| { |
| "imports": [ |
| "$import glob", |
| "$import os" |
| ], |
| "bundle_root": ".", |
| "ckpt_dir": "$@bundle_root + '/models'", |
| "output_dir": "$@bundle_root + '/eval'", |
| "dataset_dir": "$@bundle_root + '/data'", |
| "images": "$[{'artery':a, 'vein':b, 'excret':c }for a,b,c in zip(glob.glob(@dataset_dir + '/*/12.nii.gz'), glob.glob(@dataset_dir + '/*/22-.nii.gz'), glob.glob(@dataset_dir + '/*/32-.nii.gz'))]", |
| "labels": "$list(glob.glob(@dataset_dir + '/*/merged.nii.gz'))", |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
| "network_def": { |
| "_target_": "SegResNet", |
| "in_channels": 3, |
| "out_channels": 6, |
| "init_filters": 32, |
| "upsample_mode": "deconv", |
| "dropout_prob": 0.2, |
| "norm_name": "group", |
| "blocks_down": [ |
| 1, |
| 2, |
| 2, |
| 4 |
| ], |
| "blocks_up": [ |
| 1, |
| 1, |
| 1 |
| ] |
| }, |
| "network": "$@network_def.to(@device)", |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "LoadImaged", |
| "keys": [ |
| "artery", |
| "vein", |
| "excret", |
| "label" |
| ], |
| "image_only": false |
| }, |
| { |
| "_target_": "EnsureChannelFirstd", |
| "keys": [ |
| "artery", |
| "vein", |
| "excret" |
| ] |
| }, |
| { |
| "_target_": "Orientationd", |
| "keys": [ |
| "artery", |
| "vein", |
| "excret" |
| ], |
| "axcodes": "LPS" |
| }, |
| { |
| "_target_": "Spacingd", |
| "keys": [ |
| "artery", |
| "vein", |
| "excret" |
| ], |
| "pixdim": [ |
| 0.8, |
| 0.8, |
| 0.8 |
| ], |
| "mode": "bilinear" |
| }, |
| { |
| "_target_": "scripts.my_transforms.ConcatImages", |
| "keys_merge": [ |
| "artery", |
| "vein", |
| "excret" |
| ], |
| "keys_out": "image" |
| }, |
| { |
| "_target_": "ScaleIntensityRanged", |
| "keys": "image", |
| "a_min": -1000, |
| "a_max": 1000, |
| "b_min": 0.0, |
| "b_max": 1.0, |
| "clip": true |
| }, |
| { |
| "_target_": "EnsureTyped", |
| "keys": "image" |
| } |
| ] |
| }, |
| "dataset": { |
| "_target_": "Dataset", |
| "data": "$[{'label': l, **i} for i, l in zip(@images, @labels)]", |
| "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": 0.25 |
| }, |
| "postprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "Invertd", |
| "transform": "$@preprocessing", |
| "device": "@device", |
| "keys": "pred", |
| "orig_keys": "artery", |
| "meta_keys": "pred_meta_dict", |
| "nearest_interp": false, |
| "to_tensor": true |
| }, |
| { |
| "_target_": "Activationsd", |
| "keys": "pred", |
| "softmax": false, |
| "sigmoid": true |
| }, |
| { |
| "_target_": "AsDiscreted", |
| "keys": "pred", |
| "threshold": 0.5 |
| }, |
| { |
| "_target_": "scripts.my_transforms.MergeClassesd", |
| "keys": "pred" |
| }, |
| { |
| "_target_": "SaveImaged", |
| "keys": "pred", |
| "meta_keys": "pred_meta_dict", |
| "data_root_dir": "@dataset_dir", |
| "output_dir": "@output_dir" |
| }, |
| { |
| "_target_": "SaveImaged", |
| "keys": "label", |
| "data_root_dir": "@dataset_dir", |
| "output_dir": "@output_dir" |
| } |
| ] |
| }, |
| "handlers": [ |
| { |
| "_target_": "CheckpointLoader", |
| "load_path": "$@ckpt_dir + '/model.pt'", |
| "load_dict": { |
| "model": "@network" |
| }, |
| "strict": "True" |
| }, |
| { |
| "_target_": "StatsHandler", |
| "iteration_log": false |
| } |
| ], |
| "evaluator": { |
| "_target_": "SupervisedEvaluator", |
| "device": "@device", |
| "val_data_loader": "@dataloader", |
| "network": "@network", |
| "inferer": "@inferer", |
| "postprocessing": "@postprocessing", |
| "val_handlers": "@handlers", |
| "amp": false |
| }, |
| "inference": [ |
| "$setattr(torch.backends.cudnn, 'benchmark', True)", |
| "[email protected]()" |
| ] |
| } |
|
|
