[Insight-users] Gradient anisotropic filter time step?
Luis Ibanez
luis.ibanez at kitware.com
Wed Feb 17 18:24:31 EST 2010
Hi Natarajan,
Thanks for letting us know of your experiments.
I would be curious to see if the images that you used
as input had enough high contrast edges and thin spatial
features that would make visible the artifact that we are
concerned about.
Being pragmatic, you should be able to obtain a similar
degree of smoothing by running the filter with the smaller
time-step that is currently defined in ITK, and double the
number of iterations.
The limit in the time-step is the one at which the conditions
of stability break down. Playing in that borderline may not
be a good way of using the code.
BTW:Thanks for posting the link to the report.
Regards,
Luis
----------------------------------------------------------------------------------
On Tue, Feb 16, 2010 at 11:14 PM, Natarajan CS <csnataraj at gmail.com> wrote:
> 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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