Removing nan values from an array

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Question :

Removing nan values from an array

I want to figure out how to remove nan values from my array. My array looks something like this:

x = [1400, 1500, 1600, nan, nan, nan ,1700] #Not in this exact configuration

How can I remove the nan values from x?

Answer #1:

If you’re using numpy for your arrays, you can also use

x = x[numpy.logical_not(numpy.isnan(x))]


x = x[~numpy.isnan(x)]

[Thanks to chbrown for the added shorthand]


The inner function, numpy.isnan returns a boolean/logical array which has the value True everywhere that x is not-a-number. As we want the opposite, we use the logical-not operator, ~ to get an array with Trues everywhere that x is a valid number.

Lastly we use this logical array to index into the original array x, to retrieve just the non-NaN values.

Answered By: jmetz

Answer #2:

filter(lambda v: v==v, x)

works both for lists and numpy array
since v!=v only for NaN

Answered By: udibr

Answer #3:

Try this:

import math
print [value for value in x if not math.isnan(value)]

For more, read on List Comprehensions.

Answered By: liori

Answer #4:

For me the answer by @jmetz didn’t work, however using pandas isnull() did.

x = x[~pd.isnull(x)]
Answered By: Daniel Kislyuk

Answer #5:

Doing the above :

x = x[~numpy.isnan(x)]


x = x[numpy.logical_not(numpy.isnan(x))]

I found that resetting to the same variable (x) did not remove the actual nan values and had to use a different variable. Setting it to a different variable removed the nans.

y = x[~numpy.isnan(x)]
Answered By: melissaOu

Answer #6:

If you’re using numpy

# first get the indices where the values are finite
ii = np.isfinite(x)

# second get the values
x = x[ii]
Answered By: aloha

Answer #7:

As shown by others


works. But it will throw an error if the numpy dtype is not a native data type, for example if it is object. In that case you can use pandas.

x[~pandas.isna(x)] or x[~pandas.isnull(x)]
Answered By: koliyat9811

Answer #8:

The accepted answer changes shape for 2d arrays.
I present a solution here, using the Pandas dropna() functionality.
It works for 1D and 2D arrays. In the 2D case you can choose weather to drop the row or column containing np.nan.

import pandas as pd
import numpy as np

def dropna(arr, *args, **kwarg):
    assert isinstance(arr, np.ndarray)
    dropped=pd.DataFrame(arr).dropna(*args, **kwarg).values
    if arr.ndim==1:
    return dropped

x = np.array([1400, 1500, 1600, np.nan, np.nan, np.nan ,1700])
y = np.array([[1400, 1500, 1600], [np.nan, 0, np.nan] ,[1700,1800,np.nan]] )

print('='*20+' 1D Case: ' +'='*20+'nInput:n',x,sep='')

print('nn'+'='*20+' 2D Case: ' +'='*20+'nInput:n',y,sep='')
print('ndropna (rows):n',dropna(y),sep='')
print('ndropna (columns):n',dropna(y,axis=1),sep='')

print('nn'+'='*20+' x[np.logical_not(np.isnan(x))] for 2D: ' +'='*20+'nInput:n',y,sep='')


==================== 1D Case: ====================
[1400. 1500. 1600.   nan   nan   nan 1700.]

[1400. 1500. 1600. 1700.]

==================== 2D Case: ====================
[[1400. 1500. 1600.]
 [  nan    0.   nan]
 [1700. 1800.   nan]]

dropna (rows):
[[1400. 1500. 1600.]]

dropna (columns):
 [   0.]

==================== x[np.logical_not(np.isnan(x))] for 2D: ====================
[[1400. 1500. 1600.]
 [  nan    0.   nan]
 [1700. 1800.   nan]]

[1400. 1500. 1600. 1700.]
Answered By: Markus Dutschke

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