{
    "imports": [
        "$import glob",
        "$import os",
        "$import scripts",
        "$import ignite",
        "$import copy"
    ],
    "bundle_root": ".",
    "ckpt_dir": "$@bundle_root + '/models'",
    "output_dir": "$@bundle_root + '/eval'",
    "data_list_file_path": "$@bundle_root + '/configs/msd_task09_spleen_folds.json'",
    "dataset_dir": "/data/Task09_Spleen",
    "use_tensorboard": true,
    "finetune": false,
    "finetune_model_path": "$@bundle_root + '/models/model.pt'",
    "early_stop": false,
    "use_mlflow": true,
    "mlflow_dir": "$@bundle_root + '/mlruns'",
    "fold": 0,
    "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
    "epochs": 5,
    "val_interval": 1,
    "val_at_start": false,
    "sw_overlap": 0.625,
    "learning_rate": 0.0001,
    "num_patches_per_image": 1,
    "input_channels": 1,
    "output_classes": 2,
    "max_point": 5,
    "max_prompt": null,
    "max_backprompt": null,
    "max_foreprompt": null,
    "drop_label_prob": 0.25,
    "drop_point_prob": 0.25,
    "exclude_background": true,
    "label_set": null,
    "val_label_set": "@label_set",
    "amp": true,
    "train_datalist": "$monai.auto3dseg.utils.datafold_read(datalist=@data_list_file_path, basedir=@dataset_dir, fold=@fold)[0]",
    "val_datalist": "$monai.auto3dseg.utils.datafold_read(datalist=@data_list_file_path, basedir=@dataset_dir, fold=@fold)[1]",
    "patch_size": [
        128,
        128,
        128
    ],
    "patch_size_valid": "$@patch_size",
    "network_def": "$monai.networks.nets.vista3d132(in_channels=@input_channels)",
    "network": "$@network_def.to(@device)",
    "loss": {
        "_target_": "DiceCELoss",
        "include_background": true,
        "sigmoid": true,
        "smooth_dr": 1e-05,
        "smooth_nr": 0,
        "squared_pred": true,
        "to_onehot_y": false
    },
    "optimizer": {
        "_target_": "torch.optim.AdamW",
        "params": "$@network.parameters()",
        "lr": "@learning_rate",
        "weight_decay": 1e-05
    },
    "lr_schedule": {
        "activate": true,
        "lr_scheduler": {
            "_target_": "monai.optimizers.WarmupCosineSchedule",
            "optimizer": "@optimizer",
            "t_total": "$@epochs",
            "warmup_steps": 3,
            "warmup_multiplier": 0.1
        }
    },
    "resample_to_spacing": [
        1.5,
        1.5,
        1.5
    ],
    "train": {
        "deterministic_transforms": [
            {
                "_target_": "LoadImaged",
                "keys": [
                    "image",
                    "label"
                ],
                "image_only": true,
                "ensure_channel_first": true
            },
            {
                "_target_": "CropForegroundd",
                "keys": [
                    "image",
                    "label"
                ],
                "source_key": "image",
                "margin": 10,
                "allow_smaller": true,
                "start_coord_key": null,
                "end_coord_key": null
            },
            {
                "_target_": "ScaleIntensityRanged",
                "keys": "image",
                "a_min": -963.8247715525971,
                "a_max": 1053.678477684517,
                "b_min": 0.0,
                "b_max": 1.0,
                "clip": true
            },
            {
                "_target_": "Orientationd",
                "keys": [
                    "image",
                    "label"
                ],
                "axcodes": "RAS"
            },
            {
                "_target_": "Spacingd",
                "keys": [
                    "image",
                    "label"
                ],
                "pixdim": "$@resample_to_spacing",
                "mode": [
                    "bilinear",
                    "nearest"
                ]
            },
            {
                "_target_": "CastToTyped",
                "keys": [
                    "image",
                    "label"
                ],
                "dtype": [
                    "$torch.float32",
                    "$torch.uint8"
                ]
            },
            {
                "_target_": "EnsureTyped",
                "keys": [
                    "image",
                    "label"
                ],
                "track_meta": true
            },
            {
                "_target_": "SpatialPadd",
                "keys": [
                    "image",
                    "label"
                ],
                "spatial_size": "@patch_size",
                "mode": [
                    "constant",
                    "constant"
                ]
            }
        ],
        "random_transforms": [
            {
                "_target_": "RandCropByLabelClassesd",
                "keys": [
                    "image",
                    "label"
                ],
                "label_key": "label",
                "num_classes": "@output_classes",
                "spatial_size": "@patch_size",
                "num_samples": "@num_patches_per_image",
                "warn": false
            },
            {
                "_target_": "ResizeWithPadOrCropd",
                "keys": [
                    "image",
                    "label"
                ],
                "spatial_size": "@patch_size"
            },
            {
                "_target_": "RandScaleIntensityd",
                "keys": "image",
                "prob": 0.1,
                "factors": 0.1
            },
            {
                "_target_": "RandShiftIntensityd",
                "keys": "image",
                "prob": 0.1,
                "offsets": 0.1
            }
        ],
        "inferer": {
            "_target_": "SimpleInferer"
        },
        "preprocessing": {
            "_target_": "Compose",
            "transforms": "$@train#deterministic_transforms + @train#random_transforms"
        },
        "dataset": {
            "_target_": "Dataset",
            "data": "@train_datalist",
            "transform": "@train#preprocessing"
        },
        "dataloader": {
            "_target_": "DataLoader",
            "dataset": "@train#dataset",
            "batch_size": 1,
            "shuffle": true,
            "num_workers": 4,
            "pin_memory": true,
            "persistent_workers": true
        },
        "handlers": [
            {
                "_target_": "CheckpointLoader",
                "_disabled_": "$not @finetune",
                "load_path": "@finetune_model_path",
                "load_dict": {
                    "model": "@network"
                }
            },
            {
                "_target_": "LrScheduleHandler",
                "_disabled_": "$not @lr_schedule#activate",
                "lr_scheduler": "@lr_schedule#lr_scheduler",
                "print_lr": true
            },
            {
                "_target_": "ValidationHandler",
                "validator": "@validate#evaluator",
                "epoch_level": true,
                "exec_at_start": "@val_at_start",
                "interval": "@val_interval"
            },
            {
                "_target_": "TensorBoardStatsHandler",
                "_disabled_": "$not @use_tensorboard",
                "log_dir": "@output_dir",
                "tag_name": "train_loss",
                "output_transform": "$monai.handlers.from_engine(['loss'], first=True)"
            },
            {
                "_target_": "StatsHandler",
                "tag_name": "train_loss",
                "name": "StatsHandler",
                "output_transform": "$monai.handlers.from_engine(['loss'], first=True)"
            },
            {
                "_target_": "MLFlowHandler",
                "_disabled_": "$not @use_mlflow",
                "tracking_uri": "$os.path.abspath(@mlflow_dir)",
                "output_transform": "$monai.handlers.from_engine(['loss'], first=True)"
            }
        ],
        "key_metric": {
            "train_accuracy": {
                "_target_": "ignite.metrics.Accuracy",
                "output_transform": "$monai.handlers.from_engine(['pred', 'label'])"
            }
        },
        "trainer": {
            "_target_": "scripts.trainer.Vista3dTrainer",
            "max_epochs": "@epochs",
            "device": "@device",
            "train_data_loader": "@train#dataloader",
            "network": "@network",
            "loss_function": "@loss",
            "optimizer": "@optimizer",
            "inferer": "@train#inferer",
            "key_train_metric": null,
            "train_handlers": "@train#handlers",
            "amp": "@amp",
            "hyper_kwargs": {
                "output_classes": "@output_classes",
                "max_point": "@max_point",
                "max_prompt": "@max_prompt",
                "max_backprompt": "@max_backprompt",
                "max_foreprompt": "@max_foreprompt",
                "drop_label_prob": "@drop_label_prob",
                "drop_point_prob": "@drop_point_prob",
                "exclude_background": "@exclude_background",
                "label_set": "@label_set",
                "patch_size": "@patch_size",
                "user_prompt": false
            }
        }
    },
    "validate": {
        "preprocessing": {
            "_target_": "Compose",
            "transforms": "$@train#deterministic_transforms"
        },
        "postprocessing": {
            "_target_": "Compose",
            "transforms": [
                {
                    "_target_": "AsDiscreted",
                    "keys": "pred",
                    "threshold": 0.0
                }
            ]
        },
        "dataset": {
            "_target_": "Dataset",
            "data": "$@val_datalist",
            "transform": "@validate#preprocessing"
        },
        "dataloader": {
            "_target_": "DataLoader",
            "dataset": "@validate#dataset",
            "batch_size": 1,
            "shuffle": false,
            "num_workers": 4
        },
        "inferer": {
            "_target_": "scripts.inferer.Vista3dInferer",
            "roi_size": "@patch_size_valid",
            "overlap": "@sw_overlap"
        },
        "handlers": [
            {
                "_target_": "EarlyStopHandler",
                "_disabled_": "$not @early_stop",
                "trainer": null,
                "patience": 2,
                "score_function": "$scripts.score_function",
                "min_delta": 0.01
            },
            {
                "_target_": "TensorBoardStatsHandler",
                "_disabled_": "$not @use_tensorboard",
                "log_dir": "@output_dir",
                "iteration_log": false
            },
            {
                "_target_": "StatsHandler",
                "iteration_log": false,
                "name": "StatsHandler"
            },
            {
                "_target_": "CheckpointSaver",
                "save_dir": "@ckpt_dir",
                "save_dict": {
                    "model": "@network"
                },
                "save_key_metric": true,
                "key_metric_filename": "model.pt"
            },
            {
                "_target_": "MLFlowHandler",
                "_disabled_": "$not @use_mlflow",
                "iteration_log": false,
                "tracking_uri": "$os.path.abspath(@mlflow_dir)"
            }
        ],
        "key_metric": {
            "val_mean_dice": {
                "_target_": "MeanDice",
                "include_background": false,
                "output_transform": "$monai.handlers.from_engine(['pred', 'label'])",
                "num_classes": "@output_classes"
            }
        },
        "additional_metrics": {
            "val_accuracy": {
                "_target_": "ignite.metrics.Accuracy",
                "output_transform": "$monai.handlers.from_engine(['pred', 'label'])"
            }
        },
        "evaluator": {
            "_target_": "scripts.evaluator.Vista3dEvaluator",
            "device": "@device",
            "val_data_loader": "@validate#dataloader",
            "network": "@network",
            "inferer": "@validate#inferer",
            "postprocessing": "@validate#postprocessing",
            "key_val_metric": "@validate#key_metric",
            "additional_metrics": null,
            "val_handlers": "@validate#handlers",
            "amp": true,
            "hyper_kwargs": {
                "output_classes": "@output_classes",
                "drop_label_prob": "@drop_label_prob",
                "drop_point_prob": "@drop_point_prob",
                "exclude_background": "@exclude_background",
                "label_set": "@label_set",
                "val_head": "auto",
                "user_prompt": false
            }
        }
    },
    "initialize": [
        "$monai.utils.set_determinism(seed=0)"
    ],
    "run": [
        "$@validate#handlers#0.set_trainer(trainer=@train#trainer) if @early_stop else None",
        "$@train#trainer.add_event_handler(ignite.engine.Events.ITERATION_COMPLETED, ignite.handlers.TerminateOnNan())",
        "$@train#trainer.run()"
    ]
}