[Insight-developers] simplex mesh topological operators

Wed Aug 18 10:38:30 EDT 2010

Hi Alex,

depends how much of the implementation that I have to do and what
timeline you have in mind. I am on a tight schedule to produce
neurosurgery simulation results by end of December (for a NIH year-end
report on which year 2 funding hinges), which includes surface and tet
meshing, and integration with Total Lagrangian Explicit Dynamics
biomechanics, as well as get some haptic results with a 6 and 7 dof
device that will be delivered shortly. This is on year 1 of a 2-year
phase 1 budget. I would have more resources to allocate to this in
year 2 of my phase 1, which will start in March next year, assuming
the funding is renewed (but by then you are likely to have much of it
implemented, I assume).

[As for the tetrahedralization, I have a good rapport with Nikos
Chrisochoides, and in any event, I have some source by Alexander Fuchs
that produces tets with very good edge length control that I can use.
]

Do you plan on getting a start right away, or do this over the course of V4?

Best wishes,

Michel

On Wed, Aug 18, 2010 at 1:11 AM, Alexandre GOUAILLARD
<agouaillard at gmail.com> wrote:
> hi michel,
>
> in the original article, we were speaking about replacing the simplex
> implementation with QE as we wouldn't need the triangular2simplex and
> simplex2triangular and half of the currently needed filters.
>
> We never found motivation AND time to do it (we had either but not both :) )
>
> If you were willing to join the effort, and if bill or luis would be
> ok to kindly supervise/review our design along the way. I'm ok to do
> it (all design and most implementation).
>
> Here would be the proposed schedule:
>
> = core modifications =
> - implement a QE container and modify QE allocation / free mechanism (1~2 week)
> - implement a Reserve function that reserves all the containers
> (cells, edgecells, QE). Fix the current getContainer()->Reserve() bug
> found by Michel A. (1 week)
> - throw exception when non-2-manifold (2 days)
> - handle non-2-manifold to 2-manifold in some specific cases (enough
> to cover Dan M. filter) ( one week )
>
> = Simplex Meshes =
> - implement a simplex/triangular Mesh data structure ( 1~2 week )
> - recode simplex mesh (with segmentation filters) ( 1~2 weeks )
> - code 2 "functions" for T1 and T2 operators ( 1 week )
> - code the final algorithm ( ? )
>
> For tetrahedral meshing, you might want to involve vincent magnotta at
> least. He is working on very similar topic for v4, and you might want
> to tag along to be sure that eventually you'll be compatible. He is
> mister 3-manifolds, I am mister 2-manifold :-)
>
> what do you guys say?
>
> alex.
>
>
>
> On Wed, Aug 18, 2010 at 1:04 AM, Michel Audette
> <michel.audette at kitware.com> wrote:
>> Hi again,
>>
>> It does have to work properly, otherwise, I could see the topology not
>> being preserved, and introducing holes in the surface would make the
>> subsequent tetrahedralization impossible. As to the time factor,
>> depends how much time you mean. I can get by with my old code in the
>> near term (a few weeks or even months), but it would be great to
>> integrate everything under ITK ultimately.
>>
>> Would you be adding to the Quad Edge Mesh, or to the Simplex Mesh?
>> Because the balloon force, the image attraction force and the
>> regularization of the simplex model are also important to this
>> exercise.
>>
>> If you endow ITK with something like that, it has tremendous
>> implications for surface meshing, and ultimately tetrahedral meshing
>> as well. Makes ITK extremely relevant to soft-tissue motion
>> estimation, as is often needed in surgical guidance. IGSTK and SLICER
>> would benefit greatly.
>>
>> Cheers,
>>
>> Michel
>>
>>
>>
>> On Tue, Aug 17, 2010 at 12:56 PM, Alexandre GOUAILLARD
>> <agouaillard at gmail.com> wrote:
>>> yes, I think we have a shot.
>>> let me get more familiar with those two operators, and we can come up
>>> with a design quickly I think.
>>>
>>> We do you actually ned it, do we have time to make it right, or do we
>>> need to have something working quickly first and then try to make it
>>> right?
>>>
>>> alex.
>>>
>>>
>>> On Wed, Aug 18, 2010 at 12:32 AM, Michel Audette
>>> <michel.audette at kitware.com> wrote:
>>>> Hi Alex,
>>>>
>>>> the algorithm that I have in mind is my adaptation of Herve
>>>> Delingette's simplex mesh, where I use T1 and T2 operators to delete
>>>> specific edges in order to explicitly control surface mesh resolution
>>>> (prior to controlled-resolution tetrahedralization).
>>>>
>>>> The operators are on page 119 of Herve's IJCV paper General Object
>>>> Reconstruction Based on Simplex Meshes
>>>> which can still be found at
>>>> http://www-sop.inria.fr/asclepios/biblio/REP/publi.php?name=Author/DELINGETTE-H.html
>>>> .
>>>>
>>>> My adaptation appears in ICCV Workshop 2005...
>>>>
>>>> Yanxi Liu, Tianzi Jiang, Changshui Zhang  (Eds.): Computer Vision for
>>>> Biomedical Image Applications, First International Workshop, CVBIA
>>>> 2005, Beijing, China, October 21, 2005, Proceedings. Lecture Notes in
>>>> Computer Science 3765 Springer 2005, ISBN 3-540-29411-2
>>>>
>>>> Michel A. Audette, Hervé Delingette, Alexander Fuchs, Oliver R.
>>>> Astley, Kiyoyuki Chinzei:
>>>> A Topologically Faithful, Tissue-Guided, Spatially Varying Meshing
>>>> Strategy for Computing Patient-Specific Head Models for Endoscopic
>>>> Pituitary Surgery Simulation. 178-188
>>>>
>>>> (and later in Computer Aided Surgery...
>>>> http://www.informaworld.com/smpp/content~db=all~content=a770815634~frm=abslink )
>>>>
>>>> Was hoping to do this on ITK, without relying on my old code based on
>>>> stuff contributed by Herve.
>>>>
>>>> What do you think? Feasible?
>>>>
>>>> Cheers,
>>>>
>>>> Michel
>>>>
>>>> On Tue, Aug 17, 2010 at 3:03 AM, Alexandre GOUAILLARD
>>>> <agouaillard at gmail.com> wrote:
>>>>>
>>>>> hi michel,
>>>>>
>>>>> the simplex mesh code is one of the very first contribution to the
>>>>> toolkit roughly 10 years ago and it seems to be showing it s age here
>>>>> and then ( the segmentation based on simplex meshes in tk does not
>>>>> take into account spacing, move the mesh out of the image and so on).
>>>>>
>>>>> Note that simplex / triangular meshes being dual, both topologies are
>>>>> included by default in a QuadEdgeMesh. THe only thing that could be
>>>>> missing (depending on what you do) is the container for the geometry
>>>>> of the dual mesh (depending on your point of view, each can be primal
>>>>> or dual).
>>>>>
>>>>> What algorithm did you have in mind ?
>>>>>
>>>>> I'm re-motivating myself to work on QuadEdgeMesh (thanks to dan for
>>>>> pointing out a nice algorithm I'd like to work on) and that could be
>>>>> of interest to me too ;-) I could definitly help with the design, and
>>>>> even implement some.
>>>>>
>>>>> regards,
>>>>>
>>>>> alex.
>>>>>
>>>>>
>>>>> On Mon, Aug 16, 2010 at 9:51 PM, Michel Audette
>>>>> <michel.audette at kitware.com> wrote:
>>>>> > Dear fellow developers,
>>>>> >
>>>>> > I would like to find out if anyone in the community has implemented T1 and
>>>>> > T2 topological operators for the simplex mesh model. I need this kind of
>>>>> > operator to use the simplex for highly controlled decimation and high
>>>>> > quality surface triangulation. I don't see it doing a google on simplex and
>>>>> > Insight Journal.
>>>>> >
>>>>> > Best wishes,
>>>>> >
>>>>> > Michel
>>>>> >
>>>>> > --
>>>>> > Michel Audette, Ph.D.
>>>>> > R & D Engineer,
>>>>> > Kitware Inc.,
>>>>> > Chapel Hill, N.C.
>>>>> >
>>>>> >
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>>>>> >
>>>>
>>>>
>>>>
>>>> --
>>>> Michel Audette, Ph.D.
>>>> R & D Engineer,
>>>> Kitware Inc.,
>>>> Chapel Hill, N.C.
>>>>
>>>
>>
>>
>>
>> --
>> Michel Audette, Ph.D.
>> R & D Engineer,
>> Kitware Inc.,
>> Chapel Hill, N.C.
>>
>

-- 
Michel Audette, Ph.D.
R & D Engineer,
Kitware Inc.,
Chapel Hill, N.C.