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pathology_nuclick_annotation

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pathology_nuclick_annotation
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{
    "imports": [
        "$import glob",
        "$import json",
        "$import pathlib",
        "$import os"
    ],
    "bundle_root": ".",
    "output_dir": "$@bundle_root + '/eval'",
    "dataset_dir": "/workspace/data/CoNSePNuclei",
    "images": "$list(sorted(glob.glob(@dataset_dir + '/Test/Images/*.png')))[:1]",
    "centroids": "$list(sorted(glob.glob(@dataset_dir + '/Test/Centroids/*.txt')))[:1]",
    "input_data": "$[{'image': i, 'foreground': json.loads(pathlib.Path(c).read_text())} for i,c in zip(@images, @centroids)]",
    "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
    "network_def": {
        "_target_": "BasicUNet",
        "spatial_dims": 2,
        "in_channels": 5,
        "out_channels": 1,
        "features": [
            32,
            64,
            128,
            256,
            512,
            32
        ]
    },
    "network": "$@network_def.to(@device)",
    "preprocessing": {
        "_target_": "Compose",
        "transforms": [
            {
                "_target_": "LoadImaged",
                "keys": "image",
                "dtype": "uint8"
            },
            {
                "_target_": "EnsureChannelFirstd",
                "keys": "image"
            },
            {
                "_target_": "ScaleIntensityRanged",
                "keys": "image",
                "a_min": 0.0,
                "a_max": 255.0,
                "b_min": -1.0,
                "b_max": 1.0
            },
            {
                "_target_": "AddClickSignalsd",
                "image": "image",
                "foreground": "foreground",
                "gaussian": false
            },
            {
                "_target_": "SqueezeDimd",
                "keys": "image"
            }
        ]
    },
    "dataset": {
        "_target_": "Dataset",
        "data": "@input_data",
        "transform": "@preprocessing"
    },
    "dataloader": {
        "_target_": "DataLoader",
        "dataset": "@dataset",
        "batch_size": 1,
        "shuffle": false,
        "num_workers": 4
    },
    "inferer": {
        "_target_": "SimpleInferer"
    },
    "postprocessing": {
        "_target_": "Compose",
        "transforms": [
            {
                "_target_": "Activationsd",
                "keys": "pred",
                "sigmoid": true
            },
            {
                "_target_": "AsDiscreted",
                "keys": "pred",
                "threshold": 0.5
            },
            {
                "_target_": "KeepLargestConnectedComponentd",
                "keys": "pred"
            },
            {
                "_target_": "SaveImaged",
                "keys": "pred",
                "meta_keys": "pred_meta_dict",
                "output_dir": "@output_dir",
                "output_ext": ".png"
            }
        ]
    },
    "handlers": [
        {
            "_target_": "CheckpointLoader",
            "load_path": "$@bundle_root + '/models/model.pt'",
            "load_dict": {
                "model": "@network"
            }
        },
        {
            "_target_": "StatsHandler",
            "iteration_log": false
        }
    ],
    "evaluator": {
        "_target_": "SupervisedEvaluator",
        "device": "@device",
        "val_data_loader": "@dataloader",
        "network": "@network",
        "inferer": "@inferer",
        "postprocessing": "@postprocessing",
        "val_handlers": "@handlers",
        "amp": true
    },
    "initialize": [
        "$import sys",
        "$sys.path.append(@bundle_root)",
        "$monai.utils.set_determinism(seed=123)"
    ],
    "run": [
        "[email protected]()"
    ]
}