| { |
| "displayable_configs": { |
| "highres": true, |
| "init_LR": 0.0001 |
| }, |
| "imports": [ |
| "$import glob", |
| "$import os", |
| "$import ignite" |
| ], |
| "bundle_root": ".", |
| "ckpt_dir": "$@bundle_root + '/models'", |
| "output_dir": "$@bundle_root + '/eval'", |
| "dataset_dir": "sampledata", |
| "images": "$list(sorted(glob.glob(@dataset_dir + '/imagesTr/*.nii.gz')))", |
| "labels": "$list(sorted(glob.glob(@dataset_dir + '/labelsTr/*.nii.gz')))", |
| "highres": true, |
| "val_interval": 20, |
| "init_LR": 0.0001, |
| "batch_size": 4, |
| "pixdim": "$[1.5, 1.5, 1.5] if @displayable_configs#highres else [3.0, 3.0, 3.0]", |
| "modelname": "$'model.pt' if @displayable_configs#highres else 'model_lowres.pt'", |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
| "network_def": { |
| "_target_": "SegResNet", |
| "spatial_dims": 3, |
| "in_channels": 1, |
| "out_channels": 105, |
| "init_filters": 32, |
| "blocks_down": [ |
| 1, |
| 2, |
| 2, |
| 4 |
| ], |
| "blocks_up": [ |
| 1, |
| 1, |
| 1 |
| ], |
| "dropout_prob": 0.2 |
| }, |
| "network": "$@network_def.to(@device)", |
| "loss": { |
| "_target_": "DiceCELoss", |
| "to_onehot_y": true, |
| "softmax": true |
| }, |
| "optimizer": { |
| "_target_": "torch.optim.AdamW", |
| "params": "$@network.parameters()", |
| "lr": "@displayable_configs#init_LR", |
| "weight_decay": 1e-05 |
| }, |
| "train": { |
| "deterministic_transforms": [ |
| { |
| "_target_": "LoadImaged", |
| "keys": [ |
| "image", |
| "label" |
| ] |
| }, |
| { |
| "_target_": "EnsureChannelFirstd", |
| "keys": [ |
| "image", |
| "label" |
| ] |
| }, |
| { |
| "_target_": "EnsureTyped", |
| "keys": [ |
| "image", |
| "label" |
| ] |
| }, |
| { |
| "_target_": "Orientationd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "axcodes": "RAS" |
| }, |
| { |
| "_target_": "Spacingd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "pixdim": "@pixdim", |
| "mode": [ |
| "bilinear", |
| "nearest" |
| ] |
| }, |
| { |
| "_target_": "NormalizeIntensityd", |
| "keys": "image", |
| "nonzero": true |
| }, |
| { |
| "_target_": "CropForegroundd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "source_key": "image", |
| "margin": 10, |
| "k_divisible": [ |
| 96, |
| 96, |
| 96 |
| ] |
| }, |
| { |
| "_target_": "GaussianSmoothd", |
| "keys": [ |
| "image" |
| ], |
| "sigma": 0.4 |
| }, |
| { |
| "_target_": "ScaleIntensityd", |
| "keys": "image", |
| "minv": -1.0, |
| "maxv": 1.0 |
| }, |
| { |
| "_target_": "EnsureTyped", |
| "keys": [ |
| "image", |
| "label" |
| ] |
| } |
| ], |
| "random_transforms": [ |
| { |
| "_target_": "RandSpatialCropd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "roi_size": [ |
| 96, |
| 96, |
| 96 |
| ], |
| "random_size": false |
| } |
| ], |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": "$@train#deterministic_transforms + @train#random_transforms" |
| }, |
| "dataset": { |
| "_target_": "CacheDataset", |
| "data": "$[{'image': i, 'label': l} for i, l in zip(@images[:-10], @labels[:-10])]", |
| "transform": "@train#preprocessing", |
| "cache_rate": 0.4, |
| "num_workers": 4 |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@train#dataset", |
| "batch_size": "@batch_size", |
| "shuffle": true, |
| "num_workers": 4 |
| }, |
| "inferer": { |
| "_target_": "SimpleInferer" |
| }, |
| "postprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "Activationsd", |
| "keys": "pred", |
| "softmax": true |
| }, |
| { |
| "_target_": "AsDiscreted", |
| "keys": [ |
| "pred", |
| "label" |
| ], |
| "argmax": [ |
| true, |
| false |
| ], |
| "to_onehot": 105 |
| } |
| ] |
| }, |
| "handlers": [ |
| { |
| "_target_": "ValidationHandler", |
| "validator": "@validate#evaluator", |
| "epoch_level": true, |
| "interval": "@val_interval" |
| }, |
| { |
| "_target_": "StatsHandler", |
| "tag_name": "train_loss", |
| "output_transform": "$monai.handlers.from_engine(['loss'], first=True)" |
| }, |
| { |
| "_target_": "TensorBoardStatsHandler", |
| "log_dir": "@output_dir", |
| "tag_name": "train_loss", |
| "output_transform": "$monai.handlers.from_engine(['loss'], first=True)" |
| } |
| ], |
| "key_metric": { |
| "train_accuracy": { |
| "_target_": "ignite.metrics.Accuracy", |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" |
| } |
| }, |
| "trainer": { |
| "_target_": "SupervisedTrainer", |
| "max_epochs": 4000, |
| "device": "@device", |
| "train_data_loader": "@train#dataloader", |
| "network": "@network", |
| "loss_function": "@loss", |
| "optimizer": "@optimizer", |
| "inferer": "@train#inferer", |
| "postprocessing": "@train#postprocessing", |
| "key_train_metric": "@train#key_metric", |
| "train_handlers": "@train#handlers", |
| "amp": true |
| } |
| }, |
| "validate": { |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "LoadImaged", |
| "keys": [ |
| "image", |
| "label" |
| ] |
| }, |
| { |
| "_target_": "EnsureChannelFirstd", |
| "keys": [ |
| "image", |
| "label" |
| ] |
| }, |
| { |
| "_target_": "EnsureTyped", |
| "keys": [ |
| "image", |
| "label" |
| ] |
| }, |
| { |
| "_target_": "Orientationd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "axcodes": "RAS" |
| }, |
| { |
| "_target_": "Spacingd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "pixdim": "@pixdim", |
| "mode": [ |
| "bilinear", |
| "nearest" |
| ] |
| }, |
| { |
| "_target_": "NormalizeIntensityd", |
| "keys": "image", |
| "nonzero": true |
| }, |
| { |
| "_target_": "CropForegroundd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "source_key": "image", |
| "margin": 10, |
| "k_divisible": [ |
| 96, |
| 96, |
| 96 |
| ] |
| }, |
| { |
| "_target_": "GaussianSmoothd", |
| "keys": [ |
| "image" |
| ], |
| "sigma": 0.4 |
| }, |
| { |
| "_target_": "ScaleIntensityd", |
| "keys": "image", |
| "minv": -1.0, |
| "maxv": 1.0 |
| }, |
| { |
| "_target_": "CenterSpatialCropd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "roi_size": [ |
| 160, |
| 160, |
| 160 |
| ] |
| } |
| ] |
| }, |
| "postprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "Activationsd", |
| "keys": "pred", |
| "softmax": true |
| }, |
| { |
| "_target_": "AsDiscreted", |
| "keys": [ |
| "pred", |
| "label" |
| ], |
| "argmax": [ |
| true, |
| false |
| ], |
| "to_onehot": 105 |
| } |
| ] |
| }, |
| "dataset": { |
| "_target_": "Dataset", |
| "data": "$[{'image': i, 'label': l} for i, l in zip(@images[-10:], @labels[-10:])]", |
| "transform": "@validate#preprocessing" |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@validate#dataset", |
| "batch_size": 1, |
| "shuffle": false, |
| "num_workers": 4 |
| }, |
| "inferer": { |
| "_target_": "SlidingWindowInferer", |
| "roi_size": [ |
| 96, |
| 96, |
| 96 |
| ], |
| "sw_batch_size": 1, |
| "overlap": 0.25 |
| }, |
| "handlers": [ |
| { |
| "_target_": "StatsHandler", |
| "iteration_log": false |
| }, |
| { |
| "_target_": "TensorBoardStatsHandler", |
| "log_dir": "@output_dir", |
| "iteration_log": false |
| }, |
| { |
| "_target_": "CheckpointSaver", |
| "save_dir": "@ckpt_dir", |
| "save_dict": { |
| "model": "@network" |
| }, |
| "save_key_metric": true, |
| "key_metric_filename": "@modelname" |
| } |
| ], |
| "key_metric": { |
| "val_mean_dice": { |
| "_target_": "MeanDice", |
| "include_background": false, |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" |
| } |
| }, |
| "additional_metrics": { |
| "val_accuracy": { |
| "_target_": "ignite.metrics.Accuracy", |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" |
| } |
| }, |
| "evaluator": { |
| "_target_": "SupervisedEvaluator", |
| "device": "@device", |
| "val_data_loader": "@validate#dataloader", |
| "network": "@network", |
| "inferer": "@validate#inferer", |
| "postprocessing": "@validate#postprocessing", |
| "key_val_metric": "@validate#key_metric", |
| "additional_metrics": "@validate#additional_metrics", |
| "val_handlers": "@validate#handlers", |
| "amp": true |
| } |
| }, |
| "initialize": [ |
| "$monai.utils.set_determinism(seed=123)", |
| "$setattr(torch.backends.cudnn, 'benchmark', True)" |
| ], |
| "run": [ |
| "$@train#trainer.run()" |
| ] |
| } |
|
|
