[Insight-users] Chan & Vese Level Set Segmentation

Wed Feb 24 17:33:59 EST 2010

Hi Amy,

Thanks a lot for pointing these errors, and for all your suggestions to improve this code!

>>> -        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)
>>>        
/** Evaluate the derivative at the specified input position */
virtual OutputType EvaluateDerivative( const InputType&  input ) const
{
   const RealType t = ( input * this->GetOneOverEpsilon() );
   return static_cast<  OutputType>( vnl_math::one_over_pi / (1.0 + t *  t ) );
}

>>> >>>  itkRegionBasedLevelSetFunction.txx - in ComputeGlobalTerm:
>>>        
ok! Done
http://public.kitware.com/cgi-bin/viewcvs.cgi/Code/Review/itkRegionBasedLevelSetFunction.txx?root=Insight&r1=1.28&r2=1.29
>>> >>>  itkMultiphaseDenseFiniteDifferenceImageFilter
>>>        
ok! Done
I have also added accessors to m_ReinitializeCounter (Set/Get).
http://public.kitware.com/cgi-bin/viewcvs.cgi/Code/Review/itkMultiphaseDenseFiniteDifferenceImageFilter.h?root=Insight&r1=1.4&r2=1.5

>>> >>>  possibly want to make ComputeHessian virtual in
>>> >>>  itkRegionBasedLevelSetFunction.h
>>>        
ok! Done (Kishore is about to commit it)
It should appear pretty soon on the dashboard

Thanks,
Cheers

Arnaud

On 2/23/2010 5:53 PM, Kishore Mosaliganti wrote:
> 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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>>>        
>> _____________________________________
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>>
>> Visit other Kitware open-source projects at
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>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.html
>>
>> Please keep messages on-topic and check the ITK FAQ at:
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>>      
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>
> Visit other Kitware open-source projects at
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>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
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