| { |
| "imports": [ |
| "$import glob", |
| "$import os" |
| ], |
| "cudnn_opt": "$setattr(torch.backends.cudnn, 'benchmark', True)", |
| "dataset_dir": "/workspace/data/Task09_Spleen", |
| "ckpt_path": "/workspace/data/tutorials/modules/bundles/spleen_segmentation/models/model.pt", |
| "download_ckpt": "$monai.apps.utils.download_url('https://huggingface.co/MONAI/example_spleen_segmentation/resolve/main/model.pt', @ckpt_path)", |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
| "datalist": "$list(sorted(glob.glob(@dataset_dir + '/imagesTs/*.nii.gz')))", |
| "network_def": { |
| "_target_": "UNet", |
| "spatial_dims": 3, |
| "in_channels": 1, |
| "out_channels": 2, |
| "channels": [ |
| 16, |
| 32, |
| 64, |
| 128, |
| 256 |
| ], |
| "strides": [ |
| 2, |
| 2, |
| 2, |
| 2 |
| ], |
| "num_res_units": 2, |
| "norm": "batch" |
| }, |
| "network": "$@network_def.to(@device)", |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "LoadImaged", |
| "keys": "image" |
| }, |
| { |
| "_target_": "EnsureChannelFirstd", |
| "keys": "image" |
| }, |
| { |
| "_target_": "Orientationd", |
| "keys": "image", |
| "axcodes": "RAS" |
| }, |
| { |
| "_target_": "Spacingd", |
| "keys": "image", |
| "pixdim": [1.5, 1.5, 2.0], |
| "mode": "bilinear" |
| }, |
| { |
| "_target_": "ScaleIntensityRanged", |
| "keys": "image", |
| "a_min": -57, |
| "a_max": 164, |
| "b_min": 0, |
| "b_max": 1, |
| "clip": true |
| }, |
| { |
| "_target_": "EnsureTyped", |
| "keys": "image" |
| } |
| ] |
| }, |
| "dataset": { |
| "_target_": "Dataset", |
| "data": "$[{'image': i} for i in @datalist]", |
| "transform": "@preprocessing" |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@dataset", |
| "batch_size": 1, |
| "shuffle": false, |
| "num_workers": 4 |
| }, |
| "inferer": { |
| "_target_": "SlidingWindowInferer", |
| "roi_size": [ |
| 96, |
| 96, |
| 96 |
| ], |
| "sw_batch_size": 4, |
| "overlap": 0.5 |
| }, |
| "postprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "Activationsd", |
| "keys": "pred", |
| "softmax": true |
| }, |
| { |
| "_target_": "Invertd", |
| "keys": "pred", |
| "transform": "@preprocessing", |
| "orig_keys": "image", |
| "meta_key_postfix": "meta_dict", |
| "nearest_interp": false, |
| "to_tensor": true |
| }, |
| { |
| "_target_": "AsDiscreted", |
| "keys": "pred", |
| "argmax": true |
| }, |
| { |
| "_target_": "SaveImaged", |
| "keys": "pred", |
| "meta_keys": "pred_meta_dict", |
| "output_dir": "eval" |
| } |
| ] |
| }, |
| "handlers": [ |
| { |
| "_target_": "CheckpointLoader", |
| "_requires_": "@download_ckpt", |
| "_disabled_": "$not os.path.exists(@ckpt_path)", |
| "load_path": "@ckpt_path", |
| "load_dict": {"model": "@network"} |
| }, |
| { |
| "_target_": "StatsHandler", |
| "iteration_log": false |
| } |
| ], |
| "evaluator": { |
| "_target_": "SupervisedEvaluator", |
| "_requires_": "@cudnn_opt", |
| "device": "@device", |
| "val_data_loader": "@dataloader", |
| "network": "@network", |
| "inferer": "@inferer", |
| "postprocessing": "@postprocessing", |
| "val_handlers": "@handlers", |
| "amp": false |
| } |
| } |
|
|
