| { | |
| "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()" | |
| ] | |
| } | |