API Documentation¶

API reference for the FOOOF module.

Table of Contents¶

Model Objects ¶

Objects that manage data and fit the model to parameterize neural power spectra.

FOOOF Object ¶

The FOOOF object is the base object for the model, and can be used to fit individual power spectra.

FOOOF([peak_width_limits, max_n_peaks, ...])

Model a physiological power spectrum as a combination of aperiodic and periodic components.

FOOOFGroup Object ¶

The FOOOFGroup object allows for parameterizing groups of power spectra.

FOOOFGroup(*args, **kwargs)

Model a group of power spectra as a combination of aperiodic and periodic components.

Object Utilities ¶

Functions to manipulate, examine and analyze FOOOF objects, and related utilities.

`compare_info`(fooof_lst, aspect)	Compare a specified aspect of FOOOF objects across instances.
`average_fg`(fg, bands[, avg_method, regenerate])	Average across model fits in a FOOOFGroup object.
`average_reconstructions`(fg[, avg_method])	Average across model reconstructions for a group of power spectra.
`combine_fooofs`(fooofs)	Combine a group of FOOOF and/or FOOOFGroup objects into a single FOOOFGroup object.

fit_fooof_3d(fg, freqs, power_spectra[, ...])

Fit FOOOF models across a 3d array of power spectra.

Data Objects ¶

Objects to manage frequency bands, model information, and simulation parameters.

Bands Object ¶

An object to handle frequency band definitions.

Bands([input_bands])

Frequency band definitions.

Model Information ¶

Objects to store settings, metadata and results for power spectrum models.

`FOOOFSettings`(peak_width_limits, ...)	User defined settings for the fitting algorithm.
`FOOOFRunModes`(debug, check_freqs, check_data)	Checks performed and errors raised by the model.
`FOOOFMetaData`(freq_range, freq_res)	Metadata information about a power spectrum.
`FOOOFResults`(aperiodic_params, peak_params, ...)	Model results from parameterizing a power spectrum.

Simulation Parameters ¶

Object to store information about simulated data.

SimParams(aperiodic_params, periodic_params, nlv)

Parameters that define a simulated power spectrum.

Analyze Model Results ¶

Functions to analyze power spectrum models and the results parameters / components.

Analyze Model Errors ¶

Functions for analyzing the error of model fits.

Object Inputs

The following functions take in FOOOF objects directly, which is the recommended approach.

`compute_pointwise_error_fm`(fm[, ...])	Calculate the frequency by frequency error of a model fit from a FOOOF object.
`compute_pointwise_error_fg`(fg[, ...])	Calculate the frequency by frequency error of model fits from a FOOOFGroup object.

Array Inputs

The following functions operate on arrays of models and data, which may be useful for more custom work-flows.

compute_pointwise_error(model, data)

Calculate point-wise error between original data and a model fit of that data.

Analyze Periodic Components ¶

Functions for analyzing the periodic components of model fits.

Object Inputs

The following functions take in FOOOF objects directly, which is the typical use case.

`get_band_peak_fm`(fm, band[, select_highest, ...])	Extract peaks from a band of interest from a FOOOF object.
`get_band_peak_fg`(fg, band[, threshold, ...])	Extract peaks from a band of interest from a FOOOFGroup object.

Array Inputs

The following functions operate on arrays of peak parameters, which may be useful for more custom work-flows.

`get_band_peak`(peak_params, band[, ...])	Extract peaks within a given band of interest.
`get_band_peak_group`(peak_params, band, n_fits)	Extract peaks within a given band of interest, from peaks from a group fit.
`get_highest_peak`(peak_params)	Extract the highest power peak.
`threshold_peaks`(peak_params, threshold[, param])	Extract peaks that are above a given threshold value.

Simulation Code ¶

Code & utilities for simulating power spectra.

Generate Power Spectra ¶

Functions for simulating neural power spectra.

`gen_freqs`(freq_range, freq_res)	Generate a frequency vector.
`gen_power_spectrum`(freq_range, ...[, nlv, ...])	Generate a simulated power spectrum.
`gen_group_power_spectra`(n_spectra, ...[, ...])	Generate a group of simulated power spectra.

Manage Parameters ¶

Functions and objects for managing parameters for simulated power spectra.

`Stepper`(start, stop, step)	Object for stepping across parameter values.
`param_iter`(params)	Create a generator to iterate across parameter ranges.
`param_sampler`(params[, probs])	Create a generator to sample randomly from possible parameters.
`param_jitter`(params, jitters)	Create a generator that adds jitter to parameter definitions.
`update_sim_ap_params`(sim_params, delta[, field])	Update the aperiodic parameter definition in a SimParams object.

Transform Power Spectra ¶

Functions for transforming power spectra.

`translate_spectrum`(power_spectrum, delta_offset)	Translate a spectrum, changing the offset value.
`translate_sim_spectrum`(power_spectrum, ...)	Translate a simulated spectrum, updating a SimParams object.
`rotate_spectrum`(freqs, power_spectrum, ...)	Rotate a power spectrum about a frequency point, changing the aperiodic exponent.
`rotate_sim_spectrum`(freqs, power_spectrum, ...)	Rotate a simulated power spectrum, updating a SimParams object.
`compute_rotation_offset`(delta_exponent, ...)	Calculate the change in offset from a given rotation.
`compute_rotation_frequency`(delta_exponent_b, ...)	Calculate the rotation frequency between two rotated power spectra.

Simulation Utilities ¶

Utilities for simulating power spectra.

set_random_seed([seed_value])

Set the random seed value.

Plotting Functions ¶

Visualizations.

Plot Power Spectra ¶

Plots for visualizing power spectra.

plot_spectra(freqs, power_spectra[, ...])

Plot one or multiple power spectra.

Plots for plotting power spectra with shaded regions.

`plot_spectra_shading`(freqs, power_spectra, ...)	Plot one or multiple power spectra with a shaded frequency region (or regions).
`plot_spectra_yshade`(freqs, power_spectra[, ...])	Plot standard deviation or error as a shaded region around the mean spectrum.

Plot Model Properties & Parameters ¶

Plots for visualizing periodic parameters and model components.

`plot_peak_fits`(peaks[, freq_range, colors, ...])	Plot reconstructions of model peak fits.
`plot_peak_params`(peaks[, freq_range, ...])	Plot peak parameters as dots representing center frequency, power and bandwidth.

Plots for visualizing aperiodic parameters and model components.

`plot_aperiodic_fits`(aps, freq_range[, ...])	Plot reconstructions of model aperiodic fits.
`plot_aperiodic_params`(aps[, colors, labels, ax])	Plot aperiodic parameters as dots representing offset and exponent value.

Plots for visualizing model error.

plot_spectral_error(freqs, error[, shade, ...])

Plot frequency by frequency error values.

Plot FOOOF Objects ¶

Plots for visualizing models from FOOOF objects. Note that these are the same plotting functions that can be called from FOOOF objects directly.

plot_fm(fm[, plot_peaks, plot_aperiodic, ...])

Plot the power spectrum and model fit results from a FOOOF object.

plot_fg(fg[, save_fig, file_name, file_path])

Plot a figure with subplots visualizing the parameters from a FOOOFGroup object.

Annotated Plots ¶

Annotated plots that describe the model and fitting process.

`plot_annotated_model`(fm[, plt_log, ...])	Plot a an annotated power spectrum and model, from a FOOOF object.
`plot_annotated_peak_search`(fm)	Plot a series of plots illustrating the peak search from a flattened spectrum.

Plot Utilities & Styling ¶

Plot related utilies for styling and managing plots.

check_style_options()

Check the list of valid style arguments that can be passed into plot functions.

`check_ax`(ax[, figsize])	Check whether a figure axes object is defined, and define if not.
`recursive_plot`(data, plot_function, ax, **kwargs)	A utility to recursively plot sets of data.
`save_figure`(file_name[, file_path, close])	Save out a figure.

Utilities ¶

Utility functions and objects.

Data Utilities ¶

Utilities for working with data.

`trim_spectrum`(freqs, power_spectra, f_range)	Extract a frequency range from power spectra.
`interpolate_spectrum`(freqs, powers, interp_range)	Interpolate a frequency region in a power spectrum.
`interpolate_spectra`(freqs, powers, interp_range)	Interpolate a frequency region across a group of power spectra.
`subsample_spectra`(spectra, selection[, ...])	Subsample a group of power spectra.

Parameter Utilities ¶

Utilities for working with parameters

compute_knee_frequency(knee, exponent)

Compute the frequency value of the knee given the aperiodic parameter values.

Input / Output (IO)¶

`load_fooof`(file_name[, file_path, regenerate])	Load a FOOOF file into a FOOOF object.
`load_fooofgroup`(file_name[, file_path])	Load data from file into a FOOOFGroup object.

Methods Reports ¶

Utilities to creating methods reports.

`methods_report_info`([fooof_obj, concise])	Prints out a report of information required for methods reporting.
`methods_report_text`([fooof_obj])	Prints out a text template of methods reporting information.