diff --git a/models/endoscopic_tool_segmentation/configs/evaluate.json b/models/endoscopic_tool_segmentation/configs/evaluate.json index 7051a151..d81cb663 100644 --- a/models/endoscopic_tool_segmentation/configs/evaluate.json +++ b/models/endoscopic_tool_segmentation/configs/evaluate.json @@ -10,6 +10,7 @@ ], "transform": "@validate#preprocessing", "orig_keys": "image", + "meta_key_postfix": "meta_dict", "nearest_interp": [ false, true @@ -33,6 +34,7 @@ "_disabled_": true, "keys": "pred", "output_dir": "@output_dir", + "meta_keys": "pred_meta_dict", "output_ext": ".png", "resample": false, "squeeze_end_dims": true @@ -63,7 +65,7 @@ "val_iou", "val_mean_dice" ], - "batch_transform": "$lambda x: [xx['image'].meta for xx in x]", + "batch_transform": "$monai.handlers.from_engine(['image_meta_dict'])", "summary_ops": "*" } ], diff --git a/models/endoscopic_tool_segmentation/configs/inference.json b/models/endoscopic_tool_segmentation/configs/inference.json index 61200ab7..0f140d04 100644 --- a/models/endoscopic_tool_segmentation/configs/inference.json +++ b/models/endoscopic_tool_segmentation/configs/inference.json @@ -24,7 +24,8 @@ "transforms": [ { "_target_": "LoadImaged", - "keys": "image" + "keys": "image", + "image_only": false }, { "_target_": "EnsureChannelFirstd", diff --git a/models/endoscopic_tool_segmentation/configs/metadata.json b/models/endoscopic_tool_segmentation/configs/metadata.json index 984d5268..b70f30f7 100644 --- a/models/endoscopic_tool_segmentation/configs/metadata.json +++ b/models/endoscopic_tool_segmentation/configs/metadata.json @@ -2,7 +2,7 @@ "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json", "version": "0.5.5", "changelog": { - "0.5.5": "update AddChanneld with EnsureChannelFirstd and remove meta dict usage", + "0.5.5": "update AddChanneld with EnsureChannelFirstd and set image_only to False", "0.5.4": "fix the wrong GPU index issue of multi-node", "0.5.3": "remove error dollar symbol in readme", "0.5.2": "remove the CheckpointLoader from the train.json", @@ -26,7 +26,7 @@ "0.1.0": "complete the first version model package", "0.0.1": "initialize the model package structure" }, - "monai_version": "1.3.0rc5", + "monai_version": "1.3.0rc1", "pytorch_version": "1.13.1", "numpy_version": "1.22.2", "optional_packages_version": { diff --git a/models/endoscopic_tool_segmentation/configs/train.json b/models/endoscopic_tool_segmentation/configs/train.json index 15742e89..0bab96da 100644 --- a/models/endoscopic_tool_segmentation/configs/train.json +++ b/models/endoscopic_tool_segmentation/configs/train.json @@ -53,7 +53,8 @@ "keys": [ "image", "label" - ] + ], + "image_only": false }, { "_target_": "EnsureChannelFirstd",