def Fit_CosmicRay(t, Amp):
# create a set of Parameters
# time in microsecond unit
params = Parameters()
params.add('a', value=Amp[0], min=0, max=10)
params.add('A', value=1)
params.add('t0',
value=t[np.argmax(Amp)],
min=t[np.argmax(Amp) - 150],
max=t[np.argmax(Amp) + 100])
params.add('tau', value=100, min=1, max=400)
params.add('taur', value=1, min=0.2, max=20)
# do fit, here with leastsq model
result = minimize(Fit_CosmicRay_Func, params, args=(t, Amp))
# calculate final result
residual = result.residual
print(fit_report(result))
# Calculate Qc and Qi
a = result.params['a'].value
a_err = np.abs(result.params['a'].stderr / a)
A = result.params['A'].value
A_err = np.abs(result.params['A'].stderr / A)
t0 = result.params['t0'].value
t0_err = np.abs(result.params['t0'].stderr / t0)
tau = result.params['tau'].value
tau_err = np.abs(result.params['tau'].stderr / tau)
taur = result.params['taur'].value
taur_err = np.abs(result.params['taur'].stderr / taur)
return a, a_err, A, A_err, t0, t0_err, tau, tau_err, taur, taur_err, fit_report(
result), residual
def Fit_frvsT(temp, freq, fitpara):
# create a set of Parameters
params = Parameters()
print fitpara
params.add_many(('CPWC', fitpara[0], False, None, None, None),
('CPWG', fitpara[1], False, None, None, None),
('thick', fitpara[2], False, None, None, None),
('BCS', fitpara[3], False, None, None, None),
('Tc', fitpara[4], True, None, None, None),
('f0', fitpara[5], False, None, None, None),
('sigman',fitpara[6], False, None, None, None),
('A', fitpara[7], True, fitpara[7]*0.9, fitpara[7]*1.1, None))
# do fit, here with leastsq model
result = minimize(Fit_frvsT_Func, params, args=(temp, freq))
# calculate final result
residual = result.residual
Tc = result.params['Tc'].value
Tc_err = np.abs(result.params['Tc'].stderr/Tc)
A = result.params['A'].value
A_err = np.abs(result.params['A'].stderr/A)
print fit_report(result)
return Tc, Tc_err, A, A_err, fit_report(result)
def Fit_SkewedLorentizian(f, t):
params = Parameters()
params.add('A1', value=np.power(10, t[0] / 10.), min=0,
max=10) # Background
params.add('A2', value=0) #, min = -0.5, max = 0.5) # Slope
params.add('A3', value=np.power(10, np.amin(t) / 10.)) # Lowest point
params.add('A4', value=0)
params.add('fr', value=np.median(f), min=f[0], max=f[len(f) - 1])
params.add('Qr', value=10000, min=1e3, max=1e8)
result = minimize(Fit_SkewedLorentizian_Func, params, args=(f, t))
# print the fitting result
print(fit_report(result))
# get fitted value and 1 sigma error value
A1 = result.params['A1'].value
A1_err = result.params['A1'].stderr
A2 = result.params['A2'].value
A2_err = result.params['A2'].stderr
A3 = result.params['A3'].value
A3_err = result.params['A3'].stderr
A4 = result.params['A4'].value
A4_err = result.params['A4'].stderr
fr = result.params['fr'].value
fr_err = result.params['fr'].stderr
Qr = result.params['Qr'].value
Qr_err = result.params['Qr'].stderr
return A1, A1_err, A2, A2_err, A3, A3_err, A4, A4_err, fr, fr_err, Qr, Qr_err, fit_report(
result)
def Fit_frvsT(temp, freq, fitpara):
# create a set of Parameters
params = Parameters()
print fitpara
params.add_many(
('CPWC', fitpara[0], False, None, None, None),
('CPWG', fitpara[1], False, None, None, None),
('thick', fitpara[2], False, None, None, None),
('BCS', fitpara[3], False, None, None, None),
('Tc', fitpara[4], True, None, None, None),
('f0', fitpara[5], False, None, None, None),
('sigman', fitpara[6], False, None, None, None),
('A', fitpara[7], True, fitpara[7] * 0.9, fitpara[7] * 1.1, None))
# do fit, here with leastsq model
result = minimize(Fit_frvsT_Func, params, args=(temp, freq))
# calculate final result
residual = result.residual
Tc = result.params['Tc'].value
Tc_err = np.abs(result.params['Tc'].stderr / Tc)
A = result.params['A'].value
A_err = np.abs(result.params['A'].stderr / A)
print fit_report(result)
return Tc, Tc_err, A, A_err, fit_report(result)
def display_mle_fit(self, scaled=False, **kwargs):
"""Give a readable overview of the result of the MLE fitting routine.
Warning
-------
The uncertainty shown is the largest of the asymmetrical errors! Work
is being done to incorporate asymmetrical errors in the report; for
now, rely on the correlation plot."""
if hasattr(self, 'fit_mle'):
if 'show_correl' not in kwargs:
kwargs['show_correl'] = False
print('NDoF: {:d}, Chisquare: {:.8G}, Reduced Chisquare: {:.8G}'.
format(self.ndof_mle, self.chisqr_mle, self.redchi_mle))
if scaled:
print('Errors scaled with reduced chisquare.')
par = copy.deepcopy(self.fit_mle)
for p in par:
if par[p].stderr is not None:
par[p].stderr *= (self.redchi_mle**0.5)
print(lm.fit_report(par, **kwargs))
else:
print('Errors not scaled with reduced chisquare.')
print(lm.fit_report(self.fit_mle, **kwargs))
else:
print('Model has not yet been fitted with this method!')
def display_chisquare_fit(self, scaled=False, **kwargs):
"""Display all relevent info of the least-squares fitting routine,
if this has been performed.
Parameters
----------
kwargs: misc
Keywords passed on to :func:`fit_report` from the LMFit package."""
if hasattr(self, 'chisq_res_par'):
print('NDoF: {:d}, Chisquare: {:.8G}, Reduced Chisquare: {:.8G}'.
format(self.ndof_chi, self.chisqr_chi, self.redchi_chi))
print(
'Akaike Information Criterium: {:.8G}, Bayesian Information Criterium: {:.8G}'
.format(self.aic_chi, self.bic_chi))
if scaled:
print('Errors scaled with reduced chisquare.')
par = copy.deepcopy(self.chisq_res_par)
for p in par:
if par[p].stderr is not None:
par[p].stderr *= (self.redchi_chi**0.5)
print(lm.fit_report(par, **kwargs))
else:
print('Errors not scaled with reduced chisquare.')
print(lm.fit_report(self.chisq_res_par, **kwargs))
else:
print('Spectrum has not yet been fitted with this method!')
def fit(self,
mode='sig',
nmodes=1,
fitglobal=[],
init={},
fix={},
lmfit_pars={},
fitqdep={}):
'''
Function that computes the fits using lmfit's minimizer
'''
self.fitglobal = fitglobal
self.nmodes = nmodes
self.fitqdep = fitqdep
self.fix = fix
# make the parameters
if not lmfit_pars.get('is_weighted', True):
init['__lnsigma'] = 1
self._init_parameters(init, fix)
# setting the weights of the data
self._get_weights(mode)
self._minimizer = lmfit.Minimizer(self._residuals,
params=self._lmpars,
reduce_fcn=self._reduce_func,
iter_cb=self._iter_cb,
nan_policy='omit')
if bool(self.fitglobal):
# set data to fit
self._fit_data = self.cf[self.nq]
self._fit_weights = self._weights[self.nq]
# do the fit
out = self._minimizer.minimize(**lmfit_pars)
self._write_to_pars(out)
self.fit_result.append((out, lmfit.fit_report(out)))
else:
for line, qi in enumerate(self.nq):
# set data to fit
self._fit_data = self.cf[qi]
self._fit_weights = self._weights[qi]
# do the fit
out = self._minimizer.minimize(**lmfit_pars)
self._write_to_pars(out, line=line)
self.fit_result.append((out, lmfit.fit_report(out)))
self.pars['q'] = self.qv[self.nq]
self.pars = self.pars.apply(pd.to_numeric)
return self.pars, self.fit_result
def print_pars(self,fitresult=False):
""" Print a list with the parameters """
if fitresult == True:
params = self.result.params
else:
params = self.params
print lm.fit_report(params,show_correl=0)
def spectra_fit(fit_params, *args, **kwargs):
print '\nperforming minimization'
fit_kws={'nan_policy': 'omit'}
if len(args) in (1, 2, 3):
sim_data_1, meas_data_full_1, meas_data_1 = args[0]
if len(args) == 1:
print ' single sprectrum fit'
res = lmfit.minimize(minimize, fit_params, method='nelder', args=((sim_data_1, meas_data_1),), **fit_kws)
if len(args) in (2, 3):
sim_data_2, meas_data_full_2, meas_data_2= args[1]
if len(args) == 2:
print ' double spectrum fit'
res = lmfit.minimize(minimize, fit_params, args=((sim_data_1, meas_data_1), (sim_data_2, meas_data_2)), **fit_kws)
if len(args) == 3:
sim_data_3, meas_data_full_3, meas_data_3= args[2]
if len(args) == 3:
print ' triple spectrum fit'
res = lmfit.minimize(minimize, fit_params,
args=((sim_data_1, meas_data_1), (sim_data_2, meas_data_2), (sim_data_3, meas_data_3)),
**fit_kws)
if kwargs['print_info']:
print '\n',res.message
print lmfit.fit_report(res)
if kwargs['show_plots']:
if len(args) == 1:
plot_fitted_spectra( res.params['shift'].value, res.params['spread'].value,
( (res.params['alpha_1'].value,), (res.params['beta_1'].value,), (res.params['gamma_1'].value,),
(res.params['c1_1'].value,), (res.params['c2_1'].value,),
(res.params['y_scale_1'].value,), (sim_data_1,), (meas_data_full_1,), (meas_data_1,) ) )
if len(args) == 2:
plot_fitted_spectra( res.params['shift'].value, res.params['spread'].value,
( (res.params['alpha_1'].value, res.params['alpha_2'].value),
(res.params['beta_1'].value, res.params['beta_2'].value),
(res.params['gamma_1'].value, res.params['gamma_2'].value),
(res.params['c1_1'].value, res.params['c1_2'].value), (res.params['c2_1'].value, res.params['c2_2'].value),
(res.params['y_scale_1'].value, res.params['y_scale_2'].value), (sim_data_1, sim_data_2),
(meas_data_full_1, meas_data_full_2), (meas_data_1, meas_data_2) ) )
if len(args) == 3:
plot_fitted_spectra( res.params['shift'].value, res.params['spread'].value,
( (res.params['alpha_1'].value, res.params['alpha_2'].value, res.params['alpha_3'].value),
(res.params['beta_1'].value, res.params['beta_2'].value, res.params['beta_3'].value),
(res.params['gamma_1'].value, res.params['gamma_2'].value, res.params['gamma_3'].value),
(res.params['c1_1'].value, res.params['c1_2'].value, res.params['c1_3'].value),
(res.params['c2_1'].value, res.params['c2_2'].value, res.params['c2_3'].value),
(res.params['y_scale_1'].value, res.params['y_scale_2'].value, res.params['y_scale_3']),
(sim_data_1, sim_data_2, sim_data_3), (meas_data_full_1, meas_data_full_2, meas_data_full_3),
(meas_data_1, meas_data_2, meas_data_3) ) )
# get shift term
shift_term = res.params['shift'].value
spread_term = res.params['spread'].value
return shift_term, spread_term
def determine_excess(self):
B_up_slice = np.logical_and(self.min_B < self.B, self.B < self.max_B)
B_down_slice = np.logical_and(-self.max_B < self.B,
self.B < -self.min_B)
B_up = self.B[B_up_slice]
M_up = self.M[B_up_slice]
sM_up = self.sM[B_up_slice]
p_upper_fit = lmfit.Parameters()
m_up_estimate = (M_up[-1] - M_up[0]) / (B_up[-1] - B_up[0])
p_upper_fit.add("m", m_up_estimate)
p_upper_fit.add("n", B_up[0])
B_down = self.B[B_down_slice]
M_down = self.M[B_down_slice]
sM_down = self.sM[B_down_slice]
m_down_estimate = (M_down[-1] - M_down[0]) / (B_down[-1] - B_down[0])
p_lower_fit = lmfit.Parameters()
p_lower_fit.add("m", m_down_estimate)
p_lower_fit.add("n", B_down[0])
res_up = lmfit.minimize(self.residuum,
p_upper_fit,
args=(B_up, M_up, sM_up),
method='leastsq')
print(lmfit.fit_report(res_up))
res_down = lmfit.minimize(self.residuum,
p_lower_fit,
args=(B_down, M_down, sM_down),
method='leastsq')
print(lmfit.fit_report(res_down))
p_upper_fit = res_up.params
p_lower_fit = res_down.params
self.mup = p_upper_fit["m"].value
self.nup = p_upper_fit["n"].value
self.mlow = p_lower_fit["m"].value
self.nlow = p_lower_fit["n"].value
self.smup = p_upper_fit["m"].stderr
self.snup = p_upper_fit["n"].stderr
self.smlow = p_lower_fit["m"].stderr
self.snlow = p_lower_fit["n"].stderr
self.sm = 1. / self.smup**2 + 1. / self.smlow**2
self.m = (self.mup / self.smup**2 +
self.mlow / self.smlow**2) / self.sm
self.sm = np.sqrt(1. / self.sm)
self.sn = 1. / self.snup**2 + 1. / self.snlow**2
self.n = (self.nup / self.snup**2 -
self.nlow / self.snlow**2) / self.sn
self.sn = np.sqrt(1. / self.sn)
self.M_corr = self.M - self.m * self.B
self.sM_corr = self.sM
def fit_report(fit_result, modelpars=None, show_correl=True, min_correl=0.1,
sort_pars=True, _larch=None, **kws):
"""generate a report of fitting results
wrapper around lmfit.fit_report
The report contains the best-fit values for the parameters and their
uncertainties and correlations.
Parameters
----------
fit_result : result from fit
Fit Group output from fit, or lmfit.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, 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.
"""
result = getattr(fit_result, 'fit_details', fit_result)
if isinstance(result, MinimizerResult):
return lmfit.fit_report(result, modelpars=modelpars,
show_correl=show_correl,
min_correl=min_correl, sort_pars=sort_pars)
elif isinstance(result, ModelResult):
return result.fit_report(modelpars=modelpars,
show_correl=show_correl,
min_correl=min_correl, sort_pars=sort_pars)
else:
result = getattr(fit_result, 'params', fit_result)
if isinstance(result, Parameters):
return lmfit.fit_report(result, modelpars=modelpars,
show_correl=show_correl,
min_correl=min_correl, sort_pars=sort_pars)
else:
try:
result = group2params(fit_result, _larch=_larch)
return lmfit.fit_report(result, modelpars=modelpars,
show_correl=show_correl,
min_correl=min_correl, sort_pars=sort_pars)
except (ValueError, AttributeError):
pass
return "Cannot make fit report with %s" % repr(fit_result)
def get_fit(x,y,xer,yer, nsfh='Del.'):
from lmfit import Model, Parameters, minimize, fit_report, Minimizer
fit_params = Parameters()
#fit_params.add('t0', value=1., min=0, max=np.max(tt))
fit_params.add('t0', value=.5, min=0, max=14)
fit_params.add('tau', value=.1, min=0, max=100)
fit_params.add('A', value=1, min=0, max=5000)
def residual_tmp(pars):
vals = pars.valuesdict()
t0_tmp, tau_tmp, A_tmp = vals['t0'],vals['tau'],vals['A']
if nsfh == 'Del.':
model = SFH_del(t0_tmp, tau_tmp, A_tmp, tt=x)
elif nsfh == 'Decl.':
model = SFH_dec(t0_tmp, tau_tmp, A_tmp, tt=x)
elif nsfh == 'Cons.':
model = SFH_cons(t0_tmp, tau_tmp, A_tmp, tt=x)
#con = (model>minsfr)
con = (model>0)
#print(model[con])
#resid = np.abs(model - y)[con] / np.sqrt(yer[con])
#resid = np.square(model - y)[con] / np.square(yer[con])
#resid = np.square(np.log10(model[con]) - y[con]) / np.square(yer[con])
#resid = (np.log10(model[con]) - y[con]) / np.sqrt(yer[con])
resid = (np.log10(model[con]) - y[con]) / yer[con]
#print(yer[con])
#resid = (model - y)[con] / (yer[con])
# i.e. residual/sigma
return resid
out = minimize(residual_tmp, fit_params, method='powell')
#out = minimize(residual, fit_params, method='nelder')
print(fit_report(out))
t0 = out.params['t0'].value
tau = out.params['tau'].value
A = out.params['A'].value
param = [t0, tau, A]
keys = fit_report(out).split('\n')
for key in keys:
if key[4:7] == 'chi':
skey = key.split(' ')
csq = float(skey[14])
if key[4:7] == 'red':
skey = key.split(' ')
rcsq = float(skey[7])
return param, rcsq
def fit(self):
self.result = lm.minimize(fitfunc, self.params, args=(self.X, self.Y,self.EY),ftol=1e-10)
# calculate final result
if self.EY is None:
self.Yfit = self.Y + self.result.residual
else:
self.Yfit = self.Y + self.result.residual*self.EY
# write error report
print '='*80
print 'success:',self.result.success
print self.result.message
print lm.fit_report(self.result,show_correl=0)
self.plot(fitresult = True)
def residuum(self, p):
self.model.params = p
self.ptrFit.iteration += 1
self.model.updateModel()
resi = []
for i in range(self.model.nModelsets):
data = self.data.getDataset(i)
weight = self.data.dataWeights[i]
model = self.model.getModelset(i)
q_data = data.getDomain()
I_data = data.getValues()
I_error = data.getErrors()
I_model = model.getValues()
if self.fit_range is not None:
fit_range = np.logical_and(q_data > self.fit_range[0], q_data < self.fit_range[1])
q_data = q_data[fit_range]
I_data = I_data[fit_range]
I_error = I_error[fit_range]
I_model = I_model[fit_range]
addResi = np.sqrt(weight) * self.residuumFormula(q_data, I_data, I_error, I_model)
resi = np.concatenate([resi, addResi])
if self.ptrFit.printIteration is not None:
if self.ptrFit.iteration % self.ptrFit.printIteration == 0:
print(f'Iteration: {self.ptrFit.iteration}\tChi2:{np.sum(resi**2)}')
print(lmfit.fit_report(p))
return resi
def on_read_data_from_lmfit(self):
a = P4Rm()
from lmfit import fit_report
result = P4Rm.resultFit
data = []
data.append(result.success)
data.append(result.lmdif_message)
data.append(result.ier)
data.append(fit_report(result))
P4Rm.FitDict["Leastsq_report"] = data
i = 0
if a.AllDataDict["model"] == 2:
for param in result.params.values():
if i in range(1, 7):
P4Rm.ParamDict["sp"][i] = param.value
if i in range(7, 14):
P4Rm.ParamDict["dwp"][i - 7] = param.value
i += 1
else:
len_sp = int(result.params["nb_sp_val"])
len_dwp = int(result.params["nb_dwp_val"])
for ii in range(len_dwp):
name = "dwp_" + str(ii)
P4Rm.ParamDict["dwp"][ii] = result.params[name].value
for jj in range(len_sp):
name = "sp_" + str(jj)
P4Rm.ParamDict["sp"][jj] = result.params[name].value
def Fit_Million(freq, t, para_guess):
# Planar superconducting resonators with internal quality factors above one million
params = Parameters()
params.add('a', value=para_guess[0], min=-100, max=3000)
params.add('phi0', value=para_guess[1], min=-np.pi, max=np.pi)
params.add('Qi', value=para_guess[2], min=1e3, max=1e8)
params.add('Qc_scaled', value=para_guess[3], min=1e2, max=1e8)
params.add('fr', value=para_guess[4], min=freq[0], max=freq[len(freq) - 1])
params.add('aphi0', value=para_guess[5], min=-np.pi, max=np.pi)
# do fit, here with leastsq model
result = minimize(Fit_Million_Func, params, args=(freq, t))
a = result.params['a'].value
a_err = result.params['a'].stderr
phi0 = result.params['phi0'].value
phi0_err = result.params['phi0'].stderr
Qi = result.params['Qi'].value
Qi_err = result.params['Qi'].stderr
Qc_scaled = result.params['Qc_scaled'].value
Qc_scaled_err = result.params['Qc_scaled'].stderr
fr = result.params['fr'].value
fr_err = result.params['fr'].stderr
aphi0 = result.params['aphi0'].value
aphi0_err = result.params['aphi0'].stderr
# print the fitting result
print(fit_report(result))
return a, a_err, phi0, phi0_err, Qi, Qi_err, Qc_scaled, Qc_scaled_err, fr, fr_err, aphi0, aphi0_err, result
def lmfit(self, star, logger=None):
"""Fit parameters of the given star using lmfit (Levenberg-Marquardt minimization
algorithm).
:param star: A Star to fit.
:param logger: A logger object for logging debug info. [default: None]
:returns: (flux, dx, dy, scale, g1, g2, flag)
"""
import lmfit
logger = galsim.config.LoggerWrapper(logger)
params = self._lmfit_params(star)
results = self._lmfit_minimize(params, star, logger=logger)
if logger:
logger.debug(lmfit.fit_report(results))
flux, du, dv, scale, g1, g2 = results.params.valuesdict().values()
if not results.success:
raise RuntimeError("Error fitting with lmfit.")
try:
params_var = np.diag(results.covar)
except (ValueError, AttributeError) as e:
logger.warning("Failed to get params_var")
logger.warning(" -- Caught exception: %s", e)
# results.covar is either None or does not exist
params_var = np.zeros(6)
return flux, du, dv, scale, g1, g2, params_var
def fit_dunham(q, d):
print('Starting fit...')
molids, mols = read_in_dunham_config()
Ys = mols['AlCl62X_Bernath'].keys()
allowed_Ys = [
'y00', 'y01', 'y10', 'y11', 'y20', 'y21', 'y22', 'y12', 'y02'
]
params = Parameters()
for p in Ys:
if p != 'matrix':
#if p in allowed_Ys:
if p == 'y00':
params.add(p + 'A', value=0.0, vary=True)
elif p == 'y10':
params.add(p + 'A', value=0.0, max=600.0, vary=True)
elif p == 'y20':
params.add(p + 'A', value=0.0, vary=True)
else:
params.add(p + 'A', value=0.0, vary=True)
#params.add(p+'X', value = 0.0, min = -500, max = 500, vary = True)
# do fit, here with leastsq model
minner = Minimizer(fcn2min, params, fcn_args=(q, d))
result = minner.minimize()
# Store the Confidence data from the fit
con_report = lmfit.fit_report(result.params)
model = fcn2min(result.params, q, d, get_fit=True)
return (result.params, params, con_report, model)
def mostRecentModelFitReport(self):
"""returns the lmfit fit report of the most recent
lmfit model results object"""
if self.mostRecentModelResult is not None:
return lmfit.fit_report(self.mostRecentModelResult) + "\n\n"
else:
return "No fit performed"
def do_fit(x, y):
params = Parameters()
params.add('Te_1', value=0.0, min=0.0, max=340.0, vary=False)
params.add('Te_2', value=38237.0, min=0.0, max=40000.0, vary=True)
params.add('we_1', value=480.0, min=0.0, max=500.0, vary=True)
params.add('we_2', value=440.0, min=0.0, max=500.0, vary=True)
params.add('wexe_1', value=2.037, min=0.0, max=5.0, vary=True)
params.add('wexe_2', value=2.81, min=0.0, max=8.0, vary=True)
params.add('weye_1', value=0.5, min=0.0, max=5.0, vary=True)
params.add('weye_2', value=0.1, min=0.0, max=8.0, vary=True)
params.add('weze_1', value=0.5, min=0.0, max=5.0, vary=True)
params.add('weze_2', value=0.1, min=0.0, max=8.0, vary=True)
# do fit, here with leastsq model
minner = Minimizer(fcn2min, params, fcn_args=(x, y))
result = minner.minimize()
# Store the Confidence data from the fit
con_report = lmfit.fit_report(result.params)
return (result)
def CalcGwAge(self,
tracers,
FieldData,
DischData,
use_disch=0,
DischargeError=0.10):
'''Estimate the best groundwater mean age to match the given stream concentrations of tracers with age information - has_age=1.'''
C_tau = self.C_tau[1]
lb = 1.
ub = 1000. * 365. #upper limit of 100 years mean age right now. Making this longer will make inherent problems with the convolution technique be a problem. Needs to be dealt with at some point
m = CreateLmParams(C_tau, 'cTau', lb, ub)
mini = lm.Minimizer(self.MisfitAge,
m,
fcn_args=(tracers, FieldData, DischData),
fcn_kws={
'use_disch': use_disch,
'DischargeError': DischargeError
})
# fit = mini.minimize(params=m,xtol=1.e-5,ftol=1e-5,epsfcn=1.e-3)
fit = mini.minimize(params=m)
C_tau = ExtractLmParamVec(fit.params, 'cTau')
self.C_tau = (self.C_tau[0], C_tau)
self.SimRes.fit_solution = fit
self.CalcTran()
print(lm.fit_report(fit))
def CalcGwInflow(self,
tracers,
FieldData,
DischData,
DischargeError=0.10,
use_disch=1,
log_flag=1):
'''Estimate the best groundwater inflow to match the given stream concentrations.'''
qlin = self.q_lin
lb = 0.
ub = 1.
if log_flag:
qlin = np.log(qlin)
lb = -20
up = 0.
m = CreateLmParams(qlin, 'qlin', lb, ub)
mini = lm.Minimizer(self.MisfitFlux,
m,
fcn_args=(tracers, FieldData, DischData),
fcn_kws={
'DischargeError': DischargeError,
'use_disch': use_disch,
'log_flag': log_flag
})
fit = mini.minimize(params=m, ftol=1.e-5, gtol=1.e-5, xtol=1e-5)
print(lm.fit_report(fit))
self.q_lin = ExtractLmParamVec(fit.params, 'qlin')
if log_flag:
self.q_lin = np.exp(self.q_lin)
self.SimRes.fit_solution = fit
#run a last best solution
self.CalcTran()
def export_params(self, outfilename="params.txt"):
with open(outfilename, 'w') as f:
f.write("chisqr={0: f}\n".format(self.edp.chisqr))
f.write("D={0: f}\n".format(self.latt_par['D'].value))
f.write("lambda_r={0: f}\n".format(self.latt_par['lambda_r'].value))
f.write("gamma={0: f}\n\n".format(self.latt_par['gamma'].value))
f.write(lmfit.fit_report(self.edp_par))
def Gaussian_beam_propagation(meas_points,widths,lambda_beam,plot=False):
params_BeamPropagation = Parameters()
params_BeamPropagation.add('omega_zero',value=widths[0])
params_BeamPropagation.add('z0',value=0)
fit = Minimizer(__w_Gauss_freespace_residual,params_BeamPropagation,fcn_args=(meas_points,),\
fcn_kws={"meas_beamwidths":widths,"lam":lambda_beam})
fit_res = fit.minimize(maxfev=10**8)
print(fit_report(fit_res))
if plot is True:
print("Let's plot it")
fitted_w0 = fit_res.params.valuesdict()["omega_zero"]
fitted_z0 = fit_res.params.valuesdict()["z0"]
if fitted_z0<meas_points[0]:
plotpoints = np.linspace(fitted_w0,meas_points[-1],100)
elif meas_points[0]<fitted_z0<meas_points[-1]:
plotpoints = np.linspace(meas_points[0],meas_points[-1],100)
else:
plotpoints = np.linspace(meas_points[0],fitted_z0,100)
model_beamwidth = __w_Gauss_freespace_residual(fit_res.params,plotpoints,meas_beamwidths=None,lam=lambda_beam)
plt.plot(plotpoints,model_beamwidth,'b')
plt.scatter(meas_points,widths,c="r")
plt.show()
def save_txt(self,
full_path: str = None,
mode: str = 'wt',
cmd: str = '') -> None:
'''Save the optimization settings to disk as a textfile'''
logger = logging.getLogger(__name__)
if full_path is None: # pragma: no cover
full_path = save_file_full_name(self.cte.lattice,
'optimization') + '.txt'
logger.info('Saving solution as text to {}.'.format(full_path))
# print cte
with open(full_path, mode) as csvfile:
csvfile.write('Settings:\n')
csvfile.write(self.cte['config_file'])
csvfile.write('\n\nCommand used to generate data:\n')
csvfile.write(cmd)
csvfile.write('\n\n\nOptimization progress:\n')
csvfile.write(self.optim_progress[0] + '\r\n')
for update in self.optim_progress[1:]:
csvfile.write(update + '\r\n')
csvfile.write('\nOptimization statistics:\n')
csvfile.write(fit_report(self.result) + '\r\n')
csvfile.write('\r\n')
csvfile.write(f'Total time: {self.formatted_time}.' + '\r\n')
csvfile.write(f'Optimized RMS error: {self.min_f:.3e}.' + '\r\n')
csvfile.write('Parameters name and value:' + '\r\n')
for name, best_val in zip(self.result.params.keys(),
self.best_params.T):
csvfile.write(f'{name}: {best_val:.3e}.' + '\r\n')
def fit_lmfit(self, report=True, printdot=True):
import lmfit
self.lmfitparams = lmfit.Parameters()
for name in self.parameters.index:
p = self.parameters.loc[name]
self.lmfitparams.add(name,
value=p['initial'],
min=p['pmin'],
max=p['pmax'])
fit_kws = {"epsfcn": 1e-4}
self.fitresult = lmfit.minimize(self.residuals_lmfit,
self.lmfitparams,
method="leastsq",
kws={"printdot": printdot},
**fit_kws)
print('', flush=True)
print(self.fitresult.message)
if self.fitresult.success:
for name in self.parameters.index:
self.parameters.loc[name, 'optimal'] = \
self.fitresult.params.valuesdict()[name]
if hasattr(self.fitresult, 'covar'):
self.parameters['std'] = np.sqrt(np.diag(self.fitresult.covar))
self.parameters['perc_std'] = 100 * self.parameters['std'] / \
np.abs(self.parameters['optimal'])
else:
self.parameters['std'] = np.nan
self.parameters['perc_std'] = np.nan
if report:
print(lmfit.fit_report(self.fitresult))
def Fit_7para_tau(freq, t, estimateparas):
params = Parameters()
params.add('a', value=estimateparas[0]) #, min = -50, max = 50)
params.add('alpha', value=estimateparas[1], min=-np.pi, max=np.pi)
params.add('tau', value=estimateparas[2], vary=False)
params.add('phi0', value=estimateparas[3], min=-2 * np.pi, max=2 * np.pi)
params.add('fr',
value=estimateparas[4],
min=freq[0],
max=freq[len(freq) - 1])
params.add('Qr', value=estimateparas[5], min=1e3, max=1e8)
params.add('Qc', value=estimateparas[6], min=1e3, max=1e8)
result = minimize(Fit_7para_Func, params, args=(freq, t))
# print the fitting result
print(fit_report(result))
# get fitted value and 1 sigma error value
a = result.params['a'].value
a_err = result.params['a'].stderr
alpha = result.params['alpha'].value
alpha_err = result.params['alpha'].stderr
tau = result.params['tau'].value
tau_err = result.params['tau'].stderr
phi0 = result.params['phi0'].value
phi0_err = result.params['phi0'].stderr
fr = result.params['fr'].value
fr_err = result.params['fr'].stderr
Qr = result.params['Qr'].value
Qr_err = result.params['Qr'].stderr
Qc = result.params['Qc'].value
Qc_err = result.params['Qc'].stderr
return a, a_err, alpha, alpha_err, tau, tau_err, phi0, phi0_err, fr, fr_err, Qr, Qr_err, Qc, Qc_err, fit_report(
result)
def gradient_descent(self, p, flat=True):
""" Optimizes parameters following specified parameter
dependencies on task conditions (i.e. depends_on={param: cond})
::Arguments::
p (dict):
parameter dictionary
flat (bool):
if flat, yhat have ndim=1, else ndim>1
and popt lmParams will have conditional param names
::Returns::
yhat (array):
model-predicted data array
finfo (pd.Series):
fit info (AIC, BIC, chi2, redchi, etc)
popt (dict):
optimized parameters dictionary
"""
fp = self.fitparams
optkws = {'xtol': fp['tol'], 'ftol': fp['tol'], 'maxfev': fp['maxfev']}
# make lmfit Parameters object to keep track of
# parameter names and dependencies during fir
lmParams = theta.loadParameters(inits=p, pc_map=self.pc_map, is_flat=flat, kind=self.kind)
self.lmMin = minimize(self.simulator.cost_fx, lmParams, method=fp['method'], options=optkws)
#self.lmMinimizer = deepcopy(lmMinimizer)
self.param_report = fit_report(self.lmMin.params)
return self.assess_fit(flat=flat)
def lmfit(self, star, logger=None):
"""Fit parameters of the given star using lmfit (Levenberg-Marquardt minimization
algorithm).
:param star: A Star to fit.
:param logger: A logger object for logging debug info. [default: None]
:returns: (flux, dx, dy, scale, g1, g2, flag)
"""
import lmfit
logger = galsim.config.LoggerWrapper(logger)
params = self._lmfit_params(star)
results = self._lmfit_minimize(params, star, logger=logger)
if logger:
logger.debug(lmfit.fit_report(results))
flux, du, dv, scale, g1, g2 = results.params.valuesdict().values()
if not results.success:
raise RuntimeError("Error fitting with lmfit.")
try:
params_var = np.diag(results.covar)
except (ValueError, AttributeError) as e:
logger.warning("Failed to get params_var")
logger.warning(" -- Caught exception: %s",e)
# results.covar is either None or does not exist
params_var = np.zeros(6)
return flux, du, dv, scale, g1, g2, params_var
def curveFitting_lmfit(y_data, struct, lowerbound, upperbound, method):
y_data = np.array(y_data).reshape(len(struct.waves), len(struct.angles))
paras = Parameters()
no = len([i for i in struct.layers if i.coherent])
for i, l in enumerate(struct.layers):
if l.thickness < 10000:
paras.add('layer{}'.format(i),
value=l.thickness,
vary=~l.coherent,
min=lowerbound[i],
max=upperbound[i],
brute_step=2)
else:
paras.add('layer{}'.format(i), value=l.thickness, vary=False)
def residual(params, x, y):
tempstruct = copy.deepcopy(struct)
# tempstruct.waves = x
vals = params.valuesdict()
for i in range(no):
tempstruct.layers[i].thickness = vals['layer{}'.format(i)]
tempstruct.initialize()
print(np.sum(np.abs(y - tempstruct.R)))
return np.sum(np.abs(y - tempstruct.R))
out = minimize(residual, paras, args=(struct.waves, y_data), method=method)
print(fit_report(out))
ret = []
vals = out.params.valuesdict()
print(vals)
for i in range(len(vals)):
ret.append(vals['layer{}'.format(i)])
print(ret)
return ret
def doFitting(self):
#t = np.arange(1.0, 5.0, 0.01)
#s = np.sin(2*np.pi*t)
#self.ui.xplot.canvas.ax.plot(t, s)
#self.ui.xplot.canvas.draw()
filename = self.ui.fileOutput.toPlainText()
self.ui.FitResultsSummary.setPlainText("These are fitting results")
self.ui.ErrorMessages.setPlainText("")
try:
data = file1.make_numpyarray(filename)
except:
self.ui.ErrorMessages.setPlainText("Something went wrong with fitting")
return None
fit1 = file1.fit_axis(data,0)
report = fit_report(fit1[2])
self.ui.FitResultsSummary.append(report)
# rotating by 90 degrees on the other axis doesn't work well yet
#t = np.arange(1.0, 5.0, 0.01)
#s = np.sin(2*np.pi*t)
#self.myplot = self.ui.yplot.canvas.ax.plot(t, s)
#self.rotated = ndimage.rotate(self.myplot,90)
#self.rotated.draw()
self.ui.BeamDisplay.canvas.ax.pcolorfast(data)
self.ui.BeamDisplay.canvas.draw()
def on_read_data_from_lmfit(self):
a = P4Rm()
from lmfit import fit_report
result = P4Rm.resultFit
data = []
data.append(result.success)
data.append(result.lmdif_message)
data.append(result.ier)
data.append(fit_report(result))
P4Rm.FitDict['Leastsq_report'] = data
i = 0
if a.AllDataDict['model'] == 2:
for param in result.params.values():
if i in range(1, 7):
P4Rm.ParamDict['sp'][i] = param.value
if i in range(7, 14):
P4Rm.ParamDict['dwp'][i - 7] = param.value
i += 1
else:
len_sp = int(result.params['nb_sp_val'])
len_dwp = int(result.params['nb_dwp_val'])
for ii in range(len_dwp):
name = 'dwp_' + str(ii)
P4Rm.ParamDict['dwp'][ii] = result.params[name].value
for jj in range(len_sp):
name = 'sp_' + str(jj)
P4Rm.ParamDict['sp'][jj] = result.params[name].value
def fit_yb_T(x, y):
params = Parameters()
params.add('a', value=-5.0, min=-10.0, max=0.0, vary = True)
#params.add('w', value=50.0, min=1.0, max=2000, vary = True)
params.add('x_offset', value=50, min=np.min(x), max = np.max(x), vary = True)
params.add('y_offset', value=0.0, min=-2.0, max=2.0, vary = True)
params.add('T', value = 1.0, min=0.0, max=100.0, vary = True)
iso_abund = np.array([12.887, 31.896, 16.098, 16.098, 21.754, 14.216, 14.216, 3.023, 0.126])
for k in range(len(iso_abund)):
params.add('a' + str(k), value = 1.0, min = 0.0, max = 10.0, vary = True)
# print(params)
# do fit, here with leastsq model
minner = Minimizer(fcn2min, params, fcn_args=(x, y))
result = minner.minimize()
# Store the Confidence data from the fit
con_report = lmfit.fit_report(result.params)
(x_plot, model) = fcn2min(result.params, x, y, plot_fit = True)
return (x_plot, model, result)
def __init__(self, model, noise=True, weights=None, **kwargs):
import lmfit # Import Lmfit here, so it is no dependency
BaseSolver.__init__(self)
# Deal with the parameters
parameters = lmfit.Parameters()
p = model.parameters[['initial', 'pmin', 'pmax', 'vary']]
for k in p.index:
pp = np.where(p.loc[k].isnull(), None, p.loc[k])
parameters.add(k, value=pp[0], min=pp[1], max=pp[2], vary=pp[3])
# set ftol and epsfcn if no options for lmfit are provided. Only
# work with Lmfit's least squares solver method.
if not kwargs:
kwargs = {"ftol": 1e-3, "epsfcn": 1e-4}
self.fit = lmfit.minimize(fcn=self.objfunction, params=parameters,
args=(noise, model, weights), **kwargs)
# Set all parameter attributes
self.optimal_params = np.array([p.value for p in
self.fit.params.values()])
self.stderr = np.array([p.stderr for p in self.fit.params.values()])
if self.fit.covar is not None:
self.pcov = self.fit.covar
# Set all optimization attributes
self.nfev = self.fit.nfev
self.report = lmfit.fit_report(self.fit)
def test_reports_created(fitresult):
"""Verify that the fit reports are created and all headers are present."""
report_headers = [
'[[Model]]', '[[Fit Statistics]]', '[[Variables]]',
'[[Correlations]] (unreported correlations are < 0.100)'
]
report = fitresult.fit_report()
assert len(report) > 500
for header in report_headers:
assert header in report
report1 = fit_report(fitresult)
for header in report_headers[1:]:
assert header in report1
html_params = fitresult.params._repr_html_()
assert len(html_params) > 500
assert 'brute' in html_params
assert 'standard error' in html_params
assert 'relative error' in html_params
html_report = fitresult._repr_html_()
assert len(html_report) > 1000
for header in report_headers:
header_title = header.replace('[', '').replace(']', '').strip()
assert header_title in html_report
def fit(self) -> None:
self.debug('START', inspect.currentframe())
self.set_parameter()
self.result = lf.minimize(
fcn=self.objective, params=self.scf_model_parameters, kws={'E':self.xd})
if self.result.success:
self.info(self.result.message)
self.info('BEST FIT VALUES')
for name in self.result.var_names:
self.info(f'parameter of {name}')
self.info(
f' {self.result.params[name].value} +- {self.result.params[name].stderr}')
with open(self.log_file, 'w') as log:
log.write(
'--------------------------------------------------------------------\n')
log.write(lf.fit_report(self.result))
log.write('\n')
log.write(
'--------------------------------------------------------------------\n')
log.write(
f' Chi-squared value / d.o.f. = {self.result.chisqr} / {self.result.nfree}\n')
log.write(f' Reduced Chi-squared value = {self.result.redchi}\n')
log.write('\n')
self.info(f'Fitting results were recorded to {self.log_file}')
self.create_result_qdp()
if self.plot_flag:
self.plot()
self.debug('END', inspect.currentframe())
def test_bounded_jacobian():
pars = Parameters()
pars.add('x0', value=2.0)
pars.add('x1', value=2.0, min=1.5)
global jac_count
jac_count = 0
def resid(params):
x0 = params['x0'].value
x1 = params['x1'].value
return np.array([10 * (x1 - x0*x0), 1-x0])
def jac(params):
global jac_count
jac_count += 1
x0 = params['x0'].value
return np.array([[-20*x0, 10], [-1, 0]])
out0 = minimize(resid, pars, Dfun=None)
assert_paramval(out0.params['x0'], 1.2243, tol=0.02)
assert_paramval(out0.params['x1'], 1.5000, tol=0.02)
assert(jac_count == 0)
out1 = minimize(resid, pars, Dfun=jac)
assert_paramval(out1.params['x0'], 1.2243, tol=0.02)
assert_paramval(out1.params['x1'], 1.5000, tol=0.02)
assert(jac_count > 5)
print(fit_report(out1, show_correl=True))
def refine_angles(self, method='nelder', **opts):
self.set_idx()
from lmfit import minimize, fit_report
p0 = self.define_parameters(lattice=True, **opts)
self.result = minimize(self.angle_residuals, p0, method=method)
self.fit_report = fit_report(self.result)
if self.result.success:
self.get_parameters(self.result.params)
def refine_orientation_matrix(self, **opts):
self.set_idx()
from lmfit import minimize, fit_report
p0 = self.define_orientation_matrix()
self.result = minimize(self.orient_residuals, p0, **opts)
self.fit_report = fit_report(self.result)
if self.result.success:
self.get_orientation_matrix(self.result.params)
def refine_hkls(self, method='leastsq', **opts):
self.set_idx()
from lmfit import minimize, fit_report
if self.Umat is None:
raise NeXusError('No orientation matrix defined')
p0 = self.define_parameters(**opts)
self.result = minimize(self.hkl_residuals, p0, method=method)
self.fit_report = fit_report(self.result)
if self.result.success:
self.get_parameters(self.result.params)
def write_statistics(name, outf, pars, fit_result):
outf.write(name)
outf.write(fit_report(pars))
outf.write('\n')
outf.write('Norm residuals/root(N) is ' \
+ repr(LA.norm(fit_result.residual)/math.sqrt(len(fit_result.residual))))
outf.write('\n')
outf.write('Mean absolute error ' +
repr(np.mean(np.abs(fit_result.residual))))
outf.write('\n')
outf.write('-------------\n')
def save_result(self, fname=None):
"""
Parameters
----------
fname : str, optional
name of output file
"""
if not fname:
fname = self.data_title+'_out.txt'
filepath = os.path.join(self.result_folder, fname)
with open(filepath, 'w') as myfile:
myfile.write(fit_report(self.fit_result, sort_pars=True))
logger.warning('Results are saved to {}'.format(filepath))
def Fit_Qr(x, y):
# create a set of Parameters
params = Parameters()
params.add('sdelta', value= 1e-4, min = 1e-10, max = 1e-2)
params.add('Tc', value= 1.2, min = 0.1, max = 1.8)
params.add('alpha', value= 1, min = 1e-10, max = 1)
# do fit, here with leastsq model
result = minimize(Fit_Func, params, args=(x, y))
# calculate final result
residual = result.residual
# Calculate Qc and Qi
sdelta = result.params['sdelta'].value
sdelta_err = np.abs(result.params['sdelta'].stderr/sdelta)
Tc = result.params['Tc'].value
Tc_err = np.abs(result.params['Tc'].stderr/Tc)
alpha = result.params['alpha'].value
alpha_err = np.abs(result.params['alpha'].stderr/Tc)
print fit_report(result)
return sdelta, sdelta_err, Tc, Tc_err, alpha, alpha_err, fit_report(result), residual
def fit_gaussian(x_data, y_data):
""" Fit a gaussian to data """
# Setup fit
# Start values need to be ballpark correct!
params = Parameters()
params.add('A', value=-2000)
params.add('mu', value=6562.801)
params.add('sigma', value=1)
out = minimize(residual, params, args=(x_data, y_data))
print(fit_report(out.params))
plt.plot(x_data, y_data)
plt.plot(x_data, gaussian(out.params, x_data))
plt.show()
def test_bounds():
if not HAS_LEAST_SQUARES:
raise nose.SkipTest
p_true = Parameters()
p_true.add('amp', value=14.0)
p_true.add('period', value=5.4321)
p_true.add('shift', value=0.12345)
p_true.add('decay', value=0.01000)
def residual(pars, x, data=None):
amp = pars['amp']
per = pars['period']
shift = pars['shift']
decay = pars['decay']
if abs(shift) > pi/2:
shift = shift - sign(shift)*pi
model = amp*sin(shift + x/per) * exp(-x*x*decay*decay)
if data is None:
return model
return (model - data)
n = 1500
xmin = 0.
xmax = 250.0
random.seed(0)
noise = random.normal(scale=2.80, size=n)
x = linspace(xmin, xmax, n)
data = residual(p_true, x) + noise
fit_params = Parameters()
fit_params.add('amp', value=13.0, max=20, min=0.0)
fit_params.add('period', value=2, max=10)
fit_params.add('shift', value=0.0, max=pi/2., min=-pi/2.)
fit_params.add('decay', value=0.02, max=0.10, min=0.00)
min = Minimizer(residual, fit_params, (x, data))
out = min.least_squares()
assert(out.nfev > 10)
assert(out.nfree > 50)
assert(out.chisqr > 1.0)
print(fit_report(out, show_correl=True, modelpars=p_true))
assert_paramval(out.params['decay'], 0.01, tol=1.e-2)
assert_paramval(out.params['shift'], 0.123, tol=1.e-2)
def solve(self, X0, IR='IRF', RM='linear', TR=None, Cf=[1.0],
method='leastsq', period = ['01-01-1900', '01-01-2000', '01-01-2100'],
solver=1):
# Define the TFN Model
#self.IR = eval(IR) # Save the impulse response function
self.IR = getattr(self, IR)
self.RM = getattr(self, RM) # Save the recharge calculation function
if TR != None:
self.TR = getattr(self, TR)
self._TFN = IR # Save the name of the impulse response function
self._RM = RM # Save the name of the recharge model
self._index_calibration = self.data.t[(self.data.index > period[0]) &
(self.data.index < period[1]) & (self.data.Ho > -999)].tolist()
self._index_validation = self.data.t[(self.data.index > period[1]) &
(self.data.index < period[2]) & (self.data.Ho > -999)].tolist()
self.period = period
if method == 'leastsq':
X0.add('d', value=self.data.Ho.mean(), vary=True)
self.result = minimize(self.objective_function, X0,
method='leastsq', scale_covar=True)
self.parameters_optimized = self.result.params.valuesdict()
if self.result.success:
print 'Optimization completed succesfully!'
print(report_fit(self.result))
np.savetxt('Figures/fit_report_%s_%s.txt' %(self.bore, self._TFN),
(fit_report(self.result),), fmt='%str')
else:
X0.add('d', value=np.mean(self.head_observed))
self.result = minimize(self.objective_function, X0, args=(InputData,),
method=method)
self.parameters_optimized = self.result.params.valuesdict()
# Calculate statistics for both the calibration and validation period
self.result.SWSI_Cal = np.sqrt(sum(self.swsi(self._index_calibration)))
self.result.SWSI_Val = np.sqrt(sum(self.swsi(self._index_validation)))
self.result.RMSE_Cal = np.sqrt(sum(self.rmse(self._index_calibration)))
self.result.RMSE_Val = np.sqrt(sum(self.rmse(self._index_validation)))
self.result.AVGDEV_Cal = self.avg_deviation(self._index_calibration)
self.result.AVGDEV_Val = self.avg_deviation(self._index_validation)
self.result.EXPVAR_Cal = self.explained_variance(self._index_calibration)
self.result.EXPVAR_Val = self.explained_variance(self._index_validation)
def test_bounds():
p_true = Parameters()
p_true.add("amp", value=14.0)
p_true.add("period", value=5.4321)
p_true.add("shift", value=0.12345)
p_true.add("decay", value=0.01000)
def residual(pars, x, data=None):
amp = pars["amp"].value
per = pars["period"].value
shift = pars["shift"].value
decay = pars["decay"].value
if abs(shift) > pi / 2:
shift = shift - sign(shift) * pi
model = amp * sin(shift + x / per) * exp(-x * x * decay * decay)
if data is None:
return model
return model - data
n = 1500
xmin = 0.0
xmax = 250.0
random.seed(0)
noise = random.normal(scale=2.80, size=n)
x = linspace(xmin, xmax, n)
data = residual(p_true, x) + noise
fit_params = Parameters()
fit_params.add("amp", value=13.0, max=20, min=0.0)
fit_params.add("period", value=2, max=10)
fit_params.add("shift", value=0.0, max=pi / 2.0, min=-pi / 2.0)
fit_params.add("decay", value=0.02, max=0.10, min=0.00)
out = minimize(residual, fit_params, args=(x,), kws={"data": data})
fit = residual(out.params, x)
assert out.nfev > 10
assert out.nfree > 50
assert out.chisqr > 1.0
print(fit_report(out, show_correl=True, modelpars=p_true))
assert_paramval(out.params["decay"], 0.01, tol=1.0e-2)
assert_paramval(out.params["shift"], 0.123, tol=1.0e-2)
def produce_tauspectrum_noplot(freqMHz,taus,tauserr):
freqGHz = freqMHz/1000.
powmod = PowerLawModel()
powparstau = powmod.guess(taus,x=freqGHz)
tauserr = tauserr[np.nonzero(tauserr)]
taus = taus[np.nonzero(tauserr)]
freqGHz = freqGHz[np.nonzero(tauserr)]
freqMHz = freqMHz[np.nonzero(tauserr)]
powout = powmod.fit(taus,powparstau,x=freqGHz,weights=1/(np.power(tauserr,2)))
print(fit_report(powout.params))
fit = powout.best_fit
alpha = -powout.best_values['exponent']
alphaerr = powout.params['exponent'].stderr
return freqMHz, alpha, alphaerr, fit
def export_ref_fit(self):
pname = os.path.join('data', 'fit', self.label)
os.mkdir(pname)
for stim, result in zip(REF_STIM_LIST, self.ref_result_list):
fname_report = 'ref_fit_%d.txt' % stim
fname_pickle = 'ref_fit_%d.pkl' % stim
with open(os.path.join(pname, fname_report), 'w') as f:
f.write(fit_report(result))
with open(os.path.join(pname, fname_pickle), 'wb') as f:
pickle.dump(result, f)
with open(os.path.join(pname, 'ref_mean_lmpars.pkl'), 'wb') as f:
pickle.dump(self.ref_mean_lmpars, f)
# Plot
fig, axs = self.plot_ref_fit(roll=True)
fig.savefig(os.path.join(pname, 'ref_fit_roll.png'), dpi=300)
plt.close(fig)
fig, axs = self.plot_ref_fit(roll=False)
fig.savefig(os.path.join(pname, 'ref_fit_inst.png'), dpi=300)
plt.close(fig)
def fit_spectrum(self, energy, counts, energy_min=None,
energy_max=None):
work_energy = 1.0*energy
work_counts = 1.0*counts
floor = 1.e-12*np.percentile(counts, [99])[0]
work_counts[np.where(counts<floor)] = floor
if max(energy) < 250.0: # input energies are in keV
work_energy = 1000.0 * energy
self.set_fit_weight(work_energy, work_counts)
imin, imax = 0, len(counts)
if energy_min is None:
energy_min = self.energy_min
if energy_min is not None:
imin = index_of(work_energy, energy_min)
if energy_max is None:
energy_max = self.energy_max
if energy_max is not None:
imax = index_of(work_energy, energy_max)
self.fit_weight[:imin-1] = 0.0
self.fit_weight[imax+1:] = 0.0
self.fit_iter = 0
userkws = dict(data=work_counts,
index=np.arange(len(counts)))
kws = dict(method='leastsq', maxfev=4000, gtol=self.fit_toler,
ftol=self.fit_toler, xtol=self.fit_toler, epsfcn=1.e-5)
self.result = minimize(self.__resid, self.params, kws=userkws, **kws)
self.fit_report = fit_report(self.result, min_correl=0.5)
self.best_fit = self.calc_spectrum(energy, params=self.result.params)
# calculate transfer matrix for linear analysis using this model
tmat= []
for key, val in self.comps.items():
tmat.append(val / self.eigenvalues[key])
self.transfer_matrix = np.array(tmat)
def test_ci_report():
"""test confidence interval report"""
def residual(pars, x, data=None):
argu = (x*pars['decay'])**2
shift = pars['shift']
if abs(shift) > np.pi/2:
shift = shift - np.sign(shift)*np.pi
model = pars['amp']*np.sin(shift + x/pars['period']) * np.exp(-argu)
if data is None:
return model
return model - data
p_true = Parameters()
p_true.add('amp', value=14.0)
p_true.add('period', value=5.33)
p_true.add('shift', value=0.123)
p_true.add('decay', value=0.010)
n = 2500
xmin = 0.
xmax = 250.0
x = np.linspace(xmin, xmax, n)
data = residual(p_true, x) + np.random.normal(scale=0.7215, size=n)
fit_params = Parameters()
fit_params.add('amp', value=13.0)
fit_params.add('period', value=2)
fit_params.add('shift', value=0.0)
fit_params.add('decay', value=0.02)
mini = Minimizer(residual, fit_params, fcn_args=(x,),
fcn_kws={'data': data})
out = mini.leastsq()
report = fit_report(out)
assert(len(report) > 500)
ci, tr = conf_interval(mini, out, trace=True)
report = ci_report(ci)
assert(len(report) > 250)
def produce_tauspectrum_highHBA(freqMHz,taus,tauserr,freqMHzhigh,tauhigh,tauerrhigh):
freqGHz = freqMHz/1000.
powmod = PowerLawModel()
powparstau = powmod.guess(taus,x=freqGHz)
#remove tauserr = 0 entries
tauserr = tauserr[np.nonzero(tauserr)]
taus = taus[np.nonzero(tauserr)]
freqGHz = freqGHz[np.nonzero(tauserr)]
freqMHz = freqMHz[np.nonzero(tauserr)]
powout = powmod.fit(taus,powparstau,x=freqGHz,weights=1/(np.power(tauserr,2)))
print(fit_report(powout.params))
fit = powout.best_fit
alpha = -powout.best_values['exponent']
alphaerr = powout.params['exponent'].stderr
amp = powout.params['amplitude']
allfreq = np.append(freqMHz,freqMHzhigh)
fithigh = amp*np.power(allfreq/1000, -alpha)
fig = plt.figure(figsize=(12,6))
plt.errorbar(freqMHz,taus,yerr=tauserr,fmt='*-',markersize=10.0,capthick=2,linewidth=1.5,label=r'$\alpha = %.1f \pm %.1f$'%(alpha,alphaerr))
plt.errorbar(freqMHzhigh,tauhigh,yerr=tauerrhigh,fmt='o')
plt.plot(freqMHz,fit,'k--',linewidth=1.5)
plt.xscale('log')
plt.yscale('log')
plt.yticks(fontsize=12)
ticksMHz = (freqMHz).astype(np.int)[0:len(freqMHz):2]
plt.xticks(ticksMHz,ticksMHz,fontsize=12)
plt.legend(fontsize=12,numpoints=None)
plt.xlabel(r'$\nu$ (MHz)',fontsize=14, labelpad=15.0)
plt.ylabel(r'$\tau$ (sec)',fontsize=14)
plt.xlim(xmin = 0.95*freqMHz[0],xmax=1.05*freqMHzhigh[-1])
plt.gcf().subplots_adjust(bottom=0.15)
return freqMHZ, alpha, alphaerr, fit, fithigh
def fit2(self):
xdata = np.linspace(-30000.0, 30000.0, num=8000)
#ydata = UIUtils.pz_bxy_scan_data(B=xdata, B01=130, B02=-830, B03=-800, T_long=2.5*0.002, T_trans=0.002, Rp=1./(2*0.002), Rprb=1./(4*0.002), gamma=2.2, s=-1.0, xdata=xdata)
#ydata = UIUtils.pz_bxy_scan(B=xdata, B01=100, B02=1000, B03=0, T_long=2.5*0.002, T_trans=0.002, Rp=1./(2*0.002), Rprb=1./(4*0.002), gamma=2.2, s=-1.0)
ydata = UIUtils.func_scan(B=xdata, B01=0, B02=100, B03=-100, T1=2.5*0.002, T2=0.002, Rp=1./(2*0.002), Rpr=1./(4*0.002), gamma=2.2, s=-1)
#self.gui.plot.plot(xdata, ydata, pen=(0,0,255))
# create a set of Parameters
# 'value' is the initial condition
# 'min' and 'max' define your boundaries
params = Parameters()
params.add('B01', value= 0.0, vary=True, min=-10., max=300.)
params.add('B02', value= 0.0, vary=True, min=-10., max=300.)
params.add('B03', value= 0.0, vary=True, min=-300., max=300.)
params.add('T_long', value= 2.5*0.002, vary=False, min=0, max=1.0)
params.add('T_trans', value= 0.002, vary=False, min=0, max=1.0)
params.add('Rp', value= 250.0, vary=False, min=0.001, max=500)
params.add('Rprb', value= 125.0, vary=False, min=0.001, max=500)
params.add('off', value=0.0, min=0.0, max = 0.5)
# do fit
result = minimize(UIUtils.fit2, params, args=(xdata, ydata), method='nelder')
#rp = result.values['B01'], result.values['B02'], result.values['B03'], result.values['T_long'], result.values['T_trans'], result.values['Rp'], result.values['Rprb']
# write error report
print(fit_report(result))
#print(result.residual)
xplot = np.linspace(min(xdata), max(xdata), 1000)
final = ydata + result.residual
try:
self.gui.plot.plot(xdata, ydata, pen=(0,0,255), symbol='o')
self.gui.plot.plot(xdata, final, pen=(0,255,0))
except:
print('fit not successful')
pass
#print(*params)
#print(result.values['B01'])
print(final)
def inverse(self,
y_obs):
type, guess = self.guess(y_obs)
p = Parameters()
with open(self.report, 'w') as file:
file.write('** Juno Retrieval Begin **\n')
file.write('type = %s, initial guess = ' % type)
for i in range(len(guess)): file.write('%f ' % guess[i])
file.write('\n')
print type, guess
p.add('NH3', value = guess[0], min = 0.1, max = 20.)
p.add('H2O', value = guess[1], min = 0.1, max = 20.)
if type == 'sat':
p.add('stretch', value = 1., vary = False)
result = minimize(self.loss_function, p, iter_cb = self.write_iter_report,
col_deriv = True, Dfun = self.jacobian, args = (y_obs, 'f'),
xtol = 1.E-4, ftol = 1.E-8, maxfev = 100)
elif type == 'stretch':
p.add('stretch', value = guess[2], min = 0.8, max = 5.)
result = minimize(self.loss_function, p, iter_cb = self.write_iter_report,
col_deriv = True, Dfun = self.jacobian, args = (y_obs, 'f'),
xtol = 1.E-4, ftol = 1.E-8, maxfev = 100)
else:
raise ValueError('Model type not understood')
with open(self.report, 'a') as file:
file.write(fit_report(p))
file.write('\n')
# write jacobian
#file.write('Jacobian = \n')
#jacob = self.jacobian(p, y_obs)
#m, n = jacob.shape
#for i in range(m):
# for j in range(n):
# file.write('%16.4e' % jacob[i, j])
# file.write('\n')
file.write('** Juno Retrieval End **\n')
return type, parameter_to_list(p)
def Minimize(self):
result=None
report=None
# create a set of Parameters, except x
#initial values are defined here
params = lm.Parameters()
for i in range(len(self._Variables)-1):
params.add(self._Variables[i],value=0.1)
myfit = lm.Minimizer(self._ObjFunc, params, \
args=(self._Xvalues, self._Yvalues), \
fcn_kws={})
myfit.prepare_fit()
result = lm.minimize(self._ObjFunc, params, \
args=(self._Xvalues,self._Yvalues), \
method='leastsq')
report = lm.fit_report(params)
#Calculate both quality factors - R2 and ReducedChi2.
R2 = 1-result.chisqr/self._getSStotal(self._Yvalues)
RChi2 = result.redchi
return CFitReport(self._Function,R2,RChi2,result,report)
def polish(match, params0, psf, psf_err, angstrom_per_node=20):
"""Polish parameters
Given a list of match object, polish the parameters segment by segment
Args:
match (smsyn.match.Match): Match objects.
params0 (lmfit.Parameters): lmfit.Parameters object with initial guesses
angstrom_per_node (float): approximate separation between continuum and
spline nodes. Number of nodes will be rounded to nearest integer.
objective_method (string): name of objective function. Must be a method
of the Match object {'chi2med','nresid'}
Returns
dict: with following keys:
- result
- model
- wav
- resid
- objective
"""
params = lmfit.Parameters()
for name in params0.keys():
params.add(name)
params[name].value = params0[name].value
params[name].vary = params0[name].vary
params[name].min = params0[name].min
params[name].max = params0[name].max
params['vsini'].min = 0
params['logg'].min = 1.0
params['logg'].max = 5.0
params['teff'].min = 4500
params['teff'].max = 7000
params['fe'].min = -2.0
params['fe'].max = 0.5
params.add('psf')
params['psf'].vary = False
params['psf'].min = 0
params['psf'].value = psf
wavlim = match.spec['wav'][[0,-1]]
node_wav = smsyn.match.spline_nodes(
wavlim[0], wavlim[1], angstroms_per_node=angstrom_per_node,
)
for _node_wav in node_wav:
key = 'sp%d' % _node_wav
params.add(key)
params[key].value = 1.0
def chisq(params):
nresid = match.masked_nresid(params)
_chisq = np.sum(nresid**2)
return _chisq
def rchisq(params):
return chisq(params) / num_points
def objective(params):
_chisq = chisq(params)
_penalty = ((params['psf'].value - psf)/psf_err)**2.0
return _chisq + _penalty
def print_params(lmout):
lmout.params.pretty_print(columns=['value', 'vary'])
print "rchisq = {}".format(rchisq(lmout.params))
num_points = len(match.masked_nresid(params))
params_out = {}
params_out['rchisq0'] = rchisq(params)
# Fit a first time to get the chisq minimum
lmout = lmfit.minimize(
objective, params, method='powell', options=dict(disp=True)
)
print lmfit.fit_report(lmout)
print_params(lmout)
# Re-fit, but allow a prior on the psf parameter
rchisq_min = objective(lmout.params) / num_points
params = lmout.params
params['psf'].vary =True
def objective(params):
_chisq = chisq(params)
_penalty = rchisq_min * ((params['psf'].value - psf)/psf_err)**2.0
return _chisq + _penalty
lmout = lmfit.minimize(
objective, params, method='powell', options=dict(disp=True)
)
print lmfit.fit_report(lmout)
print_params(lmout)
for k in 'teff logg fe vsini psf'.split():
params_out[k] = lmout.params[k].value
params_out['rchisq1'] = rchisq(lmout.params)
resid = match.resid(lmout.params)
d = dict(
params_out=params_out,
flux=match.spec.flux,
wav=match.spec.wav,
resid=resid,
wavmask=match.wavmask,
)
return d
model_i = fitfuncs[i](x[i],
original_params[i],
*original_userargs[i],
**original_kws[i])
model = np.append(model,
model_i)
return model
if __name__ == '__main__':
from lmfit import fit_report
def gauss(x, params, *args):
"""Calculates a Gaussian model"""
p = values(params)
return p[0] + p[1] * np.exp(-((x - p[2]) / p[3])**2)
xdata = np.linspace(-4, 4, 100)
p0 = np.array([0., 1., 0., 1.])
bounds = [(-1., 1.), (0., 2.), (-3., 3.), (0.001, 2.)]
temp_pars = to_parameters(p0, bounds=bounds)
pars = to_parameters(p0 + 0.2, bounds=bounds)
ydata = gauss(xdata, temp_pars) + 0.1 * np.random.random(xdata.size)
f = CurveFitter(gauss, (xdata, ydata), pars)
f.fit()
print(fit_report(f.params))
fit_params = Parameters()
fit_params.add('scalePara', value=3.77156,vary=False)
fit_params.add('scaleCorr', value=np.random.uniform(5,25),min=0,max=30)
fit_params.add('width', value=0.2,vary=False)
fit_params.add('damp', value=100,vary=False)#1.5,min=1.0,max=100)
x=np.array([0])
data=expDr[np.logical_and(expr>rmin+0.5*rstep,expr<=rmax+0.5*rstep)]
dataErr=err[np.logical_and(expr>rmin+0.5*rstep,expr<=rmax+0.5*rstep)]
fit_kws={'sigma':err,'absolute_sigma':True}
out = minimize(residual, fit_params, args=(x,), kws={'data':data},**fit_kws)
fit = residual(fit_params, x)
print fit_report(fit_params)
rcomp = expr[np.logical_and(expr>rmin+0.5*rstep,expr<=rmax+0.5*rstep)]
diff = data-fit
chisq=np.sum((diff)**2/len(diff))
print chisq
rfull=expr[np.logical_and(expr>rcalcmin+0.5*rstep,expr<=rcalcmax+0.5*rstep)]
datafull=expDr[np.logical_and(expr>rcalcmin+0.5*rstep,expr<=rcalcmax+0.5*rstep)]
offset = 1.25*np.abs(np.min(data))
fig=plt.figure()
ax=fig.add_subplot(111)
ax.plot(rfull,datafull,marker='o',mfc='none',mec='b',linestyle='none')
def fit_report(self):
"""Return the report created by lmfit."""
return str(fit_report(self.parameters))
