Interfacing 3D surface mesh data with Numpy

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1

Hello,
I’m a new user. So, sorry if my question is too basic.
I have this simple example

import netgen.csg as csg
geo = csg.CSGeometry()
sphere = csg.Sphere(csg.Pnt(0, 0, 0), 3)
geo.Add(sphere)
mesh = geo.GenerateMesh(maxh=1.5)

and I need to store in numpy arrays the information that I am able to store in an STL file without having to export and import again in STL format. Information consists of the coordinates of the 3 points of triangles and the normal vector.

Thank you for your help.

MA

2

Hi MA,

if it is specifically only a numpy array you need to store and reload, numpy has a save function. For more general objects (including ngsolve objects, such as GridFunctions, FESpaces…), you could use pythons pickle module:

[code]import numpy as np
import pickle

x = np.array([1,2,3])
y = np.array([4,5,6])
pickle.dump([x,y], open(“filename”, “wb”))

unpickler = pickle.Unpickler( open(“filename”, “rb”) )
a,b = unpickler.load()

for i in range(len(x)):
assert a[i] == x[i]

for i in range(len(y)):
assert b[i] == y[i][/code]

Best wishes,
Henry

3

Thank you Henry.
However, I want to avoid exporting my mesh into an STL file then read it again to get it stored into a numpy array.
Is there another way to get, for a 3D surface mesh, the coordinates of the 3 points of each elementary triangle (facet) and the local normal vector?
Thanks a lot for your time.
Regards,
MA

4

Hi MA,
sorry, I misunderstood your original question. You can access the coordinates of all triangle vertices

for el in mesh.Elements2D():
	for i in range(3):
		print(mesh.Points()[el.vertices[i]])

but I guess this is not exactly what you are looking for.

Best wishes,
Henry

5

Thanks Henry,
This helps. Any idea how to find the normal vectors?
Thanks

6

not from within netgen. You could always compute a normal as
[tex]\bf n = \frac{ e_1\times e_2}{\Vert e_1\times e_2 \Vert} [/tex]
where
[tex]\bf e_i = v_i - v_3 [/tex]
for i = 1,2 are two of the triangle edges. But these might not be outward pointing.

Best wishes,
Henry