From d46c68d2dbac4bf696bf5e6202246e62fce6a301 Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Tue, 17 Oct 2023 04:44:37 +0800
Subject: [PATCH] Update spleen bundle to use MONAI v1.3 (#527)

### Description
Update the spleen bundle to use MONAI v1.3 and test it.

### Status
**Ready**

### Please ensure all the checkboxes:
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Codeformat tests passed locally by running `./runtests.sh
--codeformat`.
- [ ] In-line docstrings updated.
- [x] Update `version` and `changelog` in `metadata.json` if changing an
existing bundle.
- [ ] Please ensure the naming rules in config files meet our
requirements (please refer to: `CONTRIBUTING.md`).
- [x] Ensure versions of packages such as `monai`, `pytorch` and `numpy`
are correct in `metadata.json`.
- [ ] Descriptions should be consistent with the content, such as
`eval_metrics` of the provided weights and TorchScript modules.
- [ ] Files larger than 25MB are excluded and replaced by providing
download links in `large_file.yml`.
- [ ] Avoid using path that contains personal information within config
files (such as use `/home/your_name/` for `"bundle_root"`).

---------

Signed-off-by: KumoLiu <yunl@nvidia.com>
---
 models/spleen_ct_segmentation/configs/evaluate.json  | 4 +---
 models/spleen_ct_segmentation/configs/inference.json | 2 --
 models/spleen_ct_segmentation/configs/metadata.json  | 5 +++--
 3 files changed, 4 insertions(+), 7 deletions(-)

diff --git a/models/spleen_ct_segmentation/configs/evaluate.json b/models/spleen_ct_segmentation/configs/evaluate.json
index dd0fa811..f874330a 100644
--- a/models/spleen_ct_segmentation/configs/evaluate.json
+++ b/models/spleen_ct_segmentation/configs/evaluate.json
@@ -16,7 +16,6 @@
                 ],
                 "transform": "@validate#preprocessing",
                 "orig_keys": "image",
-                "meta_key_postfix": "meta_dict",
                 "nearest_interp": [
                     false,
                     true
@@ -39,7 +38,6 @@
                 "_target_": "SaveImaged",
                 "_disabled_": true,
                 "keys": "pred",
-                "meta_keys": "pred_meta_dict",
                 "output_dir": "@output_dir",
                 "resample": false,
                 "squeeze_end_dims": true
@@ -68,7 +66,7 @@
             "metric_details": [
                 "val_mean_dice"
             ],
-            "batch_transform": "$monai.handlers.from_engine(['image_meta_dict'])",
+            "batch_transform": "$lambda x: [xx['image'].meta for xx in x]",
             "summary_ops": "*"
         }
     ],
diff --git a/models/spleen_ct_segmentation/configs/inference.json b/models/spleen_ct_segmentation/configs/inference.json
index fa338af4..e82996d2 100644
--- a/models/spleen_ct_segmentation/configs/inference.json
+++ b/models/spleen_ct_segmentation/configs/inference.json
@@ -106,7 +106,6 @@
                 "keys": "pred",
                 "transform": "@preprocessing",
                 "orig_keys": "image",
-                "meta_key_postfix": "meta_dict",
                 "nearest_interp": false,
                 "to_tensor": true
             },
@@ -118,7 +117,6 @@
             {
                 "_target_": "SaveImaged",
                 "keys": "pred",
-                "meta_keys": "pred_meta_dict",
                 "output_dir": "@output_dir"
             }
         ]
diff --git a/models/spleen_ct_segmentation/configs/metadata.json b/models/spleen_ct_segmentation/configs/metadata.json
index c461b0a8..2cea6a99 100644
--- a/models/spleen_ct_segmentation/configs/metadata.json
+++ b/models/spleen_ct_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": "0.5.3",
+    "version": "0.5.4",
     "changelog": {
+        "0.5.4": "update to use monai 1.3.0",
         "0.5.3": "fix the wrong GPU index issue of multi-node",
         "0.5.2": "remove error dollar symbol in readme",
         "0.5.1": "add RAM warning",
@@ -31,7 +32,7 @@
         "0.1.0": "complete the model package",
         "0.0.1": "initialize the model package structure"
     },
-    "monai_version": "1.2.0",
+    "monai_version": "1.3.0",
     "pytorch_version": "1.13.1",
     "numpy_version": "1.22.2",
     "optional_packages_version": {