Enable redirection of all loggers by configuring a FileHandler within the bundle (#8142)

Fix Project-MONAI/model-zoo#658, part of #7513

### Description
Enable redirection of all loggers by configuring a FileHandler within
the bundle

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: YunLiu <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: KumoLiu

monai/bundle/scripts.py

@@ -1945,7 +1945,6 @@ def create_workflow(
 
     """
     _args = update_kwargs(args=args_file, workflow_name=workflow_name, config_file=config_file, **kwargs)
-    _log_input_summary(tag="run", args=_args)
     (workflow_name, config_file) = _pop_args(
         _args, workflow_name=ConfigWorkflow, config_file=None
     )  # the default workflow name is "ConfigWorkflow"
@@ -1969,7 +1968,7 @@ def create_workflow(
         workflow_ = workflow_class(**_args)
 
     workflow_.initialize()
-
+    _log_input_summary(tag="run", args=_args)
     return workflow_
 
 

monai/bundle/workflows.py

@@ -316,8 +316,8 @@ def __init__(
                 else:
                     raise FileNotFoundError(f"Cannot find the logging config file: {logging_file}.")
             else:
-                logger.info(f"Setting logging properties based on config: {logging_file}.")
                 fileConfig(str(logging_file), disable_existing_loggers=False)
+                logger.info(f"Setting logging properties based on config: {logging_file}.")
 
         self.parser = ConfigParser()
         self.parser.read_config(f=config_file)

monai/handlers/stats_handler.py

@@ -74,7 +74,7 @@ def __init__(
         output_transform: Callable = lambda x: x[0],
         global_epoch_transform: Callable = lambda x: x,
         state_attributes: Sequence[str] | None = None,
-        name: str | None = "StatsHandler",
+        name: str | None = "monai.handlers.StatsHandler",
         tag_name: str = DEFAULT_TAG,
         key_var_format: str = DEFAULT_KEY_VAL_FORMAT,
     ) -> None:

monai/networks/trt_compiler.py

@@ -115,7 +115,7 @@ def __init__(self, plan_path, logger=None):
           logger: optional logger object
         """
         self.plan_path = plan_path
-        self.logger = logger or get_logger("trt_compile")
+        self.logger = logger or get_logger("monai.networks.trt_compiler")
         self.logger.info(f"Loading TensorRT engine: {self.plan_path}")
         self.engine = engine_from_bytes(bytes_from_path(self.plan_path))
         self.tensors = OrderedDict()
@@ -288,7 +288,7 @@ def __init__(
         self.fallback = fallback
         self.disabled = False
 
-        self.logger = logger or get_logger("trt_compile")
+        self.logger = logger or get_logger("monai.networks.trt_compiler")
 
         # Normally we read input_names from forward() but can be overridden
         if input_names is None:
@@ -563,7 +563,7 @@ def find_sub(parent, submodule):
         else:
             wrap(model, base_path)
     else:
-        logger = logger or get_logger("trt_compile")
+        logger = logger or get_logger("monai.networks.trt_compiler")
         logger.warning("TensorRT and/or polygraphy packages are not available! trt_compile() has no effect.")
 
     return model

monai/utils/misc.py

@@ -887,7 +887,7 @@ def run_cmd(cmd_list: list[str], **kwargs: Any) -> subprocess.CompletedProcess:
     if kwargs.pop("run_cmd_verbose", False):
         import monai
 
-        monai.apps.utils.get_logger("run_cmd").info(f"{cmd_list}")  # type: ignore[attr-defined]
+        monai.apps.utils.get_logger("monai.utils.run_cmd").info(f"{cmd_list}")  # type: ignore[attr-defined]
     try:
         return subprocess.run(cmd_list, **kwargs)
     except subprocess.CalledProcessError as e: