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{
"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()"
]
}
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