def test_model_nan_policy(self):
x = np.linspace(0, 10, 201)
np.random.seed(0)
y = gaussian(x, 10.0, 6.15, 0.8)
y += gaussian(x, 8.0, 6.35, 1.1)
y += gaussian(x, 0.25, 6.00, 7.5)
y += np.random.normal(size=len(x), scale=0.5)
y[55] = y[91] = np.nan
mod = PseudoVoigtModel()
params = mod.make_params(amplitude=20, center=5.5,
sigma=1, fraction=0.25)
params['fraction'].vary = False
# with raise, should get a ValueError
result = lambda: mod.fit(y, params, x=x, nan_policy='raise')
self.assertRaises(ValueError, result)
# with propagate, should get no error, but bad results
result = mod.fit(y, params, x=x, nan_policy='propagate')
self.assertTrue(result.success)
self.assertTrue(np.isnan(result.chisqr))
self.assertTrue(np.isnan(result.aic))
self.assertFalse(result.errorbars)
self.assertTrue(result.params['amplitude'].stderr is None)
self.assertTrue(abs(result.params['amplitude'].value - 20.0) < 0.001)
# with omit, should get good results
result = mod.fit(y, params, x=x, nan_policy='omit')
self.assertTrue(result.success)
self.assertTrue(result.chisqr > 2.0)
self.assertTrue(result.aic < -100)
self.assertTrue(result.errorbars)
self.assertTrue(result.params['amplitude'].stderr > 0.1)
self.assertTrue(abs(result.params['amplitude'].value - 20.0) < 5.0)
self.assertTrue(abs(result.params['center'].value - 6.0) < 0.5)
def test_model_nan_policy(self):
x = np.linspace(0, 10, 201)
np.random.seed(0)
y = gaussian(x, 10.0, 6.15, 0.8)
y += gaussian(x, 8.0, 6.35, 1.1)
y += gaussian(x, 0.25, 6.00, 7.5)
y += np.random.normal(size=len(x), scale=0.5)
y[55] = y[91] = np.nan
mod = PseudoVoigtModel()
params = mod.make_params(amplitude=20, center=5.5,
sigma=1, fraction=0.25)
params['fraction'].vary = False
# with raise, should get a ValueError
result = lambda: mod.fit(y, params, x=x, nan_policy='raise')
self.assertRaises(ValueError, result)
# with propagate, should get no error, but bad results
result = mod.fit(y, params, x=x, nan_policy='propagate')
self.assertTrue(result.success)
self.assertTrue(np.isnan(result.chisqr))
self.assertTrue(np.isnan(result.aic))
self.assertFalse(result.errorbars)
self.assertTrue(result.params['amplitude'].stderr is None)
self.assertTrue(abs(result.params['amplitude'].value - 20.0) < 0.001)
# with omit, should get good results
result = mod.fit(y, params, x=x, nan_policy='omit')
self.assertTrue(result.success)
self.assertTrue(result.chisqr > 2.0)
self.assertTrue(result.aic < -100)
self.assertTrue(result.errorbars)
self.assertTrue(result.params['amplitude'].stderr > 0.1)
self.assertTrue(abs(result.params['amplitude'].value - 20.0) < 5.0)
self.assertTrue(abs(result.params['center'].value - 6.0) < 0.5)
def test_model_nan_policy(self):
"""Tests for nan_policy with NaN values in the input data."""
x = np.linspace(0, 10, 201)
np.random.seed(0)
y = gaussian(x, 10.0, 6.15, 0.8)
y += gaussian(x, 8.0, 6.35, 1.1)
y += gaussian(x, 0.25, 6.00, 7.5)
y += np.random.normal(size=len(x), scale=0.5)
# with NaN values in the input data
y[55] = y[91] = np.nan
mod = PseudoVoigtModel()
params = mod.make_params(amplitude=20,
center=5.5,
sigma=1,
fraction=0.25)
params['fraction'].vary = False
# with raise, should get a ValueError
result = lambda: mod.fit(y, params, x=x, nan_policy='raise')
msg = (
'NaN values detected in your input data or the output of your '
'objective/model function - fitting algorithms cannot handle this!'
)
self.assertRaisesRegex(ValueError, msg, result)
# with propagate, should get no error, but bad results
result = mod.fit(y, params, x=x, nan_policy='propagate')
self.assertTrue(result.success)
self.assertTrue(np.isnan(result.chisqr))
self.assertTrue(np.isnan(result.aic))
self.assertFalse(result.errorbars)
self.assertTrue(result.params['amplitude'].stderr is None)
self.assertTrue(abs(result.params['amplitude'].value - 20.0) < 0.001)
# with omit, should get good results
result = mod.fit(y, params, x=x, nan_policy='omit')
self.assertTrue(result.success)
self.assertTrue(result.chisqr > 2.0)
self.assertTrue(result.aic < -100)
self.assertTrue(result.errorbars)
self.assertTrue(result.params['amplitude'].stderr > 0.1)
self.assertTrue(abs(result.params['amplitude'].value - 20.0) < 5.0)
self.assertTrue(abs(result.params['center'].value - 6.0) < 0.5)
# with 'wrong_argument', should get a ValueError
err_msg = r"nan_policy must be 'propagate', 'omit', or 'raise'."
with pytest.raises(ValueError, match=err_msg):
mod.fit(y, params, x=x, nan_policy='wrong_argument')
def calc_center_pseudoVoigt(vx,vy):
mod = PseudoVoigtModel()
y = vy
pars = mod.guess(y, x=vx)
out = mod.fit(y, pars, x=vx)
center = out.best_values['center']
return center
def voigt(x, y):
# Voigt fit to a curve
x_shifted = x - x.min() # Shifting to 0
y_shifted = y - y.min() # Shifting to 0
mod = PseudoVoigtModel() # Setting model type
pars = mod.guess(y_shifted, x=x_shifted) # Estimating fit
out = mod.fit(y_shifted, pars, x=x_shifted) # Fitting fit
# print(out.fit_report(min_correl=0.25)) # Outputting best fit results
print("Voigt FWHM = ", out.params['fwhm'].value) # Outputting only FWHM
out.plot() # Plotting fit
def fit_one_Psudo_Voigt(x_lst,y_lst):
'''
Fits one Pseudo Voigt returns the
results object
'''
mod = PseudoVoigtModel(independent_vars=['x'],nan_policy='raise')
x_lst = np.asarray(x_lst)
y_lst = np.asarray(y_lst)
# Guess good values computer
mod.guess(y_lst,x = x_lst)
result = mod.fit(y_lst, x = x_lst)
return result
def center_psi(file_name):
#print(file_name)
psi, vx, vy = read_file(file_name)
vy = processing_of_data(psi,vx,vy)
legenda = file_name.split('/')[-1]
#plt.grid()
#plt.legend(loc=0)
#import pdb; pdb.set_trace()
plt.plot(vx,vy,label=legenda)
mod = PseudoVoigtModel()
y=vy
pars = mod.guess(y, x=vx)
out = mod.fit(y, pars, x=vx)
center =out.best_values['center']
print('center: {} <--> psi: {}'.format(center,psi))
return psi, center
def test_figure_title_using_title_keyword_argument(peakdata):
"""Test setting figure title using title keyword argument."""
x, y = peakdata
pvmodel = PseudoVoigtModel()
params = pvmodel.guess(y, x=x)
result = pvmodel.fit(y, params, x=x)
ax = result.plot_fit(title='test')
assert ax.axes.get_title() == 'test'
ax = result.plot_residuals(title='test')
assert ax.axes.get_title() == 'test'
fig, _ = result.plot(title='test')
assert fig.axes[0].get_title() == 'test'
assert fig.axes[1].get_title() == '' # no title for fit subplot
def test_figure_default_title(peakdata):
"""Test default figure title."""
x, y = peakdata
pvmodel = PseudoVoigtModel()
params = pvmodel.guess(y, x=x)
result = pvmodel.fit(y, params, x=x)
ax = result.plot_fit()
assert ax.axes.get_title() == 'Model(pvoigt)'
ax = result.plot_residuals()
assert ax.axes.get_title() == 'Model(pvoigt)'
fig, _ = result.plot()
assert fig.axes[0].get_title() == 'Model(pvoigt)' # default model.name
assert fig.axes[1].get_title() == '' # no title for fit subplot
def test_priority_setting_figure_title(peakdata):
"""Test for setting figure title: title keyword argument has priority."""
x, y = peakdata
pvmodel = PseudoVoigtModel()
params = pvmodel.guess(y, x=x)
result = pvmodel.fit(y, params, x=x)
ax = result.plot_fit(ax_kws={'title': 'ax_kws'}, title='test')
assert ax.axes.get_title() == 'test'
ax = result.plot_residuals(ax_kws={'title': 'ax_kws'}, title='test')
assert ax.axes.get_title() == 'test'
fig, _ = result.plot(ax_res_kws={'title': 'ax_res_kws'}, title='test')
assert fig.axes[0].get_title() == 'test'
assert fig.axes[1].get_title() == ''
fig, _ = result.plot(ax_fit_kws={'title': 'ax_fit_kws'}, title='test')
assert fig.axes[0].get_title() == 'test'
assert fig.axes[1].get_title() == ''
def test_figure_title_using_title_to_ax_kws(peakdata):
"""Test setting figure title by supplying ax_{fit,res}_kws."""
x, y = peakdata
pvmodel = PseudoVoigtModel()
params = pvmodel.guess(y, x=x)
result = pvmodel.fit(y, params, x=x)
ax = result.plot_fit(ax_kws={'title': 'ax_kws'})
assert ax.axes.get_title() == 'ax_kws'
ax = result.plot_residuals(ax_kws={'title': 'ax_kws'})
assert ax.axes.get_title() == 'ax_kws'
fig, _ = result.plot(ax_res_kws={'title': 'ax_res_kws'})
assert fig.axes[0].get_title() == 'ax_res_kws'
assert fig.axes[1].get_title() == ''
fig, _ = result.plot(ax_fit_kws={'title': 'ax_fit_kws'})
assert fig.axes[0].get_title() == 'Model(pvoigt)' # default model.name
assert fig.axes[1].get_title() == '' # no title for fit subplot
def fit_voigt(xp: XPS_experiment,
region: str,
prefix: str = 'v_',
pars: list = None,
bounds: list = None,
ax=None,
flag_plot: bool = True):
"""General method for fitting voigt model
Input
----------
xp : class XPS_experiment
XPS data
region : str
core level name
pars, bounds : list
initial guess of the fit parameters and bounds. If unspecified, guessed automatically
Returns
-----------
fitv : lmfit.model
fit result to Voigt model
"""
from lmfit.models import PseudoVoigtModel, GaussianModel
x = xp.dfx[region].dropna().energy
y = xp.dfx[region].dropna().counts
mod = PseudoVoigtModel(prefix=prefix)
if pars == None:
pars = mod.guess(y, x=x)
pars[prefix + 'sigma'].set(value=1) # Usually guessed wrong anyway
pars[prefix + 'fraction'].set(value=0.2, min=0.15, max=0.20)
fitv = mod.fit(y, pars, x=x)
xp.fit.update({region: fitv})
if flag_plot:
hatchplot_fit(xp, region, fitv, ax=ax, plot_comps=True)
return fitv
def fittingPseudoVoigt(x, y): #fits a pseudovoigt curve
mod = PseudoVoigtModel()
pars = mod.guess(y, x=x)
out = mod.fit(y, pars, x=x)
print(out.fit_report(min_correl=0.25))
return out.best_fit
# get point-spread function data
psf = pu.load_muv_point_spread_function()
# set model x and y variables
detector_pixels = np.arange(len(psf))
detector_pixel_edges = np.linspace(0, len(psf) - 1, len(psf) + 1)
# initialize model
model = PseudoVoigtModel()
# use model's built-in initial parameters guessing option
initial_parameters = model.guess(psf, x=detector_pixels)
# fit the model to the point-spread function data
result = model.fit(psf, initial_parameters, x=detector_pixels)
params = result.params
parnames = sorted(params)
# make a figure and axes
fig, axes = plt.subplots(2,
1,
figsize=(5, 4),
sharex=True,
gridspec_kw={'height_ratios': [4, 1]},
constrained_layout=True)
# plot the IUVS data
axes[0].step(detector_pixel_edges,
np.concatenate((psf, [psf[-1]])),
where='post',
def fit_double_voigt(xp: XPS_experiment,
region: str,
pars: list = None,
bounds: list = None,
sepPt: float = None,
frac: float = None,
lb: str = None,
ax=None,
flag_plot: bool = True,
plot_comps: bool = False,
DEBUG: bool = False):
"""Fitting double voigt model
Input
----------
xp : class XPS_experiment
XPS data
region : str
core level name
pars, bounds : list
initial guess of the fit parameters and bounds. If unspecified, guessed automatically
sepPt : float
separation point in energy between the two peaks. If unspecified guessed automatically
flag_plot, DEBUG : bool
flags to plot intermediate and final fit results
Returns
-----------
fitv : lmfit.model
fit result to Voigt model
"""
from lmfit.models import PseudoVoigtModel
x = xp.dfx[region].dropna().energy
y = xp.dfx[region].dropna().counts
if sepPt == None: sepPt = find_separation_point(x, y)
x1 = x[x < sepPt].values
x2 = x[x > sepPt].values
y1 = y[x < sepPt].values
y2 = y[x > sepPt].values
mod1 = PseudoVoigtModel(prefix='v1_')
mod2 = PseudoVoigtModel(prefix='v2_')
if pars == None:
pars1 = mod1.guess(y1, x=x1)
pars1['v1_sigma'].set(value=1) # Usually guessed wrong anyway
pars2 = mod2.guess(y2, x=x2)
pars2['v2_sigma'].set(value=1) # Usually guessed wrong anyway
if frac != None:
pars1['v1_fraction'].set(value=frac, vary=False)
pars2['v2_fraction'].set(value=frac, vary=False)
mod = mod1 + mod2
pars = mod.make_params()
pars.update(pars1)
pars.update(pars2)
if DEBUG: # Fit & plot individual components separately
fit1 = mod1.fit(y1, x=x1, params=pars1)
fit2 = mod2.fit(y2, x=x2, params=pars2)
plot_fit_result(xp, region, fit1)
plot_fit_result(xp, region, fit2)
fitv = mod.fit(y, pars, x=x)
xp.fit.update({region: fitv})
if flag_plot:
hatchplot_fit(xp, region, fitv, ax=ax, plot_comps=True)
return fitv