fooof.FOOOFGroup¶

class fooof.FOOOFGroup(*args, **kwargs)[source]¶

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

WARNING: FOOOF expects frequency and power values in linear space.

Passing in logged frequencies and/or power spectra is not detected, and will silently produce incorrect results.

Parameters

peak_width_limitstuple of (float, float), optional, default: (0.5, 12.0): Limits on possible peak width, in Hz, as (lower_bound, upper_bound).
max_n_peaksint, optional, default: inf: Maximum number of peaks to fit.
min_peak_heightfloat, optional, default: 0: Absolute threshold for detecting peaks. This threshold is defined in absolute units of the power spectrum (log power).
peak_thresholdfloat, optional, default: 2.0: Relative threshold for detecting peaks. This threshold is defined in relative units of the power spectrum (standard deviation).
aperiodic_mode{‘fixed’, ‘knee’}: Which approach to take for fitting the aperiodic component.
verbosebool, optional, default: True: Verbosity mode. If True, prints out warnings and general status updates.

Notes

Commonly used abbreviations used in this module include: CF: center frequency, PW: power, BW: Bandwidth, AP: aperiodic
Input power spectra must be provided in linear scale. Internally they are stored in log10 scale, as this is what the model operates upon.
Input power spectra should be smooth, as overly noisy power spectra may lead to bad fits. For example, raw FFT inputs are not appropriate. Where possible and appropriate, use longer time segments for power spectrum calculation to get smoother power spectra, as this will give better model fits.
The gaussian params are those that define the gaussian of the fit, where as the peak params are a modified version, in which the CF of the peak is the mean of the gaussian, the PW of the peak is the height of the gaussian over and above the aperiodic component, and the BW of the peak, is 2*std of the gaussian (as ‘two sided’ bandwidth).
The FOOOFGroup object inherits from the FOOOF object. As such it also has data attributes (power_spectrum & fooofed_spectrum_), and parameter attributes (aperiodic_params_, peak_params_, gaussian_params_, r_squared_, error_) which are defined in the context of individual model fits. These attributes are used during the fitting process, but in the group context do not store results post-fitting. Rather, all model fit results are collected and stored into the group_results attribute. To access individual parameters of the fit, use the get_params method.

Attributes

freqs1d array: Frequency values for the power spectra.
power_spectra2d array: Power values for the group of power spectra, as [n_power_spectra, n_freqs]. Power values are stored internally in log10 scale.
freq_rangelist of [float, float]: Frequency range of the power spectra, as [lowest_freq, highest_freq].
freq_resfloat: Frequency resolution of the power spectra.
group_resultslist of FOOOFResults: Results of FOOOF model fit for each power spectrum.
has_databool: Indicator for if the object contains data.
has_modelbool: Indicator for if the object contains model fits.
n_peaks_int: How many peaks were fit for each model.
n_null_int: How many model fits are null.
null_inds_list of int: The indices for model fits that are null.

__init__(*args, **kwargs)[source]¶: Initialize object with desired settings.

Methods

`__init__`(args, *kwargs)	Initialize object with desired settings.
`add_data`(freqs, power_spectra[, freq_range])	Add data (frequencies and power spectrum values) to the current object.
`add_meta_data`(fooof_meta_data)	Add data information into object from a FOOOFMetaData object.
`add_results`(fooof_result)	Add results data into object from a FOOOFResults object.
`add_settings`(fooof_settings)	Add settings into object from a FOOOFSettings object.
`copy`()	Return a copy of the current object.
`drop`(inds)	Drop one or more model fit results from the object.
`fit`([freqs, power_spectra, freq_range, ...])	Fit a group of power spectra.
`get_data`([component, space])	Get a data component.
`get_fooof`(ind[, regenerate])	Get a FOOOF object for a specified model fit.
`get_group`(inds)	Get a FOOOFGroup object with the specified sub-selection of model fits.
`get_meta_data`()	Return data information from the current object.
`get_model`([component, space])	Get a model component.
`get_params`(name[, col])	Return model fit parameters for specified feature(s).
`get_results`()	Return the results run across a group of power spectra.
`get_run_modes`()	Return run modes of the current object.
`get_settings`()	Return user defined settings of the current object.
`load`(file_name[, file_path])	Load FOOOFGroup data from file.
`plot`([save_fig, file_name, file_path])	Plot a figure with subplots visualizing the parameters from a FOOOFGroup object.
`print_report_issue`([concise])	Prints instructions on how to report bugs and/or problematic fits.
`print_results`([concise])	Print out FOOOFGroup results.
`print_settings`([description, concise])	Print out the current settings.
`report`([freqs, power_spectra, freq_range, ...])	Fit a group of power spectra and display a report, with a plot and printed results.
`save`(file_name[, file_path, append, ...])	Save out results and/or settings from FOOOFGroup object.
`save_model_report`(index, file_name[, ...])	"Save out an individual model report for a specified model fit.
`save_report`(file_name[, file_path, add_settings])	Generate and save out a PDF report for a group of power spectrum models.
`set_check_data_mode`(check_data)	Set check data mode, which controls if an error is raised if NaN or Inf data are added.
`set_check_modes`([check_freqs, check_data])	Set check modes, which controls if an error is raised based on check on the inputs.
`set_debug_mode`(debug)	Set debug mode, which controls if an error is raised if model fitting is unsuccessful.
`set_run_modes`(debug, check_freqs, check_data)	Simultaneously set all run modes.
`to_df`(peak_org)	Convert and extract the model results as a pandas object.

Attributes

`has_data`	Indicator for if the object contains data.
`has_model`	Indicator for if the object contains model fits.
`n_null_`	How many model fits are null.
`n_peaks_`	How many peaks were fit for each model.
`null_inds_`	The indices for model fits that are null.

add_data(freqs, power_spectra, freq_range=None)[source]¶

Add data (frequencies and power spectrum values) to the current object.

Parameters

freqs1d array: Frequency values for the power spectra, in linear space.
power_spectra2d array, shape=[n_power_spectra, n_freqs]: Matrix of power values, in linear space.
freq_rangelist of [float, float], optional: Frequency range to restrict power spectra to. If not provided, keeps the entire range.

Notes

If called on an object with existing data and/or results these will be cleared by this method call.

add_meta_data(fooof_meta_data)¶

Add data information into object from a FOOOFMetaData object.

Parameters

fooof_meta_dataFOOOFMetaData: A meta data object containing meta data information.

add_results(fooof_result)¶

Add results data into object from a FOOOFResults object.

Parameters

fooof_resultFOOOFResults: A data object containing the results from fitting a FOOOF model.

add_settings(fooof_settings)¶

Add settings into object from a FOOOFSettings object.

Parameters

fooof_settingsFOOOFSettings: A data object containing the settings for a FOOOF model.

copy()¶: Return a copy of the current object.

drop(inds)[source]¶

Drop one or more model fit results from the object.

Parameters

indsint or array_like of int or array_like of bool: Indices to drop model fit results for. If a boolean mask, True indicates indices to drop.

Notes

This method sets the model fits as null, and preserves the shape of the model fits.

fit(freqs=None, power_spectra=None, freq_range=None, n_jobs=1, progress=None)[source]¶

Fit a group of power spectra.

Parameters

freqs1d array, optional: Frequency values for the power_spectra, in linear space.
power_spectra2d array, shape: [n_power_spectra, n_freqs], optional: Matrix of power spectrum values, in linear space.
freq_rangelist of [float, float], optional: Desired frequency range to run FOOOF on. If not provided, fits the entire given range.
n_jobsint, optional, default: 1: Number of jobs to run in parallel. 1 is no parallelization. -1 uses all available cores.
progress{None, ‘tqdm’, ‘tqdm.notebook’}, optional: Which kind of progress bar to use. If None, no progress bar is used.

Notes

Data is optional, if data has already been added to the object.

get_data(component='full', space='log')¶

Get a data component.

Parameters

component{‘full’, ‘aperiodic’, ‘peak’}

Which data component to return.: ‘full’ - full power spectrum ‘aperiodic’ - isolated aperiodic data component ‘peak’ - isolated peak data component

space{‘log’, ‘linear’}

Which space to return the data component in.: ‘log’ - returns in log10 space. ‘linear’ - returns in linear space.

Returns

output1d array: Specified data component, in specified spacing.

Notes

The ‘space’ parameter doesn’t just define the spacing of the data component values, but rather defines the space of the additive data definition such that power_spectrum = aperiodic_component + peak_component. With space set as ‘log’, this combination holds in log space. With space set as ‘linear’, this combination holds in linear space.

get_fooof(ind, regenerate=True)[source]¶

Get a FOOOF object for a specified model fit.

Parameters

indint: The index of the FOOOFResults in FOOOFGroup.group_results to load.
regeneratebool, optional, default: False: Whether to regenerate the model fits from the given fit parameters.

Returns

fmFOOOF: The FOOOFResults data loaded into a FOOOF object.

get_group(inds)[source]¶

Get a FOOOFGroup object with the specified sub-selection of model fits.

Parameters

indsarray_like of int or array_like of bool: Indices to extract from the object. If a boolean mask, True indicates indices to select.

Returns

fgFOOOFGroup: The requested selection of results data loaded into a new FOOOFGroup object.

get_meta_data()¶

Return data information from the current object.

Returns

FOOOFMetaData: Object containing meta data from the current object.

get_model(component='full', space='log')¶

Get a model component.

Parameters

component{‘full’, ‘aperiodic’, ‘peak’}

Which model component to return.: ‘full’ - full model ‘aperiodic’ - isolated aperiodic model component ‘peak’ - isolated peak model component

space{‘log’, ‘linear’}

Which space to return the model component in.: ‘log’ - returns in log10 space. ‘linear’ - returns in linear space.

Returns

output1d array: Specified model component, in specified spacing.

Notes

The ‘space’ parameter doesn’t just define the spacing of the model component values, but rather defines the space of the additive model such that model = aperiodic_component + peak_component. With space set as ‘log’, this combination holds in log space. With space set as ‘linear’, this combination holds in linear space.

get_params(name, col=None)[source]¶

Return model fit parameters for specified feature(s).

Parameters

name{‘aperiodic_params’, ‘peak_params’, ‘gaussian_params’, ‘error’, ‘r_squared’}: Name of the data field to extract across the group.
col{‘CF’, ‘PW’, ‘BW’, ‘offset’, ‘knee’, ‘exponent’} or int, optional: Column name / index to extract from selected data, if requested. Only used for name of {‘aperiodic_params’, ‘peak_params’, ‘gaussian_params’}.

Returns

outndarray: Requested data.

Raises

NoModelError: If there are no model fit results available.
ValueError: If the input for the col input is not understood.

Notes

When extracting peak information (‘peak_params’ or ‘gaussian_params’), an additional column is appended to the returned array, indicating the index of the model that the peak came from.

get_results()[source]¶: Return the results run across a group of power spectra.

get_run_modes()¶

Return run modes of the current object.

Returns

FOOOFRunModes: Object containing the run modes from the current object.

get_settings()¶

Return user defined settings of the current object.

Returns

FOOOFSettings: Object containing the settings from the current object.

property has_data¶: Indicator for if the object contains data.

property has_model¶: Indicator for if the object contains model fits.

load(file_name, file_path=None)[source]¶

Load FOOOFGroup data from file.

Parameters

file_namestr: File to load data from.
file_pathPath or str, optional: Path to directory to load from. If None, loads from current directory.

property n_null_¶: How many model fits are null.

property n_peaks_¶: How many peaks were fit for each model.

property null_inds_¶: The indices for model fits that are null.

plot(save_fig=False, file_name=None, file_path=None, **plot_kwargs)[source]¶

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

Parameters

save_figbool, optional, default: False: Whether to save out a copy of the plot.
file_namestr, optional: Name to give the saved out file.
file_pathPath or str, optional: Path to directory to save to. If None, saves to current directory.
**plot_kwargs: Additional plot related keyword arguments, with styling options managed by style_plot.

Raises

NoModelError: If the FOOOF object does not have model fit data available to plot.

static print_report_issue(concise=False)¶

Prints instructions on how to report bugs and/or problematic fits.

Parameters

concisebool, optional, default: False: Whether to print the report in a concise mode, or not.

print_results(concise=False)[source]¶

Print out FOOOFGroup results.

Parameters

concisebool, optional, default: False: Whether to print the report in a concise mode, or not.

print_settings(description=False, concise=False)¶

Print out the current settings.

Parameters

descriptionbool, optional, default: False: Whether to print out a description with current settings.
concisebool, optional, default: False: Whether to print the report in a concise mode, or not.

report(freqs=None, power_spectra=None, freq_range=None, n_jobs=1, progress=None)[source]¶

Fit a group of power spectra and display a report, with a plot and printed results.

Parameters

freqs1d array, optional: Frequency values for the power_spectra, in linear space.
power_spectra2d array, shape: [n_power_spectra, n_freqs], optional: Matrix of power spectrum values, in linear space.
freq_rangelist of [float, float], optional: Desired frequency range to run FOOOF on. If not provided, fits the entire given range.
n_jobsint, optional, default: 1: Number of jobs to run in parallel. 1 is no parallelization. -1 uses all available cores.
progress{None, ‘tqdm’, ‘tqdm.notebook’}, optional: Which kind of progress bar to use. If None, no progress bar is used.

Notes

Data is optional, if data has already been added to the object.

save(file_name, file_path=None, append=False, save_results=False, save_settings=False, save_data=False)[source]¶

Save out results and/or settings from FOOOFGroup object. Saves out to a JSON file.

Parameters

file_namestr or FileObject: File to save data to.
file_pathPath or str, optional: Path to directory to load from. If None, loads from current directory.
appendbool, optional, default: False: Whether to append to an existing file, if available. This option is only valid (and only used) if ‘file_name’ is a str.
save_resultsbool, optional: Whether to save out FOOOF model fit results.
save_settingsbool, optional: Whether to save out FOOOF settings.
save_databool, optional: Whether to save out power spectra data.

Raises

ValueError: If the data or save file specified are not understood.

save_model_report(index, file_name, file_path=None, plt_log=False, add_settings=True, **plot_kwargs)[source]¶

“Save out an individual model report for a specified model fit.

Parameters

indexint: Index of the model fit to save out.
file_namestr: Name to give the saved out file.
file_pathPath or str, optional: Path to directory to save to. If None, saves to current directory.
plt_logbool, optional, default: False: Whether or not to plot the frequency axis in log space.
add_settingsbool, optional, default: True: Whether to add a print out of the model settings to the end of the report.
plot_kwargskeyword arguments: Keyword arguments to pass into the plot method.

save_report(file_name, file_path=None, add_settings=True)[source]¶

Generate and save out a PDF report for a group of power spectrum models.

Parameters

file_namestr: Name to give the saved out file.
file_pathPath or str, optional: Path to directory to save to. If None, saves to current directory.
add_settingsbool, optional, default: True: Whether to add a print out of the model settings to the end of the report.

set_check_data_mode(check_data)¶

Set check data mode, which controls if an error is raised if NaN or Inf data are added.

Parameters

check_databool: Whether to run in check data mode.

set_check_modes(check_freqs=None, check_data=None)¶

Set check modes, which controls if an error is raised based on check on the inputs.

Parameters

check_freqsbool, optional: Whether to run in check freqs mode, which checks the frequency data.
check_databool, optional: Whether to run in check data mode, which checks the power spectrum values data.

set_debug_mode(debug)¶

Set debug mode, which controls if an error is raised if model fitting is unsuccessful.

Parameters