| { |
| "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": "$@network.parameters()", |
| "lr": 0.001 |
| }, |
| "train": { |
| "deterministic_transforms": [ |
| { |
| "_target_": "LoadImaged", |
| "keys": "image" |
| }, |
| { |
| "_target_": "ToTensord", |
| "keys": "label" |
| }, |
| { |
| "_target_": "EnsureChannelFirstd", |
| "keys": "image", |
| "channel_dim": -1 |
| }, |
| { |
| "_target_": "Resized", |
| "keys": "image", |
| "spatial_size": [ |
| 256, |
| 256 |
| ], |
| "mode": "bilinear" |
| }, |
| { |
| "_target_": "CastToTyped", |
| "dtype": "$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()" |
| ] |
| } |
|
|
