Add option to validate at training start of deepedit (#515)

### Description

Modify bundle as the new feature enabled in
Project-MONAI/MONAI@fc1350a

### Status
**Ready/Work in progress/Hold**

### 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.
- [ ] 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: Mingxin Zheng <[email protected]>
Signed-off-by: KumoLiu <[email protected]>
Co-authored-by: KumoLiu <[email protected]>

models/spleen_deepedit_annotation/configs/evaluate.json

@@ -24,7 +24,6 @@
                 "_target_": "SaveImaged",
                 "_disabled_": true,
                 "keys": "pred",
-                "meta_keys": "pred_meta_dict",
                 "output_dir": "@output_dir",
                 "resample": false,
                 "squeeze_end_dims": true
@@ -53,7 +52,7 @@
             "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": "*"
         }
     ],

models/spleen_deepedit_annotation/configs/inference.json

@@ -1,11 +1,17 @@
 {
     "imports": [
         "$import glob",
+        "$import numpy",
         "$import os",
         "$import ignite"
     ],
     "bundle_root": ".",
+    "image_key": "image",
     "output_dir": "$@bundle_root + '/eval'",
+    "output_ext": ".nii.gz",
+    "output_dtype": "$numpy.float32",
+    "output_postfix": "trans",
+    "separate_folder": true,
     "dataset_dir": "/workspace/Datasets/MSD_datasets/Task09_Spleen",
     "datalist": "$list(sorted(glob.glob(@dataset_dir + '/imagesTs/*.nii.gz')))",
     "label_names": {
@@ -63,21 +69,21 @@
     "preprocessing_transforms": [
         {
             "_target_": "LoadImaged",
-            "keys": "image",
+            "keys": "@image_key",
             "reader": "ITKReader"
         },
         {
             "_target_": "EnsureChannelFirstd",
-            "keys": "image"
+            "keys": "@image_key"
         },
         {
             "_target_": "Orientationd",
-            "keys": "image",
+            "keys": "@image_key",
             "axcodes": "RAS"
         },
         {
             "_target_": "ScaleIntensityRanged",
-            "keys": "image",
+            "keys": "@image_key",
             "a_min": -175,
             "a_max": 250,
             "b_min": 0.0,
@@ -88,37 +94,37 @@
     "deepedit_transforms": [
         {
             "_target_": "scripts.transforms.OrientationGuidanceMultipleLabelDeepEditd",
-            "ref_image": "image",
+            "ref_image": "@image_key",
             "label_names": "@label_names"
         },
         {
             "_target_": "AddGuidanceFromPointsDeepEditd",
-            "ref_image": "image",
+            "ref_image": "@image_key",
             "guidance": "guidance",
             "label_names": "@label_names"
         },
         {
             "_target_": "Resized",
-            "keys": "image",
+            "keys": "@image_key",
             "spatial_size": "@spatial_size",
             "mode": "area"
         },
         {
             "_target_": "ResizeGuidanceMultipleLabelDeepEditd",
             "guidance": "guidance",
-            "ref_image": "image"
+            "ref_image": "@image_key"
         },
         {
             "_target_": "AddGuidanceSignalDeepEditd",
-            "keys": "image",
+            "keys": "@image_key",
             "guidance": "guidance",
             "number_intensity_ch": "@number_intensity_ch"
         }
     ],
     "extra_transforms": [
         {
             "_target_": "EnsureTyped",
-            "keys": "image"
+            "keys": "@image_key"
         }
     ],
     "preprocessing": {
@@ -156,8 +162,7 @@
                 "_target_": "Invertd",
                 "keys": "pred",
                 "transform": "@preprocessing",
-                "orig_keys": "image",
-                "meta_key_postfix": "meta_dict",
+                "orig_keys": "@image_key",
                 "nearest_interp": false,
                 "to_tensor": true
             },
@@ -169,8 +174,11 @@
             {
                 "_target_": "SaveImaged",
                 "keys": "pred",
-                "meta_keys": "pred_meta_dict",
-                "output_dir": "@output_dir"
+                "output_dir": "@output_dir",
+                "output_ext": "@output_ext",
+                "output_dtype": "@output_dtype",
+                "output_postfix": "@output_postfix",
+                "separate_folder": "@separate_folder"
             }
         ]
     },

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": "0.5.0",
+    "version": "0.5.1",
     "changelog": {
+        "0.5.1": "add option to validate at training start, and I/O param entries",
         "0.5.0": "enable finetune and early stop",
         "0.4.9": "fix orientation issue on clicks",
         "0.4.8": "Add infer transforms to manage clicks from viewer",
@@ -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": "1.3.0rc5",
     "pytorch_version": "1.13.1",
     "numpy_version": "1.22.2",
     "optional_packages_version": {

models/spleen_deepedit_annotation/configs/train.json

@@ -28,6 +28,7 @@
     "deepgrow_probability_train": 0.4,
     "deepgrow_probability_val": 1.0,
     "val_interval": 1,
+    "val_at_start": false,
     "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
     "network_def": {
         "_target_": "DynUNet",
@@ -324,6 +325,7 @@
                 "_target_": "ValidationHandler",
                 "validator": "@validate#evaluator",
                 "epoch_level": true,
+                "exec_at_start": "@val_at_start",
                 "interval": "@val_interval"
             },
             {