https://github.com/lmfit/lmfit-py
Raw File
Tip revision: 071b97ad88545f33cdbeede903ff156646bd8618 authored by Matthew Newville on 30 May 2017, 02:28:41 UTC
update asv conf
Tip revision: 071b97a
printfuncs.py
"""Functions to display fitting results and confidence intervals."""
from __future__ import print_function

import re

from .parameter import Parameters


def alphanumeric_sort(s, _nsre=re.compile('([0-9]+)')):
    """Sort alphanumeric string."""
    return [int(text) if text.isdigit() else text.lower()
            for text in re.split(_nsre, s)]


def getfloat_attr(obj, attr, fmt='%.3f'):
    """Format an attribute of an object for printing."""
    val = getattr(obj, attr, None)
    if val is None:
        return 'unknown'
    if isinstance(val, int):
        return '%d' % val
    if isinstance(val, float):
        return fmt % val
    else:
        return repr(val)


def gformat(val, length=11):
    """Format a number with '%g'-like format.

    The return will be length ``length`` (default is 12) and have at
    least length-6 significant digits.

    """
    length = max(length, 7)
    fmt = '{0: .%ig}' % (length-6)
    if isinstance(val, int):
        out = ('{0: .%ig}' % (length-2)).format(val)
        if len(out) > length:
            out = fmt.format(val)
    else:
        out = fmt.format(val)
    if len(out) < length:
        if 'e' in out:
            ie = out.find('e')
            if '.' not in out[:ie]:
                out = out[:ie] + '.' + out[ie:]
            out = out.replace('e', '0'*(length-len(out))+'e')
        else:
            fmt = '{0: .%ig}' % (length-1)
            out = fmt.format(val)[:length]
            if len(out) < length:
                pad = '0' if '.' in out else ' '
                out += pad*(length-len(out))
    return out


CORREL_HEAD = '[[Correlations]] (unreported correlations are < % .3f)'


def fit_report(inpars, modelpars=None, show_correl=True, min_correl=0.1,
               sort_pars=False):
    """Generate a report of the fitting results.

    The report contains the best-fit values for the parameters and their
    uncertainties and correlations.

    Parameters
    ----------
    inpars  : Parameters
       Input Parameters from fit or MinimizerResult returned from a fit.
    modelpars : Parameters, optional
       Known Model Parameters.
    show_correl : bool, optional
       Whether to show list of sorted correlations (default is True).
    min_correl : float, optional
       Smallest correlation in absolute value to show (default is 0.1).
    sort_pars : bool or callable, optional
       Whether to show parameter names sorted in alphanumerical order. If
       False (default), then the parameters will be listed in the order they
       were added to the Parameters dictionary. If callable, then this (one
       argument) function is used to extract a comparison key from each
       list element.

    Returns
    -------
    string
       Multi-line text of fit report.

    """
    if isinstance(inpars, Parameters):
        result, params = None, inpars
    if hasattr(inpars, 'params'):
        result = inpars
        params = inpars.params

    if sort_pars:
        if callable(sort_pars):
            key = sort_pars
        else:
            key = alphanumeric_sort
        parnames = sorted(params, key=key)
    else:
        # dict.keys() returns a KeysView in py3, and they're indexed
        # further down
        parnames = list(params.keys())

    buff = []
    add = buff.append
    if result is not None:
        add("[[Fit Statistics]]")
        add("    # function evals   = %s" % getfloat_attr(result, 'nfev'))
        add("    # data points      = %s" % getfloat_attr(result, 'ndata'))
        add("    # variables        = %s" % getfloat_attr(result, 'nvarys'))
        add("    chi-square         = %s" % getfloat_attr(result, 'chisqr'))
        add("    reduced chi-square = %s" % getfloat_attr(result, 'redchi'))
        add("    Akaike info crit   = %s" % getfloat_attr(result, 'aic'))
        add("    Bayesian info crit = %s" % getfloat_attr(result, 'bic'))

    namelen = max([len(n) for n in parnames])
    add("[[Variables]]")
    for name in parnames:
        par = params[name]
        space = ' '*(namelen+1-len(name))
        nout = "%s:%s" % (name, space)
        inval = '(init= ?)'
        if par.init_value is not None:
            inval = '(init=% .7g)' % par.init_value
        if modelpars is not None and name in modelpars:
            inval = '%s, model_value =% .7g' % (inval, modelpars[name].value)
        try:
            sval = gformat(par.value)
        except (TypeError, ValueError):
            sval = 'Non Numeric Value?'

        if par.stderr is not None:
            serr = gformat(par.stderr, length=9)

            try:
                spercent = '({0:.2%})'.format(abs(par.stderr/par.value))
            except ZeroDivisionError:
                spercent = ''
            sval = '%s +/-%s %s' % (sval, serr, spercent)

        if par.vary:
            add("    %s %s %s" % (nout, sval, inval))
        elif par.expr is not None:
            add("    %s %s  == '%s'" % (nout, sval, par.expr))
        else:
            add("    %s % .7g (fixed)" % (nout, par.value))

    if show_correl:
        correls = {}
        for i, name in enumerate(parnames):
            par = params[name]
            if not par.vary:
                continue
            if hasattr(par, 'correl') and par.correl is not None:
                for name2 in parnames[i+1:]:
                    if (name != name2 and name2 in par.correl and
                            abs(par.correl[name2]) > min_correl):
                        correls["%s, %s" % (name, name2)] = par.correl[name2]

        sort_correl = sorted(correls.items(), key=lambda it: abs(it[1]))
        sort_correl.reverse()
        if len(sort_correl) > 0:
            add(CORREL_HEAD % min_correl)
        for name, val in sort_correl:
            lspace = max(1, 25 - len(name))
            add('    C(%s)%s = % .3f ' % (name, (' '*30)[:lspace], val))
    return '\n'.join(buff)


def report_errors(params, **kws):
    """Print a report for fitted params: see error_report()."""
    print(fit_report(params, **kws))


def report_fit(params, **kws):
    """Print a report for fitted params: see error_report()."""
    print(fit_report(params, **kws))


def ci_report(ci, with_offset=True, ndigits=5):
    """Return text of a report for confidence intervals.

    Parameters
    ----------
    with_offset : bool, optional
        Whether to subtract best value from all other values (default is True).
    ndigits : int, optional
        Number of significant digits to show (default is 5).

    Returns
    -------
    str
       Text of formatted report on confidence intervals.

    """
    maxlen = max([len(i) for i in ci])
    buff = []
    add = buff.append

    def convp(x):
        """TODO: function docstring."""
        if abs(x[0]) < 1.e-2:
            return "_BEST_"
        return "%.2f%%" % (x[0]*100)

    title_shown = False
    fmt_best = fmt_diff = "{0:.%if}" % ndigits
    if with_offset:
        fmt_diff = "{0:+.%if}" % ndigits
    for name, row in ci.items():
        if not title_shown:
            add("".join([''.rjust(maxlen+1)] + [i.rjust(ndigits+5)
                                                for i in map(convp, row)]))
            title_shown = True
        thisrow = [" %s:" % name.ljust(maxlen)]
        offset = 0.0
        if with_offset:
            for cval, val in row:
                if abs(cval) < 1.e-2:
                    offset = val
        for cval, val in row:
            if cval < 1.e-2:
                sval = fmt_best.format(val)
            else:
                sval = fmt_diff.format(val-offset)
            thisrow.append(sval.rjust(ndigits+5))
        add("".join(thisrow))

    return '\n'.join(buff)


def report_ci(ci):
    """Print a report for confidence intervals."""
    print(ci_report(ci))
back to top