notebooks/bodytex_annotations_data.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<p>Example showing how to load and process the manual annotations</p>\n",
    "<p>We show how to load the training, validation, and test paritions. As well, we show how to load the test data for the 3 annotators.</p>"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2\n",
    "import os\n",
    "import sys\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "sys.path.insert(0, os.path.abspath(os.path.join(os.getcwd(), '../../skin3d')))\n",
    "from skin3d.bodytex import BodyTexDataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "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>subject_id</th>\n",
       "      <th>scan_name</th>\n",
       "      <th>scan_id</th>\n",
       "      <th>sex</th>\n",
       "      <th>pose</th>\n",
       "      <th>partition</th>\n",
       "      <th>selected</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>000-001</td>\n",
       "      <td>000-f-run</td>\n",
       "      <td>000</td>\n",
       "      <td>f</td>\n",
       "      <td>run</td>\n",
       "      <td>test</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>000-001</td>\n",
       "      <td>001-f-u</td>\n",
       "      <td>001</td>\n",
       "      <td>f</td>\n",
       "      <td>u</td>\n",
       "      <td>test</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>002-003</td>\n",
       "      <td>002-f-run</td>\n",
       "      <td>002</td>\n",
       "      <td>f</td>\n",
       "      <td>run</td>\n",
       "      <td>train</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>002-003</td>\n",
       "      <td>003-f-u</td>\n",
       "      <td>003</td>\n",
       "      <td>f</td>\n",
       "      <td>u</td>\n",
       "      <td>train</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>004-005</td>\n",
       "      <td>004-f-run</td>\n",
       "      <td>004</td>\n",
       "      <td>f</td>\n",
       "      <td>run</td>\n",
       "      <td>train</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  subject_id  scan_name scan_id sex pose partition  selected\n",
       "0    000-001  000-f-run     000   f  run      test      True\n",
       "1    000-001    001-f-u     001   f    u      test     False\n",
       "2    002-003  002-f-run     002   f  run     train      True\n",
       "3    002-003    003-f-u     003   f    u     train      True\n",
       "4    004-005  004-f-run     004   f  run     train      True"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# File path of the bodytex CSV.\n",
    "bodytex_csv = '../data/3dbodytex-1.1-highres/bodytex.csv'\n",
    "bodytex_df = pd.read_csv(bodytex_csv, converters={'scan_id': lambda x: str(x)})\n",
    "bodytex_df.head()\n",
    "# Each row represents a mesh, with a unique `scan_id` and `scan_name`.\n",
    "# We use the `scan_id` to identify each mesh.\n",
    "# The `scan_name` corresponds to the folder name used by 3DBodyTex.\n",
    "\n",
    "# Each subject has two meshes, that can be identified with the `subject_id`,\n",
    "# e.g., '000-001' means mesh `000` and mesh `001` are of the same subject.\n",
    "\n",
    "# Each subject is assigned to a partition (e.g., train, test).\n",
    "\n",
    "# If a mesh has `selected=True`, then we provide manual annotations.\n",
    "# Otherwise, we do not provide annotations for the mesh. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of scans annotated with lesions: 218\n",
      "Number of annotated training scans: 128\n",
      "Number of annotated validation scans: 40\n",
      "Number of annotated testing scans: 40\n",
      "Number of annotated longitudinal scans: 10\n",
      "Total number of lesions annotated: 26507\n",
      "Average annotated lesion width=22.07, height=22.95\n"
     ]
    }
   ],
   "source": [
    "bodytex = BodyTexDataset(df=bodytex_df)\n",
    "bodytex.summary()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "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>subject_id</th>\n",
       "      <th>scan_name</th>\n",
       "      <th>scan_id</th>\n",
       "      <th>sex</th>\n",
       "      <th>pose</th>\n",
       "      <th>partition</th>\n",
       "      <th>selected</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>002-003</td>\n",
       "      <td>002-f-run</td>\n",
       "      <td>002</td>\n",
       "      <td>f</td>\n",
       "      <td>run</td>\n",
       "      <td>train</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>002-003</td>\n",
       "      <td>003-f-u</td>\n",
       "      <td>003</td>\n",
       "      <td>f</td>\n",
       "      <td>u</td>\n",
       "      <td>train</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>004-005</td>\n",
       "      <td>004-f-run</td>\n",
       "      <td>004</td>\n",
       "      <td>f</td>\n",
       "      <td>run</td>\n",
       "      <td>train</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>004-005</td>\n",
       "      <td>005-f-u</td>\n",
       "      <td>005</td>\n",
       "      <td>f</td>\n",
       "      <td>u</td>\n",
       "      <td>train</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>006-007</td>\n",
       "      <td>006-f-run</td>\n",
       "      <td>006</td>\n",
       "      <td>f</td>\n",
       "      <td>run</td>\n",
       "      <td>train</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  subject_id  scan_name scan_id sex pose partition  selected\n",
       "2    002-003  002-f-run     002   f  run     train      True\n",
       "3    002-003    003-f-u     003   f    u     train      True\n",
       "4    004-005  004-f-run     004   f  run     train      True\n",
       "5    004-005    005-f-u     005   f    u     train      True\n",
       "6    006-007  006-f-run     006   f  run     train      True"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# You can get a dataframe of the data used for training.\n",
    "train_df = bodytex.annotated_samples_in_partition('train')\n",
    "train_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "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>subject_id</th>\n",
       "      <th>scan_name</th>\n",
       "      <th>scan_id</th>\n",
       "      <th>sex</th>\n",
       "      <th>pose</th>\n",
       "      <th>partition</th>\n",
       "      <th>selected</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>010-011</td>\n",
       "      <td>010-f-run</td>\n",
       "      <td>010</td>\n",
       "      <td>f</td>\n",
       "      <td>run</td>\n",
       "      <td>valid</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>010-011</td>\n",
       "      <td>011-f-u</td>\n",
       "      <td>011</td>\n",
       "      <td>f</td>\n",
       "      <td>u</td>\n",
       "      <td>valid</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>018-019</td>\n",
       "      <td>018-f-scape013</td>\n",
       "      <td>018</td>\n",
       "      <td>f</td>\n",
       "      <td>scape013</td>\n",
       "      <td>valid</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>022-023</td>\n",
       "      <td>022-f-scape061</td>\n",
       "      <td>022</td>\n",
       "      <td>f</td>\n",
       "      <td>scape061</td>\n",
       "      <td>valid</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>030-031</td>\n",
       "      <td>030-f-scape059</td>\n",
       "      <td>030</td>\n",
       "      <td>f</td>\n",
       "      <td>scape059</td>\n",
       "      <td>valid</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   subject_id       scan_name scan_id sex      pose partition  selected\n",
       "10    010-011       010-f-run     010   f       run     valid      True\n",
       "11    010-011         011-f-u     011   f         u     valid      True\n",
       "18    018-019  018-f-scape013     018   f  scape013     valid      True\n",
       "22    022-023  022-f-scape061     022   f  scape061     valid      True\n",
       "30    030-031  030-f-scape059     030   f  scape059     valid      True"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# You can get a dataframe of the validation data.\n",
    "valid_df = bodytex.annotated_samples_in_partition('valid').head()\n",
    "valid_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "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>subject_id</th>\n",
       "      <th>scan_name</th>\n",
       "      <th>scan_id</th>\n",
       "      <th>sex</th>\n",
       "      <th>pose</th>\n",
       "      <th>partition</th>\n",
       "      <th>selected</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>000-001</td>\n",
       "      <td>000-f-run</td>\n",
       "      <td>000</td>\n",
       "      <td>f</td>\n",
       "      <td>run</td>\n",
       "      <td>test</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>008-009</td>\n",
       "      <td>009-f-u</td>\n",
       "      <td>009</td>\n",
       "      <td>f</td>\n",
       "      <td>u</td>\n",
       "      <td>test</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>020-021</td>\n",
       "      <td>021-f-u</td>\n",
       "      <td>021</td>\n",
       "      <td>f</td>\n",
       "      <td>u</td>\n",
       "      <td>test</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>24</th>\n",
       "      <td>024-025</td>\n",
       "      <td>024-f-scape046</td>\n",
       "      <td>024</td>\n",
       "      <td>f</td>\n",
       "      <td>scape046</td>\n",
       "      <td>test</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>036-037</td>\n",
       "      <td>036-f-scape010</td>\n",
       "      <td>036</td>\n",
       "      <td>f</td>\n",
       "      <td>scape010</td>\n",
       "      <td>test</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   subject_id       scan_name scan_id sex      pose partition  selected\n",
       "0     000-001       000-f-run     000   f       run      test      True\n",
       "9     008-009         009-f-u     009   f         u      test      True\n",
       "21    020-021         021-f-u     021   f         u      test      True\n",
       "24    024-025  024-f-scape046     024   f  scape046      test      True\n",
       "36    036-037  036-f-scape010     036   f  scape010      test      True"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# You can get a dataframe of the test data.\n",
    "test_df = bodytex.annotated_samples_in_partition('test')\n",
    "test_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "002\n"
     ]
    },
    {
     "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>scan_id</th>\n",
       "      <th>x</th>\n",
       "      <th>y</th>\n",
       "      <th>x2</th>\n",
       "      <th>y2</th>\n",
       "      <th>width</th>\n",
       "      <th>height</th>\n",
       "      <th>annotator</th>\n",
       "      <th>lesion_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>002</td>\n",
       "      <td>779</td>\n",
       "      <td>877</td>\n",
       "      <td>797</td>\n",
       "      <td>895</td>\n",
       "      <td>18</td>\n",
       "      <td>18</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>002</td>\n",
       "      <td>1138</td>\n",
       "      <td>827</td>\n",
       "      <td>1161</td>\n",
       "      <td>846</td>\n",
       "      <td>23</td>\n",
       "      <td>19</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>002</td>\n",
       "      <td>1013</td>\n",
       "      <td>902</td>\n",
       "      <td>1033</td>\n",
       "      <td>921</td>\n",
       "      <td>20</td>\n",
       "      <td>19</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>002</td>\n",
       "      <td>702</td>\n",
       "      <td>808</td>\n",
       "      <td>721</td>\n",
       "      <td>823</td>\n",
       "      <td>19</td>\n",
       "      <td>15</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>002</td>\n",
       "      <td>685</td>\n",
       "      <td>753</td>\n",
       "      <td>702</td>\n",
       "      <td>771</td>\n",
       "      <td>17</td>\n",
       "      <td>18</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  scan_id     x    y    x2   y2  width  height annotator lesion_id\n",
       "0     002   779  877   797  895     18      18                    \n",
       "1     002  1138  827  1161  846     23      19                    \n",
       "2     002  1013  902  1033  921     20      19                    \n",
       "3     002   702  808   721  823     19      15                    \n",
       "4     002   685  753   702  771     17      18                    "
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# You can get the bounding boxes for scan_id '002'\n",
    "# that belongs to the training data.\n",
    "scan_id = train_df.scan_id.values[0]\n",
    "print(scan_id)\n",
    "bodytex.annotation(scan_id).head()\n",
    "# Each row represents a bounding box.\n",
    "# x,y indicate the bounding box starting coordinate within the texture image.\n",
    "# x2, y2 indicate the ending coordinate of the bounding box.\n",
    "# width, height are the width and height of the bounding box with respect to x,y.\n",
    "\n",
    "# (x2, y2) and (width, height) are equivalent ways of representing \n",
    "# the bounding box on the 2D texture image.\n",
    "# x + width = x2\n",
    "# y + height = y2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "010\n"
     ]
    },
    {
     "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>scan_id</th>\n",
       "      <th>x</th>\n",
       "      <th>y</th>\n",
       "      <th>x2</th>\n",
       "      <th>y2</th>\n",
       "      <th>width</th>\n",
       "      <th>height</th>\n",
       "      <th>annotator</th>\n",
       "      <th>lesion_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>010</td>\n",
       "      <td>238</td>\n",
       "      <td>1165</td>\n",
       "      <td>260</td>\n",
       "      <td>1188</td>\n",
       "      <td>22</td>\n",
       "      <td>23</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>010</td>\n",
       "      <td>204</td>\n",
       "      <td>1066</td>\n",
       "      <td>219</td>\n",
       "      <td>1081</td>\n",
       "      <td>15</td>\n",
       "      <td>15</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>010</td>\n",
       "      <td>260</td>\n",
       "      <td>1067</td>\n",
       "      <td>276</td>\n",
       "      <td>1079</td>\n",
       "      <td>16</td>\n",
       "      <td>12</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>010</td>\n",
       "      <td>1008</td>\n",
       "      <td>616</td>\n",
       "      <td>1026</td>\n",
       "      <td>631</td>\n",
       "      <td>18</td>\n",
       "      <td>15</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>010</td>\n",
       "      <td>1118</td>\n",
       "      <td>641</td>\n",
       "      <td>1140</td>\n",
       "      <td>660</td>\n",
       "      <td>22</td>\n",
       "      <td>19</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  scan_id     x     y    x2    y2  width  height annotator lesion_id\n",
       "0     010   238  1165   260  1188     22      23                    \n",
       "1     010   204  1066   219  1081     15      15                    \n",
       "2     010   260  1067   276  1079     16      12                    \n",
       "3     010  1008   616  1026   631     18      15                    \n",
       "4     010  1118   641  1140   660     22      19                    "
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Similarly, you can get the bounding boxes\n",
    "# for scan_id '010' in the validation data.\n",
    "scan_id = valid_df.scan_id.values[0]\n",
    "print(scan_id)\n",
    "bodytex.annotation(scan_id).head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "089\n"
     ]
    },
    {
     "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>scan_id</th>\n",
       "      <th>x</th>\n",
       "      <th>y</th>\n",
       "      <th>x2</th>\n",
       "      <th>y2</th>\n",
       "      <th>width</th>\n",
       "      <th>height</th>\n",
       "      <th>annotator</th>\n",
       "      <th>lesion_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>089</td>\n",
       "      <td>1287</td>\n",
       "      <td>290</td>\n",
       "      <td>1299</td>\n",
       "      <td>299</td>\n",
       "      <td>12</td>\n",
       "      <td>9</td>\n",
       "      <td>A1</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>089</td>\n",
       "      <td>1286</td>\n",
       "      <td>301</td>\n",
       "      <td>1298</td>\n",
       "      <td>313</td>\n",
       "      <td>12</td>\n",
       "      <td>12</td>\n",
       "      <td>A1</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>089</td>\n",
       "      <td>1207</td>\n",
       "      <td>252</td>\n",
       "      <td>1221</td>\n",
       "      <td>267</td>\n",
       "      <td>14</td>\n",
       "      <td>15</td>\n",
       "      <td>A1</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>089</td>\n",
       "      <td>1005</td>\n",
       "      <td>232</td>\n",
       "      <td>1020</td>\n",
       "      <td>246</td>\n",
       "      <td>15</td>\n",
       "      <td>14</td>\n",
       "      <td>A1</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>089</td>\n",
       "      <td>1307</td>\n",
       "      <td>170</td>\n",
       "      <td>1319</td>\n",
       "      <td>181</td>\n",
       "      <td>12</td>\n",
       "      <td>11</td>\n",
       "      <td>A1</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  scan_id     x    y    x2   y2  width  height annotator lesion_id\n",
       "0     089  1287  290  1299  299     12       9        A1          \n",
       "1     089  1286  301  1298  313     12      12        A1          \n",
       "2     089  1207  252  1221  267     14      15        A1          \n",
       "3     089  1005  232  1020  246     15      14        A1          \n",
       "4     089  1307  170  1319  181     12      11        A1          "
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# For testing, we evaluated against 3 annotators, \n",
    "# where each annotator provided independent bounding boxes for each test scan.\n",
    "# For scans in the \"test\" partition, you can specify the annotator \n",
    "# along with the scan_id to get the bounding boxes for a specific annotator.\n",
    "scan_id = test_df.scan_id.values[10]\n",
    "print(scan_id)\n",
    "# Here's how you specify the `annotator` for scans in the test partition.\n",
    "# (this won't work for scans that are not part of the \"test\" partition)\n",
    "bodytex.annotation(scan_id, annotator='A1').head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "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>scan_id</th>\n",
       "      <th>x</th>\n",
       "      <th>y</th>\n",
       "      <th>x2</th>\n",
       "      <th>y2</th>\n",
       "      <th>width</th>\n",
       "      <th>height</th>\n",
       "      <th>annotator</th>\n",
       "      <th>lesion_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>089</td>\n",
       "      <td>1285</td>\n",
       "      <td>301</td>\n",
       "      <td>1300</td>\n",
       "      <td>318</td>\n",
       "      <td>15</td>\n",
       "      <td>17</td>\n",
       "      <td>A2</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>089</td>\n",
       "      <td>633</td>\n",
       "      <td>1410</td>\n",
       "      <td>657</td>\n",
       "      <td>1431</td>\n",
       "      <td>24</td>\n",
       "      <td>21</td>\n",
       "      <td>A2</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>089</td>\n",
       "      <td>834</td>\n",
       "      <td>1418</td>\n",
       "      <td>854</td>\n",
       "      <td>1444</td>\n",
       "      <td>20</td>\n",
       "      <td>26</td>\n",
       "      <td>A2</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>089</td>\n",
       "      <td>713</td>\n",
       "      <td>1434</td>\n",
       "      <td>736</td>\n",
       "      <td>1461</td>\n",
       "      <td>23</td>\n",
       "      <td>27</td>\n",
       "      <td>A2</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>089</td>\n",
       "      <td>566</td>\n",
       "      <td>2134</td>\n",
       "      <td>582</td>\n",
       "      <td>2155</td>\n",
       "      <td>16</td>\n",
       "      <td>21</td>\n",
       "      <td>A2</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  scan_id     x     y    x2    y2  width  height annotator lesion_id\n",
       "0     089  1285   301  1300   318     15      17        A2          \n",
       "1     089   633  1410   657  1431     24      21        A2          \n",
       "2     089   834  1418   854  1444     20      26        A2          \n",
       "3     089   713  1434   736  1461     23      27        A2          \n",
       "4     089   566  2134   582  2155     16      21        A2          "
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Another annotator for the same test scan ID of '089'.\n",
    "bodytex.annotation(scan_id, annotator='A2').head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "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>scan_id</th>\n",
       "      <th>x</th>\n",
       "      <th>y</th>\n",
       "      <th>x2</th>\n",
       "      <th>y2</th>\n",
       "      <th>width</th>\n",
       "      <th>height</th>\n",
       "      <th>annotator</th>\n",
       "      <th>lesion_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>089</td>\n",
       "      <td>634</td>\n",
       "      <td>1407</td>\n",
       "      <td>654</td>\n",
       "      <td>1434</td>\n",
       "      <td>20</td>\n",
       "      <td>27</td>\n",
       "      <td>A3</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>089</td>\n",
       "      <td>713</td>\n",
       "      <td>1434</td>\n",
       "      <td>734</td>\n",
       "      <td>1458</td>\n",
       "      <td>21</td>\n",
       "      <td>24</td>\n",
       "      <td>A3</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>089</td>\n",
       "      <td>841</td>\n",
       "      <td>1425</td>\n",
       "      <td>857</td>\n",
       "      <td>1441</td>\n",
       "      <td>16</td>\n",
       "      <td>16</td>\n",
       "      <td>A3</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>089</td>\n",
       "      <td>557</td>\n",
       "      <td>2258</td>\n",
       "      <td>580</td>\n",
       "      <td>2282</td>\n",
       "      <td>23</td>\n",
       "      <td>24</td>\n",
       "      <td>A3</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>089</td>\n",
       "      <td>1319</td>\n",
       "      <td>2886</td>\n",
       "      <td>1342</td>\n",
       "      <td>2911</td>\n",
       "      <td>23</td>\n",
       "      <td>25</td>\n",
       "      <td>A3</td>\n",
       "      <td></td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  scan_id     x     y    x2    y2  width  height annotator lesion_id\n",
       "0     089   634  1407   654  1434     20      27        A3          \n",
       "1     089   713  1434   734  1458     21      24        A3          \n",
       "2     089   841  1425   857  1441     16      16        A3          \n",
       "3     089   557  2258   580  2282     23      24        A3          \n",
       "4     089  1319  2886  1342  2911     23      25        A3          "
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# The final annotator A3 on the test scan ID of '089'.\n",
    "bodytex.annotation(scan_id, annotator='A3').head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Please see the other example notebooks for additional details."
   ]
  }
 ],
 "metadata": {
  "interpreter": {
   "hash": "ae6326c03338b4695674937b448ebbab5b2e63f9d18074dc77b16f37539e01f3"
  },
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "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": "3.7.11"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}