{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "22332556",
   "metadata": {},
   "outputs": [
    {
     "ename": "SyntaxError",
     "evalue": "invalid syntax (55915107.py, line 1)",
     "output_type": "error",
     "traceback": [
      "  \u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[8]\u001b[39m\u001b[32m, line 1\u001b[39m\n\u001b[31m    \u001b[39m\u001b[31mfrom PRENTICE ANALYSIS import *\u001b[39m\n                  ^\n\u001b[31mSyntaxError\u001b[39m\u001b[31m:\u001b[39m invalid syntax\n"
     ]
    }
   ],
   "source": [
    "from PRENTICE ANALYSIS import *\n",
    "\n",
    "data = load_prentice_mat(\n",
    "    \"/mnt/data/flags_combined.mat\",\n",
    "    \"/mnt/data/suv_percentilesSLOthenUWM.mat\"\n",
    ")\n",
    "\n",
    "percentiles = list(range(5, 101, 5))\n",
    "\n",
    "# IMPORTANT:\n",
    "# treatment_col and ae_col below are column indices inside data[\"flags\"].\n",
    "# These still need your confirmed mapping.\n",
    "df = build_analysis_df_from_mat(\n",
    "    data,\n",
    "    treatment_col=0,\n",
    "    ae_col=5,\n",
    "    percentiles=percentiles\n",
    ")\n",
    "\n",
    "df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "4729fe28",
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'collapse_treatment_to_two_groups' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
      "\u001b[31mNameError\u001b[39m                                 Traceback (most recent call last)",
      "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[6]\u001b[39m\u001b[32m, line 9\u001b[39m\n\u001b[32m      1\u001b[39m treatment_map = {\n\u001b[32m      2\u001b[39m     \u001b[32m1\u001b[39m: \u001b[32m0\u001b[39m,   \u001b[38;5;66;03m# mono\u001b[39;00m\n\u001b[32m      3\u001b[39m     \u001b[32m2\u001b[39m: \u001b[32m0\u001b[39m,   \u001b[38;5;66;03m# mono\u001b[39;00m\n\u001b[32m   (...)\u001b[39m\u001b[32m      6\u001b[39m     \u001b[32m9\u001b[39m: \u001b[32m1\u001b[39m,   \u001b[38;5;66;03m# combo\u001b[39;00m\n\u001b[32m      7\u001b[39m }\n\u001b[32m----> \u001b[39m\u001b[32m9\u001b[39m df[\u001b[33m\"\u001b[39m\u001b[33mTreatment\u001b[39m\u001b[33m\"\u001b[39m] = \u001b[43mcollapse_treatment_to_two_groups\u001b[49m(df[\u001b[33m\"\u001b[39m\u001b[33mTreatment_raw\u001b[39m\u001b[33m\"\u001b[39m], treatment_map)\n\u001b[32m     10\u001b[39m df[\u001b[33m\"\u001b[39m\u001b[33mAE\u001b[39m\u001b[33m\"\u001b[39m] = df[\u001b[33m\"\u001b[39m\u001b[33mAE_raw\u001b[39m\u001b[33m\"\u001b[39m]\n\u001b[32m     12\u001b[39m biomarker_cols = [\u001b[33mf\u001b[39m\u001b[33m\"\u001b[39m\u001b[33mLung_SUV_\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mp\u001b[38;5;132;01m}\u001b[39;00m\u001b[33m_max\u001b[39m\u001b[33m\"\u001b[39m \u001b[38;5;28;01mfor\u001b[39;00m p \u001b[38;5;129;01min\u001b[39;00m percentiles]\n",
      "\u001b[31mNameError\u001b[39m: name 'collapse_treatment_to_two_groups' is not defined"
     ]
    }
   ],
   "source": [
    "treatment_map = {\n",
    "    1: 0,   # mono\n",
    "    2: 0,   # mono\n",
    "    3: 0,   # mono\n",
    "    5: 1,   # combo\n",
    "    9: 1,   # combo\n",
    "}\n",
    "\n",
    "df[\"Treatment\"] = collapse_treatment_to_two_groups(df[\"Treatment_raw\"], treatment_map)\n",
    "df[\"AE\"] = df[\"AE_raw\"]\n",
    "\n",
    "biomarker_cols = [f\"Lung_SUV_{p}_max\" for p in percentiles]\n",
    "results = run_prentice_multiple(df, biomarker_cols, treatment_col=\"Treatment\", ae_col=\"AE\")\n",
    "results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "43e472e1",
   "metadata": {},
   "outputs": [],
   "source": [
    "COL_PATIENT = \"Patient_ID\"\n",
    "COL_TREAT   = \"Treatment\"\n",
    "COL_AE      = \"Lung_AE_Flag\""
   ]
  }
 ],
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