edges opening after merging of two meshes

[mkondratyev85]

If I merge two meshes the n_open_edges property of resulting mesh is increasing from 0 to 4.

import pyvista as pv

clipped = pv.read('clipped.vtk')
#clipped.plot()

mesh = pv.read('mesh.vtk')
#mesh.plot()

# n_open_edges is 0
print(mesh.extract_geometry().n_open_edges)

mesh += clipped

# n_open_edges is 4
print(mesh.extract_geometry().n_open_edges)

meshes.zip

I suspect that the issue might be with these 'leafs' on the edges of the mesh:

Am I right? And if I am, how can I remove them from the "clipped" mesh.

[banesullivan]

Hm, this is odd. To start, we can figure out where the edges of the mesh are via the extract_edges filter:

import pyvista as pv

clipped = pv.read('clipped.vtk')
print(clipped.extract_geometry().n_open_edges)

mesh = pv.read('mesh.vtk')
print(mesh.extract_geometry().n_open_edges)

merged = mesh + clipped
print(merged.extract_geometry().n_open_edges)

0
0
4

geom = merged.extract_geometry()
edges = geom.extract_edges(boundary_edges=True,
                   feature_edges=False,
                   manifold_edges=False)

p = pv.Plotter()
p.add_mesh(edges, color="red", line_width=5)
p.add_mesh(mesh, opacity=0.5, color="lightblue")
p.add_mesh(clipped, opacity=0.5, color="green")
p.camera_position = [(7.801336112237166, 251.0279128488682, 236.18977047349765),
 (47.05759233540398, 50.995165371104854, 24.41602276196233),
 (0.18847718989496154, -0.6962632417999844, 0.692599340894485)]
p.show()

but those edges are not open in the original meshes, just the merged mesh. I believe what. is happening here is that there are duplicated nodes and thee + operator is merging those points and opening edges. To avoid this, you should explicitly use the merge filter (the + operator is simply calling that filter with default parameters).

merged = mesh.merge(clipped, merge_points=False)
print(merged.extract_geometry().n_open_edges)

0

[mkondratyev85]

Thank you for the answer. I've tried your suggestion and it has worked!

But when I increase the resolution of my meshes (I try to replicate simple geological structures) I meet the strange error.

meshes.zip

In the meshes.zip are two meshes I try to merge (but with slightly higher resolution). I successfully merge them with your approach. And when I read n_open_edges property of the result it is equal to 0.

Then, after I triangulate the result and save to the vtk file and check if with the Sfepy script that shows you if your mesh is OK it says me following:

sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (/tmp/question/merged.vtk)...
sfepy: ...done in 0.18 s
sfepy: CMesh: n_coor: 9692, dim 3, tdim: 3, n_el 25386
sfepy: element types: ['3_4']
sfepy: nodal BCs: []
sfepy: bounding box:
x: [ 0.0000000e+00,  1.0000000e+02]
y: [-1.7763568e-15,  1.0000000e+02]
z: [-1.4799686e+00,  5.4992756e+01]
sfepy: centre:           [ 5.0000000e+01,  5.0000000e+01,  2.6756394e+01]
sfepy: coordinates mean: [ 5.0114061e+01,  4.9927150e+01,  3.0189309e+01]
sfepy: warning: bad element orientation, trying to correct...
sfepy: ...corrected
sfepy: volumes of 44698 1D entities:
min: 0.0000000e+00 mean: 6.5867666e+00 median: 6.2928724e+00 max: 1.5499791e+01
sfepy: volumes of 60408 2D entities:
min: 0.0000000e+00 mean: 1.3895868e+01 median: 1.4366345e+01 max: 4.2905610e+01
sfepy: volumes of 25386 3D entities:
min: -0.0000000e+00 mean: 9.8874923e+00 median: 9.2336103e+00 max: 2.4642392e+01
sfepy: Euler characteristic: 16
sfepy: number of connected components: 27
sfepy: warning: mesh with topological dimension 2 lower than space dimension 3
sfepy: - element orientation not checked!
sfepy: surface Euler characteristic: 32
sfepy: surface genus: -15.0
sfepy: number of connected surface components: 27

The values of Euler characteristic and number of connected components for the volume mesh must both be equal to 1. In my case it's 16 and 27 for the volume. I don't now where to see these parameters in the pyvista, that's why I showed the result of Sfepy script.

What it could be?

[banesullivan]

Huh, I had never heard of the Euler characteristic (and we do not have a way to compute that in PyVista).

As for the connected surface components... when you merge your meshes, you will have different non-connected components in the merged mesh... in order to not, you'd need to use point merging then repair the open edges with a tool like https://pymeshfix.pyvista.org

[adamgranthendry]

@banesullivan The Euler Characteristic determines the type of surface in topology. In particular, it determines the number of holes an object has. In 3D, the Euler Characteristic is computed as V-E+F. For bodies of genus 0 (i.e. solid bodies without holes), V-E+F=2 (you get this for all the regular polyhedra, for example), where V=Vertices, E=Edges, and F=Faces.