489 lines
15 KiB
Python
489 lines
15 KiB
Python
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import numpy as np
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from numpy.testing import assert_allclose
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from pytest import raises as assert_raises
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from scipy.stats import (binned_statistic, binned_statistic_2d,
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binned_statistic_dd)
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from scipy._lib._util import check_random_state
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from .common_tests import check_named_results
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class TestBinnedStatistic(object):
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@classmethod
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def setup_class(cls):
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rng = check_random_state(9865)
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cls.x = rng.uniform(size=100)
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cls.y = rng.uniform(size=100)
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cls.v = rng.uniform(size=100)
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cls.X = rng.uniform(size=(100, 3))
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cls.w = rng.uniform(size=100)
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cls.u = rng.uniform(size=100) + 1e6
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def test_1d_count(self):
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x = self.x
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v = self.v
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count1, edges1, bc = binned_statistic(x, v, 'count', bins=10)
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count2, edges2 = np.histogram(x, bins=10)
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assert_allclose(count1, count2)
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assert_allclose(edges1, edges2)
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def test_gh5927(self):
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# smoke test for gh5927 - binned_statistic was using `is` for string
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# comparison
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x = self.x
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v = self.v
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statistics = [u'mean', u'median', u'count', u'sum']
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for statistic in statistics:
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binned_statistic(x, v, statistic, bins=10)
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def test_big_number_std(self):
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# tests for numerical stability of std calculation
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# see issue gh-10126 for more
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x = self.x
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u = self.u
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stat1, edges1, bc = binned_statistic(x, u, 'std', bins=10)
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stat2, edges2, bc = binned_statistic(x, u, np.std, bins=10)
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assert_allclose(stat1, stat2)
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def test_non_finite_inputs_and_int_bins(self):
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# if either `values` or `sample` contain np.inf or np.nan throw
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# see issue gh-9010 for more
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x = self.x
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u = self.u
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orig = u[0]
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u[0] = np.inf
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assert_raises(ValueError, binned_statistic, u, x, 'std', bins=10)
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# need to test for non-python specific ints, e.g. np.int8, np.int64
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assert_raises(ValueError, binned_statistic, u, x, 'std',
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bins=np.int64(10))
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u[0] = np.nan
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assert_raises(ValueError, binned_statistic, u, x, 'count', bins=10)
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# replace original value, u belongs the class
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u[0] = orig
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def test_1d_result_attributes(self):
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x = self.x
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v = self.v
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res = binned_statistic(x, v, 'count', bins=10)
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attributes = ('statistic', 'bin_edges', 'binnumber')
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check_named_results(res, attributes)
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def test_1d_sum(self):
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x = self.x
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v = self.v
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sum1, edges1, bc = binned_statistic(x, v, 'sum', bins=10)
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sum2, edges2 = np.histogram(x, bins=10, weights=v)
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assert_allclose(sum1, sum2)
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assert_allclose(edges1, edges2)
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def test_1d_mean(self):
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x = self.x
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v = self.v
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stat1, edges1, bc = binned_statistic(x, v, 'mean', bins=10)
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stat2, edges2, bc = binned_statistic(x, v, np.mean, bins=10)
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assert_allclose(stat1, stat2)
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assert_allclose(edges1, edges2)
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def test_1d_std(self):
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x = self.x
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v = self.v
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stat1, edges1, bc = binned_statistic(x, v, 'std', bins=10)
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stat2, edges2, bc = binned_statistic(x, v, np.std, bins=10)
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assert_allclose(stat1, stat2)
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assert_allclose(edges1, edges2)
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def test_1d_min(self):
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x = self.x
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v = self.v
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stat1, edges1, bc = binned_statistic(x, v, 'min', bins=10)
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stat2, edges2, bc = binned_statistic(x, v, np.min, bins=10)
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assert_allclose(stat1, stat2)
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assert_allclose(edges1, edges2)
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def test_1d_max(self):
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x = self.x
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v = self.v
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stat1, edges1, bc = binned_statistic(x, v, 'max', bins=10)
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stat2, edges2, bc = binned_statistic(x, v, np.max, bins=10)
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assert_allclose(stat1, stat2)
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assert_allclose(edges1, edges2)
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def test_1d_median(self):
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x = self.x
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v = self.v
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stat1, edges1, bc = binned_statistic(x, v, 'median', bins=10)
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stat2, edges2, bc = binned_statistic(x, v, np.median, bins=10)
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assert_allclose(stat1, stat2)
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assert_allclose(edges1, edges2)
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def test_1d_bincode(self):
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x = self.x[:20]
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v = self.v[:20]
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count1, edges1, bc = binned_statistic(x, v, 'count', bins=3)
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bc2 = np.array([3, 2, 1, 3, 2, 3, 3, 3, 3, 1, 1, 3, 3, 1, 2, 3, 1,
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1, 2, 1])
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bcount = [(bc == i).sum() for i in np.unique(bc)]
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assert_allclose(bc, bc2)
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assert_allclose(bcount, count1)
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def test_1d_range_keyword(self):
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# Regression test for gh-3063, range can be (min, max) or [(min, max)]
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np.random.seed(9865)
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x = np.arange(30)
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data = np.random.random(30)
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mean, bins, _ = binned_statistic(x[:15], data[:15])
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mean_range, bins_range, _ = binned_statistic(x, data, range=[(0, 14)])
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mean_range2, bins_range2, _ = binned_statistic(x, data, range=(0, 14))
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assert_allclose(mean, mean_range)
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assert_allclose(bins, bins_range)
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assert_allclose(mean, mean_range2)
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assert_allclose(bins, bins_range2)
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def test_1d_multi_values(self):
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x = self.x
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v = self.v
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w = self.w
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stat1v, edges1v, bc1v = binned_statistic(x, v, 'mean', bins=10)
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stat1w, edges1w, bc1w = binned_statistic(x, w, 'mean', bins=10)
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stat2, edges2, bc2 = binned_statistic(x, [v, w], 'mean', bins=10)
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assert_allclose(stat2[0], stat1v)
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assert_allclose(stat2[1], stat1w)
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assert_allclose(edges1v, edges2)
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assert_allclose(bc1v, bc2)
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def test_2d_count(self):
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x = self.x
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y = self.y
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v = self.v
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count1, binx1, biny1, bc = binned_statistic_2d(
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x, y, v, 'count', bins=5)
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count2, binx2, biny2 = np.histogram2d(x, y, bins=5)
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assert_allclose(count1, count2)
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assert_allclose(binx1, binx2)
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assert_allclose(biny1, biny2)
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def test_2d_result_attributes(self):
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x = self.x
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y = self.y
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v = self.v
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res = binned_statistic_2d(x, y, v, 'count', bins=5)
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attributes = ('statistic', 'x_edge', 'y_edge', 'binnumber')
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check_named_results(res, attributes)
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def test_2d_sum(self):
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x = self.x
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y = self.y
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v = self.v
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sum1, binx1, biny1, bc = binned_statistic_2d(x, y, v, 'sum', bins=5)
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sum2, binx2, biny2 = np.histogram2d(x, y, bins=5, weights=v)
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assert_allclose(sum1, sum2)
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assert_allclose(binx1, binx2)
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assert_allclose(biny1, biny2)
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def test_2d_mean(self):
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x = self.x
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y = self.y
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v = self.v
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stat1, binx1, biny1, bc = binned_statistic_2d(x, y, v, 'mean', bins=5)
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stat2, binx2, biny2, bc = binned_statistic_2d(x, y, v, np.mean, bins=5)
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assert_allclose(stat1, stat2)
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assert_allclose(binx1, binx2)
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assert_allclose(biny1, biny2)
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def test_2d_mean_unicode(self):
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x = self.x
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y = self.y
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v = self.v
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stat1, binx1, biny1, bc = binned_statistic_2d(
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x, y, v, 'mean', bins=5)
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stat2, binx2, biny2, bc = binned_statistic_2d(x, y, v, np.mean, bins=5)
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assert_allclose(stat1, stat2)
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assert_allclose(binx1, binx2)
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assert_allclose(biny1, biny2)
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def test_2d_std(self):
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x = self.x
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y = self.y
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v = self.v
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stat1, binx1, biny1, bc = binned_statistic_2d(x, y, v, 'std', bins=5)
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stat2, binx2, biny2, bc = binned_statistic_2d(x, y, v, np.std, bins=5)
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assert_allclose(stat1, stat2)
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assert_allclose(binx1, binx2)
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assert_allclose(biny1, biny2)
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def test_2d_min(self):
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x = self.x
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y = self.y
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v = self.v
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stat1, binx1, biny1, bc = binned_statistic_2d(x, y, v, 'min', bins=5)
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stat2, binx2, biny2, bc = binned_statistic_2d(x, y, v, np.min, bins=5)
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assert_allclose(stat1, stat2)
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assert_allclose(binx1, binx2)
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assert_allclose(biny1, biny2)
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def test_2d_max(self):
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x = self.x
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y = self.y
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v = self.v
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stat1, binx1, biny1, bc = binned_statistic_2d(x, y, v, 'max', bins=5)
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stat2, binx2, biny2, bc = binned_statistic_2d(x, y, v, np.max, bins=5)
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assert_allclose(stat1, stat2)
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assert_allclose(binx1, binx2)
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assert_allclose(biny1, biny2)
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def test_2d_median(self):
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x = self.x
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y = self.y
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v = self.v
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stat1, binx1, biny1, bc = binned_statistic_2d(
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x, y, v, 'median', bins=5)
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stat2, binx2, biny2, bc = binned_statistic_2d(
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x, y, v, np.median, bins=5)
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assert_allclose(stat1, stat2)
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assert_allclose(binx1, binx2)
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assert_allclose(biny1, biny2)
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def test_2d_bincode(self):
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x = self.x[:20]
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y = self.y[:20]
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v = self.v[:20]
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count1, binx1, biny1, bc = binned_statistic_2d(
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x, y, v, 'count', bins=3)
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bc2 = np.array([17, 11, 6, 16, 11, 17, 18, 17, 17, 7, 6, 18, 16,
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6, 11, 16, 6, 6, 11, 8])
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bcount = [(bc == i).sum() for i in np.unique(bc)]
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assert_allclose(bc, bc2)
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count1adj = count1[count1.nonzero()]
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assert_allclose(bcount, count1adj)
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def test_2d_multi_values(self):
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x = self.x
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y = self.y
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v = self.v
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w = self.w
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stat1v, binx1v, biny1v, bc1v = binned_statistic_2d(
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x, y, v, 'mean', bins=8)
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stat1w, binx1w, biny1w, bc1w = binned_statistic_2d(
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x, y, w, 'mean', bins=8)
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stat2, binx2, biny2, bc2 = binned_statistic_2d(
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x, y, [v, w], 'mean', bins=8)
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assert_allclose(stat2[0], stat1v)
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assert_allclose(stat2[1], stat1w)
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assert_allclose(binx1v, binx2)
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assert_allclose(biny1w, biny2)
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assert_allclose(bc1v, bc2)
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def test_2d_binnumbers_unraveled(self):
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x = self.x
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y = self.y
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v = self.v
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stat, edgesx, bcx = binned_statistic(x, v, 'mean', bins=20)
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stat, edgesy, bcy = binned_statistic(y, v, 'mean', bins=10)
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stat2, edgesx2, edgesy2, bc2 = binned_statistic_2d(
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x, y, v, 'mean', bins=(20, 10), expand_binnumbers=True)
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bcx3 = np.searchsorted(edgesx, x, side='right')
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bcy3 = np.searchsorted(edgesy, y, side='right')
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# `numpy.searchsorted` is non-inclusive on right-edge, compensate
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bcx3[x == x.max()] -= 1
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bcy3[y == y.max()] -= 1
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assert_allclose(bcx, bc2[0])
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assert_allclose(bcy, bc2[1])
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assert_allclose(bcx3, bc2[0])
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assert_allclose(bcy3, bc2[1])
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|
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|
def test_dd_count(self):
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|
X = self.X
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|
v = self.v
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|
|
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|
count1, edges1, bc = binned_statistic_dd(X, v, 'count', bins=3)
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|
|
count2, edges2 = np.histogramdd(X, bins=3)
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|
|
|
||
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|
assert_allclose(count1, count2)
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|
assert_allclose(edges1, edges2)
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|
|
|
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|
|
def test_dd_result_attributes(self):
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|
X = self.X
|
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|
|
v = self.v
|
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|
|
|
||
|
|
res = binned_statistic_dd(X, v, 'count', bins=3)
|
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|
|
attributes = ('statistic', 'bin_edges', 'binnumber')
|
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|
|
check_named_results(res, attributes)
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|
|
|
||
|
|
def test_dd_sum(self):
|
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|
|
X = self.X
|
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|
|
v = self.v
|
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|
|
|
||
|
|
sum1, edges1, bc = binned_statistic_dd(X, v, 'sum', bins=3)
|
||
|
|
sum2, edges2 = np.histogramdd(X, bins=3, weights=v)
|
||
|
|
|
||
|
|
assert_allclose(sum1, sum2)
|
||
|
|
assert_allclose(edges1, edges2)
|
||
|
|
|
||
|
|
def test_dd_mean(self):
|
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|
|
X = self.X
|
||
|
|
v = self.v
|
||
|
|
|
||
|
|
stat1, edges1, bc = binned_statistic_dd(X, v, 'mean', bins=3)
|
||
|
|
stat2, edges2, bc = binned_statistic_dd(X, v, np.mean, bins=3)
|
||
|
|
|
||
|
|
assert_allclose(stat1, stat2)
|
||
|
|
assert_allclose(edges1, edges2)
|
||
|
|
|
||
|
|
def test_dd_std(self):
|
||
|
|
X = self.X
|
||
|
|
v = self.v
|
||
|
|
|
||
|
|
stat1, edges1, bc = binned_statistic_dd(X, v, 'std', bins=3)
|
||
|
|
stat2, edges2, bc = binned_statistic_dd(X, v, np.std, bins=3)
|
||
|
|
|
||
|
|
assert_allclose(stat1, stat2)
|
||
|
|
assert_allclose(edges1, edges2)
|
||
|
|
|
||
|
|
def test_dd_min(self):
|
||
|
|
X = self.X
|
||
|
|
v = self.v
|
||
|
|
|
||
|
|
stat1, edges1, bc = binned_statistic_dd(X, v, 'min', bins=3)
|
||
|
|
stat2, edges2, bc = binned_statistic_dd(X, v, np.min, bins=3)
|
||
|
|
|
||
|
|
assert_allclose(stat1, stat2)
|
||
|
|
assert_allclose(edges1, edges2)
|
||
|
|
|
||
|
|
def test_dd_max(self):
|
||
|
|
X = self.X
|
||
|
|
v = self.v
|
||
|
|
|
||
|
|
stat1, edges1, bc = binned_statistic_dd(X, v, 'max', bins=3)
|
||
|
|
stat2, edges2, bc = binned_statistic_dd(X, v, np.max, bins=3)
|
||
|
|
|
||
|
|
assert_allclose(stat1, stat2)
|
||
|
|
assert_allclose(edges1, edges2)
|
||
|
|
|
||
|
|
def test_dd_median(self):
|
||
|
|
X = self.X
|
||
|
|
v = self.v
|
||
|
|
|
||
|
|
stat1, edges1, bc = binned_statistic_dd(X, v, 'median', bins=3)
|
||
|
|
stat2, edges2, bc = binned_statistic_dd(X, v, np.median, bins=3)
|
||
|
|
|
||
|
|
assert_allclose(stat1, stat2)
|
||
|
|
assert_allclose(edges1, edges2)
|
||
|
|
|
||
|
|
def test_dd_bincode(self):
|
||
|
|
X = self.X[:20]
|
||
|
|
v = self.v[:20]
|
||
|
|
|
||
|
|
count1, edges1, bc = binned_statistic_dd(X, v, 'count', bins=3)
|
||
|
|
bc2 = np.array([63, 33, 86, 83, 88, 67, 57, 33, 42, 41, 82, 83, 92,
|
||
|
|
32, 36, 91, 43, 87, 81, 81])
|
||
|
|
|
||
|
|
bcount = [(bc == i).sum() for i in np.unique(bc)]
|
||
|
|
|
||
|
|
assert_allclose(bc, bc2)
|
||
|
|
count1adj = count1[count1.nonzero()]
|
||
|
|
assert_allclose(bcount, count1adj)
|
||
|
|
|
||
|
|
def test_dd_multi_values(self):
|
||
|
|
X = self.X
|
||
|
|
v = self.v
|
||
|
|
w = self.w
|
||
|
|
|
||
|
|
stat1v, edges1v, bc1v = binned_statistic_dd(X, v, np.std, bins=8)
|
||
|
|
stat1w, edges1w, bc1w = binned_statistic_dd(X, w, np.std, bins=8)
|
||
|
|
stat2, edges2, bc2 = binned_statistic_dd(X, [v, w], np.std, bins=8)
|
||
|
|
|
||
|
|
assert_allclose(stat2[0], stat1v)
|
||
|
|
assert_allclose(stat2[1], stat1w)
|
||
|
|
assert_allclose(edges1v, edges2)
|
||
|
|
assert_allclose(edges1w, edges2)
|
||
|
|
assert_allclose(bc1v, bc2)
|
||
|
|
|
||
|
|
def test_dd_binnumbers_unraveled(self):
|
||
|
|
X = self.X
|
||
|
|
v = self.v
|
||
|
|
|
||
|
|
stat, edgesx, bcx = binned_statistic(X[:, 0], v, 'mean', bins=15)
|
||
|
|
stat, edgesy, bcy = binned_statistic(X[:, 1], v, 'mean', bins=20)
|
||
|
|
stat, edgesz, bcz = binned_statistic(X[:, 2], v, 'mean', bins=10)
|
||
|
|
|
||
|
|
stat2, edges2, bc2 = binned_statistic_dd(
|
||
|
|
X, v, 'mean', bins=(15, 20, 10), expand_binnumbers=True)
|
||
|
|
|
||
|
|
assert_allclose(bcx, bc2[0])
|
||
|
|
assert_allclose(bcy, bc2[1])
|
||
|
|
assert_allclose(bcz, bc2[2])
|
||
|
|
|
||
|
|
def test_dd_binned_statistic_result(self):
|
||
|
|
# NOTE: tests the reuse of bin_edges from previous call
|
||
|
|
x = np.random.random((10000, 3))
|
||
|
|
v = np.random.random((10000))
|
||
|
|
bins = np.linspace(0, 1, 10)
|
||
|
|
bins = (bins, bins, bins)
|
||
|
|
|
||
|
|
result = binned_statistic_dd(x, v, 'mean', bins=bins)
|
||
|
|
stat = result.statistic
|
||
|
|
|
||
|
|
result = binned_statistic_dd(x, v, 'mean',
|
||
|
|
binned_statistic_result=result)
|
||
|
|
stat2 = result.statistic
|
||
|
|
|
||
|
|
assert_allclose(stat, stat2)
|
||
|
|
|
||
|
|
def test_dd_zero_dedges(self):
|
||
|
|
x = np.random.random((10000, 3))
|
||
|
|
v = np.random.random((10000))
|
||
|
|
bins = np.linspace(0, 1, 10)
|
||
|
|
bins = np.append(bins, 1)
|
||
|
|
bins = (bins, bins, bins)
|
||
|
|
with assert_raises(ValueError, match='difference is numerically 0'):
|
||
|
|
binned_statistic_dd(x, v, 'mean', bins=bins)
|