| { |
| "imports": [ |
| "$import glob", |
| "$import os", |
| "$import skimage" |
| ], |
| "bundle_root": ".", |
| "ckpt_dir_stage0": "$os.path.join(@bundle_root, 'models', 'stage0')", |
| "ckpt_dir_stage1": "$os.path.join(@bundle_root, 'models')", |
| "ckpt_path_stage0": "$os.path.join(@ckpt_dir_stage0, 'model.pt')", |
| "output_dir": "$os.path.join(@bundle_root, 'eval')", |
| "dataset_dir": "/workspace/Data/Pathology/CoNSeP/Prepared/", |
| "train_images": "$list(sorted(glob.glob(@dataset_dir + '/Train/*image.npy')))", |
| "val_images": "$list(sorted(glob.glob(@dataset_dir + '/Test/*image.npy')))", |
| "train_inst_map": "$list(sorted(glob.glob(@dataset_dir + '/Train/*inst_map.npy')))", |
| "val_inst_map": "$list(sorted(glob.glob(@dataset_dir + '/Test/*inst_map.npy')))", |
| "train_type_map": "$list(sorted(glob.glob(@dataset_dir + '/Train/*type_map.npy')))", |
| "val_type_map": "$list(sorted(glob.glob(@dataset_dir + '/Test/*type_map.npy')))", |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
| "stage": 0, |
| "epochs": 50, |
| "batch_size": 16, |
| "val_interval": 1, |
| "learning_rate": 0.0001, |
| "amp": true, |
| "hovernet_mode": "fast", |
| "patch_size": 256, |
| "out_size": 164, |
| "ckpt_dir": "$@ckpt_dir_stage0 if @stage == 0 else @ckpt_dir_stage1", |
| "network_def": { |
| "_target_": "HoVerNet", |
| "mode": "@hovernet_mode", |
| "in_channels": 3, |
| "out_classes": 5, |
| "adapt_standard_resnet": true, |
| "pretrained_url": null, |
| "freeze_encoder": true |
| }, |
| "network": "$@network_def.to(@device)", |
| "loss": { |
| "_target_": "HoVerNetLoss", |
| "lambda_hv_mse": 1.0 |
| }, |
| "optimizer": { |
| "_target_": "torch.optim.Adam", |
| "params": "$filter(lambda p: p.requires_grad, @network.parameters())", |
| "lr": "@learning_rate", |
| "weight_decay": 1e-05 |
| }, |
| "lr_scheduler": { |
| "_target_": "torch.optim.lr_scheduler.StepLR", |
| "optimizer": "@optimizer", |
| "step_size": 25 |
| }, |
| "train": { |
| "preprocessing_transforms": [ |
| { |
| "_target_": "LoadImaged", |
| "keys": [ |
| "image", |
| "label_inst", |
| "label_type" |
| ] |
| }, |
| { |
| "_target_": "EnsureChannelFirstd", |
| "keys": [ |
| "image", |
| "label_inst", |
| "label_type" |
| ], |
| "channel_dim": -1 |
| }, |
| { |
| "_target_": "Lambdad", |
| "keys": "label_inst", |
| "func": "$lambda x: skimage.measure.label(x)" |
| }, |
| { |
| "_target_": "RandAffined", |
| "keys": [ |
| "image", |
| "label_inst", |
| "label_type" |
| ], |
| "prob": 1.0, |
| "rotate_range": [ |
| "$np.pi" |
| ], |
| "scale_range": [ |
| [ |
| -0.2, |
| 0.2 |
| ], |
| [ |
| -0.2, |
| 0.2 |
| ] |
| ], |
| "shear_range": [ |
| [ |
| -0.05, |
| 0.05 |
| ], |
| [ |
| -0.05, |
| 0.05 |
| ] |
| ], |
| "translate_range": [ |
| [ |
| -6, |
| 6 |
| ], |
| [ |
| -6, |
| 6 |
| ] |
| ], |
| "padding_mode": "zeros", |
| "mode": "nearest" |
| }, |
| { |
| "_target_": "CenterSpatialCropd", |
| "keys": [ |
| "image" |
| ], |
| "roi_size": [ |
| "@patch_size", |
| "@patch_size" |
| ] |
| }, |
| { |
| "_target_": "RandFlipd", |
| "keys": [ |
| "image", |
| "label_inst", |
| "label_type" |
| ], |
| "prob": 0.5, |
| "spatial_axis": 0 |
| }, |
| { |
| "_target_": "RandFlipd", |
| "keys": [ |
| "image", |
| "label_inst", |
| "label_type" |
| ], |
| "prob": 0.5, |
| "spatial_axis": 1 |
| }, |
| { |
| "_target_": "OneOf", |
| "transforms": [ |
| { |
| "_target_": "RandGaussianSmoothd", |
| "keys": [ |
| "image" |
| ], |
| "sigma_x": [ |
| 0.1, |
| 1.1 |
| ], |
| "sigma_y": [ |
| 0.1, |
| 1.1 |
| ], |
| "prob": 1.0 |
| }, |
| { |
| "_target_": "MedianSmoothd", |
| "keys": [ |
| "image" |
| ], |
| "radius": 1 |
| }, |
| { |
| "_target_": "RandGaussianNoised", |
| "keys": [ |
| "image" |
| ], |
| "std": 0.05, |
| "prob": 1.0 |
| } |
| ] |
| }, |
| { |
| "_target_": "CastToTyped", |
| "keys": "image", |
| "dtype": "$np.uint8" |
| }, |
| { |
| "_target_": "TorchVisiond", |
| "keys": "image", |
| "name": "ColorJitter", |
| "brightness": [ |
| 0.9, |
| 1.1 |
| ], |
| "contrast": [ |
| 0.95, |
| 1.1 |
| ], |
| "saturation": [ |
| 0.8, |
| 1.2 |
| ], |
| "hue": [ |
| -0.04, |
| 0.04 |
| ] |
| }, |
| { |
| "_target_": "AsDiscreted", |
| "keys": "label_type", |
| "to_onehot": 5 |
| }, |
| { |
| "_target_": "ScaleIntensityRanged", |
| "keys": "image", |
| "a_min": 0.0, |
| "a_max": 255.0, |
| "b_min": 0.0, |
| "b_max": 1.0, |
| "clip": true |
| }, |
| { |
| "_target_": "CastToTyped", |
| "keys": "label_inst", |
| "dtype": "$torch.int" |
| }, |
| { |
| "_target_": "ComputeHoVerMapsd", |
| "keys": "label_inst" |
| }, |
| { |
| "_target_": "Lambdad", |
| "keys": "label_inst", |
| "func": "$lambda x: x > 0", |
| "overwrite": "label" |
| }, |
| { |
| "_target_": "CenterSpatialCropd", |
| "keys": [ |
| "label", |
| "hover_label_inst", |
| "label_inst", |
| "label_type" |
| ], |
| "roi_size": [ |
| "@out_size", |
| "@out_size" |
| ] |
| }, |
| { |
| "_target_": "AsDiscreted", |
| "keys": "label", |
| "to_onehot": 2 |
| }, |
| { |
| "_target_": "CastToTyped", |
| "keys": [ |
| "image", |
| "label_inst", |
| "label_type" |
| ], |
| "dtype": "$torch.float32" |
| } |
| ], |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": "$@train#preprocessing_transforms" |
| }, |
| "dataset": { |
| "_target_": "CacheDataset", |
| "data": "$[{'image': i, 'label_inst': j, 'label_type': k} for i, j, k in zip(@train_images, @train_inst_map, @train_type_map)]", |
| "transform": "@train#preprocessing", |
| "cache_rate": 1.0, |
| "num_workers": 4 |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@train#dataset", |
| "batch_size": "@batch_size", |
| "shuffle": true, |
| "num_workers": 4 |
| }, |
| "inferer": { |
| "_target_": "SimpleInferer" |
| }, |
| "postprocessing_np": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "Activationsd", |
| "keys": "nucleus_prediction", |
| "softmax": true |
| }, |
| { |
| "_target_": "AsDiscreted", |
| "keys": "nucleus_prediction", |
| "argmax": true |
| } |
| ] |
| }, |
| "postprocessing": { |
| "_target_": "Lambdad", |
| "keys": "pred", |
| "func": "$@train#postprocessing_np" |
| }, |
| "handlers": [ |
| { |
| "_target_": "LrScheduleHandler", |
| "lr_scheduler": "@lr_scheduler", |
| "print_lr": true |
| }, |
| { |
| "_target_": "ValidationHandler", |
| "validator": "@validate#evaluator", |
| "epoch_level": true, |
| "interval": "@val_interval" |
| }, |
| { |
| "_target_": "CheckpointSaver", |
| "save_dir": "@ckpt_dir", |
| "save_dict": { |
| "model": "@network" |
| }, |
| "save_interval": 10, |
| "epoch_level": true, |
| "save_final": true, |
| "final_filename": "model.pt" |
| }, |
| { |
| "_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)" |
| } |
| ], |
| "extra_handlers": [ |
| { |
| "_target_": "CheckpointLoader", |
| "load_path": "$os.path.join(@ckpt_dir_stage0, 'model.pt')", |
| "load_dict": { |
| "model": "@network" |
| } |
| } |
| ], |
| "train_handlers": "$@train#extra_handlers + @train#handlers if @stage==1 else @train#handlers", |
| "key_metric": { |
| "train_mean_dice": { |
| "_target_": "MeanDice", |
| "include_background": false, |
| "output_transform": "$monai.apps.pathology.handlers.utils.from_engine_hovernet(keys=['pred', 'label'], nested_key='nucleus_prediction')" |
| } |
| }, |
| "trainer": { |
| "_target_": "SupervisedTrainer", |
| "max_epochs": "@epochs", |
| "device": "@device", |
| "train_data_loader": "@train#dataloader", |
| "prepare_batch": "$monai.apps.pathology.engines.utils.PrepareBatchHoVerNet(extra_keys=['label_type', 'hover_label_inst'])", |
| "network": "@network", |
| "loss_function": "@loss", |
| "optimizer": "@optimizer", |
| "inferer": "@train#inferer", |
| "postprocessing": "@train#postprocessing", |
| "key_train_metric": "@train#key_metric", |
| "train_handlers": "@train#train_handlers", |
| "amp": "@amp" |
| } |
| }, |
| "validate": { |
| "preprocessing_transforms": [ |
| { |
| "_target_": "LoadImaged", |
| "keys": [ |
| "image", |
| "label_inst", |
| "label_type" |
| ] |
| }, |
| { |
| "_target_": "EnsureChannelFirstd", |
| "keys": [ |
| "image", |
| "label_inst", |
| "label_type" |
| ], |
| "channel_dim": -1 |
| }, |
| { |
| "_target_": "Lambdad", |
| "keys": "label_inst", |
| "func": "$lambda x: skimage.measure.label(x)" |
| }, |
| { |
| "_target_": "CastToTyped", |
| "keys": [ |
| "image", |
| "label_inst" |
| ], |
| "dtype": "$torch.int" |
| }, |
| { |
| "_target_": "CenterSpatialCropd", |
| "keys": [ |
| "image" |
| ], |
| "roi_size": [ |
| "@patch_size", |
| "@patch_size" |
| ] |
| }, |
| { |
| "_target_": "ScaleIntensityRanged", |
| "keys": "image", |
| "a_min": 0.0, |
| "a_max": 255.0, |
| "b_min": 0.0, |
| "b_max": 1.0, |
| "clip": true |
| }, |
| { |
| "_target_": "ComputeHoVerMapsd", |
| "keys": "label_inst" |
| }, |
| { |
| "_target_": "Lambdad", |
| "keys": "label_inst", |
| "func": "$lambda x: x > 0", |
| "overwrite": "label" |
| }, |
| { |
| "_target_": "CenterSpatialCropd", |
| "keys": [ |
| "label", |
| "hover_label_inst", |
| "label_inst", |
| "label_type" |
| ], |
| "roi_size": [ |
| "@out_size", |
| "@out_size" |
| ] |
| }, |
| { |
| "_target_": "CastToTyped", |
| "keys": [ |
| "image", |
| "label_inst", |
| "label_type" |
| ], |
| "dtype": "$torch.float32" |
| } |
| ], |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": "$@validate#preprocessing_transforms" |
| }, |
| "dataset": { |
| "_target_": "CacheDataset", |
| "data": "$[{'image': i, 'label_inst': j, 'label_type': k} for i, j, k in zip(@val_images, @val_inst_map, @val_type_map)]", |
| "transform": "@validate#preprocessing", |
| "cache_rate": 1.0, |
| "num_workers": 4 |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@validate#dataset", |
| "batch_size": "@batch_size", |
| "shuffle": false, |
| "num_workers": 4 |
| }, |
| "inferer": { |
| "_target_": "SimpleInferer" |
| }, |
| "postprocessing": "$@train#postprocessing", |
| "handlers": [ |
| { |
| "_target_": "StatsHandler", |
| "iteration_log": false |
| }, |
| { |
| "_target_": "TensorBoardStatsHandler", |
| "log_dir": "@output_dir", |
| "iteration_log": false |
| }, |
| { |
| "_target_": "CheckpointSaver", |
| "save_dir": "@ckpt_dir", |
| "save_dict": { |
| "model": "@network" |
| }, |
| "save_key_metric": true |
| } |
| ], |
| "key_metric": { |
| "val_mean_dice": { |
| "_target_": "MeanDice", |
| "include_background": false, |
| "output_transform": "$monai.apps.pathology.handlers.utils.from_engine_hovernet(keys=['pred', 'label'], nested_key='nucleus_prediction')" |
| } |
| }, |
| "evaluator": { |
| "_target_": "SupervisedEvaluator", |
| "device": "@device", |
| "val_data_loader": "@validate#dataloader", |
| "prepare_batch": "$monai.apps.pathology.engines.utils.PrepareBatchHoVerNet(extra_keys=['label_type', 'hover_label_inst'])", |
| "network": "@network", |
| "inferer": "@validate#inferer", |
| "postprocessing": "@validate#postprocessing", |
| "key_val_metric": "@validate#key_metric", |
| "val_handlers": "@validate#handlers", |
| "amp": "@amp" |
| } |
| }, |
| "initialize": [ |
| "$monai.utils.set_determinism(seed=321)", |
| "$setattr(torch.backends.cudnn, 'benchmark', True)" |
| ], |
| "run": [ |
| "$@train#trainer.run()" |
| ] |
| } |
|
|
