def center_on_cos(raw_quadratures, phi0=None, omega=None, snap_omega=False):
mean = scipy.average(raw_quadratures, axis=1)
no_angles, no_pulses = raw_quadratures.shape
model = Model(cos_model)
offset, amplitude, phi0, omega = guess_initial_parameters(
mean, phi0, omega)
model.set_param_hint("offset", value=offset)
model.set_param_hint("amplitude", min=0., value=amplitude)
model.set_param_hint("phi0", value=phi0)
model.set_param_hint("omega", min=0., value=omega)
model.make_params(verbose=False)
steps = scipy.arange(no_angles)
res = model.fit(mean, x=steps, verbose=False)
omega_param = res.params["omega"]
if snap_omega:
appx_omega = float(omega_param)
no_pi_intervals = int(round(pi / appx_omega))
omega = pi / no_pi_intervals
omega_param.set(omega, vary=False)
res.fit(mean, x=steps, verbose=False)
d_value, p_value_ks = kstest(res.residual, 'norm')
mean_fit = res.eval(x=steps)
offset = mean - mean_fit
aligned_quadratures = raw_quadratures - offset[:, None]
centered_quadratures = aligned_quadratures - float(res.params["offset"])
return (centered_quadratures, float(omega_param),
float(res.params["phi0"]), p_value_ks)
def center_on_cos(raw_quadratures, phi0=None, omega=None, snap_omega=False):
mean = scipy.average(raw_quadratures, axis=1)
no_angles, no_pulses = raw_quadratures.shape
model = Model(cos_model)
offset, amplitude, phi0, omega = guess_initial_parameters(mean, phi0, omega)
model.set_param_hint("offset", value=offset)
model.set_param_hint("amplitude", min=0., value=amplitude)
model.set_param_hint("phi0", value=phi0)
model.set_param_hint("omega", min=0., value=omega)
model.make_params(verbose=False)
steps = scipy.arange(no_angles)
res = model.fit(mean, x=steps, verbose=False)
omega_param = res.params["omega"]
if snap_omega:
appx_omega = float(omega_param)
no_pi_intervals = int(round(pi/appx_omega))
omega = pi/no_pi_intervals
omega_param.set(omega, vary=False)
res.fit(mean, x=steps, verbose=False)
d_value, p_value_ks = kstest(res.residual, 'norm')
mean_fit = res.eval(x=steps)
offset = mean-mean_fit
aligned_quadratures = raw_quadratures - offset[:,None]
centered_quadratures = aligned_quadratures - float(res.params["offset"])
return (centered_quadratures,
float(omega_param), float(res.params["phi0"]), p_value_ks)
def make_models(model, peaks):
""" Make composite models for multiple peaks
Arguments:
-- models
-- peaks: dict of {prefix:"peak_name_", model_params:()}
"""
if len(peaks) < 2:
mod = Model(model, prefix=peaks[0][0])
p_guess = mod.make_params()
values = peaks[0][1:]
update_params(p_guess, values)
elif len(peaks) > 1:
mod = Model(model, prefix=peaks[0][0])
values = peaks[0][1:]
print(values)
for i in peaks[1:]:
mod += Model(model, prefix=i[0])
values.extend(i[1:])
p_guess = mod.make_params()
update_params(p_guess, values)
return mod, p_guess
def make_models(model,peaks):
""" Make composite models for multiple peaks
Arguments:
-- models
-- peaks: dict of {prefix:"peak_name_", model_params:()}
"""
if len(peaks)<2:
mod = Model(model,prefix=peaks[0][0])
p_guess = mod.make_params()
values = peaks[0][1:]
update_params(p_guess,values)
elif len(peaks)>1:
mod = Model(model,prefix=peaks[0][0])
values = peaks[0][1:]
print(values)
for i in peaks[1:]:
mod += Model(model,prefix=i[0])
values.extend(i[1:])
p_guess = mod.make_params()
update_params(p_guess,values)
return mod, p_guess
def OptimizeDevicParameters2(self):
for c in [0, 1, 2]:
fmodel = Model(self.DevicCalFunc)
# create parameters -- these are named from the function arguments --
# giving initial values
params = fmodel.make_params(A=self.DevicParam_A[c],
B=self.DevicParam_B[c],
n=self.DevicParam_n[c])
# fix n:
params['n'].vary = False
# limit parameter values
params['A'].min = 0
params['A'].max = 100
params['B'].min = 0
params['B'].max = 500
result = fmodel.fit(self.D, params, x=self.ODnet[:, c])
self.DevicParam_A[c] = result.params['A']
self.DevicParam_B[c] = result.params['B']
self.Sigma_A[c] = result.params['A'].stderr
self.Sigma_B[c] = result.params['B'].stderr
self.Sigma_n[c] = 0.0
print("Fit results for channel {}:".format(c))
# result.plot_fit()
print(result.fit_report())
print('')
self.show_calibration_plot()
def lmDDOPhaseFit(xdata, ydata, params, f0_range=1.2, Q_range=3):
f0 = params[0]
Q = 1 / (2 * params[2])
x = xdata
y = ydata
#Define a linear model and a Damped Oscillator Model
# ddophase_mod = ExpressionModel('off + m*x- arctan(1/Q * 1/(f0/x - x/f0))-')
ddophase_mod = Model(phase)
#Initial Pars for Linear Model
pars = ddophase_mod.make_params(off=0, m=0, f0=f0, Q=Q)
#Add fit parameters, Center, Amplitude, and Sigma
pars['f0'].set(min=f0 / f0_range, max=f0 * f0_range)
pars['Q'].set(min=Q / Q_range, max=Q * Q_range)
#Create full model. Add linear model and all peaks
#Initialize fit
init = ddophase_mod.eval(pars, x=x)
#Do the fit. The weight exponential can weight the points porportional to the
#amplitude of y point. In this way, points on peak can be given more weight.
out = ddophase_mod.fit(y, pars, x=x)
#Get the fit parameters
fittedf0 = out.params['f0'].value
fittedQ = out.params['Q'].value
#Returns the output fit as well as an array of the fit parameters
"""Returns output fit as will as list of important fitting parameters"""
return out, [fittedf0, np.nan, np.nan, fittedQ]
def create_xrf_line(x, params, linedict, linefunc):
funcmodel = Model(linefunc)
# start with the function parameters...
funcparams = funcmodel.make_params()
#
# copy the function based parameters from params to funcparams
#
for key in params:
if key in funcparams:
funcparams[key].value = params[key].value
funcparams[key].min = params[key].min
funcparams[key].max = params[key].max
funcparams[key].vary = params[key].vary
result = np.zeros_like(x)
sigma_keys = [s for s in funcparams.keys() if 'sigma' in s]
for key, linegroup in linedict.iteritems():
if key in params:
for line in linegroup:
# update funcparams
funcparams["area"].value = params[key].value*\
line.intensity
funcparams["center"].value = line.line_energy
for ii in sigma_keys:
funcparams[ii].value = np.sqrt(params[ii].value**2 + \
(line.line_energy*0.001))
result = result + funcmodel.eval(funcparams, x=x)
return result
def create_xrf_lmfit_parameters(exptdesc, linedict, linefunc):
funcmodel = Model(linefunc)
funcparams = funcmodel.make_params()
# remove the area and center parameter
funcparams.pop("area", None)
funcparams.pop("center", None)
# get the function name
linename = linefunc.__name__
# For each element in the linedict add a parameter
# which will control the area
for key in exptdesc["lineshape"]["element"][linename].keys():
if key in funcparams:
funcparams[key].value = \
exptdesc["lineshape"]["element"][linename][key]["value"]
funcparams[key].min = \
exptdesc["lineshape"]["element"][linename][key]["min"]
funcparams[key].max = \
exptdesc["lineshape"]["element"][linename][key]["max"]
funcparams[key].vary = \
exptdesc["lineshape"]["element"][linename][key]["vary"]
for key in linedict:
if not '+' in key:
funcparams.add(
key, **exptdesc["lineshape"]["element"][linename]["area"])
return funcparams
def decay_fitting(xdata,ydata,ystderr, init, no_trials = 1):
# Declare model and initializing data
print('Fitting now...')
lzmod = Model(exp_decay)
print(fitguess)
# Set parameter hints
lzmod.set_param_hint('amp', value = init[0])
lzmod.set_param_hint('dec', value = init[1] )
lzmod.set_param_hint('yoff', value = init[2])
lzmod.set_param_hint('ps', value = init[3])
pars = lzmod.make_params()
fit = lzmod.fit(ydata, pars, x=xdata, weights=1/ystderr, verbose=False)
#print fit.fit_report()
amp_est = fit.params['amp'].value
amp_std = fit.params['amp'].stderr
decay_est = fit.params['dec'].value
decay_std = fit.params['dec'].stderr
yoff_est = fit.params['yoff'].value
yoff_std = fit.params['yoff'].stderr
redchi = fit.redchi
# Return back the result list with the following order:
result_list = [amp_est, amp_std, decay_est, decay_std,yoff_est,yoff_std, redchi]
return (result_list,fit)
def lmDDOPhaseFit(xdata, ydata, params, f0_range = 1.2, Q_range = 3):
f0= params[0]
Q=1/(2*params[2])
x = xdata
y = ydata
#Define a linear model and a Damped Oscillator Model
# ddophase_mod = ExpressionModel('off + m*x- arctan(1/Q * 1/(f0/x - x/f0))-')
ddophase_mod = Model(phase)
#Initial Pars for Linear Model
pars = ddophase_mod.make_params(off=0, m=0, f0=f0, Q=Q)
#Add fit parameters, Center, Amplitude, and Sigma
pars['f0'].set(min=f0/f0_range, max=f0*f0_range)
pars['Q'].set(min=Q/Q_range, max=Q*Q_range)
#Create full model. Add linear model and all peaks
#Initialize fit
init = ddophase_mod.eval(pars, x=x)
#Do the fit. The weight exponential can weight the points porportional to the
#amplitude of y point. In this way, points on peak can be given more weight.
out=ddophase_mod.fit(y, pars,x=x)
#Get the fit parameters
fittedf0= out.params['f0'].value
fittedQ = out.params['Q'].value
#Returns the output fit as well as an array of the fit parameters
"""Returns output fit as will as list of important fitting parameters"""
return out, [fittedf0, np.nan, np.nan, fittedQ]
def on_fit_button_released(self):
p0 = dict()
truth_list = []
self.fit_function.__defaults__ = ()
for i in range(len(self.args)):
top_widget = self.tw.topLevelItem(i)
p0[self.args[i]] = self.tw.itemWidget(top_widget, 2).value()
truth_list.append(
bool(self.tw.itemWidget(top_widget, 0).checkState()))
fitmodel = Model(self.fit_function)
params = fitmodel.make_params(**p0)
for i, flag in enumerate(truth_list):
if not flag:
params[self.args[i]].vary = False
try:
x, y = self.data_item.getData()
if np.isnan(y).any():
end = np.isnan(y).argmax()
y = y[:end]
x = x[:end]
result = fitmodel.fit(y, params, x=x)
except Exception as e:
print(e)
self.plot_active = True
self.params = []
for i, (_, value) in enumerate(result.params.valuesdict().items()):
self.tw.topLevelItem(i).setText(3, str(value))
top_widget = self.tw.topLevelItem(i)
self.tw.itemWidget(top_widget, 2).setValue(float(value))
self.fit_function.__defaults__ = self.defaults
self.params.append(value)
self.fit_curve_drawn = True
def gauss_step_const(signal, guess):
"""
Fits high contrast data very well
"""
if guess == False:
return [0, 0]
else:
amp, centre, stdev, offset = guess
data = np.array([range(len(signal)), signal]).T
X = data[:,0]
Y = data[:,1]
# gauss_mod = Model(gaussian)
gauss_mod = Model(gaussian)
const_mod = ConstantModel()
step_mod = StepModel(prefix='step')
pars = gauss_mod.make_params(height=amp, center=centre, width=stdev / 3., offset=offset)
# pars = gauss_mod.make_params(amplitude=amp, center=centre, sigma=stdev / 3.)
gauss_mod.set_param_hint('sigma', value = stdev / 3., min=stdev / 2., max=stdev)
pars += step_mod.guess(Y, x=X, center=centre)
pars += const_mod.guess(Y, x=X)
mod = const_mod + gauss_mod + step_mod
result = mod.fit(Y, pars, x=X)
# write error report
#print result.fit_report()
print "contrast fit", result.redchi
return X, result.best_fit, result.redchi
class DLS:
"""Load DLS models for fitting autocorrelation functions using the cumulant method
A great explanation for this fitting procedure was written by Barbara Frisken
20 August 2001 Vol. 40, No. 24 APPLIED OPTICS
Arguments:
mu_2 -- Bool
fit second cumulant term, mu_2, to estimate polydispersity of sample
mu_3 -- Bool
fit third cumulant term, mu_3, to estimate skew on polydispersity
"""
def __init__(self, mu_2=True, mu_3=False, **qkwargs):
#self._q = self.q(**qkwargs)
# use only simple exp function
if not mu_2:
self.g = Model(g)
# fit mu_2 and mu_3
elif mu_3:
self.g = Model(cumulant3)
# fit only mu_2
else:
self.g = Model(cumulant2)
self.pars = self.g.make_params(D=1e-10, B=1.0, beta=0.5, mu_2=1.0e5, mu_3=1.0)
def lmfit_fourier(x, y):
x = np.array(x)
y = np.array(y)
freq = np.fft.fftfreq(len(x), (x[1] - x[0])) # assume uniform spacing
Fy = abs(np.fft.fft(y))
guess_freq = abs(freq[
np.argmax(Fy[1:]) +
1]) # excluding the zero frequency "peak", which is related to offset
guess_amp = np.std(y) * 2.**0.5
guess_offset = np.mean(y)
#guess = np.array([guess_amp, 2.*np.pi*guess_freq, 0., guess_offset])
def sinfunc(x, A, w, p, c):
return A * np.sin(w * x + p) + c
gmodel = Model(sinfunc)
params = gmodel.make_params(A=guess_amp,
w=2. * np.pi * guess_freq,
p=0.,
c=guess_offset)
sinus_fit = gmodel.fit(y, params, x=x)
return sinus_fit.best_fit
def make_lmfit(indep, dep, names, degree=2, mindep=-1.0, maxdep=0.4):
med_dep = np.median(dep)
numpts = (degree + 1)**len(indep)
names_new = [st + '_ind' for st in names]
x = np.empty(
(0, degree +
1)) # To set up grid on which true dust parameter n will be defined
per = np.percentile(indep, [1.0, 99.0], axis=1)
for i in range(len(indep)):
x = np.append(x,
np.linspace(per[0, i], per[1, i], degree + 1)[None, :],
axis=0)
xx = np.meshgrid(*x) #N-D Grid for polynomial computations
pmod = Model(polymod,
independent_vars=names_new,
param_names=['c' + str(d) for d in range(numpts)])
pars = pmod.make_params()
for i in range(numpts):
pars.add('c' + str(i),
value=med_dep,
min=mindep,
max=maxdep,
vary=True)
kwargs = {'xx': xx}
for name, ind in zip(names_new, indep):
kwargs[name] = ind
res = pmod.fit(dep, params=pars, **kwargs)
# print(res.fit_report())
return xx, res
def lorentz_fitting(data, init, no_trials=1):
# Declare model and initializing data
print('Fitting now...')
lzmod = Model(lorentzian)
xdata = data[:, 0]
ydata = data[:, 1]
ystderr = data[:, 2] / np.sqrt(no_trials)
# Set parameter hints
lzmod.set_param_hint('amp', value=init[0], min=0)
lzmod.set_param_hint('width', value=init[1], min=0)
lzmod.set_param_hint('mean', value=init[2])
pars = lzmod.make_params()
fit = lzmod.fit(ydata, pars, x=xdata, weights=1 / ystderr, verbose=False)
#print fit.fit_report()
amp_est = fit.params['amp'].value
amp_std = fit.params['amp'].stderr
width_est = fit.params['width'].value
width_std = fit.params['width'].stderr
mean_est = fit.params['mean'].value
mean_std = fit.params['mean'].stderr
redchi = fit.redchi
# Return back the result list with the following order:
result_list = [
amp_est, amp_std, width_est, width_std, mean_est, mean_std, redchi
]
return result_list
def approach_fit(y):
fmodel = Model(approach)
# initial values
params = fmodel.make_params(E=0,
E0=0,
D=1e-6,
rtip=25e-7,
k0=1,
n=1,
alpha=0.5,
T=293)
# fix parameters:
params['T'].vary = False
params['alpha'].vary = False
params['rtip'].vary = False
params['E0'].vary = False
params['E'].vary = False
# fit parameters to data with various *static* values of b:
# for b in range(10):
# params['T'].value = 293
# params['alpha'].value = 0.5
# params['rtip'].value = 25e-7
# params['E0'].value = 0
# params['E'].value = 0.4
result = fmodel.fit(i, params, x=L)
def GaussManual(signal, guess):
"""
Fits high contrast data very well
"""
amp, centre, stdev, offset = guess
data = np.array([range(len(signal)), signal]).T
X = data[:, 0]
Y = data[:, 1]
gauss_mod = Model(gaussian)
pars = gauss_mod.make_params(center=centre,
sigma=stdev,
amplitude=amp,
offset=offset)
pars['center'].vary = False
pars['sigma'].min = stdev
pars['sigma'].max = stdev + 5.
mod = gauss_mod
result = mod.fit(Y, pars, x=X)
fwhm = result.best_values['sigma'] * 2.3548
return X, result.best_fit, result.best_values['sigma'] * 4
def get_resvar(x, y, mod='linear', zero_intercept=False):
"""
If `mod == 'linear'` then uses linear regression; otherwise
`mod == 'sigmoid'` and uses sigmoid regression.
"""
assert len(x) == len(y)
if len(x) < 3 or mod == 'linear':
model = Model(linear)
params = model.make_params()
params['a'].value = (y.max() - y.min()) / (x.max() - x.min())
params['b'].value = y.min()
if zero_intercept:
params['b'].value = 0
params['b'].vary = False
modfit = model.fit(y, x=x, params=params)
else:
model = Model(sigmoid)
modfit = model.fit(y, x=x, a=y.max(), b=1 / (x.max() - x.min()),
c=x.max())
finex = np.linspace(x.min(), x.max(), 50)
result = {
'mod': mod,
'params': modfit.best_values,
'resvar': modfit.residual.var(),
'y': modfit.best_fit,
'finex': finex,
'finey': modfit.eval(x=finex),
'r2': 1 - modfit.residual.var() / np.var(y),
'modfit': modfit}
return result
def fit_lm_sin(xdata, ydata):
sinemodel = Model(sine_func)
params = sinemodel.make_params(a=1, b=0.1)
result = sinemodel.fit(ydata, params, x=xdata)
# result = sinemodel.fit(ydata, x=xdata, a=1, b=0.1) #params not required this way
return result
def gaussline(data,
flareinds,
ind,
guess_out,
plot=True,
offset=0,
mags=1,
exguess=False,
more=False):
'''
Fits gaussian+line composite model to the 13 flares.
Inputs:
-------
data: sog4
flareinds: flareinds
ind: index of flare in flareinds to fit
guess_out: gaussian output to use as a guess for the amp, cen, and wid
plot: default True -- plots best fit on flare data
offset: vertical offset
mags: original or detrended data (defaultt 1 for original data)
exguess: default False; make True if guess_out is list of guess parameters rather than gaussian result
more: returns result rather than best parameter values if True (default False)
Output:
-------
if more: returns fit result
else: returns best fit cen, amp, and wid
'''
x = data['MJD-50000'][flareinds[ind][0]:flareinds[ind][1]]
#default mag 1 is original data; 5 is detrended
if mags == 1: imag = data['I mag']
else: imag = data['I detrend 2']
y = offset + np.max(imag[flareinds[ind][0]:flareinds[ind][1]]
) - imag[flareinds[ind][0]:flareinds[ind][1]]
mod = Model(gaussian) + Model(line)
#using guesses from gaussian model
if exguess:
amp, cen, wid = guess_out[0], guess_out[1], guess_out[2]
else:
gf = guess_out[
ind].best_values #getting guesses from previous fit (just gaussian)
amp, cen, wid = gf['amplitude'], gf['center'], gf['sigma']
pars = mod.make_params(amp=amp, cen=cen, wid=wid, slope=0, intercept=1)
pars['amp'].min = 0.0
#center constrained to be within 30 days of .05 offset center
pars['cen'].min = cen - 30
pars['cen'].max = cen + 30
#positive width
pars['wid'].min = 0.0
result = mod.fit(y, pars, x=x)
if plot:
plt.plot(x, y, 'bo')
#plot best fit model and center
plt.plot(x, result.best_fit, 'r-', label='best fit')
plt.axvline(result.best_values['cen'], color='black')
plt.legend(loc='best')
plt.show()
if more: return result
else: return result.best_values
def test_unprefixed_name_collisions(self):
# tests Github Issue 710
np.random.seed(0)
x = np.linspace(0, 20, 201)
y = 6 + x * 0.55 + gaussian(x, 4.5, 8.5, 2.1) + np.random.normal(size=len(x), scale=0.03)
def myline(x, a, b):
return a + b * x
def mygauss(x, a, b, c):
return gaussian(x, a, b, c)
mod = Model(myline, prefix='line_') + Model(mygauss, prefix='peak_')
pars = mod.make_params(line_a=5, line_b=1, peak_a=10, peak_b=10, peak_c=5)
pars.add('a', expr='line_a + peak_a')
result = mod.fit(y, pars, x=x)
self.assertTrue(result.params['peak_a'].value > 4)
self.assertTrue(result.params['peak_a'].value < 5)
self.assertTrue(result.params['peak_b'].value > 8)
self.assertTrue(result.params['peak_b'].value < 9)
self.assertTrue(result.params['peak_c'].value > 1.5)
self.assertTrue(result.params['peak_c'].value < 2.5)
self.assertTrue(result.params['line_a'].value > 5.5)
self.assertTrue(result.params['line_a'].value < 6.5)
self.assertTrue(result.params['line_b'].value > 0.25)
self.assertTrue(result.params['line_b'].value < 0.75)
self.assertTrue(result.params['a'].value > 10)
self.assertTrue(result.params['a'].value < 11)
def Rturn_Vmax(r_array, v_array, negative=False):
r_array, v_array = abs(r_array), abs(v_array)
r_array = np.append(r_array, 0.1)
v_array = np.append(v_array, 5)
v0 = np.nanmedian(v_array)
try:
#x0=[250,5,0,1]
#vmax ,r_turn,beta,gamma = optimization.curve_fit(vrot, r_array, v_array, p0=x0, bounds = ([0,0,0,0],[500,60,1,50]))[0]
mod = Model(vrot)
mod.set_param_hint('v_max', value=v0, vmin=0, vmax=360)
mod.set_param_hint('beta', value=0, vary=False, min=0, max=1.0)
mod.set_param_hint('R_turn', value=5, min=0, max=35)
mod.set_param_hint('gamma', value=1, min=-2, max=12)
pars = mod.make_params()
result = mod.fit(v_array, r_sky=r_array) #, fit_method = "Powell")
best = result.best_values
vmax, r_turn, gamma, beta = best["v_max"], best["R_turn"], best[
"gamma"], best["beta"]
except (RuntimeError, TypeError, ValueError):
vmax, r_turn, gamma, beta = 500, 0, 1, 1
return vmax, r_turn, beta, gamma
def phaser(x, y, fc, y0):
def phaseFit(x, Qt, fr):
return y0 - 180 * np.arctan(2 * Qt * (x - fr) / fr) / np.pi
gmodel = Model(phaseFit)
gmodel = gmodel + LinearModel()
# print(gmodel.param_names)
# print(gmodel.independent_vars)
df = 0.002
dy = 50
Qt = 30000
dQt = Qt
params = gmodel.make_params()
params.add('y0', value=y0, min=y0 - dy, max=y0 + dy)
params.add('Qt', value=Qt, min=Qt - dQt, max=Qt + dQt)
params.add('fr', value=fc, min=fc - df, max=fc + df)
params.add('intercept', value=1, vary=True)
params.add('slope', value=0, vary=True)
result = gmodel.fit(y, params, x=x)
return result
def get_fit_result(
data,
init_params,
model_function,
):
'''
find best fit parameters.
:param data: DataFrame
raw data. index values are sampling events.
:param init_params: dict
:param model_function
function to fit data with.
:return: result: ModelResult
'''
x = data.index.values
y = data.values
model = Model(model_function)
for param, init_value in init_params.items():
model.set_param_hint(param, value=init_value)
params = model.make_params()
result = model.fit(y, params, t=x)
return result
def _fit(self, reference_point, order):
"""
This is meant to be used privately, when the pprint_disp
is handled by another function. The `fit` method is for
public use.
"""
if self.is_coeff or self.is_dispersion_array:
warnings.warn("No need to fit another curve.")
return
else:
if self.GD_mode:
order -= 1
self.fitorder = order
_function = _fit_config[order]
x, y = np.copy(self.x), np.copy(self.y)
x -= reference_point
if _has_lmfit:
fitmodel = Model(_function)
pars = fitmodel.make_params(
**{f"b{i}": 1
for i in range(order + 1)})
result = fitmodel.fit(y, x=x, params=pars)
else:
popt, pcov = curve_fit(_function, x, y, maxfev=8000)
if _has_lmfit:
dispersion, dispersion_std = transform_lmfit_params_to_dispersion(
*_unpack_lmfit(result.params.items()),
drop_first=True,
dof=1)
fit_report = result.fit_report()
self.fitted_curve = result.best_fit
else:
dispersion, dispersion_std = transform_cf_params_to_dispersion(
popt, drop_first=True, dof=1)
fit_report = (
"To display detailed results you must have `lmfit` installed."
)
self.fitted_curve = _function(x, *popt)
if self.GD_mode:
_, idx = find_nearest(self.x, reference_point)
dispersion = np.insert(dispersion, 0, self.fitted_curve[idx])
dispersion_std = np.insert(dispersion_std, 0, 0)
# The below line must have 7 elements, so slice these redundant coeffs..
dispersion, dispersion_std = dispersion[:
-1], dispersion_std[:
-1]
self.coef_array = self.coef_temp(*dispersion)
self.coef_std_array = self.coef_std_temp(*dispersion_std)
return dispersion, dispersion_std, fit_report
def Fit_Modified_SEIR(CN, missing_days=0, RN=None, fit_method="least_squares", **R_0_kwargs):
if RN is not None:
y_data = train_data [(train_data ["State"] == CN)].Fatalities.values
else:
if len(train_data ["State"] == CN) > len(train_data ["State"] == "United States"):
y_data = train_data [(train_data ["State"] == CN)].Fatalities.values
else:
y_data = train_data [train_data ["State"] == CN].Fatalities.values
Max_d = len(train_data.groupby("Date").sum().index) + missing_days
y_data = np.concatenate((np.zeros(missing_days), y_data))
# State Population
N = "please import the state population here"
# Infectious period (please read the manuscript for more information)
D = 10
x_data = np.linspace(0, Max_d - 1, Max_d, dtype=int)
# Solver
def Modified_SEIR_deaths(x, N, D, CFR_O, CFR_S, R_0_delta, **R_0_kwargs):
t_, S_, E_, I_, R_, X, R_0_, N_, CFR_ = Modified_SEIR(N, D, Max_d, CFR_O, CFR_S, R_0=New_R_0, **R_0_kwargs)
return X[x]
mod = Model(Modified_SEIR_deaths)
# Initial values and bounds
mod.set_param_hint('N', value=N, vary=False)
mod.set_param_hint('D', value=D, vary=False)
mod.set_param_hint('CFR_O', value=0.01, min=0.0001, max=0.1)
mod.set_param_hint('CFR_S', value=0.1, min=0.0001, max=1.0)
mod.set_param_hint('R_0_start', value=2.5, min=1.0, max=5.0)
mod.set_param_hint('R_0_end', value=0.7, min=0.01, max=5.0)
mod.set_param_hint('x0', value=30.0, min=0.0, max=float(Max_d))
mod.set_param_hint('k', value=0.1, min=0.01, max=5.0)
'''
if R_0_kwargs:
for arg in R_0_kwargs:
mod.set_param_hint(arg, value=R_0_kwargs[arg])
'''
params = mod.make_params()
params.add('R_0_delta', value=1.0, min=0.0, expr="R_0_start - R_0_end")
result = mod.fit(y_data, params, method=fit_method, x=x_data)
CFR_O = result.params["CFR_O"].value
CFR_S = result.params["CFR_S"].value
R_0_result_params = {}
for val in R_0_kwargs:
R_0_result_params[val] = result.params[val].value
return result, CN, y_data, N, D, Max_d, CFR_O, CFR_S, R_0_result_params
def fit_data_bg(x, y, peak_pos, peak_type="LO", width=None, bg_ord=0):
"""
Builds a lmfit model of peaks in listed by index in `peak_pos`
Parameters
----------
peak_type : string (default='lorentizian')
Peaks can be of the following types:
- 'LO' : symmetric lorentzian
- 'GA' : symmetric gaussain
- 'VO' : symmetric pseudo voigt
max_width : int (default = total points/10)
max width (in data points) that peak fitted can be
bg_ord: int
order of the background polynomial
0: constant, 1: linear, ...
Returns
-------
out:
fitted model
"""
# need to define peak width finding
if width is None:
width = guess_peak_width(x, y)
# start with polynomial background
model = PolynomialModel(bg_ord, prefix="bg_")
pars = model.make_params()
if peak_type == "LO":
peak_function = lorentzian
elif peak_type == "GA":
peak_function = gaussian
elif peak_type == "VO":
peak_function = voigt
# add peak type for all peaks
for i, peak in enumerate(peak_pos):
temp_model = Model(peak_function, prefix="p%s_" % i)
pars.update(temp_model.make_params())
model += temp_model
# set initial background as flat line at zeros
for i in range(bg_ord + 1):
pars["bg_c%i" % i].set(0)
# give values for other peaks, keeping width and height positive
for i, peak in enumerate(peak_pos):
pars["p%s_x0" % i].set(x[peak])
pars["p%s_fwhm" % i].set(width, min=0)
pars["p%s_amp" % i].set(y[peak], min=0)
out = model.fit(y, pars, x=x)
return out
def fit_data_bg(x, y, peak_pos, peak_type='LO', width=None, bg_ord=0):
"""
Builds a lmfit model of peaks in listed by index in `peak_pos`
Parameters
----------
peak_type : string (default='lorentizian')
Peaks can be of the following types:
- 'LO' : symmetric lorentzian
- 'GA' : symmetric gaussain
- 'VO' : symmetric pseudo voigt
max_width : int (default = total points/10)
max width (in data points) that peak fitted can be
bg_ord: int
order of the background polynomial
0: constant, 1: linear, ...
Returns
-------
out:
fitted model
"""
# need to define peak width finding
if width is None:
width = guess_peak_width(x, y)
# start with polynomial background
model = PolynomialModel(bg_ord, prefix='bg_')
pars = model.make_params()
if peak_type == 'LO':
peak_function = lorentzian
elif peak_type == 'GA':
peak_function = gaussian
elif peak_type == 'VO':
peak_function = voigt
# add peak type for all peaks
for i, peak in enumerate(peak_pos):
temp_model = Model(peak_function, prefix='p%s_' % i)
pars.update(temp_model.make_params())
model += temp_model
# set initial background as flat line at zeros
for i in range(bg_ord + 1):
pars['bg_c%i' % i].set(0)
# give values for other peaks, keeping width and height positive
for i, peak in enumerate(peak_pos):
pars['p%s_x0' % i].set(x[peak])
pars['p%s_fwhm' % i].set(width, min=0)
pars['p%s_amp' % i].set(y[peak], min=0)
out = model.fit(y, pars, x=x)
return out
def fit_model_error(t, y, wt=1):
gmodel = Model(correlation)
gmodel.set_param_hint('g0', value=0.1)
gmodel.set_param_hint('tauD', value=1e-4, min=1e-6, max=100)
gmodel.set_param_hint('sp', value=0.01, min=0.001, max=0.1)
gmodel.set_param_hint('bl', value=1e-6)
pars = gmodel.make_params()
return gmodel.fit(y, pars, t=t, weights=wt)
def multi_disk_fit(arcmin_sma, intens, intens_err, bounds, psf):
h_mat_0 = numpy.ones(len(bounds - 1))
mod = Model(multi_disk_func)
pars = mod.make_params(I0 = 1.0, h_mat = h_mat_0, bounds = bounds, PSF = PSF)
pars['bounds'].vary = False
pars['PSF'].vary = False
results = mod.fit(intens, params = pars, x = arcmin_sma, weights = 1.0/intens_err)
pdb.set_trace()
def lmfit(mjd,flux,fluxerr):
t0_guess = mjd[np.argmax(flux)]
tau_fall_guess = 40.
tau_rise_guess = -5.
A = 150.
B = 20.
# nflux = np.zeros(2+len(np.array(flux)))
# nfluxerr = np.ones(2+len(np.array(flux)))/10.
# nmjd = np.zeros(2+len(np.array(flux)))
#
# nflux[1:-1] = flux
# nfluxerr[1:-1] = fluxerr
# nmjd[1:-1] = mjd
# nmjd[1] = mjd[0]-100.
# nmjd[-1] = mjd[-1]+150
#
# flux = nflux
# fluxerr = nfluxerr
# mjd = nmjd
bmod = Model(bazinfunc)
bmod.set_param_hint('t0', value=t0_guess, min=t0_guess-20, max=t0_guess+20)
bmod.set_param_hint('tau_fall', value=tau_fall_guess)
bmod.set_param_hint('tau_rise', value=tau_rise_guess)
bmod.set_param_hint('A',value=A)
bmod.set_param_hint('B',value=B)
pars = bmod.make_params()
#print(bmod.param_names)
#print(bmod.independent_vars)
# print(np.array(flux))
# print(np.array(1./np.array(fluxerr)))
# print(np.array(mjd))
result = bmod.fit(np.array(flux),method='leastsq',weights=1./np.array(fluxerr), t=np.array(mjd))
#print(result.fit_report())
# plt.clf()
# plt.errorbar(np.array(mjd), np.array(flux), yerr=fluxerr,fmt='o')
# plt.plot(np.array(mjd), result.init_fit, 'k--')
# plt.plot(np.array(mjd), result.best_fit, 'r-')
# #plt.xlim(mjd[1],mjd[-2])
# plt.savefig('bazinfit.png')
chisq = result.redchi
ps = result.best_values
popt = [ps['t0'],ps['tau_fall'],ps['tau_rise'],ps['A'],ps['B']]
#print('popt',popt)
#sys.exit()
# if chisq < 2.:
# input('good chisq!')
# popt, pcov, infodict, errmsg, ier = curve_fit(bazinfunc, mjd, flux,
# sigma=fluxerr, p0=p0, maxfev=2000000, full_output=True)
#
# chisq = (infodict['fvec'] ** 2).sum() / (len(infodict['fvec']) - len(popt))
return chisq,popt
def fit_D_phi_powerlaw(phi_, D):
"""fit stuff"""
Dmod = Model(Dhop_powerlaw)
params = Dmod.make_params()
params['p'].set(0.3)
result = Dmod.fit(D, params, phi=phi_)
print result.fit_report(min_correl=0.5)
p = result.params['p'].value
return p
def fit_routine_first_order(freq, spec):
mymodel = Model(first_order)
params = mymodel.make_params(a=-2, m=-1.2e-2)
result = mymodel.fit(spec, params, x=freq)
chi2 = result.chisqr
red_chi2 = result.redchi
a = result.best_values['a']
m = result.best_values['m']
return a, m, chi2, red_chi2
def plotfile():
#------------------------------------------------------------------------------------------------------------------
# This function plots magnetization and spin current data
#------------------------------------------------------------------------------------------------------------------
#------------------------------------------------------------------------------------------------------------------
# parameters
#------------------------------------------------------------------------------------------------------------------
timestep = 100000 # number of steps
#------------------------------------------------------------------------------------------------------------------
# reading the input files of the simulation: Spin_STM-File, NN-table, DMI-vector
#------------------------------------------------------------------------------------------------------------------
job = "mag.dat"
infile = open(job, "r")
#------------------------------------------------------------------------------------------------------------------------------
# defining output arrays
#--------------------------------------------------------------------------------------------------------------------------
magx_array = []
magy_array = []
magz_array = []
time_array = []
#--------------------------------------------------------------------------------------------------------------------------------
# reading and extracting the input file
#-----------------------------------------------------------------------------------------------------------------------------------
for index, line in enumerate(infile):
current_line = line.split()
time_array.append(int(current_line[0]))
magx_array.append(float(current_line[1]))
magy_array.append(float(current_line[2]))
magz_array.append(float(current_line[3]))
#--------------------------------------------------------------------------------------------------------------------------------
# fit of the data
#-----------------------------------------------------------------------------------------------------------------------------------
def mag(x, a):
return a + 0 * x
gmodel = Model(mag)
result = gmodel.fit(magx_array, x=time_array, a=0.5)
params = gmodel.make_params()
print(result.fit_report())
#---------------------------------------------------------------------------------------------------------------------------
#creating the plots
#--------------------------------------------------------------------------------------------------------------------------
pp = PdfPages('mag_0.5.pdf')
plt.plot(time_array, magx_array, label='m_x')
plt.plot(time_array, result.best_fit, label='Fit')
plt.xlabel('time')
plt.ylabel('magnetization comp.')
plt.savefig(pp, format='pdf')
pp.close()
plt.legend()
plt.show()
def fit_model(t, y, jj, zjj, meanz, stdd):
gmodel = Model(gaus1)
gmodel.set_param_hint('a', value=zjj, min=0.8*zjj, max=1.2*zjj)
gmodel.set_param_hint('b', value=jj, min=jj-2, max=jj+2)
gmodel.set_param_hint('w', value=1.2, min=0.1, max=20)
gmodel.set_param_hint('y0', value=meanz, min=meanz -
stdd/2, max=meanz + stdd/2)
pars = gmodel.make_params()
return gmodel.fit(y, pars, t=t)
def fit_D_phi_powerlaw(phi_, D):
"""fit stuff"""
Dmod = Model(Dhop_powerlaw)
params = Dmod.make_params()
params['p'].set(0.3)
result = Dmod.fit(D, params, phi=phi_)
print result.fit_report(min_correl=0.5)
p = result.params['p'].value
return p
def fit_gaussian_peak(w,
f,
amp_hint=-0.5,
cen_hint=None,
wid_hint=0.01,
shift_hint=0.8,
minmax='min'):
"""Fit a single Gaussian to a spectrum line.
Gaussian G(x)=shift+amp*e^(-(x-cen)^2/(2*wid^2))
Uses lmfit package.
Parameters
----------
w, f : 1d arrays
Spectrum range where the minimum is located.
amp_hint : float
Amplitude value to be used as 1st guess when performing the fit.
cen_hint : float
Wavelength of the minimum location, to be used as 1st guess when fitting. If None, the mean value of `w` is used.
wid_hint : float
shift_hint : float
minmax = str
Specifies if the peak to be fitted is a minimum or a maximum, to know if the gaussian amplitude parameter `amp` must be negative or positive, respectively. Default: 'min'.
Returns
-------
lmfit results object
"""
def gaussian(x, amp=1, cen=0, wid=1, shift=0):
return shift + amp * np.exp(-(x - cen)**2 / (2 * wid**2))
# Fit model and parameters
mod = Model(gaussian)
# Amplitude `amp`
if minmax == 'min': mod.set_param_hint('amp', value=amp_hint, max=0.)
elif minmax == 'max': mod.set_param_hint('amp', value=amp_hint, min=0.)
# Center `cen`
if cen_hint is None: cen_hint = np.mean(w)
mod.set_param_hint('cen', value=cen_hint)
# Width `wid`
mod.set_param_hint('wid', value=wid_hint, min=0.)
# Shift in the y-axis `shift`
mod.set_param_hint('shift', value=shift_hint)
# mod.set_param_hint('fwhm', expr='2.35482004503*wid')
# mod.set_param_hint('height', expr='shift+amp')
gfitparams = mod.make_params()
# Fit
lmfitresult = Model(gaussian).fit(f, x=w, params=gfitparams)
return lmfitresult
def test_extra_param_issues_warning(self):
# The function accepts extra params, Model will warn but not raise.
def flexible_func(x, amplitude, center, sigma, **kwargs):
return gaussian(x, amplitude, center, sigma)
flexible_model = Model(flexible_func)
pars = flexible_model.make_params(**self.guess())
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
flexible_model.fit(self.data, pars, x=self.x, extra=5)
self.assertTrue(len(w) == 1)
self.assertTrue(issubclass(w[-1].category, UserWarning))
def fit_D_phi_alt(phi_, D, c1, c2, c1o, c2o):
"""fit stuff"""
Dmod = Model(Dhopalt)
params = Dmod.make_params()
params['c1'].set(c1, vary=False)
params['c2'].set(c2, vary=False)
params['c1o'].set(c1o, vary=False)
params['c2o'].set(c2o, vary=False)
params['c3'].set(0.25)
result = Dmod.fit(D, params, phi=phi_)
print result.fit_report(min_correl=0.5)
c3 = result.params['c3'].value
return c3
def fit_D_phi(phi_, D, c1, c2):
"""fit stuff"""
Dmod = Model(Dhop)
params = Dmod.make_params()
params['c1'].set(c1, vary=False)
params['c2'].set(c2, vary=False)
params['c3'].set(1, vary=False)
params['beta'].set(0.70, min=0)
result = Dmod.fit(D, params, phi=phi_)
print result.fit_report(min_correl=0.5)
beta = result.params['beta'].value
c3 = result.params['c3'].value
return c3, beta
def fit_Dinf_model(Input, diffusion, startindex, endindex):
time_ = diffusion[startindex:endindex,0]
D = diffusion[startindex:endindex,1]
Dmod = Model(Dinf_model)
params = Dmod.make_params()
params['var1'].set(0.1)
params['Dinf'].set(0.0001)#, min = 0, max=0.1)
result = Dmod.fit(D, params, time=time_)
print result.fit_report(min_correl=0.5)
var1 = result.params['var1'].value
Dinf = result.params['Dinf'].value
Dinfstderr = result.params['Dinf'].stderr
return var1, Dinf, Dinfstderr
def tau_fitter(data,nbins, verbose=True):
profile_peak = np.max(data)
binpeak = np.argmax(data)
modelname = GxETrain
model = Model(modelname)
model.set_param_hint('nbins', value=nbins, vary=False)
model.set_param_hint('sigma', value=15, vary=True, min =0, max = nbins)
model.set_param_hint('mu', value=binpeak, vary=True, min=0, max = nbins)
model.set_param_hint('A',value=profile_peak, vary=True, min=0)
model.set_param_hint('tau',value=200, vary=True, min=0)
model.set_param_hint('dc',value = 0, vary = True)
pars = model.make_params()
xax=np.linspace(1,nbins,nbins)
#"""Fit data"""
result = model.fit(data,pars,x=xax)
if verbose == True:
print(result.fit_report(show_correl = True))
else:
print "To see fit report, use verbose=True"
noiselessmodel = result.best_fit
besttau = result.best_values['tau']
taustd = result.params['tau'].stderr ##estimated 1 sigma error
if taustd == None:
taustd = 0
bestsig = result.best_values['sigma']
bestmu = result.best_values['mu']
bestA = result.best_values['A']
bestdc = result.best_values['dc']
bestsig_std = result.params['sigma'].stderr
bestmu_std = result.params['mu'].stderr
bestA_std = result.params['A'].stderr
bestdc_std = result.params['dc'].stderr
bestparams = np.array([bestsig,bestmu,bestA,bestdc])
bestparams_std = np.array([bestsig_std,bestmu_std,bestA_std,bestdc_std])
"""correlations with sigma"""
corsig = result.params['sigma'].correl
#corA = result.params['A'].correl
#corlist = [corsig,corA]
rchi = result.redchi
#return best values and std errors on the other parameters as well
return result, noiselessmodel, besttau, taustd, bestparams, bestparams_std, rchi, corsig
def fit_data(x, y, peak_pos, peak_type='LO', width=None):
"""
Builds a lmfit model of peaks in listed by index in `peak_pos` with lineshape
given by `peak_type`.
Parameters
----------
x : array
y : array
peak_pos : array of peak postion indices
peak_type : string
Peaks can be of the following types:
- 'LO' : symmetric lorentzian (default)
- 'GA' : symmetric gaussain
- 'VO' : symmetric pseudo voigt
width : float
amp : float
Returns
-------
out : Fitted lmfit model
"""
# get appropriate line shape function
if peak_type == 'LO':
peak_function = lorentzian
elif peak_type == 'GA':
peak_function = gaussian
elif peak_type == 'VO':
peak_function = voigt
# build model
model = Model(peak_function, prefix='p0_')
for i, p in enumerate(peak_pos[1:]):
model += Model(peak_function, prefix='p%s_' % str(i+1))
pars = model.make_params()
# initialize params
for i, p in enumerate(peak_pos):
pars['p%s_x0' % i].set(x[p])
pars['p%s_fwhm' % i].set(width, min=0)
pars['p%s_amp' % i].set(y[p], min=0)
out = model.fit(y, pars, x=x)
return out
def tau_1D_fitter(data,nbins):
profile_peak = np.max(data)
binpeak = np.argmax(data)
modelname = GxETrain1D
model = Model(modelname)
model.set_param_hint('nbins', value=nbins, vary=False)
model.set_param_hint('sigma', value=15, vary=True, min =0, max = nbins)
model.set_param_hint('mu', value=binpeak, vary=True, min=0, max = nbins)
model.set_param_hint('A',value=profile_peak, vary=True,min=0)
model.set_param_hint('tau1',value=200, vary=True, min=0)
# model.set_param_hint('tau1',value=166.792877, vary=False)
model.set_param_hint('dc',value = 0, vary = True)
pars = model.make_params()
result = model.fit(data,pars,x=np.linspace(1,nbins,nbins))
# print(result.fit_report(show_correl = False))
noiselessmodel = result.best_fit
besttau = result.best_values['tau1']
taustd = result.params['tau1'].stderr ##estimated 1 sigma error
if taustd == None:
taustd = 0
bestsig = result.best_values['sigma']
bestmu = result.best_values['mu']
bestA = result.best_values['A']
bestdc = result.best_values['dc']
bestsig_std = result.params['sigma'].stderr
bestmu_std = result.params['mu'].stderr
bestA_std = result.params['A'].stderr
bestdc_std = result.params['dc'].stderr
bestparams = np.array([bestsig,bestmu,bestA,bestdc])
bestparams_std = np.array([bestsig_std,bestmu_std,bestA_std,bestdc_std])
"""correlations with sigma"""
corsig = result.params['sigma'].correl
#corA = result.params['A'].correl
#corlist = [corsig,corA]
rchi = result.redchi
return result, noiselessmodel, besttau, taustd, bestparams, bestparams_std, rchi, corsig
def GaussManual(signal, guess):
"""
Fits high contrast data very well
"""
amp, centre, stdev, offset = guess
data = np.array([range(len(signal)), signal]).T
X = data[:,0]
Y = data[:,1]
gauss_mod = Model(gaussian)
pars = gauss_mod.make_params(center=centre, sigma=stdev, amplitude=amp, offset=offset)
pars['center'].vary = False
pars['sigma'].min = stdev
pars['sigma'].max = stdev + 5.
mod = gauss_mod
result = mod.fit(Y, pars, x=X)
fwhm = result.best_values['sigma'] * 2.3548
return X, result.best_fit, result.best_values['sigma'] * 4
def fitPeak(im,
x0,
y0,
subSize=10,
init_params={'amp': 10,
'x0': 10,
'y0': 10,
'sigma_x': 1.0,
'sigma_y': 1.0}):
subImage = im[y0 - subSize:y0 + subSize, x0 - subSize:x0 + subSize]
peakModel = Model(gaussian2d, independent_vars=['x', 'y'])
x, y = np.meshgrid(range(2 * subSize), range(2 * subSize))
p = peakModel.make_params(amp=init_params['amp'],
x0=init_params['x0'],
y0=init_params['y0'],
sigma_x=init_params['sigma_x'],
sigma_y=init_params['sigma_y'])
result = peakModel.fit(subImage,
x=x,
y=y,
params=p, method='powell')
return (result.values['x0'] + x0 - subSize,
result.values['y0'] + y0 - subSize)
def GaussStepConst(signal, guess):
"""
Fits high contrast data very well
"""
if guess == False:
return [0, 0, 0]
else:
amp, centre, stdev, offset = guess
data = np.array([range(len(signal)), signal]).T
X = data[:,0]
Y = data[:,1]
# gauss_mod = Model(gaussian)
gauss_mod = Model(gaussian)
const_mod = ConstantModel()
step_mod = StepModel(prefix='step')
gauss_mod.set_param_hint('width', value = stdev / 2., min=stdev / 3., max=stdev)
gauss_mod.set_param_hint('fwhm', expr='2.3548*width')
pars = gauss_mod.make_params(height=amp, center=centre, width=stdev / 2., offset=offset)
pars += step_mod.guess(Y, x=X, center=centre)
pars += const_mod.guess(Y, x=X)
pars['width'].vary = False
mod = const_mod + gauss_mod + step_mod
result = mod.fit(Y, pars, x=X)
# write error report
#print result.fit_report()
fwhm = result.best_values['width'] * 2.3548
return X, result.best_fit, result.redchi, fwhm
def tau_fitter(data,nbins):
profile_peak = np.max(data)
binpeak = np.argmax(data)
modelname = GxETrain
model = Model(modelname)
model.set_param_hint('nbins', value=nbins, vary=False)
model.set_param_hint('sigma', value=15, vary=True, min =0, max = nbins)
model.set_param_hint('mu', value=binpeak, vary=True, min=0, max = nbins)
model.set_param_hint('A',value=profile_peak, vary=True)
model.set_param_hint('tau',value=200, vary=True, min=0)
model.set_param_hint('dc',value = 0, vary = True)
pars = model.make_params()
#"""Fit data"""
result = model.fit(data,pars,x=np.linspace(1,nbins,nbins))
# print(result.fit_report(show_correl = False))
noiselessmodel = result.best_fit
besttau = result.best_values['tau']
taustd = result.params['tau'].stderr ##estimated 1 sigma error
return noiselessmodel, besttau, taustd
def main(spec, output, plot):
"""
"""
dD = 3 # 3 km/s Doppler FWHM for the lines
data = np.loadtxt(spec)
x = data[:,0]
y = data[:,1]
w = data[:,2]
# Catch NaNs and invalid values:
mask_x = np.ma.masked_equal(x, -9999).mask
mask_y = np.isnan(y)
mask = np.array(reduce(np.logical_or, [mask_x, mask_y]))
mx = x[~mask]
my = y[~mask]
mw = w[~mask]
# Create the model and set the parameters
mod1 = Model(Voigt, prefix='V1_')
pars = mod1.make_params()
mod2 = Model(Voigt, prefix='V2_')
pars += mod2.make_params()
mod = mod1 + mod2
# Edit the model parameter starting values, conditions, etc...
# Background parameters
pars['V1_a'].set(value=0, expr='', vary=False)
pars['V1_b'].set(value=0, expr='', vary=False)
pars['V2_a'].set(value=0, expr='', vary=False)
pars['V2_b'].set(value=0, expr='', vary=False)
# Line center
pars['V1_nu_0'].set(value=-47., vary=True, min=-50, max=-44)
pars['V2_nu_0'].set(value=-38., vary=True, min=-40, max=-36)
# Line area
pars['V1_A'].set(value=-1e-2, max=-1e-8)
pars['V2_A'].set(value=-1e-2, max=-1e-8)
# Line width
pars['V1_alphaD'].set(value=dD, vary=False)
pars['V2_alphaD'].set(value=dD, vary=False)
pars['V1_alphaL'].set(value=1, vary=True, min=0)
pars['V2_alphaL'].set(value=1, vary=True, min=0)
# Fit the model using a weight
#print len(my), len(mx)
modx = np.array([mx, mx, mx])
try:
fit = mod.fit(my, pars, nu=mx, weights=mw)
fit1 = Voigt(mx, fit.params['V1_alphaD'].value, fit.params['V1_alphaL'].value,
fit.params['V1_nu_0'].value, fit.params['V1_A'].value,
fit.params['V1_a'].value, 0)
fit2 = Voigt(mx, fit.params['V2_alphaD'].value, fit.params['V2_alphaL'].value,
fit.params['V2_nu_0'].value, fit.params['V2_A'].value, 0, 0)
fit3 = fit.best_fit
mody = np.array([fit1, fit2, fit3])
bfit = fit.best_fit
except TypeError:
bfit = np.zeros(mx.shape)
mody = np.zeros(modx.shape)
#fit1 = Voigt(mx, fit.params['V1_alphaD'].value, fit.params['V1_alphaL'].value,
#fit.params['V1_nu_0'].value, fit.params['V1_A'].value, fit.params['V1_a'].value, 0)
#fit2 = Voigt(mx, fit.params['V2_alphaD'].value, fit.params['V2_alphaL'].value,
#fit.params['V2_nu_0'].value, fit.params['V2_A'].value, 0, 0)
#fit3 = fit.best_fit
#mody = np.array([fit1, fit2, fit3])
#modx = np.array([mx, mx, mx])
if len(mx) == 0:
mx = np.zeros(10)
my = np.zeros(10)
bfit = np.zeros(10)
modx = np.array([mx, mx, mx])
mody = np.zeros(modx.shape)
crrls.plot_model(mx, my, modx, mody, plot)
np.savetxt(output, np.c_[mx, bfit])
def main(spec, output, plot):
"""
"""
dD = 3 # 3 km/s Doppler FWHM for the lines
data = np.loadtxt(spec)
x = data[:,0]
y = data[:,1]
w = data[:,2]
# Catch NaNs and invalid values:
mask_x = np.ma.masked_equal(x, -9999).mask
mask_y = np.isnan(y)
mask = np.array(reduce(np.logical_or, [mask_x, mask_y]))
mx = x[~mask]
my = y[~mask]
mw = w[~mask]
# Create the model and set the parameters
mod1 = Model(Voigt, prefix='V1_')
pars = mod1.make_params()
#mod2 = Model(Voigt, prefix='V2_')
#pars += mod2.make_params()
mod = mod1 #+ mod2
# Edit the model parameter starting values, conditions, etc...
# Background parameters
pars['V1_a'].set(value=0, expr='', vary=False)
pars['V1_b'].set(value=0, expr='', vary=False)
#pars['V2_a'].set(value=0, expr='', vary=False)
#pars['V2_b'].set(value=0, expr='', vary=False)
# Line center
pars['V1_nu_0'].set(value=-47., vary=True, min=-50, max=-45)
#pars['V2_nu_0'].set(value=-37.6, expr='V1_nu_0+9.4', vary=False)
# Line area
pars['V1_A'].set(value=-1e-2, max=-1e-8)
#pars['V2_A'].set(value=-1e-2, max=-1e-8)
# Line width
pars['V1_alphaD'].set(value=dD, vary=True, min=0.)
#pars['V2_alphaD'].set(value=dD, vary=True, min=0.)
pars['V1_alphaL'].set(value=1, vary=True, min=0, max=250.)
#pars['V2_alphaL'].set(value=1, vary=True, min=0, max=250.)
# Fit the model using a weight
fit = mod.fit(my, pars, nu=mx, weights=mw)
fit1 = Voigt(mx, fit.params['V1_alphaD'].value, fit.params['V1_alphaL'].value,
fit.params['V1_nu_0'].value, fit.params['V1_A'].value, fit.params['V1_a'].value, 0)
#fit2 = Voigt(mx, fit.params['V2_alphaD'].value, fit.params['V2_alphaL'].value,
#fit.params['V2_nu_0'].value, fit.params['V2_A'].value, 0, 0)
fit3 = fit.best_fit
#mody = np.array([fit1, fit2, fit3])
mody = np.array([fit1, fit3])
#modx = np.array([mx, mx, mx])
modx = np.array([mx, mx])
# Disable for now, and check this: http://stackoverflow.com/questions/4931376/generating-matplotlib-graphs-without-a-running-x-server
# fir a possible fix.
crrls.plot_model(mx, my, modx, mody, plot)
np.savetxt(output, np.c_[mx, fit.best_fit])
# k1 = 1.501169e-01
# 待求参数
# k2 = 1.209591e-01
# 待求参数
# k3 = 9.115386e-01
# 待求参数
# k4 = -7.802862e-01
# 待求参数
# k5 = 1.938117e+00
# 待求参数
# k6 = 9.155105e-02
if __name__ == '__main__':
x = np.linspace(1, 200, 200)
# y = 10*cos(x) + sin(x)+exp(-2)*sin(x)
y = - 1/2*sin(x+2)+1
mod = Model(my_sin) + Model(my_damping)
pars = mod.make_params(w1=6.3367e-09, k=-6.8788e+05, w2=-0.00114982, a=0.09950371, b=1.00498756, c=2,
m=0, n=10)
pars['a'].set(min=0.01, max=0.9999)
result = mod.fit(y, pars, x=x)
print(result.fit_report())
fig = plt.figure(figsize=(20, 10))
initial, = plt.plot(x, y, 'bo-')
# plt.plot(x, result.init_fit, 'k--')
best_fit, = plt.plot(x, result.best_fit, 'r*-')
plt.legend(handles=[initial, best_fit, ], labels=['initial', 'best_fit'], loc='best')
plt.show()
from lmfit import Model
data = loadtxt('model1d_gauss.dat')
x = data[:, 0]
y = data[:, 1] + 0.25*x - 1.0
def gaussian(x, amp, cen, wid):
"""1-d gaussian: gaussian(x, amp, cen, wid)"""
return (amp / (sqrt(2*pi) * wid)) * exp(-(x-cen)**2 / (2*wid**2))
def line(x, slope, intercept):
"""a line"""
return slope*x + intercept
mod = Model(gaussian) + Model(line)
pars = mod.make_params(amp=5, cen=5, wid=1, slope=0, intercept=1)
result = mod.fit(y, pars, x=x)
print(result.fit_report())
plt.plot(x, y, 'bo')
plt.plot(x, result.init_fit, 'k--')
plt.plot(x, result.best_fit, 'r-')
plt.show()
# <end examples/doc_model_two_components.py>
w50min = float((0.3/100)*P)
w50max = float((3.0/100)*P)
smin = w50min/(2*np.sqrt(2*np.log(2)))
smax = w50max/(2*np.sqrt(2*np.log(2)))
modelname = GxETrain
model = Model(modelname)
model.set_param_hint('sigma', value=s, vary=True, min=smin, max=smax)
model.set_param_hint('mu', value=m, vary=True)
model.set_param_hint('A',value=1.5, vary=True, min=0)
model.set_param_hint('tau',value=200, vary=True, min=0)
pars = model.make_params()
#print model.param_hints
#modelname2 = GxESingleFold
#model2 = Model(modelname2)
#
#model2.set_param_hint('sigma', value=s, vary=True, min=smin, max=smax)
#model2.set_param_hint('mu', value=m, vary=True)
#model2.set_param_hint('A',value=1.5, vary=True, min=0)
#model2.set_param_hint('tau',value=200, vary=True, min=0)
#pars2 = model2.make_params()
##print model2.param_hints
#
#modelname3 = GxFE
#model3 = Model(modelname3)
#
def fit_data(x, y, peak_pos, peak_type='LO', max_width=None, bg_ord=2):
""" Builds a lmfit model of peaks in listed by index in `peak_pos`
Uses some basic algorithms to determine initial parameters for
amplitude and fwhm (limit on fwhm to avoid fitting background as peaks)
Parameters
----------
peak_type : string (default='lorentizian')
Peaks can be of the following types:
- 'LO' : symmetric lorentzian
- 'GA' : symmetric gaussain
- 'VO' : symmetric pseudo voigt
max_width : int (default = total points/10)
max width (in data points) that peak fitted can be
bg_ord: int
order of the background polynomial
0: constant, 1: linear, ...
Returns
-------
pars : model parameters
model : model object
"""
# need to define peak width finding
pw = guess_peak_width(x, y)
peak_guess = x[peak_pos]
# start with polynomial background
model = PolynomialModel(bg_ord, prefix='bg_')
pars = model.make_params()
if peak_type == 'LO':
peak_function = lorentzian
elif peak_type == 'GA':
peak_function = gaussian
elif peak_type == 'VO':
peak_function = voigt
# add lorentizian peak for all peaks
for i, peak in enumerate(peak_guess):
temp_model = Model(peak_function, prefix='p%s_' % i)
pars.update(temp_model.make_params())
model += temp_model
# set inital background as flat line at zeros
for i in range(bg_ord + 1):
pars['bg_c%i' % i].set(0)
# give values for other peaks
for i, peak in enumerate(peak_pos):
# could set bounds #, min=x[peak]-5, max=x[peak]+5)
pars['p%s_x0' % i].set(x[peak])
pars['p%s_fwhm' % i].set(pw / 2, min=pw * 0.25, max=pw * 2)
# here as well #, min=0, max=2*max(y))
pars['p%s_amp' % i].set(y[peak])
out = model.fit(y, pars, x=x)
return out
def fitexps(self, x, y, amp=5):
dexpmodel = Model(doubleexp, independent_vars=['x'])
params = dexpmodel.make_params(amp=amp, C0=5, C1=1, tau0=5, tau1=0.5)
print ('Params: ', [p for p in params.values()])
self.fitresult = dexpmodel.fit(y, params, x=x)
for x in range(len(retractZ)):
if (retractZ[x] - x_shift) < 0:
originPt = x
break
# Fit WLC model to rupture
separation = (retractZ - (retractD - y_shift) - x_shift)
skipPLT5 = True
gmod = Model(WLCmodel)
gmod.set_param_hint('L_C', value = -60.0)
gmod.set_param_hint('L_P', value = -0.38, min=-0.42, max=-0.34)
gmod.set_param_hint('a', value = 0.0, min=-10.0, max=10.0)
gmod.set_param_hint('b', value = 0.0, min=-10.0, max=10.0)
params = gmod.make_params()
try:
result = gmod.fit(smooth25[originPt:ruptureI], x=separation[originPt:ruptureI]) # method='cobyla'
except Exception:
skipPLT5 = False
sys.exc_clear()
if skipPLT5:
x_off = result.params['a'].value
y_off = result.params['b'].value
WLC_P = result.params['L_P'].value
WLC_L0 = result.params['L_C'].value
else:
x_off = 0.0
y_off = 0.0
WLC_P = 0.0
WLC_L0 = 0.0
def build_model(self, peak_type='LO', max_width=None, bg_ord=2):
""" Builds a lmfit model of peaks in listed by index in `peak_pos`
Uses some basic algorithms to determine initial parameters for
amplitude and fwhm (limit on fwhm to avoid fitting background as peaks)
Parameters
----------
peak_type : string (default='lorentizian')
Peaks can be of the following types:
- 'LO' : symmetric lorentzian
- 'GA' : symmetric gaussain
max_width : int (default = total points/10)
max width (in data points) that peak fitted can be
bg_ord: int
order of the background polynomial
0: constant, 1: linear, ...
Returns
-------
pars : model parameters
model : model object
"""
x = self.x
y = self.y
pw = self.test_peak_width
peak_guess = self.x[self.peak_pos]
print("Building model ... ")
# start with polynomial background
# second order
model = PolynomialModel(bg_ord, prefix='bg_')
pars = model.make_params()
if peak_type == 'LO':
peak_function = lorentzian
self.afactor = pi
self.wfactor = 2.0
elif peak_type == 'GA':
peak_function = gaussian
self.afactor = sqrt(2 * pi)
self.wfactor = 2.354820
elif peak_type == 'VO':
peak_function = voigt
self.afactor = sqrt(2 * pi)
self.wfactor = 3.60131
# add lorentizian peak for all peaks
for i, peak in enumerate(peak_guess):
temp_model = Model(peak_function, prefix='p%s_' % i)
pars.update(temp_model.make_params())
model += temp_model
# set inital background as flat line at zeros
for i in range(bg_ord + 1):
pars['bg_c%i' % i].set(0)
# give values for other peaks
for i, peak in enumerate(self.peak_pos):
print('Peak %i: pos %s, height %s' % (i, x[peak], y[peak]))
# could set bounds #, min=x[peak]-5, max=x[peak]+5)
pars['p%s_center' % i].set(x[peak])
pars['p%s_sigma' % i].set(pw / 2, min=pw * 0.25, max=pw * 2)
# here as well #, min=0, max=2*max(y))
pars['p%s_amplitude' % i].set(self.amplitude(y[peak], (pw / 2)))
self.pars = pars
self.model = model
return self.pars, self.model
tau.append(data[:,1])
wei.append(data[:,2])
nnow = int(re.findall('\d+', stack)[0])
n.append(nnow)
dn = fc.set_dn(trans)
specie, trans, nn, freq = fc.make_line_list('CI', 1500, dn)
nii = crrls.best_match_indx2(n[i], nn)
f0.append(freq[nii])
tmin = min(tau[i])
weight = np.power(wei[i], 2)
v1 = Model(crrls.Voigt, prefix='v0_')
pars3 = v1.make_params()
mod3 = v1
pars3['v0_gamma'].set(value=0.1, vary=True, expr='', min=0.0)
pars3['v0_center'].set(value=-47., vary=True, max=-30, min=-49)
pars3['v0_amplitude'].set(value=-0.1, vary=True, max=-1e-8)
pars3['v0_sigma'].set(value=dD_fix0, vary=False)
fit3.append(mod3.fit(tau[i], pars3, x=vel[i], weights=weight))
# Plot things
res3.append(tau[i] - fit3[i].best_fit)
voigt0 = crrls.Voigt(vel[i],
fit3[i].params['v0_sigma'].value,
fit3[i].params['v0_gamma'].value,