16.02.2021       Выпуск 374 (15.02.2021 - 21.02.2021)       Статьи

Efficiently Cleaning Text with Pandas

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Introduction

It’s no secret that data cleaning is a large portion of the data analysis process. When using pandas, there are multiple techniques for cleaning text fields to prepare for further analysis. As data sets grow large, it is important to find efficient methods that perform in a reasonable time and are maintainable since the text cleaning process evolves over time.

This article will show examples of cleaning text fields in a large data file and illustrates tips for how to efficiently clean unstructured text fields using Python and pandas.

The problem

For the sake of this article, let’s say you have a brand new craft whiskey that you would like to sell. Your territory includes Iowa and there just happens to be an open data set that shows all of the liquor sales in the state. This seems like a great opportunity for you to use your analysis skills to see who the biggest accounts are in the state. Armed with that data, you can plan your sales process for each of the accounts.

Excited about the opportunity, you download the data and realize it’s pretty large. The data set for this case is a 565MB CSV file with 24 columns and 2.3M rows. This is not big data by any means but it is big enough that it can make Excel crawl. It’s also big enough that some of the pandas approaches will be relatively slow on your laptop.

For this article, I’ll be using data that includes all of 2019 sales. Due to the size, you can download it from the state site for a different time period.

Let’s get started by importing our modules and reading the data. I will also use the sidetable package to summarize the data. It’s not required for the cleaning but I wanted to highlight how useful it can be for these data exploration scenarios.

The data

Let’s get our data :

import pandas as pd
import numpy as np
import sidetable

df = pd.read_csv('2019_Iowa_Liquor_Sales.csv')

Here’s what the data looks like.

The first thing we might want to do is see how much each store purchases and rank them from the largest to the smallest. We have limited resources so we should focus on those places where we get the best bang for the buck. It will be easier for us to call on a couple of big corporate accounts instead of a lot of mom and pop stores.

sidetable is a shortcut to summarize the data in a readable format. The alternative is doing a groupby plus additional manipulation.

df.stb.freq(['Store Name'], value='Sale (Dollars)', style=True, cum_cols=False)

One thing that’s apparent is that the store names are unique per location in most cases. Ideally we would like to see all the sales for Hy-Vee, Costco, Sam’s, etc grouped together.

Looks like we need to clean the data.

Cleaning attempt #1

The first approach we can investigate is using .loc plus a boolean filter with the str accessor to search for the relevant string in the Store Name column.

df.loc[df['Store Name'].str.contains('Hy-Vee', case=False), 'Store_Group_1'] = 'Hy-Vee'

This code will search for the string ‘Hy-Vee’ using a case insensitive search and store the value “Hy-Vee” in a new column called Store_Group_1 . This code will effectively convert names like “Hy-Vee #3 / BDI / Des Moines” or “Hy-Vee Food Store / Urbandale” into a common “Hy-Vee”.

Here’s what %%timeit tells us about this performance:

1.43 s ± 31.8 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)

Normally we don’t want to optimize too early in the process but one thing we can do is use the regex=False parameter to give a speedup:

df.loc[df['Store Name'].str.contains('Hy-Vee', case=False, regex=False), 'Store_Group_1'] = 'Hy-Vee'
804 ms ± 27.9 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)

Here are the counts in the new column:

NaN       1617777
Hy-Vee     762568
Name: Store_Group_1, dtype: int64

We’ve cleaned up Hy-Vee but now there are a lot of other values we need to tackle.

The .loc approach contains a lot of code and can be slow. We can use this concept but look for some alternatives that are quicker to execute and easier to maintain.

Cleaning attempt #2

Another approach that is very performant and flexible is to use np.select to run multiple matches and apply a specified value upon match.

There are several good resources that I used to learn how to use np.select . This article from Dataquest is a good overview. I also found this presentation from Nathan Cheever very interesting and information. I encourage you to check both of these out.

The simplest explanation for what np.select does is that it evaluates a list of conditions and applies a corresponding list of values if the condition is true.

In our case, our conditions will be different string lookups and the normalized string we want to use instead will be the value.

After looking through the data, here’s a list of conditions and values in the store_patterns list. Each tuple in this list is a str.contains() lookup and the corresponding text value we want to use to group like accounts together.

store_patterns = [
    (df['Store Name'].str.contains('Hy-Vee', case=False, regex=False), 'Hy-Vee'),
    (df['Store Name'].str.contains('Central City',
                                case=False,  regex=False), 'Central City'),
    (df['Store Name'].str.contains("Smokin' Joe's",
                                case=False,  regex=False), "Smokin' Joe's"),
    (df['Store Name'].str.contains('Walmart|Wal-Mart',
                                case=False), 'Wal-Mart'),
    (df['Store Name'].str.contains('Fareway Stores',
                                case=False,  regex=False), 'Fareway Stores'),
    (df['Store Name'].str.contains("Casey's",
                                case=False,  regex=False), "Casey's General Store"),
    (df['Store Name'].str.contains("Sam's Club", case=False,  regex=False), "Sam's Club"),
    (df['Store Name'].str.contains('Kum & Go',  regex=False, case=False), 'Kum & Go'),
    (df['Store Name'].str.contains('CVS',  regex=False, case=False), 'CVS Pharmacy'),
    (df['Store Name'].str.contains('Walgreens',  regex=False, case=False), 'Walgreens'),
    (df['Store Name'].str.contains('Yesway',  regex=False, case=False), 'Yesway Store'),
    (df['Store Name'].str.contains('Target Store',  regex=False, case=False), 'Target'),
    (df['Store Name'].str.contains('Quik Trip',  regex=False, case=False), 'Quik Trip'),
    (df['Store Name'].str.contains('Circle K',  regex=False, case=False), 'Circle K'),
    (df['Store Name'].str.contains('Hometown Foods',  regex=False,
                                case=False), 'Hometown Foods'),
    (df['Store Name'].str.contains("Bucky's", case=False,  regex=False), "Bucky's Express"),
    (df['Store Name'].str.contains('Kwik', case=False,  regex=False), 'Kwik Shop')
]

One of the big challenge when working with np.select is that it is easy to get the conditions and values mismatched. I’ve decided to combine into a tuple to more easily keep track of the data matches.

Because of this data structure, we need to break the list of tuples into two separate lists. Using zip we can take the store_patterns and break into store_criteria and store_values :

store_criteria, store_values = zip(*store_patterns)
df['Store_Group_1'] = np.select(store_criteria, store_values, 'other')

This code will fill in each match with the text value. If there is no match, we’ll assign it the value ‘other’.

Here’s what it looks like now:

df.stb.freq(['Store_Group_1'], value='Sale (Dollars)', style=True, cum_cols=False)

This looks better but there is still 32.28% of our revenue in “other” accounts.

What might be nice is that if there is an account that doesn’t match, we use the Store Name instead of lumping all together in other. Here’s how we do that:

df['Store_Group_1'] = np.select(store_criteria, store_values, None)
df['Store_Group_1'] = df['Store_Group_1'].combine_first(df['Store Name'])

This uses the combine_first function to fill in all the None values with the Store Name . This is a handy trick to keep in mind when cleaning your data.

Let’s check our data:

df.stb.freq(['Store_Group_1'], value='Sale (Dollars)', style=True, cum_cols=False)

This looks better because we can continue to refine the groupings as needed. For instance, we may want to build a string lookup for Costco.

Performance is not too bad for a large data set:

13.2 s ± 328 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)

The benefit of this approach is that you can use np.select for numeric analysis as well as the text examples shown here. It is very flexible.

The one challenge with this approach is that there is a lot of code. If you had a large data set to clean, there’s a lot of data and code intermixed in this solution.

Is there another approach that might have similar performance but be a little cleaner?

Cleaning attempt #3

The next solution is based on this excellent code example from Matt Harrison who developed a generalize function that does the matching and cleaning for us. I’ve made some changes to make it consistent with this example but want to give Matt credit. I would never have thought of this solution without him doing 99% of the work!

def generalize(ser, match_name, default=None, regex=False, case=False):
    """ Search a series for text matches.
    Based on code from https://www.metasnake.com/blog/pydata-assign.html

    ser: pandas series to search
    match_name: tuple containing text to search for and text to use for normalization
    default: If no match, use this to provide a default value, otherwise use the original text
    regex: Boolean to indicate if match_name contains a  regular expression
    case: Case sensitive search

    Returns a pandas series with the matched value

    """
    seen = None
    for match, name in match_name:
        mask = ser.str.contains(match, case=case, regex=regex)
        if seen is None:
            seen = mask
        else:
            seen |= mask
        ser = ser.where(~mask, name)
    if default:
        ser = ser.where(seen, default)
    else:
        ser = ser.where(seen, ser.values)
    return ser

This function can be called on a pandas series and expects a list of tuples. The first tuple item is the value to search for and the second is the value to fill in for the matched value.

Here’s the equivalent pattern list:

store_patterns_2 = [('Hy-Vee', 'Hy-Vee'), ("Smokin' Joe's", "Smokin' Joe's"),
                    ('Central City', 'Central City'),
                    ('Costco Wholesale', 'Costco Wholesale'),
                    ('Walmart', 'Walmart'), ('Wal-Mart', 'Walmart'),
                    ('Fareway Stores', 'Fareway Stores'),
                    ("Casey's", "Casey's General Store"),
                    ("Sam's Club", "Sam's Club"), ('Kum & Go', 'Kum & Go'),
                    ('CVS', 'CVS Pharmacy'), ('Walgreens', 'Walgreens'),
                    ('Yesway', 'Yesway Store'), ('Target Store', 'Target'),
                    ('Quik Trip', 'Quik Trip'), ('Circle K', 'Circle K'),
                    ('Hometown Foods', 'Hometown Foods'),
                    ("Bucky's", "Bucky's Express"), ('Kwik', 'Kwik Shop')]

A useful benefit of this solution is that it is much easier to maintain this list than the earlier store_patterns example.

The other change I made with the generalize function is that the original value will be preserved if there is no default value provided. Instead of using combine_first , the function will take care of it all. Finally, I turned off the regex match by default for a small performance improvement.

Now that the data is all set up, calling it is simple:

df['Store_Group_2'] = generalize(df['Store Name'], store_patterns_2)

How about performance?

15.5 s ± 409 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)

It is a little slower but I think it’s a more elegant solution and what I would use in the future if I had to do a similar text cleanup.

The downside to this approach is that it is designed for string cleaning. The np.select solution is more broadly useful since it can be applied to numeric values as well.

What about data types?

In recent versions of pandas there is a dedicated string type. I tried converting the Store Name to a pandas string type to see if there was any performance improvement. I did not notice any changes. However, it’s possible there will be speed improvements in the future so keep that in mind.

While the string type did not make a difference, the category type showed a lot of promise on this data set. Refer to my previous article for details on the category data type.

We can convert the data to a category using astype :

df['Store Name'] = df['Store Name'].astype('category')

Now re-run the np.select example exactly as we did earlier:

df['Store_Group_3'] = np.select(store_criteria, store_values, None)
df['Store_Group_3'] = df['Store_Group_1'].combine_first(df['Store Name'])
786 ms ± 108 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)

We went from 13s to less than 1 second by making one simple change. Amazing!

The reason this works is pretty straightforward. When pandas converts a column to a categorical type, pandas will only call the expensive str.contains() function on each unique text value. Because this data set has a lot of repeated data, we get a huge performance boost.

Let’s see if this works for our generalize function:

df['Store_Group_4'] = generalize(df['Store Name'], store_patterns_2)

Unfortunately we get this error:

ValueError: Cannot setitem on a Categorical with a new category, set the categories first

That error highlights some of the challenge I have had in the past when dealing with Categorical data. When merging and joining categorical data, you can run into these types of challenges.

I tried to figure out a good way to modify generalize() to work but could not figure it out. Bonus points to any reader that figures it out.

However, there is a way we can replicate the Category approach by building a lookup table.

Lookup table

As we learned with the Categorical approach, this data set has a lot of duplicated data. We can build a lookup table and process the resource intensive function only one time per string.

To illustrate how this works on strings, let’s convert the value back to a string type instead of the category:

df['Store Name'] = df['Store Name'].astype('string')

First we build a lookup DataFrame that contains all the unique values and run the generalize function:

lookup_df = pd.DataFrame()
lookup_df['Store Name'] = df['Store Name'].unique()
lookup_df['Store_Group_5'] = generalize(lookup_df['Store Name'], store_patterns_2)

We can merge it back into a final DataFrame:

1.38 s ± 15.1 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)

It is slower than the np.select approach on categorical data but the performance impact might be balanced by the easier readability for maintaining the lookup list.

Also, the intermediate lookup_df could be a great output to share with an analyst that can help you clean up more of the data. That savings could be measured in hours of work!

Summary

This newsletter by Randy Au is a good discussion about the important of data cleaning and the love-hate relationship many data scientists have with this task. I agree with Randy’s premise that data cleaning is analysis.

In my experience, you can learn a lot about your underlying data by taking up the kind of cleaning activities outlined in this article.

I suspect you are going to find lots of cases in your day to day analysis where you need to do text cleaning similar to what I’ve shown in this article.

Here is a quick summary of the solutions we looked at:

Text Cleaning Options
SolutionExecution timeNotes
np.select13sCan work for non-text analysis
generalize15sText only
Category Data and np.select786msCategorical data can get tricky when merging and joining
Lookup table and generalize1.3sA lookup table can be maintained by someone else

For some data sets, performance is not an issue so pick what clicks with your brain.

However, as the data grows in size (imagine doing this analysis for 50 states worth of data), you will need to understand how to use pandas in an efficient manner for text cleaning. My hope is that you bookmark this article and come back to it when you face a similar problem.

As always, if you have some other tips that might be useful to folks, let me know in the comments. If you figure out how to make my generalize function work with categorical data, let me know too.






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