[Insight-users] Chan & Vese Level Set Segmentation

[Kishore Mosaliganti]

Hi Amy and Luis,

Thank you very much for reviewing the code and providing the feedback.
This will certainly improve the code quality.

I think the corrections can happen in the Code/Review quite easily. We
will look into the details of each issue and verify the problem before
correcting it.


Kishore

On Tue, Feb 23, 2010 at 5:14 PM, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>  Amy,
>
> Thanks a lot for contributing these comments.
>
> That's a great example of community building.
>
> --
>
> Arnaud, Kishore:
>
> Do you think what we should make some of these
> changes to the code in Insight/Code/Review ?
>
> Or should we add comments to the documentation
> of the classes ?
>
>
>    Thanks for any advice,
>
>
>             Luis
>
>
>
> -----------------------------------------
> On Tue, Feb 23, 2010 at 4:34 AM, Amy C <mathematical.coffee at gmail.com> wrote:
>> Hi,
>>
>> For a while I've been using the Chan & Vese level set segmentation classes
>> from http://www.insight-journal.org/browse/publication/322 and
>> http://www.insight-journal.org/browse/publication/323. (kudos to the
>> authors!)
>> For anyone planning to use this code in the future, here are some bugs I
>> noticed (I didn't really look at the sparse implementation, this is for the
>> function/dense filter code only):
>>
>> -        itkAtanRegularizedHeavisideStepFunction.h - in CalculateDerivative:
>> derivative should be 1/pi*1/epsilon*1/(1+(x/epsilon)^2), not
>> 1/pi*1/(1+(x/epsilon)^2)   (most people use epsilon==1 so there may be no
>> noticable difference)
>>
>> -        itkRegionBasedLevelSetFunction.txx - in ComputeGlobalTerm: in the
>> part that calculates the overlap term of the update, there's a call to
>> ComputeOverlapParameters which is only calculated when the overlap penalty
>> weight is non-zero. However ComputeOverlapParameters also calculates an
>> extra value called 'product' in the code, which holds product_{ i != current
>> function id } (1-Heaviside(level set i)). This term is required to calculate
>> the background term of the update (u_0 - backgroundAverage)^2*product. This
>> means that if the overlap penalty isn't 0 the background intensity term is
>> calculated correctly, but if the overlap penalty is 0, then '1' is used for
>> 'product' instead of product_{ i != current function id } (1-Heaviside(level
>> set i)). Should be modified so that product is calculated regardless of the
>> overlap penalty.
>>
>> -        itkMultiphaseDenseFiniteDifferenceImageFilter - in ApplyUpdate: has
>> a variable m_ReinitializeCounter that is meant to reinitalise the level set
>> function to a signed distance function every m_ReinitalizeCounter
>> iterations. However at the moment if the filter doesn't reinitalize the
>> level set function, it won't update it either. (It should update every
>> iteration, reinitalize every m_ReinitializeCounter iterations instead of
>> only update & reinitalize every m_ReinitializeCounter iterations, and do
>> nothing on the other iterations). At the moment users won't notice a
>> difference because you can't set m_ReinitializeCounter with public access.
>>
>> -        itkMultiphaseDenseFiniteDifferenceImageFilter - in
>> CopyInputToOutput - at the moment calling GetOutput() on the dense level set
>> filter will return the segmentation given by the highest-index level set
>> function. It should really give the segmentation given by all level sets -
>> according to the sparse filter, GetOutput() should return an image that is
>> default 0, and takes the value i where the i'th level set indicates this
>> region is foreground (value < 0). In the case of overlap the highest index
>> wins. Just need to initialise the output with FillBuffer(0) and remove the
>> 'else' clause from 'if (in.Get() < 0)'
>>
>> - possibly want to make ComputeHessian virtual in
>> itkRegionBasedLevelSetFunction.h so that subclasses could override it
>> (debatable, not really a bug)
>>
>> If unwilling to change the original files you could create a subclass and
>> override the respective functions with the fixes.
>>
>> cheers,
>> Amy
>>
>>
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