elli.fitting package

Submodules

elli.fitting.decorator module

Abstract base class for Decorator functions for convenient fitting

class elli.fitting.decorator.FitDecorator

Bases: abc.ABC

The abstract base class for fitting decorators. Providing features for fit, undo and redo buttons.

abstract fit(method='')

Execute lmfit with the current fitting parameters

Parameters

method (str, optional) – The fitting method to use. Any method supported by scipys curve_fit is allowed. Defaults to ‘leastsq’.

Returns

The fitting result

Return type

Result

fit_button_clicked()

Fit and update plot after the fit button has been clicked

Parameters

selected (dict) – Dict containing the current widget information of the selection dropdown.

abstract get_model_data(params=None, append_exp_data=False)

Gets the data from the provided model with the provided parameters. If no parameters are provided, the fitted parameters are used (which default to the initial parameters if no fit has been triggered).

Parameters

• params (Parameters, optional) – The parameters to calculate the model with. If not provided, the fitted parameters are used. Defaults to None.

• append_exp_data (bool, optional) – Appends the experimental data if set to True. Defaults to False.

Returns

The model results

Return type

pd.DataFrame

re_undo_button_clicked(button)

Redo or undo an operation on the paramters history object

Parameters

button (widgets.Button) – The button instance, which triggered the event.

reset_to_init_params()

Resets the parameters to the initial values

set_vary_param(change)

to_csv(fname, params=None, append_exp_data=False, *args, **kwargs)

Saves the current model to csv. This is just a wrapper to pandas Dataframe and any argument to pandas to_csv may be passed as function arguments.

Parameters

• fname (str) – The file name to save the data to.

• params (Parameters, optional) – The parameters to calculate the model with. If not provided, the fitted parameters are used. Defaults to None.

• append_exp_data (bool, optional) – Appends the experimental data if set to True. Defaults to False.

update_params(change)

Update plot after a change of fitting parameters

Parameters

• change (dict) – A dictionary containing the ipywidgets change event

• selected (dict) – The selected value of the data display dropdown widget

abstract update_selection(change=None)

Update plot after selection of displayed data

Parameters

change (dict, optional) – A dictionary containing the ipywidgets change event

update_widgets()

Updates the widget values according to the current parameters.

elli.fitting.decorator_mmatrix module

Decorator functions for convenient fitting of Mueller matrices

class elli.fitting.decorator_mmatrix.FitMuellerMatrix(exp_mm, params, model, **kwargs)

Bases: elli.fitting.decorator.FitDecorator

A class to fit mueller matrices to experimental data

Intialize the mueller matrix fitting class

Parameters

• exp_mm (pd.DataFrame) – The dataframe containing an experimental mueller matrix. It should contain 16 columns with labels Mxy, where xy are the matrix positions.

• params (Parameters) – Fitting start parameters

• model (Callable[[npt.NDArray, Parameters], Result]) – A function taking wavelengths as first parameter and fitting parameters as second, which returns a pyEllis Result object. This function contains the actual model which should be fitted

• **display_single (bool) – Returns a figure containing a single graph, if set to true. Returns a grid of figures otherwise.

• **sharex (bool) – Ties the zoom of the x-axes together for grid view.

• **full_scale (bool) – Sets the y-axis scale to [-1, 1] if set to True.

create_widgets()

Create ipywidgets for parameter estimation

fit(method='leastsq')

Execute lmfit with the current fitting parameters

Parameters

method (str, optional) – The fitting method to use. Any method supported by scipys curve_fit is allowed. Defaults to ‘leastsq’.

Returns

The fitting result

Return type

Result

fit_function(params, lbda, mueller_matrix)

The fit function to minimize the fitting problem

Parameters

• params (Parameters) – The lmfit fitting Parameters to construct the simulation

• lbda (npt.NDArray) – Wavelengths in nm

• mueller_matrix (pd.DataFrame) – The experimental data to compare to the fitted model

Returns

Residual between the calculation

with current parameters and experimental data

Return type

npt.NDArray

get_model_data(params=None, append_exp_data=False)

Gets the data from the provided model with the provided parameters. If no parameters are provided, the fitted parameters are used (which default to the initial parameters if no fit has been triggered).

Parameters

• params (Parameters, optional) – The parameters to calculate the model with. If not provided, the fitted parameters are used. Defaults to None.

• append_exp_data (bool, optional) – Appends the experimental data if set to True. Defaults to False.

Returns

The model results

Return type

pd.DataFrame

plot(**kwargs)

Plot the fit results

Parameters

• **display_single (bool) – Returns a figure containing a single graph, if set to true. Returns a grid of figures otherwise.

• **sharex (bool) – Ties the zoom of the x-axes together for grid view.

• **full_scale (bool) – Sets the y-axis scale to [-1, 1] if set to True.

Returns

The figure containing the data

Return type

go.Figure

plot_residual(**kwargs)

Plots the residual between the fit and the experimental data

Parameters

• **display_single (bool) – Returns a figure containing a single graph, if set to true. Returns a grid of figures otherwise.

• **sharex (bool) – Ties the zoom of the x-axes together for grid view.

• **full_scale (bool) – Sets the y-axis scale to [-1, 1] if set to True.

Returns

The figure containing the data

Return type

go.Figure

update_residual(change)

update_selection(_=None)

Update plot after selection of displayed data

Parameters

_ (dict, optional) – No function. Just for compliance with ABC.

elli.fitting.decorator_mmatrix.fit_mueller_matrix(exp_mm, params, **kwargs)

A parameters decorator for fitting mueller matrices. Displays an ipywidget float box for each fitting parameter and an interactive plot to estimate parameters.

Parameters

• exp_mm (pd.DataFrame) – The dataframe containing an experimental mueller matrix. It should contain 16 columns with labels Mxy, where xy are the matrix positions.

• params (Parameters) – Fitting start parameters

• **display_single (bool) – Returns a figure containing a single graph, if set to true. Returns a grid of figures otherwise.

• **sharex (bool) – Ties the zoom of the x-axes together for grid view.

• **full_scale (bool) – Sets the y-axis scale to [-1, 1] if set to True.

Returns

A function taking wavelengths as first parameter and fitting parameters as second, which returns a pyEllis Result object. This function contains the actual model which should be fitted and is automatically provided when used as a decorator.

Return type

Callable[[npt.NDArray, Parameters], Result]

elli.fitting.decorator_mmatrix.mmatrix_to_dataframe(exp_df, mueller_matrix, identifier=None)

Reshape a numpy 4x4 array containing mueller matrix elements to a dataframe with columns Mxy. The index labels for each column are taken from the provided exp_df.

Parameters

• exp_df (pd.DataFrame) – The experimental dataframe providing the index and columns for the newly generated dataframe.

• mueller_matrix (npt.NDArray) – Data to be reshaped into a dataframe

• identifier (str, optional) – An identifier to append to each column name, in the form Mxy_<identifier>, where Mxy is the old column name. Defaults to None.

Returns

Contains the data from mueller_matrix in the shape of exp_df

Return type

pd.DataFrame

elli.fitting.decorator_psi_delta module

Decorator functions for convenient fitting

class elli.fitting.decorator_psi_delta.FitRho(exp_data, params, model, angle=70)

Bases: elli.fitting.decorator.FitDecorator

A class to fit psi/delta or rho based ellipsometry data with two degress of freedom

Intialize the psi/delta fitting class

Parameters

• exp_data (pd.DataFrame) – The dataframe containing an experimental mueller matrix. It should contain 2 columns with labels Ψ and Δ.

• params (Parameters) – Fitting start parameters

• model (Callable[[npt.NDArray, Parameters], Result]) – A function taking wavelengths as first parameter and fitting parameters as second, which returns a pyEllis Result object. This function contains the actual model which should be fitted.

• angle (float, optional) – The angle of incident of the measurement. Used to calculate the Pseudo-Dielectric function. Defaults to 70.

create_widgets()

Create ipywidgets for parameter estimation

fit(method='leastsq')

Execute lmfit with the current fitting parameters

Parameters

method (str, optional) – The fitting method to use. Any method supported by scipys curve_fit is allowed. Defaults to ‘leastsq’.

Returns

The fitting result

Return type

Result

fit_function(params, lbda, rhor, rhoi)

The fit function to minimize the fitting problem

Parameters

• params (Parameters) – The lmfit fitting Parameters to construct the simulation

• lbda (npt.NDArray) – Wavelengths in nm

• rhor (npt.NDArray) – The real part of the experimental rho

• rhoi (npt.NDArray) – The imaginary part of the experimental rho

Returns

Residual between the calculation with current parameters and experimental data

Return type

npt.NDArray

get_model_data(params=None, repr='psi-delta', append_exp_data=False)

Gets the data from the provided modle with the provided parameters. If no parameters are provided, the fitted parameters are used (which default to the initial parameters if no fit has been triggered).

Parameters

• params (Parameters, optional) – The parameters to calculate the model with. If not provided, the fitted parameters are used. Defaults to None.

• repr (str, optional) – The representation of the model and experiment data. Valid values are ‘psi-delta’ or ‘rho’. Defaults to ‘psi-delta’.

• append_exp_data (bool, optional) – Appends the experimental data if set to True. Defaults to False.

Raises

ValueError – Raised if the representation is not a valid value.

Returns

The model results

Return type

pd.DataFrame

plot()

Plot the fit results as Psi/Delta

plot_rho()

Plot the fit results as Rho

set_pseudo_diel(update_exp=False, update_names=False)

Sets Plot to Pseudo Dielectric function values

Parameters

• update_exp (bool, optional) – Flag to change the experimental data as well. Defaults to False.

• update_names (bool, optional) – Flag to change the label names. Defaults to False.

set_psi_delta(update_exp=False, update_names=False)

Sets Plot to Psi/Delta values

Parameters

• update_exp (bool, optional) – Flag to change the experimental data as well. Defaults to False.

• update_names (bool, optional) – Flag to change the label names. Defaults to False.

set_residual(update_exp=False, update_names=False)

Sets plots to residual values

Parameters

• update_exp (bool, optional) – Flag to change the experimental data as well. Defaults to False.

• update_names (bool, optional) – Flag to change the label names. Defaults to False.

set_rho(update_exp=False, update_names=False)

Sets Plot to Rho values

Parameters

• update_exp (bool, optional) – Flag to change the experimental data as well. Defaults to False.

• update_names (bool, optional) – Flag to change the label names. Defaults to False.

update_selection(change=None)

Update plot after selection of displayed data

Parameters

change (dict, optional) – A dictionary containing the ipywidgets change event

elli.fitting.decorator_psi_delta.fit(exp_data, params, angle=70)

A parameters decorator for fitting psi/delta valus. Displays an ipywidget float box for each fitting parameter and an interactive plot to estimate parameters.

Parameters

• exp_data (pd.DataFrame) – The dataframe containing an experimental mueller matrix. It should contain 2 columns with labels Ψ and Δ.

• params (Parameters) – Fitting start parameters

• angle (float, optional) – The angle of incident of the measurement. Used to calculate the Pseudo-Dielectric function. Defaults to 70.

Returns

fitting parameters as second, which returns a pyEllis Result object. This function contains the actual model which should be fitted and is automatically provided when used as a decorator.

Return type

Callable[[npt.NDArray, Parameters], Result]

elli.fitting.params_hist module

ParmsHist provides a wrapper around lmfit.Parameters to keep track of the changes made to the parameters.

class elli.fitting.params_hist.ParamsHist

Bases: lmfit.parameter.Parameters

A wrapper around lmfit.Parameters to keep track of the changes made to the parameters.

Parameters

usersyms (dict, optional) – Dictionary of symbols to add to the asteval.Interpreter (default is None).

clear_history()

Clears the parameters history

commit()

Saves the current parameter set to history.

property history

Gets the entire history

Returns

The history

Return type

List[Parameters]

property history_len

The current length of the history

Returns

The length of the history

Return type

int

property max_history_len

The maximum length of the history

Returns

The maximum length of the history

Return type

int

pop()

Gets to the previous history version and deletes the current element.

revert(hist_pos)

Reverts to an older history version and keeps the entire history.

Parameters

hist_pos (int) – The history position to revert to.

tracked_add(*args, **kwargs)

Adds a parameter and keeps track of the change in history

update_params(parameters)

Updates the current paramters from a lmfit parameters object.

Parameters

parameters (lmfit.Parameters) – The lmfit paramters object to update the values from.

update_value(key, value)

Updates a parameter and keeps track of the change in history

Parameters

• key (str) – The key to be updated

• value (float) – The value the key should be updated to

Module contents