| { |
| "imports": [ |
| "$import glob", |
| "$import numpy", |
| "$import os" |
| ], |
| "bundle_root": ".", |
| "image_key": "image", |
| "output_dir": "$@bundle_root + '/eval'", |
| "output_ext": ".png", |
| "output_dtype": "$numpy.float32", |
| "output_postfix": "trans", |
| "separate_folder": true, |
| "load_pretrain": true, |
| "dataset_dir": "/workspace/data/endoscopic_tool_dataset", |
| "datalist": "$list(sorted(glob.glob(os.path.join(@dataset_dir,'test', '*', '*[!seg].jpg'))))", |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
| "network_def": { |
| "_target_": "FlexibleUNet", |
| "in_channels": 3, |
| "out_channels": 2, |
| "backbone": "efficientnet-b2", |
| "spatial_dims": 2, |
| "pretrained": false, |
| "is_pad": false, |
| "pre_conv": null |
| }, |
| "network": "$@network_def.to(@device)", |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "LoadImaged", |
| "keys": "@image_key", |
| "image_only": false |
| }, |
| { |
| "_target_": "EnsureChannelFirstd", |
| "keys": "@image_key", |
| "channel_dim": -1 |
| }, |
| { |
| "_target_": "Resized", |
| "keys": [ |
| "@image_key" |
| ], |
| "spatial_size": [ |
| 736, |
| 480 |
| ], |
| "mode": [ |
| "bilinear" |
| ] |
| }, |
| { |
| "_target_": "ScaleIntensityd", |
| "keys": [ |
| "@image_key" |
| ] |
| } |
| ] |
| }, |
| "dataset": { |
| "_target_": "Dataset", |
| "data": "$[{'image': i} for i in @datalist]", |
| "transform": "@preprocessing" |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@dataset", |
| "batch_size": 1, |
| "shuffle": false, |
| "num_workers": 4 |
| }, |
| "inferer": { |
| "_target_": "SimpleInferer" |
| }, |
| "postprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "Invertd", |
| "keys": "pred", |
| "transform": "@preprocessing", |
| "orig_keys": "@image_key", |
| "meta_key_postfix": "meta_dict", |
| "nearest_interp": false, |
| "to_tensor": true |
| }, |
| { |
| "_target_": "AsDiscreted", |
| "argmax": true, |
| "to_onehot": 2, |
| "keys": [ |
| "pred" |
| ] |
| }, |
| { |
| "_target_": "Lambdad", |
| "keys": [ |
| "pred" |
| ], |
| "func": "$lambda x : x[1:]" |
| }, |
| { |
| "_target_": "SaveImaged", |
| "keys": "pred", |
| "meta_keys": "pred_meta_dict", |
| "output_dir": "@output_dir", |
| "output_ext": "@output_ext", |
| "output_dtype": "@output_dtype", |
| "output_postfix": "@output_postfix", |
| "separate_folder": "@separate_folder", |
| "scale": 255, |
| "squeeze_end_dims": true |
| } |
| ] |
| }, |
| "handlers": [ |
| { |
| "_target_": "StatsHandler", |
| "iteration_log": false |
| } |
| ], |
| "evaluator": { |
| "_target_": "SupervisedEvaluator", |
| "device": "@device", |
| "val_data_loader": "@dataloader", |
| "network": "@network", |
| "inferer": "@inferer", |
| "postprocessing": "@postprocessing", |
| "val_handlers": "@handlers" |
| }, |
| "checkpointloader": { |
| "_target_": "CheckpointLoader", |
| "load_path": "$@bundle_root + '/models/model.pt'", |
| "load_dict": { |
| "model": "@network" |
| }, |
| "map_location": "@device" |
| }, |
| "initialize": [ |
| "$monai.utils.set_determinism(seed=123)", |
| "$@checkpointloader(@evaluator) if @load_pretrain else None" |
| ], |
| "run": [ |
| "[email protected]()" |
| ] |
| } |
|
|
