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# C/cython source files | ||
include jenkspy/src/* | ||
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include README.rst | ||
include README.md | ||
include LICENSE | ||
include tests/*.* | ||
include requirements.txt |
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# Jenkspy: Fast Fisher-Jenks breaks for Python | ||
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Compute "natural breaks" (*Fisher-Jenks algorithm*) on list / tuple / array / numpy.ndarray of integers/floats. | ||
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The algorithm implemented by this library is also sometimes referred to as *Fisher-Jenks algorithm*, *Jenks Optimisation Method* or *Fisher exact optimization method*. This is a deterministic method to calculate the optimal class boundaries. | ||
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Intended compatibility: CPython 3.6+ | ||
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Wheels are provided via PyPI for Windows / MacOS / Linux users - Also available on conda-forge channel for Anaconda users. | ||
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[![](https://github.com/mthh/jenkspy/actions/workflows/wheel.yml/badge.svg)](https://github.com/mthh/jenkspy/actions/workflows/wheel.yml) | ||
[![](https://img.shields.io/pypi/v/jenkspy.svg?color=007ec6)](https://pypi.python.org/pypi/jenkspy) | ||
[![](https://anaconda.org/conda-forge/jenkspy/badges/version.svg)](https://anaconda.org/conda-forge/jenkspy) | ||
[![](https://img.shields.io/pypi/dm/jenkspy.svg)](https://pypi.python.org/pypi/jenkspy) | ||
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## Usage | ||
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Two ways of using `jenkspy` are available: | ||
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- by using the `jenks_breaks` function which takes as input | ||
a [`list`](https://docs.python.org/3/library/stdtypes.html#list) | ||
/ [`tuple`](https://docs.python.org/3/library/stdtypes.html#tuple) | ||
/ [`array.array`](https://docs.python.org/3/library/array.html#array.array) | ||
/ [`numpy.ndarray`](https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html) of integers or floats and returns a list of values that correspond to the limits of the classes (starting with the minimum value of the series - the lower bound of the first class - and ending with its maximum value - the upper bound of the last class). | ||
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```python | ||
>>> import jenkspy | ||
>>> import json | ||
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>>> with open('tests/test.json', 'r') as f: | ||
... # Read some data from a JSON file | ||
... data = json.loads(f.read()) | ||
... | ||
>>> jenkspy.jenks_breaks(data, n_classes=5) # Asking for 5 classes | ||
[0.0028109620325267315, 2.0935479691252112, 4.205495140049607, 6.178148351609707, 8.09175917180255, 9.997982932254672] | ||
# ^ ^ ^ ^ ^ ^ | ||
# Lower bound Upper bound Upper bound Upper bound Upper bound Upper bound | ||
# 1st class 1st class 2nd class 3rd class 4th class 5th class | ||
# (Minimum value) (Maximum value) | ||
``` | ||
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- by using the `JenksNaturalBreaks` class that is inspired by `scikit-learn` classes. | ||
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The `.fit` and `.group` behavior is slightly different from `jenks_breaks`, | ||
by accepting value outside the range of the minimum and maximum value of `breaks_`, | ||
retaining the input size. It means that fit and group will use only the `inner_breaks_`. | ||
All value below the min bound will be included in the first group and all value higher than the max bound will be included in the last group. | ||
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```python | ||
>>> from jenkspy import JenksNaturalBreaks | ||
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>>> x = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11] | ||
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>>> jnb = JenksNaturalBreaks(4) # Asking for 4 clusters | ||
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>>> jnb.fit(x) # Create the clusters according to values in 'x' | ||
>>> print(jnb.labels_) # Labels for fitted data | ||
... print(jnb.groups_) # Content of each group | ||
... print(jnb.breaks_) # Break values (including min and max) | ||
... print(jnb.inner_breaks_) # Inner breaks (ie breaks_[1:-1]) | ||
[0 0 0 1 1 1 2 2 2 3 3 3] | ||
[array([0, 1, 2]), array([3, 4, 5]), array([6, 7, 8]), array([ 9, 10, 11])] | ||
[0.0, 2.0, 5.0, 8.0, 11.0] | ||
[2.0, 5.0, 8.0] | ||
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>>> print(jnb.predict(15)) # Predict the group of a value | ||
3 | ||
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>>> print(jnb.predict([2.5, 3.5, 6.5])) # Predict the group of several values | ||
[1 1 2] | ||
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>>> print(jnb.group([2.5, 3.5, 6.5])) # Group the elements into there groups | ||
[array([], dtype=float64), array([2.5, 3.5]), array([6.5]), array([], dtype=float64)] | ||
``` | ||
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## Installation | ||
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- **From pypi** | ||
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```shell | ||
pip install jenkspy | ||
``` | ||
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- **From source** | ||
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```shell | ||
git clone http://github.com/mthh/jenkspy | ||
cd jenkspy/ | ||
python setup.py install | ||
``` | ||
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- **For anaconda users** | ||
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```shell | ||
conda install -c conda-forge jenkspy | ||
``` | ||
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## Requirements | ||
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- [Numpy](https://numpy.org) | ||
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- Only for building from source: C compiler, Python C headers, setuptools and Cython. | ||
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## Motivation: | ||
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- Making a painless installing C extension so it could be used more easily | ||
as a dependency in an other package (and so learning how to build wheels | ||
using *appveyor* / *travis* at first - now it uses *GitHub Actions*). | ||
- Getting the break values! (and fast!). No fancy functionality provided, | ||
but contributions/forks/etc are welcome. | ||
- Other python implementations are currently existing but not as fast or not available on PyPi. |
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