[Insight-users] Noise simulation
Gaëtan Lehmann
gaetan.lehmann at jouy.inra.fr
Mon Mar 29 17:41:45 EDT 2010
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
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