resize.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'MIMIC': '/scratch/rc4499/thesis/data/mimic-cxr/clinicaldg/preprocessed.csv',\n",
       " 'CXP': '/scratch/rc4499/thesis/data/chexpert/clinicaldg/preprocessed.csv',\n",
       " 'NIH': '/scratch/rc4499/thesis/data/chestxray8/clinicaldg/preprocessed.csv',\n",
       " 'PAD': '/scratch/rc4499/thesis/data/padchest/clinicaldg/preprocessed.csv'}"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import pandas as pd\n",
    "import clinicaldg.cxr.Constants as cxrConstants\n",
    "import clinicaldg.cxr.process as cxrProcess\n",
    "from clinicaldg.cxr import Constants\n",
    "\n",
    "from IPython.display import display\n",
    "\n",
    "df_paths = cxrConstants.df_paths\n",
    "df_paths"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "from os.path import exists\n",
    "def img_exists(path):\n",
    "    return exists(path)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "def is_diseased(row):\n",
    "    # diseases = Constants.take_labels[1:]\n",
    "    return int((row[Constants.take_labels[1:]]).sum() > 0)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
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      "text/plain": [
       "       subject_id                                               path Sex  \\\n",
       "0        10000032  /mimic-cxr/p10/p10000032/s50414267/02aa804e-bd...   F   \n",
       "2        10000032  /mimic-cxr/p10/p10000032/s53189527/2a2277a9-b0...   F   \n",
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       "5        10000032  /mimic-cxr/p10/p10000032/s53911762/fffabebf-74...   F   \n",
       "6        10000032  /mimic-cxr/p10/p10000032/s56699142/ea030e7a-2e...   F   \n",
       "...           ...                                                ...  ..   \n",
       "376200   19999733  /mimic-cxr/p19/p19999733/s57132437/3fcd0406-9b...   F   \n",
       "376201   19999733  /mimic-cxr/p19/p19999733/s57132437/428e2c18-57...   F   \n",
       "376203   19999987  /mimic-cxr/p19/p19999987/s55368167/58766883-37...   F   \n",
       "376204   19999987  /mimic-cxr/p19/p19999987/s58621812/7ba273af-3d...   F   \n",
       "376205   19999987  /mimic-cxr/p19/p19999987/s58971208/1a1fe7e3-cb...   F   \n",
       "\n",
       "          Age    env  frontal  study_id  No Finding  Atelectasis  \\\n",
       "0       40-60  MIMIC     True  50414267         1.0          NaN   \n",
       "2       40-60  MIMIC     True  53189527         1.0          NaN   \n",
       "4       40-60  MIMIC     True  53911762         1.0          NaN   \n",
       "5       40-60  MIMIC     True  53911762         1.0          NaN   \n",
       "6       40-60  MIMIC     True  56699142         1.0          NaN   \n",
       "...       ...    ...      ...       ...         ...          ...   \n",
       "376200   0-20  MIMIC     True  57132437         1.0          NaN   \n",
       "376201   0-20  MIMIC     True  57132437         1.0          NaN   \n",
       "376203  40-60  MIMIC     True  55368167         NaN          1.0   \n",
       "376204  40-60  MIMIC     True  58621812         NaN          1.0   \n",
       "376205  40-60  MIMIC     True  58971208         NaN          1.0   \n",
       "\n",
       "        Cardiomegaly  Effusion  Pneumonia  Pneumothorax  Consolidation  Edema  \\\n",
       "0                NaN       NaN        NaN           NaN            NaN    NaN   \n",
       "2                NaN       NaN        NaN           NaN            NaN    NaN   \n",
       "4                NaN       NaN        NaN           NaN            NaN    NaN   \n",
       "5                NaN       NaN        NaN           NaN            NaN    NaN   \n",
       "6                NaN       NaN        NaN           NaN            NaN    NaN   \n",
       "...              ...       ...        ...           ...            ...    ...   \n",
       "376200           NaN       NaN        NaN           NaN            NaN    NaN   \n",
       "376201           NaN       NaN        NaN           NaN            NaN    NaN   \n",
       "376203           0.0       0.0        NaN           0.0            NaN    NaN   \n",
       "376204           NaN       NaN        NaN           NaN            NaN    NaN   \n",
       "376205           NaN       NaN        NaN           NaN            NaN    NaN   \n",
       "\n",
       "        img_exists  All  \n",
       "0             True    0  \n",
       "2             True    0  \n",
       "4             True    0  \n",
       "5             True    0  \n",
       "6             True    0  \n",
       "...            ...  ...  \n",
       "376200        True    0  \n",
       "376201        True    0  \n",
       "376203        True    1  \n",
       "376204        True    1  \n",
       "376205        True    1  \n",
       "\n",
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       "       subject_id                                               path Sex  \\\n",
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       "...           ...                                                ...  ..   \n",
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       "\n",
       "          Age  env  frontal             study_id  No Finding  Atelectasis  \\\n",
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       "...       ...  ...      ...                  ...         ...          ...   \n",
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       "\n",
       "        Cardiomegaly  Effusion  Pneumonia  Pneumothorax  Consolidation  Edema  \\\n",
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       "\n",
       "        img_exists  All  \n",
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       "       subject_id                                 path Sex    Age  env  \\\n",
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       "1               1  /chestxray8/images/00000001_001.png   M  40-60  NIH   \n",
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       "\n",
       "        frontal study_id  No Finding  Atelectasis  Cardiomegaly  Effusion  \\\n",
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       "\n",
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       "      <th>frontal</th>\n",
       "      <th>study_id</th>\n",
       "      <th>No Finding</th>\n",
       "      <th>Atelectasis</th>\n",
       "      <th>Cardiomegaly</th>\n",
       "      <th>Effusion</th>\n",
       "      <th>Pneumonia</th>\n",
       "      <th>Pneumothorax</th>\n",
       "      <th>Consolidation</th>\n",
       "      <th>Edema</th>\n",
       "      <th>img_exists</th>\n",
       "      <th>All</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>839860488694292331637988235681460987</td>\n",
       "      <td>/padchest/205366866401363482361486798914558864...</td>\n",
       "      <td>F</td>\n",
       "      <td>80-</td>\n",
       "      <td>PAD</td>\n",
       "      <td>True</td>\n",
       "      <td>20536686640136348236148679891455886468</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>0</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>313572750430997347502932654319389875966</td>\n",
       "      <td>/padchest/135803415504923515076821959678074435...</td>\n",
       "      <td>M</td>\n",
       "      <td>80-</td>\n",
       "      <td>PAD</td>\n",
       "      <td>True</td>\n",
       "      <td>135803415504923515076821959678074435083</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</td>\n",
       "      <td>0</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>50783093527901818115346441867348318648</td>\n",
       "      <td>/padchest/113855343774216031107737439268243531...</td>\n",
       "      <td>F</td>\n",
       "      <td>80-</td>\n",
       "      <td>PAD</td>\n",
       "      <td>True</td>\n",
       "      <td>113855343774216031107737439268243531979</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</td>\n",
       "      <td>0</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>93535126770783451980359712286922420997</td>\n",
       "      <td>/padchest/3137231742710829928-2476108022664036...</td>\n",
       "      <td>M</td>\n",
       "      <td>60-80</td>\n",
       "      <td>PAD</td>\n",
       "      <td>True</td>\n",
       "      <td>3137231742710829928-247610802266403640553</td>\n",
       "      <td>0</td>\n",
       "      <td>1</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>True</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>93535126770783451980359712286922420997</td>\n",
       "      <td>/padchest/313723174271082992847610802266403640...</td>\n",
       "      <td>M</td>\n",
       "      <td>60-80</td>\n",
       "      <td>PAD</td>\n",
       "      <td>True</td>\n",
       "      <td>313723174271082992847610802266403640553</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</td>\n",
       "      <td>0</td>\n",
       "      <td>True</td>\n",
       "      <td>1</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>144489</th>\n",
       "      <td>112930952416074060371371014599496493673</td>\n",
       "      <td>/padchest/128401136192941452281465412169675154...</td>\n",
       "      <td>M</td>\n",
       "      <td>60-80</td>\n",
       "      <td>PAD</td>\n",
       "      <td>True</td>\n",
       "      <td>1284011361929414522814654121696751542351444145...</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</td>\n",
       "      <td>0</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>144490</th>\n",
       "      <td>282743729971423358706056731890510600934</td>\n",
       "      <td>/padchest/128401136192941452209464657169675154...</td>\n",
       "      <td>F</td>\n",
       "      <td>60-80</td>\n",
       "      <td>PAD</td>\n",
       "      <td>True</td>\n",
       "      <td>1284011361929414522094646571696751542351444145...</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>0</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>144491</th>\n",
       "      <td>52648743308541843883453242716226652771</td>\n",
       "      <td>/padchest/128401136192941452208639063169675154...</td>\n",
       "      <td>M</td>\n",
       "      <td>40-60</td>\n",
       "      <td>PAD</td>\n",
       "      <td>True</td>\n",
       "      <td>1284011361929414522086390631696751542351444145...</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</td>\n",
       "      <td>0</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>144492</th>\n",
       "      <td>228646130593152933811948996634154201216</td>\n",
       "      <td>/padchest/128401136192941452208410890169675154...</td>\n",
       "      <td>F</td>\n",
       "      <td>60-80</td>\n",
       "      <td>PAD</td>\n",
       "      <td>True</td>\n",
       "      <td>1284011361929414522084108901696751542351444145...</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>0</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>144493</th>\n",
       "      <td>137424047230303610602080410284588825286</td>\n",
       "      <td>/padchest/128401136192941452468211919169675154...</td>\n",
       "      <td>M</td>\n",
       "      <td>60-80</td>\n",
       "      <td>PAD</td>\n",
       "      <td>True</td>\n",
       "      <td>1284011361929414524682119191696751542351444145...</td>\n",
       "      <td>0</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</td>\n",
       "      <td>True</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>99827 rows × 17 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                     subject_id  \\\n",
       "0          839860488694292331637988235681460987   \n",
       "2       313572750430997347502932654319389875966   \n",
       "3        50783093527901818115346441867348318648   \n",
       "6        93535126770783451980359712286922420997   \n",
       "7        93535126770783451980359712286922420997   \n",
       "...                                         ...   \n",
       "144489  112930952416074060371371014599496493673   \n",
       "144490  282743729971423358706056731890510600934   \n",
       "144491   52648743308541843883453242716226652771   \n",
       "144492  228646130593152933811948996634154201216   \n",
       "144493  137424047230303610602080410284588825286   \n",
       "\n",
       "                                                     path Sex    Age  env  \\\n",
       "0       /padchest/205366866401363482361486798914558864...   F    80-  PAD   \n",
       "2       /padchest/135803415504923515076821959678074435...   M    80-  PAD   \n",
       "3       /padchest/113855343774216031107737439268243531...   F    80-  PAD   \n",
       "6       /padchest/3137231742710829928-2476108022664036...   M  60-80  PAD   \n",
       "7       /padchest/313723174271082992847610802266403640...   M  60-80  PAD   \n",
       "...                                                   ...  ..    ...  ...   \n",
       "144489  /padchest/128401136192941452281465412169675154...   M  60-80  PAD   \n",
       "144490  /padchest/128401136192941452209464657169675154...   F  60-80  PAD   \n",
       "144491  /padchest/128401136192941452208639063169675154...   M  40-60  PAD   \n",
       "144492  /padchest/128401136192941452208410890169675154...   F  60-80  PAD   \n",
       "144493  /padchest/128401136192941452468211919169675154...   M  60-80  PAD   \n",
       "\n",
       "        frontal                                           study_id  \\\n",
       "0          True             20536686640136348236148679891455886468   \n",
       "2          True            135803415504923515076821959678074435083   \n",
       "3          True            113855343774216031107737439268243531979   \n",
       "6          True          3137231742710829928-247610802266403640553   \n",
       "7          True            313723174271082992847610802266403640553   \n",
       "...         ...                                                ...   \n",
       "144489     True  1284011361929414522814654121696751542351444145...   \n",
       "144490     True  1284011361929414522094646571696751542351444145...   \n",
       "144491     True  1284011361929414522086390631696751542351444145...   \n",
       "144492     True  1284011361929414522084108901696751542351444145...   \n",
       "144493     True  1284011361929414524682119191696751542351444145...   \n",
       "\n",
       "        No Finding  Atelectasis  Cardiomegaly  Effusion  Pneumonia  \\\n",
       "0                1            0             0         0          0   \n",
       "2                0            0             0         0          0   \n",
       "3                0            0             0         0          0   \n",
       "6                0            1             0         1          0   \n",
       "7                0            0             0         1          0   \n",
       "...            ...          ...           ...       ...        ...   \n",
       "144489           0            0             0         0          0   \n",
       "144490           1            0             0         0          0   \n",
       "144491           0            0             0         0          0   \n",
       "144492           1            0             0         0          0   \n",
       "144493           0            0             0         0          1   \n",
       "\n",
       "        Pneumothorax  Consolidation  Edema  img_exists  All  \n",
       "0                  0              0      0        True    0  \n",
       "2                  0              0      0        True    0  \n",
       "3                  0              0      0        True    0  \n",
       "6                  0              0      0        True    1  \n",
       "7                  0              0      0        True    1  \n",
       "...              ...            ...    ...         ...  ...  \n",
       "144489             0              0      0        True    0  \n",
       "144490             0              0      0        True    0  \n",
       "144491             0              0      0        True    0  \n",
       "144492             0              0      0        True    0  \n",
       "144493             0              0      0        True    1  \n",
       "\n",
       "[99827 rows x 17 columns]"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# loads data with random splits\n",
    "\n",
    "for data_env in cxrConstants.df_paths:\n",
    "    func = cxrProcess.get_process_func(data_env)\n",
    "    df_env = func(pd.read_csv(cxrConstants.df_paths[data_env]), only_frontal = True)\n",
    "    df_env[\"img_exists\"] = df_env[\"path\"].apply(img_exists)\n",
    "    df_env[\"All\"] = df_env.apply(is_diseased, axis=1)\n",
    "    df_env = df_env[df_env[\"img_exists\"]]\n",
    "    \n",
    "    display(df_env)\n",
    "    \n",
    "    df_env.to_csv(f\"processed/{data_env}.csv\", index=False)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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