def feffit(params, datasets, _larch=None, rmax_out=10,
path_outputs=True, **kws):
def _resid(params, datasets=None, _larch=None, **kws):
""" this is the residua function """
# print '---feffit residual '
#for i in dir(params):
# print i, getattr(params, i)
return concatenate([d.residual() for d in datasets])
if isinstance(datasets, FeffitDataSet):
datasets = [datasets]
for ds in datasets:
if not isinstance(ds, FeffitDataSet):
print "feffit needs a list of FeffitDataSets"
return
fitkws = dict(datasets=datasets)
fit = Minimizer(_resid, params, fcn_kws=fitkws, _larch=_larch)
fit.leastsq()
# scale uncertainties to sqrt(n_idp - n_varys)
n_idp = 0
for ds in datasets:
n_idp += ds.transform.n_idp
err_scale = sqrt(n_idp - params.nvarys)
for name in dir(params):
p = getattr(params, name)
if isParameter(p) and p.vary:
p.stderr *= err_scale
# here we create outputs:
for ds in datasets:
ds.save_ffts(rmax_out=rmax_out, path_outputs=path_outputs)
out = larch.Group(name='feffit fit results',
fit = fit,
params = params,
datasets = datasets)
return out
def autobk(energy, mu, group=None, rbkg=1, nknots=None, e0=None,
edge_step=None, kmin=0, kmax=None, kweight=1, dk=0,
win='hanning', k_std=None, chi_std=None, nfft=2048, kstep=0.05,
pre_edge_kws=None, debug=False, _larch=None, **kws):
"""Use Autobk algorithm to remove XAFS background
Options are:
rbkg -- distance out to which the chi(R) is minimized
"""
if _larch is None:
raise Warning("cannot calculate autobk spline -- larch broken?")
if 'kw' in kws:
kweight = kws['kw']
energy = remove_dups(energy)
# if e0 or edge_step are not specified, get them, either from the
# passed-in group or from running pre_edge()
if edge_step is None:
if _larch.symtable.isgroup(group) and hasattr(group, 'edge_step'):
edge_step = group.edge_step
if e0 is None:
if _larch.symtable.isgroup(group) and hasattr(group, 'e0'):
e0 = group.e0
if e0 is None or edge_step is None:
# need to run pre_edge:
pre_kws = dict(nnorm=3, nvict=0, pre1=None,
pre2=-50., norm1=100., norm2=None)
if pre_edge_kws is not None:
pre_kws.update(pre_edge_kws)
edge_step, e0 = pre_edge(energy, mu, group=group,
_larch=_larch, **pre_kws)
# get array indices for rkbg and e0: irbkg, ie0
ie0 = index_nearest(energy, e0)
rgrid = np.pi/(kstep*nfft)
if rbkg < 2*rgrid: rbkg = 2*rgrid
irbkg = int(1.01 + rbkg/rgrid)
# save ungridded k (kraw) and grided k (kout)
# and ftwin (*k-weighting) for FT in residual
kraw = np.sqrt(ETOK*(energy[ie0:] - e0))
if kmax is None:
kmax = max(kraw)
kout = kstep * np.arange(int(1.01+kmax/kstep), dtype='float64')
# interpolate provided chi(k) onto the kout grid
if chi_std is not None and k_std is not None:
chi_std = np.interp(kout, k_std, chi_std)
ftwin = kout**kweight * ftwindow(kout, xmin=kmin, xmax=kmax,
window=win, dx=dk)
# calc k-value and initial guess for y-values of spline params
nspline = max(4, min(60, 2*int(rbkg*(kmax-kmin)/np.pi) + 1))
spl_y = np.zeros(nspline)
spl_k = np.zeros(nspline)
spl_e = np.zeros(nspline)
for i in range(nspline):
q = kmin + i*(kmax-kmin)/(nspline - 1)
ik = index_nearest(kraw, q)
i1 = min(len(kraw)-1, ik + 5)
i2 = max(0, ik - 5)
spl_k[i] = kraw[ik]
spl_e[i] = energy[ik+ie0]
spl_y[i] = (2*mu[ik+ie0] + mu[i1+ie0] + mu[i2+ie0] ) / 4.0
# get spline represention: knots, coefs, order=3
# coefs will be varied in fit.
knots, coefs, order = splrep(spl_k, spl_y)
# set fit parameters from initial coefficients
ncoefs = len(coefs)
params = Group()
for i in range(ncoefs):
name = FMT_COEF % i
p = Parameter(coefs[i], name=name, vary=i<len(spl_y))
p._getval()
setattr(params, name, p)
initbkg, initchi = spline_eval(kraw, mu[ie0:], knots, coefs, order, kout)
fitkws = dict(ncoefs=len(coefs), chi_std=chi_std,
knots=knots, order=order, kraw=kraw, mu=mu[ie0:],
irbkg=irbkg, kout=kout, ftwin=ftwin, nfft=nfft)
# do fit
fit = Minimizer(__resid, params, fcn_kws=fitkws, _larch=_larch, toler=1.e-4)
fit.leastsq()
# write final results
coefs = [getattr(params, FMT_COEF % i) for i in range(ncoefs)]
bkg, chi = spline_eval(kraw, mu[ie0:], knots, coefs, order, kout)
obkg = np.zeros(len(mu))
obkg[:ie0] = mu[:ie0]
obkg[ie0:] = bkg
if _larch.symtable.isgroup(group):
group.bkg = obkg
group.chie = (mu-obkg)/edge_step
group.k = kout
group.chi = chi/edge_step
if debug:
group.spline_params = params
ix_bkg = np.zeros(len(mu))
ix_bkg[:ie0] = mu[:ie0]
ix_bkg[ie0:] = initbkg
group.init_bkg = ix_bkg
group.init_chi = initchi/edge_step
group.spline_e = spl_e
group.spline_y = np.array([coefs[i] for i in range(nspline)])
group.spline_yinit = spl_y
