Solving issue SimVascular#2

meshing/convert_vtu_and_vtp.py

@@ -16,7 +16,7 @@
 try:
  import meshio
 except:
- raise ImportError("Could not find meshio, please install by running" + \
+ raise ImportError("Could not find meshio, please install by running" +
  " pip install meshio")
 
 
@@ -135,16 +135,17 @@ def convert_to_dolfin_xdmf(vtp_path, vtu_path, output_path, global_node_ID_name,
  vtp_global_node_ID = msh_vtp.point_data[global_node_ID_name] - 1
 
  # Map the values from the surface to the mesh
- N = msh_vtp.cells["triangle"].shape[0]
- cells = msh_vtp.cells["triangle"].flatten()
+ N = len(msh_vtp.cells[0].data) # number of cells
+ cells = msh_vtp.cells[0].data.flatten()
  mapped_cells = vtp_global_node_ID[cells].reshape((N, 3))
- cell_data = msh_vtp.cell_data["triangle"][face_ID_name]
+ cell_data = msh_vtp.cell_data[face_ID_name]
 
  # Write the boundary markers
  facet_path = output_path.replace(".xdmf", "_facet_markers.xdmf")
  meshio.write(facet_path, meshio.Mesh(points=msh_vtu.points,
- cells={"triangle": mapped_cells},
- cell_data={"triangle": {face_ID_name: cell_data}}))
+ cells=[("triangle", mapped_cells)],
+ cell_data={"triangle": cell_data},
+ field_data={"triangle": {face_ID_name: cell_data}}))
 
 
 def read_command_line():
@@ -171,9 +172,11 @@ def read_command_line():
  if not args.output_path.endswith(".xdmf"):
  raise NameError("The output path to have an .xdmf extension")
  if not args.vtp_path.endswith(".vtp"):
- raise NameError("The input path to the VTP file has to have an .vtp extension")
+ raise NameError(
+ "The input path to the VTP file has to have an .vtp extension")
  if not args.vtu_path.endswith(".vtu"):
- raise NameError("The input path to the VTU file has to have an .vtu extension")
+ raise NameError(
+ "The input path to the VTU file has to have an .vtu extension")
 
  return args.__dict__