| { |
| "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()" |
| ] |
| } |
|
|
