Sindbad~EG File Manager
# pylint: disable-msg=W0611, W0612, W0511
"""Tests suite for MaskedArray.
Adapted from the original test_ma by Pierre Gerard-Marchant
:author: Pierre Gerard-Marchant
:contact: pierregm_at_uga_dot_edu
:version: $Id: test_extras.py 3473 2007-10-29 15:18:13Z jarrod.millman $
"""
from __future__ import division, absolute_import, print_function
import warnings
import itertools
import numpy as np
from numpy.testing import (
TestCase, run_module_suite, assert_warns, suppress_warnings,
assert_raises
)
from numpy.ma.testutils import (
assert_, assert_array_equal, assert_equal, assert_almost_equal
)
from numpy.ma.core import (
array, arange, masked, MaskedArray, masked_array, getmaskarray, shape,
nomask, ones, zeros, count
)
from numpy.ma.extras import (
atleast_1d, atleast_2d, atleast_3d, mr_, dot, polyfit, cov, corrcoef,
median, average, unique, setxor1d, setdiff1d, union1d, intersect1d, in1d,
ediff1d, apply_over_axes, apply_along_axis, compress_nd, compress_rowcols,
mask_rowcols, clump_masked, clump_unmasked, flatnotmasked_contiguous,
notmasked_contiguous, notmasked_edges, masked_all, masked_all_like, isin,
diagflat
)
import numpy.ma.extras as mae
class TestGeneric(TestCase):
#
def test_masked_all(self):
# Tests masked_all
# Standard dtype
test = masked_all((2,), dtype=float)
control = array([1, 1], mask=[1, 1], dtype=float)
assert_equal(test, control)
# Flexible dtype
dt = np.dtype({'names': ['a', 'b'], 'formats': ['f', 'f']})
test = masked_all((2,), dtype=dt)
control = array([(0, 0), (0, 0)], mask=[(1, 1), (1, 1)], dtype=dt)
assert_equal(test, control)
test = masked_all((2, 2), dtype=dt)
control = array([[(0, 0), (0, 0)], [(0, 0), (0, 0)]],
mask=[[(1, 1), (1, 1)], [(1, 1), (1, 1)]],
dtype=dt)
assert_equal(test, control)
# Nested dtype
dt = np.dtype([('a', 'f'), ('b', [('ba', 'f'), ('bb', 'f')])])
test = masked_all((2,), dtype=dt)
control = array([(1, (1, 1)), (1, (1, 1))],
mask=[(1, (1, 1)), (1, (1, 1))], dtype=dt)
assert_equal(test, control)
test = masked_all((2,), dtype=dt)
control = array([(1, (1, 1)), (1, (1, 1))],
mask=[(1, (1, 1)), (1, (1, 1))], dtype=dt)
assert_equal(test, control)
test = masked_all((1, 1), dtype=dt)
control = array([[(1, (1, 1))]], mask=[[(1, (1, 1))]], dtype=dt)
assert_equal(test, control)
def test_masked_all_like(self):
# Tests masked_all
# Standard dtype
base = array([1, 2], dtype=float)
test = masked_all_like(base)
control = array([1, 1], mask=[1, 1], dtype=float)
assert_equal(test, control)
# Flexible dtype
dt = np.dtype({'names': ['a', 'b'], 'formats': ['f', 'f']})
base = array([(0, 0), (0, 0)], mask=[(1, 1), (1, 1)], dtype=dt)
test = masked_all_like(base)
control = array([(10, 10), (10, 10)], mask=[(1, 1), (1, 1)], dtype=dt)
assert_equal(test, control)
# Nested dtype
dt = np.dtype([('a', 'f'), ('b', [('ba', 'f'), ('bb', 'f')])])
control = array([(1, (1, 1)), (1, (1, 1))],
mask=[(1, (1, 1)), (1, (1, 1))], dtype=dt)
test = masked_all_like(control)
assert_equal(test, control)
def check_clump(self, f):
for i in range(1, 7):
for j in range(2**i):
k = np.arange(i, dtype=int)
ja = np.full(i, j, dtype=int)
a = masked_array(2**k)
a.mask = (ja & (2**k)) != 0
s = 0
for sl in f(a):
s += a.data[sl].sum()
if f == clump_unmasked:
assert_equal(a.compressed().sum(), s)
else:
a.mask = ~a.mask
assert_equal(a.compressed().sum(), s)
def test_clump_masked(self):
# Test clump_masked
a = masked_array(np.arange(10))
a[[0, 1, 2, 6, 8, 9]] = masked
#
test = clump_masked(a)
control = [slice(0, 3), slice(6, 7), slice(8, 10)]
assert_equal(test, control)
self.check_clump(clump_masked)
def test_clump_unmasked(self):
# Test clump_unmasked
a = masked_array(np.arange(10))
a[[0, 1, 2, 6, 8, 9]] = masked
test = clump_unmasked(a)
control = [slice(3, 6), slice(7, 8), ]
assert_equal(test, control)
self.check_clump(clump_unmasked)
def test_flatnotmasked_contiguous(self):
# Test flatnotmasked_contiguous
a = arange(10)
# No mask
test = flatnotmasked_contiguous(a)
assert_equal(test, slice(0, a.size))
# Some mask
a[(a < 3) | (a > 8) | (a == 5)] = masked
test = flatnotmasked_contiguous(a)
assert_equal(test, [slice(3, 5), slice(6, 9)])
#
a[:] = masked
test = flatnotmasked_contiguous(a)
assert_equal(test, None)
class TestAverage(TestCase):
# Several tests of average. Why so many ? Good point...
def test_testAverage1(self):
# Test of average.
ott = array([0., 1., 2., 3.], mask=[True, False, False, False])
assert_equal(2.0, average(ott, axis=0))
assert_equal(2.0, average(ott, weights=[1., 1., 2., 1.]))
result, wts = average(ott, weights=[1., 1., 2., 1.], returned=1)
assert_equal(2.0, result)
self.assertTrue(wts == 4.0)
ott[:] = masked
assert_equal(average(ott, axis=0).mask, [True])
ott = array([0., 1., 2., 3.], mask=[True, False, False, False])
ott = ott.reshape(2, 2)
ott[:, 1] = masked
assert_equal(average(ott, axis=0), [2.0, 0.0])
assert_equal(average(ott, axis=1).mask[0], [True])
assert_equal([2., 0.], average(ott, axis=0))
result, wts = average(ott, axis=0, returned=1)
assert_equal(wts, [1., 0.])
def test_testAverage2(self):
# More tests of average.
w1 = [0, 1, 1, 1, 1, 0]
w2 = [[0, 1, 1, 1, 1, 0], [1, 0, 0, 0, 0, 1]]
x = arange(6, dtype=np.float_)
assert_equal(average(x, axis=0), 2.5)
assert_equal(average(x, axis=0, weights=w1), 2.5)
y = array([arange(6, dtype=np.float_), 2.0 * arange(6)])
assert_equal(average(y, None), np.add.reduce(np.arange(6)) * 3. / 12.)
assert_equal(average(y, axis=0), np.arange(6) * 3. / 2.)
assert_equal(average(y, axis=1),
[average(x, axis=0), average(x, axis=0) * 2.0])
assert_equal(average(y, None, weights=w2), 20. / 6.)
assert_equal(average(y, axis=0, weights=w2),
[0., 1., 2., 3., 4., 10.])
assert_equal(average(y, axis=1),
[average(x, axis=0), average(x, axis=0) * 2.0])
m1 = zeros(6)
m2 = [0, 0, 1, 1, 0, 0]
m3 = [[0, 0, 1, 1, 0, 0], [0, 1, 1, 1, 1, 0]]
m4 = ones(6)
m5 = [0, 1, 1, 1, 1, 1]
assert_equal(average(masked_array(x, m1), axis=0), 2.5)
assert_equal(average(masked_array(x, m2), axis=0), 2.5)
assert_equal(average(masked_array(x, m4), axis=0).mask, [True])
assert_equal(average(masked_array(x, m5), axis=0), 0.0)
assert_equal(count(average(masked_array(x, m4), axis=0)), 0)
z = masked_array(y, m3)
assert_equal(average(z, None), 20. / 6.)
assert_equal(average(z, axis=0), [0., 1., 99., 99., 4.0, 7.5])
assert_equal(average(z, axis=1), [2.5, 5.0])
assert_equal(average(z, axis=0, weights=w2),
[0., 1., 99., 99., 4.0, 10.0])
def test_testAverage3(self):
# Yet more tests of average!
a = arange(6)
b = arange(6) * 3
r1, w1 = average([[a, b], [b, a]], axis=1, returned=1)
assert_equal(shape(r1), shape(w1))
assert_equal(r1.shape, w1.shape)
r2, w2 = average(ones((2, 2, 3)), axis=0, weights=[3, 1], returned=1)
assert_equal(shape(w2), shape(r2))
r2, w2 = average(ones((2, 2, 3)), returned=1)
assert_equal(shape(w2), shape(r2))
r2, w2 = average(ones((2, 2, 3)), weights=ones((2, 2, 3)), returned=1)
assert_equal(shape(w2), shape(r2))
a2d = array([[1, 2], [0, 4]], float)
a2dm = masked_array(a2d, [[False, False], [True, False]])
a2da = average(a2d, axis=0)
assert_equal(a2da, [0.5, 3.0])
a2dma = average(a2dm, axis=0)
assert_equal(a2dma, [1.0, 3.0])
a2dma = average(a2dm, axis=None)
assert_equal(a2dma, 7. / 3.)
a2dma = average(a2dm, axis=1)
assert_equal(a2dma, [1.5, 4.0])
def test_onintegers_with_mask(self):
# Test average on integers with mask
a = average(array([1, 2]))
assert_equal(a, 1.5)
a = average(array([1, 2, 3, 4], mask=[False, False, True, True]))
assert_equal(a, 1.5)
def test_complex(self):
# Test with complex data.
# (Regression test for https://github.com/numpy/numpy/issues/2684)
mask = np.array([[0, 0, 0, 1, 0],
[0, 1, 0, 0, 0]], dtype=bool)
a = masked_array([[0, 1+2j, 3+4j, 5+6j, 7+8j],
[9j, 0+1j, 2+3j, 4+5j, 7+7j]],
mask=mask)
av = average(a)
expected = np.average(a.compressed())
assert_almost_equal(av.real, expected.real)
assert_almost_equal(av.imag, expected.imag)
av0 = average(a, axis=0)
expected0 = average(a.real, axis=0) + average(a.imag, axis=0)*1j
assert_almost_equal(av0.real, expected0.real)
assert_almost_equal(av0.imag, expected0.imag)
av1 = average(a, axis=1)
expected1 = average(a.real, axis=1) + average(a.imag, axis=1)*1j
assert_almost_equal(av1.real, expected1.real)
assert_almost_equal(av1.imag, expected1.imag)
# Test with the 'weights' argument.
wts = np.array([[0.5, 1.0, 2.0, 1.0, 0.5],
[1.0, 1.0, 1.0, 1.0, 1.0]])
wav = average(a, weights=wts)
expected = np.average(a.compressed(), weights=wts[~mask])
assert_almost_equal(wav.real, expected.real)
assert_almost_equal(wav.imag, expected.imag)
wav0 = average(a, weights=wts, axis=0)
expected0 = (average(a.real, weights=wts, axis=0) +
average(a.imag, weights=wts, axis=0)*1j)
assert_almost_equal(wav0.real, expected0.real)
assert_almost_equal(wav0.imag, expected0.imag)
wav1 = average(a, weights=wts, axis=1)
expected1 = (average(a.real, weights=wts, axis=1) +
average(a.imag, weights=wts, axis=1)*1j)
assert_almost_equal(wav1.real, expected1.real)
assert_almost_equal(wav1.imag, expected1.imag)
class TestConcatenator(TestCase):
# Tests for mr_, the equivalent of r_ for masked arrays.
def test_1d(self):
# Tests mr_ on 1D arrays.
assert_array_equal(mr_[1, 2, 3, 4, 5, 6], array([1, 2, 3, 4, 5, 6]))
b = ones(5)
m = [1, 0, 0, 0, 0]
d = masked_array(b, mask=m)
c = mr_[d, 0, 0, d]
self.assertTrue(isinstance(c, MaskedArray))
assert_array_equal(c, [1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1])
assert_array_equal(c.mask, mr_[m, 0, 0, m])
def test_2d(self):
# Tests mr_ on 2D arrays.
a_1 = np.random.rand(5, 5)
a_2 = np.random.rand(5, 5)
m_1 = np.round_(np.random.rand(5, 5), 0)
m_2 = np.round_(np.random.rand(5, 5), 0)
b_1 = masked_array(a_1, mask=m_1)
b_2 = masked_array(a_2, mask=m_2)
# append columns
d = mr_['1', b_1, b_2]
self.assertTrue(d.shape == (5, 10))
assert_array_equal(d[:, :5], b_1)
assert_array_equal(d[:, 5:], b_2)
assert_array_equal(d.mask, np.r_['1', m_1, m_2])
d = mr_[b_1, b_2]
self.assertTrue(d.shape == (10, 5))
assert_array_equal(d[:5,:], b_1)
assert_array_equal(d[5:,:], b_2)
assert_array_equal(d.mask, np.r_[m_1, m_2])
def test_matrix_builder(self):
assert_raises(np.ma.MAError, lambda: mr_['1, 2; 3, 4'])
def test_matrix(self):
actual = mr_['r', 1, 2, 3]
expected = np.ma.array(np.r_['r', 1, 2, 3])
assert_array_equal(actual, expected)
# outer type is masked array, inner type is matrix
assert_equal(type(actual), type(expected))
assert_equal(type(actual.data), type(expected.data))
class TestNotMasked(TestCase):
# Tests notmasked_edges and notmasked_contiguous.
def test_edges(self):
# Tests unmasked_edges
data = masked_array(np.arange(25).reshape(5, 5),
mask=[[0, 0, 1, 0, 0],
[0, 0, 0, 1, 1],
[1, 1, 0, 0, 0],
[0, 0, 0, 0, 0],
[1, 1, 1, 0, 0]],)
test = notmasked_edges(data, None)
assert_equal(test, [0, 24])
test = notmasked_edges(data, 0)
assert_equal(test[0], [(0, 0, 1, 0, 0), (0, 1, 2, 3, 4)])
assert_equal(test[1], [(3, 3, 3, 4, 4), (0, 1, 2, 3, 4)])
test = notmasked_edges(data, 1)
assert_equal(test[0], [(0, 1, 2, 3, 4), (0, 0, 2, 0, 3)])
assert_equal(test[1], [(0, 1, 2, 3, 4), (4, 2, 4, 4, 4)])
#
test = notmasked_edges(data.data, None)
assert_equal(test, [0, 24])
test = notmasked_edges(data.data, 0)
assert_equal(test[0], [(0, 0, 0, 0, 0), (0, 1, 2, 3, 4)])
assert_equal(test[1], [(4, 4, 4, 4, 4), (0, 1, 2, 3, 4)])
test = notmasked_edges(data.data, -1)
assert_equal(test[0], [(0, 1, 2, 3, 4), (0, 0, 0, 0, 0)])
assert_equal(test[1], [(0, 1, 2, 3, 4), (4, 4, 4, 4, 4)])
#
data[-2] = masked
test = notmasked_edges(data, 0)
assert_equal(test[0], [(0, 0, 1, 0, 0), (0, 1, 2, 3, 4)])
assert_equal(test[1], [(1, 1, 2, 4, 4), (0, 1, 2, 3, 4)])
test = notmasked_edges(data, -1)
assert_equal(test[0], [(0, 1, 2, 4), (0, 0, 2, 3)])
assert_equal(test[1], [(0, 1, 2, 4), (4, 2, 4, 4)])
def test_contiguous(self):
# Tests notmasked_contiguous
a = masked_array(np.arange(24).reshape(3, 8),
mask=[[0, 0, 0, 0, 1, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 1, 1],
[0, 0, 0, 0, 0, 0, 1, 0], ])
tmp = notmasked_contiguous(a, None)
assert_equal(tmp[-1], slice(23, 24, None))
assert_equal(tmp[-2], slice(16, 22, None))
assert_equal(tmp[-3], slice(0, 4, None))
#
tmp = notmasked_contiguous(a, 0)
self.assertTrue(len(tmp[-1]) == 1)
self.assertTrue(tmp[-2] is None)
assert_equal(tmp[-3], tmp[-1])
self.assertTrue(len(tmp[0]) == 2)
#
tmp = notmasked_contiguous(a, 1)
assert_equal(tmp[0][-1], slice(0, 4, None))
self.assertTrue(tmp[1] is None)
assert_equal(tmp[2][-1], slice(7, 8, None))
assert_equal(tmp[2][-2], slice(0, 6, None))
class TestCompressFunctions(TestCase):
def test_compress_nd(self):
# Tests compress_nd
x = np.array(list(range(3*4*5))).reshape(3, 4, 5)
m = np.zeros((3,4,5)).astype(bool)
m[1,1,1] = True
x = array(x, mask=m)
# axis=None
a = compress_nd(x)
assert_equal(a, [[[ 0, 2, 3, 4],
[10, 12, 13, 14],
[15, 17, 18, 19]],
[[40, 42, 43, 44],
[50, 52, 53, 54],
[55, 57, 58, 59]]])
# axis=0
a = compress_nd(x, 0)
assert_equal(a, [[[ 0, 1, 2, 3, 4],
[ 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14],
[15, 16, 17, 18, 19]],
[[40, 41, 42, 43, 44],
[45, 46, 47, 48, 49],
[50, 51, 52, 53, 54],
[55, 56, 57, 58, 59]]])
# axis=1
a = compress_nd(x, 1)
assert_equal(a, [[[ 0, 1, 2, 3, 4],
[10, 11, 12, 13, 14],
[15, 16, 17, 18, 19]],
[[20, 21, 22, 23, 24],
[30, 31, 32, 33, 34],
[35, 36, 37, 38, 39]],
[[40, 41, 42, 43, 44],
[50, 51, 52, 53, 54],
[55, 56, 57, 58, 59]]])
a2 = compress_nd(x, (1,))
a3 = compress_nd(x, -2)
a4 = compress_nd(x, (-2,))
assert_equal(a, a2)
assert_equal(a, a3)
assert_equal(a, a4)
# axis=2
a = compress_nd(x, 2)
assert_equal(a, [[[ 0, 2, 3, 4],
[ 5, 7, 8, 9],
[10, 12, 13, 14],
[15, 17, 18, 19]],
[[20, 22, 23, 24],
[25, 27, 28, 29],
[30, 32, 33, 34],
[35, 37, 38, 39]],
[[40, 42, 43, 44],
[45, 47, 48, 49],
[50, 52, 53, 54],
[55, 57, 58, 59]]])
a2 = compress_nd(x, (2,))
a3 = compress_nd(x, -1)
a4 = compress_nd(x, (-1,))
assert_equal(a, a2)
assert_equal(a, a3)
assert_equal(a, a4)
# axis=(0, 1)
a = compress_nd(x, (0, 1))
assert_equal(a, [[[ 0, 1, 2, 3, 4],
[10, 11, 12, 13, 14],
[15, 16, 17, 18, 19]],
[[40, 41, 42, 43, 44],
[50, 51, 52, 53, 54],
[55, 56, 57, 58, 59]]])
a2 = compress_nd(x, (0, -2))
assert_equal(a, a2)
# axis=(1, 2)
a = compress_nd(x, (1, 2))
assert_equal(a, [[[ 0, 2, 3, 4],
[10, 12, 13, 14],
[15, 17, 18, 19]],
[[20, 22, 23, 24],
[30, 32, 33, 34],
[35, 37, 38, 39]],
[[40, 42, 43, 44],
[50, 52, 53, 54],
[55, 57, 58, 59]]])
a2 = compress_nd(x, (-2, 2))
a3 = compress_nd(x, (1, -1))
a4 = compress_nd(x, (-2, -1))
assert_equal(a, a2)
assert_equal(a, a3)
assert_equal(a, a4)
# axis=(0, 2)
a = compress_nd(x, (0, 2))
assert_equal(a, [[[ 0, 2, 3, 4],
[ 5, 7, 8, 9],
[10, 12, 13, 14],
[15, 17, 18, 19]],
[[40, 42, 43, 44],
[45, 47, 48, 49],
[50, 52, 53, 54],
[55, 57, 58, 59]]])
a2 = compress_nd(x, (0, -1))
assert_equal(a, a2)
def test_compress_rowcols(self):
# Tests compress_rowcols
x = array(np.arange(9).reshape(3, 3),
mask=[[1, 0, 0], [0, 0, 0], [0, 0, 0]])
assert_equal(compress_rowcols(x), [[4, 5], [7, 8]])
assert_equal(compress_rowcols(x, 0), [[3, 4, 5], [6, 7, 8]])
assert_equal(compress_rowcols(x, 1), [[1, 2], [4, 5], [7, 8]])
x = array(x._data, mask=[[0, 0, 0], [0, 1, 0], [0, 0, 0]])
assert_equal(compress_rowcols(x), [[0, 2], [6, 8]])
assert_equal(compress_rowcols(x, 0), [[0, 1, 2], [6, 7, 8]])
assert_equal(compress_rowcols(x, 1), [[0, 2], [3, 5], [6, 8]])
x = array(x._data, mask=[[1, 0, 0], [0, 1, 0], [0, 0, 0]])
assert_equal(compress_rowcols(x), [[8]])
assert_equal(compress_rowcols(x, 0), [[6, 7, 8]])
assert_equal(compress_rowcols(x, 1,), [[2], [5], [8]])
x = array(x._data, mask=[[1, 0, 0], [0, 1, 0], [0, 0, 1]])
assert_equal(compress_rowcols(x).size, 0)
assert_equal(compress_rowcols(x, 0).size, 0)
assert_equal(compress_rowcols(x, 1).size, 0)
def test_mask_rowcols(self):
# Tests mask_rowcols.
x = array(np.arange(9).reshape(3, 3),
mask=[[1, 0, 0], [0, 0, 0], [0, 0, 0]])
assert_equal(mask_rowcols(x).mask,
[[1, 1, 1], [1, 0, 0], [1, 0, 0]])
assert_equal(mask_rowcols(x, 0).mask,
[[1, 1, 1], [0, 0, 0], [0, 0, 0]])
assert_equal(mask_rowcols(x, 1).mask,
[[1, 0, 0], [1, 0, 0], [1, 0, 0]])
x = array(x._data, mask=[[0, 0, 0], [0, 1, 0], [0, 0, 0]])
assert_equal(mask_rowcols(x).mask,
[[0, 1, 0], [1, 1, 1], [0, 1, 0]])
assert_equal(mask_rowcols(x, 0).mask,
[[0, 0, 0], [1, 1, 1], [0, 0, 0]])
assert_equal(mask_rowcols(x, 1).mask,
[[0, 1, 0], [0, 1, 0], [0, 1, 0]])
x = array(x._data, mask=[[1, 0, 0], [0, 1, 0], [0, 0, 0]])
assert_equal(mask_rowcols(x).mask,
[[1, 1, 1], [1, 1, 1], [1, 1, 0]])
assert_equal(mask_rowcols(x, 0).mask,
[[1, 1, 1], [1, 1, 1], [0, 0, 0]])
assert_equal(mask_rowcols(x, 1,).mask,
[[1, 1, 0], [1, 1, 0], [1, 1, 0]])
x = array(x._data, mask=[[1, 0, 0], [0, 1, 0], [0, 0, 1]])
self.assertTrue(mask_rowcols(x).all() is masked)
self.assertTrue(mask_rowcols(x, 0).all() is masked)
self.assertTrue(mask_rowcols(x, 1).all() is masked)
self.assertTrue(mask_rowcols(x).mask.all())
self.assertTrue(mask_rowcols(x, 0).mask.all())
self.assertTrue(mask_rowcols(x, 1).mask.all())
def test_dot(self):
# Tests dot product
n = np.arange(1, 7)
#
m = [1, 0, 0, 0, 0, 0]
a = masked_array(n, mask=m).reshape(2, 3)
b = masked_array(n, mask=m).reshape(3, 2)
c = dot(a, b, strict=True)
assert_equal(c.mask, [[1, 1], [1, 0]])
c = dot(b, a, strict=True)
assert_equal(c.mask, [[1, 1, 1], [1, 0, 0], [1, 0, 0]])
c = dot(a, b, strict=False)
assert_equal(c, np.dot(a.filled(0), b.filled(0)))
c = dot(b, a, strict=False)
assert_equal(c, np.dot(b.filled(0), a.filled(0)))
#
m = [0, 0, 0, 0, 0, 1]
a = masked_array(n, mask=m).reshape(2, 3)
b = masked_array(n, mask=m).reshape(3, 2)
c = dot(a, b, strict=True)
assert_equal(c.mask, [[0, 1], [1, 1]])
c = dot(b, a, strict=True)
assert_equal(c.mask, [[0, 0, 1], [0, 0, 1], [1, 1, 1]])
c = dot(a, b, strict=False)
assert_equal(c, np.dot(a.filled(0), b.filled(0)))
assert_equal(c, dot(a, b))
c = dot(b, a, strict=False)
assert_equal(c, np.dot(b.filled(0), a.filled(0)))
#
m = [0, 0, 0, 0, 0, 0]
a = masked_array(n, mask=m).reshape(2, 3)
b = masked_array(n, mask=m).reshape(3, 2)
c = dot(a, b)
assert_equal(c.mask, nomask)
c = dot(b, a)
assert_equal(c.mask, nomask)
#
a = masked_array(n, mask=[1, 0, 0, 0, 0, 0]).reshape(2, 3)
b = masked_array(n, mask=[0, 0, 0, 0, 0, 0]).reshape(3, 2)
c = dot(a, b, strict=True)
assert_equal(c.mask, [[1, 1], [0, 0]])
c = dot(a, b, strict=False)
assert_equal(c, np.dot(a.filled(0), b.filled(0)))
c = dot(b, a, strict=True)
assert_equal(c.mask, [[1, 0, 0], [1, 0, 0], [1, 0, 0]])
c = dot(b, a, strict=False)
assert_equal(c, np.dot(b.filled(0), a.filled(0)))
#
a = masked_array(n, mask=[0, 0, 0, 0, 0, 1]).reshape(2, 3)
b = masked_array(n, mask=[0, 0, 0, 0, 0, 0]).reshape(3, 2)
c = dot(a, b, strict=True)
assert_equal(c.mask, [[0, 0], [1, 1]])
c = dot(a, b)
assert_equal(c, np.dot(a.filled(0), b.filled(0)))
c = dot(b, a, strict=True)
assert_equal(c.mask, [[0, 0, 1], [0, 0, 1], [0, 0, 1]])
c = dot(b, a, strict=False)
assert_equal(c, np.dot(b.filled(0), a.filled(0)))
#
a = masked_array(n, mask=[0, 0, 0, 0, 0, 1]).reshape(2, 3)
b = masked_array(n, mask=[0, 0, 1, 0, 0, 0]).reshape(3, 2)
c = dot(a, b, strict=True)
assert_equal(c.mask, [[1, 0], [1, 1]])
c = dot(a, b, strict=False)
assert_equal(c, np.dot(a.filled(0), b.filled(0)))
c = dot(b, a, strict=True)
assert_equal(c.mask, [[0, 0, 1], [1, 1, 1], [0, 0, 1]])
c = dot(b, a, strict=False)
assert_equal(c, np.dot(b.filled(0), a.filled(0)))
def test_dot_returns_maskedarray(self):
# See gh-6611
a = np.eye(3)
b = array(a)
assert_(type(dot(a, a)) is MaskedArray)
assert_(type(dot(a, b)) is MaskedArray)
assert_(type(dot(b, a)) is MaskedArray)
assert_(type(dot(b, b)) is MaskedArray)
def test_dot_out(self):
a = array(np.eye(3))
out = array(np.zeros((3, 3)))
res = dot(a, a, out=out)
assert_(res is out)
assert_equal(a, res)
class TestApplyAlongAxis(TestCase):
# Tests 2D functions
def test_3d(self):
a = arange(12.).reshape(2, 2, 3)
def myfunc(b):
return b[1]
xa = apply_along_axis(myfunc, 2, a)
assert_equal(xa, [[1, 4], [7, 10]])
# Tests kwargs functions
def test_3d_kwargs(self):
a = arange(12).reshape(2, 2, 3)
def myfunc(b, offset=0):
return b[1+offset]
xa = apply_along_axis(myfunc, 2, a, offset=1)
assert_equal(xa, [[2, 5], [8, 11]])
class TestApplyOverAxes(TestCase):
# Tests apply_over_axes
def test_basic(self):
a = arange(24).reshape(2, 3, 4)
test = apply_over_axes(np.sum, a, [0, 2])
ctrl = np.array([[[60], [92], [124]]])
assert_equal(test, ctrl)
a[(a % 2).astype(np.bool)] = masked
test = apply_over_axes(np.sum, a, [0, 2])
ctrl = np.array([[[28], [44], [60]]])
assert_equal(test, ctrl)
class TestMedian(TestCase):
def test_pytype(self):
r = np.ma.median([[np.inf, np.inf], [np.inf, np.inf]], axis=-1)
assert_equal(r, np.inf)
def test_inf(self):
# test that even which computes handles inf / x = masked
r = np.ma.median(np.ma.masked_array([[np.inf, np.inf],
[np.inf, np.inf]]), axis=-1)
assert_equal(r, np.inf)
r = np.ma.median(np.ma.masked_array([[np.inf, np.inf],
[np.inf, np.inf]]), axis=None)
assert_equal(r, np.inf)
# all masked
r = np.ma.median(np.ma.masked_array([[np.inf, np.inf],
[np.inf, np.inf]], mask=True),
axis=-1)
assert_equal(r.mask, True)
r = np.ma.median(np.ma.masked_array([[np.inf, np.inf],
[np.inf, np.inf]], mask=True),
axis=None)
assert_equal(r.mask, True)
def test_non_masked(self):
x = np.arange(9)
assert_equal(np.ma.median(x), 4.)
assert_(type(np.ma.median(x)) is not MaskedArray)
x = range(8)
assert_equal(np.ma.median(x), 3.5)
assert_(type(np.ma.median(x)) is not MaskedArray)
x = 5
assert_equal(np.ma.median(x), 5.)
assert_(type(np.ma.median(x)) is not MaskedArray)
# integer
x = np.arange(9 * 8).reshape(9, 8)
assert_equal(np.ma.median(x, axis=0), np.median(x, axis=0))
assert_equal(np.ma.median(x, axis=1), np.median(x, axis=1))
assert_(np.ma.median(x, axis=1) is not MaskedArray)
# float
x = np.arange(9 * 8.).reshape(9, 8)
assert_equal(np.ma.median(x, axis=0), np.median(x, axis=0))
assert_equal(np.ma.median(x, axis=1), np.median(x, axis=1))
assert_(np.ma.median(x, axis=1) is not MaskedArray)
def test_docstring_examples(self):
"test the examples given in the docstring of ma.median"
x = array(np.arange(8), mask=[0]*4 + [1]*4)
assert_equal(np.ma.median(x), 1.5)
assert_equal(np.ma.median(x).shape, (), "shape mismatch")
assert_(type(np.ma.median(x)) is not MaskedArray)
x = array(np.arange(10).reshape(2, 5), mask=[0]*6 + [1]*4)
assert_equal(np.ma.median(x), 2.5)
assert_equal(np.ma.median(x).shape, (), "shape mismatch")
assert_(type(np.ma.median(x)) is not MaskedArray)
ma_x = np.ma.median(x, axis=-1, overwrite_input=True)
assert_equal(ma_x, [2., 5.])
assert_equal(ma_x.shape, (2,), "shape mismatch")
assert_(type(ma_x) is MaskedArray)
def test_axis_argument_errors(self):
msg = "mask = %s, ndim = %s, axis = %s, overwrite_input = %s"
for ndmin in range(5):
for mask in [False, True]:
x = array(1, ndmin=ndmin, mask=mask)
# Valid axis values should not raise exception
args = itertools.product(range(-ndmin, ndmin), [False, True])
for axis, over in args:
try:
np.ma.median(x, axis=axis, overwrite_input=over)
except:
raise AssertionError(msg % (mask, ndmin, axis, over))
# Invalid axis values should raise exception
args = itertools.product([-(ndmin + 1), ndmin], [False, True])
for axis, over in args:
try:
np.ma.median(x, axis=axis, overwrite_input=over)
except np.AxisError:
pass
else:
raise AssertionError(msg % (mask, ndmin, axis, over))
def test_masked_0d(self):
# Check values
x = array(1, mask=False)
assert_equal(np.ma.median(x), 1)
x = array(1, mask=True)
assert_equal(np.ma.median(x), np.ma.masked)
def test_masked_1d(self):
x = array(np.arange(5), mask=True)
assert_equal(np.ma.median(x), np.ma.masked)
assert_equal(np.ma.median(x).shape, (), "shape mismatch")
assert_(type(np.ma.median(x)) is np.ma.core.MaskedConstant)
x = array(np.arange(5), mask=False)
assert_equal(np.ma.median(x), 2.)
assert_equal(np.ma.median(x).shape, (), "shape mismatch")
assert_(type(np.ma.median(x)) is not MaskedArray)
x = array(np.arange(5), mask=[0,1,0,0,0])
assert_equal(np.ma.median(x), 2.5)
assert_equal(np.ma.median(x).shape, (), "shape mismatch")
assert_(type(np.ma.median(x)) is not MaskedArray)
x = array(np.arange(5), mask=[0,1,1,1,1])
assert_equal(np.ma.median(x), 0.)
assert_equal(np.ma.median(x).shape, (), "shape mismatch")
assert_(type(np.ma.median(x)) is not MaskedArray)
# integer
x = array(np.arange(5), mask=[0,1,1,0,0])
assert_equal(np.ma.median(x), 3.)
assert_equal(np.ma.median(x).shape, (), "shape mismatch")
assert_(type(np.ma.median(x)) is not MaskedArray)
# float
x = array(np.arange(5.), mask=[0,1,1,0,0])
assert_equal(np.ma.median(x), 3.)
assert_equal(np.ma.median(x).shape, (), "shape mismatch")
assert_(type(np.ma.median(x)) is not MaskedArray)
# integer
x = array(np.arange(6), mask=[0,1,1,1,1,0])
assert_equal(np.ma.median(x), 2.5)
assert_equal(np.ma.median(x).shape, (), "shape mismatch")
assert_(type(np.ma.median(x)) is not MaskedArray)
# float
x = array(np.arange(6.), mask=[0,1,1,1,1,0])
assert_equal(np.ma.median(x), 2.5)
assert_equal(np.ma.median(x).shape, (), "shape mismatch")
assert_(type(np.ma.median(x)) is not MaskedArray)
def test_1d_shape_consistency(self):
assert_equal(np.ma.median(array([1,2,3],mask=[0,0,0])).shape,
np.ma.median(array([1,2,3],mask=[0,1,0])).shape )
def test_2d(self):
# Tests median w/ 2D
(n, p) = (101, 30)
x = masked_array(np.linspace(-1., 1., n),)
x[:10] = x[-10:] = masked
z = masked_array(np.empty((n, p), dtype=float))
z[:, 0] = x[:]
idx = np.arange(len(x))
for i in range(1, p):
np.random.shuffle(idx)
z[:, i] = x[idx]
assert_equal(median(z[:, 0]), 0)
assert_equal(median(z), 0)
assert_equal(median(z, axis=0), np.zeros(p))
assert_equal(median(z.T, axis=1), np.zeros(p))
def test_2d_waxis(self):
# Tests median w/ 2D arrays and different axis.
x = masked_array(np.arange(30).reshape(10, 3))
x[:3] = x[-3:] = masked
assert_equal(median(x), 14.5)
assert_(type(np.ma.median(x)) is not MaskedArray)
assert_equal(median(x, axis=0), [13.5, 14.5, 15.5])
assert_(type(np.ma.median(x, axis=0)) is MaskedArray)
assert_equal(median(x, axis=1), [0, 0, 0, 10, 13, 16, 19, 0, 0, 0])
assert_(type(np.ma.median(x, axis=1)) is MaskedArray)
assert_equal(median(x, axis=1).mask, [1, 1, 1, 0, 0, 0, 0, 1, 1, 1])
def test_3d(self):
# Tests median w/ 3D
x = np.ma.arange(24).reshape(3, 4, 2)
x[x % 3 == 0] = masked
assert_equal(median(x, 0), [[12, 9], [6, 15], [12, 9], [18, 15]])
x.shape = (4, 3, 2)
assert_equal(median(x, 0), [[99, 10], [11, 99], [13, 14]])
x = np.ma.arange(24).reshape(4, 3, 2)
x[x % 5 == 0] = masked
assert_equal(median(x, 0), [[12, 10], [8, 9], [16, 17]])
def test_neg_axis(self):
x = masked_array(np.arange(30).reshape(10, 3))
x[:3] = x[-3:] = masked
assert_equal(median(x, axis=-1), median(x, axis=1))
def test_out_1d(self):
# integer float even odd
for v in (30, 30., 31, 31.):
x = masked_array(np.arange(v))
x[:3] = x[-3:] = masked
out = masked_array(np.ones(()))
r = median(x, out=out)
if v == 30:
assert_equal(out, 14.5)
else:
assert_equal(out, 15.)
assert_(r is out)
assert_(type(r) is MaskedArray)
def test_out(self):
# integer float even odd
for v in (40, 40., 30, 30.):
x = masked_array(np.arange(v).reshape(10, -1))
x[:3] = x[-3:] = masked
out = masked_array(np.ones(10))
r = median(x, axis=1, out=out)
if v == 30:
e = masked_array([0.]*3 + [10, 13, 16, 19] + [0.]*3,
mask=[True] * 3 + [False] * 4 + [True] * 3)
else:
e = masked_array([0.]*3 + [13.5, 17.5, 21.5, 25.5] + [0.]*3,
mask=[True]*3 + [False]*4 + [True]*3)
assert_equal(r, e)
assert_(r is out)
assert_(type(r) is MaskedArray)
def test_single_non_masked_value_on_axis(self):
data = [[1., 0.],
[0., 3.],
[0., 0.]]
masked_arr = np.ma.masked_equal(data, 0)
expected = [1., 3.]
assert_array_equal(np.ma.median(masked_arr, axis=0),
expected)
def test_nan(self):
with suppress_warnings() as w:
w.record(RuntimeWarning)
for mask in (False, np.zeros(6, dtype=np.bool)):
dm = np.ma.array([[1, np.nan, 3], [1, 2, 3]])
dm.mask = mask
# scalar result
r = np.ma.median(dm, axis=None)
assert_(np.isscalar(r))
assert_array_equal(r, np.nan)
r = np.ma.median(dm.ravel(), axis=0)
assert_(np.isscalar(r))
assert_array_equal(r, np.nan)
r = np.ma.median(dm, axis=0)
assert_equal(type(r), MaskedArray)
assert_array_equal(r, [1, np.nan, 3])
r = np.ma.median(dm, axis=1)
assert_equal(type(r), MaskedArray)
assert_array_equal(r, [np.nan, 2])
r = np.ma.median(dm, axis=-1)
assert_equal(type(r), MaskedArray)
assert_array_equal(r, [np.nan, 2])
dm = np.ma.array([[1, np.nan, 3], [1, 2, 3]])
dm[:, 2] = np.ma.masked
assert_array_equal(np.ma.median(dm, axis=None), np.nan)
assert_array_equal(np.ma.median(dm, axis=0), [1, np.nan, 3])
assert_array_equal(np.ma.median(dm, axis=1), [np.nan, 1.5])
assert_equal([x.category is RuntimeWarning for x in w.log],
[True]*13)
def test_out_nan(self):
with warnings.catch_warnings(record=True):
warnings.filterwarnings('always', '', RuntimeWarning)
o = np.ma.masked_array(np.zeros((4,)))
d = np.ma.masked_array(np.ones((3, 4)))
d[2, 1] = np.nan
d[2, 2] = np.ma.masked
assert_equal(np.ma.median(d, 0, out=o), o)
o = np.ma.masked_array(np.zeros((3,)))
assert_equal(np.ma.median(d, 1, out=o), o)
o = np.ma.masked_array(np.zeros(()))
assert_equal(np.ma.median(d, out=o), o)
def test_nan_behavior(self):
a = np.ma.masked_array(np.arange(24, dtype=float))
a[::3] = np.ma.masked
a[2] = np.nan
with suppress_warnings() as w:
w.record(RuntimeWarning)
assert_array_equal(np.ma.median(a), np.nan)
assert_array_equal(np.ma.median(a, axis=0), np.nan)
assert_(w.log[0].category is RuntimeWarning)
assert_(w.log[1].category is RuntimeWarning)
a = np.ma.masked_array(np.arange(24, dtype=float).reshape(2, 3, 4))
a.mask = np.arange(a.size) % 2 == 1
aorig = a.copy()
a[1, 2, 3] = np.nan
a[1, 1, 2] = np.nan
# no axis
with suppress_warnings() as w:
w.record(RuntimeWarning)
warnings.filterwarnings('always', '', RuntimeWarning)
assert_array_equal(np.ma.median(a), np.nan)
assert_(np.isscalar(np.ma.median(a)))
assert_(w.log[0].category is RuntimeWarning)
# axis0
b = np.ma.median(aorig, axis=0)
b[2, 3] = np.nan
b[1, 2] = np.nan
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings('always', '', RuntimeWarning)
assert_equal(np.ma.median(a, 0), b)
assert_equal(len(w), 1)
# axis1
b = np.ma.median(aorig, axis=1)
b[1, 3] = np.nan
b[1, 2] = np.nan
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings('always', '', RuntimeWarning)
assert_equal(np.ma.median(a, 1), b)
assert_equal(len(w), 1)
# axis02
b = np.ma.median(aorig, axis=(0, 2))
b[1] = np.nan
b[2] = np.nan
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings('always', '', RuntimeWarning)
assert_equal(np.ma.median(a, (0, 2)), b)
assert_equal(len(w), 1)
def test_ambigous_fill(self):
# 255 is max value, used as filler for sort
a = np.array([[3, 3, 255], [3, 3, 255]], dtype=np.uint8)
a = np.ma.masked_array(a, mask=a == 3)
assert_array_equal(np.ma.median(a, axis=1), 255)
assert_array_equal(np.ma.median(a, axis=1).mask, False)
assert_array_equal(np.ma.median(a, axis=0), a[0])
assert_array_equal(np.ma.median(a), 255)
def test_special(self):
for inf in [np.inf, -np.inf]:
a = np.array([[inf, np.nan], [np.nan, np.nan]])
a = np.ma.masked_array(a, mask=np.isnan(a))
assert_equal(np.ma.median(a, axis=0), [inf, np.nan])
assert_equal(np.ma.median(a, axis=1), [inf, np.nan])
assert_equal(np.ma.median(a), inf)
a = np.array([[np.nan, np.nan, inf], [np.nan, np.nan, inf]])
a = np.ma.masked_array(a, mask=np.isnan(a))
assert_array_equal(np.ma.median(a, axis=1), inf)
assert_array_equal(np.ma.median(a, axis=1).mask, False)
assert_array_equal(np.ma.median(a, axis=0), a[0])
assert_array_equal(np.ma.median(a), inf)
# no mask
a = np.array([[inf, inf], [inf, inf]])
assert_equal(np.ma.median(a), inf)
assert_equal(np.ma.median(a, axis=0), inf)
assert_equal(np.ma.median(a, axis=1), inf)
a = np.array([[inf, 7, -inf, -9],
[-10, np.nan, np.nan, 5],
[4, np.nan, np.nan, inf]],
dtype=np.float32)
a = np.ma.masked_array(a, mask=np.isnan(a))
if inf > 0:
assert_equal(np.ma.median(a, axis=0), [4., 7., -inf, 5.])
assert_equal(np.ma.median(a), 4.5)
else:
assert_equal(np.ma.median(a, axis=0), [-10., 7., -inf, -9.])
assert_equal(np.ma.median(a), -2.5)
assert_equal(np.ma.median(a, axis=1), [-1., -2.5, inf])
for i in range(0, 10):
for j in range(1, 10):
a = np.array([([np.nan] * i) + ([inf] * j)] * 2)
a = np.ma.masked_array(a, mask=np.isnan(a))
assert_equal(np.ma.median(a), inf)
assert_equal(np.ma.median(a, axis=1), inf)
assert_equal(np.ma.median(a, axis=0),
([np.nan] * i) + [inf] * j)
def test_empty(self):
# empty arrays
a = np.ma.masked_array(np.array([], dtype=float))
with suppress_warnings() as w:
w.record(RuntimeWarning)
assert_array_equal(np.ma.median(a), np.nan)
assert_(w.log[0].category is RuntimeWarning)
# multiple dimensions
a = np.ma.masked_array(np.array([], dtype=float, ndmin=3))
# no axis
with suppress_warnings() as w:
w.record(RuntimeWarning)
warnings.filterwarnings('always', '', RuntimeWarning)
assert_array_equal(np.ma.median(a), np.nan)
assert_(w.log[0].category is RuntimeWarning)
# axis 0 and 1
b = np.ma.masked_array(np.array([], dtype=float, ndmin=2))
assert_equal(np.ma.median(a, axis=0), b)
assert_equal(np.ma.median(a, axis=1), b)
# axis 2
b = np.ma.masked_array(np.array(np.nan, dtype=float, ndmin=2))
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings('always', '', RuntimeWarning)
assert_equal(np.ma.median(a, axis=2), b)
assert_(w[0].category is RuntimeWarning)
def test_object(self):
o = np.ma.masked_array(np.arange(7.))
assert_(type(np.ma.median(o.astype(object))), float)
o[2] = np.nan
assert_(type(np.ma.median(o.astype(object))), float)
class TestCov(TestCase):
def setUp(self):
self.data = array(np.random.rand(12))
def test_1d_without_missing(self):
# Test cov on 1D variable w/o missing values
x = self.data
assert_almost_equal(np.cov(x), cov(x))
assert_almost_equal(np.cov(x, rowvar=False), cov(x, rowvar=False))
assert_almost_equal(np.cov(x, rowvar=False, bias=True),
cov(x, rowvar=False, bias=True))
def test_2d_without_missing(self):
# Test cov on 1 2D variable w/o missing values
x = self.data.reshape(3, 4)
assert_almost_equal(np.cov(x), cov(x))
assert_almost_equal(np.cov(x, rowvar=False), cov(x, rowvar=False))
assert_almost_equal(np.cov(x, rowvar=False, bias=True),
cov(x, rowvar=False, bias=True))
def test_1d_with_missing(self):
# Test cov 1 1D variable w/missing values
x = self.data
x[-1] = masked
x -= x.mean()
nx = x.compressed()
assert_almost_equal(np.cov(nx), cov(x))
assert_almost_equal(np.cov(nx, rowvar=False), cov(x, rowvar=False))
assert_almost_equal(np.cov(nx, rowvar=False, bias=True),
cov(x, rowvar=False, bias=True))
#
try:
cov(x, allow_masked=False)
except ValueError:
pass
#
# 2 1D variables w/ missing values
nx = x[1:-1]
assert_almost_equal(np.cov(nx, nx[::-1]), cov(x, x[::-1]))
assert_almost_equal(np.cov(nx, nx[::-1], rowvar=False),
cov(x, x[::-1], rowvar=False))
assert_almost_equal(np.cov(nx, nx[::-1], rowvar=False, bias=True),
cov(x, x[::-1], rowvar=False, bias=True))
def test_2d_with_missing(self):
# Test cov on 2D variable w/ missing value
x = self.data
x[-1] = masked
x = x.reshape(3, 4)
valid = np.logical_not(getmaskarray(x)).astype(int)
frac = np.dot(valid, valid.T)
xf = (x - x.mean(1)[:, None]).filled(0)
assert_almost_equal(cov(x),
np.cov(xf) * (x.shape[1] - 1) / (frac - 1.))
assert_almost_equal(cov(x, bias=True),
np.cov(xf, bias=True) * x.shape[1] / frac)
frac = np.dot(valid.T, valid)
xf = (x - x.mean(0)).filled(0)
assert_almost_equal(cov(x, rowvar=False),
(np.cov(xf, rowvar=False) *
(x.shape[0] - 1) / (frac - 1.)))
assert_almost_equal(cov(x, rowvar=False, bias=True),
(np.cov(xf, rowvar=False, bias=True) *
x.shape[0] / frac))
class TestCorrcoef(TestCase):
def setUp(self):
self.data = array(np.random.rand(12))
self.data2 = array(np.random.rand(12))
def test_ddof(self):
# ddof raises DeprecationWarning
x, y = self.data, self.data2
expected = np.corrcoef(x)
expected2 = np.corrcoef(x, y)
with suppress_warnings() as sup:
warnings.simplefilter("always")
assert_warns(DeprecationWarning, corrcoef, x, ddof=-1)
sup.filter(DeprecationWarning, "bias and ddof have no effect")
# ddof has no or negligible effect on the function
assert_almost_equal(np.corrcoef(x, ddof=0), corrcoef(x, ddof=0))
assert_almost_equal(corrcoef(x, ddof=-1), expected)
assert_almost_equal(corrcoef(x, y, ddof=-1), expected2)
assert_almost_equal(corrcoef(x, ddof=3), expected)
assert_almost_equal(corrcoef(x, y, ddof=3), expected2)
def test_bias(self):
x, y = self.data, self.data2
expected = np.corrcoef(x)
# bias raises DeprecationWarning
with suppress_warnings() as sup:
warnings.simplefilter("always")
assert_warns(DeprecationWarning, corrcoef, x, y, True, False)
assert_warns(DeprecationWarning, corrcoef, x, y, True, True)
assert_warns(DeprecationWarning, corrcoef, x, bias=False)
sup.filter(DeprecationWarning, "bias and ddof have no effect")
# bias has no or negligible effect on the function
assert_almost_equal(corrcoef(x, bias=1), expected)
def test_1d_without_missing(self):
# Test cov on 1D variable w/o missing values
x = self.data
assert_almost_equal(np.corrcoef(x), corrcoef(x))
assert_almost_equal(np.corrcoef(x, rowvar=False),
corrcoef(x, rowvar=False))
with suppress_warnings() as sup:
sup.filter(DeprecationWarning, "bias and ddof have no effect")
assert_almost_equal(np.corrcoef(x, rowvar=False, bias=True),
corrcoef(x, rowvar=False, bias=True))
def test_2d_without_missing(self):
# Test corrcoef on 1 2D variable w/o missing values
x = self.data.reshape(3, 4)
assert_almost_equal(np.corrcoef(x), corrcoef(x))
assert_almost_equal(np.corrcoef(x, rowvar=False),
corrcoef(x, rowvar=False))
with suppress_warnings() as sup:
sup.filter(DeprecationWarning, "bias and ddof have no effect")
assert_almost_equal(np.corrcoef(x, rowvar=False, bias=True),
corrcoef(x, rowvar=False, bias=True))
def test_1d_with_missing(self):
# Test corrcoef 1 1D variable w/missing values
x = self.data
x[-1] = masked
x -= x.mean()
nx = x.compressed()
assert_almost_equal(np.corrcoef(nx), corrcoef(x))
assert_almost_equal(np.corrcoef(nx, rowvar=False),
corrcoef(x, rowvar=False))
with suppress_warnings() as sup:
sup.filter(DeprecationWarning, "bias and ddof have no effect")
assert_almost_equal(np.corrcoef(nx, rowvar=False, bias=True),
corrcoef(x, rowvar=False, bias=True))
try:
corrcoef(x, allow_masked=False)
except ValueError:
pass
# 2 1D variables w/ missing values
nx = x[1:-1]
assert_almost_equal(np.corrcoef(nx, nx[::-1]), corrcoef(x, x[::-1]))
assert_almost_equal(np.corrcoef(nx, nx[::-1], rowvar=False),
corrcoef(x, x[::-1], rowvar=False))
with suppress_warnings() as sup:
sup.filter(DeprecationWarning, "bias and ddof have no effect")
# ddof and bias have no or negligible effect on the function
assert_almost_equal(np.corrcoef(nx, nx[::-1]),
corrcoef(x, x[::-1], bias=1))
assert_almost_equal(np.corrcoef(nx, nx[::-1]),
corrcoef(x, x[::-1], ddof=2))
def test_2d_with_missing(self):
# Test corrcoef on 2D variable w/ missing value
x = self.data
x[-1] = masked
x = x.reshape(3, 4)
test = corrcoef(x)
control = np.corrcoef(x)
assert_almost_equal(test[:-1, :-1], control[:-1, :-1])
with suppress_warnings() as sup:
sup.filter(DeprecationWarning, "bias and ddof have no effect")
# ddof and bias have no or negligible effect on the function
assert_almost_equal(corrcoef(x, ddof=-2)[:-1, :-1],
control[:-1, :-1])
assert_almost_equal(corrcoef(x, ddof=3)[:-1, :-1],
control[:-1, :-1])
assert_almost_equal(corrcoef(x, bias=1)[:-1, :-1],
control[:-1, :-1])
class TestPolynomial(TestCase):
#
def test_polyfit(self):
# Tests polyfit
# On ndarrays
x = np.random.rand(10)
y = np.random.rand(20).reshape(-1, 2)
assert_almost_equal(polyfit(x, y, 3), np.polyfit(x, y, 3))
# ON 1D maskedarrays
x = x.view(MaskedArray)
x[0] = masked
y = y.view(MaskedArray)
y[0, 0] = y[-1, -1] = masked
#
(C, R, K, S, D) = polyfit(x, y[:, 0], 3, full=True)
(c, r, k, s, d) = np.polyfit(x[1:], y[1:, 0].compressed(), 3,
full=True)
for (a, a_) in zip((C, R, K, S, D), (c, r, k, s, d)):
assert_almost_equal(a, a_)
#
(C, R, K, S, D) = polyfit(x, y[:, -1], 3, full=True)
(c, r, k, s, d) = np.polyfit(x[1:-1], y[1:-1, -1], 3, full=True)
for (a, a_) in zip((C, R, K, S, D), (c, r, k, s, d)):
assert_almost_equal(a, a_)
#
(C, R, K, S, D) = polyfit(x, y, 3, full=True)
(c, r, k, s, d) = np.polyfit(x[1:-1], y[1:-1,:], 3, full=True)
for (a, a_) in zip((C, R, K, S, D), (c, r, k, s, d)):
assert_almost_equal(a, a_)
#
w = np.random.rand(10) + 1
wo = w.copy()
xs = x[1:-1]
ys = y[1:-1]
ws = w[1:-1]
(C, R, K, S, D) = polyfit(x, y, 3, full=True, w=w)
(c, r, k, s, d) = np.polyfit(xs, ys, 3, full=True, w=ws)
assert_equal(w, wo)
for (a, a_) in zip((C, R, K, S, D), (c, r, k, s, d)):
assert_almost_equal(a, a_)
def test_polyfit_with_masked_NaNs(self):
x = np.random.rand(10)
y = np.random.rand(20).reshape(-1, 2)
x[0] = np.nan
y[-1,-1] = np.nan
x = x.view(MaskedArray)
y = y.view(MaskedArray)
x[0] = masked
y[-1,-1] = masked
(C, R, K, S, D) = polyfit(x, y, 3, full=True)
(c, r, k, s, d) = np.polyfit(x[1:-1], y[1:-1,:], 3, full=True)
for (a, a_) in zip((C, R, K, S, D), (c, r, k, s, d)):
assert_almost_equal(a, a_)
class TestArraySetOps(TestCase):
def test_unique_onlist(self):
# Test unique on list
data = [1, 1, 1, 2, 2, 3]
test = unique(data, return_index=True, return_inverse=True)
self.assertTrue(isinstance(test[0], MaskedArray))
assert_equal(test[0], masked_array([1, 2, 3], mask=[0, 0, 0]))
assert_equal(test[1], [0, 3, 5])
assert_equal(test[2], [0, 0, 0, 1, 1, 2])
def test_unique_onmaskedarray(self):
# Test unique on masked data w/use_mask=True
data = masked_array([1, 1, 1, 2, 2, 3], mask=[0, 0, 1, 0, 1, 0])
test = unique(data, return_index=True, return_inverse=True)
assert_equal(test[0], masked_array([1, 2, 3, -1], mask=[0, 0, 0, 1]))
assert_equal(test[1], [0, 3, 5, 2])
assert_equal(test[2], [0, 0, 3, 1, 3, 2])
#
data.fill_value = 3
data = masked_array(data=[1, 1, 1, 2, 2, 3],
mask=[0, 0, 1, 0, 1, 0], fill_value=3)
test = unique(data, return_index=True, return_inverse=True)
assert_equal(test[0], masked_array([1, 2, 3, -1], mask=[0, 0, 0, 1]))
assert_equal(test[1], [0, 3, 5, 2])
assert_equal(test[2], [0, 0, 3, 1, 3, 2])
def test_unique_allmasked(self):
# Test all masked
data = masked_array([1, 1, 1], mask=True)
test = unique(data, return_index=True, return_inverse=True)
assert_equal(test[0], masked_array([1, ], mask=[True]))
assert_equal(test[1], [0])
assert_equal(test[2], [0, 0, 0])
#
# Test masked
data = masked
test = unique(data, return_index=True, return_inverse=True)
assert_equal(test[0], masked_array(masked))
assert_equal(test[1], [0])
assert_equal(test[2], [0])
def test_ediff1d(self):
# Tests mediff1d
x = masked_array(np.arange(5), mask=[1, 0, 0, 0, 1])
control = array([1, 1, 1, 4], mask=[1, 0, 0, 1])
test = ediff1d(x)
assert_equal(test, control)
assert_equal(test.filled(0), control.filled(0))
assert_equal(test.mask, control.mask)
def test_ediff1d_tobegin(self):
# Test ediff1d w/ to_begin
x = masked_array(np.arange(5), mask=[1, 0, 0, 0, 1])
test = ediff1d(x, to_begin=masked)
control = array([0, 1, 1, 1, 4], mask=[1, 1, 0, 0, 1])
assert_equal(test, control)
assert_equal(test.filled(0), control.filled(0))
assert_equal(test.mask, control.mask)
#
test = ediff1d(x, to_begin=[1, 2, 3])
control = array([1, 2, 3, 1, 1, 1, 4], mask=[0, 0, 0, 1, 0, 0, 1])
assert_equal(test, control)
assert_equal(test.filled(0), control.filled(0))
assert_equal(test.mask, control.mask)
def test_ediff1d_toend(self):
# Test ediff1d w/ to_end
x = masked_array(np.arange(5), mask=[1, 0, 0, 0, 1])
test = ediff1d(x, to_end=masked)
control = array([1, 1, 1, 4, 0], mask=[1, 0, 0, 1, 1])
assert_equal(test, control)
assert_equal(test.filled(0), control.filled(0))
assert_equal(test.mask, control.mask)
#
test = ediff1d(x, to_end=[1, 2, 3])
control = array([1, 1, 1, 4, 1, 2, 3], mask=[1, 0, 0, 1, 0, 0, 0])
assert_equal(test, control)
assert_equal(test.filled(0), control.filled(0))
assert_equal(test.mask, control.mask)
def test_ediff1d_tobegin_toend(self):
# Test ediff1d w/ to_begin and to_end
x = masked_array(np.arange(5), mask=[1, 0, 0, 0, 1])
test = ediff1d(x, to_end=masked, to_begin=masked)
control = array([0, 1, 1, 1, 4, 0], mask=[1, 1, 0, 0, 1, 1])
assert_equal(test, control)
assert_equal(test.filled(0), control.filled(0))
assert_equal(test.mask, control.mask)
#
test = ediff1d(x, to_end=[1, 2, 3], to_begin=masked)
control = array([0, 1, 1, 1, 4, 1, 2, 3],
mask=[1, 1, 0, 0, 1, 0, 0, 0])
assert_equal(test, control)
assert_equal(test.filled(0), control.filled(0))
assert_equal(test.mask, control.mask)
def test_ediff1d_ndarray(self):
# Test ediff1d w/ a ndarray
x = np.arange(5)
test = ediff1d(x)
control = array([1, 1, 1, 1], mask=[0, 0, 0, 0])
assert_equal(test, control)
self.assertTrue(isinstance(test, MaskedArray))
assert_equal(test.filled(0), control.filled(0))
assert_equal(test.mask, control.mask)
#
test = ediff1d(x, to_end=masked, to_begin=masked)
control = array([0, 1, 1, 1, 1, 0], mask=[1, 0, 0, 0, 0, 1])
self.assertTrue(isinstance(test, MaskedArray))
assert_equal(test.filled(0), control.filled(0))
assert_equal(test.mask, control.mask)
def test_intersect1d(self):
# Test intersect1d
x = array([1, 3, 3, 3], mask=[0, 0, 0, 1])
y = array([3, 1, 1, 1], mask=[0, 0, 0, 1])
test = intersect1d(x, y)
control = array([1, 3, -1], mask=[0, 0, 1])
assert_equal(test, control)
def test_setxor1d(self):
# Test setxor1d
a = array([1, 2, 5, 7, -1], mask=[0, 0, 0, 0, 1])
b = array([1, 2, 3, 4, 5, -1], mask=[0, 0, 0, 0, 0, 1])
test = setxor1d(a, b)
assert_equal(test, array([3, 4, 7]))
#
a = array([1, 2, 5, 7, -1], mask=[0, 0, 0, 0, 1])
b = [1, 2, 3, 4, 5]
test = setxor1d(a, b)
assert_equal(test, array([3, 4, 7, -1], mask=[0, 0, 0, 1]))
#
a = array([1, 2, 3])
b = array([6, 5, 4])
test = setxor1d(a, b)
assert_(isinstance(test, MaskedArray))
assert_equal(test, [1, 2, 3, 4, 5, 6])
#
a = array([1, 8, 2, 3], mask=[0, 1, 0, 0])
b = array([6, 5, 4, 8], mask=[0, 0, 0, 1])
test = setxor1d(a, b)
assert_(isinstance(test, MaskedArray))
assert_equal(test, [1, 2, 3, 4, 5, 6])
#
assert_array_equal([], setxor1d([], []))
def test_isin(self):
# the tests for in1d cover most of isin's behavior
# if in1d is removed, would need to change those tests to test
# isin instead.
a = np.arange(24).reshape([2, 3, 4])
mask = np.zeros([2, 3, 4])
mask[1, 2, 0] = 1
a = array(a, mask=mask)
b = array(data=[0, 10, 20, 30, 1, 3, 11, 22, 33],
mask=[0, 1, 0, 1, 0, 1, 0, 1, 0])
ec = zeros((2, 3, 4), dtype=bool)
ec[0, 0, 0] = True
ec[0, 0, 1] = True
ec[0, 2, 3] = True
c = isin(a, b)
assert_(isinstance(c, MaskedArray))
assert_array_equal(c, ec)
#compare results of np.isin to ma.isin
d = np.isin(a, b[~b.mask]) & ~a.mask
assert_array_equal(c, d)
def test_in1d(self):
# Test in1d
a = array([1, 2, 5, 7, -1], mask=[0, 0, 0, 0, 1])
b = array([1, 2, 3, 4, 5, -1], mask=[0, 0, 0, 0, 0, 1])
test = in1d(a, b)
assert_equal(test, [True, True, True, False, True])
#
a = array([5, 5, 2, 1, -1], mask=[0, 0, 0, 0, 1])
b = array([1, 5, -1], mask=[0, 0, 1])
test = in1d(a, b)
assert_equal(test, [True, True, False, True, True])
#
assert_array_equal([], in1d([], []))
def test_in1d_invert(self):
# Test in1d's invert parameter
a = array([1, 2, 5, 7, -1], mask=[0, 0, 0, 0, 1])
b = array([1, 2, 3, 4, 5, -1], mask=[0, 0, 0, 0, 0, 1])
assert_equal(np.invert(in1d(a, b)), in1d(a, b, invert=True))
a = array([5, 5, 2, 1, -1], mask=[0, 0, 0, 0, 1])
b = array([1, 5, -1], mask=[0, 0, 1])
assert_equal(np.invert(in1d(a, b)), in1d(a, b, invert=True))
assert_array_equal([], in1d([], [], invert=True))
def test_union1d(self):
# Test union1d
a = array([1, 2, 5, 7, 5, -1], mask=[0, 0, 0, 0, 0, 1])
b = array([1, 2, 3, 4, 5, -1], mask=[0, 0, 0, 0, 0, 1])
test = union1d(a, b)
control = array([1, 2, 3, 4, 5, 7, -1], mask=[0, 0, 0, 0, 0, 0, 1])
assert_equal(test, control)
#
assert_array_equal([], union1d([], []))
def test_setdiff1d(self):
# Test setdiff1d
a = array([6, 5, 4, 7, 7, 1, 2, 1], mask=[0, 0, 0, 0, 0, 0, 0, 1])
b = array([2, 4, 3, 3, 2, 1, 5])
test = setdiff1d(a, b)
assert_equal(test, array([6, 7, -1], mask=[0, 0, 1]))
#
a = arange(10)
b = arange(8)
assert_equal(setdiff1d(a, b), array([8, 9]))
a = array([], np.uint32, mask=[])
assert_equal(setdiff1d(a, []).dtype, np.uint32)
def test_setdiff1d_char_array(self):
# Test setdiff1d_charray
a = np.array(['a', 'b', 'c'])
b = np.array(['a', 'b', 's'])
assert_array_equal(setdiff1d(a, b), np.array(['c']))
class TestShapeBase(TestCase):
def test_atleast_2d(self):
# Test atleast_2d
a = masked_array([0, 1, 2], mask=[0, 1, 0])
b = atleast_2d(a)
assert_equal(b.shape, (1, 3))
assert_equal(b.mask.shape, b.data.shape)
assert_equal(a.shape, (3,))
assert_equal(a.mask.shape, a.data.shape)
assert_equal(b.mask.shape, b.data.shape)
def test_shape_scalar(self):
# the atleast and diagflat function should work with scalars
# GitHub issue #3367
# Additionally, the atleast functions should accept multiple scalars
# correctly
b = atleast_1d(1.0)
assert_equal(b.shape, (1,))
assert_equal(b.mask.shape, b.shape)
assert_equal(b.data.shape, b.shape)
b = atleast_1d(1.0, 2.0)
for a in b:
assert_equal(a.shape, (1,))
assert_equal(a.mask.shape, a.shape)
assert_equal(a.data.shape, a.shape)
b = atleast_2d(1.0)
assert_equal(b.shape, (1, 1))
assert_equal(b.mask.shape, b.shape)
assert_equal(b.data.shape, b.shape)
b = atleast_2d(1.0, 2.0)
for a in b:
assert_equal(a.shape, (1, 1))
assert_equal(a.mask.shape, a.shape)
assert_equal(a.data.shape, a.shape)
b = atleast_3d(1.0)
assert_equal(b.shape, (1, 1, 1))
assert_equal(b.mask.shape, b.shape)
assert_equal(b.data.shape, b.shape)
b = atleast_3d(1.0, 2.0)
for a in b:
assert_equal(a.shape, (1, 1, 1))
assert_equal(a.mask.shape, a.shape)
assert_equal(a.data.shape, a.shape)
b = diagflat(1.0)
assert_equal(b.shape, (1, 1))
assert_equal(b.mask.shape, b.data.shape)
if __name__ == "__main__":
run_module_suite()
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