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Fast Hamming distance calculation for hexadecimal strings

Project description

Pip Prs Github

What does it do?

This module performs a fast bitwise hamming distance of two hexadecimal strings.

This looks like:

DEADBEEF = 11011110101011011011111011101111
00000000 = 00000000000000000000000000000000
XOR      = 11011110101011011011111011101111
Hamming  = number of ones in DEADBEEF ^ 00000000 = 24

This essentially amounts to

>>> import gmpy
>>> gmpy.popcount(0xdeadbeef ^ 0x00000000)
24

except with Python strings, so

>>> import gmpy
>>> gmpy.popcount(int("deadbeef", 16) ^ int("00000000", 16))
24

A few assumptions are made and enforced:

  • this is a valid hexadecimal string (i.e., [a-fA-F0-9]+)
  • the strings are the same length
  • the strings do not begin with "0x"

Why yet another Hamming distance library?

There are a lot of fantastic (python) libraries that offer methods to calculate various edit distances, including Hamming distances: Distance, textdistance, scipy, jellyfish, etc.

In this case, I needed a hamming distance library that worked on hexadecimal strings (i.e., a Python str) and performed blazingly fast. Furthermore, I often did not care about hex strings greater than 256 bits. That length constraint is different vs all the other libraries and enabled me to explore vectorization techniques via numba, numpy, and SSE/AVX intrinsics.

Lastly, I wanted to minimize dependencies, meaning you do not need to install numpy, gmpy, cython, pypy, pythran, etc.

Eventually, after playing around with gmpy.popcount, numba.jit, pythran.run, numpy, I decided to write what I wanted in essentially raw C. At this point, I’m using raw char* and int*, so exploring re-writing this in Fortran makes little sense.

Installation

To install, ensure you have Python 2.7 or 3.4+. Run

pip install hexhamming

or to install from source

git clone https://github.com/mrecachinas/hexhamming
cd hexhamming
python setup.py install # or pip install .

If you want to contribute to hexhamming, you should install the dev dependencies

pip install -r requirements-dev.txt

and make sure the tests pass with

pytest -vls

Example

Using hexhamming is as simple as

>>> from hexhamming import hamming_distance
>>> hamming_distance("deadbeef", "00000000")
24

Benchmark

Below is a benchmark using pytest-benchmark with hexhamming==v1.3.2 my 2020 2.0 GHz quad-core Intel Core i5 16 GB 3733 MHz LPDDR4 macOS Catalina (10.15.5) with Python 3.7.3 and Apple clang version 11.0.3 (clang-1103.0.32.62).

Name Mean (ns) Std (ns) Median (ns) Rounds Iterations
test_hamming_distance_bench_3 93.8 10.5 94.3 53268 200
test_hamming_distance_bench_3_same 94.2 15.2 94.9 102146 100
test_check_hexstrings_within_dist_bench 231.9 104.2 216.5 195122 22
test_hamming_distance_bench_256 97.5 34.1 94.0 195122 22
test_hamming_distance_bench_1000 489.8 159.4 477.5 94411 20
test_hamming_distance_bench_1000_same 497.8 87.8 496.6 18971 20
test_hamming_distance_bench_1024 509.9 299.5 506.7 18652 10
test_hamming_distance_bench_1024_same 467.4 205.9 450.4 181819 10

Project details


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