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test_period.py
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test_period.py
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from numpy import arange, array, convolve, exp, float64, pi, random, sin, zeros
from cogent3.maths.period import _autocorr_inner2 as py_autocorr_inner
from cogent3.maths.period import _goertzel_inner as py_goertzel_inner
from cogent3.maths.period import _ipdft_inner2 as py_ipdft_inner
from cogent3.maths.period import auto_corr, dft, goertzel, hybrid, ipdft
from cogent3.maths.period_numba import autocorr_inner as numba_autocorr_inner
from cogent3.maths.period_numba import goertzel_inner as numba_goertzel_inner
from cogent3.maths.period_numba import ipdft_inner as numba_ipdft_inner
from cogent3.util.unit_test import TestCase, main
__author__ = "Hua Ying, Julien Epps and Gavin Huttley"
__copyright__ = "Copyright 2007-2020, The Cogent Project"
__credits__ = ["Julien Epps", "Hua Ying", "Gavin Huttley"]
__license__ = "BSD-3"
__version__ = "2020.7.2a"
__maintainer__ = "Gavin Huttley"
__email__ = "Gavin.Huttley@anu.edu.au"
__status__ = "Production"
class TestPeriod(TestCase):
def setUp(self):
t = arange(0, 10, 0.1)
n = random.randn(len(t))
nse = convolve(n, exp(-t / 0.05)) * 0.1
nse = nse[: len(t)]
self.sig = sin(2 * pi * t) + nse
self.p = 10
def test_inner_funcs(self):
"""python and pyrexed implementation should be the same"""
x = array(
[
0.04874203,
0.56831373,
0.94267804,
0.95664485,
0.60719478,
-0.09037356,
-0.69897319,
-1.11239811,
-0.84127485,
-0.56281126,
0.02301213,
0.56250284,
1.0258557,
1.03906527,
0.69885916,
0.10103556,
-0.43248024,
-1.03160503,
-0.84901545,
-0.84934356,
0.00323728,
0.44344594,
0.97736748,
1.01635433,
0.38538423,
0.09869918,
-0.60441861,
-0.90175391,
-1.00166887,
-0.66303249,
-0.02070569,
0.76520328,
0.93462426,
0.97011673,
0.63199999,
0.0764678,
-0.55680168,
-0.92028808,
-0.98481451,
-0.57600588,
0.0482667,
0.57572519,
1.02077883,
0.93271663,
0.41581696,
-0.07639671,
-0.71426286,
-0.97730119,
-1.0370596,
-0.67919572,
0.03779302,
0.60408759,
0.87826068,
0.79126442,
0.69769622,
0.01419442,
-0.42917556,
-1.00100485,
-0.83945546,
-0.55746313,
0.12730859,
0.60057659,
0.98059721,
0.83275501,
0.69031804,
0.02277554,
-0.63982729,
-1.23680355,
-0.79477887,
-0.67773375,
-0.05204714,
0.51765381,
0.77691955,
0.8996709,
0.5153137,
0.01840839,
-0.65124866,
-1.13269058,
-0.92342177,
-0.45673709,
0.11212881,
0.50153941,
1.09329507,
0.96457193,
0.80271578,
-0.0041043,
-0.81750772,
-0.99259986,
-0.92343788,
-0.57694955,
0.13982059,
0.56653375,
0.82217563,
0.85162513,
0.3984116,
-0.18937514,
-0.65304629,
-1.0067146,
-1.0037422,
-0.68011283,
]
)
N = 100
period = 10
self.assertFloatEqual(
py_goertzel_inner(x, N, period), numba_goertzel_inner(x, N, period)
)
ulim = 8
N = 8
x = array([0.0, 1.0, 0.0, -1.0, 0.0, 1.0, 0.0, -1.0])
X = zeros(8, dtype="complex128")
W = array(
[
1.00000000e00 + 2.44929360e-16j,
-1.00000000e00 - 1.22464680e-16j,
-5.00000000e-01 - 8.66025404e-01j,
6.12323400e-17 - 1.00000000e00j,
3.09016994e-01 - 9.51056516e-01j,
5.00000000e-01 - 8.66025404e-01j,
6.23489802e-01 - 7.81831482e-01j,
7.07106781e-01 - 7.07106781e-01j,
]
)
py_result = py_ipdft_inner(x, X, W, ulim, N)
numba_result = numba_ipdft_inner(x, X, W, ulim, N)
for i, j in zip(py_result, numba_result):
self.assertFloatEqual(abs(i), abs(j))
x = array(
[
-0.07827614,
0.56637551,
1.01320526,
1.01536245,
0.63548361,
0.08560101,
-0.46094955,
-0.78065656,
-0.8893556,
-0.56514145,
0.02325272,
0.63660719,
0.86291302,
0.82953598,
0.5706848,
0.11655242,
-0.6472655,
-0.86178218,
-0.96495057,
-0.76098445,
-0.18911517,
0.59280646,
1.00248693,
0.89241423,
0.52475111,
-0.01620599,
-0.60199278,
-0.98279829,
-1.12469771,
-0.61355799,
0.04321191,
0.52784788,
0.68508784,
0.86015123,
0.66825756,
-0.0802846,
-0.63626753,
-0.93023345,
-0.99129547,
-0.46891033,
0.04145813,
0.71226518,
1.01499246,
0.94726778,
0.63598143,
-0.21920589,
-0.48071702,
-0.86041579,
-0.9046141,
-0.55714746,
-0.10052384,
0.69708969,
1.02575789,
1.16524031,
0.49895282,
-0.13068573,
-0.45770419,
-0.86155787,
-0.9230734,
-0.6590525,
-0.05072955,
0.52380317,
1.02674335,
0.87778499,
0.4303284,
-0.01855665,
-0.62858193,
-0.93954774,
-0.94257301,
-0.49692951,
0.00699347,
0.69049074,
0.93906549,
1.06339809,
0.69337543,
0.00252569,
-0.57825881,
-0.88460603,
-0.99259672,
-0.73535697,
0.12064751,
0.91159174,
0.88966993,
1.02159917,
0.43479926,
-0.06159005,
-0.61782651,
-0.95284676,
-0.8218889,
-0.52166419,
0.021961,
0.52268762,
0.79428288,
1.01642697,
0.49060377,
-0.02183994,
-0.52743836,
-0.99363909,
-1.02963821,
-0.64249996,
]
)
py_xc = zeros(2 * len(x) - 1, dtype=float64)
numba_xc = py_xc.copy()
N = 100
py_autocorr_inner(x, py_xc, N)
numba_autocorr_inner(x, numba_xc, N)
for i, j in zip(py_xc, numba_xc):
self.assertFloatEqual(i, j)
def test_autocorr(self):
"""correctly compute autocorrelation"""
s = [1, 1, 1, 1]
X, periods = auto_corr(s, llim=-3, ulim=None)
exp_X = array([1, 2, 3, 4, 3, 2, 1], dtype=float)
self.assertEqual(X, exp_X)
auto_x, auto_periods = auto_corr(self.sig, llim=2, ulim=50)
max_idx = list(auto_x).index(max(auto_x))
auto_p = auto_periods[max_idx]
self.assertEqual(auto_p, self.p)
def test_dft(self):
"""correctly compute discrete fourier transform"""
dft_x, dft_periods = dft(self.sig)
dft_x = abs(dft_x)
max_idx = list(dft_x).index(max(dft_x))
dft_p = dft_periods[max_idx]
self.assertEqual(int(dft_p), self.p)
def test_ipdft(self):
"""correctly compute integer discrete fourier transform"""
s = [0, 1, 0, -1, 0, 1, 0, -1]
X, periods = ipdft(s, llim=1, ulim=len(s))
exp_X = abs(
array(
[
0,
0,
-1.5 + 0.866j,
-4j,
2.927 - 0.951j,
1.5 + 0.866j,
0.302 + 0.627j,
0,
]
)
)
X = abs(X)
self.assertFloatEqual(X, exp_X, eps=1e-3)
ipdft_x, ipdft_periods = ipdft(self.sig, llim=2, ulim=50)
ipdft_x = abs(ipdft_x)
max_idx = list(ipdft_x).index(max(ipdft_x))
ipdft_p = ipdft_periods[max_idx]
self.assertEqual(ipdft_p, self.p)
def test_goertzel(self):
"""goertzel and ipdft should be the same"""
ipdft_pwr, ipdft_prd = ipdft(self.sig, llim=10, ulim=10)
self.assertFloatEqual(goertzel(self.sig, 10), ipdft_pwr)
def test_hybrid(self):
"""correctly compute hybrid statistic"""
hybrid_x, hybrid_periods = hybrid(self.sig, llim=None, ulim=50)
hybrid_x = abs(hybrid_x)
max_idx = list(hybrid_x).index(max(hybrid_x))
hybrid_p = hybrid_periods[max_idx]
self.assertEqual(hybrid_p, self.p)
def test_hybrid_returns_all(self):
"""correctly returns hybrid, ipdft and autocorr statistics"""
ipdft_pwr, ipdft_prd = ipdft(self.sig, llim=2, ulim=50)
auto_x, auto_periods = auto_corr(self.sig, llim=2, ulim=50)
hybrid_x, hybrid_periods = hybrid(self.sig, llim=None, ulim=50)
hybrid_ipdft_autocorr_stats, hybrid_periods = hybrid(
self.sig, llim=None, ulim=50, return_all=True
)
self.assertEqual(hybrid_ipdft_autocorr_stats[0], hybrid_x)
self.assertEqual(hybrid_ipdft_autocorr_stats[1], ipdft_pwr)
self.assertEqual(hybrid_ipdft_autocorr_stats[2], auto_x)
ipdft_pwr, ipdft_prd = ipdft(self.sig, llim=10, ulim=10)
auto_x, auto_periods = auto_corr(self.sig, llim=10, ulim=10)
hybrid_x, hybrid_periods = hybrid(self.sig, llim=10, ulim=10)
hybrid_ipdft_autocorr_stats, hybrid_periods = hybrid(
self.sig, llim=10, ulim=10, return_all=True
)
self.assertEqual(hybrid_ipdft_autocorr_stats[0], hybrid_x)
self.assertEqual(hybrid_ipdft_autocorr_stats[1], ipdft_pwr)
self.assertEqual(hybrid_ipdft_autocorr_stats[2], auto_x)
if __name__ == "__main__":
main()