| { | |
| "data_list_file_path": "$@bundle_root + '/configs/msd_task09_spleen_folds.json'", | |
| "dataset_dir": "/data/Task09_Spleen", | |
| "output_dir": "$@bundle_root + '/eval'", | |
| "ckpt_path": "$@bundle_root + '/models/model.pt'", | |
| "patch_size": [ | |
| 128, | |
| 128, | |
| 128 | |
| ], | |
| "resample_to_spacing": [ | |
| 1.5, | |
| 1.5, | |
| 1.5 | |
| ], | |
| "label_mappings": { | |
| "default": [ | |
| [ | |
| 1, | |
| 3 | |
| ] | |
| ] | |
| }, | |
| "label_set": "$list(x[1] for x in @label_mappings#default)", | |
| "validate#evaluator#hyper_kwargs#val_head": "auto", | |
| "validate#preprocessing": { | |
| "_target_": "Compose", | |
| "transforms": [ | |
| { | |
| "_target_": "LoadImaged", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ], | |
| "image_only": true, | |
| "ensure_channel_first": true | |
| }, | |
| { | |
| "_target_": "CropForegroundd", | |
| "keys": [ | |
| "image" | |
| ], | |
| "source_key": "image", | |
| "margin": 10, | |
| "allow_smaller": true, | |
| "start_coord_key": null, | |
| "end_coord_key": null | |
| }, | |
| { | |
| "_target_": "ScaleIntensityRanged", | |
| "keys": "image", | |
| "a_min": -963.8247715525971, | |
| "a_max": 1053.678477684517, | |
| "b_min": 0.0, | |
| "b_max": 1.0, | |
| "clip": true | |
| }, | |
| { | |
| "_target_": "Orientationd", | |
| "keys": [ | |
| "image" | |
| ], | |
| "axcodes": "RAS" | |
| }, | |
| { | |
| "_target_": "Spacingd", | |
| "keys": [ | |
| "image" | |
| ], | |
| "pixdim": "$@resample_to_spacing", | |
| "mode": [ | |
| "bilinear" | |
| ] | |
| }, | |
| { | |
| "_target_": "CastToTyped", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ], | |
| "dtype": [ | |
| "$torch.float32", | |
| "$torch.uint8" | |
| ] | |
| }, | |
| { | |
| "_target_": "monai.apps.vista3d.transforms.Relabeld", | |
| "keys": "label", | |
| "label_mappings": "@label_mappings", | |
| "dtype": "$torch.uint8" | |
| } | |
| ] | |
| }, | |
| "validate#postprocessing": { | |
| "_target_": "Compose", | |
| "transforms": [ | |
| { | |
| "_target_": "EnsureTyped", | |
| "keys": [ | |
| "pred", | |
| "label" | |
| ], | |
| "device": "cpu", | |
| "_disabled_": true | |
| }, | |
| { | |
| "_target_": "monai.apps.vista3d.transforms.VistaPostTransformd", | |
| "keys": "pred" | |
| }, | |
| { | |
| "_target_": "Invertd", | |
| "keys": "pred", | |
| "transform": "$copy.deepcopy(@validate#preprocessing)", | |
| "orig_keys": "image", | |
| "nearest_interp": true, | |
| "to_tensor": true | |
| }, | |
| { | |
| "_target_": "Lambdad", | |
| "func": "$lambda x: torch.nan_to_num(x, nan=255)", | |
| "keys": "pred" | |
| }, | |
| { | |
| "_target_": "SaveImaged", | |
| "keys": "pred", | |
| "resample": false, | |
| "output_dir": "@output_dir" | |
| }, | |
| { | |
| "_target_": "monai.apps.vista3d.transforms.Relabeld", | |
| "keys": [ | |
| "pred", | |
| "label" | |
| ], | |
| "label_mappings": "${'default': [[c, i+1] for i, c in enumerate(@label_set)]}", | |
| "dtype": "$torch.uint8" | |
| } | |
| ] | |
| }, | |
| "validate#handlers": [ | |
| { | |
| "_target_": "CheckpointLoader", | |
| "load_path": "@ckpt_path", | |
| "load_dict": { | |
| "model": "@network" | |
| } | |
| }, | |
| { | |
| "_target_": "StatsHandler", | |
| "iteration_log": true, | |
| "name": "validate_stats" | |
| }, | |
| { | |
| "_target_": "MetricsSaver", | |
| "_disabled_": false, | |
| "save_dir": "@output_dir", | |
| "metrics": [ | |
| "val_mean_dice" | |
| ], | |
| "batch_transform": "$lambda x: [xx['image'].meta for xx in x]", | |
| "metric_details": "*", | |
| "summary_ops": "*" | |
| } | |
| ], | |
| "validate#dataset": { | |
| "_target_": "Dataset", | |
| "data": "$list(@val_datalist)", | |
| "transform": "@validate#preprocessing" | |
| }, | |
| "run": [ | |
| "$@validate#evaluator.run()" | |
| ] | |
| } | |