Saturday, March 18, 2017

Simple CSV Transformations

Here's an interesting question:

I came across your blog post "Introduction to using Python to process CSV files" as I'm looking to do something I'd think is easy in Python but I don't know how to do it. 

I simply want to examine a column then create a new column based on an if-then on the original column. So if my CSV has a "gender" field I'd like to do the Python equivalent of this SQL statement: 

case when gender = 'M' then 1 else 0 end as gender_m, case when gender = 'F' then 1 else 0 end as gender_f,...

I can do it in Pandas but my CSVs are too big and I run into memory issues. 

There are a number of ways to tackle this.

First -- and foremost -- this is almost always just one step in a much longer and more complex set of operations. It's a little misleading to read-and-write a CSV file to do this.

A little misleading.

It's not wrong to write a file with expanded data. But the "incrementally write new files" process can become rather complex. If we have a large number of transformations, we can wind up with many individual file-expansion steps. These things often grow organically and can get out of control. A complex set of steps should probably be collapsed into a single program that handles all of the expansions at once.

This kind of file-expansion is simple and fast. It can open a door previously closed by the in-memory problem  of trying to do the entire thing in pandas.

The general outline looks like this

from pathlib import Path
import csv
source_path = Path("some_file.csv")
target_path = Path(source_path.stem + "_1").with_suffix('.csv')

def transform(row):
    return row

with source_path.open() as source_file:
    with target_path.open('w', newline='') as target_file:
        reader = csv.DictReader(source_file)
        columns =  reader.fieldnames + ['gender_m', 'gender_f']
        writer = csv.DictWriter(target_file, columns)
        writer.writeheader()
        for row in reader:
            new_row = transform(row)
            writer.writerow(new_row)

The goal is to be able put some meaningful transformation processing in place of the build new_row comment.

The overall approach is this.

1. Create Path objects to refer to the relevant files.

2. Use with-statement context managers to handle the open files. This assures that the files are always properly closed no matter what kinds of exceptions are raised.

3. Create a dictionary-based reader for the input.  Add the additional columns and create a dictionary-based writer for the output. This allows the processing to work with each row of data as a dictionary.
This presumes that the data file actually has a single row of heading information with column names.

If column names are missing, then a fieldnames attribute can be provided when creating the DictReader(), like this: csv.DictReader(source_file, ['field', 'field', ...]).

The for statement works because a csv Reader is an iterator over each row of data.

I've omitted any definition of the transformational function. Right now, it just returns each row unmodified. We'd really like it to do some useful work.

Building The New Row

The transformation function needs to build a new row from an existing row.

Each row will be a Python dictionary. A dictionary is a mutable object. We aren't really building a completely new object -- that's a waste of memory. We'll modify the row object, and return it anyway. It will involve a microscopic redundancy of creating two references to the same dictionary object, one known by the variable name row and the other know by new_row.

Here's an example body for transform()

def transform(row):
    row['gender_m'] = 1 if row['gender'] == 'M' else 0
    row['gender_f'] = 1 if row['gender'] == 'F' else 0
    return row

This will build two new keys in the row dictionary. The exact two keys added to the fieldnames to write a new file.

Each key be associated with a value computed by a simple expression. In this case, the logical if-else operator is used to map a boolean value, row['gender'] == 'M', to one of two integer values, 1 or 0.

If this is confusing -- and it can be -- this can also be done with if statements instead of expressions.

def transform(row):
    if row['gender'] == 'M':
        row['gender_m'] = 1
    else:
        row['gender_m'] = 0
    row['gender_f'] = 1 if row['gender'] == 'F' else 0
    return row

I only rewrite the 'M' case. I'll leave the rewrite of the 'F' case to the reader.

Faster Processing with a Generator

We can simplify the body of the script slightly. This will make it work a hair faster. The following statements involve a little bit of needless overhead.

        for row in reader:
            new_row = transform(row)
            writer.writerow(new_row)

We can change this as follows:

        writer.writerows(transform(row) for row in reader)

This uses a generator expression, transform(row) for row in reader, to build individually transformed rows from a source of data. This doesn't involve executing two statements for each row of data. Therefore, it's faster.

We can also reframe it like this.

        writer.writerows(map(transform, reader))

In this example, we've replaced the generator expression with the map() function. This applies the transform() function to each row available in the reader.

In both cases, the writer.writerows() consumes the data produced by the generator expression or the map() function to create the output file.

The idea is that we can make the transform() function as complex as we need. We just have to be sure that all the new field names are handled properly when creating the writer object.