update docs for sim name update

fooof-tools · May 10, 2021 · 32c0d2f · 32c0d2f
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diff --git a/examples/manage/plot_failed_fits.py b/examples/manage/plot_failed_fits.py
@@ -11,7 +11,7 @@
 from specparam import PSDGroup
 
 # Import simulation code to create test power spectra
-from specparam.sim.gen import gen_group_power_spectra
+from specparam.sim import sim_group_power_spectra
 
 # Import FitError, which we will use to help debug model fit errors
 from specparam.core.errors import FitError
@@ -36,7 +36,7 @@
 ###################################################################################################
 
 # Simulate some example power spectra to use for the example
-freqs, powers = gen_group_power_spectra(25, [1, 50], [1, 1], [10, 0.25, 3],
+freqs, powers = sim_group_power_spectra(25, [1, 50], [1, 1], [10, 0.25, 3],
                                         nlvs=0.1, freq_res=0.25)
 
 ###################################################################################################

diff --git a/examples/manage/plot_fit_fooof_3d.py b/examples/manage/plot_fit_fooof_3d.py
@@ -58,7 +58,8 @@
 from specparam.objs import fit_models_3d, combine_model_objs
 
 # Import simulation & IO utilities to help with the example
-from specparam.sim.gen import gen_freqs, gen_group_power_spectra
+from specparam.sim import sim_group_power_spectra
+from specparam.sim.utils import create_freqs
 from specparam.sim.params import param_sampler
 from specparam.utils.io import load_group
 
@@ -89,18 +90,18 @@
 # Set up the shape of the data
 n_conditions = 3
 n_channels = 10
-n_freqs = len(gen_freqs(freq_range, freq_res))
+n_freqs = len(create_freqs(freq_range, freq_res))
 
 # Define parameters for the simulated power spectra
 ap_opts = param_sampler([[0, 1.0], [0, 1.5], [0, 2]])
 pe_opts = param_sampler([[], [10, 0.25, 1], [10, 0.25, 1, 20, 0.15, 1]])
 
 ###################################################################################################
 
-# Generate some simulated power spectra, and organize into a 3D array
+# Simulate power spectra, and organize into a 3D array
 spectra = []
 for ind in range(n_conditions):
-    freqs, powers = gen_group_power_spectra(n_channels, freq_range, ap_opts,
+    freqs, powers = sim_group_power_spectra(n_channels, freq_range, ap_opts,
                                             pe_opts, freq_res=freq_res)
     spectra.append(powers)
 

diff --git a/examples/manage/plot_freq_by_freq_error.py b/examples/manage/plot_freq_by_freq_error.py
@@ -16,7 +16,7 @@
 from specparam import PSD, PSDGroup
 
 # Import simulation utilities to create some test data
-from specparam.sim.gen import gen_power_spectrum, gen_group_power_spectra
+from specparam.sim import sim_power_spectrum, sim_group_power_spectra
 
 # Import functions to examine frequency-by-frequency error of model fits
 from specparam.analysis.error import compute_pointwise_error, compute_pointwise_error_group
@@ -53,7 +53,7 @@
 ###################################################################################################
 
 # Simulate an example power spectrum
-freqs, powers = gen_power_spectrum([3, 50], [1, 1], [10, 0.25, 0.5])
+freqs, powers = sim_power_spectrum([3, 50], [1, 1], [10, 0.25, 0.5])
 
 ###################################################################################################
 
@@ -100,7 +100,7 @@
 ###################################################################################################
 
 # Simulate a group of power spectra
-freqs, powers = gen_group_power_spectra(10, [3, 50], [1, 1], [10, 0.3, 1], nlvs=0.1)
+freqs, powers = sim_group_power_spectra(10, [3, 50], [1, 1], [10, 0.3, 1], nlvs=0.1)
 
 ###################################################################################################
 
@@ -165,7 +165,7 @@
 ###################################################################################################
 
 # Simulate a group of power spectra, with a knee
-freqs, powers = gen_group_power_spectra(10, [1, 50], [0, 10, 2],
+freqs, powers = sim_group_power_spectra(10, [1, 50], [0, 10, 2],
                                         [10, 0.3, 1], nlvs=0.01)
 
 # Parameterize our new group of power spectra

diff --git a/examples/manage/plot_manipulating_fooofs.py b/examples/manage/plot_manipulating_fooofs.py
@@ -32,7 +32,7 @@
 from specparam.objs.utils import average_group, combine_model_objs, compare_model_objs
 
 # Import simulation functions to create our example data
-from specparam.sim.gen import gen_power_spectrum
+from specparam.sim import sim_power_spectrum
 
 ###################################################################################################
 #
@@ -46,11 +46,11 @@
 freq_res = 0.25
 
 # Create some example power spectra
-freqs, powers_1 = gen_power_spectrum(freq_range, [0, 1.0], [10, 0.25, 2],
+freqs, powers_1 = sim_power_spectrum(freq_range, [0, 1.0], [10, 0.25, 2],
                                      nlv=0.00, freq_res=freq_res)
-freqs, powers_2 = gen_power_spectrum(freq_range, [0, 1.2], [9, 0.20, 1.5],
+freqs, powers_2 = sim_power_spectrum(freq_range, [0, 1.2], [9, 0.20, 1.5],
                                      nlv=0.01, freq_res=freq_res)
-freqs, powers_3 = gen_power_spectrum(freq_range, [0, 1.5], [11, 0.3, 2.5],
+freqs, powers_3 = sim_power_spectrum(freq_range, [0, 1.5], [11, 0.3, 2.5],
                                      nlv=0.02, freq_res=freq_res)
 
 ###################################################################################################

diff --git a/examples/plots/plot_fooof_models.py b/examples/plots/plot_fooof_models.py
@@ -23,12 +23,12 @@
 from specparam import PSD
 
 # Import simulation functions to create some example data
-from specparam.sim.gen import gen_power_spectrum
+from specparam.sim import sim_power_spectrum
 
 ###################################################################################################
 
-# Generate an example power spectrum
-freqs, powers = gen_power_spectrum([3, 50], [1, 1],
+# Simulate an example power spectrum
+freqs, powers = sim_power_spectrum([3, 50], [1, 1],
                                    [[9, 0.25, 0.5], [22, 0.1, 1.5], [25, 0.2, 1.]])
 
 ###################################################################################################
@@ -139,7 +139,7 @@
 ###################################################################################################
 
 # Simulate a new power spectrum, over a broader frequency region
-freqs, powers = gen_power_spectrum([1, 150], [0, 10, 1.5],
+freqs, powers = sim_power_spectrum([1, 150], [0, 10, 1.5],
                                    [[4, 0.25, 1], [12, 0.2, 1.5], [25, 0.1, 2]])
 
 ###################################################################################################

diff --git a/examples/plots/plot_model_components.py b/examples/plots/plot_model_components.py
@@ -15,7 +15,7 @@
 from specparam.analysis import get_band_peak_group
 
 # Import simulation utilities for making example data
-from specparam.sim.gen import gen_group_power_spectra
+from specparam.sim import sim_group_power_spectra
 from specparam.sim.params import param_jitter
 
 # Import plotting function for model parameters and components
@@ -60,8 +60,8 @@
 ###################################################################################################
 
 # Simulate some test data, as two groups of power spectra
-freqs, powers1 = gen_group_power_spectra(n_subjs, freq_range, g1_aps, g1_peaks)
-freqs, powers2 = gen_group_power_spectra(n_subjs, freq_range, g2_aps, g2_peaks)
+freqs, powers1 = sim_group_power_spectra(n_subjs, freq_range, g1_aps, g1_peaks)
+freqs, powers2 = sim_group_power_spectra(n_subjs, freq_range, g2_aps, g2_peaks)
 
 ###################################################################################################
 # Fit Power Spectrum Models

diff --git a/examples/plots/plot_power_spectra.py b/examples/plots/plot_power_spectra.py
@@ -14,7 +14,7 @@
 from specparam.plts.spectra import plot_spectra, plot_spectra_shading
 
 # Import simulation utilities for creating test data
-from specparam.sim.gen import gen_power_spectrum, gen_group_power_spectra
+from specparam.sim import sim_power_spectrum, sim_group_power_spectra
 from specparam.sim.params import param_iter, Stepper
 
 ###################################################################################################
@@ -49,8 +49,8 @@
 peaks = [[6, 0.2, 1], [10, 0.3, 1], [25, 0.15, 3]]
 
 # Simulate two example power spectra
-freqs, powers1 = gen_power_spectrum(freq_range, ap_1, peaks)
-freqs, powers2 = gen_power_spectrum(freq_range, ap_2, peaks)
+freqs, powers1 = sim_power_spectrum(freq_range, ap_1, peaks)
+freqs, powers2 = sim_power_spectrum(freq_range, ap_2, peaks)
 
 ###################################################################################################
 # Plotting Individual Power Spectra
@@ -142,12 +142,12 @@
 ap_params = [1, 1]
 
 # Simulate a single 10 Hz centered alpha
-freqs_al10, powers_al10 = gen_power_spectrum(freq_range, ap_params,
+freqs_al10, powers_al10 = sim_power_spectrum(freq_range, ap_params,
                                              [10, 0.25, 1], nlv=0)
 
 # Simulate spectra stepping across alpha center frequency
 cf_steps = Stepper(8, 12.5, 0.5)
-freqs_al, powers_al = gen_group_power_spectra(len(cf_steps), freq_range, ap_params,
+freqs_al, powers_al = sim_group_power_spectra(len(cf_steps), freq_range, ap_params,
                                               param_iter([cf_steps, 0.25, 1]))
 
 ###################################################################################################

diff --git a/examples/processing/plot_line_noise.py b/examples/processing/plot_line_noise.py
@@ -15,7 +15,7 @@
 from specparam.utils import trim_spectrum, interpolate_spectrum
 
 # Import simulation functions to create some example data
-from specparam.sim.gen import gen_power_spectrum
+from specparam.sim import sim_power_spectrum
 
 # Import NeuroDSP functions for simulating & processing time series
 from neurodsp.sim import sim_combined
@@ -45,11 +45,11 @@
 
 ###################################################################################################
 
-# Generate an example power spectrum, with line noise
-freqs1, powers1 = gen_power_spectrum([3, 75], [1, 1],
+# Simulate an example power spectrum, with line noise
+freqs1, powers1 = sim_power_spectrum([3, 75], [1, 1],
                                      [[10, 0.75, 2], [60, 1, 0.5]])
 
-# Visualize the generated power spectrum
+# Visualize the simulated power spectrum
 plot_spectra(freqs1, powers1, log_powers=True)
 
 ###################################################################################################
@@ -97,8 +97,8 @@
 
 ###################################################################################################
 
-# Generate an example power spectrum, with line noise & harmonics
-freqs2, powers2 = gen_power_spectrum([1, 150], [1, 500, 1.5],
+# Simulate an example power spectrum, with line noise & harmonics
+freqs2, powers2 = sim_power_spectrum([1, 150], [1, 500, 1.5],
                                      [[10, 0.5, 2], [60, 0.75, 0.5], [120, 0.5, 0.5]])
 
 # Interpolate away the line noise region & harmonics

diff --git a/examples/sims/plot_sim_params.py b/examples/sims/plot_sim_params.py
@@ -8,7 +8,7 @@
 ###################################################################################################
 
 # Import simulation functions for creating spectra
-from specparam.sim.gen import gen_power_spectrum, gen_group_power_spectra
+from specparam.sim import sim_power_spectrum, sim_group_power_spectra
 
 # Import simulation utilities for managing parameters
 from specparam.sim.params import param_sampler, param_iter, param_jitter, Stepper
@@ -49,7 +49,7 @@
 ###################################################################################################
 
 # Simulate a group of power spectra
-freqs, powers, sim_params = gen_group_power_spectra(n_spectra, freq_range, ap_params,
+freqs, powers, sim_params = sim_group_power_spectra(n_spectra, freq_range, ap_params,
                                                     pe_params, nlv, return_params=True)
 
 ###################################################################################################
@@ -62,7 +62,7 @@
 
 # You can also use a SimParams object to regenerate a particular power spectrum
 cur_params = sim_params[0]
-freqs, powers = gen_power_spectrum(freq_range, *cur_params)
+freqs, powers = sim_power_spectrum(freq_range, *cur_params)
 
 ###################################################################################################
 # Managing Parameters
@@ -98,12 +98,12 @@
 
 ###################################################################################################
 
-# Generate some power spectra, using param_sampler
-freqs, powers = gen_group_power_spectra(10, freq_range, ap_opts, pe_opts)
+# Simualte some power spectra, using param_sampler
+freqs, powers = sim_group_power_spectra(10, freq_range, ap_opts, pe_opts)
 
 ###################################################################################################
 
-# Plot some of the spectra that were generated
+# Plot some of the spectra that were simulated
 plot_spectra(freqs, powers[0:4, :], log_powers=True)
 
 ###################################################################################################
@@ -133,12 +133,12 @@
 
 ###################################################################################################
 
-# Generate some power spectra, using param_iter
-freqs, powers = gen_group_power_spectra(len(cf_steps), freq_range, ap_params, pe_params)
+# Simulate some power spectra, using param_iter
+freqs, powers = sim_group_power_spectra(len(cf_steps), freq_range, ap_params, pe_params)
 
 ###################################################################################################
 
-# Plot the generated spectra
+# Plot the simulated spectra
 plot_spectra(freqs, powers, log_freqs=True, log_powers=True)
 
 ###################################################################################################
@@ -161,16 +161,16 @@
 
 ###################################################################################################
 
-# Generate some power spectra, using param_jitter
-freqs, powers = gen_group_power_spectra(5, freq_range, ap_params, pe_params)
+# Simulate some power spectra, using param_jitter
+freqs, powers = sim_group_power_spectra(5, freq_range, ap_params, pe_params)
 
 ###################################################################################################
 
-# Plot the generated spectra
+# Plot the simulated spectra
 plot_spectra(freqs, powers, log_freqs=True, log_powers=True)
 
 ###################################################################################################
 #
-# We can see that in the generated spectra above, there is some jitter
+# We can see that in the simulated spectra above, there is some jitter
 # to the simulated aperiodic exponent values.
 #
diff --git a/examples/sims/plot_simulated_power_spectra.py b/examples/sims/plot_simulated_power_spectra.py
@@ -8,7 +8,7 @@
 ###################################################################################################
 
 # Import functions for creating simulated power spectra
-from specparam.sim.gen import gen_power_spectrum, gen_group_power_spectra
+from specparam.sim import sim_power_spectrum, sim_group_power_spectra
 
 # Import plotting functions
 from specparam.plts.spectra import plot_spectra
@@ -32,7 +32,7 @@
 #
 #   - each peak is defined with three parameters, as [center frequency, height, width]
 #
-# The :func:`~.gen_power_spectrum` function takes these parameters as input to
+# The :func:`~.sim_power_spectrum` function takes these parameters as input to
 # create and return a simulated power spectrum. Note that the parameters that define the peaks
 # are labeled as gaussian parameters, as these parameters define the simulated gaussians
 # directly, and are not the modified peak parameters that the model outputs.
@@ -47,8 +47,8 @@
 
 ###################################################################################################
 
-# Generate a simulated power spectrum
-freqs, powers = gen_power_spectrum(freq_range, aperiodic_params, periodic_params)
+# Simulate a power spectrum
+freqs, powers = sim_power_spectrum(freq_range, aperiodic_params, periodic_params)
 
 ###################################################################################################
 
@@ -93,8 +93,8 @@
 
 ###################################################################################################
 
-# Generate the new simulated power spectrum
-freqs, powers = gen_power_spectrum(freq_range, aperiodic_params,
+# Simulate the new power spectrum
+freqs, powers = sim_power_spectrum(freq_range, aperiodic_params,
                                    periodic_params, nlv, freq_res)
 
 ###################################################################################################
@@ -106,16 +106,16 @@
 # Simulating a Group of Power Spectra
 # -----------------------------------
 #
-# For simulating multiple power spectra, the :func:`~.gen_group_power_spectra` can be used.
+# For simulating multiple power spectra, the :func:`~.sim_group_power_spectra` can be used.
 #
 # This function takes the same kind of parameter definitions as
-# :func:`~.gen_power_spectrum`, and in addition takes a number specifying
+# :func:`~.sim_power_spectrum`, and in addition takes a number specifying
 # how many power spectra to simulate, returning a 2D matrix containing the
 # desired number of spectra.
 #
-# Parameters that are passed into :func:`~.gen_group_power_spectra` can be:
+# Parameters that are passed into :func:`~.sim_group_power_spectra` can be:
 #
-# - a single definition, whereby the same value is used for all generated spectra
+# - a single definition, whereby the same value is used for all simulated spectra
 # - a list of parameters, whereby each successive entry is used for each successive spectrum
 # - a function or generator that can be called to return parameters for each spectrum
 #
@@ -136,12 +136,12 @@
 ###################################################################################################
 
 # Simulate a group of power spectra
-freqs, powers = gen_group_power_spectra(n_spectra, freq_range, aperiodic_params,
+freqs, powers = sim_group_power_spectra(n_spectra, freq_range, aperiodic_params,
                                         periodic_params, nlv)
 
 ###################################################################################################
 
-# Plot the power spectra that were just generated
+# Plot the power spectra that were just simulated
 plot_spectra(freqs, powers, log_freqs=True, log_powers=True)
 
 ###################################################################################################
@@ -159,7 +159,7 @@
 ###################################################################################################
 
 # Simulate a power spectrum, returning the simulation parameter information
-freqs, powers, sp = gen_power_spectrum([1, 50], [1, 1], [10, 0.25, 1.5],
+freqs, powers, sp = sim_power_spectrum([1, 50], [1, 1], [10, 0.25, 1.5],
                                        0.01, return_params=True)
 
 # Check the information stored in the simulation params object
@@ -168,7 +168,7 @@
 ###################################################################################################
 
 # Simulate a group of power spectrum, returning the simulation parameter information
-freqs, powers, sps = gen_group_power_spectra(3, [1, 150], [1, 100, 150],
+freqs, powers, sps = sim_group_power_spectra(3, [1, 150], [1, 100, 150],
                                              [4, 0.2, 2, 22, 0.15, 3],
                                              0.01, return_params=True)