Remove outliers from pandas dataframe python

Question

I have a code that creates a dataframe using pandas

import pandas as pd
import numpy as np

x = (g[0].time[:111673])
y = (g[0].data.f[:111673])
df = pd.DataFrame({'Time': x, 'Data': y})
#df

This prints out:

          Data          Time
0        -0.704239      7.304021
1        -0.704239      7.352021
2        -0.704239      7.400021
3        -0.704239      7.448021
4        -0.825279      7.496021

Which is great but I know there are outliers in this data that I want removed so I created this dataframe below to point them out:

newdf = df.copy()
Data = newdf.groupby('Data')
newdf[np.abs(newdf.Data-newdf.Data.mean())<=(3*newdf.Data.std())]
newdf['Outlier'] = Data.transform( lambda x: abs(x-x.mean()) > 1.96*x.std() )
#newdf

This prints out:

             Data          Time  Outlier
0        -0.704239      7.304021    False
1        -0.704239      7.352021    False
2        -0.704239      7.400021    False
3        -0.704239      7.448021    False
4        -0.825279      7.496021    False

In the example of my data you cant see it but there are maybe 300 outliers and I want to remove them without messing with the original dataframe and then plot them together as a compression. My question is this: So instead of printing out false/true how can I just eliminate the outliers that are true? so I can eventually plot them in the same graph for a comparison.

Codes I have already tried:

newdf[np.abs(newdf.Data-newdf.Data.mean())<=(1.96*newdf.Data.std())]

newdf = df.copy()
def replace_outliers_with_nan(df, stdvs):
    newdf=pd.DataFrame()
    for i, col in enumerate(df.sites.unique()):
        df = pd.DataFrame(df[df.sites==col])
        idx = [np.abs(df-df.mean())<=(stdvs*df.std())] 
        df[idx==False]=np.nan  
        newdf[col] = df
    return newdf

Both of these doesn't work, they returns the same amount of data points as my original dataframe however I know that if it removed the outliers the amount of points would be less than the original.

Remove outliers from pandas dataframe python

1 Answers