[Insight-users] Noise simulation

Fri Apr 2 14:39:47 EDT 2010

Hi Gaëtan,

I downloaded and tested the revised version from the insight-journal web 
page.

http://www.insight-journal.org/browse/publication/721

It works perfect! Thanks!
I have already written and uploaded my review
with recommendation to include it into the ITK lib.

Regards,

Alex

Gaëtan Lehmann wrote:
>
> 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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>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>