def test_autocorr():
N = 128
ar_seq, _, _ = utils.ar_generator(N=N)
rxx = utils.autocorr(ar_seq)
npt.assert_(rxx[0] == rxx.max(), "Zero lag autocorrelation is not maximum autocorrelation")
rxx = utils.autocorr(ar_seq, all_lags=True)
npt.assert_(rxx[127] == rxx.max(), "Zero lag autocorrelation is not maximum autocorrelation")
def test_autocorr():
N = 128
ar_seq, _, _ = utils.ar_generator(N=N)
rxx = utils.autocorr(ar_seq)
yield nt.assert_true, rxx[0] == 1, "Zero lag autocorrelation is not equal to 1"
rxx = utils.autocorr(ar_seq, all_lags=True)
yield nt.assert_true, rxx[127] == 1, "Zero lag autocorrelation is not equal to 1"
def test_autocorr():
N = 128
ar_seq, _, _ = utils.ar_generator(N=N)
rxx = utils.autocorr(ar_seq)
nt.assert_true(rxx[0] == rxx.max(), \
'Zero lag autocorrelation is not maximum autocorrelation')
rxx = utils.autocorr(ar_seq, all_lags=True)
nt.assert_true(rxx[127] == rxx.max(), \
'Zero lag autocorrelation is not maximum autocorrelation')
def ar_nitime(x, order=1, center=False):
"""Derive a model of the noise present in the functional timeseries for
the calculation of the standardized DVARS.
- Borrowed from nipy.algorithms.AR_est_YW. aka "from nitime import
algorithms as alg".
:type x: Nibabel data
:param x: The vector of one voxel's timeseries.
:type order: int
:param order: (default: 1) Which lag of the autocorrelation of the
timeseries to use in the calculation.
:type center: bool
:param center: (default: False) Whether to center the timeseries (to
demean it).
:rtype: float
:return: The modeled noise value for the current voxel's timeseries.
"""
from nitime.lazy import scipy_linalg as linalg
import nitime.utils as utils
if center:
x = x.copy()
x = x - x.mean()
r_m = utils.autocorr(x)[:order + 1]
Tm = linalg.toeplitz(r_m[:order])
y = r_m[1:]
ak = linalg.solve(Tm, y)
return ak[0]
def ar_nitime(x, order=1, center=False):
"""Derive a model of the noise present in the functional timeseries for
the calculation of the standardized DVARS.
- Borrowed from nipy.algorithms.AR_est_YW. aka "from nitime import
algorithms as alg".
:type x: Nibabel data
:param x: The vector of one voxel's timeseries.
:type order: int
:param order: (default: 1) Which lag of the autocorrelation of the
timeseries to use in the calculation.
:type center: bool
:param center: (default: False) Whether to center the timeseries (to
demean it).
:rtype: float
:return: The modeled noise value for the current voxel's timeseries.
"""
from nitime.lazy import scipy_linalg as linalg
import nitime.utils as utils
if center:
x = x.copy()
x = x - x.mean()
r_m = utils.autocorr(x)[:order + 1]
Tm = linalg.toeplitz(r_m[:order])
y = r_m[1:]
ak = linalg.solve(Tm, y)
return ak[0]
def AR_est_YW(x, order, rxx=None):
r"""Determine the autoregressive (AR) model of a random process x using
the Yule Walker equations. The AR model takes this convention:
.. math::
x(n) = a(1)x(n-1) + a(2)x(n-2) + \dots + a(p)x(n-p) + e(n)
where e(n) is a zero-mean white noise process with variance sig_sq,
and p is the order of the AR model. This method returns the a_i and
sigma
The orthogonality property of minimum mean square error estimates
states that
.. math::
E\{e(n)x^{*}(n-k)\} = 0 \quad 1\leq k\leq p
Inserting the definition of the error signal into the equations above
yields the Yule Walker system of equations:
.. math::
R_{xx}(k) = \sum_{i=1}^{p}a(i)R_{xx}(k-i) \quad1\leq k\leq p
Similarly, the variance of the error process is
.. math::
E\{e(n)e^{*}(n)\} = E\{e(n)x^{*}(n)\} = R_{xx}(0)-\sum_{i=1}^{p}a(i)R^{*}(i)
Parameters
----------
x : ndarray
The sampled autoregressive random process
order : int
The order p of the AR system
rxx : ndarray (optional)
An optional, possibly unbiased estimate of the autocorrelation of x
Returns
-------
ak, sig_sq: The estimated AR coefficients and innovations variance
"""
if rxx is not None and type(rxx) == np.ndarray:
r_m = rxx[: order + 1]
else:
r_m = utils.autocorr(x)[: order + 1]
Tm = linalg.toeplitz(r_m[:order])
y = r_m[1:]
ak = linalg.solve(Tm, y)
sigma_v = r_m[0].real - np.dot(r_m[1:].conj(), ak).real
return ak, sigma_v
def AR_est_YW(x, order, rxx=None):
r"""Determine the autoregressive (AR) model of a random process x using
the Yule Walker equations. The AR model takes this convention:
.. math::
x(n) = a(1)x(n-1) + a(2)x(n-2) + \dots + a(p)x(n-p) + e(n)
where e(n) is a zero-mean white noise process with variance sig_sq,
and p is the order of the AR model. This method returns the a_i and
sigma
The orthogonality property of minimum mean square error estimates
states that
.. math::
E\{e(n)x^{*}(n-k)\} = 0 \quad 1\leq k\leq p
Inserting the definition of the error signal into the equations above
yields the Yule Walker system of equations:
.. math::
R_{xx}(k) = \sum_{i=1}^{p}a(i)R_{xx}(k-i) \quad1\leq k\leq p
Similarly, the variance of the error process is
.. math::
E\{e(n)e^{*}(n)\} = E\{e(n)x^{*}(n)\} = R_{xx}(0)-\sum_{i=1}^{p}a(i)R^{*}(i)
Parameters
----------
x : ndarray
The sampled autoregressive random process
order : int
The order p of the AR system
rxx : ndarray (optional)
An optional, possibly unbiased estimate of the autocorrelation of x
Returns
-------
ak, sig_sq : The estimated AR coefficients and innovations variance
"""
if rxx is not None and type(rxx) == np.ndarray:
r_m = rxx[:order + 1]
else:
r_m = utils.autocorr(x)[:order + 1]
Tm = linalg.toeplitz(r_m[:order])
y = r_m[1:]
ak = linalg.solve(Tm, y)
sigma_v = r_m[0].real - np.dot(r_m[1:].conj(), ak).real
return ak, sigma_v
def AR_est_LD(x, order, rxx=None):
"""Levinson-Durbin algorithm for solving the Hermitian Toeplitz
system R[m]w[m]=r[m+1]: (XXX review this definition for complex)
[[r(0) r(1) r(2) ... r(m-1)],
R[m] = [r*(1) r(0) r(1) ... r(m-2)],
[... ],
[r*(m-1) r*(m-2) r*(m-3)... r(0) ]]
r[m+1] = [r(1), r(2), ..., r(m)].T
r(k) = E{X(t+k)X*(t)}
and w[m] is the vector of m AR coefficients
Parameters
----------
x: ndarray
the zero-mean stochastic process
order : int
the AR model order--IE the rank of the system.
rxx : ndarray, optional
(at least) order+1 samples of the autocorrelation sequence
Returns
-------
ak, sig_sq
The AR coefficients for 1 <= k <= P, and the variance of the
driving white noise process
"""
if rxx is not None and type(rxx) == np.ndarray:
rxx_m = rxx[:order + 1]
else:
rxx_m = utils.autocorr(x)[:order + 1]
w = np.zeros((order+1,), rxx_m.dtype)
# intialize the recursion with the R[0]w[1]=r[1] solution (p=1)
b = rxx_m[0].real
w_k = rxx_m[1]/b
w[1] = w_k
p = 2
while p<=order:
b *= (1-(w_k*w_k.conj()).real)
w_k = (rxx_m[p] - (w[1:p]*rxx_m[1:p][::-1]).sum())/b
# update w_k from k=1,2,...,p-1
# with a correction from w*_i i=p-1,p-2,...,1
w[1:p] = w[1:p] - w_k*(w[1:p][::-1].conj())
w[p] = w_k
p += 1
b *= (1 - (w_k*w_k.conj()).real)
return w[1:], b
def ar_nitime(x, order=1, center=False):
"""
Borrowed from nipy.algorithms.AR_est_YW.
aka from nitime import algorithms as alg.
We could speed this up by having the autocorr only compute lag1.
"""
from nitime.lazy import scipy_linalg as linalg
import nitime.utils as utils
if center:
x = x.copy()
x = x - x.mean()
r_m = utils.autocorr(x)[:order + 1]
Tm = linalg.toeplitz(r_m[:order])
y = r_m[1:]
ak = linalg.solve(Tm, y)
return ak[0]
def ar_nitime(x, order=1, center=False):
"""
Borrowed from nipy.algorithms.AR_est_YW.
aka from nitime import algorithms as alg.
We could speed this up by having the autocorr only compute lag1.
"""
from nitime.lazy import scipy_linalg as linalg
import nitime.utils as utils
if center:
x = x.copy()
x = x - x.mean()
r_m = utils.autocorr(x)[:order + 1]
Tm = linalg.toeplitz(r_m[:order])
y = r_m[1:]
ak = linalg.solve(Tm, y)
return ak[0]
def AR_est_YW(x, order, rxx=None):
r"""Determine the autoregressive (AR) model of a random process x using
the Yule Walker equations. The AR model takes this convention:
x(n) = a(1)x(n-1) + a(2)x(n-2) + ... + a(P)x(n-P) + e(n)
where e(n) is a zero-mean white noise process with variance sig_sq,
and P is the order of the AR model. This method returns the a_i and
sigma
The orthogonality property of minimum mean square error estimates
yields the Yule Walker equations.
Parameters
----------
x : ndarray
The sampled autoregressive random process
order : int
The order P of the AR system
rxx : ndarray (optional)
An optional, possibly unbiased estimate of the autocorrelation of x
Returns
-------
ak, sig_sq: The estimated AR coefficients and innovations variance
"""
if rxx is not None and type(rxx) == np.ndarray:
r_m = rxx[:order + 1]
else:
r_m = utils.autocorr(x)[:order + 1]
Tm = linalg.toeplitz(r_m[:order])
y = r_m[1:]
ak = linalg.solve(Tm, y)
sigma_v = r_m[0].real - np.dot(r_m[1:].conj(), ak).real
return ak, sigma_v
def AR_est_LD(x, order, rxx=None):
r"""Levinson-Durbin algorithm for solving the Hermitian Toeplitz
system of Yule-Walker equations in the AR estimation problem
.. math::
T^{(p)}a^{(p)} = \gamma^{(p+1)}
where
.. math::
:nowrap:
\begin{align*}
T^{(p)} &= \begin{pmatrix}
R_{0} & R_{1}^{*} & \cdots & R_{p-1}^{*}\\
R_{1} & R_{0} & \cdots & R_{p-2}^{*}\\
\vdots & \vdots & \ddots & \vdots\\
R_{p-1}^{*} & R_{p-2}^{*} & \cdots & R_{0}
\end{pmatrix}\\
a^{(p)} &=\begin{pmatrix} a_1 & a_2 & \cdots a_p \end{pmatrix}^{T}\\
\gamma^{(p+1)}&=\begin{pmatrix}R_1 & R_2 & \cdots & R_p \end{pmatrix}^{T}
\end{align*}
and :math:`R_k` is the autocorrelation of the kth lag
Parameters
----------
x: ndarray
the zero-mean stochastic process
order : int
the AR model order--IE the rank of the system.
rxx : ndarray, optional
(at least) order+1 samples of the autocorrelation sequence
Returns
-------
ak, sig_sq
The AR coefficients for 1 <= k <= p, and the variance of the
driving white noise process
"""
if rxx is not None and type(rxx) == np.ndarray:
rxx_m = rxx[: order + 1]
else:
rxx_m = utils.autocorr(x)[: order + 1]
w = np.zeros((order + 1,), rxx_m.dtype)
# intialize the recursion with the R[0]w[1]=r[1] solution (p=1)
b = rxx_m[0].real
w_k = rxx_m[1] / b
w[1] = w_k
p = 2
while p <= order:
b *= 1 - (w_k * w_k.conj()).real
w_k = (rxx_m[p] - (w[1:p] * rxx_m[1:p][::-1]).sum()) / b
# update w_k from k=1,2,...,p-1
# with a correction from w*_i i=p-1,p-2,...,1
w[1:p] = w[1:p] - w_k * w[1:p][::-1].conj()
w[p] = w_k
p += 1
b *= 1 - (w_k * w_k.conj()).real
return w[1:], b
def dpss_windows(N, NW, Kmax, interp_from=None, interp_kind='linear'):
"""
Returns the Discrete Prolate Spheroidal Sequences of orders [0,Kmax-1]
for a given frequency-spacing multiple NW and sequence length N.
Paramters
---------
N : int
sequence length
NW : float, unitless
standardized half bandwidth corresponding to 2NW = BW*f0 = BW*N/dt
but with dt taken as 1
Kmax : int
number of DPSS windows to return is Kmax (orders 0 through Kmax-1)
interp_from: int (optional)
The dpss will can calculated using interpolation from a set of dpss
with the same NW and Kmax, but shorter N. This is the length of this
shorter set of dpss windows.
interp_kind: str (optional)
This input variable is passed to scipy.interpolate.interp1d and
specifies the kind of interpolation as a string ('linear', 'nearest',
'zero', 'slinear', 'quadratic, 'cubic') or as an integer specifying the
order of the spline interpolator to use.
Returns
-------
v, e : tuple,
v is an array of DPSS windows shaped (Kmax, N)
e are the eigenvalues
Notes
-----
Tridiagonal form of DPSS calculation from:
Slepian, D. Prolate spheroidal wave functions, Fourier analysis, and
uncertainty V: The discrete case. Bell System Technical Journal,
Volume 57 (1978), 1371430
"""
Kmax = int(Kmax)
W = float(NW) / N
nidx = np.arange(N, dtype='d')
# In this case, we create the dpss windows of the smaller size
# (interp_from) and then interpolate to the larger size (N)
if interp_from is not None:
if interp_from > N:
e_s = 'In dpss_windows, interp_from is: %s ' % interp_from
e_s += 'and N is: %s. ' % N
e_s += 'Please enter interp_from smaller than N.'
raise ValueError(e_s)
dpss = []
d, e = dpss_windows(interp_from, NW, Kmax)
for this_d in d:
x = np.arange(this_d.shape[-1])
I = interpolate.interp1d(x, this_d, kind=interp_kind)
d_temp = I(np.arange(0, this_d.shape[-1] - 1,
float(this_d.shape[-1] - 1) / N))
# Rescale:
d_temp = d_temp / np.sqrt(np.sum(d_temp ** 2))
dpss.append(d_temp)
dpss = np.array(dpss)
else:
# here we want to set up an optimization problem to find a sequence
# whose energy is maximally concentrated within band [-W,W].
# Thus, the measure lambda(T,W) is the ratio between the energy within
# that band, and the total energy. This leads to the eigen-system
# (A - (l1)I)v = 0, where the eigenvector corresponding to the largest
# eigenvalue is the sequence with maximally concentrated energy. The
# collection of eigenvectors of this system are called Slepian
# sequences, or discrete prolate spheroidal sequences (DPSS). Only the
# first K, K = 2NW/dt orders of DPSS will exhibit good spectral
# concentration
# [see http://en.wikipedia.org/wiki/Spectral_concentration_problem]
# Here I set up an alternative symmetric tri-diagonal eigenvalue
# problem such that
# (B - (l2)I)v = 0, and v are our DPSS (but eigenvalues l2 != l1)
# the main diagonal = ([N-1-2*t]/2)**2 cos(2PIW), t=[0,1,2,...,N-1]
# and the first off-diagonal = t(N-t)/2, t=[1,2,...,N-1]
# [see Percival and Walden, 1993]
diagonal = ((N - 1 - 2 * nidx) / 2.) ** 2 * np.cos(2 * np.pi * W)
off_diag = np.zeros_like(nidx)
off_diag[:-1] = nidx[1:] * (N - nidx[1:]) / 2.
# put the diagonals in LAPACK "packed" storage
ab = np.zeros((2, N), 'd')
ab[1] = diagonal
ab[0, 1:] = off_diag[:-1]
# only calculate the highest Kmax eigenvalues
w = linalg.eigvals_banded(ab, select='i',
select_range=(N - Kmax, N - 1))
w = w[::-1]
# find the corresponding eigenvectors via inverse iteration
t = np.linspace(0, np.pi, N)
dpss = np.zeros((Kmax, N), 'd')
for k in xrange(Kmax):
dpss[k] = utils.tridi_inverse_iteration(
diagonal, off_diag, w[k], x0=np.sin((k + 1) * t)
)
# By convention (Percival and Walden, 1993 pg 379)
# * symmetric tapers (k=0,2,4,...) should have a positive average.
# * antisymmetric tapers should begin with a positive lobe
fix_symmetric = (dpss[0::2].sum(axis=1) < 0)
for i, f in enumerate(fix_symmetric):
if f:
dpss[2 * i] *= -1
fix_skew = (dpss[1::2, 1] < 0)
for i, f in enumerate(fix_skew):
if f:
dpss[2 * i + 1] *= -1
# Now find the eigenvalues of the original spectral concentration problem
# Use the autocorr sequence technique from Percival and Walden, 1993 pg 390
dpss_rxx = utils.autocorr(dpss) * N
r = 4 * W * np.sinc(2 * W * nidx)
r[0] = 2 * W
eigvals = np.dot(dpss_rxx, r)
return dpss, eigvals
def AR_est_LD(x, order, rxx=None):
r"""Levinson-Durbin algorithm for solving the Hermitian Toeplitz
system of Yule-Walker equations in the AR estimation problem
.. math::
T^{(p)}a^{(p)} = \gamma^{(p+1)}
where
.. math::
:nowrap:
\begin{align*}
T^{(p)} &= \begin{pmatrix}
R_{0} & R_{1}^{*} & \cdots & R_{p-1}^{*}\\
R_{1} & R_{0} & \cdots & R_{p-2}^{*}\\
\vdots & \vdots & \ddots & \vdots\\
R_{p-1}^{*} & R_{p-2}^{*} & \cdots & R_{0}
\end{pmatrix}\\
a^{(p)} &=\begin{pmatrix} a_1 & a_2 & \cdots a_p \end{pmatrix}^{T}\\
\gamma^{(p+1)}&=\begin{pmatrix}R_1 & R_2 & \cdots & R_p \end{pmatrix}^{T}
\end{align*}
and :math:`R_k` is the autocorrelation of the kth lag
Parameters
----------
x : ndarray
the zero-mean stochastic process
order : int
the AR model order--IE the rank of the system.
rxx : ndarray, optional
(at least) order+1 samples of the autocorrelation sequence
Returns
-------
ak, sig_sq
The AR coefficients for 1 <= k <= p, and the variance of the
driving white noise process
"""
if rxx is not None and type(rxx) == np.ndarray:
rxx_m = rxx[:order + 1]
else:
rxx_m = utils.autocorr(x)[:order + 1]
w = np.zeros((order + 1, ), rxx_m.dtype)
# initialize the recursion with the R[0]w[1]=r[1] solution (p=1)
b = rxx_m[0].real
w_k = rxx_m[1] / b
w[1] = w_k
p = 2
while p <= order:
b *= 1 - (w_k * w_k.conj()).real
w_k = (rxx_m[p] - (w[1:p] * rxx_m[1:p][::-1]).sum()) / b
# update w_k from k=1,2,...,p-1
# with a correction from w*_i i=p-1,p-2,...,1
w[1:p] = w[1:p] - w_k * w[1:p][::-1].conj()
w[p] = w_k
p += 1
b *= 1 - (w_k * w_k.conj()).real
return w[1:], b