{
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "\n# Instantaneous Heart Rate\n\nThis example show how to record PPG signals using the [Nonin 3012LP\nXpod USB pulse oximeter](https://www.nonin.com/products/xpod/) and the [Nonin\n8000SM 'soft-clip' fingertip sensors](https://www.nonin.com/products/8000s/).\nPeaks are automatically labelled online and the instantaneous heart rate is\nplotted.\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "# Author: Nicolas Legrand <nicolas.legrand@cfin.au.dk>\n# Licence: Apache-2.0\n\nimport matplotlib.pyplot as plt\nimport numpy as np\nimport pandas as pd\nfrom systole import serialSim\nfrom systole.detection import ppg_peaks\nfrom systole.plots import plot_raw, plot_rr\nfrom systole.recording import Oximeter"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "## Recording\nFor the demonstration purpose, here we simulate data acquisition through\nthe pulse oximeter using pre-recorded signal.\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "ser = serialSim()"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "If you want to enable online data acquisition, you should uncomment the\nfollowing lines and provide the reference of the COM port where the pulse\noximeter is plugged in.\n\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "```python\nimport serial\nser = serial.Serial('COM4')  # Change this value according to your setup\n```\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "# Create an Oxymeter instance, initialize recording and record for 30 seconds\noxi = Oximeter(serial=ser, sfreq=75).setup()\noxi.read(30)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "## Plotting\n\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {
        "collapsed": false
      },
      "outputs": [],
      "source": [
        "signal, peaks = ppg_peaks(signal=oxi.recording, sfreq=75)\n\nfig, ax = plt.subplots(3, 1, figsize=(13, 8), sharex=True)\n\nplot_raw(signal=signal, show_heart_rate=False, ax=ax[0])\n\ntimes = pd.to_datetime(np.arange(0, len(peaks)), unit=\"ms\", origin=\"unix\")\nax[1].plot(times, peaks, \"#55a868\")\nax[1].set_title(\"Peaks vector\")\nax[1].set_ylabel(\"Peak\\n detection\")\n\nplot_rr(peaks, input_type=\"peaks\", ax=ax[2])\nplt.tight_layout()"
      ]
    }
  ],
  "metadata": {
    "kernelspec": {
      "display_name": "Python 3",
      "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": "3.11.16"
    }
  },
  "nbformat": 4,
  "nbformat_minor": 0
}