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TomDonoghueTomDonoghue
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Merge pull request #130 from fooof-tools/set_avg
Update data objects and some settings handling
2 parents 3b7abb6 + 4bc5e10 commit 1a237f4

19 files changed

+532
-348
lines changed

‎fooof/core/info.py‎

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"""Internal functions to manage info related to FOOOF objects."""
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def get_obj_desc():
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"""Get dictionary specifying FOOOF object names and kind of attributes.
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Returns
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-------
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attibutes : dict
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Mapping of FOOOF object attributes, and what kind of data they are.
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"""
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attributes = {'results' : ['aperiodic_params_', 'peak_params_',
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'r_squared_', 'error_',
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'_gaussian_params'],
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'settings' : ['peak_width_limits', 'max_n_peaks',
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'min_peak_amplitude', 'peak_threshold',
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'aperiodic_mode'],
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'data' : ['power_spectrum', 'freq_range', 'freq_res'],
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'data_info' : ['freq_range', 'freq_res'],
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'arrays' : ['freqs', 'power_spectrum', 'aperiodic_params_',
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'peak_params_', '_gaussian_params'],
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'model_components' : ['_spectrum_flat', '_spectrum_peak_rm',
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'_ap_fit', '_peak_fit']}
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return attributes
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def get_data_indices(aperiodic_mode):
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"""Get a dictionary mapping the column labels to indices in FOOOF data (FOOOFResults).
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Parameters
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----------
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aperiodic_mode : {'fixed', 'knee'}
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Which approach taken to fit the aperiodic component.
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Returns
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-------
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indices : dict
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Mapping for data columns to the column indices in which they appear.
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"""
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indices = {
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'CF' : 0,
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'Amp' : 1,
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'BW' : 2,
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'offset' : 0,
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'knee' : 1 if aperiodic_mode == 'knee' else None,
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'exponent' : 1 if aperiodic_mode == 'fixed' else 2
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}
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return indices

‎fooof/core/io.py‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,8 @@
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import json
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from json import JSONDecodeError
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8-
from fooof.core.utils import dict_array_to_lst, dict_select_keys, dict_lst_to_array, get_obj_desc
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from fooof.core.info import get_obj_desc
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from fooof.core.utils import dict_array_to_lst, dict_select_keys, dict_lst_to_array
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###################################################################################################
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###################################################################################################
@@ -89,7 +90,7 @@ def save_fm(fm, file_name, file_path=None, append=False,
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# Set and select which variables to keep. Use a set to drop any potential overlap
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# Note that results also saves frequency information to be able to recreate freq vector
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attributes = get_obj_desc()
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keep = set((attributes['results'] + attributes['freq_info'] if save_results else []) + \
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keep = set((attributes['results'] + attributes['data_info'] if save_results else []) + \
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(attributes['settings'] if save_settings else []) + \
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(attributes['data'] if save_data else []))
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obj_dict = dict_select_keys(obj_dict, keep)

‎fooof/core/strings.py‎

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -27,8 +27,8 @@ def gen_wid_warn_str(freq_res, bwl):
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output = '\n'.join([
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'',
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"FOOOF WARNING: Lower-bound peak width limit is < or ~= the frequency resolution: " + \
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"{:1.2f} <= {:1.2f}".format(freq_res, bwl),
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'FOOOF WARNING: Lower-bound peak width limit is < or ~= the frequency resolution: ' + \
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'{:1.2f} <= {:1.2f}'.format(freq_res, bwl),
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'\tLower bounds below frequency-resolution have no effect (effective lower bound is freq-res)',
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'\tToo low a limit may lead to overfitting noise as small bandwidth peaks.',
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'\tWe recommend a lower bound of approximately 2x the frequency resolution.',
@@ -57,11 +57,11 @@ def gen_settings_str(f_obj, description=False, concise=False):
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"""
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# Parameter descriptions to print out, if requested
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desc = {'aperiodic_mode' : 'The aproach taken to fitting the aperiodic component.',
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'peak_width_limits' : 'Enforced limits for peak widths, in Hz.',
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desc = {'peak_width_limits' : 'Enforced limits for peak widths, in Hz.',
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'max_n_peaks' : 'The maximum number of peaks that can be extracted.',
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'min_peak_amplitude' : "Minimum absolute amplitude of a peak, above aperiodic component.",
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'peak_threshold' : "Threshold at which to stop searching for peaks."}
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'min_peak_amplitude' : 'Minimum absolute amplitude of a peak, above aperiodic component.',
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'peak_threshold' : 'Threshold at which to stop searching for peaks.',
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'aperiodic_mode' : 'The aproach taken to fitting the aperiodic component.'}
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# Clear description for printing if not requested
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if not description:
@@ -77,16 +77,16 @@ def gen_settings_str(f_obj, description=False, concise=False):
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'',
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# Settings - include descriptions if requested
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*[el for el in ['Aperiodic Mode : {}'.format(f_obj.aperiodic_mode),
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'{}'.format(desc['aperiodic_mode']),
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'Peak Width Limits : {}'.format(f_obj.peak_width_limits),
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*[el for el in ['Peak Width Limits : {}'.format(f_obj.peak_width_limits),
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'{}'.format(desc['peak_width_limits']),
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'Max Number of Peaks : {}'.format(f_obj.max_n_peaks),
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'{}'.format(desc['max_n_peaks']),
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'Minimum Amplitude : {}'.format(f_obj.min_peak_amplitude),
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'{}'.format(desc['min_peak_amplitude']),
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'Amplitude Threshold: {}'.format(f_obj.peak_threshold),
89-
'{}'.format(desc['peak_threshold'])] if el != ''],
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'{}'.format(desc['peak_threshold']),
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'Aperiodic Mode : {}'.format(f_obj.aperiodic_mode),
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'{}'.format(desc['aperiodic_mode'])] if el != ''],
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# Footer
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'',
@@ -280,7 +280,7 @@ def gen_issue_str(concise=False):
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'If FOOOF gives you any weird / bad fits, please let us know!',
281281
'To do so, send us a FOOOF report, and a FOOOF data file, ',
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'',
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"With a FOOOF object (fm), after fitting, run the following commands:",
283+
'With a FOOOF object (fm), after fitting, run the following commands:',
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"fm.create_report('FOOOF_bad_fit_report')",
285285
"fm.save('FOOOF_bad_fit_data', True, True, True)",
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'',

‎fooof/core/utils.py‎

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Original file line numberDiff line numberDiff line change
@@ -100,53 +100,6 @@ def check_array_dim(arr):
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return np.empty([0, 3]) if arr.ndim == 1 else arr
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def get_obj_desc():
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"""Get dictionary specifying FOOOF object names and kind of attributes.
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Returns
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-------
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attibutes : dict
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Mapping of FOOOF object attributes, and what kind of data they are.
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"""
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attributes = {'results' : ['aperiodic_params_', 'peak_params_', 'error_',
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'r_squared_', '_gaussian_params'],
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'settings' : ['peak_width_limits', 'max_n_peaks', 'min_peak_amplitude',
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'peak_threshold', 'aperiodic_mode'],
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'data' : ['power_spectrum', 'freq_range', 'freq_res'],
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'freq_info' : ['freq_range', 'freq_res'],
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'arrays' : ['freqs', 'power_spectrum', 'aperiodic_params_',
119-
'peak_params_', '_gaussian_params']}
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return attributes
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def get_data_indices(aperiodic_mode):
125-
"""Get a dictionary mapping the column labels to indices in FOOOF data (FOOOFResults).
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Parameters
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----------
129-
aperiodic_mode : {'fixed', 'knee'}
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Which approach taken to fit the aperiodic component.
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Returns
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-------
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indices : dict
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Mapping for data columns to the column indices in which they appear.
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"""
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138-
indices = {
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'CF' : 0,
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'Amp' : 1,
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'BW' : 2,
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'offset' : 0,
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'knee' : 1 if aperiodic_mode == 'knee' else None,
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'exponent' : 1 if aperiodic_mode == 'fixed' else 2
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}
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return indices
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def check_iter(obj, length):
151104
"""Check an object to ensure that it is iterable, and make it iterable if not.
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‎fooof/data.py‎

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"""Data objects for FOOOF."""
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from collections import namedtuple
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###################################################################################################
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###################################################################################################
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FOOOFSettings = namedtuple('FOOOFSettings', ['peak_width_limits', 'max_n_peaks',
9+
'min_peak_amplitude', 'peak_threshold',
10+
'aperiodic_mode'])
11+
FOOOFSettings.__doc__ = """\
12+
The user defined settings for a FOOOF object.
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Attributes
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----------
16+
peak_width_limits : tuple of (float, float), optional, default: (0.5, 12.0)
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Limits on possible peak width, as (lower_bound, upper_bound).
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max_n_peaks : int, optional, default: inf
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Maximum number of gaussians to be fit in a single spectrum.
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min_peak_amplitude : float, optional, default: 0
21+
Minimum amplitude threshold for a peak to be modeled.
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peak_threshold : float, optional, default: 2.0
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Threshold for detecting peaks, units of standard deviation.
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aperiodic_mode : {'fixed', 'knee'}
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Which approach to take for fitting the aperiodic component.
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"""
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29+
FOOOFDataInfo = namedtuple('FOOOFDataInfo', ['freq_range', 'freq_res'])
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FOOOFDataInfo.__doc__ = """\
32+
Data related information for a FOOOF object.
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Attributes
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----------
36+
freq_range : list of [float, float]
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Frequency range of the power spectrum, as [lowest_freq, highest_freq].
38+
freq_res : float
39+
Frequency resolution of the power spectrum.
40+
"""
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43+
FOOOFResults = namedtuple('FOOOFResults', ['aperiodic_params', 'peak_params',
44+
'r_squared', 'error', 'gaussian_params'])
45+
FOOOFResults.__doc__ = """\
46+
The resulting parameters and associated data of a FOOOF model fit.
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48+
Attributes
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----------
50+
aperiodic_params : 1d array
51+
Parameters that define the aperiodic fit. As [Offset, (Knee), Exponent].
52+
The knee parameter is only included if aperiodic is fit with knee.
53+
peak_params : 2d array
54+
Fitted parameter values for the peaks. Each row is a peak, as [CF, Amp, BW].
55+
r_squared : float
56+
R-squared of the fit between the input power spectrum and the full model fit.
57+
error : float
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Root mean squared error of the full model fit.
59+
gaussian_params : 2d array
60+
Parameters that define the gaussian fit(s). Each row is a gaussian, as [mean, amp, std].
61+
"""
62+
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64+
SynParams = namedtuple('SynParams', ['aperiodic_params', 'gaussian_params', 'nlv'])
65+
66+
SynParams.__doc__ = """\
67+
Stores parameters used to synthesize a single power spectra.
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Attributes
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----------
71+
aperiodic_params : list, len 2 or 3
72+
Parameters that define the aperiodic fit. As [Offset, (Knee), Exponent].
73+
The knee parameter is only included if aperiodic is fit with knee. Otherwise, length is 2.
74+
gaussian_params : list or list of lists
75+
Fitted parameter values for the peaks. Each list is a peak, as [CF, Amp, BW].
76+
nlv : float
77+
Noise level added to the generated power spectrum.
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"""

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