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 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 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 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 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 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 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 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 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 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 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 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 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 __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 __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 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_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 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 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 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_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 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 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)
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)
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 make_multiplegaussian_model(self, no_of_gauss=None):
""" This method creates a model of multiple gaussians 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 lmfit.parameter.Parameters params: Returns an object of the
class Parameters with all
parameters for the
lorentzian model.
"""
model = ConstantModel()
for ii in range(no_of_gauss):
model += GaussianModel(prefix='gaussian{0}_'.format(ii))
params = model.make_params()
return model, params
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 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 GaussConst(signal, guess):
"""
Fits a Gaussian function
Plots fwhm and 2*sigma gap widths for comparison
with the analytically calculated one
"""
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-', label="Sigma * 2")
pl.plot(np.repeat(centr - fwhm * 2.3548 / 2., len(Y)),
np.arange(len(Y)), 'y--')
pl.plot(np.repeat(centr + fwhm * 2.3548 / 2., len(Y)),
np.arange(len(Y)), 'y--', label="FWHM")
return X, result.best_fit, result.best_values['gauss_sigma'] * 4, centr
def Step(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 = StepModel(prefix='step')
const_mod = ConstantModel(prefix='const_')
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()
return X, result.best_fit, result.redchi, 0
def pyfxcor(inspec, template, obj, vmin=-400., vmax=400., res=3, rej=200):
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:
plt.plot(inspec[0], inspec[1])
plt.savefig(obj+'.png', dpi=300)
pl.clf()
return 'error', ''
plt.subplot(311)
plt.plot(rv, cc)
curraxlim = plt.axis()
out.plot_fit(numpoints=100)
plt.axis(curraxlim)
plt.subplot(312)
plt.plot(obj[1][0], obj[1][1], 'r-', linewidth=0.5)
plt.subplot(313)
plt.plot(inspec[0], inspec[1], 'b-', linewidth=0.5)
plt.savefig(obj[0]+'.png', dpi=300)
plt.clf()
return ct, cterr
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
cont = 3.0 # continuum level
randamp = 3. # amplitude of gaussian noise
x = np.arange(0,xmax)
y = randamp * np.random.randn(xmax) + jrr.spec.onegaus(x, aa, bb, cc, cont)
err = randamp * np.random.randn(xmax)
plt.plot(x, y, color='black')
# Let's try fitting that gaussian w the python version of MPFIT
p0 = (50., xmax/2, 5, 2)
fa = {'x':x, 'y':y, 'err':err}
m = mpfit.mpfit(myfunct, p0, functkw=fa)
# There has got to be a less kludgy way to do line below
bestfit = jrr.spec.onegaus(x, m.params[0], m.params[1], m.params[2], m.params[3])
plt.plot(x, bestfit, color='blue')
# The same, but with LMFIT
mod1 = GaussianModel()
mod2 = ConstantModel() # The continuum level
mod = mod1 + mod2
pars = mod1.guess(y, x=x) + mod2.guess(y, x=x) # This is cool. It made rough guesses for us.
pars['c'].min = 0 # Set bounds on continuum
pars['c'].max = 10 # Set bounds on continuum
#pars['amplitude'].vary = False # Fix a parameter
out = mod.fit(y, pars, x=x, weights=1/err**2) # Fitting is done here.
plt.plot(x, out.best_fit, color='orange')
print(out.fit_report(min_correl=0.25))
plt.show()
# This is actually more elegant. I think I should learn LMFIT and use it...
def lmfit_mngauss(x,y, *params):
"""
Fit multiple gaussians from two spectra that are multiplied together
INPUT:
x - is the wavelength array
y - is the normalized flux
params - is a tuple of 2 list/arrays of initial guess values for the each spectras parameters
(this controls the number of gaussians to be fitted
number of gaussians: len(params)/3 - 3 parameters per Gaussian)
OUTPUT:
mod - the lmfit model object used for the fit
out - the lmfit fit object that contains all the results of the fit
init- array with the initial guess model (usefull to see the initial guess when plotting)
"""
m_params = params[0]
m_mods = []
prefixes = []
for i in range(0, len(m_params), 3):
pref = "gm%02i_" % (i/3)
gauss_i = GaussianModel(prefix=pref)
if i == 0:
pars = gauss_i.guess(y, x=x)
else:
pars.update(gauss_i.make_params())
A = m_params[i]
l_cen = m_params[i+1]
sigma = m_params[i+2]
pars[pref+'amplitude'].set(A)
pars[pref+'center'].set(l_cen)
pars[pref+'sigma'].set(sigma)
m_mods.append(gauss_i)
prefixes.append(pref)
m_mod = m_mods[0]
if len(m_mods) > 1:
for m in m_mods[1:]:
m_mod += m
m_one = ConstantModel(prefix="m_one_")
prefixes.append("m_one_")
pars.update(m_one.make_params())
pars['m_one_c'].set(value=1, vary=False)
try:
n_params = params[1]
n_mods = []
#prefixes = []
for j in range(0, len(n_params), 3):
pref = "gn%02i_" % (j/3)
gauss_j = GaussianModel(prefix=pref)
pars.update(gauss_j.make_params())
A = n_params[j]
l_cen = n_params[j+1]
sigma = n_params[j+2]
pars[pref+'amplitude'].set(A)
pars[pref+'center'].set(l_cen)
pars[pref+'sigma'].set(sigma)
n_mods.append(gauss_j)
prefixes.append(pref)
n_mod = n_mods[0]
if len(n_mods) > 1:
for n in n_mods[1:]:
n_mod += n
n_one = ConstantModel(prefix="n_one_")
prefixes.append("n_one_")
pars.update(n_one.make_params())
pars['n_one_c'].set(value=1, vary=False)
mod = (m_one + m_mod) * (n_one + n_mod)
except:
print("Error with second spectra, only fitting first")
mod = m_one + m_mod
init = mod.eval(pars, x=x)
out = mod.fit(y, pars, x=x)
print("Printed prefixes", prefixes)
#print(init)
return mod, out, init
def call_constant(x, y, ylock): const = ConstantModel(prefix='constant_') pars = const.guess(y, x=x) pars['constant_c'].set(ylock, min=ylock-0.01, max=ylock+0.0001) return const, pars
def CurveFitting(self, frec, Pxx, iaf, ax):
'Non-Linear Least-Squares Minimization and Curve-Fitting for Python'
# ----- adjusting a model to the obtained PSD -----
# model 1: constante
g1 = ConstantModel(prefix = 'g1_')
pars = g1.guess(Pxx, x = frec)
pars['g1_c'].set(0)
# model 2: k2/f^-1
g2 = PowerLawModel(prefix = 'g2_')
pars += g2.guess(Pxx, x = frec)
pars['g2_exponent'].set(-1)
#model 3: probability density function
g3 = GaussianModel(prefix = 'g3_')
pars += g3.guess(Pxx, x = frec)
pars['g3_center'].set(iaf, min = iaf-2, max = iaf+2)
# model 4: probability density function
g4 = GaussianModel(prefix = 'g4_')
pars += g4.guess(Pxx, x = frec)
pars['g4_center'].set(20, min = 16, max = 25)
# final model
gA = g1 + g2 + g3 + g4
outA = gA.fit(Pxx, pars, x = frec)
diffA= np.sum(Pxx - outA.best_fit)
gB = g1 + g2 + g3
outB = gB.fit(Pxx, pars, x = frec)
diffB= np.sum(Pxx - outB.best_fit)
gC = g1 + g2
outC = gC.fit(Pxx, pars, x = frec)
diffC= np.sum(Pxx - outC.best_fit)
diffs= np.abs([diffA, diffB, diffC])
idx = np.where(diffs == np.min(diffs))[0][0]
out = [outA, outB, outC][idx]
# ----- plotting the desire PSD -----
# original and fitted curves
ax.plot(frec, Pxx, 'k', linewidth = 2, label = 'PSD')
ax.plot(frec, out.best_fit, 'b.-', linewidth = 2, markersize = 9, label ='BestModel')
ax.set_xlim(frec[0], 32)
ax.set_ylim(ymin = 0)
ax.tick_params(axis = 'both', labelsize = 16)
ax.set_xlabel('Frequency [Hz]', fontsize = 'x-large')
ax.grid()
# components of the fitted curved
comps = out.eval_components(x = frec)
g12 = comps['g1_'] + comps['g2_']
ax.plot(frec, g12, 'g--', linewidth = 2, label = 'PowerLawModel')
idx1, idx2 = np.where(frec >= 5)[0][0], np.where(frec <= 15)[0][-1]
# final value on the subplot
if out != outC:
diffs = out.best_fit[idx1:idx2] - g12[idx1:idx2]
peak1 = np.amax(diffs)
idx = np.where(diffs == peak1)[0]
idx+= len(out.best_fit[:idx1])
ax.plot((frec[idx],frec[idx]), (g12[idx],out.best_fit[idx]), 'r-o', linewidth = 3, markersize = 9)
ax.text(frec[idx], g12[idx], str(np.around(peak1, decimals=2)), horizontalalignment='right', verticalalignment='top', color='r', fontsize='xx-large')
else:
peak1 = 0
# optional valued on the subplot
diffs = Pxx[idx1:idx2] - g12[idx1:idx2]
peak2 = np.amax(diffs)
idx = np.where(peak2 == diffs)[0]
idx+= len(Pxx[:idx1])
ax.plot((frec[idx],frec[idx]), (g12[idx], Pxx[idx]), 'r-*', linewidth = 3, markersize = 11)
ax.text(frec[idx], Pxx[idx], str(np.around(peak2, decimals=2)), horizontalalignment='left', verticalalignment='top', color='r', fontsize='xx-large')
ax.legend(loc='upper right', shadow=True)
return peak1, peak2
