166 lines
4.3 KiB
JSON
166 lines
4.3 KiB
JSON
{
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"imports": [
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"$import glob",
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"$import numpy",
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"$import os"
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],
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"bundle_root": ".",
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"image_key": "image",
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"output_dir": "$@bundle_root + '/eval'",
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"output_ext": ".nii.gz",
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"output_dtype": "$numpy.float32",
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"output_postfix": "trans",
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"separate_folder": true,
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"load_pretrain": true,
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"dataset_dir": "/workspace/data/Task09_Spleen",
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"datalist": "$list(sorted(glob.glob(@dataset_dir + '/imagesTs/*.nii.gz')))",
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"device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
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"network_def": {
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"_target_": "UNet",
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"spatial_dims": 3,
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"in_channels": 1,
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"out_channels": 2,
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"channels": [
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16,
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32,
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64,
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128,
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256
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],
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"strides": [
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2,
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2,
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2,
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2
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],
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"num_res_units": 2,
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"norm": "batch"
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},
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"network": "$@network_def.to(@device)",
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"preprocessing": {
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"_target_": "Compose",
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"transforms": [
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{
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"_target_": "LoadImaged",
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"keys": "@image_key"
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},
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{
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"_target_": "EnsureChannelFirstd",
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"keys": "@image_key"
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},
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{
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"_target_": "Orientationd",
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"keys": "@image_key",
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"axcodes": "RAS"
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},
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{
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"_target_": "Spacingd",
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"keys": "@image_key",
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"pixdim": [
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1.5,
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1.5,
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2.0
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],
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"mode": "bilinear"
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},
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{
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"_target_": "ScaleIntensityRanged",
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"keys": "@image_key",
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"a_min": -57,
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"a_max": 164,
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"b_min": 0,
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"b_max": 1,
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"clip": true
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},
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{
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"_target_": "EnsureTyped",
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"keys": "@image_key"
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}
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]
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},
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"dataset": {
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"_target_": "Dataset",
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"data": "$[{'image': i} for i in @datalist]",
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"transform": "@preprocessing"
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},
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"dataloader": {
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"_target_": "DataLoader",
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"dataset": "@dataset",
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"batch_size": 1,
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"shuffle": false,
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"num_workers": 4
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},
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"inferer": {
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"_target_": "SlidingWindowInferer",
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"roi_size": [
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96,
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96,
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96
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],
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"sw_batch_size": 4,
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"overlap": 0.5
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},
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"postprocessing": {
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"_target_": "Compose",
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"transforms": [
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{
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"_target_": "Activationsd",
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"keys": "pred",
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"softmax": true
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},
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{
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"_target_": "Invertd",
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"keys": "pred",
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"transform": "@preprocessing",
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"orig_keys": "@image_key",
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"nearest_interp": false,
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"to_tensor": true
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},
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{
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"_target_": "AsDiscreted",
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"keys": "pred",
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"argmax": true
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},
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{
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"_target_": "SaveImaged",
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"keys": "pred",
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"output_dir": "@output_dir",
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"output_ext": "@output_ext",
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"output_dtype": "@output_dtype",
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"output_postfix": "@output_postfix",
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"separate_folder": "@separate_folder"
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}
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]
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},
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"handlers": [
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{
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"_target_": "StatsHandler",
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"iteration_log": false
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}
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],
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"evaluator": {
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"_target_": "SupervisedEvaluator",
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"device": "@device",
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"val_data_loader": "@dataloader",
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"network": "@network",
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"inferer": "@inferer",
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"postprocessing": "@postprocessing",
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"val_handlers": "@handlers",
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"amp": true
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},
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"checkpointloader": {
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"_target_": "CheckpointLoader",
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"load_path": "$@bundle_root + '/models/model.pt'",
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"load_dict": {
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"model": "@network"
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}
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},
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"initialize": [
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"$monai.utils.set_determinism(seed=123)",
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"$@checkpointloader(@evaluator) if @load_pretrain else None"
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],
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"run": [
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"$@evaluator.run()"
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]
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}
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