| { | |
| "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": "$@network.parameters()", | |
| "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 | |
| }, | |
| { | |
| "_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": "$[{'label': l, **i} for i, l in zip(@images, @labels)]", | |
| "transform": "@train#preprocessing", | |
| "cache_rate": 1.0, | |
| "num_workers": 4 | |
| }, | |
| "dataloader": { | |
| "_target_": "DataLoader", | |
| "dataset": "@train#dataset", | |
| "batch_size": 1, | |
| "shuffle": true, | |
| "num_workers": 2 | |
| }, | |
| "inferer": { | |
| "_target_": "SimpleInferer" | |
| }, | |
| "postprocessing": { | |
| "_target_": "Compose", | |
| "transforms": [ | |
| { | |
| "_target_": "Activationsd", | |
| "keys": "pred", | |
| "softmax": false, | |
| "sigmoid": true | |
| }, | |
| { | |
| "_target_": "AsDiscreted", | |
| "keys": [ | |
| "pred", | |
| "label" | |
| ], | |
| "argmax": [ | |
| false, | |
| false | |
| ], | |
| "to_onehot": [ | |
| null, | |
| 6 | |
| ], | |
| "threshold": [ | |
| 0.5, | |
| null | |
| ] | |
| }, | |
| { | |
| "_target_": "SplitChanneld", | |
| "keys": [ | |
| "pred", | |
| "label" | |
| ], | |
| "output_postfixes": [ | |
| "bck", | |
| "ar", | |
| "ve", | |
| "ur", | |
| "tu", | |
| "ki" | |
| ] | |
| } | |
| ] | |
| }, | |
| "handlers": [ | |
| { | |
| "_target_": "CheckpointLoader", | |
| "_disabled_": "@dont_finetune", | |
| "load_path": "$@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()" | |
| ] | |
| } | |