{ "cells": [ { "cell_type": "code", "id": "initial_id", "metadata": { "collapsed": true, "ExecuteTime": { "end_time": "2025-01-23T00:25:39.409089Z", "start_time": "2025-01-23T00:25:35.577890Z" } }, "source": [ "from binascii import b2a_base64\n", "\n", "import segmentation_models_pytorch as smp\n", "import os\n", "import matplotlib.pyplot as plt\n", "from PIL import Image\n", "import numpy as np\n", "import torch\n", "from tensorflow.python.ops.gen_batch_ops import batch\n", "from torch.cuda import graph\n", "from torch.export import export\n", "from torch.fx.experimental.meta_tracer import torch_abs_override\n", "from torch.utils.data import Dataset, DataLoader\n", "from torchvision import transforms, utils\n", "import torch.nn as nn\n", "import torch.optim as optim\n", "from torch.optim import lr_scheduler\n", "import time\n", "import albumentations as Album\n", "import torch.nn.functional as Functional\n", "import pandas as pd\n", "import nibabel as nib\n", "from tqdm import tqdm\n", "from win32comext.mapi.emsabtags import PR_EMS_AB_MONITORING_ALERT_DELAY" ], "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "C:\\Users\\sammi\\anaconda3\\envs\\tensorflow-env\\lib\\site-packages\\tqdm\\auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", " from .autonotebook import tqdm as notebook_tqdm\n" ] } ], "execution_count": 1 }, { "metadata": { "ExecuteTime": { "end_time": "2025-01-23T00:26:43.170096Z", "start_time": "2025-01-23T00:26:43.161839Z" } }, "cell_type": "code", "source": [ "root_df = 'data/archive/BraTS2020_TrainingData/MICCAI_BraTS2020_TrainingData'\n", "data = pd.read_csv('data/archive/BraTS2020_TrainingData/MICCAI_BraTS2020_TrainingData/name_mapping.csv')\n", "\n", "data.head(10)" ], "id": "ca9637192280b3e7", "outputs": [ { "data": { "text/plain": [ " Grade BraTS_2017_subject_ID BraTS_2018_subject_ID TCGA_TCIA_subject_ID \\\n", "0 HGG Brats17_CBICA_AAB_1 Brats18_CBICA_AAB_1 NaN \n", "1 HGG Brats17_CBICA_AAG_1 Brats18_CBICA_AAG_1 NaN \n", "2 HGG Brats17_CBICA_AAL_1 Brats18_CBICA_AAL_1 NaN \n", "3 HGG Brats17_CBICA_AAP_1 Brats18_CBICA_AAP_1 NaN \n", "4 HGG Brats17_CBICA_ABB_1 Brats18_CBICA_ABB_1 NaN \n", "5 HGG Brats17_CBICA_ABE_1 Brats18_CBICA_ABE_1 NaN \n", "6 HGG Brats17_CBICA_ABM_1 Brats18_CBICA_ABM_1 NaN \n", "7 HGG Brats17_CBICA_ABN_1 Brats18_CBICA_ABN_1 NaN \n", "8 HGG Brats17_CBICA_ABO_1 Brats18_CBICA_ABO_1 NaN \n", "9 HGG Brats17_CBICA_ABY_1 Brats18_CBICA_ABY_1 NaN \n", "\n", " BraTS_2019_subject_ID BraTS_2020_subject_ID \n", "0 BraTS19_CBICA_AAB_1 BraTS20_Training_001 \n", "1 BraTS19_CBICA_AAG_1 BraTS20_Training_002 \n", "2 BraTS19_CBICA_AAL_1 BraTS20_Training_003 \n", "3 BraTS19_CBICA_AAP_1 BraTS20_Training_004 \n", "4 BraTS19_CBICA_ABB_1 BraTS20_Training_005 \n", "5 BraTS19_CBICA_ABE_1 BraTS20_Training_006 \n", "6 BraTS19_CBICA_ABM_1 BraTS20_Training_007 \n", "7 BraTS19_CBICA_ABN_1 BraTS20_Training_008 \n", "8 BraTS19_CBICA_ABO_1 BraTS20_Training_009 \n", "9 BraTS19_CBICA_ABY_1 BraTS20_Training_010 " ], "text/html": [ "
\n", " | Grade | \n", "BraTS_2017_subject_ID | \n", "BraTS_2018_subject_ID | \n", "TCGA_TCIA_subject_ID | \n", "BraTS_2019_subject_ID | \n", "BraTS_2020_subject_ID | \n", "
---|---|---|---|---|---|---|
0 | \n", "HGG | \n", "Brats17_CBICA_AAB_1 | \n", "Brats18_CBICA_AAB_1 | \n", "NaN | \n", "BraTS19_CBICA_AAB_1 | \n", "BraTS20_Training_001 | \n", "
1 | \n", "HGG | \n", "Brats17_CBICA_AAG_1 | \n", "Brats18_CBICA_AAG_1 | \n", "NaN | \n", "BraTS19_CBICA_AAG_1 | \n", "BraTS20_Training_002 | \n", "
2 | \n", "HGG | \n", "Brats17_CBICA_AAL_1 | \n", "Brats18_CBICA_AAL_1 | \n", "NaN | \n", "BraTS19_CBICA_AAL_1 | \n", "BraTS20_Training_003 | \n", "
3 | \n", "HGG | \n", "Brats17_CBICA_AAP_1 | \n", "Brats18_CBICA_AAP_1 | \n", "NaN | \n", "BraTS19_CBICA_AAP_1 | \n", "BraTS20_Training_004 | \n", "
4 | \n", "HGG | \n", "Brats17_CBICA_ABB_1 | \n", "Brats18_CBICA_ABB_1 | \n", "NaN | \n", "BraTS19_CBICA_ABB_1 | \n", "BraTS20_Training_005 | \n", "
5 | \n", "HGG | \n", "Brats17_CBICA_ABE_1 | \n", "Brats18_CBICA_ABE_1 | \n", "NaN | \n", "BraTS19_CBICA_ABE_1 | \n", "BraTS20_Training_006 | \n", "
6 | \n", "HGG | \n", "Brats17_CBICA_ABM_1 | \n", "Brats18_CBICA_ABM_1 | \n", "NaN | \n", "BraTS19_CBICA_ABM_1 | \n", "BraTS20_Training_007 | \n", "
7 | \n", "HGG | \n", "Brats17_CBICA_ABN_1 | \n", "Brats18_CBICA_ABN_1 | \n", "NaN | \n", "BraTS19_CBICA_ABN_1 | \n", "BraTS20_Training_008 | \n", "
8 | \n", "HGG | \n", "Brats17_CBICA_ABO_1 | \n", "Brats18_CBICA_ABO_1 | \n", "NaN | \n", "BraTS19_CBICA_ABO_1 | \n", "BraTS20_Training_009 | \n", "
9 | \n", "HGG | \n", "Brats17_CBICA_ABY_1 | \n", "Brats18_CBICA_ABY_1 | \n", "NaN | \n", "BraTS19_CBICA_ABY_1 | \n", "BraTS20_Training_010 | \n", "