| { | |
| "imports": [ | |
| "$import pandas as pd", | |
| "$import os", | |
| "$import ignite" | |
| ], | |
| "bundle_root": "/wokspace/model-zoo/models/prostate_mri_anatomy", | |
| "ckpt_dir": "$@bundle_root + '/models'", | |
| "output_dir": "$@bundle_root + '/eval'", | |
| "dataset_dir": "/workspace/data/prostate158/prostate158_train/", | |
| "images": "$list(@dataset_dir + pd.read_csv(@dataset_dir + 'train.csv').t2)", | |
| "labels": "$list(@dataset_dir + pd.read_csv(@dataset_dir + 'train.csv').t2_anatomy_reader1)", | |
| "val_images": "$list(@dataset_dir + pd.read_csv(@dataset_dir + 'valid.csv').t2)", | |
| "val_labels": "$list(@dataset_dir + pd.read_csv(@dataset_dir + 'valid.csv').t2_anatomy_reader1)", | |
| "val_interval": 5, | |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", | |
| "network_def": { | |
| "_target_": "UNet", | |
| "spatial_dims": 3, | |
| "in_channels": 1, | |
| "out_channels": 3, | |
| "channels": [ | |
| 16, | |
| 32, | |
| 64, | |
| 128, | |
| 256, | |
| 512 | |
| ], | |
| "strides": [ | |
| 2, | |
| 2, | |
| 2, | |
| 2, | |
| 2 | |
| ], | |
| "num_res_units": 4, | |
| "norm": "batch", | |
| "act": "prelu", | |
| "dropout": 0.15 | |
| }, | |
| "network": "$@network_def.to(@device)", | |
| "loss": { | |
| "_target_": "DiceFocalLoss", | |
| "to_onehot_y": true, | |
| "softmax": true, | |
| "include_background": false | |
| }, | |
| "optimizer": { | |
| "_target_": "Novograd", | |
| "params": "$@network.parameters()", | |
| "lr": 0.001, | |
| "amsgrad": true, | |
| "weight_decay": 0.01 | |
| }, | |
| "train": { | |
| "deterministic_transforms": [ | |
| { | |
| "_target_": "LoadImaged", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ] | |
| }, | |
| { | |
| "_target_": "EnsureChannelFirstd", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ] | |
| }, | |
| { | |
| "_target_": "Orientationd", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ], | |
| "axcodes": "RAS" | |
| }, | |
| { | |
| "_target_": "Spacingd", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ], | |
| "pixdim": [ | |
| 0.5, | |
| 0.5, | |
| 0.5 | |
| ], | |
| "mode": [ | |
| "bilinear", | |
| "nearest" | |
| ] | |
| }, | |
| { | |
| "_target_": "ScaleIntensityd", | |
| "keys": "image", | |
| "minv": 0, | |
| "maxv": 1 | |
| }, | |
| { | |
| "_target_": "NormalizeIntensityd", | |
| "keys": "image" | |
| }, | |
| { | |
| "_target_": "EnsureTyped", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ] | |
| } | |
| ], | |
| "random_transforms": [ | |
| { | |
| "_target_": "RandAdjustContrastd", | |
| "keys": "image", | |
| "prob": 0.15, | |
| "gamma": 2.0 | |
| }, | |
| { | |
| "_target_": "RandGaussianNoised", | |
| "keys": "image", | |
| "prob": 0.15, | |
| "mean": 0.1, | |
| "std": 0.25 | |
| }, | |
| { | |
| "_target_": "RandAffined", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ], | |
| "prob": 0.15, | |
| "rotate_range": 5, | |
| "shear_range": 0.5, | |
| "translate_range": 25 | |
| }, | |
| { | |
| "_target_": "RandBiasFieldd", | |
| "keys": "image", | |
| "prob": 0.15, | |
| "coeff_range": [ | |
| 0.0, | |
| 0.01 | |
| ], | |
| "degree": 10 | |
| }, | |
| { | |
| "_target_": "Rand3DElasticd", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ], | |
| "prob": 0.15, | |
| "magnitude_range": [ | |
| 0.5, | |
| 1.5 | |
| ], | |
| "rotate_range": 5, | |
| "shear_range": 0.5, | |
| "sigma_range": [ | |
| 0.5, | |
| 1.5 | |
| ], | |
| "translate_range": 25 | |
| }, | |
| { | |
| "_target_": "RandZoomd", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ], | |
| "prob": 0.15, | |
| "max": 1.1, | |
| "min": 0.9 | |
| }, | |
| { | |
| "_target_": "RandCropByPosNegLabeld", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ], | |
| "label_key": "label", | |
| "spatial_size": [ | |
| 96, | |
| 96, | |
| 96 | |
| ], | |
| "pos": 1, | |
| "neg": 1, | |
| "num_samples": 4, | |
| "image_key": "image", | |
| "image_threshold": 0 | |
| }, | |
| { | |
| "_target_": "RandShiftIntensityd", | |
| "keys": "image", | |
| "prob": 0.15, | |
| "offsets": 0.2 | |
| } | |
| ], | |
| "preprocessing": { | |
| "_target_": "Compose", | |
| "transforms": "$@train#deterministic_transforms + @train#random_transforms" | |
| }, | |
| "dataset": { | |
| "_target_": "PersistentDataset", | |
| "data": "$[{'image': i, 'label': l} for i, l in zip(@images, @labels)]", | |
| "transform": "@train#preprocessing", | |
| "cache_dir": "$@bundle_root + '/cache'" | |
| }, | |
| "dataloader": { | |
| "_target_": "DataLoader", | |
| "dataset": "@train#dataset", | |
| "batch_size": 2, | |
| "shuffle": true, | |
| "num_workers": 4 | |
| }, | |
| "inferer": { | |
| "_target_": "SimpleInferer" | |
| }, | |
| "postprocessing": { | |
| "_target_": "Compose", | |
| "transforms": [ | |
| { | |
| "_target_": "Activationsd", | |
| "keys": "pred", | |
| "softmax": true | |
| }, | |
| { | |
| "_target_": "AsDiscreted", | |
| "keys": [ | |
| "pred", | |
| "label" | |
| ], | |
| "argmax": [ | |
| true, | |
| false | |
| ], | |
| "to_onehot": 3 | |
| } | |
| ] | |
| }, | |
| "handlers": [ | |
| { | |
| "_target_": "ValidationHandler", | |
| "validator": "@validate#evaluator", | |
| "epoch_level": true, | |
| "interval": "@val_interval" | |
| }, | |
| { | |
| "_target_": "StatsHandler", | |
| "tag_name": "train_loss", | |
| "output_transform": "$monai.handlers.from_engine(['loss'], first=True)" | |
| }, | |
| { | |
| "_target_": "TensorBoardStatsHandler", | |
| "log_dir": "@output_dir", | |
| "tag_name": "train_loss", | |
| "output_transform": "$monai.handlers.from_engine(['loss'], first=True)" | |
| } | |
| ], | |
| "key_metric": { | |
| "train_dice": { | |
| "_target_": "MeanDice", | |
| "include_background": false, | |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" | |
| } | |
| }, | |
| "trainer": { | |
| "_target_": "SupervisedTrainer", | |
| "max_epochs": 100, | |
| "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": "%train#deterministic_transforms" | |
| }, | |
| "dataset": { | |
| "_target_": "PersistentDataset", | |
| "data": "$[{'image': i, 'label': l} for i, l in zip(@val_images, @val_labels)]", | |
| "transform": "@validate#preprocessing", | |
| "cache_dir": "$@bundle_root + '/cache'" | |
| }, | |
| "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": 16, | |
| "overlap": 0.5 | |
| }, | |
| "postprocessing": "%train#postprocessing", | |
| "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": "model.pt" | |
| } | |
| ], | |
| "key_metric": { | |
| "val_mean_dice": { | |
| "_target_": "MeanDice", | |
| "include_background": false, | |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" | |
| } | |
| }, | |
| "additional_metrics": { | |
| "val_hausdorff_distance": { | |
| "_target_": "HausdorffDistance", | |
| "include_background": false, | |
| "reduction": "mean", | |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" | |
| }, | |
| "val_surface_distance": { | |
| "_target_": "SurfaceDistance", | |
| "include_background": false, | |
| "reduction": "mean", | |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" | |
| } | |
| }, | |
| "evaluator": { | |
| "_target_": "SupervisedEvaluator", | |
| "device": "@device", | |
| "val_data_loader": "@validate#dataloader", | |
| "network": "@network", | |
| "inferer": "@validate#inferer", | |
| "postprocessing": "@validate#postprocessing", | |
| "key_val_metric": "@validate#key_metric", | |
| "additional_metrics": "@validate#additional_metrics", | |
| "val_handlers": "@validate#handlers", | |
| "amp": true | |
| } | |
| }, | |
| "training": [ | |
| "$monai.utils.set_determinism(seed=42)", | |
| "$setattr(torch.backends.cudnn, 'benchmark', True)", | |
| "$@train#trainer.run()" | |
| ] | |
| } | |