| { | |
| "imports": [ | |
| "$import glob", | |
| "$import os" | |
| ], | |
| "bundle_root": ".", | |
| "output_dir": "$os.path.join(@bundle_root, 'eval')", | |
| "dataset_dir": "/workspace/Data/Pathology/CoNSeP/Test/Images", | |
| "num_cpus": 2, | |
| "batch_size": 1, | |
| "sw_batch_size": 16, | |
| "hovernet_mode": "fast", | |
| "patch_size": 256, | |
| "out_size": 164, | |
| "device": "$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" | |
| }, | |
| "sub_keys": [ | |
| "horizontal_vertical", | |
| "nucleus_prediction", | |
| "type_prediction" | |
| ], | |
| "postprocessing": { | |
| "_target_": "Compose", | |
| "transforms": [ | |
| { | |
| "_target_": "FlattenSubKeysd", | |
| "keys": "pred", | |
| "sub_keys": "$@sub_keys", | |
| "delete_keys": true | |
| }, | |
| { | |
| "_target_": "HoVerNetInstanceMapPostProcessingd", | |
| "sobel_kernel_size": 21, | |
| "marker_threshold": 0.4, | |
| "marker_radius": 2 | |
| }, | |
| { | |
| "_target_": "HoVerNetNuclearTypePostProcessingd" | |
| }, | |
| { | |
| "_target_": "FromMetaTensord", | |
| "keys": [ | |
| "image" | |
| ] | |
| }, | |
| { | |
| "_target_": "SaveImaged", | |
| "keys": "instance_map", | |
| "meta_keys": "image_meta_dict", | |
| "output_ext": ".nii.gz", | |
| "output_dir": "@output_dir", | |
| "output_postfix": "instance_map", | |
| "output_dtype": "uint32", | |
| "separate_folder": false | |
| }, | |
| { | |
| "_target_": "SaveImaged", | |
| "keys": "type_map", | |
| "meta_keys": "image_meta_dict", | |
| "output_ext": ".nii.gz", | |
| "output_dir": "@output_dir", | |
| "output_postfix": "type_map", | |
| "output_dtype": "uint8", | |
| "separate_folder": false | |
| } | |
| ] | |
| }, | |
| "handlers": [ | |
| { | |
| "_target_": "CheckpointLoader", | |
| "load_path": "$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 | |
| }, | |
| "initialize": [ | |
| "$setattr(torch.backends.cudnn, 'benchmark', True)" | |
| ], | |
| "run": [ | |
| "$@evaluator.run()" | |
| ] | |
| } | |