How to read finite element mesh and view it as UnstructuredGrid - paraview

Question

I want to read a finite element mesh (i.e. a matrix with coordinates and a matrix with connectivity) from a HDF5 file and show it in ParaView, using the Python interface.
I know how to do something simple:
from paraview.simple import *
Sphere()
Show()
Render()
But, how to do the mesh? Let's skip the HDF5 part, and focus on this very simple 2-D mesh comprising 2-D quadrilaterals:
from paraview.simple import *
import numpy as np
coor = np.array([
[ 0.0 , 0.0 ],
[ 1.0 , 0.0 ],
[ 2.0 , 0.0 ],
[ 0.0 , 1.0 ],
[ 1.0 , 1.0 ],
[ 2.0 , 1.0 ],
])
conn = np.array([
[ 0 , 1 , 4 , 3 ],
[ 1 , 2 , 5 , 4 ],
])
Where to go from here?
Possible approach
One possible approach could be to build a vtkUnstructuredGrid. But the problem is that I don't know what to do with it. I.e. how do I tell ParaView to use it?
from paraview import vtk
points = vtk.vtkPoints()
for i,(x,y) in enumerate(coor):
points.InsertNextPoint(x,y,0.0)
grid = vtk.vtkUnstructuredGrid()
for el in conn:
cell = vtk.vtkQuad()
for i,ver in enumerate(el):
cell.GetPointIds().SetId(i,ver)
grid.InsertNextCell(cell.GetCellType(),cell.GetPointIds())
grid.SetPoints(points)
It would be extremely helpful to understand how to include cell-data and point-data, but I can probably figure this out starting from the solution to this problem.

Answer 1

First of all, it is important to note that there are a couple different "levels" of Python usage in ParaView. Your first example is from the high level Python interface to ParaView. Most things you can do in the user interface can be done in ParaView at this level through the Python Console or by running a script through the Python Console.
At a lower level, Python can be used to define operations with VTK. Programmable Filter and Programmable Source is where this level of programming is done. It is important to note that the Programmable Filter and Programmable Source do not know anything about ParaView or paraview.simple - they execute their Python scripts in a Python environment where only VTK is available. If you import paraview.simple for example, the behavior is undefined.
For your purposes, lower level Python programming seems appropriate. I would define a Programmable Source, set its Output Data Set Type to vtkUnstructuredGrid. Next, your script will look something like:
import numpy as np
coor = np.array([
[ 0.0 , 0.0 ],
[ 1.0 , 0.0 ],
[ 2.0 , 0.0 ],
[ 0.0 , 1.0 ],
[ 1.0 , 1.0 ],
[ 2.0 , 1.0 ],
])
conn = np.array([
[ 0 , 1 , 4 , 3 ],
[ 1 , 2 , 5 , 4 ],
])
import vtk
grid = self.GetOutput()
points = vtk.vtkPoints()
for i,(x,y) in enumerate(coor):
points.InsertNextPoint(x,y,0.0)
grid.SetPoints(points)
grid.Allocate()
for el in conn:
cell = vtk.vtkQuad()
for i,ver in enumerate(el):
cell.GetPointIds().InsertId(i,ver)
grid.InsertNextCell(cell.GetCellType(),cell.GetPointIds())

Answer 2

Please give credit to #CoryQuammen because it is really his solution
For future reference the full script, including some cell and point data
from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
# create a new 'Programmable Source'
mesh = ProgrammableSource()
mesh.OutputDataSetType = 'vtkUnstructuredGrid'
mesh.ScriptRequestInformation = ''
mesh.PythonPath = ''
mesh.Script = '''
import numpy as np
coor = np.array([
[ 0.0 , 0.0 ],
[ 1.0 , 0.0 ],
[ 2.0 , 0.0 ],
[ 0.0 , 1.0 ],
[ 1.0 , 1.0 ],
[ 2.0 , 1.0 ],
])
conn = np.array([
[ 0 , 1 , 4 , 3 ],
[ 1 , 2 , 5 , 4 ],
])
celldata = [
1.0 ,
2.0
]
normals = np.array([
[ -1.0 , -1.0 ],
[ 0.0 , -1.0 ],
[ +1.0 , -1.0 ],
[ -1.0 , +1.0 ],
[ 0.0 , +1.0 ],
[ +1.0 , +1.0 ],
])
normals /= np.tile(np.sqrt(np.sum(normals**2.,axis=1)).reshape(-1,1),(1,2))
import vtk
grid = self.GetOutput()
points = vtk.vtkPoints()
for i,(x,y) in enumerate(coor):
points.InsertNextPoint(x,y,0.0)
grid.SetPoints(points)
grid.Allocate()
for el in conn:
cell = vtk.vtkQuad()
for i,ver in enumerate(el):
cell.GetPointIds().InsertId(i,ver)
grid.InsertNextCell(cell.GetCellType(),cell.GetPointIds())
data = vtk.vtkDoubleArray()
data.SetName("Example data")
for i in celldata:
data.InsertNextValue(i)
grid.GetCellData().AddArray(data)
data = vtk.vtkDoubleArray()
data.SetNumberOfComponents(3)
data.SetName("Normals")
for i in normals:
data.InsertNextTuple([i[0],i[1],0.0])
grid.GetPointData().AddArray(data)
'''
# show data from mesh
Mesh = Show(mesh)
Render()