IS_evaluating_differences.ipynb

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    "\"\"\"Calculating the immunoScore\n",
    "from Data file ...\n",
    "output will be file containing for each patient_id original immuno TDy_immuno and boolean if match \"\"\"\n",
    "\n",
    "    #if img_path[-1:]=='3':\n",
    "    #    patient_dict['meanCD3_Tumor']=mean(patient_dict['Density_Tumor_images'])\n",
    "    #    patient_dict['meanCD3_InvasiveFront']=mean(patient_dict['Density_InvasiveFront_images'])\n",
    "    #elif  img_path[-1:]=='8':\n",
    "    #    patient_dict['meanCD8_Tumor']=mean(patient_dict['Density_Tumor_images'])\n",
    "    #    patient_dict['meanCD8_InvasiveFront']=mean(patient_dict['Density_InvasiveFront_images'])\n",
    "import os\n",
    "import glob\n",
    "import pandas\n",
    "\n",
    "SAVE_CLI_PATH=os.path.join('../Data_output')\n",
    "\n",
    "\n",
    "Data_IS_original=pandas.read_csv(os.path.join(SAVE_CLI_PATH,'data_HEGP_Immunoscore_original.txt'),sep=';')\n",
    "Data_IS_MDT=pandas.read_csv(os.path.join(SAVE_CLI_PATH,'HEGP_Immunoscore_mean.csv'),sep=',')\n",
    "\n",
    "with open('../Data_output/IS_check_MDT_HEGP.csv', 'w') as f:\n",
    "\n",
    "    f.write('OfficialID,Match,cd3_CT_amos,cd3_IM_amos,cd8_CT_amos,cd8_IM_amos,mean_score_amos,is_amos,is_MDT,score_cd3ct,score_cd3im,score_cd8ct,score_cd8im,score_mean)\\n')\n",
    "    for patient_id in list(Data_IS_MDT['OfficialID']):\n",
    "        idx_amos=list(Data_IS_original['OfficialID']).index(patient_id)\n",
    "            #immunoScore\n",
    "        is_amos=Data_IS_original.at[idx_amos,'immunoScore3gr']\n",
    "        cd3_CTscore_amos=Data_IS_original.at[idx_amos,'CD3.CT.score']\n",
    "        cd3_IMscore_amos=Data_IS_original.at[idx_amos,'CD3.IM.score']\n",
    "        cd8_CTscore_amos=Data_IS_original.at[idx_amos,'CD8.CT.score']\n",
    "        cd8_IMscore_amos=Data_IS_original.at[idx_amos,'CD8.IM.score']\n",
    "        mean_score_amos=Data_IS_original.at[idx_amos,'meanScore']\n",
    "\n",
    "        idx_mdt=list(Data_IS_MDT['OfficialID']).index(patient_id)\n",
    "        is_MDT=Data_IS_MDT.loc[idx_mdt,\"IS_MDT\"]\n",
    "        score_cd3ct=Data_IS_MDT.loc[idx_mdt,\"score_cd3ct\"]\n",
    "        score_cd3im=Data_IS_MDT.loc[idx_mdt,\"score_cd3im\"]\n",
    "        score_cd8ct=Data_IS_MDT.loc[idx_mdt,\"score_cd8ct\"]\n",
    "        score_cd8im=Data_IS_MDT.loc[idx_mdt,\"score_cd8im\"]\n",
    "        score_mean=Data_IS_MDT.loc[idx_mdt,\"score_mean\"]\n",
    "\n",
    "\n",
    "        if is_MDT==is_amos:\n",
    "            f.write('{},{},{},{},{},{},{},{},{},{},{},{},{},{}\\n'.format(patient_id,\"OK\",cd3_CTscore_amos,cd3_IMscore_amos,cd8_CTscore_amos,cd8_IMscore_amos,mean_score_amos,is_amos,is_MDT,score_cd3ct,\n",
    "            score_cd3im,score_cd8ct,score_cd8im,score_mean))\n",
    "        else:\n",
    "            f.write('{},{},{},{},{},{},{},{},{},{},{},{},{},{}\\n'.format(patient_id,\"False\",cd3_CTscore_amos,cd3_IMscore_amos,cd8_CTscore_amos,cd8_IMscore_amos,mean_score_amos,is_amos,is_MDT,score_cd3ct,\n",
    "            score_cd3im,score_cd8ct,score_cd8im,score_mean))\n"
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