{
    "displayable_configs": {
        "highres": true,
        "init_LR": 0.0001
    },
    "imports": [
        "$import glob",
        "$import os",
        "$import ignite"
    ],
    "bundle_root": ".",
    "ckpt_dir": "$@bundle_root + '/models'",
    "output_dir": "$@bundle_root + '/eval'",
    "dataset_dir": "sampledata",
    "images": "$list(sorted(glob.glob(@dataset_dir + '/imagesTr/*.nii.gz')))",
    "labels": "$list(sorted(glob.glob(@dataset_dir + '/labelsTr/*.nii.gz')))",
    "highres": true,
    "val_interval": 20,
    "init_LR": 0.0001,
    "batch_size": 4,
    "pixdim": "$[1.5, 1.5, 1.5] if @displayable_configs#highres else [3.0, 3.0, 3.0]",
    "modelname": "$'model.pt' if @displayable_configs#highres else 'model_lowres.pt'",
    "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
    "network_def": {
        "_target_": "SegResNet",
        "spatial_dims": 3,
        "in_channels": 1,
        "out_channels": 105,
        "init_filters": 32,
        "blocks_down": [
            1,
            2,
            2,
            4
        ],
        "blocks_up": [
            1,
            1,
            1
        ],
        "dropout_prob": 0.2
    },
    "network": "$@network_def.to(@device)",
    "loss": {
        "_target_": "DiceCELoss",
        "to_onehot_y": true,
        "softmax": true
    },
    "optimizer": {
        "_target_": "torch.optim.AdamW",
        "params": "$@network.parameters()",
        "lr": "@displayable_configs#init_LR",
        "weight_decay": 1e-05
    },
    "train": {
        "deterministic_transforms": [
            {
                "_target_": "LoadImaged",
                "keys": [
                    "image",
                    "label"
                ]
            },
            {
                "_target_": "EnsureChannelFirstd",
                "keys": [
                    "image",
                    "label"
                ]
            },
            {
                "_target_": "EnsureTyped",
                "keys": [
                    "image",
                    "label"
                ]
            },
            {
                "_target_": "Orientationd",
                "keys": [
                    "image",
                    "label"
                ],
                "axcodes": "RAS"
            },
            {
                "_target_": "Spacingd",
                "keys": [
                    "image",
                    "label"
                ],
                "pixdim": "@pixdim",
                "mode": [
                    "bilinear",
                    "nearest"
                ]
            },
            {
                "_target_": "NormalizeIntensityd",
                "keys": "image",
                "nonzero": true
            },
            {
                "_target_": "CropForegroundd",
                "keys": [
                    "image",
                    "label"
                ],
                "source_key": "image",
                "margin": 10,
                "k_divisible": [
                    96,
                    96,
                    96
                ]
            },
            {
                "_target_": "GaussianSmoothd",
                "keys": [
                    "image"
                ],
                "sigma": 0.4
            },
            {
                "_target_": "ScaleIntensityd",
                "keys": "image",
                "minv": -1.0,
                "maxv": 1.0
            },
            {
                "_target_": "EnsureTyped",
                "keys": [
                    "image",
                    "label"
                ]
            }
        ],
        "random_transforms": [
            {
                "_target_": "RandSpatialCropd",
                "keys": [
                    "image",
                    "label"
                ],
                "roi_size": [
                    96,
                    96,
                    96
                ],
                "random_size": false
            }
        ],
        "preprocessing": {
            "_target_": "Compose",
            "transforms": "$@train#deterministic_transforms + @train#random_transforms"
        },
        "dataset": {
            "_target_": "CacheDataset",
            "data": "$[{'image': i, 'label': l} for i, l in zip(@images[:-10], @labels[:-10])]",
            "transform": "@train#preprocessing",
            "cache_rate": 0.4,
            "num_workers": 4
        },
        "dataloader": {
            "_target_": "DataLoader",
            "dataset": "@train#dataset",
            "batch_size": "@batch_size",
            "shuffle": true,
            "num_workers": 4
        },
        "inferer": {
            "_target_": "SimpleInferer"
        },
        "postprocessing": {
            "_target_": "Compose",
            "transforms": [
                {
                    "_target_": "Activationsd",
                    "keys": "pred",
                    "softmax": true
                },
                {
                    "_target_": "AsDiscreted",
                    "keys": [
                        "pred",
                        "label"
                    ],
                    "argmax": [
                        true,
                        false
                    ],
                    "to_onehot": 105
                }
            ]
        },
        "handlers": [
            {
                "_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_accuracy": {
                "_target_": "ignite.metrics.Accuracy",
                "output_transform": "$monai.handlers.from_engine(['pred', 'label'])"
            }
        },
        "trainer": {
            "_target_": "SupervisedTrainer",
            "max_epochs": 4000,
            "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",
            "amp": true
        }
    },
    "validate": {
        "preprocessing": {
            "_target_": "Compose",
            "transforms": [
                {
                    "_target_": "LoadImaged",
                    "keys": [
                        "image",
                        "label"
                    ]
                },
                {
                    "_target_": "EnsureChannelFirstd",
                    "keys": [
                        "image",
                        "label"
                    ]
                },
                {
                    "_target_": "EnsureTyped",
                    "keys": [
                        "image",
                        "label"
                    ]
                },
                {
                    "_target_": "Orientationd",
                    "keys": [
                        "image",
                        "label"
                    ],
                    "axcodes": "RAS"
                },
                {
                    "_target_": "Spacingd",
                    "keys": [
                        "image",
                        "label"
                    ],
                    "pixdim": "@pixdim",
                    "mode": [
                        "bilinear",
                        "nearest"
                    ]
                },
                {
                    "_target_": "NormalizeIntensityd",
                    "keys": "image",
                    "nonzero": true
                },
                {
                    "_target_": "CropForegroundd",
                    "keys": [
                        "image",
                        "label"
                    ],
                    "source_key": "image",
                    "margin": 10,
                    "k_divisible": [
                        96,
                        96,
                        96
                    ]
                },
                {
                    "_target_": "GaussianSmoothd",
                    "keys": [
                        "image"
                    ],
                    "sigma": 0.4
                },
                {
                    "_target_": "ScaleIntensityd",
                    "keys": "image",
                    "minv": -1.0,
                    "maxv": 1.0
                },
                {
                    "_target_": "CenterSpatialCropd",
                    "keys": [
                        "image",
                        "label"
                    ],
                    "roi_size": [
                        160,
                        160,
                        160
                    ]
                }
            ]
        },
        "postprocessing": {
            "_target_": "Compose",
            "transforms": [
                {
                    "_target_": "Activationsd",
                    "keys": "pred",
                    "softmax": true
                },
                {
                    "_target_": "AsDiscreted",
                    "keys": [
                        "pred",
                        "label"
                    ],
                    "argmax": [
                        true,
                        false
                    ],
                    "to_onehot": 105
                }
            ]
        },
        "dataset": {
            "_target_": "Dataset",
            "data": "$[{'image': i, 'label': l} for i, l in zip(@images[-10:], @labels[-10:])]",
            "transform": "@validate#preprocessing"
        },
        "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": 1,
            "overlap": 0.25
        },
        "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": "@modelname"
            }
        ],
        "key_metric": {
            "val_mean_dice": {
                "_target_": "MeanDice",
                "include_background": false,
                "output_transform": "$monai.handlers.from_engine(['pred', 'label'])"
            }
        },
        "additional_metrics": {
            "val_accuracy": {
                "_target_": "ignite.metrics.Accuracy",
                "output_transform": "$monai.handlers.from_engine(['pred', 'label'])"
            }
        },
        "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
        }
    },
    "initialize": [
        "$monai.utils.set_determinism(seed=123)",
        "$setattr(torch.backends.cudnn, 'benchmark', True)"
    ],
    "run": [
        "$@train#trainer.run()"
    ]
}