| { |
| "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()" |
| ] |
| } |
|
|
