lazycsv - a memory-efficient csv parser
Developers: Michael Green, Chris Perkins
lazycsv is a C implementation of a csv parser for python. The aim of this parser is to provide for fast extraction of sequences of data from a CSV file in a memory-efficient manner, with zero dependencies.
LazyCSV utilizes memory mapped files and iterators to parse the file without persisting any significant amounts of data to physical memory. The design allows a user to generate PyObject's from a csv file lazily.
The parser works as follows:
First, The user file is memory-mapped internally to the LazyCSV object. That
file is used to generate three indexes. The first is an index of values which
correspond to the position in the user file where a given CSV field starts.
This value is always a
uint16_t which we found to be the optimal bit size for
disk usage and execution performance (This type can however be changed by
LAZYCSV_INDEX_DTYPE environment variable to any unsigned integer
type). For index values outside the range of an unsigned short, An "anchor
point" is created, which is a pair of
size_t values that mark both the value
which is subtracted from the index value such that the index value fits within
16 bits, and the first column of the CSV where the anchor value applies. This
anchor point is periodically written to the second index file when required for
a given comma index. Finally, the third index writes the index of the first
anchor point for each row of the file.
When a user requests a sequence of data (i.e. a row or a column), an iterator is created and returned. This iterator uses the value of the requested sequence and its internal position state to index into the index files the values representing the index of the requested field, and its length. Those two values are then used to create a single PyBytes object. These PyBytes objects are then yielded to the user per-iteration.
This process is lazy, only yielding data from the user file as the iterator is
consumed. It does not cache results as they are generated - it is the
responsibility of the user to store in physical memory the data which must be
persisted. The only persisted overhead in physical memory is the LazyCSV object
itself, any created iterators, a small cache of common length-0 and length-1
PyObject*'s for fast returns, and optionally the headers of the CSV file.
>>> from lazycsv import lazycsv >>> lazy = lazycsv.LazyCSV("tests/fixtures/file.csv") >>> lazy <lazycsv.LazyCSV object at 0x7f5b212ea3d0> >>> (col := lazy.sequence(col=0)) <lazycsv_iterator object at 0x7f5b212ea420> >>> next(col) b'0' >>> next(col) b'1' >>> next(col) Traceback (most recent call last): File "<stdin>", line 1, in <module> StopIteration
Since data is yielded through the iterator protocol, lazycsv pairs well with many of the builtin functional components of Python, and third-party libraries with support for iterators. This has the added benefit of keeping iterations in the C level, maximizing performance.
>>> row = lazy.sequence(row=1) >>> list(map(lambda x: x.decode('utf8'), row)) ['1', 'a1', 'b1'] >>> >>> import numpy as np >>> np.fromiter(map(int, lazy.sequence(col=0)), dtype=np.int64) array([0, 1])
lazy object also supports indexing operations for expressive iterables.
The axis for iteration can be passed as a slice object, and the index of the
iterable can be passed as a integer. Individual coordinate values can also be
passed as a pair of integers, this call will eagerly return the value at that
>>> list(lazy[::-1, 1]) [b'a1', b'a0'] >>> lazy[-1, -1] b"b1"
Iterators can be materialized at any point by calling the
to_numpy() methods on the iterator object (to enable optional numpy support,
see the Numpy section of this document). These methods exhaust the iterator,
placing the remaining PyBytes values into a PyObject.
>>> col = lazy[:, 0] >>> next(col) b'0' >>> col.to_list() [b'1'] >>>
Headers are by default parsed from the csv file and packaged into a tuple under
.headers attribute. This can be skipped by passing
the object constructor. Skipping the header parsing step results in the header
value being included in the iterator.
lazycsv makes no effort to deduplicate headers and it is the
responsibility of the user to make sure that columns are properly named.
>>> lazy.headers (b'', b'ALPHA', b'BETA') >>> (col := lazy.sequence(col=1)) <lazycsv_iterator object at 0x7f599fd86b50> >>> list(col) [b'a0', b'a1'] >>> lazy = lazycsv.LazyCSV(FPATH, skip_headers=True) >>> (col := lazy[:, 1]) <lazycsv_iterator object at 0x7f59d1b21890> >>> list(col) [b'ALPHA', b'a0', b'a1']
Fields which are double-quoted by default are yielded without quotes. This
behavior can be disabled by passing
unquoted=False to the object constructor.
>>> lazy = lazycsv.LazyCSV( ... "tests/fixtures/file_crlf2.csv" ... ) >>> lazy.headers (b'', b'This,that', b'Fizz,Buzz') >>> lazy = lazycsv.LazyCSV( ... "tests/fixtures/file_crlf2.csv", unquote=False ... ) >>> lazy.headers (b'', b'"This,that"', b'"Fizz,Buzz"')
LazyCSV also provides the option to specify a delimiter and a quote character.
Pass the keywords
quotechar= to the object contstructor to
use custom values. By default,
delimiter defaults to
>>> lazy = lazycsv.LazyCSV( ... "tests/fixtures/file_delimiter_and_quotechar.csv", ... quotechar="|", ... delimiter="\t", ... unquote=False, ... ) ... >>> open(lazy.name, "rb").read() b'INDEX\tATTR\n0\t|A|\n1\t|B|\n' >>> list(lazy[:, 1]) [b'|A|', b'|B|']
Optional, opt-in numpy support is built into the module. Access to this
extended feature set can be had by building the extension from source while
LAZYCSV_INCLUDE_NUMPY environment variable to
1. This adds a
to_numpy() method to the iterator, which allows iterators to materialize in a
1-dimensional numpy array without creating intermediary PyObject*'s for each
field of the CSV file.
Access to this feature requires numpy to be preinstalled as this feature makes numpy a compilation dependency.
$ LAZYCSV_INCLUDE_NUMPY=1 python -m pip install lazycsv
>>> import numpy as np >>> from lazycsv import lazycsv >>> lazy = lazycsv.LazyCSV("") >>> lazy = lazycsv.LazyCSV("./tests/fixtures/file.csv") >>> lazy.sequence(col=0).to_numpy().astype(np.int8) array([0, 1], dtype=int8)
Users pinned to an older version of numpy (<1.7) may wish to instead compile
LAZYCSV_INCLUDE_NUMPY_LEGACY=1 flag, which drops the API pin in the
module while still compiling with numpy support.
CPU benchmarks are included below, benchmarked on a Ryzen 7 5800X inside a stock python3.9 docker container.
root@aa9d7c7ffb59:/code# python tests/benchmark_lazy.py filesize: 0.134gb cols=10000 rows=10000 sparsity=0.95 benchmarking lazycsv: indexing lazy... time to index: 0.450414217018988 parsing cols... time to parse: 1.5233540059998631 total time: 1.9737682230188511 benchmarking datatable: 100% |██████████████████████████████████████████████████| Reading data [done] creating datatables frame... time to object: 0.40828132900060154 parsing cols... time to parse: 3.810204313998838 total time: 4.21848564299944 benchmarking polars (read): creating polars df... time to object: 2.357821761001105 parsing cols... time to parse: 1.3874979300017003 total time: 3.7453196910028055
root@aa9d7c7ffb59:/code# python tests/benchmark_lazy.py filesize: 1.387gb cols=10000 rows=100000 sparsity=0.95 benchmarking lazycsv: indexing lazy... time to index: 4.298127760004718 parsing cols... time to parse: 18.591125406033825 total time: 22.889253166038543 benchmarking datatable: 100% |██████████████████████████████████████████████████| Reading data [done] creating datatables frame... time to object: 2.4456441220027045 parsing cols... time to parse: 37.424315700998704 total time: 39.86995982300141 benchmarking polars (read): creating polars df... time to object: 22.383294907001982 parsing cols... time to parse: 14.16580996599805 total time: 36.54910487300003
filesize: 14.333gb cols=100000 rows=100000 sparsity=0.95 benchmarking lazycsv: indexing lazy... time to index: 55.42112316700002 parsing cols... time to parse: 362.268973717 total time: 417.690096884 benchmarking datatable: 58% |█████████████████████████████▍ | Reading data Killed benchmarking polars (read): Killed