I have three 3D mesh matrices (X, Y, Z) corresponding to the xyz coordinate space.
I also have a 3D Numpy matrix A where A[i,j,k] contains a float that is associated with the point (x,y,z) where x=X[i,j,k], y=Y[i,j,k], and z=Z[i,j,k]. The float values are continuous within A (i.e. the change in value between adjacent elements of A are typically small).
Is there a way to plot the surface that corresponds to a given float value in A using Matplotlib or any other Python-based graphics package? For example, if given a value 2.34, I am interested in getting a plotted contour surface of the matrix A wherever 2.34 (plus or minus some tolerance) shows up?
So far, I have been able to recover the xyz coordinates of all values in A that are within some tolerance of the target value and then make a 3D scatter plot using this (code below). Perhaps there is also a way of plotting a surface from these points?
def clean (A, t, dt):
# function for making A binary for t+-dt
# t is the target value I want in the matrix A with tolerance dt
new_A = np.copy(A)
new_A[np.logical_and(new_A > t-dt, new_A < t+dt)] = -1
new_A[new_A != -1] = 0
new_A[new_A == -1] = 1
return (new_A)
def get_surface (X, Y, Z, new_A):
x_vals = []
y_vals = []
z_vals = []
# Retrieve (x,y,z) coordinates of surface
for i in range(new_A.shape[0]):
for j in range(new_A.shape[1]):
for k in range(new_A.shape[2]):
if new_A[i,j,k] == 1.0:
x_vals.append(X[i,j,k])
y_vals.append(Y[i,j,k])
z_vals.append(Z[i,j,k])
return (np.array(x_vals), np.array(y_vals), np.array(z_vals))
cleaned_A = clean (A, t=2.5, dt=0.001)
x_f, y_f, z_f = get_surface (X, Y, Z, cleaned_A )
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d', aspect='equal')
ax.scatter(x_f, y_f, z_f, color='g', s=1)
I have also tried ax.plot_trisurf(x_f,y_f,z_f), but this gives me an poorly connected plot. I'm guessing that the ordering of values in my arrays might be affecting this, in which case is there a package that can do some kind of 3D interpolated surface plot with random ordering of points (e.g. through minimizing the surface area or something like that?)
The object that I am interested in is roughly spherical (i.e. two z's per (x,y)). I can't seem to find any working examples of someone triangulating over a closed 3D surface, but maybe I'm not looking in the right places.
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