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Numpy – Replace Nan Values with Median

In this tutorial, we will look at how to replace all occurrences of NaN values in a Numpy array with the median value in the array with the help of some examples.

How do I replace all NaN values with the median in Numpy?

replace nan values in numpy array with the median

Use boolean indexing to replace all instances of NaN in a Numpy array with the median. Here, we use the numpy.isnan() function to check whether a value inside the array is NaN or not, and if it is, we set it to the median value in the array.

The following is the syntax –

import numpy as np
ar[np.isnan(ar)] = np.nanmedian(ar)

Use the numpy.nanmedian() function to compute the median of a Numpy array containing NaN values. It calculates the median excluding the NaN values in the array.

Let’s now look at a step-by-step example of using the above syntax on a Numpy array.

Step 1 – Create a Numpy array

First, we will create a one-dimensional array that we will be using throughout this tutorial.

import numpy as np

# create numpy array
ar = np.array([1, 2, np.nan, 3, 4, np.nan, np.nan, 5, 6, 7])
# display the array
ar

Output:

array([ 1.,  2., nan,  3.,  4., nan, nan,  5.,  6.,  7.])

Here, we used the np.array() function to create a Numpy array with some numbers and some NaN values.

Step 2 – Set NaN values in the array to the median using boolean indexing

Use the numpy.isnan() function to check whether a value in the array is NaN or not. If it is, set it to the median value (use the numpy.nanmedian() function to get the median of a Numpy array with NaN values).

Let’s replace all occurrences of NaN in the above array with the median value in the array.

# replace nan with the median
ar[np.isnan(ar)] = np.nanmedian(ar)
# display the array
ar

Output:

array([1., 2., 4., 3., 4., 4., 4., 5., 6., 7.])

You can see that each instance of NaN has been replaced by 4 (which is the median value in the above array). Note that here we are modifying the original array.

You can also use this method to replace NaN values with the median in higher-dimensional arrays. For example, let’s apply this method to a two-dimensional array containing some NaN values.

# create a 2D numpy array
ar = np.array([
    [1, np.nan, 2],
    [np.nan, 3, 4],
    [5, 6, 7]
])
# display the array
ar

Output:

array([[ 1., nan,  2.],
       [nan,  3.,  4.],
       [ 5.,  6.,  7.]])

Here, we created a 2D Numpy array containing some NaN values.

Let’s now replace the NaN values in this 2D array with the overall median of the values in the 2D array.

# replace nan with the median
ar[np.isnan(ar)] = np.nanmedian(ar)
# display the array
ar

Output:

array([[1., 4., 2.],
       [4., 3., 4.],
       [5., 6., 7.]])

The array now has the median value (4) in place of the NaNs.

You can similarly use this method to replace NaN values in a Numpy array with any other value.

Summary – Replace NaN values in Numpy array with the median

In this tutorial, we looked at how to replace all NaN values in a Numpy array with the median value. The following is a short summary of the steps mentioned in this tutorial.

  1. Create a Numpy array (skip this step if you already have an array to operate on).
  2. Use the numpy.isnan() function to check whether a value in the array is NaN or not. If it is, set it to the median value in the array using boolean indexing ar[np.isnan(ar)] = np.nanmedian(ar)

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Author

  • Piyush

    Piyush is a data scientist passionate about using data to understand things better and make informed decisions. In the past, he's worked as a Data Scientist for ZS and holds an engineering degree from IIT Roorkee. His hobbies include watching cricket, reading, and working on side projects.