aperiodic exponent

Mark-Kramer · Dec 5, 2024 · d0f4cb8 · d0f4cb8
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diff --git a/.DS_Store b/.DS_Store
diff --git a/Aperiodic_Exponent_Lab.ipynb b/Aperiodic_Exponent_Lab.ipynb
@@ -0,0 +1,142 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "4df4e957-7ea5-4b20-891a-d2f4cad354a4",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "title: Aperiodic exponent example\n",
+    "project:\n",
+    "  type: website\n",
+    "format:\n",
+    "  html:\n",
+    "    code-fold: false\n",
+    "    code-tools: true\n",
+    "jupyter: python 3\n",
+    "number-sections: false\n",
+    "---"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "22374a1b-dcae-472b-8d44-68f803e630eb",
+   "metadata": {},
+   "source": [
+    "Let's try this [example code](https://fooof-tools.github.io/fooof/auto_tutorials/plot_01-ModelDescription.html#sphx-glr-auto-tutorials-plot-01-modeldescription-py)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "29838749-1da3-467c-9868-cd8afb3e1dba",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Import required code for visualizing example models\n",
+    "from fooof import FOOOF\n",
+    "from fooof.sim.gen import gen_power_spectrum\n",
+    "from fooof.sim.utils import set_random_seed\n",
+    "from fooof.plts.spectra import plot_spectra\n",
+    "from fooof.plts.annotate import plot_annotated_model"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "27503282-4a90-452e-944e-892a6d41c60e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Set random seed, for consistency generating simulated data\n",
+    "set_random_seed(21)\n",
+    "\n",
+    "# Simulate example power spectra\n",
+    "freqs1, powers1 = gen_power_spectrum([3, 40], [1, 1],\n",
+    "                                     [[10, 0.2, 1.25], [30, 0.15, 2]])\n",
+    "freqs2, powers2 = gen_power_spectrum([1, 150], [1, 125, 1.25],\n",
+    "                                     [[8, 0.15, 1.], [30, 0.1, 2]])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f9cdff44-e207-4e35-b978-a3703d89342f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Initialize power spectrum model objects and fit the power spectra\n",
+    "fm1 = FOOOF(min_peak_height=0.05, verbose=False)\n",
+    "fm2 = FOOOF(min_peak_height=0.05, aperiodic_mode='knee', verbose=False)\n",
+    "fm1.fit(freqs1, powers1)\n",
+    "fm2.fit(freqs2, powers2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "63424cc3-a85f-499d-8f32-412379f358bf",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Plot one of the example power spectra\n",
+    "plot_spectra(freqs1, powers1, log_powers=True,\n",
+    "             color='black', label='Original Spectrum')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a249c27a-e396-413f-b6ed-29ae2a96a886",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Plot an example power spectrum, with a model fit\n",
+    "fm1.plot(plot_peaks='shade', peak_kwargs={'color' : 'green'})"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2e0a0d99-aaae-4726-ba22-8e134ba70144",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Plot an annotated version of the power spectrum model\n",
+    "plot_annotated_model(fm1, annotate_aperiodic=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f29075fa-285b-425f-923d-d3d9c0b735c9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Report: fit the model, print the resulting parameters, and plot the reconstruction\n",
+    "fm1.report()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/Readings/Donoghue_2020.pdf b/Readings/Donoghue_2020.pdf
diff --git a/Readings/Gao_2017.pdf b/Readings/Gao_2017.pdf
diff --git a/Readings/Kramer_2024.pdf b/Readings/Kramer_2024.pdf
diff --git a/_extensions/.DS_Store b/_extensions/.DS_Store
diff --git a/docs/Analyzing_Rhythms_Lab_1.html b/docs/Analyzing_Rhythms_Lab_1.html
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diff --git a/docs/Analyzing_Rhythms_Lab_2a.html b/docs/Analyzing_Rhythms_Lab_2a.html
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diff --git a/docs/Analyzing_Rhythms_Lab_2b.html b/docs/Analyzing_Rhythms_Lab_2b.html
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diff --git a/docs/Analyzing_Rhythms_Lab_3.html b/docs/Analyzing_Rhythms_Lab_3.html
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