def quick_fit_peak(x, y, shape="pv", ymin_on_ymax=0.001, **kwargs):
"""
Estiamtes and fits a single peak to a set of data
Parameters
----------
x : array_like of floats
independent variable (energy, q, tth) of spectrum
y : array_like of floats
intensity data of spectrum
shape : {'g', 'l', 'pv','ag', 'al', 'apv'}
The desired peak shape. Gaussian, lorentzian and pseudovoigt (default),
with asymmetric versions, are available.
ymin_on_ymax: (optional)
The ratio of intensity, relative to the peak maximum, over which to
calculate the peak intensity.
Returns
-------
yfit : array_like of floats
The best fit to the provided data
result : dictionary
The refined parameter values (as ufloats)
"""
peak = estimate_peak(x, y, shape=shape, ymin_on_ymax=ymin_on_ymax)
pf = PeakFitter(x, [peak])
pf.refine(y)
return pf.lastfit, pf.lastresult.popitem()[1]
def refine(self, y, reestimate=False):
"""Refines the peak parameters to get a best fit with the data.
Parameters
----------
y : array_like of floats
counts data for the spectrum
reestimate : bool
If True the starting parameters for the peaks will be estimated
from the data before starting the refinement
Returns
-------
fit : array_like of floats
final output of fitting function
results : dictionary
the refined parameters of all the peaks as ufloats
"""
if not self.ready:
self.initialise()
# see if we can get errors if a uarray has been sent
unc = unumpy.std_devs(y)
unc[unc == 0] = 1.0 # if not then errors are zero and need to be 1 (unweighted)
y = unumpy.nominal_values(y)
if reestimate: # try to get a better estimate of peak values before refinement
for peak in self.peaks:
npeak = estimate_peak(self.x, y, peak.centre)
peak.centre = npeak.centre
peak.width = npeak.width
peak.area = npeak.area
# print peak.centre.value-peak.limits[0],peak.limits[1]-peak.centre.value
# cut the x,y and unc data down to the minimum we need
l, h = self.x.searchsorted([self.peaks[0].limits[0], self.peaks[-1].limits[1]])
# if (h-l) < 10:print '-->',
# print l,h
_x = self.x[l : h + 1]
_y = y[l : h + 1]
if self.use_weights:
weights = 1.0 / unc[l : h + 1]
else:
weights = np.ones_like(_y)
# do the actual fit by least squares
self._lastminimizer = minimize(
self._residual,
self._fit_params,
args=(_x, self.peaks, self.functions),
kws={"data": _y, "w": weights},
**self.lsqkwargs
)
yfit = np.zeros_like(y)
yfit[l : h + 1] = self._residual(self._fit_params, _x, self.peaks, self.functions)
self._lastresult = OrderedDict([(p.name, p.items()) for p in self.peaks])
self._lastfit = yfit
# for func in self.functions:
# for arg in inspect.getargspec(func).args[1:]:
# d[arg] = (self._fit_params[arg].value ,self._fit_params[arg].stderr)
return self.lastfit, self.lastresult