[vtkusers] Solid Voxelization with VTK
Elvis Stansvik
elvis.stansvik at orexplore.com
Mon Jun 11 02:50:17 EDT 2018
Den mån 11 juni 2018 08:33Berti Krüger <berti_krueger at hotmail.com> skrev:
> Hi David,
>
> thank you very much for all your help and for all the effort.
>
> I am sorry, but i am an absolute beginner with VTK and for me it is really
> hard to find informations / documentation / explanations beyond the doxygen
> class documentation about the advanced visualization/manipulation
> operations in VTK (the VTK User Manual sadly only covers the very basics).
>
> So thanks again for all your clarifications and all your help so far.
>
> I replaced the visualization part of my pipeline with your code which
> makes it so much clearer, shorter and better in terms of the visualization.
> And it is also easy enough so that even i get it :-)
>
> Unfortunately when i extend the simple cone source voxelization example i
> attached the last time by using general STL meshes via the vtkSTLReader, i
> get missing voxels in the visualization. To be sure that the problem is
> indeed in the visualization part and not in the voxelization part i used
> *binvox*, a mature voxelization program (http://www.patrickmin.com/binvox/
> ) to do the voxelization and the code you suggested for the visualization
> of the vtkImageData via VTK.
>
>
> Using this setup the Utah Teapot looks like this (the handle and other
> thin parts of the mesh are missing in the visualization):
>
> [image: Teapot missing voxels]
>
>
> For surface-only-voxelized meshes there even more voxels missing (the
> example here is the Stanford Bunny which has only been surface voxelized):
>
> [image: bunny surface voxelization visualization]
>
> What i don't get is that the visualization code is as simple as it gets:
>
> vtkNew<vtkThreshold> selector;
> selector->SetInputData(voxelImage);
> selector->ThresholdByUpper(1.0);
> selector->Update();
>
> vtkNew<vtkDataSetMapper> mapper;
> mapper->SetInputConnection(selector->GetOutputPort());
> mapper->ScalarVisibilityOff();
> mapper->StaticOn();
>
> When i understand it correctly, then we simply visualize every cell
> (voxel) whose threshold is equal or greater than 1.0 which means we
> visualize (filter) all voxels which are set (in my vtkImageData voxels
> which are set are 1, voxels which are not set 0) and the vtkDataSetMapper
> maps these to graphic primitives and this does the rest of the
> visualization. Not much to do wrong here and that basically should do the
> trick but it doesn't.
>
> *Any idea why this does not work correctly all the time and has problems
> with thin parts?*
>
I'm just jumping in from the side here, and I'm by no means a VTK expert.
But I think what you're seeing is simply due to how VTK does volume
rendering. It interpolates the given data points, which means you need at
least two data points to get a voxel.
I'm guessing that at the resolution you're doing the voxelization here,
your teapot handle is simply too thin to result in even a single voxel.
Think of your data points as a grid of fenceposts. You'll get a voxel in
the middle of each 2x2x2 cluster of posts.
Someone correct me if I'm wrong here.
HTH,
Elvis
>
>
> I therefore tried another approach by using the vtkGlyph3DMapper based on
> the example code from
> <https://www.vtk.org/Wiki/VTK/Examples/Cxx/Visualization/Glyph3DMapper>
>
> https://www.vtk.org/Wiki/VTK/Examples/Cxx/Visualization/Glyph3DMapper :
>
>
> vtkNew<vtkPoints> points;
>
> for (int x = 0; x < dims[0]; x++)
> {
> for (int y = 0; y < dims[1]; y++)
> {
> for (int z = 0; z < dims[2]; z++)
> {
> char* pixel = static_cast<char*>(voxelImage->GetScalarPointer(x,
> y, z));
>
> if(pixel[0] == 1) // if the voxel is set (1) in the voxel image
> points->InsertNextPoint(x, y, z);
> }
> }
> }
>
> vtkNew<vtkPolyData> polydata;
> polydata->SetPoints(points);
>
> vtkNew<vtkPolyData> glyph;
>
> vtkNew<vtkCubeSource> cubeSource;
>
> vtkNew<vtkGlyph3DMapper> glyph3Dmapper;
> glyph3Dmapper->SetSourceConnection(cubeSource->GetOutputPort());
> glyph3Dmapper->SetInputData(polydata);
> glyph3Dmapper->Update();
>
> actor->SetMapper(glyph3Dmapper);
>
>
> The visualization with this approach is a bit slower (probably because it
> does no backface culling of the backfaces of the cube polygons) but it
> seems to work correctly even with surface only voxelized meshes:
> [image: bunny ok][image: teapot]
>
>
> I attached a simple working vtk demo with both visualizations and
> integrated voxelized meshes (no external data files or other dependencies)
> as a simple cmake/vtk compileable project (
> *PolyDataToImageDataVisualizationVoxel*). Maybe it might help other vtk
> users in the future.
>
> *Are there any other possibilities (maybe faster) to do the visualization
> with vtk ?*
>
>
>
> Now having a visualization that seems to work, i tried this visualization
> with the suggested voxelization code from the vtk examples here
> https://lorensen.github.io/VTKExamples/site/Cxx/PolyData/PolyDataToImageData/
>
> and while the voxelization is lighting-fast and some example meshes did
> get correctly voxelized, i also had a lot of meshes whose voxelizations had
> misclassified voxels (e.g. voxels are set where voxels should not have been
> set and the opposite (holes)) like with the Utah Teapot here:
>
> [image: teapot errors][image: teapot errors 2][image: teapot errors3]
>
> The problem is that for my project i have to find paths through the voxel
> image. So miscIassified voxels would lead to either wrong paths found
> (paths which do not really exist like in the first image) or maybe to a
> situation where no path can be found because of holes.
>
> I attached a compileable cmake/vtk example (
> *PolyDataToImageDataVisualizationSTL*) together with some small example
> stl-mesh-files (teapot etc.) using the example code from the vtk example
> repository for showing the problem with the given approach there.
>
>
> *Is it possible by tweaking the vtk PolyDataToImageData example code to
> always get a correct voxelization or is another approach needed?*
>
>
> If you or anybody else has ideas / suggestions i would really be glad.
> Thank for reading if you managed to get this far and have not fallen
> asleep and thank you very much in advance.
>
>
> Regards
>
> Berti
>
>
> Am 06.06.2018 um 01:49 schrieb David Gobbi:
>
> Hi Berti,
>
> The correct pad filter to use for this is "vtkImageConstantPad", not
> "WrapPad", but padding really isn't necessary. Neither is the use of cell
> scalars, it's more appropriate to use point scalars when working with image
> data since each voxel is represented as a point scalar.
>
> The threshold should be set like this, for a threshold halfway between
> your "inval" and "outval":
>
> selector->ThresholdByUpper(0.5*(startLabel + endLabel));
>
> The lookup table wasn't correctly set. Calling SetRange() does not set the
> number of entries in the lookup table (by default, the lookup table has 256
> entries).
>
> lut->SetTableRange(0, 1);
> lut->SetNumberOfColors(2);
>
> Also, your color for "1" was transparent, whereas it has to be opaque in
> order to properly see a scalar-colored cone.
>
>
>
> I stripped the visualization part of your pipeline down to the following.
> No padding is done, the thresholding uses point scalars, no shifting, and
> no lookup table (instead, I call ScalarVisibilityOff() and set the color
> via the actor's property object). I replaced vtkPolyDataMapper with
> vtkDataSetMapper, which automatically skins the data.
>
>
> unsigned char startLabel = outval;
> unsigned char endLabel = inval;
>
> vtkNew<vtkThreshold> selector;
> // the call to SetInputArrayToProcess() isn't necessary, the default is
> fine
> //selector->SetInputArrayToProcess(0, 0, 0,
> //
> vtkDataObject::FIELD_ASSOCIATION_POINTS,
> // vtkDataSetAttributes::SCALARS);
> selector->SetInputData(voxelImage);
> selector->ThresholdByUpper(0.5*(startLabel + endLabel));
> selector->Update();
>
> vtkNew<vtkDataSetMapper> mapper;
> mapper->SetInputConnection(selector->GetOutputPort());
> mapper->ScalarVisibilityOff();
>
> vtkNew<vtkActor> actor;
> actor->SetMapper(mapper);
> actor->GetProperty()->SetColor(0.0, 1.0, 0.0);
>
>
> An image of the resulting cone is attached.
>
> - David
>
>
> On Tue, Jun 5, 2018 at 1:26 AM, Berti Krüger <berti_krueger at hotmail.com>
> wrote:
>
>> Hi David,
>>
>>
>> thank you very much for your help.
>>
>>
>> I tried the example from your link. Unfortunately the result is same as
>> using the vtkVoxelModeller:
>>
>>
>> [image: Screenshot result voxelization]
>> I get only a voxelization of the surface. The interior of the voxelized
>> cone is still hollow and not filled with voxels (at least this is implied
>> by the visualization).
>>
>>
>> For the visualization i use Bill Lorensen's example code from here:
>>
>>
>> https://lorensen.github.io/VTKExamples/site/Cxx/Medical/GenerateCubesFromLabels/
>>
>>
>>
>> I have attached this small example which compiles with VTK 8.1 to show
>> the issue. It basicly only consist of the example code from your link (
>> https://lorensen.github.io/VTKExamples/site/Cxx/PolyData/PolyDataToImageData/)
>> and the visualization code from the Bill Lorensen's example from the
>> link above. I have not changed much.
>>
>>
>> Any idea what is going wrong or what can i do get also voxelization of
>> the interior (solid voxelization)?
>>
>>
>> Thank you very much in advance.
>>
>>
>>
>> Regards
>>
>>
>> Berti
>> ------------------------------
>> *Von:* David Gobbi <david.gobbi at gmail.com>
>> *Gesendet:* Montag, 28. Mai 2018 23:13
>> *An:* Berti Krüger
>> *Cc:* vtkusers at vtk.org
>> *Betreff:* Re: [vtkusers] Solid Voxelization with VTK
>>
>> Hi Berti,
>>
>> If its a triangulated surface that you want to fill with voxels, use
>> vtkPolyDataToImageStencil:
>>
>> https://lorensen.github.io/VTKExamples/site/Cxx/PolyData/PolyDataToImageData/
>>
>> If its a mesh of 3D elements and you want to sample the elements to
>> create voxels, try vtkResampleToImage.
>>
>> - David
>>
>>
>>
>> On Mon, May 28, 2018 at 4:41 PM, Berti Krüger <berti_krueger at hotmail.com>
>> wrote:
>>
>> Hello Everyone.
>>
>> For my Project i have to voxelize a 3D-Triangle-Mesh. I already found the
>> vtkVoxelModeller which, while somewhat slow (only around 200 Triangles per
>> second), works, but only voxelizes the outer shell where the mesh boundary
>> triangles are. The inner part of the mesh stays hollow.
>>
>> Is there some way to get solid voxelization of 3D-Triangle-Meshes out of
>> the
>> box with VTK ?
>>
>>
>> Thank you very much in advance,
>>
>> Berti
>>
>>
>
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