ventmap_new_feature.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# API\n",
    "\n",
    "## Basics\n",
    "For reading ventilator data:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from io import open\n",
    "\n",
    "from ventmap.raw_utils import extract_raw\n",
    "\n",
    "# create generator that will iterate through file. Specify False to ensure that\n",
    "# breaths without BS/BE markers will be dropped. If you say True, then breaths\n",
    "# without BS/BE will be kept\n",
    "generator = extract_raw(open(<filepath to vent data>), False)\n",
    "for breath in generator:\n",
    "    # breath data is output in dictionary format\n",
    "    flow, pressure = breath['flow'], breath['pressure']\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If you want to preprocess a breath file for later usage, or if you intend to process it again then it is suggested to use the `process_breath_file` method"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from io import open\n",
    "\n",
    "from ventmap.raw_utils import process_breath_file, read_processed_file\n",
    "\n",
    "# This function will output 2 files. The first will just contain raw breath data\n",
    "# the other will contain higher level processed data\n",
    "process_breath_file(open(<filepath to vent data>), False, 'new_filename')\n",
    "raw_filepath_name = 'new_filename.raw.npy'\n",
    "processed_filepath_name = 'new_filename.processed.npy'\n",
    "\n",
    "for breath in read_processed_file(raw_filepath_name, processed_filepath_name):\n",
    "    # breath data is output in dictionary format\n",
    "    flow, pressure = breath['flow'], breath['pressure']\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "dict_keys(['rel_bn', 'vent_bn', 'flow', 'pressure', 'abs_bs', 'bs_time', 'frame_dur', 'dt'])"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "breath.keys()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For extracting metadata (I-Time, TVe, TVi) from files."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "from ventmap.breath_meta import get_file_breath_meta\n",
    "\n",
    "# Data output is normally in list format. Ordering information can be found in\n",
    "# ventmap.constants.META_HEADER.\n",
    "breath_meta = get_file_breath_meta(<filepath to vent data>)\n",
    "# If you want a pandas DataFrame then you can set the optional argument to_data_frame=True\n",
    "breath_meta = get_file_breath_meta(<filepath to vent data>, to_data_frame=True)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Take a look at the `metadata` dataframe"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>BN</th>\n",
       "      <th>ventBN</th>\n",
       "      <th>BS</th>\n",
       "      <th>IEnd</th>\n",
       "      <th>BE</th>\n",
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       "      <th>iTime</th>\n",
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       "      <th>tvi</th>\n",
       "      <th>...</th>\n",
       "      <th>tvi2</th>\n",
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       "      <th>abs_time_at_x0</th>\n",
       "      <th>abs_time_at_BE</th>\n",
       "      <th>rel_time_at_BS</th>\n",
       "      <th>rel_time_at_x0</th>\n",
       "      <th>rel_time_at_BE</th>\n",
       "      <th>min_pressure</th>\n",
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       "      <td>2129.422222</td>\n",
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       "      <td>2129.422222</td>\n",
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       "      <td>2016-02-17 08-38-13.587473</td>\n",
       "      <td>2016-02-17 08-38-16.087473</td>\n",
       "      <td>2016-02-17 08-38-22.967473</td>\n",
       "      <td>0.02</td>\n",
       "      <td>2.52</td>\n",
       "      <td>9.40</td>\n",
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       "      <td>11.72</td>\n",
       "      <td>18.36</td>\n",
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       "      <td>2.30</td>\n",
       "      <td>6.66</td>\n",
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       "      <td>2261.646667</td>\n",
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       "      <td>2016-02-17 08-38-31.927473</td>\n",
       "      <td>9.42</td>\n",
       "      <td>11.72</td>\n",
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       "      <td>53948</td>\n",
       "      <td>18.38</td>\n",
       "      <td>20.78</td>\n",
       "      <td>27.98</td>\n",
       "      <td>0.33241</td>\n",
       "      <td>2.40</td>\n",
       "      <td>7.22</td>\n",
       "      <td>6.237006</td>\n",
       "      <td>744.514444</td>\n",
       "      <td>...</td>\n",
       "      <td>744.514444</td>\n",
       "      <td>562.745556</td>\n",
       "      <td>120</td>\n",
       "      <td>2016-02-17 08-38-31.947473</td>\n",
       "      <td>2016-02-17 08-38-34.347473</td>\n",
       "      <td>2016-02-17 08-38-41.547473</td>\n",
       "      <td>18.38</td>\n",
       "      <td>20.78</td>\n",
       "      <td>27.98</td>\n",
       "      <td>10.08</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4</td>\n",
       "      <td>53949</td>\n",
       "      <td>28.00</td>\n",
       "      <td>29.34</td>\n",
       "      <td>30.82</td>\n",
       "      <td>0.89333</td>\n",
       "      <td>1.34</td>\n",
       "      <td>1.50</td>\n",
       "      <td>21.126761</td>\n",
       "      <td>402.528889</td>\n",
       "      <td>...</td>\n",
       "      <td>402.528889</td>\n",
       "      <td>194.674444</td>\n",
       "      <td>67</td>\n",
       "      <td>2016-02-17 08-38-41.567473</td>\n",
       "      <td>2016-02-17 08-38-42.907473</td>\n",
       "      <td>2016-02-17 08-38-44.387473</td>\n",
       "      <td>28.00</td>\n",
       "      <td>29.34</td>\n",
       "      <td>30.82</td>\n",
       "      <td>9.81</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5</td>\n",
       "      <td>53950</td>\n",
       "      <td>30.84</td>\n",
       "      <td>31.80</td>\n",
       "      <td>32.96</td>\n",
       "      <td>0.81356</td>\n",
       "      <td>0.96</td>\n",
       "      <td>1.18</td>\n",
       "      <td>28.037383</td>\n",
       "      <td>383.351111</td>\n",
       "      <td>...</td>\n",
       "      <td>383.351111</td>\n",
       "      <td>317.724167</td>\n",
       "      <td>48</td>\n",
       "      <td>2016-02-17 08-38-44.407473</td>\n",
       "      <td>2016-02-17 08-38-45.367473</td>\n",
       "      <td>2016-02-17 08-38-46.527473</td>\n",
       "      <td>30.84</td>\n",
       "      <td>31.80</td>\n",
       "      <td>32.96</td>\n",
       "      <td>9.56</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 36 columns</p>\n",
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      ],
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       "   BN  ventBN     BS   IEnd     BE  I:E ratio  iTime  eTime    inst_RR  \\\n",
       "0   1   53946   0.02   2.52   9.40    0.36232   2.50   6.90   6.382979   \n",
       "1   2   53947   9.42  11.72  18.36    0.34535   2.30   6.66   6.696429   \n",
       "2   3   53948  18.38  20.78  27.98    0.33241   2.40   7.22   6.237006   \n",
       "3   4   53949  28.00  29.34  30.82    0.89333   1.34   1.50  21.126761   \n",
       "4   5   53950  30.84  31.80  32.96    0.81356   0.96   1.18  28.037383   \n",
       "\n",
       "           tvi  ...         tvi2         tve2  x0_index  \\\n",
       "0  2129.422222  ...  2129.422222  2238.049167       125   \n",
       "1  2261.646667  ...  2261.646667  2149.061944       115   \n",
       "2   744.514444  ...   744.514444   562.745556       120   \n",
       "3   402.528889  ...   402.528889   194.674444        67   \n",
       "4   383.351111  ...   383.351111   317.724167        48   \n",
       "\n",
       "               abs_time_at_BS              abs_time_at_x0  \\\n",
       "0  2016-02-17 08-38-13.587473  2016-02-17 08-38-16.087473   \n",
       "1  2016-02-17 08-38-22.987473  2016-02-17 08-38-25.287473   \n",
       "2  2016-02-17 08-38-31.947473  2016-02-17 08-38-34.347473   \n",
       "3  2016-02-17 08-38-41.567473  2016-02-17 08-38-42.907473   \n",
       "4  2016-02-17 08-38-44.407473  2016-02-17 08-38-45.367473   \n",
       "\n",
       "               abs_time_at_BE  rel_time_at_BS  rel_time_at_x0  rel_time_at_BE  \\\n",
       "0  2016-02-17 08-38-22.967473            0.02            2.52            9.40   \n",
       "1  2016-02-17 08-38-31.927473            9.42           11.72           18.36   \n",
       "2  2016-02-17 08-38-41.547473           18.38           20.78           27.98   \n",
       "3  2016-02-17 08-38-44.387473           28.00           29.34           30.82   \n",
       "4  2016-02-17 08-38-46.527473           30.84           31.80           32.96   \n",
       "\n",
       "   min_pressure  \n",
       "0          8.81  \n",
       "1          9.53  \n",
       "2         10.08  \n",
       "3          9.81  \n",
       "4          9.56  \n",
       "\n",
       "[5 rows x 36 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "breath_meta.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "For extracting Experimental Breath Metadata from files, which have some pieces of more experimental information that have been developed since 2017 paper."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "from ventmap.breath_meta import get_file_experimental_breath_meta\n",
    "\n",
    "# Data output is normally in list format. Ordering information can be found in\n",
    "# ventmap.constants.META_HEADER.\n",
    "exp_breath_meta = get_file_experimental_breath_meta(<filepath to vent data>)\n",
    "# If you want a pandas DataFrame then you can set the optional argument to_data_frame=True\n",
    "exp_breath_meta = get_file_experimental_breath_meta(<filepath to vent data>, to_data_frame=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Take a look at the Experimental Breath Metadata dataframe"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>BN</th>\n",
       "      <th>ventBN</th>\n",
       "      <th>BS</th>\n",
       "      <th>IEnd</th>\n",
       "      <th>BE</th>\n",
       "      <th>I:E ratio</th>\n",
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       "      <th>tvi</th>\n",
       "      <th>...</th>\n",
       "      <th>dyn_compliance</th>\n",
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       "      <th>vol_at_.76_sec</th>\n",
       "      <th>vol_at_1_sec</th>\n",
       "      <th>pressure_itime_4</th>\n",
       "      <th>pressure_itime_5</th>\n",
       "      <th>pressure_itime_6</th>\n",
       "      <th>pressure_itime_by_pip5</th>\n",
       "      <th>pressure_itime_by_pip6</th>\n",
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       "      <td>0.02</td>\n",
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       "      <td>9.40</td>\n",
       "      <td>0.36232</td>\n",
       "      <td>2.50</td>\n",
       "      <td>6.90</td>\n",
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       "      <td>2129.422222</td>\n",
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       "      <td>-510.342222</td>\n",
       "      <td>-882.069167</td>\n",
       "      <td>-1095.104722</td>\n",
       "      <td>3.36</td>\n",
       "      <td>3.20</td>\n",
       "      <td>3.14</td>\n",
       "      <td>3.34</td>\n",
       "      <td>3.38</td>\n",
       "      <td>2.56</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2</td>\n",
       "      <td>53947</td>\n",
       "      <td>9.42</td>\n",
       "      <td>11.72</td>\n",
       "      <td>18.36</td>\n",
       "      <td>0.34535</td>\n",
       "      <td>2.30</td>\n",
       "      <td>6.66</td>\n",
       "      <td>6.696429</td>\n",
       "      <td>2261.646667</td>\n",
       "      <td>...</td>\n",
       "      <td>0.212441</td>\n",
       "      <td>-639.298889</td>\n",
       "      <td>-958.682778</td>\n",
       "      <td>-1147.471667</td>\n",
       "      <td>3.08</td>\n",
       "      <td>2.90</td>\n",
       "      <td>2.86</td>\n",
       "      <td>2.88</td>\n",
       "      <td>3.02</td>\n",
       "      <td>2.36</td>\n",
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       "      <td>53948</td>\n",
       "      <td>18.38</td>\n",
       "      <td>20.78</td>\n",
       "      <td>27.98</td>\n",
       "      <td>0.33241</td>\n",
       "      <td>2.40</td>\n",
       "      <td>7.22</td>\n",
       "      <td>6.237006</td>\n",
       "      <td>744.514444</td>\n",
       "      <td>...</td>\n",
       "      <td>0.081617</td>\n",
       "      <td>-186.508889</td>\n",
       "      <td>-257.480278</td>\n",
       "      <td>-305.858056</td>\n",
       "      <td>2.44</td>\n",
       "      <td>2.42</td>\n",
       "      <td>2.42</td>\n",
       "      <td>2.44</td>\n",
       "      <td>2.46</td>\n",
       "      <td>2.46</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4</td>\n",
       "      <td>53949</td>\n",
       "      <td>28.00</td>\n",
       "      <td>29.34</td>\n",
       "      <td>30.82</td>\n",
       "      <td>0.89333</td>\n",
       "      <td>1.34</td>\n",
       "      <td>1.50</td>\n",
       "      <td>21.126761</td>\n",
       "      <td>402.528889</td>\n",
       "      <td>...</td>\n",
       "      <td>0.044885</td>\n",
       "      <td>-169.228889</td>\n",
       "      <td>-198.612222</td>\n",
       "      <td>-200.667500</td>\n",
       "      <td>1.38</td>\n",
       "      <td>1.36</td>\n",
       "      <td>1.36</td>\n",
       "      <td>1.38</td>\n",
       "      <td>1.44</td>\n",
       "      <td>1.40</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5</td>\n",
       "      <td>53950</td>\n",
       "      <td>30.84</td>\n",
       "      <td>31.80</td>\n",
       "      <td>32.96</td>\n",
       "      <td>0.81356</td>\n",
       "      <td>0.96</td>\n",
       "      <td>1.18</td>\n",
       "      <td>28.037383</td>\n",
       "      <td>383.351111</td>\n",
       "      <td>...</td>\n",
       "      <td>0.043672</td>\n",
       "      <td>-195.342222</td>\n",
       "      <td>-271.551111</td>\n",
       "      <td>-316.975556</td>\n",
       "      <td>0.98</td>\n",
       "      <td>0.98</td>\n",
       "      <td>0.96</td>\n",
       "      <td>1.00</td>\n",
       "      <td>1.12</td>\n",
       "      <td>1.02</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 49 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   BN  ventBN     BS   IEnd     BE  I:E ratio  iTime  eTime    inst_RR  \\\n",
       "0   1   53946   0.02   2.52   9.40    0.36232   2.50   6.90   6.382979   \n",
       "1   2   53947   9.42  11.72  18.36    0.34535   2.30   6.66   6.696429   \n",
       "2   3   53948  18.38  20.78  27.98    0.33241   2.40   7.22   6.237006   \n",
       "3   4   53949  28.00  29.34  30.82    0.89333   1.34   1.50  21.126761   \n",
       "4   5   53950  30.84  31.80  32.96    0.81356   0.96   1.18  28.037383   \n",
       "\n",
       "           tvi  ...  dyn_compliance  vol_at_.5_sec  vol_at_.76_sec  \\\n",
       "0  2129.422222  ...        0.218268    -510.342222     -882.069167   \n",
       "1  2261.646667  ...        0.212441    -639.298889     -958.682778   \n",
       "2   744.514444  ...        0.081617    -186.508889     -257.480278   \n",
       "3   402.528889  ...        0.044885    -169.228889     -198.612222   \n",
       "4   383.351111  ...        0.043672    -195.342222     -271.551111   \n",
       "\n",
       "   vol_at_1_sec  pressure_itime_4  pressure_itime_5  pressure_itime_6  \\\n",
       "0  -1095.104722              3.36              3.20              3.14   \n",
       "1  -1147.471667              3.08              2.90              2.86   \n",
       "2   -305.858056              2.44              2.42              2.42   \n",
       "3   -200.667500              1.38              1.36              1.36   \n",
       "4   -316.975556              0.98              0.98              0.96   \n",
       "\n",
       "   pressure_itime_by_pip5  pressure_itime_by_pip6  pressure_itime_from_front  \n",
       "0                    3.34                    3.38                       2.56  \n",
       "1                    2.88                    3.02                       2.36  \n",
       "2                    2.44                    2.46                       2.46  \n",
       "3                    1.38                    1.44                       1.40  \n",
       "4                    1.00                    1.12                       1.02  \n",
       "\n",
       "[5 rows x 49 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exp_breath_meta.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(96, 49)"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exp_breath_meta.shape"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Adding new features - example\n",
    "\n",
    "The information you can use from raw data file are:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "dict_keys(['rel_bn', 'vent_bn', 'flow', 'pressure', 'abs_bs', 'bs_time', 'frame_dur', 'dt'])"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "breath.keys()\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If you want to create a new feature, first define your feature as below:\n",
    "For example, if you want to calculate the time between the Maximum of flow and the Minimun of flow for each breath."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "def time_btw_max_min_flow(breath):\n",
    "    flow = breath['flow']\n",
    "    dt = breath['dt']\n",
    "    btw_time = abs((flow.index(max(flow)) - flow.index(min(flow)))*dt)\n",
    "    return round(btw_time,2)\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "And then add you function at here, implement `extract_new_feature`, return a list `feature_values` for your new feature."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "def extract_new_feature(file):\n",
    "    feature_values = []\n",
    "    for breath in extract_raw(file, True):\n",
    "        #TODO: add new feature function\n",
    "        btw_time = time_btw_max_min_flow(breath)\n",
    "        feature_values.append(btw_time)\n",
    "    return feature_values\n",
    "\n",
    "btw_times = extract_new_feature(open(<filepath to vent data>))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Finally, add this new feature to your original dataframe."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "exp_breath_meta['time_btw_max_min'] = btw_times"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Take a look at the dataframe `exp_breath_meta` having one more feature `time_btw_max_min` at the end."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>BN</th>\n",
       "      <th>ventBN</th>\n",
       "      <th>BS</th>\n",
       "      <th>IEnd</th>\n",
       "      <th>BE</th>\n",
       "      <th>I:E ratio</th>\n",
       "      <th>iTime</th>\n",
       "      <th>eTime</th>\n",
       "      <th>inst_RR</th>\n",
       "      <th>tvi</th>\n",
       "      <th>...</th>\n",
       "      <th>vol_at_.5_sec</th>\n",
       "      <th>vol_at_.76_sec</th>\n",
       "      <th>vol_at_1_sec</th>\n",
       "      <th>pressure_itime_4</th>\n",
       "      <th>pressure_itime_5</th>\n",
       "      <th>pressure_itime_6</th>\n",
       "      <th>pressure_itime_by_pip5</th>\n",
       "      <th>pressure_itime_by_pip6</th>\n",
       "      <th>pressure_itime_from_front</th>\n",
       "      <th>time_btw_max_min</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1</td>\n",
       "      <td>53946</td>\n",
       "      <td>0.02</td>\n",
       "      <td>2.52</td>\n",
       "      <td>9.40</td>\n",
       "      <td>0.36232</td>\n",
       "      <td>2.50</td>\n",
       "      <td>6.90</td>\n",
       "      <td>6.382979</td>\n",
       "      <td>2129.422222</td>\n",
       "      <td>...</td>\n",
       "      <td>-510.342222</td>\n",
       "      <td>-882.069167</td>\n",
       "      <td>-1095.104722</td>\n",
       "      <td>3.36</td>\n",
       "      <td>3.20</td>\n",
       "      <td>3.14</td>\n",
       "      <td>3.34</td>\n",
       "      <td>3.38</td>\n",
       "      <td>2.56</td>\n",
       "      <td>1.88</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2</td>\n",
       "      <td>53947</td>\n",
       "      <td>9.42</td>\n",
       "      <td>11.72</td>\n",
       "      <td>18.36</td>\n",
       "      <td>0.34535</td>\n",
       "      <td>2.30</td>\n",
       "      <td>6.66</td>\n",
       "      <td>6.696429</td>\n",
       "      <td>2261.646667</td>\n",
       "      <td>...</td>\n",
       "      <td>-639.298889</td>\n",
       "      <td>-958.682778</td>\n",
       "      <td>-1147.471667</td>\n",
       "      <td>3.08</td>\n",
       "      <td>2.90</td>\n",
       "      <td>2.86</td>\n",
       "      <td>2.88</td>\n",
       "      <td>3.02</td>\n",
       "      <td>2.36</td>\n",
       "      <td>1.22</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>3</td>\n",
       "      <td>53948</td>\n",
       "      <td>18.38</td>\n",
       "      <td>20.78</td>\n",
       "      <td>27.98</td>\n",
       "      <td>0.33241</td>\n",
       "      <td>2.40</td>\n",
       "      <td>7.22</td>\n",
       "      <td>6.237006</td>\n",
       "      <td>744.514444</td>\n",
       "      <td>...</td>\n",
       "      <td>-186.508889</td>\n",
       "      <td>-257.480278</td>\n",
       "      <td>-305.858056</td>\n",
       "      <td>2.44</td>\n",
       "      <td>2.42</td>\n",
       "      <td>2.42</td>\n",
       "      <td>2.44</td>\n",
       "      <td>2.46</td>\n",
       "      <td>2.46</td>\n",
       "      <td>2.02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>4</td>\n",
       "      <td>53949</td>\n",
       "      <td>28.00</td>\n",
       "      <td>29.34</td>\n",
       "      <td>30.82</td>\n",
       "      <td>0.89333</td>\n",
       "      <td>1.34</td>\n",
       "      <td>1.50</td>\n",
       "      <td>21.126761</td>\n",
       "      <td>402.528889</td>\n",
       "      <td>...</td>\n",
       "      <td>-169.228889</td>\n",
       "      <td>-198.612222</td>\n",
       "      <td>-200.667500</td>\n",
       "      <td>1.38</td>\n",
       "      <td>1.36</td>\n",
       "      <td>1.36</td>\n",
       "      <td>1.38</td>\n",
       "      <td>1.44</td>\n",
       "      <td>1.40</td>\n",
       "      <td>1.20</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>5</td>\n",
       "      <td>53950</td>\n",
       "      <td>30.84</td>\n",
       "      <td>31.80</td>\n",
       "      <td>32.96</td>\n",
       "      <td>0.81356</td>\n",
       "      <td>0.96</td>\n",
       "      <td>1.18</td>\n",
       "      <td>28.037383</td>\n",
       "      <td>383.351111</td>\n",
       "      <td>...</td>\n",
       "      <td>-195.342222</td>\n",
       "      <td>-271.551111</td>\n",
       "      <td>-316.975556</td>\n",
       "      <td>0.98</td>\n",
       "      <td>0.98</td>\n",
       "      <td>0.96</td>\n",
       "      <td>1.00</td>\n",
       "      <td>1.12</td>\n",
       "      <td>1.02</td>\n",
       "      <td>0.82</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 50 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   BN  ventBN     BS   IEnd     BE  I:E ratio  iTime  eTime    inst_RR  \\\n",
       "0   1   53946   0.02   2.52   9.40    0.36232   2.50   6.90   6.382979   \n",
       "1   2   53947   9.42  11.72  18.36    0.34535   2.30   6.66   6.696429   \n",
       "2   3   53948  18.38  20.78  27.98    0.33241   2.40   7.22   6.237006   \n",
       "3   4   53949  28.00  29.34  30.82    0.89333   1.34   1.50  21.126761   \n",
       "4   5   53950  30.84  31.80  32.96    0.81356   0.96   1.18  28.037383   \n",
       "\n",
       "           tvi  ...  vol_at_.5_sec  vol_at_.76_sec  vol_at_1_sec  \\\n",
       "0  2129.422222  ...    -510.342222     -882.069167  -1095.104722   \n",
       "1  2261.646667  ...    -639.298889     -958.682778  -1147.471667   \n",
       "2   744.514444  ...    -186.508889     -257.480278   -305.858056   \n",
       "3   402.528889  ...    -169.228889     -198.612222   -200.667500   \n",
       "4   383.351111  ...    -195.342222     -271.551111   -316.975556   \n",
       "\n",
       "   pressure_itime_4  pressure_itime_5  pressure_itime_6  \\\n",
       "0              3.36              3.20              3.14   \n",
       "1              3.08              2.90              2.86   \n",
       "2              2.44              2.42              2.42   \n",
       "3              1.38              1.36              1.36   \n",
       "4              0.98              0.98              0.96   \n",
       "\n",
       "   pressure_itime_by_pip5  pressure_itime_by_pip6  pressure_itime_from_front  \\\n",
       "0                    3.34                    3.38                       2.56   \n",
       "1                    2.88                    3.02                       2.36   \n",
       "2                    2.44                    2.46                       2.46   \n",
       "3                    1.38                    1.44                       1.40   \n",
       "4                    1.00                    1.12                       1.02   \n",
       "\n",
       "   time_btw_max_min  \n",
       "0              1.88  \n",
       "1              1.22  \n",
       "2              2.02  \n",
       "3              1.20  \n",
       "4              0.82  \n",
       "\n",
       "[5 rows x 50 columns]"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exp_breath_meta.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Extras\n",
    "Clear null bytes from a file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from io import open\n",
    "\n",
    "from ventmap.clear_null_bytes import clear_descriptor_null_bytes\n",
    "\n",
    "cleared_descriptor = clear_descriptor_null_bytes(open(<filepath to vent data>))\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Cut a file into specific BN interval and store for later use"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from io import open\n",
    "\n",
    "from ventmap.cut_breath_section import cut_breath_section\n",
    "\n",
    "# get file descriptor for the truncated data\n",
    "new_descriptor = cut_breath_section(open(<filepath to vent data>), <breath start num>, <breath end num>)\n",
    "# write output to file\n",
    "with open('new_file', 'w') as f:\n",
    "    f.write(new_descriptor.read())\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Check if there is a plateau pressure in a breath"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from io import open\n",
    "\n",
    "from ventmap.raw_utils import extract_raw\n",
    "from ventmap.SAM import check_if_plat_occurs\n",
    "\n",
    "generator = extract_raw(open(<filepath to vent data>), False)\n",
    "for breath in generator:\n",
    "    flow, pressure = breath['flow'], breath['pressure']\n",
    "\n",
    "    # .02 is the sampling rate for the PB-840 corresponding with 1 obs every .02 seconds\n",
    "    did_plat_occur = check_if_plat_occurs(flow, pressure, .02)\n"
   ]
  }
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