configs/inference.json

{
    "imports": [
        "$import glob",
        "$import json",
        "$import pathlib",
        "$import os"
    ],
    "bundle_root": "/workspace/data/pathology_nuclei_classification",
    "output_dir": "$@bundle_root + '/eval'",
    "dataset_dir": "/workspace/data/CoNSePNuclei",
    "images": "$list(sorted(glob.glob(@dataset_dir + '/Test/Images/*.png')))[:1]",
    "labels": "$list(sorted(glob.glob(@dataset_dir + '/Test/Labels/*.png')))[:1]",
    "input_data": "$[{'image': i, 'label': l} for i,l in zip(@images, @labels)]",
    "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
    "network_def": {
        "_target_": "DenseNet121",
        "spatial_dims": 2,
        "in_channels": 4,
        "out_channels": 4
    },
    "network": "$@network_def.to(@device)",
    "preprocessing": {
        "_target_": "Compose",
        "transforms": [
            {
                "_target_": "LoadImaged",
                "keys": [
                    "image",
                    "label"
                ],
                "dtype": "uint8"
            },
            {
                "_target_": "EnsureChannelFirstd",
                "keys": [
                    "image",
                    "label"
                ]
            },
            {
                "_target_": "ScaleIntensityRanged",
                "keys": "image",
                "a_min": 0.0,
                "a_max": 255.0,
                "b_min": -1.0,
                "b_max": 1.0
            },
            {
                "_target_": "AddLabelAsGuidanced",
                "keys": "image",
                "source": "label"
            }
        ]
    },
    "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",
                "softmax": true
            },
            {
                "_target_": "SaveImaged",
                "keys": "pred",
                "meta_keys": "pred_meta_dict",
                "output_dir": "@output_dir",
                "output_ext": ".json"
            }
        ]
    },
    "handlers": [
        {
            "_target_": "CheckpointLoader",
            "load_path": "$@bundle_root + '/models/model.pt'",
            "load_dict": {
                "model": "@network"
            }
        },
        {
            "_target_": "StatsHandler",
            "iteration_log": false
        }
    ],
    "evaluator": {
        "_target_": "SupervisedEvaluator",
        "device": "@device",
        "val_data_loader": "@dataloader",
        "network": "@network",
        "inferer": "@inferer",
        "postprocessing": "@postprocessing",
        "val_handlers": "@handlers",
        "amp": true
    },
    "evaluating": [
        "$setattr(torch.backends.cudnn, 'benchmark', True)",
        "$import scripts",
        "$monai.data.register_writer('json', scripts.ClassificationWriter)",
        "[email protected]()"
    ]
}