more docstrings

schmidtfa · Aug 9, 2024 · e462006 · e462006
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diff --git a/README.md b/README.md
@@ -108,7 +108,7 @@ Contributions to PyRASA are welcome! Whether it's raising issues, improving docu
 
 If you are using IRASA please cite the smart people who came up with the algorithm:
 
-Wen, H., & Liu, Z. (2016). Separating fractal and oscillatory components in the power spectrum of neurophysiological signal. Brain topography, 29, 13-26.
+Wen, H., & Liu, Z. (2016). Separating fractal and oscillatory components in the power spectrum of neurophysiological signal. Brain topography, 29, 13-26. https://doi.org/10.1007/s10548-015-0448-0
 
 If you are using PyRASA it would be nice, if you could additionally cite us (whenever the paper is finally ready):
 

diff --git a/examples/basic_functionality.ipynb b/examples/basic_functionality.ipynb
@@ -630,7 +630,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 27,
    "metadata": {},
    "outputs": [
     {
@@ -645,9 +645,6 @@
     }
    ],
    "source": [
-    "import seaborn as sns\n",
-    "sns.set_style('ticks')\n",
-    "sns.set_context('talk')\n",
     "f, axes = plt.subplots(ncols=2, figsize=(8, 4))\n",
     "axes[0].plot(irasa_out.freqs, irasa_out.periodic[0,:])\n",
     "axes[0].set_ylabel('Power (a.u.)')\n",
@@ -661,51 +658,133 @@
     "axes[1].set_xlabel('Frequency (Hz)')\n",
     "axes[1].set_title('Original + \\n Aperiodic Spectrum')\n",
     "\n",
-    "f.tight_layout()\n",
-    "f.savefig('../simulations/example_knee.png')\n"
+    "f.tight_layout()"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 26,
    "metadata": {},
    "outputs": [
     {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "|   ch_name |   cf |      bw |     pw |\n",
-      "|----------:|-----:|--------:|-------:|\n",
-      "|         0 |  9.5 | 1.44337 | 0.4146 |\n"
-     ]
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>ch_name</th>\n",
+       "      <th>cf</th>\n",
+       "      <th>bw</th>\n",
+       "      <th>pw</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>0</td>\n",
+       "      <td>9.5</td>\n",
+       "      <td>1.443373</td>\n",
+       "      <td>0.4146</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "   ch_name   cf        bw      pw\n",
+       "0        0  9.5  1.443373  0.4146"
+      ]
+     },
+     "execution_count": 26,
+     "metadata": {},
+     "output_type": "execute_result"
     }
    ],
    "source": [
     "# %% get periodic stuff\n",
-    "peaks = irasa_out.get_peaks()\n",
-    "md = peaks.to_markdown(index=False)\n",
-    "print(md)"
+    "irasa_out.get_peaks()"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 25,
    "metadata": {},
    "outputs": [
     {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "|         mse |   r_squared |      BIC |      AIC | fit_type   |   ch_name |\n",
-      "|------------:|------------:|---------:|---------:|:-----------|----------:|\n",
-      "| 3.02402e-05 |    0.999894 | -2049.69 | -2062.86 | knee       |         0 |\n"
-     ]
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>Offset</th>\n",
+       "      <th>Knee</th>\n",
+       "      <th>Exponent_1</th>\n",
+       "      <th>Exponent_2</th>\n",
+       "      <th>fit_type</th>\n",
+       "      <th>Knee Frequency (Hz)</th>\n",
+       "      <th>ch_name</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>1.380983</td>\n",
+       "      <td>532.909784</td>\n",
+       "      <td>0.511999</td>\n",
+       "      <td>1.894478</td>\n",
+       "      <td>knee</td>\n",
+       "      <td>8.59554</td>\n",
+       "      <td>0</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "     Offset        Knee  Exponent_1  Exponent_2 fit_type  Knee Frequency (Hz)  \\\n",
+       "0  1.380983  532.909784    0.511999    1.894478     knee              8.59554   \n",
+       "\n",
+       "   ch_name  \n",
+       "0        0  "
+      ]
+     },
+     "execution_count": 25,
+     "metadata": {},
+     "output_type": "execute_result"
     }
    ],
    "source": [
-    "ap = irasa_out.fit_aperiodic_model(fit_func='knee').gof\n",
-    "md = ap.to_markdown(index=False)\n",
-    "print(md)"
+    "irasa_out.fit_aperiodic_model(fit_func='knee').aperiodic_params"
    ]
   },
   {