Issues with pygalmesh.generate_2d

[IgnacioEG]

Hello,

I have been using pygalmesh to generate 2D meshes from a polygon defined by points, Also pygalmesh.Extrude to do the same but for extruding and generate a volumen.

When I try some simple polygons it is OK. However,when I try to do so with some more complex polygons (polygons that do not form a convex hull for example) I get some errors and the STL created can not be read by third party softwares.

Is there any restriction on the polygon shape? (For example it has to be convex, etc...)

Regards

[nschloe]

Perhaps, you'll have to ask the cgal folks. Without and MWE, I can't say in anything.

[IgnacioEG]

Hello Nico,

Thanks for your quick response. Please find below an example:

import numpy as np import pygalmesh import pyvista as pv

points=np.array([[-69.5297,-10.9517],[-68.7862,-11.0364],[-68.2713,-11.0145],[-68.0482,-10.7121],[-67.1738,-10.3068],[-66.6469,-9.93133],[-65.3384,-9.76199],[-65.4448,-10.5115],[-65.3219,-10.8959],[-65.4023,-11.5663],[-64.3164,-12.462],[-63.1965,-12.627],[-62.8031,-13.0007],[-62.1271,-13.1988],[-61.7132,-13.4892],[-61.0841,-13.4794],[-60.5033,-13.776],[-60.4592,-14.354],[-60.2643,-14.646],[-60.2511,-15.0772],[-60.543,-15.0939],[-60.1584,-16.2583],[-58.2412,-16.2996],[-58.3881,-16.8771],[-58.2808,-17.2717],[-57.7346,-17.5525],[-57.4984,-18.1742],[-57.676,-18.9618],[-57.95,-19.4],[-57.8538,-19.97],[-58.1664,-20.1767],[-58.1835,-19.8684],[-59.115,-19.3569],[-60.0436,-19.3427],[-61.7863,-19.6337],[-62.266,-20.5137],[-62.2912,-21.0516],[-62.6851,-22.249],[-62.8465,-22.035],[-63.9868,-21.9936],[-64.377,-22.7981],[-64.9649,-22.0759],[-66.2733,-21.8323],[-67.1067,-22.7359],[-67.8282,-22.8729],[-68.2199,-21.4943],[-68.7572,-20.3727],[-68.4422,-19.4051],[-68.9668,-18.9817],[-69.1002,-18.2601],[-69.5904,-17.58],[-68.9596,-16.5007],[-69.3898,-15.6601],[-69.1603,-15.324],[-69.3395,-14.9532],[-68.9489,-14.4536],[-68.9292,-13.6027],[-68.8801,-12.8997],[-68.6651,-12.5613]])

v1=np.arange(0,len(points[:,0]+1)) v2=np.arange(1,len(points[:,0]+1)) v2=np.append(v2,0) constraints=np.hstack((v1[:,np.newaxis],v2[:,np.newaxis])) cons=np.ndarray.tolist(constraints) mesh = pygalmesh.generate_2d(points, cons, cell_size=0.25, num_lloyd_steps=10) mesh.write('example_surface.vtk') mesh2 = pv.read('example_surface.vtk') cpos = mesh2.plot(show_edges=True, color=True)

p = pygalmesh.Polygon2D(points) edge_size = 0.1 domain = pygalmesh.Extrude(p, [0.0, 0.0, 1.0], 0, edge_size) mesh = pygalmesh.generate_mesh( domain, cell_size=0.25, edge_size=edge_size, verbose=False ) mesh.write('example_volume.stl')

mesh3 = pv.read('example_volume.stl')

cpos = mesh3.plot(show_edges=True, color=True)

[nschloe]

Please use code fences. Also, this example isn't minimal. Try to boil it down to much fewer points to still see the error.

[IgnacioEG]

Hello again,

This is the maximum that I reduce the code:

import numpy as np
import pygalmesh

points=np.array([[-69.5297,-10.9517],[-68.7862,-11.0364],[-68.2713,-11.0145],[-68.0482,-10.7121],[-67.1738,-10.3068],[-66.6469,-9.93133],[-65.3384,-9.76199],[-65.4448,-10.5115],[-65.3219,-10.8959],[-65.4023,-11.5663],[-64.3164,-12.462],[-63.1965,-12.627],[-62.8031,-13.0007],[-62.1271,-13.1988],[-61.7132,-13.4892],[-61.0841,-13.4794],[-60.5033,-13.776],[-60.4592,-14.354],[-60.2643,-14.646],[-60.2511,-15.0772],[-60.543,-15.0939],[-60.1584,-16.2583],[-58.2412,-16.2996],[-58.3881,-16.8771],[-58.2808,-17.2717],[-57.7346,-17.5525],[-57.4984,-18.1742],[-57.676,-18.9618],[-57.95,-19.4],[-57.8538,-19.97],[-58.1664,-20.1767],[-58.1835,-19.8684],[-59.115,-19.3569],[-60.0436,-19.3427],[-61.7863,-19.6337],[-62.266,-20.5137],[-62.2912,-21.0516],[-62.6851,-22.249],[-62.8465,-22.035],[-63.9868,-21.9936],[-64.377,-22.7981],[-64.9649,-22.0759],[-66.2733,-21.8323],[-67.1067,-22.7359],[-67.8282,-22.8729],[-68.2199,-21.4943],[-68.7572,-20.3727],[-68.4422,-19.4051],[-68.9668,-18.9817],[-69.1002,-18.2601],[-69.5904,-17.58],[-68.9596,-16.5007],[-69.3898,-15.6601],[-69.1603,-15.324],[-69.3395,-14.9532],[-68.9489,-14.4536],[-68.9292,-13.6027],[-68.8801,-12.8997],[-68.6651,-12.5613]])

p = pygalmesh.Polygon2D(points)
domain = pygalmesh.Extrude(p, [0.0, 0.0, 1.0], 0, edge_size = 0.1)
mesh = pygalmesh.generate_mesh(domain, cell_size=0.25, edge_size=0.1, verbose=False)
mesh.write('example_volume.stl')

[nschloe]

Use triple code fences for code blocks. Also, I tried running your code and got no error.

[IgnacioEG]

Hello,

I don't get an error message either. However, when I try to import the STL with other software (I have tried CST Microwave Studio and also CURA for 3D printing) they say that the STL is corrupt. It seems that the mesh has holes in it.

Please see figures.

[nschloe]

Can you produce an example where the holes are more obvious?

[IgnacioEG]

Yes, in the same example, if you change the cell_size to 2.0 you get this:

[nschloe]

Indeed. I also noticed that you can remove the last point and still get the hole. Please make the example minimal this way, perhaps the issue will jump at us then.

[IgnacioEG]

I made it minimal, I still cannot find any issue. Am I doing something wrong or it is a bug in the code?

import numpy as np
import pygalmesh
points=np.array([[-69.5297,-10.9517],[-62.8031,-13.0007],[-60.543,-15.0939],[-58.1664,-20.1767],[-66.2733,-21.8323],[-68.9489,-14.4536]])

p = pygalmesh.Polygon2D(points)
domain = pygalmesh.Extrude(p, [0.0, 0.0, 1.0], 0, edge_size = 0.5)
mesh = pygalmesh.generate_mesh(domain, cell_size=2.0, edge_size=0.5, verbose=False)
mesh.write('example_volume.stl')

[nschloe]

Again, I can remove the last point and still get the error. Please be more diligent when creating an MWE.

[nschloe]

Also, please try to reproduce the issue with "normal" values, something between 0 and 1 perhaps. I'm sure it'll get much easier.

[IgnacioEG]

Reducing to 4 points and normalizing the coordinates, the problem is still there. Have you experienced something similar before?

import numpy as np
import pygalmesh

points=np.array([[-69.5297,-10.9517],[-60.543,-15.0939],[-58.1664,-20.1767],[-66.2733,-21.8323]])
points[:,0]=points[:,0]-np.min(points[:,0])
points[:,0]=points[:,0]/np.max(points[:,0])
points[:,1]=points[:,1]-np.min(points[:,1])
points[:,1]=points[:,1]/np.max(points[:,1])

p = pygalmesh.Polygon2D(points)
domain = pygalmesh.Extrude(p, [0.0, 0.0, 0.1]*1, 0, edge_size = 0.02)
mesh = pygalmesh.generate_mesh(domain, cell_size=0.02, edge_size=0.02, verbose=False)
mesh.write('example_volume.stl')

[nschloe]

Now it's more complicated then before!

[nschloe]

Make the code simple and easy!

[IgnacioEG]

The example is simpler than before (as it has only 4 points). The code has a couple more of lines now in order to normalize the values (as you requested).

My comment was wether I am doing something wrong or the method has a bug. Best regards

[nschloe]

I didn't request normalization, I requested easier-to-read points. I'm sure it can all be reproduced with [0.0, 0.0], [1.0, 0.7], ... etc.

[nschloe]

I cannot tell if there's an issue without doing some work. If you want me to work for you, you can at least provide a minimal example that's easy to read. It's impolite to just drop your code and expect anyone to plow through it. That said, you're doing a better job than most, I'm just guiding you to create something super simple that everyone can understand at first sight.

[IgnacioEG]

I get your point. Actually I was not expecting from you to work in my code. I just wanted an answer such us: 'actually I found some similar problem in the past with that method' or 'I have tested that method several times and it works, you must do something wrong'. I tried some really simple examples and they do work, but whenever I use some representative example of my problem is when I got troubles, that is why I asked if there was some limitations such as convex envelopes and so.

Althought I do not get the same issue, just with the simple points below, the mesh does something weird in one corner

points=np.array([[0,0],[0.1,0.75],[0.35,0.35],[1.0,0.0]])

[nschloe]

the mesh does something weird in one corner

Absolutely.

I haven't seen anything like this before, so I'll forward this to the CGAL devs. The example now really does look minimal, thanks.

[nschloe]

This has been fixed in CGAL, cf. https://github.com/CGAL/cgal/pull/5251.

[IgnacioEG]

Thanks! What should I do to get it work? I have tried to update to the latest version of pygalmesh via conda or pip but I still get the same result

[nschloe]

Install CGAL from master or wait for their next release.