Dropping infinite values from dataframes in pandas?
PythonPandasNumpyPython Problem Overview
What is the quickest/simplest way to drop nan
and inf
/-inf
values from a pandas.DataFrame
without resetting mode.use_inf_as_null
?
I'd like to be able to use the subset
and how
arguments of dropna
, except with inf
values considered missing, like:
df.dropna(subset=["col1", "col2"], how="all", with_inf=True)
Is this possible? Is there a way to tell dropna
to include inf
in its definition of missing values?
Python Solutions
Solution 1 - Python
The simplest way would be to first replace()
infs to NaN:
df.replace([np.inf, -np.inf], np.nan, inplace=True)
and then use the dropna()
:
df.replace([np.inf, -np.inf], np.nan, inplace=True) \
.dropna(subset=["col1", "col2"], how="all")
For example:
In [11]: df = pd.DataFrame([1, 2, np.inf, -np.inf])
In [12]: df.replace([np.inf, -np.inf], np.nan, inplace=True)
Out[12]:
0
0 1
1 2
2 NaN
3 NaN
The same method would work for a Series.
Solution 2 - Python
With option context, this is possible without permanently setting use_inf_as_na
. For example:
with pd.option_context('mode.use_inf_as_na', True):
df = df.dropna(subset=['col1', 'col2'], how='all')
Of course it can be set to treat inf
as NaN
permanently with
pd.set_option('use_inf_as_na', True)
For older versions, replace use_inf_as_na
with use_inf_as_null
.
Solution 3 - Python
Use (fast and simple):
df = df[np.isfinite(df).all(1)]
This answer is based on DougR's answer in an other question. Here an example code:
import pandas as pd
import numpy as np
df=pd.DataFrame([1,2,3,np.nan,4,np.inf,5,-np.inf,6])
print('Input:\n',df,sep='')
df = df[np.isfinite(df).all(1)]
print('\nDropped:\n',df,sep='')
Result:
Input:
0
0 1.0000
1 2.0000
2 3.0000
3 NaN
4 4.0000
5 inf
6 5.0000
7 -inf
8 6.0000
Dropped:
0
0 1.0
1 2.0
2 3.0
4 4.0
6 5.0
8 6.0
Solution 4 - Python
Here is another method using .loc
to replace inf with nan on a Series:
s.loc[(~np.isfinite(s)) & s.notnull()] = np.nan
So, in response to the original question:
df = pd.DataFrame(np.ones((3, 3)), columns=list('ABC'))
for i in range(3):
df.iat[i, i] = np.inf
df
A B C
0 inf 1.000000 1.000000
1 1.000000 inf 1.000000
2 1.000000 1.000000 inf
df.sum()
A inf
B inf
C inf
dtype: float64
df.apply(lambda s: s[np.isfinite(s)].dropna()).sum()
A 2
B 2
C 2
dtype: float64
Solution 5 - Python
The above solution will modify the inf
s that are not in the target columns. To remedy that,
lst = [np.inf, -np.inf]
to_replace = {v: lst for v in ['col1', 'col2']}
df.replace(to_replace, np.nan)
Solution 6 - Python
Yet another solution would be to use the isin
method. Use it to determine whether each value is infinite or missing and then chain the all
method to determine if all the values in the rows are infinite or missing.
Finally, use the negation of that result to select the rows that don't have all infinite or missing values via boolean indexing.
all_inf_or_nan = df.isin([np.inf, -np.inf, np.nan]).all(axis='columns')
df[~all_inf_or_nan]
Solution 7 - Python
You can use pd.DataFrame.mask
with np.isinf
. You should ensure first your dataframe series are all of type float
. Then use dropna
with your existing logic.
print(df)
col1 col2
0 -0.441406 inf
1 -0.321105 -inf
2 -0.412857 2.223047
3 -0.356610 2.513048
df = df.mask(np.isinf(df))
print(df)
col1 col2
0 -0.441406 NaN
1 -0.321105 NaN
2 -0.412857 2.223047
3 -0.356610 2.513048
Solution 8 - Python
To remove both Nan
, and inf
using a single command use
df = df[ np.isfinite( df ).all( axis = 1) ]
If for some reason the above doesn't work for you, please try the following 2 steps:
df = df[ ~( df.isnull().any( axis = 1 ) ) ] #to remove nan
df = df[ ~( df.isin( [np.inf, -np.inf]).any(axis =1) )] #to remove inf
Solution 9 - Python
Just stumbled upon this one and I found a one line without replace or numpy:
df = pd.DataFrame(
[[1, np.inf],
[1, -np.inf],
[1, 2]],
columns=['a', 'b']
)
df.query("b not in [inf, -inf]")
>>> a b
2 1 2.0
For some version of pandas
, one might need to use back `
around the name of the column b
.
Solution 10 - Python
Unlike other answers here, this one line code worked for me.
import numpy as np
df= df[df['required_column_name']!= np.inf]