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danibene/nk_issue_850.ipynb

Created June 26, 2023 23:42
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{
"nbformat": 4,
"nbformat_minor": 0,
"metadata": {
"colab": {
"provenance": [],
"authorship_tag": "ABX9TyPE3i/aPHt9c9RHx3p6DGvd",
"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/595f281bc118541e49b7d4462633d8ad/nk_issue_850.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "qGJepFmcEXTz",
"outputId": "c01b7a95-389c-462e-f98c-6336d654ccb0"
},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/\n",
"Requirement already satisfied: neurokit2 in /usr/local/lib/python3.10/dist-packages (0.2.4)\n",
"Requirement already satisfied: numpy in /usr/local/lib/python3.10/dist-packages (from neurokit2) (1.22.4)\n",
"Requirement already satisfied: pandas in /usr/local/lib/python3.10/dist-packages (from neurokit2) (1.5.3)\n",
"Requirement already satisfied: scipy in /usr/local/lib/python3.10/dist-packages (from neurokit2) (1.10.1)\n",
"Requirement already satisfied: scikit-learn>=1.0.0 in /usr/local/lib/python3.10/dist-packages (from neurokit2) (1.2.2)\n",
"Requirement already satisfied: matplotlib in /usr/local/lib/python3.10/dist-packages (from neurokit2) (3.7.1)\n",
"Requirement already satisfied: joblib>=1.1.1 in /usr/local/lib/python3.10/dist-packages (from scikit-learn>=1.0.0->neurokit2) (1.2.0)\n",
"Requirement already satisfied: threadpoolctl>=2.0.0 in /usr/local/lib/python3.10/dist-packages (from scikit-learn>=1.0.0->neurokit2) (3.1.0)\n",
"Requirement already satisfied: contourpy>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib->neurokit2) (1.1.0)\n",
"Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.10/dist-packages (from matplotlib->neurokit2) (0.11.0)\n",
"Requirement already satisfied: fonttools>=4.22.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib->neurokit2) (4.40.0)\n",
"Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib->neurokit2) (1.4.4)\n",
"Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib->neurokit2) (23.1)\n",
"Requirement already satisfied: pillow>=6.2.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib->neurokit2) (8.4.0)\n",
"Requirement already satisfied: pyparsing>=2.3.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib->neurokit2) (3.1.0)\n",
"Requirement already satisfied: python-dateutil>=2.7 in /usr/local/lib/python3.10/dist-packages (from matplotlib->neurokit2) (2.8.2)\n",
"Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/dist-packages (from pandas->neurokit2) (2022.7.1)\n",
"Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.10/dist-packages (from python-dateutil>=2.7->matplotlib->neurokit2) (1.16.0)\n"
]
}
],
"source": [
"!pip install neurokit2"
]
},
{
"cell_type": "code",
"source": [
"!pip install mne"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "R-7zMzdDFO5w",
"outputId": "0b4a9b53-d885-4ac9-e635-bd24c6ffe73c"
},
"execution_count": 2,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/\n",
"Requirement already satisfied: mne in /usr/local/lib/python3.10/dist-packages (1.4.2)\n",
"Requirement already satisfied: numpy>=1.15.4 in /usr/local/lib/python3.10/dist-packages (from mne) (1.22.4)\n",
"Requirement already satisfied: scipy>=1.6.3 in /usr/local/lib/python3.10/dist-packages (from mne) (1.10.1)\n",
"Requirement already satisfied: matplotlib>=3.4.0 in /usr/local/lib/python3.10/dist-packages (from mne) (3.7.1)\n",
"Requirement already satisfied: tqdm in /usr/local/lib/python3.10/dist-packages (from mne) (4.65.0)\n",
"Requirement already satisfied: pooch>=1.5 in /usr/local/lib/python3.10/dist-packages (from mne) (1.6.0)\n",
"Requirement already satisfied: decorator in /usr/local/lib/python3.10/dist-packages (from mne) (4.4.2)\n",
"Requirement already satisfied: packaging in /usr/local/lib/python3.10/dist-packages (from mne) (23.1)\n",
"Requirement already satisfied: jinja2 in /usr/local/lib/python3.10/dist-packages (from mne) (3.1.2)\n",
"Requirement already satisfied: contourpy>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib>=3.4.0->mne) (1.1.0)\n",
"Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.10/dist-packages (from matplotlib>=3.4.0->mne) (0.11.0)\n",
"Requirement already satisfied: fonttools>=4.22.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib>=3.4.0->mne) (4.40.0)\n",
"Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib>=3.4.0->mne) (1.4.4)\n",
"Requirement already satisfied: pillow>=6.2.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib>=3.4.0->mne) (8.4.0)\n",
"Requirement already satisfied: pyparsing>=2.3.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib>=3.4.0->mne) (3.1.0)\n",
"Requirement already satisfied: python-dateutil>=2.7 in /usr/local/lib/python3.10/dist-packages (from matplotlib>=3.4.0->mne) (2.8.2)\n",
"Requirement already satisfied: appdirs>=1.3.0 in /usr/local/lib/python3.10/dist-packages (from pooch>=1.5->mne) (1.4.4)\n",
"Requirement already satisfied: requests>=2.19.0 in /usr/local/lib/python3.10/dist-packages (from pooch>=1.5->mne) (2.27.1)\n",
"Requirement already satisfied: MarkupSafe>=2.0 in /usr/local/lib/python3.10/dist-packages (from jinja2->mne) (2.1.3)\n",
"Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.10/dist-packages (from python-dateutil>=2.7->matplotlib>=3.4.0->mne) (1.16.0)\n",
"Requirement already satisfied: urllib3<1.27,>=1.21.1 in /usr/local/lib/python3.10/dist-packages (from requests>=2.19.0->pooch>=1.5->mne) (1.26.16)\n",
"Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/dist-packages (from requests>=2.19.0->pooch>=1.5->mne) (2023.5.7)\n",
"Requirement already satisfied: charset-normalizer~=2.0.0 in /usr/local/lib/python3.10/dist-packages (from requests>=2.19.0->pooch>=1.5->mne) (2.0.12)\n",
"Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/dist-packages (from requests>=2.19.0->pooch>=1.5->mne) (3.4)\n"
]
}
]
},
{
"cell_type": "code",
"source": [
"import neurokit2 as nk"
],
"metadata": {
"id": "cp5tl94jEi5X"
},
"execution_count": 3,
"outputs": []
},
{
"cell_type": "code",
"source": [
"# Resample sample data from 100 Hz to 1000 Hz to try to reproduce issue\n",
"eog = nk.data(\"eog_100hz\")\n",
"desired_sampling_rate = 1000\n",
"eog_signal = nk.signal_resample(signal=eog, sampling_rate=100, desired_sampling_rate=desired_sampling_rate)"
],
"metadata": {
"id": "OIezEHH2Ej2e"
},
"execution_count": 4,
"outputs": []
},
{
"cell_type": "code",
"source": [
"eog_cleaned = nk.eog_clean(eog_signal, sampling_rate=1000, method=\"neurokit\")\n",
"peaks = nk.eog_findpeaks(eog_cleaned, sampling_rate=1000)\n",
"info = nk.eog_features(eog_cleaned, peaks,sampling_rate=1000)"
],
"metadata": {
"id": "lNUYKyJvEmfY"
},
"execution_count": 5,
"outputs": []
},
{
"cell_type": "code",
"source": [
"info"
],
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "lhQcUJ8GFLS-",
"outputId": "f03d7802-4ba3-4005-c20c-47ec0f99d17d"
},
"execution_count": 6,
"outputs": [
{
"output_type": "execute_result",
"data": {
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},
"metadata": {},
"execution_count": 6
}
]
},
{
"cell_type": "code",
"source": [],
"metadata": {
"id": "TUlTpThIFfQF"
},
"execution_count": null,
"outputs": []
}
]
}
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