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Tips for working with CSV files

How to

Typically one provides a csv filename to the data constructor like so

>>> d = data('myfile.csv')  # doctest: +SKIP

GZip extensions or collections of csv files are handled in the same manner.

>>> d = data('myfile-2014-01-*.csv.gz')  # doctest: +SKIP

In the case of collections of CSV files the files are sorted by filename and then considered to be concatenated into a single table.

How does it work?

Blaze primarily relies on Pandas to parse CSV files into DataFrames. In the case of large CSV files it may parse them into several DataFrames and then use techniques laid out in the :doc:`ooc` section.

What to do when things go wrong

The same thing that makes CSV files so popular with humans, simple readability/writability, makes them challenging for computers to reason about robustly.

Interacting with CSV files often breaks down in one of two ways

  1. We incorrectly guess the dialect of the CSV file (e.g. wrong delimiter, presence or absense of a header, ...)
  2. We incorrectly guess the type of a column with the CSV file (e.g. an integer column turns out to have floats in it)

Because Blaze operates in a lazy way, giving you access to large CSV files without reading the entire file into memory it is forced to do some guesswork. By default it guesses the dialect and types on the first few hundred lines of text. When this guesswork fails the user must supply additional information.

Correcting CSV Dialects

In the first case of incorrect guessing of CSV dialect (e.g. delimiter) Blaze respects and passes through all keyword arguments to pandas.read_csv.

Note

In the case of a CSV file with all string data, you must pass the has_header=True argument if the first row is the header row.

Correcting Column Types

In the second case of incorrect guessing of column types Blaze accepts a :doc:`datashape` as an additional keyword argument. Common practice is to create a data object around a csv file, ask for its datashape, tweak that datashape and then recreate the data object.

>>> d = data('myfile.csv')  # doctest: +SKIP
>>> d  # doctest: +SKIP
Exception: Integer column has NA values

>>> d.dshape  # Perhaps that integer column should be a float  # doctest: +SKIP
dshape("var * {name: string, amount: int64}")

# <Copy-Paste>
>>> ds = dshape("var * {name: string, amount: float64}")  # change int to float  # doctest: +SKIP

>>> d = data('myfile.csv', dshape=ds)  # doctest: +SKIP

Migrate to Binary Storage Formats

If you plan to reuse the same CSV files many times it may make sense to convert them to an efficient binary store like HDF5 (common) or BColz (less common but faster). These storage formats provide better performance on your data and also avoid the ambiguity that surrounds CSV files.

One can migrate from CSV files to a binary storage format using the odo function.

>>> from odo import odo
>>> odo('myfiles-*.csv', 'myfile.bcolz')  # doctest: +SKIP

# or

>>> odo('myfiles-*.csv', 'myfile.hdf5::/mydataset')  # doctest: +SKIP

# or

>>> odo('myfiles-*.csv', 'sqlite:///mydb.db::mytable')  # doctest: +SKIP

When migrating from a loosely formatted system like CSV to a more strict system like HDF5 or BColz there are a few things to keep in mind

  1. Neither supports variable length strings well
  2. But each supports fixed-length strings well and supports compression to cover up overly large/wasteful fixed-lengths
  3. HDF5 does not support datetimes well but can easily encode datetimes as strings
  4. BColz is a column store, offering much better performance on tables with many columns
  5. HDF5 is a standard technology with excellent library support outside of the Python ecosystem

To ensure that you encode your dataset appropriately we recommend passing a datashape explicitly. As in our previous example this can often be done by editing automatically generated datashapes

>>> d = data('myfile.csv')  # doctest: +SKIP
>>> d.dshape  # doctest: +SKIP
dshape("var * {name: string, amount: int64}")

# <Copy-Paste>
>>> ds = dshape("var * {name: string[20, 'ascii'], amount: float64}")  # doctest: +SKIP

>>> from odo import odo
>>> odo('myfiles-*.csv', 'myfile.bcolz', dshape=ds)  # doctest: +SKIP

Providing a datashape removes data type ambiguity from the transfer.