ValueError: Invalid RGBA argument: What is causing this error?

Question

I am trying to create a 3D colored bar chart using ideas from: this stackoverflow post.

First I create a 3D bar chart with the following code:

import         


        

Answer 1

The error message is misleading. You're getting a ValueError because the shape of colors is wrong, not because an RGBA value is invalid.

When coloring each bar a single color, color should be an array of length N, where N is the number of bars. Since there are 8281 bars,

In [121]: x_data.shape
Out[121]: (8281,)

colors should have shape (8281, 4). But instead, the posted code generates an array of shape (91, 91, 4):

In [123]: colors.shape
Out[123]: (91, 91, 4)

So to fix the problem, use color=colors.reshape(-1,4).

---

import numpy as np
import matplotlib.colors as colors
import matplotlib.cm as cm
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D

samples = np.random.randint(91,size=(5000,2))

F = np.zeros([91,91])
for s in samples:
    F[s[0],s[1]] += 1

fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
x_data, y_data = np.meshgrid( np.arange(F.shape[1]),
                              np.arange(F.shape[0]) )
x_data = x_data.flatten()
y_data = y_data.flatten()
z_data = F.flatten()

dz = F
offset = dz + np.abs(dz.min())
fracs = offset.astype(float)/offset.max()
norm = colors.Normalize(fracs.min(), fracs.max())
colors = cm.jet(norm(fracs))

ax.bar3d(x_data,y_data,np.zeros(len(z_data)),1,1,z_data,color=colors.reshape(-1,4) )
plt.show()

Answer 2

The color argument expects a 1D array, similar to all other arguments of bar3d.

Hence, you need to replace the line offset = dz + np.abs(dz.min())

by

offset = z_data + np.abs(z_data.min())

for your case. dz is not useful here (maybe it was in the linked example).
Note that color=np.random.rand(len(z_data),4) would equally work.

Then the result will be