def clean_up_mesh(mesh, tol):
new_mesh, _ = pymesh.remove_isolated_vertices(mesh)
new_mesh, _ = pymesh.remove_duplicated_vertices(new_mesh)
new_mesh, _ = pymesh.remove_duplicated_faces(new_mesh)
new_mesh, _ = pymesh.remove_degenerated_triangles(new_mesh)
new_mesh, _ = pymesh.collapse_short_edges(new_mesh, rel_threshold=0.2)
return new_mesh
def clean_mesh(mesh, connected=True, fill_internals=False):
print('\t - Cleaning mesh (this may take a moment)')
vert_list = []
mesh, info = pymesh.remove_isolated_vertices(mesh)
mesh, info = pymesh.remove_duplicated_vertices(mesh)
mesh, info = pymesh.remove_degenerated_triangles(mesh)
mesh, info = pymesh.remove_duplicated_faces(mesh)
if connected or fill_internals:
mesh_list = pymesh.separate_mesh(mesh, 'auto')
max_verts = 0
print(' - Total number of meshes (ideally 1): %d' % len(mesh_list))
for mesh_obj in mesh_list:
nverts = mesh_obj.num_vertices
if nverts > max_verts:
max_verts = nverts
mesh = mesh_obj
if fill_internals:
for mesh_obj in mesh_list:
if mesh_obj.num_vertices != max_verts:
vert_list.append(mesh_obj.vertices)
return mesh, vert_list
return mesh, vert_list
def fix_mesh(mesh, resolution):
bbox_min, bbox_max = mesh.bbox
diag_len = norm(bbox_max - bbox_min)
target_len = diag_len * resolution
rospy.loginfo("\tTarget resolution: {} mm".format(target_len))
count = 0
mesh, __ = pymesh.remove_degenerated_triangles(mesh, 100)
mesh, __ = pymesh.split_long_edges(mesh, target_len)
num_vertices = mesh.num_vertices
while True:
mesh, __ = pymesh.collapse_short_edges(mesh, 1e-6)
mesh, __ = pymesh.collapse_short_edges(mesh,
target_len,
preserve_feature=True)
mesh, __ = pymesh.remove_obtuse_triangles(mesh, 150.0, 100)
if mesh.num_vertices == num_vertices:
break
num_vertices = mesh.num_vertices
rospy.loginfo("\t#vertices: {}".format(num_vertices))
count += 1
if count > 2: break
mesh = pymesh.resolve_self_intersection(mesh)
mesh, __ = pymesh.remove_duplicated_faces(mesh)
mesh = pymesh.compute_outer_hull(mesh)
mesh, __ = pymesh.remove_duplicated_faces(mesh)
mesh, __ = pymesh.remove_obtuse_triangles(mesh, 179.0, 5)
mesh, __ = pymesh.remove_isolated_vertices(mesh)
return mesh
def repousse(mesh, logger):
cell_ids = mesh.get_attribute("cell").ravel().astype(int);
mesh.add_attribute("edge_length");
tol = np.amax(mesh.get_attribute("edge_length")) * 0.1;
bbox_min, bbox_max = mesh.bbox;
scaling = 2.0 / norm(bbox_max - bbox_min);
start_time = time();
num_cells = np.amax(cell_ids)+1;
results = [];
for i in range(num_cells):
to_keep = np.arange(mesh.num_faces, dtype=int)[cell_ids == i];
if not np.any(to_keep):
continue;
cut_mesh = pymesh.submesh(mesh, to_keep, 0);
pymesh.save_mesh("debug.msh", cut_mesh);
cut_mesh, __ = pymesh.remove_degenerated_triangles(cut_mesh, 100);
cut_mesh, __ = pymesh.split_long_edges(cut_mesh, tol);
dof = cut_mesh.num_vertices;
assembler = pymesh.Assembler(cut_mesh);
L = assembler.assemble("laplacian");
M = assembler.assemble("mass");
L_rhs = M * np.ones(dof) * -0.5;
bd_indices = cut_mesh.boundary_vertices;
n = len(bd_indices);
C = scipy.sparse.coo_matrix((np.ones(n),
(np.arange(n, dtype=int), bd_indices)), shape=(n, dof));
C_rhs = np.zeros(n);
A = scipy.sparse.bmat([
[-L, C.T],
[C, None]
]);
rhs = np.concatenate((L_rhs.ravel(), C_rhs));
solver = pymesh.SparseSolver.create("SparseLU");
solver.compute(A);
x = solver.solve(rhs);
z = x[:dof].reshape((-1, 1));
vertices = np.hstack((cut_mesh.vertices, z));
out_mesh = pymesh.form_mesh(vertices, cut_mesh.faces);
results.append(out_mesh);
finish_time = time();
t = finish_time - start_time;
logger.info("Repousse running time: {}".format(t));
mesh = pymesh.merge_meshes(results);
vertices = mesh.vertices[:,:2];
mesh_2d = pymesh.form_mesh(vertices, mesh.faces);
pymesh.save_mesh("out_2d.msh", mesh_2d)
return mesh;
def downsample_mesh(invert, target_size, in_file, out_file):
min_file_size = target_size * .9
max_file_size = target_size * 1.1
file_size = os.path.getsize(in_file)
mesh = pymesh.meshio.load_mesh(in_file)
temp_file = "/tmp/temp.stl"
segment_len = .40
last_size = None
increment = .1
if file_size > max_file_size:
print("initial size: %sKb, target size: %sKb" %
(f'{file_size // 1024:,}', f'{target_size // 1024:,}'))
while True:
mesh = fix_mesh(mesh, segment_len)
pymesh.meshio.save_mesh(temp_file, mesh)
new_size = os.path.getsize(temp_file)
print("size: %sKb" % (f'{new_size // 1024:,}'))
if new_size <= max_file_size and new_size >= min_file_size:
break
done = False
if last_size:
if new_size > max_file_size and last_size < min_file_size:
increment /= 2.0
segment_len += increment
done = True
elif new_size < min_file_size and last_size > max_file_size:
increment /= 2.0
segment_len -= increment
done = True
if not done:
diff = abs(target_size - new_size)
if diff > (target_size * 3):
adjust = 3
elif diff > (target_size * 2):
adjust = 2
else:
adjust = 1
if new_size > target_size:
segment_len += (adjust * increment)
else:
segment_len -= (adjust * increment)
mesh = pymesh.meshio.load_mesh(in_file)
last_size = new_size
try:
os.unlink(temp_file)
except IOError:
pass
mesh, __ = pymesh.remove_degenerated_triangles(mesh, 100)
mesh = center_around_origin(mesh)
pymesh.meshio.save_mesh(out_file, mesh)
def test_no_degeneracy(self):
mesh = generate_box_mesh(np.ones(3)*-1, np.ones(3));
result, info = remove_degenerated_triangles(mesh);
self.assertEqual(8, result.num_vertices);
self.assertEqual(12, result.num_faces);
self.assert_array_equal(np.arange(12),
sorted(info["ori_face_indices"]));
def fix_mesh(mesh, detail=5e-3):
# "normal": 5e-3
# "high": 2.5e-3
# "low": 2e-2
# "vlow": 2.5e-2
bbox_min, bbox_max = mesh.bbox
diag_len = np.linalg.norm(bbox_max - bbox_min)
if detail is None:
detail = 5e-3
target_len = diag_len * detail
print("Target resolution: {} mm".format(target_len))
count = 0
mesh, __ = pymesh.remove_degenerated_triangles(mesh, 100)
mesh, __ = pymesh.split_long_edges(mesh, target_len)
num_vertices = mesh.num_vertices
while True:
mesh, __ = pymesh.collapse_short_edges(mesh, 1e-4)
mesh, __ = pymesh.collapse_short_edges(mesh,
target_len,
preserve_feature=True)
mesh, __ = pymesh.remove_isolated_vertices(mesh)
mesh, __ = pymesh.remove_duplicated_vertices(mesh, tol=1e-4)
mesh, __ = pymesh.remove_duplicated_faces(mesh)
mesh, __ = pymesh.remove_degenerated_triangles(mesh)
mesh, __ = pymesh.remove_isolated_vertices(mesh)
mesh, __ = pymesh.remove_obtuse_triangles(mesh, 150.0, 100)
if mesh.num_vertices == num_vertices:
break
num_vertices = mesh.num_vertices
print("fix #v: {}".format(num_vertices))
count += 1
if count > 10:
break
mesh = pymesh.resolve_self_intersection(mesh)
mesh, __ = pymesh.remove_duplicated_faces(mesh)
mesh = pymesh.compute_outer_hull(mesh)
mesh, __ = pymesh.remove_duplicated_faces(mesh)
mesh, __ = pymesh.remove_obtuse_triangles(mesh, 179.0, 5)
mesh, __ = pymesh.remove_isolated_vertices(mesh)
return mesh
def test_no_degeneracy(self):
mesh = generate_box_mesh(np.ones(3) * -1, np.ones(3))
result, info = remove_degenerated_triangles(mesh)
self.assertEqual(8, result.num_vertices)
self.assertEqual(12, result.num_faces)
self.assert_array_equal(np.arange(12),
sorted(info["ori_face_indices"]))
def repousse(mesh, logger):
cell_ids = mesh.get_attribute("cell").ravel().astype(int)
mesh.add_attribute("edge_length")
tol = np.amax(mesh.get_attribute("edge_length")) * 0.1
bbox_min, bbox_max = mesh.bbox
scaling = 2.0 / norm(bbox_max - bbox_min)
start_time = time()
num_cells = np.amax(cell_ids) + 1
results = []
for i in range(num_cells):
to_keep = np.arange(mesh.num_faces, dtype=int)[cell_ids == i]
if not np.any(to_keep):
continue
cut_mesh = pymesh.submesh(mesh, to_keep, 0)
pymesh.save_mesh("debug.msh", cut_mesh)
cut_mesh, __ = pymesh.remove_degenerated_triangles(cut_mesh, 100)
cut_mesh, __ = pymesh.split_long_edges(cut_mesh, tol)
dof = cut_mesh.num_vertices
assembler = pymesh.Assembler(cut_mesh)
L = assembler.assemble("laplacian")
M = assembler.assemble("mass")
L_rhs = M * np.ones(dof) * -0.5
bd_indices = cut_mesh.boundary_vertices
n = len(bd_indices)
C = scipy.sparse.coo_matrix(
(np.ones(n), (np.arange(n, dtype=int), bd_indices)),
shape=(n, dof))
C_rhs = np.zeros(n)
A = scipy.sparse.bmat([[-L, C.T], [C, None]])
rhs = np.concatenate((L_rhs.ravel(), C_rhs))
solver = pymesh.SparseSolver.create("SparseLU")
solver.compute(A)
x = solver.solve(rhs)
z = x[:dof].reshape((-1, 1))
vertices = np.hstack((cut_mesh.vertices, z))
out_mesh = pymesh.form_mesh(vertices, cut_mesh.faces)
results.append(out_mesh)
finish_time = time()
t = finish_time - start_time
logger.info("Repousse running time: {}".format(t))
mesh = pymesh.merge_meshes(results)
vertices = mesh.vertices[:, :2]
mesh_2d = pymesh.form_mesh(vertices, mesh.faces)
pymesh.save_mesh("out_2d.msh", mesh_2d)
return mesh
def fix_meshes(mesh, detail="normal"):
meshCopy = mesh
# copy/pasta of pymesh script fix_mesh from qnzhou, see pymesh on GitHub
bbox_min, bbox_max = mesh.bbox
diag_len = np.linalg.norm(bbox_max - bbox_min)
if detail == "normal":
target_len = diag_len * 5e-3
elif detail == "high":
target_len = diag_len * 2.5e-3
elif detail == "low":
target_len = diag_len * 1e-2
count = 0
mesh, __ = pymesh.remove_degenerated_triangles(mesh, 100)
mesh, __ = pymesh.split_long_edges(mesh, target_len)
num_vertices = mesh.num_vertices
while True:
mesh, __ = pymesh.collapse_short_edges(mesh, 1e-6)
mesh, __ = pymesh.collapse_short_edges(mesh,
target_len,
preserve_feature=True)
mesh, __ = pymesh.remove_obtuse_triangles(mesh, 150.0, 100)
if mesh.num_vertices == num_vertices:
break
num_vertices = mesh.num_vertices
count += 1
if count > 10:
break
mesh = pymesh.resolve_self_intersection(mesh)
mesh, __ = pymesh.remove_duplicated_faces(mesh)
mesh = pymesh.compute_outer_hull(mesh)
mesh, __ = pymesh.remove_duplicated_faces(mesh)
mesh, __ = pymesh.remove_obtuse_triangles(mesh, 179.0, 5)
mesh, __ = pymesh.remove_isolated_vertices(mesh)
if is_mesh_broken(mesh, meshCopy) is True:
if detail == "high":
print(
f'The function fix_meshes broke mesh, trying with lower details settings'
)
fix_meshes(mesh, detail="normal")
if detail == "normal":
print(
f'The function fix_meshes broke mesh, trying with lower details settings'
)
fix_meshes(mesh, detail="low")
if detail == "low":
print(
f'The function fix_meshes broke mesh, no lower settings can be applied, no fix was done'
)
return meshCopy
else:
return mesh
def clean(vertices, faces, duplicate_tol=1e-12):
mesh = pymesh.meshio.form_mesh(vertices, faces)
mesh = pymesh.remove_isolated_vertices(mesh)[0]
mesh = pymesh.remove_duplicated_vertices(mesh, tol=duplicate_tol)[0]
mesh = remove_duplicated_faces(mesh)[0]
# mesh = pymesh.remove_duplicated_faces(mesh, fins_only=True)[0]
mesh = pymesh.remove_degenerated_triangles(mesh)[0]
mesh = pymesh.resolve_self_intersection(mesh)
# meshes = pymesh.separate_mesh(mesh)
# for i, mesh in enumerate(meshes):
# meshes[i] = make_face_normals_consistent(mesh)
# mesh = pymesh.merge_meshes(meshes)
return mesh.vertices, mesh.faces
def remesh(path1):
"""
This function takes a path to the orginal shapenet model and subsample it nicely
"""
obj1 = pymesh.load_mesh(path1)
obj1, info = pymesh.remove_isolated_vertices(obj1)
print("Removed {} isolated vertices".format(info["num_vertex_removed"]))
obj1, info = pymesh.remove_duplicated_vertices(obj1)
print("Merged {} duplicated vertices".format(info["num_vertex_merged"]))
obj1, _ = pymesh.remove_degenerated_triangles(obj1)
if len(obj1.vertices) < 5000:
while len(obj1.vertices) < 5000:
obj1 = pymesh.subdivide(obj1)
obj1 = pymesh.form_mesh(obj1.vertices, obj1.faces)
return obj1
def link(path1):
"""
This function takes a path to the orginal shapenet model and subsample it nicely
"""
obj1 = pymesh.load_mesh(path1)
# obj1, info = pymesh.remove_isolated_vertices(mesh)
obj1, info = pymesh.remove_isolated_vertices(obj1)
print("Removed {} isolated vertices".format(info["num_vertex_removed"]))
obj1, info = pymesh.remove_duplicated_vertices(obj1)
print("Merged {} duplicated vertices".format(info["num_vertex_merged"]))
obj1, info = pymesh.remove_degenerated_triangles(obj1)
new_mesh = pymesh.form_mesh(
normalize_points.BoundingBox(torch.from_numpy(obj1.vertices)).numpy(),
obj1.faces)
return new_mesh
def gre_remesh(mesh, detail="normal"):
bbox_min, bbox_max = mesh.bbox
diag_len = norm(bbox_max - bbox_min)
if detail == "normal":
target_len = diag_len * 5e-3
elif detail == "high":
target_len = diag_len * 2.5e-3
elif detail == "low":
target_len = diag_len * 1e-2
print("Target resolution: {} mm".format(target_len))
# -- pseudocódigo --
# while L is not empty
# pop one bad facet f from L
# cf = dual(f) ∩ S
# insert cf to P
# update Del(P)
# update DelS (P)
# update L, i.e.,
# remove facets of L that are no longer facets of DelS (P)
# add new bad facets of DelS (P) to L
mesh, __ = pymesh.remove_degenerated_triangles(mesh, 100)
num_vertices = mesh.num_vertices
p = mesh.vertices #conjunto P de pontos da malha
del_p, dels_p, bad_facets = delaunay_triang(p) # triagulação de Delauney
l = bad_facets #lista L de faceta ruins de Dels(P)
while True:
if len(l) == 0: break
f = l.pop()
cf = intersection(dual(f), mesh)
p.append(cf)
del_p, dels_p, bad_facets = delaunay_triang(p)
l = bad_facets
num_vertices = mesh.num_vertices
print("#v: {}".format(num_vertices))
# mesh = pymesh.resolve_self_intersection(mesh)
# mesh, __ = pymesh.remove_duplicated_faces(mesh)
# mesh = pymesh.compute_outer_hull(mesh)
# mesh, __ = pymesh.remove_duplicated_faces(mesh)
# mesh, __ = pymesh.remove_obtuse_triangles(mesh, 179.0, 5)
# mesh, __ = pymesh.remove_isolated_vertices(mesh)
return mesh
def fix_mesh(mesh):
mesh, __ = pymesh.remove_degenerated_triangles(mesh, 100)
log_mesh(mesh, "Remove degenerate faces")
mesh, __ = pymesh.collapse_short_edges(mesh, MIN_RES, preserve_feature=True)
log_mesh(mesh, "Collapse short edges")
mesh = pymesh.resolve_self_intersection(mesh)
mesh, __ = pymesh.remove_duplicated_faces(mesh)
log_mesh(mesh, "Remove self intersections")
mesh = pymesh.compute_outer_hull(mesh)
mesh, __ = pymesh.remove_duplicated_faces(mesh)
log_mesh(mesh, "New hull, remove duplicates")
mesh, __ = pymesh.remove_obtuse_triangles(mesh, 179.5, 5)
log_mesh(mesh, "Remote obtuse faces")
mesh, __ = pymesh.remove_isolated_vertices(mesh)
log_mesh(mesh, "Remove isolated vertices")
return mesh
def read_trimesh(path, normal=False, clean=True):
mesh = pymesh.load_mesh(path)
if clean:
mesh, info = pymesh.remove_isolated_vertices(mesh)
print("Removed {} isolated vertices".format(info["num_vertex_removed"]))
mesh, info = pymesh.remove_duplicated_vertices(mesh)
print("Merged {} duplicated vertices".format(info["num_vertex_merged"]))
mesh, info = pymesh.remove_degenerated_triangles(mesh)
mesh = pymesh.form_mesh(mesh.vertices, mesh.faces)
vertices = mesh.vertices
if normal:
mesh.add_attribute("vertex_normal")
vertex_normals = mesh.get_attribute("vertex_normal").reshape(-1, 3)
vertices = np.concatenate([vertices, vertex_normals], axis=-1)
return vertices, mesh.faces
def execute(self, context):
scene = context.scene
pymesh_props = scene.pymesh
obj_a = context.active_object
mesh_a = import_object(context, obj_a)
pymesh_r, info = pymesh.remove_degenerated_triangles(mesh_a)
pymesh_r, info = pymesh.remove_obtuse_triangles(pymesh_r)
pymesh_r, info = pymesh.remove_duplicated_faces(pymesh_r)
pymesh_r, info = pymesh.collapse_short_edges(pymesh_r)
pymesh_r, info = pymesh.remove_duplicated_vertices(pymesh_r)
pymesh_r, info = pymesh.remove_isolated_vertices(pymesh_r)
off_name = "Py.Clean." + obj_a.name
mesh_r = export_mesh(context, pymesh_r, off_name)
add_to_scene(context, mesh_r)
return {'FINISHED'}
def fix_mesh(mesh, detail="normal"):
bbox_min, bbox_max = mesh.bbox
diag_len = norm(bbox_max - bbox_min)
if detail == "normal":
target_len = diag_len * 1e-2
elif detail == "high":
target_len = diag_len * 5e-3
elif detail == "low":
target_len = diag_len * 0.03
print("Target resolution: {} mm".format(target_len))
count = 0
mesh, __ = pymesh.remove_degenerated_triangles(mesh, 100)
mesh, __ = pymesh.split_long_edges(mesh, target_len)
num_vertices = mesh.num_vertices
while True:
mesh, __ = pymesh.collapse_short_edges(mesh, 1e-6)
mesh, __ = pymesh.collapse_short_edges(mesh,
target_len,
preserve_feature=True)
mesh, __ = pymesh.remove_obtuse_triangles(mesh, 150.0, 100)
if mesh.num_vertices == num_vertices:
break
num_vertices = mesh.num_vertices
print("#v: {}".format(num_vertices))
count += 1
if count > 10:
break
mesh = pymesh.resolve_self_intersection(mesh)
mesh, __ = pymesh.remove_duplicated_faces(mesh)
mesh = pymesh.compute_outer_hull(mesh)
mesh, __ = pymesh.remove_duplicated_faces(mesh)
mesh, __ = pymesh.remove_obtuse_triangles(mesh, 179.0, 5)
mesh, __ = pymesh.remove_isolated_vertices(mesh)
return mesh
def scale_mesh(invert, len, in_file, out_file):
mesh = pymesh.meshio.load_mesh(in_file)
mesh = fix_mesh(mesh, len)
mesh, __ = pymesh.remove_degenerated_triangles(mesh, 100)
mesh = center_around_origin(mesh)
if mesh.num_vertices == 0 or mesh.num_faces == 0:
printf("ERROR: segment len is too small, no vertices/faces are left.")
return
if invert:
mesh = flip_mesh(mesh)
print(" flip: %d vertexes, %d faces." %
(mesh.num_vertices, mesh.num_faces))
pymesh.meshio.save_mesh(out_file, mesh)
def fix_mesh(mesh, detail="normal"):
bbox_min, bbox_max = mesh.bbox;
diag_len = norm(bbox_max - bbox_min);
if detail == "normal":
target_len = diag_len * 1e-2;
#target_len = diag_len * 5e-3;
elif detail == "enormal":
target_len = diag_len * 5e-3
elif detail == "high":
target_len = diag_len * 3e-3
#target_len = diag_len * 2.5e-3;
elif detail == "low":
target_len = diag_len * 1e-2;
elif detail == "ehigh":
target_len = diag_len * 1e-3;
print("Target resolution: {} mm".format(target_len));
count = 0;
mesh, __ = pymesh.remove_degenerated_triangles(mesh, 100);
mesh, __ = pymesh.split_long_edges(mesh, target_len);
num_vertices = mesh.num_vertices;
while True:
#mesh, __ = pymesh.collapse_short_edges(mesh, 1e-6);
if detail == "low":
mesh, __ = pymesh.collapse_short_edges(mesh, target_len, preserve_feature=False);
else:
mesh, __ = pymesh.collapse_short_edges(mesh, target_len, preserve_feature=True);
mesh, __ = pymesh.remove_obtuse_triangles(mesh, 150.0, 100);
if mesh.num_vertices == num_vertices:
break;
num_vertices = mesh.num_vertices;
print("#v: {}".format(num_vertices));
count += 1;
if count > 10: break;
mesh = pymesh.resolve_self_intersection(mesh);
mesh, __ = pymesh.remove_duplicated_faces(mesh);
mesh = pymesh.compute_outer_hull(mesh);
mesh, __ = pymesh.remove_duplicated_faces(mesh);
mesh, __ = pymesh.remove_obtuse_triangles(mesh, 179.0, 5);
mesh, __ = pymesh.remove_isolated_vertices(mesh);
return mesh;
def repousse_all(mesh, logger):
cell_ids = mesh.get_attribute("cell").ravel().astype(int);
mesh.add_attribute("edge_length");
tol = np.amax(mesh.get_attribute("edge_length")) * 0.1;
out_mesh, info = pymesh.remove_degenerated_triangles(mesh, 100);
cell_ids = cell_ids[info["ori_face_indices"]].ravel();
mesh, info = pymesh.split_long_edges(out_mesh, tol);
cell_ids = cell_ids[info["ori_face_indices"]].ravel();
mesh.enable_connectivity();
is_border = [len(np.unique(cell_ids[mesh.get_vertex_adjacent_faces(vi)])) > 1
for vi in range(mesh.num_vertices)];
start_time = time();
dof = mesh.num_vertices;
assembler = pymesh.Assembler(mesh);
L = assembler.assemble("laplacian");
M = assembler.assemble("mass");
L_rhs = M * np.ones(dof) * -1 * 1e-1;
bd_indices = np.arange(mesh.num_vertices, dtype=int)[is_border];
n = len(bd_indices);
C = scipy.sparse.coo_matrix((np.ones(n),
(np.arange(n, dtype=int), bd_indices)), shape=(n, dof));
C_rhs = np.zeros(n);
A = scipy.sparse.bmat([
[-L, C.T],
[C, None]
]);
rhs = np.concatenate((L_rhs.ravel(), C_rhs));
solver = pymesh.SparseSolver.create("SparseLU");
solver.compute(A);
x = solver.solve(rhs);
z = x[:dof].reshape((-1, 1));
vertices = np.hstack((mesh.vertices, z));
finish_time = time();
t = finish_time - start_time;
logger.info("Repousse running time: {}".format(t));
return pymesh.form_mesh(vertices, mesh.faces);
def fix_mesh(mesh, target_len):
bbox_min, bbox_max = mesh.bbox
diag_len = np.linalg.norm(bbox_max - bbox_min)
count = 0
print(" remove degenerated triangles")
mesh, __ = pymesh.remove_degenerated_triangles(mesh, 100)
print(" split long edges")
mesh, __ = pymesh.split_long_edges(mesh, target_len)
num_vertices = mesh.num_vertices
while True:
print(" pass %d" % count)
print(" collapse short edges #1")
mesh, __ = pymesh.collapse_short_edges(mesh, 1e-6)
print(" collapse short edges #2")
mesh, __ = pymesh.collapse_short_edges(mesh,
target_len,
preserve_feature=True)
print(" remove obtuse triangles")
mesh, __ = pymesh.remove_obtuse_triangles(mesh, 150.0, 100)
print(" %d of %s vertices." % (num_vertices, mesh.num_vertices))
if mesh.num_vertices == num_vertices:
break
num_vertices = mesh.num_vertices
count += 1
if count > 10: break
print(" resolve self intersection")
mesh = pymesh.resolve_self_intersection(mesh)
print(" remove duplicated faces")
mesh, __ = pymesh.remove_duplicated_faces(mesh)
print(" computer outer hull")
mesh = pymesh.compute_outer_hull(mesh)
print(" remove duplicated faces")
mesh, __ = pymesh.remove_duplicated_faces(mesh)
print(" remove obtuse triangles")
mesh, __ = pymesh.remove_obtuse_triangles(mesh, 179.0, 5)
print(" remove isolated vertices")
mesh, __ = pymesh.remove_isolated_vertices(mesh)
return mesh
def repousse_all(mesh, logger):
cell_ids = mesh.get_attribute("cell").ravel().astype(int)
mesh.add_attribute("edge_length")
tol = np.amax(mesh.get_attribute("edge_length")) * 0.1
out_mesh, info = pymesh.remove_degenerated_triangles(mesh, 100)
cell_ids = cell_ids[info["ori_face_indices"]].ravel()
mesh, info = pymesh.split_long_edges(out_mesh, tol)
cell_ids = cell_ids[info["ori_face_indices"]].ravel()
mesh.enable_connectivity()
is_border = [
len(np.unique(cell_ids[mesh.get_vertex_adjacent_faces(vi)])) > 1
for vi in range(mesh.num_vertices)
]
start_time = time()
dof = mesh.num_vertices
assembler = pymesh.Assembler(mesh)
L = assembler.assemble("laplacian")
M = assembler.assemble("mass")
L_rhs = M * np.ones(dof) * -1 * 1e-1
bd_indices = np.arange(mesh.num_vertices, dtype=int)[is_border]
n = len(bd_indices)
C = scipy.sparse.coo_matrix(
(np.ones(n), (np.arange(n, dtype=int), bd_indices)), shape=(n, dof))
C_rhs = np.zeros(n)
A = scipy.sparse.bmat([[-L, C.T], [C, None]])
rhs = np.concatenate((L_rhs.ravel(), C_rhs))
solver = pymesh.SparseSolver.create("SparseLU")
solver.compute(A)
x = solver.solve(rhs)
z = x[:dof].reshape((-1, 1))
vertices = np.hstack((mesh.vertices, z))
finish_time = time()
t = finish_time - start_time
logger.info("Repousse running time: {}".format(t))
return pymesh.form_mesh(vertices, mesh.faces)
def filter(self):
mesh = pymesh.form_mesh(self.mesh.points.values,
self.mesh.cells.values)
mesh, _ = pymesh.remove_degenerated_triangles(mesh,
self.max_iterations)
mesh, _ = pymesh.split_long_edges(mesh, self.size)
num_vertices = mesh.num_vertices
for _ in range(self.max_iterations):
mesh, _ = pymesh.collapse_short_edges(mesh,
self.size,
preserve_feature=True)
mesh, _ = pymesh.remove_obtuse_triangles(mesh, self.max_angle,
self.max_iterations)
if mesh.num_vertices == num_vertices:
break
num_vertices = mesh.num_vertices
return self.mesh.mesh_class()(mesh, parents=[self.mesh])
def fix_mesh(mesh, detail="normal"):
bbox_min, bbox_max = mesh.bbox;
diag_len = norm(bbox_max - bbox_min);
if detail == "normal":
target_len = diag_len * 5e-3;
elif detail == "high":
target_len = diag_len * 2.5e-3;
elif detail == "low":
target_len = diag_len * 1e-2;
print("Target resolution: {} mm".format(target_len));
count = 0;
mesh, __ = pymesh.remove_degenerated_triangles(mesh, 100);
mesh, __ = pymesh.split_long_edges(mesh, target_len);
num_vertices = mesh.num_vertices;
while True:
mesh, __ = pymesh.collapse_short_edges(mesh, 1e-6);
mesh, __ = pymesh.collapse_short_edges(mesh, target_len,
preserve_feature=True);
mesh, __ = pymesh.remove_obtuse_triangles(mesh, 150.0, 100);
if mesh.num_vertices == num_vertices:
break;
num_vertices = mesh.num_vertices;
print("#v: {}".format(num_vertices));
count += 1;
if count > 10: break;
mesh = pymesh.resolve_self_intersection(mesh);
mesh, __ = pymesh.remove_duplicated_faces(mesh);
mesh = pymesh.compute_outer_hull(mesh);
mesh, __ = pymesh.remove_duplicated_faces(mesh);
mesh, __ = pymesh.remove_obtuse_triangles(mesh, 179.0, 5);
mesh, __ = pymesh.remove_isolated_vertices(mesh);
return mesh;
def main():
args = parse_args()
mesh = pymesh.load_mesh(args.input_mesh)
mesh, __ = pymesh.remove_degenerated_triangles(mesh, args.num_iterations)
pymesh.save_mesh(args.output_mesh, mesh)
def regularise_mesh(mesh, tol):
"""Takes mesh & resizes triangles to tol size"""
mesh, __ = pymesh.remove_degenerated_triangles(mesh, 100)
mesh, _info = pymesh.split_long_edges(mesh, tol)
mesh, __ = pymesh.collapse_short_edges(mesh, 1e-6)
mesh, _info = pymesh.collapse_short_edges(mesh, tol, preserve_feature=True)
def fix_meshes(mesh, detail="normal"):
"""
A pipeline to optimise and fix mesh based on pymesh Mesh object.
1. A box is created around the mesh.
2. A target length is found based on diagonal of the mesh box.
3. You can choose between 3 level of details, normal details settings seems to be a good compromise between
final mesh size and sufficient number of vertices. It highly depends on your final goal.
4. Remove degenerated triangles aka collinear triangles composed of 3 aligned points. The number of iterations is 5
and should remove all degenerated triangles
5. Remove isolated vertices, not connected to any faces or edges
6. Remove self intersection edges and faces which is not realistic
7. Remove duplicated faces
8. The removing of duplicated faces can leave some vertices alone, we will removed them
9. The calculation of outer hull volume is useful to be sure that the mesh is still ok
10. Remove obtuse triangles > 179 who is not realistic and increase computation time
11. We will remove potential duplicated faces again
12. And duplicated vertices again
13. Finally we will look if the mesh is broken or not. If yes we will try lower settings, if the lowest settings
broke the mesh we will return the initial mesh. If not, we will return the optimised mesh.
:param mesh: Pymesh Mesh object to optimise
:param detail: string 'high', 'normal' or 'low' ('normal' as default), or float/int
Settings to choose the targeting minimum length of edges
:return: Pymesh Mesh object
An optimised mesh or not depending on detail settings and mesh quality
"""
meshCopy = mesh
# copy/pasta of pymesh script fix_mesh from qnzhou, see pymesh on GitHub
bbox_min, bbox_max = mesh.bbox
diag_len = np.linalg.norm(bbox_max - bbox_min)
if detail == "normal":
target_len = diag_len * 5e-3
elif detail == "high":
target_len = diag_len * 2.5e-3
elif detail == "low":
target_len = diag_len * 1e-2
elif detail is float or detail is int and detail > 0:
target_len = diag_len * detail
else:
print(
'Details settings is invalid, must be "low", "normal", "high" or positive int or float'
)
quit()
count = 0
mesh, __ = pymesh.remove_degenerated_triangles(mesh, 5)
mesh, __ = pymesh.split_long_edges(mesh, target_len)
num_vertices = mesh.num_vertices
while True:
mesh, __ = pymesh.collapse_short_edges(mesh,
target_len,
preserve_feature=True)
mesh, info = pymesh.remove_obtuse_triangles(mesh, 179.0, 5)
if mesh.num_vertices == num_vertices:
break
num_vertices = mesh.num_vertices
count += 1
if count > 10:
break
mesh, __ = pymesh.remove_duplicated_vertices(mesh)
mesh, __ = pymesh.remove_isolated_vertices(mesh)
mesh = pymesh.resolve_self_intersection(mesh)
mesh, __ = pymesh.remove_duplicated_faces(mesh)
mesh, __ = pymesh.remove_duplicated_vertices(mesh)
mesh = pymesh.compute_outer_hull(mesh)
mesh, __ = pymesh.remove_obtuse_triangles(mesh, 179.0, 5)
mesh, __ = pymesh.remove_duplicated_faces(mesh)
mesh, __ = pymesh.remove_isolated_vertices(mesh)
if is_mesh_broken(mesh, meshCopy) is True:
if detail == "high":
print(
f'The function fix_meshes broke mesh, trying with lower details settings'
)
fix_meshes(meshCopy, detail="normal")
return mesh
if detail == "normal":
print(
f'The function fix_meshes broke mesh, trying with lower details settings'
)
mesh = fix_meshes(meshCopy, detail="low")
return mesh
if detail == "low":
print(
f'The function fix_meshes broke mesh, no lower settings can be applied, no fix was done'
)
return meshCopy
else:
return mesh
def main():
args = parse_args();
mesh = pymesh.load_mesh(args.input_mesh);
mesh, __ = pymesh.remove_degenerated_triangles(mesh, args.num_iterations);
pymesh.save_mesh(args.output_mesh, mesh);
def symmetrize(verts, faces, eps=1e-3):
"""
verts: N,3 (x,y,z) tensor
faces: F,3 (0,1,2) tensor
Modifies mesh to make it symmetric about y-z plane
- Cut mesh into half
- Copy left half into right half
- merge, remove duplicate vertices
"""
# Snap vertices close to centre to centre
verts_centre_mask = (verts[:,0].abs() < eps)
verts[verts_centre_mask, 0] = 0
# import pymesh
pmesh = pymesh.form_mesh(verts.numpy(), faces.numpy())
pymesh.save_mesh(f'csm_mesh/debug/1.obj', pmesh)
# Categorize vertices into left (-1), centre(0), right(1)
verts_side = torch.sign(verts[:,0])
# Categorize faces into left (-1), centre(0), right(1)
face_verts_side = torch.index_select(verts_side, 0, faces.view(-1))
face_verts_side = face_verts_side.contiguous().view(faces.shape[0], 3)
face_left_mask = (face_verts_side[:,0]==-1) & (face_verts_side[:,1]==-1) & (face_verts_side[:,2]==-1)
face_right_mask = (face_verts_side[:,0]==1) & (face_verts_side[:,1]==1) & (face_verts_side[:,2]==1)
face_intesects_yz = (~face_left_mask) & (~face_right_mask)
# Split intersecting faces
new_verts = []
new_faces = []
for f in face_intesects_yz.nonzero().squeeze(1):
i0, i1, i2 = faces[f]
if verts_side[i0]==verts_side[i1]:
i0, i1, i2 = i2, i0, i1
elif verts_side[i2]==verts_side[i1]:
i0, i1, i2 = i0, i1, i2
elif verts_side[i0]==verts_side[i2]:
i0, i1, i2 = i1, i0, i2
elif verts_side[i0]==-1:
i0, i1, i2 = i0, i1, i2
elif verts_side[i1]==-1:
i0, i1, i2 = i1, i0, i2
elif verts_side[i2]==-1:
i0, i1, i2 = i2, i0, i1
else:
import ipdb; ipdb.set_trace()
# yz axis intersects i0->i1 & i0->i2
assert(verts_side[i0] != verts_side[i1])
assert(verts_side[i0] != verts_side[i2])
v0 = verts[i0]
v1 = verts[i1]
v2 = verts[i2]
v_n1 = (v0 * v1[0] - v1 * v0[0])/(v1[0] - v0[0])
v_n2 = (v0 * v2[0] - v2 * v0[0])/(v2[0] - v0[0])
i_n1 = verts.shape[0] + len(new_verts)
i_n2 = verts.shape[0] + len(new_verts) + 1
new_verts.append(v_n1)
new_verts.append(v_n2)
new_faces.append((i0, i_n1, i_n2))
new_faces.append((i1, i_n1, i_n2))
new_faces.append((i1, i2, i_n2))
new_verts = torch.stack(new_verts, dim=0)
new_faces = torch.tensor(new_faces, dtype=faces.dtype, device=faces.device)
verts = torch.cat([verts, new_verts], dim=0)
faces = torch.index_select(faces, 0, (~face_intesects_yz).nonzero().squeeze(1))
faces = torch.cat([faces, new_faces], dim=0)
# import pymesh
pmesh = pymesh.form_mesh(verts.numpy(), faces.numpy())
pymesh.save_mesh(f'csm_mesh/debug/2.obj', pmesh)
# Merge vertices that are very close together
vertex_mapping = []
verts_new = []
for v_id in range(verts.shape[0]):
if v_id==0:
vertex_mapping.append(0)
verts_new.append(verts[0])
continue
min_d, min_idx = (verts[0:v_id] - verts[v_id]).norm(dim=-1).min(dim=0)
if min_d < eps:
vertex_mapping.append(vertex_mapping[min_idx])
else:
vertex_mapping.append(len(verts_new))
verts_new.append(verts[v_id])
assert(len(vertex_mapping)==verts.shape[0])
vertex_mapping = torch.tensor(vertex_mapping, dtype=faces.dtype, device=faces.device)
verts = torch.stack(verts_new, dim=0)
faces = vertex_mapping[faces]
# Remove degenerate faces
faces_degenerate = (faces[:,0]==faces[:,1]) | (faces[:,0]==faces[:,2]) | (faces[:,2]==faces[:,1])
faces = torch.index_select(faces, 0, (~faces_degenerate).nonzero().squeeze(1))
# import pymesh
pmesh = pymesh.form_mesh(verts.numpy(), faces.numpy())
pymesh.save_mesh(f'csm_mesh/debug/3.obj', pmesh)
# Delete faces that lie on right side (verts_side==1)
verts_centre_mask = (verts[:,0].abs() < eps)
verts[verts_centre_mask, 0] = 0
verts_side = torch.sign(verts[:,0])
face_verts_side = torch.index_select(verts_side, 0, faces.view(-1))
face_verts_side = face_verts_side.contiguous().view(faces.shape[0], 3)
face_right_mask = (face_verts_side[:,0]==1) | (face_verts_side[:,1]==1) | (face_verts_side[:,2]==1)
faces = torch.index_select(faces, 0, (~face_right_mask).nonzero().squeeze(1))
# import pymesh
pmesh = pymesh.form_mesh(verts.numpy(), faces.numpy())
pymesh.save_mesh(f'csm_mesh/debug/4.obj', pmesh)
# Flip mesh, merge
faces_flip = faces + verts.shape[0]
faces = torch.cat([faces, faces_flip], dim=0)
verts_flip = verts * torch.tensor([-1,1,1], dtype=verts.dtype, device=verts.device)
vertex_mapping_flip = torch.arange(verts.shape[0], dtype=faces.dtype, device=faces.device)
vertex_mapping_flip[~verts_centre_mask] += verts.shape[0]
vertex_mapping = torch.arange(verts.shape[0], dtype=faces.dtype, device=faces.device)
vertex_mapping = torch.cat([vertex_mapping, vertex_mapping_flip], dim=0)
verts = torch.cat([verts, verts_flip], dim=0)
faces = vertex_mapping[faces]
# import pymesh
pmesh = pymesh.form_mesh(verts.numpy(), faces.numpy())
pymesh.save_mesh(f'csm_mesh/debug/5.obj', pmesh)
pymesh.save_mesh(f'csm_mesh/debug/5.8.obj', pmesh)
numv = pmesh.num_vertices
while True:
pmesh, __ = pymesh.collapse_short_edges(pmesh, rel_threshold=0.4)
verts = torch.as_tensor(pmesh.vertices, dtype=verts.dtype, device=verts.device)
faces = torch.as_tensor(pmesh.faces, dtype=faces.dtype, device=faces.device)
verts_centre_mask = (verts[:,0].abs() < 1e-3)
verts[verts_centre_mask, 0] = 0
pmesh = pymesh.form_mesh(verts.numpy(), faces.numpy())
pmesh, __ = pymesh.remove_isolated_vertices(pmesh)
pmesh, __ = pymesh.remove_duplicated_vertices(pmesh, tol=eps)
pmesh, __ = pymesh.remove_duplicated_faces(pmesh)
pmesh, __ = pymesh.remove_degenerated_triangles(pmesh)
pmesh, __ = pymesh.remove_isolated_vertices(pmesh)
# pmesh, __ = pymesh.remove_obtuse_triangles(pmesh, 120.0, 100)
pmesh, __ = pymesh.collapse_short_edges(pmesh, 1e-2)
pmesh, __ = pymesh.remove_duplicated_vertices(pmesh, tol=eps)
if pmesh.num_vertices==numv:
break
numv = pmesh.num_vertices
pymesh.save_mesh(f'csm_mesh/debug/5.9.obj', pmesh)
verts = torch.as_tensor(pmesh.vertices, dtype=verts.dtype, device=verts.device)
faces = torch.as_tensor(pmesh.faces, dtype=faces.dtype, device=faces.device)
# Remove unused vertices
vertices_used = torch.unique(faces.view(-1))
vertex_mapping = torch.zeros((verts.shape[0], ), dtype=faces.dtype, device=faces.device)
vertex_mapping[vertices_used] = torch.arange(vertices_used.shape[0], dtype=faces.dtype, device=faces.device)
faces = vertex_mapping[faces]
verts = verts[vertices_used]
# import pymesh
pmesh = pymesh.form_mesh(verts.numpy(), faces.numpy())
pymesh.save_mesh(f'csm_mesh/debug/6.obj', pmesh)
return verts, faces