Update to use MONAI v1.3 (#524)

Part of #509. ### Status **Ready** ### Please ensure all the checkboxes:  - [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`). - [ ] 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 <[email protected]> Co-authored-by: Wenqi Li <[email protected]>
Project-MONAI · Oct 16, 2023 · 1cff8b7 · 1cff8b7
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diff --git a/models/endoscopic_tool_segmentation/configs/metadata.json b/models/endoscopic_tool_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": "0.5.5",
+    "version": "0.5.6",
     "changelog": {
+        "0.5.6": "update to use monai 1.3.0",
         "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",
@@ -26,7 +27,7 @@
         "0.1.0": "complete the first version model package",
         "0.0.1": "initialize the model package structure"
     },
-    "monai_version": "1.3.0rc1",
+    "monai_version": "1.3.0",
     "pytorch_version": "1.13.1",
     "numpy_version": "1.22.2",
     "optional_packages_version": {

diff --git a/models/pathology_nuclick_annotation/configs/inference.json b/models/pathology_nuclick_annotation/configs/inference.json
@@ -33,7 +33,8 @@
             {
                 "_target_": "LoadImaged",
                 "keys": "image",
-                "dtype": "uint8"
+                "dtype": "uint8",
+                "image_only": false
             },
             {
                 "_target_": "EnsureChannelFirstd",

diff --git a/models/pathology_nuclick_annotation/configs/metadata.json b/models/pathology_nuclick_annotation/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": "0.1.5",
+    "version": "0.1.6",
     "changelog": {
+        "0.1.6": "set image_only to False",
         "0.1.5": "add support for TensorRT conversion and inference",
         "0.1.4": "fix the wrong GPU index issue of multi-node",
         "0.1.3": "remove error dollar symbol in readme",
@@ -18,7 +19,7 @@
         "0.0.2": "Update The Torch Vision Transform",
         "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": {

diff --git a/models/pathology_nuclick_annotation/configs/train.json b/models/pathology_nuclick_annotation/configs/train.json
@@ -51,7 +51,8 @@
                         "image",
                         "label"
                     ],
-                    "dtype": "uint8"
+                    "dtype": "uint8",
+                    "image_only": false
                 },
                 {
                     "_target_": "EnsureChannelFirstd",
@@ -207,7 +208,8 @@
                         "image",
                         "label"
                     ],
-                    "dtype": "uint8"
+                    "dtype": "uint8",
+                    "image_only": false
                 },
                 {
                     "_target_": "EnsureChannelFirstd",

diff --git a/models/renalStructures_CECT_segmentation/configs/inference.json b/models/renalStructures_CECT_segmentation/configs/inference.json
@@ -41,7 +41,8 @@
                     "vein",
                     "excret",
                     "label"
-                ]
+                ],
+                "image_only": false
             },
             {
                 "_target_": "EnsureChannelFirstd",

diff --git a/models/renalStructures_CECT_segmentation/configs/metadata.json b/models/renalStructures_CECT_segmentation/configs/metadata.json
@@ -1,10 +1,11 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
-    "version": "0.1.0",
+    "version": "0.2.0",
     "changelog": {
+        "0.2.0": "set image_only to False",
         "0.1.0": "complete the model package"
     },
-    "monai_version": "1.2.0",
+    "monai_version": "1.3.0",
     "pytorch_version": "1.13.1",
     "numpy_version": "1.24.3",
     "optional_packages_version": {

diff --git a/models/renalStructures_CECT_segmentation/configs/train.json b/models/renalStructures_CECT_segmentation/configs/train.json
@@ -73,7 +73,8 @@
                 "reader": null,
                 "overwriting": false,
                 "dtype": "float32",
-                "as_closest_canonical": true
+                "as_closest_canonical": true,
+                "image_only": false
             },
             {
                 "_target_": "EnsureChannelFirstd",
@@ -284,7 +285,7 @@
                     ]
                 },
                 {
-                    "_target_": "SplitChanneld",
+                    "_target_": "SplitDimd",
                     "keys": [
                         "pred",
                         "label"

diff --git a/models/renalStructures_UNEST_segmentation/configs/inference.json b/models/renalStructures_UNEST_segmentation/configs/inference.json
@@ -22,8 +22,9 @@
                 "keys": "image"
             },
             {
-                "_target_": "AddChanneld",
-                "keys": "image"
+                "_target_": "EnsureChannelFirstd",
+                "keys": "image",
+                "channel_dim": "no_channel"
             },
             {
                 "_target_": "Orientationd",
@@ -90,7 +91,6 @@
                 "keys": "pred",
                 "transform": "@preprocessing",
                 "orig_keys": "image",
-                "meta_key_postfix": "meta_dict",
                 "nearest_interp": false,
                 "to_tensor": true
             },
@@ -102,7 +102,6 @@
             {
                 "_target_": "SaveImaged",
                 "keys": "pred",
-                "meta_keys": "pred_meta_dict",
                 "output_dir": "@output_dir"
             }
         ]

diff --git a/models/renalStructures_UNEST_segmentation/configs/metadata.json b/models/renalStructures_UNEST_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": "0.2.2",
+    "version": "0.2.3",
     "changelog": {
+        "0.2.3": "update AddChanneld with EnsureChannelFirstd and remove meta_dict",
         "0.2.2": "add name tag",
         "0.2.1": "fix license Copyright error",
         "0.2.0": "update license files",
@@ -10,16 +11,16 @@
         "0.1.1": "fixed the model state dict name",
         "0.1.0": "complete the model package"
     },
-    "monai_version": "1.0.0",
-    "pytorch_version": "1.10.0",
-    "numpy_version": "1.21.2",
+    "monai_version": "1.3.0",
+    "pytorch_version": "1.13.1",
+    "numpy_version": "1.22.2",
     "optional_packages_version": {
         "nibabel": "3.2.1",
         "pytorch-ignite": "0.4.8",
         "einops": "0.4.1",
         "fire": "0.4.0",
         "timm": "0.6.7",
-        "torchvision": "0.11.1"
+        "torchvision": "0.14.1"
     },
     "name": "Renal structures UNEST segmentation",
     "task": "Renal segmentation",

diff --git a/models/spleen_deepedit_annotation/configs/metadata.json b/models/spleen_deepedit_annotation/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": "0.5.2",
+    "version": "0.5.3",
     "changelog": {
+        "0.5.3": "update to use monai 1.3.0",
         "0.5.2": "update the checkpoint loader logic for inference",
         "0.5.1": "add option to validate at training start, and I/O param entries",
         "0.5.0": "enable finetune and early stop",
@@ -29,7 +30,7 @@
         "0.1.0": "complete the model package",
         "0.0.1": "initialize the model package structure"
     },
-    "monai_version": "1.3.0rc5",
+    "monai_version": "1.3.0",
     "pytorch_version": "1.13.1",
     "numpy_version": "1.22.2",
     "optional_packages_version": {

diff --git a/models/swin_unetr_btcv_segmentation/configs/evaluate.json b/models/swin_unetr_btcv_segmentation/configs/evaluate.json
@@ -66,7 +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/swin_unetr_btcv_segmentation/configs/inference.json b/models/swin_unetr_btcv_segmentation/configs/inference.json
@@ -95,7 +95,6 @@
                 "keys": "pred",
                 "transform": "@preprocessing",
                 "orig_keys": "image",
-                "meta_key_postfix": "meta_dict",
                 "nearest_interp": false,
                 "to_tensor": true
             },
@@ -107,7 +106,6 @@
             {
                 "_target_": "SaveImaged",
                 "keys": "pred",
-                "meta_keys": "pred_meta_dict",
                 "output_dir": "@output_dir"
             }
         ]

diff --git a/models/swin_unetr_btcv_segmentation/configs/metadata.json b/models/swin_unetr_btcv_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": "0.5.0",
+    "version": "0.5.1",
     "changelog": {
+        "0.5.1": "remove meta_dict usage",
         "0.5.0": "fix the wrong GPU index issue of multi-node",
         "0.4.9": "remove error dollar symbol in readme",
         "0.4.8": "add RAM usage with CacheDataset",
@@ -27,7 +28,7 @@
         "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": {

diff --git a/models/ventricular_short_axis_3label/configs/inference.json b/models/ventricular_short_axis_3label/configs/inference.json
@@ -34,7 +34,8 @@
         "transforms": [
             {
                 "_target_": "LoadImaged",
-                "keys": "image"
+                "keys": "image",
+                "image_only": false
             },
             {
                 "_target_": "EnsureChannelFirstd",

diff --git a/models/ventricular_short_axis_3label/configs/metadata.json b/models/ventricular_short_axis_3label/configs/metadata.json
@@ -1,14 +1,15 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
-    "version": "0.3.2",
+    "version": "0.3.3",
     "changelog": {
+        "0.3.3": "update AddChanneld with EnsureChannelFirstd",
         "0.3.2": "add name tag",
         "0.3.1": "modify dataset key name",
         "0.3.0": "update license files",
         "0.2.0": "unify naming",
         "0.1.0": "Initial version"
     },
-    "monai_version": "1.0.1",
+    "monai_version": "1.3.0",
     "pytorch_version": "1.13.0",
     "numpy_version": "1.21.2",
     "optional_packages_version": {

diff --git a/models/ventricular_short_axis_3label/configs/train.json b/models/ventricular_short_axis_3label/configs/train.json
@@ -62,8 +62,9 @@
                 "keys": "image"
             },
             {
-                "_target_": "AddChanneld",
-                "keys": "@both_keys"
+                "_target_": "EnsureChannelFirstd",
+                "keys": "@both_keys",
+                "channel_dim": "no_channel"
             },
             {
                 "_target_": "RandAxisFlipd",
@@ -98,8 +99,7 @@
                 "translate_range": 50,
                 "scale_range": 0.25,
                 "padding_mode": "$monai.utils.GridSamplePadMode.ZEROS",
-                "mode": "$(monai.utils.GridSampleMode.BILINEAR,monai.utils.GridSampleMode.NEAREST)",
-                "as_tensor_output": false
+                "mode": "$(monai.utils.GridSampleMode.BILINEAR,monai.utils.GridSampleMode.NEAREST)"
             },
             {
                 "_target_": "RandSmoothFieldAdjustContrastd",
@@ -167,8 +167,9 @@
                 "keys": "image"
             },
             {
-                "_target_": "AddChanneld",
-                "keys": "@both_keys"
+                "_target_": "EnsureChannelFirstd",
+                "keys": "@both_keys",
+                "channel_dim": "no_channel"
             },
             {
                 "_target_": "EnsureTyped",

diff --git a/models/wholeBody_ct_segmentation/configs/evaluate.json b/models/wholeBody_ct_segmentation/configs/evaluate.json
@@ -67,7 +67,7 @@
             "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/wholeBody_ct_segmentation/configs/inference.json b/models/wholeBody_ct_segmentation/configs/inference.json
@@ -117,14 +117,12 @@
                 "keys": "pred",
                 "transform": "@preprocessing",
                 "orig_keys": "image",
-                "meta_key_postfix": "meta_dict",
                 "nearest_interp": true,
                 "to_tensor": true
             },
             {
                 "_target_": "SaveImaged",
                 "keys": "pred",
-                "meta_keys": "pred_meta_dict",
                 "output_dir": "@output_dir"
             }
         ]

diff --git a/models/wholeBody_ct_segmentation/configs/metadata.json b/models/wholeBody_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": "0.2.0",
+    "version": "0.2.1",
     "changelog": {
+        "0.2.1": "remove meta_dict usage",
         "0.2.0": "add support for TensorRT conversion and inference",
         "0.1.9": "fix the wrong GPU index issue of multi-node",
         "0.1.8": "Update evalaute doc, GPU usage details, and dataset preparation instructions",
@@ -15,7 +16,7 @@
         "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": {