By WeNYoBen


2018-11-09 02:19:22 8 Comments

I have the following DataFrame where one of the columns is an object (list type cell):

df=pd.DataFrame({'A':[1,2],'B':[[1,2],[1,2]]})
df
Out[458]: 
   A       B
0  1  [1, 2]
1  2  [1, 2]

My expected output is:

   A  B
0  1  1
1  1  2
3  2  1
4  2  2

What should I do to achieve this?


Related question

pandas: When cell contents are lists, create a row for each element in the list

Good question and answer but only handle one column with list(In my answer the self-def function will work for multiple columns, also the accepted answer is use the most time consuming apply , which is not recommended, check more info When should I ever want to use pandas apply() in my code?)

7 comments

@Ben Pap 2019-04-24 22:19:15

df=pd.DataFrame({'A':[1,2],'B':[[1,2],[1,2]]})

pd.concat([df['A'], pd.DataFrame(df['B'].values.tolist())], axis = 1)\
  .melt(id_vars = 'A', value_name = 'B')\
  .dropna()\
  .drop('variable', axis = 1)

    A   B
0   1   1
1   2   1
2   1   2
3   2   2

Any opinions on this method I thought of? or is doing both concat and melt considered too "expensive"?

@Ze Tang 2019-04-19 07:24:30

Because normally sublist length are different and join/merge is far more computational expensive. I retested the method for different length sublist and more normal columns.

MultiIndex should be also a easier way to write and has near the same performances as numpy way.

Surprisingly, in my implementation comprehension way has the best performance.

def stack(df):
    return df.set_index(['A', 'C']).B.apply(pd.Series).stack()


def comprehension(df):
    return pd.DataFrame([x + [z] for x, y in zip(df[['A', 'C']].values.tolist(), df.B) for z in y])


def multiindex(df):
    return pd.DataFrame(np.concatenate(df.B.values), index=df.set_index(['A', 'C']).index.repeat(df.B.str.len()))


def array(df):
    return pd.DataFrame(
        np.column_stack((
            np.repeat(df[['A', 'C']].values, df.B.str.len(), axis=0),
            np.concatenate(df.B.values)
        ))
    )


import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
from timeit import timeit

res = pd.DataFrame(
    index=[
        'stack',
        'comprehension',
        'multiindex',
        'array',
    ],
    columns=[1000, 2000, 5000, 10000, 20000, 50000],
    dtype=float
)

for f in res.index:
    for c in res.columns:
        df = pd.DataFrame({'A': list('abc'), 'C': list('def'), 'B': [['g', 'h', 'i'], ['j', 'k'], ['l']]})
        df = pd.concat([df] * c)
        stmt = '{}(df)'.format(f)
        setp = 'from __main__ import df, {}'.format(f)
        res.at[f, c] = timeit(stmt, setp, number=20)

ax = res.div(res.min()).T.plot(loglog=True)
ax.set_xlabel("N")
ax.set_ylabel("time (relative)")

Performance

Relative time of each method

@WeNYoBen 2018-11-09 02:20:07


As a user with both R and python, I have seen this type of question a couple of times.


In R, they have the built-in function from package tidyr called unnest. But in Python(pandas) there is no built-in function for this type of question.


I know object columns type always make the data hard to convert with a pandas' function. When I received the data like this , the first thing that came to mind was to 'flatten' or unnest the columns .


Method 1 apply + pd.Series (easy to understand but in terms of performance not recommended . )

df.set_index('A').B.apply(pd.Series).stack().reset_index(level=0).rename(columns={0:'B'})
Out[463]: 
   A  B
0  1  1
1  1  2
0  2  1
1  2  2

Method 2 using repeat with DataFrame constructor , re-create your dataframe (good at performance, not good at multiple columns )

df=pd.DataFrame({'A':df.A.repeat(df.B.str.len()),'B':np.concatenate(df.B.values)})
df
Out[465]: 
   A  B
0  1  1
0  1  2
1  2  1
1  2  2

Method 2.1 for example besides A we have A.1 .....A.n. If we still use the method(Method 2) above it is hard for us to re-create the columns one by one .

Solution : join or merge with the index after 'unnest' the single columns

s=pd.DataFrame({'B':np.concatenate(df.B.values)},index=df.index.repeat(df.B.str.len()))
s.join(df.drop('B',1),how='left')
Out[477]: 
   B  A
0  1  1
0  2  1
1  1  2
1  2  2

If you need the column order exactly the same as before, add reindex at the end.

s.join(df.drop('B',1),how='left').reindex(columns=df.columns)

Method 3 recreate the list

pd.DataFrame([[x] + [z] for x, y in df.values for z in y],columns=df.columns)
Out[488]: 
   A  B
0  1  1
1  1  2
2  2  1
3  2  2

If more than two columns

s=pd.DataFrame([[x] + [z] for x, y in zip(df.index,df.B) for z in y])
s.merge(df,left_on=0,right_index=True)
Out[491]: 
   0  1  A       B
0  0  1  1  [1, 2]
1  0  2  1  [1, 2]
2  1  1  2  [1, 2]
3  1  2  2  [1, 2]

Method 4 using reindex or loc

df.reindex(df.index.repeat(df.B.str.len())).assign(B=np.concatenate(df.B.values))
Out[554]: 
   A  B
0  1  1
0  1  2
1  2  1
1  2  2

#df.loc[df.index.repeat(df.B.str.len())].assign(B=np.concatenate(df.B.values))

Method 5 when the list only contains unique values:

df=pd.DataFrame({'A':[1,2],'B':[[1,2],[3,4]]})
from collections import ChainMap
d = dict(ChainMap(*map(dict.fromkeys, df['B'], df['A'])))
pd.DataFrame(list(d.items()),columns=df.columns[::-1])
Out[574]: 
   B  A
0  1  1
1  2  1
2  3  2
3  4  2

Method 6 using numpy for high performance:

newvalues=np.dstack((np.repeat(df.A.values,list(map(len,df.B.values))),np.concatenate(df.B.values)))
pd.DataFrame(data=newvalues[0],columns=df.columns)
   A  B
0  1  1
1  1  2
2  2  1
3  2  2

Method 7 : using base function itertools cycle and chain: Pure python solution just for fun

from itertools import cycle,chain
l=df.values.tolist()
l1=[list(zip([x[0]], cycle(x[1])) if len([x[0]]) > len(x[1]) else list(zip(cycle([x[0]]), x[1]))) for x in l]
pd.DataFrame(list(chain.from_iterable(l1)),columns=df.columns)
   A  B
0  1  1
1  1  2
2  2  1
3  2  2

Special case (two columns type object)

df=pd.DataFrame({'A':[1,2],'B':[[1,2],[3,4]],'C':[[1,2],[3,4]]})
df
Out[592]: 
   A       B       C
0  1  [1, 2]  [1, 2]
1  2  [3, 4]  [3, 4]

Self-def function

def unnesting(df, explode):
    idx = df.index.repeat(df[explode[0]].str.len())
    df1 = pd.concat([
        pd.DataFrame({x: np.concatenate(df[x].values)}) for x in explode], axis=1)
    df1.index = idx

    return df1.join(df.drop(explode, 1), how='left')


unnesting(df,['B','C'])
Out[609]: 
   B  C  A
0  1  1  1
0  2  2  1
1  3  3  2
1  4  4  2

Summary :

I am using pandas and python functions for this type of question. If you are worried about the speed of the above solutions, check user3483203's answer , since he is using numpy and most of the time numpy is faster . I recommend Cpython and numba if speed matters in your case.

@ayorgo 2018-12-11 02:05:47

My 5 cents:

df[['B', 'B2']] = pd.DataFrame(df['B'].values.tolist())

df[['A', 'B']].append(df[['A', 'B2']].rename(columns={'B2': 'B'}),
                      ignore_index=True)

and another 5

df[['B1', 'B2']] = pd.DataFrame([*df['B']]) # if values.tolist() is too boring

(pd.wide_to_long(df.drop('B', 1), 'B', 'A', '')
 .reset_index(level=1, drop=True)
 .reset_index())

both resulting in the same

   A  B
0  1  1
1  2  1
2  1  2
3  2  2

@Daniel Mesejo 2018-12-01 01:31:45

One alternative is to apply the meshgrid recipe over the rows of the columns to unnest:

import numpy as np
import pandas as pd


def unnest(frame, explode):
    def mesh(values):
        return np.array(np.meshgrid(*values)).T.reshape(-1, len(values))

    data = np.vstack(mesh(row) for row in frame[explode].values)
    return pd.DataFrame(data=data, columns=explode)


df = pd.DataFrame({'A': [1, 2], 'B': [[1, 2], [1, 2]]})
print(unnest(df, ['A', 'B']))  # base
print()

df = pd.DataFrame({'A': [1, 2], 'B': [[1, 2], [3, 4]], 'C': [[1, 2], [3, 4]]})
print(unnest(df, ['A', 'B', 'C']))  # multiple columns
print()

df = pd.DataFrame({'A': [1, 2, 3], 'B': [[1, 2], [1, 2, 3], [1]],
                   'C': [[1, 2, 3], [1, 2], [1, 2]], 'D': ['A', 'B', 'C']})

print(unnest(df, ['A', 'B']))  # uneven length lists
print()
print(unnest(df, ['D', 'B']))  # different types
print()

Output

   A  B
0  1  1
1  1  2
2  2  1
3  2  2

   A  B  C
0  1  1  1
1  1  2  1
2  1  1  2
3  1  2  2
4  2  3  3
5  2  4  3
6  2  3  4
7  2  4  4

   A  B
0  1  1
1  1  2
2  2  1
3  2  2
4  2  3
5  3  1

   D  B
0  A  1
1  A  2
2  B  1
3  B  2
4  B  3
5  C  1

@user3483203 2018-11-09 02:35:17

Option 1

If all of the sublists in the other column are the same length, numpy can be an efficient option here:

vals = np.array(df.B.values.tolist())    
a = np.repeat(df.A, vals.shape[1])

pd.DataFrame(np.column_stack((a, vals.ravel())), columns=df.columns)

   A  B
0  1  1
1  1  2
2  2  1
3  2  2

Option 2

If the sublists have different length, you need an additional step:

vals = df.B.values.tolist()
rs = [len(r) for r in vals]    
a = np.repeat(df.A, rs)

pd.DataFrame(np.column_stack((a, np.concatenate(vals))), columns=df.columns)

   A  B
0  1  1
1  1  2
2  2  1
3  2  2

Option 3

I took a shot at generalizing this to work to flatten N columns and tile M columns, I'll work later on making it more efficient:

df = pd.DataFrame({'A': [1,2,3], 'B': [[1,2], [1,2,3], [1]],
                   'C': [[1,2,3], [1,2], [1,2]], 'D': ['A', 'B', 'C']})

   A          B          C  D
0  1     [1, 2]  [1, 2, 3]  A
1  2  [1, 2, 3]     [1, 2]  B
2  3        [1]     [1, 2]  C

def unnest(df, tile, explode):
    vals = df[explode].sum(1)
    rs = [len(r) for r in vals]
    a = np.repeat(df[tile].values, rs, axis=0)
    b = np.concatenate(vals.values)
    d = np.column_stack((a, b))
    return pd.DataFrame(d, columns = tile +  ['_'.join(explode)])

unnest(df, ['A', 'D'], ['B', 'C'])

    A  D B_C
0   1  A   1
1   1  A   2
2   1  A   1
3   1  A   2
4   1  A   3
5   2  B   1
6   2  B   2
7   2  B   3
8   2  B   1
9   2  B   2
10  3  C   1
11  3  C   1
12  3  C   2

Functions

def wen1(df):
    return df.set_index('A').B.apply(pd.Series).stack().reset_index(level=0).rename(columns={0: 'B'})

def wen2(df):
    return pd.DataFrame({'A':df.A.repeat(df.B.str.len()),'B':np.concatenate(df.B.values)})

def wen3(df):
    s = pd.DataFrame({'B': np.concatenate(df.B.values)}, index=df.index.repeat(df.B.str.len()))
    return s.join(df.drop('B', 1), how='left')

def wen4(df):
    return pd.DataFrame([[x] + [z] for x, y in df.values for z in y],columns=df.columns)

def chris1(df):
    vals = np.array(df.B.values.tolist())
    a = np.repeat(df.A, vals.shape[1])
    return pd.DataFrame(np.column_stack((a, vals.ravel())), columns=df.columns)

def chris2(df):
    vals = df.B.values.tolist()
    rs = [len(r) for r in vals]
    a = np.repeat(df.A.values, rs)
    return pd.DataFrame(np.column_stack((a, np.concatenate(vals))), columns=df.columns)

Timings

import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
from timeit import timeit

res = pd.DataFrame(
       index=['wen1', 'wen2', 'wen3', 'wen4', 'chris1', 'chris2'],
       columns=[10, 50, 100, 500, 1000, 5000, 10000],
       dtype=float
)

for f in res.index:
    for c in res.columns:
        df = pd.DataFrame({'A': [1, 2], 'B': [[1, 2], [1, 2]]})
        df = pd.concat([df]*c)
        stmt = '{}(df)'.format(f)
        setp = 'from __main__ import df, {}'.format(f)
        res.at[f, c] = timeit(stmt, setp, number=50)

ax = res.div(res.min()).T.plot(loglog=True)
ax.set_xlabel("N")
ax.set_ylabel("time (relative)")

Performance

enter image description here

@U9-Forward 2018-11-09 02:40:08

Something pretty not recommended (at least work in this case):

df=pd.concat([df]*2).sort_index()
it=iter(df['B'].tolist()[0]+df['B'].tolist()[0])
df['B']=df['B'].apply(lambda x:next(it))

concat + sort_index + iter + apply + next.

Now:

print(df)

Is:

   A  B
0  1  1
0  1  2
1  2  1
1  2  2

If care about index:

df=df.reset_index(drop=True)

Now:

print(df)

Is:

   A  B
0  1  1
1  1  2
2  2  1
3  2  2

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