| { |
| "imports": [ |
| "$import glob", |
| "$import os" |
| ], |
| "bundle_root": "$os.getcwd()", |
| "output_dir": ".", |
| "dataset_dir": "CoNSeP/Test/Images", |
| "num_cpus": 2, |
| "batch_size": 1, |
| "sw_batch_size": 16, |
| "hovernet_mode": "fast", |
| "patch_size": 256, |
| "out_size": 164, |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
| "network_def": { |
| "_target_": "HoVerNet", |
| "mode": "@hovernet_mode", |
| "adapt_standard_resnet": true, |
| "in_channels": 3, |
| "out_classes": 5 |
| }, |
| "network": "$@network_def.to(@device)", |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "LoadImaged", |
| "keys": "image", |
| "reader": "$monai.data.PILReader", |
| "converter": "$lambda x: x.convert('RGB')" |
| }, |
| { |
| "_target_": "EnsureChannelFirstd", |
| "keys": "image" |
| }, |
| { |
| "_target_": "CastToTyped", |
| "keys": "image", |
| "dtype": "float32" |
| }, |
| { |
| "_target_": "ScaleIntensityRanged", |
| "keys": "image", |
| "a_min": 0.0, |
| "a_max": 255.0, |
| "b_min": 0.0, |
| "b_max": 1.0, |
| "clip": true |
| } |
| ] |
| }, |
| "data_list": "$[{'image': image} for image in glob.glob(os.path.join(@dataset_dir, '*.png'))]", |
| "dataset": { |
| "_target_": "Dataset", |
| "data": "@data_list", |
| "transform": "@preprocessing" |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@dataset", |
| "batch_size": "@batch_size", |
| "shuffle": false, |
| "num_workers": "@num_cpus", |
| "pin_memory": true |
| }, |
| "inferer": { |
| "_target_": "SlidingWindowHoVerNetInferer", |
| "roi_size": "@patch_size", |
| "sw_batch_size": "@sw_batch_size", |
| "overlap": "$1.0 - float(@out_size) / float(@patch_size)", |
| "padding_mode": "constant", |
| "cval": 0, |
| "progress": true, |
| "extra_input_padding": "$((@patch_size - @out_size) // 2,) * 4" |
| }, |
| "postprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "FlattenSubKeysd", |
| "keys": "pred", |
| "sub_keys": [ |
| "horizontal_vertical", |
| "nucleus_prediction", |
| "type_prediction" |
| ], |
| "delete_keys": true |
| }, |
| { |
| "_target_": "HoVerNetInstanceMapPostProcessingd", |
| "sobel_kernel_size": 21, |
| "marker_threshold": 0.4, |
| "marker_radius": 2 |
| }, |
| { |
| "_target_": "HoVerNetNuclearTypePostProcessingd" |
| }, |
| { |
| "_target_": "FromMetaTensord", |
| "keys": [ |
| "image" |
| ] |
| } |
| ] |
| }, |
| "handlers": [ |
| { |
| "_target_": "CheckpointLoader", |
| "load_path": "$os.path.join(@bundle_root, 'models', 'model.pt')", |
| "map_location": "@device", |
| "load_dict": { |
| "model": "@network" |
| } |
| } |
| ], |
| "evaluator": { |
| "_target_": "SupervisedEvaluator", |
| "device": "@device", |
| "val_data_loader": "@dataloader", |
| "val_handlers": "@handlers", |
| "network": "@network", |
| "postprocessing": "@postprocessing", |
| "inferer": "@inferer", |
| "amp": true |
| }, |
| "evaluating": [ |
| "$setattr(torch.backends.cudnn, 'benchmark', True)", |
| "$@evaluator.run()" |
| ] |
| } |
|
|
