How to use the dtaidistance.dtw_c.distance_matrix_nogil function in dtaidistance

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github wannesm / dtaidistance / tests / test_cython.py View on Github external
def test_numpymatrix():
    """Passing a matrix instead of a list failed because the array is now a
    view instead of the original data structure."""
    s = np.array([
        [0., 0, 1, 2, 1, 0, 1, 0, 0],
        [0., 1, 2, 0, 0, 0, 0, 0, 0],
        [1., 2, 0, 0, 0, 0, 0, 1, 0]])
    m = dtw_c.distance_matrix_nogil(s)
    m = dtw.distances_array_to_matrix(m, len(s))
    m2 = dtw.distance_matrix(s)
    correct = np.array([
        [np.inf, 1.41421356, 1.73205081],
        [np.inf, np.inf,     1.41421356],
        [np.inf, np.inf,     np.inf]])
    assert m[0, 1] == pytest.approx(math.sqrt(2))
    assert m2[0, 1] == pytest.approx(math.sqrt(2))
    np.testing.assert_almost_equal(correct, m, decimal=4)
    np.testing.assert_almost_equal(correct, m2, decimal=4)
github wannesm / dtaidistance / tests / test_cython.py View on Github external
def test_numpymatrix_compact():
    """Passing a matrix instead of a list failed because the array is now a
    view instead of the original data structure."""
    s = np.array([
        [0., 0, 1, 2, 1, 0, 1, 0, 0],
        [0., 1, 2, 0, 0, 0, 0, 0, 0],
        [1., 2, 0, 0, 0, 0, 0, 1, 0]])
    m = dtw_c.distance_matrix_nogil(s)
    m2 = dtw.distance_matrix(s, compact=True)
    correct = np.array([1.41421356, 1.73205081, 1.41421356])
    assert m[0] == pytest.approx(math.sqrt(2))
    assert m2[0] == pytest.approx(math.sqrt(2))
    np.testing.assert_almost_equal(correct, m, decimal=4)
    np.testing.assert_almost_equal(correct, m2, decimal=4)
github wannesm / dtaidistance / tests / test_dtw.py View on Github external
def test_distance_matrix1_e():
    s = [[0., 0, 1, 2, 1, 0, 1, 0, 0],
         [0., 1, 2, 0, 0, 0, 0, 0, 0],
         [1., 2, 0, 0, 0, 0, 0, 1]]
    s = [np.array(si) for si in s]
    m = dtw_c.distance_matrix_nogil(s, is_parallel=True)
    m = dtw.distances_array_to_matrix(m, len(s))
    print(m)
    assert m[0, 1] == pytest.approx(math.sqrt(2))
github wannesm / dtaidistance / tests / test_dtw.py View on Github external
def test_distance_matrix2_e():
    n = 1
    nn = 1
    s = [[0., 0, 1, 2, 1, 0, 1, 0, 0] * n,
         [0., 1, 2, 0, 0, 0, 0, 0, 0] * n,
         [1., 2, 0, 0, 0, 0, 0, 1] * n] * nn
    s = [np.array(si) for si in s]
    m1 = dtw_c.distance_matrix_nogil(s, is_parallel=True)
    m1 = dtw.distances_array_to_matrix(m1, len(s))
    m2 = dtw.distance_matrix(s, parallel=True, use_c=True, use_nogil=True)
    assert m1[0, 1] == math.sqrt(2) * n, "m1[0,1]={} != {}".format(m1[0, 1], math.sqrt(2) * n)
    assert m2[0, 1] == math.sqrt(2) * n, "m2[0,1]={} != {}".format(m2[0, 1], math.sqrt(2) * n)
github wannesm / dtaidistance / tests / test_dtw.py View on Github external
def test_distance_matrix1_d():
    s = [[0., 0, 1, 2, 1, 0, 1, 0, 0],
         [0., 1, 2, 0, 0, 0, 0, 0, 0],
         [1., 2, 0, 0, 0, 0, 0, 1]]
    s = [np.array(si) for si in s]
    m = dtw_c.distance_matrix_nogil(s)
    m = dtw.distances_array_to_matrix(m, len(s))
    assert m[0, 1] == pytest.approx(math.sqrt(2))
github wannesm / dtaidistance / tests / test_cython.py View on Github external
def test_numpymatrix_transpose():
    """Passing a matrix instead of a list failed because the array is now a
    view instead of the original data structure."""
    s = np.array([
        [0., 0., 1.,],
        [0, 1, 2],
        [1, 2, 0],
        [2, 0, 0],
        [1, 0, 0],
        [0, 0, 0],
        [1, 0, 0],
        [0, 0, 1],
        [0, 0, 0]
    ]).T
    m = dtw_c.distance_matrix_nogil(s)
    m = dtw.distances_array_to_matrix(m, len(s))
    m2 = dtw.distance_matrix(s)
    correct = np.array([
        [np.inf, 1.41421356, 1.73205081],
        [np.inf, np.inf,     1.41421356],
        [np.inf, np.inf,     np.inf]])
    assert m[0, 1] == pytest.approx(math.sqrt(2))
    assert m2[0, 1] == pytest.approx(math.sqrt(2))
    np.testing.assert_almost_equal(correct, m, decimal=4)
    np.testing.assert_almost_equal(correct, m2, decimal=4)