[Insight-users] itk LevelSetsv4

Sat Dec 10 15:59:23 EST 2011

These were great, I will try to put
them together and see how it goes

Thank you,
Cagatay

On Fri, Dec 9, 2011 at 1:26 AM, Arnaud Gelas
<arnaud_gelas at hms.harvard.edu>wrote:

>  Hi Cagatay,
>
> First, I'd like to say that it makes total sense for you to make use of
> the new framework.
> One of the main goals of the new framework is to ease the combination of
> any kind of "terms", which is the case here.
>
> In your case, if I understand correctly, you'd need to combine:
>
>    - Chan and Vese internal term
>    - Chan and Vese external term
>    - Propagation term where you'd provide your own feature image
>     - and / or Advection term where you'd provide your own vector field
>    - Curvature term (optional for regularization)
>
> The two first terms and the curvature terms are present and validated
> within the new framework.
> The propagation term is present in the framework, but the validation is
> coming along and should definitively be part of the upcoming release in
> December.
> The advection term is in its way in the framework. As Matt mentioned, the
> patch is in review and still need some validation. It will also be part of
> the upcoming release in December.
>
> While waiting for the upcoming release (which will happen within few
> weeks), I invite you to combine Chan and Vese (internal and external terms)
> with the propagation term.
> It may work fine at this point. But your feedback would definitively help
> us to improve the framework and the toolkit !!
>
> To combine the terms, you can have a look at the following tests:
>
>    - 1 level set with Chan and Vese:
>     - With a dense representation:
>       ITK/Modules/Segmentation/LevelSetsv4/test/itkSingleLevelSetDenseImage2DTest.cxx
>       - With a sparse representation
>          - Whitaker's formulation:
>          ITK/Modules/Segmentation/LevelSetsv4/test/itkSingleLevelSetWhitakerImage2DTest.cxx
>          - Shi's formulation:
>          ITK/Modules/Segmentation/LevelSetsv4/test/itkSingleLevelSetShiImage2DTest.cxx
>          - Malcolm's formulation:
>          ITK/Modules/Segmentation/LevelSetsv4/test/itkSingleLevelSetMalcolmImage2DTest.cxx
>        - 1 level set with Propagation term:
>       -
>       ITK/Modules/Segmentation/LevelSetsv4/test/itkSingleLevelSetWhitakerImage2DWithPropagationTest.cxx
>
>
> In the case if you want to see the evolution of your level set through the
> iterations, you may also want to have a look at the tests in
> ITKLevelSetsv4Visualization.
>
> If you have questions, or remarks, please let us know.
>
> Thanks,
> Arnaud
>
>
>
> On 12/09/2011 02:06 AM, cagatay bilgin wrote:
>
> Thank you very much for the clarifications
> and the pointers Matt. I checked out the
> latest release a couple of hours ago and
> see a lot of changes as you pointed out.
>
>  There is a GeodesicActiveContour class in
> the (old) LevelSet directory, which makes me
> believe that it wouldn't be too hard to come up
> with the corresponding term class for the new
> LevelSet framework. It is still not clear to me
> how to accomplish this though, I am completely
> puzzled with how it was done before.
>
>  Cagatay
>
> On Thu, Dec 8, 2011 at 6:49 PM, Matt McCormick <matt.mccormick at kitware.com
> > wrote:
>
>> Hi Cagatay,
>>
>> On Thu, Dec 8, 2011 at 8:55 PM, cagatay bilgin <bilgincc at gmail.com>
>> wrote:
>> > I am trying to understand the new level set framework
>> > and willing to use it in our project. Being able to add
>> > terms to the level set function would be really helpful
>> > I think. Is this the direction that ITK will be taking ?
>>
>>  Yes, the new level sets frame takes that direction, and it is a
>> flexible and powerful approach that allows for new avenues of
>> research.
>>
>> > I see two directories LevelSets and LevelSetsv4, one
>> > having term classes and the other not having them
>> > which makes me wonder how the framework will be
>> > working. It is a little hard to find directions and documentation
>> > for me as the framework is still being developed.
>>
>>  Currently, the old levelsets framework is in the ITKLevelSets module,
>> and the new framework is in the ITKLevelSetsv4 module.  They are not
>> compatible, and the term-based framework is ITKLevelSetsv4.
>>
>> Suggestions for disambiguation of the old and new framework are welcome.
>>
>> >
>> > I am trying to build an application that implements the
>> > geodesic chan vese algorithm which uses the internal
>> > and external terms from the chan vese algorithm and
>> > would also include the gradient information from the
>> > geodesic active contours to snap to the edges better.
>>
>>  The Chan and Vese internal and external terms have been implemented.
>> An advection term is in the works:
>>
>>  http://review.source.kitware.com/#change,2914
>>
>> Arnaud may have better suggstion on how to proceed with the
>> implementation you desire.
>>
>> You may find the MICCAI tutorial useful.
>>
>>  http://midas.kitware.com/community/view/65
>>
>> There is a copy of the presentation, but also a VirtualBox virtual
>> machine containing the code and examples.
>>
>> The code has evolved since MICCAI.  Most notably, the api has been
>> greatly simplified by not requiring different component class names to
>> correspond to each type of level set datatype (dense image, Shi,
>> Whitaker, Malcolm).
>>
>> Thanks,
>> Matt
>>
>>
>> > Should I be working on the filters defined in LevelSets
>> > or in LevelSetsv4? Is there a geodesic term class
>> > defined somewhere that I can use with other terms in
>> > LevelSetsv4 directory ?
>> >
>> > Any help would be appreciated
>> >
>> > Thank you,
>> > Cagatay
>> >
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