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danibene/nk_issue_729_orig.ipynb

Created October 13, 2022 15:29
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nk_issue_729_orig.ipynb
{
"nbformat": 4,
"nbformat_minor": 0,
"metadata": {
"colab": {
"provenance": [],
"collapsed_sections": [],
"authorship_tag": "ABX9TyMCKojK8x7rL684SjjG8LQ/",
"include_colab_link": true
},
"kernelspec": {
"name": "python3",
"display_name": "Python 3"
},
"language_info": {
"name": "python"
}
},
"cells": [
{
"cell_type": "markdown",
"metadata": {
"id": "view-in-github",
"colab_type": "text"
},
"source": [
"<a href=\"https://colab.research.google.com/gist/danibene/6cb93f7c2654698b91f0f3a5de2e8166/nk_issue_729_orig.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
]
},
{
"cell_type": "code",
"source": [
"!pip install neurokit2"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "sjisO7Eaxcz3",
"outputId": "b22a24cb-d16f-440e-e539-44cc29d88eb6"
},
"execution_count": 1,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/\n",
"Collecting neurokit2\n",
" Downloading neurokit2-0.2.1-py2.py3-none-any.whl (1.2 MB)\n",
"\u001b[K |████████████████████████████████| 1.2 MB 5.2 MB/s \n",
"\u001b[?25hRequirement already satisfied: scikit-learn>=1.0.0 in /usr/local/lib/python3.7/dist-packages (from neurokit2) (1.0.2)\n",
"Requirement already satisfied: scipy in /usr/local/lib/python3.7/dist-packages (from neurokit2) (1.7.3)\n",
"Requirement already satisfied: numpy in /usr/local/lib/python3.7/dist-packages (from neurokit2) (1.21.6)\n",
"Requirement already satisfied: matplotlib in /usr/local/lib/python3.7/dist-packages (from neurokit2) (3.2.2)\n",
"Requirement already satisfied: pandas in /usr/local/lib/python3.7/dist-packages (from neurokit2) (1.3.5)\n",
"Requirement already satisfied: threadpoolctl>=2.0.0 in /usr/local/lib/python3.7/dist-packages (from scikit-learn>=1.0.0->neurokit2) (3.1.0)\n",
"Requirement already satisfied: joblib>=0.11 in /usr/local/lib/python3.7/dist-packages (from scikit-learn>=1.0.0->neurokit2) (1.2.0)\n",
"Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib->neurokit2) (3.0.9)\n",
"Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib->neurokit2) (1.4.4)\n",
"Requirement already satisfied: python-dateutil>=2.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib->neurokit2) (2.8.2)\n",
"Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.7/dist-packages (from matplotlib->neurokit2) (0.11.0)\n",
"Requirement already satisfied: typing-extensions in /usr/local/lib/python3.7/dist-packages (from kiwisolver>=1.0.1->matplotlib->neurokit2) (4.1.1)\n",
"Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.7/dist-packages (from python-dateutil>=2.1->matplotlib->neurokit2) (1.15.0)\n",
"Requirement already satisfied: pytz>=2017.3 in /usr/local/lib/python3.7/dist-packages (from pandas->neurokit2) (2022.4)\n",
"Installing collected packages: neurokit2\n",
"Successfully installed neurokit2-0.2.1\n"
]
}
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/",
"height": 572
},
"id": "O21ViOy8xYLZ",
"outputId": "367e7868-9920-4863-fd3b-f583f20b1269"
},
"outputs": [
{
"output_type": "error",
"ename": "KeyError",
"evalue": "ignored",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m/usr/local/lib/python3.7/dist-packages/pandas/core/series.py\u001b[0m in \u001b[0;36m__setitem__\u001b[0;34m(self, key, value)\u001b[0m\n\u001b[1;32m 1061\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1062\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_set_with_engine\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1063\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mKeyError\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/usr/local/lib/python3.7/dist-packages/pandas/core/series.py\u001b[0m in \u001b[0;36m_set_with_engine\u001b[0;34m(self, key, value)\u001b[0m\n\u001b[1;32m 1094\u001b[0m \u001b[0;31m# fails with AttributeError for IntervalIndex\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1095\u001b[0;31m \u001b[0mloc\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mindex\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_engine\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_loc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1096\u001b[0m \u001b[0;31m# error: Argument 1 to \"validate_numeric_casting\" has incompatible type\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/usr/local/lib/python3.7/dist-packages/pandas/_libs/index.pyx\u001b[0m in \u001b[0;36mpandas._libs.index.IndexEngine.get_loc\u001b[0;34m()\u001b[0m\n",
"\u001b[0;32m/usr/local/lib/python3.7/dist-packages/pandas/_libs/index.pyx\u001b[0m in \u001b[0;36mpandas._libs.index.IndexEngine.get_loc\u001b[0;34m()\u001b[0m\n",
"\u001b[0;31mTypeError\u001b[0m: '[253, 474, 810, 1092, 1329, 1549, 1807, 2061, 2281, 2521, 2775, 3123, 3420, 3658, 3872, 4091, 4359, 4603, 4842, 5057, 5412, 5740, 6004, 6231, 6474, 6745, 6991, 7236, 7580, 7862, 8107, 8408, 8680, 8910, 9142, 9382, 9640, 9869, 10095, 10338, 10590, 10851, 11083, 11307, 11535, 11785, 11991, 12211, 12436, 12684, 12922, 13141, 13362, 13585, 13858, 14102, 14322, 14545, 14777, 15106, 15366, 15584, 15797, 16003, 16198, 16383, 16572, 16968, 17302, 17575, 17859, 18228, 18542, 18813, 19134, 19473, 19755, 19992, 20225, 20583, 20918, 21203, 21456, 21732, 22033, 22311, 22562, 22816, 23128, 23385, 23606, 23869, 24197, 24449, 24673, 24891, 25160, 25427, 25676, 25894, 26155, 26490, 26783, 27018, 27246, 27500, 27840, 28104, 28323, 28563, 28907, 29191, 29431, 29670, 29995, 30311, 30603, 30870, 31153, 31408, 31625, 31847, 32226, 32555, 32834, 33084, 33417, 33711, 33965, 34315, 34633, 34918, 35242, 35558, 35836, 36153, 36448, 36689, 36916, 37200, 37457, 37693, 37932, 38218, 38484, 38714, 38935, 39149, 39353, 39557, 39812, 40077, 40349, 40614, 40842, 41085, 41440, 41754, 42000, 42215, 42443, 42759, 43081, 43328, 43553, 43798, 44141, 44439, 44688, 44912, 45156, 45475, 45725, 45959, 46183, 46456, 46791, 47077, 47316, 47644, 47965, 48243, 48513, 48844, 49106, 49331, 49574, 49911, 50180, 50410, 50664, 50989, 51271, 51510, 51742, 52005, 52279, 52514, 52738, 52973, 53253, 53556, 53813, 54043, 54281, 54559, 54829, 55077, 55313, 55652, 55931, 56165, 56394, 56609, 56815, 57020, 57...",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-2-c7362faf83ab>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 9\u001b[0m \u001b[0mecg_cleaned\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnk\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mecg_clean\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecg_signal\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msampling_rate\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mHERTZ\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0m_\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrpeaks\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnk\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mecg_peaks\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecg_cleaned\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msampling_rate\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mHERTZ\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 11\u001b[0;31m \u001b[0m_\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mwaves_peak\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnk\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mecg_delineate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecg_cleaned\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrpeaks\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msampling_rate\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mHERTZ\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmethod\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"peak\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mshow\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mshow_type\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'peaks'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m/usr/local/lib/python3.7/dist-packages/neurokit2/ecg/ecg_delineate.py\u001b[0m in \u001b[0;36mecg_delineate\u001b[0;34m(ecg_cleaned, rpeaks, sampling_rate, method, show, show_type, check, **kwargs)\u001b[0m\n\u001b[1;32m 170\u001b[0m \u001b[0mwaves_noNA\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mfeature\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mx\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mwaves_noNA\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mfeature\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;34m~\u001b[0m\u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0misnan\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mx\u001b[0m \u001b[0;34m>\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 171\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 172\u001b[0;31m \u001b[0minstant_peaks\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msignal_formatpeaks\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mwaves_noNA\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdesired_length\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mecg_cleaned\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 173\u001b[0m \u001b[0msignals\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0minstant_peaks\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 174\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/usr/local/lib/python3.7/dist-packages/neurokit2/signal/signal_formatpeaks.py\u001b[0m in \u001b[0;36msignal_formatpeaks\u001b[0;34m(info, desired_length, peak_indices, other_indices)\u001b[0m\n\u001b[1;32m 19\u001b[0m \u001b[0mx\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfeature\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mx\u001b[0m \u001b[0;32min\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m\"Peak\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"Onset\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"Offset\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"Trough\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"Recovery\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 20\u001b[0m ):\n\u001b[0;32m---> 21\u001b[0;31m \u001b[0msignals\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mfeature\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_signal_from_indices\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mvalues\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdesired_length\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 22\u001b[0m \u001b[0msignals\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mfeature\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msignals\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mfeature\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mastype\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"int64\"\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;31m# indexing of feature using 1 and 0\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 23\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/usr/local/lib/python3.7/dist-packages/neurokit2/signal/signal_formatpeaks.py\u001b[0m in \u001b[0;36m_signal_from_indices\u001b[0;34m(indices, desired_length, value)\u001b[0m\n\u001b[1;32m 74\u001b[0m \u001b[0;31m# Appending single value\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 75\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mint\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfloat\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 76\u001b[0;31m \u001b[0msignal\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mindices\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 77\u001b[0m \u001b[0;31m# Appending multiple values\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 78\u001b[0m \u001b[0;32melif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mndarray\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
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"\u001b[0;32m/usr/local/lib/python3.7/dist-packages/pandas/core/series.py\u001b[0m in \u001b[0;36m_set_labels\u001b[0;34m(self, key, value)\u001b[0m\n\u001b[1;32m 1132\u001b[0m \u001b[0mmask\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mindexer\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1133\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mmask\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0many\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1134\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mKeyError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mf\"{key[mask]} not in index\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1135\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_set_values\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mindexer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1136\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mKeyError\u001b[0m: '[898750] not in index'"
]
}
],
"source": [
"import neurokit2 as nk\n",
"import pandas as pd\n",
"import numpy as np\n",
"import os\n",
"\n",
"HERTZ = 250\n",
"filin = \"https://github.com/neuropsychology/NeuroKit/files/9758396/debug.csv\"\n",
"ecg_signal = pd.read_csv(filin, header=0, names=[\"ECG\"])['ECG']\n",
"ecg_cleaned = nk.ecg_clean(ecg_signal, sampling_rate=HERTZ)\n",
"_, rpeaks = nk.ecg_peaks(ecg_cleaned, sampling_rate=HERTZ)\n",
"_, waves_peak = nk.ecg_delineate(ecg_cleaned, rpeaks, sampling_rate=HERTZ, method=\"peak\", show=False, show_type='peaks')"
]
},
{
"cell_type": "markdown",
"source": [
"Original error mentioned in https://github.com/neuropsychology/NeuroKit/issues/729 is reproduced"
],
"metadata": {
"id": "UtP-sI-49AK6"
}
}
]
}
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