{

  "nbformat": 4,

  "nbformat_minor": 0,

  "metadata": {

    "colab": {

      "name": "Copy of process_mimic.ipynb",

      "version": "0.3.2",

      "provenance": [],

      "collapsed_sections": [],

      "include_colab_link": true

    },

    "kernelspec": {

      "name": "python3",

      "display_name": "Python 3"

    }

  },

  "cells": [

    {

      "cell_type": "markdown",

      "metadata": {

        "id": "view-in-github",

        "colab_type": "text"

      },

      "source": [

        "<a href=\"https://colab.research.google.com/github/BenM1215/medgan/blob/master/process_mimic.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"

      ]

    },

    {

      "metadata": {

        "id": "dkIm2oJnyjVK",

        "colab_type": "code",

        "colab": {}

      },

      "cell_type": "code",

      "source": [

        "import sys\n",

        "import _pickle as pickle\n",

        "import numpy as np\n",

        "from datetime import datetime"

      ],

      "execution_count": 0,

      "outputs": []

    },

    {

      "metadata": {

        "id": "F3LE_9PVyBfI",

        "colab_type": "code",

        "outputId": "d6ad558d-3bd1-4da1-be4f-248213b11409",

        "colab": {

          "base_uri": "https://localhost:8080/",

          "height": 34

        }

      },

      "cell_type": "code",

      "source": [

        "from google.colab import drive\n",

        "drive.mount('/content/gdrive', force_remount=True)"

      ],

      "execution_count": 0,

      "outputs": [

        {

          "output_type": "stream",

          "text": [

            "Mounted at /content/gdrive\n"

          ],

          "name": "stdout"

        }

      ]

    },

    {

      "metadata": {

        "id": "QbwB-8Fdylim",

        "colab_type": "code",

        "colab": {}

      },

      "cell_type": "code",

      "source": [

        "def convert_to_icd9(dxStr):\n",

        "    if dxStr.startswith('E'):\n",

        "        if len(dxStr) > 4: return dxStr[:4] + '.' + dxStr[4:]\n",

        "        else: return dxStr\n",

        "    else:\n",

        "        if len(dxStr) > 3: return dxStr[:3] + '.' + dxStr[3:]\n",

        "        else: return dxStr"

      ],

      "execution_count": 0,

      "outputs": []

    },

    {

      "metadata": {

        "id": "DEHXM6G2yqLR",

        "colab_type": "code",

        "colab": {}

      },

      "cell_type": "code",

      "source": [

        "def convert_to_3digit_icd9(dxStr):\n",

        "    if dxStr.startswith('E'):\n",

        "        if len(dxStr) > 4: return dxStr[:4]\n",

        "        else: return dxStr\n",

        "    else:\n",

        "        if len(dxStr) > 3: return dxStr[:3]\n",

        "        else: return dxStr"

      ],

      "execution_count": 0,

      "outputs": []

    },

    {

      "metadata": {

        "id": "WTP8qLpe4GsQ",

        "colab_type": "code",

        "colab": {}

      },

      "cell_type": "code",

      "source": [

        "# input arguments\n",

        "binary_count = 'binary'"

      ],

      "execution_count": 0,

      "outputs": []

    },

    {

      "metadata": {

        "id": "m40Qy9Ok4KB7",

        "colab_type": "code",

        "colab": {}

      },

      "cell_type": "code",

      "source": [

        "root_dir = \"/content/gdrive/My Drive/\"\n",

        "\n",

        "if binary_count == 'count':\n",

        "  base_dir = root_dir + 'GOSH/Synthetic Data/medgan/count/'\n",

        "else:\n",

        "  base_dir = root_dir + 'GOSH/Synthetic Data/medgan/binary/'\n",

        "\n",

        "raw_data_dir = root_dir + 'GOSH/Synthetic Data/medgan/mimic/'\n",

        "processed_data_dir = base_dir + 'processed_mimic/'\n",

        "model_dir = base_dir + 'models/'\n",

        "gen_data_dir = base_dir + 'generated_data/'"

      ],

      "execution_count": 0,

      "outputs": []

    },

    {

      "metadata": {

        "id": "84a4GULe5NmG",

        "colab_type": "code",

        "colab": {}

      },

      "cell_type": "code",

      "source": [

        "admissionFile = raw_data_dir + 'ADMISSIONS.csv'\n",

        "diagnosisFile = raw_data_dir + 'DIAGNOSES_ICD.csv'\n",

        "outFile = processed_data_dir + 'processed_mimic'"

      ],

      "execution_count": 0,

      "outputs": []

    },

    {

      "metadata": {

        "id": "0o1e-8_RyttW",

        "colab_type": "code",

        "colab": {}

      },

      "cell_type": "code",

      "source": [

        "if binary_count != 'binary' and binary_count != 'count':\n",

        "    print('You must choose either binary or count.')"

      ],

      "execution_count": 0,

      "outputs": []

    },

    {

      "metadata": {

        "id": "RYeXZcXe4-Zj",

        "colab_type": "code",

        "outputId": "0c259433-92d5-497b-da62-b9357d23d938",

        "colab": {

          "base_uri": "https://localhost:8080/",

          "height": 119

        }

      },

      "cell_type": "code",

      "source": [

        "print('Building pid-admission mapping, admission-date mapping')\n",

        "pidAdmMap = {}\n",

        "admDateMap = {}\n",

        "infd = open(admissionFile, 'r')\n",

        "infd.readline()\n",

        "for line in infd:\n",

        "    tokens = line.strip().split(',')\n",

        "    pid = int(tokens[1])\n",

        "    admId = int(tokens[2])\n",

        "    admTime = datetime.strptime(tokens[3], '%Y-%m-%d %H:%M:%S')\n",

        "    admDateMap[admId] = admTime\n",

        "    if pid in pidAdmMap: pidAdmMap[pid].append(admId)\n",

        "    else: pidAdmMap[pid] = [admId]\n",

        "infd.close()\n",

        "\n",

        "print('Building admission-dxList mapping')\n",

        "admDxMap = {}\n",

        "infd = open(diagnosisFile, 'r')\n",

        "infd.readline()\n",

        "for line in infd:\n",

        "    tokens = line.strip().split(',')\n",

        "    admId = int(tokens[2])\n",

        "    # Uncomment this line and comment the line below, if you want to use the entire ICD9 digits.\n",

        "    dxStr = 'D_' + convert_to_icd9(tokens[4][1:-1])\n",

        "    #dxStr = 'D_' + convert_to_3digit_icd9(tokens[4][1:-1])\n",

        "    if admId in admDxMap: admDxMap[admId].append(dxStr)\n",

        "    else: admDxMap[admId] = [dxStr]\n",

        "infd.close()\n",

        "\n",

        "print('Building pid-sortedVisits mapping')\n",

        "pidSeqMap = {}\n",

        "for pid, admIdList in pidAdmMap.items():\n",

        "    #if len(admIdList) < 2: continue\n",

        "    sortedList = sorted([(admDateMap[admId], admDxMap[admId]) for admId in admIdList])\n",

        "    pidSeqMap[pid] = sortedList\n",

        "\n",

        "print('Building pids, dates, strSeqs')\n",

        "pids = []\n",

        "dates = []\n",

        "seqs = []\n",

        "for pid, visits in pidSeqMap.items():\n",

        "    pids.append(pid)\n",

        "    seq = []\n",

        "    date = []\n",

        "    for visit in visits:\n",

        "        date.append(visit[0])\n",

        "        seq.append(visit[1])\n",

        "    dates.append(date)\n",

        "    seqs.append(seq)\n",

        "\n",

        "print('Converting strSeqs to intSeqs, and making types')\n",

        "types = {}\n",

        "newSeqs = []\n",

        "for patient in seqs:\n",

        "    newPatient = []\n",

        "    for visit in patient:\n",

        "        newVisit = []\n",

        "        for code in visit:\n",

        "            if code in types:\n",

        "                newVisit.append(types[code])\n",

        "            else:\n",

        "                types[code] = len(types)\n",

        "                newVisit.append(types[code])\n",

        "        newPatient.append(newVisit)\n",

        "    newSeqs.append(newPatient)\n",

        "\n",

        "print('Constructing the matrix')\n",

        "numPatients = len(newSeqs)\n",

        "numCodes = len(types)\n",

        "matrix = np.zeros((numPatients, numCodes)).astype('float32')\n",

        "for i, patient in enumerate(newSeqs):\n",

        "    for visit in patient:\n",

        "        for code in visit:\n",

        "            if binary_count == 'binary':\n",

        "                matrix[i][code] = 1.\n",

        "            else:\n",

        "                matrix[i][code] += 1.\n",

        "\n",

        "pickle.dump(pids, open(outFile+'.pids', 'wb'), -1)\n",

        "pickle.dump(matrix, open(outFile+'.matrix', 'wb'), -1)\n",

        "pickle.dump(types, open(outFile+'.types', 'wb'), -1)"

      ],

      "execution_count": 0,

      "outputs": [

        {

          "output_type": "stream",

          "text": [

            "Building pid-admission mapping, admission-date mapping\n",

            "Building admission-dxList mapping\n",

            "Building pid-sortedVisits mapping\n",

            "Building pids, dates, strSeqs\n",

            "Converting strSeqs to intSeqs, and making types\n",

            "Constructing the matrix\n"

          ],

          "name": "stdout"

        }

      ]

    },

    {

      "metadata": {

        "id": "AaF-cC2t0pT6",

        "colab_type": "code",

        "colab": {}

      },

      "cell_type": "code",

      "source": [

        ""

      ],

      "execution_count": 0,

      "outputs": []

    }

  ]

}