| { | |
| "imports": [ | |
| "$import os", | |
| "$import ignite" | |
| ], | |
| "lr": 0.001, | |
| "num_epochs": 4, | |
| "val_interval": 1, | |
| "bundle_root": ".", | |
| "ckpt_dir": "$os.path.join(@bundle_root, 'models')", | |
| "output_dir": "$os.path.join(@bundle_root, 'log')", | |
| "training_file": "$os.path.join(@bundle_root, 'training.csv')", | |
| "validation_file": "$os.path.join(@bundle_root, 'validation.csv')", | |
| "dataset_dir": "/workspace/data/medical/pathology", | |
| "wsi_reader": "cuCIM", | |
| "region_size": [ | |
| 768, | |
| 768 | |
| ], | |
| "patch_size": [ | |
| 224, | |
| 224 | |
| ], | |
| "grid_shape": [ | |
| 3, | |
| 3 | |
| ], | |
| "number_intensity_ch": 3, | |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", | |
| "network_def": { | |
| "_target_": "TorchVisionFCModel", | |
| "model_name": "resnet18", | |
| "num_classes": 1, | |
| "use_conv": true, | |
| "pretrained": false | |
| }, | |
| "network": "$@network_def.to(@device)", | |
| "loss": { | |
| "_target_": "torch.nn.BCEWithLogitsLoss" | |
| }, | |
| "optimizer": { | |
| "_target_": "Novograd", | |
| "params": "[email protected]()", | |
| "lr": "@lr" | |
| }, | |
| "lr_scheduler": { | |
| "_target_": "torch.optim.lr_scheduler.CosineAnnealingLR", | |
| "optimizer": "@optimizer", | |
| "T_max": "@num_epochs" | |
| }, | |
| "train": { | |
| "preprocessing": { | |
| "_target_": "Compose", | |
| "transforms": [ | |
| { | |
| "_target_": "Lambdad", | |
| "keys": [ | |
| "label" | |
| ], | |
| "func": "$lambda x: x.reshape((1, *@grid_shape))" | |
| }, | |
| { | |
| "_target_": "GridSplitd", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ], | |
| "grid": "@grid_shape", | |
| "size": { | |
| "image": "@patch_size", | |
| "label": 1 | |
| } | |
| }, | |
| { | |
| "_target_": "ToTensord", | |
| "keys": "image" | |
| }, | |
| { | |
| "_target_": "TorchVisiond", | |
| "keys": "image", | |
| "name": "ColorJitter", | |
| "brightness": 0.25, | |
| "contrast": 0.75, | |
| "saturation": 0.25, | |
| "hue": 0.04 | |
| }, | |
| { | |
| "_target_": "ToNumpyd", | |
| "keys": "image" | |
| }, | |
| { | |
| "_target_": "RandFlipd", | |
| "keys": "image", | |
| "prob": 0.5 | |
| }, | |
| { | |
| "_target_": "RandRotate90d", | |
| "keys": "image", | |
| "prob": 0.5, | |
| "max_k": 3, | |
| "spatial_axes": [ | |
| -2, | |
| -1 | |
| ] | |
| }, | |
| { | |
| "_target_": "CastToTyped", | |
| "keys": "image", | |
| "dtype": "float32" | |
| }, | |
| { | |
| "_target_": "RandZoomd", | |
| "keys": "image", | |
| "prob": 0.5, | |
| "min_zoom": 0.9, | |
| "max_zoom": 1.1 | |
| }, | |
| { | |
| "_target_": "ScaleIntensityRanged", | |
| "keys": "image", | |
| "a_min": 0.0, | |
| "a_max": 255.0, | |
| "b_min": -1.0, | |
| "b_max": 1.0 | |
| }, | |
| { | |
| "_target_": "ToTensord", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ] | |
| } | |
| ] | |
| }, | |
| "datalist": { | |
| "_target_": "CSVDataset", | |
| "src": "@training_file", | |
| "col_groups": { | |
| "image": 0, | |
| "location": [ | |
| 2, | |
| 1 | |
| ], | |
| "label": [ | |
| 3, | |
| 6, | |
| 9, | |
| 4, | |
| 7, | |
| 10, | |
| 5, | |
| 8, | |
| 11 | |
| ] | |
| }, | |
| "kwargs_read_csv": { | |
| "header": null | |
| }, | |
| "transform": { | |
| "_target_": "Lambdad", | |
| "keys": "image", | |
| "func": "$lambda x: os.path.join(@dataset_dir, 'training/images', x + '.tif')" | |
| } | |
| }, | |
| "dataset": { | |
| "_target_": "monai.data.wsi_datasets.PatchWSIDataset", | |
| "data": "@train#datalist", | |
| "patch_level": 0, | |
| "patch_size": "@region_size", | |
| "reader": "@wsi_reader", | |
| "transform": "@train#preprocessing" | |
| }, | |
| "dataloader": { | |
| "_target_": "DataLoader", | |
| "dataset": "@train#dataset", | |
| "batch_size": 128, | |
| "pin_memory": true, | |
| "num_workers": 8 | |
| }, | |
| "inferer": { | |
| "_target_": "SimpleInferer" | |
| }, | |
| "postprocessing": { | |
| "_target_": "Compose", | |
| "transforms": [ | |
| { | |
| "_target_": "Activationsd", | |
| "keys": "pred", | |
| "sigmoid": true | |
| }, | |
| { | |
| "_target_": "AsDiscreted", | |
| "keys": "pred", | |
| "threshold": 0.5 | |
| } | |
| ] | |
| }, | |
| "handlers": [ | |
| { | |
| "_target_": "ValidationHandler", | |
| "validator": "@validate#evaluator", | |
| "epoch_level": true, | |
| "interval": "@val_interval" | |
| }, | |
| { | |
| "_target_": "StatsHandler", | |
| "tag_name": "train_loss", | |
| "output_transform": "$monai.handlers.from_engine(['loss'], first=True)" | |
| }, | |
| { | |
| "_target_": "LrScheduleHandler", | |
| "lr_scheduler": "@lr_scheduler", | |
| "print_lr": true | |
| }, | |
| { | |
| "_target_": "TensorBoardStatsHandler", | |
| "log_dir": "@output_dir", | |
| "tag_name": "train_loss", | |
| "output_transform": "$monai.handlers.from_engine(['loss'], first=True)" | |
| } | |
| ], | |
| "key_metric": { | |
| "train_acc": { | |
| "_target_": "ignite.metrics.Accuracy", | |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" | |
| } | |
| }, | |
| "trainer": { | |
| "_target_": "SupervisedTrainer", | |
| "device": "@device", | |
| "max_epochs": "@num_epochs", | |
| "train_data_loader": "@train#dataloader", | |
| "network": "@network", | |
| "optimizer": "@optimizer", | |
| "loss_function": "@loss", | |
| "inferer": "@train#inferer", | |
| "amp": true, | |
| "postprocessing": "@train#postprocessing", | |
| "key_train_metric": "@train#key_metric", | |
| "train_handlers": "@train#handlers" | |
| } | |
| }, | |
| "validate": { | |
| "preprocessing": { | |
| "_target_": "Compose", | |
| "transforms": [ | |
| { | |
| "_target_": "Lambdad", | |
| "keys": "label", | |
| "func": "$lambda x: x.reshape((1, *@grid_shape))" | |
| }, | |
| { | |
| "_target_": "GridSplitd", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ], | |
| "grid": "@grid_shape", | |
| "size": { | |
| "image": "@patch_size", | |
| "label": 1 | |
| } | |
| }, | |
| { | |
| "_target_": "CastToTyped", | |
| "keys": "image", | |
| "dtype": "float32" | |
| }, | |
| { | |
| "_target_": "ScaleIntensityRanged", | |
| "keys": "image", | |
| "a_min": 0.0, | |
| "a_max": 255.0, | |
| "b_min": -1.0, | |
| "b_max": 1.0 | |
| }, | |
| { | |
| "_target_": "ToTensord", | |
| "keys": [ | |
| "image", | |
| "label" | |
| ] | |
| } | |
| ] | |
| }, | |
| "datalist": { | |
| "_target_": "CSVDataset", | |
| "src": "@validation_file", | |
| "col_groups": { | |
| "image": 0, | |
| "location": [ | |
| 2, | |
| 1 | |
| ], | |
| "label": [ | |
| 3, | |
| 6, | |
| 9, | |
| 4, | |
| 7, | |
| 10, | |
| 5, | |
| 8, | |
| 11 | |
| ] | |
| }, | |
| "kwargs_read_csv": { | |
| "header": null | |
| }, | |
| "transform": { | |
| "_target_": "Lambdad", | |
| "keys": "image", | |
| "func": "$lambda x: os.path.join(@dataset_dir, 'training/images', x + '.tif')" | |
| } | |
| }, | |
| "dataset": { | |
| "_target_": "monai.data.wsi_datasets.PatchWSIDataset", | |
| "data": "@validate#datalist", | |
| "patch_level": 0, | |
| "patch_size": "@region_size", | |
| "reader": "@wsi_reader", | |
| "transform": "@validate#preprocessing" | |
| }, | |
| "dataloader": { | |
| "_target_": "DataLoader", | |
| "dataset": "@validate#dataset", | |
| "batch_size": 128, | |
| "pin_memory": true, | |
| "shuffle": false, | |
| "num_workers": 8 | |
| }, | |
| "inferer": { | |
| "_target_": "SimpleInferer" | |
| }, | |
| "postprocessing": "%train#postprocessing", | |
| "handlers": [ | |
| { | |
| "_target_": "StatsHandler", | |
| "iteration_log": false | |
| }, | |
| { | |
| "_target_": "TensorBoardStatsHandler", | |
| "log_dir": "@output_dir", | |
| "iteration_log": false | |
| }, | |
| { | |
| "_target_": "CheckpointSaver", | |
| "save_dir": "@ckpt_dir", | |
| "save_dict": { | |
| "model": "@network" | |
| }, | |
| "save_key_metric": true, | |
| "key_metric_filename": "model.pt" | |
| } | |
| ], | |
| "key_metric": { | |
| "valid_acc": { | |
| "_target_": "ignite.metrics.Accuracy", | |
| "output_transform": "$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", | |
| "val_handlers": "@validate#handlers", | |
| "amp": true | |
| } | |
| }, | |
| "initialize": [ | |
| "$monai.utils.set_determinism(seed=15)" | |
| ], | |
| "run": [ | |
| "$@train#trainer.run()" | |
| ] | |
| } | |