def update_spline(self, segment_number=50, fine_flag=False):
spline_points_tem = []
for i in self.tooth_list:
if i in self.existing_tooth_list:
idx = np.where(self.existing_tooth_list == i)[0][0]
points_tem = self.existing_tooth[idx].centroid
elif i in self.missing_tooth_list:
idx = np.where(self.missing_tooth_list == i)[0][0]
points_tem = self.missing_tooth[idx].centroid
spline_points_tem.append(points_tem)
self.spline_points = np.asarray(spline_points_tem)
#self.spline_points = spline_points_tem
cylindrical_center = (spline_points_tem[0] + spline_points_tem[-1]) / 2
self.spline_points_cylindrical = coordinates.convert_cylindrical(
spline_points_tem, cylindrical_center)
self.spline_points_cylindrical_center = cylindrical_center
missing_spline_points_tem = []
for tooth in self.missing_tooth:
missing_spline_points_tem.append(tooth.centroid)
self.missing_spline_points = np.asarray(missing_spline_points_tem)
del missing_spline_points_tem
if fine_flag is True:
self.spline_points_fine = fit_spline_and_split_fxt(
self.spline_points, self.missing_spline_points, segment_number)
self.spline_points_fine_cylindrical = coordinates.convert_cylindrical(
self.spline_points_fine, self.spline_points_cylindrical_center)
self.spline_points_fine_cylindrical_mid_points = check_boundary(
self.spline_points_fine_cylindrical[:, 1])
del spline_points_tem, cylindrical_center
def __init__(self,
stl_raw_points,
defined_targets,
defined_center=[0, 0, 0]):
self.all_points_cartesian = np.asarray(stl_raw_points)
self.coordinate_center = defined_center
# convert to cylindrical coordinates [r, theta, z]
self.all_points_cylindrical = coordinates.convert_cylindrical(
self.all_points_cartesian, defined_center)
self.angle_range = [
np.min(self.all_points_cylindrical[:, 1] * 180 / np.pi),
np.max(self.all_points_cylindrical[:, 1] * 180 / np.pi)
]
self.radius_range = [
np.min(self.all_points_cylindrical[:, 0]),
np.max(self.all_points_cylindrical[:, 0])
]
self.height_range = [
np.min(self.all_points_cylindrical[:, 2]),
np.max(self.all_points_cylindrical[:, 2])
]
# define targets
self.target_origins_cartesian = np.asarray(defined_targets)
self.target_origins_cylindrical = coordinates.convert_cylindrical(
self.target_origins_cartesian, defined_center)
# define multiple regions based on cylindrical coordinate angles (theta)
if np.ndim(self.target_origins_cylindrical) == 1:
self.target_angle_range = self.angle_range
else:
self.target_angle_range = []
self.target_angle_range.append(self.angle_range[0])
for i in range(len(self.target_origins_cylindrical[:, 1]) - 1):
self.target_angle_range.append(
(self.target_origins_cylindrical[i, 1] +
self.target_origins_cylindrical[i + 1, 1]) / 2 * 180 /
np.pi)
self.target_angle_range.append(self.angle_range[1])
self.target_radius_range = self.radius_range
self.target_height_range = self.height_range
self.all_regions_cartesion = []
self.all_regions_cylindrical = []
self.check_angle_range = []
self.check_radius_range = []
self.check_height_range = []
self.n_fiducial = 0
self.n_target = len(self.target_origins_cartesian)
self.default_fiducial = []
self.surface_points = []
def update_spline(self, segment_number=50, fine_flag = False):
spline_points_tem = []
for tooth in self.existing_tooth:
spline_points_tem.append(tooth.centroid)
self.spline_points = np.asarray(spline_points_tem)
cylindrical_center = (spline_points_tem[0] + spline_points_tem[-1])/2
self.spline_points_cylindrical = coordinates.convert_cylindrical(spline_points_tem, cylindrical_center)
self.spline_points_cylindrical_center = cylindrical_center
if fine_flag is True:
self.spline_points_fine = fit_spline_and_split(self.spline_points, segment_number)
self.spline_points_fine_cylindrical = coordinates.convert_cylindrical(self.spline_points_fine, self.spline_points_cylindrical_center)
self.spline_points_fine_cylindrical_mid_points = check_boundary(self.spline_points_fine_cylindrical[:,1])
del spline_points_tem, cylindrical_center
def update_spline(self, segment_number=50, fine_flag=False):
spline_points_tem = self.pyramid_fiducial_points
self.spline_points = np.asarray(spline_points_tem)
cylindrical_center = (spline_points_tem[0] + spline_points_tem[-1]) / 2
#cylindrical_center = np.array([5, -16, 233])
self.spline_points_cylindrical = coordinates.convert_cylindrical(spline_points_tem, cylindrical_center)
self.spline_points_cylindrical_center = cylindrical_center
if fine_flag is True:
self.spline_points_fine = fit_spline_and_split_splint(self.spline_points,
segment_number, self.spline_fitting_base_axis)
self.spline_points_fine_cylindrical = coordinates.convert_cylindrical(self.spline_points_fine,
self.spline_points_cylindrical_center)
self.spline_points_fine_cylindrical_mid_points = check_boundary(self.spline_points_fine_cylindrical[:, 1])
del spline_points_tem, cylindrical_center
def update_guided_spline(self, segment_number=50, fine_flag=False):
for i in self.tooth_list:
if i in self.existing_tooth_list:
idx = np.where(self.existing_tooth_list == i)[0][0]
idx2 = np.where(self.tooth_list == i)[0][0]
#print('i is', i)
#print('idx is',idx)
#print('idx2 is', idx2)
#print('tooth list is', self.existing_tooth_list)
#print('number of spline points is', np.shape(self.spline_points))
#print('spline points are', self.spline_points)
#print('shape of missing spline points is', np.shape(self.missing_spline_points))
#print('missing spline points are', self.missing_spline_points)
#print('soline_points[idx] is', self.spline_points[idx])
self.spline_guided_points[idx2] = self.spline_points[idx]
elif i in self.missing_tooth_list:
idx = np.where(self.missing_tooth_list == i)[0][0]
idx2 = np.where(self.tooth_list == i)[0][0]
self.spline_guided_points[idx2] = self.missing_spline_points[
idx]
if fine_flag is True:
points_tem = np.asarray(self.spline_guided_points)
self.spline_guided_points_fine = fit_spline_and_split(
points_tem, segment_number)
self.spline_guided_points_fine_cylindrical = coordinates.convert_cylindrical(
self.spline_guided_points_fine,
self.spline_points_cylindrical_center)
self.spline_guided_points_fine_cylindrical_mid_points = check_boundary(
self.spline_guided_points_fine_cylindrical[:, 1])
del points_tem
def update_ignore_boundary(self, ignore_tooth_list):
min_theta = []
max_theta = []
for i in ignore_tooth_list:
points_tem = self.get_tooth(i).points
points_tem_cylindrical = coordinates.convert_cylindrical(points_tem, self.spline_points_cylindrical_center)
min_theta.append(np.min(points_tem_cylindrical[:,1]))
max_theta.append(np.max(points_tem_cylindrical[:,1]))
self.ignore_boundary[0] = np.min(np.asarray(min_theta))
self.ignore_boundary[1] = np.max(np.asarray(max_theta))
def update_virtual_guided_spline(self, segment_number=50, fine_flag = False):
for i in self.tooth_list:
if i in self.existing_tooth_list:
idx = np.where(self.existing_tooth_list == i)[0][0]
idx2 = np.where(self.tooth_list == i)[0][0]
self.spline_virtual_guided_points[idx2] = self.spline_points[idx]
elif i in self.missing_tooth_list:
idx = np.where(self.missing_tooth_list == i)[0][0]
idx2 = np.where(self.tooth_list == i)[0][0]
self.spline_virtual_guided_points[idx2] = self.spline_virtual_points[idx]
if fine_flag is True:
points_tem = np.asarray(self.spline_virtual_guided_points)
fig=plt.figure()
plt.scatter(points_tem[:,0],points_tem[:,1])
plt.show()
self.spline_virtual_guided_points_fine = fit_spline_and_split(points_tem, segment_number)
self.spline_virtual_guided_points_fine_cylindrical = coordinates.convert_cylindrical(self.spline_virtual_guided_points_fine, self.spline_points_cylindrical_center)
self.spline_virtual_guided_points_fine_cylindrical_mid_points = check_boundary(self.spline_virtual_guided_points_fine_cylindrical[:,1])
splint_ground.update_spline(fine_flag=True)
splint_ios.update_spline(fine_flag=True)
#fig = plt.figure()
#plt.scatter(splint_ground.spline_points_fine[:, 0], splint_ground.spline_points_fine[:, 1], label='ground')
#plt.scatter(splint_ios.spline_points_fine[:, 0], splint_ios.spline_points_fine[:, 1], label='ios')
#plt.legend()
#plt.show()
# perform splint correction
displacement_splint = np.asarray(splint_ground.spline_points_fine) - np.asarray(splint_ios.spline_points_fine)
for i in arch_ios.existing_tooth_list:
points_tem = arch_ios.get_tooth(i).points
points_tem_transformed = transpose_pc(points_tem, modify_matrix)
points_tem_transformed_cylindrical = coordinates.convert_cylindrical(points_tem_transformed, splint_ground.spline_points_fine_cylindrical_mid_points)
points_tem_corrected_transformed = sc.displacement(points_tem_transformed, points_tem_transformed_cylindrical, splint_ground.spline_points_fine_cylindrical_mid_points, displacement_splint)
#points_tem_corrected = transpose_pc(points_tem_corrected_transformed, np.linalg.inv(modify_matrix))
points_tem_corrected = transpose_pc(points_tem_corrected_transformed, modify_matrix2)
tooth_feature_splint_correction = fe.ToothFeature(points_tem_corrected, i, 'IOS', 'IOS')
arch_ios_splint_correction.add_tooth(i, tooth_feature_splint_correction)
#target_points_transfromed = transpose_pc(arch_ios.target_points, modify_matrix)
target_points_transfromed = transpose_pc(splint_fiducial_ios[20:, :], modify_matrix)
target_points_transfromed_cylindrical = coordinates.convert_cylindrical(target_points_transfromed, splint_ground.spline_points_fine_cylindrical_mid_points)
target_points_corrected_transformed = sc.displacement(target_points_transfromed, target_points_transfromed_cylindrical, splint_ground.spline_points_fine_cylindrical_mid_points, displacement_splint)
#target_points_corrected = transpose_pc(target_points_corrected_transformed, np.linalg.inv(modify_matrix))
target_points_corrected = transpose_pc(target_points_corrected_transformed, modify_matrix2)
arch_ios_splint_correction.add_target(target_points_corrected)
print('original target points are', splint_fiducial_ios[20:, :])
print('target_points corrected are', target_points_corrected)
del points_rigid_tem, tooth_feature_rigid_tem, points_virtual_tem, tooth_feature_virtual_tem
# Update spline points
arch_ct_in_ios.update_spline(fine_flag=True)
arch_ct_to_ios.update_spline(fine_flag=True)
print('displacement check', arch_ct_to_ios.spline_points - arch_ct_in_ios.spline_points)
print('original spline is', arch_ct_in_ios.spline_points)
print('target spline is', arch_ct_to_ios.spline_points)
displacement = arch_ct_to_ios.spline_points_fine - arch_ct_in_ios.spline_points_fine
corrected_spline = sc.displacement(arch_ct_in_ios.spline_points, arch_ct_in_ios.spline_points_cylindrical, arch_ct_in_ios.spline_points_fine_cylindrical_mid_points, displacement)
print('corrected spline is', corrected_spline)
for i in arch_ct_to_ios.tooth_list:
candidate_tooth = arch_ct_in_ios.get_tooth(i).points
candidate_tooth_cylindrical = coordinates.convert_cylindrical(candidate_tooth, arch_ct_in_ios.spline_points_cylindrical_center)
corrected_tooth = sc.displacement(candidate_tooth, candidate_tooth_cylindrical,arch_ct_in_ios.spline_points_fine_cylindrical_mid_points, displacement)
corrected_tooth_feature = fe.ToothFeature(corrected_tooth, i, 'CT', 'IOS')
arch_ct_in_ios_curvilinear_correction.add_tooth(i, corrected_tooth_feature)
candidate2_tooth = arch_ios.get_tooth(i).points
candidate2_tooth_cylindrical = coordinates.convert_cylindrical(candidate2_tooth, arch_ct_in_ios.spline_points_cylindrical_center)
corrected2_tooth = sc.displacement(candidate2_tooth, candidate2_tooth_cylindrical,arch_ct_in_ios.spline_points_fine_cylindrical_mid_points, displacement)
corrected2_tooth_feature = fe.ToothFeature(corrected2_tooth, i, 'IOS', 'IOS')
arch_ios_curvilinear_correction.add_tooth(i, corrected2_tooth_feature)
del candidate_tooth, candidate2_tooth
arch_ios_curvilinear_correction.update_spline()
arch_ct_in_ios_curvilinear_correction.update_spline()
# points_tem_transformed_cylindrical = coordinates.convert_cylindrical(points_tem_transformed, splint_ground.spline_points_fine_cylindrical_mid_points)
# points_tem_corrected = sc.displacement(points_tem_transformed, points_tem_transformed_cylindrical, splint_ground.spline_points_fine_cylindrical_mid_points, displacement_splint)
# tooth_feature_splint_correction = fe.ToothFeature(points_tem_corrected, i, 'solidworks', 'IOS')
# arch_ios_splint_correction.add_tooth(i, tooth_feature_splint_correction)
# Deform stl image and save to new stl
your_mesh = mesh.Mesh.from_file(
"G:\\My Drive\\Project\\IntraOral Scanner Registration\\IOS_scan_raw_data\\IOS Splint\\demo_scan\\2nd_splint\\full_arch2\\5272021-demo_picture_full_arch-lowerjaw.stl"
)
original_stl_points = np.copy(your_mesh.points)
new_stl_points = np.copy(your_mesh.points)
for j in range(3):
points_tem = np.copy(original_stl_points[:, 3 * j:3 * (j + 1)])
points_tem_transformed = transpose_pc(points_tem, trans_rigid0)
points_tem_transformed_cylindrical = coordinates.convert_cylindrical(
points_tem_transformed,
splint_ground.spline_points_fine_cylindrical_mid_points)
points_tem_corrected = sc.displacement(
points_tem_transformed, points_tem_transformed_cylindrical,
splint_ground.spline_points_fine_cylindrical_mid_points,
displacement_splint)
new_stl_points[:, 3 * j:3 * (j + 1)] = points_tem_corrected
for i in range(np.shape(new_stl_points)[0]):
your_mesh.points[i, :] = new_stl_points[i, :]
print('original_stl_points 0 are', original_stl_points[0, :])
print('new_stl_points 0 are', new_stl_points[0, :])
print('your_mesh points 0 are', your_mesh.points[0, :])
your_mesh.save(
"G:\\My Drive\\Project\\IntraOral Scanner Registration\\IOS_scan_raw_data\\IOS Splint\\demo_scan\\2nd_splint\\full_arch2\\deformed.stl"
)
if __name__ == "__main__":
stl_base = "G:\\My Drive\\Project\\HW-9232 Registration method for edentulous\\Edentulous registration error analysis\\Typodont_scan\\Edentulous_scan\\"
all_regions = []
file = stl_base + 'full_arch.txt'
if os.path.isfile(file):
print('read txt')
full_region = Yomiread.read_csv(file, 3, -1)
else:
stl_file = 'full_arch.stl'
print('read stl')
full_region = region_points.read_regions(stl_base + stl_file,
voxel_size=2.0)
Yomiwrite.write_csv_matrix(stl_base + 'full_arch.txt', full_region)
# convert to cylindrical coordinates [r, theta, z]
full_region_cylinder = coordinates.convert_cylindrical(
full_region, [0, 0, 0])
print('point are', full_region_cylinder)
# generate target regions
# angle [90:125:160]
# radius 12~16 (inner) 16~23 (occlusal) 23~39 (outer)
# z [10:19.6:24]
ANGLE_RANGE = [90, 160]
RADIUS_RANGE = [16, 23]
HEIGHT_RANGE = [5, 34]
D_ANGLE = 2
D_HEIGHT = 1
D_RADIUS = 1
N_REGION = 2 * D_ANGLE * D_HEIGHT + D_ANGLE
splint_geometry.update_spline(fine_flag=True)
splint_ios.update_spline(fine_flag=True)
#print('splint_fine points are', splint_geometry.spline_points_fine)
#print('spline boundary is', splint_geometry.spline_points_fine_cylindrical_mid_points)
print('ground transformed ')
displacement = np.asarray(splint_geometry.spline_points_fine) - np.asarray(
splint_ios.spline_points_fine)
for i in splint_ios.pyramid_number_list:
point = splint_ios.get_pyramid(i)
print('i is', i)
print('point is', point)
point_cylindrical = coordinates.convert_cylindrical(
point, splint_ios.spline_points_cylindrical_center)
#point_cylindrical = coordinates.convert_cylindrical(point, center_2)
point_moved = sc.displacement_single_point(
point, point_cylindrical,
splint_ios.spline_points_fine_cylindrical_mid_points, displacement)
print('moved point is', point_moved)
print('target point is', splint_geometry.get_pyramid(i))
splint_ios_corrected.add_pyramid(i, point_moved)
diff_before = np.asarray(splint_geometry.pyramid_points) - np.asarray(
splint_ios.pyramid_points)
diff_after = np.asarray(splint_geometry.pyramid_points) - np.asarray(
splint_ios_corrected.pyramid_points)
diff_before_norm = np.linalg.norm(diff_before, axis=1)
diff_after_norm = np.linalg.norm(diff_after, axis=1)
diff_before_norm_2d = np.linalg.norm(diff_before[:, 0:2], axis=1)
