[Insight-users] Generate gaussian noise image

Thu Mar 6 17:13:07 EST 2014

Good call, with threadId as a seed, it works with multiple threads.

Thank you very much.
-Laurent

On Thu, Mar 6, 2014 at 5:00 PM, Wok <wokitk at gmail.com> wrote:

> > I noticed that the gaussian filter does not call Initialize of the
> NormalVariateGenerator, but I tried to add it, and it doesn't make any
> difference.
>
> As mentioned before, the thing is you can input a seed to Initialize.
> >  void itk::Statistics::NormalVariateGenerator::Initialize ( int
>  randomSeed)
>
> If your assumption about the threads is correct, I would fix the bug
> by modifying:
> >
> https://github.com/midas-journal/midas-journal-721/blob/master/noise/itkAdditiveGaussianNoiseImageFilter.txx
>
> so that Initialize is called with threadId.
> > template <class TInputImage, class TOutputImage> void
> AdditiveGaussianNoiseImageFilter<TInputImage, TOutputImage>
> ::ThreadedGenerateData( const OutputImageRegionType
> &outputRegionForThread, int threadId)
>
> Best,
>
> Wok
>
> 2014-03-06 22:40 GMT+01:00 Laurent Chauvin <lchauvin at bwh.harvard.edu>:
> > Do you mean ask the user to input a number (always different) for each
> > thread ?
> >
> > Thank you.
> > -Laurent
> >
> >
> > On Thu, Mar 6, 2014 at 4:32 PM, Bradley Lowekamp <blowekamp at mail.nih.gov
> >
> > wrote:
> >>
> >> I haven't looked at the classes closely. But would expect these filters
> >> have a user settable seed, to make the results reproduce able, and be
> the
> >> same independent with the number of threads.
> >>
> >> The trick would be to have each thread has a random number generator
> >> object, then at the beginning of each line seed it with a combination
> of the
> >> user defined seed, and the starting index of the scan-line ( perhaps
> >> multiplied by a prime number).
> >>
> >> Hope that some help... I just have some ideas in my head about some ways
> >> to do it...
> >>
> >> Brad
> >>
> >> On Mar 6, 2014, at 4:26 PM, Laurent Chauvin <lchauvin at bwh.harvard.edu>
> >> wrote:
> >>
> >> It actually works but you have to force the filter to only use 1 thread.
> >>
> >> I think otherwise all threads got the same "random" values, which
> generate
> >> same output for all threads.
> >> My guess is the image is divided in 'lines' or 'column', each of them
> >> managed by a separated thread. If all threads have same random values,
> then
> >> the output will be patterned.
> >>
> >> If it's possible to have different random values for each threads, then
> it
> >> should be possible to run it with multiple threads.
> >> I think one possibility would be to use a timestamp as seed for the
> >> NormalVariateGenerator filter.
> >> I tried with GetTimeStamp(), but this is the same timestamp for all
> >> threads.
> >> I tried with GetNumberOfThreads(), but still the same number for all
> >> threads.
> >> I tried with GetMTime(), same.
> >> I tried with 'this', but this is the same pointer too.
> >>
> >> I'm not sure which variable could be different in each thread.
> >>
> >> Thank you.
> >> -Laurent
> >>
> >>
> >> On Thu, Mar 6, 2014 at 3:56 PM, Laurent Chauvin <
> lchauvin at bwh.harvard.edu>
> >> wrote:
> >>>
> >>> I tried to use the itkAdditiveGaussianNoiseFilter, but on the output
> >>> image I obtain, the noise seems really patterned.
> >>>
> >>> I compiled the code from the article, and run exactly the same example
> >>> with same parameters and I don't have the same results as on the
> article.
> >>> As I mentionned, the noise I obtain seems really patterned.
> >>>
> >>> I enclosed the picture I obtain after running the 'gauss' example with
> >>> the same parameters as the article.
> >>>
> >>> Is it possible that the 'NormalVariateGenerator' used in the
> >>> AdditiveGaussianNoiseFilter changed since the article has been written
> ?
> >>> I noticed that the gaussian filter does not call Initialize of the
> >>> NormalVariateGenerator, but I tried to add it, and it doesn't make any
> >>> difference.
> >>>
> >>> Thank you.
> >>> -Laurent
> >>>
> >>>
> >>> On Thu, Mar 6, 2014 at 1:19 PM, Laurent Chauvin
> >>> <lchauvin at bwh.harvard.edu> wrote:
> >>>>
> >>>> I didn't look in the article for now.
> >>>>
> >>>> I was first trying to compile the code. There is a minor modification
> to
> >>>> do to be compatible with ITKv4, but otherwise it's pretty straight
> forward.
> >>>> So far I only tested itkAdditiveGaussianNoiseFilter.
> >>>>
> >>>> Thank you.
> >>>> -Laurent
> >>>>
> >>>>
> >>>> On Thu, Mar 6, 2014 at 1:11 PM, Bradley Lowekamp
> >>>> <blowekamp at mail.nih.gov> wrote:
> >>>>>
> >>>>> It would be great if you could to a brief review of the IJ article to
> >>>>> facilitate integrating it into ITK.
> >>>>>
> >>>>> Brad
> >>>>>
> >>>>> On Mar 6, 2014, at 12:17 PM, Laurent Chauvin <
> lchauvin at bwh.harvard.edu>
> >>>>> wrote:
> >>>>>
> >>>>> Thank you Bradley.
> >>>>>
> >>>>> Indeed I saw this article, but as it is from 2010, I thought maybe
> now
> >>>>> it would have been integrated into ITK.
> >>>>> I will look into that.
> >>>>>
> >>>>> Thank you.
> >>>>> -Laurent
> >>>>>
> >>>>>
> >>>>> On Thu, Mar 6, 2014 at 11:59 AM, Bradley Lowekamp
> >>>>> <blowekamp at mail.nih.gov> wrote:
> >>>>>>
> >>>>>> Have a look at this insight journal article:
> >>>>>>
> >>>>>> http://www.insight-journal.org/browse/publication/721
> >>>>>>
> >>>>>> I would also find this quite useful, and have been thinking about
> >>>>>> adding it to ITK.
> >>>>>> Brad
> >>>>>> On Mar 6, 2014, at 11:55 AM, Laurent Chauvin
> >>>>>> <lchauvin at bwh.harvard.edu> wrote:
> >>>>>>
> >>>>>> Hello,
> >>>>>>
> >>>>>> I'm trying to develop a filter, but in order to test it, I need to
> add
> >>>>>> some gaussian noise to my image.
> >>>>>> I looked for it but I couldn't find a ITK filter to generate noise.
> >>>>>>
> >>>>>> Is there a way to do this ?
> >>>>>>
> >>>>>> Thank you very much.
> >>>>>> -Laurent
> >>>>>>
> >>>>>> --
> >>>>>> Laurent Chauvin, MS
> >>>>>> Surgical Navigation and Robotics Laboratory, Radiology Department
> >>>>>> Brigham And Women's Hospital, Harvard Medical School
> >>>>>> http://wiki.ncigt.org/index.php/User:Lchauvin
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> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> Laurent Chauvin, MS
> >>>>> Surgical Navigation and Robotics Laboratory, Radiology Department
> >>>>> Brigham And Women's Hospital, Harvard Medical School
> >>>>> http://wiki.ncigt.org/index.php/User:Lchauvin
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Laurent Chauvin, MS
> >>>> Surgical Navigation and Robotics Laboratory, Radiology Department
> >>>> Brigham And Women's Hospital, Harvard Medical School
> >>>> http://wiki.ncigt.org/index.php/User:Lchauvin
> >>>
> >>>
> >>>
> >>>
> >>> --
> >>> Laurent Chauvin, MS
> >>> Surgical Navigation and Robotics Laboratory, Radiology Department
> >>> Brigham And Women's Hospital, Harvard Medical School
> >>> http://wiki.ncigt.org/index.php/User:Lchauvin
> >>
> >>
> >>
> >>
> >> --
> >> Laurent Chauvin, MS
> >> Surgical Navigation and Robotics Laboratory, Radiology Department
> >> Brigham And Women's Hospital, Harvard Medical School
> >> http://wiki.ncigt.org/index.php/User:Lchauvin
> >>
> >>
> >
> >
> >
> > --
> > Laurent Chauvin, MS
> > Surgical Navigation and Robotics Laboratory, Radiology Department
> > Brigham And Women's Hospital, Harvard Medical School
> > http://wiki.ncigt.org/index.php/User:Lchauvin
> >
> > _____________________________________
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> >
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> >
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> >
>

-- 
Laurent Chauvin, MS
Surgical Navigation and Robotics Laboratory, Radiology Department
Brigham And Women's Hospital, Harvard Medical School
http://wiki.ncigt.org/index.php/User:Lchauvin
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