Dataset Creator.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import os\n",
    "import shutil"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "# create a data for the covid +ve samples (ieee real world dataset)\n",
    "\n",
    "FILE_PATH = \"covid-chestxray-dataset-master/metadata.csv\"\n",
    "IMAGES_PATH = \"covid-chestxray-dataset-master/images\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(930, 29)\n"
     ]
    }
   ],
   "source": [
    "df = pd.read_csv(FILE_PATH)\n",
    "print(df.shape)"
   ]
  },
  {
   "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>patientid</th>\n",
       "      <th>offset</th>\n",
       "      <th>sex</th>\n",
       "      <th>age</th>\n",
       "      <th>finding</th>\n",
       "      <th>RT_PCR_positive</th>\n",
       "      <th>survival</th>\n",
       "      <th>intubated</th>\n",
       "      <th>intubation_present</th>\n",
       "      <th>went_icu</th>\n",
       "      <th>...</th>\n",
       "      <th>modality</th>\n",
       "      <th>date</th>\n",
       "      <th>location</th>\n",
       "      <th>folder</th>\n",
       "      <th>filename</th>\n",
       "      <th>doi</th>\n",
       "      <th>url</th>\n",
       "      <th>license</th>\n",
       "      <th>clinical_notes</th>\n",
       "      <th>other_notes</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>2</td>\n",
       "      <td>0.0</td>\n",
       "      <td>M</td>\n",
       "      <td>65.0</td>\n",
       "      <td>COVID-19</td>\n",
       "      <td>Y</td>\n",
       "      <td>Y</td>\n",
       "      <td>N</td>\n",
       "      <td>N</td>\n",
       "      <td>N</td>\n",
       "      <td>...</td>\n",
       "      <td>X-ray</td>\n",
       "      <td>January 22, 2020</td>\n",
       "      <td>Cho Ray Hospital, Ho Chi Minh City, Vietnam</td>\n",
       "      <td>images</td>\n",
       "      <td>auntminnie-a-2020_01_28_23_51_6665_2020_01_28_...</td>\n",
       "      <td>10.1056/nejmc2001272</td>\n",
       "      <td>https://www.nejm.org/doi/full/10.1056/NEJMc200...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>On January 22, 2020, a 65-year-old man with a ...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2</td>\n",
       "      <td>3.0</td>\n",
       "      <td>M</td>\n",
       "      <td>65.0</td>\n",
       "      <td>COVID-19</td>\n",
       "      <td>Y</td>\n",
       "      <td>Y</td>\n",
       "      <td>N</td>\n",
       "      <td>N</td>\n",
       "      <td>N</td>\n",
       "      <td>...</td>\n",
       "      <td>X-ray</td>\n",
       "      <td>January 25, 2020</td>\n",
       "      <td>Cho Ray Hospital, Ho Chi Minh City, Vietnam</td>\n",
       "      <td>images</td>\n",
       "      <td>auntminnie-b-2020_01_28_23_51_6665_2020_01_28_...</td>\n",
       "      <td>10.1056/nejmc2001272</td>\n",
       "      <td>https://www.nejm.org/doi/full/10.1056/NEJMc200...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>On January 22, 2020, a 65-year-old man with a ...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>2</td>\n",
       "      <td>5.0</td>\n",
       "      <td>M</td>\n",
       "      <td>65.0</td>\n",
       "      <td>COVID-19</td>\n",
       "      <td>Y</td>\n",
       "      <td>Y</td>\n",
       "      <td>N</td>\n",
       "      <td>N</td>\n",
       "      <td>N</td>\n",
       "      <td>...</td>\n",
       "      <td>X-ray</td>\n",
       "      <td>January 27, 2020</td>\n",
       "      <td>Cho Ray Hospital, Ho Chi Minh City, Vietnam</td>\n",
       "      <td>images</td>\n",
       "      <td>auntminnie-c-2020_01_28_23_51_6665_2020_01_28_...</td>\n",
       "      <td>10.1056/nejmc2001272</td>\n",
       "      <td>https://www.nejm.org/doi/full/10.1056/NEJMc200...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>On January 22, 2020, a 65-year-old man with a ...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>2</td>\n",
       "      <td>6.0</td>\n",
       "      <td>M</td>\n",
       "      <td>65.0</td>\n",
       "      <td>COVID-19</td>\n",
       "      <td>Y</td>\n",
       "      <td>Y</td>\n",
       "      <td>N</td>\n",
       "      <td>N</td>\n",
       "      <td>N</td>\n",
       "      <td>...</td>\n",
       "      <td>X-ray</td>\n",
       "      <td>January 28, 2020</td>\n",
       "      <td>Cho Ray Hospital, Ho Chi Minh City, Vietnam</td>\n",
       "      <td>images</td>\n",
       "      <td>auntminnie-d-2020_01_28_23_51_6665_2020_01_28_...</td>\n",
       "      <td>10.1056/nejmc2001272</td>\n",
       "      <td>https://www.nejm.org/doi/full/10.1056/NEJMc200...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>On January 22, 2020, a 65-year-old man with a ...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>F</td>\n",
       "      <td>52.0</td>\n",
       "      <td>COVID-19</td>\n",
       "      <td>Y</td>\n",
       "      <td>NaN</td>\n",
       "      <td>N</td>\n",
       "      <td>N</td>\n",
       "      <td>N</td>\n",
       "      <td>...</td>\n",
       "      <td>X-ray</td>\n",
       "      <td>January 25, 2020</td>\n",
       "      <td>Changhua Christian Hospital, Changhua City, Ta...</td>\n",
       "      <td>images</td>\n",
       "      <td>nejmc2001573_f1a.jpeg</td>\n",
       "      <td>10.1056/NEJMc2001573</td>\n",
       "      <td>https://www.nejm.org/doi/full/10.1056/NEJMc200...</td>\n",
       "      <td>NaN</td>\n",
       "      <td>diffuse infiltrates in the bilateral lower lungs</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 29 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "  patientid  offset sex   age   finding RT_PCR_positive survival intubated  \\\n",
       "0         2     0.0   M  65.0  COVID-19               Y        Y         N   \n",
       "1         2     3.0   M  65.0  COVID-19               Y        Y         N   \n",
       "2         2     5.0   M  65.0  COVID-19               Y        Y         N   \n",
       "3         2     6.0   M  65.0  COVID-19               Y        Y         N   \n",
       "4         4     0.0   F  52.0  COVID-19               Y      NaN         N   \n",
       "\n",
       "  intubation_present went_icu  ... modality              date  \\\n",
       "0                  N        N  ...    X-ray  January 22, 2020   \n",
       "1                  N        N  ...    X-ray  January 25, 2020   \n",
       "2                  N        N  ...    X-ray  January 27, 2020   \n",
       "3                  N        N  ...    X-ray  January 28, 2020   \n",
       "4                  N        N  ...    X-ray  January 25, 2020   \n",
       "\n",
       "                                            location  folder  \\\n",
       "0        Cho Ray Hospital, Ho Chi Minh City, Vietnam  images   \n",
       "1        Cho Ray Hospital, Ho Chi Minh City, Vietnam  images   \n",
       "2        Cho Ray Hospital, Ho Chi Minh City, Vietnam  images   \n",
       "3        Cho Ray Hospital, Ho Chi Minh City, Vietnam  images   \n",
       "4  Changhua Christian Hospital, Changhua City, Ta...  images   \n",
       "\n",
       "                                            filename                   doi  \\\n",
       "0  auntminnie-a-2020_01_28_23_51_6665_2020_01_28_...  10.1056/nejmc2001272   \n",
       "1  auntminnie-b-2020_01_28_23_51_6665_2020_01_28_...  10.1056/nejmc2001272   \n",
       "2  auntminnie-c-2020_01_28_23_51_6665_2020_01_28_...  10.1056/nejmc2001272   \n",
       "3  auntminnie-d-2020_01_28_23_51_6665_2020_01_28_...  10.1056/nejmc2001272   \n",
       "4                              nejmc2001573_f1a.jpeg  10.1056/NEJMc2001573   \n",
       "\n",
       "                                                 url  license  \\\n",
       "0  https://www.nejm.org/doi/full/10.1056/NEJMc200...      NaN   \n",
       "1  https://www.nejm.org/doi/full/10.1056/NEJMc200...      NaN   \n",
       "2  https://www.nejm.org/doi/full/10.1056/NEJMc200...      NaN   \n",
       "3  https://www.nejm.org/doi/full/10.1056/NEJMc200...      NaN   \n",
       "4  https://www.nejm.org/doi/full/10.1056/NEJMc200...      NaN   \n",
       "\n",
       "                                      clinical_notes other_notes  \n",
       "0  On January 22, 2020, a 65-year-old man with a ...         NaN  \n",
       "1  On January 22, 2020, a 65-year-old man with a ...         NaN  \n",
       "2  On January 22, 2020, a 65-year-old man with a ...         NaN  \n",
       "3  On January 22, 2020, a 65-year-old man with a ...         NaN  \n",
       "4   diffuse infiltrates in the bilateral lower lungs         NaN  \n",
       "\n",
       "[5 rows x 29 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Covid folder created\n"
     ]
    }
   ],
   "source": [
    "TARGET_DIR = \"Dataset/Covid\"\n",
    "\n",
    "\n",
    "if not os.path.exists(TARGET_DIR):\n",
    "    os.mkdir(TARGET_DIR)\n",
    "    print(\"Covid folder created\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Moving image 0\n",
      "Moving image 1\n",
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      "180\n"
     ]
    }
   ],
   "source": [
    "cnt = 0\n",
    "\n",
    "for (i,row) in df.iterrows(): \n",
    "    if row[\"finding\"] == \"COVID-19\" and row[\"view\"]==\"PA\":\n",
    "        filename = row[\"filename\"]\n",
    "        image_path = os.path.join(IMAGES_PATH,filename)\n",
    "        image_copy_path = os.path.join(TARGET_DIR)\n",
    "        shutil.copy2(image_path,image_copy_path)\n",
    "        print('Moving image', cnt)\n",
    "        \n",
    "        cnt += 1\n",
    "print(cnt) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "# sampling of images from the kaggle dataset (normal and pneumonia patients)\n",
    "\n",
    "import random\n",
    "KAGGLE_FILE_PATH = \"chest_xray/train/NORMAL\"\n",
    "TARGET_NORMAL_DIR = \"Dataset/Normal\"\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "image_names = os.listdir(KAGGLE_FILE_PATH)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
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       " 'NORMAL2-IM-0947-0001.jpeg',\n",
       " 'NORMAL2-IM-0948-0001.jpeg',\n",
       " 'NORMAL2-IM-0949-0001.jpeg',\n",
       " 'NORMAL2-IM-0950-0001.jpeg',\n",
       " 'NORMAL2-IM-0951-0001.jpeg',\n",
       " 'NORMAL2-IM-0952-0001.jpeg',\n",
       " 'NORMAL2-IM-0954-0001.jpeg',\n",
       " 'NORMAL2-IM-0955-0001.jpeg',\n",
       " ...]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "image_names"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "random.shuffle(image_names)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Copying image  0\n",
      "Copying image  1\n",
      "Copying image  2\n",
      "Copying image  3\n",
      "Copying image  4\n",
      "Copying image  5\n",
      "Copying image  6\n",
      "Copying image  7\n",
      "Copying image  8\n",
      "Copying image  9\n",
      "Copying image  10\n",
      "Copying image  11\n",
      "Copying image  12\n",
      "Copying image  13\n",
      "Copying image  14\n",
      "Copying image  15\n",
      "Copying image  16\n",
      "Copying image  17\n",
      "Copying image  18\n",
      "Copying image  19\n",
      "Copying image  20\n",
      "Copying image  21\n",
      "Copying image  22\n",
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      "Copying image  24\n",
      "Copying image  25\n",
      "Copying image  26\n",
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      "Copying image  145\n",
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      "Copying image  152\n",
      "Copying image  153\n",
      "Copying image  154\n",
      "Copying image  155\n",
      "Copying image  156\n",
      "Copying image  157\n",
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      "Copying image  159\n",
      "Copying image  160\n",
      "Copying image  161\n",
      "Copying image  162\n",
      "Copying image  163\n",
      "Copying image  164\n",
      "Copying image  165\n",
      "Copying image  166\n",
      "Copying image  167\n",
      "Copying image  168\n",
      "Copying image  169\n",
      "Copying image  170\n",
      "Copying image  171\n",
      "Copying image  172\n",
      "Copying image  173\n",
      "Copying image  174\n",
      "Copying image  175\n",
      "Copying image  176\n",
      "Copying image  177\n",
      "Copying image  178\n",
      "Copying image  179\n"
     ]
    }
   ],
   "source": [
    "for i in range(180):\n",
    "    \n",
    "    image_name = image_names[i]\n",
    "    image_path = os.path.join(KAGGLE_FILE_PATH,image_name)\n",
    "    \n",
    "    target_path = os.path.join(TARGET_NORMAL_DIR, image_name)\n",
    "    \n",
    "    shutil.copy2(image_path, target_path)\n",
    "    \n",
    "    print(\"Copying image \",i)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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