matplotlib 0.99 Mplot3d AttributeError: 'list' object has no attribute 'ndim'

Question

I'm trying to plot a 3d graph like this one here:

Using this code and receiving an error that says:

line 1621, in plot_surface
if Z.ndim != 2:
AttributeError: 'list' object has no attribute 'ndim'

---

import cobra
import os
from os.path import join
import matplotlib.pyplot as plt
import numpy as np
from matplotlib import cm
from mpl_toolkits.mplot3d import Axes3D
data_dir ='/Users/stephenchapman/Documents/research/FBA_algae_digesate/COBRApy/iCZ843/iCZ843_models'
model = cobra.io.read_sbml_model(join(data_dir, "iCZ843_hetero.xml"))
model.reactions[15].upper_bound = -0 #ammonia
model.reactions[15].lower_bound = -98.3
model.reactions[27].upper_bound = -0 #acetate
model.reactions[27].lower_bound = -3.3
model.reactions[14].upper_bound = -0 #phosphate
model.reactions[14].lower_bound = -10
model.reactions[16].upper_bound = -0 #nitrate
model.reactions[16].lower_bound = -30.3
model.reactions[20].upper_bound = -0 #magnesium
model.reactions[20].lower_bound = -0.56
model.reactions[18].upper_bound = -0 #iron
model.reactions[18].lower_bound = -2.16
model.objective = model.reactions[63]
solution = model.optimize()
model.summary()

ac_uptake = []
NH4_uptake = []
growth_rate = []
for i in range(0,85,5):
    model.reactions[27].lower_bound = -i #acetate uptake
    model.reactions[27].upper_bound = -i
    for j in (0,80,5):
        model.reactions[15].lower_bound = -i #NH4 uptake
        model.reactions[15].upper_bound = -i
        print(solution.f)
        growth_rate.append(solution.f)
        ac_uptake.append(model.reactions[27].lower_bound)
        NH4_uptake.append(model.reactions[15].lower_bound)
        plot_ac_uptake = list(range(0,85,5))
        plot_NH4_uptake = list(range(0,85,5))

X = (plot_ac_uptake)
Y = (plot_NH4_uptake)
X, Y = np.meshgrid(X, Y)
Z = (growth_rate)
fig = plt.figure()
ax = Axes3D(fig)
ax.plot_surface(X, Y, Z, rstride=1, cstride=1, cmap=cm.viridis)
plt.show()

Can anyone help me out please?

Answer 1

The error message

Z.ndim != 2: 
AttributeError: 'list' object has no attribute 'ndim'

is saying that the list Z has no attribute ndim. ndim is an attribute of NumPy arrays, however. So it is likely that converting Z to a NumPy array will fix the problem (or at least get you past the AttributeError):

Z = np.array(Z)

---

For example,

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

X = list(np.linspace(-4, 4, 100))
Y = list(np.linspace(-4, 4, 100))
X, Y = np.meshgrid(X, Y)
Z = np.sin((X**2 + Y**2)/4)
# Z = (np.sin((X**2 + Y**2)/4)).tolist()  
fig = plt.figure()
ax = Axes3D(fig)
ax.plot_surface(X, Y, Z, rstride=1, cstride=1, cmap=cm.viridis)
plt.show()

works fine, but if you uncomment the line

Z = (np.sin((X**2 + Y**2)/4)).tolist()  

which makes Z a list-of-lists, then you get the error message

Z.ndim != 2: 
AttributeError: 'list' object has no attribute 'ndim'