How to read points and radius info of .vtk file into ITK program

Beginner Questions
#1

Hi all,

My goal is to register 2d/3d vessel networks. The first step I’ve done is to use the VMTK module in slicer to segment out and calculate the radii of each centerline point. This saves as a .vtk file. However, while trying to use VTKPolyDataReader, I receive an error because the .vtk file is made up of binary data instead of ASCII which is one of the caveats.
I downloaded paraview and used it to save my .vtk data as ASCII. However, I’m still unable to view my points as I now see that I’m violating the primary caveat of only reading .vtk files that contain triangle meshes.
Is there some way I can read this data in such as saving the .vtk as a .stl or .obj file?

#2

Hi @Henco,

Try the MeshFileReader instead of the VTKPolyDataReader, since it supports both binary and ASCII .vtk polydata files. It also supports .obj. STL support is available with the ITKIOMeshSTL module.

#3

Hi Matt,

Thanks for the reply. I’m using this MeshReader Example to test the reader. It doesn’t seem to be working. I fed it the IDs of two points and did not receive the EuclideanDistance between the two.
I also added these lines of code at the end of the program, right before return EXIT_SUCCESS, to it to see how many points are read (I checked in paraview, should be 11836)

MeshType::Pointer mesh = reader->GetOutput();
std::cout << mesh->GetNumberOfPoints() << std::endl;

However, when I run this program, I receive no cout. I’m not sure if this is because of the program itself or because I’m dealing with a 3D collection of points in the .vtk file

#4

@Henco To print properties of the mesh and learn more about what was read, add:

mesh->Print(std::cout);
#5

Unfortunately I still do not receive any output to the command line even after adding that line.
I believe the problem lies within my data, as removing the reader->Update command causes the mesh->Print(std::cout) line to trigger and print to the command line, albeit only with the templated information.

#6

If the file is opened with a text editor, does the header contain DATASET POLYDATA? .vtk files can contain different data types – polydata is what is supported by these readers.

#7

Yes it does say DATASET POLYDATA

#8

For those following, I was able to get ITK to read in the centerlines as a mesh. I accomplished this by saving the VMTK Centerline Model as a .obj file. This allowed the itk::MeshFileReader to recognize it and read it in as a mesh.
However, this method unfortunately does not retain the radius information of each point.

#9

@Henco thanks for the update.

I am wondering if this is a locale issue, as discussed here?

CC @dzenanz