| { |
| "imports": [ |
| "$import glob", |
| "$import os", |
| "$import ignite" |
| ], |
| "bundle_root": ".", |
| "ckpt_dir": "$@bundle_root + '/models'", |
| "output_dir": "$@bundle_root + '/eval'", |
| "dataset_dir": "$@bundle_root + '/data'", |
| "images": "$[{'artery':a, 'vein':b, 'excret':c }for a,b,c in zip(glob.glob(@dataset_dir + '/*/12.nii.gz'), glob.glob(@dataset_dir + '/*/22-.nii.gz'), glob.glob(@dataset_dir + '/*/32-.nii.gz'))]", |
| "labels": "$list(glob.glob(@dataset_dir + '/*/merged.nii.gz'))", |
| "val_interval": 50, |
| "dont_finetune": true, |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
| "network_def": { |
| "_target_": "SegResNet", |
| "in_channels": 3, |
| "out_channels": 6, |
| "init_filters": 32, |
| "upsample_mode": "deconv", |
| "dropout_prob": 0.2, |
| "norm_name": "group", |
| "blocks_down": [ |
| 1, |
| 2, |
| 2, |
| 4 |
| ], |
| "blocks_up": [ |
| 1, |
| 1, |
| 1 |
| ] |
| }, |
| "network": "$@network_def.to(@device)", |
| "loss": { |
| "_target_": "DiceLoss", |
| "include_background": false, |
| "to_onehot_y": true, |
| "sigmoid": true, |
| "softmax": false, |
| "squared_pred": false, |
| "jaccard": false, |
| "reduction": "mean", |
| "smooth_nr": 0.0, |
| "smooth_dr": 1e-05, |
| "batch": false |
| }, |
| "optimizer": { |
| "_target_": "Novograd", |
| "params": "[email protected]()", |
| "lr": 0.001, |
| "betas": [ |
| 0.9, |
| 0.98 |
| ], |
| "eps": 1e-08, |
| "weight_decay": 0, |
| "grad_averaging": false, |
| "amsgrad": false |
| }, |
| "train": { |
| "deterministic_transforms": [ |
| { |
| "_target_": "LoadImaged", |
| "keys": [ |
| "artery", |
| "vein", |
| "excret", |
| "label" |
| ], |
| "reader": null, |
| "overwriting": false, |
| "dtype": "float32", |
| "as_closest_canonical": true, |
| "image_only": false |
| }, |
| { |
| "_target_": "EnsureChannelFirstd", |
| "keys": [ |
| "artery", |
| "vein", |
| "excret", |
| "label" |
| ] |
| }, |
| { |
| "_target_": "MapLabelValued", |
| "keys": "label", |
| "orig_labels": [ |
| 0, |
| 1, |
| 2, |
| 3, |
| 4, |
| 5, |
| 6 |
| ], |
| "target_labels": [ |
| 0, |
| 1, |
| 2, |
| 3, |
| 4, |
| 4, |
| 5 |
| ] |
| }, |
| { |
| "_target_": "ToTensord", |
| "keys": [ |
| "artery", |
| "vein", |
| "excret", |
| "label" |
| ] |
| }, |
| { |
| "_target_": "Spacingd", |
| "keys": [ |
| "artery", |
| "vein", |
| "excret", |
| "label" |
| ], |
| "pixdim": [ |
| 0.8, |
| 0.8, |
| 0.8 |
| ], |
| "mode": [ |
| "bilinear", |
| "bilinear", |
| "bilinear", |
| "nearest" |
| ] |
| }, |
| { |
| "_target_": "ScaleIntensityRanged", |
| "keys": [ |
| "artery", |
| "vein", |
| "excret" |
| ], |
| "a_min": -1000, |
| "a_max": 1000, |
| "b_min": 0.0, |
| "b_max": 1.0, |
| "clip": true |
| }, |
| { |
| "_target_": "scripts.my_transforms.ConcatImages", |
| "keys_merge": [ |
| "artery", |
| "vein", |
| "excret" |
| ], |
| "keys_out": "image" |
| }, |
| { |
| "_target_": "ToTensord", |
| "keys": [ |
| "image" |
| ] |
| } |
| ], |
| "random_transforms": [ |
| { |
| "_target_": "RandZoomd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "prob": 0.3 |
| }, |
| { |
| "_target_": "RandAxisFlipd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "prob": 0.3 |
| }, |
| { |
| "_target_": "RandRotate90d", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "prob": 0.3 |
| }, |
| { |
| "_target_": "RandAdjustContrastd", |
| "keys": [ |
| "image" |
| ], |
| "prob": 0.5 |
| }, |
| { |
| "_target_": "RandHistogramShiftd", |
| "keys": "image", |
| "num_control_points": 10, |
| "prob": 0.3 |
| }, |
| { |
| "_target_": "DivisiblePadd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "k": 32 |
| }, |
| { |
| "_target_": "RandCropByLabelClassesd", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "label_key": "label", |
| "num_classes": 6, |
| "spatial_size": [ |
| 96, |
| 96, |
| 96 |
| ], |
| "ratios": [ |
| 1, |
| 2, |
| 2, |
| 3, |
| 3, |
| 1 |
| ], |
| "num_samples": 4 |
| } |
| ], |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": "$@train#deterministic_transforms + @train#random_transforms" |
| }, |
| "dataset": { |
| "_target_": "CacheDataset", |
| "data": "$[{'label': l, **i} for i, l in zip(@images, @labels)]", |
| "transform": "@train#preprocessing", |
| "cache_rate": 1.0, |
| "num_workers": 4 |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@train#dataset", |
| "batch_size": 1, |
| "shuffle": true, |
| "num_workers": 2 |
| }, |
| "inferer": { |
| "_target_": "SimpleInferer" |
| }, |
| "postprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "Activationsd", |
| "keys": "pred", |
| "softmax": false, |
| "sigmoid": true |
| }, |
| { |
| "_target_": "AsDiscreted", |
| "keys": [ |
| "pred", |
| "label" |
| ], |
| "argmax": [ |
| false, |
| false |
| ], |
| "to_onehot": [ |
| null, |
| 6 |
| ], |
| "threshold": [ |
| 0.5, |
| null |
| ] |
| }, |
| { |
| "_target_": "SplitDimd", |
| "keys": [ |
| "pred", |
| "label" |
| ], |
| "output_postfixes": [ |
| "bck", |
| "ar", |
| "ve", |
| "ur", |
| "tu", |
| "ki" |
| ] |
| } |
| ] |
| }, |
| "handlers": [ |
| { |
| "_target_": "CheckpointLoader", |
| "_disabled_": "@dont_finetune", |
| "load_path": "$@ckpt_dir + '/model.pt'", |
| "load_dict": { |
| "model": "@network" |
| } |
| }, |
| { |
| "_target_": "ValidationHandler", |
| "validator": "@validate#evaluator", |
| "epoch_level": true, |
| "interval": "@val_interval" |
| }, |
| { |
| "_target_": "StatsHandler", |
| "tag_name": "train_loss", |
| "output_transform": "$monai.handlers.from_engine(['loss'], first=True)" |
| }, |
| { |
| "_target_": "TensorBoardStatsHandler", |
| "log_dir": "@output_dir", |
| "tag_name": "train_loss", |
| "output_transform": "$monai.handlers.from_engine(['loss'], first=True)" |
| } |
| ], |
| "key_metric": { |
| "train/mean_dice": { |
| "_target_": "MeanDice", |
| "include_background": false, |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" |
| } |
| }, |
| "additional_metrics": { |
| "train/tu_dice": { |
| "_target_": "MeanDice", |
| "include_background": true, |
| "output_transform": "$monai.handlers.from_engine(['pred_tu', 'label_tu'])" |
| } |
| }, |
| "trainer": { |
| "_target_": "SupervisedTrainer", |
| "max_epochs": 10000, |
| "device": "@device", |
| "train_data_loader": "@train#dataloader", |
| "network": "@network", |
| "loss_function": "@loss", |
| "optimizer": "@optimizer", |
| "inferer": "@train#inferer", |
| "postprocessing": "@train#postprocessing", |
| "key_train_metric": "@train#key_metric", |
| "train_handlers": "@train#handlers", |
| "additional_metrics": "@train#additional_metrics", |
| "amp": true |
| } |
| }, |
| "validate": { |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": "$@train#deterministic_transforms" |
| }, |
| "dataset": { |
| "_target_": "CacheDataset", |
| "data": "$[{'label': l, **i} for i, l in zip(@images, @labels)]", |
| "transform": "@validate#preprocessing", |
| "cache_rate": 1.0 |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@validate#dataset", |
| "batch_size": 1, |
| "shuffle": false, |
| "num_workers": 4 |
| }, |
| "inferer": { |
| "_target_": "SlidingWindowInferer", |
| "roi_size": [ |
| 96, |
| 96, |
| 96 |
| ], |
| "sw_batch_size": 4, |
| "overlap": 0.25 |
| }, |
| "postprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "Invertd", |
| "transform": "%validate#preprocessing", |
| "device": "@device", |
| "keys": [ |
| "pred", |
| "label" |
| ], |
| "orig_keys": [ |
| "artery", |
| "label" |
| ], |
| "meta_keys": [ |
| "pred_meta_dict", |
| "label_meta_dict" |
| ], |
| "nearest_interp": [ |
| false, |
| true |
| ], |
| "to_tensor": true |
| }, |
| "%train#postprocessing#transforms#0", |
| "%train#postprocessing#transforms#1", |
| "%train#postprocessing#transforms#2" |
| ] |
| }, |
| "handlers": [ |
| { |
| "_target_": "StatsHandler", |
| "iteration_log": false |
| }, |
| { |
| "_target_": "TensorBoardStatsHandler", |
| "log_dir": "@output_dir", |
| "iteration_log": false |
| }, |
| { |
| "_target_": "CheckpointSaver", |
| "save_dir": "@ckpt_dir", |
| "save_dict": { |
| "model": "@network" |
| }, |
| "save_key_metric": true, |
| "key_metric_filename": "model.pt" |
| } |
| ], |
| "key_metric": { |
| "val_mean_dice": { |
| "_target_": "MeanDice", |
| "include_background": false, |
| "output_transform": "$monai.handlers.from_engine(['pred', 'label'])" |
| } |
| }, |
| "additional_metrics": { |
| "ar/dice": { |
| "_target_": "MeanDice", |
| "include_background": false, |
| "output_transform": "$monai.handlers.from_engine(['pred_ar', 'label_ar'])" |
| }, |
| "ve/dice": { |
| "_target_": "MeanDice", |
| "include_background": false, |
| "output_transform": "$monai.handlers.from_engine(['pred_ve', 'label_ve'])" |
| }, |
| "ur/dice": { |
| "_target_": "MeanDice", |
| "include_background": false, |
| "output_transform": "$monai.handlers.from_engine(['pred_ur', 'label_ur'])" |
| }, |
| "ki/dice": { |
| "_target_": "MeanDice", |
| "include_background": false, |
| "output_transform": "$monai.handlers.from_engine(['pred_ki', 'label_ki'])" |
| }, |
| "tu/dice": { |
| "_target_": "MeanDice", |
| "include_background": false, |
| "output_transform": "$monai.handlers.from_engine(['pred_tu', 'label_tu'])" |
| }, |
| "tu/haunsdorff": { |
| "_target_": "HausdorffDistance", |
| "include_background": false, |
| "output_transform": "$monai.handlers.from_engine(['pred_tu', 'label_tu'])" |
| }, |
| "tu/surface": { |
| "_target_": "SurfaceDistance", |
| "include_background": false, |
| "output_transform": "$monai.handlers.from_engine(['pred_tu', 'label_tu'])" |
| } |
| }, |
| "evaluator": { |
| "_target_": "SupervisedEvaluator", |
| "device": "@device", |
| "val_data_loader": "@validate#dataloader", |
| "network": "@network", |
| "inferer": "@validate#inferer", |
| "postprocessing": "@validate#postprocessing", |
| "key_val_metric": "@validate#key_metric", |
| "additional_metrics": "@validate#additional_metrics", |
| "val_handlers": "@validate#handlers", |
| "amp": true |
| } |
| }, |
| "training": [ |
| "$monai.utils.set_determinism(seed=42)", |
| "$setattr(torch.backends.cudnn, 'benchmark', True)", |
| "$@train#trainer.run()" |
| ] |
| } |
|
|
