Trouble preparing data for contourf plot

Question

I would like to plot some data for a contourf plot in matplot lib, I would like do to do something like the following:

x = np.arange(0, 10, 0.5)
y = np.arange(0, 10, 0.5)
z = x**2 - y

fig, ax = plt.subplots()
cs = ax.contourf(x, y, z)

But this sends the following error:

TypeError: Input z must be a 2D array.

Can someone recommend a way for me to massage my data to make contourf happy. Ideally if someone who also explain why the format of my data doesn't work that would be greatly helpful as well.

Note: The actual data I'm using is read from a data file, it is the same as above, except replace x, y, z with c_a, a, Energy respectively.

c_a 
0      1.60
1      1.61
2      1.62
3      1.63
4      1.64
5      1.65
6      1.66
7      1.67
8      1.68
9      1.69
10     1.70
11     1.60
12     1.61
13     1.62
14     1.63
15     1.64
16     1.65
17     1.66
18     1.67
19     1.68
20     1.69
21     1.70
22     1.60
23     1.61
24     1.62
25     1.63
26     1.64
27     1.65
28     1.66
29     1.67
       ... 
91     1.63
92     1.64
93     1.65
94     1.66
95     1.67
96     1.68
97     1.69
98     1.70
99     1.60
100    1.61
101    1.62
102    1.63
103    1.64
104    1.65
105    1.66
106    1.67
107    1.68
108    1.69
109    1.70
110    1.60
111    1.61
112    1.62
113    1.63
114    1.64
115    1.65
116    1.66
117    1.67
118    1.68
119    1.69
120    1.70
Name: c_a, Length: 121, dtype: float64
a 
0      6.00
1      6.00
2      6.00
3      6.00
4      6.00
5      6.00
6      6.00
7      6.00
8      6.00
9      6.00
10     6.00
11     6.01
12     6.01
13     6.01
14     6.01
15     6.01
16     6.01
17     6.01
18     6.01
19     6.01
20     6.01
21     6.01
22     6.02
23     6.02
24     6.02
25     6.02
26     6.02
27     6.02
28     6.02
29     6.02
       ... 
91     6.08
92     6.08
93     6.08
94     6.08
95     6.08
96     6.08
97     6.08
98     6.08
99     6.09
100    6.09
101    6.09
102    6.09
103    6.09
104    6.09
105    6.09
106    6.09
107    6.09
108    6.09
109    6.09
110    6.10
111    6.10
112    6.10
113    6.10
114    6.10
115    6.10
116    6.10
117    6.10
118    6.10
119    6.10
120    6.10
Name: a, Length: 121, dtype: float64
Energy 
0     -250.647503
1     -250.647661
2     -250.647758
3     -250.647791
4     -250.647762
5     -250.647668
6     -250.647511
7     -250.647297
8     -250.647031
9     -250.646721
10    -250.646378
11    -250.647624
12    -250.647758
13    -250.647831
14    -250.647841
15    -250.647788
16    -250.647671
17    -250.647493
18    -250.647258
19    -250.646972
20    -250.646644
21    -250.646282
22    -250.647726
23    -250.647835
24    -250.647884
25    -250.647871
26    -250.647794
27    -250.647655
28    -250.647456
29    -250.647200
          ...    
91    -250.647657
92    -250.647449
93    -250.647182
94    -250.646860
95    -250.646488
96    -250.646071
97    -250.645620
98    -250.645140
99    -250.647896
100   -250.647841
101   -250.647729
102   -250.647559
103   -250.647330
104   -250.647043
105   -250.646702
106   -250.646310
107   -250.645876
108   -250.645407
109   -250.644912
110   -250.647847
111   -250.647769
112   -250.647635
113   -250.647444
114   -250.647193
115   -250.646887
116   -250.646526
117   -250.646116
118   -250.645665
119   -250.645180
120   -250.644669
Name: Energy, Length: 121, dtype: float64

The [documentation](https://matplotlib.org/api/_as_gen/matplotlib.pyplot.contour.html#matplotlib.pyplot.contour) and [examples](https://matplotlib.org/gallery/images_contours_and_fields/contour_demo.html#sphx-glr-gallery-images-contours-and-fields-contour-demo-py) should help — DavidG, May 03 '18 at 13:40
Recommended reading: [Why does pyplot.contour() require Z to be a 2D array?](https://stackoverflow.com/questions/42045921/why-does-pyplot-contour-require-z-to-be-a-2d-array). — ImportanceOfBeingErnest, May 03 '18 at 13:41

Jonas · Accepted Answer · 2018-05-04T07:16:58.257

2

x and y also need to be 2d (see meshgrid):

import numpy as np
import matplotlib.pyplot as plt

x = np.arange(0, 10, 0.5)
y = np.arange(0, 10, 0.5)
X, Y = np.meshgrid(x, y)
Z = X**2 - Y

fig, ax = plt.subplots()
cs = ax.contourf(X, Y, Z)
plt.show()

Output:

Edit:

If your input is in a one dimensional array you need to know how to reshape it. Maybe its sqrt(length)=11 in your case? (Assuming your domain is square)

import numpy as np
import matplotlib.pyplot as plt

c_a = np.array([np.linspace(1.6, 1.7, num=11) for _ in range(11)]).flatten()
a = np.array([[1.6+i*0.1 for j in range(11)] for i in range(11)]).flatten()
energy = np.array([-250.644-np.random.random()*0.003 for i in range(121)])

x = c_a.reshape((11, 11))
y = a.reshape((11, 11))
z = energy.reshape((11, 11))

fig, ax = plt.subplots()
cs = ax.contourf(x, y, z)
plt.show()

Output:

edited May 04 '18 at 07:16

answered May 03 '18 at 13:42

Jonas

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This wouldn't work in my case as I am reading Z directly from a file. I"m not certain what form Z should take when I don't have the luxury of regenerating it. – Daniel Marchand May 03 '18 at 13:44
`x.reshape(3,3)` converts an np.array x with 9 entries into a 3*3 np.array – Jonas May 03 '18 at 13:49
maybe you should post an example thats closer to your problem, what do x and y look like in your case? – Jonas May 03 '18 at 14:33
Clarified the underlying data. The reshape doesn't work because since I need each dimension of Z to remain the same (e.g. I would need something like 9 -> 9*9 array not 9 -> 3*3) – Daniel Marchand May 03 '18 at 15:03
See my edit. Your energy input has the same length as your a_c and a input why would you grow it by 9->9*9? maybe i still dont understand what you want to plot.. – Jonas May 04 '18 at 07:19

Trouble preparing data for contourf plot

1 Answers1