How to choose certain label in 3d array for meshing? about pygalmesh HOT 3 CLOSED

Hi @thoth291

I've tried to approach your problem from a simpler perspective: by making a simpler double-sphere inside a rectangular volume.
It has three "materials":

• 0 for "the outside"
• 1 for the inner ROI
• 2 for the outer ROI

Here's the script:

import numpy as np
import pygalmesh

Nx = 72
Ny = 41
Nz = 28
h = [0.2] * 3

vol = np.zeros((Nx, Ny, Nz))
X, Y, Z = np.meshgrid(np.linspace(0, Nx * h[0], num=Nx),
                      np.linspace(0, Ny * h[1], num=Ny),
                      np.linspace(0, Nz * h[2], num=Nz), indexing='ij')

x0, y0, z0 = X.mean(), Y.mean(), Z.mean()

# let's define spherical ROIs
roi_outer = (X-x0)**2 + (Y - y0)**2 + (Z - z0)**2 < 2**2
roi_inner = (X-x0)**2 + (Y - y0)**2 + (Z - z0)**2 < 1

# ... and assign some values to them (in reverse order else it will overwrite the previous values)
vol[roi_outer] = 2
vol[roi_inner] = 1

# and let's make a mesh with it
mesh = pygalmesh.generate_from_array(vol.astype(np.uint8), h, facet_distance=0.2, cell_size=0.5)
mesh.write("spheres_in_square.vtk")

Here's the result, visualized with Paraview:

So the implicit convention is that the outer mesh geometry will correspond to class 0. We can test this understanding by initializing the volume with a different value (e.g. 3): vol = np.zeros((Nx, Ny, Nz)) + 3.

In that case, the result is:

I hope this helps you get started.

Cheers
Florian

from pygalmesh.

I'd just play around with the code in the readme.

from pygalmesh.

@nschloe , what I did is simply something like this (not real code):

vol = (vol==1).astype(np.uint8)

And it seems to be doing something, but since I don't know how my mesh should look like in the first place I'm still exploring and testing.

from pygalmesh.