configs/inference.json

{
    "imports": [
        "$import glob",
        "$import numpy",
        "$import os",
        "$import ignite"
    ],
    "bundle_root": ".",
    "image_key": "image",
    "output_dir": "$@bundle_root + '/eval'",
    "output_ext": ".nii.gz",
    "output_dtype": "$numpy.float32",
    "output_postfix": "trans",
    "separate_folder": true,
    "load_pretrain": true,
    "dataset_dir": "/workspace/Datasets/MSD_datasets/Task09_Spleen",
    "datalist": "$list(sorted(glob.glob(@dataset_dir + '/imagesTs/*.nii.gz')))",
    "label_names": {
        "spleen": 1,
        "background": 0
    },
    "spatial_size": [
        128,
        128,
        128
    ],
    "number_intensity_ch": 1,
    "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
    "network_def": {
        "_target_": "DynUNet",
        "spatial_dims": 3,
        "in_channels": "$len(@label_names) + @number_intensity_ch",
        "out_channels": "$len(@label_names)",
        "kernel_size": [
            3,
            3,
            3,
            3,
            3,
            3
        ],
        "strides": [
            1,
            2,
            2,
            2,
            2,
            [
                2,
                2,
                1
            ]
        ],
        "upsample_kernel_size": [
            2,
            2,
            2,
            2,
            [
                2,
                2,
                1
            ]
        ],
        "norm_name": "instance",
        "deep_supervision": false,
        "res_block": true
    },
    "network": "$@network_def.to(@device)",
    "preprocessing_transforms": [
        {
            "_target_": "LoadImaged",
            "keys": "@image_key",
            "reader": "ITKReader"
        },
        {
            "_target_": "EnsureChannelFirstd",
            "keys": "@image_key"
        },
        {
            "_target_": "Orientationd",
            "keys": "@image_key",
            "axcodes": "RAS"
        },
        {
            "_target_": "ScaleIntensityRanged",
            "keys": "@image_key",
            "a_min": -175,
            "a_max": 250,
            "b_min": 0.0,
            "b_max": 1.0,
            "clip": true
        }
    ],
    "deepedit_transforms": [
        {
            "_target_": "scripts.transforms.OrientationGuidanceMultipleLabelDeepEditd",
            "ref_image": "@image_key",
            "label_names": "@label_names"
        },
        {
            "_target_": "AddGuidanceFromPointsDeepEditd",
            "ref_image": "@image_key",
            "guidance": "guidance",
            "label_names": "@label_names"
        },
        {
            "_target_": "Resized",
            "keys": "@image_key",
            "spatial_size": "@spatial_size",
            "mode": "area"
        },
        {
            "_target_": "ResizeGuidanceMultipleLabelDeepEditd",
            "guidance": "guidance",
            "ref_image": "@image_key"
        },
        {
            "_target_": "AddGuidanceSignalDeepEditd",
            "keys": "@image_key",
            "guidance": "guidance",
            "number_intensity_ch": "@number_intensity_ch"
        }
    ],
    "extra_transforms": [
        {
            "_target_": "EnsureTyped",
            "keys": "@image_key"
        }
    ],
    "preprocessing": {
        "_target_": "Compose",
        "transforms": "$@preprocessing_transforms + @deepedit_transforms + @extra_transforms"
    },
    "dataset": {
        "_target_": "Dataset",
        "data": "$[{'image': i} for i in @datalist]",
        "transform": "@preprocessing"
    },
    "dataloader": {
        "_target_": "DataLoader",
        "dataset": "@dataset",
        "batch_size": 1,
        "shuffle": false,
        "num_workers": 2
    },
    "inferer": {
        "_target_": "SimpleInferer"
    },
    "postprocessing": {
        "_target_": "Compose",
        "transforms": [
            {
                "_target_": "EnsureTyped",
                "keys": "pred"
            },
            {
                "_target_": "Activationsd",
                "keys": "pred",
                "softmax": true
            },
            {
                "_target_": "Invertd",
                "keys": "pred",
                "transform": "@preprocessing",
                "orig_keys": "@image_key",
                "nearest_interp": false,
                "to_tensor": true
            },
            {
                "_target_": "AsDiscreted",
                "keys": "pred",
                "argmax": true
            },
            {
                "_target_": "SaveImaged",
                "keys": "pred",
                "output_dir": "@output_dir",
                "output_ext": "@output_ext",
                "output_dtype": "@output_dtype",
                "output_postfix": "@output_postfix",
                "separate_folder": "@separate_folder"
            }
        ]
    },
    "handlers": [
        {
            "_target_": "StatsHandler",
            "iteration_log": false
        }
    ],
    "evaluator": {
        "_target_": "SupervisedEvaluator",
        "device": "@device",
        "val_data_loader": "@dataloader",
        "network": "@network",
        "inferer": "@inferer",
        "postprocessing": "@postprocessing",
        "val_handlers": "@handlers",
        "amp": true
    },
    "checkpointloader": {
        "_target_": "CheckpointLoader",
        "load_path": "$@bundle_root + '/models/model.pt'",
        "load_dict": {
            "model": "@network"
        }
    },
    "initialize": [
        "$monai.utils.set_determinism(seed=123)",
        "$@checkpointloader(@evaluator) if @load_pretrain else None"
    ],
    "run": [
        "$@evaluator.run()"
    ]
}