preprocess.ipynb

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     "text": [
      "1 Physical GPUs, 1 Logical GPUs\n"
     ]
    }
   ],
   "source": [
    "import os\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "from scipy.io import wavfile\n",
    "from util import util\n",
    "\n",
    "import torch\n",
    "from beats.BEATs import BEATs, BEATsConfig"
   ]
  },
  {
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      ],
      "text/plain": [
       "          ID  Sex  Age  Disease category  Narrow pitch range  \\\n",
       "0    1202f15    2   39                 1                   1   \n",
       "1    0600ve0    1   69                 2                   1   \n",
       "2    1001o7l    2   59                 2                   1   \n",
       "3    1201c1t    2   47                 1                   1   \n",
       "4    0402jvt    1   87                 1                   0   \n",
       "..       ...  ...  ...               ...                 ...   \n",
       "995  0G00ftn    1   75                 3                   0   \n",
       "996  1201pkr    1   40                 4                   0   \n",
       "997  0202p64    2   68                 3                   0   \n",
       "998  12021au    2   42                 2                   0   \n",
       "999  04027it    1   72                 2                   1   \n",
       "\n",
       "     Decreased volume  Fatigue  Dryness  Lumping  heartburn  ...  \\\n",
       "0                   1        1        1        1          0  ...   \n",
       "1                   1        1        1        0          0  ...   \n",
       "2                   1        1        1        0          0  ...   \n",
       "3                   0        1        1        1          0  ...   \n",
       "4                   0        0        0        0          0  ...   \n",
       "..                ...      ...      ...      ...        ...  ...   \n",
       "995                 0        0        0        0          0  ...   \n",
       "996                 0        1        0        0          0  ...   \n",
       "997                 1        1        0        0          0  ...   \n",
       "998                 0        1        1        1          0  ...   \n",
       "999                 1        1        1        0          0  ...   \n",
       "\n",
       "     Hypertension  CAD  Head and Neck Cancer  Head injury  CVA  \\\n",
       "0               0    0                     0            0    0   \n",
       "1               0    0                     0            0    1   \n",
       "2               0    0                     0            0    0   \n",
       "3               0    0                     0            0    0   \n",
       "4               1    0                     0            0    0   \n",
       "..            ...  ...                   ...          ...  ...   \n",
       "995             1    1                     0            0    0   \n",
       "996             0    0                     0            0    0   \n",
       "997             0    0                     0            0    0   \n",
       "998             0    0                     0            0    0   \n",
       "999             0    0                     0            0    0   \n",
       "\n",
       "     Voice handicap index - 10  setName  foldIdx  label  \\\n",
       "0                         22.0      val        4      1   \n",
       "1                         19.0    train        0      2   \n",
       "2                         18.0    train        0      2   \n",
       "3                         27.0    train        2      1   \n",
       "4                         16.0    train        0      1   \n",
       "..                         ...      ...      ...    ...   \n",
       "995                       21.0    train        1      3   \n",
       "996                       21.0    train        0      4   \n",
       "997                       27.0      val        3      3   \n",
       "998                       12.0    train        0      2   \n",
       "999                       17.0    train        4      2   \n",
       "\n",
       "                                                  path  \n",
       "0    /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "1    /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "2    /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "3    /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "4    /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "..                                                 ...  \n",
       "995  /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "996  /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "997  /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "998  /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "999  /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "\n",
       "[1000 rows x 32 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = pd.read_csv(os.path.join(util.dataPath, 'training datalist.csv'))\n",
    "df['label'] = df['Disease category']\n",
    "df['path'] = df['ID'].apply(lambda x: os.path.join(util.dataPath, 'training_voice_data', '{}.wav'.format(x)))\n",
    "outfile = os.path.join(util.dataPath, 'training.pkl')\n",
    "df"
   ]
  },
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1202v5m</td>\n",
       "      <td>2</td>\n",
       "      <td>48</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>/outerDisk1/rawDatasets/multimodalPathological...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0C01365</td>\n",
       "      <td>2</td>\n",
       "      <td>43</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>27.0</td>\n",
       "      <td>/outerDisk1/rawDatasets/multimodalPathological...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>495</th>\n",
       "      <td>0C0147g</td>\n",
       "      <td>2</td>\n",
       "      <td>39</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>30.0</td>\n",
       "      <td>/outerDisk1/rawDatasets/multimodalPathological...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>496</th>\n",
       "      <td>13021ib</td>\n",
       "      <td>2</td>\n",
       "      <td>58</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>30.0</td>\n",
       "      <td>/outerDisk1/rawDatasets/multimodalPathological...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>497</th>\n",
       "      <td>110049h</td>\n",
       "      <td>1</td>\n",
       "      <td>72</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>/outerDisk1/rawDatasets/multimodalPathological...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>498</th>\n",
       "      <td>0T01khc</td>\n",
       "      <td>2</td>\n",
       "      <td>60</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>/outerDisk1/rawDatasets/multimodalPathological...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>499</th>\n",
       "      <td>0C02cr3</td>\n",
       "      <td>2</td>\n",
       "      <td>48</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>15.0</td>\n",
       "      <td>/outerDisk1/rawDatasets/multimodalPathological...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>500 rows × 28 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          ID  Sex  Age  Narrow pitch range  Decreased volume  Fatigue  \\\n",
       "0    1301skj    2   27                   0                 1        1   \n",
       "1    1100j0u    1   50                   0                 0        0   \n",
       "2    0G00r5c    1   41                   1                 1        0   \n",
       "3    1202v5m    2   48                   1                 0        0   \n",
       "4    0C01365    2   43                   0                 1        0   \n",
       "..       ...  ...  ...                 ...               ...      ...   \n",
       "495  0C0147g    2   39                   1                 0        0   \n",
       "496  13021ib    2   58                   0                 0        1   \n",
       "497  110049h    1   72                   0                 1        1   \n",
       "498  0T01khc    2   60                   1                 0        0   \n",
       "499  0C02cr3    2   48                   1                 1        1   \n",
       "\n",
       "     Dryness  Lumping  heartburn  Choking  ...  Noise at work  \\\n",
       "0          1        1          0        0  ...              3   \n",
       "1          0        0          0        0  ...              2   \n",
       "2          0        0          0        0  ...              2   \n",
       "3          1        1          0        0  ...              1   \n",
       "4          1        0          1        1  ...              2   \n",
       "..       ...      ...        ...      ...  ...            ...   \n",
       "495        0        0          0        0  ...              2   \n",
       "496        1        0          1        0  ...              3   \n",
       "497        0        0          0        0  ...              1   \n",
       "498        0        1          0        0  ...              2   \n",
       "499        0        1          0        0  ...              2   \n",
       "\n",
       "     Occupational vocal demand  Diabetes  Hypertension  CAD  \\\n",
       "0                            1         0             0    0   \n",
       "1                            2         0             1    0   \n",
       "2                            3         0             0    0   \n",
       "3                            4         0             0    0   \n",
       "4                            1         0             0    1   \n",
       "..                         ...       ...           ...  ...   \n",
       "495                          2         0             0    0   \n",
       "496                          1         0             0    0   \n",
       "497                          3         0             1    0   \n",
       "498                          4         0             0    0   \n",
       "499                          1         0             0    0   \n",
       "\n",
       "     Head and Neck Cancer  Head injury  CVA  Voice handicap index - 10  \\\n",
       "0                       0            0    0                       30.0   \n",
       "1                       0            0    0                       30.0   \n",
       "2                       0            0    0                       29.0   \n",
       "3                       0            0    0                        5.0   \n",
       "4                       0            0    0                       27.0   \n",
       "..                    ...          ...  ...                        ...   \n",
       "495                     0            0    0                       30.0   \n",
       "496                     0            0    0                       30.0   \n",
       "497                     0            0    0                       32.0   \n",
       "498                     1            0    0                        3.0   \n",
       "499                     0            0    0                       15.0   \n",
       "\n",
       "                                                  path  \n",
       "0    /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "1    /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "2    /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "3    /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "4    /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "..                                                 ...  \n",
       "495  /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "496  /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "497  /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "498  /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "499  /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "\n",
       "[500 rows x 28 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# public test\n",
    "df = pd.read_csv(os.path.join(util.publicTestPath, 'test_datalist_public.csv'))\n",
    "df['path'] = df['ID'].apply(lambda x: os.path.join(util.publicTestPath, 'test_data_public', '{}.wav'.format(x)))\n",
    "outfile = os.path.join(util.publicTestPath, 'publitTest.pkl')\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "74d05a7d",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-05-17T11:31:51.917747Z",
     "start_time": "2023-05-17T11:31:51.895597Z"
    },
    "deletable": false,
    "editable": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<style scoped>\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ID</th>\n",
       "      <th>Sex</th>\n",
       "      <th>Age</th>\n",
       "      <th>Narrow pitch range</th>\n",
       "      <th>Decreased volume</th>\n",
       "      <th>Fatigue</th>\n",
       "      <th>Dryness</th>\n",
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       "      <th>...</th>\n",
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       "      <th>Head injury</th>\n",
       "      <th>CVA</th>\n",
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       "      <th>path</th>\n",
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       "  </thead>\n",
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       "      <td>/outerDisk1/rawDatasets/multimodalPathological...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0Y00jid</td>\n",
       "      <td>2</td>\n",
       "      <td>68</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>8.0</td>\n",
       "      <td>/outerDisk1/rawDatasets/multimodalPathological...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>0R02296</td>\n",
       "      <td>1</td>\n",
       "      <td>38</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>/outerDisk1/rawDatasets/multimodalPathological...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0W016c9</td>\n",
       "      <td>1</td>\n",
       "      <td>58</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>34.0</td>\n",
       "      <td>/outerDisk1/rawDatasets/multimodalPathological...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>11006gd</td>\n",
       "      <td>2</td>\n",
       "      <td>75</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
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       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>3</td>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>28.0</td>\n",
       "      <td>/outerDisk1/rawDatasets/multimodalPathological...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>495</th>\n",
       "      <td>1001abu</td>\n",
       "      <td>2</td>\n",
       "      <td>29</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>39.0</td>\n",
       "      <td>/outerDisk1/rawDatasets/multimodalPathological...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>496</th>\n",
       "      <td>1002ss4</td>\n",
       "      <td>2</td>\n",
       "      <td>77</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>21.0</td>\n",
       "      <td>/outerDisk1/rawDatasets/multimodalPathological...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>497</th>\n",
       "      <td>0W011bi</td>\n",
       "      <td>1</td>\n",
       "      <td>44</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>27.0</td>\n",
       "      <td>/outerDisk1/rawDatasets/multimodalPathological...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>498</th>\n",
       "      <td>0R00num</td>\n",
       "      <td>1</td>\n",
       "      <td>63</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>40.0</td>\n",
       "      <td>/outerDisk1/rawDatasets/multimodalPathological...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>499</th>\n",
       "      <td>0Y02gae</td>\n",
       "      <td>2</td>\n",
       "      <td>30</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>3</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>/outerDisk1/rawDatasets/multimodalPathological...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>500 rows × 28 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          ID  Sex  Age  Narrow pitch range  Decreased volume  Fatigue  \\\n",
       "0    0U02g8u    2   77                   0                 1        0   \n",
       "1    0Y00jid    2   68                   0                 0        1   \n",
       "2    0R02296    1   38                   0                 1        0   \n",
       "3    0W016c9    1   58                   0                 1        1   \n",
       "4    11006gd    2   75                   0                 1        1   \n",
       "..       ...  ...  ...                 ...               ...      ...   \n",
       "495  1001abu    2   29                   1                 1        1   \n",
       "496  1002ss4    2   77                   1                 1        0   \n",
       "497  0W011bi    1   44                   0                 1        1   \n",
       "498  0R00num    1   63                   0                 0        1   \n",
       "499  0Y02gae    2   30                   1                 1        0   \n",
       "\n",
       "     Dryness  Lumping  heartburn  Choking  ...  Noise at work  \\\n",
       "0          1        0          0        0  ...              1   \n",
       "1          1        1          0        1  ...              1   \n",
       "2          1        1          0        0  ...              2   \n",
       "3          0        1          0        0  ...              1   \n",
       "4          0        1          0        0  ...              1   \n",
       "..       ...      ...        ...      ...  ...            ...   \n",
       "495        0        0          0        0  ...              2   \n",
       "496        0        0          0        0  ...              1   \n",
       "497        1        1          1        0  ...              1   \n",
       "498        1        0          0        1  ...              2   \n",
       "499        0        0          0        0  ...              3   \n",
       "\n",
       "     Occupational vocal demand  Diabetes  Hypertension  CAD  \\\n",
       "0                            3         1             1    0   \n",
       "1                            4         0             0    0   \n",
       "2                            1         0             0    0   \n",
       "3                            3         0             1    0   \n",
       "4                            3         1             1    0   \n",
       "..                         ...       ...           ...  ...   \n",
       "495                          1         0             0    0   \n",
       "496                          2         0             0    0   \n",
       "497                          1         0             0    0   \n",
       "498                          2         0             0    0   \n",
       "499                          1         0             0    0   \n",
       "\n",
       "     Head and Neck Cancer  Head injury  CVA  Voice handicap index - 10  \\\n",
       "0                       0            0    1                       14.0   \n",
       "1                       0            0    0                        8.0   \n",
       "2                       1            0    0                       25.0   \n",
       "3                       0            0    0                       34.0   \n",
       "4                       0            0    0                       28.0   \n",
       "..                    ...          ...  ...                        ...   \n",
       "495                     0            0    0                       39.0   \n",
       "496                     0            0    0                       21.0   \n",
       "497                     0            0    0                       27.0   \n",
       "498                     0            0    0                       40.0   \n",
       "499                     0            0    0                       17.0   \n",
       "\n",
       "                                                  path  \n",
       "0    /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "1    /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "2    /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "3    /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "4    /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "..                                                 ...  \n",
       "495  /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "496  /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "497  /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "498  /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "499  /outerDisk1/rawDatasets/multimodalPathological...  \n",
       "\n",
       "[500 rows x 28 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# private test\n",
    "df = pd.read_csv(os.path.join(util.privateTestPath, 'test_datalist_private.csv'))\n",
    "df['path'] = df['ID'].apply(lambda x: os.path.join(util.privateTestPath, 'test_data_private', '{}.wav'.format(x)))\n",
    "outfile = os.path.join(util.privateTestPath, 'privateTest.pkl')\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "2effd768",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-05-17T11:27:37.954320Z",
     "start_time": "2023-05-17T11:27:34.627192Z"
    },
    "deletable": false,
    "editable": false,
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "tensor([[[-0.0117, -0.5506, -0.7753,  ..., -0.0241,  0.2469, -0.0137],\n",
       "         [ 0.2657, -0.2052, -0.2970,  ...,  0.1308,  0.6032, -0.1065],\n",
       "         [ 0.6168, -0.3349,  0.1502,  ...,  0.0786,  0.0810,  0.0244],\n",
       "         ...,\n",
       "         [-0.1556, -0.0361,  0.6174,  ...,  0.0835, -0.1675,  0.1355],\n",
       "         [-0.1156, -0.1233,  0.8208,  ..., -0.2111, -0.5564,  0.1147],\n",
       "         [-0.1777, -0.4909,  0.3607,  ...,  0.1084, -0.4295,  0.2782]]],\n",
       "       grad_fn=<TransposeBackward0>)"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# load the pre-trained checkpoints\n",
    "checkpoint = torch.load('BEATs_iter3_plus_AS2M.pt')\n",
    "\n",
    "cfg = BEATsConfig(checkpoint['cfg'])\n",
    "BEATs_model = BEATs(cfg)\n",
    "BEATs_model.load_state_dict(checkpoint['model'])\n",
    "BEATs_model.eval()\n",
    "\n",
    "# extract the the audio representation\n",
    "audio_input_16khz = torch.randn(1, 132300)\n",
    "padding_mask = torch.zeros(1, 132300).bool()\n",
    "\n",
    "representation = BEATs_model.extract_features(audio_input_16khz, padding_mask=padding_mask)[0]\n",
    "representation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "fe3c4cd8",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-05-17T11:34:39.850479Z",
     "start_time": "2023-05-17T11:31:59.710127Z"
    },
    "deletable": false,
    "editable": false,
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ID</th>\n",
       "      <th>Sex</th>\n",
       "      <th>Age</th>\n",
       "      <th>Narrow pitch range</th>\n",
       "      <th>Decreased volume</th>\n",
       "      <th>Fatigue</th>\n",
       "      <th>Dryness</th>\n",
       "      <th>Lumping</th>\n",
       "      <th>heartburn</th>\n",
       "      <th>Choking</th>\n",
       "      <th>...</th>\n",
       "      <th>Occupational vocal demand</th>\n",
       "      <th>Diabetes</th>\n",
       "      <th>Hypertension</th>\n",
       "      <th>CAD</th>\n",
       "      <th>Head and Neck Cancer</th>\n",
       "      <th>Head injury</th>\n",
       "      <th>CVA</th>\n",
       "      <th>Voice handicap index - 10</th>\n",
       "      <th>signal</th>\n",
       "      <th>beatsFeature</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0U02g8u</td>\n",
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       "      <td>[[0.15713872, 0.09611868, -0.027490275, 0.0898...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0Y00jid</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.68</td>\n",
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       "      <td>0</td>\n",
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       "      <td>[[0.03280581, 0.42030498, 0.0077399346, 0.3362...</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>0R02296</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.38</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.625</td>\n",
       "      <td>[-0.037384033203125, -0.037811279296875, -0.03...</td>\n",
       "      <td>[[-0.46499285, -0.07755125, -0.20460303, 0.180...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0W016c9</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.58</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
       "      <td>...</td>\n",
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       "      <td>0.850</td>\n",
       "      <td>[0.111572265625, 0.112396240234375, 0.11273193...</td>\n",
       "      <td>[[-0.14635128, 0.0033875378, -0.10318614, 0.02...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>11006gd</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.75</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
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       "    <tr>\n",
       "      <th>...</th>\n",
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       "      <td>...</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>495</th>\n",
       "      <td>1001abu</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.29</td>\n",
       "      <td>1</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.975</td>\n",
       "      <td>[-0.0367431640625, -0.043182373046875, -0.0483...</td>\n",
       "      <td>[[-0.17591335, -0.048719455, -0.19188301, 0.17...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>496</th>\n",
       "      <td>1002ss4</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.77</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.333333</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.525</td>\n",
       "      <td>[0.006805419921875, 0.007598876953125, 0.00637...</td>\n",
       "      <td>[[-0.22389068, -0.052827187, -0.25321302, 0.26...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>497</th>\n",
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       "      <td>0.44</td>\n",
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       "      <td>1</td>\n",
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       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0.675</td>\n",
       "      <td>[-0.007049560546875, -0.0037841796875, -0.0007...</td>\n",
       "      <td>[[-0.29109988, -0.15586075, 0.010163356, 0.432...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>498</th>\n",
       "      <td>0R00num</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.63</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
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       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>0.333333</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1.000</td>\n",
       "      <td>[-0.1129150390625, -0.1322021484375, -0.134124...</td>\n",
       "      <td>[[0.12534869, -0.14788422, -0.22939701, -0.018...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>499</th>\n",
       "      <td>0Y02gae</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.30</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.425</td>\n",
       "      <td>[0.021759033203125, 0.001617431640625, -0.0051...</td>\n",
       "      <td>[[-0.070778206, 0.37295544, -0.29461733, 0.110...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>500 rows × 29 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          ID  Sex   Age  Narrow pitch range  Decreased volume  Fatigue  \\\n",
       "0    0U02g8u  1.0  0.77                   0                 1        0   \n",
       "1    0Y00jid  1.0  0.68                   0                 0        1   \n",
       "2    0R02296  0.0  0.38                   0                 1        0   \n",
       "3    0W016c9  0.0  0.58                   0                 1        1   \n",
       "4    11006gd  1.0  0.75                   0                 1        1   \n",
       "..       ...  ...   ...                 ...               ...      ...   \n",
       "495  1001abu  1.0  0.29                   1                 1        1   \n",
       "496  1002ss4  1.0  0.77                   1                 1        0   \n",
       "497  0W011bi  0.0  0.44                   0                 1        1   \n",
       "498  0R00num  0.0  0.63                   0                 0        1   \n",
       "499  0Y02gae  1.0  0.30                   1                 1        0   \n",
       "\n",
       "     Dryness  Lumping  heartburn  Choking  ...  Occupational vocal demand  \\\n",
       "0          1        0          0        0  ...                   0.666667   \n",
       "1          1        1          0        1  ...                   1.000000   \n",
       "2          1        1          0        0  ...                   0.000000   \n",
       "3          0        1          0        0  ...                   0.666667   \n",
       "4          0        1          0        0  ...                   0.666667   \n",
       "..       ...      ...        ...      ...  ...                        ...   \n",
       "495        0        0          0        0  ...                   0.000000   \n",
       "496        0        0          0        0  ...                   0.333333   \n",
       "497        1        1          1        0  ...                   0.000000   \n",
       "498        1        0          0        1  ...                   0.333333   \n",
       "499        0        0          0        0  ...                   0.000000   \n",
       "\n",
       "     Diabetes Hypertension  CAD Head and Neck Cancer  Head injury CVA  \\\n",
       "0           1            1    0                    0            0   1   \n",
       "1           0            0    0                    0            0   0   \n",
       "2           0            0    0                    1            0   0   \n",
       "3           0            1    0                    0            0   0   \n",
       "4           1            1    0                    0            0   0   \n",
       "..        ...          ...  ...                  ...          ...  ..   \n",
       "495         0            0    0                    0            0   0   \n",
       "496         0            0    0                    0            0   0   \n",
       "497         0            0    0                    0            0   0   \n",
       "498         0            0    0                    0            0   0   \n",
       "499         0            0    0                    0            0   0   \n",
       "\n",
       "    Voice handicap index - 10  \\\n",
       "0                       0.350   \n",
       "1                       0.200   \n",
       "2                       0.625   \n",
       "3                       0.850   \n",
       "4                       0.700   \n",
       "..                        ...   \n",
       "495                     0.975   \n",
       "496                     0.525   \n",
       "497                     0.675   \n",
       "498                     1.000   \n",
       "499                     0.425   \n",
       "\n",
       "                                                signal  \\\n",
       "0    [-0.111175537109375, -0.11004638671875, -0.108...   \n",
       "1    [0.04358541965484619, 0.04709649085998535, 0.0...   \n",
       "2    [-0.037384033203125, -0.037811279296875, -0.03...   \n",
       "3    [0.111572265625, 0.112396240234375, 0.11273193...   \n",
       "4    [-0.0194091796875, -0.014984130859375, -0.0310...   \n",
       "..                                                 ...   \n",
       "495  [-0.0367431640625, -0.043182373046875, -0.0483...   \n",
       "496  [0.006805419921875, 0.007598876953125, 0.00637...   \n",
       "497  [-0.007049560546875, -0.0037841796875, -0.0007...   \n",
       "498  [-0.1129150390625, -0.1322021484375, -0.134124...   \n",
       "499  [0.021759033203125, 0.001617431640625, -0.0051...   \n",
       "\n",
       "                                          beatsFeature  \n",
       "0    [[0.15713872, 0.09611868, -0.027490275, 0.0898...  \n",
       "1    [[0.03280581, 0.42030498, 0.0077399346, 0.3362...  \n",
       "2    [[-0.46499285, -0.07755125, -0.20460303, 0.180...  \n",
       "3    [[-0.14635128, 0.0033875378, -0.10318614, 0.02...  \n",
       "4    [[-0.2823963, 0.1606602, -0.22187842, -0.03156...  \n",
       "..                                                 ...  \n",
       "495  [[-0.17591335, -0.048719455, -0.19188301, 0.17...  \n",
       "496  [[-0.22389068, -0.052827187, -0.25321302, 0.26...  \n",
       "497  [[-0.29109988, -0.15586075, 0.010163356, 0.432...  \n",
       "498  [[0.12534869, -0.14788422, -0.22939701, -0.018...  \n",
       "499  [[-0.070778206, 0.37295544, -0.29461733, 0.110...  \n",
       "\n",
       "[500 rows x 29 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df['Age'] /= 100\n",
    "\n",
    "onehotCols = ['label', 'Smoking', 'Drinking', 'Onset of dysphonia ', 'Diurnal pattern']\n",
    "for col in onehotCols:\n",
    "    if col in df:\n",
    "        df[col] = pd.Series(pd.get_dummies(df[col]).values.tolist())\n",
    "minmaxCols = ['Sex', 'PPD', 'frequency', 'Noise at work', 'Occupational vocal demand', 'Voice handicap index - 10']\n",
    "for col in minmaxCols:\n",
    "    df[col] = df[col].fillna(0)\n",
    "    df[col] = (df[col] - df[col].min()) / (df[col].max() - df[col].min())\n",
    "\n",
    "df['signal'] = df['path'].apply(lambda x: wavfile.read(x)[1] / 2**31)\n",
    "maxSize = df['signal'].apply(lambda x: x.shape[0]).max()\n",
    "df['signal'] = df['signal'].apply(lambda x: np.concatenate([x] * int(np.ceil(maxSize / x.shape[0])))[:maxSize])\n",
    "\n",
    "df['beatsFeature'] = df['signal'].apply(lambda x: BEATs_model.extract_features(torch.from_numpy(np.expand_dims(x, 0).astype(np.float32)), padding_mask=torch.zeros(1, x.shape[0]).bool())[0].detach().numpy()[0])\n",
    "\n",
    "del df['path']\n",
    "df.to_pickle(outfile)\n",
    "\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "db190d59",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-05-13T14:12:42.460009Z",
     "start_time": "2023-05-13T14:12:42.052830Z"
    },
    "deletable": false,
    "editable": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Disease category\n",
       "1    0.536\n",
       "2    0.220\n",
       "3    0.168\n",
       "4    0.044\n",
       "5    0.032\n",
       "Name: ID, dtype: float64"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = pd.read_pickle(os.path.join(util.dataPath, 'training.pkl'))\n",
    "df.groupby(\"Disease category\").count()['ID'] / len(df)"
   ]
  }
 ],
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