import gmsh
import sys
import math

gmsh.initialize(sys.argv)

# merge STL, create surface patches that are reparametrizable (so we can remesh
# them) and compute the parametrizations
gmsh.merge('aneurysm_data.stl')
gmsh.model.mesh.classifySurfaces(math.pi, True, True)
gmsh.model.mesh.createGeometry()

# make extrusions only return "top" surfaces and volumes, not lateral surfaces
gmsh.option.setNumber('Geometry.ExtrudeReturnLateralEntities', 0)

# extrude a boundary layer of 4 elements using mesh normals (thickness = 0.5)
gmsh.model.geo.extrudeBoundaryLayer(gmsh.model.getEntities(2), [4], [0.5], True)

# extrude a second boundary layer in the opposite direction (note the `second ==
# True' argument to distinguish it from the first one)
e = gmsh.model.geo.extrudeBoundaryLayer(gmsh.model.getEntities(2), [4], [-0.5],
                                        True, True)

# get "top" surfaces created by extrusion
top_ent = [s for s in e if s[0] == 2]
top_surf = [s[1] for s in top_ent]

# get boundary of top surfaces, i.e. boundaries of holes
gmsh.model.geo.synchronize()
bnd_ent = gmsh.model.getBoundary(top_ent)
bnd_curv = [c[1] for c in bnd_ent]

# create plane surfaces filling the holes
loops = gmsh.model.geo.addCurveLoops(bnd_curv)
for l in loops:
    top_surf.append(gmsh.model.geo.addPlaneSurface([l]))

# create the inner volume
gmsh.model.geo.addVolume([gmsh.model.geo.addSurfaceLoop(top_surf)])
gmsh.model.geo.synchronize()

# use MeshAdapt for the resulting not-so-smooth parametrizations
gmsh.option.setNumber('Mesh.Algorithm', 1)
gmsh.option.setNumber('Mesh.MeshSizeFactor', 0.1)

if '-nopopup' not in sys.argv:
    gmsh.fltk.run()

gmsh.finalize()
