| { |
| "imports": [ |
| "$import glob", |
| "$import os" |
| ], |
| "bundle_root": ".", |
| "ckpt_dir": "$@bundle_root + '/models'", |
| "output_dir": "$@bundle_root + '/eval'", |
| "data_list_file_path": "$@bundle_root + '/configs/datalist.json'", |
| "dataset_dir": "/workspace/data/medical/brats2018challenge", |
| "test_datalist": "$monai.data.load_decathlon_datalist(@data_list_file_path, data_list_key='testing', base_dir=@dataset_dir)", |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
| "amp": true, |
| "network_def": { |
| "_target_": "SegResNet", |
| "blocks_down": [ |
| 1, |
| 2, |
| 2, |
| 4 |
| ], |
| "blocks_up": [ |
| 1, |
| 1, |
| 1 |
| ], |
| "init_filters": 16, |
| "in_channels": 4, |
| "out_channels": 3, |
| "dropout_prob": 0.2 |
| }, |
| "network": "$@network_def.to(@device)", |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "LoadImaged", |
| "keys": "image", |
| "image_only": false |
| }, |
| { |
| "_target_": "NormalizeIntensityd", |
| "keys": "image", |
| "nonzero": true, |
| "channel_wise": true |
| } |
| ] |
| }, |
| "dataset": { |
| "_target_": "Dataset", |
| "data": "@test_datalist", |
| "transform": "@preprocessing" |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@dataset", |
| "batch_size": 1, |
| "shuffle": true, |
| "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_": "Invertd", |
| "keys": "pred", |
| "transform": "@preprocessing", |
| "orig_keys": "image", |
| "meta_keys": "pred_meta_dict", |
| "nearest_interp": false, |
| "to_tensor": true |
| }, |
| { |
| "_target_": "AsDiscreted", |
| "keys": "pred", |
| "threshold": 0.5 |
| }, |
| { |
| "_target_": "Lambdad", |
| "keys": "pred", |
| "func": "$lambda x: torch.where(x[[2]] > 0, 4, torch.where(x[[0]] > 0, 1, torch.where(x[[1]] > 0, 2, 0)))" |
| }, |
| { |
| "_target_": "SaveImaged", |
| "keys": "pred", |
| "meta_keys": "pred_meta_dict", |
| "output_dir": "@output_dir", |
| "output_postfix": "seg", |
| "output_dtype": "uint8", |
| "resample": false, |
| "squeeze_end_dims": true |
| } |
| ] |
| }, |
| "handlers": [ |
| { |
| "_target_": "CheckpointLoader", |
| "load_path": "$@bundle_root + '/models/model.pt'", |
| "load_dict": { |
| "model": "@network" |
| } |
| }, |
| { |
| "_target_": "StatsHandler", |
| "iteration_log": false |
| } |
| ], |
| "evaluator": { |
| "_target_": "SupervisedEvaluator", |
| "device": "@device", |
| "val_data_loader": "@dataloader", |
| "network": "@network", |
| "inferer": "@inferer", |
| "postprocessing": "@postprocessing", |
| "val_handlers": "@handlers", |
| "amp": true |
| }, |
| "initialize": [ |
| "$setattr(torch.backends.cudnn, 'benchmark', True)" |
| ], |
| "run": [ |
| "$@evaluator.run()" |
| ] |
| } |
|
|
