pandas: resample a multi-index dataframe

Question

I have a dataframe with a multi-index: "subject" and "datetime". Each row corresponds to a subject and a datetime, and columns of the dataframe correspond to various measurements.

The range of days differ per subject and some days can be missing for a given subject (see example). Moreover, a subject can have one or several values for a given day.

I want to resample the dataframe so that:

• there is only one row per day per subject (I do not care about time of day),
• each column value is the last non-NaN of the day (and NaN if there is no value for that day),
• days with no values on any column are not created or kept.

For instance, the following dataframe example:

                                a       b
subject  datetime                        
patient1 2018-01-01 00:00:00  2.0    high
         2018-01-01 01:00:00  NaN  medium
         2018-01-01 02:00:00  6.0     NaN
         2018-01-01 03:00:00  NaN     NaN
         2018-01-02 00:00:00  4.3     low
patient2 2018-01-01 00:00:00  NaN  medium
         2018-01-01 02:00:00  NaN     NaN
         2018-01-01 03:00:00  5.0     NaN
         2018-01-03 00:00:00  9.0     NaN
         2018-01-04 02:00:00  NaN     NaN

should return:

                                a       b
subject  datetime                        
patient1 2018-01-01 00:00:00  6.0  medium
         2018-01-02 00:00:00  4.3     low
patient2 2018-01-01 00:00:00  5.0  medium
         2018-01-03 00:00:00  9.0     NaN

I spent too much time trying to obtain this using resample with the 'pad' option, but I always get errors or not the result I want. Can anybody help?

Note: Here is a code to create the example dataframe:

import pandas as pd
import numpy as np

index = pd.MultiIndex.from_product([['patient1', 'patient2'], pd.date_range('20180101', periods=4,
                                      freq='h')])

df = pd.DataFrame({'a': [2, np.nan, 6, np.nan, np.nan, np.nan, np.nan, 5], 'b': ['high', 'medium', np.nan, np.nan, 'medium', 'low', np.nan, np.nan]},
                  index=index)
df.index.names = ['subject', 'datetime']

df = df.drop(df.index[5])
df.at[('patient2', '2018-01-03 00:00:00'), 'a'] = 9
df.at[('patient2', '2018-01-04 02:00:00'), 'a'] = None
df.at[('patient1', '2018-01-02 00:00:00'), 'a'] = 4.3
df.at[('patient1', '2018-01-02 00:00:00'), 'b'] = 'low'

df = df.sort_index(level=['subject', 'datetime'])

Answer 1

Let's floor the datetime on daily frequency, then groupby the dataframe on subject + floored timestamp and agg using last, finally drop the rows having all NaN's:

i = pd.to_datetime(df.index.get_level_values(1)).floor('d')
df1 = df.groupby(['subject', i]).agg('last').dropna(how='all')

---

                       a       b
subject  datetime               
patient1 2018-01-01  6.0  medium
         2018-01-02  4.3     low
patient2 2018-01-01  5.0  medium
         2018-01-03  9.0     NaN

Answer 2

# drop a et b we don't need them when they ='re both na
df = df.reset_index().dropna(subset=["a", "b"], how="all")

#add a day columns we need it to keep last value
df["dt_day"] = df["datetime"].dt.date

#d1 result dataframe which we add a et b
 
d1 = df.copy().drop_duplicates(subset=["subject", "dt_day"]).loc[:, ["subject", "datetime"]].reset_index(drop=True)

#add a et b to ou dataframe result

for col in ["a", "b"]:
    d1.loc[:,col] = (df.copy().
                     dropna(subset=[col]).drop_duplicates(subset=["subject", "dt_day"], keep="last")[col]
                     .reset_index(drop=True))

Wall time: 24 ms

@Shubham Sharma code => Wall time: 2.94 ms

    subject   datetime    a       b
0  patient1 2018-01-01  6.0  medium
1  patient1 2018-01-02  4.3     low
2  patient2 2018-01-01  5.0  medium
3  patient2 2018-01-03  9.0     NaN

thanks for your question :)

Answer 3

This should do the job:

def day_agg(series_):
    try:
        return series_.dropna().iloc[-1]
    except IndexError:
        return float("nan")

df = df.reset_index().sort_values("datetime")
df.groupby([df["subject"],df.datetime.map(lambda x:datetime(year=x.year,month=x.month,day=x.day))])\
    .agg({"a":day_agg, "b":day_agg})\
    .dropna(how="all")