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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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"$import torch", |
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"$import numpy as np" |
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], |
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"bundle_root": "/workspace/bundle/endoscopic_tool_segmentation", |
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"ckpt_dir": "$@bundle_root + '/models'", |
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"output_dir": "$@bundle_root + '/eval'", |
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"dataset_dir": "/workspace/data/endoscopic_tool_dataset", |
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"images": "$list(sorted(glob.glob(os.path.join(@dataset_dir,'train', '*', '*[!seg].jpg'))))", |
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"labels": "$[x.replace('.jpg', '_seg.jpg') for x in @images]", |
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"val_images": "$list(sorted(glob.glob(os.path.join(@dataset_dir,'val', '*', '*[!seg].jpg'))))", |
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"val_labels": "$[x.replace('.jpg', '_seg.jpg') for x in @val_images]", |
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"val_interval": 1, |
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"device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
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"network_def": { |
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"_target_": "FlexibleUNet", |
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"in_channels": 3, |
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"out_channels": 2, |
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"backbone": "efficientnet-b2", |
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"spatial_dims": 2, |
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"dropout": 0.5, |
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"pretrained": true, |
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"is_pad": false, |
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"pre_conv": null |
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}, |
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"network": "$@network_def.to(@device)", |
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"loss": { |
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"_target_": "DiceLoss", |
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"include_background": false, |
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"to_onehot_y": true, |
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"softmax": true, |
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"jaccard": true |
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}, |
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"optimizer": { |
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"_target_": "torch.optim.Adam", |
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"params": "$@network.parameters()", |
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"lr": 0.0001 |
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}, |
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"lr_scheduler": { |
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"_target_": "torch.optim.lr_scheduler.CosineAnnealingWarmRestarts", |
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"optimizer": "@optimizer", |
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"T_0": 100, |
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"T_mult": 1 |
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}, |
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"train": { |
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"deterministic_transforms": [ |
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{ |
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"_target_": "LoadImaged", |
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"keys": [ |
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"image", |
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"label" |
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] |
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}, |
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{ |
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"_target_": "AsChannelFirstd", |
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"keys": "image" |
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}, |
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{ |
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"_target_": "AddChanneld", |
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"keys": "label" |
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}, |
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{ |
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"_target_": "Resized", |
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"keys": [ |
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"image", |
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"label" |
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], |
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"spatial_size": [ |
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736, |
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480 |
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], |
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"mode": [ |
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"bilinear", |
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"nearest" |
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] |
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}, |
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{ |
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"_target_": "ScaleIntensityd", |
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"keys": [ |
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"image", |
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"label" |
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] |
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} |
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], |
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"random_transforms": [ |
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{ |
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"_target_": "RandRotated", |
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"keys": [ |
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"image", |
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"label" |
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], |
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"range_x": "$np.pi", |
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"prob": 0.8, |
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"mode": [ |
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"bilinear", |
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"nearest" |
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] |
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}, |
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{ |
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"_target_": "RandZoomd", |
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"keys": [ |
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"image", |
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"label" |
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], |
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"min_zoom": 0.8, |
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"max_zoom": 1.2, |
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"prob": 0.2, |
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"mode": [ |
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"bilinear", |
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"nearest" |
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] |
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} |
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], |
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"preprocessing": { |
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"_target_": "Compose", |
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"transforms": "$@train#deterministic_transforms + @train#random_transforms" |
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}, |
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"dataset": { |
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"_target_": "CacheDataset", |
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"data": "$[{'image': i, 'label': l} for i, l in zip(@images, @labels)]", |
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"transform": "@train#preprocessing", |
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"cache_rate": 0.1, |
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"num_workers": 4 |
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}, |
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"dataloader": { |
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"_target_": "DataLoader", |
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"dataset": "@train#dataset", |
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"batch_size": 8, |
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"shuffle": true, |
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"num_workers": 4 |
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}, |
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"inferer": { |
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"_target_": "SimpleInferer" |
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}, |
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"handlers": [ |
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{ |
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"_target_": "ValidationHandler", |
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"validator": "@validate#evaluator", |
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"epoch_level": true, |
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"interval": "@val_interval" |
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}, |
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{ |
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"_target_": "StatsHandler", |
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"tag_name": "train_loss", |
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"output_transform": "$monai.handlers.from_engine(['loss'], first=True)" |
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}, |
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{ |
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"_target_": "TensorBoardStatsHandler", |
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"log_dir": "@output_dir", |
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"tag_name": "train_loss", |
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"output_transform": "$monai.handlers.from_engine(['loss'], first=True)" |
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}, |
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{ |
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"_target_": "LrScheduleHandler", |
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"lr_scheduler": "@lr_scheduler", |
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"print_lr": true |
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} |
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], |
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"key_metric": { |
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"train_iou": { |
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"_target_": "MeanIoUHandler", |
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"include_background": false, |
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"reduction": "mean", |
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"output_transform": "$monai.handlers.from_engine(['pred', 'label'])" |
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} |
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}, |
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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_": "AsDiscreted", |
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"argmax": [ |
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true, |
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false |
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], |
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"to_onehot": [ |
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2, |
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2 |
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], |
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"keys": [ |
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"pred", |
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"label" |
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] |
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} |
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] |
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}, |
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"trainer": { |
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"_target_": "SupervisedTrainer", |
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"max_epochs": 100, |
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"device": "@device", |
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"train_data_loader": "@train#dataloader", |
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"network": "@network", |
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"loss_function": "@loss", |
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"optimizer": "@optimizer", |
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"inferer": "@train#inferer", |
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"postprocessing": "@train#postprocessing", |
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"key_train_metric": "@train#key_metric", |
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"train_handlers": "@train#handlers" |
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} |
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}, |
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"validate": { |
|
"preprocessing": { |
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"_target_": "Compose", |
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"transforms": "%train#deterministic_transforms" |
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}, |
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"dataset": { |
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"_target_": "CacheDataset", |
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"data": "$[{'image': i, 'label': l} for i, l in zip(@val_images, @val_labels)]", |
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"transform": "@validate#preprocessing", |
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"cache_rate": 0.1 |
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}, |
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"dataloader": { |
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"_target_": "DataLoader", |
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"dataset": "@validate#dataset", |
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"batch_size": 8, |
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"shuffle": false, |
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"num_workers": 4 |
|
}, |
|
"inferer": { |
|
"_target_": "SimpleInferer" |
|
}, |
|
"postprocessing": { |
|
"_target_": "Compose", |
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"transforms": "%train#postprocessing" |
|
}, |
|
"handlers": [ |
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{ |
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"_target_": "StatsHandler", |
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"iteration_log": false |
|
}, |
|
{ |
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"_target_": "TensorBoardStatsHandler", |
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"log_dir": "@output_dir", |
|
"iteration_log": false |
|
}, |
|
{ |
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"_target_": "CheckpointSaver", |
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"save_dir": "@ckpt_dir", |
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"save_dict": { |
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"model": "@network" |
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}, |
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"save_key_metric": true, |
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"key_metric_filename": "model.pt" |
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} |
|
], |
|
"additional_metrics": { |
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"val_mean_dice": { |
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"_target_": "MeanDice", |
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"include_background": false, |
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"reduction": "mean", |
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"output_transform": "$monai.handlers.from_engine(['pred', 'label'])" |
|
} |
|
}, |
|
"key_metric": { |
|
"val_iou": { |
|
"_target_": "MeanIoUHandler", |
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"include_background": false, |
|
"reduction": "mean", |
|
"output_transform": "$monai.handlers.from_engine(['pred', 'label'])" |
|
} |
|
}, |
|
"evaluator": { |
|
"_target_": "SupervisedEvaluator", |
|
"device": "@device", |
|
"val_data_loader": "@validate#dataloader", |
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"network": "@network", |
|
"inferer": "@validate#inferer", |
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"postprocessing": "@validate#postprocessing", |
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"key_val_metric": "@validate#key_metric", |
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"additional_metrics": "@validate#additional_metrics", |
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"val_handlers": "@validate#handlers" |
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} |
|
}, |
|
"training": [ |
|
"$monai.utils.set_determinism(seed=0)", |
|
"$setattr(torch.backends.cudnn, 'benchmark', True)", |
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"$@train#trainer.run()" |
|
] |
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} |
|
|