| { | |
| "imports": [ | |
| "$import glob", | |
| "$import os", | |
| "$import ignite", | |
| "$import scripts" | |
| ], | |
| "bundle_root": ".", | |
| "ckpt_dir": "$@bundle_root + '/models'", | |
| "output_dir": "$@bundle_root + '/eval'", | |
| "dataset_dir": "/workspace/Datasets/MSD_datasets/Task09_Spleen", | |
| "images": "$list(sorted(glob.glob(@dataset_dir + '/imagesTr/*.nii.gz')))", | |
| "labels": "$list(sorted(glob.glob(@dataset_dir + '/labelsTr/*.nii.gz')))", | |
| "label_names": { | |
| "spleen": 1, | |
| "background": 0 | |
| }, | |
| "finetune": false, | |
| "finetune_model_path": "$@bundle_root + '/models/model.pt'", | |
| "early_stop": false, | |
| "epochs": 500, | |
| "spatial_size": [ | |
| 128, | |
| 128, | |
| 128 | |
| ], | |
| "number_intensity_ch": 1, | |
| "deepgrow_probability_train": 0.4, | |
| "deepgrow_probability_val": 1.0, | |
| "val_interval": 1, | |
| "val_at_start": false, | |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", | |
| "network_def": { | |
| "_target_": "DynUNet", | |
| "spatial_dims": 3, | |
| "in_channels": "$len(@label_names) + @number_intensity_ch", | |
| "out_channels": "$len(@label_names)", | |
| "kernel_size": [ | |
| 3, | |
| 3, | |
| 3, | |
| 3, | |
| 3, | |
| 3 | |
| ], | |
| "strides": [ | |
| 1, | |
| 2, | |
| 2, | |
| 2, | |
| 2, | |
| [ | |
| 2, | |
| 2, | |
| 1 | |
| ] | |
| ], | |
| "upsample_kernel_size": [ | |
| 2, | |
| 2, | |
| 2, | |
| 2, | |
| [ | |
| 2, | |
| 2, | |
| 1 | |
| ] | |
| ], | |
| "norm_name": "instance", | |
| "deep_supervision": false, | |
| "res_block": true | |
| }, | |
| "network": "$@network_def.to(@device)", | |
| "loss": { | |
| "_target_": "DiceCELoss", | |
| "to_onehot_y": true, | |
| "softmax": true | |
| }, | |
| "optimizer": { | |
| "_target_": "torch.optim.Adam", | |
| "params": "$@network.parameters()", | |
| "lr": 0.0001 | |
| }, | |
| "lr_scheduler": { | |
| "_target_": "torch.optim.lr_scheduler.StepLR", | |
| "optimizer": "@optimizer", | |
| "step_size": 1000, | |
| "gamma": 0.1 | |
| }, | |
| "train": { | |
| "preprocessing_transforms": [ | |
| { | |
| "_target_": "LoadImaged", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ], | |
| "reader": "ITKReader" | |
| }, | |
| { | |
| "_target_": "NormalizeLabelsInDatasetd", | |
| "keys": "label", | |
| "label_names": "@label_names" | |
| }, | |
| { | |
| "_target_": "EnsureChannelFirstd", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ] | |
| }, | |
| { | |
| "_target_": "Orientationd", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ], | |
| "axcodes": "RAS" | |
| }, | |
| { | |
| "_target_": "ScaleIntensityRanged", | |
| "keys": "image", | |
| "a_min": -175, | |
| "a_max": 250, | |
| "b_min": 0.0, | |
| "b_max": 1.0, | |
| "clip": true | |
| } | |
| ], | |
| "random_transforms": [ | |
| { | |
| "_target_": "RandFlipd", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ], | |
| "spatial_axis": [ | |
| 0 | |
| ], | |
| "prob": 0.1 | |
| }, | |
| { | |
| "_target_": "RandFlipd", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ], | |
| "spatial_axis": [ | |
| 1 | |
| ], | |
| "prob": 0.1 | |
| }, | |
| { | |
| "_target_": "RandFlipd", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ], | |
| "spatial_axis": [ | |
| 2 | |
| ], | |
| "prob": 0.1 | |
| }, | |
| { | |
| "_target_": "RandRotate90d", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ], | |
| "prob": 0.1, | |
| "max_k": 3 | |
| }, | |
| { | |
| "_target_": "RandShiftIntensityd", | |
| "keys": "image", | |
| "offsets": 0.1, | |
| "prob": 0.5 | |
| } | |
| ], | |
| "deepedit_transforms": [ | |
| { | |
| "_target_": "Resized", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ], | |
| "spatial_size": "@spatial_size", | |
| "mode": [ | |
| "area", | |
| "nearest" | |
| ] | |
| }, | |
| { | |
| "_target_": "FindAllValidSlicesMissingLabelsd", | |
| "keys": "label", | |
| "sids": "sids" | |
| }, | |
| { | |
| "_target_": "AddInitialSeedPointMissingLabelsd", | |
| "keys": "label", | |
| "guidance": "guidance", | |
| "sids": "sids" | |
| }, | |
| { | |
| "_target_": "AddGuidanceSignalDeepEditd", | |
| "keys": "image", | |
| "guidance": "guidance", | |
| "number_intensity_ch": "@number_intensity_ch" | |
| }, | |
| { | |
| "_target_": "ToTensord", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ] | |
| } | |
| ], | |
| "preprocessing": { | |
| "_target_": "Compose", | |
| "transforms": "$@train#preprocessing_transforms + @train#random_transforms + @train#deepedit_transforms" | |
| }, | |
| "click_transforms": { | |
| "_target_": "Compose", | |
| "transforms": [ | |
| { | |
| "_target_": "Activationsd", | |
| "keys": "pred", | |
| "softmax": true | |
| }, | |
| { | |
| "_target_": "AsDiscreted", | |
| "keys": "pred", | |
| "argmax": true | |
| }, | |
| { | |
| "_target_": "ToNumpyd", | |
| "keys": [ | |
| "image", | |
| "label", | |
| "pred" | |
| ] | |
| }, | |
| { | |
| "_target_": "FindDiscrepancyRegionsDeepEditd", | |
| "keys": "label", | |
| "pred": "pred", | |
| "discrepancy": "discrepancy" | |
| }, | |
| { | |
| "_target_": "AddRandomGuidanceDeepEditd", | |
| "keys": "NA", | |
| "guidance": "guidance", | |
| "discrepancy": "discrepancy", | |
| "probability": "probability" | |
| }, | |
| { | |
| "_target_": "AddGuidanceSignalDeepEditd", | |
| "keys": "image", | |
| "guidance": "guidance", | |
| "number_intensity_ch": "@number_intensity_ch" | |
| }, | |
| { | |
| "_target_": "ToTensord", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ] | |
| } | |
| ] | |
| }, | |
| "dataset": { | |
| "_target_": "CacheDataset", | |
| "data": "$[{'image': i, 'label': l} for i, l in zip(@images[:-9], @labels[:-9])]", | |
| "transform": "@train#preprocessing", | |
| "cache_rate": 1.0, | |
| "num_workers": 4 | |
| }, | |
| "dataloader": { | |
| "_target_": "DataLoader", | |
| "dataset": "@train#dataset", | |
| "batch_size": 1, | |
| "shuffle": true, | |
| "num_workers": 0 | |
| }, | |
| "inferer": { | |
| "_target_": "SimpleInferer" | |
| }, | |
| "postprocessing": { | |
| "_target_": "Compose", | |
| "transforms": [ | |
| { | |
| "_target_": "Activationsd", | |
| "keys": "pred", | |
| "softmax": true | |
| }, | |
| { | |
| "_target_": "AsDiscreted", | |
| "keys": [ | |
| "pred", | |
| "label" | |
| ], | |
| "argmax": [ | |
| true, | |
| false | |
| ], | |
| "to_onehot": "$len(@label_names)+1" | |
| } | |
| ] | |
| }, | |
| "handlers": [ | |
| { | |
| "_target_": "CheckpointLoader", | |
| "_disabled_": "$not @finetune", | |
| "load_path": "@finetune_model_path", | |
| "load_dict": { | |
| "model": "@network" | |
| } | |
| }, | |
| { | |
| "_target_": "LrScheduleHandler", | |
| "lr_scheduler": "@lr_scheduler", | |
| "print_lr": true | |
| }, | |
| { | |
| "_target_": "ValidationHandler", | |
| "validator": "@validate#evaluator", | |
| "epoch_level": true, | |
| "exec_at_start": "@val_at_start", | |
| "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_dice": { | |
| "_target_": "MeanDice", | |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" | |
| } | |
| }, | |
| "train_iteration_update": { | |
| "_target_": "Interaction", | |
| "deepgrow_probability": "@deepgrow_probability_train", | |
| "transforms": "@train#click_transforms", | |
| "click_probability_key": "probability", | |
| "train": true, | |
| "label_names": "@label_names" | |
| }, | |
| "trainer": { | |
| "_target_": "SupervisedTrainer", | |
| "device": "@device", | |
| "max_epochs": "@epochs", | |
| "train_data_loader": "@train#dataloader", | |
| "network": "@network", | |
| "optimizer": "@optimizer", | |
| "loss_function": "@loss", | |
| "inferer": "@train#inferer", | |
| "amp": true, | |
| "postprocessing": "@train#postprocessing", | |
| "key_train_metric": "@train#key_metric", | |
| "train_handlers": "@train#handlers", | |
| "iteration_update": "@train#train_iteration_update" | |
| } | |
| }, | |
| "validate": { | |
| "preprocessing": { | |
| "_target_": "Compose", | |
| "transforms": "$@train#preprocessing_transforms + @train#deepedit_transforms" | |
| }, | |
| "dataset": { | |
| "_target_": "CacheDataset", | |
| "data": "$[{'image': i, 'label': l} for i, l in zip(@images[-9:], @labels[-9:])]", | |
| "transform": "@validate#preprocessing", | |
| "cache_rate": 1.0, | |
| "num_workers": 4 | |
| }, | |
| "dataloader": { | |
| "_target_": "DataLoader", | |
| "dataset": "@validate#dataset", | |
| "batch_size": 1, | |
| "shuffle": false, | |
| "num_workers": 0 | |
| }, | |
| "inferer": { | |
| "_target_": "SimpleInferer" | |
| }, | |
| "postprocessing": "%train#postprocessing", | |
| "handlers": [ | |
| { | |
| "_target_": "EarlyStopHandler", | |
| "_disabled_": "$not @early_stop", | |
| "trainer": null, | |
| "patience": 1, | |
| "score_function": "$scripts.score_function", | |
| "min_delta": 0.01 | |
| }, | |
| { | |
| "_target_": "StatsHandler", | |
| "iteration_log": false | |
| }, | |
| { | |
| "_target_": "TensorBoardStatsHandler", | |
| "log_dir": "@output_dir", | |
| "iteration_log": false | |
| }, | |
| { | |
| "_target_": "CheckpointSaver", | |
| "save_dir": "@ckpt_dir", | |
| "save_dict": { | |
| "model": "@network" | |
| }, | |
| "save_key_metric": true, | |
| "key_metric_filename": "model.pt" | |
| } | |
| ], | |
| "key_metric": { | |
| "val_mean_dice": { | |
| "_target_": "MeanDice", | |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" | |
| } | |
| }, | |
| "val_iteration_update": { | |
| "_target_": "Interaction", | |
| "deepgrow_probability": "@deepgrow_probability_val", | |
| "transforms": "@train#click_transforms", | |
| "click_probability_key": "probability", | |
| "train": false, | |
| "label_names": "@label_names" | |
| }, | |
| "evaluator": { | |
| "_target_": "SupervisedEvaluator", | |
| "device": "@device", | |
| "val_data_loader": "@validate#dataloader", | |
| "network": "@network", | |
| "inferer": "@validate#inferer", | |
| "postprocessing": "@validate#postprocessing", | |
| "key_val_metric": "@validate#key_metric", | |
| "val_handlers": "@validate#handlers", | |
| "iteration_update": "@validate#val_iteration_update", | |
| "amp": true | |
| } | |
| }, | |
| "initialize": [ | |
| "$monai.utils.set_determinism(seed=123)" | |
| ], | |
| "run": [ | |
| "$@validate#handlers#0.set_trainer(trainer=@train#trainer) if @early_stop else None", | |
| "$@train#trainer.run()" | |
| ] | |
| } | |