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{
"imports": [
"$import glob",
"$import os",
"$import ignite",
"$import scripts"
],
"bundle_root": ".",
"ckpt_dir": "$@bundle_root + '/models'",
"output_dir": "$@bundle_root + '/eval'",
"dataset_dir": "/workspace/Datasets/MSD_datasets/Task09_Spleen",
"images": "$list(sorted(glob.glob(@dataset_dir + '/imagesTr/*.nii.gz')))",
"labels": "$list(sorted(glob.glob(@dataset_dir + '/labelsTr/*.nii.gz')))",
"label_names": {
"spleen": 1,
"background": 0
},
"finetune": false,
"finetune_model_path": "$@bundle_root + '/models/model.pt'",
"early_stop": false,
"epochs": 500,
"spatial_size": [
128,
128,
128
],
"number_intensity_ch": 1,
"deepgrow_probability_train": 0.4,
"deepgrow_probability_val": 1.0,
"val_interval": 1,
"val_at_start": false,
"device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
"network_def": {
"_target_": "DynUNet",
"spatial_dims": 3,
"in_channels": "$len(@label_names) + @number_intensity_ch",
"out_channels": "$len(@label_names)",
"kernel_size": [
3,
3,
3,
3,
3,
3
],
"strides": [
1,
2,
2,
2,
2,
[
2,
2,
1
]
],
"upsample_kernel_size": [
2,
2,
2,
2,
[
2,
2,
1
]
],
"norm_name": "instance",
"deep_supervision": false,
"res_block": true
},
"network": "$@network_def.to(@device)",
"loss": {
"_target_": "DiceCELoss",
"to_onehot_y": true,
"softmax": true
},
"optimizer": {
"_target_": "torch.optim.Adam",
"params": "$@network.parameters()",
"lr": 0.0001
},
"lr_scheduler": {
"_target_": "torch.optim.lr_scheduler.StepLR",
"optimizer": "@optimizer",
"step_size": 1000,
"gamma": 0.1
},
"train": {
"preprocessing_transforms": [
{
"_target_": "LoadImaged",
"keys": [
"image",
"label"
],
"reader": "ITKReader"
},
{
"_target_": "NormalizeLabelsInDatasetd",
"keys": "label",
"label_names": "@label_names"
},
{
"_target_": "EnsureChannelFirstd",
"keys": [
"image",
"label"
]
},
{
"_target_": "Orientationd",
"keys": [
"image",
"label"
],
"axcodes": "RAS"
},
{
"_target_": "ScaleIntensityRanged",
"keys": "image",
"a_min": -175,
"a_max": 250,
"b_min": 0.0,
"b_max": 1.0,
"clip": true
}
],
"random_transforms": [
{
"_target_": "RandFlipd",
"keys": [
"image",
"label"
],
"spatial_axis": [
0
],
"prob": 0.1
},
{
"_target_": "RandFlipd",
"keys": [
"image",
"label"
],
"spatial_axis": [
1
],
"prob": 0.1
},
{
"_target_": "RandFlipd",
"keys": [
"image",
"label"
],
"spatial_axis": [
2
],
"prob": 0.1
},
{
"_target_": "RandRotate90d",
"keys": [
"image",
"label"
],
"prob": 0.1,
"max_k": 3
},
{
"_target_": "RandShiftIntensityd",
"keys": "image",
"offsets": 0.1,
"prob": 0.5
}
],
"deepedit_transforms": [
{
"_target_": "Resized",
"keys": [
"image",
"label"
],
"spatial_size": "@spatial_size",
"mode": [
"area",
"nearest"
]
},
{
"_target_": "FindAllValidSlicesMissingLabelsd",
"keys": "label",
"sids": "sids"
},
{
"_target_": "AddInitialSeedPointMissingLabelsd",
"keys": "label",
"guidance": "guidance",
"sids": "sids"
},
{
"_target_": "AddGuidanceSignalDeepEditd",
"keys": "image",
"guidance": "guidance",
"number_intensity_ch": "@number_intensity_ch"
},
{
"_target_": "ToTensord",
"keys": [
"image",
"label"
]
}
],
"preprocessing": {
"_target_": "Compose",
"transforms": "$@train#preprocessing_transforms + @train#random_transforms + @train#deepedit_transforms"
},
"click_transforms": {
"_target_": "Compose",
"transforms": [
{
"_target_": "Activationsd",
"keys": "pred",
"softmax": true
},
{
"_target_": "AsDiscreted",
"keys": "pred",
"argmax": true
},
{
"_target_": "ToNumpyd",
"keys": [
"image",
"label",
"pred"
]
},
{
"_target_": "FindDiscrepancyRegionsDeepEditd",
"keys": "label",
"pred": "pred",
"discrepancy": "discrepancy"
},
{
"_target_": "AddRandomGuidanceDeepEditd",
"keys": "NA",
"guidance": "guidance",
"discrepancy": "discrepancy",
"probability": "probability"
},
{
"_target_": "AddGuidanceSignalDeepEditd",
"keys": "image",
"guidance": "guidance",
"number_intensity_ch": "@number_intensity_ch"
},
{
"_target_": "ToTensord",
"keys": [
"image",
"label"
]
}
]
},
"dataset": {
"_target_": "CacheDataset",
"data": "$[{'image': i, 'label': l} for i, l in zip(@images[:-9], @labels[:-9])]",
"transform": "@train#preprocessing",
"cache_rate": 1.0,
"num_workers": 4
},
"dataloader": {
"_target_": "DataLoader",
"dataset": "@train#dataset",
"batch_size": 1,
"shuffle": true,
"num_workers": 0
},
"inferer": {
"_target_": "SimpleInferer"
},
"postprocessing": {
"_target_": "Compose",
"transforms": [
{
"_target_": "Activationsd",
"keys": "pred",
"softmax": true
},
{
"_target_": "AsDiscreted",
"keys": [
"pred",
"label"
],
"argmax": [
true,
false
],
"to_onehot": "$len(@label_names)+1"
}
]
},
"handlers": [
{
"_target_": "CheckpointLoader",
"_disabled_": "$not @finetune",
"load_path": "@finetune_model_path",
"load_dict": {
"model": "@network"
}
},
{
"_target_": "LrScheduleHandler",
"lr_scheduler": "@lr_scheduler",
"print_lr": true
},
{
"_target_": "ValidationHandler",
"validator": "@validate#evaluator",
"epoch_level": true,
"exec_at_start": "@val_at_start",
"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_dice": {
"_target_": "MeanDice",
"output_transform": "$monai.handlers.from_engine(['pred', 'label'])"
}
},
"train_iteration_update": {
"_target_": "Interaction",
"deepgrow_probability": "@deepgrow_probability_train",
"transforms": "@train#click_transforms",
"click_probability_key": "probability",
"train": true,
"label_names": "@label_names"
},
"trainer": {
"_target_": "SupervisedTrainer",
"device": "@device",
"max_epochs": "@epochs",
"train_data_loader": "@train#dataloader",
"network": "@network",
"optimizer": "@optimizer",
"loss_function": "@loss",
"inferer": "@train#inferer",
"amp": true,
"postprocessing": "@train#postprocessing",
"key_train_metric": "@train#key_metric",
"train_handlers": "@train#handlers",
"iteration_update": "@train#train_iteration_update"
}
},
"validate": {
"preprocessing": {
"_target_": "Compose",
"transforms": "$@train#preprocessing_transforms + @train#deepedit_transforms"
},
"dataset": {
"_target_": "CacheDataset",
"data": "$[{'image': i, 'label': l} for i, l in zip(@images[-9:], @labels[-9:])]",
"transform": "@validate#preprocessing",
"cache_rate": 1.0,
"num_workers": 4
},
"dataloader": {
"_target_": "DataLoader",
"dataset": "@validate#dataset",
"batch_size": 1,
"shuffle": false,
"num_workers": 0
},
"inferer": {
"_target_": "SimpleInferer"
},
"postprocessing": "%train#postprocessing",
"handlers": [
{
"_target_": "EarlyStopHandler",
"_disabled_": "$not @early_stop",
"trainer": null,
"patience": 1,
"score_function": "$scripts.score_function",
"min_delta": 0.01
},
{
"_target_": "StatsHandler",
"iteration_log": false
},
{
"_target_": "TensorBoardStatsHandler",
"log_dir": "@output_dir",
"iteration_log": false
},
{
"_target_": "CheckpointSaver",
"save_dir": "@ckpt_dir",
"save_dict": {
"model": "@network"
},
"save_key_metric": true,
"key_metric_filename": "model.pt"
}
],
"key_metric": {
"val_mean_dice": {
"_target_": "MeanDice",
"output_transform": "$monai.handlers.from_engine(['pred', 'label'])"
}
},
"val_iteration_update": {
"_target_": "Interaction",
"deepgrow_probability": "@deepgrow_probability_val",
"transforms": "@train#click_transforms",
"click_probability_key": "probability",
"train": false,
"label_names": "@label_names"
},
"evaluator": {
"_target_": "SupervisedEvaluator",
"device": "@device",
"val_data_loader": "@validate#dataloader",
"network": "@network",
"inferer": "@validate#inferer",
"postprocessing": "@validate#postprocessing",
"key_val_metric": "@validate#key_metric",
"val_handlers": "@validate#handlers",
"iteration_update": "@validate#val_iteration_update",
"amp": true
}
},
"initialize": [
"$monai.utils.set_determinism(seed=123)"
],
"run": [
"$@validate#handlers#0.set_trainer(trainer=@train#trainer) if @early_stop else None",
"$@train#trainer.run()"
]
}
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