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Merge pull request #37 from arvkevi/refactor_data_generator
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move data variables from test_sample.py to staticmethods in data_generator.py
fixes #36
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@arvkevi
arvkevi authored Aug 3, 2019
2 parents cee53e0 + 06e86ca commit 9e522f9
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Showing 2 changed files with 82 additions and 39 deletions.
61 changes: 61 additions & 0 deletions kneed/data_generator.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -43,3 +43,64 @@ def decreasing():
x = [1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000]
y = [2314, 802, 519, 417, 358, 318, 302, 284, 280]
return x, y

@staticmethod
def convex_increasing():
"""Generate a sample increasing convex function
:returns: tuple(x, y)
:rtypes: (array, array)
"""
x = np.arange(0, 10)
y_convex_inc = np.array([1, 2, 3, 4, 5, 10, 15, 20, 40, 100])
return x, y_convex_inc

@staticmethod
def convex_decreasing():
"""Generate a sample decreasing convex function
:returns: tuple(x, y)
:rtypes: (array, array)
"""
x = np.arange(0, 10)
y_convex_dec = np.array([100, 40, 20, 15, 10, 5, 4, 3, 2, 1])
return x, y_convex_dec

@staticmethod
def concave_decreasing():
"""Generate a sample decreasing concave function
:returns: tuple(x, y)
:rtypes: (array, array)
"""
x = np.arange(0, 10)
y_concave_dec = np.array([99, 98, 97, 96, 95, 90, 85, 80, 60, 0])
return x, y_concave_dec

@staticmethod
def concave_increasing():
"""Generate a sample increasing concave function
:returns: tuple(x, y)
:rtypes: (array, array)
"""
x = np.arange(0, 10)
y_concave_inc = np.array([0, 60, 80, 85, 90, 95, 96, 97, 98, 99])
return x, y_concave_inc

@staticmethod
def bumpy():
"""Generate a sample function with local minima/maxima
:returns: tuple(x, y)
:rtypes: (array, array)
"""
x_bumpy = list(range(90))
y_bumpy = [7305., 6979., 6666.6, 6463.2, 6326.5, 6048.8, 6032.8, 5762.,
5742.8, 5398.2, 5256.8, 5227., 5001.7, 4942., 4854.2, 4734.6,
4558.7, 4491.1, 4411.6, 4333., 4234.6, 4139.1, 4056.8, 4022.5,
3868., 3808.3, 3745.3, 3692.3, 3645.6, 3618.3, 3574.3, 3504.3,
3452.4, 3401.2, 3382.4, 3340.7, 3301.1, 3247.6, 3190.3, 3180.,
3154.2, 3089.5, 3045.6, 2989., 2993.6, 2941.3, 2875.6, 2866.3,
2834.1, 2785.1, 2759.7, 2763.2, 2720.1, 2660.1, 2690.2, 2635.7,
2632.9, 2574.6, 2556., 2545.7, 2513.4, 2491.6, 2496., 2466.5,
2442.7, 2420.5, 2381.5, 2388.1, 2340.6, 2335., 2318.9, 2319.,
2308.2, 2262.2, 2235.8, 2259.3, 2221., 2202.7, 2184.3, 2170.1,
2160., 2127.7, 2134.7, 2102., 2101.4, 2066.4, 2074.3, 2063.7,
2048.1, 2031.9]
return x_bumpy, y_bumpy
60 changes: 21 additions & 39 deletions tests/test_sample.py
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Original file line number Diff line number Diff line change
@@ -1,106 +1,88 @@
import math
import numpy as np
import pytest
from kneed.data_generator import DataGenerator
from kneed.data_generator import DataGenerator as dg
from kneed.knee_locator import KneeLocator

x = np.arange(0, 10)
y_convex_inc = np.array([1, 2, 3, 4, 5, 10, 15, 20, 40, 100])
y_convex_dec = np.array(y_convex_inc[::-1])
y_concave_dec = np.array(100 - y_convex_inc)
y_concave_inc = np.array(100 - y_convex_dec)
x_bumpy = list(range(90))
y_bumpy = [7305., 6979., 6666.6, 6463.2, 6326.5, 6048.8, 6032.8, 5762.,
5742.8, 5398.2, 5256.8, 5227., 5001.7, 4942., 4854.2, 4734.6,
4558.7, 4491.1, 4411.6, 4333., 4234.6, 4139.1, 4056.8, 4022.5,
3868., 3808.3, 3745.3, 3692.3, 3645.6, 3618.3, 3574.3, 3504.3,
3452.4, 3401.2, 3382.4, 3340.7, 3301.1, 3247.6, 3190.3, 3180.,
3154.2, 3089.5, 3045.6, 2989., 2993.6, 2941.3, 2875.6, 2866.3,
2834.1, 2785.1, 2759.7, 2763.2, 2720.1, 2660.1, 2690.2, 2635.7,
2632.9, 2574.6, 2556., 2545.7, 2513.4, 2491.6, 2496., 2466.5,
2442.7, 2420.5, 2381.5, 2388.1, 2340.6, 2335., 2318.9, 2319.,
2308.2, 2262.2, 2235.8, 2259.3, 2221., 2202.7, 2184.3, 2170.1,
2160., 2127.7, 2134.7, 2102., 2101.4, 2066.4, 2074.3, 2063.7,
2048.1, 2031.9]


@pytest.mark.parametrize("interp_method", ['interp1d', 'polynomial'])
def test_figure2(interp_method):
"""From the kneedle manuscript"""
DG = DataGenerator()
x, y = DG.figure2()
x, y = dg.figure2()
kl = KneeLocator(x, y, S=1.0, curve='concave', interp_method=interp_method)
assert math.isclose(kl.knee, 0.22, rel_tol=0.05)


@pytest.mark.parametrize("interp_method", ['interp1d', 'polynomial'])
def test_NoisyGaussian(interp_method):
"""From the Kneedle manuscript"""
DG = DataGenerator()
x, y = DG.noisy_gaussian(mu=50, sigma=10, N=10000)
x, y = dg.noisy_gaussian(mu=50, sigma=10, N=10000)
kl = KneeLocator(x, y, S=1.0, curve='concave', interp_method=interp_method)
assert math.isclose(kl.knee, 60.5, rel_tol=7.0)


@pytest.mark.parametrize("interp_method", ['interp1d', 'polynomial'])
def test_concave_increasing(interp_method):
"""test a concave increasing function"""
kn = KneeLocator(x, y_concave_inc, curve='concave', interp_method=interp_method)
x, y = dg.concave_increasing()
kn = KneeLocator(x, y, curve='concave', interp_method=interp_method)
assert kn.knee == 2


@pytest.mark.parametrize("interp_method", ['interp1d', 'polynomial'])
def test_concave_decreasing(interp_method):
"""test a concave decreasing function"""
kn = KneeLocator(x, y_concave_dec, curve='concave',
direction='decreasing', interp_method=interp_method)
x, y = dg.concave_decreasing()
kn = KneeLocator(x, y, curve='concave', direction='decreasing', interp_method=interp_method)
assert kn.knee == 7


@pytest.mark.parametrize("interp_method", ['interp1d', 'polynomial'])
def test_convex_increasing(interp_method):
"""test a convex increasing function"""
kl = KneeLocator(x, y_convex_inc, curve='convex', interp_method=interp_method)
x, y = dg.convex_increasing()
kl = KneeLocator(x, y, curve='convex', interp_method=interp_method)
assert kl.knee == 7


@pytest.mark.parametrize("interp_method", ['interp1d', 'polynomial'])
def test_convex_decreasing(interp_method):
"""test a convex decreasing function"""
kl = KneeLocator(x, y_convex_dec, curve='convex',
direction='decreasing', interp_method=interp_method)
x, y = dg.convex_decreasing()
kl = KneeLocator(x, y, curve='convex', direction='decreasing', interp_method=interp_method)
assert kl.knee == 2


@pytest.mark.parametrize("interp_method", ['interp1d', 'polynomial'])
def test_concave_increasing_truncated(interp_method):
"""test a truncated concave increasing function"""
kl = KneeLocator(x[:-3] / 10, y_concave_inc[:-3] / 10,
curve='concave', interp_method=interp_method)
x, y = dg.concave_increasing()
kl = KneeLocator(x[:-3] / 10, y[:-3] / 10, curve='concave', interp_method=interp_method)
assert kl.knee == 0.2


@pytest.mark.parametrize("interp_method", ['interp1d', 'polynomial'])
def test_concave_decreasing_truncated(interp_method):
"""test a truncated concave decreasing function"""
kl = KneeLocator(x[:-3] / 10, y_concave_dec[:-3] / 10,
curve='concave', direction='decreasing', interp_method=interp_method)
x, y = dg.concave_decreasing()
kl = KneeLocator(x[:-3] / 10, y[:-3] / 10, curve='concave', direction='decreasing', interp_method=interp_method)
assert kl.knee == 0.4


@pytest.mark.parametrize("interp_method", ['interp1d', 'polynomial'])
def test_convex_increasing_truncated(interp_method):
"""test a truncated convex increasing function"""
kl = KneeLocator(x[:-3] / 10, y_convex_inc[:-3] / 10,
curve='convex', interp_method=interp_method)
x, y = dg.convex_increasing()
kl = KneeLocator(x[:-3] / 10, y[:-3] / 10, curve='convex', interp_method=interp_method)
assert kl.knee == 0.4


@pytest.mark.parametrize("interp_method", ['interp1d', 'polynomial'])
def test_convex_decreasing_truncated(interp_method):
"""test a truncated convex decreasing function"""
kl = KneeLocator(x[:-3] / 10, y_convex_dec[:-3] / 10,
curve='convex', direction='decreasing', interp_method=interp_method)
x, y = dg.convex_decreasing()
kl = KneeLocator(x[:-3] / 10, y[:-3] / 10, curve='convex', direction='decreasing', interp_method=interp_method)
assert kl.knee == 0.2


Expand All @@ -110,8 +92,8 @@ def test_convex_decreasing_truncated(interp_method):
])
def test_convex_decreasing_bumpy(interp_method, expected):
"""test a bumpy convex decreasing function"""
kl = KneeLocator(x_bumpy, y_bumpy, curve='convex',
direction='decreasing', interp_method=interp_method)
x, y = dg.bumpy()
kl = KneeLocator(x, y, curve='convex', direction='decreasing', interp_method=interp_method)
assert kl.knee == expected


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