[DLMED] update patterns

Nic-Ma · Nic-Ma · commit f9cb68aa9e0e · 2022-03-10T23:20:25.000+08:00
Signed-off-by: Nic Ma &lt;nma@nvidia.com&gt;
diff --git a/monai/bundle/config_parser.py b/monai/bundle/config_parser.py
@@ -38,19 +38,17 @@ class ConfigParser:
         config = {
             "my_dims": 2,
             "dims_1": "$@my_dims + 1",
-            "my_xform": {"<name>": "LoadImage"},
-            "my_net": {"<name>": "BasicUNet",
-                       "<args>": {"spatial_dims": "@dims_1", "in_channels": 1, "out_channels": 4}},
-            "trainer": {"<name>": "SupervisedTrainer",
-                        "<args>": {"network": "@my_net", "preprocessing": "@my_xform"}}
+            "my_xform": {"_name_": "LoadImage"},
+            "my_net": {"_name_": "BasicUNet", "spatial_dims": "@dims_1", "in_channels": 1, "out_channels": 4},
+            "trainer": {"_name_": "SupervisedTrainer", "network": "@my_net", "preprocessing": "@my_xform"}
         }
         # in the example $@my_dims + 1 is an expression, which adds 1 to the value of @my_dims
         parser = ConfigParser(config)
 
         # get/set configuration content, the set method should happen before calling parse()
-        print(parser["my_net"]["<args>"]["in_channels"])  # original input channels 1
-        parser["my_net"]["<args>"]["in_channels"] = 4  # change input channels to 4
-        print(parser["my_net"]["<args>"]["in_channels"])
+        print(parser["my_net"]["in_channels"])  # original input channels 1
+        parser["my_net"]["in_channels"] = 4  # change input channels to 4
+        print(parser["my_net"]["in_channels"])
 
         # instantiate the network component
         parser.parse(True)
@@ -107,7 +105,7 @@ def __getitem__(self, id: Union[str, int]):
             id: id of the ``ConfigItem``, ``"#"`` in id are interpreted as special characters to
                 go one level further into the nested structures.
                 Use digits indexing from "0" for list or other strings for dict.
-                For example: ``"xform#5"``, ``"net#<args>#channels"``. ``""`` indicates the entire ``self.config``.
+                For example: ``"xform#5"``, ``"net#channels"``. ``""`` indicates the entire ``self.config``.
 
         """
         if id == "":
@@ -129,7 +127,7 @@ def __setitem__(self, id: Union[str, int], config: Any):
             id: id of the ``ConfigItem``, ``"#"`` in id are interpreted as special characters to
                 go one level further into the nested structures.
                 Use digits indexing from "0" for list or other strings for dict.
-                For example: ``"xform#5"``, ``"net#<args>#channels"``. ``""`` indicates the entire ``self.config``.
+                For example: ``"xform#5"``, ``"net#channels"``. ``""`` indicates the entire ``self.config``.
             config: config to set at location ``id``.
 
         """
@@ -171,7 +169,7 @@ def _do_resolve(self, config: Any):
         """
         Recursively resolve the config content to replace the macro tokens with target content.
         The macro tokens start with "%", can be from another structured file, like:
-        ``{"net": "%default_net"}``, ``{"net": "%/data/config.json#net#<args>"}``.
+        ``{"net": "%default_net"}``, ``{"net": "%/data/config.json#net"}``.
 
         Args:
             config: input config file to resolve.
@@ -190,7 +188,7 @@ def resolve_macro(self):
         """
         Recursively resolve `self.config` to replace the macro tokens with target content.
         The macro tokens are marked as starting with "%", can be from another structured file, like:
-        ``"%default_net"``, ``"%/data/config.json#net#<args>"``.
+        ``"%default_net"``, ``"%/data/config.json#net"``.
 
         """
         self.set(self._do_resolve(config=deepcopy(self.get())))
@@ -204,7 +202,7 @@ def _do_parse(self, config, id: str = ""):
             id: id of the ``ConfigItem``, ``"#"`` in id are interpreted as special characters to
                 go one level further into the nested structures.
                 Use digits indexing from "0" for list or other strings for dict.
-                For example: ``"xform#5"``, ``"net#<args>#channels"``. ``""`` indicates the entire ``self.config``.
+                For example: ``"xform#5"``, ``"net#channels"``. ``""`` indicates the entire ``self.config``.
 
         """
         if isinstance(config, (dict, list)):
@@ -248,7 +246,7 @@ def get_parsed_content(self, id: str = "", **kwargs):
             id: id of the ``ConfigItem``, ``"#"`` in id are interpreted as special characters to
                 go one level further into the nested structures.
                 Use digits indexing from "0" for list or other strings for dict.
-                For example: ``"xform#5"``, ``"net#<args>#channels"``. ``""`` indicates the entire ``self.config``.
+                For example: ``"xform#5"``, ``"net#channels"``. ``""`` indicates the entire ``self.config``.
             kwargs: additional keyword arguments to be passed to ``_resolve_one_item``.
                 Currently support ``reset`` (for parse), ``instantiate`` and ``eval_expr``. All defaulting to True.
 
diff --git a/monai/bundle/config_reader.py b/monai/bundle/config_reader.py
@@ -38,7 +38,7 @@ class ConfigReader:
     suffixes = ("json", "yaml", "yml")
     suffix_match = rf"\.({'|'.join(suffixes)})"
     path_match = rf"(.*{suffix_match}$)"
-    meta_key = "<meta>"  # field key to save metadata
+    meta_key = "_meta_"  # field key to save metadata
     sep = "#"  # separator for file path and the id of content in the file
 
     def __init__(self):
@@ -122,7 +122,7 @@ def split_path_id(cls, src: str) -> Tuple[str, str]:
     def read_meta(self, f: Union[PathLike, Sequence[PathLike], Dict], **kwargs):
         """
         Read the metadata from specified JSON or YAML file.
-        The metadata as a dictionary will be stored at ``self.config["<meta>"]``.
+        The metadata as a dictionary will be stored at ``self.config["_meta_"]``.
 
         Args:
             f: filepath of the metadata file, the content must be a dictionary,
diff --git a/monai/bundle/reference_resolver.py b/monai/bundle/reference_resolver.py
@@ -47,8 +47,8 @@ class ReferenceResolver:
     _vars = "__local_refs"
     sep = "#"  # separator for key indexing
     ref = "@"  # reference prefix
-    # match a reference string, e.g. "@id#key", "@id#key#0", "@<test>#<args>#key"
-    id_matcher = re.compile(rf"{ref}(?:(?:<\w*>)|(?:\w*))(?:(?:{sep}<\w*>)|(?:{sep}\w*))*")
+    # match a reference string, e.g. "@id#key", "@id#key#0", "@_name_#key"
+    id_matcher = re.compile(rf"{ref}(?:\w*)(?:{sep}\w*)*")
 
     def __init__(self, items: Optional[Sequence[ConfigItem]] = None):
         # save the items in a dictionary with the `ConfigItem.id` as key
diff --git a/monai/bundle/scripts.py b/monai/bundle/scripts.py
@@ -34,13 +34,13 @@ def run(
         python -m monai.bundle run --meta_file <meta path> --config_file <config path> --target_id trainer
 
         # Override config values at runtime by specifying the component id and its new value:
-        python -m monai.bundle run --"net#<args>#input_chns" 1 ...
+        python -m monai.bundle run --net#input_chns 1 ...
 
         # Override config values with another config file `/path/to/another.json`:
-        python -m monai.bundle run --"net#<args>" "%/path/to/another.json" ...
+        python -m monai.bundle run --net %/path/to/another.json ...
 
         # Override config values with part content of another config file:
-        python -m monai.bundle run --"net#<args>" "%/data/other.json#net_arg" ...
+        python -m monai.bundle run --net %/data/other.json#net_arg ...
 
         # Set default args of `run` in a JSON / YAML file, help to record and simplify the command line.
         # Other args still can override the default args at runtime:
@@ -55,7 +55,7 @@ def run(
         args_file: a JSON or YAML file to provide default values for `meta_file`, `config_file`,
             `target_id` and override pairs. so that the command line inputs can be simplified.
         override: id-value pairs to override or add the corresponding config content.
-            e.g. ``--"net#<args>#input_chns" 42``.
+            e.g. ``--net#input_chns 42``.
 
     """
     k_v = zip(["meta_file", "config_file", "target_id"], [meta_file, config_file, target_id])
diff --git a/tests/test_bundle_run.py b/tests/test_bundle_run.py
@@ -60,20 +60,20 @@ def test_shape(self, config_file, expected_shape):
             saver = LoadImage(image_only=True)
 
             if sys.platform == "win32":
-                override = "--network $@network_def.to(@device) --dataset#<name> Dataset"
+                override = "--network $@network_def.to(@device) --dataset#_name_ Dataset"
             else:
-                override = f"--network %{overridefile1}#move_net --dataset#<name> %{overridefile2}"
+                override = f"--network %{overridefile1}#move_net --dataset#_name_ %{overridefile2}"
             # test with `monai.bundle` as CLI entry directly
             cmd = "-m monai.bundle run --target_id evaluator"
-            cmd += f" --postprocessing#<args>#transforms#2#<args>#output_postfix seg {override}"
+            cmd += f" --postprocessing#transforms#2#output_postfix seg {override}"
             la = [f"{sys.executable}"] + cmd.split(" ") + ["--meta_file", meta_file] + ["--config_file", config_file]
             ret = subprocess.check_call(la + ["--args_file", def_args_file])
             self.assertEqual(ret, 0)
             self.assertTupleEqual(saver(os.path.join(tempdir, "image", "image_seg.nii.gz")).shape, expected_shape)
 
             # here test the script with `google fire` tool as CLI
             cmd = "-m fire monai.bundle.scripts run --target_id evaluator"
-            cmd += f" --evaluator#<args>#amp False {override}"
+            cmd += f" --evaluator#amp False {override}"
             la = [f"{sys.executable}"] + cmd.split(" ") + ["--meta_file", meta_file] + ["--config_file", config_file]
             ret = subprocess.check_call(la)
             self.assertEqual(ret, 0)
diff --git a/tests/test_config_item.py b/tests/test_config_item.py
@@ -34,10 +34,7 @@
 # test `_disabled_` with string
 TEST_CASE_5 = [{"_name_": "LoadImaged", "_disabled_": "true", "keys": ["image"]}, dict]
 # test non-monai modules and excludes
-TEST_CASE_6 = [
-    {"_path_": "torch.optim.Adam", "params": torch.nn.PReLU().parameters(), "lr": 1e-4},
-    torch.optim.Adam,
-]
+TEST_CASE_6 = [{"_path_": "torch.optim.Adam", "params": torch.nn.PReLU().parameters(), "lr": 1e-4}, torch.optim.Adam]
 TEST_CASE_7 = [{"_name_": "decollate_batch", "detach": True, "pad": True}, partial]
 # test args contains "name" field
 TEST_CASE_8 = [
diff --git a/tests/test_config_parser.py b/tests/test_config_parser.py
@@ -25,24 +25,21 @@
 TEST_CASE_1 = [
     {
         "transform": {
-            "<name>": "Compose",
-            "<args>": {
-                "transforms": [
-                    {"<name>": "LoadImaged", "<args>": {"keys": "image"}},
-                    {
-                        "<name>": "RandTorchVisiond",
-                        "<args>": {"keys": "image", "name": "ColorJitter", "brightness": 0.25},
-                    },
-                ]
-            },
+            "_name_": "Compose",
+            "transforms": [
+                {"_name_": "LoadImaged", "keys": "image"},
+                {"_name_": "RandTorchVisiond", "keys": "image", "name": "ColorJitter", "brightness": 0.25},
+            ],
         },
-        "dataset": {"<name>": "Dataset", "<args>": {"data": [1, 2], "transform": "@transform"}},
+        "dataset": {"_name_": "Dataset", "data": [1, 2], "transform": "@transform"},
         "dataloader": {
-            "<name>": "DataLoader",
-            "<args>": {"dataset": "@dataset", "batch_size": 2, "collate_fn": "monai.data.list_data_collate"},
+            "_name_": "DataLoader",
+            "dataset": "@dataset",
+            "batch_size": 2,
+            "collate_fn": "monai.data.list_data_collate",
         },
     },
-    ["transform", "transform#<args>#transforms#0", "transform#<args>#transforms#1", "dataset", "dataloader"],
+    ["transform", "transform#transforms#0", "transform#transforms#1", "dataset", "dataloader"],
     [Compose, LoadImaged, RandTorchVisiond, Dataset, DataLoader],
 ]
 
@@ -67,9 +64,9 @@ def __call__(self, a, b):
         "cls_func": "$TestClass.cls_compute",
         "lambda_static_func": "$lambda x, y: TestClass.compute(x, y)",
         "lambda_cls_func": "$lambda x, y: TestClass.cls_compute(x, y)",
-        "compute": {"<path>": "tests.test_config_parser.TestClass.compute", "<args>": {"func": "@basic_func"}},
-        "cls_compute": {"<path>": "tests.test_config_parser.TestClass.cls_compute", "<args>": {"func": "@basic_func"}},
-        "call_compute": {"<path>": "tests.test_config_parser.TestClass"},
+        "compute": {"_path_": "tests.test_config_parser.TestClass.compute", "func": "@basic_func"},
+        "cls_compute": {"_path_": "tests.test_config_parser.TestClass.cls_compute", "func": "@basic_func"},
+        "call_compute": {"_path_": "tests.test_config_parser.TestClass"},
         "error_func": "$TestClass.__call__",
         "<test>": "$lambda x, y: x + y",
     }
@@ -78,17 +75,17 @@ def __call__(self, a, b):
 
 class TestConfigComponent(unittest.TestCase):
     def test_config_content(self):
-        test_config = {"preprocessing": [{"<name>": "LoadImage"}], "dataset": {"<name>": "Dataset"}}
+        test_config = {"preprocessing": [{"_name_": "LoadImage"}], "dataset": {"_name_": "Dataset"}}
         parser = ConfigParser(config=test_config)
         # test `get`, `set`, `__getitem__`, `__setitem__`
         self.assertEqual(str(parser.get()), str(test_config))
         parser.set(config=test_config)
         self.assertListEqual(parser["preprocessing"], test_config["preprocessing"])
-        parser["dataset"] = {"<name>": "CacheDataset"}
-        self.assertEqual(parser["dataset"]["<name>"], "CacheDataset")
+        parser["dataset"] = {"_name_": "CacheDataset"}
+        self.assertEqual(parser["dataset"]["_name_"], "CacheDataset")
         # test nested ids
-        parser["dataset#<name>"] = "Dataset"
-        self.assertEqual(parser["dataset#<name>"], "Dataset")
+        parser["dataset#_name_"] = "Dataset"
+        self.assertEqual(parser["dataset#_name_"], "Dataset")
         # test int id
         parser.set(["test1", "test2", "test3"])
         parser[1] = "test4"
@@ -99,11 +96,11 @@ def test_config_content(self):
     def test_parse(self, config, expected_ids, output_types):
         parser = ConfigParser(config=config, globals={"monai": "monai"})
         # test lazy instantiation with original config content
-        parser["transform"]["<args>"]["transforms"][0]["<args>"]["keys"] = "label1"
-        self.assertEqual(parser.get_parsed_content(id="transform#<args>#transforms#0").keys[0], "label1")
+        parser["transform"]["transforms"][0]["keys"] = "label1"
+        self.assertEqual(parser.get_parsed_content(id="transform#transforms#0").keys[0], "label1")
         # test nested id
-        parser["transform#<args>#transforms#0#<args>#keys"] = "label2"
-        self.assertEqual(parser.get_parsed_content(id="transform#<args>#transforms#0").keys[0], "label2")
+        parser["transform#transforms#0#keys"] = "label2"
+        self.assertEqual(parser.get_parsed_content(id="transform#transforms#0").keys[0], "label2")
         for id, cls in zip(expected_ids, output_types):
             self.assertTrue(isinstance(parser.get_parsed_content(id), cls))
         # test root content
diff --git a/tests/test_reference_resolver.py b/tests/test_reference_resolver.py
@@ -27,11 +27,10 @@
 TEST_CASE_1 = [
     {
         # all the recursively parsed config items
-        "transform#1": {"<name>": "LoadImaged", "<args>": {"keys": ["image"]}},
-        "transform#1#<name>": "LoadImaged",
-        "transform#1#<args>": {"keys": ["image"]},
-        "transform#1#<args>#keys": ["image"],
-        "transform#1#<args>#keys#0": "image",
+        "transform#1": {"_name_": "LoadImaged", "keys": ["image"]},
+        "transform#1#_name_": "LoadImaged",
+        "transform#1#keys": ["image"],
+        "transform#1#keys#0": "image",
     },
     "transform#1",
     LoadImaged,
@@ -40,20 +39,15 @@
 TEST_CASE_2 = [
     {
         # some the recursively parsed config items
-        "dataloader": {
-            "<name>": "DataLoader",
-            "<args>": {"dataset": "@dataset", "collate_fn": "$monai.data.list_data_collate"},
-        },
-        "dataset": {"<name>": "Dataset", "<args>": {"data": [1, 2]}},
-        "dataloader#<name>": "DataLoader",
-        "dataloader#<args>": {"dataset": "@dataset", "collate_fn": "$monai.data.list_data_collate"},
-        "dataloader#<args>#dataset": "@dataset",
-        "dataloader#<args>#collate_fn": "$monai.data.list_data_collate",
-        "dataset#<name>": "Dataset",
-        "dataset#<args>": {"data": [1, 2]},
-        "dataset#<args>#data": [1, 2],
-        "dataset#<args>#data#0": 1,
-        "dataset#<args>#data#1": 2,
+        "dataloader": {"_name_": "DataLoader", "dataset": "@dataset", "collate_fn": "$monai.data.list_data_collate"},
+        "dataset": {"_name_": "Dataset", "data": [1, 2]},
+        "dataloader#_name_": "DataLoader",
+        "dataloader#dataset": "@dataset",
+        "dataloader#collate_fn": "$monai.data.list_data_collate",
+        "dataset#_name_": "Dataset",
+        "dataset#data": [1, 2],
+        "dataset#data#0": 1,
+        "dataset#data#1": 2,
     },
     "dataloader",
     DataLoader,
@@ -62,15 +56,11 @@
 TEST_CASE_3 = [
     {
         # all the recursively parsed config items
-        "transform#1": {
-            "<name>": "RandTorchVisiond",
-            "<args>": {"keys": "image", "name": "ColorJitter", "brightness": 0.25},
-        },
-        "transform#1#<name>": "RandTorchVisiond",
-        "transform#1#<args>": {"keys": "image", "name": "ColorJitter", "brightness": 0.25},
-        "transform#1#<args>#keys": "image",
-        "transform#1#<args>#name": "ColorJitter",
-        "transform#1#<args>#brightness": 0.25,
+        "transform#1": {"_name_": "RandTorchVisiond", "keys": "image", "name": "ColorJitter", "brightness": 0.25},
+        "transform#1#_name_": "RandTorchVisiond",
+        "transform#1#keys": "image",
+        "transform#1#name": "ColorJitter",
+        "transform#1#brightness": 0.25,
     },
     "transform#1",
     RandTorchVisiond,
@@ -97,7 +87,7 @@ def test_resolve(self, configs, expected_id, output_type):
         # test lazy instantiation
         item = resolver.get_item(expected_id, resolve=True)
         config = item.get_config()
-        config["<disabled>"] = False
+        config["_disabled_"] = False
         item.update_config(config=config)
         if isinstance(item, ConfigComponent):
             result = item.instantiate()
diff --git a/tests/testing_data/inference.json b/tests/testing_data/inference.json
diff --git a/tests/testing_data/inference.yaml b/tests/testing_data/inference.yaml
