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pep8

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pbrod 9 years ago
parent 00f3ce12d8
commit 436a9f9ba9
2 changed files with 105 additions and 105 deletions
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6
wafo/doc/rainflow_example.py
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@ -4,7 +4,6 @@ import logging
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
import itertools import itertools
# import sys # import sys
import itertools
log = logging.getLogger(__name__) log = logging.getLogger(__name__)
log.setLevel(logging.DEBUG) log.setLevel(logging.DEBUG)
@ -14,6 +13,7 @@ MARKERS = ('o', 'x', '+', '.', '<', '>', '^', 'v')
def set_windows_title(title='', log=None): def set_windows_title(title='', log=None):
pass pass
def plot_varying_symbols(x, y, color='red', size=5): def plot_varying_symbols(x, y, color='red', size=5):
""" """
Create a plot with varying symbols Create a plot with varying symbols
@ -29,7 +29,9 @@ def plot_varying_symbols(x, y, color='red', size=5):
""" """
markers = itertools.cycle(MARKERS) markers = itertools.cycle(MARKERS)
for q, p in zip(x, y): for q, p in zip(x, y):
plt.plot(q, p, marker=markers.next(), linestyle='', color=color, markersize=size) plt.plot(q, p, marker=markers.next(), linestyle='', color=color,
markersize=size)
def damage_vs_S(S, beta, K): def damage_vs_S(S, beta, K):
""" """

194
wafo/stats/estimation.py
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@ -36,9 +36,9 @@ arr = asarray
all = alltrue # @ReservedAssignment all = alltrue # @ReservedAssignment
def _burr_link(x, logSF, phat, ix): def _burr_link(x, logsf, phat, ix):
c, d, loc, scale = phat c, d, loc, scale = phat
logp = log(-expm1(logSF)) logp = log(-expm1(logsf))
xn = (x - loc) / scale xn = (x - loc) / scale
if ix == 1: if ix == 1:
return -logp / log1p(xn**(-c)) return -logp / log1p(xn**(-c))
@ -51,28 +51,28 @@ def _burr_link(x, logSF, phat, ix):
raise IndexError('Index to the fixed parameter is out of bounds') raise IndexError('Index to the fixed parameter is out of bounds')
def _expon_link(x, logSF, phat, ix): def _expon_link(x, logsf, phat, ix):
if ix == 1: if ix == 1:
return - (x - phat[0]) / logSF return - (x - phat[0]) / logsf
if ix == 0: if ix == 0:
return x + phat[1] * logSF return x + phat[1] * logsf
raise IndexError('Index to the fixed parameter is out of bounds') raise IndexError('Index to the fixed parameter is out of bounds')
def _weibull_min_link(x, logSF, phat, ix): def _weibull_min_link(x, logsf, phat, ix):
c, loc, scale = phat c, loc, scale = phat
if ix == 0: if ix == 0:
return log(-logSF) / log((x - loc) / scale) return log(-logsf) / log((x - loc) / scale)
if ix == 1: if ix == 1:
return x - scale * (-logSF) ** (1. / c) return x - scale * (-logsf) ** (1. / c)
if ix == 2: if ix == 2:
return (x - loc) / (-logSF) ** (1. / c) return (x - loc) / (-logsf) ** (1. / c)
raise IndexError('Index to the fixed parameter is out of bounds') raise IndexError('Index to the fixed parameter is out of bounds')
def _exponweib_link(x, logSF, phat, ix): def _exponweib_link(x, logsf, phat, ix):
a, c, loc, scale = phat a, c, loc, scale = phat
logP = -log(-expm1(logSF)) logP = -log(-expm1(logsf))
xn = (x - loc) / scale xn = (x - loc) / scale
if ix == 0: if ix == 0:
return - logP / log(-expm1(-xn**c)) return - logP / log(-expm1(-xn**c))
@ -85,7 +85,7 @@ def _exponweib_link(x, logSF, phat, ix):
raise IndexError('Index to the fixed parameter is out of bounds') raise IndexError('Index to the fixed parameter is out of bounds')
def _genpareto_link(x, logSF, phat, ix): def _genpareto_link(x, logsf, phat, ix):
# Reference # Reference
# Stuart Coles (2004) # Stuart Coles (2004)
# "An introduction to statistical modelling of extreme values". # "An introduction to statistical modelling of extreme values".
@ -94,27 +94,27 @@ def _genpareto_link(x, logSF, phat, ix):
if ix == 2: if ix == 2:
# Reorganizing w.r.t.scale, Eq. 4.13 and 4.14, pp 81 in # Reorganizing w.r.t.scale, Eq. 4.13 and 4.14, pp 81 in
# Coles (2004) gives # Coles (2004) gives
# link = -(x-loc)*c/expm1(-c*logSF) # link = -(x-loc)*c/expm1(-c*logsf)
if c != 0.0: if c != 0.0:
phati = (x - loc) * c / expm1(-c * logSF) phati = (x - loc) * c / expm1(-c * logsf)
else: else:
phati = -(x - loc) / logSF phati = -(x - loc) / logsf
elif ix == 1: elif ix == 1:
if c != 0: if c != 0:
phati = x + scale * expm1(c * logSF) / c phati = x + scale * expm1(c * logsf) / c
else: else:
phati = x + scale * logSF phati = x + scale * logsf
elif ix == 0: elif ix == 0:
raise NotImplementedError( raise NotImplementedError(
'link(x,logSF,phat,i) where i=0 is not implemented!') 'link(x,logsf,phat,i) where i=0 is not implemented!')
else: else:
raise IndexError('Index to the fixed parameter is out of bounds') raise IndexError('Index to the fixed parameter is out of bounds')
return phati return phati
def _genextreme_link(x, logSF, phat, ix): def _genextreme_link(x, logsf, phat, ix):
c, loc, scale = phat c, loc, scale = phat
loglogP = log(-log(-expm1(logSF))) loglogP = log(-log(-expm1(logsf)))
if ix == 2: if ix == 2:
# link = -(x-loc)*c/expm1(c*log(-logP)) # link = -(x-loc)*c/expm1(c*log(-logP))
if c != 0.0: if c != 0.0:
@ -126,40 +126,40 @@ def _genextreme_link(x, logSF, phat, ix):
return x + scale * loglogP return x + scale * loglogP
if ix == 0: if ix == 0:
raise NotImplementedError( raise NotImplementedError(
'link(x,logSF,phat,i) where i=0 is not implemented!') 'link(x,logsf,phat,i) where i=0 is not implemented!')
raise IndexError('Index to the fixed parameter is out of bounds') raise IndexError('Index to the fixed parameter is out of bounds')
def _genexpon_link(x, logSF, phat, ix): def _genexpon_link(x, logsf, phat, ix):
a, b, c, loc, scale = phat a, b, c, loc, scale = phat
xn = (x - loc) / scale xn = (x - loc) / scale
fact1 = (xn + expm1(-c * xn) / c) fact1 = (xn + expm1(-c * xn) / c)
if ix == 0: if ix == 0:
return b * fact1 + logSF # a return b * fact1 + logsf # a
if ix == 1: if ix == 1:
return (a - logSF) / fact1 # b return (a - logsf) / fact1 # b
if ix in [2, 3, 4]: if ix in [2, 3, 4]:
raise NotImplementedError('Only implemented for index in [0,1]!') raise NotImplementedError('Only implemented for index in [0,1]!')
raise IndexError('Index to the fixed parameter is out of bounds') raise IndexError('Index to the fixed parameter is out of bounds')
def _rayleigh_link(x, logSF, phat, ix): def _rayleigh_link(x, logsf, phat, ix):
if ix == 1: if ix == 1:
return x - phat[0] / sqrt(-2.0 * logSF) return x - phat[0] / sqrt(-2.0 * logsf)
if ix == 0: if ix == 0:
return x - phat[1] * sqrt(-2.0 * logSF) return x - phat[1] * sqrt(-2.0 * logsf)
raise IndexError('Index to the fixed parameter is out of bounds') raise IndexError('Index to the fixed parameter is out of bounds')
def _trunclayleigh_link(x, logSF, phat, ix): def _trunclayleigh_link(x, logsf, phat, ix):
c, loc, scale = phat c, loc, scale = phat
if ix == 0: if ix == 0:
xn = (x - loc) / scale xn = (x - loc) / scale
return - 2 * logSF / xn - xn / 2.0 return - 2 * logsf / xn - xn / 2.0
if ix == 2: if ix == 2:
return x - loc / (sqrt(c * c - 2 * logSF) - c) return x - loc / (sqrt(c * c - 2 * logsf) - c)
if ix == 1: if ix == 1:
return x - scale * (sqrt(c * c - 2 * logSF) - c) return x - scale * (sqrt(c * c - 2 * logsf) - c)
raise IndexError('Index to the fixed parameter is out of bounds') raise IndexError('Index to the fixed parameter is out of bounds')
@ -240,9 +240,9 @@ class Profile(object):
>>> phat = FitDistribution(ws.weibull_min, R, 1, scale=1, floc=0.0) >>> phat = FitDistribution(ws.weibull_min, R, 1, scale=1, floc=0.0)
# Better 90% CI for phat.par[i=0] # Better 90% CI for phat.par[i=0]
>>> Lp = Profile(phat, i=0) >>> profile_phat_i = Profile(phat, i=0)
>>> Lp.plot() >>> profile_phat_i.plot()
>>> phat_ci = Lp.get_bounds(alpha=0.1) >>> phat_ci = profile_phat_i.get_bounds(alpha=0.1)
''' '''
def __init__(self, fit_dist, i=None, pmin=None, pmax=None, n=100, def __init__(self, fit_dist, i=None, pmin=None, pmax=None, n=100,
@ -558,16 +558,13 @@ def plot_all_profiles(phats, plot=None):
n = len(indices) n = len(indices)
for j, k in enumerate(indices): for j, k in enumerate(indices):
plt.subplot(n, 1, j+1) plt.subplot(n, 1, j+1)
Lp1 = Profile(phats, i=k) profile_phat_k = Profile(phats, i=k)
m = 0 m = 0
while hasattr(Lp1, 'best_par') and m < 7: while hasattr(profile_phat_k, 'best_par') and m < 7:
phats.fit(*Lp1.best_par) phats.fit(*profile_phat_k.best_par)
# phats = FitDistribution(dist, data, args=Lp1.best_par, profile_phat_k = Profile(phats, i=k)
# method=method, search=True)
Lp1 = Profile(phats, i=k)
m += 1 m += 1
Lp1.plot() profile_phat_k.plot()
if j != 0: if j != 0:
plt.title('') plt.title('')
if j != n//2: if j != n//2:
@ -600,9 +597,9 @@ class ProfileQuantile(Profile):
alpha : real scalar alpha : real scalar
confidence coefficent (default 0.05) confidence coefficent (default 0.05)
link : function connecting the x-quantile and the survival probability link : function connecting the x-quantile and the survival probability
(SF) with the fixed distribution parameter, i.e.: (sf) with the fixed distribution parameter, i.e.:
self.par[i] = link(x, logSF, self.par, i), where self.par[i] = link(x, logsf, self.par, i), where
logSF = log(Prob(X>x;phat)). logsf = log(Prob(X>x;phat)).
(default is fetched from the LINKS dictionary) (default is fetched from the LINKS dictionary)
Returns Returns
@ -625,8 +622,8 @@ class ProfileQuantile(Profile):
Lmax : Maximum value of profile function Lmax : Maximum value of profile function
alpha_cross_level : alpha_cross_level :
PROFILE is a utility function for making inferences either on a particular ProfileQuantile is a utility function for making inferences on the
component of the vector phat or the quantile, x, or the probability, SF. quantile, x.
This is usually more accurate than using the delta method assuming This is usually more accurate than using the delta method assuming
asymptotic normality of the ML estimator or the MPS estimator. asymptotic normality of the ML estimator or the MPS estimator.
@ -641,9 +638,9 @@ class ProfileQuantile(Profile):
>>> x = phat.isf(sf) >>> x = phat.isf(sf)
# 80% CI for x # 80% CI for x
>>> Lx = ProfileQuantile(phat, x) >>> profile_x = ProfileQuantile(phat, x)
>>> Lx.plot() >>> profile_x.plot()
>>> x_ci = Lx.get_bounds(alpha=0.2) >>> x_ci = profile_x.get_bounds(alpha=0.2)
''' '''
def __init__(self, fit_dist, x, i=None, pmin=None, pmax=None, n=100, def __init__(self, fit_dist, x, i=None, pmin=None, pmax=None, n=100,
alpha=0.05, link=None): alpha=0.05, link=None):
@ -709,9 +706,9 @@ class ProfileProbability(Profile):
alpha : real scalar alpha : real scalar
confidence coefficent (default 0.05) confidence coefficent (default 0.05)
link : function connecting the x-quantile and the survival probability link : function connecting the x-quantile and the survival probability
(SF) with the fixed distribution parameter, i.e.: (sf) with the fixed distribution parameter, i.e.:
self.par[i] = link(x, logSF, self.par, i), where self.par[i] = link(x, logsf, self.par, i), where
logSF = log(Prob(X>x;phat)). logsf = log(Prob(X>x;phat)).
(default is fetched from the LINKS dictionary) (default is fetched from the LINKS dictionary)
Returns Returns
@ -734,7 +731,7 @@ class ProfileProbability(Profile):
Lmax : Maximum value of profile function Lmax : Maximum value of profile function
alpha_cross_level : alpha_cross_level :
PROFILE is a utility function for making inferences the survival ProfileProbability is a utility function for making inferences the survival
probability (sf). probability (sf).
This is usually more accurate than using the delta method assuming This is usually more accurate than using the delta method assuming
asymptotic normality of the ML estimator or the MPS estimator. asymptotic normality of the ML estimator or the MPS estimator.
@ -749,9 +746,9 @@ class ProfileProbability(Profile):
>>> sf = 1./990 >>> sf = 1./990
# 80% CI for sf # 80% CI for sf
>>> Lsf = ProfileProbability(phat, np.log(sf)) >>> profile_logsf = ProfileProbability(phat, np.log(sf))
>>> Lsf.plot() >>> profile_logsf.plot()
>>> sf_ci = Lsf.get_bounds(alpha=0.2) >>> logsf_ci = profile_logsf.get_bounds(alpha=0.2)
''' '''
def __init__(self, fit_dist, logsf, i=None, pmin=None, pmax=None, n=100, def __init__(self, fit_dist, logsf, i=None, pmin=None, pmax=None, n=100,
alpha=0.05, link=None): alpha=0.05, link=None):
@ -776,8 +773,8 @@ class ProfileProbability(Profile):
def _myprbfun(self, phatnotfixed): def _myprbfun(self, phatnotfixed):
mphat = self._par.copy() mphat = self._par.copy()
mphat[self.i_notfixed] = phatnotfixed mphat[self.i_notfixed] = phatnotfixed
logSF = self.fit_dist.dist.logsf(self.x, *mphat) logsf = self.fit_dist.dist.logsf(self.x, *mphat)
return np.where(np.isfinite(logSF), logSF, np.nan) return np.where(np.isfinite(logsf), logsf, np.nan)
def _get_variance(self): def _get_variance(self):
i_notfixed = self.i_notfixed i_notfixed = self.i_notfixed
@ -872,23 +869,23 @@ class FitDistribution(rv_frozen):
# phat.par_upper upper CI for parameters # phat.par_upper upper CI for parameters
# phat.par_lower lower CI for parameters # phat.par_lower lower CI for parameters
#Better CI for phat.par[0] # Better 90% CI for phat.par[0]
>>> Lp = phat.profile(i=0) >>> profile_phat_i = phat.profile(i=0)
>>> Lp.plot() >>> profile_phat_i.plot()
>>> p_ci = Lp.get_bounds(alpha=0.1) >>> p_ci = profile_phat_i.get_bounds(alpha=0.1)
>>> SF = 1./990
>>> x = phat.isf(SF)
# CI for x >>> sf = 1./990
>>> Lx = phat.profile_quantile(x=x) >>> x = phat.isf(sf)
>>> Lx.plot()
>>> x_ci = Lx.get_bounds(alpha=0.2)
# CI for logSF=log(SF) # 80% CI for x
>>> Lsf = phat.profile_probability(log(SF)) >>> profile_x = phat.profile_quantile(x=x)
>>> Lsf.plot() >>> profile_x.plot()
>>> sf_ci = Lsf.get_bounds(alpha=0.2) >>> x_ci = profile_x.get_bounds(alpha=0.2)
# 80% CI for logsf=log(sf)
>>> profile_logsf = phat.profile_probability(log(sf))
>>> profile_logsf.plot()
>>> sf_ci = profile_logsf.get_bounds(alpha=0.2)
''' '''
def __init__(self, dist, data, args=(), method='ML', alpha=0.05, def __init__(self, dist, data, args=(), method='ML', alpha=0.05,
@ -1021,9 +1018,9 @@ class FitDistribution(rv_frozen):
else: else:
kwds[key] = val kwds[key] = val
args = list(args) args = list(args)
Nargs = len(args) nargs = len(args)
fixedn = [] fixedn = []
names = ['f%d' % n for n in range(Nargs - 2)] + ['floc', 'fscale'] names = ['f%d' % n for n in range(nargs - 2)] + ['floc', 'fscale']
x0 = [] x0 = []
for n, key in enumerate(names): for n, key in enumerate(names):
if key in kwds: if key in kwds:
@ -1038,7 +1035,7 @@ class FitDistribution(rv_frozen):
func = fitfun func = fitfun
restore = None restore = None
else: else:
if len(fixedn) == Nargs: if len(fixedn) == nargs:
raise ValueError("All parameters fixed. " + raise ValueError("All parameters fixed. " +
"There is nothing to optimize.") "There is nothing to optimize.")
@ -1047,7 +1044,7 @@ class FitDistribution(rv_frozen):
# This allows the non-fixed values to vary, but # This allows the non-fixed values to vary, but
# we still call self.nnlf with all parameters. # we still call self.nnlf with all parameters.
i = 0 i = 0
for n in range(Nargs): for n in range(nargs):
if n not in fixedn: if n not in fixedn:
args[n] = theta[i] args[n] = theta[i]
i += 1 i += 1
@ -1189,7 +1186,8 @@ class FitDistribution(rv_frozen):
return -np.sum(logD[finiteD], axis=0) + penalty return -np.sum(logD[finiteD], axis=0) + penalty
return -np.sum(logD, axis=0) return -np.sum(logD, axis=0)
def _get_optimizer(self, kwds): @staticmethod
def _get_optimizer(kwds):
optimizer = kwds.pop('optimizer', optimize.fmin) optimizer = kwds.pop('optimizer', optimize.fmin)
# convert string to function in scipy.optimize # convert string to function in scipy.optimize
if not callable(optimizer) and isinstance(optimizer, string_types): if not callable(optimizer) and isinstance(optimizer, string_types):
@ -1203,14 +1201,14 @@ class FitDistribution(rv_frozen):
def _fit_start(self, data, args, kwds): def _fit_start(self, data, args, kwds):
dist = self.dist dist = self.dist
Narg = len(args) narg = len(args)
if Narg > dist.numargs + 2: if narg > dist.numargs + 2:
raise ValueError("Too many input arguments.") raise ValueError("Too many input arguments.")
if (Narg < dist.numargs + 2) or not ('loc' in kwds and if (narg < dist.numargs + 2) or not ('loc' in kwds and
'scale' in kwds): 'scale' in kwds):
# get distribution specific starting locations # get distribution specific starting locations
start = dist._fitstart(data) start = dist._fitstart(data)
args += start[Narg:] args += start[narg:]
loc = kwds.pop('loc', args[-2]) loc = kwds.pop('loc', args[-2])
scale = kwds.pop('scale', args[-1]) scale = kwds.pop('scale', args[-1])
args = args[:-2] + (loc, scale) args = args[:-2] + (loc, scale)
@ -1315,9 +1313,9 @@ class FitDistribution(rv_frozen):
>>> x = phat.isf(sf) >>> x = phat.isf(sf)
# 80% CI for x # 80% CI for x
>>> Lx = phat.profile_quantile(x) >>> profile_x = phat.profile_quantile(x)
>>> Lx.plot() >>> profile_x.plot()
>>> x_ci = Lx.get_bounds(alpha=0.2) >>> x_ci = profile_x.get_bounds(alpha=0.2)
''' '''
return ProfileQuantile(self, x, **kwds) return ProfileQuantile(self, x, **kwds)
@ -1335,9 +1333,9 @@ class FitDistribution(rv_frozen):
>>> log_sf = np.log(1./990) >>> log_sf = np.log(1./990)
# 80% CI for log_sf # 80% CI for log_sf
>>> Lsf = phat.profile_probability(log_sf) >>> profile_logsf = phat.profile_probability(log_sf)
>>> Lsf.plot() >>> profile_logsf.plot()
>>> log_sf_ci = Lsf.get_bounds(alpha=0.2) >>> log_sf_ci = profile_logsf.get_bounds(alpha=0.2)
''' '''
return ProfileProbability(self, log_sf, **kwds) return ProfileProbability(self, log_sf, **kwds)
@ -1392,10 +1390,10 @@ class FitDistribution(rv_frozen):
Other distribution types will introduce deviations in the plot. Other distribution types will introduce deviations in the plot.
''' '''
n = len(self.data) n = len(self.data)
SF = (arange(n, 0, -1)) / n sf = (arange(n, 0, -1)) / n
plt.semilogy( plt.semilogy(
self.data, SF, symb2, self.data, self.sf(self.data), symb1) self.data, sf, symb2, self.data, self.sf(self.data), symb1)
# plt.plot(self.data,SF,'b.',self.data,self.sf(self.data),'r-') # plt.plot(self.data,sf,'b.',self.data,self.sf(self.data),'r-')
plt.xlabel('x') plt.xlabel('x')
plt.ylabel('F(x) (%s)' % self.dist.name) plt.ylabel('F(x) (%s)' % self.dist.name)
plt.title('Empirical SF plot') plt.title('Empirical SF plot')
@ -1575,9 +1573,9 @@ def test1():
x = phat.isf(sf) x = phat.isf(sf)
# 80% CI for x # 80% CI for x
Lx = ProfileQuantile(phat, x) profile_x = ProfileQuantile(phat, x)
Lx.plot() profile_x.plot()
# x_ci = Lx.get_bounds(alpha=0.2) # x_ci = profile_x.get_bounds(alpha=0.2)
plt.figure(5) plt.figure(5)
@ -1585,9 +1583,9 @@ def test1():
x = phat.isf(sf) x = phat.isf(sf)
# 80% CI for x # 80% CI for x
Lsf = ProfileProbability(phat, np.log(sf)) profile_logsf = ProfileProbability(phat, np.log(sf))
Lsf.plot() profile_logsf.plot()
# logsf_ci = Lsf.get_bounds(alpha=0.2) # logsf_ci = profile_logsf.get_bounds(alpha=0.2)
plt.show('hold') plt.show('hold')

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