示例#1
0
def line_fit(p, x, y, y_error, x_error=False, iterations=10000):
    """
    Linear Fit to data, taking either errors in y or both in x and y into
    account.

    Parameters
    ----------

    p : list
        Containg slope (m) and y-axis intersection (b) p=[m, b]. Same as in
        :func:`line` and :func:`antiline`.
    x : float or list
        x measurements. Data.
    y : float or list
        y measurements. Data.
    y_error : float or list
        The y measurment errors.
    x_error : float or list
        The x measurment errors. If unset only errors in y are taken into
        account.
    """
    p1, cov, info, mesg, success = least(linear_error_function, p,
                                         args=(x, y, y_error, x_error),
                                         maxfev=int(iterations), full_output=1)
    dof = len(x) - len(p) - 1  # degrees of Freedom
    chisq = sum(info['fvec'] * info['fvec']) / dof
    Error = std(info['fvec'])
    return p1, chisq, Error
示例#2
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def _grid_fit(data, beta, nu_or_lambda='nu', fit_beta=False, rawChiSq=False,
             kappa='Kruegel'):
    r"""
    Different approach to find the best fitting SED using certain ranges of
    temperatures and masses to avoid unreasonably high values.

    Not sure about the functionality and the code is badly written with the
    temperature and mass ranges hard coded. Thats why its not public.
    Once approved it may be made public again.

    Parameters
    ----------
    data : array
        Same format as in grey_body_fit.
    beta :
        The beta value. If fit_beta=True this is varied in the fits.
    kappa :
        As in :func:`greybody`.

    Other Parameters
    ----------------
    fit_beta: True or False
        Steers if beta is fittet or not.
    rawChisq: True or False
        Returns chi square without normalisation, or not.
    """
    def _err(p, x, y, y_error, nu_or_lambda):
        """
        The function to be minimized by scipy.optimize.leastsq. It returns the
        difference between the measured fluxes, y, and the calculated fluxes
        for the parameters p of the SED at the given frequency x.

        Parameters
        ----------
        p : list
            same start start_parameter as in grey_body_fit
        x and y :
         The two rows, data[0] and data[1] of the data variable from
         grey_body_fit.
        y_error : The absolute error on the flux measurement.

        Other Parameters
        ----------------
        nu_or_lambda : string
            Specify whether x is a frequency :math:`\nu` ``'nu'`` or
            a wavelenght :math:`\lambda` ``'lambda'``; default is ``'nu'``.::
            **Don't** use ``'lambda'`` as this part of the
            :py:func:`grey_body` is not up-to-date.

        Notes
        -----
        This function caluclates the residuals that are minimized by
        :func:`leastsq`, thus it calculates:

        .. math::

            (model-measurement)/\sigma

        Note the :math:`\chi^2` is defined as:

        .. math::

            \chi^2 = \frac{1}{N} \sum{(model-measurement)/\sigma}

        :warning:`Formula has to be checked.`

        This functions is different from the _err functions in grey_body_fit
        because the start parameters are handles differently.
        """
        if not fit_beta:
            pMulti = [T, p, beta]
            print pMulti
        if fit_beta:
            pMulti = [Temps, p]
            print pMulti
        return (((multi_component_grey_body(pMulti, x, nu_or_lambda, kappa)[0])
                - y) / y_error)
    beta = [beta]
    T1 = arange(5, 70, 1)
    T2 = arange(20, 100, 1)
    chisqList = {}
    chisqList1 = []
    for i in T1:
        for j in T2:
            T = [i, j]
            N = [1e2, 1]
            if not fit_beta:
                p = N
            if fit_beta:
                p = N + beta
            p2, cov, info, mesg, success = least(_err, p, args=(data[0],
                                                 data[1], data[2],
                                                 nu_or_lambda),
                                                 maxfev=int(1e9),
                                                 full_output=1)
            dof = len(data[0]) - len(p) - 1  # Degrees of Freedom
            chisq = sum(info['fvec'] * info['fvec']) / dof  # see above
            rawchisq = sum(info['fvec'] * info['fvec'])
            chisqList[chisq] = [[i, j], p2]
            chisqList1 += [chisq]
    chisq = sorted(chisqList)[0]
    T, p2 = chisqList[sorted(chisqList)[0]]
    if not fit_beta:
        numberOfComponents = len(p)
        p2 = [T, p2, beta]
    if fit_beta:
        numberOfComponents = (len(p) - 1)
        p2 = [Temps, list(p2[0:numberOfComponents]), [p2[len(p) - 1]]]
    if not rawChiSq:
        return p2, chisq
    if rawChiSq:
        return p2, rawchisq
    return sorted(chisq)[0]
示例#3
0
def grey_body_fit(data, start_parameter, nu_or_lambda='nu', fit_beta=False,
                fix_temperature=False, rawChiSq=None, kappa='Kruegel',
                residuals=False, iterations=1e9):
    r"""
    This function fits a multi component grey body model to an observed SED for
    the optical thin case.

    Parameters
    ----------
    data : array
        The obseved data. Array of shape(3, x) first row has to be the X values
        (Frequency in [GHz]) of the measurements, second row the Y values
        (Flux [Jy]), and the third row  the Z values the errors on the
        fluxes i.e.:
        data = array([[X1, X2, X3, ...], [Y1, Y2, Y3,...], [Z1, Z2,
        Z3, ...]])
    start_parameter : array
        Array of a first guess of the parameters of the grey_body components.
        The number of components is arbitrary.
        start_parameter = [[T1, T2, T3,...], [N1, N2, N3, ...], beta]

    fit_beta : True or False
        If True Beta is allowed to vary. Default is False.

    fix_temperature : True or False
        If True the Temperature is fixed allowed to vary.

    rawChiSq :
        if None the function gives the reduced chisq Value. If True the
        function gives chisq without dividing it by the dof

    Returns
    -------
    p2 : list
        The final grey_body parameters that reduce the least squares for the
        given dataset.
    chisq/rawChiSq :
        chisq is reduced chisq with degrees of freedom:
        dof= #dataPoints-#freeFitParameters-1

    Other Parameters
    ----------------
    nu_or_lambda : string
        Specify whether x is a frequency :math:`\nu` ``'nu'`` or
        a wavelenght :math:`\lambda` ``'lambda'``; default is ``'nu'``.::
        **Don't** use ``'lambda'`` as this part of the
        :py:func:`grey_body` is not up-to-date.

    See Also
    --------
    scipy.optimize.leastsq: This function is used to perform the least squares
    fit.
    multi_component_grey_body, grey_body, black_body: Defining the function to
    be fittet to the data.

    Notes
    -----
    A one component fit has four free parameters if beta is allowed to vary or
    three if beta is fixed (one more than parameters to fit). Each additional
    component adds two more free paramters to fit.
    Assure that:
    number of data points > number of free parameters.
    """
    # Distinguish between the different options and build the parameter list
    # needed by optimize.leastsq()
    if not fit_beta:
        if not fix_temperature:
            p = start_parameter[0] + start_parameter[1]
            beta = start_parameter[2]
        if fix_temperature:
            p = start_parameter[1]
            Temps = start_parameter[0]
            beta = start_parameter[2]
    if fit_beta:
        if not fix_temperature:
            p = start_parameter[0] + start_parameter[1] + start_parameter[2]
        if fix_temperature:
            p = start_parameter[1] + start_parameter[2]
            Temps = start_parameter[0]

    def _err(p, x, y, y_error, nu_or_lambda):
        """
        The function to be minimized by scipy.optimize.leastsq. It returns the
        difference between the measured fluxes, y, and the calculated fluxes
        for the parameters p of the SED at the given frequency x.

        Parameters
        ----------
        p : list
            same start start_parameter as in grey_body_fit
        x and y :
         The two rows, data[0] and data[1] of the data variable from
         grey_body_fit.
        y_error : The absolute error on the flux measurement.

        Other Parameters
        ----------------
        nu_or_lambda : string
            Specify whether x is a frequency :math:`\nu` ``'nu'`` or
            a wavelenght :math:`\lambda` ``'lambda'``; default is ``'nu'``.::
            **Don't** use ``'lambda'`` as this part of the
            :py:func:`grey_body` is not up-to-date.

        Notes
        -----
        This function caluclates the residuals that are minimized by
        :func:`leastsq`, thus it calculates:

        .. math::

            (model-measurement)/\sigma

        Note the :math:`\chi^2` is defined as:

        .. math::

            \chi^2 = \frac{1}{N} \sum{(model-measurement)/\sigma}

        :warning:`Formula has to be checked.`
        """
        if not fit_beta:
            if not fix_temperature:
                numberOfComponents = (len(p)) / 2
                pMulti = [list(p[0:numberOfComponents]),
                          list(p[numberOfComponents:numberOfComponents * 2])]
                pMulti += [beta]
            if fix_temperature:
                pMulti = [Temps, p, beta]

        if fit_beta:
            if not fix_temperature:
                numberOfComponents = (len(p) - 1) / 2
                pMulti = [list(p[0:numberOfComponents]),
                          list(p[numberOfComponents:numberOfComponents * 2]),
                          p[len(p) - 1]]

            if fix_temperature:
                numberOfComponents = len(p) - 1
                pMulti = [Temps, list(p[0:numberOfComponents]), p[len(p) - 1]]

        return (((multi_component_grey_body(pMulti, x, nu_or_lambda,
                kappa=kappa)[0]) - y) / y_error)
    # The actual fit
    # maxfev : Number of integrations
    # full_output: Additional informations
    # args: X and Y data
    p2, cov, info, mesg, success = least(_err, p, args=(data[0], data[1],
                                         data[2], nu_or_lambda),
                                         maxfev=int(iterations), full_output=1)
    # return of the optimized parameters
    dof = len(data[0]) - len(p) - 1  # degrees of Freedom
    chisq = sum(info['fvec'] * info['fvec']) / dof  # see above
    rawchisq = sum(info['fvec'] * info['fvec'])

    if not fit_beta:
        if not fix_temperature:
            numberOfComponents = (len(p)) / 2
            p2 = [list(p2[0:numberOfComponents]),
                  list(p2[numberOfComponents:numberOfComponents * 2]), beta]
        if fix_temperature:
            numberOfComponents = len(p)
            p2 = [Temps, p2, beta]

    if fit_beta:
        if not fix_temperature:
            numberOfComponents = (len(p) - 1) / 2
            p2 = [list(p2[0:numberOfComponents]),
                  list(p2[numberOfComponents:numberOfComponents * 2]),
                  [p2[len(p) - 1]]]
        if fix_temperature:
            numberOfComponents = (len(p) - 1)
            p2 = [Temps, list(p2[0:numberOfComponents]), [p2[len(p) - 1]]]
    if residuals:
        return p2, chisq, info['fvec']
    if rawChiSq == None:
        return p2, chisq
    if rawChiSq:
        return p2, rawchisq