Adding error bars in line figure with missing data

Question

I want to draw lines between missing data as suggested here but with error bars.

This is my code.

import matplotlib.pyplot as plt
import numpy as np

x = [1, 2, 3, 4, 5]
y_value = [12, None, 18, None, 20]
y_error = [1, None, 3, None, 2]

fig = plt.figure()
ax = fig.add_subplot(111)
plt.axis([0, 6, 0, 25])
ax.plot(x, y_value, linestyle = '-', color = 'b', marker = 'o')
ax.errorbar(x, y_value, yerr = y_error, linestyle = '' , color = 'b')
plt.show()

But because of the missing data, I get

TypeError: unsupported operand type(s) for -: 'NoneType' and 'NoneType'

What should I do?

Paul H · Accepted Answer · 2016-01-06 07:44:48Z

2

You just need to use numpy (which you've imported) to mask the missing values:

import matplotlib.pyplot as plt
import numpy as np

x = [1, 2, 3, 4, 5]
y_value = np.ma.masked_object([12, None, 18, None, 20], None)
y_error = np.ma.masked_object([1, None, 3, None, 2], None)

fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_xlim([0, 6])
ax.set_ylim([0, 25])
ax.plot(x, y_value, linestyle = '-', color = 'b', marker = 'o')
ax.errorbar(x, y_value, yerr = y_error, linestyle = '' , color = 'b')

answered Jan 6, 2016 at 7:44

Paul H

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1 Comment

owl Over a year ago

Thanks to your help and this page, I was able to create a figure I wanted, which I will post for your reference.

owl · Accepted Answer · 2016-01-06 09:51:25Z

0

Thanks to Paul's answer, this is the revised code.

import matplotlib.pyplot as plt
import numpy as np

x = np.array([1, 2, 3, 4, 5])
y_value = np.ma.masked_object([12, None, 18, None, 20], None).astype(np.double)
y_error = np.ma.masked_object([1, None, 3, None, 2], None).astype(np.double)

masked_v = np.isfinite(y_value)
masked_e = np.isfinite(y_error)

fig = plt.figure()
ax = fig.add_subplot(111)
plt.axis([0, 6, 0, 25])
ax.plot(x[masked_v], y_value[masked_v], linestyle = '-', color = 'b', marker = 'o')
ax.errorbar(x[masked_e], y_value[masked_e], yerr = y_error[masked_e], linestyle = '' , color = 'b')
plt.show()

AlthoughI am still not sure what isfinite does, even after reading the definition page...

answered Jan 6, 2016 at 9:51

owl

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