[vtkusers] VTKPolyData to 3D image

[Bill Lorensen]

Compiles for me.

On Tue, Apr 20, 2010 at 11:45 AM, David Welch
<dmwelch at engineering.uiowa.edu> wrote:
> Okay, I'm in the home stretch here... I've changed the code slightly to
> output a XMLImageData file and take an input surface.  CMake runs fine on
> it, but it dies in the make process with this error:
>
> CMakeFiles/SurfaceToImage.dir/SurfaceToImage.cxx.o: In function
> `vtkSmartPointer<vtkPolyDataToImageStencil>::New()':
> /usr/local/include/vtk-5.7/vtkSmartPointer.h:113: undefined reference to
> `vtkPolyDataToImageStencil::New()'
>
> The smart pointer line is fundamentally no different than any other line of
> code.  ???  Here's my code:
> ____________________________________________________________________________________________________________________
> #include <vtkSmartPointer.h>
> #include <vtkPolyData.h>
> #include <vtkImageData.h>
> #include <vtkPolyDataReader.h>
> #include <vtkXMLImageDataWriter.h>
> #include <vtkPolyDataToImageStencil.h>
> #include <vtkImageStencil.h>
> #include <vtkPointData.h>
>
> /**
>  * This program generates a sphere (closed surface, vtkPolyData) and
> converts it into volume
>  * representation (vtkImageData) where the foreground voxels are 1 and the
> background voxels are
>  * 0. Internally vtkPolyDataToImageStencil is utilized. The resultant image
> is saved to disk
>  * in XML image data format.
>  */
> int main (int argc, char *argv[])
> {
>   if( argc < 3 )
>   {
>     std::cerr << "Usage: " << argv[0];
>     std::cerr << " inputImageFile outputImageFile " << std::endl;
>     return EXIT_FAILURE;
>   }
>
>   vtkSmartPointer<vtkPolyDataReader> surfaceSource =
> vtkSmartPointer<vtkPolyDataReader>::New();
>   surfaceSource->SetFileName( argv[1] );
>   vtkSmartPointer<vtkPolyData> pd = surfaceSource->GetOutput();
>   surfaceSource->Update();
>
>   vtkSmartPointer<vtkImageData> whiteImage =
> vtkSmartPointer<vtkImageData>::New();
>   double bounds[6];
>   pd->GetBounds(bounds);
>   double spacing[3]; // desired volume spacing
>   spacing[0] = 0.5;
>   spacing[1] = 0.5;
>   spacing[2] = 0.5;
>   whiteImage->SetSpacing(spacing);
>
>   // compute dimensions
>   int dim[3];
>   for (int i = 0; i < 3; i++)
>   {
>     dim[i] = static_cast<int>(ceil((bounds[i * 2 + 1] - bounds[i * 2]) /
> spacing[i]));
>   }
>   whiteImage->SetDimensions(dim);
>   whiteImage->SetExtent(0, dim[0] - 1, 0, dim[1] - 1, 0, dim[2] - 1);
>
>   double origin[3];
>   // NOTE: I am not sure whether or not we had to add some offset!
>   origin[0] = bounds[0];// + spacing[0] / 2;
>   origin[1] = bounds[2];// + spacing[1] / 2;
>   origin[2] = bounds[4];// + spacing[2] / 2;
>   whiteImage->SetOrigin(origin);
>
>   whiteImage->SetScalarTypeToUnsignedChar();
>   whiteImage->AllocateScalars();
>
>   // fill the image with foreground voxels:
>   unsigned char inval = 255;
>   unsigned char outval = 0;
>   vtkIdType count = whiteImage->GetNumberOfPoints();
>   for (vtkIdType i = 0; i < count; ++i)
>   {
>     whiteImage->GetPointData()->GetScalars()->SetTuple1(i, inval);
>   }
>
>   // polygonal data --> image stencil:
>   vtkSmartPointer<vtkPolyDataToImageStencil> pol2stenc =
> vtkSmartPointer<vtkPolyDataToImageStencil>::New(); //<---- This is the
> 'problem'???
>   pol2stenc->SetInput(pd);
>   pol2stenc->SetOutputOrigin(origin);
>   pol2stenc->SetOutputSpacing(spacing);
>   pol2stenc->SetOutputWholeExtent(whiteImage->GetExtent());
>   pol2stenc->Update();
>
>   // cut the corresponding white image and set the background:
>   vtkSmartPointer<vtkImageStencil> imgstenc =
> vtkSmartPointer<vtkImageStencil>::New();
>   imgstenc->SetInput(whiteImage);
>   imgstenc->SetStencil(pol2stenc->GetOutput());
>   imgstenc->ReverseStencilOff();
>   imgstenc->SetBackgroundValue(outval);
>   imgstenc->Update();
>
>   vtkSmartPointer<vtkXMLImageDataWriter> writer =
> vtkSmartPointer<vtkXMLImageDataWriter>::New();
>   writer->SetFileName( argv[2] ); //"SphereVolume.mhd");
>   writer->SetInput(imgstenc->GetOutput());
>   writer->Write();
>
>   return EXIT_SUCCESS;
> }
> ____________________________________________________________________________________________________________________
>
>
>
> On Tue, Apr 20, 2010 at 6:37 AM, David Doria <daviddoria+vtk at gmail.com>
> wrote:
>>
>> On Tue, Apr 20, 2010 at 3:34 AM, Lars Friedrich Lars
>> <lars-friedrich at gmx.net> wrote:
>>>
>>> Hello David Welch,
>>>
>>> referring to your original question "how to voxelize a simple surface" I
>>> added a VTK wiki example:
>>>
>>> http://www.cmake.org/Wiki/VTK/Examples/PolyDataToImageData
>>>
>>> It shows how we could incorporate vtkPolyDataToImageStencil into
>>> voxelizing a *closed* surface.
>>>
>>> Please NOTE: as I wrote on the example page I'm not sure about the image
>>> origin. The visual agreement in the sphere-image-overlay (paraview) is not
>>> perfect and I'm not sure whether or not we had to introduce some
>>> spacing-dependent image origin offset to compensate that. If you use that
>>> code and find out something in this direction it would be great if you
>>> contributed it to that example!
>>>
>>> HTH,
>>>
>>> lars
>>>
>>
>> David W -
>> Yes, the normals are definitely necessary. With a mesh, you can simply run
>> vtkPolyDataNormals. With a point set, you'd have to use my
>> vtkPointSetNormalEstimation and vtkPointSetNormalOrientation filters (part
>> of the same surface reconstruction journal submission). Unfortunately I
>> don't know what it means by the missing ImageData element.
>> Lars -
>> Looks great, thanks! Hopefully David W will play around with it and solve
>> the mystery of the origin problem.
>> Thanks,
>>
>> David
>
>
> --
> David Welch
> Graduate Student
> Dept. of Biomedical Engineering
> University of Iowa
> Lab: (319) 335-5279
>
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