[vtkusers] Solid Voxelization with VTK

Sun Sep 23 14:31:22 EDT 2018

Looks like I should add some examples!

On Sun, Sep 23, 2018, 9:15 AM David Gobbi <david.gobbi at gmail.com> wrote:

> Hi Berti,
>
> Thanks for the code, I'm sure that people will find it useful.  The
> vtkImageStencilData class isn't described in much detail in the VTK
> documentation, but I can provide a brief description.
>
> The vtkImageStencilData object stores each raster-line of a binary image
> as a list of (begin, end) pairs.  That is, each raster line has zero or
> more non-overlapping (begin, end) pairs.  When vtkImageStencil operates on
> an image, it simply iterates through the (begin, end) pairs to figure out
> what parts of the image to copy.  One way to think about this is that if
> the original binary image volume is stored as O(n^3) voxels, the
> vtkImageStencilData stores O(n^2) values.
>
> When a vtkImageStencilData is created, it allocates enough memory to store
> one (begin, end) pair per raster line, since this matches the most common
> use case (i.e. a mask that corresponds to a convex object). Thereafter it
> performs additional allocations as necessary.
>
> As for vtkPolyDataToImageStencil, it works by cutting your STL object
> along each XY plane to create polygons (zero or more polygons per slice),
> and then it rasterizes each polygon to create the (begin, end) pairs for
> each raster line.
>
>
> One comment about your code: it would be more efficient to use
> vtkImageStencilToImage instead of vtkImageStencil and vtkImageCast.  The
> vtkImageStencilToImage filter requires only one input (the stencil), i.e.
> it doesn't require 'binaryLabelMap' as input.  Also, you can set the data
> type of the image that it produces as output, so it doesn't have to be
> followed by a cast.
>
> Cheers,
>  - David
>
> On Sat, Sep 22, 2018 at 10:29 PM Berti Krüger <berti_krueger at hotmail.com>
> wrote:
>
>> Hi all.
>>
>>
>> I am very sorry to revive this ancient thread.
>>
>>
>> But i thought that maybe it could help other vtk users in the future to
>> have a compilable and working example of the final result. If someone
>> thinks that this code could be useful as an vtk example then feel free to
>> modify / correct / pimp / add this to the vtk examples on github.
>>
>>
>> I adapted the 3D slicer vtk code Csaba has pointed me to and incorporated
>> the hints from David and everything works like a charm:
>>
>>
>>
>> The whole procedure is incredibly simple. Basically the vtkPolyData of
>> the mesh is converted via the vtkPolyDataToImageStencil filter to a
>> vtkImageStencil and the rest of the whole magic is only done by the
>> vtkImageStencil filter:
>>
>>
>> *// Convert stencil to image*
>> *vtkNew<vtkImageStencil> stencil;*
>> *stencil->SetInputData(binaryLabelMap);*
>> *stencil->SetStencilConnection(polyDataToImageStencil->GetOutputPort());*
>> *stencil->ReverseStencilOn();*
>> *stencil->SetBackgroundValue(1); // General foreground value is 1
>> (background value because of reverse **stencil)*
>>
>> I would really like to know very roughly how the vtkImageStencil works
>> internally without digging through all of the source code. Because it is
>> really fast (some kind of rasterization maybe ?). If someone could drop me
>> a line on how it works only in principle  that would be really great.
>>
>>
>> So thanks again to Bill, Csaba, David, Elvis and everyone else on this
>> thread.
>>
>>
>>
>> Kind regards,
>>
>>
>> Berti
>>
>>
>>
>> PS: Example code, CMakeLists and example STL mesh are attached
>>
>> ------------------------------
>> *Von:* Csaba Pinter <csaba.pinter at queensu.ca>
>> *Gesendet:* Montag, 11. Juni 2018 12:45
>> *An:* Berti Krüger
>> *Cc:* vtkusers at vtk.org
>> *Betreff:* RE: [vtkusers] Solid Voxelization with VTK
>>
>>
>> Hi Berti,
>>
>>
>>
>> That code is under BSD-style license, so you’re free to do basically
>> anything with it. This implementation is already pretty simple; just a
>> concatenation of several VTK filters, so you can just give it a try by
>> copy-pasting the relevant part of that function into your code and see if
>> it works. If you’re interested in using the vtkSegmentation library, let me
>> know though!
>>
>>
>>
>> Best,
>>
>> csaba
>>
>>
>>
>> *From:* Berti Krüger <berti_krueger at hotmail.com>
>> *Sent:* Monday, June 11, 2018 02:46
>> *To:* Csaba Pinter <csaba.pinter at queensu.ca>; David Gobbi <
>> david.gobbi at gmail.com>
>> *Cc:* vtkusers at vtk.org
>> *Subject:* Re: [vtkusers] Solid Voxelization with VTK
>>
>>
>>
>> Hi Csaba,
>>
>>
>>
>> thank you very much for you answer and for offering your help.
>>
>>
>>
>> I already have looked at it and i think if no simpler option will come
>> up, i will give it a try (hoping not to have to change too much to get it
>> working with my pipeline since i am an absolute vtk beginner :-) ).
>>
>>
>>
>> How is this code licensed ? (i am only doing research work at the moment,
>> the whole project i am working on is internal and just for testing and part
>> of some larger work, it might be open sourced one day in the very far
>> future but could even be not at all  and it will never be used
>> commercially).
>>
>>
>>
>>
>>
>> Regards
>>
>>
>>
>> Berti
>>
>>
>>
>>
>>
>> Am 05.06.2018 um 16:14 schrieb Csaba Pinter:
>>
>> Hi Berti,
>>
>>
>>
>> There is a pretty robust conversion algorithm implemented within 3D
>> Slicer but using solely VTK:
>>
>>
>> https://github.com/Slicer/Slicer/blob/master/Libs/vtkSegmentationCore/vtkClosedSurfaceToBinaryLabelmapConversionRule.cxx#L118
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FSlicer%2FSlicer%2Fblob%2Fmaster%2FLibs%2FvtkSegmentationCore%2FvtkClosedSurfaceToBinaryLabelmapConversionRule.cxx%23L118&data=02%7C01%7Ccsaba.pinter%40queensu.ca%7C3aab37ccc6914427982508d5cf66eedc%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636642963366161717&sdata=p0ekXyWC0VAuADrfhvReHFywfi8%2BD7jhe59iVCIZmqs%3D&reserved=0>
>>
>> It consists of a short pipeline of standard VTK filters (some
>> preprocessing then vtkPolyDataToImageStencil and vtkImageStencil).
>>
>>
>>
>> Let me know if you have any questions.
>>
>>
>>
>> csaba
>>
>>
>>
>>
>>
>> *From:* vtkusers <vtkusers-bounces at public.kitware.com>
>> <vtkusers-bounces at public.kitware.com> *On Behalf Of *Berti Krüger
>> *Sent:* Tuesday, June 5, 2018 03:26
>> *To:* David Gobbi <david.gobbi at gmail.com> <david.gobbi at gmail.com>
>> *Cc:* vtkusers at vtk.org
>> *Subject:* Re: [vtkusers] Solid Voxelization with VTK
>>
>>
>>
>> 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/
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Florensen.github.io%2FVTKExamples%2Fsite%2FCxx%2FMedical%2FGenerateCubesFromLabels%2F&data=02%7C01%7Ccsaba.pinter%40queensu.ca%7C63496d6b50e24ff32f7808d5cab5a98b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636637804016225671&sdata=4TKi7VbGBfbM4DpQuLib1m0YGmLJO%2FU7BAO6ZKCUpVU%3D&reserved=0>
>>
>>
>>
>>
>>
>> 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/
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Florensen.github.io%2FVTKExamples%2Fsite%2FCxx%2FPolyData%2FPolyDataToImageData%2F&data=02%7C01%7Ccsaba.pinter%40queensu.ca%7C63496d6b50e24ff32f7808d5cab5a98b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636637804016225671&sdata=hXqgnekqjjNPflRneU0sU7DFo%2B%2FcdBfIFDcpE%2FZXiOg%3D&reserved=0>)
>> 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
>>
>>
>>
>> PolyDataToImageData - lorensen.github.io
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Florensen.github.io%2FVTKExamples%2Fsite%2FCxx%2FPolyData%2FPolyDataToImageData%2F&data=02%7C01%7Ccsaba.pinter%40queensu.ca%7C63496d6b50e24ff32f7808d5cab5a98b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636637804016225671&sdata=hXqgnekqjjNPflRneU0sU7DFo%2B%2FcdBfIFDcpE%2FZXiOg%3D&reserved=0>
>>
>> lorensen.github.io
>>
>> If VTK is not installed but compiled on your system, you will need to
>> specify the path to your VTK build:
>>
>>
>>
>>
>>
>> GenerateCubesFromLabels - GitHub Pages
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Florensen.github.io%2FVTKExamples%2Fsite%2FCxx%2FMedical%2FGenerateCubesFromLabels%2F&data=02%7C01%7Ccsaba.pinter%40queensu.ca%7C63496d6b50e24ff32f7808d5cab5a98b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636637804016225671&sdata=4TKi7VbGBfbM4DpQuLib1m0YGmLJO%2FU7BAO6ZKCUpVU%3D&reserved=0>
>>
>> lorensen.github.io
>>
>> Usage: GenerateCubesFromLabels FullHead.mhd StartLabel EndLabel where
>> InputVolume is a meta file containing a 3 volume of discrete labels.
>>
>>
>>
>>
>> ------------------------------
>>
>> *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/
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Florensen.github.io%2FVTKExamples%2Fsite%2FCxx%2FPolyData%2FPolyDataToImageData%2F&data=02%7C01%7Ccsaba.pinter%40queensu.ca%7C63496d6b50e24ff32f7808d5cab5a98b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636637804016225671&sdata=hXqgnekqjjNPflRneU0sU7DFo%2B%2FcdBfIFDcpE%2FZXiOg%3D&reserved=0>
>>
>> PolyDataToImageData - lorensen.github.io
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Florensen.github.io%2FVTKExamples%2Fsite%2FCxx%2FPolyData%2FPolyDataToImageData%2F&data=02%7C01%7Ccsaba.pinter%40queensu.ca%7C63496d6b50e24ff32f7808d5cab5a98b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636637804016225671&sdata=hXqgnekqjjNPflRneU0sU7DFo%2B%2FcdBfIFDcpE%2FZXiOg%3D&reserved=0>
>>
>> lorensen.github.io
>>
>> If VTK is not installed but compiled on your system, you will need to
>> specify the path to your VTK build:
>>
>>
>>
>>
>>
>> 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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