def check_all_normals(self, interval=100) -> None:
centroid = math.mean(self)
scale = np.mean(self.nn_weights[:, 3])
normals = self.point_normals[:, ::interval]*scale
pyplot.plot3d(*self[:, ::interval], '.', alpha=1, markersize=1)
pyplot.quiver3d(
*self[:, ::interval],
*normals)
pyplot.equal_aspect_3d_centered(centroid)
pyplot.show()
def check_normals_n_at_a_time(self, interval=1000, n_normals=3) -> None:
scale = np.mean(self.nn_weights[:, 3])
for i, (point, normal) in enumerate(
zip(self.T, self.point_normals.T)):
if i % interval == 0:
normal = normal*scale
I_nearest = self.nn_indices[i]
# nn = self[:, I_nearest]
# nn_normals = self.point_normals[I_nearest]
pyplot.plot3d(*self, '.', alpha=1, markersize=1)
pyplot.quiver3d(*point, *normal)
pyplot.equal_aspect_3d_centered(point)
pyplot.show()
perpendicularPointDict = centerline_main.findPointPairsAtPerpendicularDistance(centerline_bifur, distance=landmark.bar, resolution=0.0001)
print("the data required:\n", perpendicularPointDict)
# %%
pt_main, pt_bifur, error, vector = perpendicularPointDict.values()
# %%
plt.figure_3d()
centerline_main.plot3d('b')
centerline_bifur.plot3d('r')
vector.quiver3d(origin=pt_main)
pt_main.scatter3d(color='green')
pt_bifur.scatter3d(color='red')
plt.equal_aspect_3d_centered(pt_main)
plt.show()
# %% [markdown]
# Originally our transport frames are not oriented along the centerline. But since we now have an approximation to of the orientation of our frames we can now orient our transport frames.
# %%
orientedTransportFrames, origin_id = centerline_main.oriented_transport_frames(
pt_main, vector
)
mainTransportFrames = centerline_main.transport_frames()
plt.figure_3d()
centerline_main.plot3d('g')
centerline_bifur.plot3d('r')
# the now oriented transport frames
def post_plot(self, ax):
pyplot.equal_aspect_3d_centered(self.data.mean(axis=-1), ax=ax)
file = data_folder/'00000.vtk'
pv_obj = pv.read(file)
points = pv_obj.points.T
test_points = points[:, ::20]*1000
# test_points = points*1000
psurf = Pointsurface(
test_points, leafsize=100, neighbours=13, external=True)
psurf.compute_all_normals()
psurf.compute_principle_curvatures(n_processors=5)
psurf
if False:
ii = 500
ids = psurf.nn_indices[ii]
xx, yy = psurf.principle_directions[ii].T
X, Y, Z = psurf.point_basis[ii].T
pyplot.plot3d(*psurf, '.', alpha=0.5, markersize=2)
pyplot.plot3d(*psurf[:, ii, None], 'go')
pyplot.plot3d(*psurf[:, ids], 'ro')
pyplot.quiver3d(*psurf[:, ii, None], *X[:, None], color='blue')
pyplot.quiver3d(*psurf[:, ii, None], *Y[:, None], color='blue')
pyplot.quiver3d(*psurf[:, ii, None], *Z[:, None], color='green')
pyplot.quiver3d(*psurf[:, ii, None], *xx[:, None], color='red')
pyplot.quiver3d(*psurf[:, ii, None], *yy[:, None], color='red')
pyplot.equal_aspect_3d_centered(psurf[:, ii, None])
pyplot.show()
# psurf.plot_curvature()
# pyplot.show()
# psurf.check_all_normals(interval=1)
print('done')