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vista2d
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{
    "imports": [
        "$import numpy as np"
    ],
    "bundle_root": ".",
    "ckpt_dir": "$@bundle_root + '/models'",
    "output_dir": "$@bundle_root + '/eval'",
    "output_ext": ".tif",
    "output_postfix": "trans",
    "roi_size": [
        256,
        256
    ],
    "input_dict": "${'image': '/cellpose_dataset/test/001_img.png'}",
    "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
    "sam_ckpt_path": "$@ckpt_dir + '/sam_vit_b_01ec64.pth'",
    "pretrained_ckpt_path": "$@ckpt_dir + '/model.pt'",
    "image_key": "image",
    "channels_last": true,
    "use_amp": true,
    "amp_dtype": "$torch.float",
    "network_def": {
        "_target_": "monai.networks.nets.cell_sam_wrapper.CellSamWrapper",
        "checkpoint": "@sam_ckpt_path"
    },
    "network": "$@network_def.to(@device)",
    "preprocessing_transforms": [
        {
            "_target_": "scripts.components.LoadTiffd",
            "keys": "@image_key"
        },
        {
            "_target_": "EnsureTyped",
            "keys": "@image_key",
            "data_type": "tensor",
            "dtype": "$torch.float"
        },
        {
            "_target_": "ScaleIntensityd",
            "keys": "@image_key",
            "minv": 0,
            "maxv": 1,
            "channel_wise": true
        },
        {
            "_target_": "ScaleIntensityRangePercentilesd",
            "keys": "image",
            "lower": 1,
            "upper": 99,
            "b_min": 0.0,
            "b_max": 1.0,
            "channel_wise": true,
            "clip": true
        }
    ],
    "preprocessing": {
        "_target_": "Compose",
        "transforms": "$@preprocessing_transforms "
    },
    "dataset": {
        "_target_": "Dataset",
        "data": "$[@input_dict]",
        "transform": "@preprocessing"
    },
    "dataloader": {
        "_target_": "ThreadDataLoader",
        "dataset": "@dataset",
        "batch_size": 1,
        "shuffle": false,
        "num_workers": 0
    },
    "inferer": {
        "_target_": "SlidingWindowInfererAdapt",
        "roi_size": "@roi_size",
        "sw_batch_size": 1,
        "overlap": 0.625,
        "mode": "gaussian",
        "cache_roi_weight_map": true,
        "progress": false
    },
    "postprocessing": {
        "_target_": "Compose",
        "transforms": [
            {
                "_target_": "ToDeviced",
                "keys": "pred",
                "device": "cpu"
            },
            {
                "_target_": "scripts.components.LogitsToLabelsd",
                "keys": "pred"
            },
            {
                "_target_": "scripts.components.SaveTiffExd",
                "keys": "pred",
                "output_dir": "@output_dir",
                "output_ext": "@output_ext",
                "output_postfix": "@output_postfix"
            }
        ]
    },
    "handlers": [
        {
            "_target_": "StatsHandler",
            "iteration_log": false
        }
    ],
    "checkpointloader": {
        "_target_": "CheckpointLoader",
        "load_path": "@pretrained_ckpt_path",
        "map_location": "cpu",
        "load_dict": {
            "state_dict": "@network"
        }
    },
    "evaluator": {
        "_target_": "SupervisedEvaluator",
        "device": "@device",
        "val_data_loader": "@dataloader",
        "network": "@network",
        "inferer": "@inferer",
        "postprocessing": "@postprocessing",
        "val_handlers": "@handlers",
        "amp": true
    },
    "initialize": [
        "$monai.utils.set_determinism(seed=123)",
        "$@checkpointloader(@evaluator)"
    ],
    "run": [
        "$@evaluator.run()"
    ]
}