{ "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": [ "\"Open" ] }, { "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": [] } ] }