prepare_dataset.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "import transformers"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Paths:\n",
    "physionet_dir = '/home/user/datasets/physionet.org/files'  # Where MIMIC-CXR, MIMIC-CXR-JPG, and MIMIC-IV-ED are stored.\n",
    "dataset_dir = '/home/user/datasets'  # Some outputs of prepare_data() will be stored here.\n",
    "database_path = '/home/user/database/cxrmate_ed.db'  # The DuckDB database used to manage the tables of the dataset will be saved here."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Prepare the MIMIC-CXR & MIMIC-IV-ED dataset:\n",
    "model = transformers.AutoModel.from_pretrained('aehrc/cxrmate-ed', trust_remote_code=True)\n",
    "model.prepare_data(\n",
    "    physionet_dir=physionet_dir,\n",
    "    dataset_dir=dataset_dir,\n",
    "    database_path=database_path,\n",
    ")"
   ]
  }
 ],
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