from __future__ import division, absolute_import, print_function import numpy as np from numpy.lib.histograms import histogram, histogramdd, histogram_bin_edges from numpy.testing import ( run_module_suite, assert_, assert_equal, assert_array_equal, assert_almost_equal, assert_array_almost_equal, assert_raises, assert_allclose, assert_array_max_ulp, assert_warns, assert_raises_regex, dec, suppress_warnings, HAS_REFCOUNT, ) class TestHistogram(object): def setup(self): pass def teardown(self): pass def test_simple(self): n = 100 v = np.random.rand(n) (a, b) = histogram(v) # check if the sum of the bins equals the number of samples assert_equal(np.sum(a, axis=0), n) # check that the bin counts are evenly spaced when the data is from # a linear function (a, b) = histogram(np.linspace(0, 10, 100)) assert_array_equal(a, 10) def test_one_bin(self): # Ticket 632 hist, edges = histogram([1, 2, 3, 4], [1, 2]) assert_array_equal(hist, [2, ]) assert_array_equal(edges, [1, 2]) assert_raises(ValueError, histogram, [1, 2], bins=0) h, e = histogram([1, 2], bins=1) assert_equal(h, np.array([2])) assert_allclose(e, np.array([1., 2.])) def test_normed(self): # Check that the integral of the density equals 1. n = 100 v = np.random.rand(n) a, b = histogram(v, normed=True) area = np.sum(a * np.diff(b)) assert_almost_equal(area, 1) # Check with non-constant bin widths (buggy but backwards # compatible) v = np.arange(10) bins = [0, 1, 5, 9, 10] a, b = histogram(v, bins, normed=True) area = np.sum(a * np.diff(b)) assert_almost_equal(area, 1) def test_density(self): # Check that the integral of the density equals 1. n = 100 v = np.random.rand(n) a, b = histogram(v, density=True) area = np.sum(a * np.diff(b)) assert_almost_equal(area, 1) # Check with non-constant bin widths v = np.arange(10) bins = [0, 1, 3, 6, 10] a, b = histogram(v, bins, density=True) assert_array_equal(a, .1) assert_equal(np.sum(a * np.diff(b)), 1) # Variale bin widths are especially useful to deal with # infinities. v = np.arange(10) bins = [0, 1, 3, 6, np.inf] a, b = histogram(v, bins, density=True) assert_array_equal(a, [.1, .1, .1, 0.]) # Taken from a bug report from N. Becker on the numpy-discussion # mailing list Aug. 6, 2010. counts, dmy = np.histogram( [1, 2, 3, 4], [0.5, 1.5, np.inf], density=True) assert_equal(counts, [.25, 0]) def test_outliers(self): # Check that outliers are not tallied a = np.arange(10) + .5 # Lower outliers h, b = histogram(a, range=[0, 9]) assert_equal(h.sum(), 9) # Upper outliers h, b = histogram(a, range=[1, 10]) assert_equal(h.sum(), 9) # Normalization h, b = histogram(a, range=[1, 9], normed=True) assert_almost_equal((h * np.diff(b)).sum(), 1, decimal=15) # Weights w = np.arange(10) + .5 h, b = histogram(a, range=[1, 9], weights=w, normed=True) assert_equal((h * np.diff(b)).sum(), 1) h, b = histogram(a, bins=8, range=[1, 9], weights=w) assert_equal(h, w[1:-1]) def test_type(self): # Check the type of the returned histogram a = np.arange(10) + .5 h, b = histogram(a) assert_(np.issubdtype(h.dtype, np.integer)) h, b = histogram(a, normed=True) assert_(np.issubdtype(h.dtype, np.floating)) h, b = histogram(a, weights=np.ones(10, int)) assert_(np.issubdtype(h.dtype, np.integer)) h, b = histogram(a, weights=np.ones(10, float)) assert_(np.issubdtype(h.dtype, np.floating)) def test_f32_rounding(self): # gh-4799, check that the rounding of the edges works with float32 x = np.array([276.318359, -69.593948, 21.329449], dtype=np.float32) y = np.array([5005.689453, 4481.327637, 6010.369629], dtype=np.float32) counts_hist, xedges, yedges = np.histogram2d(x, y, bins=100) assert_equal(counts_hist.sum(), 3.) def test_weights(self): v = np.random.rand(100) w = np.ones(100) * 5 a, b = histogram(v) na, nb = histogram(v, normed=True) wa, wb = histogram(v, weights=w) nwa, nwb = histogram(v, weights=w, normed=True) assert_array_almost_equal(a * 5, wa) assert_array_almost_equal(na, nwa) # Check weights are properly applied. v = np.linspace(0, 10, 10) w = np.concatenate((np.zeros(5), np.ones(5))) wa, wb = histogram(v, bins=np.arange(11), weights=w) assert_array_almost_equal(wa, w) # Check with integer weights wa, wb = histogram([1, 2, 2, 4], bins=4, weights=[4, 3, 2, 1]) assert_array_equal(wa, [4, 5, 0, 1]) wa, wb = histogram( [1, 2, 2, 4], bins=4, weights=[4, 3, 2, 1], normed=True) assert_array_almost_equal(wa, np.array([4, 5, 0, 1]) / 10. / 3. * 4) # Check weights with non-uniform bin widths a, b = histogram( np.arange(9), [0, 1, 3, 6, 10], weights=[2, 1, 1, 1, 1, 1, 1, 1, 1], density=True) assert_almost_equal(a, [.2, .1, .1, .075]) def test_exotic_weights(self): # Test the use of weights that are not integer or floats, but e.g. # complex numbers or object types. # Complex weights values = np.array([1.3, 2.5, 2.3]) weights = np.array([1, -1, 2]) + 1j * np.array([2, 1, 2]) # Check with custom bins wa, wb = histogram(values, bins=[0, 2, 3], weights=weights) assert_array_almost_equal(wa, np.array([1, 1]) + 1j * np.array([2, 3])) # Check with even bins wa, wb = histogram(values, bins=2, range=[1, 3], weights=weights) assert_array_almost_equal(wa, np.array([1, 1]) + 1j * np.array([2, 3])) # Decimal weights from decimal import Decimal values = np.array([1.3, 2.5, 2.3]) weights = np.array([Decimal(1), Decimal(2), Decimal(3)]) # Check with custom bins wa, wb = histogram(values, bins=[0, 2, 3], weights=weights) assert_array_almost_equal(wa, [Decimal(1), Decimal(5)]) # Check with even bins wa, wb = histogram(values, bins=2, range=[1, 3], weights=weights) assert_array_almost_equal(wa, [Decimal(1), Decimal(5)]) def test_no_side_effects(self): # This is a regression test that ensures that values passed to # ``histogram`` are unchanged. values = np.array([1.3, 2.5, 2.3]) np.histogram(values, range=[-10, 10], bins=100) assert_array_almost_equal(values, [1.3, 2.5, 2.3]) def test_empty(self): a, b = histogram([], bins=([0, 1])) assert_array_equal(a, np.array([0])) assert_array_equal(b, np.array([0, 1])) def test_error_binnum_type (self): # Tests if right Error is raised if bins argument is float vals = np.linspace(0.0, 1.0, num=100) histogram(vals, 5) assert_raises(TypeError, histogram, vals, 2.4) def test_finite_range(self): # Normal ranges should be fine vals = np.linspace(0.0, 1.0, num=100) histogram(vals, range=[0.25,0.75]) assert_raises(ValueError, histogram, vals, range=[np.nan,0.75]) assert_raises(ValueError, histogram, vals, range=[0.25,np.inf]) def test_bin_edge_cases(self): # Ensure that floating-point computations correctly place edge cases. arr = np.array([337, 404, 739, 806, 1007, 1811, 2012]) hist, edges = np.histogram(arr, bins=8296, range=(2, 2280)) mask = hist > 0 left_edges = edges[:-1][mask] right_edges = edges[1:][mask] for x, left, right in zip(arr, left_edges, right_edges): assert_(x >= left) assert_(x < right) def test_last_bin_inclusive_range(self): arr = np.array([0., 0., 0., 1., 2., 3., 3., 4., 5.]) hist, edges = np.histogram(arr, bins=30, range=(-0.5, 5)) assert_equal(hist[-1], 1) def test_unsigned_monotonicity_check(self): # Ensures ValueError is raised if bins not increasing monotonically # when bins contain unsigned values (see #9222) arr = np.array([2]) bins = np.array([1, 3, 1], dtype='uint64') with assert_raises(ValueError): hist, edges = np.histogram(arr, bins=bins) def test_object_array_of_0d(self): # gh-7864 assert_raises(ValueError, histogram, [np.array([0.4]) for i in range(10)] + [-np.inf]) assert_raises(ValueError, histogram, [np.array([0.4]) for i in range(10)] + [np.inf]) # these should not crash np.histogram([np.array([0.5]) for i in range(10)] + [.500000000000001]) np.histogram([np.array([0.5]) for i in range(10)] + [.5]) def test_some_nan_values(self): # gh-7503 one_nan = np.array([0, 1, np.nan]) all_nan = np.array([np.nan, np.nan]) # the internal commparisons with NaN give warnings sup = suppress_warnings() sup.filter(RuntimeWarning) with sup: # can't infer range with nan assert_raises(ValueError, histogram, one_nan, bins='auto') assert_raises(ValueError, histogram, all_nan, bins='auto') # explicit range solves the problem h, b = histogram(one_nan, bins='auto', range=(0, 1)) assert_equal(h.sum(), 2) # nan is not counted h, b = histogram(all_nan, bins='auto', range=(0, 1)) assert_equal(h.sum(), 0) # nan is not counted # as does an explicit set of bins h, b = histogram(one_nan, bins=[0, 1]) assert_equal(h.sum(), 2) # nan is not counted h, b = histogram(all_nan, bins=[0, 1]) assert_equal(h.sum(), 0) # nan is not counted def test_datetime(self): begin = np.datetime64('2000-01-01', 'D') offsets = np.array([0, 0, 1, 1, 2, 3, 5, 10, 20]) bins = np.array([0, 2, 7, 20]) dates = begin + offsets date_bins = begin + bins td = np.dtype('timedelta64[D]') # Results should be the same for integer offsets or datetime values. # For now, only explicit bins are supported, since linspace does not # work on datetimes or timedeltas d_count, d_edge = histogram(dates, bins=date_bins) t_count, t_edge = histogram(offsets.astype(td), bins=bins.astype(td)) i_count, i_edge = histogram(offsets, bins=bins) assert_equal(d_count, i_count) assert_equal(t_count, i_count) assert_equal((d_edge - begin).astype(int), i_edge) assert_equal(t_edge.astype(int), i_edge) assert_equal(d_edge.dtype, dates.dtype) assert_equal(t_edge.dtype, td) def do_precision_lower_bound(self, float_small, float_large): eps = np.finfo(float_large).eps arr = np.array([1.0], float_small) range = np.array([1.0 + eps, 2.0], float_large) # test is looking for behavior when the bounds change between dtypes if range.astype(float_small)[0] != 1: return # previously crashed count, x_loc = np.histogram(arr, bins=1, range=range) assert_equal(count, [1]) # gh-10322 means that the type comes from arr - this may change assert_equal(x_loc.dtype, float_small) def do_precision_upper_bound(self, float_small, float_large): eps = np.finfo(float_large).eps arr = np.array([1.0], float_small) range = np.array([0.0, 1.0 - eps], float_large) # test is looking for behavior when the bounds change between dtypes if range.astype(float_small)[-1] != 1: return # previously crashed count, x_loc = np.histogram(arr, bins=1, range=range) assert_equal(count, [1]) # gh-10322 means that the type comes from arr - this may change assert_equal(x_loc.dtype, float_small) def do_precision(self, float_small, float_large): self.do_precision_lower_bound(float_small, float_large) self.do_precision_upper_bound(float_small, float_large) def test_precision(self): # not looping results in a useful stack trace upon failure self.do_precision(np.half, np.single) self.do_precision(np.half, np.double) self.do_precision(np.half, np.longdouble) self.do_precision(np.single, np.double) self.do_precision(np.single, np.longdouble) self.do_precision(np.double, np.longdouble) def test_histogram_bin_edges(self): hist, e = histogram([1, 2, 3, 4], [1, 2]) edges = histogram_bin_edges([1, 2, 3, 4], [1, 2]) assert_array_equal(edges, e) arr = np.array([0., 0., 0., 1., 2., 3., 3., 4., 5.]) hist, e = histogram(arr, bins=30, range=(-0.5, 5)) edges = histogram_bin_edges(arr, bins=30, range=(-0.5, 5)) assert_array_equal(edges, e) hist, e = histogram(arr, bins='auto', range=(0, 1)) edges = histogram_bin_edges(arr, bins='auto', range=(0, 1)) assert_array_equal(edges, e) class TestHistogramOptimBinNums(object): """ Provide test coverage when using provided estimators for optimal number of bins """ def test_empty(self): estimator_list = ['fd', 'scott', 'rice', 'sturges', 'doane', 'sqrt', 'auto'] # check it can deal with empty data for estimator in estimator_list: a, b = histogram([], bins=estimator) assert_array_equal(a, np.array([0])) assert_array_equal(b, np.array([0, 1])) def test_simple(self): """ Straightforward testing with a mixture of linspace data (for consistency). All test values have been precomputed and the values shouldn't change """ # Some basic sanity checking, with some fixed data. # Checking for the correct number of bins basic_test = {50: {'fd': 4, 'scott': 4, 'rice': 8, 'sturges': 7, 'doane': 8, 'sqrt': 8, 'auto': 7}, 500: {'fd': 8, 'scott': 8, 'rice': 16, 'sturges': 10, 'doane': 12, 'sqrt': 23, 'auto': 10}, 5000: {'fd': 17, 'scott': 17, 'rice': 35, 'sturges': 14, 'doane': 17, 'sqrt': 71, 'auto': 17}} for testlen, expectedResults in basic_test.items(): # Create some sort of non uniform data to test with # (2 peak uniform mixture) x1 = np.linspace(-10, -1, testlen // 5 * 2) x2 = np.linspace(1, 10, testlen // 5 * 3) x = np.concatenate((x1, x2)) for estimator, numbins in expectedResults.items(): a, b = np.histogram(x, estimator) assert_equal(len(a), numbins, err_msg="For the {0} estimator " "with datasize of {1}".format(estimator, testlen)) def test_small(self): """ Smaller datasets have the potential to cause issues with the data adaptive methods, especially the FD method. All bin numbers have been precalculated. """ small_dat = {1: {'fd': 1, 'scott': 1, 'rice': 1, 'sturges': 1, 'doane': 1, 'sqrt': 1}, 2: {'fd': 2, 'scott': 1, 'rice': 3, 'sturges': 2, 'doane': 1, 'sqrt': 2}, 3: {'fd': 2, 'scott': 2, 'rice': 3, 'sturges': 3, 'doane': 3, 'sqrt': 2}} for testlen, expectedResults in small_dat.items(): testdat = np.arange(testlen) for estimator, expbins in expectedResults.items(): a, b = np.histogram(testdat, estimator) assert_equal(len(a), expbins, err_msg="For the {0} estimator " "with datasize of {1}".format(estimator, testlen)) def test_incorrect_methods(self): """ Check a Value Error is thrown when an unknown string is passed in """ check_list = ['mad', 'freeman', 'histograms', 'IQR'] for estimator in check_list: assert_raises(ValueError, histogram, [1, 2, 3], estimator) def test_novariance(self): """ Check that methods handle no variance in data Primarily for Scott and FD as the SD and IQR are both 0 in this case """ novar_dataset = np.ones(100) novar_resultdict = {'fd': 1, 'scott': 1, 'rice': 1, 'sturges': 1, 'doane': 1, 'sqrt': 1, 'auto': 1} for estimator, numbins in novar_resultdict.items(): a, b = np.histogram(novar_dataset, estimator) assert_equal(len(a), numbins, err_msg="{0} estimator, " "No Variance test".format(estimator)) def test_outlier(self): """ Check the FD, Scott and Doane with outliers. The FD estimates a smaller binwidth since it's less affected by outliers. Since the range is so (artificially) large, this means more bins, most of which will be empty, but the data of interest usually is unaffected. The Scott estimator is more affected and returns fewer bins, despite most of the variance being in one area of the data. The Doane estimator lies somewhere between the other two. """ xcenter = np.linspace(-10, 10, 50) outlier_dataset = np.hstack((np.linspace(-110, -100, 5), xcenter)) outlier_resultdict = {'fd': 21, 'scott': 5, 'doane': 11} for estimator, numbins in outlier_resultdict.items(): a, b = np.histogram(outlier_dataset, estimator) assert_equal(len(a), numbins) def test_simple_range(self): """ Straightforward testing with a mixture of linspace data (for consistency). Adding in a 3rd mixture that will then be completely ignored. All test values have been precomputed and the shouldn't change. """ # some basic sanity checking, with some fixed data. # Checking for the correct number of bins basic_test = { 50: {'fd': 8, 'scott': 8, 'rice': 15, 'sturges': 14, 'auto': 14}, 500: {'fd': 15, 'scott': 16, 'rice': 32, 'sturges': 20, 'auto': 20}, 5000: {'fd': 33, 'scott': 33, 'rice': 69, 'sturges': 27, 'auto': 33} } for testlen, expectedResults in basic_test.items(): # create some sort of non uniform data to test with # (3 peak uniform mixture) x1 = np.linspace(-10, -1, testlen // 5 * 2) x2 = np.linspace(1, 10, testlen // 5 * 3) x3 = np.linspace(-100, -50, testlen) x = np.hstack((x1, x2, x3)) for estimator, numbins in expectedResults.items(): a, b = np.histogram(x, estimator, range = (-20, 20)) msg = "For the {0} estimator".format(estimator) msg += " with datasize of {0}".format(testlen) assert_equal(len(a), numbins, err_msg=msg) def test_simple_weighted(self): """ Check that weighted data raises a TypeError """ estimator_list = ['fd', 'scott', 'rice', 'sturges', 'auto'] for estimator in estimator_list: assert_raises(TypeError, histogram, [1, 2, 3], estimator, weights=[1, 2, 3]) class TestHistogramdd(object): def test_simple(self): x = np.array([[-.5, .5, 1.5], [-.5, 1.5, 2.5], [-.5, 2.5, .5], [.5, .5, 1.5], [.5, 1.5, 2.5], [.5, 2.5, 2.5]]) H, edges = histogramdd(x, (2, 3, 3), range=[[-1, 1], [0, 3], [0, 3]]) answer = np.array([[[0, 1, 0], [0, 0, 1], [1, 0, 0]], [[0, 1, 0], [0, 0, 1], [0, 0, 1]]]) assert_array_equal(H, answer) # Check normalization ed = [[-2, 0, 2], [0, 1, 2, 3], [0, 1, 2, 3]] H, edges = histogramdd(x, bins=ed, normed=True) assert_(np.all(H == answer / 12.)) # Check that H has the correct shape. H, edges = histogramdd(x, (2, 3, 4), range=[[-1, 1], [0, 3], [0, 4]], normed=True) answer = np.array([[[0, 1, 0, 0], [0, 0, 1, 0], [1, 0, 0, 0]], [[0, 1, 0, 0], [0, 0, 1, 0], [0, 0, 1, 0]]]) assert_array_almost_equal(H, answer / 6., 4) # Check that a sequence of arrays is accepted and H has the correct # shape. z = [np.squeeze(y) for y in np.split(x, 3, axis=1)] H, edges = histogramdd( z, bins=(4, 3, 2), range=[[-2, 2], [0, 3], [0, 2]]) answer = np.array([[[0, 0], [0, 0], [0, 0]], [[0, 1], [0, 0], [1, 0]], [[0, 1], [0, 0], [0, 0]], [[0, 0], [0, 0], [0, 0]]]) assert_array_equal(H, answer) Z = np.zeros((5, 5, 5)) Z[list(range(5)), list(range(5)), list(range(5))] = 1. H, edges = histogramdd([np.arange(5), np.arange(5), np.arange(5)], 5) assert_array_equal(H, Z) def test_shape_3d(self): # All possible permutations for bins of different lengths in 3D. bins = ((5, 4, 6), (6, 4, 5), (5, 6, 4), (4, 6, 5), (6, 5, 4), (4, 5, 6)) r = np.random.rand(10, 3) for b in bins: H, edges = histogramdd(r, b) assert_(H.shape == b) def test_shape_4d(self): # All possible permutations for bins of different lengths in 4D. bins = ((7, 4, 5, 6), (4, 5, 7, 6), (5, 6, 4, 7), (7, 6, 5, 4), (5, 7, 6, 4), (4, 6, 7, 5), (6, 5, 7, 4), (7, 5, 4, 6), (7, 4, 6, 5), (6, 4, 7, 5), (6, 7, 5, 4), (4, 6, 5, 7), (4, 7, 5, 6), (5, 4, 6, 7), (5, 7, 4, 6), (6, 7, 4, 5), (6, 5, 4, 7), (4, 7, 6, 5), (4, 5, 6, 7), (7, 6, 4, 5), (5, 4, 7, 6), (5, 6, 7, 4), (6, 4, 5, 7), (7, 5, 6, 4)) r = np.random.rand(10, 4) for b in bins: H, edges = histogramdd(r, b) assert_(H.shape == b) def test_weights(self): v = np.random.rand(100, 2) hist, edges = histogramdd(v) n_hist, edges = histogramdd(v, normed=True) w_hist, edges = histogramdd(v, weights=np.ones(100)) assert_array_equal(w_hist, hist) w_hist, edges = histogramdd(v, weights=np.ones(100) * 2, normed=True) assert_array_equal(w_hist, n_hist) w_hist, edges = histogramdd(v, weights=np.ones(100, int) * 2) assert_array_equal(w_hist, 2 * hist) def test_identical_samples(self): x = np.zeros((10, 2), int) hist, edges = histogramdd(x, bins=2) assert_array_equal(edges[0], np.array([-0.5, 0., 0.5])) def test_empty(self): a, b = histogramdd([[], []], bins=([0, 1], [0, 1])) assert_array_max_ulp(a, np.array([[0.]])) a, b = np.histogramdd([[], [], []], bins=2) assert_array_max_ulp(a, np.zeros((2, 2, 2))) def test_bins_errors(self): # There are two ways to specify bins. Check for the right errors # when mixing those. x = np.arange(8).reshape(2, 4) assert_raises(ValueError, np.histogramdd, x, bins=[-1, 2, 4, 5]) assert_raises(ValueError, np.histogramdd, x, bins=[1, 0.99, 1, 1]) assert_raises( ValueError, np.histogramdd, x, bins=[1, 1, 1, [1, 2, 2, 3]]) assert_raises( ValueError, np.histogramdd, x, bins=[1, 1, 1, [1, 2, 3, -3]]) assert_(np.histogramdd(x, bins=[1, 1, 1, [1, 2, 3, 4]])) def test_inf_edges(self): # Test using +/-inf bin edges works. See #1788. with np.errstate(invalid='ignore'): x = np.arange(6).reshape(3, 2) expected = np.array([[1, 0], [0, 1], [0, 1]]) h, e = np.histogramdd(x, bins=[3, [-np.inf, 2, 10]]) assert_allclose(h, expected) h, e = np.histogramdd(x, bins=[3, np.array([-1, 2, np.inf])]) assert_allclose(h, expected) h, e = np.histogramdd(x, bins=[3, [-np.inf, 3, np.inf]]) assert_allclose(h, expected) def test_rightmost_binedge(self): # Test event very close to rightmost binedge. See Github issue #4266 x = [0.9999999995] bins = [[0., 0.5, 1.0]] hist, _ = histogramdd(x, bins=bins) assert_(hist[0] == 0.0) assert_(hist[1] == 1.) x = [1.0] bins = [[0., 0.5, 1.0]] hist, _ = histogramdd(x, bins=bins) assert_(hist[0] == 0.0) assert_(hist[1] == 1.) x = [1.0000000001] bins = [[0., 0.5, 1.0]] hist, _ = histogramdd(x, bins=bins) assert_(hist[0] == 0.0) assert_(hist[1] == 1.) x = [1.0001] bins = [[0., 0.5, 1.0]] hist, _ = histogramdd(x, bins=bins) assert_(hist[0] == 0.0) assert_(hist[1] == 0.0) def test_finite_range(self): vals = np.random.random((100, 3)) histogramdd(vals, range=[[0.0, 1.0], [0.25, 0.75], [0.25, 0.5]]) assert_raises(ValueError, histogramdd, vals, range=[[0.0, 1.0], [0.25, 0.75], [0.25, np.inf]]) assert_raises(ValueError, histogramdd, vals, range=[[0.0, 1.0], [np.nan, 0.75], [0.25, 0.5]]) if __name__ == "__main__": run_module_suite()