def FWHM(counts, lower_bound, upper_bound):
X = range(lower_bound, upper_bound)
Y = counts[lower_bound:upper_bound]
# Fit a guassian
mean = sum(X * Y) / sum(Y)
sigma = np.sqrt(sum(Y * (X - mean)**2) / sum(Y))
# pi = [max(Y),mean,sigma]
# popt, pcov = curve_fit(gauss, X, Y, p0=pi)
# print(popt)
# fit_a, fit_mu, fit_stdev = popt
# fit guassian using other method
model = GaussianModel(prefix='peak_') + ConstantModel()
# make a model that is a Gaussian + a constant:
model = GaussianModel(prefix='peak_') + ConstantModel()
# make parameters with starting values:
params = model.make_params(c=1.0,
peak_center=mean,
peak_sigma=sigma,
peak_amplitude=max(Y))
# run fit
result = model.fit(Y, params, x=X)
print('fwhm: ', result.params['peak_fwhm'].value, 'centroid: ',
result.params['peak_center'].value)
# find FWHM
# fwhm = 2*np.sqrt(2*np.log(2))*np.abs(fit_stdev)
# cent = fit_mu
return result.params['peak_fwhm'].value, result.params['peak_center'].value
def fitNpeaks(f,
y,
npeaks=5,
thres=0.02,
min_dist=5,
width=300,
plot_prefix=None,
model=SkewedGaussianModel,
offset=True):
# Guess initial peak centres using peakutils
indexes = peakutils.indexes(y, thres=thres, min_dist=min_dist)
peaksfound = len(indexes)
assert peaksfound >= npeaks, "Looking for %s or more peaks only found %s of them!" % (
npeaks, peaksfound)
peak_f = peakutils.interpolate(f, y, ind=indexes)
# Oder peaks by decreaing height and keep only the first npeaks
peak_heights = indexes
peak_order = peak_heights.argsort()[::-1]
peak_heights = peak_heights[peak_order[:npeaks]]
peak_f = peak_f[peak_order[:npeaks]]
amplitude_scale = 1.0
peak_amplitudes = peak_heights * amplitude_scale # This is lmfit's annoying definition of a Gaussian `amplitude'
print('Initial peaks guessed at ', peak_f)
# Make multipeak model
peaks = []
for i in range(npeaks):
prefix = 'g{:d}_'.format(i + 1)
peaks.append(model(prefix=prefix))
if i == 0:
pars = peaks[i].make_params(x=f)
else:
pars.update(peaks[i].make_params())
if model == SkewedGaussianModel:
pars[prefix + 'center'].set(peak_f[i], min=f.min(), max=f.max())
pars[prefix + 'sigma'].set(width, min=0.1 * width, max=10 * width)
pars[prefix + 'gamma'].set(0, min=-5, max=5)
pars[prefix + 'amplitude'].set(peak_amplitudes[i])
elif model == GaussianModel:
pars[prefix + 'center'].set(peak_f[i], min=f.min(), max=f.max())
pars[prefix + 'sigma'].set(width, min=0.1 * width, max=10 * width)
pars[prefix + 'amplitude'].set(peak_amplitudes[i])
model = peaks[0]
for i in range(1, npeaks):
model += peaks[i]
if offset:
model += ConstantModel()
pars.update(ConstantModel().make_params())
pars['c'].set(0)
# Fit first spectrum, creating the ModelResult object which will be used over and over
fit = model.fit(y, pars, x=f)
return fit
def fit_peaks(
x,
y,
peak_pos,
bg="constant",
sigma_guess=2,
center_pm=20,
sigma_min=0.5,
amplitude_max_m=3.0,
bg_pm=100,
):
mod = ConstantModel()
for i, p in enumerate(peak_pos):
mod += LorentzianModel(prefix="p%s_" % i)
pars = mod.make_params()
for i, p in enumerate(peak_pos):
pars["p%s_center" % i].set(p, min=p - center_pm, max=p + center_pm)
pars["p%s_sigma" % i].set(sigma_guess, min=sigma_min)
# pars['p%s_amplitude' % i].set(10**2, min=0.0)
pars["p%s_amplitude" % i].set(
amplitude_max_m * y[find_nearest_index(x, p)], min=0.0
)
pars["c"].set(0, min=-1 * bg_pm, max=bg_pm)
out = mod.fit(y, pars, x=x, method="leastsq")
out.peak_pos = peak_pos
return out
def make_gaussian_model(self):
""" This method creates a model of a gaussian with an offset.
@return tuple: (object model, object params)
Explanation of the objects:
object lmfit.model.CompositeModel model:
A model the lmfit module will use for that fit. Here a
gaussian model. Returns an object of the class
lmfit.model.CompositeModel.
object lmfit.parameter.Parameters params:
It is basically an OrderedDict, so a dictionary, with keys
denoting the parameters as string names and values which are
lmfit.parameter.Parameter (without s) objects, keeping the
information about the current value.
The used model has the Parameter with the meaning:
'amplitude' : amplitude
'center' : center
'sigm' : sigma
'fwhm' : full width half maximum
'c' : offset
For further information have a look in:
http://cars9.uchicago.edu/software/python/lmfit/builtin_models.html#models.GaussianModel
"""
model = GaussianModel() + ConstantModel()
params = model.make_params()
return model, params
def pyfxcor(inspec, template, vmin=-200., vmax=200., res=3, rej=1000):
rv, cc = pyasl.crosscorrRV(inspec[0],
inspec[1],
template[0],
template[1],
vmin,
vmax,
res,
skipedge=rej)
cen_gs = np.argmax(cc)
perfx, perfy = rv[cen_gs - 5:cen_gs + 6], cc[cen_gs - 5:cen_gs + 6]
try:
gauss = ConstantModel() + GaussianModel()
pars = gauss.make_params()
pars['center'].set(value=rv[np.argmax(cc)], vary=True)
pars['amplitude'].set(value=max(cc), vary=True)
pars['sigma'].set(vary=True)
pars['c'].set(value=0, vary=True)
out = gauss.fit(perfy, pars, x=perfx)
ct = out.best_values['center']
cterr = out.params['center'].stderr
except:
return 'error', ''
return ct, cterr
def GaussConst(signal, guess):
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 = GaussianModel(prefix='gauss_')
const_mod = ConstantModel(prefix='const_')
#pars = lorentz_mod.make_params(amplitude=amp, center=centre, sigma=stdev / 3.)
#lorentz_mod.set_param_hint('sigma', value = stdev / 3., min=0., max=stdev)
pars = gauss_mod.guess(Y, x=X, center=centre, sigma=stdev / 3., amplitude=amp)
#pars += step_mod.guess(Y, x=X, center=centre)
pars += const_mod.guess(Y, x=X)
pars['gauss_sigma'].vary = False
mod = gauss_mod + const_mod
result = mod.fit(Y, pars, x=X)
# write error report
#print result.fit_report()
fwhm = result.best_values['gauss_sigma'] * 2.3548
return X, result.best_fit, result.redchi, fwhm
def GaussConst(signal, guess):
amp, centre, stdev, offset = guess
data = np.array([range(len(signal)), signal]).T
X = data[:, 0]
Y = data[:, 1]
gauss_mod = GaussianModel(prefix='gauss_')
const_mod = ConstantModel(prefix='const_')
pars = gauss_mod.make_params(center=centre, sigma=stdev, amplitude=amp)
pars += const_mod.guess(Y, x=X)
pars['gauss_center'].min = centre - 5.
pars['gauss_center'].max = centre + 5.
pars['gauss_sigma'].max = stdev + 5.
mod = gauss_mod + const_mod
result = mod.fit(Y, pars, x=X)
fwhm = result.best_values['gauss_sigma'] #* 2.3548
centr = result.best_values['gauss_center']
# Values within two stdevs i.e. 95%
pl.plot(np.repeat(centr - fwhm * 2, len(Y)), np.arange(len(Y)), 'b-')
pl.plot(np.repeat(centr + fwhm * 2, len(Y)), np.arange(len(Y)), 'b-')
return X, result.best_fit, result.best_values['gauss_sigma'] * 4
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
def model_at_depth(tree, depth, property_name):
r"""Generate a fit model at a particular tree depth
Parameters
----------
tree : :class:`~idpflex.cnextend.Tree`
Hierarchical tree
depth: int
depth level, starting from the tree's root (depth=0)
property_name : str
Name of the property to create the model for
Returns
-------
:class:`~lmfit.model.CompositeModel`
A model composed of a :class:`~idpflex.bayes.TabulatedFunctionModel`
for each node plus a :class:`~lmfit.models.ConstantModel` accounting
for a flat background
""" # noqa: E501
mod = ConstantModel()
for node in tree.nodes_at_depth(depth):
p = node[property_name]
m = TabulatedFunctionModel(p.x, p.y, prefix='n{}_'.format(node.id))
m.set_param_hint('center', vary=False)
m.set_param_hint('amplitude', value=1.0 / (1 + depth))
mod += m
return mod
def Box(signal, guess):
amp, centre, stdev, offset = guess
data = np.array([range(len(signal)), signal]).T
X = data[:, 0]
Y = data[:, 1]
gauss_mod = RectangleModel(prefix='gauss_', mode='logistic')
const_mod = ConstantModel(prefix='const_')
pars = gauss_mod.make_params(center1=centre - stdev * 3,
center2=centre + stdev * 3,
sigma1=0,
sigma2=0,
amplitude=amp)
pars += const_mod.guess(Y, x=X)
pars['gauss_center1'].min = centre - stdev * 3 - 3
pars['gauss_center2'].max = centre - stdev * 3 + 3
pars['gauss_center2'].min = centre + stdev * 3 - 3
pars['gauss_center2'].max = centre + stdev * 3 + 3
mod = gauss_mod + const_mod
result = mod.fit(Y, pars, x=X)
c1 = result.best_values['gauss_center1']
c2 = result.best_values['gauss_center2']
pl.legend()
return X, result.best_fit, c2 - c1
def fitgaussian_sample(sample, components, svg, verbose, center, cmin, cmax,
amp, amin, sigma, smin):
'''Fits gaussian curve to dyad coverage for a single sample.'''
print('Fits gaussian curve to dyad coverage of sample {}'.format(sample))
input = sample + '-dyad.txt'
dyads = pd.read_csv(input, sep='\t', index_col=0, comment='#')
x = dyads.index.values
y = dyads['Relative Frequency'].values
if not amp:
amp = dyads['Relative Frequency'].max() * 100
if not center:
center = 0.0
if not sigma:
sigma = dyads.index.max() / 2
plt.figure()
plt.title(sample)
plt.xlabel('Position relative to dyad (bp)')
plt.ylabel('Relative Frequency')
plt.xlim(x[0], x[len(x) - 1])
plt.xticks(list(range(x[0], x[len(x) - 1] + 1, 25)))
plt.plot(dyads.index.values,
dyads['Relative Frequency'].values,
color='red')
plot_output = sample + '-dyad-gaussian.png'
try:
constant = ConstantModel(prefix='c_')
pars = constant.make_params()
pars['c_c'].set(value=dyads['Relative Frequency'].min(),
min=0.0,
max=dyads['Relative Frequency'].max())
gauss = GaussianModel(prefix='g_')
pars.update(gauss.make_params())
pars['g_center'].set(value=center, min=cmin, max=cmax)
pars['g_sigma'].set(value=sigma, min=smin)
pars['g_amplitude'].set(value=amp, min=amin)
mod = constant + gauss
init = mod.eval(pars, x=x)
out = mod.fit(y, pars, x=x)
if components:
plt.plot(x, init, 'b--', label='Initial fit')
if verbose:
print(out.fit_report(min_correl=0.5))
plt.plot(x, out.best_fit, 'b-', label='Best fit')
if components:
comps = out.eval_components(x=x)
plt.plot(x,
np.repeat(comps['c_'], len(x)),
'g--',
label='Constant component')
plt.plot(x, comps['g_'], 'm--', label='Gaussian component')
except Exception as e:
logging.warning(
'could not fit gaussian curve to sample {}'.format(sample), e)
if components:
plt.legend(loc='lower right')
plt.savefig(plot_output)
if svg:
plot_svg_output = sample + '-dyad-gaussian.svg'
plt.savefig(plot_svg_output, transparent=True)
plt.close()
def Rectangle(signal, guess):
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]
step_mod = Rectangle()
const_mod = ConstantModel()
pars = step_mod.guess(Y, x=X, center=centre)
pars += const_mod.guess(Y, x=X)
mod = step_mod + const_mod
result = mod.fit(Y, pars, x=X)
# write error report
#print result.fit_report()
fwhm = result.best_values['sigma'] * 2.3548
print fwhm
return X, result.best_fit, result.redchi, 0
def fit_s21mag(x_val, y_val):
peak = LorentzianModel()
offset = ConstantModel()
model = peak
pars = peak.guess(y_val, x=x_val, amplitude=-0.05)
result = model.fit(y_val, pars, x=x_val)
return result
def fit_s21mag(x_val, y_val):
peak = GaussianModel()
offset = ConstantModel()
model = peak + offset
pars = offset.make_params(c=np.median(y_val))
pars += peak.guess(y_val, x=x_val, amplitude=-0.5)
result = model.fit(y_val, pars, x=x_val)
return result
def __init__(self, nexp=0, moddef=" "):
self.definition = moddef
self.model = ConstantModel()
self.nexp = 0
self.errors = None
self.params = None
self.res = None
for _ in range(nexp):
self.add_exp()
def xrf_calib_init_roi(mca, roiname):
"""initial calibration step for MCA:
find energy locations for one ROI
"""
if not isLarchMCAGroup(mca):
print('Not a valid MCA')
return
energy = 1.0 * mca.energy
chans = 1.0 * np.arange(len(energy))
counts = mca.counts
bgr = getattr(mca, 'bgr', None)
if bgr is not None:
counts = counts - bgr
if not hasattr(mca, 'init_calib'):
mca.init_calib = OrderedDict()
roi = None
for xroi in mca.rois:
if xroi.name == roiname:
roi = xroi
break
if roi is None:
return
words = roiname.split()
elem = words[0].title()
family = 'Ka'
if len(words) > 1:
family = words[1].title()
if family == 'Lb':
family = 'Lb1'
try:
eknown = xray_line(elem, family).energy / 1000.0
except:
eknown = 0.001
llim = max(0, roi.left - roi.bgr_width)
hlim = min(len(chans) - 1, roi.right + roi.bgr_width)
segcounts = counts[llim:hlim]
maxcounts = max(segcounts)
ccen = llim + np.where(segcounts == maxcounts)[0][0]
ecen = ccen * mca.slope + mca.offset
bkgcounts = counts[llim] + counts[hlim]
if maxcounts < 2 * bkgcounts:
mca.init_calib[roiname] = (eknown, ecen, 0.0, ccen, None)
else:
model = GaussianModel() + ConstantModel()
params = model.make_params(amplitude=maxcounts,
sigma=(chans[hlim] - chans[llim]) / 2.0,
center=ccen - llim,
c=0.00)
params['center'].min = -10
params['center'].max = hlim - llim + 10
params['c'].min = -10
out = model.fit(counts[llim:hlim], params, x=chans[llim:hlim])
ccen = llim + out.params['center'].value
ecen = ccen * mca.slope + mca.offset
fwhm = out.params['fwhm'].value * mca.slope
mca.init_calib[roiname] = (eknown, ecen, fwhm, ccen, out)
def __init__(self, nexp=0, sum_one=False):
self.sum_one_flag = sum_one
self.model = ConstantModel()
self.nexp = 0
self.errors = None
self.params = None
self.res = None
for _ in range(nexp):
self.add_exp()
def model(self):
"""Returns the sum of all peak models."""
model = ConstantModel(prefix="BASE_")
model.set_param_hint("c", vary=False, value=0)
self.params += model.make_params()
for peak in self._peaks:
model += peak.model
return model
def fit_lm_g(x,y,inits): ##https://stackoverflow.com/questions/44573896/python-fit-gaussian-to-noisy-data-with-lmfit
# gmodel = LorentzianModel()
# gmodel = VoigtModel()
gmodel = GaussianModel()
cmodel = ConstantModel()
model = gmodel + cmodel
params = model.make_params(sigma = inits[2], amplitude = inits[0], center = inits[1])
result = model.fit(y, params, x=x)
# print(params)
return result
def fit_s21mag(x_val, y_val):
x_val_midpoint = int(np.round(len(x_val) / 2))
peak = GaussianModel()
offset = ConstantModel()
model = peak + offset
pars = offset.make_params(c=np.median(y_val))
pars += peak.guess(y_val,
x=x_val,
amplitude=-0.05,
center=x_val[x_val_midpoint])
result = model.fit(y_val, pars, x=x_val)
return result
def abel_invert(self, y_lim, x_range, parameters=None, model=None):
if model is None:
# Create the lmfit model
model = GaussianModel()
model += ConstantModel()
params = model.make_params()
params['c'].set(0.45)
params['center'].set(0, vary=False)
params['sigma'].set(min=0.001)
if parameters is not None:
for key, value in parameters.items():
params[key].set(**value)
f = FloatProgress(min=0.3, max=4.5)
display(f)
fit_data = []
abel_data = []
xx = x_range
self.abel_extent = [-xx, xx, y_lim[0], y_lim[1]]
for yy in np.arange(y_lim[0], y_lim[1], 1 / self.scale):
f.value = yy
self.create_lineout(start=(yy, -xx),
end=(yy, xx),
lineout_width_mm=1 / self.scale)
# The data obtained by the lineout
y = self.lo
x = self.mm
out = model.fit(y, params, x=x)
fit_data.append(out.best_fit)
abel_data.append(
self.abel_gauss(x, out.best_values['sigma'],
out.best_values['amplitude']) *
10) #*10 converts from mm^-1 to cm^-1
# Change the lists to numpy arrays and flip them
fit_data = np.array(fit_data)[::-1]
abel_data = np.array(abel_data)[::-1]
extent = [-x_range, x_range, y_lim[0], y_lim[1]]
origin = [
int(len(fit_data) + y_lim[0] * self.scale),
int(len(fit_data[0]) / 2)
]
self.fit = DMFromArray(fit_data,
self.scale,
extent=extent,
origin=origin)
self.abel = DMFromArray(abel_data,
self.scale,
extent=extent,
origin=origin)
return self.fit, self.abel
def FitSpectrumInit(self, label):
"""
Fit the spectrum with the fit params of another spectrum (given by label) as initial values. Useful when you fit big number of similar spectra.
"""
borders = np.genfromtxt(label + '/spectrumborders_' + label + '.txt',
unpack=True)
np.savetxt(self.label + '/spectrumborders_' + self.label + '.txt',
borders)
self.y = self.y[(self.x > borders[0]) & (self.x < borders[-1])]
self.x = self.x[(self.x > borders[0]) & (self.x < borders[-1])]
FitData = np.load(label + '/fitparams_' + label + '.npz')
baseline = FitData['c'] / self.maxyvalue
ctr = FitData['x0']
sigma = FitData['sigma']
gamma = FitData['gamma']
ramanmodel = ConstantModel()
ramanmodel.set_param_hint('c', value=baseline[0], min=0)
for i in range(len(sigma)):
prefix = 'p' + str(i + 1)
tempvoigt = Model(func=voigt, prefix=prefix)
tempvoigt.set_param_hint(prefix + 'x0', value=ctr[i], min=0)
tempvoigt.set_param_hint(prefix + 'sigma', value=sigma[i], min=0)
tempvoigt.set_param_hint(prefix + 'gamma', value=gamma[i], min=0)
tempvoigt.set_param_hint(prefix + 'height',
expr='wofz(((0) + 1j*' + prefix +
'gamma) / ' + prefix +
'sigma / sqrt(2)).real')
tempvoigt.set_param_hint(prefix + 'fwhm',
expr='0.5346 * 2 *' + prefix +
'gamma + sqrt(0.2166 * (2*' + prefix +
'gamma)**2 + (2 * ' + prefix +
'sigma * sqrt(2 * log(2) ) )**2 )')
ramanmodel += tempvoigt
pars = ramanmodel.make_params()
fitresult = ramanmodel.fit(self.y, pars, x=self.x, scale_covar=True)
plt.clf()
comps = fitresult.eval_components()
xplot = np.linspace(self.x[0], self.x[-1], 1000)
plt.plot(self.x, self.y * self.maxyvalue, 'r-')
plt.plot(self.x, fitresult.best_fit * self.maxyvalue)
for i in range(0, len(sigma)):
plt.plot(
self.x, comps['p' + str(i + 1)] * self.maxyvalue +
comps['constant'] * self.maxyvalue, 'k-')
plt.savefig(self.label + '/rawplot_' + self.label + '.pdf')
save_modelresult(fitresult,
self.label + '/modelresult_' + self.label + '.sav')
plt.clf()
def prepare_model(nexp):
emodel = ConstantModel() + ExponentialModel(prefix='a') + ExponentialModel(
prefix='b')
pars.add('e', value=0, min=0)
pars.add('cntrl', value=1, min=1 - 1e-5, max=1 + 1e-5)
pars['cntrl'].expr = 'c'
pars['cntrl'].vary = True
expr = '{}amplitude'
all_expr = ''
for i in range(1, 1):
pars['cntrl'].expr += ' + ' + expr.format(Prefixes[i])
return emodel, pars
def FitSpectrum(self):
"""
Fit Spectrum with initial values provided by SelectBaseline() and SelectPeaks()
"""
polyparams = self.Fitbaseline(self)
base = polyparams[0].n
ramanmodel = ConstantModel()
ramanmodel.set_param_hint('c', value=base, min=0)
globwidth = 1
xpeak, ypeak = np.genfromtxt(self.peakfile, unpack=True)
if type(xpeak) == np.float64:
xpeak = [xpeak]
ypeak = [ypeak]
for i in range(0, len(xpeak)):
prefix = 'p' + str(i + 1)
tempvoigt = Model(func=voigt, prefix=prefix)
tempvoigt.set_param_hint(prefix + 'x0', value=xpeak[i], min=0)
tempvoigt.set_param_hint(prefix + 'sigma', value=globwidth, min=0)
tempvoigt.set_param_hint(prefix + 'gamma', value=globwidth, min=0)
tempvoigt.set_param_hint(prefix + 'height',
value=ypeak[i],
expr='wofz(((0) + 1j*' + prefix +
'gamma) / ' + prefix +
'sigma / sqrt(2)).real')
tempvoigt.set_param_hint(prefix + 'fwhm',
expr='0.5346 * 2 *' + prefix +
'gamma + sqrt(0.2166 * (2*' + prefix +
'gamma)**2 + (2 * ' + prefix +
'sigma * sqrt(2 * log(2) ) )**2 )')
ramanmodel += tempvoigt
pars = ramanmodel.make_params()
fitresult = ramanmodel.fit(self.y, pars, x=self.x, scale_covar=True)
print(fitresult.fit_report(min_correl=0.5))
comps = fitresult.eval_components()
xplot = np.linspace(self.x[0], self.x[-1], 1000)
plt.plot(self.x, self.y * self.maxyvalue, 'rx')
plt.plot(self.x, fitresult.best_fit * self.maxyvalue)
for i in range(0, len(xpeak)):
plt.plot(
self.x, comps['p' + str(i + 1)] * self.maxyvalue +
comps['constant'] * self.maxyvalue, 'k-')
plt.show()
plt.savefig(self.label + '/rawplot_' + self.label + '.pdf')
save_modelresult(fitresult,
self.label + '/modelresult_' + self.label + '.sav')
def BuiltInModels(self) :
FitInfo = self.FitInfo
ModelString = list()
for key in FitInfo['Models'] :
ModelString.append((key,FitInfo['Models'][key]['model']))
for Model in ModelString :
try :
FitModel
except :
if Model[1] == 'Constant' :
FitModel = ConstantModel(prefix=Model[0]+'_')
if Model[1] == 'Linear' :
FitModel = LinearModel(prefix=Model[0]+'_')
if Model[1] == 'Gaussian' :
FitModel = GaussianModel(prefix=Model[0]+'_')
if Model[1] == 'SkewedGaussian' :
FitModel = SkewedGaussianModel(prefix=Model[0]+'_')
if Model[1] == 'Voigt' :
FitModel = VoigtModel(prefix=Model[0]+'_')
else :
if Model[1] == 'Constant' :
FitModel = FitModel + ConstantModel(prefix=Model[0]+'_')
if Model[1] == 'Linear' :
FitModel = FitModel + LinearModel(prefix=Model[0]+'_')
if Model[1] == 'Gaussian' :
FitModel = FitModel + GaussianModel(prefix=Model[0]+'_')
if Model[1] == 'SkewedGaussian' :
FitModel = FitModel + SkewedGaussianModel(prefix=Model[0]+'_')
if Model[1] == 'Voigt' :
FitModel = FitModel + VoigtModel(prefix=Model[0]+'_')
self.FitModel = FitModel
self.ModelParameters = FitModel.make_params()
def fit_data(x, y, xmin=None, xmax=None):
if y is None:
return "No spectrum! Fit not performed!"
else:
if xmin is None:
xmin = x.min()
elif xmin < x.min():
xmin = x.min()
if xmax is None:
xmax = x.max()
elif xmax < x.max():
xmax = x.max()
y = np.copy(y[np.logical_and(x > xmin, x < xmax)])
x = np.copy(x[np.logical_and(x > xmin, x < xmax)])
x, y = remove_spike(y, x=x)
mod = (ConstantModel() + PseudoVoigtModel(prefix="peak1_") +
PseudoVoigtModel(prefix="peak2_"))
params = mod.make_params()
ymax_ind = np.argmax(y)
xmax = x[ymax_ind]
params["c"].set(0)
params.add("psplit", value=1.5, vary=True, min=0.5, max=2.0)
params["peak2_center"].set(xmax, min=xmax - 0.5, max=x.max())
params["peak2_sigma"].set(0.5, min=0.01)
params["peak2_amplitude"].set(y[ymax_ind] * 0.5 * np.sqrt(2 * np.pi),
min=0)
params["peak2_fraction"].set(0.5, min=0, max=1)
params["peak1_center"].set(vary=False, expr="peak2_center-psplit")
params["peak1_sigma"].set(0.5, min=0.01)
params["peak1_amplitude"].set(y[ymax_ind] * 0.5 * np.sqrt(2 * np.pi) /
2,
min=0)
params["peak1_fraction"].set(0.5, min=0, max=1)
fit = mod.fit(y, params, x=x)
return fit
def make_lorentzian_model(self):
""" This method creates a model of lorentzian with an offset. The
parameters are: 'amplitude', 'center', 'sigma, 'fwhm' and offset
'c'. For function see:
http://cars9.uchicago.edu/software/python/lmfit/builtin_models.html#models.LorentzianModel
@return lmfit.model.CompositeModel model: Returns an object of the
class CompositeModel
@return object params: lmfit.parameter.Parameters object, returns an
object of the class Parameters with all
parameters for the lorentzian model.
"""
model = LorentzianModel() + ConstantModel()
params = model.make_params()
return model, params
def fit_peak_df(df, model=GaussianModel, params=None, fit_range=(-np.inf, np.inf), x_field=None, fit_field='nphe2_mean', out_field='peak_fit'):
"""
Fits DataFrame with selected peak model. Appends residuals column to DataFrame.
"""
# Data
fit_min, fit_max = fit_range
df_ranged = df[(df.index > fit_min) & (df.index < fit_max)]
if x_field:
x = np.array(df_ranged[x_field])
full_x = np.array(df[x_field])
else:
x = np.array(df_ranged.index.get_values())
full_x = np.array(df.index.get_values())
y = np.array(df_ranged[fit_field].values)
full_y = np.array(df[fit_field].values)
# Models
if isinstance(model, str):
try:
model = PEAK_MODELS[model]
except KeyError:
print("Undefined model: {}, using default".format(model))
peak_mod = model(prefix='peak_')
const_mod = ConstantModel(prefix='const_')
result_model = const_mod + peak_mod
# Parameters
if not params:
pars = const_mod.make_params(c=y.min())
pars += peak_mod.guess(y, x=x, center=0)
else:
pars = params
# Fitting
result = result_model.fit(y, params=pars, x=x)
peak_eval = result.eval(x=full_x)
y_res = full_y - peak_eval
df[out_field] = pd.Series(peak_eval, index=df.index)
df[out_field + '_res'] = pd.Series(y_res, index=df.index)
return df, result
def gaussian_fit(self, x, y, paras=None, method=None):
g1model = GaussianModel(prefix='g1_')
g2model = GaussianModel(prefix='g2_')
g3model = GaussianModel(prefix='g3_')
cmodel = ConstantModel()
paras_fit = g1model.guess(data=y, x=x)
paras_fit.update(g2model.make_params())
paras_fit.update(g3model.make_params())
paras_fit['g1_amplitude'].set(min=0.)
paras_fit['g2_amplitude'].set(min=0.)
paras_fit['g3_amplitude'].set(min=0.)
paras_fit['g1_center'].set(min=paras['g1_center'] - 300.,
value=paras['g1_center'],
max=paras['g1_center'] + 300.)
paras_fit['g2_center'].set(min=paras['g2_center'] - 300.,
value=paras['g2_center'],
max=paras['g2_center'] + 300.)
paras_fit['g3_center'].set(min=paras['g3_center'] - 300.,
value=paras['g3_center'],
max=paras['g3_center'] + 300.)
paras_fit['g1_sigma'].set(min=100,
value=paras['g1_sigma'],
max=paras['g1_sigma'] + 50.)
paras_fit['g2_sigma'].set(min=100,
value=paras['g2_sigma'],
max=paras['g2_sigma'] + 50.)
paras_fit['g3_sigma'].set(min=100,
value=paras['g3_sigma'],
max=paras['g3_sigma'] + 50.)
paras_fit.update(cmodel.make_params())
model = g1model + g2model + g3model + cmodel
result = model.fit(y, x=x, params=paras_fit, mothod=method)
yfit = result.best_fit
y_para = result.best_values
residual = y - yfit
return yfit, y_para, result, residual
def test_stepmodel_erf():
x, y = get_data()
stepmod = StepModel(form='linear')
const = ConstantModel()
pars = stepmod.guess(y, x)
pars = pars + const.make_params(c=3 * y.min())
mod = stepmod + const
out = mod.fit(y, pars, x=x)
assert (out.nfev > 5)
assert (out.nvarys == 4)
assert (out.chisqr > 1)
assert (out.params['c'].value > 3)
assert (out.params['center'].value > 1)
assert (out.params['center'].value < 4)
assert (out.params['amplitude'].value > 50)
assert (out.params['sigma'].value > 0.2)
assert (out.params['sigma'].value < 1.5)
