{"metadata":{"kernelspec":{"language":"python","display_name":"Python 3","name":"python3"},"language_info":{"pygments_lexer":"ipython3","nbconvert_exporter":"python","version":"3.6.4","file_extension":".py","codemirror_mode":{"name":"ipython","version":3},"name":"python","mimetype":"text/x-python"}},"nbformat_minor":4,"nbformat":4,"cells":[{"cell_type":"code","source":"import pandas as pd\nfrom fastai.vision.all import *\n\npath = Path('../input/rsna-miccai-brain-tumor-radiogenomic-classification')","metadata":{"_uuid":"8f2839f25d086af736a60e9eeb907d3b93b6e0e5","_cell_guid":"b1076dfc-b9ad-4769-8c92-a6c4dae69d19","execution":{"iopub.status.busy":"2021-09-23T14:32:28.237067Z","iopub.execute_input":"2021-09-23T14:32:28.237464Z","iopub.status.idle":"2021-09-23T14:32:30.855029Z","shell.execute_reply.started":"2021-09-23T14:32:28.237378Z","shell.execute_reply":"2021-09-23T14:32:30.853979Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"train_df = pd.read_csv('../input/rsna-miccai-brain-tumor-radiogenomic-classification/train_labels.csv')\ntrain_df","metadata":{"execution":{"iopub.status.busy":"2021-09-23T14:36:18.782117Z","iopub.execute_input":"2021-09-23T14:36:18.783361Z","iopub.status.idle":"2021-09-23T14:36:18.799106Z","shell.execute_reply.started":"2021-09-23T14:36:18.783314Z","shell.execute_reply":"2021-09-23T14:36:18.798206Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"# Exclusion of three cases from training cohort\n# https://www.kaggle.com/c/rsna-miccai-brain-tumor-radiogenomic-classification/discussion/262046\n# 00109\n# 00123\n# 00709\n\n#show dropped \ndisplay(train_df[train_df['BraTS21ID'].isin([109, 123, 709])])\ntrain_df = train_df[~train_df['BraTS21ID'].isin([109, 123, 709])]","metadata":{"execution":{"iopub.status.busy":"2021-09-23T14:36:31.314083Z","iopub.execute_input":"2021-09-23T14:36:31.314406Z","iopub.status.idle":"2021-09-23T14:36:31.328284Z","shell.execute_reply.started":"2021-09-23T14:36:31.314377Z","shell.execute_reply":"2021-09-23T14:36:31.327026Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"temp = []\ntemp1 = []\nfor i in train_df.iterrows():\n    imageid = str(i[1][0]).zfill(5)\n    x = path/'train'/imageid\n    for j in os.listdir(x):\n        for k in os.listdir(x/j):\n            temp.append([imageid, j, k, str(i[1][1]), x/j/k])\n\ntrain_dcm_df = pd.DataFrame(temp,columns=['BraTS21ID', \"Method\", \"FileName\", 'MGMT_value', 'filepath'])\ntrain_dcm_df.to_csv('train_dcm.csv', index=False)\ntrain_dcm_df","metadata":{"execution":{"iopub.status.busy":"2021-09-14T12:20:13.460952Z","iopub.execute_input":"2021-09-14T12:20:13.461349Z","iopub.status.idle":"2021-09-14T12:20:14.596946Z","shell.execute_reply.started":"2021-09-14T12:20:13.461314Z","shell.execute_reply":"2021-09-14T12:20:14.595922Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"png_path = Path('../input/rsna-miccai-png')\n\ntemp = []\nfor i in train_df.iterrows():\n    imageid = str(i[1][0]).zfill(5)\n    x = png_path/'train'/imageid\n    for j in os.listdir(x):\n        num = len(os.listdir(x/j))\n        if num >= 20:\n            images = sorted([int(pngFile.split('.')[0].split('-')[1]) for pngFile in os.listdir(x/j)])[num-10:num+10]\n        else:\n            images = sorted([int(pngFile.split('.')[0].split('-')[1]) for pngFile in os.listdir(x/j)])\n        for image_num in images:\n            pngPath = x/j/('Image-' + str(image_num) + '.png')\n            temp1.append([imageid, j, image_num, str(i[1][1]), pngPath])\n        for k in os.listdir(x/j):\n            temp.append([imageid, j, k, str(i[1][1]), x/j/k])\n\ntrain_png_df = pd.DataFrame(temp,columns=['BraTS21ID', \"Method\", \"FileName\", 'MGMT_value', 'filepath'])\ntrain_png_df.to_csv('train_png.csv', index=False)\ntrain_png_df","metadata":{"execution":{"iopub.status.busy":"2021-09-14T12:20:14.598676Z","iopub.execute_input":"2021-09-14T12:20:14.598948Z","iopub.status.idle":"2021-09-14T12:20:15.033845Z","shell.execute_reply.started":"2021-09-14T12:20:14.598918Z","shell.execute_reply":"2021-09-14T12:20:15.032963Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"train_midPng_df = pd.DataFrame(temp1,columns=['BraTS21ID', \"Method\", \"ImageNum\", 'MGMT_value', 'filepath'])\ntrain_midPng_df.to_csv('train_mid_png.csv', index=False)\ntrain_midPng_df","metadata":{"execution":{"iopub.status.busy":"2021-09-14T12:20:15.0349Z","iopub.execute_input":"2021-09-14T12:20:15.035121Z","iopub.status.idle":"2021-09-14T12:20:15.061565Z","shell.execute_reply.started":"2021-09-14T12:20:15.035097Z","shell.execute_reply":"2021-09-14T12:20:15.060457Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"# submission_df = pd.read_csv('../input/rsna-miccai-brain-tumor-radiogenomic-classification/sample_submission.csv')\n# submission_df","metadata":{"execution":{"iopub.status.busy":"2021-09-14T12:20:15.062721Z","iopub.execute_input":"2021-09-14T12:20:15.063017Z","iopub.status.idle":"2021-09-14T12:20:15.072051Z","shell.execute_reply.started":"2021-09-14T12:20:15.062984Z","shell.execute_reply":"2021-09-14T12:20:15.070548Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"# temp = []\n# for i in submission_df.iterrows():\n#     imageid = str(int(i[1][0])).zfill(5)\n#     x = path/'test'/imageid\n#     for j in os.listdir(x):\n#         for k in os.listdir(x/j):\n#             temp.append([int(i[1][0]), j, k, i[1][1], 'test/'+imageid+'/'+j+'/'+k])\n\n# submission_df = pd.DataFrame(temp, columns=['BraTS21ID', \"Method\", \"FileName\", 'MGMT_value', 'filepath'])\n# submission_df.to_csv('sample_submission.csv', index=False)\n# submission_df","metadata":{"execution":{"iopub.status.busy":"2021-09-14T12:20:15.073461Z","iopub.execute_input":"2021-09-14T12:20:15.073932Z","iopub.status.idle":"2021-09-14T12:20:15.086051Z","shell.execute_reply.started":"2021-09-14T12:20:15.07389Z","shell.execute_reply":"2021-09-14T12:20:15.084812Z"},"trusted":true},"execution_count":null,"outputs":[]},{"cell_type":"code","source":"","metadata":{},"execution_count":null,"outputs":[]}]}