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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": "/workspace/bundle/endoscopic_tool_segmentation", |
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"output_dir": "$@bundle_root + '/eval'", |
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"dataset_dir": "/workspace/data/endoscopic_tool_dataset", |
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"datalist": "$list(sorted(glob.glob(os.path.join(@dataset_dir,'test', '*', '*[!seg].jpg'))))", |
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"device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
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"network_def": { |
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"_target_": "FlexibleUNet", |
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"in_channels": 3, |
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"out_channels": 2, |
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"backbone": "efficientnet-b2", |
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"spatial_dims": 2, |
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"pretrained": false, |
|
"is_pad": false, |
|
"pre_conv": null |
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}, |
|
"network": "$@network_def.to(@device)", |
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"preprocessing": { |
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"_target_": "Compose", |
|
"transforms": [ |
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{ |
|
"_target_": "LoadImaged", |
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"keys": [ |
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"image" |
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] |
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}, |
|
{ |
|
"_target_": "AsChannelFirstd", |
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"keys": [ |
|
"image" |
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] |
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}, |
|
{ |
|
"_target_": "Resized", |
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"keys": [ |
|
"image" |
|
], |
|
"spatial_size": [ |
|
736, |
|
480 |
|
], |
|
"mode": [ |
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"bilinear" |
|
] |
|
}, |
|
{ |
|
"_target_": "ScaleIntensityd", |
|
"keys": [ |
|
"image" |
|
] |
|
} |
|
] |
|
}, |
|
"dataset": { |
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"_target_": "Dataset", |
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"data": "$[{'image': i} for i in @datalist]", |
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"transform": "@preprocessing" |
|
}, |
|
"dataloader": { |
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"_target_": "DataLoader", |
|
"dataset": "@dataset", |
|
"batch_size": 1, |
|
"shuffle": false, |
|
"num_workers": 4 |
|
}, |
|
"inferer": { |
|
"_target_": "SimpleInferer" |
|
}, |
|
"postprocessing": { |
|
"_target_": "Compose", |
|
"transforms": [ |
|
{ |
|
"_target_": "Invertd", |
|
"keys": "pred", |
|
"transform": "@preprocessing", |
|
"orig_keys": "image", |
|
"meta_key_postfix": "meta_dict", |
|
"nearest_interp": false, |
|
"to_tensor": true |
|
}, |
|
{ |
|
"_target_": "AsDiscreted", |
|
"argmax": true, |
|
"to_onehot": 2, |
|
"keys": [ |
|
"pred" |
|
] |
|
}, |
|
{ |
|
"_target_": "Lambdad", |
|
"keys": [ |
|
"pred" |
|
], |
|
"func": "$lambda x : x[1:]" |
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}, |
|
{ |
|
"_target_": "SaveImaged", |
|
"keys": "pred", |
|
"meta_keys": "pred_meta_dict", |
|
"output_dir": "@output_dir", |
|
"output_ext": ".png", |
|
"scale": 255, |
|
"squeeze_end_dims": true |
|
} |
|
] |
|
}, |
|
"handlers": [ |
|
{ |
|
"_target_": "CheckpointLoader", |
|
"load_path": "$@bundle_root + '/models/model.pt'", |
|
"load_dict": { |
|
"model": "@network" |
|
} |
|
}, |
|
{ |
|
"_target_": "StatsHandler", |
|
"iteration_log": false |
|
} |
|
], |
|
"evaluator": { |
|
"_target_": "SupervisedEvaluator", |
|
"device": "@device", |
|
"val_data_loader": "@dataloader", |
|
"network": "@network", |
|
"inferer": "@inferer", |
|
"postprocessing": "@postprocessing", |
|
"val_handlers": "@handlers" |
|
}, |
|
"evaluating": [ |
|
"$setattr(torch.backends.cudnn, 'benchmark', True)", |
|
"$@evaluator.run()" |
|
] |
|
} |
|
|