| { |
| "imports": [ |
| "$import datetime", |
| "$import numpy", |
| "$import torch", |
| "$import ignite", |
| "$import scripts" |
| ], |
| "bundle_root": ".", |
| "ckpt_path": "$@bundle_root + '/models/model.pt'", |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
| "val_interval": 1, |
| "num_iters": 400, |
| "batch_size": 600, |
| "num_epochs": 100, |
| "num_substeps": 3, |
| "learning_rate": 0.0001, |
| "num_workers": 8, |
| "dataset_dir": ".", |
| "dataset_file": "$@dataset_dir + '/valvelandmarks.npz'", |
| "output_dir": "$datetime.datetime.now().strftime('./results/output_%y%m%d_%H%M%S')", |
| "network_def": { |
| "_target_": "scripts.valve_landmarks.PointRegressor", |
| "in_shape": [ |
| 1, |
| 256, |
| 256 |
| ], |
| "out_shape": [ |
| 2, |
| 10 |
| ], |
| "channels": [ |
| 8, |
| 16, |
| 32, |
| 64, |
| 128 |
| ], |
| "strides": [ |
| 2, |
| 2, |
| 2, |
| 2, |
| 2 |
| ] |
| }, |
| "network": "$@network_def.to(@device)", |
| "im_shape": [ |
| 1, |
| 256, |
| 256 |
| ], |
| "both_keys": [ |
| "image", |
| "label" |
| ], |
| "rand_prob": 0.5, |
| "train_transforms": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "EnsureTyped", |
| "keys": "@both_keys", |
| "data_type": "numpy", |
| "dtype": "$(numpy.float32, numpy.int32)" |
| }, |
| { |
| "_target_": "EnsureTyped", |
| "keys": "@both_keys" |
| }, |
| { |
| "_target_": "ScaleIntensityd", |
| "keys": "image" |
| }, |
| { |
| "_target_": "EnsureChannelFirstd", |
| "keys": "@both_keys", |
| "channel_dim": "no_channel" |
| }, |
| { |
| "_target_": "RandAxisFlipd", |
| "keys": "@both_keys", |
| "prob": "@rand_prob" |
| }, |
| { |
| "_target_": "RandRotate90d", |
| "keys": "@both_keys", |
| "prob": "@rand_prob" |
| }, |
| { |
| "_target_": "RandSmoothFieldAdjustIntensityd", |
| "keys": "image", |
| "prob": "@rand_prob", |
| "spatial_size": "@im_shape", |
| "rand_size": [ |
| 5, |
| 5 |
| ], |
| "gamma": [ |
| 0.1, |
| 1 |
| ], |
| "mode": "$monai.utils.InterpolateMode.BICUBIC", |
| "align_corners": true |
| }, |
| { |
| "_target_": "RandGaussianNoised", |
| "keys": "image", |
| "prob": "@rand_prob", |
| "std": 0.05 |
| }, |
| { |
| "_target_": "scripts.valve_landmarks.RandFourierDropoutd", |
| "keys": "image", |
| "prob": "@rand_prob" |
| }, |
| { |
| "_target_": "scripts.valve_landmarks.RandImageLMDeformd", |
| "prob": "@rand_prob", |
| "spatial_size": [ |
| 256, |
| 256 |
| ], |
| "rand_size": [ |
| 7, |
| 7 |
| ], |
| "pad": 2, |
| "field_mode": "$monai.utils.InterpolateMode.BICUBIC", |
| "align_corners": true, |
| "def_range": 0.05 |
| }, |
| { |
| "_target_": "scripts.valve_landmarks.RandLMShiftd", |
| "keys": "@both_keys", |
| "prob": "@rand_prob", |
| "spatial_size": [ |
| 256, |
| 256 |
| ], |
| "max_shift": 8 |
| }, |
| { |
| "_target_": "Lambdad", |
| "keys": "label", |
| "func": "$scripts.valve_landmarks.convert_lm_image_t" |
| } |
| ] |
| }, |
| "eval_transforms": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "EnsureTyped", |
| "keys": "@both_keys", |
| "data_type": "numpy", |
| "dtype": "$(numpy.float32, numpy.int32)" |
| }, |
| { |
| "_target_": "EnsureTyped", |
| "keys": "@both_keys" |
| }, |
| { |
| "_target_": "ScaleIntensityd", |
| "keys": "image" |
| }, |
| { |
| "_target_": "EnsureChannelFirstd", |
| "keys": "@both_keys", |
| "channel_dim": "no_channel" |
| }, |
| { |
| "_target_": "Lambdad", |
| "keys": "label", |
| "func": "$scripts.valve_landmarks.convert_lm_image_t" |
| } |
| ] |
| }, |
| "train_dataset": { |
| "_target_": "NPZDictItemDataset", |
| "npzfile": "$@dataset_file", |
| "keys": { |
| "trainImgs": "image", |
| "trainLMImgs": "label" |
| }, |
| "transform": "@train_transforms" |
| }, |
| "eval_dataset": { |
| "_target_": "NPZDictItemDataset", |
| "npzfile": "$@dataset_file", |
| "keys": { |
| "testImgs": "image", |
| "testLMImgs": "label" |
| }, |
| "transform": "@eval_transforms" |
| }, |
| "sampler": { |
| "_target_": "torch.utils.data.WeightedRandomSampler", |
| "weights": "$torch.ones(len(@train_dataset))", |
| "replacement": true, |
| "num_samples": "$@num_iters*@batch_size" |
| }, |
| "train_dataloader": { |
| "_target_": "ThreadDataLoader", |
| "dataset": "@train_dataset", |
| "batch_size": "@batch_size", |
| "repeats": "@num_substeps", |
| "num_workers": "@num_workers", |
| "sampler": "@sampler" |
| }, |
| "eval_dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@eval_dataset", |
| "batch_size": "@batch_size", |
| "num_workers": "@num_workers" |
| }, |
| "lossfn": { |
| "_target_": "torch.nn.L1Loss" |
| }, |
| "optimizer": { |
| "_target_": "torch.optim.Adam", |
| "params": "$@network.parameters()", |
| "lr": "@learning_rate" |
| }, |
| "evaluator": { |
| "_target_": "SupervisedEvaluator", |
| "device": "@device", |
| "val_data_loader": "@eval_dataloader", |
| "network": "@network", |
| "key_val_metric": { |
| "val_mean_dist": { |
| "_target_": "ignite.metrics.MeanPairwiseDistance", |
| "output_transform": "$scripts.valve_landmarks._output_lm_trans" |
| } |
| }, |
| "metric_cmp_fn": "$lambda current, prev: prev < 0 or current < prev", |
| "val_handlers": [ |
| { |
| "_target_": "StatsHandler", |
| "output_transform": "$lambda x: None" |
| } |
| ] |
| }, |
| "handlers": [ |
| { |
| "_target_": "ValidationHandler", |
| "validator": "@evaluator", |
| "epoch_level": true, |
| "interval": "@val_interval" |
| }, |
| { |
| "_target_": "CheckpointSaver", |
| "save_dir": "@output_dir", |
| "save_dict": { |
| "net": "@network" |
| }, |
| "save_interval": 1, |
| "save_final": true, |
| "epoch_level": true |
| } |
| ], |
| "trainer": { |
| "_target_": "SupervisedTrainer", |
| "max_epochs": "@num_epochs", |
| "device": "@device", |
| "train_data_loader": "@train_dataloader", |
| "network": "@network", |
| "loss_function": "@lossfn", |
| "optimizer": "@optimizer", |
| "key_train_metric": null, |
| "train_handlers": "@handlers" |
| }, |
| "training": [ |
| "$@trainer.run()" |
| ] |
| } |
|
|
