| { |
| "imports": [ |
| "$import glob", |
| "$import os", |
| "$import scripts", |
| "$import ignite", |
| "$import copy" |
| ], |
| "bundle_root": ".", |
| "ckpt_dir": "$@bundle_root + '/models'", |
| "output_dir": "$@bundle_root + '/eval'", |
| "data_list_file_path": "$@bundle_root + '/configs/msd_task09_spleen_folds.json'", |
| "dataset_dir": "/data/Task09_Spleen", |
| "use_tensorboard": true, |
| "finetune": false, |
| "finetune_model_path": "$@bundle_root + '/models/model.pt'", |
| "early_stop": false, |
| "use_mlflow": true, |
| "mlflow_dir": "$@bundle_root + '/mlruns'", |
| "fold": 0, |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
| "epochs": 5, |
| "val_interval": 1, |
| "val_at_start": false, |
| "sw_overlap": 0.625, |
| "learning_rate": 0.0001, |
| "num_patches_per_image": 1, |
| "input_channels": 1, |
| "output_classes": 2, |
| "max_point": 5, |
| "max_prompt": null, |
| "max_backprompt": null, |
| "max_foreprompt": null, |
| "drop_label_prob": 0.25, |
| "drop_point_prob": 0.25, |
| "exclude_background": true, |
| "label_set": null, |
| "val_label_set": "@label_set", |
| "amp": true, |
| "train_datalist": "$monai.auto3dseg.utils.datafold_read(datalist=@data_list_file_path, basedir=@dataset_dir, fold=@fold)[0]", |
| "val_datalist": "$monai.auto3dseg.utils.datafold_read(datalist=@data_list_file_path, basedir=@dataset_dir, fold=@fold)[1]", |
| "patch_size": [ |
| 128, |
| 128, |
| 128 |
| ], |
| "patch_size_valid": "$@patch_size", |
| "network_def": "$monai.networks.nets.vista3d132(in_channels=@input_channels)", |
| "network": "$@network_def.to(@device)", |
| "loss": { |
| "_target_": "DiceCELoss", |
| "include_background": true, |
| "sigmoid": true, |
| "smooth_dr": 1e-05, |
| "smooth_nr": 0, |
| "squared_pred": true, |
| "to_onehot_y": false |
| }, |
| "optimizer": { |
| "_target_": "torch.optim.AdamW", |
| "params": "$@network.parameters()", |
| "lr": "@learning_rate", |
| "weight_decay": 1e-05 |
| }, |
| "lr_schedule": { |
| "activate": true, |
| "lr_scheduler": { |
| "_target_": "monai.optimizers.WarmupCosineSchedule", |
| "optimizer": "@optimizer", |
| "t_total": "$@epochs", |
| "warmup_steps": 3, |
| "warmup_multiplier": 0.1 |
| } |
| }, |
| "resample_to_spacing": [ |
| 1.5, |
| 1.5, |
| 1.5 |
| ], |
| "train": { |
| "deterministic_transforms": [ |
| { |
| "_target_": "LoadImaged", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "image_only": true, |
| "ensure_channel_first": true |
| }, |
| { |
| "_target_": "CropForegroundd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "source_key": "image", |
| "margin": 10, |
| "allow_smaller": true, |
| "start_coord_key": null, |
| "end_coord_key": null |
| }, |
| { |
| "_target_": "ScaleIntensityRanged", |
| "keys": "image", |
| "a_min": -963.8247715525971, |
| "a_max": 1053.678477684517, |
| "b_min": 0.0, |
| "b_max": 1.0, |
| "clip": true |
| }, |
| { |
| "_target_": "Orientationd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "axcodes": "RAS" |
| }, |
| { |
| "_target_": "Spacingd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "pixdim": "$@resample_to_spacing", |
| "mode": [ |
| "bilinear", |
| "nearest" |
| ] |
| }, |
| { |
| "_target_": "CastToTyped", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "dtype": [ |
| "$torch.float32", |
| "$torch.uint8" |
| ] |
| }, |
| { |
| "_target_": "EnsureTyped", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "track_meta": true |
| }, |
| { |
| "_target_": "SpatialPadd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "spatial_size": "@patch_size", |
| "mode": [ |
| "constant", |
| "constant" |
| ] |
| } |
| ], |
| "random_transforms": [ |
| { |
| "_target_": "RandCropByLabelClassesd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "label_key": "label", |
| "num_classes": "@output_classes", |
| "spatial_size": "@patch_size", |
| "num_samples": "@num_patches_per_image", |
| "warn": false |
| }, |
| { |
| "_target_": "ResizeWithPadOrCropd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "spatial_size": "@patch_size" |
| }, |
| { |
| "_target_": "RandScaleIntensityd", |
| "keys": "image", |
| "prob": 0.1, |
| "factors": 0.1 |
| }, |
| { |
| "_target_": "RandShiftIntensityd", |
| "keys": "image", |
| "prob": 0.1, |
| "offsets": 0.1 |
| } |
| ], |
| "inferer": { |
| "_target_": "SimpleInferer" |
| }, |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": "$@train#deterministic_transforms + @train#random_transforms" |
| }, |
| "dataset": { |
| "_target_": "Dataset", |
| "data": "@train_datalist", |
| "transform": "@train#preprocessing" |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@train#dataset", |
| "batch_size": 1, |
| "shuffle": true, |
| "num_workers": 4, |
| "pin_memory": true, |
| "persistent_workers": true |
| }, |
| "handlers": [ |
| { |
| "_target_": "CheckpointLoader", |
| "_disabled_": "$not @finetune", |
| "load_path": "@finetune_model_path", |
| "load_dict": { |
| "model": "@network" |
| } |
| }, |
| { |
| "_target_": "LrScheduleHandler", |
| "_disabled_": "$not @lr_schedule#activate", |
| "lr_scheduler": "@lr_schedule#lr_scheduler", |
| "print_lr": true |
| }, |
| { |
| "_target_": "ValidationHandler", |
| "validator": "@validate#evaluator", |
| "epoch_level": true, |
| "exec_at_start": "@val_at_start", |
| "interval": "@val_interval" |
| }, |
| { |
| "_target_": "TensorBoardStatsHandler", |
| "_disabled_": "$not @use_tensorboard", |
| "log_dir": "@output_dir", |
| "tag_name": "train_loss", |
| "output_transform": "$monai.handlers.from_engine(['loss'], first=True)" |
| }, |
| { |
| "_target_": "StatsHandler", |
| "tag_name": "train_loss", |
| "name": "StatsHandler", |
| "output_transform": "$monai.handlers.from_engine(['loss'], first=True)" |
| }, |
| { |
| "_target_": "MLFlowHandler", |
| "_disabled_": "$not @use_mlflow", |
| "tracking_uri": "$os.path.abspath(@mlflow_dir)", |
| "output_transform": "$monai.handlers.from_engine(['loss'], first=True)" |
| } |
| ], |
| "key_metric": { |
| "train_accuracy": { |
| "_target_": "ignite.metrics.Accuracy", |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" |
| } |
| }, |
| "trainer": { |
| "_target_": "scripts.trainer.Vista3dTrainer", |
| "max_epochs": "@epochs", |
| "device": "@device", |
| "train_data_loader": "@train#dataloader", |
| "network": "@network", |
| "loss_function": "@loss", |
| "optimizer": "@optimizer", |
| "inferer": "@train#inferer", |
| "key_train_metric": null, |
| "train_handlers": "@train#handlers", |
| "amp": "@amp", |
| "hyper_kwargs": { |
| "output_classes": "@output_classes", |
| "max_point": "@max_point", |
| "max_prompt": "@max_prompt", |
| "max_backprompt": "@max_backprompt", |
| "max_foreprompt": "@max_foreprompt", |
| "drop_label_prob": "@drop_label_prob", |
| "drop_point_prob": "@drop_point_prob", |
| "exclude_background": "@exclude_background", |
| "label_set": "@label_set", |
| "patch_size": "@patch_size", |
| "user_prompt": false |
| } |
| } |
| }, |
| "validate": { |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": "$@train#deterministic_transforms" |
| }, |
| "postprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "AsDiscreted", |
| "keys": "pred", |
| "threshold": 0.0 |
| } |
| ] |
| }, |
| "dataset": { |
| "_target_": "Dataset", |
| "data": "$@val_datalist", |
| "transform": "@validate#preprocessing" |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@validate#dataset", |
| "batch_size": 1, |
| "shuffle": false, |
| "num_workers": 4 |
| }, |
| "inferer": { |
| "_target_": "scripts.inferer.Vista3dInferer", |
| "roi_size": "@patch_size_valid", |
| "overlap": "@sw_overlap" |
| }, |
| "handlers": [ |
| { |
| "_target_": "EarlyStopHandler", |
| "_disabled_": "$not @early_stop", |
| "trainer": null, |
| "patience": 2, |
| "score_function": "$scripts.score_function", |
| "min_delta": 0.01 |
| }, |
| { |
| "_target_": "TensorBoardStatsHandler", |
| "_disabled_": "$not @use_tensorboard", |
| "log_dir": "@output_dir", |
| "iteration_log": false |
| }, |
| { |
| "_target_": "StatsHandler", |
| "iteration_log": false, |
| "name": "StatsHandler" |
| }, |
| { |
| "_target_": "CheckpointSaver", |
| "save_dir": "@ckpt_dir", |
| "save_dict": { |
| "model": "@network" |
| }, |
| "save_key_metric": true, |
| "key_metric_filename": "model.pt" |
| }, |
| { |
| "_target_": "MLFlowHandler", |
| "_disabled_": "$not @use_mlflow", |
| "iteration_log": false, |
| "tracking_uri": "$os.path.abspath(@mlflow_dir)" |
| } |
| ], |
| "key_metric": { |
| "val_mean_dice": { |
| "_target_": "MeanDice", |
| "include_background": false, |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])", |
| "num_classes": "@output_classes" |
| } |
| }, |
| "additional_metrics": { |
| "val_accuracy": { |
| "_target_": "ignite.metrics.Accuracy", |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" |
| } |
| }, |
| "evaluator": { |
| "_target_": "scripts.evaluator.Vista3dEvaluator", |
| "device": "@device", |
| "val_data_loader": "@validate#dataloader", |
| "network": "@network", |
| "inferer": "@validate#inferer", |
| "postprocessing": "@validate#postprocessing", |
| "key_val_metric": "@validate#key_metric", |
| "additional_metrics": null, |
| "val_handlers": "@validate#handlers", |
| "amp": true, |
| "hyper_kwargs": { |
| "output_classes": "@output_classes", |
| "drop_label_prob": "@drop_label_prob", |
| "drop_point_prob": "@drop_point_prob", |
| "exclude_background": "@exclude_background", |
| "label_set": "@label_set", |
| "val_head": "auto", |
| "user_prompt": false |
| } |
| } |
| }, |
| "initialize": [ |
| "$monai.utils.set_determinism(seed=0)" |
| ], |
| "run": [ |
| "$@validate#handlers#0.set_trainer(trainer=@train#trainer) if @early_stop else None", |
| "$@train#trainer.add_event_handler(ignite.engine.Events.ITERATION_COMPLETED, ignite.handlers.TerminateOnNan())", |
| "$@train#trainer.run()" |
| ] |
| } |
|
|
