Does marching cubes in vtk require specific input?

Question

The marching cubes class does not generate anything after I passed a ImageData to it.

I am trying to generate surface from a 3D numpy array. I used evtk to export the array to a .vti (Structured Points) file and stored as pointData. Then, read the file by vtkXMLImageDataReader. After passing the output of the Reader (vtkImageData) to vtkMarchingCubes class, the class returns a vtkPolyData with no point or cell, vtkImageData were used in vtk wiki's example, the MarchingCubes class should have no problem to handle it.

I tried to export the ImageData generated by the Reader, the output can be visualized by ParaView without any problem.

I just wondering are there any special requirement for the marching cubes in vtk to generate the surface? It will be even better if the 3D numpy can directly transform to data type that suitable for the MarchingCubes.

Here is my code to read the .vki file and pass it to marching cubes:

dataReader = vtk.vtkXMLImageDataReader()
dataReader.SetFileName('model_name.vti')
dataReader.Update()
contacts = vtk.vtkDiscreteMarchingCubes()
contacts.SetInputConnection(dataReader.GetOutputPort())
contacts.SetValue(0,1)
contacts.ComputeNormalsOn()
contacts.Update()
result = contacts.GetOutput()

Is it possible that the values you specify do not make sense for the input data? — mdurant, Jul 31 '14 at 03:05
The data are ranged [1,7]. I compared the input with examples from vtk. Seems the XMLImageDataReader does not convert the PointDataArray to the scalar and MarchingCubes won't work without scalar... — YC.Chui, Jul 31 '14 at 03:36

score 1 · Answer 1 · answered Jul 31 '14 at 01:09

If you wish to do this in the python/numpy world, then I would suggest using the marching cubes implementation from here (or look at isosurface routines in pyqtgraph, mayavi ...). Although there are many tutorials on moving data to and from VTK, if you are already programming with numpy, I wouldn't mix the two methodologies.

score 0 · Answer 2 · answered May 01 '21 at 18:05

Although this question is quite old already, I ran into a very similar problem.

As YC.Chui pointed out in his comment, we need to set the scalar values in the read data. For me this helped:

reader = vtk.vtkXMLImageDataReader()
reader.SetFileName('model_name.vti')
reader.Update()

readData = reader.GetOutput()
readData.GetPointData().SetScalars(readData.GetPointData().GetArray(0))

I am quite new to VTK and have absolutely no idea why this solves the problem and whether there is a better way. Feel free to comment and correct me!

Does marching cubes in vtk require specific input?

2 Answers2