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--- |
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imports: |
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- "$import glob" |
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- "$import os" |
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- "$import scripts.monai_utils" |
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workflow_type: inference |
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input_channels: 1 |
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output_classes: 4 |
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output_channels: 4 |
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bundle_root: "." |
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output_dir: "$@bundle_root + '/eval/segresnet_FT'" |
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dataset_dir: "/processed/Public/CT_TotalSegmentator/TS_split/test/" |
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data_list_file_path: "$@bundle_root + '/configs/TS_test.json'" |
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datalist: "$monai.data.load_decathlon_datalist(@data_list_file_path, data_list_key='validation')" |
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device: "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')" |
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spatial_size: |
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- 96 |
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- 96 |
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- 96 |
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spatial_dims: "$len(@spatial_size)" |
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labels: |
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background: 0 |
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liver: 1 |
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spleen: 2 |
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pancreas: 3 |
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network_def: |
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_target_: monai.networks.nets.SegResNet |
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blocks_down: |
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- 1 |
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- 2 |
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- 2 |
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- 4 |
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blocks_up: |
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- 1 |
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- 1 |
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- 1 |
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init_filters: 16 |
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in_channels: "@input_channels" |
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out_channels: "@output_channels" |
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dropout_prob: 0.0 |
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network: "$@network_def.to(@device)" |
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image_key: image |
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preprocessing: |
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_target_: Compose |
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transforms: |
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- _target_: LoadImaged |
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keys: "@image_key" |
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reader: ITKReader |
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- _target_: EnsureChannelFirstd |
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keys: "@image_key" |
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- _target_: Orientationd |
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keys: image |
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axcodes: RAS |
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- _target_: Spacingd |
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keys: |
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- "@image_key" |
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pixdim: |
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- 1.5 |
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- 1.5 |
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- 3.0 |
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mode: |
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- bilinear |
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- _target_: ScaleIntensityRanged |
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keys: "@image_key" |
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a_min: -250 |
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a_max: 400 |
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b_min: 0 |
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b_max: 1 |
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clip: true |
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- _target_: CropForegroundd |
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keys: |
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- "@image_key" |
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source_key: "@image_key" |
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mode: |
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- "minimum" |
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- _target_: EnsureTyped |
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keys: image |
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- _target_: CastToTyped |
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keys: "@image_key" |
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dtype: "$torch.float32" |
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dataset: |
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_target_: Dataset |
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data: "@datalist" |
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transform: "@preprocessing" |
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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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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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sw_batch_size: 4 |
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overlap: 0.75 |
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postprocessing: |
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_target_: Compose |
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transforms: |
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- _target_: Activationsd |
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keys: pred |
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softmax: true |
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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 |
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meta_key_postfix: meta_dict |
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nearest_interp: false |
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to_tensor: true |
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- _target_: AsDiscreted |
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keys: pred |
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argmax: true |
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- _target_: SaveImaged |
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keys: pred |
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meta_keys: pred_meta_dict |
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output_dir: "@output_dir" |
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separate_folder: false |
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output_dtype: "$torch.int16" |
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handlers: |
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- _target_: CheckpointLoader |
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load_path: "$@bundle_root + '/models/segresnet_FT.pt'" |
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load_dict: |
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model: "@network" |
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- _target_: StatsHandler |
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iteration_log: false |
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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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initialize: |
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- "$setattr(torch.backends.cudnn, 'benchmark', True)" |
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run: |
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- "$@evaluator.run()" |
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