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   "source": [
    "## mixing state calculator"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d185087a",
   "metadata": {},
   "source": [
    "This script is used for calculating [mixing state index](https://doi.org/10.5194/acp-13-11423-2013)   \n",
    "**Step 0**: click the link [here](https://mybinder.org/v2/gh/zhonghua-zheng/pmcpy/HEAD?filepath=docs%2Fnotebooks) to launch a jupyter notebook  \n",
    "**Step 1**: upload your own csv file (each `row` is a `particle`, each \n",
    "`column` is the `mass` of a `species`)    \n",
    "![upload_csv](./figures/upload_csv.png)\n",
    "\n",
    "**Step 2**: edit the `file_name` and `group_list` below   \n",
    "Below is an exmaple with three `surrogate species`  \n",
    "The definition of surrogate species is [here](https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2020EA001500) (Figure 2)   \n",
    "- surrogate species 1: \"BC\" and \"POM\"    \n",
    "- surrogate species 2: \"DUST\"    \n",
    "- surrogate species 3: \"SS\"    \n",
    "\n",
    "**Step 3**: click `Run` button on the top of your jupyter notebook  \n",
    "![run_cell](./figures/run_cell.png)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "26c77ea2",
   "metadata": {},
   "source": [
    "**Please edit the \"file_name\" and \"group_list\", then run the code below**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "a9cb7470",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "mixing state index: 0.9408323695414793\n",
      "average particle (alpha) species diversity: 2.838147712915256\n",
      "bulk population (gamma) species diversity: 2.9537462489849164\n"
     ]
    }
   ],
   "source": [
    "file_name = \"sample_data.csv\"\n",
    "group_list = [[\"BC\",\"POM\"],\n",
    "              [\"DUST\"],\n",
    "              [\"SS\"]]\n",
    "\n",
    "# ====== please don't change ======\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import pmcpy\n",
    "\n",
    "# load data\n",
    "df = pd.read_csv(file_name)\n",
    "# get matrix for calculation\n",
    "da = np.concatenate([df[group].values.sum(axis=1).reshape(-1,1) for group in group_list],axis=1)\n",
    "# calculate mixing state index\n",
    "D_alpha, D_gamma, chi = pmcpy.get_chi(da)\n",
    "print(\"mixing state index:\", chi)\n",
    "print(\"average particle (alpha) species diversity:\", D_alpha)\n",
    "print(\"bulk population (gamma) species diversity:\", D_gamma)"
   ]
  }
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