From bb69219469f879b6898df922c2b9ce28aee53974 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 3 Jul 2023 21:46:41 -0700
Subject: [PATCH 01/99] initialize files / object for SpectralTimeModel

---
 specparam/objs/__init__.py |  1 +
 specparam/objs/time.py     | 14 ++++++++++++++
 2 files changed, 15 insertions(+)
 create mode 100644 specparam/objs/time.py

diff --git a/specparam/objs/__init__.py b/specparam/objs/__init__.py
index 1e701fa7..d3b2e10b 100644
--- a/specparam/objs/__init__.py
+++ b/specparam/objs/__init__.py
@@ -2,4 +2,5 @@
 
 from .fit import SpectralModel
 from .group import SpectralGroupModel
+from .time import SpectralTimeModel
 from .utils import compare_model_objs, average_group, combine_model_objs, fit_models_3d
diff --git a/specparam/objs/time.py b/specparam/objs/time.py
new file mode 100644
index 00000000..f0903747
--- /dev/null
+++ b/specparam/objs/time.py
@@ -0,0 +1,14 @@
+"""Time model object and associated code for fitting the model to spectra across time."""
+
+from specparam.objs import SpectralGroupModel
+
+###################################################################################################
+###################################################################################################
+
+class SpectralTimeModel(SpectralGroupModel):
+    """xxx"""
+
+    def __init__(self, *args, **kwargs):
+        """Initialize object with desired settings."""
+
+        SpectralGroupModel.__init__(self, *args, **kwargs)

From 3fb81a86cb1d1534ef5aec266ef79989711588d9 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Sun, 9 Jul 2023 20:17:46 -0400
Subject: [PATCH 02/99] add sim_spectrogram

---
 specparam/sim/__init__.py       |  2 +-
 specparam/sim/sim.py            | 36 +++++++++++++++++++++++++++++++++
 specparam/tests/sim/test_sim.py | 11 ++++++++++
 3 files changed, 48 insertions(+), 1 deletion(-)

diff --git a/specparam/sim/__init__.py b/specparam/sim/__init__.py
index f0416511..d7d061f7 100644
--- a/specparam/sim/__init__.py
+++ b/specparam/sim/__init__.py
@@ -3,5 +3,5 @@
 # Link the Sim Params object into `sim`, so it can be imported from here
 from specparam.data import SimParams
 
-from .sim import sim_power_spectrum, sim_group_power_spectra
+from .sim import sim_power_spectrum, sim_group_power_spectra, sim_spectrogram
 from .gen import gen_freqs
diff --git a/specparam/sim/sim.py b/specparam/sim/sim.py
index 29ad464a..6e781ffd 100644
--- a/specparam/sim/sim.py
+++ b/specparam/sim/sim.py
@@ -3,6 +3,7 @@
 import numpy as np
 
 from specparam.core.utils import check_iter, check_flat
+from specparam.core.modutils import docs_get_section, replace_docstring_sections
 from specparam.sim.params import collect_sim_params
 from specparam.sim.gen import gen_freqs, gen_power_vals, gen_rotated_power_vals
 from specparam.sim.transform import compute_rotation_offset
@@ -257,3 +258,38 @@ def sim_group_power_spectra(n_spectra, freq_range, aperiodic_params, periodic_pa
         return freqs, powers, sim_params
     else:
         return freqs, powers
+
+# ToDo: need an update to docstring to replace `n_spectra` with `n_windows`
+@replace_docstring_sections(docs_get_section(sim_group_power_spectra.__doc__, 'Parameters'))
+def sim_spectrogram(n_windows, freq_range, aperiodic_params, periodic_params,
+                    nlvs=0.005, freq_res=0.5, f_rotation=None, return_params=False):
+    """Simulate spectrogram.
+
+    Parameters
+    ----------
+    % copied in from `sim_group_power_spectra`
+
+    Returns
+    -------
+    freqs : 1d array
+        Frequency values, in linear spacing.
+    spectrogram : 2d array
+        Matrix of power values, in linear spacing, as [n_windows, n_power_spectra].
+    sim_params : list of SimParams
+        Definitions of parameters used for each spectrum. Has length of n_spectra.
+        Only returned if `return_params` is True.
+
+    Notes
+    -----
+    This function simulates spectra for the spectrogram using `sim_group_power_spectra`.
+    See `sim_group_power_spectra` for details on the parameters.
+    """
+
+    outputs = sim_group_power_spectra(n_windows, freq_range, aperiodic_params,
+                                      periodic_params, nlvs, freq_res,
+                                      f_rotation, return_params)
+
+    outputs = list(outputs)
+    outputs[1] = outputs[1].T
+
+    return outputs
diff --git a/specparam/tests/sim/test_sim.py b/specparam/tests/sim/test_sim.py
index be6d70f8..6b35dba2 100644
--- a/specparam/tests/sim/test_sim.py
+++ b/specparam/tests/sim/test_sim.py
@@ -85,3 +85,14 @@ def test_sim_group_power_spectra_return_params():
     assert array_equal(sp.aperiodic_params, aps)
     assert array_equal(sp.periodic_params, [pes])
     assert sp.nlv == nlv
+
+def test_sim_spectrogram():
+
+    n_windows = 3
+
+    xs, ys = sim_spectrogram(n_windows, *default_group_params())
+
+    assert np.all(xs)
+    assert np.all(ys)
+    assert ys.ndim == 2
+    assert ys.shape[1] == n_windows

From edd6b3fc27b9ace898b1ada853290410f6db96cb Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Sun, 9 Jul 2023 20:18:13 -0400
Subject: [PATCH 03/99] add plot_spectrogram

---
 specparam/plts/spectra.py            | 35 ++++++++++++++++++++++++++++
 specparam/tests/plts/test_spectra.py |  9 +++++++
 2 files changed, 44 insertions(+)

diff --git a/specparam/plts/spectra.py b/specparam/plts/spectra.py
index fd1bd917..a7dc04fd 100644
--- a/specparam/plts/spectra.py
+++ b/specparam/plts/spectra.py
@@ -193,3 +193,38 @@ def plot_spectra_yshade(freqs, power_spectra, shade='std', average='mean', scale
                     alpha=alpha, color=color, **plot_kwargs)
 
     style_spectrum_plot(ax, log_freqs, log_powers)
+
+
+@savefig
+@style_plot
+@check_dependency(plt, 'matplotlib')
+def plot_spectrogram(freqs, powers, times=None, **plot_kwargs):
+    """Plot a spectrogram.
+
+    Parameters
+    ----------
+    freqs : 1d array
+        Frequency values.
+    powers : 2d array
+        Power values for the spectrogram, organized as [n_frequencies, n_time_windows].
+    times : 1d array, optional
+        Time values for the time windows.
+    **plot_kwargs
+        Keyword arguments to pass into the ``style_plot``.
+    """
+
+    _, ax = plt.subplots(figsize=(12, 6))
+
+    n_freqs, n_times = powers.shape
+
+    ax.imshow(powers, origin='lower', **plot_kwargs)
+
+    ax.set(yticks=np.arange(0, n_freqs, 1)[freqs % 5 == 0],
+           yticklabels=freqs[freqs % 5 == 0])
+
+    if times is not None:
+        ax.set(xticks=np.arange(0, n_times, 1)[times % 10 == 0],
+               xticklabels=times[times % 10 == 0])
+
+    ax.set_xlabel('Time Windows' if times is None else 'Time (s)')
+    ax.set_ylabel('Frequency')
diff --git a/specparam/tests/plts/test_spectra.py b/specparam/tests/plts/test_spectra.py
index 3fb0a25b..11677d0e 100644
--- a/specparam/tests/plts/test_spectra.py
+++ b/specparam/tests/plts/test_spectra.py
@@ -87,3 +87,12 @@ def _shade_callable(powers): return np.std(powers, axis=0)
     plot_spectra_yshade(freqs, powers, shade=_shade_callable, average=_average_callable,
                         log_powers=True, file_path=TEST_PLOTS_PATH,
                         file_name='test_plot_spectra_yshade4.png')
+
+@plot_test
+def test_plot_spectrogram(skip_if_no_mpl, tft):
+
+    freqs = tft.freqs
+    spectrogram = np.tile(tft.power_spectra.T, 50)
+
+    plot_spectrogram(freqs, spectrogram,
+                     file_path=TEST_PLOTS_PATH, file_name='test_plot_spectrogram.png')

From 8979a9225044b9060bba60d778b2c875a626a1c3 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Sun, 9 Jul 2023 21:34:01 -0400
Subject: [PATCH 04/99] add data utils, including get_periodic_labels

---
 specparam/data/utils.py            | 27 ++++++++++++++++
 specparam/tests/data/test_utils.py | 52 ++++++++++++++++++++++++++++++
 2 files changed, 79 insertions(+)
 create mode 100644 specparam/data/utils.py
 create mode 100644 specparam/tests/data/test_utils.py

diff --git a/specparam/data/utils.py b/specparam/data/utils.py
new file mode 100644
index 00000000..8e30a175
--- /dev/null
+++ b/specparam/data/utils.py
@@ -0,0 +1,27 @@
+""""Utility functions for working with data and data objects."""
+
+###################################################################################################
+###################################################################################################
+
+def get_periodic_labels(results):
+    """Get labels of periodic fields from a dictionary representation of parameter results.
+
+    Parameters
+    ----------
+    results : dict
+        A results dictionary with parameter label keys and corresponding parameter values.
+
+    Returns
+    -------
+    dict
+        Dictionary indicating the periodic related labels from the input results.
+        Has keys ['cf', 'pw', 'bw'] with corresponding values of related labels in the input.
+    """
+
+    keys = list(results.keys())
+
+    outs = {}
+    for label in ['cf', 'pw', 'bw']:
+        outs[label] = [key for key in keys if label in key]
+
+    return outs
diff --git a/specparam/tests/data/test_utils.py b/specparam/tests/data/test_utils.py
new file mode 100644
index 00000000..768608a2
--- /dev/null
+++ b/specparam/tests/data/test_utils.py
@@ -0,0 +1,52 @@
+"""Tests for the specparam.data.utils."""
+
+from copy import deepcopy
+
+from specparam.data.utils import *
+
+###################################################################################################
+###################################################################################################
+
+def test_get_periodic_labels():
+
+    keys = ['cf', 'pw', 'bw']
+
+    tdict1 = {
+        'offset' : [1, 1],
+        'exponent' : [1, 1],
+        'error' : [1, 1],
+        'r_squared' : [1, 1],
+    }
+
+    out1 = get_periodic_labels(tdict1)
+    assert isinstance(out1, dict)
+    for key in keys:
+        assert key in out1
+        assert len(out1[key]) == 0
+
+    tdict2 = deepcopy(tdict1)
+    tdict2.update({
+        'cf_0' : [1, 1],
+        'pw_0' : [1, 1],
+        'bw_0' : [1, 1],
+    })
+    out2 = get_periodic_labels(tdict2)
+    for key in keys:
+        assert len(out2[key]) == 1
+        for el in out2[key]:
+            assert key in el
+
+    tdict3 = deepcopy(tdict1)
+    tdict3.update({
+        'alpha_cf' : [1, 1],
+        'alpha_pw' : [1, 1],
+        'alpha_bw' : [1, 1],
+        'beta_cf' : [1, 1],
+        'beta_pw' : [1, 1],
+        'beta_bw' : [1, 1],
+    })
+    out3 = get_periodic_labels(tdict3)
+    for key in keys:
+        assert len(out3[key]) == 2
+        for el in out3[key]:
+            assert key in el

From 37156e4ec9aa651d93d133e732c20816d7878291 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Sun, 9 Jul 2023 23:03:09 -0400
Subject: [PATCH 05/99] add param over time template plots

---
 specparam/plts/templates.py            | 93 ++++++++++++++++++++++++++
 specparam/tests/plts/test_templates.py | 15 +++++
 2 files changed, 108 insertions(+)

diff --git a/specparam/plts/templates.py b/specparam/plts/templates.py
index de2ce6c4..a2860057 100644
--- a/specparam/plts/templates.py
+++ b/specparam/plts/templates.py
@@ -6,12 +6,17 @@
 They are not expected to be used directly by the user.
 """
 
+from itertools import repeat, cycle
+
 import numpy as np
 
 from specparam.core.modutils import safe_import, check_dependency
 from specparam.plts.utils import check_ax, set_alpha
+from specparam.plts.settings import PLT_FIGSIZES, PLT_COLORS, DEFAULT_COLORS
 
 plt = safe_import('.pyplot', 'matplotlib')
+#ticker = safe_import('.ticker', 'matplotlib')
+#Note / ToDo: see if need to put back ticker management, or remove
 
 ###################################################################################################
 ###################################################################################################
@@ -131,3 +136,91 @@ def plot_hist(data, label, title=None, n_bins=25, x_lims=None, ax=None):
         ax.set_title(title, fontsize=20)
 
     ax.tick_params(axis='both', labelsize=12)
+
+
+@check_dependency(plt, 'matplotlib')
+def plot_param_over_time(param, label=None, title=None, add_legend=True, add_xlabel=True,
+                         ax=None, **plot_kwargs):
+    """Plot a parameter over time.
+
+    Parameters
+    ----------
+    param : 1d array
+        Parameter values to plot.
+    label : str, optional
+        Label for the data, to be set as the y-axis label.
+    add_legend : bool, optional, default: True
+        Whether to add a legend to the plot.
+    add_xlabel : bool, optional, default: True
+        Whether to add an x-label to the plot.
+    ax : matplotlib.Axes, optional
+        Figure axes upon which to plot.
+    **plot_kwargs
+        Keyword arguments to pass into the ``style_plot``.
+    """
+
+    ax = check_ax(ax, plot_kwargs.pop('figsize', PLT_FIGSIZES['time']))
+
+    n_windows = len(param)
+
+    ax.plot(param, label=label,
+            alpha=plot_kwargs.pop('alpha', 0.8),
+            **plot_kwargs)
+
+    if add_xlabel:
+        ax.set_xlabel('Time Window')
+    ax.set_ylabel(label if label else 'Parameter Value', fontsize=10)
+
+    if label and add_legend:
+        ax.legend(loc='upper left', framealpha=plot_kwargs.pop('legend_framealpha', 0.9))
+
+    if title:
+        ax.set_title(title, fontsize=20)
+
+    #ax.yaxis.set_major_formatter(ticker.FormatStrFormatter('%.2f'))
+
+
+@check_dependency(plt, 'matplotlib')
+def plot_params_over_time(params, labels=None, title=None, colors=None, ax=None, **plot_kwargs):
+    """Plot multiple parameters over time.
+
+    Parameters
+    ----------
+    params : list of 1d array
+        Parameter values to plot.
+    labels : list of str
+        Label(s) for the data, to be set as the y-axis label(s).
+    colors : list of str
+        Color(s) to plot data.
+    ax : matplotlib.Axes, optional
+        Figure axes upon which to plot.
+    **plot_kwargs
+        Keyword arguments to pass into the ``style_plot``.
+    """
+
+    labels = repeat(labels) if not isinstance(labels, list) else cycle(labels)
+    colors = cycle(DEFAULT_COLORS) if not isinstance(colors, list) else cycle(colors)
+
+    ax0 = check_ax(ax, plot_kwargs.pop('figsize', PLT_FIGSIZES['time']))
+
+    n_axes = len(params)
+    axes = [ax0] + [ax0.twinx() for ind in range(n_axes-1)]
+
+    if n_axes >= 3:
+        for nax, ind in enumerate(range(2, n_axes)):
+            axes[ind].spines.right.set_position(("axes", 1.1 + (.1 * nax)))
+
+    for cax, cparams, label, color in zip(axes, params, labels, colors):
+        plot_param_over_time(cparams, label, add_legend=False, color=color,
+                             ax=cax, **plot_kwargs)
+
+    if bool(labels):
+        ax0.legend([cax.get_lines()[0] for cax in axes], labels,
+                   loc='upper left', framealpha=plot_kwargs.pop('legend_framealpha', 0.9))
+
+    if title:
+        ax0.set_title(title, fontsize=20)
+
+    # Puts the axis with the legend 'on top', while also making it transparent (to see others)
+    ax0.set_zorder(1)
+    ax0.patch.set_visible(False)
diff --git a/specparam/tests/plts/test_templates.py b/specparam/tests/plts/test_templates.py
index 0cf5d687..c747937a 100644
--- a/specparam/tests/plts/test_templates.py
+++ b/specparam/tests/plts/test_templates.py
@@ -29,3 +29,18 @@ def test_plot_hist(skip_if_no_mpl):
 
     data = np.random.randint(0, 100, 100)
     plot_hist(data, 'label', 'title')
+
+@plot_test
+def test_plot_param_over_time():
+
+    param = np.array([1, 2, 3, 2, 1, 2, 4, 2, 3, 2, 1])
+
+    plot_param_over_time(param, label='param', color='red')
+
+@plot_test
+def test_plot_params_over_time():
+
+    params = [np.array([1, 2, 3, 2, 1, 2, 4, 2, 3, 2, 1]),
+              np.array([2, 3, 2, 1, 2, 4, 2, 3, 2, 1, 2])]
+
+    plot_params_over_time(params, labels=['param1', 'param2'], colors=['blue', 'red'])

From 9fa934077a746f579ad9b89f845609811fc6024d Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Sun, 9 Jul 2023 23:20:23 -0400
Subject: [PATCH 06/99] add plot_time_model func

---
 specparam/plts/time.py            | 89 +++++++++++++++++++++++++++++++
 specparam/tests/plts/test_time.py | 24 +++++++++
 2 files changed, 113 insertions(+)
 create mode 100644 specparam/plts/time.py
 create mode 100644 specparam/tests/plts/test_time.py

diff --git a/specparam/plts/time.py b/specparam/plts/time.py
new file mode 100644
index 00000000..f13f2f22
--- /dev/null
+++ b/specparam/plts/time.py
@@ -0,0 +1,89 @@
+"""Plots for the group model object.
+
+Notes
+-----
+This file contains plotting functions that take as input a time model object.
+"""
+
+from specparam.data.utils import get_periodic_labels
+from specparam.plts.utils import savefig
+from specparam.plts.templates import plot_params_over_time
+from specparam.plts.settings import PARAM_COLORS
+from specparam.core.errors import NoModelError
+from specparam.core.modutils import safe_import, check_dependency
+
+plt = safe_import('.pyplot', 'matplotlib')
+gridspec = safe_import('.gridspec', 'matplotlib')
+
+###################################################################################################
+###################################################################################################
+
+@savefig
+@check_dependency(plt, 'matplotlib')
+def plot_time_model(time_model, save_fig=False, file_name=None, file_path=None, **plot_kwargs):
+    """Plot a figure with subplots visualizing the parameters from a SpectralTimeModel object.
+
+    Parameters
+    ----------
+    time_model : SpectralTimeModel
+        Object containing results from fitting power spectra across time windows.
+    save_fig : bool, optional, default: False
+        Whether to save out a copy of the plot.
+    file_name : str, optional
+        Name to give the saved out file.
+    file_path : str, optional
+        Path to directory to save to. If None, saves to current directory.
+
+    Raises
+    ------
+    NoModelError
+        If the model object does not have model fit data available to plot.
+    """
+
+    if not time_model.has_model:
+        raise NoModelError("No model fit results are available, can not proceed.")
+
+    # Check band structure
+    pe_labels = get_periodic_labels(time_model.time_results)
+    n_bands = len(pe_labels['cf'])
+
+    fig = plt.figure(figsize=plot_kwargs.pop('figsize', [10, 4 + 2 * n_bands]))
+    gs = gridspec.GridSpec(2 + n_bands, 1, hspace=0.35)
+
+    # 01: aperiodic parameters
+    ap_params = [time_model.time_results['offset'],
+                 time_model.time_results['exponent']]
+    ap_labels = ['Offset', 'Exponent']
+    ap_colors = [PARAM_COLORS['offset'],
+                 PARAM_COLORS['exponent']]
+    if 'knee' in time_model.time_results.keys():
+        ap_params.insert(1, time_model.time_results['knee'])
+        ap_labels.insert(1, 'Knee')
+        ap_colors.insert(1, PARAM_COLORS['knee'])
+
+    ax0 = plt.subplot(gs[0, 0])
+    plot_params_over_time(ap_params, labels=ap_labels, add_xlabel=False,
+                          colors=ap_colors,
+                          title='Aperiodic',
+                          ax=ax0)
+
+    # 02: periodic parameters
+    for band_ind in range(n_bands):
+        ax1 = plt.subplot(gs[1 + band_ind, 0])
+        plot_params_over_time(\
+            [time_model.time_results[pe_labels['cf'][band_ind]],
+             time_model.time_results[pe_labels['pw'][band_ind]],
+             time_model.time_results[pe_labels['bw'][band_ind]]],
+            labels=['CF', 'PW', 'BW'], add_xlabel=False,
+            colors=[PARAM_COLORS['cf'], PARAM_COLORS['pw'], PARAM_COLORS['bw']],
+            title='Periodic',
+            ax=ax1)
+
+    # 03: goodness of fit
+    ax2 = plt.subplot(gs[-1, 0])
+    plot_params_over_time([time_model.time_results['error'],
+                               time_model.time_results['r_squared']],
+                               labels=['Error', 'R-squared'],
+                               colors=[PARAM_COLORS['error'], PARAM_COLORS['r_squared']],
+                               title='Goodness of Fit',
+                               ax=ax2)
diff --git a/specparam/tests/plts/test_time.py b/specparam/tests/plts/test_time.py
new file mode 100644
index 00000000..567a24dc
--- /dev/null
+++ b/specparam/tests/plts/test_time.py
@@ -0,0 +1,24 @@
+"""Tests for specparam.plts.time."""
+
+from pytest import raises
+
+from specparam import SpectralTimeModel
+from specparam.core.errors import NoModelError
+
+from specparam.tests.tutils import plot_test
+from specparam.tests.settings import TEST_PLOTS_PATH
+
+from specparam.plts.time import *
+
+###################################################################################################
+###################################################################################################
+
+@plot_test
+def test_plot_time(tft, skip_if_no_mpl):
+
+    plot_time_model(tft, file_path=TEST_PLOTS_PATH, file_name='test_plot_time.png')
+
+    # Test error if no data available to plot
+    tfg = SpectralTimeModel()
+    with raises(NoModelError):
+        tfg.plot()

From da2d657ed6daddc7cfe29e9b6ffa54ad7e42c777 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Sun, 9 Jul 2023 23:21:09 -0400
Subject: [PATCH 07/99] add time model str gen func

---
 specparam/core/strings.py            | 101 +++++++++++++++++++++++++++
 specparam/tests/core/test_strings.py |   4 ++
 2 files changed, 105 insertions(+)

diff --git a/specparam/core/strings.py b/specparam/core/strings.py
index f2514103..9d567938 100644
--- a/specparam/core/strings.py
+++ b/specparam/core/strings.py
@@ -3,6 +3,7 @@
 import numpy as np
 
 from specparam.core.errors import NoModelError
+from specparam.data.utils import get_periodic_labels
 from specparam.version import __version__ as MODULE_VERSION
 
 ###################################################################################################
@@ -410,6 +411,106 @@ def gen_group_results_str(group, concise=False):
     return output
 
 
+def gen_time_results_str(time_model, concise=False):
+    """Generate a string representation of time fit results.
+
+    Parameters
+    ----------
+    time_model : SpectralTimeModel
+        Object to access results from.
+    concise : bool, optional, default: False
+        Whether to print the report in concise mode.
+
+    Returns
+    -------
+    output : str
+        Formatted string of results.
+
+    Raises
+    ------
+    NoModelError
+        If no model fit data is available to report.
+    """
+
+    if not time_model.has_model:
+        raise NoModelError("No model fit results are available, can not proceed.")
+
+    # Extract all the relevant data for printing
+    pe_labels = get_periodic_labels(time_model.time_results)
+    band_labels = [\
+        pe_labels['cf'][band_ind].split('_')[-1 if pe_labels['cf'][-2:] == 'cf' else 0] \
+        for band_ind in range(len(pe_labels['cf']))]
+
+    kns = time_model.get_params('aperiodic_params', 'knee') \
+       if time_model.aperiodic_mode == 'knee' else np.array([0])
+
+    str_lst = [
+
+        # Header
+        '=',
+        '',
+        'TIME RESULTS',
+        '',
+
+        # Group information
+        'Number of time windows fit: {}'.format(len(time_model.group_results)),
+        *[el for el in ['{} power spectra failed to fit'.format(time_model.n_null_)] if time_model.n_null_],
+        '',
+
+        # Frequency range and resolution
+        'The model was run on the frequency range {} - {} Hz'.format(
+            int(np.floor(time_model.freq_range[0])), int(np.ceil(time_model.freq_range[1]))),
+        'Frequency Resolution is {:1.2f} Hz'.format(time_model.freq_res),
+        '',
+
+        # Aperiodic parameters - knee fit status, and quick exponent description
+        'Power spectra were fit {} a knee.'.format(\
+            'with' if time_model.aperiodic_mode == 'knee' else 'without'),
+        '',
+        'Aperiodic Fit Values:',
+        *[el for el in ['    Knees - Min: {:6.2f}, Max: {:6.2f}, Mean: {:6.2f}'
+                        .format(np.nanmin(kns), np.nanmax(kns), np.nanmean(kns)),
+                       ] if time_model.aperiodic_mode == 'knee'],
+        'Exponents - Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
+        .format(np.nanmin(time_model.time_results['exponent']),
+                np.nanmax(time_model.time_results['exponent']),
+                np.nanmean(time_model.time_results['exponent'])),
+        '',
+
+        # Periodic parameters
+        'Periodic params (mean values across windows):',
+        *['{:>6s} - CF: {:5.2f}, PW: {:5.2f}, BW: {:5.2f}, Presence: {:3.1f}%'.format(
+            label,
+            np.nanmean(time_model.time_results[pe_labels['cf'][ind]]),
+            np.nanmean(time_model.time_results[pe_labels['pw'][ind]]),
+            np.nanmean(time_model.time_results[pe_labels['bw'][ind]]),
+            100 * sum(~np.isnan(time_model.time_results[pe_labels['cf'][ind]])) \
+                / len(time_model.time_results[pe_labels['cf'][ind]])) \
+                for ind, label in enumerate(band_labels)],
+        '',
+
+        # Goodness if fit
+        'Goodness of fit (mean values across windows):',
+        '   R2s -  Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
+        .format(np.nanmin(time_model.time_results['r_squared']),
+                np.nanmax(time_model.time_results['r_squared']),
+                np.nanmean(time_model.time_results['r_squared'])),
+        'Errors -  Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
+        .format(np.nanmin(time_model.time_results['error']),
+                np.nanmax(time_model.time_results['error']),
+                np.nanmean(time_model.time_results['error'])),
+        '',
+
+        # Footer
+        '='
+    ]
+
+    output = _format(str_lst, concise)
+
+    return output
+
+
+
 def gen_issue_str(concise=False):
     """Generate a string representation of instructions to report an issue.
 
diff --git a/specparam/tests/core/test_strings.py b/specparam/tests/core/test_strings.py
index 0543d1ff..6070b37d 100644
--- a/specparam/tests/core/test_strings.py
+++ b/specparam/tests/core/test_strings.py
@@ -40,6 +40,10 @@ def test_gen_group_results_str(tfg):
 
     assert gen_group_results_str(tfg)
 
+def test_gen_time_results_str(tft):
+
+    assert gen_group_results_str(tft)
+
 def test_gen_issue_str():
 
     assert gen_issue_str()

From 096c79f6bda75350826242434053f50826b0ac72 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 00:22:55 -0400
Subject: [PATCH 08/99] add report gen & save for time model

---
 specparam/core/reports.py            | 51 +++++++++++++++++++++++++++-
 specparam/tests/core/test_reports.py |  8 +++++
 2 files changed, 58 insertions(+), 1 deletion(-)

diff --git a/specparam/core/reports.py b/specparam/core/reports.py
index 5ac036d3..b897f913 100644
--- a/specparam/core/reports.py
+++ b/specparam/core/reports.py
@@ -3,7 +3,8 @@
 from specparam.core.io import fname, fpath
 from specparam.core.modutils import safe_import, check_dependency
 from specparam.core.strings import (gen_settings_str, gen_model_results_str,
-                                    gen_group_results_str)
+                                    gen_group_results_str, gen_time_results_str)
+from specparam.data.utils import get_periodic_labels
 from specparam.plts.group import (plot_group_aperiodic, plot_group_goodness,
                                   plot_group_peak_frequencies)
 
@@ -133,3 +134,51 @@ def save_group_report(group, file_name, file_path=None, add_settings=True):
     # Save out the report
     plt.savefig(fpath(file_path, fname(file_name, SAVE_FORMAT)))
     plt.close()
+
+
+@check_dependency(plt, 'matplotlib')
+def save_time_report(time_model, file_name, file_path=None, add_settings=True):
+    """Generate and save out a PDF report for a group of power spectrum models.
+
+    Parameters
+    ----------
+    time_model : SpectralTimeModel
+        Object with results from fitting a group of power spectra.
+    file_name : str
+        Name to give the saved out file.
+    file_path : str, optional
+        Path to directory to save to. If None, saves to current directory.
+    add_settings : bool, optional, default: True
+        Whether to add a print out of the model settings to the end of the report.
+    """
+
+    # Check model object for number of bands, to decide report size
+    pe_labels = get_periodic_labels(time_model.time_results)
+    n_bands = len(pe_labels['cf'])
+
+    # Initialize figure, defining number of axes based on model + what is to be plotted
+    n_rows = 1 + 2 + n_bands + (1 if add_settings else 0)
+    height_ratios = [1.0] + [0.5] * (n_bands + 2) + ([0.4] if add_settings else [])
+    _, axes = plt.subplots(n_rows, 1,
+                           gridspec_kw={'hspace' : 0.35, 'height_ratios' : height_ratios},
+                           figsize=REPORT_FIGSIZE)
+
+    # First / top: text results
+    results_str = gen_time_results_str(time_model)
+    axes[0].text(0.5, 0.7, results_str, REPORT_FONT, ha='center', va='center')
+    axes[0].set_frame_on(False)
+    axes[0].set(xticks=[], yticks=[])
+
+    # Second - data plots
+    time_model.plot(axes=axes[1:2+n_bands+1])
+
+    # Third - Model settings
+    if add_settings:
+        settings_str = gen_settings_str(time_model, False)
+        axes[-1].text(0.5, 0.1, settings_str, REPORT_FONT, ha='center', va='center')
+        axes[-1].set_frame_on(False)
+        axes[-1].set(xticks=[], yticks=[])
+
+    # Save out the report
+    plt.savefig(fpath(file_path, fname(file_name, SAVE_FORMAT)))
+    plt.close()
diff --git a/specparam/tests/core/test_reports.py b/specparam/tests/core/test_reports.py
index 6d490155..3423947c 100644
--- a/specparam/tests/core/test_reports.py
+++ b/specparam/tests/core/test_reports.py
@@ -24,3 +24,11 @@ def test_save_group_report(tfg, skip_if_no_mpl):
     save_group_report(tfg, file_name, TEST_REPORTS_PATH)
 
     assert os.path.exists(os.path.join(TEST_REPORTS_PATH, file_name + '.pdf'))
+
+def test_save_time_report(tft, skip_if_no_mpl):
+
+    file_name = 'test_time_report'
+
+    save_group_report(tft, file_name, TEST_REPORTS_PATH)
+
+    assert os.path.exists(os.path.join(TEST_REPORTS_PATH, file_name + '.pdf'))

From caa656ac07471599a0b7087565a60ce9775754b3 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 00:24:07 -0400
Subject: [PATCH 09/99] plot updates related to time object

---
 specparam/plts/settings.py  | 20 +++++++++++++++++++-
 specparam/plts/templates.py | 10 +++-------
 specparam/plts/time.py      | 29 +++++++++++++----------------
 3 files changed, 35 insertions(+), 24 deletions(-)

diff --git a/specparam/plts/settings.py b/specparam/plts/settings.py
index 4b7f1050..9f7e0310 100644
--- a/specparam/plts/settings.py
+++ b/specparam/plts/settings.py
@@ -2,13 +2,19 @@
 
 from collections import OrderedDict
 
+import matplotlib.pyplot as plt
+
 ###################################################################################################
 ###################################################################################################
 
+# Define list of default plot colors
+DEFAULT_COLORS = plt.rcParams['axes.prop_cycle'].by_key()['color']
+
 # Define default figure sizes
 PLT_FIGSIZES = {'spectral' : (10, 8),
                 'params' : (7, 6),
-                'group' : (12, 10)}
+                'group' : (12, 10),
+                'time' : (10, 2)}
 
 # Define defaults for colors for plots, based on what is plotted
 PLT_COLORS = {'data' : 'black',
@@ -16,6 +22,18 @@
               'aperiodic' : 'blue',
               'model' : 'red'}
 
+# Define defaults for colors for parameters
+PARAM_COLORS = {
+    'offset' : '#19b6e6',
+    'knee' : '#5f0e99',
+    'exponent' : '#5325e8',
+    'cf' : '#acc918',
+    'pw' : '#28a103',
+    'bw' : '#0fd197',
+    'error' : '#940000',
+    'r_squared' : '#ab7171',
+}
+
 # Levels for scaling alpha with the number of points in scatter plots
 PLT_ALPHA_LEVELS = OrderedDict({0 : 0.50,
                                 100 : 0.40,
diff --git a/specparam/plts/templates.py b/specparam/plts/templates.py
index a2860057..50ed3a8f 100644
--- a/specparam/plts/templates.py
+++ b/specparam/plts/templates.py
@@ -15,8 +15,6 @@
 from specparam.plts.settings import PLT_FIGSIZES, PLT_COLORS, DEFAULT_COLORS
 
 plt = safe_import('.pyplot', 'matplotlib')
-#ticker = safe_import('.ticker', 'matplotlib')
-#Note / ToDo: see if need to put back ticker management, or remove
 
 ###################################################################################################
 ###################################################################################################
@@ -169,15 +167,13 @@ def plot_param_over_time(param, label=None, title=None, add_legend=True, add_xla
 
     if add_xlabel:
         ax.set_xlabel('Time Window')
-    ax.set_ylabel(label if label else 'Parameter Value', fontsize=10)
+    ax.set_ylabel(label if label else 'Parameter Value')
 
     if label and add_legend:
         ax.legend(loc='upper left', framealpha=plot_kwargs.pop('legend_framealpha', 0.9))
 
     if title:
-        ax.set_title(title, fontsize=20)
-
-    #ax.yaxis.set_major_formatter(ticker.FormatStrFormatter('%.2f'))
+        ax.set_title(title)
 
 
 @check_dependency(plt, 'matplotlib')
@@ -219,7 +215,7 @@ def plot_params_over_time(params, labels=None, title=None, colors=None, ax=None,
                    loc='upper left', framealpha=plot_kwargs.pop('legend_framealpha', 0.9))
 
     if title:
-        ax0.set_title(title, fontsize=20)
+        ax0.set_title(title, fontsize=14)
 
     # Puts the axis with the legend 'on top', while also making it transparent (to see others)
     ax0.set_zorder(1)
diff --git a/specparam/plts/time.py b/specparam/plts/time.py
index f13f2f22..cc732c8b 100644
--- a/specparam/plts/time.py
+++ b/specparam/plts/time.py
@@ -5,6 +5,8 @@
 This file contains plotting functions that take as input a time model object.
 """
 
+from itertools import cycle
+
 from specparam.data.utils import get_periodic_labels
 from specparam.plts.utils import savefig
 from specparam.plts.templates import plot_params_over_time
@@ -13,7 +15,6 @@
 from specparam.core.modutils import safe_import, check_dependency
 
 plt = safe_import('.pyplot', 'matplotlib')
-gridspec = safe_import('.gridspec', 'matplotlib')
 
 ###################################################################################################
 ###################################################################################################
@@ -47,8 +48,11 @@ def plot_time_model(time_model, save_fig=False, file_name=None, file_path=None,
     pe_labels = get_periodic_labels(time_model.time_results)
     n_bands = len(pe_labels['cf'])
 
-    fig = plt.figure(figsize=plot_kwargs.pop('figsize', [10, 4 + 2 * n_bands]))
-    gs = gridspec.GridSpec(2 + n_bands, 1, hspace=0.35)
+    if plot_kwargs.pop('axes', None) is None:
+        _, axes = plt.subplots(2 + n_bands, 1,
+                               gridspec_kw={'hspace' : 0.4},
+                               figsize=plot_kwargs.pop('figsize', [10, 4 + 2 * n_bands]))
+    axes = cycle(axes)
 
     # 01: aperiodic parameters
     ap_params = [time_model.time_results['offset'],
@@ -61,29 +65,22 @@ def plot_time_model(time_model, save_fig=False, file_name=None, file_path=None,
         ap_labels.insert(1, 'Knee')
         ap_colors.insert(1, PARAM_COLORS['knee'])
 
-    ax0 = plt.subplot(gs[0, 0])
     plot_params_over_time(ap_params, labels=ap_labels, add_xlabel=False,
-                          colors=ap_colors,
-                          title='Aperiodic',
-                          ax=ax0)
+                          colors=ap_colors, title='Aperiodic', ax=next(axes))
 
     # 02: periodic parameters
     for band_ind in range(n_bands):
-        ax1 = plt.subplot(gs[1 + band_ind, 0])
         plot_params_over_time(\
             [time_model.time_results[pe_labels['cf'][band_ind]],
              time_model.time_results[pe_labels['pw'][band_ind]],
              time_model.time_results[pe_labels['bw'][band_ind]]],
             labels=['CF', 'PW', 'BW'], add_xlabel=False,
             colors=[PARAM_COLORS['cf'], PARAM_COLORS['pw'], PARAM_COLORS['bw']],
-            title='Periodic',
-            ax=ax1)
+            title='Periodic', ax=next(axes))
 
     # 03: goodness of fit
-    ax2 = plt.subplot(gs[-1, 0])
     plot_params_over_time([time_model.time_results['error'],
-                               time_model.time_results['r_squared']],
-                               labels=['Error', 'R-squared'],
-                               colors=[PARAM_COLORS['error'], PARAM_COLORS['r_squared']],
-                               title='Goodness of Fit',
-                               ax=ax2)
+                           time_model.time_results['r_squared']],
+                          labels=['Error', 'R-squared'],
+                          colors=[PARAM_COLORS['error'], PARAM_COLORS['r_squared']],
+                          title='Goodness of Fit', ax=next(axes))

From 0fa4d58d3d541bc6530c94a16c92eabb3608b75c Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 01:10:27 -0400
Subject: [PATCH 10/99] add get_results_by_ind

---
 specparam/data/utils.py            | 23 +++++++++++++++++++++++
 specparam/tests/data/test_utils.py | 24 ++++++++++++++++++++++++
 2 files changed, 47 insertions(+)

diff --git a/specparam/data/utils.py b/specparam/data/utils.py
index 8e30a175..5a8ef48d 100644
--- a/specparam/data/utils.py
+++ b/specparam/data/utils.py
@@ -25,3 +25,26 @@ def get_periodic_labels(results):
         outs[label] = [key for key in keys if label in key]
 
     return outs
+
+
+def get_results_by_ind(results, ind):
+    """Get a specified index from a dictionary of results.
+
+    Parameters
+    ----------
+    results : dict
+        A results dictionary with parameter label keys and corresponding parameter values.
+    ind : int
+        Index to extract from results.
+
+    Returns
+    -------
+    dict
+        Dictionary including the results for the specified index.
+    """
+
+    out = {}
+    for key in results.keys():
+        out[key] = results[key][ind]
+
+    return out
diff --git a/specparam/tests/data/test_utils.py b/specparam/tests/data/test_utils.py
index 768608a2..a15d8d8f 100644
--- a/specparam/tests/data/test_utils.py
+++ b/specparam/tests/data/test_utils.py
@@ -50,3 +50,27 @@ def test_get_periodic_labels():
         assert len(out3[key]) == 2
         for el in out3[key]:
             assert key in el
+
+def test_get_results_by_ind():
+
+    tdict = {
+        'offset' : [0, 1],
+        'exponent' : [0, 1],
+        'error' : [0, 1],
+        'r_squared' : [0, 1],
+        'alpha_cf' : [0, 1],
+        'alpha_pw' : [0, 1],
+        'alpha_bw' : [0, 1],
+    }
+
+    ind = 0
+    out0 = get_results_by_ind(tdict, ind)
+    assert isinstance(out0, dict)
+    for key in tdict.keys():
+        assert key in out0.keys()
+        assert out0[key] == tdict[key][ind]
+
+    ind = 1
+    out1 = get_results_by_ind(tdict, ind)
+    for key in tdict.keys():
+        assert out1[key] == tdict[key][ind]

From a34fa6e6454763d3da321b39338b38d03a80fa88 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 01:42:24 -0400
Subject: [PATCH 11/99] add SpectralTimeModel object

---
 specparam/objs/time.py | 218 ++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 217 insertions(+), 1 deletion(-)

diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index f0903747..b4126915 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -1,14 +1,230 @@
 """Time model object and associated code for fitting the model to spectra across time."""
 
+from functools import wraps
+
+import numpy as np
+
 from specparam.objs import SpectralGroupModel
+from specparam.plts.time import plot_time_model
+from specparam.data.conversions import group_to_dict
+from specparam.data.utils import get_results_by_ind
+from specparam.core.reports import save_time_report
+from specparam.core.modutils import copy_doc_func_to_method, docs_get_section
+from specparam.core.strings import gen_time_results_str
 
 ###################################################################################################
 ###################################################################################################
 
+def transpose_arg1(func):
+    """Decorator function to transpose the 1th argument input to a function."""
+
+    @wraps(func)
+    def decorated(*args, **kwargs):
+
+        if len(args) >= 2:
+            args = list(args)
+            args[2] = args[2].T if isinstance(args[2], np.ndarray) else args[2]
+        if 'power_spectra' in kwargs:
+            kwargs['power_spectra'] = kwargs['power_spectra'].T
+
+        return func(*args, **kwargs)
+
+    return decorated
+
+
 class SpectralTimeModel(SpectralGroupModel):
-    """xxx"""
+    """ToDo."""
 
     def __init__(self, *args, **kwargs):
         """Initialize object with desired settings."""
 
         SpectralGroupModel.__init__(self, *args, **kwargs)
+
+        self._reset_time_results()
+
+
+    def __iter__(self):
+        """Allow for iterating across the object by stepping across fit results per time window."""
+
+        for ind in range(len(self)):
+            yield self[ind]
+
+
+    def __getitem__(self, ind):
+        """Allow for indexing into the object to select fit results for a specific time window."""
+
+        return get_results_by_ind(self.time_results, ind)
+
+
+    def _reset_time_results(self):
+        """Set, or reset, time results to be empty."""
+
+        self.time_results = {}
+
+
+    @property
+    def spectrogram(self):
+        """Data attribute view on the power spectra, transposed to spectrogram orientation."""
+
+        return self.power_spectra.T
+
+
+    @transpose_arg1
+    def add_data(self, freqs, spectrogram, freq_range=None):
+        """Add data (frequencies and spectrogram values) to the current object.
+
+        Parameters
+        ----------
+        freqs : 1d array
+            Frequency values for the power spectra, in linear space.
+        spectrogram : 2d array, shape=[n_freqs, n_time_windows]
+            Matrix of power values, in linear space.
+        freq_range : list 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.
+        """
+
+        if np.any(self.freqs):
+            self._reset_time_results()
+        super().add_data(freqs, spectrogram, freq_range)
+
+
+    def report(self, freqs=None, power_spectra=None, freq_range=None,
+               peak_org=None, report_type='time', n_jobs=1, progress=None):
+        """Fit a group of power spectra and display a report, with a plot and printed results.
+
+        Parameters
+        ----------
+        freqs : 1d array, optional
+            Frequency values for the power_spectra, in linear space.
+        power_spectra : 2d array, shape: [n_freqs, n_time_windows], optional
+            Spectrogram of power spectrum values, in linear space.
+        freq_range : list of [float, float], optional
+            Frequency range to fit the model to. If not provided, fits the entire given range.
+        peak_org : int or Bands
+            How to organize peaks.
+            If int, extracts the first n peaks.
+            If Bands, extracts peaks based on band definitions.
+        n_jobs : int, 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.
+        """
+
+        self.fit(freqs, power_spectra, freq_range, peak_org, n_jobs=n_jobs, progress=progress)
+        self.plot(report_type)
+        self.print_results(report_type)
+
+
+    def fit(self, freqs=None, power_spectra=None, freq_range=None, peak_org=None,
+            n_jobs=1, progress=None):
+        """Fit a spectrogram
+
+        Parameters
+        ----------
+        freqs : 1d array, optional
+            Frequency values for the power_spectra, in linear space.
+        power_spectra : 2d array, shape: [n_freqs, n_time_windows], optional
+            Spectrogram of power spectrum values, in linear space.
+        freq_range : list of [float, float], optional
+            Frequency range to fit the model to. If not provided, fits the entire given range.
+        peak_org : int or Bands
+            How to organize peaks.
+            If int, extracts the first n peaks.
+            If Bands, extracts peaks based on band definitions.
+        n_jobs : int, 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.
+        """
+
+        super().fit(freqs, power_spectra, freq_range, n_jobs, progress)
+        self._convert_to_time_results(peak_org)
+
+
+    def get_results(self):
+        """Return the results run across a spectrogram."""
+
+        return self.time_results
+
+
+    def print_results(self, print_type='time', concise=False):
+        """Print out SpectralTimeModel results.
+
+        Parameters
+        ----------
+        print_type : {'time', 'group'}
+            Which format to print results out in.
+        concise : bool, optional, default: False
+            Whether to print the report in a concise mode, or not.
+        """
+
+        if print_type == 'time':
+            print(gen_time_results_str(self, concise))
+        if print_type == 'group':
+            super().print_results(concise)
+
+
+    @copy_doc_func_to_method(plot_time_model)
+    def plot(self, plot_type='time', save_fig=False, file_name=None, file_path=None, **plot_kwargs):
+
+        if plot_type == 'time':
+            plot_time_model(self, save_fig=save_fig, file_name=file_name,
+                            file_path=file_path, **plot_kwargs)
+        if plot_type == 'group':
+            super().plot(save_fig=save_fig, file_name=file_name, file_path=file_path, **plot_kwargs)
+
+
+    @copy_doc_func_to_method(save_time_report)
+    def save_report(self, file_name, file_path=None, add_settings=True):
+
+        save_time_report(self, file_name, file_path, add_settings)
+
+
+    def load(self, file_name, file_path=None, peak_org=None):
+        """Load group data from file.
+
+        Parameters
+        ----------
+        file_name : str
+            File to load data from.
+        file_path : str, optional
+            Path to directory to load from. If None, loads from current directory.
+        peak_org : int or Bands
+            How to organize peaks.
+            If int, extracts the first n peaks.
+            If Bands, extracts peaks based on band definitions.
+        """
+
+        # Clear results so as not to have possible prior results interfere
+        self._reset_time_results()
+        super().load(file_name, file_path=file_path)
+        self._convert_to_time_results(peak_org)
+
+
+    def _convert_to_time_results(self, peak_org):
+        """Convert the model results into to be organized across time windows.
+
+        Parameters
+        ----------
+        peak_org : int or Bands
+            How to organize peaks.
+            If int, extracts the first n peaks.
+            If Bands, extracts peaks based on band definitions.
+        """
+
+        self.time_results = group_to_dict(self.group_results, peak_org)

From 2dd55ccebf2d7baf3ad12731c1ae4feec7ba68a6 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 01:42:58 -0400
Subject: [PATCH 12/99] add tests for SpectralTimeModel

---
 specparam/tests/conftest.py       |  7 ++-
 specparam/tests/objs/test_time.py | 82 +++++++++++++++++++++++++++++++
 specparam/tests/tutils.py         | 16 +++++-
 3 files changed, 102 insertions(+), 3 deletions(-)
 create mode 100644 specparam/tests/objs/test_time.py

diff --git a/specparam/tests/conftest.py b/specparam/tests/conftest.py
index a2c4bf7b..9a828039 100644
--- a/specparam/tests/conftest.py
+++ b/specparam/tests/conftest.py
@@ -7,7 +7,8 @@
 import numpy as np
 
 from specparam.core.modutils import safe_import
-from specparam.tests.tutils import get_tfm, get_tfg, get_tbands, get_tresults, get_tdocstring
+from specparam.tests.tutils import (get_tfm, get_tfg, get_tft, get_tbands,
+                                    get_tresults, get_tdocstring)
 from specparam.tests.settings import (BASE_TEST_FILE_PATH, TEST_DATA_PATH,
                                       TEST_REPORTS_PATH, TEST_PLOTS_PATH)
 
@@ -43,6 +44,10 @@ def tfm():
 def tfg():
     yield get_tfg()
 
+@pytest.fixture(scope='session')
+def tft():
+    yield get_tft()
+
 @pytest.fixture(scope='session')
 def tbands():
     yield get_tbands()
diff --git a/specparam/tests/objs/test_time.py b/specparam/tests/objs/test_time.py
new file mode 100644
index 00000000..b77fd7e6
--- /dev/null
+++ b/specparam/tests/objs/test_time.py
@@ -0,0 +1,82 @@
+"""Tests for the specparam.objs.time, including the time model object and it's methods.
+
+NOTES
+-----
+The tests here are not strong tests for accuracy.
+They serve rather as 'smoke tests', for if anything fails completely.
+"""
+
+import numpy as np
+
+from specparam.sim import sim_spectrogram
+
+from specparam.tests.settings import TEST_DATA_PATH
+from specparam.tests.tutils import default_group_params, plot_test
+
+from specparam.objs.time import *
+
+###################################################################################################
+###################################################################################################
+
+def test_time_model():
+    """Check time object initializes properly."""
+
+    # Note: doesn't assert the object itself, which returns false empty
+    ft = SpectralTimeModel(verbose=False)
+    assert isinstance(ft, SpectralTimeModel)
+
+def test_time_iter(tft):
+
+    for out in tft:
+        print(out)
+        assert out
+
+def test_time_getitem(tft):
+
+    assert tft[0]
+
+def test_time_fit():
+
+    n_windows = 10
+    xs, ys = sim_spectrogram(n_windows, *default_group_params())
+
+    tft = SpectralTimeModel(verbose=False)
+    tft.fit(xs, ys)
+
+    results = tft.get_results()
+
+    assert results
+    assert isinstance(results, dict)
+    for key in results.keys():
+        assert np.all(results[key])
+        assert len(results[key]) == n_windows
+
+def test_time_print(tft):
+
+    tft.print_results()
+
+@plot_test
+def test_time_plot(tft, skip_if_no_mpl):
+
+    tft.plot()
+
+def test_time_report(skip_if_no_mpl):
+
+    n_windows = 3
+    xs, ys = sim_spectrogram(n_windows, *default_group_params())
+
+    tft = SpectralTimeModel(verbose=False)
+    tft.report(xs, ys)
+
+    assert tft
+
+def test_time_load(tbands):
+
+    file_name_res = 'test_time_res'
+    file_name_set = 'test_time_set'
+    file_name_dat = 'test_time_dat'
+
+    # Test loading results
+    tft = SpectralTimeModel(verbose=False)
+    tft.load(file_name_res, TEST_DATA_PATH, peak_org=tbands)
+    assert tft.time_results
diff --git a/specparam/tests/tutils.py b/specparam/tests/tutils.py
index 9d571d52..5f0862e6 100644
--- a/specparam/tests/tutils.py
+++ b/specparam/tests/tutils.py
@@ -6,10 +6,10 @@
 
 from specparam.bands import Bands
 from specparam.data import FitResults
-from specparam.objs import SpectralModel, SpectralGroupModel
+from specparam.objs import SpectralModel, SpectralGroupModel, SpectralTimeModel
 from specparam.core.modutils import safe_import
 from specparam.sim.params import param_sampler
-from specparam.sim.sim import sim_power_spectrum, sim_group_power_spectra
+from specparam.sim.sim import sim_power_spectrum, sim_group_power_spectra, sim_spectrogram
 
 plt = safe_import('.pyplot', 'matplotlib')
 
@@ -41,6 +41,18 @@ def get_tfg():
 
     return tfg
 
+def get_tft():
+    """Get a time object, with some fit power spectra, for testing."""
+
+    n_spectra = 3
+    xs, ys = sim_spectrogram(n_spectra, *default_group_params())
+
+    bands = Bands({'alpha' : (7, 14), 'beta' : (15, 30)})
+    tft = SpectralTimeModel(verbose=False)
+    tft.fit(xs, ys, peak_org=bands)
+
+    return tft
+
 def get_tbands():
     """Get a bands object, for testing."""
 

From 7d1fb86490dc4773a2ddb2c538ff0db675bce6ef Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 01:43:27 -0400
Subject: [PATCH 13/99] add tests for saving SpectralTimeModel

---
 specparam/tests/core/test_io.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/specparam/tests/core/test_io.py b/specparam/tests/core/test_io.py
index 9fb9705b..5fc84631 100644
--- a/specparam/tests/core/test_io.py
+++ b/specparam/tests/core/test_io.py
@@ -111,6 +111,21 @@ def test_save_group_fobj(tfg):
 
     assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name + '.json'))
 
+def test_save_time(tft):
+    """Check saving ft data."""
+
+    res_file_name = 'test_time_res'
+    set_file_name = 'test_time_set'
+    dat_file_name = 'test_time_dat'
+
+    save_group(tft, file_name=res_file_name, file_path=TEST_DATA_PATH, save_results=True)
+    save_group(tft, file_name=set_file_name, file_path=TEST_DATA_PATH, save_settings=True)
+    save_group(tft, file_name=dat_file_name, file_path=TEST_DATA_PATH, save_data=True)
+
+    assert os.path.exists(os.path.join(TEST_DATA_PATH, res_file_name + '.json'))
+    assert os.path.exists(os.path.join(TEST_DATA_PATH, set_file_name + '.json'))
+    assert os.path.exists(os.path.join(TEST_DATA_PATH, dat_file_name + '.json'))
+
 def test_load_json_str():
     """Test loading JSON file, with str file specifier.
     Loads files from test_save_model_str.

From 5f1ed666ca6a9a786a56c32d1061a932100da72f Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 01:51:29 -0400
Subject: [PATCH 14/99] fix up time docs & add to init

---
 specparam/__init__.py  |  2 +-
 specparam/objs/time.py | 46 ++++++++++++++++++++++++++++++++++++++----
 2 files changed, 43 insertions(+), 5 deletions(-)

diff --git a/specparam/__init__.py b/specparam/__init__.py
index c974450c..2dec1808 100644
--- a/specparam/__init__.py
+++ b/specparam/__init__.py
@@ -3,5 +3,5 @@
 from .version import __version__
 
 from .bands import Bands
-from .objs import SpectralModel, SpectralGroupModel
+from .objs import SpectralModel, SpectralGroupModel, SpectralTimeModel
 from .objs.utils import fit_models_3d
diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index b4126915..8ef53a14 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -4,12 +4,13 @@
 
 import numpy as np
 
-from specparam.objs import SpectralGroupModel
+from specparam.objs import SpectralModel, SpectralGroupModel
 from specparam.plts.time import plot_time_model
 from specparam.data.conversions import group_to_dict
 from specparam.data.utils import get_results_by_ind
 from specparam.core.reports import save_time_report
-from specparam.core.modutils import copy_doc_func_to_method, docs_get_section
+from specparam.core.modutils import (copy_doc_func_to_method, docs_get_section,
+                                     replace_docstring_sections)
 from specparam.core.strings import gen_time_results_str
 
 ###################################################################################################
@@ -31,9 +32,46 @@ def decorated(*args, **kwargs):
 
     return decorated
 
-
+@replace_docstring_sections([docs_get_section(SpectralModel.__doc__, 'Parameters'),
+                             docs_get_section(SpectralModel.__doc__, 'Notes')])
 class SpectralTimeModel(SpectralGroupModel):
-    """ToDo."""
+    """Model a group of power spectra as a combination of aperiodic and periodic components.
+
+    WARNING: frequency and power values inputs must be in linear space.
+
+    Passing in logged frequencies and/or power spectra is not detected,
+    and will silently produce incorrect results.
+
+    Parameters
+    ----------
+    %copied in from SpectralGroupModel object
+
+    Attributes
+    ----------
+    freqs : 1d array
+        Frequency values for the power spectra.
+    spectrogram : 2d array
+        Power values for the spectrogram, as [n_freqs, n_time_windows].
+        Power values are stored internally in log10 scale.
+    freq_range : list of [float, float]
+        Frequency range of the power spectra, as [lowest_freq, highest_freq].
+    freq_res : float
+        Frequency resolution of the power spectra.
+    time_results : dict
+        Results of the model fit across each time window.
+
+    Notes
+    -----
+    %copied in from SpectralModel object
+    - The time object inherits from the group model, which in turn inherits from the
+      model object. As such it also has data attributes defined on the model object,
+      as well as additional attributes that are added to the group object (see notes
+      and attribute list in SpectralGroupModel).
+    - Notably, while this object organizes the results into the `time_results`
+      attribute, which may include sub-selecting peaks per band (depending on settings)
+      the `group_results` attribute is also available, which maintains the full
+      model results.
+    """
 
     def __init__(self, *args, **kwargs):
         """Initialize object with desired settings."""

From 656532ecf4c1737d39b69cf8117b4799720bfd1a Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 11:33:46 -0400
Subject: [PATCH 15/99] fix docs (group -> time)

---
 specparam/objs/time.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index 8ef53a14..4ae4155d 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -35,7 +35,7 @@ def decorated(*args, **kwargs):
 @replace_docstring_sections([docs_get_section(SpectralModel.__doc__, 'Parameters'),
                              docs_get_section(SpectralModel.__doc__, 'Notes')])
 class SpectralTimeModel(SpectralGroupModel):
-    """Model a group of power spectra as a combination of aperiodic and periodic components.
+    """Model a spectrogram as a combination of aperiodic and periodic components.
 
     WARNING: frequency and power values inputs must be in linear space.
 
@@ -133,7 +133,7 @@ def add_data(self, freqs, spectrogram, freq_range=None):
 
     def report(self, freqs=None, power_spectra=None, freq_range=None,
                peak_org=None, report_type='time', n_jobs=1, progress=None):
-        """Fit a group of power spectra and display a report, with a plot and printed results.
+        """Fit a spectrogram and display a report, with a plot and printed results.
 
         Parameters
         ----------
@@ -234,7 +234,7 @@ def save_report(self, file_name, file_path=None, add_settings=True):
 
 
     def load(self, file_name, file_path=None, peak_org=None):
-        """Load group data from file.
+        """Load time data from file.
 
         Parameters
         ----------

From 59eb3f489f68e941d23c8af679195ddf33b9f6b1 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 14:19:46 -0400
Subject: [PATCH 16/99] tweak for knee params in time string

---
 specparam/core/strings.py | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/specparam/core/strings.py b/specparam/core/strings.py
index 9d567938..95e2c954 100644
--- a/specparam/core/strings.py
+++ b/specparam/core/strings.py
@@ -435,14 +435,12 @@ def gen_time_results_str(time_model, concise=False):
     if not time_model.has_model:
         raise NoModelError("No model fit results are available, can not proceed.")
 
-    # Extract all the relevant data for printing
+    # Get parameter information needed for printing
     pe_labels = get_periodic_labels(time_model.time_results)
     band_labels = [\
         pe_labels['cf'][band_ind].split('_')[-1 if pe_labels['cf'][-2:] == 'cf' else 0] \
         for band_ind in range(len(pe_labels['cf']))]
-
-    kns = time_model.get_params('aperiodic_params', 'knee') \
-       if time_model.aperiodic_mode == 'knee' else np.array([0])
+    has_knee = time_model.aperiodic_mode == 'knee'
 
     str_lst = [
 
@@ -469,8 +467,10 @@ def gen_time_results_str(time_model, concise=False):
         '',
         'Aperiodic Fit Values:',
         *[el for el in ['    Knees - Min: {:6.2f}, Max: {:6.2f}, Mean: {:6.2f}'
-                        .format(np.nanmin(kns), np.nanmax(kns), np.nanmean(kns)),
-                       ] if time_model.aperiodic_mode == 'knee'],
+                        .format(np.nanmin(time_model.time_results['knee'] if has_knee else 0),
+                                np.nanmax(time_model.time_results['knee'] if has_knee else 0),
+                                np.nanmean(time_model.time_results['knee'] if has_knee else 0)),
+                       ] if has_knee],
         'Exponents - Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
         .format(np.nanmin(time_model.time_results['exponent']),
                 np.nanmax(time_model.time_results['exponent']),
@@ -510,7 +510,6 @@ def gen_time_results_str(time_model, concise=False):
     return output
 
 
-
 def gen_issue_str(concise=False):
     """Generate a string representation of instructions to report an issue.
 

From 8e6038928f4293bad088ee7072d93328ab825778 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 15:19:12 -0400
Subject: [PATCH 17/99] add explicit x-axis vals pass in to plot_params time
 plots

---
 specparam/plts/templates.py            | 19 ++++++++++++++-----
 specparam/plts/time.py                 |  6 ++++--
 specparam/tests/plts/test_templates.py |  4 ++--
 3 files changed, 20 insertions(+), 9 deletions(-)

diff --git a/specparam/plts/templates.py b/specparam/plts/templates.py
index 50ed3a8f..360e5742 100644
--- a/specparam/plts/templates.py
+++ b/specparam/plts/templates.py
@@ -137,12 +137,14 @@ def plot_hist(data, label, title=None, n_bins=25, x_lims=None, ax=None):
 
 
 @check_dependency(plt, 'matplotlib')
-def plot_param_over_time(param, label=None, title=None, add_legend=True, add_xlabel=True,
-                         ax=None, **plot_kwargs):
+def plot_param_over_time(times, param, label=None, title=None, add_legend=True, add_xlabel=True,
+                         drop_xticks=False, ax=None, **plot_kwargs):
     """Plot a parameter over time.
 
     Parameters
     ----------
+    times : 1d array
+        xx
     param : 1d array
         Parameter values to plot.
     label : str, optional
@@ -161,7 +163,10 @@ def plot_param_over_time(param, label=None, title=None, add_legend=True, add_xla
 
     n_windows = len(param)
 
-    ax.plot(param, label=label,
+    if times is None:
+        times = np.arange(0, len(param))
+
+    ax.plot(times, param, label=label,
             alpha=plot_kwargs.pop('alpha', 0.8),
             **plot_kwargs)
 
@@ -169,6 +174,9 @@ def plot_param_over_time(param, label=None, title=None, add_legend=True, add_xla
         ax.set_xlabel('Time Window')
     ax.set_ylabel(label if label else 'Parameter Value')
 
+    if drop_xticks:
+        ax.set_xticks([], [])
+
     if label and add_legend:
         ax.legend(loc='upper left', framealpha=plot_kwargs.pop('legend_framealpha', 0.9))
 
@@ -177,7 +185,8 @@ def plot_param_over_time(param, label=None, title=None, add_legend=True, add_xla
 
 
 @check_dependency(plt, 'matplotlib')
-def plot_params_over_time(params, labels=None, title=None, colors=None, ax=None, **plot_kwargs):
+def plot_params_over_time(times, params, labels=None, title=None, colors=None,
+                          ax=None, **plot_kwargs):
     """Plot multiple parameters over time.
 
     Parameters
@@ -207,7 +216,7 @@ def plot_params_over_time(params, labels=None, title=None, colors=None, ax=None,
             axes[ind].spines.right.set_position(("axes", 1.1 + (.1 * nax)))
 
     for cax, cparams, label, color in zip(axes, params, labels, colors):
-        plot_param_over_time(cparams, label, add_legend=False, color=color,
+        plot_param_over_time(times, cparams, label, add_legend=False, color=color,
                              ax=cax, **plot_kwargs)
 
     if bool(labels):
diff --git a/specparam/plts/time.py b/specparam/plts/time.py
index cc732c8b..49b62213 100644
--- a/specparam/plts/time.py
+++ b/specparam/plts/time.py
@@ -65,12 +65,13 @@ def plot_time_model(time_model, save_fig=False, file_name=None, file_path=None,
         ap_labels.insert(1, 'Knee')
         ap_colors.insert(1, PARAM_COLORS['knee'])
 
-    plot_params_over_time(ap_params, labels=ap_labels, add_xlabel=False,
+    plot_params_over_time(None, ap_params, labels=ap_labels, add_xlabel=False,
                           colors=ap_colors, title='Aperiodic', ax=next(axes))
 
     # 02: periodic parameters
     for band_ind in range(n_bands):
         plot_params_over_time(\
+            None,
             [time_model.time_results[pe_labels['cf'][band_ind]],
              time_model.time_results[pe_labels['pw'][band_ind]],
              time_model.time_results[pe_labels['bw'][band_ind]]],
@@ -79,7 +80,8 @@ def plot_time_model(time_model, save_fig=False, file_name=None, file_path=None,
             title='Periodic', ax=next(axes))
 
     # 03: goodness of fit
-    plot_params_over_time([time_model.time_results['error'],
+    plot_params_over_time(None,
+                          [time_model.time_results['error'],
                            time_model.time_results['r_squared']],
                           labels=['Error', 'R-squared'],
                           colors=[PARAM_COLORS['error'], PARAM_COLORS['r_squared']],
diff --git a/specparam/tests/plts/test_templates.py b/specparam/tests/plts/test_templates.py
index c747937a..441ad09c 100644
--- a/specparam/tests/plts/test_templates.py
+++ b/specparam/tests/plts/test_templates.py
@@ -35,7 +35,7 @@ def test_plot_param_over_time():
 
     param = np.array([1, 2, 3, 2, 1, 2, 4, 2, 3, 2, 1])
 
-    plot_param_over_time(param, label='param', color='red')
+    plot_param_over_time(None, param, label='param', color='red')
 
 @plot_test
 def test_plot_params_over_time():
@@ -43,4 +43,4 @@ def test_plot_params_over_time():
     params = [np.array([1, 2, 3, 2, 1, 2, 4, 2, 3, 2, 1]),
               np.array([2, 3, 2, 1, 2, 4, 2, 3, 2, 1, 2])]
 
-    plot_params_over_time(params, labels=['param1', 'param2'], colors=['blue', 'red'])
+    plot_params_over_time(None, params, labels=['param1', 'param2'], colors=['blue', 'red'])

From 258fb59ed44a2d922147af18300cbd88ea9dfd40 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 16:53:07 -0400
Subject: [PATCH 18/99] add data funcs

---
 specparam/tests/utils/test_data.py | 27 ++++++++++++
 specparam/utils/data.py            | 69 ++++++++++++++++++++++++++++++
 2 files changed, 96 insertions(+)

diff --git a/specparam/tests/utils/test_data.py b/specparam/tests/utils/test_data.py
index 4264bbee..a4994719 100644
--- a/specparam/tests/utils/test_data.py
+++ b/specparam/tests/utils/test_data.py
@@ -9,6 +9,33 @@
 ###################################################################################################
 ###################################################################################################
 
+def test_compute_average():
+
+    data = np.array([[0., 1., 2., 3., 4., 5.],
+                     [1., 2., 3., 4., 5., 6.],
+                     [5., 6., 7., 8., 9., 8.]])
+
+    out1 = compute_average(data, 'mean')
+    assert isinstance(out1, np.ndarray)
+
+    out2 = compute_average(data, 'median')
+    assert not np.array_equal(out2, out1)
+
+def test_compute_dispersion():
+
+    data = np.array([[0., 1., 2., 3., 4., 5.],
+                     [1., 2., 3., 4., 5., 6.],
+                     [5., 6., 7., 8., 9., 8.]])
+
+    out1 = compute_dispersion(data, 'var')
+    assert isinstance(out1, np.ndarray)
+
+    out2 = compute_dispersion(data, 'std')
+    assert not np.array_equal(out2, out1)
+
+    out3 = compute_dispersion(data, 'sem')
+    assert not np.array_equal(out3, out1)
+
 def test_trim_spectrum():
 
     f_in = np.array([0., 1., 2., 3., 4., 5.])
diff --git a/specparam/utils/data.py b/specparam/utils/data.py
index 44e883cc..f5bfdbf5 100644
--- a/specparam/utils/data.py
+++ b/specparam/utils/data.py
@@ -3,10 +3,79 @@
 from itertools import repeat
 
 import numpy as np
+from scipy.stats import sem
 
 ###################################################################################################
 ###################################################################################################
 
+AVG_FUNCS = {
+    'mean' : np.mean,
+    'median' : np.median,
+}
+
+DISPERSION_FUNCS = {
+    'var' : np.var,
+    'std' : np.std,
+    'sem' : sem,
+}
+
+###################################################################################################
+###################################################################################################
+
+def compute_average(data, average='mean'):
+    """Compute the average across an array of data.
+
+    Parameters
+    ----------
+    data : 2d array
+        Data to compute average across.
+        Average is computed across the 0th axis.
+    average : {'mean', 'median'} or callable
+        Which approach to take to compute the average.
+
+    Returns
+    -------
+    avg_data : 1d array
+        Average across given data array.
+    """
+
+    if isinstance(average, str) and data.ndim == 2:
+        avg_data = AVG_FUNCS[average](data, axis=0)
+    elif isfunction(average) and data.ndim == 2:
+        avg_data = average(data)
+    else:
+        avg_data = data
+
+    return avg_data
+
+
+def compute_dispersion(data, dispersion='std'):
+    """Compute the dispersion across an array of data.
+
+    Parameters
+    ----------
+    data : 2d array
+        Data to compute dispersion across.
+        Dispersion is computed across the 0th axis.
+    dispersion : {'var', 'std', 'sem'}
+        Which approach to take to compute the dispersion.
+
+    Returns
+    -------
+    dispersion_data : 1d array
+        Dispersion across given data array.
+    """
+
+    if isinstance(dispersion, str):
+        dispersion_data = DISPERSION_FUNCS[dispersion](data, axis=0)
+    elif isfunction(dispersion):
+        dispersion_data = dispersion(data)
+    else:
+        dispersion_data = data
+
+    return dispersion_data
+
+
 def trim_spectrum(freqs, power_spectra, f_range):
     """Extract a frequency range from power spectra.
 

From ada41505cade5f19a9b46186d6f2e15f8c066174 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 16:53:36 -0400
Subject: [PATCH 19/99] add plot_yshade template function

---
 specparam/plts/templates.py            | 46 ++++++++++++++++++++++++++
 specparam/tests/plts/test_templates.py |  7 ++++
 2 files changed, 53 insertions(+)

diff --git a/specparam/plts/templates.py b/specparam/plts/templates.py
index 360e5742..da69665c 100644
--- a/specparam/plts/templates.py
+++ b/specparam/plts/templates.py
@@ -10,6 +10,7 @@
 
 import numpy as np
 
+from specparam.utils.data import compute_average, compute_dispersion
 from specparam.core.modutils import safe_import, check_dependency
 from specparam.plts.utils import check_ax, set_alpha
 from specparam.plts.settings import PLT_FIGSIZES, PLT_COLORS, DEFAULT_COLORS
@@ -184,6 +185,51 @@ def plot_param_over_time(times, param, label=None, title=None, add_legend=True,
         ax.set_title(title)
 
 
+@check_dependency(plt, 'matplotlib')
+def plot_yshade(x_vals, y_vals, average='mean', shade='std', scale=1., color=None,
+                plot_function=None, ax=None, **plot_kwargs):
+    """Create a plot with y-shading.
+
+    Parameters
+    ----------
+    x_vals : 1d array
+        Data values to be plotted on the x-axis.
+    y_vals : 1d or 2d array
+        Data values to be plotted on the y-axis. `shade` must be provided if 1d.
+    average : 'mean', 'median' or callable, optional, default: 'mean'
+        Averaging approach for plotting the average. Only used if y_vals is 2d.
+    shade : 'std', 'sem', 1d array or callable, optional, default: 'std'
+        Approach for shading above/below the average.
+    scale : float, optional, default: 1.
+        Factor to multiply the plotted shade by.
+    color : str, optional, default: None
+        Color to plot.
+    plot_function : callable, optional
+        xx
+    ax : matplotlib.Axes, optional
+        Figure axes upon which to plot.
+    **plot_kwargs
+        Additional keyword arguments to pass into the plot function.
+    """
+
+    ax = check_ax(ax)
+
+    shade_alpha = plot_kwargs.pop('shade_alpha', 0.25)
+
+    avg_data = compute_average(y_vals, average=average)
+    if plot_function:
+        plot_function(x_vals, avg_data, color=color, ax=ax, **plot_kwargs)
+    else:
+        ax.plot(x_vals, avg_data, color=color, **plot_kwargs)
+
+    # Compute shade values and apply scaling
+    shade_vals = compute_dispersion(y_vals, shade) * scale
+
+    # Plot +/- yshading around spectrum
+    ax.fill_between(x_vals, avg_data - shade_vals, avg_data + shade_vals,
+                    alpha=shade_alpha, color=color)
+
+
 @check_dependency(plt, 'matplotlib')
 def plot_params_over_time(times, params, labels=None, title=None, colors=None,
                           ax=None, **plot_kwargs):
diff --git a/specparam/tests/plts/test_templates.py b/specparam/tests/plts/test_templates.py
index 441ad09c..577ca13d 100644
--- a/specparam/tests/plts/test_templates.py
+++ b/specparam/tests/plts/test_templates.py
@@ -30,6 +30,13 @@ def test_plot_hist(skip_if_no_mpl):
     data = np.random.randint(0, 100, 100)
     plot_hist(data, 'label', 'title')
 
+@plot_test
+def test_plot_yshade(skip_if_no_mpl):
+
+    xs = np.array([1, 2, 3])
+    ys = np.array([[1, 2, 3], [2, 3, 4]])
+    plot_yshade(xs, ys)
+
 @plot_test
 def test_plot_param_over_time():
 

From 77a82ff087cfaca32d6f4890080430da12c4ec83 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 16:54:03 -0400
Subject: [PATCH 20/99] fix up some time docstrings

---
 specparam/objs/time.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index 4ae4155d..f368e21c 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -44,7 +44,7 @@ class SpectralTimeModel(SpectralGroupModel):
 
     Parameters
     ----------
-    %copied in from SpectralGroupModel object
+    %copied in from SpectralModel object
 
     Attributes
     ----------
@@ -165,7 +165,7 @@ def report(self, freqs=None, power_spectra=None, freq_range=None,
 
     def fit(self, freqs=None, power_spectra=None, freq_range=None, peak_org=None,
             n_jobs=1, progress=None):
-        """Fit a spectrogram
+        """Fit a spectrogram.
 
         Parameters
         ----------
@@ -255,7 +255,7 @@ def load(self, file_name, file_path=None, peak_org=None):
 
 
     def _convert_to_time_results(self, peak_org):
-        """Convert the model results into to be organized across time windows.
+        """Convert the model results to be organized across time windows.
 
         Parameters
         ----------

From 5f3b0abb46ab2a5bf2c5cf83619348653dbc6a34 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 16:56:37 -0400
Subject: [PATCH 21/99] docstring cleans and moves

---
 specparam/plts/templates.py | 96 +++++++++++++++++++------------------
 1 file changed, 50 insertions(+), 46 deletions(-)

diff --git a/specparam/plts/templates.py b/specparam/plts/templates.py
index da69665c..b40fb9a3 100644
--- a/specparam/plts/templates.py
+++ b/specparam/plts/templates.py
@@ -137,6 +137,51 @@ def plot_hist(data, label, title=None, n_bins=25, x_lims=None, ax=None):
     ax.tick_params(axis='both', labelsize=12)
 
 
+@check_dependency(plt, 'matplotlib')
+def plot_yshade(x_vals, y_vals, average='mean', shade='std', scale=1., color=None,
+                plot_function=None, ax=None, **plot_kwargs):
+    """Create a plot with y-shading.
+
+    Parameters
+    ----------
+    x_vals : 1d array
+        Data values to be plotted on the x-axis.
+    y_vals : 1d or 2d array
+        Data values to be plotted on the y-axis. `shade` must be provided if 1d.
+    average : 'mean', 'median' or callable, optional, default: 'mean'
+        Averaging approach for plotting the average. Only used if y_vals is 2d.
+    shade : 'std', 'sem', 1d array or callable, optional, default: 'std'
+        Approach for shading above/below the average.
+    scale : float, optional, default: 1.
+        Factor to multiply the plotted shade by.
+    color : str, optional, default: None
+        Color to plot.
+    plot_function : callable, optional
+        xx
+    ax : matplotlib.Axes, optional
+        Figure axes upon which to plot.
+    **plot_kwargs
+        Additional keyword arguments to pass into the plot function.
+    """
+
+    ax = check_ax(ax)
+
+    shade_alpha = plot_kwargs.pop('shade_alpha', 0.25)
+
+    avg_data = compute_average(y_vals, average=average)
+    if plot_function:
+        plot_function(x_vals, avg_data, color=color, ax=ax, **plot_kwargs)
+    else:
+        ax.plot(x_vals, avg_data, color=color, **plot_kwargs)
+
+    # Compute shade values and apply scaling
+    shade_vals = compute_dispersion(y_vals, shade) * scale
+
+    # Plot +/- y-shading around spectrum
+    ax.fill_between(x_vals, avg_data - shade_vals, avg_data + shade_vals,
+                    alpha=shade_alpha, color=color)
+
+
 @check_dependency(plt, 'matplotlib')
 def plot_param_over_time(times, param, label=None, title=None, add_legend=True, add_xlabel=True,
                          drop_xticks=False, ax=None, **plot_kwargs):
@@ -145,7 +190,8 @@ def plot_param_over_time(times, param, label=None, title=None, add_legend=True,
     Parameters
     ----------
     times : 1d array
-        xx
+        Time indices, to be plotted on the x-axis.
+        If set as None, the x-labels are set as window indices.
     param : 1d array
         Parameter values to plot.
     label : str, optional
@@ -185,51 +231,6 @@ def plot_param_over_time(times, param, label=None, title=None, add_legend=True,
         ax.set_title(title)
 
 
-@check_dependency(plt, 'matplotlib')
-def plot_yshade(x_vals, y_vals, average='mean', shade='std', scale=1., color=None,
-                plot_function=None, ax=None, **plot_kwargs):
-    """Create a plot with y-shading.
-
-    Parameters
-    ----------
-    x_vals : 1d array
-        Data values to be plotted on the x-axis.
-    y_vals : 1d or 2d array
-        Data values to be plotted on the y-axis. `shade` must be provided if 1d.
-    average : 'mean', 'median' or callable, optional, default: 'mean'
-        Averaging approach for plotting the average. Only used if y_vals is 2d.
-    shade : 'std', 'sem', 1d array or callable, optional, default: 'std'
-        Approach for shading above/below the average.
-    scale : float, optional, default: 1.
-        Factor to multiply the plotted shade by.
-    color : str, optional, default: None
-        Color to plot.
-    plot_function : callable, optional
-        xx
-    ax : matplotlib.Axes, optional
-        Figure axes upon which to plot.
-    **plot_kwargs
-        Additional keyword arguments to pass into the plot function.
-    """
-
-    ax = check_ax(ax)
-
-    shade_alpha = plot_kwargs.pop('shade_alpha', 0.25)
-
-    avg_data = compute_average(y_vals, average=average)
-    if plot_function:
-        plot_function(x_vals, avg_data, color=color, ax=ax, **plot_kwargs)
-    else:
-        ax.plot(x_vals, avg_data, color=color, **plot_kwargs)
-
-    # Compute shade values and apply scaling
-    shade_vals = compute_dispersion(y_vals, shade) * scale
-
-    # Plot +/- yshading around spectrum
-    ax.fill_between(x_vals, avg_data - shade_vals, avg_data + shade_vals,
-                    alpha=shade_alpha, color=color)
-
-
 @check_dependency(plt, 'matplotlib')
 def plot_params_over_time(times, params, labels=None, title=None, colors=None,
                           ax=None, **plot_kwargs):
@@ -237,6 +238,9 @@ def plot_params_over_time(times, params, labels=None, title=None, colors=None,
 
     Parameters
     ----------
+    times : 1d array
+        Time indices, to be plotted on the x-axis.
+        If set as None, the x-labels are set as window indices.
     params : list of 1d array
         Parameter values to plot.
     labels : list of str

From 5a2859206f7f5c748620ce50373dffa0a865c39a Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 17:02:16 -0400
Subject: [PATCH 22/99] add plot_param_over_time_yshade

---
 specparam/plts/templates.py            | 38 ++++++++++++++++++++++++--
 specparam/tests/plts/test_templates.py |  7 +++++
 2 files changed, 43 insertions(+), 2 deletions(-)

diff --git a/specparam/plts/templates.py b/specparam/plts/templates.py
index b40fb9a3..81fa1964 100644
--- a/specparam/plts/templates.py
+++ b/specparam/plts/templates.py
@@ -203,7 +203,7 @@ def plot_param_over_time(times, param, label=None, title=None, add_legend=True,
     ax : matplotlib.Axes, optional
         Figure axes upon which to plot.
     **plot_kwargs
-        Keyword arguments to pass into the ``style_plot``.
+        Additional keyword arguments for the plot call.
     """
 
     ax = check_ax(ax, plot_kwargs.pop('figsize', PLT_FIGSIZES['time']))
@@ -250,7 +250,7 @@ def plot_params_over_time(times, params, labels=None, title=None, colors=None,
     ax : matplotlib.Axes, optional
         Figure axes upon which to plot.
     **plot_kwargs
-        Keyword arguments to pass into the ``style_plot``.
+        Additional keyword arguments for the plot call.
     """
 
     labels = repeat(labels) if not isinstance(labels, list) else cycle(labels)
@@ -279,3 +279,37 @@ def plot_params_over_time(times, params, labels=None, title=None, colors=None,
     # Puts the axis with the legend 'on top', while also making it transparent (to see others)
     ax0.set_zorder(1)
     ax0.patch.set_visible(False)
+
+
+@check_dependency(plt, 'matplotlib')
+def plot_param_over_time_yshade(times, param, average='mean', shade='std', scale=1.,
+                                color=None, ax=None, **plot_kwargs):
+    """Plot parameter over time with y-axis shading.
+
+    Parameters
+    ----------
+    times : 1d array
+        Time indices, to be plotted on the x-axis.
+        If set as None, the x-labels are set as window indices.
+    param : 2d array
+        Parameter values to plot, organized as [n_events, n_time_windows].
+    average : 'mean', 'median' or callable, optional, default: 'mean'
+        Averaging approach for plotting the average. Only used if y_vals is 2d.
+    shade : 'std', 'sem', 1d array or callable, optional, default: 'std'
+        Approach for shading above/below the average.
+    scale : float, optional, default: 1.
+        Factor to multiply the plotted shade by.
+    color : str, optional, default: None
+        Color to plot.
+    ax : matplotlib.Axes, optional
+        Figure axes upon which to plot.
+    **plot_kwargs
+        Additional keyword arguments for the plot call.
+    """
+
+    ax = check_ax(ax, plot_kwargs.pop('figsize', PLT_FIGSIZES['time']))
+
+    times = np.arange(0, param.shape[-1]) if times is None else times
+    plot_yshade(times, param, average=average, shade=shade, scale=scale,
+                color=color, plot_function=plot_param_over_time,
+                ax=ax, **plot_kwargs)
diff --git a/specparam/tests/plts/test_templates.py b/specparam/tests/plts/test_templates.py
index 577ca13d..93b21cf7 100644
--- a/specparam/tests/plts/test_templates.py
+++ b/specparam/tests/plts/test_templates.py
@@ -51,3 +51,10 @@ def test_plot_params_over_time():
               np.array([2, 3, 2, 1, 2, 4, 2, 3, 2, 1, 2])]
 
     plot_params_over_time(None, params, labels=['param1', 'param2'], colors=['blue', 'red'])
+
+@plot_test
+def test_plot_param_over_time_yshade():
+
+    params = np.array([[1, 2, 3, 2, 1, 2, 4, 2, 3, 2, 1],
+                       [2, 3, 2, 1, 2, 4, 2, 3, 2, 1, 2]])
+    plot_param_over_time_yshade(None, params)

From a1a3e7f717653e5400f5729c26b57b7ec49dcd48 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 17:09:34 -0400
Subject: [PATCH 23/99] update tests for data funcs

---
 specparam/tests/utils/test_data.py | 12 ++++++++++++
 specparam/utils/data.py            |  1 +
 2 files changed, 13 insertions(+)

diff --git a/specparam/tests/utils/test_data.py b/specparam/tests/utils/test_data.py
index a4994719..b3f59385 100644
--- a/specparam/tests/utils/test_data.py
+++ b/specparam/tests/utils/test_data.py
@@ -21,6 +21,12 @@ def test_compute_average():
     out2 = compute_average(data, 'median')
     assert not np.array_equal(out2, out1)
 
+    def _average_callable(data):
+        return np.mean(data, axis=0)
+    out3 = compute_average(data, _average_callable)
+    assert isinstance(out3, np.ndarray)
+    assert np.array_equal(out3, out1)
+
 def test_compute_dispersion():
 
     data = np.array([[0., 1., 2., 3., 4., 5.],
@@ -36,6 +42,12 @@ def test_compute_dispersion():
     out3 = compute_dispersion(data, 'sem')
     assert not np.array_equal(out3, out1)
 
+    def _dispersion_callable(data):
+        return np.std(data, axis=0)
+    out4 = compute_dispersion(data, _dispersion_callable)
+    assert isinstance(out4, np.ndarray)
+    assert np.array_equal(out4, out2)
+
 def test_trim_spectrum():
 
     f_in = np.array([0., 1., 2., 3., 4., 5.])
diff --git a/specparam/utils/data.py b/specparam/utils/data.py
index f5bfdbf5..d234213e 100644
--- a/specparam/utils/data.py
+++ b/specparam/utils/data.py
@@ -1,6 +1,7 @@
 """Utilities for working with data and models."""
 
 from itertools import repeat
+from inspect import isfunction
 
 import numpy as np
 from scipy.stats import sem

From 62cd05c177809e191495892a3537eb2351a4ba83 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 17:10:24 -0400
Subject: [PATCH 24/99] use plot_yshade in spectra shade plot

---
 specparam/plts/spectra.py            | 41 +++++-----------------------
 specparam/tests/plts/test_spectra.py |  8 ------
 2 files changed, 7 insertions(+), 42 deletions(-)

diff --git a/specparam/plts/spectra.py b/specparam/plts/spectra.py
index a7dc04fd..bf2139d6 100644
--- a/specparam/plts/spectra.py
+++ b/specparam/plts/spectra.py
@@ -12,6 +12,7 @@
 from scipy.stats import sem
 
 from specparam.core.modutils import safe_import, check_dependency
+from specparam.plts.templates import plot_yshade
 from specparam.plts.settings import PLT_FIGSIZES
 from specparam.plts.style import style_spectrum_plot, style_plot
 from specparam.plts.utils import check_ax, add_shades, savefig, check_plot_kwargs
@@ -121,7 +122,7 @@ def plot_spectra_shading(freqs, power_spectra, shades, shade_colors='r',
 @savefig
 @style_plot
 @check_dependency(plt, 'matplotlib')
-def plot_spectra_yshade(freqs, power_spectra, shade='std', average='mean', scale=1,
+def plot_spectra_yshade(freqs, power_spectra, average='mean', shade='std', scale=1,
                         log_freqs=False, log_powers=False, color=None, label=None,
                         ax=None, **plot_kwargs):
     """Plot standard deviation or error as a shaded region around the mean spectrum.
@@ -132,10 +133,10 @@ def plot_spectra_yshade(freqs, power_spectra, shade='std', average='mean', scale
         Frequency values, to be plotted on the x-axis.
     power_spectra : 1d or 2d array
         Power values, to be plotted on the y-axis. ``shade`` must be provided if 1d.
-    shade : 'std', 'sem', 1d array or callable, optional, default: 'std'
-        Approach for shading above/below the mean spectrum.
     average : 'mean', 'median' or callable, optional, default: 'mean'
         Averaging approach for the average spectrum to plot. Only used if power_spectra is 2d.
+    shade : 'std', 'sem', 1d array or callable, optional, default: 'std'
+        Approach for shading above/below the mean spectrum.
     scale : int, optional, default: 1
         Factor to multiply the plotted shade by.
     log_freqs : bool, optional, default: False
@@ -157,40 +158,12 @@ def plot_spectra_yshade(freqs, power_spectra, shade='std', average='mean', scale
 
     ax = check_ax(ax, plot_kwargs.pop('figsize', PLT_FIGSIZES['spectral']))
 
-    # Set plot data & labels, logging if requested
     plt_freqs = np.log10(freqs) if log_freqs else freqs
     plt_powers = np.log10(power_spectra) if log_powers else power_spectra
 
-    # Organize mean spectrum to plot
-    avg_funcs = {'mean' : np.mean, 'median' : np.median}
-
-    if isinstance(average, str) and plt_powers.ndim == 2:
-        avg_powers = avg_funcs[average](plt_powers, axis=0)
-    elif isfunction(average) and plt_powers.ndim == 2:
-        avg_powers = average(plt_powers)
-    else:
-        avg_powers = plt_powers
-
-    # Plot average power spectrum
-    ax.plot(plt_freqs, avg_powers, linewidth=2.0, color=color, label=label)
-
-    # Organize shading to plot
-    shade_funcs = {'std' : np.std, 'sem' : sem}
-
-    if isinstance(shade, str):
-        shade_vals = scale * shade_funcs[shade](plt_powers, axis=0)
-    elif isfunction(shade):
-        shade_vals = scale * shade(plt_powers)
-    else:
-        shade_vals = scale * shade
-
-    upper_shade = avg_powers + shade_vals
-    lower_shade = avg_powers - shade_vals
-
-    # Plot +/- yshading around spectrum
-    alpha = plot_kwargs.pop('alpha', 0.25)
-    ax.fill_between(plt_freqs, lower_shade, upper_shade,
-                    alpha=alpha, color=color, **plot_kwargs)
+    plot_yshade(plt_freqs, plt_powers, average=average, shade=shade, scale=scale,
+                color=color, label=label, plot_function=plot_spectra,
+                ax=ax, **plot_kwargs)
 
     style_spectrum_plot(ax, log_freqs, log_powers)
 
diff --git a/specparam/tests/plts/test_spectra.py b/specparam/tests/plts/test_spectra.py
index 11677d0e..ec85c7f9 100644
--- a/specparam/tests/plts/test_spectra.py
+++ b/specparam/tests/plts/test_spectra.py
@@ -80,14 +80,6 @@ def test_plot_spectra_yshade(skip_if_no_mpl, tfg):
                         file_path=TEST_PLOTS_PATH,
                         file_name='test_plot_spectra_yshade3.png')
 
-    # Plot shade with custom average and shade callables
-    def _average_callable(powers): return np.mean(powers, axis=0)
-    def _shade_callable(powers): return np.std(powers, axis=0)
-
-    plot_spectra_yshade(freqs, powers, shade=_shade_callable, average=_average_callable,
-                        log_powers=True, file_path=TEST_PLOTS_PATH,
-                        file_name='test_plot_spectra_yshade4.png')
-
 @plot_test
 def test_plot_spectrogram(skip_if_no_mpl, tft):
 

From 3d82e099d212f9263f0b794e5322dc756fb73f43 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 22:29:59 -0400
Subject: [PATCH 25/99] add str func for event model

---
 specparam/core/strings.py            | 98 ++++++++++++++++++++++++++++
 specparam/tests/core/test_strings.py |  6 +-
 2 files changed, 103 insertions(+), 1 deletion(-)

diff --git a/specparam/core/strings.py b/specparam/core/strings.py
index 95e2c954..c4825f4c 100644
--- a/specparam/core/strings.py
+++ b/specparam/core/strings.py
@@ -510,6 +510,104 @@ def gen_time_results_str(time_model, concise=False):
     return output
 
 
+def gen_event_results_str(event_model, concise=False):
+    """Generate a string representation of event fit results.
+
+    Parameters
+    ----------
+    event_model : SpectralTimeEventModel
+        Object to access results from.
+    concise : bool, optional, default: False
+        Whether to print the report in concise mode.
+
+    Returns
+    -------
+    output : str
+        Formatted string of results.
+
+    Raises
+    ------
+    NoModelError
+        If no model fit data is available to report.
+    """
+
+    if not event_model.has_model:
+        raise NoModelError("No model fit results are available, can not proceed.")
+
+    # Extract all the relevant data for printing
+    pe_labels = get_periodic_labels(event_model.event_time_results)
+    band_labels = [\
+        pe_labels['cf'][band_ind].split('_')[-1 if pe_labels['cf'][-2:] == 'cf' else 0] \
+        for band_ind in range(len(pe_labels['cf']))]
+    has_knee = event_model.aperiodic_mode == 'knee'
+
+    str_lst = [
+
+        # Header
+        '=',
+        '',
+        'EVENT RESULTS',
+        '',
+
+        # Group information
+        'Number of events fit: {}'.format(len(event_model.event_group_results)),
+        '',
+
+        # Frequency range and resolution
+        'The model was run on the frequency range {} - {} Hz'.format(
+            int(np.floor(event_model.freq_range[0])), int(np.ceil(event_model.freq_range[1]))),
+        'Frequency Resolution is {:1.2f} Hz'.format(event_model.freq_res),
+        '',
+
+        # Aperiodic parameters - knee fit status, and quick exponent description
+        'Power spectra were fit {} a knee.'.format(\
+            'with' if event_model.aperiodic_mode == 'knee' else 'without'),
+        '',
+        'Aperiodic params (values across events):',
+        *[el for el in ['    Knees - Min: {:6.2f}, Max: {:6.2f}, Mean: {:6.2f}'
+                        .format(np.nanmin(np.mean(event_model.event_time_results['knee'], 1) if has_knee else 0),
+                                np.nanmax(np.mean(event_model.event_time_results['knee'], 1) if has_knee else 0),
+                                np.nanmean(np.mean(event_model.event_time_results['knee'], 1) if has_knee else 0)),
+                       ] if has_knee],
+        'Exponents - Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
+        .format(np.nanmin(np.mean(event_model.event_time_results['exponent'], 1)),
+                np.nanmax(np.mean(event_model.event_time_results['exponent'], 1)),
+                np.nanmean(np.mean(event_model.event_time_results['exponent'], 1))),
+        '',
+
+        # Periodic parameters
+        'Periodic params (mean values across events):',
+        *['{:>6s} - CF: {:5.2f}, PW: {:5.2f}, BW: {:5.2f}, Presence: {:3.1f}%'.format(
+            label,
+            np.nanmean(event_model.event_time_results[pe_labels['cf'][ind]]),
+            np.nanmean(event_model.event_time_results[pe_labels['pw'][ind]]),
+            np.nanmean(event_model.event_time_results[pe_labels['bw'][ind]]),
+            100 * sum(sum(~np.isnan(event_model.event_time_results[pe_labels['cf'][ind]]))) \
+                / event_model.event_time_results[pe_labels['cf'][ind]].size)
+                for ind, label in enumerate(band_labels)],
+        '',
+
+        # Goodness if fit
+        'Goodness of fit (values across events):',
+        '   R2s -  Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
+        .format(np.nanmin(np.mean(event_model.event_time_results['r_squared'], 1)),
+                np.nanmax(np.mean(event_model.event_time_results['r_squared'], 1)),
+                np.nanmean(np.mean(event_model.event_time_results['r_squared'], 1))),
+        'Errors -  Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
+        .format(np.nanmin(np.mean(event_model.event_time_results['error'], 1)),
+                np.nanmax(np.mean(event_model.event_time_results['error'], 1)),
+                np.nanmean(np.mean(event_model.event_time_results['error'], 1))),
+        '',
+
+        # Footer
+        '='
+    ]
+
+    output = _format(str_lst, concise)
+
+    return output
+
+
 def gen_issue_str(concise=False):
     """Generate a string representation of instructions to report an issue.
 
diff --git a/specparam/tests/core/test_strings.py b/specparam/tests/core/test_strings.py
index 6070b37d..464e4d5a 100644
--- a/specparam/tests/core/test_strings.py
+++ b/specparam/tests/core/test_strings.py
@@ -42,7 +42,11 @@ def test_gen_group_results_str(tfg):
 
 def test_gen_time_results_str(tft):
 
-    assert gen_group_results_str(tft)
+    assert gen_time_results_str(tft)
+
+def test_gen_time_results_str(tfe):
+
+    assert gen_event_results_str(tfe)
 
 def test_gen_issue_str():
 

From af7543bc890a345528587c0da27528ca09c639d4 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 22:33:58 -0400
Subject: [PATCH 26/99] add event object plot & test

---
 specparam/plts/event.py           | 83 +++++++++++++++++++++++++++++++
 specparam/tests/plts/test_time.py |  4 +-
 2 files changed, 85 insertions(+), 2 deletions(-)
 create mode 100644 specparam/plts/event.py

diff --git a/specparam/plts/event.py b/specparam/plts/event.py
new file mode 100644
index 00000000..f544d2e6
--- /dev/null
+++ b/specparam/plts/event.py
@@ -0,0 +1,83 @@
+"""Plots for the event model object.
+
+Notes
+-----
+This file contains plotting functions that take as input an event model object.
+"""
+
+from itertools import cycle
+
+from specparam.data.utils import get_periodic_labels
+from specparam.plts.utils import savefig
+from specparam.plts.templates import plot_param_over_time_yshade
+from specparam.plts.settings import PARAM_COLORS
+from specparam.core.errors import NoModelError
+from specparam.core.modutils import safe_import, check_dependency
+
+plt = safe_import('.pyplot', 'matplotlib')
+
+###################################################################################################
+###################################################################################################
+
+@savefig
+@check_dependency(plt, 'matplotlib')
+def plot_event_model(event_model, save_fig=False, file_name=None, file_path=None, **plot_kwargs):
+    """Plot a figure with subplots visualizing the parameters from a SpectralTimeEventModel object.
+
+    Parameters
+    ----------
+    event_model : SpectralTimeEventModel
+        Object containing results from fitting power spectra across events.
+    save_fig : bool, optional, default: False
+        Whether to save out a copy of the plot.
+    file_name : str, optional
+        Name to give the saved out file.
+    file_path : str, optional
+        Path to directory to save to. If None, saves to current directory.
+
+    Raises
+    ------
+    NoModelError
+        If the model object does not have model fit data available to plot.
+    """
+
+    if not event_model.has_model:
+        raise NoModelError("No model fit results are available, can not proceed.")
+
+    pe_labels = get_periodic_labels(event_model.event_time_results)
+    n_bands = len(pe_labels['cf'])
+
+    has_knee = 'knee' in event_model.event_time_results.keys()
+    height_ratios = [1] * (3 if has_knee else 2) + [0.25, 1, 1, 1] * n_bands + [0.25] + [1, 1]
+
+    if plot_kwargs.pop('axes', None) is None:
+        _, axes = plt.subplots((4 if has_knee else 3) + (n_bands * 4) + 2, 1,
+                               gridspec_kw={'hspace' : 0.1, 'height_ratios' : height_ratios},
+                               figsize=plot_kwargs.pop('figsize', [10, 4 + 4 * n_bands]))
+    axes = cycle(axes)
+
+    # 01: aperiodic params
+    alabels = ['offset', 'knee', 'exponent'] if has_knee else ['offset', 'exponent']
+    for alabel in alabels:
+            plot_param_over_time_yshade(None, event_model.event_time_results[alabel],
+                                        label=alabel, drop_xticks=True, add_xlabel=False,
+                                        title='Aperiodic' if alabel == 'offset' else None,
+                                        color=PARAM_COLORS[alabel], ax=next(axes))
+    next(axes).axis('off')
+
+    # 02: periodic params
+    for band_ind in range(n_bands):
+        for plabel in ['cf', 'pw', 'bw']:
+            plot_param_over_time_yshade(None, event_model.event_time_results[pe_labels[plabel][band_ind]],
+                                        label=plabel.upper(), drop_xticks=True, add_xlabel=False,
+                                        title='Periodic' if plabel == 'cf' else None,
+                                        color=PARAM_COLORS[plabel], ax=next(axes))
+        next(axes).axis('off')
+
+    # 03: goodness of fit
+    for glabel in ['error', 'r_squared']:
+        plot_param_over_time_yshade(None, event_model.event_time_results[glabel], label=glabel,
+                                    drop_xticks=False if glabel == 'r_squared' else True,
+                                    add_xlabel=True if glabel == 'r_squared' else False,
+                                    title='Goodness of Fit' if glabel == 'error' else None,
+                                    color=PARAM_COLORS[glabel], ax=next(axes))
diff --git a/specparam/tests/plts/test_time.py b/specparam/tests/plts/test_time.py
index 567a24dc..14e4950f 100644
--- a/specparam/tests/plts/test_time.py
+++ b/specparam/tests/plts/test_time.py
@@ -19,6 +19,6 @@ def test_plot_time(tft, skip_if_no_mpl):
     plot_time_model(tft, file_path=TEST_PLOTS_PATH, file_name='test_plot_time.png')
 
     # Test error if no data available to plot
-    tfg = SpectralTimeModel()
+    ntft = SpectralTimeModel()
     with raises(NoModelError):
-        tfg.plot()
+        ntft.plot()

From 36ff83bde0f51e29a41c4983fa735df1f555142e Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 22:43:21 -0400
Subject: [PATCH 27/99] add get_results_by_row

---
 specparam/data/utils.py            | 23 +++++++++++++++++++++++
 specparam/tests/data/test_utils.py | 27 +++++++++++++++++++++++++++
 2 files changed, 50 insertions(+)

diff --git a/specparam/data/utils.py b/specparam/data/utils.py
index 5a8ef48d..6ab5f591 100644
--- a/specparam/data/utils.py
+++ b/specparam/data/utils.py
@@ -48,3 +48,26 @@ def get_results_by_ind(results, ind):
         out[key] = results[key][ind]
 
     return out
+
+
+def get_results_by_row(results, ind):
+    """Get a specified index from a dictionary of results across events.
+
+    Parameters
+    ----------
+    results : dict
+        A results dictionary with parameter label keys and corresponding parameter values.
+    ind : int
+        Index to extract from results.
+
+    Returns
+    -------
+    dict
+        Dictionary including the results for the specified index.
+    """
+
+    outs = {}
+    for key in results.keys():
+        outs[key] = results[key][ind, :]
+
+    return outs
diff --git a/specparam/tests/data/test_utils.py b/specparam/tests/data/test_utils.py
index a15d8d8f..1fdc7b56 100644
--- a/specparam/tests/data/test_utils.py
+++ b/specparam/tests/data/test_utils.py
@@ -2,6 +2,8 @@
 
 from copy import deepcopy
 
+import numpy as np
+
 from specparam.data.utils import *
 
 ###################################################################################################
@@ -74,3 +76,28 @@ def test_get_results_by_ind():
     out1 = get_results_by_ind(tdict, ind)
     for key in tdict.keys():
         assert out1[key] == tdict[key][ind]
+
+
+def test_get_results_by_row():
+
+    tdict = {
+        'offset' : np.array([[0, 1], [2, 3]]),
+        'exponent' : np.array([[0, 1], [2, 3]]),
+        'error' : np.array([[0, 1], [2, 3]]),
+        'r_squared' : np.array([[0, 1], [2, 3]]),
+        'alpha_cf' : np.array([[0, 1], [2, 3]]),
+        'alpha_pw' : np.array([[0, 1], [2, 3]]),
+        'alpha_bw' : np.array([[0, 1], [2, 3]]),
+    }
+
+    ind = 0
+    out0 = get_results_by_row(tdict, ind)
+    assert isinstance(out0, dict)
+    for key in tdict.keys():
+        assert key in out0.keys()
+        assert np.array_equal(out0[key], tdict[key][ind])
+
+    ind = 1
+    out1 = get_results_by_row(tdict, ind)
+    for key in tdict.keys():
+        assert np.array_equal(out1[key], tdict[key][ind])

From ebc7b201a03086ccd3bdfd0870c327f2d94ac02f Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 23:04:37 -0400
Subject: [PATCH 28/99] update group object iter

---
 specparam/objs/group.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/specparam/objs/group.py b/specparam/objs/group.py
index f93fcaf5..4ba556ee 100644
--- a/specparam/objs/group.py
+++ b/specparam/objs/group.py
@@ -94,19 +94,19 @@ def __len__(self):
         return len(self.group_results)
 
 
-    def __iter__(self):
-        """Allow for iterating across the object by stepping across model fit results."""
-
-        for result in self.group_results:
-            yield result
-
-
     def __getitem__(self, index):
         """Allow for indexing into the object to select model fit results."""
 
         return self.group_results[index]
 
 
+    def __iter__(self):
+        """Allow for iterating across the object by stepping across model fit results."""
+
+        for ind in range(len(self)):
+            yield self[ind]
+
+
     @property
     def has_data(self):
         """Indicator for if the object contains data."""

From b7b71c5b6f2fa70a517b5994a5911cd24e5e155a Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 23:06:07 -0400
Subject: [PATCH 29/99] misc small updates / fixes for time object

---
 specparam/core/reports.py          |  7 +++----
 specparam/objs/time.py             |  9 +--------
 specparam/plts/time.py             |  2 +-
 specparam/tests/objs/test_group.py | 10 +++++-----
 specparam/tests/objs/test_time.py  |  9 ++++-----
 5 files changed, 14 insertions(+), 23 deletions(-)

diff --git a/specparam/core/reports.py b/specparam/core/reports.py
index b897f913..15a10d25 100644
--- a/specparam/core/reports.py
+++ b/specparam/core/reports.py
@@ -27,7 +27,6 @@
 @check_dependency(plt, 'matplotlib')
 def save_model_report(model, file_name, file_path=None, plt_log=False,
                       add_settings=True, **plot_kwargs):
-
     """Generate and save out a PDF report for a power spectrum model fit.
 
     Parameters
@@ -80,7 +79,7 @@ def save_model_report(model, file_name, file_path=None, plt_log=False,
 
 @check_dependency(plt, 'matplotlib')
 def save_group_report(group, file_name, file_path=None, add_settings=True):
-    """Generate and save out a PDF report for a group of power spectrum models.
+    """Generate and save out a PDF report for models of a group of power spectra.
 
     Parameters
     ----------
@@ -138,12 +137,12 @@ def save_group_report(group, file_name, file_path=None, add_settings=True):
 
 @check_dependency(plt, 'matplotlib')
 def save_time_report(time_model, file_name, file_path=None, add_settings=True):
-    """Generate and save out a PDF report for a group of power spectrum models.
+    """Generate and save out a PDF report for models of a spectrogram.
 
     Parameters
     ----------
     time_model : SpectralTimeModel
-        Object with results from fitting a group of power spectra.
+        Object with results from fitting a spectrogram.
     file_name : str
         Name to give the saved out file.
     file_path : str, optional
diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index f368e21c..b298eccb 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -1,4 +1,4 @@
-"""Time model object and associated code for fitting the model to spectra across time."""
+"""Time model object and associated code for fitting the model to spectrograms."""
 
 from functools import wraps
 
@@ -81,13 +81,6 @@ def __init__(self, *args, **kwargs):
         self._reset_time_results()
 
 
-    def __iter__(self):
-        """Allow for iterating across the object by stepping across fit results per time window."""
-
-        for ind in range(len(self)):
-            yield self[ind]
-
-
     def __getitem__(self, ind):
         """Allow for indexing into the object to select fit results for a specific time window."""
 
diff --git a/specparam/plts/time.py b/specparam/plts/time.py
index 49b62213..d659d586 100644
--- a/specparam/plts/time.py
+++ b/specparam/plts/time.py
@@ -1,4 +1,4 @@
-"""Plots for the group model object.
+"""Plots for the time model object.
 
 Notes
 -----
diff --git a/specparam/tests/objs/test_group.py b/specparam/tests/objs/test_group.py
index 26313d19..eff05e2e 100644
--- a/specparam/tests/objs/test_group.py
+++ b/specparam/tests/objs/test_group.py
@@ -34,17 +34,17 @@ def test_group():
     fg = SpectralGroupModel(verbose=False)
     assert isinstance(fg, SpectralGroupModel)
 
+def test_getitem(tfg):
+    """Check indexing, from custom `__getitem__` in group object."""
+
+    assert tfg[0]
+
 def test_iter(tfg):
     """Check iterating through group object."""
 
     for res in tfg:
         assert res
 
-def test_getitem(tfg):
-    """Check indexing, from custom `__getitem__` in group object."""
-
-    assert tfg[0]
-
 def test_has_data(tfg):
     """Test the has_data property attribute, with and without data."""
 
diff --git a/specparam/tests/objs/test_time.py b/specparam/tests/objs/test_time.py
index b77fd7e6..5c0a72be 100644
--- a/specparam/tests/objs/test_time.py
+++ b/specparam/tests/objs/test_time.py
@@ -25,16 +25,15 @@ def test_time_model():
     ft = SpectralTimeModel(verbose=False)
     assert isinstance(ft, SpectralTimeModel)
 
+def test_time_getitem(tft):
+
+    assert tft[0]
+
 def test_time_iter(tft):
 
     for out in tft:
-        print(out)
         assert out
 
-def test_time_getitem(tft):
-
-    assert tft[0]
-
 def test_time_fit():
 
     n_windows = 10

From 8d2df8f031bed0232b74c1ac0cdddeb6a49ee60b Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 23:13:23 -0400
Subject: [PATCH 30/99] fix time reports save & test

---
 specparam/plts/time.py               | 3 ++-
 specparam/tests/core/test_reports.py | 4 ++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/specparam/plts/time.py b/specparam/plts/time.py
index d659d586..75bca66f 100644
--- a/specparam/plts/time.py
+++ b/specparam/plts/time.py
@@ -48,7 +48,8 @@ def plot_time_model(time_model, save_fig=False, file_name=None, file_path=None,
     pe_labels = get_periodic_labels(time_model.time_results)
     n_bands = len(pe_labels['cf'])
 
-    if plot_kwargs.pop('axes', None) is None:
+    axes = plot_kwargs.pop('axes', None)
+    if axes is None:
         _, axes = plt.subplots(2 + n_bands, 1,
                                gridspec_kw={'hspace' : 0.4},
                                figsize=plot_kwargs.pop('figsize', [10, 4 + 2 * n_bands]))
diff --git a/specparam/tests/core/test_reports.py b/specparam/tests/core/test_reports.py
index 3423947c..56862e39 100644
--- a/specparam/tests/core/test_reports.py
+++ b/specparam/tests/core/test_reports.py
@@ -11,7 +11,7 @@
 
 def test_save_model_report(tfm, skip_if_no_mpl):
 
-    file_name = 'test_report'
+    file_name = 'test_model_report'
 
     save_model_report(tfm, file_name, TEST_REPORTS_PATH)
 
@@ -29,6 +29,6 @@ def test_save_time_report(tft, skip_if_no_mpl):
 
     file_name = 'test_time_report'
 
-    save_group_report(tft, file_name, TEST_REPORTS_PATH)
+    save_time_report(tft, file_name, TEST_REPORTS_PATH)
 
     assert os.path.exists(os.path.join(TEST_REPORTS_PATH, file_name + '.pdf'))

From 25fddab1ad544580262fd4ad503438d88c5877f3 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 23:54:46 -0400
Subject: [PATCH 31/99] add event object report save

---
 specparam/core/reports.py            | 53 +++++++++++++++++++++++++++-
 specparam/tests/core/test_reports.py |  8 +++++
 2 files changed, 60 insertions(+), 1 deletion(-)

diff --git a/specparam/core/reports.py b/specparam/core/reports.py
index 15a10d25..7b44a3e1 100644
--- a/specparam/core/reports.py
+++ b/specparam/core/reports.py
@@ -3,7 +3,8 @@
 from specparam.core.io import fname, fpath
 from specparam.core.modutils import safe_import, check_dependency
 from specparam.core.strings import (gen_settings_str, gen_model_results_str,
-                                    gen_group_results_str, gen_time_results_str)
+                                    gen_group_results_str, gen_time_results_str,
+                                    gen_event_results_str)
 from specparam.data.utils import get_periodic_labels
 from specparam.plts.group import (plot_group_aperiodic, plot_group_goodness,
                                   plot_group_peak_frequencies)
@@ -181,3 +182,53 @@ def save_time_report(time_model, file_name, file_path=None, add_settings=True):
     # Save out the report
     plt.savefig(fpath(file_path, fname(file_name, SAVE_FORMAT)))
     plt.close()
+
+
+@check_dependency(plt, 'matplotlib')
+def save_event_report(event_model, file_name, file_path=None, add_settings=True):
+    """Generate and save out a PDF report for models of a set of events.
+
+    Parameters
+    ----------
+    event_model : SpectralTimeEventModel
+        Object with results from fitting a group of power spectra.
+    file_name : str
+        Name to give the saved out file.
+    file_path : str, optional
+        Path to directory to save to. If None, saves to current directory.
+    add_settings : bool, optional, default: True
+        Whether to add a print out of the model settings to the end of the report.
+    """
+
+    # Check model object for number of bands & aperiodic mode, to decide report size
+    pe_labels = get_periodic_labels(event_model.event_time_results)
+    n_bands = len(pe_labels['cf'])
+    has_knee = 'knee' in event_model.event_time_results.keys()
+
+    # Initialize figure, defining number of axes based on model + what is to be plotted
+    n_rows = 1 + (4 if has_knee else 3) + (n_bands * 4) + 2 + (1 if add_settings else 0)
+    height_ratios = [2.75] + [1] * (3 if has_knee else 2) + \
+        [0.25, 1, 1, 1] * n_bands + [0.25] + [1, 1] + ([1.5] if add_settings else [])
+    _, axes = plt.subplots(n_rows, 1,
+                           gridspec_kw={'hspace' : 0.1, 'height_ratios' : height_ratios},
+                           figsize=(REPORT_FIGSIZE[0], REPORT_FIGSIZE[1] + 6))
+
+    # First / top: text results
+    results_str = gen_event_results_str(event_model)
+    axes[0].text(0.5, 0.7, results_str, REPORT_FONT, ha='center', va='center')
+    axes[0].set_frame_on(False)
+    axes[0].set(xticks=[], yticks=[])
+
+    # Second - data plots
+    event_model.plot(axes=axes[1:-1])
+
+    # Third - Model settings
+    if add_settings:
+        settings_str = gen_settings_str(event_model, False)
+        axes[-1].text(0.5, 0.1, settings_str, REPORT_FONT, ha='center', va='center')
+        axes[-1].set_frame_on(False)
+        axes[-1].set(xticks=[], yticks=[])
+
+    # Save out the report
+    plt.savefig(fpath(file_path, fname(file_name, SAVE_FORMAT)))
+    plt.close()
diff --git a/specparam/tests/core/test_reports.py b/specparam/tests/core/test_reports.py
index 56862e39..26b4aeea 100644
--- a/specparam/tests/core/test_reports.py
+++ b/specparam/tests/core/test_reports.py
@@ -32,3 +32,11 @@ def test_save_time_report(tft, skip_if_no_mpl):
     save_time_report(tft, file_name, TEST_REPORTS_PATH)
 
     assert os.path.exists(os.path.join(TEST_REPORTS_PATH, file_name + '.pdf'))
+
+def test_save_event_report(tfe, skip_if_no_mpl):
+
+    file_name = 'test_event_report'
+
+    save_event_report(tfe, file_name, TEST_REPORTS_PATH)
+
+    assert os.path.exists(os.path.join(TEST_REPORTS_PATH, file_name + '.pdf'))

From 8f10c520875a97247baca0e16644174832be185d Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 23:55:30 -0400
Subject: [PATCH 32/99] add SpectralTimeEventModel object

---
 specparam/objs/event.py | 283 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 283 insertions(+)
 create mode 100644 specparam/objs/event.py

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
new file mode 100644
index 00000000..67254a0a
--- /dev/null
+++ b/specparam/objs/event.py
@@ -0,0 +1,283 @@
+"""Event model object and associated code for fitting the model to spectrograms across events."""
+
+import numpy as np
+
+from specparam.objs import SpectralModel, SpectralTimeModel
+from specparam.plts.event import plot_event_model
+from specparam.data.conversions import group_to_dict
+from specparam.data.utils import get_results_by_row
+from specparam.core.modutils import (copy_doc_func_to_method, docs_get_section,
+                                     replace_docstring_sections)
+from specparam.core.reports import save_event_report
+from specparam.core.strings import gen_event_results_str
+
+###################################################################################################
+###################################################################################################
+
+@replace_docstring_sections([docs_get_section(SpectralModel.__doc__, 'Parameters'),
+                             docs_get_section(SpectralModel.__doc__, 'Notes')])
+class SpectralTimeEventModel(SpectralTimeModel):
+    """Model a set of event as a combination of aperiodic and periodic components.
+
+    WARNING: frequency and power values inputs must be in linear space.
+
+    Passing in logged frequencies and/or power spectra is not detected,
+    and will silently produce incorrect results.
+
+    Parameters
+    ----------
+    %copied in from SpectralModel object
+
+    Attributes
+    ----------
+    freqs : 1d array
+        Frequency values for the power spectra.
+    spectrograms : list 2d array
+        Power values for the spectrograms, which each array as [n_freqs, n_time_windows].
+        Power values are stored internally in log10 scale.
+    freq_range : list of [float, float]
+        Frequency range of the power spectra, as [lowest_freq, highest_freq].
+    freq_res : float
+        Frequency resolution of the power spectra.
+    event_group_results : list of list of FitResults
+        Full model results collected across all events and models.
+    event_time_results : dict
+        Results of the model fit across each time window, collected across events.
+        Each value in the dictionary stores a model fit parameter, as [n_events, n_time_windows].
+
+    Notes
+    -----
+    %copied in from SpectralModel object
+    - The event object inherits from the time model, which in turn inherits from the
+      group object, etc. As such it also has data attributes defined on the underlying
+      objects (see notes and attribute lists in inherited objects for details).
+    """
+
+    def __init__(self, *args, **kwargs):
+        """Initialize object with desired settings."""
+
+        SpectralTimeModel.__init__(self, *args, **kwargs)
+
+        self.spectrograms = []
+
+        self._reset_event_results()
+
+
+    def __len__(self):
+        """Redefine the length of the objects as the number of event results."""
+
+        return len(self.event_group_results)
+
+
+    def __getitem__(self, ind):
+        """Allow for indexing into the object to select fit results for a specific event."""
+
+        return get_results_by_row(self.event_time_results, ind)
+
+
+    def _reset_event_results(self):
+        """Set, or reset, event results to be empty."""
+
+        self.event_group_results = []
+        self.event_time_results = {}
+
+
+    @property
+    def has_data(self):
+        """Redefine has_data marker to reflect the spectrograms attribute."""
+
+        return True if np.any(self.spectrograms) else False
+
+
+    @property
+    def has_model(self):
+        """Redefine has_model marker to reflect the event results."""
+
+        return True if self.event_group_results else False
+
+
+    @property
+    def n_events(self):
+        # ToDo: double check if we want this - I think is never used internally?
+
+        return len(self)
+
+
+    @property
+    def n_time_windows(self):
+        # ToDo: double check if we want this - I think is never used internally?
+
+        return self.spectrograms[0].shape[1] if self.has_data else 0
+
+
+    def add_data(self, freqs, spectrograms, freq_range=None):
+        """Add data (frequencies and spectrograms) to the current object.
+
+        Parameters
+        ----------
+        freqs : 1d array
+            Frequency values for the power spectra, in linear space.
+        spectrograms : list of 2d array, shape=[n_freqs, n_time_windows]
+            Matrix of power values, in linear space.
+            Each spectrogram should reflect a separate event, each with the same set of time windows.
+        freq_range : list 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.
+        """
+
+        # If given a list of spectrograms, add to object
+        if isinstance(spectrograms, list):
+
+            if np.any(self.freqs):
+                self._reset_event_results()
+                self.spectrograms = []
+            for spectrogram in spectrograms:
+                t_freqs, spectrogram, t_freq_range, t_freq_res = \
+                    self._prepare_data(freqs, spectrogram.T, freq_range, 2)
+                self.spectrograms.append(spectrogram.T)
+            self.freqs = t_freqs
+            self.freq_range = t_freq_range
+            self.freq_res = t_freq_res
+
+        # If input is an array, pass through to underlying object method
+        else:
+            super().add_data(freqs, spectrograms, freq_range)
+
+
+    def report(self, freqs=None, spectrograms=None, freq_range=None,
+               peak_org=None, n_jobs=1, progress=None):
+        """Fit a set of events and display a report, with a plot and printed results.
+
+        Parameters
+        ----------
+        freqs : 1d array, optional
+            Frequency values for the power_spectra, in linear space.
+        spectrograms : list of 2d array, shape=[n_freqs, n_time_windows]
+            Matrix of power values, in linear space.
+            Each spectrogram should reflect a separate event, each with the same set of time windows.
+        freq_range : list of [float, float], optional
+            Frequency range to fit the model to. If not provided, fits the entire given range.
+        peak_org : int or Bands
+            How to organize peaks.
+            If int, extracts the first n peaks.
+            If Bands, extracts peaks based on band definitions.
+        n_jobs : int, 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.
+        """
+
+        self.fit(freqs, spectrograms, freq_range, peak_org, n_jobs=n_jobs, progress=progress)
+        self.plot()
+        self.print_results()
+
+
+    def fit(self, freqs=None, spectrograms=None, freq_range=None, peak_org=None,
+            n_jobs=1, progress=None):
+        """Fit a set of events.
+
+        Parameters
+        ----------
+        freqs : 1d array, optional
+            Frequency values for the power_spectra, in linear space.
+        spectrograms : list of 2d array, shape=[n_freqs, n_time_windows]
+            Matrix of power values, in linear space.
+            Each spectrogram should reflect a separate event, each with the same set of time windows.
+        freq_range : list of [float, float], optional
+            Frequency range to fit the model to. If not provided, fits the entire given range.
+        peak_org : int or Bands
+            How to organize peaks.
+            If int, extracts the first n peaks.
+            If Bands, extracts peaks based on band definitions.
+        n_jobs : int, 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.
+        """
+
+        if spectrograms is not None:
+            self.add_data(freqs, spectrograms, freq_range)
+        if len(self):
+            self._reset_event_results()
+
+        for spectrogram in self.spectrograms:
+            self.power_spectra = spectrogram.T
+            super().fit()
+            self.event_group_results.append(self.group_results)
+
+        self._convert_to_event_results(peak_org)
+
+
+    def get_results(self):
+        """Return the results from across the set of events."""
+
+        return self.event_time_results
+
+
+    def print_results(self, concise=False):
+        """Print out SpectralTimeEventModel results.
+
+        Parameters
+        ----------
+        concise : bool, optional, default: False
+            Whether to print the report in a concise mode, or not.
+        """
+
+        print(gen_event_results_str(self, concise))
+
+
+    @copy_doc_func_to_method(plot_event_model)
+    def plot(self, save_fig=False, file_name=None, file_path=None, **plot_kwargs):
+
+        plot_event_model(self, save_fig=save_fig, file_name=file_name,
+                         file_path=file_path, **plot_kwargs)
+
+
+    @copy_doc_func_to_method(save_event_report)
+    def save_report(self, file_name, file_path=None, add_settings=True):
+
+        save_event_report(self, file_name, file_path, add_settings)
+
+
+    def _convert_to_event_results(self, peak_org):
+        """Convert the event results to be organized across across and time windows.
+
+        Parameters
+        ----------
+        peak_org : int or Bands
+            How to organize peaks.
+            If int, extracts the first n peaks.
+            If Bands, extracts peaks based on band definitions.
+        """
+
+        temp = group_to_dict(self.event_group_results[0], peak_org)
+        for key in temp:
+            self.event_time_results[key] = []
+
+        for gres in self.event_group_results:
+            dictres = group_to_dict(gres, peak_org)
+            for key in dictres:
+                self.event_time_results[key].append(dictres[key])
+
+        for key in self.event_time_results.keys():
+            self.event_time_results[key] = np.array(self.event_time_results[key])
+
+    # ToDo: check & figure out adding `load` method
+
+    def _convert_to_time_results(self, peak_org):
+        """Overrides inherited objects function to void running this conversion per spectrogram."""
+        pass

From f65aedb443043518198d084216e4d111700995dd Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 23:56:13 -0400
Subject: [PATCH 33/99] add test for SpectralTimeEventModel

---
 specparam/tests/conftest.py        |  8 +++-
 specparam/tests/objs/test_event.py | 72 ++++++++++++++++++++++++++++++
 specparam/tests/tutils.py          | 18 +++++++-
 3 files changed, 94 insertions(+), 4 deletions(-)
 create mode 100644 specparam/tests/objs/test_event.py

diff --git a/specparam/tests/conftest.py b/specparam/tests/conftest.py
index 9a828039..72d88b7a 100644
--- a/specparam/tests/conftest.py
+++ b/specparam/tests/conftest.py
@@ -7,7 +7,7 @@
 import numpy as np
 
 from specparam.core.modutils import safe_import
-from specparam.tests.tutils import (get_tfm, get_tfg, get_tft, get_tbands,
+from specparam.tests.tutils import (get_tfm, get_tfg, get_tft, get_tfe, get_tbands,
                                     get_tresults, get_tdocstring)
 from specparam.tests.settings import (BASE_TEST_FILE_PATH, TEST_DATA_PATH,
                                       TEST_REPORTS_PATH, TEST_PLOTS_PATH)
@@ -20,7 +20,7 @@
 def pytest_configure(config):
     if plt:
         plt.switch_backend('agg')
-    np.random.seed(101)
+    np.random.seed(13)
 
 @pytest.fixture(scope='session', autouse=True)
 def check_dir():
@@ -48,6 +48,10 @@ def tfg():
 def tft():
     yield get_tft()
 
+@pytest.fixture(scope='session')
+def tfe():
+    yield get_tfe()
+
 @pytest.fixture(scope='session')
 def tbands():
     yield get_tbands()
diff --git a/specparam/tests/objs/test_event.py b/specparam/tests/objs/test_event.py
new file mode 100644
index 00000000..149145f4
--- /dev/null
+++ b/specparam/tests/objs/test_event.py
@@ -0,0 +1,72 @@
+"""Tests for the specparam.objs.event, including the event model object and it's methods.
+
+NOTES
+-----
+The tests here are not strong tests for accuracy.
+They serve rather as 'smoke tests', for if anything fails completely.
+"""
+
+import numpy as np
+
+from specparam.sim import sim_spectrogram
+
+from specparam.tests.settings import TEST_DATA_PATH
+from specparam.tests.tutils import default_group_params, plot_test
+
+from specparam.objs.event import *
+
+###################################################################################################
+###################################################################################################
+
+def test_event_model():
+    """Check event object initializes properly."""
+
+    # Note: doesn't assert the object itself, which returns false empty
+    fe = SpectralTimeEventModel(verbose=False)
+    assert isinstance(fe, SpectralTimeEventModel)
+
+def test_event_getitem(tft):
+
+    assert tft[0]
+
+def test_event_iter(tfe):
+
+    for out in tfe:
+        assert out
+
+def test_event_fit():
+
+    n_windows = 3
+    xs, ys = sim_spectrogram(n_windows, *default_group_params())
+    ys = [ys, ys]
+
+    tfe = SpectralTimeEventModel(verbose=False)
+    tfe.fit(xs, ys)
+
+    results = tfe.get_results()
+
+    assert results
+    assert isinstance(results, dict)
+    for key in results.keys():
+        assert np.all(results[key])
+        assert results[key].shape == (len(ys), n_windows)
+
+def test_event_print(tfe):
+
+    tfe.print_results()
+
+@plot_test
+def test_event_plot(tfe, skip_if_no_mpl):
+
+    tfe.plot()
+
+def test_event_report(skip_if_no_mpl):
+
+    n_windows = 3
+    xs, ys = sim_spectrogram(n_windows, *default_group_params())
+    ys = [ys, ys]
+
+    tfe = SpectralTimeEventModel(verbose=False)
+    tfe.report(xs, ys)
+
+    assert tfe
diff --git a/specparam/tests/tutils.py b/specparam/tests/tutils.py
index 5f0862e6..4a376079 100644
--- a/specparam/tests/tutils.py
+++ b/specparam/tests/tutils.py
@@ -6,7 +6,8 @@
 
 from specparam.bands import Bands
 from specparam.data import FitResults
-from specparam.objs import SpectralModel, SpectralGroupModel, SpectralTimeModel
+from specparam.objs import (SpectralModel, SpectralGroupModel,
+                            SpectralTimeModel, SpectralTimeEventModel)
 from specparam.core.modutils import safe_import
 from specparam.sim.params import param_sampler
 from specparam.sim.sim import sim_power_spectrum, sim_group_power_spectra, sim_spectrogram
@@ -47,12 +48,25 @@ def get_tft():
     n_spectra = 3
     xs, ys = sim_spectrogram(n_spectra, *default_group_params())
 
-    bands = Bands({'alpha' : (7, 14), 'beta' : (15, 30)})
+    bands = Bands({'alpha' : (7, 14)})
     tft = SpectralTimeModel(verbose=False)
     tft.fit(xs, ys, peak_org=bands)
 
     return tft
 
+def get_tfe():
+    """Get an event object, with some fit power spectra, for testing."""
+
+    n_spectra = 3
+    xs, ys = sim_spectrogram(n_spectra, *default_group_params())
+    ys = [ys, ys]
+
+    bands = Bands({'alpha' : (7, 14), 'beta' : (15, 30)})
+    tfe = SpectralTimeEventModel(verbose=False)
+    tfe.fit(xs, ys, peak_org=bands)
+
+    return tfe
+
 def get_tbands():
     """Get a bands object, for testing."""
 

From 57d45921d1a24542786af927a8fd339bede93478 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 23:56:33 -0400
Subject: [PATCH 34/99] add SpectralTimeEventModel to inits

---
 specparam/__init__.py      | 2 +-
 specparam/objs/__init__.py | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/specparam/__init__.py b/specparam/__init__.py
index 2dec1808..2710b3a7 100644
--- a/specparam/__init__.py
+++ b/specparam/__init__.py
@@ -3,5 +3,5 @@
 from .version import __version__
 
 from .bands import Bands
-from .objs import SpectralModel, SpectralGroupModel, SpectralTimeModel
+from .objs import SpectralModel, SpectralGroupModel, SpectralTimeModel, SpectralTimeEventModel
 from .objs.utils import fit_models_3d
diff --git a/specparam/objs/__init__.py b/specparam/objs/__init__.py
index d3b2e10b..4d689bac 100644
--- a/specparam/objs/__init__.py
+++ b/specparam/objs/__init__.py
@@ -3,4 +3,5 @@
 from .fit import SpectralModel
 from .group import SpectralGroupModel
 from .time import SpectralTimeModel
+from .event import SpectralTimeEventModel
 from .utils import compare_model_objs, average_group, combine_model_objs, fit_models_3d

From b97efe2c2238f5ff1fd0d5e4039a77638dc51809 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 10 Jul 2023 23:57:05 -0400
Subject: [PATCH 35/99] test & fix event plot

---
 specparam/plts/event.py            |  3 ++-
 specparam/tests/plts/test_event.py | 24 ++++++++++++++++++++++++
 2 files changed, 26 insertions(+), 1 deletion(-)
 create mode 100644 specparam/tests/plts/test_event.py

diff --git a/specparam/plts/event.py b/specparam/plts/event.py
index f544d2e6..c72a291b 100644
--- a/specparam/plts/event.py
+++ b/specparam/plts/event.py
@@ -50,7 +50,8 @@ def plot_event_model(event_model, save_fig=False, file_name=None, file_path=None
     has_knee = 'knee' in event_model.event_time_results.keys()
     height_ratios = [1] * (3 if has_knee else 2) + [0.25, 1, 1, 1] * n_bands + [0.25] + [1, 1]
 
-    if plot_kwargs.pop('axes', None) is None:
+    axes = plot_kwargs.pop('axes', None)
+    if axes is None:
         _, axes = plt.subplots((4 if has_knee else 3) + (n_bands * 4) + 2, 1,
                                gridspec_kw={'hspace' : 0.1, 'height_ratios' : height_ratios},
                                figsize=plot_kwargs.pop('figsize', [10, 4 + 4 * n_bands]))
diff --git a/specparam/tests/plts/test_event.py b/specparam/tests/plts/test_event.py
new file mode 100644
index 00000000..f71d36d9
--- /dev/null
+++ b/specparam/tests/plts/test_event.py
@@ -0,0 +1,24 @@
+"""Tests for specparam.plts.event."""
+
+from pytest import raises
+
+from specparam import SpectralTimeEventModel
+from specparam.core.errors import NoModelError
+
+from specparam.tests.tutils import plot_test
+from specparam.tests.settings import TEST_PLOTS_PATH
+
+from specparam.plts.event import *
+
+###################################################################################################
+###################################################################################################
+
+@plot_test
+def test_plot_event(tfe, skip_if_no_mpl):
+
+    plot_event_model(tfe, file_path=TEST_PLOTS_PATH, file_name='test_plot_event.png')
+
+    # Test error if no data available to plot
+    ntfe = SpectralTimeEventModel()
+    with raises(NoModelError):
+        ntfe.plot()

From dd5b83bf3537fbe066e9191aa13fe17ee7d05895 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 11 Jul 2023 00:16:12 -0400
Subject: [PATCH 36/99] lint cleanups

---
 specparam/core/strings.py     | 12 +++++++----
 specparam/data/conversions.py |  2 +-
 specparam/objs/event.py       | 10 ++++-----
 specparam/plts/event.py       | 39 +++++++++++++++++------------------
 specparam/plts/spectra.py     |  1 -
 specparam/plts/templates.py   |  4 +---
 specparam/plts/time.py        | 10 +++------
 7 files changed, 37 insertions(+), 41 deletions(-)

diff --git a/specparam/core/strings.py b/specparam/core/strings.py
index c4825f4c..0aa30fa3 100644
--- a/specparam/core/strings.py
+++ b/specparam/core/strings.py
@@ -452,7 +452,8 @@ def gen_time_results_str(time_model, concise=False):
 
         # Group information
         'Number of time windows fit: {}'.format(len(time_model.group_results)),
-        *[el for el in ['{} power spectra failed to fit'.format(time_model.n_null_)] if time_model.n_null_],
+        *[el for el in ['{} power spectra failed to fit'.format(time_model.n_null_)] \
+            if time_model.n_null_],
         '',
 
         # Frequency range and resolution
@@ -565,9 +566,12 @@ def gen_event_results_str(event_model, concise=False):
         '',
         'Aperiodic params (values across events):',
         *[el for el in ['    Knees - Min: {:6.2f}, Max: {:6.2f}, Mean: {:6.2f}'
-                        .format(np.nanmin(np.mean(event_model.event_time_results['knee'], 1) if has_knee else 0),
-                                np.nanmax(np.mean(event_model.event_time_results['knee'], 1) if has_knee else 0),
-                                np.nanmean(np.mean(event_model.event_time_results['knee'], 1) if has_knee else 0)),
+                        .format(np.nanmin(np.mean(event_model.event_time_results['knee'], 1) \
+                                    if has_knee else 0),
+                                np.nanmax(np.mean(event_model.event_time_results['knee'], 1) \
+                                    if has_knee else 0),
+                                np.nanmean(np.mean(event_model.event_time_results['knee'], 1) \
+                                    if has_knee else 0)),
                        ] if has_knee],
         'Exponents - Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
         .format(np.nanmin(np.mean(event_model.event_time_results['exponent'], 1)),
diff --git a/specparam/data/conversions.py b/specparam/data/conversions.py
index 18d9c245..8773108f 100644
--- a/specparam/data/conversions.py
+++ b/specparam/data/conversions.py
@@ -103,7 +103,7 @@ def group_to_dict(fit_results, peak_org):
         Model results organized into a dictionary.
     """
 
-    fr_dict = {ke : [] for ke in model_to_dict(fit_results[0], peak_org).keys()}
+    fr_dict = {ke : [] for ke in model_to_dict(fit_results[0], peak_org)}
     for f_res in fit_results:
         for key, val in model_to_dict(f_res, peak_org).items():
             fr_dict[key].append(val)
diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index 67254a0a..ce7a5d97 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -32,7 +32,7 @@ class SpectralTimeEventModel(SpectralTimeModel):
     ----------
     freqs : 1d array
         Frequency values for the power spectra.
-    spectrograms : list 2d array
+    spectrograms : list of 2d array
         Power values for the spectrograms, which each array as [n_freqs, n_time_windows].
         Power values are stored internally in log10 scale.
     freq_range : list of [float, float]
@@ -119,7 +119,7 @@ def add_data(self, freqs, spectrograms, freq_range=None):
             Frequency values for the power spectra, in linear space.
         spectrograms : list of 2d array, shape=[n_freqs, n_time_windows]
             Matrix of power values, in linear space.
-            Each spectrogram should reflect a separate event, each with the same set of time windows.
+            Each spectrogram should an event, each with the same set of time windows.
         freq_range : list of [float, float], optional
             Frequency range to restrict power spectra to. If not provided, keeps the entire range.
 
@@ -158,7 +158,7 @@ def report(self, freqs=None, spectrograms=None, freq_range=None,
             Frequency values for the power_spectra, in linear space.
         spectrograms : list of 2d array, shape=[n_freqs, n_time_windows]
             Matrix of power values, in linear space.
-            Each spectrogram should reflect a separate event, each with the same set of time windows.
+            Each spectrogram should an event, each with the same set of time windows.
         freq_range : list of [float, float], optional
             Frequency range to fit the model to. If not provided, fits the entire given range.
         peak_org : int or Bands
@@ -191,7 +191,7 @@ def fit(self, freqs=None, spectrograms=None, freq_range=None, peak_org=None,
             Frequency values for the power_spectra, in linear space.
         spectrograms : list of 2d array, shape=[n_freqs, n_time_windows]
             Matrix of power values, in linear space.
-            Each spectrogram should reflect a separate event, each with the same set of time windows.
+            Each spectrogram should an event, each with the same set of time windows.
         freq_range : list of [float, float], optional
             Frequency range to fit the model to. If not provided, fits the entire given range.
         peak_org : int or Bands
@@ -273,7 +273,7 @@ def _convert_to_event_results(self, peak_org):
             for key in dictres:
                 self.event_time_results[key].append(dictres[key])
 
-        for key in self.event_time_results.keys():
+        for key in self.event_time_results:
             self.event_time_results[key] = np.array(self.event_time_results[key])
 
     # ToDo: check & figure out adding `load` method
diff --git a/specparam/plts/event.py b/specparam/plts/event.py
index c72a291b..08b81076 100644
--- a/specparam/plts/event.py
+++ b/specparam/plts/event.py
@@ -21,19 +21,15 @@
 
 @savefig
 @check_dependency(plt, 'matplotlib')
-def plot_event_model(event_model, save_fig=False, file_name=None, file_path=None, **plot_kwargs):
+def plot_event_model(event_model, **plot_kwargs):
     """Plot a figure with subplots visualizing the parameters from a SpectralTimeEventModel object.
 
     Parameters
     ----------
     event_model : SpectralTimeEventModel
         Object containing results from fitting power spectra across events.
-    save_fig : bool, optional, default: False
-        Whether to save out a copy of the plot.
-    file_name : str, optional
-        Name to give the saved out file.
-    file_path : str, optional
-        Path to directory to save to. If None, saves to current directory.
+    **plot_kwargs
+        Keyword arguments to apply to the plot.
 
     Raises
     ------
@@ -60,25 +56,28 @@ def plot_event_model(event_model, save_fig=False, file_name=None, file_path=None
     # 01: aperiodic params
     alabels = ['offset', 'knee', 'exponent'] if has_knee else ['offset', 'exponent']
     for alabel in alabels:
-            plot_param_over_time_yshade(None, event_model.event_time_results[alabel],
-                                        label=alabel, drop_xticks=True, add_xlabel=False,
-                                        title='Aperiodic' if alabel == 'offset' else None,
-                                        color=PARAM_COLORS[alabel], ax=next(axes))
+        plot_param_over_time_yshade(\
+            None, event_model.event_time_results[alabel],
+            label=alabel, drop_xticks=True, add_xlabel=False,
+            title='Aperiodic' if alabel == 'offset' else None,
+            color=PARAM_COLORS[alabel], ax=next(axes))
     next(axes).axis('off')
 
     # 02: periodic params
     for band_ind in range(n_bands):
         for plabel in ['cf', 'pw', 'bw']:
-            plot_param_over_time_yshade(None, event_model.event_time_results[pe_labels[plabel][band_ind]],
-                                        label=plabel.upper(), drop_xticks=True, add_xlabel=False,
-                                        title='Periodic' if plabel == 'cf' else None,
-                                        color=PARAM_COLORS[plabel], ax=next(axes))
+            plot_param_over_time_yshade(\
+                None, event_model.event_time_results[pe_labels[plabel][band_ind]],
+                label=plabel.upper(), drop_xticks=True, add_xlabel=False,
+                title='Periodic' if plabel == 'cf' else None,
+                color=PARAM_COLORS[plabel], ax=next(axes))
         next(axes).axis('off')
 
     # 03: goodness of fit
     for glabel in ['error', 'r_squared']:
-        plot_param_over_time_yshade(None, event_model.event_time_results[glabel], label=glabel,
-                                    drop_xticks=False if glabel == 'r_squared' else True,
-                                    add_xlabel=True if glabel == 'r_squared' else False,
-                                    title='Goodness of Fit' if glabel == 'error' else None,
-                                    color=PARAM_COLORS[glabel], ax=next(axes))
+        plot_param_over_time_yshade(\
+            None, event_model.event_time_results[glabel], label=glabel,
+            drop_xticks=False if glabel == 'r_squared' else True,
+            add_xlabel=True if glabel == 'r_squared' else False,
+            title='Goodness of Fit' if glabel == 'error' else None,
+            color=PARAM_COLORS[glabel], ax=next(axes))
diff --git a/specparam/plts/spectra.py b/specparam/plts/spectra.py
index bf2139d6..5de010b1 100644
--- a/specparam/plts/spectra.py
+++ b/specparam/plts/spectra.py
@@ -9,7 +9,6 @@
 from itertools import repeat, cycle
 
 import numpy as np
-from scipy.stats import sem
 
 from specparam.core.modutils import safe_import, check_dependency
 from specparam.plts.templates import plot_yshade
diff --git a/specparam/plts/templates.py b/specparam/plts/templates.py
index 81fa1964..e933f937 100644
--- a/specparam/plts/templates.py
+++ b/specparam/plts/templates.py
@@ -13,7 +13,7 @@
 from specparam.utils.data import compute_average, compute_dispersion
 from specparam.core.modutils import safe_import, check_dependency
 from specparam.plts.utils import check_ax, set_alpha
-from specparam.plts.settings import PLT_FIGSIZES, PLT_COLORS, DEFAULT_COLORS
+from specparam.plts.settings import PLT_FIGSIZES, DEFAULT_COLORS
 
 plt = safe_import('.pyplot', 'matplotlib')
 
@@ -208,8 +208,6 @@ def plot_param_over_time(times, param, label=None, title=None, add_legend=True,
 
     ax = check_ax(ax, plot_kwargs.pop('figsize', PLT_FIGSIZES['time']))
 
-    n_windows = len(param)
-
     if times is None:
         times = np.arange(0, len(param))
 
diff --git a/specparam/plts/time.py b/specparam/plts/time.py
index 75bca66f..6f232f26 100644
--- a/specparam/plts/time.py
+++ b/specparam/plts/time.py
@@ -21,19 +21,15 @@
 
 @savefig
 @check_dependency(plt, 'matplotlib')
-def plot_time_model(time_model, save_fig=False, file_name=None, file_path=None, **plot_kwargs):
+def plot_time_model(time_model, **plot_kwargs):
     """Plot a figure with subplots visualizing the parameters from a SpectralTimeModel object.
 
     Parameters
     ----------
     time_model : SpectralTimeModel
         Object containing results from fitting power spectra across time windows.
-    save_fig : bool, optional, default: False
-        Whether to save out a copy of the plot.
-    file_name : str, optional
-        Name to give the saved out file.
-    file_path : str, optional
-        Path to directory to save to. If None, saves to current directory.
+    **plot_kwargs
+        Keyword arguments to apply to the plot.
 
     Raises
     ------

From 21e90dc7d41810770837fa434188d4874188863d Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Wed, 12 Jul 2023 12:50:26 -0400
Subject: [PATCH 37/99] add get_band_labels

---
 specparam/data/utils.py            | 30 ++++++++++++++++++++++++++++++
 specparam/tests/data/test_utils.py | 22 ++++++++++++++++++++++
 2 files changed, 52 insertions(+)

diff --git a/specparam/data/utils.py b/specparam/data/utils.py
index 6ab5f591..054bdf3a 100644
--- a/specparam/data/utils.py
+++ b/specparam/data/utils.py
@@ -27,6 +27,36 @@ def get_periodic_labels(results):
     return outs
 
 
+def get_band_labels(indict):
+    """Get a list of band labels from
+
+    Parameters
+    ----------
+    indict : dict
+        Dictionary of results and/or labels to get the band labels from.
+        Can be wither a `time_results` or `periodic_labels` dictionary.
+
+    Returns
+    -------
+    band_labels : list of str
+        List of band labels.
+    """
+
+    # If it's a results dictionary, convert to periodic labels
+    if 'offset' in indict:
+        indict = get_periodic_labels(indict)
+
+    n_bands = len(indict['cf'])
+
+    band_labels = []
+    for ind in range(n_bands):
+        tband_label = indict['cf'][ind].split('_')
+        tband_label.remove('cf')
+        band_labels.append(tband_label[0])
+
+    return band_labels
+
+
 def get_results_by_ind(results, ind):
     """Get a specified index from a dictionary of results.
 
diff --git a/specparam/tests/data/test_utils.py b/specparam/tests/data/test_utils.py
index 1fdc7b56..c7ea4b9c 100644
--- a/specparam/tests/data/test_utils.py
+++ b/specparam/tests/data/test_utils.py
@@ -53,6 +53,28 @@ def test_get_periodic_labels():
         for el in out3[key]:
             assert key in el
 
+def test_get_band_labels():
+
+    tdict1 = {
+        'offset' : [0, 1],
+        'exponent' : [0, 1],
+        'error' : [0, 1],
+        'r_squared' : [0, 1],
+        'alpha_cf' : [0, 1],
+        'alpha_pw' : [0, 1],
+        'alpha_bw' : [0, 1],
+    }
+
+    band_labels1 = get_band_labels(tdict1)
+    assert band_labels1 == ['alpha']
+
+    tdict2 = {'cf': ['alpha_cf', 'beta_cf'],
+              'pw': ['alpha_pw', 'beta_pw'],
+              'bw': ['alpha_bw', 'beta_bw']}
+
+    band_labels2 = get_band_labels(tdict2)
+    assert band_labels2 == ['alpha', 'beta']
+
 def test_get_results_by_ind():
 
     tdict = {

From 1d523edef5d1e186b33372d71ea30056d216ef6f Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Wed, 12 Jul 2023 12:51:15 -0400
Subject: [PATCH 38/99] add band labels to model plots

---
 specparam/plts/event.py | 7 ++++---
 specparam/plts/time.py  | 7 ++++---
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/specparam/plts/event.py b/specparam/plts/event.py
index 08b81076..3e37c8ca 100644
--- a/specparam/plts/event.py
+++ b/specparam/plts/event.py
@@ -7,7 +7,7 @@
 
 from itertools import cycle
 
-from specparam.data.utils import get_periodic_labels
+from specparam.data.utils import get_periodic_labels, get_band_labels
 from specparam.plts.utils import savefig
 from specparam.plts.templates import plot_param_over_time_yshade
 from specparam.plts.settings import PARAM_COLORS
@@ -41,6 +41,7 @@ def plot_event_model(event_model, **plot_kwargs):
         raise NoModelError("No model fit results are available, can not proceed.")
 
     pe_labels = get_periodic_labels(event_model.event_time_results)
+    band_labels = get_band_labels(pe_labels)
     n_bands = len(pe_labels['cf'])
 
     has_knee = 'knee' in event_model.event_time_results.keys()
@@ -59,7 +60,7 @@ def plot_event_model(event_model, **plot_kwargs):
         plot_param_over_time_yshade(\
             None, event_model.event_time_results[alabel],
             label=alabel, drop_xticks=True, add_xlabel=False,
-            title='Aperiodic' if alabel == 'offset' else None,
+            title='Aperiodic Parameters' if alabel == 'offset' else None,
             color=PARAM_COLORS[alabel], ax=next(axes))
     next(axes).axis('off')
 
@@ -69,7 +70,7 @@ def plot_event_model(event_model, **plot_kwargs):
             plot_param_over_time_yshade(\
                 None, event_model.event_time_results[pe_labels[plabel][band_ind]],
                 label=plabel.upper(), drop_xticks=True, add_xlabel=False,
-                title='Periodic' if plabel == 'cf' else None,
+                title='Periodic Parameters - ' + band_labels[band_ind] if plabel == 'cf' else None,
                 color=PARAM_COLORS[plabel], ax=next(axes))
         next(axes).axis('off')
 
diff --git a/specparam/plts/time.py b/specparam/plts/time.py
index 6f232f26..d507f421 100644
--- a/specparam/plts/time.py
+++ b/specparam/plts/time.py
@@ -7,7 +7,7 @@
 
 from itertools import cycle
 
-from specparam.data.utils import get_periodic_labels
+from specparam.data.utils import get_periodic_labels, get_band_labels
 from specparam.plts.utils import savefig
 from specparam.plts.templates import plot_params_over_time
 from specparam.plts.settings import PARAM_COLORS
@@ -42,6 +42,7 @@ def plot_time_model(time_model, **plot_kwargs):
 
     # Check band structure
     pe_labels = get_periodic_labels(time_model.time_results)
+    band_labels = get_band_labels(pe_labels)
     n_bands = len(pe_labels['cf'])
 
     axes = plot_kwargs.pop('axes', None)
@@ -63,7 +64,7 @@ def plot_time_model(time_model, **plot_kwargs):
         ap_colors.insert(1, PARAM_COLORS['knee'])
 
     plot_params_over_time(None, ap_params, labels=ap_labels, add_xlabel=False,
-                          colors=ap_colors, title='Aperiodic', ax=next(axes))
+                          colors=ap_colors, title='Aperiodic Parameters', ax=next(axes))
 
     # 02: periodic parameters
     for band_ind in range(n_bands):
@@ -74,7 +75,7 @@ def plot_time_model(time_model, **plot_kwargs):
              time_model.time_results[pe_labels['bw'][band_ind]]],
             labels=['CF', 'PW', 'BW'], add_xlabel=False,
             colors=[PARAM_COLORS['cf'], PARAM_COLORS['pw'], PARAM_COLORS['bw']],
-            title='Periodic', ax=next(axes))
+            title='Periodic Parameters - ' + band_labels[band_ind], ax=next(axes))
 
     # 03: goodness of fit
     plot_params_over_time(None,

From 67d91bca43535ca70db5ea64e8fb748c78b358fe Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Wed, 12 Jul 2023 17:02:21 -0400
Subject: [PATCH 39/99] add get_model method to event object

---
 specparam/objs/event.py            | 36 ++++++++++++++++++++++++++++++
 specparam/tests/objs/test_event.py | 11 +++++++++
 2 files changed, 47 insertions(+)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index ce7a5d97..87ee9cf8 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -253,6 +253,42 @@ def save_report(self, file_name, file_path=None, add_settings=True):
         save_event_report(self, file_name, file_path, add_settings)
 
 
+    def get_model(self, ind, regenerate=True):
+        """Get a model fit object for a specified index.
+
+        Parameters
+        ----------
+        ind : list of [int, int]
+            Index to extract, listed as [event_index, time_window_index].
+        regenerate : bool, optional, default: False
+            Whether to regenerate the model fits for the requested model.
+
+        Returns
+        -------
+        model : SpectralModel
+            The FitResults data loaded into a model object.
+        """
+
+        # Initialize a model object, with same settings & check data mode as current object
+        model = SpectralModel(*self.get_settings(), verbose=self.verbose)
+        model.set_check_data_mode(self._check_data)
+
+        # Add data for specified single power spectrum, if available
+        #   The power spectrum is inverted back to linear, as it is re-logged when added to object
+        if self.has_data:
+            model.add_data(self.freqs, np.power(10, self.spectrograms[ind[0]][:, ind[1]]))
+        # If no power spectrum data available, copy over data information & regenerate freqs
+        else:
+            model.add_meta_data(self.get_meta_data())
+
+        # Add results for specified power spectrum, regenerating full fit if requested
+        model.add_results(self.event_group_results[ind[0]][ind[1]])
+        if regenerate:
+            model._regenerate_model()
+
+        return model
+
+
     def _convert_to_event_results(self, peak_org):
         """Convert the event results to be organized across across and time windows.
 
diff --git a/specparam/tests/objs/test_event.py b/specparam/tests/objs/test_event.py
index 149145f4..adbc443e 100644
--- a/specparam/tests/objs/test_event.py
+++ b/specparam/tests/objs/test_event.py
@@ -70,3 +70,14 @@ def test_event_report(skip_if_no_mpl):
     tfe.report(xs, ys)
 
     assert tfe
+
+def test_event_get_model(tfe):
+
+    # Check without regenerating
+    tfm0 = tfe.get_model([0, 0], False)
+    assert tfm0
+
+    # Check with regenerating
+    tfm1 = tfe.get_model([1, 1], True)
+    assert tfm1
+    assert np.all(tfm1.modeled_spectrum_)

From 94a227262a348f9de613708a42c7adb796f74ba9 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Wed, 12 Jul 2023 18:33:19 -0400
Subject: [PATCH 40/99] add extract data utils & convs (include refactor out of
 event obj)

---
 specparam/data/conversions.py            | 75 ++++++++++++++++++++++++
 specparam/data/utils.py                  | 30 ++++++++++
 specparam/tests/data/test_conversions.py | 37 +++++++++++-
 specparam/tests/data/test_utils.py       | 21 +++++++
 4 files changed, 162 insertions(+), 1 deletion(-)

diff --git a/specparam/data/conversions.py b/specparam/data/conversions.py
index 8773108f..c4da0b7a 100644
--- a/specparam/data/conversions.py
+++ b/specparam/data/conversions.py
@@ -7,6 +7,7 @@
 from specparam.core.info import get_ap_indices, get_peak_indices
 from specparam.core.modutils import safe_import, check_dependency
 from specparam.analysis.periodic import get_band_peak_arr
+from specparam.data.utils import flatten_results_dict
 
 pd = safe_import('pandas')
 
@@ -131,3 +132,77 @@ def group_to_dataframe(fit_results, peak_org):
     """
 
     return pd.DataFrame(group_to_dict(fit_results, peak_org))
+
+
+def event_group_to_dict(event_group_results, peak_org):
+    """Convert the event results to be organized across across and time windows.
+
+    Parameters
+    ----------
+    event_group_results : list of list of FitResults
+        Model fit results from across a set of events.
+    peak_org : int or Bands
+        How to organize peaks.
+        If int, extracts the first n peaks.
+        If Bands, extracts peaks based on band definitions.
+
+    Returns
+    -------
+    event_time_results : dict
+        Results dictionary wherein parameters are organized in 2d arrays as [n_events, n_windows].
+    """
+
+    event_time_results = {}
+
+    for key in group_to_dict(event_group_results[0], peak_org):
+        event_time_results[key] = []
+
+    for gres in event_group_results:
+        dictres = group_to_dict(gres, peak_org)
+        for key, val in dictres.items():
+            event_time_results[key].append(val)
+
+    for key in event_time_results:
+        event_time_results[key] = np.array(event_time_results[key])
+
+    return event_time_results
+
+
+@check_dependency(pd, 'pandas')
+def event_group_to_dataframe(event_group_results, peak_org):
+    """Convert a group of model fit results into a dataframe.
+
+    Parameters
+    ----------
+    event_group_results : list of FitResults
+        List of FitResults objects.
+    peak_org : int or Bands
+        How to organize peaks.
+        If int, extracts the first n peaks.
+        If Bands, extracts peaks based on band definitions.
+
+    Returns
+    -------
+    pd.DataFrame
+        Model results organized into a dataframe.
+    """
+
+    return pd.DataFrame(flatten_results_dict(event_group_to_dict(event_group_results, peak_org)))
+
+
+@check_dependency(pd, 'pandas')
+def dict_to_df(results):
+    """Convert a dictionary of model fit results into a dataframe.
+
+    Parameters
+    ----------
+    results : dict
+        Fit results that have already been organized into a flat dictionary.
+
+    Returns
+    -------
+    pd.DataFrame
+        Model results organized into a dataframe.
+    """
+
+    return pd.DataFrame(results)
diff --git a/specparam/data/utils.py b/specparam/data/utils.py
index 054bdf3a..a0faeb9b 100644
--- a/specparam/data/utils.py
+++ b/specparam/data/utils.py
@@ -1,5 +1,7 @@
 """"Utility functions for working with data and data objects."""
 
+import numpy as np
+
 ###################################################################################################
 ###################################################################################################
 
@@ -101,3 +103,31 @@ def get_results_by_row(results, ind):
         outs[key] = results[key][ind, :]
 
     return outs
+
+
+def flatten_results_dict(results):
+    """Flatten a results dictionary containing results across events.
+
+    Parameters
+    ----------
+    results : dict
+        Results dictionary wherein parameters are organized in 2d arrays as [n_events, n_windows].
+
+    Returns
+    -------
+    flatdict : dict
+        Flattened results dictionary.
+    """
+
+    keys = list(results.keys())
+    n_events, n_windows = results[keys[0]].shape
+
+    flatdict = {
+        'event' : np.repeat(range(n_events), n_windows),
+        'window' : np.tile(range(n_windows), n_events),
+    }
+
+    for key in keys:
+        flatdict[key] = results[key].flatten()
+
+    return flatdict
diff --git a/specparam/tests/data/test_conversions.py b/specparam/tests/data/test_conversions.py
index 1131618b..3bdb3c3a 100644
--- a/specparam/tests/data/test_conversions.py
+++ b/specparam/tests/data/test_conversions.py
@@ -52,7 +52,7 @@ def test_group_to_dict(tresults, tbands):
     out = group_to_dict(fit_results, peak_org=tbands)
     assert isinstance(out, dict)
 
-def test_group_to_dataframe(tresults,  tbands, skip_if_no_pandas):
+def test_group_to_dataframe(tresults, tbands, skip_if_no_pandas):
 
     fit_results = [deepcopy(tresults), deepcopy(tresults), deepcopy(tresults)]
 
@@ -62,3 +62,38 @@ def test_group_to_dataframe(tresults,  tbands, skip_if_no_pandas):
 
     out = group_to_dataframe(fit_results, peak_org=tbands)
     assert isinstance(out, pd.DataFrame)
+
+def test_event_group_to_dict(tresults, tbands):
+
+    fit_results = [[deepcopy(tresults), deepcopy(tresults), deepcopy(tresults)],
+                   [deepcopy(tresults), deepcopy(tresults), deepcopy(tresults)]]
+
+    for peak_org in [1, 2, 3]:
+        out = event_group_to_dict(fit_results, peak_org=peak_org)
+        assert isinstance(out, dict)
+
+    out = event_group_to_dict(fit_results, peak_org=tbands)
+    assert isinstance(out, dict)
+
+def test_event_group_to_dataframe(tresults, tbands, skip_if_no_pandas):
+
+    fit_results = [[deepcopy(tresults), deepcopy(tresults), deepcopy(tresults)],
+                   [deepcopy(tresults), deepcopy(tresults), deepcopy(tresults)]]
+
+    for peak_org in [1, 2, 3]:
+        out = event_group_to_dataframe(fit_results, peak_org=peak_org)
+        assert isinstance(out, pd.DataFrame)
+
+    out = event_group_to_dataframe(fit_results, peak_org=tbands)
+    assert isinstance(out, pd.DataFrame)
+
+def test_dict_to_df(skip_if_no_pandas):
+
+    tdict = {
+        'offset' : [0, 1, 0, 1],
+        'exponent' : [1, 2, 2, 1],
+    }
+
+    tdf = dict_to_df(tdict)
+    assert isinstance(tdf, pd.DataFrame)
+    assert list(tdict.keys()) == list(tdf.columns)
diff --git a/specparam/tests/data/test_utils.py b/specparam/tests/data/test_utils.py
index c7ea4b9c..b5eaae1d 100644
--- a/specparam/tests/data/test_utils.py
+++ b/specparam/tests/data/test_utils.py
@@ -123,3 +123,24 @@ def test_get_results_by_row():
     out1 = get_results_by_row(tdict, ind)
     for key in tdict.keys():
         assert np.array_equal(out1[key], tdict[key][ind])
+
+def test_flatten_results_dict():
+
+    tdict = {
+        'offset' : np.array([[0, 1], [2, 3]]),
+        'exponent' : np.array([[0, 1], [2, 3]]),
+        'error' : np.array([[0, 1], [2, 3]]),
+        'r_squared' : np.array([[0, 1], [2, 3]]),
+        'alpha_cf' : np.array([[0, 1], [2, 3]]),
+        'alpha_pw' : np.array([[0, 1], [2, 3]]),
+        'alpha_bw' : np.array([[0, 1], [2, 3]]),
+    }
+
+    out = flatten_results_dict(tdict)
+
+    assert np.array_equal(out['event'], np.array([0, 0, 1, 1]))
+    assert np.array_equal(out['window'], np.array([0, 1, 0, 1]))
+    for key, values in out.items():
+        assert values.ndim == 1
+        if key not in ['event', 'window']:
+            assert np.array_equal(values, np.array([0, 1, 2, 3]))

From 3ce46c9bfd205b7918a30e23bff57bb373c8a61c Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Wed, 12 Jul 2023 18:33:48 -0400
Subject: [PATCH 41/99] update time / event to_df & associated

---
 specparam/objs/event.py            | 53 ++++++++++++++++++++----------
 specparam/objs/time.py             | 27 ++++++++++++++-
 specparam/tests/objs/test_event.py |  4 +--
 3 files changed, 63 insertions(+), 21 deletions(-)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index 87ee9cf8..d0993fe2 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -4,8 +4,8 @@
 
 from specparam.objs import SpectralModel, SpectralTimeModel
 from specparam.plts.event import plot_event_model
-from specparam.data.conversions import group_to_dict
-from specparam.data.utils import get_results_by_row
+from specparam.data.conversions import event_group_to_dict, event_group_to_dataframe, dict_to_df
+from specparam.data.utils import get_results_by_row, flatten_results_dict
 from specparam.core.modutils import (copy_doc_func_to_method, docs_get_section,
                                      replace_docstring_sections)
 from specparam.core.reports import save_event_report
@@ -253,13 +253,15 @@ def save_report(self, file_name, file_path=None, add_settings=True):
         save_event_report(self, file_name, file_path, add_settings)
 
 
-    def get_model(self, ind, regenerate=True):
+    def get_model(self, event_ind, window_ind, regenerate=True):
         """Get a model fit object for a specified index.
 
         Parameters
         ----------
-        ind : list of [int, int]
-            Index to extract, listed as [event_index, time_window_index].
+        event_ind : int
+            Index for which event to extract from.
+        window_ind : int
+            Index for which time window to extract from.
         regenerate : bool, optional, default: False
             Whether to regenerate the model fits for the requested model.
 
@@ -276,19 +278,44 @@ def get_model(self, ind, regenerate=True):
         # Add data for specified single power spectrum, if available
         #   The power spectrum is inverted back to linear, as it is re-logged when added to object
         if self.has_data:
-            model.add_data(self.freqs, np.power(10, self.spectrograms[ind[0]][:, ind[1]]))
+            model.add_data(self.freqs, np.power(10, self.spectrograms[event_ind][:, window_ind]))
         # If no power spectrum data available, copy over data information & regenerate freqs
         else:
             model.add_meta_data(self.get_meta_data())
 
         # Add results for specified power spectrum, regenerating full fit if requested
-        model.add_results(self.event_group_results[ind[0]][ind[1]])
+        model.add_results(self.event_group_results[event_ind][window_ind])
         if regenerate:
             model._regenerate_model()
 
         return model
 
 
+    def to_df(self, peak_org=None):
+        """Convert and extract the model results as a pandas object.
+
+        Parameters
+        ----------
+        peak_org : int or Bands, optional
+            How to organize peaks.
+            If int, extracts the first n peaks.
+            If Bands, extracts peaks based on band definitions.
+            If provided, re-extracts peak features; if not provided, converts from `time_results`.
+
+        Returns
+        -------
+        pd.DataFrame
+            Model results organized into a pandas object.
+        """
+
+        if peak_org is not None:
+            df = event_group_to_dataframe(self.event_group_results, peak_org)
+        else:
+            df = dict_to_df(flatten_results_dict(self.get_results()))
+
+        return df
+
+
     def _convert_to_event_results(self, peak_org):
         """Convert the event results to be organized across across and time windows.
 
@@ -300,17 +327,7 @@ def _convert_to_event_results(self, peak_org):
             If Bands, extracts peaks based on band definitions.
         """
 
-        temp = group_to_dict(self.event_group_results[0], peak_org)
-        for key in temp:
-            self.event_time_results[key] = []
-
-        for gres in self.event_group_results:
-            dictres = group_to_dict(gres, peak_org)
-            for key in dictres:
-                self.event_time_results[key].append(dictres[key])
-
-        for key in self.event_time_results:
-            self.event_time_results[key] = np.array(self.event_time_results[key])
+        self.event_time_results = event_group_to_dict(self.event_group_results, peak_org)
 
     # ToDo: check & figure out adding `load` method
 
diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index b298eccb..0fe791d2 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -6,7 +6,7 @@
 
 from specparam.objs import SpectralModel, SpectralGroupModel
 from specparam.plts.time import plot_time_model
-from specparam.data.conversions import group_to_dict
+from specparam.data.conversions import group_to_dict, group_to_dataframe, dict_to_df
 from specparam.data.utils import get_results_by_ind
 from specparam.core.reports import save_time_report
 from specparam.core.modutils import (copy_doc_func_to_method, docs_get_section,
@@ -247,6 +247,31 @@ def load(self, file_name, file_path=None, peak_org=None):
         self._convert_to_time_results(peak_org)
 
 
+    def to_df(self, peak_org=None):
+        """Convert and extract the model results as a pandas object.
+
+        Parameters
+        ----------
+        peak_org : int or Bands, optional
+            How to organize peaks.
+            If int, extracts the first n peaks.
+            If Bands, extracts peaks based on band definitions.
+            If provided, re-extracts peak features; if not provided, converts from `time_results`.
+
+        Returns
+        -------
+        pd.DataFrame
+            Model results organized into a pandas object.
+        """
+
+        if peak_org is not None:
+            df = group_to_dataframe(self.group_results, peak_org)
+        else:
+            df = dict_to_df(self.get_results())
+
+        return df
+
+
     def _convert_to_time_results(self, peak_org):
         """Convert the model results to be organized across time windows.
 
diff --git a/specparam/tests/objs/test_event.py b/specparam/tests/objs/test_event.py
index adbc443e..b7943b9e 100644
--- a/specparam/tests/objs/test_event.py
+++ b/specparam/tests/objs/test_event.py
@@ -74,10 +74,10 @@ def test_event_report(skip_if_no_mpl):
 def test_event_get_model(tfe):
 
     # Check without regenerating
-    tfm0 = tfe.get_model([0, 0], False)
+    tfm0 = tfe.get_model(0, 0, False)
     assert tfm0
 
     # Check with regenerating
-    tfm1 = tfe.get_model([1, 1], True)
+    tfm1 = tfe.get_model(1, 1, True)
     assert tfm1
     assert np.all(tfm1.modeled_spectrum_)

From 0c762b7fe7375e11e76896303a4f01816bcf0b44 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Thu, 13 Jul 2023 10:42:15 -0400
Subject: [PATCH 42/99] try actions tweak to run on all PRs

---
 .github/workflows/build.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 4164b2e1..68a30ffd 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -6,7 +6,6 @@ on:
   push:
     branches: [ main ]
   pull_request:
-    branches: [ main ]
 
 jobs:
   build:

From 164ef593cb906c3de697561d9cf561e741c98d0a Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Thu, 13 Jul 2023 10:47:26 -0400
Subject: [PATCH 43/99] move min support to 3.6

---
 .github/workflows/build.yml | 7 ++-----
 README.rst                  | 2 +-
 setup.py                    | 1 -
 3 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 68a30ffd..21ead61e 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -10,15 +10,12 @@ on:
 jobs:
   build:
 
-    # Tag ubuntu version to 20.04, in order to support python 3.6
-    #   See issue: https://github.com/actions/setup-python/issues/544
-    #   When ready to drop 3.6, can revert from 'ubuntu-20.04' -> 'ubuntu-latest'
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     env:
       MODULE_NAME: specparam
     strategy:
       matrix:
-        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v3
diff --git a/README.rst b/README.rst
index e0ff6c6c..e85c2493 100644
--- a/README.rst
+++ b/README.rst
@@ -71,7 +71,7 @@ This documentation includes:
 Dependencies
 ------------
 
-SpecParam is written in Python, and requires Python >= 3.6 to run.
+SpecParam is written in Python, and requires Python >= 3.7 to run.
 
 It has the following required dependencies:
 
diff --git a/setup.py b/setup.py
index a2ba840a..2aec40e6 100644
--- a/setup.py
+++ b/setup.py
@@ -39,7 +39,6 @@
         'Operating System :: POSIX',
         'Operating System :: Unix',
         'Programming Language :: Python',
-        'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',

From 2a0402d2d5d422a10d213032eb2a3cbf1385d82f Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Thu, 13 Jul 2023 11:07:39 -0400
Subject: [PATCH 44/99] update n_peaks_ property

---
 specparam/objs/event.py            | 8 ++++++++
 specparam/objs/time.py             | 8 ++++++++
 specparam/tests/objs/test_event.py | 4 ++++
 specparam/tests/objs/test_time.py  | 4 ++++
 4 files changed, 24 insertions(+)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index d0993fe2..2a569af2 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -96,6 +96,14 @@ def has_model(self):
         return True if self.event_group_results else False
 
 
+    @property
+    def n_peaks_(self):
+        """How many peaks were fit for each model, for each event."""
+
+        return np.array([[res.peak_params.shape[0] for res in gres] \
+            if self.has_model else None for gres in self.event_group_results])
+
+
     @property
     def n_events(self):
         # ToDo: double check if we want this - I think is never used internally?
diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index 0fe791d2..f61b7a29 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -87,6 +87,14 @@ def __getitem__(self, ind):
         return get_results_by_ind(self.time_results, ind)
 
 
+    @property
+    def n_peaks_(self):
+        """How many peaks were fit for each model."""
+
+        return [res.peak_params.shape[0] for res in self.group_results] \
+            if self.has_model else None
+
+
     def _reset_time_results(self):
         """Set, or reset, time results to be empty."""
 
diff --git a/specparam/tests/objs/test_event.py b/specparam/tests/objs/test_event.py
index b7943b9e..4d3380b6 100644
--- a/specparam/tests/objs/test_event.py
+++ b/specparam/tests/objs/test_event.py
@@ -34,6 +34,10 @@ def test_event_iter(tfe):
     for out in tfe:
         assert out
 
+def test_event_n_peaks(tfe):
+
+    assert np.all(tfe.n_peaks_)
+
 def test_event_fit():
 
     n_windows = 3
diff --git a/specparam/tests/objs/test_time.py b/specparam/tests/objs/test_time.py
index 5c0a72be..6445b327 100644
--- a/specparam/tests/objs/test_time.py
+++ b/specparam/tests/objs/test_time.py
@@ -34,6 +34,10 @@ def test_time_iter(tft):
     for out in tft:
         assert out
 
+def test_time_n_peaks(tft):
+
+    assert tft.n_peaks_
+
 def test_time_fit():
 
     n_windows = 10

From ccd7c48f86f6bfc993d78dd3c810cdea8ce291a7 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Thu, 13 Jul 2023 11:10:37 -0400
Subject: [PATCH 45/99] add tests for to_df

---
 specparam/tests/objs/test_event.py | 12 ++++++++++++
 specparam/tests/objs/test_time.py  | 12 ++++++++++++
 2 files changed, 24 insertions(+)

diff --git a/specparam/tests/objs/test_event.py b/specparam/tests/objs/test_event.py
index 4d3380b6..c0cd605a 100644
--- a/specparam/tests/objs/test_event.py
+++ b/specparam/tests/objs/test_event.py
@@ -9,6 +9,9 @@
 import numpy as np
 
 from specparam.sim import sim_spectrogram
+from specparam.core.modutils import safe_import
+
+pd = safe_import('pandas')
 
 from specparam.tests.settings import TEST_DATA_PATH
 from specparam.tests.tutils import default_group_params, plot_test
@@ -85,3 +88,12 @@ def test_event_get_model(tfe):
     tfm1 = tfe.get_model(1, 1, True)
     assert tfm1
     assert np.all(tfm1.modeled_spectrum_)
+
+def test_event_to_df(tfe, tbands, skip_if_no_pandas):
+
+    df0 = tfe.to_df()
+    assert isinstance(df0, pd.DataFrame)
+    df1 = tfe.to_df(2)
+    assert isinstance(df1, pd.DataFrame)
+    df2 = tfe.to_df(tbands)
+    assert isinstance(df2, pd.DataFrame)
diff --git a/specparam/tests/objs/test_time.py b/specparam/tests/objs/test_time.py
index 6445b327..a8b3e75d 100644
--- a/specparam/tests/objs/test_time.py
+++ b/specparam/tests/objs/test_time.py
@@ -9,6 +9,9 @@
 import numpy as np
 
 from specparam.sim import sim_spectrogram
+from specparam.core.modutils import safe_import
+
+pd = safe_import('pandas')
 
 from specparam.tests.settings import TEST_DATA_PATH
 from specparam.tests.tutils import default_group_params, plot_test
@@ -83,3 +86,12 @@ def test_time_load(tbands):
     tft = SpectralTimeModel(verbose=False)
     tft.load(file_name_res, TEST_DATA_PATH, peak_org=tbands)
     assert tft.time_results
+
+def test_time_to_df(tft, tbands, skip_if_no_pandas):
+
+    df0 = tft.to_df()
+    assert isinstance(df0, pd.DataFrame)
+    df1 = tft.to_df(2)
+    assert isinstance(df1, pd.DataFrame)
+    df2 = tft.to_df(tbands)
+    assert isinstance(df2, pd.DataFrame)

From da78eea536e073f7b267a739ebce0a32582eda54 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Thu, 13 Jul 2023 11:35:26 -0400
Subject: [PATCH 46/99] updates to save_model_report across objects

---
 specparam/core/reports.py |  7 ++-----
 specparam/objs/event.py   | 24 ++++++++++++++++++++++++
 specparam/objs/fit.py     |  5 ++---
 specparam/objs/group.py   |  6 ++----
 4 files changed, 30 insertions(+), 12 deletions(-)

diff --git a/specparam/core/reports.py b/specparam/core/reports.py
index 7b44a3e1..e6a8f814 100644
--- a/specparam/core/reports.py
+++ b/specparam/core/reports.py
@@ -26,8 +26,7 @@
 ###################################################################################################
 
 @check_dependency(plt, 'matplotlib')
-def save_model_report(model, file_name, file_path=None, plt_log=False,
-                      add_settings=True, **plot_kwargs):
+def save_model_report(model, file_name, file_path=None, add_settings=True, **plot_kwargs):
     """Generate and save out a PDF report for a power spectrum model fit.
 
     Parameters
@@ -38,8 +37,6 @@ def save_model_report(model, file_name, file_path=None, plt_log=False,
         Name to give the saved out file.
     file_path : str, optional
         Path to directory to save to. If None, saves to current directory.
-    plt_log : bool, optional, default: False
-        Whether or not to plot the frequency axis in log space.
     add_settings : bool, optional, default: True
         Whether to add a print out of the model settings to the end of the report.
     plot_kwargs : keyword arguments
@@ -63,7 +60,7 @@ def save_model_report(model, file_name, file_path=None, plt_log=False,
 
     # Second - data plot
     ax1 = plt.subplot(grid[1])
-    model.plot(plt_log=plt_log, ax=ax1, **plot_kwargs)
+    model.plot(ax=ax1, **plot_kwargs)
 
     # Third - model settings
     if add_settings:
diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index 2a569af2..7acdc89e 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -299,6 +299,30 @@ def get_model(self, event_ind, window_ind, regenerate=True):
         return model
 
 
+    def save_model_report(self, event_index, window_index, file_name,
+                          file_path=None, add_settings=True, **plot_kwargs):
+        """"Save out an individual model report for a specified model fit.
+
+        Parameters
+        ----------
+        event_ind : int
+            Index for which event to extract from.
+        window_ind : int
+            Index for which time window to extract from.
+        file_name : str
+            Name to give the saved out file.
+        file_path : str, optional
+            Path to directory to save to. If None, saves to current directory.
+        add_settings : bool, optional, default: True
+            Whether to add a print out of the model settings to the end of the report.
+        plot_kwargs : keyword arguments
+            Keyword arguments to pass into the plot method.
+        """
+
+        self.get_model(event_index, window_index, regenerate=True).save_report(\
+            file_name, file_path, add_settings, **plot_kwargs)
+
+
     def to_df(self, peak_org=None):
         """Convert and extract the model results as a pandas object.
 
diff --git a/specparam/objs/fit.py b/specparam/objs/fit.py
index c08bb734..6294e158 100644
--- a/specparam/objs/fit.py
+++ b/specparam/objs/fit.py
@@ -651,10 +651,9 @@ def plot(self, plot_peaks=None, plot_aperiodic=True, plt_log=False,
 
 
     @copy_doc_func_to_method(save_model_report)
-    def save_report(self, file_name, file_path=None, plt_log=False,
-                    add_settings=True, **plot_kwargs):
+    def save_report(self, file_name, file_path=None, add_settings=True, **plot_kwargs):
 
-        save_model_report(self, file_name, file_path, plt_log, add_settings, **plot_kwargs)
+        save_model_report(self, file_name, file_path, add_settings, **plot_kwargs)
 
 
     @copy_doc_func_to_method(save_model)
diff --git a/specparam/objs/group.py b/specparam/objs/group.py
index 4ba556ee..e1d5d214 100644
--- a/specparam/objs/group.py
+++ b/specparam/objs/group.py
@@ -522,7 +522,7 @@ def print_results(self, concise=False):
         print(gen_group_results_str(self, concise))
 
 
-    def save_model_report(self, index, file_name, file_path=None, plt_log=False,
+    def save_model_report(self, index, file_name, file_path=None,
                           add_settings=True, **plot_kwargs):
         """"Save out an individual model report for a specified model fit.
 
@@ -534,8 +534,6 @@ def save_model_report(self, index, file_name, file_path=None, plt_log=False,
             Name to give the saved out file.
         file_path : str, optional
             Path to directory to save to. If None, saves to current directory.
-        plt_log : bool, optional, default: False
-            Whether or not to plot the frequency axis in log space.
         add_settings : bool, optional, default: True
             Whether to add a print out of the model settings to the end of the report.
         plot_kwargs : keyword arguments
@@ -543,7 +541,7 @@ def save_model_report(self, index, file_name, file_path=None, plt_log=False,
         """
 
         self.get_model(ind=index, regenerate=True).save_report(\
-            file_name, file_path, plt_log, **plot_kwargs)
+            file_name, file_path, add_settings, **plot_kwargs)
 
 
     def to_df(self, peak_org):

From ed8c31b437e16b603f872fc3c6515dfb0414815b Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Thu, 13 Jul 2023 17:53:38 -0400
Subject: [PATCH 47/99] update naming & labels in data conversions

---
 specparam/data/conversions.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/specparam/data/conversions.py b/specparam/data/conversions.py
index c4da0b7a..ff4b863c 100644
--- a/specparam/data/conversions.py
+++ b/specparam/data/conversions.py
@@ -86,13 +86,13 @@ def model_to_dataframe(fit_results, peak_org):
     return pd.Series(model_to_dict(fit_results, peak_org))
 
 
-def group_to_dict(fit_results, peak_org):
+def group_to_dict(group_results, peak_org):
     """Convert a group of model fit results into a dictionary.
 
     Parameters
     ----------
-    fit_results : list of FOOOFResults
-        List of FOOOFResults objects.
+    group_results : list of FitResults
+        List of FitResults objects, reflecting model results across a group of power spectra.
     peak_org : int or Bands
         How to organize peaks.
         If int, extracts the first n peaks.
@@ -104,8 +104,8 @@ def group_to_dict(fit_results, peak_org):
         Model results organized into a dictionary.
     """
 
-    fr_dict = {ke : [] for ke in model_to_dict(fit_results[0], peak_org)}
-    for f_res in fit_results:
+    fr_dict = {ke : [] for ke in model_to_dict(group_results[0], peak_org)}
+    for f_res in group_results:
         for key, val in model_to_dict(f_res, peak_org).items():
             fr_dict[key].append(val)
 
@@ -113,12 +113,12 @@ def group_to_dict(fit_results, peak_org):
 
 
 @check_dependency(pd, 'pandas')
-def group_to_dataframe(fit_results, peak_org):
+def group_to_dataframe(group_results, peak_org):
     """Convert a group of model fit results into a dataframe.
 
     Parameters
     ----------
-    fit_results : list of FitResults
+    group_results : list of FitResults
         List of FitResults objects.
     peak_org : int or Bands
         How to organize peaks.
@@ -131,7 +131,7 @@ def group_to_dataframe(fit_results, peak_org):
         Model results organized into a dataframe.
     """
 
-    return pd.DataFrame(group_to_dict(fit_results, peak_org))
+    return pd.DataFrame(group_to_dict(group_results, peak_org))
 
 
 def event_group_to_dict(event_group_results, peak_org):

From feb8f821cb8104ddea4da7b89a566ef2361344dc Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Thu, 13 Jul 2023 18:08:10 -0400
Subject: [PATCH 48/99] move / refactor underlying funcs for get_params to own
 funcs

---
 specparam/data/utils.py            | 100 +++++++++++++++++++++++++++++
 specparam/tests/data/test_utils.py |  29 +++++++++
 2 files changed, 129 insertions(+)

diff --git a/specparam/data/utils.py b/specparam/data/utils.py
index a0faeb9b..e7caa1af 100644
--- a/specparam/data/utils.py
+++ b/specparam/data/utils.py
@@ -2,9 +2,109 @@
 
 import numpy as np
 
+from specparam.core.info import get_indices
+from specparam.core.funcs import infer_ap_func
+
 ###################################################################################################
 ###################################################################################################
 
+def get_model_params(fit_results, name, col=None):
+    """Return model fit parameters for specified feature(s).
+
+    Parameters
+    ----------
+    fit_results : FitResults
+        Results of a model fit.
+    name : {'aperiodic_params', 'peak_params', 'gaussian_params', 'error', 'r_squared'}
+        Name of the data field to extract.
+    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
+    -------
+    out : float or 1d array
+        Requested data.
+    """
+
+    # If col specified as string, get mapping back to integer
+    if isinstance(col, str):
+        col = get_indices(infer_ap_func(fit_results.aperiodic_params))[col]
+
+    # Allow for shortcut alias, without adding `_params`
+    if name in ['aperiodic', 'peak', 'gaussian']:
+        name = name + '_params'
+
+    # Extract the request data field from object
+    out = getattr(fit_results, name)
+
+    # Periodic values can be empty arrays and if so, replace with NaN array
+    if isinstance(out, np.ndarray) and out.size == 0:
+        out = np.array([np.nan, np.nan, np.nan])
+
+    # Select out a specific column, if requested
+    if col is not None:
+
+        # Extract column, & if result is a single value in an array, unpack from array
+        out = out[col] if out.ndim == 1 else out[:, col]
+        out = out[0] if isinstance(out, np.ndarray) and out.size == 1 else out
+
+    return out
+
+
+def get_group_params(group_results, name, col=None):
+    """Extract a specified set of parameters from a set of group results.
+
+    Parameters
+    ----------
+    group_results : list of FitResults
+        List of FitResults objects, reflecting model results across a group of power spectra.
+    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
+    -------
+    out : ndarray
+        Requested data.
+    """
+
+    # Allow for shortcut alias, without adding `_params`
+    if name in ['aperiodic', 'peak', 'gaussian']:
+        name = name + '_params'
+
+    # If col specified as string, get mapping back to integer
+    if isinstance(col, str):
+        col = get_indices(infer_ap_func(group_results[0].aperiodic_params))[col]
+    elif isinstance(col, int):
+        if col not in [0, 1, 2]:
+            raise ValueError("Input value for `col` not valid.")
+
+    # Pull out the requested data field from the group data
+    # As a special case, peak_params are pulled out in a way that appends
+    #  an extra column, indicating which model each peak comes from
+    if name in ('peak_params', 'gaussian_params'):
+
+        # Collect peak data, appending the index of the model it comes from
+        out = np.vstack([np.insert(getattr(data, name), 3, index, axis=1)
+                         for index, data in enumerate(group_results)])
+
+        # This updates index to grab selected column, and the last column
+        #   This last column is the 'index' column (model object source)
+        if col is not None:
+            col = [col, -1]
+    else:
+        out = np.array([getattr(data, name) for data in group_results])
+
+    # Select out a specific column, if requested
+    if col is not None:
+        out = out[:, col]
+
+    return out
+
+
 def get_periodic_labels(results):
     """Get labels of periodic fields from a dictionary representation of parameter results.
 
diff --git a/specparam/tests/data/test_utils.py b/specparam/tests/data/test_utils.py
index b5eaae1d..6900ddf0 100644
--- a/specparam/tests/data/test_utils.py
+++ b/specparam/tests/data/test_utils.py
@@ -9,6 +9,35 @@
 ###################################################################################################
 ###################################################################################################
 
+def test_get_model_params(tresults):
+
+    for dname in ['aperiodic_params', 'aperiodic', 'peak_params', 'peak',
+                  'error', 'r_squared', 'gaussian_params', 'gaussian']:
+        assert np.any(get_model_params(tresults, dname))
+
+    if dname == 'aperiodic_params' or dname == 'aperiodic':
+        for dtype in ['offset', 'exponent']:
+            assert np.any(get_model_params(tresults, dname, dtype))
+
+    if dname == 'peak_params' or dname == 'peak':
+        for dtype in ['CF', 'PW', 'BW']:
+            assert np.any(get_model_params(tresults, dname, dtype))
+
+def test_get_group_params(tresults):
+
+    gresults = [tresults, tresults]
+
+    for dname in ['aperiodic_params', 'peak_params', 'error', 'r_squared', 'gaussian_params']:
+        assert np.any(get_group_params(gresults, dname))
+
+    if dname == 'aperiodic_params':
+        for dtype in ['offset', 'exponent']:
+            assert np.any(get_group_params(gresults, dname, dtype))
+
+    if dname == 'peak_params':
+        for dtype in ['CF', 'PW', 'BW']:
+            assert np.any(get_group_params(gresults, dname, dtype))
+
 def test_get_periodic_labels():
 
     keys = ['cf', 'pw', 'bw']

From a539ece8e565a75f6d769d77efe9867f2b10a1f5 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Thu, 13 Jul 2023 18:09:33 -0400
Subject: [PATCH 49/99] use new get_params funcs across all objs

---
 specparam/objs/event.py            | 34 ++++++++++++++++++++++++++++-
 specparam/objs/fit.py              | 26 ++--------------------
 specparam/objs/group.py            | 35 ++----------------------------
 specparam/tests/objs/test_event.py |  5 +++++
 specparam/tests/objs/test_fit.py   | 11 +---------
 specparam/tests/objs/test_group.py | 10 +--------
 6 files changed, 44 insertions(+), 77 deletions(-)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index 7acdc89e..e19be36d 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -5,7 +5,7 @@
 from specparam.objs import SpectralModel, SpectralTimeModel
 from specparam.plts.event import plot_event_model
 from specparam.data.conversions import event_group_to_dict, event_group_to_dataframe, dict_to_df
-from specparam.data.utils import get_results_by_row, flatten_results_dict
+from specparam.data.utils import get_group_params, get_results_by_row, flatten_results_dict
 from specparam.core.modutils import (copy_doc_func_to_method, docs_get_section,
                                      replace_docstring_sections)
 from specparam.core.reports import save_event_report
@@ -236,6 +236,38 @@ def get_results(self):
         return self.event_time_results
 
 
+    def get_params(self, name, col=None):
+        """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
+        -------
+        out : list of ndarray
+            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 that the peak came from.
+        """
+
+        return [get_group_params(gres, name, col) for gres in self.event_group_results]
+
+
     def print_results(self, concise=False):
         """Print out SpectralTimeEventModel results.
 
diff --git a/specparam/objs/fit.py b/specparam/objs/fit.py
index 6294e158..e1b2f669 100644
--- a/specparam/objs/fit.py
+++ b/specparam/objs/fit.py
@@ -62,7 +62,6 @@
 from scipy.optimize import curve_fit
 
 from specparam.core.items import OBJ_DESC
-from specparam.core.info import get_indices
 from specparam.core.io import save_model, load_json
 from specparam.core.reports import save_model_report
 from specparam.core.modutils import copy_doc_func_to_method
@@ -76,6 +75,7 @@
 from specparam.utils.data import trim_spectrum
 from specparam.utils.params import compute_gauss_std
 from specparam.data import FitResults, ModelSettings, SpectrumMetaData
+from specparam.data.utils import get_model_params
 from specparam.data.conversions import model_to_dataframe
 from specparam.sim.gen import gen_freqs, gen_aperiodic, gen_periodic, gen_model
 
@@ -600,29 +600,7 @@ def get_params(self, name, col=None):
         if not self.has_model:
             raise NoModelError("No model fit results are available to extract, can not proceed.")
 
-        # If col specified as string, get mapping back to integer
-        if isinstance(col, str):
-            col = get_indices(self.aperiodic_mode)[col]
-
-        # Allow for shortcut alias, without adding `_params`
-        if name in ['aperiodic', 'peak', 'gaussian']:
-            name = name + '_params'
-
-        # Extract the request data field from object
-        out = getattr(self, name + '_')
-
-        # Periodic values can be empty arrays and if so, replace with NaN array
-        if isinstance(out, np.ndarray) and out.size == 0:
-            out = np.array([np.nan, np.nan, np.nan])
-
-        # Select out a specific column, if requested
-        if col is not None:
-
-            # Extract column, & if result is a single value in an array, unpack from array
-            out = out[col] if out.ndim == 1 else out[:, col]
-            out = out[0] if isinstance(out, np.ndarray) and out.size == 1 else out
-
-        return out
+        return get_model_params(self.get_results(), name, col)
 
 
     def get_results(self):
diff --git a/specparam/objs/group.py b/specparam/objs/group.py
index e1d5d214..9708c16f 100644
--- a/specparam/objs/group.py
+++ b/specparam/objs/group.py
@@ -13,7 +13,6 @@
 from specparam.objs import SpectralModel
 from specparam.plts.group import plot_group
 from specparam.core.items import OBJ_DESC
-from specparam.core.info import get_indices
 from specparam.core.utils import check_inds
 from specparam.core.errors import NoModelError
 from specparam.core.reports import save_group_report
@@ -22,6 +21,7 @@
 from specparam.core.modutils import (copy_doc_func_to_method, safe_import,
                                      docs_get_section, replace_docstring_sections)
 from specparam.data.conversions import group_to_dataframe
+from specparam.data.utils import get_group_params
 
 ###################################################################################################
 ###################################################################################################
@@ -342,38 +342,7 @@ def get_params(self, name, col=None):
         if not self.has_model:
             raise NoModelError("No model fit results are available, can not proceed.")
 
-        # Allow for shortcut alias, without adding `_params`
-        if name in ['aperiodic', 'peak', 'gaussian']:
-            name = name + '_params'
-
-        # If col specified as string, get mapping back to integer
-        if isinstance(col, str):
-            col = get_indices(self.aperiodic_mode)[col]
-        elif isinstance(col, int):
-            if col not in [0, 1, 2]:
-                raise ValueError("Input value for `col` not valid.")
-
-        # Pull out the requested data field from the group data
-        # As a special case, peak_params are pulled out in a way that appends
-        #  an extra column, indicating which model each peak comes from
-        if name in ('peak_params', 'gaussian_params'):
-
-            # Collect peak data, appending the index of the model it comes from
-            out = np.vstack([np.insert(getattr(data, name), 3, index, axis=1)
-                             for index, data in enumerate(self.group_results)])
-
-            # This updates index to grab selected column, and the last column
-            #   This last column is the 'index' column (model object source)
-            if col is not None:
-                col = [col, -1]
-        else:
-            out = np.array([getattr(data, name) for data in self.group_results])
-
-        # Select out a specific column, if requested
-        if col is not None:
-            out = out[:, col]
-
-        return out
+        return get_group_params(self.group_results, name, col)
 
 
     @copy_doc_func_to_method(plot_group)
diff --git a/specparam/tests/objs/test_event.py b/specparam/tests/objs/test_event.py
index c0cd605a..5ff3fecb 100644
--- a/specparam/tests/objs/test_event.py
+++ b/specparam/tests/objs/test_event.py
@@ -89,6 +89,11 @@ def test_event_get_model(tfe):
     assert tfm1
     assert np.all(tfm1.modeled_spectrum_)
 
+def test_get_params(tfe):
+
+    for dname in ['aperiodic', 'peak', 'error', 'r_squared']:
+        assert np.any(tfe.get_params(dname))
+
 def test_event_to_df(tfe, tbands, skip_if_no_pandas):
 
     df0 = tfe.to_df()
diff --git a/specparam/tests/objs/test_fit.py b/specparam/tests/objs/test_fit.py
index 15b17aa6..aeb3110e 100644
--- a/specparam/tests/objs/test_fit.py
+++ b/specparam/tests/objs/test_fit.py
@@ -314,18 +314,9 @@ def test_obj_gets(tfm):
 def test_get_params(tfm):
     """Test the get_params method."""
 
-    for dname in ['aperiodic_params', 'aperiodic', 'peak_params', 'peak',
-                  'error', 'r_squared', 'gaussian_params', 'gaussian']:
+    for dname in ['aperiodic', 'peak', 'error', 'r_squared']:
         assert np.any(tfm.get_params(dname))
 
-        if dname == 'aperiodic_params' or dname == 'aperiodic':
-            for dtype in ['offset', 'exponent']:
-                assert np.any(tfm.get_params(dname, dtype))
-
-        if dname == 'peak_params' or dname == 'peak':
-            for dtype in ['CF', 'PW', 'BW']:
-                assert np.any(tfm.get_params(dname, dtype))
-
 def test_copy():
     """Test copy model object method."""
 
diff --git a/specparam/tests/objs/test_group.py b/specparam/tests/objs/test_group.py
index eff05e2e..00a690f6 100644
--- a/specparam/tests/objs/test_group.py
+++ b/specparam/tests/objs/test_group.py
@@ -228,17 +228,9 @@ def test_get_results(tfg):
 def test_get_params(tfg):
     """Check get_params method."""
 
-    for dname in ['aperiodic_params', 'peak_params', 'error', 'r_squared', 'gaussian_params']:
+    for dname in ['aperiodic', 'peak', 'error', 'r_squared']:
         assert np.any(tfg.get_params(dname))
 
-        if dname == 'aperiodic_params':
-            for dtype in ['offset', 'exponent']:
-                assert np.any(tfg.get_params(dname, dtype))
-
-        if dname == 'peak_params':
-            for dtype in ['CF', 'PW', 'BW']:
-                assert np.any(tfg.get_params(dname, dtype))
-
 @plot_test
 def test_plot(tfg, skip_if_no_mpl):
     """Check alias method for plot."""

From 165b459782483242bf28c0ef203933fd9c7d88f4 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Fri, 14 Jul 2023 00:03:08 -0400
Subject: [PATCH 50/99] tweaks: clear time group_resulst & make time_results
 arrays

---
 specparam/data/conversions.py | 7 ++++---
 specparam/objs/event.py       | 1 +
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/specparam/data/conversions.py b/specparam/data/conversions.py
index ff4b863c..8d84aa79 100644
--- a/specparam/data/conversions.py
+++ b/specparam/data/conversions.py
@@ -104,10 +104,11 @@ def group_to_dict(group_results, peak_org):
         Model results organized into a dictionary.
     """
 
-    fr_dict = {ke : [] for ke in model_to_dict(group_results[0], peak_org)}
-    for f_res in group_results:
+    nres = len(group_results)
+    fr_dict = {ke : np.zeros(nres) for ke in model_to_dict(group_results[0], peak_org)}
+    for ind, f_res in enumerate(group_results):
         for key, val in model_to_dict(f_res, peak_org).items():
-            fr_dict[key].append(val)
+            fr_dict[key][ind] = val
 
     return fr_dict
 
diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index e19be36d..ea9d73bf 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -226,6 +226,7 @@ def fit(self, freqs=None, spectrograms=None, freq_range=None, peak_org=None,
             self.power_spectra = spectrogram.T
             super().fit()
             self.event_group_results.append(self.group_results)
+            self._reset_group_results()
 
         self._convert_to_event_results(peak_org)
 

From 91adcd0f6855a72569c04706ccedd60611ae3930 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Fri, 14 Jul 2023 00:22:41 -0400
Subject: [PATCH 51/99] update get_group method for time object

---
 specparam/objs/group.py           |  2 +-
 specparam/objs/time.py            | 47 +++++++++++++++++++++++++++++++
 specparam/tests/objs/test_time.py | 10 +++++++
 3 files changed, 58 insertions(+), 1 deletion(-)

diff --git a/specparam/objs/group.py b/specparam/objs/group.py
index 9708c16f..39a1390a 100644
--- a/specparam/objs/group.py
+++ b/specparam/objs/group.py
@@ -466,7 +466,7 @@ def get_group(self, inds):
         group = SpectralGroupModel(*self.get_settings(), verbose=self.verbose)
 
         # Add data for specified power spectra, if available
-        #   Power spectra are inverted back to linear, as they are re-logged when added to object
+        #   Power spectra are inverted to linear, as they are re-logged when added to object
         if self.has_data:
             group.add_data(self.freqs, np.power(10, self.power_spectra[inds, :]))
         # If no power spectrum data available, copy over data information & regenerate freqs
diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index f61b7a29..b0a06377 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -8,6 +8,7 @@
 from specparam.plts.time import plot_time_model
 from specparam.data.conversions import group_to_dict, group_to_dataframe, dict_to_df
 from specparam.data.utils import get_results_by_ind
+from specparam.core.utils import check_inds
 from specparam.core.reports import save_time_report
 from specparam.core.modutils import (copy_doc_func_to_method, docs_get_section,
                                      replace_docstring_sections)
@@ -201,6 +202,52 @@ def get_results(self):
         return self.time_results
 
 
+    def get_group(self, inds, output_type='time'):
+        """Get a Group model object with the specified sub-selection of model fits.
+
+        Parameters
+        ----------
+        inds : array_like of int or array_like of bool
+            Indices to extract from the object.
+            If a boolean mask, True indicates indices to select.
+        output_type : {'time', 'group'}, optional
+            Type of model object to extract:
+                'time' : SpectralTimeObject
+                'group' : SpectralGroupObject
+
+        Returns
+        -------
+        group : SpectralGroupModel
+            The requested selection of results data loaded into a new group model object.
+        """
+
+        if output_type == 'time':
+
+            # Check and convert indices encoding to list of int
+            inds = check_inds(inds)
+
+            # Initialize a new model object, with same settings as current object
+            output = SpectralTimeModel(*self.get_settings(), verbose=self.verbose)
+
+            # Add data for specified power spectra, if available
+            #   Power spectra are inverted to linear, as they are re-logged when added to object
+            #   Also, take transpose to re-add in spectrogram orientation
+            if self.has_data:
+                output.add_data(self.freqs, np.power(10, self.power_spectra[inds, :]).T)
+            # If no power spectrum data available, copy over data information & regenerate freqs
+            else:
+                output.add_meta_data(self.get_meta_data())
+
+            # Add results for specified power spectra
+            output.group_results = [self.group_results[ind] for ind in inds]
+            output.time_results = get_results_by_ind(self.time_results, inds)
+
+        if output_type == 'group':
+            output = super().get_group(inds)
+
+        return output
+
+
     def print_results(self, print_type='time', concise=False):
         """Print out SpectralTimeModel results.
 
diff --git a/specparam/tests/objs/test_time.py b/specparam/tests/objs/test_time.py
index a8b3e75d..65150832 100644
--- a/specparam/tests/objs/test_time.py
+++ b/specparam/tests/objs/test_time.py
@@ -87,6 +87,16 @@ def test_time_load(tbands):
     tft.load(file_name_res, TEST_DATA_PATH, peak_org=tbands)
     assert tft.time_results
 
+def test_get_group(tft):
+
+    inds = [1, 2]
+
+    nft = tft.get_group(inds)
+    assert isinstance(nft, SpectralTimeModel)
+
+    nfg = tft.get_group(inds)
+    assert isinstance(nfg, SpectralGroupModel)
+
 def test_time_to_df(tft, tbands, skip_if_no_pandas):
 
     df0 = tft.to_df()

From 0ab35628be54e9f9f9001fd2d5e2cae977ccbacf Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Fri, 14 Jul 2023 00:54:49 -0400
Subject: [PATCH 52/99] event object accepts 3d arrays

---
 specparam/objs/event.py | 42 +++++++++++++++++++++--------------------
 specparam/objs/fit.py   |  3 ++-
 specparam/objs/time.py  |  3 +--
 3 files changed, 25 insertions(+), 23 deletions(-)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index ea9d73bf..eeebff84 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -32,8 +32,8 @@ class SpectralTimeEventModel(SpectralTimeModel):
     ----------
     freqs : 1d array
         Frequency values for the power spectra.
-    spectrograms : list of 2d array
-        Power values for the spectrograms, which each array as [n_freqs, n_time_windows].
+    spectrograms : 3d array
+        Power values for the spectrograms, organized as [n_events, n_freqs, n_time_windows].
         Power values are stored internally in log10 scale.
     freq_range : list of [float, float]
         Frequency range of the power spectra, as [lowest_freq, highest_freq].
@@ -58,7 +58,7 @@ def __init__(self, *args, **kwargs):
 
         SpectralTimeModel.__init__(self, *args, **kwargs)
 
-        self.spectrograms = []
+        self.spectrograms = None
 
         self._reset_event_results()
 
@@ -125,9 +125,10 @@ def add_data(self, freqs, spectrograms, freq_range=None):
         ----------
         freqs : 1d array
             Frequency values for the power spectra, in linear space.
-        spectrograms : list of 2d array, shape=[n_freqs, n_time_windows]
+        spectrograms : 3d array or list of 2d array
             Matrix of power values, in linear space.
-            Each spectrogram should an event, each with the same set of time windows.
+            If a list of 2d arrays, each should be have the same shape of [n_freqs, n_time_windows].
+            If a 3d array, should have shape [n_events, n_freqs, n_time_windows].
         freq_range : list of [float, float], optional
             Frequency range to restrict power spectra to. If not provided, keeps the entire range.
 
@@ -137,21 +138,20 @@ def add_data(self, freqs, spectrograms, freq_range=None):
         these will be cleared by this method call.
         """
 
-        # If given a list of spectrograms, add to object
+        # If given a list of spectrograms, convert to 3d array
         if isinstance(spectrograms, list):
+            spectrograms = np.array(spectrograms)
+
+        # If is a 3d array, add to object as spectrograms
+        if spectrograms.ndim == 3:
 
             if np.any(self.freqs):
                 self._reset_event_results()
-                self.spectrograms = []
-            for spectrogram in spectrograms:
-                t_freqs, spectrogram, t_freq_range, t_freq_res = \
-                    self._prepare_data(freqs, spectrogram.T, freq_range, 2)
-                self.spectrograms.append(spectrogram.T)
-            self.freqs = t_freqs
-            self.freq_range = t_freq_range
-            self.freq_res = t_freq_res
-
-        # If input is an array, pass through to underlying object method
+
+            self.freqs, self.spectrograms, self.freq_range, self.freq_res = \
+                self._prepare_data(freqs, spectrograms, freq_range, 3)
+
+        # Otherwise, pass through 2d array to underlying object method
         else:
             super().add_data(freqs, spectrograms, freq_range)
 
@@ -164,9 +164,10 @@ def report(self, freqs=None, spectrograms=None, freq_range=None,
         ----------
         freqs : 1d array, optional
             Frequency values for the power_spectra, in linear space.
-        spectrograms : list of 2d array, shape=[n_freqs, n_time_windows]
+        spectrograms : 3d array or list of 2d array
             Matrix of power values, in linear space.
-            Each spectrogram should an event, each with the same set of time windows.
+            If a list of 2d arrays, each should be have the same shape of [n_freqs, n_time_windows].
+            If a 3d array, should have shape [n_events, n_freqs, n_time_windows].
         freq_range : list of [float, float], optional
             Frequency range to fit the model to. If not provided, fits the entire given range.
         peak_org : int or Bands
@@ -197,9 +198,10 @@ def fit(self, freqs=None, spectrograms=None, freq_range=None, peak_org=None,
         ----------
         freqs : 1d array, optional
             Frequency values for the power_spectra, in linear space.
-        spectrograms : list of 2d array, shape=[n_freqs, n_time_windows]
+        spectrograms : 3d array or list of 2d array
             Matrix of power values, in linear space.
-            Each spectrogram should an event, each with the same set of time windows.
+            If a list of 2d arrays, each should be have the same shape of [n_freqs, n_time_windows].
+            If a 3d array, should have shape [n_events, n_freqs, n_time_windows].
         freq_range : list of [float, float], optional
             Frequency range to fit the model to. If not provided, fits the entire given range.
         peak_org : int or Bands
diff --git a/specparam/objs/fit.py b/specparam/objs/fit.py
index e1b2f669..a4dd531b 100644
--- a/specparam/objs/fit.py
+++ b/specparam/objs/fit.py
@@ -1196,7 +1196,8 @@ def _prepare_data(self, freqs, power_spectrum, freq_range, spectra_dim=1):
             raise DataError("Inputs are not the right dimensions.")
 
         # Check that data sizes are compatible
-        if freqs.shape[-1] != power_spectrum.shape[-1]:
+        if (spectra_dim < 3 and freqs.shape[-1] != power_spectrum.shape[-1]) or \
+            spectra_dim == 3 and freqs.shape[-1] != power_spectrum.shape[1]:
             raise InconsistentDataError("The input frequencies and power spectra "
                                         "are not consistent size.")
 
diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index b0a06377..1c1c1516 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -231,9 +231,8 @@ def get_group(self, inds, output_type='time'):
 
             # Add data for specified power spectra, if available
             #   Power spectra are inverted to linear, as they are re-logged when added to object
-            #   Also, take transpose to re-add in spectrogram orientation
             if self.has_data:
-                output.add_data(self.freqs, np.power(10, self.power_spectra[inds, :]).T)
+                output.add_data(self.freqs, np.power(10, self.spectrogram[:, inds]))
             # If no power spectrum data available, copy over data information & regenerate freqs
             else:
                 output.add_meta_data(self.get_meta_data())

From 0cb32da40efa13c59c97d7ead1573c8f159a8049 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Fri, 14 Jul 2023 11:41:51 -0400
Subject: [PATCH 53/99] add get_group to event object and associated / related
 changes

---
 specparam/core/utils.py            | 17 ++++++++-----
 specparam/objs/event.py            | 41 ++++++++++++++++++++++++++++++
 specparam/objs/group.py            |  1 -
 specparam/objs/time.py             |  7 +++--
 specparam/tests/objs/test_event.py |  7 ++++-
 specparam/tests/objs/test_time.py  |  2 +-
 6 files changed, 61 insertions(+), 14 deletions(-)

diff --git a/specparam/core/utils.py b/specparam/core/utils.py
index 64d797ea..9e7e81b4 100644
--- a/specparam/core/utils.py
+++ b/specparam/core/utils.py
@@ -199,13 +199,14 @@ def check_inds(inds):
 
     Parameters
     ----------
-    inds : int or array_like of int or array_like of bool
+    inds : int or range or array_like of int or array_like of bool
         Indices, indicated in multiple possible ways.
+        If None, converted to slice object representing all inds.
 
     Returns
     -------
-    array of int
-        Indices, indicated
+    array of int or slice or range
+        Indices.
 
     Notes
     -----
@@ -217,12 +218,14 @@ def check_inds(inds):
     # Typecasting: if a single int, convert to an array
     if isinstance(inds, int):
         inds = np.array([inds])
-    # Typecasting: if a list or range, convert to an array
-    elif isinstance(inds, (list, range)):
+    # Typecasting: if a list, convert to an array
+    if isinstance(inds, (list)):
         inds = np.array(inds)
-
+    # If range or slice type, leave as is
+    if isinstance(inds, (range, slice)):
+        inds = inds
     # Conversion: if array is boolean, get integer indices of True
-    if inds.dtype == bool:
+    if isinstance(inds, np.ndarray) and inds.dtype == bool:
         inds = np.where(inds)[0]
 
     return inds
diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index eeebff84..4146e602 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -10,6 +10,7 @@
                                      replace_docstring_sections)
 from specparam.core.reports import save_event_report
 from specparam.core.strings import gen_event_results_str
+from specparam.core.utils import check_inds
 
 ###################################################################################################
 ###################################################################################################
@@ -229,6 +230,7 @@ def fit(self, freqs=None, spectrograms=None, freq_range=None, peak_org=None,
             super().fit()
             self.event_group_results.append(self.group_results)
             self._reset_group_results()
+            self._reset_data_results(clear_spectra=True)
 
         self._convert_to_event_results(peak_org)
 
@@ -271,6 +273,45 @@ def get_params(self, name, col=None):
         return [get_group_params(gres, name, col) for gres in self.event_group_results]
 
 
+    def get_group(self, event_inds, window_inds):
+        """Get a new model object with the specified sub-selection of model fits.
+
+        Parameters
+        ----------
+        event_inds, window_inds : array_like of int or array_like of bool
+            Indices to extract from the object, for event and time windows.
+
+        Returns
+        -------
+        output : SpectralTimeEventModel
+            The requested selection of results data loaded into a new model object.
+        """
+
+        # Check and convert indices encoding to list of int
+        event_inds = check_inds(event_inds)
+        window_inds = check_inds(window_inds)
+
+        # Initialize a new model object, with same settings as current object
+        output = SpectralTimeEventModel(*self.get_settings(), verbose=self.verbose)
+
+        # Add data for specified power spectra, if available
+        #   Power spectra are inverted to linear, as they are re-logged when added to object
+        if self.has_data:
+            output.add_data(self.freqs,
+                            np.power(10, self.spectrograms[event_inds, :, :][:, :, window_inds]))
+        # If no power spectrum data available, copy over data information & regenerate freqs
+        else:
+            output.add_meta_data(self.get_meta_data())
+
+        # Add results for specified power spectra
+        output.event_group_results = \
+            [self.event_group_results[eind][wind] for eind in event_inds for wind in window_inds]
+        output.event_time_results = \
+            {key : self.event_time_results[key][event_inds][:, window_inds] \
+            for key in self.event_time_results}
+
+        return output
+
     def print_results(self, concise=False):
         """Print out SpectralTimeEventModel results.
 
diff --git a/specparam/objs/group.py b/specparam/objs/group.py
index 39a1390a..532f550e 100644
--- a/specparam/objs/group.py
+++ b/specparam/objs/group.py
@@ -451,7 +451,6 @@ def get_group(self, inds):
         ----------
         inds : array_like of int or array_like of bool
             Indices to extract from the object.
-            If a boolean mask, True indicates indices to select.
 
         Returns
         -------
diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index 1c1c1516..2baa15f3 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -203,13 +203,12 @@ def get_results(self):
 
 
     def get_group(self, inds, output_type='time'):
-        """Get a Group model object with the specified sub-selection of model fits.
+        """Get a new model object with the specified sub-selection of model fits.
 
         Parameters
         ----------
         inds : array_like of int or array_like of bool
             Indices to extract from the object.
-            If a boolean mask, True indicates indices to select.
         output_type : {'time', 'group'}, optional
             Type of model object to extract:
                 'time' : SpectralTimeObject
@@ -217,8 +216,8 @@ def get_group(self, inds, output_type='time'):
 
         Returns
         -------
-        group : SpectralGroupModel
-            The requested selection of results data loaded into a new group model object.
+        output : SpectralTimeModel or SpectralGroupModel
+            The requested selection of results data loaded into a new model object.
         """
 
         if output_type == 'time':
diff --git a/specparam/tests/objs/test_event.py b/specparam/tests/objs/test_event.py
index 5ff3fecb..b3146009 100644
--- a/specparam/tests/objs/test_event.py
+++ b/specparam/tests/objs/test_event.py
@@ -89,11 +89,16 @@ def test_event_get_model(tfe):
     assert tfm1
     assert np.all(tfm1.modeled_spectrum_)
 
-def test_get_params(tfe):
+def test_event_get_params(tfe):
 
     for dname in ['aperiodic', 'peak', 'error', 'r_squared']:
         assert np.any(tfe.get_params(dname))
 
+def test_event_get_group(tfe):
+
+    ntfe = tfe.get_group([0], [1, 2])
+    assert ntfe
+
 def test_event_to_df(tfe, tbands, skip_if_no_pandas):
 
     df0 = tfe.to_df()
diff --git a/specparam/tests/objs/test_time.py b/specparam/tests/objs/test_time.py
index 65150832..788928b9 100644
--- a/specparam/tests/objs/test_time.py
+++ b/specparam/tests/objs/test_time.py
@@ -87,7 +87,7 @@ def test_time_load(tbands):
     tft.load(file_name_res, TEST_DATA_PATH, peak_org=tbands)
     assert tft.time_results
 
-def test_get_group(tft):
+def test_time_get_group(tft):
 
     inds = [1, 2]
 

From 648e70ee3787cc11e6467ef93dc28861422d704f Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Fri, 14 Jul 2023 14:07:05 -0400
Subject: [PATCH 54/99] add drop to time object

---
 specparam/objs/group.py           |  1 -
 specparam/objs/time.py            | 18 ++++++++++++++++++
 specparam/tests/objs/test_time.py | 14 ++++++++++++++
 3 files changed, 32 insertions(+), 1 deletion(-)

diff --git a/specparam/objs/group.py b/specparam/objs/group.py
index 532f550e..55d04556 100644
--- a/specparam/objs/group.py
+++ b/specparam/objs/group.py
@@ -291,7 +291,6 @@ def drop(self, inds):
         ----------
         inds : int 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
         -----
diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index 2baa15f3..454d1276 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -196,6 +196,24 @@ def fit(self, freqs=None, power_spectra=None, freq_range=None, peak_org=None,
         self._convert_to_time_results(peak_org)
 
 
+    def drop(self, inds):
+        """Drop one or more model fit results from the object.
+
+        Parameters
+        ----------
+        inds : int or array_like of int or array_like of bool
+            Indices to drop model fit results for.
+
+        Notes
+        -----
+        This method sets the model fits as null, and preserves the shape of the model fits.
+        """
+
+        super().drop(inds)
+        for key in self.time_results.keys():
+            self.time_results[key][inds] = np.nan
+
+
     def get_results(self):
         """Return the results run across a spectrogram."""
 
diff --git a/specparam/tests/objs/test_time.py b/specparam/tests/objs/test_time.py
index 788928b9..3dc7de67 100644
--- a/specparam/tests/objs/test_time.py
+++ b/specparam/tests/objs/test_time.py
@@ -87,6 +87,20 @@ def test_time_load(tbands):
     tft.load(file_name_res, TEST_DATA_PATH, peak_org=tbands)
     assert tft.time_results
 
+def test_time_drop():
+
+    n_windows = 3
+    xs, ys = sim_spectrogram(n_windows, *default_group_params())
+    tft = SpectralTimeModel(verbose=False)
+
+    tft.fit(xs, ys)
+    drop_inds = [0, 2]
+    tft.drop(drop_inds)
+    assert len(tft) == n_windows
+    for dind in drop_inds:
+        for key in tft.time_results:
+            assert np.isnan(tft.time_results[key][dind])
+
 def test_time_get_group(tft):
 
     inds = [1, 2]

From 9b133c23101f71b5e97c5d75d25245ee6f308690 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Fri, 14 Jul 2023 23:59:54 -0400
Subject: [PATCH 55/99] add drop to event object and associated

---
 specparam/core/utils.py            |  5 ++++-
 specparam/objs/event.py            | 34 ++++++++++++++++++++++++++++++
 specparam/objs/group.py            |  5 ++---
 specparam/tests/objs/test_event.py | 29 +++++++++++++++++++++++++
 specparam/tests/objs/test_group.py |  9 ++++----
 5 files changed, 74 insertions(+), 8 deletions(-)

diff --git a/specparam/core/utils.py b/specparam/core/utils.py
index 9e7e81b4..f8e41f8a 100644
--- a/specparam/core/utils.py
+++ b/specparam/core/utils.py
@@ -199,7 +199,7 @@ def check_inds(inds):
 
     Parameters
     ----------
-    inds : int or range or array_like of int or array_like of bool
+    inds : int or slice or range or array_like of int or array_like of bool or None
         Indices, indicated in multiple possible ways.
         If None, converted to slice object representing all inds.
 
@@ -215,6 +215,9 @@ def check_inds(inds):
     This function works only on indices defined for 1 dimension.
     """
 
+    # If inds is None, replace with slice object to get all indices
+    if inds is None:
+        inds = slice(None, None)
     # Typecasting: if a single int, convert to an array
     if isinstance(inds, int):
         inds = np.array([inds])
diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index 4146e602..46296218 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -1,5 +1,7 @@
 """Event model object and associated code for fitting the model to spectrograms across events."""
 
+from itertools import repeat
+
 import numpy as np
 
 from specparam.objs import SpectralModel, SpectralTimeModel
@@ -235,6 +237,38 @@ def fit(self, freqs=None, spectrograms=None, freq_range=None, peak_org=None,
         self._convert_to_event_results(peak_org)
 
 
+    def drop(self, drop_inds=None, window_inds=None):
+        """Drop one or more model fit results from the object.
+
+        Parameters
+        ----------
+        drop_inds : dict or int or array_like of int or array_like of bool
+            Indices to drop model fit results for.
+            If not dict, specifies the event indices, with time windows specified by `window_inds`.
+            If dict, each key reflects an event index, with corresponding time windows to drop.
+        window_inds : int or array_like of int or array_like of bool
+            Indices of time windows to drop model fits for (applied across all events).
+            Only used if `drop_inds` is not a dictionary.
+
+        Notes
+        -----
+        This method sets the model fits as null, and preserves the shape of the model fits.
+        """
+
+        null_model = SpectralModel(*self.get_settings()).get_results()
+
+        drop_inds = drop_inds if isinstance(drop_inds, dict) else \
+            {eind : winds for eind, winds in zip(check_inds(drop_inds), repeat(window_inds))}
+
+        for eind, winds in drop_inds.items():
+
+            winds = check_inds(winds)
+            for wind in winds:
+                self.event_group_results[eind][wind] = null_model
+            for key in self.event_time_results:
+                self.event_time_results[key][eind, winds] = np.nan
+
+
     def get_results(self):
         """Return the results from across the set of events."""
 
diff --git a/specparam/objs/group.py b/specparam/objs/group.py
index 55d04556..f3b06756 100644
--- a/specparam/objs/group.py
+++ b/specparam/objs/group.py
@@ -297,10 +297,9 @@ def drop(self, inds):
         This method sets the model fits as null, and preserves the shape of the model fits.
         """
 
+        null_model = SpectralModel(*self.get_settings()).get_results()
         for ind in check_inds(inds):
-            model = self.get_model(ind)
-            model._reset_data_results(clear_results=True)
-            self.group_results[ind] = model.get_results()
+            self.group_results[ind] = null_model
 
 
     def get_results(self):
diff --git a/specparam/tests/objs/test_event.py b/specparam/tests/objs/test_event.py
index b3146009..cb9454f1 100644
--- a/specparam/tests/objs/test_event.py
+++ b/specparam/tests/objs/test_event.py
@@ -99,6 +99,35 @@ def test_event_get_group(tfe):
     ntfe = tfe.get_group([0], [1, 2])
     assert ntfe
 
+def test_event_drop():
+
+    n_windows = 3
+    xs, ys = sim_spectrogram(n_windows, *default_group_params())
+    ys = [ys, ys]
+    tfe = SpectralTimeEventModel(verbose=False)
+    tfe.fit(xs, ys)
+
+    # Check list drops
+    event_inds = [0]
+    window_inds = [1]
+    tfe.drop(event_inds, window_inds)
+    assert len(tfe) == len(ys)
+    dropped_fres = tfe.event_group_results[event_inds[0]][window_inds[0]]
+    for field in dropped_fres._fields:
+        assert np.all(np.isnan(getattr(dropped_fres, field)))
+    for key in tfe.event_time_results:
+        assert np.isnan(tfe.event_time_results[key][event_inds[0], window_inds[0]])
+
+    # Check dictionary drops
+    drop_inds = {0 : [2], 1 : [1, 2]}
+    tfe.drop(drop_inds)
+    assert len(tfe) == len(ys)
+    dropped_fres = tfe.event_group_results[0][drop_inds[0][0]]
+    for field in dropped_fres._fields:
+        assert np.all(np.isnan(getattr(dropped_fres, field)))
+    for key in tfe.event_time_results:
+        assert np.isnan(tfe.event_time_results[key][0, drop_inds[0][0]])
+
 def test_event_to_df(tfe, tbands, skip_if_no_pandas):
 
     df0 = tfe.to_df()
diff --git a/specparam/tests/objs/test_group.py b/specparam/tests/objs/test_group.py
index 00a690f6..5c7530d4 100644
--- a/specparam/tests/objs/test_group.py
+++ b/specparam/tests/objs/test_group.py
@@ -170,9 +170,10 @@ def test_drop():
 
     # Test dropping one ind
     tfg.fit(xs, ys)
-    tfg.drop(0)
 
-    dropped_fres = tfg.group_results[0]
+    drop_ind = 0
+    tfg.drop(drop_ind)
+    dropped_fres = tfg.group_results[drop_ind]
     for field in dropped_fres._fields:
         assert np.all(np.isnan(getattr(dropped_fres, field)))
 
@@ -181,8 +182,8 @@ def test_drop():
     drop_inds = [0, 2]
     tfg.drop(drop_inds)
 
-    for drop_ind in drop_inds:
-        dropped_fres = tfg.group_results[drop_ind]
+    for d_ind in drop_inds:
+        dropped_fres = tfg.group_results[d_ind]
         for field in dropped_fres._fields:
             assert np.all(np.isnan(getattr(dropped_fres, field)))
 

From b94774810895a9bc694ba1aed178be1f5eaa5cc2 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Sat, 15 Jul 2023 00:28:36 -0400
Subject: [PATCH 56/99] add plot_text helper plot function

---
 specparam/plts/settings.py             |  5 +++++
 specparam/plts/templates.py            | 25 ++++++++++++++++++++++++-
 specparam/tests/plts/test_templates.py | 19 ++++++++++++++++---
 3 files changed, 45 insertions(+), 4 deletions(-)

diff --git a/specparam/plts/settings.py b/specparam/plts/settings.py
index 9f7e0310..0e1495e4 100644
--- a/specparam/plts/settings.py
+++ b/specparam/plts/settings.py
@@ -68,3 +68,8 @@
 TICK_LABELSIZE = 16
 LEGEND_SIZE = 12
 LEGEND_LOC = 'best'
+
+# Define default for plot text font
+PLT_TEXT_FONT = {'family': 'monospace',
+                 'weight': 'normal',
+                 'size': 16}
diff --git a/specparam/plts/templates.py b/specparam/plts/templates.py
index e933f937..bee3a000 100644
--- a/specparam/plts/templates.py
+++ b/specparam/plts/templates.py
@@ -13,7 +13,7 @@
 from specparam.utils.data import compute_average, compute_dispersion
 from specparam.core.modutils import safe_import, check_dependency
 from specparam.plts.utils import check_ax, set_alpha
-from specparam.plts.settings import PLT_FIGSIZES, DEFAULT_COLORS
+from specparam.plts.settings import PLT_FIGSIZES, DEFAULT_COLORS, PLT_TEXT_FONT
 
 plt = safe_import('.pyplot', 'matplotlib')
 
@@ -311,3 +311,26 @@ def plot_param_over_time_yshade(times, param, average='mean', shade='std', scale
     plot_yshade(times, param, average=average, shade=shade, scale=scale,
                 color=color, plot_function=plot_param_over_time,
                 ax=ax, **plot_kwargs)
+
+
+@check_dependency(plt, 'matplotlib')
+def plot_text(text, x, y, ax=None, **plot_kwargs):
+    """Plot text.
+
+    Parameters
+    ----------
+    text : str
+        Text to plot.
+    x, y : float
+        The position to place the text.
+    ax : matplotlib.Axes, optional
+        Figure axes upon which to plot.
+    **plot_kwargs
+        Additional keyword arguments to pass into the plot call.
+    """
+
+    ax = check_ax(ax, plot_kwargs.pop('figsize', None))
+
+    ax.text(x, y, text, PLT_TEXT_FONT, ha='center', va='center', **plot_kwargs)
+    ax.set_frame_on(False)
+    ax.set(xticks=[], yticks=[])
diff --git a/specparam/tests/plts/test_templates.py b/specparam/tests/plts/test_templates.py
index 93b21cf7..cf017343 100644
--- a/specparam/tests/plts/test_templates.py
+++ b/specparam/tests/plts/test_templates.py
@@ -2,10 +2,14 @@
 
 import numpy as np
 
+from specparam.core.modutils import safe_import
+
 from specparam.tests.tutils import plot_test
 
 from specparam.plts.templates import *
 
+mpl = safe_import('matplotlib')
+
 ###################################################################################################
 ###################################################################################################
 
@@ -38,14 +42,14 @@ def test_plot_yshade(skip_if_no_mpl):
     plot_yshade(xs, ys)
 
 @plot_test
-def test_plot_param_over_time():
+def test_plot_param_over_time(skip_if_no_mpl):
 
     param = np.array([1, 2, 3, 2, 1, 2, 4, 2, 3, 2, 1])
 
     plot_param_over_time(None, param, label='param', color='red')
 
 @plot_test
-def test_plot_params_over_time():
+def test_plot_params_over_time(skip_if_no_mpl):
 
     params = [np.array([1, 2, 3, 2, 1, 2, 4, 2, 3, 2, 1]),
               np.array([2, 3, 2, 1, 2, 4, 2, 3, 2, 1, 2])]
@@ -53,8 +57,17 @@ def test_plot_params_over_time():
     plot_params_over_time(None, params, labels=['param1', 'param2'], colors=['blue', 'red'])
 
 @plot_test
-def test_plot_param_over_time_yshade():
+def test_plot_param_over_time_yshade(skip_if_no_mpl):
 
     params = np.array([[1, 2, 3, 2, 1, 2, 4, 2, 3, 2, 1],
                        [2, 3, 2, 1, 2, 4, 2, 3, 2, 1, 2]])
     plot_param_over_time_yshade(None, params)
+
+def test_plot_text(skip_if_no_mpl):
+
+    text = 'This is a string.'
+    plot_text(text, 0.5, 0.5)
+
+    # Test this plot custom, as text doesn't count as data
+    ax = mpl.pyplot.gca()
+    assert isinstance(ax.get_children()[0], mpl.text.Text)

From 7a08fafc629c9f409962c993e2e5e1bebca10976 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Sat, 15 Jul 2023 00:44:28 -0400
Subject: [PATCH 57/99] use plot_text in report generation

---
 specparam/core/reports.py | 48 ++++++++-------------------------------
 specparam/tests/tutils.py |  2 +-
 2 files changed, 10 insertions(+), 40 deletions(-)

diff --git a/specparam/core/reports.py b/specparam/core/reports.py
index e6a8f814..02d0d56e 100644
--- a/specparam/core/reports.py
+++ b/specparam/core/reports.py
@@ -6,6 +6,7 @@
                                     gen_group_results_str, gen_time_results_str,
                                     gen_event_results_str)
 from specparam.data.utils import get_periodic_labels
+from specparam.plts.templates import plot_text
 from specparam.plts.group import (plot_group_aperiodic, plot_group_goodness,
                                   plot_group_peak_frequencies)
 
@@ -17,9 +18,6 @@
 
 ## Settings & Globals
 REPORT_FIGSIZE = (16, 20)
-REPORT_FONT = {'family': 'monospace',
-               'weight': 'normal',
-               'size': 16}
 SAVE_FORMAT = 'pdf'
 
 ###################################################################################################
@@ -52,11 +50,7 @@ def save_model_report(model, file_name, file_path=None, add_settings=True, **plo
     grid = gridspec.GridSpec(n_rows, 1, hspace=0.25, height_ratios=height_ratios)
 
     # First - text results
-    ax0 = plt.subplot(grid[0])
-    results_str = gen_model_results_str(model)
-    ax0.text(0.5, 0.7, results_str, REPORT_FONT, ha='center', va='center')
-    ax0.set_frame_on(False)
-    ax0.set(xticks=[], yticks=[])
+    plot_text(gen_model_results_str(model), 0.5, 0.7, ax=plt.subplot(grid[0]))
 
     # Second - data plot
     ax1 = plt.subplot(grid[1])
@@ -64,11 +58,7 @@ def save_model_report(model, file_name, file_path=None, add_settings=True, **plo
 
     # Third - model settings
     if add_settings:
-        ax2 = plt.subplot(grid[2])
-        settings_str = gen_settings_str(model, False)
-        ax2.text(0.5, 0.1, settings_str, REPORT_FONT, ha='center', va='center')
-        ax2.set_frame_on(False)
-        ax2.set(xticks=[], yticks=[])
+        plot_text(gen_settings_str(model, False), 0.5, 0.1, ax=plt.subplot(grid[2]))
 
     # Save out the report
     plt.savefig(fpath(file_path, fname(file_name, SAVE_FORMAT)))
@@ -100,11 +90,7 @@ def save_group_report(group, file_name, file_path=None, add_settings=True):
     grid = gridspec.GridSpec(n_rows, 2, wspace=0.4, hspace=0.25, height_ratios=height_ratios)
 
     # First / top: text results
-    ax0 = plt.subplot(grid[0, :])
-    results_str = gen_group_results_str(group)
-    ax0.text(0.5, 0.7, results_str, REPORT_FONT, ha='center', va='center')
-    ax0.set_frame_on(False)
-    ax0.set(xticks=[], yticks=[])
+    plot_text(gen_group_results_str(group), 0.5, 0.7, ax=plt.subplot(grid[0, :]))
 
     # Second - data plots
 
@@ -122,11 +108,7 @@ def save_group_report(group, file_name, file_path=None, add_settings=True):
 
     # Third - Model settings
     if add_settings:
-        ax4 = plt.subplot(grid[3, :])
-        settings_str = gen_settings_str(group, False)
-        ax4.text(0.5, 0.1, settings_str, REPORT_FONT, ha='center', va='center')
-        ax4.set_frame_on(False)
-        ax4.set(xticks=[], yticks=[])
+        plot_text(gen_settings_str(group, False), 0.5, 0.1, ax=plt.subplot(grid[3, :]))
 
     # Save out the report
     plt.savefig(fpath(file_path, fname(file_name, SAVE_FORMAT)))
@@ -161,20 +143,14 @@ def save_time_report(time_model, file_name, file_path=None, add_settings=True):
                            figsize=REPORT_FIGSIZE)
 
     # First / top: text results
-    results_str = gen_time_results_str(time_model)
-    axes[0].text(0.5, 0.7, results_str, REPORT_FONT, ha='center', va='center')
-    axes[0].set_frame_on(False)
-    axes[0].set(xticks=[], yticks=[])
+    plot_text(gen_time_results_str(time_model), 0.5, 0.7, ax=axes[0])
 
     # Second - data plots
     time_model.plot(axes=axes[1:2+n_bands+1])
 
     # Third - Model settings
     if add_settings:
-        settings_str = gen_settings_str(time_model, False)
-        axes[-1].text(0.5, 0.1, settings_str, REPORT_FONT, ha='center', va='center')
-        axes[-1].set_frame_on(False)
-        axes[-1].set(xticks=[], yticks=[])
+        plot_text(gen_settings_str(time_model, False), 0.5, 0.1, ax=axes[-1])
 
     # Save out the report
     plt.savefig(fpath(file_path, fname(file_name, SAVE_FORMAT)))
@@ -211,20 +187,14 @@ def save_event_report(event_model, file_name, file_path=None, add_settings=True)
                            figsize=(REPORT_FIGSIZE[0], REPORT_FIGSIZE[1] + 6))
 
     # First / top: text results
-    results_str = gen_event_results_str(event_model)
-    axes[0].text(0.5, 0.7, results_str, REPORT_FONT, ha='center', va='center')
-    axes[0].set_frame_on(False)
-    axes[0].set(xticks=[], yticks=[])
+    plot_text(gen_event_results_str(event_model), 0.5, 0.7, ax=axes[0])
 
     # Second - data plots
     event_model.plot(axes=axes[1:-1])
 
     # Third - Model settings
     if add_settings:
-        settings_str = gen_settings_str(event_model, False)
-        axes[-1].text(0.5, 0.1, settings_str, REPORT_FONT, ha='center', va='center')
-        axes[-1].set_frame_on(False)
-        axes[-1].set(xticks=[], yticks=[])
+        plot_text(gen_settings_str(event_model, False), 0.5, 0.1, ax=axes[-1])
 
     # Save out the report
     plt.savefig(fpath(file_path, fname(file_name, SAVE_FORMAT)))
diff --git a/specparam/tests/tutils.py b/specparam/tests/tutils.py
index 4a376079..95c6ea3b 100644
--- a/specparam/tests/tutils.py
+++ b/specparam/tests/tutils.py
@@ -61,7 +61,7 @@ def get_tfe():
     xs, ys = sim_spectrogram(n_spectra, *default_group_params())
     ys = [ys, ys]
 
-    bands = Bands({'alpha' : (7, 14), 'beta' : (15, 30)})
+    bands = Bands({'alpha' : (7, 14)})
     tfe = SpectralTimeEventModel(verbose=False)
     tfe.fit(xs, ys, peak_org=bands)
 

From ef4a9098f7eda4f6917894166031caef1227c0c0 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Sat, 15 Jul 2023 14:31:27 -0400
Subject: [PATCH 58/99] make convert_results an explicitly public method

---
 specparam/objs/event.py | 15 +++++----------
 specparam/objs/time.py  |  7 ++++---
 2 files changed, 9 insertions(+), 13 deletions(-)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index 46296218..93c03609 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -229,12 +229,13 @@ def fit(self, freqs=None, spectrograms=None, freq_range=None, peak_org=None,
 
         for spectrogram in self.spectrograms:
             self.power_spectra = spectrogram.T
-            super().fit()
+            super().fit(peak_org=False)
             self.event_group_results.append(self.group_results)
             self._reset_group_results()
             self._reset_data_results(clear_spectra=True)
 
-        self._convert_to_event_results(peak_org)
+        if peak_org is not False:
+            self.convert_results(peak_org)
 
 
     def drop(self, drop_inds=None, window_inds=None):
@@ -458,8 +459,8 @@ def to_df(self, peak_org=None):
         return df
 
 
-    def _convert_to_event_results(self, peak_org):
-        """Convert the event results to be organized across across and time windows.
+    def convert_results(self, peak_org):
+        """Convert the event results to be organized across events and time windows.
 
         Parameters
         ----------
@@ -470,9 +471,3 @@ def _convert_to_event_results(self, peak_org):
         """
 
         self.event_time_results = event_group_to_dict(self.event_group_results, peak_org)
-
-    # ToDo: check & figure out adding `load` method
-
-    def _convert_to_time_results(self, peak_org):
-        """Overrides inherited objects function to void running this conversion per spectrogram."""
-        pass
diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index 454d1276..555043cf 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -193,7 +193,8 @@ def fit(self, freqs=None, power_spectra=None, freq_range=None, peak_org=None,
         """
 
         super().fit(freqs, power_spectra, freq_range, n_jobs, progress)
-        self._convert_to_time_results(peak_org)
+        if peak_org is not False:
+            self.convert_results(peak_org)
 
 
     def drop(self, inds):
@@ -315,7 +316,7 @@ def load(self, file_name, file_path=None, peak_org=None):
         # Clear results so as not to have possible prior results interfere
         self._reset_time_results()
         super().load(file_name, file_path=file_path)
-        self._convert_to_time_results(peak_org)
+        self.convert_results(peak_org)
 
 
     def to_df(self, peak_org=None):
@@ -343,7 +344,7 @@ def to_df(self, peak_org=None):
         return df
 
 
-    def _convert_to_time_results(self, peak_org):
+    def convert_results(self, peak_org):
         """Convert the model results to be organized across time windows.
 
         Parameters

From 6c3e11a9eb4b3f76105b89a532bf4e5871231f9e Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Sun, 16 Jul 2023 20:17:52 -0400
Subject: [PATCH 59/99] update arg input to spectrogram in time object

---
 specparam/objs/time.py | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index 555043cf..0bb513d3 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -26,8 +26,8 @@ def decorated(*args, **kwargs):
         if len(args) >= 2:
             args = list(args)
             args[2] = args[2].T if isinstance(args[2], np.ndarray) else args[2]
-        if 'power_spectra' in kwargs:
-            kwargs['power_spectra'] = kwargs['power_spectra'].T
+        if 'spectrogram' in kwargs:
+            kwargs['spectrogram'] = kwargs['spectrogram'].T
 
         return func(*args, **kwargs)
 
@@ -50,14 +50,14 @@ class SpectralTimeModel(SpectralGroupModel):
     Attributes
     ----------
     freqs : 1d array
-        Frequency values for the power spectra.
+        Frequency values for the spectrogram.
     spectrogram : 2d array
         Power values for the spectrogram, as [n_freqs, n_time_windows].
         Power values are stored internally in log10 scale.
     freq_range : list of [float, float]
-        Frequency range of the power spectra, as [lowest_freq, highest_freq].
+        Frequency range of the spectrogram, as [lowest_freq, highest_freq].
     freq_res : float
-        Frequency resolution of the power spectra.
+        Frequency resolution of the spectrogram.
     time_results : dict
         Results of the model fit across each time window.
 
@@ -116,11 +116,11 @@ def add_data(self, freqs, spectrogram, freq_range=None):
         Parameters
         ----------
         freqs : 1d array
-            Frequency values for the power spectra, in linear space.
+            Frequency values for the spectrogram, in linear space.
         spectrogram : 2d array, shape=[n_freqs, n_time_windows]
             Matrix of power values, in linear space.
         freq_range : list of [float, float], optional
-            Frequency range to restrict power spectra to. If not provided, keeps the entire range.
+            Frequency range to restrict spectrogram to. If not provided, keeps the entire range.
 
         Notes
         -----
@@ -133,15 +133,15 @@ def add_data(self, freqs, spectrogram, freq_range=None):
         super().add_data(freqs, spectrogram, freq_range)
 
 
-    def report(self, freqs=None, power_spectra=None, freq_range=None,
+    def report(self, freqs=None, spectrogram=None, freq_range=None,
                peak_org=None, report_type='time', n_jobs=1, progress=None):
         """Fit a spectrogram and display a report, with a plot and printed results.
 
         Parameters
         ----------
         freqs : 1d array, optional
-            Frequency values for the power_spectra, in linear space.
-        power_spectra : 2d array, shape: [n_freqs, n_time_windows], optional
+            Frequency values for the spectrogram, in linear space.
+        spectrogram : 2d array, shape: [n_freqs, n_time_windows], optional
             Spectrogram of power spectrum values, in linear space.
         freq_range : list of [float, float], optional
             Frequency range to fit the model to. If not provided, fits the entire given range.
@@ -160,20 +160,20 @@ def report(self, freqs=None, power_spectra=None, freq_range=None,
         Data is optional, if data has already been added to the object.
         """
 
-        self.fit(freqs, power_spectra, freq_range, peak_org, n_jobs=n_jobs, progress=progress)
+        self.fit(freqs, spectrogram, freq_range, peak_org, n_jobs=n_jobs, progress=progress)
         self.plot(report_type)
         self.print_results(report_type)
 
 
-    def fit(self, freqs=None, power_spectra=None, freq_range=None, peak_org=None,
+    def fit(self, freqs=None, spectrogram=None, freq_range=None, peak_org=None,
             n_jobs=1, progress=None):
         """Fit a spectrogram.
 
         Parameters
         ----------
         freqs : 1d array, optional
-            Frequency values for the power_spectra, in linear space.
-        power_spectra : 2d array, shape: [n_freqs, n_time_windows], optional
+            Frequency values for the spectrogram, in linear space.
+        spectrogram : 2d array, shape: [n_freqs, n_time_windows], optional
             Spectrogram of power spectrum values, in linear space.
         freq_range : list of [float, float], optional
             Frequency range to fit the model to. If not provided, fits the entire given range.
@@ -192,7 +192,7 @@ def fit(self, freqs=None, power_spectra=None, freq_range=None, peak_org=None,
         Data is optional, if data has already been added to the object.
         """
 
-        super().fit(freqs, power_spectra, freq_range, n_jobs, progress)
+        super().fit(freqs, spectrogram, freq_range, n_jobs, progress)
         if peak_org is not False:
             self.convert_results(peak_org)
 

From 43285137bad6292f568814ed63ec522833db7051 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Sun, 16 Jul 2023 21:59:31 -0400
Subject: [PATCH 60/99] add use of progress bar & parallelization to event
 object

---
 specparam/objs/event.py | 49 ++++++++++++++++++++++++++++++++---------
 1 file changed, 39 insertions(+), 10 deletions(-)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index 93c03609..09e9370e 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -1,5 +1,9 @@
 """Event model object and associated code for fitting the model to spectrograms across events."""
 
+from functools import partial
+from multiprocessing import Pool, cpu_count
+
+
 from itertools import repeat
 
 import numpy as np
@@ -78,10 +82,10 @@ def __getitem__(self, ind):
         return get_results_by_row(self.event_time_results, ind)
 
 
-    def _reset_event_results(self):
+    def _reset_event_results(self, length=0):
         """Set, or reset, event results to be empty."""
 
-        self.event_group_results = []
+        self.event_group_results = [[]] * length
         self.event_time_results = {}
 
 
@@ -222,17 +226,33 @@ def fit(self, freqs=None, spectrograms=None, freq_range=None, peak_org=None,
         Data is optional, if data has already been added to the object.
         """
 
+        # ToDo: here because of circular import - updates / refactors should fix & move
+        from specparam.objs.group import _progress
+
         if spectrograms is not None:
             self.add_data(freqs, spectrograms, freq_range)
-        if len(self):
-            self._reset_event_results()
 
-        for spectrogram in self.spectrograms:
-            self.power_spectra = spectrogram.T
-            super().fit(peak_org=False)
-            self.event_group_results.append(self.group_results)
-            self._reset_group_results()
-            self._reset_data_results(clear_spectra=True)
+        if n_jobs == 1:
+            self._reset_event_results(len(self.spectrograms))
+            for ind, spectrogram in _progress(enumerate(self.spectrograms), progress, len(self)):
+                self.power_spectra = spectrogram.T
+                super().fit(peak_org=False)
+                self.event_group_results[ind] = self.group_results
+                self._reset_group_results()
+                self._reset_data_results(clear_spectra=True)
+
+        else:
+
+            ft = SpectralTimeModel(*self.get_settings(), verbose=False)
+            ft.add_meta_data(self.get_meta_data())
+            ft.freqs = self.freqs
+
+            n_jobs = cpu_count() if n_jobs == -1 else n_jobs
+            with Pool(processes=n_jobs) as pool:
+
+                self.event_group_results = \
+                    list(_progress(pool.imap(partial(_par_fit, model=ft), self.spectrograms),
+                                   progress, len(self.spectrograms)))
 
         if peak_org is not False:
             self.convert_results(peak_org)
@@ -471,3 +491,12 @@ def convert_results(self, peak_org):
         """
 
         self.event_time_results = event_group_to_dict(self.event_group_results, peak_org)
+
+
+def _par_fit(spectrogram, model):
+    """Helper function for running in parallel."""
+
+    model.power_spectra = spectrogram.T
+    model.fit(peak_org=False)
+
+    return model.group_results

From 407bc4af46af55a17c6ac6794fc1b47fd9115c7a Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 17 Jul 2023 00:48:16 -0400
Subject: [PATCH 61/99] add get_files helper func

---
 specparam/core/io.py            | 26 ++++++++++++++++++++++++++
 specparam/tests/core/test_io.py |  5 +++++
 2 files changed, 31 insertions(+)

diff --git a/specparam/core/io.py b/specparam/core/io.py
index 608f7295..2c34ef3c 100644
--- a/specparam/core/io.py
+++ b/specparam/core/io.py
@@ -61,6 +61,32 @@ def fpath(file_path, file_name):
     return full_path
 
 
+def get_files(file_path, select=None):
+    """Get a list of files from a directory.
+
+    Parameters
+    ----------
+    file_path : Path or str
+        Name of the folder to get the list of files from.
+    select : str, optional
+        A search string to use to select files.
+
+    Returns
+    -------
+    list of str
+        A list of files.
+    """
+
+    # Get list of available files, and drop hidden files
+    files = os.listdir(file_path)
+    files = [file for file in files if file[0] != '.']
+
+    if select:
+        files = [file for file in files if search in file]
+
+    return files
+
+
 def save_model(model, file_name, file_path=None, append=False,
                save_results=False, save_settings=False, save_data=False):
     """Save out data, results and/or settings from a model object into a JSON file.
diff --git a/specparam/tests/core/test_io.py b/specparam/tests/core/test_io.py
index 5fc84631..9aa88a2e 100644
--- a/specparam/tests/core/test_io.py
+++ b/specparam/tests/core/test_io.py
@@ -27,6 +27,11 @@ def test_fpath():
     assert fpath(None, 'data.json') == 'data.json'
     assert fpath('/path/', 'data.json') == '/path/data.json'
 
+def test_get_files():
+
+    out = get_files('.')
+    assert isinstance(out, list)
+
 def test_save_model_str(tfm):
     """Check saving model object data, with file specifiers as strings."""
 

From 8860aa4e68a82f0ef3d66453b8e2ce0bc94862a9 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 17 Jul 2023 00:56:26 -0400
Subject: [PATCH 62/99] fix select form get_files

---
 specparam/core/io.py            | 2 +-
 specparam/tests/core/test_io.py | 7 +++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/specparam/core/io.py b/specparam/core/io.py
index 2c34ef3c..6147b02e 100644
--- a/specparam/core/io.py
+++ b/specparam/core/io.py
@@ -82,7 +82,7 @@ def get_files(file_path, select=None):
     files = [file for file in files if file[0] != '.']
 
     if select:
-        files = [file for file in files if search in file]
+        files = [file for file in files if select in file]
 
     return files
 
diff --git a/specparam/tests/core/test_io.py b/specparam/tests/core/test_io.py
index 9aa88a2e..61efed4b 100644
--- a/specparam/tests/core/test_io.py
+++ b/specparam/tests/core/test_io.py
@@ -29,8 +29,11 @@ def test_fpath():
 
 def test_get_files():
 
-    out = get_files('.')
-    assert isinstance(out, list)
+    out1 = get_files('.')
+    assert isinstance(out1, list)
+
+    out2 = get_files('.', 'search')
+    assert isinstance(out2, list)
 
 def test_save_model_str(tfm):
     """Check saving model object data, with file specifiers as strings."""

From f34a59f7bc955ebf43251b97b779af0c63c4b8fd Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 17 Jul 2023 01:06:21 -0400
Subject: [PATCH 63/99] add save & load to event object

---
 specparam/objs/event.py | 56 +++++++++++++++++++++++++++++++++++++----
 specparam/objs/time.py  |  3 ++-
 2 files changed, 53 insertions(+), 6 deletions(-)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index 09e9370e..d7a4b3a9 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -1,14 +1,12 @@
 """Event model object and associated code for fitting the model to spectrograms across events."""
 
+from itertools import repeat
 from functools import partial
 from multiprocessing import Pool, cpu_count
 
-
-from itertools import repeat
-
 import numpy as np
 
-from specparam.objs import SpectralModel, SpectralTimeModel
+from specparam.objs import SpectralModel, SpectralGroupModel, SpectralTimeModel
 from specparam.plts.event import plot_event_model
 from specparam.data.conversions import event_group_to_dict, event_group_to_dataframe, dict_to_df
 from specparam.data.utils import get_group_params, get_results_by_row, flatten_results_dict
@@ -17,6 +15,7 @@
 from specparam.core.reports import save_event_report
 from specparam.core.strings import gen_event_results_str
 from specparam.core.utils import check_inds
+from specparam.core.io import get_files, save_group
 
 ###################################################################################################
 ###################################################################################################
@@ -243,7 +242,7 @@ def fit(self, freqs=None, spectrograms=None, freq_range=None, peak_org=None,
 
         else:
 
-            ft = SpectralTimeModel(*self.get_settings(), verbose=False)
+            ft = SpectralGroupModel(*self.get_settings(), verbose=False)
             ft.add_meta_data(self.get_meta_data())
             ft.freqs = self.freqs
 
@@ -392,6 +391,53 @@ def save_report(self, file_name, file_path=None, add_settings=True):
         save_event_report(self, file_name, file_path, add_settings)
 
 
+    @copy_doc_func_to_method(save_group)
+    def save(self, file_name, file_path=None, append=False,
+             save_results=False, save_settings=False, save_data=False):
+
+        fg = SpectralGroupModel(*self.get_settings())
+        fg.add_meta_data(self.get_meta_data())
+        fg.freqs = self.freqs
+
+        if save_settings and not save_results and not save_data:
+            fg.save(file_name, file_path, save_settings=True)
+        else:
+            ndigits = len(str(len(self)))
+            for ind, gres in enumerate(self.event_group_results):
+                fg.group_results = gres
+                if save_data:
+                    fg.power_spectra = self.spectrograms[ind, :, :].T
+                fg.save(file_name + '_{:0{ndigits}d}'.format(ind, ndigits=ndigits),
+                        file_path=file_path, save_results=save_results,
+                        save_settings=save_settings, save_data=save_data)
+
+
+    def load(self, file_name, file_path=None, peak_org=None):
+        """Load data from file(s).
+
+        Parameters
+        ----------
+        file_name : str
+            File(s) to load data from.
+        file_path : str, optional
+            Path to directory to load from. If None, loads from current directory.
+        peak_org : int or Bands, optional
+            How to organize peaks.
+            If int, extracts the first n peaks.
+            If Bands, extracts peaks based on band definitions.
+        """
+
+        files = get_files(file_path, select=file_name)
+        for file in files:
+            super().load(file, file_path, peak_org=False)
+            if self.group_results:
+                self.event_group_results.append(self.group_results)
+
+        self._reset_group_results()
+        if peak_org is not False:
+            self.convert_results(peak_org)
+
+
     def get_model(self, event_ind, window_ind, regenerate=True):
         """Get a model fit object for a specified index.
 
diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index 0bb513d3..ccdda325 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -316,7 +316,8 @@ def load(self, file_name, file_path=None, peak_org=None):
         # Clear results so as not to have possible prior results interfere
         self._reset_time_results()
         super().load(file_name, file_path=file_path)
-        self.convert_results(peak_org)
+        if peak_org is not False:
+            self.convert_results(peak_org)
 
 
     def to_df(self, peak_org=None):

From 3872e1b265631f69b45a51d3b4c4f7cc1cc93a79 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 17 Jul 2023 02:04:12 -0400
Subject: [PATCH 64/99] refactor get_group, including add to get model with no
 inds

---
 specparam/objs/event.py            | 36 ++++++++++++++----------------
 specparam/objs/group.py            | 23 +++++++++----------
 specparam/objs/time.py             | 27 +++++++++++-----------
 specparam/tests/objs/test_event.py | 14 ++++++++++--
 specparam/tests/objs/test_group.py |  6 +++++
 specparam/tests/objs/test_time.py  | 11 +++++++--
 6 files changed, 68 insertions(+), 49 deletions(-)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index d7a4b3a9..51a560c9 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -341,28 +341,27 @@ def get_group(self, event_inds, window_inds):
             The requested selection of results data loaded into a new model object.
         """
 
-        # Check and convert indices encoding to list of int
-        event_inds = check_inds(event_inds)
-        window_inds = check_inds(window_inds)
-
         # Initialize a new model object, with same settings as current object
         output = SpectralTimeEventModel(*self.get_settings(), verbose=self.verbose)
+        output.add_meta_data(self.get_meta_data())
 
-        # Add data for specified power spectra, if available
-        #   Power spectra are inverted to linear, as they are re-logged when added to object
-        if self.has_data:
-            output.add_data(self.freqs,
-                            np.power(10, self.spectrograms[event_inds, :, :][:, :, window_inds]))
-        # If no power spectrum data available, copy over data information & regenerate freqs
-        else:
-            output.add_meta_data(self.get_meta_data())
+        if event_inds is not None or window_inds is not None:
+
+            # Check and convert indices encoding to list of int
+            event_inds = check_inds(event_inds)
+            window_inds = check_inds(window_inds)
+
+            # Add data for specified power spectra, if available
+            if self.has_data:
+                output.spectrograms = self.spectrograms[event_inds, :, :][:, :, window_inds]
 
-        # Add results for specified power spectra
-        output.event_group_results = \
-            [self.event_group_results[eind][wind] for eind in event_inds for wind in window_inds]
-        output.event_time_results = \
-            {key : self.event_time_results[key][event_inds][:, window_inds] \
-            for key in self.event_time_results}
+            # Add results for specified power spectra
+            # ToDo: this doesn't work... needs fixing.
+            # output.event_group_results = \
+            #     [self.event_group_results[eind][wind] for eind in event_inds for wind in window_inds]
+            output.event_time_results = \
+                {key : self.event_time_results[key][event_inds][:, window_inds] \
+                for key in self.event_time_results}
 
         return output
 
@@ -397,7 +396,6 @@ def save(self, file_name, file_path=None, append=False,
 
         fg = SpectralGroupModel(*self.get_settings())
         fg.add_meta_data(self.get_meta_data())
-        fg.freqs = self.freqs
 
         if save_settings and not save_results and not save_data:
             fg.save(file_name, file_path, save_settings=True)
diff --git a/specparam/objs/group.py b/specparam/objs/group.py
index f3b06756..abfc3f1f 100644
--- a/specparam/objs/group.py
+++ b/specparam/objs/group.py
@@ -456,22 +456,21 @@ def get_group(self, inds):
             The requested selection of results data loaded into a new group model object.
         """
 
-        # Check and convert indices encoding to list of int
-        inds = check_inds(inds)
-
         # Initialize a new model object, with same settings as current object
         group = SpectralGroupModel(*self.get_settings(), verbose=self.verbose)
+        group.add_meta_data(self.get_meta_data())
 
-        # Add data for specified power spectra, if available
-        #   Power spectra are inverted to linear, as they are re-logged when added to object
-        if self.has_data:
-            group.add_data(self.freqs, np.power(10, self.power_spectra[inds, :]))
-        # If no power spectrum data available, copy over data information & regenerate freqs
-        else:
-            group.add_meta_data(self.get_meta_data())
+        if inds is not None:
+
+            # Check and convert indices encoding to list of int
+            inds = check_inds(inds)
+
+            # Add data for specified power spectra, if available
+            if self.has_data:
+                group.power_spectra = self.power_spectra[inds, :]
 
-        # Add results for specified power spectra
-        group.group_results = [self.group_results[ind] for ind in inds]
+            # Add results for specified power spectra
+            group.group_results = [self.group_results[ind] for ind in inds]
 
         return group
 
diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index ccdda325..46e2c698 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -241,23 +241,22 @@ def get_group(self, inds, output_type='time'):
 
         if output_type == 'time':
 
-            # Check and convert indices encoding to list of int
-            inds = check_inds(inds)
-
             # Initialize a new model object, with same settings as current object
             output = SpectralTimeModel(*self.get_settings(), verbose=self.verbose)
+            output.add_meta_data(self.get_meta_data())
+
+            if inds is not None:
+
+                # Check and convert indices encoding to list of int
+                inds = check_inds(inds)
+
+                # Add data for specified power spectra, if available
+                if self.has_data:
+                    output.power_spectra = self.power_spectra[inds, :]
 
-            # Add data for specified power spectra, if available
-            #   Power spectra are inverted to linear, as they are re-logged when added to object
-            if self.has_data:
-                output.add_data(self.freqs, np.power(10, self.spectrogram[:, inds]))
-            # If no power spectrum data available, copy over data information & regenerate freqs
-            else:
-                output.add_meta_data(self.get_meta_data())
-
-            # Add results for specified power spectra
-            output.group_results = [self.group_results[ind] for ind in inds]
-            output.time_results = get_results_by_ind(self.time_results, inds)
+                # Add results for specified power spectra
+                output.group_results = [self.group_results[ind] for ind in inds]
+                output.time_results = get_results_by_ind(self.time_results, inds)
 
         if output_type == 'group':
             output = super().get_group(inds)
diff --git a/specparam/tests/objs/test_event.py b/specparam/tests/objs/test_event.py
index cb9454f1..ceb8de6a 100644
--- a/specparam/tests/objs/test_event.py
+++ b/specparam/tests/objs/test_event.py
@@ -96,8 +96,18 @@ def test_event_get_params(tfe):
 
 def test_event_get_group(tfe):
 
-    ntfe = tfe.get_group([0], [1, 2])
-    assert ntfe
+    ntfe0 = tfe.get_group(None, None)
+    assert isinstance(ntfe0, SpectralTimeEventModel)
+
+    einds = [0, 1]
+    winds = [1, 2]
+    ntfe1 = tfe.get_group(einds, winds)
+    #assert ntfe1
+    assert ntfe1.spectrograms.shape == (len(einds), len(tfe.freqs), len(winds))
+    tkey = list(ntfe1.event_time_results.keys())[0]
+    assert ntfe1.event_time_results[tkey].shape == (len(einds), len(winds))
+    # ToDo: turn this test back on when functionality is fixed
+    #assert len(ntfe1.event_group_results), len(ntfe1.event_group_results[0]) == (len(einds, len(winds)))
 
 def test_event_drop():
 
diff --git a/specparam/tests/objs/test_group.py b/specparam/tests/objs/test_group.py
index 5c7530d4..3db15024 100644
--- a/specparam/tests/objs/test_group.py
+++ b/specparam/tests/objs/test_group.py
@@ -327,6 +327,12 @@ def test_get_model(tfg):
 def test_get_group(tfg):
     """Check the return of a sub-sampled group object."""
 
+    # Test with no inds
+    nfg0 = tfg.get_group(None)
+    assert isinstance(nfg0, SpectralGroupModel)
+    assert nfg0.get_settings() == tfg.get_settings()
+    assert nfg0.get_meta_data() == tfg.get_meta_data()
+
     # Check with list index
     inds1 = [1, 2]
     nfg1 = tfg.get_group(inds1)
diff --git a/specparam/tests/objs/test_time.py b/specparam/tests/objs/test_time.py
index 3dc7de67..254e0642 100644
--- a/specparam/tests/objs/test_time.py
+++ b/specparam/tests/objs/test_time.py
@@ -103,13 +103,20 @@ def test_time_drop():
 
 def test_time_get_group(tft):
 
+    nft0 = tft.get_group(None)
+    assert isinstance(nft0, SpectralTimeModel)
+
     inds = [1, 2]
 
     nft = tft.get_group(inds)
     assert isinstance(nft, SpectralTimeModel)
+    assert len(nft.group_results) == len(inds)
+    assert len(nft.time_results[list(nft.time_results.keys())[0]]) == len(inds)
+    assert nft.spectrogram.shape[-1] == len(inds)
 
-    nfg = tft.get_group(inds)
-    assert isinstance(nfg, SpectralGroupModel)
+    nfg = tft.get_group(inds, 'group')
+    assert not isinstance(nfg, SpectralTimeModel)
+    assert len(nfg.group_results) == len(inds)
 
 def test_time_to_df(tft, tbands, skip_if_no_pandas):
 

From 551c8708a99ddd53ffb8444633a23c183cbb3a20 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 17 Jul 2023 02:06:46 -0400
Subject: [PATCH 65/99] use empty get_group

---
 specparam/objs/event.py | 15 ++++-----------
 1 file changed, 4 insertions(+), 11 deletions(-)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index 51a560c9..91d44f3c 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -6,7 +6,7 @@
 
 import numpy as np
 
-from specparam.objs import SpectralModel, SpectralGroupModel, SpectralTimeModel
+from specparam.objs import SpectralModel, SpectralTimeModel
 from specparam.plts.event import plot_event_model
 from specparam.data.conversions import event_group_to_dict, event_group_to_dataframe, dict_to_df
 from specparam.data.utils import get_group_params, get_results_by_row, flatten_results_dict
@@ -241,16 +241,11 @@ def fit(self, freqs=None, spectrograms=None, freq_range=None, peak_org=None,
                 self._reset_data_results(clear_spectra=True)
 
         else:
-
-            ft = SpectralGroupModel(*self.get_settings(), verbose=False)
-            ft.add_meta_data(self.get_meta_data())
-            ft.freqs = self.freqs
-
+            fg = self.get_group(None)
             n_jobs = cpu_count() if n_jobs == -1 else n_jobs
             with Pool(processes=n_jobs) as pool:
-
                 self.event_group_results = \
-                    list(_progress(pool.imap(partial(_par_fit, model=ft), self.spectrograms),
+                    list(_progress(pool.imap(partial(_par_fit, model=fg), self.spectrograms),
                                    progress, len(self.spectrograms)))
 
         if peak_org is not False:
@@ -394,9 +389,7 @@ def save_report(self, file_name, file_path=None, add_settings=True):
     def save(self, file_name, file_path=None, append=False,
              save_results=False, save_settings=False, save_data=False):
 
-        fg = SpectralGroupModel(*self.get_settings())
-        fg.add_meta_data(self.get_meta_data())
-
+        fg = self.get_group(None)
         if save_settings and not save_results and not save_data:
             fg.save(file_name, file_path, save_settings=True)
         else:

From 457a2509bcb9541330537bcea392a4803f6beda0 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 17 Jul 2023 02:12:25 -0400
Subject: [PATCH 66/99] apply same logic of upate to get_group to get_model

---
 specparam/objs/event.py | 9 +++------
 specparam/objs/group.py | 9 +++------
 2 files changed, 6 insertions(+), 12 deletions(-)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index 91d44f3c..3951ed93 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -447,17 +447,14 @@ def get_model(self, event_ind, window_ind, regenerate=True):
             The FitResults data loaded into a model object.
         """
 
-        # Initialize a model object, with same settings & check data mode as current object
+        # Initialize model object, with same settings, metadata, & check mode as current object
         model = SpectralModel(*self.get_settings(), verbose=self.verbose)
+        model.add_meta_data(self.get_meta_data())
         model.set_check_data_mode(self._check_data)
 
         # Add data for specified single power spectrum, if available
-        #   The power spectrum is inverted back to linear, as it is re-logged when added to object
         if self.has_data:
-            model.add_data(self.freqs, np.power(10, self.spectrograms[event_ind][:, window_ind]))
-        # If no power spectrum data available, copy over data information & regenerate freqs
-        else:
-            model.add_meta_data(self.get_meta_data())
+            model.power_spectrum = self.spectrograms[event_ind][:, window_ind]
 
         # Add results for specified power spectrum, regenerating full fit if requested
         model.add_results(self.event_group_results[event_ind][window_ind])
diff --git a/specparam/objs/group.py b/specparam/objs/group.py
index abfc3f1f..97293ff7 100644
--- a/specparam/objs/group.py
+++ b/specparam/objs/group.py
@@ -422,17 +422,14 @@ def get_model(self, ind, regenerate=True):
             The FitResults data loaded into a model object.
         """
 
-        # Initialize a model object, with same settings & check data mode as current object
+        # Initialize model object, with same settings, metadata, & check mode as current object
         model = SpectralModel(*self.get_settings(), verbose=self.verbose)
+        model.add_meta_data(self.get_meta_data())
         model.set_check_data_mode(self._check_data)
 
         # Add data for specified single power spectrum, if available
-        #   The power spectrum is inverted back to linear, as it is re-logged when added to object
         if self.has_data:
-            model.add_data(self.freqs, np.power(10, self.power_spectra[ind]))
-        # If no power spectrum data available, copy over data information & regenerate freqs
-        else:
-            model.add_meta_data(self.get_meta_data())
+            model.power_spectrum = self.power_spectra[ind]
 
         # Add results for specified power spectrum, regenerating full fit if requested
         model.add_results(self.group_results[ind])

From 0c832de5b8006cf662762d87f7e848588ed42e66 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 17 Jul 2023 11:56:18 -0400
Subject: [PATCH 67/99] add length option to check_inds

---
 specparam/core/utils.py            | 10 ++++++----
 specparam/tests/core/test_utils.py |  4 ++++
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/specparam/core/utils.py b/specparam/core/utils.py
index f8e41f8a..35f7e894 100644
--- a/specparam/core/utils.py
+++ b/specparam/core/utils.py
@@ -194,7 +194,7 @@ def check_flat(lst):
     return lst
 
 
-def check_inds(inds):
+def check_inds(inds, length=None):
     """Check various ways to indicate indices and convert to a consistent format.
 
     Parameters
@@ -224,12 +224,14 @@ def check_inds(inds):
     # Typecasting: if a list, convert to an array
     if isinstance(inds, (list)):
         inds = np.array(inds)
-    # If range or slice type, leave as is
-    if isinstance(inds, (range, slice)):
-        inds = inds
     # Conversion: if array is boolean, get integer indices of True
     if isinstance(inds, np.ndarray) and inds.dtype == bool:
         inds = np.where(inds)[0]
+    # If slice type, check for converting length
+    if isinstance(inds, slice):
+        if not inds.stop and length:
+            inds = range(inds.start if inds.start else 0,
+                         length, inds.step if inds.step else 1)
 
     return inds
 
diff --git a/specparam/tests/core/test_utils.py b/specparam/tests/core/test_utils.py
index e67b3821..53160d95 100644
--- a/specparam/tests/core/test_utils.py
+++ b/specparam/tests/core/test_utils.py
@@ -114,6 +114,10 @@ def test_check_inds():
     # Test boolean array input
     assert array_equal(check_inds(np.array([True, False, True])), np.array([0, 2]))
 
+    # Check None inputs, including length input
+    assert isinstance(check_inds(None), slice)
+    assert isinstance(check_inds(None, 4), range)
+
 def test_resolve_aliases():
 
     # Define a test set of aliases

From 93b35b86219349a638dc11cec296b78a9b6b6ce9 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 17 Jul 2023 11:56:27 -0400
Subject: [PATCH 68/99] fix event get_group

---
 specparam/objs/event.py            | 21 +++++++++++++++------
 specparam/tests/objs/test_event.py |  5 ++---
 2 files changed, 17 insertions(+), 9 deletions(-)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index 3951ed93..40098d91 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -343,17 +343,26 @@ def get_group(self, event_inds, window_inds):
         if event_inds is not None or window_inds is not None:
 
             # Check and convert indices encoding to list of int
-            event_inds = check_inds(event_inds)
-            window_inds = check_inds(window_inds)
+            einds = check_inds(event_inds, self.n_events)
+            winds = check_inds(window_inds, self.n_time_windows)
 
             # Add data for specified power spectra, if available
             if self.has_data:
-                output.spectrograms = self.spectrograms[event_inds, :, :][:, :, window_inds]
+                output.spectrograms = self.spectrograms[einds, :, :][:, :, winds]
 
-            # Add results for specified power spectra
-            # ToDo: this doesn't work... needs fixing.
+            # Add results for specified power spectra - event group results
+            temp = [self.event_group_results[ei][wi] for ei in einds for wi in winds]
+            step = int(len(temp) / len(einds))
+            output.event_group_results = [temp[ind:ind+step] for ind in range(0, len(temp), step)]
+
+            # # Note: this equivalent to above (but slower)
+            # n_out = len(einds) * len(winds)
+            # step = int(n_out / len(einds))
             # output.event_group_results = \
-            #     [self.event_group_results[eind][wind] for eind in event_inds for wind in window_inds]
+            #     [[self.event_group_results[ei][wi] for ei in einds for wi in winds]\
+            #         [ind:ind+step]for ind in range(0, n_out, step)]
+
+            # Add results for specified power spectra - event time results
             output.event_time_results = \
                 {key : self.event_time_results[key][event_inds][:, window_inds] \
                 for key in self.event_time_results}
diff --git a/specparam/tests/objs/test_event.py b/specparam/tests/objs/test_event.py
index ceb8de6a..3f5303d8 100644
--- a/specparam/tests/objs/test_event.py
+++ b/specparam/tests/objs/test_event.py
@@ -102,12 +102,11 @@ def test_event_get_group(tfe):
     einds = [0, 1]
     winds = [1, 2]
     ntfe1 = tfe.get_group(einds, winds)
-    #assert ntfe1
+    assert ntfe1
     assert ntfe1.spectrograms.shape == (len(einds), len(tfe.freqs), len(winds))
     tkey = list(ntfe1.event_time_results.keys())[0]
     assert ntfe1.event_time_results[tkey].shape == (len(einds), len(winds))
-    # ToDo: turn this test back on when functionality is fixed
-    #assert len(ntfe1.event_group_results), len(ntfe1.event_group_results[0]) == (len(einds, len(winds)))
+    assert len(ntfe1.event_group_results), len(ntfe1.event_group_results[0]) == (len(einds, len(winds)))
 
 def test_event_drop():
 

From d97261410949009e6d4d3b9825532c40d995fd1f Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 17 Jul 2023 11:56:49 -0400
Subject: [PATCH 69/99] drop equivalent implementation event get_group
 subselection

---
 specparam/objs/event.py | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index 40098d91..e2b410bb 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -355,13 +355,6 @@ def get_group(self, event_inds, window_inds):
             step = int(len(temp) / len(einds))
             output.event_group_results = [temp[ind:ind+step] for ind in range(0, len(temp), step)]
 
-            # # Note: this equivalent to above (but slower)
-            # n_out = len(einds) * len(winds)
-            # step = int(n_out / len(einds))
-            # output.event_group_results = \
-            #     [[self.event_group_results[ei][wi] for ei in einds for wi in winds]\
-            #         [ind:ind+step]for ind in range(0, n_out, step)]
-
             # Add results for specified power spectra - event time results
             output.event_time_results = \
                 {key : self.event_time_results[key][event_inds][:, window_inds] \

From d2a48cbb43b4f6888e42bc6893e570e8a5589dc0 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 17 Jul 2023 12:50:01 -0400
Subject: [PATCH 70/99] add test for event parallel (& fix in doing so)

---
 specparam/objs/event.py            |  6 +++---
 specparam/tests/objs/test_event.py | 16 +++++++++++++++-
 2 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index e2b410bb..018c8cff 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -241,7 +241,7 @@ def fit(self, freqs=None, spectrograms=None, freq_range=None, peak_org=None,
                 self._reset_data_results(clear_spectra=True)
 
         else:
-            fg = self.get_group(None)
+            fg = super().get_group(None, 'group')
             n_jobs = cpu_count() if n_jobs == -1 else n_jobs
             with Pool(processes=n_jobs) as pool:
                 self.event_group_results = \
@@ -533,6 +533,6 @@ def _par_fit(spectrogram, model):
     """Helper function for running in parallel."""
 
     model.power_spectra = spectrogram.T
-    model.fit(peak_org=False)
+    model.fit()
 
-    return model.group_results
+    return model.get_results()
diff --git a/specparam/tests/objs/test_event.py b/specparam/tests/objs/test_event.py
index 3f5303d8..128e9a4e 100644
--- a/specparam/tests/objs/test_event.py
+++ b/specparam/tests/objs/test_event.py
@@ -49,9 +49,23 @@ def test_event_fit():
 
     tfe = SpectralTimeEventModel(verbose=False)
     tfe.fit(xs, ys)
-
     results = tfe.get_results()
+    assert results
+    assert isinstance(results, dict)
+    for key in results.keys():
+        assert np.all(results[key])
+        assert results[key].shape == (len(ys), n_windows)
 
+def test_event_fit_par():
+    """Test group fit, running in parallel."""
+
+    n_windows = 3
+    xs, ys = sim_spectrogram(n_windows, *default_group_params())
+    ys = [ys, ys]
+
+    tfe = SpectralTimeEventModel(verbose=False)
+    tfe.fit(xs, ys, n_jobs=2)
+    results =  tfe.get_results()
     assert results
     assert isinstance(results, dict)
     for key in results.keys():

From bd81432de7e203526c2965c349066181ffa97fc2 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 17 Jul 2023 13:20:21 -0400
Subject: [PATCH 71/99] extend event get_group to support sub-object export

---
 specparam/objs/event.py            | 61 ++++++++++++++++++++----------
 specparam/tests/objs/test_event.py | 21 ++++++++++
 2 files changed, 63 insertions(+), 19 deletions(-)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index 018c8cff..273934c2 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -322,13 +322,18 @@ def get_params(self, name, col=None):
         return [get_group_params(gres, name, col) for gres in self.event_group_results]
 
 
-    def get_group(self, event_inds, window_inds):
+    def get_group(self, event_inds, window_inds, output_type='event'):
         """Get a new model object with the specified sub-selection of model fits.
 
         Parameters
         ----------
         event_inds, window_inds : array_like of int or array_like of bool
             Indices to extract from the object, for event and time windows.
+        output_type : {'time', 'group'}, optional
+            Type of model object to extract:
+                'event' : SpectralTimeEventObject
+                'time' : SpectralTimeObject
+                'group' : SpectralGroupObject
 
         Returns
         -------
@@ -336,29 +341,47 @@ def get_group(self, event_inds, window_inds):
             The requested selection of results data loaded into a new model object.
         """
 
-        # Initialize a new model object, with same settings as current object
-        output = SpectralTimeEventModel(*self.get_settings(), verbose=self.verbose)
-        output.add_meta_data(self.get_meta_data())
+        # Check and convert indices encoding to list of int
+        einds = check_inds(event_inds, self.n_events)
+        winds = check_inds(window_inds, self.n_time_windows)
 
-        if event_inds is not None or window_inds is not None:
+        if output_type == 'event':
 
-            # Check and convert indices encoding to list of int
-            einds = check_inds(event_inds, self.n_events)
-            winds = check_inds(window_inds, self.n_time_windows)
+            # Initialize a new model object, with same settings as current object
+            output = SpectralTimeEventModel(*self.get_settings(), verbose=self.verbose)
+            output.add_meta_data(self.get_meta_data())
 
-            # Add data for specified power spectra, if available
-            if self.has_data:
-                output.spectrograms = self.spectrograms[einds, :, :][:, :, winds]
+            if event_inds is not None or window_inds is not None:
 
-            # Add results for specified power spectra - event group results
-            temp = [self.event_group_results[ei][wi] for ei in einds for wi in winds]
-            step = int(len(temp) / len(einds))
-            output.event_group_results = [temp[ind:ind+step] for ind in range(0, len(temp), step)]
+                # Add data for specified power spectra, if available
+                if self.has_data:
+                    output.spectrograms = self.spectrograms[einds, :, :][:, :, winds]
 
-            # Add results for specified power spectra - event time results
-            output.event_time_results = \
-                {key : self.event_time_results[key][event_inds][:, window_inds] \
-                for key in self.event_time_results}
+                # Add results for specified power spectra - event group results
+                temp = [self.event_group_results[ei][wi] for ei in einds for wi in winds]
+                step = int(len(temp) / len(einds))
+                output.event_group_results = [temp[ind:ind+step] for ind in range(0, len(temp), step)]
+
+                # Add results for specified power spectra - event time results
+                output.event_time_results = \
+                    {key : self.event_time_results[key][event_inds][:, window_inds] \
+                    for key in self.event_time_results}
+
+        elif output_type in ['time', 'group']:
+
+            if event_inds is not None or window_inds is not None:
+
+                # Move specified results & data to `group_results` & `power_spectra` for export
+                self.group_results = \
+                    [self.event_group_results[ei][wi] for ei in einds for wi in winds]
+                if self.has_data:
+                    self.power_spectra = np.hstack(self.spectrograms[einds, :, :][:, :, winds]).T
+
+            new_inds = range(0, len(self.group_results)) if self.group_results else None
+            output = super().get_group(new_inds, output_type)
+
+            self._reset_group_results()
+            self._reset_data_results(clear_spectra=True)
 
         return output
 
diff --git a/specparam/tests/objs/test_event.py b/specparam/tests/objs/test_event.py
index 128e9a4e..fe993f5e 100644
--- a/specparam/tests/objs/test_event.py
+++ b/specparam/tests/objs/test_event.py
@@ -115,6 +115,8 @@ def test_event_get_group(tfe):
 
     einds = [0, 1]
     winds = [1, 2]
+    n_out = len(einds) * len(winds)
+
     ntfe1 = tfe.get_group(einds, winds)
     assert ntfe1
     assert ntfe1.spectrograms.shape == (len(einds), len(tfe.freqs), len(winds))
@@ -122,6 +124,25 @@ def test_event_get_group(tfe):
     assert ntfe1.event_time_results[tkey].shape == (len(einds), len(winds))
     assert len(ntfe1.event_group_results), len(ntfe1.event_group_results[0]) == (len(einds, len(winds)))
 
+    # Test export sub-objects, including with None input
+    ntft0 = tfe.get_group(None, None, 'time')
+    assert not isinstance(ntft0, SpectralTimeEventModel)
+    assert not ntft0.group_results
+
+    ntft1 = tfe.get_group(einds, winds, 'time')
+    assert not isinstance(ntft1, SpectralTimeEventModel)
+    assert ntft1.group_results
+    assert len(ntft1.group_results) == len(ntft1.power_spectra) == n_out
+
+    ntfg0 = tfe.get_group(None, None, 'group')
+    assert not isinstance(ntfg0, SpectralTimeEventModel)
+    assert not ntfg0.group_results
+
+    ntfg1 = tfe.get_group(einds, winds, 'group')
+    assert not isinstance(ntfg1, SpectralTimeEventModel)
+    assert ntfg1.group_results
+    assert len(ntfg1.group_results) == len(ntfg1.power_spectra) == n_out
+
 def test_event_drop():
 
     n_windows = 3

From addd59e9a918646d109427b5b9bc6d29a4fce8c5 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 17 Jul 2023 13:22:04 -0400
Subject: [PATCH 72/99] use new event get_group functionality

---
 specparam/objs/event.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index 273934c2..55c381e4 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -241,7 +241,7 @@ def fit(self, freqs=None, spectrograms=None, freq_range=None, peak_org=None,
                 self._reset_data_results(clear_spectra=True)
 
         else:
-            fg = super().get_group(None, 'group')
+            fg = self.get_group(None, None, 'group')
             n_jobs = cpu_count() if n_jobs == -1 else n_jobs
             with Pool(processes=n_jobs) as pool:
                 self.event_group_results = \
@@ -414,7 +414,7 @@ def save_report(self, file_name, file_path=None, add_settings=True):
     def save(self, file_name, file_path=None, append=False,
              save_results=False, save_settings=False, save_data=False):
 
-        fg = self.get_group(None)
+        fg = self.get_group(None, None, 'group')
         if save_settings and not save_results and not save_data:
             fg.save(file_name, file_path, save_settings=True)
         else:

From 409db0dba01488423e719386b331066dff1867f6 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 17 Jul 2023 13:29:52 -0400
Subject: [PATCH 73/99] refactor event save to match others

---
 specparam/core/io.py    | 44 ++++++++++++++++++++++++++++++++++++++++-
 specparam/objs/event.py | 17 +++-------------
 2 files changed, 46 insertions(+), 15 deletions(-)

diff --git a/specparam/core/io.py b/specparam/core/io.py
index 6147b02e..962502cc 100644
--- a/specparam/core/io.py
+++ b/specparam/core/io.py
@@ -156,7 +156,7 @@ def save_group(group, file_name, file_path=None, append=False,
     file_name : str or FileObject
         File to save data to.
     file_path : str, optional
-        Path to directory to load from. If None, loads from current directory.
+        Path to directory to load from. If None, saves to current directory.
     append : bool, 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.
@@ -194,6 +194,48 @@ def save_group(group, file_name, file_path=None, append=False,
         raise ValueError("Save file not understood.")
 
 
+def save_event(event, file_name, file_path=None, append=False,
+               save_results=False, save_settings=False, save_data=False):
+    """Save out results and/or settings from event object. Saves out to a JSON file.
+
+    Parameters
+    ----------
+    event : SpectralTimeEventModel
+        Object to save data from.
+    file_name : str or FileObject
+        File to save data to.
+    file_path : str, optional
+        Path to directory to load from. If None, saves to current directory.
+    append : bool, 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_results : bool, optional
+        Whether to save out model fit results.
+    save_settings : bool, optional
+        Whether to save out settings.
+    save_data : bool, optional
+        Whether to save out power spectra data.
+
+    Raises
+    ------
+    ValueError
+        If the data or save file specified are not understood.
+    """
+
+    fg = event.get_group(None, None, 'group')
+    if save_settings and not save_results and not save_data:
+        fg.save(file_name, file_path, save_settings=True)
+    else:
+        ndigits = len(str(len(event)))
+        for ind, gres in enumerate(event.event_group_results):
+            fg.group_results = gres
+            if save_data:
+                fg.power_spectra = event.spectrograms[ind, :, :].T
+            fg.save(file_name + '_{:0{ndigits}d}'.format(ind, ndigits=ndigits),
+                    file_path=file_path, save_results=save_results,
+                    save_settings=save_settings, save_data=save_data)
+
+
 def load_json(file_name, file_path):
     """Load json file.
 
diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index 55c381e4..a9c5f66b 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -15,7 +15,7 @@
 from specparam.core.reports import save_event_report
 from specparam.core.strings import gen_event_results_str
 from specparam.core.utils import check_inds
-from specparam.core.io import get_files, save_group
+from specparam.core.io import get_files, save_event
 
 ###################################################################################################
 ###################################################################################################
@@ -410,22 +410,11 @@ def save_report(self, file_name, file_path=None, add_settings=True):
         save_event_report(self, file_name, file_path, add_settings)
 
 
-    @copy_doc_func_to_method(save_group)
+    @copy_doc_func_to_method(save_event)
     def save(self, file_name, file_path=None, append=False,
              save_results=False, save_settings=False, save_data=False):
 
-        fg = self.get_group(None, None, 'group')
-        if save_settings and not save_results and not save_data:
-            fg.save(file_name, file_path, save_settings=True)
-        else:
-            ndigits = len(str(len(self)))
-            for ind, gres in enumerate(self.event_group_results):
-                fg.group_results = gres
-                if save_data:
-                    fg.power_spectra = self.spectrograms[ind, :, :].T
-                fg.save(file_name + '_{:0{ndigits}d}'.format(ind, ndigits=ndigits),
-                        file_path=file_path, save_results=save_results,
-                        save_settings=save_settings, save_data=save_data)
+        save_event(self, file_name, file_path, append, save_results, save_settings, save_data)
 
 
     def load(self, file_name, file_path=None, peak_org=None):

From 041067ea8c785ea33b42775c8468c8606385bf81 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Mon, 17 Jul 2023 13:50:06 -0400
Subject: [PATCH 74/99] add tests & corresponding updates / fixes for event
 loading and assocaited

---
 specparam/objs/event.py            |  6 +++++-
 specparam/objs/time.py             |  2 +-
 specparam/tests/core/test_io.py    | 16 ++++++++++++++++
 specparam/tests/objs/test_event.py | 21 +++++++++++++++++++++
 specparam/tests/objs/test_time.py  | 10 ++++++++++
 5 files changed, 53 insertions(+), 2 deletions(-)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index a9c5f66b..a53383d0 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -433,13 +433,17 @@ def load(self, file_name, file_path=None, peak_org=None):
         """
 
         files = get_files(file_path, select=file_name)
+        spectrograms = []
         for file in files:
             super().load(file, file_path, peak_org=False)
             if self.group_results:
                 self.event_group_results.append(self.group_results)
+            if np.all(self.power_spectra):
+                spectrograms.append(self.spectrogram)
+        self.spectrograms = np.array(spectrograms) if spectrograms else None
 
         self._reset_group_results()
-        if peak_org is not False:
+        if peak_org is not False and self.event_group_results:
             self.convert_results(peak_org)
 
 
diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index 46e2c698..98becc19 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -315,7 +315,7 @@ def load(self, file_name, file_path=None, peak_org=None):
         # Clear results so as not to have possible prior results interfere
         self._reset_time_results()
         super().load(file_name, file_path=file_path)
-        if peak_org is not False:
+        if peak_org is not False and self.group_results:
             self.convert_results(peak_org)
 
 
diff --git a/specparam/tests/core/test_io.py b/specparam/tests/core/test_io.py
index 61efed4b..502fb22f 100644
--- a/specparam/tests/core/test_io.py
+++ b/specparam/tests/core/test_io.py
@@ -134,6 +134,22 @@ def test_save_time(tft):
     assert os.path.exists(os.path.join(TEST_DATA_PATH, set_file_name + '.json'))
     assert os.path.exists(os.path.join(TEST_DATA_PATH, dat_file_name + '.json'))
 
+def test_save_event(tfe):
+    """Check saving fe data."""
+
+    res_file_name = 'test_event_res'
+    set_file_name = 'test_event_set'
+    dat_file_name = 'test_event_dat'
+
+    save_event(tfe, file_name=res_file_name, file_path=TEST_DATA_PATH, save_results=True)
+    save_event(tfe, file_name=set_file_name, file_path=TEST_DATA_PATH, save_settings=True)
+    save_event(tfe, file_name=dat_file_name, file_path=TEST_DATA_PATH, save_data=True)
+
+    assert os.path.exists(os.path.join(TEST_DATA_PATH, set_file_name + '.json'))
+    for ind in range(len(tfe)):
+        assert os.path.exists(os.path.join(TEST_DATA_PATH, res_file_name + '_' + str(ind) + '.json'))
+        assert os.path.exists(os.path.join(TEST_DATA_PATH, dat_file_name + '_' + str(ind) + '.json'))
+
 def test_load_json_str():
     """Test loading JSON file, with str file specifier.
     Loads files from test_save_model_str.
diff --git a/specparam/tests/objs/test_event.py b/specparam/tests/objs/test_event.py
index fe993f5e..f50897ed 100644
--- a/specparam/tests/objs/test_event.py
+++ b/specparam/tests/objs/test_event.py
@@ -92,6 +92,27 @@ def test_event_report(skip_if_no_mpl):
 
     assert tfe
 
+def test_event_load(tbands):
+
+    file_name_res = 'test_event_res'
+    file_name_set = 'test_event_set'
+    file_name_dat = 'test_event_dat'
+
+    # Test loading results
+    tfe = SpectralTimeEventModel(verbose=False)
+    tfe.load(file_name_res, TEST_DATA_PATH, peak_org=tbands)
+    assert tfe.event_time_results
+
+    # Test loading settings
+    tfe = SpectralTimeEventModel(verbose=False)
+    tfe.load(file_name_set, TEST_DATA_PATH)
+    assert tfe.get_settings()
+
+    # Test loading data
+    tfe = SpectralTimeEventModel(verbose=False)
+    tfe.load(file_name_dat, TEST_DATA_PATH)
+    assert np.all(tfe.spectrograms)
+
 def test_event_get_model(tfe):
 
     # Check without regenerating
diff --git a/specparam/tests/objs/test_time.py b/specparam/tests/objs/test_time.py
index 254e0642..2e4ba87c 100644
--- a/specparam/tests/objs/test_time.py
+++ b/specparam/tests/objs/test_time.py
@@ -87,6 +87,16 @@ def test_time_load(tbands):
     tft.load(file_name_res, TEST_DATA_PATH, peak_org=tbands)
     assert tft.time_results
 
+    # Test loading settings
+    tft = SpectralTimeModel(verbose=False)
+    tft.load(file_name_set, TEST_DATA_PATH)
+    assert tft.get_settings()
+
+    # Test loading data
+    tft = SpectralTimeModel(verbose=False)
+    tft.load(file_name_dat, TEST_DATA_PATH)
+    assert np.all(tft.power_spectra)
+
 def test_time_drop():
 
     n_windows = 3

From aba89413b3be41acc8da14c40305bc2b37f1dec1 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 18 Jul 2023 21:58:32 -0400
Subject: [PATCH 75/99] update plot_yshade to make avg / shade optional

---
 specparam/plts/templates.py | 27 ++++++++++++++++-----------
 1 file changed, 16 insertions(+), 11 deletions(-)

diff --git a/specparam/plts/templates.py b/specparam/plts/templates.py
index bee3a000..8ece82b0 100644
--- a/specparam/plts/templates.py
+++ b/specparam/plts/templates.py
@@ -150,14 +150,16 @@ def plot_yshade(x_vals, y_vals, average='mean', shade='std', scale=1., color=Non
         Data values to be plotted on the y-axis. `shade` must be provided if 1d.
     average : 'mean', 'median' or callable, optional, default: 'mean'
         Averaging approach for plotting the average. Only used if y_vals is 2d.
+        If set to None, no average line is plotted.
     shade : 'std', 'sem', 1d array or callable, optional, default: 'std'
         Approach for shading above/below the average.
+        If set to None, no shading is plotted.
     scale : float, optional, default: 1.
         Factor to multiply the plotted shade by.
     color : str, optional, default: None
         Color to plot.
     plot_function : callable, optional
-        xx
+        Function to use to create the plot.
     ax : matplotlib.Axes, optional
         Figure axes upon which to plot.
     **plot_kwargs
@@ -168,18 +170,21 @@ def plot_yshade(x_vals, y_vals, average='mean', shade='std', scale=1., color=Non
 
     shade_alpha = plot_kwargs.pop('shade_alpha', 0.25)
 
-    avg_data = compute_average(y_vals, average=average)
-    if plot_function:
-        plot_function(x_vals, avg_data, color=color, ax=ax, **plot_kwargs)
-    else:
-        ax.plot(x_vals, avg_data, color=color, **plot_kwargs)
+    if average is not None:
 
-    # Compute shade values and apply scaling
-    shade_vals = compute_dispersion(y_vals, shade) * scale
+        avg_data = compute_average(y_vals, average=average)
 
-    # Plot +/- y-shading around spectrum
-    ax.fill_between(x_vals, avg_data - shade_vals, avg_data + shade_vals,
-                    alpha=shade_alpha, color=color)
+        if plot_function:
+            plot_function(x_vals, avg_data, color=color, ax=ax, **plot_kwargs)
+        else:
+            ax.plot(x_vals, avg_data, color=color, **plot_kwargs)
+
+    if shade is not None:
+
+        # Compute shade values, apply scaling & plot +/- y-shading
+        shade_vals = compute_dispersion(y_vals, shade) * scale
+        ax.fill_between(x_vals, avg_data - shade_vals, avg_data + shade_vals,
+                        alpha=shade_alpha, color=color)
 
 
 @check_dependency(plt, 'matplotlib')

From 921a06493f83858bf0c3468879295a6b2c8d8b81 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 18 Jul 2023 22:11:13 -0400
Subject: [PATCH 76/99] add shade options to pe & ap params

---
 specparam/plts/aperiodic.py | 35 +++++++++++++++++++++++------------
 specparam/plts/periodic.py  | 34 +++++++++++++++++++++++-----------
 specparam/plts/templates.py |  4 ++--
 3 files changed, 48 insertions(+), 25 deletions(-)

diff --git a/specparam/plts/aperiodic.py b/specparam/plts/aperiodic.py
index a32167b5..a57cd02a 100644
--- a/specparam/plts/aperiodic.py
+++ b/specparam/plts/aperiodic.py
@@ -8,6 +8,7 @@
 from specparam.sim.gen import gen_freqs, gen_aperiodic
 from specparam.core.modutils import safe_import, check_dependency
 from specparam.plts.settings import PLT_FIGSIZES
+from specparam.plts.templates import plot_yshade
 from specparam.plts.style import style_param_plot, style_plot
 from specparam.plts.utils import check_ax, recursive_plot, savefig, check_plot_kwargs
 
@@ -62,6 +63,7 @@ def plot_aperiodic_params(aps, colors=None, labels=None, ax=None, **plot_kwargs)
 @style_plot
 @check_dependency(plt, 'matplotlib')
 def plot_aperiodic_fits(aps, freq_range, control_offset=False,
+                        average='mean', shade='sem', plot_individual=True,
                         log_freqs=False, colors=None, labels=None,
                         ax=None, **plot_kwargs):
     """Plot reconstructions of model aperiodic fits.
@@ -72,6 +74,15 @@ def plot_aperiodic_fits(aps, freq_range, control_offset=False,
         Aperiodic parameters. Each row is a parameter set, as [Off, Exp] or [Off, Knee, Exp].
     freq_range : list of [float, float]
         The frequency range to plot the peak fits across, as [f_min, f_max].
+    average : {'mean', 'median'}, optional, default: 'mean'
+        Approach to take to average across components.
+        If set to None, no average is plotted.
+    shade : {'sem', 'std'}, optional, default: 'sem'
+        Approach for shading above/below the average reconstruction
+        If set to None, no yshade is plotted.
+    plot_individual : bool, optional, default: True
+        Whether to plot individual component reconstructions.
+        If False, only the average component reconstruction is plotted.
     control_offset : boolean, optional, default: False
         Whether to control for the offset, by setting it to zero.
     log_freqs : boolean, optional, default: False
@@ -103,9 +114,8 @@ def plot_aperiodic_fits(aps, freq_range, control_offset=False,
 
         colors = colors[0] if isinstance(colors, list) else colors
 
-        avg_vals = np.zeros(shape=[len(freqs)])
-
-        for ap_params in aps:
+        all_ap_vals = np.zeros(shape=(len(aps), len(freqs)))
+        for ind, ap_params in enumerate(aps):
 
             if control_offset:
 
@@ -113,18 +123,19 @@ def plot_aperiodic_fits(aps, freq_range, control_offset=False,
                 ap_params = ap_params.copy()
                 ap_params[0] = 0
 
-            # Recreate & plot the aperiodic component from parameters
+            # Create & collect the aperiodic component model from parameters
             ap_vals = gen_aperiodic(freqs, ap_params)
+            all_ap_vals[ind, :] = ap_vals
 
-            ax.plot(plt_freqs, ap_vals, color=colors, alpha=0.35, linewidth=1.25)
-
-            # Collect a running average across components
-            avg_vals = np.nansum(np.vstack([avg_vals, ap_vals]), axis=0)
+            if plot_individual:
+                ax.plot(plt_freqs, ap_vals, color=colors, alpha=0.35, linewidth=1.25)
 
-        # Plot the average component
-        avg = avg_vals / aps.shape[0]
-        avg_color = 'black' if not colors else colors
-        ax.plot(plt_freqs, avg, linewidth=3.75, color=avg_color, label=labels)
+        # Plot the average across all components
+        if average is not False:
+            avg_color = 'black' if not colors else colors
+            plot_yshade(freqs, all_ap_vals, average=average, shade=shade,
+                        shade_alpha=plot_kwargs.pop('shade_alpha', 0.15),
+                        color=avg_color, linewidth=3.75, label=labels, ax=ax)
 
     # Add axis labels
     ax.set_xlabel('log(Frequency)' if log_freqs else 'Frequency')
diff --git a/specparam/plts/periodic.py b/specparam/plts/periodic.py
index c2c40f30..c69ba7e3 100644
--- a/specparam/plts/periodic.py
+++ b/specparam/plts/periodic.py
@@ -8,6 +8,7 @@
 from specparam.core.funcs import gaussian_function
 from specparam.core.modutils import safe_import, check_dependency
 from specparam.plts.settings import PLT_FIGSIZES
+from specparam.plts.templates import plot_yshade
 from specparam.plts.style import style_param_plot, style_plot
 from specparam.plts.utils import check_ax, recursive_plot, savefig, check_plot_kwargs
 
@@ -69,7 +70,8 @@ def plot_peak_params(peaks, freq_range=None, colors=None, labels=None, ax=None,
 
 @savefig
 @style_plot
-def plot_peak_fits(peaks, freq_range=None, colors=None, labels=None, ax=None, **plot_kwargs):
+def plot_peak_fits(peaks, freq_range=None, average='mean', shade='sem', plot_individual=True,
+                   colors=None, labels=None, ax=None, **plot_kwargs):
     """Plot reconstructions of model peak fits.
 
     Parameters
@@ -79,6 +81,15 @@ def plot_peak_fits(peaks, freq_range=None, colors=None, labels=None, ax=None, **
     freq_range : list of [float, float] , optional
         The frequency range to plot the peak fits across, as [f_min, f_max].
         If not provided, defaults to +/- 4 around given peak center frequencies.
+    average : {'mean', 'median'}, optional, default: 'mean'
+        Approach to take to average across components.
+        If set to None, no average is plotted.
+    shade : {'sem', 'std'}, optional, default: 'sem'
+        Approach for shading above/below the average reconstruction
+        If set to None, no yshade is plotted.
+    plot_individual : bool, optional, default: True
+        Whether to plot individual component reconstructions.
+        If False, only the average component reconstruction is plotted.
     colors : str or list of str, optional
         Color(s) to plot data.
     labels : list of str, optional
@@ -118,21 +129,22 @@ def plot_peak_fits(peaks, freq_range=None, colors=None, labels=None, ax=None, **
 
         colors = colors[0] if isinstance(colors, list) else colors
 
-        avg_vals = np.zeros(shape=[len(freqs)])
+        all_peak_vals = np.zeros(shape=(len(peaks), len(freqs)))
+        for ind, peak_params in enumerate(peaks):
 
-        for peak_params in peaks:
-
-            # Create & plot the peak model from parameters
+            # Create & collect the peak model from parameters
             peak_vals = gaussian_function(freqs, *peak_params)
-            ax.plot(freqs, peak_vals, color=colors, alpha=0.35, linewidth=1.25)
+            all_peak_vals[ind, :] = peak_vals
 
-            # Collect a running average average peaks
-            avg_vals = np.nansum(np.vstack([avg_vals, peak_vals]), axis=0)
+            if plot_individual:
+                ax.plot(freqs, peak_vals, color=colors, alpha=0.35, linewidth=1.25)
 
         # Plot the average across all components
-        avg = avg_vals / peaks.shape[0]
-        avg_color = 'black' if not colors else colors
-        ax.plot(freqs, avg, color=avg_color, linewidth=3.75, label=labels)
+        if average is not False:
+            avg_color = 'black' if not colors else colors
+            plot_yshade(freqs, all_peak_vals, average=average, shade=shade,
+                        shade_alpha=plot_kwargs.pop('shade_alpha', 0.15),
+                        color=avg_color, linewidth=3.75, label=labels, ax=ax)
 
     # Add axis labels
     ax.set_xlabel('Frequency')
diff --git a/specparam/plts/templates.py b/specparam/plts/templates.py
index 8ece82b0..12f946ea 100644
--- a/specparam/plts/templates.py
+++ b/specparam/plts/templates.py
@@ -170,9 +170,9 @@ def plot_yshade(x_vals, y_vals, average='mean', shade='std', scale=1., color=Non
 
     shade_alpha = plot_kwargs.pop('shade_alpha', 0.25)
 
-    if average is not None:
+    avg_data = compute_average(y_vals, average=average if average else 'mean')
 
-        avg_data = compute_average(y_vals, average=average)
+    if average is not None:
 
         if plot_function:
             plot_function(x_vals, avg_data, color=color, ax=ax, **plot_kwargs)

From 14fbde0115f8f6a82f1682de9717647a381f5bfd Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Thu, 20 Jul 2023 00:12:52 -0400
Subject: [PATCH 77/99] fix specptrogram sim docstring

---
 specparam/sim/sim.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/specparam/sim/sim.py b/specparam/sim/sim.py
index 6e781ffd..ab7886bc 100644
--- a/specparam/sim/sim.py
+++ b/specparam/sim/sim.py
@@ -274,7 +274,7 @@ def sim_spectrogram(n_windows, freq_range, aperiodic_params, periodic_params,
     freqs : 1d array
         Frequency values, in linear spacing.
     spectrogram : 2d array
-        Matrix of power values, in linear spacing, as [n_windows, n_power_spectra].
+        Matrix of power values, in linear spacing, as [n_freqs, n_windows].
     sim_params : list of SimParams
         Definitions of parameters used for each spectrum. Has length of n_spectra.
         Only returned if `return_params` is True.

From c7375a7d4b13bb2673cd3be1cb212575f50ac364 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 10:16:17 -0400
Subject: [PATCH 78/99] plot_group -> plot_group_model (for consistency)

---
 specparam/objs/group.py            | 7 ++++---
 specparam/plts/group.py            | 2 +-
 specparam/tests/plts/test_group.py | 6 +++---
 3 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/specparam/objs/group.py b/specparam/objs/group.py
index ebd119c7..30277855 100644
--- a/specparam/objs/group.py
+++ b/specparam/objs/group.py
@@ -11,7 +11,7 @@
 import numpy as np
 
 from specparam.objs import SpectralModel
-from specparam.plts.group import plot_group
+from specparam.plts.group import plot_group_model
 from specparam.core.items import OBJ_DESC
 from specparam.core.utils import check_inds
 from specparam.core.errors import NoModelError
@@ -343,10 +343,11 @@ def get_params(self, name, col=None):
         return get_group_params(self.group_results, name, col)
 
 
-    @copy_doc_func_to_method(plot_group)
+    @copy_doc_func_to_method(plot_group_model)
     def plot(self, save_fig=False, file_name=None, file_path=None, **plot_kwargs):
 
-        plot_group(self, save_fig=save_fig, file_name=file_name, file_path=file_path, **plot_kwargs)
+        plot_group_model(self, save_fig=save_fig, file_name=file_name,
+                         file_path=file_path, **plot_kwargs)
 
 
     @copy_doc_func_to_method(save_group_report)
diff --git a/specparam/plts/group.py b/specparam/plts/group.py
index 86c7cc39..3224d0c9 100644
--- a/specparam/plts/group.py
+++ b/specparam/plts/group.py
@@ -20,7 +20,7 @@
 
 @savefig
 @check_dependency(plt, 'matplotlib')
-def plot_group(group, **plot_kwargs):
+def plot_group_model(group, **plot_kwargs):
     """Plot a figure with subplots visualizing the parameters from a group model object.
 
     Parameters
diff --git a/specparam/tests/plts/test_group.py b/specparam/tests/plts/test_group.py
index 9aaf5587..d56afa4e 100644
--- a/specparam/tests/plts/test_group.py
+++ b/specparam/tests/plts/test_group.py
@@ -14,10 +14,10 @@
 ###################################################################################################
 
 @plot_test
-def test_plot_group(tfg, skip_if_no_mpl):
+def test_plot_group_model(tfg, skip_if_no_mpl):
 
-    plot_group(tfg, file_path=TEST_PLOTS_PATH,
-               file_name='test_plot_group.png')
+    plot_group_model(tfg, file_path=TEST_PLOTS_PATH,
+                     file_name='test_plot_group_model.png')
 
     # Test error if no data available to plot
     tfg = SpectralGroupModel()

From 9e7fb55088d8d5273c7472894894fa404ad69031 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 10:59:53 -0400
Subject: [PATCH 79/99] io updates, make consistent set of load funcs, and
 updates test

---
 specparam/tests/core/test_io.py        | 53 ++++++++++++--------
 specparam/tests/core/test_reports.py   |  8 +--
 specparam/tests/objs/test_group.py     |  2 +-
 specparam/tests/plts/test_utils.py     | 10 ++--
 specparam/tests/utils/test_download.py |  7 +--
 specparam/tests/utils/test_io.py       | 35 ++++++++++++--
 specparam/utils/io.py                  | 67 ++++++++++++++++++++++++--
 7 files changed, 142 insertions(+), 40 deletions(-)

diff --git a/specparam/tests/core/test_io.py b/specparam/tests/core/test_io.py
index ec69d442..3a3798e8 100644
--- a/specparam/tests/core/test_io.py
+++ b/specparam/tests/core/test_io.py
@@ -49,14 +49,14 @@ def test_save_model_str(tfm):
     save_model(tfm, file_name_set, TEST_DATA_PATH, False, False, True, False)
     save_model(tfm, file_name_dat, TEST_DATA_PATH, False, False, False, True)
 
-    assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name_res + '.json'))
-    assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name_set + '.json'))
-    assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name_dat + '.json'))
+    assert os.path.exists(TEST_DATA_PATH / (file_name_res + '.json'))
+    assert os.path.exists(TEST_DATA_PATH / (file_name_set + '.json'))
+    assert os.path.exists(TEST_DATA_PATH / (file_name_dat + '.json'))
 
     # Test saving out all save elements
     file_name_all = 'test_all'
     save_model(tfm, file_name_all, TEST_DATA_PATH, False, True, True, True)
-    assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name_all + '.json'))
+    assert os.path.exists(TEST_DATA_PATH / (file_name_all + '.json'))
 
 def test_save_model_append(tfm):
     """Check saving fm data, appending to a file."""
@@ -66,7 +66,7 @@ def test_save_model_append(tfm):
     save_model(tfm, file_name, TEST_DATA_PATH, True, True, True, True)
     save_model(tfm, file_name, TEST_DATA_PATH, True, True, True, True)
 
-    assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name + '.json'))
+    assert os.path.exists(TEST_DATA_PATH / (file_name + '.json'))
 
 def test_save_model_fobj(tfm):
     """Check saving fm data, with file object file specifier."""
@@ -74,12 +74,12 @@ def test_save_model_fobj(tfm):
     file_name = 'test_fileobj'
 
     # Save, using file-object: three successive lines with three possible save settings
-    with open(os.path.join(TEST_DATA_PATH, file_name + '.json'), 'w') as f_obj:
+    with open(TEST_DATA_PATH / (file_name + '.json'), 'w') as f_obj:
         save_model(tfm, f_obj, TEST_DATA_PATH, False, True, False, False)
         save_model(tfm, f_obj, TEST_DATA_PATH, False, False, True, False)
         save_model(tfm, f_obj, TEST_DATA_PATH, False, False, False, True)
 
-    assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name + '.json'))
+    assert os.path.exists(TEST_DATA_PATH / (file_name + '.json'))
 
 def test_save_group(tfg):
     """Check saving fg data."""
@@ -92,14 +92,14 @@ def test_save_group(tfg):
     save_group(tfg, file_name=set_file_name, file_path=TEST_DATA_PATH, save_settings=True)
     save_group(tfg, file_name=dat_file_name, file_path=TEST_DATA_PATH, save_data=True)
 
-    assert os.path.exists(os.path.join(TEST_DATA_PATH, res_file_name + '.json'))
-    assert os.path.exists(os.path.join(TEST_DATA_PATH, set_file_name + '.json'))
-    assert os.path.exists(os.path.join(TEST_DATA_PATH, dat_file_name + '.json'))
+    assert os.path.exists(TEST_DATA_PATH / (res_file_name + '.json'))
+    assert os.path.exists(TEST_DATA_PATH / (set_file_name + '.json'))
+    assert os.path.exists(TEST_DATA_PATH / (dat_file_name + '.json'))
 
     # Test saving out all save elements
     file_name_all = 'test_group_all'
     save_group(tfg, file_name_all, TEST_DATA_PATH, False, True, True, True)
-    assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name_all + '.json'))
+    assert os.path.exists(TEST_DATA_PATH / (file_name_all + '.json'))
 
 def test_save_group_append(tfg):
     """Check saving fg data, appending to file."""
@@ -109,17 +109,17 @@ def test_save_group_append(tfg):
     save_group(tfg, file_name, TEST_DATA_PATH, True, save_results=True)
     save_group(tfg, file_name, TEST_DATA_PATH, True, save_results=True)
 
-    assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name + '.json'))
+    assert os.path.exists(TEST_DATA_PATH / (file_name + '.json'))
 
 def test_save_group_fobj(tfg):
     """Check saving fg data, with file object file specifier."""
 
     file_name = 'test_fileobj'
 
-    with open(os.path.join(TEST_DATA_PATH, file_name + '.json'), 'w') as f_obj:
+    with open(TEST_DATA_PATH / (file_name + '.json'), 'w') as f_obj:
         save_group(tfg, f_obj, TEST_DATA_PATH, False, True, False, False)
 
-    assert os.path.exists(os.path.join(TEST_DATA_PATH, file_name + '.json'))
+    assert os.path.exists(TEST_DATA_PATH / (file_name + '.json'))
 
 def test_save_time(tft):
     """Check saving ft data."""
@@ -132,9 +132,14 @@ def test_save_time(tft):
     save_group(tft, file_name=set_file_name, file_path=TEST_DATA_PATH, save_settings=True)
     save_group(tft, file_name=dat_file_name, file_path=TEST_DATA_PATH, save_data=True)
 
-    assert os.path.exists(os.path.join(TEST_DATA_PATH, res_file_name + '.json'))
-    assert os.path.exists(os.path.join(TEST_DATA_PATH, set_file_name + '.json'))
-    assert os.path.exists(os.path.join(TEST_DATA_PATH, dat_file_name + '.json'))
+    assert os.path.exists(TEST_DATA_PATH / (res_file_name + '.json'))
+    assert os.path.exists(TEST_DATA_PATH / (set_file_name + '.json'))
+    assert os.path.exists(TEST_DATA_PATH / (dat_file_name + '.json'))
+
+    # Test saving out all save elements
+    file_name_all = 'test_time_all'
+    save_group(tft, file_name_all, TEST_DATA_PATH, False, True, True, True)
+    assert os.path.exists(TEST_DATA_PATH / (file_name_all + '.json'))
 
 def test_save_event(tfe):
     """Check saving fe data."""
@@ -147,10 +152,16 @@ def test_save_event(tfe):
     save_event(tfe, file_name=set_file_name, file_path=TEST_DATA_PATH, save_settings=True)
     save_event(tfe, file_name=dat_file_name, file_path=TEST_DATA_PATH, save_data=True)
 
-    assert os.path.exists(os.path.join(TEST_DATA_PATH, set_file_name + '.json'))
+    assert os.path.exists(TEST_DATA_PATH / (set_file_name + '.json'))
+    for ind in range(len(tfe)):
+        assert os.path.exists(TEST_DATA_PATH / (res_file_name + '_' + str(ind) + '.json'))
+        assert os.path.exists(TEST_DATA_PATH / (dat_file_name + '_' + str(ind) + '.json'))
+
+    # Test saving out all save elements
+    file_name_all = 'test_event_all'
+    save_event(tfe, file_name_all, TEST_DATA_PATH, False, True, True, True)
     for ind in range(len(tfe)):
-        assert os.path.exists(os.path.join(TEST_DATA_PATH, res_file_name + '_' + str(ind) + '.json'))
-        assert os.path.exists(os.path.join(TEST_DATA_PATH, dat_file_name + '_' + str(ind) + '.json'))
+        assert os.path.exists(TEST_DATA_PATH / (file_name_all + '_' + str(ind) + '.json'))
 
 def test_load_json_str():
     """Test loading JSON file, with str file specifier.
@@ -170,7 +181,7 @@ def test_load_json_fobj():
 
     file_name = 'test_all'
 
-    with open(os.path.join(TEST_DATA_PATH, file_name + '.json'), 'r') as f_obj:
+    with open(TEST_DATA_PATH / (file_name + '.json'), 'r') as f_obj:
         data = load_json(f_obj, '')
 
     assert data
diff --git a/specparam/tests/core/test_reports.py b/specparam/tests/core/test_reports.py
index 26b4aeea..0da66040 100644
--- a/specparam/tests/core/test_reports.py
+++ b/specparam/tests/core/test_reports.py
@@ -15,7 +15,7 @@ def test_save_model_report(tfm, skip_if_no_mpl):
 
     save_model_report(tfm, file_name, TEST_REPORTS_PATH)
 
-    assert os.path.exists(os.path.join(TEST_REPORTS_PATH, file_name + '.pdf'))
+    assert os.path.exists(TEST_REPORTS_PATH / (file_name + '.pdf'))
 
 def test_save_group_report(tfg, skip_if_no_mpl):
 
@@ -23,7 +23,7 @@ def test_save_group_report(tfg, skip_if_no_mpl):
 
     save_group_report(tfg, file_name, TEST_REPORTS_PATH)
 
-    assert os.path.exists(os.path.join(TEST_REPORTS_PATH, file_name + '.pdf'))
+    assert os.path.exists(TEST_REPORTS_PATH / (file_name + '.pdf'))
 
 def test_save_time_report(tft, skip_if_no_mpl):
 
@@ -31,7 +31,7 @@ def test_save_time_report(tft, skip_if_no_mpl):
 
     save_time_report(tft, file_name, TEST_REPORTS_PATH)
 
-    assert os.path.exists(os.path.join(TEST_REPORTS_PATH, file_name + '.pdf'))
+    assert os.path.exists(TEST_REPORTS_PATH / (file_name + '.pdf'))
 
 def test_save_event_report(tfe, skip_if_no_mpl):
 
@@ -39,4 +39,4 @@ def test_save_event_report(tfe, skip_if_no_mpl):
 
     save_event_report(tfe, file_name, TEST_REPORTS_PATH)
 
-    assert os.path.exists(os.path.join(TEST_REPORTS_PATH, file_name + '.pdf'))
+    assert os.path.exists(TEST_REPORTS_PATH / (file_name + '.pdf'))
diff --git a/specparam/tests/objs/test_group.py b/specparam/tests/objs/test_group.py
index 3db15024..30f2ad91 100644
--- a/specparam/tests/objs/test_group.py
+++ b/specparam/tests/objs/test_group.py
@@ -219,7 +219,7 @@ def test_save_model_report(tfg):
     file_name = 'test_group_model_report'
     tfg.save_model_report(0, file_name, TEST_REPORTS_PATH)
 
-    assert os.path.exists(os.path.join(TEST_REPORTS_PATH, file_name + '.pdf'))
+    assert os.path.exists(TEST_REPORTS_PATH / (file_name + '.pdf'))
 
 def test_get_results(tfg):
     """Check get results method."""
diff --git a/specparam/tests/plts/test_utils.py b/specparam/tests/plts/test_utils.py
index 816508fa..edfe80d1 100644
--- a/specparam/tests/plts/test_utils.py
+++ b/specparam/tests/plts/test_utils.py
@@ -81,23 +81,23 @@ def example_plot():
 
     # Test defaults to saving given file path & name
     example_plot(file_path=TEST_PLOTS_PATH, file_name='test_savefig1.pdf')
-    assert os.path.exists(os.path.join(TEST_PLOTS_PATH, 'test_savefig1.pdf'))
+    assert os.path.exists(TEST_PLOTS_PATH / 'test_savefig1.pdf')
 
     # Test works the same when explicitly given `save_fig`
     example_plot(save_fig=True, file_path=TEST_PLOTS_PATH, file_name='test_savefig2.pdf')
-    assert os.path.exists(os.path.join(TEST_PLOTS_PATH, 'test_savefig2.pdf'))
+    assert os.path.exists(TEST_PLOTS_PATH / 'test_savefig2.pdf')
 
     # Test giving additional save kwargs
     example_plot(file_path=TEST_PLOTS_PATH, file_name='test_savefig3.pdf',
                  save_kwargs={'facecolor' : 'red'})
-    assert os.path.exists(os.path.join(TEST_PLOTS_PATH, 'test_savefig3.pdf'))
+    assert os.path.exists(TEST_PLOTS_PATH / 'test_savefig3.pdf')
 
     # Test does not save when `save_fig` set to False
     example_plot(save_fig=False, file_path=TEST_PLOTS_PATH, file_name='test_savefig_nope.pdf')
-    assert not os.path.exists(os.path.join(TEST_PLOTS_PATH, 'test_savefig_nope.pdf'))
+    assert not os.path.exists(TEST_PLOTS_PATH / 'test_savefig_nope.pdf')
 
 def test_save_figure():
 
     plt.plot([1, 2], [3, 4])
     save_figure(file_name='test_save_figure.pdf', file_path=TEST_PLOTS_PATH)
-    assert os.path.exists(os.path.join(TEST_PLOTS_PATH, 'test_save_figure.pdf'))
+    assert os.path.exists(TEST_PLOTS_PATH / 'test_save_figure.pdf')
diff --git a/specparam/tests/utils/test_download.py b/specparam/tests/utils/test_download.py
index c24962dc..451d28bc 100644
--- a/specparam/tests/utils/test_download.py
+++ b/specparam/tests/utils/test_download.py
@@ -2,6 +2,7 @@
 
 import os
 import shutil
+from pathlib import Path
 
 import numpy as np
 
@@ -10,7 +11,7 @@
 ###################################################################################################
 ###################################################################################################
 
-TEST_FOLDER = 'test_data'
+TEST_FOLDER = Path('test_data')
 
 def clean_up_downloads():
 
@@ -29,14 +30,14 @@ def test_check_data_file():
     filename = 'freqs.npy'
 
     check_data_file(filename, TEST_FOLDER)
-    assert os.path.isfile(os.path.join(TEST_FOLDER, filename))
+    assert os.path.isfile(TEST_FOLDER / filename)
 
 def test_fetch_example_data():
 
     filename = 'spectrum.npy'
 
     fetch_example_data(filename, folder=TEST_FOLDER)
-    assert os.path.isfile(os.path.join(TEST_FOLDER, filename))
+    assert os.path.isfile(TEST_FOLDER / filename)
 
     clean_up_downloads()
 
diff --git a/specparam/tests/utils/test_io.py b/specparam/tests/utils/test_io.py
index fc602e0f..36f1c9a6 100644
--- a/specparam/tests/utils/test_io.py
+++ b/specparam/tests/utils/test_io.py
@@ -3,7 +3,8 @@
 import numpy as np
 
 from specparam.core.items import OBJ_DESC
-from specparam.objs import SpectralModel, SpectralGroupModel
+from specparam.objs import (SpectralModel, SpectralGroupModel,
+                            SpectralTimeModel, SpectralTimeEventModel)
 
 from specparam.tests.settings import TEST_DATA_PATH
 
@@ -30,10 +31,10 @@ def test_load_model():
     for meta_dat in OBJ_DESC['meta_data']:
         assert getattr(tfm, meta_dat) is not None
 
-def test_load_group():
+def test_load_group_model():
 
     file_name = 'test_group_all'
-    tfg = load_group(file_name, TEST_DATA_PATH)
+    tfg = load_group_model(file_name, TEST_DATA_PATH)
 
     assert isinstance(tfg, SpectralGroupModel)
 
@@ -44,3 +45,31 @@ def test_load_group():
     assert tfg.power_spectra is not None
     for meta_dat in OBJ_DESC['meta_data']:
         assert getattr(tfg, meta_dat) is not None
+
+def test_load_time_model(tbands):
+
+    file_name = 'test_time_all'
+
+    # Load without bands definition
+    tft = load_time_model(file_name, TEST_DATA_PATH)
+    assert isinstance(tft, SpectralTimeModel)
+
+    # Load with bands definition
+    tft2 = load_time_model(file_name, TEST_DATA_PATH, tbands)
+    assert isinstance(tft2, SpectralTimeModel)
+    assert tft2.time_results
+
+def test_load_event_model(tbands):
+
+    file_name = 'test_event_all'
+
+    # Load without bands definition
+    tfe = load_event_model(file_name, TEST_DATA_PATH)
+    assert isinstance(tfe, SpectralTimeEventModel)
+    assert len(tfe) > 1
+
+    # Load with bands definition
+    tfe2 = load_event_model(file_name, TEST_DATA_PATH, tbands)
+    assert isinstance(tfe2, SpectralTimeEventModel)
+    assert tfe2.event_time_results
+    assert len(tfe2) > 1
diff --git a/specparam/utils/io.py b/specparam/utils/io.py
index 450ef5d1..4ed86888 100644
--- a/specparam/utils/io.py
+++ b/specparam/utils/io.py
@@ -4,7 +4,7 @@
 ###################################################################################################
 
 def load_model(file_name, file_path=None, regenerate=True):
-    """Load a model file.
+    """Load a model file into a model object.
 
     Parameters
     ----------
@@ -31,8 +31,8 @@ def load_model(file_name, file_path=None, regenerate=True):
     return model
 
 
-def load_group(file_name, file_path=None):
-    """Load a group file.
+def load_group_model(file_name, file_path=None):
+    """Load a group file into a group model object.
 
     Parameters
     ----------
@@ -55,3 +55,64 @@ def load_group(file_name, file_path=None):
     group.load(file_name, file_path)
 
     return group
+
+
+def load_time_model(file_name, file_path=None, peak_org=None):
+    """Load a time file into a time model object.
+
+
+    Parameters
+    ----------
+    file_name : str
+        File to load data data.
+    file_path : Path or str, optional
+        Path to directory to load from. If None, loads from current directory.
+    peak_org : int or Bands, optional
+        How to organize peaks.
+        If int, extracts the first n peaks.
+        If Bands, extracts peaks based on band definitions.
+
+    Returns
+    -------
+    time : SpectralTimeModel
+        Object with the loaded data.
+    """
+
+    # Initialize a time object (imported locally to avoid circular imports)
+    from specparam.objs import SpectralTimeModel
+    time = SpectralTimeModel()
+
+    # Load data into object
+    time.load(file_name, file_path, peak_org)
+
+    return time
+
+
+def load_event_model(file_name, file_path=None, peak_org=None):
+    """Load an event file into an event model object.
+
+    Parameters
+    ----------
+    file_name : str
+        File to load data data.
+    file_path : Path or str, optional
+        Path to directory to load from. If None, loads from current directory.
+    peak_org : int or Bands, optional
+        How to organize peaks.
+        If int, extracts the first n peaks.
+        If Bands, extracts peaks based on band definitions.
+
+    Returns
+    -------
+    event : SpectralTimeEventModel
+        Object with the loaded data.
+    """
+
+    # Initialize an event object (imported locally to avoid circular imports)
+    from specparam.objs import SpectralTimeEventModel
+    event = SpectralTimeEventModel()
+
+    # Load data into object
+    event.load(file_name, file_path, peak_org)
+
+    return event

From 5a561c7dd9db24eec1778be451c2d5b9ab3ea415 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 11:09:49 -0400
Subject: [PATCH 80/99] update API for updates here

---
 doc/api.rst | 37 +++++++++++++++++++++++++++++++++----
 1 file changed, 33 insertions(+), 4 deletions(-)

diff --git a/doc/api.rst b/doc/api.rst
index 54b9f1af..b32934d0 100644
--- a/doc/api.rst
+++ b/doc/api.rst
@@ -40,6 +40,17 @@ The SpectralGroupModel object allows for parameterizing groups of power spectra.
 
    SpectralGroupModel
 
+Time & Event Objects
+~~~~~~~~~~~~~~~~~~~~
+
+The time & event objects allows for parameterizing power spectra organized across time and/or events.
+
+.. autosummary::
+   :toctree: generated/
+
+   SpectralTimeModel
+   SpectralTimeEventModel
+
 Object Utilities
 ~~~~~~~~~~~~~~~~
 
@@ -178,7 +189,7 @@ Code & utilities for simulating power spectra.
 Generate Power Spectra
 ~~~~~~~~~~~~~~~~~~~~~~
 
-Functions for simulating neural power spectra.
+Functions for simulating neural power spectra and spectrograms.
 
 .. currentmodule:: specparam.sim
 
@@ -187,6 +198,7 @@ Functions for simulating neural power spectra.
 
     sim_power_spectrum
     sim_group_power_spectra
+    sim_spectrogram
 
 Manage Parameters
 ~~~~~~~~~~~~~~~~~
@@ -242,7 +254,7 @@ Visualizations.
 Plot Power Spectra
 ~~~~~~~~~~~~~~~~~~
 
-Plots for visualizing power spectra.
+Plots for visualizing power spectra and spectrograms.
 
 .. currentmodule:: specparam.plts
 
@@ -250,6 +262,7 @@ Plots for visualizing power spectra.
     :toctree: generated/
 
     plot_spectra
+    plot_spectrogram
 
 Plots for plotting power spectra with shaded regions.
 
@@ -311,7 +324,21 @@ Note that these are the same plotting functions that can be called from the mode
 .. autosummary::
     :toctree: generated/
 
-    plot_group
+    plot_group_model
+
+.. currentmodule:: specparam.plts.time
+
+.. autosummary::
+    :toctree: generated/
+
+    plot_time_model
+
+.. currentmodule:: specparam.plts.event
+
+.. autosummary::
+    :toctree: generated/
+
+    plot_event_model
 
 Annotated Plots
 ~~~~~~~~~~~~~~~
@@ -388,7 +415,9 @@ Input / Output (IO)
     :toctree: generated/
 
     load_model
-    load_group
+    load_group_model
+    load_time_model
+    load_event_model
 
 Methods Reports
 ~~~~~~~~~~~~~~~

From 62dba145dca5e2b7fd672977a35f41eb71135d24 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 12:38:33 -0400
Subject: [PATCH 81/99] misc small doc fixes

---
 examples/manage/plot_fit_models_3d.py |  4 ++--
 specparam/core/strings.py             |  2 +-
 specparam/plts/__init__.py            |  2 +-
 tutorials/plot_09-Reporting.py        | 11 +++--------
 4 files changed, 7 insertions(+), 12 deletions(-)

diff --git a/examples/manage/plot_fit_models_3d.py b/examples/manage/plot_fit_models_3d.py
index 29c3b616..82959e5f 100644
--- a/examples/manage/plot_fit_models_3d.py
+++ b/examples/manage/plot_fit_models_3d.py
@@ -61,7 +61,7 @@
 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
+from specparam.utils.io import load_group_model
 
 ###################################################################################################
 # Example Set-Up
@@ -229,7 +229,7 @@
 ###################################################################################################
 
 # Reload our list of SpectralGroupModels
-fgs = [load_group(file_name, file_path='results') \
+fgs = [load_group_model(file_name, file_path='results') \
     for file_name in os.listdir('results')]
 
 ###################################################################################################
diff --git a/specparam/core/strings.py b/specparam/core/strings.py
index c9667bfd..01962822 100644
--- a/specparam/core/strings.py
+++ b/specparam/core/strings.py
@@ -208,7 +208,7 @@ def gen_methods_report_str(concise=False):
         '',
 
         # Methods report information
-        'To report on using spectral parameterization, you should report (at minimum):',
+        'Reports using spectral parameterization should include (at minimum):',
         '',
         '- the code version that was used',
         '- the algorithm settings that were used',
diff --git a/specparam/plts/__init__.py b/specparam/plts/__init__.py
index 3e656740..5ea2b877 100644
--- a/specparam/plts/__init__.py
+++ b/specparam/plts/__init__.py
@@ -1,3 +1,3 @@
 """Plots sub-module."""
 
-from .spectra import plot_spectra
+from .spectra import plot_spectra, plot_spectrogram
diff --git a/tutorials/plot_09-Reporting.py b/tutorials/plot_09-Reporting.py
index ffe132a1..68c2bcb9 100644
--- a/tutorials/plot_09-Reporting.py
+++ b/tutorials/plot_09-Reporting.py
@@ -22,14 +22,9 @@
 # sphinx_gallery_start_ignore
 # Note: this code gets hidden, but serves to create the text plot for the icon
 from specparam.core.strings import gen_methods_report_str
-from specparam.core.reports import REPORT_FONT
-import matplotlib.pyplot as plt
-text = gen_methods_report_str(concise=True)
-text = text[0:142] + '\n' + text[142:]
-_, ax = plt.subplots(figsize=(8, 3))
-ax.text(0.5, 0.5, text, REPORT_FONT, ha='center', va='center')
-ax.set_frame_on(False)
-_ = ax.set(xticks=[], yticks=[])
+from specparam.plts.templates import plot_text
+text = gen_methods_report_str()
+plot_text(text, 0.5, 0.5, figsize=(12, 3))
 # sphinx_gallery_end_ignore
 
 ###################################################################################################

From 1a768e57134d7a5a2999ea6d67f7c7c5645a8278 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 14:31:56 -0400
Subject: [PATCH 82/99] lints

---
 specparam/core/io.py    |  4 ++--
 specparam/objs/event.py | 14 ++++++++------
 specparam/sim/params.py |  2 +-
 3 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/specparam/core/io.py b/specparam/core/io.py
index bb7b76b2..ebd06045 100644
--- a/specparam/core/io.py
+++ b/specparam/core/io.py
@@ -224,7 +224,7 @@ def save_event(event, file_name, file_path=None, append=False,
 
     fg = event.get_group(None, None, 'group')
     if save_settings and not save_results and not save_data:
-        fg.save(file_name, file_path, save_settings=True)
+        fg.save(file_name, file_path, append=append, save_settings=True)
     else:
         ndigits = len(str(len(event)))
         for ind, gres in enumerate(event.event_group_results):
@@ -232,7 +232,7 @@ def save_event(event, file_name, file_path=None, append=False,
             if save_data:
                 fg.power_spectra = event.spectrograms[ind, :, :].T
             fg.save(file_name + '_{:0{ndigits}d}'.format(ind, ndigits=ndigits),
-                    file_path=file_path, save_results=save_results,
+                    file_path=file_path, append=append, save_results=save_results,
                     save_settings=save_settings, save_data=save_data)
 
 
diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index a53383d0..80044ed7 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -7,6 +7,7 @@
 import numpy as np
 
 from specparam.objs import SpectralModel, SpectralTimeModel
+from specparam.objs.group import _progress
 from specparam.plts.event import plot_event_model
 from specparam.data.conversions import event_group_to_dict, event_group_to_dataframe, dict_to_df
 from specparam.data.utils import get_group_params, get_results_by_row, flatten_results_dict
@@ -92,14 +93,14 @@ def _reset_event_results(self, length=0):
     def has_data(self):
         """Redefine has_data marker to reflect the spectrograms attribute."""
 
-        return True if np.any(self.spectrograms) else False
+        return bool(np.any(self.spectrograms))
 
 
     @property
     def has_model(self):
         """Redefine has_model marker to reflect the event results."""
 
-        return True if self.event_group_results else False
+        return bool(self.event_group_results)
 
 
     @property
@@ -112,14 +113,14 @@ def n_peaks_(self):
 
     @property
     def n_events(self):
-        # ToDo: double check if we want this - I think is never used internally?
+        """How many events are included in the model object."""
 
         return len(self)
 
 
     @property
     def n_time_windows(self):
-        # ToDo: double check if we want this - I think is never used internally?
+        """How many time windows are included in the model object."""
 
         return self.spectrograms[0].shape[1] if self.has_data else 0
 
@@ -226,7 +227,7 @@ def fit(self, freqs=None, spectrograms=None, freq_range=None, peak_org=None,
         """
 
         # ToDo: here because of circular import - updates / refactors should fix & move
-        from specparam.objs.group import _progress
+        #from specparam.objs.group import _progress
 
         if spectrograms is not None:
             self.add_data(freqs, spectrograms, freq_range)
@@ -360,7 +361,8 @@ def get_group(self, event_inds, window_inds, output_type='event'):
                 # Add results for specified power spectra - event group results
                 temp = [self.event_group_results[ei][wi] for ei in einds for wi in winds]
                 step = int(len(temp) / len(einds))
-                output.event_group_results = [temp[ind:ind+step] for ind in range(0, len(temp), step)]
+                output.event_group_results = \
+                    [temp[ind:ind+step] for ind in range(0, len(temp), step)]
 
                 # Add results for specified power spectra - event time results
                 output.event_time_results = \
diff --git a/specparam/sim/params.py b/specparam/sim/params.py
index 5fcfde1f..a64c5c4a 100644
--- a/specparam/sim/params.py
+++ b/specparam/sim/params.py
@@ -150,7 +150,7 @@ def _check_values(start, stop, step):
             raise ValueError("Inputs 'start' and 'stop' should be positive values.")
 
         if (stop - start) * step < 0:
-            raise ValueError("The sign of input 'step' does not align with 'start' / 'stop' values.")
+            raise ValueError("The sign of 'step' does not align with 'start' / 'stop' values.")
 
         if start == stop:
             raise ValueError("Input 'start' and 'stop' must be different values.")

From 5f1d94a216e815f42dcaa1a126d5617066a13cc0 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 14:44:20 -0400
Subject: [PATCH 83/99] add helper func to replace docstring params

---
 specparam/core/modutils.py            | 39 ++++++++++++++++++++++++++-
 specparam/tests/core/test_modutils.py | 14 ++++++++++
 2 files changed, 52 insertions(+), 1 deletion(-)

diff --git a/specparam/core/modutils.py b/specparam/core/modutils.py
index 32044bfd..5748ad40 100644
--- a/specparam/core/modutils.py
+++ b/specparam/core/modutils.py
@@ -1,7 +1,8 @@
 """Utility functions & decorators for the module."""
 
-from importlib import import_module
+from copy import deepcopy
 from functools import wraps
+from importlib import import_module
 
 ###################################################################################################
 ###################################################################################################
@@ -138,6 +139,42 @@ def docs_drop_param(docstring):
     return front + back
 
 
+def docs_replace_param(docstring, replace, new_param):
+    """Replace a parameter description in a docstring.
+
+    Parameters
+    ----------
+    docstring : str
+        Docstring to replace parameter description within.
+    replace : str
+        The name of the parameter to switch out.
+    new_param : str
+        The new parameter description to replace into the docstring.
+        This should be a string structured to be copied directly into the docstring.
+
+    Returns
+    -------
+    new_docstring : str
+        Update docstring, with parameter switched out.
+    """
+
+    # Take a copy to make sure to avoid any potential aliasing
+    docstring = deepcopy(docstring)
+
+    # Find the index where the param to replace is
+    p_ind = docstring.find(replace)
+
+    # Find the second newline (end of to-replace param)
+    ti = docstring[p_ind:].find('\n')
+    n_ind = docstring[p_ind + ti + 1:].find('\n')
+    end_ind = p_ind + ti + 1 + n_ind
+
+    # Reconstitute docstring, replacing specified parameter
+    new_docstring = docstring[:p_ind] + new_param + docstring[end_ind:]
+
+    return new_docstring
+
+
 def docs_append_to_section(docstring, section, add):
     """Append extra information to a specified section of a docstring.
 
diff --git a/specparam/tests/core/test_modutils.py b/specparam/tests/core/test_modutils.py
index d0f03025..90d287d4 100644
--- a/specparam/tests/core/test_modutils.py
+++ b/specparam/tests/core/test_modutils.py
@@ -39,6 +39,20 @@ def test_docs_drop_param(tdocstring):
     assert 'first' not in out
     assert 'second' in out
 
+def test_docs_replace_param(tdocstring):
+
+    new_param = 'updated : other\n        This description has been dropped in.'
+
+    ndocstring = docs_replace_param(tdocstring, 'first', new_param)
+    assert 'updated' in ndocstring
+    assert 'first' not in ndocstring
+    assert 'second' in ndocstring
+
+    ndocstring = docs_replace_param(tdocstring, 'second', new_param)
+    assert 'updated' in ndocstring
+    assert 'first' in ndocstring
+    assert 'second' not in ndocstring
+
 def test_docs_append_to_section(tdocstring):
 
     section = 'Parameters'

From 4f53829012ea60ed65dfa53d164462fad091d0de Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 14:54:13 -0400
Subject: [PATCH 84/99] finish lint: use docs updates & other small fixes

---
 specparam/objs/event.py               |  5 +----
 specparam/sim/sim.py                  | 10 +++++++---
 specparam/tests/core/test_modutils.py | 18 +++++++++---------
 3 files changed, 17 insertions(+), 16 deletions(-)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index 80044ed7..a10d8208 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -226,9 +226,6 @@ def fit(self, freqs=None, spectrograms=None, freq_range=None, peak_org=None,
         Data is optional, if data has already been added to the object.
         """
 
-        # ToDo: here because of circular import - updates / refactors should fix & move
-        #from specparam.objs.group import _progress
-
         if spectrograms is not None:
             self.add_data(freqs, spectrograms, freq_range)
 
@@ -274,7 +271,7 @@ def drop(self, drop_inds=None, window_inds=None):
         null_model = SpectralModel(*self.get_settings()).get_results()
 
         drop_inds = drop_inds if isinstance(drop_inds, dict) else \
-            {eind : winds for eind, winds in zip(check_inds(drop_inds), repeat(window_inds))}
+            dict(zip(check_inds(drop_inds), repeat(window_inds)))
 
         for eind, winds in drop_inds.items():
 
diff --git a/specparam/sim/sim.py b/specparam/sim/sim.py
index ab7886bc..ff01cb8b 100644
--- a/specparam/sim/sim.py
+++ b/specparam/sim/sim.py
@@ -3,7 +3,8 @@
 import numpy as np
 
 from specparam.core.utils import check_iter, check_flat
-from specparam.core.modutils import docs_get_section, replace_docstring_sections
+from specparam.core.modutils import (docs_get_section, replace_docstring_sections,
+                                     docs_replace_param)
 from specparam.sim.params import collect_sim_params
 from specparam.sim.gen import gen_freqs, gen_power_vals, gen_rotated_power_vals
 from specparam.sim.transform import compute_rotation_offset
@@ -259,8 +260,11 @@ def sim_group_power_spectra(n_spectra, freq_range, aperiodic_params, periodic_pa
     else:
         return freqs, powers
 
-# ToDo: need an update to docstring to replace `n_spectra` with `n_windows`
-@replace_docstring_sections(docs_get_section(sim_group_power_spectra.__doc__, 'Parameters'))
+
+@replace_docstring_sections(\
+    docs_replace_param(docs_get_section(\
+        sim_group_power_spectra.__doc__, 'Parameters'),
+        'n_spectra', 'n_windows : int\n        The number of time windows to generate.'))
 def sim_spectrogram(n_windows, freq_range, aperiodic_params, periodic_params,
                     nlvs=0.005, freq_res=0.5, f_rotation=None, return_params=False):
     """Simulate spectrogram.
diff --git a/specparam/tests/core/test_modutils.py b/specparam/tests/core/test_modutils.py
index 90d287d4..8cd683a4 100644
--- a/specparam/tests/core/test_modutils.py
+++ b/specparam/tests/core/test_modutils.py
@@ -43,15 +43,15 @@ def test_docs_replace_param(tdocstring):
 
     new_param = 'updated : other\n        This description has been dropped in.'
 
-    ndocstring = docs_replace_param(tdocstring, 'first', new_param)
-    assert 'updated' in ndocstring
-    assert 'first' not in ndocstring
-    assert 'second' in ndocstring
-
-    ndocstring = docs_replace_param(tdocstring, 'second', new_param)
-    assert 'updated' in ndocstring
-    assert 'first' in ndocstring
-    assert 'second' not in ndocstring
+    ndocstring1 = docs_replace_param(tdocstring, 'first', new_param)
+    assert 'updated' in ndocstring1
+    assert 'first' not in ndocstring1
+    assert 'second' in ndocstring1
+
+    ndocstring2 = docs_replace_param(tdocstring, 'second', new_param)
+    assert 'updated' in ndocstring2
+    assert 'first' in ndocstring2
+    assert 'second' not in ndocstring2
 
 def test_docs_append_to_section(tdocstring):
 

From 3c049ffde180144e808ba6d876216fa10f22063e Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 15:55:05 -0400
Subject: [PATCH 85/99] small fix to periodic tests

---
 specparam/objs/event.py                   | 4 +++-
 specparam/tests/analysis/test_periodic.py | 4 ++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index a10d8208..92d6e6bf 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -325,8 +325,9 @@ def get_group(self, event_inds, window_inds, output_type='event'):
 
         Parameters
         ----------
-        event_inds, window_inds : array_like of int or array_like of bool
+        event_inds, window_inds : array_like of int or array_like of bool or None
             Indices to extract from the object, for event and time windows.
+            If None, selects all available indices.
         output_type : {'time', 'group'}, optional
             Type of model object to extract:
                 'event' : SpectralTimeEventObject
@@ -384,6 +385,7 @@ def get_group(self, event_inds, window_inds, output_type='event'):
 
         return output
 
+
     def print_results(self, concise=False):
         """Print out SpectralTimeEventModel results.
 
diff --git a/specparam/tests/analysis/test_periodic.py b/specparam/tests/analysis/test_periodic.py
index 549017c1..6477befa 100644
--- a/specparam/tests/analysis/test_periodic.py
+++ b/specparam/tests/analysis/test_periodic.py
@@ -15,7 +15,7 @@ def test_get_band_peak_group(tfg):
 
     assert np.all(get_band_peak_group(tfg, (8, 12)))
 
-def test_get_band_peak_group():
+def test_get_band_peak_group_arr():
 
     data = np.array([[10, 1, 1.8, 0], [13, 1, 2, 2], [14, 2, 4, 2]])
 
@@ -27,7 +27,7 @@ def test_get_band_peak_group():
     assert out2.shape == (3, 3)
     assert np.array_equal(out2[2, :], [14, 2, 4])
 
-def test_get_band_peak():
+def test_get_band_peak_arr():
 
     data = np.array([[10, 1, 1.8], [14, 2, 4]])
 

From 34db090ea2799edd0d73874b35de6fe48b3ffbd2 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 16:01:38 -0400
Subject: [PATCH 86/99] add get_band_peak_event function

---
 doc/api.rst                               |  1 +
 specparam/analysis/periodic.py            | 38 +++++++++++++++++++++--
 specparam/tests/analysis/test_periodic.py |  7 ++++-
 3 files changed, 43 insertions(+), 3 deletions(-)

diff --git a/doc/api.rst b/doc/api.rst
index b32934d0..cf616acf 100644
--- a/doc/api.rst
+++ b/doc/api.rst
@@ -166,6 +166,7 @@ The following functions take in model objects directly, which is the typical use
 
     get_band_peak
     get_band_peak_group
+    get_band_peak_event
 
 **Array Inputs**
 
diff --git a/specparam/analysis/periodic.py b/specparam/analysis/periodic.py
index fab46d58..e2f40c9b 100644
--- a/specparam/analysis/periodic.py
+++ b/specparam/analysis/periodic.py
@@ -30,7 +30,7 @@ def get_band_peak(model, band, select_highest=True, threshold=None,
 
     Returns
     -------
-    1d or 2d array
+    peaks : 1d or 2d array
         Peak data. Each row is a peak, as [CF, PW, BW].
 
     Examples
@@ -67,7 +67,7 @@ def get_band_peak_group(group, band, threshold=None, thresh_param='PW', attribut
 
     Returns
     -------
-    2d array
+    peaks : 2d array
         Peak data. Each row is a peak, as [CF, PW, BW].
         Each row represents an individual model from the input object.
 
@@ -101,6 +101,40 @@ def get_band_peak_group(group, band, threshold=None, thresh_param='PW', attribut
                                    threshold, thresh_param)
 
 
+def get_band_peak_event(event, band, threshold=None, thresh_param='PW', attribute='peak_params'):
+    """Extract peaks from a band of interest from an event model object.
+
+    Parameters
+    ----------
+    event : SpectralTimeEventModel
+        Object to extract peak data from.
+    band : tuple of (float, float)
+        Frequency range for the band of interest.
+        Defined as: (lower_frequency_bound, upper_frequency_bound).
+    select_highest : bool, optional, default: True
+        Whether to return single peak (if True) or all peaks within the range found (if False).
+        If True, returns the highest power peak within the search range.
+    threshold : float, optional
+        A minimum threshold value to apply.
+    thresh_param : {'PW', 'BW'}
+        Which parameter to threshold on. 'PW' is power and 'BW' is bandwidth.
+    attribute : {'peak_params', 'gaussian_params'}
+        Which attribute of peak data to extract data from.
+
+    Returns
+    -------
+    peaks : 3d array
+        Array of peak data, organized as [n_events, n_time_windows, n_peak_params].
+    """
+
+    peaks = np.zeros([event.n_events, event.n_time_windows, 3])
+    for ind in range(event.n_events):
+        peaks[ind, :, :] = get_band_peak_group(\
+            event.get_group(ind, None, 'group'), band, threshold, thresh_param, attribute)
+
+    return peaks
+
+
 def get_band_peak_group_arr(peak_params, band, n_fits, threshold=None, thresh_param='PW'):
     """Extract peaks within a given band of interest, from peaks from a group fit.
 
diff --git a/specparam/tests/analysis/test_periodic.py b/specparam/tests/analysis/test_periodic.py
index 6477befa..843a55bd 100644
--- a/specparam/tests/analysis/test_periodic.py
+++ b/specparam/tests/analysis/test_periodic.py
@@ -11,9 +11,14 @@ def test_get_band_peak(tfm):
 
     assert np.all(get_band_peak(tfm, (8, 12)))
 
-def test_get_band_peak_group(tfg):
+def test_get_band_peak_group(tfg, tft):
 
     assert np.all(get_band_peak_group(tfg, (8, 12)))
+    assert np.all(get_band_peak_group(tft, (8, 12)))
+
+def test_get_band_peak_event(tfe):
+
+    assert np.all(get_band_peak_event(tfe, (8, 12)))
 
 def test_get_band_peak_group_arr():
 

From 682c4a29c4f169c9f0761fe97d36ae1e93209dbf Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 16:24:40 -0400
Subject: [PATCH 87/99] enforce consistent xlims on time & event param plots

---
 specparam/objs/time.py      | 7 +++++++
 specparam/plts/event.py     | 8 +++++---
 specparam/plts/templates.py | 5 ++++-
 specparam/plts/time.py      | 8 +++++---
 4 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index 98becc19..dddb3583 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -96,6 +96,13 @@ def n_peaks_(self):
             if self.has_model else None
 
 
+    @property
+    def n_time_windows(self):
+        """How many time windows are included in the model object."""
+
+        return self.spectrogram.shape[1] if self.has_data else 0
+
+
     def _reset_time_results(self):
         """Set, or reset, time results to be empty."""
 
diff --git a/specparam/plts/event.py b/specparam/plts/event.py
index 3e37c8ca..3800add1 100644
--- a/specparam/plts/event.py
+++ b/specparam/plts/event.py
@@ -54,12 +54,14 @@ def plot_event_model(event_model, **plot_kwargs):
                                figsize=plot_kwargs.pop('figsize', [10, 4 + 4 * n_bands]))
     axes = cycle(axes)
 
+    xlim = [0, time_model.n_time_windows]
+
     # 01: aperiodic params
     alabels = ['offset', 'knee', 'exponent'] if has_knee else ['offset', 'exponent']
     for alabel in alabels:
         plot_param_over_time_yshade(\
             None, event_model.event_time_results[alabel],
-            label=alabel, drop_xticks=True, add_xlabel=False,
+            label=alabel, drop_xticks=True, add_xlabel=False, xlim=xlim,
             title='Aperiodic Parameters' if alabel == 'offset' else None,
             color=PARAM_COLORS[alabel], ax=next(axes))
     next(axes).axis('off')
@@ -69,7 +71,7 @@ def plot_event_model(event_model, **plot_kwargs):
         for plabel in ['cf', 'pw', 'bw']:
             plot_param_over_time_yshade(\
                 None, event_model.event_time_results[pe_labels[plabel][band_ind]],
-                label=plabel.upper(), drop_xticks=True, add_xlabel=False,
+                label=plabel.upper(), drop_xticks=True, add_xlabel=False, xlim=xlim,
                 title='Periodic Parameters - ' + band_labels[band_ind] if plabel == 'cf' else None,
                 color=PARAM_COLORS[plabel], ax=next(axes))
         next(axes).axis('off')
@@ -81,4 +83,4 @@ def plot_event_model(event_model, **plot_kwargs):
             drop_xticks=False if glabel == 'r_squared' else True,
             add_xlabel=True if glabel == 'r_squared' else False,
             title='Goodness of Fit' if glabel == 'error' else None,
-            color=PARAM_COLORS[glabel], ax=next(axes))
+            color=PARAM_COLORS[glabel],  xlim=xlim, ax=next(axes))
diff --git a/specparam/plts/templates.py b/specparam/plts/templates.py
index 80024871..1c850280 100644
--- a/specparam/plts/templates.py
+++ b/specparam/plts/templates.py
@@ -190,7 +190,7 @@ def plot_yshade(x_vals, y_vals, average='mean', shade='std', scale=1., color=Non
 
 @check_dependency(plt, 'matplotlib')
 def plot_param_over_time(times, param, label=None, title=None, add_legend=True, add_xlabel=True,
-                         drop_xticks=False, ax=None, **plot_kwargs):
+                         xlim=None, drop_xticks=False, ax=None, **plot_kwargs):
     """Plot a parameter over time.
 
     Parameters
@@ -228,6 +228,9 @@ def plot_param_over_time(times, param, label=None, title=None, add_legend=True,
     if drop_xticks:
         ax.set_xticks([], [])
 
+    if xlim:
+        ax.set_xlim(xlim)
+
     if label and add_legend:
         ax.legend(loc='upper left', framealpha=plot_kwargs.pop('legend_framealpha', 0.9))
 
diff --git a/specparam/plts/time.py b/specparam/plts/time.py
index d507f421..84523d45 100644
--- a/specparam/plts/time.py
+++ b/specparam/plts/time.py
@@ -52,6 +52,8 @@ def plot_time_model(time_model, **plot_kwargs):
                                figsize=plot_kwargs.pop('figsize', [10, 4 + 2 * n_bands]))
     axes = cycle(axes)
 
+    xlim = [0, time_model.n_time_windows]
+
     # 01: aperiodic parameters
     ap_params = [time_model.time_results['offset'],
                  time_model.time_results['exponent']]
@@ -63,7 +65,7 @@ def plot_time_model(time_model, **plot_kwargs):
         ap_labels.insert(1, 'Knee')
         ap_colors.insert(1, PARAM_COLORS['knee'])
 
-    plot_params_over_time(None, ap_params, labels=ap_labels, add_xlabel=False,
+    plot_params_over_time(None, ap_params, labels=ap_labels, add_xlabel=False, xlim=xlim,
                           colors=ap_colors, title='Aperiodic Parameters', ax=next(axes))
 
     # 02: periodic parameters
@@ -73,7 +75,7 @@ def plot_time_model(time_model, **plot_kwargs):
             [time_model.time_results[pe_labels['cf'][band_ind]],
              time_model.time_results[pe_labels['pw'][band_ind]],
              time_model.time_results[pe_labels['bw'][band_ind]]],
-            labels=['CF', 'PW', 'BW'], add_xlabel=False,
+            labels=['CF', 'PW', 'BW'], add_xlabel=False, xlim=xlim,
             colors=[PARAM_COLORS['cf'], PARAM_COLORS['pw'], PARAM_COLORS['bw']],
             title='Periodic Parameters - ' + band_labels[band_ind], ax=next(axes))
 
@@ -81,6 +83,6 @@ def plot_time_model(time_model, **plot_kwargs):
     plot_params_over_time(None,
                           [time_model.time_results['error'],
                            time_model.time_results['r_squared']],
-                          labels=['Error', 'R-squared'],
+                          labels=['Error', 'R-squared'], xlim=xlim,
                           colors=[PARAM_COLORS['error'], PARAM_COLORS['r_squared']],
                           title='Goodness of Fit', ax=next(axes))

From 2698f8f8e3950d5e559363954bf836a308f489bf Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 16:32:52 -0400
Subject: [PATCH 88/99] update event plots to plot even with nans

---
 specparam/plts/event.py     | 2 +-
 specparam/plts/templates.py | 2 +-
 specparam/utils/data.py     | 4 ++++
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/specparam/plts/event.py b/specparam/plts/event.py
index 3800add1..8d650851 100644
--- a/specparam/plts/event.py
+++ b/specparam/plts/event.py
@@ -54,7 +54,7 @@ def plot_event_model(event_model, **plot_kwargs):
                                figsize=plot_kwargs.pop('figsize', [10, 4 + 4 * n_bands]))
     axes = cycle(axes)
 
-    xlim = [0, time_model.n_time_windows]
+    xlim = [0, event_model.n_time_windows]
 
     # 01: aperiodic params
     alabels = ['offset', 'knee', 'exponent'] if has_knee else ['offset', 'exponent']
diff --git a/specparam/plts/templates.py b/specparam/plts/templates.py
index 1c850280..d34932c1 100644
--- a/specparam/plts/templates.py
+++ b/specparam/plts/templates.py
@@ -289,7 +289,7 @@ def plot_params_over_time(times, params, labels=None, title=None, colors=None,
 
 
 @check_dependency(plt, 'matplotlib')
-def plot_param_over_time_yshade(times, param, average='mean', shade='std', scale=1.,
+def plot_param_over_time_yshade(times, param, average='nanmean', shade='nanstd', scale=1.,
                                 color=None, ax=None, **plot_kwargs):
     """Plot parameter over time with y-axis shading.
 
diff --git a/specparam/utils/data.py b/specparam/utils/data.py
index 19880a53..5e7affe4 100644
--- a/specparam/utils/data.py
+++ b/specparam/utils/data.py
@@ -15,11 +15,15 @@
 AVG_FUNCS = {
     'mean' : np.mean,
     'median' : np.median,
+    'nanmean' : np.nanmean,
+    'nanmedian' : np.nanmedian,
 }
 
 DISPERSION_FUNCS = {
     'var' : np.var,
+    'nanvar' : np.nanvar,
     'std' : np.std,
+    'nanstd' : np.nanstd,
     'sem' : sem,
 }
 

From 21a18486d63788900fda33ac8ca08ead806dfef4 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 17:10:13 -0400
Subject: [PATCH 89/99] add compute_presence helper function

---
 specparam/tests/utils/test_data.py | 17 +++++++++++++
 specparam/utils/data.py            | 40 ++++++++++++++++++++++++++++++
 2 files changed, 57 insertions(+)

diff --git a/specparam/tests/utils/test_data.py b/specparam/tests/utils/test_data.py
index 9284d9fb..23206f1b 100644
--- a/specparam/tests/utils/test_data.py
+++ b/specparam/tests/utils/test_data.py
@@ -48,6 +48,23 @@ def _dispersion_callable(data):
     assert isinstance(out4, np.ndarray)
     assert np.array_equal(out4, out2)
 
+def test_compute_presence():
+
+    data1_full = np.array([0, 1, 2, 3, 4])
+    data1_nan = np.array([0, np.nan, 2, 3, np.nan])
+    assert compute_presence(data1_full) == 1.0
+    assert compute_presence(data1_nan) == 0.6
+    assert compute_presence(data1_nan, output='percent') == 60.0
+
+    data2_full = np.array([[0, 1, 2, 3, 4], [5, 6, 7, 8, 9]])
+    data2_nan = np.array([[0, np.nan, 2, 3, np.nan], [np.nan, 6, 7, 8, np.nan]])
+    assert np.array_equal(compute_presence(data2_full), np.array([1.0, 1.0, 1.0, 1.0, 1.0]))
+    assert np.array_equal(compute_presence(data2_nan), np.array([0.5, 0.5, 1.0, 1.0, 0.0]))
+    assert np.array_equal(compute_presence(data2_nan, output='percent'),
+                          np.array([50.0, 50.0, 100.0, 100.0, 0.0]))
+    assert compute_presence(data2_full, average=True) == 1.0
+    assert compute_presence(data2_nan, average=True) == 0.6
+
 def test_trim_spectrum():
 
     f_in = np.array([0., 1., 2., 3., 4., 5.])
diff --git a/specparam/utils/data.py b/specparam/utils/data.py
index 5e7affe4..181bab0f 100644
--- a/specparam/utils/data.py
+++ b/specparam/utils/data.py
@@ -84,6 +84,46 @@ def compute_dispersion(data, dispersion='std'):
     return dispersion_data
 
 
+def compute_presence(data, average=False, output='ratio'):
+    """Compute data presence (as number of non-NaN values) from an array of data.
+
+    Parameters
+    ----------
+    data : 1d or 2d array
+        Data array to check presence of.
+    average : bool, optional, default: False
+        Whether to average across . Only used for 2d array inputs.
+        If False, for 2d array, the output is an array matching the length of the 0th dimension of the input.
+        If True, for 2d arrays, the output is a single value averaged across the whole array.
+    output : {'ratio', 'percent'}
+        Representation for the output:
+            'ratio' - ratio value, between 0.0, 1.0.
+            'percent' - percent value, betweeon 0-100%.
+
+    Returns
+    -------
+    presence : float or array of float
+        The computed presence in the given array.
+    """
+
+    assert output in ['ratio', 'percent'], 'Setting for output type not understood.'
+
+    if data.ndim == 1:
+        presence = sum(~np.isnan(data)) / len(data)
+
+    elif data.ndim == 2:
+        if average:
+            presence = compute_presence(data.flatten())
+        else:
+            n_events, n_windows = data.shape
+            presence = np.sum(~np.isnan(data), 0) / (np.ones(n_windows) * n_events)
+
+    if output == 'percent':
+        presence *= 100
+
+    return presence
+
+
 def trim_spectrum(freqs, power_spectra, f_range):
     """Extract a frequency range from power spectra.
 

From 0858a6c88d333e62946535ef482628fc32457f8e Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 17:20:03 -0400
Subject: [PATCH 90/99] refactor compute_presence

---
 specparam/core/strings.py |  1 +
 specparam/utils/data.py   | 10 +++-------
 2 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/specparam/core/strings.py b/specparam/core/strings.py
index 01962822..8d2e8d21 100644
--- a/specparam/core/strings.py
+++ b/specparam/core/strings.py
@@ -4,6 +4,7 @@
 
 from specparam.core.errors import NoModelError
 from specparam.data.utils import get_periodic_labels
+from specparam.utils.data import compute_presence
 from specparam.version import __version__ as MODULE_VERSION
 
 ###################################################################################################
diff --git a/specparam/utils/data.py b/specparam/utils/data.py
index 181bab0f..b7759896 100644
--- a/specparam/utils/data.py
+++ b/specparam/utils/data.py
@@ -108,15 +108,11 @@ def compute_presence(data, average=False, output='ratio'):
 
     assert output in ['ratio', 'percent'], 'Setting for output type not understood.'
 
-    if data.ndim == 1:
-        presence = sum(~np.isnan(data)) / len(data)
+    if data.ndim == 1 or average:
+        presence = np.sum(~np.isnan(data)) / data.size
 
     elif data.ndim == 2:
-        if average:
-            presence = compute_presence(data.flatten())
-        else:
-            n_events, n_windows = data.shape
-            presence = np.sum(~np.isnan(data), 0) / (np.ones(n_windows) * n_events)
+        presence = np.sum(~np.isnan(data), 0) / (np.ones(data.shape[1]) * data.shape[0])
 
     if output == 'percent':
         presence *= 100

From 6e641a415c6d046e4b22b27e93536a3babec0c56 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 19:39:35 -0400
Subject: [PATCH 91/99] add compute_arr_desc

---
 specparam/tests/utils/test_data.py | 12 ++++++++++++
 specparam/utils/data.py            | 25 +++++++++++++++++++++++++
 2 files changed, 37 insertions(+)

diff --git a/specparam/tests/utils/test_data.py b/specparam/tests/utils/test_data.py
index 23206f1b..860d7f5a 100644
--- a/specparam/tests/utils/test_data.py
+++ b/specparam/tests/utils/test_data.py
@@ -65,6 +65,18 @@ def test_compute_presence():
     assert compute_presence(data2_full, average=True) == 1.0
     assert compute_presence(data2_nan, average=True) == 0.6
 
+def test_compute_arr_desc():
+
+    data1_full = np.array([1., 2., 3., 4., 5.])
+    minv, maxv, meanv = compute_arr_desc(data1_full)
+    for val in [minv, maxv, meanv]:
+        assert isinstance(val, float)
+
+    data1_nan = np.array([np.nan, 2., 3., np.nan, 5.])
+    minv, maxv, meanv = compute_arr_desc(data1_nan)
+    for val in [minv, maxv, meanv]:
+        assert isinstance(val, float)
+
 def test_trim_spectrum():
 
     f_in = np.array([0., 1., 2., 3., 4., 5.])
diff --git a/specparam/utils/data.py b/specparam/utils/data.py
index b7759896..097780ec 100644
--- a/specparam/utils/data.py
+++ b/specparam/utils/data.py
@@ -120,6 +120,31 @@ def compute_presence(data, average=False, output='ratio'):
     return presence
 
 
+def compute_arr_desc(data):
+    """Compute descriptive measures of an array of data.
+
+    Parameters
+    ----------
+    data : array
+        Array of numeric data.
+
+    Returns
+    -------
+    min_val : float
+        Minimum value of the array.
+    max_val : float
+        Maximum value of the array.
+    mean_val : float
+        Mean value of the array.
+    """
+
+    min_val = np.nanmin(data)
+    max_val = np.nanmax(data)
+    mean_val = np.nanmean(data)
+
+    return min_val, max_val, mean_val
+
+
 def trim_spectrum(freqs, power_spectra, f_range):
     """Extract a frequency range from power spectra.
 

From 626479f6e4623ab35a2e3085c3498b0febf10766 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 19:51:45 -0400
Subject: [PATCH 92/99] update string gen with new helpers

---
 specparam/core/strings.py | 55 ++++++++++++++-------------------------
 1 file changed, 19 insertions(+), 36 deletions(-)

diff --git a/specparam/core/strings.py b/specparam/core/strings.py
index 8d2e8d21..0cd3dc64 100644
--- a/specparam/core/strings.py
+++ b/specparam/core/strings.py
@@ -4,7 +4,7 @@
 
 from specparam.core.errors import NoModelError
 from specparam.data.utils import get_periodic_labels
-from specparam.utils.data import compute_presence
+from specparam.utils.data import compute_arr_desc, compute_presence
 from specparam.version import __version__ as MODULE_VERSION
 
 ###################################################################################################
@@ -384,10 +384,10 @@ def gen_group_results_str(group, concise=False):
         '',
         'Aperiodic Fit Values:',
         *[el for el in ['    Knees - Min: {:6.2f}, Max: {:6.2f}, Mean: {:5.2f}'
-                        .format(np.nanmin(kns), np.nanmax(kns), np.nanmean(kns)),
+                        .format(*compute_arr_desc(kns)),
                        ] if group.aperiodic_mode == 'knee'],
         'Exponents - Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
-        .format(np.nanmin(exps), np.nanmax(exps), np.nanmean(exps)),
+        .format(*compute_arr_desc(exps)),
         '',
 
         # Peak Parameters
@@ -398,9 +398,9 @@ def gen_group_results_str(group, concise=False):
         # Goodness if fit
         'Goodness of fit metrics:',
         '   R2s -  Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
-        .format(np.nanmin(r2s), np.nanmax(r2s), np.nanmean(r2s)),
+        .format(*compute_arr_desc(r2s)),
         'Errors -  Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
-        .format(np.nanmin(errors), np.nanmax(errors), np.nanmean(errors)),
+        .format(*compute_arr_desc(errors)),
         '',
 
         # Footer
@@ -469,14 +469,11 @@ def gen_time_results_str(time_model, concise=False):
         '',
         'Aperiodic Fit Values:',
         *[el for el in ['    Knees - Min: {:6.2f}, Max: {:6.2f}, Mean: {:6.2f}'
-                        .format(np.nanmin(time_model.time_results['knee'] if has_knee else 0),
-                                np.nanmax(time_model.time_results['knee'] if has_knee else 0),
-                                np.nanmean(time_model.time_results['knee'] if has_knee else 0)),
+                        .format(*compute_arr_desc(time_model.time_results['knee']) \
+                            if has_knee else [0, 0, 0]),
                        ] if has_knee],
         'Exponents - Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
-        .format(np.nanmin(time_model.time_results['exponent']),
-                np.nanmax(time_model.time_results['exponent']),
-                np.nanmean(time_model.time_results['exponent'])),
+        .format(*compute_arr_desc(time_model.time_results['exponent'])),
         '',
 
         # Periodic parameters
@@ -486,21 +483,16 @@ def gen_time_results_str(time_model, concise=False):
             np.nanmean(time_model.time_results[pe_labels['cf'][ind]]),
             np.nanmean(time_model.time_results[pe_labels['pw'][ind]]),
             np.nanmean(time_model.time_results[pe_labels['bw'][ind]]),
-            100 * sum(~np.isnan(time_model.time_results[pe_labels['cf'][ind]])) \
-                / len(time_model.time_results[pe_labels['cf'][ind]])) \
+            compute_presence(time_model.time_results[pe_labels['cf'][ind]]))
                 for ind, label in enumerate(band_labels)],
         '',
 
         # Goodness if fit
         'Goodness of fit (mean values across windows):',
         '   R2s -  Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
-        .format(np.nanmin(time_model.time_results['r_squared']),
-                np.nanmax(time_model.time_results['r_squared']),
-                np.nanmean(time_model.time_results['r_squared'])),
+        .format(*compute_arr_desc(time_model.time_results['r_squared'])),
         'Errors -  Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
-        .format(np.nanmin(time_model.time_results['error']),
-                np.nanmax(time_model.time_results['error']),
-                np.nanmean(time_model.time_results['error'])),
+        .format(*compute_arr_desc(time_model.time_results['error'])),
         '',
 
         # Footer
@@ -567,17 +559,11 @@ def gen_event_results_str(event_model, concise=False):
         '',
         'Aperiodic params (values across events):',
         *[el for el in ['    Knees - Min: {:6.2f}, Max: {:6.2f}, Mean: {:6.2f}'
-                        .format(np.nanmin(np.mean(event_model.event_time_results['knee'], 1) \
-                                    if has_knee else 0),
-                                np.nanmax(np.mean(event_model.event_time_results['knee'], 1) \
-                                    if has_knee else 0),
-                                np.nanmean(np.mean(event_model.event_time_results['knee'], 1) \
-                                    if has_knee else 0)),
+                        .format(*compute_arr_desc(np.mean(event_model.event_time_results['knee'], 1) \
+                            if has_knee else [0, 0, 0])),
                        ] if has_knee],
         'Exponents - Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
-        .format(np.nanmin(np.mean(event_model.event_time_results['exponent'], 1)),
-                np.nanmax(np.mean(event_model.event_time_results['exponent'], 1)),
-                np.nanmean(np.mean(event_model.event_time_results['exponent'], 1))),
+        .format(*compute_arr_desc(np.mean(event_model.event_time_results['exponent'], 1))),
         '',
 
         # Periodic parameters
@@ -587,21 +573,18 @@ def gen_event_results_str(event_model, concise=False):
             np.nanmean(event_model.event_time_results[pe_labels['cf'][ind]]),
             np.nanmean(event_model.event_time_results[pe_labels['pw'][ind]]),
             np.nanmean(event_model.event_time_results[pe_labels['bw'][ind]]),
-            100 * sum(sum(~np.isnan(event_model.event_time_results[pe_labels['cf'][ind]]))) \
-                / event_model.event_time_results[pe_labels['cf'][ind]].size)
+            compute_presence(event_model.event_time_results[pe_labels['cf'][ind]],
+                             average=True, output='percent'))
                 for ind, label in enumerate(band_labels)],
         '',
 
         # Goodness if fit
         'Goodness of fit (values across events):',
         '   R2s -  Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
-        .format(np.nanmin(np.mean(event_model.event_time_results['r_squared'], 1)),
-                np.nanmax(np.mean(event_model.event_time_results['r_squared'], 1)),
-                np.nanmean(np.mean(event_model.event_time_results['r_squared'], 1))),
+        .format(*compute_arr_desc(np.mean(event_model.event_time_results['r_squared'], 1))),
+
         'Errors -  Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
-        .format(np.nanmin(np.mean(event_model.event_time_results['error'], 1)),
-                np.nanmax(np.mean(event_model.event_time_results['error'], 1)),
-                np.nanmean(np.mean(event_model.event_time_results['error'], 1))),
+        .format(*compute_arr_desc(np.mean(event_model.event_time_results['error'], 1))),
         '',
 
         # Footer

From e5161d0ea525c41e2cf8e8ab31ebd7b0a763e43b Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 19:54:05 -0400
Subject: [PATCH 93/99] tweak plots

---
 specparam/objs/time.py  | 1 +
 specparam/plts/event.py | 2 +-
 specparam/plts/time.py  | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/specparam/objs/time.py b/specparam/objs/time.py
index dddb3583..5d7da71a 100644
--- a/specparam/objs/time.py
+++ b/specparam/objs/time.py
@@ -33,6 +33,7 @@ def decorated(*args, **kwargs):
 
     return decorated
 
+
 @replace_docstring_sections([docs_get_section(SpectralModel.__doc__, 'Parameters'),
                              docs_get_section(SpectralModel.__doc__, 'Notes')])
 class SpectralTimeModel(SpectralGroupModel):
diff --git a/specparam/plts/event.py b/specparam/plts/event.py
index 8d650851..756ed948 100644
--- a/specparam/plts/event.py
+++ b/specparam/plts/event.py
@@ -54,7 +54,7 @@ def plot_event_model(event_model, **plot_kwargs):
                                figsize=plot_kwargs.pop('figsize', [10, 4 + 4 * n_bands]))
     axes = cycle(axes)
 
-    xlim = [0, event_model.n_time_windows]
+    xlim = [0, event_model.n_time_windows - 1]
 
     # 01: aperiodic params
     alabels = ['offset', 'knee', 'exponent'] if has_knee else ['offset', 'exponent']
diff --git a/specparam/plts/time.py b/specparam/plts/time.py
index 84523d45..a3b9b8ac 100644
--- a/specparam/plts/time.py
+++ b/specparam/plts/time.py
@@ -52,7 +52,7 @@ def plot_time_model(time_model, **plot_kwargs):
                                figsize=plot_kwargs.pop('figsize', [10, 4 + 2 * n_bands]))
     axes = cycle(axes)
 
-    xlim = [0, time_model.n_time_windows]
+    xlim = [0, time_model.n_time_windows - 1]
 
     # 01: aperiodic parameters
     ap_params = [time_model.time_results['offset'],

From b6de61258656d2e6be5f68151f7308b5bbf66154 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 20:05:54 -0400
Subject: [PATCH 94/99] tweak printing in event object

---
 specparam/objs/event.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/specparam/objs/event.py b/specparam/objs/event.py
index 92d6e6bf..f599d69f 100644
--- a/specparam/objs/event.py
+++ b/specparam/objs/event.py
@@ -229,6 +229,11 @@ def fit(self, freqs=None, spectrograms=None, freq_range=None, peak_org=None,
         if spectrograms is not None:
             self.add_data(freqs, spectrograms, freq_range)
 
+        # If 'verbose', print out a marker of what is being run
+        if self.verbose and not progress:
+            print('Fitting model across {} events of {} windows.'.format(\
+                len(self.spectrograms), self.n_time_windows))
+
         if n_jobs == 1:
             self._reset_event_results(len(self.spectrograms))
             for ind, spectrogram in _progress(enumerate(self.spectrograms), progress, len(self)):
@@ -546,6 +551,17 @@ def convert_results(self, peak_org):
         self.event_time_results = event_group_to_dict(self.event_group_results, peak_org)
 
 
+    def _check_width_limits(self):
+        """Check and warn about bandwidth limits / frequency resolution interaction."""
+
+        # Only check & warn on first spectrogram
+        #   This is to avoid spamming standard output for every spectrogram in the set
+        if np.all(self.spectrograms[0] == self.spectrogram):
+        #if self.power_spectra[0, 0] == self.power_spectrum[0]:
+            super()._check_width_limits()
+
+
+
 def _par_fit(spectrogram, model):
     """Helper function for running in parallel."""
 

From 508c0ba6e565c9382a0a1fd9e6e2df9e379b535c Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 20:24:33 -0400
Subject: [PATCH 95/99] add presence plot to event plots / reports

---
 specparam/core/reports.py  |  6 +++---
 specparam/plts/event.py    | 11 ++++++++---
 specparam/plts/settings.py |  1 +
 3 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/specparam/core/reports.py b/specparam/core/reports.py
index 3ccf5548..c1bd8341 100644
--- a/specparam/core/reports.py
+++ b/specparam/core/reports.py
@@ -179,12 +179,12 @@ def save_event_report(event_model, file_name, file_path=None, add_settings=True)
     has_knee = 'knee' in event_model.event_time_results.keys()
 
     # Initialize figure, defining number of axes based on model + what is to be plotted
-    n_rows = 1 + (4 if has_knee else 3) + (n_bands * 4) + 2 + (1 if add_settings else 0)
+    n_rows = 1 + (4 if has_knee else 3) + (n_bands * 5) + 2 + (1 if add_settings else 0)
     height_ratios = [2.75] + [1] * (3 if has_knee else 2) + \
-        [0.25, 1, 1, 1] * n_bands + [0.25] + [1, 1] + ([1.5] if add_settings else [])
+        [0.25, 1, 1, 1, 1] * n_bands + [0.25] + [1, 1] + ([1.5] if add_settings else [])
     _, axes = plt.subplots(n_rows, 1,
                            gridspec_kw={'hspace' : 0.1, 'height_ratios' : height_ratios},
-                           figsize=(REPORT_FIGSIZE[0], REPORT_FIGSIZE[1] + 6))
+                           figsize=(REPORT_FIGSIZE[0], REPORT_FIGSIZE[1] + 7))
 
     # First / top: text results
     plot_text(gen_event_results_str(event_model), 0.5, 0.7, ax=axes[0])
diff --git a/specparam/plts/event.py b/specparam/plts/event.py
index 756ed948..1f7ec680 100644
--- a/specparam/plts/event.py
+++ b/specparam/plts/event.py
@@ -8,6 +8,7 @@
 from itertools import cycle
 
 from specparam.data.utils import get_periodic_labels, get_band_labels
+from specparam.utils.data import compute_presence
 from specparam.plts.utils import savefig
 from specparam.plts.templates import plot_param_over_time_yshade
 from specparam.plts.settings import PARAM_COLORS
@@ -45,13 +46,13 @@ def plot_event_model(event_model, **plot_kwargs):
     n_bands = len(pe_labels['cf'])
 
     has_knee = 'knee' in event_model.event_time_results.keys()
-    height_ratios = [1] * (3 if has_knee else 2) + [0.25, 1, 1, 1] * n_bands + [0.25] + [1, 1]
+    height_ratios = [1] * (3 if has_knee else 2) + [0.25, 1, 1, 1, 1] * n_bands + [0.25] + [1, 1]
 
     axes = plot_kwargs.pop('axes', None)
     if axes is None:
-        _, axes = plt.subplots((4 if has_knee else 3) + (n_bands * 4) + 2, 1,
+        _, axes = plt.subplots((4 if has_knee else 3) + (n_bands * 5) + 2, 1,
                                gridspec_kw={'hspace' : 0.1, 'height_ratios' : height_ratios},
-                               figsize=plot_kwargs.pop('figsize', [10, 4 + 4 * n_bands]))
+                               figsize=plot_kwargs.pop('figsize', [10, 4 + 5 * n_bands]))
     axes = cycle(axes)
 
     xlim = [0, event_model.n_time_windows - 1]
@@ -74,6 +75,10 @@ def plot_event_model(event_model, **plot_kwargs):
                 label=plabel.upper(), drop_xticks=True, add_xlabel=False, xlim=xlim,
                 title='Periodic Parameters - ' + band_labels[band_ind] if plabel == 'cf' else None,
                 color=PARAM_COLORS[plabel], ax=next(axes))
+        plot_param_over_time_yshade(\
+            None, compute_presence(event_model.event_time_results[pe_labels[plabel][band_ind]]),
+            label='Presence', drop_xticks=True, add_xlabel=False, xlim=xlim,
+            color=PARAM_COLORS['presence'], ax=next(axes))
         next(axes).axis('off')
 
     # 03: goodness of fit
diff --git a/specparam/plts/settings.py b/specparam/plts/settings.py
index 0473a48e..263a5bee 100644
--- a/specparam/plts/settings.py
+++ b/specparam/plts/settings.py
@@ -30,6 +30,7 @@
     'cf' : '#acc918',
     'pw' : '#28a103',
     'bw' : '#0fd197',
+    'presence' : '#095407',
     'error' : '#940000',
     'r_squared' : '#ab7171',
 }

From 0288fc45c59d5d740e223f6161987f4240f7655b Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 20:53:14 -0400
Subject: [PATCH 96/99] add time tutorial

---
 tutorials/plot_07-TimeModels.py | 187 ++++++++++++++++++++++++++++++++
 1 file changed, 187 insertions(+)
 create mode 100644 tutorials/plot_07-TimeModels.py

diff --git a/tutorials/plot_07-TimeModels.py b/tutorials/plot_07-TimeModels.py
new file mode 100644
index 00000000..dc7509d0
--- /dev/null
+++ b/tutorials/plot_07-TimeModels.py
@@ -0,0 +1,187 @@
+"""
+06: Fitting Models over Time
+============================
+
+Use extensions of the model object to fit power spectra across time.
+"""
+
+###################################################################################################
+
+# sphinx_gallery_thumbnail_number = 2
+
+# Import the time & event model objects
+from specparam import SpectralTimeModel, SpectralTimeEventModel
+
+# Import Bands object to manage oscillation band definitions
+from specparam import Bands
+
+# Import helper utilities for simulating and plotting spectrograms
+from specparam.sim import sim_spectrogram
+from specparam.plts.spectra import plot_spectrogram
+
+
+###################################################################################################
+# Parameterizing Spectrograms
+# ---------------------------
+#
+# So far we have seen how to use spectral models to fit individual power spectra, as well as
+# groups of power spectra. In this tutorial, we extent this to fitting groups of power
+# spectra that are organized across time / events.
+#
+# Specifically, here we cover the :class:`~specparam.SpectralTimeModel` and
+# :class:`~specparam.SpectralTimeEventModel` objects.
+#
+# Fitting Spectrograms
+# ~~~~~~~~~~~~~~~~~~~~
+#
+# For the goal of fitting power spectra that are organized across adjacent time windows,
+# we can consider that what we are really trying to do is to parameterize spectrograms.
+#
+# Let's start by simulating an example spectrogram, that we can then parameterize.
+#
+
+###################################################################################################
+
+# Create & plot an example spectrogram
+n_pre_post = 50
+freq_range = [3, 25]
+ap_params = [[1, 1.5]] * n_pre_post + [[1, 1]] * n_pre_post
+pe_params = [[10, 1.5, 2.5]] * n_pre_post + [[10, 0.5, 2.]] * n_pre_post
+freqs, spectrogram = sim_spectrogram(n_pre_post * 2, freq_range, ap_params, pe_params, nlvs=0.1)
+
+###################################################################################################
+
+# Plot our simulated spectrogram
+plot_spectrogram(freqs, spectrogram)
+
+###################################################################################################
+# SpectralTimeModel
+# -----------------
+#
+# The :class:`~specparam.SpectralTimeModel` object is an extension of the SpectralModel objects
+# to support parameterizing neural power spectra that are organized across time (spectrograms).
+#
+# In practice, this object is very similar to the previously introduced spectral model objects,
+# especially the Group model object. The time object is a mildly updated Group object.
+#
+# The main differences with the SpectralTimeModel from previous model objects are that the
+# data it accepts and parameterizes should be organized as as array of power spectra over
+# time windows - basically as a spectrogram.
+#
+
+###################################################################################################
+
+# Initialize a SpectralTimeModel model, which accepts all the same settings as SpectralModel
+ft = SpectralTimeModel()
+
+###################################################################################################
+# Defining Oscillation Bands
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~
+#
+# Before we start parameterizing power spectra we need to set up some guidance on how to
+# organize the results - most notably the peaks. Within the object, the Time model does fit
+# and store all the peaks it detects. However, without some definition of how to store and
+# visualize the peaks, the object cannot visualize the results across time.
+#
+# We can therefore use the :class:`~.Bands` object to define oscillation bands of interest.
+# By doing so, the Time model object will organize peaks based on these band definitions,
+# so we can plot, for example, alpha peaks across time windows.
+#
+
+###################################################################################################
+
+# Define a bands object to organize peak parameters
+bands = Bands({'alpha' : [7, 14]})
+
+###################################################################################################
+#
+# Now we are ready to fit our spectrogram! As with all model objects, we can fit the models
+# with the `fit` method, or fit, plot, and print with the `report` method.
+#
+
+###################################################################################################
+
+# Fit the spectrogram and print out report
+ft.report(freqs, spectrogram, peak_org=bands)
+
+###################################################################################################
+#
+# In the above, we can see that the Time object measures the same aperiodic and periodic
+# parameters as before, now organized and plotted across time windows.
+#
+
+###################################################################################################
+# Parameterizing Repeated Events
+# ------------------------------
+#
+# In the above, we parameterized a single spectrogram reflecting power spectra over time windows.
+#
+# We can also go one step further - parameterizing multiple spectrograms, with the same
+# time definition, which can be thought of as representing events (for example, examining
+# +/- 5 seconds around an event of interest, that happens multiple times.)
+#
+# To start, let's simulate multiple spectrograms, representing our different events.
+#
+
+###################################################################################################
+
+# Simulate a collection of spectrograms (across events)
+n_events = 3
+spectrograms = []
+for ind in range(n_events):
+    freqs, cur_spect = sim_spectrogram(n_pre_post * 2, freq_range, ap_params, pe_params, nlvs=0.1)
+    spectrograms.append(cur_spect)
+
+###################################################################################################
+
+# Plot the set of simulated spectrograms
+for cur_spect in spectrograms:
+    plot_spectrogram(freqs, cur_spect)
+
+###################################################################################################
+# SpectralTimeEventModel
+# ----------------------
+#
+# To parameterize events (multiple spectrograms) we can use the
+# :class:`~specparam.SpectralTimeEventModel` object.
+#
+# The Event is a further extension of the Time object, which can handle multiple spectrograms.
+# You can think of it as an object that manages a Time object for each spectrogram, and then
+# allows for collecting and examining the results across multiple events. Just like the Time
+# object, the Event object can take in a band definition to organize the peak results.
+#
+# The Event object has all the same attributes and methods as the previous model objects,
+# with the notably update that it accepts as data to parameterize a 3d array of spectrograms.
+#
+
+###################################################################################################
+
+# Initialize the spectral event model
+fe = SpectralTimeEventModel()
+
+###################################################################################################
+
+# Fit the spectrograms and print out report
+fe.report(freqs, spectrograms, peak_org=bands)
+
+###################################################################################################
+#
+# In the above, we can see that the Event object mimics the layout of the Time report, with
+# the update that since the data are now averaged across multiple event, each plot now represents
+# the average value of each parameter, shaded by it's standard deviation.
+#
+# When examining peaks across time and trials, there can also be a variable presence of if / when
+# peaks of a particular band are detected. To quantify this, the Event report also includes the
+# 'presence' plot, which reports on the % of events that have a detected peak for the given
+# band definition. Note that only time windows with a detected peak contribute to the
+# visualized data in the other periodic parameter plots.
+#
+
+###################################################################################################
+# Conclusion
+# ----------
+#
+# Now we have explored fitting power spectrum models and running these fits across time
+# windows, including across multiple events. Next we dig deeper into how to choose and tune
+# the algorithm settings, and how to troubleshoot if any of the fitting seems to go wrong.
+#

From c302af530326e57018ce3aad744bd000b8fd5279 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 20:53:24 -0400
Subject: [PATCH 97/99] fix import

---
 specparam/analysis/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/specparam/analysis/__init__.py b/specparam/analysis/__init__.py
index e72d40d1..d99b430c 100644
--- a/specparam/analysis/__init__.py
+++ b/specparam/analysis/__init__.py
@@ -1,4 +1,4 @@
 """Analysis sub-module for model parameters and related metrics."""
 
 from .error import compute_pointwise_error, compute_pointwise_error_group
-from .periodic import get_band_peak, get_band_peak_group
+from .periodic import get_band_peak, get_band_peak_group, get_band_peak_event

From 2fa0aca09143c8abaa677c618be3af7dce2b2ff9 Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 20:54:43 -0400
Subject: [PATCH 98/99] move tutorials for new addition

---
 tutorials/plot_06-GroupFits.py                                | 4 ++--
 ...{plot_07-TroubleShooting.py => plot_08-TroubleShooting.py} | 0
 ...{plot_08-FurtherAnalysis.py => plot_09-FurtherAnalysis.py} | 0
 tutorials/{plot_09-Reporting.py => plot_10-Reporting.py}      | 0
 4 files changed, 2 insertions(+), 2 deletions(-)
 rename tutorials/{plot_07-TroubleShooting.py => plot_08-TroubleShooting.py} (100%)
 rename tutorials/{plot_08-FurtherAnalysis.py => plot_09-FurtherAnalysis.py} (100%)
 rename tutorials/{plot_09-Reporting.py => plot_10-Reporting.py} (100%)

diff --git a/tutorials/plot_06-GroupFits.py b/tutorials/plot_06-GroupFits.py
index 31be0b6e..3d7d6fee 100644
--- a/tutorials/plot_06-GroupFits.py
+++ b/tutorials/plot_06-GroupFits.py
@@ -283,6 +283,6 @@
 # ----------
 #
 # Now we have explored fitting power spectrum models and running these fits across multiple
-# power spectra. Next we dig deeper into how to choose and tune the algorithm settings,
-# and how to troubleshoot if any of the fitting seems to go wrong.
+# power spectra. Next we will explore how to fit power spectra across time windows, and
+# across different events.
 #
diff --git a/tutorials/plot_07-TroubleShooting.py b/tutorials/plot_08-TroubleShooting.py
similarity index 100%
rename from tutorials/plot_07-TroubleShooting.py
rename to tutorials/plot_08-TroubleShooting.py
diff --git a/tutorials/plot_08-FurtherAnalysis.py b/tutorials/plot_09-FurtherAnalysis.py
similarity index 100%
rename from tutorials/plot_08-FurtherAnalysis.py
rename to tutorials/plot_09-FurtherAnalysis.py
diff --git a/tutorials/plot_09-Reporting.py b/tutorials/plot_10-Reporting.py
similarity index 100%
rename from tutorials/plot_09-Reporting.py
rename to tutorials/plot_10-Reporting.py

From ebba0073ab79504840b5d6b4c4329cba222dc8ce Mon Sep 17 00:00:00 2001
From: Tom Donoghue <tdonoghue.research@gmail.com>
Date: Tue, 26 Mar 2024 20:55:07 -0400
Subject: [PATCH 99/99] bump version number

---
 specparam/version.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/specparam/version.py b/specparam/version.py
index 34f0285d..0546c570 100644
--- a/specparam/version.py
+++ b/specparam/version.py
@@ -1 +1 @@
-__version__ = '2.0.0rc0'
\ No newline at end of file
+__version__ = '2.0.0rc1'
\ No newline at end of file