| { | |
| "imports": [ | |
| "$import torch", | |
| "$import json", | |
| "$import ignite", | |
| "$import os" | |
| ], | |
| "bundle_root": ".", | |
| "ckpt_dir": "$@bundle_root + '/models'", | |
| "output_dir": "$@bundle_root + '/eval'", | |
| "dataset_dir": "/workspace/data/endoscopic_inbody_classification", | |
| "train_json": "$@bundle_root+'/label/train_samples.json'", | |
| "val_json": "$@bundle_root+'/label/val_samples.json'", | |
| "train_fp": "$open(@train_json,'r', encoding='utf8')", | |
| "train_dict": "$json.load(@train_fp)", | |
| "val_fp": "$open(@val_json,'r', encoding='utf8')", | |
| "val_dict": "$json.load(@val_fp)", | |
| "val_interval": 1, | |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", | |
| "network_def": { | |
| "_target_": "SEResNet50", | |
| "spatial_dims": 2, | |
| "in_channels": 3, | |
| "num_classes": 2 | |
| }, | |
| "network": "$@network_def.to(@device)", | |
| "loss": { | |
| "_target_": "torch.nn.CrossEntropyLoss", | |
| "reduction": "sum" | |
| }, | |
| "optimizer": { | |
| "_target_": "torch.optim.Adam", | |
| "params": "[email protected]()", | |
| "lr": 0.001 | |
| }, | |
| "train": { | |
| "deterministic_transforms": [ | |
| { | |
| "_target_": "LoadImaged", | |
| "keys": "image" | |
| }, | |
| { | |
| "_target_": "ToTensord", | |
| "keys": "label" | |
| }, | |
| { | |
| "_target_": "AsChannelFirstd", | |
| "keys": "image" | |
| }, | |
| { | |
| "_target_": "Resized", | |
| "keys": "image", | |
| "spatial_size": [ | |
| 256, | |
| 256 | |
| ], | |
| "mode": "bilinear" | |
| }, | |
| { | |
| "_target_": "CastToTyped", | |
| "dtype": "$torch.float32", | |
| "keys": "image" | |
| }, | |
| { | |
| "_target_": "NormalizeIntensityd", | |
| "nonzero": true, | |
| "channel_wise": true, | |
| "keys": "image" | |
| }, | |
| { | |
| "_target_": "EnsureTyped", | |
| "keys": "image" | |
| } | |
| ], | |
| "random_transforms": [ | |
| { | |
| "_target_": "RandRotated", | |
| "range_x": 0.3, | |
| "prob": 0.2, | |
| "mode": "bilinear", | |
| "keys": "image" | |
| }, | |
| { | |
| "_target_": "RandScaleIntensityd", | |
| "factors": 0.3, | |
| "prob": 0.5, | |
| "keys": "image" | |
| }, | |
| { | |
| "_target_": "RandShiftIntensityd", | |
| "offsets": 0.1, | |
| "prob": 0.5, | |
| "keys": "image" | |
| }, | |
| { | |
| "_target_": "RandGaussianNoised", | |
| "std": 0.01, | |
| "prob": 0.15, | |
| "keys": "image" | |
| }, | |
| { | |
| "_target_": "RandFlipd", | |
| "spatial_axis": 0, | |
| "prob": 0.5, | |
| "keys": "image" | |
| }, | |
| { | |
| "_target_": "RandFlipd", | |
| "spatial_axis": 1, | |
| "prob": 0.5, | |
| "keys": "image" | |
| } | |
| ], | |
| "preprocessing": { | |
| "_target_": "Compose", | |
| "transforms": "$@train#deterministic_transforms + @train#random_transforms" | |
| }, | |
| "dataset": { | |
| "_target_": "Dataset", | |
| "data": "@train_dict", | |
| "transform": "@train#preprocessing" | |
| }, | |
| "dataloader": { | |
| "_target_": "DataLoader", | |
| "dataset": "@train#dataset", | |
| "batch_size": 64, | |
| "shuffle": true, | |
| "num_workers": 4 | |
| }, | |
| "inferer": { | |
| "_target_": "SimpleInferer" | |
| }, | |
| "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_accu": { | |
| "_target_": "ignite.metrics.Accuracy", | |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" | |
| } | |
| }, | |
| "postprocessing": { | |
| "_target_": "Compose", | |
| "transforms": [ | |
| { | |
| "_target_": "AsDiscreted", | |
| "argmax": [ | |
| true, | |
| false | |
| ], | |
| "to_onehot": [ | |
| 2, | |
| 2 | |
| ], | |
| "keys": [ | |
| "pred", | |
| "label" | |
| ] | |
| } | |
| ] | |
| }, | |
| "trainer": { | |
| "_target_": "SupervisedTrainer", | |
| "max_epochs": 25, | |
| "device": "@device", | |
| "train_data_loader": "@train#dataloader", | |
| "network": "@network", | |
| "loss_function": "@loss", | |
| "optimizer": "@optimizer", | |
| "inferer": "@train#inferer", | |
| "postprocessing": "@train#postprocessing", | |
| "key_train_metric": "@train#key_metric", | |
| "train_handlers": "@train#handlers" | |
| } | |
| }, | |
| "validate": { | |
| "preprocessing": { | |
| "_target_": "Compose", | |
| "transforms": "%train#deterministic_transforms" | |
| }, | |
| "dataset": { | |
| "_target_": "Dataset", | |
| "data": "@val_dict", | |
| "transform": "@validate#preprocessing" | |
| }, | |
| "dataloader": { | |
| "_target_": "DataLoader", | |
| "dataset": "@validate#dataset", | |
| "batch_size": 64, | |
| "shuffle": false, | |
| "num_workers": 4 | |
| }, | |
| "inferer": { | |
| "_target_": "SimpleInferer" | |
| }, | |
| "postprocessing": { | |
| "_target_": "Compose", | |
| "transforms": "%train#postprocessing" | |
| }, | |
| "handlers": [ | |
| { | |
| "_target_": "StatsHandler", | |
| "iteration_log": false | |
| }, | |
| { | |
| "_target_": "TensorBoardStatsHandler", | |
| "log_dir": "@output_dir", | |
| "iteration_log": false | |
| }, | |
| { | |
| "_target_": "CheckpointSaver", | |
| "save_dir": "@ckpt_dir", | |
| "save_dict": { | |
| "model": "@network" | |
| }, | |
| "save_key_metric": true, | |
| "key_metric_filename": "model.pt" | |
| } | |
| ], | |
| "key_metric": { | |
| "val_accu": { | |
| "_target_": "ignite.metrics.Accuracy", | |
| "output_transform": "$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" | |
| } | |
| }, | |
| "initialize": [ | |
| "$monai.utils.set_determinism(seed=123)" | |
| ], | |
| "run": [ | |
| "$@train#trainer.run()" | |
| ], | |
| "finalize": [ | |
| "$@train_fp.close()", | |
| "$@val_fp.close()" | |
| ] | |
| } | |