https://github.com/lmfit/lmfit-py
Tip revision: 4b5dde4c5bd8b1f063b5a656fbf0c7c898a9027e authored by Matt Newville on 20 August 2014, 19:11:04 UTC
tweak doc html header
tweak doc html header
Tip revision: 4b5dde4
printfuncs.py
# -*- coding: utf-8 -*-
"""
Created on Fri Apr 20 19:24:21 2012
@author: Tillsten
Changes:
- 13-Feb-2013 M Newville
complemented "report_errors" and "report_ci" with
"error_report" and "ci_report" (respectively) which
return the text of the report. Thus report_errors()
is simply:
def report_errors(params, modelpars=None, show_correl=True):
print error_report(params, modelpars=modelpars,
show_correl=show_correl)
and similar for report_ci() / ci_report()
"""
from __future__ import print_function
from .parameter import Parameters
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)
CORREL_HEAD = '[[Correlations]] (unreported correlations are < % .3f)'
def fit_report(inpars, modelpars=None, show_correl=True, min_correl=0.1):
"""return text of a report for fitted params best-fit values,
uncertainties and correlations
arguments
----------
inpars Parameters from fit or Minizer object returned from a fit.
modelpars Optional Known Model Parameters [None]
show_correl whether to show list of sorted correlations [True]
min_correl smallest correlation absolute value to show [0.1]
"""
if isinstance(inpars, Parameters):
result, params = None, inpars
if hasattr(inpars, 'params'):
result = inpars
params = inpars.params
parnames = sorted(params)
parnames = sorted(params)
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'))
namelen = max([len(n) for n in parnames])
add("[[Variables]]")
for name in parnames:
par = params[name]
space = ' '*(namelen+2 - len(name))
nout = "%s: %s" % (name, space)
inval = 'inital = ?'
if par.init_value is not None:
inval = 'initial = % .7g' % par.init_value
if modelpars is not None and name in modelpars:
inval = '%s, model_value =% .7g' % (inval, modelpars[name].value)
try:
sval = '% .7g' % par.value
except (TypeError, ValueError):
sval = 'Non Numeric Value?'
if par.stderr is not None:
sval = '% .7g +/- %.7g' % (par.value, par.stderr)
try:
sval = '%s (%.2f%%)' % (sval, abs(par.stderr/par.value)*100)
except ZeroDivisionError:
pass
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:
add(CORREL_HEAD % min_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
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()
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):
"""return text of a report for confidence intervals"""
maxlen = max([len(i) for i in ci])
buff = []
add = buff.append
convp = lambda x: ("%.2f" % (x[0]*100))+'%'
conv = lambda x: "%.5f" % x[1]
title_shown = False
for name, row in ci.items():
if not title_shown:
add("".join([''.rjust(maxlen)]+[i.rjust(10)
for i in map(convp, row)]))
title_shown = True
add("".join([name.rjust(maxlen)]+[i.rjust(10)
for i in map(conv, row)]))
return '\n'.join(buff)
def report_ci(ci):
"""print a report for confidence intervals"""
print(ci_report(ci))