nk_issue_824_c.ipynb

nk_issue_824_c.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "provenance": [],
      "authorship_tag": "ABX9TyODax6x+khQ4nFDGtjQeqPp",
      "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/177a9e9c98e3696c92a2e0d0317cb37c/nk_issue_824_c.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 numpy==1.22\n",
        "!pip install biosppy==0.6.1\n",
        "!pip install neurokit2==0.2.4"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "ALWWASrMiC9n",
        "outputId": "dc4db867-3c20-49df-c052-d0d7df828fa7"
      },
      "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",
            "Requirement already satisfied: numpy==1.22 in /usr/local/lib/python3.10/dist-packages (1.22.0)\n",
            "Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/\n",
            "Requirement already satisfied: biosppy==0.6.1 in /usr/local/lib/python3.10/dist-packages (0.6.1)\n",
            "Requirement already satisfied: bidict in /usr/local/lib/python3.10/dist-packages (from biosppy==0.6.1) (0.22.1)\n",
            "Requirement already satisfied: h5py in /usr/local/lib/python3.10/dist-packages (from biosppy==0.6.1) (3.8.0)\n",
            "Requirement already satisfied: matplotlib in /usr/local/lib/python3.10/dist-packages (from biosppy==0.6.1) (3.7.1)\n",
            "Requirement already satisfied: numpy in /usr/local/lib/python3.10/dist-packages (from biosppy==0.6.1) (1.22.0)\n",
            "Requirement already satisfied: scikit-learn in /usr/local/lib/python3.10/dist-packages (from biosppy==0.6.1) (1.2.2)\n",
            "Requirement already satisfied: scipy in /usr/local/lib/python3.10/dist-packages (from biosppy==0.6.1) (1.10.1)\n",
            "Requirement already satisfied: shortuuid in /usr/local/lib/python3.10/dist-packages (from biosppy==0.6.1) (1.0.11)\n",
            "Requirement already satisfied: six in /usr/local/lib/python3.10/dist-packages (from biosppy==0.6.1) (1.16.0)\n",
            "Requirement already satisfied: contourpy>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib->biosppy==0.6.1) (1.0.7)\n",
            "Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.10/dist-packages (from matplotlib->biosppy==0.6.1) (0.11.0)\n",
            "Requirement already satisfied: fonttools>=4.22.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib->biosppy==0.6.1) (4.39.3)\n",
            "Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib->biosppy==0.6.1) (1.4.4)\n",
            "Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib->biosppy==0.6.1) (23.1)\n",
            "Requirement already satisfied: pillow>=6.2.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib->biosppy==0.6.1) (8.4.0)\n",
            "Requirement already satisfied: pyparsing>=2.3.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib->biosppy==0.6.1) (3.0.9)\n",
            "Requirement already satisfied: python-dateutil>=2.7 in /usr/local/lib/python3.10/dist-packages (from matplotlib->biosppy==0.6.1) (2.8.2)\n",
            "Requirement already satisfied: joblib>=1.1.1 in /usr/local/lib/python3.10/dist-packages (from scikit-learn->biosppy==0.6.1) (1.2.0)\n",
            "Requirement already satisfied: threadpoolctl>=2.0.0 in /usr/local/lib/python3.10/dist-packages (from scikit-learn->biosppy==0.6.1) (3.1.0)\n",
            "Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/\n",
            "Requirement already satisfied: neurokit2==0.2.4 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==0.2.4) (1.22.0)\n",
            "Requirement already satisfied: pandas in /usr/local/lib/python3.10/dist-packages (from neurokit2==0.2.4) (1.5.3)\n",
            "Requirement already satisfied: scipy in /usr/local/lib/python3.10/dist-packages (from neurokit2==0.2.4) (1.10.1)\n",
            "Requirement already satisfied: scikit-learn>=1.0.0 in /usr/local/lib/python3.10/dist-packages (from neurokit2==0.2.4) (1.2.2)\n",
            "Requirement already satisfied: matplotlib in /usr/local/lib/python3.10/dist-packages (from neurokit2==0.2.4) (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==0.2.4) (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==0.2.4) (3.1.0)\n",
            "Requirement already satisfied: contourpy>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib->neurokit2==0.2.4) (1.0.7)\n",
            "Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.10/dist-packages (from matplotlib->neurokit2==0.2.4) (0.11.0)\n",
            "Requirement already satisfied: fonttools>=4.22.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib->neurokit2==0.2.4) (4.39.3)\n",
            "Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib->neurokit2==0.2.4) (1.4.4)\n",
            "Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib->neurokit2==0.2.4) (23.1)\n",
            "Requirement already satisfied: pillow>=6.2.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib->neurokit2==0.2.4) (8.4.0)\n",
            "Requirement already satisfied: pyparsing>=2.3.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib->neurokit2==0.2.4) (3.0.9)\n",
            "Requirement already satisfied: python-dateutil>=2.7 in /usr/local/lib/python3.10/dist-packages (from matplotlib->neurokit2==0.2.4) (2.8.2)\n",
            "Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/dist-packages (from pandas->neurokit2==0.2.4) (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==0.2.4) (1.16.0)\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "import neurokit2 as nk\n",
        "import biosppy\n",
        "import numpy as np"
      ],
      "metadata": {
        "id": "cRYIjMO1iLm1"
      },
      "execution_count": 2,
      "outputs": []
    },
    {
      "cell_type": "code",
      "execution_count": 3,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "yqpAXjFliCbU",
        "outputId": "907b4fd7-7395-4d5f-ec65-93893934d9fe"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stderr",
          "text": [
            "/usr/local/lib/python3.10/dist-packages/biosppy/signals/eda.py:239: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.\n",
            "  scrs = np.array(scrs)\n"
          ]
        }
      ],
      "source": [
        "sampling_rate = 1000\n",
        "eda = nk.eda_simulate(\n",
        "    duration=30 * 20,\n",
        "    sampling_rate=sampling_rate,\n",
        "    scr_number=6 * 20,\n",
        "    noise=0,\n",
        "    drift=0.01,\n",
        "    random_state=42,\n",
        ")\n",
        "eda_phasic = nk.eda_phasic(nk.standardize(eda), method=\"highpass\")[\"EDA_Phasic\"].values\n",
        "\n",
        "signals, info = nk.eda_peaks(eda_phasic, method=\"gamboa2008\")\n",
        "onsets, peaks, amplitudes = biosppy.eda.basic_scr(eda_phasic, sampling_rate=1000)\n",
        "assert np.allclose((info[\"SCR_Peaks\"] - peaks).mean(), 0, atol=1e-5)\n",
        "\n",
        "signals, info = nk.eda_peaks(eda_phasic, method=\"kim2004\")\n",
        "onsets, peaks, amplitudes = biosppy.eda.kbk_scr(eda_phasic, sampling_rate=1000)"
      ]
    },
    {
      "cell_type": "code",
      "source": [],
      "metadata": {
        "id": "-h0PmfDmlzzg"
      },
      "execution_count": null,
      "outputs": []
    }
  ]
}