https://github.com/ei-grad/bincount

No-copy parallelized bincount returning dict
https://github.com/ei-grad/bincount

bincount cython numpy python statistics

Last synced: 9 days ago
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No-copy parallelized bincount returning dict

• Host: GitHub
• URL: https://github.com/ei-grad/bincount
• Owner: ei-grad
• Created: 2018-11-19T15:30:14.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2024-04-09T06:11:12.000Z (9 months ago)
• Last Synced: 2024-12-15T11:17:03.836Z (14 days ago)
• Topics: bincount, cython, numpy, python, statistics
• Language: Cython
• Homepage:
• Size: 3.91 KB
• Stars: 2
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst

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README

        
bincount

========

No-copy parallelized bincount returning dict.

Install

-------

Prequirements: C-compiler with OpenMP support.

Install with pip:

.. code-block::

   pip install bincount

Usage

-----

There is a ``bincount`` (a parallel version) and a ``bincount_single`` (which don't

parallelize the calculation) functions, both returning the dict containing the

number of occurrences of each byte value in the passed bytes-like object:

.. code-block::

   >>> from bincount import bincount

   >>> bincount(open('a-tiny-file.txt', 'rb').read())

   {59: 2, 65: 5, 66: 1, 67: 3, 68: 2, 69: 3, 73: 4, 76: 7, 84: 3, 86: 1, 95: 4}

Motivation

----------

As of Nov 2018, ``np.bincount`` is unusable with large memmaps:

.. code-block::

   >>> import numpy as np

   >>> np.bincount(np.memmap('some-5gb-file.txt', mode='r'))

   Traceback (most recent call last):

     File "", line 1, in 

   MemoryError

The most effective pure-python solution for ``wc -l`` is a bit slow:

.. code-block::

   In [6]: %%time

      ...: sum(1 for i in open('some-5gb-file.txt', mode='rb'))

      ...:

   CPU times: user 3.5 s, sys: 878 ms, total: 4.38 s

   Wall time: 4.38 s

   Out[6]: 58941384

It is 3x times slower than ``wc -l``:

.. code-block::

   In [1]: %%time

      ...: !wc -l some-5gb-file.txt

      ...:

   58941384 some-5gb-file.txt

   CPU times: user 1.48 ms, sys: 3.48 ms, total: 4.96 ms

   Wall time: 1.24 s

While it should be faster on modern multicore SMP systems:

.. code-block::

   In [1]: import numpy as np

   In [2]: from bincount import bincount

   In [3]: %%time

      ...: bincount(np.memmap('some-5gb-file.txt', mode='r'))[10]

      ...:

   CPU times: user 6.83 s, sys: 354 ms, total: 7.19 s

   Wall time: 705 ms

   Out[4]: 58941384