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#! /usr/bin/env python
# Last Change: Fri Dec 15 10:00 PM 2006 J
from numpy.testing import *
from numpy.random import randn, seed
from numpy import correlate, array, concatenate, require, corrcoef
from numpy.fft import fft, ifft
from numpy.ctypeslib import ndpointer, load_library
from ctypes import c_uint
set_package_path()
from cdavid.autocorr import _raw_autocorr_1d, _raw_autocorr_1d_noncontiguous
from cdavid.autocorr import autocorr_oneside_nofft as autocorr
from cdavid.autocorr import autocorr_fft , nextpow2
from cdavid.autocorr import _autocorr_oneside_nofft_py as autocorr_py
restore_path()
import numpy
# number of decimals to check
nd = 20
# minimum number of correct decimals required
md = 12
a = array([1, 2, 3.])
b = a + 3
x = concatenate((a, b)).reshape(2, 3)
# float and double C order
xc = require(x, dtype = numpy.float64, requirements = 'C')
xcf = require(x, dtype = numpy.float32, requirements = 'C')
xc1 = xc[0]
xcf1 = xcf[0]
# float and double F order
xf = require(x, dtype = numpy.float64, requirements = 'FORTRAN')
xff = require(x, dtype = numpy.float32, requirements = 'FORTRAN')
xf1 = xf[0]
xff1 = xff[0]
# This class tests the C functions directly. This is more a debugging tool
# that a test case, as the tested functions are not part of the public API
class test_ctype_1d(NumpyTestCase):
def check_contiguous_double(self):
# double test
xt = xc1
yt = _raw_autocorr_1d(xt, xt.size - 1)
yr = correlate(xt, xt, mode = 'full')
yr = yr[xt.size-1:]
assert_array_equal(yt, yr)
def check_contiguous_float(self):
# float test
xt = xcf1
yt = _raw_autocorr_1d(xt, xt.size - 1)
yr = correlate(xt, xt, mode = 'full')
yr = yr[xt.size-1:]
assert_array_equal(yt, yr)
def check_non_contiguous_double(self):
# double test
xt = xf1
yt = _raw_autocorr_1d_noncontiguous(xt, xt.size - 1)
yr = correlate(xt, xt, mode = 'full')
yr = yr[xt.size-1:]
assert_array_equal(yt, yr)
def check_non_contiguous_float(self):
# float test
xt = xff1
yt = _raw_autocorr_1d_noncontiguous(xt, xt.size - 1)
yr = correlate(xt, xt, mode = 'full')
yr = yr[xt.size-1:]
assert_array_equal(yt, yr)
# Test autocorrelation for rank 1 arrays
class test_autocorr_1d(NumpyTestCase):
def check_contiguous_double(self):
# double test
xt = xc1
yt = autocorr(xt, xt.size - 1)
yr = correlate(xt, xt, mode = 'full')
yr = yr[xt.size-1:]
assert_array_equal(yt, yr)
def check_contiguous_float(self):
# float test
xt = xcf1
yt = autocorr(xt, xt.size - 1)
yr = correlate(xt, xt, mode = 'full')
yr = yr[xt.size-1:]
assert_array_equal(yt, yr)
def check_non_contiguous_double(self):
# double test
xt = xf1
yt = autocorr(xt, xt.size - 1)
yr = correlate(xt, xt, mode = 'full')
yr = yr[xt.size-1:]
assert_array_equal(yt, yr)
def check_non_contiguous_float(self):
# float test
xt = xff1
yt = autocorr(xt, xt.size - 1)
yr = correlate(xt, xt, mode = 'full')
yr = yr[xt.size-1:]
assert_array_equal(yt, yr)
# This class is a pure python implementation of autocorrelation
# with rank 2 arrays. This will be used in the above test cases;
# this function implements the expected behaviour of the public
# autocorr function.
class test_autocorr_py(NumpyTestCase):
def check_full(self):
xt = xc
axis = -1
lag = xt.shape[axis] - 1
yt = autocorr_py(xt, lag, axis = axis)
yr = yt.copy()
for i in range(xt.shape[(axis +1) % 2]):
tmp = correlate(xt[i], xt[i], 'full')
center = xt[i].size - 1
assert_array_equal(tmp[center:center+1+lag], yt[i])
xt = xc
axis = 0
lag = xt.shape[axis] - 1
yt = autocorr_py(xt, lag, axis = axis)
yr = yt.copy()
for i in range(xt.shape[(axis +1) % 2]):
tmp = correlate(xt[:, i], xt[:, i], 'full')
center = xt[:,i].size - 1
assert_array_equal(tmp[center:center+1+lag], yt[:, i])
def check_partial(self):
xt = xc
axis = -1
lag = 1
yt = autocorr_py(xt, lag, axis = axis)
yr = yt.copy()
for i in range(xt.shape[(axis +1) % 2]):
tmp = correlate(xt[i], xt[i], 'full')
center = xt[i].size - 1
assert_array_equal(tmp[center:center+1+lag], yt[i])
xt = xc
axis = 0
lag = 1
yt = autocorr_py(xt, lag, axis = axis)
yr = yt.copy()
for i in range(xt.shape[(axis +1) % 2]):
tmp = correlate(xt[:, i], xt[:, i], 'full')
center = xt[:,i].size - 1
assert_array_equal(tmp[center:center+1+lag], yt[:, i])
# Test autocorrelation for rank 2 arrays
class test_autocorr_2d(NumpyTestCase):
def check_double_full(self):
# C, axis 1 test
xt = xc
axis = -1
lag = xt.shape[axis] - 1
yt = autocorr(xt, lag, axis = axis)
yr = autocorr_py(xt, lag, axis = axis)
assert_array_equal(yt, yr)
# C, axis 0 test
xt = xc
axis = 0
lag = xt.shape[axis] - 1
yt = autocorr(xt, lag, axis = axis)
yr = autocorr_py(xt, lag, axis = axis)
assert_array_equal(yt, yr)
# F, axis 0 test
xt = xf
axis = 0
lag = xt.shape[axis] - 1
yt = autocorr(xt, lag, axis = axis)
yr = autocorr_py(xt, lag, axis = axis)
assert_array_equal(yt, yr)
# F, axis 1 test
xt = xf
axis = -1
lag = xt.shape[axis] - 1
yt = autocorr(xt, lag, axis = axis)
yr = autocorr_py(xt, lag, axis = axis)
assert_array_equal(yt, yr)
def check_float(self):
# C, axis 1 test
xt = xcf
axis = -1
lag = xt.shape[axis] - 1
yt = autocorr(xt, lag, axis = axis)
yr = autocorr_py(xt, lag, axis = axis)
assert_array_equal(yt, yr)
# C, axis 0 test
xt = xcf
axis = 0
lag = xt.shape[axis] - 1
yt = autocorr(xt, lag, axis = axis)
yr = autocorr_py(xt, lag, axis = axis)
assert_array_equal(yt, yr)
# F, axis 0 test
xt = xff
axis = 0
lag = xt.shape[axis] - 1
yt = autocorr(xt, lag, axis = axis)
yr = autocorr_py(xt, lag, axis = axis)
assert_array_equal(yt, yr)
# F, axis 1 test
xt = xff
axis = -1
lag = xt.shape[axis] - 1
yt = autocorr(xt, lag, axis = axis)
yr = autocorr_py(xt, lag, axis = axis)
assert_array_equal(yt, yr)
def check_double_partial(self):
# C, axis 1 test
xt = xc
axis = -1
lag = 1
yt = autocorr(xt, lag, axis = axis)
yr = autocorr_py(xt, lag, axis = axis)
assert_array_equal(yt, yr)
# C, axis 0 test
xt = xc
axis = 0
lag = 0
yt = autocorr(xt, lag, axis = axis)
yr = autocorr_py(xt, lag, axis = axis)
assert_array_equal(yt, yr)
# F, axis 0 test
xt = xf
axis = 1
lag = xt.shape[axis] - 1
yt = autocorr(xt, lag, axis = axis)
yr = autocorr_py(xt, lag, axis = axis)
assert_array_equal(yt, yr)
# F, axis 1 test
xt = xf
axis = -1
lag = 1
yt = autocorr(xt, lag, axis = axis)
yr = autocorr_py(xt, lag, axis = axis)
assert_array_equal(yt, yr)
class test_autocorr_fft(NumpyTestCase):
n = 5
d = 3
def check_nextpow2(self):
assert(nextpow2(255) == 8)
assert(nextpow2(256) == 8)
assert(nextpow2(257) == 9)
def check_r1r(self):
"""real case, rank 1"""
a = randn(self.n)
aref = correlate(a, a, mode = 'full')
atest = autocorr_fft(a)
assert_array_almost_equal(atest, aref, decimal = md)
assert atest.dtype == a.dtype
def check_r1c(self):
"""complex case, rank 1"""
a = randn(self.n) + 1.0j * randn(self.n)
atest = autocorr_fft(a)
aref = numpy.sum(a * numpy.conj(a))
assert_array_almost_equal(atest[self.n - 1], aref, decimal = md)
assert atest.dtype == a.dtype
def check_r2c(self):
"""complex case, rank 2"""
pass
def check_r2r(self):
"""real case, rank 2"""
# axis 0
a = randn(self.n, self.d)
axis = 0
c = [correlate(a[:, i], a[:, i], mode = 'full') for i in range(self.d)]
aref = array(c).T
atest = autocorr_fft(a, axis = axis)
assert_array_almost_equal(atest, aref, decimal = md)
# axis 1
a = randn(self.n, self.d)
axis = 1
c = [correlate(a[i], a[i], mode = 'full') for i in range(self.n)]
aref = array(c)
atest = autocorr_fft(a, axis = axis)
assert_array_almost_equal(atest, aref, decimal = md)
if __name__ == "__main__":
NumpyTest().run()
#class test_autocorr_2d(NumpyTestCase):
# def check_double(self):
# # C, axis 1 test
# xt = xc
# axis = -1
# lag = xt.shape[axis] - 1
# yt = autocorr(xt, lag, axis = axis)
#
# yr = yt.copy()
# for i in range(xt.shape[(axis +1) % 2]):
# tmp = correlate(xt[i], xt[i], 'full')
# assert_array_equal(tmp[lag:], yt[i])
#
# # C, axis 0 test
# xt = xc
# axis = 0
# lag = xt.shape[axis] - 1
# yt = autocorr(xt, lag, axis = axis)
#
# yr = yt.copy()
# for i in range(xt.shape[(axis +1) % 2]):
# tmp = correlate(xt[:, i], xt[:, i], 'full')
# assert_array_equal(tmp[lag:], yt[:, i])
#
# # F, axis 0 test
# xt = xf
# axis = 0
# lag = xt.shape[axis] - 1
# yt = autocorr(xt, lag, axis = axis)
#
# yr = yt.copy()
# for i in range(xt.shape[(axis +1) % 2]):
# tmp = correlate(xt[:, i], xt[:, i], 'full')
# assert_array_equal(tmp[lag:], yt[:, i])
#
# # F, axis 1 test
# xt = xf
# axis = -1
# lag = xt.shape[axis] - 1
# yt = autocorr(xt, lag, axis = axis)
#
# yr = yt.copy()
# for i in range(xt.shape[(axis +1) % 2]):
# tmp = correlate(xt[i], xt[i], 'full')
# assert_array_equal(tmp[lag:], yt[i])
#
# def check_float(self):
# # C, axis 1 test
# xt = xcf
# axis = -1
# lag = xt.shape[axis] - 1
# yt = autocorr(xt, lag, axis = axis)
#
# yr = yt.copy()
# for i in range(xt.shape[(axis +1) % 2]):
# tmp = correlate(xt[i], xt[i], 'full')
# assert_array_equal(tmp[lag:], yt[i])
#
# # C, axis 0 test
# xt = xcf
# axis = 0
# lag = xt.shape[axis] - 1
# yt = autocorr(xt, lag, axis = axis)
#
# yr = yt.copy()
# for i in range(xt.shape[(axis +1) % 2]):
# tmp = correlate(xt[:, i], xt[:, i], 'full')
# assert_array_equal(tmp[lag:], yt[:, i])
#
# # F, axis 0 test
# xt = xff
# axis = 0
# lag = xt.shape[axis] - 1
# yt = autocorr(xt, lag, axis = axis)
#
# yr = yt.copy()
# for i in range(xt.shape[(axis +1) % 2]):
# tmp = correlate(xt[:, i], xt[:, i], 'full')
# assert_array_equal(tmp[lag:], yt[:, i])
#
# # F, axis 1 test
# xt = xff
# axis = -1
# lag = xt.shape[axis] - 1
# yt = autocorr(xt, lag, axis = axis)
#
# yr = yt.copy()
# for i in range(xt.shape[(axis +1) % 2]):
# tmp = correlate(xt[i], xt[i], 'full')
# assert_array_equal(tmp[lag:], yt[i])
#
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