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{ |
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"imports": [ |
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"$import glob", |
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"$import os" |
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], |
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"bundle_root": "$os.getcwd()", |
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"output_dir": ".", |
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"dataset_dir": "CoNSeP/Test/Images", |
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"num_cpus": 6, |
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"batch_size": 1, |
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"sw_batch_size": 16, |
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"hovernet_mode": "fast", |
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"patch_size": 256, |
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"out_size": 164, |
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"device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
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"network_def": { |
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"_target_": "HoVerNet", |
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"mode": "@hovernet_mode", |
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"adapt_standard_resnet": true, |
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"in_channels": 3, |
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"out_classes": 5 |
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}, |
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"network": "$@network_def.to(@device)", |
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"preprocessing": { |
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"_target_": "Compose", |
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"transforms": [ |
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{ |
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"_target_": "LoadImaged", |
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"keys": "image", |
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"reader": "$monai.data.PILReader", |
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"converter": "$lambda x: x.convert('RGB')" |
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}, |
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{ |
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"_target_": "EnsureChannelFirstd", |
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"keys": "image" |
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}, |
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{ |
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"_target_": "CastToTyped", |
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"keys": "image", |
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"dtype": "float32" |
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}, |
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{ |
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"_target_": "ScaleIntensityRanged", |
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"keys": "image", |
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"a_min": 0.0, |
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"a_max": 255.0, |
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"b_min": 0.0, |
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"b_max": 1.0, |
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"clip": true |
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} |
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] |
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}, |
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"data_list": "$[{'image': image} for image in glob.glob(os.path.join(@dataset_dir, '*.png'))]", |
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"dataset": { |
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"_target_": "Dataset", |
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"data": "@data_list", |
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"transform": "@preprocessing" |
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}, |
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"dataloader": { |
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"_target_": "DataLoader", |
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"dataset": "@dataset", |
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"batch_size": "@batch_size", |
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"shuffle": false, |
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"num_workers": "@num_cpus", |
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"pin_memory": true |
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}, |
|
"inferer": { |
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"_target_": "SlidingWindowHoVerNetInferer", |
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"roi_size": "@patch_size", |
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"sw_batch_size": "@sw_batch_size", |
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"overlap": "$1.0 - float(@out_size) / float(@patch_size)", |
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"padding_mode": "constant", |
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"cval": 0, |
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"progress": true, |
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"extra_input_padding": "$((@patch_size - @out_size) // 2,) * 4" |
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}, |
|
"postprocessing": { |
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"_target_": "Compose", |
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"transforms": [ |
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{ |
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"_target_": "FlattenSubKeysd", |
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"keys": "pred", |
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"sub_keys": [ |
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"horizontal_vertical", |
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"nucleus_prediction", |
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"type_prediction" |
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], |
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"delete_keys": true |
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}, |
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{ |
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"_target_": "HoVerNetInstanceMapPostProcessingd", |
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"sobel_kernel_size": 21, |
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"marker_threshold": 0.4, |
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"marker_radius": 2 |
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}, |
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{ |
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"_target_": "HoVerNetNuclearTypePostProcessingd" |
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}, |
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{ |
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"_target_": "FromMetaTensord", |
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"keys": [ |
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"image" |
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] |
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} |
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] |
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}, |
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"handlers": [ |
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{ |
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"_target_": "CheckpointLoader", |
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"load_path": "$os.path.join(@bundle_root, 'models', 'model.pt')", |
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"map_location": "@device", |
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"load_dict": { |
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"model": "@network" |
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} |
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} |
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], |
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"evaluator": { |
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"_target_": "SupervisedEvaluator", |
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"device": "@device", |
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"val_data_loader": "@dataloader", |
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"val_handlers": "@handlers", |
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"network": "@network", |
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"postprocessing": "@postprocessing", |
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"inferer": "@inferer", |
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"amp": true |
|
}, |
|
"evaluating": [ |
|
"$setattr(torch.backends.cudnn, 'benchmark', True)", |
|
"$@evaluator.run()" |
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] |
|
} |
|
|