| { |
| "imports": [ |
| "$import glob", |
| "$import ignite", |
| "$import json", |
| "$import pathlib", |
| "$import os" |
| ], |
| "bundle_root": ".", |
| "ckpt_dir": "$@bundle_root + '/models'", |
| "output_dir": "$@bundle_root + '/eval'", |
| "dataset_dir": "/workspace/data/CoNSePNuclei", |
| "dataset_json": "$@dataset_dir + '/dataset.json'", |
| "train_datalist": "$json.loads(pathlib.Path(@dataset_json).read_text())['training']", |
| "val_datalist": "$json.loads(pathlib.Path(@dataset_json).read_text())['validation']", |
| "val_interval": 1, |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
| "network_def": { |
| "_target_": "DenseNet121", |
| "spatial_dims": 2, |
| "in_channels": 4, |
| "out_channels": 4 |
| }, |
| "network": "$@network_def.to(@device)", |
| "loss": { |
| "_target_": "torch.nn.CrossEntropyLoss" |
| }, |
| "optimizer": { |
| "_target_": "torch.optim.Adam", |
| "params": "$@network.parameters()", |
| "lr": 0.0001, |
| "weight_decay": 1e-05 |
| }, |
| "lr_scheduler": { |
| "_target_": "torch.optim.lr_scheduler.StepLR", |
| "optimizer": "@optimizer", |
| "step_size": 50 |
| }, |
| "max_epochs": 100, |
| "train": { |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "LoadImaged", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "dtype": "uint8", |
| "image_only": false |
| }, |
| { |
| "_target_": "EnsureChannelFirstd", |
| "keys": [ |
| "image", |
| "label" |
| ] |
| }, |
| { |
| "_target_": "SplitLabeld", |
| "keys": "label", |
| "mask_value": "", |
| "others_value": 255, |
| "to_binary_mask": false |
| }, |
| { |
| "_target_": "RandTorchVisiond", |
| "keys": "image", |
| "name": "ColorJitter", |
| "brightness": 0.25, |
| "contrast": 0.75, |
| "saturation": 0.25, |
| "hue": 0.04 |
| }, |
| { |
| "_target_": "RandFlipd", |
| "keys": [ |
| "image", |
| "label", |
| "others" |
| ], |
| "prob": 0.5 |
| }, |
| { |
| "_target_": "RandRotate90d", |
| "keys": [ |
| "image", |
| "label", |
| "others" |
| ], |
| "prob": 0.5 |
| }, |
| { |
| "_target_": "ScaleIntensityRanged", |
| "keys": "image", |
| "a_min": 0.0, |
| "a_max": 255.0, |
| "b_min": -1.0, |
| "b_max": 1.0 |
| }, |
| { |
| "_target_": "AddLabelAsGuidanced", |
| "keys": "image", |
| "source": "label" |
| }, |
| { |
| "_target_": "SetLabelClassd", |
| "keys": "label", |
| "offset": -1 |
| }, |
| { |
| "_target_": "SelectItemsd", |
| "keys": [ |
| "image", |
| "label" |
| ] |
| } |
| ] |
| }, |
| "dataset": { |
| "_target_": "CacheDataset", |
| "data": "@train_datalist", |
| "transform": "@train#preprocessing", |
| "cache_rate": 1.0, |
| "num_workers": 4 |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@train#dataset", |
| "batch_size": 64, |
| "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": 4 |
| }, |
| { |
| "_target_": "ToTensord", |
| "keys": [ |
| "pred", |
| "label" |
| ], |
| "device": "@device" |
| } |
| ] |
| }, |
| "handlers": [ |
| { |
| "_target_": "LrScheduleHandler", |
| "lr_scheduler": "@lr_scheduler", |
| "print_lr": true |
| }, |
| { |
| "_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": "$monai.handlers.from_engine(['loss'], first=True)" |
| }, |
| { |
| "_target_": "scripts.TensorBoardImageHandler", |
| "class_names": { |
| "0": "Other", |
| "1": "Inflammatory", |
| "2": "Epithelial", |
| "3": "Spindle-Shaped" |
| }, |
| "log_dir": "@output_dir", |
| "batch_limit": 4, |
| "tag_name": "train" |
| } |
| ], |
| "key_metric": { |
| "train_f1": { |
| "_target_": "ConfusionMatrix", |
| "metric_name": "f1 score", |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" |
| } |
| }, |
| "trainer": { |
| "_target_": "SupervisedTrainer", |
| "max_epochs": "@max_epochs", |
| "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": [ |
| { |
| "_target_": "LoadImaged", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "dtype": "uint8", |
| "image_only": false |
| }, |
| { |
| "_target_": "EnsureChannelFirstd", |
| "keys": [ |
| "image", |
| "label" |
| ] |
| }, |
| { |
| "_target_": "SplitLabeld", |
| "keys": "label", |
| "mask_value": "", |
| "others_value": 255, |
| "to_binary_mask": false |
| }, |
| { |
| "_target_": "ScaleIntensityRanged", |
| "keys": "image", |
| "a_min": 0.0, |
| "a_max": 255.0, |
| "b_min": -1.0, |
| "b_max": 1.0 |
| }, |
| { |
| "_target_": "AddLabelAsGuidanced", |
| "keys": "image", |
| "source": "label" |
| }, |
| { |
| "_target_": "SetLabelClassd", |
| "keys": "label", |
| "offset": -1 |
| }, |
| { |
| "_target_": "SelectItemsd", |
| "keys": [ |
| "image", |
| "label", |
| "image_meta_dict" |
| ] |
| } |
| ] |
| }, |
| "dataset": { |
| "_target_": "CacheDataset", |
| "data": "@val_datalist", |
| "transform": "@validate#preprocessing", |
| "cache_rate": 1.0 |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@validate#dataset", |
| "batch_size": 64, |
| "shuffle": false, |
| "num_workers": 4 |
| }, |
| "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" |
| }, |
| { |
| "_target_": "scripts.TensorBoardImageHandler", |
| "class_names": { |
| "0": "Other", |
| "1": "Inflammatory", |
| "2": "Epithelial", |
| "3": "Spindle-Shaped" |
| }, |
| "log_dir": "@output_dir", |
| "batch_limit": 8, |
| "tag_name": "val" |
| } |
| ], |
| "key_metric": { |
| "val_f1": { |
| "_target_": "ConfusionMatrix", |
| "metric_name": "f1 score", |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" |
| } |
| }, |
| "additional_metrics": { |
| "val_accuracy": { |
| "_target_": "ignite.metrics.Accuracy", |
| "output_transform": "$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", |
| "additional_metrics": "@validate#additional_metrics", |
| "val_handlers": "@validate#handlers", |
| "amp": true |
| } |
| }, |
| "initialize": [ |
| "$import sys", |
| "$sys.path.append(@bundle_root)", |
| "$monai.utils.set_determinism(seed=123)" |
| ], |
| "run": [ |
| "$@train#trainer.run()" |
| ] |
| } |
|
|
