def fit_quadrature(orth, nodes, weights, solves, retall=False,
norms=None, **kws):
"""
Using spectral projection to create a polynomial approximation over
distribution space.
Parameters
----------
orth : Poly
Orthogonal polynomial expansion. Must be orthogonal for the
approximation to be accurate.
nodes : array_like
Where to evaluate the polynomial expansion and model to
approximate.
nodes.shape==(D,K) where D is the number of dimensions and K is
the number of nodes.
weights : array_like
Weights when doing numerical integration.
weights.shape==(K,)
solves : array_like, callable
The model to approximate.
If array_like is provided, it must have len(solves)==K.
If callable, it must take a single argument X with len(X)==D,
and return a consistent numpy compatible shape.
norms : array_like
In the of TTR using coefficients to estimate the polynomial
norm is more stable than manual calculation.
Calculated using quadrature if no provided.
norms.shape==(len(orth),)
"""
orth = po.Poly(orth)
nodes = np.asfarray(nodes)
weights = np.asfarray(weights)
if hasattr(solves, "__call__"):
solves = [solves(q) for q in nodes.T]
solves = np.asfarray(solves)
shape = solves.shape
solves = solves.reshape(weights.size, solves.size/weights.size)
ovals = orth(*nodes)
vals1 = [(val*solves.T*weights).T for val in ovals]
if norms is None:
vals2 = [(val**2*weights).T for val in ovals]
norms = np.sum(vals2, 1)
else:
norms = np.array(norms).flatten()
assert len(norms)==len(orth)
coefs = (np.sum(vals1, 1).T/norms).T
coefs = coefs.reshape(len(coefs), *shape[1:])
Q = po.transpose(po.sum(orth*coefs.T, -1))
if retall:
return Q, coefs
return Q
def orth_pcd(order, dist, eps=1.e-16, normed=False, **kws):
"""
Create orthogonal polynomial expansion from pivoted Cholesky
decompostion.
Parameters
----------
order : int
Order of polynomial expansion
dist : Dist
Distribution space where polynomials are orthogonal
normed : bool
If True orthonormal polynomials will be used instead of monic.
**kws : optional
Extra keywords passed to dist.mom
Examples
--------
# >>> Z = cp.Normal()
# >>> print cp.orth_pcd(2, Z)
# [1.0, q0^2-1.0, q0]
"""
raise DeprecationWarning("Obsolete. Use orth_chol instead.")
dim = len(dist)
basis = po.basis(1, order, dim)
C = Cov(basis, dist)
N = len(basis)
L, P = pcd(C, approx=1, pivot=1, tol=eps)
Li = np.dot(P, np.linalg.inv(L.T))
if normed:
for i in xrange(N):
Li[:, i] /= np.sum(Li[:, i] * P[:, i])
E_ = -po.sum(E(basis, dist, **kws) * Li.T, -1)
coefs = np.zeros((N + 1, N + 1))
coefs[1:, 1:] = Li
coefs[0, 0] = 1
coefs[0, 1:] = E_
out = {}
out[(0, ) * dim] = coefs[0]
basis = list(basis)
for i in xrange(N):
I = basis[i].keys[0]
out[I] = coefs[i + 1]
P = po.Poly(out, dim, coefs.shape[1:], float)
return P
def orth_pcd(order, dist, eps=1.e-16, normed=False, **kws):
"""
Create orthogonal polynomial expansion from pivoted Cholesky
decompostion.
Parameters
----------
order : int
Order of polynomial expansion
dist : Dist
Distribution space where polynomials are orthogonal
normed : bool
If True orthonormal polynomials will be used instead of monic.
**kws : optional
Extra keywords passed to dist.mom
Examples
--------
# >>> Z = cp.Normal()
# >>> print cp.orth_pcd(2, Z)
# [1.0, q0^2-1.0, q0]
"""
raise DeprecationWarning("Obsolete. Use orth_chol instead.")
dim = len(dist)
basis = po.basis(1,order,dim)
C = Cov(basis, dist)
N = len(basis)
L, P = pcd(C, approx=1, pivot=1, tol=eps)
Li = np.dot(P, np.linalg.inv(L.T))
if normed:
for i in xrange(N):
Li[:,i] /= np.sum(Li[:,i]*P[:,i])
E_ = -po.sum(E(basis, dist, **kws)*Li.T, -1)
coefs = np.zeros((N+1, N+1))
coefs[1:,1:] = Li
coefs[0,0] = 1
coefs[0,1:] = E_
out = {}
out[(0,)*dim] = coefs[0]
basis = list(basis)
for i in xrange(N):
I = basis[i].keys[0]
out[I] = coefs[i+1]
P = po.Poly(out, dim, coefs.shape[1:], float)
return P
def lagrange_polynomial(X, sort="GR"):
"""
Lagrange Polynomials
X : array_like
Sample points where the lagrange polynomials shall be
"""
X = np.asfarray(X)
if len(X.shape) == 1:
X = X.reshape(1, X.size)
dim, size = X.shape
order = 1
while ber.terms(order, dim) <= size:
order += 1
indices = np.array(ber.bindex(1, order, dim, sort)[:size])
s, t = np.mgrid[:size, :size]
M = np.prod(X.T[s]**indices[t], -1)
det = np.linalg.det(M)
if det == 0:
raise np.linalg.LinAlgError, "invertable matrix"
v = po.basis(1, order, dim, sort)[:size]
coeffs = np.zeros((size, size))
if size == 2:
coeffs = np.linalg.inv(M)
else:
for i in xrange(size):
for j in xrange(size):
coeffs[i, j] += np.linalg.det(M[1:, 1:])
M = np.roll(M, -1, axis=0)
M = np.roll(M, -1, axis=1)
coeffs /= det
return po.sum(v * (coeffs.T), 1)
def lagrange_polynomial(X, sort="GR"):
"""
Lagrange Polynomials
X : array_like
Sample points where the lagrange polynomials shall be
"""
X = np.asfarray(X)
if len(X.shape)==1:
X = X.reshape(1,X.size)
dim,size = X.shape
order = 1
while ber.terms(order, dim)<=size: order += 1
indices = np.array(ber.bindex(1, order, dim, sort)[:size])
s,t = np.mgrid[:size, :size]
M = np.prod(X.T[s]**indices[t], -1)
det = np.linalg.det(M)
if det==0:
raise np.linalg.LinAlgError, "invertable matrix"
v = po.basis(1, order, dim, sort)[:size]
coeffs = np.zeros((size, size))
if size==2:
coeffs = np.linalg.inv(M)
else:
for i in xrange(size):
for j in xrange(size):
coeffs[i,j] += np.linalg.det(M[1:,1:])
M = np.roll(M, -1, axis=0)
M = np.roll(M, -1, axis=1)
coeffs /= det
return po.sum(v*(coeffs.T), 1)
def orth_svd(order, dist, eps=1.e-300, normed=False, **kws):
"""
Create orthogonal polynomial expansion from pivoted Cholesky
decompostion. If eigenvalue of covariance matrix is bellow eps, the
polynomial is subset.
Parameters
----------
order : int
Order of polynomial expansion
dist : Dist
Distribution space where polynomials are orthogonal
eps : float
Threshold for when to subset the expansion.
normed : bool
If True, polynomial will be orthonormal.
**kws : optional
Extra keywords passed to dist.mom
Examples
--------
# >>> Z = cp.Normal()
# >>> print cp.orth_svd(2, Z)
# [1.0, q0^2-1.0, q0]
"""
dim = len(dist)
if isinstance(order, po.Poly):
basis = order
else:
basis = po.basis(1,order,dim)
basis = list(basis)
C = Cov(basis, dist, **kws)
L, P = pcd(C, approx=0, pivot=1, tol=eps)
N = L.shape[-1]
if len(L)!=N:
I = [_.tolist().index(1) for _ in P]
b_ = [0]*N
for i in xrange(N):
b_[i] = basis[I[i]]
basis = b_
C = Cov(basis, dist, **kws)
L, P = pcd(C, approx=0, pivot=1, tol=eps)
N = L.shape[-1]
basis = po.Poly(basis)
Li = rlstsq(L, P, alpha=1.e-300).T
E_ = -po.sum(E(basis, dist, **kws)*Li.T, -1)
coefs = np.zeros((N+1, N+1))
coefs[1:,1:] = Li
coefs[0,0] = 1
coefs[0,1:] = E_
out = {}
out[(0,)*dim] = coefs[0]
for i in xrange(N):
I = basis[i].keys[0]
out[I] = coefs[i+1]
P = po.Poly(out, dim, coefs.shape[1:], float)
if normed:
norm = np.sqrt(Var(P, dist, **kws))
norm[0] = 1
P = P/norm
return P
def fit_regression(P, x, u, rule="LS", retall=False, **kws):
"""
Fit a polynomial chaos expansion using linear regression.
Parameters
----------
P : Poly
Polynomial chaos expansion with `P.shape=(M,)` and `P.dim=D`.
x : array_like
Collocation nodes with `x.shape=(D,K)`.
u : array_like
Model evaluations with `len(u)=K`.
retall : bool
If True return uhat in addition to R
rule : str
Regression method used.
The follwong methods uses scikits-learn as backend.
See `sklearn.linear_model` for more details.
Key Scikit-learn Description
--- ------------ -----------
Parameters Description
---------- -----------
"BARD" ARDRegression Bayesian ARD Regression
n_iter=300 Maximum iterations
tol=1e-3 Optimization tolerance
alpha_1=1e-6 Gamma scale parameter
alpha_2=1e-6 Gamma inverse scale parameter
lambda_1=1e-6 Gamma shape parameter
lambda_2=1e-6 Gamma inverse scale parameter
threshold_lambda=1e-4 Upper pruning threshold
"BR" BayesianRidge Bayesian Ridge Regression
n_iter=300 Maximum iterations
tol=1e-3 Optimization tolerance
alpha_1=1e-6 Gamma scale parameter
alpha_2=1e-6 Gamma inverse scale parameter
lambda_1=1e-6 Gamma shape parameter
lambda_2=1e-6 Gamma inverse scale parameter
"EN" ElastiNet Elastic Net
alpha=1.0 Dampening parameter
rho Mixing parameter in [0,1]
max_iter=300 Maximum iterations
tol Optimization tolerance
"ENC" ElasticNetCV EN w/Cross Validation
rho Dampening parameter(s)
eps=1e-3 min(alpha)/max(alpha)
n_alphas Number of alphas
alphas List of alphas
max_iter Maximum iterations
tol Optimization tolerance
cv=3 Cross validation folds
"LA" Lars Least Angle Regression
n_nonzero_coefs Number of non-zero coefficients
eps Cholesky regularization
"LAC" LarsCV LAR w/Cross Validation
max_iter Maximum iterations
cv=5 Cross validation folds
max_n_alphas Max points for residuals in cv
"LAS" Lasso Least Absolute Shrinkage and
Selection Operator
alpha=1.0 Dampening parameter
max_iter Maximum iterations
tol Optimization tolerance
"LASC" LassoCV LAS w/Cross Validation
eps=1e-3 min(alpha)/max(alpha)
n_alphas Number of alphas
alphas List of alphas
max_iter Maximum iterations
tol Optimization tolerance
cv=3 Cross validation folds
"LL" LassoLars Lasso and Lars model
max_iter Maximum iterations
eps Cholesky regularization
"LLC" LassoLarsCV LL w/Cross Validation
max_iter Maximum iterations
cv=5 Cross validation folds
max_n_alphas Max points for residuals in cv
eps Cholesky regularization
"LLIC" LassoLarsIC LL w/AIC or BIC
criterion "AIC" or "BIC" criterion
max_iter Maximum iterations
eps Cholesky regularization
"OMP" OrthogonalMatchingPursuit
n_nonzero_coefs Number of non-zero coefficients
tol Max residual norm (instead of non-zero coef)
Local methods
Key Description
--- -----------
"LS" Ordenary Least Squares
"T" Ridge Regression/Tikhonov Regularization
order Order of regularization (or custom matrix)
alpha Dampning parameter (else estimated from gcv)
"TC" T w/Cross Validation
order Order of regularization (or custom matrix)
alpha Dampning parameter (else estimated from gcv)
Returns
-------
R[, uhat]
R : Poly
Fitted polynomial with `R.shape=u.shape[1:]` and `R.dim=D`.
uhat : np.ndarray
The Fourier coefficients in the estimation.
Examples
--------
>>> P = cp.Poly([1, x, y])
>>> s = [[-1,-1,1,1], [-1,1,-1,1]]
>>> u = [0,1,1,2]
>>> print fit_regression(P, s, u)
0.5q1+0.5q0+1.0
"""
x = np.array(x)
if len(x.shape) == 1:
x = x.reshape(1, *x.shape)
u = np.array(u)
Q = P(*x).T
shape = u.shape[1:]
u = u.reshape(u.shape[0], int(np.prod(u.shape[1:])))
rule = rule.upper()
# Local rules
if rule == "LS":
uhat = la.lstsq(Q, u)[0].T
elif rule == "T":
uhat, alphas = rlstsq(Q, u, kws.get("order", 0),
kws.get("alpha", None), False, True)
uhat = uhat.T
elif rule == "TC":
uhat = rlstsq(Q, u, kws.get("order", 0), kws.get("alpha", None), True)
uhat = uhat.T
else:
# Scikit-learn wrapper
try:
_ = lm
except:
raise NotImplementedError("sklearn not installed")
if rule == "BARD":
solver = lm.ARDRegression(fit_intercept=False, copy_X=False, **kws)
elif rule == "BR":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.BayesianRidge(**kws)
elif rule == "EN":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.ElasticNet(**kws)
elif rule == "ENC":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.ElasticNetCV(**kws)
elif rule == "LA": # success
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.Lars(**kws)
elif rule == "LAC":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.LarsCV(**kws)
elif rule == "LAS":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.Lasso(**kws)
elif rule == "LASC":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.LassoCV(**kws)
elif rule == "LL":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.LassoLars(**kws)
elif rule == "LLC":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.LassoLarsCV(**kws)
elif rule == "LLIC":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.LassoLarsIC(**kws)
elif rule == "OMP":
solver = lm.OrthogonalMatchingPursuit(**kws)
uhat = solver.fit(Q, u).coef_
u = u.reshape(u.shape[0], *shape)
R = po.sum((P * uhat), -1)
R = po.reshape(R, shape)
if retall == 1:
return R, uhat
elif retall == 2:
if rule == "T":
return R, uhat, Q, alphas
return R, uhat, Q
return R
def pcm_gq(func,
order,
dist_out,
dist_in=None,
acc=None,
orth=None,
retall=False,
sparse=False):
"""
Probabilistic Collocation Method using optimal Gaussian quadrature
Parameters
----------
Required arguments
func : callable
The model to be approximated.
Must accept arguments on the form `func(z, *args, **kws)`
where `z` is an 1-dimensional array with `len(z)==len(dist)`.
order : int
The order of the polynomial approximation
dist_out : Dist
Distributions for models parameter
Optional arguments
dist_in : Dist
If included, space will be mapped using a Rosenblatt
transformation from dist_out to dist_in before creating an
expansin in terms of dist_in
acc : float
The order of the sample scheme used
If omitted order+1 will be used
orth : int, str, callable, Poly
Orthogonal polynomial generation.
int, str :
orth will be passed to orth_select
for selection of orthogonalization.
See orth_select doc for more details.
callable :
the return of orth(M, dist) will be used.
Poly :
it will be used directly.
All polynomials must be orthogonal for method to work
properly.
args : itterable
Extra positional arguments passed to `func`.
kws : dict
Extra keyword arguments passed to `func`.
retall : bool
If True, return also number of evaluations
sparse : bool
If True, Smolyak sparsegrid will be used instead of full
tensorgrid
Returns
-------
Q[, X]
Q : Poly
Polynomial estimate of a given a model.
X : np.ndarray
Values used in evaluation
# Examples
# --------
# Define function:
# >>> func = lambda z: z[1]*z[0]
#
# Define distribution:
# >>> dist = cp.J(cp.Normal(), cp.Normal())
#
# Perform pcm:
# >>> p, x, w, y = cp.pcm_gq(func, 2, dist, acc=3, retall=True)
# >>> print cp.around(p, 10)
# q0q1
# >>> print len(w)
# 16
"""
if acc is None:
acc = order + 1
if dist_in is None:
z, w = qu.generate_quadrature(acc,
dist_out,
100,
sparse=sparse,
rule="G")
x = z
dist = dist_out
else:
z, w = qu.generate_quadrature(acc,
dist_in,
100,
sparse=sparse,
rule="G")
x = dist_out.ppf(dist_in.cdf(z))
dist = dist_in
y = np.array(map(func, x.T))
shape = y.shape
y = y.reshape(w.size, y.size / w.size)
if orth is None:
if dist.dependent:
orth = "chol"
else:
orth = "ttr"
if isinstance(orth, (str, int, long)):
orth = orth_select(orth)
if not isinstance(orth, po.Poly):
orth = orth(order, dist)
ovals = orth(*z)
vals1 = [(val * y.T * w).T for val in ovals]
vals2 = [(val**2 * w).T for val in ovals]
coef = (np.sum(vals1, 1).T / np.sum(vals2, 1)).T
coef = coef.reshape(len(coef), *shape[1:])
Q = po.transpose(po.sum(orth * coef.T, -1))
if retall:
return Q, x, w, y
return Q
def fit_quadrature(orth,
nodes,
weights,
solves,
retall=False,
norms=None,
**kws):
"""
Using spectral projection to create a polynomial approximation over
distribution space.
Parameters
----------
orth : Poly
Orthogonal polynomial expansion. Must be orthogonal for the
approximation to be accurate.
nodes : array_like
Where to evaluate the polynomial expansion and model to
approximate.
nodes.shape==(D,K) where D is the number of dimensions and K is
the number of nodes.
weights : array_like
Weights when doing numerical integration.
weights.shape==(K,)
solves : array_like, callable
The model to approximate.
If array_like is provided, it must have len(solves)==K.
If callable, it must take a single argument X with len(X)==D,
and return a consistent numpy compatible shape.
norms : array_like
In the of TTR using coefficients to estimate the polynomial
norm is more stable than manual calculation.
Calculated using quadrature if no provided.
norms.shape==(len(orth),)
"""
orth = po.Poly(orth)
nodes = np.asfarray(nodes)
weights = np.asfarray(weights)
if hasattr(solves, "__call__"):
solves = [solves(q) for q in nodes.T]
solves = np.asfarray(solves)
shape = solves.shape
solves = solves.reshape(weights.size, solves.size / weights.size)
ovals = orth(*nodes)
vals1 = [(val * solves.T * weights).T for val in ovals]
if norms is None:
vals2 = [(val**2 * weights).T for val in ovals]
norms = np.sum(vals2, 1)
else:
norms = np.array(norms).flatten()
assert len(norms) == len(orth)
coefs = (np.sum(vals1, 1).T / norms).T
coefs = coefs.reshape(len(coefs), *shape[1:])
Q = po.transpose(po.sum(orth * coefs.T, -1))
if retall:
return Q, coefs
return Q
def fit_adaptive(func,
poly,
dist,
abserr=1.e-8,
relerr=1.e-8,
budget=0,
norm=0,
bufname="",
retall=False):
"""Adaptive estimation of Fourier coefficients.
Parameters
----------
func : callable
Should take a single argument `q` which is 1D array
`len(q)=len(dist)`.
Must return something compatible with np.ndarray.
poly : Poly
Polynomial vector for which to create Fourier coefficients for.
dist : Dist
A distribution to optimize the Fourier coefficients to.
abserr : float
Absolute error tolerance.
relerr : float
Relative error tolerance.
budget : int
Soft maximum number of function evaluations.
0 means unlimited.
norm : int
Specifies the norm that is used to measure the error and
determine convergence properties (irrelevant for single-valued
functions). The `norm` argument takes one of the values:
0 : L0-norm
1 : L0-norm on top of paired the L2-norm. Good for complex
numbers where each conseqtive pair of the solution is real
and imaginery.
2 : L2-norm
3 : L1-norm
4 : L_infinity-norm
bufname : str, optional
Buffer evaluations to file such that the fit_adaptive can be
run again without redooing all evaluations.
retall : bool
If true, returns extra values.
Returns
-------
estimate[, coeffs, norms, coeff_error, norm_error]
estimate : Poly
The polynomial chaos expansion representation of func.
coeffs : np.ndarray
The Fourier coefficients.
norms : np.ndarray
The norm of the orthogonal polynomial squared.
coeff_error : np.ndarray
Estimated integration error of the coeffs.
norm_error : np.ndarray
Estimated integration error of the norms.
Examples
--------
>>> func = lambda q: q[0]*q[1]
>>> poly = cp.basis(0,2,2)
>>> dist = cp.J(cp.Uniform(0,1), cp.Uniform(0,1))
>>> res = cp.fit_adaptive(func, poly, dist, budget=100)
>>> print res
"""
if bufname:
func = lazy_eval(func, load=bufname)
dim = len(dist)
n = [0, 0]
dummy_x = dist.inv(.5 * np.ones(dim, dtype=np.float64))
val = np.array(func(dummy_x), np.float64)
xmin = np.zeros(dim, np.float64)
xmax = np.ones(dim, np.float64)
def f1(u, ns, *args):
qs = dist.inv(u.reshape(ns, dim))
out = (poly(*qs.T)**2).T.flatten()
return out
dim1 = len(poly)
val1 = np.empty(dim1, dtype=np.float64)
err1 = np.empty(dim1, dtype=np.float64)
_cubature(f1, dim1, xmin, xmax, (), "h", abserr, relerr, norm, budget,
True, val1, err1)
val1 = np.tile(val1, val.size)
dim2 = np.prod(val.shape) * dim1
val2 = np.empty(dim2, dtype=np.float64)
err2 = np.empty(dim2, dtype=np.float64)
def f2(u, ns, *args):
n[0] += ns
n[1] += 1
qs = dist.inv(u.reshape(ns, dim))
Y = np.array([func(q) for q in qs])
Q = poly(*qs.T)
out = np.array([Y.T * q1 for q1 in Q]).T.flatten()
out = out / np.tile(val1, ns)
return out
try:
_ = _cubature
except:
raise NotImplementedError("cubature not install properly")
_cubature(f2, dim2, xmin, xmax, (), "h", abserr, relerr, norm, budget,
True, val2, err2)
shape = (dim1, ) + val.shape
val2 = val2.reshape(shape[::-1]).T
out = po.transpose(po.sum(poly * val2.T, -1))
if retall:
return out, val2, val1, err2, err1
return val2
def orth_svd(order, dist, eps=1.e-300, normed=False, **kws):
"""
Create orthogonal polynomial expansion from pivoted Cholesky
decompostion. If eigenvalue of covariance matrix is bellow eps, the
polynomial is subset.
Parameters
----------
order : int
Order of polynomial expansion
dist : Dist
Distribution space where polynomials are orthogonal
eps : float
Threshold for when to subset the expansion.
normed : bool
If True, polynomial will be orthonormal.
**kws : optional
Extra keywords passed to dist.mom
Examples
--------
# >>> Z = cp.Normal()
# >>> print cp.orth_svd(2, Z)
# [1.0, q0^2-1.0, q0]
"""
raise DeprecationWarning("Obsolete")
dim = len(dist)
if isinstance(order, po.Poly):
basis = order
else:
basis = po.basis(1, order, dim)
basis = list(basis)
C = Cov(basis, dist, **kws)
L, P = pcd(C, approx=0, pivot=1, tol=eps)
N = L.shape[-1]
if len(L) != N:
I = [_.tolist().index(1) for _ in P]
b_ = [0] * N
for i in xrange(N):
b_[i] = basis[I[i]]
basis = b_
C = Cov(basis, dist, **kws)
L, P = pcd(C, approx=0, pivot=1, tol=eps)
N = L.shape[-1]
basis = po.Poly(basis)
Li = rlstsq(L, P, alpha=1.e-300).T
E_ = -po.sum(E(basis, dist, **kws) * Li.T, -1)
coefs = np.zeros((N + 1, N + 1))
coefs[1:, 1:] = Li
coefs[0, 0] = 1
coefs[0, 1:] = E_
out = {}
out[(0, ) * dim] = coefs[0]
for i in xrange(N):
I = basis[i].keys[0]
out[I] = coefs[i + 1]
P = po.Poly(out, dim, coefs.shape[1:], float)
if normed:
norm = np.sqrt(Var(P, dist, **kws))
norm[0] = 1
P = P / norm
return P
def fit_adaptive(func, poly, dist, abserr=1.e-8, relerr=1.e-8,
budget=0, norm=0, bufname="", retall=False):
"""Adaptive estimation of Fourier coefficients.
Parameters
----------
func : callable
Should take a single argument `q` which is 1D array
`len(q)=len(dist)`.
Must return something compatible with np.ndarray.
poly : Poly
Polynomial vector for which to create Fourier coefficients for.
dist : Dist
A distribution to optimize the Fourier coefficients to.
abserr : float
Absolute error tolerance.
relerr : float
Relative error tolerance.
budget : int
Soft maximum number of function evaluations.
0 means unlimited.
norm : int
Specifies the norm that is used to measure the error and
determine convergence properties (irrelevant for single-valued
functions). The `norm` argument takes one of the values:
0 : L0-norm
1 : L0-norm on top of paired the L2-norm. Good for complex
numbers where each conseqtive pair of the solution is real
and imaginery.
2 : L2-norm
3 : L1-norm
4 : L_infinity-norm
bufname : str, optional
Buffer evaluations to file such that the fit_adaptive can be
run again without redooing all evaluations.
retall : bool
If true, returns extra values.
Returns
-------
estimate[, coeffs, norms, coeff_error, norm_error]
estimate : Poly
The polynomial chaos expansion representation of func.
coeffs : np.ndarray
The Fourier coefficients.
norms : np.ndarray
The norm of the orthogonal polynomial squared.
coeff_error : np.ndarray
Estimated integration error of the coeffs.
norm_error : np.ndarray
Estimated integration error of the norms.
Examples
--------
>>> func = lambda q: q[0]*q[1]
>>> poly = cp.basis(0,2,2)
>>> dist = cp.J(cp.Uniform(0,1), cp.Uniform(0,1))
>>> res = cp.fit_adaptive(func, poly, dist, budget=100)
>>> print res
"""
if bufname:
func = lazy_eval(func, load=bufname)
dim = len(dist)
n = [0,0]
dummy_x = dist.inv(.5*np.ones(dim, dtype=np.float64))
val = np.array(func(dummy_x), np.float64)
xmin = np.zeros(dim, np.float64)
xmax = np.ones(dim, np.float64)
def f1(u, ns, *args):
qs = dist.inv(u.reshape(ns, dim))
out = (poly(*qs.T)**2).T.flatten()
return out
dim1 = len(poly)
val1 = np.empty(dim1, dtype=np.float64)
err1 = np.empty(dim1, dtype=np.float64)
_cubature(f1, dim1, xmin, xmax, (), "h", abserr, relerr, norm,
budget, True, val1, err1)
val1 = np.tile(val1, val.size)
dim2 = np.prod(val.shape)*dim1
val2 = np.empty(dim2, dtype=np.float64)
err2 = np.empty(dim2, dtype=np.float64)
def f2(u, ns, *args):
n[0] += ns
n[1] += 1
qs = dist.inv(u.reshape(ns, dim))
Y = np.array([func(q) for q in qs])
Q = poly(*qs.T)
out = np.array([Y.T*q1 for q1 in Q]).T.flatten()
out = out/np.tile(val1, ns)
return out
try:
_ = _cubature
except:
raise NotImplementedError(
"cubature not install properly")
_cubature(f2, dim2, xmin, xmax, (), "h", abserr, relerr, norm,
budget, True, val2, err2)
shape = (dim1,)+val.shape
val2 = val2.reshape(shape[::-1]).T
out = po.transpose(po.sum(poly*val2.T, -1))
if retall:
return out, val2, val1, err2, err1
return val2
def fit_regression(P, x, u, rule="LS", retall=False, **kws):
"""
Fit a polynomial chaos expansion using linear regression.
Parameters
----------
P : Poly
Polynomial chaos expansion with `P.shape=(M,)` and `P.dim=D`.
x : array_like
Collocation nodes with `x.shape=(D,K)`.
u : array_like
Model evaluations with `len(u)=K`.
retall : bool
If True return uhat in addition to R
rule : str
Regression method used.
The follwong methods uses scikits-learn as backend.
See `sklearn.linear_model` for more details.
Key Scikit-learn Description
--- ------------ -----------
Parameters Description
---------- -----------
"BARD" ARDRegression Bayesian ARD Regression
n_iter=300 Maximum iterations
tol=1e-3 Optimization tolerance
alpha_1=1e-6 Gamma scale parameter
alpha_2=1e-6 Gamma inverse scale parameter
lambda_1=1e-6 Gamma shape parameter
lambda_2=1e-6 Gamma inverse scale parameter
threshold_lambda=1e-4 Upper pruning threshold
"BR" BayesianRidge Bayesian Ridge Regression
n_iter=300 Maximum iterations
tol=1e-3 Optimization tolerance
alpha_1=1e-6 Gamma scale parameter
alpha_2=1e-6 Gamma inverse scale parameter
lambda_1=1e-6 Gamma shape parameter
lambda_2=1e-6 Gamma inverse scale parameter
"EN" ElastiNet Elastic Net
alpha=1.0 Dampening parameter
rho Mixing parameter in [0,1]
max_iter=300 Maximum iterations
tol Optimization tolerance
"ENC" ElasticNetCV EN w/Cross Validation
rho Dampening parameter(s)
eps=1e-3 min(alpha)/max(alpha)
n_alphas Number of alphas
alphas List of alphas
max_iter Maximum iterations
tol Optimization tolerance
cv=3 Cross validation folds
"LA" Lars Least Angle Regression
n_nonzero_coefs Number of non-zero coefficients
eps Cholesky regularization
"LAC" LarsCV LAR w/Cross Validation
max_iter Maximum iterations
cv=5 Cross validation folds
max_n_alphas Max points for residuals in cv
"LAS" Lasso Least Absolute Shrinkage and
Selection Operator
alpha=1.0 Dampening parameter
max_iter Maximum iterations
tol Optimization tolerance
"LASC" LassoCV LAS w/Cross Validation
eps=1e-3 min(alpha)/max(alpha)
n_alphas Number of alphas
alphas List of alphas
max_iter Maximum iterations
tol Optimization tolerance
cv=3 Cross validation folds
"LL" LassoLars Lasso and Lars model
max_iter Maximum iterations
eps Cholesky regularization
"LLC" LassoLarsCV LL w/Cross Validation
max_iter Maximum iterations
cv=5 Cross validation folds
max_n_alphas Max points for residuals in cv
eps Cholesky regularization
"LLIC" LassoLarsIC LL w/AIC or BIC
criterion "AIC" or "BIC" criterion
max_iter Maximum iterations
eps Cholesky regularization
"OMP" OrthogonalMatchingPursuit
n_nonzero_coefs Number of non-zero coefficients
tol Max residual norm (instead of non-zero coef)
Local methods
Key Description
--- -----------
"LS" Ordenary Least Squares
"T" Ridge Regression/Tikhonov Regularization
order Order of regularization (or custom matrix)
alpha Dampning parameter (else estimated from gcv)
"TC" T w/Cross Validation
order Order of regularization (or custom matrix)
alpha Dampning parameter (else estimated from gcv)
Returns
-------
R[, uhat]
R : Poly
Fitted polynomial with `R.shape=u.shape[1:]` and `R.dim=D`.
uhat : np.ndarray
The Fourier coefficients in the estimation.
Examples
--------
>>> P = cp.Poly([1, x, y])
>>> x = [[-1,-1,1,1], [-1,1,-1,1]]
>>> u = [0,1,1,2]
>>> print fit_regression(P, x, u)
0.5q1+0.5q0+1.0
"""
x = np.array(x)
if len(x.shape)==1:
x = x.reshape(1, *x.shape)
u = np.array(u)
Q = P(*x).T
shape = u.shape[1:]
u = u.reshape(u.shape[0], np.prod(u.shape[1:]))
rule = rule.upper()
# Local rules
if rule=="LS":
uhat = la.lstsq(Q, u)[0]
elif rule=="T":
uhat = rlstsq(Q, u, kws.get("order",0),
kws.get("alpha", None), False)
elif rule=="TC":
uhat = rlstsq(Q, u, kws.get("order",0),
kws.get("alpha", None), True)
else:
# Scikit-learn wrapper
try:
_ = lm
except:
raise NotImplementedError(
"sklearn not installed")
if rule=="BARD":
solver = lm.ARDRegression(fit_intercept=False,
copy_X=False, **kws)
elif rule=="BR":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.BayesianRidge(**kws)
elif rule=="EN":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.ElasticNet(**kws)
elif rule=="ENC":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.ElasticNetCV(**kws)
elif rule=="LA":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.Lars(**kws)
elif rule=="LAC":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.LarsCV(**kws)
elif rule=="LAS":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.Lasso(**kws)
elif rule=="LASC":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.LassoCV(**kws)
elif rule=="LL":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.LassoLars(**kws)
elif rule=="LLC":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.LassoLarsCV(**kws)
elif rule=="LLIC":
kws["fit_intercept"] = kws.get("fit_intercept", False)
solver = lm.LassoLarsIC(**kws)
elif rule=="OMP":
solver = lm.OrthogonalMatchingPursuit(**kws)
uhat = solver.fit(Q, u).coef_
u = u.reshape(u.shape[0], *shape)
R = po.sum((P*uhat.T), -1)
R = po.reshape(R, shape)
if retall==1:
return R, uhat
elif retall==2:
return R, uhat, Q
return R
def pcm_gq(func, order, dist_out, dist_in=None, acc=None,
orth=None, retall=False, sparse=False):
"""
Probabilistic Collocation Method using optimal Gaussian quadrature
Parameters
----------
Required arguments
func : callable
The model to be approximated.
Must accept arguments on the form `func(z, *args, **kws)`
where `z` is an 1-dimensional array with `len(z)==len(dist)`.
order : int
The order of the polynomial approximation
dist_out : Dist
Distributions for models parameter
Optional arguments
dist_in : Dist
If included, space will be mapped using a Rosenblatt
transformation from dist_out to dist_in before creating an
expansin in terms of dist_in
acc : float
The order of the sample scheme used
If omitted order+1 will be used
orth : int, str, callable, Poly
Orthogonal polynomial generation.
int, str :
orth will be passed to orth_select
for selection of orthogonalization.
See orth_select doc for more details.
callable :
the return of orth(M, dist) will be used.
Poly :
it will be used directly.
All polynomials must be orthogonal for method to work
properly.
args : itterable
Extra positional arguments passed to `func`.
kws : dict
Extra keyword arguments passed to `func`.
retall : bool
If True, return also number of evaluations
sparse : bool
If True, Smolyak sparsegrid will be used instead of full
tensorgrid
Returns
-------
Q[, X]
Q : Poly
Polynomial estimate of a given a model.
X : np.ndarray
Values used in evaluation
# Examples
# --------
# Define function:
# >>> func = lambda z: z[1]*z[0]
#
# Define distribution:
# >>> dist = cp.J(cp.Normal(), cp.Normal())
#
# Perform pcm:
# >>> p, x, w, y = cp.pcm_gq(func, 2, dist, acc=3, retall=True)
# >>> print cp.around(p, 10)
# q0q1
# >>> print len(w)
# 16
"""
if acc is None:
acc = order+1
if dist_in is None:
z,w = qu.generate_quadrature(acc, dist_out, 100, sparse=sparse,
rule="G")
x = z
dist = dist_out
else:
z,w = qu.generate_quadrature(acc, dist_in, 100, sparse=sparse,
rule="G")
x = dist_out.ppf(dist_in.cdf(z))
dist = dist_in
y = np.array(map(func, x.T))
shape = y.shape
y = y.reshape(w.size, y.size/w.size)
if orth is None:
if dist.dependent:
orth = "chol"
else:
orth = "ttr"
if isinstance(orth, (str, int, long)):
orth = orth_select(orth)
if not isinstance(orth, po.Poly):
orth = orth(order, dist)
ovals = orth(*z)
vals1 = [(val*y.T*w).T for val in ovals]
vals2 = [(val**2*w).T for val in ovals]
coef = (np.sum(vals1, 1).T/np.sum(vals2, 1)).T
coef = coef.reshape(len(coef), *shape[1:])
Q = po.transpose(po.sum(orth*coef.T, -1))
if retall:
return Q, x, w, y
return Q
