configs/train_continual.json

{
    "data_list_file_path": "$@bundle_root + '/configs/msd_task09_spleen_folds.json'",
    "dataset_dir": "/data/Task09_Spleen",
    "finetune": true,
    "val_at_start": true,
    "finetune_model_path": "$@bundle_root + '/models/model.pt'",
    "n_train_samples": null,
    "n_val_samples": null,
    "val_interval": 1,
    "learning_rate": 5e-05,
    "lr_schedule#activate": false,
    "loss#smooth_dr": 0.01,
    "loss#smooth_nr": 0.0001,
    "train_dataset_cache_rate": 1.0,
    "val_dataset_cache_rate": 1.0,
    "num_cache_workers": 4,
    "label_mappings": {
        "default": [
            [
                1,
                3
            ]
        ]
    },
    "patch_size": [
        128,
        128,
        128
    ],
    "label_set": "$[0] + list(x[1] for x in @label_mappings#default)",
    "val_label_set": "$[0] + list(x[0] for x in @label_mappings#default)",
    "num_classes": 255,
    "output_classes": "$len(@label_set)",
    "optimizer": {
        "_target_": "torch.optim.AdamW",
        "lr": "@learning_rate",
        "params": "$@network.parameters()"
    },
    "show_cache_progress": true,
    "resample_to_spacing": [
        1.5,
        1.5,
        1.5
    ],
    "cache_cls_idx": {
        "activate": true,
        "indices_key": "$'label_cls_indices' if @cache_cls_idx#activate else None"
    },
    "train#random_transforms": [
        {
            "_target_": "ClassesToIndicesd",
            "_disabled_": "$not @cache_cls_idx#activate",
            "keys": "label",
            "num_classes": "@num_classes",
            "indices_postfix": "_cls_indices",
            "max_samples_per_class": "$int(10 * @epochs)"
        },
        {
            "_target_": "RandCropByLabelClassesd",
            "keys": [
                "image",
                "label"
            ],
            "label_key": "label",
            "num_classes": "@num_classes",
            "spatial_size": "@patch_size",
            "num_samples": "@num_patches_per_image",
            "ratios": "$tuple(float(i>=0) for i in range(@num_classes))",
            "indices_key": "$@cache_cls_idx#indices_key",
            "warn": false
        },
        {
            "_target_": "RandZoomd",
            "keys": [
                "image",
                "label"
            ],
            "min_zoom": 0.8,
            "max_zoom": 1.2,
            "mode": [
                "trilinear",
                "nearest"
            ],
            "prob": 0.2,
            "allow_missing_keys": true
        },
        {
            "_target_": "RandSimulateLowResolutiond",
            "keys": [
                "image"
            ],
            "zoom_range": [
                0.3,
                1
            ],
            "prob": 0.2,
            "allow_missing_keys": true
        },
        {
            "_target_": "RandGaussianSmoothd",
            "keys": [
                "image"
            ],
            "prob": 0.2,
            "sigma_x": [
                0.5,
                1.0
            ],
            "sigma_y": [
                0.5,
                1.0
            ],
            "sigma_z": [
                0.5,
                1.0
            ]
        },
        {
            "_target_": "RandScaleIntensityd",
            "keys": [
                "image"
            ],
            "factors": 0.1,
            "prob": 0.2
        },
        {
            "_target_": "RandShiftIntensityd",
            "keys": [
                "image"
            ],
            "offsets": 0.1,
            "prob": 0.2
        },
        {
            "_target_": "RandGaussianNoised",
            "keys": [
                "image"
            ],
            "prob": 0.2,
            "mean": 0.0,
            "std": 0.2
        },
        {
            "_target_": "monai.apps.vista3d.transforms.Relabeld",
            "keys": "label",
            "label_mappings": "@label_mappings",
            "dtype": "$torch.uint8"
        }
    ],
    "train#handlers#0#strict": false,
    "train#dataset": {
        "_target_": "CacheDataset",
        "data": "$@train_datalist[:@n_train_samples]",
        "transform": "@train#preprocessing",
        "cache_rate": "@train_dataset_cache_rate",
        "hash_as_key": true,
        "num_workers": "@num_cache_workers",
        "progress": "@show_cache_progress"
    },
    "validate#dataset": {
        "_target_": "CacheDataset",
        "data": "$@val_datalist[:@n_val_samples]",
        "transform": "@validate#preprocessing",
        "cache_rate": "@val_dataset_cache_rate",
        "hash_as_key": true,
        "num_workers": "@num_cache_workers",
        "progress": "@show_cache_progress"
    },
    "validate#evaluator#hyper_kwargs#val_label_set": "$list(range(len(@val_label_set)))",
    "validate#preprocessing#transforms": "$@train#deterministic_transforms + [@valid_remap]",
    "valid_remap": {
        "_target_": "monai.apps.vista3d.transforms.Relabeld",
        "keys": "label",
        "label_mappings": "${'default': [[c, i] for i, c in enumerate(@val_label_set)]}",
        "dtype": "$torch.uint8"
    },
    "validate#handlers#3#key_metric_filename": "model_finetune.pt"
}