[Insight-users] Chan & Vese Level Set Segmentation

[Luis Ibanez]

  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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