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aaronreidsmith / scipy   python

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Version: 1.3.3 

/ optimize / minpack.py

from __future__ import division, print_function, absolute_import

import threading
import warnings
from . import _minpack

import numpy as np
from numpy import (atleast_1d, dot, take, triu, shape, eye,
                   transpose, zeros, prod, greater, array,
                   all, where, isscalar, asarray, inf, abs,
                   finfo, inexact, issubdtype, dtype)
from scipy.linalg import svd, cholesky, solve_triangular, LinAlgError
from scipy._lib._util import _asarray_validated, _lazywhere
from .optimize import OptimizeResult, _check_unknown_options, OptimizeWarning
from ._lsq import least_squares
from ._lsq.common import make_strictly_feasible
from ._lsq.least_squares import prepare_bounds

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 += "."
            msg += 'Shape should be %s but it is %s.' % (output_shape, shape(res))
            raise TypeError(msg)
    if issubdtype(res.dtype, inexact):
        dt = res.dtype
    else:
        dt = dtype(float)
    return shape(res), dt


def fsolve(func, x0, args=(), fprime=None, full_output=0,
           col_deriv=0, xtol=1.49012e-8, maxfev=0, band=None,
           epsfcn=None, 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,
        and returns a value of the same length.
    x0 : ndarray
        The starting estimate for the roots of ``func(x) = 0``.
    args : tuple, optional
        Any extra arguments to `func`.
    fprime : callable ``f(x, *args)``, optional
        A function to compute the Jacobian of `func` with derivatives
        across the rows. By default, the Jacobian will be estimated.
    full_output : bool, optional
        If True, return optional outputs.
    col_deriv : bool, optional
        Specify whether the Jacobian function computes derivatives down
        the columns (faster, because there is no transpose operation).
    xtol : float, optional
        The calculation will terminate if the relative error between two
        consecutive iterates is at most `xtol`.
    maxfev : int, optional
        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, optional
        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, optional
        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, optional
        A parameter determining the initial step bound
        (``factor * || diag * x||``).  Should be in the interval
        ``(0.1, 100)``.
    diag : sequence, optional
        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).
    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 the 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.

    See Also
    --------
    root : Interface to root finding algorithms for multivariate
           functions. See the ``method=='hybr'`` 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}

    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:
        status = res['status']
        msg = res['message']
        if status == 0:
            raise TypeError(msg)
        elif status == 1:
            pass
        elif status in [2, 3, 4, 5]:
            warnings.warn(msg, RuntimeWarning)
        else:
            raise TypeError(msg)
        return res['x']


def _root_hybr(func, x0, args=(), jac=None,
               col_deriv=0, xtol=1.49012e-08, maxfev=0, band=None, eps=None,
               factor=100, diag=None, **unknown_options):
    """
    Find the roots of a multivariate function using MINPACK's hybrd and
    hybrj routines (modified Powell method).

    Options
    -------
    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.

    """
    _check_unknown_options(unknown_options)
    epsfcn = eps

    x0 = asarray(x0).flatten()
    n = len(x0)
    if not isinstance(args, tuple):
        args = (args,)
    shape, dtype = _check_func('fsolve', 'func', func, x0, args, n, (n,))
    if epsfcn is None:
        epsfcn = finfo(dtype).eps
    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.",
              1: "The solution converged.",
              2: "The number of calls to function has "
                  "reached maxfev = %d." % maxfev,
              3: "xtol=%f is too small, no further improvement "
                  "in the approximate\n  solution "
                  "is possible." % xtol,
              4: "The iteration is not making good progress, as measured "
                  "by the \n  improvement from the last five "
                  "Jacobian evaluations.",
              5: "The iteration is not making good progress, "
                  "as measured by the \n  improvement from the last "
                  "ten iterations.",
              'unknown': "An error occurred."}

    info = retval[1]
    info['fun'] = info.pop('fvec')
    sol = OptimizeResult(x=x, success=(status == 1), status=status)
    sol.update(info)
    try:
        sol['message'] = errors[status]
    except KeyError:
        sol['message'] = errors['unknown']

    return sol


LEASTSQ_SUCCESS = [1, 2, 3, 4]
LEASTSQ_FAILURE = [5, 6, 7, 8]


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=None, 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. It must not return NaNs or
        fitting might fail.
    x0 : ndarray
        The starting estimate for the minimization.
    args : tuple, optional
        Any extra arguments to func are placed in this tuple.
    Dfun : callable, optional
        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, optional
        non-zero to return all optional outputs.
    col_deriv : bool, optional
        non-zero to specify that the Jacobian function computes derivatives
        down the columns (faster, because there is no transpose operation).
    ftol : float, optional
        Relative error desired in the sum of squares.
    xtol : float, optional
        Relative error desired in the approximate solution.
    gtol : float, optional
        Orthogonality desired between the function vector and the columns of
        the Jacobian.
    maxfev : int, optional
        The maximum number of calls to the function. If `Dfun` is provided
        then the default `maxfev` is 100*(N+1) where N is the number of elements
        in x0, otherwise the default `maxfev` is 200*(N+1).
    epsfcn : float, optional
        A variable used in determining a suitable step length for the forward-
        difference approximation of the Jacobian (for Dfun=None).
        Normally the actual step length will be sqrt(epsfcn)*x
        If epsfcn is less than the machine precision, it is assumed that the
        relative errors are of the order of the machine precision.
    factor : float, optional
        A parameter determining the initial step bound
        (``factor * || diag * x||``). Should be in interval ``(0.1, 100)``.
    diag : sequence, optional
        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
        The inverse of the Hessian. `fjac` and `ipvt` are used to construct an
        estimate of the Hessian. A value of None indicates a singular matrix,
        which means the curvature in parameters `x` is numerically flat. To
        obtain the covariance matrix of the parameters `x`, `cov_x` must be
        multiplied by the variance of the residuals -- see curve_fit.
    infodict : dict
        a dictionary of optional outputs with the keys:

        ``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
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