[Insight-users] Gradient anisotropic filter time step?
Natarajan CS
csnataraj at gmail.com
Tue Feb 16 23:14:40 EST 2010
Hello Luis,
just an update on the time step question. For my data I don't see any
undesirable side effects like what you described. I also tested
corresponding values for a 2D image, same thing! It seems that <=
1/2^dimension should work! However, this comes with the caveat that image
analysis is not my expertise!! It would be nice to get a affirmation from a
more reliable source!
Nonetheless, I really appreciate you guys making ITK open source and being
great with answering questions!
Cheers,
C.S.N
On Mon, Feb 15, 2010 at 5:01 PM, Natarajan CS <csnataraj at gmail.com> wrote:
> Hi Luis,
> sure, sounds like a good plan. I am heading out right now, but
> hopefully I should be able to get it done by tomorrow! I will try with time
> steps at 1/2^N, 1/2^(N+1), and 1.5/2^N and send out another e-mail.
>
> Cheers,
>
> C.S.N
>
> P.S :- Just in case anyone is interested, the paper is available as a tech
> report from Berkeley
>
> http://digitalassets.lib.berkeley.edu/techreports/ucb/text/CSD-88-483.pdf
>
>
> On Mon, Feb 15, 2010 at 3:58 PM, Luis Ibanez <luis.ibanez at kitware.com>wrote:
>
>> Hi Natarajan,
>>
>> You are right, the code is actually testing for
>>
>> 1/2^(N+1)
>>
>> not for
>>
>> 1/2^(N)
>>
>> as I incorrectly wrote in my email.
>>
>>
>> This filter is intended to be the implementation of
>> the Perona-Malik method, as described in:
>>
>> * Pietro Perona and Jalhandra Malik, ``Scale-space and edge detection
>> using
>> * anisotropic diffusion,'' IEEE Transactions on Pattern Analysis Machine
>> * Intelligence, vol. 12, pp. 629-639, 1990.
>>
>>
>> I don't have at hand the Perona Malik paper,
>> so let's do this:
>>
>>
>> Could you please modify the code locally in your ITK code,
>> and run it with a couple of cases, using a timestep that is
>> in the range:
>>
>> 1/2^(N+1) < t < 1/2^(N)
>>
>> and let us know if the output looks correct ?
>>
>> ---
>>
>> Typically when you use a timestep that is too large, you
>> will see intensity artifacts that look like rhomboids in the
>> borders of the objects in the image.
>>
>>
>> Please let us know what you find,
>>
>>
>> Thanks
>>
>>
>> Luis
>>
>>
>>
>> ---------------------------------------------------------------------------
>> On Mon, Feb 15, 2010 at 3:34 PM, Natarajan CS <csnataraj at gmail.com>
>> wrote:
>> > Hi Luis,
>> > thanks for the quick reply. Nope, I do not believe I have enabled
>> this
>> > flag. I am confused, I did take a look at the code snippet you suggested
>> and
>> > figured that time step is <= 1/2^(N+1) not 1/2^N (Judging from line 75
>> > and/through 81). In reality I believe this has to be 1/2^N as you
>> suggested,
>> > at least if the implementation is same as Perona and Malik..
>> >
>> > just in case my metadata looks as follows :
>> >
>> > NDims = 3
>> > DimSize = 256 256 256
>> > ElementType = MET_SHORT
>> > ElementDataFile = raw256.raw
>> >
>> >
>> > Again, thanks for the help!
>> >
>> > Cheers,
>> >
>> > C.S.N
>> >
>> >
>> >
>> > On Mon, Feb 15, 2010 at 2:00 PM, Luis Ibanez <luis.ibanez at kitware.com>
>> > wrote:
>> >>
>> >> Hi Natarajan,
>> >>
>> >>
>> >>
>> >> "Glimpsing at the Source, leaves no doubt"
>> >>
>> >>
>> >> This is what the file:
>> >>
>> >>
>> Insight/Code/BasicFilters/itkAnisotropicDiffusionImageFilter.txx
>> >>
>> >> has in lines 75-82:
>> >>
>> >>
>> >> if ( m_TimeStep > (minSpacing / vcl_pow(2.0,
>> >> static_cast<double>(ImageDimension) + 1)) )
>> >> {
>> >> // f->SetTimeStep(1.0 / vcl_pow(2.0,
>> >> static_cast<double>(ImageDimension)));
>> >> itkWarningMacro( << "Anisotropic diffusion unstable time step: "
>> >> << m_TimeStep << std::endl
>> >> << "Stable time step for this image must be smaller
>> >> than "
>> >> << minSpacing / vcl_pow(2.0,
>> >> static_cast<double>(ImageDimension+1)));
>> >> }
>> >>
>> >>
>> >> In summary:
>> >>
>> >> Timestep < pixelSpacing / ( 2^N )
>> >>
>> >> where N is the image dimension (e.g. 3 for 3D images, and 2 for 2D
>> >> images).
>> >>
>> >>
>> >>
>> >>
>> >> Did you enable the flag:
>> >>
>> >> UseImageSpacing ?
>> >>
>> >> If so, what is the pixel spacing of your image ?
>> >>
>> >>
>> >> Regards,
>> >>
>> >>
>> >>
>> >> Luis
>> >>
>> >>
>> >> -------------------------------------------
>> >> On Mon, Feb 15, 2010 at 12:27 PM, Natarajan CS <csnataraj at gmail.com>
>> >> wrote:
>> >> > Hello all,
>> >> > Not sure if this is a bug or a implementation detail I am
>> >> > overlooking,
>> >> > I am tending towards the latter, so any info would be helpful !
>> >> > I get the following warning from the
>> >> > GradientAnisotropicDiffusionImageFilter (The filter is being applied
>> to
>> >> > a
>> >> > 256^3 dataset of type short)
>> >> >
>> >> > WARNING: In
>> >> >
>> >> >
>> /hpc/soft/natac0/itk/include/InsightToolkit/BasicFilters/itkAnisotropicDiffusionImageFilter.txx,
>> >> > line 78
>> >> > GradientAnisotropicDiffusionImageFilter (0xbc4120): Anisotropic
>> >> > diffusion
>> >> > unstable time step: 0.07
>> >> > Stable time step for this image must be smaller than 0.0625
>> >> >
>> >> > i was under the impression that the ITK implimentation was a explicit
>> >> > method
>> >> > with the time step requirement for 3D images is <= 1/8 and <= 1/4 for
>> >> > 2D. Am
>> >> > i completely off-track here?
>> >> >
>> >> > Appreciate any help!
>> >> >
>> >> > Thanks,
>> >> >
>> >> > C.S.N
>> >> >
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