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Interfacing 3D surface mesh data with Numpy
4 years 7 months ago #1898
by MA
Interfacing 3D surface mesh data with Numpy was created by MA
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
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
4 years 7 months ago #1899
by hvwahl
Replied by hvwahl on topic Interfacing 3D surface mesh data with Numpy
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:
Best wishes,
Henry
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]
Best wishes,
Henry
4 years 7 months ago - 4 years 7 months ago #1902
by MA
Replied by MA on topic Interfacing 3D surface mesh data with Numpy
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
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
Last edit: 4 years 7 months ago by MA.
4 years 7 months ago #1904
by hvwahl
Replied by hvwahl on topic Interfacing 3D surface mesh data with Numpy
Hi MA,
sorry, I misunderstood your original question. You can access the coordinates of all triangle vertices
but I guess this is not exactly what you are looking for.
Best wishes,
Henry
sorry, I misunderstood your original question. You can access the coordinates of all triangle vertices
Code:
for el in mesh.Elements2D():
for i in range(3):
print(mesh.Points()[el.vertices[i]])
Best wishes,
Henry
4 years 7 months ago #1906
by MA
Replied by MA on topic Interfacing 3D surface mesh data with Numpy
Thanks Henry,
This helps. Any idea how to find the normal vectors?
Thanks
This helps. Any idea how to find the normal vectors?
Thanks
4 years 7 months ago #1909
by hvwahl
Replied by hvwahl on topic Interfacing 3D surface mesh data with Numpy
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
[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
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