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import numpy as npfrom uncertainties import ufloat
import lmfitfrom lmfit.models import (ConstantModel, ComplexConstantModel, LinearModel, QuadraticModel, PolynomialModel, SineModel, GaussianModel, Gaussian2dModel, LorentzianModel, SplitLorentzianModel, VoigtModel, PseudoVoigtModel, MoffatModel, Pearson7Model, StudentsTModel, BreitWignerModel, LognormalModel, DampedOscillatorModel, ExponentialGaussianModel, SkewedGaussianModel, SkewedVoigtModel, ThermalDistributionModel, DoniachModel, PowerLawModel, ExponentialModel, StepModel, RectangleModel, ExpressionModel, DampedHarmonicOscillatorModel)from lmfit.models import (guess_from_peak, guess_from_peak2d, fwhm_expr, height_expr, update_param_vals)from lmfit.lineshapes import (not_zero, breit_wigner, damped_oscillator, dho, doniach, expgaussian, exponential, gaussian, gaussian2d, linear, lognormal, lorentzian, moffat, parabolic, pearson7, powerlaw, pvoigt, rectangle, sine, skewed_gaussian, skewed_voigt, split_lorentzian, step, students_t, thermal_distribution, tiny, voigt)from lmfit import Modelimport numpy as npfrom numpy import (arctan, copysign, cos, exp, isclose, isnan, log, pi, real, sin, sqrt, where)from scipy.special import erf, erfcfrom scipy.special import gamma as gamfcnfrom scipy.special import wofzfrom scipy.optimize import curve_fit
import xarray as xr
import copy
log2 = log(2)s2pi = sqrt(2*pi)s2 = sqrt(2.0)
def gaussianWithOffset(x, amplitude=1.0, center=0.0, sigma=1.0, offset=0.0): """Return a 1-dimensional Gaussian function with an offset.
gaussian(x, amplitude, center, sigma) = (amplitude/(s2pi*sigma)) * exp(-(1.0*x-center)**2 / (2*sigma**2))
"""
return ((amplitude/(max(tiny, s2pi*sigma))) * exp(-(1.0*x-center)**2 / max(tiny, (2*sigma**2))) + offset)
def lorentzianWithOffset(x, amplitude=1.0, center=0.0, sigma=1.0, offset=0.0): return ((amplitude/(1 + ((1.0*x-center)/max(tiny, sigma))**2)) / max(tiny, (pi*sigma)) + offset)
def exponentialWithOffset(x, amplitude=1.0, decay=1.0, offset=0.0): decay = not_zero(decay) return amplitude * exp(-x/decay) + offset
def expansion(x, amplitude=1.0, offset=0.0): return np.sqrt(amplitude*x*x + offset)
def dampingOscillation(x, center=0, amplitude=1.0, frequency=1.0, decay=1.0, offset=0.0): return amplitude * np.exp(-decay*x)*np.sin(2*np.pi*frequency*(x-center)) + offset
def two_gaussian2d(x, y=0.0, A_amplitude=1.0, A_centerx=0.0, A_centery=0.0, A_sigmax=1.0, A_sigmay=1.0, B_amplitude=1.0, B_centerx=0.0, B_centery=0.0, B_sigmax=1.0, B_sigmay=1.0): """Return a 2-dimensional Gaussian function.
gaussian2d(x, y, amplitude, centerx, centery, sigmax, sigmay) = amplitude/(2*pi*sigmax*sigmay) * exp(-(x-centerx)**2/(2*sigmax**2) -(y-centery)**2/(2*sigmay**2))
"""
z = A_amplitude*(gaussian(x, amplitude=1, center=A_centerx, sigma=A_sigmax) * gaussian(y, amplitude=1, center=A_centery, sigma=A_sigmay)) z += B_amplitude*(gaussian(x, amplitude=1, center=B_centerx, sigma=B_sigmax) * gaussian(y, amplitude=1, center=B_centery, sigma=B_sigmay)) return z
def ThomasFermi_2d(x, y=0.0, centerx=0.0, centery=0.0, amplitude=1.0, sigmax=1.0, sigmay=1.0): res = (1- ((x-centerx)/(sigmax))**2 - ((y-centery)/(sigmay))**2)**(3 / 2) return amplitude * 5 / 2 / np.pi / max(tiny, sigmax * sigmay) * np.where(res > 0, res, 0)
def polylog(power, numerator): order = 20 dataShape = numerator.shape numerator = np.tile(numerator, (order, 1)) numerator = np.power(numerator.T, np.arange(1, order+1)).T
denominator = np.arange(1, order+1) denominator = np.tile(denominator, (dataShape[0], 1)) denominator = denominator.T
data = numerator/ np.power(denominator, power)
return np.sum(data, axis=0)
def polylog2_2d(x, y=0.0, centerx=0.0, centery=0.0, amplitude=1.0, sigmax=1.0, sigmay=1.0): ## Approximation of the polylog function with 2D gaussian as argument. -> discribes the thermal part of the cloud return amplitude / 2 / np.pi / 1.20206 / max(tiny, sigmax * sigmay) * polylog(2, np.exp( -((x-centerx)**2/(2 * (sigmax)**2))-((y-centery)**2/( 2 * (sigmay)**2)) ))
def density_profile_BEC_2d(x, y=0.0, BEC_amplitude=1.0, thermal_amplitude=1.0, BEC_centerx=0.0, BEC_centery=0.0, thermal_centerx=0.0, thermal_centery=0.0, BEC_sigmax=1.0, BEC_sigmay=1.0, thermal_sigmax=1.0, thermal_sigmay=1.0): return ThomasFermi_2d(x=x, y=y, centerx=BEC_centerx, centery=BEC_centery, amplitude=BEC_amplitude, sigmax=BEC_sigmax, sigmay=BEC_sigmay ) + polylog2_2d(x=x, y=y, centerx=thermal_centerx, centery=thermal_centery, amplitude=thermal_amplitude, sigmax=thermal_sigmax, sigmay=thermal_sigmay)
class GaussianWithOffsetModel(Model): fwhm_factor = 2*np.sqrt(2*np.log(2)) height_factor = 1./np.sqrt(2*np.pi) def __init__(self, independent_vars=['x'], nan_policy='raise', prefix='', name=None, **kwargs): kwargs.update({'prefix': prefix, 'nan_policy': nan_policy, 'independent_vars': independent_vars}) super().__init__(gaussianWithOffset, **kwargs) self._set_paramhints_prefix()
def _set_paramhints_prefix(self): self.set_param_hint('sigma', min=0) self.set_param_hint('fwhm', expr=fwhm_expr(self)) self.set_param_hint('height', expr=height_expr(self)) def guess(self, data, x, negative=False, **kwargs): offset = np.min(data) data = data - offset pars = guess_from_peak(self, data, x, negative) pars.add('offset', value=offset) return update_param_vals(pars, self.prefix, **kwargs)
class LorentzianWithOffsetModel(Model):
fwhm_factor = 2.0 height_factor = 1./np.pi
def __init__(self, independent_vars=['x'], prefix='', nan_policy='raise', **kwargs): kwargs.update({'prefix': prefix, 'nan_policy': nan_policy, 'independent_vars': independent_vars}) super().__init__(lorentzianWithOffset, **kwargs) self._set_paramhints_prefix()
def _set_paramhints_prefix(self): self.set_param_hint('sigma', min=0) self.set_param_hint('fwhm', expr=fwhm_expr(self)) self.set_param_hint('height', expr=height_expr(self))
def guess(self, data, x, negative=False, **kwargs): """Estimate initial model parameter values from data.""" offset = np.min(data) data = data - offset pars = guess_from_peak(self, data, x, negative, ampscale=1.25) pars.add('offset', value=offset) return update_param_vals(pars, self.prefix, **kwargs)
class ExponentialWithOffsetModel(Model):
def __init__(self, independent_vars=['x'], prefix='', nan_policy='raise', **kwargs): kwargs.update({'prefix': prefix, 'nan_policy': nan_policy, 'independent_vars': independent_vars}) super().__init__(exponentialWithOffset, **kwargs)
def guess(self, data, x, **kwargs): """Estimate initial model parameter values from data.""" offset = np.min(data) data = data - offset try: sval, oval = np.polyfit(x, np.log(abs(data)+1.e-15), 1) except TypeError: sval, oval = 1., np.log(abs(max(data)+1.e-9)) pars = self.make_params(amplitude=np.exp(oval), decay=-1.0/sval) pars.add('offset', value=offset) return update_param_vals(pars, self.prefix, **kwargs)
class ExpansionModel(Model):
def __init__(self, independent_vars=['x'], prefix='', nan_policy='raise', **kwargs): kwargs.update({'prefix': prefix, 'nan_policy': nan_policy, 'independent_vars': independent_vars}) super().__init__(expansion, **kwargs)
def guess(self, data, x, **kwargs): """Estimate initial model parameter values from data.""" popt1, pcov1 = curve_fit(expansion, x, data) pars = self.make_params(amplitude=popt1[0], offset=popt1[1]) return update_param_vals(pars, self.prefix, **kwargs)
class DampingOscillationModel(Model): def __init__(self, independent_vars=['x'], prefix='', nan_policy='raise', **kwargs): kwargs.update({'prefix': prefix, 'nan_policy': nan_policy, 'independent_vars': independent_vars}) super().__init__(dampingOscillation, **kwargs)
def guess(self, data, x, **kwargs): """Estimate initial model parameter values from data.""" try: popt1, pcov1 = curve_fit(dampingOscillation, x, data, np.array(0, 5, 5e2, 1e3, 16)) pars = self.make_params(center=popt1[0], amplitude=popt1[1], frequency=popt1[2], decay=popt1[3], offset=popt1[4]) except: pars = self.make_params(center=0, amplitude=5.0, frequency=5e2, decay=1.0e3, offset=16.0) return update_param_vals(pars, self.prefix, **kwargs)
class TwoGaussian2dModel(Model): fwhm_factor = 2*np.sqrt(2*np.log(2)) height_factor = 1./2*np.pi
def __init__(self, independent_vars=['x', 'y'], prefix='', nan_policy='raise', **kwargs): kwargs.update({'prefix': prefix, 'nan_policy': nan_policy, 'independent_vars': independent_vars}) self.helperModel = Gaussian2dModel() super().__init__(two_gaussian2d, **kwargs) self._set_paramhints_prefix()
def _set_paramhints_prefix(self): self.set_param_hint('delta', value=-1, max=0) self.set_param_hint('A_sigmax', expr=f'{self.prefix}delta + {self.prefix}B_sigmax')
def guess(self, data, x, y, negative=False, **kwargs): pars_guess = guess_from_peak2d(self.helperModel, data, x, y, negative) pars = self.make_params(A_amplitude=pars_guess['amplitude'].value, A_centerx=pars_guess['centerx'].value, A_centery=pars_guess['centery'].value, A_sigmax=pars_guess['sigmax'].value, A_sigmay=pars_guess['sigmay'].value, B_amplitude=pars_guess['amplitude'].value, B_centerx=pars_guess['centerx'].value, B_centery=pars_guess['centery'].value, B_sigmax=pars_guess['sigmax'].value, B_sigmay=pars_guess['sigmay'].value) pars[f'{self.prefix}A_sigmax'].set(expr=f'delta + {self.prefix}B_sigmax') pars.add(f'{self.prefix}delta', value=-1, max=0, min=-np.inf, vary=True) pars[f'{self.prefix}A_sigmay'].set(min=0.0) pars[f'{self.prefix}B_sigmax'].set(min=0.0) pars[f'{self.prefix}B_sigmay'].set(min=0.0) return pars
class Polylog22dModel(Model):
fwhm_factor = 2*np.sqrt(2*np.log(2)) height_factor = 1./2*np.pi
def __init__(self, independent_vars=['x', 'y'], prefix='', nan_policy='raise', **kwargs): kwargs.update({'prefix': prefix, 'nan_policy': nan_policy, 'independent_vars': independent_vars}) super().__init__(polylog2_2d, **kwargs) self._set_paramhints_prefix()
def _set_paramhints_prefix(self): self.set_param_hint('Rx', min=0) self.set_param_hint('Ry', min=0)
def guess(self, data, x, y, negative=False, **kwargs): """Estimate initial model parameter values from data.""" pars = guess_from_peak2d(self, data, x, y, negative) return update_param_vals(pars, self.prefix, **kwargs)
class ThomasFermi2dModel(Model):
fwhm_factor = 1 height_factor = 0.5
def __init__(self, independent_vars=['x', 'y'], prefix='', nan_policy='raise', **kwargs): kwargs.update({'prefix': prefix, 'nan_policy': nan_policy, 'independent_vars': independent_vars}) super().__init__(ThomasFermi_2d, **kwargs) self._set_paramhints_prefix()
def _set_paramhints_prefix(self): self.set_param_hint('Rx', min=0) self.set_param_hint('Ry', min=0)
def guess(self, data, x, y, negative=False, **kwargs): """Estimate initial model parameter values from data.""" pars = guess_from_peak2d(self, data, x, y, negative) # amplitude = pars['amplitude'].value # simgax = pars['sigmax'].value # sigmay = pars['sigmay'].value # pars['amplitude'].set(value=amplitude/s2pi/simgax/sigmay) simgax = pars['sigmax'].value sigmay = pars['sigmay'].value pars['simgax'].set(value=simgax / 2.355) pars['sigmay'].set(value=sigmay / 2.355) return update_param_vals(pars, self.prefix, **kwargs)
class DensityProfileBEC2dModel(Model):
fwhm_factor = 2*np.sqrt(2*np.log(2)) height_factor = 1./2*np.pi
def __init__(self, independent_vars=['x', 'y'], prefix='', nan_policy='raise', **kwargs): kwargs.update({'prefix': prefix, 'nan_policy': nan_policy, 'independent_vars': independent_vars}) super().__init__(density_profile_BEC_2d, **kwargs) self._set_paramhints_prefix()
def _set_paramhints_prefix(self): # self.set_param_hint('BEC_sigmax', min=0) self.set_param_hint('deltax', min=0) self.set_param_hint('BEC_sigmax', expr=f'3 * {self.prefix}thermal_sigmax - {self.prefix}deltax') self.set_param_hint('BEC_sigmay', min=0) self.set_param_hint('thermal_sigmax', min=0) # self.set_param_hint('thermal_sigmay', min=0) self.set_param_hint('BEC_amplitude', min=0) self.set_param_hint('thermal_amplitude', min=0) self.set_param_hint('thermalAspectRatio', min=0.8, max=1.2) self.set_param_hint('thermal_sigmay', expr=f'{self.prefix}thermalAspectRatio * {self.prefix}thermal_sigmax') # self.set_param_hint('betax', value=0) # self.set_param_hint('BEC_centerx', expr=f'{self.prefix}thermal_sigmax - {self.prefix}betax') self.set_param_hint('condensate_fraction', expr=f'{self.prefix}BEC_amplitude / ({self.prefix}BEC_amplitude + {self.prefix}thermal_amplitude)')
def guess(self, data, x, y, negative=False, pureBECThreshold=0.5, noBECThThreshold=0.0, **kwargs): """Estimate initial model parameter values from data.""" fitModel = TwoGaussian2dModel() pars = fitModel.guess(data, x=x, y=y, negative=negative) pars['A_amplitude'].set(min=0) pars['B_amplitude'].set(min=0) pars['A_centerx'].set(min=pars['A_centerx'].value - 3 * pars['A_sigmax'], max=pars['A_centerx'].value + 3 * pars['A_sigmax'],) pars['A_centery'].set(min=pars['A_centery'].value - 3 * pars['A_sigmay'], max=pars['A_centery'].value + 3 * pars['A_sigmay'],) pars['B_centerx'].set(min=pars['B_centerx'].value - 3 * pars['B_sigmax'], max=pars['B_centerx'].value + 3 * pars['B_sigmax'],) pars['B_centery'].set(min=pars['B_centery'].value - 3 * pars['B_sigmay'], max=pars['B_centery'].value + 3 * pars['B_sigmay'],) fitResult = fitModel.fit(data, x=x, y=y, params=pars, **kwargs) pars_guess = fitResult.params BEC_amplitude = pars_guess['A_amplitude'].value thermal_amplitude = pars_guess['B_amplitude'].value pars = self.make_params(BEC_amplitude=BEC_amplitude, thermal_amplitude=thermal_amplitude, BEC_centerx=pars_guess['A_centerx'].value, BEC_centery=pars_guess['A_centery'].value, # BEC_sigmax=(pars_guess['A_sigmax'].value / 2.355), deltax = 3 * (pars_guess['B_sigmax'].value * s2) - (pars_guess['A_sigmax'].value / 2.355), BEC_sigmay=(pars_guess['A_sigmay'].value / 2.355), thermal_centerx=pars_guess['B_centerx'].value, thermal_centery=pars_guess['B_centery'].value, thermal_sigmax=(pars_guess['B_sigmax'].value * s2), thermalAspectRatio=(pars_guess['B_sigmax'].value * s2) / (pars_guess['B_sigmay'].value * s2) # thermal_sigmay=(pars_guess['B_sigmay'].value * s2) ) nBEC = pars[f'{self.prefix}BEC_amplitude'] / 2 / np.pi / 5.546 / pars[f'{self.prefix}BEC_sigmay'] / pars[f'{self.prefix}BEC_sigmax'] if (pars[f'{self.prefix}condensate_fraction']>0.95) and (np.max(data) > 1.05 * nBEC): temp = ((np.max(data) - nBEC) * s2pi * pars[f'{self.prefix}thermal_sigmay'] / pars[f'{self.prefix}thermal_sigmax']) if temp > pars[f'{self.prefix}BEC_amplitude']: pars[f'{self.prefix}thermal_amplitude'].set(value=pars[f'{self.prefix}BEC_amplitude'] / 2) else: pars[f'{self.prefix}thermal_amplitude'].set(value=temp * 10) if BEC_amplitude / (thermal_amplitude + BEC_amplitude) > pureBECThreshold: pars[f'{self.prefix}thermal_amplitude'].set(value=0) pars[f'{self.prefix}BEC_amplitude'].set(value=(thermal_amplitude + BEC_amplitude)) if BEC_amplitude / (thermal_amplitude + BEC_amplitude) < noBECThThreshold: pars[f'{self.prefix}BEC_amplitude'].set(value=0) pars[f'{self.prefix}thermal_amplitude'].set(value=(thermal_amplitude + BEC_amplitude)) pars[f'{self.prefix}BEC_centerx'].set( min=pars[f'{self.prefix}BEC_centerx'].value - 10 * pars[f'{self.prefix}BEC_sigmax'].value, max=pars[f'{self.prefix}BEC_centerx'].value + 10 * pars[f'{self.prefix}BEC_sigmax'].value, ) pars[f'{self.prefix}thermal_centerx'].set( min=pars[f'{self.prefix}thermal_centerx'].value - 3 * pars[f'{self.prefix}thermal_sigmax'].value, max=pars[f'{self.prefix}thermal_centerx'].value + 3 * pars[f'{self.prefix}thermal_sigmax'].value, ) pars[f'{self.prefix}BEC_centery'].set( min=pars[f'{self.prefix}BEC_centery'].value - 10 * pars[f'{self.prefix}BEC_sigmay'].value, max=pars[f'{self.prefix}BEC_centery'].value + 10 * pars[f'{self.prefix}BEC_sigmay'].value, ) pars[f'{self.prefix}thermal_centery'].set( min=pars[f'{self.prefix}thermal_centery'].value - 3 * pars[f'{self.prefix}thermal_sigmay'].value, max=pars[f'{self.prefix}thermal_centery'].value + 3 * pars[f'{self.prefix}thermal_sigmay'].value, ) pars[f'{self.prefix}BEC_sigmay'].set( max=5 * pars[f'{self.prefix}BEC_sigmay'].value, ) pars[f'{self.prefix}thermal_sigmax'].set( max=5 * pars[f'{self.prefix}thermal_sigmax'].value, ) return update_param_vals(pars, self.prefix, **kwargs)
class NewFitModel(Model): def __init__(self, func, independent_vars=['x'], prefix='', nan_policy='raise', **kwargs): kwargs.update({'prefix': prefix, 'nan_policy': nan_policy, 'independent_vars': independent_vars}) super().__init__(func, **kwargs) def guess(self, *args, **kwargs): return self.make_params()
lmfit_models = {'Constant': ConstantModel, 'Complex Constant': ComplexConstantModel, 'Linear': LinearModel, 'Quadratic': QuadraticModel, 'Polynomial': PolynomialModel, 'Gaussian': GaussianModel, 'Gaussian-2D': Gaussian2dModel, 'Lorentzian': LorentzianModel, 'Split-Lorentzian': SplitLorentzianModel, 'Voigt': VoigtModel, 'PseudoVoigt': PseudoVoigtModel, 'Moffat': MoffatModel, 'Pearson7': Pearson7Model, 'StudentsT': StudentsTModel, 'Breit-Wigner': BreitWignerModel, 'Log-Normal': LognormalModel, 'Damped Oscillator': DampedOscillatorModel, 'Damped Harmonic Oscillator': DampedHarmonicOscillatorModel, 'Exponential Gaussian': ExponentialGaussianModel, 'Skewed Gaussian': SkewedGaussianModel, 'Skewed Voigt': SkewedVoigtModel, 'Thermal Distribution': ThermalDistributionModel, 'Doniach': DoniachModel, 'Power Law': PowerLawModel, 'Exponential': ExponentialModel, 'Step': StepModel, 'Rectangle': RectangleModel, 'Expression': ExpressionModel, 'Gaussian With Offset':GaussianWithOffsetModel, 'Lorentzian With Offset':LorentzianWithOffsetModel, 'Expansion':ExpansionModel, 'Damping Oscillation Model':DampingOscillationModel, 'Two Gaussian-2D':TwoGaussian2dModel, }
class FitAnalyser(): """This is a class integrated all the functions to do a fit.
"""
def __init__(self, fitModel, fitDim=1, **kwargs) -> None: """Initialize function
:param fitModel: The fitting model of fit function :type fitModel: lmfit Model :param fitDim: The dimension of the fit, defaults to 1 :type fitDim: int, optional """
if isinstance(fitModel, str): self.fitModel = lmfit_models[fitModel](**kwargs) else: self.fitModel = fitModel self.fitDim = fitDim
def print_params_set_template(self, params=None): """Print a template to manually set the initial parameters of the fit
:param params: An object of Parameters class to print, defaults to None :type params: lmfit Paraemters, optional """
if params is None: params = self.fitModel.make_params() for key in params: res = "params.add(" res += "name=\"" + key + "\", " if not params[key].expr is None: res += "expr=\"" + params[key].expr +"\")" else: res += "value=" + f'{params[key].value:3g}' + ", " if str(params[key].max)=="inf": res += "max=np.inf, " else: res += "max=" + f'{params[key].max:3g}' + ", " if str(params[key].min)=="-inf": res += "min=-np.inf, " else: res += "min=" + f'{params[key].min:3g}' + ", " res += "vary=" + str(params[key].vary) + ")" print(res) def _guess_1D(self, data, x, **kwargs): """Call the guess function of the 1D fit model to guess the initial value.
:param data: The data to fit :type data: 1D numpy array :param x: The data of x axis :type x: 1D numpy array :return: The guessed initial parameters for the fit :rtype: lmfit Parameters """
return self.fitModel.guess(data=data, x=x, **kwargs) def _guess_2D(self, data, x, y, **kwargs): """Call the guess function of the 2D fit model to guess the initial value.
:param data: The flattened data to fit :type data: 1D numpy array :param x: The flattened data of x axis :type x: 1D numpy array :param y: The flattened data of y axis :type y: 1D numpy array :return: The guessed initial parameters for the fit :rtype: lmfit Parameters """
data = data.flatten(order='F') return self.fitModel.guess(data=data, x=x, y=y, **kwargs) def guess(self, dataArray, x=None, y=None, guess_kwargs={}, input_core_dims=None, dask='parallelized', vectorize=True, keep_attrs=True, daskKwargs=None, **kwargs): """Call the guess function of the fit model to guess the initial value.
:param dataArray: The data for the fit :type dataArray: xarray DataArray :param x: The name of x axis in data or the data of x axis, defaults to None :type x: str or numpy array, optional :param y: The name of y axis in data or the data of y axis, defaults to None :type y: str or numpy array, optional :param guess_kwargs: the keyworded arguments to send to the guess function, defaults to {} :type guess_kwargs: dict, optional :param input_core_dims: over write of the same argument in xarray.apply_ufunc, defaults to None :type input_core_dims: list or array like, optional :param dask: over write of the same argument in xarray.apply_ufunc,, defaults to 'parallelized' :type dask: str, optional :param vectorize: over write of the same argument in xarray.apply_ufunc, defaults to True :type vectorize: bool, optional :param keep_attrs: over write of the same argument in xarray.apply_ufunc, defaults to True :type keep_attrs: bool, optional :param daskKwargs: over write of the same argument in xarray.apply_ufunc, defaults to None :type daskKwargs: dict, optional :return: The guessed initial parameters for the fit :rtype: xarray DataArray """
kwargs.update( { "dask": dask, "vectorize": vectorize, "input_core_dims": input_core_dims, 'keep_attrs': keep_attrs,
} )
if not daskKwargs is None: kwargs.update({"dask_gufunc_kwargs": daskKwargs})
if input_core_dims is None: kwargs.update( { "input_core_dims": [['x']], } )
if x is None: if 'x' in dataArray.dims: x = dataArray['x'].to_numpy() else: if isinstance(x, str): if input_core_dims is None: kwargs.update( { "input_core_dims": [[x]], } ) x = dataArray[x].to_numpy()
if self.fitDim == 1: guess_kwargs.update( { 'x':x, } ) return xr.apply_ufunc(self._guess_1D, dataArray, kwargs=guess_kwargs, output_dtypes=[type(self.fitModel.make_params())], **kwargs ) if self.fitDim == 2: if y is None: if 'y' in dataArray.dims: y = dataArray['y'].to_numpy() if input_core_dims is None: kwargs.update( { "input_core_dims": [['x', 'y']], } ) else: if isinstance(y, str): kwargs["input_core_dims"][0] = np.append(kwargs["input_core_dims"][0], y) y = dataArray[y].to_numpy() elif input_core_dims is None: kwargs.update( { "input_core_dims": [['x', 'y']], } ) _x, _y = np.meshgrid(x, y) _x = _x.flatten() _y = _y.flatten()
# dataArray = dataArray.stack(_z=(kwargs["input_core_dims"][0][0], kwargs["input_core_dims"][0][1])) # kwargs["input_core_dims"][0] = ['_z']
guess_kwargs.update( { 'x':_x, 'y':_y, } ) return xr.apply_ufunc(self._guess_2D, dataArray, kwargs=guess_kwargs, output_dtypes=[type(self.fitModel.make_params())], **kwargs ) def _fit_1D(self, data, params, x): """Call the fit function of the 1D fit model to do the fit.
:param data: The data to fit :type data: 1D numpy array :param params: The initial paramters of the fit :type params: lmfit Parameters :param x: The data of x axis :type x: 1D numpy array :return: The result of the fit :rtype: lmfit FitResult """
return self.fitModel.fit(data=data, x=x, params=params, nan_policy='omit')
def _fit_2D(self, data, params, x, y): """Call the fit function of the 2D fit model to do the fit.
:param data: The flattened data to fit :type data: 1D numpy array :param params: The flattened initial paramters of the fit :type params: lmfit Parameters :param x: The flattened data of x axis :type x: 1D numpy array :param y: The flattened data of y axis :type y: 1D numpy array :return: The result of the fit :rtype: lmfit FitResult """
data = data.flatten(order='F') return self.fitModel.fit(data=data, x=x, y=y, params=params, nan_policy='omit')
def fit(self, dataArray, paramsArray, x=None, y=None, input_core_dims=None, dask='parallelized', vectorize=True, keep_attrs=True, daskKwargs=None, **kwargs): """Call the fit function of the fit model to do the fit.
:param dataArray: The data for the fit :type dataArray: xarray DataArray :param paramsArray: The flattened initial paramters of the fit :type paramsArray: xarray DataArray or lmfit Parameters :param x: The name of x axis in data or the data of x axis, defaults to None :type x: str or numpy array, optional :param y: The name of y axis in data or the data of y axis, defaults to None :type y: str or numpy array, optional :param input_core_dims: over write of the same argument in xarray.apply_ufunc, defaults to None, defaults to None :type input_core_dims: list or array like, optional :param dask: over write of the same argument in xarray.apply_ufunc, defaults to None, defaults to 'parallelized' :type dask: str, optional :param vectorize: over write of the same argument in xarray.apply_ufunc, defaults to None, defaults to True :type vectorize: bool, optional :param keep_attrs: over write of the same argument in xarray.apply_ufunc, defaults to None, defaults to True :type keep_attrs: bool, optional :param daskKwargs: over write of the same argument in xarray.apply_ufunc, defaults to None, defaults to None :type daskKwargs: dict, optional :return: The fit result :rtype: xarray DataArray """
kwargs.update( { "dask": dask, "vectorize": vectorize, "input_core_dims": input_core_dims, 'keep_attrs': keep_attrs, } )
if not daskKwargs is None: kwargs.update({"dask_gufunc_kwargs": daskKwargs}) if isinstance(paramsArray, type(self.fitModel.make_params())):
if input_core_dims is None: kwargs.update( { "input_core_dims": [['x']], } )
if x is None: if 'x' in dataArray.dims: x = dataArray['x'].to_numpy() else: if isinstance(x, str): if input_core_dims is None: kwargs.update( { "input_core_dims": [[x]], } ) x = dataArray[x].to_numpy()
if self.fitDim == 1: res = xr.apply_ufunc(self._fit_1D, dataArray, kwargs={'params':paramsArray,'x':x}, output_dtypes=[type(lmfit.model.ModelResult(self.fitModel, self.fitModel.make_params()))], **kwargs) if keep_attrs: res.attrs = copy.copy(dataArray.attrs) return res if self.fitDim == 2: if y is None: if 'y' in dataArray.dims: y = dataArray['y'].to_numpy() if input_core_dims is None: kwargs.update( { "input_core_dims": [['x', 'y']], } ) else: if isinstance(y, str): kwargs["input_core_dims"][0] = np.append(kwargs["input_core_dims"][0], y) y = dataArray[y].to_numpy() elif input_core_dims is None: kwargs.update( { "input_core_dims": [['x', 'y']], } ) _x, _y = np.meshgrid(x, y) _x = _x.flatten() _y = _y.flatten()
# dataArray = dataArray.stack(_z=(kwargs["input_core_dims"][0][0], kwargs["input_core_dims"][0][1]))
# kwargs["input_core_dims"][0] = ['_z']
res = xr.apply_ufunc(self._fit_2D, dataArray, kwargs={'params':paramsArray,'x':_x, 'y':_y}, output_dtypes=[type(lmfit.model.ModelResult(self.fitModel, self.fitModel.make_params()))], **kwargs) if keep_attrs: res.attrs = copy.copy(dataArray.attrs) return res
else:
if input_core_dims is None: kwargs.update( { "input_core_dims": [['x'], []], } )
if x is None: if 'x' in dataArray.dims: x = dataArray['x'].to_numpy() else: if isinstance(x, str): if input_core_dims is None: kwargs.update( { "input_core_dims": [[x], []], } ) x = dataArray[x].to_numpy()
if self.fitDim == 1: return xr.apply_ufunc(self._fit_1D, dataArray, paramsArray, kwargs={'x':x}, output_dtypes=[type(lmfit.model.ModelResult(self.fitModel, self.fitModel.make_params()))], **kwargs)
if self.fitDim == 2:
if input_core_dims is None: kwargs.update( { "input_core_dims": [['x', 'y'], []], } ) if y is None: if 'y' in dataArray.dims: y = dataArray['y'].to_numpy() else: if isinstance(y, str): y = dataArray[y].to_numpy() kwargs["input_core_dims"][0] = np.append(kwargs["input_core_dims"][0], y) _x, _y = np.meshgrid(x, y) _x = _x.flatten() _y = _y.flatten()
# dataArray = dataArray.stack(_z=(kwargs["input_core_dims"][0][0], kwargs["input_core_dims"][0][1]))
# kwargs["input_core_dims"][0] = ['_z']
return xr.apply_ufunc(self._fit_2D, dataArray, paramsArray, kwargs={'x':_x, 'y':_y}, output_dtypes=[type(lmfit.model.ModelResult(self.fitModel, self.fitModel.make_params()))], **kwargs)
def _eval_1D(self, fitResult, x): """Call the eval function of the 1D fit model to calculate the curve.
:param fitResult: The result of fit :type fitResult: lmfit FitResult :param x: The data of x axis :type x: 1D numpy array :return: The curve based on the fit result :rtype: 1D numpy array """
return self.fitModel.eval(x=x, **fitResult.best_values) def _eval_2D(self, fitResult, x, y, shape): """Call the eval function of the 2D fit model to calculate the curve.
:param fitResult: The result of fit :type fitResult: lmfit FitResult :param x: The data of x axis :type x: 1D numpy array :param y: The flattened data of y axis :type y: 1D numpy array :param shape: The desired shape for output :type shape: list, tuple or array like :return: The curve based on the fit result :rtype: 2D numpy array """
res = self.fitModel.eval(x=x, y=y, **fitResult.best_values) return res.reshape(shape, order='F')
def eval(self, fitResultArray, x=None, y=None, output_core_dims=None, prefix="", dask='parallelized', vectorize=True, daskKwargs=None, **kwargs): """Call the eval function of the fit model to calculate the curve.
:param fitResultArray: The result of fit :type fitResultArray: xarray DataArray :param x: The name of x axis in data or the data of x axis, defaults to None :type x: str or numpy array, optional :param y: The name of y axis in data or the data of y axis, defaults to None :type y: str or numpy array, optional :param output_core_dims: over write of the same argument in xarray.apply_ufunc, defaults to None :type output_core_dims: list, optional :param prefix: prefix str of the fit model, defaults to "" :type prefix: str, optional :param dask: over write of the same argument in xarray.apply_ufunc, defaults to 'parallelized' :type dask: str, optional :param vectorize: over write of the same argument in xarray.apply_ufunc, defaults to True :type vectorize: bool, optional :param daskKwargs: over write of the same argument in xarray.apply_ufunc, defaults to None :type daskKwargs: dict, optional :return: The curve based on the fit result :rtype: xarray """
kwargs.update( { "dask": dask, "vectorize": vectorize, "output_core_dims": output_core_dims, } )
if daskKwargs is None: daskKwargs = {}
if self.fitDim == 1:
if output_core_dims is None: kwargs.update( { "output_core_dims": prefix+'x', } ) output_core_dims = [prefix+'x'] daskKwargs.update( { 'output_sizes': { output_core_dims[0]: np.size(x), }, 'meta': np.ndarray((0,0), dtype=float) } )
kwargs.update( { "dask_gufunc_kwargs": daskKwargs, } )
res = xr.apply_ufunc(self._eval_1D, fitResultArray, kwargs={"x":x}, **kwargs) return res.assign_coords({prefix+'x':np.array(x)})
if self.fitDim == 2: if output_core_dims is None: kwargs.update( { "output_core_dims": [[prefix+'x', prefix+'y']], } ) output_core_dims = [prefix+'x', prefix+'y']
daskKwargs.update( { 'output_sizes': { output_core_dims[0]: np.size(x), output_core_dims[1]: np.size(y), }, 'meta': np.ndarray((0,0), dtype=float) }, ) kwargs.update( { "dask_gufunc_kwargs": daskKwargs, } )
_x, _y = np.meshgrid(x, y) _x = _x.flatten() _y = _y.flatten()
res = xr.apply_ufunc(self._eval_2D, fitResultArray, kwargs={"x":_x, "y":_y, "shape":(len(x), len(y))}, **kwargs) return res.assign_coords({prefix+'x':np.array(x), prefix+'y':np.array(y)})
def _get_fit_value_single(self, fitResult, key): """get value of one single parameter from fit result
:param fitResult: The result of the fit :type fitResult: lmfit FitResult :param key: The name of the parameter :type key: str :return: The vaule of the parameter :rtype: float """
return fitResult.params[key].value
def _get_fit_value(self, fitResult, params): """get value of parameters from fit result
:param fitResult: The result of the fit :type fitResult: lmfit FitResult :param params: A list of the name of paramerters to read :type params: list or array like :return: The vaule of the parameter :rtype: 1D numpy array """
func = np.vectorize(self._get_fit_value_single) res = tuple( func(fitResult, key) for key in params )
return res
def get_fit_value(self, fitResult, dask='parallelized', **kwargs): """get value of parameters from fit result
:param fitResult: The result of the fit :type fitResult: lmfit FitResult :param dask: over write of the same argument in xarray.apply_ufunc, defaults to 'parallelized' :type dask: str, optional :return: The vaule of the parameter :rtype: xarray DataArray """
firstIndex = { key: fitResult[key][0] for key in fitResult.dims } firstFitResult = fitResult.sel(firstIndex).item()
params = list(firstFitResult.params.keys())
output_core_dims=[ [] for _ in range(len(params))]
kwargs.update( { "dask": dask, "output_core_dims": output_core_dims, } )
value = xr.apply_ufunc(self._get_fit_value, fitResult, kwargs=dict(params=params), **kwargs)
value = xr.Dataset( data_vars={ params[i]: value[i] for i in range(len(params)) }, attrs=fitResult.attrs )
return value
def _get_fit_std_single(self, fitResult, key): """get standard deviation of one single parameter from fit result
:param fitResult: The result of the fit :type fitResult: lmfit FitResult :param key: The name of the parameter :type key: str :return: The vaule of the parameter :rtype: float """
return fitResult.params[key].stderr
def _get_fit_std(self, fitResult, params): """get standard deviation of parameters from fit result
:param fitResult: The result of the fit :type fitResult: lmfit FitResult :param params: A list of the name of paramerters to read :type params: list or array like :return: The vaule of the parameter :rtype: 1D numpy array """
func = np.vectorize(self._get_fit_std_single) res = tuple( func(fitResult, key) for key in params )
return res
def get_fit_std(self, fitResult, dask='parallelized', **kwargs): """get standard deviation of parameters from fit result
:param fitResult: The result of the fit :type fitResult: lmfit FitResult :param dask: over write of the same argument in xarray.apply_ufunc, defaults to 'parallelized' :type dask: str, optional :return: The vaule of the parameter :rtype: xarray DataArray """
firstIndex = { key: fitResult[key][0] for key in fitResult.dims } firstFitResult = fitResult.sel(firstIndex).item()
params = list(firstFitResult.params.keys())
output_core_dims=[ [] for _ in range(len(params))]
kwargs.update( { "dask": dask, "output_core_dims": output_core_dims, } )
value = xr.apply_ufunc(self._get_fit_std, fitResult, kwargs=dict(params=params), **kwargs)
value = xr.Dataset( data_vars={ params[i]: value[i] for i in range(len(params)) }, attrs=fitResult.attrs )
return value
def _get_fit_full_result_single(self, fitResult, key): """get the full result of one single parameter from fit result
:param fitResult: The result of the fit :type fitResult: lmfit FitResult :param key: The name of the parameter :type key: str :return: The vaule of the parameter :rtype: float """
if not fitResult.params[key].value is None: value = fitResult.params[key].value else: value = np.nan if not fitResult.params[key].stderr is None: std = fitResult.params[key].stderr else: std = np.nan return ufloat(value, std)
def _get_fit_full_result(self, fitResult, params): """get the full result of parameters from fit result
:param fitResult: The result of the fit :type fitResult: lmfit FitResult :param params: A list of the name of paramerters to read :type params: list or array like :return: The vaule of the parameter :rtype: 1D numpy array """
func = np.vectorize(self._get_fit_full_result_single) res = tuple( func(fitResult, key) for key in params )
return res
def get_fit_full_result(self, fitResult, dask='parallelized', **kwargs): """get the full result of parameters from fit result
:param fitResult: The result of the fit :type fitResult: lmfit FitResult :param dask: over write of the same argument in xarray.apply_ufunc, defaults to 'parallelized' :type dask: str, optional :return: The vaule of the parameter :rtype: xarray DataArray """
firstIndex = { key: fitResult[key][0] for key in fitResult.dims } firstFitResult = fitResult.sel(firstIndex).item()
params = list(firstFitResult.params.keys())
output_core_dims=[ [] for _ in range(len(params))]
kwargs.update( { "dask": dask, "output_core_dims": output_core_dims, } )
value = xr.apply_ufunc(self._get_fit_full_result, fitResult, kwargs=dict(params=params), **kwargs)
value = xr.Dataset( data_vars={ params[i]: value[i] for i in range(len(params)) }, attrs=fitResult.attrs )
return value
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