From 05e4d375aa96073c916734a023b17b6bf1626261 Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Thu, 5 Sep 2024 17:31:03 +0800
Subject: [PATCH 01/16] add packaging

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 monai/data/image_reader.py       | 2 +-
 monai/handlers/mlflow_handler.py | 2 ++
 setup.cfg                        | 1 +
 tests/min_tests.py               | 1 +
 tests/test_gdsdataset.py         | 7 ++++---
 5 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/monai/data/image_reader.py b/monai/data/image_reader.py
index aab1e03898..821cab0f43 100644
--- a/monai/data/image_reader.py
+++ b/monai/data/image_reader.py
@@ -34,7 +34,7 @@
 )
 from monai.utils import MetaKeys, SpaceKeys, TraceKeys, ensure_tuple, optional_import, require_pkg
 
-# workaround for https://github.com/Project-MONAI/MONAI/issues/8061
+# workaround for https://github.com/Project-MONAI/MONAI/issues/8060
 warnings.filterwarnings("ignore", category=DeprecationWarning, module="nptyping")
 
 if TYPE_CHECKING:
diff --git a/monai/handlers/mlflow_handler.py b/monai/handlers/mlflow_handler.py
index 6d19579d9e..f3865e45ae 100644
--- a/monai/handlers/mlflow_handler.py
+++ b/monai/handlers/mlflow_handler.py
@@ -25,6 +25,8 @@
 from monai.config import IgniteInfo
 from monai.utils import CommonKeys, ensure_tuple, min_version, optional_import
 
+# workaround for https://github.com/Project-MONAI/MONAI/issues/8061
+warnings.filterwarnings("ignore", category=DeprecationWarning, module="mlflow")
 Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
 mlflow, _ = optional_import("mlflow", descriptor="Please install mlflow before using MLFlowHandler.")
 mlflow.entities, _ = optional_import(
diff --git a/setup.cfg b/setup.cfg
index c97118d43a..694dc969d9 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -40,6 +40,7 @@ python_requires = >= 3.9
 setup_requires =
     torch
     ninja
+    packaging
 install_requires =
     torch>=1.9
     numpy>=1.24,<2.0
diff --git a/tests/min_tests.py b/tests/min_tests.py
index 632355b5c6..642273acd7 100644
--- a/tests/min_tests.py
+++ b/tests/min_tests.py
@@ -212,6 +212,7 @@ def run_testsuit():
         "test_ultrasound_confidence_map_transform",
         "test_vista3d_utils",
         "test_vista3d_transforms",
+        "test_matshow3d"
     ]
     assert sorted(exclude_cases) == sorted(set(exclude_cases)), f"Duplicated items in {exclude_cases}"
 
diff --git a/tests/test_gdsdataset.py b/tests/test_gdsdataset.py
index f0a419dcf5..5d2e2aa013 100644
--- a/tests/test_gdsdataset.py
+++ b/tests/test_gdsdataset.py
@@ -23,7 +23,7 @@
 from monai.data import GDSDataset, json_hashing
 from monai.transforms import Compose, Flip, Identity, LoadImaged, SimulateDelayd, Transform
 from monai.utils import optional_import
-from tests.utils import TEST_NDARRAYS, assert_allclose
+from tests.utils import TEST_NDARRAYS, assert_allclose, skip_if_no_cuda
 
 _, has_cp = optional_import("cupy")
 nib, has_nib = optional_import("nibabel")
@@ -70,9 +70,9 @@ def __call__(self, data):
         return data
 
 
+@skip_if_no_cuda
 @unittest.skipUnless(has_cp, "Requires CuPy library.")
-@unittest.skipUnless(has_nib, "Requires nibabel package.")
-@unittest.skipUnless(has_kvikio_numpy, "Requires scikit-image library.")
+@unittest.skipUnless(has_cp and has_kvikio_numpy, "Requires CuPy and kvikio library.")
 class TestDataset(unittest.TestCase):
 
     def test_cache(self):
@@ -131,6 +131,7 @@ def test_dtype(self):
                 self.assertEqual(ds[0].dtype, DTYPES[_dtype])
                 self.assertEqual(ds1[0].dtype, DTYPES[_dtype])
 
+    @unittest.skipUnless(has_nib, "Requires nibabel package.")
     @parameterized.expand([TEST_CASE_1, TEST_CASE_2, TEST_CASE_3])
     def test_shape(self, transform, expected_shape):
         test_image = nib.Nifti1Image(np.random.randint(0, 2, size=[128, 128, 128]).astype(float), np.eye(4))

From a05c5c04b2062b2be2d40ec7de48176c484ed8a4 Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Thu, 5 Sep 2024 17:37:18 +0800
Subject: [PATCH 02/16] add packaging in pyproject.toml

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 53ca608d20..c2ab92a43d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,6 +4,7 @@ requires = [
   "setuptools",
   "torch>=1.9",
   "ninja",
+  "packaging"
 ]
 
 [tool.black]

From 73f176747d51a320789282cda24e3c0410aa2f87 Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Thu, 5 Sep 2024 21:52:32 +0800
Subject: [PATCH 03/16] add warning filter

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 monai/__init__.py       | 12 +++++++++++-
 monai/networks/utils.py |  3 +++
 monai/utils/module.py   |  3 +++
 tests/min_tests.py      |  2 +-
 4 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/monai/__init__.py b/monai/__init__.py
index cb0ccd36f8..0897bf0f3a 100644
--- a/monai/__init__.py
+++ b/monai/__init__.py
@@ -13,9 +13,19 @@
 
 import os
 import sys
-
+import warnings
 from ._version import get_versions
 
+
+def custom_warning_handler(message, category, filename, lineno, file=None, line=None):
+    message1 = "`TorchScript` support for functional optimizers is deprecated and will be removed in a future PyTorch release. Consider using the `torch.compile` optimizer instead."
+    message2 = "`torch.library.impl_abstract` was renamed to `torch.library.register_fake`. Please use that instead; we will remove `torch.library.impl_abstract` in a future version of PyTorch."
+    if message1 or message2 in message:
+        return
+    warnings.showwarning(message, category, filename, lineno, file, line)
+
+
+warnings.showwarning = custom_warning_handler
 PY_REQUIRED_MAJOR = 3
 PY_REQUIRED_MINOR = 9
 
diff --git a/monai/networks/utils.py b/monai/networks/utils.py
index d0150b4e5b..fd32fe526e 100644
--- a/monai/networks/utils.py
+++ b/monai/networks/utils.py
@@ -37,6 +37,9 @@
 onnxreference, _ = optional_import("onnx.reference")
 onnxruntime, _ = optional_import("onnxruntime")
 polygraphy, polygraphy_imported = optional_import("polygraphy")
+
+# workaround for https://github.com/Project-MONAI/MONAI/issues/8060
+warnings.filterwarnings("ignore", category=DeprecationWarning, module="torch_tensorrt")
 torch_tensorrt, _ = optional_import("torch_tensorrt", "1.4.0")
 
 __all__ = [
diff --git a/monai/utils/module.py b/monai/utils/module.py
index 78087aef84..50eb25789f 100644
--- a/monai/utils/module.py
+++ b/monai/utils/module.py
@@ -399,6 +399,9 @@ def optional_import(
     else:
         actual_cmd = f"import {module}"
     try:
+        # workaround for https://github.com/Project-MONAI/MONAI/issues/8060
+        warnings.filterwarnings("ignore", module="pydantic")
+        warnings.filterwarnings("ignore", category=ResourceWarning)
         pkg = __import__(module)  # top level module
         the_module = import_module(module)
         if not allow_namespace_pkg:
diff --git a/tests/min_tests.py b/tests/min_tests.py
index 642273acd7..f39d3f9843 100644
--- a/tests/min_tests.py
+++ b/tests/min_tests.py
@@ -212,7 +212,7 @@ def run_testsuit():
         "test_ultrasound_confidence_map_transform",
         "test_vista3d_utils",
         "test_vista3d_transforms",
-        "test_matshow3d"
+        "test_matshow3d",
     ]
     assert sorted(exclude_cases) == sorted(set(exclude_cases)), f"Duplicated items in {exclude_cases}"
 

From 6e36ebeefa255b4330185a137e470331c9bd13a8 Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Thu, 5 Sep 2024 21:56:49 +0800
Subject: [PATCH 04/16] workaround for #8060

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 monai/handlers/mlflow_handler.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/monai/handlers/mlflow_handler.py b/monai/handlers/mlflow_handler.py
index f3865e45ae..eb93c5b49b 100644
--- a/monai/handlers/mlflow_handler.py
+++ b/monai/handlers/mlflow_handler.py
@@ -25,7 +25,7 @@
 from monai.config import IgniteInfo
 from monai.utils import CommonKeys, ensure_tuple, min_version, optional_import
 
-# workaround for https://github.com/Project-MONAI/MONAI/issues/8061
+# workaround for https://github.com/Project-MONAI/MONAI/issues/8060
 warnings.filterwarnings("ignore", category=DeprecationWarning, module="mlflow")
 Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
 mlflow, _ = optional_import("mlflow", descriptor="Please install mlflow before using MLFlowHandler.")

From f719f4cec5de3c73a456a77e015aced8ea2be4be Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Thu, 5 Sep 2024 22:25:07 +0800
Subject: [PATCH 05/16] minor fix

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 monai/__init__.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/monai/__init__.py b/monai/__init__.py
index 0897bf0f3a..2be56dfb6a 100644
--- a/monai/__init__.py
+++ b/monai/__init__.py
@@ -18,9 +18,10 @@
 
 
 def custom_warning_handler(message, category, filename, lineno, file=None, line=None):
-    message1 = "`TorchScript` support for functional optimizers is deprecated and will be removed in a future PyTorch release. Consider using the `torch.compile` optimizer instead."
-    message2 = "`torch.library.impl_abstract` was renamed to `torch.library.register_fake`. Please use that instead; we will remove `torch.library.impl_abstract` in a future version of PyTorch."
-    if message1 or message2 in message:
+    message1 = "`TorchScript` support for functional optimizers is deprecated and will be removed"
+    message2 = "`torch.library.impl_abstract` was renamed to `torch.library.register_fake`."
+
+    if message1 in str(message) or message2 in str(message):
         return
     warnings.showwarning(message, category, filename, lineno, file, line)
 

From 5cca0251c399050a26b1959f1f7f4b09a640c577 Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Thu, 5 Sep 2024 22:37:53 +0800
Subject: [PATCH 06/16] use filename instead of message

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 monai/__init__.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/monai/__init__.py b/monai/__init__.py
index 2be56dfb6a..be0be71c79 100644
--- a/monai/__init__.py
+++ b/monai/__init__.py
@@ -18,10 +18,9 @@
 
 
 def custom_warning_handler(message, category, filename, lineno, file=None, line=None):
-    message1 = "`TorchScript` support for functional optimizers is deprecated and will be removed"
-    message2 = "`torch.library.impl_abstract` was renamed to `torch.library.register_fake`."
-
-    if message1 in str(message) or message2 in str(message):
+    filename1 = "ignite/handlers/checkpoint.py"
+    filename2 = "modelopt/torch/quantization/tensor_quant.py"
+    if filename1 in filename or filename2 in filename:
         return
     warnings.showwarning(message, category, filename, lineno, file, line)
 

From 8ef5c0617d02605a2cc29d9c1122b7497a1bbc5f Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Thu, 5 Sep 2024 23:04:27 +0800
Subject: [PATCH 07/16] Update monai/__init__.py

Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 monai/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/monai/__init__.py b/monai/__init__.py
index be0be71c79..c2b28f4d78 100644
--- a/monai/__init__.py
+++ b/monai/__init__.py
@@ -17,12 +17,13 @@
 from ._version import get_versions
 
 
+old_showwarning = warnings.showwarning
 def custom_warning_handler(message, category, filename, lineno, file=None, line=None):
     filename1 = "ignite/handlers/checkpoint.py"
     filename2 = "modelopt/torch/quantization/tensor_quant.py"
     if filename1 in filename or filename2 in filename:
         return
-    warnings.showwarning(message, category, filename, lineno, file, line)
+    old_showwarning(message, category, filename, lineno, file, line)
 
 
 warnings.showwarning = custom_warning_handler

From 998af8fc327c500725c5ea55324ed697561135b5 Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Thu, 5 Sep 2024 23:23:05 +0800
Subject: [PATCH 08/16] fix format

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 monai/__init__.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/monai/__init__.py b/monai/__init__.py
index c2b28f4d78..efab9c52e6 100644
--- a/monai/__init__.py
+++ b/monai/__init__.py
@@ -18,6 +18,8 @@
 
 
 old_showwarning = warnings.showwarning
+
+
 def custom_warning_handler(message, category, filename, lineno, file=None, line=None):
     filename1 = "ignite/handlers/checkpoint.py"
     filename2 = "modelopt/torch/quantization/tensor_quant.py"

From 5577b85352e9e550d7a4860a669828015194e6bf Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Fri, 6 Sep 2024 12:49:53 +0800
Subject: [PATCH 09/16] add rest warning

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 monai/__init__.py          | 12 +++++++++---
 monai/data/image_reader.py |  3 ---
 monai/networks/utils.py    |  5 ++---
 monai/utils/module.py      |  9 ++++++---
 4 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/monai/__init__.py b/monai/__init__.py
index efab9c52e6..536c9b0047 100644
--- a/monai/__init__.py
+++ b/monai/__init__.py
@@ -21,13 +21,19 @@
 
 
 def custom_warning_handler(message, category, filename, lineno, file=None, line=None):
-    filename1 = "ignite/handlers/checkpoint.py"
-    filename2 = "modelopt/torch/quantization/tensor_quant.py"
-    if filename1 in filename or filename2 in filename:
+    ignore_files = [
+        "ignite/handlers/checkpoint",
+        "modelopt/torch/quantization/tensor_quant",
+        "nptyping/typing_",
+        "pydantic/_internal/_config",
+        "tempfile",
+    ]
+    if any(ignore in filename for ignore in ignore_files):
         return
     old_showwarning(message, category, filename, lineno, file, line)
 
 
+# workaround for https://github.com/Project-MONAI/MONAI/issues/8060
 warnings.showwarning = custom_warning_handler
 PY_REQUIRED_MAJOR = 3
 PY_REQUIRED_MINOR = 9
diff --git a/monai/data/image_reader.py b/monai/data/image_reader.py
index 821cab0f43..f5e199e2a3 100644
--- a/monai/data/image_reader.py
+++ b/monai/data/image_reader.py
@@ -34,9 +34,6 @@
 )
 from monai.utils import MetaKeys, SpaceKeys, TraceKeys, ensure_tuple, optional_import, require_pkg
 
-# workaround for https://github.com/Project-MONAI/MONAI/issues/8060
-warnings.filterwarnings("ignore", category=DeprecationWarning, module="nptyping")
-
 if TYPE_CHECKING:
     import itk
     import nibabel as nib
diff --git a/monai/networks/utils.py b/monai/networks/utils.py
index fd32fe526e..a7beba3ace 100644
--- a/monai/networks/utils.py
+++ b/monai/networks/utils.py
@@ -38,9 +38,8 @@
 onnxruntime, _ = optional_import("onnxruntime")
 polygraphy, polygraphy_imported = optional_import("polygraphy")
 
-# workaround for https://github.com/Project-MONAI/MONAI/issues/8060
-warnings.filterwarnings("ignore", category=DeprecationWarning, module="torch_tensorrt")
-torch_tensorrt, _ = optional_import("torch_tensorrt", "1.4.0")
+torch_tensorrt, _ = optional_import("torch_tensorrt", "1.4.0", reset_warning=True)
+
 
 __all__ = [
     "one_hot",
diff --git a/monai/utils/module.py b/monai/utils/module.py
index 50eb25789f..13a18cb91f 100644
--- a/monai/utils/module.py
+++ b/monai/utils/module.py
@@ -345,6 +345,7 @@ def optional_import(
     version_args: Any = None,
     allow_namespace_pkg: bool = False,
     as_type: str = "default",
+    reset_warning: bool = False,
 ) -> tuple[Any, bool]:
     """
     Imports an optional module specified by `module` string.
@@ -363,6 +364,7 @@ def optional_import(
             a base class, or a decorator, the exceptions should raise accordingly. The current supported values
             are "default" (call once to raise), "decorator" (call the constructor and the second call to raise),
             and anything else will return a lazy class that can be used as a base class (call the constructor to raise).
+        reset_warning: whether to reset the warnings.showwarning to the original function during the import.
 
     Returns:
         The imported module and a boolean flag indicating whether the import is successful.
@@ -399,10 +401,11 @@ def optional_import(
     else:
         actual_cmd = f"import {module}"
     try:
-        # workaround for https://github.com/Project-MONAI/MONAI/issues/8060
-        warnings.filterwarnings("ignore", module="pydantic")
-        warnings.filterwarnings("ignore", category=ResourceWarning)
+        if reset_warning:
+            old_showwarning = warnings.showwarning
         pkg = __import__(module)  # top level module
+        if reset_warning:
+            warnings.showwarning = old_showwarning
         the_module = import_module(module)
         if not allow_namespace_pkg:
             is_namespace = getattr(the_module, "__file__", None) is None and hasattr(the_module, "__path__")

From ec5e743a5448c5d97754d55f25eba65f99dfafa5 Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Fri, 6 Sep 2024 14:03:55 +0800
Subject: [PATCH 10/16] add reset_warning

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 monai/__init__.py                | 2 ++
 monai/data/image_reader.py       | 2 +-
 monai/data/image_writer.py       | 2 +-
 monai/data/itk_torch_bridge.py   | 2 +-
 monai/handlers/mlflow_handler.py | 2 --
 monai/utils/module.py            | 5 ++++-
 6 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/monai/__init__.py b/monai/__init__.py
index 536c9b0047..937bf82bc5 100644
--- a/monai/__init__.py
+++ b/monai/__init__.py
@@ -27,6 +27,8 @@ def custom_warning_handler(message, category, filename, lineno, file=None, line=
         "nptyping/typing_",
         "pydantic/_internal/_config",
         "tempfile",
+        "mlflow/gateway",
+        "mlflow/utils",
     ]
     if any(ignore in filename for ignore in ignore_files):
         return
diff --git a/monai/data/image_reader.py b/monai/data/image_reader.py
index f5e199e2a3..555738ecd9 100644
--- a/monai/data/image_reader.py
+++ b/monai/data/image_reader.py
@@ -44,7 +44,7 @@
 
     has_nrrd = has_itk = has_nib = has_pil = has_pydicom = True
 else:
-    itk, has_itk = optional_import("itk", allow_namespace_pkg=True)
+    itk, has_itk = optional_import("itk", allow_namespace_pkg=True, reset_warning=True)
     nib, has_nib = optional_import("nibabel")
     Nifti1Image, _ = optional_import("nibabel.nifti1", name="Nifti1Image")
     PILImage, has_pil = optional_import("PIL.Image")
diff --git a/monai/data/image_writer.py b/monai/data/image_writer.py
index b9e8b9e68e..2cf094264f 100644
--- a/monai/data/image_writer.py
+++ b/monai/data/image_writer.py
@@ -46,7 +46,7 @@
     import nibabel as nib
     from PIL import Image as PILImage
 else:
-    itk, _ = optional_import("itk", allow_namespace_pkg=True)
+    itk, _ = optional_import("itk", allow_namespace_pkg=True, reset_warning=True)
     nib, _ = optional_import("nibabel")
     PILImage, _ = optional_import("PIL.Image")
 
diff --git a/monai/data/itk_torch_bridge.py b/monai/data/itk_torch_bridge.py
index 4671cd112b..47e52a9c68 100644
--- a/monai/data/itk_torch_bridge.py
+++ b/monai/data/itk_torch_bridge.py
@@ -28,7 +28,7 @@
 
     has_itk = True
 else:
-    itk, has_itk = optional_import("itk")
+    itk, has_itk = optional_import("itk", reset_warning=True)
 
 __all__ = [
     "itk_image_to_metatensor",
diff --git a/monai/handlers/mlflow_handler.py b/monai/handlers/mlflow_handler.py
index eb93c5b49b..6d19579d9e 100644
--- a/monai/handlers/mlflow_handler.py
+++ b/monai/handlers/mlflow_handler.py
@@ -25,8 +25,6 @@
 from monai.config import IgniteInfo
 from monai.utils import CommonKeys, ensure_tuple, min_version, optional_import
 
-# workaround for https://github.com/Project-MONAI/MONAI/issues/8060
-warnings.filterwarnings("ignore", category=DeprecationWarning, module="mlflow")
 Events, _ = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
 mlflow, _ = optional_import("mlflow", descriptor="Please install mlflow before using MLFlowHandler.")
 mlflow.entities, _ = optional_import(
diff --git a/monai/utils/module.py b/monai/utils/module.py
index 13a18cb91f..808143f2db 100644
--- a/monai/utils/module.py
+++ b/monai/utils/module.py
@@ -364,7 +364,8 @@ def optional_import(
             a base class, or a decorator, the exceptions should raise accordingly. The current supported values
             are "default" (call once to raise), "decorator" (call the constructor and the second call to raise),
             and anything else will return a lazy class that can be used as a base class (call the constructor to raise).
-        reset_warning: whether to reset the warnings.showwarning to the original function during the import.
+        reset_warning: whether to reset the warnings.showwarning and warnings.formatwarning to
+            the original function during the import.
 
     Returns:
         The imported module and a boolean flag indicating whether the import is successful.
@@ -403,9 +404,11 @@ def optional_import(
     try:
         if reset_warning:
             old_showwarning = warnings.showwarning
+            old_formatwarning = warnings.formatwarning
         pkg = __import__(module)  # top level module
         if reset_warning:
             warnings.showwarning = old_showwarning
+            warnings.formatwarning = old_formatwarning
         the_module = import_module(module)
         if not allow_namespace_pkg:
             is_namespace = getattr(the_module, "__file__", None) is None and hasattr(the_module, "__path__")

From 449b88c6a4a83b0cd8e2f10cf426d1a575f9adce Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Fri, 6 Sep 2024 14:10:04 +0800
Subject: [PATCH 11/16] minor fix

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 monai/networks/utils.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/monai/networks/utils.py b/monai/networks/utils.py
index a7beba3ace..ce53ff9755 100644
--- a/monai/networks/utils.py
+++ b/monai/networks/utils.py
@@ -37,7 +37,6 @@
 onnxreference, _ = optional_import("onnx.reference")
 onnxruntime, _ = optional_import("onnxruntime")
 polygraphy, polygraphy_imported = optional_import("polygraphy")
-
 torch_tensorrt, _ = optional_import("torch_tensorrt", "1.4.0", reset_warning=True)
 
 

From 0faf233a63fe4929a2b2ecbe65e6be4bc4df1858 Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Fri, 6 Sep 2024 16:36:59 +0800
Subject: [PATCH 12/16] add log warning filter

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 monai/__init__.py              | 34 +++++++++++++++++++++++++++++-----
 monai/data/image_reader.py     |  2 +-
 monai/data/image_writer.py     |  2 +-
 monai/data/itk_torch_bridge.py |  2 +-
 monai/networks/utils.py        |  2 +-
 monai/utils/module.py          |  8 --------
 6 files changed, 33 insertions(+), 17 deletions(-)

diff --git a/monai/__init__.py b/monai/__init__.py
index 937bf82bc5..c2c73077e5 100644
--- a/monai/__init__.py
+++ b/monai/__init__.py
@@ -13,6 +13,7 @@
 
 import os
 import sys
+import logging
 import warnings
 from ._version import get_versions
 
@@ -24,19 +25,42 @@ def custom_warning_handler(message, category, filename, lineno, file=None, line=
     ignore_files = [
         "ignite/handlers/checkpoint",
         "modelopt/torch/quantization/tensor_quant",
-        "nptyping/typing_",
-        "pydantic/_internal/_config",
-        "tempfile",
-        "mlflow/gateway",
-        "mlflow/utils",
     ]
     if any(ignore in filename for ignore in ignore_files):
         return
     old_showwarning(message, category, filename, lineno, file, line)
 
+class DeprecatedTypesWarningFilter(logging.Filter):
+    def filter(self, record):
+        deprecated_aliases = [
+            "np.bool8",
+            "np.object0",
+            "np.int0",
+            "np.uint0",
+            "np.void0",
+            "np.str0",
+            "np.bytes0",
+            "@validator",
+            "@root_validator",
+            "class-based `config`",
+            "pkg_resources",
+            "Implicitly cleaning up"
+            ]
+        for alias in deprecated_aliases:
+            if alias in record.getMessage():
+                return False
+        return True
 
 # workaround for https://github.com/Project-MONAI/MONAI/issues/8060
+# Set the custom warning handler to filter warning
 warnings.showwarning = custom_warning_handler
+# Get the logger for warnings
+logger = logging.getLogger("py.warnings")
+# Create and add the filter to the logger
+filter = DeprecatedTypesWarningFilter()
+logger.addFilter(filter)
+
+
 PY_REQUIRED_MAJOR = 3
 PY_REQUIRED_MINOR = 9
 
diff --git a/monai/data/image_reader.py b/monai/data/image_reader.py
index 555738ecd9..f5e199e2a3 100644
--- a/monai/data/image_reader.py
+++ b/monai/data/image_reader.py
@@ -44,7 +44,7 @@
 
     has_nrrd = has_itk = has_nib = has_pil = has_pydicom = True
 else:
-    itk, has_itk = optional_import("itk", allow_namespace_pkg=True, reset_warning=True)
+    itk, has_itk = optional_import("itk", allow_namespace_pkg=True)
     nib, has_nib = optional_import("nibabel")
     Nifti1Image, _ = optional_import("nibabel.nifti1", name="Nifti1Image")
     PILImage, has_pil = optional_import("PIL.Image")
diff --git a/monai/data/image_writer.py b/monai/data/image_writer.py
index 2cf094264f..b9e8b9e68e 100644
--- a/monai/data/image_writer.py
+++ b/monai/data/image_writer.py
@@ -46,7 +46,7 @@
     import nibabel as nib
     from PIL import Image as PILImage
 else:
-    itk, _ = optional_import("itk", allow_namespace_pkg=True, reset_warning=True)
+    itk, _ = optional_import("itk", allow_namespace_pkg=True)
     nib, _ = optional_import("nibabel")
     PILImage, _ = optional_import("PIL.Image")
 
diff --git a/monai/data/itk_torch_bridge.py b/monai/data/itk_torch_bridge.py
index 47e52a9c68..4671cd112b 100644
--- a/monai/data/itk_torch_bridge.py
+++ b/monai/data/itk_torch_bridge.py
@@ -28,7 +28,7 @@
 
     has_itk = True
 else:
-    itk, has_itk = optional_import("itk", reset_warning=True)
+    itk, has_itk = optional_import("itk")
 
 __all__ = [
     "itk_image_to_metatensor",
diff --git a/monai/networks/utils.py b/monai/networks/utils.py
index ce53ff9755..1826e9ae1f 100644
--- a/monai/networks/utils.py
+++ b/monai/networks/utils.py
@@ -37,7 +37,7 @@
 onnxreference, _ = optional_import("onnx.reference")
 onnxruntime, _ = optional_import("onnxruntime")
 polygraphy, polygraphy_imported = optional_import("polygraphy")
-torch_tensorrt, _ = optional_import("torch_tensorrt", "1.4.0", reset_warning=True)
+torch_tensorrt, _ = optional_import("torch_tensorrt", "1.4.0")
 
 
 __all__ = [
diff --git a/monai/utils/module.py b/monai/utils/module.py
index 808143f2db..59fe906bdd 100644
--- a/monai/utils/module.py
+++ b/monai/utils/module.py
@@ -364,8 +364,6 @@ def optional_import(
             a base class, or a decorator, the exceptions should raise accordingly. The current supported values
             are "default" (call once to raise), "decorator" (call the constructor and the second call to raise),
             and anything else will return a lazy class that can be used as a base class (call the constructor to raise).
-        reset_warning: whether to reset the warnings.showwarning and warnings.formatwarning to
-            the original function during the import.
 
     Returns:
         The imported module and a boolean flag indicating whether the import is successful.
@@ -402,13 +400,7 @@ def optional_import(
     else:
         actual_cmd = f"import {module}"
     try:
-        if reset_warning:
-            old_showwarning = warnings.showwarning
-            old_formatwarning = warnings.formatwarning
         pkg = __import__(module)  # top level module
-        if reset_warning:
-            warnings.showwarning = old_showwarning
-            warnings.formatwarning = old_formatwarning
         the_module = import_module(module)
         if not allow_namespace_pkg:
             is_namespace = getattr(the_module, "__file__", None) is None and hasattr(the_module, "__path__")

From b65ad148a80326d772775f7a46cdcbb04f69a855 Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Fri, 6 Sep 2024 16:37:40 +0800
Subject: [PATCH 13/16] fix format

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 monai/__init__.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/monai/__init__.py b/monai/__init__.py
index c2c73077e5..a7910b6618 100644
--- a/monai/__init__.py
+++ b/monai/__init__.py
@@ -22,14 +22,12 @@
 
 
 def custom_warning_handler(message, category, filename, lineno, file=None, line=None):
-    ignore_files = [
-        "ignite/handlers/checkpoint",
-        "modelopt/torch/quantization/tensor_quant",
-    ]
+    ignore_files = ["ignite/handlers/checkpoint", "modelopt/torch/quantization/tensor_quant"]
     if any(ignore in filename for ignore in ignore_files):
         return
     old_showwarning(message, category, filename, lineno, file, line)
 
+
 class DeprecatedTypesWarningFilter(logging.Filter):
     def filter(self, record):
         deprecated_aliases = [
@@ -44,13 +42,14 @@ def filter(self, record):
             "@root_validator",
             "class-based `config`",
             "pkg_resources",
-            "Implicitly cleaning up"
-            ]
+            "Implicitly cleaning up",
+        ]
         for alias in deprecated_aliases:
             if alias in record.getMessage():
                 return False
         return True
 
+
 # workaround for https://github.com/Project-MONAI/MONAI/issues/8060
 # Set the custom warning handler to filter warning
 warnings.showwarning = custom_warning_handler

From 7955e5a7c824e66d98c8b90974196411e9b16581 Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Fri, 6 Sep 2024 16:39:43 +0800
Subject: [PATCH 14/16] minor fix

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 monai/networks/utils.py | 1 -
 monai/utils/module.py   | 1 -
 2 files changed, 2 deletions(-)

diff --git a/monai/networks/utils.py b/monai/networks/utils.py
index 1826e9ae1f..d0150b4e5b 100644
--- a/monai/networks/utils.py
+++ b/monai/networks/utils.py
@@ -39,7 +39,6 @@
 polygraphy, polygraphy_imported = optional_import("polygraphy")
 torch_tensorrt, _ = optional_import("torch_tensorrt", "1.4.0")
 
-
 __all__ = [
     "one_hot",
     "predict_segmentation",
diff --git a/monai/utils/module.py b/monai/utils/module.py
index 59fe906bdd..78087aef84 100644
--- a/monai/utils/module.py
+++ b/monai/utils/module.py
@@ -345,7 +345,6 @@ def optional_import(
     version_args: Any = None,
     allow_namespace_pkg: bool = False,
     as_type: str = "default",
-    reset_warning: bool = False,
 ) -> tuple[Any, bool]:
     """
     Imports an optional module specified by `module` string.

From e46040142f59b4ffa64085ca2ef9c9e18b95d4f4 Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Fri, 6 Sep 2024 17:13:43 +0800
Subject: [PATCH 15/16] address comments

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 monai/__init__.py | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/monai/__init__.py b/monai/__init__.py
index a7910b6618..200acc72e4 100644
--- a/monai/__init__.py
+++ b/monai/__init__.py
@@ -30,7 +30,7 @@ def custom_warning_handler(message, category, filename, lineno, file=None, line=
 
 class DeprecatedTypesWarningFilter(logging.Filter):
     def filter(self, record):
-        deprecated_aliases = [
+        message_bodies_to_ignore = [
             "np.bool8",
             "np.object0",
             "np.int0",
@@ -44,20 +44,18 @@ def filter(self, record):
             "pkg_resources",
             "Implicitly cleaning up",
         ]
-        for alias in deprecated_aliases:
-            if alias in record.getMessage():
+        for message in message_bodies_to_ignore:
+            if message in record.getMessage():
                 return False
         return True
 
 
 # workaround for https://github.com/Project-MONAI/MONAI/issues/8060
+#TODO: remove this workaround after upstream fixed the warning
 # Set the custom warning handler to filter warning
 warnings.showwarning = custom_warning_handler
-# Get the logger for warnings
-logger = logging.getLogger("py.warnings")
-# Create and add the filter to the logger
-filter = DeprecatedTypesWarningFilter()
-logger.addFilter(filter)
+# Get the logger for warnings and add the filter to the logger
+logging.getLogger("py.warnings").addFilter(DeprecatedTypesWarningFilter())
 
 
 PY_REQUIRED_MAJOR = 3

From 5ad5eca078bbea1239ff1f8191e8e092b6bff9bd Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Fri, 6 Sep 2024 18:33:49 +0800
Subject: [PATCH 16/16] fix format

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 monai/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/monai/__init__.py b/monai/__init__.py
index 200acc72e4..3f6b12c407 100644
--- a/monai/__init__.py
+++ b/monai/__init__.py
@@ -51,7 +51,7 @@ def filter(self, record):
 
 
 # workaround for https://github.com/Project-MONAI/MONAI/issues/8060
-#TODO: remove this workaround after upstream fixed the warning
+# TODO: remove this workaround after upstream fixed the warning
 # Set the custom warning handler to filter warning
 warnings.showwarning = custom_warning_handler
 # Get the logger for warnings and add the filter to the logger