[Insight-users] calculate normal

Alexandre GOUAILLARD hanfei at caltech.edu
Thu Feb 21 16:36:56 EST 2008 

Hi rashed,


Usually the answer is application dependent. If there is a point you're
especially interested in, it's **your** job to find it first and then to
call ComputeNormal.

If you don't know which point you're dealing with, it usually means you want
to process all the points. You can just loop over all the points and call
ComputeNormal for all of them.

You might want to see the API of itkPointSet from which SimplexMesh
inherits. Once again, the software manual is your friend:
Chapter 4.2 "PointSet"
SubChapter 4.2.2 "Getting access to Points" is worth reading.

Especially, depending on the traits (to come back to your previous
question), the container of the pointSet can be a map, which means that the
Ids of the points can be not consecutive (i.e. There can be a point whose ID
is 1, then a point whose ID is 3 even though there would be no point whose
ID is 2). You might want to use an iterator on the container to avoid
non-consecutive IDs problem.

That also answers your old question:
>>>>> Is there also a way to iterate through every point
>>>>> on
>>>>> the mesh?  

My 2 cents comments, you're welcome to skip or ignore.

ItkSimplexMesh is not really made to be used on its own. You 'd better see
it as a component of a deformable framework and as such, its methods are
tailored to fit the segmentation goal. It means that some of the method are
not designed to be used outside a very specific context. There is a handfull
of classes related to that specific deformable framework; you can see some
of them here:
http://www.itk.org/Doxygen/html/group__MeshSegmentation.html

The best entrance point to use them, as leila mentioned, is in the related
InsightApplication directory (it's a separate tarball, from a separate cvs
repository than ITK. It requires ITK):
Your_Path_To_InsightApplication\DeformableSimplexMesh\
It will provide vtk-ITK glue for vizualization and a GUI. As it implements
all the framework, you might to start your experimentation from there.

Note that vtk provides normal and curvature filters for example:
VtkPolyDataNormals, vtkCurvatures


At that point, I would recommend you take time to read the software Guide
enterely at least once. It might save you a lot of time.

Cheers,

Alex.

On 2/21/08 11:50 AM, "rashedk" <rashed.vtk at googlemail.com> wrote:

> 
> Hi, 
> 
> In the documentation of ComputeNormal of SimplexMesh it says:
> 
> CovariantVectorType itk::SimplexMesh< TPixelType, VDimension, TMeshTraits
>> ::ComputeNormal   (   unsigned long     idx    )     const
> 
> compute the normal vector in the specified mesh point
> 
> I need to pass in the index of the mesh point as a parameter. Which function
> returns the index of a mesh point on a simplex mesh??
> 
> Thanks, 
> Rashed
> 
> 
> 
> Alex. GOUAILLARD-2 wrote:
>> 
>> Hi rashed,
>> 
>> The meshtraits is a list of type definition to finely tune your structure
>> depending on your usage. You can read more in the itk software guide:
>> Chapter 4.3.4 "Customizing the Mesh", page 70.
>> 
>> A meshtrait is provided by default, so you can basically ignore that for
>> your first experiments and use the itk:SimplexMesh as if it was templated
>> only over the PixelType and the Dimension. (Note, the Dimension also has a
>> default value, so theoretically, you only need to define a PixelType)
>> 
>> 
>> //----------------- original code
>> 
>> // NOTE see the default values for Vdimension and TMeshTraits
>> template < typename TPixelType,
>>            unsigned int VDimension = 3,
>>            typename TMeshTraits = DefaultStaticMeshTraits< TPixelType,
>>                                                            VDimension,
>>                                                            VDimension,
>>                                                            TPixelType,
>>                                                            TPixelType,
>>                                                            TPixelType >
>>> 
>> class SimplexMesh : public Mesh<TPixelType, VDimension, TMeshTraits>
>> 
>> 
>> //-----------------
>> 
>> 
>> Possible usages:
>> 
>> // simplest
>> Typedef itk::SimplexMesh< float >      MyFirstSimplexMeshType;
>> 
>> // same thing with second template parameter explicitly set
>> Typedef itk::SimplexMesh< float, 3 >   MySecondSimplexMeshType;
>> 
>> // full options - stay away from that unless you **really** know what you
>> do
>> Typedef float PointAndCellDataType;
>> typedef float                Coord;
>> const unsigned int  SDimension = 3; // space dimension
>> Const unsigned int  TDimension = 2; // max topological dim. Surface => 2
>> 
>> typedef itk:: DefaultStaticMeshTraits<
>>       PointAndCellDataType,
>>       SDimension,
>>       TDimension,
>>       Coord,
>>       Coord,
>>       PointAndCellDataType           >    MeshTraitsType;
>>  
>> typedef SimplexMesh< PointAndCellDataType, SDimension, MeshTraitsType >
>>                                           MeshType;
>> 
>> 
>> On 2/20/08 10:18 AM, "rashedk" <rashed.vtk at googlemail.com> wrote:
>> 
>>> 
>>> Thanks! 
>>> 
>>> What is TMeshTraits in itk::SimplexMesh< TPixelType, VDimension,
>>> TMeshTraits
>>>> ??
>>> 
>>> What should I pass for TMeshTraits?
>>> 
>>> 
>>> 
>>> 
>>> Leila Baghdadi-2 wrote:
>>>> 
>>>> check InsightApplication/DeformableModel...
>>>> 
>>>> I think that code needs work but I am sure I have the part where it
>>>> converts the mesh to pass to vtk.
>>>> 
>>>> HTH
>>>> 
>>>> Leila
>>>> 
>>>> On Wed, 2008-20-02 at 09:21 -0800, rashedk wrote:
>>>>> 
>>>>> Thanks, but now I am stuck trying to display a simplex mesh in VTK. How
>>>>> do I
>>>>> visualize this mesh? Is there also a way to iterate through every point
>>>>> on
>>>>> the mesh?  
>>>>> 
>>>>> Rashed. 
>>>>> 
>>>>> 
>>>>> Leila Baghdadi-2 wrote:
>>>>>> 
>>>>>> Yep that's right and another note,
>>>>>> 
>>>>>> you "must" create a triangle mesh in order to create a simplex mesh!
>>>>>> 
>>>>>> If you are unsure about how it is done, check the paper
>>>>>> simplex mesh
>>>>>> by herve delingette of INRIA france
>>>>>> 
>>>>>> good luck
>>>>>> 
>>>>>> Leila
>>>>>> 
>>>>>> On Wed, 2008-20-02 at 12:47 +0100, Iván Macía wrote:
>>>>>>> Hi Rashed,
>>>>>>> 
>>>>>>> You can do what you mention with VTK or directly in ITK use
>>>>>>> itk::BinaryMask3DMeshSource, which is the equivalent of Marching
>>>>>>> Cubes
>>>>> in
>>>>>>> ITK. As the name implies, you need a binary mask (segmentation) as
>>>>> input.
>>>>>>> 
>>>>>>> HTH
>>>>>>> 
>>>>>>> Ivan
>>>>>>> 
>>>>>>> -----Mensaje original-----
>>>>>>> De: insight-users-bounces+imacia=vicomtech.org at itk.org
>>>>>>> [mailto:insight-users-bounces+imacia=vicomtech.org at itk.org] En nombre
>>>>> de
>>>>>>> rashedk
>>>>>>> Enviado el: miércoles, 20 de febrero de 2008 12:06
>>>>>>> Para: insight-users at itk.org
>>>>>>> Asunto: Re: [Insight-users] calculate normal
>>>>>>> 
>>>>>>> 
>>>>>>> Hi, 
>>>>>>> 
>>>>>>> How do I convert my 3D image data to a simplex mesh in order to
>>>>> compute
>>>>>>> the
>>>>>>> normals? Checking the class documentation for itk::SimplexMesh
>>>>>>> reveals
>>>>>>> that
>>>>>>> one has to generate a triangle mesh and then use the
>>>>>>> itkTriangleMeshToSimplexMeshFilter. But then how do I convert my 3D
>>>>> image
>>>>>>> data to a triangle mesh?? Do I use vtkContour to produce polyData and
>>>>>>> then
>>>>>>> convert it to itkMesh using appropriate filters?
>>>>>>> 
>>>>>>> Any help will be appreciated,
>>>>>>> 
>>>>>>> Thanks
>>>>>>> Rashed 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> Luis Ibanez wrote:
>>>>>>>> 
>>>>>>>> Hi Tony,
>>>>>>>> 
>>>>>>>> 
>>>>>>>> Well.... if you only have a point, then there is no normal to
>>>>> compute.
>>>>>>>> 
>>>>>>>> You probably are thinking of a point from a surface, where a point
>>>>>>>> belongs to several faces and have other points as neighbors.
>>>>>>>> 
>>>>>>>> 
>>>>>>>> In that case you may want to look at the itk::SimplexMesh
>>>>>>>> http://www.itk.org/Insight/Doxygen/html/classitk_1_1SimplexMesh.html
>>>>>>>> 
>>>>>>>> and its "ComputeNormal" method:
>>>>>>>> 
>>>>>>> 
>>>>> http://www.itk.org/Insight/Doxygen/html/classitk_1_1SimplexMesh.html#itk_1
>>>>> _1
>>>>>>> SimplexMesha5
>>>>>>>> 
>>>>>>>> 
>>>>>>>>     Regards,
>>>>>>>> 
>>>>>>>> 
>>>>>>>>        Luis
>>>>>>>> 
>>>>>>>> 
>>>>>>>> -------------------
>>>>>>>> tony hakki wrote:
>>>>>>>>> Is it possible to calculate normal of a point in ITK? If yes, Could
>>>>>>> you 
>>>>>>>>> tell which class should be used?
>>>>>>>>> thank you
>>>>>>>>>  
>>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> Insight-users mailing list
>>>>>>>> Insight-users at itk.org
>>>>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>>>> 
>>>>>>>> 
>>>>>>> 
>>>>>> 
>>>>>> _______________________________________________
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>>>>>> 
>>>>>> 
>>>>> 
>>>> 
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>>>> 
>> 
>> 
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