Python | Replace NaN values with average of columns

In machine learning and data analytics data visualization is one of the most important steps. Cleaning and arranging data is done by different algorithms. Sometimes in data sets, we get NaN (not a number) values which are not possible to use for data visualization.

To solve this problem, one possible method is to replace nan values with an average of columns. Given below are a few methods to solve this problem.

Method #1: Using np.colmean and np.take

# Python code to demonstrate
# to replace nan values
# with an average of columns

import numpy as np

# Initialising numpy array
ini_array = np.array([[1.3, 2.5, 3.6, np.nan],
                      [2.6, 3.3, np.nan, 5.5],
                      [2.1, 3.2, 5.4, 6.5]])

# printing initial array
print ("initial array", ini_array)

# column mean
col_mean = np.nanmean(ini_array, axis = 0)

# printing column mean
print ("columns mean", str(col_mean))

# find indices where nan value is present
inds = np.where(np.isnan(ini_array))

# replace inds with avg of column
ini_array[inds] = np.take(col_mean, inds[1])

# printing final array
print ("final array", ini_array)

Output:

initial array [[ 1.3  2.5  3.6  nan]
 [ 2.6  3.3  nan  5.5]
 [ 2.1  3.2  5.4  6.5]]
columns mean [ 2.   3.   4.5  6. ]

final array [[ 1.3  2.5  3.6  6. ]
 [ 2.6  3.3  4.5  5.5]
 [ 2.1  3.2  5.4  6.5]]

Method #2: Using np.ma and np.where

# Python code to demonstrate
# to replace nan values
# with average of columns

import numpy as np

# Initialising numpy array
ini_array = np.array([[1.3, 2.5, 3.6, np.nan],
                      [2.6, 3.3, np.nan, 5.5],
                      [2.1, 3.2, 5.4, 6.5]])

# printing initial array
print ("initial array", ini_array)

# replace nan with col means
res = np.where(np.isnan(ini_array), np.ma.array(ini_array,
               mask = np.isnan(ini_array)).mean(axis = 0), ini_array)

# printing final array
print ("final array", res)

Output:

initial array [[ 1.3  2.5  3.6  nan]
 [ 2.6  3.3  nan  5.5]
 [ 2.1  3.2  5.4  6.5]]
final array [[ 1.3  2.5  3.6  6. ]
 [ 2.6  3.3  4.5  5.5]
 [ 2.1  3.2  5.4  6.5]]

Method #3: Using Naive and zip

# Python code to demonstrate
# to replace nan values
# with average of columns

import numpy as np

# Initialising numpy array
ini_array = np.array([[1.3, 2.5, 3.6, np.nan],
                      [2.6, 3.3, np.nan, 5.5],
                      [2.1, 3.2, 5.4, 6.5]])

# printing initial array
print ("initial array", ini_array)

# indices where values is nan in array
indices = np.where(np.isnan(ini_array))

# Iterating over numpy array to replace nan with values
for row, col in zip(*indices):
    ini_array[row, col] = np.mean(ini_array[
           ~np.isnan(ini_array[:, col]), col])

# printing final array
print ("final array", ini_array)

Output:

initial array [[ 1.3  2.5  3.6  nan]
 [ 2.6  3.3  nan  5.5]
 [ 2.1  3.2  5.4  6.5]]
final array [[ 1.3  2.5  3.6  6. ]
 [ 2.6  3.3  4.5  5.5]
 [ 2.1  3.2  5.4  6.5]]