[vtkusers] Re : Re : Re : Build 3D Mesh from vtkImageData using vtkMarchingCubes - holes filling ?

[Malsoaz James]

Dominique, I have been thinking about closing but I'm afraid it will have bad effect on the mesh topology.

Anyway, I can give it a try, which filter should I use to perform morphological operations on a 3D mesh ?

Best.



________________________________
 De : Malsoaz James <jmalsoaz at yahoo.fr>
À : Dominique Töpfer <dominique at toepfer-web.de> 
Cc : "vtkusers at vtk.org" <vtkusers at vtk.org> 
Envoyé le : Mercredi 7 Décembre 2011 10h06
Objet : [vtkusers] Re : Re : Build 3D Mesh from vtkImageData using vtkMarchingCubes - holes filling ?
 

Thank you, I will look into this and let you know.

Regarding the use of a vtkRectilinearGrid, is there a class/filter to convert my vtkImageData to a vtkRectilinearGrid or should I build it manually ?

Best.



________________________________
 De : Dominique Töpfer <dominique at toepfer-web.de>
À : Malsoaz James <jmalsoaz at yahoo.fr> 
Cc : Bill Lorensen <bill.lorensen at gmail.com>; "vtkusers at vtk.org" <vtkusers at vtk.org> 
Envoyé le : Mardi 6 Décembre 2011 19h19
Objet : Re: [vtkusers] Re : Build 3D Mesh from vtkImageData using vtkMarchingCubes - holes filling ?
 

Hi,

maybe morphological closing on your 3D build is also an option.

HTH
Dominique

On 06.12.2011 19:09, Malsoaz James wrote: 
Thank you Bill for your answer.
>
>The input vtkImageData is the result of a segmentation process.
        Sometimes, the segmentation is not perfect, part of the object
        can be missing on a slice. For now, I can't know automatically
        if a slice is missing or not before the 3D build. Thus, I can't
        create it manually. I thought Marching cubes was able to deal
        with this kind of problem, apparently not.
>
>I will look at your solution and let you know.
>
>In any case, the resampler solution works, it is just not really
        suitable for bad resolution.
>
>Best.
>
>
>
>________________________________
> De : Bill Lorensen <bill.lorensen at gmail.com>
>À : Malsoaz James <jmalsoaz at yahoo.fr> 
>Cc : "vtkusers at vtk.org" <vtkusers at vtk.org> 
>Envoyé le : Mardi 6 Décembre 2011 18h19
>Objet : Re: [vtkusers] Build 3D Mesh from vtkImageData using vtkMarchingCubes - holes filling ?
> 
>Another possible solution is to convert your image data to a
>rectilinear grid. The rectilinear grid supports non uniform
            spacing.
>Once converted you would use vtkContourFilter rather than
            Marching
>Cubes. It will be slower.
>
>Bill
>
>On Tue, Dec 6, 2011 at 12:16 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>> Marching Cubes is the correct filter and your results
            look good
>> (except for the missing slice. You could try to create
            a missing slice
>> by creating a new slice. Maybe by averaging the slice
            above and below
>> the missing slice.
>>
>> Why is the data missing?
>>
>> On Tue, Dec 6, 2011 at 12:03 PM, Malsoaz James <jmalsoaz at yahoo.fr> wrote:
>>> Dear VTK users
>>>
>>> I'm trying to build a 3D mesh from a vtkImageData
            using vtkMarchingCubes.
>>> The vtkImageData is build from a list of 2D binary
            slices.
>>>
>>> vtkMarchingCubes works great. But when a slice(s)
            is(are) missing, it
>>> creates a hole in the 3D mesh (see image in
            attachment).
>>>
>>> 1 - How can I fill this kind of hole ? Ideally, I
            would like to link the two
>>> parts of the mesh
>>>
>>> 2 - I found a solution in the use of a resampler
            (vtkImageResample,
>>> vtkImageShrink3D, don't know which one is
            recommanded). Unfortunately, it
>>> sometimes produces ugly mesh with "stair effect"
            when the spacing is too big
>>> (still there after decimate and smooth). Is it a
            good solution ? How to
>>> solve the stair problem ?
>>>
>>> 3 - Browsing the mailing list brings me to the
            notion of "repair hole" for
>>> marching cubes. I don't know a lot about it. But
            should I look into this ?
>>> Some solutions exist for this such as http://www.opentopology.org/
>>>
>>> 4 - Is vtkMarchingCubes the class I should use for
            my purpose or should I
>>> look at vtkVoxelContoursSurfaceFilter or any other
            filter ?
>>>
>>>
>>> Thank you for you help.
>>> Best.
>>>
>>>
>>>
>>>
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>>
>>
>> --
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>
>
>
>-- 
>Unpaid intern in BillsBasement at noware dot com
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>
>
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-- 
Dominique Töpfer, Dipl.-Inform.
Institute of Medical Physics
University of Erlangen


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