[python] How to store a dataframe using Pandas

Right now I'm importing a fairly large CSV as a dataframe every time I run the script. Is there a good solution for keeping that dataframe constantly available in between runs so I don't have to spend all that time waiting for the script to run?

pyarrow compatibility across versions

Overall move has been to pyarrow/feather (deprecation warnings from pandas/msgpack). However I have a challenge with pyarrow with transient in specification Data serialized with pyarrow 0.15.1 cannot be deserialized with 0.16.0 ARROW-7961. I'm using serialization to use redis so have to use a binary encoding.

I've retested various options (using jupyter notebook)

import sys, pickle, zlib, warnings, io
class foocls:
    def pyarrow(out): return pa.serialize(out).to_buffer().to_pybytes()
    def msgpack(out): return out.to_msgpack()
    def pickle(out): return pickle.dumps(out)
    def feather(out): return out.to_feather(io.BytesIO())
    def parquet(out): return out.to_parquet(io.BytesIO())

warnings.filterwarnings("ignore")
for c in foocls.__dict__.values():
    sbreak = True
    try:
        c(out)
        print(c.__name__, "before serialization", sys.getsizeof(out))
        print(c.__name__, sys.getsizeof(c(out)))
        %timeit -n 50 c(out)
        print(c.__name__, "zlib", sys.getsizeof(zlib.compress(c(out))))
        %timeit -n 50 zlib.compress(c(out))
    except TypeError as e:
        if "not callable" in str(e): sbreak = False
        else: raise
    except (ValueError) as e: print(c.__name__, "ERROR", e)
    finally: 
        if sbreak: print("=+=" * 30)        
warnings.filterwarnings("default")

With following results for my data frame (in out jupyter variable)

pyarrow before serialization 533366
pyarrow 120805
1.03 ms ± 43.9 µs per loop (mean ± std. dev. of 7 runs, 50 loops each)
pyarrow zlib 20517
2.78 ms ± 81.8 µs per loop (mean ± std. dev. of 7 runs, 50 loops each)
=+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+=
msgpack before serialization 533366
msgpack 109039
1.74 ms ± 72.8 µs per loop (mean ± std. dev. of 7 runs, 50 loops each)
msgpack zlib 16639
3.05 ms ± 71.7 µs per loop (mean ± std. dev. of 7 runs, 50 loops each)
=+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+=
pickle before serialization 533366
pickle 142121
733 µs ± 38.3 µs per loop (mean ± std. dev. of 7 runs, 50 loops each)
pickle zlib 29477
3.81 ms ± 60.4 µs per loop (mean ± std. dev. of 7 runs, 50 loops each)
=+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+=
feather ERROR feather does not support serializing a non-default index for the index; you can .reset_index() to make the index into column(s)
=+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+=
parquet ERROR Nested column branch had multiple children: struct<x: double, y: double>
=+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+=

feather and parquet do not work for my data frame. I'm going to continue using pyarrow. However I will supplement with pickle (no compression). When writing to cache store pyarrow and pickle serialised forms. When reading from cache fallback to pickle if pyarrow deserialisation fails.

Numpy file formats are pretty fast for numerical data

I prefer to use numpy files since they're fast and easy to work with. Here's a simple benchmark for saving and loading a dataframe with 1 column of 1million points.

import numpy as np
import pandas as pd

num_dict = {'voltage': np.random.rand(1000000)}
num_df = pd.DataFrame(num_dict)

using ipython's %%timeit magic function

%%timeit
with open('num.npy', 'wb') as np_file:
    np.save(np_file, num_df)

the output is

100 loops, best of 3: 5.97 ms per loop

to load the data back into a dataframe

%%timeit
with open('num.npy', 'rb') as np_file:
    data = np.load(np_file)

data_df = pd.DataFrame(data)

the output is

100 loops, best of 3: 5.12 ms per loop

NOT BAD!

CONS

There's a problem if you save the numpy file using python 2 and then try opening using python 3 (or vice versa).

https://docs.python.org/3/library/pickle.html

The pickle protocol formats:

Protocol version 0 is the original “human-readable” protocol and is backwards compatible with earlier versions of Python.

Protocol version 1 is an old binary format which is also compatible with earlier versions of Python.

Protocol version 2 was introduced in Python 2.3. It provides much more efficient pickling of new-style classes. Refer to PEP 307 for information about improvements brought by protocol 2.

Protocol version 3 was added in Python 3.0. It has explicit support for bytes objects and cannot be unpickled by Python 2.x. This is the default protocol, and the recommended protocol when compatibility with other Python 3 versions is required.

Protocol version 4 was added in Python 3.4. It adds support for very large objects, pickling more kinds of objects, and some data format optimizations. Refer to PEP 3154 for information about improvements brought by protocol 4.

As already mentioned there are different options and file formats (HDF5, JSON, CSV, parquet, SQL) to store a data frame. However, pickle is not a first-class citizen (depending on your setup), because:

1. pickle is a potential security risk. Form the Python documentation for pickle:

Warning The pickle module is not secure against erroneous or maliciously constructed data. Never unpickle data received from an untrusted or unauthenticated source.

2. pickle is slow. Find here and here benchmarks.

Depending on your setup/usage both limitations do not apply, but I would not recommend pickle as the default persistence for pandas data frames.

Pandas DataFrames have the to_pickle function which is useful for saving a DataFrame:

import pandas as pd

a = pd.DataFrame({'A':[0,1,0,1,0],'B':[True, True, False, False, False]})
print a
#    A      B
# 0  0   True
# 1  1   True
# 2  0  False
# 3  1  False
# 4  0  False

a.to_pickle('my_file.pkl')

b = pd.read_pickle('my_file.pkl')
print b
#    A      B
# 0  0   True
# 1  1   True
# 2  0  False
# 3  1  False
# 4  0  False

Although there are already some answers I found a nice comparison in which they tried several ways to serialize Pandas DataFrames: Efficiently Store Pandas DataFrames.

They compare:

• pickle: original ASCII data format
• cPickle, a C library
• pickle-p2: uses the newer binary format
• json: standardlib json library
• json-no-index: like json, but without index
• msgpack: binary JSON alternative
• CSV
• hdfstore: HDF5 storage format

In their experiment, they serialize a DataFrame of 1,000,000 rows with the two columns tested separately: one with text data, the other with numbers. Their disclaimer says:

You should not trust that what follows generalizes to your data. You should look at your own data and run benchmarks yourself

The source code for the test which they refer to is available online. Since this code did not work directly I made some minor changes, which you can get here: serialize.py I got the following results:

They also mention that with the conversion of text data to categorical data the serialization is much faster. In their test about 10 times as fast (also see the test code).

Edit: The higher times for pickle than CSV can be explained by the data format used. By default pickle uses a printable ASCII representation, which generates larger data sets. As can be seen from the graph however, pickle using the newer binary data format (version 2, pickle-p2) has much lower load times.

Some other references:

• In the question Fastest Python library to read a CSV file there is a very detailed answer which compares different libraries to read csv files with a benchmark. The result is that for reading csv files numpy.fromfile is the fastest.
• Another serialization test shows msgpack, ujson, and cPickle to be the quickest in serializing.

You can use feather format file. It is extremely fast.

df.to_feather('filename.ft')

Arctic is a high performance datastore for Pandas, numpy and other numeric data. It sits on top of MongoDB. Perhaps overkill for the OP, but worth mentioning for other folks stumbling across this post

Pickle works good!

import pandas as pd
df.to_pickle('123.pkl')    #to save the dataframe, df to 123.pkl
df1 = pd.read_pickle('123.pkl') #to load 123.pkl back to the dataframe df

Another quite fresh test with to_pickle().

I have 25 .csv files in total to process and the final dataframe consists of roughly 2M items.

(Note: Besides loading the .csv files, I also manipulate some data and extend the data frame by new columns.)

Going through all 25 .csv files and create the dataframe takes around 14 sec.

Loading the whole dataframe from a pkl file takes less than 1 sec

If I understand correctly, you're already using pandas.read_csv() but would like to speed up the development process so that you don't have to load the file in every time you edit your script, is that right? I have a few recommendations:

1. you could load in only part of the CSV file using pandas.read_csv(..., nrows=1000) to only load the top bit of the table, while you're doing the development

2. use ipython for an interactive session, such that you keep the pandas table in memory as you edit and reload your script.

3. convert the csv to an HDF5 table

4. updated use DataFrame.to_feather() and pd.read_feather() to store data in the R-compatible feather binary format that is super fast (in my hands, slightly faster than pandas.to_pickle() on numeric data and much faster on string data).

You might also be interested in this answer on stackoverflow.