Create a model/mesh in python from array of vertices and triangles?

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Hi,
I am trying to create a model in python. The model data, i.e. the raw vertices, vertex normals and triangles, will come from reading a non-standard file format in this extension. (Background: The extension will eventually be able to read data exported from an electroanatomic mapping system such as this one.)
I’ve found some guidance here and here, but I am stuck.

I’ve tried:

cubeVerts = [[1.0, 1.0, 1.0],
             [1.0, -1.0, 1.0],
             [-1.0, -1.0, 1.0],
             [-1.0, 1.0, 1.0],
             [1.0, 1.0, -1.0],
             [1.0, -1.0, -1.0],
             [-1.0, -1.0, -1.0],
             [-1.0, 1.0, -1.0]]

cubeTris = [[0,1,2],
            [0,2,3],
            [0,1,5],
            [0,5,4],
            [0,4,7],
            [0,7,3],
            [3,2,6],
            [3,6,7],
            [1,5,7],
            [1,6,2],
            [4,5,6],
            [4,6,7]] 

modelNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLModelNode')
modelPolyData = modelNode.GetPolyData()
modelPolyData.SetVerts(cube)

But since the model created does not contain any points initially, modelPolyData = modelNode.GetPolyData() return nothing and modelPolyData.SetVerts fails with AttributeError: 'NoneType' object has no attribute 'SetVerts'.

I considered using the approach in this example in the script repository and create a dummy sphere first which is then overwritten by the actual data, but here I ran into another problem: vtkPolyData::SetVerts needs a vtkCellArray and I could not find any member function of this type that simply takes an array of point coordinates together with another array of connectivity information.

I even thought about simply writing out a .vtk file line by line from the python script and re-load it into Slicer, but I am sure there is a more elegant solution…

Any help would be appreciated.

Thanks
Stephan

2

In the meantime I have found some very valuable additional resources here, here, and here and have been able to solve the issue.

If someone has the same question in the future: this was my solution (based on the references above).

def mkVtkIdList(it):
  vil = vtk.vtkIdList()
  for i in it:
    vil.InsertNextId(int(i))
  return vil

def CreateMesh(modeNode, arrayVertices, arrayVertexNormals, arrayTriangles, labelsScalars, arrayScalars):
  # modelNode : a vtkMRMLModelNode in the Slicer scene which will hold the mesh
  # arrayVertices : list of triples [[x1,y1,z2], [x2,y2,z2], ... ,[xn,yn,zn]] of vertex coordinates
  # arrayVertexNormals : list of triples [[nx1,ny1,nz2], [nx2,ny2,nz2], ... ] of vertex normals
  # arrayTriangles : list of triples of 0-based indices defining triangles
  # labelsScalars : list of strings such as ["bipolar", "unipolar"] to label the individual scalars data sets
  # arrayScalars : an array of n rows for n vertices and m colums for m inidividual scalar sets

  # create the building blocks of polydata including data attributes.
  mesh    = vtk.vtkPolyData()
  points  = vtk.vtkPoints()
  normals = vtk.vtkFloatArray()
  polys   = vtk.vtkCellArray()
  
  # load the array data into the respective VTK data structures
  for i in range(len(arrayVertices)):
    points.InsertPoint(i, arrayVertices[i])
  
  for i in range(len(arrayTriangles)):
    polys.InsertNextCell(mkVtkIdList(arrayTriangles[i]))
  
  for i in range(len(arrayVertexNormals)):
    normals.InsertTuple3(i, arrayVertexNormals[i][0], arrayVertexNormals[i][1], arrayVertexNormals[i][2])
  
  # put together the mesh object
  mesh.SetPoints(points)
  mesh.SetPolys(polys)
  if(len(arrayVertexNormals) == len(arrayVertices)):
    mesh.GetPointData().SetNormals(normals)
  
  # Add scalars
  scalars = []
  for j in range(len(labelsScalars)):
    scalars.append(vtk.vtkFloatArray())
    
    for i in range(len(arrayVertices)):
      scalars[j].InsertTuple1(i,arrayScalars[i][j])
    
    scalars[j].SetName(labelsScalars[j])
    mesh.GetPointData().AddArray(scalars[j])
  
  modelNode.SetAndObservePolyData(mesh)
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Thank you for the solution, it saved me a lot of time. Ludek