Update spleen bundle to support checkpoint loader

ci/unit_tests/test_spleen_ct_segmentation.py

@@ -44,6 +44,19 @@
 ]
 
 
+def test_order(test_name1, test_name2):
+    def get_order(name):
+        if "train" in name:
+            return 1
+        if "eval" in name:
+            return 2
+        if "infer" in name:
+            return 3
+        return 4
+
+    return get_order(test_name1) - get_order(test_name2)
+
+
 class TestSpleenCTSeg(unittest.TestCase):
     def setUp(self):
         self.dataset_dir = tempfile.mkdtemp()
@@ -102,4 +115,6 @@ def test_infer_config(self, override):
 
 
 if __name__ == "__main__":
-    unittest.main()
+    loader = unittest.TestLoader()
+    loader.sortTestMethodsUsing = test_order
+    unittest.main(testLoader=loader)

models/spleen_ct_segmentation/configs/inference.json

@@ -1,10 +1,16 @@
 {
     "imports": [
         "$import glob",
+        "$import numpy",
         "$import os"
     ],
     "bundle_root": ".",
+    "image_key": "image",
     "output_dir": "$@bundle_root + '/eval'",
+    "output_ext": ".nii.gz",
+    "output_dtype": "$numpy.float32",
+    "output_postfix": "trans",
+    "separate_folder": true,
     "dataset_dir": "/workspace/data/Task09_Spleen",
     "datalist": "$list(sorted(glob.glob(@dataset_dir + '/imagesTs/*.nii.gz')))",
     "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
@@ -35,20 +41,20 @@
         "transforms": [
             {
                 "_target_": "LoadImaged",
-                "keys": "image"
+                "keys": "@image_key"
             },
             {
                 "_target_": "EnsureChannelFirstd",
-                "keys": "image"
+                "keys": "@image_key"
             },
             {
                 "_target_": "Orientationd",
-                "keys": "image",
+                "keys": "@image_key",
                 "axcodes": "RAS"
             },
             {
                 "_target_": "Spacingd",
-                "keys": "image",
+                "keys": "@image_key",
                 "pixdim": [
                     1.5,
                     1.5,
@@ -58,7 +64,7 @@
             },
             {
                 "_target_": "ScaleIntensityRanged",
-                "keys": "image",
+                "keys": "@image_key",
                 "a_min": -57,
                 "a_max": 164,
                 "b_min": 0,
@@ -67,7 +73,7 @@
             },
             {
                 "_target_": "EnsureTyped",
-                "keys": "image"
+                "keys": "@image_key"
             }
         ]
     },
@@ -105,7 +111,7 @@
                 "_target_": "Invertd",
                 "keys": "pred",
                 "transform": "@preprocessing",
-                "orig_keys": "image",
+                "orig_keys": "@image_key",
                 "nearest_interp": false,
                 "to_tensor": true
             },
@@ -117,18 +123,15 @@
             {
                 "_target_": "SaveImaged",
                 "keys": "pred",
-                "output_dir": "@output_dir"
+                "output_dir": "@output_dir",
+                "output_ext": "@output_ext",
+                "output_dtype": "@output_dtype",
+                "output_postfix": "@output_postfix",
+                "separate_folder": "@separate_folder"
             }
         ]
     },
     "handlers": [
-        {
-            "_target_": "CheckpointLoader",
-            "load_path": "$@bundle_root + '/models/model.pt'",
-            "load_dict": {
-                "model": "@network"
-            }
-        },
         {
             "_target_": "StatsHandler",
             "iteration_log": false
@@ -144,8 +147,16 @@
         "val_handlers": "@handlers",
         "amp": true
     },
+    "checkpointloader": {
+        "_target_": "CheckpointLoader",
+        "load_path": "$@bundle_root + '/models/model.pt'",
+        "load_dict": {
+            "model": "@network"
+        }
+    },
     "initialize": [
-        "$monai.utils.set_determinism(seed=123)"
+        "$monai.utils.set_determinism(seed=123)",
+        "$@checkpointloader(@evaluator)"
     ],
     "run": [
         "$@evaluator.run()"

models/spleen_ct_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)"
+    ]
 }

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": "0.5.4",
+    "version": "0.5.5",
     "changelog": {
+        "0.5.5": "add checkpoint loader for infer",
         "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",