| { | |
| "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 | |
| } | |
| } | |