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{
"data_list_file_path": "$@bundle_root + '/configs/msd_task09_spleen_folds.json'",
"dataset_dir": "/data/Task09_Spleen",
"output_dir": "$@bundle_root + '/eval'",
"ckpt_path": "$@bundle_root + '/models/model.pt'",
"patch_size": [
128,
128,
128
],
"resample_to_spacing": [
1.5,
1.5,
1.5
],
"label_mappings": {
"default": [
[
1,
3
]
]
},
"label_set": "$list(x[1] for x in @label_mappings#default)",
"validate#evaluator#hyper_kwargs#val_head": "auto",
"validate#preprocessing": {
"_target_": "Compose",
"transforms": [
{
"_target_": "LoadImaged",
"keys": [
"image",
"label"
],
"image_only": true,
"ensure_channel_first": true
},
{
"_target_": "CropForegroundd",
"keys": [
"image"
],
"source_key": "image",
"margin": 10,
"allow_smaller": true,
"start_coord_key": null,
"end_coord_key": null
},
{
"_target_": "ScaleIntensityRanged",
"keys": "image",
"a_min": -963.8247715525971,
"a_max": 1053.678477684517,
"b_min": 0.0,
"b_max": 1.0,
"clip": true
},
{
"_target_": "Orientationd",
"keys": [
"image"
],
"axcodes": "RAS"
},
{
"_target_": "Spacingd",
"keys": [
"image"
],
"pixdim": "$@resample_to_spacing",
"mode": [
"bilinear"
]
},
{
"_target_": "CastToTyped",
"keys": [
"image",
"label"
],
"dtype": [
"$torch.float32",
"$torch.uint8"
]
},
{
"_target_": "monai.apps.vista3d.transforms.Relabeld",
"keys": "label",
"label_mappings": "@label_mappings",
"dtype": "$torch.uint8"
}
]
},
"validate#postprocessing": {
"_target_": "Compose",
"transforms": [
{
"_target_": "EnsureTyped",
"keys": [
"pred",
"label"
],
"device": "cpu",
"_disabled_": true
},
{
"_target_": "monai.apps.vista3d.transforms.VistaPostTransformd",
"keys": "pred"
},
{
"_target_": "Invertd",
"keys": "pred",
"transform": "$copy.deepcopy(@validate#preprocessing)",
"orig_keys": "image",
"nearest_interp": true,
"to_tensor": true
},
{
"_target_": "Lambdad",
"func": "$lambda x: torch.nan_to_num(x, nan=255)",
"keys": "pred"
},
{
"_target_": "SaveImaged",
"keys": "pred",
"resample": false,
"output_dir": "@output_dir"
},
{
"_target_": "monai.apps.vista3d.transforms.Relabeld",
"keys": [
"pred",
"label"
],
"label_mappings": "${'default': [[c, i+1] for i, c in enumerate(@label_set)]}",
"dtype": "$torch.uint8"
}
]
},
"validate#handlers": [
{
"_target_": "CheckpointLoader",
"load_path": "@ckpt_path",
"load_dict": {
"model": "@network"
}
},
{
"_target_": "StatsHandler",
"iteration_log": true,
"name": "validate_stats"
},
{
"_target_": "MetricsSaver",
"_disabled_": false,
"save_dir": "@output_dir",
"metrics": [
"val_mean_dice"
],
"batch_transform": "$lambda x: [xx['image'].meta for xx in x]",
"metric_details": "*",
"summary_ops": "*"
}
],
"validate#dataset": {
"_target_": "Dataset",
"data": "$list(@val_datalist)",
"transform": "@validate#preprocessing"
},
"run": [
"$@validate#evaluator.run()"
]
}
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