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Refactored smoothn into SmoothNd and _Filter classes

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master
Per A Brodtkorb 9 years ago
parent 8e411b384d
commit f207791b6e
1 changed files with 289 additions and 211 deletions
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wafo/sg_filter.py
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@ -286,6 +286,238 @@ def evar(y):
return noisevar
class _Filter(object):
def __init__(self, y, z0, weightstr, weights, s, robust, maxiter, tolz):
self.y = y
self.z0 = z0
self.weightstr = weightstr
self.s = s
self.robust = robust
self.maxiter = maxiter
self.tolz = tolz
self.auto_smooth = s is None
self.is_finite = np.isfinite(y)
self.nof = self.is_finite.sum() # number of finite elements
self.W = self._normalized_weights(weights, self.is_finite)
self.gamma = self._gamma_fun(y)
self.N = self._tensor_rank(y)
self.s_min, self.s_max = self._smoothness_limits(self.N)
# Initialize before iterating
self.Wtot = self.W
self.is_weighted = (self.W < 1).any() # Weighted or missing data?
self.z0 = self._get_start_condition(y, z0)
self.y[~self.is_finite] = 0 # arbitrary values for missing y-data
# Error on p. Smoothness parameter s = 10^p
self.errp = 0.1
# Relaxation factor RF: to speedup convergence
self.RF = 1.75 if self.is_weighted else 1.0
@staticmethod
def _tensor_rank(y):
"""tensor rank of the y-array"""
return (np.array(y.shape) != 1).sum()
@staticmethod
def _smoothness_limits(n):
"""
Return upper and lower bound for the smoothness parameter
The average leverage (h) is by definition in [0 1]. Weak smoothing
occurs if h is close to 1, while over-smoothing appears when h is
near 0. Upper and lower bounds for h are given to avoid under- or
over-smoothing. See equation relating h to the smoothness parameter
(Equation #12 in the referenced CSDA paper).
"""
h_min = 1e-6 ** (2. / n)
h_max = 0.99 ** (2. / n)
s_min = (((1 + sqrt(1 + 8 * h_max)) / 4. / h_max) ** 2 - 1) / 16
s_max = (((1 + sqrt(1 + 8 * h_min)) / 4. / h_min) ** 2 - 1) / 16
return s_min, s_max
@staticmethod
def _lambda_tensor(y):
"""
Return the Lambda tensor
Lambda contains the eigenvalues of the difference matrix used in this
penalized least squares process.
"""
d = y.ndim
Lambda = np.zeros(y.shape)
shape0 = [1, ] * d
for i in range(d):
shape0[i] = y.shape[i]
Lambda = Lambda + \
np.cos(pi * np.arange(y.shape[i]) / y.shape[i]).reshape(shape0)
shape0[i] = 1
Lambda = -2 * (d - Lambda)
return Lambda
def _gamma_fun(self, y):
Lambda = self._lambda_tensor(y)
def gamma(s):
return 1. / (1 + s * Lambda ** 2)
return gamma
@staticmethod
def _initial_guess(y, I):
# Initial Guess with weighted/missing data
# nearest neighbor interpolation (in case of missing values)
z = y
if (1 - I).any():
notI = ~I
z, L = distance_transform_edt(notI, return_indices=True)
z[notI] = y[L.flat[notI]]
# coarse fast smoothing using one-tenth of the DCT coefficients
shape = z.shape
d = z.ndim
z = dctn(z)
for k in range(d):
z[int((shape[k] + 0.5) / 10) + 1::, ...] = 0
z = z.reshape(np.roll(shape, -k))
z = z.transpose(np.roll(range(d), -1))
# z = shiftdim(z,1);
return idctn(z)
def _get_start_condition(self, y, z0):
# Initial conditions for z
if self.is_weighted:
# With weighted/missing data
# An initial guess is provided to ensure faster convergence. For
# that purpose, a nearest neighbor interpolation followed by a
# coarse smoothing are performed.
if z0 is None:
z = self._initial_guess(y, self.is_finite)
else:
z = z0 # an initial guess (z0) has been provided
else:
z = np.zeros(y.shape)
return z
@staticmethod
def _normalized_weights(weight, is_finite):
""" Return normalized weights.
Zero weights are assigned to not finite values (Inf or NaN),
(Inf/NaN values = missing data).
"""
weights = weight * is_finite
if (weights < 0).any():
raise ValueError('Weights must all be >=0')
return weights / weights.max()
@staticmethod
def _studentized_residuals(r, I, h):
median_abs_deviation = np.median(abs(r[I] - np.median(r[I])))
return abs(r / (1.4826 * median_abs_deviation) / sqrt(1 - h))
def robust_weights(self, r, I, h):
"""Return weights for robust smoothing."""
def bisquare(u):
c = 4.685
return (1 - (u / c) ** 2) ** 2 * ((u / c) < 1)
def talworth(u):
c = 2.795
return u < c
def cauchy(u):
c = 2.385
return 1. / (1 + (u / c) ** 2)
u = self._studentized_residuals(r, I, h)
wfun = {'cauchy': cauchy, 'talworth': talworth}.get(self.weightstr,
bisquare)
weights = wfun(u)
weights[np.isnan(weights)] = 0
return weights
@staticmethod
def _average_leverage(s, N):
h = sqrt(1 + 16 * s)
h = sqrt(1 + h) / sqrt(2) / h
return h ** N
def check_smooth_parameter(self, s):
if self.auto_smooth:
if abs(np.log10(s) - np.log10(self.s_min)) < self.errp:
warnings.warn('''s = %g: the lower bound for s has been reached.
Put s as an input variable if required.''' % s)
elif abs(np.log10(s) - np.log10(self.s_max)) < self.errp:
warnings.warn('''s = %g: the Upper bound for s has been reached.
Put s as an input variable if required.''' % s)
def gcv(self, p, aow, DCTy, y, Wtot):
# Search the smoothing parameter s that minimizes the GCV score
s = 10.0 ** p
Gamma = self.gamma(s)
if aow > 0.9: # aow = 1 means that all of the data are equally weighted
# very much faster: does not require any inverse DCT
residual = DCTy.ravel() * (Gamma.ravel() - 1)
else:
# take account of the weights to calculate RSS:
is_finite = self.is_finite
yhat = idctn(Gamma * DCTy)
residual = sqrt(Wtot[is_finite]) * (y[is_finite] - yhat[is_finite])
TrH = Gamma.sum()
RSS = linalg.norm(residual)**2 # Residual sum-of-squares
GCVscore = RSS / self.nof / (1.0 - TrH / y.size) ** 2
return GCVscore
def __call__(self, z, s):
auto_smooth = self.auto_smooth
norm = linalg.norm
y = self.y
Wtot = self.Wtot
Gamma = 1
if s is not None:
Gamma = self.gamma(s)
# "amount" of weights (see the function GCVscore)
aow = Wtot.sum() / y.size # 0 < aow <= 1
for nit in range(self.maxiter):
DCTy = dctn(Wtot * (y - z) + z)
if auto_smooth and not np.remainder(np.log2(nit + 1), 1):
# The generalized cross-validation (GCV) method is used.
# We seek the smoothing parameter s that minimizes the GCV
# score i.e. s = Argmin(GCVscore).
# Because this process is time-consuming, it is performed from
# time to time (when nit is a power of 2)
log10s = optimize.fminbound(
self.gcv, np.log10(self.s_min), np.log10(self.s_max),
args=(aow, DCTy, y, Wtot),
xtol=self.errp, full_output=False, disp=False)
s = 10 ** log10s
Gamma = self.gamma(s)
z0 = z
z = self.RF * idctn(Gamma * DCTy) + (1 - self.RF) * z
# if no weighted/missing data => tol=0 (no iteration)
tol = norm(z0.ravel() - z.ravel()) / norm(z.ravel())
converged = tol <= self.tolz or not self.is_weighted
if converged:
break
if self.robust:
# -- Robust Smoothing: iteratively re-weighted process
h = self._average_leverage(s, self.N)
self.Wtot = self.W * self.robust_weights(y - z, self.is_finite, h)
# re-initialize for another iterative weighted process
self.is_weighted = True
return z, s, converged
def smoothn(data, s=None, weight=None, robust=False, z0=None, tolz=1e-3,
maxiter=100, fulloutput=False):
'''
@ -414,219 +646,65 @@ def smoothn(data, s=None, weight=None, robust=False, z0=None, tolz=1e-3,
http://www.biomecardio.com/matlab/smoothn.html
for more details about SMOOTHN
'''
return SmoothNd(s, weight, robust, z0, tolz, maxiter, fulloutput)(data)
y = np.atleast_1d(data)
sizy = y.shape
noe = y.size
if noe < 2:
return data
weightstr = 'bisquare'
W = np.ones(sizy)
# Smoothness parameter and weights
if weight is None:
pass
elif isinstance(weight, str):
weightstr = weight.lower()
else:
W = weight
# Weights. Zero weights are assigned to not finite values (Inf or NaN),
# (Inf/NaN values = missing data).
IsFinite = np.isfinite(y)
nof = IsFinite.sum() # number of finite elements
W = W * IsFinite
if (W < 0).any():
raise ValueError('Weights must all be >=0')
W = W / W.max()
isweighted = (W < 1).any() # Weighted or missing data?
isauto = s is None # Automatic smoothing?
# Creation of the Lambda tensor
# Lambda contains the eingenvalues of the difference matrix used in this
# penalized least squares process.
d = y.ndim
Lambda = np.zeros(sizy)
siz0 = [1, ] * d
for i in range(d):
siz0[i] = sizy[i]
Lambda = Lambda + \
np.cos(pi * np.arange(sizy[i]) / sizy[i]).reshape(siz0)
siz0[i] = 1
Lambda = -2 * (d - Lambda)
if not isauto:
Gamma = 1. / (1 + s * Lambda ** 2)
# Upper and lower bound for the smoothness parameter
# The average leverage (h) is by definition in [0 1]. Weak smoothing occurs
# if h is close to 1, while over-smoothing appears when h is near 0. Upper
# and lower bounds for h are given to avoid under- or over-smoothing. See
# equation relating h to the smoothness parameter (Equation #12 in the
# referenced CSDA paper).
N = (np.array(sizy) != 1).sum() # tensor rank of the y-array
hMin = 1e-6
hMax = 0.99
sMinBnd = (((1 + sqrt(1 + 8 * hMax ** (2. / N))) / 4. /
hMax ** (2. / N)) ** 2 - 1) / 16
sMaxBnd = (((1 + sqrt(1 + 8 * hMin ** (2. / N))) / 4. /
hMin ** (2. / N)) ** 2 - 1) / 16
# Initialize before iterating
class SmoothNd(object):
def __init__(self, s=None, weight=None, robust=False, z0=None, tolz=1e-3,
maxiter=100, fulloutput=False):
self.s = s
self.weight = weight
self.robust = robust
self.z0 = z0
self.tolz = tolz
self.maxiter = maxiter
self.fulloutput = fulloutput
Wtot = W
# Initial conditions for z
if isweighted:
# With weighted/missing data
# An initial guess is provided to ensure faster convergence. For that
# purpose, a nearest neighbor interpolation followed by a coarse
# smoothing are performed.
@property
def weightstr(self):
if isinstance(self._weight, str):
return self._weight.lower()
return 'bisquare'
if z0 is None:
z = InitialGuess(y, IsFinite)
else:
# an initial guess (z0) has been provided
z = z0
else:
z = np.zeros(sizy)
z0 = z
y[~IsFinite] = 0 # arbitrary values for missing y-data
@property
def weight(self):
if self._weight is None or isinstance(self._weight, str):
return 1.0
return self._weight
tol = 1
RobustIterativeProcess = True
RobustStep = 1
@weight.setter
def weight(self, weight):
self._weight = weight
# Error on p. Smoothness parameter s = 10^p
errp = 0.1
def _init_filter(self, y):
return _Filter(y, self.z0, self.weightstr, self.weight, self.s,
self.robust, self.maxiter, self.tolz)
# Relaxation factor RF: to speedup convergence
RF = 1.75 if isweighted else 1.0
def __call__(self, data):
norm = linalg.norm
# Main iterative process
while RobustIterativeProcess:
# "amount" of weights (see the function GCVscore)
aow = Wtot.sum() / noe # 0 < aow <= 1
exitflag = True
for nit in range(1, maxiter + 1):
DCTy = dctn(Wtot * (y - z) + z)
if isauto and not np.remainder(np.log2(nit), 1):
y = np.atleast_1d(data)
if y.size < 2:
return data
# The generalized cross-validation (GCV) method is used.
# We seek the smoothing parameter s that minimizes the GCV
# score i.e. s = Argmin(GCVscore).
# Because this process is time-consuming, it is performed from
# time to time (when nit is a power of 2)
log10s = optimize.fminbound(
gcv, np.log10(sMinBnd), np.log10(sMaxBnd),
args=(aow, Lambda, DCTy, y, Wtot, IsFinite, nof, noe),
xtol=errp, full_output=False, disp=False)
s = 10 ** log10s
Gamma = 1.0 / (1 + s * Lambda ** 2)
z = RF * idctn(Gamma * DCTy) + (1 - RF) * z
_filter = self._init_filter(y)
z = _filter.z0
s = _filter.s
num_steps = 3 if self.robust else 1
converged = False
for i in range(num_steps):
z, s, converged = _filter(z, s)
# if no weighted/missing data => tol=0 (no iteration)
tol = norm(z0.ravel() - z.ravel()) / norm(
z.ravel()) if isweighted else 0.0
if tol <= tolz:
if converged and num_steps <= i+1:
break
z0 = z # re-initialization
else:
exitflag = False # nit<MaxIter;
msg = '''Maximum number of iterations (%d) has been exceeded.
Increase MaxIter option or decrease TolZ value.''' % (self.maxiter)
warnings.warn(msg)
if robust:
# -- Robust Smoothing: iteratively re-weighted process
# --- average leverage
h = sqrt(1 + 16 * s)
h = sqrt(1 + h) / sqrt(2) / h
h = h ** N
# take robust weights into account
Wtot = W * RobustWeights(y - z, IsFinite, h, weightstr)
# re-initialize for another iterative weighted process
isweighted = True
tol = 1
RobustStep = RobustStep + 1
# 3 robust steps are enough.
RobustIterativeProcess = RobustStep < 4
else:
RobustIterativeProcess = False # stop the whole process
# Warning messages
if isauto:
if abs(np.log10(s) - np.log10(sMinBnd)) < errp:
warnings.warn('''s = %g: the lower bound for s has been reached.
Put s as an input variable if required.''' % s)
elif abs(np.log10(s) - np.log10(sMaxBnd)) < errp:
warnings.warn('''s = %g: the Upper bound for s has been reached.
Put s as an input variable if required.''' % s)
_filter.check_smooth_parameter(s)
if not exitflag:
warnings.warn('''Maximum number of iterations (%d) has been exceeded.
Increase MaxIter option or decrease TolZ value.''' % (maxiter))
if fulloutput:
if self.fulloutput:
return z, s
else:
return z
def gcv(p, aow, Lambda, DCTy, y, Wtot, IsFinite, nof, noe):
# Search the smoothing parameter s that minimizes the GCV score
s = 10.0 ** p
Gamma = 1.0 / (1 + s * Lambda ** 2)
# RSS = Residual sum-of-squares
if aow > 0.9: # aow = 1 means that all of the data are equally weighted
# very much faster: does not require any inverse DCT
RSS = linalg.norm(DCTy.ravel() * (Gamma.ravel() - 1)) ** 2
else:
# take account of the weights to calculate RSS:
yhat = idctn(Gamma * DCTy)
RSS = linalg.norm(sqrt(Wtot[IsFinite]) *
(y[IsFinite] - yhat[IsFinite])) ** 2
TrH = Gamma.sum()
GCVscore = RSS / nof / (1.0 - TrH / noe) ** 2
return GCVscore
def RobustWeights(r, I, h, wstr):
# weights for robust smoothing.
MAD = np.median(abs(r[I] - np.median(r[I]))) # median absolute deviation
u = abs(r / (1.4826 * MAD) / sqrt(1 - h)) # studentized residuals
if wstr == 'cauchy':
c = 2.385
W = 1. / (1 + (u / c) ** 2) # Cauchy weights
elif wstr == 'talworth':
c = 2.795
W = u < c # Talworth weights
else: # bisquare weights
c = 4.685
W = (1 - (u / c) ** 2) ** 2 * ((u / c) < 1)
W[np.isnan(W)] = 0
return W
def InitialGuess(y, I):
# Initial Guess with weighted/missing data
# nearest neighbor interpolation (in case of missing values)
z = y
if (1 - I).any():
notI = ~I
z, L = distance_transform_edt(notI, return_indices=True)
z[notI] = y[L.flat[notI]]
# coarse fast smoothing using one-tenth of the DCT coefficients
siz = z.shape
d = z.ndim
z = dctn(z)
for k in range(d):
z[int((siz[k] + 0.5) / 10) + 1::, ...] = 0
z = z.reshape(np.roll(siz, -k))
z = z.transpose(np.roll(range(z.ndim), -1))
# z = shiftdim(z,1);
z = idctn(z)
return z
@ -1476,11 +1554,11 @@ def test_docstrings():
if __name__ == '__main__':
# test_docstrings()
test_kalman_sine()
# test_kalman_sine()
# test_tide_filter()
# demo_hampel()
# test_kalman()
# test_smooth()
# test_hodrick_cardioid()
# test_smoothn_1d()
test_smoothn_1d()
# test_smoothn_cardioid()

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