Fast NumPy array functions written in C
Project description
Bottleneck is a collection of fast NumPy array functions written in C.
Let’s give it a try. Create a NumPy array:
>>> import numpy as np >>> a = np.array([1, 2, np.nan, 4, 5])
Find the nanmean:
>>> import bottleneck as bn >>> bn.nanmean(a) 3.0
Moving window mean:
>>> bn.move_mean(a, window=2, min_count=1) array([ 1. , 1.5, 2. , 4. , 4.5])
Benchmark
Bottleneck comes with a benchmark suite:
>>> bn.bench() Bottleneck performance benchmark Bottleneck 1.3.0.dev0; Numpy 1.12.1 Speed is NumPy time divided by Bottleneck time NaN means approx one-fifth NaNs; float64 used no NaN no NaN NaN no NaN NaN (100,) (1000,1000)(1000,1000)(1000,1000)(1000,1000) axis=0 axis=0 axis=0 axis=1 axis=1 nansum 67.3 0.3 0.7 2.5 2.4 nanmean 194.8 1.9 2.1 3.4 3.1 nanstd 241.5 1.6 2.1 2.7 2.6 nanvar 229.7 1.7 2.1 2.7 2.5 nanmin 34.1 0.7 1.1 0.8 2.6 nanmax 45.6 0.7 2.7 1.0 3.7 median 111.0 1.3 5.6 1.0 4.8 nanmedian 108.8 5.9 6.7 5.6 6.7 ss 16.3 1.1 1.2 1.6 1.6 nanargmin 89.2 2.9 5.1 2.2 5.6 nanargmax 107.4 3.0 5.4 2.2 5.8 anynan 19.4 0.3 35.0 0.5 29.9 allnan 39.9 146.6 128.3 115.8 75.6 rankdata 55.0 2.6 2.3 2.9 2.8 nanrankdata 59.8 2.8 2.2 3.2 2.5 partition 4.4 1.2 1.6 1.0 1.4 argpartition 3.5 1.1 1.4 1.1 1.6 replace 17.7 1.4 1.4 1.3 1.4 push 3440.0 7.8 9.5 20.0 15.5 move_sum 4743.0 75.7 156.1 195.4 211.1 move_mean 8760.9 116.2 167.4 252.1 258.8 move_std 8979.9 96.1 196.3 144.0 256.3 move_var 11216.8 127.3 243.9 225.9 321.4 move_min 2245.3 20.6 36.7 23.2 42.1 move_max 2223.7 20.5 37.2 24.1 42.4 move_argmin 3664.0 48.2 73.3 40.2 83.9 move_argmax 3916.9 42.0 75.4 41.5 81.2 move_median 2023.3 166.8 173.7 153.8 154.3 move_rank 1208.5 1.9 1.9 2.5 2.8
You can also run a detailed benchmark for a single function using, for example, the command:
>>> bn.bench_detailed("move_median", fraction_nan=0.3)
Only arrays with data type (dtype) int32, int64, float32, and float64 are accelerated. All other dtypes result in calls to slower, unaccelerated functions. In the rare case of a byte-swapped input array (e.g. a big-endian array on a little-endian operating system) the function will not be accelerated regardless of dtype.
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License
Bottleneck is distributed under a Simplified BSD license. See the LICENSE file for details.
Install
Requirements:
Bottleneck |
Python 2.7, 3.5, 3.6; NumPy 1.12.1 |
Compile |
gcc, clang, MinGW or MSVC |
Unit tests |
nose |
To install Bottleneck on GNU/Linux, Mac OS X, et al.:
$ sudo python setup.py install
To install bottleneck on Windows, first install MinGW and add it to your system path. Then install Bottleneck with the commands:
python setup.py install --compiler=mingw32
Alternatively, you can use the Windows binaries created by Christoph Gohlke: http://www.lfd.uci.edu/~gohlke/pythonlibs/#bottleneck
Unit tests
After you have installed Bottleneck, run the suite of unit tests:
>>> import bottleneck as bn >>> bn.test() <snip> Ran 169 tests in 57.205s OK <nose.result.TextTestResult run=169 errors=0 failures=0>
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