Merge pull request #129 from fooof-tools/audit

Audit & misc fixes for 1.0 release

Author: TomDonoghue

doc/api.rst

@@ -31,14 +31,25 @@ FOOOFGroup Object
 
    FOOOFGroup
 
-FOOOF Object Functions
-----------------------
+Bands
+-----
+
+.. currentmodule:: fooof.bands
+
+.. autosummary::
+   :toctree: generated/
+
+   Bands
+
+FOOOF Functions
+---------------
 
 .. currentmodule:: fooof.funcs
 
 .. autosummary::
    :toctree: generated/
 
+   average_fg
    combine_fooofs
    fit_fooof_group_3d
 
@@ -51,16 +62,20 @@ Analysis Functions
     :toctree: generated/
 
     get_band_peak
+    get_band_peak_fm
+    get_band_peak_fg
     get_band_peak_group
     get_highest_peak
 
-Synth Code
-----------
+Sim Code
+--------
+
+Code & utilities for simulating power spectra.
 
 Generating Power Spectra
 ~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. currentmodule:: fooof.synth.gen
+.. currentmodule:: fooof.sim.gen
 
 .. autosummary::
     :toctree: generated/
@@ -72,27 +87,28 @@ Generating Power Spectra
 Parameter Management
 ~~~~~~~~~~~~~~~~~~~~
 
-.. currentmodule:: fooof.synth.params
+.. currentmodule:: fooof.sim.params
 
 .. autosummary::
     :toctree: generated/
 
     Stepper
     param_iter
     param_sampler
+    update_sim_ap_params
 
 Transforming Power Spectra
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. currentmodule:: fooof.synth.transform
+.. currentmodule:: fooof.sim.transform
 
 .. autosummary::
     :toctree: generated/
 
     translate_spectrum
-    translate_syn_spectrum
+    translate_sim_spectrum
     rotate_spectrum
-    rotate_syn_spectrum
+    rotate_sim_spectrum
     compute_rotation_offset
 
 Plotting Functions
@@ -117,7 +133,5 @@ Utility Functions
     :toctree: generated/
 
     trim_spectrum
-    get_settings
-    get_data_info
-    compare_settings
-    compare_data_info
+    get_info
+    compare_info

examples/plot_fit_fooof_3d.py

@@ -12,20 +12,20 @@
 # FOOOF imports
 from fooof import FOOOFGroup
 from fooof.funcs import fit_fooof_group_3d, combine_fooofs
-from fooof.synth.gen import gen_group_power_spectra
-from fooof.synth.params import param_sampler
+from fooof.sim.gen import gen_group_power_spectra
+from fooof.sim.params import param_sampler
 
 ###################################################################################################
 
-# Settings for creating synthetic data
+# Settings for creating simulated data
 n_spectra = 10
 freq_range = [3, 40]
 ap_opts = param_sampler([[0, 1.0], [0, 1.5], [0, 2]])
 gauss_opts = param_sampler([[], [10, 1, 1], [10, 1, 1, 20, 2, 1]])
 
 ###################################################################################################
 
-# Generate some synthetic power spectra, and organize into a 3D matrix
+# Generate some simulated power spectra, and organize into a 3D matrix
 spectra = []
 for ind in range(3):
     fs, ps, _ = gen_group_power_spectra(n_spectra, freq_range, ap_opts, gauss_opts)

examples/plot_plots.py

@@ -13,10 +13,10 @@
 
 ###################################################################################################
 
-# Create a couple synthetic power spectra to explore plotting with
+# Create a couple simulated power spectra to explore plotting with
 #   Here we create two spectra, with different aperiodic components
 #   but each with the same oscillations (a theta, alpha & beta)
-from fooof.synth.gen import gen_group_power_spectra
+from fooof.sim.gen import gen_group_power_spectra
 fs, ps, _ = gen_group_power_spectra(2, [3, 40], [[0.75, 1.5], [0.25, 1]],
                                     [6, 0.2, 1, 10, 0.3, 1, 25, 0.15, 3])
 ps1, ps2 = ps

examples/plot_synth_params.py renamed to examples/plot_sim_params.py

@@ -1,35 +1,35 @@
 """
-Synthetic Parameters
+Simulated Parameters
 ====================
 
-Manage parameters for creating synthetic power spectra.
+Manage parameters for creating simulated power spectra.
 """
 
 ###################################################################################################
 
 # Import fooof functions for creating spectra and managing parameters
-from fooof.synth.params import param_sampler, param_iter, Stepper
-from fooof.synth.gen import gen_power_spectrum, gen_group_power_spectra
+from fooof.sim.params import param_sampler, param_iter, Stepper
+from fooof.sim.gen import gen_power_spectrum, gen_group_power_spectra
 
 # Import some fooof plotting functions
 from fooof.plts.spectra import plot_spectrum, plot_spectra
 
 ###################################################################################################
-# SynParams
+# SimParams
 # ~~~~~~~~~
 #
-# When you synthesize multiple power spectra, FOOOF uses `SynParams` objects to
+# When you simulate multiple power spectra, FOOOF uses `SimParams` objects to
 # keep track of the parameters used for each power spectrum.
 #
-# SynParams objects are named tuples with the following fields:
+# SimParams objects are named tuples with the following fields:
 # - `aperiodic_params`
 # - `gaussian_params`
 # - `nlv`
 #
 
 ###################################################################################################
 
-# Set up settings for synthesizing a group of power spectra
+# Set up settings for simulating a group of power spectra
 n_spectra = 2
 freq_range = [3, 40]
 ap_params = [[0.5, 1], [1, 1.5]]
@@ -38,19 +38,19 @@
 
 ###################################################################################################
 
-# Synthesize a group of power spectra
-fs, ps, syn_params = gen_group_power_spectra(n_spectra, freq_range, ap_params, gauss_params, nlv)
+# Simulate a group of power spectra
+fs, ps, sim_params = gen_group_power_spectra(n_spectra, freq_range, ap_params, gauss_params, nlv)
 
 ###################################################################################################
 
-# Print out the SynParams objects that track the parameters used to create power spectra
-for syn_param in syn_params:
-    print(syn_param)
+# Print out the SimParams objects that track the parameters used to create power spectra
+for sim_param in sim_params:
+    print(sim_param)
 
 ###################################################################################################
 
-# You can also use a SynParams object to regenerate a particular power spectrum
-cur_params = syn_params[0]
+# You can also use a SimParams object to regenerate a particular power spectrum
+cur_params = sim_params[0]
 fs, ps = gen_power_spectrum(freq_range, *cur_params)
 
 ###################################################################################################
@@ -83,7 +83,7 @@
 ###################################################################################################
 
 # Generate some power spectra, using the param samplers
-fs, ps, syn_params = gen_group_power_spectra(10, [3, 40], ap_opts, gauss_opts)
+fs, ps, sim_params = gen_group_power_spectra(10, [3, 40], ap_opts, gauss_opts)
 
 ###################################################################################################
 
@@ -113,7 +113,7 @@
 ###################################################################################################
 
 # Generate some power spectra, using param iter
-fs, ps, syn_params = gen_group_power_spectra(len(cf_steps), [3, 40], ap_params, gauss_params)
+fs, ps, sim_params = gen_group_power_spectra(len(cf_steps), [3, 40], ap_params, gauss_params)
 
 ###################################################################################################
 

examples/plot_synthetic_power_spectra.py renamed to examples/plot_simulated_power_spectra.py

@@ -1,55 +1,55 @@
 """
-Creating Synthetic Power Spectra
+Creating Simulated Power Spectra
 ================================
 
-Use FOOOF to create synthetic power spectra.
+Use FOOOF to create simulated power spectra.
 """
 
 ###################################################################################################
 
-# Import fooof functions for creating synthetic power spectra
-from fooof.synth.gen import gen_power_spectrum, gen_group_power_spectra
+# Import fooof functions for creating simulated power spectra
+from fooof.sim.gen import gen_power_spectrum, gen_group_power_spectra
 
 # Import some fooof plotting functions
 from fooof.plts.spectra import plot_spectrum, plot_spectra
 
 ###################################################################################################
-# Creating Synthetic Power Spectra
+# Creating Simulated Power Spectra
 # --------------------------------
 #
-# FOOOF has utilities to create synthetic power spectra, whereby spectra
+# FOOOF has utilities to create simulated power spectra, whereby spectra
 # are simulated with an aperiodic component with overlying peaks,
 # using specified parameters.
 #
-# The :func:`gen_power_spectrum` function can be used to synthesize a power
+# The :func:`gen_power_spectrum` function can be used to simulate a power
 # spectrum with specified parameters.
 #
-# Note that all FOOOF functions that synthesize power spectra take in
+# Note that all FOOOF functions that simulate power spectra take in
 # gaussian parameters, not the modified peak parameters.
 #
 
 ###################################################################################################
 
-# Settings for creating a synthetic power spectrum
+# Settings for creating a simulated power spectrum
 freq_range = [3, 40]            # The frequency range to simulate
 aperiodic_params = [1, 1]       # Parameters defining the aperiodic component
 gaussian_params = [10, 0.3, 1]  # Parameters for any periodic components
 
 ###################################################################################################
 
-# Generate a synthetic power spectrum
+# Generate a simulated power spectrum
 fs, ps = gen_power_spectrum(freq_range, aperiodic_params, gaussian_params)
 
 ###################################################################################################
 
-# Plot the synthetic power spectrum
+# Plot the simulated power spectrum
 plot_spectrum(fs, ps, log_freqs=True, log_powers=False)
 
 ###################################################################################################
 # Simulating With Different Parameters
 # ------------------------------------
 #
-# Power spectra can be synthesized with any desired parameters for the FOOOF power spectra model.
+# Power spectra can be simulated with any desired parameters for the FOOOF power spectra model.
 #
 # The aperiodic mode for the simulated power spectrum is inferred from the parameters provided.
 # If two parameters are provided, this is interpreted as [offset, exponent] for simulating
@@ -67,19 +67,19 @@
 
 ###################################################################################################
 
-# Set up new settings for creating a different synthetic power spectrum
+# Set up new settings for creating a different simulated power spectrum
 freq_range = [1, 60]
 aperiodic_params = [1, 500, 2]            # Specify three values as [offset, knee, exponent]
 gaussian_params = [9, 0.4, 1, 24, 0.2, 3]  # Add peaks - can also be [[9, 0.4, 1], [24, 0.2, 3]]
 nlv = 0.01                                 # The amount of noise to add to the spectrum
 freq_res = 0.25                            # Specific the frequency resolution to simulate
 
-# Generate the new synthetic power spectrum
+# Generate the new simulated power spectrum
 fs, ps = gen_power_spectrum(freq_range, aperiodic_params, gaussian_params, nlv, freq_res)
 
 ###################################################################################################
 
-# Plot the new synthetic power spectrum
+# Plot the new simulated power spectrum
 plot_spectrum(fs, ps, log_powers=True)
 
 ###################################################################################################
@@ -100,7 +100,7 @@
 
 ###################################################################################################
 
-# Create some new settings for synthesizing a group of power spectra
+# Create some new settings for simulating a group of power spectra
 n_spectra = 2
 freq_range = [3, 40]
 ap_params = [[0.5, 1], [1, 1.5]]
@@ -109,8 +109,8 @@
 
 ###################################################################################################
 
-# Synthesize a group of power spectra
-fs, ps, syn_params = gen_group_power_spectra(n_spectra, freq_range, ap_params, gauss_params, nlv)
+# Simulate a group of power spectra
+fs, ps, sim_params = gen_group_power_spectra(n_spectra, freq_range, ap_params, gauss_params, nlv)
 
 ###################################################################################################
 
@@ -119,8 +119,8 @@
 
 ###################################################################################################
 #
-# Note that when you simulate a group of power spectra, FOOOF returns SynParam objects that
+# Note that when you simulate a group of power spectra, FOOOF returns SimParam objects that
 # keep track of the simulations. This, and other utilties to manage parameters and provide
-# parameter definitions for synthesizing groups of power spectra are covered in the
-# `Synthetic Parameters` example.
+# parameter definitions for simulating groups of power spectra are covered in the
+# `Simulated Parameters` example.
 #

examples/plot_transforms.py

@@ -8,14 +8,14 @@
 ###################################################################################################
 
 # Imports
-from fooof.synth.gen import gen_power_spectrum
-from fooof.synth.transform import rotate_spectrum
+from fooof.sim.gen import gen_power_spectrum
+from fooof.sim.transform import rotate_spectrum
 
 from fooof.plts.spectra import plot_spectra
 
 ###################################################################################################
 
-# Generate a synthetic power spectrum
+# Generate a simulated power spectrum
 fs, ps = gen_power_spectrum([3, 40], [1, 1], [10, 0.5, 1])
 
 ###################################################################################################

fooof/analysis.py

@@ -29,7 +29,7 @@ def get_band_peak_fm(fm, band, ret_one=True, attribute='peak_params'):
     return get_band_peak(getattr(fm, attribute + '_'), band, ret_one)
 
 
-def get_band_peaks_fg(fg, band, attribute='peak_params'):
+def get_band_peak_fg(fg, band, attribute='peak_params'):
     """Extract peaks from a band of interest from a FOOOF object.
 
     Parameters
@@ -47,10 +47,10 @@ def get_band_peaks_fg(fg, band, attribute='peak_params'):
         Peak data. Each row is a peak, as [CF, Amp, BW].
     """
 
-    return get_band_peaks_group(fg.get_all_data(attribute), band, len(fg))
+    return get_band_peak_group(fg.get_params(attribute), band, len(fg))
 
 
-def get_band_peaks_group(peak_params, band, n_fits):
+def get_band_peak_group(peak_params, band, n_fits):
     """Extracts peaks within a given band of interest.
 
     Parameters