{ "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 } }