| { |
| "imports": [ |
| "$import glob", |
| "$import json", |
| "$import pathlib", |
| "$import os" |
| ], |
| "bundle_root": ".", |
| "checkpoint": "$@bundle_root + '/models/model.pt'", |
| "output_dir": "$@bundle_root + '/eval'", |
| "dataset_dir": "/workspace/data/CoNSePNuclei", |
| "images": "$list(sorted(glob.glob(@dataset_dir + '/Test/Images/*.png')))[:1]", |
| "labels": "$list(sorted(glob.glob(@dataset_dir + '/Test/Labels/*.png')))[:1]", |
| "input_data": "$[{'image': i, 'label': l} for i,l in zip(@images, @labels)]", |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
| "network_def": { |
| "_target_": "DenseNet121", |
| "spatial_dims": 2, |
| "in_channels": 4, |
| "out_channels": 4 |
| }, |
| "network": "$@network_def.to(@device)", |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "LoadImaged", |
| "keys": [ |
| "image", |
| "label" |
| ], |
| "dtype": "uint8", |
| "image_only": false |
| }, |
| { |
| "_target_": "EnsureChannelFirstd", |
| "keys": [ |
| "image", |
| "label" |
| ] |
| }, |
| { |
| "_target_": "ScaleIntensityRanged", |
| "keys": "image", |
| "a_min": 0.0, |
| "a_max": 255.0, |
| "b_min": -1.0, |
| "b_max": 1.0 |
| }, |
| { |
| "_target_": "AddLabelAsGuidanced", |
| "keys": "image", |
| "source": "label" |
| } |
| ] |
| }, |
| "dataset": { |
| "_target_": "Dataset", |
| "data": "@input_data", |
| "transform": "@preprocessing" |
| }, |
| "dataloader": { |
| "_target_": "DataLoader", |
| "dataset": "@dataset", |
| "batch_size": 1, |
| "shuffle": false, |
| "num_workers": 4 |
| }, |
| "inferer": { |
| "_target_": "SimpleInferer" |
| }, |
| "postprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "Activationsd", |
| "keys": "pred", |
| "softmax": true |
| }, |
| { |
| "_target_": "SaveImaged", |
| "keys": "pred", |
| "meta_keys": "pred_meta_dict", |
| "output_dir": "@output_dir", |
| "output_ext": ".json" |
| } |
| ] |
| }, |
| "handlers": [ |
| { |
| "_target_": "CheckpointLoader", |
| "load_path": "$@checkpoint", |
| "load_dict": { |
| "model": "@network" |
| } |
| }, |
| { |
| "_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 |
| }, |
| "initialize": [ |
| "$monai.utils.set_determinism(seed=123)", |
| "$import scripts", |
| "$monai.data.register_writer('json', scripts.ClassificationWriter)" |
| ], |
| "run": [ |
| "$@evaluator.run()" |
| ] |
| } |
|
|
