| { |
| "imports": [ |
| "$import numpy as np" |
| ], |
| "bundle_root": ".", |
| "ckpt_dir": "$@bundle_root + '/models'", |
| "output_dir": "$@bundle_root + '/eval'", |
| "output_ext": ".tif", |
| "output_postfix": "trans", |
| "roi_size": [ |
| 256, |
| 256 |
| ], |
| "input_dict": "${'image': '/cellpose_dataset/test/001_img.png'}", |
| "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", |
| "sam_ckpt_path": "$@ckpt_dir + '/sam_vit_b_01ec64.pth'", |
| "pretrained_ckpt_path": "$@ckpt_dir + '/model.pt'", |
| "image_key": "image", |
| "channels_last": true, |
| "use_amp": true, |
| "amp_dtype": "$torch.float", |
| "network_def": { |
| "_target_": "monai.networks.nets.cell_sam_wrapper.CellSamWrapper", |
| "checkpoint": "@sam_ckpt_path" |
| }, |
| "network": "$@network_def.to(@device)", |
| "preprocessing_transforms": [ |
| { |
| "_target_": "scripts.components.LoadTiffd", |
| "keys": "@image_key" |
| }, |
| { |
| "_target_": "EnsureTyped", |
| "keys": "@image_key", |
| "data_type": "tensor", |
| "dtype": "$torch.float" |
| }, |
| { |
| "_target_": "ScaleIntensityd", |
| "keys": "@image_key", |
| "minv": 0, |
| "maxv": 1, |
| "channel_wise": true |
| }, |
| { |
| "_target_": "ScaleIntensityRangePercentilesd", |
| "keys": "image", |
| "lower": 1, |
| "upper": 99, |
| "b_min": 0.0, |
| "b_max": 1.0, |
| "channel_wise": true, |
| "clip": true |
| } |
| ], |
| "preprocessing": { |
| "_target_": "Compose", |
| "transforms": "$@preprocessing_transforms " |
| }, |
| "dataset": { |
| "_target_": "Dataset", |
| "data": "$[@input_dict]", |
| "transform": "@preprocessing" |
| }, |
| "dataloader": { |
| "_target_": "ThreadDataLoader", |
| "dataset": "@dataset", |
| "batch_size": 1, |
| "shuffle": false, |
| "num_workers": 0 |
| }, |
| "inferer": { |
| "_target_": "SlidingWindowInfererAdapt", |
| "roi_size": "@roi_size", |
| "sw_batch_size": 1, |
| "overlap": 0.625, |
| "mode": "gaussian", |
| "cache_roi_weight_map": true, |
| "progress": false |
| }, |
| "postprocessing": { |
| "_target_": "Compose", |
| "transforms": [ |
| { |
| "_target_": "ToDeviced", |
| "keys": "pred", |
| "device": "cpu" |
| }, |
| { |
| "_target_": "scripts.components.LogitsToLabelsd", |
| "keys": "pred" |
| }, |
| { |
| "_target_": "scripts.components.SaveTiffExd", |
| "keys": "pred", |
| "output_dir": "@output_dir", |
| "output_ext": "@output_ext", |
| "output_postfix": "@output_postfix" |
| } |
| ] |
| }, |
| "handlers": [ |
| { |
| "_target_": "StatsHandler", |
| "iteration_log": false |
| } |
| ], |
| "checkpointloader": { |
| "_target_": "CheckpointLoader", |
| "load_path": "@pretrained_ckpt_path", |
| "map_location": "cpu", |
| "load_dict": { |
| "state_dict": "@network" |
| } |
| }, |
| "evaluator": { |
| "_target_": "SupervisedEvaluator", |
| "device": "@device", |
| "val_data_loader": "@dataloader", |
| "network": "@network", |
| "inferer": "@inferer", |
| "postprocessing": "@postprocessing", |
| "val_handlers": "@handlers", |
| "amp": true |
| }, |
| "initialize": [ |
| "$monai.utils.set_determinism(seed=123)", |
| "$@checkpointloader(@evaluator)" |
| ], |
| "run": [ |
| "$@evaluator.run()" |
| ] |
| } |
|
|
