| { | |
| "imports": [ | |
| "$import glob", | |
| "$import os" | |
| ], | |
| "bundle_root": ".", | |
| "output_dir": "$os.path.join(@bundle_root, 'eval')", | |
| "dataset_dir": "/workspace/data/medical/pathology", | |
| "testing_file": "$os.path.join(@bundle_root, 'testing.csv')", | |
| "wsi_reader": "cuCIM", | |
| "patch_size": [ | |
| 224, | |
| 224 | |
| ], | |
| "number_intensity_ch": 3, | |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", | |
| "network_def": { | |
| "_target_": "TorchVisionFCModel", | |
| "model_name": "resnet18", | |
| "num_classes": 1, | |
| "use_conv": true, | |
| "pretrained": true | |
| }, | |
| "network": "$@network_def.to(@device)", | |
| "preprocessing": { | |
| "_target_": "Compose", | |
| "transforms": [ | |
| { | |
| "_target_": "CastToTyped", | |
| "keys": "image", | |
| "dtype": "float32" | |
| }, | |
| { | |
| "_target_": "ScaleIntensityRanged", | |
| "keys": "image", | |
| "a_min": 0.0, | |
| "a_max": 255.0, | |
| "b_min": -1.0, | |
| "b_max": 1.0 | |
| }, | |
| { | |
| "_target_": "ToTensord", | |
| "keys": "image" | |
| } | |
| ] | |
| }, | |
| "datalist": { | |
| "_target_": "CSVDataset", | |
| "src": "@testing_file", | |
| "kwargs_read_csv": { | |
| "names": [ | |
| "image" | |
| ], | |
| "header": null | |
| }, | |
| "transform": { | |
| "_target_": "Lambdad", | |
| "keys": "image", | |
| "func": "$lambda x: os.path.join(@dataset_dir, 'testing/images', x + '.tif')" | |
| } | |
| }, | |
| "dataset": { | |
| "_target_": "MaskedPatchWSIDataset", | |
| "data": "@datalist", | |
| "mask_level": 6, | |
| "patch_size": "@patch_size", | |
| "transform": "@preprocessing", | |
| "reader": "@wsi_reader" | |
| }, | |
| "dataloader": { | |
| "_target_": "DataLoader", | |
| "dataset": "@dataset", | |
| "batch_size": 400, | |
| "shuffle": false, | |
| "num_workers": 8 | |
| }, | |
| "inferer": { | |
| "_target_": "SimpleInferer" | |
| }, | |
| "postprocessing": { | |
| "_target_": "Compose", | |
| "transforms": [ | |
| { | |
| "_target_": "EnsureTyped", | |
| "keys": "pred" | |
| }, | |
| { | |
| "_target_": "Activationsd", | |
| "keys": "pred", | |
| "sigmoid": true | |
| }, | |
| { | |
| "_target_": "ToNumpyd", | |
| "keys": "pred" | |
| } | |
| ] | |
| }, | |
| "handlers": [ | |
| { | |
| "_target_": "CheckpointLoader", | |
| "load_path": "$@bundle_root + '/models/model.pt'", | |
| "load_dict": { | |
| "model": "@network" | |
| } | |
| }, | |
| { | |
| "_target_": "StatsHandler", | |
| "tag_name": "progress", | |
| "iteration_print_logger": "$lambda engine: print(f'image: \"{engine.state.batch[\"image\"].meta[\"name\"][0]}\", iter: {engine.state.iteration}/{engine.state.epoch_length}') if engine.state.iteration % 100 == 0 else None", | |
| "output_transform": "$lambda x: None" | |
| }, | |
| { | |
| "_target_": "monai.handlers.ProbMapProducer", | |
| "output_dir": "@output_dir" | |
| } | |
| ], | |
| "evaluator": { | |
| "_target_": "SupervisedEvaluator", | |
| "device": "@device", | |
| "val_data_loader": "@dataloader", | |
| "network": "@network", | |
| "inferer": "@inferer", | |
| "postprocessing": "@postprocessing", | |
| "val_handlers": "@handlers", | |
| "amp": true, | |
| "decollate": false | |
| }, | |
| "run": [ | |
| "[email protected]()" | |
| ] | |
| } | |