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monai-test
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brats_mri_segmentation

monai
medical
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brats_mri_segmentation
File size: 2,764 Bytes 
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{
    "validate#postprocessing": {
        "_target_": "Compose",
        "transforms": [
            {
                "_target_": "Activationsd",
                "keys": "pred",
                "sigmoid": true
            },
            {
                "_target_": "Invertd",
                "keys": "pred",
                "transform": "@validate#preprocessing",
                "orig_keys": "image",
                "meta_keys": "pred_meta_dict",
                "nearest_interp": false,
                "to_tensor": true,
                "device": "@validate#evaluator#device"
            },
            {
                "_target_": "AsDiscreted",
                "keys": "pred",
                "threshold": 0.5
            },
            {
                "_target_": "SplitDimd",
                "keys": [
                    "pred",
                    "label"
                ],
                "output_postfixes": [
                    "tc",
                    "wt",
                    "et"
                ]
            },
            {
                "_target_": "CopyItemsd",
                "keys": "pred",
                "names": "pred_combined",
                "times": 1
            },
            {
                "_target_": "Lambdad",
                "keys": "pred_combined",
                "func": "$lambda x: torch.where(x[[2]] > 0, 4, torch.where(x[[0]] > 0, 1, torch.where(x[[1]] > 0, 2, 0)))"
            },
            {
                "_target_": "SaveImaged",
                "keys": "pred_combined",
                "meta_keys": "pred_meta_dict",
                "output_dir": "@output_dir",
                "output_postfix": "seg",
                "output_dtype": "uint8",
                "resample": false,
                "squeeze_end_dims": true
            }
        ]
    },
    "validate#handlers": [
        {
            "_target_": "CheckpointLoader",
            "load_path": "$@ckpt_dir + '/model.pt'",
            "load_dict": {
                "model": "@network"
            }
        },
        {
            "_target_": "StatsHandler",
            "iteration_log": false
        },
        {
            "_target_": "MetricsSaver",
            "save_dir": "@output_dir",
            "metrics": [
                "val_mean_dice",
                "val_mean_dice_tc",
                "val_mean_dice_wt",
                "val_mean_dice_et"
            ],
            "metric_details": [
                "val_mean_dice"
            ],
            "batch_transform": "$monai.handlers.from_engine(['image_meta_dict'])",
            "summary_ops": "*"
        }
    ],
    "initialize": [
        "$setattr(torch.backends.cudnn, 'benchmark', True)"
    ],
    "run": [
        "$@validate#evaluator.run()"
    ]
}