import warnings
import _minpack
from numpy import atleast_1d, dot, take, triu, shape, eye, \
transpose, zeros, product, greater, array, \
all, where, isscalar, asarray, inf, abs
from optimize import Result, _check_unknown_options
error = _minpack.error
__all__ = ['fsolve', 'leastsq', 'fixed_point', 'curve_fit']
def _check_func(checker, argname, thefunc, x0, args, numinputs, output_shape=None):
res = atleast_1d(thefunc(*((x0[:numinputs],) + args)))
if (output_shape is not None) and (shape(res) != output_shape):
if (output_shape[0] != 1):
if len(output_shape) > 1:
if output_shape[1] == 1:
return shape(res)
msg = "%s: there is a mismatch between the input and output " \
"shape of the '%s' argument" % (checker, argname)
func_name = getattr(thefunc, '__name__', None)
if func_name:
msg += " '%s'." % func_name
else:
msg += "."
raise TypeError(msg)
return shape(res)
def fsolve(func, x0, args=(), fprime=None, full_output=0,
col_deriv=0, xtol=1.49012e-8, maxfev=0, band=None,
epsfcn=0.0, factor=100, diag=None):
"""
Find the roots of a function.
Return the roots of the (non-linear) equations defined by
``func(x) = 0`` given a starting estimate.
Parameters
----------
func : callable ``f(x, *args)``
A function that takes at least one (possibly vector) argument.
x0 : ndarray
The starting estimate for the roots of ``func(x) = 0``.
args : tuple
Any extra arguments to `func`.
fprime : callable(x)
A function to compute the Jacobian of `func` with derivatives
across the rows. By default, the Jacobian will be estimated.
full_output : bool
If True, return optional outputs.
col_deriv : bool
Specify whether the Jacobian function computes derivatives down
the columns (faster, because there is no transpose operation).
Returns
-------
x : ndarray
The solution (or the result of the last iteration for
an unsuccessful call).
infodict : dict
A dictionary of optional outputs with the keys::
* 'nfev': number of function calls
* 'njev': number of Jacobian calls
* 'fvec': function evaluated at the output
* 'fjac': the orthogonal matrix, q, produced by the QR
factorization of the final approximate Jacobian
matrix, stored column wise
* 'r': upper triangular matrix produced by QR factorization of same
matrix
* 'qtf': the vector ``(transpose(q) * fvec)``
ier : int
An integer flag. Set to 1 if a solution was found, otherwise refer
to `mesg` for more information.
mesg : str
If no solution is found, `mesg` details the cause of failure.
Other Parameters
----------------
xtol : float
The calculation will terminate if the relative error between two
consecutive iterates is at most `xtol`.
maxfev : int
The maximum number of calls to the function. If zero, then
``100*(N+1)`` is the maximum where N is the number of elements
in `x0`.
band : tuple
If set to a two-sequence containing the number of sub- and
super-diagonals within the band of the Jacobi matrix, the
Jacobi matrix is considered banded (only for ``fprime=None``).
epsfcn : float
A suitable step length for the forward-difference
approximation of the Jacobian (for ``fprime=None``). If
`epsfcn` is less than the machine precision, it is assumed
that the relative errors in the functions are of the order of
the machine precision.
factor : float
A parameter determining the initial step bound
(``factor * || diag * x||``). Should be in the interval
``(0.1, 100)``.
diag : sequence
N positive entries that serve as a scale factors for the
variables.
See also
--------
root: Interface to root finding algorithms for multivariate
functions. See the 'hybr' `method` in particular.
Notes
-----
``fsolve`` is a wrapper around MINPACK's hybrd and hybrj algorithms.
"""
options = {'col_deriv': col_deriv,
'xtol': xtol,
'maxfev': maxfev,
'band': band,
'eps': epsfcn,
'factor': factor,
'diag': diag,
'full_output': full_output}
res = _root_hybr(func, x0, args, jac=fprime, **options)
if full_output:
x = res['x']
info = dict((k, res.get(k))
for k in ('nfev', 'njev', 'fjac', 'r', 'qtf') if k in res)
info['fvec'] = res['fun']
return x, info, res['status'], res['message']
else:
return res['x']
def _root_hybr(func, x0, args=(), jac=None,
col_deriv=0, xtol=1.49012e-08, maxfev=0, band=None, eps=0.0,
factor=100, diag=None, full_output=0, **unknown_options):
"""
Find the roots of a multivariate function using MINPACK's hybrd and
hybrj routines (modified Powell method).
Options for the hybrd algorithm are:
col_deriv : bool
Specify whether the Jacobian function computes derivatives down
the columns (faster, because there is no transpose operation).
xtol : float
The calculation will terminate if the relative error between two
consecutive iterates is at most `xtol`.
maxfev : int
The maximum number of calls to the function. If zero, then
``100*(N+1)`` is the maximum where N is the number of elements
in `x0`.
band : tuple
If set to a two-sequence containing the number of sub- and
super-diagonals within the band of the Jacobi matrix, the
Jacobi matrix is considered banded (only for ``fprime=None``).
eps : float
A suitable step length for the forward-difference
approximation of the Jacobian (for ``fprime=None``). If
`eps` is less than the machine precision, it is assumed
that the relative errors in the functions are of the order of
the machine precision.
factor : float
A parameter determining the initial step bound
(``factor * || diag * x||``). Should be in the interval
``(0.1, 100)``.
diag : sequence
N positive entries that serve as a scale factors for the
variables.
This function is called by the `root` function with `method=hybr`. It
is not supposed to be called directly.
"""
_check_unknown_options(unknown_options)
epsfcn = eps
x0 = array(x0, ndmin=1)
n = len(x0)
if type(args) != type(()):
args = (args,)
_check_func('fsolve', 'func', func, x0, args, n, (n,))
Dfun = jac
if Dfun is None:
if band is None:
ml, mu = -10,-10
else:
ml, mu = band[:2]
if (maxfev == 0):
maxfev = 200*(n + 1)
retval = _minpack._hybrd(func, x0, args, 1, xtol, maxfev,
ml, mu, epsfcn, factor, diag)
else:
_check_func('fsolve', 'fprime', Dfun, x0, args, n, (n,n))
if (maxfev == 0):
maxfev = 100*(n + 1)
retval = _minpack._hybrj(func, Dfun, x0, args, 1,
col_deriv, xtol, maxfev, factor,diag)
x, status = retval[0], retval[-1]
errors = {0:["Improper input parameters were entered.",TypeError],
1:["The solution converged.", None],
2:["The number of calls to function has "
"reached maxfev = %d." % maxfev, ValueError],
3:["xtol=%f is too small, no further improvement "
"in the approximate\n solution "
"is possible." % xtol, ValueError],
4:["The iteration is not making good progress, as measured "
"by the \n improvement from the last five "
"Jacobian evaluations.", ValueError],
5:["The iteration is not making good progress, "
"as measured by the \n improvement from the last "
"ten iterations.", ValueError],
'unknown': ["An error occurred.", TypeError]}
if status != 1 and not full_output:
if status in [2,3,4,5]:
msg = errors[status][0]
warnings.warn(msg, RuntimeWarning)
else:
try:
raise errors[status][1](errors[status][0])
except KeyError:
raise errors['unknown'][1](errors['unknown'][0])
info = retval[1]
info['fun'] = info.pop('fvec')
sol = Result(x=x, success=(status==1), status=status)
sol.update(info)
try:
sol['message'] = errors[status][0]
except KeyError:
info['message'] = errors['unknown'][0]
return sol
def leastsq(func, x0, args=(), Dfun=None, full_output=0,
col_deriv=0, ftol=1.49012e-8, xtol=1.49012e-8,
gtol=0.0, maxfev=0, epsfcn=0.0, factor=100, diag=None):
"""
Minimize the sum of squares of a set of equations.
::
x = arg min(sum(func(y)**2,axis=0))
y
Parameters
----------
func : callable
should take at least one (possibly length N vector) argument and
returns M floating point numbers.
x0 : ndarray
The starting estimate for the minimization.
args : tuple
Any extra arguments to func are placed in this tuple.
Dfun : callable
A function or method to compute the Jacobian of func with derivatives
across the rows. If this is None, the Jacobian will be estimated.
full_output : bool
non-zero to return all optional outputs.
col_deriv : bool
non-zero to specify that the Jacobian function computes derivatives
down the columns (faster, because there is no transpose operation).
ftol : float
Relative error desired in the sum of squares.
xtol : float
Relative error desired in the approximate solution.
gtol : float
Orthogonality desired between the function vector and the columns of
the Jacobian.
maxfev : int
The maximum number of calls to the function. If zero, then 100*(N+1) is
the maximum where N is the number of elements in x0.
epsfcn : float
A suitable step length for the forward-difference approximation of the
Jacobian (for Dfun=None). If epsfcn is less than the machine precision,
it is assumed that the relative errors in the functions are of the
order of the machine precision.
factor : float
A parameter determining the initial step bound
(``factor * || diag * x||``). Should be in interval ``(0.1, 100)``.
diag : sequence
N positive entries that serve as a scale factors for the variables.
Returns
-------
x : ndarray
The solution (or the result of the last iteration for an unsuccessful
call).
cov_x : ndarray
Uses the fjac and ipvt optional outputs to construct an
estimate of the jacobian around the solution. ``None`` if a
singular matrix encountered (indicates very flat curvature in
some direction). This matrix must be multiplied by the
residual variance to get the covariance of the
parameter estimates -- see curve_fit.
infodict : dict
a dictionary of optional outputs with the key s::
- 'nfev' : the number of function calls
- 'fvec' : the function evaluated at the output
- 'fjac' : A permutation of the R matrix of a QR
factorization of the final approximate
Jacobian matrix, stored column wise.
Together with ipvt, the covariance of the
estimate can be approximated.
- 'ipvt' : an integer array of length N which defines
a permutation matrix, p, such that
fjac*p = q*r, where r is upper triangular
with diagonal elements of nonincreasing
magnitude. Column j of p is column ipvt(j)
of the identity matrix.
- 'qtf' : the vector (transpose(q) * fvec).
mesg : str
A string message giving information about the cause of failure.
ier : int
An integer flag. If it is equal to 1, 2, 3 or 4, the solution was
found. Otherwise, the solution was not found. In either case, the
optional output variable 'mesg' gives more information.
Notes
-----
"leastsq" is a wrapper around MINPACK's lmdif and lmder algorithms.
cov_x is a Jacobian approximation to the Hessian of the least squares
objective function.
This approximation assumes that the objective function is based on the
difference between some observed target data (ydata) and a (non-linear)
function of the parameters `f(xdata, params)` ::
func(params) = ydata - f(xdata, params)
so that the objective function is ::
min sum((ydata - f(xdata, params))**2, axis=0)
params
"""
x0 = array(x0, ndmin=1)
n = len(x0)
if type(args) != type(()):
args = (args,)
m = _check_func('leastsq', 'func', func, x0, args, n)[0]
if n > m:
raise TypeError('Improper input: N=%s must not exceed M=%s' % (n,m))
if Dfun is None:
if (maxfev == 0):
maxfev = 200*(n + 1)
retval = _minpack._lmdif(func, x0, args, full_output, ftol, xtol,
gtol, maxfev, epsfcn, factor, diag)
else:
if col_deriv:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (n,m))
else:
_check_func('leastsq', 'Dfun', Dfun, x0, args, n, (m,n))
if (maxfev == 0):
maxfev = 100*(n + 1)
retval = _minpack._lmder(func, Dfun, x0, args, full_output, col_deriv,
ftol, xtol, gtol, maxfev, factor, diag)
errors = {0:["Improper input parameters.", TypeError],
1:["Both actual and predicted relative reductions "
"in the sum of squares\n are at most %f" % ftol, None],
2:["The relative error between two consecutive "
"iterates is at most %f" % xtol, None],
3:["Both actual and predicted relative reductions in "
"the sum of squares\n are at most %f and the "
"relative error between two consecutive "
"iterates is at \n most %f" % (ftol,xtol), None],
4:["The cosine of the angle between func(x) and any "
"column of the\n Jacobian is at most %f in "
"absolute value" % gtol, None],
5:["Number of calls to function has reached "
"maxfev = %d." % maxfev, ValueError],
6:["ftol=%f is too small, no further reduction "
"in the sum of squares\n is possible.""" % ftol, ValueError],
7:["xtol=%f is too small, no further improvement in "
"the approximate\n solution is possible." % xtol, ValueError],
8:["gtol=%f is too small, func(x) is orthogonal to the "
"columns of\n the Jacobian to machine "
"precision." % gtol, ValueError],
'unknown':["Unknown error.", TypeError]}
info = retval[-1] # The FORTRAN return value
if (info not in [1,2,3,4] and not full_output):
if info in [5,6,7,8]:
warnings.warn(errors[info][0], RuntimeWarning)
else:
try:
raise errors[info][1](errors[info][0])
except KeyError:
raise errors['unknown'][1](errors['unknown'][0])
mesg = errors[info][0]
if full_output:
cov_x = None
if info in [1,2,3,4]:
from numpy.dual import inv
from numpy.linalg import LinAlgError
perm = take(eye(n),retval[1]['ipvt']-1,0)
r = triu(transpose(retval[1]['fjac'])[:n,:])
R = dot(r, perm)
try:
cov_x = inv(dot(transpose(R),R))
except LinAlgError:
pass
return (retval[0], cov_x) + retval[1:-1] + (mesg, info)
else:
return (retval[0], info)
def _general_function(params, xdata, ydata, function):
return function(xdata, *params) - ydata
def _weighted_general_function(params, xdata, ydata, function, weights):
return weights * (function(xdata, *params) - ydata)
def curve_fit(f, xdata, ydata, p0=None, sigma=None, **kw):
"""
Use non-linear least squares to fit a function, f, to data.
Assumes ``ydata = f(xdata, *params) + eps``
Parameters
----------
f : callable
The model function, f(x, ...). It must take the independent
variable as the first argument and the parameters to fit as
separate remaining arguments.
xdata : An N-length sequence or an (k,N)-shaped array
for functions with k predictors.
The independent variable where the data is measured.
ydata : N-length sequence
The dependent data --- nominally f(xdata, ...)
p0 : None, scalar, or M-length sequence
Initial guess for the parameters. If None, then the initial
values will all be 1 (if the number of parameters for the function
can be determined using introspection, otherwise a ValueError
is raised).
sigma : None or N-length sequence
If not None, it represents the standard-deviation of ydata.
This vector, if given, will be used as weights in the
least-squares problem.
Returns
-------
popt : array
Optimal values for the parameters so that the sum of the squared error
of ``f(xdata, *popt) - ydata`` is minimized
pcov : 2d array
The estimated covariance of popt. The diagonals provide the variance
of the parameter estimate.
See Also
--------
leastsq
Notes
-----
The algorithm uses the Levenburg-Marquardt algorithm through `leastsq`.
Additional keyword arguments are passed directly to that algorithm.
Examples
--------
>>> import numpy as np
>>> from scipy.optimize import curve_fit
>>> def func(x, a, b, c):
... return a*np.exp(-b*x) + c
>>> x = np.linspace(0,4,50)
>>> y = func(x, 2.5, 1.3, 0.5)
>>> yn = y + 0.2*np.random.normal(size=len(x))
>>> popt, pcov = curve_fit(func, x, yn)
"""
if p0 is None:
# determine number of parameters by inspecting the function
import inspect
args, varargs, varkw, defaults = inspect.getargspec(f)
if len(args) < 2:
msg = "Unable to determine number of fit parameters."
raise ValueError(msg)
if 'self' in args:
p0 = [1.0] * (len(args)-2)
else:
p0 = [1.0] * (len(args)-1)
if isscalar(p0):
p0 = array([p0])
args = (xdata, ydata, f)
if sigma is None:
func = _general_function
else:
func = _weighted_general_function
args += (1.0/asarray(sigma),)
# Remove full_output from kw, otherwise we're passing it in twice.
return_full = kw.pop('full_output', False)
res = leastsq(func, p0, args=args, full_output=1, **kw)
(popt, pcov, infodict, errmsg, ier) = res
if ier not in [1,2,3,4]:
msg = "Optimal parameters not found: " + errmsg
raise RuntimeError(msg)
if (len(ydata) > len(p0)) and pcov is not None:
s_sq = (func(popt, *args)**2).sum()/(len(ydata)-len(p0))
pcov = pcov * s_sq
else:
pcov = inf
if return_full:
return popt, pcov, infodict, errmsg, ier
else:
return popt, pcov
def check_gradient(fcn, Dfcn, x0, args=(), col_deriv=0):
"""Perform a simple check on the gradient for correctness.
"""
x = atleast_1d(x0)
n = len(x)
x = x.reshape((n,))
fvec = atleast_1d(fcn(x,*args))
m = len(fvec)
fvec = fvec.reshape((m,))
ldfjac = m
fjac = atleast_1d(Dfcn(x,*args))
fjac = fjac.reshape((m,n))
if col_deriv == 0:
fjac = transpose(fjac)
xp = zeros((n,), float)
err = zeros((m,), float)
fvecp = None
_minpack._chkder(m, n, x, fvec, fjac, ldfjac, xp, fvecp, 1, err)
fvecp = atleast_1d(fcn(xp,*args))
fvecp = fvecp.reshape((m,))
_minpack._chkder(m, n, x, fvec, fjac, ldfjac, xp, fvecp, 2, err)
good = (product(greater(err, 0.5), axis=0))
return (good, err)
# Steffensen's Method using Aitken's Del^2 convergence acceleration.
def fixed_point(func, x0, args=(), xtol=1e-8, maxiter=500):
"""Find the point where func(x) == x
Given a function of one or more variables and a starting point, find a
fixed-point of the function: i.e. where func(x)=x.
Uses Steffensen's Method using Aitken's Del^2 convergence acceleration.
See Burden, Faires, "Numerical Analysis", 5th edition, pg. 80
Examples
--------
>>> from numpy import sqrt, array
>>> from scipy.optimize import fixed_point
>>> def func(x, c1, c2):
return sqrt(c1/(x+c2))
>>> c1 = array([10,12.])
>>> c2 = array([3, 5.])
>>> fixed_point(func, [1.2, 1.3], args=(c1,c2))
array([ 1.4920333 , 1.37228132])
"""
if not isscalar(x0):
x0 = asarray(x0)
p0 = x0
for iter in range(maxiter):
p1 = func(p0, *args)
p2 = func(p1, *args)
d = p2 - 2.0 * p1 + p0
p = where(d == 0, p2, p0 - (p1 - p0)*(p1 - p0) / d)
relerr = where(p0 == 0, p, (p-p0)/p0)
if all(abs(relerr) < xtol):
return p
p0 = p
else:
p0 = x0
for iter in range(maxiter):
p1 = func(p0, *args)
p2 = func(p1, *args)
d = p2 - 2.0 * p1 + p0
if d == 0.0:
return p2
else:
p = p0 - (p1 - p0)*(p1 - p0) / d
if p0 == 0:
relerr = p
else:
relerr = (p - p0)/p0
if abs(relerr) < xtol:
return p
p0 = p
msg = "Failed to converge after %d iterations, value is %s" % (maxiter, p)
raise RuntimeError(msg)