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{ |
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"imports": [ |
|
"$import glob", |
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"$import os" |
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], |
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"bundle_root": ".", |
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"ckpt_dir": "$@bundle_root + '/models'", |
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"output_dir": "$@bundle_root + '/eval'", |
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"dataset_dir": "$@bundle_root + '/data'", |
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"images": "$[{'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'))]", |
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"labels": "$list(glob.glob(@dataset_dir + '/*/merged.nii.gz'))", |
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"device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
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"network_def": { |
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"_target_": "SegResNet", |
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"in_channels": 3, |
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"out_channels": 6, |
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"init_filters": 32, |
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"upsample_mode": "deconv", |
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"dropout_prob": 0.2, |
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"norm_name": "group", |
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"blocks_down": [ |
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1, |
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2, |
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2, |
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4 |
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], |
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"blocks_up": [ |
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1, |
|
1, |
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1 |
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] |
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}, |
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"network": "$@network_def.to(@device)", |
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"preprocessing": { |
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"_target_": "Compose", |
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"transforms": [ |
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{ |
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"_target_": "LoadImaged", |
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"keys": [ |
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"artery", |
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"vein", |
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"excret", |
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"label" |
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] |
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}, |
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{ |
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"_target_": "EnsureChannelFirstd", |
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"keys": [ |
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"artery", |
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"vein", |
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"excret" |
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] |
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}, |
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{ |
|
"_target_": "Orientationd", |
|
"keys": [ |
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"artery", |
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"vein", |
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"excret" |
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], |
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"axcodes": "LPS" |
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}, |
|
{ |
|
"_target_": "Spacingd", |
|
"keys": [ |
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"artery", |
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"vein", |
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"excret" |
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], |
|
"pixdim": [ |
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0.8, |
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0.8, |
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0.8 |
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], |
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"mode": "bilinear" |
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}, |
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{ |
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"_target_": "scripts.my_transforms.ConcatImages", |
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"keys_merge": [ |
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"artery", |
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"vein", |
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"excret" |
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], |
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"keys_out": "image" |
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}, |
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{ |
|
"_target_": "ScaleIntensityRanged", |
|
"keys": "image", |
|
"a_min": -1000, |
|
"a_max": 1000, |
|
"b_min": 0.0, |
|
"b_max": 1.0, |
|
"clip": true |
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}, |
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{ |
|
"_target_": "EnsureTyped", |
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"keys": "image" |
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} |
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] |
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}, |
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"dataset": { |
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"_target_": "Dataset", |
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"data": "$[{'label': l, **i} for i, l in zip(@images, @labels)]", |
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"transform": "@preprocessing" |
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}, |
|
"dataloader": { |
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"_target_": "DataLoader", |
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"dataset": "@dataset", |
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"batch_size": 1, |
|
"shuffle": false, |
|
"num_workers": 4 |
|
}, |
|
"inferer": { |
|
"_target_": "SlidingWindowInferer", |
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"roi_size": [ |
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96, |
|
96, |
|
96 |
|
], |
|
"sw_batch_size": 4, |
|
"overlap": 0.25 |
|
}, |
|
"postprocessing": { |
|
"_target_": "Compose", |
|
"transforms": [ |
|
{ |
|
"_target_": "Invertd", |
|
"transform": "$@preprocessing", |
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"device": "@device", |
|
"keys": "pred", |
|
"orig_keys": "artery", |
|
"meta_keys": "pred_meta_dict", |
|
"nearest_interp": false, |
|
"to_tensor": true |
|
}, |
|
{ |
|
"_target_": "Activationsd", |
|
"keys": "pred", |
|
"softmax": false, |
|
"sigmoid": true |
|
}, |
|
{ |
|
"_target_": "AsDiscreted", |
|
"keys": "pred", |
|
"threshold": 0.5 |
|
}, |
|
{ |
|
"_target_": "scripts.my_transforms.MergeClassesd", |
|
"keys": "pred" |
|
}, |
|
{ |
|
"_target_": "SaveImaged", |
|
"keys": "pred", |
|
"meta_keys": "pred_meta_dict", |
|
"data_root_dir": "@dataset_dir", |
|
"output_dir": "@output_dir" |
|
}, |
|
{ |
|
"_target_": "SaveImaged", |
|
"keys": "label", |
|
"data_root_dir": "@dataset_dir", |
|
"output_dir": "@output_dir" |
|
} |
|
] |
|
}, |
|
"handlers": [ |
|
{ |
|
"_target_": "CheckpointLoader", |
|
"load_path": "$@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": [ |
|
"$setattr(torch.backends.cudnn, 'benchmark', True)", |
|
"$@evaluator.run()" |
|
] |
|
} |
|
|