diff --git a/models/brats_mri_segmentation/configs/inference.json b/models/brats_mri_segmentation/configs/inference.json index e7dafc82..04e673b4 100644 --- a/models/brats_mri_segmentation/configs/inference.json +++ b/models/brats_mri_segmentation/configs/inference.json @@ -1,11 +1,17 @@ { "imports": [ "$import glob", + "$import numpy", "$import os" ], "bundle_root": ".", + "image_key": "image", "ckpt_dir": "$@bundle_root + '/models'", "output_dir": "$@bundle_root + '/eval'", + "output_ext": ".nii.gz", + "output_dtype": "uint8", + "output_postfix": "seg", + "separate_folder": true, "data_list_file_path": "$@bundle_root + '/configs/datalist.json'", "dataset_dir": "/workspace/data/medical/brats2018challenge", "test_datalist": "$monai.data.load_decathlon_datalist(@data_list_file_path, data_list_key='testing', base_dir=@dataset_dir)", @@ -35,12 +41,12 @@ "transforms": [ { "_target_": "LoadImaged", - "keys": "image", + "keys": "@image_key", "image_only": false }, { "_target_": "NormalizeIntensityd", - "keys": "image", + "keys": "@image_key", "nonzero": true, "channel_wise": true } @@ -80,7 +86,7 @@ "_target_": "Invertd", "keys": "pred", "transform": "@preprocessing", - "orig_keys": "image", + "orig_keys": "@image_key", "meta_keys": "pred_meta_dict", "nearest_interp": false, "to_tensor": true @@ -100,21 +106,16 @@ "keys": "pred", "meta_keys": "pred_meta_dict", "output_dir": "@output_dir", - "output_postfix": "seg", - "output_dtype": "uint8", + "output_ext": "@output_ext", + "output_dtype": "@output_dtype", + "output_postfix": "@output_postfix", + "separate_folder": "@separate_folder", "resample": false, "squeeze_end_dims": true } ] }, "handlers": [ - { - "_target_": "CheckpointLoader", - "load_path": "$@bundle_root + '/models/model.pt'", - "load_dict": { - "model": "@network" - } - }, { "_target_": "StatsHandler", "iteration_log": false @@ -130,8 +131,16 @@ "val_handlers": "@handlers", "amp": true }, + "checkpointloader": { + "_target_": "CheckpointLoader", + "load_path": "$@bundle_root + '/models/model.pt'", + "load_dict": { + "model": "@network" + } + }, "initialize": [ - "$setattr(torch.backends.cudnn, 'benchmark', True)" + "$setattr(torch.backends.cudnn, 'benchmark', True)", + "$@checkpointloader(@evaluator)" ], "run": [ "$@evaluator.run()" diff --git a/models/brats_mri_segmentation/configs/inference_trt.json b/models/brats_mri_segmentation/configs/inference_trt.json index adfbca41..ec1e88ab 100644 --- a/models/brats_mri_segmentation/configs/inference_trt.json +++ b/models/brats_mri_segmentation/configs/inference_trt.json @@ -4,7 +4,9 @@ "$import os", "$import torch_tensorrt" ], - "handlers#0#_disabled_": true, "network_def": "$torch.jit.load(@bundle_root + '/models/model_trt.ts')", - "evaluator#amp": false + "evaluator#amp": false, + "initialize": [ + "$monai.utils.set_determinism(seed=123)" + ] } diff --git a/models/brats_mri_segmentation/configs/metadata.json b/models/brats_mri_segmentation/configs/metadata.json index 2ca65cea..9679fa09 100644 --- a/models/brats_mri_segmentation/configs/metadata.json +++ b/models/brats_mri_segmentation/configs/metadata.json @@ -1,7 +1,8 @@ { "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json", - "version": "0.4.8", + "version": "0.4.9", "changelog": { + "0.4.9": "add checkpoint loader for infer", "0.4.8": "fix the wrong GPU index issue of multi-node", "0.4.7": "enhance prepare datalist file", "0.4.6": "add dataset dir example",