sp.png
> ./median sp.png out.png
>
> it is very efficient for this kind of noise.
>
> 3)
> dzyubak at helium: /Original_Images$ ./gauss cthead1.tif
> cthead1_gauss_s22_8_m0.png 22.8 0.0 | grep " Number Of Threads"
> Number Of Threads: 16
> Global Maximum Number Of Threads: 128
> Global Default Number Of Threads: 16
>
> The image has the same seeding problem as in the previous version.
> No changes at all.
>
>
> err, yes, my fault. I forgot that this filter was not using the
> mersenne twister generator.
> It's fixed now, by using the same random generator as in the other
> filters :-)
>
> 4)
> dzyubak at helium: /Original_Images$ ./sp cthead1.tif
> cthead1_sp_001.png 0.01 | grep " Number Of Threads"
>
> Number Of Threads: 16
> Global Maximum Number Of Threads: 128
> Global Default Number Of Threads: 16
>
> Surprisingly, now cthead1_sp_001.png looks similar to that
> from your submission. The incorrect seeding problem is gone.
> Noise really looks random. However, I noticed that your image is
> "noisier".
> Did you use the same parameter "0.01" or that is still the seeding
> problem?
>
> noiser? can your provide the images?
>
>
> 5)
> The shot and spekle noise generators work fine and my images
> are identical to yours.
>
> great :-)
>
>
> 6)
> Peak signal to noise ratio. In your submission you have 20 dB. Mine
> is below.
>
> dzyubak at helium: /Original_Images$ ./psnr cthead1.tif
> cthead1_median.png
> PSNR: 37.3425 dB
>
> dzyubak at helium: /Original_Images$ ./psnr cthead1.tif
> cthead1_gauss_s22_8_m0.png
> PSNR: 20.0251 dB
>
> dzyubak at helium: /Original_Images$ ./psnr cthead1.tif
> cthead1_shot_s015.png
> PSNR: 20.0429 dB
>
> dzyubak at helium: /Original_Images$ ./psnr cthead1.tif
> cthead1_spekle_s024.png
> PSNR: 20.0901 dB
>
> dzyubak at helium: /Original_Images$ ./psnr cthead1.tif
> cthead1_sp_001.png
> PSNR: 22.4873 dB
>
> Interesting, the utility says that my salt and pepper is noisier,
> but just visual test yours is as twice noisier. Subjective judgment?
>
> PSNR is only a (not so bad) approximation of the image degradation
> as perceived by a human.
> Our brain very capable to ignore the noise, and for some case like
> the salt and pepper case, the PSNR is not very representative of our
> feeling.
>
>
> Summing up.
> 1) What is the need for median.cxx ?
> Can't be this utility just removed from the submission?
>
> 2) The seeding problem in the Gauss noise generator is still there.
>
> Regards,
>
> Alex
>
>
> Gaëtan Lehmann wrote:
>
> Le 25 mars 10 à 23:27, Gaëtan Lehmann a écrit :
>
>
> Hi Alex,
>
> I think there is a problem with multithreading and the random
> generator - more specifically, the seeds are the same in all the
> threads.
> I didn't noticed this on my macbook with only 2 cores, even when
> increasing the number of threads to a higher number than the number
> of cores, but I see the same behavior on my workstation with 16
> threads.
>
> How many threads are running in parallel on your system? The number
> is displayed while running one of the noise generator
>
> [glehmann at gbook build]$ ./shot ../images/cthead1.tif toto.png | grep
> " Number Of Threads:"
> Number Of Threads: 2
> Number Of Threads: 2
>
> You can limit the number of threads to a small number, or even to 1,
> with
>
> export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
>
> to workaround the problem.
>
> I will restore the (non thread safe) seeding behavior in
> ThreadSafeMersenneTwisterRandomVariateGenerator and make it thread
> safe with a lock so that 2 threads can't get the same seed.
>
>
> This is fixed in the main repository:
>
> http://mima2.jouy.inra.fr/darcs/contrib-itk/noise/
>
> As well as the problem you have reported in median.cxx.
> Please let me know if there is something else wrong!
>
> Gaëtan
>
>
> Thanks for the report!
>
> Gaëtan
>
>
> Le 25 mars 10 à 22:47, Oleksandr Dzyubak a écrit :
>
> Dear ITK users,
>
> Did anybody tested the noise simulation codes from the submission
> "Noise simulation" http://hdl.handle.net/10380/3158 ?
> The most needed (for me at least) noise generators
> (Gauss and salt and pepper)
> produce corrupted images with periodic line patterns
> (see attached images). To generate those images, I followed
> the parameter recommendations taken from the submission.
>
> ./gauss cthead1.tif cthead1_gauss_s22_8_m0.png 22.8 0
> ./sp cthead1.tif cthead1_sp_0016.png 0.016
>
> Did anybody get similar results?
>
> Alex
>
>
>
> Oleksandr Dzyubak wrote:
> Hi Gaëtan,
>
> Nice and long awaited work.
> I found a tiny typo in your code that prevents the submitted codes
> from
> being compiled.
> At least on my Linux box. The typo is sitting in your median.cxx and
> the
> fix is below.
>
> // Part that gives the errors.
> /*
> FilterType::RadiusType r;
> r.Fill(2);
> // filter->SetRadius(r);
> */
>
> // this fix solves the problem.
> IType::SizeType r;
> r[0] = 1;
> r[1] = 1;
> filter->SetRadius(r);
>
> Could you please add the fix and upload the code?
>
> Thanks,
> Alex
>
>
> <cthead1_gauss_s22_8_m0.png><cthead1_sp_0016.png>
>
> --
> 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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>
>
>
>
>
>
> --
> 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
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
>
>
>
> --
> 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
>
>
>
--
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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