| { |
| "displayable_configs": { |
| "highres": true, |
| "sw_overlap": 0.25, |
| "sw_batch_size": 1 |
| }, |
| "imports": [ |
| "$import glob", |
| "$import numpy", |
| "$import os" |
| ], |
| "bundle_root": ".", |
| "image_key": "image", |
| "output_dir": "$@bundle_root + '/eval'", |
| "output_ext": ".nii.gz", |
| "output_dtype": "$numpy.float32", |
| "output_postfix": "trans", |
| "separate_folder": true, |
| "load_pretrain": true, |
| "dataset_dir": "sampledata", |
| "datalist": "$list(sorted(glob.glob(@dataset_dir + '/imagesTs/*.nii.gz')))", |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
| "pixdim": "$[1.5, 1.5, 1.5] if @displayable_configs#highres else [3.0, 3.0, 3.0]", |
| "modelname": "$'model.pt' if @displayable_configs#highres else 'model_lowres.pt'", |
| "network_def": { |
| "_target_": "SegResNet", |
| "spatial_dims": 3, |
| "in_channels": 1, |
| "out_channels": 105, |
| "init_filters": 32, |
| "blocks_down": [ |
| 1, |
| 2, |
| 2, |
| 4 |
| ], |
| "blocks_up": [ |
| 1, |
| 1, |
| 1 |
| ], |
| "dropout_prob": 0.2 |
| }, |
| "network": "$@network_def.to(@device)", |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "LoadImaged", |
| "keys": "@image_key" |
| }, |
| { |
| "_target_": "EnsureTyped", |
| "keys": "@image_key" |
| }, |
| { |
| "_target_": "EnsureChannelFirstd", |
| "keys": "@image_key" |
| }, |
| { |
| "_target_": "Orientationd", |
| "keys": "@image_key", |
| "axcodes": "RAS" |
| }, |
| { |
| "_target_": "Spacingd", |
| "keys": "@image_key", |
| "pixdim": "@pixdim", |
| "mode": "bilinear" |
| }, |
| { |
| "_target_": "NormalizeIntensityd", |
| "keys": "@image_key", |
| "nonzero": true |
| }, |
| { |
| "_target_": "ScaleIntensityd", |
| "keys": "@image_key", |
| "minv": -1.0, |
| "maxv": 1.0 |
| } |
| ] |
| }, |
| "dataset": { |
| "_target_": "Dataset", |
| "data": "$[{'image': i} for i in @datalist]", |
| "transform": "@preprocessing" |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@dataset", |
| "batch_size": 1, |
| "shuffle": false, |
| "num_workers": 1 |
| }, |
| "inferer": { |
| "_target_": "SlidingWindowInferer", |
| "roi_size": [ |
| 96, |
| 96, |
| 96 |
| ], |
| "sw_batch_size": "@displayable_configs#sw_batch_size", |
| "overlap": "@displayable_configs#sw_overlap", |
| "padding_mode": "replicate", |
| "mode": "gaussian", |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')" |
| }, |
| "postprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "Activationsd", |
| "keys": "pred", |
| "softmax": true |
| }, |
| { |
| "_target_": "AsDiscreted", |
| "keys": "pred", |
| "argmax": true |
| }, |
| { |
| "_target_": "Invertd", |
| "keys": "pred", |
| "transform": "@preprocessing", |
| "orig_keys": "@image_key", |
| "nearest_interp": true, |
| "to_tensor": 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": "$@bundle_root + '/models/' + @modelname", |
| "load_dict": { |
| "model": "@network" |
| } |
| }, |
| "initialize": [ |
| "$setattr(torch.backends.cudnn, 'benchmark', True)", |
| "$@checkpointloader(@evaluator) if @load_pretrain else None" |
| ], |
| "run": [ |
| "$@evaluator.run()" |
| ] |
| } |
|
|
