| { |
| "imports": [ |
| "$import glob", |
| "$import os" |
| ], |
| "bundle_root": ".", |
| "ckpt_dir": "$@bundle_root + '/models'", |
| "output_dir": "$@bundle_root + '/eval'", |
| "data_list_file_path": "$@bundle_root + '/configs/datalist.json'", |
| "dataset_dir": "/workspace/data/medical/brats2018challenge", |
| "train_datalist": "$monai.data.load_decathlon_datalist(@data_list_file_path, data_list_key='training', base_dir=@dataset_dir)", |
| "val_datalist": "$monai.data.load_decathlon_datalist(@data_list_file_path, data_list_key='validation', base_dir=@dataset_dir)", |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
| "epochs": 300, |
| "val_interval": 1, |
| "learning_rate": 0.0001, |
| "amp": true, |
| "network_def": { |
| "_target_": "SegResNet", |
| "blocks_down": [ |
| 1, |
| 2, |
| 2, |
| 4 |
| ], |
| "blocks_up": [ |
| 1, |
| 1, |
| 1 |
| ], |
| "init_filters": 16, |
| "in_channels": 4, |
| "out_channels": 3, |
| "dropout_prob": 0.2 |
| }, |
| "network": "$@network_def.to(@device)", |
| "loss": { |
| "_target_": "DiceLoss", |
| "smooth_nr": 0, |
| "smooth_dr": 1e-05, |
| "squared_pred": true, |
| "to_onehot_y": false, |
| "sigmoid": true |
| }, |
| "optimizer": { |
| "_target_": "torch.optim.Adam", |
| "params": "$@network.parameters()", |
| "lr": "@learning_rate", |
| "weight_decay": 1e-05 |
| }, |
| "lr_scheduler": { |
| "_target_": "torch.optim.lr_scheduler.CosineAnnealingLR", |
| "optimizer": "@optimizer", |
| "T_max": "@epochs" |
| }, |
| "train": { |
| "preprocessing_transforms": [ |
| { |
| "_target_": "LoadImaged", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "image_only": false |
| }, |
| { |
| "_target_": "ConvertToMultiChannelBasedOnBratsClassesd", |
| "keys": "label" |
| }, |
| { |
| "_target_": "NormalizeIntensityd", |
| "keys": "image", |
| "nonzero": true, |
| "channel_wise": true |
| } |
| ], |
| "random_transforms": [ |
| { |
| "_target_": "RandSpatialCropd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "roi_size": [ |
| 224, |
| 224, |
| 144 |
| ], |
| "random_size": false |
| }, |
| { |
| "_target_": "RandFlipd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "prob": 0.5, |
| "spatial_axis": 0 |
| }, |
| { |
| "_target_": "RandFlipd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "prob": 0.5, |
| "spatial_axis": 1 |
| }, |
| { |
| "_target_": "RandFlipd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "prob": 0.5, |
| "spatial_axis": 2 |
| }, |
| { |
| "_target_": "RandScaleIntensityd", |
| "keys": "image", |
| "factors": 0.1, |
| "prob": 1.0 |
| }, |
| { |
| "_target_": "RandShiftIntensityd", |
| "keys": "image", |
| "offsets": 0.1, |
| "prob": 1.0 |
| } |
| ], |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": "$@train#preprocessing_transforms + @train#random_transforms" |
| }, |
| "dataset": { |
| "_target_": "Dataset", |
| "data": "@train_datalist", |
| "transform": "@train#preprocessing" |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@train#dataset", |
| "batch_size": 1, |
| "shuffle": true, |
| "num_workers": 4 |
| }, |
| "inferer": { |
| "_target_": "SimpleInferer" |
| }, |
| "postprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "Activationsd", |
| "keys": "pred", |
| "sigmoid": true |
| }, |
| { |
| "_target_": "AsDiscreted", |
| "keys": "pred", |
| "threshold": 0.5 |
| } |
| ] |
| }, |
| "handlers": [ |
| { |
| "_target_": "LrScheduleHandler", |
| "lr_scheduler": "@lr_scheduler", |
| "print_lr": true |
| }, |
| { |
| "_target_": "ValidationHandler", |
| "validator": "@validate#evaluator", |
| "epoch_level": true, |
| "interval": "@val_interval" |
| }, |
| { |
| "_target_": "StatsHandler", |
| "tag_name": "train_loss", |
| "output_transform": "$monai.handlers.from_engine(['loss'], first=True)" |
| }, |
| { |
| "_target_": "TensorBoardStatsHandler", |
| "log_dir": "@output_dir", |
| "tag_name": "train_loss", |
| "output_transform": "$monai.handlers.from_engine(['loss'], first=True)" |
| } |
| ], |
| "key_metric": { |
| "train_mean_dice": { |
| "_target_": "MeanDice", |
| "include_background": true, |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" |
| } |
| }, |
| "trainer": { |
| "_target_": "SupervisedTrainer", |
| "max_epochs": "@epochs", |
| "device": "@device", |
| "train_data_loader": "@train#dataloader", |
| "network": "@network", |
| "loss_function": "@loss", |
| "optimizer": "@optimizer", |
| "inferer": "@train#inferer", |
| "postprocessing": "@train#postprocessing", |
| "key_train_metric": "@train#key_metric", |
| "train_handlers": "@train#handlers", |
| "amp": "@amp" |
| } |
| }, |
| "validate": { |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": "$@train#preprocessing_transforms" |
| }, |
| "dataset": { |
| "_target_": "Dataset", |
| "data": "@val_datalist", |
| "transform": "@validate#preprocessing" |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@validate#dataset", |
| "batch_size": 1, |
| "shuffle": false, |
| "num_workers": 4 |
| }, |
| "inferer": { |
| "_target_": "SlidingWindowInferer", |
| "roi_size": [ |
| 240, |
| 240, |
| 160 |
| ], |
| "sw_batch_size": 1, |
| "overlap": 0.5 |
| }, |
| "postprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "Activationsd", |
| "keys": "pred", |
| "sigmoid": true |
| }, |
| { |
| "_target_": "AsDiscreted", |
| "keys": "pred", |
| "threshold": 0.5 |
| }, |
| { |
| "_target_": "SplitDimd", |
| "keys": [ |
| "pred", |
| "label" |
| ], |
| "output_postfixes": [ |
| "tc", |
| "wt", |
| "et" |
| ] |
| } |
| ] |
| }, |
| "handlers": [ |
| { |
| "_target_": "StatsHandler", |
| "iteration_log": false |
| }, |
| { |
| "_target_": "TensorBoardStatsHandler", |
| "log_dir": "@output_dir", |
| "iteration_log": false |
| }, |
| { |
| "_target_": "CheckpointSaver", |
| "save_dir": "@ckpt_dir", |
| "save_dict": { |
| "model": "@network" |
| }, |
| "save_key_metric": true, |
| "key_metric_filename": "model.pt" |
| } |
| ], |
| "key_metric": { |
| "val_mean_dice": { |
| "_target_": "MeanDice", |
| "include_background": true, |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" |
| } |
| }, |
| "additional_metrics": { |
| "val_mean_dice_tc": { |
| "_target_": "MeanDice", |
| "include_background": true, |
| "output_transform": "$monai.handlers.from_engine(['pred_tc', 'label_tc'])" |
| }, |
| "val_mean_dice_wt": { |
| "_target_": "MeanDice", |
| "include_background": true, |
| "output_transform": "$monai.handlers.from_engine(['pred_wt', 'label_wt'])" |
| }, |
| "val_mean_dice_et": { |
| "_target_": "MeanDice", |
| "include_background": true, |
| "output_transform": "$monai.handlers.from_engine(['pred_et', 'label_et'])" |
| } |
| }, |
| "evaluator": { |
| "_target_": "SupervisedEvaluator", |
| "device": "@device", |
| "val_data_loader": "@validate#dataloader", |
| "network": "@network", |
| "inferer": "@validate#inferer", |
| "postprocessing": "@validate#postprocessing", |
| "key_val_metric": "@validate#key_metric", |
| "additional_metrics": "@validate#additional_metrics", |
| "val_handlers": "@validate#handlers", |
| "amp": "@amp" |
| } |
| }, |
| "initialize": [ |
| "$monai.utils.set_determinism(seed=123)", |
| "$setattr(torch.backends.cudnn, 'benchmark', True)" |
| ], |
| "run": [ |
| "$@train#trainer.run()" |
| ] |
| } |
|
|
