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

[Bill Lorensen]

You will need to create it manually.

2011/12/7 Malsoaz James <jmalsoaz at yahoo.fr>:
> 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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>>
>>
>>
>> --
>> Unpaid intern in BillsBasement at noware dot com
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com
>
>
>
>
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>
> --
> Dominique Töpfer, Dipl.-Inform.
> Institute of Medical Physics
> University of Erlangen
>
>
>



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