Merge branch 'dev' into swin-unetr-extended

Author: KumoLiu

monai/bundle/reference_resolver.py

@@ -192,6 +192,16 @@ def get_resolved_content(self, id: str, **kwargs: Any) -> ConfigExpression | str
         """
         return self._resolve_one_item(id=id, **kwargs)
 
+    def remove_resolved_content(self, id: str) -> Any | None:
+        """
+        Remove the resolved ``ConfigItem`` by id.
+
+        Args:
+            id: id name of the expected item.
+
+        """
+        return self.resolved_content.pop(id) if id in self.resolved_content else None
+
     @classmethod
     def normalize_id(cls, id: str | int) -> str:
         """

monai/bundle/workflows.py

@@ -394,8 +394,23 @@ def check_properties(self) -> list[str] | None:
             ret.extend(wrong_props)
         return ret
 
-    def _run_expr(self, id: str, **kwargs: dict) -> Any:
-        return self.parser.get_parsed_content(id, **kwargs) if id in self.parser else None
+    def _run_expr(self, id: str, **kwargs: dict) -> list[Any]:
+        """
+        Evaluate the expression or expression list given by `id`. The resolved values from the evaluations are not stored,
+        allowing this to be evaluated repeatedly (eg. in streaming applications) without restarting the hosting process.
+        """
+        ret = []
+        if id in self.parser:
+            # suppose all the expressions are in a list, run and reset the expressions
+            if isinstance(self.parser[id], list):
+                for i in range(len(self.parser[id])):
+                    sub_id = f"{id}{ID_SEP_KEY}{i}"
+                    ret.append(self.parser.get_parsed_content(sub_id, **kwargs))
+                    self.parser.ref_resolver.remove_resolved_content(sub_id)
+            else:
+                ret.append(self.parser.get_parsed_content(id, **kwargs))
+                self.parser.ref_resolver.remove_resolved_content(id)
+        return ret
 
     def _get_prop_id(self, name: str, property: dict) -> Any:
         prop_id = property[BundlePropertyConfig.ID]

tests/test_bundle_workflow.py

@@ -26,7 +26,7 @@
 from monai.data import Dataset
 from monai.inferers import SimpleInferer, SlidingWindowInferer
 from monai.networks.nets import UNet
-from monai.transforms import Compose, LoadImage
+from monai.transforms import Compose, LoadImage, LoadImaged, SaveImaged
 from tests.nonconfig_workflow import NonConfigWorkflow
 
 TEST_CASE_1 = [os.path.join(os.path.dirname(__file__), "testing_data", "inference.json")]
@@ -35,6 +35,8 @@
 
 TEST_CASE_3 = [os.path.join(os.path.dirname(__file__), "testing_data", "config_fl_train.json")]
 
+TEST_CASE_4 = [os.path.join(os.path.dirname(__file__), "testing_data", "responsive_inference.json")]
+
 TEST_CASE_NON_CONFIG_WRONG_LOG = [None, "logging.conf", "Cannot find the logging config file: logging.conf."]
 
 
@@ -45,7 +47,9 @@ def setUp(self):
         self.expected_shape = (128, 128, 128)
         test_image = np.random.rand(*self.expected_shape)
         self.filename = os.path.join(self.data_dir, "image.nii")
+        self.filename1 = os.path.join(self.data_dir, "image1.nii")
         nib.save(nib.Nifti1Image(test_image, np.eye(4)), self.filename)
+        nib.save(nib.Nifti1Image(test_image, np.eye(4)), self.filename1)
 
     def tearDown(self):
         shutil.rmtree(self.data_dir)
@@ -115,6 +119,35 @@ def test_inference_config(self, config_file):
         self._test_inferer(inferer)
         self.assertEqual(inferer.workflow_type, None)
 
+    @parameterized.expand([TEST_CASE_4])
+    def test_responsive_inference_config(self, config_file):
+        input_loader = LoadImaged(keys="image")
+        output_saver = SaveImaged(keys="pred", output_dir=self.data_dir, output_postfix="seg")
+
+        # test standard MONAI model-zoo config workflow
+        inferer = ConfigWorkflow(
+            workflow_type="infer",
+            config_file=config_file,
+            logging_file=os.path.join(os.path.dirname(__file__), "testing_data", "logging.conf"),
+        )
+        # FIXME: temp add the property for test, we should add it to some formal realtime infer properties
+        inferer.add_property(name="dataflow", required=True, config_id="dataflow")
+
+        inferer.initialize()
+        inferer.dataflow.update(input_loader({"image": self.filename}))
+        inferer.run()
+        output_saver(inferer.dataflow)
+        self.assertTrue(os.path.exists(os.path.join(self.data_dir, "image", "image_seg.nii.gz")))
+
+        # bundle is instantiated and idle, just change the input for next inference
+        inferer.dataflow.clear()
+        inferer.dataflow.update(input_loader({"image": self.filename1}))
+        inferer.run()
+        output_saver(inferer.dataflow)
+        self.assertTrue(os.path.exists(os.path.join(self.data_dir, "image1", "image1_seg.nii.gz")))
+
+        inferer.finalize()
+
     @parameterized.expand([TEST_CASE_3])
     def test_train_config(self, config_file):
         # test standard MONAI model-zoo config workflow

tests/test_module_list.py

@@ -58,13 +58,17 @@ def test_transform_api(self):
                 continue
             with self.subTest(n=n):
                 basename = n[:-1]  # Transformd basename is Transform
+
+                # remove aliases to check, do this before the assert below so that a failed assert does skip this
+                for postfix in ("D", "d", "Dict"):
+                    remained.remove(f"{basename}{postfix}")
+
                 for docname in (f"{basename}", f"{basename}d"):
                     if docname in to_exclude_docs:
                         continue
                     if (contents is not None) and f"`{docname}`" not in f"{contents}":
                         self.assertTrue(False, f"please add `{docname}` to docs/source/transforms.rst")
-                for postfix in ("D", "d", "Dict"):
-                    remained.remove(f"{basename}{postfix}")
+
         self.assertFalse(remained)
 
 

tests/testing_data/responsive_inference.json

@@ -0,0 +1,101 @@
+{
+    "imports": [
+        "$from collections import defaultdict"
+    ],
+    "bundle_root": "will override",
+    "device": "$torch.device('cpu')",
+    "network_def": {
+        "_target_": "UNet",
+        "spatial_dims": 3,
+        "in_channels": 1,
+        "out_channels": 2,
+        "channels": [
+            2,
+            2,
+            4,
+            8,
+            4
+        ],
+        "strides": [
+            2,
+            2,
+            2,
+            2
+        ],
+        "num_res_units": 2,
+        "norm": "batch"
+    },
+    "network": "$@network_def.to(@device)",
+    "dataflow": "$defaultdict()",
+    "preprocessing": {
+        "_target_": "Compose",
+        "transforms": [
+            {
+                "_target_": "EnsureChannelFirstd",
+                "keys": "image"
+            },
+            {
+                "_target_": "ScaleIntensityd",
+                "keys": "image"
+            },
+            {
+                "_target_": "RandRotated",
+                "_disabled_": true,
+                "keys": "image"
+            }
+        ]
+    },
+    "dataset": {
+        "_target_": "Dataset",
+        "data": [
+            "@dataflow"
+        ],
+        "transform": "@preprocessing"
+    },
+    "dataloader": {
+        "_target_": "DataLoader",
+        "dataset": "@dataset",
+        "batch_size": 1,
+        "shuffle": false,
+        "num_workers": 0
+    },
+    "inferer": {
+        "_target_": "SlidingWindowInferer",
+        "roi_size": [
+            64,
+            64,
+            32
+        ],
+        "sw_batch_size": 4,
+        "overlap": 0.25
+    },
+    "postprocessing": {
+        "_target_": "Compose",
+        "transforms": [
+            {
+                "_target_": "Activationsd",
+                "keys": "pred",
+                "softmax": true
+            },
+            {
+                "_target_": "AsDiscreted",
+                "keys": "pred",
+                "argmax": true
+            }
+        ]
+    },
+    "evaluator": {
+        "_target_": "SupervisedEvaluator",
+        "device": "@device",
+        "val_data_loader": "@dataloader",
+        "network": "@network",
+        "inferer": "@inferer",
+        "postprocessing": "@postprocessing",
+        "amp": false,
+        "epoch_length": 1
+    },
+    "run": [
+        "[email protected]()",
+        "[email protected](@evaluator.state.output[0])"
+    ]
+}