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 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 supports(self, c):
other = pymesh.form_mesh(
c.component_mesh.vertices - numpy.array([0, 0, (c.z - self.z)]),
c.component_mesh.faces)
pymesh.remove_duplicated_vertices(other)
pymesh.remove_duplicated_faces(other)
intersection = pymesh.boolean(self.component_mesh, other,
'intersection')
pymesh.remove_duplicated_vertices(intersection)
pymesh.remove_duplicated_faces(intersection)
intersection.add_attribute("face_area")
intersection_area = sum(intersection.get_attribute("face_area"))
return intersection_area >= 0.2 * self.area()
def main():
args = parse_args();
mesh = pymesh.load_mesh(args.in_mesh);
if (args.with_rounding):
mesh = pymesh.form_mesh(
np.round(mesh.vertices, args.precision),
mesh.faces);
intersecting_faces = pymesh.detect_self_intersection(mesh);
counter = 0;
while len(intersecting_faces) > 0 and counter < args.max_iterations:
if (args.with_rounding):
involved_vertices = np.unique(mesh.faces[intersecting_faces].ravel());
mesh.vertices_ref[involved_vertices, :] =\
np.round(mesh.vertices[involved_vertices, :],
args.precision//2);
mesh = pymesh.resolve_self_intersection(mesh, "igl");
mesh, __ = pymesh.remove_duplicated_faces(mesh, fins_only=True);
if (args.with_rounding):
mesh = pymesh.form_mesh(
np.round(mesh.vertices, args.precision),
mesh.faces);
intersecting_faces = pymesh.detect_self_intersection(mesh);
counter += 1;
if len(intersecting_faces) > 0:
logging.warn("Resolving failed: max iteration reached!");
pymesh.save_mesh(args.out_mesh, 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 hipp_cut(hipp_filename):
hipp_img = nib.load(hipp_filename)
hipp_matrix = hipp_img.get_fdata()
hipp_matrix_s = scipy.ndimage.filters.gaussian_filter(hipp_matrix, sigma=1)
#mesh it
verts, faces, normals, values = skimage.measure.marching_cubes_lewiner(hipp_matrix_s, level=0.5)
hipp_mesh = pymesh.form_mesh(verts, faces)
hipp_mesh, info = pymesh.remove_duplicated_faces(hipp_mesh)
assembler = pymesh.Assembler(hipp_mesh)
L = assembler.assemble('laplacian').toarray()
eigen = sciLA.eigh(L)
for i in range(50):
#print(eigen[0][i])
#Plot_3D.plot_eigh(hipp_mesh, eigen[1][:, i])
if (eigen[0][i] > 0.0000000001):
eigen_cut = segment(eigen[1][:, i])
mean_first = np.mean(verts[np.where(eigen_cut==0), :], axis=1)
mean_last = np.mean(verts[np.where(eigen_cut==(NUM_CUT-1)), :], axis=1)
diff = -mean_first[0, 1] + mean_last[0, 1] + mean_first[0, 2] - mean_last[0, 2]
eigen_cut_output = copy.copy(eigen_cut)
if diff < 0:
for i in range(NUM_CUT):
eigen_cut_output[np.where(eigen_cut==i)] = NUM_CUT-i-1
#Plot_3D.plot_eigh(hipp_mesh, eigen_cut)
break
return eigen_cut_output, hipp_mesh
def main():
args = parse_args()
mesh = pymesh.load_mesh(args.in_mesh)
if (args.with_rounding):
mesh = pymesh.form_mesh(np.round(mesh.vertices, args.precision),
mesh.faces)
intersecting_faces = pymesh.detect_self_intersection(mesh)
counter = 0
while len(intersecting_faces) > 0 and counter < args.max_iterations:
if (args.with_rounding):
involved_vertices = np.unique(
mesh.faces[intersecting_faces].ravel())
mesh.vertices_ref[involved_vertices, :] =\
np.round(mesh.vertices[involved_vertices, :],
args.precision//2)
mesh = pymesh.resolve_self_intersection(mesh, "igl")
mesh, __ = pymesh.remove_duplicated_faces(mesh, fins_only=True)
if (args.with_rounding):
mesh = pymesh.form_mesh(np.round(mesh.vertices, args.precision),
mesh.faces)
intersecting_faces = pymesh.detect_self_intersection(mesh)
counter += 1
if len(intersecting_faces) > 0:
logging.warn("Resolving failed: max iteration reached!")
pymesh.save_mesh(args.out_mesh, 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 finalMesh(z):
poolWarning = None
# Check if pools will overflow mesh
if z > zMax:
z = zMax
poolWarning = 'The pool have a greater volume than the mesh can contain. Pool set to fill entire mesh.'
# Create Bbox
bMesh = createBbox(z)
# Make intersection
newMesh, bottomFaces, boolWarning = intersectAndBottomFaces(bMesh, z)
# Create volume mesh
volMesh = getVolMesh(newMesh, bottomFaces, z)
volMesh.add_attribute('voxel_volume')
volVol = volMesh.get_attribute('voxel_volume')
volVol = sum(list(map(abs, volVol)))
# Clean up mesh
volMesh, info = pm.remove_isolated_vertices(volMesh)
#print('num vertex removed', info["num_vertex_removed"])
volMesh, info = pm.remove_duplicated_faces(volMesh)
return volMesh, volVol, poolWarning, poolWarning
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 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 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 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 inc_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 * 2.5e-2
print("Target resolution: {} mm".format(target_len))
count = 1
#
# 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_isolated_vertices(mesh)
num_vertices = mesh.num_vertices
low = 4 / 5 * target_len
high = 4 / 3 * target_len
while True:
print()
print("[iteration " + str(count) + "]")
# mesh, __ = pymesh.split_long_edges(mesh, high)
# print("<split_long_edges> : DONE")
# mesh, __ = pymesh.collapse_short_edges(mesh, low, preserve_feature=True)
# print("<collapse_short_edges> : DONE")
check_mesh(mesh)
mesh = equalize_valences(mesh)
print("<equalize_valences> : DONE")
# mesh = tangential_relaxation(mesh)
# print("<tangential_relaxation> : DONE")
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)
check_mesh(mesh)
return mesh
def load_mesh(path: Path) -> "threedframe.lib.PyMesh.python.Mesh.Mesh":
mesh = pymesh.load_mesh(str(path))
mesh, _ = pymesh.remove_duplicated_faces(mesh)
mesh, _ = pymesh.remove_duplicated_vertices(mesh)
mesh.add_attribute("face_area")
mesh.add_attribute("face_normal")
mesh.add_attribute("face_centroid")
mesh.add_attribute("vertex_normal")
mesh.enable_connectivity()
return mesh
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 __fix_mesh(self, mesh, improvement_thres=0.8):
mesh, __ = pymesh.split_long_edges(mesh, self.mesh_target_len)
num_vertices = len(mesh.vertices)
for __ in range(10):
mesh, __ = pymesh.collapse_short_edges(mesh, 1e-6)
mesh, __ = pymesh.collapse_short_edges(
mesh, self.mesh_target_len, preserve_feature=True
)
mesh, __ = pymesh.remove_obtuse_triangles(mesh, 150.0, 100)
if len(mesh.vertices) < num_vertices * improvement_thres:
break
mesh = pymesh.resolve_self_intersection(mesh)
mesh, __ = pymesh.collapse_short_edges(mesh, 1e-6)
mesh, __ = pymesh.remove_duplicated_faces(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 old_fix_mesh(vertices, faces, detail="normal"):
bbox_min = np.amin(vertices, axis=0)
bbox_max = np.amax(vertices, axis=0)
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
vertices, faces = pymesh.split_long_edges(vertices, faces, target_len)
num_vertices = len(vertices)
while True:
vertices, faces = pymesh.collapse_short_edges(vertices, faces, 1e-6)
vertices, faces = pymesh.collapse_short_edges(vertices,
faces,
target_len,
preserve_feature=True)
vertices, faces = pymesh.remove_obtuse_triangles(
vertices, faces, 150.0, 100)
if num_vertices == len(vertices):
break
num_vertices = len(vertices)
print("#v: {}".format(num_vertices))
count += 1
if count > 10: break
vertices, faces = pymesh.resolve_self_intersection(vertices, faces)
vertices, faces = pymesh.remove_duplicated_faces(vertices, faces)
vertices, faces, _ = pymesh.compute_outer_hull(vertices, faces, False)
vertices, faces = pymesh.remove_duplicated_faces(vertices, faces)
vertices, faces = pymesh.remove_obtuse_triangles(vertices, faces, 179.0, 5)
vertices, faces, voxels = pymesh.remove_isolated_vertices(vertices, faces)
return vertices, faces
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.in_mesh);
intersecting_faces = pymesh.detect_self_intersection(mesh);
counter = 0;
while len(intersecting_faces) > 0 and counter < args.max_iterations:
mesh = pymesh.resolve_self_intersection(mesh, "igl");
mesh, __ = pymesh.remove_duplicated_faces(mesh, fins_only=True);
intersecting_faces = pymesh.detect_self_intersection(mesh);
counter += 1;
if len(intersecting_faces) > 0:
logging.warn("Resolving failed: max iteration reached!");
pymesh.save_mesh(args.out_mesh, mesh);
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'}
if left != None:
b = left
elif right != None:
b = right
if front != None:
c = front
elif back != None:
c = back
a, info = pymesh.remove_isolated_vertices(a)
b, info = pymesh.remove_isolated_vertices(b)
c, info = pymesh.remove_isolated_vertices(c)
a, info = pymesh.remove_duplicated_faces(a)
b, info = pymesh.remove_duplicated_faces(b)
c, info = pymesh.remove_duplicated_faces(c)
if a == None and b == None and c == None:
print('No mesh to convert')
exit()
elif a != None and b != None and c != None:
a = pymesh.boolean(a, c, operation="intersection")
# a = pymesh.boolean(b, a, operation="intersection")
elif a != None and b != None and c == None:
a = pymesh.boolean(a, b, operation="intersection")
elif a != None and b == None and c != None:
from mesh_utils import *
# from greedy_remesh_remesh import gre_remesh
# from variational_remesh import var_remesh
from incremental_remesh import inc_remesh
mesh = pymesh.load_mesh(str(sys.argv[1]))
# mesh, __ = pymesh.remove_degenerated_triangles(mesh, 100)
# 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)
mesh, __ = pymesh.remove_duplicated_faces(mesh)
mesh, __ = pymesh.remove_isolated_vertices(mesh)
mesh.enable_connectivity()
edges = get_edges(mesh)
check_mesh(mesh)
start = timeit.default_timer()
mesh = equalize_valences(mesh)
stop = timeit.default_timer()
print('Time: ', stop - start)
# mesh = tangential_relaxation(mesh)
# edges = get_edges(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
def main():
args = parse_args();
mesh = pymesh.load_mesh(args.input_mesh);
mesh, __ = pymesh.remove_duplicated_faces(mesh);
pymesh.save_mesh(args.output_mesh, mesh);
def preprocess_mesh(input_mesh, prevent_nonmanifold_edges=True):
r"""Removes duplicated vertices, duplicated faces, zero-area faces, and
optionally faces the insertion of which would cause an edge of the mesh to
become non-manifold. In particular, an iteration is performed over all faces
in the mesh, keeping track of the half-edges in each face, and if a face
contains a half-edge already found in one of the faces previously processed,
it gets removed from the mesh.
Args:
input_mesh (pymesh.Mesh.Mesh): Mesh to preprocess.
prevent_nonmanifold_edges (bool, optional): If True, faces that would
cause an edge to become non-manifold are removed from the mesh (cf.
above). (default: :obj:`True`)
Returns:
output_mesh (pymesh.Mesh.Mesh): Mesh after preprocessing.
"""
halfedges_found = set()
new_faces = np.empty([input_mesh.num_faces, 3])
# Remove duplicated vertices.
input_mesh = pymesh.remove_duplicated_vertices(input_mesh)[0]
# Remove duplicated faces.
input_mesh = pymesh.remove_duplicated_faces(input_mesh)[0]
num_valid_faces = 0
# Compute face areas so that zero-are faces can be removed.
input_mesh.add_attribute("face_area")
face_areas = input_mesh.get_face_attribute("face_area")
assert (len(face_areas) == len(input_mesh.faces))
for face, face_area in zip(input_mesh.faces, face_areas):
# Do not include the face if it does not have three different
# vertices.
if (face[0] == face[1] or face[0] == face[2] or face[1] == face[2]):
continue
# Do not include zero-area faces.
if (face_area == 0):
continue
# Optionally prevent non-manifold edges.
if (prevent_nonmanifold_edges):
new_halfedges_in_face = set()
for idx in range(3):
halfedge = (face[idx], face[(idx + 1) % 3])
if (halfedge[0] != halfedge[1]): # Exclude self-loops.
if (halfedge not in halfedges_found):
# Half-edge not found previously. -> The edge is
# manifold so far.
new_halfedges_in_face.add(halfedge)
if (len(new_halfedges_in_face) == 3):
# Face does not introduce non-manifold edges.
halfedges_found.update(new_halfedges_in_face)
new_faces[num_valid_faces] = face
num_valid_faces += 1
# Here one can compute the face features already.
else:
new_faces[num_valid_faces] = face
num_valid_faces += 1
new_faces = new_faces[:num_valid_faces]
output_mesh = pymesh.form_mesh(input_mesh.vertices, new_faces)
# Not including faces might have caused vertices to become isolated.
output_mesh = pymesh.remove_isolated_vertices(output_mesh)[0]
return output_mesh
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_duplicated_faces(mesh)
pymesh.save_mesh(args.output_mesh, mesh)
