[Python] Gmsh: “Wrong topology of boundary mesh for parametrization” or endless “Partitioning...

I’m trying to turn a 3D STL surface (exported from ImageJ/Fiji segmentation) into a volume mesh in Gmsh using the typical workflow given by the official tutorial (t13). I’m running this with the Gmsh Python API:

n_file = "Birch_745_746-1_Extract3.stl"

gmsh.initialize()
gmsh.clear()
gmsh.model.add(n_file[:-4])
gmsh.merge(n_file)

angle = 40
forceParametrizablePatches = True
includeBoundary = True
curveAngle = 180
gmsh.model.mesh.classifySurfaces(
angle * math.pi / 180.,
includeBoundary,
forceParametrizablePatches,
curveAngle * math.pi / 180.
)


gmsh.model.mesh.createGeometry()

s = gmsh.model.getEntities(2)
l = gmsh.model.geo.addSurfaceLoop([e[1] for e in s])
gmsh.model.geo.addVolume([l])

gmsh.model.geo.synchronize()

gmsh.model.mesh.generate(3)

gmsh.write(f'{n_file[:-4]}.msh')

gmsh.finalize()


with forceParametrizablePatches = True, the method createGeometry raised the error:

Info : [ 10%] Discrete surface 28 is planar, simplifying parametrization
Error : Wrong topology of boundary mesh for parametrization
Exception: Wrong topology of boundary mesh for parametrization


with forceParametrizablePatches = False: tens of thousands of warnings like:

Warning : Partitioning face 1 with 2 triangles that all have the same partition - changing tolerance to 30.55
...
Warning : Tolerance too large - aborting partitioning
Info : Level ... Poincaré characteristic ... not 0


and it never seems to finish.

My STL file comes from the Image/FidJ plugin BoneJ and is a small part of tomography.

You can find the file in the GitHub repository: https://github.com/npistenon/Wood-tomogram.git

What I tried:

• Cleaned STL with various plugin in ImageJ/FidJ and MeshLab
• Cleaning with trimesh package in Python
• Several values for angles But without any improvement.
• Tried gmsh.model.mesh.createTopology() instead of gmsh.model.mesh.createGeometry() and I have got the error:

gmsh.model.mesh.generate(3)
~~~~~~~~~~~~~~~~~~~~~~~~^^^
File "\gmsh.py", line 2060, in generate
raise Exception(logger.getLastError())
Exception: Invalid boundary mesh (overlapping facets) on surface 1 surface 1


Question What exactly causes these “Wrong topology” / “changing tolerance” loops when creating geometry from a surface mesh? How can I get the 3D mesh from my STL file for use in finite element simulation?

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