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{
"imports": [
"$import glob",
"$import os"
],
"bundle_root": "$os.getcwd()",
"output_dir": ".",
"dataset_dir": "CoNSeP/Test/Images",
"num_cpus": 6,
"batch_size": 1,
"sw_batch_size": 16,
"hovernet_mode": "fast",
"patch_size": 256,
"out_size": 164,
"device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
"network_def": {
"_target_": "HoVerNet",
"mode": "@hovernet_mode",
"adapt_standard_resnet": true,
"in_channels": 3,
"out_classes": 5
},
"network": "$@network_def.to(@device)",
"preprocessing": {
"_target_": "Compose",
"transforms": [
{
"_target_": "LoadImaged",
"keys": "image",
"reader": "$monai.data.PILReader",
"converter": "$lambda x: x.convert('RGB')"
},
{
"_target_": "EnsureChannelFirstd",
"keys": "image"
},
{
"_target_": "CastToTyped",
"keys": "image",
"dtype": "float32"
},
{
"_target_": "ScaleIntensityRanged",
"keys": "image",
"a_min": 0.0,
"a_max": 255.0,
"b_min": 0.0,
"b_max": 1.0,
"clip": true
}
]
},
"data_list": "$[{'image': image} for image in glob.glob(os.path.join(@dataset_dir, '*.png'))]",
"dataset": {
"_target_": "Dataset",
"data": "@data_list",
"transform": "@preprocessing"
},
"dataloader": {
"_target_": "DataLoader",
"dataset": "@dataset",
"batch_size": "@batch_size",
"shuffle": false,
"num_workers": "@num_cpus",
"pin_memory": true
},
"inferer": {
"_target_": "SlidingWindowHoVerNetInferer",
"roi_size": "@patch_size",
"sw_batch_size": "@sw_batch_size",
"overlap": "$1.0 - float(@out_size) / float(@patch_size)",
"padding_mode": "constant",
"cval": 0,
"progress": true,
"extra_input_padding": "$((@patch_size - @out_size) // 2,) * 4"
},
"postprocessing": {
"_target_": "Compose",
"transforms": [
{
"_target_": "FlattenSubKeysd",
"keys": "pred",
"sub_keys": [
"horizontal_vertical",
"nucleus_prediction",
"type_prediction"
],
"delete_keys": true
},
{
"_target_": "HoVerNetInstanceMapPostProcessingd",
"sobel_kernel_size": 21,
"marker_threshold": 0.4,
"marker_radius": 2
},
{
"_target_": "HoVerNetNuclearTypePostProcessingd"
},
{
"_target_": "FromMetaTensord",
"keys": [
"image"
]
}
]
},
"handlers": [
{
"_target_": "CheckpointLoader",
"load_path": "$os.path.join(@bundle_root, 'models', 'model.pt')",
"map_location": "@device",
"load_dict": {
"model": "@network"
}
}
],
"evaluator": {
"_target_": "SupervisedEvaluator",
"device": "@device",
"val_data_loader": "@dataloader",
"val_handlers": "@handlers",
"network": "@network",
"postprocessing": "@postprocessing",
"inferer": "@inferer",
"amp": true
},
"evaluating": [
"$setattr(torch.backends.cudnn, 'benchmark', True)",
"$@evaluator.run()"
]
}
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